Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery
and replicability rates on the bases of test-statistics of published studies. The package
provides functions for fitting the new density and EM version
(Bartoš & Schimmack, 2020, <doi:10.31234/osf.io/urgtn>) as well as the original density
z-curve (Brunner & Schimmack, 2017, <doi:10.31219/osf.io/wr93f>). Furthermore, the package
provides summarizing and plotting functions for the fitted z-curve objects. See the
aforementioned articles for more information about the z-curves, expected discovery
and replicability rates, validation studies, and limitations.
Author: František Bartoš [aut, cre],
Ulrich Schimmack [aut]
Maintainer: František Bartoš <f.bartos96@gmail.com>
Diff between zcurve versions 1.0.0 dated 2020-03-31 and 1.0.6 dated 2020-09-26
DESCRIPTION | 8 - MD5 | 37 +++--- NAMESPACE | 15 ++ R/main.R | 80 ++++++++------ R/tools.R | 239 ++++++++++++++++++++++++++++++++++++++++-- R/zcurve_EM.R | 40 +++---- R/zcurve_density.R | 80 +++++++------- README.md | 9 + build/partial.rdb |binary inst/CITATION | 2 man/OSC.z.Rd | 4 man/control_EM.Rd | 2 man/control_density.Rd | 2 man/control_density_v1.Rd | 2 man/is.zcurve.Rd |only man/power_to_z.Rd | 9 - man/print.estimates.zcurve.Rd |only man/print.summary.zcurve.Rd | 36 +++--- man/print.zcurve.Rd | 36 +++--- man/z_to_power.Rd | 4 man/zcurve.estimates.Rd |only 21 files changed, 434 insertions(+), 171 deletions(-)
Title: Add Gate Information to Your Tibble
Description: It interactively or programmatically label points within custom gates on two dimensions.
The information is added to your tibble. It is based on the package 'gatepoints' from Wajid Jawaid.
The benefits are (i) in interactive mode you can draw your gates on extensive 'ggplot'-like scatter plots;
(ii) you can draw multiple gates; and (iii) you can save your gates and apply the programmatically.
Author: Stefano Mangiola [aut, cre],
Wajid Jawaid [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidygate versions 0.2.7 dated 2020-07-06 and 0.2.8 dated 2020-09-26
DESCRIPTION | 8 +++---- MD5 | 16 +++++++-------- NAMESPACE | 3 ++ R/functions.R | 47 ++++++++++++++++++++++++++++---------------- R/methods.R | 51 ++++++++++++++++++++++++++++++------------------ build/tidygate.pdf |binary build/vignette.rds |binary man/gate-methods.Rd | 13 ++++++++---- man/gate_interactive.Rd | 3 ++ 9 files changed, 89 insertions(+), 52 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 1.10.0 dated 2020-08-06 and 1.10.1 dated 2020-09-26
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 7 ++++++- R/Connection.R | 4 ++-- R/Options.R | 2 +- R/View.R | 4 ++-- inst/doc/getting_started.Rmd | 2 +- inst/doc/getting_started.html | 2 +- vignettes/getting_started.Rmd | 2 +- 9 files changed, 25 insertions(+), 20 deletions(-)
Title: Comfortable Search for R Packages on CRAN, Either Directly from
the R Console or with an R Studio Add-in
Description: Search for R packages on CRAN directly from the R console, based on the packages' titles, short and long descriptions, or other fields. Combine multiple keywords with logical operators ('and', 'or'), view detailed information on any package and keep track of the latest package contributions to CRAN. If you don't want to search from the R console, use the comfortable R Studio add-in.
Author: Joachim Zuckarelli [aut, cre] (<https://orcid.org/0000-0002-9280-3016>)
Maintainer: Joachim Zuckarelli <joachim@zuckarelli.de>
Diff between packagefinder versions 0.3.0 dated 2020-09-14 and 0.3.1 dated 2020-09-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/packagefinder.r | 10 ++++++---- README.md | 8 +++++++- 5 files changed, 29 insertions(+), 13 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations for a wide variety of models (see support list of insight; Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), used in the computation of marginal means, contrast analysis and predictions.
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between modelbased versions 0.1.2 dated 2020-03-12 and 0.3.0 dated 2020-09-26
DESCRIPTION | 15 - MD5 | 93 ++++---- NAMESPACE | 14 + NEWS.md | 23 ++ R/estimate_contrasts.bayesian.R | 54 +++-- R/estimate_contrasts.frequentist.R | 36 ++- R/estimate_means.bayesian.R | 58 ++--- R/estimate_means.frequentist.R | 30 +- R/estimate_response.bayesian.R | 37 ++- R/estimate_response.frequentist.R | 19 + R/estimate_slopes.R | 81 +++++-- R/estimate_smooth.R | 19 + R/print.R | 2 R/reshape_draws.R | 2 R/signal.R | 3 R/utils.R | 11 - R/utils_clean_names.R |only R/utils_emmeans_wrapper.R | 89 ++++---- R/utils_estimate_response_init.R | 1 R/utils_guess_arguments.R |only R/utils_predict_wrapper.R | 79 +++++-- R/visualisation_matrix.R | 33 ++- README.md | 90 ++++---- inst |only man/as.numeric_ifnumeric.Rd | 41 +-- man/dot-uniroot.all.Rd | 40 +-- man/estimate_contrasts.lm.Rd | 138 ++++++------ man/estimate_contrasts.stanreg.Rd | 197 +++++++++--------- man/estimate_means.lm.Rd | 121 +++++------ man/estimate_means.stanreg.Rd | 139 ++++++------ man/estimate_response.glm.Rd | 138 ++++++------ man/estimate_response.stanreg.Rd | 268 ++++++++++++------------- man/estimate_slopes.Rd | 100 +++++---- man/estimate_slopes.lm.Rd | 86 ++++---- man/estimate_slopes.stanreg.Rd | 146 ++++++------- man/estimate_smooth.Rd | 80 +++---- man/estimate_smooth.stanreg.Rd | 106 ++++----- man/figures/unnamed-chunk-13-1.png |binary man/figures/unnamed-chunk-5-1.png |binary man/figures/unnamed-chunk-8-1.png |binary man/find_inversions.Rd | 43 +--- tests/testthat/test-attributes_visualisation.R | 3 tests/testthat/test-estimate_contrasts.R | 141 +++++++++++-- tests/testthat/test-estimate_means.R | 146 ++++++++++++- tests/testthat/test-estimate_response.R | 55 +++-- tests/testthat/test-estimate_slopes.R | 27 +- tests/testthat/test-estimate_smooth.R | 11 - tests/testthat/test-glmmTMB.R |only tests/testthat/test-mgcv.R |only tests/testthat/test-visualisation_matrix.R | 4 50 files changed, 1658 insertions(+), 1161 deletions(-)
Title: Covariate-Adaptive Randomization for Clinical Trials
Description: Provides functions and command-line user interface to generate allocation sequence by covariate-adaptive randomization for clinical trials. The package currently supports six covariate-adaptive randomization procedures. Three hypothesis testing methods that are valid and robust under covariate-adaptive randomization are also available in the package to facilitate the inference for treatment effect under the included randomization procedures. Additionally, the package provides comprehensive and efficient tools to allow one to evaluate and compare the performance of randomization procedures and tests based on various criteria.
Author: Fuyi Tu [aut],
Xiaoqing Ye [aut, cre],
Wei Ma [aut, ths],
Feifang Hu [aut, ths]
Maintainer: Xiaoqing Ye <ye_xiaoq@163.com>
Diff between carat versions 1.3 dated 2020-09-08 and 1.4 dated 2020-09-26
carat-1.3/carat/R/class_plottest.R |only carat-1.3/carat/man/print.carandom.Rd |only carat-1.3/carat/src/All.cpp |only carat-1.4/carat/DESCRIPTION | 26 - carat-1.4/carat/MD5 | 51 +- carat-1.4/carat/NAMESPACE | 10 carat-1.4/carat/R/RcppExports.R | 602 ++++++++++++++++----------------- carat-1.4/carat/R/class_plotrandtest.R |only carat-1.4/carat/R/rand_CLI.R | 14 carat-1.4/carat/R/rand_evalRand.R | 1 carat-1.4/carat/R/test_Rfunction.R | 357 +++++++++---------- carat-1.4/carat/data/pats.rda |binary carat-1.4/carat/inst/NEWS.Rd | 17 carat-1.4/carat/man/AdjBCD.sim.Rd | 3 carat-1.4/carat/man/AdjBCD.ui.Rd | 3 carat-1.4/carat/man/DoptBCD.sim.Rd | 3 carat-1.4/carat/man/DoptBCD.ui.Rd | 3 carat-1.4/carat/man/HuHuCAR.sim.Rd | 3 carat-1.4/carat/man/HuHuCAR.ui.Rd | 3 carat-1.4/carat/man/PocSimMIN.sim.Rd | 3 carat-1.4/carat/man/PocSimMIN.ui.Rd | 3 carat-1.4/carat/man/StrBCD.sim.Rd | 3 carat-1.4/carat/man/StrBCD.ui.Rd | 3 carat-1.4/carat/man/StrPBR.sim.Rd | 3 carat-1.4/carat/man/StrPBR.ui.Rd | 3 carat-1.4/carat/man/carat-package.Rd | 78 ++-- carat-1.4/carat/src/InnerFun.cpp |only carat-1.4/carat/src/Makevars | 5 carat-1.4/carat/src/RcppExports.cpp | 12 29 files changed, 609 insertions(+), 600 deletions(-)
Title: Software for Project AERO
Description: Implements methods for anticipating the emergence and eradication
of infectious diseases from surveillance time series. Also provides support
for computational experiments testing the performance of such methods.
Author: Eamon O'Dea [aut, cre]
Maintainer: Eamon O'Dea <odea35@gmail.com>
Diff between spaero versions 0.5.0 dated 2019-05-24 and 0.6.0 dated 2020-09-26
DESCRIPTION | 12 ++++---- MD5 | 16 +++++------ NEWS.md | 5 +++ R/simulation.R | 54 +++++++++------------------------------ README.md | 3 -- build/vignette.rds |binary inst/doc/spaero-introduction.pdf |binary man/create_simulator.Rd | 14 +++++----- man/get_stats.Rd | 15 +++++++--- 9 files changed, 52 insertions(+), 67 deletions(-)
Title: Methods and Measures for Semantic Network Analysis
Description: Implements several functions for the analysis of semantic networks including different network estimation algorithms, partial node bootstrapping (Kenett, Anaki, & Faust, 2014 <doi:10.3389/fnhum.2014.00407>), random walk simulation (Kenett & Austerweil, 2016 <http://alab.psych.wisc.edu/papers/files/Kenett16CreativityRW.pdf>), and a function to compute global network measures. Significance tests and plotting features are also implemented.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>),
Yoed N. Kenett [aut, ctb] (<https://orcid.org/0000-0003-3872-7689>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNeT versions 1.3.0 dated 2020-06-09 and 1.4.0 dated 2020-09-26
SemNeT-1.3.0/SemNeT/build |only SemNeT-1.3.0/SemNeT/inst/doc |only SemNeT-1.3.0/SemNeT/vignettes |only SemNeT-1.4.0/SemNeT/DESCRIPTION | 20 SemNeT-1.4.0/SemNeT/MD5 | 93 - SemNeT-1.4.0/SemNeT/NAMESPACE | 14 SemNeT-1.4.0/SemNeT/NEWS | 55 SemNeT-1.4.0/SemNeT/R/ASPL.R |only SemNeT-1.4.0/SemNeT/R/CC.R |only SemNeT-1.4.0/SemNeT/R/CN.R | 17 SemNeT-1.4.0/SemNeT/R/NRW.R | 10 SemNeT-1.4.0/SemNeT/R/PF.R | 109 - SemNeT-1.4.0/SemNeT/R/Q.R |only SemNeT-1.4.0/SemNeT/R/SemNeTShiny.R | 6 SemNeT-1.4.0/SemNeT/R/TMFG.R |only SemNeT-1.4.0/SemNeT/R/bootSemNeT.R | 219 ++- SemNeT-1.4.0/SemNeT/R/compare_nets.R | 20 SemNeT-1.4.0/SemNeT/R/convert2cytoscape.R | 8 SemNeT-1.4.0/SemNeT/R/convert2igraph.R |only SemNeT-1.4.0/SemNeT/R/equate.R | 5 SemNeT-1.4.0/SemNeT/R/methods.R | 6 SemNeT-1.4.0/SemNeT/R/permSemNeT.R |only SemNeT-1.4.0/SemNeT/R/plot.bootSemNeT.R | 2 SemNeT-1.4.0/SemNeT/R/randnet.test.R | 38 SemNeT-1.4.0/SemNeT/R/randwalk.R | 121 + SemNeT-1.4.0/SemNeT/R/semnetmeas.R | 13 SemNeT-1.4.0/SemNeT/R/test.bootSemNeT.R | 300 ++-- SemNeT-1.4.0/SemNeT/R/utils-SemNeT.R | 896 +++++++------- SemNeT-1.4.0/SemNeT/R/utils-SemNeTShiny.R | 1355 ++++++++++++--------- SemNeT-1.4.0/SemNeT/R/zzz.R | 5 SemNeT-1.4.0/SemNeT/data/open.clean.RData |binary SemNeT-1.4.0/SemNeT/data/two.result.RData |binary SemNeT-1.4.0/SemNeT/inst/Shiny/server.R | 1718 ++++++++++++++++++++++++--- SemNeT-1.4.0/SemNeT/inst/Shiny/ui.R | 279 +++- SemNeT-1.4.0/SemNeT/man/ASPL.Rd |only SemNeT-1.4.0/SemNeT/man/CC.Rd |only SemNeT-1.4.0/SemNeT/man/CN.Rd | 7 SemNeT-1.4.0/SemNeT/man/NRW.Rd | 2 SemNeT-1.4.0/SemNeT/man/PF.Rd | 8 SemNeT-1.4.0/SemNeT/man/Q.Rd |only SemNeT-1.4.0/SemNeT/man/SemNeTShiny.Rd | 6 SemNeT-1.4.0/SemNeT/man/TMFG.Rd |only SemNeT-1.4.0/SemNeT/man/bootSemNeT.Rd | 22 SemNeT-1.4.0/SemNeT/man/compare_nets.Rd | 6 SemNeT-1.4.0/SemNeT/man/convert2cytoscape.Rd | 8 SemNeT-1.4.0/SemNeT/man/convert2igraph.Rd |only SemNeT-1.4.0/SemNeT/man/equate.Rd | 3 SemNeT-1.4.0/SemNeT/man/plot.animateShiny.Rd |only SemNeT-1.4.0/SemNeT/man/plot.compareShiny.Rd | 6 SemNeT-1.4.0/SemNeT/man/randnet.test.Rd | 16 SemNeT-1.4.0/SemNeT/man/randwalk.Rd | 14 SemNeT-1.4.0/SemNeT/man/semnetmeas.Rd | 4 SemNeT-1.4.0/SemNeT/man/test.bootSemNeT.Rd | 38 53 files changed, 3870 insertions(+), 1579 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-20 0.1.4
Title: FDR Power
Description: This is a package for calculating two differing notions of power, or deriving sample
sizes for specified requisite power in multiple testing experiments under a variety of methods for
control of the distribution of the False Discovery Proportion (FDP). More specifically, one can
choose to control the FDP distribution according to control of its (i) mean, e.g. the usual BH-FDR
procedure, or via the probability that it exceeds a given value, delta, via (ii) the Romano
procedure, or via (iii) my procedure based upon asymptotic approximation. Likewise, we can think of
the power in multiple testing experiments in terms of a summary of the distribution of the
True Positive Proportion (TPP). The package will compute power, sample size or any other missing
parameter required for power based upon (i) the mean of the TPP which is the average power
(ii) the probability that the TPP exceeds a given value, lambda, via my asymptotic approximation
procedure. The theoretical results are described in Izmirlian, G. (2020) Stat. and Prob. letters,
<doi:10.1016/j.spl.2020.108713>, and an applied paper describing the methodology with a
simulation study is in preparation.
Author: Grant Izmirlian Jr <izmirlig@mail.nih.gov>
Maintainer: Grant Izmirlian Jr <izmirlig@mail.nih.gov>
Diff between pwrFDR versions 1.95 dated 2018-08-22 and 2.8.4 dated 2020-09-26
pwrFDR-1.95/pwrFDR/man/Ch02-controlFDF.Rd |only pwrFDR-1.95/pwrFDR/man/Ch03-dists.Rd |only pwrFDR-1.95/pwrFDR/man/Ch04-detail.Rd |only pwrFDR-1.95/pwrFDR/man/Ch05-cCDF.SoM.Rd |only pwrFDR-1.95/pwrFDR/man/Ch06-cCDF.ToJ.Rd |only pwrFDR-1.95/pwrFDR/man/Ch07-CDF.Pval.Rd |only pwrFDR-1.95/pwrFDR/man/Ch08-CDF.Pval.HA.Rd |only pwrFDR-1.95/pwrFDR/man/Ch09-var.J.o.rtm.Rd |only pwrFDR-1.95/pwrFDR/man/Ch10-var.rtm.SoM.Rd |only pwrFDR-1.95/pwrFDR/man/Ch11-var.rtm.ToJ.Rd |only pwrFDR-1.95/pwrFDR/man/Ch12-logit.Rd |only pwrFDR-1.95/pwrFDR/man/Ch13-logitInv.Rd |only pwrFDR-1.95/pwrFDR/man/Ch14-over.Rd |only pwrFDR-1.95/pwrFDR/man/Ch15-concat.Rd |only pwrFDR-1.95/pwrFDR/man/Ch16-gentempfilenm.Rd |only pwrFDR-2.8.4/pwrFDR/DESCRIPTION | 25 pwrFDR-2.8.4/pwrFDR/MD5 | 54 pwrFDR-2.8.4/pwrFDR/NAMESPACE | 11 pwrFDR-2.8.4/pwrFDR/R/pwrFDR.R | 2672 ++++++++++++----------- pwrFDR-2.8.4/pwrFDR/man/Ch01-pwrFDR.Rd | 463 ++- pwrFDR-2.8.4/pwrFDR/man/Ch02-pwrFDR-grid.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch03-controlFDP.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch04-dists.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch05-detail.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch06-cCDF-Rom.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch07-cCDF-ToM.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch08-cCDF-VoR.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch09-CDF-Pval.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch10-CDF-Pval-HA.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch11-sd-rtm-Rom.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch12-sd-rtm-ToM.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch13-sd-rtm-VoR.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch14-logit.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch15-logitInv.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch16-over.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch17-concat.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch18-gentempfilenm.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch19-CDF-Pval-ua-eq-u.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch20-CDF-Pval-ar-eq-u.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch21-cc-ROC.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch22-es-ROC.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch23-criterion.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch24-arg-vals.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch25-if-0-rm.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch26-if-na-x.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch27-if-y-z.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch28-nna.Rd |only pwrFDR-2.8.4/pwrFDR/src/pwrFDRsim.c | 115 pwrFDR-2.8.4/pwrFDR/src/pwrFDRsimCS.c | 103 49 files changed, 2012 insertions(+), 1431 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>),
Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>),
Jeff Farrell [ctb],
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb],
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>
Diff between Seurat versions 3.2.1 dated 2020-09-07 and 3.2.2 dated 2020-09-26
DESCRIPTION | 10 MD5 | 44 +-- NAMESPACE | 1 NEWS.md | 8 R/clustering.R | 6 R/dimensional_reduction.R | 18 - R/generics.R | 14 - R/integration.R | 408 ++++++++++++++++++------------------ R/objects.R | 18 - R/preprocessing.R | 10 R/utilities.R | 2 R/visualization.R | 32 +- README.md | 2 man/AddModuleScore.Rd | 2 man/FindIntegrationAnchors.Rd | 36 +-- man/FindTransferAnchors.Rd | 66 ++--- man/GetTransferPredictions.Rd | 6 man/IntegrateData.Rd | 62 ++--- man/PrepSCTIntegration.Rd | 22 - man/SelectIntegrationFeatures.Rd | 12 - man/TransferData.Rd | 42 +-- tests/testthat/test_objects.R | 15 - tests/testthat/test_preprocessing.R | 16 - 23 files changed, 435 insertions(+), 417 deletions(-)
Title: Dictionaries for the 'SemNetCleaner' Package
Description: Implements dictionaries that can be used in the 'SemNetCleaner' package. Also includes several functions aimed at facilitating the text cleaning analysis in the 'SemNetCleaner' package. This package is designed to integrate and update word lists and dictionaries based on each user's individual needs by allowing users to store and save their own dictionaries. Dictionaries can be added to the 'SemNetDictionaries' package by submitting user-defined dictionaries to <https://github.com/AlexChristensen/SemNetDictionaries>.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNetDictionaries versions 0.1.6 dated 2020-06-08 and 0.1.7 dated 2020-09-26
SemNetDictionaries-0.1.6/SemNetDictionaries/build |only SemNetDictionaries-0.1.6/SemNetDictionaries/inst/doc |only SemNetDictionaries-0.1.6/SemNetDictionaries/vignettes |only SemNetDictionaries-0.1.7/SemNetDictionaries/DESCRIPTION | 15 +++--- SemNetDictionaries-0.1.7/SemNetDictionaries/MD5 | 23 +++------- SemNetDictionaries-0.1.7/SemNetDictionaries/NEWS | 7 +++ SemNetDictionaries-0.1.7/SemNetDictionaries/R/append.dictionary.R | 18 +++---- SemNetDictionaries-0.1.7/SemNetDictionaries/R/find.dictionaries.R | 15 ++++-- SemNetDictionaries-0.1.7/SemNetDictionaries/R/load.dictionaries.R | 20 +++++--- SemNetDictionaries-0.1.7/SemNetDictionaries/R/zzz.R | 4 - SemNetDictionaries-0.1.7/SemNetDictionaries/man/find.dictionaries.Rd | 6 +- SemNetDictionaries-0.1.7/SemNetDictionaries/man/load.dictionaries.Rd | 10 +++- 12 files changed, 66 insertions(+), 52 deletions(-)
More information about SemNetDictionaries at CRAN
Permanent link
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2019) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.6.7 dated 2020-03-05 and 1.6.8 dated 2020-09-26
lava-1.6.7/lava/NEWS |only lava-1.6.7/lava/inst/doc/reference.pdf |only lava-1.6.7/lava/inst/gof1.png |only lava-1.6.7/lava/inst/lava1.png |only lava-1.6.7/lava/inst/me1.png |only lava-1.6.7/lava/inst/mediation1.png |only lava-1.6.7/lava/inst/mediation2.png |only lava-1.6.8/lava/DESCRIPTION | 25 +-- lava-1.6.8/lava/MD5 | 134 +++++++++-------- lava-1.6.8/lava/NAMESPACE | 1 lava-1.6.8/lava/NEWS.md |only lava-1.6.8/lava/R/addhook.R | 2 lava-1.6.8/lava/R/complik.R | 13 - lava-1.6.8/lava/R/constrain.R | 6 lava-1.6.8/lava/R/covariance.R | 6 lava-1.6.8/lava/R/estimate.lvm.R | 2 lava-1.6.8/lava/R/mixture.R | 54 +++--- lava-1.6.8/lava/R/mvnmix.R | 61 +++---- lava-1.6.8/lava/R/normal.R | 4 lava-1.6.8/lava/R/parameter.R | 1 lava-1.6.8/lava/R/profile.R | 5 lava-1.6.8/lava/R/twostage.R | 37 +++- lava-1.6.8/lava/R/utils.R | 6 lava-1.6.8/lava/R/wkm.R | 10 - lava-1.6.8/lava/README.md |only lava-1.6.8/lava/build |only lava-1.6.8/lava/data/bmd.rda |binary lava-1.6.8/lava/data/bmidata.rda |binary lava-1.6.8/lava/data/brisa.rda |binary lava-1.6.8/lava/data/calcium.rda |binary lava-1.6.8/lava/data/hubble.rda |binary lava-1.6.8/lava/data/hubble2.rda |binary lava-1.6.8/lava/data/indoorenv.rda |binary lava-1.6.8/lava/data/missingdata.rda |binary lava-1.6.8/lava/data/nldata.rda |binary lava-1.6.8/lava/data/nsem.rda |binary lava-1.6.8/lava/data/semdata.rda |binary lava-1.6.8/lava/data/serotonin.rda |binary lava-1.6.8/lava/data/serotonin2.rda |binary lava-1.6.8/lava/data/twindata.rda |binary lava-1.6.8/lava/inst/doc/correlation.R |only lava-1.6.8/lava/inst/doc/correlation.Rmd |only lava-1.6.8/lava/inst/doc/correlation.html |only lava-1.6.8/lava/inst/doc/gof.R |only lava-1.6.8/lava/inst/doc/gof.Rmd |only lava-1.6.8/lava/inst/doc/gof.html |only lava-1.6.8/lava/inst/doc/nonlinear.R |only lava-1.6.8/lava/inst/doc/nonlinear.Rmd |only lava-1.6.8/lava/inst/doc/nonlinear.html |only lava-1.6.8/lava/man/bmd.Rd | 4 lava-1.6.8/lava/man/bmidata.Rd | 4 lava-1.6.8/lava/man/brisa.Rd | 4 lava-1.6.8/lava/man/calcium.Rd | 6 lava-1.6.8/lava/man/complik.Rd | 4 lava-1.6.8/lava/man/figures |only lava-1.6.8/lava/man/hubble.Rd | 4 lava-1.6.8/lava/man/hubble2.Rd | 4 lava-1.6.8/lava/man/indoorenv.Rd | 4 lava-1.6.8/lava/man/missingdata.Rd | 4 lava-1.6.8/lava/man/mixture.Rd | 14 + lava-1.6.8/lava/man/nldata.Rd | 4 lava-1.6.8/lava/man/nsem.Rd | 4 lava-1.6.8/lava/man/semdata.Rd | 4 lava-1.6.8/lava/man/serotonin.Rd | 4 lava-1.6.8/lava/man/serotonin2.Rd | 4 lava-1.6.8/lava/man/twindata.Rd | 4 lava-1.6.8/lava/man/twostageCV.Rd | 11 - lava-1.6.8/lava/tests/testthat/test-constrain.R | 21 +- lava-1.6.8/lava/tests/testthat/test-estimate_default.R | 16 +- lava-1.6.8/lava/tests/testthat/test-inference.R | 82 +++++----- lava-1.6.8/lava/vignettes |only 71 files changed, 333 insertions(+), 240 deletions(-)
Title: Interactive Interface to Data Envelopment Analysis Modeling
Description: Allows the user to execute interactively radial data envelopment analysis models. The user has the ability to upload a data frame,
select the input/output variables, choose the technology assumption to adopt and decide whether to run an input or an output oriented model.
When the model is executed a set of results are displayed which include efficiency scores, peers' determination, scale efficiencies' evaluation
and slacks' calculation. Fore more information about the theoretical background of the package,
please refer to Bogetoft & Otto (2011) <doi:10.1007/978-1-4419-7961-2>.
Author: Mohamed El Fodil Ihaddaden
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between farrell versions 0.2.0 dated 2020-06-03 and 0.2.1 dated 2020-09-26
DESCRIPTION | 8 - LICENSE | 4 MD5 | 31 +++-- NAMESPACE | 10 - NEWS.md |only R/farrell.R | 17 +-- R/globals.R | 6 - R/utils-pipe.R | 22 ++-- README.md | 254 +++++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/Intro.R | 5 inst/doc/Intro.Rmd | 229 ++++++++++++++++++++++++------------------- inst/doc/Intro.html | 58 +++++++++- inst/rstudio/addins.dcf | 10 - man/farrell.Rd | 42 +++---- man/pipe.Rd | 24 ++-- vignettes/Intro.Rmd | 229 ++++++++++++++++++++++++------------------- 17 files changed, 529 insertions(+), 420 deletions(-)
Title: Helper Functions for Bayesian Analyses
Description: Functions to 'numericise' 'R' objects (coerce to numeric objects)
and summarise 'MCMC' (Monte Carlo Markov Chain) samples
as well as 'R' translations of 'BUGS' (Bayesian Using Gibbs Sampling)
and 'JAGS' (Just Another Gibbs Sampler) functions.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Kirill Müller [ctb] (<https://orcid.org/0000-0002-1416-3412>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between extras versions 0.0.1 dated 2020-06-16 and 0.1.0 dated 2020-09-26
DESCRIPTION | 15 +++++++--- MD5 | 54 +++++++++++++++++++++++++------------- NAMESPACE | 9 ++++++ NEWS.md | 7 ++++ R/as-list.R |only R/chk-index.R |only R/chk-indices.R |only R/chk-pars.R | 13 +++------ R/par-pattern.R |only R/params.R | 2 + R/pextreme.R |only R/pvalue.R | 2 - R/sextreme.R |only R/svalue.R | 2 - README.md | 4 +- inst/WORDLIST | 4 +- man/as_list_unnamed.Rd |only man/chk_index.Rd |only man/chk_indices.Rd |only man/chk_pars.Rd | 5 ++- man/extras-package.Rd | 3 +- man/ilogit.Rd | 2 - man/logit.Rd | 2 - man/par_pattern.Rd |only man/params.Rd | 3 ++ man/pextreme.Rd |only man/phi.Rd | 2 - man/pvalue.Rd | 2 - man/sextreme.Rd |only man/svalue.Rd | 2 - tests/testthat/test-as-list.R |only tests/testthat/test-chk-index.R |only tests/testthat/test-chk-indices.R |only tests/testthat/test-chk-pars.R | 15 ++-------- tests/testthat/test-par-pattern.R |only tests/testthat/test-pextreme.R |only tests/testthat/test-sextreme.R |only 37 files changed, 92 insertions(+), 56 deletions(-)
Title: Cycle Routing and Data for Cycling Advocacy
Description: An interface to the cycle routing/data services provided by 'CycleStreets',
a not-for-profit social enterprise and advocacy organisation.
The application programming interfaces (APIs) provided by 'CycleStreets' are documented at (<https://www.cyclestreets.net/api/>).
The focus of this package is the journey planning API, which aims to emulate the routes taken by a knowledgeable cyclist.
An innovative feature of the routing service of its provision of fastest, quietest and balanced profiles.
These represent routes taken to minimise time, avoid traffic and compromise between the two, respectively.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Martin Lucas-Smith [aut],
Eric Krueger [ctb],
Joey Talbot [aut] (<https://orcid.org/0000-0002-6520-4560>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between cyclestreets versions 0.1.5 dated 2018-05-06 and 0.3.0 dated 2020-09-26
cyclestreets-0.1.5/cyclestreets/R/hello.R |only cyclestreets-0.3.0/cyclestreets/DESCRIPTION | 21 cyclestreets-0.3.0/cyclestreets/MD5 | 27 - cyclestreets-0.3.0/cyclestreets/NAMESPACE | 1 cyclestreets-0.3.0/cyclestreets/NEWS.md | 6 cyclestreets-0.3.0/cyclestreets/R/data.R |only cyclestreets-0.3.0/cyclestreets/R/journey.R | 238 +++++++++- cyclestreets-0.3.0/cyclestreets/README.md | 30 - cyclestreets-0.3.0/cyclestreets/data |only cyclestreets-0.3.0/cyclestreets/inst/extdata/journey-2018.json |only cyclestreets-0.3.0/cyclestreets/inst/extdata/journey.json | 2 cyclestreets-0.3.0/cyclestreets/inst/gradient-tests.R |only cyclestreets-0.3.0/cyclestreets/man/cyclestreets_column_names.Rd |only cyclestreets-0.3.0/cyclestreets/man/figures/README-example-1.png |binary cyclestreets-0.3.0/cyclestreets/man/figures/README-unnamed-chunk-2-1.png |binary cyclestreets-0.3.0/cyclestreets/man/journey.Rd | 55 +- cyclestreets-0.3.0/cyclestreets/man/json2sf_cs.Rd | 38 + cyclestreets-0.3.0/cyclestreets/man/smooth_with_cutoffs.Rd |only 18 files changed, 361 insertions(+), 57 deletions(-)
Title: Measuring Morphological Diversity and Evolutionary Tempo
Description: Measures morphological diversity from discrete character data and
estimates evolutionary tempo on phylogenetic trees. Imports morphological
data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>)
format with read_nexus_matrix(), and writes to both #NEXUS and TNT format
(Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main
functions are test_rates(), which implements AIC and likelihood
ratio tests for discrete character rates introduced across Lloyd et al.
(2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014)
<doi:10.1016/j.cub.2014.08.034>, Close et al. (2015)
<doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>,
and MatrixDistances(), which implements multiple discrete character
distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998)
<doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>, and
Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. This also includes
the GED correction from Lehmann et al. (2019) <doi:10.1111/pala.12430>.
Multiple functions implement morphospace plots:
plot_chronophylomorphospace() implements Sakamoto and Ruta (2012)
<doi:10.1371/journal.pone.0039752>, plot_morphospace() implements Wills et
al. (1994) <doi:10.1017/S009483730001263X>, plot_changes_on_tree()
implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and
plot_morphospace_stack() implements Foote (1993)
<doi:10.1017/S0094837300015864>. Other functions include
safe_taxonomic_reduction(), which implements Wilkinson (1995)
<doi:10.1093/sysbio/44.4.501>, map_dollo_changes() implements
the Dollo stochastic character mapping of Tarver et al. (2018)
<doi:10.1093/gbe/evy096>, and estimate_ancestral_states() implements
the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>.
Author: Graeme T. Lloyd [aut, cre, cph],
Thomas Guillerme [aut, cph],
Emma Sherratt [aut, cph],
Steve C. Wang [aut, cph]
Maintainer: Graeme T. Lloyd <graemetlloyd@gmail.com>
Diff between Claddis versions 0.6.1 dated 2020-08-26 and 0.6.3 dated 2020-09-26
CHANGELOG | 21 +++++++++++ DESCRIPTION | 11 ++--- MD5 | 59 ++++++++++++++++--------------- NAMESPACE | 13 +++++- R/Claddis-package.R | 1 R/assign_taxa_to_bins.R | 2 - R/bin_character_completeness.R | 3 + R/build_cladistic_matrix.R | 10 ++++- R/calculate_morphological_distances.R | 7 ++- R/compactify_matrix.R | 9 +++- R/constructors.r |only R/estimate_ancestral_states.R | 7 ++- R/map_stochastic_changes.R | 5 ++ R/ordinate_cladistic_matrix.R | 3 + R/plot_morphospace.R | 3 - R/plot_morphospace_stack.R | 19 +++++++-- R/print.cladisticMatrix.r |only R/prune_cladistic_matrix.R | 6 +++ R/read_nexus_matrix.R | 15 +++++-- R/safe_taxonomic_reduction.R | 3 + R/test_rates.R | 9 +++- R/trim_marginal_whitespace.r |only R/write_nexus_matrix.R | 3 + R/write_tnt_matrix.R | 3 + README.md | 30 +++++++++++---- data/day_2016.RData |binary data/gauthier_1986.RData |binary data/michaux_1989.RData |binary man/calculate_morphological_distances.Rd | 2 - man/plot_morphospace.Rd | 3 - man/print.cladisticMatrix.Rd |only man/test_rates.Rd | 4 +- man/trim_marginal_whitespace.Rd |only 33 files changed, 176 insertions(+), 75 deletions(-)