Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as getting database specific taxonomic identifiers, verifying
species names, getting taxonomic hierarchies, fetching downstream and
upstream taxonomic names, getting taxonomic synonyms, converting
scientific to common names and vice versa, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Eduard Szoecs [aut],
Zachary Foster [aut],
Zebulun Arendsee [aut],
Carl Boettiger [ctb],
Karthik Ram [ctb],
Ignasi Bartomeus [ctb],
John Baumgartner [ctb],
James O'Donnell [ctb],
Jari Oksanen [ctb],
Bastian Greshake Tzovaras [ctb],
Philippe Marchand [ctb],
Vinh Tran [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.9.2 dated 2018-03-01 and 0.9.3 dated 2018-03-20
DESCRIPTION | 16 ++- MD5 | 56 +++++------ NEWS.md | 19 +++ R/classification.R | 38 ++++--- R/comm2sci.R | 2 R/genbank2uid.R | 47 +++++---- R/get_tolid.R | 1 R/get_uid.R | 30 ++++-- R/getkey.R | 16 ++- R/ncbi_children.R | 131 +++++++++++++++------------ R/ncbi_get_taxon_summary.R | 66 ++++++++----- R/sci2comm.R | 12 +- R/zzz.R | 7 + README.md | 23 ++++ build/vignette.rds |binary inst/CITATION | 10 +- man/classification.Rd | 8 - man/genbank2uid.Rd | 14 ++ man/getkey.Rd | 16 ++- man/ncbi_children.Rd | 68 ++++++++------ man/ncbi_get_taxon_summary.Rd | 32 ++++-- tests/testthat/Rplots.pdf |binary tests/testthat/test-classification.R | 64 ++++++------- tests/testthat/test-gbif_parse.R | 8 - tests/testthat/test-get_gbifid.R | 20 ++-- tests/testthat/test-gnr_resolve.R | 2 tests/testthat/test-iucn_id.R | 8 + tests/testthat/test-iucn_summary.R | 20 +++- tests/testthat/test-ncbi_get_taxon_summary.R | 2 29 files changed, 456 insertions(+), 280 deletions(-)
Title: Tools for Assessment the Association Between Two Spatial
Processes
Description: Tools to assess the association between two spatial processes. Currently,
four methodologies are implemented: A modified t-test to perform hypothesis testing
about the independence between the processes, a suitable nonparametric correlation
coefficient, the codispersion coefficient, and an F test for assessing the multiple
correlation between one spatial process and several others. SpatialPack gives methods
to complement methodologies that are available in geoR for one spatial process.
Author: Felipe Osorio [aut, cre],
Ronny Vallejos [aut],
Francisco Cuevas [ctb],
Diego Mancilla [ctb]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between SpatialPack versions 0.2-3 dated 2014-08-08 and 0.3 dated 2018-03-20
ChangeLog |only DESCRIPTION | 37 +++++---- MD5 | 33 +++++--- NAMESPACE | 15 +++ R/modified.Ftest.R |only R/modified.ttest.R | 8 +- data/radiata.rda |only inst/CITATION | 26 +++--- man/codisp.Rd | 58 ++++++++------ man/cor.spatial.Rd | 59 +++++++-------- man/modified.Ftest.Rd |only man/modified.ttest.Rd | 69 ++++++++--------- man/murray.Rd | 22 +++-- man/radiata.Rd |only src/base.h | 11 ++ src/mod_ttest.c | 195 ++++++++++++++++++++++++-------------------------- src/mod_ttest.h | 2 src/similarity.c |only src/similarity.h |only src/stats.c | 47 ++++++++---- src/stats.h | 1 21 files changed, 324 insertions(+), 259 deletions(-)
Title: R Commander Miscellaneous Functions
Description: Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut, cre],
Robert Muenchen [ctb],
Dan Putler [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between RcmdrMisc versions 1.0-8 dated 2018-02-23 and 1.0-9 dated 2018-03-20
DESCRIPTION | 8 +++--- MD5 | 6 ++-- NEWS | 4 +++ R/discretePlot.R | 68 +++++++++++++++++++++++++++---------------------------- 4 files changed, 45 insertions(+), 41 deletions(-)
Title: Continuous Development Models for Incremental Time-Series
Analysis
Description: Using the Bayesian state-space approach, we developed a continuous development model to quantify dynamic incremental changes in the response variable. While the model was originally developed for daily changes in forest green-up, the model can be used to predict any similar process. The CDM can capture both timing and rate of nonlinear processes. Unlike statics methods, which aggregate variations into a single metric, our dynamic model tracks the changing impacts over time. The CDM accommodates nonlinear responses to variation in predictors, which changes throughout development.
Author: Bijan Seyednasrollah, Jennifer Swenson, Jean-Christophe Domec, James S. Clark
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>
Diff between phenoCDM versions 0.0.2 dated 2018-02-16 and 0.1.2 dated 2018-03-20
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- inst/CITATION | 34 ++++++++++++++++++++++++++++------ 3 files changed, 37 insertions(+), 15 deletions(-)
Title: Arrays with Arbitrary Offsets
Description: Generalise the starting point of the array index.
Author: Jonathan Rougier <j.c.rougier@bristol.ac.uk>
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between Oarray versions 1.4-7 dated 2018-03-19 and 1.4-9 dated 2018-03-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/Oarray.R | 1 - man/internal.Rd | 11 ++--------- 4 files changed, 8 insertions(+), 16 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Mikael Dubik (lart and glouvain functions). The package uses functions from dlib, Eigen, Spectra and eclat libraries, whose code has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 1.1.2 dated 2018-03-19 and 1.1.3 dated 2018-03-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/lib/dlib/smart_pointers/shared_ptr.h | 8 ++++---- src/multinet/community/community_evaluation.cpp | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) chngpt: threshold regression model estimation and inference, BMC Bioinformatics, in press, <DOI:10.1186/s12859-017-1863-x>.
Author: Youyi Fong
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2018.1-3 dated 2018-01-04 and 2018.3-20 dated 2018-03-20
DESCRIPTION | 6 - MD5 | 20 ++--- R/chngpt.test.R | 129 ++++++++++++++++++++++++------------- R/chngptm.R | 59 +++++++++++----- R/sim.chngpt.R | 104 ++++++++++++++++------------- inst/doc/chngpt-vignette.pdf |binary inst/unitTests/runit.chngpt.test.R | 2 inst/unitTests/runit.chngptm.R | 27 ++++--- man/chngpt.test.Rd | 10 ++ man/sim.chngpt.Rd | 5 - tests/doRUnit.R | 4 - 11 files changed, 222 insertions(+), 144 deletions(-)
Title: Marine Benthic Ecosystem Analysis
Description: Preprocessing tools and biodiversity measures
(species abundance, species richness, population heterogeneity and
sensitivity) for analysing marine benthic data. See Van Loon et al.
(2015) <doi:10.1016/j.seares.2015.05.002> for an application of
these tools.
Author: Dennis Walvoort [aut, cre, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between benthos versions 1.3-4 dated 2017-11-22 and 1.3-5 dated 2018-03-20
DESCRIPTION | 8 MD5 | 8 R/io.R | 12 build/vignette.rds |binary inst/doc/benthos.html | 1281 +++++++++++++++++++++++++------------------------- 5 files changed, 655 insertions(+), 654 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [aut],
Charles Spanbauer [aut],
Matthew Pratola [aut],
Jean-Sebastien Roy [ctb],
Makoto Matsumoto [ctb],
Takuji Nishimura [ctb],
Bill Venables [ctb],
Brian Ripley [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 1.5 dated 2018-02-08 and 1.6 dated 2018-03-20
DESCRIPTION | 8 MD5 | 123 ++++++------ NEWS | 27 ++ R/bartModelMatrix.R | 12 + R/crisk.bart.R | 35 ++- R/crisk.pre.bart.R | 29 +- R/mc.crisk.bart.R | 7 R/mc.recur.bart.R | 4 R/mc.surv.bart.R | 4 R/pbart.R | 13 + R/recur.bart.R | 3 R/surv.bart.R | 4 R/surv.pre.bart.R | 45 +++- R/wbart.R | 13 + build/vignette.rds |binary cleanup | 1 cleanup.win | 1 data/ACTG175.rda |binary data/arq.rda |binary data/bladder.rda |binary data/lung.rda |binary data/transplant.rda |binary data/xdm20.test.rda |binary data/xdm20.train.rda |binary data/ydm20.test.rda |binary data/ydm20.train.rda |binary demo/00Index | 3 demo/concord.surv.bart.R |only demo/liver50.crisk.bart.R |only demo/lung.surv.bart.R | 8 demo/lung.surv.lbart.R | 10 - demo/trees.pbart.R |only inst/cxx-ex/bart.cpp | 54 ++--- inst/cxx-ex/bart.h | 19 + inst/cxx-ex/bartfuns.cpp | 24 +- inst/cxx-ex/cpbart.cpp | 17 + inst/cxx-ex/cwbart.cpp | 15 + inst/doc/bincat.Rnw | 80 ++++---- inst/doc/bincat.pdf |binary inst/doc/computing.Rnw | 72 ++++++- inst/doc/computing.pdf |binary inst/doc/cont1.Rnw |only inst/doc/cont1.pdf |only inst/doc/cont2.R |only inst/doc/cont2.Rnw |only inst/doc/cont2.pdf |only inst/doc/hwbart.pdf |binary inst/doc/time-to-event.Rnw | 396 ++++++++++++++++++++++------------------ inst/doc/time-to-event.pdf |binary man/crisk.bart.Rd | 9 man/crisk.pre.bart.Rd | 11 - man/pbart.Rd | 5 man/surv.bart.Rd | 11 - man/surv.pre.bart.Rd | 7 man/wbart.Rd | 13 - src/bart.cpp | 54 ++--- src/bart.h | 19 + src/bartfuns.cpp | 24 +- src/cpbart.cpp | 17 + src/cwbart.cpp | 15 + src/init.c | 8 vignettes/bincat.Rnw | 80 ++++---- vignettes/computing.Rnw | 72 ++++++- vignettes/cont1.Rnw |only vignettes/cont2.Rnw |only vignettes/references.bib | 188 ++++++++++++++++++ vignettes/time-to-event.Rnw | 396 ++++++++++++++++++++++------------------ vignettes/time-to-event.pdfsync |only 68 files changed, 1302 insertions(+), 654 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, with optional sampling techniques and kernel term.
Author: Alencar Xavier, William Muir, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 1.5.1 dated 2018-02-26 and 1.5.2 dated 2018-03-20
bWGR-1.5.1/bWGR/src/wgr022618.cpp |only bWGR-1.5.2/bWGR/DESCRIPTION | 8 +-- bWGR-1.5.2/bWGR/MD5 | 13 ++--- bWGR-1.5.2/bWGR/R/RcppExports.R | 86 ++++++++++++++++++------------------ bWGR-1.5.2/bWGR/R/emcv.R |only bWGR-1.5.2/bWGR/man/bWGR.Rd | 4 - bWGR-1.5.2/bWGR/man/em.Rd | 52 +++++++-------------- bWGR-1.5.2/bWGR/src/RcppExports.cpp | 39 ++++++++++++---- bWGR-1.5.2/bWGR/src/wgr032018.cpp |only 9 files changed, 103 insertions(+), 99 deletions(-)
Title: Turner Miscellaneous
Description: Miscellaneous utility functions for data manipulation,
data tidying, and working with gene expression data.
Author: Stephen Turner [aut, cre] (<https://orcid.org/0000-0001-9140-9028>)
Maintainer: Stephen Turner <vustephen@gmail.com>
Diff between Tmisc versions 0.1.17 dated 2017-06-01 and 0.1.19 dated 2018-03-20
Tmisc-0.1.17/Tmisc/R/beep.R |only Tmisc-0.1.17/Tmisc/R/clean_names.R |only Tmisc-0.1.17/Tmisc/R/convert_to_NA.R |only Tmisc-0.1.17/Tmisc/R/remove_empty_cols.R |only Tmisc-0.1.17/Tmisc/R/remove_empty_rows.R |only Tmisc-0.1.17/Tmisc/R/unrowname.R |only Tmisc-0.1.17/Tmisc/inst/sounds |only Tmisc-0.1.17/Tmisc/man/beep.Rd |only Tmisc-0.1.17/Tmisc/man/clean_names.Rd |only Tmisc-0.1.17/Tmisc/man/convert_to_NA.Rd |only Tmisc-0.1.17/Tmisc/man/remove_empty_cols.Rd |only Tmisc-0.1.17/Tmisc/man/remove_empty_rows.Rd |only Tmisc-0.1.17/Tmisc/man/unrowname.Rd |only Tmisc-0.1.19/Tmisc/DESCRIPTION | 12 +++++------ Tmisc-0.1.19/Tmisc/MD5 | 29 ++++++++-------------------- Tmisc-0.1.19/Tmisc/NAMESPACE | 9 -------- Tmisc-0.1.19/Tmisc/NEWS.md | 13 ++++++++++++ Tmisc-0.1.19/Tmisc/R/addins.R | 2 - Tmisc-0.1.19/Tmisc/R/aliases.R | 6 ----- Tmisc-0.1.19/Tmisc/R/propmiss.R | 1 Tmisc-0.1.19/Tmisc/inst/rmarkdown |only Tmisc-0.1.19/Tmisc/man/aliases.Rd | 2 - 22 files changed, 30 insertions(+), 44 deletions(-)
Title: Power Analysis for Longitudinal Multilevel Models
Description: Calculate power for two- and three-level multilevel longitudinal
studies with missing data. Both the third-level factor (e.g. therapists,
schools, or physicians), and the second-level factor (e.g. subjects),
can be assigned random slopes. Studies with partially nested designs,
unequal cluster sizes, unequal allocation to treatment arms, and different
dropout patterns per treatment are supported. For all designs power can be
calculated both analytically and via simulations. The analytical
calculations extends the method described in Galbraith et al. (2002)
<doi:10.1016/S0197-2456(02)00205-2>, to three-level models.
Additionally, the simulation tools provides flexible ways to investigate
bias, Type I errors and the consequences of model misspecification.
Author: Kristoffer Magnusson [aut, cre]
Maintainer: Kristoffer Magnusson <hello@kristoffer.email>
Diff between powerlmm versions 0.1.0 dated 2017-09-11 and 0.2.0 dated 2018-03-20
DESCRIPTION | 20 MD5 | 125 +- NAMESPACE | 25 NEWS.md |only R/DEFT.R | 15 R/VPC.r | 83 + R/helpers.R | 179 ++- R/missing_data.R | 1 R/power.R | 1273 +++++++++++++++++++------- R/powerlmm-package.R | 29 R/satterthwaite.R |only R/setup.R | 835 +++++++++++------ R/simulate.R | 758 ++++++++++----- R/simulate_3lvl_data.R | 29 README.md | 148 ++- build/vignette.rds |binary inst/doc/simulations.R | 15 inst/doc/simulations.Rmd | 32 inst/doc/simulations.html | 51 - inst/doc/technical.Rmd | 46 inst/doc/technical.pdf |binary inst/doc/three-level.R | 22 inst/doc/three-level.Rmd | 71 + inst/doc/three-level.html | 360 ++++--- inst/doc/two-level.R | 2 inst/doc/two-level.Rmd | 15 inst/doc/two-level.html | 109 +- inst/shiny_powerlmm/server.r | 33 inst/shiny_powerlmm/ui.r | 4 man/create_lmer_formula.Rd |only man/get_DEFT.Rd | 4 man/get_ICC_pre_subjects.Rd | 6 man/get_ICC_slope.Rd | 3 man/get_VPC.Rd | 2 man/get_monte_carlo_se.Rd | 16 man/get_power.Rd | 45 man/get_power_table.Rd | 13 man/plot.plcp.Rd | 8 man/plot.plcp_ICC2.Rd |only man/powerlmm.Rd | 27 man/print.plcp_multi.Rd |only man/print.plcp_multi_power.Rd |only man/print.plcp_multi_sim_summary.Rd |only man/print.plcp_sim_summary.Rd | 4 man/simulate.plcp.Rd | 56 - man/simulate_data.Rd | 14 man/study_parameters.Rd | 76 + man/sub-.plcp_multi_power.Rd |only man/summary.plcp_multi_sim.Rd | 5 man/summary.plcp_sim.Rd | 5 man/unequal_clusters.Rd | 43 tests/testthat/tests.get_DEFT.r |only tests/testthat/tests.get_sample_size.R | 30 tests/testthat/tests.helpers.R | 164 +++ tests/testthat/tests.helpers_create_formula.R |only tests/testthat/tests.power.R | 419 ++++++-- tests/testthat/tests.power_satterth_df.R |only tests/testthat/tests.power_table.R | 12 tests/testthat/tests.setup_2lvl.R | 309 +++--- tests/testthat/tests.setup_3lvl.R | 739 ++++++++++----- tests/testthat/tests.setup_print.R | 55 - tests/testthat/tests.simulate_data.R | 186 +++ tests/testthat/tests.simulation.R | 95 + tests/testthat/tests.simulation_multi.R | 5 vignettes/citations.bib | 21 vignettes/simulations.Rmd | 32 vignettes/technical.Rmd | 46 vignettes/three-level.Rmd | 71 + vignettes/two-level.Rmd | 15 69 files changed, 4835 insertions(+), 1971 deletions(-)
Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'.
Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions,
conditioned scatter plot with marginal densities,
box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between WVPlots versions 0.2.9 dated 2018-03-13 and 0.3.0 dated 2018-03-20
WVPlots-0.2.9/WVPlots/man/reexports.Rd |only WVPlots-0.3.0/WVPlots/DESCRIPTION | 17 ++++---- WVPlots-0.3.0/WVPlots/MD5 | 40 +++++++++---------- WVPlots-0.3.0/WVPlots/NAMESPACE | 17 +------- WVPlots-0.3.0/WVPlots/NEWS.md | 6 ++ WVPlots-0.3.0/WVPlots/R/ClevelandDotPlot.R | 1 WVPlots-0.3.0/WVPlots/R/DiscreteDistribution.R | 1 WVPlots-0.3.0/WVPlots/R/DistributionPlot.R | 2 WVPlots-0.3.0/WVPlots/R/DoubleDensity.R | 2 WVPlots-0.3.0/WVPlots/R/DoubleHistogram.R | 11 ++--- WVPlots-0.3.0/WVPlots/R/FitHistoryPlot.R | 4 + WVPlots-0.3.0/WVPlots/R/GainCurve.R | 16 +++++++ WVPlots-0.3.0/WVPlots/R/ROC.R | 8 +++ WVPlots-0.3.0/WVPlots/R/ScatterHist.R | 7 +++ WVPlots-0.3.0/WVPlots/R/ScatterHistC.R | 8 +++ WVPlots-0.3.0/WVPlots/R/ShadedDensity.R | 4 - WVPlots-0.3.0/WVPlots/R/WVPlots.R | 30 -------------- WVPlots-0.3.0/WVPlots/R/sharedFunctions.R | 2 WVPlots-0.3.0/WVPlots/R/wv_gapply.R |only WVPlots-0.3.0/WVPlots/build/vignette.rds |binary WVPlots-0.3.0/WVPlots/inst/doc/WVPlots_concept.html | 4 - WVPlots-0.3.0/WVPlots/inst/doc/WVPlots_examples.html | 4 - 22 files changed, 97 insertions(+), 87 deletions(-)
Title: Scale Invariant Probabilistic Neural Networks
Description: Scale invariant version of the original PNN proposed by Specht (1990) <doi:10.1016/0893-6080(90)90049-q> with the added functionality of allowing for smoothing along multiple dimensions while accounting for covariances within the data set. It is written in the R statistical programming language. Given a data set with categorical variables, we use this algorithm to estimate the probabilities of a new observation vector belonging to a specific category. This type of neural network provides the benefits of fast training time relative to backpropagation and statistical generalization with only a small set of known observations.
Author: Romin Ebrahimi
Maintainer: Romin Ebrahimi <romin.ebrahimi@utexas.edu>
Diff between spnn versions 1.0 dated 2018-03-16 and 1.1 dated 2018-03-20
DESCRIPTION | 6 +- MD5 | 10 +-- R/pnn.learn.R | 8 +-- R/spnn-internal.R | 144 +++--------------------------------------------------- build/partial.rdb |binary man/pnn.learn.Rd | 4 + 6 files changed, 22 insertions(+), 150 deletions(-)
Title: Some Latent Variable Models
Description: Contains some procedures for latent variable modelling with a
particular focus on multilevel data.
The 'LAM' package contains mean and covariance structure modelling
for multivariate normally distributed data (mlnormal()),
a general Metropolis-Hastings algorithm (amh()) and penalized
maximum likelihood estimation (pmle()).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between LAM versions 0.1-22 dated 2017-11-24 and 0.2-9 dated 2018-03-20
DESCRIPTION | 21 +++++++++++---------- MD5 | 27 +++++++++++++++------------ NAMESPACE | 5 +++++ R/amh.R | 11 +++++------ R/amh_proposal_refresh.R | 5 +++-- R/loglike_mvnorm.R | 13 ++++++++----- R/loglike_mvnorm_NA_pattern.R |only R/pmle.R | 11 ++++++----- R/pmle_eval_posterior.R | 5 +++-- R/suff_stat_NA_pattern.R |only README.md | 1 - data/data.HT12.rda |binary inst/NEWS | 27 ++++++++++++++++++++++----- man/LAM-package.Rd | 10 +++++----- man/loglike_mvnorm.Rd | 28 ++++++++++++++++++++++++++-- man/suff_stat_NA_pattern.Rd |only 16 files changed, 109 insertions(+), 55 deletions(-)
Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values
in univariate time series.
Offers several imputation functions
and missing data plots.
Available imputation algorithms include:
'Mean', 'LOCF', 'Interpolation',
'Moving Average', 'Seasonal Decomposition',
'Kalman Smoothing on Structural Time Series models',
'Kalman Smoothing on ARIMA models'.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between imputeTS versions 2.5 dated 2017-06-13 and 2.6 dated 2018-03-20
imputeTS-2.5/imputeTS/vignettes/placeins.sty |only imputeTS-2.5/imputeTS/vignettes/titleps.sty |only imputeTS-2.5/imputeTS/vignettes/titlesec.sty |only imputeTS-2.5/imputeTS/vignettes/titletoc.sty |only imputeTS-2.6/imputeTS/DESCRIPTION | 8 ++--- imputeTS-2.6/imputeTS/MD5 | 16 +++------- imputeTS-2.6/imputeTS/NEWS | 10 +++++- imputeTS-2.6/imputeTS/README.md | 2 - imputeTS-2.6/imputeTS/inst/CITATION | 14 ++++++++ imputeTS-2.6/imputeTS/inst/doc/imputeTS-Time-Series-Missing-Value-Imputation-in-R.pdf |binary imputeTS-2.6/imputeTS/tests/testthat/test-na.seasplit.R | 3 - 11 files changed, 33 insertions(+), 20 deletions(-)
Title: Regression Helper Functions
Description: Methods for manipulating regression models and for describing these in a style adapted for medical journals.
Contains functions for generating an HTML table with crude and adjusted estimates, plotting hazard ratio, plotting model
estimates and confidence intervals using forest plots, extending this to comparing multiple models in a single forest plots.
In addition to the descriptive methods, there are add-ons for the robust covariance matrix provided by the 'sandwich'
package, a function for adding non-linearities to a model, and a wrapper around the 'Epi' package's Lexis() functions for
time-splitting a dataset when modeling non-proportional hazards in Cox regressions.
Author: Max Gordon [aut, cre],
Reinhard Seifert [aut] (Author of original plotHR)
Maintainer: Max Gordon <max@gforge.se>
Diff between Greg versions 1.2 dated 2016-03-28 and 1.2.1 dated 2018-03-20
DESCRIPTION | 18 MD5 | 223 - NAMESPACE | 158 - NEWS | 164 - R/Greg.R | 90 R/addNonlinearity.R | 664 ++-- R/confint_robust.R | 104 R/forestplotCombineRegrObj.R | 342 +- R/forestplotRegrObj.R | 838 ++--- R/getCrudeAndAdjustedModelData.R | 392 +- R/getCrudeAndAdjustedModelData.rms.R | 286 - R/getModelData4Forestplot.R | 130 R/isFitCoxPH.R | 38 R/isFitLogit.R | 38 R/plotHR.R | 678 ++-- R/printCrudeAndAdjustedModel.R | 1310 ++++---- R/private_functions.R | 1418 ++++----- R/private_getCaA.R | 278 - R/private_plotHR.R | 600 +-- R/private_printCaA.R | 2162 ++++++------- R/rms_SandwichAddon.R | 426 +- R/simpleRmsAnova.R | 268 - R/timeSplitter.R | 475 +-- README.md | 66 build/vignette.rds |binary inst/doc/Print_crude_and_adjusted_models.R | 156 inst/doc/Print_crude_and_adjusted_models.Rmd | 254 - inst/doc/Print_crude_and_adjusted_models.html | 2977 +++++++++---------- inst/doc/timeSplitter.R | 800 ++--- inst/doc/timeSplitter.Rmd | 1092 +++--- inst/doc/timeSplitter.html | 1293 ++++---- inst/examples/addNonlinearity_example.R | 58 inst/examples/confint_robust_example.R | 14 inst/examples/forestplotCombineRegrObj_example.R | 84 inst/examples/forestplotRegrObj_example.R | 88 inst/examples/getCphRegrObjData_example.R | 34 inst/examples/getCrudeAndAdjustedModelData_example.R | 56 inst/examples/isFitCoxPH_example.R | 76 inst/examples/isFitLogit_example.R | 104 inst/examples/plotHR_example.R | 120 inst/examples/printCrudeAndAdjustedModel_example.R | 263 - inst/examples/printSimpleFit_example.R | 34 inst/examples/rms_SandwichAddon_example.R | 54 inst/examples/simpleRmsAnova_example.R | 92 inst/examples/timeSplitter_example.R | 30 man/GetCoefAndCI.Rd | 96 man/Greg-package.Rd | 116 man/SimpleRmsAnova.Rd | 185 - man/addNonlinearity.Rd | 171 - man/bread.ols.Rd | 103 man/caDescribeOpts.Rd | 81 man/confint.ols.Rd | 123 man/confint_robust.Rd | 109 man/estfun.ols.Rd | 109 man/forestplotCombineRegrObj.Rd | 222 - man/forestplotRegrObj.Rd | 256 - man/getCrudeAndAdjustedModelData.Rd | 199 - man/getModelData4Forestplot.Rd | 155 man/hatvalues.ols.Rd | 107 man/isFitFn.Rd | 239 - man/model.matrix.ols.Rd | 47 man/plotHR.Rd | 368 +- man/prCaAddRefAndStat.Rd | 133 man/prCaAddReference.Rd | 107 man/prCaAddUserReferences.Rd | 105 man/prCaGetImputationCols.Rd | 85 man/prCaGetRowname.Rd | 73 man/prCaGetVnStats.Rd | 113 man/prCaPrepareCrudeAndAdjusted.Rd | 79 man/prCaReorder.Rd | 79 man/prCaReorderReferenceDescribe.Rd | 139 man/prCaSelectAndOrderVars.Rd | 75 man/prCaSetRownames.Rd | 79 man/prClearPCAclass.Rd | 37 man/prConvertShowMissing.Rd | 41 man/prEnvModelCall.Rd | 49 man/prExtractOutcomeFromModel.Rd | 49 man/prFindRownameMatches.Rd | 59 man/prGetFpDataFromFit.Rd | 59 man/prGetFpDataFromGlmFit.Rd | 55 man/prGetFpDataFromSurvivalFit.Rd | 55 man/prGetModelData.Rd | 43 man/prGetModelVariables.Rd | 65 man/prGetStatistics.Rd | 111 man/prMapVariable2Name.Rd | 71 man/prNlChooseDf.Rd | 97 man/prPhConfIntPlot.Rd | 59 man/prPhDensityPlot.Rd | 41 man/prPhEstimate.Rd | 69 man/prPhNewData.Rd | 49 man/prPhRugPlot.Rd | 37 man/prPrintCAstring.Rd | 55 man/printCrudeAndAdjustedModel.Rd | 599 +-- man/robcov_alt.Rd | 111 man/timeSplitter.Rd | 143 tests/test-interval-timeSplitter.R | 80 tests/test-nonlin_4_coxph.R | 88 tests/testthat.R | 8 tests/testthat/Rplots.pdf |only tests/testthat/test-addNonlinearity.R | 266 - tests/testthat/test-confint_robust.R | 146 tests/testthat/test-fit.mult.impute-C&A.R | 502 +-- tests/testthat/test-forestplotCombineRegrObj.R | 274 - tests/testthat/test-forestplotRegrObj.R | 110 tests/testthat/test-getCrudeAndAdjustedModelData.R | 662 ++-- tests/testthat/test-isFit.R | 144 tests/testthat/test-plotHR.R | 448 +- tests/testthat/test-printCrudeAndAdjustedModel.R | 441 +- tests/testthat/test-private_functions.R | 874 ++--- tests/testthat/test-simpleRmsAnova.R | 122 tests/testthat/test-timeSplitter.R | 218 - vignettes/Print_crude_and_adjusted_models.Rmd | 254 - vignettes/timeSplitter.Rmd | 1092 +++--- 113 files changed, 15107 insertions(+), 15174 deletions(-)
Title: Fst-Heterozygosity Smoothed Quantiles
Description: A program to generate smoothed quantiles for the Fst-heterozygosity distribution. Designed for use with large numbers of loci (e.g., genome-wide SNPs). The best case for analyzing the Fst-heterozygosity distribution is when many populations (>10) have been sampled. See Flanagan & Jones (2017) <doi:10.1093/jhered/esx048>.
Author: Sarah P. Flanagan and Adam G. Jones
Maintainer: Sarah P. Flanagan <spflanagan.phd@gmail.com>
Diff between fsthet versions 1.0.0 dated 2017-11-02 and 1.0.1 dated 2018-03-20
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/fsthet.R | 10 +++++----- build/vignette.rds |binary data/bins.rda |binary data/cis.list.rda |binary data/cis.rda |binary data/fsts.beta.rda |binary data/fsts.betahat.rda |binary data/fsts.rda |binary data/fsts.theta.rda |binary data/gpop.rda |binary data/quant.out.rda |binary man/fst.boot.Rd | 3 ++- man/make.bins.Rd | 3 ++- 15 files changed, 26 insertions(+), 24 deletions(-)
Title: eBird Data Extraction and Processing with AWK
Description: Extract and process bird sightings records from eBird
(<http://ebird.org>), an online tool for recording bird observations.
Public access to the full eBird database is via the eBird Basic Dataset
(EBD; see <http://ebird.org/ebird/data/download> for access), a downloadable
text file. This package is an interface to AWK for extracting data from the
EBD based on taxonomic, spatial, or temporal filters, to produce a
manageable file size that can be imported into R.
Author: Matthew Strimas-Mackey [aut, cre]
(<https://orcid.org/0000-0001-8929-7776>),
Eliot Miller [aut],
Wesley Hochachka [aut],
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between auk versions 0.1.0 dated 2017-10-21 and 0.2.0 dated 2018-03-20
DESCRIPTION | 27 MD5 | 135 +- NAMESPACE | 21 NEWS.md | 13 R/auk-clean.r | 62 - R/auk-complete.r | 11 R/auk-country.r | 44 R/auk-date.r | 46 R/auk-distance.r | 12 R/auk-duration.r | 11 R/auk-ebd.r | 50 R/auk-extent.r | 15 R/auk-filter.r | 180 ++- R/auk-last-edited.r | 11 R/auk-project.r | 11 R/auk-protocol.r | 21 R/auk-rollup.r | 91 + R/auk-sampling.r |only R/auk-select.r |only R/auk-species.r | 6 R/auk-split.r |only R/auk-state.r |only R/auk-time.r | 11 R/auk-unique.r | 14 R/auk-version-date.r | 7 R/auk-zerofill.r | 16 R/data.r | 20 R/read.r | 22 R/utils.r | 1 R/zzz.r | 14 build/vignette.rds |binary data/ebird_states.rda |only inst/doc/auk.R | 36 inst/doc/auk.Rmd | 52 inst/doc/auk.html | 307 ++--- inst/doc/development.Rmd | 2 inst/extdata/ebd-rollup-ex.txt | 273 ---- inst/extdata/ebd-sample.txt | 1002 ++++++++--------- inst/extdata/ebd-sample_messy.txt | 202 +-- inst/extdata/zerofill-ex_ebd.txt | 514 ++++---- inst/extdata/zerofill-ex_sampling.txt | 1923 +++++++++++++++++++-------------- man/auk_clean.Rd | 29 man/auk_complete.Rd | 7 man/auk_country.Rd | 9 man/auk_date.Rd | 22 man/auk_distance.Rd | 7 man/auk_duration.Rd | 7 man/auk_ebd.Rd | 24 man/auk_extent.Rd | 11 man/auk_filter.Rd | 45 man/auk_last_edited.Rd | 7 man/auk_project.Rd | 7 man/auk_protocol.Rd | 15 man/auk_rollup.Rd | 72 + man/auk_sampling.Rd |only man/auk_select.Rd |only man/auk_species.Rd | 6 man/auk_split.Rd |only man/auk_state.Rd |only man/auk_time.Rd | 7 man/auk_version_date.Rd | 5 man/auk_zerofill.Rd | 5 man/ebird_states.Rd |only man/read_ebd.Rd | 17 tests/testthat/test_auk-filter.r | 61 - tests/testthat/test_auk-keep-drop.r | 4 tests/testthat/test_auk-rollup.r | 12 tests/testthat/test_auk-select.r |only tests/testthat/test_auk-split.r |only tests/testthat/test_auk-zerofill.r | 2 tests/testthat/test_filters.r | 88 + tests/testthat/test_filters_sampling.r |only tests/testthat/test_read.r | 8 vignettes/auk.Rmd | 52 vignettes/development.Rmd | 2 75 files changed, 3348 insertions(+), 2366 deletions(-)
Title: Functions for Phylogenetically Based Statistical Analyses
Description: Manipulation and analysis of phylogenetically simulated
data sets and phylogenetically based analyses using GLS.
Author: Ramon Diaz-Uriarte <rdiaz@cnio.es> and Theodore Garland, Jr
<theodore.garland@ucr.edu>
Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
Diff between PHYLOGR versions 1.0.8 dated 2014-11-09 and 1.0.10 dated 2018-03-20
CHANGES | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 30 ++++++++++++++++++++++++++---- R/PHYLOGR.R | 2 +- 5 files changed, 41 insertions(+), 13 deletions(-)
Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new
approach to the statistical analysis of multi-valued data, we consider
histogram-valued data, i.e., data described by univariate histograms. The
methods and the basic statistics for histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., the Euclidean metric
between quantile functions. The package contains unsupervised classification
techniques, least square regression and tools for histogram-valued data and for
histogram time series. An introducing paper is Irpino A. Verde R. (2015) <doi:10.1007/s11634-014-0176-4>.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unicampania.it>
Diff between HistDAWass versions 1.0.0 dated 2017-12-07 and 1.0.1 dated 2018-03-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Kohonen_maps.R | 2 +- src/Utility_fun.cpp | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Generalized Logistic Distribution
Description: Provides basic distribution functions for a generalized logistic distribution proposed by Rathie and Swamee (2006) <https://www.rroij.com/open-access/on-new-generalized-logistic-distributions-and-applicationsbarreto-fhs-mota-jma-and-rathie-pn-.pdf>. It also has an interactive 'RStudio' plot for better guessing dynamically of initial values for ease of included optimization and simulating.
Author: Eduardo Hellas [aut, cre],
Eduardo Monteiro [ctb]
Maintainer: Eduardo Hellas <ehellas@gmail.com>
Diff between genlogis versions 0.5.0 dated 2017-10-31 and 1.0.0 dated 2018-03-20
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/distributions_genlogis.R | 6 ++++-- R/genlog_simu.R | 22 ++++++++++++++++------ man/distrib.Rd | 3 ++- man/genlog_simu.Rd | 4 +++- man/genlog_simu_sk.Rd | 4 +++- 7 files changed, 39 insertions(+), 22 deletions(-)
Title: Fast Marching Method for Modelling Evolving Boundaries
Description: Fast Marching Method (FMM) first developed by Sethian (1996) <http://www.pnas.org/content/93/4/1591.short>, and further extended by including a second-order approximation, the first-arrival rule, additive weights, and non-homogeneous domains following Silva and Steele (2012) <doi:10.1142/S0219525911003293> and Silva and Steele (2014) <doi:10.1016/j.jas.2014.04.021>.
Author: Fabio Silva
Maintainer: Fabio Silva <fsilva@iphes.cat>
Diff between fastmaRching versions 1.0.0 dated 2018-01-22 and 1.1.0 dated 2018-03-20
DESCRIPTION | 6 +++--- MD5 | 5 +++-- NEWS.md |only R/FMM.R | 2 +- 4 files changed, 7 insertions(+), 6 deletions(-)
Title: Parses LaTeX Documents for Errors
Description: Checks LaTeX documents and .bib files for typing errors, such as spelling errors, incorrect quotation marks. Also provides useful functions for parsing and linting bibliography files.
Author: Hugh Parsonage
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between TeXCheckR versions 0.4.4 dated 2017-11-04 and 0.5.1 dated 2018-03-20
TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/lost-entry/a.aux |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/lost-entry/a.bbl |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/lost-entry/a.bcf |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/lost-entry/a.blg |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/lost-entry/a.log |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/lost-entry/a.run.xml |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/no-journal-title/a.aux |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/no-journal-title/a.bbl |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/no-journal-title/a.bcf |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/no-journal-title/a.blg |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/no-journal-title/a.log |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/no-journal-title/a.pdf |only TeXCheckR-0.4.4/TeXCheckR/tests/testthat/check-biber/no-journal-title/a.run.xml |only TeXCheckR-0.5.1/TeXCheckR/DESCRIPTION | 19 TeXCheckR-0.5.1/TeXCheckR/MD5 | 215 +- TeXCheckR-0.5.1/TeXCheckR/NAMESPACE | 8 TeXCheckR-0.5.1/TeXCheckR/NEWS.md | 37 TeXCheckR-0.5.1/TeXCheckR/R/TexCheckR-package.R | 3 TeXCheckR-0.5.1/TeXCheckR/R/any_bib_duplicates.R | 346 ++-- TeXCheckR-0.5.1/TeXCheckR/R/bib_parser.R | 14 TeXCheckR-0.5.1/TeXCheckR/R/check_all_figs_tbls_refd.R | 4 TeXCheckR-0.5.1/TeXCheckR/R/check_biber.R | 4 TeXCheckR-0.5.1/TeXCheckR/R/check_consecutive_words.R | 113 + TeXCheckR-0.5.1/TeXCheckR/R/check_dashes.R | 48 TeXCheckR-0.5.1/TeXCheckR/R/check_escapes.R | 13 TeXCheckR-0.5.1/TeXCheckR/R/check_footnote_typography.R | 738 +++++----- TeXCheckR-0.5.1/TeXCheckR/R/check_labels.R | 60 TeXCheckR-0.5.1/TeXCheckR/R/check_log.R | 6 TeXCheckR-0.5.1/TeXCheckR/R/check_quote_marks.R | 4 TeXCheckR-0.5.1/TeXCheckR/R/check_sentence_ending_periods.R | 13 TeXCheckR-0.5.1/TeXCheckR/R/check_spelling.R | 191 +- TeXCheckR-0.5.1/TeXCheckR/R/check_unclosed_parentheses.R | 145 + TeXCheckR-0.5.1/TeXCheckR/R/check_xrefs.R | 121 + TeXCheckR-0.5.1/TeXCheckR/R/commands_used.R | 2 TeXCheckR-0.5.1/TeXCheckR/R/extract_mandatory_LaTeX_argument.R | 27 TeXCheckR-0.5.1/TeXCheckR/R/extract_optional_LaTeX_argument.R | 322 ++-- TeXCheckR-0.5.1/TeXCheckR/R/extract_valid_abbreviations.R | 7 TeXCheckR-0.5.1/TeXCheckR/R/fill_nth_LaTeX_argument.R |only TeXCheckR-0.5.1/TeXCheckR/R/inputs_of.R | 3 TeXCheckR-0.5.1/TeXCheckR/R/lint_bib.R | 6 TeXCheckR-0.5.1/TeXCheckR/R/locate_mandatory_LaTeX_argument.R |only TeXCheckR-0.5.1/TeXCheckR/R/minimal_bib.R |only TeXCheckR-0.5.1/TeXCheckR/R/nth_arg_positions.R | 441 +++-- TeXCheckR-0.5.1/TeXCheckR/R/parse_tex.R | 139 + TeXCheckR-0.5.1/TeXCheckR/R/positions_of_strings.R | 2 TeXCheckR-0.5.1/TeXCheckR/R/read_tex_document.R |only TeXCheckR-0.5.1/TeXCheckR/R/remove_valid_contractions.R | 3 TeXCheckR-0.5.1/TeXCheckR/R/report_error.R | 171 +- 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TeXCheckR-0.5.1/TeXCheckR/man/extract_mandatory_LaTeX_argument.Rd | 3 TeXCheckR-0.5.1/TeXCheckR/man/extract_validate_abbreviations.Rd | 1 TeXCheckR-0.5.1/TeXCheckR/man/locate_mandatory_LaTeX_argument.Rd |only TeXCheckR-0.5.1/TeXCheckR/man/minimal_bib.Rd |only TeXCheckR-0.5.1/TeXCheckR/man/parse_tex.Rd | 18 TeXCheckR-0.5.1/TeXCheckR/man/read_tex_document.Rd |only TeXCheckR-0.5.1/TeXCheckR/man/report_error.Rd | 7 TeXCheckR-0.5.1/TeXCheckR/man/separate_sentences.Rd | 4 TeXCheckR-0.5.1/TeXCheckR/man/split_report.Rd |only TeXCheckR-0.5.1/TeXCheckR/man/strip_comments.Rd |only TeXCheckR-0.5.1/TeXCheckR/man/veto_sic.Rd |only TeXCheckR-0.5.1/TeXCheckR/tests/testthat/Engaging-students/Report.tex | 1 TeXCheckR-0.5.1/TeXCheckR/tests/testthat/Engaging-students/logos |only TeXCheckR-0.5.1/TeXCheckR/tests/testthat/check-xrefs/case-sensitive-C.tex |only TeXCheckR-0.5.1/TeXCheckR/tests/testthat/check-xrefs/case-sensitive-both.tex |only 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123 files changed, 2521 insertions(+), 1616 deletions(-)
Title: Regularized Autoregressive Hidden Semi Markov Model
Description: Fit Gaussian hidden Markov (or semi-Markov) models with / without autoregressive coefficients and with / without regularization. The fitting algorithm for the hidden Markov model is illustrated by Rabiner (1989) <doi:10.1109/5.18626>. The shrinkage estimation on the covariance matrices is based on the method by Ledoit et al. (2004) <doi:10.1016/S0047-259X(03)00096-4>. The shrinkage estimation on the autoregressive coefficients uses the elastic net shrinkage detailed in Zou et al. (2005) <doi:10.1111/j.1467-9868.2005.00503.x>.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun Xu <zekunxu@gmail.com>
Diff between rarhsmm versions 1.0.5 dated 2017-10-17 and 1.0.7 dated 2018-03-20
DESCRIPTION | 8 ++--- MD5 | 18 +++++------ NAMESPACE | 2 + R/RcppExports.R | 8 ++--- R/em.hmm.R | 68 +++++++++++++++++++++++++------------------ R/em.semi.R | 15 ++++++++- R/package.R | 6 ++- man/package-rarhsmm.Rd | 4 +- src/RcppExports.cpp | 24 +++++++-------- src/rcpparma_hello_world.cpp | 55 ++++++++++++---------------------- 10 files changed, 111 insertions(+), 97 deletions(-)
Title: Differentially Private Regularized Logistic Regression
Description: Implements two differentially private algorithms for
estimating L2-regularized logistic regression coefficients. A randomized
algorithm F is epsilon-differentially private (C. Dwork, Differential
Privacy, ICALP 2006 <DOI:10.1007/11681878_14>), if
|log(P(F(D) in S)) - log(P(F(D') in S))| <= epsilon
for any pair D, D' of datasets that differ in exactly one record, any
measurable set S, and the randomness is taken over the choices F makes.
Author: Staal A. Vinterbo <Staal.Vinterbo@ntnu.no>
Maintainer: Staal A. Vinterbo <Staal.Vinterbo@ntnu.no>
Diff between PrivateLR versions 1.2-21 dated 2014-10-31 and 1.2-22 dated 2018-03-20
DESCRIPTION | 20 ++++++++++---------- MD5 | 4 ++-- NAMESPACE | 18 +++++++++++++++++- 3 files changed, 29 insertions(+), 13 deletions(-)
Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built on
top of the 'libuv' C library.
Author: Jim Hester [aut, cre],
Hadley Wickham [aut],
libuv project contributors [cph] (libuv library),
Joyent, Inc. and other Node contributors [cph] (libuv library),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between fs versions 1.2.0 dated 2018-03-13 and 1.2.1 dated 2018-03-20
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 13 +++++++++++++ R/copy.R | 4 ++-- R/create.R | 6 +++--- R/file.R | 2 +- R/fs_perms.R | 6 +++--- R/path.R | 21 ++++++++++++++------- R/utils.R | 13 +++++++++++-- man/path_math.Rd | 4 ++-- src/file.cc | 6 ++++++ src/path.cc | 4 +++- tests/testthat/test-path.R | 12 +++++++++++- 13 files changed, 84 insertions(+), 37 deletions(-)
Title: Analysis of Ecotoxicology
Description: A simple approach to using a probit or logit analysis to calculate
lethal concentration (LC) or time (LT) and the appropriate fiducial
confidence limits desired for selected LC or LT for
ecotoxicology studies (Finney 1971; Wheeler et al. 2006;
Robertson et al. 2007). The simplicity of 'ecotox' comes from the
syntax it implies within its functions which are similar to functions
like glm() and lm(). In addition to the simplicity of the syntax,
a comprehensive data frame is produced which gives the user a
predicted LC or LT value for the desired level and a suite of important
parameters such as fiducial confidence limits and slope.
Finney, D.J. (1971, ISBN: 052108041X);
Wheeler, M.W., Park, R.M., and Bailer, A.J. (2006) <doi:10.1897/05-320R.1>;
Robertson, J.L., Savin, N.E., Russell, R.M., and Preisler, H.K.
(2007, ISBN: 0849323312).
Author: Benjamin L Hlina [aut, cre]
Maintainer: Benjamin L Hlina <benjamin.hlina@gmail.com>
Diff between ecotox versions 1.3.0 dated 2017-12-08 and 1.3.1 dated 2018-03-20
ecotox-1.3.0/ecotox/man/LC.Rd |only ecotox-1.3.0/ecotox/man/LT.Rd |only ecotox-1.3.1/ecotox/DESCRIPTION | 18 ecotox-1.3.1/ecotox/MD5 | 42 - ecotox-1.3.1/ecotox/NAMESPACE | 3 ecotox-1.3.1/ecotox/R/LCx.R | 588 +++++++------------- ecotox-1.3.1/ecotox/R/LTx.R | 517 +++++------------ ecotox-1.3.1/ecotox/R/lampreytime.R | 2 ecotox-1.3.1/ecotox/R/lampreytox.R | 2 ecotox-1.3.1/ecotox/README.md | 28 ecotox-1.3.1/ecotox/data/lampreytime.rda |binary ecotox-1.3.1/ecotox/data/lampreytox.rda |binary ecotox-1.3.1/ecotox/inst/CITATION | 8 ecotox-1.3.1/ecotox/man/LC_logit.Rd | 50 - ecotox-1.3.1/ecotox/man/LC_probit.Rd | 52 - ecotox-1.3.1/ecotox/man/LT_logit.Rd | 25 ecotox-1.3.1/ecotox/man/LT_probit.Rd | 24 ecotox-1.3.1/ecotox/man/lampreytime.Rd | 2 ecotox-1.3.1/ecotox/man/lampreytox.Rd | 2 ecotox-1.3.1/ecotox/tests/testthat/test-LC_logit.R | 29 ecotox-1.3.1/ecotox/tests/testthat/test-LC_probit.R | 33 - ecotox-1.3.1/ecotox/tests/testthat/test-LT_logit.R | 17 ecotox-1.3.1/ecotox/tests/testthat/test-LT_probit.R | 17 23 files changed, 576 insertions(+), 883 deletions(-)
Title: Meta-Analysis
Description: Functions for simple fixed and random effects
meta-analysis for two-sample comparisons and cumulative
meta-analyses. Draws standard summary plots, funnel plots, and
computes summaries and tests for association and heterogeneity.
Author: Thomas Lumley
Maintainer: Thomas Lumley <t.lumley@auckland.ac.nz>
Diff between rmeta versions 2.16 dated 2009-09-29 and 3.0 dated 2018-03-20
rmeta-2.16/rmeta/data/catheter.R |only rmeta-3.0/rmeta/Changes | 2 ++ rmeta-3.0/rmeta/DESCRIPTION | 17 +++++++++-------- rmeta-3.0/rmeta/MD5 |only rmeta-3.0/rmeta/NAMESPACE |only rmeta-3.0/rmeta/R/forestplot-grid.R | 3 --- rmeta-3.0/rmeta/R/forestplot.R | 2 +- rmeta-3.0/rmeta/R/meta.R | 2 +- rmeta-3.0/rmeta/data/catheter.rda |only rmeta-3.0/rmeta/man/forestplot.Rd | 27 ++++++++++++++++----------- rmeta-3.0/rmeta/man/meta.MH.Rd | 1 - rmeta-3.0/rmeta/man/meta.cum.Rd | 21 +++++++++++++++------ 12 files changed, 44 insertions(+), 31 deletions(-)
Title: Multivariate Polynomials
Description: Various utilities to manipulate multivariate polynomials.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between multipol versions 1.0-6 dated 2013-01-21 and 1.0-7 dated 2018-03-20
DESCRIPTION | 13 +++++----- MD5 | 16 +++++++------ NAMESPACE | 14 +++++++++++ R/multipol.R | 2 + build |only inst/doc/multipol.R |only inst/doc/multipol.pdf |binary man/multipol-package.Rd | 2 - man/print.Rd | 23 +++++++++++++++---- tests/aaa.R | 58 +++++++++++++++++++++++++++++++++++++++++++++--- 10 files changed, 107 insertions(+), 21 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi
platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 0.8.1.6 dated 2017-11-15 and 0.8.5 dated 2018-03-20
jmvcore-0.8.1.6/jmvcore/tests/testthat/test-profiletable.R |only jmvcore-0.8.5/jmvcore/DESCRIPTION | 8 +- jmvcore-0.8.5/jmvcore/MD5 | 18 +++--- jmvcore-0.8.5/jmvcore/R/analysis.R | 11 +-- jmvcore-0.8.5/jmvcore/R/array.R | 25 ++++++--- jmvcore-0.8.5/jmvcore/R/cell.R | 4 + jmvcore-0.8.5/jmvcore/R/options.R | 28 ++++++++-- jmvcore-0.8.5/jmvcore/R/results.R | 12 +++- jmvcore-0.8.5/jmvcore/R/table.R | 2 jmvcore-0.8.5/jmvcore/R/utils.R | 36 ++++++++++--- jmvcore-0.8.5/jmvcore/tests/testthat/test-parseaddress.R |only 11 files changed, 102 insertions(+), 42 deletions(-)
Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework
<http://taf.ices.dk> to organize data, methods, and results used in ICES
assessments. ICES is an organization facilitating international collaboration
in marine science.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesTAF versions 1.5-0 dated 2018-01-25 and 1.5-1 dated 2018-03-20
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 10 ++++++++++ R/flr2taf.R | 14 ++++++++++++-- R/makeAll.R | 2 +- R/msg.R | 2 +- R/sourceTAF.R | 25 +++++++++++++++---------- man/flr2taf.Rd | 7 ++++++- man/makeAll.Rd | 2 +- man/msg.Rd | 2 +- man/sourceTAF.Rd | 11 ++++++----- 11 files changed, 67 insertions(+), 36 deletions(-)
Title: Extreme Values in R
Description: Functions for extreme value theory, which may be
divided into the following groups; exploratory data analysis,
block maxima, peaks over thresholds (univariate and bivariate),
point processes, gev/gpd distributions.
Author: Bernhard Pfaff [aut, cre],
Eric Zivot [ctb],
Alexander McNeil [aut] (S original (EVIS)),
Alec Stephenson [trl] (R port of EVIS)
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between evir versions 1.7-3 dated 2012-07-26 and 1.7-4 dated 2018-03-20
DESCRIPTION | 33 ++++++++++++++++----------------- MD5 | 18 +++++++++--------- NAMESPACE | 14 ++++++++++---- data/bmw.rda |binary data/danish.rda |binary data/nidd.annual.rda |binary data/nidd.thresh.rda |binary data/siemens.rda |binary data/sp.raw.rda |binary data/spto87.rda |binary 10 files changed, 35 insertions(+), 30 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Description: Contains:
1) Facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear contrasts.
3) Miscellaneous other utilities.
Author: Søren Højsgaard <sorenh@math.aau.dk> and Ulrich Halekoh
<uhalekoh@health.sdu.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.5-15 dated 2016-03-31 and 4.6-1 dated 2018-03-20
doBy-4.5-15/doBy/R/BY-funBy.R |only doBy-4.5-15/doBy/R/BY-lapplyBy.R |only doBy-4.5-15/doBy/R/BY-lmBy.R |only doBy-4.5-15/doBy/R/BY-sampleBy.R |only doBy-4.5-15/doBy/R/BY-scaleBy2.R |only doBy-4.5-15/doBy/R/HmiscStuff.R |only doBy-4.5-15/doBy/R/linest.R |only doBy-4.5-15/doBy/R/linestGet.R |only doBy-4.5-15/doBy/R/linestLSmatrix.R |only doBy-4.5-15/doBy/R/linestUtilities.R |only doBy-4.5-15/doBy/data/beets.txt.gz |only doBy-4.5-15/doBy/data/budworm.txt.gz |only doBy-4.5-15/doBy/data/carcass.txt.gz |only doBy-4.5-15/doBy/data/carcassall.txt.gz |only doBy-4.5-15/doBy/inst/doc/LSmeans.R |only doBy-4.5-15/doBy/inst/doc/LSmeans.Rnw |only doBy-4.5-15/doBy/inst/doc/LSmeans.pdf |only doBy-4.5-15/doBy/man/DATA-NIRmilk.Rd |only doBy-4.5-15/doBy/man/DATA-beets.Rd |only doBy-4.5-15/doBy/man/DATA-breastcancer.Rd |only doBy-4.5-15/doBy/man/DATA-budworm.Rd |only doBy-4.5-15/doBy/man/DATA-carcass.Rd |only doBy-4.5-15/doBy/man/DATA-codstom.Rd |only doBy-4.5-15/doBy/man/DATA-crimeRate.Rd |only doBy-4.5-15/doBy/man/DATA-dietox.Rd |only doBy-4.5-15/doBy/man/DATA-haldCement.Rd |only doBy-4.5-15/doBy/man/DATA-milkman.Rd |only doBy-4.5-15/doBy/man/DATA-potatoes.Rd |only doBy-4.5-15/doBy/man/LSmeans.Rd |only doBy-4.5-15/doBy/man/createFunBy.Rd |only doBy-4.5-15/doBy/man/doBy.Rd |only doBy-4.5-15/doBy/man/is_estimable.Rd |only doBy-4.5-15/doBy/man/lapplyBy.Rd |only doBy-4.5-15/doBy/man/lmBy.Rd |only doBy-4.5-15/doBy/man/null_basis.Rd |only doBy-4.5-15/doBy/man/orderBy.Rd |only doBy-4.5-15/doBy/man/sampleBy.Rd |only doBy-4.5-15/doBy/man/scaleBy.Rd |only doBy-4.5-15/doBy/man/splitBy.Rd |only doBy-4.5-15/doBy/man/subsetBy.Rd |only doBy-4.5-15/doBy/man/summaryBy.Rd |only doBy-4.5-15/doBy/man/transformBy.Rd |only doBy-4.5-15/doBy/vignettes/LSmeans.Rnw |only doBy-4.6-1/doBy/ChangeLog | 1209 +++++++++---------- doBy-4.6-1/doBy/DESCRIPTION | 33 doBy-4.6-1/doBy/MD5 | 159 +- doBy-4.6-1/doBy/NAMESPACE | 247 ++- doBy-4.6-1/doBy/R/BY-orderBy.R | 211 +-- doBy-4.6-1/doBy/R/BY-splitBy2.R | 205 +-- doBy-4.6-1/doBy/R/BY-subsetBy.R | 143 +- doBy-4.6-1/doBy/R/BY-summaryBy2.R | 746 +++++++---- doBy-4.6-1/doBy/R/BY-transformBy.R | 85 - doBy-4.6-1/doBy/R/data-NIRmilk.R |only doBy-4.6-1/doBy/R/data-breastcancer.R |only doBy-4.6-1/doBy/R/data-budworm.R |only doBy-4.6-1/doBy/R/data-codstom.R |only doBy-4.6-1/doBy/R/data-crimerate.R |only doBy-4.6-1/doBy/R/data-doBy.R |only doBy-4.6-1/doBy/R/data-haldCement.R |only doBy-4.6-1/doBy/R/data-milkman.R |only doBy-4.6-1/doBy/R/data-potatoes.R |only doBy-4.6-1/doBy/R/descStat.R | 50 doBy-4.6-1/doBy/R/doby-utilities.R |only doBy-4.6-1/doBy/R/esticon.R | 634 ++++++---- doBy-4.6-1/doBy/R/firstlastObs.R | 117 + doBy-4.6-1/doBy/R/linest_LSmeans.R |only doBy-4.6-1/doBy/R/linest_compute.R |only doBy-4.6-1/doBy/R/linest_get.R |only doBy-4.6-1/doBy/R/linest_matrix.R |only doBy-4.6-1/doBy/R/linest_utilities.R |only doBy-4.6-1/doBy/R/recodeVar.R | 121 + doBy-4.6-1/doBy/R/renameCol.R | 129 +- doBy-4.6-1/doBy/R/subSeq.R | 172 +- doBy-4.6-1/doBy/R/timeSinceEvent.R | 474 ++++--- doBy-4.6-1/doBy/R/which.maxn.R | 87 - doBy-4.6-1/doBy/README.md |only doBy-4.6-1/doBy/build/vignette.rds |binary doBy-4.6-1/doBy/data/beets.RData |only doBy-4.6-1/doBy/data/budworm.RData |only doBy-4.6-1/doBy/data/carcass.RData |only doBy-4.6-1/doBy/data/carcassall.RData |only doBy-4.6-1/doBy/data/crimeRate.RData |only doBy-4.6-1/doBy/data/datalist | 5 doBy-4.6-1/doBy/data/fatacid.RData |only doBy-4.6-1/doBy/data/haldCement.RData |only doBy-4.6-1/doBy/data/potatoes.RData |only doBy-4.6-1/doBy/inst/doc/doBy.R | 292 +--- doBy-4.6-1/doBy/inst/doc/doBy.Rnw | 1701 ++++++++++++++------------- doBy-4.6-1/doBy/inst/doc/doBy.pdf |binary doBy-4.6-1/doBy/inst/doc/linest-lsmeans.R |only doBy-4.6-1/doBy/inst/doc/linest-lsmeans.Rnw |only doBy-4.6-1/doBy/inst/doc/linest-lsmeans.pdf |only doBy-4.6-1/doBy/man/by-order.Rd |only doBy-4.6-1/doBy/man/by-split.Rd |only doBy-4.6-1/doBy/man/by-subset.Rd |only doBy-4.6-1/doBy/man/by-summary.Rd |only doBy-4.6-1/doBy/man/by-transform.Rd |only doBy-4.6-1/doBy/man/data-NIRmilk.Rd |only doBy-4.6-1/doBy/man/data-beets.Rd |only doBy-4.6-1/doBy/man/data-breastcancer.Rd |only doBy-4.6-1/doBy/man/data-budworm.Rd |only doBy-4.6-1/doBy/man/data-carcass.Rd |only doBy-4.6-1/doBy/man/data-codstom.Rd |only doBy-4.6-1/doBy/man/data-crimeRate.Rd |only doBy-4.6-1/doBy/man/data-dietox.Rd |only doBy-4.6-1/doBy/man/data-haldCement.Rd |only doBy-4.6-1/doBy/man/data-milkman.Rd |only doBy-4.6-1/doBy/man/data-potatoes.Rd |only doBy-4.6-1/doBy/man/descStat.Rd | 84 - doBy-4.6-1/doBy/man/doBy-internal.Rd | 162 +- doBy-4.6-1/doBy/man/esticon.Rd | 308 ++-- doBy-4.6-1/doBy/man/fatacid.Rd |only doBy-4.6-1/doBy/man/firstlastobs.Rd | 125 + doBy-4.6-1/doBy/man/is-estimable.Rd |only doBy-4.6-1/doBy/man/linest-get.Rd |only doBy-4.6-1/doBy/man/linest-matrix.Rd |only doBy-4.6-1/doBy/man/linest.Rd | 168 +- doBy-4.6-1/doBy/man/ls-means.Rd |only doBy-4.6-1/doBy/man/null-basis.Rd |only doBy-4.6-1/doBy/man/parseGroupFormula.Rd | 75 - doBy-4.6-1/doBy/man/recodeVar.Rd | 90 - doBy-4.6-1/doBy/man/renameCol.Rd | 93 - doBy-4.6-1/doBy/man/subSeq.Rd | 101 - doBy-4.6-1/doBy/man/timeSinceEvent.Rd | 144 +- doBy-4.6-1/doBy/man/which.maxn.Rd | 99 - doBy-4.6-1/doBy/vignettes/doBy.Rnw | 1701 ++++++++++++++------------- doBy-4.6-1/doBy/vignettes/linest-lsmeans.Rnw |only 127 files changed, 5402 insertions(+), 4568 deletions(-)
Title: Categorical Data Analysis Program Package
Description: Categorical data analysis by AIC. The methodology is described in
Sakamoto (1992) <ISBN 978-0-7923-1429-5>.
Author: The Institute of Statistical Mathematics
Maintainer: Masami Saga <msaga@mtb.biglobe.ne.jp>
Diff between catdap versions 1.2.4 dated 2016-09-08 and 1.3.4 dated 2018-03-20
catdap-1.2.4/catdap/src/catdap1.c |only catdap-1.3.4/catdap/DESCRIPTION | 14 catdap-1.3.4/catdap/MD5 | 39 catdap-1.3.4/catdap/NAMESPACE | 2 catdap-1.3.4/catdap/R/catdap.R | 1925 +++++++++++++++---------- catdap-1.3.4/catdap/data/HealthData.rda |binary catdap-1.3.4/catdap/data/HelloGoodbye.rda |binary catdap-1.3.4/catdap/data/JNcharacter.rda |binary catdap-1.3.4/catdap/data/MissingHealthData.rda |only catdap-1.3.4/catdap/data/datalist | 1 catdap-1.3.4/catdap/inst/AUTHORS | 8 catdap-1.3.4/catdap/man/Barplot2WayTable.Rd | 28 catdap-1.3.4/catdap/man/HealthData.Rd | 31 catdap-1.3.4/catdap/man/HelloGoodbye.Rd | 3 catdap-1.3.4/catdap/man/JNcharacter.Rd | 31 catdap-1.3.4/catdap/man/MissingHealthData.Rd |only catdap-1.3.4/catdap/man/catdap-package.Rd | 56 catdap-1.3.4/catdap/man/catdap1.Rd | 66 catdap-1.3.4/catdap/man/catdap2.Rd | 218 +- catdap-1.3.4/catdap/src/catdap1m.c |only catdap-1.3.4/catdap/src/catdap2m.c | 70 catdap-1.3.4/catdap/src/catdap2mf.f | 762 +++++++-- catdap-1.3.4/catdap/src/init.c |only 23 files changed, 2163 insertions(+), 1091 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-04 3.1.1
2016-07-03 3.1.0
2015-08-17 0.1
Title: Fast Multivariate Log-Concave Density Estimation
Description: A fast solver for the maximum likelihood estimator (MLE) of a
multivariate log-concave probability function. Given a sample X, it estimates
a non-parametric density function whose logarithm is a concave function. Many
well-known parametric densities belong to that class, among them the normal
density, the uniform density, the exponential distribution and many more. This
package provides functions for the estimation of a log-concave density and
a mixture of log-concave densities in multiple dimensions. While being similar
to the package LogConcDEAD, fmlogcondens provides much fast run times for
large samples (>= 250 points). As a reference see Fabian Rathke, Christoph
Schnörr (2015), <doi:10.1515/auom-2015-0053>.
Author: Fabian Rathke [aut, cre],
Christoph Schnörr [aut],
Giovanni Garberoglio [cph]
Maintainer: Fabian Rathke <frathke@gmail.com>
Diff between fmlogcondens versions 1.0.0 dated 2018-03-09 and 1.0.1 dated 2018-03-20
fmlogcondens-1.0.0/fmlogcondens/man/calcExactIntegralC.Rd |only fmlogcondens-1.0.0/fmlogcondens/man/calcKernelDens.Rd |only fmlogcondens-1.0.0/fmlogcondens/man/callCalcExactIntegralC.Rd |only fmlogcondens-1.0.0/fmlogcondens/man/callNewtonBFGSLC.Rd |only fmlogcondens-1.0.0/fmlogcondens/man/callNewtonBFGSLInitC.Rd |only fmlogcondens-1.0.0/fmlogcondens/man/newtonBFGSLC.Rd |only fmlogcondens-1.0.0/fmlogcondens/man/newtonBFGSLInitC.Rd |only fmlogcondens-1.0.0/fmlogcondens/man/printAVXInfo.Rd |only fmlogcondens-1.0.0/fmlogcondens/man/recalcParamsC.Rd |only fmlogcondens-1.0.1/fmlogcondens/DESCRIPTION | 6 fmlogcondens-1.0.1/fmlogcondens/MD5 | 53 +++----- fmlogcondens-1.0.1/fmlogcondens/NAMESPACE | 8 + fmlogcondens-1.0.1/fmlogcondens/NEWS.md | 10 + fmlogcondens-1.0.1/fmlogcondens/R/callerFunctions.R | 61 ---------- fmlogcondens-1.0.1/fmlogcondens/R/correctIntegral.R | 4 fmlogcondens-1.0.1/fmlogcondens/R/paramFitGammaOne.R | 8 - fmlogcondens-1.0.1/fmlogcondens/build/vignette.rds |binary fmlogcondens-1.0.1/fmlogcondens/inst/doc/documentation.Rmd | 8 - fmlogcondens-1.0.1/fmlogcondens/inst/doc/documentation.html | 49 ++++---- fmlogcondens-1.0.1/fmlogcondens/src/AVXinfo.c | 8 + fmlogcondens-1.0.1/fmlogcondens/src/bfgsFullC.c | 31 +++-- fmlogcondens-1.0.1/fmlogcondens/src/bfgsInitC.c | 4 fmlogcondens-1.0.1/fmlogcondens/src/calcExactIntegral.c | 3 fmlogcondens-1.0.1/fmlogcondens/src/calcGradAVX.c | 3 fmlogcondens-1.0.1/fmlogcondens/src/calcGradC.c | 2 fmlogcondens-1.0.1/fmlogcondens/src/calcGradFloatC.c | 3 fmlogcondens-1.0.1/fmlogcondens/src/calcGradFullAVXC.c | 4 fmlogcondens-1.0.1/fmlogcondens/src/makeGridC.c | 18 ++ fmlogcondens-1.0.1/fmlogcondens/src/preCondGradAVXC.c | 21 ++- fmlogcondens-1.0.1/fmlogcondens/src/preCondGradFloatC.c | 20 ++- fmlogcondens-1.0.1/fmlogcondens/src/util.c | 10 + fmlogcondens-1.0.1/fmlogcondens/vignettes/documentation.Rmd | 8 - 32 files changed, 172 insertions(+), 170 deletions(-)
Title: Run 'roxygen2' on (Chunks of) Single Code Files
Description: Have you ever been tempted to create 'roxygen2'-style documentation
comments for one of your functions that was not part of one of your
packages (yet)?
This is exactly what this package is about: running 'roxygen2' on
(chunks of) a single code file.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <adc-r@arcor.de>
Diff between document versions 3.0.0 dated 2018-02-11 and 3.0.1 dated 2018-03-20
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/document.R | 2 +- inst/doc/Introduction_to_document.R | 8 +++++--- inst/doc/Introduction_to_document.Rmd | 10 ++++++---- inst/doc/Introduction_to_document.html | 17 +++++++++-------- vignettes/Introduction_to_document.Rmd | 10 ++++++---- 8 files changed, 41 insertions(+), 30 deletions(-)
Title: Multidimensional Scaling
Description: Provides the following approaches for multidimensional scaling (MDS) based on stress minimization using majorization (smacof): basic MDS on symmetric dissimilarity matrices,
MDS with external constraints on the configuration, individual differences scaling (idioscal, indscal, and friends), MDS with spherical restrictions, and unfolding. The MDS type can be ratio, interval, ordinal, and monotone splines.
Various tools and extensions like jackknife MDS, bootstrap MDS, permutation tests, MDS biplots, gravity models, inverse MDS, unidimensional scaling, drift vectors (asymmetric MDS), classical scaling, and Procrustes are implemented as well.
Author: Patrick Mair [aut, cre],
Jan De Leeuw [aut],
Ingwer Borg [ctb],
Patrick J. F. Groenen [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between smacof versions 1.9-6 dated 2017-05-11 and 1.10-5 dated 2018-03-20
DESCRIPTION | 8 - MD5 | 51 +++--- NAMESPACE | 3 R/nextperm.R | 4 R/plot.mdsbi.R | 2 R/plot.smacof.R | 11 - R/plot.smacofID.r | 8 - R/plot.smacofR.R | 138 +++++++++++------- R/plot.smacofboot.R | 16 +- R/print.smacofR.R | 11 - R/print.uniscale.R | 2 R/smacofRect.R | 367 +++++++++++++++++++++++++++++++++++++----------- R/smacofSphere.R | 2 R/smacofSym.R | 4 R/uniscale.R | 7 build/vignette.rds |binary data/perception.rda |binary inst/NEWS.Rd | 54 +++++++ inst/doc/smacof.pdf |binary man/Procrustes.Rd | 6 man/biplotmds.smacof.Rd | 5 man/bootmds.smacofB.Rd | 2 man/plot.smacof.rd | 13 - man/smacofRect.Rd | 69 +++++++-- man/smacofSym.Rd | 2 man/transform.Rd |only man/uniscale.Rd | 5 27 files changed, 566 insertions(+), 224 deletions(-)
Title: Event Data Repository
Description: Event dataset repository including both real-life and artificial event logs. They can be used in combination with functionalities provided by the 'bupaR' packages 'edeaR', 'processmapR', etc.
Author: Gert Janssenswillen [aut, cre]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between eventdataR versions 0.1.2 dated 2017-12-05 and 0.2.0 dated 2018-03-20
eventdataR-0.1.2/eventdataR/data/BPIC14_incident_case_attributes.rda |only eventdataR-0.1.2/eventdataR/data/BPIC14_incident_log.rda |only eventdataR-0.1.2/eventdataR/data/BPIC15_1.rda |only eventdataR-0.1.2/eventdataR/man/BPIC14_incident_case_attributes.Rd |only eventdataR-0.1.2/eventdataR/man/BPIC14_incident_log.Rd |only eventdataR-0.1.2/eventdataR/man/BPIC15_1.Rd |only eventdataR-0.2.0/eventdataR/DESCRIPTION | 8 - eventdataR-0.2.0/eventdataR/LICENSE | 2 eventdataR-0.2.0/eventdataR/MD5 | 29 ++-- eventdataR-0.2.0/eventdataR/R/datasets_documentation.R | 61 ++++++---- eventdataR-0.2.0/eventdataR/build/vignette.rds |binary eventdataR-0.2.0/eventdataR/data/datalist |only eventdataR-0.2.0/eventdataR/data/hospital.rda |only eventdataR-0.2.0/eventdataR/data/hospital_billing.rda |only eventdataR-0.2.0/eventdataR/data/patients.rda |binary eventdataR-0.2.0/eventdataR/data/sepsis.rda |binary eventdataR-0.2.0/eventdataR/data/traffic_fines.rda |only eventdataR-0.2.0/eventdataR/inst/doc/eventdataR.html | 4 eventdataR-0.2.0/eventdataR/man/hospital.Rd |only eventdataR-0.2.0/eventdataR/man/hospital_billing.Rd |only eventdataR-0.2.0/eventdataR/man/sepsis.Rd | 2 eventdataR-0.2.0/eventdataR/man/traffic_fines.Rd |only 22 files changed, 60 insertions(+), 46 deletions(-)
Title: Generate Descriptive Statistics & Explore Statistical
Distributions
Description: Generate descriptive statistics such as measures of location,
dispersion, frequency tables, cross tables, group summaries and multiple
one/two way tables. Visualize and compute percentiles/probabilities of
normal, t, f, chi square and binomial distributions.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between descriptr versions 0.4.0 dated 2018-02-10 and 0.4.1 dated 2018-03-20
DESCRIPTION | 8 MD5 | 110 ++++++------ NAMESPACE | 15 + NEWS.md | 42 ++++ R/dist-binomial.R | 46 +++-- R/dist-chisquare.R | 40 ++-- R/dist-f.R | 41 ++-- R/dist-normal.R | 38 ++-- R/dist-t.R | 36 ++-- R/ds-cross-mult.R | 2 R/ds-cross-table.R | 109 ++++++++---- R/ds-describe.R | 255 +++++++++++++++++++++++++---- R/ds-descriptr.R | 2 R/ds-freq-cont.R | 91 ++++++---- R/ds-freq-mult.R | 32 +++ R/ds-freq-table.R | 71 +++++--- R/ds-group-summary.R | 67 +++++-- R/ds-multistats.R | 29 ++- R/ds-output.R | 146 +++++++++++++--- R/ds-screener.R | 62 +++---- R/ds-summary-stats.R | 67 ++----- R/ds-utils.R | 33 +++ README.md | 50 +++-- build/vignette.rds |binary inst/application/logic/logic_exit_button.R |only inst/application/server.R | 1 inst/application/ui.R | 5 inst/application/ui/ui_analyze.R | 2 inst/application/ui/ui_exit_button.R |only inst/doc/descriptive-stats.R | 9 - inst/doc/descriptive-stats.Rmd | 18 +- inst/doc/descriptive-stats.html | 219 ++++++++++++++---------- man/dist_binom_plot.Rd | 31 +-- man/dist_chi_plot.Rd | 27 +-- man/dist_f_plot.Rd | 32 +-- man/dist_norm_plot.Rd | 25 +- man/dist_t.Rd | 24 +- man/ds_cross_table.Rd | 53 ++---- man/ds_css.Rd | 4 man/ds_cvar.Rd | 4 man/ds_extreme_obs.Rd |only man/ds_freq_cont.Rd | 38 +--- man/ds_freq_table.Rd | 28 +-- man/ds_gmean.Rd | 4 man/ds_group_summary.Rd | 39 ++-- man/ds_hmean.Rd | 4 man/ds_kurtosis.Rd | 4 man/ds_mdev.Rd | 4 man/ds_measures_location.Rd |only man/ds_measures_symmetry.Rd |only man/ds_measures_variation.Rd |only man/ds_mode.Rd | 4 man/ds_multi_stats.Rd | 13 - man/ds_percentiles.Rd |only man/ds_range.Rd | 4 man/ds_screener.Rd | 52 ++--- man/ds_skewness.Rd | 4 man/ds_std_error.Rd |only man/ds_summary_stats.Rd | 47 ----- vignettes/descriptive-stats.Rmd | 18 +- 60 files changed, 1364 insertions(+), 745 deletions(-)
Title: Tools for Preprocessing Visual World Data
Description: Gaze data from the Visual World Paradigm requires significant
preprocessing prior to plotting and analyzing the data. This package
provides functions for preparing visual world eye-tracking data for
statistical analysis and plotting. It can prepare data for linear
analyses (e.g., ANOVA, Gaussian-family LMER, Gaussian-family GAMM) as
well as logistic analyses (e.g., binomial-family LMER and binomial-family GAMM).
Additionally, it contains various plotting functions for creating grand average and
conditional average plots. See the vignette for samples of the functionality.
Currently, the functions in this package are designed for handling data
collected with SR Research Eyelink eye trackers using Sample Reports created
in SR Research Data Viewer. While we would like to add functionality
for data collected with other systems in the future, the current package is
considered to be feature-complete; further updates will mainly entail maintenance
and the addition of minor functionality.
Author: Vincent Porretta [aut, cre],
Aki-Juhani Kyröläinen [aut],
Jacolien van Rij [ctb],
Juhani Järvikivi [ctb]
Maintainer: Vincent Porretta <vincentporretta@gmail.com>
Diff between VWPre versions 1.0.1 dated 2017-12-04 and 1.1.0 dated 2018-03-20
DESCRIPTION | 10 MD5 | 51 - NAMESPACE | 1 R/VWPre.R | 4 R/checking.R | 48 + R/formatting.R | 362 ++++++++--- R/interactive.R | 1138 +++++++++++++++++------------------ R/plotting.R | 13 R/zzz.R | 58 - build/vignette.rds |binary inst/CITATION | 41 - inst/NEWS | 475 +++++++------- inst/doc/SR_Basic_Preprocessing.R | 10 inst/doc/SR_Basic_Preprocessing.Rmd | 16 inst/doc/SR_Basic_Preprocessing.html | 203 +++--- inst/doc/SR_Interest_Areas.html | 106 +-- inst/doc/SR_Message_Alignment.html | 156 ++-- inst/doc/SR_Plotting.Rmd | 2 inst/doc/SR_Plotting.html | 144 ++-- man/VWPre.Rd | 4 man/check_eye_recording.Rd | 5 man/plot_avg.Rd | 4 man/plot_avg_diff.Rd | 6 man/rm_extra_DVcols.Rd |only man/select_recorded_eye.Rd | 8 vignettes/SR_Basic_Preprocessing.Rmd | 16 vignettes/SR_Plotting.Rmd | 2 27 files changed, 1595 insertions(+), 1288 deletions(-)
Title: Spatial Predictive Modeling
Description: Introduction to some novel accurate hybrid methods of geostatistical and machine learning methods for spatial predictive modelling. It contains two commonly used geostatistical methods, two machine learning methods, four hybrid methods and two averaging methods. For each method, two functions are provided. One function is for assessing the predictive errors and accuracy of the method based on cross-validation. The other one is for generating spatial predictions using the method. For details please see: Li, J., Potter, A., Huang, Z., Daniell, J. J. and Heap, A. (2010) <https:www.ga.gov.au/metadata-gateway/metadata/record/gcat_71407>
Li, J., Heap, A. D., Potter, A., Huang, Z. and Daniell, J. (2011) <doi:10.1016/j.csr.2011.05.015>
Li, J., Heap, A. D., Potter, A. and Daniell, J. (2011) <doi:10.1016/j.envsoft.2011.07.004>
Li, J., Potter, A., Huang, Z. and Heap, A. (2012) <https:www.ga.gov.au/metadata-gateway/metadata/record/74030>.
Author: Jin Li [aut, cre]
Maintainer: Jin Li <jin.li@ga.gov.au>
Diff between spm versions 1.0.0 dated 2017-08-25 and 1.1.0 dated 2018-03-20
DESCRIPTION | 10 +- MD5 | 104 +++++++++++++++------------ NAMESPACE | 9 ++ R/RFcv.R | 19 +--- R/gbmcv.R | 6 - R/gbmidwcv.R | 2 R/gbmokcv.R | 4 - R/gbmokgbmidwcv.R | 4 - R/gbmokgbmidwpred.R | 11 +- R/gbmokpred.R | 11 +- R/gbmpred.R | 4 - R/idwcv.R | 2 R/okcv.R | 2 R/okpred.R | 14 +-- R/pred.acc.R | 62 ++++++++++++---- R/rfidwcv.R | 2 R/rfokcv.R | 2 R/rfokpred.R | 13 +-- R/rfokrfidwcv.R | 2 R/rfokrfidwpred.R | 13 +-- R/rgcv.R |only R/rgidwcv.R |only R/rgidwpred.R |only R/rgokcv.R |only R/rgokpred.R |only R/rgokrgidwcv.R |only R/rgokrgidwpred.R |only R/rgpred.R |only R/tovecv.acc.R |only R/vecv.acc.R | 1 data/hard.rda |binary inst/doc/spm.R | 122 +++++++++++++++---------------- inst/doc/spm.Rmd | 173 ++++++++++++++++++++++++--------------------- inst/doc/spm.html | 187 +++++++++++++++++++++++++------------------------ man/RFcv.Rd | 11 +- man/gbmcv.Rd | 6 - man/gbmidwcv.Rd | 2 man/gbmokcv.Rd | 4 - man/gbmokgbmidwcv.Rd | 4 - man/gbmokgbmidwpred.Rd | 3 man/gbmokpred.Rd | 3 man/gbmpred.Rd | 4 - man/hard.Rd | 6 - man/idwcv.Rd | 2 man/okcv.Rd | 2 man/okpred.Rd | 2 man/pred.acc.Rd | 20 ++++- man/rfidwcv.Rd | 2 man/rfokcv.Rd | 2 man/rfokpred.Rd | 5 - man/rfokrfidwcv.Rd | 2 man/rfokrfidwpred.Rd | 5 - man/rgcv.Rd |only man/rgidwcv.Rd |only man/rgidwpred.Rd |only man/rgokcv.Rd |only man/rgokpred.Rd |only man/rgokrgidwcv.Rd |only man/rgokrgidwpred.Rd |only man/rgpred.Rd |only man/tovecv.Rd |only vignettes/spm.Rmd | 173 ++++++++++++++++++++++++--------------------- 62 files changed, 575 insertions(+), 462 deletions(-)