Title: Analysis of RD Designs with Multiple Cutoffs or Scores
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. The 'rdmulti' package provides tools to analyze RD designs with multiple cutoffs or scores: rdmc() estimates pooled and cutoff specific effects for multi-cutoff designs, rdmcplot() draws RD plots for multi-cutoff designs and rdms() estimates effects in cumulative cutoffs or multi-score designs. See Cattaneo, Titiunik and Vazquez-Bare (2020) <https://rdpackages.github.io/references/Cattaneo-Titiunik-VazquezBare_2020_Stata.pdf> for further methodological details.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@econ.ucsb.edu>
Diff between rdmulti versions 0.9 dated 2022-06-22 and 1.0 dated 2023-01-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/rdmc.R | 5 +++-- R/rdmcplot.R | 5 +++-- R/rdms.R | 2 +- R/rdmulti_package.R | 6 +++--- man/rdmulti-package.Rd | 4 ++-- 7 files changed, 22 insertions(+), 20 deletions(-)
Title: Create the Tree of Science from WoS and Scopus
Description: The goal of 'tosr' is to create the Tree of Science from
Web of Science (WoS) and Scopus data. It can read files
from both sources at the same time. More information
can be found in Valencia-Hernández (2020)
<https://revistas.unal.edu.co/index.php/ingeinv/article/view/77718>.
Author: Sebastian Robledo [aut, cre] ,
Martha Zuluaga [aut] ,
Oscar Arbelaez Echeverry [aut]
,
Luis Alexander Valencia Hernandez [aut],
Centro de Bioinformatica y Biologia computacional de Colombia - BIOS
[cph, fnd]
Maintainer: Sebastian Robledo <sebastian.robledogi@amigo.edu.co>
Diff between tosr versions 0.1.1 dated 2022-01-14 and 0.1.2 dated 2023-01-13
DESCRIPTION | 6 - MD5 | 8 - build/vignette.rds |binary inst/doc/ToS-dummy.html | 217 ++++++++++++++++++++++++++++++++++++++-- tests/testthat/test-tosr_load.R | 2 5 files changed, 218 insertions(+), 15 deletions(-)
Title: Business Analytics using R and Shiny
Description: A platform-independent browser-based interface for business
analytics in R, based on the shiny package. The application combines the
functionality of 'radiant.data', 'radiant.design', 'radiant.basics',
'radiant.model', and 'radiant.multivariate'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant versions 1.4.4 dated 2022-08-08 and 1.5.0 dated 2023-01-13
DESCRIPTION | 18 ++--- MD5 | 24 +++---- NEWS.md | 4 + README.md | 4 - build/build.R | 35 ++++++----- build/build_mac.R | 3 build/build_win.R | 16 ++++- build/vignette.rds |binary inst/doc/programming.html | 144 +++++++++++++++++++++++----------------------- man/launcher.Rd | 4 - man/lin_launcher.Rd | 4 - man/mac_launcher.Rd | 4 - man/win_launcher.Rd | 4 - 13 files changed, 144 insertions(+), 120 deletions(-)
Title: Small Helpers and Tricks for Epidemics Analysis
Description: A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymize data, and fitting discretized Gamma distributions.
Author: Thibaut Jombart [aut, cre],
Anne Cori [aut],
Zhian N. Kamvar [ctb],
Dirk Schumacher [ctb],
Flavio Finger [aut],
Charlie Whittaker [ctb]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between epitrix versions 0.2.2 dated 2019-01-15 and 0.4.0 dated 2023-01-13
epitrix-0.2.2/epitrix/tests/testthat/rds |only epitrix-0.4.0/epitrix/DESCRIPTION | 28 epitrix-0.4.0/epitrix/LICENSE | 2 epitrix-0.4.0/epitrix/MD5 | 86 +- epitrix-0.4.0/epitrix/NAMESPACE | 16 epitrix-0.4.0/epitrix/NEWS.md | 57 + epitrix-0.4.0/epitrix/R/clean_labels.R | 85 +- epitrix-0.4.0/epitrix/R/estimate_incubation.R |only epitrix-0.4.0/epitrix/R/final_size.R |only epitrix-0.4.0/epitrix/R/fit_discrete.R | 41 - epitrix-0.4.0/epitrix/R/gamma_tools.R | 17 epitrix-0.4.0/epitrix/R/hash_names.R | 78 +- epitrix-0.4.0/epitrix/R/sim_linelist.R |only epitrix-0.4.0/epitrix/build/vignette.rds |binary epitrix-0.4.0/epitrix/inst/doc/epitrix.R | 30 epitrix-0.4.0/epitrix/inst/doc/epitrix.Rmd | 25 epitrix-0.4.0/epitrix/inst/doc/epitrix.html | 385 +++++----- epitrix-0.4.0/epitrix/inst/doc/estimate_incubation.R |only epitrix-0.4.0/epitrix/inst/doc/estimate_incubation.Rmd |only epitrix-0.4.0/epitrix/inst/doc/estimate_incubation.html |only epitrix-0.4.0/epitrix/man/AR2R0.Rd |only epitrix-0.4.0/epitrix/man/R02AR.Rd |only epitrix-0.4.0/epitrix/man/R02herd_immunity_threshold.Rd |only epitrix-0.4.0/epitrix/man/clean_labels.Rd | 57 + epitrix-0.4.0/epitrix/man/empirical_incubation_dist.Rd |only epitrix-0.4.0/epitrix/man/figures |only epitrix-0.4.0/epitrix/man/fit_disc_gamma.Rd | 11 epitrix-0.4.0/epitrix/man/fit_gamma_incubation_dist.Rd |only epitrix-0.4.0/epitrix/man/gamma_tools.Rd | 12 epitrix-0.4.0/epitrix/man/hash_names.Rd | 43 - epitrix-0.4.0/epitrix/man/sim_linelist.Rd |only epitrix-0.4.0/epitrix/tests/testthat/_snaps |only epitrix-0.4.0/epitrix/tests/testthat/test_estimate_incubation.R |only epitrix-0.4.0/epitrix/tests/testthat/test_final_size.R |only epitrix-0.4.0/epitrix/tests/testthat/test_fit_discrete.R | 31 epitrix-0.4.0/epitrix/tests/testthat/test_gamma.R | 1 epitrix-0.4.0/epitrix/tests/testthat/test_hash_names.R | 35 epitrix-0.4.0/epitrix/tests/testthat/test_r_to_R0.R | 7 epitrix-0.4.0/epitrix/tests/testthat/test_rename.R | 47 - epitrix-0.4.0/epitrix/tests/testthat/test_sim_linelist.R |only epitrix-0.4.0/epitrix/vignettes/epitrix.Rmd | 25 epitrix-0.4.0/epitrix/vignettes/estimate_incubation.Rmd |only epitrix-0.4.0/epitrix/vignettes/figs-overview |only 43 files changed, 758 insertions(+), 361 deletions(-)
Title: Routines for Descriptive and Model-Based APC Analysis
Description: Age-Period-Cohort (APC) analyses are used to differentiate relevant drivers for long-term developments.
The 'APCtools' package offers visualization techniques and general routines to simplify the workflow of an APC analysis.
Sophisticated functions are available both for descriptive and regression model-based analyses.
For the former, we use density (or ridgeline) matrices and (hexagonally binned) heatmaps as innovative visualization
techniques building on the concept of Lexis diagrams.
Model-based analyses build on the separation of the temporal dimensions based on generalized additive models,
where a tensor product interaction surface (usually between age and period) is utilized
to represent the third dimension (usually cohort) on its diagonal.
Such tensor product surfaces can also be estimated while accounting for
further covariates in the regression model.
See Weigert et al. (2021) <doi:10.1177/1354816620987198> for methodological details.
Author: Alexander Bauer [aut, cre] ,
Maximilian Weigert [aut] ,
Hawre Jalal [aut]
Maintainer: Alexander Bauer <alexander.bauer@stat.uni-muenchen.de>
Diff between APCtools versions 1.0.1 dated 2022-01-11 and 1.0.4 dated 2023-01-13
DESCRIPTION | 16 LICENSE | 4 MD5 | 68 +-- NAMESPACE | 1 NEWS.md | 18 R/create_APCsummary.R | 20 - R/create_modelSummary.R | 49 +- R/data.R | 8 R/plot_APCheatmap.R | 3 R/plot_APChexamap.R | 48 +- R/plot_density.R | 1 R/plot_densityMatrix.R | 92 +++- R/plot_jointMarginalAPCeffects.R | 32 + R/plot_linearEffects.R | 89 ++++ R/plot_partialAPCeffects.R | 10 R/plot_smoothEffects.R | 78 ++-- README.md | 98 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/main_functionality.R | 4 inst/doc/main_functionality.Rmd | 6 inst/doc/main_functionality.html | 601 +++++++++++++++++++++++-------- man/create_APCsummary.Rd | 9 man/create_modelSummary.Rd | 13 man/extract_summary_linearEffects.Rd | 11 man/plot_1Dsmooth.Rd | 10 man/plot_densityMatrix.Rd | 25 - man/plot_density_categorical.Rd | 4 man/plot_density_metric.Rd | 6 man/plot_jointMarginalAPCeffects.Rd | 17 man/plot_linearEffects.Rd | 14 man/travel.Rd | 8 tests/testthat/test-modelSummaries.R | 4 tests/testthat/test-plots_covarEffects.R | 13 vignettes/main_functionality.Rmd | 6 35 files changed, 1029 insertions(+), 357 deletions(-)
Title: Functional Analysis of Phenotypic Growth Data to Smooth and
Extract Traits
Description: Assists in the plotting and functional smoothing of traits
measured over time and the extraction of features from these traits,
implementing the SET (Smoothing and Extraction of Traits) method
described in Brien et al. (2020) Plant Methods, 16. Smoothing of
growth trends for individual plants using natural cubic smoothing
splines or P-splines is available for removing transient effects and
segmented smoothing is available to deal with discontinuities in
growth trends. There are graphical tools for assessing the adequacy
of trait smoothing, both when using this and other packages, such as
those that fit nonlinear growth models. A range of per-unit (plant,
pot, plot) growth traits or features can be extracted from the
data, including single time points, interval growth rates and other
growth statistics, such as maximum growth or days to maximum growth.
The package also has tools adapted to inputting data from
high-throughput phenotyping facilities, such from a Lemna-Tec
Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 2.1.16 dated 2022-11-15 and 2.1.17 dated 2023-01-13
growthPheno-2.1.16/growthPheno/tests/testthat/Rplots.pdf |only growthPheno-2.1.17/growthPheno/DESCRIPTION | 12 - growthPheno-2.1.17/growthPheno/MD5 | 21 +- growthPheno-2.1.17/growthPheno/R/dataLongi_v9.r | 20 +- growthPheno-2.1.17/growthPheno/R/traitSmooth.r | 31 ++- growthPheno-2.1.17/growthPheno/build/partial.rdb |binary growthPheno-2.1.17/growthPheno/inst/News.Rd | 6 growthPheno-2.1.17/growthPheno/inst/doc/Rice.pdf |binary growthPheno-2.1.17/growthPheno/inst/doc/Tomato.pdf |binary growthPheno-2.1.17/growthPheno/inst/doc/growthPheno-manual.pdf |binary growthPheno-2.1.17/growthPheno/tests/testthat/testProbeSmooths.r | 10 + growthPheno-2.1.17/growthPheno/tests/testthat/testTraitWrappers.r | 79 +++++++--- 12 files changed, 126 insertions(+), 53 deletions(-)
Title: Spatially Explicit Capture-Recapture by Inverse Prediction
Description: Estimates the density of a spatially distributed animal population
sampled with an array of passive detectors, such as traps. Models incorporating
distance-dependent detection are fitted by simulation and inverse prediction
as proposed by Efford (2004) <doi:10.1111/j.0030-1299.2004.13043.x>.
Author: Murray Efford [aut, cre]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between ipsecr versions 1.3.0 dated 2022-09-09 and 1.4.0 dated 2023-01-13
DESCRIPTION | 13 + MD5 | 52 +++---- NAMESPACE | 7 - NEWS | 19 ++ R/RcppExports.R | 4 R/ipsecr.fit.R | 273 +++++++++++++++++++++++----------------- R/plotProxy.R | 1 R/proxyfn.R | 124 +++++++++++------- R/simCH.R | 29 +++- R/simpop.R | 2 R/utility.R | 27 ++- inst/doc/ipsecr-vignette.R | 62 ++++++++- inst/doc/ipsecr-vignette.Rmd | 115 ++++++++++++++-- inst/doc/ipsecr-vignette.pdf |binary inst/example/fittedmodels.RData |binary inst/example/ip.Fr.RData |binary man/details.Rd | 4 man/ipsecr-internal.Rd | 19 ++ man/ipsecr-package.Rd | 32 ++-- man/ipsecr.fit.Rd | 11 + src/RcppExports.cpp | 15 +- src/armaCH.cpp | 110 ++++++++++++---- tests/testthat/test-ipsecr.R | 10 - tests/testthat/test-nontarget.R | 49 ++++--- tests/testthat/test-proxy.R | 13 + tests/testthat/test-simCH.R | 14 +- vignettes/ipsecr-vignette.Rmd | 115 ++++++++++++++-- 27 files changed, 786 insertions(+), 334 deletions(-)
Title: Estimation of Transition Probabilities in Multistate Models
Description: Estimation of transition probabilities for the
illness-death model and or the three-state progressive model.
Author: Artur Araujo [aut, cre] ,
Javier Roca-Pardinas [aut] ,
Luis Meira-Machado [aut]
Maintainer: Artur Araujo <artur.stat@gmail.com>
Diff between TPmsm versions 1.2.5 dated 2021-10-15 and 1.2.7 dated 2023-01-13
DESCRIPTION | 10 - MD5 | 180 ++++++++++++++++---------------- R/BtoTPCmsm.R | 6 - R/BtoTPmsm.R | 22 ++-- R/Clean.R | 6 - R/OutTPmsm.R | 6 - R/Outetm.R | 46 ++++---- R/Outp3state.R | 6 - R/TPmsmOut.R | 38 +++--- R/Trans.R | 86 +++++++-------- R/TransBoot.R | 122 +++++++++++----------- R/TransCheck.R | 258 +++++++++++++++++++++++------------------------ R/TransMatrix.R | 82 +++++++------- R/TransMethod.R | 40 +++---- R/TransPROB.R | 90 ++++++++-------- R/TransWidth.R | 30 ++--- R/addlegend.R | 30 ++--- R/as.data.frame.survTP.R | 14 +- R/contour.TPCmsm.R | 122 +++++++++++----------- R/corrTP.R | 58 +++++----- R/csample.int.R | 8 - R/dgpTP.R | 20 +-- R/image.TPCmsm.R | 190 +++++++++++++++++----------------- R/lines.TPCmsm.R | 150 +++++++++++++-------------- R/lines.TPmsm.R | 62 +++++------ R/methods.R | 62 +++++------ R/object.R | 14 +- R/plot.TPCmsm.R | 170 +++++++++++++++--------------- R/plot.TPmsm.R | 68 ++++++------ R/print.TPCmsm.R | 46 ++++---- R/print.TPmsm.R | 52 ++++----- R/setPackageSeedTP.R | 26 ++-- R/setSeedTP.R | 50 ++++----- R/setThreadsTP.R | 16 +- R/survTP.R | 88 ++++++++-------- R/toTPCmsm.R | 6 - R/toTPmsm.R | 22 ++-- R/transAJ.R | 18 +-- R/transIPCW.R | 30 ++--- R/transKMPW.R | 24 ++-- R/transKMW.R | 24 ++-- R/transLIN.R | 32 ++--- R/transLS.R | 28 ++--- R/transPAJ.R | 18 +-- R/uniqueTP.R | 14 +- R/zzz.R | 6 - README.md | 21 +++ build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 235 ++++++++++++++++++++++-------------------- inst/doc/TPmsm.Rnw | 13 -- inst/doc/TPmsm.pdf |binary man/TPmsm-package.Rd | 9 + man/dgpTP.Rd | 7 + src/BtoTPCmsm.c | 34 +++--- src/BtoTPmsm.c | 68 ++++++------ src/RngArray.c | 8 - src/RngArray.h | 4 src/RngBoot.c | 54 ++++----- src/RngStream.c | 6 - src/dgpTP.c | 20 +-- src/get.c | 89 ++++++++-------- src/init.c | 2 src/kmsurv.c | 24 ++-- src/logistic.c | 81 +++++++------- src/logistic.h | 5 src/quantile.c | 24 ++-- src/rseed.c | 2 src/sample.c | 2 src/sort.c | 161 ++++++++++++++--------------- src/toTPCmsm.c | 34 +++--- src/toTPmsm.c | 66 ++++++------ src/transAJ.c | 88 ++++++++-------- src/transIPCW1.c | 128 +++++++++++------------ src/transIPCW2.c | 202 ++++++++++++++++++------------------ src/transKMPW1.c | 144 +++++++++++++------------- src/transKMPW2.c | 152 +++++++++++++-------------- src/transKMW.c | 36 +++--- src/transKMW1.c | 96 ++++++++--------- src/transKMW2.c | 96 ++++++++--------- src/transLIN1.c | 78 +++++++------- src/transLIN2.c | 110 ++++++++++---------- src/transLS.c | 237 ++++++++++++++++++++----------------------- src/transPAJ.c | 102 +++++++++--------- src/unique.c | 20 +-- src/uniqueTP.c | 64 +++++------ src/unload.c | 2 src/wikmsurv.c | 34 +++--- src/window.c | 256 +++++++++++++++++++++++----------------------- src/wkmsurv.c | 34 +++--- vignettes/TPmsm.Rnw | 13 -- 91 files changed, 2697 insertions(+), 2660 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 0.9.1 dated 2022-10-25 and 0.9.2 dated 2023-01-13
tidytable-0.9.1/tidytable/R/compat-lifecycle.R |only tidytable-0.9.2/tidytable/DESCRIPTION | 14 - tidytable-0.9.2/tidytable/MD5 | 114 +++++----- tidytable-0.9.2/tidytable/NAMESPACE | 12 + tidytable-0.9.2/tidytable/NEWS.md | 25 ++ tidytable-0.9.2/tidytable/R/as_tidytable.R | 4 tidytable-0.9.2/tidytable/R/extract.R | 26 +- tidytable-0.9.2/tidytable/R/group_by.R | 10 tidytable-0.9.2/tidytable/R/group_cols.R |only tidytable-0.9.2/tidytable/R/join.R | 56 ++++ tidytable-0.9.2/tidytable/R/mutate.R | 3 tidytable-0.9.2/tidytable/R/na_if.R | 10 tidytable-0.9.2/tidytable/R/pick.R |only tidytable-0.9.2/tidytable/R/pivot_longer.R | 7 tidytable-0.9.2/tidytable/R/pivot_wider.R | 52 ++-- tidytable-0.9.2/tidytable/R/purrr-map.R | 15 + tidytable-0.9.2/tidytable/R/purrr-map2.R | 7 tidytable-0.9.2/tidytable/R/purrr-pmap.R | 7 tidytable-0.9.2/tidytable/R/rowwise.R | 2 tidytable-0.9.2/tidytable/R/select.R | 22 - tidytable-0.9.2/tidytable/R/separate.R | 53 +++- tidytable-0.9.2/tidytable/R/separate_longer_delim.R |only tidytable-0.9.2/tidytable/R/separate_rows.R | 7 tidytable-0.9.2/tidytable/R/separate_wider_delim.R |only tidytable-0.9.2/tidytable/R/separate_wider_regex.R |only tidytable-0.9.2/tidytable/R/summarize.R | 2 tidytable-0.9.2/tidytable/R/tidytable-package.R | 2 tidytable-0.9.2/tidytable/R/unite.R | 2 tidytable-0.9.2/tidytable/R/unnest_longer.R | 29 +- tidytable-0.9.2/tidytable/R/utils-across.R | 53 ++-- tidytable-0.9.2/tidytable/R/utils-general.R | 68 +++-- tidytable-0.9.2/tidytable/R/utils-prep_exprs.R | 50 ++-- tidytable-0.9.2/tidytable/R/utils-stringr.R | 14 - tidytable-0.9.2/tidytable/man/cross_join.Rd |only tidytable-0.9.2/tidytable/man/extract..Rd | 4 tidytable-0.9.2/tidytable/man/extract.Rd | 4 tidytable-0.9.2/tidytable/man/group_cols.Rd |only tidytable-0.9.2/tidytable/man/map.Rd | 11 tidytable-0.9.2/tidytable/man/na_if..Rd | 2 tidytable-0.9.2/tidytable/man/na_if.Rd | 2 tidytable-0.9.2/tidytable/man/pick.Rd |only tidytable-0.9.2/tidytable/man/pivot_wider..Rd | 14 - tidytable-0.9.2/tidytable/man/pivot_wider.Rd | 14 - tidytable-0.9.2/tidytable/man/separate..Rd | 9 tidytable-0.9.2/tidytable/man/separate.Rd | 9 tidytable-0.9.2/tidytable/man/separate_longer_delim.Rd |only tidytable-0.9.2/tidytable/man/separate_rows..Rd | 7 tidytable-0.9.2/tidytable/man/separate_rows.Rd | 7 tidytable-0.9.2/tidytable/man/separate_wider_delim.Rd |only tidytable-0.9.2/tidytable/man/separate_wider_regex.Rd |only tidytable-0.9.2/tidytable/man/unnest_longer..Rd | 3 tidytable-0.9.2/tidytable/man/unnest_longer.Rd | 3 tidytable-0.9.2/tidytable/tests/testthat/test-across.R | 11 tidytable-0.9.2/tidytable/tests/testthat/test-cur-context.R | 13 - tidytable-0.9.2/tidytable/tests/testthat/test-extract.R | 74 +++--- tidytable-0.9.2/tidytable/tests/testthat/test-join.R | 28 ++ tidytable-0.9.2/tidytable/tests/testthat/test-na_if.R | 29 ++ tidytable-0.9.2/tidytable/tests/testthat/test-pick.R |only tidytable-0.9.2/tidytable/tests/testthat/test-pivot_wider.R | 17 + tidytable-0.9.2/tidytable/tests/testthat/test-purrr.R | 8 tidytable-0.9.2/tidytable/tests/testthat/test-select.R | 9 tidytable-0.9.2/tidytable/tests/testthat/test-separate.R | 44 +++ tidytable-0.9.2/tidytable/tests/testthat/test-separate_longer_delim.R |only tidytable-0.9.2/tidytable/tests/testthat/test-separate_wider_delim.R |only tidytable-0.9.2/tidytable/tests/testthat/test-separate_wider_regex.R |only tidytable-0.9.2/tidytable/tests/testthat/test-unnest_longer.R | 11 66 files changed, 675 insertions(+), 324 deletions(-)
Title: Factorization of Sparse Counts Matrices Through Poisson
Likelihood
Description: Creates a non-negative low-rank approximate factorization of a sparse counts matrix by maximizing Poisson
likelihood with L1/L2 regularization (e.g. for implicit-feedback recommender systems or bag-of-words-based topic modeling)
(Cortes, (2018) <arXiv:1811.01908>), which usually leads to very sparse user and item factors (over 90% zero-valued).
Similar to hierarchical Poisson factorization (HPF), but follows an optimization-based approach with regularization
instead of a hierarchical prior, and is fit through gradient-based methods instead of variational inference.
Author: David Cortes [aut, cre, cph],
Jean-Sebastien Roy [cph] ,
Stephen Nash [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between poismf versions 0.4.0-2 dated 2022-10-25 and 0.4.0-3 dated 2023-01-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- configure | 9 +++------ configure.ac | 4 +++- 4 files changed, 12 insertions(+), 13 deletions(-)
More information about multilevelcoda at CRAN
Permanent link
Title: Tidy Presentation of Clinical Reporting
Description: Streamlined statistical reporting in 'Rmarkdown' environments.
Facilitates the automated reporting of descriptive statistics, multiple
univariate models, multivariable models and tables combining these outputs.
Plotting functions include customisable survival curves, forest plots from
logistic and ordinal regression and bivariate comparison plots.
Author: Lisa Avery [cre, aut],
Ryan Del Bel [aut],
Osvaldo Espin-Garcia [aut],
Tyler Pittman [aut] ,
Yanning Wang [ctr],
Jessica Weiss [aut],
Wei Xu [aut]
Maintainer: Lisa Avery <lisa.avery@uhn.ca>
Diff between reportRmd versions 0.0.1 dated 2022-10-17 and 0.0.2 dated 2023-01-13
DESCRIPTION | 12 MD5 | 40 NAMESPACE | 2 NEWS.md | 17 R/helper.R | 1277 ++--- R/main.R | 7883 +++++++++++++++---------------- README.md | 51 build/vignette.rds |binary inst/doc/reportRmd.R | 6 inst/doc/reportRmd.Rmd | 771 +-- inst/doc/reportRmd.pdf |binary man/cap.Rd | 30 man/covsum.Rd | 222 man/figures/README-unnamed-chunk-7-1.png |binary man/forestplot2.Rd | 104 man/plotuv.Rd | 152 man/rm_covsum.Rd | 299 - man/rm_mvsum.Rd | 217 man/rm_survsum.Rd | 210 man/rm_uvsum.Rd | 314 - vignettes/reportRmd.Rmd | 771 +-- 21 files changed, 6323 insertions(+), 6055 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis. Please see Vinue (2017) <doi:10.18637/jss.v077.i06>.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between Anthropometry versions 1.17 dated 2021-12-09 and 1.18 dated 2023-01-13
DESCRIPTION | 11 +++---- MD5 | 37 +++++++++++++------------ NAMESPACE | 6 ++-- NEWS | 5 +++ R/figures8landm.R | 40 ++++++++++++++-------------- R/shapes3dShapes.R | 4 +- build/partial.rdb |binary inst/doc/Anthropometry.pdf |binary man/Anthropometry-internalHipamAnthropom.Rd | 4 +- man/Anthropometry-internalPlotTree.Rd | 4 +- man/Anthropometry-package.Rd | 4 +- man/checkBranchLocalIMO.Rd | 4 +- man/checkBranchLocalMO.Rd | 4 +- man/getBestPamsamIMO.Rd | 4 +- man/getBestPamsamMO.Rd | 4 +- man/hipamAnthropom.Rd | 4 +- man/plotTreeHipamAnthropom.Rd | 6 ++-- src/cast.c | 3 -- src/cast.h |only src/init.c | 9 ------ 20 files changed, 75 insertions(+), 78 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.33.0 dated 2022-12-14 and 1.34.0 dated 2023-01-13
DESCRIPTION | 6 ++--- MD5 | 25 ++++++++++++----------- NEWS.md | 47 +++++++++++++++++++++++++++++++++++++------- R/000.import.R |only R/availableConnections.R | 5 ++-- R/availableCores.R | 5 +--- R/availableWorkers.R | 27 +++++++++++++++++++------ R/makeClusterPSOCK.R | 2 - R/options.R | 6 ++--- R/utils.R | 31 ----------------------------- man/availableConnections.Rd | 5 ++-- man/availableWorkers.Rd | 11 ++++++++-- man/parallelly.options.Rd | 4 +-- tests/makeClusterPSOCK.R | 17 +++++++++++++++ 14 files changed, 117 insertions(+), 74 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-14 0.1.6
2016-11-22 0.1.5
2016-11-13 0.1.2
Title: Create Custom Plots for Viewing Genetic Association Results
Description: A collection of functions for visualizing,exploring and annotating genetic association results.Association results from multiple traits can be viewed simultaneously along with gene annotation, over the entire genome (Manhattan plot) or in the more detailed regional view.
Author: Genuity Science [cph],
Thorhildur Juliusdottir [aut, cre],
Andri Stefansson [aut]
Maintainer: Thorhildur Juliusdottir <thorhildur@genuitysci.com>
Diff between topr versions 1.1.1 dated 2022-11-04 and 1.1.2 dated 2023-01-13
topr-1.1.1/topr/man/figures/topr_v.1.1.0.gif |only topr-1.1.2/topr/DESCRIPTION | 6 - topr-1.1.2/topr/MD5 | 65 +++++++--------- topr-1.1.2/topr/NEWS.md | 6 + topr-1.1.2/topr/R/dat_checks.R | 2 topr-1.1.2/topr/R/data.R | 1 topr-1.1.2/topr/R/deprec_funcs.R | 4 topr-1.1.2/topr/R/effectplot.R | 22 +++-- topr-1.1.2/topr/R/get_genes_and_annotation.R | 7 + topr-1.1.2/topr/R/locuszoomplot.R | 9 +- topr-1.1.2/topr/R/manhattan.R | 39 +++++---- topr-1.1.2/topr/R/plot_functions.R | 40 +++++---- topr-1.1.2/topr/R/qqtopr.R | 7 + topr-1.1.2/topr/R/regionplot.R | 12 ++ topr-1.1.2/topr/R/setters_and_getters.R | 6 + topr-1.1.2/topr/R/topr.R | 3 topr-1.1.2/topr/man/CD_FINNGEN.Rd | 1 topr-1.1.2/topr/man/annotate_with_nearest_gene.Rd | 2 topr-1.1.2/topr/man/create_snpset.Rd | 2 topr-1.1.2/topr/man/effectplot.Rd | 4 topr-1.1.2/topr/man/flip_to_positive_allele_for_dat1.Rd | 2 topr-1.1.2/topr/man/get_best_snp_per_MB.Rd | 2 topr-1.1.2/topr/man/get_genes_in_region.Rd | 5 - topr-1.1.2/topr/man/get_lead_snps.Rd | 2 topr-1.1.2/topr/man/get_overlapping_snps_by_pos.Rd | 2 topr-1.1.2/topr/man/get_snpset.Rd | 4 topr-1.1.2/topr/man/get_snpset_code.Rd | 2 topr-1.1.2/topr/man/locuszoom.Rd | 24 ++++- topr-1.1.2/topr/man/manhattan.Rd | 29 +++---- topr-1.1.2/topr/man/match_by_alleles.Rd | 2 topr-1.1.2/topr/man/match_by_pos.Rd | 2 topr-1.1.2/topr/man/qqtopr.Rd | 9 +- topr-1.1.2/topr/man/regionplot.Rd | 10 +- topr-1.1.2/topr/man/topr.Rd | 3 34 files changed, 203 insertions(+), 133 deletions(-)
Title: Data Frames with Persistent Columns and Attributes
Description: Provides data frames that hold certain columns and attributes
persistently for data processing in 'dplyr'.
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>
Diff between stickyr versions 0.1.0 dated 2022-11-07 and 0.1.1 dated 2023-01-13
DESCRIPTION | 10 ++++++---- MD5 | 13 +++++++------ NEWS.md | 5 +++++ R/distinct.R | 7 +++++-- R/sticky_tbl_df.R | 12 +++++++----- README.md | 11 +++++++++-- man/new_sticky_tibble.Rd | 12 +++++++----- tests/testthat/test-distinct.R |only 8 files changed, 46 insertions(+), 24 deletions(-)
Title: Simulator for Spatially Resolved Transcriptomics
Description: An independent, reproducible, and flexible Spatially Resolved Transcriptomics (SRT) simulation framework that can be used to facilitate the development of SRT analytical methods for a wide variety of SRT-specific analyses. It utilizes spatial localization information to simulate SRT expression count data in a reproducible and scalable fashion. Two major simulation schemes are implemented in 'SRTsim': reference-based and reference-free.
Author: Jiaqiang Zhu [aut, ctb, cre] ,
Lulu Shang [aut] ,
Xiang Zhou [aut]
Maintainer: Jiaqiang Zhu <jiaqiang@umich.edu>
Diff between SRTsim versions 0.99.3 dated 2022-11-20 and 0.99.6 dated 2023-01-13
SRTsim-0.99.3/SRTsim/NEWS |only SRTsim-0.99.6/SRTsim/DESCRIPTION | 15 ++++++++------- SRTsim-0.99.6/SRTsim/MD5 | 23 +++++++++++++---------- SRTsim-0.99.6/SRTsim/NAMESPACE | 8 ++++++++ SRTsim-0.99.6/SRTsim/R/SRTcci.R |only SRTsim-0.99.6/SRTsim/R/SRTfit.R | 12 +++++++++++- SRTsim-0.99.6/SRTsim/R/SRTsim_class.R | 19 +++++++++++++++++++ SRTsim-0.99.6/SRTsim/R/simSRTLocs.R | 6 ++---- SRTsim-0.99.6/SRTsim/inst/doc/SRTsim.R | 12 +++++++++++- SRTsim-0.99.6/SRTsim/inst/doc/SRTsim.Rmd | 12 +++++++++++- SRTsim-0.99.6/SRTsim/inst/doc/SRTsim.html | 27 ++++++++++++++------------- SRTsim-0.99.6/SRTsim/man/simNewLocs.Rd |only SRTsim-0.99.6/SRTsim/man/srtsim_cci_free.Rd |only SRTsim-0.99.6/SRTsim/man/srtsim_cci_ref.Rd |only SRTsim-0.99.6/SRTsim/vignettes/SRTsim.Rmd | 12 +++++++++++- 15 files changed, 108 insertions(+), 38 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430>.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb]
Maintainer: Samuel Marsh <samuel.marsh@childrens.harvard.edu>
Diff between scCustomize versions 1.1.0 dated 2022-12-23 and 1.1.1 dated 2023-01-13
DESCRIPTION | 13 MD5 | 76 +- NAMESPACE | 4 NEWS.md | 25 R/Color_Palettes.R | 128 ++-- R/Internal_Utilities.R | 64 +- R/LIGER_Plotting.R | 55 - R/LIGER_Utilities.R | 76 +- R/Nebulosa_Plotting.R | 38 - R/Object_Utilities.R | 341 ++++-------- R/Plotting_Utilities.R | 2 R/QC_Plotting_Seq_10X.R | 273 ++++----- R/QC_Plotting_Seurat.R | 5 R/Read_&_Write_Data.R | 205 ++++--- R/Seurat_Iterative_Plotting.R | 272 +++++---- R/Seurat_Plotting.R | 1040 ++++++++++++++++++------------------- R/Statistics.R | 8 R/Statistics_Plotting.R | 18 R/Utilities.R | 288 ++++++++-- README.md | 44 - build/partial.rdb |binary man/Cluster_Highlight_Plot.Rd | 9 man/ColorBlind_Pal.Rd | 2 man/Dark2_Pal.Rd | 2 man/DiscretePalette_scCustomize.Rd | 2 man/Fetch_Meta.Rd | 16 man/Hue_Pal.Rd | 2 man/JCO_Four.Rd | 2 man/Merge_Seurat_List.Rd | 2 man/Meta_Highlight_Plot.Rd | 6 man/NavyAndOrange.Rd | 2 man/PalettePlot.Rd | 9 man/Rename_Clusters.Rd | 2 man/Single_Color_Palette.Rd | 2 man/Stacked_VlnPlot.Rd | 3 man/UnRotate_X.Rd | 2 man/Variable_Features_ALL_LIGER.Rd | 2 man/scCustomize_Palette.Rd | 2 man/viridis_shortcut.Rd | 16 39 files changed, 1643 insertions(+), 1415 deletions(-)
Title: Probabilistic Forecast Combination Using CRPS Learning
Description: Combine probabilistic forecasts using CRPS learning algorithms proposed in Berrisch, Ziel (2021) <arXiv:2102.00968> <doi:10.1016/j.jeconom.2021.11.008>. The package implements multiple online learning algorithms like Bernstein online aggregation; see Wintenberger (2014) <arXiv:1404.1356>. Quantile regression is also implemented for comparison purposes. Model parameters can be tuned automatically with respect to the loss of the forecast combination. Methods like predict(), update(), plot() and print() are available for convenience. This package utilizes the optim C++ library for numeric optimization <https://github.com/kthohr/optim>.
Author: Jonathan Berrisch [cre] ,
Florian Ziel [aut]
Maintainer: Jonathan Berrisch <Jonathan@Berrisch.biz>
Diff between profoc versions 1.0.0 dated 2022-12-23 and 1.1.0 dated 2023-01-13
DESCRIPTION | 10 +- MD5 | 28 +++--- NAMESPACE | 1 NEWS.md | 11 ++ R/RcppExports.R | 44 ++++++++++ README.md | 4 build/partial.rdb |binary man/penalty.Rd |only man/profoc-package.Rd | 5 + src/RcppExports.cpp | 26 ++++++ src/splines.cpp | 118 +++++++++++++++++++++------- tests/testthat/test-grids.R | 18 ++-- tests/testthat/test-penalty.R |only tests/testthat/test-save_past_performance.R | 14 +-- tests/testthat/test-save_predictions_grid.R | 31 ++++--- tests/testthat/test-sobolev.R | 2 16 files changed, 239 insertions(+), 73 deletions(-)
Title: Calculation of the Integrated Flow of Particles Between Polygons
Description: Calculate the flow of particles between polygons by two integration methods:
integration by a cubature method and integration on a grid of points.
Annie Bouvier, Kien Kieu, Kasia Adamczyk and Herve Monod (2009)
<doi:10.1016/j.envsoft.2008.11.006>.
Author: Annie Bouvier [aut, cph],
Kien Kieu [aut, cph],
Kasia Adamczyk [aut, cph],
Herve Monod [aut, cph],
Jean-Francois Rey [cre]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
Diff between RCALI versions 0.3.4 dated 2022-09-26 and 0.3.5 dated 2023-01-13
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- src/Adapt.cc | 2 +- src/Adapt.h | 1 + src/Point.h | 4 ++-- src/Triangle.cc | 4 ++-- src/Vector.cc | 10 +++++----- src/crConvexSp.cc | 14 +++++++------- src/fluxsd.cc | 44 ++++++++++++++++++++++---------------------- src/geom.cc | 8 ++++---- src/go.cc | 16 ++++++++-------- src/intersection.cc | 4 ++-- src/methodAdapt.cc | 8 ++++---- src/methodGrid.cc | 14 +++++++------- src/methodIntegr.h | 4 ++-- src/read1Poly.cc | 26 +++++++++++++------------- src/readPoly.cc | 32 ++++++++++++++++---------------- src/zoneintegration.cc | 4 ++-- 18 files changed, 119 insertions(+), 118 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions where showing the progress is
useful (e.g. bootstrap). The type and style of the
progress bar (with percentages or remaining time)
can be set through options.
Supports several parallel processing backends including future.
Author: Peter Solymos [aut, cre] ,
Zygmunt Zawadzki [aut],
Henrik Bengtsson [ctb],
R Core Team [cph, ctb]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between pbapply versions 1.6-0 dated 2022-11-15 and 1.7-0 dated 2023-01-13
pbapply-1.6-0/pbapply/tests/file-1.csv |only pbapply-1.6-0/pbapply/tests/file-2.csv |only pbapply-1.6-0/pbapply/tests/file-3.csv |only pbapply-1.7-0/pbapply/DESCRIPTION | 36 +++++++++--- pbapply-1.7-0/pbapply/MD5 | 23 ++++---- pbapply-1.7-0/pbapply/NAMESPACE | 4 + pbapply-1.7-0/pbapply/NEWS.md |only pbapply-1.7-0/pbapply/R/pbapply.R | 93 ++++++++++++++++++++++++++++++++- pbapply-1.7-0/pbapply/R/pbby.R |only pbapply-1.7-0/pbapply/R/pbeapply.R |only pbapply-1.7-0/pbapply/R/pblapply.R | 29 +++++++++- pbapply-1.7-0/pbapply/R/pbmapply.R | 5 + pbapply-1.7-0/pbapply/R/pbvapply.R |only pbapply-1.7-0/pbapply/inst/WORDLIST | 1 pbapply-1.7-0/pbapply/man/pbapply.Rd | 75 ++++++++++++++++++++++++-- pbapply-1.7-0/pbapply/tests/tests.R | 71 +++++++++++++++++++++++++ 16 files changed, 307 insertions(+), 30 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for performing variation partitioning, calculating several measures of model discrimination and calibration, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: Barbosa A.M., Brown J.A., Jimenez-Valverde A., Real R.
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.8.4 dated 2022-10-30 and 3.9 dated 2023-01-13
modEvA-3.8.4/modEvA/R/pseudoRsq.R |only modEvA-3.9/modEvA/DESCRIPTION | 13 ++- modEvA-3.9/modEvA/MD5 | 43 ++++++------ modEvA-3.9/modEvA/NAMESPACE | 6 - modEvA-3.9/modEvA/NEWS | 111 +++++++++++++++++++++++++++++++- modEvA-3.9/modEvA/R/Dsquared.R | 108 ++++++++++++++++++++----------- modEvA-3.9/modEvA/R/MESS.R | 7 +- modEvA-3.9/modEvA/R/MillerCalib.R | 16 ++-- modEvA-3.9/modEvA/R/RMSE.R |only modEvA-3.9/modEvA/R/RsqGLM.R | 23 ++++-- modEvA-3.9/modEvA/R/lollipop.R |only modEvA-3.9/modEvA/R/mod2obspred.R | 8 +- modEvA-3.9/modEvA/R/predDensity.R | 62 +++++++++++------ modEvA-3.9/modEvA/R/ptsrast2obspred.R | 30 ++++---- modEvA-3.9/modEvA/R/threshMeasures.R | 44 ++++++------ modEvA-3.9/modEvA/R/varImp.R |only modEvA-3.9/modEvA/data/rotif.mods.rda |binary modEvA-3.9/modEvA/man/Dsquared.Rd | 28 ++++---- modEvA-3.9/modEvA/man/RMSE.Rd |only modEvA-3.9/modEvA/man/RsqGLM.Rd | 10 +- modEvA-3.9/modEvA/man/lollipop.Rd |only modEvA-3.9/modEvA/man/modEvA-package.Rd | 12 ++- modEvA-3.9/modEvA/man/modEvAmethods.Rd | 2 modEvA-3.9/modEvA/man/predDensity.Rd | 34 ++++++--- modEvA-3.9/modEvA/man/threshMeasures.Rd | 13 ++- modEvA-3.9/modEvA/man/varImp.Rd |only 26 files changed, 382 insertions(+), 188 deletions(-)
Title: Sensitivities of Prices of Financial Options and Implied
Volatilites
Description: Methods to calculate sensitivities of financial option prices for
European, Asian, American and Digital Options options in the Black Scholes
model, and in more general jump diffusion models. A shiny app to interactively
view plot the results is included. Furthermore, methods to
compute implied volatilities are provided for a wide range of option types and
custom payoff functions. Classical formulas are implemented for European
options in the Black Scholes Model, as is presented in Hull, J. C. (2017).
Options, Futures, and Other Derivatives, Global Edition (9th Edition). Pearson.
In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see
Hudde, A. & Rüschendorf, L. (2016). European and Asian Greeks for exponential
Lévy processes. <arXiv:1603.00920>. For American options, the Binomial Tree
Method is implemented, as is presented in Hull, J. C. (2017).
Author: Anselm Hudde [aut, cre]
Maintainer: Anselm Hudde <anselmhudde@gmx.de>
Diff between greeks versions 0.7.0 dated 2022-08-26 and 0.8.0 dated 2023-01-13
greeks-0.7.0/greeks/R/BS_European_Greeks_test.R |only greeks-0.7.0/greeks/man/BS_European_Greeks_test.Rd |only greeks-0.8.0/greeks/DESCRIPTION | 13 - greeks-0.8.0/greeks/MD5 | 16 - greeks-0.8.0/greeks/NAMESPACE | 8 greeks-0.8.0/greeks/R/BS_Implied_Volatility.R | 101 +++------ greeks-0.8.0/greeks/R/Greeks_UI.R |only greeks-0.8.0/greeks/R/Implied_Volatility_test.R |only greeks-0.8.0/greeks/R/greeks-package.R |only greeks-0.8.0/greeks/man/BS_European_Greeks.Rd | 4 greeks-0.8.0/greeks/man/Greeks_UI.Rd |only greeks-0.8.0/greeks/man/Malliavin_Asian_Greeks.Rd | 216 ++++++++++----------- 12 files changed, 173 insertions(+), 185 deletions(-)
Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography
formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and
'Bibentry'. Includes a port of the 'bibutils' utilities by Chris
Putnam <https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in
'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] ),
Chris Putman [aut] ,
Richard Mathar [ctb] ,
Johannes Wilm [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between rbibutils versions 2.2.12 dated 2023-01-10 and 2.2.13 dated 2023-01-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 11 ++++++++++- build/partial.rdb |binary src/common_bt_btd_blt.c | 2 +- src/common_bt_btd_blt.h | 2 +- 6 files changed, 20 insertions(+), 11 deletions(-)
Title: Multi-Way Component Analysis
Description: For single tensor data, any matrix factorization method can be specified the matricised tensor in each dimension by Multi-way Component Analysis (MWCA). An originally extended MWCA is also implemented to specify and decompose multiple matrices and tensors simultaneously (CoupledMWCA). See the reference section of GitHub README.md <https://github.com/rikenbit/mwTensor>, for details of the methods.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between mwTensor versions 1.0.0 dated 2023-01-12 and 1.0.1 dated 2023-01-13
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- build/partial.rdb |binary inst/NEWS | 4 ++++ man/CoupledMWCA.Rd | 17 +++++++++++++---- man/MWCA.Rd | 5 +++-- man/defaultCoupledMWCAParams.Rd | 10 ++++++---- man/defaultMWCAParams.Rd | 6 ++++-- man/myALS_SVD.Rd | 1 + man/myCX.Rd | 1 + man/myICA.Rd | 1 + man/myNMF.Rd | 1 + man/mySVD.Rd | 1 + man/toyModel.Rd | 7 ++++++- 14 files changed, 57 insertions(+), 29 deletions(-)
Title: Mutational Signature Analysis Tools
Description: Utility functions for mutational signature analysis
as described in Alexandrov, L. B. (2020)
<doi:10.1038/s41586-020-1943-3>.
This package provides two groups of functions. One is
for dealing with mutational signature "exposures"
(i.e. the counts of mutations in a sample that are
due to each mutational signature). The other group of
functions is for matching or comparing sets of
mutational signatures. 'mSigTools' stands for
mutational Signature analysis Tools.
Author: Steven Rozen [aut, cre] ,
Nanhai Jiang [aut]
Maintainer: Steven Rozen <steverozen@pm.me>
Diff between mSigTools versions 1.0.5 dated 2022-08-30 and 1.0.7 dated 2023-01-13
DESCRIPTION | 31 ++++++++++------------ MD5 | 29 ++++++++++++-------- NAMESPACE | 2 + NEWS.md | 15 +++++++++- R/exposure_related_functions.R | 15 ++++++---- R/find_best_reconstruction_QP.R |only R/optimize_exposure_QP.R |only R/sig_dist_matrix.R | 10 ++++++- README.md | 4 ++ inst/CITATION | 10 +++---- inst/WORDLIST | 4 ++ man/find_best_reconstruction_QP.Rd |only man/optimize_exposure_QP.Rd |only man/plot_exposure.Rd | 3 +- man/plot_exposure_internal.Rd | 3 +- man/plot_exposure_to_pdf.Rd | 3 +- tests/testthat/test_find_best_reconstruction_QP.R |only tests/testthat/test_optimize_exposure_QP.R |only tests/testthat/testdata/SBS96_spectrum.csv |only 19 files changed, 84 insertions(+), 45 deletions(-)
Title: Inequality Measures for Weighted Data
Description: Computes inequality measures of a given variable taking into account weights. Bootstrap method provides distribution of inequality measures and several additional statistics.
Author: Sebastian Wojcik [aut, cre] ,
Agnieszka Giemza [aut],
Katarzyna Machowska [aut],
Jaroslaw Napora [aut]
Maintainer: Sebastian Wojcik <S.Wojcik@stat.gov.pl>
Diff between wINEQ versions 1.0.1 dated 2022-02-11 and 1.1.1 dated 2023-01-13
DESCRIPTION | 24 +- MD5 | 43 ++-- NEWS.md |only R/inequalityMeasure.R | 481 +++++++++++++++++++++++++++++++++++++--------- R/inequalityMeasureBoot.R | 86 +++++--- data |only man/Allison_and_Foster.Rd | 30 ++ man/Atkinson.Rd | 29 ++ man/CoefVar.Rd | 26 ++ man/Entropy.Rd | 29 ++ man/Gini.Rd | 29 ++ man/Hoover.Rd | 25 ++ man/Jenkins.Rd | 42 +++- man/Kolm.Rd | 36 ++- man/Leti.Rd | 28 ++ man/Palma.Rd | 29 ++ man/Prop20_20.Rd | 25 +- man/RicciSchutz.Rd | 29 ++ man/Theil_L.Rd | 26 ++ man/Theil_T.Rd | 30 ++ man/Tourism.Rd |only man/Well_being.Rd |only man/ineq_weighted.Rd | 37 ++- man/ineq_weighted_boot.Rd | 49 +++- 24 files changed, 892 insertions(+), 241 deletions(-)
Title: Distances on Directed Graphs
Description: Distances on dual-weighted directed graphs using
priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>).
Weighted directed graphs have weights from A to B which may differ
from those from B to A. Dual-weighted directed graphs have two sets
of such weights. A canonical example is a street network to be used
for routing in which routes are calculated by weighting distances
according to the type of way and mode of transport, yet lengths of
routes must be calculated from direct distances.
Author: Mark Padgham [aut, cre],
Andreas Petutschnig [aut],
David Cooley [aut],
Robin Lovelace [ctb],
Andrew Smith [ctb],
Malcolm Morgan [ctb],
Shane Saunders [cph]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between dodgr versions 0.2.18 dated 2022-12-07 and 0.2.19 dated 2023-01-13
DESCRIPTION | 9 ++- MD5 | 24 ++++----- NEWS.md | 11 ++++ README.md | 15 +++++- inst/doc/dists-categorical.html | 14 ++--- inst/doc/dodgr.html | 100 ++++++++++++---------------------------- inst/doc/flows.html | 4 - inst/doc/parallel.html | 4 - inst/doc/times.R | 22 +++++--- inst/doc/times.Rmd | 26 ++++++---- inst/doc/times.html | 32 +++++++----- tests/testthat/test-iso.R | 2 vignettes/times.Rmd | 26 ++++++---- 13 files changed, 149 insertions(+), 140 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 4.0.1 dated 2022-09-16 and 4.1.0 dated 2023-01-13
DESCRIPTION | 12 MD5 | 83 NAMESPACE | 6 NEWS | 14 R/authorProdOverTime.R | 2 R/bib2df.R | 9 R/bradford.R | 2 R/cocMatrix.R | 28 R/conceptualStructure.R | 23 R/couplingMap.R | 19 R/csvLens2df.R | 2 R/csvScopus2df.R | 2 R/customTheme.R |only R/dimensions2df.R | 12 R/histNetwork.R | 11 R/histPlot.R | 36 R/keywordGrowth.R | 4 R/metaTagExtraction.R | 5 R/missingData.R |only R/networkPlot.R | 31 R/plotThematicEvolution.R | 13 R/rpys.R | 138 R/summary.bibliometrix.R | 6 R/sysdata.rda |only R/tableTag.R | 2 R/thematicEvolution.R | 25 R/thematicMap.R | 32 R/threeFieldsPlot.R | 13 R/toUpper.R | 2 R/zzz.R | 199 build/partial.rdb |binary data/bibtag.rda |binary data/countries.rda |binary data/customTheme.rda |only data/logo.rda |binary data/stopwords.rda |binary inst/biblioshiny/libraries.R |only inst/biblioshiny/rsconnect/shinyapps.io/massimoaria/biblioshiny.dcf | 8 inst/biblioshiny/server.R | 4473 ++-------- inst/biblioshiny/ui.R | 3835 +++++++- inst/biblioshiny/utils.R | 550 - man/customTheme.Rd |only man/missingData.Rd |only man/rpys.Rd | 4 man/thematicEvolution.Rd | 4 man/thematicMap.Rd | 5 46 files changed, 5651 insertions(+), 3959 deletions(-)
Title: 'Rcpp' Integration for the 'mlpack' Library
Description: A fast, flexible machine learning library, written in C++, that
aims to provide fast, extensible implementations of cutting-edge
machine learning algorithms. See also Curtin et al. (2018)
<doi:10.21105/joss.00726>.
Author: Yashwant Singh Parihar [aut, ctb, cph],
Ryan Curtin [aut, ctb, cph, cre],
Dirk Eddelbuettel [aut, ctb, cph],
James Balamuta [aut, ctb, cph],
Bill March [ctb, cph],
Dongryeol Lee [ctb, cph],
Nishant Mehta [ctb, cph],
Parikshit Ram [ctb, cph],
James Cl [...truncated...]
Maintainer: Ryan Curtin <ryan@ratml.org>
Diff between mlpack versions 4.0.0 dated 2022-10-28 and 4.0.1 dated 2023-01-13
DESCRIPTION | 12 MD5 | 209 +++++++-------- R/RcppExports.R | 4 R/adaboost.R | 4 R/approx_kfn.R | 6 R/bayesian_linear_regression.R | 4 R/cf.R | 4 R/dbscan.R | 2 R/decision_tree.R | 2 R/det.R | 4 R/emst.R | 2 R/fastmks.R | 4 R/gmm_probability.R | 2 R/gmm_train.R | 2 R/hmm_loglik.R | 2 R/hmm_viterbi.R | 2 R/image_converter.R | 2 R/kde.R | 4 R/kernel_pca.R | 2 R/kfn.R | 6 R/kmeans.R | 4 R/knn.R | 6 R/krann.R | 4 R/lars.R | 6 R/linear_regression.R | 4 R/linear_svm.R | 4 R/lmnn.R | 4 R/local_coordinate_coding.R | 6 R/logistic_regression.R | 4 R/lsh.R | 4 R/mean_shift.R | 2 R/nbc.R | 4 R/nca.R | 2 R/nmf.R | 6 R/pca.R | 2 R/perceptron.R | 4 R/preprocess_binarize.R | 2 R/preprocess_describe.R | 2 R/preprocess_one_hot_encoding.R | 2 R/preprocess_scale.R | 2 R/preprocess_split.R | 2 R/radical.R | 2 R/random_forest.R | 4 R/softmax_regression.R | 4 R/sparse_coding.R | 6 R/test_r_binding.R | 8 inst/include/mlpack.h | 10 man/test_r_binding.Rd | 3 src/RcppExports.cpp | 9 src/cereal/access.hpp | 4 src/cereal/archives/adapters.hpp | 4 src/cereal/archives/binary.hpp | 4 src/cereal/archives/json.hpp | 35 +- src/cereal/archives/portable_binary.hpp | 4 src/cereal/archives/xml.hpp | 4 src/cereal/cereal.hpp | 43 ++- src/cereal/details/helpers.hpp | 4 src/cereal/details/polymorphic_impl.hpp | 41 ++ src/cereal/details/polymorphic_impl_fwd.hpp | 4 src/cereal/details/static_object.hpp | 9 src/cereal/details/traits.hpp | 4 src/cereal/details/util.hpp | 4 src/cereal/external/LICENSE |only src/cereal/external/base64.hpp | 4 src/cereal/external/rapidjson/LICENSE |only src/cereal/external/rapidjson/document.h | 19 - src/cereal/external/rapidjson/msinttypes/LICENSE |only src/cereal/external/rapidxml/license.txt |only src/cereal/external/rapidxml/manual.html |only src/cereal/macros.hpp | 10 src/cereal/specialize.hpp | 4 src/cereal/types/array.hpp | 4 src/cereal/types/atomic.hpp | 4 src/cereal/types/base_class.hpp | 4 src/cereal/types/bitset.hpp | 4 src/cereal/types/boost_variant.hpp | 4 src/cereal/types/chrono.hpp | 4 src/cereal/types/common.hpp | 4 src/cereal/types/complex.hpp | 4 src/cereal/types/concepts/pair_associative_container.hpp | 4 src/cereal/types/deque.hpp | 4 src/cereal/types/forward_list.hpp | 4 src/cereal/types/functional.hpp | 4 src/cereal/types/list.hpp | 4 src/cereal/types/map.hpp | 4 src/cereal/types/memory.hpp | 6 src/cereal/types/optional.hpp | 9 src/cereal/types/polymorphic.hpp | 6 src/cereal/types/queue.hpp | 4 src/cereal/types/set.hpp | 4 src/cereal/types/stack.hpp | 4 src/cereal/types/string.hpp | 4 src/cereal/types/tuple.hpp | 4 src/cereal/types/unordered_map.hpp | 4 src/cereal/types/unordered_set.hpp | 4 src/cereal/types/utility.hpp | 4 src/cereal/types/valarray.hpp | 2 src/cereal/types/variant.hpp | 17 - src/cereal/types/vector.hpp | 6 src/cereal/version.hpp | 6 src/mlpack/base.hpp | 4 src/mlpack/bindings/R/print_input_processing.hpp | 31 ++ src/mlpack/bindings/R/tests/test_r_binding_main.cpp | 61 +++- src/mlpack/core/util/gitversion.hpp | 2 src/mlpack/core/util/version.hpp | 2 src/r_util.cpp | 5 src/rcpp_mlpack.h | 2 tests/testthat/test-R_binding.R | 11 108 files changed, 508 insertions(+), 352 deletions(-)
Title: Delete-d Jackknife for Point and Interval Estimation
Description: This function creates jackknife samples from the data by
sequentially removing d observations from the data, performs estimation
using the jackknife samples and calculates the jackknife coefficients, bias,
standard error and confidence intervals based on the methodology discussed by
Quenouille (1956) <doi:10.2307/2332914>,
Tukey (1958) <doi:10.1214/aoms/1177706647> and
Shi (1988) <doi:10.1016/0167-7152(88)90011-9>.
Author: S. Mohanasundaram [aut, cre]
Maintainer: S. Mohanasundaram <s.mohanasundaram@outlook.com>
Diff between jackknifeR versions 0.1.1 dated 2022-12-02 and 1.0.0 dated 2023-01-13
DESCRIPTION | 19 ++++----- MD5 | 20 +++++---- NAMESPACE | 4 + NEWS.md | 18 ++++++++ R/jackknife.R |only R/jackknife.cor.R | 29 +++++++++----- R/jackknife.lm.R | 36 +++++++++++------ README.md | 5 -- build/partial.rdb |binary man/jackknife.Rd |only man/jackknife.cor.Rd | 99 +++++++++++++++++++++++++----------------------- man/jackknife.lm.Rd | 104 +++++++++++++++++++++++++-------------------------- 12 files changed, 190 insertions(+), 144 deletions(-)
Title: Fit Hidden Markov Models using Template Model Builder
Description: Fitting hidden Markov models using automatic differentiation
and Laplace approximation, allowing for fast inference and flexible covariate
effects (including random effects and smoothing splines) on model parameters.
The package is described by Michelot (2022) <arXiv:2211.14139>.
Author: Theo Michelot [aut, cre],
Richard Glennie [aut, ctb]
Maintainer: Theo Michelot <theo.michelot@dal.ca>
Diff between hmmTMB versions 1.0.0 dated 2023-01-11 and 1.0.1 dated 2023-01-13
hmmTMB-1.0.0/hmmTMB/inst/doc/hmmTMB_dist_list.R |only hmmTMB-1.0.0/hmmTMB/inst/doc/hmmTMB_dist_list.Rmd |only hmmTMB-1.0.0/hmmTMB/inst/doc/hmmTMB_dist_list.pdf |only hmmTMB-1.0.0/hmmTMB/inst/doc/hmmTMB_example_stan.R |only hmmTMB-1.0.0/hmmTMB/inst/doc/hmmTMB_example_stan.Rmd |only hmmTMB-1.0.0/hmmTMB/inst/doc/hmmTMB_example_stan.pdf |only hmmTMB-1.0.0/hmmTMB/inst/doc/hmmTMB_workflow.R |only hmmTMB-1.0.0/hmmTMB/inst/doc/hmmTMB_workflow.Rmd |only hmmTMB-1.0.0/hmmTMB/inst/doc/hmmTMB_workflow.pdf |only hmmTMB-1.0.0/hmmTMB/vignettes/hmmTMB_dist_list.Rmd |only hmmTMB-1.0.0/hmmTMB/vignettes/hmmTMB_example_stan.Rmd |only hmmTMB-1.0.0/hmmTMB/vignettes/hmmTMB_workflow.Rmd |only hmmTMB-1.0.1/hmmTMB/DESCRIPTION | 6 +- hmmTMB-1.0.1/hmmTMB/MD5 | 21 ++-------- hmmTMB-1.0.1/hmmTMB/build/vignette.rds |binary hmmTMB-1.0.1/hmmTMB/inst/doc/hmmTMB_list_of_online_resources.Rmd |only hmmTMB-1.0.1/hmmTMB/inst/doc/hmmTMB_list_of_online_resources.pdf |only hmmTMB-1.0.1/hmmTMB/vignettes/hmmTMB_list_of_online_resources.Rmd |only hmmTMB-1.0.1/hmmTMB/vignettes/refs.bib | 7 +++ 19 files changed, 16 insertions(+), 18 deletions(-)
Title: Genetic Analysis Package
Description: As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18.
<doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data
analysis of both population and family data. Currently, it contains functions for
sample size calculations of both population-based and family-based designs, probability
of familial disease aggregation, kinship calculation, statistics in linkage analysis,
and association analysis involving genetic markers including haplotype analysis with or
without environmental covariates. Over years, the package has been developed in-between
many projects hence also in line with the name (gap).
Author: Jing Hua Zhao [aut, cre] ,
Kurt Hornik [ctb],
Brian Ripley [ctb],
Uwe Liggs [ctb],
Achim Zeileis [ctb]
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>
Diff between gap versions 1.4-2 dated 2023-01-09 and 1.5 dated 2023-01-13
ChangeLog | 7 DESCRIPTION | 14 MD5 | 35 - R/gap-package.R | 6 R/read.ms.output.R | 2 inst/doc/gap.Rmd | 27 inst/doc/gap.html | 96 +-- inst/doc/jss.pdf |binary inst/doc/shinygap.Rmd | 39 - inst/doc/shinygap.html | 1335 +++++++++++++++++++++++++++++++++++++++++++++---- man/gap-package.Rd | 6 man/read.ms.output.Rd | 2 src/gcontrol_c.c | 4 src/pgc.h | 3 src/pgc_c.c | 18 vignettes/HR.txt |only vignettes/gap.Rmd | 27 vignettes/gap.bib | 71 +- vignettes/shinygap.Rmd | 39 - 19 files changed, 1456 insertions(+), 275 deletions(-)
Title: Biodiversity Data from the Living Atlas Community
Description: The living atlas community provides tools to enable users to find,
access, combine and visualise data on biodiversity. 'galah' enables the R
community to directly access data and resources hosted by the living atlases.
Author: Martin Westgate [aut, cre],
Matilda Stevenson [aut],
Dax Kellie [aut],
Peggy Newman [aut]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
Diff between galah versions 1.5.0 dated 2022-10-27 and 1.5.1 dated 2023-01-13
galah-1.5.0/galah/R/atlas_GET.R |only galah-1.5.0/galah/R/atlas_POST.R |only galah-1.5.0/galah/R/atlas_download.R |only galah-1.5.0/galah/R/atlas_url.R |only galah-1.5.0/galah/inst/doc/international_atlases.Rmd |only galah-1.5.0/galah/inst/doc/international_atlases.html |only galah-1.5.0/galah/inst/doc/syntax_changes.Rmd |only galah-1.5.0/galah/inst/doc/syntax_changes.html |only galah-1.5.0/galah/man/atlas_url.Rd |only galah-1.5.0/galah/tests/fixtures/IA_Austria_atlas_counts2.yml |only galah-1.5.0/galah/tests/fixtures/IA_Austria_atlas_counts3.yml |only galah-1.5.0/galah/tests/fixtures/IA_Austria_search_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Austria_show_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Austria_show_values.yml |only galah-1.5.0/galah/tests/fixtures/IA_Brazil_atlas_counts2.yml |only galah-1.5.0/galah/tests/fixtures/IA_Brazil_atlas_counts3.yml |only galah-1.5.0/galah/tests/fixtures/IA_Brazil_search_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Brazil_show_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Estonia_atlas_counts3.yml |only galah-1.5.0/galah/tests/fixtures/IA_Estonia_search_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Estonia_show_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_France_atlas_counts.yml |only galah-1.5.0/galah/tests/fixtures/IA_France_atlas_counts2.yml |only galah-1.5.0/galah/tests/fixtures/IA_France_atlas_counts3.yml |only galah-1.5.0/galah/tests/fixtures/IA_France_search_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_France_show_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Guatemala_atlas_counts2.yml |only galah-1.5.0/galah/tests/fixtures/IA_Guatemala_atlas_counts3.yml |only galah-1.5.0/galah/tests/fixtures/IA_Guatemala_search_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Guatemala_show_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Portugal_atlas_counts2.yml |only galah-1.5.0/galah/tests/fixtures/IA_Portugal_atlas_counts3.yml |only galah-1.5.0/galah/tests/fixtures/IA_Portugal_search_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Portugal_show_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Portugal_show_values.yml |only galah-1.5.0/galah/tests/fixtures/IA_Spain_atlas_counts2.yml |only galah-1.5.0/galah/tests/fixtures/IA_Spain_atlas_counts3.yml |only galah-1.5.0/galah/tests/fixtures/IA_Spain_search_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Spain_show_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Spain_show_values.yml |only galah-1.5.0/galah/tests/fixtures/IA_Sweden_search_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_Sweden_show_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_United_Kingdom_atlas_counts2.yml |only galah-1.5.0/galah/tests/fixtures/IA_United_Kingdom_atlas_counts3.yml |only galah-1.5.0/galah/tests/fixtures/IA_United_Kingdom_atlas_counts_records.yml |only galah-1.5.0/galah/tests/fixtures/IA_United_Kingdom_atlas_counts_species.yml |only galah-1.5.0/galah/tests/fixtures/IA_United_Kingdom_search_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_United_Kingdom_show_all.yml |only galah-1.5.0/galah/tests/fixtures/IA_United_Kingdom_show_all_fields.yml |only galah-1.5.0/galah/tests/fixtures/IA_United_Kingdom_show_field_values.yml |only galah-1.5.0/galah/tests/fixtures/IA_United_Kingdom_show_values.yml |only galah-1.5.0/galah/tests/fixtures/IA_search_taxa_multiple_UK.yml |only galah-1.5.0/galah/tests/fixtures/IA_search_taxa_types_UK.yml |only galah-1.5.0/galah/tests/fixtures/atlas_count.yml |only galah-1.5.0/galah/tests/fixtures/atlas_media-1.yml |only galah-1.5.0/galah/tests/fixtures/atlas_media-2.yml |only galah-1.5.0/galah/tests/fixtures/multiple_group_by_counts.yml |only galah-1.5.0/galah/tests/fixtures/paginated_counts.yml |only galah-1.5.0/galah/tests/fixtures/piped_counts_1.yml |only galah-1.5.0/galah/tests/fixtures/piped_counts_2.yml |only galah-1.5.0/galah/tests/fixtures/piped_counts_3_groups.yml |only galah-1.5.0/galah/tests/fixtures/piped_counts_bbox.yml |only galah-1.5.0/galah/tests/fixtures/piped_counts_polygon.yml |only galah-1.5.0/galah/tests/fixtures/record_count_group_by.yml |only galah-1.5.0/galah/tests/fixtures/record_count_group_by_with_limit.yml |only galah-1.5.0/galah/tests/fixtures/record_count_no_limit.yml |only galah-1.5.0/galah/tests/fixtures/species_count.yml |only galah-1.5.0/galah/tests/fixtures/species_count_group_by.yml |only galah-1.5.0/galah/tests/fixtures/species_group_by_counts.yml |only galah-1.5.0/galah/tests/fixtures/taxa_count.yml |only galah-1.5.0/galah/tests/fixtures/taxonConceptID_group_by_counts.yml |only galah-1.5.0/galah/vignettes/galah-DiagrammeR-plot.png |only galah-1.5.0/galah/vignettes/international_atlases.Rmd |only galah-1.5.0/galah/vignettes/syntax_changes.Rmd |only galah-1.5.1/galah/DESCRIPTION | 23 galah-1.5.1/galah/MD5 | 487 galah-1.5.1/galah/NAMESPACE | 45 galah-1.5.1/galah/NEWS.md | 42 galah-1.5.1/galah/R/atlas_citation.R | 3 galah-1.5.1/galah/R/atlas_counts.R | 244 galah-1.5.1/galah/R/atlas_media.R | 103 galah-1.5.1/galah/R/atlas_occurrences.R | 372 galah-1.5.1/galah/R/atlas_species.R | 109 galah-1.5.1/galah/R/atlas_taxonomy.R | 33 galah-1.5.1/galah/R/build_predicates.R |only galah-1.5.1/galah/R/clear_cached_files.R | 24 galah-1.5.1/galah/R/collect_media.R | 24 galah-1.5.1/galah/R/collect_occurrences.R | 45 galah-1.5.1/galah/R/count.R |only galah-1.5.1/galah/R/deprecated_functions.R | 8 galah-1.5.1/galah/R/filter.R |only galah-1.5.1/galah/R/galah-package.R | 75 galah-1.5.1/galah/R/galah_apply_profile.R | 17 galah-1.5.1/galah/R/galah_bbox.R | 55 galah-1.5.1/galah/R/galah_call.R | 82 galah-1.5.1/galah/R/galah_config.R | 201 galah-1.5.1/galah/R/galah_down_to.R | 33 galah-1.5.1/galah/R/galah_filter.R | 170 galah-1.5.1/galah/R/galah_geolocate.R | 107 galah-1.5.1/galah/R/galah_group_by.R | 85 galah-1.5.1/galah/R/galah_identify.R | 86 galah-1.5.1/galah/R/galah_internal_cache.R | 7 galah-1.5.1/galah/R/galah_polygon.R | 88 galah-1.5.1/galah/R/galah_select.R | 112 galah-1.5.1/galah/R/group_by.R |only galah-1.5.1/galah/R/grouped_counts_GBIF.R |only galah-1.5.1/galah/R/grouped_counts_LA.R |only galah-1.5.1/galah/R/identify.R |only galah-1.5.1/galah/R/occurrences_GBIF.R |only galah-1.5.1/galah/R/occurrences_LA.R |only galah-1.5.1/galah/R/onload.R | 5 galah-1.5.1/galah/R/print.R |only galah-1.5.1/galah/R/reexports.R |only galah-1.5.1/galah/R/search_all.R | 102 galah-1.5.1/galah/R/search_identifiers.R | 53 galah-1.5.1/galah/R/search_media.R | 22 galah-1.5.1/galah/R/search_taxa.R | 102 galah-1.5.1/galah/R/select.R |only galah-1.5.1/galah/R/show_all.R | 312 galah-1.5.1/galah/R/show_values.R | 113 galah-1.5.1/galah/R/slice_head.R |only galah-1.5.1/galah/R/st_crop.R |only galah-1.5.1/galah/R/sysdata.rda |binary galah-1.5.1/galah/R/url_GET.R |only galah-1.5.1/galah/R/url_POST.R |only galah-1.5.1/galah/R/url_download.R |only galah-1.5.1/galah/R/url_lookup.R |only galah-1.5.1/galah/R/url_paginate.R |only galah-1.5.1/galah/R/url_queue.R |only galah-1.5.1/galah/R/utilities_internal.R | 163 galah-1.5.1/galah/R/utilities_occurrences.R |only galah-1.5.1/galah/README.md | 6 galah-1.5.1/galah/build/vignette.rds |binary galah-1.5.1/galah/inst/doc/choosing_an_atlas.Rmd |only galah-1.5.1/galah/inst/doc/choosing_an_atlas.html |only galah-1.5.1/galah/inst/doc/download_data.Rmd | 71 galah-1.5.1/galah/inst/doc/download_data.html | 217 galah-1.5.1/galah/inst/doc/look_up_information.Rmd | 107 galah-1.5.1/galah/inst/doc/look_up_information.html | 220 galah-1.5.1/galah/inst/doc/narrow_your_results.Rmd | 176 galah-1.5.1/galah/inst/doc/narrow_your_results.html | 287 galah-1.5.1/galah/inst/doc/piping.Rmd |only galah-1.5.1/galah/inst/doc/piping.html |only galah-1.5.1/galah/inst/doc/quick_start_guide.Rmd | 84 galah-1.5.1/galah/inst/doc/quick_start_guide.html | 220 galah-1.5.1/galah/man/atlas_citation.Rd | 5 galah-1.5.1/galah/man/atlas_counts.Rd | 87 galah-1.5.1/galah/man/atlas_media.Rd | 64 galah-1.5.1/galah/man/atlas_occurrences.Rd | 42 galah-1.5.1/galah/man/atlas_species.Rd | 70 galah-1.5.1/galah/man/atlas_taxonomy.Rd | 111 galah-1.5.1/galah/man/clear_cached_files.Rd | 20 galah-1.5.1/galah/man/collect_media.Rd | 18 galah-1.5.1/galah/man/collect_occurrences.Rd | 16 galah-1.5.1/galah/man/count.data_request.Rd |only galah-1.5.1/galah/man/deprecated.Rd | 2 galah-1.5.1/galah/man/filter.data_request.Rd |only galah-1.5.1/galah/man/galah.Rd | 72 galah-1.5.1/galah/man/galah_apply_profile.Rd | 16 galah-1.5.1/galah/man/galah_bbox.Rd | 51 galah-1.5.1/galah/man/galah_call.Rd | 66 galah-1.5.1/galah/man/galah_config.Rd | 100 galah-1.5.1/galah/man/galah_down_to.Rd | 69 galah-1.5.1/galah/man/galah_filter.Rd | 143 galah-1.5.1/galah/man/galah_geolocate.Rd | 107 galah-1.5.1/galah/man/galah_group_by.Rd | 73 galah-1.5.1/galah/man/galah_identify.Rd | 62 galah-1.5.1/galah/man/galah_polygon.Rd | 39 galah-1.5.1/galah/man/galah_select.Rd | 25 galah-1.5.1/galah/man/group_by.data_request.Rd |only galah-1.5.1/galah/man/identify.data_request.Rd |only galah-1.5.1/galah/man/reexports.Rd |only galah-1.5.1/galah/man/search_all.Rd | 58 galah-1.5.1/galah/man/search_identifiers.Rd | 25 galah-1.5.1/galah/man/search_media.Rd | 13 galah-1.5.1/galah/man/search_taxa.Rd | 101 galah-1.5.1/galah/man/select.data_request.Rd |only galah-1.5.1/galah/man/show_all.Rd | 37 galah-1.5.1/galah/man/show_values.Rd | 6 galah-1.5.1/galah/man/slice_head.data_request.Rd |only galah-1.5.1/galah/man/st_crop.data_request.Rd |only galah-1.5.1/galah/tests/fixtures/IA_Austria_atlas_counts.yml | 16 galah-1.5.1/galah/tests/fixtures/IA_Austria_atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/IA_Austria_atlas_counts_identify.yml |only galah-1.5.1/galah/tests/fixtures/IA_Austria_search_all_taxa.yml |only galah-1.5.1/galah/tests/fixtures/IA_Austria_show_all_assertions.yml |only galah-1.5.1/galah/tests/fixtures/IA_Austria_show_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_Austria_show_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_Austria_show_all_fields.yml | 20 galah-1.5.1/galah/tests/fixtures/IA_Austria_show_all_lists.yml |only galah-1.5.1/galah/tests/fixtures/IA_Austria_show_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_Austria_show_all_reasons.yml |only galah-1.5.1/galah/tests/fixtures/IA_Austria_show_values_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_Austria_show_values_profiles.yml |only galah-1.5.1/galah/tests/fixtures/IA_Brazil_atlas_counts.yml | 24 galah-1.5.1/galah/tests/fixtures/IA_Brazil_atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/IA_Brazil_atlas_counts_identify.yml |only galah-1.5.1/galah/tests/fixtures/IA_Brazil_search_all_taxa.yml |only galah-1.5.1/galah/tests/fixtures/IA_Brazil_show_all_assertions.yml |only galah-1.5.1/galah/tests/fixtures/IA_Brazil_show_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_Brazil_show_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_Brazil_show_all_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_Brazil_show_all_lists.yml |only galah-1.5.1/galah/tests/fixtures/IA_Brazil_show_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_Brazil_show_values.yml | 292 galah-1.5.1/galah/tests/fixtures/IA_Estonia_atlas_counts.yml | 20 galah-1.5.1/galah/tests/fixtures/IA_Estonia_atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/IA_Estonia_search_all_taxa.yml |only galah-1.5.1/galah/tests/fixtures/IA_Estonia_show_all_assertions.yml |only galah-1.5.1/galah/tests/fixtures/IA_Estonia_show_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_Estonia_show_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_Estonia_show_all_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_Estonia_show_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_Estonia_show_values.yml | 10 galah-1.5.1/galah/tests/fixtures/IA_France_atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/IA_France_atlas_counts_identify.yml |only galah-1.5.1/galah/tests/fixtures/IA_France_atlas_counts_records.yml |only galah-1.5.1/galah/tests/fixtures/IA_France_atlas_counts_species.yml |only galah-1.5.1/galah/tests/fixtures/IA_France_search_all_taxa.yml |only galah-1.5.1/galah/tests/fixtures/IA_France_show_all_assertions.yml |only galah-1.5.1/galah/tests/fixtures/IA_France_show_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_France_show_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_France_show_all_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_France_show_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_France_show_values.yml | 35 galah-1.5.1/galah/tests/fixtures/IA_GBIF_atlas_counts.yml |only galah-1.5.1/galah/tests/fixtures/IA_GBIF_atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/IA_GBIF_atlas_counts_identify.yml |only galah-1.5.1/galah/tests/fixtures/IA_GBIF_search_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_GBIF_search_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_GBIF_search_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_GBIF_search_all_taxa.yml |only galah-1.5.1/galah/tests/fixtures/IA_GBIF_show_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_GBIF_show_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_GBIF_show_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_GBIF_show_values.yml |only galah-1.5.1/galah/tests/fixtures/IA_Guatemala_atlas_counts.yml | 16 galah-1.5.1/galah/tests/fixtures/IA_Guatemala_atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/IA_Guatemala_atlas_counts_identify.yml |only galah-1.5.1/galah/tests/fixtures/IA_Guatemala_search_all_taxa.yml |only galah-1.5.1/galah/tests/fixtures/IA_Guatemala_show_all_assertions.yml |only galah-1.5.1/galah/tests/fixtures/IA_Guatemala_show_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_Guatemala_show_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_Guatemala_show_all_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_Guatemala_show_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_Guatemala_show_all_reasons.yml |only galah-1.5.1/galah/tests/fixtures/IA_Guatemala_show_values.yml | 10 galah-1.5.1/galah/tests/fixtures/IA_Guatemala_show_values_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_Portugal_atlas_counts.yml | 20 galah-1.5.1/galah/tests/fixtures/IA_Portugal_atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/IA_Portugal_atlas_counts_identify.yml |only galah-1.5.1/galah/tests/fixtures/IA_Portugal_search_all_taxa.yml |only galah-1.5.1/galah/tests/fixtures/IA_Portugal_show_all_assertions.yml |only galah-1.5.1/galah/tests/fixtures/IA_Portugal_show_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_Portugal_show_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_Portugal_show_all_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_Portugal_show_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_Portugal_show_all_reasons.yml |only galah-1.5.1/galah/tests/fixtures/IA_Portugal_show_values_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_atlas_counts.yml | 24 galah-1.5.1/galah/tests/fixtures/IA_Spain_atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_atlas_counts_identify.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_search_all_identifiers.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_search_all_taxa.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_search_all_taxa_df.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_all_assertions.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_all_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_all_licences.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_all_lists.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_all_profiles.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_all_reasons.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_values_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_Spain_show_values_profiles.yml |only galah-1.5.1/galah/tests/fixtures/IA_Sweden_atlas_counts.yml | 20 galah-1.5.1/galah/tests/fixtures/IA_Sweden_atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/IA_Sweden_search_all_taxa.yml |only galah-1.5.1/galah/tests/fixtures/IA_Sweden_show_all_assertions.yml |only galah-1.5.1/galah/tests/fixtures/IA_Sweden_show_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_Sweden_show_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_Sweden_show_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_Sweden_show_all_reasons.yml |only galah-1.5.1/galah/tests/fixtures/IA_Sweden_show_values.yml | 27 galah-1.5.1/galah/tests/fixtures/IA_UK_atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_atlas_counts_identify.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_atlas_counts_records.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_atlas_counts_species.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_search_all_taxa.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_search_taxa_multiple.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_search_taxa_types.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_show_all_assertions.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_show_all_collections.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_show_all_datasets.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_show_all_fields.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_show_all_lists.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_show_all_providers.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_show_all_reasons.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_show_list_values.yml |only galah-1.5.1/galah/tests/fixtures/IA_UK_show_values_field.yml |only galah-1.5.1/galah/tests/fixtures/apply_profile_counts.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_group_by.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_group_by_taxonConceptID.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_group_by_with_limit.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_identify.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_multiple_group_by.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_no_args.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_no_limit.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_pagination.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_piped_1.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_piped_2.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_piped_3_groups.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_piped_bbox.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_piped_polygon.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_startup.yml | 5159 ---------- galah-1.5.1/galah/tests/fixtures/atlas_counts_type_species.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_type_species_group_by.yml |only galah-1.5.1/galah/tests/fixtures/atlas_counts_type_species_group_by_2.yml |only galah-1.5.1/galah/tests/fixtures/count_test.yml |only galah-1.5.1/galah/tests/fixtures/galah_filter_startup.yml | 330 galah-1.5.1/galah/tests/fixtures/galah_identify_search_1.yml | 12 galah-1.5.1/galah/tests/fixtures/galah_identify_search_2.yml | 48 galah-1.5.1/galah/tests/fixtures/galah_identify_search_3.yml | 175 galah-1.5.1/galah/tests/fixtures/identify_test.yml |only galah-1.5.1/galah/tests/fixtures/logger_config.yml | 96 galah-1.5.1/galah/tests/fixtures/search_identifiers_id_search.yml | 45 galah-1.5.1/galah/tests/fixtures/search_identifiers_invalid.yml | 15 galah-1.5.1/galah/tests/fixtures/search_taxa_df.yml | 30 galah-1.5.1/galah/tests/fixtures/search_taxa_invalid.yml | 15 galah-1.5.1/galah/tests/fixtures/search_taxa_multiple.yml | 45 galah-1.5.1/galah/tests/fixtures/search_taxa_rank_search.yml | 15 galah-1.5.1/galah/tests/fixtures/search_taxa_simple.yml | 15 galah-1.5.1/galah/tests/fixtures/search_taxa_valid_invalid.yml | 60 galah-1.5.1/galah/tests/fixtures/select_taxa.yml | 15 galah-1.5.1/galah/tests/fixtures/slice_head.yml |only galah-1.5.1/galah/tests/fixtures/taxonomy_tree_with_pipes.yml | 204 galah-1.5.1/galah/tests/testthat/test-atlas_counts.R | 50 galah-1.5.1/galah/tests/testthat/test-atlas_media.R | 2 galah-1.5.1/galah/tests/testthat/test-atlas_occurrences.R | 1 galah-1.5.1/galah/tests/testthat/test-atlas_species.R | 7 galah-1.5.1/galah/tests/testthat/test-galah_apply_profile.R |only galah-1.5.1/galah/tests/testthat/test-galah_config.R | 2 galah-1.5.1/galah/tests/testthat/test-galah_select.R | 8 galah-1.5.1/galah/tests/testthat/test-international-Austria.R | 122 galah-1.5.1/galah/tests/testthat/test-international-Brazil.R | 121 galah-1.5.1/galah/tests/testthat/test-international-Estonia.R | 96 galah-1.5.1/galah/tests/testthat/test-international-France.R | 167 galah-1.5.1/galah/tests/testthat/test-international-GBIF.R |only galah-1.5.1/galah/tests/testthat/test-international-Guatemala.R | 108 galah-1.5.1/galah/tests/testthat/test-international-Portugal.R | 106 galah-1.5.1/galah/tests/testthat/test-international-Spain.R | 198 galah-1.5.1/galah/tests/testthat/test-international-Sweden.R | 169 galah-1.5.1/galah/tests/testthat/test-international-UK.R | 139 galah-1.5.1/galah/tests/testthat/test-masked-functions.R |only galah-1.5.1/galah/tests/testthat/test-search_all.R | 2 galah-1.5.1/galah/tests/testthat/test-search_taxa.R | 4 galah-1.5.1/galah/vignettes/atlases_plot.R |only galah-1.5.1/galah/vignettes/atlases_plot.png |only galah-1.5.1/galah/vignettes/choosing_an_atlas.Rmd |only galah-1.5.1/galah/vignettes/download_data.Rmd | 71 galah-1.5.1/galah/vignettes/look_up_information.Rmd | 107 galah-1.5.1/galah/vignettes/narrow_your_results.Rmd | 176 galah-1.5.1/galah/vignettes/piping.Rmd |only galah-1.5.1/galah/vignettes/quick_start_guide.Rmd | 84 365 files changed, 4944 insertions(+), 10047 deletions(-)
Title: Generating Funky Heatmaps for Data Frames
Description: Allows generating heatmap-like visualisations for benchmark data
frames. Funky heatmaps can be fine-tuned by providing annotations of the
columns and rows, which allows assigning multiple palettes or geometries
or grouping rows and columns together in categories.
Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between funkyheatmap versions 0.1.0 dated 2022-11-28 and 0.2.0 dated 2023-01-13
funkyheatmap-0.1.0/funkyheatmap/R/process_geom_params.R |only funkyheatmap-0.1.0/funkyheatmap/man/figures/README-example-heatmap-1.png |only funkyheatmap-0.1.0/funkyheatmap/man/figures/README-view-heatmap-1.png |only funkyheatmap-0.1.0/funkyheatmap/man/figures/README-view-heatmap-with-colinfo-1.png |only funkyheatmap-0.1.0/funkyheatmap/man/figures/lifecycle-archived.svg |only funkyheatmap-0.1.0/funkyheatmap/man/figures/lifecycle-defunct.svg |only funkyheatmap-0.1.0/funkyheatmap/man/figures/lifecycle-deprecated.svg |only funkyheatmap-0.1.0/funkyheatmap/man/figures/lifecycle-experimental.svg |only funkyheatmap-0.1.0/funkyheatmap/man/figures/lifecycle-maturing.svg |only funkyheatmap-0.1.0/funkyheatmap/man/figures/lifecycle-questioning.svg |only funkyheatmap-0.1.0/funkyheatmap/man/figures/lifecycle-stable.svg |only funkyheatmap-0.1.0/funkyheatmap/man/figures/lifecycle-superseded.svg |only funkyheatmap-0.2.0/funkyheatmap/DESCRIPTION | 12 funkyheatmap-0.2.0/funkyheatmap/MD5 | 59 funkyheatmap-0.2.0/funkyheatmap/NAMESPACE | 2 funkyheatmap-0.2.0/funkyheatmap/NEWS.md | 17 funkyheatmap-0.2.0/funkyheatmap/R/dynbenchmark_data.R | 7 funkyheatmap-0.2.0/funkyheatmap/R/funky_heatmap.R | 59 funkyheatmap-0.2.0/funkyheatmap/R/funkyheatmap-package.R | 3 funkyheatmap-0.2.0/funkyheatmap/R/verify_column_info.R | 62 funkyheatmap-0.2.0/funkyheatmap/README.md | 37 funkyheatmap-0.2.0/funkyheatmap/build/partial.rdb |binary funkyheatmap-0.2.0/funkyheatmap/data/dynbenchmark_data.rda |binary funkyheatmap-0.2.0/funkyheatmap/inst/CITATION | 2 funkyheatmap-0.2.0/funkyheatmap/inst/REFERENCES.bib |only funkyheatmap-0.2.0/funkyheatmap/inst/doc/dynbenchmark.R | 172 funkyheatmap-0.2.0/funkyheatmap/inst/doc/dynbenchmark.Rmd | 231 funkyheatmap-0.2.0/funkyheatmap/inst/doc/dynbenchmark.html | 3609 +++++++++- funkyheatmap-0.2.0/funkyheatmap/inst/doc/mtcars.html | 13 funkyheatmap-0.2.0/funkyheatmap/man/dynbenchmark_data.Rd | 9 funkyheatmap-0.2.0/funkyheatmap/man/figures/README-heatmap1-1.png |only funkyheatmap-0.2.0/funkyheatmap/man/figures/README-heatmap2-1.png |only funkyheatmap-0.2.0/funkyheatmap/man/funky_heatmap.Rd | 19 funkyheatmap-0.2.0/funkyheatmap/man/verify_column_groups.Rd | 17 funkyheatmap-0.2.0/funkyheatmap/man/verify_column_info.Rd | 17 funkyheatmap-0.2.0/funkyheatmap/man/verify_palettes.Rd | 17 funkyheatmap-0.2.0/funkyheatmap/tests/testthat/test-verify_column_info.R | 26 funkyheatmap-0.2.0/funkyheatmap/vignettes/dynbenchmark.Rmd | 231 38 files changed, 3954 insertions(+), 667 deletions(-)
Title: Cox Mixed-Effects Models for Genome-Wide Association Studies
Description: Fast algorithms for fitting a Cox mixed-effects model for e.g., genome-wide association studies. See Liang He and Alexander Kulminski (2020) <doi: 10.1534/genetics.119.302940>.
Author: Liang He, Stephanie Gogarten
Maintainer: Liang He <lianghe@health.sdu.dk>
Diff between coxmeg versions 1.1.2 dated 2023-01-10 and 1.1.4 dated 2023-01-13
DESCRIPTION | 8 +- MD5 | 18 +++--- build/partial.rdb |binary inst/doc/COXMEG_example.Rmd | 2 inst/doc/COXMEG_example.html | 108 +++++++++++++++++++-------------------- inst/doc/coxmeg_gds_example.R | 10 ++- inst/doc/coxmeg_gds_example.Rmd | 10 ++- inst/doc/coxmeg_gds_example.html | 15 +++-- vignettes/COXMEG_example.Rmd | 2 vignettes/coxmeg_gds_example.Rmd | 10 ++- 10 files changed, 96 insertions(+), 87 deletions(-)
Title: DBI Connector to Presto
Description: Implements a 'DBI' compliant interface to Presto. Presto is
an open source distributed SQL query engine for running interactive
analytic queries against data sources of all sizes ranging from
gigabytes to petabytes: <https://prestodb.io/>.
Author: Onur Ismail Filiz [aut],
Sergey Goder [aut],
Jarod G.R. Meng [aut, cre],
Thomas J. Leeper [ctb],
John Myles White [ctb]
Maintainer: Jarod G.R. Meng <jarodm@fb.com>
Diff between RPresto versions 1.4.1 dated 2022-11-15 and 1.4.2 dated 2023-01-13
DESCRIPTION | 17 +++---- MD5 | 73 ++++++++++++++++--------------- NAMESPACE | 6 ++ NEWS.md | 10 ++++ R/chunk.R | 43 +++++++++++------- R/dbAppendTable.R | 5 +- R/dbConnect.R | 15 ++++++ R/dbCreateTableAs.R | 10 ---- R/dbExistsTable.R | 8 +-- R/dbListFields.R | 44 +++++++++++++----- R/dbQuoteIdentifier.R |only R/dbReadTable.R | 22 ++++++++- R/dbRemoveTable.R | 2 R/dbRenameTable.R |only R/dbWriteTable.R | 27 +++++------ R/dbplyr-src.R | 3 - R/request_headers.R | 19 ++++++++ README.md | 21 ++++++++ inst/doc/common-table-expressions.html | 2 inst/doc/complex-types.R | 2 inst/doc/complex-types.Rmd | 2 inst/doc/complex-types.html | 63 +++++++++++++------------- inst/doc/primitive-types.html | 7 ++ man/PrestoConnection-class.Rd | 59 +++++++++++++++++++------ man/add_chunk.Rd | 22 ++++----- man/dbRenameTable.Rd |only man/dummyPrestoConnection.Rd |only man/kerberos_configs.Rd |only tests/testthat/credentials.dcf | 2 tests/testthat/test-add_chunk.R | 25 ++++++---- tests/testthat/test-copy_to.src_presto.R | 14 +++++ tests/testthat/test-dbAppendTable.R | 16 ++++++ tests/testthat/test-dbExistsTable.R | 4 + tests/testthat/test-dbListFields.R | 10 +++- tests/testthat/test-dbQuoteLiteral.R | 4 - tests/testthat/test-dbReadTable.R | 15 ++++++ tests/testthat/test-dbRemoveTable.R | 25 ++++++++++ tests/testthat/test-dbRenameTable.R |only tests/testthat/test-dbWriteTable.R | 16 ++++++ tests/testthat/test-headers.R |only vignettes/complex-types.Rmd | 2 41 files changed, 437 insertions(+), 178 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), used in the computation of
marginal means, contrast analysis and predictions.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between modelbased versions 0.8.5 dated 2022-08-17 and 0.8.6 dated 2023-01-13
DESCRIPTION | 27 +-- MD5 | 108 +++++++------- NEWS.md | 8 - R/clean_names.R |only R/describe_nonlinear.R | 4 R/estimate_contrasts.R | 67 +++++--- R/estimate_grouplevel.R | 3 R/estimate_means.R | 110 +++----------- R/estimate_predicted.R | 14 + R/estimate_slopes.R | 5 R/get_emmeans.R | 4 R/get_emtrends.R | 4 R/get_marginalcontrasts.R |only R/get_marginaleffects.R | 2 R/get_marginalmeans.R |only R/modelbased-package.R |only R/reshape_grouplevel.R | 35 ++-- R/smoothing.R | 4 R/visualisation_matrix.R | 2 R/visualisation_recipe.estimate_means.R | 58 +++++-- R/visualisation_recipe.estimate_predicted.R | 34 ++-- R/visualisation_recipe.estimate_slopes.R | 2 R/zero_crossings.R | 4 README.md | 190 ++++++++++++------------- build/vignette.rds |binary inst/doc/overview_of_vignettes.html | 14 - man/estimate_contrasts.Rd | 57 ++++--- man/estimate_grouplevel.Rd | 9 - man/estimate_means.Rd | 4 man/figures/unnamed-chunk-10-1.png |binary man/figures/unnamed-chunk-12-1.png |binary man/figures/unnamed-chunk-14-1.png |binary man/figures/unnamed-chunk-15-1.png |binary man/figures/unnamed-chunk-16-1.png |binary man/figures/unnamed-chunk-17-1.png |binary man/figures/unnamed-chunk-3-1.png |binary man/figures/unnamed-chunk-4-1.png |binary man/figures/unnamed-chunk-6-1.png |binary man/figures/unnamed-chunk-8-1.png |binary man/figures/unnamed-chunk-9-1.png |binary man/modelbased-package.Rd |only man/visualisation_matrix.Rd | 19 +- man/visualisation_recipe.estimate_predicted.Rd | 10 - tests/testthat.R | 25 +-- tests/testthat/helper.R |only tests/testthat/test-attributes_visualisation.R | 2 tests/testthat/test-brms.R |only tests/testthat/test-describe_nonlinear.R | 38 ++++- tests/testthat/test-estimate_contrasts.R | 101 ++++++++----- tests/testthat/test-estimate_expectation.R | 2 tests/testthat/test-estimate_grouplevel.R | 2 tests/testthat/test-estimate_means.R | 74 +++++---- tests/testthat/test-estimate_predicted.R | 44 ++--- tests/testthat/test-estimate_slopes.R | 6 tests/testthat/test-get_marginaleffects.R | 2 tests/testthat/test-get_marginalmeans.R |only tests/testthat/test-glmmTMB.R | 2 tests/testthat/test-mgcv.R | 4 tests/testthat/test-signal.R | 2 59 files changed, 590 insertions(+), 512 deletions(-)
Title: Maps of Finland
Description: Maps and other related data of Finland.
Author: Jari Haukka [aut, cre]
Maintainer: Jari Haukka <jari.haukka@helsinki.fi>
Diff between mapsFinland versions 0.2.0 dated 2023-01-12 and 0.2.1 dated 2023-01-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++-- R/data.R | 6 ++++-- 4 files changed, 12 insertions(+), 10 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] ,
Joseph Larmarange [aut] ,
Michael Curry [aut] ,
Jessica Lavery [aut] ,
Karissa Whiting [aut] ,
Emily C. Zabor [aut] ,
Xing Bai [ctb],
Esther Drill [ctb] ,
Jessica Flynn [ctb] ,
Margie Hannum [ctb] ,
Stephanie Lobaugh [c [...truncated...]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.6.3 dated 2022-12-06 and 1.7.0 dated 2023-01-13
gtsummary-1.6.3/gtsummary/tests/testthat/test-modify_cols_merge.R |only gtsummary-1.7.0/gtsummary/DESCRIPTION | 27 gtsummary-1.7.0/gtsummary/MD5 | 466 +- gtsummary-1.7.0/gtsummary/NAMESPACE | 3 gtsummary-1.7.0/gtsummary/NEWS.md | 2277 +++++----- gtsummary-1.7.0/gtsummary/R/aaa.R |only gtsummary-1.7.0/gtsummary/R/add_ci.R | 489 +- gtsummary-1.7.0/gtsummary/R/add_difference.R | 15 gtsummary-1.7.0/gtsummary/R/add_glance.R | 7 gtsummary-1.7.0/gtsummary/R/add_global_p.R | 44 gtsummary-1.7.0/gtsummary/R/add_n.R | 2 gtsummary-1.7.0/gtsummary/R/add_nevent.R | 2 gtsummary-1.7.0/gtsummary/R/add_overall.R | 29 gtsummary-1.7.0/gtsummary/R/add_p.R | 83 gtsummary-1.7.0/gtsummary/R/add_q.R | 2 gtsummary-1.7.0/gtsummary/R/add_significance_stars.R | 24 gtsummary-1.7.0/gtsummary/R/add_stat.R | 27 gtsummary-1.7.0/gtsummary/R/add_vif.R | 2 gtsummary-1.7.0/gtsummary/R/as_flex_table.R | 59 gtsummary-1.7.0/gtsummary/R/as_gt.R | 48 gtsummary-1.7.0/gtsummary/R/as_hux_table.R | 49 gtsummary-1.7.0/gtsummary/R/as_kable.R | 33 gtsummary-1.7.0/gtsummary/R/as_kable_extra.R | 106 gtsummary-1.7.0/gtsummary/R/as_tibble.R | 38 gtsummary-1.7.0/gtsummary/R/assert_package.R | 2 gtsummary-1.7.0/gtsummary/R/bold_italicise_labels_levels.R | 64 gtsummary-1.7.0/gtsummary/R/combine_terms.R | 2 gtsummary-1.7.0/gtsummary/R/custom_tidiers.R | 47 gtsummary-1.7.0/gtsummary/R/deprecated.R | 18 gtsummary-1.7.0/gtsummary/R/inline_text.R | 83 gtsummary-1.7.0/gtsummary/R/modify.R | 47 gtsummary-1.7.0/gtsummary/R/modify_column_alignment.R | 1 gtsummary-1.7.0/gtsummary/R/modify_column_indent.R | 2 gtsummary-1.7.0/gtsummary/R/modify_column_merge.R | 13 gtsummary-1.7.0/gtsummary/R/modify_table_styling.R | 26 gtsummary-1.7.0/gtsummary/R/plot.R | 2 gtsummary-1.7.0/gtsummary/R/print.R | 3 gtsummary-1.7.0/gtsummary/R/remove_row_type.R | 4 gtsummary-1.7.0/gtsummary/R/separate_p_footnotes.R | 16 gtsummary-1.7.0/gtsummary/R/set_gtsummary_theme.R | 26 gtsummary-1.7.0/gtsummary/R/style_pvalue.R | 3 gtsummary-1.7.0/gtsummary/R/style_sigfig.R | 2 gtsummary-1.7.0/gtsummary/R/sysdata.rda |binary gtsummary-1.7.0/gtsummary/R/tbl_butcher.R | 24 gtsummary-1.7.0/gtsummary/R/tbl_continuous.R | 39 gtsummary-1.7.0/gtsummary/R/tbl_cross.R | 7 gtsummary-1.7.0/gtsummary/R/tbl_custom_summary.R | 83 gtsummary-1.7.0/gtsummary/R/tbl_merge.R | 32 gtsummary-1.7.0/gtsummary/R/tbl_regression.R | 24 gtsummary-1.7.0/gtsummary/R/tbl_regression_methods.R | 16 gtsummary-1.7.0/gtsummary/R/tbl_split.R | 2 gtsummary-1.7.0/gtsummary/R/tbl_stack.R | 6 gtsummary-1.7.0/gtsummary/R/tbl_strata.R | 104 gtsummary-1.7.0/gtsummary/R/tbl_summary.R | 25 gtsummary-1.7.0/gtsummary/R/tbl_survfit.R | 14 gtsummary-1.7.0/gtsummary/R/tbl_svysummary.R | 64 gtsummary-1.7.0/gtsummary/R/tbl_uvregression.R | 56 gtsummary-1.7.0/gtsummary/R/theme_gtsummary.R | 87 gtsummary-1.7.0/gtsummary/R/tidy_plus_plus_dots.R |only gtsummary-1.7.0/gtsummary/R/utils-add_p.R | 28 gtsummary-1.7.0/gtsummary/R/utils-add_p_tests.R | 151 gtsummary-1.7.0/gtsummary/R/utils-as.R | 13 gtsummary-1.7.0/gtsummary/R/utils-gtsummary_core.R | 21 gtsummary-1.7.0/gtsummary/R/utils-man_images.R | 1 gtsummary-1.7.0/gtsummary/R/utils-misc.R | 78 gtsummary-1.7.0/gtsummary/R/utils-tbl_custom_summary.R | 23 gtsummary-1.7.0/gtsummary/R/utils-tbl_regression.R | 10 gtsummary-1.7.0/gtsummary/R/utils-tbl_summary.R | 113 gtsummary-1.7.0/gtsummary/README.md | 7 gtsummary-1.7.0/gtsummary/build/gtsummary.pdf |binary gtsummary-1.7.0/gtsummary/inst/WORDLIST | 3 gtsummary-1.7.0/gtsummary/inst/doc/gallery.R | 84 gtsummary-1.7.0/gtsummary/inst/doc/gallery.Rmd | 84 gtsummary-1.7.0/gtsummary/inst/doc/gallery.html | 1601 +++---- gtsummary-1.7.0/gtsummary/inst/doc/gtsummary_definition.R | 118 gtsummary-1.7.0/gtsummary/inst/doc/gtsummary_definition.Rmd | 118 gtsummary-1.7.0/gtsummary/inst/doc/gtsummary_definition.html | 660 +- gtsummary-1.7.0/gtsummary/inst/doc/inline_text.R | 32 gtsummary-1.7.0/gtsummary/inst/doc/inline_text.Rmd | 32 gtsummary-1.7.0/gtsummary/inst/doc/inline_text.html | 282 - gtsummary-1.7.0/gtsummary/inst/doc/rmarkdown.R | 78 gtsummary-1.7.0/gtsummary/inst/doc/rmarkdown.Rmd | 82 gtsummary-1.7.0/gtsummary/inst/doc/rmarkdown.html | 204 gtsummary-1.7.0/gtsummary/inst/doc/tbl_regression.R | 108 gtsummary-1.7.0/gtsummary/inst/doc/tbl_regression.Rmd | 108 gtsummary-1.7.0/gtsummary/inst/doc/tbl_regression.html | 862 +-- gtsummary-1.7.0/gtsummary/inst/doc/tbl_summary.R | 135 gtsummary-1.7.0/gtsummary/inst/doc/tbl_summary.Rmd | 139 gtsummary-1.7.0/gtsummary/inst/doc/tbl_summary.html | 1616 +++---- gtsummary-1.7.0/gtsummary/inst/doc/themes.R | 37 gtsummary-1.7.0/gtsummary/inst/doc/themes.Rmd | 37 gtsummary-1.7.0/gtsummary/inst/doc/themes.html | 592 +- gtsummary-1.7.0/gtsummary/man/add_ci.Rd | 113 gtsummary-1.7.0/gtsummary/man/add_global_p.Rd | 7 gtsummary-1.7.0/gtsummary/man/add_n.tbl_summary.Rd | 1 gtsummary-1.7.0/gtsummary/man/add_n.tbl_survfit.Rd | 2 gtsummary-1.7.0/gtsummary/man/add_nevent.tbl_survfit.Rd | 2 gtsummary-1.7.0/gtsummary/man/add_overall.Rd | 7 gtsummary-1.7.0/gtsummary/man/add_p.tbl_summary.Rd | 4 gtsummary-1.7.0/gtsummary/man/add_p.tbl_survfit.Rd | 2 gtsummary-1.7.0/gtsummary/man/add_p.tbl_svysummary.Rd | 6 gtsummary-1.7.0/gtsummary/man/add_q.Rd | 3 gtsummary-1.7.0/gtsummary/man/add_significance_stars.Rd | 15 gtsummary-1.7.0/gtsummary/man/add_stat_label.Rd | 1 gtsummary-1.7.0/gtsummary/man/add_vif.Rd | 2 gtsummary-1.7.0/gtsummary/man/as_flex_table.Rd | 2 gtsummary-1.7.0/gtsummary/man/as_gt.Rd | 4 gtsummary-1.7.0/gtsummary/man/as_hux_table.Rd | 2 gtsummary-1.7.0/gtsummary/man/as_kable.Rd | 4 gtsummary-1.7.0/gtsummary/man/as_kable_extra.Rd | 2 gtsummary-1.7.0/gtsummary/man/as_tibble.gtsummary.Rd | 3 gtsummary-1.7.0/gtsummary/man/bold_italicize_labels_levels.Rd | 1 gtsummary-1.7.0/gtsummary/man/combine_terms.Rd | 2 gtsummary-1.7.0/gtsummary/man/continuous_summary.Rd | 2 gtsummary-1.7.0/gtsummary/man/custom_tidiers.Rd | 7 gtsummary-1.7.0/gtsummary/man/deprecated.Rd | 6 gtsummary-1.7.0/gtsummary/man/inline_text.tbl_summary.Rd | 1 gtsummary-1.7.0/gtsummary/man/inline_text.tbl_survfit.Rd | 3 gtsummary-1.7.0/gtsummary/man/modify.Rd | 1 gtsummary-1.7.0/gtsummary/man/modify_column_merge.Rd | 3 gtsummary-1.7.0/gtsummary/man/plot.Rd | 2 gtsummary-1.7.0/gtsummary/man/proportion_summary.Rd | 6 gtsummary-1.7.0/gtsummary/man/ratio_summary.Rd | 2 gtsummary-1.7.0/gtsummary/man/separate_p_footnotes.Rd | 1 gtsummary-1.7.0/gtsummary/man/tbl_butcher.Rd | 24 gtsummary-1.7.0/gtsummary/man/tbl_custom_summary.Rd | 13 gtsummary-1.7.0/gtsummary/man/tbl_merge.Rd | 1 gtsummary-1.7.0/gtsummary/man/tbl_regression.Rd | 3 gtsummary-1.7.0/gtsummary/man/tbl_split.Rd | 1 gtsummary-1.7.0/gtsummary/man/tbl_stack.Rd | 1 gtsummary-1.7.0/gtsummary/man/tbl_strata.Rd | 19 gtsummary-1.7.0/gtsummary/man/tbl_summary.Rd | 1 gtsummary-1.7.0/gtsummary/man/tbl_survfit.Rd | 2 gtsummary-1.7.0/gtsummary/man/tbl_svysummary.Rd | 2 gtsummary-1.7.0/gtsummary/man/tbl_uvregression.Rd | 3 gtsummary-1.7.0/gtsummary/man/tests.Rd | 1 gtsummary-1.7.0/gtsummary/man/theme_gtsummary.Rd | 2 gtsummary-1.7.0/gtsummary/man/tidy_plus_plus_dots.Rd |only gtsummary-1.7.0/gtsummary/tests/spelling.R | 9 gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_ci.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_difference.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_glance.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_global_p.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_n.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_nevent.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_overall.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_p.tbl_continuous.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_p.tbl_cross.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_p.tbl_summary.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_p.tbl_survfit.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_p.tbl_svysummary.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_p_test_safe.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_q.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_significance_stars.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_stat_label.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/add_vif.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/as_flex_table.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/as_gt.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/as_hux_table.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/as_kable.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/as_kable_extra.md | 721 +++ gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/as_tibble.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/bold_italicize_labels_levels.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/bold_p.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/combine_terms.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/custom_tidiers.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/filter_p.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_caption.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_column_alignment.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_column_hide.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_column_indent.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_column_merge.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_fmt_fun.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_footnote.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_header.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_spanning_header.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_table_body.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/modify_table_styling.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/remove_row_type.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/select_helpers.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/separate_p_footnotes.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/set_gtsummary_theme.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/sort_p.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_butcher.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_continuous.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_cross.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_custom_summary.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_merge.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_regression.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_split.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_stack.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_strata.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_summary.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_survfit.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_svysummary.md |only gtsummary-1.7.0/gtsummary/tests/testthat/_snaps/tbl_uvregression.md |only gtsummary-1.7.0/gtsummary/tests/testthat/helper-render_as_html.R |only gtsummary-1.7.0/gtsummary/tests/testthat/test-add_ci.R | 107 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_difference.R | 71 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_glance.R | 17 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_global_p.R | 18 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_n.R | 161 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_nevent.R | 96 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_overall.R | 74 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_p.tbl_continuous.R | 33 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_p.tbl_cross.R | 67 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_p.tbl_summary.R | 209 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_p.tbl_survfit.R | 61 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_p.tbl_svysummary.R | 27 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_p_test_safe.R | 44 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_q.R | 4 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_significance_stars.R | 13 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_stat_label.R | 32 gtsummary-1.7.0/gtsummary/tests/testthat/test-add_vif.R | 36 gtsummary-1.7.0/gtsummary/tests/testthat/test-as_flex_table.R | 40 gtsummary-1.7.0/gtsummary/tests/testthat/test-as_gt.R | 30 gtsummary-1.7.0/gtsummary/tests/testthat/test-as_hux_table.R | 33 gtsummary-1.7.0/gtsummary/tests/testthat/test-as_hux_xlsx.R | 4 gtsummary-1.7.0/gtsummary/tests/testthat/test-as_kable.R | 34 gtsummary-1.7.0/gtsummary/tests/testthat/test-as_kable_extra.R | 62 gtsummary-1.7.0/gtsummary/tests/testthat/test-as_tibble.R | 10 gtsummary-1.7.0/gtsummary/tests/testthat/test-bold_italicize_labels_levels.R | 25 gtsummary-1.7.0/gtsummary/tests/testthat/test-bold_p.R | 5 gtsummary-1.7.0/gtsummary/tests/testthat/test-combine_terms.R | 47 gtsummary-1.7.0/gtsummary/tests/testthat/test-custom_tidiers.R | 49 gtsummary-1.7.0/gtsummary/tests/testthat/test-filter_p.R | 6 gtsummary-1.7.0/gtsummary/tests/testthat/test-inline_text.R | 23 gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_caption.R | 6 gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_column_alignment.R | 6 gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_column_hide.R | 6 gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_column_indent.R | 1 gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_column_merge.R |only gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_fmt_fun.R | 1 gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_footnote.R | 33 gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_header.R | 17 gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_spanning_header.R | 14 gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_table_body.R | 1 gtsummary-1.7.0/gtsummary/tests/testthat/test-modify_table_styling.R | 20 gtsummary-1.7.0/gtsummary/tests/testthat/test-plot.R | 2 gtsummary-1.7.0/gtsummary/tests/testthat/test-remove_row_type.R | 3 gtsummary-1.7.0/gtsummary/tests/testthat/test-select_helpers.R | 24 gtsummary-1.7.0/gtsummary/tests/testthat/test-separate_p_footnotes.R | 2 gtsummary-1.7.0/gtsummary/tests/testthat/test-set_gtsummary_theme.R | 98 gtsummary-1.7.0/gtsummary/tests/testthat/test-sort_p.R | 6 gtsummary-1.7.0/gtsummary/tests/testthat/test-style_number.R | 1 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_butcher.R | 1 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_continuous.R | 9 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_cross.R | 61 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_custom_summary.R | 72 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_merge.R | 64 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_regression.R | 113 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_split.R | 8 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_stack.R | 32 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_strata.R | 61 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_summary.R | 178 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_survfit.R | 67 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_svysummary.R | 110 gtsummary-1.7.0/gtsummary/tests/testthat/test-tbl_uvregression.R | 156 gtsummary-1.7.0/gtsummary/vignettes/gallery.Rmd | 84 gtsummary-1.7.0/gtsummary/vignettes/gtsummary_definition.Rmd | 118 gtsummary-1.7.0/gtsummary/vignettes/inline_text.Rmd | 32 gtsummary-1.7.0/gtsummary/vignettes/rmarkdown.Rmd | 82 gtsummary-1.7.0/gtsummary/vignettes/tbl_regression.Rmd | 108 gtsummary-1.7.0/gtsummary/vignettes/tbl_summary.Rmd | 139 gtsummary-1.7.0/gtsummary/vignettes/themes.Rmd | 37 265 files changed, 9221 insertions(+), 7245 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii)
Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v)
Matrix functions, (vi) Projector and canonical efficiency functions, and (vii)
Miscellaneous functions. There is a vignette describing how to use the
design functions for randomizing and assessing designs available as a
vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of
information when the 'Error' function has been used in the call to 'aov'.
The package 'dae' can also be installed from
<http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between dae versions 3.2-13 dated 2021-11-17 and 3.2-14 dated 2023-01-13
DESCRIPTION | 8 ++-- MD5 | 74 ++++++++++++++++++++-------------------- R/designGGPlot.v1.r | 12 ++---- R/fac.gen.r | 2 - R/fac.match.r | 2 - R/mat.functions.r | 21 +++++++++-- R/proj.r | 2 - build/partial.rdb |binary build/vignette.rds |binary data/ABC.Interact.dat.rda |binary data/BIBDWheat.dat.rda |binary data/Cabinet1.des.rda |binary data/Casuarina.dat.rda |binary data/Exp249.munit.des.rda |binary data/Fac4Proc.dat.rda |binary data/LatticeSquare_t49.des.rda |binary data/McIntyreTMV.dat.rda |binary data/Oats.dat.rda |binary data/SPLGrass.dat.rda |binary data/Sensory3Phase.dat.rda |binary data/Sensory3PhaseShort.dat.rda |binary inst/NEWS.Rd | 5 ++ inst/doc/DesignNotes.pdf |binary inst/doc/dae-manual.pdf |binary man/BIBDWheat.dat.Rd | 2 - man/Casuarina.dat.Rd | 2 - man/Exp249.munit.des.Rd | 2 - man/LatticeSquare_t49.des.Rd | 2 - man/McIntyreTMV.dat.Rd | 2 - man/Sensory3Phase.dat.Rd | 2 - man/dae-package.Rd | 7 ++- man/designAmeasures.Rd | 37 ++++++++++++++------ man/designAnatomy.Rd | 15 +++++--- man/designGGPlot.Rd | 2 - man/designRandomize.Rd | 4 +- man/designTwoPhaseAnatomies.Rd | 3 + man/fac.divide.Rd | 6 +-- tests/testthat/testAmeasures.r | 51 +++++++++++++++++++++++++++ 38 files changed, 180 insertions(+), 83 deletions(-)
Title: A Tree and Forest Tool for Classification and Regression
Description: Build decision trees and random forests for classification and regression. The implementation strikes a balance between minimizing computing efforts and maximizing the expected predictive accuracy, thus scales well to large data sets. Multi-threading is available through 'OpenMP' <https://gcc.gnu.org/wiki/openmp>.
Author: Yanchao Liu [aut, cre]
Maintainer: Yanchao Liu <yanchaoliu@wayne.edu>
Diff between brif versions 1.2.0 dated 2022-12-01 and 1.4.0 dated 2023-01-13
DESCRIPTION | 10 MD5 | 17 - NAMESPACE | 27 +- R/RcppExports.R | 94 +++---- R/brif.R | 193 +++++++++++---- man/brif.trainpredict.Rd | 17 + man/brif_write_data.Rd |only src/Rcpp_brif.cpp | 14 - src/brif.cpp | 588 ++++++++++++++++++++++++++++++++--------------- src/brif.h | 25 + 10 files changed, 660 insertions(+), 325 deletions(-)