Title: Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
Description: Articles in the 'R Journal' were first authored in 'LaTeX', which performs
admirably for 'PDF' files but is less than ideal for modern online interfaces.
The 'texor' package does all the transitional chores and conversions necessary
to move to the online versions.
Author: Abhishek Ulayil [aut, cre, cph]
,
Heather Turner [ctb] ,
Christophe Dervieux [ctb] ,
Mitchell O'Hara-Wild [ctb] ,
Dianne Cook [ctb] ,
Yinxiang Huang [ctb]
Maintainer: Abhishek Ulayil <perricoq@outlook.com>
Diff between texor versions 1.5.0 dated 2024-10-15 and 1.5.3 dated 2024-12-13
DESCRIPTION | 6 - MD5 | 21 ++--- NEWS.md | 8 ++ R/rnw-tools.R | 11 ++ build/vignette.rds |binary inst/doc/How-texor-convert-Sweave-to-R-Markdown.html | 4 - inst/doc/environment-handling.html | 71 +++++++++---------- inst/doc/introduction-to-texor.html | 1 inst/fig_code_chunk.lua | 2 tests/testthat/test-code-tools.R |only tests/testthat/test-file-tools.R | 9 ++ tests/testthat/test-rnw-tools.R | 2 12 files changed, 84 insertions(+), 51 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut],
Alba Estrada [ctb],
Paul Melloy [ctb],
Jose Carlos Guerrero [fnd],
A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.26 dated 2024-10-30 and 4.29 dated 2024-12-13
DESCRIPTION | 14 ++++++++---- MD5 | 20 +++++++++--------- NEWS | 47 ++++++++++++++++++++++++++++++++++++++---- R/cleanCoords.R | 19 ++++++++++++----- R/fuzzyOverlay.R | 8 +++++-- R/getRegion.R | 12 ++++++++-- man/cleanCoords.Rd | 7 +++--- man/fuzzySim-package.Rd | 4 +-- man/getRegion.Rd | 53 +++++++++++++++++++++++++++++++++++++++++++++--- man/gridRecords.Rd | 8 +++---- man/selectAbsences.Rd | 25 ++++++++++++++++------ 11 files changed, 168 insertions(+), 49 deletions(-)
Title: Fast Access to Large ASCII Files
Description: Methods for fast access to large ASCII files. Currently the
following file formats are supported: comma separated format (CSV) and fixed
width format. It is assumed that the files are too large to fit into memory,
although the package can also be used to efficiently access files that do
fit into memory. Methods are provided to access and process files blockwise.
Furthermore, an opened file can be accessed as one would an ordinary
data.frame. The LaF vignette gives an overview of the functionality
provided.
Author: Jan van der Laan [aut, cre]
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between LaF versions 0.8.4 dated 2020-03-23 and 0.8.6 dated 2024-12-13
DESCRIPTION | 21 ++++++++++++++------- MD5 | 28 +++++++++++++++------------- NEWS | 13 +++++++++++++ R/meta.R | 2 +- R/open.R | 8 +++++++- R/read_dm_blaise.R | 5 +++-- build/vignette.rds |binary inst/doc/LaF-benchmark.pdf |binary inst/doc/LaF-manual.pdf |binary man/laf_open.Rd | 2 +- man/laf_open_csv.Rd | 6 ++++++ man/laf_open_fwf.Rd | 2 +- man/read_dm_blaise.Rd | 4 +++- src/csvreader.cpp | 31 ++++++++++++++++++++++++++----- tests/testthat/test_blaise.R |only tests/testthat/test_firstlineseparator.R |only 16 files changed, 90 insertions(+), 32 deletions(-)
Title: 'ggplot2' Pattern Geoms
Description: Provides 'ggplot2' geoms filled with various patterns. Includes a patterned version of every 'ggplot2' geom that has a region that can be filled with a pattern. Provides a suite of 'ggplot2' aesthetics and scales for controlling pattern appearances. Supports over a dozen builtin patterns (every pattern implemented by 'gridpattern') as well as allowing custom user-defined patterns.
Author: Mike FC [aut],
Trevor L. Davis [aut, cre] ,
ggplot2 authors [aut]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between ggpattern versions 1.1.1 dated 2024-06-04 and 1.1.3 dated 2024-12-13
DESCRIPTION | 8 ++-- MD5 | 62 +++++++++++++++++----------------- NEWS.md | 7 +++ R/geom-.R | 2 - R/scale-pattern-alpha.R | 6 +-- R/scale-pattern-brewer.R | 4 +- R/scale-pattern-linetype.R | 2 - R/scale-pattern-viridis.R | 6 +-- README.md | 36 ++++++++++--------- build/vignette.rds |binary inst/doc/developing-patterns.R | 2 - inst/doc/developing-patterns.Rmd | 2 - inst/doc/developing-patterns.html | 4 +- inst/doc/patterns-noise.R | 16 ++++---- inst/doc/patterns-noise.Rmd | 16 ++++---- inst/doc/patterns-noise.html | 16 ++++---- inst/doc/patterns-points.R | 14 +++---- inst/doc/patterns-points.Rmd | 14 +++---- inst/doc/patterns-points.html | 14 +++---- inst/doc/patterns-stripes.R | 18 ++++----- inst/doc/patterns-stripes.Rmd | 18 ++++----- inst/doc/patterns-stripes.html | 18 ++++----- man/draw_key_polygon_pattern.Rd | 2 - man/ggpattern.Rd | 2 - man/scale_pattern_alpha_continuous.Rd | 6 +-- man/scale_pattern_colour_brewer.Rd | 4 +- man/scale_pattern_colour_viridis_d.Rd | 6 +-- man/scale_pattern_linetype.Rd | 2 - vignettes/developing-patterns.Rmd | 2 - vignettes/patterns-noise.Rmd | 16 ++++---- vignettes/patterns-points.Rmd | 14 +++---- vignettes/patterns-stripes.Rmd | 18 ++++----- 32 files changed, 183 insertions(+), 174 deletions(-)
Title: Libraries, Data Dictionaries, and a Data Step for R
Description: Contains a set of functions to create data libraries,
generate data dictionaries, and simulate a data step.
The libname() function will load a directory of data into
a library in one line of code. The dictionary() function
will generate data dictionaries for individual
data frames or an entire library. And the datestep() function
will perform row-by-row data processing.
Author: David Bosak [aut, cre],
Brian Varney [ctb],
Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between libr versions 1.3.7 dated 2024-11-06 and 1.3.8 dated 2024-12-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 - NEWS.md | 3 +++ R/libname.R | 1 - 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Simulation of Daily and Monthly Time Series
Description: Flexible simulation of time series using time series
components, including seasonal, calendar and outlier effects. Main
algorithm described in Ollech, D. (2021) <doi:10.1515/jtse-2020-0028>.
Author: Daniel Ollech [aut, cre]
Maintainer: Daniel Ollech <daniel.ollech@bundesbank.de>
Diff between tssim versions 0.1.7 dated 2021-06-25 and 0.2.7 dated 2024-12-13
DESCRIPTION | 23 +++++++---------- MD5 | 28 +++++++++++++-------- NAMESPACE | 4 +++ NEWS.md | 14 ++++++++++ R/sim_daily.R | 63 ++++++++++++++++++++++++++++++++++-------------- R/sim_daily_hs.R |only R/sim_daily_mstl.R |only R/sim_monthly.R | 8 +++--- R/sim_monthly_hs.R |only R/sim_monthly_mstl.R |only R/sim_sfac.R | 59 +++++++++++++++++++++++++++++--------------- build/partial.rdb |binary man/sim_daily.Rd | 29 ++++++++++++---------- man/sim_daily_hs.Rd |only man/sim_daily_mstl.Rd |only man/sim_monthly.Rd | 14 +++++++--- man/sim_monthly_hs.Rd |only man/sim_monthly_mstl.Rd |only man/sim_sfac.Rd | 21 +++++++++------- 19 files changed, 173 insertions(+), 90 deletions(-)
Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or
data scientist to get quick and robust results, without the need of repetitive coding or
advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.2.9 dated 2024-09-12 and 5.2.10 dated 2024-12-13
lares-5.2.10/lares/DESCRIPTION | 11 +- lares-5.2.10/lares/MD5 | 30 ++++--- lares-5.2.10/lares/NAMESPACE | 7 + lares-5.2.10/lares/R/checks.R | 23 ++++- lares-5.2.10/lares/R/crossbrand.R |only lares-5.2.10/lares/R/crossbrand2.R |only lares-5.2.10/lares/R/family.R |only lares-5.2.10/lares/R/lares.R | 7 + lares-5.2.10/lares/R/lasso.R | 1 lares-5.2.10/lares/R/model_functions.R | 1 lares-5.2.10/lares/R/model_predict.R | 2 lares-5.2.10/lares/R/onehotencoding.R | 131 +++++++++++++++---------------- lares-5.2.10/lares/R/wrangling.R | 31 ++++--- lares-5.2.10/lares/man/checks.Rd | 56 +++++++++++++ lares-5.2.10/lares/man/format_string.Rd | 3 lares-5.2.10/lares/man/holidays.Rd | 5 - lares-5.2.10/lares/man/robyn_crossmmm.Rd |only lares-5.2.10/lares/man/seq_surnames.Rd |only lares-5.2.9/lares/man/is_url.Rd |only 19 files changed, 205 insertions(+), 103 deletions(-)
Title: Random Fields on Metric Graphs
Description: Facilitates creation and manipulation of metric graphs, such as street or river networks. Further facilitates operations and visualizations of data on metric graphs, and the creation of a large class of random fields and stochastic partial differential equations on such spaces. These random fields can be used for simulation, prediction and inference. In particular, linear mixed effects models including random field components can be fitted to data based on computationally efficient sparse matrix representations. Interfaces to the R packages 'INLA' and 'inlabru' are also provided, which facilitate working with Bayesian statistical models on metric graphs. The main references for the methods are Bolin, Simas and Wallin (2024) <doi:10.3150/23-BEJ1647>, Bolin, Kovacs, Kumar and Simas (2023) <doi:10.1090/mcom/3929> and Bolin, Simas and Wallin (2023) <doi:10.48550/arXiv.2304.03190> and <doi:10.48550/arXiv.2304.10372>.
Author: David Bolin [cre, aut],
Alexandre Simas [aut],
Jonas Wallin [aut]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between MetricGraph versions 1.3.0 dated 2024-02-27 and 1.4.0 dated 2024-12-13
MetricGraph-1.3.0/MetricGraph/tests/testthat/test_cgeneric.R |only MetricGraph-1.4.0/MetricGraph/DESCRIPTION | 17 MetricGraph-1.4.0/MetricGraph/MD5 | 91 MetricGraph-1.4.0/MetricGraph/NAMESPACE | 12 MetricGraph-1.4.0/MetricGraph/NEWS.md | 27 MetricGraph-1.4.0/MetricGraph/R/MetricGraph-package.R | 18 MetricGraph-1.4.0/MetricGraph/R/RcppExports.R | 12 MetricGraph-1.4.0/MetricGraph/R/data.R | 32 MetricGraph-1.4.0/MetricGraph/R/graph_inference.R | 13 MetricGraph-1.4.0/MetricGraph/R/graph_likelihoods.R | 13 MetricGraph-1.4.0/MetricGraph/R/graph_lme.R | 22 MetricGraph-1.4.0/MetricGraph/R/graph_spde.R | 877 +- MetricGraph-1.4.0/MetricGraph/R/metric_graph.R | 4385 +++++++--- MetricGraph-1.4.0/MetricGraph/R/spde_covariance.R | 188 MetricGraph-1.4.0/MetricGraph/R/spde_posteriors.R | 215 MetricGraph-1.4.0/MetricGraph/R/spde_precision.R | 183 MetricGraph-1.4.0/MetricGraph/R/spde_sampling.R | 69 MetricGraph-1.4.0/MetricGraph/R/util.R | 444 - MetricGraph-1.4.0/MetricGraph/build/vignette.rds |binary MetricGraph-1.4.0/MetricGraph/data/pems.rda |binary MetricGraph-1.4.0/MetricGraph/data/pems_repl.rda |only MetricGraph-1.4.0/MetricGraph/inst/CITATION | 10 MetricGraph-1.4.0/MetricGraph/inst/doc/MetricGraph_pkg.Rmd | 27 MetricGraph-1.4.0/MetricGraph/inst/doc/MetricGraph_pkg.html | 36 MetricGraph-1.4.0/MetricGraph/man/graph_components.Rd | 6 MetricGraph-1.4.0/MetricGraph/man/graph_data_spde.Rd | 13 MetricGraph-1.4.0/MetricGraph/man/graph_lme.Rd | 8 MetricGraph-1.4.0/MetricGraph/man/graph_spde.Rd | 33 MetricGraph-1.4.0/MetricGraph/man/graph_spde_basis.Rd | 2 MetricGraph-1.4.0/MetricGraph/man/graph_starting_values.Rd | 8 MetricGraph-1.4.0/MetricGraph/man/metric_graph.Rd | 712 + MetricGraph-1.4.0/MetricGraph/man/pems.Rd | 11 MetricGraph-1.4.0/MetricGraph/man/pems_repl.Rd |only MetricGraph-1.4.0/MetricGraph/man/plot.graph_bru_proc_pred.Rd |only MetricGraph-1.4.0/MetricGraph/man/predict.inla_metric_graph_spde.Rd | 20 MetricGraph-1.4.0/MetricGraph/man/process_rspde_predictions.Rd |only MetricGraph-1.4.0/MetricGraph/man/sample_spde.Rd | 3 MetricGraph-1.4.0/MetricGraph/man/spde_covariance.Rd | 4 MetricGraph-1.4.0/MetricGraph/man/spde_variance.Rd |only MetricGraph-1.4.0/MetricGraph/man/summary.metric_graph.Rd | 12 MetricGraph-1.4.0/MetricGraph/src/CB.cpp | 195 MetricGraph-1.4.0/MetricGraph/src/RcppExports.cpp | 48 MetricGraph-1.4.0/MetricGraph/src/aux_functions.cpp | 114 MetricGraph-1.4.0/MetricGraph/tests/testthat/test.alpha2.R | 10 MetricGraph-1.4.0/MetricGraph/tests/testthat/test.graph.R | 4 MetricGraph-1.4.0/MetricGraph/tests/testthat/test.variance.R | 5 MetricGraph-1.4.0/MetricGraph/tests/testthat/test_directional.R |only MetricGraph-1.4.0/MetricGraph/tests/testthat/test_exp.R | 2 MetricGraph-1.4.0/MetricGraph/tests/testthat/test_isoExp.R | 4 MetricGraph-1.4.0/MetricGraph/vignettes/MetricGraph_pkg.Rmd | 27 50 files changed, 6045 insertions(+), 1887 deletions(-)
Title: Sign-Simplicity-Regression-Solver
Description: Implementation of the SSR-Algorithm. The Sign-Simplicity-Regression model is a nonparametric statistical model which is based on residual signs and simplicity assumptions on the regression function. Goal is to calculate the most parsimonious regression function satisfying the statistical adequacy requirements. Theory and functions are specified in Metzner (2020, ISBN: 979-8-68239-420-3, "Trendbasierte Prognostik") and Metzner (2021, ISBN: 979-8-59347-027-0, "Adäquates Maschinelles Lernen").
Author: Lars Metzner [aut, cre]
Maintainer: Lars Metzner <lars.metzner@ppi.de>
Diff between sisireg versions 1.1.1 dated 2023-09-20 and 1.1.2 dated 2024-12-13
DESCRIPTION | 8 - MD5 | 20 ++-- NAMESPACE | 1 R/ssr.R | 12 ++ R/ssr3d.R | 40 +++++---- R/ssrMLP.R | 220 ++++++++++++++++++++++++++++++++++++++++++++-------- R/ssrnd.R | 9 +- man/onnx_load.Rd | 56 +++++++------ man/onnx_save.Rd | 46 +++++----- man/ssrmlp_train.Rd | 8 + src/ssrnd.c | 2 11 files changed, 303 insertions(+), 119 deletions(-)
Title: Bias Diagnostic for Linear Mixed Models
Description: Provides a function to perform bias diagnostics on linear mixed models fitted with lmer() from the 'lme4' package. Implements permutation tests for assessing the bias of fixed effects, as described in Karl and Zimmerman (2021) <doi:10.1016/j.jspi.2020.06.004>. Karl and Zimmerman (2020) <doi:10.17632/tmynggddfm.1> provide R code for implementing the test using 'mvglmmRank' output. Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mixedbiastest versions 0.2.1 dated 2024-12-05 and 0.3.0 dated 2024-12-13
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/list_fixed.R | 4 ++-- R/mixedbiastest.R | 4 ++-- R/plot.R | 30 ++++++++++++------------------ man/list_fixed_effects.Rd | 4 ++-- man/mixedbiastest.Rd | 4 ++-- 7 files changed, 31 insertions(+), 37 deletions(-)
Title: An 'Armadillo' Interface
Description: Provides function declarations and inline function definitions that
facilitate communication between R and the 'Armadillo' 'C++' library for
linear algebra and scientific computing. This implementation is detailed
in Vargas Sepulveda and Schneider Malamud (2024)
<doi:10.48550/arXiv.2408.11074>.
Author: Mauricio Vargas Sepulveda [aut, cre]
,
Jonathan Schneider Malamud [ctb],
Conrad Sanderson [aut] )
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Diff between cpp11armadillo versions 0.3.3 dated 2024-09-02 and 0.4.0 dated 2024-12-13
cpp11armadillo-0.3.3/cpp11armadillo/inst/extdata/src/Makevars |only cpp11armadillo-0.3.3/cpp11armadillo/inst/include/armadillo/r_messages.hpp |only cpp11armadillo-0.4.0/cpp11armadillo/DESCRIPTION | 8 cpp11armadillo-0.4.0/cpp11armadillo/MD5 | 218 +- cpp11armadillo-0.4.0/cpp11armadillo/NEWS.md | 18 cpp11armadillo-0.4.0/cpp11armadillo/R/version.R | 2 cpp11armadillo-0.4.0/cpp11armadillo/README.md | 34 cpp11armadillo-0.4.0/cpp11armadillo/build/vignette.rds |binary cpp11armadillo-0.4.0/cpp11armadillo/configure |only cpp11armadillo-0.4.0/cpp11armadillo/configure.win |only cpp11armadillo-0.4.0/cpp11armadillo/inst/doc/usage.Rmd | 55 cpp11armadillo-0.4.0/cpp11armadillo/inst/doc/usage.html | 88 cpp11armadillo-0.4.0/cpp11armadillo/inst/extdata/README | 17 cpp11armadillo-0.4.0/cpp11armadillo/inst/extdata/cleanup |only cpp11armadillo-0.4.0/cpp11armadillo/inst/extdata/configure |only cpp11armadillo-0.4.0/cpp11armadillo/inst/extdata/src/Makevars.in |only cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo.hpp | 2 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Base_bones.hpp | 12 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Col_bones.hpp | 2 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Col_meat.hpp | 6 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/CubeToMatOp_bones.hpp | 5 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Cube_bones.hpp | 15 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Cube_meat.hpp | 38 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Gen_bones.hpp | 5 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Glue_bones.hpp | 3 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Glue_meat.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/MapMat_meat.hpp | 65 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Mat_bones.hpp | 18 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Mat_meat.hpp | 14 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Op_bones.hpp | 3 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Op_meat.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Proxy.hpp | 16 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Row_bones.hpp | 2 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/Row_meat.hpp | 6 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/SpBase_bones.hpp | 12 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/SpMat_meat.hpp | 25 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/SpToDGlue_bones.hpp | 5 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/SpToDOp_bones.hpp | 5 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/arma_forward.hpp | 3 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/arma_rng.hpp | 56 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/arma_rng_cxx03.hpp | 4 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/arma_version.hpp | 4 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/auxlib_bones.hpp | 46 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/auxlib_meat.hpp | 896 +++++++++- cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/compiler_check.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/compiler_setup.hpp | 9 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/config.hpp | 33 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/config.hpp.cmake | 25 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/debug.hpp | 20 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/def_lapack.hpp | 198 ++ cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/diagview_bones.hpp | 3 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/diagview_meat.hpp | 48 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/eGlue_bones.hpp | 3 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/eGlue_meat.hpp | 6 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/eOp_bones.hpp | 3 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/eOp_meat.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/fft_engine_fftw3.hpp | 44 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/fn_accu.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/fn_misc.hpp | 57 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/fn_powext.hpp | 25 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/glue_solve_bones.hpp | 5 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/glue_solve_meat.hpp | 124 + cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/glue_times_meat.hpp | 29 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/gmm_diag_meat.hpp | 4 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/gmm_full_meat.hpp | 4 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/memory.hpp | 52 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/mp_misc.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/mtGlue_bones.hpp | 3 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/mtGlue_meat.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/mtOp_bones.hpp | 3 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/mtOp_meat.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/mul_gemv.hpp | 4 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/mul_herk.hpp | 4 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/mul_syrk.hpp | 4 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_cond_meat.hpp | 12 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_dot_meat.hpp | 12 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_expmat_meat.hpp | 18 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_inv_gen_meat.hpp | 64 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_inv_spd_meat.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_log_det_meat.hpp | 2 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_logmat_meat.hpp | 6 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_max_meat.hpp | 44 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_min_meat.hpp | 44 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_norm_meat.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_pinv_meat.hpp | 9 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_powmat_meat.hpp | 42 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_rank_meat.hpp | 9 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_rcond_meat.hpp | 30 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/op_sqrtmat_meat.hpp | 6 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/operator_minus.hpp | 56 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/operator_plus.hpp | 56 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/sp_auxlib_meat.hpp | 12 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/subview_bones.hpp | 7 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/subview_cube_each_bones.hpp | 2 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/subview_each_bones.hpp | 2 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/subview_each_meat.hpp | 4 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/subview_elem1_bones.hpp | 3 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/subview_elem1_meat.hpp | 56 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/subview_elem2_bones.hpp | 3 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/subview_elem2_meat.hpp | 9 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/subview_meat.hpp | 8 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/sym_helper.hpp | 189 +- cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/traits.hpp | 10 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/translate_lapack.hpp | 208 ++ cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/typedef_elem.hpp | 5 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/armadillo/unwrap.hpp | 21 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/cpp11armadillo.hpp | 108 + cpp11armadillo-0.4.0/cpp11armadillo/inst/include/r_messages.hpp |only cpp11armadillo-0.4.0/cpp11armadillo/inst/include/wrappers/matrices.hpp | 13 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/wrappers/sparse_matrices.hpp | 34 cpp11armadillo-0.4.0/cpp11armadillo/inst/include/wrappers/vectors.hpp | 40 cpp11armadillo-0.4.0/cpp11armadillo/man/figures/logo.svg | 851 +++------ cpp11armadillo-0.4.0/cpp11armadillo/tests/testthat/test-version.R | 2 cpp11armadillo-0.4.0/cpp11armadillo/vignettes/usage.Rmd | 55 114 files changed, 2890 insertions(+), 1660 deletions(-)
More information about cpp11armadillo at CRAN
Permanent link
Title: Structural Modeling for Multiple Latent Class Variables
Description: Provides comprehensive tools for the implementation of Structural Latent Class Models (SLCM), including
Latent Transition Analysis (LTA; Linda M. Collins and Stephanie T. Lanza, 2009) <doi:10.1002/9780470567333>,
Latent Class Profile Analysis (LCPA; Hwan Chung et al., 2010) <doi:10.1111/j.1467-985x.2010.00674.x>, and
Joint Latent Class Analysis (JLCA; Saebom Jeon et al., 2017) <doi:10.1080/10705511.2017.1340844>, and
any other extended models involving multiple latent class variables.
Author: Youngsun Kim [aut, cre] ,
Hwan Chung [aut]
Maintainer: Youngsun Kim <yskstat@gmail.com>
Diff between slca versions 1.2.0 dated 2024-11-01 and 1.3.0 dated 2024-12-12
slca-1.2.0/slca/R/addhealth.R |only slca-1.2.0/slca/R/gss7677.R |only slca-1.2.0/slca/R/nlys97.R |only slca-1.2.0/slca/R/regression.R |only slca-1.2.0/slca/R/simulate.slca.R |only slca-1.2.0/slca/man/confint.slca.Rd |only slca-1.2.0/slca/man/examples/diag.R |only slca-1.2.0/slca/man/examples/reg.R |only slca-1.2.0/slca/man/reorder.slca.Rd |only slca-1.3.0/slca/DESCRIPTION | 6 slca-1.3.0/slca/MD5 | 72 +++--- slca-1.3.0/slca/NAMESPACE | 22 + slca-1.3.0/slca/R/data.R |only slca-1.3.0/slca/R/data_encode.R | 25 ++ slca-1.3.0/slca/R/diagnostic.R | 80 +++---- slca-1.3.0/slca/R/estimate.R | 48 ++-- slca-1.3.0/slca/R/methods.R | 340 +++++++++++++++--------------- slca-1.3.0/slca/R/nlsy_fit.R | 9 slca-1.3.0/slca/R/plot.slca.R | 85 +++---- slca-1.3.0/slca/R/regress.R |only slca-1.3.0/slca/R/simulate.R |only slca-1.3.0/slca/R/slca.R | 97 +++++--- slca-1.3.0/slca/R/slcaControl.R | 24 +- slca-1.3.0/slca/data/nlsy_jlcpa.rda |binary slca-1.3.0/slca/data/nlsy_jlta.rda |only slca-1.3.0/slca/man/addhealth.Rd | 27 +- slca-1.3.0/slca/man/compare.Rd | 22 - slca-1.3.0/slca/man/confint.slcafit.Rd |only slca-1.3.0/slca/man/estimate.Rd | 65 ++++- slca-1.3.0/slca/man/examples/diagnostic.R |only slca-1.3.0/slca/man/examples/estimate.R |only slca-1.3.0/slca/man/examples/gss7677.R | 14 - slca-1.3.0/slca/man/examples/regress.R |only slca-1.3.0/slca/man/examples/sim.R | 82 ++++++- slca-1.3.0/slca/man/examples/simulate.R |only slca-1.3.0/slca/man/examples/slca.R | 24 +- slca-1.3.0/slca/man/gof.Rd | 31 +- slca-1.3.0/slca/man/gss7677.Rd | 56 ++-- slca-1.3.0/slca/man/nlsy97.Rd | 43 +-- slca-1.3.0/slca/man/nlsy_jlcpa.Rd | 11 slca-1.3.0/slca/man/param.Rd | 24 +- slca-1.3.0/slca/man/predict.slcafit.Rd |only slca-1.3.0/slca/man/regress.Rd | 52 ++-- slca-1.3.0/slca/man/reorder.slcafit.Rd |only slca-1.3.0/slca/man/simulate.slca.Rd | 62 +++-- slca-1.3.0/slca/man/slca.Rd | 105 +++++---- slca-1.3.0/slca/man/slcaControl.Rd | 27 +- 47 files changed, 833 insertions(+), 620 deletions(-)
Title: Computational Methods for Economic Complexity
Description: A wrapper of different methods from Linear Algebra for the equations
introduced in The Atlas of Economic Complexity and related literature. This
package provides standard matrix and graph output that can be used seamlessly
with other packages. See <doi:10.21105/joss.01866> for a summary
of these methods and its evolution in literature.
Author: Mauricio Vargas Sepulveda [aut, cre, cph]
,
Carlo Bottai [ctb] ,
Diego Kozlowski [ctb] ,
Nico Pintar [rev] ,
The World Bank [dtc] ,
Open Trade Statistics [dtc]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Diff between economiccomplexity versions 1.5.0 dated 2023-08-07 and 2.0.0 dated 2024-12-12
economiccomplexity-1.5.0/economiccomplexity/R/economiccomplexity-internals.R |only economiccomplexity-1.5.0/economiccomplexity/man/eigenvalues_method.Rd |only economiccomplexity-1.5.0/economiccomplexity/man/fitness_method.Rd |only economiccomplexity-1.5.0/economiccomplexity/man/reflections_method.Rd |only economiccomplexity-2.0.0/economiccomplexity/DESCRIPTION | 15 economiccomplexity-2.0.0/economiccomplexity/MD5 | 80 economiccomplexity-2.0.0/economiccomplexity/NAMESPACE | 10 economiccomplexity-2.0.0/economiccomplexity/R/balassa_index.R | 64 economiccomplexity-2.0.0/economiccomplexity/R/complexity_measures.R | 199 - economiccomplexity-2.0.0/economiccomplexity/R/complexity_outlook.R | 25 economiccomplexity-2.0.0/economiccomplexity/R/cpp11.R |only economiccomplexity-2.0.0/economiccomplexity/R/density.R | 7 economiccomplexity-2.0.0/economiccomplexity/R/distance.R | 21 economiccomplexity-2.0.0/economiccomplexity/R/economiccomplexity-package.R |only economiccomplexity-2.0.0/economiccomplexity/R/helpers.R |only economiccomplexity-2.0.0/economiccomplexity/R/productivity_levels.R | 41 economiccomplexity-2.0.0/economiccomplexity/R/projections.R | 40 economiccomplexity-2.0.0/economiccomplexity/R/proximity.R | 46 economiccomplexity-2.0.0/economiccomplexity/build/partial.rdb |binary economiccomplexity-2.0.0/economiccomplexity/build/vignette.rds |binary economiccomplexity-2.0.0/economiccomplexity/cleanup |only economiccomplexity-2.0.0/economiccomplexity/configure |only economiccomplexity-2.0.0/economiccomplexity/data/economiccomplexity_output.rda |binary economiccomplexity-2.0.0/economiccomplexity/inst/doc/economiccomplexity.R | 131 - economiccomplexity-2.0.0/economiccomplexity/inst/doc/economiccomplexity.Rmd | 161 - economiccomplexity-2.0.0/economiccomplexity/inst/doc/economiccomplexity.html | 1217 ++++------ economiccomplexity-2.0.0/economiccomplexity/man/balassa_index.Rd | 25 economiccomplexity-2.0.0/economiccomplexity/man/complexity_measures.Rd | 7 economiccomplexity-2.0.0/economiccomplexity/man/complexity_outlook.Rd | 9 economiccomplexity-2.0.0/economiccomplexity/man/country_aggregation.Rd | 2 economiccomplexity-2.0.0/economiccomplexity/man/country_product_aggregation.Rd | 2 economiccomplexity-2.0.0/economiccomplexity/man/dataframe_to_matrix.Rd | 2 economiccomplexity-2.0.0/economiccomplexity/man/density.Rd | 7 economiccomplexity-2.0.0/economiccomplexity/man/distance.Rd | 7 economiccomplexity-2.0.0/economiccomplexity/man/economiccomplexity-package.Rd |only economiccomplexity-2.0.0/economiccomplexity/man/economiccomplexity_output.Rd | 19 economiccomplexity-2.0.0/economiccomplexity/man/productivity_levels.Rd | 20 economiccomplexity-2.0.0/economiccomplexity/man/projections.Rd | 9 economiccomplexity-2.0.0/economiccomplexity/man/proximity.Rd | 7 economiccomplexity-2.0.0/economiccomplexity/man/world_gdp_avg_1998_to_2000.Rd | 22 economiccomplexity-2.0.0/economiccomplexity/man/world_trade_avg_1998_to_2000.Rd | 24 economiccomplexity-2.0.0/economiccomplexity/src |only economiccomplexity-2.0.0/economiccomplexity/tests/testthat/test-balassa_index.R | 21 economiccomplexity-2.0.0/economiccomplexity/tests/testthat/test-productivity_levels.R | 13 economiccomplexity-2.0.0/economiccomplexity/vignettes/economiccomplexity.Rmd | 161 - 45 files changed, 1189 insertions(+), 1225 deletions(-)
More information about economiccomplexity at CRAN
Permanent link
Title: Hexagonal Hierarchical Geospatial Indexing System
Description: Provides access to Uber's 'H3' geospatial indexing system via 'h3lib'
<https://CRAN.R-project.org/package=h3lib>. 'h3r' is designed to mimic the 'H3'
Application Programming Interface (API) <https://h3geo.org/docs/api/indexing/>,
so that any function in the API is also available in 'h3r'.
Author: David Cooley [aut, cre],
Ray Shao [aut]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between h3r versions 0.1.1 dated 2024-03-12 and 0.1.2 dated 2024-12-12
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/h3r-package.R | 2 +- man/stations.Rd | 2 +- src/h3rUtils.c | 3 ++- 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Personalised Synthetic Controls
Description: Allows the comparison of data cohorts (DC) against a Counter Factual Model (CFM) and measures the difference in terms of an efficacy parameter. Allows the application of Personalised Synthetic Controls.
Author: Richard Jackson [cre, aut]
Maintainer: Richard Jackson <richJ23@liverpool.ac.uk>
Diff between psc versions 1.0.0 dated 2024-11-20 and 1.1.0 dated 2024-12-12
psc-1.0.0/psc/R/psc_ite.R |only psc-1.0.0/psc/man/psc_ite.Rd |only psc-1.1.0/psc/DESCRIPTION | 11 psc-1.1.0/psc/MD5 | 137 +- psc-1.1.0/psc/NAMESPACE | 9 psc-1.1.0/psc/NEWS.md | 2 psc-1.1.0/psc/R/acc.R | 2 psc-1.1.0/psc/R/bin.mod.R | 16 psc-1.1.0/psc/R/coef.psc.R | 3 psc-1.1.0/psc/R/cont.mod.R | 20 psc-1.1.0/psc/R/count.mod.R | 18 psc-1.1.0/psc/R/data.R | 3 psc-1.1.0/psc/R/dataComb.R | 8 psc-1.1.0/psc/R/dataComb.flexsurvreg.R | 28 psc-1.1.0/psc/R/dataComb.glm.R | 32 psc-1.1.0/psc/R/dataSumm.R |only psc-1.1.0/psc/R/data_match.R |only psc-1.1.0/psc/R/initParm.R | 6 psc-1.1.0/psc/R/lik.flexsurvreg.R | 18 psc-1.1.0/psc/R/lik.flexsurvreg.mtc.R | 17 psc-1.1.0/psc/R/lik.glm.R | 12 psc-1.1.0/psc/R/lik.glm.mtc.R | 11 psc-1.1.0/psc/R/linPred.R | 16 psc-1.1.0/psc/R/modelExtract.flexsurvreg.R | 16 psc-1.1.0/psc/R/modelExtract.glm.R | 10 psc-1.1.0/psc/R/modp.R | 3 psc-1.1.0/psc/R/plot.R | 82 - psc-1.1.0/psc/R/plot.psc.binary.R |only psc-1.1.0/psc/R/plot.psc.cont.R |only psc-1.1.0/psc/R/plot.psc.count.R |only psc-1.1.0/psc/R/plot.psc.flexsurvreg.R |only psc-1.1.0/psc/R/pscEst.flexsurvreg.R | 7 psc-1.1.0/psc/R/pscEst.glm.R | 7 psc-1.1.0/psc/R/pscSumm.R | 28 psc-1.1.0/psc/R/pscfit.R | 13 psc-1.1.0/psc/R/summary.R | 3 psc-1.1.0/psc/R/surv.mod.R | 9 psc-1.1.0/psc/R/surv_fpm.R | 13 psc-1.1.0/psc/README.md | 12 psc-1.1.0/psc/inst/doc/psc-vignette.R | 26 psc-1.1.0/psc/inst/doc/psc-vignette.Rmd | 204 ++-- psc-1.1.0/psc/inst/doc/psc-vignette.html | 1177 +++++++++++++++++++----- psc-1.1.0/psc/man/acc.Rd | 2 psc-1.1.0/psc/man/bin.mod.Rd | 16 psc-1.1.0/psc/man/coef.psc.Rd | 3 psc-1.1.0/psc/man/cont.mod.Rd | 20 psc-1.1.0/psc/man/count.mod.Rd | 18 psc-1.1.0/psc/man/data.Rd | 3 psc-1.1.0/psc/man/dataComb.Rd | 8 psc-1.1.0/psc/man/dataComb.flexsurvreg.Rd | 12 psc-1.1.0/psc/man/dataComb.glm.Rd | 14 psc-1.1.0/psc/man/dataSumm.Rd |only psc-1.1.0/psc/man/data_match.Rd |only psc-1.1.0/psc/man/figures/README-pressure-1.png |binary psc-1.1.0/psc/man/figures/example_plot.png |only psc-1.1.0/psc/man/initParm.Rd | 6 psc-1.1.0/psc/man/lik.flexsurvreg.Rd | 10 psc-1.1.0/psc/man/lik.flexsurvreg.mtc.Rd | 10 psc-1.1.0/psc/man/lik.glm.Rd | 10 psc-1.1.0/psc/man/lik.glm.mtc.Rd | 10 psc-1.1.0/psc/man/linPred.Rd | 9 psc-1.1.0/psc/man/modelExtract.flexsurvreg.Rd | 14 psc-1.1.0/psc/man/modelExtract.glm.Rd | 10 psc-1.1.0/psc/man/modp.Rd | 3 psc-1.1.0/psc/man/plot.psc.Rd | 19 psc-1.1.0/psc/man/plot.psc.binary.Rd |only psc-1.1.0/psc/man/plot.psc.cont.Rd |only psc-1.1.0/psc/man/plot.psc.count.Rd |only psc-1.1.0/psc/man/plot.psc.flexsurvreg.Rd |only psc-1.1.0/psc/man/pscEst.flexsurvreg.Rd | 6 psc-1.1.0/psc/man/pscEst.glm.Rd | 6 psc-1.1.0/psc/man/pscSumm.Rd | 5 psc-1.1.0/psc/man/pscfit.Rd | 13 psc-1.1.0/psc/man/summary.psc.Rd | 3 psc-1.1.0/psc/man/surv.mod.Rd | 10 psc-1.1.0/psc/man/surv_fpm.Rd | 11 psc-1.1.0/psc/vignettes/psc-vignette.Rmd | 204 ++-- 77 files changed, 1759 insertions(+), 675 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell V. Lenth [aut, cre, cph],
Balazs Banfai [ctb],
Ben Bolker [ctb],
Paul Buerkner [ctb],
Iago Gine-Vazquez [ctb],
Maxime Herve [ctb],
Maarten Jung [ctb],
Jonathon Love [ctb],
Fernando Miguez [ctb],
Julia Piaskowski [ctb],
Hannes Riebl [ctb],
Hen [...truncated...]
Maintainer: Russell V. Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.10.5 dated 2024-10-14 and 1.10.6 dated 2024-12-12
DESCRIPTION | 8 +- MD5 | 62 +++++++++++----------- NAMESPACE | 1 NEWS.md | 12 +++- R/eff-size.R | 19 ++++-- R/emmGrid-methods.R | 5 + R/factors.R | 28 +++++++++ R/rbind.R | 2 R/test.R | 3 - build/vignette.rds |binary inst/doc/AQuickStart.html | 4 - inst/doc/FAQs.html | 6 +- inst/doc/basics.html | 4 - inst/doc/comparisons.html | 10 +-- inst/doc/confidence-intervals.html | 14 ++-- inst/doc/interactions.html | 18 +++--- inst/doc/messy-data.html | 4 - inst/doc/models.Rmd | 5 + inst/doc/models.html | 104 +++++++++++++++++++------------------ inst/doc/predictions.html | 4 - inst/doc/re-engineering-clds.html | 4 - inst/doc/sophisticated.html | 4 - inst/doc/transformations.html | 4 - inst/doc/utilities.html | 4 - inst/doc/vignette-topics.html | 4 - inst/doc/xplanations.html | 4 - inst/doc/xtending.html | 8 +- man/eff_size.Rd | 11 +-- man/joint_tests.Rd | 3 - man/manip-factors.Rd | 20 +++++++ man/update.emmGrid.Rd | 5 + vignettes/models.Rmd | 5 + 32 files changed, 238 insertions(+), 151 deletions(-)
Title: Padronizador de Endereços Brasileiros (Brazilian Addresses
Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes
critérios. Os métodos de padronização incluem apenas manipulações
básicas de strings, não oferecendo suporte a correspondências
probabilísticas entre strings. (Standardizes brazilian addresses using
different criteria. Standardization methods include only basic string
manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Lucas Mation [aut]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between enderecobr versions 0.2.1 dated 2024-11-18 and 0.3.0 dated 2024-12-12
DESCRIPTION | 6 MD5 | 26 +- NEWS.md | 10 R/padronizar_ceps.R | 4 R/padronizar_enderecos.R | 42 ++- R/padronizar_estados.R | 49 ++-- build/vignette.rds |binary inst/doc/enderecobr.R | 2 inst/doc/enderecobr.html | 4 man/padronizar_enderecos.Rd | 6 man/padronizar_estados.Rd | 7 tests/testthat/_snaps/padronizar_enderecos.md | 318 +++++++++++++------------- tests/testthat/test-padronizar_enderecos.R | 28 ++ tests/testthat/test-padronizar_estados.R | 34 ++ 14 files changed, 323 insertions(+), 213 deletions(-)
Title: Simple, Consistent Package Options
Description: Simple mechanisms for defining and interpreting package options. Provides
helpers for interpreting environment variables, global options, defining
default values and more.
Author: Doug Kelkhoff [aut, cre]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Diff between options versions 0.2.0 dated 2024-05-12 and 0.3.0 dated 2024-12-12
DESCRIPTION | 12 ++-- MD5 | 25 ++++----- NAMESPACE | 3 + NEWS.md | 10 +++ R/envvars.R | 2 R/naming.R | 43 ++++++++++++++++ R/options_get.R | 71 ++++++++++++++++++++++++-- README.md | 2 inst/doc/envvars.R | 4 + inst/doc/envvars.html | 4 - inst/doc/options.R | 106 ++++++++++++++++++++-------------------- man/opt.Rd | 55 ++++++++++++++++++-- tests/testthat/test-envvars.R | 1 tests/testthat/test-opts_list.R |only 14 files changed, 249 insertions(+), 89 deletions(-)
Title: Superefficient Estimation of Future Conditional Hazards Based on
Marker Information
Description: Provides a nonparametric smoothed kernel density estimator for the future conditional hazard when time-dependent covariates are present. It also provides pointwise and uniform confidence bands and a bandwidth selection.
Author: Dimitrios Bagkavos [aut, cre],
Alex Isakson [ctb],
Enno Mammen [ctb],
Jens Nielsen [ctb],
Cecile Proust-Lima [ctb]
Maintainer: Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>
Diff between HQM versions 0.1.2 dated 2024-12-04 and 0.1.4 dated 2024-12-12
DESCRIPTION | 6 ++-- MD5 | 4 +-- man/h_xt_vec.Rd | 68 +++++++++++++++++++++----------------------------------- 3 files changed, 31 insertions(+), 47 deletions(-)
Title: Packages and Functions for 'CourseKata' Courses
Description: Easily install and load all packages and functions used in
'CourseKata' courses. Aid teaching with helper functions and augment
generic functions to provide cohesion between the network of packages.
Learn more about 'CourseKata' at <https://coursekata.org>.
Author: Adam Blake [cre, aut] ,
Ji Son [aut] ,
Jim Stigler [aut]
Maintainer: Adam Blake <adam@coursekata.org>
Diff between coursekata versions 0.18.0 dated 2024-08-16 and 0.18.1 dated 2024-12-12
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/data.R | 6 ++++-- build/partial.rdb |binary data/Fingers.rda |binary data/FingersMessy.rda |binary man/Fingers.Rd | 3 ++- man/FingersMessy.Rd | 3 ++- 9 files changed, 24 insertions(+), 16 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.2.2 dated 2024-11-28 and 1.2.3 dated 2024-12-12
DESCRIPTION | 6 - MD5 | 16 +- NEWS.md | 4 R/addIntersect.R | 7 - inst/doc/cohort-intersect.html | 68 ++++++------ inst/doc/concept-intersect.html | 92 ++++++++-------- inst/doc/demographics.html | 218 ++++++++++++++++++++-------------------- inst/doc/summarise.html | 192 +++++++++++++++++------------------ inst/doc/table-intersect.html | 86 +++++++-------- 9 files changed, 346 insertions(+), 343 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: PD-Clustering and Related Methods
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution-free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership under the constraint that the product of the probability and the distance of each point to any cluster center is a constant. PD-clustering is a flexible method that can be used with elliptical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different sizes. GPDC and TPDC use a dissimilarity measure based on densities. Factor PD-clustering (FPDC) is a factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high-dimensional data sets.
Author: Cristina Tortora [aut, cre, cph],
Noe Vidales [aut],
Francesco Palumbo [aut],
Tina Kalra [aut],
Paul D. McNicholas [fnd]
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between FPDclustering versions 2.3.1 dated 2024-01-29 and 2.3.2 dated 2024-12-12
DESCRIPTION | 36 ++++++++++++++++++++++++++++-------- MD5 | 3 ++- inst |only 3 files changed, 30 insertions(+), 9 deletions(-)
Title: Correct for Verification Bias in Diagnostic Accuracy & Agreement
Description: A standard test is observed on all specimens. We treat the second test (or sampled test) as being conducted on only a stratified sample of specimens. Verification Bias is this situation when the specimens for doing the second (sampled) test is not under investigator control. We treat the total sample as stratified two-phase sampling and use inverse probability weighting. We estimate diagnostic accuracy (category-specific classification probabilities; for binary tests reduces to specificity and sensitivity, and also predictive values) and agreement statistics (percent agreement, percent agreement by category, Kappa (unweighted), Kappa (quadratic weighted) and symmetry tests (reduces to McNemar's test for binary tests)). See: Katki HA, Li Y, Edelstein DW, Castle PE. Estimating the agreement and diagnostic accuracy of two diagnostic tests when one test is conducted on only a subsample of specimens. Stat Med. 2012 Feb 28; 31(5) <doi:10.1002/sim.4422>.
Author: Hormuzd A. Katki [aut],
David W. Edelstein [aut],
Hormuzd Katki [cre]
Maintainer: Hormuzd Katki <katkih@mail.nih.gov>
Diff between CompareTests versions 1.2 dated 2017-02-06 and 1.3 dated 2024-12-12
DESCRIPTION | 25 ++++++++++++++++++------- MD5 | 6 +++--- man/CompareTests.Rd | 4 ++-- man/fulltable.Rd | 4 ++-- 4 files changed, 25 insertions(+), 14 deletions(-)
Title: Cluster Analysis with Missing Values by Multiple Imputation
Description: Allows clustering of incomplete observations by addressing missing values using multiple imputation. For achieving this goal, the methodology consists in three steps, following Audigier and Niang 2022 <doi:10.1007/s11634-022-00519-1>. I) Missing data imputation using dedicated models. Four multiple imputation methods are proposed, two are based on joint modelling and two are fully sequential methods, as discussed in Audigier et al. (2021) <doi:10.48550/arXiv.2106.04424>. II) cluster analysis of imputed data sets. Six clustering methods are available (distances-based or model-based), but custom methods can also be easily used. III) Partition pooling. The set of partitions is aggregated using Non-negative Matrix Factorization based method. An associated instability measure is computed by bootstrap (see Fang, Y. and Wang, J., 2012 <doi:10.1016/j.csda.2011.09.003>). Among applications, this instability measure can be used to choose a number of clusters with missing value [...truncated...]
Author: Vincent Audigier [aut, cre] ,
Hang Joon Kim [ctb]
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between clusterMI versions 1.2.2 dated 2024-10-23 and 1.3 dated 2024-12-12
DESCRIPTION | 8 - MD5 | 50 +++++------ R/calculintra.intern.R | 7 + R/chooseB.R | 2 R/choosem.R | 2 R/choosemaxit.R | 2 R/choosenbclust.R | 109 ++++++------------------ R/chooser.R | 3 R/clusterMI-package.R | 2 R/clusterMI.R | 43 ++++++--- R/fastnmf.R | 20 +++- R/imputedata.R | 205 +++++++++++++++++++++++------------------------ R/myem.mix.R | 4 R/overimpute.R | 2 R/varselbest.R | 2 man/chooseB.Rd | 2 man/choosem.Rd | 2 man/choosemaxit.Rd | 2 man/choosenbclust.Rd | 2 man/chooser.Rd | 2 man/clusterMI-package.Rd | 2 man/clusterMI.Rd | 4 man/fastnmf.Rd | 4 man/imputedata.Rd | 2 man/overimpute.Rd | 2 man/varselbest.Rd | 2 26 files changed, 234 insertions(+), 253 deletions(-)
Title: Common Public Health Statistics and their Confidence Intervals
Description: Functions to calculate commonly used public health statistics and
their confidence intervals using methods approved for use in the production
of Public Health England indicators such as those presented via Fingertips
(<https://fingertips.phe.org.uk/>). It provides functions for the generation
of proportions, crude rates, means, directly standardised rates, indirectly
standardised rates, standardised mortality ratios, slope and relative index
of inequality and life expectancy.
Statistical methods are referenced in the following publications.
Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>.
Dobson et al (1991) <doi:10.1002/sim.4780100317>.
Armitage P, Berry G (2002) <doi:10.1002/9780470773666>.
Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>.
Altman DG et al (2000, ISBN: 978-0-727-91375-3).
Chiang CL. (1968, ISBN: 978-0-882-75200-6).
Newell C. (1994, ISBN: 978-0-898-62451-9).
Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>.
S [...truncated...]
Author: Georgina Anderson [aut, cre],
Sebastian Fox [ctb],
Matthew Francis [ctb],
Paul Fryers [ctb],
Emma Clegg [ctb],
Annabel Westermann [ctb],
Joshua Woolner [ctb],
Charlotte Fellows [ctb],
Olivia Box Power [ctb]
Maintainer: Georgina Anderson <georgina.anderson@dhsc.gov.uk>
Diff between PHEindicatormethods versions 2.0.2 dated 2024-01-25 and 2.1.0 dated 2024-12-12
PHEindicatormethods-2.0.2/PHEindicatormethods/R/PHEindicatormethods.R |only PHEindicatormethods-2.0.2/PHEindicatormethods/man/PHEindicatormethods.Rd |only PHEindicatormethods-2.1.0/PHEindicatormethods/DESCRIPTION | 57 PHEindicatormethods-2.1.0/PHEindicatormethods/MD5 | 92 PHEindicatormethods-2.1.0/PHEindicatormethods/NAMESPACE | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/NEWS.md | 8 PHEindicatormethods-2.1.0/PHEindicatormethods/R/DSR.R | 625 +++-- PHEindicatormethods-2.1.0/PHEindicatormethods/R/ISRate.R | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/R/ISRatio.R | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/R/LifeExpectancy.R | 3 PHEindicatormethods-2.1.0/PHEindicatormethods/R/Means.R | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/R/PHEindicatormethods-package.R |only PHEindicatormethods-2.1.0/PHEindicatormethods/R/Proportions.R | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/R/Rates.R | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/R/phe_DSR.R |only PHEindicatormethods-2.1.0/PHEindicatormethods/R/sysdata.rda |binary PHEindicatormethods-2.1.0/PHEindicatormethods/R/utils.R | 8 PHEindicatormethods-2.1.0/PHEindicatormethods/build/partial.rdb |only PHEindicatormethods-2.1.0/PHEindicatormethods/build/vignette.rds |binary PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/DSR-vignette.R | 151 + PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/DSR-vignette.Rmd | 345 +-- PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/DSR-vignette.html | 784 ++++--- PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/Introduction_to_PHEindicatormethods.R | 141 + PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/Introduction_to_PHEindicatormethods.Rmd | 102 PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/Introduction_to_PHEindicatormethods.html | 1104 +++++----- PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/WorkedExamples_phe_sii.R | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/WorkedExamples_phe_sii.Rmd | 10 PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/WorkedExamples_phe_sii.html | 500 +++- PHEindicatormethods-2.1.0/PHEindicatormethods/man/PHEindicatormethods-package.Rd |only PHEindicatormethods-2.1.0/PHEindicatormethods/man/assign_funnel_significance.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/man/calculate_ISRate.Rd | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/man/calculate_ISRatio.Rd | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/man/calculate_dsr.Rd |only PHEindicatormethods-2.1.0/PHEindicatormethods/man/calculate_funnel_limits.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/man/calculate_funnel_points.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/man/figures |only PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_dsr.Rd | 41 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_life_expectancy.Rd | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_mean.Rd | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_proportion.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_quantile.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_rate.Rd | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_sii.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/tests/testthat/testDSRs.R | 478 +++- PHEindicatormethods-2.1.0/PHEindicatormethods/tests/testthat/testLifeExpectancy.R | 9 PHEindicatormethods-2.1.0/PHEindicatormethods/tests/testthat/testdata_DSR_ISR.xlsx |binary PHEindicatormethods-2.1.0/PHEindicatormethods/tests/testthat/testpheDSRs.R |only PHEindicatormethods-2.1.0/PHEindicatormethods/vignettes/DSR-vignette.Rmd | 345 +-- PHEindicatormethods-2.1.0/PHEindicatormethods/vignettes/Introduction_to_PHEindicatormethods.Rmd | 102 PHEindicatormethods-2.1.0/PHEindicatormethods/vignettes/WorkedExamples_phe_sii.Rmd | 10 50 files changed, 3122 insertions(+), 1841 deletions(-)
More information about PHEindicatormethods at CRAN
Permanent link
Title: Statistical Methods for Survival Data with Dependent Censoring
Description: Several statistical methods for analyzing survival data under various forms of dependent
censoring are implemented in the package. In addition to accounting for dependent censoring, it
offers tools to adjust for unmeasured confounding factors. The implemented approaches allow
users to estimate the dependency between survival time and dependent censoring time, based
solely on observed survival data. For more details on the methods, refer to Deresa and Van
Keilegom (2021) <doi:10.1093/biomet/asaa095>, Czado and Van Keilegom (2023)
<doi:10.1093/biomet/asac067>, Crommen et al. (2024) <doi:10.1007/s11749-023-00903-9>,
Deresa and Van Keilegom (2024) <doi:10.1080/01621459.2022.2161387> and Willems et al. (2024+)
<doi:10.48550/arXiv.2403.11860> and Ding and Van Keilegom (2024).
Author: Ilias Willems [aut] ,
Gilles Crommen [aut] ,
Negera Wakgari Deresa [aut, cre]
,
Jie Ding [aut] ,
Claudia Czado [aut] ,
Ingrid Van Keilegom [aut]
Maintainer: Negera Wakgari Deresa <negera.deresa@gmail.com>
Diff between depCensoring versions 0.1.4 dated 2024-12-04 and 0.1.5 dated 2024-12-12
DESCRIPTION | 17 ++++++++------ MD5 | 28 ++++++++++++++++++++--- NAMESPACE | 19 +++++++++++++++ NEWS.md | 36 +++++++++++++++--------------- R/SemiParametricCopulawithoutCovariates.R |only man/Kernel.Rd |only man/Likelihood.Parametric.Rd |only man/Likelihood.Profile.Kernel.Rd |only man/Likelihood.Profile.Solve.Rd |only man/Likelihood.Semiparametric.Rd |only man/Parameters.Constraints.Rd |only man/SurvDC.GoF.Rd |only man/SurvDC.Rd |only man/SurvFunc.CG.Rd |only man/SurvFunc.KM.Rd |only man/SurvMLE.Likelihood.Rd |only man/SurvMLE.Rd |only man/control.arguments.Rd |only man/copdist.Archimedean.Rd |only man/cophfunc.Rd |only man/coppar.to.ktau.Rd |only man/generator.Archimedean.Rd |only man/ktau.to.coppar.Rd |only man/parafam.d.Rd |only man/parafam.p.Rd |only man/parafam.trunc.Rd |only 26 files changed, 73 insertions(+), 27 deletions(-)
Title: Covariate-Based Covariance Functions for Nonstationary Spatial
Modeling
Description: Estimation, prediction, and simulation of nonstationary Gaussian process with modular covariate-based covariance functions.
Sources of nonstationarity, such as spatial mean, variance, geometric anisotropy, smoothness, and nugget, can be considered based on spatial characteristics.
An induced compact-supported nonstationary covariance function is provided, enabling fast and memory-efficient computations when handling densely sampled domains.
Author: Federico Blasi [aut, cre] ,
Reinhard Furrer [ctb]
Maintainer: Federico Blasi <federico.blasi@gmail.com>
Diff between cocons versions 0.1.3 dated 2024-10-15 and 0.1.4 dated 2024-12-12
cocons-0.1.3/cocons/man/getTrend.Rd |only cocons-0.1.3/cocons/man/show-methods.Rd |only cocons-0.1.4/cocons/DESCRIPTION | 12 cocons-0.1.4/cocons/MD5 | 51 +- cocons-0.1.4/cocons/NEWS.md | 30 + cocons-0.1.4/cocons/R/checkFunctions.R | 33 + cocons-0.1.4/cocons/R/cocons.R | 19 cocons-0.1.4/cocons/R/getFunctions.R | 56 +- cocons-0.1.4/cocons/R/methods.R | 85 --- cocons-0.1.4/cocons/R/neg2loglikelihood.R | 106 +++- cocons-0.1.4/cocons/R/optim.R | 63 +- cocons-0.1.4/cocons/R/plot.R | 18 cocons-0.1.4/cocons/R/predict.R | 57 +- cocons-0.1.4/cocons/R/sim.R | 7 cocons-0.1.4/cocons/inst/doc/cocons.pdf |binary cocons-0.1.4/cocons/man/GetNeg2loglikelihoodProfile.Rd | 2 cocons-0.1.4/cocons/man/GetNeg2loglikelihoodREML.Rd |only cocons-0.1.4/cocons/man/coco.Rd | 10 cocons-0.1.4/cocons/man/cocoOptim.Rd | 16 cocons-0.1.4/cocons/man/cocoPredict.Rd | 10 cocons-0.1.4/cocons/man/cocoSim.Rd | 2 cocons-0.1.4/cocons/man/cocons-package.Rd | 4 cocons-0.1.4/cocons/man/getCIs.Rd | 2 cocons-0.1.4/cocons/man/getDensityFromDelta.Rd |only cocons-0.1.4/cocons/man/getHessian.Rd | 2 cocons-0.1.4/cocons/man/getSpatMean.Rd |only cocons-0.1.4/cocons/src/cocons_full.cpp | 410 +++++++++++------ cocons-0.1.4/cocons/src/cocons_taper.cpp | 243 ++++++++-- cocons-0.1.4/cocons/src/cocons_types.h | 16 29 files changed, 842 insertions(+), 412 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between RODBC versions 1.3-25.1 dated 2024-12-11 and 1.3-26 dated 2024-12-12
ChangeLog | 10 +++++++++- DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- inst/doc/RODBC.pdf |binary src/RODBC.c | 24 ++++++++++++++++++++---- 5 files changed, 38 insertions(+), 14 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr [aut, cre]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between rms versions 6.8-2 dated 2024-08-23 and 6.9-0 dated 2024-12-12
rms-6.8-2/rms/R/lrm.fit.bare.r |only rms-6.8-2/rms/R/lrm.fit.s |only rms-6.8-2/rms/R/lrm.fit.strat.s |only rms-6.8-2/rms/man/lrm.fit.bare.Rd |only rms-6.8-2/rms/src/lrmfit.f |only rms-6.8-2/rms/src/ormuv.f |only rms-6.8-2/rms/src/robcovf.f |only rms-6.9-0/rms/DESCRIPTION | 10 - rms-6.9-0/rms/MD5 | 77 ++++---- rms-6.9-0/rms/NAMESPACE | 4 rms-6.9-0/rms/NEWS | 33 ++- rms-6.9-0/rms/R/LRchunktest.r | 6 rms-6.9-0/rms/R/anova.rms.s | 6 rms-6.9-0/rms/R/bootcov.s | 16 - rms-6.9-0/rms/R/lrm.fit.r |only rms-6.9-0/rms/R/lrm.s | 133 ++++---------- rms-6.9-0/rms/R/orm.fit.s | 72 +------ rms-6.9-0/rms/R/orm.s | 2 rms-6.9-0/rms/R/pentrace.s | 132 +++++++------- rms-6.9-0/rms/R/predab.resample.s | 9 rms-6.9-0/rms/R/recode2integer.r |only rms-6.9-0/rms/R/robcov.s | 2 rms-6.9-0/rms/R/val.prob.s | 2 rms-6.9-0/rms/R/validate.lrm.s | 80 ++++---- rms-6.9-0/rms/inst/tests/anova-lr.r | 5 rms-6.9-0/rms/inst/tests/lrm.ols.penalty.r | 4 rms-6.9-0/rms/inst/tests/lrm3.r |only rms-6.9-0/rms/inst/tests/lrmMean.s | 3 rms-6.9-0/rms/inst/tests/orm-bootcov.r | 3 rms-6.9-0/rms/inst/tests/robcov4.r |only rms-6.9-0/rms/inst/tests/robcov_Yuqi.r | 2 rms-6.9-0/rms/inst/tests/scale.r | 6 rms-6.9-0/rms/inst/tests/val.prob.r | 8 rms-6.9-0/rms/man/anova.rms.Rd | 6 rms-6.9-0/rms/man/bootcov.Rd | 3 rms-6.9-0/rms/man/gIndex.Rd | 9 rms-6.9-0/rms/man/lrm.Rd | 98 ++++------ rms-6.9-0/rms/man/lrm.fit.Rd | 273 ++++++++++++++--------------- rms-6.9-0/rms/man/orm.Rd | 2 rms-6.9-0/rms/man/orm.fit.Rd | 11 - rms-6.9-0/rms/man/pentrace.Rd | 8 rms-6.9-0/rms/man/recode2integer.Rd |only rms-6.9-0/rms/man/validate.lrm.Rd | 15 - rms-6.9-0/rms/src/init.c | 8 rms-6.9-0/rms/src/lrmll.f90 |only rms-6.9-0/rms/src/ormuv.f90 |only rms-6.9-0/rms/src/robcovf.f90 |only 47 files changed, 475 insertions(+), 573 deletions(-)
Title: Soil Defense Investments in Italy: Data Retrieval, Analysis,
Visualization
Description: Facilitates the retrieval and analysis of financial data related to public works in Italy,
focusing on soil defense investments. It extracts data from 'OpenCoesione', 'OpenBDAP',
and the 'ReNDiS' database, eliminating the need for direct access to these platforms.
The package boasts a user-friendly design, featuring real time updates and a set of functions
tailored for data retrieval and visualization.
See the webpages for further information
<http://www.rendis.isprambiente.it/rendisweb/>,
<https://opencoesione.gov.it/en/>, and
<https://bdap-opendata.rgs.mef.gov.it/>.
Author: Lorena Ricciotti [aut, cre] ,
Alessio Pollice [ths]
Maintainer: Lorena Ricciotti <lorena.ricciotti@uniba.it>
Diff between PublicWorksFinanceIT versions 0.3.0 dated 2024-10-29 and 0.3.1 dated 2024-12-12
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS.md | 38 ++++++++++++++++++++------------------ 3 files changed, 25 insertions(+), 23 deletions(-)
More information about PublicWorksFinanceIT at CRAN
Permanent link
Title: Generate Generative Data for a Data Source
Description: Generative Adversarial Networks are applied to generate generative data for a data source. A generative model consisting of a generator and a discriminator network is trained. During iterative training the distribution of generated data is converging to that of the data source. Direct applications of generative data are the created functions for data evaluation, missing data completion and data classification. A software service for accelerated training of generative models on graphics processing units is available. Reference: Goodfellow et al. (2014) <doi:10.48550/arXiv.1406.2661>.
Author: Werner Mueller [aut, cre]
Maintainer: Werner Mueller <werner.mueller5@chello.at>
Diff between ganGenerativeData versions 2.1.3 dated 2024-10-07 and 2.1.4 dated 2024-12-12
DESCRIPTION | 10 ++--- MD5 | 34 +++++++++-------- NAMESPACE | 2 + R/RcppExports.R | 29 ++++++++++++-- R/dsInt.R | 37 ++++++++++++++++++ R/gdTrain.R | 5 ++ R/gdTrainGenerate.R | 37 ++++++++++++++---- man/dsCalculateDensityValues.Rd |only man/dsDensityValueInverseQuantile.Rd |only man/figures/dvh.png |only man/figures/dviq.png |only man/ganGenerativeData-package.Rd | 62 ++++++++++++++++++++++++------- man/gdComplete.Rd | 2 - man/gdKNearestNeighbors.Rd | 4 +- man/gdTrainParameters.Rd | 2 - src/RcppExports.cpp | 30 +++++++++++++-- src/density.h | 3 + src/dsInt.cpp | 69 ++++++++++++++++++++++++++++++++--- src/gdInt.cpp | 7 +-- src/vpTree.h | 22 ++++++++++- 20 files changed, 290 insertions(+), 65 deletions(-)
More information about ganGenerativeData at CRAN
Permanent link
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood and Laplace approximation model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
See <https://samuel-watson.github.io/glmmr-web/> for a detailed manual.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 0.11.1 dated 2024-12-09 and 0.11.2 dated 2024-12-12
glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_bernoulli.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_beta.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_binomial.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_gamma.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_gaussian.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_poisson.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_quantile.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_bernoulli.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_beta.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_binomial.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_gamma.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_gaussian.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_poisson.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_quantile.stan |only glmmrBase-0.11.1/glmmrBase/src/covariance_module.cpp |only glmmrBase-0.11.1/glmmrBase/src/linpred_module.cpp |only glmmrBase-0.11.1/glmmrBase/src/model_module_2.cpp |only glmmrBase-0.11.1/glmmrBase/src/model_module_extension.cpp |only glmmrBase-0.11.1/glmmrBase/src/openmp_utils.cpp |only glmmrBase-0.11.1/glmmrBase/src/other_functions.cpp |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_bernoulli.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_bernoulli.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_beta.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_beta.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_binomial.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_binomial.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_gamma.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_gamma.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_gaussian.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_gaussian.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_poisson.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_poisson.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_quantile.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_quantile.h |only glmmrBase-0.11.2/glmmrBase/DESCRIPTION | 8 glmmrBase-0.11.2/glmmrBase/MD5 | 135 glmmrBase-0.11.2/glmmrBase/R/R6Model.R | 113 glmmrBase-0.11.2/glmmrBase/R/RcppExports.R | 88 glmmrBase-0.11.2/glmmrBase/R/extrafunctions.R | 68 glmmrBase-0.11.2/glmmrBase/R/stanmodels.R | 10 glmmrBase-0.11.2/glmmrBase/build/partial.rdb |binary glmmrBase-0.11.2/glmmrBase/inst/cmdstan/mcml.stan |only glmmrBase-0.11.2/glmmrBase/inst/include/glmmr.h | 1 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/calculator.hpp | 9 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/covariance.hpp | 23 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/family.hpp | 39 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/formulaparse.h | 16 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/general.h | 331 - glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/griddata.hpp | 1 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/interpreter.h | 99 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/maths.h | 32 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/model.hpp | 6 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/modelbits.hpp | 1 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/modelmatrix.hpp | 71 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/modeloptim.hpp | 10 glmmrBase-0.11.2/glmmrBase/inst/stan/mcml.stan |only glmmrBase-0.11.2/glmmrBase/man/Beta.Rd | 34 glmmrBase-0.11.2/glmmrBase/man/Salamanders.Rd | 28 glmmrBase-0.11.2/glmmrBase/man/SimGeospat.Rd | 48 glmmrBase-0.11.2/glmmrBase/man/SimTrial.Rd | 50 glmmrBase-0.11.2/glmmrBase/man/coef.Model.Rd | 38 glmmrBase-0.11.2/glmmrBase/man/coef.mcml.Rd | 38 glmmrBase-0.11.2/glmmrBase/man/confint.mcml.Rd | 38 glmmrBase-0.11.2/glmmrBase/man/family.Model.Rd | 40 glmmrBase-0.11.2/glmmrBase/man/family.mcml.Rd | 38 glmmrBase-0.11.2/glmmrBase/man/fitted.Model.Rd | 44 glmmrBase-0.11.2/glmmrBase/man/fitted.mcml.Rd | 40 glmmrBase-0.11.2/glmmrBase/man/fixed.effects.Rd | 34 glmmrBase-0.11.2/glmmrBase/man/formula.Model.Rd | 40 glmmrBase-0.11.2/glmmrBase/man/formula.mcml.Rd | 44 glmmrBase-0.11.2/glmmrBase/man/lme4_to_glmmr.Rd | 60 glmmrBase-0.11.2/glmmrBase/man/logLik.Model.Rd | 38 glmmrBase-0.11.2/glmmrBase/man/logLik.mcml.Rd | 50 glmmrBase-0.11.2/glmmrBase/man/mcml_lmer.Rd | 132 glmmrBase-0.11.2/glmmrBase/man/predict.Model.Rd | 62 glmmrBase-0.11.2/glmmrBase/man/predict.mcml.Rd | 40 glmmrBase-0.11.2/glmmrBase/man/random.effects.Rd | 34 glmmrBase-0.11.2/glmmrBase/man/residuals.Model.Rd | 56 glmmrBase-0.11.2/glmmrBase/man/residuals.mcml.Rd | 50 glmmrBase-0.11.2/glmmrBase/man/setParallel.Rd | 42 glmmrBase-0.11.2/glmmrBase/man/summary.Model.Rd | 42 glmmrBase-0.11.2/glmmrBase/man/vcov.Model.Rd | 44 glmmrBase-0.11.2/glmmrBase/man/vcov.mcml.Rd | 46 glmmrBase-0.11.2/glmmrBase/src/RcppExports.cpp | 164 glmmrBase-0.11.2/glmmrBase/src/heckman.cpp |only glmmrBase-0.11.2/glmmrBase/src/model_module.cpp | 2025 ++++++++++ glmmrBase-0.11.2/glmmrBase/src/stanExports_mcml.cc |only glmmrBase-0.11.2/glmmrBase/src/stanExports_mcml.h |only 88 files changed, 3239 insertions(+), 1261 deletions(-)
Title: Interface to 'JDemetra+' Seasonal Adjustment Software
Description: Interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially
recommended to the members of the European Statistical System (ESS) and the European System of Central Banks.
It offers full access to all options and outputs of 'JDemetra+', including the two leading seasonal adjustment methods
TRAMO/SEATS+ and X-12ARIMA/X-13ARIMA-SEATS.
Author: Alain Quartier-la-Tente [aut, cre]
,
Anna Michalek [aut],
Jean Palate [aut],
Raf Baeyens [aut]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between RJDemetra versions 0.2.7 dated 2024-10-01 and 0.2.8 dated 2024-12-12
DESCRIPTION | 6 - MD5 | 26 ++--- NEWS.md | 13 ++ R/export_workspace.R | 163 ++++++++++++++++++++----------- R/get_jmodel.R | 42 +++++--- R/get_jspec.R | 4 R/import_workspace.R | 73 ++++++++------ R/jsa2r.R | 2 R/regarima_rslts.R | 28 +++-- R/spec_rjd.R | 262 +++++++++++++++++++++++++++++++++------------------ R/tramoseats.R | 29 +++-- R/x13.R | 28 +++-- man/add_sa_item.Rd | 2 man/get_model.Rd | 18 +++ 14 files changed, 446 insertions(+), 250 deletions(-)
Title: Check if a Remote Computer is Up
Description: Check if a remote computer is up. It can either just call the
system ping command, or check a specified TCP port.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pingr versions 2.0.4 dated 2024-10-28 and 2.0.5 dated 2024-12-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/dns.c | 25 +++++++++++++++++++++++++ tests/testthat/test-tcp.R | 4 ++-- 5 files changed, 38 insertions(+), 9 deletions(-)
Title: Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Description: An EM algorithm, Karl et al. (2013) <doi:10.1016/j.csda.2012.10.004>, is used to estimate the generalized, variable, and complete persistence models, Mariano et al. (2010) <doi:10.3102/1076998609346967>. These are multiple-membership linear mixed models with teachers modeled as "G-side" effects and students modeled with either "G-side" or "R-side" effects.
Author: Andrew Karl [cre, aut] ,
Yan Yang [aut],
Sharon Lohr [aut]
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between GPvam versions 3.1-2 dated 2024-11-17 and 3.2-0 dated 2024-12-12
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NEWS | 4 +++ R/bias.test.custom.R | 58 ++++++++++++------------------------------------ man/bias.test.custom.Rd | 12 +-------- 5 files changed, 29 insertions(+), 61 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Roger Bivand [ctb] ,
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.7-83 dated 2024-10-14 and 1.8-5 dated 2024-12-12
DESCRIPTION | 8 MD5 | 219 +++---- NAMESPACE | 62 - NEWS.md | 58 + R/Agenerics.R | 787 ++++++++++++------------- R/RGB.R | 31 R/Zdeprecated.R | 42 - R/aggregate.R | 2 R/app.R | 5 R/generics.R | 18 R/geom.R | 15 R/graticule.R | 26 R/lapp.R | 12 R/levels.R | 34 - R/plot.R | 11 R/plot_legend.R | 16 R/plot_let.R | 40 + R/plot_raster.R | 63 +- R/predict.R | 11 R/rast.R | 5 R/read.R | 128 ++-- R/replace_values.R | 18 R/rowSums.R | 168 ++--- R/sample.R | 18 R/show.R | 1280 ++++++++++++++++++++--------------------- R/tags.R | 62 + R/tapp.R | 18 R/tempfiles.R | 4 R/values.R | 5 R/vect.R | 9 R/wrap.R | 99 ++- R/zonal.R | 10 configure | 644 +++++++++++--------- configure.ac | 46 - inst/tinytest/test_rasterize.R | 2 man/RGB.Rd | 10 man/clamp.Rd | 2 man/classify.Rd | 2 man/compareGeom.Rd | 2 man/contour.Rd | 10 man/deprecated.Rd | 11 man/expanse.Rd | 4 man/global.Rd | 2 man/gridDist.Rd | 4 man/inplace.Rd | 2 man/lapp.Rd | 7 man/mappal.Rd | 14 man/metags.Rd | 4 man/patches.Rd | 13 man/plet.Rd | 10 man/plot.Rd | 6 man/rast.Rd | 12 man/rowSums.Rd |only man/selectHigh.Rd | 80 +- man/serialize.Rd | 2 man/sieve.Rd | 90 +- man/split.Rd | 2 man/subst.Rd | 2 man/surfArea.Rd |only man/tapp.Rd | 2 man/terra-package.Rd | 7 man/toMemory.Rd |only man/vect.Rd | 1 man/wrap.Rd | 2 man/writeVector.Rd | 5 src/RcppFunctions.cpp | 2 src/RcppModule.cpp | 14 src/arith.cpp | 38 - src/crs.cpp | 2 src/distRaster.cpp | 16 src/distance.cpp | 31 src/distance.h | 2 src/extract.cpp | 2 src/file_utils.cpp | 6 src/focal.cpp | 2 src/gdal_algs.cpp | 298 ++++++++- src/gdalio.cpp | 43 + src/geos_methods.cpp | 84 +- src/geos_spat.h | 2 src/geosphere.cpp | 2 src/math_utils.cpp | 2 src/mediancut.cpp | 2 src/memory.cpp | 2 src/movingWindow.cpp | 2 src/patches.cpp |only src/ram.cpp | 2 src/raster_methods.cpp | 216 +++++- src/raster_stats.cpp | 2 src/rasterize.cpp | 200 +++--- src/read.cpp | 2 src/read_gdal.cpp | 115 ++- src/read_ogr.cpp | 22 src/sample.cpp | 2 src/spatBase.cpp | 2 src/spatDataframe.cpp | 45 - src/spatDataframe.h | 1 src/spatRaster.cpp | 156 +++- src/spatRaster.h | 26 src/spatRasterMultiple.cpp | 46 + src/spatRasterMultiple.h | 9 src/spatSources.cpp | 2 src/spatTime.cpp | 22 src/spatVector.cpp | 4 src/spatVector2.cpp | 2 src/string_utils.cpp | 2 src/surfArea.cpp |only src/vecmath.cpp | 2 src/vecmath.h | 1 src/vecmathse.cpp | 2 src/vector_methods.cpp | 2 src/write.cpp | 2 src/write_gdal.cpp | 47 + src/write_ogr.cpp | 2 113 files changed, 3479 insertions(+), 2293 deletions(-)
Title: Pathways Longitudinal and Differential Analysis in Metabolomics
Description: Perform a differential analysis at pathway level based on metabolite quantifications and information on pathway metabolite composition.
The method is based on a Principal Component Analysis step and on a linear mixed model.
Automatic query of metabolic pathways is also implemented.
Author: Camille Guilmineau [aut, cre],
Remi Servien [aut] ,
Nathalie Vialaneix [aut]
Maintainer: Camille Guilmineau <camille.guilmineau@inrae.fr>
Diff between phoenics versions 0.3 dated 2024-07-22 and 0.4 dated 2024-12-12
DESCRIPTION | 10 MD5 | 16 - NAMESPACE | 10 NEWS.md | 16 + R/pathwayRes-class.R | 139 +++++++++-- R/test_pathway.R | 95 +++++-- inst/adddata/ASICS_library_codes.txt | 434 +++++++++++++++++------------------ man/pathwayRes.Rd | 17 + man/test_pathway.Rd | 35 +- 9 files changed, 477 insertions(+), 295 deletions(-)
Title: Generate and Plot Voronoi or Sunburst Treemaps from Hierarchical
Data
Description: Treemaps are a visually appealing graphical representation of
numerical data using a space-filling approach. A plane or 'map' is
subdivided into smaller areas called cells. The cells in the map are
scaled according to an underlying metric which allows to grasp the
hierarchical organization and relative importance of many objects at
once. This package contains two different implementations of treemaps,
Voronoi treemaps and Sunburst treemaps. The Voronoi treemap function
subdivides the plot area in polygonal cells according to the highest
hierarchical level, then continues to subdivide those parental cells
on the next lower hierarchical level, and so on. The Sunburst treemap
is a computationally less demanding treemap that does not require
iterative refinement, but simply generates circle sectors that are
sized according to predefined weights. The Voronoi tesselation is
based on functions from Paul Murrell (2012)
<https://www.stat.auckland.ac.nz/~paul/Reports/VoronoiTreemap/voronoi [...truncated...]
Author: Michael Jahn [aut, cre] ,
David Leslie [aut],
Ahmadou Dicko [aut] ,
Dunipace Eric [aut] ,
Paul Murrell [aut, cph]
Maintainer: Michael Jahn <jahn@mpusp.mpg.de>
Diff between WeightedTreemaps versions 0.1.3 dated 2024-11-04 and 0.1.4 dated 2024-12-12
DESCRIPTION | 9 + MD5 | 18 +-- NEWS.md | 6 + R/drawTreemap.R | 14 ++- R/drawUtils.R | 98 +++++++++++---------- README.md | 5 - inst/doc/WeightedTreemaps.R | 186 ++++++++++++++++++++--------------------- inst/doc/WeightedTreemaps.html | 4 man/drawTreemap.Rd | 12 ++ src/Makevars | 2 10 files changed, 194 insertions(+), 160 deletions(-)
More information about WeightedTreemaps at CRAN
Permanent link
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic models
(assuming either presence or absence of the effect, heterogeneity, and
publication bias). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2022,
<doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022,
<doi:10.1037/met0000405>). Users can define a wide range of non-informative
or informative prior distributions for the effect size, heterogeneity,
and publication bias components (including selection models and PET-PEESE).
The package provides convenient functions for summary, visualizations, and
fit diagnostics.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut] ,
Eric-Jan Wagenmakers [ths] ,
Joris Goosen [ctb],
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBMA versions 3.1.0 dated 2023-07-18 and 3.2.0 dated 2024-12-12
DESCRIPTION | 16 +- MD5 | 117 ++++++++++--------- NAMESPACE | 2 NEWS.md | 18 ++- R/BiBMA.R | 59 +++++++++ R/NoBMA.R | 14 +- R/RoBMA-reg.R | 55 +++++++-- R/RoBMA.R | 36 ++++-- R/datasets.R | 19 +++ R/fit-and-marglik.R | 4 R/summary-heterogeneity.R |only R/summary.R | 33 +---- R/tools.R | 73 +++++++++++- R/utilities.R | 8 + R/zzz.R | 4 README.md | 137 +++++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary data/Andrews2021.RData |only inst/REFERENCES.bib | 79 +++++++++++-- inst/doc/CustomEnsembles.R | 76 ++++++------ inst/doc/CustomEnsembles.Rmd | 29 ++-- inst/doc/CustomEnsembles.html | 141 ++++++++++++----------- inst/doc/HierarchicalBMA.R | 64 +++++----- inst/doc/HierarchicalBMA.Rmd | 24 ++-- inst/doc/HierarchicalBMA.html | 128 ++++++++++----------- inst/doc/MedicineBMA.R | 38 +++--- inst/doc/MedicineBMA.Rmd | 26 ++-- inst/doc/MedicineBMA.html | 158 +++++++++++++------------- inst/doc/MedicineBiBMA.R |only inst/doc/MedicineBiBMA.Rmd |only inst/doc/MedicineBiBMA.html |only inst/doc/MetaRegression.R |only inst/doc/MetaRegression.Rmd |only inst/doc/MetaRegression.html |only inst/doc/ReproducingBMA.R | 58 ++++----- inst/doc/ReproducingBMA.Rmd | 20 +-- inst/doc/ReproducingBMA.html | 166 ++++++++++++++-------------- inst/doc/Tutorial.R | 28 ++-- inst/doc/Tutorial.Rmd | 42 +++---- inst/doc/Tutorial.html | 143 ++++++++++++------------ man/Andrews2021.Rd |only man/BiBMA.Rd | 42 ++++++- man/NoBMA.Rd | 12 +- man/NoBMA.reg.Rd | 23 ++- man/RoBMA-package.Rd | 1 man/RoBMA.Rd | 18 +-- man/RoBMA.reg.Rd | 68 ++++++++--- man/check_RoBMA.Rd | 7 + man/check_setup.reg.Rd | 24 ++-- man/figures/README-fig_PETPEESE-1.png |binary man/figures/README-fig_forest-1.png |binary man/figures/README-fig_mu-1.png |binary man/figures/README-fig_mu_chain-1.png |binary man/figures/README-fig_mu_ind-1.png |binary man/figures/README-fig_tau-1.png |binary man/figures/README-fig_weightfunction-1.png |binary man/summary_heterogeneity.Rd |only tests/testthat/Rplots.pdf |only vignettes/CustomEnsembles.Rmd | 29 ++-- vignettes/HierarchicalBMA.Rmd | 24 ++-- vignettes/MedicineBMA.Rmd | 26 ++-- vignettes/MedicineBiBMA.Rmd |only vignettes/MetaRegression.Rmd |only vignettes/ReproducingBMA.Rmd | 20 +-- vignettes/Tutorial.Rmd | 42 +++---- 66 files changed, 1296 insertions(+), 855 deletions(-)
Title: 'GNU Unifont' Hex Fonts
Description: Contains most of the hex font files from the 'GNU Unifont Project' <https://unifoundry.com/unifont/> compressed by 'xz'. 'GNU Unifont' is a duospaced bitmap font that attempts to cover all the official Unicode glyphs plus several of the artificial scripts in the '(Under-)ConScript Unicode Registry' <https://www.kreativekorp.com/ucsur/>. Provides a convenience function for loading in several of them at the same time as a 'bittermelon' bitmap font object for easy rendering of the glyphs in an 'R' terminal or graphics device.
Author: Trevor L. Davis [aut, cre] ,
GNU Unifont authors [cph]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between hexfont versions 0.4.0 dated 2023-12-18 and 0.5.1 dated 2024-12-12
DESCRIPTION | 22 - MD5 | 66 ++--- NEWS.md | 17 + R/unifont.R | 45 +++ README.md | 83 ++---- build/vignette.rds |binary inst/doc/hexfont.R |only inst/doc/hexfont.Rmd | 34 +- inst/doc/hexfont.html | 85 +++--- inst/font/ChangeLog | 243 ++++++++++++++++++- inst/font/plane00/plane00-combining.txt | 1 inst/font/plane00/plane00-unassigned.hex.xz |binary inst/font/plane00csur/plane00csur-combining.txt | 32 ++ inst/font/plane00csur/plane00csur-unassigned.hex.xz |binary inst/font/plane00csur/plane00csur.hex.xz |binary inst/font/plane01/plane01-combining.txt | 60 ++++ inst/font/plane01/plane01-noscript.hex.xz |binary inst/font/plane01/plane01-unassigned.hex.xz |binary inst/font/plane01/plane01.hex.xz |binary inst/font/plane02/zh-plane02.hex.xz |binary inst/font/plane03/jp-plane03.hex.xz |only inst/font/plane03/zh-plane03.hex.xz |binary inst/font/plane0Fcsur/plane0Fcsur-combining.txt | 15 + inst/font/plane0Fcsur/plane0Fcsur-nonprinting.hex.xz |binary inst/font/plane0Fcsur/plane0Fcsur.hex.xz |binary inst/font/precompiled/unifont.hex.xz |binary inst/font/precompiled/unifont_jp.hex.xz |binary inst/font/precompiled/unifont_jp_sample.hex.xz |binary inst/font/precompiled/unifont_sample.hex.xz |binary inst/font/precompiled/unifont_upper.hex.xz |binary inst/font/precompiled/unifont_upper_sample.hex.xz |binary man/unifont.Rd | 24 + tests/testthat/test-combining.R | 8 tests/testthat/test-unifont.R | 4 vignettes/hexfont.Rmd | 34 +- 35 files changed, 581 insertions(+), 192 deletions(-)
Title: Extremal Dependence Models
Description: A set of procedures for parametric and non-parametric modelling of the dependence structure of multivariate extreme-values is provided. The statistical inference is performed with non-parametric estimators, likelihood-based estimators and Bayesian techniques. It adapts the methodologies of Beranger and Padoan (2015) <doi:10.48550/arXiv.1508.05561>, Marcon et al. (2016) <doi:10.1214/16-EJS1162>, Marcon et al. (2017) <doi:10.1002/sta4.145>, Marcon et al. (2017) <doi:10.1016/j.jspi.2016.10.004> and Beranger et al. (2021) <doi:10.1007/s10687-019-00364-0>. This package also allows for the modelling of spatial extremes using flexible max-stable processes. It provides simulation algorithms and fitting procedures relying on the Stephenson-Tawn likelihood as per Beranger at al. (2021) <doi:10.1007/s10687-020-00376-1>.
Author: Boris Beranger [aut],
Simone Padoan [cre, aut],
Giulia Marcon [aut],
Steven G. Johnson [ctb] ,
Rudolf Schuerer [ctb] ,
Brian Gough [ctb] ,
Alec G. Stephenson [ctb],
Anne Sabourin [ctb] ,
Philippe Naveau [ctb]
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Diff between ExtremalDep versions 0.0.4-2 dated 2024-10-06 and 0.0.4-3 dated 2024-12-12
DESCRIPTION | 16 +++++++++------- MD5 | 6 ++++-- NAMESPACE | 11 ++++++----- R/PAMfmado.R |only man/PAMfmado.Rd |only 5 files changed, 19 insertions(+), 14 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep' and 'HCP' preprocessed
datasets and 'HippUnfold' hippocampal segmentation outputs for a given
sample by restructuring the data values into a single file. The single
file can then be used by the package for analyses independently from
its base dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.1.0 dated 2024-10-09 and 1.2.0 dated 2024-12-12
DESCRIPTION | 12 - MD5 | 65 +++++----- NAMESPACE | 3 NEWS.md |only R/CAT12vextract.R |only R/FSLRvextract.R | 12 + R/HIPvextract.R | 6 R/SURFvextract.R | 30 +++- R/VWRfirstrun.R | 169 ++++++++++++++++----------- R/miniconda_installer_url_py39.r |only R/otherfunc.R | 51 +++++--- R/plot_surf.R | 4 R/plot_surf3d.R | 4 R/python_custominstall.r | 4 R/vertTFCE.R | 8 - R/vertmixedTFCE.R | 5 R/vertwise.R | 15 +- README.md | 10 + inst/CITATION |only inst/doc/VertexWiseR_Example_1.html | 9 - inst/doc/VertexWiseR_Example_2.html | 100 +++++++++------ inst/doc/VertexWiseR_surface_extraction.html | 119 +++++++++++++++---- inst/python/brainstat.stats.SLM_VWR.py | 7 - man/CAT12vextract.Rd |only man/FSLRvextract.Rd | 2 man/RFT_vertex_analysis.Rd | 6 man/SURFvextract.Rd | 10 + man/TFCE_vertex_analysis.Rd | 2 man/TFCE_vertex_analysis_mixed.Rd | 2 man/plot_surf3d.Rd | 2 vignettes/FINK_tstatmaps.png |only vignettes/Python_troubleshooting.Rmd |only vignettes/SPRENG_tstatmaps.png |only vignettes/VertexWiseR_Example_1.Rmd | 2 vignettes/VertexWiseR_surface_extraction.Rmd | 62 ++++++++- vignettes/references.bib | 25 +++ vignettes/surfextract.jpg |binary vignettes/traj.png |only 38 files changed, 510 insertions(+), 236 deletions(-)
Title: Enhance Reproducibility of R Code
Description: A collection of high-level, machine- and OS-independent tools
for making reproducible and reusable content in R.
The two workhorse functions are Cache() and prepInputs(). Cache()
allows for nested caching, is robust to environments and objects with
environments (like functions), and deals with some classes of
file-backed R objects e.g., from terra and raster packages.
Both functions have been developed to
be foundational components of data retrieval
and processing in continuous workflow situations. In both functions,
efforts are made to make the first and subsequent calls of functions have
the same result, but faster at subsequent times by way of checksums
and digesting. Several features are still under development, including
cloud storage of cached objects allowing for sharing between users. Several
advanced options are available, see ?reproducibleOptions().
Author: Eliot J B McIntire [aut, cre] ,
Alex M Chubaty [aut] ,
Tati Micheletti [ctb] ,
Ceres Barros [ctb] ,
Ian Eddy [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 2.1.0 dated 2024-05-29 and 2.1.2 dated 2024-12-12
DESCRIPTION | 25 MD5 | 92 - NEWS.md | 27 R/DBI.R | 7 R/cache-helpers.R | 4 R/cache.R | 35 R/download.R | 618 ++++++-- R/exportedMethods.R | 34 R/helpers.R | 46 R/messages.R | 177 +- R/options.R | 23 R/paths.R | 19 R/postProcessTo.R | 53 R/preProcess.R | 309 ++-- R/prepInputs.R | 386 ++--- R/robustDigest.R | 66 R/showCacheEtc.R | 12 R/zzz.R | 8 build/vignette.rds |binary inst/WORDLIST | 11 inst/doc/Intro-to-Cache.html | 2169 ++++++++++++++--------------- inst/examples/example_postProcess.R | 13 inst/examples/example_postProcessTo.R | 2 man/Cache.Rd | 21 man/downloadFile.Rd | 9 man/downloadRemote.Rd | 9 man/gdalwarpFns.Rd | 2 man/messageColoured.Rd | 2 man/postProcess.Rd | 13 man/postProcessTo.Rd | 5 man/preProcess.Rd | 2 man/prepInputs.Rd | 5 man/purge.Rd | 8 man/reproducibleOptions.Rd | 13 man/viewCache.Rd | 3 tests/testthat/helper-allEqual.R | 43 tests/testthat/test-cache.R | 345 ---- tests/testthat/test-cacheGeo.R | 4 tests/testthat/test-cloud.R | 6 tests/testthat/test-cluster.R | 12 tests/testthat/test-examples.R | 7 tests/testthat/test-gis.R | 4 tests/testthat/test-misc.R | 26 tests/testthat/test-postProcess.R | 22 tests/testthat/test-postProcessTerra.R | 18 tests/testthat/test-preProcessDoesntWork.R | 65 tests/testthat/test-prepInputs.R | 142 + 47 files changed, 2706 insertions(+), 2216 deletions(-)
Title: Gaussian Processes on Graphs and Lattices in 'Stan'
Description: Gaussian processes are flexible distributions to model functional data. Whilst
theoretically appealing, they are computationally cumbersome except for small datasets.
This package implements two methods for scaling Gaussian process inference in 'Stan'. First, a
sparse approximation of the likelihood that is generally applicable and, second, an exact method
for regularly spaced data modeled by stationary kernels using fast Fourier methods. Utility
functions are provided to compile and fit 'Stan' models using the 'cmdstanr' interface.
References: Hoffmann and Onnela (2022) <doi:10.48550/arXiv.2301.08836>.
Author: Till Hoffmann [aut, cre] ,
Jukka-Pekka Onnela [ctb]
Maintainer: Till Hoffmann <thoffmann@hsph.harvard.edu>
Diff between gptoolsStan versions 0.1.0 dated 2023-12-19 and 0.2.0 dated 2024-12-12
DESCRIPTION | 12 - MD5 | 24 +- NEWS.md | 5 R/model.R | 22 ++ README.md | 2 inst/doc/getting_started.R | 2 inst/doc/getting_started.Rmd | 2 inst/doc/getting_started.html | 28 +-- inst/extdata/gptools/fft1.stan | 7 inst/extdata/gptools/fft2.stan | 7 inst/extdata/gptools/graph.stan | 367 +++++++++++++++++++++++++++++++++++++++- man/gptools_include_path.Rd | 4 vignettes/getting_started.Rmd | 2 13 files changed, 433 insertions(+), 51 deletions(-)
Title: Efficient Serialization of R Objects
Description: Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Francesc Alted [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs2 versions 0.1.3 dated 2024-12-02 and 0.1.4 dated 2024-12-12
ChangeLog | 7 +++++-- DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/qx_functions.R | 2 +- man/qx_dump.Rd | 2 +- src/io/zstd_module.h | 3 ++- src/qx_dump.h | 9 ++++++--- src/qx_functions.cpp | 8 +++++--- 8 files changed, 31 insertions(+), 22 deletions(-)
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is
a C++ library for translating between absolute and civil times using the rules
of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License,
is included in this package. See <https://github.com/google/cctz> for more
details.
Author: Dirk Eddelbuettel [aut, cre] ,
Bradley White [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.2.12 dated 2022-11-06 and 0.2.13 dated 2024-12-11
ChangeLog | 29 +++++++++++++++++++++++++++++ DESCRIPTION | 16 ++++++++++------ MD5 | 16 ++++++++-------- README.md | 2 +- inst/NEWS.Rd | 25 +++++++++++++++++++++---- src/Makevars | 4 ---- src/Makevars.ucrt | 3 --- src/Makevars.win | 4 ---- src/examples.cpp | 2 +- 9 files changed, 70 insertions(+), 31 deletions(-)
Title: Search and Retrieve Data from the BC Data Catalogue
Description: Search, query, and download tabular and
'geospatial' data from the British Columbia Data Catalogue
(<https://catalogue.data.gov.bc.ca/>). Search catalogue data records
based on keywords, data licence, sector, data format, and B.C.
government organization. View metadata directly in R, download many
data formats, and query 'geospatial' data available via the B.C.
government Web Feature Service ('WFS') using 'dplyr' syntax.
Author: Andy Teucher [aut, cre] ,
Sam Albers [aut, ctb] ,
Stephanie Hazlitt [aut, ctb] ,
Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gmail.com>
Diff between bcdata versions 0.4.1 dated 2023-03-18 and 0.5.0 dated 2024-12-11
DESCRIPTION | 13 MD5 | 122 ++--- NEWS.md | 181 +++++-- R/bcdata-package.R | 7 R/bcdc-get-citation.R | 4 R/bcdc-web-services.R | 5 R/bcdc_options.R | 124 +++-- R/bcdc_search.R | 4 R/describe-feature.R | 6 R/utils-classes.R | 21 R/utils.R | 66 +- R/zzz.R | 2 README.md | 12 build/vignette.rds |binary inst/doc/bcdata.Rmd | 227 +++++---- inst/doc/bcdata.html | 228 +++++----- inst/doc/efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd | 181 ++++--- inst/doc/efficiently-query-spatial-data-in-the-bc-data-catalogue.html | 162 +++---- inst/doc/explore-silviculture-data-using-bcdata.Rmd | 68 +- inst/doc/explore-silviculture-data-using-bcdata.html | 69 +-- inst/doc/local-filter.Rmd | 41 - inst/doc/local-filter.html | 38 - man/bcdc_options.Rd | 48 +- man/bcdc_preview.Rd | 2 man/bcdc_query_geodata.Rd | 3 man/bcdc_search_facets.Rd | 6 man/filter.Rd | 2 tests/testthat.R | 25 - tests/testthat/helper-bcdata.R | 7 tests/testthat/test-bcdc-get-citation.R | 5 tests/testthat/test-browse.R | 2 tests/testthat/test-cql-string.R | 3 tests/testthat/test-describe-feature.R | 5 tests/testthat/test-edge-cases.R | 6 tests/testthat/test-geom-operators.R | 33 - tests/testthat/test-get-data.R | 201 ++++++-- tests/testthat/test-get_record.R | 76 ++- tests/testthat/test-options.R | 24 - tests/testthat/test-print-methods.R | 6 tests/testthat/test-query-geodata-base-methods.R | 7 tests/testthat/test-query-geodata-collect.R | 83 ++- tests/testthat/test-query-geodata-filter.R | 36 - tests/testthat/test-query-geodata-mutate.R | 2 tests/testthat/test-query-geodata-select.R | 18 tests/testthat/test-query-geodata.R | 16 tests/testthat/test-search.R | 21 tests/testthat/test-utils.R | 9 vignettes/bcdata.Rmd | 227 +++++---- vignettes/bcdata.Rmd.orig | 2 vignettes/efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd | 181 ++++--- vignettes/efficiently-query-spatial-data-in-the-bc-data-catalogue.Rmd.orig | 2 vignettes/explore-silviculture-data-using-bcdata.Rmd | 68 +- vignettes/local-filter.Rmd | 41 - vignettes/vignette-fig-air_zones-1.png |binary vignettes/vignette-fig-bbox-1.png |binary vignettes/vignette-fig-district_parks-1.png |binary vignettes/vignette-fig-dp_join-1.png |binary vignettes/vignette-fig-map-larch-plantations-dpg-1.png |binary vignettes/vignette-fig-plot-dpg-1.png |binary vignettes/vignette-fig-regional_districts-1.png |binary vignettes/vignette-fig-unnamed-chunk-1-1.png |binary vignettes/vignette-fig-unnamed-chunk-3-1.png |binary 62 files changed, 1550 insertions(+), 1198 deletions(-)
Title: Exposes the 'Uber' 'H3' Library to R Packages
Description: 'H3' is a hexagonal hierarchical spatial index developed by 'Uber' <https://h3geo.org/>.
This package exposes the source code of 'H3' (written in 'C') to routines that are callable through 'R'.
Author: David Cooley [aut, cre],
Ray Shao [ctb]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between h3lib versions 0.1.3 dated 2024-01-30 and 0.1.4 dated 2024-12-11
DESCRIPTION | 8 +- MD5 | 42 ++++++----- NEWS.md | 4 + inst/include/h3libapi.h | 1 src/algos.c | 19 +++-- src/bbox.c | 138 +++++++++++++++++++++++++++++++++++++ src/bbox.h | 10 ++ src/constants.h | 29 +++++-- src/coordijk.c | 56 +++++++-------- src/faceijk.c | 19 ++--- src/h3Index.c | 132 +++++++++++++++++++++++------------- src/h3Index.h | 27 +++---- src/h3api.h | 33 +++++++-- src/iterators.c | 26 ++++--- src/iterators.h | 1 src/latLng.c | 41 ++++++++--- src/latLng.h | 8 ++ src/localij.c | 16 +--- src/mathExtensions.h | 19 ++++- src/polyfill.c |only src/polyfill.h |only src/polygon.c | 175 ++++++++++++++++++++++++++++++++++++++++++++++++ src/polygon.h | 29 +++++++ 23 files changed, 651 insertions(+), 182 deletions(-)
Title: Miscellaneous Functions for Passive Acoustic Analysis
Description: A collection of miscellaneous functions for passive acoustics.
Much of the content here is adapted to R from code written by other people.
If you have any ideas of functions to add, please contact Taiki Sakai.
Author: Taiki Sakai [aut, cre],
Jay Barlow [ctb],
Julie Oswald [ctb],
Val Schmidt [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMmisc versions 1.12.1 dated 2024-06-10 and 1.12.3 dated 2024-12-11
DESCRIPTION | 15 ++++----- MD5 | 46 +++++++++++++++++------------ NAMESPACE | 11 ++++++ NEWS.md | 18 ++++++++++- R/PAMmisc-package.R |only R/decimateWavFiles.R | 8 +---- R/erddapToEdinfo.R | 49 ++++++++++++++++++++++++++++--- R/fastReadWave.R |only R/matchEnvData.R | 24 +++++++++++---- R/ncToData.R | 7 +++- R/ncUtils.R | 14 +++++--- R/peakTrough.R | 1 R/plotPresBar.R | 2 - R/plotPresGrid.R | 24 ++++++++++----- R/pwelch.R |only R/soundtrapQAQC.R | 74 +++++++++++++++++++++++++++++++++-------------- R/writeAMWave.R | 2 - R/writeClickWave.R | 2 - inst/extdata/testWav.wav |only man/decimateWavFiles.Rd | 8 +---- man/fastReadWave.Rd |only man/plotPresBar.Rd | 2 - man/pwelch.Rd |only man/soundtrapQAQC.Rd | 3 + man/writeAMWave.Rd | 2 - man/writeClickWave.Rd | 2 - src |only 27 files changed, 222 insertions(+), 92 deletions(-)
Title: Design on-Farm Precision Field Agronomic Trials
Description: A comprehensive system for designing and implementing on-farm precision field agronomic trials. You provide field data, tell 'ofpetrial' how to design a trial, and get readily-usable trial design files and a report checks the validity and reliability of the trial design.
Author: Taro Mieno [aut, cre, cph] ,
Brittani Edge [aut, ctb]
Maintainer: Taro Mieno <tmieno2@unl.edu>
Diff between ofpetrial versions 0.1.1 dated 2024-05-15 and 0.1.2 dated 2024-12-11
DESCRIPTION | 13 - MD5 | 45 +-- NAMESPACE | 1 NEWS.md | 5 R/assign_rates.R | 348 ++++++++++++++++++--------- R/diagnose.R | 4 R/make_exp_plots.R | 11 R/make_trial_report.R | 226 ++++++++++-------- R/prepare_plot_info.R | 76 +++--- R/prepare_rate_info.R | 152 ++++++++---- R/utility.R | 6 R/utility_spatial.R | 51 +--- README.md | 39 ++- build/vignette.rds |binary data/exp_data.rda |binary data/rate_info.rda |binary data/td_curved.rda |binary data/td_single_input.rda |binary data/td_two_input.rda |binary inst/doc/basic-work-flow.html | 389 +++++++++++++++---------------- man/assign_rates_conditional.Rd |only man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/ofpetrial-package.Rd | 4 24 files changed, 814 insertions(+), 556 deletions(-)
Title: Robust Score Testing in GLMs, by Sign-Flip Contributions
Description: Provides robust tests for testing in GLMs, by sign-flipping score contributions. The tests are robust against overdispersion, heteroscedasticity and, in some cases, ignored nuisance variables. See Hemerik, Goeman and Finos (2020) <doi:10.1111/rssb.12369>.
Author: Livio Finos [cre, aut] ,
Jelle J. Goeman [ctb],
Jesse Hemerik [ctb],
Riccardo De Santis [ctb]
Maintainer: Livio Finos <livio.finos@unipd.it>
Diff between flipscores versions 1.3.1 dated 2024-11-22 and 1.3.2 dated 2024-12-11
DESCRIPTION | 8 +- MD5 | 14 ++-- R/compute_flips.R | 22 +++--- R/compute_scores.R | 77 +++++++++++----------- R/flipscores.R | 109 ++++++++++++++++--------------- R/utiliy_score_functions.R | 71 ++++++++++---------- man/compute_scores.Rd | 4 - man/flipscores.Rd | 156 ++++++++++++++++++++++----------------------- 8 files changed, 235 insertions(+), 226 deletions(-)
Title: 2D and 3D Movement-Based Kernel Density Estimates (MKDEs)
Description: Provides functions to compute and visualize movement-based kernel density estimates (MKDEs) for animal utilization distributions in 2 or 3 spatial dimensions.
Author: Jeff A. Tracey [aut],
James Sheppard [aut],
Jun Zhu [aut],
Amit Chourasia [aut],
Glenn Lockwood [aut],
Matthew Wang [aut],
Robert N. Fisher [aut],
Robert Sinkovits [aut, cre]
Maintainer: Robert Sinkovits <sinkovit@sdsc.edu>
Diff between mkde versions 0.3 dated 2024-07-02 and 0.4 dated 2024-12-11
mkde-0.3/mkde/man/mkdeToRaster.Rd |only mkde-0.3/mkde/man/readdem_example.Rd |only mkde-0.4/mkde/DESCRIPTION | 44 ++++++++++++++++++++++++++++++----- mkde-0.4/mkde/MD5 | 13 ++++++---- mkde-0.4/mkde/NAMESPACE | 3 -- mkde-0.4/mkde/R/mkdeFunctions.R | 19 ++++----------- mkde-0.4/mkde/man/condordem.Rd |only mkde-0.4/mkde/man/condordem120.Rd |only mkde-0.4/mkde/man/dugongdem.Rd |only mkde-0.4/mkde/man/mkdeToTerra.Rd |only mkde-0.4/mkde/man/pandadem.Rd |only 11 files changed, 53 insertions(+), 26 deletions(-)
Title: Markov Chain Monte Carlo Small Area Estimation
Description: Fit multi-level models with possibly correlated
random effects using Markov Chain Monte Carlo simulation.
Such models allow smoothing over space and time and are useful in,
for example, small area estimation.
Author: Harm Jan Boonstra [aut, cre],
Grzegorz Baltissen [ctb]
Maintainer: Harm Jan Boonstra <hjboonstra@gmail.com>
Diff between mcmcsae versions 0.7.7 dated 2024-02-26 and 0.7.8 dated 2024-12-11
mcmcsae-0.7.7/mcmcsae/man/compute_GMRF_matrices.Rd |only mcmcsae-0.7.7/mcmcsae/man/nchains-ndraws-nvars.Rd |only mcmcsae-0.7.7/mcmcsae/tests/testthat/test_linalg_closures.R |only mcmcsae-0.7.8/mcmcsae/DESCRIPTION | 27 mcmcsae-0.7.8/mcmcsae/MD5 | 180 +- mcmcsae-0.7.8/mcmcsae/NAMESPACE | 15 mcmcsae-0.7.8/mcmcsae/NEWS | 19 mcmcsae-0.7.8/mcmcsae/R/AR1_sampler.R |only mcmcsae-0.7.8/mcmcsae/R/GMRF_extension.R |only mcmcsae-0.7.8/mcmcsae/R/MCMCsim.R | 170 +- mcmcsae-0.7.8/mcmcsae/R/MH.R | 169 +- mcmcsae-0.7.8/mcmcsae/R/MatrixUtils.R | 114 - mcmcsae-0.7.8/mcmcsae/R/RcppExports.R | 4 mcmcsae-0.7.8/mcmcsae/R/TMVN_methods.R | 30 mcmcsae-0.7.8/mcmcsae/R/TMVN_sampler.R | 979 +++++------- mcmcsae-0.7.8/mcmcsae/R/aux_closures.R | 463 ++--- mcmcsae-0.7.8/mcmcsae/R/cMVN_sampler.R | 184 +- mcmcsae-0.7.8/mcmcsae/R/cholesky.R | 80 mcmcsae-0.7.8/mcmcsae/R/conjugate_gradients.R | 40 mcmcsae-0.7.8/mcmcsae/R/f_gamma.R |only mcmcsae-0.7.8/mcmcsae/R/f_poisson.R |only mcmcsae-0.7.8/mcmcsae/R/family.R | 294 --- mcmcsae-0.7.8/mcmcsae/R/formulas.R | 106 - mcmcsae-0.7.8/mcmcsae/R/kronprod.R | 64 mcmcsae-0.7.8/mcmcsae/R/mc_bart.R | 63 mcmcsae-0.7.8/mcmcsae/R/mc_block.R | 110 - mcmcsae-0.7.8/mcmcsae/R/mc_gen.R | 448 +++-- mcmcsae-0.7.8/mcmcsae/R/mc_gl.R | 22 mcmcsae-0.7.8/mcmcsae/R/mc_mec.R | 104 - mcmcsae-0.7.8/mcmcsae/R/mc_offset.R |only mcmcsae-0.7.8/mcmcsae/R/mc_reg.R | 135 - mcmcsae-0.7.8/mcmcsae/R/mc_vfac.R | 9 mcmcsae-0.7.8/mcmcsae/R/mc_vreg.R | 9 mcmcsae-0.7.8/mcmcsae/R/mcmcsae.R | 21 mcmcsae-0.7.8/mcmcsae/R/model_eval.R | 80 mcmcsae-0.7.8/mcmcsae/R/modelmatrix.R | 54 mcmcsae-0.7.8/mcmcsae/R/models.R | 529 ++++-- mcmcsae-0.7.8/mcmcsae/R/opts.R | 4 mcmcsae-0.7.8/mcmcsae/R/parallel.R | 29 mcmcsae-0.7.8/mcmcsae/R/plots.R | 27 mcmcsae-0.7.8/mcmcsae/R/prediction.R | 35 mcmcsae-0.7.8/mcmcsae/R/priors.R | 93 + mcmcsae-0.7.8/mcmcsae/R/projection.R |only mcmcsae-0.7.8/mcmcsae/R/random.R | 4 mcmcsae-0.7.8/mcmcsae/R/samplers.R | 290 +-- mcmcsae-0.7.8/mcmcsae/R/sbc.R | 10 mcmcsae-0.7.8/mcmcsae/R/sparse_template.R | 93 - mcmcsae-0.7.8/mcmcsae/R/tabMatrix.R | 11 mcmcsae-0.7.8/mcmcsae/R/utils.R | 20 mcmcsae-0.7.8/mcmcsae/build/vignette.rds |binary mcmcsae-0.7.8/mcmcsae/inst/doc/area_level.html | 73 mcmcsae-0.7.8/mcmcsae/inst/doc/linear_weighting.html | 51 mcmcsae-0.7.8/mcmcsae/inst/doc/unit_level.html | 325 +-- mcmcsae-0.7.8/mcmcsae/man/GMRF_structure.Rd |only mcmcsae-0.7.8/mcmcsae/man/SBC_test.Rd | 8 mcmcsae-0.7.8/mcmcsae/man/TMVN-methods.Rd | 28 mcmcsae-0.7.8/mcmcsae/man/brt.Rd | 2 mcmcsae-0.7.8/mcmcsae/man/correlation.Rd | 72 mcmcsae-0.7.8/mcmcsae/man/create_TMVN_sampler.Rd | 12 mcmcsae-0.7.8/mcmcsae/man/create_block_cMVN_sampler.Rd |only mcmcsae-0.7.8/mcmcsae/man/create_cMVN_sampler.Rd | 29 mcmcsae-0.7.8/mcmcsae/man/create_sampler.Rd | 9 mcmcsae-0.7.8/mcmcsae/man/gen.Rd | 30 mcmcsae-0.7.8/mcmcsae/man/gen_control.Rd | 4 mcmcsae-0.7.8/mcmcsae/man/generate_data.Rd | 3 mcmcsae-0.7.8/mcmcsae/man/mc_offset.Rd |only mcmcsae-0.7.8/mcmcsae/man/mcmcsae-family.Rd | 60 mcmcsae-0.7.8/mcmcsae/man/model_matrix.Rd | 5 mcmcsae-0.7.8/mcmcsae/man/n_chains-n_draws-n_vars.Rd |only mcmcsae-0.7.8/mcmcsae/man/plot_coef.Rd | 4 mcmcsae-0.7.8/mcmcsae/man/pr_beta.Rd |only mcmcsae-0.7.8/mcmcsae/man/pr_truncnormal.Rd |only mcmcsae-0.7.8/mcmcsae/man/pr_unif.Rd |only mcmcsae-0.7.8/mcmcsae/man/residuals-fitted-values.Rd | 8 mcmcsae-0.7.8/mcmcsae/man/sampler_control.Rd | 2 mcmcsae-0.7.8/mcmcsae/man/set_MH.Rd |only mcmcsae-0.7.8/mcmcsae/man/sim_marg_var.Rd |only mcmcsae-0.7.8/mcmcsae/man/subset.dc.Rd | 10 mcmcsae-0.7.8/mcmcsae/src/RcppExports.cpp | 13 mcmcsae-0.7.8/mcmcsae/src/TN.cpp | 2 mcmcsae-0.7.8/mcmcsae/src/mcmcsae_init.c | 5 mcmcsae-0.7.8/mcmcsae/src/speed_ups.cpp | 28 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_AR1.R |only mcmcsae-0.7.8/mcmcsae/tests/testthat/test_Cholesky.R | 16 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_GMRF_extensions.R |only mcmcsae-0.7.8/mcmcsae/tests/testthat/test_GMRF_matrices.R | 16 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_Poisson.R | 34 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_TMVN.R | 107 + mcmcsae-0.7.8/mcmcsae/tests/testthat/test_bart.R | 10 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_cMVNsampler.R |only mcmcsae-0.7.8/mcmcsae/tests/testthat/test_checks.R | 7 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_gammareg.R | 15 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_gen.R | 22 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_grouplevel.R | 6 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_linalg.R | 26 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_linreg.R | 23 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_mat_sum.R | 76 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_modelmatrix.R | 11 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_offset.R |only mcmcsae-0.7.8/mcmcsae/tests/testthat/test_output.R | 2 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_predict.R | 14 mcmcsae-0.7.8/mcmcsae/tests/testthat/test_sim.R |only mcmcsae-0.7.8/mcmcsae/tests/testthat/test_spatial.R |only 103 files changed, 3379 insertions(+), 2927 deletions(-)
Title: Causal Modeling in Epidemiology
Description: Create causal models for use in epidemiological studies,
including sufficient-component cause models as introduced by
Rothman (1976) <doi:10.1093/oxfordjournals.aje.a112335>.
Author: Felix Forster [aut, cre, cph]
Maintainer: Felix Forster <felix.forster@med.uni-muenchen.de>
Diff between epicmodel versions 0.1.1 dated 2024-11-08 and 0.2.0 dated 2024-12-11
epicmodel-0.1.1/epicmodel/R/server_utils.R |only epicmodel-0.2.0/epicmodel/DESCRIPTION | 13 - epicmodel-0.2.0/epicmodel/MD5 | 93 +++---- epicmodel-0.2.0/epicmodel/NAMESPACE | 3 epicmodel-0.2.0/epicmodel/NEWS.md | 12 epicmodel-0.2.0/epicmodel/R/check_steplist.R | 2 epicmodel-0.2.0/epicmodel/R/create_scc.R | 78 +++++- epicmodel-0.2.0/epicmodel/R/intervention.R | 26 +- epicmodel-0.2.0/epicmodel/R/launch_steplist_creator.R | 2 epicmodel-0.2.0/epicmodel/R/mechanism.R | 2 epicmodel-0.2.0/epicmodel/R/prevent.R |only epicmodel-0.2.0/epicmodel/R/process_steplist.R | 2 epicmodel-0.2.0/epicmodel/R/process_steplist_user.R | 7 epicmodel-0.2.0/epicmodel/R/scc_utils.R | 10 epicmodel-0.2.0/epicmodel/README.md | 13 - epicmodel-0.2.0/epicmodel/build/partial.rdb |binary epicmodel-0.2.0/epicmodel/build/vignette.rds |binary epicmodel-0.2.0/epicmodel/inst/CITATION | 2 epicmodel-0.2.0/epicmodel/inst/doc/epicmodel.R | 17 - epicmodel-0.2.0/epicmodel/inst/doc/epicmodel.Rmd | 22 + epicmodel-0.2.0/epicmodel/inst/doc/epicmodel.html | 127 ++++++---- epicmodel-0.2.0/epicmodel/inst/doc/glossary.Rmd | 5 epicmodel-0.2.0/epicmodel/inst/doc/glossary.html | 14 - epicmodel-0.2.0/epicmodel/inst/doc/modules.R | 7 epicmodel-0.2.0/epicmodel/inst/doc/modules.Rmd | 1 epicmodel-0.2.0/epicmodel/inst/doc/modules.html | 3 epicmodel-0.2.0/epicmodel/inst/doc/scc.R | 12 epicmodel-0.2.0/epicmodel/inst/doc/scc.Rmd | 14 - epicmodel-0.2.0/epicmodel/inst/doc/scc.html | 16 - epicmodel-0.2.0/epicmodel/inst/doc/steplist.R | 124 ++++----- epicmodel-0.2.0/epicmodel/inst/doc/steplist.Rmd | 2 epicmodel-0.2.0/epicmodel/inst/doc/steplist.html | 2 epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/R/icc.R | 2 epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/R/server_utils.R |only epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/R/ui_utils.R | 92 ++++--- epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/R/upload.R | 2 epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/server.R | 93 +++++-- epicmodel-0.2.0/epicmodel/inst/shiny/steplist_creator/ui.R | 3 epicmodel-0.2.0/epicmodel/man/mechanism.Rd | 2 epicmodel-0.2.0/epicmodel/man/necessary_causes.Rd |only epicmodel-0.2.0/epicmodel/man/prevent.Rd |only epicmodel-0.2.0/epicmodel/man/uncheck_steplist.Rd |only epicmodel-0.2.0/epicmodel/tests/testthat/test-create_scc.R | 28 ++ epicmodel-0.2.0/epicmodel/tests/testthat/test-intervention.R | 13 + epicmodel-0.2.0/epicmodel/tests/testthat/test-prevent.R |only epicmodel-0.2.0/epicmodel/tests/testthat/test-server_utils.R | 2 epicmodel-0.2.0/epicmodel/vignettes/epicmodel.Rmd | 22 + epicmodel-0.2.0/epicmodel/vignettes/glossary.Rmd | 5 epicmodel-0.2.0/epicmodel/vignettes/modules.Rmd | 1 epicmodel-0.2.0/epicmodel/vignettes/scc.Rmd | 14 - epicmodel-0.2.0/epicmodel/vignettes/steplist.Rmd | 2 51 files changed, 618 insertions(+), 294 deletions(-)
Title: Effect Plots
Description: High-performance implementation of various effect plots
useful for regression and probabilistic classification tasks. The
package includes partial dependence plots (Friedman, 2021,
<doi:10.1214/aos/1013203451>), accumulated local effect plots and
M-plots (both from Apley and Zhu, 2016, <doi:10.1111/rssb.12377>), as
well as plots that describe the statistical associations between model
response and features. It supports visualizations with either
'ggplot2' or 'plotly', and is compatible with most models, including
'Tidymodels', models wrapped in 'DALEX' explainers, or models with
case weights.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between effectplots versions 0.1.0 dated 2024-11-18 and 0.2.0 dated 2024-12-11
effectplots-0.1.0/effectplots/src/clamp2.cpp |only effectplots-0.2.0/effectplots/DESCRIPTION | 7 effectplots-0.2.0/effectplots/MD5 | 86 - effectplots-0.2.0/effectplots/NAMESPACE | 4 effectplots-0.2.0/effectplots/NEWS.md | 47 effectplots-0.2.0/effectplots/R/RcppExports.R | 31 effectplots-0.2.0/effectplots/R/ale.R | 131 + effectplots-0.2.0/effectplots/R/average_observed.R | 25 effectplots-0.2.0/effectplots/R/average_predicted.R | 13 effectplots-0.2.0/effectplots/R/bias.R | 9 effectplots-0.2.0/effectplots/R/crunch.R | 197 +- effectplots-0.2.0/effectplots/R/feature_effects.R | 262 ++- effectplots-0.2.0/effectplots/R/importance.R | 10 effectplots-0.2.0/effectplots/R/input.R | 7 effectplots-0.2.0/effectplots/R/partial_dependence.R | 71 effectplots-0.2.0/effectplots/R/plot.R | 144 +- effectplots-0.2.0/effectplots/R/update.R | 79 - effectplots-0.2.0/effectplots/R/utils.R | 70 effectplots-0.2.0/effectplots/README.md | 107 + effectplots-0.2.0/effectplots/man/ale.Rd | 120 + effectplots-0.2.0/effectplots/man/average_observed.Rd | 65 effectplots-0.2.0/effectplots/man/average_predicted.Rd | 168 +- effectplots-0.2.0/effectplots/man/bias.Rd | 155 +- effectplots-0.2.0/effectplots/man/dot-ale.Rd | 155 +- effectplots-0.2.0/effectplots/man/dot-pd.Rd | 126 - effectplots-0.2.0/effectplots/man/effect_importance.Rd | 80 - effectplots-0.2.0/effectplots/man/fcut.Rd |only effectplots-0.2.0/effectplots/man/feature_effects.Rd | 470 +++--- effectplots-0.2.0/effectplots/man/figures/avg_obs.svg | 594 ++++---- effectplots-0.2.0/effectplots/man/figures/bias.svg | 716 +++++----- effectplots-0.2.0/effectplots/man/figures/classification.svg |only effectplots-0.2.0/effectplots/man/figures/dalex.svg | 450 +++--- effectplots-0.2.0/effectplots/man/figures/feature_effects.svg | 469 +++--- effectplots-0.2.0/effectplots/man/figures/tidymodels.svg |only effectplots-0.2.0/effectplots/man/figures/train_test.svg | 472 +++--- effectplots-0.2.0/effectplots/man/partial_dependence.Rd | 98 - effectplots-0.2.0/effectplots/man/plot.EffectData.Rd | 262 +-- effectplots-0.2.0/effectplots/man/update.EffectData.Rd | 144 +- effectplots-0.2.0/effectplots/src/RcppExports.cpp | 25 effectplots-0.2.0/effectplots/src/findInterval_equi.cpp | 57 effectplots-0.2.0/effectplots/tests/testthat/test-ale.R | 1 effectplots-0.2.0/effectplots/tests/testthat/test-bias.R | 4 effectplots-0.2.0/effectplots/tests/testthat/test-crunch.R | 244 ++- effectplots-0.2.0/effectplots/tests/testthat/test-feature_effects.R | 20 effectplots-0.2.0/effectplots/tests/testthat/test-partial_dependence.R | 40 effectplots-0.2.0/effectplots/tests/testthat/test-update.R |only effectplots-0.2.0/effectplots/tests/testthat/test-utils.R |only 47 files changed, 3584 insertions(+), 2651 deletions(-)
Title: High-Level Functions for Tabulating, Charting and Reporting
Survey Data
Description: Craft polished tables and plots in Markdown reports.
Simply choose whether to treat your data as counts or metrics,
and the package will automatically generate well-designed default tables and plots for you.
Boiled down to the basics, with labeling features and simple interactive reports.
All functions are 'tidyverse' compatible.
Author: Jakob Juenger [aut, cre, cph] ,
Henrieke Kotthoff [aut, ctb],
Chantal Gaertner [ctb]
Maintainer: Jakob Juenger <jakob.juenger@uni-muenster.de>
Diff between volker versions 2.1.0 dated 2024-09-10 and 3.0.0 dated 2024-12-11
volker-2.1.0/volker/man/idx_alpha.Rd |only volker-3.0.0/volker/DESCRIPTION | 8 volker-3.0.0/volker/LICENSE | 4 volker-3.0.0/volker/MD5 | 443 volker-3.0.0/volker/NAMESPACE | 187 volker-3.0.0/volker/NEWS.md | 66 volker-3.0.0/volker/R/checks.R | 198 volker-3.0.0/volker/R/clean.R | 757 - volker-3.0.0/volker/R/cluster.R |only volker-3.0.0/volker/R/config.R | 241 volker-3.0.0/volker/R/data.R | 42 volker-3.0.0/volker/R/effects.R | 2516 ++--- volker-3.0.0/volker/R/factor.R |only volker-3.0.0/volker/R/idx.R | 223 volker-3.0.0/volker/R/import-standalone-purrr.R | 488 volker-3.0.0/volker/R/imports.R | 204 volker-3.0.0/volker/R/labels.R | 1876 +-- volker-3.0.0/volker/R/plots.R | 4898 +++++----- volker-3.0.0/volker/R/report.R | 1110 +- volker-3.0.0/volker/R/skim.R | 222 volker-3.0.0/volker/R/tables.R | 3814 +++---- volker-3.0.0/volker/R/utils.R | 158 volker-3.0.0/volker/R/volker-package.R | 16 volker-3.0.0/volker/README.md | 43 volker-3.0.0/volker/inst/doc/introduction.R | 39 volker-3.0.0/volker/inst/doc/introduction.Rmd | 801 - volker-3.0.0/volker/inst/doc/introduction.html | 2300 ++++ volker-3.0.0/volker/inst/extdata/header.tex | 14 volker-3.0.0/volker/inst/extdata/styles.css | 96 volker-3.0.0/volker/inst/rmarkdown/templates/volker-report/skeleton/skeleton.Rmd | 100 volker-3.0.0/volker/inst/rmarkdown/templates/volker-report/template.yaml | 8 volker-3.0.0/volker/man/VLKR_FIG_SETTINGS.Rd | 36 volker-3.0.0/volker/man/VLKR_FILLDISCRETE.Rd | 32 volker-3.0.0/volker/man/VLKR_FILLGRADIENT.Rd | 32 volker-3.0.0/volker/man/VLKR_FILLPOLARIZED.Rd | 32 volker-3.0.0/volker/man/VLKR_NA_LEVELS.Rd | 32 volker-3.0.0/volker/man/VLKR_NA_NUMBERS.Rd | 32 volker-3.0.0/volker/man/VLKR_NORMAL_DIGITS.Rd | 32 volker-3.0.0/volker/man/VLKR_PLOT_LABELWRAP.Rd | 36 volker-3.0.0/volker/man/VLKR_POINT_ALPHA.Rd | 32 volker-3.0.0/volker/man/VLKR_POINT_MEAN_SHAPE.Rd | 32 volker-3.0.0/volker/man/VLKR_POINT_SIZE.Rd | 32 volker-3.0.0/volker/man/VLKR_WRAP_SEPARATOR.Rd | 32 volker-3.0.0/volker/man/add_clusters.Rd |only volker-3.0.0/volker/man/add_factors.Rd |only volker-3.0.0/volker/man/add_index.Rd |only volker-3.0.0/volker/man/cfg_get_na_numbers.Rd | 46 volker-3.0.0/volker/man/chatgpt.Rd | 72 volker-3.0.0/volker/man/check_has_column.Rd | 44 volker-3.0.0/volker/man/check_is_dataframe.Rd | 44 volker-3.0.0/volker/man/check_is_param.Rd | 48 volker-3.0.0/volker/man/cluster_plot.Rd |only volker-3.0.0/volker/man/cluster_tab.Rd |only volker-3.0.0/volker/man/codebook.Rd | 60 volker-3.0.0/volker/man/data_clean.Rd | 62 volker-3.0.0/volker/man/data_clean_sosci.Rd | 84 volker-3.0.0/volker/man/data_prepare.Rd | 60 volker-3.0.0/volker/man/data_rev.Rd |only volker-3.0.0/volker/man/data_rm_missings.Rd | 40 volker-3.0.0/volker/man/data_rm_na_levels.Rd | 46 volker-3.0.0/volker/man/data_rm_na_numbers.Rd | 48 volker-3.0.0/volker/man/data_rm_negatives.Rd | 40 volker-3.0.0/volker/man/data_rm_zeros.Rd | 40 volker-3.0.0/volker/man/dot-add_to_vlkr_rprt.Rd | 44 volker-3.0.0/volker/man/dot-attr_insert.Rd | 48 volker-3.0.0/volker/man/dot-attr_transfer.Rd | 44 volker-3.0.0/volker/man/dot-density_mode.Rd | 40 volker-3.0.0/volker/man/dot-effect_correlations.Rd | 54 volker-3.0.0/volker/man/dot-effect_npmi.Rd | 62 volker-3.0.0/volker/man/dot-factor_with_attr.Rd | 40 volker-3.0.0/volker/man/dot-get_fig_settings.Rd | 30 volker-3.0.0/volker/man/dot-iqr.Rd | 36 volker-3.0.0/volker/man/dot-knit_plot.Rd | 64 volker-3.0.0/volker/man/dot-knit_prepare.Rd | 40 volker-3.0.0/volker/man/dot-knit_table.Rd | 36 volker-3.0.0/volker/man/dot-outliers.Rd | 36 volker-3.0.0/volker/man/dot-plot_bars.Rd | 80 volker-3.0.0/volker/man/dot-plot_cor.Rd | 72 volker-3.0.0/volker/man/dot-plot_lines.Rd | 52 volker-3.0.0/volker/man/dot-plot_scree.Rd |only volker-3.0.0/volker/man/dot-plot_summary.Rd | 72 volker-3.0.0/volker/man/dot-report_cls.Rd |only volker-3.0.0/volker/man/dot-report_fct.Rd |only volker-3.0.0/volker/man/dot-report_idx.Rd | 80 volker-3.0.0/volker/man/dot-tab_split.Rd | 48 volker-3.0.0/volker/man/dot-to_vlkr_df.Rd | 36 volker-3.0.0/volker/man/dot-to_vlkr_list.Rd | 42 volker-3.0.0/volker/man/dot-to_vlkr_plot.Rd | 72 volker-3.0.0/volker/man/dot-to_vlkr_rprt.Rd | 40 volker-3.0.0/volker/man/dot-to_vlkr_tab.Rd | 48 volker-3.0.0/volker/man/dot-whisker_lower.Rd | 36 volker-3.0.0/volker/man/dot-whisker_upper.Rd | 36 volker-3.0.0/volker/man/effect_counts.Rd | 118 volker-3.0.0/volker/man/effect_counts_items.Rd | 68 volker-3.0.0/volker/man/effect_counts_items_cor.Rd | 52 volker-3.0.0/volker/man/effect_counts_items_cor_items.Rd | 52 volker-3.0.0/volker/man/effect_counts_items_grouped.Rd | 52 volker-3.0.0/volker/man/effect_counts_items_grouped_items.Rd | 52 volker-3.0.0/volker/man/effect_counts_one.Rd | 66 volker-3.0.0/volker/man/effect_counts_one_cor.Rd | 52 volker-3.0.0/volker/man/effect_counts_one_grouped.Rd | 76 volker-3.0.0/volker/man/effect_metrics.Rd | 118 volker-3.0.0/volker/man/effect_metrics_items.Rd | 68 volker-3.0.0/volker/man/effect_metrics_items_cor.Rd | 94 volker-3.0.0/volker/man/effect_metrics_items_cor_items.Rd | 100 volker-3.0.0/volker/man/effect_metrics_items_grouped.Rd | 90 volker-3.0.0/volker/man/effect_metrics_items_grouped_items.Rd | 52 volker-3.0.0/volker/man/effect_metrics_one.Rd | 66 volker-3.0.0/volker/man/effect_metrics_one_cor.Rd | 90 volker-3.0.0/volker/man/effect_metrics_one_grouped.Rd | 104 volker-3.0.0/volker/man/ends_with.Rd | 18 volker-3.0.0/volker/man/factor_plot.Rd |only volker-3.0.0/volker/man/factor_tab.Rd |only volker-3.0.0/volker/man/figures/lifecycle-archived.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-defunct.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-deprecated.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-experimental.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-maturing.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-questioning.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-soft-deprecated.svg | 42 volker-3.0.0/volker/man/figures/lifecycle-stable.svg | 58 volker-3.0.0/volker/man/figures/lifecycle-superseded.svg | 42 volker-3.0.0/volker/man/filter.Rd | 18 volker-3.0.0/volker/man/get_alpha.Rd |only volker-3.0.0/volker/man/get_angle.Rd | 48 volker-3.0.0/volker/man/get_baseline.Rd | 40 volker-3.0.0/volker/man/get_ci.Rd | 40 volker-3.0.0/volker/man/get_direction.Rd | 50 volker-3.0.0/volker/man/get_gini.Rd | 36 volker-3.0.0/volker/man/get_limits.Rd | 60 volker-3.0.0/volker/man/get_prefix.Rd | 64 volker-3.0.0/volker/man/get_stars.Rd | 36 volker-3.0.0/volker/man/get_title.Rd | 44 volker-3.0.0/volker/man/html_report.Rd | 64 volker-3.0.0/volker/man/idx_add.Rd | 52 volker-3.0.0/volker/man/knit_print.vlkr_plt.Rd | 56 volker-3.0.0/volker/man/label_scale.Rd | 42 volker-3.0.0/volker/man/labs_apply.Rd | 176 volker-3.0.0/volker/man/labs_clear.Rd | 52 volker-3.0.0/volker/man/labs_impute.Rd | 36 volker-3.0.0/volker/man/labs_replace.Rd | 82 volker-3.0.0/volker/man/labs_restore.Rd | 66 volker-3.0.0/volker/man/labs_store.Rd | 62 volker-3.0.0/volker/man/mutate.Rd | 18 volker-3.0.0/volker/man/pdf_report.Rd | 62 volker-3.0.0/volker/man/pipe.Rd | 40 volker-3.0.0/volker/man/plot_counts.Rd | 156 volker-3.0.0/volker/man/plot_counts_items.Rd | 130 volker-3.0.0/volker/man/plot_counts_items_cor.Rd | 120 volker-3.0.0/volker/man/plot_counts_items_cor_items.Rd | 78 volker-3.0.0/volker/man/plot_counts_items_grouped.Rd | 118 volker-3.0.0/volker/man/plot_counts_items_grouped_items.Rd | 78 volker-3.0.0/volker/man/plot_counts_one.Rd | 118 volker-3.0.0/volker/man/plot_counts_one_cor.Rd | 142 volker-3.0.0/volker/man/plot_counts_one_grouped.Rd | 142 volker-3.0.0/volker/man/plot_metrics.Rd | 154 volker-3.0.0/volker/man/plot_metrics_items.Rd | 104 volker-3.0.0/volker/man/plot_metrics_items_cor.Rd | 104 volker-3.0.0/volker/man/plot_metrics_items_cor_items.Rd | 104 volker-3.0.0/volker/man/plot_metrics_items_grouped.Rd | 98 volker-3.0.0/volker/man/plot_metrics_items_grouped_items.Rd | 78 volker-3.0.0/volker/man/plot_metrics_one.Rd | 104 volker-3.0.0/volker/man/plot_metrics_one_cor.Rd | 106 volker-3.0.0/volker/man/plot_metrics_one_grouped.Rd | 110 volker-3.0.0/volker/man/prepare_scale.Rd | 36 volker-3.0.0/volker/man/print.vlkr_list.Rd | 56 volker-3.0.0/volker/man/print.vlkr_plt.Rd | 62 volker-3.0.0/volker/man/print.vlkr_rprt.Rd | 56 volker-3.0.0/volker/man/print.vlkr_tbl.Rd | 56 volker-3.0.0/volker/man/report_counts.Rd | 150 volker-3.0.0/volker/man/report_metrics.Rd | 158 volker-3.0.0/volker/man/select.Rd | 18 volker-3.0.0/volker/man/skim_boxplot.Rd | 28 volker-3.0.0/volker/man/skim_metrics.Rd | 48 volker-3.0.0/volker/man/starts_with.Rd | 18 volker-3.0.0/volker/man/tab_counts.Rd | 142 volker-3.0.0/volker/man/tab_counts_items.Rd | 96 volker-3.0.0/volker/man/tab_counts_items_cor.Rd | 126 volker-3.0.0/volker/man/tab_counts_items_cor_items.Rd | 78 volker-3.0.0/volker/man/tab_counts_items_grouped.Rd | 120 volker-3.0.0/volker/man/tab_counts_items_grouped_items.Rd | 78 volker-3.0.0/volker/man/tab_counts_one.Rd | 90 volker-3.0.0/volker/man/tab_counts_one_cor.Rd | 102 volker-3.0.0/volker/man/tab_counts_one_grouped.Rd | 102 volker-3.0.0/volker/man/tab_metrics.Rd | 142 volker-3.0.0/volker/man/tab_metrics_items.Rd | 90 volker-3.0.0/volker/man/tab_metrics_items_cor.Rd | 106 volker-3.0.0/volker/man/tab_metrics_items_cor_items.Rd | 112 volker-3.0.0/volker/man/tab_metrics_items_grouped.Rd | 96 volker-3.0.0/volker/man/tab_metrics_items_grouped_items.Rd | 78 volker-3.0.0/volker/man/tab_metrics_one.Rd | 90 volker-3.0.0/volker/man/tab_metrics_one_cor.Rd | 102 volker-3.0.0/volker/man/tab_metrics_one_grouped.Rd | 96 volker-3.0.0/volker/man/theme_set.Rd | 18 volker-3.0.0/volker/man/theme_vlkr.Rd | 88 volker-3.0.0/volker/man/tibble.Rd | 18 volker-3.0.0/volker/man/tidy_lm_levels.Rd | 42 volker-3.0.0/volker/man/tribble.Rd | 18 volker-3.0.0/volker/man/trim_label.Rd | 44 volker-3.0.0/volker/man/trim_prefix.Rd | 47 volker-3.0.0/volker/man/trunc_labels.Rd | 40 volker-3.0.0/volker/man/vlkr_colors_discrete.Rd | 48 volker-3.0.0/volker/man/vlkr_colors_polarized.Rd | 36 volker-3.0.0/volker/man/vlkr_colors_sequential.Rd | 36 volker-3.0.0/volker/man/volker-package.Rd | 72 volker-3.0.0/volker/man/wrap_label.Rd | 40 volker-3.0.0/volker/man/zip_tables.Rd | 56 volker-3.0.0/volker/tests/testthat.R | 24 volker-3.0.0/volker/tests/testthat/_markdown/plots.Rmd | 332 volker-3.0.0/volker/tests/testthat/_markdown/reports.Rmd | 173 volker-3.0.0/volker/tests/testthat/_markdown/tables.Rmd | 292 volker-3.0.0/volker/tests/testthat/_snaps/clean.md | 26 volker-3.0.0/volker/tests/testthat/_snaps/clusters.md |only volker-3.0.0/volker/tests/testthat/_snaps/effects.md | 858 - volker-3.0.0/volker/tests/testthat/_snaps/factors.md |only volker-3.0.0/volker/tests/testthat/_snaps/idx.md |only volker-3.0.0/volker/tests/testthat/_snaps/labels.md | 15 volker-3.0.0/volker/tests/testthat/_snaps/skim.md | 94 volker-3.0.0/volker/tests/testthat/_snaps/tables.md | 451 volker-3.0.0/volker/tests/testthat/test-checks.R | 142 volker-3.0.0/volker/tests/testthat/test-clean.R | 207 volker-3.0.0/volker/tests/testthat/test-clusters.R |only volker-3.0.0/volker/tests/testthat/test-effects.R | 228 volker-3.0.0/volker/tests/testthat/test-factors.R |only volker-3.0.0/volker/tests/testthat/test-idx.R |only volker-3.0.0/volker/tests/testthat/test-labels.R | 453 volker-3.0.0/volker/tests/testthat/test-markdown.R | 54 volker-3.0.0/volker/tests/testthat/test-plots.R | 164 volker-3.0.0/volker/tests/testthat/test-tables.R | 495 - volker-3.0.0/volker/tests/testthat/test-theme.R | 106 volker-3.0.0/volker/tests/testthat/test-utils.R | 62 volker-3.0.0/volker/tests/testthat/test_skim.R | 50 volker-3.0.0/volker/vignettes/introduction.Rmd | 801 - 233 files changed, 19794 insertions(+), 16724 deletions(-)
Title: Interact with Simile Models
Description: Allows a Simile model saved as a compiled binary to be
loaded, parameterized, executed and interrogated. This version works
with Simile v6 on.
Author: Simulistics Ltd [cph],
Jasper Taylor [aut, cre]
Maintainer: Jasper Taylor <support@simulistics.com>
Diff between Simile versions 1.3.3 dated 2015-02-19 and 1.3.4 dated 2024-12-11
DESCRIPTION | 22 +++++++++++++++------- MD5 | 12 ++++++------ NAMESPACE | 14 +++++--------- man/Simile-package.Rd | 10 +++++----- man/get.model.property.Rd | 4 ++-- man/list.objects.Rd | 4 ++-- man/load.model.Rd | 4 ++-- 7 files changed, 37 insertions(+), 33 deletions(-)
Title: General Purpose Client for 'ERDDAP™' Servers
Description: General purpose R client for 'ERDDAP™' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP™' information:
<https://upwell.pfeg.noaa.gov/erddap/information.html>.
Author: Scott Chamberlain [aut],
Ben Tupper [ctb],
Salvador Jesus Fernandez Bejarano [ctb],
Roy Mendelssohn [cre, ctb]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddap versions 1.1.0 dated 2024-01-12 and 1.2.0 dated 2024-12-11
DESCRIPTION | 19 MD5 | 82 +-- NEWS.md | 7 R/browse.R | 20 R/convert_time.R | 6 R/default-url.R | 2 R/fipscounty.R | 2 R/global_search.R | 6 R/grid.R | 12 R/info.R | 6 R/keywords.R | 4 R/rerddap-package.r | 10 R/search.R | 6 R/search_adv.R | 4 R/servers.R | 6 R/table.R | 113 +++- R/utils.R | 2 R/version.R | 4 R/zzz.r | 19 build/vignette.rds |binary inst/doc/Using_rerddap.R | 825 ++++++++++++++++++---------------- inst/doc/Using_rerddap.Rmd | 130 ++++- inst/doc/Using_rerddap.html | 1039 +++++++++++++++++++++++--------------------- inst/doc/rerddap.Rmd | 10 inst/doc/rerddap.html | 24 - man/browse.Rd | 5 man/convert_time.Rd | 6 man/disk.Rd | 4 man/ed_search.Rd | 8 man/ed_search_adv.Rd | 6 man/eurl.Rd | 4 man/fipscounty.Rd | 2 man/global_search.Rd | 6 man/griddap.Rd | 4 man/info.Rd | 8 man/key_words.Rd | 4 man/rerddap.Rd | 12 man/servers.Rd | 8 man/tabledap.Rd | 21 man/version.Rd | 6 vignettes/Using_rerddap.Rmd | 130 ++++- vignettes/rerddap.Rmd | 10 42 files changed, 1482 insertions(+), 1120 deletions(-)
Title: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Description: Methods for Cluster analysis. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Author: Martin Maechler [aut, cre] ,
Peter Rousseeuw [aut] ,
Anja Struyf [aut] ,
Mia Hubert [aut] ,
Kurt Hornik [trl, ctb] ,
<https://orcid.org/0000-0003-4198-9911>),
Matthias Studer [ctb],
Pierre Roudier [ctb],
Juan Gonzalez [ctb],
Kamil Kozlowski [ctb],
Er [...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cluster versions 2.1.7 dated 2024-12-08 and 2.1.8 dated 2024-12-11
DESCRIPTION | 11 ++++---- MD5 | 12 ++++----- R/agnes.q | 41 ++++++++++++++++---------------- R/daisy.q | 27 +++++++++++---------- R/diana.q | 24 ++++++++++--------- inst/NEWS.Rd | 17 +++++++++---- src/daisy.c | 74 +++++++++++++++++++++++++++-------------------------------- 7 files changed, 108 insertions(+), 98 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.
Author: Marcelo Araya-Salas [aut, cre]
,
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between warbleR versions 1.1.32 dated 2024-08-19 and 1.1.33 dated 2024-12-11
warbleR-1.1.32/warbleR/inst/doc/annotation_data_format.R |only warbleR-1.1.32/warbleR/inst/doc/annotation_data_format.Rmd |only warbleR-1.1.32/warbleR/inst/doc/annotation_data_format.html |only warbleR-1.1.32/warbleR/inst/doc/warbleR.R |only warbleR-1.1.32/warbleR/inst/doc/warbleR.Rmd |only warbleR-1.1.32/warbleR/inst/doc/warbleR.html |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_01.R |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_01.Rmd |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_01.html |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_02.R |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_02.Rmd |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_02.html |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_03.R |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_03.Rmd |only warbleR-1.1.32/warbleR/inst/doc/warbleR_workflow_03.html |only warbleR-1.1.32/warbleR/vignettes/annotation_data_format.Rmd |only warbleR-1.1.32/warbleR/vignettes/warbleR.Rmd |only warbleR-1.1.32/warbleR/vignettes/warbleR_workflow_01.Rmd |only warbleR-1.1.32/warbleR/vignettes/warbleR_workflow_02.Rmd |only warbleR-1.1.32/warbleR/vignettes/warbleR_workflow_03.Rmd |only warbleR-1.1.33/warbleR/DESCRIPTION | 10 warbleR-1.1.33/warbleR/MD5 | 100 ++--- warbleR-1.1.33/warbleR/NAMESPACE | 2 warbleR-1.1.33/warbleR/NEWS.md | 16 warbleR-1.1.33/warbleR/R/compare_methods.R | 2 warbleR-1.1.33/warbleR/R/freq_ts.R | 2 warbleR-1.1.33/warbleR/R/internal_functions.R | 9 warbleR-1.1.33/warbleR/R/move_images.R | 4 warbleR-1.1.33/warbleR/R/open_wd.R | 2 warbleR-1.1.33/warbleR/R/overlapping_sels.R | 2 warbleR-1.1.33/warbleR/R/phylo_spectro.R | 8 warbleR-1.1.33/warbleR/R/plot_coordination.R | 2 warbleR-1.1.33/warbleR/R/read_sound_file.R | 19 - warbleR-1.1.33/warbleR/R/read_wave.R | 169 ---------- warbleR-1.1.33/warbleR/R/selection_table.R | 2 warbleR-1.1.33/warbleR/R/spectro_analysis.R | 5 warbleR-1.1.33/warbleR/R/sth_annotations-data.R | 2 warbleR-1.1.33/warbleR/R/test_coordination.R | 19 - warbleR-1.1.33/warbleR/R/warbleR-package.R | 2 warbleR-1.1.33/warbleR/README.md | 13 warbleR-1.1.33/warbleR/build/vignette.rds |binary warbleR-1.1.33/warbleR/data/comp_matrix.rda |binary warbleR-1.1.33/warbleR/data/lbh_selec_table.rda |binary warbleR-1.1.33/warbleR/data/sim_coor_sing.rda |binary warbleR-1.1.33/warbleR/data/sth_annotations.rda |binary warbleR-1.1.33/warbleR/inst/doc/a_warbleR.R |only warbleR-1.1.33/warbleR/inst/doc/a_warbleR.Rmd |only warbleR-1.1.33/warbleR/inst/doc/a_warbleR.html |only warbleR-1.1.33/warbleR/inst/doc/b_annotation_data_format.R |only warbleR-1.1.33/warbleR/inst/doc/b_annotation_data_format.Rmd |only warbleR-1.1.33/warbleR/inst/doc/b_annotation_data_format.html |only warbleR-1.1.33/warbleR/inst/doc/c_warbleR_workflow_02.R |only warbleR-1.1.33/warbleR/inst/doc/c_warbleR_workflow_02.Rmd |only warbleR-1.1.33/warbleR/inst/doc/c_warbleR_workflow_02.html |only warbleR-1.1.33/warbleR/inst/doc/d_warbleR_workflow_03.R |only warbleR-1.1.33/warbleR/inst/doc/d_warbleR_workflow_03.Rmd |only warbleR-1.1.33/warbleR/inst/doc/d_warbleR_workflow_03.html |only warbleR-1.1.33/warbleR/man/move_images.Rd | 4 warbleR-1.1.33/warbleR/man/open_wd.Rd | 2 warbleR-1.1.33/warbleR/man/phylo_spectro.Rd | 6 warbleR-1.1.33/warbleR/man/plot_coordination.Rd | 2 warbleR-1.1.33/warbleR/man/read_wave.Rd | 31 - warbleR-1.1.33/warbleR/man/selection_table.Rd | 2 warbleR-1.1.33/warbleR/man/spectro_analysis.Rd | 3 warbleR-1.1.33/warbleR/man/test_coordination.Rd | 2 warbleR-1.1.33/warbleR/vignettes/a_warbleR.Rmd |only warbleR-1.1.33/warbleR/vignettes/b_annotation_data_format.Rmd |only warbleR-1.1.33/warbleR/vignettes/c_warbleR_workflow_02.Rmd |only warbleR-1.1.33/warbleR/vignettes/d_warbleR_workflow_03.Rmd |only 69 files changed, 157 insertions(+), 285 deletions(-)
Title: Analyzing the Orientation of Maximum Horizontal Stress
Description: Models the direction of the maximum horizontal stress using
relative plate motion parameters. Statistical algorithms to evaluate
the modeling results compared with the observed data. Provides plots
to visualize the results. Methods described in Stephan et al. (2023)
<doi:10.1038/s41598-023-42433-2> and Wdowinski (1998)
<doi:10.1016/S0079-1946(98)00091-3>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between tectonicr versions 0.4.0 dated 2024-08-21 and 0.4.4 dated 2024-12-11
tectonicr-0.4.0/tectonicr/man/compact_grid.Rd |only tectonicr-0.4.0/tectonicr/man/figures/Figure_07_san_andreas_data.png |only tectonicr-0.4.4/tectonicr/DESCRIPTION | 8 tectonicr-0.4.4/tectonicr/MD5 | 143 tectonicr-0.4.4/tectonicr/NAMESPACE | 5 tectonicr-0.4.4/tectonicr/NEWS.md | 263 - tectonicr-0.4.4/tectonicr/R/coordinates.R | 921 ++-- tectonicr-0.4.4/tectonicr/R/interpolation.R | 371 + tectonicr-0.4.4/tectonicr/R/plotting.R | 127 tectonicr-0.4.4/tectonicr/R/stat_tests.R | 17 tectonicr-0.4.4/tectonicr/R/statistics.R | 2282 +++++----- tectonicr-0.4.4/tectonicr/R/trigonometry_degrees.R | 722 +-- tectonicr-0.4.4/tectonicr/R/various.R | 51 tectonicr-0.4.4/tectonicr/README.md | 117 tectonicr-0.4.4/tectonicr/build/vignette.rds |binary tectonicr-0.4.4/tectonicr/data/iceland.rda |binary tectonicr-0.4.4/tectonicr/data/san_andreas.rda |binary tectonicr-0.4.4/tectonicr/data/tibet.rda |binary tectonicr-0.4.4/tectonicr/inst/doc/A_tectonicr.Rmd | 453 - tectonicr-0.4.4/tectonicr/inst/doc/A_tectonicr.html | 22 tectonicr-0.4.4/tectonicr/inst/doc/B_datasets.html | 44 tectonicr-0.4.4/tectonicr/inst/doc/C_stress_trajectories.html | 4 tectonicr-0.4.4/tectonicr/inst/doc/D_statistics.R | 11 tectonicr-0.4.4/tectonicr/inst/doc/D_statistics.Rmd | 380 - tectonicr-0.4.4/tectonicr/inst/doc/D_statistics.html | 140 tectonicr-0.4.4/tectonicr/inst/doc/E_interpolation.R | 22 tectonicr-0.4.4/tectonicr/inst/doc/E_interpolation.Rmd | 340 - tectonicr-0.4.4/tectonicr/inst/doc/E_interpolation.html | 44 tectonicr-0.4.4/tectonicr/inst/doc/F_spatial.R |only tectonicr-0.4.4/tectonicr/inst/doc/F_spatial.Rmd |only tectonicr-0.4.4/tectonicr/inst/doc/F_spatial.html |only tectonicr-0.4.4/tectonicr/man/PoR_coordinates.Rd | 66 tectonicr-0.4.4/tectonicr/man/PoR_distance.Rd |only tectonicr-0.4.4/tectonicr/man/PoR_map.Rd | 4 tectonicr-0.4.4/tectonicr/man/PoR_stress2grid.Rd | 20 tectonicr-0.4.4/tectonicr/man/circle_stats.Rd | 3 tectonicr-0.4.4/tectonicr/man/circular_dispersion_boot.Rd | 2 tectonicr-0.4.4/tectonicr/man/circular_mode.Rd |only tectonicr-0.4.4/tectonicr/man/circular_qqplot.Rd | 102 tectonicr-0.4.4/tectonicr/man/circular_summary.Rd | 14 tectonicr-0.4.4/tectonicr/man/compact-grid.Rd |only tectonicr-0.4.4/tectonicr/man/dispersion.Rd | 2 tectonicr-0.4.4/tectonicr/man/figures/Figure_07_san_andreas_data_low.jpg |only tectonicr-0.4.4/tectonicr/man/figures/logo.png |only tectonicr-0.4.4/tectonicr/man/figures/logo_hi.png |only tectonicr-0.4.4/tectonicr/man/figures/logo_lo.png |only tectonicr-0.4.4/tectonicr/man/figures/logo_med.png |only tectonicr-0.4.4/tectonicr/man/figures/logo_orig.svg |only tectonicr-0.4.4/tectonicr/man/import_WSM2016.Rd | 7 tectonicr-0.4.4/tectonicr/man/kernel_dispersion.Rd | 12 tectonicr-0.4.4/tectonicr/man/line_azimuth.Rd | 8 tectonicr-0.4.4/tectonicr/man/mean_SC.Rd | 4 tectonicr-0.4.4/tectonicr/man/plot_density.Rd | 21 tectonicr-0.4.4/tectonicr/man/prd_err.Rd | 7 tectonicr-0.4.4/tectonicr/man/quick_plot.Rd | 8 tectonicr-0.4.4/tectonicr/man/rose.Rd | 11 tectonicr-0.4.4/tectonicr/man/rose_stats.Rd | 7 tectonicr-0.4.4/tectonicr/man/sample_median.Rd | 2 tectonicr-0.4.4/tectonicr/man/spherical_angle.Rd | 4 tectonicr-0.4.4/tectonicr/man/stress2grid.Rd | 42 tectonicr-0.4.4/tectonicr/man/stress_data.Rd | 6 tectonicr-0.4.4/tectonicr/man/vm_qqplot.Rd | 106 tectonicr-0.4.4/tectonicr/tests/testthat/Rplots.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots1.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots10.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots11.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots12.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots13.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots14.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots15.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots16.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots17.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots18.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots19.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots2.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots20.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots21.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots22.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots23.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots24.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots25.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots26.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots27.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots3.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots4.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots5.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots6.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots7.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots8.pdf |only tectonicr-0.4.4/tectonicr/tests/testthat/Rplots9.pdf |only tectonicr-0.4.4/tectonicr/vignettes/A_tectonicr.Rmd | 453 - tectonicr-0.4.4/tectonicr/vignettes/D_statistics.Rmd | 380 - tectonicr-0.4.4/tectonicr/vignettes/E_interpolation.Rmd | 340 - tectonicr-0.4.4/tectonicr/vignettes/F_spatial.Rmd |only 94 files changed, 4361 insertions(+), 3757 deletions(-)
Title: Spatial Data Science Complementary Features
Description: Wrapping and supplementing commonly used functions in the R ecosystem related to spatial data science,
while serving as a basis for other packages maintained by Wenbo Lv.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between sdsfun versions 0.5.0 dated 2024-11-25 and 0.6.0 dated 2024-12-11
DESCRIPTION | 6 - MD5 | 25 +++--- NAMESPACE | 2 NEWS.md | 10 ++ R/RcppExports.R | 12 ++ R/linear_regression.R |only R/spvar.R | 3 R/stratification.R | 177 +++++++++++++++++++++--------------------- R/utils.R | 195 +++++++++++++++++++++++++++-------------------- man/hclustgeo_disc.Rd | 96 +++++++++++++---------- man/rm_lineartrend.Rd |only man/spvar.Rd | 2 man/tbl_xyz2mat.Rd |only src/LinearRegression.cpp |only src/RcppExports.cpp | 39 +++++++++ src/Tbl2Mat.cpp |only 16 files changed, 342 insertions(+), 225 deletions(-)
Title: Functional Control Charts
Description: Provides functional control charts
for statistical process monitoring of functional data,
using the methods of Capezza et al. (2020) <doi:10.1002/asmb.2507>,
Centofanti et al. (2021) <doi:10.1080/00401706.2020.1753581>,
Capezza et al. (2024) <doi:10.1080/00401706.2024.2327346>,
Capezza et al. (2024) <doi:10.1080/00224065.2024.2383674>,
Centofanti et al. (2022) <doi:10.48550/arXiv.2205.06256>.
The package is thoroughly illustrated in the paper of
Capezza et al (2023) <doi:10.1080/00224065.2023.2219012>.
Author: Christian Capezza [cre, aut],
Fabio Centofanti [aut],
Antonio Lepore [aut],
Biagio Palumbo [aut],
Alessandra Menafoglio [ctb],
Simone Vantini [ctb]
Maintainer: Christian Capezza <christian.capezza@unina.it>
Diff between funcharts versions 1.5.0 dated 2024-07-19 and 1.6.0 dated 2024-12-11
DESCRIPTION | 25 +- MD5 | 109 ++++++----- NAMESPACE | 15 + NEWS.md | 18 + R/00_mfd.R | 134 +++++++++++++ R/02_fof_pc.R | 3 R/02_sof_pc.R | 3 R/04_phaseII.R | 4 R/05_fault_detection.R | 6 R/FRTM.R |only R/FRTM_plot_functions.R |only R/FRTM_scamfunctions.R |only R/FRTM_util.R |only R/RcppExports.R | 20 ++ R/amfewma.R | 7 R/funcharts-package.R | 48 +++- R/real_time_01_pca.mfd.R | 1 R/real_time_02_fof_pc.R | 1 R/real_time_02_sof_pc.R | 1 R/rmfcc.R | 22 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/capezza2020.html | 8 inst/doc/centofanti2021.html | 10 - inst/doc/colosimo2010.html | 12 - inst/doc/mfd.html | 6 man/AMFEWMA_PhaseI.Rd | 411 +++++++++++++++++++++--------------------- man/AMFEWMA_PhaseII.Rd | 6 man/FRTM_PhaseI.Rd |only man/FRTM_PhaseII.Rd |only man/OEBFDTW.Rd |only man/RoMFCC_PhaseI.Rd | 6 man/RoMFCC_PhaseII.Rd | 6 man/RoMFDI.Rd | 185 +++++++++--------- man/control_charts_pca.Rd | 1 man/control_charts_sof_pc.Rd | 3 man/cor_mfd.Rd |only man/cov_mfd.Rd |only man/fof_pc.Rd | 3 man/fof_pc_real_time.Rd | 3 man/funcharts-package.Rd | 35 +++ man/functional_filter.Rd | 5 man/mFPCA.Rd |only man/mean_mfd.Rd |only man/par.FDTW.Rd |only man/par.mFPCA.Rd |only man/par.rtr.Rd |only man/pca_mfd_real_time.Rd | 3 man/plot.FRTM_PhaseI.Rd |only man/plot.mFPCA.Rd |only man/plot_bootstrap_sof_pc.Rd | 3 man/predict_fof_pc.Rd | 4 man/predict_sof_pc.Rd | 3 man/regr_cc_fof.Rd | 3 man/regr_cc_sof.Rd | 3 man/rpca_mfd.Rd | 6 man/simulate_data_FRTM.Rd |only man/sof_pc.Rd | 3 man/sof_pc_real_time.Rd | 3 src/RcppExports.cpp | 99 ++++++++++ src/src.cpp | 357 ++++++++++++++++++++++++++++++++++++ tests/testthat/Rplots.pdf |only tests/testthat/test_FRTM.R |only tests/testthat/test_OEBFDTW.R |only tests/testthat/test_mFPCA.R |only tests/testthat/test_mfd.R | 12 + 66 files changed, 1214 insertions(+), 402 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.0.4 dated 2024-07-26 and 5.0.5 dated 2024-12-11
UComp-5.0.4/UComp/R/PTSS3functions.R |only UComp-5.0.4/UComp/R/PTSfunctions.R |only UComp-5.0.4/UComp/man/ARIMAmodel.Rd |only UComp-5.0.4/UComp/man/ETSmodel.Rd |only UComp-5.0.4/UComp/man/PTS.Rd |only UComp-5.0.4/UComp/man/PTS2modelUC.Rd |only UComp-5.0.4/UComp/man/PTScomponents.Rd |only UComp-5.0.4/UComp/man/PTSestim.Rd |only UComp-5.0.4/UComp/man/PTSmodel.Rd |only UComp-5.0.4/UComp/man/PTSsetup.Rd |only UComp-5.0.4/UComp/man/PTSvalidate.Rd |only UComp-5.0.4/UComp/man/TETSmodel.Rd |only UComp-5.0.4/UComp/man/UCmodel.Rd |only UComp-5.0.4/UComp/man/modelUC2PTS.Rd |only UComp-5.0.4/UComp/man/modelUC2arma.Rd |only UComp-5.0.4/UComp/man/summary.PTS.Rd |only UComp-5.0.5/UComp/ChangeLog | 4 UComp-5.0.5/UComp/DESCRIPTION | 10 +- UComp-5.0.5/UComp/MD5 | 146 ++++++++++++++------------------ UComp-5.0.5/UComp/NAMESPACE | 24 +---- UComp-5.0.5/UComp/R/ARIMAS3functions.R | 14 +-- UComp-5.0.5/UComp/R/ARIMAestim.R | 4 UComp-5.0.5/UComp/R/ARIMAmodel.R | 29 +++--- UComp-5.0.5/UComp/R/ARIMAvalidate.R | 7 - UComp-5.0.5/UComp/R/ETSS3functions.R | 20 ++-- UComp-5.0.5/UComp/R/ETScomponents.R | 4 UComp-5.0.5/UComp/R/ETSestim.R | 4 UComp-5.0.5/UComp/R/ETSmodel.R | 30 +++--- UComp-5.0.5/UComp/R/ETSvalidate.R | 68 ++++++++++---- UComp-5.0.5/UComp/R/TETSS3functions.R | 20 ++-- UComp-5.0.5/UComp/R/TETScomponents.R | 4 UComp-5.0.5/UComp/R/TETSestim.R | 4 UComp-5.0.5/UComp/R/TETSmodel.R | 27 +++-- UComp-5.0.5/UComp/R/TETSvalidate.R | 68 ++++++++++---- UComp-5.0.5/UComp/R/UCS3functions.R | 50 +++++----- UComp-5.0.5/UComp/R/UCcomponents.R | 4 UComp-5.0.5/UComp/R/UCestim.R | 2 UComp-5.0.5/UComp/R/UCfilter.R | 8 - UComp-5.0.5/UComp/R/UCmodel.R | 20 ++-- UComp-5.0.5/UComp/R/UCvalidate.R | 2 UComp-5.0.5/UComp/R/onAttach.R | 2 UComp-5.0.5/UComp/R/tools.R | 4 UComp-5.0.5/UComp/man/AIC.UComp.Rd | 4 UComp-5.0.5/UComp/man/ARIMA.Rd | 6 - UComp-5.0.5/UComp/man/ARIMAestim.Rd | 4 UComp-5.0.5/UComp/man/ARIMAforecast.Rd |only UComp-5.0.5/UComp/man/ARIMAsetup.Rd | 6 - UComp-5.0.5/UComp/man/ARIMAvalidate.Rd | 6 - UComp-5.0.5/UComp/man/BIC.UComp.Rd | 4 UComp-5.0.5/UComp/man/ETS.Rd | 6 - UComp-5.0.5/UComp/man/ETScomponents.Rd | 4 UComp-5.0.5/UComp/man/ETSestim.Rd | 4 UComp-5.0.5/UComp/man/ETSforecast.Rd |only UComp-5.0.5/UComp/man/ETSsetup.Rd | 6 - UComp-5.0.5/UComp/man/ETSvalidate.Rd | 6 - UComp-5.0.5/UComp/man/TETS.Rd | 6 - UComp-5.0.5/UComp/man/TETScomponents.Rd | 4 UComp-5.0.5/UComp/man/TETSestim.Rd | 4 UComp-5.0.5/UComp/man/TETSforecast.Rd |only UComp-5.0.5/UComp/man/TETSsetup.Rd | 6 - UComp-5.0.5/UComp/man/TETSvalidate.Rd | 6 - UComp-5.0.5/UComp/man/UC.Rd | 2 UComp-5.0.5/UComp/man/UCcomponents.Rd | 4 UComp-5.0.5/UComp/man/UCdisturb.Rd | 2 UComp-5.0.5/UComp/man/UCestim.Rd | 2 UComp-5.0.5/UComp/man/UCfilter.Rd | 2 UComp-5.0.5/UComp/man/UCforecast.Rd |only UComp-5.0.5/UComp/man/UChp.Rd | 2 UComp-5.0.5/UComp/man/UCsetup.Rd | 4 UComp-5.0.5/UComp/man/UCsmooth.Rd | 2 UComp-5.0.5/UComp/man/UCvalidate.Rd | 2 UComp-5.0.5/UComp/man/box.cox.Rd | 2 UComp-5.0.5/UComp/man/fitted.Rd | 25 +---- UComp-5.0.5/UComp/man/getp0.Rd | 6 - UComp-5.0.5/UComp/man/inv.box.cox.Rd | 2 UComp-5.0.5/UComp/man/plot.ARIMA.Rd | 4 UComp-5.0.5/UComp/man/plot.Rd | 25 +---- UComp-5.0.5/UComp/man/predict.UComp.Rd | 4 UComp-5.0.5/UComp/man/print.Rd | 28 +----- UComp-5.0.5/UComp/man/residuals.Rd | 25 +---- UComp-5.0.5/UComp/man/summary.ARIMA.Rd | 4 UComp-5.0.5/UComp/man/summary.ETS.Rd | 4 UComp-5.0.5/UComp/man/summary.TETS.Rd | 4 UComp-5.0.5/UComp/src/UCompC.cpp | 38 ++------ 84 files changed, 406 insertions(+), 448 deletions(-)
Title: Feature Stores for the 'diseasy' Framework
Description: Simple feature stores and tools for creating personalised feature stores.
'diseasystore' powers feature stores which can automatically link and aggregate features to a given stratification
level. These feature stores are automatically time-versioned (powered by the 'SCDB' package) and allows you to easily
and dynamically compute features as part of your continuous integration.
Author: Rasmus Skytte Randloev [aut, cre]
,
Kaare Graesboell [rev] ,
Kasper Schou Telkamp [rev] ,
Lasse Engbo Christiansen [rev]
,
Marcus Munch Gruenewald [rev] ,
Sofia Myrup Otero [rev],
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between diseasystore versions 0.2.2 dated 2024-07-15 and 0.3.0 dated 2024-12-11
diseasystore-0.2.2/diseasystore/R/0_locks.R |only diseasystore-0.3.0/diseasystore/DESCRIPTION | 26 diseasystore-0.3.0/diseasystore/MD5 | 118 diseasystore-0.3.0/diseasystore/NAMESPACE | 12 diseasystore-0.3.0/diseasystore/NEWS.md | 240 - diseasystore-0.3.0/diseasystore/R/0_R6_utils.R | 116 diseasystore-0.3.0/diseasystore/R/0_documentation.R | 76 diseasystore-0.3.0/diseasystore/R/0_linters.R | 8 diseasystore-0.3.0/diseasystore/R/0_miscellaneous.R |only diseasystore-0.3.0/diseasystore/R/2_FeatureHandler.R | 9 diseasystore-0.3.0/diseasystore/R/3_feature_store_helpers.R | 23 diseasystore-0.3.0/diseasystore/R/DiseasystoreBase.R | 200 diseasystore-0.3.0/diseasystore/R/DiseasystoreEcdcRespiratoryViruses.R | 28 diseasystore-0.3.0/diseasystore/R/DiseasystoreGoogleCovid19.R | 73 diseasystore-0.3.0/diseasystore/R/DiseasystoreSimulist.R |only diseasystore-0.3.0/diseasystore/R/age_helpers.R |only diseasystore-0.3.0/diseasystore/R/data.R |only diseasystore-0.3.0/diseasystore/R/drop_diseasystore.R | 17 diseasystore-0.3.0/diseasystore/R/test_diseasystore.R | 285 + diseasystore-0.3.0/diseasystore/README.md | 12 diseasystore-0.3.0/diseasystore/build/partial.rdb |only diseasystore-0.3.0/diseasystore/build/vignette.rds |binary diseasystore-0.3.0/diseasystore/data |only diseasystore-0.3.0/diseasystore/inst/WORDLIST | 12 diseasystore-0.3.0/diseasystore/inst/doc/benchmarks.R |only diseasystore-0.3.0/diseasystore/inst/doc/benchmarks.Rmd |only diseasystore-0.3.0/diseasystore/inst/doc/benchmarks.html |only diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.R | 8 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.Rmd | 8 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.html | 25 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-google-covid-19.R | 8 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-google-covid-19.Rmd | 10 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore-google-covid-19.html | 20 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore.R | 20 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore.Rmd | 43 diseasystore-0.3.0/diseasystore/inst/doc/diseasystore.html | 339 - diseasystore-0.3.0/diseasystore/inst/doc/extending-diseasystore-example.R |only diseasystore-0.3.0/diseasystore/inst/doc/extending-diseasystore-example.Rmd |only diseasystore-0.3.0/diseasystore/inst/doc/extending-diseasystore-example.html |only diseasystore-0.3.0/diseasystore/inst/doc/extending-diseasystore.Rmd | 97 diseasystore-0.3.0/diseasystore/inst/doc/extending-diseasystore.html | 142 diseasystore-0.3.0/diseasystore/inst/extdata |only diseasystore-0.3.0/diseasystore/man/DiseasystoreBase.Rd | 34 diseasystore-0.3.0/diseasystore/man/DiseasystoreEcdcRespiratoryViruses.Rd | 23 diseasystore-0.3.0/diseasystore/man/DiseasystoreGoogleCovid19.Rd | 1 diseasystore-0.3.0/diseasystore/man/DiseasystoreSimulist.Rd |only diseasystore-0.3.0/diseasystore/man/FeatureHandler.Rd | 7 diseasystore-0.3.0/diseasystore/man/add_years.Rd |only diseasystore-0.3.0/diseasystore/man/age_labels.Rd | 10 diseasystore-0.3.0/diseasystore/man/age_on_date.Rd |only diseasystore-0.3.0/diseasystore/man/diseasyoption.Rd | 10 diseasystore-0.3.0/diseasystore/man/diseasystore-package.Rd | 2 diseasystore-0.3.0/diseasystore/man/drop_diseasystore.Rd | 4 diseasystore-0.3.0/diseasystore/man/simulist_data.Rd |only diseasystore-0.3.0/diseasystore/man/test_diseasystore.Rd | 17 diseasystore-0.3.0/diseasystore/tests/spelling.R | 10 diseasystore-0.3.0/diseasystore/tests/testthat/helper-setup.R | 45 diseasystore-0.3.0/diseasystore/tests/testthat/test-0_R6_utils.R | 36 diseasystore-0.3.0/diseasystore/tests/testthat/test-DiseasystoreBase.R | 195 diseasystore-0.3.0/diseasystore/tests/testthat/test-DiseasystoreSimulist.R |only diseasystore-0.3.0/diseasystore/tests/testthat/test-FeatureHandler.R | 4 diseasystore-0.3.0/diseasystore/tests/testthat/test-age_helpers.R |only diseasystore-0.3.0/diseasystore/tests/testthat/test-drop_diseasystore.R | 155 diseasystore-0.3.0/diseasystore/tests/testthat/test-truncate_interlace.R | 20 diseasystore-0.3.0/diseasystore/tests/testthat/test_data/data/snapshots/2023-11-24_ILIARIRates.csv | 2002 +++++----- diseasystore-0.3.0/diseasystore/vignettes/benchmarks.Rmd |only diseasystore-0.3.0/diseasystore/vignettes/diseasystore-ecdc-respiratory-viruses.Rmd | 8 diseasystore-0.3.0/diseasystore/vignettes/diseasystore-google-covid-19.Rmd | 10 diseasystore-0.3.0/diseasystore/vignettes/diseasystore.Rmd | 43 diseasystore-0.3.0/diseasystore/vignettes/extending-diseasystore-example.Rmd |only diseasystore-0.3.0/diseasystore/vignettes/extending-diseasystore.Rmd | 97 71 files changed, 2718 insertions(+), 1990 deletions(-)
Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between tree versions 1.0-43 dated 2023-02-05 and 1.0-44 dated 2024-12-11
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- src/grow.c | 12 ++++++------ 3 files changed, 14 insertions(+), 14 deletions(-)
Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table',
giving users the speed of 'data.table' while using tidyverse-like syntax.
Author: Mark Fairbanks [aut, cre],
Abdessabour Moutik [ctb],
Matt Carlson [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb],
Robert On [ctb],
Alexander Sevostianov [ctb],
Koen ter Berg [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.11.1 dated 2024-07-18 and 0.11.2 dated 2024-12-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/case.R | 8 +------- R/dt.R | 10 +++++----- R/utils-general.R | 6 ++---- tests/testthat/test-dt.R | 6 ++++++ 7 files changed, 29 insertions(+), 26 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between RODBC versions 1.3-23 dated 2023-11-25 and 1.3-25.1 dated 2024-12-11
ChangeLog | 4 DESCRIPTION | 14 +- MD5 | 10 +- build/vignette.rds |binary inst/doc/RODBC.pdf |binary src/RODBC.c | 253 ++++++++++++++++++++++++++--------------------------- 6 files changed, 143 insertions(+), 138 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
Author: Craig Gower-Page [aut, cre],
Alessandro Noci [aut],
Marcel Wolbers [ctb],
Isaac Gravestock [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Craig Gower-Page <craig.gower-page@roche.com>
Diff between rbmi versions 1.3.0 dated 2024-10-16 and 1.3.1 dated 2024-12-11
DESCRIPTION | 8 +++++--- MD5 | 21 +++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/utilities.R | 36 +++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/advanced.html | 2 +- inst/doc/quickstart.html | 40 ++++++++++++++++++++-------------------- man/get_session_hash.Rd |only man/rbmi-package.Rd | 1 + tests/testthat/test-longData.R | 33 +++++++++++++++++++++++++++++++++ tests/testthat/test-utilities.R | 19 +++++++++++++++++++ 12 files changed, 126 insertions(+), 39 deletions(-)
Title: Statistical Tools for Quantitative Genetic Analyses
Description: Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses.
Rohde et al. (2019) <doi:10.1101/503631>.
Author: Peter Soerensen [aut, cre],
Palle Duun Rohde [aut],
Izel Fourie Soerensen [aut]
Maintainer: Peter Soerensen <peter.sorensen@r-qgg.org>
Diff between qgg versions 1.1.2 dated 2023-09-07 and 1.1.3 dated 2024-12-11
qgg-1.1.2/qgg/man/qcStat.Rd |only qgg-1.1.3/qgg/DESCRIPTION | 12 qgg-1.1.3/qgg/MD5 | 126 qgg-1.1.3/qgg/NAMESPACE | 22 qgg-1.1.3/qgg/NEWS.md | 2 qgg-1.1.3/qgg/R/RcppExports.R | 28 qgg-1.1.3/qgg/R/genomic_bayes.R | 3292 +++++++++++++++++++------ qgg-1.1.3/qgg/R/genomic_correlation.R | 85 qgg-1.1.3/qgg/R/genomic_matrix.R | 626 +++- qgg-1.1.3/qgg/R/genomic_reml.R | 2 qgg-1.1.3/qgg/R/genomic_score.R | 62 qgg-1.1.3/qgg/R/genomic_simulation.R | 241 + qgg-1.1.3/qgg/R/genomic_statistics.R | 97 qgg-1.1.3/qgg/R/multiple_marker_test.R | 517 +++ qgg-1.1.3/qgg/R/qgg.R | 11 qgg-1.1.3/qgg/README.md | 177 + qgg-1.1.3/qgg/man/acc.Rd | 36 qgg-1.1.3/qgg/man/adjLDStat.Rd | 76 qgg-1.1.3/qgg/man/adjStat.Rd | 106 qgg-1.1.3/qgg/man/adjustB.Rd | 74 qgg-1.1.3/qgg/man/adjustMapLD.Rd | 54 qgg-1.1.3/qgg/man/auc.Rd | 34 qgg-1.1.3/qgg/man/checkStat.Rd |only qgg-1.1.3/qgg/man/computeROC.Rd | 40 qgg-1.1.3/qgg/man/createLDsets.Rd |only qgg-1.1.3/qgg/man/gbayes.Rd | 3 qgg-1.1.3/qgg/man/getG.Rd | 118 qgg-1.1.3/qgg/man/getLD.Rd | 56 qgg-1.1.3/qgg/man/getLDscores.Rd |only qgg-1.1.3/qgg/man/getLDsets.Rd | 38 qgg-1.1.3/qgg/man/getMap.Rd | 44 qgg-1.1.3/qgg/man/getMarkers.Rd | 46 qgg-1.1.3/qgg/man/getPos.Rd | 44 qgg-1.1.3/qgg/man/getSparseLD.Rd | 76 qgg-1.1.3/qgg/man/gfilter.Rd | 126 qgg-1.1.3/qgg/man/glma.Rd | 268 +- qgg-1.1.3/qgg/man/gmap.Rd | 405 +-- qgg-1.1.3/qgg/man/gprep.Rd | 2 qgg-1.1.3/qgg/man/gsea.Rd | 1 qgg-1.1.3/qgg/man/gsim.Rd | 122 qgg-1.1.3/qgg/man/gsimC.Rd |only qgg-1.1.3/qgg/man/gsimR.Rd |only qgg-1.1.3/qgg/man/hwe.Rd | 30 qgg-1.1.3/qgg/man/ldsc.Rd | 245 - qgg-1.1.3/qgg/man/ldscore.Rd | 82 qgg-1.1.3/qgg/man/magma.Rd |only qgg-1.1.3/qgg/man/mapSets.Rd | 52 qgg-1.1.3/qgg/man/mapStat.Rd | 136 - qgg-1.1.3/qgg/man/mtadj.Rd | 194 - qgg-1.1.3/qgg/man/plotBayes.Rd | 42 qgg-1.1.3/qgg/man/plotForest.Rd | 96 qgg-1.1.3/qgg/man/plotLD.Rd | 50 qgg-1.1.3/qgg/man/plotROC.Rd | 40 qgg-1.1.3/qgg/man/pops.Rd |only qgg-1.1.3/qgg/man/predict_auc_mt_cc.Rd | 78 qgg-1.1.3/qgg/man/predict_auc_mt_continuous.Rd | 70 qgg-1.1.3/qgg/man/predict_auc_st.Rd | 56 qgg-1.1.3/qgg/man/predict_r2_mt.Rd | 60 qgg-1.1.3/qgg/man/predict_r2_st.Rd | 48 qgg-1.1.3/qgg/man/rnag.Rd | 34 qgg-1.1.3/qgg/man/splitWithOverlap.Rd | 46 qgg-1.1.3/qgg/man/vegas.Rd |only qgg-1.1.3/qgg/man/writeBED.Rd |only qgg-1.1.3/qgg/src/Makevars.win | 2 qgg-1.1.3/qgg/src/RcppExports.cpp | 124 qgg-1.1.3/qgg/src/bedfunc.cpp | 153 - qgg-1.1.3/qgg/src/gbayes.cpp | 735 ++++- qgg-1.1.3/qgg/src/mtgbayes.cpp | 2289 ++++++++++++++++- qgg-1.1.3/qgg/src/qgg_init.c | 24 69 files changed, 8595 insertions(+), 3160 deletions(-)
Title: Penalized Smoothing Splines
Description: Smoothing splines with penalties on order m derivatives.
Author: S original by Jim Ramsey <ramsay@psych.mcgill.ca>.
R port by Brian Ripley <Brian.Ripley@R-project.org>.
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between pspline versions 1.0-20 dated 2024-05-25 and 1.0-21 dated 2024-12-11
ChangeLog | 2 ++ DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- 3 files changed, 10 insertions(+), 8 deletions(-)
Title: Estimation/Multiple Imputation for Mixed Categorical and
Continuous Data
Description: Estimation/multiple imputation programs for mixed categorical
and continuous data.
Author: Joseph L. Schafer [aut],
Brian Ripley [aut, trl, cre]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between mix versions 1.0-12 dated 2024-05-13 and 1.0-13 dated 2024-12-11
DESCRIPTION | 22 ++++++++++++++++------ MD5 | 4 ++-- data/stlouis.rda |binary 3 files changed, 18 insertions(+), 8 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.6 dated 2024-11-15 and 1.3.8 dated 2024-12-11
DESCRIPTION | 10 MD5 | 34 - NAMESPACE | 3 NEWS.md | 6 R/CreateTableOneJS.R | 159 ++++---- R/forestcox.R | 2 R/forestglm.R | 572 ++++++++++++++++++++++---------- R/svyCreateTableOneJS.R | 164 +++++---- inst/doc/jstable.html | 30 - man/CreateTableOne2.Rd | 5 man/CreateTableOneJS.Rd | 5 man/TableSubgroupGLM.Rd | 2 man/count_event_by.Rd | 2 man/svyCreateTableOne2.Rd | 5 man/svyCreateTableOneJS.Rd | 5 tests/testthat/test-CreateTableOneJS.R | 14 tests/testthat/test-forestglm.R | 4 tests/testthat/test-svyCreateTableOne.R | 9 18 files changed, 672 insertions(+), 359 deletions(-)
Title: Generalized Estimation Equation Solver
Description: Generalized Estimation Equation solver.
Author: Vincent J Carey [aut],
Thomas S Lumley [trl] ,
Cleve Moler [ctb] ,
Brian Ripley [trl, cre, ctb]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between gee versions 4.13-27 dated 2024-05-25 and 4.13-29 dated 2024-12-11
DESCRIPTION | 12 +++++----- MD5 | 4 +-- src/ugee.c | 72 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 44 insertions(+), 44 deletions(-)
Title: Imputation Procedures and Quality Tests for Fuzzy Data
Description: Special procedures for the imputation of missing fuzzy numbers are still underdeveloped. The goal of the package is to provide the new d-imputation method (DIMP for short, Romaniuk, M. and Grzegorzewski, P. (2023) "Fuzzy Data Imputation with DIMP and FGAIN" RB/23/2023) and covert some classical ones applied in R packages ('missForest','miceRanger','knn') for use with fuzzy datasets. Additionally, specially tailored benchmarking tests are provided to check and compare these imputation procedures with fuzzy datasets.
Author: Maciej Romaniuk [cre, aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyImputationTest versions 0.3.4 dated 2024-10-30 and 0.3.6 dated 2024-12-11
DESCRIPTION | 6 +- MD5 | 66 ++++++++++++++-------- R/ApplyStatisticalTests.R | 6 +- R/CalculateFuzzyMeasures.R | 58 +++++++++++++++++++- R/ErrorMatrix.R | 26 ++++++--- R/FuzzifyMatrix.R | 6 +- R/FuzzyNumbersToMatrix.R | 38 ++++++++++++- R/ImputationDimp.R | 2 R/ImputationTests.R | 69 +++++++++++++++++++++--- R/IntroducingNA.R | 11 ++- R/MatrixToFuzzyNumbers.R | 40 +++++++++++++ R/MeasureAHD.R | 45 +++++++++++++++ R/MeasureEuclidean.R | 47 ++++++++++++++++ R/MeasureHSD.R | 46 ++++++++++++++++ R/MethodsComparison.R | 48 ++++++++++++++++ R/RemoveNotFuzzy.R | 4 - R/StatisticalMeasures.R | 57 ++++++++++++++++++- R/utils.R | 15 +++++ man/ErrorMatrix.Rd | 6 +- man/FuzzifyMatrix.Rd | 4 - man/ImputationTests.Rd | 2 tests/testthat/_snaps/ApplyStatisticalTests.md | 36 ++++++++++++ tests/testthat/_snaps/CalculateFuzzyMeasures.md |only tests/testthat/_snaps/FuzzyNumbersToMatrix.md |only tests/testthat/_snaps/ImputationTests.md |only tests/testthat/_snaps/MatrixToFuzzyNumbers.md |only tests/testthat/_snaps/MeasureAHD.md |only tests/testthat/_snaps/MeasureEuclidean.md |only tests/testthat/_snaps/MeasureHSD.md |only tests/testthat/_snaps/MethodsComparison.md |only tests/testthat/_snaps/StatisticalMeasures.md |only tests/testthat/test-ApplyStatisticalTests.R | 30 ++++++++++ tests/testthat/test-CalculateFuzzyMeasures.R |only tests/testthat/test-ErrorMatrix.R | 4 - tests/testthat/test-FuzzyNumbersToMatrix.R |only tests/testthat/test-ImputationTests.R |only tests/testthat/test-IntroducingNA.R | 8 +- tests/testthat/test-MatrixToFuzzyNumbers.R |only tests/testthat/test-MeasureAHD.R |only tests/testthat/test-MeasureEuclidean.R |only tests/testthat/test-MeasureHSD.R |only tests/testthat/test-MethodsComparison.R |only tests/testthat/test-StatisticalMeasures.R |only 43 files changed, 606 insertions(+), 74 deletions(-)
More information about FuzzyImputationTest at CRAN
Permanent link
Title: FastICA Algorithms to Perform ICA and Projection Pursuit
Description: Implementation of FastICA algorithm to perform Independent
Component Analysis (ICA) and Projection Pursuit.
Author: Jonathan L Marchini [aut],
Chris Heaton [aut],
Brian Ripley [aut, cre]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between fastICA versions 1.2-5.1 dated 2024-08-21 and 1.2-7 dated 2024-12-11
DESCRIPTION | 21 +++++---- MD5 | 4 - src/ica.c | 130 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 79 insertions(+), 76 deletions(-)
Title: Species Distribution Modeling and Ecological Niche Modeling
Description: Implements species distribution modeling and ecological niche
modeling, including: bias correction, spatial cross-validation, model
evaluation, raster interpolation, biotic "velocity" (speed and
direction of movement of a "mass" represented by a raster), interpolating
across a time series of rasters, and use of spatially imprecise records.
The heart of the package is a set of "training" functions which
automatically optimize model complexity based number of available
occurrences. These algorithms include MaxEnt, MaxNet, boosted regression
trees/gradient boosting machines, generalized additive models,
generalized linear models, natural splines, and random forests. To enhance
interoperability with other modeling packages, no new classes are created.
The package works with 'PROJ6' geodetic objects and coordinate reference
systems.
Author: Adam B. Smith [cre, aut]
Maintainer: Adam B. Smith <adam.smith@mobot.org>
Diff between enmSdmX versions 1.1.9 dated 2024-11-03 and 1.2.10 dated 2024-12-11
enmSdmX-1.1.9/enmSdmX/R/trainBRT.r |only enmSdmX-1.1.9/enmSdmX/R/trainGAM.r |only enmSdmX-1.1.9/enmSdmX/R/trainGLM.r |only enmSdmX-1.1.9/enmSdmX/R/trainNS.r |only enmSdmX-1.1.9/enmSdmX/R/trainRF.r |only enmSdmX-1.2.10/enmSdmX/DESCRIPTION | 10 enmSdmX-1.2.10/enmSdmX/MD5 | 116 - enmSdmX-1.2.10/enmSdmX/NAMESPACE | 106 - enmSdmX-1.2.10/enmSdmX/NEWS.md | 6 enmSdmX-1.2.10/enmSdmX/R/aaa.r | 6 enmSdmX-1.2.10/enmSdmX/R/geoFold.r | 2 enmSdmX-1.2.10/enmSdmX/R/predict_maxent.r | 174 - enmSdmX-1.2.10/enmSdmX/R/trainBrt.r |only enmSdmX-1.2.10/enmSdmX/R/trainGam.r |only enmSdmX-1.2.10/enmSdmX/R/trainGlm.r |only enmSdmX-1.2.10/enmSdmX/R/trainNs.r |only enmSdmX-1.2.10/enmSdmX/R/trainRf.r |only enmSdmX-1.2.10/enmSdmX/README.md | 230 +- enmSdmX-1.2.10/enmSdmX/inst/CITATION | 2 enmSdmX-1.2.10/enmSdmX/inst/extdata/canada_level0_gadm41.gpkg |binary enmSdmX-1.2.10/enmSdmX/man/bioticVelocity.Rd | 1016 +++++----- enmSdmX-1.2.10/enmSdmX/man/canada.Rd | 48 enmSdmX-1.2.10/enmSdmX/man/compareResponse.Rd | 178 - enmSdmX-1.2.10/enmSdmX/man/customAlbers.Rd | 182 - enmSdmX-1.2.10/enmSdmX/man/dot-calcWeights.Rd | 48 enmSdmX-1.2.10/enmSdmX/man/dot-cardinalDistance.Rd | 106 - enmSdmX-1.2.10/enmSdmX/man/dot-scalePredictors.Rd | 38 enmSdmX-1.2.10/enmSdmX/man/elimCellDuplicates.Rd | 78 enmSdmX-1.2.10/enmSdmX/man/enmSdmX.Rd | 254 +- enmSdmX-1.2.10/enmSdmX/man/evalAUC.Rd | 118 - enmSdmX-1.2.10/enmSdmX/man/evalContBoyce.Rd | 154 - enmSdmX-1.2.10/enmSdmX/man/evalMultiAUC.Rd | 106 - enmSdmX-1.2.10/enmSdmX/man/evalTSS.Rd | 134 - enmSdmX-1.2.10/enmSdmX/man/evalThreshold.Rd | 148 - enmSdmX-1.2.10/enmSdmX/man/evalThresholdStats.Rd | 160 - enmSdmX-1.2.10/enmSdmX/man/evalTjursR2.Rd | 118 - enmSdmX-1.2.10/enmSdmX/man/examples/customCRS_examples.r | 8 enmSdmX-1.2.10/enmSdmX/man/extentToVect.Rd | 70 enmSdmX-1.2.10/enmSdmX/man/geoFold.Rd | 186 - enmSdmX-1.2.10/enmSdmX/man/geoFoldContrast.Rd | 182 - enmSdmX-1.2.10/enmSdmX/man/geoThin.Rd | 128 - enmSdmX-1.2.10/enmSdmX/man/getCRS.Rd | 86 enmSdmX-1.2.10/enmSdmX/man/globalx.Rd | 78 enmSdmX-1.2.10/enmSdmX/man/interpolateRasts.Rd | 242 +- enmSdmX-1.2.10/enmSdmX/man/mad0.Rd | 54 enmSdmX-1.2.10/enmSdmX/man/mad1.Rd | 54 enmSdmX-1.2.10/enmSdmX/man/nearestEnvPoints.Rd | 392 +-- enmSdmX-1.2.10/enmSdmX/man/nearestGeogPoints.Rd | 500 ++-- enmSdmX-1.2.10/enmSdmX/man/nicheOverlapMetrics.Rd | 124 - enmSdmX-1.2.10/enmSdmX/man/predictEnmSdm.Rd | 532 ++--- enmSdmX-1.2.10/enmSdmX/man/predictMaxEnt.Rd | 560 ++--- enmSdmX-1.2.10/enmSdmX/man/predictMaxNet.Rd | 526 ++--- enmSdmX-1.2.10/enmSdmX/man/summaryByCrossValid.Rd | 440 ++-- enmSdmX-1.2.10/enmSdmX/man/trainBRT.Rd | 2 enmSdmX-1.2.10/enmSdmX/man/trainByCrossValid.Rd | 504 ++-- enmSdmX-1.2.10/enmSdmX/man/trainESM.Rd | 342 +-- enmSdmX-1.2.10/enmSdmX/man/trainGAM.Rd | 2 enmSdmX-1.2.10/enmSdmX/man/trainGLM.Rd | 19 enmSdmX-1.2.10/enmSdmX/man/trainMaxEnt.Rd | 610 +++--- enmSdmX-1.2.10/enmSdmX/man/trainMaxNet.Rd | 584 ++--- enmSdmX-1.2.10/enmSdmX/man/trainNS.Rd | 23 enmSdmX-1.2.10/enmSdmX/man/trainRF.Rd | 2 enmSdmX-1.2.10/enmSdmX/man/troubleshooting_parallel_operations.Rd | 72 enmSdmX-1.2.10/enmSdmX/man/weightByDist.Rd | 90 64 files changed, 4994 insertions(+), 4956 deletions(-)
Title: 'Rcpp' Integration for 'CGAL'
Description: Creates a header only package to link to the 'CGAL'
(Computational Geometry Algorithms Library)
header files in 'Rcpp'. There are a variety of potential uses for
the software such as Hilbert sorting, K-D Tree nearest neighbors,
and convex hull algorithms. For more information about how to use the header files,
see the 'CGAL' documentation at <https://www.cgal.org>. Currently
downloads version 6.0.1 of the 'CGAL' header files.
Author: Eric Dunipace [aut, cre] ,
Tyler Morgan-Wall [ctb],
The CGAL Project [cph]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Diff between RcppCGAL versions 5.6.4 dated 2024-07-04 and 6.0 dated 2024-12-11
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- R/downloader.R | 10 +++++----- README.md | 7 ++++++- build/vignette.rds |binary inst/WORDLIST | 2 ++ inst/doc/Installation.R | 10 +++++----- inst/doc/Installation.html | 4 ++-- inst/include/CGAL_zip.tar.xz |binary man/RcppCGAL-package.Rd | 2 +- tools/config/configure.R | 4 ++-- tools/config/downloader_functions.R | 3 +++ 12 files changed, 43 insertions(+), 33 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut] ,
Yoonkyoung Jeon [aut],
Jaewoong Heo [aut],
Youngsun Park [aut] ,
Hyungwoo Jo [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.5.9 dated 2024-10-17 and 1.6.0 dated 2024-12-11
DESCRIPTION | 14 ++++--- MD5 | 22 ++++++------ NAMESPACE | 1 NEWS.md | 9 ++++ R/bar.R | 2 - R/box.R | 3 + R/coxph.R | 89 +++++++++++++++++++++++++++++++++++-------------- R/forestcox.R | 40 +++++++++++++++++++--- R/kaplan.R | 80 +++++++++++++++++++++++++++++++++++++++----- R/line.R | 72 ++++++++++++++++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/jsmodule.html | 4 +- 12 files changed, 271 insertions(+), 65 deletions(-)
Title: Searching Shared HLA Amino Acid Residue Prevalence
Description: Processes amino acid alignments produced by the 'IPD-IMGT/HLA (Immuno Polymorphism-ImMunoGeneTics/Human Leukocyte Antigen) Database' to identify user-defined amino acid residue motifs shared across HLA alleles, HLA alleles, or HLA haplotypes, and calculates frequencies based on HLA allele frequency data. 'SSHAARP' (Searching Shared HLA Amino Acid Residue Prevalence) uses 'Generic Mapping Tools (GMT)' software and the 'GMT' R package to generate global frequency heat maps that illustrate the distribution of each user-defined map around the globe. 'SSHAARP' analyzes the allele frequency data described by Solberg et al. (2008) <doi:10.1016/j.humimm.2008.05.001>, a global set of 497 population samples from 185 published datasets, representing 66,800 individuals total. Users may also specify their own datasets, but file conventions must follow the prebundled Solberg dataset, or the mock haplotype dataset.
Author: Livia Tran [aut, cre],
Steven Mack [aut],
Josh Bredeweg [ctb],
Dale Steinhardt [ctb]
Maintainer: Livia Tran <livia.tran@ucsf.edu>
Diff between SSHAARP versions 1.1.0 dated 2021-09-17 and 2.0.5 dated 2024-12-11
SSHAARP-1.1.0/SSHAARP/R/BLAASD.R |only SSHAARP-1.1.0/SSHAARP/R/checkMotif.R |only SSHAARP-1.1.0/SSHAARP/data/AA_atlas.rda |only SSHAARP-1.1.0/SSHAARP/data/IMGTprotalignments.rda |only SSHAARP-1.1.0/SSHAARP/man/AA_atlas.Rd |only SSHAARP-1.1.0/SSHAARP/man/BLAASD.Rd |only SSHAARP-1.1.0/SSHAARP/man/IMGTprotalignments.Rd |only SSHAARP-1.1.0/SSHAARP/man/checkMotif.Rd |only SSHAARP-1.1.0/SSHAARP/vignettes/basemap_bw.jpg |only SSHAARP-2.0.5/SSHAARP/DESCRIPTION | 15 SSHAARP-2.0.5/SSHAARP/MD5 | 73 +- SSHAARP-2.0.5/SSHAARP/NAMESPACE | 30 SSHAARP-2.0.5/SSHAARP/NEWS | 35 - SSHAARP-2.0.5/SSHAARP/R/PALM.R | 583 +++++++++++------- SSHAARP-2.0.5/SSHAARP/R/checkAlleleSyntax.R |only SSHAARP-2.0.5/SSHAARP/R/checkHaplotypeSyntax.R |only SSHAARP-2.0.5/SSHAARP/R/checkLocusANHIG.R |only SSHAARP-2.0.5/SSHAARP/R/checkLocusDataset.R |only SSHAARP-2.0.5/SSHAARP/R/checkMotifSyntax.R |only SSHAARP-2.0.5/SSHAARP/R/checkPosition.R |only SSHAARP-2.0.5/SSHAARP/R/data.R | 33 - SSHAARP-2.0.5/SSHAARP/R/dataSubset.R | 70 +- SSHAARP-2.0.5/SSHAARP/R/dataSubsetHaplo.R |only SSHAARP-2.0.5/SSHAARP/R/findMotif.R | 59 - SSHAARP-2.0.5/SSHAARP/R/getVariantInfo.R |only SSHAARP-2.0.5/SSHAARP/R/isNamePresent.R |only SSHAARP-2.0.5/SSHAARP/R/readFileName.R |only SSHAARP-2.0.5/SSHAARP/R/verifyAlleleANHIG.R |only SSHAARP-2.0.5/SSHAARP/R/verifyAlleleANHIGHaplo.R |only SSHAARP-2.0.5/SSHAARP/R/verifyAlleleDataset.R |only SSHAARP-2.0.5/SSHAARP/build/vignette.rds |binary SSHAARP-2.0.5/SSHAARP/data/mock_haplotype_dataset.rda |only SSHAARP-2.0.5/SSHAARP/data/solberg_dataset.rda |binary SSHAARP-2.0.5/SSHAARP/inst/doc/vignette.R | 9 SSHAARP-2.0.5/SSHAARP/inst/doc/vignette.Rmd | 145 ++-- SSHAARP-2.0.5/SSHAARP/inst/doc/vignette.html | 257 +++++-- SSHAARP-2.0.5/SSHAARP/man/PALM.Rd | 73 +- SSHAARP-2.0.5/SSHAARP/man/checkAlleleSyntax.Rd |only SSHAARP-2.0.5/SSHAARP/man/checkHaplotypeSyntax.Rd |only SSHAARP-2.0.5/SSHAARP/man/checkLocusANHIG.Rd |only SSHAARP-2.0.5/SSHAARP/man/checkLocusDataset.Rd |only SSHAARP-2.0.5/SSHAARP/man/checkMotifSyntax.Rd |only SSHAARP-2.0.5/SSHAARP/man/checkPosition.Rd |only SSHAARP-2.0.5/SSHAARP/man/dataSubset.Rd | 12 SSHAARP-2.0.5/SSHAARP/man/dataSubsetHaplo.Rd |only SSHAARP-2.0.5/SSHAARP/man/findMotif.Rd | 23 SSHAARP-2.0.5/SSHAARP/man/getVariantInfo.Rd |only SSHAARP-2.0.5/SSHAARP/man/isNamePresent.Rd |only SSHAARP-2.0.5/SSHAARP/man/mock_haplotype_dataset.Rd |only SSHAARP-2.0.5/SSHAARP/man/readFilename.Rd |only SSHAARP-2.0.5/SSHAARP/man/verifyAlleleANHIG.Rd |only SSHAARP-2.0.5/SSHAARP/man/verifyAlleleANHIGHaplo.Rd |only SSHAARP-2.0.5/SSHAARP/man/verifyAlleleDataset.Rd |only SSHAARP-2.0.5/SSHAARP/vignettes/allele_bw.jpg |only SSHAARP-2.0.5/SSHAARP/vignettes/basemap_color.jpg |binary SSHAARP-2.0.5/SSHAARP/vignettes/haplo_color.jpg |only SSHAARP-2.0.5/SSHAARP/vignettes/vignette.Rmd | 145 ++-- 57 files changed, 968 insertions(+), 594 deletions(-)
Title: Sequential Imputation with Bayesian Trees Mixed-Effects Models
for Longitudinal Data
Description: Implements a sequential imputation framework using Bayesian Mixed-Effects Trees ('SBMTrees') for handling missing data in longitudinal studies. The package supports a variety of models, including non-linear relationships and non-normal random effects and residuals, leveraging Dirichlet Process priors for increased flexibility. Key features include handling Missing at Random (MAR) longitudinal data, imputation of both covariates and outcomes, and generating posterior predictive samples for further analysis. The methodology is designed for applications in epidemiology, biostatistics, and other fields requiring robust handling of missing data in longitudinal settings.
Author: Jungang Zou [aut, cre],
Liangyuan Hu [aut],
Robert McCulloch [ctb],
Rodney Sparapani [ctb],
Charles Spanbauer [ctb]
Maintainer: Jungang Zou <jungang.zou@gmail.com>
Diff between SBMTrees versions 1.1 dated 2024-12-09 and 1.2 dated 2024-12-11
DESCRIPTION | 6 - MD5 | 30 ++++---- NEWS.md | 9 ++ R/BMTrees_prediction.R | 10 ++ R/sequential_imputation.R | 10 ++ README.md | 16 ++++ inst/doc/SBMTrees_Introduction.R | 6 - inst/doc/SBMTrees_Introduction.Rmd | 10 +- inst/doc/SBMTrees_Introduction.html | 121 +++++++++++++++++++----------------- man/BMTrees_prediction.Rd | 8 +- man/SBMTrees-package.Rd | 9 +- man/sequential_imputation.Rd | 10 ++ src/BART/bart.h | 9 +- src/DP_lambda.h | 6 + src/sequential_imputation.cpp | 4 - vignettes/SBMTrees_Introduction.Rmd | 10 +- 16 files changed, 165 insertions(+), 109 deletions(-)
Title: Graphs and Tables for OMOP Results
Description: Provides methods to transform omop_result objects into
formatted tables and figures, facilitating the visualization of study
results working with the Observational Medical Outcomes Partnership
(OMOP) Common Data Model.
Author: Marti Catala [aut] ,
Nuria Mercade-Besora [aut, cre]
,
Yuchen Guo [ctb] ,
Elin Rowlands [ctb] ,
Edward Burn [ctb]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between visOmopResults versions 0.5.0 dated 2024-11-24 and 0.5.1 dated 2024-12-10
visOmopResults-0.5.0/visOmopResults/R/helperTableFunctions.R |only visOmopResults-0.5.0/visOmopResults/tests/testthat/test-helperTableFunctions.R |only visOmopResults-0.5.1/visOmopResults/DESCRIPTION | 15 visOmopResults-0.5.1/visOmopResults/MD5 | 67 visOmopResults-0.5.1/visOmopResults/NAMESPACE | 2 visOmopResults-0.5.1/visOmopResults/R/datatableInternal.R |only visOmopResults-0.5.1/visOmopResults/R/formatEstimateName.R | 380 +-- visOmopResults-0.5.1/visOmopResults/R/formatEstimateValue.R | 166 - visOmopResults-0.5.1/visOmopResults/R/formatTable.R | 22 visOmopResults-0.5.1/visOmopResults/R/helperFunctions.R |only visOmopResults-0.5.1/visOmopResults/R/plot.R | 43 visOmopResults-0.5.1/visOmopResults/R/plottingThemes.R | 112 - visOmopResults-0.5.1/visOmopResults/R/reexports.R | 198 - visOmopResults-0.5.1/visOmopResults/R/utilities.R | 453 ++-- visOmopResults-0.5.1/visOmopResults/R/visOmopTable.R | 539 ++--- visOmopResults-0.5.1/visOmopResults/build/vignette.rds |binary visOmopResults-0.5.1/visOmopResults/inst/doc/plots.Rmd | 604 ++--- visOmopResults-0.5.1/visOmopResults/inst/doc/plots.html | 26 visOmopResults-0.5.1/visOmopResults/inst/doc/tables.Rmd | 886 ++++---- visOmopResults-0.5.1/visOmopResults/inst/doc/tables.html | 1078 ++++------ visOmopResults-0.5.1/visOmopResults/man/barPlot.Rd | 20 visOmopResults-0.5.1/visOmopResults/man/formatTable.Rd | 12 visOmopResults-0.5.1/visOmopResults/man/plotColumns.Rd |only visOmopResults-0.5.1/visOmopResults/man/scatterPlot.Rd | 2 visOmopResults-0.5.1/visOmopResults/man/tableColumns.Rd |only visOmopResults-0.5.1/visOmopResults/man/tableOptions.Rd | 2 visOmopResults-0.5.1/visOmopResults/man/tableStyle.Rd | 2 visOmopResults-0.5.1/visOmopResults/man/tableType.Rd | 2 visOmopResults-0.5.1/visOmopResults/man/themeVisOmop.Rd | 2 visOmopResults-0.5.1/visOmopResults/man/visOmopTable.Rd | 27 visOmopResults-0.5.1/visOmopResults/tests/testthat/test-formatEstimateName.R | 912 ++++---- visOmopResults-0.5.1/visOmopResults/tests/testthat/test-formatEstimateValue.R | 630 ++--- visOmopResults-0.5.1/visOmopResults/tests/testthat/test-formatTable.R | 160 + visOmopResults-0.5.1/visOmopResults/tests/testthat/test-helperFunctions.R |only visOmopResults-0.5.1/visOmopResults/tests/testthat/test-plot.R | 26 visOmopResults-0.5.1/visOmopResults/tests/testthat/test-visOmopTable.R | 634 +++-- visOmopResults-0.5.1/visOmopResults/vignettes/plots.Rmd | 604 ++--- visOmopResults-0.5.1/visOmopResults/vignettes/tables.Rmd | 886 ++++---- 38 files changed, 4305 insertions(+), 4207 deletions(-)
More information about visOmopResults at CRAN
Permanent link
Title: Load 'Overture' Datasets as 'dbplyr' and 'sf'-Ready Data Frames
Description: An integrated R interface to the 'Overture' API
(<https://docs.overturemaps.org/>). Allows R users to return 'Overture' data as
'dbplyr' data frames or materialized 'sf' spatial data frames.
Author: Arthur Gailes [aut, cre, cph]
Maintainer: Arthur Gailes <agailes1@gmail.com>
Diff between overtureR versions 0.2.3 dated 2024-09-04 and 0.2.4 dated 2024-12-10
DESCRIPTION | 6 MD5 | 10 - NEWS.md | 54 +++--- R/open_curtain.R | 444 ++++++++++++++++++++++++++-------------------------- R/utils.R | 62 +++---- man/open_curtain.Rd | 2 6 files changed, 296 insertions(+), 282 deletions(-)
Title: Download Geospatial Data Available from Several Federated Data
Sources
Description: Download geospatial data available
from several federated data sources (mainly sources maintained by the
US Federal government). Currently, the package enables extraction from
nine datasets: The National Elevation Dataset digital elevation
models (<https://www.usgs.gov/3d-elevation-program> 1 and 1/3 arc-second;
USGS); The National Hydrography Dataset
(<https://www.usgs.gov/national-hydrography/national-hydrography-dataset>;
USGS); The Soil Survey Geographic (SSURGO) database from the National
Cooperative Soil Survey (<https://websoilsurvey.sc.egov.usda.gov/>; NCSS),
which is led by the Natural Resources
Conservation Service (NRCS) under the USDA;
the Global Historical Climatology Network (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>; GHCN), coordinated by National Climatic Data
Center at NOAA; the Daymet gridded estimates of daily weather
parameters for North America, version 4, available from the Oak Ridge [...truncated...]
Author: R. Kyle Bocinsky [aut, cre, cph]
,
Dylan Beaudette [ctb],
Scott Chamberlain [ctb, rev],
Jeffrey Hollister [ctb],
Julia Gustavsen [rev]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 4.1.0 dated 2024-11-11 and 4.2.0 dated 2024-12-10
DESCRIPTION | 13 +- MD5 | 52 ++++---- NAMESPACE | 2 NEWS.md | 3 R/DAYMET_FUNCTIONS.R | 2 R/GHCN_FUNCTIONS.R | 2 R/ITRDB_FUNCTIONS.R | 2 R/NASS_FUNCTIONS.R | 2 R/NED_FUNCTIONS.R | 2 R/NHD_FUNCTIONS.R | 83 +++++------- R/NLCD_FUNCTIONS.R | 4 R/PADUS_FUNCTIONS.R | 48 +++---- R/SSURGO_FUNCTIONS.R | 2 R/UTILITY_FUNCTIONS.R | 276 ++++++++++++++++++++++++++++++++++++++++++- man/agol_filter.Rd |only man/agol_filter_httr.Rd |only man/get_daymet.Rd | 2 man/get_ghcn_daily.Rd | 2 man/get_itrdb.Rd | 8 - man/get_nass_cdl.Rd | 2 man/get_ned.Rd | 2 man/get_nhd.Rd | 2 man/get_nlcd.Rd | 2 man/get_nlcd_annual.Rd | 6 man/get_padus.Rd | 2 man/get_ssurgo.Rd | 31 ++-- man/plot_nhd.Rd | 2 tests/testthat/test.SSURGO.R | 4 28 files changed, 413 insertions(+), 145 deletions(-)
Title: Determine and Evaluate Optimal Cutpoints in Binary
Classification Tasks
Description: Estimate cutpoints that optimize a specified metric in binary classification tasks
and validate performance using bootstrapping. Some methods for more robust cutpoint
estimation are supported, e.g. a parametric method assuming normal distributions,
bootstrapped cutpoints, and smoothing of the metric values per cutpoint using
Generalized Additive Models. Various plotting functions are included. For an overview
of the package see Thiele and Hirschfeld (2021) <doi:10.18637/jss.v098.i11>.
Author: Christian Thiele [cre, aut]
Maintainer: Christian Thiele <c.thiele@gmx-topmail.de>
Diff between cutpointr versions 1.1.2 dated 2022-04-13 and 1.2.0 dated 2024-12-10
cutpointr-1.1.2/cutpointr/man/cutpoint_knots.Rd |only cutpointr-1.1.2/cutpointr/man/maximize_spline_metric.Rd |only cutpointr-1.1.2/cutpointr/tests/testthat/Rplots.pdf |only cutpointr-1.2.0/cutpointr/DESCRIPTION | 12 cutpointr-1.2.0/cutpointr/MD5 | 223 +-- cutpointr-1.2.0/cutpointr/NAMESPACE | 205 +-- cutpointr-1.2.0/cutpointr/NEWS.md | 10 cutpointr-1.2.0/cutpointr/R/add_metric.R | 324 ++-- cutpointr-1.2.0/cutpointr/R/boot_ci.R | 172 +- cutpointr-1.2.0/cutpointr/R/compat-lifecycle.R | 520 +++---- cutpointr-1.2.0/cutpointr/R/cutpointr.R | 7 cutpointr-1.2.0/cutpointr/R/grid_arrange_shared_legend.R | 82 - cutpointr-1.2.0/cutpointr/R/metrics.R | 1 cutpointr-1.2.0/cutpointr/R/oc_manual.R | 30 cutpointr-1.2.0/cutpointr/R/oc_mean.R | 48 cutpointr-1.2.0/cutpointr/R/oc_median.R | 40 cutpointr-1.2.0/cutpointr/R/oc_youden_kernel.R | 186 +- cutpointr-1.2.0/cutpointr/R/oc_youden_normal.R | 128 - cutpointr-1.2.0/cutpointr/R/optimize_metric.R | 156 -- cutpointr-1.2.0/cutpointr/R/plot.cutpointr.R | 102 - cutpointr-1.2.0/cutpointr/R/plot.multi_cutpointr.R | 24 cutpointr-1.2.0/cutpointr/R/plot_cut_boot.R | 136 +- cutpointr-1.2.0/cutpointr/R/plot_roc.R | 208 +-- cutpointr-1.2.0/cutpointr/R/plot_x.R | 210 +-- cutpointr-1.2.0/cutpointr/R/predict.cutpointr.R | 154 +- cutpointr-1.2.0/cutpointr/R/prep.R | 108 - cutpointr-1.2.0/cutpointr/R/print.cutpointr.R | 46 cutpointr-1.2.0/cutpointr/R/print.multi_cutpointr.R | 24 cutpointr-1.2.0/cutpointr/R/print.summary_cutpointr.R | 4 cutpointr-1.2.0/cutpointr/R/roc.R | 228 +-- cutpointr-1.2.0/cutpointr/build/vignette.rds |binary cutpointr-1.2.0/cutpointr/inst/doc/cutpointr.R | 263 +-- cutpointr-1.2.0/cutpointr/inst/doc/cutpointr.Rmd | 253 +-- cutpointr-1.2.0/cutpointr/inst/doc/cutpointr.html | 542 +++++--- cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_benchmarks.R | 18 cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_benchmarks.html | 260 ++- cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_bootstrapping.R | 2 cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_bootstrapping.html | 417 +++--- cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_estimation.R | 12 cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_estimation.Rmd | 18 cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_estimation.html | 407 +++--- cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_plotting.R | 10 cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_plotting.html | 296 ++-- cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_roc.R | 8 cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_roc.html | 261 ++- cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_user_functions.R | 4 cutpointr-1.2.0/cutpointr/inst/doc/cutpointr_user_functions.html | 239 ++- cutpointr-1.2.0/cutpointr/man/F1_score.Rd | 122 - cutpointr-1.2.0/cutpointr/man/Jaccard.Rd | 122 - cutpointr-1.2.0/cutpointr/man/abs_d_ppv_npv.Rd | 127 - cutpointr-1.2.0/cutpointr/man/abs_d_sens_spec.Rd | 128 - cutpointr-1.2.0/cutpointr/man/accuracy.Rd | 122 - cutpointr-1.2.0/cutpointr/man/add_metric.Rd | 96 - cutpointr-1.2.0/cutpointr/man/auc.Rd | 52 cutpointr-1.2.0/cutpointr/man/boot_ci.Rd | 108 - cutpointr-1.2.0/cutpointr/man/boot_test.Rd | 188 +- cutpointr-1.2.0/cutpointr/man/cohens_kappa.Rd | 136 +- cutpointr-1.2.0/cutpointr/man/cutpoint.Rd | 116 - cutpointr-1.2.0/cutpointr/man/cutpointr.Rd | 673 ++++------ cutpointr-1.2.0/cutpointr/man/cutpointr_.Rd | 210 +-- cutpointr-1.2.0/cutpointr/man/false_omission_rate.Rd | 130 - cutpointr-1.2.0/cutpointr/man/maximize_boot_metric.Rd | 263 +-- cutpointr-1.2.0/cutpointr/man/maximize_gam_metric.Rd | 243 +-- cutpointr-1.2.0/cutpointr/man/maximize_loess_metric.Rd | 281 ++-- cutpointr-1.2.0/cutpointr/man/maximize_metric.Rd | 203 +-- cutpointr-1.2.0/cutpointr/man/metric_constrain.Rd | 302 ++-- cutpointr-1.2.0/cutpointr/man/misclassification_cost.Rd | 132 - cutpointr-1.2.0/cutpointr/man/multi_cutpointr.Rd | 132 - cutpointr-1.2.0/cutpointr/man/npv.Rd | 122 - cutpointr-1.2.0/cutpointr/man/oc_manual.Rd | 71 - cutpointr-1.2.0/cutpointr/man/oc_mean.Rd | 87 - cutpointr-1.2.0/cutpointr/man/oc_median.Rd | 79 - cutpointr-1.2.0/cutpointr/man/oc_youden_kernel.Rd | 147 +- cutpointr-1.2.0/cutpointr/man/oc_youden_normal.Rd | 119 - cutpointr-1.2.0/cutpointr/man/odds_ratio.Rd | 122 - cutpointr-1.2.0/cutpointr/man/p_chisquared.Rd | 120 - cutpointr-1.2.0/cutpointr/man/plot.cutpointr.Rd | 76 - cutpointr-1.2.0/cutpointr/man/plot.multi_cutpointr.Rd | 32 cutpointr-1.2.0/cutpointr/man/plot.roc_cutpointr.Rd | 84 - cutpointr-1.2.0/cutpointr/man/plot_cut_boot.Rd | 70 - cutpointr-1.2.0/cutpointr/man/plot_cutpointr.Rd | 154 +- cutpointr-1.2.0/cutpointr/man/plot_metric.Rd | 98 - cutpointr-1.2.0/cutpointr/man/plot_metric_boot.Rd | 74 - cutpointr-1.2.0/cutpointr/man/plot_precision_recall.Rd | 80 - cutpointr-1.2.0/cutpointr/man/plot_roc.Rd | 104 - cutpointr-1.2.0/cutpointr/man/plot_sensitivity_specificity.Rd | 80 - cutpointr-1.2.0/cutpointr/man/plot_x.Rd | 80 - cutpointr-1.2.0/cutpointr/man/plr.Rd | 130 - cutpointr-1.2.0/cutpointr/man/ppv.Rd | 122 - cutpointr-1.2.0/cutpointr/man/precision.Rd | 122 - cutpointr-1.2.0/cutpointr/man/predict.cutpointr.Rd | 82 - cutpointr-1.2.0/cutpointr/man/print.cutpointr.Rd | 54 cutpointr-1.2.0/cutpointr/man/print.multi_cutpointr.Rd | 44 cutpointr-1.2.0/cutpointr/man/prod_ppv_npv.Rd | 128 - cutpointr-1.2.0/cutpointr/man/prod_sens_spec.Rd | 126 - cutpointr-1.2.0/cutpointr/man/prostate_nodal.Rd | 52 cutpointr-1.2.0/cutpointr/man/recall.Rd | 122 - cutpointr-1.2.0/cutpointr/man/risk_ratio.Rd | 122 - cutpointr-1.2.0/cutpointr/man/roc.Rd | 140 +- cutpointr-1.2.0/cutpointr/man/roc01.Rd | 138 +- cutpointr-1.2.0/cutpointr/man/sensitivity.Rd | 114 - cutpointr-1.2.0/cutpointr/man/specificity.Rd | 112 - cutpointr-1.2.0/cutpointr/man/suicide.Rd | 64 cutpointr-1.2.0/cutpointr/man/sum_ppv_npv.Rd | 128 - cutpointr-1.2.0/cutpointr/man/sum_sens_spec.Rd | 126 - cutpointr-1.2.0/cutpointr/man/total_utility.Rd | 160 +- cutpointr-1.2.0/cutpointr/man/tp.Rd | 144 +- cutpointr-1.2.0/cutpointr/man/tpr.Rd | 152 +- cutpointr-1.2.0/cutpointr/man/user_span_cutpointr.Rd | 46 cutpointr-1.2.0/cutpointr/man/youden.Rd | 126 - cutpointr-1.2.0/cutpointr/tests/testthat.R | 8 cutpointr-1.2.0/cutpointr/tests/testthat/test-cutpointr.R | 65 cutpointr-1.2.0/cutpointr/vignettes/cutpointr.Rmd | 253 +-- cutpointr-1.2.0/cutpointr/vignettes/cutpointr_estimation.Rmd | 18 114 files changed, 7506 insertions(+), 7475 deletions(-)
Title: Clustering of Weighted Data
Description: Clusters state sequences and weighted data. It provides an optimized weighted PAM algorithm as well as functions for aggregating replicated cases, computing cluster quality measures for a range of clustering solutions and plotting (fuzzy) clusters of state sequences. Parametric bootstraps methods to validate typology of sequences are also provided. Finally, it provides a fuzzy and crisp CLARA algorithm to cluster large database with sequence analysis.
Author: Matthias Studer [aut, cre]
Maintainer: Matthias Studer <matthias.studer@unige.ch>
Diff between WeightedCluster versions 1.8-0 dated 2024-10-02 and 1.8-1 dated 2024-12-10
DESCRIPTION | 11 +-- MD5 | 40 +++++++---- NEWS | 9 ++ R/zzz.R | 10 +- build/vignette.rds |binary inst/doc/BigDataSA.R |only inst/doc/BigDataSA.Rmd |only inst/doc/BigDataSA.html |only inst/doc/ClusterExternalValidSA.R |only inst/doc/ClusterExternalValidSA.Rmd |only inst/doc/ClusterExternalValidSA.html |only inst/doc/ClusterValidSA.R |only inst/doc/ClusterValidSA.Rmd |only inst/doc/ClusterValidSA.html |only inst/doc/FuzzySA.R |only inst/doc/FuzzySA.Rmd |only inst/doc/FuzzySA.html |only inst/doc/WeightedCluster.R | 18 ++--- inst/doc/WeightedCluster.pdf |binary inst/doc/WeightedClusterFR.R | 18 ++--- inst/doc/WeightedClusterFR.pdf |binary inst/doc/WeightedClusterPreview.R | 8 +- inst/doc/WeightedClusterPreview.pdf |binary src/cluster.h | 2 vignettes/BigDataSA.Rmd |only vignettes/ClusterExternalValidSA.Rmd |only vignettes/ClusterValidSA.Rmd |only vignettes/FuzzySA.Rmd |only vignettes/manual.bib | 125 +++++++++++++++++++++++++++++++---- 29 files changed, 184 insertions(+), 57 deletions(-)
More information about WeightedCluster at CRAN
Permanent link
Title: Rosenthal's Fail Safe Number and Related Functions
Description: Estimation of Rosenthal's fail safe number including confidence intervals. The relevant papers are the following. Konstantinos C. Fragkos, Michail Tsagris and Christos C. Frangos (2014). "Publication Bias in Meta-Analysis: Confidence Intervals for Rosenthal's Fail-Safe Number". International Scholarly Research Notices, Volume 2014. <doi:10.1155/2014/825383>. Konstantinos C. Fragkos, Michail Tsagris and Christos C. Frangos (2017). "Exploring the distribution for the estimator of Rosenthal's fail-safe number of unpublished studies in meta-analysis". Communications in Statistics-Theory and Methods, 46(11):5672--5684. <doi:10.1080/03610926.2015.1109664>.
Author: Michail Tsagris [aut, cre],
Constantinos Frangos [aut],
Christos Frangos [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between fsn versions 0.2 dated 2022-03-09 and 0.4 dated 2024-12-10
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/convergence.rate.R | 12 +++++------- R/den.plot.R | 4 ++-- R/foldnorm.nr.density.R | 2 ++ R/rosenthal.R | 2 ++ R/truncnorm.nr.density.R | 2 ++ man/fsn-package.Rd | 4 ++-- man/halfnorm.fixednr.ci.Rd | 2 +- man/halfnorm.randomnr.ci.Rd | 2 +- man/rosenthal.Rd | 2 +- 12 files changed, 35 insertions(+), 31 deletions(-)
Title: Publication-Ready Tables for 'manymome' Results
Description: Converts results from the 'manymome' package,
presented in Cheung and Cheung (2023)
<doi:10.3758/s13428-023-02224-z>, to publication-ready
tables.
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome.table versions 0.3.0 dated 2024-03-04 and 0.4.0 dated 2024-12-10
DESCRIPTION | 8 +-- MD5 | 21 +++++---- NEWS.md | 14 ++++++ R/as_flextable.cond_indirect_effects.R | 65 ++++++++++++++++++++++++------ R/as_flextable.indirect_list.R | 7 ++- README.md | 2 build/vignette.rds |binary inst/doc/manymome.table.html | 31 +++++++++----- inst/tinytest/test_cond_effect.R |only inst/tinytest/test_cond_ind.R | 5 +- man/as_flextable.cond_indirect_effects.Rd | 15 ++++++ man/as_flextable.indirect_list.Rd | 5 +- 12 files changed, 130 insertions(+), 43 deletions(-)
More information about manymome.table at CRAN
Permanent link
Title: Easily Install and Load 'tesselle' Packages
Description: Easy install and load key packages from the 'tesselle' suite
in a single step. The 'tesselle' suite is a collection of packages for
research and teaching in archaeology. These packages focus on
quantitative analysis methods developed for archaeology. The
'tesselle' packages are designed to work seamlessly together and to
complement general-purpose and other specialized statistical packages.
These packages can be used to explore and analyze common data types in
archaeology: count data, compositional data and chronological data.
Learn more about 'tesselle' at <https://www.tesselle.org>.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tesselle versions 1.4.0 dated 2023-11-30 and 1.5.0 dated 2024-12-10
DESCRIPTION | 25 +++++++++----------- MD5 | 18 +++++++------- NEWS.md | 10 ++++++++ R/attach.R | 8 +++--- R/tesselle-internal.R | 20 ++++++++-------- R/tesselle-package.R | 2 - R/zzz.R | 5 +--- README.md | 59 +++++++++++++++++++++++++----------------------- inst/CITATION | 19 +++++++++++++-- man/tesselle-package.Rd | 3 -- 10 files changed, 96 insertions(+), 73 deletions(-)
Title: Inference for Released Plug-in Sampling Single Synthetic Dataset
Description: Considering the singly imputed synthetic data generated via plug-in sampling under the multivariate normal model, draws inference procedures including the generalized variance, the sphericity test, the test for independence between two subsets of variables, and the test for the regression of one set of variables on the other. For more details see Klein et al. (2021) <doi:10.1007/s13571-019-00215-9>.
Author: Ricardo Moura [aut, cre, cph] ,
Mina Norouzirad [aut] ,
Vitor Augusto [aut] ,
Miguel Fonseca [ctb] ,
FCT, I.P. [fnd] )
Maintainer: Ricardo Moura <rp.moura@fct.unl.pt>
Diff between PSinference versions 0.2.1 dated 2024-09-19 and 0.2.2 dated 2024-12-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 14 +++++++++----- R/Sphdist.R | 2 +- R/simSynthData.R | 5 +++-- 5 files changed, 21 insertions(+), 16 deletions(-)
Title: Hierarchical Partitioning of Marginal R2 for Generalized
Mixed-Effect Models
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor (fixed effects) towards marginal R2 for generalized linear mixed-effect model (including lm, glm and glmm) based on output of r.squaredGLMM() in 'MuMIn', applying the algorithm of Lai J.,Zou Y., Zhang S.,Zhang X.,Mao L.(2022)glmm.hp: an R package for computing individual effect of predictors in generalized linear mixed models.Journal of Plant Ecology,15(6)1302-1307<doi:10.1093/jpe/rtac096>.
Author: Jiangshan Lai [aut, cre] ,
Kim Nimon [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between glmm.hp versions 0.1-6 dated 2024-10-26 and 0.1-7 dated 2024-12-10
DESCRIPTION | 8 - MD5 | 9 - R/glmm.hp.r | 353 +++++++++++++++++++++++++++++++++++++++++++++------------ R/zzz.R |only inst/CITATION | 29 ++-- man/glmm.hp.Rd | 9 + 6 files changed, 311 insertions(+), 97 deletions(-)
Title: Generation of Different Animated Christmas Cards
Description: Generation of different Christmas cards, most of them being
animated. Most of the cards can be generated in three languages (English,
Catalan and Spanish). The collection started in 2009.
Author: Jose Barrera-Gomez [aut, cre]
Maintainer: Jose Barrera-Gomez <jose.barrera@uab.cat>
Diff between christmas versions 1.3.0 dated 2023-12-06 and 1.4.0 dated 2024-12-10
DESCRIPTION | 14 +++++++------- MD5 | 14 ++++++++------ NAMESPACE | 1 + NEWS | 5 +++++ R/auxiliarFunctions.R | 46 ++++++++++++++++++++++++++++++++++++++++++++++ R/xmasfractaltree.R |only README.md | 2 +- man/christmas-package.Rd | 2 +- man/xmasfractaltree.Rd |only 9 files changed, 69 insertions(+), 15 deletions(-)
Title: Progress Bar for Parallel Tasks
Description: A simple interface in the form of R6 classes for executing tasks in
parallel, tracking their progress, and displaying accurate progress bars.
Author: Mihai Constantin [aut, cre]
Maintainer: Mihai Constantin <mihai@mihaiconstantin.com>
Diff between parabar versions 1.2.1 dated 2024-10-17 and 1.3.0 dated 2024-12-10
parabar-1.2.1/parabar/R/Service.R |only parabar-1.2.1/parabar/man/Service.Rd |only parabar-1.3.0/parabar/DESCRIPTION | 17 parabar-1.3.0/parabar/MD5 | 112 - parabar-1.3.0/parabar/NAMESPACE | 3 parabar-1.3.0/parabar/NEWS.md | 47 parabar-1.3.0/parabar/R/AsyncBackend.R | 90 - parabar-1.3.0/parabar/R/Backend.R | 9 parabar-1.3.0/parabar/R/BackendFactory.R | 2 parabar-1.3.0/parabar/R/BackendService.R |only parabar-1.3.0/parabar/R/Context.R | 18 parabar-1.3.0/parabar/R/ContextFactory.R | 5 parabar-1.3.0/parabar/R/Exception.R | 12 parabar-1.3.0/parabar/R/Helper.R | 8 parabar-1.3.0/parabar/R/Options.R | 13 parabar-1.3.0/parabar/R/ProgressTrackingContext.R | 8 parabar-1.3.0/parabar/R/SessionState.R |only parabar-1.3.0/parabar/R/Specification.R | 26 parabar-1.3.0/parabar/R/SyncBackend.R | 23 parabar-1.3.0/parabar/R/TaskState.R | 6 parabar-1.3.0/parabar/R/Warning.R | 23 parabar-1.3.0/parabar/R/exports.R | 20 parabar-1.3.0/parabar/README.md | 18 parabar-1.3.0/parabar/inst/doc/comparison.Rmd | 212 +- parabar-1.3.0/parabar/inst/doc/comparison.html | 883 +++++----- parabar-1.3.0/parabar/man/AsyncBackend.Rd | 39 parabar-1.3.0/parabar/man/Backend.Rd | 27 parabar-1.3.0/parabar/man/BackendFactory.Rd | 2 parabar-1.3.0/parabar/man/BackendService.Rd |only parabar-1.3.0/parabar/man/Context.Rd | 18 parabar-1.3.0/parabar/man/ContextFactory.Rd | 4 parabar-1.3.0/parabar/man/Exception.Rd | 3 parabar-1.3.0/parabar/man/Helper.Rd | 2 parabar-1.3.0/parabar/man/Options.Rd | 10 parabar-1.3.0/parabar/man/ProgressTrackingContext.Rd | 10 parabar-1.3.0/parabar/man/SessionState.Rd |only parabar-1.3.0/parabar/man/Specification.Rd | 10 parabar-1.3.0/parabar/man/SyncBackend.Rd | 26 parabar-1.3.0/parabar/man/TaskState.Rd | 5 parabar-1.3.0/parabar/man/Warning.Rd | 1 parabar-1.3.0/parabar/man/clear.Rd | 4 parabar-1.3.0/parabar/man/evaluate.Rd | 4 parabar-1.3.0/parabar/man/export.Rd | 4 parabar-1.3.0/parabar/man/figures/parabar-design.png |binary parabar-1.3.0/parabar/man/par_apply.Rd | 2 parabar-1.3.0/parabar/man/par_lapply.Rd | 2 parabar-1.3.0/parabar/man/par_sapply.Rd | 2 parabar-1.3.0/parabar/man/parabar-package.Rd | 38 parabar-1.3.0/parabar/man/peek.Rd | 4 parabar-1.3.0/parabar/man/start_backend.Rd | 8 parabar-1.3.0/parabar/man/stop_backend.Rd | 4 parabar-1.3.0/parabar/tests/testthat/helpers.R | 40 parabar-1.3.0/parabar/tests/testthat/test-async-backend.R | 75 parabar-1.3.0/parabar/tests/testthat/test-backend-finalizer.R |only parabar-1.3.0/parabar/tests/testthat/test-options.R | 1 parabar-1.3.0/parabar/tests/testthat/test-service.R | 20 parabar-1.3.0/parabar/tests/testthat/test-specification.R | 35 parabar-1.3.0/parabar/tests/testthat/test-states.R |only parabar-1.3.0/parabar/tests/testthat/test-user-api.R | 5 parabar-1.3.0/parabar/vignettes/comparison-benchmarks-1.png |binary parabar-1.3.0/parabar/vignettes/comparison.Rmd | 212 +- 61 files changed, 1273 insertions(+), 899 deletions(-)
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 0.9.91 dated 2024-11-11 and 0.9.92 dated 2024-12-10
DESCRIPTION | 6 MD5 | 50 ++--- NEWS.md | 16 + R/as_discrete.R | 3 R/case.R | 38 ++-- R/cpp11.R | 8 R/dots.R | 2 R/extras.R | 11 - R/factors.R | 2 R/get_breaks.R | 170 ------------------ R/lists.R | 3 R/new_df.R | 16 + R/scalars.R | 37 ++- R/utils.R | 60 ++++-- README.md | 188 +++++++++++++------- man/as_discrete.Rd | 3 man/figures/README-unnamed-chunk-30-1.png |only man/figures/README-unnamed-chunk-30-2.png |only man/get_breaks.Rd | 156 ++++++++-------- src/cheapr.h | 3 src/cpp11.cpp | 16 + src/nas.cpp | 41 +--- src/scalars.cpp | 265 ++++++++++++++++++++++++++++ src/sequences.cpp | 278 ++++++++++++++++++++++++++++++ src/utils.cpp | 5 src/which.cpp | 154 ++++++++++++++++ tests/testthat/test-get_breaks.R |only tests/testthat/test-scalars.R |only 28 files changed, 1107 insertions(+), 424 deletions(-)
Title: Analysis of Chronological Patterns from Archaeological Count
Data
Description: A toolkit for absolute and relative dating and analysis of
chronological patterns. This package includes functions for
chronological modeling and dating of archaeological assemblages from
count data. It provides methods for matrix seriation. It also allows
to compute time point estimates and density estimates of the
occupation and duration of an archaeological site.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Ben Marwick [ctb] ,
Anne Philippe [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between kairos versions 2.1.1 dated 2024-07-26 and 2.2.0 dated 2024-12-10
kairos-2.1.1/kairos/R/permute.R |only kairos-2.1.1/kairos/R/seriate_average.R |only kairos-2.1.1/kairos/R/seriate_rank.R |only kairos-2.1.1/kairos/R/seriate_refine.R |only kairos-2.1.1/kairos/R/summary.R |only kairos-2.1.1/kairos/inst/examples/ex-appotion.R |only kairos-2.1.1/kairos/inst/tinytest/_tinysnapshot/plot_event_activ-FALSE.svg |only kairos-2.1.1/kairos/inst/tinytest/_tinysnapshot/plot_event_activ-TRUE.svg |only kairos-2.1.1/kairos/man/RefinePermutationOrder-class.Rd |only kairos-2.1.1/kairos/man/model.Rd |only kairos-2.1.1/kairos/man/seriate_refine.Rd |only kairos-2.2.0/kairos/DESCRIPTION | 36 kairos-2.2.0/kairos/MD5 | 180 +- kairos-2.2.0/kairos/NAMESPACE | 9 kairos-2.2.0/kairos/NEWS.md | 16 kairos-2.2.0/kairos/R/AllClasses.R | 31 kairos-2.2.0/kairos/R/AllGenerics.R | 758 +++++----- kairos-2.2.0/kairos/R/aoristic.R | 10 kairos-2.2.0/kairos/R/apportion.R | 7 kairos-2.2.0/kairos/R/event_date.R | 317 +++- kairos-2.2.0/kairos/R/event_model.R | 29 kairos-2.2.0/kairos/R/event_plot.R | 83 - kairos-2.2.0/kairos/R/event_resample.R | 116 - kairos-2.2.0/kairos/R/fit.R | 11 kairos-2.2.0/kairos/R/kairos-deprecated.R | 128 + kairos-2.2.0/kairos/R/kairos-internal.R | 22 kairos-2.2.0/kairos/R/kairos-package.R | 12 kairos-2.2.0/kairos/R/mcd.R | 19 kairos-2.2.0/kairos/R/mutators.R | 17 kairos-2.2.0/kairos/R/seriation_assess.R |only kairos-2.2.0/kairos/R/seriation_average.R |only kairos-2.2.0/kairos/R/seriation_coerce.R |only kairos-2.2.0/kairos/R/seriation_permute.R |only kairos-2.2.0/kairos/R/seriation_rank.R |only kairos-2.2.0/kairos/R/seriation_refine.R |only kairos-2.2.0/kairos/R/show.R | 34 kairos-2.2.0/kairos/R/validate.R | 18 kairos-2.2.0/kairos/R/zzz.R | 3 kairos-2.2.0/kairos/README.md | 309 +++- kairos-2.2.0/kairos/build/partial.rdb |binary kairos-2.2.0/kairos/build/vignette.rds |binary kairos-2.2.0/kairos/inst/doc/event.R | 12 kairos-2.2.0/kairos/inst/doc/event.Rmd | 12 kairos-2.2.0/kairos/inst/doc/event.html | 117 - kairos-2.2.0/kairos/inst/doc/seriation.R | 26 kairos-2.2.0/kairos/inst/doc/seriation.Rmd | 27 kairos-2.2.0/kairos/inst/doc/seriation.html | 73 kairos-2.2.0/kairos/inst/examples/ex-apportion.R |only kairos-2.2.0/kairos/inst/examples/ex-assess.R |only kairos-2.2.0/kairos/inst/examples/ex-seriation.R | 9 kairos-2.2.0/kairos/inst/po |only kairos-2.2.0/kairos/inst/tinytest/_snaps/accumulation.rds |only kairos-2.2.0/kairos/inst/tinytest/_snaps/aoristic.rds |only kairos-2.2.0/kairos/inst/tinytest/_snaps/aoristic_group.rds |binary kairos-2.2.0/kairos/inst/tinytest/_snaps/aoristic_raw.rds |binary kairos-2.2.0/kairos/inst/tinytest/_snaps/aoristic_weight.rds |binary kairos-2.2.0/kairos/inst/tinytest/_snaps/event_jackknife.rds |binary kairos-2.2.0/kairos/inst/tinytest/_snaps/event_summary.rds |only kairos-2.2.0/kairos/inst/tinytest/_snaps/fit.rds |binary kairos-2.2.0/kairos/inst/tinytest/_tinysnapshot/plot_event_activity1.svg |only kairos-2.2.0/kairos/inst/tinytest/_tinysnapshot/plot_event_activity2.svg |only kairos-2.2.0/kairos/inst/tinytest/test_aoristic.R | 9 kairos-2.2.0/kairos/inst/tinytest/test_event.R | 36 kairos-2.2.0/kairos/inst/tinytest/test_fit.R | 5 kairos-2.2.0/kairos/inst/tinytest/test_mcd.R | 3 kairos-2.2.0/kairos/inst/tinytest/test_seriation.R | 37 kairos-2.2.0/kairos/inst/tinytest/test_spartaas.R |only kairos-2.2.0/kairos/man/AoristicSum-class.Rd | 6 kairos-2.2.0/kairos/man/CountApportion-class.Rd | 3 kairos-2.2.0/kairos/man/EventDate-class.Rd | 3 kairos-2.2.0/kairos/man/IncrementTest-class.Rd | 3 kairos-2.2.0/kairos/man/MeanDate-class.Rd | 3 kairos-2.2.0/kairos/man/PermutationOrder-class.Rd | 3 kairos-2.2.0/kairos/man/RateOfChange-class.Rd | 3 kairos-2.2.0/kairos/man/aoristic.Rd | 9 kairos-2.2.0/kairos/man/apportion.Rd | 27 kairos-2.2.0/kairos/man/as_seriation.Rd |only kairos-2.2.0/kairos/man/assess.Rd |only kairos-2.2.0/kairos/man/data.frame.Rd | 1 kairos-2.2.0/kairos/man/density_event.Rd |only kairos-2.2.0/kairos/man/event.Rd | 35 kairos-2.2.0/kairos/man/figures/README-aoristic-2.png |binary kairos-2.2.0/kairos/man/fit.Rd | 5 kairos-2.2.0/kairos/man/kairos-deprecated.Rd | 20 kairos-2.2.0/kairos/man/kairos-package.Rd | 12 kairos-2.2.0/kairos/man/mcd.Rd | 9 kairos-2.2.0/kairos/man/model_event.Rd |only kairos-2.2.0/kairos/man/mutators.Rd | 1 kairos-2.2.0/kairos/man/order.Rd |only kairos-2.2.0/kairos/man/permute.Rd | 50 kairos-2.2.0/kairos/man/plot_aoristic.Rd | 12 kairos-2.2.0/kairos/man/plot_event.Rd | 17 kairos-2.2.0/kairos/man/plot_fit.Rd | 12 kairos-2.2.0/kairos/man/plot_mcd.Rd | 12 kairos-2.2.0/kairos/man/plot_time.Rd | 7 kairos-2.2.0/kairos/man/predict_event.Rd | 52 kairos-2.2.0/kairos/man/refine.Rd |only kairos-2.2.0/kairos/man/resample_event.Rd | 32 kairos-2.2.0/kairos/man/resample_mcd.Rd | 7 kairos-2.2.0/kairos/man/roc.Rd | 9 kairos-2.2.0/kairos/man/seriate_average.Rd | 46 kairos-2.2.0/kairos/man/seriate_rank.Rd | 18 kairos-2.2.0/kairos/man/series.Rd | 7 kairos-2.2.0/kairos/man/subset.Rd | 1 kairos-2.2.0/kairos/po |only kairos-2.2.0/kairos/vignettes/event.Rmd | 12 kairos-2.2.0/kairos/vignettes/seriation.Rmd | 27 107 files changed, 1906 insertions(+), 1089 deletions(-)
Title: Univariate Time Series Forecasting
Description: An engine for univariate time series forecasting using
different regression models in an autoregressive way. The engine
provides an uniform interface for applying the different models.
Furthermore, it is extensible so that users can easily apply their
own regression models to univariate time series forecasting and
benefit from all the features of the engine, such as preprocessings
or estimation of forecast accuracy.
Author: Maria Pilar Frias-Bustamante [aut]
,
Francisco Martinez [aut, cre, cph]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between utsf versions 1.0.0 dated 2024-10-14 and 1.1.0 dated 2024-12-10
utsf-1.0.0/utsf/man/differences.Rd |only utsf-1.1.0/utsf/DESCRIPTION | 6 utsf-1.1.0/utsf/MD5 | 39 ++--- utsf-1.1.0/utsf/NAMESPACE | 5 utsf-1.1.0/utsf/NEWS.md | 7 utsf-1.1.0/utsf/R/build_examples.R | 18 ++ utsf-1.1.0/utsf/R/build_models.R | 7 utsf-1.1.0/utsf/R/do_tuneGrid.R | 2 utsf-1.1.0/utsf/R/estimate_accuracy.R | 107 +++++++++---- utsf-1.1.0/utsf/R/first_differences.R | 31 ++- utsf-1.1.0/utsf/R/forecast.R | 82 +++++----- utsf-1.1.0/utsf/R/plot.R | 12 + utsf-1.1.0/utsf/R/print_utsf.R | 13 + utsf-1.1.0/utsf/R/recursive_prediction.R | 4 utsf-1.1.0/utsf/build/vignette.rds |binary utsf-1.1.0/utsf/inst/doc/utsf.R | 41 ++--- utsf-1.1.0/utsf/inst/doc/utsf.Rmd | 81 ++++------ utsf-1.1.0/utsf/inst/doc/utsf.html | 241 +++++++++++++++---------------- utsf-1.1.0/utsf/man/evaluation.Rd |only utsf-1.1.0/utsf/man/forecast.Rd | 30 +-- utsf-1.1.0/utsf/man/trend.Rd |only utsf-1.1.0/utsf/vignettes/utsf.Rmd | 81 ++++------ 22 files changed, 443 insertions(+), 364 deletions(-)
Title: Unit Testing for R
Description: Software testing is important, but, in part because it is
frustrating and boring, many of us avoid it. 'testthat' is a testing
framework for R that is easy to learn and use, and integrates with
your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb] )
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between testthat versions 3.2.1.1 dated 2024-04-13 and 3.2.2 dated 2024-12-10
DESCRIPTION | 15 MD5 | 176 +-- NAMESPACE | 4 NEWS.md | 509 +++++----- R/describe.R | 15 R/edition.R | 1 R/expect-condition.R | 44 R/expect-constant.R | 23 R/expect-inheritance.R | 29 R/expect-invisible.R | 4 R/expect-no-condition.R | 14 R/expect-self-test.R | 85 + R/expect-setequal.R | 14 R/expect-vector.R | 5 R/expectation.R | 1 R/expectations-matches.R | 1 R/local.R | 7 R/mock.R | 19 R/reporter-progress.R | 4 R/reporter-zzz.R | 2 R/reporter.R | 2 R/skip.R | 10 R/snapshot-file.R | 2 R/snapshot-reporter.R | 3 R/snapshot.R | 12 R/source.R | 2 R/test-example.R | 2 R/test-files.R | 12 R/test-that.R | 8 README.md | 2 build/vignette.rds |binary inst/doc/custom-expectation.html | 2 inst/doc/parallel.html | 2 inst/doc/skipping.R | 36 inst/doc/skipping.html | 2 inst/doc/snapshotting.R | 4 inst/doc/snapshotting.html | 34 inst/doc/special-files.R | 14 inst/doc/special-files.Rmd | 4 inst/doc/special-files.html | 6 inst/doc/test-fixtures.R | 80 - inst/doc/test-fixtures.Rmd | 2 inst/doc/test-fixtures.html | 8 inst/doc/third-edition.R | 4 inst/doc/third-edition.html | 39 inst/include/testthat/testthat.h | 2 man/Reporter.Rd | 2 man/describe.Rd | 10 man/expect_match.Rd | 1 man/expect_null.Rd | 1 man/expect_success.Rd | 22 man/expect_vector.Rd | 4 man/expectation.Rd | 1 man/inheritance-expectations.Rd | 5 man/local_edition.Rd | 1 man/local_test_context.Rd | 2 man/logical-expectations.Rd | 3 man/skip.Rd | 2 man/test_dir.Rd | 1 man/with_mock.Rd | 17 tests/testthat/_snaps/R4.4 |only tests/testthat/_snaps/expect-condition.md | 20 tests/testthat/_snaps/expect-constant.md | 7 tests/testthat/_snaps/expect-inheritance.md | 16 tests/testthat/_snaps/expect-invisible.md |only tests/testthat/_snaps/expect-setequal.md | 24 tests/testthat/_snaps/mock.md |only tests/testthat/_snaps/reporter-debug.md | 8 tests/testthat/_snaps/skip.md | 2 tests/testthat/_snaps/snapshot.md | 8 tests/testthat/test-examples.R | 2 tests/testthat/test-expect-condition.R | 18 tests/testthat/test-expect-constant.R | 6 tests/testthat/test-expect-inheritance.R | 18 tests/testthat/test-expect-invisible.R | 7 tests/testthat/test-expect-no-condition.R | 16 tests/testthat/test-expect-self-test.R | 16 tests/testthat/test-expect-setequal.R | 12 tests/testthat/test-local.R | 2 tests/testthat/test-mock.R | 152 -- tests/testthat/test-parallel-crash.R | 17 tests/testthat/test-parallel/crash/tests/testthat/test-crash-3.R | 2 tests/testthat/test-reporter-debug.R | 5 tests/testthat/test-snapshot-reporter.R | 4 tests/testthat/test-snapshot.R | 13 tests/testthat/test-verify-conditions-lines.txt | 4 tests/testthat/test-verify-conditions.txt | 4 tests/testthat/test-verify-output.R | 6 vignettes/special-files.Rmd | 4 vignettes/test-fixtures.Rmd | 2 90 files changed, 951 insertions(+), 782 deletions(-)
Title: Scoring Methodology for Ordered Factors
Description: Starting from a given object representing a fitted model
(within a certain set of model classes) whose (non-)linear predictor
includes some ordered factor(s) among the explanatory variables, a new
model is constructed and fitted where each named factor is replaced by a
single numeric score, suitably chosen so that the new variable produces a
fit comparable with the standard methodology based on a set of polynomial
contrasts. Two variants of the present approach have been developed, one in
each of the next references: Azzalini (2023) <doi:10.1002/sta4.624>, (2024)
<doi:10.48550/arXiv.2406.15933>.
Author: Adelchi Azzalini [aut, cre]
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between smof versions 1.2.1 dated 2024-10-30 and 1.2.2 dated 2024-12-10
DESCRIPTION | 10 +- MD5 | 16 ++-- NAMESPACE | 12 +-- R/smof-methods.R | 25 +++---- R/smof.R | 142 ++++++++++++++++++++++++++++------------ build/partial.rdb |binary inst/NEWS.Rd | 36 +++++++--- man/smof.Rd | 190 ++++++++++++++++++++++++++++++++++++------------------ man/smof_refit.Rd | 25 +++---- 9 files changed, 300 insertions(+), 156 deletions(-)
Title: Expanded Replacement and Extension of the 'optim' Function
Description: Provides a replacement and extension of the optim()
function to call to several function minimization codes in R in a single
statement. These methods handle smooth, possibly box constrained functions
of several or many parameters. Note that function 'optimr()' was prepared to
simplify the incorporation of minimization codes going forward. Also implements some
utility codes and some extra solvers, including safeguarded Newton methods.
Many methods previously separate are now included here.
This is the version for CRAN.
Author: John C Nash [aut, cre],
Ravi Varadhan [aut],
Hans W Borchers [ctb],
Gabor Grothendieck [ctb]
Maintainer: John C Nash <profjcnash@gmail.com>
Diff between optimx versions 2023-10.21 dated 2023-10-24 and 2024-12.2 dated 2024-12-10
optimx-2023-10.21/optimx/inst/doc/examples/onepar_test.R |only optimx-2023-10.21/optimx/inst/doc/examples/ox.R |only optimx-2023-10.21/optimx/inst/doc/replaced2021 |only optimx-2023-10.21/optimx/inst/doc/replaced2023 |only optimx-2023-10.21/optimx/inst/doc/vignette-source/ExplainGradMinR.pdf |only optimx-2023-10.21/optimx/inst/doc/vignette-source/Extend-optimx.pdf |only optimx-2023-10.21/optimx/inst/doc/vignette-source/Intro-to-optimx.pdf |only optimx-2023-10.21/optimx/inst/doc/vignette-source/Rvmmin.pdf |only optimx-2023-10.21/optimx/inst/doc/vignette-source/SNewton.pdf |only optimx-2023-10.21/optimx/man/Rcgminb.Rd |only optimx-2023-10.21/optimx/man/Rcgminu.Rd |only optimx-2023-10.21/optimx/man/Rvmminb.Rd |only optimx-2023-10.21/optimx/man/Rvmminu.Rd |only optimx-2023-10.21/optimx/man/tn.Rd |only optimx-2023-10.21/optimx/man/tnbc.Rd |only optimx-2024-12.2/optimx/DESCRIPTION | 27 +- optimx-2024-12.2/optimx/MD5 | 82 ++++----- optimx-2024-12.2/optimx/NAMESPACE | 2 optimx-2024-12.2/optimx/NEWS | 60 ++++++ optimx-2024-12.2/optimx/R/Rcgminb.R | 8 optimx-2024-12.2/optimx/R/Rcgminu.R | 9 optimx-2024-12.2/optimx/R/checksolver.R | 7 optimx-2024-12.2/optimx/R/grfwd.R | 2 optimx-2024-12.2/optimx/R/ncg.R | 35 +++ optimx-2024-12.2/optimx/R/opm.R | 8 optimx-2024-12.2/optimx/R/opm2optimr.R |only optimx-2024-12.2/optimx/R/optimr.R | 35 ++- optimx-2024-12.2/optimx/R/optimr2opm.R |only optimx-2024-12.2/optimx/R/proptimr.R | 12 - optimx-2024-12.2/optimx/R/tn.R | 16 + optimx-2024-12.2/optimx/R/tnbc.R | 22 +- optimx-2024-12.2/optimx/README.md |only optimx-2024-12.2/optimx/build/vignette.rds |binary optimx-2024-12.2/optimx/inst/doc/AddPracmaNM2optimx.pdf |only optimx-2024-12.2/optimx/inst/doc/AddPracmaNM2optimx.pdf.asis |only optimx-2024-12.2/optimx/inst/doc/ExplainGradMinR.pdf |binary optimx-2024-12.2/optimx/inst/doc/Intro-to-optimx.pdf |binary optimx-2024-12.2/optimx/inst/doc/SNewton.pdf |binary optimx-2024-12.2/optimx/inst/doc/examples/simfunX.R |only optimx-2024-12.2/optimx/inst/doc/ncgqs2204.R | 1 optimx-2024-12.2/optimx/inst/doc/optcontrol.xls |binary optimx-2024-12.2/optimx/inst/doc/vignette-source/AddPracmaNM2optimx.Rmd |only optimx-2024-12.2/optimx/inst/doc/vignette-source/ExplainGradMinR.Rmd | 10 - optimx-2024-12.2/optimx/man/Rcgmin.Rd | 91 ++++------ optimx-2024-12.2/optimx/man/Rtnmin.Rd |only optimx-2024-12.2/optimx/man/Rvmmin.Rd | 11 - optimx-2024-12.2/optimx/man/fnchk.Rd | 2 optimx-2024-12.2/optimx/man/grpracma.Rd | 6 optimx-2024-12.2/optimx/man/ncg.Rd |only optimx-2024-12.2/optimx/man/nvm.Rd |only optimx-2024-12.2/optimx/man/opm2optimr.Rd |only optimx-2024-12.2/optimx/man/optimr.Rd | 31 ++- optimx-2024-12.2/optimx/man/optimx-package.Rd | 4 optimx-2024-12.2/optimx/man/proptimr.Rd | 5 optimx-2024-12.2/optimx/vignettes/AddPracmaNM2optimx.pdf.asis |only 55 files changed, 316 insertions(+), 170 deletions(-)
Title: Multivariate Data Analysis
Description: Simple Principal Components Analysis (PCA) and (Multiple)
Correspondence Analysis (CA) based on the Singular Value Decomposition
(SVD). This package provides S4 classes and methods to compute,
extract, summarize and visualize results of multivariate data
analysis. It also includes methods for partial bootstrap validation
described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et
al. (2006, ISBN: 978-2-10-049616-7).
Author: Nicolas Frerebeau [aut, cre] ,
Jean-Baptiste Fourvel [ctb] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between dimensio versions 0.10.0 dated 2024-11-08 and 0.10.1 dated 2024-12-10
DESCRIPTION | 8 - MD5 | 110 ++++++++++++------------ NEWS.md | 8 + R/AllClasses.R | 2 R/AllGenerics.R | 5 - R/annotations.R | 2 R/ca.R | 4 R/dimensio-internal.R | 5 + R/dimensio-package.R | 2 R/screeplot.R | 17 ++- R/show.R | 61 ++++++++----- R/viz_contributions.R | 2 R/viz_coordinates.R | 14 +-- R/viz_cos2.R | 4 R/viz_ellipse.R | 2 R/viz_hull.R | 2 README.md | 16 +++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/pca.R | 18 +-- inst/doc/pca.html | 12 +- inst/examples/ex-contributions.R | 2 inst/po/fr/LC_MESSAGES/R-dimensio.mo |binary inst/tinytest/_tinysnapshot/CA_eig_0-0.svg | 2 inst/tinytest/_tinysnapshot/CA_eig_0-1.svg | 4 inst/tinytest/_tinysnapshot/CA_eig_1-1.svg | 2 inst/tinytest/_tinysnapshot/CA_ind_contrib.svg | 2 inst/tinytest/_tinysnapshot/CA_var_contrib.svg | 2 inst/tinytest/_tinysnapshot/CA_var_cos2.svg | 68 +++++++------- inst/tinytest/_tinysnapshot/PCA_eig_0-1.svg | 2 inst/tinytest/_tinysnapshot/PCA_eig_1-1.svg | 2 inst/tinytest/_tinysnapshot/PCA_ind_contrib.svg | 2 inst/tinytest/_tinysnapshot/PCA_var_contrib.svg | 2 inst/tinytest/_tinysnapshot/PCA_var_cos2.svg | 44 ++++----- inst/tinytest/test_bootstrap_ca.R | 8 - inst/tinytest/test_bootstrap_pca.R | 2 inst/tinytest/test_ca.R | 2 inst/tinytest/test_mca.R | 2 inst/tinytest/test_pca.R | 2 inst/tinytest/test_plot_ca.R | 2 inst/tinytest/test_plot_pca.R | 2 man/biplot.Rd | 3 man/dimensio-package.Rd | 2 man/figures/README-biplot-1.png |binary man/figures/README-plot-var-1.png |binary man/figures/README-plot-var-2.png |binary man/label.Rd | 8 - man/plot.Rd | 2 man/prepare_plot.Rd | 2 man/viz_contributions.Rd | 4 man/viz_individuals.Rd | 12 ++ man/viz_points.Rd | 2 man/viz_variables.Rd | 8 + man/viz_wrap.Rd | 2 po/R-dimensio.pot | 86 ++++++++++++++++++ po/R-fr.po | 87 ++++++++++++++++++ 56 files changed, 452 insertions(+), 214 deletions(-)
Title: Variable Selection Algorithms Using the Distance Correlation
Description: The 'FBED' and 'mmpc' variable selection algorithms have been implemented using the distance correlation. The references include: Tsamardinos I., Aliferis C. F. and Statnikov A. (2003). "Time and sample efficient discovery of Markovblankets and direct causal relations". In Proceedings of the ninth ACM SIGKDD international Conference. <doi:10.1145/956750.956838>. Borboudakis G. and Tsamardinos I. (2019). "Forward-backward selection with early dropping". Journal of Machine Learning Research, 20(8): 1--39. <doi:10.48550/arXiv.1705.10770>. Huo X. and Szekely G.J. (2016). "Fast computing for distance covariance". Technometrics, 58(4): 435--447. <doi:10.1080/00401706.2015.1054435>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between dcorVS versions 1.0 dated 2023-10-18 and 1.1 dated 2024-12-10
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- man/dcor.bsmmpc.Rd | 9 ++++++--- man/dcor.mmpc.Rd | 6 +++++- man/dcorVS-package.Rd | 4 ++-- 5 files changed, 22 insertions(+), 14 deletions(-)
Title: Archaeological Time Series
Description: A toolkit for archaeological time series and time intervals.
This package provides a system of classes and methods to represent and
work with archaeological time series and time intervals. Dates are
represented as "rata die" and can be converted to (virtually) any
calendar defined by Reingold and Dershowitz (2018)
<doi:10.1017/9781107415058>. This packages offers a simple API that
can be used by other specialized packages.
Author: Nicolas Frerebeau [aut, cre] ,
Joe Roe [aut] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between aion versions 1.2.0 dated 2024-11-13 and 1.3.0 dated 2024-12-10
DESCRIPTION | 10 +-- MD5 | 48 +++++++++---------- NAMESPACE | 1 NEWS.md | 7 ++ R/AllGenerics.R | 19 +++++-- R/aion-package.R | 4 - R/calendar.R | 14 +++-- R/show.R | 23 +++++---- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/aion.html | 22 ++++---- inst/doc/extending.Rmd | 2 inst/doc/extending.html | 8 +-- inst/po/fr/LC_MESSAGES/R-aion.mo |binary inst/tinytest/_tinysnapshot/show_calendar_CE.txt | 2 inst/tinytest/_tinysnapshot/show_calendar_julian.txt | 2 inst/tinytest/_tinysnapshot/show_rata_die.txt | 2 inst/tinytest/_tinysnapshot/show_time_series.txt | 2 inst/tinytest/test_calendar.R | 6 +- man/aion-package.Rd | 4 - man/calendar_get.Rd | 19 +++++-- po/R-aion.pot | 37 ++++++++------ po/R-fr.po | 40 ++++++++------- vignettes/extending.Rmd | 2 25 files changed, 160 insertions(+), 116 deletions(-)
Title: Interface for 'Google Gemini' API
Description: Provides a comprehensive interface for Google Gemini API,
enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R.
This package facilitates seamless integration with Google Gemini, allowing for advanced language processing,
text generation, and other AI-driven capabilities within the R environment.
For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.
Author: Jinhwan Kim [aut, cre, cph] ,
Maciej Nasinski [ctb]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>
Diff between gemini.R versions 0.5.2 dated 2024-08-26 and 0.6.1 dated 2024-12-10
DESCRIPTION | 17 ++++++++-------- MD5 | 16 +++++++++------ NAMESPACE | 4 +++ NEWS.md | 2 + R/gen_docs.R |only R/setAPI.R | 3 ++ README.md | 49 ++++++++++++++++++++++++++++++++++++------------ inst |only man/figures/roxygen.gif |only man/gen_docs.Rd |only man/setAPI.Rd | 5 ++++ 11 files changed, 70 insertions(+), 26 deletions(-)
Title: Causal Inference with Continuous (Multiple Time Point)
Interventions
Description: Estimation of counterfactual outcomes for multiple values of continuous interventions at different time points, and plotting of causal dose-response curves. Details are given in Schomaker, McIlleron, Denti, Diaz (2024) <doi:10.48550/arXiv.2305.06645>.
Author: Michael Schomaker [aut, cre]
Maintainer: Michael Schomaker <michael.schomaker@stat.uni-muenchen.de>
Diff between CICI versions 0.9.3 dated 2024-11-01 and 0.9.4 dated 2024-12-10
DESCRIPTION | 8 +-- MD5 | 10 ++-- R/gformula.r | 105 +++++++++++++++++++++++++--------------------------- R/helper.r | 25 ++++++++---- R/plot.gformula.r | 3 - man/CICI-package.Rd | 4 - 6 files changed, 82 insertions(+), 73 deletions(-)
Title: Approximate String Matching, Fuzzy Text Search, and String
Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Also offers fuzzy text search based on various string
distance measures. Can calculate various string distances based on edits
(Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q-
gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An
implementation of soundex is provided as well. Distances can be computed between
character vectors while taking proper care of encoding or between integer
vectors representing generic sequences. This package is built for speed and
runs in parallel by using 'openMP'. An API for C or C++ is exposed as well.
Reference: MPJ van der Loo (2014) <doi:10.32614/RJ-2014-011>.
Author: Mark van der Loo [aut, cre] ,
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb],
Chris Muir [ctb],
Johannes Gruber [ctb],
Brian Ripley [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.12 dated 2023-11-28 and 0.9.14 dated 2024-12-10
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS | 7 +++++++ R/doc_metrics.R | 2 +- R/phonetic.R | 2 +- R/qgrams.R | 9 +++++++++ R/stringdist.R | 2 +- build/vignette.rds |binary inst/doc/RJournal_6_111-122-2014.pdf |binary inst/doc/stringdist_C-Cpp_api.pdf |binary inst/tinytest/test_qgrams.R | 2 +- man/phonetic.Rd | 2 +- man/stringdist-metrics.Rd | 2 +- man/stringdist-package.Rd | 22 ++++++++++++++++++++++ src/qgram.c | 3 ++- 15 files changed, 64 insertions(+), 25 deletions(-)
Title: Nonparametric Kernel Smoothing Methods for Mixed Data Types
Description: Nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would also like to acknowledge the contributions of the GNU GSL authors. In particular, we adapt the GNU GSL B-spline routine gsl_bspline.c adding automated support for quantile knots (in addition to uniform knots), providing missing functionality for derivatives, and for extending the splines beyond their endpoints.
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between np versions 0.60-17 dated 2023-03-13 and 0.60-18 dated 2024-12-10
CHANGELOG | 13 +++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- NAMESPACE | 1 + R/np.kernel.R | 16 ++++++++++++---- R/np.regression.R | 20 +++++++++++++++----- R/zzz.R | 2 +- build/vignette.rds |binary data/cps71.rda |binary inst/doc/entropy_np.pdf |binary inst/doc/np.pdf |binary inst/doc/np_faq.Rnw | 33 ++++++++++++++++++++++++++++----- inst/doc/np_faq.pdf |binary man/b.star.Rd | 2 +- man/np-package.Rd | 1 + man/np.deptest.Rd | 4 ++-- man/np.sdeptest.Rd | 4 ++-- man/np.symtest.Rd | 2 +- man/npuniden.boundary.Rd | 22 ++++++++++++---------- man/npuniden.sc.Rd | 4 ++-- src/nr.c | 2 +- vignettes/np_faq.Rnw | 33 ++++++++++++++++++++++++++++----- 22 files changed, 145 insertions(+), 64 deletions(-)
Title: Easily Scrape and Process AFL Data
Description: An easy package for scraping and processing Australia Rules Football (AFL)
data. 'fitzRoy' provides a range of functions for accessing publicly available data
from 'AFL Tables' <https://afltables.com/afl/afl_index.html>, 'Footy Wire' <https://www.footywire.com> and
'The Squiggle' <https://squiggle.com.au>. Further functions allow for easy processing,
cleaning and transformation of this data into formats that can be used for analysis.
Author: James Day [cre, aut],
Robert Nguyen [aut],
Matthew Erbs [ctb],
Oscar Lane [aut],
Jason Zivkovic [ctb],
Jacob Holden [ctb]
Maintainer: James Day <jamesthomasday@gmail.com>
Diff between fitzRoy versions 1.5.0 dated 2024-07-30 and 1.6.0 dated 2024-12-10
fitzRoy-1.5.0/fitzRoy/R/fetch_lineup.R |only fitzRoy-1.5.0/fitzRoy/data/player_mapping_afltables.rda |only fitzRoy-1.5.0/fitzRoy/man/player_mapping_afltables.Rd |only fitzRoy-1.5.0/fitzRoy/tests/testthat/test-fetch_lineup.R |only fitzRoy-1.6.0/fitzRoy/DESCRIPTION | 10 fitzRoy-1.6.0/fitzRoy/MD5 | 103 ++--- fitzRoy-1.6.0/fitzRoy/NAMESPACE | 5 fitzRoy-1.6.0/fitzRoy/R/data.R | 8 fitzRoy-1.6.0/fitzRoy/R/fetch-coaches-votes.R | 15 fitzRoy-1.6.0/fitzRoy/R/fetch-ladder.R | 34 + fitzRoy-1.6.0/fitzRoy/R/fetch-lineup.R |only fitzRoy-1.6.0/fitzRoy/R/fetch-player-details.R | 27 - fitzRoy-1.6.0/fitzRoy/R/fetch-player-stats.R | 9 fitzRoy-1.6.0/fitzRoy/R/fetch-results.R | 4 fitzRoy-1.6.0/fitzRoy/R/helper-aflcoaches.R | 19 - fitzRoy-1.6.0/fitzRoy/R/helpers-afl.R | 3 fitzRoy-1.6.0/fitzRoy/R/helpers-afltables-playerstats.R | 18 fitzRoy-1.6.0/fitzRoy/R/helpers-footywire-playerdetails.R | 97 +++-- fitzRoy-1.6.0/fitzRoy/R/helpers-general.R | 124 ++++++ fitzRoy-1.6.0/fitzRoy/R/plot-score-worm.R |only fitzRoy-1.6.0/fitzRoy/R/team_colour_palettes.R | 18 fitzRoy-1.6.0/fitzRoy/R/utils-pipe.R |only fitzRoy-1.6.0/fitzRoy/build/vignette.rds |binary fitzRoy-1.6.0/fitzRoy/data/dictionary_afltables.rda |binary fitzRoy-1.6.0/fitzRoy/data/mapping_afltables.rda |binary fitzRoy-1.6.0/fitzRoy/inst/WORDLIST | 16 fitzRoy-1.6.0/fitzRoy/inst/doc/aflca-coaches-votes.R | 76 ++-- fitzRoy-1.6.0/fitzRoy/inst/doc/aflca-coaches-votes.html | 4 fitzRoy-1.6.0/fitzRoy/inst/doc/docker-support.html | 4 fitzRoy-1.6.0/fitzRoy/inst/doc/elo-ratings-example.R | 92 ++-- fitzRoy-1.6.0/fitzRoy/inst/doc/elo-ratings-example.html | 8 fitzRoy-1.6.0/fitzRoy/inst/doc/fitzRoy.R | 188 +++++----- fitzRoy-1.6.0/fitzRoy/inst/doc/fitzRoy.html | 4 fitzRoy-1.6.0/fitzRoy/inst/doc/main-fetch-functions.R | 64 +-- fitzRoy-1.6.0/fitzRoy/inst/doc/main-fetch-functions.html | 4 fitzRoy-1.6.0/fitzRoy/inst/doc/player-details.R | 24 - fitzRoy-1.6.0/fitzRoy/inst/doc/player-details.html | 4 fitzRoy-1.6.0/fitzRoy/inst/doc/score-worms.R |only fitzRoy-1.6.0/fitzRoy/inst/doc/score-worms.Rmd |only fitzRoy-1.6.0/fitzRoy/inst/doc/score-worms.html |only fitzRoy-1.6.0/fitzRoy/inst/doc/using-fryzigg-stats.R | 6 fitzRoy-1.6.0/fitzRoy/inst/doc/using-fryzigg-stats.html | 4 fitzRoy-1.6.0/fitzRoy/inst/doc/using-squiggle-api.R | 54 +- fitzRoy-1.6.0/fitzRoy/inst/doc/using-squiggle-api.html | 4 fitzRoy-1.6.0/fitzRoy/inst/doc/womens-stats.R | 166 ++++---- fitzRoy-1.6.0/fitzRoy/inst/doc/womens-stats.html | 4 fitzRoy-1.6.0/fitzRoy/man/dictionary_afltables.Rd | 2 fitzRoy-1.6.0/fitzRoy/man/fetch_lineup.Rd | 2 fitzRoy-1.6.0/fitzRoy/man/fetch_player_details.Rd | 10 fitzRoy-1.6.0/fitzRoy/man/fetch_score_worm_data.Rd |only fitzRoy-1.6.0/fitzRoy/man/parse_team_abbr.Rd |only fitzRoy-1.6.0/fitzRoy/man/pipe.Rd |only fitzRoy-1.6.0/fitzRoy/man/plot_score_worm.Rd |only fitzRoy-1.6.0/fitzRoy/man/plot_score_worm_totals.Rd |only fitzRoy-1.6.0/fitzRoy/tests/testthat/test-fetch-betting-odds.R | 3 fitzRoy-1.6.0/fitzRoy/tests/testthat/test-fetch-lineup.R |only fitzRoy-1.6.0/fitzRoy/tests/testthat/test-fetch-player-stats.R | 44 +- fitzRoy-1.6.0/fitzRoy/tests/testthat/test-fetch-results.R | 3 fitzRoy-1.6.0/fitzRoy/tests/testthat/test-helpers-afl.R | 7 fitzRoy-1.6.0/fitzRoy/tests/testthat/test-team_colour_palettes.R | 11 fitzRoy-1.6.0/fitzRoy/vignettes/score-worms.Rmd |only 61 files changed, 774 insertions(+), 528 deletions(-)
Title: Wrapper Functions Around 'Charles Schwab Individual Trader API'
Description: For those wishing to interact with the 'Charles Schwab Individual Trader API' (<https://developer.schwab.com/products/trader-api--individual>) with R in a simplified manner, this package offers wrapper functions around authentication and the available API calls to streamline the process.
Author: Nick Bultman [aut, cre, cph]
Maintainer: Nick Bultman <njbultman74@gmail.com>
Diff between charlesschwabapi versions 1.0.3 dated 2024-09-14 and 1.0.4 dated 2024-12-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/get_authentication_tokens.R | 38 +++++++++++++++++++++++++++----------- 3 files changed, 32 insertions(+), 16 deletions(-)
More information about charlesschwabapi at CRAN
Permanent link
Title: Visualizing the Elements Within Bio-Sequences
Description: Visualizing the types and distribution of elements within
bio-sequences. At the same time, We have developed a geom layer,
geom_rrect(), that can generate rounded rectangles. No external references
are used in the development of this package.
Author: Shiqi Zhao [aut, cre, cph]
Maintainer: Shiqi Zhao <zhaosq89@163.com>
Diff between BioVizSeq versions 0.1.1 dated 2024-11-27 and 0.1.2 dated 2024-12-10
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++----- NAMESPACE | 5 ++++- NEWS.md | 10 +++++++--- R/combi_plot.R |only R/globalvariables.R |only R/zzz.R | 2 +- man/combi_p.Rd |only man/globalVariables.Rd | 24 ++++++++++++------------ 9 files changed, 36 insertions(+), 26 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Procedures are available for choosing models that
conform to the hierarchy or marginality principle, for fitting and choosing between
two-dimensional spatial models using correlation, natural cubic smoothing spline and
P-spline models. A history of the fitting of a sequence of models is kept in a data frame.
Also used to compute functions and contrasts of, to investigate differences between and
to plot predictions obtained using any model fitting function. The content falls into
the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model
selection and description functions, (iv) Model diagnostics and simulation functions,
(v) Prediction production and presentation functions, (vi) Response transformation
functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions
(for further details see 'asremlPlus-package' in help). The [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.4.40 dated 2024-10-27 and 4.4.43 dated 2024-12-10
asremlPlus-4.4.40/asremlPlus/R/spatial.funcs.v8.r |only asremlPlus-4.4.40/asremlPlus/R/spatial.funcs.v9.r |only asremlPlus-4.4.40/asremlPlus/R/spatial.utilities.v2.r |only asremlPlus-4.4.40/asremlPlus/inst/doc/Ladybird.asreml.pdf |only asremlPlus-4.4.40/asremlPlus/inst/doc/Ladybird.asreml.pdf.asis |only asremlPlus-4.4.40/asremlPlus/inst/doc/Ladybird.lm.pdf |only asremlPlus-4.4.40/asremlPlus/inst/doc/Ladybird.lm.pdf.asis |only asremlPlus-4.4.40/asremlPlus/vignettes/Ladybird.asreml.pdf.asis |only asremlPlus-4.4.40/asremlPlus/vignettes/Ladybird.lm.pdf.asis |only asremlPlus-4.4.43/asremlPlus/DESCRIPTION | 8 - asremlPlus-4.4.43/asremlPlus/MD5 | 63 ++++---- asremlPlus-4.4.43/asremlPlus/R/LSDutilities.R | 22 +-- asremlPlus-4.4.43/asremlPlus/R/alldiffs.v4.r | 26 +-- asremlPlus-4.4.43/asremlPlus/R/asremlPlusObjUtils.r | 42 ++++- asremlPlus-4.4.43/asremlPlus/R/asremlPlusUtilities.r | 7 asremlPlus-4.4.43/asremlPlus/R/pairTrans.r | 6 asremlPlus-4.4.43/asremlPlus/R/plotLSDs.r | 12 - asremlPlus-4.4.43/asremlPlus/R/plotPvalues.r | 4 asremlPlus-4.4.43/asremlPlus/R/reml4.v11.r | 73 +++++++--- asremlPlus-4.4.43/asremlPlus/R/spatial.funcs.v10.r |only asremlPlus-4.4.43/asremlPlus/R/spatial.utilities.v3.r |only asremlPlus-4.4.43/asremlPlus/build/partial.rdb |binary asremlPlus-4.4.43/asremlPlus/build/vignette.rds |binary asremlPlus-4.4.43/asremlPlus/inst/NEWS.Rd | 18 ++ asremlPlus-4.4.43/asremlPlus/inst/doc/LadybirdEMMs.asreml.pdf |only asremlPlus-4.4.43/asremlPlus/inst/doc/LadybirdEMMs.asreml.pdf.asis |only asremlPlus-4.4.43/asremlPlus/inst/doc/LadybirdEMMs.lm.pdf |only asremlPlus-4.4.43/asremlPlus/inst/doc/LadybirdEMMs.lm.pdf.asis |only asremlPlus-4.4.43/asremlPlus/inst/doc/Wheat.analysis.pdf |binary asremlPlus-4.4.43/asremlPlus/inst/doc/Wheat.infoCriteria.pdf |binary asremlPlus-4.4.43/asremlPlus/inst/doc/WheatSpatialModels.pdf |binary asremlPlus-4.4.43/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-4.4.43/asremlPlus/man/as.asrtests.Rd | 2 asremlPlus-4.4.43/asremlPlus/man/getTestEntry.asrtests.Rd | 5 asremlPlus-4.4.43/asremlPlus/man/print.test.summary.Rd | 6 asremlPlus-4.4.43/asremlPlus/tests/testthat/test42EstimateV.r | 6 asremlPlus-4.4.43/asremlPlus/tests/testthat/test42GeneticCane.R | 9 - asremlPlus-4.4.43/asremlPlus/tests/testthat/test42PredictionsPresentation.r | 6 asremlPlus-4.4.43/asremlPlus/tests/testthat/test42SpatialModels.r | 10 - asremlPlus-4.4.43/asremlPlus/vignettes/LadybirdEMMs.asreml.pdf.asis |only asremlPlus-4.4.43/asremlPlus/vignettes/LadybirdEMMs.lm.pdf.asis |only 41 files changed, 202 insertions(+), 123 deletions(-)
Title: Indices of Effect Size
Description: Provide utilities to work with indices of effect size for a wide
variety of models and hypothesis tests (see list of supported models using
the function 'insight::supported_models()'), allowing computation of and
conversion between indices such as Cohen's d, r, odds, etc.
References: Ben-Shachar et al. (2020) <doi:10.21105/joss.02815>.
Author: Mattan S. Ben-Shachar [aut, cre]
,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [aut] ,
Ken Kelley [ctb],
David Stanley [ctb],
Aaron Caldwell [ctb] ,
Jessica Burnett [rev] ,
Johan [...truncated...]
Maintainer: Mattan S. Ben-Shachar <mattansb@msbstats.info>
Diff between effectsize versions 0.8.9 dated 2024-07-03 and 1.0.0 dated 2024-12-10
DESCRIPTION | 41 ++--- MD5 | 76 +++++----- NAMESPACE | 14 - NEWS.md | 14 + R/convert_between_d_to_r.R | 47 ++++-- R/interpret.R | 11 + R/interpret_bf.R | 10 - R/interpret_direction.R | 8 - R/interpret_oddsratio.R | 40 +---- R/interpret_rope.R | 5 R/rank_ANOVA.R | 11 + R/zzz_deprecated.R | 80 ----------- README.md | 18 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/anovaES.html | 7 inst/doc/convert_p_OR_RR.html | 7 inst/doc/convert_r_d_OR.html | 7 inst/doc/effectsize.html | 233 ++++++++++++++++----------------- inst/doc/effectsize_API.html | 4 inst/doc/from_test_statistics.html | 7 inst/doc/interpret.html | 7 inst/doc/standardized_differences.R | 26 +-- inst/doc/standardized_differences.html | 110 ++++++--------- inst/doc/statistical_power.html | 49 +++--- inst/doc/xtabs.R | 44 +++--- inst/doc/xtabs.html | 117 +++++++--------- man/d_to_r.Rd | 10 - man/effectsize-package.Rd | 12 - man/effectsize.Rd | 8 - man/effectsize_CIs.Rd | 12 - man/effectsize_deprecated.Rd | 33 ---- man/interpret.Rd | 4 man/interpret_direction.Rd | 1 man/interpret_oddsratio.Rd | 20 +- man/interpret_rope.Rd | 7 tests/testthat/test-convert_between.R | 39 +++++ tests/testthat/test-htest_data.R | 4 tests/testthat/test-interpret.R | 189 +++++++++++++++----------- 39 files changed, 634 insertions(+), 698 deletions(-)
Title: DDI with R
Description: Useful functions for various DDI (Data Documentation Initiative)
related inputs and outputs. Converts data files to and from DDI, SPSS,
Stata, SAS, R and Excel, including user declared missing values.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between DDIwR versions 0.18 dated 2024-01-08 and 0.19 dated 2024-12-10
DDIwR-0.18/DDIwR/R/exportDDI.R |only DDIwR-0.18/DDIwR/R/getMetadata.R |only DDIwR-0.18/DDIwR/man/exportDDI.Rd |only DDIwR-0.18/DDIwR/man/getMetadata.Rd |only DDIwR-0.19/DDIwR/DESCRIPTION | 8 DDIwR-0.19/DDIwR/MD5 | 46 DDIwR-0.19/DDIwR/NAMESPACE | 2 DDIwR-0.19/DDIwR/R/DDI_Codebook_2.6.R |15952 +++++++++++++++++++-------------- DDIwR-0.19/DDIwR/R/DDIwR_package.R | 7 DDIwR-0.19/DDIwR/R/children.R | 54 DDIwR-0.19/DDIwR/R/convert.R | 147 DDIwR-0.19/DDIwR/R/exportCodebook.R |only DDIwR-0.19/DDIwR/R/getCodebook.R |only DDIwR-0.19/DDIwR/R/internals.R | 403 DDIwR-0.19/DDIwR/R/makeElement.R | 26 DDIwR-0.19/DDIwR/R/searchFor.R | 87 DDIwR-0.19/DDIwR/R/setupfile.R | 16 DDIwR-0.19/DDIwR/R/showDetails.R | 220 DDIwR-0.19/DDIwR/R/testValid.R | 6 DDIwR-0.19/DDIwR/R/updateCodebook.R | 11 DDIwR-0.19/DDIwR/inst/ChangeLog | 275 DDIwR-0.19/DDIwR/man/DDIwR_internal.Rd | 12 DDIwR-0.19/DDIwR/man/DDIwR_package.Rd | 7 DDIwR-0.19/DDIwR/man/convert.Rd | 25 DDIwR-0.19/DDIwR/man/exportCodebook.Rd |only DDIwR-0.19/DDIwR/man/getCodebook.Rd |only DDIwR-0.19/DDIwR/man/makeElement.Rd | 15 DDIwR-0.19/DDIwR/man/searchFor.Rd | 13 28 files changed, 10335 insertions(+), 6997 deletions(-)
Title: Utilities and Design Aids for Up-and-Down Dose-Finding Studies
Description: Up-and-Down is the most popular design approach for dose-finding, but has been severely under-served by the statistical computing community. This is the first package to address Up-and-Down's needs. For a recent methodological tutorial on Up-and-Down, see Oron et al. (2022) <doi:10.1097/ALN.0000000000004282>.
Author: Assaf P. Oron [cre, aut]
Maintainer: Assaf P. Oron <assaf.oron@gmail.com>
Diff between upndown versions 0.1.0 dated 2023-06-07 and 0.2.0 dated 2024-12-10
upndown-0.1.0/upndown/man/adaptmean.Rd |only upndown-0.2.0/upndown/DESCRIPTION | 12 upndown-0.2.0/upndown/MD5 | 52 +- upndown-0.2.0/upndown/NAMESPACE | 7 upndown-0.2.0/upndown/R/averaging.r | 148 +++++-- upndown-0.2.0/upndown/R/bootstrap.r |only upndown-0.2.0/upndown/R/cirWrappers.r | 75 +++ upndown-0.2.0/upndown/R/genutils.r | 22 - upndown-0.2.0/upndown/R/matrixFunctions.r | 25 - upndown-0.2.0/upndown/R/simulate.r |only upndown-0.2.0/upndown/R/vectorFunctions.r | 93 +++- upndown-0.2.0/upndown/build/vignette.rds |binary upndown-0.2.0/upndown/inst/doc/upndown_basics.R | 12 upndown-0.2.0/upndown/inst/doc/upndown_basics.Rmd | 90 ++-- upndown-0.2.0/upndown/inst/doc/upndown_basics.html | 401 ++++++++++++--------- upndown-0.2.0/upndown/inst/examples/avgExamples.r | 35 + upndown-0.2.0/upndown/inst/examples/simExample.r |only upndown-0.2.0/upndown/inst/examples/vecExamples.r | 6 upndown-0.2.0/upndown/man/bcdmat.Rd | 6 upndown-0.2.0/upndown/man/dfboot.Rd |only upndown-0.2.0/upndown/man/dfsim.Rd |only upndown-0.2.0/upndown/man/dixonmood.Rd | 37 + upndown-0.2.0/upndown/man/drplot.Rd | 5 upndown-0.2.0/upndown/man/dynamean.Rd |only upndown-0.2.0/upndown/man/krow.Rd |only upndown-0.2.0/upndown/man/pivec.Rd | 19 upndown-0.2.0/upndown/man/reversmean.Rd | 77 ++-- upndown-0.2.0/upndown/man/udest.Rd | 23 - upndown-0.2.0/upndown/man/udplot.Rd | 15 upndown-0.2.0/upndown/man/validUDinput.Rd | 8 upndown-0.2.0/upndown/vignettes/upndown_basics.Rmd | 90 ++-- 31 files changed, 828 insertions(+), 430 deletions(-)
Title: Tools for Analyzing Shapes and Patterns
Description: This is an evolving and growing collection of tools for the quantification, assessment, and comparison of shape and pattern. This collection provides tools for: (1) the spatial decomposition of planar shapes using 'ShrinkShape' to incrementally shrink shapes to extinction while computing area, perimeter, and number of parts at each iteration of shrinking; the spectra of results are returned in graphic and tabular formats (Remmel 2015) <doi:10.1111/cag.12222>, (2) simulating landscape patterns, (3) provision of tools for estimating composition and configuration parameters from a categorical (binary) landscape map (grid) and then simulates a selected number of statistically similar landscapes. Class-focused pattern metrics are computed for each simulated map to produce empirical distributions against which statistical comparisons can be made. The code permits the analysis of single maps or pairs of maps (Remmel and Fortin 2013) <doi:10.1007/s10980-013-9905-x>, (4) counting th [...truncated...]
Author: Tarmo K. Remmel [aut, cre] ,
Marie-Josee Fortin [ctb],
Ferenc Csillag [ctb],
Sandor Kabos [ctb]
Maintainer: Tarmo K. Remmel <remmelt@yorku.ca>
Diff between ShapePattern versions 3.0.1 dated 2023-08-22 and 3.1.0 dated 2024-12-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/ssr.R | 13 +++++++------ build/partial.rdb |binary man/ssr.Rd | 2 +- 6 files changed, 23 insertions(+), 15 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.77 dated 2024-11-19 and 2.0.78 dated 2024-12-09
DESCRIPTION | 8 - MD5 | 24 +-- NEWS | 7 R/epi.insthaz.R | 219 ++++++++++++++--------------- build/vignette.rds |binary inst/doc/epiR_descriptive.R | 2 inst/doc/epiR_descriptive.Rmd | 2 inst/doc/epiR_descriptive.html | 22 +- inst/doc/epiR_measures_of_association.html | 28 ++- inst/doc/epiR_sample_size.html | 4 inst/doc/epiR_surveillance.html | 27 ++- man/epi.insthaz.Rd | 90 ++++++----- vignettes/epiR_descriptive.Rmd | 2 13 files changed, 239 insertions(+), 196 deletions(-)
Title: Statistical Tests of Familial Hypotheses
Description: Provides functionality for testing familial hypotheses. Supports testing centers
belonging to the Huber family. Testing is carried out using the Bayesian bootstrap. One- and
two-sample tests are supported, as are directional tests. Methods for visualizing output are
provided.
Author: Ryan Thompson [aut, cre]
Maintainer: Ryan Thompson <ryan.thompson-1@uts.edu.au>
Diff between familial versions 1.0.6 dated 2024-11-28 and 1.0.7 dated 2024-12-09
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ R/fit-family.R | 2 +- man/plot.fit.family.Rd | 2 +- 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 0.7.1 dated 2024-09-06 and 0.8.0 dated 2024-12-09
DrugUtilisation-0.7.1/DrugUtilisation/R/addIndication.R |only DrugUtilisation-0.7.1/DrugUtilisation/R/assert.R |only DrugUtilisation-0.7.1/DrugUtilisation/R/checkInputs.R |only DrugUtilisation-0.7.1/DrugUtilisation/R/plotProportionOfPatientsCovered.R |only DrugUtilisation-0.7.1/DrugUtilisation/R/summariseIndication.R |only DrugUtilisation-0.7.1/DrugUtilisation/R/summariseTreatment.R |only DrugUtilisation-0.7.1/DrugUtilisation/man/defaultTableOptions.Rd |only DrugUtilisation-0.7.1/DrugUtilisation/tests/testthat/test-drugUse.R |only DrugUtilisation-0.8.0/DrugUtilisation/DESCRIPTION | 19 DrugUtilisation-0.8.0/DrugUtilisation/MD5 | 254 DrugUtilisation-0.8.0/DrugUtilisation/NAMESPACE | 152 DrugUtilisation-0.8.0/DrugUtilisation/NEWS.md | 72 DrugUtilisation-0.8.0/DrugUtilisation/R/addDrugUse.R | 1095 DrugUtilisation-0.8.0/DrugUtilisation/R/addDrugUtilisation.R | 2286 - DrugUtilisation-0.8.0/DrugUtilisation/R/addIntersect.R |only DrugUtilisation-0.8.0/DrugUtilisation/R/benchmarkDrugUtilisation.R | 409 DrugUtilisation-0.8.0/DrugUtilisation/R/cohortUtilities.R | 260 DrugUtilisation-0.8.0/DrugUtilisation/R/dailyDose.R | 598 DrugUtilisation-0.8.0/DrugUtilisation/R/data.R | 68 DrugUtilisation-0.8.0/DrugUtilisation/R/documentationHelpers.R |only DrugUtilisation-0.8.0/DrugUtilisation/R/erafyCohort.R |only DrugUtilisation-0.8.0/DrugUtilisation/R/generateAtcCohortSet.R | 237 DrugUtilisation-0.8.0/DrugUtilisation/R/generateDrugUtilisationCohortSet.R | 448 DrugUtilisation-0.8.0/DrugUtilisation/R/generateIngredientCohortSet.R | 420 DrugUtilisation-0.8.0/DrugUtilisation/R/mockDrugUtilisation.R | 1112 DrugUtilisation-0.8.0/DrugUtilisation/R/pattern.R | 640 DrugUtilisation-0.8.0/DrugUtilisation/R/plots.R | 995 DrugUtilisation-0.8.0/DrugUtilisation/R/readConceptList.R | 79 DrugUtilisation-0.8.0/DrugUtilisation/R/reexports.R | 86 DrugUtilisation-0.8.0/DrugUtilisation/R/require.R | 720 DrugUtilisation-0.8.0/DrugUtilisation/R/summariseDrugRestart.R | 775 DrugUtilisation-0.8.0/DrugUtilisation/R/summariseDrugUse.R | 166 DrugUtilisation-0.8.0/DrugUtilisation/R/summariseDrugUtilisation.R | 410 DrugUtilisation-0.8.0/DrugUtilisation/R/summariseIntersect.R |only DrugUtilisation-0.8.0/DrugUtilisation/R/summariseProportionOfPatientsCovered.R | 638 DrugUtilisation-0.8.0/DrugUtilisation/R/tables.R | 1310 DrugUtilisation-0.8.0/DrugUtilisation/R/validate.R |only DrugUtilisation-0.8.0/DrugUtilisation/README.md | 427 DrugUtilisation-0.8.0/DrugUtilisation/build/vignette.rds |binary DrugUtilisation-0.8.0/DrugUtilisation/inst/CITATION | 22 DrugUtilisation-0.8.0/DrugUtilisation/inst/Concept/asthma.json | 36 DrugUtilisation-0.8.0/DrugUtilisation/inst/acetaminophen.json | 24 DrugUtilisation-0.8.0/DrugUtilisation/inst/concepts/acetaminophen.json | 24 DrugUtilisation-0.8.0/DrugUtilisation/inst/concepts/influenza.json | 24 DrugUtilisation-0.8.0/DrugUtilisation/inst/doc/create_cohorts.R | 764 DrugUtilisation-0.8.0/DrugUtilisation/inst/doc/create_cohorts.Rmd | 1288 DrugUtilisation-0.8.0/DrugUtilisation/inst/doc/create_cohorts.html | 2000 - DrugUtilisation-0.8.0/DrugUtilisation/inst/doc/drug_utilisation.R | 331 DrugUtilisation-0.8.0/DrugUtilisation/inst/doc/drug_utilisation.Rmd | 578 DrugUtilisation-0.8.0/DrugUtilisation/inst/doc/drug_utilisation.html |15119 +++++----- DrugUtilisation-0.8.0/DrugUtilisation/inst/pattern_assessment_for_dose_final.csv | 84 DrugUtilisation-0.8.0/DrugUtilisation/man/DrugUtilisation-package.Rd | 81 DrugUtilisation-0.8.0/DrugUtilisation/man/addCumulativeDose.Rd | 119 DrugUtilisation-0.8.0/DrugUtilisation/man/addCumulativeQuantity.Rd | 124 DrugUtilisation-0.8.0/DrugUtilisation/man/addDailyDose.Rd | 74 DrugUtilisation-0.8.0/DrugUtilisation/man/addDaysExposed.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/addDaysPrescribed.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/addDrugRestart.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/addDrugUse.Rd | 226 DrugUtilisation-0.8.0/DrugUtilisation/man/addDrugUtilisation.Rd | 204 DrugUtilisation-0.8.0/DrugUtilisation/man/addExposedTime.Rd | 114 DrugUtilisation-0.8.0/DrugUtilisation/man/addIndication.Rd | 152 DrugUtilisation-0.8.0/DrugUtilisation/man/addInitialDailyDose.Rd | 119 DrugUtilisation-0.8.0/DrugUtilisation/man/addInitialExposureDuration.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/addInitialQuantity.Rd | 124 DrugUtilisation-0.8.0/DrugUtilisation/man/addNumberEras.Rd | 132 DrugUtilisation-0.8.0/DrugUtilisation/man/addNumberExposures.Rd | 124 DrugUtilisation-0.8.0/DrugUtilisation/man/addRoute.Rd | 58 DrugUtilisation-0.8.0/DrugUtilisation/man/addTimeToExposure.Rd | 124 DrugUtilisation-0.8.0/DrugUtilisation/man/addTreatment.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/benchmarkDrugUtilisation.Rd | 30 DrugUtilisation-0.8.0/DrugUtilisation/man/cdmDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/censorDateDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/cohortDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/cohortGapEra.Rd | 86 DrugUtilisation-0.8.0/DrugUtilisation/man/cohortIdDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/compNameDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/conceptSetDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/dailyDoseCoverage.Rd | 43 DrugUtilisation-0.8.0/DrugUtilisation/man/daysPrescribedDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/drugUtilisationDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/erafyCohort.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/gapEraDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/generateAtcCohortSet.Rd | 169 DrugUtilisation-0.8.0/DrugUtilisation/man/generateDrugUtilisationCohortSet.Rd | 170 DrugUtilisation-0.8.0/DrugUtilisation/man/generateIngredientCohortSet.Rd | 198 DrugUtilisation-0.8.0/DrugUtilisation/man/indexDateDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/ingredientConceptIdDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/mockDrugUtilisation.Rd | 88 DrugUtilisation-0.8.0/DrugUtilisation/man/nameStyleDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/newNameDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/numberExposuresDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/patternTable.Rd | 57 DrugUtilisation-0.8.0/DrugUtilisation/man/patternsWithFormula.Rd | 38 DrugUtilisation-0.8.0/DrugUtilisation/man/plotDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/plotDrugRestart.Rd | 111 DrugUtilisation-0.8.0/DrugUtilisation/man/plotDrugUtilisation.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/plotIndication.Rd | 115 DrugUtilisation-0.8.0/DrugUtilisation/man/plotProportionOfPatientsCovered.Rd | 83 DrugUtilisation-0.8.0/DrugUtilisation/man/plotTreatment.Rd | 98 DrugUtilisation-0.8.0/DrugUtilisation/man/readConceptList.Rd | 50 DrugUtilisation-0.8.0/DrugUtilisation/man/reexports.Rd | 56 DrugUtilisation-0.8.0/DrugUtilisation/man/requireDrugInDateRange.Rd | 106 DrugUtilisation-0.8.0/DrugUtilisation/man/requireIsFirstDrugEntry.Rd | 84 DrugUtilisation-0.8.0/DrugUtilisation/man/requireObservationBeforeDrug.Rd | 98 DrugUtilisation-0.8.0/DrugUtilisation/man/requirePriorDrugWashout.Rd | 104 DrugUtilisation-0.8.0/DrugUtilisation/man/restrictIncidentDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/resultDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/strataDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/stratifyByUnit.Rd | 71 DrugUtilisation-0.8.0/DrugUtilisation/man/summariseDoseCoverage.Rd | 89 DrugUtilisation-0.8.0/DrugUtilisation/man/summariseDrugRestart.Rd | 139 DrugUtilisation-0.8.0/DrugUtilisation/man/summariseDrugUse.Rd | 88 DrugUtilisation-0.8.0/DrugUtilisation/man/summariseDrugUtilisation.Rd | 211 DrugUtilisation-0.8.0/DrugUtilisation/man/summariseIndication.Rd | 163 DrugUtilisation-0.8.0/DrugUtilisation/man/summariseProportionOfPatientsCovered.Rd | 69 DrugUtilisation-0.8.0/DrugUtilisation/man/summariseTreatment.Rd | 124 DrugUtilisation-0.8.0/DrugUtilisation/man/tableDoc.Rd |only DrugUtilisation-0.8.0/DrugUtilisation/man/tableDoseCoverage.Rd | 111 DrugUtilisation-0.8.0/DrugUtilisation/man/tableDrugRestart.Rd | 130 DrugUtilisation-0.8.0/DrugUtilisation/man/tableDrugUtilisation.Rd | 128 DrugUtilisation-0.8.0/DrugUtilisation/man/tableIndication.Rd | 115 DrugUtilisation-0.8.0/DrugUtilisation/man/tableProportionOfPatientsCovered.Rd | 105 DrugUtilisation-0.8.0/DrugUtilisation/man/tableTreatment.Rd | 114 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat.R | 24 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/_snaps/addDrugUtilisation.md | 144 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/setup.R | 85 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-addDrugUtilisation.R | 774 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-benchmarkDrugUtilisation.R | 60 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-dailyDose.R | 540 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-erafyCohort.R |only DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-generateDrugUtilisationCohortSet.R | 345 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-generatedAtcCohortSet.R | 56 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-generatedIngredientCohortSet.R | 258 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-indication.R | 1354 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-patterns.R | 128 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-plotProportionOfPatientsCovered.R | 292 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-plotTreatment.R | 182 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-plots.R | 214 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-readConceptList.R | 39 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-require.R | 1265 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-summariseDrugRestart.R | 449 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-summariseDrugUtilisation.R | 235 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-summariseProportionOfPatientsCovered.R | 1200 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-summariseTreatment.R | 108 DrugUtilisation-0.8.0/DrugUtilisation/tests/testthat/test-tables.R | 956 DrugUtilisation-0.8.0/DrugUtilisation/vignettes/create_cohorts.Rmd | 1288 DrugUtilisation-0.8.0/DrugUtilisation/vignettes/drug_utilisation.Rmd | 578 148 files changed, 24986 insertions(+), 24774 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Phase I/II CRM Based Drug Combination Design
Description: Implements the adaptive designs for integrated phase I/II trials of drug combinations via continual reassessment method (CRM) to evaluate toxicity and efficacy simultaneously for each enrolled patient cohort based on Bayesian inference. It supports patients assignment guidance in a single trial using current enrolled data, as well as conducting extensive simulation studies to evaluate operating characteristics before the trial starts. It includes various link functions such as empiric, one-parameter logistic, two-parameter logistic, and hyperbolic tangent, as well as considering multiple prior distributions of the parameters like normal distribution, gamma distribution and exponential distribution to accommodate diverse clinical scenarios. Method using Bayesian framework with empiric link function is described in: Wages and Conaway (2014) <doi:10.1002/sim.6097>.
Author: Junying Wang [cre, aut],
Song Wu [aut],
Jie Yang [aut]
Maintainer: Junying Wang <junying.wang@stonybrook.edu>
Diff between crm12Comb versions 0.1.8 dated 2024-11-03 and 0.1.9 dated 2024-12-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/priorSkeletons.R | 4 ++-- data/examples_results.RData |binary inst/doc/crm12Comb.R | 2 +- inst/doc/crm12Comb.Rmd | 2 +- inst/doc/crm12Comb.html | 10 +++++----- vignettes/crm12Comb.Rmd | 2 +- 8 files changed, 20 insertions(+), 20 deletions(-)
Title: Download Air Quality and Meteorological Information of Chile
Description: Download air quality and meteorological information of Chile from the National Air Quality System (S.I.N.C.A.)<https://sinca.mma.gob.cl/> dependent on the Ministry of the Environment and the Meteorological Directorate of Chile (D.M.C.)<https://www.meteochile.gob.cl/> dependent on the Directorate General of Civil Aeronautics.
Author: Francisco Catalan Meyer [aut, cre]
,
Manuel Leiva [aut] ,
Richard Toro [aut]
Maintainer: Francisco Catalan Meyer <francisco.catalan@ug.uchile.cl>
Diff between AtmChile versions 1.0.1 dated 2022-08-29 and 1.0.2 dated 2024-12-09
DESCRIPTION | 12 - MD5 | 16 - R/ChileAirQuality.R | 431 ++++++++++++++---------------------- R/ChileAirQualityApp.R | 16 + README.md | 8 inst/CITATION | 29 +- inst/shiny/app.R | 21 - inst/shiny/complementaryFunctions.R | 92 +++---- man/ChileClimateData.Rd | 92 +++---- 9 files changed, 331 insertions(+), 386 deletions(-)
Title: Measuring Association with Recursive Binning
Description: An iterative implementation of a recursive binary partitioning algorithm to measure pairwise dependence with a modular design that allows user specification of the splitting logic and stop criteria. Helper functions provide suggested versions of both and support visualization and the computation of summary statistics on final binnings. For a complete description of the functionality and algorithm, see Salahub and Oldford (2023) <doi:10.48550/arXiv.2311.08561>.
Author: Chris Salahub [aut, cre]
Maintainer: Chris Salahub <chris.salahub@uwaterloo.ca>
Diff between AssocBin versions 1.0-0 dated 2024-06-28 and 1.0-2 dated 2024-12-09
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/dispatch.R | 26 ++++++++++++++------------ R/splitters.R | 41 +++++++++++++++++++++++++---------------- build/vignette.rds |binary data/heart.rda |binary data/sp500pseudo.rda |binary inst/doc/AssocBin.html | 2 +- inst/doc/complex.html | 16 ++++++++-------- man/methods.Rd | 8 +++++--- 10 files changed, 65 insertions(+), 52 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn [aut, cre] ,
Jed Wing [ctb],
Steve Weston [ctb],
Andre Williams [ctb],
Chris Keefer [ctb],
Allan Engelhardt [ctb],
Tony Cooper [ctb],
Zachary Mayer [ctb],
Brenton Kenkel [ctb],
R Core Team [ctb],
Michael Benesty [ctb],
Reynald Lescarbeau [ct [...truncated...]
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between caret versions 6.0-94 dated 2023-03-21 and 7.0-1 dated 2024-12-09
DESCRIPTION | 11 MD5 | 136 ++-- NAMESPACE | 14 R/aaa.R | 2 R/adaptive.R | 56 +- R/additive.R | 4 R/avNNet.R | 2 R/bag.R | 4 R/bagEarth.R | 2 R/bagFDA.R | 2 R/calibration.R | 4 R/classDist.R | 2 R/classLevels.R | 2 R/confusionMatrix.R | 2 R/createDataPartition.R | 28 - R/createResample.R | 2 R/expoTrans.R | 28 - R/extractPrediction.R | 2 R/extractProb.R | 2 R/featurePlot.R | 2 R/findCorrelation.R | 74 +- R/findLinearCombos.R | 27 R/gafs.R | 22 R/ggplot.R | 2 R/heldout.R | 2 R/knn3.R | 3 R/learning_curve.R | 2 R/lift.R | 10 R/maxDissim.R | 8 R/misc.R | 47 - R/modelLookup.R | 4 R/panel.needle.R | 2 R/plsda.R | 6 R/preProcess.R | 8 R/predict.PLS.R | 21 R/predictors.R | 6 R/print.mars.R | 9 R/print.train.R | 4 R/resamples.R | 44 - R/rfe.R | 20 R/safs.R | 22 R/sampling.R | 2 R/selectByFilter.R | 14 R/sensitivity.R | 3 R/sortImp.R | 2 R/specificity.R | 1 R/train.default.R | 17 R/train_recipes.R | 36 - R/twoClassSim.R | 4 R/varImp.R | 2 R/varImp.train.R | 2 R/workflows.R | 30 - build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 11 inst/doc/caret.html | 868 +++++++++---------------------- man/calibration.Rd | 4 man/findCorrelation.Rd | 14 man/findLinearCombos.Rd | 6 man/maxDissim.Rd | 2 man/plsda.Rd | 2 man/sensitivity.Rd | 2 man/train.Rd | 2 tests/testthat/test_Dummies.R | 11 tests/testthat/test_misc.R | 3 tests/testthat/test_multiclassSummary.R | 2 tests/testthat/test_preProcess_methods.R | 9 tests/testthat/test_recipe_upsample.R | 25 tests/testthat/test_resamples.R | 2 69 files changed, 694 insertions(+), 1032 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood and Laplace approximation model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
See <https://samuel-watson.github.io/glmmr-web/> for a detailed manual.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 0.10.5 dated 2024-09-07 and 0.11.1 dated 2024-12-09
glmmrBase-0.10.5/glmmrBase/data/yexample312a.rda |only glmmrBase-0.10.5/glmmrBase/data/yexample312b.rda |only glmmrBase-0.10.5/glmmrBase/data/yexample312c.rda |only glmmrBase-0.10.5/glmmrBase/data/ytest1.rda |only glmmrBase-0.10.5/glmmrBase/man/yexample312a.Rd |only glmmrBase-0.10.5/glmmrBase/man/yexample312b.Rd |only glmmrBase-0.10.5/glmmrBase/man/yexample312c.Rd |only glmmrBase-0.10.5/glmmrBase/man/ytest1.Rd |only glmmrBase-0.10.5/glmmrBase/src/heckman.cpp |only glmmrBase-0.11.1/glmmrBase/DESCRIPTION | 12 glmmrBase-0.11.1/glmmrBase/MD5 | 116 +- glmmrBase-0.11.1/glmmrBase/R/R6Model.R | 484 ++++++---- glmmrBase-0.11.1/glmmrBase/R/R6covariance.R | 81 + glmmrBase-0.11.1/glmmrBase/R/R6meanfunction.R | 1 glmmrBase-0.11.1/glmmrBase/R/RcppExports.R | 36 glmmrBase-0.11.1/glmmrBase/R/extrafunctions.R | 55 - glmmrBase-0.11.1/glmmrBase/R/lme4_functions.R | 16 glmmrBase-0.11.1/glmmrBase/R/printfunctions.R | 7 glmmrBase-0.11.1/glmmrBase/README.md |only glmmrBase-0.11.1/glmmrBase/build/partial.rdb |binary glmmrBase-0.11.1/glmmrBase/data/Salamanders.rda |only glmmrBase-0.11.1/glmmrBase/data/SimGeospat.rda |only glmmrBase-0.11.1/glmmrBase/data/SimTrial.rda |only glmmrBase-0.11.1/glmmrBase/inst/include/glmmr/covariance.hpp | 89 + glmmrBase-0.11.1/glmmrBase/inst/include/glmmr/formula.hpp | 6 glmmrBase-0.11.1/glmmrBase/inst/include/glmmr/general.h | 42 glmmrBase-0.11.1/glmmrBase/inst/include/glmmr/linearpredictor.hpp | 12 glmmrBase-0.11.1/glmmrBase/inst/include/glmmr/matrixfield.h | 6 glmmrBase-0.11.1/glmmrBase/inst/include/glmmr/model.hpp | 36 glmmrBase-0.11.1/glmmrBase/inst/include/glmmr/modelbits.hpp | 32 glmmrBase-0.11.1/glmmrBase/inst/include/glmmr/modelmatrix.hpp | 401 ++++++-- glmmrBase-0.11.1/glmmrBase/inst/include/glmmr/modeloptim.hpp | 179 +++ glmmrBase-0.11.1/glmmrBase/man/Beta.Rd | 34 glmmrBase-0.11.1/glmmrBase/man/MeanFunction.Rd | 8 glmmrBase-0.11.1/glmmrBase/man/Model.Rd | 187 +++ glmmrBase-0.11.1/glmmrBase/man/Salamanders.Rd |only glmmrBase-0.11.1/glmmrBase/man/SimGeospat.Rd |only glmmrBase-0.11.1/glmmrBase/man/SimTrial.Rd |only glmmrBase-0.11.1/glmmrBase/man/coef.Model.Rd | 38 glmmrBase-0.11.1/glmmrBase/man/coef.mcml.Rd | 38 glmmrBase-0.11.1/glmmrBase/man/confint.mcml.Rd | 38 glmmrBase-0.11.1/glmmrBase/man/family.Model.Rd | 40 glmmrBase-0.11.1/glmmrBase/man/family.mcml.Rd | 38 glmmrBase-0.11.1/glmmrBase/man/fitted.Model.Rd | 44 glmmrBase-0.11.1/glmmrBase/man/fitted.mcml.Rd | 40 glmmrBase-0.11.1/glmmrBase/man/fixed.effects.Rd | 34 glmmrBase-0.11.1/glmmrBase/man/formula.Model.Rd | 40 glmmrBase-0.11.1/glmmrBase/man/formula.mcml.Rd | 44 glmmrBase-0.11.1/glmmrBase/man/lme4_to_glmmr.Rd | 60 - glmmrBase-0.11.1/glmmrBase/man/logLik.Model.Rd | 38 glmmrBase-0.11.1/glmmrBase/man/logLik.mcml.Rd | 50 - glmmrBase-0.11.1/glmmrBase/man/mcml_glmer.Rd | 132 +- glmmrBase-0.11.1/glmmrBase/man/mcml_lmer.Rd | 132 +- glmmrBase-0.11.1/glmmrBase/man/predict.Model.Rd | 62 - glmmrBase-0.11.1/glmmrBase/man/predict.mcml.Rd | 40 glmmrBase-0.11.1/glmmrBase/man/random.effects.Rd | 34 glmmrBase-0.11.1/glmmrBase/man/residuals.Model.Rd | 56 - glmmrBase-0.11.1/glmmrBase/man/residuals.mcml.Rd | 50 - glmmrBase-0.11.1/glmmrBase/man/setParallel.Rd | 42 glmmrBase-0.11.1/glmmrBase/man/summary.Model.Rd | 42 glmmrBase-0.11.1/glmmrBase/man/vcov.Model.Rd | 44 glmmrBase-0.11.1/glmmrBase/man/vcov.mcml.Rd | 46 glmmrBase-0.11.1/glmmrBase/src/RcppExports.cpp | 105 +- glmmrBase-0.11.1/glmmrBase/src/covariance_module.cpp | 3 glmmrBase-0.11.1/glmmrBase/src/model_module.cpp | 12 glmmrBase-0.11.1/glmmrBase/src/model_module_2.cpp | 56 + glmmrBase-0.11.1/glmmrBase/src/model_module_extension.cpp | 56 - 67 files changed, 2131 insertions(+), 1163 deletions(-)
Title: (Robust) Mediation Analysis
Description: Perform mediation analysis via the fast-and-robust bootstrap test ROBMED (Alfons, Ates & Groenen, 2022a; <doi:10.1177/1094428121999096>), as well as various other methods. Details on the implementation and code examples can be found in Alfons, Ates, and Groenen (2022b) <doi:10.18637/jss.v103.i13>.
Author: Andreas Alfons [aut, cre] ,
Nufer Y. Ates [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robmed versions 1.1.0 dated 2024-11-03 and 1.2.0 dated 2024-12-09
DESCRIPTION | 8 +- MD5 | 62 +++++++++--------- NAMESPACE | 2 NEWS | 11 +++ R/control.R | 73 ++++++++++++++++++---- R/fit_mediation.R | 42 +++++++----- R/regression.R | 9 +- R/test_mediation.R | 39 +++++++---- build/partial.rdb |binary inst/CITATION | 37 ++++++++++- inst/doc/robmed-intro.pdf |binary man/fit_mediation.Rd | 19 +++-- man/reg_control.Rd | 57 ++++++++++++++--- man/test_mediation.Rd | 19 +++-- tests/testthat/test_boot_multiple_covariates.R | 12 ++- tests/testthat/test_boot_multiple_no_covariates.R | 12 ++- tests/testthat/test_boot_parallel_covariates.R | 12 ++- tests/testthat/test_boot_parallel_no_covariates.R | 12 ++- tests/testthat/test_boot_serial_covariates.R | 12 ++- tests/testthat/test_boot_serial_no_covariates.R | 12 ++- tests/testthat/test_boot_simple_covariates.R | 12 ++- tests/testthat/test_boot_simple_no_covariates.R | 12 ++- tests/testthat/test_fit_multiple_covariates.R | 10 +-- tests/testthat/test_fit_multiple_no_covariates.R | 10 +-- tests/testthat/test_fit_parallel_covariates.R | 10 +-- tests/testthat/test_fit_parallel_no_covariates.R | 10 +-- tests/testthat/test_fit_serial_covariates.R | 10 +-- tests/testthat/test_fit_serial_no_covariates.R | 10 +-- tests/testthat/test_fit_simple_covariates.R | 10 +-- tests/testthat/test_fit_simple_no_covariates.R | 10 +-- tests/testthat/test_sobel_simple_covariates.R | 12 ++- tests/testthat/test_sobel_simple_no_covariates.R | 12 ++- 32 files changed, 389 insertions(+), 189 deletions(-)
Title: Recognize and Parse Dates in Various Formats, Including All ISO
8601 Formats
Description: Parse dates automatically, without the need of specifying a
format. Currently it includes the git date parser. It can also
recognize and parse all ISO 8601 formats.
Author: Gabor Csardi [aut, cre],
Linus Torvalds [aut]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between parsedate versions 1.3.1 dated 2022-10-27 and 1.3.2 dated 2024-12-09
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/parsedate-package.r | 5 ++--- README.md | 25 ++++++++++++------------- man/parse_date.Rd | 2 +- man/parsedate-package.Rd | 9 +++++++++ src/rdate.c | 5 +++-- tests/testthat.R | 25 +++++++++++++++++-------- tests/testthat/test-corner-cases.R | 15 +++++++-------- tests/testthat/test-git.r | 5 ++--- tests/testthat/test-iso8601.r | 9 ++++----- tests/testthat/test-time-zones.R | 3 +-- 13 files changed, 89 insertions(+), 66 deletions(-)
Title: Processing and Analysing Animal Trajectories
Description: Tools to handle, manipulate and explore trajectory data, with an emphasis on data from tracked animals. The package is designed to support large studies with several million location records and keep track of units where possible. Data import directly from 'movebank' <https://www.movebank.org/cms/movebank-main> and files is facilitated.
Author: Bart Kranstauber [aut, cre] ,
Kamran Safi [aut] ,
Anne K. Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move2 versions 0.3.0 dated 2024-05-22 and 0.4.0 dated 2024-12-09
DESCRIPTION | 10 MD5 | 152 ++- NEWS.md | 10 R/assertions.R | 8 R/movebank_api.R | 44 - R/movebank_api_helper.R | 50 - R/movebank_constants.R | 553 +++++++------ R/movebank_credentials.R | 12 R/movebank_get_vocabulary.R | 25 R/mt_aeqd_crs.R | 16 R/mt_as_track_attribute.R | 4 R/mt_distance.R | 4 R/mt_filter_per_interval.R | 4 R/mt_filter_unique.R | 13 R/mt_interpolate.R | 2 R/mt_read.R | 8 R/mt_segments.R | 2 R/mt_sim_brownian_motion.R | 42 - R/mt_time.R | 2 R/mt_track_id.R | 10 R/new_move.R | 14 inst/CITATION |only inst/WORDLIST | 4 inst/doc/albatross.R | 42 - inst/doc/albatross.Rmd | 42 - inst/doc/albatross.html | 869 +++++++++----------- inst/doc/convert.html | 246 ++--- inst/doc/filtering_tracks.R | 4 inst/doc/filtering_tracks.Rmd | 6 inst/doc/filtering_tracks.html | 1086 ++++++++++++-------------- inst/doc/movebank.R | 101 +- inst/doc/movebank.Rmd | 194 +++- inst/doc/movebank.html | 1044 ++++++++++++------------ inst/doc/programming_move2_object.Rmd | 8 inst/doc/programming_move2_object.html | 416 +++------ inst/doc/trajectory_analysis.R | 15 inst/doc/trajectory_analysis.Rmd | 15 inst/doc/trajectory_analysis.html | 552 ++++++------- man/movebank_download_study.Rd | 2 man/movebank_get_vocabulary.Rd | 7 man/mt_filter_unique.Rd | 11 tests/testthat/test-assertions.R | 42 - tests/testthat/test-calculate_properties.R | 102 +- tests/testthat/test-movebank_api.R | 60 - tests/testthat/test-movebank_constants.R |only tests/testthat/test-movebank_get_vocabulary.R | 32 tests/testthat/test-movebank_speed.R | 23 tests/testthat/test-mt_aeqd_crs.R | 26 tests/testthat/test-mt_as_move2.R | 41 tests/testthat/test-mt_as_track_attribute.R | 30 tests/testthat/test-mt_filter_unique.R | 80 - tests/testthat/test-mt_interpolate.R | 85 +- tests/testthat/test-mt_read.R | 19 tests/testthat/test-mt_read_speed.R | 6 tests/testthat/test-mt_set_track_id.R | 2 tests/testthat/test-mt_sim_brownian_motion.R | 68 - tests/testthat/test-mt_stack.R | 160 ++- tests/testthat/test-mt_track_id.R | 4 tests/testthat/test-print.R | 49 - tests/testthat/test-round_trip_rbind.R | 10 tests/testthat/test-segments.R | 20 tests/testthat/test-sf.R | 2 tests/testthat/test-subset.R | 20 tests/testthat/test-tidyr.R | 12 vignettes/albatross.Rmd | 42 - vignettes/filtering_tracks.Rmd | 6 vignettes/movebank.Rmd | 194 +++- vignettes/programming_move2_object.Rmd | 8 vignettes/rosm.cache |only vignettes/trajectory_analysis.Rmd | 15 70 files changed, 3560 insertions(+), 3247 deletions(-)
Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its
application to forecasting. The main scope of the package is in variables selection
and models specification for cases of time series data. This includes promotional
modelling, selection between different dynamic regressions with non-standard
distributions of errors, selection based on cross validation, solutions to the fat
regression model problem and more. Models developed in the package are tailored
specifically for forecasting purposes. So as a results there are several methods
that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] ,
Yves R. Sagaert [ctb]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Diff between greybox versions 2.0.2 dated 2024-08-27 and 2.0.3 dated 2024-12-09
greybox-2.0.2/greybox/R/nemenyi.R |only greybox-2.0.3/greybox/DESCRIPTION | 16 greybox-2.0.3/greybox/MD5 | 131 ++-- greybox-2.0.3/greybox/NAMESPACE | 3 greybox-2.0.3/greybox/NEWS | 14 greybox-2.0.3/greybox/R/AutomaticDemandIdentifier.R | 42 + greybox-2.0.3/greybox/R/coefbootstrap.R | 28 greybox-2.0.3/greybox/R/dsrboot.R | 14 greybox-2.0.3/greybox/R/greybox-package.R | 3 greybox-2.0.3/greybox/R/ro.R | 63 +- greybox-2.0.3/greybox/R/tableplot.R | 1 greybox-2.0.3/greybox/inst/doc/alm.html | 581 ++++++++++---------- greybox-2.0.3/greybox/inst/doc/greybox.html | 217 +++---- greybox-2.0.3/greybox/inst/doc/maUsingGreybox.html | 242 ++++---- greybox-2.0.3/greybox/inst/doc/ro.html | 113 +-- greybox-2.0.3/greybox/man/ALaplace.Rd | 2 greybox-2.0.3/greybox/man/BCNormal.Rd | 2 greybox-2.0.3/greybox/man/Distributions.Rd | 2 greybox-2.0.3/greybox/man/FNormal.Rd | 2 greybox-2.0.3/greybox/man/InformationCriteria.Rd | 2 greybox-2.0.3/greybox/man/Laplace.Rd | 2 greybox-2.0.3/greybox/man/LogitNormal.Rd | 2 greybox-2.0.3/greybox/man/SDistribution.Rd | 2 greybox-2.0.3/greybox/man/TPLNormal.Rd | 2 greybox-2.0.3/greybox/man/accuracy.Rd | 2 greybox-2.0.3/greybox/man/actuals.Rd | 2 greybox-2.0.3/greybox/man/aid.Rd | 2 greybox-2.0.3/greybox/man/alm.Rd | 2 greybox-2.0.3/greybox/man/association.Rd | 2 greybox-2.0.3/greybox/man/coef.alm.Rd | 2 greybox-2.0.3/greybox/man/coefbootstrap.Rd | 2 greybox-2.0.3/greybox/man/cramer.Rd | 2 greybox-2.0.3/greybox/man/detectdst.Rd | 2 greybox-2.0.3/greybox/man/determination.Rd | 2 greybox-2.0.3/greybox/man/dsrboot.Rd | 4 greybox-2.0.3/greybox/man/error-measures.Rd | 2 greybox-2.0.3/greybox/man/errorType.Rd | 2 greybox-2.0.3/greybox/man/extractScale.Rd | 2 greybox-2.0.3/greybox/man/greybox.Rd | 4 greybox-2.0.3/greybox/man/hm.Rd | 2 greybox-2.0.3/greybox/man/implant.Rd | 2 greybox-2.0.3/greybox/man/isFunctions.Rd | 2 greybox-2.0.3/greybox/man/lmCombine.Rd | 2 greybox-2.0.3/greybox/man/lmDynamic.Rd | 2 greybox-2.0.3/greybox/man/mcor.Rd | 2 greybox-2.0.3/greybox/man/measures.Rd | 2 greybox-2.0.3/greybox/man/nparam.Rd | 2 greybox-2.0.3/greybox/man/outlierdummy.Rd | 2 greybox-2.0.3/greybox/man/pcor.Rd | 2 greybox-2.0.3/greybox/man/pinball.Rd | 2 greybox-2.0.3/greybox/man/plot.greybox.Rd | 2 greybox-2.0.3/greybox/man/pointIC.Rd | 2 greybox-2.0.3/greybox/man/pointLik.Rd | 2 greybox-2.0.3/greybox/man/polyprod.Rd | 2 greybox-2.0.3/greybox/man/predict.greybox.Rd | 2 greybox-2.0.3/greybox/man/rectNormal.Rd | 2 greybox-2.0.3/greybox/man/rmcb.Rd | 2 greybox-2.0.3/greybox/man/ro.Rd | 12 greybox-2.0.3/greybox/man/sm.Rd | 2 greybox-2.0.3/greybox/man/spread.Rd | 2 greybox-2.0.3/greybox/man/stepwise.Rd | 2 greybox-2.0.3/greybox/man/tableplot.Rd | 2 greybox-2.0.3/greybox/man/temporaldummy.Rd | 2 greybox-2.0.3/greybox/man/xregExpander.Rd | 2 greybox-2.0.3/greybox/man/xregMultiplier.Rd | 2 greybox-2.0.3/greybox/man/xregTransformer.Rd | 2 greybox-2.0.3/greybox/src/polyMult.cpp | 4 67 files changed, 823 insertions(+), 765 deletions(-)
Title: Tools for Cleaning Rectangular Data
Description: A dependency-free collection of simple functions for cleaning
rectangular data. This package allows to detect, count and replace
values or discard rows/columns using a predicate function. In
addition, it provides tools to check conditions and return informative
error messages.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between arkhe versions 1.8.0 dated 2024-11-07 and 1.9.0 dated 2024-12-09
DESCRIPTION | 7 ++-- MD5 | 52 +++++++++++++++++----------------- NAMESPACE | 9 ++++-- NEWS.md | 9 +++++- R/AllGenerics.R | 20 ++++++------- R/arkhe-deprecated.R | 25 +++++++++++++++- R/arkhe-package.R | 6 ++-- R/assert.R | 9 ++++-- R/compact.R | 4 +- R/discard.R | 4 +- R/keep.R | 4 +- R/seek.R | 13 ++------ README.md | 64 +++++++++++++++++++++++++++---------------- build/partial.rdb |binary inst/tinytest/test_assert.R | 1 inst/tinytest/test_compact.R | 10 +++--- inst/tinytest/test_discard.R | 8 ++--- inst/tinytest/test_keep.R | 10 +++--- inst/tinytest/test_seek.R | 8 ++--- man/arkhe-deprecated.Rd | 11 ++++++- man/arkhe-package.Rd | 6 ++-- man/assert_length.Rd | 12 ++++++-- man/assert_type.Rd | 2 - man/compact.Rd | 10 +++--- man/discard.Rd | 10 +++--- man/keep.Rd | 10 +++--- man/seek.Rd | 2 - 27 files changed, 194 insertions(+), 132 deletions(-)
Title: Extract 'REDCap' Databases into Tidy 'Tibble's
Description: Convert 'REDCap' exports into tidy tables for easy handling of 'REDCap' repeat instruments and event arms.
Author: Richard Hanna [aut, cre] ,
Stephan Kadauke [aut] ,
Ezra Porter [aut]
Maintainer: Richard Hanna <richardshanna91@gmail.com>
Diff between REDCapTidieR versions 1.2.0 dated 2024-10-23 and 1.2.1 dated 2024-12-09
DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++------------ NAMESPACE | 1 NEWS.md | 7 +++++- R/REDCapTidieR-package.R | 1 R/checks.R | 10 ++++----- R/clean_redcap_long.R | 2 - R/combine_checkboxes.R | 18 ++++++++--------- R/read_redcap.R | 39 ++++++++++++++++++++++---------------- R/utils.R | 6 ++++- inst/doc/REDCapTidieR.R | 2 - tests/testthat/test-read_redcap.R | 14 ++++++++++++- tests/testthat/test-utils.R | 6 +++++ 13 files changed, 87 insertions(+), 51 deletions(-)
Title: Agreement of Nominal Scale Raters (with a Gold Standard)
Description: Estimate agreement of a group of raters with a gold standard rating
on a nominal scale. For a single gold standard rater the average pairwise
agreement of raters with this gold standard is provided. For a group of (gold
standard) raters the approach of S. Vanbelle, A. Albert (2009)
<doi:10.1007/s11336-009-9116-1> is implemented. Bias and standard error are
estimated via delete-1 jackknife.
Author: Matthias Kuhn [aut, cre] ,
Jonas Breidenstein [aut]
Maintainer: Matthias Kuhn <matthias.kuhn@tu-dresden.de>
Diff between kappaGold versions 0.3.2 dated 2024-09-30 and 0.4.0 dated 2024-12-09
DESCRIPTION | 17 ++-- MD5 | 37 +++++---- NAMESPACE | 5 + NEWS.md | 8 +- R/data.R | 42 ++++++++++ R/kappa.R | 135 ++++++++++------------------------- R/kappaGold-package.R | 4 - R/kappa_inference.R |only R/vanbelle.R | 34 ++++---- README.md | 69 +++++++++++++---- build/partial.rdb |binary data/agreem_binary.rda |only data/depression.rda |only man/agreem_binary.Rd |only man/depression.Rd |only man/kappa2.Rd | 18 ++-- man/kappa_test.Rd | 26 +++--- man/kappa_test_corr.Rd |only man/kappam_gold.Rd | 25 ++++-- man/kappam_vanbelle.Rd | 16 +--- tests/testthat/test-kappa.R | 30 +------ tests/testthat/test-kappaInference.R |only tests/testthat/test-vanbelle.R | 14 ++- 23 files changed, 266 insertions(+), 214 deletions(-)
Title: Client for World Banks's 'Indicators' and 'Poverty and
Inequality Platform (PIP)' APIs
Description: Download and search data from the 'World Bank Indicators
API', which provides access to nearly 16,000 time series indicators.
See
<https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api-documentation>
for further details about the API.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between worldbank versions 0.3.0 dated 2024-08-26 and 0.4.0 dated 2024-12-09
worldbank-0.3.0/worldbank/tests/testthat/_snaps/api.md |only worldbank-0.4.0/worldbank/DESCRIPTION | 10 worldbank-0.4.0/worldbank/MD5 | 23 + worldbank-0.4.0/worldbank/NAMESPACE | 2 worldbank-0.4.0/worldbank/NEWS.md | 6 worldbank-0.4.0/worldbank/R/assertions.R | 4 worldbank-0.4.0/worldbank/R/fone.R |only worldbank-0.4.0/worldbank/R/indicators.R | 28 +- worldbank-0.4.0/worldbank/R/pip.R | 14 - worldbank-0.4.0/worldbank/R/utils.R | 9 worldbank-0.4.0/worldbank/README.md | 125 +++++----- worldbank-0.4.0/worldbank/man/figures/README-plotting-1.png |binary worldbank-0.4.0/worldbank/man/fone.Rd |only worldbank-0.4.0/worldbank/tests/testthat/_snaps/indicators.md |only worldbank-0.4.0/worldbank/tests/testthat/test-fone.R |only 15 files changed, 121 insertions(+), 100 deletions(-)
Title: 'shiny' App to Analyze Pakistan's Population Census Data
Description: Provides tools for analyzing Pakistan's Population Censuses data via the 'PakPC2023' and 'PakPC2017' R packages. Designed for researchers, policymakers, and professionals, the app enables in-depth numerical and graphical analysis, including detailed cross-tabulations and insights. With diverse statistical models and visualization options, it supports informed decision-making in social and economic policy. This tool enhances users' ability to explore and interpret census data, providing valuable insights for effective planning and analysis across various fields.
Author: Muhammad Yaseen [aut, cre, cph]
,
Muhammad Arfan Dilber [ctb],
Zahid Asghar [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PakPC versions 0.2.0 dated 2024-11-11 and 0.3.0 dated 2024-12-09
DESCRIPTION | 6 MD5 | 10 - NEWS.md | 8 + README.md | 16 ++ inst/shinyapp/rsconnect/shinyapps.io/myaseen208/PakPC.dcf | 2 inst/shinyapp/ui.R | 87 ++++++++++++-- 6 files changed, 105 insertions(+), 24 deletions(-)
Title: OPTICS K-Xi Density-Based Clustering
Description: Density-based clustering methods are well adapted to the clustering of high-dimensional data and enable the discovery of core groups of various shapes despite large amounts of noise. This package provides a novel density-based cluster extraction method, OPTICS k-Xi, and a framework to compare k-Xi models using distance-based metrics to investigate datasets with unknown number of clusters. The vignette first introduces density-based algorithms with simulated datasets, then presents and evaluates the k-Xi cluster extraction method. Finally, the models comparison framework is described and experimented on 2 genetic datasets to identify groups and their discriminating features. The k-Xi algorithm is a novel OPTICS cluster extraction method that specifies directly the number of clusters and does not require fine-tuning of the steepness parameter as the OPTICS Xi method. Combined with a framework that compares models with varying parameters, the OPTICS k-Xi method can identify groups in nois [...truncated...]
Author: Thomas Charlon [aut, cre]
Maintainer: Thomas Charlon <charlon@protonmail.com>
Diff between opticskxi versions 0.1 dated 2019-07-18 and 1.1.0 dated 2024-12-09
opticskxi-0.1/opticskxi/LICENSE |only opticskxi-0.1/opticskxi/README.md |only opticskxi-1.1.0/opticskxi/DESCRIPTION | 25 +++--- opticskxi-1.1.0/opticskxi/MD5 | 49 +++++++------ opticskxi-1.1.0/opticskxi/NAMESPACE | 11 ++ opticskxi-1.1.0/opticskxi/NEWS.md |only opticskxi-1.1.0/opticskxi/R/0_imports.R | 5 + opticskxi-1.1.0/opticskxi/R/ensemble_models.R |only opticskxi-1.1.0/opticskxi/R/ggpairs.R | 10 +- opticskxi-1.1.0/opticskxi/R/m_psychwords.R |only opticskxi-1.1.0/opticskxi/R/optics_plots.R | 13 ++- opticskxi-1.1.0/opticskxi/R/psych_kxi_example.R |only opticskxi-1.1.0/opticskxi/R/rm_huge_clusters.R |only opticskxi-1.1.0/opticskxi/R/utils.R | 5 - opticskxi-1.1.0/opticskxi/build/vignette.rds |binary opticskxi-1.1.0/opticskxi/data/m_psychwords.rda |only opticskxi-1.1.0/opticskxi/inst/doc/opticskxi.R | 1 opticskxi-1.1.0/opticskxi/inst/doc/opticskxi.pdf |binary opticskxi-1.1.0/opticskxi/man/ensemble_metrics.Rd |only opticskxi-1.1.0/opticskxi/man/ensemble_models.Rd |only opticskxi-1.1.0/opticskxi/man/fortify_dimred.Rd | 9 +- opticskxi-1.1.0/opticskxi/man/ggpairs.Rd | 14 ++- opticskxi-1.1.0/opticskxi/man/ggplot_kxi_metrics.Rd | 3 opticskxi-1.1.0/opticskxi/man/ggplot_optics.Rd | 8 +- opticskxi-1.1.0/opticskxi/man/m_psychwords.Rd |only opticskxi-1.1.0/opticskxi/man/multishapes.Rd | 6 + opticskxi-1.1.0/opticskxi/man/opticskxi.Rd | 9 +- opticskxi-1.1.0/opticskxi/man/opticskxi_pipeline.Rd | 11 +- opticskxi-1.1.0/opticskxi/man/psych_kxi_ensemble_models.Rd |only opticskxi-1.1.0/opticskxi/man/psych_kxi_pipeline.Rd |only opticskxi-1.1.0/opticskxi/tests/testthat/test-ggpairs.R |only opticskxi-1.1.0/opticskxi/tests/testthat/test-opticskxi.R | 12 ++- opticskxi-1.1.0/opticskxi/tests/testthat/test-psychkxi.R |only 33 files changed, 128 insertions(+), 63 deletions(-)
Title: Real-Time Disease Surveillance
Description: Supports modelling real-time case data to facilitate the real-time
surveillance of infectious diseases and other point phenomena. The package provides automated computational grid generation over
an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts,
and predictions and visualisation. Both Bayesian and maximum likelihood methods are provided. Log-Gaussian Cox Processes are described by
Diggle et al. (2013) <doi:10.1214/13-STS441> and we provide both the low-rank approximation for Gaussian processes
described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and Riutort-Mayol et al (2023) <doi:10.1007/s11222-022-10167-2> and the
nearest neighbour Gaussian process described by Datta et al (2016) <doi:10.1080/01621459.2015.1044091>. 'cmdstanr' can be downloaded at <https://mc-stan.org/cmdstanr/>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between rts2 versions 0.7.6 dated 2024-09-06 and 0.7.7 dated 2024-12-09
DESCRIPTION | 8 +- MD5 | 53 ++++++++------- README.md |only build/partial.rdb |binary man/birmingham_crime.Rd | 34 +++++----- man/boundary.Rd | 32 ++++----- man/coef.rtsFit.Rd | 38 +++++------ man/confint.rtsFit.Rd | 38 +++++------ man/covariance.parameters.Rd | 34 +++++----- man/example_points.Rd | 34 +++++----- man/family.rtsFit.Rd | 38 +++++------ man/fitted.rtsFit.Rd | 40 +++++------ man/fixed.effects.Rd | 34 +++++----- man/formula.grid.Rd | 42 ++++++------ man/formula.rtsFit.Rd | 42 ++++++------ man/logLik.rtsFit.Rd | 40 +++++------ man/predict.grid.Rd | 138 ++++++++++++++++++++--------------------- man/predict.rtsFit.Rd | 40 +++++------ man/print.rtsFit.Rd | 50 +++++++------- man/print.rtsFitSummary.Rd | 44 ++++++------- man/random.effects.Rd | 34 +++++----- man/residuals.grid.Rd | 44 ++++++------- man/residuals.rtsFit.Rd | 44 ++++++------- man/summary.grid.Rd | 38 +++++------ man/summary.rtsFit.Rd | 48 +++++++------- man/vcov.grid.Rd | 40 +++++------ man/vcov.rtsFit.Rd | 40 +++++------ src/model_module_extension.cpp | 8 ++ 28 files changed, 541 insertions(+), 534 deletions(-)
Title: Econometric Tools for Performance and Risk Analysis
Description: Collection of econometric functions for performance and risk
analysis. In addition to standard risk and performance metrics, this
package aims to aid practitioners and researchers in utilizing the latest
research in analysis of non-normal return streams. In general, it is most
tested on return (rather than price) data on a regular scale, but most
functions will work with irregular return data as well, and increasing
numbers of functions will work with P&L or price data where possible.
Author: Brian G. Peterson [cre, aut, cph],
Peter Carl [aut, cph],
Kris Boudt [ctb, cph],
Ross Bennett [ctb],
Joshua Ulrich [ctb],
Eric Zivot [ctb],
Dries Cornilly [ctb],
Eric Hung [ctb],
Matthieu Lestel [ctb],
Kyle Balkissoon [ctb],
Diethelm Wuertz [ctb],
An [...truncated...]
Maintainer: Brian G. Peterson <brian@braverock.com>
Diff between PerformanceAnalytics versions 2.0.4 dated 2020-02-06 and 2.0.8 dated 2024-12-09
PerformanceAnalytics-2.0.4/PerformanceAnalytics/NEWS |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/inst/doc/PA-Bacon.R |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/inst/doc/PA-Bacon.Rnw |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/inst/doc/PA-Bacon.pdf |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/inst/doc/textplotPresentation-CRUG-2011.R |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/inst/doc/textplotPresentation-CRUG-2011.Rnw |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/man/CAPM.alpha.Rd |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/man/CAPM.beta.Rd |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/tests/Examples |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/vignettes/PA-Bacon.Rnw |only PerformanceAnalytics-2.0.4/PerformanceAnalytics/vignettes/textplotPresentation-CRUG-2011.Rnw |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/DESCRIPTION | 25 PerformanceAnalytics-2.0.8/PerformanceAnalytics/MD5 | 525 ++--- PerformanceAnalytics-2.0.8/PerformanceAnalytics/NAMESPACE | 23 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/ActivePremium.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/AdjustedSharpeRatio.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/AppraisalRatio.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/BernadoLedoitratio.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/BurkeRatio.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/CAPM.alpha.R | 129 - PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/CAPM.beta.R | 321 +-- PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/CAPM.epsilon.R | 26 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/CAPM.jensenAlpha.R | 51 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/CAPM.utils.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/CDAR.alpha.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/CDAR.beta.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/CalmarRatio.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/CoMoments.R | 24 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/DRatio.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/DownsideDeviation.R | 69 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/DownsideFrequency.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/DownsideSharpeRatio.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/DrawdownPeak.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Drawdowns.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/ES.R | 92 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/FamaBeta.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Frequency.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/HerfindahlIndex.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/HurstIndex.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/InformationRatio.R | 8 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Kappa.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/KellyRatio.R | 8 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/M2Sortino.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/MM.NCE.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/MSquared.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/MSquaredExcess.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/MartinRatio.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/MeanAbsoluteDeviation.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/MultivariateMoments.R | 99 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/NetSelectivity.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Omega.R | 47 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/OmegaExcessReturn.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/OmegaSharpeRatio.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/PainIndex.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/PainRatio.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/PerformanceAnalytics-package.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/PortfolioRisk.R | 78 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/ProspectRatio.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/RPESE.control.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/RachevRatio.R | 40 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Return.Geltner.R | 8 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Return.annualized.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Return.calculate.R | 36 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Return.clean.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Return.cumulative.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Return.excess.R | 10 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Return.locScaleRob.R | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Return.portfolio.R | 12 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Return.read.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Return.relative.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/SFM.coefficients.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/SFM.fit.models.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/Selectivity.R | 9 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/SemiDeviation.R | 62 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/SharpeRatio.R | 109 - PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/SharpeRatio.annualized.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/SkewnessKurtosisRatio.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/SmoothingIndex.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/SortinoRatio.R | 51 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/SpecificRisk.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/StdDev.R | 215 +- PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/StdDev.annualized.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/SystematicRisk.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/TotalRisk.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/TrackingError.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/TreynorRatio.R | 8 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/UlcerIndex.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/UpDownRatios.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/UpsideFrequency.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/UpsidePotentialRatio.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/UpsideRisk.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/VaR.Marginal.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/VaR.R | 113 - PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/VolatilitySkewness.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/apply.fromstart.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/apply.rolling.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.ACF.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.ACFplus.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.Bar.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.BarVaR.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.Boxplot.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.CaptureRatios.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.Correlation.R | 34 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.CumReturns.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.Drawdown.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.ECDF.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.Events.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.Histogram.R | 11 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.QQPlot.R | 14 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.Regression.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.RelativePerformance.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.RiskReturnScatter.R | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.RollingCorrelation.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.RollingMean.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.RollingPerformance.R | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.RollingQuantileRegression.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.RollingRegression.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.SFM.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.Scatter.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.SnailTrail.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.StackedBar.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.TimeSeries.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.TimeSeries.base.R | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.TimeSeries.builtin.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/chart.VaRSensitivity.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/charts.Bar.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/charts.BarVaR.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/charts.PerformanceSummary.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/charts.RollingPerformance.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/charts.RollingRegression.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/charts.TimeSeries.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/checkData.R | 8 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/findDrawdowns.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/kurtosis.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/legend.R | 16 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/lpm.R | 33 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/maxDrawdown.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/mean.utils.R | 47 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/na.skip.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/replaceTabs.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/skewness.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/sortDrawdowns.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.AnnualizedReturns.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.Arbitrary.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.Autocorrelation.R | 94 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.CAPM.R | 52 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.CalendarReturns.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.CaptureRatios.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.Correlation.R | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.Distributions.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.DownsideRisk.R | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.DownsideRiskRatio.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.Drawdowns.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.DrawdownsRatio.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.HigherMoments.R | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.InformationRatio.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.MonthlyReturns.R | 11 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.RollingPeriods.R | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.SpecificRisk.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.UpDownRatios.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/table.Variability.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/textplot.R | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/to.period.contributions.R | 8 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/utils.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/zerofill.R | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/R/zzz.R | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/README.md | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/build/vignette.rds |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/data/edhec.rda |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/data/managers.rda |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/data/portfolio_bacon.rda |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/data/test_returns.rda |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/data/test_weights.rda |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/data/weights.rda |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/EstimationComoments.R | 77 PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/EstimationComoments.Rnw | 13 PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/EstimationComoments.pdf |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/PA-charts.R | 10 PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/PA-charts.Rnw | 11 PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/PA-charts.pdf |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/PA_StandardErrors.pdf |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/PerformanceAnalyticsChartsPresentation-Meielisalp-2007.R | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/PerformanceAnalyticsChartsPresentation-Meielisalp-2007.Rnw | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/PerformanceAnalyticsChartsPresentation-Meielisalp-2007.pdf |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/PerformanceAnalyticsPresentation-UseR-2007.R | 10 PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/PerformanceAnalyticsPresentation-UseR-2007.Rnw | 9 PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/PerformanceAnalyticsPresentation-UseR-2007.pdf |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/portfolio_returns.R | 1 PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/portfolio_returns.pdf |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/textplotPresentation-CRUG-2011.pdf |binary PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/doc/textplotPresentation-CRUG-2011.pdf.asis |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/tinytest/test_CAPM.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/inst/tinytest/test_Return.portfolio.arithmetic.R |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/AdjustedSharpeRatio.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/CAPM.RiskPremium.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/CAPM.jensenAlpha.Rd | 17 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/CDD.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/CDaR.alpha.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/CDaR.beta.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/CoMoments.Rd | 8 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/DownsideDeviation.Rd | 10 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/DownsideSharpeRatio.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/ES.Rd | 20 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/EWMAMoments.Rd | 3 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/InformationRatio.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/KellyRatio.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/MCA.Rd | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/NCE.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/Omega.Rd | 9 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/PerformanceAnalytics-package.Rd | 995 ++++++++-- PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/RPESE.control.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/RachevRatio.Rd | 17 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/Return.Geltner.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/Return.calculate.Rd | 32 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/Return.locScaleRob.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/Return.portfolio.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/SFM.alpha.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/SFM.beta.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/SFM.coefficients.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/SFM.fit.models.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/Selectivity.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/SharpeRatio.Rd | 13 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/ShrinkageMoments.Rd | 13 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/SortinoRatio.Rd | 12 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/StdDev.Rd | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/StdDev.annualized.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/StructuredMoments.Rd | 15 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/SystematicRisk.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/TreynorRatio.Rd | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/UlcerIndex.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/UpsidePotentialRatio.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/VaR.Rd | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/centeredmoments.Rd | 15 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.ACF.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.Correlation.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.ECDF.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.Histogram.Rd | 3 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.QQPlot.Rd | 11 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.RiskReturnScatter.Rd | 3 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.RollingCorrelation.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.RollingMean.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.RollingPerformance.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.RollingRegression.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.SFM.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.StackedBar.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/chart.TimeSeries.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/charts.RollingPerformance.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/dot-coefficients.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/edhec.Rd | 9 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/legend.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/managers.Rd | 2 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/mean.geometric.Rd | 8 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/portfolio-moments.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.AnnualizedReturns.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.Autocorrelation.Rd | 7 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.CAPM.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.CalendarReturns.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.Correlation.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.Distributions.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.DownsideRisk.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.DownsideRiskRatio.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.DrawdownsRatio.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.HigherMoments.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.InformationRatio.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.MonthlyReturns.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.RollingPeriods.Rd | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.SpecificRisk.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/table.Variability.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/test_returns.Rd | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/test_weights.Rd | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/textplot.Rd | 4 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/to.period.contributions.Rd | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/man/unique-comoments.Rd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/src/NCEHelper.c |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/src/comomentsEstimators.c | 6 PerformanceAnalytics-2.0.8/PerformanceAnalytics/src/init.c | 11 PerformanceAnalytics-2.0.8/PerformanceAnalytics/vignettes/EstimationComoments.Rnw | 13 PerformanceAnalytics-2.0.8/PerformanceAnalytics/vignettes/PA-Bacon.Rmd |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/vignettes/PA-Bacon.pdf |only PerformanceAnalytics-2.0.8/PerformanceAnalytics/vignettes/PA-charts.Rnw | 11 PerformanceAnalytics-2.0.8/PerformanceAnalytics/vignettes/PerformanceAnalyticsChartsPresentation-Meielisalp-2007.Rnw | 5 PerformanceAnalytics-2.0.8/PerformanceAnalytics/vignettes/PerformanceAnalyticsPresentation-UseR-2007.Rnw | 9 PerformanceAnalytics-2.0.8/PerformanceAnalytics/vignettes/textplotPresentation-CRUG-2011.pdf.asis |only 283 files changed, 2856 insertions(+), 1636 deletions(-)
More information about PerformanceAnalytics at CRAN
Permanent link
Title: Copernicus Digital Elevation Models
Description: Copernicus Digital Elevation Model datasets (DEM) of 90 and 30 meters resolution using the 'awscli' command line tool. The Copernicus (DEM) is included in the Registry of Open Data on 'AWS (Amazon Web Services)' and represents the surface of the Earth including buildings, infrastructure and vegetation.
Author: Lampros Mouselimis [aut, cre]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between CopernicusDEM versions 1.0.4 dated 2024-08-17 and 1.0.5 dated 2024-12-09
DESCRIPTION | 11 MD5 | 22 - NEWS.md | 6 README.md | 2 inst/doc/Copernicus_Digital_Elevation_Models.R | 289 ++++++++++------------ inst/doc/Copernicus_Digital_Elevation_Models.Rmd | 143 +++++----- inst/doc/Copernicus_Digital_Elevation_Models.html | 206 ++++++++------- vignettes/Copernicus_Digital_Elevation_Models.Rmd | 143 +++++----- vignettes/leaflet_map.png |binary vignettes/progress_logs.png |binary vignettes/tarandus_elevation.png |binary vignettes/wolves_elevation.png |binary 12 files changed, 421 insertions(+), 401 deletions(-)
Title: Fitting Latent Class Vector-Autoregressive (VAR) Models
Description: Estimates latent class vector-autoregressive models via EM algorithm on time-series data for model-based clustering and classification. Includes model selection criteria for selecting the number of lags and clusters.
Author: Anja Ernst [aut, cre],
Jonas Haslbeck [aut]
Maintainer: Anja Ernst <a.f.ernst@rug.nl>
Diff between ClusterVAR versions 0.0.7 dated 2024-07-10 and 0.0.8 dated 2024-12-09
ClusterVAR-0.0.7/ClusterVAR/data/datalist |only ClusterVAR-0.0.8/ClusterVAR/DESCRIPTION | 6 - ClusterVAR-0.0.8/ClusterVAR/MD5 | 28 ++--- ClusterVAR-0.0.8/ClusterVAR/NEWS | 12 +- ClusterVAR-0.0.8/ClusterVAR/R/LCVAR.R | 21 ++-- ClusterVAR-0.0.8/ClusterVAR/R/callEMFuncsPARALLELIZED.R | 2 ClusterVAR-0.0.8/ClusterVAR/R/checkSingularitySigma.R | 2 ClusterVAR-0.0.8/ClusterVAR/R/checkVarianceY.R |only ClusterVAR-0.0.8/ClusterVAR/R/createX.R | 22 ++-- ClusterVAR-0.0.8/ClusterVAR/R/plot.ClusterVAR.R | 35 +++++-- ClusterVAR-0.0.8/ClusterVAR/R/plotHeat.R | 75 ++++------------ ClusterVAR-0.0.8/ClusterVAR/build/partial.rdb |binary ClusterVAR-0.0.8/ClusterVAR/man/LCVAR.Rd | 17 +++ ClusterVAR-0.0.8/ClusterVAR/man/clusterVAR_internal.Rd | 3 ClusterVAR-0.0.8/ClusterVAR/man/coef.ClusterVAR.Rd | 2 ClusterVAR-0.0.8/ClusterVAR/man/plot.ClusterVAR.Rd | 4 16 files changed, 118 insertions(+), 111 deletions(-)
Title: Methods for Quantitative Magnetic Resonance Imaging ('qMRI')
Description: Implementation of methods for estimation of quantitative maps
from Multi-Parameter Mapping (MPM) acquisitions (Weiskopf et al. (2013)
<doi:10.3389/fnins.2013.00095>) and analysis of Inversion Recovery MRI data.
Usage of the package is described in
Polzehl and Tabelow (2023),
"Magnetic Resonance Brain Imaging", 2nd Edition, Chapter 6 and 7, Springer, Use R! Series.
<doi:10.1007/978-3-031-38949-8>.
J. Polzehl and K. Tabelow (2023), "Magnetic Resonance Brain Imaging - Modeling and Data Analysis Using R: Code and Data."
<doi:10.20347/WIAS.DATA.6> provides extensive example code and data.
Author: Joerg Polzehl [aut],
Karsten Tabelow [aut, cre],
WIAS Berlin [cph, fnd]
Maintainer: Karsten Tabelow <karsten.tabelow@wias-berlin.de>
Diff between qMRI versions 1.2.7.6 dated 2024-05-22 and 1.2.7.8 dated 2024-12-09
qMRI-1.2.7.6/qMRI/tests |only qMRI-1.2.7.8/qMRI/DESCRIPTION | 8 +++---- qMRI-1.2.7.8/qMRI/MD5 | 26 +++++++++++------------- qMRI-1.2.7.8/qMRI/R/estimateIR.R | 6 ++--- qMRI-1.2.7.8/qMRI/build/partial.rdb |binary qMRI-1.2.7.8/qMRI/inst/doc/IRMRI-Example.R | 2 - qMRI-1.2.7.8/qMRI/inst/doc/IRMRI-Example.Rnw | 2 - qMRI-1.2.7.8/qMRI/inst/doc/IRMRI-Example.pdf |binary qMRI-1.2.7.8/qMRI/inst/doc/qMRI-Example.pdf |binary qMRI-1.2.7.8/qMRI/vignettes/IRMRI-Example-2.pdf |binary qMRI-1.2.7.8/qMRI/vignettes/IRMRI-Example-9.pdf |binary qMRI-1.2.7.8/qMRI/vignettes/IRMRI-Example.Rnw | 2 - qMRI-1.2.7.8/qMRI/vignettes/qMRI-Example-11.pdf |binary qMRI-1.2.7.8/qMRI/vignettes/qMRI-Example-8.pdf |binary 14 files changed, 22 insertions(+), 24 deletions(-)
Title: Library Search Against Electron Ionization Mass Spectral
Databases
Description: Perform library searches against electron ionization mass spectral
databases using either the API provided by 'MS Search' software
(<https://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:nistlibs>) or
custom implementations of the Identity and Similarity algorithms.
Author: Andrey Samokhin [aut, cre, cph]
Maintainer: Andrey Samokhin <andrey.s.samokhin@gmail.com>
Diff between mssearchr versions 0.1.1 dated 2024-06-25 and 0.2.0 dated 2024-12-09
mssearchr-0.1.1/mssearchr/tests/testthat/data/SRCRESLT.TXT |only mssearchr-0.1.1/mssearchr/tests/testthat/data/intst_presence.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/library_search_alkanes.rda |only mssearchr-0.1.1/mssearchr/tests/testthat/data/library_search_synthetic.rda |only mssearchr-0.1.1/mssearchr/tests/testthat/data/merging_synon_fields.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/ms_delimiters.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/ms_number_format.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/mz_presence.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/name_absence.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/nonunique_field.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/numpeaks_absence.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/numpeaks_incorrect.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/reading_cas_and_nist.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/reading_cas_and_nist2.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/reading_ordinary_fields.msp |only mssearchr-0.1.1/mssearchr/tests/testthat/data/srcreslt.rda |only mssearchr-0.1.1/mssearchr/tests/testthat/data/synthetic_spectra.rda |only mssearchr-0.1.1/mssearchr/tests/testthat/test-msp_format.R |only mssearchr-0.2.0/mssearchr/DESCRIPTION | 8 mssearchr-0.2.0/mssearchr/MD5 | 71 +-- mssearchr-0.2.0/mssearchr/NAMESPACE | 18 mssearchr-0.2.0/mssearchr/NEWS.md | 18 mssearchr-0.2.0/mssearchr/R/RcppExports.R | 7 mssearchr-0.2.0/mssearchr/R/library_search_nist_api.R | 11 mssearchr-0.2.0/mssearchr/R/library_search_r.R | 50 +- mssearchr-0.2.0/mssearchr/R/mass_spectra_preprocessing.R | 80 ++- mssearchr-0.2.0/mssearchr/R/msp_format.R | 10 mssearchr-0.2.0/mssearchr/inst/CITATION |only mssearchr-0.2.0/mssearchr/man/LibrarySearch.Rd | 175 ++++--- mssearchr-0.2.0/mssearchr/man/LibrarySearchUsingNistApi.Rd | 224 +++++----- mssearchr-0.2.0/mssearchr/man/PreprocessMassSpectra.Rd | 161 +++---- mssearchr-0.2.0/mssearchr/man/WriteMsp.Rd | 108 ++-- mssearchr-0.2.0/mssearchr/src/RcppExports.cpp | 9 mssearchr-0.2.0/mssearchr/src/identity_algorithm.cpp | 66 +- mssearchr-0.2.0/mssearchr/tests/testthat/data/library_search |only mssearchr-0.2.0/mssearchr/tests/testthat/data/parse_srcreslt |only mssearchr-0.2.0/mssearchr/tests/testthat/data/read_msp |only mssearchr-0.2.0/mssearchr/tests/testthat/test-library_search_nist_api.R | 4 mssearchr-0.2.0/mssearchr/tests/testthat/test-library_search_r.R | 24 - mssearchr-0.2.0/mssearchr/tests/testthat/test-mass_spectra_preprocessing.R | 2 mssearchr-0.2.0/mssearchr/tests/testthat/test-read_msp.R |only mssearchr-0.2.0/mssearchr/tests/testthat/test-write_msp.R |only 42 files changed, 557 insertions(+), 489 deletions(-)
Title: Classes for Relational Data
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre],
David Hunter [ctb],
Mark Handcock [ctb],
Skye Bender-deMoll [ctb],
Jeffrey Horner [ctb],
Li Wang [ctb],
Pavel N. Krivitsky [ctb] ,
Brendan Knapp [ctb] ,
Michal Bojanowski [ctb] ,
Chad Klumb [ctb]
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between network versions 1.18.2 dated 2023-12-05 and 1.19.0 dated 2024-12-09
ChangeLog | 15 ++ DESCRIPTION | 10 - MD5 | 105 +++++++------- NAMESPACE | 2 R/access.R | 148 +++++++------------- R/as.edgelist.R | 2 R/coercion.R | 20 +- R/constructors.R | 7 R/fileio.R | 6 R/layout.R | 2 R/misc.R | 5 R/network-package.R | 8 - R/operators.R | 8 - R/plot.R | 6 build/partial.rdb |only build/vignette.rds |binary inst/doc/networkVignette.pdf |binary man/add.edges.Rd | 2 man/add.vertices.Rd | 2 man/as.edgelist.Rd | 2 man/as.matrix.network.Rd | 6 man/as.network.matrix.Rd | 2 man/as.sociomatrix.Rd | 2 man/attribute.methods.Rd | 2 man/deletion.methods.Rd | 2 man/edgeset.constructors.Rd | 2 man/get.edges.Rd | 2 man/get.inducedSubgraph.Rd | 7 man/get.neighborhood.Rd | 2 man/is.adjacent.Rd | 2 man/loading.attributes.Rd | 2 man/network-internal.Rd | 1 man/network-operators.Rd | 2 man/network-package.Rd | 7 man/network.Rd | 2 man/network.arrow.Rd | 2 man/network.density.Rd | 2 man/network.dyadcount.Rd | 2 man/network.edgecount.Rd | 2 man/network.extraction.Rd | 2 man/network.indicators.Rd | 2 man/network.initialize.Rd | 2 man/network.layout.Rd | 2 man/network.naedgecount.Rd | 2 man/network.size.Rd | 2 man/network.vertex.Rd | 2 man/permute.vertexIDs.Rd | 9 - man/plot.network.Rd | 2 man/prod.network.Rd | 2 man/read.paj.Rd | 6 man/sum.network.Rd | 2 man/which.matrix.type.Rd | 2 src/access.c | 75 +++++++--- tests/testthat/test-read.paj.R | 302 ++++++++++++++++++++--------------------- 54 files changed, 422 insertions(+), 393 deletions(-)
Title: Get Data from the Swiss Federal Statistical Office
Description: Search and download data from the Swiss Federal Statistical Office (BFS) APIs <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre, cph]
,
Janosch Brenzel-Weiss [ctb],
Joao Martins [ctb],
Philipp Baumann [ctb]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between BFS versions 0.5.11 dated 2024-11-27 and 0.5.12 dated 2024-12-09
DESCRIPTION | 6 ++-- MD5 | 14 ++++----- NEWS.md | 5 +++ R/bfs_get_base_maps.R | 25 +++++++++-------- README.md | 45 +++++++++++++++++++++++++++++++- man/bfs_get_base_maps.Rd | 5 ++- man/figures/base_maps.png |binary tests/testthat/test-bfs_get_base_maps.R | 16 +++++++++++ 8 files changed, 93 insertions(+), 23 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm
(Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6>. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Hege Boevelstad [ctb] ,
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 0.9.0 dated 2024-09-24 and 0.9.2 dated 2024-12-09
DESCRIPTION | 10 - MD5 | 46 ++--- NAMESPACE | 6 NEWS.md | 50 ++++++ R/Candidates.R | 2 R/GaussSuppressionFromData.R | 27 ++- R/MagnitudeRule.R | 211 +++++++++++++++++++++++---- R/MaxContribution.R | 15 + R/SuppressDominantCells.R | 27 +++ R/SuppressSmallCounts.R | 11 + R/reexport.R | 12 + inst/doc/Magnitude_table_suppression.R | 2 inst/doc/Magnitude_table_suppression.Rmd | 2 inst/doc/Magnitude_table_suppression.html | 63 +++++--- man/FindDominantCells.Rd | 6 man/GaussSuppressionFromData.Rd | 6 man/MagnitudeRule.Rd | 51 +++++- man/SuppressDominantCells.Rd | 32 +++- man/SuppressFewContributors.Rd | 4 man/SuppressSmallCounts.Rd | 15 + man/reexports.Rd | 4 tests/testthat/test-DominanceRule.R | 133 ++++++++++++++++- tests/testthat/test-Wrappers.R | 234 ++++++++++++++++++++++++++++++ vignettes/Magnitude_table_suppression.Rmd | 2 24 files changed, 856 insertions(+), 115 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: Small Count Rounding of Tabular Data
Description: A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398_An_Algorithm_for_Small_Count_Rounding_of_Tabular_Data>.
Author: Oeyvind Langsrud [aut, cre],
Johan Heldal [aut]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SmallCountRounding versions 1.0.8 dated 2024-10-22 and 1.1.0 dated 2024-12-09
DESCRIPTION | 10 ++++---- MD5 | 18 +++++++-------- NEWS.md | 27 +++++++++++++++++++++++ R/PLSrounding.R | 25 ++++++++++++++++++--- inst/doc/Introduction_to_SmallCountRounding.R | 11 +++++---- inst/doc/Introduction_to_SmallCountRounding.Rmd | 17 +++++++------- inst/doc/Introduction_to_SmallCountRounding.html | 27 +++++++++++------------ man/PLSrounding.Rd | 15 ++++++++++-- tests/testthat/test-PLSrounding.R | 25 ++++++++++++--------- vignettes/Introduction_to_SmallCountRounding.Rmd | 17 +++++++------- 10 files changed, 128 insertions(+), 64 deletions(-)
More information about SmallCountRounding at CRAN
Permanent link
Title: Transcriptomic Atlas of Neuroimaging Derived Phenotypes
Description: Contains functions to query and visualize the Neuroimaging features
associated with genetically regulated gene expression (GReX). The primary utility,
neuroimaGene(), relies on a list of user-defined genes and returns a table of
neuroimaging features (NIDPs) associated with each gene. This resource
is designed to assist in the interpretation of genome-wide and transcriptome-wide
association studies that evaluate brain related traits. Bledsoe (2024)
<doi:10.1016/j.ajhg.2024.06.002>. In addition there are several visualization
functions that generate summary plots and 2-dimensional visualizations of regional
brain measures. Mowinckel (2020).
Author: Xavier Bledsoe [aut, cre] ,
Eric Gamazon [aut]
Maintainer: Xavier Bledsoe <xavier.bledsoe@vanderbilt.edu>
Diff between neuroimaGene versions 0.1.1 dated 2024-09-20 and 0.1.2 dated 2024-12-09
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ R/anno_doc.R | 4 ++-- R/plot_gn_nidp.R | 6 +++--- R/plot_nidps.R | 7 +++---- README.md |only data/nidp_anno.RData |binary man/anno.Rd | 4 ++-- 8 files changed, 21 insertions(+), 21 deletions(-)
Title: Mean Comparison in 'ggplot2'
Description: Add mean comparison annotations to a 'ggplot'.
This package provides an easy way to indicate if two or more groups are significantly different in a 'ggplot'.
Usually you do not need to specify the test method, you only need to tell stat_compare() whether you want to perform a parametric test or a nonparametric test, and stat_compare() will automatically choose the appropriate test method based on your data.
For comparisons between two groups, the p-value is calculated by t-test (parametric) or Wilcoxon rank sum test (nonparametric). For comparisons among more than two groups, the p-value is calculated by One-way ANOVA (parametric) or Kruskal-Wallis test (nonparametric).
Author: Hao Wang [aut, cre]
Maintainer: Hao Wang <wanghao8772@gmail.com>
Diff between ggcompare versions 0.0.2 dated 2024-10-07 and 0.0.3 dated 2024-12-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 ++++++-- R/GGExtensions.R | 10 +++++++--- man/geom_bracket.Rd | 2 ++ man/stat_compare.Rd | 8 +++++--- 6 files changed, 28 insertions(+), 16 deletions(-)
Title: An Extension of the Gap Statistic for Ordinal/Categorical Data
Description: The gap statistic approach is extended to estimate the number of clusters for categorical response format data. This approach and accompanying software is designed to be used with the output of any clustering algorithm and with distances specifically designed for categorical (i.e. multiple choice) or ordinal survey response data.
Author: Jeffrey Miecznikowski [aut],
Eduardo Cortes [aut, cre]
Maintainer: Eduardo Cortes <ecortesg@buffalo.edu>
Diff between DiscreteGapStatistic versions 0.1.0 dated 2024-10-25 and 1.0.0 dated 2024-12-09
DESCRIPTION | 11 - MD5 | 29 ++- NAMESPACE | 2 R/AuxFuns.R |only R/DiscreteClusGapFuns.R | 243 +++++++++++++++++++++++++++---- R/VisualFuns.R | 39 ++++ README.md | 210 +++++++++++++++++++++++--- man/ResHeatmap.Rd | 12 + man/clusGapDiscr.Rd | 18 +- man/clusGapDiscr0.Rd |only man/clusterFunSel.Rd |only man/figures/README-clusGapDiscrFit-1.png |binary man/figures/README-clusGapDiscrFit-2.png |binary man/figures/README-clusGapDiscrFit-3.png |binary man/figures/README-clusterRun-1.png |only man/figures/README-clusterRun-2.png |only man/figures/README-hclustRun-1.png |only man/figures/README-hclustRun-2.png |only man/figures/README-hclustRun-3.png |only man/kmodesD.Rd |only 20 files changed, 482 insertions(+), 82 deletions(-)
More information about DiscreteGapStatistic at CRAN
Permanent link
Title: Create Flashcards of Terms and Definitions
Description: Provides functions for creating flashcard decks of terms and
definitions. This package creates HTML slides using 'revealjs' that can be
viewed in the 'RStudio' viewer or a web browser. Users can create
flashcards from either existing built-in decks or create their own from CSV
files or vectors of function names.
Author: Jeffrey R. Stevens [aut, cre, cph]
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@protonmail.com>
Diff between flashr versions 0.1.2 dated 2024-03-15 and 0.2.0 dated 2024-12-08
DESCRIPTION | 13 ++--- MD5 | 35 ++++++++----- NAMESPACE | 4 + NEWS.md | 5 + R/extract_functions.R |only R/flashcard.R | 81 ++++++++++++++++++++------------ R/flashr-package.R |only R/utils.R | 2 README.md | 12 +++- build/vignette.rds |binary inst/doc/flashr.R | 22 ++++---- inst/doc/flashr.Rmd | 14 +++-- inst/doc/flashr.html | 77 ++++++++++++++++++------------ man/build_functions_df.Rd |only man/extract_code.Rd |only man/extract_functions.Rd |only man/fail_gracefully.Rd | 2 man/flashr-package.Rd |only tests/testthat/test-extract_functions.R |only tests/testthat/test-flashcard.R | 46 +++++++++++++----- tests/testthat/test-utils.R | 1 vignettes/flashr.Rmd | 14 +++-- 22 files changed, 216 insertions(+), 112 deletions(-)
Title: Tidy Integration of Large Language Models
Description: A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'Openai', 'Groq','Mistral' and local models via 'Ollama' into R workflows. The package supports text and media-based interactions, interactive message history, batch request APIs, and a tidy, pipeline-oriented interface for streamlined integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://groq.com>, <https://mistral.ai/> and <https://ollama.com>.
Author: Eduard Bruell [aut, cre],
Jia Zhang [ctb]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>
Diff between tidyllm versions 0.2.0 dated 2024-11-07 and 0.3.0 dated 2024-12-08
tidyllm-0.2.0/tidyllm/R/azure_openai.R |only tidyllm-0.2.0/tidyllm/R/claude.R |only tidyllm-0.2.0/tidyllm/R/groq.R |only tidyllm-0.2.0/tidyllm/R/mistral.R |only tidyllm-0.2.0/tidyllm/R/ollama.R |only tidyllm-0.2.0/tidyllm/R/openai.R |only tidyllm-0.2.0/tidyllm/R/perform_api_request.R |only tidyllm-0.2.0/tidyllm/R/streaming_callback.R |only tidyllm-0.2.0/tidyllm/R/tidyllm.R |only tidyllm-0.2.0/tidyllm/man/generate_callback_function.Rd |only tidyllm-0.2.0/tidyllm/man/initialize_api_env.Rd |only tidyllm-0.2.0/tidyllm/man/last_reply.Rd |only tidyllm-0.2.0/tidyllm/man/last_reply_data.Rd |only tidyllm-0.2.0/tidyllm/man/last_user_message.Rd |only tidyllm-0.2.0/tidyllm/man/parse_duration_to_seconds.Rd |only tidyllm-0.2.0/tidyllm/man/perform_api_request.Rd |only tidyllm-0.2.0/tidyllm/man/ratelimit_from_header.Rd |only tidyllm-0.2.0/tidyllm/man/update_rate_limit.Rd |only tidyllm-0.2.0/tidyllm/tests/testthat/openai/api.openai.com/v1/chat/completions-65bf96-POST.R |only tidyllm-0.2.0/tidyllm/tests/testthat/test_claude.R |only tidyllm-0.2.0/tidyllm/tests/testthat/test_groq.R |only tidyllm-0.2.0/tidyllm/tests/testthat/test_mistral.R |only tidyllm-0.2.0/tidyllm/tests/testthat/test_ollama.R |only tidyllm-0.2.0/tidyllm/tests/testthat/test_openai.R |only tidyllm-0.3.0/tidyllm/DESCRIPTION | 29 tidyllm-0.3.0/tidyllm/MD5 | 170 +-- tidyllm-0.3.0/tidyllm/NAMESPACE | 38 tidyllm-0.3.0/tidyllm/NEWS.md | 274 +++++ tidyllm-0.3.0/tidyllm/R/APIProvider.R |only tidyllm-0.3.0/tidyllm/R/LLMMessage.R |only tidyllm-0.3.0/tidyllm/R/api_azure_openai.R |only tidyllm-0.3.0/tidyllm/R/api_claude.R |only tidyllm-0.3.0/tidyllm/R/api_gemini.R |only tidyllm-0.3.0/tidyllm/R/api_groq.R |only tidyllm-0.3.0/tidyllm/R/api_mistral.R |only tidyllm-0.3.0/tidyllm/R/api_ollama.R |only tidyllm-0.3.0/tidyllm/R/api_openai.R |only tidyllm-0.3.0/tidyllm/R/api_perplexity.R |only tidyllm-0.3.0/tidyllm/R/llm_message.R |only tidyllm-0.3.0/tidyllm/R/llm_verbs.R |only tidyllm-0.3.0/tidyllm/R/media.R | 1 tidyllm-0.3.0/tidyllm/R/message_retrieval.R | 146 ++ tidyllm-0.3.0/tidyllm/R/perform_api_requests.R |only tidyllm-0.3.0/tidyllm/R/rate_limits.R | 149 -- tidyllm-0.3.0/tidyllm/R/tidyllm-package.R | 2 tidyllm-0.3.0/tidyllm/R/tidyllm_schema.R | 61 + tidyllm-0.3.0/tidyllm/R/utilites.R | 93 + tidyllm-0.3.0/tidyllm/R/zzz.R | 17 tidyllm-0.3.0/tidyllm/README.md | 37 tidyllm-0.3.0/tidyllm/inst/doc/tidyllm.R | 308 ++++- tidyllm-0.3.0/tidyllm/inst/doc/tidyllm.Rmd | 258 +++- tidyllm-0.3.0/tidyllm/inst/doc/tidyllm.html | 517 ++++++---- tidyllm-0.3.0/tidyllm/man/LLMMessage.Rd | 204 --- tidyllm-0.3.0/tidyllm/man/azure_openai.Rd | 95 - tidyllm-0.3.0/tidyllm/man/azure_openai_chat.Rd |only tidyllm-0.3.0/tidyllm/man/azure_openai_embedding.Rd |only tidyllm-0.3.0/tidyllm/man/cancel_openai_batch.Rd |only tidyllm-0.3.0/tidyllm/man/chat.Rd |only tidyllm-0.3.0/tidyllm/man/chatgpt.Rd | 81 - tidyllm-0.3.0/tidyllm/man/check_batch.Rd |only tidyllm-0.3.0/tidyllm/man/check_claude_batch.Rd | 2 tidyllm-0.3.0/tidyllm/man/check_mistral_batch.Rd |only tidyllm-0.3.0/tidyllm/man/check_openai_batch.Rd | 2 tidyllm-0.3.0/tidyllm/man/claude.Rd | 76 - tidyllm-0.3.0/tidyllm/man/claude_chat.Rd |only tidyllm-0.3.0/tidyllm/man/df_llm_message.Rd | 20 tidyllm-0.3.0/tidyllm/man/embed.Rd |only tidyllm-0.3.0/tidyllm/man/fetch_batch.Rd |only tidyllm-0.3.0/tidyllm/man/fetch_claude_batch.Rd | 2 tidyllm-0.3.0/tidyllm/man/fetch_mistral_batch.Rd |only tidyllm-0.3.0/tidyllm/man/fetch_openai_batch.Rd | 2 tidyllm-0.3.0/tidyllm/man/gemini.Rd |only tidyllm-0.3.0/tidyllm/man/gemini_chat.Rd |only tidyllm-0.3.0/tidyllm/man/gemini_delete_file.Rd |only tidyllm-0.3.0/tidyllm/man/gemini_embedding.Rd |only tidyllm-0.3.0/tidyllm/man/gemini_file_metadata.Rd |only tidyllm-0.3.0/tidyllm/man/gemini_list_files.Rd |only tidyllm-0.3.0/tidyllm/man/gemini_upload_file.Rd |only tidyllm-0.3.0/tidyllm/man/get_metadata.Rd |only tidyllm-0.3.0/tidyllm/man/get_reply.Rd | 21 tidyllm-0.3.0/tidyllm/man/get_reply_data.Rd | 21 tidyllm-0.3.0/tidyllm/man/get_user_message.Rd | 14 tidyllm-0.3.0/tidyllm/man/groq.Rd | 83 - tidyllm-0.3.0/tidyllm/man/groq_chat.Rd |only tidyllm-0.3.0/tidyllm/man/groq_transcribe.Rd | 2 tidyllm-0.3.0/tidyllm/man/list_batches.Rd |only tidyllm-0.3.0/tidyllm/man/list_claude_batches.Rd | 2 tidyllm-0.3.0/tidyllm/man/list_mistral_batches.Rd |only tidyllm-0.3.0/tidyllm/man/list_openai_batches.Rd | 2 tidyllm-0.3.0/tidyllm/man/llm_message.Rd | 14 tidyllm-0.3.0/tidyllm/man/mistral.Rd | 63 - tidyllm-0.3.0/tidyllm/man/mistral_chat.Rd |only tidyllm-0.3.0/tidyllm/man/mistral_embedding.Rd | 6 tidyllm-0.3.0/tidyllm/man/ollama.Rd | 114 -- tidyllm-0.3.0/tidyllm/man/ollama_chat.Rd |only tidyllm-0.3.0/tidyllm/man/ollama_download_model.Rd | 7 tidyllm-0.3.0/tidyllm/man/ollama_embedding.Rd | 6 tidyllm-0.3.0/tidyllm/man/ollama_list_models.Rd | 2 tidyllm-0.3.0/tidyllm/man/openai.Rd | 84 - tidyllm-0.3.0/tidyllm/man/openai_chat.Rd |only tidyllm-0.3.0/tidyllm/man/openai_embedding.Rd | 15 tidyllm-0.3.0/tidyllm/man/perplexity.Rd |only tidyllm-0.3.0/tidyllm/man/perplexity_chat.Rd |only tidyllm-0.3.0/tidyllm/man/send_batch.Rd |only tidyllm-0.3.0/tidyllm/man/send_claude_batch.Rd | 2 tidyllm-0.3.0/tidyllm/man/send_mistral_batch.Rd |only tidyllm-0.3.0/tidyllm/man/send_openai_batch.Rd | 8 tidyllm-0.3.0/tidyllm/man/tidyllm-package.Rd | 5 tidyllm-0.3.0/tidyllm/man/tidyllm_schema.Rd | 4 tidyllm-0.3.0/tidyllm/tests/testthat/claude/api.anthropic.com/v1/messages-e050b5-POST.R | 18 tidyllm-0.3.0/tidyllm/tests/testthat/openai/api.openai.com/v1/chat/completions-00dde8-POST.R |only tidyllm-0.3.0/tidyllm/tests/testthat/openai_schema_multiple |only tidyllm-0.3.0/tidyllm/tests/testthat/openai_schema_single |only tidyllm-0.3.0/tidyllm/tests/testthat/test_api_claude.R |only tidyllm-0.3.0/tidyllm/tests/testthat/test_api_gemini.R |only tidyllm-0.3.0/tidyllm/tests/testthat/test_api_groq.R |only tidyllm-0.3.0/tidyllm/tests/testthat/test_api_mistral.R |only tidyllm-0.3.0/tidyllm/tests/testthat/test_api_ollama.R |only tidyllm-0.3.0/tidyllm/tests/testthat/test_api_openai.R |only tidyllm-0.3.0/tidyllm/tests/testthat/test_llm_message.R | 107 -- tidyllm-0.3.0/tidyllm/tests/testthat/test_message_retrieval.R | 194 ++- tidyllm-0.3.0/tidyllm/tests/testthat/test_pdf_page_batch.R | 10 tidyllm-0.3.0/tidyllm/vignettes/tidyllm.Rmd | 258 +++- 123 files changed, 2115 insertions(+), 1531 deletions(-)
Title: Create 'shiny' Applications for Cox Proportional Hazards Models
Description: Takes one or more fitted Cox proportional hazards models and writes
a 'shiny' application to a directory specified by the user. The 'shiny'
application displays predicted survival curves based on user input, and
contains none of the original data used to create the Cox model or models.
The goal is towards visualization and presentation of predicted survival
curves.
Author: Harrison Clement [aut, cre],
Subodh Selukar [aut],
Stanley Pounds [aut],
St Jude Children's Research Hospital [fnd]
Maintainer: Harrison Clement <harrisonclement16@gmail.com>
Diff between shinyCox versions 1.1.1 dated 2024-10-06 and 1.1.2 dated 2024-12-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/misc_functions.R | 4 ++-- R/shine_coxph.R | 4 ++-- R/shinybuilder.R | 4 ++-- 6 files changed, 18 insertions(+), 14 deletions(-)
Title: Comparing and Visualizing Differences Between Surveys
Description: Easily analyze and visualize differences between samples (e.g., benchmark comparisons, nonresponse comparisons in surveys) on three levels. The comparisons can be univariate, bivariate or multivariate. On univariate level the variables of interest of a survey and a comparison survey (i.e. benchmark) are compared, by calculating one of several difference measures (e.g., relative difference in mean), and an average difference between the surveys. On bivariate level a function can calculate significant differences in correlations for the surveys. And on multivariate levels a function can calculate significant differences in model coefficients between the surveys of comparison. All of those differences can be easily plotted and outputted as a table. For more detailed information on the methods and example use see Rohr, B., Silber, H., & Felderer, B. (2024). Comparing the Accuracy of Univariate, Bivariate, and Multivariate Estimates across Probability and Nonprobability Surveys with Po [...truncated...]
Author: Bjoern Rohr [aut, cre, cph],
Barbara Felderer [aut]
Maintainer: Bjoern Rohr <bjoern.rohr@gesis.org>
Diff between sampcompR versions 0.2.4 dated 2024-11-10 and 0.2.6 dated 2024-12-08
DESCRIPTION | 14 MD5 | 67 + NEWS.md | 12 R/Bivdiff.R | 19 R/Bivdiff_Plot.R | 11 R/Data_equalizer_Function.R | 2 R/Multidiff.R | 24 R/Multidiff_Plot.R | 20 R/Output_Tables.R | 125 ++- R/Unidiff.R | 860 +++++++++++++------------ R/Unidiff_Plot.R | 9 R/card.R |only README.md | 372 +++++----- data |only man/R_indicator.Rd | 4 man/biv_compare.Rd | 8 man/biv_compare_table.Rd | 8 man/biv_per_variable.Rd | 7 man/card.Rd |only man/dataequalizer.Rd | 2 man/figures/README-adding_logit_models-1.png |binary man/figures/README-bivariate_comparison-1.png |binary man/figures/README-ols_models-1.png |binary man/figures/README-univariate_comparison-1.png |binary man/multi_compare.Rd | 12 man/multi_compare_merge.Rd | 10 man/multi_compare_table.Rd | 12 man/multi_per_variable.Rd | 11 man/plot_biv_compare.Rd | 8 man/plot_multi_compare.Rd | 12 man/plot_uni_compare.Rd | 4 man/uni_compare.Rd | 25 man/uni_compare_table.Rd | 8 tests/testthat/helper_biv_compare.R | 22 tests/testthat/helper_multi_compare2.R | 28 tests/testthat/helper_uni_compare.R | 28 36 files changed, 912 insertions(+), 832 deletions(-)
Title: Less Code, More Results
Description: Each function replaces multiple standard R functions. For example, two function calls, Read() and CountAll(), generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for summary statistics via pivot tables, a comprehensive regression analysis, ANOVA and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, time series with aggregation and forecasting, color themes, and Trellis graphics. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, generation and rendering of regression instructions for interpretative output, and interactive visualizations.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.3.8 dated 2024-10-07 and 4.3.9 dated 2024-12-08
DESCRIPTION | 8 - MD5 | 35 +++--- NEWS.md | 39 ++++++- R/Plot.R | 285 +++++++++++++++++++++++++++++++++------------------- R/STL.R | 128 ++++++++++++++--------- R/Write.R | 6 - R/plt.forecast.R |only R/plt.main.R | 144 ++++++++------------------ R/plt.txt.R | 14 +- R/zzz.R | 95 ++++++++++------- inst/doc/intro.R | 3 inst/doc/intro.Rmd | 19 ++- inst/doc/intro.html | 261 ++++++++++++++++++++++++++--------------------- man/Plot.Rd | 45 ++++---- man/STL.Rd | 11 +- man/pivot.Rd | 2 man/reshape_long.Rd | 2 man/reshape_wide.Rd | 2 vignettes/intro.Rmd | 19 ++- 19 files changed, 643 insertions(+), 475 deletions(-)
Title: Model Consistent Lasso Estimation Through the Bootstrap
Description: Implements the bolasso algorithm for consistent variable selection
and estimation accuracy. Includes support for many parallel backends via the
future package. For details see: Bach (2008),
'Bolasso: model consistent Lasso estimation through the bootstrap',
<doi:10.48550/arXiv.0804.1302>.
Author: Daniel Molitor [aut, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between bolasso versions 0.2.0 dated 2022-05-10 and 0.3.0 dated 2024-12-08
bolasso-0.2.0/bolasso/build |only bolasso-0.2.0/bolasso/man/selected_vars.Rd |only bolasso-0.3.0/bolasso/DESCRIPTION | 20 bolasso-0.3.0/bolasso/LICENSE | 4 bolasso-0.3.0/bolasso/MD5 | 57 bolasso-0.3.0/bolasso/NAMESPACE | 13 bolasso-0.3.0/bolasso/NEWS.md | 63 bolasso-0.3.0/bolasso/R/bolasso.R | 121 + bolasso-0.3.0/bolasso/R/bolasso_fast.R |only bolasso-0.3.0/bolasso/R/data.R |only bolasso-0.3.0/bolasso/R/methods.R | 79 - bolasso-0.3.0/bolasso/R/plot.R |only bolasso-0.3.0/bolasso/R/tidy.R | 36 bolasso-0.3.0/bolasso/R/utils.R | 314 +++- bolasso-0.3.0/bolasso/README.md | 692 +++++++--- bolasso-0.3.0/bolasso/data |only bolasso-0.3.0/bolasso/inst/REFERENCES.bib | 28 bolasso-0.3.0/bolasso/man/bolasso.Rd | 223 +-- bolasso-0.3.0/bolasso/man/figures/README-unnamed-chunk-10-1.png |only bolasso-0.3.0/bolasso/man/figures/README-unnamed-chunk-11-1.png |only bolasso-0.3.0/bolasso/man/figures/README-unnamed-chunk-12-1.png |only bolasso-0.3.0/bolasso/man/figures/README-unnamed-chunk-13-1.png |only bolasso-0.3.0/bolasso/man/figures/README-unnamed-chunk-16-1.png |only bolasso-0.3.0/bolasso/man/figures/README-unnamed-chunk-7-1.png |binary bolasso-0.3.0/bolasso/man/plot.bolasso.Rd |only bolasso-0.3.0/bolasso/man/plot_selected_variables.Rd |only bolasso-0.3.0/bolasso/man/plot_selection_thresholds.Rd |only bolasso-0.3.0/bolasso/man/reexports.Rd |only bolasso-0.3.0/bolasso/man/selected_variables.Rd |only bolasso-0.3.0/bolasso/man/selection_thresholds.Rd |only bolasso-0.3.0/bolasso/man/tidy.bolasso.Rd |only bolasso-0.3.0/bolasso/man/transactions.Rd |only bolasso-0.3.0/bolasso/tests/testthat.R | 8 bolasso-0.3.0/bolasso/tests/testthat/test-main.R | 50 bolasso-0.3.0/bolasso/tests/testthat/test-model-matrix.R | 66 bolasso-0.3.0/bolasso/tests/testthat/test-tidy.R | 24 bolasso-0.3.0/bolasso/tests/testthat/test-translate.R | 102 - bolasso-0.3.0/bolasso/tests/testthat/test-utils.R | 80 - bolasso-0.3.0/bolasso/tests/testthat/test-validation.R | 47 39 files changed, 1342 insertions(+), 685 deletions(-)
Title: 'pinp' is not 'PNAS'
Description: A 'PNAS'-alike style for 'rmarkdown', derived from the 'Proceedings of the
National Academy of Sciences of the United States of America' ('PNAS') 'LaTeX' style,
and adapted for use with 'markdown' and 'pandoc'.
Author: Dirk Eddelbuettel [aut, cre] ,
James Joseph Balamuta [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between pinp versions 0.0.10 dated 2020-10-01 and 0.0.11 dated 2024-12-08
ChangeLog | 50 ++++++++++++++++++++ DESCRIPTION | 27 ++++++---- MD5 | 22 ++++---- R/pinp.R | 4 - README.md | 12 ++-- build/vignette.rds |binary inst/NEWS.Rd | 8 +++ inst/doc/pinp.Rmd | 6 +- inst/doc/pinp.pdf |binary inst/rmarkdown/templates/pdf/resources/template.tex | 2 man/pinp.Rd | 4 - vignettes/pinp.Rmd | 6 +- 12 files changed, 101 insertions(+), 40 deletions(-)
Title: Transforms Institutional Data into Text Files for IPEDS
Automated Import/Upload
Description: Starting from user-supplied institutional data, these scripts
transform, aggregate, and reshape the information to produce
key-value pair data files that are able to be uploaded to IPEDS (Integrated Postsecondary Education Data System)
through their submission portal <https://surveys.nces.ed.gov/ipeds/>. Starting data specifications can be found in the vignettes.
Final files are saved locally to a location of the user's choice.
User-friendly readable files can also be produced for purposes of data review and validation.
Author: Alison Lanski [aut, cre],
Shiloh Fling [aut]
Maintainer: Alison Lanski <alanski@nd.edu>
Diff between IPEDSuploadables versions 2.9.0 dated 2024-08-29 and 2.10.0 dated 2024-12-08
DESCRIPTION | 6 MD5 | 247 +++++++++++++-------------- NAMESPACE | 1 NEWS.md | 9 R/create_dummy_data_ef1.R | 2 R/make_com_part_A.R | 2 R/make_com_part_B.R | 2 R/make_com_part_C.R | 2 R/make_com_part_D.R | 2 R/make_com_part_E.R | 2 R/make_e1d_part_A.R | 2 R/make_e1d_part_B.R | 2 R/make_e1d_part_C.R | 2 R/make_e1d_part_D.R | 2 R/make_e1d_part_E.R | 2 R/make_e1d_part_F.R | 2 R/make_ef1_part_A.R | 2 R/make_ef1_part_B.R | 2 R/make_ef1_part_C.R | 2 R/make_ef1_part_D.R | 2 R/make_ef1_part_E.R | 2 R/make_ef1_part_F.R | 2 R/make_ef1_part_G.R | 2 R/make_ef1_part_H.R | 2 R/make_gr200.R | 2 R/make_gr_part_B.R | 2 R/make_gr_part_C.R | 2 R/make_gr_part_E.R | 2 R/make_hr_part_A1.R | 2 R/make_hr_part_A2.R | 2 R/make_hr_part_B1.R | 2 R/make_hr_part_B2.R | 2 R/make_hr_part_B3.R | 2 R/make_hr_part_D1.R | 2 R/make_hr_part_D2.R | 2 R/make_hr_part_D3.R | 2 R/make_hr_part_D4.R | 2 R/make_hr_part_G1.R | 2 R/make_hr_part_G2.R | 2 R/make_hr_part_H1.R | 2 R/make_hr_part_H2.R | 2 R/make_om_part_A.R | 2 R/make_om_part_B.R | 2 R/make_om_part_C.R | 2 R/make_om_part_D.R | 2 R/prep_com_data_frame.R | 2 R/prep_ef1_data_frame.R | 2 R/prep_hr_data_frame.R | 2 R/prep_om_awards.R | 2 R/prep_om_data_frame.R | 12 + README.md | 23 +- data/specs_OM.rda |binary inst/WORDLIST |only inst/doc/howto_overall_ipedsuploadables.Rmd | 4 inst/doc/howto_overall_ipedsuploadables.html | 13 - inst/doc/setup_for_12monthenrollment.R | 6 inst/doc/setup_for_12monthenrollment.Rmd | 4 inst/doc/setup_for_completions.R | 12 - inst/doc/setup_for_completions.Rmd | 10 - inst/doc/setup_for_fallenrollment.R | 6 inst/doc/setup_for_fallenrollment.Rmd | 4 inst/doc/setup_for_gr.R | 6 inst/doc/setup_for_gr.Rmd | 4 inst/doc/setup_for_gr200.R | 6 inst/doc/setup_for_gr200.Rmd | 4 inst/doc/setup_for_hr.R | 6 inst/doc/setup_for_hr.Rmd | 4 inst/doc/setup_for_om.R | 6 inst/doc/setup_for_om.Rmd | 4 inst/doc/setup_for_om.html | 2 man/create_dummy_data_ef1.Rd | 2 man/make_com_part_A.Rd | 2 man/make_com_part_B.Rd | 2 man/make_com_part_C.Rd | 2 man/make_com_part_D.Rd | 2 man/make_com_part_E.Rd | 2 man/make_e1d_part_A.Rd | 2 man/make_e1d_part_B.Rd | 2 man/make_e1d_part_C.Rd | 2 man/make_e1d_part_D.Rd | 2 man/make_e1d_part_E.Rd | 2 man/make_e1d_part_F.Rd | 2 man/make_ef1_part_A.Rd | 2 man/make_ef1_part_B.Rd | 2 man/make_ef1_part_C.Rd | 2 man/make_ef1_part_D.Rd | 2 man/make_ef1_part_E.Rd | 2 man/make_ef1_part_F.Rd | 2 man/make_ef1_part_G.Rd | 2 man/make_ef1_part_H.Rd | 2 man/make_gr200.Rd | 2 man/make_gr_part_B.Rd | 2 man/make_gr_part_C.Rd | 2 man/make_gr_part_E.Rd | 2 man/make_hr_part_A1.Rd | 2 man/make_hr_part_A2.Rd | 2 man/make_hr_part_B1.Rd | 2 man/make_hr_part_B2.Rd | 2 man/make_hr_part_B3.Rd | 2 man/make_hr_part_D1.Rd | 2 man/make_hr_part_D2.Rd | 2 man/make_hr_part_D3.Rd | 2 man/make_hr_part_D4.Rd | 2 man/make_hr_part_G1.Rd | 2 man/make_hr_part_G2.Rd | 2 man/make_hr_part_H1.Rd | 2 man/make_hr_part_H2.Rd | 2 man/make_om_part_A.Rd | 2 man/make_om_part_B.Rd | 2 man/make_om_part_C.Rd | 2 man/make_om_part_D.Rd | 2 man/prep_com_data_frame.Rd | 2 man/prep_ef1_data_frame.Rd | 2 man/prep_hr_data_frame.Rd | 2 man/prep_om_awards.Rd | 2 man/prep_om_data_frame.Rd | 2 tests/testthat/test-prep-scripts.R | 7 vignettes/howto_overall_ipedsuploadables.Rmd | 4 vignettes/setup_for_12monthenrollment.Rmd | 4 vignettes/setup_for_completions.Rmd | 10 - vignettes/setup_for_fallenrollment.Rmd | 4 vignettes/setup_for_gr.Rmd | 4 vignettes/setup_for_gr200.Rmd | 4 vignettes/setup_for_hr.Rmd | 4 vignettes/setup_for_om.Rmd | 4 125 files changed, 316 insertions(+), 310 deletions(-)
More information about IPEDSuploadables at CRAN
Permanent link
Title: Sparse Matrix C++ Classes Including Sparse Cholesky LDL
Decomposition of Symmetric Matrices
Description: 'C++' classes for sparse matrix methods including implementation of sparse LDL decomposition of symmetric matrices and solvers described by Timothy A. Davis (2016)
<https://fossies.org/linux/SuiteSparse/LDL/Doc/ldl_userguide.pdf>. Provides a set of C++ classes for basic sparse
matrix specification and linear algebra, and a class to implement sparse LDL decomposition and solvers. See <https://github.com/samuel-watson/SparseChol>
for details.
Author: Sam Watson [aut, cre],
Timothy A. Davis [aut, ctb]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between SparseChol versions 0.3.1 dated 2024-01-08 and 0.3.2 dated 2024-12-08
DESCRIPTION | 8 ++-- MD5 | 15 ++++---- README.md |only build/partial.rdb |binary inst/include/sparsematrix.h | 78 +++++++++++++++++++++++++++--------------- man/LDL_Cholesky.Rd | 36 +++++++++---------- man/LL_Cholesky.Rd | 36 +++++++++---------- man/dense_to_sparse.Rd | 48 +++++++++++++------------- man/sparse_chol_crs.Rd | 80 ++++++++++++++++++++++---------------------- 9 files changed, 162 insertions(+), 139 deletions(-)
Title: Inference for Panel Partially Observed Markov Processes
Description: Data analysis based on panel partially-observed Markov process (PanelPOMP) models. To implement such models, simulate them and fit them to panel data, 'panelPomp' extends some of the facilities provided for time series data by the 'pomp' package. Implemented methods include filtering (panel particle filtering) and maximum likelihood estimation (Panel Iterated Filtering) as proposed in Breto, Ionides and King (2020) "Panel Data Analysis via Mechanistic Models" <doi:10.1080/01621459.2019.1604367>.
Author: Carles Breto [aut] ,
Edward L. Ionides [aut] ,
Aaron A. King [aut] ,
Jesse Wheeler [aut, cre] ,
Aaron Abkemeier [ctb]
Maintainer: Jesse Wheeler <jeswheel@umich.edu>
Diff between panelPomp versions 1.4 dated 2024-09-12 and 1.5.0.0 dated 2024-12-08
DESCRIPTION | 18 +++-- MD5 | 51 ++++++++------ NAMESPACE | 1 R/panelMeasles.R |only R/panelPomp.R | 4 - R/panelPomp_methods.R | 147 ++++++++++++++++++------------------------ R/sysdata.rda |only R/twentycities.R |only R/uk_measles.R |only README.md | 7 -- build/partial.rdb |binary build/vignette.rds |binary data |only inst/CITATION | 3 inst/NEWS | 23 ++++++ inst/NEWS.Rd | 19 +++++ inst/doc/getting-started.html | 2 man/contacts.Rd | 1 man/macros/cite.Rd | 4 + man/panelGompertz.Rd | 1 man/panelMeasles.Rd |only man/panelPomp-package.Rd | 5 + man/panelPomp.Rd | 4 - man/panelPomp_methods.Rd | 15 ++-- man/panelRandomWalk.Rd | 3 man/twentycities.Rd |only man/uk_measles.Rd |only tests/panelMeasles.R |only tests/panelMeasles.Rout.save |only tests/panelPomp.R | 7 +- tests/panelPomp.Rout.save | 7 +- 31 files changed, 188 insertions(+), 134 deletions(-)
Title: Estimate Orientation of an Inertial Measurement Unit
Description: Estimate the orientation of an inertial measurement unit
(IMU) with a 3-axis accelerometer and a 3-axis gyroscope using a
complementary filter. 'imuf' takes an IMU's accelerometer and gyroscope
readings, time duration, its initial orientation, and a gain factor as
inputs, and returns an estimate of the IMU's final orientation.
Author: Felix Chan [aut, cre, cph]
Maintainer: Felix Chan <chanfelix@gmail.com>
Diff between imuf versions 0.3.0 dated 2024-11-06 and 0.4.0 dated 2024-12-08
DESCRIPTION | 11 +++++--- MD5 | 27 +++++++++++++------- NAMESPACE | 11 ++++---- NEWS.md | 6 ++++ R/RcppExports.R | 28 ++++++++++++++++++++- R/walking_shin_1.R |only README.md | 8 ++++++ build |only data |only inst |only man/compUpdate.Rd | 60 +++++++++++++++++++++++---------------------- man/rotV.Rd |only man/walking_shin_1.Rd |only src/RcppExports.cpp | 13 +++++++++ src/imuf.cpp | 38 +++++++++++++++++++++++++++- tests/testthat/test-imuf.R | 7 +++++ vignettes |only 17 files changed, 160 insertions(+), 49 deletions(-)
Title: Mediation, Moderation and Moderated-Mediation After Model
Fitting
Description: Computes indirect effects, conditional effects, and conditional
indirect effects in a structural equation model or path model after model
fitting, with no need to define any user parameters or label any paths in
the model syntax, using the approach presented in Cheung and Cheung
(2023) <doi:10.3758/s13428-023-02224-z>. Can also form bootstrap
confidence intervals by doing bootstrapping only once and reusing the
bootstrap estimates in all subsequent computations. Supports bootstrap
confidence intervals for standardized (partially or completely) indirect
effects, conditional effects, and conditional indirect effects as described
in Cheung (2009) <doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui,
and Vong (2022) <doi:10.1037/hea0001188>. Model fitting can be done by
structural equation modeling using lavaan() or regression using lm().
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome versions 0.2.4 dated 2024-10-04 and 0.2.5 dated 2024-12-08
DESCRIPTION | 6 MD5 | 84 +-- NAMESPACE | 1 NEWS.md | 61 ++ R/boot2est_lavaan.R | 53 + R/boot2est_lm.R | 5 R/cond_indirect.R | 26 R/helpers.R |only R/merge_mod_levels.R | 8 R/print_cond_indirect_effect.R | 545 +++++++++++++++----- R/print_indirect_list.R | 5 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/do_boot.Rmd | 2 inst/doc/do_boot.html | 4 inst/doc/do_mc.Rmd | 2 inst/doc/do_mc.html | 4 inst/doc/do_mc_lavaan_mi.Rmd | 2 inst/doc/do_mc_lavaan_mi.html | 4 inst/doc/manymome.Rmd | 2 inst/doc/manymome.html | 4 inst/doc/med_lav.Rmd | 2 inst/doc/med_lav.html | 4 inst/doc/med_lm.Rmd | 2 inst/doc/med_lm.html | 4 inst/doc/mod_levels.html | 4 inst/doc/mome_lm.Rmd | 2 inst/doc/mome_lm.html | 4 inst/extdata/mi_test_data.RData |binary man/cond_indirect.Rd | 5 man/indirect_effects_from_list.Rd | 5 man/print.cond_indirect_effects.Rd | 69 ++ tests/testthat/test_cond_indirect_effects_lm_kway.R | 2 tests/testthat/test_cond_indirect_effects_to_df.R |only tests/testthat/test_merge_mod_levels_one_level.R |only tests/testthat/test_one_y.R |only vignettes/articles/med_mg.Rmd | 4 vignettes/do_boot.Rmd | 2 vignettes/do_mc.Rmd | 2 vignettes/do_mc_lavaan_mi.Rmd | 2 vignettes/manymome.Rmd | 2 vignettes/med_lav.Rmd | 2 vignettes/med_lm.Rmd | 2 vignettes/mome_lm.Rmd | 2 45 files changed, 722 insertions(+), 219 deletions(-)
Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl],
Paul Pearson [ctb],
Daniel Muellner [ctb],
Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>
Diff between MapperAlgo versions 1.0 dated 2024-09-18 and 1.0.1 dated 2024-12-08
MapperAlgo-1.0.1/MapperAlgo/DESCRIPTION | 11 MapperAlgo-1.0.1/MapperAlgo/MD5 | 29 + MapperAlgo-1.0.1/MapperAlgo/NAMESPACE | 7 MapperAlgo-1.0.1/MapperAlgo/R/Cluster.R |only MapperAlgo-1.0.1/MapperAlgo/R/ConvertLevelsets.R |only MapperAlgo-1.0.1/MapperAlgo/R/Cover.R |only MapperAlgo-1.0.1/MapperAlgo/R/MapperAlgo.R | 174 ---------- MapperAlgo-1.0.1/MapperAlgo/R/SimplicialComplex.R |only MapperAlgo-1.0.1/MapperAlgo/README.md | 54 +++ MapperAlgo-1.0.1/MapperAlgo/man/MapperAlgo.Rd | 94 +---- MapperAlgo-1.0.1/MapperAlgo/man/cluster_cutoff_at_first_empty_bin.Rd | 2 MapperAlgo-1.0.1/MapperAlgo/man/cover_points.Rd | 2 MapperAlgo-1.0.1/MapperAlgo/man/figures |only MapperAlgo-1.0.1/MapperAlgo/man/find_best_k_for_kmeans.Rd |only MapperAlgo-1.0.1/MapperAlgo/man/perform_clustering.Rd | 10 MapperAlgo-1.0.1/MapperAlgo/man/simplcial_complex.Rd |only MapperAlgo-1.0.1/MapperAlgo/man/to_lsfi.Rd |only MapperAlgo-1.0.1/MapperAlgo/man/to_lsmi.Rd |only MapperAlgo-1.0/MapperAlgo/man/lsfi_from_lsmi.Rd |only MapperAlgo-1.0/MapperAlgo/man/lsmi_from_lsfi.Rd |only 20 files changed, 138 insertions(+), 245 deletions(-)
Title: Make Dealing with Dates a Little Easier
Description: Functions to work with date-times and time-spans: fast and
user friendly parsing of date-time data, extraction and updating of
components of a date-time (years, months, days, hours, minutes, and
seconds), algebraic manipulation on date-time and time-span objects.
The 'lubridate' package has a consistent and memorable syntax that
makes working with dates easy and fun.
Author: Vitalie Spinu [aut, cre],
Garrett Grolemund [aut],
Hadley Wickham [aut],
Davis Vaughan [ctb],
Ian Lyttle [ctb],
Imanuel Costigan [ctb],
Jason Law [ctb],
Doug Mitarotonda [ctb],
Joseph Larmarange [ctb],
Jonathan Boiser [ctb],
Chel Hee Lee [ctb]
Maintainer: Vitalie Spinu <spinuvit@gmail.com>
Diff between lubridate versions 1.9.3 dated 2023-09-27 and 1.9.4 dated 2024-12-08
DESCRIPTION | 10 MD5 | 67 ++-- NEWS.md | 37 +- R/Dates.r | 2 R/POSIXt.r | 2 R/accessors-date.R | 2 R/durations.r | 2 R/format_ISO8601.r | 10 R/intervals.r | 4 R/ops-m+.r | 2 R/periods.r | 2 R/pretty.r | 6 R/tzdir.R | 8 README.md | 66 ++-- build/vignette.rds |binary inst/WORDLIST |only inst/doc/lubridate.Rmd | 4 inst/doc/lubridate.html | 465 +++++++++++++++++++--------------- man/DateTimeUpdate.Rd | 2 man/Duration-class.Rd | 2 man/Period-class.Rd | 2 man/date.Rd | 2 man/date_utils.Rd | 2 man/force_tz.Rd | 2 man/format_ISO8601.Rd | 10 man/format_ISO8601_precision_check.Rd | 6 man/interval.Rd | 4 man/mplus.Rd | 2 man/posix_utils.Rd | 2 man/pretty_dates.Rd | 6 tests/testthat/_snaps/vctrs.md | 120 +++++--- tests/testthat/test-format_ISO8601.R | 16 - tests/testthat/test-parsers.R | 4 tests/testthat/test-periods.R | 2 vignettes/lubridate.Rmd | 4 35 files changed, 485 insertions(+), 392 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.1.3 dated 2024-11-21 and 1.1.3-1 dated 2024-12-08
DESCRIPTION | 9 +- MD5 | 83 +++++++++++++-------------- NEWS.md | 27 ++++++++ R/Driver.R | 19 +++++- R/cpp11.R | 8 +- R/dbConnect__duckdb_driver.R | 4 - R/dbSendQuery__duckdb_connection_character.R | 21 ++++++ R/rethrow-gen.R | 8 +- R/zzz.R | 2 cleanup | 6 + inst/include/cpp11.hpp | 4 - inst/include/cpp11/R.hpp | 7 +- inst/include/cpp11/altrep.hpp | 46 +------------- inst/include/cpp11/as.hpp | 4 - inst/include/cpp11/attribute_proxy.hpp | 4 - inst/include/cpp11/data_frame.hpp | 4 - inst/include/cpp11/declarations.hpp | 15 +--- inst/include/cpp11/doubles.hpp | 6 - inst/include/cpp11/environment.hpp | 18 ----- inst/include/cpp11/external_pointer.hpp | 7 +- inst/include/cpp11/function.hpp | 4 - inst/include/cpp11/integers.hpp | 6 - inst/include/cpp11/list.hpp | 6 - inst/include/cpp11/list_of.hpp | 4 - inst/include/cpp11/logicals.hpp | 6 - inst/include/cpp11/matrix.hpp | 4 - inst/include/cpp11/named_arg.hpp | 4 - inst/include/cpp11/protect.hpp | 21 +----- inst/include/cpp11/r_bool.hpp | 4 - inst/include/cpp11/r_string.hpp | 4 - inst/include/cpp11/r_vector.hpp | 13 ++-- inst/include/cpp11/raws.hpp | 6 - inst/include/cpp11/sexp.hpp | 4 - inst/include/cpp11/strings.hpp | 6 - man/duckdb.Rd | 15 +++- src/cpp11.cpp | 16 ++--- src/database.cpp | 14 +++- src/duckdb.tar.xz |binary src/include/rapi.hpp | 6 + src/register.cpp | 42 +++++++++++++ src/statement.cpp | 28 ++++++--- src/types.cpp | 5 - tests/testthat/test-scan.R |only 43 files changed, 298 insertions(+), 222 deletions(-)
Title: Trajectory Miner: a Sequence Analysis Toolkit
Description: Set of sequence analysis tools for manipulating, describing and rendering categorical sequences, and more generally mining sequence data in the field of social sciences. Although this sequence analysis package is primarily intended for state or event sequences that describe time use or life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and functions for extracting the most frequent event subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph] ,
Nicolas Mueller [aut],
Reto Buergin [aut] ,
Pierre-Alexandre Fonta [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 2.2-10 dated 2024-05-21 and 2.2-11 dated 2024-12-08
TraMineR-2.2-10/TraMineR/data/ex1.rda |only TraMineR-2.2-10/TraMineR/data/ex1.txt.gz |only TraMineR-2.2-10/TraMineR/data/ex2.rda |only TraMineR-2.2-10/TraMineR/data/famform.rda |only TraMineR-2.2-11/TraMineR/DESCRIPTION | 8 TraMineR-2.2-11/TraMineR/MD5 | 28 TraMineR-2.2-11/TraMineR/NEWS | 17 TraMineR-2.2-11/TraMineR/R/dissrep.R | 11 TraMineR-2.2-11/TraMineR/R/seqecreate.R | 345 +++++----- TraMineR-2.2-11/TraMineR/data/ex1.R |only TraMineR-2.2-11/TraMineR/data/ex1.txt |only TraMineR-2.2-11/TraMineR/data/ex2.R |only TraMineR-2.2-11/TraMineR/data/famform.R |only TraMineR-2.2-11/TraMineR/inst/NEWS.Rd | 24 TraMineR-2.2-11/TraMineR/inst/doc/TraMineR-state-sequence.pdf |binary TraMineR-2.2-11/TraMineR/man/TraMineR-package.Rd | 2 TraMineR-2.2-11/TraMineR/man/seqplot.Rd | 2 TraMineR-2.2-11/TraMineR/man/seqstatl.Rd | 2 TraMineR-2.2-11/TraMineR/src/tmrsequence.cpp | 3 19 files changed, 255 insertions(+), 187 deletions(-)
Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'DDIwR', 'QCA' and 'venn'.
Interprets and translates, factorizes and negates SOP - Sum of Products
expressions, for both binary and multi-value crisp sets, and extracts
information (set names, set values) from those expressions. Other functions
perform various other checks if possibly numeric (even if all numbers reside
in a character vector) and coerce to numeric, or check if the numbers are
whole. It also offers, among many others, a highly versatile recoding
routine and some more flexible alternatives to the base functions 'with()'
and 'within()'.
SOP simplification functions in this package use related minimization from
package 'QCA', which is recommended to be installed despite not being listed
in the Imports field, due to circular dependency issues.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between admisc versions 0.36 dated 2024-09-11 and 0.37 dated 2024-12-08
DESCRIPTION | 15 - MD5 | 139 +++++++------ NAMESPACE | 4 R/asNumeric.R | 41 ++-- R/asSOP.R | 30 ++- R/betweenQuotes.R | 28 ++ R/brackets.R | 73 ++----- R/change.R | 54 ++--- R/checkMV.R | 52 ++--- R/checkSubset.R | 26 ++ R/checkValid.R | 33 ++- R/classify.R | 26 ++ R/coerceMode.R | 33 ++- R/combnk.R | 55 +++-- R/compute.R | 74 ++----- R/dimnames.R | 46 +++- R/equality.R | 42 ++-- R/expand.R | 87 ++------ R/export.R | 92 ++++++--- R/factorize.R | 141 ++------------ R/finvert.R | 41 +++- R/frelevel.R | 54 +++-- R/getInfo.R | 230 +++++++++++------------ R/getLevels.R | 107 ++++++---- R/getMatrix.R | 35 ++- R/getName.R | 65 ++---- R/hclr.R | 26 ++ R/inside.R | 44 ++-- R/intersection.R | 89 ++------ R/invert.R | 80 ++------ R/listRDA.R | 26 ++ R/mvSOP.R | 48 ++-- R/negate.R | 90 ++------- R/numdec.R | 72 +++---- R/objRDA.R | 26 ++ R/onLoad.R | 27 ++ R/overwrite.R | 27 ++ R/pad.R | 29 ++ R/permutations.R | 48 +++- R/possibleNumeric.R | 52 +++-- R/prettyString.R | 43 ++-- R/prettyTable.R | 38 ++- R/print.R | 99 ++------- R/recode.R | 124 +++--------- R/recreate.R | 83 ++------ R/reload.R | 29 ++ R/replaceText.R | 69 ++---- R/scan.clipboard.R | 29 ++ R/simplify.R | 60 ++---- R/sortExpressions.R | 58 ++++- R/stopError.R | 31 ++- R/string.R | 153 ++------------- R/tagged.R | 37 ++- R/tilde.R | 32 ++- R/translate.R | 201 +++----------------- R/tryCatchWEM.R | 29 ++ R/unicode.R | 33 ++- R/uninstall.R | 26 ++ R/unload.R | 30 ++- R/update.R |only R/using.R | 158 +++++---------- R/validateNames.R | 55 +++-- R/verify.R | 38 ++- R/wholeNumeric.R | 38 ++- R/write.clipboard.R | 27 ++ R/writePrimeimp.R | 38 ++- build/partial.rdb |binary inst/ChangeLog | 440 ++++++++++++++++++++++---------------------- man/admisc_package.Rd | 4 man/export.Rd | 14 - src/registerDynamicSymbol.c | 6 71 files changed, 2229 insertions(+), 2100 deletions(-)
Title: Regularized Joint Assignment Forest with Treatment Arm
Clustering
Description: Personalized assignment to one of many treatment arms via regularized and clustered joint assignment forests as described in Ladhania, Spiess, Ungar, and Wu (2023) <doi:10.48550/arXiv.2311.00577>. The algorithm pools information across treatment arms: it considers a regularized forest-based assignment algorithm based on greedy recursive partitioning that shrinks effect estimates across arms; and it incorporates a clustering scheme that combines treatment arms with consistently similar outcomes.
Author: Wenbo Wu [aut, cph] ,
Xinyi Zhang [aut, cre, cph] ,
Jann Spiess [aut, cph] ,
Rahul Ladhania [aut, cph]
Maintainer: Xinyi Zhang <zhang.xinyi@nyu.edu>
Diff between rjaf versions 0.1.0 dated 2024-11-11 and 0.1.1 dated 2024-12-08
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ R/RcppExports.R | 4 +-- R/rjaf.R | 34 +++++++++++++++--------------- man/rjaf.Rd | 18 ++++++++-------- src/RcppExports.cpp | 8 +++---- src/rjaf.cpp | 50 ++++++++++++++++++++++----------------------- tests/testthat/test-rjaf.R | 6 +---- 8 files changed, 69 insertions(+), 71 deletions(-)
Title: Measuring Ecosystem Multi-Functionality and Its Decomposition
Description: Provide simple functions to (i) compute a class of
multi-functionality measures for a single ecosystem for given
function weights, (ii) decompose gamma multi-functionality
for pairs of ecosystems and K ecosystems (K can be greater than 2)
into a within-ecosystem component (alpha multi-functionality)
and an among-ecosystem component (beta multi-functionality).
In each case, the correlation between functions can be corrected for.
Based on biodiversity and ecosystem function data, this software
also facilitates graphics for assessing biodiversity-ecosystem
functioning relationships across scales.
Author: Anne Chao [aut, cre],
Chun-Yu Liu [ctb],
KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between MF.beta4 versions 1.1.0 dated 2024-11-03 and 1.1.1 dated 2024-12-08
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS | 5 ++++- build/vignette.rds |binary inst/doc/Introduction.Rnw | 2 +- inst/doc/Introduction.pdf |binary man/MF.beta4-package.Rd | 10 ++++++---- vignettes/Introduction.Rnw | 2 +- vignettes/mypaper.pdf |binary 9 files changed, 23 insertions(+), 18 deletions(-)
Title: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Description: Methods for Cluster analysis. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Author: Martin Maechler [aut, cre] ,
Peter Rousseeuw [aut] ,
Anja Struyf [aut] ,
Mia Hubert [aut] ,
Kurt Hornik [trl, ctb] ,
<https://orcid.org/0000-0003-4198-9911>),
Matthias Studer [ctb],
Pierre Roudier [ctb],
Juan Gonzalez [ctb],
Kamil Kozlowski [ctb],
Er [...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cluster versions 2.1.6 dated 2023-12-01 and 2.1.7 dated 2024-12-08
cluster-2.1.6/cluster/src/daisy.f |only cluster-2.1.6/cluster/src/dysta.f |only cluster-2.1.7/cluster/DESCRIPTION | 9 +++-- cluster-2.1.7/cluster/MD5 | 40 ++++++++++++------------- cluster-2.1.7/cluster/R/agnes.q | 4 +- cluster-2.1.7/cluster/R/daisy.q | 2 - cluster-2.1.7/cluster/R/mona.q | 4 +- cluster-2.1.7/cluster/R/plotpart.q | 4 +- cluster-2.1.7/cluster/build/partial.rdb |binary cluster-2.1.7/cluster/inst/NEWS.Rd | 28 +++++++++++++++++ cluster-2.1.7/cluster/man/pam.Rd | 16 +++++++--- cluster-2.1.7/cluster/po/R-cluster.pot | 2 - cluster-2.1.7/cluster/src/clara.c | 5 +++ cluster-2.1.7/cluster/src/cluster.h | 24 ++++----------- cluster-2.1.7/cluster/src/daisy.c |only cluster-2.1.7/cluster/src/dysta.c |only cluster-2.1.7/cluster/src/fanny.c | 24 +++++++-------- cluster-2.1.7/cluster/src/init.c | 18 +++-------- cluster-2.1.7/cluster/src/mona.c | 2 - cluster-2.1.7/cluster/src/pam.c | 3 - cluster-2.1.7/cluster/src/twins.c | 8 +---- cluster-2.1.7/cluster/tests/fanny-ex.R | 14 +++++++- cluster-2.1.7/cluster/tests/fanny-ex.Rout.save | 24 ++++++++++----- 23 files changed, 136 insertions(+), 95 deletions(-)
Title: Quantitative Text Kit
Description: Support package for the textbook "An Introduction to
Quantitative Text Analysis for Linguists: Reproducible Research Using
R" (Francom, 2024) <doi:10.4324/9781003393764>. Includes functions to
acquire, clean, and analyze text data as well as functions to document
and share the results of text analysis. The package is designed to be
used in conjunction with the book, but can also be used as a standalone
package for text analysis.
Author: Jerid Francom [aut, cre, cph]
Maintainer: Jerid Francom <francojc@wfu.edu>
Diff between qtkit versions 1.0.0 dated 2024-08-17 and 1.1.0 dated 2024-12-07
DESCRIPTION | 13 - MD5 | 119 +++++++++----- NAMESPACE | 15 - NEWS.md | 35 +++- R/add_pkg_to_bib.R | 33 ++-- R/calc_assoc_metrics.R | 106 ++++++++++--- R/calc_disp.R | 111 +++++++++++-- R/calc_normalized_entropy.R |only R/calc_type_metrics.R | 209 ++++++++++++++------------ R/confirm_permission.R | 20 +- R/create_data_dictionary.R | 23 +- R/create_data_origin.R | 111 +++++++------ R/curate_enntt_data.R |only R/curate_swda_data.R |only R/find_outliers.R | 176 ++++++++++++--------- R/get_archive_data.R | 110 ++++++++++--- R/get_gutenberg_data.R | 180 ++++++++++------------ R/write_gg.R | 120 +++++++------- R/write_kbl.R | 81 ++++++---- R/write_obj.R | 88 ++++++---- README.md | 14 - build/vignette.rds |binary inst/doc/document.R | 87 ++++++++++ inst/doc/document.Rmd | 162 +++++++++++++++++++- inst/doc/document.html | 163 +++++++++++++++++++- inst/doc/reports.R | 92 +++++++++++ inst/doc/reports.Rmd | 186 ++++++++++++++++++++++- inst/doc/reports.html | 174 ++++++++++++++++++++- inst/extdata/bigrams.R | 10 - inst/extdata/simul_enntt |only inst/extdata/simul_swda |only inst/extdata/tokenized.R | 19 +- inst/extdata/types_data.rds |binary man/add_pkg_to_bib.Rd | 27 ++- man/calc_df.Rd |only man/calc_dp.Rd |only man/calc_idf.Rd |only man/calc_normalized_entropy.Rd |only man/calc_orf.Rd |only man/calc_rf.Rd | 62 ++++++- man/calc_type_metrics.Rd | 80 +++++---- man/calculate_bigram_probabilities.Rd |only man/calculate_metrics.Rd |only man/clean_filenames.Rd |only man/confirm_if_needed.Rd |only man/create_data_origin.Rd | 33 ++-- man/curate_enntt_data.Rd |only man/curate_enntt_file.Rd |only man/curate_swda_data.Rd |only man/curate_swda_file.Rd |only man/download_and_decompress.Rd |only man/extract_dat_attrs.Rd |only man/extract_speaker_info.Rd |only man/extract_utterances.Rd |only man/find_enntt_files.Rd |only man/find_outliers.Rd | 53 +++++- man/get_archive_data.Rd | 55 ++++-- man/get_gutenberg_data.Rd | 13 - man/process_speaker_info.Rd |only man/validate_dir_path.Rd |only man/validate_file_extension.Rd |only man/validate_inputs_cam.Rd |only man/validate_inputs_ctm.Rd |only man/write_gg.Rd | 31 ++- man/write_kbl.Rd | 46 +++-- man/write_obj.Rd | 27 ++- tests/testthat/test-calc_normalized_entropy.R |only tests/testthat/test-calc_type_metrics.R | 17 +- tests/testthat/test-create_data_dictionary.R | 11 - tests/testthat/test-curate_enntt_data.R |only tests/testthat/test-curate_swda_data.R |only tests/testthat/test-get_gutenberg_data.R | 10 - vignettes/document.Rmd | 162 +++++++++++++++++++- vignettes/reports.Rmd | 186 ++++++++++++++++++++++- 74 files changed, 2460 insertions(+), 810 deletions(-)
Title: Document a Universe of Packages
Description: Creates a data frame containing the metadata associated with
the documentation of a collection of R packages. It allows for linking
topic names to their corresponding documentation online. If you
maintain a universe meta-package, it helps create a comprehensive
reference for its website.
Author: Mauro Lepore [aut, cre, cph]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between dverse versions 0.1.0 dated 2024-11-22 and 0.2.0 dated 2024-12-07
DESCRIPTION | 8 ++++---- MD5 | 19 +++++++++++-------- NAMESPACE | 1 + NEWS.md | 16 +++++++--------- R/document_universe.R | 30 +++++++++++++++++++++++------- R/is_online.R |only R/s3_strip_class.R | 12 ++++++------ README.md | 6 +++--- inst/WORDLIST | 1 + man/is_online.Rd |only tests/testthat/test-document_universe.R | 21 ++++++++++++--------- tests/testthat/test-is_online.R |only 12 files changed, 68 insertions(+), 46 deletions(-)
Title: Friendly R Startup Configuration
Description: Adds support for R startup configuration via '.Renviron.d' and '.Rprofile.d' directories in addition to '.Renviron' and '.Rprofile' files. This makes it possible to keep private / secret environment variables separate from other environment variables. It also makes it easier to share specific startup settings by simply copying a file to a directory.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between startup versions 0.22.0 dated 2024-07-29 and 0.23.0 dated 2024-12-07
DESCRIPTION | 6 +- MD5 | 42 ++++++++------ NEWS.md | 34 +++++++++++ R/debug.R | 39 +++++++++++++ R/is_ark.R |only R/is_positron.R |only R/is_webr.R | 2 R/is_wine.R | 4 - R/options.R | 17 +++++ R/renviron_d.R | 14 +++- R/rprofile_d.R | 34 +++++++++-- R/startup.R | 126 +++++++++++++++++++++++++++----------------- R/sysinfo.R | 14 ++-- README.md | 33 ++++++++--- build/vignette.rds |binary inst/WORDLIST | 6 ++ inst/doc/startup-intro.html | 65 ++++++++++++++++++---- inst/doc/startup-intro.md | 33 ++++++++--- man/is_ark.Rd |only man/is_positron.Rd |only man/is_webr.Rd | 2 man/is_wine.Rd | 4 - man/startup.options.Rd | 17 +++++ vignettes/startup-intro.md | 33 ++++++++--- 24 files changed, 388 insertions(+), 137 deletions(-)
Title: Spatial Modeling of Infectious Disease with Reinfection
Description: Geographically Dependent Individual Level Models (GDILMs) within the Susceptible-Exposed-Infectious-Recovered-Susceptible (SEIRS) framework are applied to model infectious disease transmission, incorporating reinfection dynamics. This package employs a likelihood based Monte Carlo Expectation Conditional Maximization (MCECM) algorithm for estimating model parameters. It also provides tools for GDILM fitting, parameter estimation, AIC calculation on real pandemic data, and simulation studies customized to user-defined model settings.
Author: Amin Abed [aut, cre, cph] ,
Mahmoud Torabi [ths],
Zeinab Mashreghi [ths]
Maintainer: Amin Abed <abeda@myumanitoba.ca>
Diff between GDILM.SEIRS versions 0.0.1 dated 2024-12-05 and 0.0.2 dated 2024-12-07
DESCRIPTION | 10 +- MD5 | 14 ++-- R/GDILM_SEIRS_Par_Est.R | 84 ++++++++++++++++-------- R/GDILM_SEIRS_Sim_Par_Est.R | 89 +++++++++++++++++--------- man/GDILM_SEIRS_Par_Est.Rd | 7 +- man/GDILM_SEIRS_Sim_Par_Est.Rd | 7 +- tests/testthat/test-GDILM_SEIRS_Par_Est.R | 2 tests/testthat/test-GDILM_SEIRS_Sim_Par_Est.R | 2 8 files changed, 140 insertions(+), 75 deletions(-)
Title: An API Wrapper for 'DAWA' - 'The Danish Address Web API'
Description: Functions for interacting with all sections of
the official 'Danish Address Web API' (also known as 'DAWA')
<https://api.dataforsyningen.dk>. The development of this package is
completely independent from the government agency, Klimadatastyrelsen,
who maintains the API.
Author: Aleksander Bang-Larsen [aut, cre, cph]
,
Agency of Climate Data [ctb]
Maintainer: Aleksander Bang-Larsen <contact@aleksanderbl.dk>
Diff between dawaR versions 0.2.6 dated 2024-11-24 and 0.2.7 dated 2024-12-07
DESCRIPTION | 26 ++-- MD5 | 124 +++++++++++++-------- NEWS.md | 4 R/base_api.R | 31 ++++- R/get_data.R | 14 ++ R/get_map_data.R | 12 ++ R/status_check.R | 12 +- README.md | 2 inst/CITATION | 15 ++ inst/WORDLIST | 22 +++ inst/doc/dawaR.R | 6 - inst/doc/dawaR.Rmd | 6 - inst/doc/dawaR.html | 2 inst/doc/status.html | 8 - man/autocomplete.Rd | 4 man/dawa.Rd | 6 - man/get_data.Rd | 11 + man/get_map_data.Rd | 5 man/reverse.Rd | 4 man/status_check.Rd | 13 +- tests/fixtures |only tests/testthat/_snaps/afstemningsomraader.md | 14 +- tests/testthat/_snaps/autocomplete.md | 32 ++--- tests/testthat/_snaps/base_api.md | 4 tests/testthat/_snaps/get_data.md | 68 +++++------ tests/testthat/_snaps/get_map_data-kommuner.md | 2 tests/testthat/_snaps/get_map_data-politikredse.md | 58 ++++----- tests/testthat/_snaps/get_map_data-regioner.md | 18 +-- tests/testthat/_snaps/get_map_data-vote.md | 2 tests/testthat/_snaps/reverse.md | 19 ++- tests/testthat/_snaps/status_check.md | 8 - tests/testthat/helper-vcr.R |only tests/testthat/test-1-dawa-sections.R | 1 tests/testthat/test-3-get_map_data-sections.R | 1 tests/testthat/test-afstemningsomraader.R | 66 +++++++---- tests/testthat/test-autocomplete.R | 115 +++++++++++++++---- tests/testthat/test-base_api.R | 40 ++++-- tests/testthat/test-get_data.R | 39 +++++- tests/testthat/test-get_map_data-kommuner.R | 2 tests/testthat/test-get_map_data-politikredse.R | 4 tests/testthat/test-get_map_data-postnumre.R | 6 - tests/testthat/test-get_map_data-regioner.R | 4 tests/testthat/test-get_map_data-vote.R | 2 tests/testthat/test-get_map_data.R | 1 tests/testthat/test-reverse.R | 50 +++++--- tests/testthat/test-status_check.R | 2 vignettes/dawaR.Rmd | 6 - 47 files changed, 600 insertions(+), 291 deletions(-)
Title: Self-Validated Ensemble Models with Elastic Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM, Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using Elastic Net regression via 'glmnet' (Friedman et al. <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). \\Code for the whole model test was taken from the supplementary material of Karl (2024). Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 1.1.1 dated 2024-11-29 and 1.2.1 dated 2024-12-07
DESCRIPTION | 11 - MD5 | 30 ++-- NAMESPACE | 8 + NEWS | 5 R/SVEMnet-package.R | 1 R/globals.R | 2 R/predict.svem_lasso.R | 3 R/svem_significance_test.R | 23 ++- R/svem_significance_test_parallel.R |only inst/doc/SVEMnet_vignette.R | 2 inst/doc/SVEMnet_vignette.Rmd | 50 +++----- inst/doc/SVEMnet_vignette.html | 204 ++++++++++++++++----------------- man/SVEMnet-package.Rd | 1 man/svem_significance_test.Rd | 14 +- man/svem_significance_test_parallel.Rd |only vignettes/SVEMnet_vignette.Rmd | 50 +++----- vignettes/figures/whole_model_2.png |binary 17 files changed, 213 insertions(+), 191 deletions(-)
Title: The Cauchy-Cacoullos (Discrete Cauchy) Distribution
Description: Maximum likelihood estimation of the Cauchy-Cacoullos (discrete Cauchy) distribution. Probability mass, distribution and quantile function are also included. The reference paper is: Papadatos N. (2022). "The Characteristic Function of the Discrete Cauchy Distribution in Memory of T. Cacoullos". Journal of Statistical Theory Practice, 16(3): 47. <doi:10.1007/s42519-022-00268-6>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CCd versions 1.0 dated 2024-09-26 and 1.1 dated 2024-12-07
DESCRIPTION | 11 ++++++----- MD5 | 18 ++++++++++-------- NAMESPACE | 4 ++-- R/cc.mle.R | 4 ++-- R/cc.reg.R |only R/loc0.test.R | 2 +- man/CCd-package.Rd | 7 +++---- man/cc.mle.Rd | 20 ++++++++++++++------ man/cc.reg.Rd |only man/dcc.Rd | 5 ++--- man/loc0.test.Rd | 3 +-- 11 files changed, 41 insertions(+), 33 deletions(-)
Title: Miscellaneous, Analytic R Kernels
Description: Miscellaneous functions and wrappers for development in other
packages created, maintained by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre]
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>
Diff between mark versions 0.8.1 dated 2024-09-29 and 0.8.2 dated 2024-12-07
DESCRIPTION | 9 +- MD5 | 19 ++--- NAMESPACE | 1 NEWS.md | 8 ++ R/clipboard.R | 136 ++++++++++++++++++++++++++-------------- README.md | 2 man/clipboard.Rd | 7 +- tests/testthat/Rplots.pdf |only tests/testthat/test-clipboard.R | 68 +++++++++++++++----- tests/testthat/test-diff-time.R | 2 tests/testthat/test-strings.R | 1 11 files changed, 173 insertions(+), 80 deletions(-)
Title: Rewrite of gWidgets API for Simplified GUI Construction
Description: Re-implementation of the 'gWidgets' API. The API is defined in this
package. A second, toolkit-specific package is required to use it. At this point only 'gWidgets2tcltk' is viable.
Author: John Verzani [aut, cre]
Maintainer: John Verzani <jverzani@gmail.com>
Diff between gWidgets2 versions 1.0-9 dated 2022-01-10 and 1.0-10 dated 2024-12-07
DESCRIPTION | 11 +-- MD5 | 24 +++--- NAMESPACE | 8 ++ R/gWidgets2-package.R | 166 +++++++++++++++++++++++------------------------ R/icons.R | 13 +-- man/add.Rd | 2 man/gWidgets2-package.Rd | 6 - man/gedit.Rd | 2 man/gfile.Rd | 7 + man/gmenu.Rd | 2 man/gnotebook.Rd | 2 man/gtoolbar.Rd | 2 man/gwindow.Rd | 4 - 13 files changed, 128 insertions(+), 121 deletions(-)
Title: Categorical Landscape Simulation Facility
Description: Simulates categorical maps on actual geographical realms, starting from either empty landscapes or landscapes provided by the user (e.g. land use maps). Allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscapes in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion) and von Neumann neighbourhood (four cells, aka Rook case). Outputs are raster dataset exportable to any common GIS format.
Author: Dario Masante [aut, cre],
Lora Murphy [ctb]
Maintainer: Dario Masante <dario.masante@gmail.com>
Diff between landscapeR versions 1.3 dated 2024-11-01 and 1.3.1 dated 2024-12-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ inst/doc/landscapeR.Rmd | 9 +++------ inst/doc/landscapeR.html | 34 ++++++++++++++++------------------ vignettes/landscapeR.Rmd | 9 +++------ 6 files changed, 36 insertions(+), 39 deletions(-)
Title: Helper Functions for Creating Tutorials
Description: Helper functions for creating, editing, and testing tutorials
created with the 'learnr' package. Provides a simple method for allowing
students to download their answers to tutorial questions. For examples
of its use, see the 'r4ds.tutorials' package.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between tutorial.helpers versions 0.3.0 dated 2024-06-26 and 0.3.1 dated 2024-12-07
DESCRIPTION | 8 MD5 | 44 ++-- NEWS.md | 6 README.md | 11 - build/vignette.rds |binary inst/doc/addins.R | 45 ++++ inst/doc/addins.Rmd | 17 - inst/doc/addins.html | 15 - inst/doc/books.Rmd | 12 - inst/doc/books.html | 12 - inst/doc/cloud.Rmd | 4 inst/doc/cloud.html | 4 inst/doc/downloads.Rmd | 6 inst/doc/downloads.html | 5 inst/doc/instructions.Rmd | 167 +++++++++-------- inst/doc/instructions.html | 156 ++++++++-------- inst/tutorials/getting-started/tutorial.Rmd | 72 ++++++- inst/tutorials/getting-started/tutorial.html | 254 +++++++++++++++------------ vignettes/addins.Rmd | 17 - vignettes/books.Rmd | 12 - vignettes/cloud.Rmd | 4 vignettes/downloads.Rmd | 6 vignettes/instructions.Rmd | 167 +++++++++-------- 23 files changed, 598 insertions(+), 446 deletions(-)
More information about tutorial.helpers at CRAN
Permanent link
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and
much more.
Author: Gabor Csardi [aut] ,
Tamas Nepusz [aut] ,
Vincent Traag [aut] ,
Szabolcs Horvat [aut] ,
Fabio Zanini [aut] ,
Daniel Noom [aut],
Kirill Mueller [aut, cre] ,
Maelle Salmon [ctb],
Michael Antonov [ctb],
Chan Zuckerberg Initiative [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between igraph versions 2.1.1 dated 2024-10-19 and 2.1.2 dated 2024-12-07
DESCRIPTION | 11 ++- MD5 | 104 ++++++++++++++++++------------------ NEWS.md | 25 ++++++++ R/centrality.R | 2 R/community.R | 21 +++---- R/foreign.R | 27 +++++++-- R/interface.R | 4 - R/motifs.R | 21 ++++++- R/palette.R | 4 - R/paths.R | 10 +-- build/partial.rdb |binary build/vignette.rds |binary configure | 2 inst/doc/igraph.R | 26 ++++----- inst/doc/igraph.html | 70 ++++++++++++------------ inst/doc/igraph_ES.R | 28 +++++---- inst/doc/igraph_ES.html | 70 ++++++++++++------------ man/all_simple_paths.Rd | 10 +-- man/as_directed.Rd | 2 man/as_graphnel.Rd | 2 man/cluster_fast_greedy.Rd | 3 - man/cluster_label_prop.Rd | 2 man/cluster_leiden.Rd | 2 man/cluster_louvain.Rd | 2 man/cluster_optimal.Rd | 7 +- man/cluster_spinglass.Rd | 3 - man/cluster_walktrap.Rd | 2 man/diverging_pal.Rd | 2 man/fastgreedy.community.Rd | 3 - man/fit_hrg.Rd | 2 man/graph.motifs.est.Rd | 3 - man/graph_from_graphnel.Rd | 2 man/label.propagation.community.Rd | 2 man/layout_in_circle.Rd | 2 man/multilevel.community.Rd | 2 man/optimal.community.Rd | 7 +- man/predict_edges.Rd | 2 man/read_graph.Rd | 2 man/sample_degseq.Rd | 4 - man/sample_motifs.Rd | 5 + man/sample_pref.Rd | 4 - man/sequential_pal.Rd | 2 man/spinglass.community.Rd | 3 - man/walktrap.community.Rd | 2 man/write.graph.Rd | 2 man/write_graph.Rd | 29 ++++++++-- src/rinterface_extra.c | 17 ++--- tests/testthat/_snaps/centrality.md | 71 ------------------------ tests/testthat/test-centrality.R | 9 ++- tests/testthat/test-get.adjlist.R | 42 ++++++++++++++ tests/testthat/test-interface.R | 61 +++++++++++++++++++++ tests/testthat/test-motifs.R | 16 +++++ tests/testthat/test-plot.R | 2 53 files changed, 450 insertions(+), 308 deletions(-)
Title: Precipitation R Recipes
Description: An open-access tool/framework to download, validate, visualize, and
analyze multi-source precipitation data. More information and an example of
implementation can be found in Vargas Godoy and Markonis (2023,
<doi:10.1016/j.envsoft.2023.105711>).
Author: Mijael Rodrigo Vargas Godoy [aut, cre]
,
Yannis Markonis [aut, ths]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Diff between pRecipe versions 3.0.1-3 dated 2024-01-31 and 3.0.2 dated 2024-12-07
pRecipe-3.0.1-3/pRecipe/R/crop_data.R |only pRecipe-3.0.1-3/pRecipe/R/csi.R |only pRecipe-3.0.1-3/pRecipe/R/download_e_obs.R |only pRecipe-3.0.1-3/pRecipe/R/download_trmm_3b43.R |only pRecipe-3.0.1-3/pRecipe/R/download_udel.R |only pRecipe-3.0.1-3/pRecipe/R/far.R |only pRecipe-3.0.1-3/pRecipe/R/fldmean.R |only pRecipe-3.0.1-3/pRecipe/R/infoNC.R |only pRecipe-3.0.1-3/pRecipe/R/label.R |only pRecipe-3.0.1-3/pRecipe/R/muldpm.R |only pRecipe-3.0.1-3/pRecipe/R/nse.R |only pRecipe-3.0.1-3/pRecipe/R/pRecipe_masks.R |only pRecipe-3.0.1-3/pRecipe/R/pod.R |only pRecipe-3.0.1-3/pRecipe/R/remap.R |only pRecipe-3.0.1-3/pRecipe/R/saveNC.R |only pRecipe-3.0.1-3/pRecipe/R/subset_data.R |only pRecipe-3.0.1-3/pRecipe/R/tabular.R |only pRecipe-3.0.1-3/pRecipe/R/trend.R |only pRecipe-3.0.1-3/pRecipe/R/yearstat.R |only pRecipe-3.0.1-3/pRecipe/man/crop_data.Rd |only pRecipe-3.0.1-3/pRecipe/man/csi.Rd |only pRecipe-3.0.1-3/pRecipe/man/download_e_obs.Rd |only pRecipe-3.0.1-3/pRecipe/man/download_trmm_3b43.Rd |only pRecipe-3.0.1-3/pRecipe/man/download_udel.Rd |only pRecipe-3.0.1-3/pRecipe/man/far.Rd |only pRecipe-3.0.1-3/pRecipe/man/fldmean.Rd |only pRecipe-3.0.1-3/pRecipe/man/infoNC.Rd |only pRecipe-3.0.1-3/pRecipe/man/label.Rd |only pRecipe-3.0.1-3/pRecipe/man/muldpm.Rd |only pRecipe-3.0.1-3/pRecipe/man/nse.Rd |only pRecipe-3.0.1-3/pRecipe/man/pRecipe_masks.Rd |only pRecipe-3.0.1-3/pRecipe/man/pod.Rd |only pRecipe-3.0.1-3/pRecipe/man/remap.Rd |only pRecipe-3.0.1-3/pRecipe/man/saveNC.Rd |only pRecipe-3.0.1-3/pRecipe/man/subset_data.Rd |only pRecipe-3.0.1-3/pRecipe/man/tabular.Rd |only pRecipe-3.0.1-3/pRecipe/man/trend.Rd |only pRecipe-3.0.1-3/pRecipe/man/yearstat.Rd |only pRecipe-3.0.2/pRecipe/DESCRIPTION | 23 pRecipe-3.0.2/pRecipe/MD5 | 201 +--- pRecipe-3.0.2/pRecipe/NAMESPACE | 42 pRecipe-3.0.2/pRecipe/NEWS.md | 6 pRecipe-3.0.2/pRecipe/R/core_functions.R |only pRecipe-3.0.2/pRecipe/R/dataset_check.R | 16 pRecipe-3.0.2/pRecipe/R/download_20cr.R | 7 pRecipe-3.0.2/pRecipe/R/download_all.R | 4 pRecipe-3.0.2/pRecipe/R/download_chirps.R | 6 pRecipe-3.0.2/pRecipe/R/download_cmap.R | 5 pRecipe-3.0.2/pRecipe/R/download_cmorph.R | 7 pRecipe-3.0.2/pRecipe/R/download_cpc.R | 6 pRecipe-3.0.2/pRecipe/R/download_cru_ts.R | 4 pRecipe-3.0.2/pRecipe/R/download_data.R | 6 pRecipe-3.0.2/pRecipe/R/download_em_earth.R | 4 pRecipe-3.0.2/pRecipe/R/download_era20c.R | 5 pRecipe-3.0.2/pRecipe/R/download_era5.R | 3 pRecipe-3.0.2/pRecipe/R/download_era5_land.R |only pRecipe-3.0.2/pRecipe/R/download_fldas.R | 4 pRecipe-3.0.2/pRecipe/R/download_ghcn.R | 4 pRecipe-3.0.2/pRecipe/R/download_gldas_clsm.R | 6 pRecipe-3.0.2/pRecipe/R/download_gldas_noah.R | 5 pRecipe-3.0.2/pRecipe/R/download_gldas_vic.R | 5 pRecipe-3.0.2/pRecipe/R/download_gpcc.R | 5 pRecipe-3.0.2/pRecipe/R/download_gpcp.R | 7 pRecipe-3.0.2/pRecipe/R/download_gpm_imerg.R | 7 pRecipe-3.0.2/pRecipe/R/download_gsmap.R |only pRecipe-3.0.2/pRecipe/R/download_jra55.R | 7 pRecipe-3.0.2/pRecipe/R/download_merra2.R | 7 pRecipe-3.0.2/pRecipe/R/download_mswep.R | 7 pRecipe-3.0.2/pRecipe/R/download_ncep_doe.R | 7 pRecipe-3.0.2/pRecipe/R/download_ncep_ncar.R | 7 pRecipe-3.0.2/pRecipe/R/download_persiann.R | 7 pRecipe-3.0.2/pRecipe/R/download_precl.R | 4 pRecipe-3.0.2/pRecipe/R/download_terraclimate.R | 4 pRecipe-3.0.2/pRecipe/R/globals.R | 6 pRecipe-3.0.2/pRecipe/R/plot_map.R | 85 - pRecipe-3.0.2/pRecipe/R/plot_taylor.R | 9 pRecipe-3.0.2/pRecipe/build/partial.rdb |binary pRecipe-3.0.2/pRecipe/build/vignette.rds |binary pRecipe-3.0.2/pRecipe/inst/doc/case_study.R |only pRecipe-3.0.2/pRecipe/inst/doc/case_study.Rmd |only pRecipe-3.0.2/pRecipe/inst/doc/case_study.html |only pRecipe-3.0.2/pRecipe/inst/doc/introduction.R | 140 +- pRecipe-3.0.2/pRecipe/inst/doc/introduction.Rmd | 218 ++-- pRecipe-3.0.2/pRecipe/inst/doc/introduction.html | 770 ++++------------ pRecipe-3.0.2/pRecipe/man/download_20cr.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_chirps.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_cmorph.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_cpc.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_em_earth.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_era20c.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_era5_land.Rd |only pRecipe-3.0.2/pRecipe/man/download_gldas_clsm.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_gpcp.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_gpm_imerg.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_gsmap.Rd |only pRecipe-3.0.2/pRecipe/man/download_jra55.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_merra2.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_mswep.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_ncep_doe.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_ncep_ncar.Rd | 1 pRecipe-3.0.2/pRecipe/man/download_persiann.Rd | 1 pRecipe-3.0.2/pRecipe/man/plot_map.Rd | 16 pRecipe-3.0.2/pRecipe/man/plot_taylor.Rd | 9 pRecipe-3.0.2/pRecipe/man/reexports.Rd |only pRecipe-3.0.2/pRecipe/vignettes/case_study.Rmd |only pRecipe-3.0.2/pRecipe/vignettes/introduction.Rmd | 218 ++-- pRecipe-3.0.2/pRecipe/vignettes/pRecipe.bib | 27 pRecipe-3.0.2/pRecipe/vignettes/plots/box.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/box_bo.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/box_sa.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/case_study_01.png |only pRecipe-3.0.2/pRecipe/vignettes/plots/case_study_02.png |only pRecipe-3.0.2/pRecipe/vignettes/plots/case_study_03.png |only pRecipe-3.0.2/pRecipe/vignettes/plots/case_study_04.png |only pRecipe-3.0.2/pRecipe/vignettes/plots/case_study_05.png |only pRecipe-3.0.2/pRecipe/vignettes/plots/density.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/density_bo.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/density_sa.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/heatmap.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/heatmap_bo.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/heatmap_sa.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/line.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/line_bo.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/line_sa.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/map.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/map_bo.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/map_sa.png |binary pRecipe-3.0.2/pRecipe/vignettes/plots/summary.png |binary 128 files changed, 844 insertions(+), 1107 deletions(-)
Title: Testing DBI Backends
Description: A helper that tests DBI back ends for conformity to the
interface.
Author: Kirill Mueller [aut, cre] ,
RStudio [cph],
R Consortium [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between DBItest versions 1.8.1 dated 2024-03-31 and 1.8.2 dated 2024-12-07
DESCRIPTION | 12 +-- MD5 | 112 +++++++++++++++---------------- NEWS.md | 19 +++++ R/spec-meta-bind-.R | 20 ++--- R/spec-meta-bind-arrow-stream.R | 50 ++++++------- R/spec-meta-bind-arrow.R | 18 ++-- R/spec-meta-bind-expr.R | 8 +- R/spec-meta-bind-runner.R | 34 +++++---- R/spec-meta-bind-stream.R | 50 ++++++------- R/spec-meta-bind.R | 22 +++--- R/spec-result-roundtrip.R | 10 +- R/spec-sql-write-table.R | 16 ++-- build/vignette.rds |binary inst/doc/DBItest.html | 2 man/context.Rd | 4 - man/spec_arrow_append_table_arrow.Rd | 6 - man/spec_arrow_create_table_arrow.Rd | 4 - man/spec_arrow_get_query_arrow.Rd | 4 - man/spec_arrow_read_table_arrow.Rd | 6 - man/spec_arrow_send_query_arrow.Rd | 12 +-- man/spec_arrow_write_table_arrow.Rd | 6 - man/spec_compliance_methods.Rd | 6 - man/spec_driver_connect.Rd | 2 man/spec_driver_constructor.Rd | 2 man/spec_driver_data_type.Rd | 2 man/spec_get_info.Rd | 16 ++-- man/spec_meta_bind.Rd | 42 +++++------ man/spec_meta_column_info.Rd | 2 man/spec_meta_get_row_count.Rd | 8 +- man/spec_meta_get_rows_affected.Rd | 8 +- man/spec_meta_get_statement.Rd | 6 - man/spec_meta_has_completed.Rd | 8 +- man/spec_meta_is_valid.Rd | 12 +-- man/spec_result_clear_result.Rd | 2 man/spec_result_execute.Rd | 4 - man/spec_result_fetch.Rd | 2 man/spec_result_get_query.Rd | 4 - man/spec_result_roundtrip.Rd | 4 - man/spec_result_send_query.Rd | 12 +-- man/spec_result_send_statement.Rd | 12 +-- man/spec_sql_append_table.Rd | 6 - man/spec_sql_create_table.Rd | 4 - man/spec_sql_exists_table.Rd | 6 - man/spec_sql_list_fields.Rd | 4 - man/spec_sql_list_objects.Rd | 14 +-- man/spec_sql_list_tables.Rd | 2 man/spec_sql_quote_identifier.Rd | 6 - man/spec_sql_quote_literal.Rd | 4 - man/spec_sql_quote_string.Rd | 4 - man/spec_sql_read_table.Rd | 8 +- man/spec_sql_remove_table.Rd | 8 +- man/spec_sql_unquote_identifier.Rd | 10 +- man/spec_sql_write_table.Rd | 10 +- man/spec_transaction_with_transaction.Rd | 6 - man/test_data_type.Rd | 2 man/tweaks.Rd | 4 - tests/testthat/test-DBItest.R | 2 57 files changed, 349 insertions(+), 320 deletions(-)
Title: Seamless Integration Between R and 'Julia'
Description: Provides an R interface to 'Julia',
which is a high-level, high-performance dynamic programming language
for numerical computing, see <https://julialang.org/> for more information.
It provides a high-level interface as well as a low-level interface.
Using the high level interface, you could call any 'Julia' function just like
any R function with automatic type conversion. Using the low level interface,
you could deal with C-level SEXP directly while enjoying the convenience of
using a high-level programming language like 'Julia'.
Author: Changcheng Li [aut, cre],
Christopher Rackauckas [ctb],
Randy Lai [ctb],
Dmitri Grominski [ctb],
Nagi Teramo [ctb]
Maintainer: Changcheng Li <cxl508@psu.edu>
Diff between JuliaCall versions 0.17.5 dated 2022-09-08 and 0.17.6 dated 2024-12-07
DESCRIPTION | 16 LICENSE | 4 MD5 | 202 ++-- NAMESPACE | 166 +-- NEWS.md | 674 ++++++------- R/JuliaCall.R | 116 +- R/JuliaObject.R | 298 +++--- R/JuliaObjectExt.R | 106 +- R/JuliaPlain.R | 52 - R/Jupyter.R | 10 R/RMarkdown.R | 403 ++++---- R/RcppExports.R | 38 R/aaa.R | 204 ++-- R/argument.R | 18 R/console.R | 132 +- R/dispatch.R | 364 +++---- R/installJulia.R | 295 ++---- R/interface.R | 456 ++++----- R/internal_generic.R | 34 R/package.R | 128 +- R/package_wrap.R | 154 +-- R/piper.R | 52 - R/plotsViewer.R | 42 R/util.R | 30 R/zzz.R | 520 +++++----- README.md | 730 +++++++------- build/vignette.rds |binary inst/CITATION | 30 inst/doc/JuliaCall_in_Jupyter_R_Notebook.R | 12 inst/doc/JuliaCall_in_Jupyter_R_Notebook.Rmd | 48 inst/doc/JuliaCall_in_Jupyter_R_Notebook.html | 1129 +++++++++++------------ inst/doc/Julia_in_RMarkdown.R | 6 inst/doc/Julia_in_RMarkdown.Rmd | 28 inst/doc/Julia_in_RMarkdown.html | 809 ++++++++-------- inst/js/plotly-latest.min.js | 154 +-- inst/julia/JuliaObject.jl | 198 ++-- inst/julia/REPLhook.jl | 26 inst/julia/RmdStd.jl | 58 - inst/julia/asR.jl | 28 inst/julia/convert.jl | 34 inst/julia/dispatch.jl | 200 ++-- inst/julia/display/IRjulia.jl | 132 +- inst/julia/display/RmdJulia.jl | 78 - inst/julia/display/basic.jl | 96 - inst/julia/display/plotsViewer.jl | 90 - inst/julia/incomplete_console.jl | 16 inst/julia/install_dependency.jl | 84 - inst/julia/interface1.jl | 70 - inst/julia/libjulia.jl | 34 inst/julia/rebuildRCall.jl | 116 +- inst/julia/setup.jl | 498 +++++----- man/JuliaCall.Rd | 118 +- man/JuliaObject.Rd | 56 - man/JuliaObjectFields.Rd | 68 - man/autowrap.Rd | 38 man/call.Rd | 116 +- man/eng_juliacall.Rd | 38 man/grapes-greater-than-J-grapes.Rd | 50 - man/install_julia.Rd | 40 man/julia_assign.Rd | 54 - man/julia_command.Rd | 64 - man/julia_console.Rd | 34 man/julia_eval.Rd | 74 - man/julia_exists.Rd | 46 man/julia_help.Rd | 46 man/julia_markdown_setup.Rd | 36 man/julia_notebook_setup.Rd | 30 man/julia_package.Rd | 94 - man/julia_pkg_wrap.Rd | 90 - man/julia_setup.Rd | 129 +- man/julia_source.Rd | 28 man/plotsViewer.Rd | 22 src/libjulia.cpp | 2 src/libjulia.h | 2 tests/testthat.R | 8 tests/testthat/Rmd_error_test.Rmd | 38 tests/testthat/Rmd_error_test1.Rmd | 40 tests/testthat/Rmd_test.Rmd | 78 - tests/testthat/Rmd_test.md | 96 - tests/testthat/simplesource.jl | 2 tests/testthat/test_AD.R | 168 +-- tests/testthat/test_JuliaObject.R | 150 +-- tests/testthat/test_JuliaTuple.R | 30 tests/testthat/test_RCall.R | 28 tests/testthat/test_arguments.R | 28 tests/testthat/test_array_related_dispatching.R | 82 - tests/testthat/test_asR.R | 18 tests/testthat/test_autowrap_JuliaObject.R | 56 - tests/testthat/test_basic.R | 56 - tests/testthat/test_dispatch.R | 238 ++-- tests/testthat/test_error.R | 24 tests/testthat/test_ifelse_related_dispatching.R | 132 +- tests/testthat/test_julia_package.R | 32 tests/testthat/test_julia_source.R | 22 tests/testthat/test_pkgwrap.R | 30 tests/testthat/test_rebuild.R | 22 tests/testthat/test_rmd.R | 26 tests/testthat/test_rmd_error.R | 24 vignettes/JuliaCall_in_Jupyter_R_Notebook.Rmd | 48 vignettes/JuliaCall_in_Jupyter_R_Notebook1.md | 530 +++++----- vignettes/JuliaCall_in_RMarkdown.md | 124 +- vignettes/Julia_in_RMarkdown.Rmd | 28 102 files changed, 6321 insertions(+), 6330 deletions(-)
Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Maximum likelihood estimation of smooth transition vector
autoregressive models with various types of transition weight functions,
conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, and calculation of impulse
response functions, generalized impulse response functions, and generalized
forecast error variance decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2024) <doi:10.48550/arXiv.2403.14216>,
Savi Virolainen (2024) <doi:10.48550/arXiv.2404.19707>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.1.0 dated 2024-11-29 and 1.1.1 dated 2024-12-07
sstvars-1.1.0/sstvars/tests |only sstvars-1.1.0/sstvars/vignettes/figures/profilelogliks.png |only sstvars-1.1.0/sstvars/vignettes/figures/seriesplot.png |only sstvars-1.1.1/sstvars/DESCRIPTION | 6 sstvars-1.1.1/sstvars/MD5 | 62 - sstvars-1.1.1/sstvars/NEWS.md | 10 sstvars-1.1.1/sstvars/R/LSest.R |only sstvars-1.1.1/sstvars/R/MAINest.R | 6 sstvars-1.1.1/sstvars/R/STVARconstruction.R | 2 sstvars-1.1.1/sstvars/R/eigens.R | 2 sstvars-1.1.1/sstvars/R/moreEst.R | 730 ------------- sstvars-1.1.1/sstvars/R/printMethods.R | 3 sstvars-1.1.1/sstvars/data/acidata.rda |binary sstvars-1.1.1/sstvars/data/gdpdef.rda |binary sstvars-1.1.1/sstvars/data/usacpu.rda |binary sstvars-1.1.1/sstvars/data/usamone.rda |binary sstvars-1.1.1/sstvars/inst/doc/sstvars-vignette.Rnw | 75 - sstvars-1.1.1/sstvars/inst/doc/sstvars-vignette.pdf |binary sstvars-1.1.1/sstvars/man/estim_LS.Rd | 6 sstvars-1.1.1/sstvars/man/estim_NLS.Rd | 6 sstvars-1.1.1/sstvars/man/fitSTVAR.Rd | 6 sstvars-1.1.1/sstvars/vignettes/figures/profilelogliks.pdf |only sstvars-1.1.1/sstvars/vignettes/figures/seriesplot.pdf |only sstvars-1.1.1/sstvars/vignettes/sstvars-vignette.Rnw | 75 - 24 files changed, 138 insertions(+), 851 deletions(-)
Title: Data and Software for "Lessons in Statistical Thinking"
Description: "Lessons in Statistical Thinking" D.T. Kaplan (2014)
<https://dtkaplan.github.io/Lessons-in-statistical-thinking/>
is a textbook for a first or second course in statistics that embraces
data wrangling, causal reasoning, modeling, statistical adjustment,
and simulation. 'LSTbook' supports the student-centered, tidy,
pipeline-oriented computing style featured in the book.
Author: Daniel Kaplan [aut, cre],
Randall Pruim [aut]
Maintainer: Daniel Kaplan <dtkaplan@gmail.com>
Diff between LSTbook versions 0.5.0 dated 2024-02-23 and 0.6 dated 2024-12-07
LSTbook-0.5.0/LSTbook/R/pointplot.R |only LSTbook-0.5.0/LSTbook/R/sample.R |only LSTbook-0.5.0/LSTbook/data/FEV.rda |only LSTbook-0.5.0/LSTbook/man/FEV.Rd |only LSTbook-0.5.0/LSTbook/man/sample.Rd |only LSTbook-0.6/LSTbook/DESCRIPTION | 15 - LSTbook-0.6/LSTbook/MD5 | 121 ++++---- LSTbook-0.6/LSTbook/NAMESPACE | 13 LSTbook-0.6/LSTbook/NEWS.md | 33 ++ LSTbook-0.6/LSTbook/R/AAUP.R | 2 LSTbook-0.6/LSTbook/R/FARS.R | 2 LSTbook-0.6/LSTbook/R/FEV.R | 4 LSTbook-0.6/LSTbook/R/data_from_tilde.R | 21 + LSTbook-0.6/LSTbook/R/datasim_helpers.R | 4 LSTbook-0.6/LSTbook/R/model_eval.R | 24 - LSTbook-0.6/LSTbook/R/model_plot.R | 7 LSTbook-0.6/LSTbook/R/model_skeleton.R | 2 LSTbook-0.6/LSTbook/R/model_type.R | 8 LSTbook-0.6/LSTbook/R/mosaic-do.R | 2 LSTbook-0.6/LSTbook/R/ntiles.R | 4 LSTbook-0.6/LSTbook/R/point_plot.R |only LSTbook-0.6/LSTbook/R/print.R | 1 LSTbook-0.6/LSTbook/R/print_model_object.R | 1 LSTbook-0.6/LSTbook/R/random_terms.R |only LSTbook-0.6/LSTbook/R/regression_summary.R | 2 LSTbook-0.6/LSTbook/R/sims.R | 2 LSTbook-0.6/LSTbook/R/take_sample.R |only LSTbook-0.6/LSTbook/R/trials.R | 2 LSTbook-0.6/LSTbook/R/zzz.R | 6 LSTbook-0.6/LSTbook/README.md | 52 +-- LSTbook-0.6/LSTbook/build/vignette.rds |binary LSTbook-0.6/LSTbook/data/CRDS.rda |only LSTbook-0.6/LSTbook/inst/Natality_2014.R |only LSTbook-0.6/LSTbook/inst/doc/DAGs.R | 26 - LSTbook-0.6/LSTbook/inst/doc/DAGs.Rmd | 26 - LSTbook-0.6/LSTbook/inst/doc/DAGs.html | 206 +++----------- LSTbook-0.6/LSTbook/inst/doc/LSTbook.R | 2 LSTbook-0.6/LSTbook/inst/doc/LSTbook.Rmd | 30 +- LSTbook-0.6/LSTbook/inst/doc/LSTbook.html | 135 +++------ LSTbook-0.6/LSTbook/inst/doc/modeling.Rmd | 4 LSTbook-0.6/LSTbook/inst/doc/modeling.html | 23 - LSTbook-0.6/LSTbook/man/AAUP.Rd | 2 LSTbook-0.6/LSTbook/man/CRDS.Rd |only LSTbook-0.6/LSTbook/man/FARS.Rd | 2 LSTbook-0.6/LSTbook/man/add_plot_labels.Rd | 2 LSTbook-0.6/LSTbook/man/datasim_make.Rd | 2 LSTbook-0.6/LSTbook/man/figures/README-README1euiBE-1.png |binary LSTbook-0.6/LSTbook/man/figures/README-README2lz92Z-1.png |binary LSTbook-0.6/LSTbook/man/figures/README-READMEDfxgmm-1.png |binary LSTbook-0.6/LSTbook/man/model_eval.Rd | 4 LSTbook-0.6/LSTbook/man/model_skeleton.Rd | 2 LSTbook-0.6/LSTbook/man/mosaic_cull_for_do.Rd | 2 LSTbook-0.6/LSTbook/man/ntiles.Rd | 4 LSTbook-0.6/LSTbook/man/point_plot.Rd | 2 LSTbook-0.6/LSTbook/man/random_terms.Rd |only LSTbook-0.6/LSTbook/man/regression_summaries.Rd | 2 LSTbook-0.6/LSTbook/man/take_sample.Rd |only LSTbook-0.6/LSTbook/man/trials.Rd | 2 LSTbook-0.6/LSTbook/tests/testthat/test-dags.R | 10 LSTbook-0.6/LSTbook/tests/testthat/test-dagsim.R | 40 +- LSTbook-0.6/LSTbook/tests/testthat/test-mix_with.R | 6 LSTbook-0.6/LSTbook/tests/testthat/test-model_eval.R | 6 LSTbook-0.6/LSTbook/tests/testthat/test-model_train.R | 6 LSTbook-0.6/LSTbook/tests/testthat/test-pointplot.R | 8 LSTbook-0.6/LSTbook/tests/testthat/test-sample.R | 20 - LSTbook-0.6/LSTbook/vignettes/DAGs.Rmd | 26 - LSTbook-0.6/LSTbook/vignettes/LSTbook.Rmd | 30 +- LSTbook-0.6/LSTbook/vignettes/modeling.Rmd | 4 68 files changed, 435 insertions(+), 527 deletions(-)
Title: A Wrapper for the Phonetic Software 'Praat'
Description: It allows running 'Praat' scripts from R and it provides some
wrappers for basic plotting. It also adds support for literate markdown
tangling. The package is designed to bring reproducible phonetic research
into R.
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between speakr versions 3.2.2 dated 2024-01-29 and 3.2.4 dated 2024-12-07
speakr-3.2.2/speakr/man/figures/logo.png |only speakr-3.2.2/speakr/man/figures/vowels.png |only speakr-3.2.4/speakr/DESCRIPTION | 19 ++--- speakr-3.2.4/speakr/MD5 | 32 ++++----- speakr-3.2.4/speakr/NEWS.md | 8 ++ speakr-3.2.4/speakr/build/vignette.rds |binary speakr-3.2.4/speakr/inst/doc/praat-lmt.html | 2 speakr-3.2.4/speakr/inst/doc/praat-plot.R | 14 ++-- speakr-3.2.4/speakr/inst/doc/praat-plot.html | 2 speakr-3.2.4/speakr/inst/doc/run-praat.R | 54 ++++++++-------- speakr-3.2.4/speakr/inst/doc/run-praat.html | 8 +- speakr-3.2.4/speakr/man/figures/README-vowel-plot-1.png |binary speakr-3.2.4/speakr/man/get_praat_path.Rd | 2 speakr-3.2.4/speakr/man/praat_path.Rd | 2 speakr-3.2.4/speakr/man/praat_plot.Rd | 14 ++-- speakr-3.2.4/speakr/man/praat_run.Rd | 4 - speakr-3.2.4/speakr/man/set_praat_path.Rd | 2 speakr-3.2.4/speakr/man/speakr-package.Rd | 4 - 18 files changed, 85 insertions(+), 82 deletions(-)
Title: Tidy Prediction and Plotting of Generalised Additive Models
Description: Provides functions that compute predictions from Generalised
Additive Models (GAMs) fitted with 'mgcv' and return them as a tibble.
These can be plotted with a generic plot()-method that uses 'ggplot2' or
plotted as any other data frame. The main function is predict_gam().
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between tidygam versions 0.2.0 dated 2023-05-09 and 0.2.2 dated 2024-12-07
DESCRIPTION | 12 ++-- MD5 | 14 ++--- NEWS.md | 10 +++ README.md | 4 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/get-started.R | 2 inst/doc/get-started.html | 119 +++++++++++++++++++++++++--------------------- 8 files changed, 92 insertions(+), 69 deletions(-)
Title: Fast Imputation of Missing Values
Description: Alternative implementation of the beautiful 'MissForest'
algorithm used to impute mixed-type data sets by chaining random
forests, introduced by Stekhoven, D.J. and Buehlmann, P. (2012)
<doi:10.1093/bioinformatics/btr597>. Under the hood, it uses the
lightning fast random forest package 'ranger'. Between the iterative
model fitting, we offer the option of using predictive mean matching.
This firstly avoids imputation with values not already present in the
original data (like a value 0.3334 in 0-1 coded variable). Secondly,
predictive mean matching tries to raise the variance in the resulting
conditional distributions to a realistic level. This would allow,
e.g., to do multiple imputation when repeating the call to
missRanger(). Out-of-sample application is supported as well.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between missRanger versions 2.6.0 dated 2024-08-17 and 2.6.1 dated 2024-12-07
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/missRanger.R | 17 +++++++++++++---- inst/doc/missRanger.html | 4 ++-- inst/doc/multiple_imputation.html | 4 ++-- inst/doc/working_with_censoring.html | 4 ++-- tests/testthat/test-helper.R | 8 ++++++++ 8 files changed, 44 insertions(+), 20 deletions(-)
Title: Codon Usage Bias Analysis
Description: A suite of functions for rapid and flexible analysis of codon
usage bias. It provides in-depth analysis at the codon level, including
relative synonymous codon usage (RSCU), tRNA weight calculations, machine
learning predictions for optimal or preferred codons, and visualization of
codon-anticodon pairing. Additionally, it can calculate various gene-
specific codon indices such as codon adaptation index (CAI), effective
number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation
index (tAI), mean codon stabilization coefficients (CSCg), and GC contents
(GC/GC3s/GC4d). It also supports both standard and non-standard genetic
code tables found in NCBI, as well as custom genetic code tables.
Author: Hong Zhang [aut, cre] ,
Mengyue Liu [aut],
Bu Zi [aut]
Maintainer: Hong Zhang <mt1022.dev@gmail.com>
Diff between cubar versions 1.0.0 dated 2024-08-01 and 1.1.0 dated 2024-12-07
cubar-1.0.0/cubar/tests/testthat/test-codon_weight.R |only cubar-1.1.0/cubar/DESCRIPTION | 12 + cubar-1.1.0/cubar/MD5 | 65 ++++----- cubar-1.1.0/cubar/NEWS.md | 6 cubar-1.1.0/cubar/R/codon_info.R | 8 - cubar-1.1.0/cubar/R/codon_weight.R | 40 +++-- cubar-1.1.0/cubar/R/gene_index.R | 100 +++++++++----- cubar-1.1.0/cubar/R/sequences.R | 2 cubar-1.1.0/cubar/R/utils.R | 6 cubar-1.1.0/cubar/R/window.R | 6 cubar-1.1.0/cubar/README.md | 7 cubar-1.1.0/cubar/inst/doc/cubar.html | 31 ++-- cubar-1.1.0/cubar/inst/doc/non_standard_genetic_code.html | 2 cubar-1.1.0/cubar/man/codon_diff.Rd | 3 cubar-1.1.0/cubar/man/codon_optimize.Rd | 3 cubar-1.1.0/cubar/man/count_codons.Rd | 2 cubar-1.1.0/cubar/man/create_codon_table.Rd | 2 cubar-1.1.0/cubar/man/est_csc.Rd | 2 cubar-1.1.0/cubar/man/est_optimal_codons.Rd | 10 - cubar-1.1.0/cubar/man/est_rscu.Rd | 18 +- cubar-1.1.0/cubar/man/est_trna_weight.Rd | 2 cubar-1.1.0/cubar/man/get_cai.Rd | 8 - cubar-1.1.0/cubar/man/get_codon_table.Rd | 4 cubar-1.1.0/cubar/man/get_cscg.Rd | 4 cubar-1.1.0/cubar/man/get_dp.Rd | 21 ++ cubar-1.1.0/cubar/man/get_enc.Rd | 9 - cubar-1.1.0/cubar/man/get_fop.Rd | 9 - cubar-1.1.0/cubar/man/get_gc3s.Rd | 9 - cubar-1.1.0/cubar/man/get_gc4d.Rd | 10 - cubar-1.1.0/cubar/man/get_tai.Rd | 4 cubar-1.1.0/cubar/man/plot_ca_pairing.Rd | 3 cubar-1.1.0/cubar/man/show_codon_tables.Rd | 2 cubar-1.1.0/cubar/man/slide_apply.Rd | 4 cubar-1.1.0/cubar/man/slide_plot.Rd | 2 34 files changed, 253 insertions(+), 163 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.3.6 dated 2024-11-07 and 0.4.0 dated 2024-12-07
DESCRIPTION | 13 +- MD5 | 186 +++++++++++++++++++++--------------------- NAMESPACE | 4 R/areaplot.R | 5 - R/barplot.R | 38 +++++++- R/boxviolinplot.R | 20 ++++ R/chordplot.R | 7 + R/clustreeplot.R | 7 + R/common_args.R | 3 R/corplot.R | 17 +++ R/densityplot.R | 21 ++++ R/dimplot.R | 12 ++ R/dotplot.R | 13 ++ R/enrich.R | 10 +- R/heatmap.R | 117 ++++++++++++++++---------- R/lineplot.R | 6 + R/piechart.R | 6 + R/radarplot.R | 10 +- R/rarefractionplot.R | 6 + R/ringplot.R | 7 + R/roccurve.R |only R/scatterplot.R | 8 + R/theming.R | 19 +++- R/trendplot.R | 6 + R/upsetplot.R | 4 R/utils.R | 50 +++++++++++ R/venndiagram.R | 4 R/volcanoplot.R | 12 +- R/wordcloudplot.R | 4 README.md | 11 +- man/AreaPlot.Rd | 8 + man/AreaPlotAtomic.Rd | 7 + man/BarPlotAtomic.Rd | 11 ++ man/BarPlotGrouped.Rd | 11 ++ man/BarPlotSingle.Rd | 7 + man/BoxViolinPlot-internal.Rd | 10 +- man/BoxViolinPlotAtomic.Rd | 10 +- man/ChordPlotAtomic.Rd | 7 + man/ClustreePlot.Rd | 9 +- man/ClustreePlotAtomic.Rd | 7 + man/CorPairsPlot.Rd | 10 +- man/CorPlot.Rd | 9 +- man/CorPlotAtomic.Rd | 7 + man/DensityHistoPlotAtomic.Rd | 7 + man/DimPlotAtomic.Rd | 7 + man/DotPlotAtomic.Rd | 7 + man/EnrichMapAtomic.Rd | 7 + man/EnrichNetworkAtomic.Rd | 7 + man/Heatmap.Rd | 25 +++++ man/HeatmapAtomic.Rd | 16 +++ man/LinePlot.Rd | 9 +- man/LinePlotAtomic.Rd | 7 + man/LinePlotGrouped.Rd | 7 + man/LinePlotSingle.Rd | 7 + man/Network.Rd | 7 + man/PieChart.Rd | 9 +- man/PieChartAtomic.Rd | 7 + man/ROCCurve.Rd |only man/ROCCurveAtomic.Rd |only man/RadarPlotAtomic.Rd | 7 + man/RarefactionPlot.Rd | 9 +- man/RarefactionPlotAtomic.Rd | 7 + man/RidgePlot.Rd | 9 +- man/RidgePlotAtomic.Rd | 7 + man/RingPlot.Rd | 10 +- man/RingPlotAtomic.Rd | 7 + man/ScatterPlot.Rd | 11 ++ man/ScatterPlotAtomic.Rd | 7 + man/SplitBarPlotAtomic.Rd | 7 + man/TrendPlot.Rd | 9 +- man/TrendPlotAtomic.Rd | 7 + man/UpsetPlotAtomic.Rd | 7 + man/VennDiagramAtomic.Rd | 7 + man/VolcanoPlot.Rd | 10 +- man/VolcanoPlotAtomic.Rd | 7 + man/WordCloudPlot.Rd | 7 + man/WordCloudPlotAtomic.Rd | 7 + man/barplot.Rd | 14 ++- man/boxviolinplot.Rd | 20 +++- man/check_palcolor.Rd |only man/check_palette.Rd |only man/chordplot.Rd | 9 +- man/common_args.Rd | 7 + man/densityhistoplot.Rd | 11 ++ man/dimplot.Rd | 11 ++ man/dotplot.Rd | 12 ++ man/enrichmap1.Rd | 9 +- man/figures/area-trend.png |binary man/get_cutoffs_data.Rd |only man/gsea.Rd | 7 + man/palette_this.Rd | 8 + man/radarplot.Rd | 9 +- man/sankeyplot.Rd | 7 + man/upsetplot1.Rd | 7 + man/validate_common_args.Rd | 7 + man/venndiagram1.Rd | 7 + tests |only 97 files changed, 845 insertions(+), 310 deletions(-)
Title: Transform Microplate Data into Tibbles
Description: The goal of 'tidyplate' is to help researchers convert
different types of microplates into tibbles which can be used in data
analysis. It accepts xlsx and csv files formatted in a specific way as
input. It supports all types of standard microplate formats such as
6-well, 12-well, 24-well, 48-well, 96-well, 384-well, and, 1536-well
plates.
Author: Shubham Dutta [aut, cre, cph]
Maintainer: Shubham Dutta <shubhamdutta26@gmail.com>
Diff between tidyplate versions 2.1.0 dated 2024-11-18 and 2.2.0 dated 2024-12-06
DESCRIPTION | 6 MD5 | 63 +++++++-- NEWS.md | 7 + R/utils.R | 5 README.md | 5 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/comparison.R |only inst/doc/comparison.Rmd |only inst/doc/comparison.html |only inst/extdata/example_12_well.csv | 22 +++ inst/extdata/example_1536_well.csv | 138 +++++++++++++++++++- inst/extdata/example_384_well.csv | 72 ++++++++++ inst/extdata/example_96_well.csv | 64 ++++----- inst/performance_tidy.R |only tests/spelling.R | 4 tests/testthat/template_6-well.csv |only tests/testthat/test-build_plate.R | 16 +- tests/testthat/test-tidy_plate.R | 12 + tests/testthat/test_data/12/allPlatesChar.csv |only tests/testthat/test_data/12/allPlatesChar.xlsx |only tests/testthat/test_data/12/allPlatesNumeric.csv |only tests/testthat/test_data/12/allPlatesNumeric.xlsx |only tests/testthat/test_data/1536/allPlatesChar.csv |only tests/testthat/test_data/1536/allPlatesChar.xlsx |only tests/testthat/test_data/1536/allPlatesNumeric.csv |only tests/testthat/test_data/1536/allPlatesNumeric.xlsx |only tests/testthat/test_data/24/allPlatesChar.csv |only tests/testthat/test_data/24/allPlatesChar.xlsx |only tests/testthat/test_data/24/allPlatesNumeric.csv |only tests/testthat/test_data/24/allPlatesNumeric.xlsx |only tests/testthat/test_data/384/allPlatesChar.csv |only tests/testthat/test_data/384/allPlatesChar.xlsx |only tests/testthat/test_data/384/allPlatesNumeric.csv |only tests/testthat/test_data/384/allPlatesNumeric.xlsx |only tests/testthat/test_data/48/allPlatesChar.csv |only tests/testthat/test_data/48/allPlatesChar.xlsx |only tests/testthat/test_data/48/allPlatesNumeric.csv |only tests/testthat/test_data/48/allPlatesNumeric.xlsx |only tests/testthat/test_data/6/allPlatesChar.csv |only tests/testthat/test_data/6/allPlatesChar.xlsx |only tests/testthat/test_data/6/allPlatesNumeric.csv |only tests/testthat/test_data/6/allPlatesNumeric.xlsx |only tests/testthat/test_data/6/badColRowName.csv | 2 tests/testthat/test_data/96/allPlatesChar.csv |only tests/testthat/test_data/96/allPlatesChar.xlsx |only tests/testthat/test_data/96/allPlatesNumeric.csv |only tests/testthat/test_data/96/allPlatesNumeric.xlsx |only vignettes/comparison.Rmd |only vignettes/images |only 50 files changed, 351 insertions(+), 66 deletions(-)
Title: Get and Modify 'oTree' Data
Description: Efficiently manage and process data from 'oTree' experiments.
Import 'oTree' data and clean them by using functions that handle
messy data, dropouts, and other problematic cases. Create IDs,
calculate the time, transfer variables between app data frames, and
delete sensitive information. Review your experimental data prior to
running the experiment and automatically generate a detailed summary
of the variables used in your 'oTree' code. Information on 'oTree' is
found in Chen, D. L., Schonger, M., & Wickens, C. (2016)
<doi:10.1016/j.jbef.2015.12.001>.
Author: Patricia F. Zauchner [aut, trl, cre, cph]
Maintainer: Patricia F. Zauchner <patricia.zauchner@gmx.at>
Diff between gmoTree versions 1.3.0 dated 2024-12-06 and 1.3.1 dated 2024-12-06
gmoTree-1.3.0/gmoTree/vignettes/title.PNG |only gmoTree-1.3.1/gmoTree/DESCRIPTION | 6 +++--- gmoTree-1.3.1/gmoTree/MD5 | 10 +++++----- gmoTree-1.3.1/gmoTree/NEWS.md | 4 ++++ gmoTree-1.3.1/gmoTree/inst/CITATION | 4 ++-- gmoTree-1.3.1/gmoTree/inst/doc/intro_to_gmoTree.html | 18 +++++++++--------- gmoTree-1.3.1/gmoTree/vignettes/title.png |only 7 files changed, 23 insertions(+), 19 deletions(-)
Title: Statistical Quality Control Simulation
Description: This is a set of statistical quality control functions, that allows plotting control charts and its iterations, process capability for variable and attribute control, highlighting the xrs_gr() function, like a first iteration for variable chart, meanwhile the we_rules() function detects non random patterns in sample.
Author: Erick Marroquin [aut, cre]
Maintainer: Erick Marroquin <ericksuhel@gmail.com>
Diff between XRSCC versions 0.1 dated 2016-11-11 and 0.2 dated 2024-12-06
DESCRIPTION | 17 +++++++++++------ MD5 | 6 +++--- man/C_it.Rd | 3 +-- man/c_gr.Rd | 2 -- 4 files changed, 15 insertions(+), 13 deletions(-)
Title: Generalized Latent Markov Models
Description: Latent Markov models for longitudinal continuous and categorical data. See Bartolucci, Pandolfi, Pennoni (2017)<doi:10.18637/jss.v081.i04>.
Author: Francesco Bartolucci [aut, cre],
Silvia Pandolfi [aut],
Fulvia Pennoni [aut],
Alessio Farcomeni [ctb],
Alessio Serafini [ctb]
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between LMest versions 3.2.3 dated 2024-11-05 and 3.2.4 dated 2024-12-06
DESCRIPTION | 8 ++--- MD5 | 46 +++++++++++++++--------------- R/bootstrap.R | 13 ++++++-- R/draw.R | 27 +++++++++++++++-- R/est_multilogit.R | 5 +-- R/expit.R | 7 ++-- R/functions.R | 1 R/lk_comp_latent_cont.R | 16 ++++++++-- R/lk_obs_latent.R | 14 ++++----- R/lk_obs_latent_cont.R | 25 ++++++++++------ R/lmbasic.cont.R | 2 - R/lmcovlatent.cont.R | 14 ++++----- R/lmestCont.R | 7 ++-- R/lmestDecoding.R | 15 ++++++--- R/lmestMc.R | 64 ++++++++++++++---------------------------- R/mccov.R | 6 +-- R/plot.LMbasic.R | 42 ++++++++++++++++++--------- R/plot.LMbasiccont.R | 31 +++++++++++++------- R/plot.LMlatent.R | 42 ++++++++++++++++++--------- R/plot.LMlatentcont.R | 30 +++++++++++++------ R/plot.LMsearch.R | 3 + R/prob_multilogit.R | 67 ++++++++++++++++++++++---------------------- R/prob_post_cov_cont.R | 66 +++++++++++++++++++++++++++++-------------- inst/doc/vignetteLMest.html | 14 ++++----- 24 files changed, 336 insertions(+), 229 deletions(-)
Title: Piecewise Geodesic Smoothing for Spherical Data
Description: Fitting a smooth path to a given set of noisy spherical data observed at known time points. It implements a piecewise geodesic curve fitting method on the unit sphere based on a velocity-based penalization scheme. The proposed approach is implemented using the Riemannian block coordinate descent algorithm. To understand the method and algorithm, one can refer to Bak, K. Y., Shin, J. K., & Koo, J. Y. (2023) <doi:10.1080/02664763.2022.2054962> for the case of order 1. Additionally, this package includes various functions necessary for handling spherical data.
Author: Jae-Hwan Jhong [aut] ,
Ja-Yong Koo [aut] ,
Seyoung Lee [aut] ,
Kwan-Young Bak [aut, cre, cph]
Maintainer: Kwan-Young Bak <kybak@sungshin.ac.kr>
Diff between spheresmooth versions 0.1.0 dated 2024-04-18 and 0.1.3 dated 2024-12-06
spheresmooth-0.1.0/spheresmooth/man/Exp.Rd |only spheresmooth-0.1.0/spheresmooth/man/Normalize.Rd |only spheresmooth-0.1.0/spheresmooth/man/cross_normalized.Rd |only spheresmooth-0.1.3/spheresmooth/DESCRIPTION | 35 + spheresmooth-0.1.3/spheresmooth/MD5 | 34 - spheresmooth-0.1.3/spheresmooth/NAMESPACE | 13 spheresmooth-0.1.3/spheresmooth/R/linear-spherical-spline.R | 210 ++++------ spheresmooth-0.1.3/spheresmooth/README.md | 71 ++- spheresmooth-0.1.3/spheresmooth/data/apw_spherical.rda |binary spheresmooth-0.1.3/spheresmooth/data/goni_spherical.rda |binary spheresmooth-0.1.3/spheresmooth/man/cartesian_to_spherical.Rd | 14 spheresmooth-0.1.3/spheresmooth/man/cross.Rd | 4 spheresmooth-0.1.3/spheresmooth/man/exp_map.Rd |only spheresmooth-0.1.3/spheresmooth/man/figures/README-unnamed-chunk-6-1.png |binary spheresmooth-0.1.3/spheresmooth/man/figures/README-unnamed-chunk-7-1.png |binary spheresmooth-0.1.3/spheresmooth/man/geodesic.Rd | 8 spheresmooth-0.1.3/spheresmooth/man/geodesic_lower.Rd |only spheresmooth-0.1.3/spheresmooth/man/normalize.Rd |only spheresmooth-0.1.3/spheresmooth/man/normalize_lower.Rd |only spheresmooth-0.1.3/spheresmooth/man/penalized_linear_spherical_spline.Rd | 16 spheresmooth-0.1.3/spheresmooth/man/spheresmooth.Rd |only spheresmooth-0.1.3/spheresmooth/man/spherical_to_cartesian.Rd | 10 22 files changed, 226 insertions(+), 189 deletions(-)
Title: Nested Data Summary, Adverse Events and REDCap
Description: Tools and code snippets for summarizing nested data, adverse events
and REDCap study information.
Author: Lisa Avery [aut] ,
Zeynep Baskurt [aut],
Osvaldo Espin-Garcia [aut],
Katrina Hueniken [aut],
Katherine Lajkosz [aut] ,
Xuan Li [aut],
Tyler Pittman [cre, aut] ,
Anna Santiago [aut] ,
Jessica Weiss [aut],
Wei Xu [aut]
Maintainer: Tyler Pittman <tyler.pittman@uhn.ca>
Diff between BiostatsUHNplus versions 0.0.10 dated 2024-05-24 and 1.0.1 dated 2024-12-06
DESCRIPTION | 6 MD5 | 70 +++++----- NEWS.md | 4 R/ae_timeline_plot.R | 5 R/covsum_nested.R | 9 - R/dsmb_ccru.R | 39 +++-- R/redcap_data_out.R | 16 +- README.md | 35 ++--- man/ae_timeline_plot.Rd | 5 man/covsum_nested.Rd | 4 man/figures/ae_category_attribStart_timeline_plot.png |binary man/figures/ae_category_timeline_plot.png |binary man/figures/ae_detail_timeline_plot.png |binary man/figures/ana10-1.png |binary man/figures/ana9-1.png |binary man/figures/caterpillar_plot_Cows_Model.png |binary man/figures/caterpillar_plot_Yards_Model.png |binary man/figures/caterpillar_plot_ae_category.png |binary man/figures/caterpillar_plot_subject.png |binary man/figures/variance_pie_plot.png |binary man/rm_covsum_nested.Rd | 5 man/tables/ae_detail_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY__30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY__30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY__30OCT2020.xlsx |binary 36 files changed, 107 insertions(+), 91 deletions(-)
More information about BiostatsUHNplus at CRAN
Permanent link
Title: Ultrasound Tongue Imaging
Description: A tool for processing Articulate
Assistant Advanced™ (AAA) export files and plot tongue contour data from any
system.
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between rticulate versions 1.7.3 dated 2022-09-04 and 1.7.4 dated 2024-12-06
DESCRIPTION | 10 - MD5 | 20 +- NEWS.md | 5 build/vignette.rds |binary inst/doc/overview.html | 4 inst/doc/polar-gams.html | 380 +++++++++++++++++++++--------------------- inst/doc/tongue-imaging.R | 2 inst/doc/tongue-imaging.html | 204 +++++++++++----------- inst/doc/transform-coord.html | 100 +++++------ vignettes/filter-signals.R |only vignettes/filter-signals.html |only vignettes/kinematics.R |only vignettes/kinematics.html |only 13 files changed, 370 insertions(+), 355 deletions(-)
Title: Network Analysis of Dependencies of CRAN Packages
Description: The dependencies of CRAN packages can be analysed in a network fashion. For each package we can obtain the packages that it depends, imports, suggests, etc. By iterating this procedure over a number of packages, we can build, visualise, and analyse the dependency network, enabling us to have a bird's-eye view of the CRAN ecosystem. One aspect of interest is the number of reverse dependencies of the packages, or equivalently the in-degree distribution of the dependency network. This can be fitted by the power law and/or an extreme value mixture distribution <doi:10.1111/stan.12355>, of which functions are provided.
Author: Clement Lee [aut, cre]
Maintainer: Clement Lee <clement.lee.tm@outlook.com>
Diff between crandep versions 0.3.10 dated 2024-08-18 and 0.3.11 dated 2024-12-06
crandep-0.3.10/crandep/man/topo_sort_kahn.Rd |only crandep-0.3.11/crandep/DESCRIPTION | 6 +- crandep-0.3.11/crandep/MD5 | 27 ++++------ crandep-0.3.11/crandep/NAMESPACE | 5 - crandep-0.3.11/crandep/NEWS.md | 8 +++ crandep-0.3.11/crandep/R/data.R | 2 crandep-0.3.11/crandep/R/graph.R | 57 --------------------- crandep-0.3.11/crandep/build/vignette.rds |binary crandep-0.3.11/crandep/inst/doc/cran.html | 49 +++++++++--------- crandep-0.3.11/crandep/inst/doc/degree.html | 52 +++++++++---------- crandep-0.3.11/crandep/inst/doc/introduction.R | 11 ---- crandep-0.3.11/crandep/inst/doc/introduction.Rmd | 24 --------- crandep-0.3.11/crandep/inst/doc/introduction.html | 58 ++-------------------- crandep-0.3.11/crandep/man/chi_citations.Rd | 2 crandep-0.3.11/crandep/vignettes/introduction.Rmd | 24 --------- 15 files changed, 85 insertions(+), 240 deletions(-)
Title: Tidy Geospatial Networks
Description: Provides a tidy approach to spatial network
analysis, in the form of classes and functions that enable a seamless
interaction between the network analysis package 'tidygraph' and the
spatial analysis package 'sf'.
Author: Lucas van der Meer [aut, cre] ,
Lorena Abad [aut] ,
Andrea Gilardi [aut] ,
Robin Lovelace [aut]
Maintainer: Lucas van der Meer <luukvandermeer@live.nl>
Diff between sfnetworks versions 0.6.4 dated 2024-04-09 and 0.6.5 dated 2024-12-06
DESCRIPTION | 8 MD5 | 171 +- NAMESPACE | 505 +++---- NEWS.md | 515 +++---- R/agr.R | 228 +-- R/attrs.R | 602 ++++---- R/bbox.R | 136 +- R/blend.R | 1014 +++++++------- R/checks.R | 372 ++--- R/edge.R | 616 ++++----- R/geom.R | 436 +++--- R/igraph.R |only R/join.R | 142 +- R/messages.R | 136 +- R/morphers.R | 2377 +++++++++++++++++------------------ R/node.R | 458 +++--- R/paths.R | 874 ++++++------ R/plot.R | 178 +- R/require.R | 296 ++-- R/roxel.R | 32 R/s2.R | 18 R/sf.R | 1526 +++++++++++----------- R/sfnetwork.R | 950 ++++++------- R/sfnetworks-package.R | 16 R/spatstat.R | 158 +- R/tibble.R | 152 +- R/tidygraph.R | 314 ++-- R/utils.R | 912 ++++++------- R/zzz.R | 208 +-- README.md | 130 - build/vignette.rds |binary inst/doc/sfn01_structure.R | 418 +++--- inst/doc/sfn01_structure.Rmd | 714 +++++----- inst/doc/sfn01_structure.html | 2241 ++++++++++++++++---------------- inst/doc/sfn02_preprocess_clean.R | 672 ++++----- inst/doc/sfn02_preprocess_clean.Rmd | 938 ++++++------- inst/doc/sfn02_preprocess_clean.html | 2272 ++++++++++++++++----------------- inst/doc/sfn03_join_filter.R | 542 +++---- inst/doc/sfn03_join_filter.Rmd | 770 +++++------ inst/doc/sfn03_join_filter.html | 2021 ++++++++++++++--------------- inst/doc/sfn04_routing.R | 694 +++++----- inst/doc/sfn04_routing.Rmd | 930 ++++++------- inst/doc/sfn04_routing.html | 1990 ++++++++++++++--------------- inst/doc/sfn05_morphers.R | 538 +++---- inst/doc/sfn05_morphers.Rmd | 784 +++++------ inst/doc/sfn05_morphers.html | 2140 +++++++++++++++---------------- man/as.linnet.Rd | 58 man/as_sfnetwork.Rd | 194 +- man/as_tibble.Rd | 104 - man/autoplot.Rd | 50 man/figures/hexlogo.R | 122 - man/is.sfnetwork.Rd | 52 man/node_coordinates.Rd | 126 - man/plot.sfnetwork.Rd | 106 - man/reexports.Rd | 36 man/roxel.Rd | 56 man/s2.Rd | 34 man/sf.Rd | 450 +++--- man/sf_attr.Rd | 70 - man/sfnetwork.Rd | 246 +-- man/sfnetworks-package.Rd | 66 man/spatial_edge_measures.Rd | 178 +- man/spatial_edge_predicates.Rd | 228 +-- man/spatial_morphers.Rd | 530 +++---- man/spatial_node_predicates.Rd | 210 +-- man/st_network_bbox.Rd | 120 - man/st_network_blend.Rd | 212 +-- man/st_network_cost.Rd | 252 +-- man/st_network_join.Rd | 108 - man/st_network_paths.Rd | 344 ++--- tests/testthat.R | 8 tests/testthat/test_bbox.R | 66 tests/testthat/test_blend.R | 76 - tests/testthat/test_edges_nodes.R | 454 +++--- tests/testthat/test_join.R | 142 +- tests/testthat/test_morphers.R | 572 ++++---- tests/testthat/test_paths.R | 488 +++---- tests/testthat/test_plot.R | 44 tests/testthat/test_sf.R | 428 +++--- tests/testthat/test_sfnetworks.R | 118 - tests/testthat/test_spatstat.R | 38 tests/testthat/test_tidygraph.R | 42 vignettes/sfn01_structure.Rmd | 714 +++++----- vignettes/sfn02_preprocess_clean.Rmd | 938 ++++++------- vignettes/sfn03_join_filter.Rmd | 770 +++++------ vignettes/sfn04_routing.Rmd | 930 ++++++------- vignettes/sfn05_morphers.Rmd | 784 +++++------ 87 files changed, 20842 insertions(+), 20866 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] ,
Danielle Navarro [aut],
Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between rstanemax versions 0.1.6 dated 2024-12-05 and 0.1.7 dated 2024-12-06
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/posterior_predict.R | 18 ++++++++++++++---- inst/doc/emaxmodel.html | 4 ++-- man/posterior_predict.Rd | 7 +++++-- tests/testthat/test-posterior_predict.R | 2 +- tests/testthat/test-stan_emax_binary.R | 1 + 8 files changed, 40 insertions(+), 19 deletions(-)
Title: Communicate with 'Ollama' to Run Large Language Models Locally
Description: Wraps the 'Ollama' <https://ollama.com> API, which can be used to
communicate with generative large language models locally.
Author: Johannes B. Gruber [aut, cre] ,
Maximilian Weber [aut, ctb]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between rollama versions 0.1.0 dated 2024-05-01 and 0.2.0 dated 2024-12-06
rollama-0.1.0/rollama/vignettes/bench |only rollama-0.1.0/rollama/vignettes/benchmarking.Rmd.orig |only rollama-0.2.0/rollama/DESCRIPTION | 17 rollama-0.2.0/rollama/MD5 | 93 +-- rollama-0.2.0/rollama/NAMESPACE | 1 rollama-0.2.0/rollama/NEWS.md | 13 rollama-0.2.0/rollama/R/chat.r | 272 +++++++-- rollama-0.2.0/rollama/R/embedding.r | 83 +- rollama-0.2.0/rollama/R/lib.R | 195 ++++-- rollama-0.2.0/rollama/R/models.r | 47 + rollama-0.2.0/rollama/R/rollama-package.R | 9 rollama-0.2.0/rollama/R/utils.r | 109 +++ rollama-0.2.0/rollama/README.md | 370 ++++++------ rollama-0.2.0/rollama/build/vignette.rds |binary rollama-0.2.0/rollama/inst/WORDLIST | 16 rollama-0.2.0/rollama/inst/doc/annotation.Rmd | 326 ++++++---- rollama-0.2.0/rollama/inst/doc/annotation.html | 419 +++++++------- rollama-0.2.0/rollama/inst/doc/hf-gguf.Rmd |only rollama-0.2.0/rollama/inst/doc/hf-gguf.html |only rollama-0.2.0/rollama/inst/doc/image-annotation.Rmd | 46 - rollama-0.2.0/rollama/inst/doc/image-annotation.html | 42 - rollama-0.2.0/rollama/inst/doc/text-embedding.Rmd | 129 ++-- rollama-0.2.0/rollama/inst/doc/text-embedding.html | 149 ++-- rollama-0.2.0/rollama/inst/extdata/logo.png |only rollama-0.2.0/rollama/man/chat_history.Rd | 3 rollama-0.2.0/rollama/man/check_model_installed.Rd | 11 rollama-0.2.0/rollama/man/create_model.Rd | 4 rollama-0.2.0/rollama/man/embed_text.Rd | 14 rollama-0.2.0/rollama/man/list_models.Rd | 2 rollama-0.2.0/rollama/man/make_query.Rd |only rollama-0.2.0/rollama/man/ping_ollama.Rd | 2 rollama-0.2.0/rollama/man/pull_model.Rd | 24 rollama-0.2.0/rollama/man/query.Rd | 81 +- rollama-0.2.0/rollama/man/rollama-options.Rd | 8 rollama-0.2.0/rollama/man/rollama-package.Rd | 3 rollama-0.2.0/rollama/tests/testthat/_snaps |only rollama-0.2.0/rollama/tests/testthat/setup-models.R | 1 rollama-0.2.0/rollama/tests/testthat/test-aaa.R |only rollama-0.2.0/rollama/tests/testthat/test-chat.R | 55 + rollama-0.2.0/rollama/tests/testthat/test-embedding.R | 2 rollama-0.2.0/rollama/tests/testthat/test-make_query.R |only rollama-0.2.0/rollama/tests/testthat/test-models.R | 11 rollama-0.2.0/rollama/tests/testthat/test-utils.R | 2 rollama-0.2.0/rollama/vignettes/README.md | 6 rollama-0.2.0/rollama/vignettes/annotation.Rmd | 326 ++++++---- rollama-0.2.0/rollama/vignettes/annotation.Rmd.orig | 222 ++++--- rollama-0.2.0/rollama/vignettes/figures/smldemo-1.png |binary rollama-0.2.0/rollama/vignettes/hf-gguf.Rmd |only rollama-0.2.0/rollama/vignettes/hf-gguf.Rmd.orig |only rollama-0.2.0/rollama/vignettes/image-annotation.Rmd | 46 - rollama-0.2.0/rollama/vignettes/image-annotation.Rmd.orig | 4 rollama-0.2.0/rollama/vignettes/text-embedding.Rmd | 129 ++-- rollama-0.2.0/rollama/vignettes/text-embedding.Rmd.orig | 14 53 files changed, 1987 insertions(+), 1319 deletions(-)
Title: Project Future Case Incidence
Description: Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>. The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.
Author: Thibaut Jombart [aut, cre],
Pierre Nouvellet [aut],
Sangeeta Bhatia [ctb],
Zhian N. Kamvar [ctb],
Tim Taylor [ctb],
Stephane Ghozzi [ctb]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between projections versions 0.6.0 dated 2023-03-23 and 0.6.1 dated 2024-12-06
DESCRIPTION | 8 - MD5 | 41 ++++++---- NEWS.md | 9 ++ R/summary.R | 1 man/figures |only man/summary.projections.Rd | 37 ++++----- tests/testthat/_snaps/plots/basic-example-plot.svg | 14 +-- tests/testthat/_snaps/plots/evd-proj-box-no-outliers.svg | 14 +-- tests/testthat/_snaps/plots/evd-proj-no-box-custom-lines.svg | 16 +-- tests/testthat/_snaps/plots/evd-proj-no-ribbon.svg | 16 +-- tests/testthat/_snaps/plots/evd-proj-red-box.svg | 14 +-- tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-and-custom.svg | 30 +++---- tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-no-box.svg | 14 +-- tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence.svg | 16 +-- tests/testthat/_snaps/plots/evd-proj.svg | 16 +-- tests/testthat/test-project.R | 6 - 16 files changed, 138 insertions(+), 114 deletions(-)