Title: 'Toggl.com' Api for 'Rstudio'
Description: Use the <http://toggl.com> time tracker api through R.
Author: Vincent Guyader [aut, cre],
ThinkR [cph, fnd]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between togglr versions 0.1.3 dated 2017-12-07 and 0.1.33 dated 2018-08-13
togglr-0.1.3/togglr/man/open_toggl_website.Rd |only togglr-0.1.33/togglr/DESCRIPTION | 27 ++--- togglr-0.1.33/togglr/MD5 | 57 +++++----- togglr-0.1.33/togglr/NAMESPACE | 15 ++ togglr-0.1.33/togglr/R/client.R | 8 - togglr-0.1.33/togglr/R/get_dashboard.R | 12 +- togglr-0.1.33/togglr/R/get_project.R | 45 ++++++++ togglr-0.1.33/togglr/R/get_time_entries.R |only togglr-0.1.33/togglr/R/onAttach.R | 3 togglr-0.1.33/togglr/R/open_toggl.R | 19 ++- togglr-0.1.33/togglr/R/put.R | 6 - togglr-0.1.33/togglr/R/put_project.R | 6 - togglr-0.1.33/togglr/R/tools.R | 3 togglr-0.1.33/togglr/README.md | 89 ++++++++++++++--- togglr-0.1.33/togglr/build/vignette.rds |binary togglr-0.1.33/togglr/inst/dependencies.R |only togglr-0.1.33/togglr/inst/doc/togglr.R | 3 togglr-0.1.33/togglr/inst/doc/togglr.Rmd | 13 +- togglr-0.1.33/togglr/inst/doc/togglr.html | 21 ++-- togglr-0.1.33/togglr/man/correct_date.Rd | 2 togglr-0.1.33/togglr/man/create_client.Rd | 7 - togglr-0.1.33/togglr/man/get_all_project_names.Rd | 2 togglr-0.1.33/togglr/man/get_dashboard.Rd | 2 togglr-0.1.33/togglr/man/get_project_id.Rd | 7 - togglr-0.1.33/togglr/man/get_project_id_and_name.Rd |only togglr-0.1.33/togglr/man/get_project_total.Rd | 5 togglr-0.1.33/togglr/man/get_time_entries.Rd |only togglr-0.1.33/togglr/man/open_toggl_website_app.Rd |only togglr-0.1.33/togglr/man/open_toggl_website_profile.Rd |only togglr-0.1.33/togglr/man/toggl_create.Rd | 4 togglr-0.1.33/togglr/man/toggl_create_project.Rd | 6 - togglr-0.1.33/togglr/man/toggl_start.Rd | 5 togglr-0.1.33/togglr/vignettes/togglr.Rmd | 13 +- 33 files changed, 264 insertions(+), 116 deletions(-)
Title: Core Utilities for Developing and Running Spatially Explicit
Discrete Event Simulation Models
Description: Provide the core discrete event simulation (DES) framework for
implementing spatially explicit simulation models. The core DES components
facilitate modularity, and easily enable the user to include additional
functionality by running user-built simulation modules.
Author: Alex M Chubaty [aut, cre] (<https://orcid.org/0000-0001-7146-8135>),
Eliot J B McIntire [aut] (<https://orcid.org/0000-0002-6914-8316>),
Yong Luo [ctb],
Steve Cumming [ctb],
Ceres Barros [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>
Diff between SpaDES.core versions 0.2.1 dated 2018-08-09 and 0.2.2 dated 2018-08-13
DESCRIPTION | 12 MD5 | 22 NEWS.md | 12 R/cache.R | 10 R/simulation-spades.R | 3 build/vignette.rds |binary inst/doc/i-introduction.html | 375 +++- inst/doc/ii-modules.html | 3412 +++++++++++++++++++++++++++++++++----- tests/testthat/helper-initTests.R | 8 tests/testthat/test-cache.R | 5 tests/testthat/test-checkpoint.R | 12 tests/testthat/test-timeunits.R | 23 12 files changed, 3383 insertions(+), 511 deletions(-)
Title: Connectivity Scores with Factor Analysis
Description: Applies factor analysis methodology to microarray data in order
to derive connectivity scores between compounds. The package also contains an
implementation of the connectivity score algorithm by Zhang and Gant (2008) <doi:10.1186/1471-2105-9-258>.
Author: Ewoud De Troyer
Maintainer: Ewoud De Troyer <ewoud.detroyer@uhasselt.be>
Diff between CSFA versions 1.1.0 dated 2018-06-13 and 1.2.0 dated 2018-08-13
DESCRIPTION | 8 ++--- MD5 | 22 +++++++------ NAMESPACE | 2 + R/ClusterCS.R |only R/extra.R | 10 +++--- R/method_structure.R | 40 ++++++++++++------------- inst/doc/CSFA.pdf |binary man/CSanalysis-matrix-matrix-CSfabia-method.Rd | 10 +++--- man/CSanalysis-matrix-matrix-CSmfa-method.Rd | 10 +++--- man/CSanalysis-matrix-matrix-CSpca-method.Rd | 10 +++--- man/CSanalysis-matrix-matrix-CSsmfa-method.Rd | 10 +++--- man/CScluster.Rd |only man/CSlabelscompare.Rd | 6 +-- 13 files changed, 66 insertions(+), 62 deletions(-)
Title: Fast Generators and Iterators for Permutations, Combinations and
Partitions
Description: Fast generators and iterators for permutations, combinations
and partitions. The iterators allow users to generate arrangements in
a memory efficient manner and the generated arrangements are in
lexicographical (dictionary) order. Permutations and combinations can
be drawn with/without replacement and support multisets. It has been
demonstrated that 'arrangements' outperforms most of the existing
packages of similar kind. Some benchmarks could be found at
<https://randy3k.github.io/arrangements/articles/benchmark.html>.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between arrangements versions 1.0.3 dated 2018-08-05 and 1.1.0 dated 2018-08-13
arrangements-1.0.3/arrangements/src/arrangements.h |only arrangements-1.0.3/arrangements/src/k_partitions.c |only arrangements-1.0.3/arrangements/src/k_permutations.c |only arrangements-1.0.3/arrangements/src/multiset_combinations.c |only arrangements-1.0.3/arrangements/src/multiset_permutations.c |only arrangements-1.0.3/arrangements/src/next |only arrangements-1.0.3/arrangements/src/replace_combinations.c |only arrangements-1.0.3/arrangements/src/replace_permutations.c |only arrangements-1.1.0/arrangements/DESCRIPTION | 8 arrangements-1.1.0/arrangements/MD5 | 113 +- arrangements-1.1.0/arrangements/NAMESPACE | 1 arrangements-1.1.0/arrangements/R/arrangements.R | 1 arrangements-1.1.0/arrangements/R/combinations.R | 307 ++---- arrangements-1.1.0/arrangements/R/partitions.R | 261 +---- arrangements-1.1.0/arrangements/R/permutations.R | 348 ++----- arrangements-1.1.0/arrangements/R/utils.R | 33 arrangements-1.1.0/arrangements/man/combinations.Rd | 41 arrangements-1.1.0/arrangements/man/icombinations.Rd | 22 arrangements-1.1.0/arrangements/man/ipartitions.Rd | 8 arrangements-1.1.0/arrangements/man/ipermutations.Rd | 22 arrangements-1.1.0/arrangements/man/ncombinations.Rd | 17 arrangements-1.1.0/arrangements/man/npermutations.Rd | 19 arrangements-1.1.0/arrangements/man/partitions.Rd | 12 arrangements-1.1.0/arrangements/man/permutations.Rd | 47 - arrangements-1.1.0/arrangements/src/Makevars | 10 arrangements-1.1.0/arrangements/src/arrangements.c | 40 arrangements-1.1.0/arrangements/src/combinations |only arrangements-1.1.0/arrangements/src/combinations.c | 340 ++----- arrangements-1.1.0/arrangements/src/combinations.h |only arrangements-1.1.0/arrangements/src/combinatorics |only arrangements-1.1.0/arrangements/src/combinatorics.c |only arrangements-1.1.0/arrangements/src/combinatorics.h |only arrangements-1.1.0/arrangements/src/gmp_utils.c |only arrangements-1.1.0/arrangements/src/gmp_utils.h |only arrangements-1.1.0/arrangements/src/macros.h |only arrangements-1.1.0/arrangements/src/partitions |only arrangements-1.1.0/arrangements/src/partitions.c | 454 +--------- arrangements-1.1.0/arrangements/src/partitions.h |only arrangements-1.1.0/arrangements/src/permutations |only arrangements-1.1.0/arrangements/src/permutations.c | 381 ++------ arrangements-1.1.0/arrangements/src/permutations.h |only arrangements-1.1.0/arrangements/src/utils.c | 217 +++- arrangements-1.1.0/arrangements/src/utils.h | 21 arrangements-1.1.0/arrangements/tests/testthat/test_combinations.R | 115 +- arrangements-1.1.0/arrangements/tests/testthat/test_k_partitions.R | 152 +-- arrangements-1.1.0/arrangements/tests/testthat/test_k_permutations.R | 197 +--- arrangements-1.1.0/arrangements/tests/testthat/test_multiset_combinations.R | 83 + arrangements-1.1.0/arrangements/tests/testthat/test_multiset_permutations.R |only arrangements-1.1.0/arrangements/tests/testthat/test_partitions.R | 142 +-- arrangements-1.1.0/arrangements/tests/testthat/test_permutations.R | 158 --- arrangements-1.1.0/arrangements/tests/testthat/test_replace_combinations.R | 83 + arrangements-1.1.0/arrangements/tests/testthat/test_replace_permutations.R | 83 + 52 files changed, 1539 insertions(+), 2197 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 3.0.3 dated 2018-08-06 and 3.0.4 dated 2018-08-13
DESCRIPTION | 6 MD5 | 38 NEWS | 13 R/rpart.model.frame.R | 99 + R/rpart.rules.R | 89 + R/split.labs.R | 18 inst/doc/prp.pdf | 1525 +++++++++++++++--------------- inst/slowtests/rpart.report.R | 24 inst/slowtests/rpart.report.Rout.save | 187 +++ inst/slowtests/test.prp.Rout.save | 10 inst/slowtests/test.rpart.plot.Rout.save | 96 + inst/slowtests/test.rpart.rules.R | 97 + inst/slowtests/test.rpart.rules.Rout.save | 814 +++++++++++++++- inst/slowtests/vignette.R | 23 inst/slowtests/vignette.Rout.save | 23 man/prp.Rd | 2 man/rpart.predict.Rd | 4 man/rpart.rules.Rd | 7 tests/test.rpart.plot.R | 3 tests/test.rpart.plot.Rout.save | 10 20 files changed, 2110 insertions(+), 978 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 1.3 dated 2018-06-04 and 1.4 dated 2018-08-13
DESCRIPTION | 7 - MD5 | 38 +++--- R/ThU.R | 158 ++++++++++++++-------------- R/age.R | 31 +++++ R/cad.R | 38 +++++- R/evolution.R | 287 ++++++++++++++++++++++++++++++++++------------------ R/kde.R | 38 +++++- R/peakfit.R | 51 +++++++-- R/radialplot.R | 53 +++++++-- R/titterington.R | 12 +- R/weightedmean.R | 247 +++++++++++++++++++++++++++----------------- R/york.R | 4 inst/constants.json | 2 man/age.Rd | 28 ++++- man/cad.Rd | 36 +++++- man/evolution.Rd | 30 ++++- man/kde.Rd | 39 +++++-- man/peakfit.Rd | 27 ++++ man/radialplot.Rd | 37 +++++- man/weightedmean.Rd | 115 ++++++++++++++------ 20 files changed, 880 insertions(+), 398 deletions(-)
Title: Reading Bibliometric Data from Lattes Platform
Description: A simple API for downloading and reading xml data directly from Lattes <http://lattes.cnpq.br/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetLattesData versions 0.9 dated 2017-11-28 and 1.0 dated 2018-08-13
DESCRIPTION | 10 +-- MD5 | 22 +++--- NEWS.md | 8 ++ R/gld_get_lattes_data.R | 55 +++++++++++++---- R/gld_read_lattes_zip.R | 12 ++- R/gld_utils.R | 20 ++++-- README.md | 2 build/vignette.rds |binary inst/doc/gld_vignette-ReadLattes.R | 90 ++++++++++++++-------------- inst/doc/gld_vignette-ReadLattes.Rmd | 22 +++--- inst/doc/gld_vignette-ReadLattes.html | 108 +++++++++++++++++++++++++++++----- vignettes/gld_vignette-ReadLattes.Rmd | 22 +++--- 12 files changed, 249 insertions(+), 122 deletions(-)
Title: Estimation of Parameter-Dependent Network Centrality Measures
Description: Provides methods for estimating parameter-dependent network centrality measures with linear-in-means models. Both non linear least squares and maximum likelihood estimators are implemented. The methods allow for both link and node heterogeneity in network effects, endogenous network formation and the presence of unconnected nodes. The routines also compare the explanatory power of parameter-dependent network centrality measures with those of standard measures of network centrality. Benefits and features of the 'econet' package are illustrated using data from Battaglini and Patacchini (2018), which examine the determinants of US campaign contributions when legislators care about the behavior of other legislators to whom they are socially connected. For additional details, see the vignette.
Author: Marco Battaglini [aut] (<https://orcid.org/0000-0001-9690-0721>),
Valerio Leone Sciabolazza [aut, cre]
(<https://orcid.org/0000-0003-2537-3084>),
Eleonora Patacchini [aut] (<https://orcid.org/0000-0002-3510-2969>),
Sida Peng [aut] (<https://orcid.org/0000-0002-2151-0523>)
Maintainer: Valerio Leone Sciabolazza <valerio.leonesciabolazza@uniparthenope.it>
Diff between econet versions 0.1.6 dated 2018-07-05 and 0.1.7 dated 2018-08-13
DESCRIPTION | 8 MD5 | 52 - NAMESPACE | 18 R/AIC.R |only R/a_G_alumni_109.R | 2 R/boot.R | 92 +- R/formula.R |only R/horse_race.R | 44 - R/logLik.R |only R/mle_compet_het.R | 2 R/mle_compet_lim.R | 2 R/mle_het.R | 4 R/mle_party.R | 2 R/net_dep.R | 62 - R/parameter_dependent_centrality.R | 28 R/print.R |only R/quantify.R | 145 ++- R/select_X.R | 4 R/summary.R |only R/time_party_connection.R | 2 R/vcov.R |only build/vignette.rds |binary inst/doc/econet.pdf |binary man/a_G_alumni_109.Rd | 4 man/boot.Rd | 22 man/horse_race.Rd | 41 - man/net_dep.Rd | 39 man/quantify.Rd | 35 vignettes/econet.tex | 1458 +++++++++++++++++-------------------- vignettes/econet_refs.bib | 52 - 30 files changed, 1086 insertions(+), 1032 deletions(-)
Title: Bayesian Analysis of Change Point Problems
Description: Provides an implementation of the Barry and Hartigan (1993) product
partition model for the normal errors change point problem using Markov Chain
Monte Carlo. It also extends the methodology to regression models on a connected
graph (Wang and Emerson, 2015); this allows estimation of change point models
with multivariate responses. Parallel MCMC, previously available in bcp v.3.0.0,
is currently not implemented.
Author: Xiaofei Wang, Chandra Erdman, and John W. Emerson
Maintainer: Xiaofei Wang <xiaofei.wang@yale.edu>
Diff between bcp versions 4.0.2 dated 2018-06-08 and 4.0.3 dated 2018-08-13
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- R/output.R | 13 +++++++------ man/bcp.Rd | 6 +++--- man/plot.bcp.Rd | 16 ++++++++++------ src/HelperVariables.h | 4 ++-- 6 files changed, 33 insertions(+), 27 deletions(-)
Title: Example T1 Structural Data from the Multi-Modal MRI
'Reproducibility' Resource
Description: Structural T1 magnetic resonance imaging ('MRI')
data from the 'Kirby21' 'reproducibility' study
<doi:10.1016/j.neuroimage.2010.11.047>.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between kirby21.t1 versions 1.6.0 dated 2018-02-01 and 1.7.0 dated 2018-08-13
DESCRIPTION | 18 +++++++++--------- MD5 | 8 +++++--- NAMESPACE | 2 ++ NEWS.md | 7 +++++++ R/delete_t1_data.R |only man/delete_t1_data.Rd |only 6 files changed, 23 insertions(+), 12 deletions(-)
Title: Example Functional Imaging Data from the Multi-Modal MRI
'Reproducibility' Resource
Description: Functional magnetic resonance imaging ('fMRI')
data from the 'Kirby21' 'reproducibility' study
<doi:10.1016/j.neuroimage.2010.11.047>.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between kirby21.fmri versions 1.6.0 dated 2018-02-01 and 1.7.0 dated 2018-08-13
DESCRIPTION | 20 ++++++++++---------- MD5 | 8 +++++--- NAMESPACE | 2 ++ NEWS.md | 8 ++++++++ R/delete_fmri_data.R |only man/delete_fmri_data.Rd |only 6 files changed, 25 insertions(+), 13 deletions(-)
Title: Boosted Multivariate Trees for Longitudinal Data
Description: Implements Friedman's gradient descent boosting algorithm for longitudinal data using multivariate tree base learners. A time-covariate interaction effect is modeled using penalized B-splines (P-splines) with estimated adaptive smoothing parameter.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Amol Pande <amoljpande@gmail.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between boostmtree versions 1.2.1 dated 2018-02-12 and 1.3.0 dated 2018-08-13
DESCRIPTION | 8 - MD5 | 36 +++--- NAMESPACE | 5 R/boostmtree.R | 211 +++++++++++++++++++++++++++++++---------- R/boostmtree.news.R | 6 - R/generic.predict.boostmtree.R | 26 +---- R/marginalPlot.R |only R/partialPlot.R | 34 +++++- R/plot.boostmtree.R | 6 - R/predict.boostmtree.R | 6 - R/print.boostmtree.R | 6 - R/simLong.R | 6 - R/utilities.R | 77 +++++++++++++- R/vimpPlot.R |only R/zzz.R | 6 - data/spirometry.RData |binary inst/NEWS | 19 ++- man/boostmtree.Rd | 62 +++++++----- man/marginalPlot.Rd |only man/partialPlot.Rd | 16 ++- man/vimpPlot.Rd |only 21 files changed, 367 insertions(+), 163 deletions(-)
Title: Multivariate Functional Principal Component Analysis for Data
Observed on Different Dimensional Domains
Description: Calculate a multivariate functional principal component analysis
for data observed on different dimensional domains. The estimation algorithm
relies on univariate basis expansions for each element of the multivariate
functional data (Happ & Greven, 2018) <doi:10.1080/01621459.2016.1273115>. Multivariate and univariate functional data objects are
represented by S4 classes for this type of data implemented in the package
'funData'. For more details on the general concepts of both packages and a case study, see Happ (2018) <arXiv:1707.02129>.
Author: Clara Happ [aut, cre] (<https://orcid.org/0000-0003-4737-3835>)
Maintainer: Clara Happ <clara.happ@stat.uni-muenchen.de>
Diff between MFPCA versions 1.2-3 dated 2018-07-03 and 1.3 dated 2018-08-13
DESCRIPTION | 11 +++--- MD5 | 41 +++++++++++++------------ NAMESPACE | 1 NEWS.md | 7 ++++ R/FCP_TPA.R | 2 - R/MFPCA_calculation.R | 47 ++++++++++++++++++----------- R/univDecomp.R | 57 ++++++++++++++++++++++++++++++------ R/univariateExpansions.R | 1 README.md | 4 +- build/partial.rdb |binary configure.ac | 2 - inst/CITATION | 6 ++- man/FCP_TPA.Rd | 2 - man/MFPCA.Rd | 36 ++++++++++++---------- man/dctBasis2D.Rd | 4 +- man/fdaBasis.Rd |only man/givenBasis.Rd | 4 +- man/umpcaBasis.Rd | 2 - man/univDecomp.Rd | 4 +- tests/testthat/Rplots.pdf | 6 +-- tests/testthat/test_univDecomp.R | 27 ++++++++++++++++- tests/testthat/test_univExpansion.R | 3 + 22 files changed, 182 insertions(+), 85 deletions(-)
Title: Cross-Validated (Nested) Forward Selection
Description: Implementation of forward selection based on cross-validated
linear and logistic regression.
Author: Marco Colombo [aut, cre] (<https://orcid.org/0000-0001-6672-0623>),
Felix Agakov [ctb]
Maintainer: Marco Colombo <m.colombo@ed.ac.uk>
Diff between nestfs versions 0.8.5 dated 2018-08-02 and 0.8.6 dated 2018-08-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/nestfs.R | 31 +++++++++++++++++++++++++++---- man/forward.selection.Rd | 16 ++++++++++++++-- 4 files changed, 48 insertions(+), 13 deletions(-)
Title: An Interface for MATLAB using System Calls
Description: Provides users to call MATLAB from using the "system" command.
Allows users to submit lines of code or MATLAB m files.
This is in comparison to 'R.matlab', which creates a MATLAB server.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between matlabr versions 1.5.0 dated 2018-02-01 and 1.5.2 dated 2018-08-13
DESCRIPTION | 10 +++++----- MD5 | 16 +++++++++------- NAMESPACE | 3 +++ NEWS.md | 5 +++++ R/add_path.R |only R/matlab_script.R | 25 ++++++++++++++++++++++--- man/add_path.Rd |only man/get_matlab.Rd | 5 ++++- man/run_matlab_code.Rd | 13 +++++++++++-- man/run_matlab_script.Rd | 8 ++++++-- 10 files changed, 65 insertions(+), 20 deletions(-)
Title: Read Large Text Files
Description: Read large text files by splitting them in smaller files.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigreadr versions 0.1.0 dated 2018-07-30 and 0.1.3 dated 2018-08-13
DESCRIPTION | 10 ++++----- MD5 | 26 ++++++++++++------------- R/nlines.R | 4 +-- R/read.R | 45 +++++++++++++++++++++++++++++++++++--------- R/split.R | 2 - R/utils.R | 16 +++++++++++++++ README.md | 3 -- man/big_fread2.Rd | 17 +++++++++++----- man/fread2.Rd | 2 - man/fwrite2.Rd | 7 +++--- man/nlines.Rd | 4 +-- man/split_file.Rd | 2 - tests/testthat/test-read.R | 30 +++++++++++++++-------------- tests/testthat/test-split.R | 9 ++++++-- 14 files changed, 117 insertions(+), 60 deletions(-)
Title: Pedigree Inference from SNPs
Description: Fast multi-generational pedigree inference from incomplete data on
hundreds of SNPs, including parentage assignment and sibship clustering.
See citation('sequoia') for more information.
Author: Jisca Huisman [aut, cre]
Maintainer: Jisca Huisman <jisca.huisman@gmail.com>
Diff between sequoia versions 1.0.2 dated 2018-04-01 and 1.1.1 dated 2018-08-13
sequoia-1.0.2/sequoia/man/Merge.Rd |only sequoia-1.1.1/sequoia/DESCRIPTION | 10 sequoia-1.1.1/sequoia/MD5 | 51 sequoia-1.1.1/sequoia/NAMESPACE | 2 sequoia-1.1.1/sequoia/R/ComparePeds.R | 2 sequoia-1.1.1/sequoia/R/GenoConvert.R | 39 sequoia-1.1.1/sequoia/R/Prepare.R | 50 sequoia-1.1.1/sequoia/R/SNPstats.R | 2 sequoia-1.1.1/sequoia/R/Sequoia_F90wrappers.R | 6 sequoia-1.1.1/sequoia/R/Sequoia_Main.R | 42 sequoia-1.1.1/sequoia/R/Utils.R | 12 sequoia-1.1.1/sequoia/R/Utils_hermaphrodites.R | 4 sequoia-1.1.1/sequoia/R/WriteToFiles.R | 55 sequoia-1.1.1/sequoia/build/vignette.rds |binary sequoia-1.1.1/sequoia/inst/Fortran/sequoia.f90 | 1624 +++++++++++++++---------- sequoia-1.1.1/sequoia/inst/doc/sequoia.R | 76 - sequoia-1.1.1/sequoia/inst/doc/sequoia.Rnw | 67 - sequoia-1.1.1/sequoia/inst/doc/sequoia.pdf |binary sequoia-1.1.1/sequoia/man/CheckGeno.Rd |only sequoia-1.1.1/sequoia/man/LHConvert.Rd | 4 sequoia-1.1.1/sequoia/man/MergeFill.Rd |only sequoia-1.1.1/sequoia/man/PedCompare.Rd | 2 sequoia-1.1.1/sequoia/man/SeqPrep.Rd | 3 sequoia-1.1.1/sequoia/man/SimGeno.Rd | 4 sequoia-1.1.1/sequoia/man/SnpStats.Rd | 2 sequoia-1.1.1/sequoia/man/sequoia.Rd | 14 sequoia-1.1.1/sequoia/src/sequoia.f90 | 1624 +++++++++++++++---------- sequoia-1.1.1/sequoia/vignettes/sequoia.Rnw | 67 - 28 files changed, 2354 insertions(+), 1408 deletions(-)
Title: Example Data from the Multi-Modal MRI 'Reproducibility' Resource
Description: Multi-modal magnetic resonance imaging ('MRI')
data from the 'Kirby21' 'reproducibility' study
<https://www.nitrc.org/projects/multimodal/>, including functional
and structural imaging.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between kirby21.base versions 1.6.0 dated 2017-10-11 and 1.7.0 dated 2018-08-13
DESCRIPTION | 10 +++++----- MD5 | 18 ++++++++++-------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/delete_kirby21_data.R |only R/download_kirby21_data.R | 17 +++++++++++++---- R/get_image_filenames.R | 16 ++++++++++++++-- man/delete_kirby21_data.Rd |only man/download_kirby21_data.Rd | 5 ++++- man/get_image_filenames_df.Rd | 5 ++++- man/get_par_filenames.Rd | 4 ++-- 11 files changed, 60 insertions(+), 23 deletions(-)
Title: Access to Spotify API
Description: Provides an interface to the Spotify API <https://developer.spotify.com/documentation/web-api/>.
Author: Tiago Mendes Dantas
Maintainer: Tiago Mendes Dantas <t.mendesdantas@gmail.com>
Diff between Rspotify versions 0.1.0 dated 2018-08-07 and 0.1.2 dated 2018-08-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++++-- NAMESPACE | 2 ++ R/getTopTracks.R |only R/getTrack.R |only man/getTopTracks.Rd |only man/getTrack.Rd |only 7 files changed, 11 insertions(+), 5 deletions(-)
Title: Fitting User-Specified Models with Group Lasso Penalty
Description: Fits user-specified (GLM-) models with group lasso penalty.
Author: Lukas Meier
Maintainer: Lukas Meier <meier@stat.math.ethz.ch>
Diff between grplasso versions 0.4-5 dated 2015-01-23 and 0.4-6 dated 2018-08-13
DESCRIPTION | 12 ++++++------ MD5 | 25 +++++++++++++------------ NAMESPACE | 2 ++ build |only man/grpl.control.Rd | 2 +- man/grpl.model-class.Rd | 2 +- man/grpl.model.Rd | 4 ++-- man/grplasso-internal.Rd | 4 ++-- man/grplasso-package.Rd | 47 +++++++++++++---------------------------------- man/grplasso.Rd | 5 ++--- man/lambdamax.Rd | 5 ++++- man/plot.grplasso.Rd | 2 +- man/predict.grplasso.Rd | 2 +- man/splice.Rd | 2 +- 14 files changed, 49 insertions(+), 65 deletions(-)
Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Maximum likelihood estimation of Gaussian Mixture Vector Autoregressive (GMVAR)
model, quantile residual tests, graphical diagnostics, forecasting and simulations. Applying
general linear constraints to the autoregressive parameters is supported.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 1.0.0 dated 2018-07-28 and 1.0.1 dated 2018-08-13
gmvarkit-1.0.0/gmvarkit/man/gmvarkit.Rd |only gmvarkit-1.0.1/gmvarkit/DESCRIPTION | 6 gmvarkit-1.0.1/gmvarkit/MD5 | 59 - gmvarkit-1.0.1/gmvarkit/NAMESPACE | 1 gmvarkit-1.0.1/gmvarkit/R/GMVARconstruction.R | 27 gmvarkit-1.0.1/gmvarkit/R/MAINest.R | 69 - gmvarkit-1.0.1/gmvarkit/R/argumentChecks.R | 17 gmvarkit-1.0.1/gmvarkit/R/diagnosticPlot.R | 2 gmvarkit-1.0.1/gmvarkit/R/generateParams.R | 4 gmvarkit-1.0.1/gmvarkit/R/geneticAlgorithm.R | 805 +++++++--------- gmvarkit-1.0.1/gmvarkit/R/gmvarkit.R | 2 gmvarkit-1.0.1/gmvarkit/R/loglikelihood.R | 17 gmvarkit-1.0.1/gmvarkit/R/miscS3methods.R | 3 gmvarkit-1.0.1/gmvarkit/R/numericalDifferentiation.R | 2 gmvarkit-1.0.1/gmvarkit/R/parameterReforms.R | 17 gmvarkit-1.0.1/gmvarkit/R/plotMethods.R | 39 gmvarkit-1.0.1/gmvarkit/R/predictMethod.R | 6 gmvarkit-1.0.1/gmvarkit/R/printMethods.R | 6 gmvarkit-1.0.1/gmvarkit/R/quantileResidualTests.R | 59 - gmvarkit-1.0.1/gmvarkit/R/standardErrors.R | 311 +++--- gmvarkit-1.0.1/gmvarkit/inst/doc/intro-to-gmvarkit.Rmd | 248 ++-- gmvarkit-1.0.1/gmvarkit/inst/doc/intro-to-gmvarkit.html | 30 gmvarkit-1.0.1/gmvarkit/man/GAfit.Rd | 13 gmvarkit-1.0.1/gmvarkit/man/GMVAR.Rd | 3 gmvarkit-1.0.1/gmvarkit/man/aa_gmvarkit.Rd |only gmvarkit-1.0.1/gmvarkit/man/add_data.Rd | 8 gmvarkit-1.0.1/gmvarkit/man/check_null_data.Rd |only gmvarkit-1.0.1/gmvarkit/man/fitGMVAR.Rd | 2 gmvarkit-1.0.1/gmvarkit/man/loglikelihood.Rd | 8 gmvarkit-1.0.1/gmvarkit/man/quantile_residual_tests.Rd | 16 gmvarkit-1.0.1/gmvarkit/man/regime_distance.Rd | 8 gmvarkit-1.0.1/gmvarkit/vignettes/intro-to-gmvarkit.Rmd | 248 ++-- 32 files changed, 1068 insertions(+), 968 deletions(-)
Title: ANSI Control Sequence Aware String Functions
Description: Counterparts to R string manipulation functions that account for
the effects of ANSI text formatting control sequences.
Author: Brodie Gaslam [aut, cre],
Elliott Sales De Andrade [ctb],
R Core Team [cph] (UTF8 byte length calcs from src/util.c)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between fansi versions 0.2.3 dated 2018-05-06 and 0.3.0 dated 2018-08-13
DESCRIPTION | 11 - MD5 | 105 +++++++------ NAMESPACE | 3 NEWS.md | 18 ++ R/fansi-package.R | 21 +- R/has.R | 2 R/internal.R | 13 + R/load.R | 9 - R/misc.R | 242 ++++++++++++++++++++++++++++++ R/nchar.R | 6 R/strip.R | 8 R/strsplit.R | 2 R/strtrim.R | 2 R/strwrap.R | 2 R/substr2.R | 2 README.md | 16 + build |only inst |only man/fansi.Rd | 19 +- man/html_code_block.Rd |only man/html_esc.Rd |only man/nchar_ctl.Rd | 2 man/set_knit_hooks.Rd |only man/strtrim_ctl.Rd | 2 man/strwrap_ctl.Rd | 2 man/substr_ctl.Rd | 2 src/fansi.h | 15 + src/init.c | 2 src/read.c | 4 src/rnchar.c | 4 src/state.c | 4 src/strip.c | 20 +- src/tohtml.c | 4 src/utf8.c | 27 ++- src/utils.c | 16 + tests/run.R | 14 + tests/unitizer/has.R | 9 + tests/unitizer/has.unitizer/data.rds |binary tests/unitizer/misc.R | 122 +++++++++++++++ tests/unitizer/misc.unitizer/data.rds |binary tests/unitizer/nchar.R | 14 + tests/unitizer/nchar.unitizer/data.rds |binary tests/unitizer/strip.R | 20 ++ tests/unitizer/strip.unitizer/data.rds |binary tests/unitizer/strsplit.R | 12 + tests/unitizer/strsplit.unitizer/data.rds |binary tests/unitizer/substr.R | 15 + tests/unitizer/substr.unitizer/data.rds |binary tests/unitizer/tabs.R | 5 tests/unitizer/tabs.unitizer/data.rds |binary tests/unitizer/tohtml.R | 12 + tests/unitizer/tohtml.unitizer/data.rds |binary tests/unitizer/wrap.R | 43 +++++ tests/unitizer/wrap.unitizer/data.rds |binary vignettes |only 55 files changed, 719 insertions(+), 132 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-08 0.5.5
2016-11-07 0.5.4
2016-07-29 0.5.2
2016-03-23 0.5.1
2016-01-22 0.4.2
2015-12-23 0.4.1
2015-11-03 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-03 0.4
2016-03-15 0.3
2015-12-11 0.2
2015-04-09 0.1.4.0
2015-02-24 0.1.3.3
2014-12-24 0.1.3.2
2014-10-07 0.1.3.1
2014-07-02 0.1.2-1
2014-06-30 0.1.2
2013-09-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-21 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-02 0.3-6
2012-12-03 0.3-5
2012-03-16 0.3-4
2012-01-30 0.3-3
2011-02-10 0.3-2
2010-08-06 0.3-1
2010-06-19 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-23 0.9.4
2018-03-01 0.7.5
2018-02-20 0.7.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-17 0.2
2012-02-13 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-30 0.1.5
2018-06-01 0.1.4
2018-03-03 0.1.3
2017-11-19 0.1.2
2017-05-24 0.1.1
2017-03-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-02 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-17 0.1.3
2017-11-02 0.1.1
2017-10-27 0.1.0
Title: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages
Description: Individual based simulations of hybridizing populations, where the accumulation of junctions is tracked. Furthermore, mathematical equations are provided to verify simulation outcomes. Both simulations and mathematical equations are based on Janzen (2018) <doi:10.1101/058107>.
Author: Thijs Janzen [aut, cre]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between junctions versions 1.0.1 dated 2018-04-17 and 1.1 dated 2018-08-13
DESCRIPTION | 8 - MD5 | 22 +-- README.md | 2 inst/doc/junctions_vignette.R | 2 inst/doc/junctions_vignette.Rmd | 4 inst/doc/junctions_vignette.html | 12 +- man/junctions-package.Rd | 2 src/Fish.cpp | 221 ++++++++++++++++++++++++++++----------- src/Fish.h | 6 - src/random_functions.cpp | 10 + src/random_functions.h | 1 vignettes/junctions_vignette.Rmd | 4 12 files changed, 202 insertions(+), 92 deletions(-)
Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://www.activinsights.com/products/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing.
Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut],
Aimee Gott [aut],
Joss Langford [aut],
Charles Sweetland [aut, cre],
Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>
Diff between GENEAclassify versions 1.4.13 dated 2018-08-02 and 1.4.14 dated 2018-08-13
DESCRIPTION | 10 - MD5 | 18 +-- R/dataImport.R | 5 R/stepCounter.R | 255 +++++++++++++++++++++++++++++------------------- man/classifyGENEA.Rd | 23 ++-- man/createGENEAmodel.Rd | 7 - man/getGENEAsegments.Rd | 8 - man/segmentation.Rd | 4 man/stepCounter.Rd | 12 +- man/stepCounter2.Rd | 10 - 10 files changed, 209 insertions(+), 143 deletions(-)
Title: Very Large Numbers in R
Description: Handles very large numbers in R. Real numbers are held
using their natural logarithms, plus a logical flag indicating
sign. The package includes a vignette that gives a
step-by-step introduction to using S4 methods.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between Brobdingnag versions 1.2-5 dated 2018-03-18 and 1.2-6 dated 2018-08-13
Brobdingnag-1.2-5/Brobdingnag/inst/doc/brob.R |only Brobdingnag-1.2-5/Brobdingnag/inst/doc/brob.Rnw |only Brobdingnag-1.2-5/Brobdingnag/inst/doc/brob.pdf |only Brobdingnag-1.2-5/Brobdingnag/vignettes/brob.Rnw |only Brobdingnag-1.2-6/Brobdingnag/DESCRIPTION | 9 +- Brobdingnag-1.2-6/Brobdingnag/MD5 | 25 +++--- Brobdingnag-1.2-6/Brobdingnag/build/partial.rdb |only Brobdingnag-1.2-6/Brobdingnag/build/vignette.rds |binary Brobdingnag-1.2-6/Brobdingnag/inst/doc/S4_brob.R |only Brobdingnag-1.2-6/Brobdingnag/inst/doc/S4_brob.Rnw |only Brobdingnag-1.2-6/Brobdingnag/inst/doc/S4_brob.pdf |only Brobdingnag-1.2-6/Brobdingnag/inst/doc/brobpaper.R | 4 - Brobdingnag-1.2-6/Brobdingnag/inst/doc/brobpaper.Rnw | 9 -- Brobdingnag-1.2-6/Brobdingnag/inst/doc/brobpaper.pdf |binary Brobdingnag-1.2-6/Brobdingnag/man/Brobdingnag-package.Rd | 55 ++++++--------- Brobdingnag-1.2-6/Brobdingnag/man/brob.Rd | 27 +++++-- Brobdingnag-1.2-6/Brobdingnag/vignettes/S4_brob.Rnw |only Brobdingnag-1.2-6/Brobdingnag/vignettes/brobpaper.Rnw | 9 -- 18 files changed, 71 insertions(+), 67 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-03 2.7.4
2017-03-06 2.3.1
2016-09-28 2.0
2015-11-03 1.1.1
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models.
Author: Stefan Widgren [aut, cre] (<https://orcid.org/0000-0001-5745-2284>),
Robin Eriksson [aut] (<https://orcid.org/0000-0002-4291-712X>),
Stefan Engblom [aut] (<https://orcid.org/0000-0002-3614-1732>),
Pavol Bauer [aut] (<https://orcid.org/0000-0003-4328-7171>),
Attractive Chaos [cph] (Author of 'kvec.h', a generic dynamic array)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 6.0.0 dated 2018-04-20 and 6.1.0 dated 2018-08-13
DESCRIPTION | 11 MD5 | 44 +- NEWS | 16 R/SimInf_model.R | 7 R/distance.R | 10 build/vignette.rds |binary configure | 51 --- configure.ac | 38 -- inst/CITATION | 5 inst/doc/SimInf.R | 169 ++++------ inst/doc/SimInf.Rnw | 724 +++++++++++++++++++++----------------------- inst/doc/SimInf.pdf |binary man/SISe.Rd | 8 man/SISe3.Rd | 8 man/SISe3_sp.Rd | 9 man/mparse.Rd | 7 man/plot.Rd | 5 src/Makevars.win | 2 src/solvers/SimInf_solver.c | 159 +++++++++ tests/model_builder.R | 59 +++ tests/package_skeleton.R | 21 + vignettes/SimInf.Rnw | 724 +++++++++++++++++++++----------------------- vignettes/SimInf.bib | 45 +- 23 files changed, 1111 insertions(+), 1011 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The
package should add new functionality to R such as the possibility to
manipulate 'NeXML' objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Hilmar Lapp [aut] (<https://orcid.org/0000-0001-9107-0714>),
Kseniia Shumelchyk [aut],
Rutger Vos [aut] (<https://orcid.org/0000-0001-9254-7318>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.1.1 dated 2018-05-07 and 2.1.2 dated 2018-08-13
DESCRIPTION | 15 MD5 | 66 +-- NEWS.md | 6 R/add_basic_meta.R | 4 R/add_characters.R | 2 R/get_metadata.R | 2 R/get_trees.R | 24 - R/nexml_get.R | 6 R/nexml_publish.R | 2 R/simmap.R | 2 R/taxize_nexml.R | 2 build/vignette.rds |binary inst/WORDLIST |only inst/doc/S4.Rmd | 2 inst/doc/S4.html | 316 ++++++++++++-- inst/doc/metadata.R | 8 inst/doc/metadata.Rmd | 6 inst/doc/metadata.html | 893 ++++++++++++++++++++++++----------------- inst/doc/simmap.html | 334 ++++++++++++--- inst/doc/sparql.html | 454 +++++++++++++++----- man/add_basic_meta.Rd | 4 man/add_characters.Rd | 2 man/flatten_multiphylo.Rd | 4 man/get_flat_trees.Rd | 2 man/get_metadata.Rd | 2 man/get_trees.Rd | 8 man/get_trees_list.Rd | 10 man/nexml_get.Rd | 6 man/nexml_publish.Rd | 2 man/simmap_to_nexml.Rd | 2 man/taxize_nexml.Rd | 2 tests/spelling.R |only tests/testthat/test_taxonomy.R | 19 vignettes/S4.Rmd | 2 vignettes/metadata.Rmd | 6 35 files changed, 1523 insertions(+), 692 deletions(-)
Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs, pairwise comparisons, graphical approaches, assesses variance homogeneity and normality of data in each group via tests and plots.
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between onewaytests versions 1.7 dated 2018-06-04 and 1.8 dated 2018-08-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/citation | 12 +++++++++--- 3 files changed, 15 insertions(+), 9 deletions(-)
Title: Integrating R with QGIS
Description: Establishes an interface between R and 'QGIS', i.e. it allows
the user to access 'QGIS' functionalities from the R console. It achieves this
by using the 'QGIS' Python API via the command line. Hence, RQGIS extends R's
statistical power by the incredible vast geo-functionality of 'QGIS' (including
also 'GDAL', 'SAGA'- and 'GRASS'-GIS among other third-party providers).
This in turn creates a powerful environment for advanced and innovative
(geo-)statistical geocomputing. 'QGIS' is licensed under GPL version 2 or
greater and is available from <http://www.qgis.org/en/site/>.
Author: Jannes Muenchow [aut, cre] (<https://orcid.org/0000-0001-7834-4717>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Jannes Muenchow <jannes.muenchow@uni-jena.de>
Diff between RQGIS versions 1.0.3 dated 2018-01-23 and 1.0.4 dated 2018-08-13
DESCRIPTION | 16 MD5 | 113 - NAMESPACE | 78 NEWS | 259 +- NEWS.md | 241 +- R/RQGIS.R | 40 R/data.R | 172 + R/helper_funs.R | 1363 ++++++------- R/init.R | 62 R/processing.R | 2278 +++++++++++------------ build/vignette.rds |binary data/comm.rda |only data/random_points.rda |binary data/study_area.rda |only inst/CITATION | 39 inst/doc/install_guide.R | 21 inst/doc/install_guide.Rmd | 707 +++---- inst/doc/install_guide.html | 905 +++++---- inst/python/python_funs.py | 510 ++--- inst/test-scripts/3_python3_reticulate_testing.R |only inst/test-scripts/linux_map_canvas.py | 220 +- inst/test-scripts/linux_run_qgis.R | 318 +-- inst/test-scripts/python_manual_processing.py | 47 inst/test-scripts/reticulate.R | 660 +++--- inst/test-scripts/saga_test.R | 104 - inst/travis/gdal-abi.sh | 12 man/RQGIS-package.Rd | 90 man/check_apps.Rd | 66 man/check_for_server.Rd | 30 man/comm.Rd |only man/dem.Rd | 50 man/find_algorithms.Rd | 100 - man/get_args_man.Rd | 108 - man/get_extent.Rd | 104 - man/get_options.Rd | 68 man/get_usage.Rd | 74 man/ndvi.Rd | 46 man/open_app.Rd | 68 man/open_grass_help.Rd | 50 man/open_help.Rd | 90 man/pass_args.Rd | 183 - man/qgis_session_info.Rd | 74 man/random_points.Rd | 46 man/reset_path.Rd | 38 man/run_ini.Rd | 58 man/run_qgis.Rd | 194 - man/save_spatial_objects.Rd | 94 man/set_env.Rd | 98 man/setup_linux.Rd | 54 man/setup_mac.Rd | 54 man/setup_win.Rd | 56 man/study_area.Rd |only tests/testthat.R | 14 tests/testthat/test-get-options.R | 28 tests/testthat/test-get-usage.R | 26 tests/testthat/test-paper-analysis.R | 318 +-- tests/testthat/test-pass_args.R | 172 - tests/testthat/test-qgis-prerun.R | 106 - tests/testthat/test-run-qgis.R | 253 +- vignettes/install_guide.Rmd | 707 +++---- 60 files changed, 5992 insertions(+), 5690 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on undirected graphical models for accomplishing three important and interrelated goals in genetics: (1) linkage map construction, (2) reconstructing intra- and inter-chromosomal conditional interactions (linkage disequilibrium) networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-phenotype-environment interactions network. For this purpose, we use conditional (in)dependence relationships between variables. The netgwas package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The package is implemented the recent developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <arXiv:1710.01063>.
NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between netgwas versions 1.5.0 dated 2018-05-16 and 1.7.0 dated 2018-08-13
DESCRIPTION | 16 - MD5 | 40 ++- NAMESPACE | 32 +- R/cal.pos.R |only R/cross2netgwas.R |only R/detect.err.R |only R/netgwas2cross.R |only R/netmap.R | 555 ++++++++++++++++++++++++------------------------- man/R.approx.Rd | 88 +++---- man/R.gibbs.Rd | 98 ++++---- man/cal.pos.Rd |only man/cross2netgwas.Rd |only man/cutoffs.Rd | 92 ++++---- man/detect.err.Rd |only man/netgwas-package.Rd | 2 man/netgwas2cross.Rd |only man/netmap.Rd | 180 +++++++-------- man/netphenogeno.Rd | 164 +++++++------- man/netsnp.Rd | 164 +++++++------- man/selectnet.Rd | 188 ++++++++-------- man/simGeno.Rd | 158 ++++++------- tests |only 22 files changed, 900 insertions(+), 877 deletions(-)
Title: Univariate and Multivariate Model-Based Clustering in
Group-Specific Functional Subspaces
Description: The funHDDC algorithm (Schmutz et al., 2017) allows to cluster functional univariate or multivariate data by modeling each group within a specific functional subspace.
Author: A Schmutz, J. Jacques & C. Bouveyron
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>
Diff between funHDDC versions 2.0 dated 2018-04-18 and 2.1.0 dated 2018-08-13
funHDDC-2.0/funHDDC/man/funHDDC-package.Rd |only funHDDC-2.1.0/funHDDC/DESCRIPTION | 10 funHDDC-2.1.0/funHDDC/MD5 | 27 - funHDDC-2.1.0/funHDDC/R/funHDDC.R | 648 ++++++++++++--------------- funHDDC-2.1.0/funHDDC/R/mfpca.R | 160 ++---- funHDDC-2.1.0/funHDDC/R/plot.mfpca.R | 218 +++------ funHDDC-2.1.0/funHDDC/R/predict.funHDDC.R | 65 ++ funHDDC-2.1.0/funHDDC/R/slopeHeuristic.R | 47 + funHDDC-2.1.0/funHDDC/inst/doc/funHDDC.pdf |binary funHDDC-2.1.0/funHDDC/man/funHDDC.Rd | 37 - funHDDC-2.1.0/funHDDC/man/mfpca.Rd | 14 funHDDC-2.1.0/funHDDC/man/plot.mfpca.Rd | 14 funHDDC-2.1.0/funHDDC/man/predict.funHDDC.Rd | 30 - funHDDC-2.1.0/funHDDC/man/slopeHeuristic.Rd | 41 - funHDDC-2.1.0/funHDDC/man/trigo.Rd | 37 - 15 files changed, 594 insertions(+), 754 deletions(-)
Title: Empirical Likelihood (EL) for Comparing Two Survival Functions
Description: Functions for computing critical values and implementing the one-sided/two-sided EL tests.
Author: Hsin-wen Chang [aut, cre] <hwchang@stat.sinica.edu.tw>
Maintainer: Guo-You Lan <jj6020770416jj@gmail.com>
Diff between EL2Surv versions 1.0 dated 2017-06-28 and 1.1 dated 2018-08-13
DESCRIPTION | 10 - MD5 | 25 +-- NAMESPACE | 20 +- R/hazardcross.R |only R/hepatitis.R | 48 +++--- R/intELtest.R | 368 +++++++++++++++++++++++++-------------------------- R/ptwiseELtest.R | 134 +++++++++--------- R/supELtest.R | 140 +++++++++---------- data/hazardcross.rda |only data/hepatitis.rda |binary man/hazardcross.Rd |only man/hepatitis.Rd | 76 +++++----- man/intELtest.Rd | 265 ++++++++++++++++++------------------ man/ptwiseELtest.Rd | 156 ++++++++++----------- man/supELtest.Rd | 164 +++++++++++----------- 15 files changed, 711 insertions(+), 695 deletions(-)
Title: Computational Graphs
Description: Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various functions including basic arithmetic, trigonometry functions, and linear algebra functions. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
Author: Ron Triepels
Maintainer: Ron Triepels <dev@cgraph.org>
Diff between cgraph versions 2.0.0 dated 2018-08-05 and 2.0.1 dated 2018-08-13
cgraph-2.0.0/cgraph/R/fun.R |only cgraph-2.0.0/cgraph/src/fun.c |only cgraph-2.0.1/cgraph/DESCRIPTION | 6 cgraph-2.0.1/cgraph/MD5 | 30 - cgraph-2.0.1/cgraph/NAMESPACE | 4 cgraph-2.0.1/cgraph/NEWS.md | 18 cgraph-2.0.1/cgraph/R/cgraph.R | 14 cgraph-2.0.1/cgraph/R/internal.R |only cgraph-2.0.1/cgraph/R/session.R | 12 cgraph-2.0.1/cgraph/man/address.Rd | 2 cgraph-2.0.1/cgraph/man/bsum.Rd | 2 cgraph-2.0.1/cgraph/man/cg.name.Rd | 11 cgraph-2.0.1/cgraph/man/name.Rd | 11 cgraph-2.0.1/cgraph/src/cgraph.c | 671 ++++++++++++++++++------------------- cgraph-2.0.1/cgraph/src/init.c | 21 - cgraph-2.0.1/cgraph/src/internal.c |only cgraph-2.0.1/cgraph/src/stack.c | 30 - cgraph-2.0.1/cgraph/src/stack.h | 2 18 files changed, 416 insertions(+), 418 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-29 1.2
Title: Manage Sub-Processes in R
Description: Create and handle multiple sub-processes in R, exchange
data over standard input and output streams, control their life cycle.
Author: Lukasz Bartnik [aut, cre]
Maintainer: Lukasz Bartnik <l.bartnik@gmail.com>
Diff between subprocess versions 0.8.2 dated 2017-10-22 and 0.8.3 dated 2018-08-13
DESCRIPTION | 6 - MD5 | 55 +++++----- NAMESPACE | 1 NEWS.md | 8 + R/package.R | 12 +- R/readwrite.R | 73 ++++++-------- R/signals.R | 56 +++++------ R/subprocess.R | 191 ++++++++++++++++++++------------------ R/tests.R | 2 man/process_exists.Rd |only man/readwrite.Rd | 44 ++++---- man/signals.Rd | 14 +- man/spawn_process.Rd | 4 man/subprocess.Rd | 8 - man/terminating.Rd | 10 - src/config-os.h | 4 src/rapi.cc | 33 ++++-- src/rapi.h | 2 src/registration.cpp | 1 src/sub-linux.cc | 164 ++++++++++++++------------------ src/sub-windows.cc | 53 ++++++---- src/subprocess.h | 38 ++++--- tests/testthat/helper-processes.R | 31 +----- tests/testthat/signal-trap.sh | 2 tests/testthat/test-parameters.R | 12 +- tests/testthat/test-signals.R | 55 ++++++---- tests/testthat/test-subprocess.R | 12 +- tests/testthat/test-termination.R | 4 tests/testthat/test-utf8.R | 3 29 files changed, 472 insertions(+), 426 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Also contains two-stage binomial modelling that can do pairwise odds-ratio
dependence modelling based marginal logistic regression models. This is an
alternative to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.2.3.1 dated 2018-04-30 and 1.2.4 dated 2018-08-13
DESCRIPTION | 10 MD5 | 89 - NAMESPACE | 18 NEWS | 13 R/daggregate.R | 6 R/dtransform.R | 32 R/dutils.R | 980 +++++++++----- R/gof-phreg.R | 159 ++ R/phreg.R | 363 ++++- R/pmvn.R | 78 + R/recurrent.marginal.R | 1450 +++++++++++++++------- R/twinsim.R | 5 R/twostage.R | 1052 +++++++++++++++ build/vignette.rds |binary data/base1cumhaz.txt.gz |binary data/base4cumhaz.txt.gz |binary data/drcumhaz.txt.gz |binary inst/doc/basic-dutils.pdf |binary inst/doc/binomial-case-control-ascertainment.ltx | 88 - inst/doc/binomial-case-control-ascertainment.pdf |binary inst/doc/binomial-family.pdf |binary inst/doc/binomial-twin.pdf |binary inst/doc/quantitative-twin.pdf |binary inst/include/mets_RcppExports.h | 40 man/LinSpline.Rd |only man/basehazplot.phreg.Rd | 15 man/cif.Rd |only man/count.history.Rd | 4 man/covarianceRecurrent.Rd | 9 man/dspline.Rd |only man/gofG.phreg.Rd | 6 man/gofM.phreg.Rd | 13 man/km.Rd |only man/phreg.Rd | 8 man/pmvn.Rd | 5 man/predict.phreg.Rd | 1 man/prob.exceed.recurrent.Rd | 35 man/recurrentMarginal.Rd | 40 man/simRecurrent.Rd | 3 man/simRecurrentII.Rd | 12 man/survival.iterative.Rd |only man/survival.twostage.Rd | 34 src/RcppExports.cpp | 68 + src/fastcox.cpp | 29 src/mvn.cpp | 74 + src/survival-twostage.cpp | 28 vignettes/binomial-case-control-ascertainment.ltx | 88 - vignettes/binomial-case-control-ascertainment.org | 225 ++- 48 files changed, 3890 insertions(+), 1190 deletions(-)
Title: Tools for Conducting and Analyzing Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct
respirometry experiments. Strong emphasis is on aquatic respirometry. Tools
focus on helping the researcher setup and conduct experiments. Analysis of the
resulting data is not a focus since analyses are often specific to a particular
setup, and thus are better created by the researcher individually. This
package provides tools for intermittent, flow-through, and closed respirometry
techniques.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between respirometry versions 0.6.0 dated 2018-01-24 and 0.7.0 dated 2018-08-13
DESCRIPTION | 14 +++++++------- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 1 + NEWS | 12 ++++++++++-- R/calc_MO2.R | 9 +++------ R/calc_b.R | 9 +++++---- R/guess_TA.R | 4 ++-- R/import_firesting.R | 10 +++------- R/make_bins.R |only R/scale_MO2.R | 21 +++++++++++++++++---- man/calc_MO2.Rd | 12 +++++------- man/co2_flush.Rd | 5 +++-- man/co2_rate.Rd | 4 ++-- man/conv_resp_unit.Rd | 4 ++-- man/import_firesting.Rd | 13 +++++-------- man/make_bins.Rd |only man/scale_MO2.Rd | 21 +++++++++++++++++---- 17 files changed, 98 insertions(+), 71 deletions(-)