Title: Mapping Fisheries Data and Spatial Analysis Tools
Description: This software has evolved from fisheries research conducted at the
Pacific Biological Station (PBS) in 'Nanaimo', British Columbia, Canada. It
extends the R language to include two-dimensional plotting features similar
to those commonly available in a Geographic Information System (GIS).
Embedded C code speeds algorithms from computational geometry, such as
finding polygons that contain specified point events or converting between
longitude-latitude and Universal Transverse Mercator (UTM) coordinates.
Additionally, we include 'C++' code developed by Angus Johnson for the
'Clipper' library, data for a global shoreline, and other data sets in the
public domain. Under the user's R library directory '.libPaths()',
specifically in './PBSmapping/doc', a complete user's guide is offered and
should be consulted to use package functions effectively.
Author: Jon T. Schnute [aut],
Nicholas Boers [aut],
Rowan Haigh [aut, cre],
Alex Couture-Beil [ctb],
Denis Chabot [ctb],
Chris Grandin [ctb],
Angus Johnson [ctb],
Paul Wessel [ctb],
Franklin Antonio [ctb],
Nicholas J. Lewin-Koh [ctb],
Roger Bivand [ctb]
Maintainer: Rowan Haigh <rowan.haigh@dfo-mpo.gc.ca>
Diff between PBSmapping versions 2.70.4 dated 2017-06-29 and 2.70.5 dated 2018-06-06
PBSmapping-2.70.4/PBSmapping/inst/doc/index.html |only PBSmapping-2.70.5/PBSmapping/DESCRIPTION | 27 PBSmapping-2.70.5/PBSmapping/MD5 | 10 PBSmapping-2.70.5/PBSmapping/R/PBSmapping.r | 32 PBSmapping-2.70.5/PBSmapping/inst/doc/ChangeLog.txt | 1152 +++++++++++--------- PBSmapping-2.70.5/PBSmapping/inst/doc/Links.html |only PBSmapping-2.70.5/PBSmapping/src/clipper.cpp | 2 7 files changed, 728 insertions(+), 495 deletions(-)
More information about plotlyGeoAssets at CRAN
Permanent link
More information about kendallRandomWalks at CRAN
Permanent link
Title: Score Test and Meta-Analysis Based on Saddlepoint Approximation
Description: Performs score test using saddlepoint approximation to estimate the null distribution. Also prepares summary statistics for meta-analysis and performs meta-analysis to combine multiple association results. For the latest version, please check <https://github.com/leeshawn/SPAtest>.
Author: Rounak Dey, Seunggeun Lee
Maintainer: Rounak Dey <deyrnk@umich.edu>
Diff between SPAtest versions 2.0.2 dated 2017-11-03 and 3.0.0 dated 2018-06-06
DESCRIPTION | 12 MD5 | 12 NAMESPACE | 4 R/SPA_functions.R | 973 ++++++++++++++++++++++++++++-- man/SPAmeta.Rd |only man/ScoreTest_SPA.Rd | 4 man/ScoreTest_SPA_wMeta.Rd |only man/ScoreTest_wSaddleApprox_NULL_Model.Rd | 2 8 files changed, 954 insertions(+), 53 deletions(-)
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.0.10 dated 2018-04-25 and 1.0.11 dated 2018-06-06
DESCRIPTION | 11 +- MD5 | 54 +++++------ NAMESPACE | 4 NEWS.md | 15 +++ R/as_labelled.R | 201 ++++++++++++++++++++++------------------- R/get_label.R | 72 +++++++------- R/get_labels.R | 37 ------- R/get_model_labels.R | 32 +++++- R/get_values.R | 2 R/helpfunctions.R | 4 R/read_write.R | 13 +- R/set_label.R | 4 R/set_labels.R | 4 R/tidiers.R | 9 + R/zap_labels.R | 8 - README.md | 73 +++++++------- inst/CITATION | 8 - inst/doc/intro_sjlabelled.html | 79 ++++++++-------- inst/doc/labelleddata.html | 4 man/get_label.Rd | 3 man/get_labels.Rd | 39 ------- man/get_term_labels.Rd | 6 + man/get_values.Rd | 2 man/read_spss.Rd | 2 man/set_label.Rd | 6 - man/set_labels.Rd | 5 - man/write_spss.Rd | 7 - man/zap_labels.Rd | 8 - 28 files changed, 347 insertions(+), 365 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains some auxiliary functions for multiple
imputation which complements existing functionality
in R.
In addition to some utility functions, main features
include plausible value imputation, multilevel
imputation functions (arbitrary number of levels,
hierarchical and non-hierarchical datasets),
imputation using partial least squares (PLS) for
high dimensional predictors, and nested multiple
imputation.
Author: Alexander Robitzsch [aut, cre], Simon Grund [aut],
Thorsten Henke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 2.11-87 dated 2018-05-21 and 2.12-24 dated 2018-06-06
DESCRIPTION | 10 - MD5 | 124 +++++++++------- NAMESPACE | 4 R/MIwaldtest.R | 213 +++++++---------------------- R/MIwaldtest_qhat2list.R |only R/MIwaldtest_u2list.R |only R/NMIwaldtest.R | 164 +++++----------------- R/NMIwaldtest_compute_statistic.R |only R/NMIwaldtest_qhat2list.R |only R/NMIwaldtest_u2list.R |only R/NestedImputationList.R | 14 - R/RcppExports.R | 2 R/create_interactions.R | 12 - R/datalist2mids.R | 23 --- R/datlist_create.R | 16 +- R/ma_exists.R |only R/ma_exists_get.R |only R/mice.1chain.R | 80 +++------- R/mice.impute.2l.pls2.R | 16 +- R/mice.impute.2lonly.function.R | 38 +++-- R/mice.impute.ml.lmer.R | 26 +-- R/mice.impute.norm3.R | 9 - R/mice.impute.plausible.values.R | 29 +-- R/mice.impute.pls.R | 20 +- R/mice_imputation_extract_list_arguments.R | 6 R/mice_imputation_get_states.R | 20 +- R/mice_imputation_pls_do_impute.R | 5 R/mice_imputation_prepare_2l_functions.R | 50 ++++-- R/mice_inits.R |only R/mice_ml_lmer_extract_input.R | 12 - R/mice_ml_lmer_interactions_pls.R | 2 R/mice_multilevel_imputation_pmm5.R | 9 - R/micombine.cor.R | 74 +++++----- R/micombine.cov.R | 50 +++--- R/norm.draw3.R | 6 R/plot.mids.1chain.R |only R/rcpp_create_header_file.R | 4 R/string_extract_part.R | 11 + R/summary.MIwaldtest.R |only R/summary.NMIwaldtest.R |only R/summaryMIwaldtest_linear_hyp.R |only inst/NEWS | 24 ++- man/Rhat.mice.Rd | 4 man/complete.miceadds.Rd | 6 man/data.graham.Rd | 4 man/datlist_create.Rd | 4 man/filename_split.Rd | 6 man/lm.cluster.Rd | 4 man/ma.wtd.statNA.Rd | 6 man/mi.anova.Rd | 6 man/mice.1chain.Rd | 36 +--- man/mice.impute.2l.contextual.pmm.Rd | 4 man/mice.impute.2l.latentgroupmean.ml.Rd | 6 man/mice.impute.2lonly.function.Rd | 39 ++--- man/mice.impute.bygroup.Rd | 10 - man/mice.impute.grouped.Rd | 4 man/mice.impute.hotDeck.Rd | 4 man/mice.impute.ml.lmer.Rd | 18 +- man/mice.impute.plausible.values.Rd | 43 ++--- man/mice.impute.pls.Rd | 10 - man/mice.impute.tricube.pmm.Rd | 12 - man/mice.impute.weighted.pmm.Rd | 6 man/mice.nmi.Rd | 6 man/mice_impute_2l_lmer.Rd | 32 ++-- man/mice_inits.Rd |only man/miceadds-utilities.Rd |only man/micombine.cor.Rd | 6 man/visitSequence.determine.Rd | 8 - man/write.datlist.Rd | 5 src/RcppExports.cpp | 2 70 files changed, 601 insertions(+), 763 deletions(-)
Title: Distributions for Generalized Additive Models for Location Scale
and Shape
Description: A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a ''log'' or a ''logit' transformation respectively.
Author: Mikis Stasinopoulos [aut, cre, cph],
Robert Rigby [aut],
Calliope Akantziliotou [ctb],
Vlasios Voudouris [ctb],
Gillian Heller [ctb],
Raydonal Ospina [ctb],
Nicoletta Motpan [ctb],
Fiona McElduff [ctb],
Majid Djennad [ctb],
Marco Enea [ctb],
Alexios Ghalanos [ctb],
Christos Argyropoulos [ctb],
Almond Stocker [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.dist versions 5.0-5 dated 2018-04-30 and 5.0-6 dated 2018-06-06
gamlss.dist-5.0-5/gamlss.dist/man/gamlss.dist.package.Rd |only gamlss.dist-5.0-6/gamlss.dist/DESCRIPTION | 39 +++++++---- gamlss.dist-5.0-6/gamlss.dist/MD5 | 15 ++-- gamlss.dist-5.0-6/gamlss.dist/NAMESPACE | 1 gamlss.dist-5.0-6/gamlss.dist/R/SIMPLEX.R |only gamlss.dist-5.0-6/gamlss.dist/R/genFamily.R | 52 +++++++-------- gamlss.dist-5.0-6/gamlss.dist/build |only gamlss.dist-5.0-6/gamlss.dist/man/BE.Rd | 12 +-- gamlss.dist-5.0-6/gamlss.dist/man/SIMPLEX.Rd |only gamlss.dist-5.0-6/gamlss.dist/man/gamlss.dist-package.Rd |only gamlss.dist-5.0-6/gamlss.dist/man/gamlss.family.Rd | 2 11 files changed, 70 insertions(+), 51 deletions(-)
Title: Extreme Value Mixture Modelling, Threshold Estimation and
Boundary Corrected Kernel Density Estimation
Description: The usual distribution functions, maximum likelihood inference and
model diagnostics for univariate stationary extreme value mixture models
are provided. Kernel density estimation including various boundary
corrected kernel density estimation methods and a wide choice of kernels,
with cross-validation likelihood based bandwidth estimator.
Reasonable consistency with the base functions in the 'evd' package is
provided, so that users can safely interchange most code.
Author: Carl Scarrott, Yang Hu and Alfadino Akbar, University of Canterbury
Maintainer: Carl Scarrott <carl.scarrott@canterbury.ac.nz>
Diff between evmix versions 2.10 dated 2018-04-15 and 2.11 dated 2018-06-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/evmix-package.r | 6 ++++-- inst/doc/Rd2.pdf |binary inst/doc/UserGuide_compressed.pdf |binary man/evmix-package.Rd | 4 ++-- 6 files changed, 15 insertions(+), 13 deletions(-)
Title: Cross-Recurrence Quantification Analysis for Categorical and
Continuous Time-Series
Description: Cross-recurrence quantification analysis
of two time-series, of either categorical or
continuous values. It provides different methods
for profiling cross-recurrence, i.e., only looking
at the diagonal recurrent points, as well as more
in-depth measures of the whole cross-recurrence plot,
e.g., recurrence rate. Please refer to by Coco and Dale (2014)
<doi:10.3389/fpsyg.2014.00510> for further details about the method.
Author: Moreno I. Coco and Rick Dale with contributions of James D. Dixon and John Nash
Maintainer: Moreno I. Coco <moreno.cocoi@gmail.com>
Diff between crqa versions 1.0.6 dated 2015-07-15 and 1.0.7 dated 2018-06-06
DESCRIPTION | 14 - MD5 | 26 +- NAMESPACE | 52 ++-- R/crqa.R | 570 +++++++++++++++++++++++++++--------------------------- R/drpdfromts.R | 170 +++++++--------- R/plotRP.R |only R/runcrqa.R | 304 ++++++++++++++-------------- R/tt.R | 282 +++++++++++++------------- R/wincrqa.R | 170 ++++++++-------- R/windowdrp.R | 33 +-- README.md |only man/crqa.Rd | 251 +++++++++++------------ man/drpdfromts.Rd | 135 +++++++----- man/plotRP.Rd |only man/windowdrp.Rd | 180 +++++++++-------- src/crqa_init.c |only 16 files changed, 1124 insertions(+), 1063 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models and mixed effects models. However, some of the functions
also deal with other statistical measures, like Cronbach's Alpha,
Cramer's V, Phi etc.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.14.3 dated 2018-05-02 and 0.15.0 dated 2018-06-06
sjstats-0.14.3/sjstats/R/sum.R |only sjstats-0.14.3/sjstats/man/mn.Rd |only sjstats-0.15.0/sjstats/DESCRIPTION | 20 sjstats-0.15.0/sjstats/MD5 | 112 ++-- sjstats-0.15.0/sjstats/NAMESPACE | 19 sjstats-0.15.0/sjstats/NEWS.md | 28 + sjstats-0.15.0/sjstats/R/HDI.R | 228 ++++++-- sjstats-0.15.0/sjstats/R/S3-methods.R | 156 ++++- sjstats-0.15.0/sjstats/R/check_model_assumptions.R | 5 sjstats-0.15.0/sjstats/R/efc.R | 8 sjstats-0.15.0/sjstats/R/equi_test.R |only sjstats-0.15.0/sjstats/R/eta_sq.R | 24 sjstats-0.15.0/sjstats/R/grpmean.R | 5 sjstats-0.15.0/sjstats/R/helpfunctions.R | 6 sjstats-0.15.0/sjstats/R/icc.R | 15 sjstats-0.15.0/sjstats/R/mean_n.R | 8 sjstats-0.15.0/sjstats/R/mediation.R |only sjstats-0.15.0/sjstats/R/merMod_p.R | 84 ++- sjstats-0.15.0/sjstats/R/mwu.R | 2 sjstats-0.15.0/sjstats/R/n_eff.R | 36 - sjstats-0.15.0/sjstats/R/pred_vars.R | 55 +- sjstats-0.15.0/sjstats/R/pseudo_r2.R | 135 ++++- sjstats-0.15.0/sjstats/R/rmse.R | 4 sjstats-0.15.0/sjstats/R/rope.R | 42 - sjstats-0.15.0/sjstats/R/se.R | 22 sjstats-0.15.0/sjstats/R/sjStatistics.R | 7 sjstats-0.15.0/sjstats/R/std_b.R | 316 ++++++------ sjstats-0.15.0/sjstats/R/tidy_stan.R | 49 + sjstats-0.15.0/sjstats/R/weight.R | 2 sjstats-0.15.0/sjstats/R/xtab_statistics.R | 4 sjstats-0.15.0/sjstats/README.md | 120 ++-- sjstats-0.15.0/sjstats/build/partial.rdb |binary sjstats-0.15.0/sjstats/build/vignette.rds |binary sjstats-0.15.0/sjstats/inst/doc/anova-statistics.html | 30 - sjstats-0.15.0/sjstats/inst/doc/bayesian-statistics.R |only sjstats-0.15.0/sjstats/inst/doc/bayesian-statistics.Rmd |only sjstats-0.15.0/sjstats/inst/doc/bayesian-statistics.html |only sjstats-0.15.0/sjstats/inst/doc/mixedmodels-statistics.R | 11 sjstats-0.15.0/sjstats/inst/doc/mixedmodels-statistics.Rmd | 16 sjstats-0.15.0/sjstats/inst/doc/mixedmodels-statistics.html | 96 +-- sjstats-0.15.0/sjstats/man/check_assumptions.Rd | 5 sjstats-0.15.0/sjstats/man/cod.Rd | 2 sjstats-0.15.0/sjstats/man/efc.Rd | 8 sjstats-0.15.0/sjstats/man/eta_sq.Rd | 2 sjstats-0.15.0/sjstats/man/grpmean.Rd | 4 sjstats-0.15.0/sjstats/man/hdi.Rd | 195 ++++++- sjstats-0.15.0/sjstats/man/mean_n.Rd | 8 sjstats-0.15.0/sjstats/man/mwu.Rd | 6 sjstats-0.15.0/sjstats/man/p_value.Rd | 17 sjstats-0.15.0/sjstats/man/pred_vars.Rd | 3 sjstats-0.15.0/sjstats/man/r2.Rd | 17 sjstats-0.15.0/sjstats/man/reliab_test.Rd | 4 sjstats-0.15.0/sjstats/man/rmse.Rd | 4 sjstats-0.15.0/sjstats/man/sjstats-package.Rd | 2 sjstats-0.15.0/sjstats/man/std_beta.Rd | 6 sjstats-0.15.0/sjstats/man/table_values.Rd | 7 sjstats-0.15.0/sjstats/man/tidy_stan.Rd | 12 sjstats-0.15.0/sjstats/man/weight.Rd | 2 sjstats-0.15.0/sjstats/man/xtab_statistics.Rd | 4 sjstats-0.15.0/sjstats/vignettes/bayesian-statistics.Rmd |only sjstats-0.15.0/sjstats/vignettes/mixedmodels-statistics.Rmd | 16 61 files changed, 1339 insertions(+), 650 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-27 0.1.1
Title: GEO RNA-Seq Experiments Processing Pipeline
Description: An R based pipeline to download and process Gene Expression Omnibus (GEO) RNA-seq data.
For a given GEO series accession ID, this pipeline generates metadata,
both gene and transcript level counts, and quality control (QC) report.
This package is mainly developed to process the GEO RNA-seq datasets
for the web platform GREIN. More details about GREP2 and GREIN can be
found here <doi:10.1101/326223>.
Author: Naim Al Mahi [cre, aut],
Mario Medvedovic [aut, ctb]
Maintainer: Naim Al Mahi <mahina@mail.uc.edu>
Diff between GREP2 versions 0.99.9 dated 2018-06-04 and 1.0.0 dated 2018-06-06
DESCRIPTION | 11 ++-- MD5 | 25 +++++---- R/process_geo_rnaseq.R | 13 ++--- R/run_multiqc.R | 5 + R/trim_fastq.R | 9 +-- README.md | 101 +++++++++++++++++++++++++++++++++++++++- inst/CITATION |only inst/doc/vignette.R | 72 +++++++++++++--------------- inst/doc/vignette.Rmd | 78 ++++++++++++++---------------- inst/doc/vignette.html | 116 +++++++++++++++++++++++----------------------- man/process_geo_rnaseq.Rd | 12 +--- man/run_multiqc.Rd | 5 + man/trim_fastq.Rd | 11 +--- vignettes/vignette.Rmd | 78 ++++++++++++++---------------- 14 files changed, 311 insertions(+), 225 deletions(-)
Title: High Precision Timing of R Expressions
Description: Tools to accurately benchmark and analyze execution times for R expressions.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between bench versions 1.0.0 dated 2018-05-27 and 1.0.1 dated 2018-06-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ README.md | 18 ++++++++++-------- src/nanotime.c | 18 +++++++++++------- tests/testthat/test-system_time.R | 2 ++ 6 files changed, 36 insertions(+), 23 deletions(-)