Title: Robust Variance Meta-Regression
Description: Functions for conducting robust variance estimation (RVE) meta-regression using both large and small sample RVE estimators under various weighting schemes. These methods are distribution free and provide valid point estimates, standard errors and hypothesis tests even when the degree and structure of dependence between effect sizes is unknown. Also included are functions for conducting sensitivity analyses under correlated effects weighting and producing RVE-based forest plots.
Author: Zachary Fisher [aut, cre],
Elizabeth Tipton [aut],
Hou Zhipeng [aut]
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between robumeta versions 2.0 dated 2017-05-29 and 2.1 dated 2023-03-27
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/predict.robu.R | 4 ++-- R/print.robu.R | 2 +- build/vignette.rds |binary man/corrdat.Rd | 6 ++++-- man/corrdat.sm.Rd | 6 ++++-- man/hedgesdat.Rd | 4 +++- man/hierdat.Rd | 6 ++++-- man/oswald2013.Rd | 6 ++++-- man/oswald2013.ex1.Rd | 6 ++++-- man/robu.Rd | 13 +++++++++++-- 12 files changed, 53 insertions(+), 32 deletions(-)
Title: R-Squared Measures for Multilevel Models
Description: Generates both total- and level-specific R-squared measures from
Rights and Sterba’s (2019) <doi:10.1037/met0000184> framework of R-squared measures for multilevel
models with random intercepts and/or slopes, which is based on a complete
decomposition of variance. Additionally generates graphical
representations of these R-squared measures to allow visualizing and
interpreting all measures in the framework together as an integrated set.
This framework subsumes 10 previously-developed R-squared measures for
multilevel models as special cases of 5 measures from the framework, and it
also includes several newly-developed measures. Measures in the framework
can be used to compute R-squared differences when comparing multilevel
models (following procedures in Rights & Sterba (2020) <doi:10.1080/00273171.2019.1660605>).
Author: Mairead Shaw [aut, cre],
Jason Rights [aut],
Sonya Sterba [aut],
Jessica Flake [aut]
Maintainer: Mairead Shaw <mairead.shaw@mail.mcgill.ca>
Diff between r2mlm versions 0.3.2 dated 2022-07-06 and 0.3.3 dated 2023-03-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/r2mlm3_manual.R | 4 ++-- README.md | 30 ++++++++++++++++-------------- man/figures/README-example-1.png |binary 6 files changed, 33 insertions(+), 24 deletions(-)
Title: E-Value in the Omics Data Association Studies
Description: In the omics data association studies, it is common to conduct the p-value corrections to control the false significance. Among those p-value correction methods, E-value is recently studied based on V. Vovk and R. Wang (2021) <doi:10.1214/20-AOS2020>. This package provides e-value calculation for several types of omics data association studies. Currently, four data formats are supported: BiSeq, MDRfinder, methylKit and metilene data. The relevant references are listed below: Katja Hebestreit and Hans-Ulrich Klein (2022) <doi:10.18129/B9.bioc.BiSeq>; Altuna Akalin et.al (2012) <doi:10.18129/B9.bioc.methylKit>.
Author: Yifan Yang [aut, cre, cph],
Xiaoqing Pan [aut],
Haoyuan Liu [aut]
Maintainer: Yifan Yang <yfyang.86@hotmail.com>
Diff between metevalue versions 0.1.13 dated 2022-11-21 and 0.1.14 dated 2023-03-27
DESCRIPTION | 11 MD5 | 28 R/evalue_data_chk.R | 16 R/evalue_data_metilene.R | 10 build/partial.rdb |binary inst/doc/metevalue.R | 82 -- inst/doc/metevalue.Rmd | 274 ++++++--- inst/doc/metevalue.html | 1149 ++++++++++++++++++++++---------------- man/metevalue.DMRfinder.chk.Rd | 4 man/metevalue.biseq.chk.Rd | 4 man/metevalue.methylKit.chk.Rd | 4 man/metevalue.metilene.Rd | 10 man/metevalue.metilene.chk.Rd | 4 tests/testthat/test-evalue_main.R | 48 - vignettes/metevalue.Rmd | 274 ++++++--- 15 files changed, 1203 insertions(+), 715 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized
additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between gam versions 1.22-1 dated 2023-01-28 and 1.22-2 dated 2023-03-27
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- tests/testthat/test_example.R | 11 +++++++++++ 4 files changed, 20 insertions(+), 7 deletions(-)
Title: Query the Breeding Management System(s)
Description: Linking data management systems to analytics is an important step in breeding
digitization. Breeders can use this R package to Query the Breeding Management
System(s) like 'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, and
'GIGWA' <https://southgreen.fr/content/gigwa> (using 'BrAPI' <https://brapi.org> calls)
and help them to retrieve phenotypic and genotypic data directly into their analyzing
pipelines.
Author: Khaled Al-Shamaa [aut, cre],
Mariano Omar Crimi [ctb],
Zakaria Kehel [ctb],
Johan Aparicio [ctb],
ICARDA [cph]
Maintainer: Khaled Al-Shamaa <k.el-shamaa@cgiar.org>
Diff between QBMS versions 0.8.0 dated 2022-05-19 and 0.9.0 dated 2023-03-27
QBMS-0.8.0/QBMS/man/get_crop_locations.Rd |only QBMS-0.9.0/QBMS/DESCRIPTION | 29 QBMS-0.9.0/QBMS/MD5 | 52 QBMS-0.9.0/QBMS/NAMESPACE | 6 QBMS-0.9.0/QBMS/NEWS.md | 12 QBMS-0.9.0/QBMS/R/qbms.R | 1173 +++++++++++++++++---- QBMS-0.9.0/QBMS/README.md | 127 ++ QBMS-0.9.0/QBMS/build/partial.rdb |only QBMS-0.9.0/QBMS/build/vignette.rds |binary QBMS-0.9.0/QBMS/inst/doc/bms_example.Rmd | 24 QBMS-0.9.0/QBMS/inst/doc/bms_example.html | 262 ++++ QBMS-0.9.0/QBMS/inst/doc/breedbase_example.Rmd | 17 QBMS-0.9.0/QBMS/inst/doc/breedbase_example.html | 261 ++++ QBMS-0.9.0/QBMS/inst/doc/gigwa_example.Rmd | 20 QBMS-0.9.0/QBMS/inst/doc/gigwa_example.html | 355 +++++- QBMS-0.9.0/QBMS/inst/doc/terraclimate_example.Rmd |only QBMS-0.9.0/QBMS/inst/doc/terraclimate_example.html |only QBMS-0.9.0/QBMS/man/brapi_get_call.Rd | 4 QBMS-0.9.0/QBMS/man/brapi_headers.Rd |only QBMS-0.9.0/QBMS/man/calc_biovars.Rd |only QBMS-0.9.0/QBMS/man/get_async_page.Rd |only QBMS-0.9.0/QBMS/man/get_async_pages.Rd |only QBMS-0.9.0/QBMS/man/get_germplasm_attributes.Rd |only QBMS-0.9.0/QBMS/man/get_germplasm_data.Rd | 10 QBMS-0.9.0/QBMS/man/get_germplasm_id.Rd |only QBMS-0.9.0/QBMS/man/get_qbms_connection.Rd |only QBMS-0.9.0/QBMS/man/get_terraclimate.Rd |only QBMS-0.9.0/QBMS/man/gigwa_get_metadata.Rd |only QBMS-0.9.0/QBMS/man/list_locations.Rd |only QBMS-0.9.0/QBMS/man/set_qbms_config.Rd | 5 QBMS-0.9.0/QBMS/man/set_qbms_connection.Rd |only QBMS-0.9.0/QBMS/vignettes/bms_example.Rmd | 24 QBMS-0.9.0/QBMS/vignettes/breedbase_example.Rmd | 17 QBMS-0.9.0/QBMS/vignettes/gigwa_example.Rmd | 20 QBMS-0.9.0/QBMS/vignettes/terraclimate_example.Rmd |only 35 files changed, 1989 insertions(+), 429 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Complete analytical environment for the construction and analysis
of matrix population models and integral projection models.
Includes the ability to construct historical matrices, which are
2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices and raw and function-based
Leslie matrices.
Author: Richard P. Shefferson [aut, cre]
,
Johan Ehrlen [aut]
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 5.5.0 dated 2022-09-13 and 6.0.0 dated 2023-03-27
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Title: Two-Stage Difference-in-Differences Following Gardner (2021)
Description: Estimates Two-way Fixed Effects difference-in-differences/event-study models using the approach proposed by Gardner (2021). To avoid the problems caused by OLS estimation of the Two-way Fixed Effects model, this function first estimates the fixed effects and covariates using untreated observations and then in a second stage, estimates the treatment effects.
Author: Kyle Butts [aut, cre] ,
John Gardner [aut] ,
Grant McDermott [ctb] ,
Laurent Berge [ctb]
Maintainer: Kyle Butts <kyle.butts@colorado.edu>
Diff between did2s versions 1.0.0 dated 2023-03-11 and 1.0.1 dated 2023-03-27
DESCRIPTION | 8 MD5 | 15 NEWS.md | 4 R/did2s.R | 18 inst/doc/Two-Stage-Difference-in-Differences.html | 401 +++++++++++----------- vignettes/event_study_cache |only 6 files changed, 236 insertions(+), 210 deletions(-)
Title: A Comprehensive R Interface for the DSSAT Cropping Systems Model
Description: The purpose of this package is to provide a comprehensive
R interface to the Decision Support System for Agrotechnology
Transfer Cropping Systems Model (DSSAT-CSM; see <https://dssat.net> for more information).
The package provides cross-platform functions to read and
write input files, run DSSAT-CSM, and read output files.
Author: Phillip D. Alderman [aut, cre]
Maintainer: Phillip D. Alderman <phillip.alderman@okstate.edu>
Diff between DSSAT versions 0.0.6 dated 2022-01-19 and 0.0.7 dated 2023-03-27
DESCRIPTION | 16 ++++--- MD5 | 68 ++++++++++++++++-------------- NAMESPACE | 15 ++++-- NEWS.md | 12 +++++ R/calc_TAV_AMP.R |only R/combine_multi_section.R | 6 +- R/combine_tiers.R | 32 ++++++-------- R/extract_comments.R | 5 +- R/header_to_fwf_position.R | 8 +-- R/process_dssat_output_header.R | 4 - R/read_casupro_eco.R | 1 R/read_filex.R | 48 ++++++++++++++++----- R/read_tier_data.R | 41 +++++++++++------- R/reconcile_gaps.R | 6 +- R/splice_in_col_name.R | 4 - R/test_cols_check.R |only R/v_fmt_filex.R | 13 +++-- R/v_fmt_to_col_types.R |only R/v_fmt_to_fwf_pos.R |only R/v_fmt_to_fwf_widths.R |only R/v_fmt_wth.R |only R/write_filex.R | 2 R/write_tier.R | 7 +-- R/write_wth.R | 83 ++++++++++++++++++++++++++++++++----- inst/CITATION | 19 ++++---- inst/extdata/SAMPLE.OUT | 38 ---------------- inst/extdata/SAMPLE.WTH | 1 man/calc_AMP.Rd |only man/calc_TAV.Rd |only man/header_to_fwf_position.Rd | 2 man/process_dssat_output_header.Rd | 2 man/read_casupro_eco.Rd | 1 man/read_filex.Rd | 7 ++- man/read_tier_data.Rd | 3 - man/splice_in_col_name.Rd | 2 man/write_dssbatch.Rd | 10 ---- man/write_dssbatch.data.frame.Rd | 10 ---- man/write_dssbatch.tbl_df.Rd | 10 ---- man/write_wth.Rd | 43 ++++++++++++++++++- 39 files changed, 318 insertions(+), 201 deletions(-)
Title: Load Data for Analysis System
Description: Provides a framework to load text and excel files through a 'shiny' graphical interface. It allows renaming, transforming, ordering and removing variables. It includes basic exploratory methods such as the mean, median, mode, normality test, histogram and correlation.
Author: Oldemar Rodriguez [aut, cre],
Diego Jimenez [aut],
Joseline Quiros [aut]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between loadeR versions 1.1.3 dated 2023-01-24 and 1.1.6 dated 2023-03-27
DESCRIPTION | 17 ++++--- MD5 | 32 +++++++------- NAMESPACE | 6 +- NEWS.md | 14 ++++++ R/app_server.R | 2 R/golem_utils_ui.R | 77 +++++++++++++++++------------------ R/loadeR.R | 4 - R/mod_acercade.R | 2 R/mod_carga_datos.R | 3 - R/mod_carga_datos_fct.R | 8 +-- R/mod_carga_datos_utils.R | 21 ++++++--- inst/app/lang/diccionario.csv | 3 - inst/app/lang/translation_loadeR.bin |binary inst/golem-config.yml | 2 man/carga.datos.excel.Rd | 2 man/loadeR.Rd | 4 - man/menu.idioma.Rd | 60 --------------------------- 17 files changed, 110 insertions(+), 147 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi:10.1002/9781119942283>.
Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <m.quartagno@ucl.ac.uk>
Diff between jomo versions 2.7-4 dated 2022-09-17 and 2.7-5 dated 2023-03-27
DESCRIPTION | 10 +++---- MD5 | 16 +++++------ NAMESPACE | 14 ++++----- inst/CITATION | 2 - src/jomo1ranhrsmcC.c | 48 +++++++++++++++++++--------------- src/jomo1ransmcC.c | 48 +++++++++++++++++++--------------- src/jomo1smcC.c | 48 +++++++++++++++++++--------------- src/jomo2hrsmcC.c | 72 +++++++++++++++++++++++++++------------------------ src/jomo2smcC.c | 72 +++++++++++++++++++++++++++------------------------ 9 files changed, 180 insertions(+), 150 deletions(-)
Title: User-Friendly GUI Plotting Tools
Description: Create a user-friendly plotting GUI for 'R'.
In addition, one purpose of creating the 'R' package is to facilitate third-party software to call 'R' for drawing, for example, 'Phoenix WinNonlin' software calls 'R' to draw the drug concentration versus time curve.
Author: Fu Yongchao [aut, cre, cph]
Maintainer: Fu Yongchao <3212418315@qq.com>
Diff between guiplot versions 0.3.1 dated 2022-12-07 and 0.4.0 dated 2023-03-27
DESCRIPTION | 6 +-- MD5 | 14 +++---- NEWS | 14 +++++++ R/ggplotcodes.R | 17 ++++---- R/guiplot.R | 6 +-- R/guiplotServer.R | 106 ++++++++++++++++++++++++++++++++++++++++++++---------- R/guiplotUI.R | 15 +++++-- R/optioncodes.R | 2 - 8 files changed, 135 insertions(+), 45 deletions(-)
Title: Query the 'UniProtKB' REST API
Description: Retrieve protein information from
the 'UniProtKB' REST API (see <https://www.uniprot.org/help/api_queries>).
Author: Guillaume Voisinne [aut, cre]
Maintainer: Guillaume Voisinne <voisinne@gmail.com>
Diff between queryup versions 1.0.2 dated 2023-02-10 and 1.0.3 dated 2023-03-27
DESCRIPTION | 6 ++--- MD5 | 10 ++++---- NEWS.md | 4 +++ R/get_uniprot_data.R | 18 ++++++++++++--- inst/doc/queryup.html | 39 ++++++++++++--------------------- tests/testthat/test-get_uniprot_data.R | 4 +-- 6 files changed, 44 insertions(+), 37 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] ,
Gregor Gorjanc [ctb] ,
John Hickey [ctb] ,
Daniel Money [ctb] ,
David Wilson [ctb],
Thiago Oliveira [ctb] ,
Audrey Martin [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 1.3.4 dated 2022-12-09 and 1.4.2 dated 2023-03-27
DESCRIPTION | 17 LICENSE | 2 MD5 | 348 +- NAMESPACE | 320 +- NEWS.md | 732 +++--- R/AlphaSimR.R | 58 R/Class-HybridPop.R | 256 +- R/Class-LociMap.R | 752 +++--- R/Class-Pop.R | 1998 ++++++++-------- R/Class-RRsol.R | 54 R/Class-SimParam.R | 4752 +++++++++++++++++++-------------------- R/GS.R | 3036 ++++++++++++------------ R/RcppExports.R | 718 ++--- R/crossing.R | 1786 +++++++------- R/founderPop.R | 1166 ++++----- R/hybrids.R | 854 +++---- R/importData.R | 592 ++-- R/mergePops.R | 296 +- R/misc.R | 1578 ++++++------ R/phenotypes.R | 526 ++-- R/polyploids.R | 608 ++-- R/popSummary.R | 1248 +++++----- R/pullGeno.R | 2218 +++++++++--------- R/selection.R | 922 +++---- R/writePlink.R | 276 +- R/writeRecords.R | 214 - README.md | 64 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 27 inst/REFERENCES.bib | 340 +- inst/doc/intro.R | 100 inst/doc/intro.Rmd | 264 +- inst/doc/intro.html | 1194 ++++----- inst/doc/traits.Rmd | 372 +-- inst/doc/traits.pdf |binary man/AlphaSimR-package.Rd | 97 man/HybridPop-class.Rd | 122 - man/LociMap-class.Rd | 42 man/MapPop-class.Rd | 102 man/MegaPop-class.Rd | 102 man/NamedMapPop-class.Rd | 96 man/Pop-class.Rd | 148 - man/RRBLUP.Rd | 130 - man/RRBLUP2.Rd | 222 - man/RRBLUPMemUse.Rd | 56 man/RRBLUP_D.Rd | 132 - man/RRBLUP_D2.Rd | 176 - man/RRBLUP_GCA.Rd | 134 - man/RRBLUP_GCA2.Rd | 174 - man/RRBLUP_SCA.Rd | 132 - man/RRBLUP_SCA2.Rd | 182 - man/RRsol-class.Rd | 52 man/RawPop-class.Rd | 122 - man/SimParam.Rd | 3481 ++++++++++++++-------------- man/TraitA-class.Rd | 36 man/TraitA2-class.Rd | 34 man/TraitA2D-class.Rd | 32 man/TraitAD-class.Rd | 32 man/TraitADE-class.Rd | 32 man/TraitADEG-class.Rd | 40 man/TraitADG-class.Rd | 40 man/TraitAE-class.Rd | 32 man/TraitAEG-class.Rd | 40 man/TraitAG-class.Rd | 40 man/aa.Rd | 62 man/addSegSite.Rd | 80 man/attrition.Rd | 72 man/bv.Rd | 60 man/cChr.Rd | 54 man/calcGCA.Rd | 72 man/dd.Rd | 60 man/dot-newPop.Rd | 108 man/doubleGenome.Rd | 78 man/ebv.Rd | 58 man/editGenome.Rd | 96 man/editGenomeTopQtl.Rd | 88 man/fastRRBLUP.Rd | 154 - man/genParam.Rd | 128 - man/genicVarA.Rd | 60 man/genicVarAA.Rd | 62 man/genicVarD.Rd | 60 man/genicVarG.Rd | 60 man/getGenMap.Rd | 80 man/getMisc.Rd | 112 man/getNumThreads.Rd | 38 man/getPed.Rd | 66 man/getQtlMap.Rd | 86 man/getSnpMap.Rd | 88 man/gv.Rd | 56 man/hybridCross.Rd | 100 man/importGenMap.Rd | 64 man/importHaplo.Rd | 124 - man/importInbredGeno.Rd | 122 - man/isFemale.Rd | 76 man/isPop.Rd | 56 man/makeCross.Rd | 82 man/makeCross2.Rd | 86 man/makeDH.Rd | 84 man/meanG.Rd | 56 man/meanP.Rd | 56 man/mergeGenome.Rd | 84 man/mergePops.Rd | 64 man/mutate.Rd | 92 man/nInd.Rd | 56 man/newEmptyPop.Rd | 68 man/newMapPop.Rd | 106 man/newMegaPop.Rd | 68 man/newPop.Rd | 78 man/pedigreeCross.Rd | 158 - man/pheno.Rd | 56 man/popVar.Rd | 40 man/pullIbdHaplo.Rd | 80 man/pullMarkerGeno.Rd | 88 man/pullMarkerHaplo.Rd | 98 man/pullQtlGeno.Rd | 82 man/pullQtlHaplo.Rd | 104 man/pullSegSiteGeno.Rd | 80 man/pullSegSiteHaplo.Rd | 100 man/pullSnpGeno.Rd | 82 man/pullSnpHaplo.Rd | 104 man/quickHaplo.Rd | 70 man/randCross.Rd | 106 man/randCross2.Rd | 124 - man/reduceGenome.Rd | 108 man/resetPop.Rd | 72 man/runMacs.Rd | 158 - man/runMacs2.Rd | 162 - man/sampleHaplo.Rd | 66 man/selIndex.Rd | 90 man/selInt.Rd | 36 man/selectCross.Rd | 174 - man/selectFam.Rd | 164 - man/selectInd.Rd | 148 - man/selectOP.Rd | 154 - man/selectWithinFam.Rd | 166 - man/self.Rd | 82 man/setEBV.Rd | 132 - man/setMarkerHaplo.Rd | 100 man/setMisc.Rd | 114 man/setPheno.Rd | 220 - man/setPhenoGCA.Rd | 164 - man/setPhenoProgTest.Rd | 182 - man/smithHazel.Rd | 60 man/solveMKM.Rd | 48 man/solveMVM.Rd | 48 man/solveRRBLUP.Rd | 36 man/solveRRBLUPMK.Rd | 40 man/solveRRBLUPMV.Rd | 44 man/solveRRBLUP_EM.Rd | 60 man/solveRRBLUP_EM2.Rd | 68 man/solveRRBLUP_EM3.Rd | 76 man/solveUVM.Rd | 40 man/transMat.Rd | 98 man/usefulness.Rd | 122 - man/varA.Rd | 60 man/varAA.Rd | 62 man/varD.Rd | 60 man/varG.Rd | 56 man/varP.Rd | 56 man/writePlink.Rd | 138 - man/writeRecords.Rd | 80 src/RcppExports.cpp | 26 src/ibd.cpp | 340 +- src/meiosis.cpp | 2 tests/testthat.R | 8 tests/testthat/test-addTrait.R | 212 - tests/testthat/test-crossing.R | 256 +- tests/testthat/test-editGenome.R | 30 tests/testthat/test-hybrids.R | 128 - tests/testthat/test-importData.R | 94 tests/testthat/test-statistics.R | 60 vignettes/AlphaSimR.bib | 288 +- vignettes/intro.Rmd | 264 +- vignettes/traits.Rmd | 372 +-- 175 files changed, 22319 insertions(+), 22085 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-01 0.1.2
2021-05-20 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-07 1.2.5
2022-11-16 1.2.4
2022-10-18 1.2.3
2022-06-07 1.2.2
2022-06-01 1.2.1
2022-04-07 1.2.0
2022-01-12 1.1.1
2021-10-18 1.1.0
2021-09-14 1.0.0
2021-07-16 0.7.0
2021-06-13 0.6.1
2021-05-30 0.6.0
2021-04-03 0.5.1
2021-03-29 0.5.0
2021-03-19 0.4.2
2021-01-17 0.4.1
2020-11-23 0.4.0
2020-11-09 0.3.1
2020-10-28 0.3.0
2020-10-08 0.2.1
2020-09-28 0.2.0
2020-09-02 0.1.0
2020-07-03 0.0.2
2020-06-22 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-01 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-17 2.8.2
2022-05-31 2.8.1
2022-04-07 2.8.0
2022-01-19 2.7.0
2021-11-16 2.6.2
2021-01-18 2.6.1
2020-11-21 2.6.0
2020-10-22 2.5.0
2020-10-08 2.4.0
2020-09-29 2.3.0
2020-09-01 2.2.1
2020-07-18 2.2.0
2020-07-03 2.1.0
2020-05-31 2.0.0
2020-04-19 1.0.0
2020-03-18 0.1.3
2019-09-25 0.1.2
2018-08-19 0.1.1.1
2018-05-14 0.1.1
2017-07-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-18 1.0.2
2022-06-09 1.0.1
2021-10-19 1.0.0
2021-07-16 0.4.2
2021-05-31 0.4.1
2021-04-05 0.4.0
2020-11-06 0.3.0
2020-10-09 0.2.0
2020-10-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-05 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-16 1.0.6
2022-09-08 1.0.5
2022-05-20 1.0.4
2021-03-05 1.0.3
2020-10-21 1.0.2
2020-07-02 1.0.1
2020-03-04 1.0.0
2020-01-27 0.5.10
2019-12-15 0.5.9
2019-10-11 0.5.8
2019-09-20 0.5.7
2019-04-22 0.5.6
2018-05-09 0.5.5
2018-02-19 0.5.4
2017-08-03 0.5.3
2017-07-27 0.5.2
2017-04-24 0.5.1
2017-04-03 0.5.0
2017-03-03 0.4.0
2017-01-21 0.3.0
2017-01-08 0.2.0
2016-12-31 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-17 0.2.2
2022-06-07 0.2.1
2021-03-14 0.2.0
2020-11-05 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-28 0.2.7
2023-01-06 0.2.6
2022-11-16 0.2.5
2022-11-10 0.2.4
2022-10-03 0.2.3
2022-08-07 0.2.2
2022-07-19 0.2.1
2022-06-09 0.2.0
2022-04-26 0.1.9
2022-02-25 0.1.8
2021-12-11 0.1.7
2021-12-04 0.1.6
2021-11-10 0.1.5
2021-10-31 0.1.4
2021-08-23 0.1.3
2021-06-25 0.1.2
2021-02-09 0.1.1
2021-01-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-18 0.2.0
2022-04-25 0.1.9
2022-02-27 0.1.8
2022-01-05 0.1.7
2021-08-20 0.1.6
2021-06-22 0.1.5
2021-06-13 0.1.4
2021-06-03 0.1.3
2021-02-23 0.1.2
2020-12-04 0.1.1
2020-12-03 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-01 0.1.2
2019-03-11 0.1.1
2017-09-03 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-31 1.1.0
2021-05-27 1.0.6
2020-10-29 1.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-08 1.3.2
2022-11-15 1.3.1
2022-11-07 1.3.0
2022-06-17 1.2.0
2022-05-18 1.1.0
2022-02-11 1.0.0
2022-01-07 0.1.91
2022-01-04 0.1.9
2021-09-21 0.1.8
2021-06-12 0.1.7
2021-04-07 0.1.6
2020-11-11 0.1.5
2020-09-04 0.1.4
2020-06-07 0.1.3
2020-02-23 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-21 1.0.3
2022-01-21 1.0.2
2021-08-23 1.0.1
2021-02-17 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-23 0.39.1
2022-09-20 0.39
2021-12-19 0.37
2019-03-14 0.36
2019-03-02 0.35
2017-09-27 0.34
2017-09-07 0.33
2017-08-02 0.32
2017-06-07 0.31
2017-05-20 0.30
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-01 0.0.12
2023-01-12 0.0.11
2022-11-16 0.0.10
2022-10-04 0.0.9
2022-07-04 0.0.8
2022-04-29 0.0.7
2022-02-27 0.0.6
2022-01-07 0.0.5
2021-12-08 0.0.4
2021-11-23 0.0.3
2021-09-02 0.0.2
2021-08-20 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-23 0.2.3
2023-02-11 0.2.2
2022-11-15 0.2.1
2022-07-14 0.2.0
2022-03-28 0.1.1
2022-02-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-19 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-06 0.1.0
Title: Main Existing Human Datasets
Description: Shiny for Open Science to visualize, share, and inventory the
main existing human datasets for researchers.
Author: Etienne Camenen [aut, cre],
Baptiste Couvy-Duchesne [aut]
Maintainer: Etienne Camenen <etienne.camenen@gmail.com>
Diff between MainExistingDatasets versions 1.0.1 dated 2022-06-27 and 1.0.2 dated 2023-03-27
DESCRIPTION | 11 + MD5 | 12 +- NAMESPACE | 2 R/MainExistingDatasets-package.R | 3 build/vignette.rds |binary inst/doc/Tutorial.html | 227 ++++++++++++++++++++++++++++++++++++--- inst/golem-config.yml | 2 7 files changed, 229 insertions(+), 28 deletions(-)
More information about MainExistingDatasets at CRAN
Permanent link
Title: Utilities for Graphical Rendering and Fonts Management
Description: Tools are provided to compute metrics of
formatted strings and to check the availability of a font.
Another set of functions is provided to support the collection
of fonts from 'Google Fonts' in a cache. Their use is simple within
'R Markdown' documents and 'shiny' applications but also with graphic
productions generated with the 'ggiraph', 'ragg' and 'svglite' packages
or with tabular productions from the 'flextable' package.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut] ,
Yixuan Qiu [ctb],
R Core Team [cph] ,
ArData [cph],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.3.2 dated 2023-03-13 and 0.3.3 dated 2023-03-27
DESCRIPTION | 12 ++++++------ MD5 | 9 +++++---- NAMESPACE | 1 - NEWS | 7 +++++++ R/font-caching.R | 5 +++-- R/sysdata.rda |only 6 files changed, 21 insertions(+), 13 deletions(-)
More information about SherlockHolmes at CRAN
Permanent link
More information about IncidencePrevalence at CRAN
Permanent link
Title: Censored Regression with Conditional Heteroscedasticity
Description: Different approaches to censored or truncated regression with
conditional heteroscedasticity are provided. First, continuous
distributions can be used for the (right and/or left censored or truncated)
response with separate linear predictors for the mean and variance.
Second, cumulative link models for ordinal data
(obtained by interval-censoring continuous data) can be employed for
heteroscedastic extended logistic regression (HXLR). In the latter type of
models, the intercepts depend on the thresholds that define the intervals.
Infrastructure for working with censored or truncated normal, logistic,
and Student-t distributions, i.e., d/p/q/r functions and distributions3
objects.
Author: Jakob Messner [aut, cre] ,
Achim Zeileis [aut] ,
Reto Stauffer [aut]
Maintainer: Jakob Messner <jakob.messner@posteo.net>
Diff between crch versions 1.1-1 dated 2022-09-09 and 1.1-2 dated 2023-03-27
DESCRIPTION | 8 +-- MD5 | 14 +++--- NEWS.md | 5 ++ R/crch.R | 8 +-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 120 +++++++++++++++++------------------------------------ inst/doc/crch.pdf |binary 8 files changed, 60 insertions(+), 95 deletions(-)
More information about AcademicThemes at CRAN
Permanent link
Title: General Network (HTTP/FTP/...) Client Interface for R
Description: A wrapper for 'libcurl' <https://curl.se/libcurl/>
Provides functions to allow one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: CRAN Team [ctb, cre] ,
Duncan Temple Lang [aut]
Maintainer: CRAN Team <CRAN@r-project.org>
Diff between RCurl versions 1.98-1.10 dated 2023-01-27 and 1.98-1.12 dated 2023-03-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/curl.S | 2 +- src/Makevars.ucrt | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Optimal Channel Networks
Description: Generate and analyze Optimal Channel Networks (OCNs):
oriented spanning trees reproducing all scaling features characteristic
of real, natural river networks. As such, they can be used in a variety
of numerical experiments in the fields of hydrology, ecology and
epidemiology. See Carraro et al. (2020) <doi:10.1002/ece3.6479>
for a presentation of the package; Rinaldo et al. (2014)
<doi:10.1073/pnas.1322700111> for a theoretical overview on the OCN
concept; Furrer and Sain (2010) <doi:10.18637/jss.v036.i10> for the
construct used.
Author: Luca Carraro [aut, cre],
Florian Altermatt [ctb],
Emanuel A. Fronhofer [ctb],
Reinhard Furrer [ctb],
Isabelle Gounand [ctb],
Andrea Rinaldo [ctb],
Enrico Bertuzzo [aut]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between OCNet versions 0.7.1 dated 2023-03-07 and 1.0.0 dated 2023-03-27
DESCRIPTION | 6 +- MD5 | 92 +++++++++++++++---------------- NAMESPACE | 4 + NEWS.md | 9 +++ R/aggregate_OCN.R | 75 ++++++++++++++++++------- R/continue_OCN.R | 16 +++-- R/create_OCN.R | 112 +++++++++++++++++++++++++++++++++++++- R/create_general_contour_OCN.R | 6 +- R/create_peano.R | 6 +- R/draw_elev2D_OCN.R | 4 - R/draw_elev3D_OCN.R | 4 - R/draw_subcatchments_OCN.R | 4 - R/draw_thematic_OCN.R | 3 - R/paths_OCN.R | 39 +------------ data/OCN_20.rda |binary data/OCN_250_PB.rda |binary data/OCN_250_T.rda |binary data/OCN_300_4out.rda |binary data/OCN_300_4out_PB_hot.rda |binary data/OCN_4.rda |binary data/OCN_400_Allout.rda |binary man/OCN_20.Rd | 2 man/OCN_250_PB.Rd | 2 man/OCN_250_T.Rd | 2 man/OCN_300_4out.Rd | 2 man/OCN_300_4out_PB_hot.Rd | 2 man/OCN_4.Rd | 2 man/OCN_400_Allout.Rd | 2 man/OCN_to_SSN.Rd | 3 - man/OCN_to_igraph.Rd | 2 man/aggregate_OCN.Rd | 23 +++++-- man/continue_OCN.Rd | 4 - man/create_OCN.Rd | 6 +- man/create_general_contour_OCN.Rd | 2 man/create_peano.Rd | 2 man/draw_contour_OCN.Rd | 2 man/draw_elev2D_OCN.Rd | 2 man/draw_elev3D_OCN.Rd | 2 man/draw_elev3Drgl_OCN.Rd | 2 man/draw_simple_OCN.Rd | 4 - man/draw_subcatchments_OCN.Rd | 2 man/draw_thematic_OCN.Rd | 4 - man/find_area_threshold_OCN.Rd | 2 man/landscape_OCN.Rd | 8 +- man/paths_OCN.Rd | 6 +- man/plot.Rd |only man/river-class.Rd |only man/rivergeometry_OCN.Rd | 4 - 48 files changed, 309 insertions(+), 165 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library providing high-performance scalability protocols, a
cross-platform standard for messaging and communications. Serves as a
concurrency framework for building distributed applications, utilising 'aio'
objects which resolve automatically upon completion of asynchronous
operations. Implements synchronisation primitives, allowing R to wait upon
events being signalled by concurrent messaging threads.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 0.8.0 dated 2023-03-03 and 0.8.1 dated 2023-03-27
DESCRIPTION | 17 - MD5 | 69 ++-- NAMESPACE | 15 + NEWS.md | 18 + R/aio.R | 56 +++ R/context.R | 44 +++ R/listdial.R | 16 - R/messenger.R | 15 - R/nano.R | 18 + R/nanonext-package.R | 11 R/ncurl.R | 14 R/opts.R | 14 R/socket.R | 13 R/sync.R |only R/tls.R | 39 ++ R/utils.R | 21 + README.md | 185 ++++++++++--- man/close.Rd | 18 - man/cv.Rd |only man/dial.Rd | 6 man/dot-unresolved.Rd |only man/is_aio.Rd | 2 man/listen.Rd | 12 man/msg_pipe.Rd |only man/nanonext-package.Rd | 11 man/ncurl_session.Rd | 13 man/opt.Rd | 14 man/pipe_notify.Rd |only man/recv_aio.Rd | 36 ++ man/request.Rd | 40 ++ man/sha1.Rd |only man/weakref-set.Rd |only src/aio.c | 681 ++++++++++++++++++++++++++++++++++++++++++++++-- src/core.c | 13 src/init.c | 24 + src/nanonext.h | 20 + src/thread.c | 10 src/tls.c | 51 +++ tests/tests.R | 112 +++++-- 39 files changed, 1438 insertions(+), 190 deletions(-)
Title: Support for the Multicriteria Decision Aiding Process
Description: Support for the analyst in a Multicriteria Decision Aiding (MCDA) process with algorithms,
preference elicitation and data visualisation functions. Sébastien Bigaret, Richard Hodgett, Patrick Meyer,
Tatyana Mironova, Alexandru Olteanu (2017) Supporting the multi-criteria decision aiding process :
R and the MCDA package, Euro Journal On Decision Processes, Volume 5, Issue 1 - 4,
pages 169 - 194 <doi:10.1007/s40070-017-0064-1>.
Author: Patrick Meyer, Sebastien Bigaret, Richard Hodgett, Alexandru-Liviu Olteanu
Maintainer: Patrick Meyer <patrick.meyer@imt-atlantique.fr>
Diff between MCDA versions 0.0.22 dated 2022-09-20 and 0.0.24 dated 2023-03-27
DESCRIPTION | 10 - MD5 | 47 ++-- NAMESPACE | 1 R/ELECTRE3.R |only R/LPDMRSortIdentifyIncompatibleAssignments.R | 161 +++-------------- R/LPDMRSortInferenceExact.R | 56 ----- R/MRSortIdentifyIncompatibleAssignments.R | 160 +++------------- R/MRSortInferenceExact.R | 90 ++------- R/SRMPInference.R | 4 R/SRMPInferenceFixedLexicographicOrder.R | 102 ++-------- R/SRMPInferenceFixedProfilesNumber.R | 4 R/SRMPInferenceNoInconsist.R | 4 R/SRMPInferenceNoInconsistFixedLexicographicOrder.R | 98 ++-------- R/SRMPInferenceNoInconsistFixedProfilesNumber.R | 16 - man/ELECTRE3.Rd |only man/LPDMRSortIdentifyIncompatibleAssignments.Rd | 8 man/LPDMRSortInferenceExact.Rd | 10 - man/MRSortIdentifyIncompatibleAssignments.Rd | 8 man/MRSortInferenceExact.Rd | 10 - man/SRMPInference.Rd | 10 - man/SRMPInferenceFixedLexicographicOrder.Rd | 9 man/SRMPInferenceFixedProfilesNumber.Rd | 9 man/SRMPInferenceNoInconsist.Rd | 10 - man/SRMPInferenceNoInconsistFixedLexicographicOrder.Rd | 9 man/SRMPInferenceNoInconsistFixedProfilesNumber.Rd | 9 tests/ELECTRE.R |only 26 files changed, 204 insertions(+), 641 deletions(-)
Title: Standardize Plant Names According to World Flora Online
Taxonomic Backbone
Description: World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. The World Flora Online Taxonomic Backbone is an updated version of The Plant List (<http://www.theplantlist.org/>), a working list of plant names that has become static since 2013.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between WorldFlora versions 1.12 dated 2023-01-06 and 1.13 dated 2023-03-27
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++-------- NAMESPACE | 1 R/WFO.acceptable.match.R |only R/WFO.download.R | 21 ++++++++++++---- R/WFO.match.R | 6 +++- R/WFO.remember.R | 55 ++++++++++++++++++++++---------------------- inst/CITATION | 29 ++++++++++++----------- inst/ChangeLog | 20 ++++++++++++++++ man/WFO.acceptable.match.Rd |only man/WFO.match2.Rd | 8 ++++++ man/WFO.remember.Rd | 10 ++++---- 12 files changed, 114 insertions(+), 64 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Umer Zeeshan Ijaz [ctb],
Chenhao Li [ctb],
Yang Cao [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 0.14.1 dated 2023-02-20 and 0.15.0 dated 2023-03-27
DESCRIPTION | 6 MD5 | 42 - R/microtable.R | 94 ++- R/trans_alpha.R | 305 +++++------ R/trans_beta.R | 2 R/trans_classifier.R | 187 ++++-- R/trans_diff.R | 1310 +++++++++++++++++++++++++----------------------- R/trans_env.R | 50 + R/trans_func.R | 26 R/trans_network.R | 581 ++++++++++----------- R/trans_nullmodel.R | 12 R/trans_venn.R | 154 ++++- R/utility.R | 16 man/microtable.Rd | 35 + man/trans_alpha.Rd | 6 man/trans_classifier.Rd | 62 +- man/trans_diff.Rd | 30 - man/trans_env.Rd | 18 man/trans_func.Rd | 11 man/trans_network.Rd | 7 man/trans_nullmodel.Rd | 24 man/trans_venn.Rd | 53 + 22 files changed, 1697 insertions(+), 1334 deletions(-)
Title: Graph-Constrained Functional Pruning Optimal Partitioning
Description: Penalized parametric change-point detection by functional pruning dynamic programming algorithm. The successive means are constrained using a graph structure with edges defining the nature of the changes These changes can be unconstrained (type std), up or down constrained (type up and down) or constrained by a minimal size jump (type abs). The type null means that the graph allows us to stay on the same segment. To each edge we can associate some additional properties: a minimal gap size, a penalty, some robust parameters (K,a) for biweight (K) and Huber losses (K and a). The user can also constrain the inferred means to lie between some minimal and maximal values. Data is modeled by a cost with possible use of a robust loss, biweight and Huber (see edge parameters K and a). These costs should have a quadratic, log-linear or a log-log representation. This includes quadratic Gaussian cost (type = 'mean'), log-linear cost (type = 'variance', 'poisson' or 'exp') and log-log cost (type = [...truncated...]
Author: Vincent Runge [aut, cre],
Toby Hocking [aut],
Guillem Rigaill [aut],
Daniel Grose [aut],
Gaetano Romano [aut],
Fatemeh Afghah [aut],
Paul Fearnhead [aut],
Michel Koskas [ctb],
Arnaud Liehrmann [ctb]
Maintainer: Vincent Runge <vincent.runge@univ-evry.fr>
Diff between gfpop versions 1.1.0 dated 2022-03-10 and 1.1.1 dated 2023-03-27
DESCRIPTION | 11 +++++------ MD5 | 21 ++++++++++++++++----- NAMESPACE | 7 +++++++ R/gfpop.R | 8 ++++++-- R/graph.R | 2 +- R/plot.R | 18 +++++++++--------- R/print.R |only R/summary.R |only README.md |only inst |only man/print.gfpop.Rd |only man/summary.gfpop.Rd |only tests |only 13 files changed, 44 insertions(+), 23 deletions(-)
Title: Variable Table for Variable Documentation
Description: Automatically generates HTML variable documentation including variable names, labels, classes, value labels (if applicable), value ranges, and summary statistics. See the vignette "vtable" for a package overview.
Author: Nick Huntington-Klein [aut, cre]
Maintainer: Nick Huntington-Klein <nhuntington-klein@seattleu.edu>
Diff between vtable versions 1.4.2 dated 2023-03-14 and 1.4.3 dated 2023-03-27
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/helpers.R | 20 +++++++++++++++----- inst/doc/dftotable.html | 4 ++-- inst/doc/labeltable.html | 4 ++-- inst/doc/sumtable.html | 4 ++-- inst/doc/vtable.html | 4 ++-- inst/doc/vtablefunction.html | 4 ++-- inst/doc/vtablehelpers.html | 10 +++++----- 10 files changed, 46 insertions(+), 32 deletions(-)
Title: A Collection of Methods to Estimate Parameters of Different
Tempered Stable Distributions
Description: A collection of methods to estimate parameters of different tempered stable
distributions. Currently, there are three different tempered stable
distributions to choose from: Tempered stable subordinator distribution,
classical tempered stable distribution, normal tempered stable distribution.
The package also provides functions to compute density and probability
functions and tools to run Monte Carlo simulations.
This package has already been used for the estimation of tempered stable
distributions (Massing (2023) <arXiv:2303.07060>).
The following references form the theoretical background for various functions
in this package. References for each function are explicitly listed in its
documentation:
Carrasco (2017) <doi:10.1017/S0266466616000025>
Feuerverger (1981) <doi:10.1111/j.2517-6161.1981.tb01143.x>
Hansen et al. (1996) <doi:10.1080/07350015.1996.10524656>
Hansen (1982) <doi:10.2307/1912775>
Kawai & Masuda (2011) <doi:10.1016/j.cam.2010.12.01 [...truncated...]
Author: Till Massing [aut],
Cedric Maximilian Juessen [cre]
Maintainer: Cedric Maximilian Juessen <cedric.juessen@vwl.uni-due.de>
Diff between TempStable versions 0.1.0 dated 2023-03-17 and 0.1.1 dated 2023-03-27
DESCRIPTION | 18 +-- MD5 | 14 +- NEWS.md | 9 + README.md | 25 +++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/my-vignette.html | 196 -------------------------------------- tests/testthat/test_MasterEstim.R | 54 +++++----- 8 files changed, 71 insertions(+), 245 deletions(-)
Title: Interface to the 'nanoarrow' 'C' Library
Description: Provides an 'R' interface to the 'nanoarrow' 'C' library and the
'Apache Arrow' application binary interface. Functions to import and
export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures
to and from 'R' objects are provided alongside helpers to facilitate zero-copy
data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C'
data interface.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between nanoarrow versions 0.1.0.1 dated 2023-03-10 and 0.1.0.2 dated 2023-03-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/as_array.c | 12 ++++++++++-- tests/testthat/test-as-array.R | 6 +++--- tests/testthat/test-convert-array.R | 4 ++-- 5 files changed, 22 insertions(+), 14 deletions(-)
Title: Generalized Linear Models Extended
Description: Extended techniques for generalized linear models (GLMs), especially for binary responses,
including parametric links and heteroscedastic latent variables.
Author: Achim Zeileis [aut, cre] ,
Roger Koenker [aut] ,
Philipp Doebler [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between glmx versions 0.1-3 dated 2022-04-19 and 0.2-0 dated 2023-03-27
glmx-0.1-3/glmx/NEWS |only glmx-0.2-0/glmx/DESCRIPTION | 20 +++++------ glmx-0.2-0/glmx/MD5 | 18 +++++----- glmx-0.2-0/glmx/NEWS.md |only glmx-0.2-0/glmx/R/glmx.R | 32 +++++++++++++----- glmx-0.2-0/glmx/R/hetglm.R | 27 ++++----------- glmx-0.2-0/glmx/build/partial.rdb |binary glmx-0.2-0/glmx/man/MexicanLabor.Rd | 2 - glmx-0.2-0/glmx/tests/Examples/glmx-Ex.Rout.save | 40 +++++++---------------- glmx-0.2-0/glmx/tests/hetglm.R | 6 +-- glmx-0.2-0/glmx/tests/hetglm.Rout.save | 12 +++--- 11 files changed, 73 insertions(+), 84 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 2.7 dated 2022-12-14 and 2.8 dated 2023-03-27
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 2 +- R/MFA.R | 6 ++++-- R/print.condes.R | 2 +- R/tab.disjonctif.R | 6 ++++-- man/AovSum.Rd | 3 ++- src/init.c | 2 +- 8 files changed, 23 insertions(+), 18 deletions(-)
Title: Tools for Handling Extraction of Features from Time Series
Description: Consolidates and calculates different sets of time-series features from multiple
'R' and 'Python' packages including 'Rcatch22' Henderson, T. (2021) <doi:10.5281/zenodo.5546815>,
'feasts' O'Hara-Wild, M., Hyndman, R., and Wang, E. (2021) <https://CRAN.R-project.org/package=feasts>,
'tsfeatures' Hyndman, R., Kang, Y., Montero-Manso, P., Talagala, T., Wang, E., Yang, Y., and O'Hara-Wild, M. (2020)
<https://CRAN.R-project.org/package=tsfeatures>, 'tsfresh' Christ, M., Braun, N., Neuffer, J.,
and Kempa-Liehr A.W. (2018) <doi:10.1016/j.neucom.2018.03.067>, 'TSFEL' Barandas, M., et al. (2020)
<doi:10.1016/j.softx.2020.100456>, and 'Kats' Facebook Infrastructure Data Science (2021)
<https://facebookresearch.github.io/Kats/>. Provides a standardised workflow from feature calculation to
feature processing, machine learning classification procedures, and the production of statistical graphics.
Author: Trent Henderson [cre, aut],
Annie Bryant [ctb]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between theft versions 0.4.2.3 dated 2023-02-07 and 0.4.2.4 dated 2023-03-27
theft-0.4.2.3/theft/vignettes/multi_outputs.rda |only theft-0.4.2.3/theft/vignettes/outputs.rda |only theft-0.4.2.4/theft/DESCRIPTION | 8 theft-0.4.2.4/theft/LICENSE | 2 theft-0.4.2.4/theft/MD5 | 103 theft-0.4.2.4/theft/NAMESPACE | 208 - theft-0.4.2.4/theft/R/calculate_features.R | 951 ++-- theft-0.4.2.4/theft/R/check_vector_quality.R | 20 theft-0.4.2.4/theft/R/compute_top_features.R | 758 +-- theft-0.4.2.4/theft/R/data.R | 52 theft-0.4.2.4/theft/R/fit_multi_feature_classifier.R | 1962 +++++----- theft-0.4.2.4/theft/R/fit_single_feature_classifier.R | 1610 ++++---- theft-0.4.2.4/theft/R/init_theft.R | 30 theft-0.4.2.4/theft/R/normalise.R | 132 theft-0.4.2.4/theft/R/plots.R | 878 ++-- theft-0.4.2.4/theft/R/process_hctsa_file.R | 142 theft-0.4.2.4/theft/R/reduce_dims.R | 198 - theft-0.4.2.4/theft/R/rescalers.R | 178 theft-0.4.2.4/theft/R/theft.R | 52 theft-0.4.2.4/theft/README.md | 230 - theft-0.4.2.4/theft/build/vignette.rds |binary theft-0.4.2.4/theft/inst/doc/theft.R | 243 - theft-0.4.2.4/theft/inst/doc/theft.Rmd | 650 +-- theft-0.4.2.4/theft/inst/doc/theft.html | 1750 ++++---- theft-0.4.2.4/theft/inst/python/kats_calculator.py | 64 theft-0.4.2.4/theft/inst/python/tsfel_calculator.py | 46 theft-0.4.2.4/theft/inst/python/tsfresh_calculator.py | 46 theft-0.4.2.4/theft/man/calculate_features.Rd | 112 theft-0.4.2.4/theft/man/check_vector_quality.Rd | 40 theft-0.4.2.4/theft/man/compute_top_features.Rd | 194 theft-0.4.2.4/theft/man/feature_list.Rd | 40 theft-0.4.2.4/theft/man/fit_multi_feature_classifier.Rd | 152 theft-0.4.2.4/theft/man/fit_single_feature_classifier.Rd | 104 theft-0.4.2.4/theft/man/init_theft.Rd | 44 theft-0.4.2.4/theft/man/minmax_scaler.Rd | 40 theft-0.4.2.4/theft/man/normalise.Rd | 44 theft-0.4.2.4/theft/man/plot.feature_calculations.Rd | 76 theft-0.4.2.4/theft/man/plot.low_dimension.Rd | 48 theft-0.4.2.4/theft/man/process_hctsa_file.Rd | 56 theft-0.4.2.4/theft/man/reduce_dims.Rd | 68 theft-0.4.2.4/theft/man/robustsigmoid_scaler.Rd | 50 theft-0.4.2.4/theft/man/sigmoid_scaler.Rd | 44 theft-0.4.2.4/theft/man/simData.Rd | 44 theft-0.4.2.4/theft/man/theft.Rd | 18 theft-0.4.2.4/theft/man/zscore_scaler.Rd | 44 theft-0.4.2.4/theft/tests/testthat.R | 8 theft-0.4.2.4/theft/tests/testthat/helper-core_data.R | 22 theft-0.4.2.4/theft/tests/testthat/test-calculate_features.R | 66 theft-0.4.2.4/theft/tests/testthat/test-compute_top_features.R | 262 - theft-0.4.2.4/theft/tests/testthat/test-fit_multi_feature_classifier.R | 100 theft-0.4.2.4/theft/tests/testthat/test-process_hctsa_file.R | 18 theft-0.4.2.4/theft/vignettes/FeatureFeatureCorrelationPlot.png |only theft-0.4.2.4/theft/vignettes/FeatureSetResultsPlot.png |only theft-0.4.2.4/theft/vignettes/ViolinPlots.png |only theft-0.4.2.4/theft/vignettes/theft.Rmd | 650 +-- 55 files changed, 6273 insertions(+), 6384 deletions(-)
Title: Companion Datasets and Functions for Research Design in the
Social Sciences
Description: Helper functions to accompany the Blair, Coppock, and Humphreys (2022) "Research Design in the Social Sciences: Declaration, Diagnosis, and Redesign" <https://book.declaredesign.org>. 'rdss' includes datasets, helper functions, and plotting components to enable use and replication of the book.
Author: Graeme Blair [aut, cre] ,
Alexander Coppock [aut] ,
Macartan Humphreys [aut]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Diff between rdss versions 1.0.0 dated 2023-01-17 and 1.0.2 dated 2023-03-27
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NEWS.md | 4 ++++ R/data.R | 11 +++++++++++ data/lapop_brazil.rda |only man/lapop_brazil.Rd |only 6 files changed, 23 insertions(+), 6 deletions(-)
Title: Drugs Databases Parser
Description: This tool is for parsing public drug databases such as 'DrugBank' XML database <https://go.drugbank.com/>.
The parsed data are then returned in a proper 'R' object called 'dvobject'.
Author: Mohammed Ali [aut, cre],
Ali Ezzat [aut],
Hao Zhu [rev],
Emma Mendelsohn [rev]
Maintainer: Mohammed Ali <moh_fcis@yahoo.com>
Diff between dbparser versions 2.0.0 dated 2023-03-17 and 2.0.1 dated 2023-03-27
DESCRIPTION | 6 MD5 | 30 NEWS.md | 10 R/drug_common_utilities.R | 24 R/drugbank_parser.R | 84 - README.md | 10 inst/doc/dbparser.R | 7 inst/doc/dbparser.Rmd | 7 inst/doc/dbparser.html | 29 man/cett_nodes_options.Rd | 8 man/drug_node_options.Rd | 8 man/parseDrugBank.Rd | 30 man/references_node_options.Rd | 8 tests/testthat/_snaps/drugbank-parser.md | 2282 ++++++++----------------------- tests/testthat/test-drugbank-parser.R | 124 - vignettes/dbparser.Rmd | 7 16 files changed, 866 insertions(+), 1808 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-07 0.1.1
2022-01-27 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-04 1.4.3
2021-06-22 1.4.2
2020-12-04 1.4.1
2020-09-26 1.4.0
2020-06-09 1.3.0
2020-03-21 1.2.0
2020-02-07 1.1.3
2019-10-28 1.1.2
2019-09-27 1.1.1
2019-08-05 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-10 1.4.5
2022-12-14 1.4.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-21 0.1.0