Title: SNPs Enrichment Analysis
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal).
Author: Mickael Canouil [aut, cre],
Loic Yengo [ctb]
Maintainer: Mickael Canouil <mickael.canouil@cnrs.fr>
Diff between snpEnrichment versions 1.6.3 dated 2015-02-09 and 1.7.0 dated 2015-10-01
snpEnrichment-1.6.3/snpEnrichment/README.md |only snpEnrichment-1.7.0/snpEnrichment/ChangeLog | 18 ++++++++++ snpEnrichment-1.7.0/snpEnrichment/DESCRIPTION | 14 +++---- snpEnrichment-1.7.0/snpEnrichment/MD5 | 16 ++++---- snpEnrichment-1.7.0/snpEnrichment/NAMESPACE | 10 ++++- snpEnrichment-1.7.0/snpEnrichment/R/Global.R | 2 - snpEnrichment-1.7.0/snpEnrichment/R/enrichment.R | 15 +++++++- snpEnrichment-1.7.0/snpEnrichment/data/toyEnrichment.RData |binary snpEnrichment-1.7.0/snpEnrichment/man/snpEnrichment-package.Rd | 4 +- snpEnrichment-1.7.0/snpEnrichment/tests |only 10 files changed, 56 insertions(+), 23 deletions(-)
Title: Statistical Comparison of Multiple Algorithms in Multiple
Problems
Description: Given a matrix with results of different algorithms for different problems, the package uses statistical tests and corrections to assess the differences between algorithms.
Author: Borja Calvo [aut, cre],
Guzman Santafe [aut]
Maintainer: Borja Calvo <borja.calvo@ehu.eus>
Diff between scmamp versions 0.2.1 dated 2015-09-23 and 0.2.3 dated 2015-10-01
DESCRIPTION | 10 +- MD5 | 33 ++++----- NAMESPACE | 1 R/plotting.R | 159 ++++++++++++++++++++++++++++++++++++++++++++-- R/post_hoc.R | 16 ++-- R/scmamp.R | 106 ++++++++++++++++++++++++++---- R/sysdata.rda |binary build/vignette.rds |binary data/data_blum_2015.RData |binary data/data_gh_2008.RData |binary data/data_gh_2010.RData |binary man/adjustFinner.Rd | 4 - man/adjustHolland.Rd | 4 - man/adjustLi.Rd | 4 - man/adjustRom.Rd | 4 - man/drawAlgorithmGraph.Rd | 2 man/plotCD.Rd | 2 man/plotRanking.Rd |only 18 files changed, 289 insertions(+), 56 deletions(-)
Title: Distance Weighted Discrimination (DWD) and Kernel Methods
Description: A novel implementation that solves the DWD and the kernel DWD which can be hundred times faster than the existing implementation of DWD based on the second-order-cone programming (SOCP). The package also handles some other general loss functions including large-margin unified machines (LUM).
Author: Boxiang Wang <boxiang@umn.edu>, Hui Zou <hzou@stat.umn.edu>
Maintainer: Boxiang Wang <boxiang@umn.edu>
Diff between kerndwd versions 1.1.1 dated 2015-09-06 and 1.1.2 dated 2015-10-01
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/cv.kerndwd.R | 10 +++++++--- R/kerndwd.R | 3 ++- R/predict.kerndwd.R | 8 ++++++-- R/utilities.R | 4 ++-- man/cv.kerndwd.Rd | 2 +- man/dots.Rd | 8 ++++---- man/kerndwd.Rd | 4 ++-- 9 files changed, 37 insertions(+), 28 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Testing
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace and GraceR tests to perform graph-guided hypothesis test on the association between the response and the predictor.
Author: Sen Zhao
Maintainer: Sen Zhao <senz@uw.edu>
Diff between Grace versions 0.1 dated 2015-08-18 and 0.1.1 dated 2015-10-01
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/grace.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Cleaning Geometries from Spatial Objects
Description:
Provides a set of utility tools to inspect spatial objects, facilitate
handling and reporting of topology errors and geometry validity issues.
Finally, it provides a geometry cleaner that will fix all geometry problems,
and eliminate (at least reduce) the likelihood of having issues when doing
spatial data processing.
Author: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between cleangeo versions 0.1-0 dated 2015-09-27 and 0.1-1 dated 2015-10-01
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++++------- R/cleangeo.R | 4 ++-- R/clgeo_Clean.R | 39 ++++++++++++++++++++------------------- README.md | 5 +++-- build |only inst/doc |only man/cleangeo.Rd | 4 ++-- tests/testthat/test_Clean.R | 9 ++++++++- vignettes/quickstart.Rmd | 12 +++++------- 10 files changed, 57 insertions(+), 45 deletions(-)
Title: Species Richness Estimation and Modeling
Description: Species richness estimation is an important problem in biodiversity analysis. This package provides methods for total species richness estimation (observed plus unobserved) and a method for modelling total diversity with covariates. breakaway() estimates total (observed plus unobserved) species richness. Microbial diversity datasets are characterized by a large number of rare species and a small number of highly abundant species. The class of models implemented by breakaway() is flexible enough to model both these features. breakaway_nof1() implements a similar procedure however does not require a singleton count. betta() provides a method for modelling total diversity with covariates in a way that accounts for its estimated nature and thus accounts for unobserved taxa.
Author: Amy Willis and John Bunge
Maintainer: Amy Willis <adw96@cornell.edu>
Diff between breakaway versions 1.0 dated 2014-08-04 and 2.0 dated 2015-10-01
breakaway-1.0/breakaway/R/betta_basic.R |only breakaway-1.0/breakaway/man/betta_basic.Rd |only breakaway-2.0/breakaway/DESCRIPTION | 12 +-- breakaway-2.0/breakaway/MD5 | 19 +++-- breakaway-2.0/breakaway/NAMESPACE | 9 ++ breakaway-2.0/breakaway/R/betta.R |only breakaway-2.0/breakaway/R/breakaway_nof1.R | 78 ++++++++++++++--------- breakaway-2.0/breakaway/R/hawaii.R |only breakaway-2.0/breakaway/man/betta.Rd |only breakaway-2.0/breakaway/man/betta_pic.Rd |only breakaway-2.0/breakaway/man/breakaway-package.Rd | 17 ++--- breakaway-2.0/breakaway/man/breakaway.Rd | 11 +-- breakaway-2.0/breakaway/man/breakaway_nof1.Rd | 11 +-- breakaway-2.0/breakaway/man/hawaii.Rd |only 14 files changed, 94 insertions(+), 63 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Taxonomic information from around the web. This package
interacts with a suite of web 'APIs' for taxonomic tasks, such
as verifying species names, getting taxonomic hierarchies,
and verifying name spelling.
Author: Scott Chamberlain [aut, cre],
Eduard Szoecs [aut],
Zachary Foster [aut],
Carl Boettiger [aut],
Karthik Ram [aut],
Ignasi Bartomeus [aut],
John Baumgartner [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.6.2 dated 2015-08-07 and 0.6.6 dated 2015-10-01
taxize-0.6.2/taxize/man/get_ubioid.Rd |only taxize-0.6.2/taxize/man/ubio_classification.Rd |only taxize-0.6.2/taxize/man/ubio_classification_search.Rd |only taxize-0.6.2/taxize/man/ubio_id.Rd |only taxize-0.6.2/taxize/man/ubio_search.Rd |only taxize-0.6.2/taxize/man/ubio_synonyms.Rd |only taxize-0.6.2/taxize/tests/testthat/test-ubio_classification.R |only taxize-0.6.6/taxize/DESCRIPTION | 10 taxize-0.6.6/taxize/MD5 | 225 +++++----- taxize-0.6.6/taxize/NAMESPACE | 4 taxize-0.6.6/taxize/R/children.R | 23 - taxize-0.6.6/taxize/R/classification.R | 4 taxize-0.6.6/taxize/R/comm2sci.R | 7 taxize-0.6.6/taxize/R/eol_dataobjects.R | 22 taxize-0.6.6/taxize/R/gbif_parse.R | 2 taxize-0.6.6/taxize/R/get_eolid.R | 16 taxize-0.6.6/taxize/R/get_gbifid.R | 24 - taxize-0.6.6/taxize/R/get_ids.R | 18 taxize-0.6.6/taxize/R/get_nbnid.R | 51 -- taxize-0.6.6/taxize/R/get_tsn.R | 2 taxize-0.6.6/taxize/R/get_ubioid.R | 125 +---- taxize-0.6.6/taxize/R/get_uid.R | 20 taxize-0.6.6/taxize/R/gni_parse.R | 30 - taxize-0.6.6/taxize/R/gnr_resolve.R | 157 +++--- taxize-0.6.6/taxize/R/iplant_resolve.R | 3 taxize-0.6.6/taxize/R/ipni_search.R | 34 - taxize-0.6.6/taxize/R/itis.R | 89 ++- taxize-0.6.6/taxize/R/itis_downstream.R | 62 +- taxize-0.6.6/taxize/R/itis_getrecord.R | 26 - taxize-0.6.6/taxize/R/itis_hierarchy.R | 19 taxize-0.6.6/taxize/R/itis_kingdomnames.R | 18 taxize-0.6.6/taxize/R/itis_lsid.R | 16 taxize-0.6.6/taxize/R/itis_native.R | 22 taxize-0.6.6/taxize/R/itis_refs.R | 7 taxize-0.6.6/taxize/R/itis_taxrank.R | 12 taxize-0.6.6/taxize/R/iucn_getname.R | 3 taxize-0.6.6/taxize/R/iucn_id.R |only taxize-0.6.6/taxize/R/iucn_summary.R | 3 taxize-0.6.6/taxize/R/names_list.r | 3 taxize-0.6.6/taxize/R/nbn_classification.R | 7 taxize-0.6.6/taxize/R/nbn_search.R | 13 taxize-0.6.6/taxize/R/nbn_synonyms.R | 3 taxize-0.6.6/taxize/R/ncbi_children.R | 10 taxize-0.6.6/taxize/R/ncbi_get_taxon_summary.R | 13 taxize-0.6.6/taxize/R/phylomatic_format.R | 2 taxize-0.6.6/taxize/R/ping.R | 19 taxize-0.6.6/taxize/R/plantminer.R | 56 +- taxize-0.6.6/taxize/R/scrapenames.r | 2 taxize-0.6.6/taxize/R/synonyms.R | 31 - taxize-0.6.6/taxize/R/tax_name.R | 34 - taxize-0.6.6/taxize/R/tax_rank.R | 10 taxize-0.6.6/taxize/R/taxize-package.R | 16 taxize-0.6.6/taxize/R/taxize_cite.R | 17 taxize-0.6.6/taxize/R/tnrs.R | 8 taxize-0.6.6/taxize/R/tnrs_sources.r | 4 taxize-0.6.6/taxize/R/tp_refs.R | 3 taxize-0.6.6/taxize/R/ubio_classification.R | 75 --- taxize-0.6.6/taxize/R/ubio_classification_search.R | 35 - taxize-0.6.6/taxize/R/ubio_id.R | 91 ---- taxize-0.6.6/taxize/R/ubio_search.R | 67 -- taxize-0.6.6/taxize/R/ubio_synonyms.R | 59 -- taxize-0.6.6/taxize/R/upstream.R | 6 taxize-0.6.6/taxize/R/vascan_search.r | 49 +- taxize-0.6.6/taxize/R/zzz.R | 3 taxize-0.6.6/taxize/README.md | 63 -- taxize-0.6.6/taxize/build/vignette.rds |binary taxize-0.6.6/taxize/data/rank_ref.RData |binary taxize-0.6.6/taxize/inst/doc/taxize_infotable.Rmd | 40 - taxize-0.6.6/taxize/inst/doc/taxize_infotable.html | 126 +---- taxize-0.6.6/taxize/inst/doc/taxize_vignette.Rmd | 80 --- taxize-0.6.6/taxize/inst/doc/taxize_vignette.html | 79 --- taxize-0.6.6/taxize/inst/vign/taxize_infotable.Rmd | 40 - taxize-0.6.6/taxize/inst/vign/taxize_infotable.md | 40 - taxize-0.6.6/taxize/inst/vign/taxize_vignette.Rmd | 7 taxize-0.6.6/taxize/inst/vign/taxize_vignette.md | 80 --- taxize-0.6.6/taxize/man/eol_dataobjects.Rd | 10 taxize-0.6.6/taxize/man/get_eolid.Rd | 2 taxize-0.6.6/taxize/man/get_ids.Rd | 12 taxize-0.6.6/taxize/man/get_ubioid-defunct.Rd |only taxize-0.6.6/taxize/man/get_uid.Rd | 14 taxize-0.6.6/taxize/man/getitistermsfromcommonname.Rd | 4 taxize-0.6.6/taxize/man/getjurisdictionaloriginfromtsn.Rd | 2 taxize-0.6.6/taxize/man/gettsnbyvernacularlanguage.Rd | 2 taxize-0.6.6/taxize/man/gnr_resolve.Rd | 41 + taxize-0.6.6/taxize/man/ipni_search.Rd | 4 taxize-0.6.6/taxize/man/itis_getrecord.Rd | 7 taxize-0.6.6/taxize/man/itis_hierarchy.Rd | 7 taxize-0.6.6/taxize/man/itis_kingdomnames.Rd | 7 taxize-0.6.6/taxize/man/itis_lsid.Rd | 4 taxize-0.6.6/taxize/man/itis_native.Rd | 3 taxize-0.6.6/taxize/man/itis_refs.Rd | 5 taxize-0.6.6/taxize/man/itis_taxrank.Rd | 2 taxize-0.6.6/taxize/man/iucn_id.Rd |only taxize-0.6.6/taxize/man/ncbi_children.Rd | 7 taxize-0.6.6/taxize/man/ncbi_get_taxon_summary.Rd | 4 taxize-0.6.6/taxize/man/ping.Rd | 4 taxize-0.6.6/taxize/man/plantminer.Rd | 24 - taxize-0.6.6/taxize/man/searchforanymatchpaged.Rd | 4 taxize-0.6.6/taxize/man/synonyms.Rd | 16 taxize-0.6.6/taxize/man/tax_rank.Rd | 4 taxize-0.6.6/taxize/man/taxize-defunct.Rd | 7 taxize-0.6.6/taxize/man/taxize-package.Rd | 6 taxize-0.6.6/taxize/man/taxize_cite.Rd | 1 taxize-0.6.6/taxize/man/tnrs.Rd | 6 taxize-0.6.6/taxize/man/ubio_classification-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_classification_search-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_id-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_ping-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_search-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_synonyms-defunct.Rd |only taxize-0.6.6/taxize/man/vascan_search.Rd | 12 taxize-0.6.6/taxize/tests/testthat/Rplots.pdf |only taxize-0.6.6/taxize/tests/testthat/test-eol_dataobjects.R | 2 taxize-0.6.6/taxize/tests/testthat/test-gbif_parse.R | 11 taxize-0.6.6/taxize/tests/testthat/test-gnr_resolve.R | 36 - taxize-0.6.6/taxize/tests/testthat/test-ipni_search.R |only taxize-0.6.6/taxize/tests/testthat/test-itis_lsid.R | 2 taxize-0.6.6/taxize/tests/testthat/test-iucn_id.R |only taxize-0.6.6/taxize/tests/testthat/test-phylomatic_tree.R | 1 taxize-0.6.6/taxize/tests/testthat/test-ping.R | 6 taxize-0.6.6/taxize/tests/testthat/test-plantminer.R | 18 taxize-0.6.6/taxize/vignettes/taxize_infotable.Rmd | 40 - taxize-0.6.6/taxize/vignettes/taxize_vignette.Rmd | 80 --- 123 files changed, 1026 insertions(+), 1636 deletions(-)
Title: Spatial Analysis and Modelling
Description: Utilities to support spatial data manipulation, query, sampling and modelling.
Functions include models for species population density, download utilities for
climate and global deforestation spatial products, spatial smoothing,
multivariate separability, point process model for creating pseudo-absences
and sub-sampling, polygon and point-distance landscape metrics, auto-logistic
model, sampling models, cluster optimization and statistical exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 0.1-1 dated 2015-02-24 and 0.1-2 dated 2015-10-01
DESCRIPTION | 24 ++++--- MD5 | 146 +++++++++++++++++++++++++-------------------- NAMESPACE | 14 ++++ R/bearing.distance.R |only R/breeding.density.R | 35 +++++----- R/concordance.R |only R/conf.interval.R |only R/correlogram.R | 18 ++--- R/csi.R | 7 +- R/download.daymet.R | 5 - R/download.hansen.R | 5 - R/download.prism.R | 7 +- R/group.pdf.R | 10 +-- R/hexagons.R | 7 +- R/idw.smoothing.R | 4 - R/kl.divergence.R | 4 - R/land.metrics.R | 20 +++--- R/local.min.max.R | 25 +++---- R/loess.boot.R |only R/loess.ci.R |only R/logistic.regression.R | 20 +++--- R/moments.R | 52 ++++++++-------- R/nni.R | 2 R/o.ring.R | 27 ++++---- R/optimal.k.R | 9 +- R/outliers.R | 11 +-- R/parea.sample.R | 7 +- R/plot.loess.boot.R |only R/point.in.poly.R | 4 - R/pp.subsample.R | 13 ++-- R/print.loess.boot.R |only R/pseudo.absence.R | 27 ++++---- R/raster.entropy.R | 6 - R/raster.vol.R |only R/sample.line.R |only R/separability.R | 36 +++++------ R/sp.na.omit.R | 3 R/stratified.random.R | 3 R/summary.loess.boot.R |only R/tpi.R |only R/trend.line.R | 24 +++---- R/wt.centroids.R | 5 - R/zonal.stats.R | 12 +-- inst/CITATION | 4 - inst/NEWS | 10 +++ man/bearing.distance.Rd |only man/breeding.density.Rd | 2 man/concordance.Rd |only man/conf.interval.Rd |only man/correlogram.Rd | 2 man/csi.Rd | 2 man/download.daymet.Rd | 2 man/download.hansen.Rd | 2 man/download.prism.Rd | 2 man/group.pdf.Rd | 84 ++++++++++++------------- man/hexagons.Rd | 76 +++++++++++------------ man/idw.smoothing.Rd | 2 man/kl.divergence.Rd | 74 +++++++++++----------- man/land.metrics.Rd | 11 +-- man/local.min.max.Rd | 2 man/loess.boot.Rd |only man/loess.ci.Rd |only man/logistic.regression.Rd | 10 +-- man/moments.Rd | 2 man/nni.Rd | 2 man/o.ring.Rd | 14 ++-- man/optimal.k.Rd | 2 man/outliers.Rd | 2 man/parea.sample.Rd | 2 man/plot.loess.boot.Rd |only man/point.in.poly.Rd | 104 ++++++++++++++++---------------- man/pp.subsample.Rd | 2 man/print.loess.boot.Rd |only man/pseudo.absence.Rd | 2 man/raster.entropy.Rd | 102 +++++++++++++++---------------- man/raster.vol.Rd |only man/sample.line.Rd |only man/separability.Rd | 2 man/sp.na.omit.Rd | 90 +++++++++++++-------------- man/stratified.random.Rd | 2 man/summary.loess.boot.Rd |only man/tpi.Rd |only man/trend.line.Rd | 2 man/wt.centroid.Rd | 86 +++++++++++++------------- man/zonal.stats.Rd | 132 ++++++++++++++++++++-------------------- 85 files changed, 743 insertions(+), 682 deletions(-)
Title: Sparse Bayesian Models for Regression, Subgroup Analysis, and
Panel Data
Description: Sparse modeling provides a mean selecting a small number of non-zero effects from a large possible number of candidate effects. This package includes a suite of methods for sparse modeling: estimation via EM or MCMC, approximate confidence intervals with nominal coverage, and diagnostic and summary plots. Beyond regression analyses, applications include subgroup analysis, particularly for conjoint experiments, and panel data. Future versions will include extensions to limited dependent variables, models with truncated outcomes, and propensity score and instrumental variable analysis.
Author: Marc Ratkovic and Dustin Tingley
Maintainer: Marc Ratkovic <ratkovic@princeton.edu>
Diff between sparsereg versions 1.0 dated 2015-07-21 and 1.1 dated 2015-10-01
sparsereg-1.0/sparsereg/R/type2tobit.R |only sparsereg-1.0/sparsereg/man/type2tobit.Rd |only sparsereg-1.0/sparsereg/man/volcanoplot.Rd |only sparsereg-1.1/sparsereg/ChangeLog |only sparsereg-1.1/sparsereg/DESCRIPTION | 12 - sparsereg-1.1/sparsereg/MD5 | 29 +- sparsereg-1.1/sparsereg/NAMESPACE | 7 sparsereg-1.1/sparsereg/R/subgroup.R | 248 +++++++++++++++++++---- sparsereg-1.1/sparsereg/R/updateREs.R | 16 + sparsereg-1.1/sparsereg/R/utility.R | 2 sparsereg-1.1/sparsereg/man/difference.Rd | 2 sparsereg-1.1/sparsereg/man/plot.sparsereg.Rd | 6 sparsereg-1.1/sparsereg/man/print.sparsereg.Rd | 5 sparsereg-1.1/sparsereg/man/sparsereg-package.Rd | 2 sparsereg-1.1/sparsereg/man/sparsereg.Rd | 52 ++-- sparsereg-1.1/sparsereg/man/summary.sparsereg.Rd | 4 sparsereg-1.1/sparsereg/man/violinplot.Rd |only sparsereg-1.1/sparsereg/src/subgroup.cpp | 15 - 18 files changed, 288 insertions(+), 112 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of
Microdata and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
In addition, various risk estimation methods are included.
Note that the package 'sdcMicroGUI' includes a graphical user interface for various methods
in this package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 4.5.0 dated 2015-05-04 and 4.6.0 dated 2015-10-01
sdcMicro-4.5.0/sdcMicro/R/localSupp2.R |only sdcMicro-4.5.0/sdcMicro/R/localSupp2Wrapper.R |only sdcMicro-4.5.0/sdcMicro/R/plot.localSuppression.R |only sdcMicro-4.5.0/sdcMicro/R/print.freqCalc.R |only sdcMicro-4.5.0/sdcMicro/R/print.indivRisk.R |only sdcMicro-4.5.0/sdcMicro/R/print.localSuppression.R |only sdcMicro-4.5.0/sdcMicro/R/print.micro.R |only sdcMicro-4.5.0/sdcMicro/R/summary.freqCalc.R |only sdcMicro-4.5.0/sdcMicro/R/summary.micro.R |only sdcMicro-4.5.0/sdcMicro/R/summary.pram.r |only sdcMicro-4.5.0/sdcMicro/R/swappNum.R |only sdcMicro-4.5.0/sdcMicro/inst/templates/template-report-html.brew |only sdcMicro-4.5.0/sdcMicro/inst/templates/template-report-latex.brew |only sdcMicro-4.5.0/sdcMicro/inst/templates/template-report-text.brew |only sdcMicro-4.5.0/sdcMicro/man/extractManipData-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/groupVars-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/localSupp2.Rd |only sdcMicro-4.5.0/sdcMicro/man/localSupp2Wrapper.Rd |only sdcMicro-4.5.0/sdcMicro/man/removeDirectID-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/renameVars-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/sdcMicro-deprecated.Rd |only sdcMicro-4.5.0/sdcMicro/man/swappNum-deprecated.Rd |only sdcMicro-4.5.0/sdcMicro/man/swappNum.Rd |only sdcMicro-4.5.0/sdcMicro/man/varToFactor-methods.Rd |only sdcMicro-4.6.0/sdcMicro/DESCRIPTION | 47 sdcMicro-4.6.0/sdcMicro/MD5 | 238 - sdcMicro-4.6.0/sdcMicro/NAMESPACE | 236 - sdcMicro-4.6.0/sdcMicro/R/0classes.r | 304 + sdcMicro-4.6.0/sdcMicro/R/GUIfunctions.R | 319 + sdcMicro-4.6.0/sdcMicro/R/LLmodGlobalRisk.R | 371 - sdcMicro-4.6.0/sdcMicro/R/LocalRecProg.R | 261 - sdcMicro-4.6.0/sdcMicro/R/RcppExports.R |only sdcMicro-4.6.0/sdcMicro/R/addNoise.r | 245 - sdcMicro-4.6.0/sdcMicro/R/aux_functions.r | 523 +- sdcMicro-4.6.0/sdcMicro/R/dRisk.R | 114 sdcMicro-4.6.0/sdcMicro/R/dRiskRMD.R | 237 - sdcMicro-4.6.0/sdcMicro/R/dUtility.R | 161 sdcMicro-4.6.0/sdcMicro/R/dataGen.r | 125 sdcMicro-4.6.0/sdcMicro/R/dataSets.R |only sdcMicro-4.6.0/sdcMicro/R/freqCalc.r | 968 ++--- sdcMicro-4.6.0/sdcMicro/R/globalRecode.R | 120 sdcMicro-4.6.0/sdcMicro/R/indivRisk.R | 246 - sdcMicro-4.6.0/sdcMicro/R/localSupp.R | 144 sdcMicro-4.6.0/sdcMicro/R/localSuppression.R | 814 +++- sdcMicro-4.6.0/sdcMicro/R/maG.R | 478 +- sdcMicro-4.6.0/sdcMicro/R/mafast.R | 234 - sdcMicro-4.6.0/sdcMicro/R/mdav.R | 53 sdcMicro-4.6.0/sdcMicro/R/measure_risk.R | 723 ++- sdcMicro-4.6.0/sdcMicro/R/methods.r | 224 - sdcMicro-4.6.0/sdcMicro/R/microaggregation.R | 1883 +++++----- sdcMicro-4.6.0/sdcMicro/R/modRisk.R |only sdcMicro-4.6.0/sdcMicro/R/plotFunctions.R |only sdcMicro-4.6.0/sdcMicro/R/plotMicro.R | 271 - sdcMicro-4.6.0/sdcMicro/R/pram.R | 749 ++- sdcMicro-4.6.0/sdcMicro/R/printFunctions.R | 467 +- sdcMicro-4.6.0/sdcMicro/R/rankSwap.R | 194 - sdcMicro-4.6.0/sdcMicro/R/report.R | 811 +--- sdcMicro-4.6.0/sdcMicro/R/sdcMicro-package.R |only sdcMicro-4.6.0/sdcMicro/R/show_sdcMicroObj.R | 57 sdcMicro-4.6.0/sdcMicro/R/shuffle.R | 721 +-- sdcMicro-4.6.0/sdcMicro/R/suda2.R | 220 - sdcMicro-4.6.0/sdcMicro/R/timeEstimation.R | 82 sdcMicro-4.6.0/sdcMicro/R/topBotCoding.R | 171 sdcMicro-4.6.0/sdcMicro/R/valTable.R | 246 - sdcMicro-4.6.0/sdcMicro/R/zzz.R | 20 sdcMicro-4.6.0/sdcMicro/build/vignette.rds |binary sdcMicro-4.6.0/sdcMicro/data/CASCrefmicrodata.rda |binary sdcMicro-4.6.0/sdcMicro/data/EIA.rda |binary sdcMicro-4.6.0/sdcMicro/data/Tarragona.rda |binary sdcMicro-4.6.0/sdcMicro/data/casc1.rda |binary sdcMicro-4.6.0/sdcMicro/data/francdat.rda |binary sdcMicro-4.6.0/sdcMicro/data/free1.rda |binary sdcMicro-4.6.0/sdcMicro/data/microData.rda |binary sdcMicro-4.6.0/sdcMicro/data/testdata.RData |binary sdcMicro-4.6.0/sdcMicro/data/testdata2.RData |binary sdcMicro-4.6.0/sdcMicro/inst/CITATION |only sdcMicro-4.6.0/sdcMicro/inst/doc/sdc_guidelines.R | 208 - sdcMicro-4.6.0/sdcMicro/inst/doc/sdc_guidelines.pdf |binary sdcMicro-4.6.0/sdcMicro/inst/templates/report-template.rmd |only sdcMicro-4.6.0/sdcMicro/inst/templates/report.css | 34 sdcMicro-4.6.0/sdcMicro/man/CASCrefmicrodata.Rd | 82 sdcMicro-4.6.0/sdcMicro/man/EIA.Rd | 203 - sdcMicro-4.6.0/sdcMicro/man/LLmodGlobalRisk.Rd | 127 sdcMicro-4.6.0/sdcMicro/man/LocalRecProg.Rd | 193 - sdcMicro-4.6.0/sdcMicro/man/Tarragona.Rd | 81 sdcMicro-4.6.0/sdcMicro/man/addNoise.Rd | 236 - sdcMicro-4.6.0/sdcMicro/man/calcRisks.Rd | 42 sdcMicro-4.6.0/sdcMicro/man/casc1.Rd | 38 sdcMicro-4.6.0/sdcMicro/man/dRisk.Rd | 133 sdcMicro-4.6.0/sdcMicro/man/dRiskRMD.Rd | 166 sdcMicro-4.6.0/sdcMicro/man/dUtility.Rd | 165 sdcMicro-4.6.0/sdcMicro/man/dataGen.Rd | 132 sdcMicro-4.6.0/sdcMicro/man/extractManipData.Rd |only sdcMicro-4.6.0/sdcMicro/man/francdat.Rd | 67 sdcMicro-4.6.0/sdcMicro/man/free1.Rd | 55 sdcMicro-4.6.0/sdcMicro/man/freqCalc.Rd | 161 sdcMicro-4.6.0/sdcMicro/man/generateStrata.Rd | 65 sdcMicro-4.6.0/sdcMicro/man/globalRecode.Rd | 133 sdcMicro-4.6.0/sdcMicro/man/groupVars.Rd |only sdcMicro-4.6.0/sdcMicro/man/indivRisk.Rd | 87 sdcMicro-4.6.0/sdcMicro/man/localSupp.Rd | 153 sdcMicro-4.6.0/sdcMicro/man/localSuppression.Rd | 194 - sdcMicro-4.6.0/sdcMicro/man/mafast.Rd | 166 sdcMicro-4.6.0/sdcMicro/man/measure_risk.Rd | 254 - sdcMicro-4.6.0/sdcMicro/man/microData.Rd | 40 sdcMicro-4.6.0/sdcMicro/man/microaggrGower.Rd | 161 sdcMicro-4.6.0/sdcMicro/man/microaggregation.Rd | 353 - sdcMicro-4.6.0/sdcMicro/man/modRisk.Rd |only sdcMicro-4.6.0/sdcMicro/man/plot.localSuppression.Rd | 75 sdcMicro-4.6.0/sdcMicro/man/plot.sdcMicroObj.Rd |only sdcMicro-4.6.0/sdcMicro/man/plotMicro.Rd | 80 sdcMicro-4.6.0/sdcMicro/man/pram.Rd | 194 - sdcMicro-4.6.0/sdcMicro/man/print.freqCalc.Rd | 60 sdcMicro-4.6.0/sdcMicro/man/print.indivRisk.Rd | 68 sdcMicro-4.6.0/sdcMicro/man/print.localSuppression.Rd | 60 sdcMicro-4.6.0/sdcMicro/man/print.micro.Rd | 58 sdcMicro-4.6.0/sdcMicro/man/print.modrisk.Rd |only sdcMicro-4.6.0/sdcMicro/man/print.pram.Rd |only sdcMicro-4.6.0/sdcMicro/man/print.sdcMicroObj.Rd | 75 sdcMicro-4.6.0/sdcMicro/man/print.suda2.Rd | 60 sdcMicro-4.6.0/sdcMicro/man/rankSwap.Rd | 220 - sdcMicro-4.6.0/sdcMicro/man/removeDirectID.Rd |only sdcMicro-4.6.0/sdcMicro/man/renameVars.Rd |only sdcMicro-4.6.0/sdcMicro/man/report.Rd | 66 sdcMicro-4.6.0/sdcMicro/man/sdcMicro-package.Rd | 517 +- sdcMicro-4.6.0/sdcMicro/man/sdcMicroObj-class.Rd | 211 - sdcMicro-4.6.0/sdcMicro/man/shuffle.Rd | 248 - sdcMicro-4.6.0/sdcMicro/man/suda2.Rd | 191 - sdcMicro-4.6.0/sdcMicro/man/summary.freqCalc.Rd | 87 sdcMicro-4.6.0/sdcMicro/man/summary.micro.Rd | 110 sdcMicro-4.6.0/sdcMicro/man/summary.pram.Rd | 80 sdcMicro-4.6.0/sdcMicro/man/testdata.Rd | 119 sdcMicro-4.6.0/sdcMicro/man/topBotCoding.Rd | 111 sdcMicro-4.6.0/sdcMicro/man/valTable.Rd | 130 sdcMicro-4.6.0/sdcMicro/man/varToFactor.Rd |only sdcMicro-4.6.0/sdcMicro/src/RcppExports.cpp |only sdcMicro-4.6.0/sdcMicro/src/calcSuppInds.cpp |only sdcMicro-4.6.0/sdcMicro/tests/globalRecoding_test.R | 18 sdcMicro-4.6.0/sdcMicro/tests/microaggregation_test.R | 28 sdcMicro-4.6.0/sdcMicro/tests/reporting_test.R | 41 sdcMicro-4.6.0/sdcMicro/tests/testhat.R |only sdcMicro-4.6.0/sdcMicro/tests/testthat |only 142 files changed, 11288 insertions(+), 8425 deletions(-)
Title: Stratified Analysis with Nonparametric Covariable Adjustment
Description: There are several functions to implement the method for analysis in a randomized clinical trial with strata with following key features. A stratified Mann-Whitney estimator addresses the comparison between two randomized groups for a strictly ordinal response variable. The multivariate vector of such stratified Mann-Whitney estimators for multivariate response variables can be considered for one or more response variables such as in repeated measurements and these can have missing completely at random (MCAR) data. Non-parametric covariance adjustment is also considered with the minimal assumption of randomization. The p-value for hypothesis test and confidence interval are provided.
Author: Atsushi Kawaguchi
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>
Diff between sanon versions 1.4 dated 2014-09-04 and 1.5 dated 2015-10-01
DESCRIPTION | 12 +-- MD5 | 49 +++++++------- NAMESPACE | 32 ++++++++- R/sanon.r | 29 +++++++- data/cpain.rda |binary data/heartburn.rda |binary data/resp.rda |binary data/sebor.rda |binary data/skin.rda |binary inst |only man/catecovar.Rd | 18 ++--- man/coef.sanon.Rd | 20 ++--- man/confint.sanon.Rd | 39 +++-------- man/contrast.Rd | 55 ++++++--------- man/covar.Rd | 10 +- man/cpain.Rd | 30 +++----- man/grp.Rd | 13 +-- man/heartburn.Rd | 44 +++++------- man/resp.Rd | 53 +++++---------- man/sanon-package.Rd | 17 ++-- man/sanon.Rd | 176 ++++++++++++++++++--------------------------------- man/sebor.Rd | 47 +++++-------- man/skin.Rd | 43 ++++-------- man/strt.Rd | 11 +-- man/summary.sanon.Rd | 27 +++---- man/vcov.sanon.Rd | 17 ++-- 26 files changed, 331 insertions(+), 411 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 1.5.2 dated 2015-02-04 and 1.5.3 dated 2015-10-01
DESCRIPTION | 13 +- MD5 | 26 ++-- NAMESPACE | 4 NEWS | 6 + R/branches.R | 3 R/lib.R | 45 ++++++- R/node.labs.R | 2 R/prp.R | 6 - inst/doc/prp.pdf |binary inst/slowtests/make.bat | 2 inst/slowtests/test.prp.R | 168 +++++++++++++++++----------- inst/slowtests/test.prp.Rout.save | 223 ++++++++++++++++++++++---------------- inst/slowtests/user-manual-figs.R | 20 +++ inst/slowtests/webpage-figs.R | 4 14 files changed, 334 insertions(+), 188 deletions(-)
Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions
from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh,
R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton <charlton@usgs.gov>
Diff between phreeqc versions 1.0-9102 dated 2014-12-11 and 3.3.1 dated 2015-10-01
DESCRIPTION | 24 - MD5 | 242 +++++++------- NAMESPACE | 2 R/phreeqc.R | 2 data/databases.rda |binary data/examples.rda |binary man/Amm.dat.Rd | 19 - man/ex1.Rd | 33 + man/ex10.Rd | 45 +- man/ex11.Rd | 43 +- man/ex12.Rd | 59 +-- man/ex13.Rd | 42 +- man/ex14.Rd | 52 +-- man/ex15.Rd | 47 +- man/ex15.dat.Rd | 16 man/ex16.Rd | 53 +-- man/ex17.Rd | 52 +-- man/ex18.Rd | 72 ++-- man/ex19.Rd | 38 +- man/ex2.Rd | 29 - man/ex20.Rd | 57 +-- man/ex21.Rd | 52 +-- man/ex22.Rd | 46 +- man/ex3.Rd | 51 +-- man/ex4.Rd | 54 +-- man/ex5.Rd | 41 +- man/ex6.Rd | 36 +- man/ex7.Rd | 61 +-- man/ex8.Rd | 38 +- man/ex9.Rd | 62 +-- man/iso.dat.Rd | 18 - man/llnl.dat.Rd | 17 - man/minteq.dat.Rd | 14 man/minteq.v4.dat.Rd | 14 man/phrAccumulateLine.Rd | 12 man/phrClearAccumulatedLines.Rd | 11 man/phrGetAccumulatedLines.Rd | 6 man/phrGetComponentList.Rd | 5 man/phrGetDumpFileName.Rd | 17 - man/phrGetDumpFileOn.Rd | 12 man/phrGetDumpStrings.Rd | 16 man/phrGetDumpStringsOn.Rd | 12 man/phrGetErrorFileName.Rd | 18 - man/phrGetErrorFileOn.Rd | 12 man/phrGetErrorStrings.Rd | 28 - man/phrGetErrorStringsOn.Rd | 12 man/phrGetLogFileName.Rd | 15 man/phrGetLogFileOn.Rd | 12 man/phrGetLogStrings.Rd | 12 man/phrGetLogStringsOn.Rd | 12 man/phrGetOutputFileName.Rd | 15 man/phrGetOutputFileOn.Rd | 12 man/phrGetOutputStrings.Rd | 12 man/phrGetOutputStringsOn.Rd | 12 man/phrGetSelectedOutput.Rd | 30 - man/phrGetSelectedOutputFileName.Rd | 15 man/phrGetWarningStrings.Rd | 14 man/phrLoadDatabase.Rd | 7 man/phrLoadDatabaseString.Rd | 9 man/phrRunAccumulated.Rd | 27 - man/phrRunFile.Rd | 6 man/phrRunString.Rd | 18 - man/phrSetDumpFileName.Rd | 19 - man/phrSetDumpFileOn.Rd | 20 - man/phrSetDumpStringsOn.Rd | 22 - man/phrSetErrorFileName.Rd | 17 - man/phrSetErrorFileOn.Rd | 23 - man/phrSetErrorStringsOn.Rd | 25 - man/phrSetLogFileName.Rd | 21 - man/phrSetLogFileOn.Rd | 24 - man/phrSetLogStringsOn.Rd | 22 - man/phrSetOutputFileName.Rd | 20 - man/phrSetOutputFileOn.Rd | 22 - man/phrSetOutputStringsOn.Rd | 22 - man/phrSetSelectedOutputFileName.Rd | 20 - man/phrSetSelectedOutputFileOn.Rd | 22 - man/phreeqc-package.Rd | 26 - man/phreeqc.dat.Rd | 17 - man/pitzer.dat.Rd | 17 - man/sit.dat.Rd | 17 - man/wateq4f.dat.Rd | 15 src/IPhreeqc.cpp | 118 +++++-- src/IPhreeqc.h | 30 + src/IPhreeqcLib.cpp | 16 src/IPhreeqchpp.h | 9 src/phreeqcpp/ChartHandler.cpp | 2 src/phreeqcpp/ChartObject.cpp | 20 - src/phreeqcpp/GasPhase.cpp | 18 - src/phreeqcpp/NameDouble.cpp | 1 src/phreeqcpp/PBasic.cpp | 326 ++++++++++++++++++- src/phreeqcpp/PBasic.h | 4 src/phreeqcpp/PPassemblage.cpp | 1 src/phreeqcpp/Phreeqc.cpp | 6 src/phreeqcpp/Phreeqc.h | 43 ++ src/phreeqcpp/Solution.cpp | 61 +++ src/phreeqcpp/Solution.h | 2 src/phreeqcpp/StorageBinList.cpp | 29 + src/phreeqcpp/SurfaceCharge.cpp | 44 ++ src/phreeqcpp/SurfaceCharge.h | 2 src/phreeqcpp/basicsubs.cpp | 444 +++++++++++++++++++++++++- src/phreeqcpp/cvdense.cpp | 5 src/phreeqcpp/cvode.cpp | 9 src/phreeqcpp/dumper.cpp | 4 src/phreeqcpp/dw.cpp | 3 src/phreeqcpp/gases.cpp | 23 + src/phreeqcpp/integrate.cpp | 9 src/phreeqcpp/inverse.cpp | 19 - src/phreeqcpp/isotopes.cpp | 22 + src/phreeqcpp/kinetics.cpp | 4 src/phreeqcpp/mainsubs.cpp | 53 +++ src/phreeqcpp/model.cpp | 170 ++++++++-- src/phreeqcpp/pitzer.cpp | 604 +++++++++++++++++++++++++++++------- src/phreeqcpp/pitzer_structures.cpp | 15 src/phreeqcpp/prep.cpp | 39 +- src/phreeqcpp/print.cpp | 41 ++ src/phreeqcpp/read.cpp | 15 src/phreeqcpp/sit.cpp | 387 +++++++++++++++++++++-- src/phreeqcpp/step.cpp | 4 src/phreeqcpp/structures.cpp | 48 +- src/phreeqcpp/tally.cpp | 8 src/phreeqcpp/tidy.cpp | 67 +++ src/phreeqcpp/utilities.cpp | 5 122 files changed, 3494 insertions(+), 1447 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table, actuarial tables (also multiple decrement tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein.
Author: Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb], Kevin J. Owens [ctb], Christophe Dutang [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between lifecontingencies versions 1.1.9 dated 2015-07-10 and 1.1.10 dated 2015-10-01
ChangeLog | 4 DESCRIPTION | 10 MD5 | 34 NEWS | 10 R/3_demographicFunctions.R | 4 R/5_actuarialFunctions.R | 904 ++++++++------ R/8_mdtFunctions.R | 8 README.md | 3 build/vignette.rds |binary data/demoGermany.rda |only inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary inst/doc/introToLifecontingencies.Rmd | 2 inst/doc/introToLifecontingencies.pdf |binary man/demoGermany.Rd |only man/demoIta.Rd | 2 man/lifecontingencies-package.Rd | 4 vignettes/introToLifecontingencies.Rmd | 2 vignettes/introToLifecontingencies_files |only 18 files changed, 585 insertions(+), 402 deletions(-)
More information about lifecontingencies at CRAN
Permanent link
Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging
For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of
CppJieba
Maintainer: Qin Wenfeng <mail@qinwenfeng.com>
Diff between jiebaR versions 0.5 dated 2015-04-29 and 0.6 dated 2015-10-01
DESCRIPTION | 10 - MD5 | 102 +++++++++------ NAMESPACE | 5 NEWS | 10 + R/RcppExports.R | 24 ++- R/filter.R | 41 +++++- R/jiebar.R | 48 +++++-- R/print.R | 11 + R/quick.R | 2 R/segment.R | 21 ++- R/tagger.R | 17 +- R/words_freq.R |only R/zzz.R | 3 README.md | 3 build/vignette.rds |binary inst/include/jiebaRAPI.h |only inst/include/lib/DictTrie.hpp | 7 - inst/include/lib/HMMSegment.hpp | 2 inst/include/segtype.hpp | 253 ++++++++++++++++++++------------------ man/DICTPATH.Rd | 2 man/distance.Rd | 2 man/edit_dict.Rd | 2 man/filecoding.Rd | 2 man/filter_segment.Rd | 6 man/freq.Rd |only man/jiebaR.Rd | 2 man/keywords.Rd | 2 man/less-than-equals-.keywords.Rd | 2 man/less-than-equals-.qseg.Rd | 2 man/less-than-equals-.segment.Rd | 2 man/less-than-equals-.simhash.Rd | 2 man/less-than-equals-.tagger.Rd | 2 man/print.hmmseg.Rd | 5 man/segment.Rd | 2 man/set_qsegmodel.Rd | 2 man/show_dictpath.Rd | 2 man/simhash.Rd | 2 man/tagging.Rd | 2 man/worker.Rd | 8 - src/RcppExports.cpp | 146 ++++++++++++--------- src/detect.cpp | 3 src/init.c |only src/segtype.cpp | 99 ++++++++++---- src/word_freq.cpp |only tests/testthat/CPP_API |only tests/testthat/C_API |only tests/testthat/test-api.R |only tests/testthat/test-cut.R | 39 +++++ 48 files changed, 571 insertions(+), 326 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting
for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Lash T.L, Fox M.P, and Fink A.K.
"Applying Quantitative Bias Analysis to Epidemiologic Data",
'Springer', 2009.
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <denis.haine@gmail.com>
Diff between episensr versions 0.6.0 dated 2015-03-31 and 0.7.0 dated 2015-10-01
DESCRIPTION | 17 +- MD5 | 58 ++++--- NAMESPACE | 37 ++++ R/confounders.R | 96 +++++++++++- R/confounders.emm.R | 119 +++++++++++++-- R/confounders.limit.R | 27 +++ R/confounders.poly.R | 114 +++++++++++++-- R/mbias.R |only R/misclassification.R | 79 +++++++++- R/multidimBias.R | 62 ++++++++ R/plot.mbias.R |only R/print.mbias.R |only R/probsens.R | 311 +++++++++++++++++++++++++++++++++++------ R/probsens.conf.R | 245 ++++++++++++++++++++++++++++---- R/probsens.irr.R |only R/probsens.irr.conf.R |only R/probsens.sel.R | 101 +++++++++++-- R/selection.R | 40 +++++ README.md | 105 +++++++++++++ man/confounders.Rd | 128 +++++++++------- man/confounders.emm.Rd | 161 +++++++++++---------- man/confounders.limit.Rd | 54 ++++--- man/confounders.poly.Rd | 170 +++++++++++----------- man/mbias.Rd |only man/misclassification.Rd | 121 ++++++++------- man/multidimBias.Rd | 128 +++++++++------- man/plot.mbias.Rd |only man/print.mbias.Rd |only man/probsens.Rd | 145 ++++++++++--------- man/probsens.conf.Rd | 114 ++++++++------- man/probsens.irr.Rd |only man/probsens.irr.conf.Rd |only man/probsens.sel.Rd | 88 ++++++----- man/selection.Rd | 74 +++++---- tests/testthat/test-probsens.R | 154 ++++++++++++++++++++ 35 files changed, 2064 insertions(+), 684 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data analysis
by a unified model specification, along with some data manipulation functions.
This package covers fitting of variety models including Cox regression models,
linear regression models, Poisson regression models, logistic models and
others whose likelihood is expressed in negative binomial, gamma and Weibull
distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.0.2 dated 2015-09-01 and 0.0.3 dated 2015-10-01
DESCRIPTION | 8 +- MD5 | 18 ++--- NAMESPACE | 1 NEWS | 7 ++ R/epifit-package.R | 7 +- R/epifit.R | 75 ++++++++++++++------- R/modules.R | 172 +++++++++++++++++++++++++++++++------------------- R/pytable.R |only man/epifit-package.Rd | 7 +- man/epifit.Rd | 42 +++++++++--- man/pytable.Rd |only 11 files changed, 223 insertions(+), 114 deletions(-)
Title: Statistical Functions for the Censored and Uncensored
Epanechnikov Distribution
Description: Analyzing censored variables usually requires the use of optimization algorithms. This package provides an alternative algebraic approach to the task of determining the expected value of a random censored variable with a known censoring point. Likewise this approach allows for the determination of the censoring point if the expected value is known. These results are derived under the assumption that the variable follows an Epanechnikov kernel distribution with known mean and range prior to censoring. Statistical functions related to the uncensored Epanechnikov distribution are also provided by this package.
Author: Mathias Borritz Milfeldt [aut, cre]
Maintainer: Mathias Borritz Milfeldt <mathias@milfeldt.dk>
Diff between epandist versions 1.0.0 dated 2015-09-27 and 1.0.1 dated 2015-10-01
DESCRIPTION | 6 ++-- MD5 | 34 +++++++++++++------------- R/cepan.R | 2 - R/depan.R | 2 - R/evepan.R | 4 +-- R/pepan.R | 2 - R/qepan.R | 2 - R/repan.R | 2 - inst/doc/Vignette_epandist.R | 15 ++++++++++- inst/doc/Vignette_epandist.Rmd | 44 +++++++++++++++++++++++++++++++--- inst/doc/Vignette_epandist.html | 51 +++++++++++++++++++++++++++++++--------- man/cepan.Rd | 2 - man/depan.Rd | 2 - man/evepan.Rd | 4 +-- man/pepan.Rd | 2 - man/qepan.Rd | 2 - man/repan.Rd | 2 - vignettes/Vignette_epandist.Rmd | 44 +++++++++++++++++++++++++++++++--- 18 files changed, 168 insertions(+), 54 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat for some core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between dbmss versions 2.2.2 dated 2015-09-17 and 2.2.3 dated 2015-10-01
DESCRIPTION | 8 MD5 | 18 - NEWS | 9 inst/CITATION | 37 +- inst/doc/dbmss.R | 2 inst/doc/dbmss.Rnw | 18 - inst/doc/dbmss.pdf |binary man/dbmss-package.Rd | 4 vignettes/dbmss.Rnw | 18 - vignettes/dbmss.bib | 816 +++++++++++++++++++++++++-------------------------- 10 files changed, 474 insertions(+), 456 deletions(-)
Title: Simultaneous Variables Clustering and Regression
Description: The R package clere implements an empirical Bayes approach for simultaneous variable clustering and regression. This version also (re)implements in C++ an R script proposed by Howard Bondell that fits the Pairwise Absolute Clustering and Sparsity (PACS) methodology (see Sharma DB et al. - 2013).
Author: Loic Yengo, Mickael Canouil
Maintainer: Loic Yengo <loic.yengo@gmail.com>
Diff between clere versions 1.1 dated 2014-02-21 and 1.1.1 dated 2015-10-01
clere-1.1.1/clere/DESCRIPTION | 22 ++-- clere-1.1.1/clere/MD5 | 46 ++++++---- clere-1.1.1/clere/NAMESPACE | 5 + clere-1.1.1/clere/R/Clere.R | 91 ------------------- clere-1.1.1/clere/R/fitClere.R |only clere-1.1.1/clere/R/fitPacs.R |only clere-1.1.1/clere/build |only clere-1.1.1/clere/data |only clere-1.1.1/clere/inst |only clere-1.1.1/clere/man/Clere-class.Rd | 138 ++++++++++++++---------------- clere-1.1.1/clere/man/Pacs-class.Rd |only clere-1.1.1/clere/man/algoComp.Rd |only clere-1.1.1/clere/man/clere-package.Rd | 35 +++---- clere-1.1.1/clere/man/clusters-methods.Rd | 18 +-- clere-1.1.1/clere/man/fitClere.Rd |only clere-1.1.1/clere/man/fitPacs.Rd |only clere-1.1.1/clere/man/is.clere.Rd | 16 +-- clere-1.1.1/clere/man/numExpRealData.Rd |only clere-1.1.1/clere/man/numExpSimData.Rd |only clere-1.1.1/clere/man/plot-methods.Rd | 16 +-- clere-1.1.1/clere/man/predict-methods.Rd | 18 +-- clere-1.1.1/clere/man/summary-methods.Rd | 16 +-- clere-1.1.1/clere/src/Model.cpp | 26 +++-- clere-1.1.1/clere/src/clere.cpp | 8 - clere-1.1.1/clere/src/pacs.cpp |only clere-1.1.1/clere/vignettes |only clere-1.1/clere/R/fit.clere.R |only clere-1.1/clere/man/fit.clere.Rd |only clere-1.1/clere/man/ggPlot-methods.Rd |only 29 files changed, 190 insertions(+), 265 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors with or without shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The cone information criterion (CIC) may be used to select the best combination of variables and shapes. This package depends on the R package coneproj.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between cgam versions 1.2 dated 2014-09-10 and 1.3 dated 2015-10-01
DESCRIPTION | 13 +-- MD5 | 10 +- NAMESPACE | 5 + R/cgam.R | 193 +++++++++++++++++++++++++++++++++++++++++++------------ man/cgam.Rd | 4 - man/plotpersp.Rd | 26 +++++-- 6 files changed, 189 insertions(+), 62 deletions(-)
Title: Tools for Spatial Data Analysis
Description: Tools for spatial data analysis. Emphasis on kriging. Provides functions for prediction and simulation. Intended to be relatively straightforward, fast, and flexible.
Author: Joshua French <joshua.french@ucdenver.edu>
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between SpatialTools versions 0.5.8 dated 2014-07-02 and 1.0.0 dated 2015-10-01
SpatialTools-0.5.8/SpatialTools/R/old_code.R |only SpatialTools-0.5.8/SpatialTools/man/mspe.uk.Rd |only SpatialTools-0.5.8/SpatialTools/man/pweights.uk.Rd |only SpatialTools-1.0.0/SpatialTools/DESCRIPTION | 10 - SpatialTools-1.0.0/SpatialTools/MD5 | 25 +- SpatialTools-1.0.0/SpatialTools/NAMESPACE | 10 - SpatialTools-1.0.0/SpatialTools/NEWS | 2 SpatialTools-1.0.0/SpatialTools/R/arg_check.R | 110 ----------- SpatialTools-1.0.0/SpatialTools/R/contour_tools.R | 4 SpatialTools-1.0.0/SpatialTools/R/cov.R | 4 SpatialTools-1.0.0/SpatialTools/R/generate_norm.R | 2 SpatialTools-1.0.0/SpatialTools/R/krige_tools.R | 194 +-------------------- SpatialTools-1.0.0/SpatialTools/man/krige.ok.Rd | 11 - SpatialTools-1.0.0/SpatialTools/man/krige.sk.Rd | 10 - SpatialTools-1.0.0/SpatialTools/man/krige.uk.Rd | 10 - 15 files changed, 61 insertions(+), 331 deletions(-)
Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal .
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
Diff between Rsomoclu versions 1.4.1 dated 2014-09-07 and 1.5 dated 2015-10-01
Rsomoclu-1.4.1/Rsomoclu/src/somocluWrap.h |only Rsomoclu-1.4.1/Rsomoclu/src/trainOneEpoch.cpp |only Rsomoclu-1.5/Rsomoclu/DESCRIPTION | 12 - Rsomoclu-1.5/Rsomoclu/MD5 | 32 +- Rsomoclu-1.5/Rsomoclu/R/Rsomoclu.R | 19 + Rsomoclu-1.5/Rsomoclu/configure |only Rsomoclu-1.5/Rsomoclu/data/rgbs.txt.gz |binary Rsomoclu-1.5/Rsomoclu/man/Rsomoclu.train.Rd | 46 ++-- Rsomoclu-1.5/Rsomoclu/src/Makefile.in |only Rsomoclu-1.5/Rsomoclu/src/Makefile.root.in |only Rsomoclu-1.5/Rsomoclu/src/Rsomoclu.cpp | 238 +++++++-------------- Rsomoclu-1.5/Rsomoclu/src/config.h.in |only Rsomoclu-1.5/Rsomoclu/src/configure |only Rsomoclu-1.5/Rsomoclu/src/denseCpuKernels.cpp | 88 ++++--- Rsomoclu-1.5/Rsomoclu/src/denseGpuKernels.cu |only Rsomoclu-1.5/Rsomoclu/src/install-sh |only Rsomoclu-1.5/Rsomoclu/src/mapDistanceFunctions.cpp | 62 +++-- Rsomoclu-1.5/Rsomoclu/src/somoclu.h | 152 +++++++------ Rsomoclu-1.5/Rsomoclu/src/sparseCpuKernels.cpp | 101 ++++---- Rsomoclu-1.5/Rsomoclu/src/training.cpp |only Rsomoclu-1.5/Rsomoclu/src/uMatrix.cpp | 35 +-- Rsomoclu-1.5/Rsomoclu/tests/R_interface_test.R | 8 22 files changed, 398 insertions(+), 395 deletions(-)
Title: Rcmdr Evidence Based Medicine Plug-in Package
Description: Rcmdr plug-in GUI extension for Evidence Based Medicine medical indicators calculations (Sensitivity, specificity, absolute risk reduction, relative risk, ...).
Author: Daniel-Corneliu Leucuta <danny.ldc@gmail.com>
Maintainer: Daniel-Corneliu Leucuta <danny.ldc@gmail.com>
Diff between RcmdrPlugin.EBM versions 1.0-8 dated 2014-09-08 and 1.0-10 dated 2015-10-01
DESCRIPTION | 12 - MD5 | 8 - NAMESPACE | 2 R/CrossTab.R | 429 ++++++++++++++++++++++++++++++----------------------------- inst/CHANGES | 4 5 files changed, 240 insertions(+), 215 deletions(-)
More information about RcmdrPlugin.EBM at CRAN
Permanent link
Title: A Tool for Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.4 dated 2015-08-04 and 0.4.1 dated 2015-10-01
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 4 ++-- R/manage_expansion_sim.R | 12 +----------- R/range_raster.R | 3 +-- build/vignette.rds |binary data/cabrera.rda |binary data/landscape_change.rda |binary data/mc_df.rda |binary data/occ.landscape.rda |binary data/occ.landscape2.rda |binary data/param1.rda |binary data/rg_exp.rda |binary data/rland.rda |binary inst/doc/MetaLandSim.pdf |binary inst/logo/logo.gif |binary inst/logo/logo2.gif |binary man/MetaLandSim-package.Rd | 4 ++-- 18 files changed, 27 insertions(+), 38 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for binary classification models using weight-of-evidence (WOE) and information value (IV). In order to make the package as efficient as possible, aggregations are done in data.table and creation of WOE vectors can be distributed across multiple cores. The package also supports exploration for uplift models (NWOE and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.3 dated 2015-09-16 and 0.0.4 dated 2015-10-01
DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++----------- R/CheckInputs.R | 2 + R/Information.R | 39 ++++++++++++++++++++++++------------- R/create_infotables.R | 7 +++++- R/plot_infotables.R | 21 ++++++++++++++----- build/vignette.rds |binary inst/doc/Information-vignette.Rmd | 2 - inst/doc/Information-vignette.html | 4 +-- man/Information.Rd | 37 +++++++++++++++++++++++------------ man/create_infotables.Rd | 4 +-- man/plot_infotables.Rd | 21 ++++++++++++++----- vignettes/Information-vignette.Rmd | 2 - 13 files changed, 111 insertions(+), 60 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between InvariantCausalPrediction versions 0.3-4 dated 2015-09-17 and 0.4-0 dated 2015-10-01
DESCRIPTION | 8 +-- MD5 | 25 ++++++----- NAMESPACE | 3 - R/ICP.R | 64 +++++++++++++++++------------- R/getpval.R | 13 ++++-- R/getpvalClassif.R | 29 +++++++------ R/hiddenICP.R | 34 +++++++++++++-- R/plot.InvariantCausalPrediction.R | 2 R/print.InvariantCausalPrediction.R | 31 +++++++------- R/print.hiddenInvariantCausalPrediction.R |only R/pvalfunc.R | 19 +++++++- R/summary.InvariantCausalPrediction.R | 25 +---------- man/ICP.Rd | 61 +++++++++++++++------------- man/hiddenICP.Rd | 45 +++++++++++---------- 14 files changed, 206 insertions(+), 153 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Retrospective Noise Control for fMRI
Description: Useful functions for fMRI preprocessing.
Author: Tim Tierney
Maintainer: Tim Tierney <fiachmri@gmail.com>
Diff between FIACH versions 0.1.0 dated 2015-09-30 and 0.1.1 dated 2015-10-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars | 1 - 3 files changed, 5 insertions(+), 6 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include productivity evaluation using distance measures, benchmarking,
risk analysis, technology adoption model, inverse optimization, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 1.0 dated 2015-09-27 and 1.5 dated 2015-10-01
DESCRIPTION | 8 - MD5 | 40 ++++---- NAMESPACE | 1 R/DJL-internal.R | 251 ++++++++++++++++++++++++++--------------------------- R/dm.ddf.R | 7 - R/dm.sf.R | 7 - R/map.soa.ddf.R | 43 +++++---- R/map.soa.dea.R | 43 +++++---- R/map.soa.sbm.R | 41 +++++--- R/map.soa.sf.R | 43 +++++---- R/roc.dea.R | 7 - R/roc.sf.R |only man/dm.ddf.Rd | 11 +- man/dm.dea.Rd | 7 - man/dm.sbm.Rd | 8 - man/dm.sf.Rd | 9 - man/map.soa.ddf.Rd | 10 +- man/map.soa.dea.Rd | 11 +- man/map.soa.sbm.Rd | 10 +- man/map.soa.sf.Rd | 39 +++++--- man/roc.dea.Rd | 1 man/roc.sf.Rd |only 22 files changed, 338 insertions(+), 259 deletions(-)