Title: Parametric Survival Simulation with Parameter Uncertainty
Description: Perform survival simulation with parametric survival model generated from 'survreg' function in 'survival' package.
In each simulation coefficients are resampled from variance-covariance matrix of parameter estimates to
capture uncertainty in model parameters.
Prediction intervals of Kaplan-Meier estimates and hazard ratio of treatment effect can be further calculated using simulated survival data.
Author: Kenta Yoshida [aut, cre] (<https://orcid.org/0000-0003-4967-3831>),
Laurent Claret [aut]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between survParamSim versions 0.1.4 dated 2020-12-08 and 0.1.5 dated 2021-04-26
DESCRIPTION | 20 MD5 | 65 +- NAMESPACE | 6 NEWS.md | 14 R/calc_hr_pi.R | 129 +++- R/calc_km_pi.R | 144 +++-- R/extract_pi.R | 121 +++- R/extract_raw_sim.R | 107 +++- R/survParamSim-package.R |only R/surv_param_sim.R | 48 + R/surv_param_sim_pre_resampled.R |only R/surv_param_sim_resample.R | 41 + R/yyy.R | 9 README.md | 71 +- build/survParamSim.pdf |only inst/doc/survParamSim.R | 3 inst/doc/survParamSim.Rmd | 12 inst/doc/survParamSim.html | 546 ++++++--------------- man/calc_hr_pi.Rd | 12 man/calc_km_pi.Rd | 18 man/extractpi.Rd | 35 - man/extractpi_deprecated.Rd |only man/extractrawsim.Rd | 25 man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/plot_hr_pi.Rd | 4 man/surv_param_sim_pre_resampled.Rd |only man/survparamsim.Rd | 27 - tests/testthat/test-calc_hr_pi.R | 61 +- tests/testthat/test-calc_km_pi.R | 59 +- tests/testthat/test-surv_param_sim.R | 10 tests/testthat/test-surv_param_sim_pre_resampled.R |only tests/testthat/test-surv_param_sim_resample.R | 46 + vignettes/survParamSim.Rmd | 12 41 files changed, 950 insertions(+), 695 deletions(-)
Title: Extracts Environmental Data from 'ERDDAP' Web Services
Description: Contains three functions that access
environmental data from any 'ERDDAP' data web service. The rxtracto() function extracts
data along a trajectory for a given "radius" around the point. The
rxtracto_3D() function extracts data in a box. The rxtractogon() function
extracts data in a polygon. All of those three function use the 'rerddap' package
to extract the data, and should work with any 'ERDDAP' server.
There are also two functions, plotBBox() and plotTrack() that use the 'plotdap'
package to simplify the creation of maps of the data.
Author: Roy Mendelssohn [aut, cre]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddapXtracto versions 1.0.2 dated 2020-11-03 and 1.1.0 dated 2021-04-26
DESCRIPTION | 8 MD5 | 25 - NEWS.md | 6 R/data_extract_read.R | 2 R/getFIleCoords.R | 2 R/interp.R |only R/rxtracto.R | 21 + README.md | 15 - build/vignette.rds |binary inst/doc/UsingrerddapXtracto.R | 34 +- inst/doc/UsingrerddapXtracto.Rmd | 65 +++- inst/doc/UsingrerddapXtracto.html | 564 ++++++++++++-------------------------- man/rxtracto.Rd | 6 vignettes/UsingrerddapXtracto.Rmd | 65 +++- 14 files changed, 379 insertions(+), 434 deletions(-)
More information about rerddapXtracto at CRAN
Permanent link
Title: Fit Continuous-Time State-Space and Latent Variable Models for
Quality Control of Argos Satellite (and Other) Telemetry Data
and for Estimating Movement Behaviour
Description: Fits continuous-time random walk and correlated random walk state-space models for quality control animal tracking data ('Argos', processed light-level 'geolocation', 'GPS'). Template Model Builder ('TMB') is used for fast estimation. The 'Argos' data can be: (older) least squares-based locations; (newer) Kalman filter-based locations with error ellipse information; or a mixture of both. The models estimate two sets of location states corresponding to: 1) each observation, which are (usually) irregularly timed; and 2) user-specified time intervals (regular or irregular). Latent variable models are provided to estimate move persistence along tracks as an index of behaviour. Track simulation functions are provided. 'Jonsen I', 'McMahon CR', 'Patterson TA', 'Auger-Méthé M', 'Harcourt R', 'Hindell MA', 'Bestley S' (2019) Movement responses to environment: fast inference of variation among southern elephant seals with a mixed effects model. Ecology 100:e02566 <doi:10.1002/ecy.2566>.
Author: Ian Jonsen [aut, cre, cph],
Toby Patterson [aut, ctb]
Maintainer: Ian Jonsen <ian.jonsen@mq.edu.au>
Diff between foieGras versions 0.7-5 dated 2021-04-24 and 0.7-6 dated 2021-04-26
foieGras-0.7-5/foieGras/data/xs.RData |only foieGras-0.7-5/foieGras/man/xs.Rd |only foieGras-0.7-6/foieGras/DESCRIPTION | 16 - foieGras-0.7-6/foieGras/MD5 | 76 +++--- foieGras-0.7-6/foieGras/R/fit_mpm.R | 4 foieGras-0.7-6/foieGras/R/foieGras-package.R | 11 foieGras-0.7-6/foieGras/R/grab.R | 6 foieGras-0.7-6/foieGras/R/join.R | 5 foieGras-0.7-6/foieGras/R/mpm_control.R | 4 foieGras-0.7-6/foieGras/R/osar.r | 11 foieGras-0.7-6/foieGras/R/plot.fG_mpm.R | 5 foieGras-0.7-6/foieGras/R/plot.fG_osar.R | 8 foieGras-0.7-6/foieGras/R/plot.fG_simfit.R | 4 foieGras-0.7-6/foieGras/R/plot.fG_ssm.R | 6 foieGras-0.7-6/foieGras/R/print.ssm.R | 6 foieGras-0.7-6/foieGras/build/vignette.rds |binary foieGras-0.7-6/foieGras/data/sese2.RData |only foieGras-0.7-6/foieGras/data/xm.RData |binary foieGras-0.7-6/foieGras/inst/doc/basics.html | 158 ++++++-------- foieGras-0.7-6/foieGras/man/fit_mpm.Rd | 4 foieGras-0.7-6/foieGras/man/grab.Rd | 6 foieGras-0.7-6/foieGras/man/join.Rd | 5 foieGras-0.7-6/foieGras/man/mpm_control.Rd | 5 foieGras-0.7-6/foieGras/man/osar.Rd | 11 foieGras-0.7-6/foieGras/man/plot.fG_mpm.Rd | 5 foieGras-0.7-6/foieGras/man/plot.fG_osar.Rd | 8 foieGras-0.7-6/foieGras/man/plot.fG_simfit.Rd | 4 foieGras-0.7-6/foieGras/man/plot.fG_ssm.Rd | 6 foieGras-0.7-6/foieGras/man/print.ssm.Rd | 6 foieGras-0.7-6/foieGras/man/sese2.Rd |only foieGras-0.7-6/foieGras/src/Makevars | 2 foieGras-0.7-6/foieGras/src/Makevars.win | 2 foieGras-0.7-6/foieGras/tests/testthat/test-fit_mpm.R | 8 foieGras-0.7-6/foieGras/tests/testthat/test-fmap.R | 6 foieGras-0.7-6/foieGras/tests/testthat/test-grab.R | 6 foieGras-0.7-6/foieGras/tests/testthat/test-join.R | 6 foieGras-0.7-6/foieGras/tests/testthat/test-osar.R | 7 foieGras-0.7-6/foieGras/tests/testthat/test-plot_mpm.R | 5 foieGras-0.7-6/foieGras/tests/testthat/test-plot_simfit.R | 4 foieGras-0.7-6/foieGras/tests/testthat/test-plot_ssm.R | 6 foieGras-0.7-6/foieGras/tests/testthat/test-sim.R | 5 41 files changed, 248 insertions(+), 189 deletions(-)
Title: Non-Parametric Bayesian Analyses of Animal Movement
Description: Methods for assessing animal movement from telemetry and biologging
data using non-parametric Bayesian methods. This includes features for pre-
processing and analysis of data, as well as the visualization of results
from the models. This framework does not rely on standard parametric density
functions, which provides flexibility during model fitting.
Author: Joshua Cullen [aut, cre, cph] (<https://orcid.org/0000-0002-6935-9340>),
Denis Valle [aut, cph]
Maintainer: Joshua Cullen <joshcullen10@gmail.com>
Diff between bayesmove versions 0.1.0 dated 2020-10-16 and 0.2.0 dated 2021-04-26
DESCRIPTION | 14 +- MD5 | 72 ++++++++----- NAMESPACE | 7 + NEWS.md | 14 ++ R/LDA_gibbs_sampler.R | 4 R/LDA_helper_functions.R | 14 +- R/RcppExports.R | 24 ++++ R/mixmod_gibbs_functions.R |only R/mixmod_gibbs_sampler.R |only R/segmentation_gibbs_functions.R | 2 R/segmentation_gibbs_sampler.R | 34 ++++-- R/segmentation_helper_functions.R | 174 ++++++++++++++++++++++++++++----- R/shinyapp.R |only README.md | 61 +++++++++-- inst/WORDLIST | 11 ++ man/StoreZ.Rd |only man/SummarizeDat.Rd |only man/behav_gibbs_sampler.Rd | 5 man/cluster_obs.Rd |only man/cluster_segments.Rd | 4 man/discrete_move_var.Rd | 3 man/filter_time.Rd | 3 man/get.llk.mixmod.Rd |only man/get_behav_hist.Rd | 10 - man/insert_NAs.Rd |only man/prep_data.Rd | 23 ++-- man/prep_data_internal.Rd | 4 man/round_track_time.Rd | 9 + man/sample.gamma.mixmod.Rd |only man/sample.phi.mixmod.Rd |only man/sample.v.mixmod.Rd |only man/sample.z.mixmod.Rd |only man/segment_behavior.Rd | 6 - man/shiny_tracks.Rd |only src/RcppExports.cpp | 30 +++++ src/mixmod_aux1.cpp |only tests/testthat/test-assign_tseg.R | 5 tests/testthat/test-cluster_obs.R |only tests/testthat/test-df_to_list.R | 3 tests/testthat/test-filter_time.R | 3 tests/testthat/test-get_behav_hist.R | 6 - tests/testthat/test-insert_NAs.R |only tests/testthat/test-prep_data.R | 3 tests/testthat/test-round_track_time.R | 3 tests/testthat/test-segment_behavior.R | 13 +- 45 files changed, 436 insertions(+), 128 deletions(-)
Title: Board Game Graphics
Description: Functions to make board game graphics. Specializes in game diagrams, animations, and "Print & Play" layouts for the 'piecepack' <https://www.ludism.org/ppwiki> but can make graphics for other board game systems. Includes configurations for several public domain game systems.
Author: Trevor L Davis [aut, cre],
Delapouite <https://delapouite.com/> [dtc] (Meeple shape extracted from
"Meeple icon" <https://game-icons.net/1x1/delapouite/meeple.html> /
"CC BY 3.0" <https://creativecommons.org/licenses/by/3.0/>)
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between piecepackr versions 1.7.1 dated 2021-03-25 and 1.7.2 dated 2021-04-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 9 ++++++++- R/sysdata.rda |binary 4 files changed, 15 insertions(+), 8 deletions(-)
Title: Dirichlet Process Bayesian Clustering, Profile Regression
Description: Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership. The package allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as well as Normal and discrete covariates. It also allows for fixed effects in the response model, where a spatial CAR (conditional autoregressive) term can be also included. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to fitting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection. The main reference for the package is Liverani, Hastie, Azizi, Papathomas and Richardson (2015) <doi:10.18637/jss.v064.i07>.
Author: David I. Hastie, Silvia Liverani <liveranis@gmail.com> and Sylvia Richardson with contributions from Aurore J. Lavigne, Lucy Leigh, Lamiae Azizi, Xi Liu, Ruizhu Huang, Austin Gratton, Wei Jing
Maintainer: Silvia Liverani <liveranis@gmail.com>
Diff between PReMiuM versions 3.2.5 dated 2021-04-08 and 3.2.6 dated 2021-04-26
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/PReMiuM.cpp | 18 +++++++++--------- tests/testthat/test-calcAvgRisk.R | 4 ++-- tests/testthat/test-profRegr.R | 2 +- 5 files changed, 19 insertions(+), 19 deletions(-)
Title: Document Unit Tests Roxygen-Style
Description: Much as 'roxygen2' allows one to document functions in the same file as the function itself, 'roxut' allows one to write the unit tests in the same file as the function. Once processed, the unit tests are moved to the appropriate directory. Currently supports 'testthat' and 'tinytest' frameworks. The 'roxygen2' package provides much of the infrastructure.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>),
Hadley Wickham [aut, cph] (roxygen2 code),
Peter Danenberg [aut, cph] (roxygen2 code),
Gábor Csárdi [aut] (roxygen2 code),
Manuel Eugster [aut, cph] (roxygen2 code),
RStudio [cph] (roxygen2 code)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between roxut versions 0.2.23 dated 2020-07-06 and 0.2.40 dated 2021-04-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 ++++++ inst/tinytest/test_roxutTestPkg.R | 33 ++++++++++++++++++++++++--------- 4 files changed, 37 insertions(+), 16 deletions(-)
Title: Visualizes a Matrix as Heatmap
Description: Visualizes a matrix object plainly as heatmap. It provides S3 functions to plot simple matrices and loading matrices.
Author: Sigbert Klinke [aut, cre],
Frédéric Chevalier [ctb]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Diff between plot.matrix versions 1.5.2 dated 2020-11-01 and 1.6 dated 2021-04-26
DESCRIPTION | 10 MD5 | 24 +- NAMESPACE | 1 R/fmt.R |only R/plot.matrix.R | 42 ++- README.md | 4 build/vignette.rds |binary inst/doc/plot.matrix.R | 77 +++++++ inst/doc/plot.matrix.Rmd | 110 ++++++++++ inst/doc/plot.matrix.html | 495 +++++++++++++++++----------------------------- inst/png |only man/fmt.Rd |only man/plot.matrix.Rd | 93 ++++---- vignettes/plot.matrix.Rmd | 110 ++++++++++ 14 files changed, 574 insertions(+), 392 deletions(-)
Title: Obtain 'jQuery' as an HTML Dependency Object
Description: Obtain any major version of 'jQuery' (<https://code.jquery.com/>) and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown').
Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.
Author: Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Joe Cheng [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/lib/jquery-AUTHORS.txt)
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between jquerylib versions 0.1.3 dated 2020-12-17 and 0.1.4 dated 2021-04-26
jquerylib-0.1.3/jquerylib/inst/lib/jquery-1.12.4.js |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-1.12.4.min.js |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-1.12.4.min.map |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-2.2.4.js |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-2.2.4.min.js |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-2.2.4.min.map |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-3.5.1.js |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-3.5.1.min.js |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-3.5.1.min.map |only jquerylib-0.1.4/jquerylib/DESCRIPTION | 8 +-- jquerylib-0.1.4/jquerylib/MD5 | 31 +++++++-------- jquerylib-0.1.4/jquerylib/NEWS.md | 5 ++ jquerylib-0.1.4/jquerylib/R/jquery.R | 4 - jquerylib-0.1.4/jquerylib/README.md | 17 +++----- jquerylib-0.1.4/jquerylib/inst/lib/1.12.4 |only jquerylib-0.1.4/jquerylib/inst/lib/2.2.4 |only jquerylib-0.1.4/jquerylib/inst/lib/3.6.0 |only jquerylib-0.1.4/jquerylib/tests/testthat/_snaps |only jquerylib-0.1.4/jquerylib/tests/testthat/test-jquery.R | 20 +-------- jquerylib-0.1.4/jquerylib/tools/download.R | 7 ++- 20 files changed, 43 insertions(+), 49 deletions(-)
Title: Statistical Analysis of Mixed Ploidy Populations
Description: Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation
Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single
ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values
around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to
utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects
allowing integration with other packages such adegenet.
Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. <doi:10.1111/1755-0998.12129> for the appropriate citation and user manual. Thank you in advance.
Author: LW Pembleton
Maintainer: LW Pembleton <luke.pembleton@agriculture.vic.gov.au>
Diff between StAMPP versions 1.6.1 dated 2020-03-20 and 1.6.2 dated 2021-04-26
StAMPP-1.6.1/StAMPP/ChangeLog |only StAMPP-1.6.2/StAMPP/DESCRIPTION | 14 ++++++++------ StAMPP-1.6.2/StAMPP/MD5 | 11 +++++++---- StAMPP-1.6.2/StAMPP/NAMESPACE | 1 + StAMPP-1.6.2/StAMPP/NEWS.md |only StAMPP-1.6.2/StAMPP/R/stamppAmova.R | 12 +++--------- StAMPP-1.6.2/StAMPP/README.md |only StAMPP-1.6.2/StAMPP/inst/StAMPP.png |only StAMPP-1.6.2/StAMPP/inst/StAMPP.svg |only 9 files changed, 19 insertions(+), 19 deletions(-)
Title: Add More 'AdminLTE2' Components to 'shinydashboard'
Description: Extend 'shinydashboard' with 'AdminLTE2' components.
'AdminLTE2' is a free 'Bootstrap 3' dashboard template available
at <https://adminlte.io>. Customize boxes, add timelines and a lot more.
Author: David Granjon [aut, cre],
RinteRface [cph],
Almasaeed Studio [ctb, cph] (AdminLTE2 theme for Bootstrap 3),
Guang Yang [ctb, cph] (ygdashboard original template),
Winston Chang [ctb, cph] (Functions from shinydashboard),
Victor Perrier [ctb] (improved the shinydashboardPlusGallery)
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between shinydashboardPlus versions 2.0.0 dated 2021-03-07 and 2.0.1 dated 2021-04-26
DESCRIPTION | 9 - MD5 | 34 +-- NEWS.md | 12 + R/boxes.R | 2 R/dashboardPage.R | 5 R/useful-items.R | 2 build/shinydashboardPlus.pdf |binary inst/doc/box-elements.html | 4 inst/doc/controlbar.html | 4 inst/doc/css-preloader.html | 4 inst/doc/enhanced-header.html | 4 inst/doc/improved-boxes.html | 4 inst/doc/more-skins.html | 4 inst/doc/shinydashboardPlus.html | 2 inst/shinydashboardPlus-2.0.0/js/shinydashboardPlus.js | 89 +++++----- inst/shinydashboardPlus-2.0.0/js/shinydashboardPlus.min.js | 2 inst/shinydashboardPlus-2.0.0/js/shinydashboardPlus.min.js.map | 2 man/dashboardPage.Rd | 6 18 files changed, 104 insertions(+), 85 deletions(-)
More information about shinydashboardPlus at CRAN
Permanent link
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also contains a
number of lower level 'CLI' elements: rules, boxes, trees, and
'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and
text styles as well.
Author: Gábor Csárdi [aut, cre],
Hadley Wickham [ctb],
Kirill Müller [ctb],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cli versions 2.4.0 dated 2021-04-05 and 2.5.0 dated 2021-04-26
cli-2.4.0/cli/R/lazyrmd.R |only cli-2.4.0/cli/R/memo.R |only cli-2.4.0/cli/man/cli_memo.Rd |only cli-2.4.0/cli/tests/testthat/_snaps/memo.md |only cli-2.4.0/cli/tests/testthat/test-memo.R |only cli-2.5.0/cli/DESCRIPTION | 14 cli-2.5.0/cli/MD5 | 132 ++++---- cli-2.5.0/cli/NAMESPACE | 31 + cli-2.5.0/cli/NEWS.md | 24 + cli-2.5.0/cli/R/aaa-utils.R | 18 - cli-2.5.0/cli/R/ansi.R | 31 + cli-2.5.0/cli/R/ansiex.R | 64 +++ cli-2.5.0/cli/R/app.R | 8 cli-2.5.0/cli/R/boxes.R | 4 cli-2.5.0/cli/R/bullets.R |only cli-2.5.0/cli/R/cli.R | 42 ++ cli-2.5.0/cli/R/cliapp-docs.R | 67 ++-- cli-2.5.0/cli/R/cliapp.R | 43 -- cli-2.5.0/cli/R/containers.R | 15 cli-2.5.0/cli/R/format-conditions.R |only cli-2.5.0/cli/R/format.R | 20 - cli-2.5.0/cli/R/inline.R | 241 ++++++++++----- cli-2.5.0/cli/R/internals.R | 7 cli-2.5.0/cli/R/num-ansi-colors.R | 17 - cli-2.5.0/cli/R/onload.R | 6 cli-2.5.0/cli/R/rules.R | 4 cli-2.5.0/cli/R/simple-theme.R | 10 cli-2.5.0/cli/R/status-bar.R | 10 cli-2.5.0/cli/R/symbol.R | 2 cli-2.5.0/cli/R/test.R |only cli-2.5.0/cli/R/themes.R | 61 ++- cli-2.5.0/cli/R/tree.R | 6 cli-2.5.0/cli/R/zzz.R | 63 +++ cli-2.5.0/cli/man/ansi-styles.Rd | 62 +++ cli-2.5.0/cli/man/ansi_align.Rd | 1 cli-2.5.0/cli/man/ansi_columns.Rd | 1 cli-2.5.0/cli/man/ansi_nchar.Rd | 1 cli-2.5.0/cli/man/ansi_strsplit.Rd | 1 cli-2.5.0/cli/man/ansi_strtrim.Rd | 1 cli-2.5.0/cli/man/ansi_strwrap.Rd | 1 cli-2.5.0/cli/man/ansi_substr.Rd | 1 cli-2.5.0/cli/man/ansi_substring.Rd | 1 cli-2.5.0/cli/man/ansi_toupper.Rd |only cli-2.5.0/cli/man/ansi_trimws.Rd | 3 cli-2.5.0/cli/man/chunks/pluralization.Rmd | 118 +++---- cli-2.5.0/cli/man/cli_bullets.Rd |only cli-2.5.0/cli/man/cli_format.Rd | 8 cli-2.5.0/cli/man/cli_process_start.Rd | 2 cli-2.5.0/cli/man/cli_status.Rd | 10 cli-2.5.0/cli/man/cli_status_clear.Rd | 2 cli-2.5.0/cli/man/cli_vec.Rd | 4 cli-2.5.0/cli/man/format_error.Rd |only cli-2.5.0/cli/man/inline-markup.Rd | 43 +- cli-2.5.0/cli/man/test_that_cli.Rd |only cli-2.5.0/cli/man/themes.Rd | 24 + cli-2.5.0/cli/tests/testthat/_snaps/ansiex.md | 66 ++++ cli-2.5.0/cli/tests/testthat/_snaps/bullets.md |only cli-2.5.0/cli/tests/testthat/_snaps/cat-helpers.md | 10 cli-2.5.0/cli/tests/testthat/_snaps/format-conditions.md |only cli-2.5.0/cli/tests/testthat/_snaps/inline-2.md | 150 ++++++++- cli-2.5.0/cli/tests/testthat/_snaps/inline.md | 2 cli-2.5.0/cli/tests/testthat/_snaps/lists.md | 42 +- cli-2.5.0/cli/tests/testthat/_snaps/pluralization.md | 6 cli-2.5.0/cli/tests/testthat/_snaps/text.md | 3 cli-2.5.0/cli/tests/testthat/_snaps/themes.md | 60 +++ cli-2.5.0/cli/tests/testthat/helper.R | 34 -- cli-2.5.0/cli/tests/testthat/test-ansiex.R | 36 ++ cli-2.5.0/cli/tests/testthat/test-bullets.R |only cli-2.5.0/cli/tests/testthat/test-format-conditions.R |only cli-2.5.0/cli/tests/testthat/test-inline-2.R | 56 +++ cli-2.5.0/cli/tests/testthat/test-inline.R | 2 cli-2.5.0/cli/tests/testthat/test-pluralization.R | 6 cli-2.5.0/cli/tests/testthat/test-text.R | 6 cli-2.5.0/cli/tests/testthat/test-themes.R | 45 ++ cli-2.5.0/cli/tests/testthat/test-tree.R | 9 75 files changed, 1270 insertions(+), 487 deletions(-)
Title: Maximum Likelihood Multiple Imputation
Description: Implements so called Maximum Likelihood Multiple Imputation as described by von Hippel and Bartlett (2019) <arXiv:1210.0870v10>. A number of different imputations are available, by utilising the 'norm', 'cat' and 'mix' packages. Inferences can be performed either using combination rules similar to Rubin's or using a likelihood score based approach based on theory by Wang and Robins (1998) <doi:10.1093/biomet/85.4.935>.
Author: Jonathan Bartlett
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>
Diff between mlmi versions 1.0.0 dated 2019-08-02 and 1.1.0 dated 2021-04-26
DESCRIPTION | 12 +-- MD5 | 30 +++++--- NAMESPACE | 1 NEWS.md |only R/data.r |only R/refBasedCts.r |only R/sb.r | 6 - R/wb.r | 6 - README.md | 4 - build |only data |only man/catImp.Rd | 11 ++- man/ctsTrialWide.Rd |only man/mixImp.Rd | 15 +++- man/normImp.Rd | 136 +++++++++++++++++++------------------- man/refBasedCts.Rd |only man/scoreBased.Rd | 9 +- man/withinBetween.Rd | 6 - tests/testthat/test_normimp.r | 13 --- tests/testthat/test_refBasedCts.R |only 20 files changed, 132 insertions(+), 117 deletions(-)
Title: Extended Empirical Saddlepoint Density Approximations
Description: Tools for fitting the Extended Empirical Saddlepoint (EES) density of Fasiolo et al. (2018) <doi:10.1214/18-EJS1433>.
Author: Matteo Fasiolo and Simon N. Wood
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between esaddle versions 0.0.6 dated 2020-01-10 and 0.0.7 dated 2021-04-26
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- build/vignette.rds |binary inst/doc/esaddle.R | 14 +++++++------- inst/doc/esaddle.Rmd | 2 +- inst/doc/esaddle.html | 12 ++++++------ man/selectDecay.Rd | 8 ++++---- vignettes/esaddle.Rmd | 2 +- 8 files changed, 31 insertions(+), 31 deletions(-)
Title: User Friendly Bayesian Data Analysis for Psychology
Description: Contains several Bayesian models for data analysis of psychological tests. A user friendly interface for these models should enable students and researchers to perform professional level Bayesian data analysis without advanced knowledge in programming and Bayesian statistics. This package is based on the Stan platform (Carpenter et el. 2017 <doi:10.18637/jss.v076.i01>).
Author: Jure Demšar [cre, aut],
Grega Repovš [aut],
Erik Štrumbelj [aut],
Trustees of Columbia University [cph],
John Kruschke [cph] (R/shared_functions.R - mcmc_hdi,
src/stan_files/ttest.stan),
Rasmus Baath [cph] (R/b_bootstrap.R)
Maintainer: Jure Demšar <jure.demsar@fri.uni-lj.si>
Diff between bayes4psy versions 1.2.5 dated 2020-12-07 and 1.2.6 dated 2021-04-26
DESCRIPTION | 8 +- MD5 | 16 ++--- inst/doc/adaptation_level.R | 10 --- inst/doc/adaptation_level.Rmd | 10 --- inst/doc/adaptation_level.html | 58 +++++++++------------ inst/doc/afterimages.html | 16 ++--- inst/doc/flanker.html | 110 ++++++++++++++++++++--------------------- inst/doc/stroop.html | 38 +++++++------- vignettes/adaptation_level.Rmd | 10 --- 9 files changed, 122 insertions(+), 154 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares
or REML by adding the function r() to formulas of lm() and glm(). A collection of
text-book statistics for higher education is also included, e.g. modifications
of the functions lm(), glm() and associated summaries from the package 'stats'.
Author: Kristian Hovde Liland [aut, cre],
Solve S<e6>b<f8> [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.2.4 dated 2019-12-13 and 1.2.5 dated 2021-04-26
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- NEWS | 8 ++++++++ R/lm.R | 2 +- R/statistics.R | 6 ++---- 5 files changed, 19 insertions(+), 14 deletions(-)
Title: Run Time-Course MBNMA Models
Description: Fits Bayesian time-course models for model-based network meta-analysis (MBNMA) that allows inclusion of multiple
time-points from studies. Repeated measures over time are accounted for within studies by applying different time-course functions,
following the method of Pedder et al. (2019) <doi:10.1002/jrsm.1351>.
The method allows synthesis of studies with multiple follow-up measurements that can account for time-course for a single or multiple
treatment comparisons. Several general time-course functions are provided; others may be added
by the user. Various characteristics can be flexibly added to the models, such as correlation between time points and shared
class effects. The consistency of direct and indirect evidence in the network can be assessed using unrelated mean effects
models and/or by node-splitting.
Author: Hugo Pedder [aut, cre],
Tobias Saueressig [rev],
Nicky Welton [ctb, rev],
Sofia Dias [ctb, rev],
Meg Bennetts [ctb, rev],
Martin Boucher [ctb, rev]
Maintainer: Hugo Pedder <hugopedder@gmail.com>
Diff between MBNMAtime versions 0.1.3 dated 2020-03-04 and 0.2.0 dated 2021-04-26
MBNMAtime-0.1.3/MBNMAtime/R/write.functions.R |only MBNMAtime-0.1.3/MBNMAtime/inst/extdata/nodesplit1.RData |only MBNMAtime-0.1.3/MBNMAtime/inst/extdata/nodesplit2.RData |only MBNMAtime-0.1.3/MBNMAtime/inst/extdata/ranks.RData |only MBNMAtime-0.1.3/MBNMAtime/inst/extdata/umelist1.Rdata |only MBNMAtime-0.1.3/MBNMAtime/inst/extdata/umelist2.RData |only MBNMAtime-0.1.3/MBNMAtime/inst/extdata/vignettedata.rda |only MBNMAtime-0.1.3/MBNMAtime/man/compound.beta.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/mb.emax.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/mb.emax.hill.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/mb.exponential.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/mb.fract.first.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/mb.fract.second.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/mb.linear.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/mb.piecelinear.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/mb.quadratic.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/print.mb.nodesplit.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/summary.mb.nodesplit.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/time.fun.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/write.alpha.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/write.fract.poly.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/write.inserts.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/write.piece.fract.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/write.piecelinear.Rd |only MBNMAtime-0.1.3/MBNMAtime/man/write.remove.loops.Rd |only MBNMAtime-0.2.0/MBNMAtime/DESCRIPTION | 31 MBNMAtime-0.2.0/MBNMAtime/MD5 | 203 - MBNMAtime-0.2.0/MBNMAtime/NAMESPACE | 26 MBNMAtime-0.2.0/MBNMAtime/NEWS.md | 23 MBNMAtime-0.2.0/MBNMAtime/R/MBNMAtime.R | 36 MBNMAtime-0.2.0/MBNMAtime/R/datasets.R | 43 MBNMAtime-0.2.0/MBNMAtime/R/globals.R | 7 MBNMAtime-0.2.0/MBNMAtime/R/mb.network-class.R |only MBNMAtime-0.2.0/MBNMAtime/R/mb.predict-class.R |only MBNMAtime-0.2.0/MBNMAtime/R/mb.rank-class.R |only MBNMAtime-0.2.0/MBNMAtime/R/mbnma-class.R |only MBNMAtime-0.2.0/MBNMAtime/R/nodesplit-class.R |only MBNMAtime-0.2.0/MBNMAtime/R/nodesplit.functions.R | 337 - MBNMAtime-0.2.0/MBNMAtime/R/plot.functions.R | 995 +---- MBNMAtime-0.2.0/MBNMAtime/R/predict.functions.R | 692 --- MBNMAtime-0.2.0/MBNMAtime/R/prepare.functions.R | 594 ++- MBNMAtime-0.2.0/MBNMAtime/R/print.sum.functions.R | 606 --- MBNMAtime-0.2.0/MBNMAtime/R/rank.functions.R | 240 - MBNMAtime-0.2.0/MBNMAtime/R/run.functions.R | 1656 +-------- MBNMAtime-0.2.0/MBNMAtime/R/time.functions.R |only MBNMAtime-0.2.0/MBNMAtime/R/write.jags.R |only MBNMAtime-0.2.0/MBNMAtime/README.md | 23 MBNMAtime-0.2.0/MBNMAtime/build/partial.rdb |binary MBNMAtime-0.2.0/MBNMAtime/build/vignette.rds |binary MBNMAtime-0.2.0/MBNMAtime/data/copd.rda |only MBNMAtime-0.2.0/MBNMAtime/inst/REFERENCES.bib | 107 MBNMAtime-0.2.0/MBNMAtime/inst/doc/MBNMAtime.R | 595 +-- MBNMAtime-0.2.0/MBNMAtime/inst/doc/MBNMAtime.Rmd | 836 ++-- MBNMAtime-0.2.0/MBNMAtime/inst/doc/MBNMAtime.html | 1835 +++++----- MBNMAtime-0.2.0/MBNMAtime/inst/extdata/nd.exp.rda |only MBNMAtime-0.2.0/MBNMAtime/inst/extdata/nodesplit.rda |only MBNMAtime-0.2.0/MBNMAtime/inst/extdata/ranks.rda |only MBNMAtime-0.2.0/MBNMAtime/man/MBNMAtime-package.Rd | 44 MBNMAtime-0.2.0/MBNMAtime/man/add_index.Rd | 2 MBNMAtime-0.2.0/MBNMAtime/man/alog_pcfb.Rd | 12 MBNMAtime-0.2.0/MBNMAtime/man/copd.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/devplot.Rd | 24 MBNMAtime-0.2.0/MBNMAtime/man/figures/functionstructure.png |binary MBNMAtime-0.2.0/MBNMAtime/man/fitplot.Rd | 25 MBNMAtime-0.2.0/MBNMAtime/man/gen.parameters.to.save.Rd | 8 MBNMAtime-0.2.0/MBNMAtime/man/genspline.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/get.earliest.time.Rd | 2 MBNMAtime-0.2.0/MBNMAtime/man/get.latest.time.Rd | 2 MBNMAtime-0.2.0/MBNMAtime/man/get.model.vals.Rd | 24 MBNMAtime-0.2.0/MBNMAtime/man/get.prior.Rd | 6 MBNMAtime-0.2.0/MBNMAtime/man/getjagsdata.Rd | 35 MBNMAtime-0.2.0/MBNMAtime/man/getnmadata.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/goutSUA_CFB.Rd | 6 MBNMAtime-0.2.0/MBNMAtime/man/goutSUA_CFBcomb.Rd | 6 MBNMAtime-0.2.0/MBNMAtime/man/inconsistency.loops.Rd | 4 MBNMAtime-0.2.0/MBNMAtime/man/mb.network.Rd | 42 MBNMAtime-0.2.0/MBNMAtime/man/mb.nodesplit.Rd | 93 MBNMAtime-0.2.0/MBNMAtime/man/mb.nodesplit.comparisons.Rd | 6 MBNMAtime-0.2.0/MBNMAtime/man/mb.run.Rd | 343 - MBNMAtime-0.2.0/MBNMAtime/man/mb.update.Rd | 10 MBNMAtime-0.2.0/MBNMAtime/man/mb.validate.data.Rd | 8 MBNMAtime-0.2.0/MBNMAtime/man/mb.write.Rd | 126 MBNMAtime-0.2.0/MBNMAtime/man/nma.run.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/obesityBW_CFB.Rd | 10 MBNMAtime-0.2.0/MBNMAtime/man/osteopain.Rd | 6 MBNMAtime-0.2.0/MBNMAtime/man/pDcalc.Rd | 20 MBNMAtime-0.2.0/MBNMAtime/man/plot.mb.predict.Rd | 59 MBNMAtime-0.2.0/MBNMAtime/man/plot.mb.rank.Rd | 23 MBNMAtime-0.2.0/MBNMAtime/man/plot.mbnma.Rd | 19 MBNMAtime-0.2.0/MBNMAtime/man/predict.mbnma.Rd | 65 MBNMAtime-0.2.0/MBNMAtime/man/print.mb.network.Rd | 2 MBNMAtime-0.2.0/MBNMAtime/man/print.mb.predict.Rd | 2 MBNMAtime-0.2.0/MBNMAtime/man/print.mb.rank.Rd | 2 MBNMAtime-0.2.0/MBNMAtime/man/print.nodesplit.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/rank.mb.predict.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/rank.mbnma.Rd | 37 MBNMAtime-0.2.0/MBNMAtime/man/rankauc.Rd | 31 MBNMAtime-0.2.0/MBNMAtime/man/ref.synth.Rd | 29 MBNMAtime-0.2.0/MBNMAtime/man/remove.loops.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/replace.prior.Rd | 2 MBNMAtime-0.2.0/MBNMAtime/man/summary.mb.network.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/summary.mb.predict.Rd | 12 MBNMAtime-0.2.0/MBNMAtime/man/summary.mbnma.Rd | 6 MBNMAtime-0.2.0/MBNMAtime/man/summary.nodesplit.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/temax.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/texp.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/tfpoly.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/timeplot.Rd | 28 MBNMAtime-0.2.0/MBNMAtime/man/tloglin.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/tpoly.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/tspline.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/tuser.Rd |only MBNMAtime-0.2.0/MBNMAtime/man/write.beta.Rd | 22 MBNMAtime-0.2.0/MBNMAtime/man/write.check.Rd | 91 MBNMAtime-0.2.0/MBNMAtime/man/write.cor.Rd | 19 MBNMAtime-0.2.0/MBNMAtime/man/write.likelihood.Rd | 39 MBNMAtime-0.2.0/MBNMAtime/man/write.model.Rd | 4 MBNMAtime-0.2.0/MBNMAtime/man/write.ref.synth.Rd | 91 MBNMAtime-0.2.0/MBNMAtime/man/write.timecourse.Rd |only MBNMAtime-0.2.0/MBNMAtime/tests/testthat/test_nodesplit.functions.R | 423 +- MBNMAtime-0.2.0/MBNMAtime/tests/testthat/test_plot.functions.R | 665 +-- MBNMAtime-0.2.0/MBNMAtime/tests/testthat/test_postest.functions.R | 542 -- MBNMAtime-0.2.0/MBNMAtime/tests/testthat/test_prepare.functions.R | 106 MBNMAtime-0.2.0/MBNMAtime/tests/testthat/test_print.sum.functions.R | 338 - MBNMAtime-0.2.0/MBNMAtime/tests/testthat/test_rank.functions.R |only MBNMAtime-0.2.0/MBNMAtime/tests/testthat/test_run.functions.R | 511 +- MBNMAtime-0.2.0/MBNMAtime/tests/testthat/test_time.functions.R |only MBNMAtime-0.2.0/MBNMAtime/tests/testthat/test_write.functions.R | 506 -- MBNMAtime-0.2.0/MBNMAtime/vignettes/MBNMAtime.Rmd | 836 ++-- MBNMAtime-0.2.0/MBNMAtime/vignettes/REFERENCES.bib | 107 130 files changed, 5945 insertions(+), 8421 deletions(-)
Title: Cartography for Statistical Analysis
Description: Creating maps for statistical analysis such as proportional circles, chroropleth, typology and flows. Some functions use 'shiny' or 'leaflet' technologies for dynamism and interactivity.
The great features are :
- Create maps in a web environment where the parameters are modifiable on the fly ('shiny' and 'leaflet' technology).
- Create interactive maps through zoom and pop-up ('leaflet' technology).
- Create frozen maps with the possibility to add labels.
Author: Sébastien CALVET - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [cre, aut],
Sophie AUDRIC - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [aut],
SED - DR Hauts-de-France - INSEE [ctb],
PSAR-SL - DR Auvergne-Rhone-Alpes - INSEE [ctb],
PSAR-EEP - DR Occitanie - INSEE [ctb],
SED - DR Pays-de-la-Loire - INSEE [ctb]
Maintainer: Sébastien CALVET <sebastien.calvet@insee.fr>
Diff between oceanis versions 1.7.5.1 dated 2021-02-05 and 1.7.5.2 dated 2021-04-26
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NEWS | 7 +++++++ R/calcul_bornes.R | 2 ++ R/leaflet_classes.R | 10 +++++----- R/leaflet_classes_ronds.R | 10 +++++----- R/leaflet_ronds_classes.R | 10 +++++----- R/plot_classes.R | 6 +++--- R/plot_classes_ronds.R | 6 +++--- R/plot_ronds_classes.R | 6 +++--- R/plot_typo.R | 1 + R/shiny_classes.R | 14 +++++++------- R/shiny_classes_ronds.R | 16 ++++++++-------- R/shiny_ronds.R | 2 +- R/shiny_ronds_classes.R | 16 ++++++++-------- README.md | 2 +- inst/doc/integration_shiny.html | 13 ++++++++++--- inst/doc/oceanis.html | 13 ++++++++++--- 18 files changed, 100 insertions(+), 76 deletions(-)
Title: Multimodal and Multilevel Network Analysis
Description: A set of tools that extend common social network analysis packages
for analysing multimodal and multilevel networks.
It includes functions for one- and two-mode (and sometimes three-mode)
centrality, centralization, clustering, and constraint,
as well as for one- and two-mode network regression and block-modelling.
All functions operate with matrices, edge lists,
and 'igraph', 'network'/'sna', and 'tidygraph' objects.
The package is released as a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book.
Author: James Hollway [cph, cre, aut, ctb] (IHEID,
<https://orcid.org/0000-0002-8361-9647>)
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 0.6.2 dated 2021-04-15 and 0.6.3 dated 2021-04-26
migraph-0.6.2/migraph/R/convert.R |only migraph-0.6.2/migraph/R/sample.R |only migraph-0.6.2/migraph/man/convert.Rd |only migraph-0.6.2/migraph/man/sample.Rd |only migraph-0.6.2/migraph/tests/testthat/test-convert.R |only migraph-0.6.2/migraph/tests/testthat/test-sample.R |only migraph-0.6.3/migraph/DESCRIPTION | 8 - migraph-0.6.3/migraph/MD5 | 47 ++++++----- migraph-0.6.3/migraph/NAMESPACE | 16 ++- migraph-0.6.3/migraph/NEWS.md | 40 +++++++++ migraph-0.6.3/migraph/R/blockmodel.R | 39 --------- migraph-0.6.3/migraph/R/coercion.R |only migraph-0.6.3/migraph/R/create.R | 64 ++++++++------- migraph-0.6.3/migraph/R/data_bristol.R | 8 + migraph-0.6.3/migraph/R/generate.R |only migraph-0.6.3/migraph/R/is.R |only migraph-0.6.3/migraph/R/plot.R | 46 ++++++++++- migraph-0.6.3/migraph/R/read_ucinet.R |only migraph-0.6.3/migraph/README.md | 71 ++++++++++++++--- migraph-0.6.3/migraph/inst/CITATION |only migraph-0.6.3/migraph/man/blockmodel.Rd | 3 migraph-0.6.3/migraph/man/coercion.Rd |only migraph-0.6.3/migraph/man/create.Rd | 25 +++-- migraph-0.6.3/migraph/man/generate.Rd |only migraph-0.6.3/migraph/man/is.Rd |only migraph-0.6.3/migraph/man/mpn_bristol.Rd | 6 - migraph-0.6.3/migraph/man/plot.blockmodel.Rd |only migraph-0.6.3/migraph/man/plot.igraph.Rd | 2 migraph-0.6.3/migraph/man/read.Rd |only migraph-0.6.3/migraph/tests/testthat/test-blockmodel.R | 5 + migraph-0.6.3/migraph/tests/testthat/test-coercion.R |only migraph-0.6.3/migraph/tests/testthat/test-create.R | 15 ++- migraph-0.6.3/migraph/tests/testthat/test-generate.R |only migraph-0.6.3/migraph/tests/testthat/test-is.R |only 34 files changed, 269 insertions(+), 126 deletions(-)
Title: Lightweight Infrastructure for Handling Multiple R Markdown
Documents
Description: Provides an infrastructure for handling multiple R Markdown
reports, including automated curation and time-stamping of outputs,
parameterisation and provision of helper functions to manage dependencies.
Author: Thibaut Jombart [aut],
Amy Gimma [ctb],
Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between reportfactory versions 0.2.0 dated 2021-03-11 and 0.3.0 dated 2021-04-26
DESCRIPTION | 10 +-- MD5 | 20 +++---- NEWS.md | 6 ++ R/compile_reports.R | 24 +++++++- R/list_reports.R | 2 R/new_factory.R | 22 ++++++- man/compile_reports.Rd | 4 + man/new_factory.Rd | 9 ++- tests/testthat.R | 10 ++- tests/testthat/test-compile_reports.R | 94 ++++++++++++++++++++++++++++++++++ tests/testthat/test-new_factory.R | 4 + 11 files changed, 177 insertions(+), 28 deletions(-)
Title: Refitting and Spatial Analysis in Archaeology
Description: Methods to analyse fragmented objects in archaeology using refitting relationships between fragments scattered in archaeological spatial units (e.g. stratigraphic layers). Graphs and graph theory are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. An empirical dataset is also provided as an example.
Author: Sebastien Plutniak [aut, cre] (<https://orcid.org/0000-0002-6674-3806>)
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeofrag versions 0.6.0 dated 2020-11-27 and 0.7 dated 2021-04-26
DESCRIPTION | 14 - MD5 | 84 ++++---- NAMESPACE | 13 - NEWS.md |only R/frag.cycles.R | 9 R/frag.diameters.R | 4 R/frag.edges.weighting.R | 190 ++++++++++++++++++-- R/frag.get.layers.R | 9 R/frag.get.layers.pair.R | 22 +- R/frag.get.parameters.R | 30 ++- R/frag.graph.plot.R | 26 ++ R/frag.layers.admixture.R | 30 ++- R/frag.layers.cohesion.R | 68 +++++-- R/frag.observer.failure.R |only R/frag.path.lengths.R | 3 R/frag.relations.by.layers.R | 15 - R/frag.simul.compare.R |only R/frag.simul.process.R | 118 ++++++++++-- R/frag.simul.summarise.R |only R/make_frag_object.R | 127 ++++++++----- data/LiangAbu.RData |binary inst/doc/archeofrag-vignette.R | 4 inst/doc/archeofrag-vignette.Rmd | 13 + inst/doc/archeofrag-vignette.html | 355 +++++++++++++++++--------------------- man/Frag.object-class.Rd | 27 +- man/LiangAbu.Rd | 33 ++- man/archeofrag-package.Rd | 12 - man/frag.cycles.Rd | 10 - man/frag.diameters.Rd | 8 man/frag.edges.weighting.Rd | 46 +++- man/frag.get.layers.Rd | 8 man/frag.get.layers.pair.Rd | 6 man/frag.get.parameters.Rd | 6 man/frag.graph.plot.Rd | 10 - man/frag.layers.admixture.Rd | 25 +- man/frag.layers.cohesion.Rd | 32 +-- man/frag.observer.failure.Rd |only man/frag.path.lengths.Rd | 8 man/frag.relations.by.layers.Rd | 8 man/frag.simul.compare.Rd |only man/frag.simul.process.Rd | 27 +- man/frag.simul.summarise.Rd |only man/make_cr_graph.Rd | 8 man/make_crsr_graph.Rd | 20 -- man/make_frag_object.Rd | 6 man/make_sr_graph.Rd |only vignettes/archeofrag-vignette.Rmd | 13 + 47 files changed, 937 insertions(+), 510 deletions(-)
More information about ganGenerativeData at CRAN
Permanent link
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and R maintainer until
2009),
Atkinson Elizabeth [ctb],
Crowson Cynthia [ctb]
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 3.2-10 dated 2021-03-16 and 3.2-11 dated 2021-04-26
DESCRIPTION | 8 +- MD5 | 130 ++++++++++++++++++++++---------------------- R/attrassign.R | 2 R/coxph.R | 6 +- R/coxph.getdata.R | 6 +- R/model.matrix.coxph.R | 2 R/parsecovar.R | 4 - R/plot.survfit.R | 46 +++++++++++---- R/print.coxph.R | 2 R/print.summary.coxph.R | 2 R/pseudo.R | 6 +- R/pyears.R | 5 + R/residuals.survfit.R | 4 - R/stacker.R | 2 R/survcheck.R | 8 +- R/survfit.R | 8 +- R/survfit.coxphms.R | 11 ++- R/survfitCI.R | 2 R/survfitms.R | 25 +++++--- R/yates.R | 1 build/vignette.rds |binary inst/NEWS.Rd | 22 +++++++ inst/doc/adjcurve.pdf |binary inst/doc/approximate.pdf |binary inst/doc/compete.pdf |binary inst/doc/concordance.pdf |binary inst/doc/multi.pdf |binary inst/doc/other.pdf |binary inst/doc/population.pdf |binary inst/doc/splines.pdf |binary inst/doc/survival.Rnw | 2 inst/doc/survival.pdf |binary inst/doc/tiedtimes.pdf |binary inst/doc/timedep.pdf |binary inst/doc/validate.pdf |binary man/concordance.Rd | 7 +- man/frailty.Rd | 2 man/gbsg.Rd | 6 +- man/rhDNase.Rd | 2 man/rotterdam.Rd | 10 +-- man/summary.survfit.Rd | 11 +++ man/survfit.Rd | 3 - man/survfit.coxph.Rd | 36 ++++++++---- noweb/code.nw | 130 +++++++++++++++++++++++++------------------- noweb/concordance.Rnw | 4 - noweb/coxph.Rnw | 6 +- noweb/coxsurv3.Rnw | 32 ++++++---- noweb/parse.Rnw | 4 - noweb/plot.Rnw | 24 +++++--- noweb/pyears.Rnw | 5 + noweb/residuals.survfit.Rnw | 4 - noweb/survexpm.Rnw | 10 +-- noweb/survfit.Rnw | 8 +- noweb/survfitCI.Rnw | 7 +- noweb/survfitms.Rnw | 25 +++++--- noweb/yates.Rnw | 1 src/cdecomp.c | 10 +-- src/concordance3.c | 2 tests/coxsurv5.R | 8 ++ tests/coxsurv5.Rout.save | 16 ++++- tests/mstrata.R | 23 +++++++ tests/mstrata.Rout.save | 29 ++++++++- tests/multi2.R | 2 tests/multi2.Rout.save | 8 +- vignettes/refer.bib | 26 ++++++++ vignettes/survival.Rnw | 2 66 files changed, 485 insertions(+), 282 deletions(-)
Title: Interactive Q-Q and Manhattan Plots Using 'plotly.js'
Description: Create interactive manhattan, Q-Q and volcano plots that are usable from the R console,
in 'Dash' apps, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps.
Hover the mouse pointer over a point to show details or drag a rectangle to
zoom. A manhattan plot is a popular graphical method for visualizing results
from high-dimensional data analysis such as a (epi)genome wide association study
(GWAS or EWAS), in which p-values, Z-scores, test statistics are plotted on a scatter
plot against their genomic position. Manhattan plots are used for visualizing
potential regions of interest in the genome that are associated with a phenotype.
Interactive manhattan plots allow the inspection of specific value (e.g. rs number or
gene name) by hovering the mouse over a cell, as well as zooming into a region of the
genome (e.g. a chromosome) by dragging a rectangle around the relevant area.
This work is based on the 'qqman' package and the 'plotly.js'
engine. It produces similar manhattan and Q-Q plots as the 'manhattan' and 'qq'
functions in the 'qqman' package, with the advantage of including extra annotation
information and interactive web-based visualizations directly from R.
Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them)
can be viewed and modified in a web browser.
Author: Sahir Bhatnagar [aut, cre] (http://sahirbhatnagar.com/)
Maintainer: Sahir Bhatnagar <sahir.bhatnagar@gmail.com>
Diff between manhattanly versions 0.2.0 dated 2016-11-15 and 0.3.0 dated 2021-04-26
DESCRIPTION | 27 +- MD5 | 55 ++-- NAMESPACE | 3 NEWS.md | 23 ++ R/manhattanly.R | 112 +-------- R/manhattanr.R | 88 ++----- R/qqly.R | 231 ++++++++++---------- R/qqr.R | 40 +-- R/utils.R |only R/volcanoly.R | 460 ++++++++++++++++++---------------------- R/volcanor.R | 135 +++++------ README.md | 20 + build/vignette.rds |binary inst/doc/manhattanly.R | 130 ++++++----- inst/doc/manhattanly.Rmd | 161 +++++++------- inst/doc/manhattanly.html | 522 +++++++++++++++++++++++++++------------------- man/HapMap.Rd | 7 man/manhattanly.Rd | 49 ++-- man/manhattanr.Rd | 29 +- man/qqly.Rd | 50 ++-- man/qqr.Rd | 7 man/significantSNP.Rd | 5 man/volcanoly.Rd | 125 ++++++----- man/volcanor.Rd | 54 ++-- tests |only vignettes/manhattanly.Rmd | 161 +++++++------- vignettes/web_only |only 27 files changed, 1270 insertions(+), 1224 deletions(-)
Title: Small Count Rounding of Tabular Data
Description: A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398_An_Algorithm_for_Small_Count_Rounding_of_Tabular_Data>.
Author: Øyvind Langsrud [aut, cre],
Johan Heldal [aut]
Maintainer: Øyvind Langsrud <oyl@ssb.no>
Diff between SmallCountRounding versions 0.7.0 dated 2021-03-09 and 0.8.0 dated 2021-04-26
SmallCountRounding-0.7.0/SmallCountRounding/R/ModelMatrixExtra.R |only SmallCountRounding-0.7.0/SmallCountRounding/data |only SmallCountRounding-0.7.0/SmallCountRounding/man/sosialFiktiv.Rd |only SmallCountRounding-0.8.0/SmallCountRounding/DESCRIPTION | 8 SmallCountRounding-0.8.0/SmallCountRounding/MD5 | 60 - SmallCountRounding-0.8.0/SmallCountRounding/NAMESPACE | 3 SmallCountRounding-0.8.0/SmallCountRounding/NEWS.md | 8 SmallCountRounding-0.8.0/SmallCountRounding/R/PLSrounding.R | 65 + SmallCountRounding-0.8.0/SmallCountRounding/R/RoundViaDummy.R | 19 SmallCountRounding-0.8.0/SmallCountRounding/R/SmallCountData.R | 55 - SmallCountRounding-0.8.0/SmallCountRounding/build/partial.rdb |only SmallCountRounding-0.8.0/SmallCountRounding/inst/doc/Introduction_to_SmallCountRounding.html | 4 SmallCountRounding-0.8.0/SmallCountRounding/man/FindMaxDiff.Rd | 52 - SmallCountRounding-0.8.0/SmallCountRounding/man/HDutility.Rd | 88 +- SmallCountRounding-0.8.0/SmallCountRounding/man/Lists2formula.Rd | 44 - SmallCountRounding-0.8.0/SmallCountRounding/man/MakeControl.Rd | 44 - SmallCountRounding-0.8.0/SmallCountRounding/man/PLS2way.Rd | 68 +- SmallCountRounding-0.8.0/SmallCountRounding/man/PLSrounding.Rd | 287 ++++---- SmallCountRounding-0.8.0/SmallCountRounding/man/Round2.Rd | 118 +-- SmallCountRounding-0.8.0/SmallCountRounding/man/RoundViaDummy.Rd | 335 +++++----- SmallCountRounding-0.8.0/SmallCountRounding/man/RoundViaDummy2.Rd | 82 +- SmallCountRounding-0.8.0/SmallCountRounding/man/SmallCountData.Rd | 68 +- SmallCountRounding-0.8.0/SmallCountRounding/man/SmallCountRounding-package.Rd | 50 - SmallCountRounding-0.8.0/SmallCountRounding/man/aggrtab.Rd | 66 - SmallCountRounding-0.8.0/SmallCountRounding/man/makeroundtabs.Rd | 154 ++-- SmallCountRounding-0.8.0/SmallCountRounding/man/print.PLSrounded.Rd | 44 - SmallCountRounding-0.8.0/SmallCountRounding/man/redcube.Rd | 88 +- SmallCountRounding-0.8.0/SmallCountRounding/man/roundcube.Rd | 86 +- SmallCountRounding-0.8.0/SmallCountRounding/tests/testthat/test-PLSrounding.R | 33 29 files changed, 995 insertions(+), 934 deletions(-)
More information about SmallCountRounding at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-18 0.1.103
2019-08-05 0.1.102
2019-05-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-13 0.1.2
2020-05-14 0.1.1
2019-02-22 0.1.0
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal
and Skew-Normal distributions, considering appropriate parameterizations of
the variance-covariance matrix that takes into account the intrinsic nature of
interval data, and lead to four different possible configuration structures.
The Skew-Normal parameters can be estimated by maximum likelihood, while Normal
parameters may be estimated by maximum likelihood or robust trimmed maximum
likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito
<mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 2.5.0 dated 2020-09-24 and 2.6.0 dated 2021-04-26
CHANGELOG | 24 ++++++ DESCRIPTION | 9 +- MD5 | 87 +++++++++++++----------- NAMESPACE | 7 + R/AgrMcDt.R | 2 R/CPLogLik.grads.R | 10 -- R/ClasGenMetDef.R | 10 ++ R/ConfMatrix.R |only R/CorrHetSNSol.R | 3 R/DACrossVal.R | 26 +++++-- R/IData.R | 158 +++++++++++++++++++-------------------------- R/IdtMaxLikN.R | 29 +++++--- R/IdtMaxLikSN.R | 6 - R/IdtMclust_methods.R | 6 - R/RepLOptim.R | 6 - R/RestCPMaxLik.R | 15 +--- R/Rfasttle.R | 3 R/RobMxtDEst.R | 11 +-- R/SNmle.R | 2 R/fasttle.R | 7 - R/fulltle.R | 5 - R/lqda.R | 10 -- R/mle.R | 11 +-- R/mleVCOV.R | 7 - R/sknda.R | 4 - man/AgrMcDt.Rd | 4 + man/ConfMat.Rd |only man/DACrossVal.Rd | 4 - man/IData.Rd | 11 +-- man/Idtmclust-methods.Rd | 2 man/MAINT.Data-internal.Rd | 5 + man/MAINT.Data-package.Rd | 4 - man/MANOVA-methods.Rd | 8 +- man/Robda-methods.Rd | 6 + man/fasttle-methods.Rd | 10 +- man/fulltle-methods.Rd | 12 +-- man/lda-methods.Rd | 7 + man/mle-methods.Rd | 6 - man/qda-methods.Rd | 4 - man/snda-methods.Rd | 6 + src/msnCP_dev_grad.cpp | 5 - tests |only 42 files changed, 291 insertions(+), 261 deletions(-)
Title: Data Sets for Predictive Analytics Exam
Description: Contains all data sets for Exam PA: Predictive Analytics at
<https://exampa.net/>.
Author: Guanglai Li [aut, cre],
Sam Castillo [aut]
Maintainer: Guanglai Li <liguanglai@gmail.com>
Diff between ExamPAData versions 0.2.1 dated 2021-03-23 and 0.3.0 dated 2021-04-26
DESCRIPTION | 8 ++++---- MD5 | 5 ++++- R/bike_sharing_demand.R |only data/bike_sharing_demand.RData |only man/bike_sharing_demand.Rd |only 5 files changed, 8 insertions(+), 5 deletions(-)