Title: Differential Gene Expression (DGE) Analysis Utility Toolkit
Description: Provides a function toolkit to facilitate reproducible RNA-Seq Differential Gene Expression (DGE)
analysis (Law (2015) <doi:10.12688/f1000research.9005.3>). The tools include both analysis
work-flow and utility functions: mapping/unit conversion, count normalization, accounting for
unknown covariates, and more. This is a complement/cohort to the 'DGEobj' package that
provides a flexible container to manage and annotate Differential Gene Expression analysis results.
Author: John Thompson [aut],
Connie Brett [aut, cre],
Isaac Neuhaus [aut],
Ryan Thompson [aut]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between DGEobj.utils versions 1.0.5 dated 2022-05-10 and 1.0.6 dated 2022-05-19
DESCRIPTION | 14 - MD5 | 88 ++++---- NAMESPACE | 21 - NEWS.md | 3 R/convertCounts.R | 136 +++++++++--- R/lowIntFilter.R | 4 R/rsqCalc.R | 10 R/runContrasts.R | 89 +++++++- R/runEdgeRNorm.R | 26 +- R/runIHW.R | 9 R/runPower.R | 43 +++- R/runQvalue.R | 26 ++ R/runSVA.R | 37 +++ R/runVoom.R | 330 +++++++++++++++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/DGEobj.utils_Workflow.Rmd | 40 +-- inst/doc/DGEobj.utils_Workflow.html | 42 +-- man/convertCounts.Rd | 38 +-- man/rsqCalc.Rd | 10 man/runContrasts.Rd | 2 man/runEdgeRNorm.Rd | 4 man/runIHW.Rd | 5 man/runPower.Rd | 4 man/runQvalue.Rd | 4 man/runSVA.Rd | 4 man/runVoom.Rd | 15 - man/tpm.on.subset.Rd | 9 tests/testthat/Rplots.pdf |binary tests/testthat/setup.R | 26 ++ tests/testthat/test_convertCounts.R | 1 tests/testthat/test_extractCol.R | 1 tests/testthat/test_lowIntFilter.R | 3 tests/testthat/test_rsqCalc.R | 1 tests/testthat/test_runContrasts.R | 2 tests/testthat/test_runEdgeRNorm.R | 2 tests/testthat/test_runIHW.R | 4 tests/testthat/test_runPower.R | 8 tests/testthat/test_runQvalue.R | 2 tests/testthat/test_runSVA.R | 2 tests/testthat/test_runVoom.R | 7 tests/testthat/test_summarizeSigCounts.R | 1 tests/testthat/test_topTable.merge.R | 1 vignettes/DGEobj.utils_Workflow.Rmd | 40 +-- vignettes/DGEobj.utils_Workflow.Rmd.orig | 1 45 files changed, 799 insertions(+), 316 deletions(-)
Title: Feature Selection Algorithms for Computer Aided Diagnosis
Description: Contains a set of utilities for building and testing statistical models (linear, logistic,ordinal or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya, Israel Alanis and Jorge Orozco
Maintainer: Jose Gerardo Tamez-Pena <jose.tamezpena@tec.mx>
Diff between FRESA.CAD versions 3.3.1 dated 2021-08-17 and 3.4.2 dated 2022-05-19
DESCRIPTION | 10 MD5 | 64 +-- NAMESPACE | 2 NEWS | 10 R/BSWiMS.r | 21 - R/CoxBenchmark.R | 4 R/FRESA.Model.R | 4 R/FRESAModelingFunctions.R | 499 +++++++++++++---------------- R/FRESAScale.r | 2 R/GMVECluster.r | 2 R/baggedModel.R | 6 R/binaryBenchMark.R | 4 R/bootstrapValidation.Bin.R | 4 R/bootstrapValidation.Res.R | 4 R/featureAdjustment.R | 111 +----- R/getKNNpredictionFromFormula.R | 4 R/heatMaps.R | 10 R/modelFitting.R | 4 R/nearestCentroid.r | 4 R/predictionStats.R | 54 +-- R/randomCV.R | 90 ++--- R/randomCVFunctions.R | 305 ++++++++++++------ R/rankInverseNormalDataFrame.R | 2 R/rpredict.R | 39 +- R/supervisedDecorrelation.r | 670 ++++++++++++++++++++++++++++++---------- man/FRESA.CAD-package.Rd | 4 man/HCLAS_KNN_CLASS.Rd | 2 man/featureAdjustment.Rd | 10 man/filteredFit.Rd | 8 man/predictionStats.Rd | 5 man/randomCV.Rd | 5 man/supervisedDecorrelation.Rd | 147 ++++++-- src/FRESAcommons.cpp | 4 33 files changed, 1266 insertions(+), 848 deletions(-)
Title: Classification Based on Association Rules
Description: Provides the infrastructure for association rule-based classification including the algorithms CBA, CMAR, CPAR, C4.5, FOIL, PART, PRM, RCAR, and RIPPER to build associative classifiers.
Author: Michael Hahsler [aut, cre, cph],
Ian Johnson [aut, cph],
Tyler Giallanza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesCBA versions 1.2.1 dated 2021-11-20 and 1.2.2 dated 2022-05-19
DESCRIPTION | 8 +- MD5 | 14 ++-- NEWS.md | 5 + R/CBA_ruleset.R | 6 - R/LUCS_KDD_CBA.R | 30 ++++++--- R/formula.R | 14 +++- README.md | 170 ++++++++++++++++++++++++++++++++++-------------------- build/partial.rdb |binary 8 files changed, 159 insertions(+), 88 deletions(-)
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Seqinr includes
utilities for sequence data management under the ACNUC system
described in Gouy, M. et al. (1984) Nucleic Acids Res.
12:121-127 <doi:10.1093/nar/12.1Part1.121>.
Author: Delphine Charif [aut],
Olivier Clerc [ctb],
Carolin Frank [ctb],
Jean R. Lobry [aut, cph],
Anamaria Necşulea [ctb],
Leonor Palmeira [ctb],
Simon Penel [cre],
Guy Perriere [ctb]
Maintainer: Simon Penel <simon.penel@univ-lyon1.fr>
Diff between seqinr versions 4.2-8 dated 2021-06-09 and 4.2-16 dated 2022-05-19
DESCRIPTION | 16 - MD5 | 72 ++++---- R/dotchart.uco.R | 6 build/partial.rdb |binary data/AnoukResult.RData |binary data/ECH.RData |binary data/EXP.RData |binary data/JLO.RData |binary data/SEQINR.UTIL.RData |binary data/aacost.RData |binary data/aaindex.RData |binary data/caitab.RData |binary data/chargaff.RData |binary data/clustal.RData |binary data/dinucl.RData |binary data/ec999.RData |binary data/fasta.RData |binary data/gcO2.rda |binary data/gcT.rda |binary data/gs500liz.RData |binary data/identifiler.RData |binary data/kaksTorture.RData |binary data/m16j.RData |binary data/mase.RData |binary data/msf.RData |binary data/pK.RData |binary data/phylip.RData |binary data/prochlo.RData |binary data/revaligntest.RData |binary data/sysdata.rda |binary data/toyaa.RData |binary data/toycodon.RData |binary data/waterabs.RData |binary man/choosebank.Rd | 2 man/dotchart.uco.Rd | 15 - man/test.co.recstat.Rd | 2 src/alignment.c | 396 ++++++++++++++++++++++-------------------------- 37 files changed, 242 insertions(+), 267 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre' (BSD license, see <http://www.pcre.org/licence.txt>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stefan Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.5.2 dated 2022-03-29 and 0.5.3 dated 2022-05-19
DESCRIPTION | 8 +- MD5 | 30 ++++---- NEWS.md | 19 +++++ R/checks.R | 51 +++++++------- R/cl.R | 43 ++++++------ R/cqp.R | 2 R/cwb.R | 30 +++++++- inst/extdata/cwb/registry/unga | 2 man/checks.Rd | 8 +- man/cwb_utils.Rd | 9 +- man/registry_info.Rd | 3 src/Makevars.ucrt | 2 src/addons.cpp | 127 ++++++++++++++++++------------------ src/cl.cpp | 6 + tests/testthat/test_delete_corpus.R | 4 - tests/testthat/test_registry_info.R | 14 +++ 16 files changed, 220 insertions(+), 138 deletions(-)
Title: Maximum Kernel Likelihood Estimation
Description: Package for fast computation of the maximum kernel likelihood estimator (mkle).
Author: Thomas Jaki
Maintainer: Thomas Jaki <thomas.jaki@protonmail.com>
Diff between MKLE versions 0.05 dated 2009-01-26 and 1.0.0 dated 2022-05-19
DESCRIPTION | 22 ++++++++++++---------- MD5 |only NAMESPACE |only man/opt.bw.Rd | 52 ++++++++++++++++++++++++++-------------------------- 4 files changed, 38 insertions(+), 36 deletions(-)
Title: Moderation Analysis for Two-Instance Repeated Measures Designs
Description: Multiple moderation analysis for two-instance repeated measures designs, with up to three simultaneous moderators (dichotomous and/or continuous) with additive or multiplicative relationship. Includes analyses of simple slopes and conditional effects at (automatically determined or manually set) values of the moderator(s). Based on Montoya, A. K. (2018) "Moderation analysis in two-instance repeated measures designs: Probing methods and multiple moderator models" <doi:10.3758/s13428-018-1088-6> .
Author: Matthias Forstmann [aut, cre]
Maintainer: Matthias Forstmann <matthias.forstmann@uzh.ch>
Diff between mod2rm versions 0.0.2 dated 2022-05-02 and 0.1.0 dated 2022-05-19
DESCRIPTION | 12 MD5 | 12 NAMESPACE | 1 R/mod2rm.r | 603 +++++++++++++++++++++++++++++++++++++++----------- R/summary.mod2rm.r | 182 +++++++++++---- man/mod2rm.Rd | 60 +++- man/summary.mod2rm.Rd | 8 7 files changed, 670 insertions(+), 208 deletions(-)
Title: Managing Larger Data on a GitHub Repository
Description: Because larger (> 50 MB) data files cannot easily be committed to git,
a different approach is required to manage data associated with an analysis in a
GitHub repository. This package provides a simple work-around by allowing larger
(up to 2 GB) data files to piggyback on a repository as assets attached to individual
GitHub releases. These files are not handled by git in any way, but instead are
uploaded, downloaded, or edited directly by calls through the GitHub API. These
data files can be versioned manually by creating different releases. This approach
works equally well with public or private repositories. Data can be uploaded
and downloaded programmatically from scripts. No authentication is required to
download data from public repositories.
Author: Carl Boettiger [aut, cre, cph]
,
Mark Padgham [ctb] ,
Jeffrey O Hanson [ctb] ,
Kevin Kuo [ctb] ,
Tan Ho [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between piggyback versions 0.1.2 dated 2022-04-26 and 0.1.3 dated 2022-05-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/pb_upload.R | 6 +++++- R/utils.R | 4 ++-- inst/doc/alternatives.html | 4 ++-- inst/doc/intro.html | 4 ++-- 7 files changed, 25 insertions(+), 16 deletions(-)
Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management
system developed by the New Zealand Institute of Language, Brain
and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>.
This package defines functions for accessing corpus data in a 'LaBB-CAT'
instance. You must have at least version 20220401.1842 of 'LaBB-CAT'
to use this package.
For more information about 'LaBB-CAT', see
Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142>
or
Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre]
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>
Diff between nzilbb.labbcat versions 1.1-0 dated 2022-04-12 and 1.1-1 dated 2022-05-19
DESCRIPTION | 8 +- MD5 | 26 +++---- NEWS.md | 11 +++ R/getAnnotatorDescriptor.R | 1 R/praatScriptIntensity.R | 76 ++++++++++++++++++++-- R/praatScriptPitch.R | 81 ++++++++++++++++++++++-- R/saveLayer.R | 4 - build/partial.rdb |binary man/getAnnotatorDescriptor.Rd | 1 man/praatScriptIntensity.Rd | 31 ++++++++- man/praatScriptPitch.Rd | 23 ++++++ man/saveLayer.Rd | 4 - tests/testthat/test-praatScriptIntensity.R | 79 +++++++++++++++++++++-- tests/testthat/test-praatScriptPitch.R | 97 ++++++++++++++++++++++++++--- 14 files changed, 392 insertions(+), 50 deletions(-)
More information about nzilbb.labbcat at CRAN
Permanent link
Title: Automated Cleaning of Fossil Occurrence Data
Description: Functions to automate the detection and resolution of taxonomic and stratigraphic errors in fossil occurrence datasets. Functions were developed using data from the Paleobiology Database.
Author: Joe Flannery-Sutherland [aut, cre]
,
Nussaïbah Raja-Schoob [aut, ctb],
Ádam Kocsis [aut, ctb],
Wolfgang Kiessling [aut]
Maintainer: Joe Flannery-Sutherland <jf15558@bristol.ac.uk>
Diff between fossilbrush versions 1.0 dated 2022-05-09 and 1.0.1 dated 2022-05-19
DESCRIPTION | 8 MD5 | 32 +- R/GTS2020_scale.R | 252 ++++++++--------- R/age_ranges.R | 210 +++++++------- R/assess_duplicates.R | 10 R/densify.R | 380 +++++++++++++------------- R/flag_ranges.R | 553 +++++++++++++++++++------------------- R/get_pbdb.R | 12 R/pacmacro_ranges.R | 5 R/revise_ranges.R | 5 R/spell_check.R | 4 R/threshold_peaks.R | 7 R/threshold_ranges.R | 4 data/GTS2020.rda |binary inst/doc/fossilbrush_vignette.pdf |binary man/GTS2020_scale.Rd | 10 man/flag_ranges.Rd | 14 17 files changed, 770 insertions(+), 736 deletions(-)
Title: Supervised Cluster Analysis
Description: Clusters features under the assumption that each cluster has a
random effect and there is an outcome variable that is related to the random
effects by a linear regression. In this way the cluster analysis is
``supervised'' by the outcome variable. An alternate specification is that
features in each cluster have the same compound symmetric normal distribution,
and the conditional distribution of the outcome given the features
has the same coefficient for each feature in a cluster.
Author: David A. Schoenfeld,
Jesse Hsu
Maintainer: David A. Schoenfeld <dschoenfeld@mgh.harvard.edu>
Diff between supcluster versions 1.0 dated 2015-05-18 and 1.0.1 dated 2022-05-19
DESCRIPTION | 10 MD5 | 29 - NAMESPACE | 11 R/binary_link.R |only R/concordmap.R | 172 ++++----- R/generate.cluster.data.R | 57 +-- R/supcluster.R | 786 ++++++++++++++++++++++++++----------------- R/tab1.R | 2 man/beta.by.gene.Rd | 80 ++-- man/binaryLink.Rd |only man/binaryOutcome.Rd |only man/compare.chains.Rd | 4 man/concordmap.Rd | 116 +++--- man/coxLink.Rd |only man/gene_names.Rd | 56 +-- man/generate.cluster.data.Rd | 84 ++-- man/supcluster.Rd | 203 +++++------ man/survivalOutcome.Rd |only 18 files changed, 914 insertions(+), 696 deletions(-)
Title: Matrices in Data Frames
Description: Provides functions to collapse a tidy data frame into matrices in a data frame
and expand a data frame of matrices into a tidy data frame.
Author: Matthew Heun [aut, cre]
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsindf versions 0.3.10 dated 2021-12-17 and 0.3.11 dated 2022-05-19
DESCRIPTION | 10 LICENSE | 2 MD5 | 34 +- NEWS.md | 15 + R/collapse.R | 2 R/matsindf_apply.R | 9 R/utilities.R | 68 ++--- build/vignette.rds |binary inst/CITATION | 8 inst/WORDLIST | 1 inst/doc/iris_pca.html | 229 ++++++++++++++++++- inst/doc/matsindf.html | 440 ++++++++++++++++++++++++++++++++------ inst/doc/midf_apply_primer.html | 352 +++++++++++++++++++++++++++--- man/collapse_to_matrices.Rd | 2 man/everything_except.Rd | 10 man/group_by_everything_except.Rd | 6 man/mat_to_rowcolval.Rd | 16 - man/rowcolval_to_mat.Rd | 18 - 18 files changed, 1025 insertions(+), 197 deletions(-)
Title: Combined Analysis of Pleiotropy and Epistasis for Diversity
Outbred Mice
Description: Combined Analysis of Pleiotropy and Epistasis infers predictive
networks between genetic variants and phenotypes. It can be used with
standard two-parent populations as well as multi-parent populations, such
as the Diversity Outbred (DO) mice, Collaborative Cross (CC) mice, or the
multi-parent advanced generation intercross (MAGIC) population of Arabidopsis
thaliana. It uses complementary information of pleiotropic gene variants across
different phenotypes to resolve models of epistatic interactions between alleles.
To do this, cape reparametrizes main effect and interaction coefficients from
pairwise variant regressions into directed influence parameters. These
parameters describe how alleles influence each other, in terms of suppression
and enhancement, as well as how gene variants influence phenotypes. All of the
final interactions are reported as directed interactions between pairs of
parental alleles. For detailed descriptions of the methods used in this package
please see the following references.
Carter, G. W., Hays, M., Sherman, A. & Galitski, T. (2012) <doi:10.1371/journal.pgen.1003010>.
Tyler, A. L., Lu, W., Hendrick, J. J., Philip, V. M. & Carter, G. W. (2013) <doi:10.1371/journal.pcbi.1003270>.
Author: Anna Tyler [aut, cre],
Jake Emerson [aut],
Baha El Kassaby [aut],
Ann Wells [aut],
Georgi Kolishovski [aut],
Vivek Philip [aut],
Gregory Carter [aut]
Maintainer: Anna Tyler <anna.tyler@jax.org>
Diff between cape versions 3.1.0 dated 2021-02-10 and 3.1.1 dated 2022-05-19
DESCRIPTION | 16 +-- MD5 | 110 +++++++++++++------------- NAMESPACE | 1 NEWS.md | 45 +++++++++++ R/Cape.R | 13 +-- R/bin_curve.R | 2 R/calc_delta_errors.R | 5 - R/calc_m.R | 3 R/cape2mpp.R | 20 ++-- R/direct_influence.R | 4 R/error_prop.R | 2 R/genome_wide_threshold_1D.R | 4 R/get_allele_colors.R | 3 R/get_geno.R | 3 R/get_marker_covar.R | 67 +++++++--------- R/get_marker_name.R | 2 R/get_network.R | 44 +++------- R/get_pairs_for_pairscan.R | 5 - R/get_stats_multiallele.R | 4 R/impute_missing_geno.R | 2 R/kin_adjust.R | 3 R/kinship.R | 27 +++--- R/linkage_blocks_network.R | 21 +---- R/load_input_and_run_cape.R | 91 ++++++++++++++++++++-- R/one_pairscan_parallel.R | 4 R/one_singlescanDO.R | 2 R/pairscan_kin.R | 4 R/plot_effects.R | 31 +++++-- R/plot_full_network.R | 3 R/plot_pairscan.R | 4 R/read_population.R | 139 +++++++++++++++++++++------------- R/remove_kin_ind.R | 3 R/remove_unused_markers.R | 1 R/run_cape.R | 97 +++++++++++++++-------- R/select_markers_for_pairscan.R | 25 ++++-- R/singlescan.R | 3 R/write_population.R | 3 demo/00Index | 1 demo/demo_plink.R | 2 demo/demo_qtl.R | 5 - demo/demo_qtl2.R | 2 demo/demo_rds |only demo/demo_rds.R |only inst/doc/cape.Rmd | 2 inst/doc/cape.html | 55 ++----------- man/Cape-class.Rd | 9 +- man/direct_influence.Rd | 2 man/get_allele_colors.Rd | 3 man/get_marker_name.Rd | 2 man/load_input_and_run_cape.Rd | 18 +++- man/plot_effects.Rd | 11 +- man/plot_full_network.Rd | 3 man/plot_pairscan.Rd | 6 - man/run_cape.Rd | 11 +- tests/testthat/testdata/demo_rds_data |only vignettes/cape.Rmd | 2 vignettes/cape.md | 2 57 files changed, 581 insertions(+), 371 deletions(-)
Title: Simulating Forest Growth using the 3-PG Model
Description: Provides a flexible and easy-to-use interface for the Physiological Processes Predicting Growth (3-PG) model written in Fortran. The r3PG serves as a flexible and easy-to-use interface for the 3-PGpjs (monospecific, evenaged and evergreen forests) described in Landsberg & Waring (1997) <doi:10.1016/S0378-1127(97)00026-1> and the 3-PGmix (deciduous, uneven-aged or mixed-species forests) described in Forrester & Tang (2016) <doi:10.1016/j.ecolmodel.2015.07.010>.
Author: Volodymyr Trotsiuk [aut, cre] ,
Florian Hartig [aut] ,
David Forrester [aut],
Ramiro Silveyra Gonzalez [aut]
Maintainer: Volodymyr Trotsiuk <volodymyr.trotsiuk@wsl.ch>
Diff between r3PG versions 0.1.3 dated 2021-02-19 and 0.1.4 dated 2022-05-19
r3PG-0.1.3/r3PG/data/i_output.rda |only r3PG-0.1.3/r3PG/data/i_parameters.rda |only r3PG-0.1.3/r3PG/data/i_sizeDist.rda |only r3PG-0.1.4/r3PG/DESCRIPTION | 17 r3PG-0.1.4/r3PG/MD5 | 63 - r3PG-0.1.4/r3PG/NAMESPACE | 7 r3PG-0.1.4/r3PG/NEWS | 25 r3PG-0.1.4/r3PG/R/data.R | 145 +++ r3PG-0.1.4/r3PG/R/get_parameters.R |only r3PG-0.1.4/r3PG/R/prepare_climate.R | 10 r3PG-0.1.4/r3PG/R/prepare_input.R | 14 r3PG-0.1.4/r3PG/R/prepare_parameters.R | 8 r3PG-0.1.4/r3PG/R/prepare_site.R |only r3PG-0.1.4/r3PG/R/prepare_sizeDist.R | 10 r3PG-0.1.4/r3PG/R/prepare_species.R |only r3PG-0.1.4/r3PG/R/prepare_thinning.R | 7 r3PG-0.1.4/r3PG/R/r3PG.R | 2 r3PG-0.1.4/r3PG/R/run_3PG.R | 6 r3PG-0.1.4/r3PG/R/sysdata.rda |binary r3PG-0.1.4/r3PG/build/partial.rdb |binary r3PG-0.1.4/r3PG/build/vignette.rds |binary r3PG-0.1.4/r3PG/data/d_climate.rda |binary r3PG-0.1.4/r3PG/data/d_parameters.rda |binary r3PG-0.1.4/r3PG/data/d_site.rda |binary r3PG-0.1.4/r3PG/data/d_sizeDist.rda |binary r3PG-0.1.4/r3PG/data/d_species.rda |binary r3PG-0.1.4/r3PG/data/d_thinning.rda |binary r3PG-0.1.4/r3PG/inst/doc/r3PG-ReferenceManual.html | 891 +++++++++++-------- r3PG-0.1.4/r3PG/inst/examples/get_parameters-help.R |only r3PG-0.1.4/r3PG/inst/examples/prepare_site-help.R |only r3PG-0.1.4/r3PG/inst/examples/prepare_species-help.R |only r3PG-0.1.4/r3PG/man/get_parameters.Rd |only r3PG-0.1.4/r3PG/man/i_parameters_lit.Rd |only r3PG-0.1.4/r3PG/man/prepare_input.Rd | 6 r3PG-0.1.4/r3PG/man/prepare_site.Rd |only r3PG-0.1.4/r3PG/man/prepare_species.Rd |only r3PG-0.1.4/r3PG/man/r3PG.Rd | 2 r3PG-0.1.4/r3PG/man/run_3PG.Rd | 2 r3PG-0.1.4/r3PG/src/md_3PG.f95 | 1 39 files changed, 800 insertions(+), 416 deletions(-)
Title: R Interface to NLopt
Description: Solve optimization problems using an R interface to NLopt. NLopt is a
free/open-source library for nonlinear optimization, providing a common
interface for a number of different free optimization routines available
online as well as original implementations of various other algorithms.
See <https://nlopt.readthedocs.io/en/latest/NLopt_Algorithms/> for more
information on the available algorithms. Building from included sources
requires 'CMake'. On Linux and 'macOS', if a suitable system build of
NLopt (2.7.0 or later) is found, it is used; otherwise, it is built
from included sources via 'CMake'. On Windows, NLopt is obtained through
'rwinlib' for 'R <= 4.1.x' or grabbed from the 'Rtools42 toolchain' for
'R >= 4.2.0'.
Author: Jelmer Ypma [aut],
Steven G. Johnson [aut] ,
Hans W. Borchers [ctb],
Dirk Eddelbuettel [ctb],
Brian Ripley [ctb] ,
Kurt Hornik [ctb] ,
Julien Chiquet [ctb],
Avraham Adler [ctb] ,
Xiongtao Dai [ctb],
Aymeric Stamm [ctb, cre] ,
Jeroen Ooms [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@math.cnrs.fr>
Diff between nloptr versions 2.0.1 dated 2022-05-03 and 2.0.2 dated 2022-05-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 13 +++++++++++++ configure | 2 +- configure.ac | 2 +- inst/doc/nloptr.html | 4 ++-- 6 files changed, 26 insertions(+), 13 deletions(-)
Title: Interface to 'X12-ARIMA'/'X13-ARIMA-SEATS' and Structure for
Batch Processing of Seasonal Adjustment
Description: The 'X13-ARIMA-SEATS' <https://www.census.gov/data/software/x13as.html> methodology and software is a widely used software and developed by the US Census Bureau. It can be accessed from 'R' with this package and 'X13-ARIMA-SEATS' binaries are provided by the 'R' package 'x13binary'.
Author: Alexander Kowarik <alexander.kowarik@statistik.gv.at>, Angelika Meraner
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between x12 versions 1.10.2 dated 2022-02-02 and 1.10.3 dated 2022-05-19
DESCRIPTION | 8 - MD5 | 14 +- R/class.R | 2 R/parameter-methods.R | 8 - R/readx12Out.R | 2 R/x12-methods.R | 254 ++++++++++++++++++++++++------------------------ man/crossVal-methods.Rd | 230 +++++++++++++++++++++---------------------- man/x12-methods.Rd | 6 - 8 files changed, 262 insertions(+), 262 deletions(-)
Title: Infrastructure for Partially Observable Markov Decision
Processes (POMDP)
Description: Provides the infrastructure to define and analyze the solutions of Partially Observable Markov Decision Process (POMDP) models. Interfaces for various exact and approximate solution algorithms are available including value iteration, point-based value iteration and SARSOP. Smallwood and Sondik (1973) <doi:10.1287/opre.21.5.1071>.
Author: Michael Hahsler [aut, cph, cre],
Hossein Kamalzadeh [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between pomdp versions 1.0.2 dated 2022-05-17 and 1.0.3 dated 2022-05-19
DESCRIPTION | 12 +-- MD5 | 14 ++-- NEWS.md | 3 R/round_stochchastic.R | 23 +++---- README.md | 156 +++++++++++++++++++++++++++++------------------- inst/README_files |only inst/doc/POMDP.html | 2 man/round_stochastic.Rd | 13 ++-- 8 files changed, 133 insertions(+), 90 deletions(-)
Title: Process and Analyse Data from m-Path Sense
Description: Overcomes one of the major challenges in mobile (passive) sensing, namely
being able to pre-process the raw data that comes from a mobile sensing app,
specifically "m-Path Sense" <https://m-path.io>. The main task of 'mpathsenser' is
therefore to read "m-Path Sense" JSON files into a database and provide several
convenience functions to aid in data processing.
Author: Koen Niemeijer [aut, cre]
Maintainer: Koen Niemeijer <koen.niemeijer@kuleuven.be>
Diff between mpathsenser versions 1.0.0 dated 2022-05-17 and 1.0.1 dated 2022-05-19
DESCRIPTION | 6 +-- MD5 | 22 +++++------ NEWS.md | 3 + R/database.R | 11 ++++- R/functions.R | 2 - inst/extdata/dbdef.sql | 2 - man/close_db.Rd | 5 ++ man/open_db.Rd | 10 ++++- tests/testthat/test-data.R | 4 +- tests/testthat/test-database.R | 14 +++---- tests/testthat/test-import-functions.R | 62 ++++++++++++++++----------------- tests/testthat/test-sensor_functions.R | 22 +++++------ 12 files changed, 91 insertions(+), 72 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-3 dated 2022-01-13 and 1.1-4 dated 2022-05-19
DESCRIPTION | 12 +-- MD5 | 21 +++--- build/vignette.rds |binary inst/NEWS.Rd | 7 ++ inst/doc/mlt.Rnw | 8 -- inst/doc/mlt.pdf |binary tests/KM-Ex.R |only tests/KM-Ex.Rout.save |only tests/orm-Ex.Rout.save |only tests/timedep_covar.R | 5 - tests/timedep_covar.Rout.save | 13 +-- vignettes/mlt.Rnw | 8 -- vignettes/mlt.bib | 138 ++++++++++++++++++++++++++++++++++++++++-- 13 files changed, 172 insertions(+), 40 deletions(-)
Title: EcoPhyloMapper
Description: Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography.
Author: Pascal Title [aut, cre] ,
Donald Swiderski [aut],
Miriam Zelditch [aut]
Maintainer: Pascal Title <pascal.title@stonybrook.edu>
Diff between epm versions 1.0.0 dated 2022-05-17 and 1.0.1 dated 2022-05-19
DESCRIPTION | 8 - MD5 | 10 - R/betadiv_phylogenetic.R | 140 ------------------- R/createEPMgrid.R | 339 ----------------------------------------------- R/gridMetrics.R | 45 ------ src/epm_cppFunctions.cpp | 4 6 files changed, 12 insertions(+), 534 deletions(-)
Title: Core Functions for Data Quality Assessment
Description: Perform data quality assessment ('DQA') of electronic health
records ('EHR'). Publication: Kapsner et al. (2021)
<doi:10.1055/s-0041-1733847>.
Author: Lorenz A. Kapsner [cre, aut] ,
Jonathan M. Mang [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen [cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@uk-erlangen.de>
Diff between DQAstats versions 0.2.6 dated 2022-03-02 and 0.3.0 dated 2022-05-19
DESCRIPTION | 13 MD5 | 80 - NAMESPACE | 1 R/DQA.R | 11 R/conformance.R | 185 ++- R/create_markdown.R |only R/dataloading.R | 239 ++-- R/datetime_restrictions.R | 120 +- R/etl.R | 357 +++--- R/format_value_conformance_results.R |only R/mdr.R | 54 R/report.R | 786 +++++--------- R/utils.R | 56 README.md | 14 build |only inst/demo_data/utilities/MDR/mdr_example_data.csv | 50 inst/demo_data/utilities/RMD/DQA_report.Rmd | 6 inst/doc |only man/apply_time_restriciton.Rd | 16 man/create_markdown.Rd | 2 man/dqa.Rd | 8 man/format_value_conformance_results.Rd |only man/parallel.Rd | 4 man/read_mdr.Rd | 2 tests/testthat.R | 17 tests/testthat/_snaps |only tests/testthat/test-DQA.R | 138 +- tests/testthat/test-MDR.R | 192 +-- tests/testthat/test-check_date_restriction_requirements.R | 108 - tests/testthat/test-completeness.R | 2 tests/testthat/test-conformance.R | 2 tests/testthat/test-dataloading.R | 326 ++--- tests/testthat/test-datamap.R | 2 tests/testthat/test-descriptive_results.R | 638 +++++------ tests/testthat/test-etl_checks.R | 2 tests/testthat/test-export.R | 2 tests/testthat/test-helper_vars.R | 294 ++--- tests/testthat/test-import.R | 212 +-- tests/testthat/test-plausibilities.R | 2 tests/testthat/test-readme.R | 132 +- tests/testthat/test-reduce_cat.R | 2 tests/testthat/test-render_conformance.R |only tests/testthat/test-stats.R | 110 - vignettes |only 44 files changed, 2116 insertions(+), 2069 deletions(-)
More information about chromatographR at CRAN
Permanent link
Title: Tools for Approximate Bayesian Computation (ABC)
Description: Implements several ABC algorithms for
performing parameter estimation, model selection, and goodness-of-fit.
Cross-validation tools are also available for measuring the
accuracy of ABC estimates, and to calculate the
misclassification probabilities of different models.
Author: Csillery Katalin [aut],
Lemaire Louisiane [aut],
Francois Olivier [aut],
Blum Michael [aut, cre]
Maintainer: Blum Michael <michael.blum.temp@gmail.com>
Diff between abc versions 2.1 dated 2015-05-05 and 2.2.1 dated 2022-05-19
CHANGES | 160 ++++++++++++++++++++++++----------------------- DESCRIPTION | 12 +-- MD5 | 21 +++--- NAMESPACE | 10 ++ R/abc.R | 3 R/cv4postpr.R | 2 README.md |only build/vignette.rds |binary inst/CITATION | 2 inst/doc/abcvignette.pdf |binary man/abc.Rd | 3 man/cv4abc.Rd | 2 12 files changed, 116 insertions(+), 99 deletions(-)
Title: Analytical Tools for Radiation Oncology
Description: Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from multiple treatment planning system platforms and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data.
Author: Reid F. Thompson <reid.thompson@gmail.com>
Maintainer: Reid F. Thompson <reid.thompson@gmail.com>
Diff between RadOnc versions 1.1.5 dated 2019-03-20 and 1.1.6 dated 2022-05-19
DESCRIPTION | 12 ++++----- MD5 | 49 ++++++++++++++++++++------------------- NAMESPACE | 2 - R/CLASSES.R | 14 +++++------ R/compareStructures.R | 2 - R/convert.DVH.R | 6 ++-- R/mean.DVH.R | 14 +++++------ R/plot.DVH.R | 21 ---------------- R/read.DICOM.RT.R | 37 ++++++++++++++++++++++++----- R/read.DVH.R | 47 ++++++++++++++++++++++++++++--------- R/structure.list.R | 55 -------------------------------------------- R/structure3D.R | 26 -------------------- R/t.test.DVH.R | 2 - R/wilcox.DVH.R | 2 - build/partial.rdb |binary build/vignette.rds |only inst/NEWS.Rd | 33 ++++++++++++++++++++++++++ inst/doc/RadOnc.R |only inst/doc/RadOnc.Rnw |only inst/doc/RadOnc.pdf |binary man/DVH-class.Rd | 2 - man/DVH.list-class.Rd | 2 - man/read.DVH.Rd | 2 - man/structure.list-class.Rd | 4 --- man/structure3D-class.Rd | 6 ---- man/zDVH-class.Rd | 4 --- vignettes/RadOnc.Rnw | 16 ------------ 27 files changed, 156 insertions(+), 202 deletions(-)
Title: Query the Breeding Management System(s)
Description: Query the Breeding Management System(s) like BMS <https://bmspro.io>,
BreeBase <https://breedbase.org>, and GIGWA <https://southgreen.fr/content/gigwa>
(using 'BrAPI' <https://brapi.org> calls) to help breeders as targeted end-users
retrieve phenotypic and genotypic data directly into their analyzing pipelines.
Author: Khaled Al-Shamaa [aut, cre],
Mariano Omar Crimi [ctb],
Zakaria Kehel [ctb],
ICARDA [cph]
Maintainer: Khaled Al-Shamaa <k.el-shamaa@cgiar.org>
Diff between QBMS versions 0.7.0 dated 2022-03-02 and 0.8.0 dated 2022-05-19
QBMS-0.7.0/QBMS/inst/doc/tutorial.Rmd |only QBMS-0.7.0/QBMS/inst/doc/tutorial.html |only QBMS-0.7.0/QBMS/vignettes/tutorial.Rmd |only QBMS-0.8.0/QBMS/DESCRIPTION | 18 QBMS-0.8.0/QBMS/MD5 | 50 +- QBMS-0.8.0/QBMS/NAMESPACE | 9 QBMS-0.8.0/QBMS/NEWS.md | 5 QBMS-0.8.0/QBMS/R/qbms.R | 558 +++++++++++++++++++++++- QBMS-0.8.0/QBMS/README.md | 76 --- QBMS-0.8.0/QBMS/build/vignette.rds |binary QBMS-0.8.0/QBMS/inst/doc/bms_example.Rmd |only QBMS-0.8.0/QBMS/inst/doc/bms_example.html |only QBMS-0.8.0/QBMS/inst/doc/breedbase_example.Rmd | 13 QBMS-0.8.0/QBMS/inst/doc/breedbase_example.html | 30 - QBMS-0.8.0/QBMS/inst/doc/gigwa_example.Rmd |only QBMS-0.8.0/QBMS/inst/doc/gigwa_example.html |only QBMS-0.8.0/QBMS/man/build_pedigree_table.Rd | 58 +- QBMS-0.8.0/QBMS/man/get_parents.Rd | 42 - QBMS-0.8.0/QBMS/man/get_pedigree_table.Rd | 166 +++---- QBMS-0.8.0/QBMS/man/gigwa_get_samples.Rd |only QBMS-0.8.0/QBMS/man/gigwa_get_variants.Rd |only QBMS-0.8.0/QBMS/man/gigwa_list_dbs.Rd |only QBMS-0.8.0/QBMS/man/gigwa_list_projects.Rd |only QBMS-0.8.0/QBMS/man/gigwa_list_runs.Rd |only QBMS-0.8.0/QBMS/man/gigwa_set_db.Rd |only QBMS-0.8.0/QBMS/man/gigwa_set_project.Rd |only QBMS-0.8.0/QBMS/man/gigwa_set_run.Rd |only QBMS-0.8.0/QBMS/man/login_bms.Rd | 8 QBMS-0.8.0/QBMS/man/login_gigwa.Rd |only QBMS-0.8.0/QBMS/man/rbindlistx.Rd | 34 - QBMS-0.8.0/QBMS/man/rbindx.Rd | 38 - QBMS-0.8.0/QBMS/man/set_qbms_config.Rd | 6 QBMS-0.8.0/QBMS/vignettes/bms_example.Rmd |only QBMS-0.8.0/QBMS/vignettes/breedbase_example.Rmd | 13 QBMS-0.8.0/QBMS/vignettes/gigwa_example.Rmd |only 35 files changed, 806 insertions(+), 318 deletions(-)
Title: Power Analyses for the Affected Sib Pair and the TDT Design
Description: There are two main functions: (1) To estimate the power of testing for linkage using an
affected sib pair design, as a function of the recurrence risk
ratios. We will use analytical power formulae as implemented in
R. These are based on a Mathematica notebook created by Martin
Farrall. (2) To examine how the power of the transmission
disequilibrium test (TDT) depends on the disease allele
frequency, the marker allele frequency, the strength of the
linkage disequilibrium, and the magnitude of the genetic
effect. We will use an R program that implements the power
formulae of Abel and Muller-Myhsok (1998). These formulae allow
one to quickly compute power of the TDT approach under a
variety of different conditions. This R program was modeled on
Martin Farrall's Mathematica notebook.
Author: Daniel E. Weeks
Maintainer: Daniel E. Weeks <weeks@pitt.edu>
Diff between powerpkg versions 1.5 dated 2012-10-11 and 1.6 dated 2022-05-19
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- NAMESPACE | 5 +++++ R/normplot.R | 2 +- 4 files changed, 16 insertions(+), 10 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between inti versions 0.5.5 dated 2022-04-01 and 0.5.6 dated 2022-05-19
DESCRIPTION | 10 ++-- MD5 | 36 ++++++++--------- NAMESPACE | 1 NEWS.md | 10 ++++ R/plot_smr.R | 12 ++--- R/split_folder.R |only R/web_table.R | 20 ++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/apps.Rmd | 14 ------ inst/doc/apps.html | 16 ------- inst/doc/rticles.html | 2 inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 6 +- inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf | 6 +- inst/yupana/server.R | 10 ++-- inst/yupana/ui.R | 19 ++++++++ man/plot_smr.Rd | 6 +- man/split_folder.Rd |only man/web_table.Rd | 10 +++- vignettes/apps.Rmd | 14 ------ 20 files changed, 100 insertions(+), 92 deletions(-)
Title: Robust Gene-Environment Interaction Analysis
Description: Description: For the risk, progression, and response to treatment of many complex diseases, it has been increasingly recognized that gene-environment interactions play important roles beyond the main genetic and environmental effects. In practical interaction analyses, outliers in response variables and covariates are not uncommon. In addition, missingness in environmental factors is routinely encountered in epidemiological studies. The developed package consists of five robust approaches to address the outliers problems, among which two approaches can also accommodate missingness in environmental factors. Both continuous and right censored responses are considered. The proposed approaches are based on penalization and sparse boosting techniques for identifying important interactions, which are realized using efficient algorithms. Beyond the gene-environment analysis, the developed package can also be adopted to conduct analysis on interactions between other types of low-dimensional and high-dimensional data. (Mengyun Wu et al (2017), <doi:10.1080/00949655.2018.1523411>; Mengyun Wu et al (2017), <doi:10.1002/gepi.22055>; Yaqing Xu et al (2018), <doi:10.1080/00949655.2018.1523411>; Yaqing Xu et al (2019), <doi:10.1016/j.ygeno.2018.07.006>; Mengyun Wu et al (2021), <doi:10.1093/bioinformatics/btab318>).
Author: Mengyun Wu [aut],
Xing Qin [aut, cre],
Shuangge Ma [aut]
Maintainer: Xing Qin <qin.xing@163.sufe.edu.cn>
Diff between GEInter versions 0.3.1 dated 2021-07-10 and 0.3.2 dated 2022-05-19
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- NEWS.md | 5 ++++- 3 files changed, 13 insertions(+), 10 deletions(-)
Title: Finite Moment Stable Distributions
Description: Some basic procedures for dealing
with log maximally skew stable distributions, which are also
called finite moment log stable distributions.
Author: Geoff Robinson
Maintainer: Daniel Wilson <hmp.R.package@gmail.com>
Diff between FMStable versions 0.1-2 dated 2012-09-06 and 0.1-3 dated 2022-05-19
DESCRIPTION | 14 ++++++++------ MD5 | 7 ++++--- NAMESPACE | 3 ++- R/functions.R | 12 ++++++------ src/init.c |only 5 files changed, 20 insertions(+), 16 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-06 1.0.0