Title: An Alternative Conflict Resolution Strategy
Description: R's default conflict management system gives the most recently
loaded package precedence. This can make it hard to detect conflicts,
particularly when they arise because a package update creates ambiguity
that did not previously exist. 'conflicted' takes a different approach,
making every conflict an error and forcing you to choose which function
to use.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between conflicted versions 1.0.1 dated 2018-10-02 and 1.0.2 dated 2019-03-29
DESCRIPTION | 10 +-- MD5 | 10 +-- NEWS.md | 4 + R/conflicts.R | 5 - R/shim.R | 138 +++++++++++++++++++++++++++++++++++++++------ tests/testthat/test-shim.R | 28 +++++---- 6 files changed, 153 insertions(+), 42 deletions(-)
Title: Automatic Fixed Rank Kriging
Description: Automatic fixed rank kriging for (irregularly located)
spatial data using a class of basis functions with multi-resolution features
and ordered in terms of their resolutions. The model parameters are estimated
by maximum likelihood (ML) and the number of basis functions is determined
by Akaike's information criterion (AIC). For spatial data with either one
realization or independent replicates, the ML estimates and AIC are efficiently
computed using their closed-form expressions when no missing value occurs. Details
regarding the basis function construction, parameter estimation, and AIC calculation
can be found in Tzeng and Huang (2018) <doi:10.1080/00401706.2017.1345701>. For
data with missing values, the ML estimates are obtained using the expectation-
maximization algorithm. Apart from the number of basis functions, there are
no other tuning parameters, making the method fully automatic. Users can also
include a stationary structure in the spatial covariance, which utilizes
'LatticeKrig' package.
Author: ShengLi Tzeng [aut, cre], Hsin-Cheng Huang [aut], Wen-Ting Wang [ctb], Douglas Nychka [ctb], Colin Gillespie [ctb]
Maintainer: ShengLi Tzeng <slt.cmu@gmail.com>
Diff between autoFRK versions 1.0.0 dated 2018-04-05 and 1.1.0 dated 2019-03-29
DESCRIPTION | 12 ++++----- MD5 | 12 ++++----- NAMESPACE | 3 +- R/autoFRK.R | 71 +++++++++++++++++++++++++++++++++++++++++++------------ man/autoFRK.Rd | 2 - src/Makevars | 2 - src/Makevars.win | 2 - 7 files changed, 73 insertions(+), 31 deletions(-)
Title: Snipping Methods for Robust Estimation and Clustering
Description: Snipping methods optimally removing scattered cells for robust estimation and cluster analysis.
Author: Alessio Farcomeni, Andy Leung
Maintainer: Alessio Farcomeni <alessio.farcomeni@uniroma1.it>
Diff between snipEM versions 1.0 dated 2014-10-06 and 1.0.1 dated 2019-03-29
DESCRIPTION | 14 +++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 4 ++-- man/ldmvnorm.Rd | 3 +-- man/sclust.Rd | 17 ++++++++--------- man/skmeans.Rd | 18 ++++++++---------- man/snipEM.Rd | 18 ++++-------------- man/stEM.Rd | 45 +++++++++++++-------------------------------- man/sumlog.Rd | 3 +-- 9 files changed, 52 insertions(+), 86 deletions(-)
Title: Single Cell Genomics for Enhancing Cell Composition Inference
from Bulk Genomics Data
Description: Cellular population mapping (CPM) a deconvolution algorithm in which single-cell genomics is required in only one or a few samples, where in other samples of the same tissue, only bulk genomics is measured and the underlying fine resolution cellular heterogeneity is inferred.
Author: Amit Frishberg [aut, cre], Naama Peshes-Yaloz [aut], Irit Gat-Viks [aut]
Maintainer: Amit Frishberg <amfrishberg@gmail.com>
Diff between scBio versions 0.1.3 dated 2019-03-24 and 0.1.4 dated 2019-03-29
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/scBio.R | 19 +++++++++++++++++-- 3 files changed, 22 insertions(+), 7 deletions(-)
Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu et al. (2014) <doi:10.4172/2155-6180.1000189> "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189; and Yu et al.(2017) <DOI:10.1016/j.sste.2017.02.001> "Exploring racial disparity in obesity: a mediation analysis considering geo-coded environmental factors", published on Spatial and Spatio-temporal Epidemiology, 21, 13-23.
Author: Qingzhao Yu and Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mma versions 7.0-0 dated 2018-11-20 and 8.0-0 dated 2019-03-29
DESCRIPTION | 13 MD5 | 38 NAMESPACE | 4 R/mma.r | 2630 +++++++++++++++++++++++++++++++----------------- R/moderation.R |only man/boot.med.Rd | 46 man/boot.med.par.Rd | 22 man/boot.mod.Rd |only man/data.org.Rd | 16 man/form.interaction.Rd | 13 man/med.Rd | 28 man/mma-package.Rd | 4 man/mma.Rd | 32 man/mma.par.Rd | 22 man/moderate.Rd |only man/plot.mma.Rd | 8 man/plot2.mma.Rd |only man/print.med.Rd | 10 man/print.mma.Rd | 10 man/summary.med_iden.Rd | 8 man/summary.mma.Rd | 13 man/test.moderation.Rd | 20 22 files changed, 1964 insertions(+), 973 deletions(-)
Title: Interactively Visualize Genomic Mutation Data using a
Lollipop-Diagram
Description: R interface for 'g3-lollipop' JavaScript library.
Visualize genomic mutation data using an interactive lollipop diagram in Rstudio or your browser.
Author: Xin Guo [aut, cre]
Maintainer: Xin Guo <g3viz.group@gmail.com>
Diff between g3viz versions 0.1.4 dated 2019-01-23 and 1.0.0 dated 2019-03-29
g3viz-0.1.4/g3viz/R/g3Lollipop.options.R |only g3viz-0.1.4/g3viz/inst/htmlwidgets/lib/g3Lollipop |only g3viz-0.1.4/g3viz/vignettes/figures/CCLE_APC.png |only g3viz-0.1.4/g3viz/vignettes/figures/MSK_IMPACT_2017_TP53.png |only g3viz-0.1.4/g3viz/vignettes/figures/TCGA_BRCA_PIK3CA.png |only g3viz-1.0.0/g3viz/DESCRIPTION | 23 g3viz-1.0.0/g3viz/MD5 | 68 g3viz-1.0.0/g3viz/NAMESPACE | 1 g3viz-1.0.0/g3viz/R/data.R | 8 g3viz-1.0.0/g3viz/R/g3Lollipop.R | 138 g3viz-1.0.0/g3viz/R/g3LollipopOptions.R |only g3viz-1.0.0/g3viz/R/g3LollipopTheme.R |only g3viz-1.0.0/g3viz/R/getMutationsFromCbioportal.R | 71 g3viz-1.0.0/g3viz/R/hgnc2pfam.R | 2 g3viz-1.0.0/g3viz/R/mapMutationTypeToMutationClass.R | 52 g3viz-1.0.0/g3viz/R/readMAF.R | 52 g3viz-1.0.0/g3viz/R/zzz.R | 2 g3viz-1.0.0/g3viz/build/vignette.rds |binary g3viz-1.0.0/g3viz/data/mutation.table.df.rda |binary g3viz-1.0.0/g3viz/inst/doc/introduction.R | 219 + g3viz-1.0.0/g3viz/inst/doc/introduction.Rmd | 517 ++- g3viz-1.0.0/g3viz/inst/doc/introduction.html | 1732 +++++++++-- g3viz-1.0.0/g3viz/inst/htmlwidgets/g3Lollipop.js | 104 g3viz-1.0.0/g3viz/inst/htmlwidgets/g3Lollipop.yaml | 8 g3viz-1.0.0/g3viz/inst/htmlwidgets/lib/g3viz |only g3viz-1.0.0/g3viz/man/g3Lollipop-shiny.Rd | 4 g3viz-1.0.0/g3viz/man/g3Lollipop.Rd | 114 g3viz-1.0.0/g3viz/man/g3Lollipop.options.Rd | 71 g3viz-1.0.0/g3viz/man/g3Lollipop.theme.Rd |only g3viz-1.0.0/g3viz/man/getMutationsFromCbioportal.Rd | 64 g3viz-1.0.0/g3viz/man/hgnc2pfam.df.Rd | 3 g3viz-1.0.0/g3viz/man/mapMutationTypeToMutationClass.Rd | 50 g3viz-1.0.0/g3viz/man/readMAF.Rd | 40 g3viz-1.0.0/g3viz/vignettes/figures/cbioportal_theme.png |only g3viz-1.0.0/g3viz/vignettes/figures/color_scheme.png |only g3viz-1.0.0/g3viz/vignettes/figures/customized_plot.png |only g3viz-1.0.0/g3viz/vignettes/figures/default_theme.png |only g3viz-1.0.0/g3viz/vignettes/figures/ggplot2_theme.png |only g3viz-1.0.0/g3viz/vignettes/figures/nature_theme.png |only g3viz-1.0.0/g3viz/vignettes/figures/simple_theme.png |only g3viz-1.0.0/g3viz/vignettes/introduction.Rmd | 517 ++- 41 files changed, 3014 insertions(+), 846 deletions(-)
Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in handy
if you are developing R packages and can not use a proper build
system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fakemake versions 1.4.0 dated 2018-11-02 and 1.4.1 dated 2019-03-29
DESCRIPTION | 16 +++++----- MD5 | 12 +++---- NEWS.md | 4 ++ README.md | 16 +++++++--- inst/doc/An_Introduction_to_fakemake.Rmd | 4 +- inst/doc/An_Introduction_to_fakemake.html | 48 +++++++++++++++--------------- vignettes/An_Introduction_to_fakemake.Rmd | 4 +- 7 files changed, 58 insertions(+), 46 deletions(-)
Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analysis functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: OECD <http://www.oecd.org/>, including PISA, TALIS, PIAAC, and IEA <http://www.iea.nl/>, including TIMSS, TIMSS Advanced, PIRLS, ICCS, ICILS, and CivEd.
Author: Paul Bailey [aut, cre], Ren C'deBaca [ctb], Ahmad Emad [aut], Huade Huo [aut], Michael Lee [aut], Yuqi Liao [aut], Alex Lishinski [aut], Trang Nguyen [aut], Qingshu Xie [aut], Jiao Yu [aut], Ting Zhang [aut]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between EdSurvey versions 2.2.3 dated 2019-03-18 and 2.3.2 dated 2019-03-29
DESCRIPTION | 12 MD5 | 195 NAMESPACE | 16 R/achievementLevels.R | 18 R/cacheMetaReqUpdate.R | 5 R/dim.edsurvey.data.frame.R | 40 R/downloadPISA.R | 29 R/edsurvey-package.R | 3 R/edsurvey.data.frame.R | 294 R/edsurveyTable.R | 53 R/gap.R | 348 R/getAttributes.R | 7 R/getData.R | 528 - R/glm.sdf.R | 219 R/levelsSDF.R | 8 R/lm.sdf.R | 121 R/mixed.sdf.R | 34 R/mvrlm.sdf.R | 36 R/percentile.R | 62 R/readBB_2001.R |only R/readBB_2012.R |only R/readECLS_K1998.R | 598 + R/readECLS_K2011.R | 752 - R/readICCS.R | 156 R/readICILS.R | 377 R/readNAEP.r | 53 R/readPIAAC.R | 37 R/readPIRLS.R | 504 - R/readPISA.R | 937 +- R/readTALIS.R | 81 R/readTIMSS.R | 677 - R/readTIMSSAdv.R | 314 R/read_ePIRLS.R | 61 R/rebindAttributes.R | 2 R/rename.sdf.R | 99 R/rq.sdf.R |only R/searchSDF.R | 194 R/showCodebook.R | 42 R/summary2.R | 109 R/zzz.R | 3 inst/NEWS.Rd | 17 inst/suggestWeights |only man/EdSurvey-package.Rd | 3 man/achievementLevels.Rd | 18 man/downloadPISA.Rd | 20 man/edsurvey-class.Rd | 102 man/edsurveyTable.Rd | 16 man/examples/downloadPISA.R | 8 man/examples/getData.R | 2 man/examples/glm.sdf.R | 7 man/examples/lm.sdf.R | 7 man/examples/mvrlm.sdf.R | 18 man/examples/oddsRatio.R | 2 man/examples/percentile.R | 4 man/examples/readBB_2001.R |only man/examples/readBB_2012.R |only man/examples/rebindAttributes.R | 2 man/examples/rq.sdf.R |only man/examples/searchSDF.R | 7 man/examples/subset.edsurvey.data.frame.R | 5 man/examples/summary2.R | 4 man/gap.Rd | 41 man/getData.Rd | 10 man/glm.sdf.Rd | 51 man/lm.sdf.Rd | 45 man/mvrlm.sdf.Rd | 54 man/percentile.Rd | 31 man/readBB_2001.Rd |only man/readBB_2012.Rd |only man/readECLS_K1998.Rd | 10 man/readECLS_K2011.Rd | 12 man/readICILS.Rd | 10 man/readPIRLS.Rd | 20 man/readPISA.Rd | 28 man/readTIMSS.Rd | 24 man/readTIMSSAdv.Rd | 14 man/rebindAttributes.Rd | 4 man/rq.sdf.Rd |only man/searchSDF.Rd | 19 man/showCodebook.Rd | 6 man/subset.Rd | 5 man/summary2.Rd | 25 tests/Examples/edsurvey-Ex.Rout.save |11479 +++++++++++++++--------------- tests/testthat/REF-0-main.R |only tests/testthat/REF-1-lesdf.R |only tests/testthat/REF-2-esdfl.R |only tests/testthat/REF-3-TIMSS.R |only tests/testthat/REF-4-pisa.R |only tests/testthat/REF-5-piaac.R |only tests/testthat/REF-6-ECLS_K.R |only tests/testthat/gd8.rds |binary tests/testthat/gddat.rds |binary tests/testthat/lm1t.rds |binary tests/testthat/lm2t.rds |binary tests/testthat/searchSDFLevels.rds |only tests/testthat/searchSDFOr.rds |only tests/testthat/searchSDFVector.rds |only tests/testthat/showCodebook.rds |only tests/testthat/showCodebookRecodes.rds |only tests/testthat/test-0-main.R | 204 tests/testthat/test-1-lesdf.R | 16 tests/testthat/test-2-esdfl.R | 31 tests/testthat/test-3-TIMSS.R | 25 tests/testthat/test-4-pisa.R | 13 tests/testthat/test-5-piaac.R | 8 tests/testthat/test-6-ECLS_K.R | 12 tests/testthat/test-mixed.R | 30 tests/testthat/test-mvrlm.R | 7 tests/testthat_tests.R | 1 109 files changed, 10264 insertions(+), 9237 deletions(-)
More information about intensity.analysis at CRAN
Permanent link
Title: Extensions of Package 'distr'
Description: Extends package 'distr' by functionals, distances, and conditional distributions.
Author: Matthias Kohl [cre, cph],
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between distrEx versions 2.7.0 dated 2018-07-22 and 2.8.0 dated 2019-03-29
DESCRIPTION | 22 MD5 | 58 +- NAMESPACE | 9 R/AllClass.R | 5 R/AsymTotalVarDist.R | 113 +++- R/CvMDist.R | 23 R/DiagnUtils.R |only R/DiscreteMVDistribution.R | 8 R/Expectation.R | 818 +++++++++++++++++++++---------- R/GammaWeibullExpectation.R |only R/HellingerDist.R | 59 +- R/Internalfunctions.R | 19 R/OAsymTotalVarDist.R | 84 ++- R/TotalVarDist.R | 39 + R/distrExIntegrate.R | 174 +++++- R/liesInSupport.R | 6 R/sysdata.rda |binary inst/NEWS | 81 +++ man/0distrEx-package.Rd | 22 man/AsymTotalVarDist.Rd | 23 man/CvMDist.Rd | 17 man/DiscreteMVDistribution-class.Rd | 5 man/E.Rd | 165 ++++-- man/HellingerDist.Rd | 24 man/OAsymTotalVarDist.Rd | 24 man/TotalVarDist.Rd | 26 man/distrExIntegrate.Rd | 62 ++ man/internals.Rd | 76 ++ man/liesInSupport.Rd | 8 tests/Examples/distrEx-Ex_i386.Rout.save | 134 +---- tests/Examples/distrEx-Ex_x64.Rout.save | 134 +---- 31 files changed, 1516 insertions(+), 722 deletions(-)
More information about IndexConstruction at CRAN
Permanent link
Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with
spatially correlated errors by robust and Gaussian (Restricted)
Maximum Likelihood and for computing robust and customary point
and block external-drift Kriging predictions, along with utility
functions for variogram modelling in ad hoc geostatistical analyses,
model building, model evaluation by cross-validation, (conditional)
simulation of Gaussian processes, unbiased back-transformation of
Kriging predictions of log-transformed data.
Author: Andreas Papritz [cre, aut],
Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>
Diff between georob versions 0.3-7 dated 2018-08-27 and 0.3-8 dated 2019-03-29
ChangeLog | 11 +++++++ DESCRIPTION | 10 +++--- MD5 | 30 ++++++++++---------- NAMESPACE | 2 - NEWS | 4 ++ R/georob.predict.R | 2 - R/georob.private.functions.R | 52 ++++++++++++++++++++++++++++++----- R/georob.simulation.R | 14 +++++++-- build/vignette.rds |binary inst/doc/georob_vignette.Rnw | 22 ++++++++------ inst/doc/georob_vignette.pdf |binary man/georob.Rd | 6 ++-- man/georobSimulation.Rd | 6 ++-- vignettes/georob_vignette.Rnw | 22 ++++++++------ vignettes/r_coalash_objects.RData |binary vignettes/r_meuse_zinc_objects.RData |binary 16 files changed, 123 insertions(+), 58 deletions(-)
Title: Genomic Data Management
Description: Manage and analyze high-dimensional SNP data from chips with multiple densities.
Author: Gamal Abdel-Azim [aut, cre]
Maintainer: Gamal Abdel-Azim <gamal.azim@gmail.com>
Diff between gdmp versions 0.1.0 dated 2016-09-29 and 0.2.0 dated 2019-03-29
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/dataEdit.R | 9 +++++---- man/read.findhap.Rd | 6 +++--- src/cGetHCS.c | 2 +- src/cIdentical.c | 2 +- src/gt.c | 2 +- src/readGenotypes.c | 4 ++-- 8 files changed, 25 insertions(+), 24 deletions(-)
Title: Estimation and Prediction of Skewed Spatial Processes
Description: MCMC method to estimate and predict skewed spatial processes. A real data set is included. Reference: Wang, Yang and Majumdar (2018) <doi.org/10.1007/s00180-017-0741-3>.
Author: Jiangyan Wang, Miao Yang and Anandamayee Majumdar
Maintainer: "Jiangyan Wang" <wangjiangyan2007@126.com>
Diff between DZEXPM versions 1.0 dated 2017-06-24 and 2.0 dated 2019-03-29
DZEXPM-1.0/DZEXPM/R/dzexpm.R |only DZEXPM-1.0/DZEXPM/man/DZEXPM-package.Rd |only DZEXPM-2.0/DZEXPM/DESCRIPTION | 12 ++++++------ DZEXPM-2.0/DZEXPM/MD5 | 10 +++++----- DZEXPM-2.0/DZEXPM/R/dzexpm.r |only DZEXPM-2.0/DZEXPM/man/MaxTemp03.Rd | 2 +- DZEXPM-2.0/DZEXPM/man/dzexpm-package.Rd |only DZEXPM-2.0/DZEXPM/man/dzexpm.Rd | 5 ++--- 8 files changed, 14 insertions(+), 15 deletions(-)
Title: Exploring Genomic Relations for Enhanced Interpretation Through
Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR by Fang et al. (2016) <doi:10.1186/s13073-016-0384-y> is to provide a data interpretation system necessary to do "big data" science. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.1.4 dated 2018-08-14 and 1.1.5 dated 2019-03-29
XGR-1.1.4/XGR/R/xBigraph.r |only XGR-1.1.4/XGR/R/xBiheatmap.r |only XGR-1.1.4/XGR/R/xBiproject.r |only XGR-1.1.4/XGR/R/xCorrelation.r |only XGR-1.1.4/XGR/R/xCrosstalk.r |only XGR-1.1.4/XGR/R/xFunArgs.r |only XGR-1.1.4/XGR/R/xGR2xNet.r |only XGR-1.1.4/XGR/R/xGRkaryogram.r |only XGR-1.1.4/XGR/R/xGRmanhattan.r |only XGR-1.1.4/XGR/R/xGRoverlap.r |only XGR-1.1.4/XGR/R/xGRtrack.r |only XGR-1.1.4/XGR/R/xGScore.r |only XGR-1.1.4/XGR/R/xGScoreAdv.r |only XGR-1.1.4/XGR/R/xGraphSplit.r |only XGR-1.1.4/XGR/R/xHEB.r |only XGR-1.1.4/XGR/R/xLDblock.r |only XGR-1.1.4/XGR/R/xLDenricher.r |only XGR-1.1.4/XGR/R/xLDsampling.r |only XGR-1.1.4/XGR/R/xPCHiCplot.r |only XGR-1.1.4/XGR/R/xPolarBar.r |only XGR-1.1.4/XGR/R/xPolarDot.r |only XGR-1.1.4/XGR/R/xRPS.r |only XGR-1.1.4/XGR/R/xRWenricher.r |only XGR-1.1.4/XGR/R/xRWkernel.r |only XGR-1.1.4/XGR/R/xRd2HTML.r |only XGR-1.1.4/XGR/R/xRdWrap.r |only XGR-1.1.4/XGR/R/xRegress.r |only XGR-1.1.4/XGR/R/xRepurpose.r |only XGR-1.1.4/XGR/R/xVisInterp.r |only XGR-1.1.4/XGR/R/xVisInterpAnimate.r |only XGR-1.1.4/XGR/R/xVolcano.r |only XGR-1.1.4/XGR/inst/DR.html |only XGR-1.1.4/XGR/inst/bLD.html |only XGR-1.1.4/XGR/inst/cPath.html |only XGR-1.1.4/XGR/inst/mSeed.html |only XGR-1.1.4/XGR/inst/xBigraph.html |only XGR-1.1.4/XGR/inst/xBiheatmap.html |only XGR-1.1.4/XGR/inst/xBiproject.html |only XGR-1.1.4/XGR/inst/xCorrelation.html |only XGR-1.1.4/XGR/inst/xCrosstalk.html |only XGR-1.1.4/XGR/inst/xFunArgs.html |only XGR-1.1.4/XGR/inst/xGR2xNet.html |only XGR-1.1.4/XGR/inst/xGRkaryogram.html |only XGR-1.1.4/XGR/inst/xGRmanhattan.html |only XGR-1.1.4/XGR/inst/xGRoverlap.html |only XGR-1.1.4/XGR/inst/xGRtrack.html |only XGR-1.1.4/XGR/inst/xGScore.html |only XGR-1.1.4/XGR/inst/xGScoreAdv.html |only XGR-1.1.4/XGR/inst/xGraphSplit.html |only XGR-1.1.4/XGR/inst/xHEB.html |only XGR-1.1.4/XGR/inst/xLDblock.html |only XGR-1.1.4/XGR/inst/xLDenricher.html |only XGR-1.1.4/XGR/inst/xLDsampling.html |only XGR-1.1.4/XGR/inst/xPCHiCplot.html |only XGR-1.1.4/XGR/inst/xPolarBar.html |only XGR-1.1.4/XGR/inst/xPolarDot.html |only XGR-1.1.4/XGR/inst/xRPS.html |only XGR-1.1.4/XGR/inst/xRWenricher.html |only XGR-1.1.4/XGR/inst/xRWkernel.html |only XGR-1.1.4/XGR/inst/xRd2HTML.html |only XGR-1.1.4/XGR/inst/xRdWrap.html |only XGR-1.1.4/XGR/inst/xRegress.html |only XGR-1.1.4/XGR/inst/xRepurpose.html |only XGR-1.1.4/XGR/inst/xVisInterp.html |only XGR-1.1.4/XGR/inst/xVisInterpAnimate.html |only XGR-1.1.4/XGR/inst/xVolcano.html |only XGR-1.1.4/XGR/man/DR.Rd |only XGR-1.1.4/XGR/man/bLD.Rd |only XGR-1.1.4/XGR/man/cPath.Rd |only XGR-1.1.4/XGR/man/mSeed.Rd |only XGR-1.1.4/XGR/man/xBigraph.Rd |only XGR-1.1.4/XGR/man/xBiheatmap.Rd |only XGR-1.1.4/XGR/man/xBiproject.Rd |only XGR-1.1.4/XGR/man/xCorrelation.Rd |only XGR-1.1.4/XGR/man/xCrosstalk.Rd |only XGR-1.1.4/XGR/man/xFunArgs.Rd |only XGR-1.1.4/XGR/man/xGR2xNet.Rd |only XGR-1.1.4/XGR/man/xGRkaryogram.Rd |only XGR-1.1.4/XGR/man/xGRmanhattan.Rd |only XGR-1.1.4/XGR/man/xGRoverlap.Rd |only XGR-1.1.4/XGR/man/xGRtrack.Rd |only XGR-1.1.4/XGR/man/xGScore.Rd |only XGR-1.1.4/XGR/man/xGScoreAdv.Rd |only XGR-1.1.4/XGR/man/xGraphSplit.Rd |only XGR-1.1.4/XGR/man/xHEB.Rd |only XGR-1.1.4/XGR/man/xLDblock.Rd |only XGR-1.1.4/XGR/man/xLDenricher.Rd |only XGR-1.1.4/XGR/man/xLDsampling.Rd |only XGR-1.1.4/XGR/man/xPCHiCplot.Rd |only XGR-1.1.4/XGR/man/xPolarBar.Rd |only XGR-1.1.4/XGR/man/xPolarDot.Rd |only XGR-1.1.4/XGR/man/xRPS.Rd |only XGR-1.1.4/XGR/man/xRWenricher.Rd |only XGR-1.1.4/XGR/man/xRWkernel.Rd |only XGR-1.1.4/XGR/man/xRd2HTML.Rd |only XGR-1.1.4/XGR/man/xRdWrap.Rd |only XGR-1.1.4/XGR/man/xRegress.Rd |only XGR-1.1.4/XGR/man/xRepurpose.Rd |only XGR-1.1.4/XGR/man/xVisInterp.Rd |only XGR-1.1.4/XGR/man/xVisInterpAnimate.Rd |only XGR-1.1.4/XGR/man/xVolcano.Rd |only XGR-1.1.5/XGR/DESCRIPTION | 64 +-- XGR-1.1.5/XGR/MD5 | 509 ++++++++++++-------------- XGR-1.1.5/XGR/NAMESPACE | 84 +--- XGR-1.1.5/XGR/R/ClassMethod-XGR.r | 194 --------- XGR-1.1.5/XGR/R/xAddCoords.r | 15 XGR-1.1.5/XGR/R/xAuxEmbed.r |only XGR-1.1.5/XGR/R/xAuxFunArgs.r |only XGR-1.1.5/XGR/R/xAuxRd2HTML.r |only XGR-1.1.5/XGR/R/xAuxRdWrap.r |only XGR-1.1.5/XGR/R/xCheckParallel.r | 2 XGR-1.1.5/XGR/R/xColormap.r | 103 +++++ XGR-1.1.5/XGR/R/xCombineNet.r | 10 XGR-1.1.5/XGR/R/xConverter.r | 239 +++++++++--- XGR-1.1.5/XGR/R/xCtree.r |only XGR-1.1.5/XGR/R/xDAGsim.r | 2 XGR-1.1.5/XGR/R/xDefineEQTL.r | 120 +++++- XGR-1.1.5/XGR/R/xDefineGenomicAnno.r | 8 XGR-1.1.5/XGR/R/xDefineHIC.r | 23 - XGR-1.1.5/XGR/R/xDefineNet.r | 25 + XGR-1.1.5/XGR/R/xDefineOntology.r | 245 ++++++++---- XGR-1.1.5/XGR/R/xEnrichBarplot.r | 2 XGR-1.1.5/XGR/R/xEnrichChord.r |only XGR-1.1.5/XGR/R/xEnrichCtree.r |only XGR-1.1.5/XGR/R/xEnrichD3.r |only XGR-1.1.5/XGR/R/xEnrichDotplot.r |only XGR-1.1.5/XGR/R/xEnrichForest.r | 21 - XGR-1.1.5/XGR/R/xEnrichGGraph.r |only XGR-1.1.5/XGR/R/xEnrichLadder.r | 7 XGR-1.1.5/XGR/R/xEnrichMatrix.r | 16 XGR-1.1.5/XGR/R/xEnrichRadial.r |only XGR-1.1.5/XGR/R/xEnrichTreemap.r | 92 +++- XGR-1.1.5/XGR/R/xEnrichViewer.r | 12 XGR-1.1.5/XGR/R/xEnricher.r | 2 XGR-1.1.5/XGR/R/xEnricherGenes.r | 53 +- XGR-1.1.5/XGR/R/xEnricherGenesAdv.r | 17 XGR-1.1.5/XGR/R/xEnricherSNPs.r | 4 XGR-1.1.5/XGR/R/xEnricherYours.r | 4 XGR-1.1.5/XGR/R/xGGnetwork.r | 69 ++- XGR-1.1.5/XGR/R/xGGraph.r |only XGR-1.1.5/XGR/R/xGR2xGeneAnno.r | 107 +++-- XGR-1.1.5/XGR/R/xGR2xGeneAnnoAdv.r | 27 - XGR-1.1.5/XGR/R/xGR2xGeneScores.r | 4 XGR-1.1.5/XGR/R/xGR2xGenes.r | 24 - XGR-1.1.5/XGR/R/xGRcse.r | 2 XGR-1.1.5/XGR/R/xGRviaGeneAnno.r | 2 XGR-1.1.5/XGR/R/xGRviaGeneAnnoAdv.r | 2 XGR-1.1.5/XGR/R/xGRviaGenomicAnnoAdv.r | 2 XGR-1.1.5/XGR/R/xGeneID2Symbol.r |only XGR-1.1.5/XGR/R/xGraphML.r | 31 + XGR-1.1.5/XGR/R/xGraphML2AA.r |only XGR-1.1.5/XGR/R/xHeatmap.r | 7 XGR-1.1.5/XGR/R/xHeatmapAdv.r | 9 XGR-1.1.5/XGR/R/xLayout.r |only XGR-1.1.5/XGR/R/xMEabf.r |only XGR-1.1.5/XGR/R/xObjSize.r |only XGR-1.1.5/XGR/R/xPieplot.r |only XGR-1.1.5/XGR/R/xRDataLoader.r | 10 XGR-1.1.5/XGR/R/xReport.r |only XGR-1.1.5/XGR/R/xSM2DF.r | 4 XGR-1.1.5/XGR/R/xSNP2cGenes.r |only XGR-1.1.5/XGR/R/xSNP2eGenes.r |only XGR-1.1.5/XGR/R/xSNP2nGenes.r | 17 XGR-1.1.5/XGR/R/xSocialiser.r | 2 XGR-1.1.5/XGR/R/xSocialiserGenes.r | 2 XGR-1.1.5/XGR/R/xSocialiserSNPs.r | 2 XGR-1.1.5/XGR/R/xSubneterGR.r | 29 - XGR-1.1.5/XGR/R/xSubneterGenes.r | 23 - XGR-1.1.5/XGR/R/xSubneterSNPs.r | 29 - XGR-1.1.5/XGR/R/xSymbol2GeneID.r | 30 + XGR-1.1.5/XGR/R/xVisNet.r | 2 XGR-1.1.5/XGR/data/Haploid_regulators.RData |binary XGR-1.1.5/XGR/data/ImmunoBase.RData |binary XGR-1.1.5/XGR/data/JKscience_TS2A.RData |binary XGR-1.1.5/XGR/inst/DynamicReport |only XGR-1.1.5/XGR/inst/NEWS | 32 + XGR-1.1.5/XGR/inst/eTerm.html | 3 XGR-1.1.5/XGR/inst/xAddCoords.html | 30 + XGR-1.1.5/XGR/inst/xAuxEmbed.html |only XGR-1.1.5/XGR/inst/xAuxFunArgs.html |only XGR-1.1.5/XGR/inst/xAuxRd2HTML.html |only XGR-1.1.5/XGR/inst/xAuxRdWrap.html |only XGR-1.1.5/XGR/inst/xCheckParallel.html | 4 XGR-1.1.5/XGR/inst/xCircos.html | 4 XGR-1.1.5/XGR/inst/xColormap.html | 46 +- XGR-1.1.5/XGR/inst/xConverter.html | 44 +- XGR-1.1.5/XGR/inst/xCtree.html |only XGR-1.1.5/XGR/inst/xDAGsim.html | 5 XGR-1.1.5/XGR/inst/xDefineEQTL.html | 168 +++++++- XGR-1.1.5/XGR/inst/xDefineGenomicAnno.html | 33 + XGR-1.1.5/XGR/inst/xDefineHIC.html | 22 - XGR-1.1.5/XGR/inst/xDefineOntology.html | 67 ++- XGR-1.1.5/XGR/inst/xEnrichBarplot.html | 7 XGR-1.1.5/XGR/inst/xEnrichChord.html |only XGR-1.1.5/XGR/inst/xEnrichCompare.html | 6 XGR-1.1.5/XGR/inst/xEnrichCtree.html |only XGR-1.1.5/XGR/inst/xEnrichD3.html |only XGR-1.1.5/XGR/inst/xEnrichDAGplot.html | 12 XGR-1.1.5/XGR/inst/xEnrichDAGplotAdv.html | 9 XGR-1.1.5/XGR/inst/xEnrichDotplot.html |only XGR-1.1.5/XGR/inst/xEnrichForest.html | 24 - XGR-1.1.5/XGR/inst/xEnrichGGraph.html |only XGR-1.1.5/XGR/inst/xEnrichHeatmap.html | 6 XGR-1.1.5/XGR/inst/xEnrichLadder.html | 16 XGR-1.1.5/XGR/inst/xEnrichMatrix.html | 15 XGR-1.1.5/XGR/inst/xEnrichNetplot.html | 7 XGR-1.1.5/XGR/inst/xEnrichRadial.html |only XGR-1.1.5/XGR/inst/xEnrichTreemap.html | 25 - XGR-1.1.5/XGR/inst/xEnrichViewer.html | 6 XGR-1.1.5/XGR/inst/xEnricher.html | 11 XGR-1.1.5/XGR/inst/xEnricherGenes.html | 34 - XGR-1.1.5/XGR/inst/xEnricherGenesAdv.html | 27 - XGR-1.1.5/XGR/inst/xEnricherSNPs.html | 16 XGR-1.1.5/XGR/inst/xEnricherYours.html | 8 XGR-1.1.5/XGR/inst/xGGnetwork.html | 40 +- XGR-1.1.5/XGR/inst/xGGraph.html |only XGR-1.1.5/XGR/inst/xGR.html | 4 XGR-1.1.5/XGR/inst/xGR2nGenes.html | 3 XGR-1.1.5/XGR/inst/xGR2xGeneAnno.html | 54 +- XGR-1.1.5/XGR/inst/xGR2xGeneAnnoAdv.html | 28 - XGR-1.1.5/XGR/inst/xGR2xGeneScores.html | 2 XGR-1.1.5/XGR/inst/xGR2xGenes.html | 20 - XGR-1.1.5/XGR/inst/xGRcse.html | 4 XGR-1.1.5/XGR/inst/xGRviaGeneAnno.html | 20 - XGR-1.1.5/XGR/inst/xGRviaGeneAnnoAdv.html | 23 - XGR-1.1.5/XGR/inst/xGRviaGenomicAnno.html | 12 XGR-1.1.5/XGR/inst/xGRviaGenomicAnnoAdv.html | 9 XGR-1.1.5/XGR/inst/xGeneID2Symbol.html |only XGR-1.1.5/XGR/inst/xGraphML.html | 33 + XGR-1.1.5/XGR/inst/xGraphML2AA.html |only XGR-1.1.5/XGR/inst/xHeatmap.html | 18 XGR-1.1.5/XGR/inst/xHeatmapAdv.html | 28 - XGR-1.1.5/XGR/inst/xLayout.html |only XGR-1.1.5/XGR/inst/xLiftOver.html | 7 XGR-1.1.5/XGR/inst/xMEabf.html |only XGR-1.1.5/XGR/inst/xOBOcode.html | 11 XGR-1.1.5/XGR/inst/xObjSize.html |only XGR-1.1.5/XGR/inst/xPieplot.html |only XGR-1.1.5/XGR/inst/xRDataLoader.html | 18 XGR-1.1.5/XGR/inst/xReport.html |only XGR-1.1.5/XGR/inst/xSM2DF.html | 4 XGR-1.1.5/XGR/inst/xSNP2GeneScores.html | 16 XGR-1.1.5/XGR/inst/xSNP2cGenes.html |only XGR-1.1.5/XGR/inst/xSNP2eGenes.html |only XGR-1.1.5/XGR/inst/xSNP2nGenes.html | 14 XGR-1.1.5/XGR/inst/xSNPlocations.html | 4 XGR-1.1.5/XGR/inst/xSocialiser.html | 5 XGR-1.1.5/XGR/inst/xSocialiserDAGplot.html | 13 XGR-1.1.5/XGR/inst/xSocialiserDAGplotAdv.html | 5 XGR-1.1.5/XGR/inst/xSocialiserGenes.html | 5 XGR-1.1.5/XGR/inst/xSocialiserNetplot.html | 14 XGR-1.1.5/XGR/inst/xSocialiserSNPs.html | 10 XGR-1.1.5/XGR/inst/xSubneterGR.html | 50 ++ XGR-1.1.5/XGR/inst/xSubneterGenes.html | 17 XGR-1.1.5/XGR/inst/xSubneterSNPs.html | 62 ++- XGR-1.1.5/XGR/inst/xSymbol2GeneID.html | 13 XGR-1.1.5/XGR/inst/xVisNet.html | 12 XGR-1.1.5/XGR/man/eTerm.Rd | 3 XGR-1.1.5/XGR/man/xAddCoords.Rd | 30 + XGR-1.1.5/XGR/man/xAuxEmbed.Rd |only XGR-1.1.5/XGR/man/xAuxFunArgs.Rd |only XGR-1.1.5/XGR/man/xAuxRd2HTML.Rd |only XGR-1.1.5/XGR/man/xAuxRdWrap.Rd |only XGR-1.1.5/XGR/man/xCheckParallel.Rd | 4 XGR-1.1.5/XGR/man/xCircos.Rd | 4 XGR-1.1.5/XGR/man/xColormap.Rd | 40 +- XGR-1.1.5/XGR/man/xConverter.Rd | 44 +- XGR-1.1.5/XGR/man/xCtree.Rd |only XGR-1.1.5/XGR/man/xDAGsim.Rd | 5 XGR-1.1.5/XGR/man/xDefineEQTL.Rd | 94 ++++ XGR-1.1.5/XGR/man/xDefineGenomicAnno.Rd | 27 - XGR-1.1.5/XGR/man/xDefineHIC.Rd | 22 - XGR-1.1.5/XGR/man/xDefineOntology.Rd | 63 ++- XGR-1.1.5/XGR/man/xEnrichBarplot.Rd | 7 XGR-1.1.5/XGR/man/xEnrichChord.Rd |only XGR-1.1.5/XGR/man/xEnrichCompare.Rd | 6 XGR-1.1.5/XGR/man/xEnrichCtree.Rd |only XGR-1.1.5/XGR/man/xEnrichD3.Rd |only XGR-1.1.5/XGR/man/xEnrichDAGplot.Rd | 12 XGR-1.1.5/XGR/man/xEnrichDAGplotAdv.Rd | 9 XGR-1.1.5/XGR/man/xEnrichDotplot.Rd |only XGR-1.1.5/XGR/man/xEnrichForest.Rd | 22 - XGR-1.1.5/XGR/man/xEnrichGGraph.Rd |only XGR-1.1.5/XGR/man/xEnrichHeatmap.Rd | 6 XGR-1.1.5/XGR/man/xEnrichLadder.Rd | 14 XGR-1.1.5/XGR/man/xEnrichMatrix.Rd | 13 XGR-1.1.5/XGR/man/xEnrichNetplot.Rd | 7 XGR-1.1.5/XGR/man/xEnrichRadial.Rd |only XGR-1.1.5/XGR/man/xEnrichTreemap.Rd | 21 - XGR-1.1.5/XGR/man/xEnrichViewer.Rd | 4 XGR-1.1.5/XGR/man/xEnricher.Rd | 11 XGR-1.1.5/XGR/man/xEnricherGenes.Rd | 32 - XGR-1.1.5/XGR/man/xEnricherGenesAdv.Rd | 27 - XGR-1.1.5/XGR/man/xEnricherSNPs.Rd | 16 XGR-1.1.5/XGR/man/xEnricherYours.Rd | 8 XGR-1.1.5/XGR/man/xGGnetwork.Rd | 36 + XGR-1.1.5/XGR/man/xGGraph.Rd |only XGR-1.1.5/XGR/man/xGR.Rd | 4 XGR-1.1.5/XGR/man/xGR2nGenes.Rd | 3 XGR-1.1.5/XGR/man/xGR2xGeneAnno.Rd | 46 +- XGR-1.1.5/XGR/man/xGR2xGeneAnnoAdv.Rd | 28 - XGR-1.1.5/XGR/man/xGR2xGeneScores.Rd | 2 XGR-1.1.5/XGR/man/xGR2xGenes.Rd | 18 XGR-1.1.5/XGR/man/xGRcse.Rd | 2 XGR-1.1.5/XGR/man/xGRviaGeneAnno.Rd | 20 - XGR-1.1.5/XGR/man/xGRviaGeneAnnoAdv.Rd | 23 - XGR-1.1.5/XGR/man/xGRviaGenomicAnno.Rd | 12 XGR-1.1.5/XGR/man/xGRviaGenomicAnnoAdv.Rd | 9 XGR-1.1.5/XGR/man/xGeneID2Symbol.Rd |only XGR-1.1.5/XGR/man/xGraphML.Rd | 31 - XGR-1.1.5/XGR/man/xGraphML2AA.Rd |only XGR-1.1.5/XGR/man/xHeatmap.Rd | 16 XGR-1.1.5/XGR/man/xHeatmapAdv.Rd | 26 - XGR-1.1.5/XGR/man/xLayout.Rd |only XGR-1.1.5/XGR/man/xLiftOver.Rd | 7 XGR-1.1.5/XGR/man/xMEabf.Rd |only XGR-1.1.5/XGR/man/xOBOcode.Rd | 11 XGR-1.1.5/XGR/man/xObjSize.Rd |only XGR-1.1.5/XGR/man/xPieplot.Rd |only XGR-1.1.5/XGR/man/xRDataLoader.Rd | 18 XGR-1.1.5/XGR/man/xReport.Rd |only XGR-1.1.5/XGR/man/xSM2DF.Rd | 4 XGR-1.1.5/XGR/man/xSNP2GeneScores.Rd | 16 XGR-1.1.5/XGR/man/xSNP2cGenes.Rd |only XGR-1.1.5/XGR/man/xSNP2eGenes.Rd |only XGR-1.1.5/XGR/man/xSNP2nGenes.Rd | 14 XGR-1.1.5/XGR/man/xSNPlocations.Rd | 4 XGR-1.1.5/XGR/man/xSocialiser.Rd | 5 XGR-1.1.5/XGR/man/xSocialiserDAGplot.Rd | 13 XGR-1.1.5/XGR/man/xSocialiserDAGplotAdv.Rd | 5 XGR-1.1.5/XGR/man/xSocialiserGenes.Rd | 5 XGR-1.1.5/XGR/man/xSocialiserNetplot.Rd | 14 XGR-1.1.5/XGR/man/xSocialiserSNPs.Rd | 10 XGR-1.1.5/XGR/man/xSubneterGR.Rd | 40 +- XGR-1.1.5/XGR/man/xSubneterGenes.Rd | 15 XGR-1.1.5/XGR/man/xSubneterSNPs.Rd | 52 ++ XGR-1.1.5/XGR/man/xSymbol2GeneID.Rd | 11 XGR-1.1.5/XGR/man/xVisNet.Rd | 12 338 files changed, 2905 insertions(+), 1752 deletions(-)
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are
a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
This package is based on 'XenaR' package.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Martin Morgan [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaTools versions 1.0.1 dated 2019-03-07 and 1.1.0 dated 2019-03-29
DESCRIPTION | 6 MD5 | 105 +++- NAMESPACE | 1 NEWS.md | 10 R/XenaHub-class.R | 115 ++--- R/api.R |only R/data.R | 4 R/download.R | 57 +- R/query.R | 14 R/simplify.R | 18 R/zzz.R | 2 README.md | 56 +- build/vignette.rds |binary data/XenaData.rda |binary inst/doc/USCSXenaTools.R | 13 inst/doc/USCSXenaTools.Rmd | 36 - inst/doc/USCSXenaTools.html | 787 +++++++++++++++++------------------ inst/doc/xena-apis.R |only inst/doc/xena-apis.Rmd |only inst/doc/xena-apis.html |only inst/queries |only inst/test_api.R |only man/XenaBrowse.Rd | 4 man/XenaData.Rd | 4 man/XenaDownload.Rd | 10 man/XenaFilter.Rd | 2 man/XenaGenerate.Rd | 4 man/XenaHub.Rd | 15 man/XenaPrepare.Rd | 6 man/XenaQuery.Rd | 6 man/cohorts.Rd | 2 man/datasets.Rd | 2 man/hosts.Rd | 2 man/samples.Rd | 2 man/to_snake.Rd |only man/xena_default_hosts.Rd | 2 tests/testthat/test-basic-workflow.R | 2 vignettes/USCSXenaTools.Rmd | 36 - vignettes/xena-apis.Rmd |only 39 files changed, 696 insertions(+), 627 deletions(-)
Title: High-Dimensional Inference
Description: Implementation of multiple approaches to perform inference in high-dimensional models.
Author: Lukas Meier [aut, cre], Ruben Dezeure [aut], Nicolai Meinshausen [aut], Martin Maechler [aut], Peter Buehlmann [aut]
Maintainer: Lukas Meier <meier@stat.math.ethz.ch>
Diff between hdi versions 0.1-6 dated 2016-03-21 and 0.1-7 dated 2019-03-29
DESCRIPTION | 13 +-- MD5 | 34 ++++---- NAMESPACE | 1 R/boot.lasso-proj.R |only R/helpers.R | 166 ++++++++++++++++++++++++++++++++++++++++- R/helpers.nodewise.R | 193 +++++++++++++++++++++++++++++++++++++++++++++--- R/lasso-proj.R | 104 +++++++++---------------- R/methods.R | 24 +++++ R/ridge-proj.R | 38 +++------ build/partial.rdb |binary data/riboflavin.RData |binary inst/NEWS.Rd | 13 +++ man/boot.lasso.proj.Rd |only man/groupBound.rd | 2 man/lasso.proj.Rd | 22 ++++- tests/ex-lasso.proj.R | 5 + tests/groupTsts.R | 6 + tests/test-lasso.R | 5 - tests/test-multisplit.R | 5 - 19 files changed, 497 insertions(+), 134 deletions(-)
Title: Imputation of Count Data using Side Information
Description: Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear model where main row and column effects are decomposed as regression terms on known covariates. A residual low-rank interaction term is also fitted. LORI returns estimates of covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure.
Author: Genevieve Robin [aut, cre]
Maintainer: Genevieve Robin <genevieve.robin@polytechnique.edu>
Diff between lori versions 2.1.2 dated 2019-03-07 and 2.1.3 dated 2019-03-29
lori-2.1.2/lori/inst |only lori-2.1.3/lori/DESCRIPTION | 13 +- lori-2.1.3/lori/MD5 | 25 ++--- lori-2.1.3/lori/NAMESPACE | 8 - lori-2.1.3/lori/R/altmin.R | 30 +++--- lori-2.1.3/lori/R/covmat.R | 2 lori-2.1.3/lori/R/cv.lori.R | 129 ++++++++++----------------- lori-2.1.3/lori/R/lori.R | 165 ++++++++++++++++++++++++++++++++--- lori-2.1.3/lori/R/mi.lori.R | 47 ++++++++- lori-2.1.3/lori/R/plot.interaction.R | 1 lori-2.1.3/lori/man/covmat.Rd | 2 lori-2.1.3/lori/man/cv.lori.Rd | 8 - lori-2.1.3/lori/man/lori.Rd | 4 lori-2.1.3/lori/man/mi.lori.Rd | 7 - 14 files changed, 295 insertions(+), 146 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to
information contained in various R models, like model formulas, model terms,
information about random effects, data that was used to fit the model or
data from response variables. 'insight' mainly revolves around two types
of functions: Functions that find (the names of) information, starting with
'find_', and functions that get the underlying data, starting with 'get_'.
The package has a consistent syntax and works with many different model
objects, where otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.1.2 dated 2019-03-05 and 0.2.0 dated 2019-03-29
DESCRIPTION | 16 - MD5 | 139 +++++++++----- NAMESPACE | 123 ++++++++++++ NEWS.md | 36 +++ R/all_equal_models.R |only R/clean_names.R | 8 R/colour_tools.R |only R/compute_variances.R |only R/download_model.R |only R/find_algorithm.R |only R/find_formula.R | 156 +++++++++++++++- R/find_parameters.R | 178 +++++++++++++++--- R/find_predictors.R | 18 + R/find_random_slopes.R |only R/find_response.R | 34 ++- R/find_terms.R | 4 R/find_variables.R | 5 R/get_data.R | 184 ++++++++++++++---- R/get_nested_lme_varcorr.R |only R/get_parameters.R | 302 +++++++++++++++++++++++++++---- R/get_priors.R |only R/get_variances.R |only R/helper_functions.R | 110 ++++++++++- R/is_model.R |only R/is_multivariate.R | 3 R/link_function.R | 79 ++++++++ R/link_inverse.R | 55 +++++ R/model_info.R | 152 +++++++++++++-- R/n_obs.R | 26 ++ build |only man/all_models_equal.Rd |only man/dot-badlink.Rd |only man/dot-collapse_cond.Rd |only man/dot-compute_variance_dispersion.Rd |only man/dot-compute_variance_distribution.Rd |only man/dot-compute_variance_fixed.Rd |only man/dot-compute_variance_random.Rd |only man/dot-download_data_github.Rd |only man/dot-get_variance_beta_family.Rd |only man/dot-get_variance_default.Rd |only man/dot-get_variance_dist.Rd |only man/dot-get_variance_information.Rd |only man/dot-get_variance_nbinom_family.Rd |only man/dot-get_variance_tweedie_family.Rd |only man/dot-null_model.Rd |only man/dot-random_slopes.Rd |only man/download_model.Rd |only man/find_algorithm.Rd |only man/find_formula.Rd | 7 man/find_parameters.Rd | 16 + man/find_predictors.Rd | 5 man/find_random_slopes.Rd |only man/find_terms.Rd | 7 man/find_variables.Rd | 6 man/get_data.Rd | 12 + man/get_parameters.Rd | 47 +++- man/get_priors.Rd |only man/get_variance.Rd |only man/is_model.Rd |only man/is_multivariate.Rd | 3 man/model_info.Rd | 5 man/print_color.Rd |only tests/testthat/test-GLMMadaptive.R | 18 + tests/testthat/test-Gam2.R | 10 - tests/testthat/test-betareg.R | 23 ++ tests/testthat/test-blmer.R |only tests/testthat/test-brms.R | 52 +++-- tests/testthat/test-crch.R |only tests/testthat/test-felm.R | 46 +++- tests/testthat/test-gam.R | 23 +- tests/testthat/test-gamlss.R |only tests/testthat/test-gamm.R | 18 - tests/testthat/test-gamm4.R | 13 - tests/testthat/test-gee.R | 6 tests/testthat/test-geeglm.R |only tests/testthat/test-glm.R | 4 tests/testthat/test-glmRob.R |only tests/testthat/test-glmmTMB.R | 56 +++++ tests/testthat/test-glmrob_base.R |only tests/testthat/test-gls.R | 21 +- tests/testthat/test-iv_robust.R |only tests/testthat/test-lm.R | 4 tests/testthat/test-lmRob.R |only tests/testthat/test-lm_robust.R |only tests/testthat/test-lme.R | 26 ++ tests/testthat/test-lmer.R | 53 +++++ tests/testthat/test-lmrob_base.R |only tests/testthat/test-logistf.R |only tests/testthat/test-mixed.R |only tests/testthat/test-rlmer.R |only tests/testthat/test-rms.R |only tests/testthat/test-rq.R |only tests/testthat/test-rstanarm.R | 30 ++- tests/testthat/test-survreg.R |only tests/testthat/test-tobit.R |only tests/testthat/test-vgam.R | 6 96 files changed, 1835 insertions(+), 310 deletions(-)
Title: Search and Retrieve Scientific Publication Records from PubMed
Description: Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.
Author: Damiano Fantini
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>
Diff between easyPubMed versions 2.12 dated 2019-03-06 and 2.13 dated 2019-03-29
easyPubMed-2.12/easyPubMed/R/article_to_df.R |only easyPubMed-2.12/easyPubMed/R/articles_to_list.R |only easyPubMed-2.12/easyPubMed/R/batch_pubmed_download.R |only easyPubMed-2.12/easyPubMed/R/custom_grep.R |only easyPubMed-2.12/easyPubMed/R/easyPubMed-internal.R |only easyPubMed-2.12/easyPubMed/R/fetch_all_pubmed_ids.R |only easyPubMed-2.12/easyPubMed/R/fetch_pubmed_data.R |only easyPubMed-2.12/easyPubMed/R/get_pubmed_ids.R |only easyPubMed-2.12/easyPubMed/R/get_pubmed_ids_by_fulltitle.R |only easyPubMed-2.12/easyPubMed/R/table_articles_byAuth.R |only easyPubMed-2.12/easyPubMed/R/trim_address.R |only easyPubMed-2.12/easyPubMed/data/NUBL_1618.rda |only easyPubMed-2.12/easyPubMed/man/NUBL_1618.Rd |only easyPubMed-2.13/easyPubMed/DESCRIPTION | 10 easyPubMed-2.13/easyPubMed/MD5 | 54 +-- easyPubMed-2.13/easyPubMed/NAMESPACE | 16 easyPubMed-2.13/easyPubMed/R/easyPubMed_scr.R |only easyPubMed-2.13/easyPubMed/build/vignette.rds |binary easyPubMed-2.13/easyPubMed/data/EPMsamples.rda |only easyPubMed-2.13/easyPubMed/inst/doc/getting_started_with_easyPubMed.R | 35 -- easyPubMed-2.13/easyPubMed/inst/doc/getting_started_with_easyPubMed.Rmd | 38 +- easyPubMed-2.13/easyPubMed/inst/doc/getting_started_with_easyPubMed.html | 167 +++++++--- easyPubMed-2.13/easyPubMed/man/EPMsamples.Rd |only easyPubMed-2.13/easyPubMed/man/PubMed_stopwords.Rd | 27 - easyPubMed-2.13/easyPubMed/man/article_to_df.Rd | 94 +++-- easyPubMed-2.13/easyPubMed/man/articles_to_list.Rd | 66 ++- easyPubMed-2.13/easyPubMed/man/batch_pubmed_download.Rd | 96 +++-- easyPubMed-2.13/easyPubMed/man/custom_grep.Rd | 53 +-- easyPubMed-2.13/easyPubMed/man/easyPubMed-package.Rd | 59 ++- easyPubMed-2.13/easyPubMed/man/fetch_all_pubmed_ids.Rd | 34 +- easyPubMed-2.13/easyPubMed/man/fetch_pubmed_data.Rd | 86 +++-- easyPubMed-2.13/easyPubMed/man/get_pubmed_ids.Rd | 57 ++- easyPubMed-2.13/easyPubMed/man/get_pubmed_ids_by_fulltitle.Rd | 64 ++- easyPubMed-2.13/easyPubMed/man/table_articles_byAuth.Rd | 95 +++-- easyPubMed-2.13/easyPubMed/man/trim_address.Rd | 29 - easyPubMed-2.13/easyPubMed/vignettes/getting_started_with_easyPubMed.Rmd | 38 +- 36 files changed, 659 insertions(+), 459 deletions(-)
Title: Export 'grid' Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG
format. Additional functions provide access to SVG features that
are not available in standard R graphics, such as hyperlinks,
animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut],
Simon Potter [aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridSVG versions 1.7-0 dated 2019-02-12 and 1.7-1 dated 2019-03-29
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/animate.R | 23 +++++++++++++++++++---- inst/NEWS.Rd | 5 +++++ inst/doc/animation.pdf |binary inst/doc/extensibility.pdf |binary inst/doc/gridSVG.pdf |binary 7 files changed, 33 insertions(+), 13 deletions(-)
Title: Combine and Export Data Frames
Description: Functions to combine data.frames in ways that require additional effort in
base R, and to add metadata (id, title, ...) that can be used for printing and
xlsx export. The 'Tatoo_report' class is provided as a
convenient helper to write several such tables to a workbook, one table per
worksheet. Tatoo is built on top of 'openxlsx', but intimate knowledge of
that package is not required to use tatoo.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between tatoo versions 1.1.0 dated 2018-02-12 and 1.1.1 dated 2019-03-29
tatoo-1.1.0/tatoo/tests/testthat/manual_tests/test_as_lines.R |only tatoo-1.1.1/tatoo/DESCRIPTION | 12 tatoo-1.1.1/tatoo/MD5 | 90 - tatoo-1.1.1/tatoo/NAMESPACE | 1 tatoo-1.1.1/tatoo/NEWS.md | 121 - tatoo-1.1.1/tatoo/R/Composite_table.R | 15 tatoo-1.1.1/tatoo/R/Mashed_table.R | 37 tatoo-1.1.1/tatoo/R/Stacked_table.R | 10 tatoo-1.1.1/tatoo/R/Tagged_table.R | 899 +++++----- tatoo-1.1.1/tatoo/R/Tatoo_report.R | 9 tatoo-1.1.1/tatoo/R/as_latex.R | 2 tatoo-1.1.1/tatoo/R/as_lines.R | 39 tatoo-1.1.1/tatoo/R/as_workbook.R | 101 - tatoo-1.1.1/tatoo/R/regions.R | 138 - tatoo-1.1.1/tatoo/R/tatoo-package.R | 1 tatoo-1.1.1/tatoo/R/utils-hammr.R | 804 ++++---- tatoo-1.1.1/tatoo/R/utils-sfmisc.R |only tatoo-1.1.1/tatoo/R/utils.R | 26 tatoo-1.1.1/tatoo/R/walk_regions.R | 5 tatoo-1.1.1/tatoo/README.md | 16 tatoo-1.1.1/tatoo/build/vignette.rds |binary tatoo-1.1.1/tatoo/inst/doc/named_regions.R | 4 tatoo-1.1.1/tatoo/inst/doc/named_regions.Rmd | 6 tatoo-1.1.1/tatoo/inst/doc/named_regions.html | 64 tatoo-1.1.1/tatoo/inst/doc/tatoo.html | 340 ++- tatoo-1.1.1/tatoo/man/Composite_table.Rd | 1 tatoo-1.1.1/tatoo/man/Mashed_table.Rd | 1 tatoo-1.1.1/tatoo/man/Stacked_table.Rd | 1 tatoo-1.1.1/tatoo/man/Tagged_table.Rd | 1 tatoo-1.1.1/tatoo/man/as.data.table.Composite_table.Rd | 7 tatoo-1.1.1/tatoo/man/as.data.table.Mashed_table.Rd | 17 tatoo-1.1.1/tatoo/man/as_Composite_table.Rd | 14 tatoo-1.1.1/tatoo/man/as_latex.Composite_table.Rd | 1 tatoo-1.1.1/tatoo/man/as_latex.Mashed_table.Rd | 1 tatoo-1.1.1/tatoo/man/as_latex.Rd | 1 tatoo-1.1.1/tatoo/man/as_latex.Tagged_table.Rd | 1 tatoo-1.1.1/tatoo/man/as_latex.Tatoo_report.Rd | 1 tatoo-1.1.1/tatoo/man/as_latex.data.frame.Rd | 4 tatoo-1.1.1/tatoo/man/as_workbook.Rd | 11 tatoo-1.1.1/tatoo/man/cmash.Rd | 4 tatoo-1.1.1/tatoo/man/is_class.Rd | 8 tatoo-1.1.1/tatoo/man/tatoo.Rd | 8 tatoo-1.1.1/tatoo/man/tatoo_table.Rd | 1 tatoo-1.1.1/tatoo/man/tt_meta.Rd | 18 tatoo-1.1.1/tatoo/man/walk_regions.Rd | 3 tatoo-1.1.1/tatoo/man/write_worksheet.Rd | 20 tatoo-1.1.1/tatoo/vignettes/named_regions.Rmd | 6 47 files changed, 1483 insertions(+), 1387 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 0.3.2 dated 2019-03-21 and 0.3.3 dated 2019-03-29
DESCRIPTION | 9 +++++---- MD5 | 23 ++++++++++++----------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/arg.R | 10 ++++++---- R/cnd.R | 8 ++++++++ build/rlang.pdf |binary man/missing_arg.Rd | 9 ++++++--- src/lib/vec-lgl.c | 7 ++++++- tests/testthat/helper-trace.R | 17 +++++++++++++++++ tests/testthat/test-c-api.R | 10 +++++++++- tests/testthat/test-trace.R | 10 ++++++++++ tests/testthat/test-trace.Rmd |only 13 files changed, 87 insertions(+), 24 deletions(-)
Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between rJava versions 0.9-10 dated 2018-05-29 and 0.9-11 dated 2019-03-29
DESCRIPTION | 6 MD5 | 118 +++++----- NEWS | 51 ++++ R/windows/FirstLib.R | 2 R/zzz.R.in | 1 configure | 58 ++++ configure.ac | 34 +- inst/javadoc/ArrayDimensionException.html | 4 inst/javadoc/ArrayWrapper.html | 4 inst/javadoc/ArrayWrapper_Test.html | 4 inst/javadoc/DummyPoint.html | 4 inst/javadoc/FlatException.html | 4 inst/javadoc/NotAnArrayException.html | 4 inst/javadoc/NotComparableException.html | 4 inst/javadoc/ObjectArrayException.html | 4 inst/javadoc/PrimitiveArrayException.html | 4 inst/javadoc/RJavaArrayIterator.html | 4 inst/javadoc/RJavaArrayTools.ArrayDimensionMismatchException.html | 4 inst/javadoc/RJavaArrayTools.html | 4 inst/javadoc/RJavaArrayTools_Test.html | 4 inst/javadoc/RJavaClassLoader.html | 4 inst/javadoc/RJavaComparator.html | 4 inst/javadoc/RJavaImport.html | 4 inst/javadoc/RJavaTools.html | 4 inst/javadoc/RJavaTools_Test.DummyNonStaticClass.html | 4 inst/javadoc/RJavaTools_Test.TestException.html | 4 inst/javadoc/RJavaTools_Test.html | 4 inst/javadoc/RectangularArrayBuilder.html | 4 inst/javadoc/RectangularArrayBuilder_Test.html | 4 inst/javadoc/RectangularArrayExamples.html | 4 inst/javadoc/RectangularArraySummary.html | 4 inst/javadoc/TestException.html | 4 inst/javadoc/allclasses-frame.html | 4 inst/javadoc/allclasses-noframe.html | 4 inst/javadoc/constant-values.html | 4 inst/javadoc/deprecated-list.html | 4 inst/javadoc/help-doc.html | 4 inst/javadoc/index-all.html | 4 inst/javadoc/index.html | 2 inst/javadoc/overview-tree.html | 4 inst/javadoc/package-frame.html | 4 inst/javadoc/package-summary.html | 4 inst/javadoc/package-tree.html | 4 inst/javadoc/serialized-form.html | 4 inst/jri/JRIEngine.jar |binary inst/jri/REngine.jar |binary jri/Makevars.win | 1 jri/configure | 31 ++ jri/configure.ac | 39 ++- jri/configure.win | 8 jri/src/Rinit.c | 1 jri/src/jri.c | 4 jri/src/jri.h | 14 - jri/src/win32/findjava.c | 24 +- man/javaImport.Rd | 2 src/init.c | 96 ++++++-- src/jri_glue.c | 2 src/jvm-w32/findjava.c | 37 ++- src/rJava.c | 7 src/rJava.h | 2 60 files changed, 468 insertions(+), 216 deletions(-)