Title: Calculates Conditional Mahalanobis Distances
Description: Calculates a Mahalanobis distance for every row of a set of
outcome variables (Mahalanobis, 1936
<doi:10.1007/s13171-019-00164-5>). The conditional Mahalanobis
distance is calculated using a conditional covariance matrix (i.e., a
covariance matrix of the outcome variables after controlling for a set
of predictors). Plotting the output of the cond_maha() function can
help identify which elements of a profile are unusual after
controlling for the predictors.
Author: W. Joel Schneider [aut, cre] ,
Feng Ji [aut]
Maintainer: W. Joel Schneider <w.joel.schneider@gmail.com>
Diff between unusualprofile versions 0.1.1 dated 2022-11-29 and 0.1.2 dated 2022-12-13
DESCRIPTION | 8 MD5 | 30 +-- NEWS.md | 7 R/main.R | 50 ++--- README.md | 2 inst/WORDLIST | 1 inst/doc/unusualprofile_calculations.R | 12 - inst/doc/unusualprofile_calculations.Rmd | 12 - inst/doc/unusualprofile_calculations.html | 8 man/figures/README-example-1.png |binary man/plot.cond_maha.Rd | 2 man/plot.maha.Rd | 2 tests/testthat/test-main.R | 291 ++++++++++++++++++++++++++++-- vignettes/Reading.pdf |binary vignettes/Reading.svg | 106 +++++----- vignettes/unusualprofile_calculations.Rmd | 12 - 16 files changed, 409 insertions(+), 134 deletions(-)
More information about unusualprofile at CRAN
Permanent link
Title: Two One-Sided Tests (TOST) Equivalence Testing
Description: Two one-sided tests (TOST) procedure to test equivalence for t-tests, correlations, differences between proportions, and meta-analyses, including power analysis for t-tests and correlations. Allows you to specify equivalence bounds in raw scale units or in terms of effect sizes. See: Lakens (2017) <doi:10.1177/1948550617697177>.
Author: Daniel Lakens [aut],
Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between TOSTER versions 0.4.2 dated 2022-09-20 and 0.6.0 dated 2022-12-13
DESCRIPTION | 8 MD5 | 291 +-- NAMESPACE | 180 + NEWS.md | 203 +- R/00jmv.R |only R/TOSTmeta.R | 230 +- R/TOSTone.R | 230 +- R/TOSTone.raw.R | 222 +- R/TOSTpaired.R | 258 +- R/TOSTpaired.raw.R | 232 +- R/TOSTr.R | 222 +- R/TOSTtwo.R | 314 +-- R/TOSTtwo.prop.R | 290 +-- R/TOSTtwo.raw.R | 300 +-- R/anova_summary.R | 470 ++--- R/boot_compare_smd.R |only R/boot_log_TOST.R |only R/boot_t_TOST.R | 983 +++++----- R/cohend_calcs.R | 1042 ++++++++--- R/compare_cor.R |only R/compare_smd.R |only R/compare_smd_functions.R |only R/corr_calcs.R | 270 +- R/data.R | 14 R/datatostone.b.R | 358 ++- R/datatostone.h.R | 991 +++++----- R/datatostpaired.b.R | 809 ++++---- R/datatostpaired.h.R | 971 +++++----- R/datatostr.b.R | 393 ++-- R/datatostr.h.R | 655 +++---- R/datatosttwo.b.R | 603 +++--- R/datatosttwo.h.R | 1149 ++++++------ R/datatosttwoprop.b.R | 248 +- R/datatosttwoprop.h.R | 713 +++---- R/equ_anova.R | 172 - R/equ_ftest.R | 193 +- R/extract_r_paired.R |only R/gg_curv_t.R | 388 ++-- R/globals.R | 10 R/htest.R |only R/jamovi_functions.R |only R/log_TOST.R |only R/log_pair.R |only R/methods.TOSTnp.R | 118 - R/methods.TOSTt.R | 1163 ++++++------ R/others.R |only R/pes_calc.R | 440 ++-- R/plot.R | 53 R/plot_corr.R | 73 R/plot_pes.R | 85 R/plot_scripts.R | 195 +- R/plot_smd.R | 111 - R/powerTOSTanova.R | 111 - R/powerTOSTone.R | 106 - R/powerTOSTone.raw.R | 108 - R/powerTOSTpaired.R | 102 - R/powerTOSTpaired.raw.R | 120 - R/powerTOSTr.R | 116 - R/powerTOSTtwo.R | 102 - R/powerTOSTtwo.prop.R | 142 - R/powerTOSTtwo.raw.R | 120 - R/power_TOST_functions.R | 596 +++--- R/power_t_TOST.R | 205 +- R/rbs.R | 332 ++- R/rbs_calcs.R | 186 +- R/ses_calc.R |only R/smd_calc.R |only R/t_TOST.R | 877 +++++---- R/tsum_TOST.R | 692 +++---- R/tsum_funcs.R | 240 +- R/wilcox_TOST.R | 636 +++---- README.md | 98 - build/vignette.rds |binary inst/CITATION | 15 inst/doc/IntroTOSTt.R | 446 ++-- inst/doc/IntroTOSTt.Rmd | 627 +++--- inst/doc/IntroTOSTt.html | 1495 ++++++++-------- inst/doc/IntroductionToTOSTER.R | 46 inst/doc/IntroductionToTOSTER.Rmd | 315 +-- inst/doc/IntroductionToTOSTER.html | 1731 +++++++++---------- inst/doc/SMD_calcs.R | 85 inst/doc/SMD_calcs.Rmd | 1035 +++++++---- inst/doc/SMD_calcs.html | 1892 ++++++++++++-------- inst/doc/robustTOST.R | 98 - inst/doc/robustTOST.Rmd | 392 ++-- inst/doc/robustTOST.html | 1441 +++++++++------ inst/doc/the_ftestTOSTER.R | 66 inst/doc/the_ftestTOSTER.Rmd | 232 +- inst/doc/the_ftestTOSTER.html | 1144 ++++++------ man/TOSTmeta.Rd | 106 - man/TOSTnp-methods.Rd | 52 man/TOSTone.Rd | 96 - man/TOSTone.raw.Rd | 96 - man/TOSTpaired.Rd | 120 - man/TOSTpaired.raw.Rd | 120 - man/TOSTr.Rd | 74 man/TOSTt-methods.Rd | 83 man/TOSTtwo.Rd | 154 - man/TOSTtwo.prop.Rd | 120 - man/TOSTtwo.raw.Rd | 154 - man/as_htest.Rd |only man/boot_compare_smd.Rd |only man/boot_log_TOST.Rd |only man/boot_t_TOST.Rd | 196 +- man/compare_cor.Rd |only man/compare_smd.Rd |only man/dataTOSTone.Rd | 165 - man/dataTOSTpaired.Rd | 195 +- man/dataTOSTr.Rd | 125 - man/dataTOSTtwo.Rd | 211 +- man/datatosttwoprop.Rd | 121 - man/equ_anova.Rd | 82 man/equ_ftest.Rd | 94 - man/extract_r_paired.Rd |only man/hawthorne.Rd | 38 man/log_TOST.Rd |only man/plot_cor.Rd | 76 man/plot_pes.Rd | 76 man/plot_smd.Rd | 92 - man/powerTOSTone.Rd | 92 - man/powerTOSTone.raw.Rd | 96 - man/powerTOSTpaired.Rd | 88 man/powerTOSTpaired.raw.Rd | 106 - man/powerTOSTr.Rd | 78 man/powerTOSTtwo.Rd | 88 man/powerTOSTtwo.prop.Rd | 152 - man/powerTOSTtwo.raw.Rd | 112 - man/power_eq_f.Rd | 75 man/power_t_TOST.Rd | 106 - man/rbs.Rd | 160 - man/ses_calc.Rd |only man/smd_calc.Rd |only man/t_TOST.Rd | 211 +- man/tsum_TOST.Rd | 174 + man/wilcox_TOST.Rd | 197 +- tests/testthat.R | 8 tests/testthat/Rplots.pdf |binary tests/testthat/test-NCSS1.R | 162 - tests/testthat/test-bootTOST.R | 452 ++-- tests/testthat/test-compare_smds.R |only tests/testthat/test-data_summary_equivalent.R | 190 +- tests/testthat/test-ftests.R | 224 +- tests/testthat/test-jamovi.R | 1273 +++++++------- tests/testthat/test-known_results.R | 570 +++--- tests/testthat/test-log.R |only tests/testthat/test-old_errors.R | 516 ++--- tests/testthat/test-power_consistent.R | 146 - tests/testthat/test-power_t_TOST.R | 708 ++++--- tests/testthat/test-powerraw.R | 158 - tests/testthat/test-tTOST.R | 2354 ++++++++++++++------------ tests/testthat/test-wilcox.R | 335 ++- vignettes/IntroTOSTt.Rmd | 627 +++--- vignettes/IntroductionToTOSTER.Rmd | 315 +-- vignettes/SMD_calcs.Rmd | 1035 +++++++---- vignettes/anovaTOSTER.R | 56 vignettes/anovaTOSTER.html | 976 +++++----- vignettes/references.bib | 349 ++- vignettes/robustTOST.Rmd | 392 ++-- vignettes/the_ftestTOSTER.Rmd | 232 +- 159 files changed, 25133 insertions(+), 21925 deletions(-)
Title: Repeated Measures Correlation
Description: Compute the repeated measures correlation, a statistical technique
for determining the overall within-individual relationship among paired measures
assessed on two or more occasions, first introduced by Bland and Altman (1995).
Includes functions for diagnostics, p-value, effect size with confidence
interval including optional bootstrapping, as well as graphing. Also includes
several example datasets. For more details, see the web documentation
<https://lmarusich.github.io/rmcorr/index.html> and the
original paper: Bakdash and Marusich (2017) <doi:10.3389/fpsyg.2017.00456>.
Author: Jonathan Z. Bakdash [aut] ,
Laura R. Marusich [aut, cre]
Maintainer: Laura R. Marusich <lmarusich@gmail.com>
Diff between rmcorr versions 0.5.2 dated 2022-08-25 and 0.5.4 dated 2022-12-13
DESCRIPTION | 13 MD5 | 67 NEWS.md | 10 R/data.R | 2 R/rmcorr-package.R | 8 R/rmcorr.R | 24 R/rmcorr_mat.R | 13 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/CI_fix.R |only inst/doc/CI_fix.Rmd |only inst/doc/CI_fix.html |only inst/doc/FAQ_and_limitations.html | 115 - inst/doc/New_rmcorr_paper_analyses_figures.R | 55 inst/doc/New_rmcorr_paper_analyses_figures.Rmd | 57 inst/doc/New_rmcorr_paper_analyses_figures.html | 1842 ++++++++++++------------ inst/doc/compcor.R | 5 inst/doc/compcor.Rmd | 7 inst/doc/compcor.html | 637 ++++---- inst/doc/rmcorr_mat.R | 5 inst/doc/rmcorr_mat.Rmd | 6 inst/doc/rmcorr_mat.html | 281 +-- man/bland1995.Rd | 2 man/rmcorr-package.Rd | 6 man/rmcorr.Rd | 17 man/rmcorr_mat.Rd | 8 tests/testthat/Rplots.pdf |only tests/testthat/_snaps |only tests/testthat/test-rmcorr-mat.R | 65 tests/testthat/test-rmcorr-plot.R |only tests/testthat/test-rmcorr.R | 41 vignettes/CI_fix.Rmd |only vignettes/New_rmcorr_paper_analyses_figures.Rmd | 57 vignettes/compcor.Rmd | 7 vignettes/rmcorr_mat.Rmd | 6 36 files changed, 1874 insertions(+), 1484 deletions(-)
Title: Extracts Environmental Data from 'ERDDAP' Web Services
Description: Contains three functions that access
environmental data from any 'ERDDAP' data web service. The rxtracto() function extracts
data along a trajectory for a given "radius" around the point. The
rxtracto_3D() function extracts data in a box. The rxtractogon() function
extracts data in a polygon. All of those three function use the 'rerddap' package
to extract the data, and should work with any 'ERDDAP' server.
There are also two functions, plotBBox() and plotTrack() that use the 'plotdap'
package to simplify the creation of maps of the data.
Author: Roy Mendelssohn [aut, cre],
Marie Auger-Methe [ctb]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddapXtracto versions 1.1.3 dated 2022-10-16 and 1.1.4 dated 2022-12-13
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/data_extract_read.R | 1 - R/rxtracto.R | 9 ++++----- R/rxtracto_3D.R | 7 +++---- R/rxtractogon.R | 20 +++++++++----------- README.md | 2 +- build/vignette.rds |binary inst/doc/UsingrerddapXtracto.html | 4 ++-- man/rxtracto.Rd | 9 ++++----- man/rxtracto_3D.Rd | 7 +++---- man/rxtractogon.Rd | 19 ++++++++----------- 13 files changed, 55 insertions(+), 61 deletions(-)
More information about rerddapXtracto at CRAN
Permanent link
Title: Create and Maintain a Relational Database of Data from
PubMed/MEDLINE
Description: Provides a simple interface for extracting various elements from
the publicly available PubMed XML files, incorporating PubMed's regular
updates, and combining the data with the NIH Open Citation Collection. See
Schoenbachler and Hughey (2021) <doi:10.7717/peerj.11071>.
Author: Jake Hughey [aut, cre],
Josh Schoenbachler [aut],
Elliot Outland [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between pmparser versions 1.0.13 dated 2022-11-24 and 1.0.15 dated 2022-12-13
pmparser-1.0.13/pmparser/tests/testthat/pubmed_sample/baseline/pubmed22n1114.xml.gz |only pmparser-1.0.13/pmparser/tests/testthat/pubmed_sample/baseline/pubmed22n1114.xml.gz.md5 |only pmparser-1.0.13/pmparser/tests/testthat/pubmed_sample/pubmed22n1114.rds |only pmparser-1.0.13/pmparser/tests/testthat/pubmed_sample/pubmed22n1115.rds |only pmparser-1.0.13/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed22n1115.xml.gz |only pmparser-1.0.13/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed22n1115.xml.gz.md5 |only pmparser-1.0.15/pmparser/DESCRIPTION | 8 pmparser-1.0.15/pmparser/MD5 | 56 pmparser-1.0.15/pmparser/NEWS.md | 7 pmparser-1.0.15/pmparser/R/get_citation.R | 8 pmparser-1.0.15/pmparser/R/get_parsing_tables.R | 4 pmparser-1.0.15/pmparser/R/get_pubmed_files.R | 9 pmparser-1.0.15/pmparser/R/parse_element.R | 13 pmparser-1.0.15/pmparser/R/utilities.R | 16 pmparser-1.0.15/pmparser/inst/doc/data_dictionary.html | 16 pmparser-1.0.15/pmparser/inst/extdata/data_dictionary.csv | 6 pmparser-1.0.15/pmparser/man/parseElement.Rd | 5 pmparser-1.0.15/pmparser/tests/testthat/parsing_tables/create_parsing_tables_no_suffix.db |binary pmparser-1.0.15/pmparser/tests/testthat/parsing_tables/create_parsing_tables_with_suffix.db |binary pmparser-1.0.15/pmparser/tests/testthat/parsing_tables/get_parsing_tables_no_suffix.rds |binary pmparser-1.0.15/pmparser/tests/testthat/parsing_tables/get_parsing_tables_with_suffix.rds |binary pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/baseline/pubmed23n1166.xml.gz |only pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/baseline/pubmed23n1166.xml.gz.md5 |only pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/file_info_postdown.csv | 8 pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/file_info_predown_all.csv | 2715 ++++------ pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/file_info_predown_baseline.csv | 2280 ++++---- pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/open_citation_collection.zip |binary pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/pmdb_sample_create.db |binary pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/pmdb_sample_update.db |binary pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/pubmed23n1166.rds |only pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/pubmed23n1167.rds |only pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed23n1167.xml.gz |only pmparser-1.0.15/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed23n1167.xml.gz.md5 |only pmparser-1.0.15/pmparser/tests/testthat/test_parse_element.R | 2 pmparser-1.0.15/pmparser/tests/testthat/test_utilities.R | 2 35 files changed, 2431 insertions(+), 2724 deletions(-)
Title: Two-Steps Benchmarks for Time Series Disaggregation
Description: The twoStepsBenchmark() and threeRuleSmooth() functions allow you to
disaggregate a low-frequency time series with higher frequency time series,
using the French National Accounts methodology. The aggregated sum of the
resulting time series is strictly equal to the low-frequency time series within the
benchmarking window. Typically, the low-frequency time series is an annual one,
unknown for the last year, and the high frequency one is either quarterly or
monthly. See "Methodology of quarterly national accounts", Insee Méthodes
N°126, by Insee (2012, ISBN:978-2-11-068613-8, <https://www.insee.fr/en/information/2579410>).
Author: Arnaud Feldmann [aut] ,
Franck Arnaud [ctb] ,
Thomas Laurent [cre],
Institut national de la statistique et des etudes economiques [cph]
Maintainer: Thomas Laurent <thomas.laurent@insee.fr>
Diff between disaggR versions 1.0.3.1 dated 2022-03-04 and 1.0.4.1 dated 2022-12-13
DESCRIPTION | 9 MD5 | 74 NEWS.md | 8 R/data.R | 22 R/in.R | 3 R/plot.R | 4 R/reView.R | 82 R/twoStepsBenchmark.R | 12 R/utils.R | 12 build/vignette.rds |binary data/consumption_catering.RData |only data/turnover_catering.RData |only inst/doc/disaggr.html | 503 +- inst/doc/disaggr_outlier.R |only inst/doc/disaggr_outlier.Rmd |only inst/doc/disaggr_outlier.html |only man/consumption_catering.Rd |only man/disaggR-package.Rd | 1 man/rePort.Rd | 6 man/turnover_catering.Rd |only man/twoStepsBenchmark.Rd | 2 tests/testthat/_snaps/in.md | 940 +-- tests/testthat/_snaps/methods.md | 464 - tests/testthat/_snaps/plot/gg-ctb-showlegendf.svg | 1464 +++--- tests/testthat/_snaps/plot/gg-indicator-contributions-2008-4-2012-7-smooth.svg | 212 tests/testthat/_snaps/plot/gg-indicator-contributions-2008-4-2012-7.svg | 318 - tests/testthat/_snaps/plot/gg-indicator-contributions-nowin-smooth.svg | 980 ++-- tests/testthat/_snaps/plot/gg-indicator-contributions-nowin.svg | 1470 +++--- tests/testthat/_snaps/plot/gg-inrevisions-contributions-2008-4-2012-7-smooth.svg | 212 tests/testthat/_snaps/plot/gg-inrevisions-contributions-2008-4-2012-7.svg | 318 - tests/testthat/_snaps/plot/gg-inrevisions-contributions-nowin-smooth.svg | 980 ++-- tests/testthat/_snaps/plot/gg-inrevisions-contributions-nowin.svg | 1470 +++--- tests/testthat/_snaps/plot/gg-main-ctb-smooth.svg | 980 ++-- tests/testthat/_snaps/plot/gg-mts-ctb.svg | 2408 +++++----- tests/testthat/_snaps/plot/gg-plot-main-ctb.svg | 1470 +++--- tests/testthat/_snaps/plot/ggplot-indicator-contributions-outlier.svg | 1470 +++--- tests/testthat/_snaps/threeRuleSmooth.md | 734 +-- tests/testthat/_snaps/twoStepsBenchmark.md | 650 +- tests/testthat/test-in.R | 1 tests/testthat/test-plot.R | 15 tests/testthat/test-reView.R | 523 +- vignettes/disaggr_outlier.Rmd |only 42 files changed, 9103 insertions(+), 8714 deletions(-)
Title: High Dimensional Penalized Generalized Linear Mixed Models
(pGLMM)
Description: Fits high dimensional penalized generalized linear
mixed models using
the Monte Carlo Expectation Conditional Minimization (MCECM) algorithm.
The purpose of the package is to perform variable selection on both the fixed and
random effects simultaneously for generalized linear mixed models.
The package supports fitting of Binomial, Gaussian, and Poisson data with canonical links, and
supports penalization using the MCP, SCAD, or LASSO penalties. The MCECM algorithm
is described in Rashid et al. (2020) <doi:10.1080/01621459.2019.1671197>.
The techniques used in the minimization portion of the procedure (the M-step) are
derived from the procedures of the 'ncvreg' package (Breheny and Huang (2011)
<doi:10.1214/10-AOAS388>) and 'grpreg' package (Breheny and Huang (2015)
<doi:10.1007/s11222-013-9424-2>), with
appropriate modifications to account for the estimation and penalization of
the random effects. The 'ncvreg' and 'grpreg' packages also describe the MCP, SCAD,
and LAS [...truncated...]
Author: Hillary Heiling [aut, cre],
Naim Rashid [aut],
Quefeng Li [aut]
Maintainer: Hillary Heiling <hheiling@live.unc.edu>
Diff between glmmPen versions 1.5.1.10 dated 2022-04-29 and 1.5.2.11 dated 2022-12-13
glmmPen-1.5.1.10/glmmPen/R/glmmPen_FineSearch.R |only glmmPen-1.5.1.10/glmmPen/inst/glmmPen_1.5.1.10.pdf |only glmmPen-1.5.1.10/glmmPen/man/fit_dat.Rd |only glmmPen-1.5.1.10/glmmPen/man/glmmPen_FineSearch.Rd |only glmmPen-1.5.1.10/glmmPen/man/select_tune.Rd |only glmmPen-1.5.1.10/glmmPen/src/grp_CD_XZ_fast.cpp |only glmmPen-1.5.2.11/glmmPen/DESCRIPTION | 8 glmmPen-1.5.2.11/glmmPen/MD5 | 81 + glmmPen-1.5.2.11/glmmPen/NAMESPACE | 4 glmmPen-1.5.2.11/glmmPen/R/E_step_final_FA.R |only glmmPen-1.5.2.11/glmmPen/R/M_step.R | 19 glmmPen-1.5.2.11/glmmPen/R/M_step_FA.R |only glmmPen-1.5.2.11/glmmPen/R/RcppExports.R | 20 glmmPen-1.5.2.11/glmmPen/R/SetClassDefn.R | 26 glmmPen-1.5.2.11/glmmPen/R/basal_dataset.R | 3 glmmPen-1.5.2.11/glmmPen/R/control_options.R | 163 +++ glmmPen-1.5.2.11/glmmPen/R/estimate_r.R |only glmmPen-1.5.2.11/glmmPen/R/fit_dat.R | 279 +++--- glmmPen-1.5.2.11/glmmPen/R/fit_dat_FA.R |only glmmPen-1.5.2.11/glmmPen/R/glmmPen.R | 477 ++++++++--- glmmPen-1.5.2.11/glmmPen/R/glmmPen_FA.R |only glmmPen-1.5.2.11/glmmPen/R/logLik_Pajor_FA.R |only glmmPen-1.5.2.11/glmmPen/R/methods.R | 26 glmmPen-1.5.2.11/glmmPen/R/prescreen.R | 40 glmmPen-1.5.2.11/glmmPen/R/prescreen_FA.R |only glmmPen-1.5.2.11/glmmPen/R/select_tune.R | 126 +- glmmPen-1.5.2.11/glmmPen/R/select_tune_FA.R |only glmmPen-1.5.2.11/glmmPen/R/sim_generation.R | 34 glmmPen-1.5.2.11/glmmPen/R/sim_generation_FA.R |only glmmPen-1.5.2.11/glmmPen/inst/glmmPen_1.5.2.11.pdf |only glmmPen-1.5.2.11/glmmPen/inst/stan/poisson_log_model.stan | 3 glmmPen-1.5.2.11/glmmPen/inst/update.R | 14 glmmPen-1.5.2.11/glmmPen/man/LambdaSeq.Rd | 3 glmmPen-1.5.2.11/glmmPen/man/basal.Rd | 3 glmmPen-1.5.2.11/glmmPen/man/glmm.Rd | 3 glmmPen-1.5.2.11/glmmPen/man/glmmPen.Rd | 15 glmmPen-1.5.2.11/glmmPen/man/glmmPen_FA.Rd |only glmmPen-1.5.2.11/glmmPen/man/glmm_FA.Rd |only glmmPen-1.5.2.11/glmmPen/man/optimControl.Rd | 50 + glmmPen-1.5.2.11/glmmPen/man/pglmmObj-class.Rd | 10 glmmPen-1.5.2.11/glmmPen/man/plot_mcmc.Rd | 3 glmmPen-1.5.2.11/glmmPen/man/rControl.Rd | 19 glmmPen-1.5.2.11/glmmPen/man/sim.data.Rd | 48 - glmmPen-1.5.2.11/glmmPen/src/RcppExports.cpp | 106 ++ glmmPen-1.5.2.11/glmmPen/src/coord_descent.cpp | 8 glmmPen-1.5.2.11/glmmPen/src/grp_CD_XZ_FA_step.cpp |only glmmPen-1.5.2.11/glmmPen/src/grp_CD_XZ_step.cpp |only glmmPen-1.5.2.11/glmmPen/src/stanExports_poisson_log_model.h | 4 glmmPen-1.5.2.11/glmmPen/src/utility_CD.h | 34 glmmPen-1.5.2.11/glmmPen/src/utility_FA.cpp |only glmmPen-1.5.2.11/glmmPen/src/utility_glm.cpp | 5 glmmPen-1.5.2.11/glmmPen/src/utility_grpCD.cpp | 149 ++- 52 files changed, 1246 insertions(+), 537 deletions(-)
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://eppn2020.plant-phenotyping.eu/>).
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml>).
Author: Emilie J Millet [aut] ,
Maria Xose Rodriguez Alvarez [aut]
,
Diana Marcela Perez Valencia [aut]
,
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre]
,
Fred van Eeuwijk [aut] ,
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.5 dated 2021-09-15 and 1.0.6 dated 2022-12-13
statgenHTP-1.0.5/statgenHTP/man/plot.HTPSplineEst.Rd |only statgenHTP-1.0.6/statgenHTP/DESCRIPTION | 16 statgenHTP-1.0.6/statgenHTP/MD5 | 103 - statgenHTP-1.0.6/statgenHTP/NAMESPACE | 8 statgenHTP-1.0.6/statgenHTP/NEWS.md | 27 statgenHTP-1.0.6/statgenHTP/R/correctSpatial.R | 12 statgenHTP-1.0.6/statgenHTP/R/createFitMod.R | 53 statgenHTP-1.0.6/statgenHTP/R/detectSerieOut.R | 6 statgenHTP-1.0.6/statgenHTP/R/detectSingleOut.R | 16 statgenHTP-1.0.6/statgenHTP/R/detectSingleOutMaize.R | 4 statgenHTP-1.0.6/statgenHTP/R/estimateSplineParameters.R | 188 + statgenHTP-1.0.6/statgenHTP/R/fitModels.R | 3 statgenHTP-1.0.6/statgenHTP/R/fitSpline.R | 166 - statgenHTP-1.0.6/statgenHTP/R/fitSplineHDM.R |only statgenHTP-1.0.6/statgenHTP/R/fitSplineHDMHelperFunctions.R |only statgenHTP-1.0.6/statgenHTP/R/plot.psHDM.R |only statgenHTP-1.0.6/statgenHTP/R/predict.psHDM.R |only statgenHTP-1.0.6/statgenHTP/R/reexport.R |only statgenHTP-1.0.6/statgenHTP/R/utils.R | 55 statgenHTP-1.0.6/statgenHTP/README.md | 8 statgenHTP-1.0.6/statgenHTP/build/partial.rdb |binary statgenHTP-1.0.6/statgenHTP/build/vignette.rds |binary statgenHTP-1.0.6/statgenHTP/inst/doc/Overview_HTP.R | 83 statgenHTP-1.0.6/statgenHTP/inst/doc/Overview_HTP.Rmd | 193 +- statgenHTP-1.0.6/statgenHTP/inst/doc/Overview_HTP.html | 958 ++++++++-- statgenHTP-1.0.6/statgenHTP/inst/tinytest/coefDat |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corr1Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corr2Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corr3Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corr4Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corr5Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corr6Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corrAs1Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corrAs2Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corrAs3Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corrAs4Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corrAs5Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/corrAs6Comp |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/genoLevel |only statgenHTP-1.0.6/statgenHTP/inst/tinytest/plotLevel |only statgenHTP-1.0.6/statgenHTP/inst/tinytest/popLevel |only statgenHTP-1.0.6/statgenHTP/inst/tinytest/predDat |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/predHDM |only statgenHTP-1.0.6/statgenHTP/inst/tinytest/predHDMse |only statgenHTP-1.0.6/statgenHTP/inst/tinytest/serieOut |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/splineEst |binary statgenHTP-1.0.6/statgenHTP/inst/tinytest/splineEstHDM |only statgenHTP-1.0.6/statgenHTP/inst/tinytest/test_detectSerieOut.R | 12 statgenHTP-1.0.6/statgenHTP/inst/tinytest/test_detectSingleOut.R | 14 statgenHTP-1.0.6/statgenHTP/inst/tinytest/test_estimateSplineParameters.R | 56 statgenHTP-1.0.6/statgenHTP/inst/tinytest/test_fitSplineHDM.R |only statgenHTP-1.0.6/statgenHTP/inst/tinytest/test_getVar.R | 12 statgenHTP-1.0.6/statgenHTP/inst/tinytest/test_plot.psHDM.R |only statgenHTP-1.0.6/statgenHTP/inst/tinytest/test_predict.psHDM.R |only statgenHTP-1.0.6/statgenHTP/man/estimateSplineParameters.Rd | 76 statgenHTP-1.0.6/statgenHTP/man/fitSplineHDM.Rd |only statgenHTP-1.0.6/statgenHTP/man/plot.psHDM.Rd |only statgenHTP-1.0.6/statgenHTP/man/plot.splineEst.Rd |only statgenHTP-1.0.6/statgenHTP/man/predict.psHDM.Rd |only statgenHTP-1.0.6/statgenHTP/man/statgenHTP-package.Rd | 8 statgenHTP-1.0.6/statgenHTP/vignettes/Overview_HTP.Rmd | 193 +- statgenHTP-1.0.6/statgenHTP/vignettes/bibliography.bib | 27 62 files changed, 1677 insertions(+), 620 deletions(-)
Title: Text Analysis Through the 'Receptiviti' API
Description: Send text to the <https://www.receptiviti.com> API to be scored
by all available frameworks.
Author: Receptiviti Inc. [fnd, cph],
Kent English [cre],
Micah Iserman [aut, ctr]
Maintainer: Kent English <kenglish@receptiviti.com>
Diff between receptiviti versions 0.1.2 dated 2022-10-06 and 0.1.3 dated 2022-12-13
DESCRIPTION | 9 ++++----- MD5 | 14 +++++++------- NEWS.md | 7 ++++++- R/receptiviti.R | 1 + R/receptiviti_status.R | 5 +++-- README.md | 4 ++-- tests/testthat/test-receptiviti.R | 4 ++-- tests/testthat/test-receptiviti_status.R | 7 ++++--- 8 files changed, 29 insertions(+), 22 deletions(-)
Title: Tracking Geo Code Change of Regional Granularity in Norway
Description: Regional granularity levels in Norway which are depicted by different codes,
have undergone several changes over the years.
Identifying when codes have changed and how many changes have taken place
can be troublesome. This package will help to identify these changes and when the changes
have taken place. One of the limitation of this package is that it is heavily depending
on the codes available from SSB website <https://data.ssb.no/api/klass/v1/api-guide.html>.
Author: Yusman Kamaleri [aut, cre]
Maintainer: Yusman Kamaleri <ybkamaleri@gmail.com>
Diff between norgeo versions 2.1.2 dated 2022-11-07 and 2.1.3 dated 2022-12-13
DESCRIPTION | 8 LICENSE | 4 MD5 | 72 +- NEWS.md | 205 +++--- R/cast-geo.R | 548 +++++++++--------- R/data.R | 22 R/env.R | 32 - R/get-change.R | 524 ++++++++--------- R/get-code.R | 230 +++---- R/get-correspond.R | 226 +++---- R/globals.R | 58 - R/norgeo.R | 12 R/save_geo.R | 140 ++-- R/track-change.R | 292 ++++----- R/track-merge.R | 46 - R/track-split.R | 46 - R/utils.R | 100 +-- R/zzz.R | 8 README.md | 130 ++-- build/vignette.rds |binary inst/doc/use-api.R | 36 - inst/doc/use-api.Rmd | 118 ++-- inst/doc/use-api.html | 796 +++++++++++++-------------- inst/test-data/cast_2020.rds |binary inst/test-data/trackChangeKomm_2017_2020.rds |binary tests/fixtures/change.yml | 216 +++---- tests/fixtures/codes-fromto.yml | 122 ++-- tests/fixtures/correspond.yml | 764 ++++++++++++------------- tests/testthat.R | 8 tests/testthat/setup-norgeo.R | 40 - tests/testthat/test-Save_file.R | 14 tests/testthat/test-cast-geo.R | 12 tests/testthat/test-get-change.R | 58 - tests/testthat/test-get-code.R | 26 tests/testthat/test-get-correspond.R | 18 tests/testthat/test-track-change.R | 34 - vignettes/use-api.Rmd | 118 ++-- 37 files changed, 2541 insertions(+), 2542 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [aut, cre] ,
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Jeroen Ooms [ctb],
Barret Schloerke [ctb],
Adam Ryczkowski [ctb],
Hiroaki Yutani [ctb],
Michel Lang [ctb],
Karolis Koncevičius [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between evaluate versions 0.18 dated 2022-11-07 and 0.19 dated 2022-12-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/eval.r | 16 +++++++++------- R/parse.r | 2 +- 5 files changed, 25 insertions(+), 16 deletions(-)
Title: R and C++ Interfaces to 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides
many desirable features. This package bundles these header files for easy use by R packages
from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSpdlog versions 0.0.10 dated 2022-11-17 and 0.0.11 dated 2022-12-13
ChangeLog | 26 ++++++++++++ DESCRIPTION | 10 ++-- MD5 | 32 +++++++-------- R/RcppExports.R | 10 ++++ README.md | 6 ++ build/partial.rdb |binary inst/NEWS.Rd | 8 +++ inst/doc/introduction.html | 2 inst/doc/introduction.md | 3 - inst/include/RcppSpdlog_RcppExports.h | 41 ++++++++++++++++++++ inst/include/rcpp_sink.h | 1 inst/include/spdl.h | 6 ++ man/log_setup.Rd | 9 +++- src/RcppExports.cpp | 69 ++++++++++++++++++++++++++++++++-- src/formatter.cpp | 2 src/interface.cpp | 25 +++++++++++- vignettes/introduction.md | 3 - 17 files changed, 222 insertions(+), 31 deletions(-)
Title: Genealogical Data Analysis
Description: Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations. See: "GENLIB: an R package for the analysis of genealogical data" Gauvin et al. (2015) <doi:10.1186/s12859-015-0581-5>.
Author: Louis Houde [aut],
Jean-Francois Lefebvre [aut],
Valery Roy-Lagace [aut],
Sebastien Lemieux [aut],
Michael J. Fromberger [ctb],
Jarno van der Kolk [ctb],
Mohan Rakesh [ctb],
Marie-Helene Roy-Gagnon [cre]
Maintainer: Marie-Helene Roy-Gagnon <mroygagn@uottawa.ca>
Diff between GENLIB versions 1.1.7 dated 2022-11-16 and 1.1.8 dated 2022-12-13
DESCRIPTION | 10 MD5 | 18 - NAMESPACE | 2 R/fonctionsSimul.R | 25 + man/gen.simuHaplo.Rd | 8 man/gen.simuHaplo_IBD_compare.Rd |only man/gen.simuHaplo_traceback.Rd |only src/fondateur.cpp | 608 ++++++++++++++++++++++++++++++++++++++- src/fondateur.h | 5 src/interface.cpp | 71 ++++ src/interface.h | 2 11 files changed, 728 insertions(+), 21 deletions(-)
Title: Pretty Summaries of Generalized Linear Model Coefficients
Description: One of the main advantages of using Generalised Linear Models
is their interpretability. The goal of 'prettyglm' is to provide a
set of functions which easily create beautiful coefficient summaries
which can readily be shared and explained. 'prettyglm' helps users
create coefficient summaries which include categorical base levels,
variable importance and type III p.values. 'prettyglm' also creates
beautiful relativity plots for categorical, continuous and splined
coefficients.
Author: Jared Fowler [cre, aut]
Maintainer: Jared Fowler <jared.fowler8@gmail.com>
Diff between prettyglm versions 0.1.0 dated 2021-06-24 and 1.0.0 dated 2022-12-13
prettyglm-0.1.0/prettyglm/man/figures/full_table.png |only prettyglm-0.1.0/prettyglm/man/figures/table.png |only prettyglm-1.0.0/prettyglm/DESCRIPTION | 29 prettyglm-1.0.0/prettyglm/MD5 | 61 prettyglm-1.0.0/prettyglm/NAMESPACE | 12 prettyglm-1.0.0/prettyglm/NEWS.md | 12 prettyglm-1.0.0/prettyglm/R/actual_expected_bucketed.R |only prettyglm-1.0.0/prettyglm/R/bank.R | 2 prettyglm-1.0.0/prettyglm/R/clean_coefficients.R | 137 prettyglm-1.0.0/prettyglm/R/cut3.R |only prettyglm-1.0.0/prettyglm/R/globals.R |only prettyglm-1.0.0/prettyglm/R/one_way_ave.R |only prettyglm-1.0.0/prettyglm/R/predict_outcome.R |only prettyglm-1.0.0/prettyglm/R/pretty_coefficients.R | 152 prettyglm-1.0.0/prettyglm/R/pretty_relativities.R | 1408 +++ prettyglm-1.0.0/prettyglm/R/splineit.R |only prettyglm-1.0.0/prettyglm/README.md | 184 prettyglm-1.0.0/prettyglm/build/vignette.rds |binary prettyglm-1.0.0/prettyglm/inst/doc/prettyglm-vignette.R | 214 prettyglm-1.0.0/prettyglm/inst/doc/prettyglm-vignette.Rmd | 424 prettyglm-1.0.0/prettyglm/inst/doc/prettyglm-vignette.html | 5550 ++++--------- prettyglm-1.0.0/prettyglm/man/actual_expected_bucketed.Rd |only prettyglm-1.0.0/prettyglm/man/bank_data.Rd | 2 prettyglm-1.0.0/prettyglm/man/clean_coefficients.Rd | 20 prettyglm-1.0.0/prettyglm/man/cut3.Rd |only prettyglm-1.0.0/prettyglm/man/figures/ageave.png |only prettyglm-1.0.0/prettyglm/man/figures/agerel.png |only prettyglm-1.0.0/prettyglm/man/figures/aveband.png |only prettyglm-1.0.0/prettyglm/man/figures/bank_overall_ave.png |only prettyglm-1.0.0/prettyglm/man/figures/defualtloanrel.png |only prettyglm-1.0.0/prettyglm/man/figures/educationave.png |only prettyglm-1.0.0/prettyglm/man/figures/importancetable.png |only prettyglm-1.0.0/prettyglm/man/figures/indextable.png |only prettyglm-1.0.0/prettyglm/man/figures/logo.png |binary prettyglm-1.0.0/prettyglm/man/figures/maritalrel.png |only prettyglm-1.0.0/prettyglm/man/figures/simpletable.png |only prettyglm-1.0.0/prettyglm/man/figures/splinetable.png |only prettyglm-1.0.0/prettyglm/man/figures/type3table.png |only prettyglm-1.0.0/prettyglm/man/one_way_ave.Rd |only prettyglm-1.0.0/prettyglm/man/predict_outcome.Rd |only prettyglm-1.0.0/prettyglm/man/pretty_coefficients.Rd | 56 prettyglm-1.0.0/prettyglm/man/pretty_relativities.Rd | 93 prettyglm-1.0.0/prettyglm/man/splineit.Rd |only prettyglm-1.0.0/prettyglm/vignettes/prettyglm-vignette.Rmd | 424 44 files changed, 4699 insertions(+), 4081 deletions(-)
Title: Cross-Validated (Nested) Forward Selection
Description: Implementation of forward selection based on cross-validated
linear and logistic regression.
Author: Marco Colombo [aut, cre] ,
Felix Agakov [ctb]
Maintainer: Marco Colombo <mar.colombo13@gmail.com>
Diff between nestfs versions 1.0.2 dated 2022-05-10 and 1.0.3 dated 2022-12-13
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/misc.R | 8 ++++++-- build/partial.rdb |binary tests/testthat/test_arguments.R | 14 ++++++++++++++ 6 files changed, 35 insertions(+), 12 deletions(-)
Title: Fuzzy Inference System Design and Optimization
Description: Fuzzy inference systems are based on fuzzy rules, which have a good capability for managing progressive phenomenons.
This package is a basic implementation of the main functions to use a Fuzzy Inference System (FIS) provided by the open source software 'FisPro' <https://www.fispro.org>.
'FisPro' allows to create fuzzy inference systems and to use them for reasoning purposes, especially for simulating a physical or biological system.
Author: Serge Guillaume [aut],
Brigitte Charnomordic [aut],
Jean-Luc Lablee [aut, cre],
Hazael Jones [ctb],
Lydie Desperben [ctb],
INRAE [cph]
Maintainer: Jean-Luc Lablee <jean-luc.lablee@inrae.fr>
Diff between FisPro versions 1.1.1 dated 2022-04-19 and 1.1.2 dated 2022-12-13
DESCRIPTION | 8 - MD5 | 32 +++---- NEWS.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/user-guide.html | 16 ++- inst/include/base/common.h | 1 inst/include/base/fis.h | 22 ++-- inst/include/base/rule.h | 4 src/Makevars | 2 src/base/aggreg.cpp | 6 - src/base/common.cpp | 24 ++--- src/base/fis.cpp | 203 +++++++++++++++++++++++---------------------- src/base/in.cpp | 69 ++++++++------- src/base/mf.cpp | 5 - src/base/out.cpp | 30 +++--- src/base/rule.cpp | 12 +- 17 files changed, 238 insertions(+), 200 deletions(-)
Title: Adaptive Trial Simulator
Description: Package that simulates adaptive clinical trials using adaptive
stopping, adaptive arm dropping, and/or adaptive randomisation.
Developed as part of the INCEPT (Intensive Care Platform Trial) project
(<https://incept.dk/>), which is primarily supported by a grant
from Sygeforsikringen "danmark" (<https://www.sygeforsikring.dk/>).
Author: Anders Granholm [aut, cre] ,
Benjamin Skov Kaas-Hansen [aut]
,
Aksel Karl Georg Jensen [ctb] ,
Theis Lange [ctb]
Maintainer: Anders Granholm <andersgran@gmail.com>
Diff between adaptr versions 1.1.1 dated 2022-08-16 and 1.2.0 dated 2022-12-13
DESCRIPTION | 11 MD5 | 191 - NAMESPACE | 5 NEWS.md | 179 - R/adaptr-package.R | 24 R/check_performance.R |only R/extract_results.R | 544 +-- R/find_beta_params.R | 28 R/plot_convergence.R |only R/plot_history.R | 492 +- R/plot_status.R | 445 +- R/print.R | 144 R/prob_funs.R | 408 +- R/run_trial.R | 1376 ++++---- R/run_trials.R | 717 ++-- R/setup_trial.R | 383 +- R/summary.R | 297 - R/test_helpers.R | 61 R/update_saved_trials.R |only R/utils.R | 520 +-- R/utils_plots.R | 16 R/zzz.R | 88 README.md | 88 inst/doc/Advanced-example.Rmd | 820 ++-- inst/doc/Advanced-example.html | 40 inst/doc/Basic-examples.R | 34 inst/doc/Basic-examples.Rmd | 57 inst/doc/Basic-examples.html | 211 - inst/doc/Overview.R | 18 inst/doc/Overview.Rmd | 407 +- inst/doc/Overview.html | 429 +- inst/testdata/binom__result__3_arms__common_control__equivalence__futility__softened.RData |binary inst/testdata/binom__result__3_arms__no_control__equivalence__softened.RData |binary inst/testdata/binom__result__3_arms__no_control__equivalence__softened__sparse.RData |only inst/testdata/binom__results__3_arms__common_control__equivalence__futility__softened.RData |binary inst/testdata/binom__results__3_arms__no_control__equivalence__softened.RData |binary inst/testdata/binom__results__3_arms__no_control__equivalence__softened__sparse.RData |only inst/testdata/binom__setup__3_arms__common_control__equivalence__futility__softened.RData |binary inst/testdata/binom__setup__3_arms__no_control__equivalence__softened.RData |binary inst/testdata/norm__result__3_arms__common_control__fixed__all_arms_fixed.RData |only inst/testdata/norm__results__3_arms__common_control__fixed__all_arms_fixed.RData |only inst/testdata/norm__setup__3_arms__common_control__fixed__all_arms_fixed.RData |only inst/testdata/norm__setup__3_arms__common_control__matched__varying_probs.RData |only man/adaptr-package.Rd | 24 man/assert_pkgs.Rd | 5 man/calculate_idp.Rd |only man/check_performance.Rd |only man/dispatch_trial_runs.Rd | 9 man/extract_history.Rd | 27 man/extract_results.Rd | 21 man/extract_statuses.Rd | 11 man/figures/README-plot-1.png |binary man/find_beta_params.Rd | 4 man/make_x_scale.Rd | 5 man/make_y_scale.Rd | 15 man/plot_convergence.Rd |only man/plot_history.Rd | 20 man/plot_status.Rd | 44 man/print.Rd | 29 man/replace_nonfinite.Rd |only man/replace_null.Rd | 2 man/run_trial.Rd | 145 man/run_trials.Rd | 20 man/setup_trial.Rd | 131 man/setup_trial_binom.Rd | 106 man/setup_trial_norm.Rd | 106 man/stop0_warning0.Rd |only man/summarise_num.Rd |only man/summary.Rd | 83 man/update_saved_trials.Rd |only man/validate_trial.Rd | 104 man/vapply_helpers.Rd | 3 tests/testthat/_snaps/check_performance.md |only tests/testthat/_snaps/extract.md | 1710 +++++----- tests/testthat/_snaps/plot_convergence |only tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct-followed-n.svg |only tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct-total-n.svg |only tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct.svg | 26 tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-prob.svg | 24 tests/testthat/_snaps/plot_history/history-plot-binomial-single-n-look.svg |only tests/testthat/_snaps/plot_history/history-plot-binomial-single-pct-all-look.svg |only tests/testthat/_snaps/plot_history/history-plot-binomial-single-pct-look.svg |only tests/testthat/_snaps/plot_history/history-plot-binomial-single-prob-followed-n.svg |only tests/testthat/_snaps/plot_history/history-plot-binomial-single-prob-total-n.svg |only tests/testthat/_snaps/plot_history/history-plot-binomial-single-ratio-ys-all-look.svg |only tests/testthat/_snaps/plot_history/history-plot-binomial-single-ratio-ys-look.svg |only tests/testthat/_snaps/plot_status.md | 333 + tests/testthat/_snaps/plot_status/status-plot-across-arms-binomial.svg | 44 tests/testthat/_snaps/plot_status/status-plot-for-all-arms-binomial.svg |only tests/testthat/_snaps/plot_status/status-plot-for-arm-c-binom.svg | 134 tests/testthat/_snaps/run_trials.md | 708 ++-- tests/testthat/_snaps/setup_trial.md | 240 - tests/testthat/_snaps/summary-print.md | 534 ++- tests/testthat/_snaps/utils.md |only tests/testthat/setup_testdata_files.R | 52 tests/testthat/test-check_performance.R |only tests/testthat/test-extract.R | 35 tests/testthat/test-find_beta_params.R | 10 tests/testthat/test-plot_convergence.R |only tests/testthat/test-plot_history.R | 42 tests/testthat/test-plot_status.R | 16 tests/testthat/test-prob_funs.R | 14 tests/testthat/test-run_trials.R | 207 + tests/testthat/test-setup_trial.R | 131 tests/testthat/test-summary-print.R | 29 tests/testthat/test-update_saved_trials.R |only tests/testthat/test-utils.R | 25 vignettes/Advanced-example.Rmd | 820 ++-- vignettes/Basic-examples.Rmd | 57 vignettes/Overview.Rmd | 407 +- 110 files changed, 8333 insertions(+), 6212 deletions(-)
Title: Robust Estimation in the Presence of Cellwise and Casewise
Contamination and Missing Data
Description: Robust Estimation of Multivariate Location and Scatter in the
Presence of Cellwise and Casewise Contamination and Missing Data.
Author: Andy Leung, Mike Danilov, Victor Yohai, Ruben Zamar
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>
Diff between GSE versions 4.2 dated 2019-04-12 and 4.2-1 dated 2022-12-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/boston.Rd | 2 +- man/calcium.Rd | 4 ++-- src/cov-em.cpp | 4 ++-- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Spatial Structural Diversity Quantification in Raster Data
Description: Spatial structural diversity refers to the spatial, i.e.
horizontal arrangement of landscape elements and can reveal itself as
landscape features, such as patches and linear features. The 'R' package
'StrucDiv' provides methods to quantify spatial structural diversity
in continuous remote sensing data, or in other data in raster format.
Structure is based on the spatial arrangement of value pairs. The 'R' package 'StrucDiv'
includes methods to combine information from different spatial scales, which allows to quantify
multi-scale spatial structural diversity.
Author: Leila Schuh [aut, cre] ,
Reinhard Furrer [aut] ,
Kalina Cherneva [ctb, ctr],
Kirill Mueller [ctr],
Patrick Schratz [ctr],
University Research Priority Progam Global Change and Biodiversity of
the University of Zurich [fnd]
Maintainer: Leila Schuh <l.schuh@posteo.net>
Diff between StrucDiv versions 0.1.1 dated 2022-08-11 and 0.2.0 dated 2022-12-13
StrucDiv-0.1.1/StrucDiv/NEWS.md |only StrucDiv-0.1.1/StrucDiv/man/StrucDiv.Rd |only StrucDiv-0.1.1/StrucDiv/man/metric.Rd |only StrucDiv-0.2.0/StrucDiv/DESCRIPTION | 41 StrucDiv-0.2.0/StrucDiv/MD5 | 111 + StrucDiv-0.2.0/StrucDiv/NAMESPACE | 19 StrucDiv-0.2.0/StrucDiv/R/RcppExports.R | 156 ++ StrucDiv-0.2.0/StrucDiv/R/StrucDiv.R | 144 +- StrucDiv-0.2.0/StrucDiv/R/data.R | 21 StrucDiv-0.2.0/StrucDiv/R/diversity_ref_switch_function.R |only StrucDiv-0.2.0/StrucDiv/R/diversity_switch_function.R | 187 +-- StrucDiv-0.2.0/StrucDiv/R/getValuesWindow.R | 55 StrucDiv-0.2.0/StrucDiv/R/strucDivDom.R |only StrucDiv-0.2.0/StrucDiv/R/strucDivNest.R |only StrucDiv-0.2.0/StrucDiv/README.md | 189 ++- StrucDiv-0.2.0/StrucDiv/data/patch.rda |only StrucDiv-0.2.0/StrucDiv/inst/doc/StrucDiv.R | 2 StrucDiv-0.2.0/StrucDiv/inst/doc/StrucDiv.Rmd | 73 - StrucDiv-0.2.0/StrucDiv/inst/doc/StrucDiv.html | 88 - StrucDiv-0.2.0/StrucDiv/man/Diversity.Rd |only StrucDiv-0.2.0/StrucDiv/man/DiversityDom.Rd |only StrucDiv-0.2.0/StrucDiv/man/figures/README-plot-1.png |binary StrucDiv-0.2.0/StrucDiv/man/getValuesWindow.Rd |only StrucDiv-0.2.0/StrucDiv/man/ndvi.15gl.Rd | 10 StrucDiv-0.2.0/StrucDiv/man/ndvi.Rd | 1 StrucDiv-0.2.0/StrucDiv/man/patch.Rd |only StrucDiv-0.2.0/StrucDiv/man/strucDiv.Rd |only StrucDiv-0.2.0/StrucDiv/man/strucDivDom.Rd |only StrucDiv-0.2.0/StrucDiv/man/strucDivNest.Rd |only StrucDiv-0.2.0/StrucDiv/src/ContrastRankNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/ContrastRankRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/ContrastValueNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/ContrastValueRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/DissimilarityRank.cpp | 2 StrucDiv-0.2.0/StrucDiv/src/DissimilarityRankNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/DissimilarityRankRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/DissimilarityValue.cpp | 2 StrucDiv-0.2.0/StrucDiv/src/DissimilarityValueNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/DissimilarityValueRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/Entropy.cpp | 9 StrucDiv-0.2.0/StrucDiv/src/EntropyNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/EntropyRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/HomogeneityRankNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/HomogeneityRankRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/HomogeneityValueNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/HomogeneityValueRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/NormalizedEntropyNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/NormalizedEntropyRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix0.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix0Dynamic.cpp | 2 StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix0Nested.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix0Post.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix135.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix135Dynamic.cpp | 2 StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix135Nested.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix135Post.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix45.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix45Dynamic.cpp | 4 StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix45Nested.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix45Post.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix90.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix90Dynamic.cpp | 2 StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix90Nested.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrix90Post.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrixAll.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrixAllDynamic.cpp | 10 StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrixAllNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/ProbabilityMatrixAllPost.cpp |only StrucDiv-0.2.0/StrucDiv/src/RcppExports.cpp | 575 ++++++++++ StrucDiv-0.2.0/StrucDiv/src/WeightedEntropyAbsRank.cpp | 2 StrucDiv-0.2.0/StrucDiv/src/WeightedEntropyAbsRankNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/WeightedEntropyAbsRankRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/WeightedEntropyAbsValueNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/WeightedEntropyAbsValueRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/WeightedEntropySqrRankNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/WeightedEntropySqrRankRef.cpp |only StrucDiv-0.2.0/StrucDiv/src/WeightedEntropySqrValueNested.cpp |only StrucDiv-0.2.0/StrucDiv/src/WeightedEntropySqrValueRef.cpp |only StrucDiv-0.2.0/StrucDiv/tests/Examples/StrucDiv-Ex.Rout.save | 148 ++ StrucDiv-0.2.0/StrucDiv/tests/testthat.Rout.save | 4 StrucDiv-0.2.0/StrucDiv/tests/testthat/test_rasterlayer.R | 20 StrucDiv-0.2.0/StrucDiv/vignettes/StrucDiv.Rmd | 73 - StrucDiv-0.2.0/StrucDiv/vignettes/bibliography.bib | 30 83 files changed, 1600 insertions(+), 382 deletions(-)
Title: Sparse Logistic Functional Principal Component Analysis
Description: Implementation for sparse logistic functional principal component analysis (SLFPCA). SLFPCA is specifically developed for functional binary data, and the estimated eigenfunction can be strictly zero on some sub-intervals, which is helpful for interpretation. The crucial function of this package is SLFPCA().
Author: Rou Zhong [aut, cre],
Jingxiao Zhang [aut]
Maintainer: Rou Zhong <zhong_rou@163.com>
Diff between SLFPCA versions 2.0 dated 2022-02-03 and 3.0 dated 2022-12-13
SLFPCA-2.0/SLFPCA/R/gcvscoremu.R |only SLFPCA-3.0/SLFPCA/DESCRIPTION | 6 SLFPCA-3.0/SLFPCA/MD5 | 11 - SLFPCA-3.0/SLFPCA/R/SLFPCA.R | 20 +- SLFPCA-3.0/SLFPCA/R/SLFPCA_sub.R | 292 +++++++++++++++++----------------- SLFPCA-3.0/SLFPCA/R/init_mu_setting.R | 2 SLFPCA-3.0/SLFPCA/man/SLFPCA.Rd | 16 - 7 files changed, 172 insertions(+), 175 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
RStudio, PBC [cph],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.42 dated 2022-09-27 and 0.43 dated 2022-12-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/install.R | 2 +- R/tlmgr.R | 3 ++- man/check_installed.Rd | 2 ++ 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre] ,
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Siddharth Agrawal [cph] ),
Brendan Frey [cph] ),
Delbert Dueck [cph] ,
Vitalie Spinu [ctb]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.2.8 dated 2022-12-03 and 1.2.9 dated 2022-12-13
DESCRIPTION | 10 MD5 | 14 - NEWS.md | 5 R/clustering_functions.R | 3 README.md | 4 build/vignette.rds |binary inst/doc/the_clusterR_package.html | 12 tests/testthat/test-gmm.R | 504 ++++++++++++++++++------------------- 8 files changed, 277 insertions(+), 275 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] ,
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] ,
Aust Frederik [ctb] ,
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Christophe Dervieux [ctb],
Clift [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.30 dated 2022-11-09 and 0.31 dated 2022-12-13
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- R/gitbook.R | 2 +- R/render.R | 2 +- 4 files changed, 10 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-27 0.0.3
Title: An Inclusive, Unifying API for Progress Updates
Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will als [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressr versions 0.11.0 dated 2022-09-02 and 0.12.0 dated 2022-12-13
DESCRIPTION | 14 MD5 | 85 ++- NAMESPACE | 1 NEWS.md | 46 ++ R/global_progression_handler.R | 9 R/handler_cli.R |only R/handler_pbcol.R | 42 + R/handler_pbmcapply.R | 42 + R/handler_progress.R | 47 +- R/handler_txtprogressbar.R | 115 +++-- R/make_progression_handler.R | 14 R/progressor.R | 16 R/slow_sum.R | 5 R/utils.R | 13 R/with_progress.R | 13 R/without_progress.R | 4 build/vignette.rds |binary inst/WORDLIST | 98 ++-- inst/doc/progressr-intro.html | 307 +++++++++++--- inst/doc/progressr-intro.md | 369 +++++++++++++---- man/figures/handler_cli-default.svg |only man/figures/handler_cli-format-1.svg |only man/figures/handler_pbcol-adjust-mid.svg |only man/figures/handler_pbcol-adjust-right-complete.svg |only man/figures/handler_pbcol-default.svg |only man/figures/handler_pbmcapply-default.svg |only man/figures/handler_progress-complete.svg |only man/figures/handler_progress-default.svg |only man/figures/handler_progress-format-1.svg |only man/figures/handler_progress-format-2.svg |only man/figures/handler_txtprogressbar-1.svg |only man/figures/handler_txtprogressbar-char-ansi.svg |only man/figures/handler_txtprogressbar-char-width-2.svg |only man/figures/handler_txtprogressbar-char.svg |only man/figures/handler_txtprogressbar-default.svg |only man/figures/handler_txtprogressbar-style-1.svg |only man/figures/handler_txtprogressbar-style-2.svg |only man/figures/handler_txtprogressbar-style-3.svg |only man/handler_cli.Rd |only man/handler_pbcol.Rd | 36 + man/handler_pbmcapply.Rd | 22 - man/handler_progress.Rd | 30 - man/handler_txtprogressbar.Rd | 49 +- man/progressor.Rd | 15 man/roxygen |only man/with_progress.Rd | 3 tests/handler_cli.R |only tests/incl/start,load-only.R | 6 tests/zzz,doFuture.R | 8 tests/zzz,furrr.R | 8 tests/zzz,future.apply.R | 8 vignettes/imgs/handler_cli-default.svg |only vignettes/imgs/handler_pbcol-adjust-right-complete.svg |only vignettes/imgs/handler_progress-default.svg |only vignettes/imgs/handler_txtprogressbar-char-ansi.svg |only vignettes/imgs/handler_txtprogressbar-default.svg |only vignettes/progressr-intro.md | 369 +++++++++++++---- 57 files changed, 1391 insertions(+), 403 deletions(-)
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] ,
Alessandro Gasparini [ctb] ,
Benjie Gillam [ctb],
Claus Thorn Ekstroem [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Deo Salil [ctb],
Emi Tanaka [ctb],
Garrick Aden-Buie [ctb] ,
Inaki Ucar [ctb] ,
John Little [ctb],
Joselyn Ch [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.27 dated 2022-11-07 and 0.28 dated 2022-12-13
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- R/utils.R | 2 +- 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] ,
Romain Lesur [aut, cph] ,
Brent Thorne [aut] ,
Xianying Tan [aut] ,
Christophe Dervieux [ctb] ,
Atsushi Yasumoto [ctb] ,
RStudio, PBC [cph],
Adam Hyde [ctb] ,
Min-Zhong Lu [ctb] ,
Zulko [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.19 dated 2022-09-26 and 0.20 dated 2022-12-13
DESCRIPTION | 7 ++++--- MD5 | 8 ++++---- NEWS.md | 8 +++++++- R/chrome.R | 11 +++++++++-- README.md | 2 +- 5 files changed, 25 insertions(+), 11 deletions(-)
Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package
supports the static site generator 'Hugo' (<https://gohugo.io>) best,
and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo'
(<https://hexo.io>).
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Alison Presmanes Hill [aut] ,
Amber Thomas [ctb],
Beilei Bian [ctb],
Brandon Greenwell [ctb],
Brian Barkley [ctb],
Deependra Dhakal [ctb],
Eric Nantz [ctb],
Forest Fang [ctb],
Garrick Aden-Buie [ctb] [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between blogdown versions 1.15 dated 2022-11-07 and 1.16 dated 2022-12-13
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- R/format.R | 6 +++--- R/hugo.R | 2 +- R/render.R | 4 ++-- man/html_page.Rd | 2 +- 6 files changed, 18 insertions(+), 17 deletions(-)