Title: Polynomial Spline Routines
Description: Routines for the polynomial spline fitting routines
hazard regression, hazard estimation with flexible tails, logspline,
lspec, polyclass, and polymars, by C. Kooperberg and co-authors.
Author: Charles Kooperberg <clk@fredhutch.org>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between polspline versions 1.1.14 dated 2019-02-28 and 1.1.15 dated 2019-06-13
DESCRIPTION | 8 - MD5 | 8 - R/polspline.R | 50 +------ src/lsdall.c | 287 -------------------------------------------- src/registerDynamicSymbol.c | 2 5 files changed, 15 insertions(+), 340 deletions(-)
Title: Routines for Logspline Density Estimation
Description: Contains routines for logspline density estimation.
The function oldlogspline() uses the same algorithm as the logspline package
version 1.0.x; i.e. the Kooperberg and Stone (1992)
algorithm (with an improved interface). The recommended routine logspline()
uses an algorithm from Stone et al (1997) <DOI:10.1214/aos/1031594728>.
Author: Charles Kooperberg <clk@fredhutch.org>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between logspline versions 2.1.12 dated 2019-02-05 and 2.1.13 dated 2019-06-13
DESCRIPTION | 8 - MD5 | 8 - R/logspline.R | 48 ------- src/lsdall.c | 287 -------------------------------------------- src/registerDynamicSymbol.c | 2 5 files changed, 14 insertions(+), 339 deletions(-)
Title: Creates Page Layout Visualizations
Description: Facilitates the creation of page layout
visualizations in which words are represented as rectangles with sizes
relating to the length of the words. Which then is divided in lines
and pages for easy overview of up to quite large texts.
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between ggpage versions 0.2.2 dated 2018-07-27 and 0.2.3 dated 2019-06-13
ggpage-0.2.2/ggpage/man/figures/README-gif.gif |only ggpage-0.2.2/ggpage/man/figures/README-unnamed-chunk-3-1.png |only ggpage-0.2.2/ggpage/man/figures/README-unnamed-chunk-5-1.png |only ggpage-0.2.3/ggpage/DESCRIPTION | 36 +- ggpage-0.2.3/ggpage/MD5 | 18 - ggpage-0.2.3/ggpage/NEWS.md | 2 ggpage-0.2.3/ggpage/R/ggpage_build.R | 17 - ggpage-0.2.3/ggpage/README.md | 83 ++--- ggpage-0.2.3/ggpage/build/vignette.rds |binary ggpage-0.2.3/ggpage/inst/doc/different-features.html | 181 ++++++----- ggpage-0.2.3/ggpage/man/figures/README-unnamed-chunk-4-1.png |only ggpage-0.2.3/ggpage/man/figures/README-unnamed-chunk-6-1.png |only ggpage-0.2.3/ggpage/man/figures/logo.png |only 13 files changed, 179 insertions(+), 158 deletions(-)
Title: An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of one or more categorical
variables; paired(), a Table-1-like summary of multiple variable types paired across
two time points; modelsum(), which performs simple model fits on one or more endpoints
for many variables (univariate or adjusted for covariates);
freqlist(), a powerful frequency table across many categorical variables;
comparedf(), a function for comparing data.frames; and
write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre],
Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb],
Maddie McCullough [art]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between arsenal versions 3.1.0 dated 2019-05-03 and 3.2.0 dated 2019-06-13
DESCRIPTION | 8 +-- MD5 | 60 ++++++++++++------------- NEWS.md | 30 ++++++++++++ R/arsenal_table.R | 14 +++++ R/comparedf.R | 8 +-- R/comparedf.internal.R | 7 ++ R/modelsum.R | 7 ++ R/modelsum.control.R | 12 ++++- R/paired.R | 3 - R/summary.comparedf.R | 8 ++- R/summary.tableby.R | 5 +- R/tableby.R | 3 - R/tableby.internal.R | 3 - R/write2.R | 2 inst/doc/comparedf.html | 54 +++++++++++----------- inst/doc/freqlist.html | 2 inst/doc/labels.html | 2 inst/doc/modelsum.Rmd | 3 + inst/doc/modelsum.html | 8 ++- inst/doc/paired.html | 2 inst/doc/tableby.html | 2 inst/doc/write2.html | 2 man/write2.Rd | 2 tests/testthat/test_comparedf.R | 88 +++++++++++++++++++++++++------------ tests/testthat/test_lhs_tableby.R | 45 ++++++++++++++++++ tests/testthat/test_paired.R | 4 - tests/testthat/test_tableby.R | 27 +++++++++++ tests/testthat/test_write2.R | 4 - tests/testthat/write2.lm.pdf.Rmd | 2 tests/testthat/write2.yaml.pdf.Rmd | 2 vignettes/modelsum.Rmd | 3 + 31 files changed, 299 insertions(+), 123 deletions(-)
Title: Dynamic Functional Connectivity Analysis
Description: An implementation of multivariate linear process bootstrap (MLPB) method and sliding window technique to assess the dynamic functional connectivity (dFC) estimate by providing its confidence bands, based on Maria Kudela (2017) <doi: 10.1016/j.neuroimage.2017.01.056>.
It also integrates features to visualize non-zero coverage for selected a-priori regions of interest estimated by the dynamic functional connectivity model (dFCM) and dynamic functional connectivity (dFC) curves for reward-related a-priori regions of interest where the activation-based analysis reported.
Author: Zikai Lin [aut, cre],
Maria Kudela [aut],
Jaroslaw Harezlak [aut],
Mario Dzemidzic [aut]
Maintainer: Zikai Lin <ziklin@iu.edu>
Diff between dfConn versions 0.2.0 dated 2019-05-31 and 0.2.1 dated 2019-06-13
DESCRIPTION | 6 - MD5 | 10 +- R/lme_model0.r | 2 R/lme_model6.r | 2 R/mlpb.R | 2 R/utils.r | 198 --------------------------------------------------------- 6 files changed, 11 insertions(+), 209 deletions(-)
Title: Implementation Helper for '[' and '[<-' of Custom Matrix-Like
Types
Description: Functions to help implement the extraction / subsetting / indexing
function '[' and replacement function '[<-' of custom matrix-like types
(based on S3, S4, etc.), modeled as closely to the base matrix class as
possible (with tests to prove it).
Author: Alexander Grueneberg [aut, cre]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between crochet versions 2.1.0 dated 2018-08-06 and 2.2.0 dated 2019-06-13
crochet-2.1.0/crochet/man/examples |only crochet-2.1.0/crochet/tests/testthat/helper.R |only crochet-2.1.0/crochet/tests/testthat/test-crochet-extract.R |only crochet-2.1.0/crochet/tests/testthat/test-crochet-replace.R |only crochet-2.2.0/crochet/DESCRIPTION | 21 - crochet-2.2.0/crochet/MD5 | 36 +- crochet-2.2.0/crochet/NAMESPACE | 4 crochet-2.2.0/crochet/NEWS.md | 7 crochet-2.2.0/crochet/R/crochet.R | 107 ------ crochet-2.2.0/crochet/README.md | 212 ------------ crochet-2.2.0/crochet/build |only crochet-2.2.0/crochet/inst |only crochet-2.2.0/crochet/man/convertIndex.Rd | 45 +- crochet-2.2.0/crochet/man/crochet-package.Rd |only crochet-2.2.0/crochet/man/extract.Rd | 72 ++-- crochet-2.2.0/crochet/man/ijtok.Rd | 34 + crochet-2.2.0/crochet/man/ktoij.Rd | 29 - crochet-2.2.0/crochet/man/replace.Rd | 71 ++-- crochet-2.2.0/crochet/tests/testthat/test-stringmatrix.R |only crochet-2.2.0/crochet/vignettes |only 20 files changed, 194 insertions(+), 444 deletions(-)
Title: Quantile Regression Neural Network
Description: Fit quantile regression neural network models with optional
left censoring, partial monotonicity constraints, generalized additive
model constraints, and the ability to fit multiple non-crossing quantile
functions following Cannon (2011) <doi:10.1016/j.cageo.2010.07.005>
and Cannon (2018) <doi:10.1007/s00477-018-1573-6>.
Author: Alex J. Cannon [aut, cre] (<https://orcid.org/0000-0002-8025-3790>)
Maintainer: Alex J. Cannon <alex.cannon@canada.ca>
Diff between qrnn versions 2.0.3 dated 2018-06-26 and 2.0.4 dated 2019-06-13
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/mcqrnn.R | 2 +- R/qrnn.R | 4 ++-- R/qrnn2.R | 6 +++--- inst/CITATION | 6 +++--- man/composite.stack.Rd | 8 ++++---- man/mcqrnn.Rd | 10 +++++----- man/qrnn-package.Rd | 8 ++++---- man/qrnn.fit.Rd | 14 +++++++------- man/qrnn2.Rd | 10 +++++----- 11 files changed, 47 insertions(+), 47 deletions(-)
Title: Hierarchical Item Response Theory Models
Description: Implementation of a class of hierarchical item response
theory (IRT) models where both the mean and the variance of latent preferences
(ability parameters) may depend on observed covariates. The current
implementation includes both the two-parameter latent trait model for binary data and the
graded response model for ordinal data. Both are fitted via the Expectation-Maximization (EM)
algorithm. Asymptotic standard errors are derived from the observed information
matrix.
Author: Xiang Zhou [aut, cre]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>
Diff between hIRT versions 0.1.3 dated 2018-09-16 and 0.2.0 dated 2019-06-13
hIRT-0.1.3/hIRT/man/coef.hIRT.Rd |only hIRT-0.2.0/hIRT/DESCRIPTION | 6 - hIRT-0.2.0/hIRT/MD5 | 31 +++++----- hIRT-0.2.0/hIRT/NAMESPACE | 4 - hIRT-0.2.0/hIRT/R/coef.R | 106 +++++++++++++---------------------- hIRT-0.2.0/hIRT/R/hgrm.R | 54 ++++++++++------- hIRT-0.2.0/hIRT/R/hltm.R | 46 ++++++++------- hIRT-0.2.0/hIRT/R/predict_hIRT.R |only hIRT-0.2.0/hIRT/R/print.R | 2 hIRT-0.2.0/hIRT/R/summary.R | 8 +- hIRT-0.2.0/hIRT/R/utils.R | 7 -- hIRT-0.2.0/hIRT/R/utils_grm.R | 7 ++ hIRT-0.2.0/hIRT/man/coef_item.Rd | 20 +++--- hIRT-0.2.0/hIRT/man/hgrm.Rd | 8 +- hIRT-0.2.0/hIRT/man/hltm.Rd | 10 +-- hIRT-0.2.0/hIRT/man/latent_scores.Rd | 2 hIRT-0.2.0/hIRT/man/predict_hIRT.Rd |only hIRT-0.2.0/hIRT/man/print.hIRT.Rd | 2 18 files changed, 158 insertions(+), 155 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, stats, geoms and scales for plotting
"light" spectra with 'ggplot2', together with specializations of ggplot()
and autoplot() methods for spectral data and waveband definitions
stored in objects of classes defined in package 'photobiology'. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.3.2 dated 2019-02-20 and 0.3.3.1 dated 2019-06-13
ggspectra-0.3.2/ggspectra/man/ggtitle_spct.Rd |only ggspectra-0.3.3.1/ggspectra/DESCRIPTION | 18 ggspectra-0.3.3.1/ggspectra/MD5 | 95 ggspectra-0.3.3.1/ggspectra/NAMESPACE | 3 ggspectra-0.3.3.1/ggspectra/NEWS | 18 ggspectra-0.3.3.1/ggspectra/R/autoplot-calibration-spct.R | 2 ggspectra-0.3.3.1/ggspectra/R/autoplot-cps-spct.r | 2 ggspectra-0.3.3.1/ggspectra/R/autoplot-filter-spct.r | 10 ggspectra-0.3.3.1/ggspectra/R/autoplot-raw-spct.r | 2 ggspectra-0.3.3.1/ggspectra/R/autoplot-response-spct.r | 2 ggspectra-0.3.3.1/ggspectra/R/autoplot-source-spct.r | 2 ggspectra-0.3.3.1/ggspectra/R/autoplot-waveband.R | 2 ggspectra-0.3.3.1/ggspectra/R/decoration.R | 178 + ggspectra-0.3.3.1/ggspectra/R/ggplot-methods.R | 4 ggspectra-0.3.3.1/ggspectra/R/multiplot.R | 66 ggspectra-0.3.3.1/ggspectra/R/stat-label-peaks.R | 17 ggspectra-0.3.3.1/ggspectra/R/stat-peaks.R | 16 ggspectra-0.3.3.1/ggspectra/R/stat-wb-box.R | 7 ggspectra-0.3.3.1/ggspectra/R/stat-wb-label.R | 10 ggspectra-0.3.3.1/ggspectra/R/stat-wl-strip.R | 5 ggspectra-0.3.3.1/ggspectra/R/title-utils.R | 94 ggspectra-0.3.3.1/ggspectra/README.md | 4 ggspectra-0.3.3.1/ggspectra/build/vignette.rds |binary ggspectra-0.3.3.1/ggspectra/inst/doc/userguide1-grammar.R | 63 ggspectra-0.3.3.1/ggspectra/inst/doc/userguide1-grammar.Rmd | 55 ggspectra-0.3.3.1/ggspectra/inst/doc/userguide1-grammar.html | 1367 +++++----- ggspectra-0.3.3.1/ggspectra/inst/doc/userguide2-autoplot-methods.R | 12 ggspectra-0.3.3.1/ggspectra/inst/doc/userguide2-autoplot-methods.Rmd | 46 ggspectra-0.3.3.1/ggspectra/inst/doc/userguide2-autoplot-methods.html | 511 ++- ggspectra-0.3.3.1/ggspectra/man/autoplot.calibration_spct.Rd | 3 ggspectra-0.3.3.1/ggspectra/man/autoplot.cps_spct.Rd | 3 ggspectra-0.3.3.1/ggspectra/man/autoplot.filter_spct.Rd | 3 ggspectra-0.3.3.1/ggspectra/man/autoplot.object_spct.Rd | 3 ggspectra-0.3.3.1/ggspectra/man/autoplot.raw_spct.Rd | 3 ggspectra-0.3.3.1/ggspectra/man/autoplot.reflector_spct.Rd | 3 ggspectra-0.3.3.1/ggspectra/man/autoplot.response_spct.Rd | 3 ggspectra-0.3.3.1/ggspectra/man/autoplot.source_spct.Rd | 3 ggspectra-0.3.3.1/ggspectra/man/autoplot.waveband.Rd | 3 ggspectra-0.3.3.1/ggspectra/man/autotitle.Rd |only ggspectra-0.3.3.1/ggspectra/man/decode_annotations.Rd | 3 ggspectra-0.3.3.1/ggspectra/man/figures/README-example0-1.png |only ggspectra-0.3.3.1/ggspectra/man/figures/README-example1-1.png |only ggspectra-0.3.3.1/ggspectra/man/multiplot.Rd | 31 ggspectra-0.3.3.1/ggspectra/man/set_annotations_default.Rd |only ggspectra-0.3.3.1/ggspectra/man/stat_label_peaks.Rd | 9 ggspectra-0.3.3.1/ggspectra/man/stat_peaks.Rd | 24 ggspectra-0.3.3.1/ggspectra/man/stat_wb_box.Rd | 5 ggspectra-0.3.3.1/ggspectra/man/stat_wb_label.Rd | 4 ggspectra-0.3.3.1/ggspectra/man/stat_wl_strip.Rd | 4 ggspectra-0.3.3.1/ggspectra/vignettes/userguide1-grammar.Rmd | 55 ggspectra-0.3.3.1/ggspectra/vignettes/userguide2-autoplot-methods.Rmd | 46 51 files changed, 1799 insertions(+), 1020 deletions(-)
Title: Odds Ratio Calculation for GAM(M)s & GLM(M)s
Description: Simplified odds ratio calculation of GAM(M)s &
GLM(M)s. Provides structured output (data frame) of all predictors
and their corresponding odds ratios and confident intervals for
further analyses. It helps to avoid false references of predictors
and increments by specifying these parameters in a list instead of
using 'exp(coef(model))' (standard approach of odds ratio calculation
for GLMs) which just returns a plain numeric output. For GAM(M)s,
odds ratio calculation is highly simplified with this package since it
takes care of the multiple 'predict()' calls of the chosen predictor
while holding other predictors constant. Also, this package allows
odds ratio calculation of percentage steps across the whole predictor
distribution range for GAM(M)s. In both cases, confident intervals
are returned additionally. Calculated odds ratio of GAM(M)s can be
inserted into the smooth function plot.
Author: Patrick Schratz [aut, cre] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between oddsratio versions 1.0.3 dated 2018-07-25 and 2.0.0 dated 2019-06-13
oddsratio-1.0.3/oddsratio/NEWS |only oddsratio-1.0.3/oddsratio/inst/Plots |only oddsratio-1.0.3/oddsratio/inst/convert_to_ascii_news.sh |only oddsratio-1.0.3/oddsratio/inst/doc/function_tutorial.R |only oddsratio-1.0.3/oddsratio/inst/doc/function_tutorial.Rmd |only oddsratio-1.0.3/oddsratio/inst/doc/function_tutorial.html |only oddsratio-1.0.3/oddsratio/inst/wordpress.Rmd |only oddsratio-1.0.3/oddsratio/inst/wordpress.md |only oddsratio-1.0.3/oddsratio/inst/wordpress_files |only oddsratio-1.0.3/oddsratio/vignettes/function_tutorial.Rmd |only oddsratio-2.0.0/oddsratio/DESCRIPTION | 55 +++-- oddsratio-2.0.0/oddsratio/MD5 | 60 ++--- oddsratio-2.0.0/oddsratio/NAMESPACE | 5 oddsratio-2.0.0/oddsratio/NEWS.md | 7 oddsratio-2.0.0/oddsratio/R/data.R | 6 oddsratio-2.0.0/oddsratio/R/helper_funs.R | 26 +- oddsratio-2.0.0/oddsratio/R/insert_or.R | 143 ++++++++------ oddsratio-2.0.0/oddsratio/R/or_gam.R | 129 ++++++------ oddsratio-2.0.0/oddsratio/R/or_glm.R | 85 ++++---- oddsratio-2.0.0/oddsratio/R/plot_gam.R | 23 +- oddsratio-2.0.0/oddsratio/build/vignette.rds |binary oddsratio-2.0.0/oddsratio/inst/doc/oddsratio.R |only oddsratio-2.0.0/oddsratio/inst/doc/oddsratio.Rmd |only oddsratio-2.0.0/oddsratio/inst/doc/oddsratio.html |only oddsratio-2.0.0/oddsratio/man/data_gam.Rd | 2 oddsratio-2.0.0/oddsratio/man/data_glm.Rd | 2 oddsratio-2.0.0/oddsratio/man/gam_to_df.Rd | 11 - oddsratio-2.0.0/oddsratio/man/insert_or.Rd | 52 ++--- oddsratio-2.0.0/oddsratio/man/no_plot.Rd | 8 oddsratio-2.0.0/oddsratio/man/or_gam.Rd | 75 +++---- oddsratio-2.0.0/oddsratio/man/or_glm.Rd | 39 ++- oddsratio-2.0.0/oddsratio/man/plot_gam.Rd | 9 oddsratio-2.0.0/oddsratio/tests/testthat/test-insert-or.R | 10 oddsratio-2.0.0/oddsratio/tests/testthat/test-or-gam.R | 40 ++- oddsratio-2.0.0/oddsratio/tests/testthat/test-or-glm.R | 14 - oddsratio-2.0.0/oddsratio/vignettes/oddsratio.Rmd |only 36 files changed, 437 insertions(+), 364 deletions(-)
Title: Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
Description: Bayesian reconstruction of disease outbreaks using epidemiological
and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser
C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F,
Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.
Author: Thibaut Jombart [aut],
Finlay Campbell [aut, cre],
Rich Fitzjohn [aut],
Gerry Tonkin-Hill [ctb],
Alexis Robert [ctb]
Maintainer: Finlay Campbell <f.campbell15@imperial.ac.uk>
Diff between outbreaker2 versions 1.0.1 dated 2018-03-06 and 1.1.0 dated 2019-06-13
DESCRIPTION | 23 MD5 | 148 NAMESPACE | 4 NEWS.md | 19 R/create_config.R | 1104 +- R/custom_likelihoods.R | 2 R/internals.R | 114 R/outbreaker_chains_methods.R | 134 R/outbreaker_data.R | 346 R/outbreaker_find_imports.R | 138 R/outbreaker_init_mcmc.R | 4 R/outbreaker_move.R | 66 R/ref_likelihoods.R | 10 R/sim_ctd.R | 12 README.md | 18 build/vignette.rds |binary data/fake_outbreak.RData |binary inst/doc/Rcpp_API.html | 348 inst/doc/customisation.html | 1810 ++-- inst/doc/introduction.R | 12 inst/doc/introduction.Rmd | 24 inst/doc/introduction.html | 6114 +++++++++++++++- inst/doc/overview.html | 321 man/bind_to_function.Rd | 2 man/create_config.Rd | 7 man/fake_outbreak.Rd | 2 man/outbreaker_chains.Rd | 21 man/outbreaker_data.Rd | 14 src/likelihoods.cpp | 53 src/moves.cpp | 8 tests/testthat/test_config.R | 3 tests/testthat/test_data.R | 175 tests/testthat/test_find_imports.R | 1 tests/testthat/test_likelihoods.R | 23 tests/testthat/test_moves.R | 41 tests/testthat/test_non_exported.R | 4 tests/testthat/test_outbreaker.R | 80 vignettes/figs-customisation/f_pi-1.png |binary vignettes/figs-customisation/null_net-1.png |binary vignettes/figs-customisation/null_trees-1.png |binary vignettes/figs-customisation/res_new_move-1.png |binary vignettes/figs-customisation/res_new_move-2.png |binary vignettes/figs-customisation/res_null_diag-1.png |binary vignettes/figs-customisation/res_null_diag-2.png |binary vignettes/figs-customisation/res_null_model-1.png |binary vignettes/figs-customisation/res_null_model-2.png |binary vignettes/figs-customisation/res_null_model-3.png |binary vignettes/figs-customisation/res_null_priors-1.png |binary vignettes/figs-customisation/res_null_priors-2.png |binary vignettes/figs-customisation/res_wt-1.png |binary vignettes/figs-customisation/res_wt-2.png |binary vignettes/figs-customisation/res_wt-3.png |binary vignettes/figs-customisation/run_custom_move_mu-1.png |binary vignettes/figs-customisation/run_custom_move_mu-2.png |binary vignettes/figs-customisation/run_custom_move_mu-3.png |binary vignettes/figs-customisation/traces_custom_priors-1.png |binary vignettes/figs-customisation/traces_custom_priors-2.png |binary vignettes/figs-customisation/traces_custom_priors-3.png |binary vignettes/figs-customisation/traces_custom_priors-4.png |binary vignettes/figs-customisation/traces_custom_priors-5.png |binary vignettes/figs-customisation/wt_net-1.png |binary vignettes/figs-introduction/basic_trace-1.png |binary vignettes/figs-introduction/basic_trace_burn-1.png |binary vignettes/figs-introduction/config2-1.png |binary vignettes/figs-introduction/config2-2.png |binary vignettes/figs-introduction/many_plots-1.png |binary vignettes/figs-introduction/many_plots-2.png |binary vignettes/figs-introduction/many_plots-3.png |binary vignettes/figs-introduction/many_plots-4.png |binary vignettes/figs-introduction/many_plots-5.png |binary vignettes/figs-introduction/traces-1.png |binary vignettes/figs-introduction/traces-2.png |binary vignettes/figs-introduction/traces-3.png |binary vignettes/figs-introduction/w-1.png |binary vignettes/introduction.Rmd | 24 75 files changed, 8965 insertions(+), 2264 deletions(-)
Title: Latent Variable Models for Networks
Description: Latent variable models for network data using fast inferential
procedures. For more information please visit: <http://igollini.github.io/lvm4net/>.
Author: Isabella Gollini [aut, cre] (<https://orcid.org/0000-0002-7738-5688>)
Maintainer: Isabella Gollini <igollini.stats@gmail.com>
Diff between lvm4net versions 0.2.1 dated 2018-10-07 and 0.3 dated 2019-06-13
DESCRIPTION | 21 +++++++++------ MD5 | 64 ++++++++++++++++++++++++++++++++++++------------ NAMESPACE | 8 ++++++ R/AitkenAcc.R |only R/PPIgen.R | 2 - R/PPIphy.R | 2 - R/ResTable.R |only R/XtoS.R |only R/buildYYh.R |only R/cls.R |only R/f_lca.R |only R/f_lca_nstarts.R |only R/f_lta.R |only R/f_lta_nstarts.R |only R/f_mlta.R |only R/f_mlta_methods.R |only R/f_mlta_nstarts.R |only R/f_mlta_nstarts_wfix.R |only R/f_mlta_wfix.R |only R/fvg.R |only R/ggLLlta.R |only R/is.adjacency.R | 2 - R/lca.R |only R/lift.R |only R/lsjm.R | 3 -- R/lsm.R | 4 +-- R/lta.R |only R/lvm4net-package.R | 13 +++++++-- R/mlta.R |only R/plot.lsjm.R | 2 - R/plot.lsm.R | 2 - R/print.mlta.R |only R/print.mmlta.R |only R/tableBIC.R |only README.md | 11 ++++++-- build |only inst/doc |only man/PPIgen.Rd | 3 ++ man/PPIphy.Rd | 3 ++ man/lca.Rd |only man/lift.Rd |only man/lsjm.Rd | 8 +++--- man/lsm.Rd | 8 +++--- man/lta.Rd |only man/lvm4net-package.Rd | 11 ++++++-- man/mlta.Rd |only vignettes |only 47 files changed, 120 insertions(+), 47 deletions(-)
Title: Longitudinal Cascade
Description: Creates a series of set of graphics and statistics related to the longitudinal cascade, all included in a single object. The longitudinal cascade inputs longitudinal data to identify gaps in the HIV and related cascades by observing differences using time to event and survival methods. The stage definitions are set by the user, with default standard options. Outputs include graphics, datasets, and formal statistical tests.
Author: Noah Haber [aut, cre]
Maintainer: Noah Haber <noahhaber@gmail.com>
Diff between longitudinalcascade versions 0.2.1.1 dated 2019-04-03 and 0.3.1.1 dated 2019-06-13
longitudinalcascade-0.2.1.1/longitudinalcascade/data/events_long.rdata |only longitudinalcascade-0.3.1.1/longitudinalcascade/DESCRIPTION | 6 longitudinalcascade-0.3.1.1/longitudinalcascade/MD5 | 8 longitudinalcascade-0.3.1.1/longitudinalcascade/R/longitudinalcascade.R | 992 +++++++--- longitudinalcascade-0.3.1.1/longitudinalcascade/data/events_long.RData |only longitudinalcascade-0.3.1.1/longitudinalcascade/man/longitudinalcascade.Rd | 37 6 files changed, 778 insertions(+), 265 deletions(-)
More information about longitudinalcascade at CRAN
Permanent link
Title: Parallel Implementation of 'ETERNA 3.40' for Prediction and
Analysis of Earth Tides
Description: This is a port of 'Fortran ETERNA 3.4'
<http://igets.u-strasbg.fr/soft_and_tool.php> by H.G. Wenzel
for calculating synthetic Earth tides using the
Hartmann and Wenzel (1994) <doi:10.1029/95GL03324> or
Kudryavtsev (2004) <doi:10.1007/s00190-003-0361-2> tidal catalogs.
Author: Jonathan Kennel [aut, cre, trl],
Beth Parker [ths],
Wenzel Hans-Georg [ctb]
Maintainer: Jonathan Kennel <jkennel@uoguelph.ca>
Diff between earthtide versions 0.0.6 dated 2019-05-05 and 0.0.8 dated 2019-06-13
DESCRIPTION | 9 MD5 | 43 +- NAMESPACE | 1 NEWS.md |only R/RcppExports.R | 8 R/calc_earthtide.R | 49 ++ R/earthtide_class.R | 283 ++++++++++++---- R/get_main_frequency.R |only R/gravity_station.R | 6 R/sysdata.rda |binary build/partial.rdb |binary inst/CITATION |only inst/doc/introduction.R | 157 ++++----- inst/doc/introduction.Rmd | 212 +++++------- inst/doc/introduction.html | 520 ++++++++++++++++++++++--------- man/Earthtide_class.Rd | 17 - man/calc_earthtide.Rd | 17 - man/get_main_frequency.Rd |only src/RcppExports.cpp | 18 - src/astro.cpp | 103 +++--- tests/testthat/test-earthtide.R | 83 ++++ tests/testthat/test-et_analyze.R | 35 ++ tests/testthat/test-get_main_frequency.R |only tests/testthat/test-gravity_station.R | 4 vignettes/introduction.Rmd | 212 +++++------- 25 files changed, 1129 insertions(+), 648 deletions(-)
Title: Pulls Information from Prov.Json Files
Description: R functions to access provenance information collected by 'rdt' or
'rdtLite'. The information is stored inside a 'ProvInfo' object and can be
accessed through a collection of functions that will return the requested
data. The exact format of the JSON created by 'rdt' and 'rdtLite' is described
in <https://github.com/End-to-end-provenance/ExtendedProvJson>.
Author: Orenna Brand [aut],
Joseph Wonsil [aut],
Emery Boose [aut],
Barbara Lerner [cre]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Diff between provParseR versions 0.1.1 dated 2018-12-27 and 0.1.2 dated 2019-06-13
DESCRIPTION | 9 - MD5 | 24 +- NAMESPACE | 3 NEWS.md | 7 R/provParse.R | 288 +++++++++++++++++++++++++++-------- inst/testdata/cases |only inst/testdata/ddg.json | 32 +-- inst/testdata/expected |only man/access.Rd | 38 ++++ tests/ddg.json | 32 +-- tests/testthat/test_elapsedTime.R |only tests/testthat/test_provParse.R | 16 + tests/testthat/test_provParse2.R | 29 +++ tests/testthat/test_sourcedScripts.R |only 14 files changed, 361 insertions(+), 117 deletions(-)
Title: Normal aka Gaussian (1-d) Mixture Models (S3 Classes and
Methods)
Description: Onedimensional Normal (i.e. Gaussian) Mixture Models Classes,
for, e.g., density estimation or clustering algorithms research and teaching;
providing the widely used Marron-Wand densities. Efficient random
number generation and graphics. Fitting to data by efficient ML (Maximum
Likelihood) or traditional EM estimation.
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Friedrich Leisch [ctb] (norMixEM(),
<https://orcid.org/0000-0001-7278-1983>),
Erik Jørgensen [ctb] (pnorMix(), qnorMix())
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between nor1mix versions 1.2-3 dated 2017-08-30 and 1.3-0 dated 2019-06-13
nor1mix-1.2-3/nor1mix/tests/ex.R |only nor1mix-1.3-0/nor1mix/ChangeLog | 23 +++ nor1mix-1.3-0/nor1mix/DESCRIPTION | 33 +++-- nor1mix-1.3-0/nor1mix/MD5 | 31 ++--- nor1mix-1.3-0/nor1mix/NAMESPACE | 3 nor1mix-1.3-0/nor1mix/R/norMix.R | 167 +++++++++++++++++++++------ nor1mix-1.3-0/nor1mix/R/norMixEM.R | 11 + nor1mix-1.3-0/nor1mix/build |only nor1mix-1.3-0/nor1mix/man/MarronWand.Rd | 9 + nor1mix-1.3-0/nor1mix/man/llnorMix.Rd | 63 ++++++---- nor1mix-1.3-0/nor1mix/man/nor1mix-package.Rd |only nor1mix-1.3-0/nor1mix/man/norMix.Rd | 2 nor1mix-1.3-0/nor1mix/man/norMix2call.Rd |only nor1mix-1.3-0/nor1mix/man/norMixFit.Rd | 9 + nor1mix-1.3-0/nor1mix/man/pnorMix.Rd | 2 nor1mix-1.3-0/nor1mix/man/rnorMix.Rd | 4 nor1mix-1.3-0/nor1mix/tests/MW.R | 6 nor1mix-1.3-0/nor1mix/tests/par.R | 27 +++- nor1mix-1.3-0/nor1mix/tests/qnorMix-ex.R |only 19 files changed, 288 insertions(+), 102 deletions(-)
Title: A Fully Featured Logging Framework
Description: A flexible, feature-rich yet light-weight logging
framework based on 'R6' classes. It supports hierarchical loggers,
custom log levels, arbitrary data fields in log events, logging to
plaintext, 'JSON', (rotating) files, memory buffers, and databases, as
well as email and push notifications. For a full list of features with
examples please refer to the package vignette.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between lgr versions 0.3.0 dated 2019-05-30 and 0.3.1 dated 2019-06-13
DESCRIPTION | 20 MD5 | 121 ++-- NAMESPACE | 10 NEWS.md | 15 R/Appender.R | 254 +++++++++- R/Layout.R | 28 + R/Logger.R | 21 R/basic_config.R |only R/default_functions.R | 10 R/get_logger.R | 66 +- R/logger_tree.R |only R/print_Appender.R |only R/print_Logger.R | 11 R/simple_logging.R | 307 +----------- R/utils.R | 20 README.md | 92 +-- inst/WORDLIST | 2 inst/benchmarks/benchmarks.html |only inst/doc/lgr.R | 9 inst/doc/lgr.Rmd | 38 + inst/doc/lgr.html | 731 ++++++++++++++--------------- man/Appender.Rd | 1 man/AppenderBuffer.Rd | 6 man/AppenderConsole.Rd | 3 man/AppenderDbi.Rd | 4 man/AppenderDigest.Rd | 2 man/AppenderDt.Rd | 3 man/AppenderFile.Rd | 3 man/AppenderFileRotating.Rd | 2 man/AppenderGmail.Rd | 5 man/AppenderJson.Rd | 3 man/AppenderMail.Rd | 2 man/AppenderMemory.Rd | 5 man/AppenderPushbullet.Rd | 9 man/AppenderRjdbc.Rd | 4 man/AppenderSendmail.Rd | 5 man/AppenderTable.Rd | 2 man/LayoutDbi.Rd | 1 man/LayoutFormat.Rd | 1 man/LayoutGlue.Rd | 1 man/LayoutJson.Rd | 1 man/basic_config.Rd | 23 man/default_exception_handler.Rd | 5 man/default_should_flush.Rd | 4 man/get_logger.Rd | 12 man/logger_tree.Rd |only man/print.Appender.Rd |only man/print.logger_tree.Rd |only man/simple_logging.Rd | 93 +-- tests/testthat/test_Appender.R | 54 +- tests/testthat/test_AppenderDbi.R | 4 tests/testthat/test_AppenderFileRotating.R | 44 - tests/testthat/test_Filter.R | 4 tests/testthat/test_Filterable.R | 4 tests/testthat/test_Layout.R | 2 tests/testthat/test_LogEvent.R | 6 tests/testthat/test_Logger.R | 44 - tests/testthat/test_get_logger.R | 73 ++ tests/testthat/test_log_levels.R | 8 tests/testthat/test_logger_config.R | 13 tests/testthat/test_logger_tree.R |only tests/testthat/test_print_Appender.R |only tests/testthat/test_print_Logger.R | 2 tests/testthat/test_read_json_log.R | 2 tests/testthat/test_simple_logging.R | 26 - vignettes/lgr.Rmd | 38 + 66 files changed, 1321 insertions(+), 958 deletions(-)
Title: Simultaneous Confidence Intervals for Ranks
Description: Algorithms to construct simultaneous confidence intervals for the ranks of means mu_1,...,mu_n based on an independent Gaussian sample using multiple testing techniques.
Author: Diaa Al Mohamad and Erik W. van Zwet and Jelle J. Goeman
Maintainer: Diaa Al Mohamad <diaa.almohamad@gmail.com>
Diff between ICRanks versions 2.0 dated 2018-12-13 and 3.0 dated 2019-06-13
DESCRIPTION | 10 MD5 | 14 NAMESPACE | 3 R/RcppExports.R | 28 R/ic.ranks.R | 466 +++------ man/ic.ranks.Rd | 54 - src/PartitionByBlock.cpp | 2350 ++++++++++++++++++++++++++++++++++++++++++++++- src/RcppExports.cpp | 138 ++ 8 files changed, 2706 insertions(+), 357 deletions(-)
Title: Toolkit to Validate New Data for a Predictive Model
Description: A lightweight toolkit to validate new observations when computing
their predictions with a predictive model. The validation process
consists of two steps: (1) record relevant statistics and meta data of the
variables in the original training data for the predictive model and
(2) use these data to run a set of basic validation tests on the new set of
observations.
Author: Lars Kjeldgaard [aut, cre]
Maintainer: Lars Kjeldgaard <lars_kjeldgaard@hotmail.com>
Diff between recorder versions 0.8.1 dated 2019-05-21 and 0.8.2 dated 2019-06-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/get_clean_rows.R | 5 +++-- inst/doc/recorder.html | 33 +++++++++++++++++++++++++++++---- inst/extdata/config.yml | 2 +- tests/testthat/test_get_failed_tests.R | 16 ++++++++++++++++ 6 files changed, 57 insertions(+), 15 deletions(-)
Title: Creates and Plots P-Value Functions, S-Value Functions,
Confidence Distributions and Confidence Densities
Description: Contains functions to compute and plot confidence distributions, confidence densities, p-value functions and s-value (surprisal) functions for several commonly used estimates. Instead of just calculating one p-value and one confidence interval, p-value functions display p-values and confidence intervals for many levels thereby allowing to gauge the compatibility of several parameter values with the data. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>; Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>; Bender R, Berg G, Zeeb H. (2005) <doi:10.1002/bimj.200410104> ; Singh K, Xie M, Strawderman WE. (2007) <doi:10.1214/074921707000000102>; Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052); Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>; and Greenland S. (2019) <doi:10.1080/00031305.2018.1529625>.
Author: Denis Infanger [aut, cre] (<https://orcid.org/0000-0001-9028-7110>)
Maintainer: Denis Infanger <denis.infanger@unibas.ch>
Diff between pvaluefunctions versions 1.1.0 dated 2019-05-22 and 1.2.0 dated 2019-06-13
DESCRIPTION | 6 MD5 | 35 ++ NEWS | 9 R/confidence_distributions.R | 504 +++++++++++++++++++++++++++++++------------ README.md | 254 ++++++++++++++++----- inst/doc/pvaluefun.R | 93 +++++++ inst/doc/pvaluefun.Rmd | 123 +++++++++- inst/doc/pvaluefun.html | 138 ++++++++++- man/conf_dist.Rd | 155 ++++++++----- man/figures |only vignettes/pvaluefun.Rmd | 123 +++++++++- 11 files changed, 1132 insertions(+), 308 deletions(-)
More information about pvaluefunctions at CRAN
Permanent link
Title: Various Programming Utilities
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.utils versions 2.8.0 dated 2019-02-14 and 2.9.0 dated 2019-06-13
R.utils-2.8.0/R.utils/R/arrayIndex.R |only R.utils-2.8.0/R.utils/R/resetWarnings.R |only R.utils-2.8.0/R.utils/man/arrayIndex.Rd |only R.utils-2.8.0/R.utils/man/resetWarnings.Rd |only R.utils-2.9.0/R.utils/DESCRIPTION | 7 - R.utils-2.9.0/R.utils/MD5 | 81 ++++++++++----------- R.utils-2.9.0/R.utils/NAMESPACE | 4 - R.utils-2.9.0/R.utils/NEWS | 21 +++++ R.utils-2.9.0/R.utils/R/Assert.R | 3 R.utils-2.9.0/R.utils/R/createLink.R | 17 +++- R.utils-2.9.0/R.utils/R/sourceDirectory.R | 3 R.utils-2.9.0/R.utils/R/withCapture.R | 6 - R.utils-2.9.0/R.utils/R/withTimeout.R | 6 - R.utils-2.9.0/R.utils/inst/WORDLIST | 2 R.utils-2.9.0/R.utils/man/MultiVerbose.Rd | 6 - R.utils-2.9.0/R.utils/man/Options.Rd | 4 - R.utils-2.9.0/R.utils/man/Verbose.Rd | 4 - R.utils-2.9.0/R.utils/man/callHooks.Rd | 6 - R.utils-2.9.0/R.utils/man/capitalize.Rd | 2 R.utils-2.9.0/R.utils/man/createFileAtomically.Rd | 16 ++-- R.utils-2.9.0/R.utils/man/findSourceTraceback.Rd | 32 ++++---- R.utils-2.9.0/R.utils/man/pushBackupFile.Rd | 23 ++--- R.utils-2.9.0/R.utils/man/readBinFragments.Rd | 4 - R.utils-2.9.0/R.utils/man/whichVector.logical.Rd | 46 +++++------ R.utils-2.9.0/R.utils/man/withCapture.Rd | 14 +-- R.utils-2.9.0/R.utils/man/withTimeout.Rd | 1 R.utils-2.9.0/R.utils/man/wrap.array.Rd | 8 +- R.utils-2.9.0/R.utils/tests/MultiVerbose.R | 4 - R.utils-2.9.0/R.utils/tests/Options.R | 4 - R.utils-2.9.0/R.utils/tests/Verbose.R | 4 - R.utils-2.9.0/R.utils/tests/callHooks.R | 6 - R.utils-2.9.0/R.utils/tests/capitalize.R | 2 R.utils-2.9.0/R.utils/tests/createFileAtomically.R | 1 R.utils-2.9.0/R.utils/tests/createLink.R | 4 - R.utils-2.9.0/R.utils/tests/filePath.R | 2 R.utils-2.9.0/R.utils/tests/findSourceTraceback.R | 32 ++++---- R.utils-2.9.0/R.utils/tests/hpaste.R | 6 - R.utils-2.9.0/R.utils/tests/isReplicated.R | 2 R.utils-2.9.0/R.utils/tests/pushBackupFile.R | 24 +++--- R.utils-2.9.0/R.utils/tests/readBinFragments.R | 4 - R.utils-2.9.0/R.utils/tests/sourceDirectory.R |only R.utils-2.9.0/R.utils/tests/use.R | 2 R.utils-2.9.0/R.utils/tests/withCapture.R | 7 + R.utils-2.9.0/R.utils/tests/wrap.array.R | 8 +- 44 files changed, 222 insertions(+), 206 deletions(-)
Title: Object-Oriented Implementation of CRM Designs
Description: Implements a wide range of model-based dose
escalation designs, ranging from classical and modern continual
reassessment methods (CRMs) based on dose-limiting toxicity endpoints to
dual-endpoint designs taking into account a biomarker/efficacy outcome. The
focus is on Bayesian inference, making it very easy to setup a new design
with its own JAGS code. However, it is also possible to implement 3+3
designs for comparison or models with non-Bayesian estimation. The whole
package is written in a modular form in the S4 class system, making it very
flexible for adaptation to new models, escalation or stopping rules.
Author: Daniel Sabanes Bove [aut],
Wai Yin Yeung [aut],
Giuseppe Palermo [aut, cre],
Thomas Jaki [aut]
Maintainer: Giuseppe Palermo <giuseppe.palermo@roche.com>
Diff between crmPack versions 0.2.9 dated 2018-12-21 and 1.0.0 dated 2019-06-13
crmPack-0.2.9/crmPack/inst/doc/jss2762.R |only crmPack-0.2.9/crmPack/inst/doc/jss2762.Rnw |only crmPack-0.2.9/crmPack/inst/doc/jss2762.pdf |only crmPack-0.2.9/crmPack/vignettes/jss2762.Rnw |only crmPack-0.2.9/crmPack/vignettes/jss2762.bib |only crmPack-0.2.9/crmPack/vignettes/mySweave.sty |only crmPack-1.0.0/crmPack/DESCRIPTION | 9 crmPack-1.0.0/crmPack/MD5 | 30 +- crmPack-1.0.0/crmPack/NEWS.md | 4 crmPack-1.0.0/crmPack/R/crmPack-package.R | 9 crmPack-1.0.0/crmPack/build/vignette.rds |binary crmPack-1.0.0/crmPack/inst/CITATION |only crmPack-1.0.0/crmPack/inst/doc/crmPack-jss-paper.R |only crmPack-1.0.0/crmPack/inst/doc/crmPack-jss-paper.Rnw |only crmPack-1.0.0/crmPack/inst/doc/crmPack-jss-paper.pdf |only crmPack-1.0.0/crmPack/inst/doc/example.Rnw | 1 crmPack-1.0.0/crmPack/inst/doc/example.pdf |binary crmPack-1.0.0/crmPack/inst/doc/guidelines.html | 194 +++++++++++++++++- crmPack-1.0.0/crmPack/man/crmPack-package.Rd | 11 - crmPack-1.0.0/crmPack/vignettes/crmPack-jss-paper.Rnw |only crmPack-1.0.0/crmPack/vignettes/crmPack-jss-paper.bib |only crmPack-1.0.0/crmPack/vignettes/example.Rnw | 1 22 files changed, 230 insertions(+), 29 deletions(-)
Title: Adapted Pair Correlation Function
Description: The adapted pair correlation function transfers the concept of the
pair correlation function from point patterns to patterns of objects of
finite size and irregular shape (e.g. lakes within a country). This is a
reimplementation of the method suggested by Nuske et al. (2009)
<doi:10.1016/j.foreco.2009.09.050> using the libraries 'GEOS' and 'GDAL'
directly instead of through 'PostGIS'.
Author: Robert Nuske [aut, cre] (<https://orcid.org/0000-0001-9773-2061>)
Maintainer: Robert Nuske <robert.nuske@mailbox.org>
Diff between apcf versions 0.1.2 dated 2019-01-17 and 0.1.3 dated 2019-06-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 3 +++ README.md | 1 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro.html | 25 ++++++++++++++----------- src/Makevars.win | 1 + 8 files changed, 29 insertions(+), 21 deletions(-)