Title: Weighted Linear Fixed Effects Regression Models for Causal
Inference
Description: Provides a computationally efficient way of fitting
weighted linear fixed effects estimators for causal
inference with various weighting schemes. Weighted linear
fixed effects estimators can be used to estimate the
average treatment effects under different identification
strategies. This includes stratified randomized
experiments, matching and stratification for
observational studies, first differencing, and
difference-in-differences. The package implements methods
described in Imai and Kim (2017) "When should We Use
Linear Fixed Effects Regression Models for Causal
Inference with Longitudinal Data?", available at
<https://imai.fas.harvard.edu/research/FEmatch.html>.
Author: In Song Kim [aut, cre],
Kosuke Imai [aut]
Maintainer: In Song Kim <insong@mit.edu>
Diff between wfe versions 1.8 dated 2019-01-09 and 1.9.1 dated 2019-04-17
Changelog | 5 DESCRIPTION | 8 - MD5 | 10 - R/wfe.R | 464 ++++++++++++++++++++++-------------------------------------- man/wfe.Rd | 6 src/wfe.c | 14 - 6 files changed, 196 insertions(+), 311 deletions(-)
Title: Machine Learning of Hyperrectangular Gating Strategies for
High-Dimensional Cytometry
Description: Given a high-dimensional dataset that typically represents a cytometry dataset, and a subset of the datapoints, this algorithm outputs an hyperrectangle so that datapoints within the hyperrectangle best correspond to the specified subset. In essence, this allows the conversion of clustering algorithms' outputs to gating strategies outputs.
Author: Etienne Becht [cre, aut],
Samuel Granjeaud [ctb]
Maintainer: Etienne Becht <etienne.becht@protonmail.com>
Diff between hypergate versions 0.8 dated 2018-08-31 and 0.8.1 dated 2019-04-17
DESCRIPTION | 10 MD5 | 8 R/hypergate.R | 2 build/vignette.rds |binary inst/doc/Hypergate.html | 697 ++++++++++++++++++------------------------------ 5 files changed, 279 insertions(+), 438 deletions(-)
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in Gjessing, HK and Lie, RT (2006) <doi:10.1111/j.1529-8817.2005.00218.x>.
Author: Hakon K. Gjessing [aut, cre],
Miriam Gjerdevik [ctb] (functions 'lineByLine' and 'convertPed'),
Julia Romanowska [ctb] (new data format, parallelisation, new
documentation),
Oivind Skare [ctb] (TDT tests)
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>
Diff between Haplin versions 7.0.0 dated 2018-05-27 and 7.1.0 dated 2019-04-17
Haplin-7.0.0/Haplin/vignettes/C_Running_Haplin_files |only Haplin-7.1.0/Haplin/DESCRIPTION | 10 Haplin-7.1.0/Haplin/MD5 | 85 Haplin-7.1.0/Haplin/NAMESPACE | 3 Haplin-7.1.0/Haplin/R/f.check.pars.R | 7 Haplin-7.1.0/Haplin/R/f.data.R | 4 Haplin-7.1.0/Haplin/R/f.make.out.filename.R | 2 Haplin-7.1.0/Haplin/R/genDataLoad.R | 8 Haplin-7.1.0/Haplin/R/genDataRead.R | 98 Haplin-7.1.0/Haplin/R/hapCovar.R | 4 Haplin-7.1.0/Haplin/R/hapPower.R | 4 Haplin-7.1.0/Haplin/R/hapRelEff.R |only Haplin-7.1.0/Haplin/R/nfam.R |only Haplin-7.1.0/Haplin/R/nindiv.R |only Haplin-7.1.0/Haplin/R/nsnps.R |only Haplin-7.1.0/Haplin/R/print.haplin.data.R | 10 Haplin-7.1.0/Haplin/R/print.haplin.ready.R | 10 Haplin-7.1.0/Haplin/R/showGen.R |only Haplin-7.1.0/Haplin/R/showPheno.R |only Haplin-7.1.0/Haplin/build/vignette.rds |binary Haplin-7.1.0/Haplin/inst/doc/A_Haplin_intro_installation.Rmd | 2 Haplin-7.1.0/Haplin/inst/doc/A_Haplin_intro_installation.html | 502 +-- Haplin-7.1.0/Haplin/inst/doc/B_Reading_data.R | 56 Haplin-7.1.0/Haplin/inst/doc/B_Reading_data.Rmd | 100 Haplin-7.1.0/Haplin/inst/doc/B_Reading_data.html | 785 +++-- Haplin-7.1.0/Haplin/inst/doc/C_Running_Haplin.html | 1537 ++++------ Haplin-7.1.0/Haplin/inst/doc/D_Running_Haplin_on_cluster.html | 531 ++- Haplin-7.1.0/Haplin/inst/doc/hapRelEff.R |only Haplin-7.1.0/Haplin/inst/doc/hapRelEff.Rmd |only Haplin-7.1.0/Haplin/inst/doc/hapRelEff.html |only Haplin-7.1.0/Haplin/inst/extdata/add_cov_data.dat |only Haplin-7.1.0/Haplin/inst/extdata/add_cov_data2.dat |only Haplin-7.1.0/Haplin/man/f.convert.matrix.ff.Rd | 4 Haplin-7.1.0/Haplin/man/genDataGetPart.Rd | 5 Haplin-7.1.0/Haplin/man/genDataRead.Rd | 41 Haplin-7.1.0/Haplin/man/hapPower.Rd | 6 Haplin-7.1.0/Haplin/man/hapPowerAsymp.Rd | 18 Haplin-7.1.0/Haplin/man/hapRelEff.Rd |only Haplin-7.1.0/Haplin/man/hapRun.Rd | 6 Haplin-7.1.0/Haplin/man/nfam.Rd |only Haplin-7.1.0/Haplin/man/nindiv.Rd |only Haplin-7.1.0/Haplin/man/nsnps.Rd |only Haplin-7.1.0/Haplin/man/plot.haplinSlide.Rd | 4 Haplin-7.1.0/Haplin/man/plot.haplinStrat.Rd | 4 Haplin-7.1.0/Haplin/man/rbindFiles.Rd | 2 Haplin-7.1.0/Haplin/man/showGen.Rd |only Haplin-7.1.0/Haplin/man/showPheno.Rd |only Haplin-7.1.0/Haplin/man/snpPower.Rd | 3 Haplin-7.1.0/Haplin/man/snpSampleSize.Rd | 4 Haplin-7.1.0/Haplin/vignettes/A_Haplin_intro_installation.Rmd | 2 Haplin-7.1.0/Haplin/vignettes/B_Reading_data.Rmd | 100 Haplin-7.1.0/Haplin/vignettes/Styrke_artikkel_rmd.bib |only Haplin-7.1.0/Haplin/vignettes/hapRelEff.Rmd |only 53 files changed, 2363 insertions(+), 1594 deletions(-)
Title: Conditional Akaike Information Criterion for 'lme4'
Description: Provides functions for the estimation of the conditional Akaike
information in generalized mixed-effect models fitted with (g)lmer()
from 'lme4'.
Author: Benjamin Saefken and David Ruegamer, with contributions from Sonja
Greven and Thomas Kneib
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between cAIC4 versions 0.7 dated 2019-02-02 and 0.8 dated 2019-04-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + R/bcMer.R | 5 +---- R/biasCorrectionBernoulli.R | 2 +- R/getcondLL.R | 11 ++++++++++- build/partial.rdb |binary 7 files changed, 23 insertions(+), 16 deletions(-)
Title: Tools to Handle Taxonomic Lists
Description: Some tools to work with taxonomic name lists.
Author: Vijay Barve [aut, cre] (<https://orcid.org/0000-0002-4852-2567>)
Maintainer: Vijay Barve <vijay.barve@gmail.com>
Diff between taxotools versions 0.0.20 dated 2019-04-08 and 0.0.23 dated 2019-04-17
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++++----------- NAMESPACE | 7 +++++++ NEWS | 9 +++++++-- R/cast_cs_field.R | 2 +- R/list_higher_taxo.R |only R/match_lists.R | 2 ++ R/melt_cs_field.R |only R/taxotools.R | 8 +++++--- man/cast_cs_field.Rd | 5 ++++- man/check_scientific.Rd | 3 ++- man/expand_name.Rd | 3 ++- man/guess_taxo_level.Rd | 2 +- man/list_higher_taxo.Rd |only man/melt_cs_field.Rd |only man/taxotools.Rd | 10 +++++++--- 16 files changed, 58 insertions(+), 29 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis
of chemical toxicokinetics ("TK") as in Pearce et al. (2017)
<doi:10.18637/jss.v079.i04>. Chemical-specific in vitro
data have been obtained from relatively high throughput
experiments. Both physiologically-based ("PBTK") and empirical
(e.g., one compartment) "TK" models can be parameterized for
several hundred chemicals and multiple species. These models are
solved efficiently, often using compiled (C-based) code. A Monte
Carlo sampler is included for simulating biological variability
(Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>)
and measurement limitations. Calibrated methods are included for
predicting tissue:plasma partition coefficients and volume of
distribution
(Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>).
These functions and data provide a set of tools for
in vitro-in vivo extrapolation ("IVIVE") of high throughput
screening data (e.g., Tox21, ToxCast) to real-world exposures via
reverse dosimetry (also known as "RTK")
(Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).
Author: John Wambaugh [aut, cre],
Robert Pearce [aut],
Caroline Ring [aut],
Greg Honda [aut],
Jimena Davis [ctb],
Nisha Sipes [ctb],
Barbara Wetmore [ctb],
Woodrow Setzer [ctb]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.9 dated 2019-02-04 and 1.9.1 dated 2019-04-17
DESCRIPTION | 8 - MD5 | 43 +++++----- NEWS |binary R/3compPBPKmodel_inits.R |only R/Parameterize_SteadyState.R | 11 +- R/calc_analytic_css.R | 13 +-- build/partial.rdb |binary inst/doc/Pearce_2017_partitioning_plots.html | 4 inst/doc/Ring_2017_supplemental_vignette_age_dist.html | 4 inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.html | 4 inst/doc/Ring_2017_supplemental_vignette_globalsensitivityplot.html | 4 inst/doc/Ring_2017_supplemental_vignette_heightweight_splines_kde.html | 4 inst/doc/Ring_2017_supplemental_vignette_hematocrit_splines.html | 4 inst/doc/Ring_2017_supplemental_vignette_plot_css95.html | 4 inst/doc/Ring_2017_supplemental_vignette_serumcreat_splines_kde.html | 4 inst/doc/Ring_2017_vignette01_subpopulations.html | 4 inst/doc/Ring_2017_vignette02_evalmodelsubpop.html | 4 inst/doc/Ring_2017_vignette03_paper_fig2.html | 4 inst/doc/Ring_2017_vignette04_paper_fig3.html | 4 inst/doc/Ring_2017_vignette05b_plothowgatejohnson.html | 4 inst/doc/Ring_2017_vignette06_aerplotting.html | 4 inst/doc/Ring_2017_vignette_05a_virtualstudypops.html | 4 inst/doc/Wambaugh_2018_Figures.html | 4 23 files changed, 71 insertions(+), 68 deletions(-)
Title: Interactive Interfaces for Results Exploration
Description: Shiny interfaces and graphical functions for multivariate analysis results exploration.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between explor versions 0.3.4 dated 2018-09-13 and 0.3.5 dated 2019-04-17
explor-0.3.4/explor/NEWS |only explor-0.3.5/explor/DESCRIPTION | 14 explor-0.3.5/explor/MD5 | 50 explor-0.3.5/explor/NAMESPACE | 3 explor-0.3.5/explor/NEWS.md |only explor-0.3.5/explor/R/MCA_plots.R | 147 ++ explor-0.3.5/explor/R/explor_multi.R | 217 ++- explor-0.3.5/explor/R/explor_multi_CA.R | 230 +-- explor-0.3.5/explor/R/explor_multi_MCA.R | 620 ++++++---- explor-0.3.5/explor/R/explor_multi_PCA.R | 397 +++--- explor-0.3.5/explor/R/prepare_results_dudi_coa.R | 4 explor-0.3.5/explor/R/prepare_results_dudi_mca.R | 4 explor-0.3.5/explor/R/prepare_results_dudi_pca.R | 4 explor-0.3.5/explor/README.md | 17 explor-0.3.5/explor/build/vignette.rds |binary explor-0.3.5/explor/inst/doc/introduction_en.html | 33 explor-0.3.5/explor/inst/doc/introduction_fr.html | 33 explor-0.3.5/explor/inst/po/en@quot/LC_MESSAGES/R-explor.mo |binary explor-0.3.5/explor/inst/po/fr/LC_MESSAGES/R-explor.mo |binary explor-0.3.5/explor/man/MCA_biplot.Rd |only explor-0.3.5/explor/man/explor.Rd | 4 explor-0.3.5/explor/man/figures |only explor-0.3.5/explor/po/R-explor.pot | 61 explor-0.3.5/explor/po/R-fr.mo |binary explor-0.3.5/explor/po/R-fr.po | 63 - explor-0.3.5/explor/tests/testthat/test_prepare_results_dudi.acm.R | 4 explor-0.3.5/explor/tests/testthat/test_prepare_results_dudi.coa.R | 4 explor-0.3.5/explor/tests/testthat/test_prepare_results_dudi.pca.R | 4 28 files changed, 1209 insertions(+), 704 deletions(-)
Title: Computation of Optimal Transport Plans and Wasserstein Distances
Description: Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
Author: Dominic Schuhmacher [aut, cre],
Björn Bähre [aut] (aha and power diagrams),
Carsten Gottschlich [aut] (simplex and shortlist),
Valentin Hartmann [aut] (semidiscrete1),
Florian Heinemann [aut] (transport_track),
Bernhard Schmitzer [aut] (shielding),
Jörn Schrieber [aut] (subsampling),
Timo Wilm [ctb] (wpp)
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between transport versions 0.11-0 dated 2019-02-04 and 0.11-1 dated 2019-04-17
DESCRIPTION | 8 ++-- MD5 | 10 +++--- NEWS | 28 ++++++++++++++++ R/fundament.R | 1 R/subsampling.R | 83 ++++++++++++++++++++++++++++++++++---------------- man/subwasserstein.Rd | 9 ++--- 6 files changed, 99 insertions(+), 40 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.2.6 dated 2018-09-22 and 2.2.7 dated 2019-04-17
DESCRIPTION | 8 MD5 | 19 - R/gjamHfunctions.R | 451 +++++++++++++++++++++++--------------------- R/gjamPriorTemplate.r | 78 +++---- build/vignette.rds |binary inst/doc/gjamVignette.R | 1 inst/doc/gjamVignette.Rmd | 1 inst/doc/gjamVignette.html | 438 +++++++++++++++++++++--------------------- man/gjam-package.Rd | 4 man/gjamFillMissingTimes.Rd |only vignettes/gjamVignette.Rmd | 1 11 files changed, 522 insertions(+), 479 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.
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 0.1-2 dated 2019-03-21 and 0.2-0 dated 2019-04-17
nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.countAnnotations.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getAnchors.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getAnnotations.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getAvailableMedia.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getCorpusIds.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getGraphIds.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getGraphIdsInCorpus.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getGraphIdsWithParticipant.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getId.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getLayer.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getLayerIds.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getLayers.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getMatchingGraphIdsPage.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getMedia.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getMediaTracks.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getParticipantIds.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.getSoundFragment.Rd |only nzilbb.labbcat-0.1-2/nzilbb.labbcat/man/labbcat.instance.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/DESCRIPTION | 10 nzilbb.labbcat-0.2-0/nzilbb.labbcat/MD5 | 47 nzilbb.labbcat-0.2-0/nzilbb.labbcat/NAMESPACE | 21 nzilbb.labbcat-0.2-0/nzilbb.labbcat/R/nzilbb.labbcat.R | 721 ++++++---- nzilbb.labbcat-0.2-0/nzilbb.labbcat/build/partial.rdb |binary nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/countAnnotations.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getAnchors.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getAnnotationLabels.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getAnnotations.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getAvailableMedia.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getCorpusIds.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getGraphIds.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getGraphIdsInCorpus.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getGraphIdsWithParticipant.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getId.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getLayer.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getLayerIds.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getLayers.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getMatchingGraphIds.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getMedia.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getMediaTracks.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getParticipantIds.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/getSoundFragment.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/labbcatCredentials.Rd |only nzilbb.labbcat-0.2-0/nzilbb.labbcat/man/nzilbb.labbcat.Rd | 20 43 files changed, 562 insertions(+), 257 deletions(-)
More information about nzilbb.labbcat at CRAN
Permanent link
Title: Generalized Additive Models for Bivariate Conditional Dependence
Structures and Vine Copulas
Description: Implementation of various inference and simulation tools to
apply generalized additive models to bivariate dependence structures and
non-simplified vine copulas.
Author: Thomas Nagler [aut],
Thibault Vatter [aut, cre]
Maintainer: Thibault Vatter <thibault.vatter@gmail.com>
Diff between gamCopula versions 0.0-4 dated 2017-08-17 and 0.0-5 dated 2019-04-17
DESCRIPTION | 10 MD5 | 30 - NAMESPACE | 6 NEWS.md | 16 R/gamBiCopPDF.R | 3 R/gamVine.R | 13 R/gamVinePDF.R |only R/gamVineSeqFit.R | 3 R/gamVineStructureSelect.R | 768 ++++++++++++++++++++++-------------------- README.md | 4 man/gamBiCopFit.Rd | 5 man/gamBiCopPDF.Rd | 3 man/gamBiCopSelect.Rd | 9 man/gamBiCopSimulate.Rd | 4 man/gamVinePDF.Rd |only man/gamVineSeqFit.Rd | 5 man/gamVineStructureSelect.Rd | 103 ++--- 17 files changed, 525 insertions(+), 457 deletions(-)
Title: Mapping Markers to the Nearest Genomic Feature
Description: Allows the user to generate a list of features (gene, pseudo, RNA,
CDS, and/or UTR) directly from NCBI database for any species with a current
build available. Option to save downloaded and formatted files is available,
and the user can prioritize the feature list based on type and assembly builds
present in the current build used. The user can then use the list of features
generated or provide a list to map a set of markers (designed for SNP markers
with a single base pair position available) to the closest feature based on
the map build. This function does require map positions of the markers to be
provided and the positions should be based on the build being queried through
NCBI.
Author: Lauren L. Hulsman Hanna and David G. Riley
Maintainer: Lauren Hanna <Lauren.Hanna@ndsu.edu>
Diff between Map2NCBI versions 1.1 dated 2015-11-13 and 1.2 dated 2019-04-17
Map2NCBI-1.1/Map2NCBI/data/Example10MarkerFile.rda |only Map2NCBI-1.2/Map2NCBI/DESCRIPTION | 14 - Map2NCBI-1.2/Map2NCBI/MD5 | 20 +- Map2NCBI-1.2/Map2NCBI/NAMESPACE | 3 Map2NCBI-1.2/Map2NCBI/R/GetGeneList.R | 177 ++++++++++--------- Map2NCBI-1.2/Map2NCBI/R/MapMarkers.R | 81 ++++---- Map2NCBI-1.2/Map2NCBI/data/Example10MarkerFile.RData |only Map2NCBI-1.2/Map2NCBI/data/GeneList_BTA1.rda |binary Map2NCBI-1.2/Map2NCBI/man/Example10MarkerFile.Rd | 2 Map2NCBI-1.2/Map2NCBI/man/GetGeneList.Rd | 73 +++---- Map2NCBI-1.2/Map2NCBI/man/Map2NCBI-package.Rd | 6 Map2NCBI-1.2/Map2NCBI/man/MapMarkers.Rd | 42 ++-- 12 files changed, 219 insertions(+), 199 deletions(-)
Title: React Helpers
Description: Make it easy to use 'React' in R with 'htmlwidget' scaffolds,
helper dependency functions, an embedded 'Babel' 'transpiler',
and examples.
Author: Facebook Inc [aut, cph] (React library in lib,
https://facebook.github.io/react; see AUTHORS for full list of
contributors),
Kent Russell [aut, cre] (R interface),
Alan Dipert [aut] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between reactR versions 0.3.0 dated 2019-01-15 and 0.4.0 dated 2019-04-17
reactR-0.3.0/reactR/R/scaffold.R |only reactR-0.3.0/reactR/build/getreact.R |only reactR-0.3.0/reactR/inst/examples/bizcharts.R |only reactR-0.3.0/reactR/inst/examples/blueprint.R |only reactR-0.3.0/reactR/inst/examples/react-sparklines.r |only reactR-0.3.0/reactR/inst/examples/react-virtualized.R |only reactR-0.3.0/reactR/inst/examples/semiotic.R |only reactR-0.3.0/reactR/inst/examples/victory-chart.R |only reactR-0.3.0/reactR/inst/templates/widget_package.json.txt |only reactR-0.3.0/reactR/inst/templates/widget_webpack.config.js.txt |only reactR-0.4.0/reactR/DESCRIPTION | 11 reactR-0.4.0/reactR/MD5 | 68 - reactR-0.4.0/reactR/NAMESPACE | 2 reactR-0.4.0/reactR/NEWS.md | 18 reactR-0.4.0/reactR/R/babel.R | 2 reactR-0.4.0/reactR/R/meta.R | 2 reactR-0.4.0/reactR/R/reacttools.R | 62 + reactR-0.4.0/reactR/R/scaffold_input.R |only reactR-0.4.0/reactR/R/scaffold_utils.R |only reactR-0.4.0/reactR/R/scaffold_widget.R |only reactR-0.4.0/reactR/README.md | 27 reactR-0.4.0/reactR/build/vignette.rds |binary reactR-0.4.0/reactR/inst/doc/intro_htmlwidgets.R | 48 reactR-0.4.0/reactR/inst/doc/intro_htmlwidgets.Rmd | 69 - reactR-0.4.0/reactR/inst/doc/intro_htmlwidgets.html | 230 +-- reactR-0.4.0/reactR/inst/doc/intro_inputs.R |only reactR-0.4.0/reactR/inst/doc/intro_inputs.Rmd |only reactR-0.4.0/reactR/inst/doc/intro_inputs.html |only reactR-0.4.0/reactR/inst/doc/intro_reactR.html | 493 ++++---- reactR-0.4.0/reactR/inst/templates/input_app.R.txt |only reactR-0.4.0/reactR/inst/templates/input_js.txt |only reactR-0.4.0/reactR/inst/templates/input_r.txt |only reactR-0.4.0/reactR/inst/templates/package.json.txt |only reactR-0.4.0/reactR/inst/templates/webpack.config.js.txt |only reactR-0.4.0/reactR/inst/templates/widget_r.txt | 4 reactR-0.4.0/reactR/inst/templates/widget_yaml.txt |only reactR-0.4.0/reactR/inst/www/react-tools/react-tools.js | 602 ++++++++-- reactR-0.4.0/reactR/inst/www/react-tools/react-tools.js.map |only reactR-0.4.0/reactR/inst/www/react/react-dom.min.js | 402 +++--- reactR-0.4.0/reactR/inst/www/react/react.min.js | 49 reactR-0.4.0/reactR/man/createReactShinyInput.Rd |only reactR-0.4.0/reactR/man/reactMarkup.Rd | 2 reactR-0.4.0/reactR/man/scaffoldReactShinyInput.Rd |only reactR-0.4.0/reactR/man/scaffoldReactWidget.Rd | 13 reactR-0.4.0/reactR/vignettes/input_app.jpg |only reactR-0.4.0/reactR/vignettes/input_sketchpicker.jpg |only reactR-0.4.0/reactR/vignettes/input_sketchpicker.mp4 |only reactR-0.4.0/reactR/vignettes/intro_htmlwidgets.Rmd | 69 - reactR-0.4.0/reactR/vignettes/intro_inputs.Rmd |only reactR-0.4.0/reactR/vignettes/logo.svg |only 50 files changed, 1339 insertions(+), 834 deletions(-)
Title: Fast, Dependency-Free Geodesic Distance Calculations
Description: Dependency-free, ultra fast calculation of geodesic distances.
Includes the reference nanometre-accuracy geodesic distances of Karney
(2013) <doi:10.1007/s00190-012-0578-z>, as used by the 'sf' package, as well
as Haversine and Vincenty distances. Default distance measure is the "Mapbox
cheap ruler" which is generally more accurate than Haversine or Vincenty for
distances out to a few hundred kilometres, and is considerably faster. The
main function accepts one or two inputs in almost any generic rectangular
form, and returns either matrices of pairwise distances, or vectors of
sequential distances.
Author: Mark Padgham [aut, cre],
Michael D. Sumner [aut],
Charles F.F Karney [cph] (Original author of included code for geodesic
distances)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between geodist versions 0.0.2 dated 2019-03-22 and 0.0.3 dated 2019-04-17
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/geodist.R | 41 +++++++++++++++++++++++++---------------- R/georange.R | 24 ++++++++++++------------ build/vignette.rds |binary inst/doc/geodist.html | 4 ++-- src/dists_seq.c | 18 ++++++++++++++++-- tests/testthat/test-georange.R | 2 +- 9 files changed, 72 insertions(+), 44 deletions(-)
Title: Simple Key-Value Database
Description: Implements a simple key-value style database where character string keys
are associated with data values that are stored on the disk. A simple interface is provided for inserting,
retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be
treated much like environments and lists are already used in R. These utilities are provided to encourage
interactive and exploratory analysis on large datasets. Three different file formats for representing the
database are currently available and new formats can easily be incorporated by third parties for use in the
'filehash' framework.
Author: Roger D. Peng <rdpeng@jhu.edu>
Maintainer: Roger D. Peng <rdpeng@jhu.edu>
Diff between filehash versions 2.4-1 dated 2017-04-07 and 2.4-2 dated 2019-04-17
DESCRIPTION | 6 +- MD5 | 12 ++--- build/vignette.rds |binary inst/doc/filehash.pdf |binary src/readKeyMap.c | 94 +++++++++++++++++++++++----------------------- tests/reg-tests.R | 16 +++---- tests/reg-tests.Rout.save | 25 ++++++------ 7 files changed, 79 insertions(+), 74 deletions(-)
Title: Continuous Time Distance-Based and Network-Based Individual
Level Models for Epidemics
Description: Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks.
Author: Waleed Almutiry, Vineetha Warriyar K. V. and Rob Deardon
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>
Diff between EpiILMCT versions 1.1.2 dated 2018-03-28 and 1.1.3 dated 2019-04-17
EpiILMCT-1.1.2/EpiILMCT/man/epiplot.Rd |only EpiILMCT-1.1.3/EpiILMCT/DESCRIPTION | 17 EpiILMCT-1.1.3/EpiILMCT/MD5 | 62 EpiILMCT-1.1.3/EpiILMCT/NAMESPACE | 16 EpiILMCT-1.1.3/EpiILMCT/R/datgen.r | 886 ++-- EpiILMCT-1.1.3/EpiILMCT/R/epictmcmc.r | 3846 ++++++++++++++------- EpiILMCT-1.1.3/EpiILMCT/R/epiplot.r | 1134 +++--- EpiILMCT-1.1.3/EpiILMCT/R/loglikelihoodepiILM.r | 664 ++- EpiILMCT-1.1.3/EpiILMCT/R/netdis.r | 240 - EpiILMCT-1.1.3/EpiILMCT/data/NetworkData.RData |binary EpiILMCT-1.1.3/EpiILMCT/data/NetworkDataSINR.RData |binary EpiILMCT-1.1.3/EpiILMCT/data/SpatialData.RData |binary EpiILMCT-1.1.3/EpiILMCT/data/SpatialNetData.RData |binary EpiILMCT-1.1.3/EpiILMCT/data/tswv.RData |binary EpiILMCT-1.1.3/EpiILMCT/man/NetworkData.Rd | 72 EpiILMCT-1.1.3/EpiILMCT/man/NetworkDataSINR.Rd | 43 EpiILMCT-1.1.3/EpiILMCT/man/SpatialData.Rd | 72 EpiILMCT-1.1.3/EpiILMCT/man/SpatialNetData.Rd | 76 EpiILMCT-1.1.3/EpiILMCT/man/as.datagen.Rd |only EpiILMCT-1.1.3/EpiILMCT/man/contactnet.Rd | 67 EpiILMCT-1.1.3/EpiILMCT/man/datagen.Rd | 141 EpiILMCT-1.1.3/EpiILMCT/man/epictmcmc.Rd | 256 - EpiILMCT-1.1.3/EpiILMCT/man/loglikelihoodepiILM.Rd | 69 EpiILMCT-1.1.3/EpiILMCT/man/plot.contactnet.Rd |only EpiILMCT-1.1.3/EpiILMCT/man/plot.datagen.Rd |only EpiILMCT-1.1.3/EpiILMCT/man/plot.epictmcmc.Rd | 8 EpiILMCT-1.1.3/EpiILMCT/man/print.epictmcmc.Rd | 2 EpiILMCT-1.1.3/EpiILMCT/man/summary.epictmcmc.Rd | 6 EpiILMCT-1.1.3/EpiILMCT/man/tswv.Rd | 10 EpiILMCT-1.1.3/EpiILMCT/src/datsim.f95 | 10 EpiILMCT-1.1.3/EpiILMCT/src/freginf.c | 35 EpiILMCT-1.1.3/EpiILMCT/src/mcmcsinr2.f95 |only EpiILMCT-1.1.3/EpiILMCT/src/mcmcsir2.f95 |only EpiILMCT-1.1.3/EpiILMCT/tests |only 34 files changed, 4783 insertions(+), 2949 deletions(-)
Title: Quantitative Exploration of Elastic Net Families for Generalized
Linear Models
Description: Provides a quantitative toolkit to explore elastic net families and to uncover correlates contributing to prediction under a cross-validation framework. Fits linear, binomial (logistic) and multinomial models. Candia J and Tsang JS, BMC Bioinformatics (2019) 20:189 <doi:10.1186/s12859-019-2778-5>.
Author: Julian Candia and John S. Tsang
Maintainer: Julian Candia <julian.candia@nih.gov>
Diff between eNetXplorer versions 1.0.1 dated 2018-06-10 and 1.0.2 dated 2019-04-17
ChangeLog | 16 - DESCRIPTION | 14 MD5 | 52 ++- NAMESPACE | 1 R/eNetXplorer.R | 12 R/eNetXplorerBinomial.R | 453 ++++++++++++++++++------------- R/eNetXplorerGaussian.R | 380 ++++++++++++++------------ R/eNetXplorerMultinomial.R | 531 ++++++++++++++++++++----------------- R/plotFeatureCaterpillar.R | 122 ++++---- R/plotFeatureCaterpillarMultinom.R | 122 ++++---- R/plotSummary.R | 54 ++- build |only data/Leukemia_miR.RData |binary inst/CITATION | 13 inst/doc |only man/H1N1_Flow.Rd | 6 man/Leuk_miR_filt.Rd |only man/Leuk_miR_full.Rd |only man/Leukemia_miR.Rd | 21 - man/QuickStartEx.Rd | 2 man/eNetXplorer-internal.Rd | 6 man/eNetXplorer-package.Rd | 10 man/eNetXplorer.Rd | 32 +- man/plot.eNetXplorer.Rd | 2 man/plotSummary.Rd | 4 man/summaryPDF.Rd | 2 vignettes |only 27 files changed, 1036 insertions(+), 819 deletions(-)
Title: Import Surface Meteorological Data from NOAA Integrated Surface
Database (ISD)
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface
Database (ISD, see <https://www.ncdc.noaa.gov/isd>).
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 0.8.4 dated 2018-02-27 and 0.8.7 dated 2019-04-17
worldmet-0.8.4/worldmet/R/meta.R |only worldmet-0.8.4/worldmet/data/meta.rda |only worldmet-0.8.4/worldmet/man/meta.Rd |only worldmet-0.8.7/worldmet/DESCRIPTION | 11 worldmet-0.8.7/worldmet/MD5 | 34 worldmet-0.8.7/worldmet/NAMESPACE | 40 - worldmet-0.8.7/worldmet/R/exportADMS.R | 234 +++--- worldmet-0.8.7/worldmet/R/getMeta.R | 409 +++++----- worldmet-0.8.7/worldmet/R/metNOAA.R | 995 +++++++++++++------------- worldmet-0.8.7/worldmet/R/sysdata.rda |binary worldmet-0.8.7/worldmet/R/weatherCodes.R | 30 worldmet-0.8.7/worldmet/R/worldmet-package.R | 58 - worldmet-0.8.7/worldmet/README.md | 138 +-- worldmet-0.8.7/worldmet/data/weatherCodes.rda |binary worldmet-0.8.7/worldmet/man/exportADMS.Rd | 72 - worldmet-0.8.7/worldmet/man/getMeta.Rd | 161 ++-- worldmet-0.8.7/worldmet/man/getMetaLive.Rd |only worldmet-0.8.7/worldmet/man/importNOAA.Rd | 252 +++--- worldmet-0.8.7/worldmet/man/weatherCodes.Rd | 36 worldmet-0.8.7/worldmet/man/worldmet.Rd | 68 - 20 files changed, 1294 insertions(+), 1244 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-14 0.1.1
2019-04-02 0.1.0
2018-07-05 0.0.7
Title: Sliding Window Discrete Fourier Transform (SWDFT)
Description: Implements the Sliding Window Discrete Fourier Transform (SWDFT). Also provides
statistical methods based on the SWDFT, and graphical tools to display the outputs.
Author: Lee F. Richardson [aut, cre]
Maintainer: Lee F. Richardson <leerichardson2013@gmail.com>
Diff between swdft versions 0.0.1 dated 2018-07-30 and 1.0.0 dated 2019-04-17
swdft-0.0.1/swdft/R/data.R |only swdft-0.0.1/swdft/R/fit-cosine-signal.R |only swdft-0.0.1/swdft/data |only swdft-0.0.1/swdft/man/c1kp.Rd |only swdft-0.0.1/swdft/man/c2kp.Rd |only swdft-0.0.1/swdft/man/coef_to_search.Rd |only swdft-0.0.1/swdft/man/compute_mse.Rd |only swdft-0.0.1/swdft/man/fit_local_cosine.Rd |only swdft-0.0.1/swdft/man/get_grid.Rd |only swdft-0.0.1/swdft/man/grid_search.Rd |only swdft-0.0.1/swdft/man/plot_mvts.Rd |only swdft-0.0.1/swdft/man/plot_swdft.Rd |only swdft-0.0.1/swdft/man/star.Rd |only swdft-0.0.1/swdft/tests/testthat/test-fit-cosine.R |only swdft-1.0.0/swdft/DESCRIPTION | 16 - swdft-1.0.0/swdft/MD5 | 103 +++++- swdft-1.0.0/swdft/NAMESPACE | 24 + swdft-1.0.0/swdft/NEWS.md | 8 swdft-1.0.0/swdft/R/cosine-regression.R |only swdft-1.0.0/swdft/R/covariance.R |only swdft-1.0.0/swdft/R/demod.R |only swdft-1.0.0/swdft/R/dirichlet.R | 29 + swdft-1.0.0/swdft/R/helpers.R |only swdft-1.0.0/swdft/R/local-cosine-regression.R |only swdft-1.0.0/swdft/R/signals.R | 12 swdft-1.0.0/swdft/R/smoothers.R |only swdft-1.0.0/swdft/R/swdft.R | 84 ++++- swdft-1.0.0/swdft/R/swdft2d.R |only swdft-1.0.0/swdft/R/swdft3d.R |only swdft-1.0.0/swdft/R/tapers.R |only swdft-1.0.0/swdft/R/visualization.R | 231 +++++++-------- swdft-1.0.0/swdft/README.md | 21 + swdft-1.0.0/swdft/build |only swdft-1.0.0/swdft/inst |only swdft-1.0.0/swdft/man/coefficients.swdft_mod.Rd |only swdft-1.0.0/swdft/man/complex_demod.Rd |only swdft-1.0.0/swdft/man/cosine_taper.Rd |only swdft-1.0.0/swdft/man/cosreg.Rd |only swdft-1.0.0/swdft/man/cov_swdft_cnum.Rd |only swdft-1.0.0/swdft/man/demod_swdft.Rd |only swdft-1.0.0/swdft/man/dirichlet.Rd |only swdft-1.0.0/swdft/man/fitted.swdft_mod.Rd |only swdft-1.0.0/swdft/man/get_aphi.Rd |only swdft-1.0.0/swdft/man/get_freq_range.Rd |only swdft-1.0.0/swdft/man/get_loglik.Rd |only swdft-1.0.0/swdft/man/get_max_freq.Rd |only swdft-1.0.0/swdft/man/get_p_range.Rd |only swdft-1.0.0/swdft/man/get_sigma.Rd |only swdft-1.0.0/swdft/man/get_sl.Rd |only swdft-1.0.0/swdft/man/get_taper.Rd |only swdft-1.0.0/swdft/man/lcr_loglik.Rd |only swdft-1.0.0/swdft/man/local_cosreg.Rd |only swdft-1.0.0/swdft/man/matching_demod.Rd |only swdft-1.0.0/swdft/man/moving_average.Rd |only swdft-1.0.0/swdft/man/new_swdft.Rd |only swdft-1.0.0/swdft/man/new_swdft2d.Rd |only swdft-1.0.0/swdft/man/new_swdft3d.Rd |only swdft-1.0.0/swdft/man/new_swdft_cosreg.Rd |only swdft-1.0.0/swdft/man/new_swdft_demod.Rd |only swdft-1.0.0/swdft/man/new_swdft_local_cosreg.Rd |only swdft-1.0.0/swdft/man/new_swdft_matching_demod.Rd |only swdft-1.0.0/swdft/man/plot.swdft.Rd |only swdft-1.0.0/swdft/man/plot.swdft_mod.Rd |only swdft-1.0.0/swdft/man/residuals.swdft_mod.Rd |only swdft-1.0.0/swdft/man/smooth_pgram.Rd |only swdft-1.0.0/swdft/man/smooth_swdft.Rd |only swdft-1.0.0/swdft/man/swdft.Rd | 30 + swdft-1.0.0/swdft/man/swdft2d.Rd |only swdft-1.0.0/swdft/man/swdft2d_fft.Rd |only swdft-1.0.0/swdft/man/swdft2d_fftw.Rd |only swdft-1.0.0/swdft/man/swdft3d.Rd |only swdft-1.0.0/swdft/man/swdft_base_3d.Rd |only swdft-1.0.0/swdft/man/swdft_fft.Rd | 6 swdft-1.0.0/swdft/man/swdft_fftw.Rd | 6 swdft-1.0.0/swdft/man/swdft_to_props.Rd |only swdft-1.0.0/swdft/man/unwrap_phase.Rd |only swdft-1.0.0/swdft/tests/testthat/test-cosreg.R |only swdft-1.0.0/swdft/tests/testthat/test-demod.R |only swdft-1.0.0/swdft/tests/testthat/test-dirichlet-kernel.R |only swdft-1.0.0/swdft/tests/testthat/test-smooth-taper.R |only swdft-1.0.0/swdft/tests/testthat/test-swdft.R | 8 swdft-1.0.0/swdft/tests/testthat/test-swdft2d.R |only swdft-1.0.0/swdft/tests/testthat/test-visualization.R |only swdft-1.0.0/swdft/vignettes |only 84 files changed, 376 insertions(+), 202 deletions(-)