Title: Blind Source Separation and Supervised Dimension Reduction for
Time Series
Description: Different estimators are provided to solve the blind source separation problem for multivariate time series with stochastic volatility (Matilainen, Nordhausen and Oja (2015) <doi:10.1016/j.spl.2015.04.033>; Matilainen, Miettinen, Nordhausen, Oja and Taskinen (2017) <doi:10.17713/ajs.v46i3-4.671>) and supervised dimension reduction problem for multivariate time series (Matilainen, Croux, Nordhausen and Oja (2017) <doi:10.1016/j.ecosta.2017.04.002>). Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace.
Author: Markus Matilainen [cre, aut] (<https://orcid.org/0000-0002-5597-2670>),
Christophe Croux [aut],
Jari Miettinen [aut] (<https://orcid.org/0000-0002-3270-7014>),
Klaus Nordhausen [aut] (<https://orcid.org/0000-0002-3758-8501>),
Hannu Oja [aut],
Sara Taskinen [aut] (<https://orcid.org/0000-0001-9470-7258>),
Joni Virta [aut] (<https://orcid.org/0000-0002-2150-2769>)
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>
Diff between tsBSS versions 0.5.6 dated 2020-11-18 and 0.5.7 dated 2021-04-01
DESCRIPTION | 27 ++++++++++++++++----- MD5 | 64 +++++++++++++++++++++++++-------------------------- NAMESPACE | 2 - R/AMUSEasymp.R | 2 - R/AMUSEboot.R | 10 +++---- R/AMUSEladle.R | 2 - R/FixNA.R | 2 - R/LADLEinternal.R | 4 +-- R/PVC.R | 2 - R/SOBIasymp.R | 2 - R/SOBIboot.R | 10 +++---- R/SOBIladle.R | 2 - R/gFOBI.R | 2 - R/gJADE.R | 2 - R/gSOBI.R | 2 - R/tssdr.R | 2 - R/vSOBI.R | 2 - inst/ChangeLog | 4 +++ man/AMUSEasymp.Rd | 2 - man/FixNA.Rd | 2 - man/PVC.Rd | 2 - man/SOBIasymp.Rd | 2 - man/SOBIboot.Rd | 2 - man/SOBIladle.Rd | 2 - man/gFOBI.Rd | 2 - man/gJADE.Rd | 2 - man/gSOBI.Rd | 6 ++-- man/lbtest.Rd | 4 +-- man/tsBSS-package.Rd | 11 ++++---- man/vSOBI.Rd | 2 - src/bb.c | 2 - src/tsBSS.cpp | 23 ------------------ src/tsBSS.h | 1 33 files changed, 101 insertions(+), 107 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 Bakdash and Marusich (2017) <doi:10.3389/fpsyg.2017.00456>.
Author: Jonathan Z. Bakdash, Laura R. Marusich
Maintainer: Laura R. Marusich <laura.m.cooper20.civ@mail.mil>
Diff between rmcorr versions 0.4.2 dated 2021-03-30 and 0.4.3 dated 2021-04-01
rmcorr-0.4.2/rmcorr/vignettes/plots |only rmcorr-0.4.3/rmcorr/DESCRIPTION | 8 rmcorr-0.4.3/rmcorr/MD5 | 36 --- rmcorr-0.4.3/rmcorr/NEWS.md | 4 rmcorr-0.4.3/rmcorr/build/partial.rdb |binary rmcorr-0.4.3/rmcorr/build/vignette.rds |binary rmcorr-0.4.3/rmcorr/inst/doc/New_rmcorr_paper_analyses_figures.R | 57 +++-- rmcorr-0.4.3/rmcorr/inst/doc/New_rmcorr_paper_analyses_figures.Rmd | 77 ++++--- rmcorr-0.4.3/rmcorr/inst/doc/New_rmcorr_paper_analyses_figures.html | 106 ++++------ rmcorr-0.4.3/rmcorr/vignettes/New_rmcorr_paper_analyses_figures.Rmd | 77 ++++--- 10 files changed, 193 insertions(+), 172 deletions(-)
Title: UCA Rcmdr Plug-in
Description: Some extensions to Rcmdr (R Commander), randomness test,
variance test for one normal sample and predictions using active model,
made by R-UCA project and used in teaching statistics at University of Cadiz (UCA).
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between RcmdrPlugin.UCA versions 4.3-4 dated 2021-03-01 and 4.4-2 dated 2021-04-01
ChangeLog | 5 DESCRIPTION | 15 - MD5 | 33 +-- NAMESPACE | 35 +++ R/RcmdrPlugin.UCA.R | 73 +++++-- R/globals.R | 2 R/qualitycontrol.R |only build/vignette.rds |binary inst/doc/additions.html | 4 inst/doc/adiciones.html | 4 inst/etc/menus.txt | 66 ++++++ inst/po/es/LC_MESSAGES/R-RcmdrPlugin.UCA.mo |binary man/RcmdrPlugin.UCA-internal.Rd | 28 ++ man/RcmdrPlugin.UCA-package.Rd | 4 man/RcmdrPlugin.UCA.es-package.Rd | 4 po/R-RcmdrPlugin.UCA-es.mo |binary po/R-RcmdrPlugin.UCA-es.po | 265 +++++++++++++++++++++++++--- po/R-RcmdrPlugin.UCA.pot | 263 +++++++++++++++++++++++++-- 18 files changed, 692 insertions(+), 109 deletions(-)
More information about RcmdrPlugin.UCA at CRAN
Permanent link
Title: Propensity Score Weighting for Causal Inference with
Observational Studies and Randomized Trials
Description: Supports propensity score weighting analysis of observational studies and randomized trials. Enables the estimation and inference of average causal effects with binary and multiple treatments using overlap weights (ATO), inverse probability of treatment weights (ATE), average treatment effect among the treated weights (ATT), matching weights (ATM) and entropy weights (ATEN), with and without propensity score trimming. These weights are members of the family of balancing weights introduced in Li, Morgan and Zaslavsky (2018) <doi:10.1080/01621459.2016.1260466> and Li and Li (2019) <doi:10.1214/19-AOAS1282>.
Author: Tianhui Zhou [aut, cre],
Guangyu Tong [aut],
Fan Li [aut],
Laine Thomas [aut],
Fan Li [aut]
Maintainer: Tianhui Zhou <tianhui.zhou@duke.edu>
Diff between PSweight versions 1.1.3 dated 2021-02-25 and 1.1.4 dated 2021-04-01
PSweight-1.1.3/PSweight/R/Outmethod.R |only PSweight-1.1.4/PSweight/DESCRIPTION | 8 PSweight-1.1.4/PSweight/MD5 | 30 + PSweight-1.1.4/PSweight/NAMESPACE | 2 PSweight-1.1.4/PSweight/R/NCDS.R | 126 ++++---- PSweight-1.1.4/PSweight/R/OUTmethod.R |only PSweight-1.1.4/PSweight/R/PSmethod.R | 379 +++++++++++++----------- PSweight-1.1.4/PSweight/R/PStrim.R | 476 +++++++++++++++---------------- PSweight-1.1.4/PSweight/R/PSweight.R | 28 - PSweight-1.1.4/PSweight/R/SumStat.R | 18 - PSweight-1.1.4/PSweight/R/bin_est.R | 20 - PSweight-1.1.4/PSweight/R/mul_est.R | 16 - PSweight-1.1.4/PSweight/man/NCDS.Rd | 8 PSweight-1.1.4/PSweight/man/OUTmethod.Rd |only PSweight-1.1.4/PSweight/man/PSmethod.Rd |only PSweight-1.1.4/PSweight/man/PStrim.Rd | 10 PSweight-1.1.4/PSweight/man/PSweight.Rd | 24 - PSweight-1.1.4/PSweight/man/SumStat.Rd | 18 - 18 files changed, 603 insertions(+), 560 deletions(-)
Title: Do 16s Data Analysis and Generate Figures
Description: Provides functions to enhance the available
statistical analysis procedures in R by providing simple functions to
analysis and visualize the 16S rRNA data.Here we present a tutorial
with minimum working examples to demonstrate usage and dependencies.
Author: Kai Guo [aut, cre],
Pan Gao [aut]
Maintainer: Kai Guo <guokai8@gmail.com>
Diff between microbial versions 0.0.18 dated 2021-03-31 and 0.0.19 dated 2021-04-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/dada2.R | 21 +++++++++++++++++---- man/processSeq.Rd | 3 +++ 4 files changed, 26 insertions(+), 10 deletions(-)
Title: Latent (Variable) Analysis with Bayesian Learning
Description: A variety of models to analyze latent variables based on Bayesian learning: the partially CFA (Chen, Guo, Zhang, & Pan, 2020) <DOI: 10.1037/met0000293>; generalized PCFA; partially confirmatory IRM (Chen, 2020) <DOI: 10.1007/s11336-020-09724-3>; Bayesian regularized EFA <DOI: 10.1080/10705511.2020.1854763>; Fully and partially EFA.
Author: Jinsong Chen [aut, cre, cph]
Maintainer: Jinsong Chen <jinsong.chen@live.com>
Diff between LAWBL versions 1.3.0 dated 2020-11-03 and 1.4.0 dated 2021-04-01
LAWBL-1.3.0/LAWBL/R/plot_eigen.R |only LAWBL-1.3.0/LAWBL/inst/doc/gpcfa-examples.R |only LAWBL-1.3.0/LAWBL/inst/doc/gpcfa-examples.Rmd |only LAWBL-1.3.0/LAWBL/inst/doc/gpcfa-examples.html |only LAWBL-1.3.0/LAWBL/inst/doc/pcfa-examples.R |only LAWBL-1.3.0/LAWBL/inst/doc/pcfa-examples.Rmd |only LAWBL-1.3.0/LAWBL/inst/doc/pcfa-examples.html |only LAWBL-1.3.0/LAWBL/inst/doc/pcirm-examples.R |only LAWBL-1.3.0/LAWBL/inst/doc/pcirm-examples.Rmd |only LAWBL-1.3.0/LAWBL/inst/doc/pcirm-examples.html |only LAWBL-1.3.0/LAWBL/man/plot_eigen.Rd |only LAWBL-1.3.0/LAWBL/vignettes/gpcfa-examples.Rmd |only LAWBL-1.3.0/LAWBL/vignettes/pcfa-examples.Rmd |only LAWBL-1.3.0/LAWBL/vignettes/pcirm-examples.Rmd |only LAWBL-1.4.0/LAWBL/DESCRIPTION | 9 +- LAWBL-1.4.0/LAWBL/MD5 | 75 ++++++++---------- LAWBL-1.4.0/LAWBL/NAMESPACE | 27 +++--- LAWBL-1.4.0/LAWBL/NEWS.md | 9 ++ LAWBL-1.4.0/LAWBL/R/Gibbs_pefa_main.R |only LAWBL-1.4.0/LAWBL/R/Init.R | 9 +- LAWBL-1.4.0/LAWBL/R/LAWBL-package.R | 41 ++++++--- LAWBL-1.4.0/LAWBL/R/datasets.R | 22 ++++- LAWBL-1.4.0/LAWBL/R/pcfa.R | 53 ++++++------ LAWBL-1.4.0/LAWBL/R/pcirm.R | 38 ++++----- LAWBL-1.4.0/LAWBL/R/pefa.R |only LAWBL-1.4.0/LAWBL/R/plot_lawbl.R |only LAWBL-1.4.0/LAWBL/R/summary.lawbl.R | 60 +++++++++----- LAWBL-1.4.0/LAWBL/R/utils.R | 27 +++--- LAWBL-1.4.0/LAWBL/R/zzz.R |only LAWBL-1.4.0/LAWBL/README.md | 103 +++++++++---------------- LAWBL-1.4.0/LAWBL/build/vignette.rds |binary LAWBL-1.4.0/LAWBL/data/nlsy27.RData |only LAWBL-1.4.0/LAWBL/data/sim18ccfa40.RData |binary LAWBL-1.4.0/LAWBL/data/sim18ccfa41.RData |binary LAWBL-1.4.0/LAWBL/data/sim18cfa0.RData |binary LAWBL-1.4.0/LAWBL/data/sim18cfa1.RData |binary LAWBL-1.4.0/LAWBL/data/sim18mcfa41.RData |binary LAWBL-1.4.0/LAWBL/data/sim24ccfa21.RData |binary LAWBL-1.4.0/LAWBL/inst/doc/LAWBL.Rmd |only LAWBL-1.4.0/LAWBL/inst/doc/LAWBL.html |only LAWBL-1.4.0/LAWBL/man/LAWBL-package.Rd | 38 +++++---- LAWBL-1.4.0/LAWBL/man/nlsy27.Rd |only LAWBL-1.4.0/LAWBL/man/pcfa.Rd | 17 ++-- LAWBL-1.4.0/LAWBL/man/pcirm.Rd | 10 +- LAWBL-1.4.0/LAWBL/man/pefa.Rd |only LAWBL-1.4.0/LAWBL/man/plot_lawbl.Rd |only LAWBL-1.4.0/LAWBL/man/sim18ccfa40.Rd | 2 LAWBL-1.4.0/LAWBL/man/sim18ccfa41.Rd | 2 LAWBL-1.4.0/LAWBL/man/sim18mcfa41.Rd | 4 LAWBL-1.4.0/LAWBL/man/summary.lawbl.Rd | 5 - LAWBL-1.4.0/LAWBL/vignettes/LAWBL.Rmd |only 51 files changed, 297 insertions(+), 254 deletions(-)
Title: 'GitHub' 'API'
Description: Minimal client to access the 'GitHub' 'API'.
Author: Gábor Csárdi [cre, ctb],
Jennifer Bryan [aut],
Hadley Wickham [aut],
RStudio [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between gh versions 1.2.0 dated 2020-11-27 and 1.2.1 dated 2021-04-01
DESCRIPTION | 9 MD5 | 30 +-- NEWS.md | 9 R/errors.R | 253 ++++++++++++++++++++++---- R/gh_token.R | 23 +- R/gh_whoami.R | 7 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/managing-personal-access-tokens.Rmd | 2 inst/doc/managing-personal-access-tokens.html | 51 +---- man/gh_token.Rd | 2 man/gh_whoami.Rd | 7 tests/testthat/helper-offline.R | 2 tests/testthat/test-gh_token.R | 6 tests/testthat/test-mock-repos.R | 4 vignettes/managing-personal-access-tokens.Rmd | 2 16 files changed, 294 insertions(+), 114 deletions(-)
Title: Sensitivity Analyses for Unmeasured Confounding and Other Biases
in Observational Studies and Meta-Analyses
Description: Conducts sensitivity analyses for unmeasured confounding, selection bias, and measurement error (individually or in combination; VanderWeele & Ding (2017) <doi:10.7326/M16-2607>; Smith & VanderWeele (2019) <doi:10.1097/EDE.0000000000001032>; VanderWeele & Li (2019) <doi:10.1093/aje/kwz133>; Smith & VanderWeele (2021) <arXiv:2005.02908>). Also conducts sensitivity analyses for unmeasured confounding in meta-analyses (Mathur & VanderWeele (2020a) <doi:10.1080/01621459.2018.1529598>; Mathur & VanderWeele (2020b) <doi:10.1097/EDE.0000000000001180>) and for additive measures of effect modification (Mathur et al., under review).
Author: Maya B. Mathur [cre, aut],
Louisa H. Smith [aut],
Peng Ding [aut],
Tyler J. VanderWeele [aut]
Maintainer: Maya B. Mathur <mmathur@stanford.edu>
Diff between EValue versions 4.1.1 dated 2021-01-04 and 4.1.2 dated 2021-04-01
DESCRIPTION | 8 - MD5 | 25 ++-- NAMESPACE | 1 R/EValue.R | 17 +- R/effect_modification.R |only R/meta-analysis.R | 58 ++++------ R/utils.R | 15 ++ README.md | 10 + inst/doc/meta-analysis.html | 8 - man/confounded_meta.Rd | 5 man/evalue.Rd | 8 + man/evalues.IC.Rd |only man/sens_plot.Rd | 2 tests/testthat/test-effect-mod.R |only tests/testthat/testthat.R | 223 ++++++++------------------------------- 15 files changed, 141 insertions(+), 239 deletions(-)
Title: Complex Split Procedures in Random Forests Through Candidate
Split Sampling
Description: Implements interaction forests [1], which are specific diversity forests, and
the basic form of diversity forests that uses univariable, binary splitting [2].
Interaction forests (IFs) are ensembles of decision trees that model quantitative and
qualitative interaction effects using bivariable splitting. IFs come with the
Effect Importance Measure (EIM), which can be used to identify variable pairs that
feature quantitative and qualitative interaction effects with high predictive
relevance. IFs and EIM focus on well interpretable forms of interactions.
The package also offers plot functions for visualising the estimated forms of
interaction effects.
Categorical, metric, and survival outcomes are supported.
This is a fork of the R package 'ranger' (main author: Marvin N. Wright) that
implements random forests using an efficient C++ implementation.
References:
[1] Hornung, R. & Boulesteix, A.-L. (2021) Interaction Forests: Identifying and
exploiting interpretable quantitative and qualitative interaction effects.
Technical Report No. 237, Department of Statistics, University of Munich
[2] Hornung, R. (2020) Diversity Forests: Using split sampling to allow for complex
split procedures in random forest. Technical Report No. 234, Department of Statistics,
University of Munich.
Author: Roman Hornung [aut, cre], Marvin N. Wright [ctb, cph]
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between diversityForest versions 0.2.0 dated 2020-01-29 and 0.3.0 dated 2021-04-01
diversityForest-0.2.0/diversityForest/R/predict.R |only diversityForest-0.2.0/diversityForest/man/predictions.divfor.Rd |only diversityForest-0.2.0/diversityForest/man/predictions.divfor.prediction.Rd |only diversityForest-0.2.0/diversityForest/man/print.divfor.Rd |only diversityForest-0.2.0/diversityForest/man/print.divfor.forest.Rd |only diversityForest-0.2.0/diversityForest/man/print.divfor.prediction.Rd |only diversityForest-0.2.0/diversityForest/man/print.tunedivfor.Rd |only diversityForest-0.3.0/diversityForest/DESCRIPTION | 55 diversityForest-0.3.0/diversityForest/MD5 | 105 diversityForest-0.3.0/diversityForest/NAMESPACE | 26 diversityForest-0.3.0/diversityForest/NEWS | 5 diversityForest-0.3.0/diversityForest/R/RcppExports.R | 4 diversityForest-0.3.0/diversityForest/R/diversityForest-package.R |only diversityForest-0.3.0/diversityForest/R/divfor.R | 1768 +++--- diversityForest-0.3.0/diversityForest/R/getPromispairs.R |only diversityForest-0.3.0/diversityForest/R/interactionfor.R |only diversityForest-0.3.0/diversityForest/R/plot.interactionfor.R |only diversityForest-0.3.0/diversityForest/R/plotEffects.R |only diversityForest-0.3.0/diversityForest/R/plotPair.R |only diversityForest-0.3.0/diversityForest/R/predict.divfor.R |only diversityForest-0.3.0/diversityForest/R/predict.interactionfor.R |only diversityForest-0.3.0/diversityForest/R/predictions.R | 44 diversityForest-0.3.0/diversityForest/R/print.R | 104 diversityForest-0.3.0/diversityForest/R/stock.R |only diversityForest-0.3.0/diversityForest/R/tunedivfor.R | 10 diversityForest-0.3.0/diversityForest/R/zoo.R |only diversityForest-0.3.0/diversityForest/build/partial.rdb |binary diversityForest-0.3.0/diversityForest/data |only diversityForest-0.3.0/diversityForest/man/diversityForest-package.Rd |only diversityForest-0.3.0/diversityForest/man/divfor.Rd | 91 diversityForest-0.3.0/diversityForest/man/interactionfor.Rd |only diversityForest-0.3.0/diversityForest/man/plot.interactionfor.Rd |only diversityForest-0.3.0/diversityForest/man/plotEffects.Rd |only diversityForest-0.3.0/diversityForest/man/plotPair.Rd |only diversityForest-0.3.0/diversityForest/man/predict.divfor.Rd | 28 diversityForest-0.3.0/diversityForest/man/predict.interactionfor.Rd |only diversityForest-0.3.0/diversityForest/man/stock.Rd |only diversityForest-0.3.0/diversityForest/man/tunedivfor.Rd | 19 diversityForest-0.3.0/diversityForest/man/zoo.Rd |only diversityForest-0.3.0/diversityForest/src/Data.cpp | 7 diversityForest-0.3.0/diversityForest/src/Data.h | 3 diversityForest-0.3.0/diversityForest/src/Forest.cpp | 254 diversityForest-0.3.0/diversityForest/src/Forest.h | 88 diversityForest-0.3.0/diversityForest/src/ForestClassification.cpp | 51 diversityForest-0.3.0/diversityForest/src/ForestClassification.h | 6 diversityForest-0.3.0/diversityForest/src/ForestProbability.cpp | 19 diversityForest-0.3.0/diversityForest/src/ForestProbability.h | 3 diversityForest-0.3.0/diversityForest/src/ForestRegression.cpp | 47 diversityForest-0.3.0/diversityForest/src/ForestRegression.h | 4 diversityForest-0.3.0/diversityForest/src/ForestSurvival.cpp | 22 diversityForest-0.3.0/diversityForest/src/ForestSurvival.h | 3 diversityForest-0.3.0/diversityForest/src/RcppExports.cpp | 14 diversityForest-0.3.0/diversityForest/src/Tree.cpp | 2638 +++++++--- diversityForest-0.3.0/diversityForest/src/Tree.h | 62 diversityForest-0.3.0/diversityForest/src/TreeClassification.cpp | 192 diversityForest-0.3.0/diversityForest/src/TreeClassification.h | 11 diversityForest-0.3.0/diversityForest/src/TreeProbability.cpp | 169 diversityForest-0.3.0/diversityForest/src/TreeProbability.h | 9 diversityForest-0.3.0/diversityForest/src/TreeRegression.cpp | 187 diversityForest-0.3.0/diversityForest/src/TreeRegression.h | 11 diversityForest-0.3.0/diversityForest/src/TreeSurvival.cpp | 163 diversityForest-0.3.0/diversityForest/src/TreeSurvival.h | 8 diversityForest-0.3.0/diversityForest/src/divforCpp.cpp | 73 diversityForest-0.3.0/diversityForest/src/globals.h | 2 diversityForest-0.3.0/diversityForest/src/utility.cpp | 53 diversityForest-0.3.0/diversityForest/src/utility.h | 31 66 files changed, 4578 insertions(+), 1811 deletions(-)
More information about diversityForest at CRAN
Permanent link
Title: Deep Learning for General Purpose
Description: Aims to provide simple intuitive functions to create quick prototypes of artificial neural network or deep learning models. In addition novel ensemble models like 'deeptree' and 'deepforest' has been included which combines decision trees and neural network.
Author: Rajesh Balakrishnan
Maintainer: Rajesh Balakirshnan <rajeshbalakrishnan24@gmail.com>
Diff between deepdive versions 1.0.1 dated 2020-03-26 and 1.0.2 dated 2021-04-01
deepdive-1.0.1/deepdive/man/figures |only deepdive-1.0.2/deepdive/DESCRIPTION | 10 deepdive-1.0.2/deepdive/LICENSE | 4 deepdive-1.0.2/deepdive/MD5 | 62 - deepdive-1.0.2/deepdive/NAMESPACE | 44 - deepdive-1.0.2/deepdive/NEWS.md |only deepdive-1.0.2/deepdive/R/backProp.R | 242 +++--- deepdive-1.0.2/deepdive/R/deepForest.R | 622 ++++++++--------- deepdive-1.0.2/deepdive/R/deepnet.R | 710 ++++++++++---------- deepdive-1.0.2/deepdive/R/deeptree.R | 508 +++++++------- deepdive-1.0.2/deepdive/R/feedForward.R | 176 ++-- deepdive-1.0.2/deepdive/R/miniBatchCreate.R | 62 - deepdive-1.0.2/deepdive/R/multiActivationList.R | 44 - deepdive-1.0.2/deepdive/R/multiDataCut.R | 114 +-- deepdive-1.0.2/deepdive/R/multiLayerIntialiser.R | 50 - deepdive-1.0.2/deepdive/R/multiVariableCut.R | 56 - deepdive-1.0.2/deepdive/R/optimiserAdjust.R | 142 ++-- deepdive-1.0.2/deepdive/R/predict.deepforest.R | 166 ++-- deepdive-1.0.2/deepdive/R/predict.deepnet.R | 235 +++--- deepdive-1.0.2/deepdive/R/predict.deeptree.R | 306 ++++---- deepdive-1.0.2/deepdive/R/shuffler.R | 120 +-- deepdive-1.0.2/deepdive/R/variableImportance.R | 152 ++-- deepdive-1.0.2/deepdive/R/weightIntialiser.R | 44 - deepdive-1.0.2/deepdive/R/weightUpdate.R | 304 ++++---- deepdive-1.0.2/deepdive/R/weightUpdateInitialiser.R | 40 - deepdive-1.0.2/deepdive/README.md | 171 ++-- deepdive-1.0.2/deepdive/man/deepforest.Rd | 294 ++++---- deepdive-1.0.2/deepdive/man/deepnet.Rd | 216 +++--- deepdive-1.0.2/deepdive/man/deeptree.Rd | 262 +++---- deepdive-1.0.2/deepdive/man/predict.deepforest.Rd | 42 - deepdive-1.0.2/deepdive/man/predict.deepnet.Rd | 42 - deepdive-1.0.2/deepdive/man/predict.deeptree.Rd | 50 - deepdive-1.0.2/deepdive/man/variableImportance.Rd | 50 - 33 files changed, 2674 insertions(+), 2666 deletions(-)
Title: Spatial Absorbing Markov Chains
Description: Implements functions for working with absorbing Markov chains. The
implementation is based on the framework described in "Toward a unified
framework for connectivity that disentangles movement and mortality in space
and time" by Fletcher et al. (2019) <doi:10.1111/ele.13333>, which applies
them to spatial ecology. This framework incorporates both resistance and
absorption with spatial absorbing Markov chains (SAMC) to provide several
short-term and long-term predictions for metrics related to connectivity in
landscapes. Despite the ecological context of the framework, this package
can be used in any application of absorbing Markov chains.
Author: Andrew Marx [aut, cre, cph] (<https://orcid.org/0000-0002-7456-1631>),
Robert Fletcher [ctb] (<https://orcid.org/0000-0003-1717-5707>),
Miguel Acevedo [ctb] (<https://orcid.org/0000-0002-8289-1497>),
Jorge Sefair [ctb] (<https://orcid.org/0000-0002-5887-8938>),
Chao Wang [ctb] (<https://orcid.org/0000-0003-2706-5122>)
Maintainer: Andrew Marx <andrewjmarx@ufl.edu>
Diff between samc versions 1.2.1 dated 2020-11-02 and 1.3.0 dated 2021-04-01
DESCRIPTION | 20 +- MD5 | 105 ++++++----- NEWS.md | 13 + R/check.R | 35 ++- R/cond_passage.R | 36 ++- R/dispersal.R | 73 ++++--- R/distribution.R | 41 ++-- R/internal-functions.R | 83 +++++++- R/locate.R | 7 R/location-class.R |only R/map.R | 10 - R/mortality.R | 69 ++++--- R/pairwise.R |only R/samc.R | 125 +++++++++---- R/survival.R | 6 R/visitation.R | 40 +++- build/vignette.rds |binary inst/doc/code-snippets.R |only inst/doc/code-snippets.Rmd |only inst/doc/code-snippets.html |only inst/doc/overview.R | 2 inst/doc/overview.Rmd | 11 - inst/doc/overview.html | 94 ++++----- inst/doc/performance.html | 23 -- inst/doc/troubleshooting.html | 136 ++++++-------- inst/doc/tutorial-animations.R | 2 inst/doc/tutorial-animations.html | 188 +++++++++---------- inst/doc/tutorial-basic.R | 2 inst/doc/tutorial-basic.Rmd | 2 inst/doc/tutorial-basic.html | 304 +++++++++++++++----------------- inst/doc/tutorial-ggplot.html | 252 ++++++++++++-------------- inst/doc/tutorial-locations.R |only inst/doc/tutorial-locations.Rmd |only inst/doc/tutorial-locations.html |only inst/doc/tutorial-temporal.R | 2 inst/doc/tutorial-temporal.Rmd | 2 inst/doc/tutorial-temporal.html | 224 +++++++++++------------ inst/examples/locate.R |only inst/examples/pairwise.R |only man/cond_passage.Rd | 31 +-- man/dispersal.Rd | 48 ++--- man/distribution.Rd | 28 +- man/locate.Rd | 56 ++--- man/location-class.Rd |only man/mortality.Rd | 40 ++-- man/pairwise.Rd |only man/samc.Rd | 73 +++++-- man/visitation.Rd | 28 +- tests/testthat/test-check.R |only tests/testthat/test-cond_passage.R | 70 ++++--- tests/testthat/test-dispersal.R | 147 ++++++--------- tests/testthat/test-distribution.R | 85 ++++---- tests/testthat/test-mortality.R | 161 ++++++++-------- tests/testthat/test-samc.R | 4 tests/testthat/test-visitation.R | 50 ++--- vignettes/code-snippets.Rmd |only vignettes/overview.Rmd | 11 - vignettes/scripts/tutorial-animations.R | 2 vignettes/tutorial-basic.Rmd | 2 vignettes/tutorial-locations.Rmd |only vignettes/tutorial-temporal.Rmd | 2 61 files changed, 1458 insertions(+), 1287 deletions(-)
Title: A Parallelized General-Purpose Optimization Based on
Marquardt-Levenberg Algorithm
Description: This algorithm provides a numerical solution to the
problem of unconstrained local minimization (or maximization). It is particularly suited for complex problems and more efficient than
the Gauss-Newton-like algorithm when starting from points very
far from the final minimum (or maximum). Each iteration is parallelized and convergence relies on a stringent stopping criterion based on the first and second derivatives. See Philipps et al, 2020 <arXiv:2009.03840>.
Author: Viviane Philipps, Cecile Proust-Lima, Melanie Prague, Boris Hejblum, Daniel Commenges, Amadou Diakite
Maintainer: Viviane Philipps <viviane.philipps@u-bordeaux.fr>
Diff between marqLevAlg versions 2.0.4 dated 2020-09-12 and 2.0.5 dated 2021-04-01
marqLevAlg-2.0.4/marqLevAlg/man/ForInternalUse.Rd |only marqLevAlg-2.0.5/marqLevAlg/DESCRIPTION | 14 marqLevAlg-2.0.5/marqLevAlg/MD5 | 49 - marqLevAlg-2.0.5/marqLevAlg/R/deriva.R | 2 marqLevAlg-2.0.5/marqLevAlg/R/deriva_grad.R | 1 marqLevAlg-2.0.5/marqLevAlg/R/func.R | 3 marqLevAlg-2.0.5/marqLevAlg/R/func1.R | 3 marqLevAlg-2.0.5/marqLevAlg/R/ghg.R | 4 marqLevAlg-2.0.5/marqLevAlg/R/marqLevAlg-package.R | 4 marqLevAlg-2.0.5/marqLevAlg/R/marqLevAlg.R | 12 marqLevAlg-2.0.5/marqLevAlg/R/print.marqLevAlg.R | 24 marqLevAlg-2.0.5/marqLevAlg/R/searpas.R | 3 marqLevAlg-2.0.5/marqLevAlg/R/summary.marqLevAlg.R | 33 + marqLevAlg-2.0.5/marqLevAlg/R/sup.R | 3 marqLevAlg-2.0.5/marqLevAlg/R/valfpa.R | 1 marqLevAlg-2.0.5/marqLevAlg/build/partial.rdb |binary marqLevAlg-2.0.5/marqLevAlg/inst/doc/mla.R | 332 +++++++++-- marqLevAlg-2.0.5/marqLevAlg/inst/doc/mla.Rmd | 526 +++++++++++++++--- marqLevAlg-2.0.5/marqLevAlg/inst/doc/mla.pdf |binary marqLevAlg-2.0.5/marqLevAlg/man/dataEx.Rd | 6 marqLevAlg-2.0.5/marqLevAlg/man/marqLevAlg-package.Rd | 4 marqLevAlg-2.0.5/marqLevAlg/man/marqLevAlg.Rd | 62 +- marqLevAlg-2.0.5/marqLevAlg/man/print.marqLevAlg.Rd | 81 +- marqLevAlg-2.0.5/marqLevAlg/man/summary.marqLevAlg.Rd | 104 +-- marqLevAlg-2.0.5/marqLevAlg/vignettes/mla.Rmd | 526 +++++++++++++++--- marqLevAlg-2.0.5/marqLevAlg/vignettes/mla.bib | 78 ++ 26 files changed, 1503 insertions(+), 372 deletions(-)
Title: Representation of DET Curve with Confidence Intervals
Description: Builds both ROC (Receiver Operating Characteristic) and DET (Detection Error Tradeoff) curves from a set of predictors, which are the
results of a binary classification system. The curves give a general vision of the performance of the classifier,
and are useful for comparing performance of different systems.
Author: García-Ródenas, Álvaro [aut, cre],
Franco, Manuel [aut],
Vivo, Juana-María [aut],
Fernández-Breis, Jesualdo T. [aut],
Font, Roberto [aut]
Maintainer: "García-Ródenas, Álvaro" <alvaro.garcia9@um.es>
Diff between DET versions 2.0.2 dated 2020-03-29 and 3.0.0 dated 2021-04-01
DET-2.0.2/DET/R/detcurve.R |only DET-2.0.2/DET/R/print.R |only DET-2.0.2/DET/man/detc.CI.Rd |only DET-2.0.2/DET/man/printDET.Rd |only DET-3.0.0/DET/DESCRIPTION | 10 +- DET-3.0.0/DET/MD5 | 36 ++++--- DET-3.0.0/DET/NAMESPACE | 52 +++++----- DET-3.0.0/DET/NEWS.md | 65 ++++++++----- DET-3.0.0/DET/R/classDefinitions.R |only DET-3.0.0/DET/R/detc.R |only DET-3.0.0/DET/R/internalFunctions.R |only DET-3.0.0/DET/R/measures.R |only DET-3.0.0/DET/R/ovarianCancer-data.R | 76 ++++++++------- DET-3.0.0/DET/R/plot.R |only DET-3.0.0/DET/R/show.R |only DET-3.0.0/DET/R/speaker-data.R | 79 ++++++++-------- DET-3.0.0/DET/man/EER.Rd |only DET-3.0.0/DET/man/detc.Rd | 170 ++++++++++++++++++----------------- DET-3.0.0/DET/man/detc.ci.Rd |only DET-3.0.0/DET/man/minDcf.Rd |only DET-3.0.0/DET/man/ovarianCancer.Rd | 36 ++++--- DET-3.0.0/DET/man/plot.DET.Rd |only DET-3.0.0/DET/man/plot.DETs.Rd |only DET-3.0.0/DET/man/plotROC.Rd |only DET-3.0.0/DET/man/plotROCs.Rd |only DET-3.0.0/DET/man/pointsEER.Rd |only DET-3.0.0/DET/man/show.DETs.Rd |only DET-3.0.0/DET/man/speaker.Rd | 46 +++++---- DET-3.0.0/DET/tests |only 29 files changed, 312 insertions(+), 258 deletions(-)
Title: 'shiny' App to Discover Cocktails
Description: A 'shiny' app to discover cocktails. The
app allows one to search for cocktails by ingredient,
filter on rating, and number of ingredients. The
package also contains data with the ingredients of
nearly 26 thousand cocktails scraped from the web.
Author: Steven E. Pav [aut, cre] (<https://orcid.org/0000-0002-4197-6195>)
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between cocktailApp versions 0.2.1 dated 2019-07-02 and 0.2.2 dated 2021-04-01
ChangeLog | 6 ++ DESCRIPTION | 9 +--- MD5 | 18 ++++---- R/cocktailApp.r | 92 +++++++++++++++++++++++++++++++++----------- README.md | 11 ++--- data/cocktails.rda |binary man/NEWS.Rd | 9 ++++ man/cocktailApp.Rd | 4 - man/cocktails.Rd | 14 +++--- tests/testthat/test-basic.r | 61 +++++++++++++++++++++++++++-- 10 files changed, 171 insertions(+), 53 deletions(-)
Title: Extracts the Backbone from Weighted Graphs
Description: Provides methods for extracting from a weighted graph
a binary or signed backbone that retains only the significant edges.
The user may input a weighted graph, or a bipartite graph
from which a weighted graph is first constructed via projection.
Backbone extraction methods include the stochastic degree sequence model (Neal, Z. P. (2014). <doi:10.1016/j.socnet.2014.06.001>),
hypergeometric model (Neal, Z. (2013). <doi:10.1007/s13278-013-0107-y>),
the fixed degree sequence model (Zweig, K. A., and Kaufmann, M. (2011). <doi:10.1007/s13278-011-0021-0>),
fixed column model, fixed fill model,
as well as a universal threshold method.
Author: Rachel Domagalski [aut, cre],
Zachary Neal [aut],
Bruce Sagan [aut]
Maintainer: Rachel Domagalski <domagal9@msu.edu>
Diff between backbone versions 1.3.1 dated 2021-02-16 and 1.4.0 dated 2021-04-01
backbone-1.3.1/backbone/R/hyperg.R |only backbone-1.3.1/backbone/man/bipartite.null.Rd |only backbone-1.3.1/backbone/man/class.convert.Rd |only backbone-1.3.1/backbone/man/rna.Rd |only backbone-1.3.1/backbone/tests/testthat/test-bipartite.null.R |only backbone-1.3.1/backbone/tests/testthat/test-class.convert.R |only backbone-1.3.1/backbone/vignettes/pandoc1c18612a2cfe.html |only backbone-1.3.1/backbone/vignettes/pandoc2fb8dd87a1d.html |only backbone-1.4.0/backbone/DESCRIPTION | 14 backbone-1.4.0/backbone/MD5 | 61 - backbone-1.4.0/backbone/NAMESPACE | 4 backbone-1.4.0/backbone/NEWS.md | 10 backbone-1.4.0/backbone/R/backbone.R | 27 backbone-1.4.0/backbone/R/backbone.extract.R | 19 backbone-1.4.0/backbone/R/fdsm.R | 38 backbone-1.4.0/backbone/R/fixedcol.R |only backbone-1.4.0/backbone/R/fixedfill.R |only backbone-1.4.0/backbone/R/fixedrow.R |only backbone-1.4.0/backbone/R/model.helpers.R | 292 ++--- backbone-1.4.0/backbone/R/sdsm.R | 35 backbone-1.4.0/backbone/R/universal.R | 22 backbone-1.4.0/backbone/README.md | 77 + backbone-1.4.0/backbone/build/partial.rdb |binary backbone-1.4.0/backbone/inst/doc/backbone.R | 14 backbone-1.4.0/backbone/inst/doc/backbone.Rmd | 91 + backbone-1.4.0/backbone/inst/doc/backbone.html | 489 +++++----- backbone-1.4.0/backbone/man/backbone.Rd | 27 backbone-1.4.0/backbone/man/backbone.extract.Rd | 10 backbone-1.4.0/backbone/man/fdsm.Rd | 3 backbone-1.4.0/backbone/man/figures |only backbone-1.4.0/backbone/man/fixedcol.Rd |only backbone-1.4.0/backbone/man/fixedfill.Rd |only backbone-1.4.0/backbone/man/fixedrow.Rd |only backbone-1.4.0/backbone/man/frommatrix.Rd |only backbone-1.4.0/backbone/man/hyperg.Rd | 9 backbone-1.4.0/backbone/man/sdsm.Rd | 5 backbone-1.4.0/backbone/man/tomatrix.Rd |only backbone-1.4.0/backbone/tests/testthat/test-backbone.extract.R | 8 backbone-1.4.0/backbone/tests/testthat/test-frommatrix.R |only backbone-1.4.0/backbone/tests/testthat/test-tomatrix.R |only backbone-1.4.0/backbone/vignettes/backbone.Rmd | 91 + 41 files changed, 731 insertions(+), 615 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre],
Ruth Keogh [aut],
Claus Thorn Ekstrøm [ctb],
Edouard F. Bonneville [ctb]
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>
Diff between smcfcs versions 1.4.2 dated 2020-12-07 and 1.5.0 dated 2021-04-01
DESCRIPTION | 8 MD5 | 87 - NAMESPACE | 17 R/data.r | 273 ++-- R/plot_convergence.R | 398 +++--- R/smcfcs.r | 2187 +++++++++++++++++---------------- README.md | 22 build/partial.rdb |only build/vignette.rds |binary data/ex_cc.rda |binary data/ex_compet.rda |binary data/ex_coxquad.rda |binary data/ex_dtsam.rda |only data/ex_lininter.rda |binary data/ex_linquad.rda |binary data/ex_logisticquad.rda |binary data/ex_ncc.rda |binary data/ex_poisson.rda |binary inst/doc/smcfcs-vignette.R | 96 - inst/doc/smcfcs-vignette.Rmd | 278 ++-- inst/doc/smcfcs-vignette.html | 959 +++++--------- inst/doc/smcfcs_coverror-vignette.R | 168 +- inst/doc/smcfcs_coverror-vignette.Rmd | 262 +-- inst/doc/smcfcs_coverror-vignette.html | 907 +++++-------- man/ex_cc.Rd | 50 man/ex_compet.Rd | 48 man/ex_coxquad.Rd | 50 man/ex_dtsam.Rd |only man/ex_lininter.Rd | 44 man/ex_linquad.Rd | 48 man/ex_logisticquad.Rd | 48 man/ex_ncc.Rd | 52 man/ex_poisson.Rd | 46 man/plot.smcfcs.Rd | 126 - man/smcfcs.Rd | 423 +++--- man/smcfcs.casecohort.Rd | 202 +-- man/smcfcs.dtsam.Rd |only man/smcfcs.nestedcc.Rd | 216 +-- tests/testthat/test_casecohort.r | 166 +- tests/testthat/test_coxph.r | 96 - tests/testthat/test_dtsam.r |only tests/testthat/test_errorchecks.R | 434 +++--- tests/testthat/test_measerror.r | 168 +- tests/testthat/test_nestedcc.R | 272 ++-- tests/testthat/test_weibull.r | 126 - vignettes/smcfcs-vignette.Rmd | 278 ++-- vignettes/smcfcs_coverror-vignette.Rmd | 262 +-- 47 files changed, 4268 insertions(+), 4549 deletions(-)
Title: R Package Installation from Remote Repositories, Including
'GitHub'
Description: Download and install R packages stored in 'GitHub', 'GitLab',
'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git' repositories.
This package provides the 'install_*' functions in 'devtools'. Indeed most
of the code was copied over from 'devtools'.
Author: Jim Hester [aut, cre],
Gábor Csárdi [aut],
Hadley Wickham [aut],
Winston Chang [aut],
RStudio [cph],
Martin Morgan [aut],
Dan Tenenbaum [aut],
Mango Solutions [cph]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between remotes versions 2.2.0 dated 2020-07-21 and 2.3.0 dated 2021-04-01
DESCRIPTION | 8 - MD5 | 87 +++++++-------- NEWS.md | 22 +++ R/bioc-standalone.R | 4 R/deps.R | 26 +++- R/download.R | 2 R/github.R | 19 ++- R/install-bioc.R | 5 R/install-bitbucket.R | 2 R/install-cran.R | 2 R/install-github.R | 5 R/install-gitlab.R | 11 + R/install-remote.R | 16 ++ R/install.R | 7 - R/system_requirements.R | 73 +++++++++--- README.md | 15 -- build/vignette.rds |binary inst/doc/dependencies.html | 39 ++++++ inst/install-github.R | 170 +++++++++++++++++++++--------- man/github_remote.Rd | 2 man/install_bioc.Rd | 7 - man/install_bitbucket.Rd | 11 - man/install_cran.Rd | 9 - man/install_deps.Rd | 9 - man/install_git.Rd | 7 - man/install_github.Rd | 12 +- man/install_gitlab.Rd | 14 +- man/install_local.Rd | 7 - man/install_remote.Rd | 7 - man/install_svn.Rd | 7 - man/install_url.Rd | 7 - man/install_version.Rd | 7 - man/package_deps.Rd | 9 - man/standardise_dep.Rd | 2 man/system_requirements.Rd | 15 ++ man/update_packages.Rd | 7 - tests/testthat/helper.R | 2 tests/testthat/test-bioc.R | 2 tests/testthat/test-deps.R | 24 ++++ tests/testthat/test-download.R | 155 +++++++++++++-------------- tests/testthat/test-github.R | 10 + tests/testthat/test-install-gitlab.R | 12 ++ tests/testthat/test-install.R | 25 +--- tests/testthat/test-system_requirements.R | 12 ++ tests/testthat/urlremotes |only 45 files changed, 567 insertions(+), 327 deletions(-)
Title: Hazard Function Estimation in Survival Analysis
Description: Produces a smooth estimate of the hazard
function for censored data.
Author: S original by Kenneth Hess,
R port by R. Gentleman
Maintainer: David Winsemius <dwinsemius@comcast.net>
Diff between muhaz versions 1.2.6.2 dated 2021-03-29 and 1.2.6.3 dated 2021-04-01
DESCRIPTION | 10 +++++----- MD5 | 3 ++- src/init.c |only 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Bayesian Summary Data Models for Mendelian Randomization Studies
Description: Bayesian estimation of inverse variance weighted (IVW), Burgess
et al. (2013) <doi:10.1002/gepi.21758>, and MR-Egger, Bowden et
al. (2015) <doi:10.1093/ije/dyv080>, summary data models for Mendelian
randomization analyses.
Author: Okezie Uche-Ikonne [aut, cre] (<https://orcid.org/0000-0002-8461-8099>),
Frank Dondelinger [aut] (<https://orcid.org/0000-0003-1816-6300>),
Tom Palmer [aut] (<https://orcid.org/0000-0003-4655-4511>)
Maintainer: Okezie Uche-Ikonne <o.uche-ikonne@lancaster.ac.uk>
Diff between mrbayes versions 0.2.0 dated 2020-05-28 and 0.3.0 dated 2021-04-01
mrbayes-0.2.0/mrbayes/R/do_data.R |only mrbayes-0.2.0/mrbayes/data/do_data.rda |only mrbayes-0.2.0/mrbayes/man/do_data.Rd |only mrbayes-0.3.0/mrbayes/DESCRIPTION | 12 mrbayes-0.3.0/mrbayes/MD5 | 112 - mrbayes-0.3.0/mrbayes/NAMESPACE | 50 mrbayes-0.3.0/mrbayes/NEWS.md | 18 mrbayes-0.3.0/mrbayes/R/bmi_insulin.R | 34 mrbayes-0.3.0/mrbayes/R/dodata.R |only mrbayes-0.3.0/mrbayes/R/mr_egger_rjags.R | 723 +++++----- mrbayes-0.3.0/mrbayes/R/mr_egger_stan.R | 160 +- mrbayes-0.3.0/mrbayes/R/mr_format.R | 78 - mrbayes-0.3.0/mrbayes/R/mr_ivw_rjags.R | 471 +++--- mrbayes-0.3.0/mrbayes/R/mr_ivw_stan.R | 135 - mrbayes-0.3.0/mrbayes/R/mr_radialegger_rjags.R | 713 ++++----- mrbayes-0.3.0/mrbayes/R/mr_radialegger_stan.R | 155 +- mrbayes-0.3.0/mrbayes/R/mrbayes-package.r | 31 mrbayes-0.3.0/mrbayes/R/mrinput_mrformat.R |only mrbayes-0.3.0/mrbayes/R/mvmr_egger_rjags.R |only mrbayes-0.3.0/mrbayes/R/mvmr_egger_stan.R |only mrbayes-0.3.0/mrbayes/R/mvmr_format.R |only mrbayes-0.3.0/mrbayes/R/mvmr_ivw_rjags.R |only mrbayes-0.3.0/mrbayes/R/mvmr_ivw_stan.R |only mrbayes-0.3.0/mrbayes/R/stanmodels.R | 56 mrbayes-0.3.0/mrbayes/R/tsmr_mrformat.R |only mrbayes-0.3.0/mrbayes/README.md | 88 - mrbayes-0.3.0/mrbayes/build |only mrbayes-0.3.0/mrbayes/configure.win | 8 mrbayes-0.3.0/mrbayes/data/dodata.rda |only mrbayes-0.3.0/mrbayes/inst/stan/include/license.stan | 28 mrbayes-0.3.0/mrbayes/inst/stan/mregger.stan | 190 +- mrbayes-0.3.0/mrbayes/inst/stan/mrivw.stan | 88 - mrbayes-0.3.0/mrbayes/inst/stan/mrradialegger.stan | 190 +- mrbayes-0.3.0/mrbayes/inst/stan/mvmregger.stan |only mrbayes-0.3.0/mrbayes/inst/stan/mvmrivw.stan |only mrbayes-0.3.0/mrbayes/man/bmi_insulin.Rd | 58 mrbayes-0.3.0/mrbayes/man/dodata.Rd |only mrbayes-0.3.0/mrbayes/man/mr_egger_rjags.Rd | 148 +- mrbayes-0.3.0/mrbayes/man/mr_egger_stan.Rd | 116 - mrbayes-0.3.0/mrbayes/man/mr_format.Rd | 70 mrbayes-0.3.0/mrbayes/man/mr_ivw_rjags.Rd | 132 - mrbayes-0.3.0/mrbayes/man/mr_ivw_stan.Rd | 104 - mrbayes-0.3.0/mrbayes/man/mr_radialegger_rjags.Rd | 148 +- mrbayes-0.3.0/mrbayes/man/mr_radialegger_stan.Rd | 116 - mrbayes-0.3.0/mrbayes/man/mrbayes-package.Rd | 27 mrbayes-0.3.0/mrbayes/man/mrinput_mr_format.Rd |only mrbayes-0.3.0/mrbayes/man/mvmr_egger_rjags.Rd |only mrbayes-0.3.0/mrbayes/man/mvmr_egger_stan.Rd |only mrbayes-0.3.0/mrbayes/man/mvmr_format.Rd |only mrbayes-0.3.0/mrbayes/man/mvmr_ivw_rjags.Rd |only mrbayes-0.3.0/mrbayes/man/mvmr_ivw_stan.Rd |only mrbayes-0.3.0/mrbayes/src/Makevars | 10 mrbayes-0.3.0/mrbayes/src/Makevars.win | 11 mrbayes-0.3.0/mrbayes/src/RcppExports.cpp | 4 mrbayes-0.3.0/mrbayes/src/stanExports_mregger.h | 20 mrbayes-0.3.0/mrbayes/src/stanExports_mrivw.h | 20 mrbayes-0.3.0/mrbayes/src/stanExports_mrradialegger.h | 20 mrbayes-0.3.0/mrbayes/src/stanExports_mvmregger.cc |only mrbayes-0.3.0/mrbayes/src/stanExports_mvmregger.h |only mrbayes-0.3.0/mrbayes/src/stanExports_mvmrivw.cc |only mrbayes-0.3.0/mrbayes/src/stanExports_mvmrivw.h |only mrbayes-0.3.0/mrbayes/tests/testthat.R | 8 mrbayes-0.3.0/mrbayes/tests/testthat/test-mr_egger_rjags.R | 223 +-- mrbayes-0.3.0/mrbayes/tests/testthat/test-mr_egger_stan.R | 146 +- mrbayes-0.3.0/mrbayes/tests/testthat/test-mr_ivw_rjags.R | 152 +- mrbayes-0.3.0/mrbayes/tests/testthat/test-mr_ivw_stan.R | 114 - mrbayes-0.3.0/mrbayes/tests/testthat/test-mr_radialegger_rjags.R | 222 +-- mrbayes-0.3.0/mrbayes/tests/testthat/test-mr_radialegger_stan.R | 146 +- mrbayes-0.3.0/mrbayes/tests/testthat/test-mvmr_egger_rjags.R |only mrbayes-0.3.0/mrbayes/tests/testthat/test-mvmr_egger_stan.R |only mrbayes-0.3.0/mrbayes/tests/testthat/test-mvmr_ivw_rjags.R |only mrbayes-0.3.0/mrbayes/tests/testthat/test-mvmr_ivw_stan.R |only 72 files changed, 2861 insertions(+), 2494 deletions(-)
Title: Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) Files
Description: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it contains
or can be specified by the user.
Author: Marc Schwartz <marc_schwartz@me.com> and various authors for Perl modules listed in each .pm file.
Maintainer: Marc Schwartz <marc_schwartz@me.com>
Diff between WriteXLS versions 6.2.0 dated 2021-02-22 and 6.3.0 dated 2021-04-01
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/WriteXLS.R | 2 +- R/testPerl.R | 2 +- inst/Perl/WriteXLS.pl | 16 ++++++++++++++-- inst/Perl/WriteXLSX.pl | 16 ++++++++++++++-- 6 files changed, 39 insertions(+), 15 deletions(-)
Title: Extract Tables and Sentences from PDFs with User Interface
Description: The PDE (Pdf Data Extractor) allows the extraction of
information and tables optionally based on search words from
PDF (Portable Document Format) files and enables the visualization
of the results, both by providing a convenient user-interface.
Author: Erik Stricker [aut, cre]
Maintainer: Erik Stricker <erik.stricker@gmx.com>
Diff between PDE versions 1.1.2 dated 2020-11-26 and 1.2.1 dated 2021-04-01
PDE-1.1.2/PDE/man/PDE_install_XpdfReader4.02.Rd |only PDE-1.1.2/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.input_output_MTX_example.png |only PDE-1.1.2/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.input_output_empty.png |only PDE-1.2.1/PDE/DESCRIPTION | 9 PDE-1.2.1/PDE/MD5 | 63 PDE-1.2.1/PDE/NAMESPACE | 1 PDE-1.2.1/PDE/NEWS.md | 17 PDE-1.2.1/PDE/R/PDE.R | 1099 +++++----- PDE-1.2.1/PDE/README.md | 153 - PDE-1.2.1/PDE/inst/doc/PDE.R | 15 PDE-1.2.1/PDE/inst/doc/PDE.Rmd | 125 - PDE-1.2.1/PDE/inst/doc/PDE.html | 93 PDE-1.2.1/PDE/man/PDE-deprecated.Rd | 2 PDE-1.2.1/PDE/man/PDE.Rd | 4 PDE-1.2.1/PDE/man/PDE_analyzer.Rd | 3 PDE-1.2.1/PDE/man/PDE_extr_data_from_pdfs.Rd | 30 PDE-1.2.1/PDE/man/PDE_path.Rd | 2 PDE-1.2.1/PDE/man/PDE_pdfs2table.Rd | 12 PDE-1.2.1/PDE/man/PDE_pdfs2table_searchandfilter.Rd | 22 PDE-1.2.1/PDE/man/PDE_pdfs2txt_searchandfilter.Rd | 16 PDE-1.2.1/PDE/man/dot-PDE_extr_data_from_pdf.Rd | 26 PDE-1.2.1/PDE/vignettes/PDE.Rmd | 125 - PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.choose_variables_empty.png |binary PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.docus_MTX_example.png |binary PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.docus_empty.png |binary PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.filter_words_MTX_example.png |only PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.filter_words_empty.png |only PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.parameters_MTX_example.png |binary PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.parameters_empty.png |binary PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.search_words_MTX_example.png |only PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.search_words_empty.png |only PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.start_MTX_example.png |binary PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface_MTX_example.png |binary PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface_empty_linux.png |binary PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface_empty_mac.png |binary PDE-1.2.1/PDE/vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface_empty_win.png |binary 36 files changed, 1016 insertions(+), 801 deletions(-)
Title: Bootstrap Inference for Multiple Imputation
Description: Bootstraps and imputes incomplete datasets. Then performs inference on estimates obtained from analysing the imputed datasets as proposed by von Hippel and Bartlett (2019) <arXiv:1210.0870v10>.
Author: Jonathan Bartlett
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>
Diff between bootImpute versions 1.1.0 dated 2020-07-10 and 1.2.0 dated 2021-04-01
DESCRIPTION | 6 +- MD5 | 16 ++--- NEWS.md | 9 --- R/bootImpute.R | 32 ++++++++--- R/bootMice.R | 16 +++-- R/bootSmcfcs.R | 12 ++-- man/bootImpute.Rd | 35 +++++++----- tests/testthat/test_bootImpute.r | 110 ++++++++++++++++++++++++++++++++------- tests/testthat/test_parallel.R | 68 +++++++++++++++++------- 9 files changed, 215 insertions(+), 89 deletions(-)
Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scattered points by 3rd dimension,
enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings,
use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays,
fit multiple functions.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between berryFunctions versions 1.19.1 dated 2020-06-06 and 1.20.1 dated 2021-04-01
berryFunctions-1.19.1/berryFunctions/inst/extdata/RainfallStationsMap.pdf |only berryFunctions-1.20.1/berryFunctions/DESCRIPTION | 12 berryFunctions-1.20.1/berryFunctions/MD5 | 183 +-- berryFunctions-1.20.1/berryFunctions/NAMESPACE | 7 berryFunctions-1.20.1/berryFunctions/NEWS | 20 berryFunctions-1.20.1/berryFunctions/R/TFtest.R | 6 berryFunctions-1.20.1/berryFunctions/R/checkFile.R | 33 berryFunctions-1.20.1/berryFunctions/R/classify.R | 27 berryFunctions-1.20.1/berryFunctions/R/climateGraph.R | 24 berryFunctions-1.20.1/berryFunctions/R/colPoints.R | 2 berryFunctions-1.20.1/berryFunctions/R/combineFiles.R | 3 berryFunctions-1.20.1/berryFunctions/R/compareDist.R |only berryFunctions-1.20.1/berryFunctions/R/compareFiles.R | 2 berryFunctions-1.20.1/berryFunctions/R/createPres.R | 63 + berryFunctions-1.20.1/berryFunctions/R/dataStr.R | 55 - berryFunctions-1.20.1/berryFunctions/R/distance.R | 3 berryFunctions-1.20.1/berryFunctions/R/funnelPlot.R | 8 berryFunctions-1.20.1/berryFunctions/R/getName.R | 4 berryFunctions-1.20.1/berryFunctions/R/gof.R | 4 berryFunctions-1.20.1/berryFunctions/R/googleLink2pdf.R | 4 berryFunctions-1.20.1/berryFunctions/R/groupHist.R | 5 berryFunctions-1.20.1/berryFunctions/R/if.error.R |only berryFunctions-1.20.1/berryFunctions/R/insertRows.R | 2 berryFunctions-1.20.1/berryFunctions/R/l2array.R | 3 berryFunctions-1.20.1/berryFunctions/R/l2df.R | 10 berryFunctions-1.20.1/berryFunctions/R/learnVocab.R | 2 berryFunctions-1.20.1/berryFunctions/R/library2.R | 14 berryFunctions-1.20.1/berryFunctions/R/linLogTrans.R | 6 berryFunctions-1.20.1/berryFunctions/R/locatorRS.R |only berryFunctions-1.20.1/berryFunctions/R/logSpaced.R | 4 berryFunctions-1.20.1/berryFunctions/R/logVals.R | 3 berryFunctions-1.20.1/berryFunctions/R/lsMem.R | 2 berryFunctions-1.20.1/berryFunctions/R/lsc.R | 6 berryFunctions-1.20.1/berryFunctions/R/mReg.R | 2 berryFunctions-1.20.1/berryFunctions/R/normalizePathCP.R | 2 berryFunctions-1.20.1/berryFunctions/R/owa.R | 8 berryFunctions-1.20.1/berryFunctions/R/pal.R | 12 berryFunctions-1.20.1/berryFunctions/R/popleaf.R | 15 berryFunctions-1.20.1/berryFunctions/R/rescale.R | 2 berryFunctions-1.20.1/berryFunctions/R/runTime.R |only berryFunctions-1.20.1/berryFunctions/R/seasonality.R | 2 berryFunctions-1.20.1/berryFunctions/R/seqR.R | 3 berryFunctions-1.20.1/berryFunctions/R/smallPlot.R | 2 berryFunctions-1.20.1/berryFunctions/R/sumatraInitialize.R | 49 berryFunctions-1.20.1/berryFunctions/R/testExamples.R | 1 berryFunctions-1.20.1/berryFunctions/R/textField.R | 4 berryFunctions-1.20.1/berryFunctions/R/timer.R | 2 berryFunctions-1.20.1/berryFunctions/R/traceCall.R | 7 berryFunctions-1.20.1/berryFunctions/R/tryStack.R | 8 berryFunctions-1.20.1/berryFunctions/R/unitHydrograph.R | 9 berryFunctions-1.20.1/berryFunctions/README.md | 8 berryFunctions-1.20.1/berryFunctions/build/vignette.rds |binary berryFunctions-1.20.1/berryFunctions/inst/doc/berryFunctions.html | 541 +++------- berryFunctions-1.20.1/berryFunctions/man/TFtest.Rd | 1 berryFunctions-1.20.1/berryFunctions/man/catPal.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/checkFile.Rd | 6 berryFunctions-1.20.1/berryFunctions/man/classify.Rd | 17 berryFunctions-1.20.1/berryFunctions/man/climateGraph.Rd | 391 +++---- berryFunctions-1.20.1/berryFunctions/man/colPoints.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/combineFiles.Rd | 3 berryFunctions-1.20.1/berryFunctions/man/compareDist.Rd |only berryFunctions-1.20.1/berryFunctions/man/compareFiles.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/createPres.Rd | 7 berryFunctions-1.20.1/berryFunctions/man/dataStr.Rd | 25 berryFunctions-1.20.1/berryFunctions/man/distance.Rd | 3 berryFunctions-1.20.1/berryFunctions/man/divPal.Rd | 6 berryFunctions-1.20.1/berryFunctions/man/funnelPlot.Rd | 8 berryFunctions-1.20.1/berryFunctions/man/getName.Rd | 4 berryFunctions-1.20.1/berryFunctions/man/gof.Rd | 4 berryFunctions-1.20.1/berryFunctions/man/googleLink2pdf.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/groupHist.Rd | 3 berryFunctions-1.20.1/berryFunctions/man/if.error.Rd |only berryFunctions-1.20.1/berryFunctions/man/insertRows.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/l2array.Rd | 3 berryFunctions-1.20.1/berryFunctions/man/l2df.Rd | 10 berryFunctions-1.20.1/berryFunctions/man/learnVocab.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/library2.Rd | 10 berryFunctions-1.20.1/berryFunctions/man/linLogTrans.Rd | 6 berryFunctions-1.20.1/berryFunctions/man/locatorRS.Rd |only berryFunctions-1.20.1/berryFunctions/man/logSpaced.Rd | 4 berryFunctions-1.20.1/berryFunctions/man/logVals.Rd | 3 berryFunctions-1.20.1/berryFunctions/man/lsMem.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/lsc.Rd | 6 berryFunctions-1.20.1/berryFunctions/man/mReg.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/owa.Rd | 8 berryFunctions-1.20.1/berryFunctions/man/popleaf.Rd | 19 berryFunctions-1.20.1/berryFunctions/man/rescale.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/runTime.Rd |only berryFunctions-1.20.1/berryFunctions/man/seasonality.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/seqPal.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/seqR.Rd | 3 berryFunctions-1.20.1/berryFunctions/man/showPal.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/sumatraInitialize.Rd | 5 berryFunctions-1.20.1/berryFunctions/man/textField.Rd | 4 berryFunctions-1.20.1/berryFunctions/man/timer.Rd | 2 berryFunctions-1.20.1/berryFunctions/man/tryStack.Rd | 8 berryFunctions-1.20.1/berryFunctions/man/unitHydrograph.Rd | 9 97 files changed, 933 insertions(+), 863 deletions(-)
More information about berryFunctions at CRAN
Permanent link
Title: A 'HTTP' Server Graphics Device
Description: A graphics device for R that is accessible via network protocols.
This package was created to make it easier to embed live R graphics in
integrated development environments and other applications.
The included 'HTML/JavaScript' client (plot viewer) aims to provide a better overall user experience when dealing with R graphics.
The device asynchronously serves 'SVG' graphics via 'HTTP' and 'WebSockets'.
Author: Florian Rupprecht [aut, cre] (<https://orcid.org/0000-0002-1795-8624>),
Kun Ren [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Hadley Wickham [cph] (Author of included svglite code),
Lionel Henry [cph] (Author of included svglite code),
Thomas Lin Pedersen [cph] (Author and creator of included svglite code),
T Jake Luciani [cph] (Author of included svglite code),
Matthieu Decorde [cph] (Author of included svglite code),
Vaudor Lise [cph] (Author of included svglite code),
Tony Plate [cph] (Contributor to included svglite code),
David Gohel [cph] (Contributor to included svglite code),
Yixuan Qiu [cph] (Contributor to included svglite code),
Håkon Malmedal [cph] (Contributor to included svglite code),
RStudio [cph] (Copyright holder of included svglite code),
Brett Robinson [cph] (Author of included belle library),
Google [cph] (Copyright holder of included material design icons),
Victor Zverovich [cph] (Author of included fmt library)
Maintainer: Florian Rupprecht <floruppr@gmail.com>
Diff between httpgd versions 1.0.1 dated 2021-01-21 and 1.1.0 dated 2021-04-01
DESCRIPTION | 14 MD5 | 86 - NAMESPACE | 1 NEWS.md | 12 R/cpp11.R | 26 R/httpgd.R | 330 ++++-- README.md | 94 - build |only inst/doc |only inst/www/httpgd.js | 487 +++++---- inst/www/index.html | 346 +++--- inst/www/plot-none.svg |only inst/www/style.css |only man/hgd.Rd | 8 man/hgd_browse.Rd | 6 man/hgd_clear.Rd | 2 man/hgd_close.Rd | 5 man/hgd_id.Rd |only man/hgd_inline.Rd | 10 man/hgd_remove.Rd | 8 man/hgd_state.Rd | 4 man/hgd_svg.Rd | 16 man/hgd_url.Rd | 23 src/DrawData.cpp | 860 +++++++--------- src/DrawData.h | 330 +++--- src/Httpgd.cpp | 93 + src/HttpgdApi.h | 12 src/HttpgdApiAsync.cpp | 30 src/HttpgdApiAsync.h | 9 src/HttpgdCommons.h | 20 src/HttpgdDataStore.cpp | 175 ++- src/HttpgdDataStore.h | 63 - src/HttpgdDev.cpp | 198 ++- src/HttpgdDev.h | 16 src/HttpgdGeom.h |only src/HttpgdWebServer.cpp | 200 ++- src/HttpgdWebServer.h | 1 src/Makevars.win | 2 src/cpp11.cpp | 38 src/devGeneric.cpp | 8 src/lib/fmt/core.h | 448 ++++++-- src/lib/fmt/format-inl.h | 1896 +++++++++++++++++++++++++++++++------ src/lib/fmt/format.h | 1157 +++++++++++++--------- src/lib/fmt/ostream.h | 28 src/lib/svglite_utils.h | 54 - tests/testthat/test-svglite-rect.R | 6 vignettes |only 47 files changed, 4728 insertions(+), 2394 deletions(-)
Title: Interactive Genomic Visualization of Biological Data
Description: Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions
of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces
a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data
associated with chromosome elements (like gene expression) in the form of heat colors which can be highly
advantageous in the scientific interpretations and research work. Because of the large size of the chromosomes,
it is impractical to visualize each element on the same plot. However, the plot provides a magnified view for each
of chromosome locus to render additional information and visualization specific for that location. You can map
thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings
(like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the
chromosome at a location showing each mapped element in sequential order. The package provide multiple features
like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling.
The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R 'Shiny' applications.
Author: Lakshay Anand [aut, cre]
Maintainer: Lakshay Anand <lakshayanand15@gmail.com>
Diff between chromoMap versions 0.3 dated 2021-01-13 and 0.3.1 dated 2021-04-01
DESCRIPTION | 6 MD5 | 29 NAMESPACE | 2 R/chromoMap.R | 390 +++++-- inst/doc/chromoMap.R | 254 ++++ inst/doc/chromoMap.Rmd | 395 +++++++ inst/doc/chromoMap.html | 1111 ++++++++++++++++++-- inst/htmlwidgets/chromoMap.js | 10 inst/htmlwidgets/lib/chromoMap-3.0/chromoMap-3.0.js | 630 +++++++++++ man/chromoMap.Rd | 52 vignettes/chromoMap.Rmd | 395 +++++++ vignettes/data/ANNO_DATA_FOR_CATSCATTER.txt |only vignettes/data/SLINK22.csv |only vignettes/data/SLINK_anno.txt |only vignettes/data/SLINK_chr.txt |only vignettes/data/SLINK_link1.csv |only vignettes/data/SLINK_link2.csv |only vignettes/data/TEST_LINKSSS.csv |only vignettes/data/TEST_anno.txt |only vignettes/data/TEST_chr.txt |only 20 files changed, 3052 insertions(+), 222 deletions(-)
Title: Origin Estimation for Propagation Processes on Complex Networks
Description: Performs network-based source estimation. Different approaches are available: effective distance median, recursive backtracking, and centrality-based source estimation. Additionally, we provide public transportation network data as well as methods for data preparation, source estimation performance analysis and visualization.
Author: Juliane Manitz [aut, cre],
Jonas Harbering [ctb],
Jun Li [ctb]
Maintainer: Juliane Manitz <r@manitz.org>
Diff between NetOrigin versions 1.0-3 dated 2018-04-19 and 1.1-2 dated 2021-04-01
NetOrigin-1.0-3/NetOrigin/man/plot.Rd |only NetOrigin-1.1-2/NetOrigin/DESCRIPTION | 24 NetOrigin-1.1-2/NetOrigin/MD5 | 60 NetOrigin-1.1-2/NetOrigin/NAMESPACE | 83 - NetOrigin-1.1-2/NetOrigin/R/0_helper_net.r | 192 +- NetOrigin-1.1-2/NetOrigin/R/NetOrigin.r | 40 NetOrigin-1.1-2/NetOrigin/R/compute_mu_lambda.R |only NetOrigin-1.1-2/NetOrigin/R/data.r | 256 +-- NetOrigin-1.1-2/NetOrigin/R/data_handling.r | 144 - NetOrigin-1.1-2/NetOrigin/R/distance.r | 276 +-- NetOrigin-1.1-2/NetOrigin/R/initial_condition_sib_model.R |only NetOrigin-1.1-2/NetOrigin/R/origin_helper.r | 626 ++++--- NetOrigin-1.1-2/NetOrigin/R/origin_methods.r | 862 ++++++----- NetOrigin-1.1-2/NetOrigin/R/robustness.r | 274 +-- NetOrigin-1.1-2/NetOrigin/R/stochastic_sib_model.R |only NetOrigin-1.1-2/NetOrigin/README.md |only NetOrigin-1.1-2/NetOrigin/man/NetOrigin.Rd | 48 NetOrigin-1.1-2/NetOrigin/man/aggr_data.Rd | 51 NetOrigin-1.1-2/NetOrigin/man/analyze_ptn.Rd | 91 - NetOrigin-1.1-2/NetOrigin/man/compute_mu_lambda.Rd |only NetOrigin-1.1-2/NetOrigin/man/delay-data.Rd | 131 - NetOrigin-1.1-2/NetOrigin/man/eff_dist.Rd | 106 - NetOrigin-1.1-2/NetOrigin/man/initial_condition_sib_model.Rd |only NetOrigin-1.1-2/NetOrigin/man/origin-methods.Rd | 127 - NetOrigin-1.1-2/NetOrigin/man/origin.Rd | 305 ++- NetOrigin-1.1-2/NetOrigin/man/origin_multiple.Rd | 104 - NetOrigin-1.1-2/NetOrigin/man/performance.Rd | 39 NetOrigin-1.1-2/NetOrigin/man/plot_performance.Rd | 148 - NetOrigin-1.1-2/NetOrigin/man/plot_ptn.Rd | 76 NetOrigin-1.1-2/NetOrigin/man/ptn-data.Rd | 95 - NetOrigin-1.1-2/NetOrigin/man/read_DB_data.Rd | 43 NetOrigin-1.1-2/NetOrigin/man/robustness-methods.Rd | 71 NetOrigin-1.1-2/NetOrigin/man/robustness.Rd | 124 - NetOrigin-1.1-2/NetOrigin/man/stochastic_sib_model.Rd |only NetOrigin-1.1-2/NetOrigin/man/var_wtd_mean_cochran.Rd | 53 35 files changed, 2316 insertions(+), 2133 deletions(-)
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Ziyu Tao [aut] (<https://orcid.org/0000-0003-3272-1227>),
Huimin Li [aut] (<https://orcid.org/0000-0003-1683-9057>),
Tao Wu [aut] (<https://orcid.org/0000-0002-8999-9628>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 1.2.5 dated 2021-02-19 and 2.0.0 dated 2021-04-01
sigminer-1.2.5/sigminer/R/CN-mutex-classification-methed.R |only sigminer-1.2.5/sigminer/R/get_tidy_parameter.R |only sigminer-1.2.5/sigminer/R/helper_calc_sum_of_events.R |only sigminer-1.2.5/sigminer/R/helper_fit_cn_components.R |only sigminer-1.2.5/sigminer/R/show_sig_number_survey.R |only sigminer-1.2.5/sigminer/R/show_sig_number_survey2.R |only sigminer-1.2.5/sigminer/man/get_tidy_parameter.Rd |only sigminer-1.2.5/sigminer/man/show_sig_number_survey.Rd |only sigminer-1.2.5/sigminer/man/show_sig_number_survey2.Rd |only sigminer-2.0.0/sigminer/DESCRIPTION | 29 - sigminer-2.0.0/sigminer/MD5 | 125 ++-- sigminer-2.0.0/sigminer/NAMESPACE | 3 sigminer-2.0.0/sigminer/NEWS.md | 35 + sigminer-2.0.0/sigminer/R/CN-mutex-classification-method.R |only sigminer-2.0.0/sigminer/R/best_practice.R | 30 - sigminer-2.0.0/sigminer/R/generate_matrices.R | 2 sigminer-2.0.0/sigminer/R/get.R | 196 ------- sigminer-2.0.0/sigminer/R/get_reconstructed_similarity.R | 45 + sigminer-2.0.0/sigminer/R/get_shannon_diversity_index.R | 3 sigminer-2.0.0/sigminer/R/get_sig_cancer_type_index.R | 12 sigminer-2.0.0/sigminer/R/get_sig_db.R | 54 ++ sigminer-2.0.0/sigminer/R/get_sig_feature_association.R | 2 sigminer-2.0.0/sigminer/R/get_sig_similarity.R | 10 sigminer-2.0.0/sigminer/R/get_sv.R | 130 ++--- sigminer-2.0.0/sigminer/R/group_enrichment.R | 1 sigminer-2.0.0/sigminer/R/helper_normalize_by_feature.R | 66 -- sigminer-2.0.0/sigminer/R/output.R | 9 sigminer-2.0.0/sigminer/R/read_vcf.R | 27 - sigminer-2.0.0/sigminer/R/show_catalogue.R | 21 sigminer-2.0.0/sigminer/R/show_cn_components.R | 234 +-------- sigminer-2.0.0/sigminer/R/show_cn_features.R | 129 ---- sigminer-2.0.0/sigminer/R/show_cn_group_profile.R | 6 sigminer-2.0.0/sigminer/R/show_group_enrichment.R | 83 ++- sigminer-2.0.0/sigminer/R/show_sig_profile.R | 103 --- sigminer-2.0.0/sigminer/R/show_sig_profile_heatmap.R | 2 sigminer-2.0.0/sigminer/R/sig_estimate.R | 260 +++++++++- sigminer-2.0.0/sigminer/R/sig_fit.R | 13 sigminer-2.0.0/sigminer/R/sig_tally.R | 115 ---- sigminer-2.0.0/sigminer/R/sigminer.R | 1 sigminer-2.0.0/sigminer/R/utils.R | 21 sigminer-2.0.0/sigminer/R/zzz.R | 2 sigminer-2.0.0/sigminer/README.md | 9 sigminer-2.0.0/sigminer/build/partial.rdb |binary sigminer-2.0.0/sigminer/inst/doc/sigminer.html | 45 + sigminer-2.0.0/sigminer/inst/extdata/e1.RData |only sigminer-2.0.0/sigminer/inst/extdata/toy_copynumber_tally_M.RData |binary sigminer-2.0.0/sigminer/man/bp.Rd | 20 sigminer-2.0.0/sigminer/man/figures/README-unnamed-chunk-1-1.png |binary sigminer-2.0.0/sigminer/man/figures/README-unnamed-chunk-2-1.png |binary sigminer-2.0.0/sigminer/man/figures/README-unnamed-chunk-3-1.png |binary sigminer-2.0.0/sigminer/man/figures/README-unnamed-chunk-4-1.png |binary sigminer-2.0.0/sigminer/man/figures/README-unnamed-chunk-5-1.png |binary sigminer-2.0.0/sigminer/man/figures/README-unnamed-chunk-8-1.png |binary sigminer-2.0.0/sigminer/man/get_sig_db.Rd | 3 sigminer-2.0.0/sigminer/man/get_sig_feature_association.Rd | 4 sigminer-2.0.0/sigminer/man/get_sig_rec_similarity.Rd | 2 sigminer-2.0.0/sigminer/man/get_sig_similarity.Rd | 7 sigminer-2.0.0/sigminer/man/read_sv_as_rs.Rd | 14 sigminer-2.0.0/sigminer/man/read_vcf.Rd | 7 sigminer-2.0.0/sigminer/man/show_catalogue.Rd | 11 sigminer-2.0.0/sigminer/man/show_cn_components.Rd | 30 - sigminer-2.0.0/sigminer/man/show_cn_features.Rd | 16 sigminer-2.0.0/sigminer/man/show_cosmic_sig_profile.Rd | 3 sigminer-2.0.0/sigminer/man/show_group_enrichment.Rd | 15 sigminer-2.0.0/sigminer/man/show_sig_profile.Rd | 37 - sigminer-2.0.0/sigminer/man/sig_estimate.Rd | 134 ++++- sigminer-2.0.0/sigminer/man/sig_fit.Rd | 7 sigminer-2.0.0/sigminer/man/sig_fit_bootstrap.Rd | 3 sigminer-2.0.0/sigminer/man/sig_tally.Rd | 59 -- 69 files changed, 1047 insertions(+), 1148 deletions(-)
Title: Reading Annual Financial Reports from Bovespa's DFP, FRE and FCA
System
Description: Reads annual financial reports including assets, liabilities, dividends history, stockholder composition and much more from Bovespa's DFP, FRE and FCA systems <http://www.b3.com.br/pt_br/produtos-e-servicos/negociacao/renda-variavel/empresas-listadas.htm>.
These are web based interfaces for all financial reports of companies traded at Bovespa. The package is specially designed for large scale data importation, keeping a tabular (long) structure for easier processing.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetDFPData versions 1.5.3 dated 2020-05-18 and 1.6 dated 2021-04-01
DESCRIPTION | 16 - MD5 | 16 - NEWS.md | 5 R/gdfpd_utils.R | 18 + README.md | 11 - build/vignette.rds |binary inst/doc/gdfpd-vignette-introduction.Rmd | 8 inst/doc/gdfpd-vignette-introduction.html | 306 +++++++----------------------- vignettes/gdfpd-vignette-introduction.Rmd | 8 9 files changed, 129 insertions(+), 259 deletions(-)
Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor
(Pya and Wood, 2015) <doi:10.1007/s11222-013-9448-7>.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of gam()
in package 'mgcv' are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-10 dated 2021-02-01 and 1.2-11 dated 2021-04-01
ChangeLog | 13 DESCRIPTION | 8 MD5 | 52 - NAMESPACE | 32 + R/bfgs.r | 4 R/estimate.scam.R | 2 R/plot.r | 19 R/print.scam.R | 1 R/scam.r | 28 - R/summary.scam.R | 143 ++--- R/uni.smooth.const-with-po.r | 840 ++++++++++++++++++++++++++++++- build/partial.rdb |binary man/Predict.matrix.mpi.smooth.Rd | 16 man/linear.functional.terms.Rd | 42 + man/plot.scam.Rd | 6 man/predict.scam.Rd | 14 man/scam.Rd | 117 +--- man/smooth.construct.cv.smooth.spec.rd | 79 ++ man/smooth.construct.cx.smooth.spec.Rd | 113 ++-- man/smooth.construct.mdcv.smooth.spec.Rd | 45 + man/smooth.construct.mdcx.smooth.spec.Rd | 47 + man/smooth.construct.micv.smooth.spec.Rd | 52 + man/smooth.construct.micx.smooth.spec.Rd | 56 +- man/smooth.construct.mpd.smooth.spec.Rd | 86 ++- man/smooth.construct.mpi.smooth.spec.Rd | 102 +++ man/summary.scam.Rd | 4 man/vis.scam.Rd | 13 27 files changed, 1567 insertions(+), 367 deletions(-)
Title: Utilities for Handling Strings and Text
Description: Utilities for handling character vectors
that store human-readable text (either plain or with
markup, such as HTML or LaTeX). The package provides,
in particular, functions that help with the
preparation of plain-text reports, e.g. for expanding
and aligning strings that form the lines of such
reports. The package also provides generic functions for
transforming R objects to HTML and to plain text.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between textutils versions 0.2-0 dated 2020-01-07 and 0.2-1 dated 2021-04-01
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ NAMESPACE | 1 + NEWS | 16 ++++++++++++++++ R/functions.R | 27 +++++++++++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/btable.pdf |binary inst/tinytest/test_HTMLdecode.R | 9 +++++++++ inst/tinytest/test_toHTML.R |only man/btable.Rd | 2 +- man/dctable.Rd | 2 +- man/toHTML.Rd | 7 ++++++- man/toText.Rd | 6 +++--- 14 files changed, 75 insertions(+), 28 deletions(-)
Title: Sign-Simplicity-Regression-Solver
Description: Implementation of the SSR-Algorithm. The Sign-Simplicity-Regression model is a nonparametric statistical model which is based on residual signs and simplicity assumptions on the regression function. Goal is to calculate the most parsimonious regression function satisfying the statistical adequacy requirements. Theory and functions are specified in Metzner (2020, ISBN: 979-8-68239-420-3, "Trendbasierte Prognostik") and Metzner (2021, ISBN: 979-8-59347-027-0, "Adäquates Maschinelles Lernen").
Author: Lars Metzner [aut, cre]
Maintainer: Lars Metzner <lars.metzner@ppi.de>
Diff between sisireg versions 0.8.1 dated 2021-01-25 and 0.9.0 dated 2021-04-01
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++----- NAMESPACE | 2 +- R/ssrMLP.R |only man/psvalid.Rd | 3 ++- man/runvalid.Rd | 3 ++- man/ssr.Rd | 11 +++++++---- man/ssrmlp_predict.Rd |only man/ssrmlp_train.Rd |only 9 files changed, 24 insertions(+), 16 deletions(-)
Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the first and
the second edition of "Numerical Methods and Optimization
in Finance" by M. Gilli, D. Maringer and E. Schumann
(2019, ISBN:978-0128150658). The package provides
implementations of optimisation heuristics (Differential
Evolution, Genetic Algorithms, Particle Swarm
Optimisation, Simulated Annealing and Threshold
Accepting), and other optimisation tools, such as grid
search and greedy search. There are also functions for
the valuation of financial instruments such as bonds and
options, for portfolio selection and functions that help
with stochastic simulations.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between NMOF versions 2.3-1 dated 2021-01-19 and 2.4-0 dated 2021-04-01
DESCRIPTION | 8 +-- MD5 | 50 ++++++++++--------- NEWS | 16 ++++++ R/callHestoncf.R | 10 +-- R/market_data.R | 96 ++++++++++++++++++++++++++++--------- R/portfolio.R | 29 +++++++++++ R/randomReturns.R | 9 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/An_overview.pdf |binary inst/doc/DEnss.pdf |binary inst/doc/LSqueens.pdf |binary inst/doc/LSselect.pdf |binary inst/doc/PSlms.pdf |binary inst/doc/TAportfolio.pdf |binary inst/doc/portfolio.pdf |binary inst/doc/qTableEx.pdf |binary inst/doc/repair.pdf |binary inst/doc/vectorise.pdf |binary inst/tinytest/test_French.R |only inst/tinytest/test_portfolio.R | 58 ++++++++++++++++++++-- inst/tinytest/test_randomReturns.R |only inst/unitTests/runTests.R | 2 inst/unitTests/test_results.txt | 38 ++++++++------ man/callHestoncf.Rd | 7 +- man/randomReturns.Rd | 5 + man/xtContractValue.Rd | 2 27 files changed, 248 insertions(+), 82 deletions(-)
Title: Utilities for Dates and Times
Description: Utilities for handling dates and times, such
as selecting particular days of the week or month,
formatting timestamps as required by RSS feeds, or
converting timestamp representations of other software
(such as 'MATLAB' and 'Excel') to R. The package is
lightweight (no dependencies, pure R implementations) and
relies only on R's standard classes to represent dates
and times ('Date' and 'POSIXt'); it aims to provide
efficient implementations, through vectorisation and the
use of R's native numeric representations of timestamps
where possible.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>),
Unicode, Inc. [dtc, cph] (source of timezone names in 'tznames')
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between datetimeutils versions 0.4-0 dated 2020-03-25 and 0.5-0 dated 2021-04-01
datetimeutils-0.4-0/datetimeutils/inst/unitTests |only datetimeutils-0.5-0/datetimeutils/DESCRIPTION | 9 - datetimeutils-0.5-0/datetimeutils/MD5 | 31 +-- datetimeutils-0.5-0/datetimeutils/NEWS | 16 + datetimeutils-0.5-0/datetimeutils/R/functions.R | 84 +++++++--- datetimeutils-0.5-0/datetimeutils/build/partial.rdb |binary datetimeutils-0.5-0/datetimeutils/build/vignette.rds |binary datetimeutils-0.5-0/datetimeutils/data/tznames.RData |binary datetimeutils-0.5-0/datetimeutils/inst/doc/datetimeutils_examples.R | 2 datetimeutils-0.5-0/datetimeutils/inst/doc/datetimeutils_examples.Rnw | 16 - datetimeutils-0.5-0/datetimeutils/inst/doc/datetimeutils_examples.pdf |binary datetimeutils-0.5-0/datetimeutils/inst/tinytest |only datetimeutils-0.5-0/datetimeutils/man/convertDate.Rd | 10 - datetimeutils-0.5-0/datetimeutils/man/guess_datetime.Rd | 41 +++- datetimeutils-0.5-0/datetimeutils/man/rfc822t.Rd | 4 datetimeutils-0.5-0/datetimeutils/tests |only datetimeutils-0.5-0/datetimeutils/vignettes/datetimeutils_examples.Rnw | 16 - 17 files changed, 151 insertions(+), 78 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Mattan S. Ben-Shachar [aut, ctb]
(<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.13.1 dated 2021-02-22 and 0.13.2 dated 2021-04-01
DESCRIPTION | 14 MD5 | 209 +++++---- NAMESPACE | 72 +++ NEWS.md | 461 ++------------------- R/clean_names.R | 32 + R/clean_parameters.R | 56 +- R/colour_tools.R | 16 R/compute_variances.R | 125 ++++- R/display.R | 2 R/ellipsis_info.R | 40 - R/export_table.R | 24 + R/find_formula.R | 85 +++ R/find_interactions.R | 18 R/find_parameter_zi.R | 52 ++ R/find_parameters.R | 78 --- R/find_parameters_emmeans.R |only R/find_parameters_other.R | 82 +++ R/find_predictors.R | 5 R/find_response.R | 86 +++ R/find_statistic.R | 11 R/find_weights.R | 6 R/format_p.R | 31 + R/format_table.R | 202 ++++++--- R/format_value.R | 49 +- R/get_auxiliary.R | 5 R/get_call.R | 6 R/get_data.R | 35 + R/get_deviance.R | 10 R/get_df.R | 6 R/get_family.R |only R/get_loglikelihood.R | 50 +- R/get_parameters.R | 50 ++ R/get_parameters_bayesian.R | 16 R/get_parameters_emmeans.R | 17 R/get_parameters_mixed.R | 8 R/get_parameters_others.R | 32 + R/get_parameters_zi.R | 73 +++ R/get_predicted.R | 696 ++++++++++++++------------------ R/get_predicted_ci.R |only R/get_predicted_methods.R |only R/get_priors.R | 56 ++ R/get_residuals.R | 9 R/get_sigma.R | 9 R/get_statistic.R | 171 +++++++ R/get_varcov.R | 28 + R/get_variances.R | 23 - R/get_weights.R | 4 R/helper_functions.R | 101 ++++ R/is_gam_model.R |only R/is_model.R | 347 ++++----------- R/is_model_supported.R | 113 +---- R/link_function.R | 9 R/link_inverse.R | 8 R/model_info.R | 29 + R/n_obs.R | 35 + R/n_parameters.R | 7 R/print_color.R | 40 + R/print_parameters.R | 102 +++- R/reshape_ci.R |only R/utils_model_info.R | 20 README.md | 40 - build/partial.rdb |binary inst/WORDLIST | 9 inst/doc/display.R | 8 inst/doc/display.Rmd | 36 - inst/doc/display.html | 290 +++++-------- man/display.Rd | 6 man/ellipsis_info.Rd | 24 - man/export_table.Rd | 30 - man/find_interactions.Rd | 104 ++-- man/find_parameters.Rd | 1 man/find_parameters.averaging.Rd | 146 +++--- man/find_parameters.emmGrid.Rd |only man/find_parameters.zeroinfl.Rd | 114 ++--- man/find_response.Rd | 68 +-- man/format_ci.Rd | 7 man/format_p.Rd | 11 man/format_rope.Rd | 7 man/format_table.Rd | 182 ++++---- man/format_value.Rd | 34 + man/get_family.Rd |only man/get_parameters.betareg.Rd | 123 ++--- man/get_parameters.emmGrid.Rd | 90 ++-- man/get_parameters.glmm.Rd | 122 ++--- man/get_parameters.zeroinfl.Rd | 98 ++-- man/get_predicted.Rd | 104 +--- man/get_predicted_ci.Rd |only man/get_sigma.Rd | 98 ++-- man/get_statistic.Rd | 3 man/is_gam_model.Rd |only man/model_info.Rd | 1 man/n_parameters.Rd | 178 ++++---- man/print_color.Rd | 79 ++- man/print_parameters.Rd | 226 +++++----- man/reshape_ci.Rd |only tests/testthat/test-BayesFactorBF.R | 27 - tests/testthat/test-Gam2.R | 5 tests/testthat/test-brms.R | 24 - tests/testthat/test-fixest.R | 9 tests/testthat/test-gamm4.R | 4 tests/testthat/test-get_loglikelihood.R | 13 tests/testthat/test-get_predicted.R | 353 ++++++++++------ tests/testthat/test-get_variance.R | 53 +- tests/testthat/test-lme.R | 2 tests/testthat/test-lmer.R | 3 tests/testthat/test-metaBMA.R | 4 tests/testthat/test-model_data.R | 15 tests/testthat/test-panelr.R | 20 tests/testthat/test-standardize_names.R | 6 tests/testthat/test-tidymodels.R | 5 vignettes/display.Rmd | 36 - 111 files changed, 3829 insertions(+), 2860 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-17 1.2.3
2021-02-15 1.2.2
2020-12-17 1.2.1
2020-11-04 1.2
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Author: Niels Waller [aut, cre],
Jeff Jones [ctb],
Casey Giordano [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 1.96.3 dated 2020-06-03 and 1.97 dated 2021-04-01
DESCRIPTION | 11 +-- MD5 | 78 +++++++++++++------------ NAMESPACE | 1 R/eigGen.R | 7 +- R/faAlign.R | 56 +++++++++++++++--- R/faLocalMin.R |only R/faMain.R | 16 ++--- R/fungibleExtrema.R | 150 ++++++++++++++++++++++++++++++++++--------------- R/rGivens.R | 5 + R/rMAP.R | 15 +++- R/simFA.R | 22 ++++--- R/summary.faMain.R | 7 +- R/tetcor.R | 4 - inst/CITATION | 8 +- man/BiFAD.Rd | 1 man/Box26.Rd | 1 man/GenerateBoxData.Rd | 1 man/Ledermann.Rd | 1 man/SLi.Rd | 1 man/SchmidLeiman.Rd | 1 man/faAlign.Rd | 1 man/faEKC.Rd | 1 man/faIB.Rd | 1 man/faLocalMin.Rd |only man/faMB.Rd | 1 man/faMain.Rd | 1 man/faScores.Rd | 1 man/faSort.Rd | 1 man/faStandardize.Rd | 1 man/faX.Rd | 1 man/fals.Rd | 1 man/fapa.Rd | 1 man/fareg.Rd | 1 man/fungibleExtrema.Rd | 69 +++++++++++++++++----- man/orderFactors.Rd | 1 man/print.faMB.Rd | 1 man/print.faMain.Rd | 1 man/promaxQ.Rd | 1 man/simFA.Rd | 15 ++-- man/summary.faMB.Rd | 1 man/summary.faMain.Rd | 4 - 41 files changed, 342 insertions(+), 149 deletions(-)
Title: Data-Limited Methods Toolkit
Description: A collection of data-limited management procedures that can be evaluated
with management strategy evaluation with the 'MSEtool' package, or applied to
fishery data to provide management recommendations.
Author: Tom Carruthers [aut],
Quang Huynh [aut],
Adrian Hordyk [aut, cre],
M. Bryan [ctb],
HF. Geremont [ctb],
C. Grandin [ctb],
W. Harford [ctb],
Q. Huynh [ctb],
C. Walters [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between DLMtool versions 6.0.0 dated 2021-01-13 and 6.0.1 dated 2021-04-01
DESCRIPTION | 9 - MD5 | 141 ++++++++++---------- NEWS.md | 6 R/MPs_Input.R | 138 ++++++++++++-------- README.md | 38 +++-- man/AvC.Rd | 122 ++++++++--------- man/AvC_MLL.Rd | 124 +++++++++--------- man/BK.Rd | 228 ++++++++++++++++----------------- man/CC.Rd | 52 +++---- man/CC1.Rd | 214 +++++++++++++++---------------- man/CompSRA.Rd | 150 +++++++++++----------- man/CompSRA_.Rd | 44 +++--- man/DBSRA.Rd | 224 ++++++++++++++++---------------- man/DBSRA_.Rd | 48 +++---- man/DBSRAopt.Rd | 62 ++++----- man/DCAC.Rd | 354 ++++++++++++++++++++++++++-------------------------- man/DCAC_.Rd | 52 +++---- man/DD.Rd | 174 ++++++++++++------------- man/DD_.Rd | 44 +++--- man/DD_R.Rd | 94 ++++++------- man/DDe.Rd | 166 ++++++++++++------------ man/DTe40.Rd | 132 +++++++++---------- man/DynF.Rd | 168 ++++++++++++------------ man/EtargetLopt.Rd | 120 ++++++++--------- man/Fadapt.Rd | 210 +++++++++++++++--------------- man/Fdem.Rd | 174 ++++++++++++------------- man/Fdem_.Rd | 42 +++--- man/FilterSmooth.Rd | 48 +++---- man/Fratio.Rd | 244 +++++++++++++++++------------------ man/Fratio_.Rd | 42 +++--- man/GB_CC.Rd | 140 ++++++++++---------- man/GB_slope.Rd | 164 ++++++++++++------------ man/GB_target.Rd | 176 ++++++++++++------------- man/Gcontrol.Rd | 172 ++++++++++++------------- man/ICI.Rd | 200 ++++++++++++++--------------- man/IT5.Rd | 154 +++++++++++----------- man/ITM.Rd | 106 +++++++-------- man/IT_.Rd | 56 ++++---- man/ITe5.Rd | 142 ++++++++++---------- man/Iratio.Rd | 152 +++++++++++----------- man/Islope1.Rd | 202 ++++++++++++++--------------- man/Islope_.Rd | 52 +++---- man/Itarget1.Rd | 226 ++++++++++++++++----------------- man/Itarget1_MPA.Rd | 176 ++++++++++++------------- man/ItargetE1.Rd | 210 +++++++++++++++--------------- man/Itarget_.Rd | 64 ++++----- man/Itargeteff_.Rd | 58 ++++---- man/LBSPR.Rd | 200 ++++++++++++++--------------- man/LBSPR_.Rd | 50 +++---- man/LBSPRgen.Rd | 130 +++++++++---------- man/Lratio_BHI.Rd | 198 ++++++++++++++--------------- man/LstepCC1.Rd | 306 ++++++++++++++++++++++---------------------- man/LstepCE1.Rd | 210 +++++++++++++++--------------- man/Ltarget1.Rd | 266 +++++++++++++++++++-------------------- man/LtargetE1.Rd | 180 +++++++++++++------------- man/MCD.Rd | 138 ++++++++++---------- man/MRreal.Rd | 122 ++++++++--------- man/Rcontrol.Rd | 216 +++++++++++++++---------------- man/SBT1.Rd | 238 +++++++++++++++++----------------- man/SPMSY.Rd | 150 +++++++++++----------- man/SPSRA.Rd | 168 ++++++++++++------------ man/SPSRA_.Rd | 84 ++++++------ man/SPmod.Rd | 162 +++++++++++------------ man/SPslope.Rd | 186 +++++++++++++-------------- man/YPR.Rd | 184 +++++++++++++-------------- man/YPR_.Rd | 96 +++++++------- man/curE.Rd | 122 ++++++++--------- man/demographic2.Rd | 86 ++++++------ man/figures |only man/getr.Rd | 62 ++++----- man/iVB.Rd | 42 +++--- man/matlenlim.Rd | 230 ++++++++++++++++----------------- 72 files changed, 4993 insertions(+), 4947 deletions(-)