Title: Who are You? Bayesian Prediction of Racial Category Using
Surname and Geolocation
Description: Predicts individual race/ethnicity using surname, geolocation, and other
attributes, such as gender and age. The method utilizes the Bayes' Rule to compute
the posterior probability of each racial category for any given individual.
The package implements methods described in Imai and Khanna (2015) "Improving
Ecological Inference by Predicting Individual Ethnicity from Voter Registration
Records" <DOI:10.1093/pan/mpw001>.
Author: Kabir Khanna [aut, cre], Kosuke Imai [aut, cre], Hubert Jin [ctb]
Maintainer: Kabir Khanna <kkhanna@princeton.edu>
Diff between wru versions 0.1-4 dated 2017-05-04 and 0.1-5 dated 2017-06-08
ChangeLog | 1 + DESCRIPTION | 10 +++++----- MD5 | 42 +++++++++++++++++++++--------------------- R/census_geo_api.R | 18 +++++++++--------- R/census_helper.R | 4 ++-- R/get_census_api.R | 8 ++++---- R/get_census_api_2.R | 8 ++++---- R/get_census_data.R | 4 ++-- R/vec_to_chunk.R | 2 +- man/State.FIPS.Rd | 1 - man/census_geo_api.Rd | 5 ++--- man/census_helper.Rd | 3 +-- man/get_census_api.Rd | 9 ++++----- man/get_census_api_2.Rd | 9 ++++----- man/get_census_data.Rd | 3 +-- man/merge_surnames.Rd | 1 - man/pid.Rd | 1 - man/predict_race.Rd | 1 - man/surnames.Rd | 1 - man/surnames2000.Rd | 1 - man/vec_to_chunk.Rd | 3 +-- man/voters.Rd | 1 - 22 files changed, 62 insertions(+), 74 deletions(-)
Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez R. with contributions from Carlos Aguero, Olger Calderon, Roberto Zuniga and Jorge Arce
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between RSDA versions 1.4 dated 2017-05-30 and 2.0 dated 2017-06-08
DESCRIPTION | 12 - MD5 | 106 ++++++++--- NAMESPACE | 10 - R/RSDA.R | 5 R/RSDA.to.latex.j.r |only R/SDS.to.RSDA.R | 146 ++++++++------- R/SODAS.to.RSDA.R | 53 ++--- R/centers.interval.j.r |only R/cfa.scatterplot.R | 24 +- R/change.coord.j.r |only R/classic.to.sym.R | 6 R/cor.sym.data.table.R | 2 R/data.R | 174 +++++++----------- R/data.frame.to.RSDA.inteval.table.j.r |only R/data.frame.to.sym.inteval.j.r |only R/desv.fun.j.r |only R/dist.interval.R |only R/dist.set.R |only R/dist.vect.R | 2 R/dist.vect.matrix.R | 2 R/generate.columns.interval.j.r |only R/generate.columns.multivalued.j.r |only R/generate.columns.set.j.r |only R/get.rotation.matrix.j.r |only R/interscal.R | 12 - R/interval.histogram.plot.R |only R/is.vertex.j.r |only R/meta.to.RSDA.j.r |only R/neg.desv.fun.j.r |only R/optim.desv.fun.interval.j.r |only R/optim.pca.distance.j.r |only R/optim.pca.variance.j.r |only R/pca.supplementary.vertex.fun.j.r |only R/pca.supplementary.vertex.lambda.fun.j.r |only R/principal.axis.i.j.r |only R/process.modal.variable.R | 36 +-- R/scatter.sym.j.r |only R/sym.cfa.R | 21 +- R/sym.histogram.pca.R | 6 R/sym.interval.pc.2.j.r |only R/sym.interval.pc.limits.2.j.r |only R/sym.interval.pca.R | 275 ++++++++++++++++-------------- R/sym.interval.pca.limits.new.j.r |only R/sym.interval.vertex.pca.j.r |only R/sym.radar.plot.R |only R/sym.scale.interval.j.r |only R/sym.table.to.latex.j.r |only R/vertex.interval.new.j.r |only R/vertex.pca.j.r |only R/whiskers.j.r |only data/table7.rda |only man/RSDA.Rd | 2 man/Table7.Rd |only man/USCrime.Rd | 4 man/classic.to.sym.Rd | 2 man/cor.Rd | 2 man/dist.interval.Rd |only man/dist.set.Rd |only man/dist.vect.Rd | 2 man/dist.vect.matrix.Rd | 2 man/ex1_db2so.Rd | 2 man/example1.Rd | 41 ++-- man/example2.Rd | 12 - man/example3.Rd | 16 - man/example4.Rd | 14 - man/example5.Rd | 12 - man/example6.Rd | 12 - man/example7.Rd | 12 - man/interscal.Rd | 2 man/interval.histogram.plot.Rd |only man/sym.Interval.distance.Rd |only man/sym.Multieval.distance.Rd |only man/sym.interval.pca.Rd | 3 man/sym.radar.plot..Rd |only man/sym.radar.plot.Rd |only 75 files changed, 534 insertions(+), 498 deletions(-)
Title: Quantifying Systematic Heterogeneity in Meta-Analysis
Description: Quantifying systematic heterogeneity in meta-analysis using R.
The M statistic aggregates heterogeneity information across multiple
variants to, identify systematic heterogeneity patterns and their direction
of effect in meta-analysis. It's primary use is to identify outlier studies,
which either show "null" effects or consistently show stronger or weaker
genetic effects than average across, the panel of variants examined in a
GWAS meta-analysis. In contrast to conventional heterogeneity metrics
(Q-statistic, I-squared and tau-squared) which measure random heterogeneity
at individual variants, M measures systematic (non-random)
heterogeneity across multiple independently associated variants. Systematic
heterogeneity can arise in a meta-analysis due to differences in the study
characteristics of participating studies. Some of the differences may
include: ancestry, allele frequencies, phenotype definition, age-of-disease
onset, family-history, gender, linkage disequilibrium and quality control
thresholds. See <https://magosil86.github.io/getmstatistic/> for statistical
statistical theory, documentation and examples.
Author: Lerato E Magosi [aut],
Jemma C Hopewell [aut],
Martin Farrall [aut],
Lerato E Magosi [cre]
Maintainer: Lerato E Magosi <lmagosi@well.ox.ac.uk>
Diff between getmstatistic versions 0.1.0 dated 2017-06-05 and 0.1.1 dated 2017-06-08
DESCRIPTION | 10 +++---- MD5 | 22 ++++++++--------- R/compute_mstatistics.R | 4 +-- R/data.R | 7 +++-- R/util_draw_table.R | 29 ++++++++++++---------- inst/CITATION | 10 +++---- inst/doc/getmstatistic-tutorial.Rmd | 2 - inst/doc/getmstatistic-tutorial.html | 6 ++-- man/draw_table.Rd | 45 ++++++++++++++++++----------------- man/heartgenes214.Rd | 7 +++-- vignettes/getmstatistic-tutorial.Rmd | 2 - vignettes/getmstatistic-tutorial.md | 4 +-- 12 files changed, 78 insertions(+), 70 deletions(-)
Title: Fill Missing Values in Satellite Data
Description: Tools to fill missing values in satellite data and to develop new
gap-fill algorithms. The methods are tailored to data (images) observed
at equally-spaced points in time. The package is illustrated with MODIS
NDVI data.
Author: Florian Gerber
Maintainer: Florian Gerber <florian.gerber@math.uzh.ch>
Diff between gapfill versions 0.9.5-2 dated 2017-01-19 and 0.9.5-3 dated 2017-06-08
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++----------------- R/RcppExports.R | 2 +- R/gapfill.R | 12 ++++++------ man/Array2Matrix.Rd | 7 +++---- man/ArrayAround.Rd | 1 - man/EstimateQuantile.Rd | 7 +++---- man/Extend.Rd | 9 ++++----- man/Gapfill.Rd | 11 +++++------ man/Image.Rd | 19 +++++++++---------- man/Index.Rd | 4 ++-- man/Score.Rd | 7 +++---- man/Subset-Predict.Rd | 14 +++++++------- man/Validate.Rd | 1 - man/gapfill-package.Rd | 10 +++++----- man/ndvi.Rd | 1 - src/RcppExports.cpp | 20 +++++++++++++++----- tests/testthat/test-Score.R | 2 +- 18 files changed, 86 insertions(+), 85 deletions(-)
Title: Connect to 'DocuSign' API
Description: Connect to the 'DocuSign' Rest API <https://www.docusign.com/p/RESTAPIGuide/RESTAPIGuide.htm>,
which supports embedded signing, and sending of documents.
Author: Carl Ganz [aut, cre],
CannaData Solutions [cph]
Maintainer: Carl Ganz <carl@cannadatasolutions.com>
Diff between docuSignr versions 0.0.1 dated 2017-04-14 and 0.0.2 dated 2017-06-08
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NAMESPACE | 1 NEWS.md |only R/httr.R | 60 ++++++++++++++++++++++++++++++++++++---- README.md | 19 +++++++----- man/docu_embedded_sign.Rd | 11 ++++--- man/docu_envelope.Rd | 3 +- man/docu_templates.Rd |only tests/testthat/test-2-signing.R | 7 ++-- tests/testthat/test-3-sending.R | 4 -- 11 files changed, 93 insertions(+), 36 deletions(-)
Title: Data and Methods Around Reference Values in Pediatrics
Description: Calculation of standard deviation scores adduced from different
growth standards (WHO, UK, Germany, Italy, China, etc). Therefore, the calculation of SDS-values
for different measures like BMI, weight, height, head circumference, different
ratios, etc. are easy to carry out. Also, references for laboratory values in
children are available: serum lipids, iron-related blood parameters. In the
new version, there are also functions combining the gamlss lms() function with
resampling methods for using with repeated measurements and family dependencies.
Author: Mandy Vogel [aut, cre]
Maintainer: Mandy Vogel <mandy.vogel@googlemail.com>
Diff between childsds versions 0.6.1 dated 2017-05-07 and 0.6.2 dated 2017-06-08
DESCRIPTION | 11 +++--- MD5 | 24 +++++++++------ NAMESPACE | 2 + NEWS.md | 11 +++++- R/createlms.R | 3 + R/data.R | 18 +++++++++++ R/misc.R | 55 +++++++++++++++++++++------------- R/refsclass.r | 72 --------------------------------------------- R/sdsvals.r |only data/belgium.ref.rda |only data/kiggs_bp.ref.rda |only man/belgium.ref.Rd |only man/kiggs_bp.ref.Rd |only man/make_percentile_tab.Rd | 6 +-- man/sds.Rd | 2 - man/sds_2d.Rd |only 16 files changed, 91 insertions(+), 113 deletions(-)
Title: Functional Linear Mixed Models for Irregularly or Sparsely
Sampled Data
Description: Estimation of functional linear mixed models for irregularly or
sparsely sampled data based on functional principal component analysis.
Author: Jona Cederbaum
Maintainer: Jona Cederbaum <Jona.Cederbaum@stat.uni-muenchen.de>
Diff between sparseFLMM versions 0.1.0 dated 2017-01-14 and 0.1.1 dated 2017-06-08
DESCRIPTION | 8 - MD5 | 18 +- R/call_all_functions.R | 22 +-- R/cov_estimation_tri_constr.R | 217 +++++++++++++++---------------- man/Predict.matrix.symm.smooth.Rd | 1 man/acoustic.Rd | 1 man/acoustic_subset.Rd | 1 man/make_summation_matrix.Rd | 1 man/smooth.construct.symm.smooth.spec.Rd | 1 man/sparseFLMM.Rd | 28 ++-- 10 files changed, 149 insertions(+), 149 deletions(-)
Title: Probabilistic Latent Feature Analysis
Description: Functions for estimating probabilistic latent feature models with a disjunctive, conjunctive or additive mapping rule on (aggregated) binary three-way data.
Author: Michel Meulders [aut, cre], Philippe De Bruecker [ctb]
Maintainer: Michel Meulders <michel.meulders@kuleuven.be>
Diff between plfm versions 2.1 dated 2015-12-16 and 2.2 dated 2017-06-08
plfm-2.1/plfm/src/Main.cpp |only plfm-2.2/plfm/DESCRIPTION | 10 plfm-2.2/plfm/MD5 | 26 plfm-2.2/plfm/NAMESPACE | 5 plfm-2.2/plfm/R/plfm.R | 1427 +++++++++++++++++++++++++--- plfm-2.2/plfm/man/LCplfm.Rd | 69 + plfm-2.2/plfm/man/gendat.Rd | 15 plfm-2.2/plfm/man/gendatLCplfm.Rd | 21 plfm-2.2/plfm/man/plfm-package.Rd | 8 plfm-2.2/plfm/man/plfm.Rd | 20 plfm-2.2/plfm/man/stepLCplfm.Rd | 7 plfm-2.2/plfm/man/stepplfm.Rd | 14 plfm-2.2/plfm/man/summary.stepLCplfm.Rd | 4 plfm-2.2/plfm/src/main.cpp |only plfm-2.2/plfm/src/plfm-win.def |only plfm-2.2/plfm/src/registerDynamicSymbol.cpp |only 16 files changed, 1438 insertions(+), 188 deletions(-)
Title: Regularized Structural Equation Modeling
Description: Uses both ridge and lasso penalties (and extensions) to penalize
specific parameters in structural equation models. The package offers additional
cost functions, cross validation, and other extensions beyond traditional structural
equation models.
Author: Ross Jacobucci[aut,cre],
Kevin J. Grimm [ctb],
Andreas M. Brandmaier [ctb]
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>
Diff between regsem versions 0.7.0 dated 2017-03-02 and 0.8.1 dated 2017-06-08
regsem-0.7.0/regsem/R/plot_cv.R |only regsem-0.7.0/regsem/R/summary.R |only regsem-0.7.0/regsem/man/plot_cv.Rd |only regsem-0.7.0/regsem/src/init.c |only regsem-0.7.0/regsem/src/registerDynamicSymbol.c |only regsem-0.8.1/regsem/DESCRIPTION | 16 regsem-0.8.1/regsem/MD5 | 47 +- regsem-0.8.1/regsem/NAMESPACE | 6 regsem-0.8.1/regsem/R/RcppExports.R | 10 regsem-0.8.1/regsem/R/coord_desc.R | 322 +++++++++++++---- regsem-0.8.1/regsem/R/cv_regsem.R | 395 +++++++++++++++++++-- regsem-0.8.1/regsem/R/fit_indices.R | 43 +- regsem-0.8.1/regsem/R/multi_optim.R | 27 + regsem-0.8.1/regsem/R/parse_parameters.R |only regsem-0.8.1/regsem/R/plot.R |only regsem-0.8.1/regsem/R/regsem.R | 124 +++--- regsem-0.8.1/regsem/R/soft.R | 8 regsem-0.8.1/regsem/R/summary.cvregsem.R |only regsem-0.8.1/regsem/R/summary.regsem.R |only regsem-0.8.1/regsem/R/xmed_cat.R |only regsem-0.8.1/regsem/man/cv_regsem.Rd | 27 - regsem-0.8.1/regsem/man/multi_optim.Rd | 24 - regsem-0.8.1/regsem/man/parse_parameters.Rd |only regsem-0.8.1/regsem/man/plot.cvregsem.Rd |only regsem-0.8.1/regsem/man/rcpp_quasi_calc.Rd |only regsem-0.8.1/regsem/man/regsem.Rd | 33 + regsem-0.8.1/regsem/man/summary.cvregsem.Rd |only regsem-0.8.1/regsem/man/summary.regsem.Rd | 2 regsem-0.8.1/regsem/man/xmed_cat.Rd |only regsem-0.8.1/regsem/src/RcppExports.cpp | 14 regsem-0.8.1/regsem/src/regsem_init.c |only regsem-0.8.1/regsem/src/regsem_rcpp_fit_fun.cpp | 2 regsem-0.8.1/regsem/src/regsem_rcpp_quasi_calc.cpp |only 33 files changed, 849 insertions(+), 251 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK").
Author: John Wambaugh, Robert Pearce, Caroline Ring, Jimena Davis, Nisha Sipes, and R. Woodrow Setzer
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.5 dated 2017-03-03 and 1.6 dated 2017-06-08
DESCRIPTION | 19 MD5 | 193 +- NAMESPACE | 9 NEWS |binary R/Calc_Hepatic_Clearance.r | 17 R/Calc_elimination_rate.R | 14 R/Calc_ratioblood2plasma.R | 10 R/Calc_total_clearance.R | 6 R/Calc_volume_of_distribution.R | 17 R/Parameterize_3comp.r | 10 R/Parameterize_PBTK.r | 48 R/Parameterize_SteadyState.R | 38 R/Predict_partitioning_Schmitt.R | 107 - R/add_chemtable.R | 2 R/age_draw_smooth.R | 3 R/available_rblood2plasma.R |only R/calc_analytic_css.R | 43 R/calc_css.R | 19 R/calc_mc_css.R | 30 R/convert_httk.R | 35 R/draw_fup_clint.R | 6 R/get_cheminfo.R | 6 R/get_httk_params.R | 15 R/get_rblood2plasma.R | 3 R/lump_tissues.R | 46 R/parameterize_1comp.R | 12 R/parameterize_schmitt.R | 19 R/solve_1comp.R | 7 R/solve_3comp.R | 7 R/solve_pbtk.R | 8 R/tissue_mass_functions.R | 774 +++++----- build/partial.rdb |only build/vignette.rds |binary data/Tables.RData |binary data/datalist | 2 data/httkpop.RData |binary data/vignettes.RData |binary inst/doc/httk.pdf |binary inst/doc/partitioning_plots.R |only inst/doc/partitioning_plots.Rmd |only inst/doc/partitioning_plots.html |only inst/doc/supplemental_vignette_age_dist.html | 4 inst/doc/supplemental_vignette_globalsensitivityanalysis.Rmd | 2 inst/doc/supplemental_vignette_globalsensitivityanalysis.html | 6 inst/doc/supplemental_vignette_globalsensitivityplot.Rmd | 2 inst/doc/supplemental_vignette_globalsensitivityplot.html | 6 inst/doc/supplemental_vignette_heightweight_splines_kde.html | 4 inst/doc/supplemental_vignette_hematocrit_splines.html | 4 inst/doc/supplemental_vignette_plot_css95.html | 4 inst/doc/supplemental_vignette_serumcreat_splines_kde.html | 4 inst/doc/vignette01_subpopulations.R | 2 inst/doc/vignette01_subpopulations.Rmd | 2 inst/doc/vignette01_subpopulations.html | 4 inst/doc/vignette02_evalmodelsubpop.html | 4 inst/doc/vignette03_paper_fig2.html | 4 inst/doc/vignette04_paper_fig3.html | 4 inst/doc/vignette05b_plothowgatejohnson.html | 4 inst/doc/vignette06_aerplotting.html | 4 inst/doc/vignette_05a_virtualstudypops.html | 4 man/Calc_elimination_rate.Rd | 8 man/Calc_ratioblood2plasma.Rd | 12 man/Calc_volume_of_distriution.Rd | 15 man/PK_physiology_data.Rd | 2 man/Parameterize_PBTK.Rd | 7 man/Parameterize_SteadyState.Rd | 4 man/Wetmore.data.Rd | 2 man/Wetmore_Css.Rd | 1 man/add_chemtable.Rd | 6 man/available_ratioblood2plasma.Rd |only man/calc_analytic_css.Rd | 18 man/calc_css.Rd | 51 man/calc_hepatic_clearance.Rd | 11 man/calc_mc_css.Rd | 32 man/calc_stats.Rd | 7 man/calc_total_clearance.Rd | 13 man/chem_invivo_PK_data.Rd | 4 man/chem_invivo_PK_summary_data.Rd | 2 man/chem_physical_and_invitro_data.Rd | 8 man/convert_httk.Rd | 7 man/draw_fup_clint.Rd | 3 man/get_cheminfo.Rd | 4 man/get_httk_params.Rd | 7 man/get_rblood2plasma.Rd | 1 man/httk-package.Rd |only man/httkpop_generate.Rd | 3 man/monte_carlo.Rd | 33 man/parameterize_1comp.Rd | 16 man/parameterize_3comp.Rd | 14 man/parameterize_schmitt.Rd | 16 man/pc.data.Rd |only man/predict_partitioning_schmitt.Rd | 16 man/solve_1comp_pk.Rd | 8 man/solve_3comp_pbpk.Rd | 5 man/solve_pbtk.Rd | 24 man/tissue_data.Rd | 16 tests/cheminfo_test.Rout.save | 28 tests/other_tests.R | 2 tests/other_tests.Rout.save | 80 - vignettes/partitioning_plots.Rmd |only vignettes/supplemental_vignette_globalsensitivityanalysis.Rmd | 2 vignettes/supplemental_vignette_globalsensitivityplot.Rmd | 2 vignettes/vignette01_subpopulations.Rmd | 2 102 files changed, 1182 insertions(+), 903 deletions(-)
Title: Substitution and Indel Distances to Infer Evolutionary
Relationships
Description: Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.
Author: A. Jesus Muñoz Pajares
Maintainer: A.J. Muñoz-Pajares <ajesusmp@ugr.es>
Diff between sidier versions 4.0.1 dated 2017-06-06 and 4.0.2 dated 2017-06-08
DESCRIPTION | 8 ++-- MD5 | 8 ++-- NEWS | 8 ++++ R/barcode.summary.R | 9 ++-- man/sidier-package.Rd | 98 +++++++++++++++++++++++++------------------------- 5 files changed, 70 insertions(+), 61 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH
Zurich, quite a few related to graphics; some were ported from S-plus.
Author: Martin Maechler et al.
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-0 dated 2016-02-23 and 1.1-1 dated 2017-06-08
sfsmisc-1.1-0/sfsmisc/ChangeLog |only sfsmisc-1.1-0/sfsmisc/man/pmax.sa.Rd |only sfsmisc-1.1-1/sfsmisc/DESCRIPTION | 12 ++--- sfsmisc-1.1-1/sfsmisc/MD5 | 47 ++++++++++---------- sfsmisc-1.1-1/sfsmisc/NAMESPACE | 2 sfsmisc-1.1-1/sfsmisc/R/Defunct.R | 17 +++++++ sfsmisc-1.1-1/sfsmisc/R/Deprecated.R | 39 +++------------- sfsmisc-1.1-1/sfsmisc/R/integratexy.R | 21 ++++----- sfsmisc-1.1-1/sfsmisc/R/misc-goodies.R | 26 ----------- sfsmisc-1.1-1/sfsmisc/R/mult.fig.R | 8 +-- sfsmisc-1.1-1/sfsmisc/R/p.ts.R | 2 sfsmisc-1.1-1/sfsmisc/R/prettylab.R | 23 ++++++---- sfsmisc-1.1-1/sfsmisc/R/sessionInfo-ext.R | 62 +++++++++++++++++++-------- sfsmisc-1.1-1/sfsmisc/R/zzz.R | 19 +------- sfsmisc-1.1-1/sfsmisc/TODO | 14 ++++-- sfsmisc-1.1-1/sfsmisc/inst/NEWS.Rd | 24 ++++++++++ sfsmisc-1.1-1/sfsmisc/man/Deprecated.Rd | 40 +++++------------ sfsmisc-1.1-1/sfsmisc/man/eaxis.Rd | 22 +++++++-- sfsmisc-1.1-1/sfsmisc/man/mult.fig.Rd | 26 +++++------ sfsmisc-1.1-1/sfsmisc/man/plotDS.Rd | 1 sfsmisc-1.1-1/sfsmisc/man/primes.Rd | 6 +- sfsmisc-1.1-1/sfsmisc/man/read.org.table.Rd | 7 +-- sfsmisc-1.1-1/sfsmisc/man/roundfixS.Rd | 4 - sfsmisc-1.1-1/sfsmisc/man/sessionInfoX.Rd | 19 +++++++- sfsmisc-1.1-1/sfsmisc/man/sfsmisc-defunct.Rd |only sfsmisc-1.1-1/sfsmisc/tests/misc.R | 13 +++++ 26 files changed, 251 insertions(+), 203 deletions(-)
Title: Multiple-Instance Logistic Regression with LASSO Penalty
Description: The multiple instance data set consists of many independent
subjects (called bags) and each subject is composed of several components
(called instances). The outcomes of such data set are binary or categorical responses,
and, we can only observe the subject-level outcomes. For example, in manufacturing
processes, a subject is labeled as "defective" if at least one of its own
components is defective, and otherwise, is labeled as "non-defective". The
'milr' package focuses on the predictive model for the multiple instance
data set with binary outcomes and performs the maximum likelihood estimation
with the Expectation-Maximization algorithm under the framework of logistic
regression. Moreover, the LASSO penalty is attached to the likelihood function
for simultaneous parameter estimation and variable selection.
Author: Ping-Yang Chen [aut, cre],
ChingChuan Chen [aut],
Chun-Hao Yang [aut],
Sheng-Mao Chang [aut]
Maintainer: Ping-Yang Chen <pychen.ping@gmail.com>
Diff between milr versions 0.2.0 dated 2017-01-10 and 0.3.0 dated 2017-06-08
milr-0.2.0/milr/src/Makevars.win |only milr-0.3.0/milr/DESCRIPTION | 49 ++++---- milr-0.3.0/milr/LICENSE | 4 milr-0.3.0/milr/MD5 | 60 ++++++---- milr-0.3.0/milr/NAMESPACE | 7 - milr-0.3.0/milr/R/DGP.R | 78 +++++++------ milr-0.3.0/milr/R/RcppExports.R | 68 +++++++---- milr-0.3.0/milr/R/milr-package.R | 56 ++++----- milr-0.3.0/milr/R/milr.R | 188 +++++++++++++++++---------------- milr-0.3.0/milr/R/softmax.R | 50 ++++---- milr-0.3.0/milr/build |only milr-0.3.0/milr/inst |only milr-0.3.0/milr/man/DGP.Rd | 53 ++++----- milr-0.3.0/milr/man/fitted.milr.Rd | 1 milr-0.3.0/milr/man/fitted.softmax.Rd | 1 milr-0.3.0/milr/man/logit.Rd | 42 +++---- milr-0.3.0/milr/man/milr-package.Rd | 49 ++++---- milr-0.3.0/milr/man/milr.Rd | 31 +++-- milr-0.3.0/milr/man/predict.milr.Rd | 1 milr-0.3.0/milr/man/predict.softmax.Rd | 1 milr-0.3.0/milr/man/softmax.Rd | 7 - milr-0.3.0/milr/src/Makevars | 1 milr-0.3.0/milr/src/RcppExports.cpp | 70 +++++++++++- milr-0.3.0/milr/src/common.cpp |only milr-0.3.0/milr/src/common.h |only milr-0.3.0/milr/src/getLogLikMilr.cpp |only milr-0.3.0/milr/src/getMilrProb.cpp |only milr-0.3.0/milr/src/getSoftmaxBag.cpp |only milr-0.3.0/milr/src/milr.cpp | 137 ++++++++---------------- milr-0.3.0/milr/src/softmaxlogL.cpp |only milr-0.3.0/milr/tests |only milr-0.3.0/milr/vignettes |only 32 files changed, 507 insertions(+), 447 deletions(-)
Title: Multi-Scale Motions Separation with Kolmogorov-Zurbenko
Periodogram Signals
Description: Separation of wave motions in different scales and directions based on
Kolmogorov-Zurbenko Periodograms and Kolmogorov-Zurbenko Fourier Transform.
Author: Ming Luo <ml226662@gmail.com> and Igor Zurbenko <IZurbenko@albany.edu>
Maintainer: Ming Luo <ml226662@gmail.com>
Diff between kzfs versions 1.0.1.5 dated 2016-09-23 and 1.5.0.1 dated 2017-06-08
kzfs-1.0.1.5/kzfs/man/kz.ft.Rd |only kzfs-1.0.1.5/kzfs/man/kz.rc2.Rd |only kzfs-1.0.1.5/kzfs/man/kzpdr.demo.Rd |only kzfs-1.5.0.1/kzfs/DESCRIPTION | 10 kzfs-1.5.0.1/kzfs/MD5 | 55 ++- kzfs-1.5.0.1/kzfs/NAMESPACE | 9 kzfs-1.5.0.1/kzfs/R/drsp.R | 53 ++- kzfs-1.5.0.1/kzfs/R/drsub.R | 17 - kzfs-1.5.0.1/kzfs/R/eval.R | 58 ++-- kzfs-1.5.0.1/kzfs/R/gtwv.R | 489 ++++++++++++++++++++++++++--------- kzfs-1.5.0.1/kzfs/R/kz.ft.R | 262 ++++++++++++------ kzfs-1.5.0.1/kzfs/R/kzfs.R | 95 ++++-- kzfs-1.5.0.1/kzfs/R/kzmd.R | 14 - kzfs-1.5.0.1/kzfs/R/kzp2.R | 195 +++++++++---- kzfs-1.5.0.1/kzfs/R/opt.kz.R |only kzfs-1.5.0.1/kzfs/R/smpg.R | 6 kzfs-1.5.0.1/kzfs/data/kzp2.QF.rda |only kzfs-1.5.0.1/kzfs/data/kzp2.demo.rda |only kzfs-1.5.0.1/kzfs/data/kzpdr.QF.rda |only kzfs-1.5.0.1/kzfs/man/eval.Rd | 9 kzfs-1.5.0.1/kzfs/man/getwave.Rd | 100 ++++++- kzfs-1.5.0.1/kzfs/man/kzfs.Rd | 55 ++- kzfs-1.5.0.1/kzfs/man/kzft.Rd |only kzfs-1.5.0.1/kzfs/man/kzmd.Rd | 5 kzfs-1.5.0.1/kzfs/man/kzp2.QF.Rd |only kzfs-1.5.0.1/kzfs/man/kzp2.Rd | 23 - kzfs-1.5.0.1/kzfs/man/kzpdr.QF.Rd |only kzfs-1.5.0.1/kzfs/man/kzpdr.Rd | 3 kzfs-1.5.0.1/kzfs/man/kzrc2.Rd |only kzfs-1.5.0.1/kzfs/man/opt.kz.Rd |only kzfs-1.5.0.1/kzfs/man/smpg.Rd | 3 kzfs-1.5.0.1/kzfs/man/spikes.Rd | 1 kzfs-1.5.0.1/kzfs/man/tolerance.Rd | 1 kzfs-1.5.0.1/kzfs/man/valid.Rd | 1 kzfs-1.5.0.1/kzfs/src/kzfs_init.c |only 35 files changed, 1015 insertions(+), 449 deletions(-)
Title: A Universal Non-Uniform Random Number Generator
Description: A universal non-uniform random number generator
for quite arbitrary distributions with piecewise twice
differentiable densities.
Author: Josef Leydold, Carsten Botts and Wolfgang H\"ormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Tinflex versions 1.1 dated 2015-07-17 and 1.2 dated 2017-06-08
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ NAMESPACE | 3 ++- NEWS | 6 ++++++ R/sample.R | 2 +- R/setup.R | 2 +- man/Tinflex-package.Rd | 4 ++-- src/init.c |only 8 files changed, 24 insertions(+), 16 deletions(-)
Title: El Nino/Southern Oscillation (ENSO) Index
Description: Downloads Southern Oscillation Index from <https://www.ncdc.noaa.gov/teleconnections/enso/indicators/soi/> and Oceanic Nino Index data from <http://www.cpc.ncep.noaa.gov/products/analysis_monitoring/ensostuff/detrend.nino34.ascii.txt>.
Author: Sam Albers [aut, cre]
Maintainer: Sam Albers <sam.albers@gmail.com>
Diff between rsoi versions 0.2.2 dated 2017-05-31 and 0.2.3 dated 2017-06-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- data/enso.rda |binary tests/testthat/test_download_soi.R | 17 ++--------------- 4 files changed, 8 insertions(+), 21 deletions(-)
Title: Analyzing Archival Tagging Data
Description: A set of functions to generate, access and analyze standard data products from archival tagging data.
Author: Robert Bauer
Maintainer: Robert Bauer <robert.bauer@ird.fr>
Diff between RchivalTag versions 0.0.4 dated 2017-04-25 and 0.0.5 dated 2017-06-08
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/hidden_functions.r | 22 ++++++++++++++++++++++ R/read_histos.r | 7 +++++-- R/ts2histos.r | 4 +++- inst/doc/RchivalTag.pdf |binary man/read_histos.Rd | 36 +++++++++++++++++++++++++++++++++--- man/ts2histos.Rd | 25 ++++++++++++++++++++++++- 9 files changed, 102 insertions(+), 19 deletions(-)
Title: List with Defaults
Description: Provides a function that, as an alternative to base::list, allows
default values to be inherited from another list.
Author: Russell S. Pierce
Maintainer: Russell S. Pierce <russell.s.pierce@gmail.com>
Diff between listWithDefaults versions 1.1.0 dated 2017-01-06 and 1.2.0 dated 2017-06-08
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/listWithDefaults.R | 6 +++++- README.md | 4 ++-- man/listWithDefaults.Rd | 4 ++-- tests/testthat/test.listWithDefault.R | 1 + 7 files changed, 25 insertions(+), 16 deletions(-)
More information about listWithDefaults at CRAN
Permanent link
Title: Computation of Parameters Used in Preliminary Assessment of
Conservation Status
Description: Multi-species estimation of geographical range parameters
for preliminary assessment of conservation status following Criterion B of the
International Union for Conservation of Nature (IUCN,
see <http://www.iucnredlist.org>).
Author: Gilles Dauby
Maintainer: Gilles Dauby <gildauby@gmail.com>
Diff between ConR versions 1.1 dated 2016-11-28 and 1.2 dated 2017-06-08
ConR-1.1/ConR/data/Malagasy_amphibian.RData |only ConR-1.1/ConR/man/Malagasy_amphibian.Rd |only ConR-1.2/ConR/DESCRIPTION | 10 ConR-1.2/ConR/MD5 | 58 - ConR-1.2/ConR/NAMESPACE | 8 ConR-1.2/ConR/R/IUCNeval.functionv11.R | 487 +++++----- ConR-1.2/ConR/build/partial.rdb |binary ConR-1.2/ConR/build/vignette.rds |binary ConR-1.2/ConR/data/Malagasy.amphibian.RData |only ConR-1.2/ConR/data/datalist | 2 ConR-1.2/ConR/inst/doc/my-vignette.R | 16 ConR-1.2/ConR/inst/doc/my-vignette.Rmd | 36 ConR-1.2/ConR/inst/doc/my-vignette.html | 181 +-- ConR-1.2/ConR/man/EOO.computing.Rd | 15 ConR-1.2/ConR/man/IUCN.eval.Rd | 29 ConR-1.2/ConR/man/Malagasy.amphibian.Rd |only ConR-1.2/ConR/vignettes/IUCN__results_map/IUCN_Anodonthyla_moramora.png |binary ConR-1.2/ConR/vignettes/IUCN__results_map/IUCN_Berlinia_bruneelii.png |binary ConR-1.2/ConR/vignettes/IUCN__results_map/IUCN_Oncocalamus_mannii.png |binary ConR-1.2/ConR/vignettes/IUCN__results_map/IUCN_Platycoryne_guingangae.png |binary ConR-1.2/ConR/vignettes/IUCN__results_map/IUCN_Psychotria_minuta.png |binary ConR-1.2/ConR/vignettes/IUCN__results_map/IUCN_species_1.png |binary ConR-1.2/ConR/vignettes/IUCN__results_map/number_threatened_sp.png |binary ConR-1.2/ConR/vignettes/IUCN__results_map/proportion_threatened_sp.png |binary ConR-1.2/ConR/vignettes/IUCN__results_map/species_richness.png |binary ConR-1.2/ConR/vignettes/loc1_results_map/loc1Anodonthyla_moramora.png |binary ConR-1.2/ConR/vignettes/loc2_results_map/loc2Anodonthyla_moramora.png |binary ConR-1.2/ConR/vignettes/loc3_results_map/loc3Anodonthyla_moramora.png |binary ConR-1.2/ConR/vignettes/my-vignette.Rmd | 36 ConR-1.2/ConR/vignettes/protec2_results_map/protec2Anodonthyla_moramora.png |binary ConR-1.2/ConR/vignettes/protec_results_map/protecAnodonthyla_moramora.png |binary ConR-1.2/ConR/vignettes/slide_results_map/slideAnodonthyla_moramora.png |binary 32 files changed, 497 insertions(+), 381 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: State space modelling is an efficient and flexible method for
statistical inference of a broad class of time series and other data. KFAS
includes fast functions for Kalman filtering, smoothing, forecasting, and
simulation of multivariate exponential family state space models, with
observations from Gaussian, Poisson, binomial, negative binomial, and gamma
distributions.
Author: Jouni Helske <jouni.helske@iki.fi>
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between KFAS versions 1.2.6 dated 2017-04-18 and 1.2.8 dated 2017-06-08
ChangeLog | 9 DESCRIPTION | 14 MD5 | 80 ++--- R/KFAS-package.R | 20 + R/logLik.SSModel.R | 2 build/vignette.rds |binary inst/CITATION | 39 +- inst/doc/KFAS.Rnw | 8 inst/doc/KFAS.pdf |binary man/Extract.SSModel.Rd | 3 man/GlobalTemp.Rd | 1 man/KFAS-defunct.Rd | 8 man/KFAS.Rd | 17 + man/KFS.Rd | 1 man/SSModel.Rd | 4 man/alcohol.Rd | 1 man/approxSSM.Rd | 1 man/artransform.Rd | 1 man/boat.Rd | 1 man/checkModel.Rd | 1 man/coef.SSModel.Rd | 8 man/fitSSM.Rd | 1 man/fitted.SSModel.Rd | 2 man/hatvalues.KFS.Rd | 1 man/importanceSSM.Rd | 1 man/ldl.Rd | 1 man/logLik.SSModel.Rd | 3 man/mvInnovations.Rd | 1 man/plot.SSModel.Rd | 1 man/predict.SSModel.Rd | 3 man/print.KFS.Rd | 1 man/print.SSModel.Rd | 1 man/rename_states.Rd | 1 man/residuals.KFS.Rd | 1 man/rstandard.KFS.Rd | 1 man/sexratio.Rd | 1 man/signal.Rd | 1 man/simulateSSM.Rd | 1 man/transformSSM.Rd | 1 vignettes/KFAS.Rnw | 8 vignettes/KFAS.bib | 706 +++++++++++++++++++++++++------------------------ 41 files changed, 499 insertions(+), 457 deletions(-)
Title: Loading Facebook and Instagram Advertising Data from
'Smartly.io'
Description: Aims at loading Facebook and Instagram advertising data from
'Smartly.io' into R. 'Smartly.io' is an online advertising service that enables
advertisers to display commercial ads on social media networks (see <http://www.smartly.io/> for more information).
The package offers an interface to query the 'Smartly.io' API and loads data directly into R for further data processing and data analysis.
Author: Johannes Burkhardt <johannes.burkhardt@gmail.com>
Maintainer: Johannes Burkhardt <johannes.burkhardt@gmail.com>
Diff between RSmartlyIO versions 0.1.1 dated 2017-01-09 and 0.1.2 dated 2017-06-08
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- NEWS |only R/getSmartlyData.R | 4 ++-- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Diff between mvMORPH versions 1.0.8 dated 2016-10-25 and 1.0.9 dated 2017-06-08
DESCRIPTION | 8 MD5 | 51 NAMESPACE | 6 NEWS.md |only R/estim.r | 28 R/fun.r | 2389 ++++++++++++++++++++------------------- R/mvBM.r | 20 R/mvBMTS.r | 10 R/mvEB.r | 12 R/mvLLIK.r | 6 R/mvOU.r | 34 R/mvOUTS.r | 42 R/mvSHIFT.r | 24 R/mvSIM.r | 67 - R/pruning.r |only R/zzz.r | 2 README.md | 25 build/vignette.rds |binary inst/CITATION | 2 inst/doc/How_to_use_mvMORPH.R | 6 inst/doc/How_to_use_mvMORPH.Rmd | 6 inst/doc/How_to_use_mvMORPH.pdf |binary inst/doc/tutorial_mvMORPH.pdf |binary man/estim.Rd | 2 man/mvMORPH-package.Rd | 2 man/pruning.Rd |only src/mvMORPH_init.c |only src/sqrtMat.c |only vignettes/How_to_use_mvMORPH.Rmd | 6 29 files changed, 1457 insertions(+), 1291 deletions(-)
Title: The Moving Epidemics Method Shiny Web Application
Description: Web application created in the Shiny framework for the 'mem' R package.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between memapp versions 2.0 dated 2017-06-06 and 2.1 dated 2017-06-08
DESCRIPTION | 20 +++--- MD5 | 8 +- README.md | 10 --- inst/shinyapp/server.R | 149 +++++++++++++++++++++++++++++++++++++------------ inst/shinyapp/ui.R | 115 ++++++++----------------------------- 5 files changed, 155 insertions(+), 147 deletions(-)
Title: The Moving Epidemics Method R Package
Description: Tools to model influenza epidemics and to monitor influenza surveillance.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between mem versions 2.6 dated 2017-06-06 and 2.7 dated 2017-06-08
DESCRIPTION | 18 ++++--- MD5 | 8 +-- NAMESPACE | 3 - R/memsurveillance.animated.R | 100 ++++++++++++++++++++-------------------- man/memsurveillance.animated.Rd | 2 5 files changed, 67 insertions(+), 64 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 4.0.0 dated 2017-06-05 and 4.0.1 dated 2017-06-08
DESCRIPTION | 8 MD5 | 35 R/compare-clusterings.R | 2034 +++++++++++++++++------------------ R/dtw-lb.R | 91 + R/tsclust.R | 1604 +++++++++++++-------------- inst/NEWS.Rd | 7 inst/doc/dtwclust.pdf |binary inst/include/dtwclust.hpp | 8 man/compare_clusterings.Rd | 4 man/dtw_lb.Rd | 2 src/dtw-lb.cpp |only src/dtwclustpp.h | 2 src/init.cpp | 2 src/lbs.cpp | 4 tests/testthat/acceptance/dtwb.R | 162 +- tests/testthat/acceptance/gak.R | 110 - tests/testthat/acceptance/lbs.R | 153 +- tests/testthat/system/hierarchical.R | 2 tests/testthat/unit/distances.R | 333 ++--- 19 files changed, 2302 insertions(+), 2259 deletions(-)
Title: Implementation of Adaptive or Non-Adaptive Differentiable Lasso
and SCAD Penalties in Linear Models
Description: An implementation of the differentiable lasso (dlasso) and SCAD (dSCAD) using iterative ridge algorithm. This package allows selecting the tuning parameter by AIC, BIC, GIC and GIC.
Author: Hamed Haseli Mashhadi <hamedhaseli@gmail.com>
Maintainer: Hamed Haseli Mashhadi <hamedhaseli@gmail.com>
Diff between DLASSO versions 2.0.1 dated 2017-06-02 and 2.0.2 dated 2017-06-08
DESCRIPTION | 6 ++-- MD5 | 8 ++--- R/auxilary.R | 4 +- R/main.R | 82 +++++++++++++++++++--------------------------------------- man/dlasso.Rd | 12 ++++---- 5 files changed, 42 insertions(+), 70 deletions(-)
Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO
Network
Description: Computes the Weighted Topological Overlap (wTO) networks. Once a data.frame containing the count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction.It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a Consensus network, based on multiple wTOs. Also includes a visualization tool for the final network.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy@bioinf.uni-leipzig.de>
Diff between wTO versions 1.1.0 dated 2017-05-29 and 1.2.0 dated 2017-06-08
DESCRIPTION | 6 MD5 | 42 +-- NAMESPACE | 86 +++--- R/Cut.off2.R | 140 +++++------ R/ExampledfExpression.R | 2 R/NetVis.R | 329 +++++++++++++------------- R/wTO.Complete.R | 556 +++++++++++++++++++++++---------------------- R/wTO.Consensus.R | 22 - R/wTO.R | 58 ++-- R/wTO.aux.each.R | 115 ++++----- R/wTO.in.line.R | 7 man/Correlation.Overlap.Rd | 46 +-- man/Cut.off.Rd | 40 +-- man/ExampleGRF.Rd | 28 +- man/ExampledfExpression.Rd | 28 +- man/NetVis.Rd | 124 +++++----- man/sample_ind.Rd | 34 +- man/wTO.Complete.Rd | 122 ++++----- man/wTO.Consensus.Rd | 60 ++-- man/wTO.Rd | 46 +-- man/wTO.aux.each.Rd | 46 +-- man/wTO.in.line.Rd | 34 +- 22 files changed, 1015 insertions(+), 956 deletions(-)
Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test
code with earlier versions of those same objects. If objects are unchanged
the tests pass, otherwise execution stops with error details. If in
interactive mode, tests can be reviewed through the provided interactive
environment.
Author: Brodie Gaslam [aut, cre]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between unitizer versions 1.4.2 dated 2017-04-09 and 1.4.3 dated 2017-06-08
unitizer-1.4.2/unitizer/tests/testthat/testthat.rename.R |only unitizer-1.4.2/unitizer/tests/testthat/testthat.repairenvs.R |only unitizer-1.4.2/unitizer/tests/testthat/testthat.unitize.R |only unitizer-1.4.2/unitizer/tests/testthat/testthat.unitize2.R |only unitizer-1.4.3/unitizer/DESCRIPTION | 6 unitizer-1.4.3/unitizer/MD5 | 100 ++-- unitizer-1.4.3/unitizer/NEWS.md | 12 unitizer-1.4.3/unitizer/R/asciiml.R | 13 unitizer-1.4.3/unitizer/R/browse.R | 47 +- unitizer-1.4.3/unitizer/R/browse.struct.R | 9 unitizer-1.4.3/unitizer/R/capture.R | 2 unitizer-1.4.3/unitizer/R/conditions.R | 7 unitizer-1.4.3/unitizer/R/demo.R | 2 unitizer-1.4.3/unitizer/R/deparse.R | 18 unitizer-1.4.3/unitizer/R/exec.R | 8 unitizer-1.4.3/unitizer/R/get.R | 19 unitizer-1.4.3/unitizer/R/global.R | 11 unitizer-1.4.3/unitizer/R/heal.R | 10 unitizer-1.4.3/unitizer/R/item.R | 4 unitizer-1.4.3/unitizer/R/item.sub.R | 3 unitizer-1.4.3/unitizer/R/load.R | 25 - unitizer-1.4.3/unitizer/R/ls.R | 4 unitizer-1.4.3/unitizer/R/misc.R | 18 unitizer-1.4.3/unitizer/R/parse.R | 225 +++++++--- unitizer-1.4.3/unitizer/R/prompt.R | 14 unitizer-1.4.3/unitizer/R/rename.R | 4 unitizer-1.4.3/unitizer/R/search.R | 57 +- unitizer-1.4.3/unitizer/R/shims.R | 2 unitizer-1.4.3/unitizer/R/size.R | 2 unitizer-1.4.3/unitizer/R/state.R | 4 unitizer-1.4.3/unitizer/R/test.R | 4 unitizer-1.4.3/unitizer/R/unitize.R | 3 unitizer-1.4.3/unitizer/R/unitize.core.R | 168 ++++--- unitizer-1.4.3/unitizer/R/unitizer.R | 27 + unitizer-1.4.3/unitizer/R/unitizer.add.R | 19 unitizer-1.4.3/unitizer/R/upgrade.R | 11 unitizer-1.4.3/unitizer/README.md | 34 - unitizer-1.4.3/unitizer/build/vignette.rds |binary unitizer-1.4.3/unitizer/inst/doc/unitizer.html | 4 unitizer-1.4.3/unitizer/inst/doc/unitizer_index.html | 4 unitizer-1.4.3/unitizer/inst/doc/unitizer_interactive_env.html | 4 unitizer-1.4.3/unitizer/inst/doc/unitizer_miscellaneous.html | 4 unitizer-1.4.3/unitizer/inst/doc/unitizer_reproducible_tests.html | 4 unitizer-1.4.3/unitizer/inst/doc/unitizer_tests.html | 4 unitizer-1.4.3/unitizer/tests/testthat/helper/runtt.R | 4 unitizer-1.4.3/unitizer/tests/testthat/testthat.get.R | 68 ++- unitizer-1.4.3/unitizer/tests/testthat/testthat.parse.R | 11 unitizer-1.4.3/unitizer/tests/testthat/testthat.prompt.R | 4 unitizer-1.4.3/unitizer/tests/testthat/testthat.rrename.R |only unitizer-1.4.3/unitizer/tests/testthat/testthat.rrepairenvs.R |only unitizer-1.4.3/unitizer/tests/testthat/testthat.search.R | 9 unitizer-1.4.3/unitizer/tests/testthat/testthat.text.R | 9 unitizer-1.4.3/unitizer/tests/testthat/testthat.upgrade.R | 25 + unitizer-1.4.3/unitizer/tests/testthat/testthat.utz1.R |only unitizer-1.4.3/unitizer/tests/testthat/testthat.utz2.R |only 55 files changed, 732 insertions(+), 314 deletions(-)
Title: Accesses Air Quality Data from the Open Data Platform OpenAQ
Description: Allows access to air quality data from the API of the OpenAQ
platform <https://docs.openaq.org/>, with the different services the API offers
(getting measurements for a given query, getting latest measurements, getting
lists of available countries/cities/locations).
Author: Maëlle Salmon [aut, cre],
Andrew MacDonald [ctb] (Andrew MacDonald reviewed the package for
rOpenSci, see https://github.com/ropensci/onboarding/issues/24),
Andy Teucher [ctb] (Andy Teucher reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/24),
Mikayla Murphy [ctb]
Maintainer: Maëlle Salmon <maelle.salmon@yahoo.se>
Diff between ropenaq versions 0.2.0 dated 2017-04-28 and 0.2.1 dated 2017-06-08
DESCRIPTION | 6 +- MD5 | 22 +++++----- NEWS.md | 6 ++ R/locations.R | 2 inst/doc/Ropenaq-vignette.Rmd | 2 inst/doc/Ropenaq-vignette.html | 6 +- inst/doc/graphics_of_pm_25_concentrations_in_several_countries.html | 6 +- inst/doc/mapping_openaq_monitors.html | 6 +- inst/doc/using_openair_package_with_openaq_data.html | 10 ++-- man/aq_locations.Rd | 2 tests/testthat/test-buildQueries.R | 1 vignettes/Ropenaq-vignette.Rmd | 1 12 files changed, 38 insertions(+), 32 deletions(-)
Title: Radiomics Image Analysis Toolbox for Grayscale Images
Description: Radiomics image analysis toolbox for grayscale 2D and 3D images. RIA calculates first-order,
gray level co-occurrence matrix, gray level run length matrix and geometry-based statistics.
Almost all calculations are done using vectorized formulas to optimize run speeds. Calculation
of several thousands of parameters only takes minutes on a single core of a conventional PC.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <marton.kolossvary@cirg.hu>
Diff between RIA versions 1.0.1 dated 2017-05-04 and 1.1.0 dated 2017-06-08
DESCRIPTION | 12 +++--- MD5 | 51 ++++++++++++++------------ R/ZZZ.R | 3 + R/check_data_in.R | 68 +++++++++++++++++++---------------- R/dichotomize.R | 11 +++-- R/first_order.R | 30 +++++++++++++-- R/geometry.R | 102 ++++++++++++++++++++++++++++++----------------------- R/glcm.R | 47 +++++++++++++++++++++--- R/glcm_stat.R | 26 +++++++++++-- R/glcm_stat_plus.R | 2 - R/glrlm.R | 43 +++++++++++++++++++--- R/glrlm_stat.R | 27 ++++++++++++-- R/load_dicom.R | 18 ++++----- build |only inst/doc |only man/DICOM_codes.Rd | 1 man/NRS.Rd | 1 man/Non_NRS.Rd | 1 man/dichotomize.Rd | 5 +- man/first_order.Rd | 10 +++-- man/geometry.Rd | 37 ++++++++----------- man/glcm.Rd | 9 +++- man/glcm_stat.Rd | 8 +++- man/glrlm.Rd | 9 +++- man/glrlm_stat.Rd | 8 +++- man/load_dicom.Rd | 1 vignettes |only 27 files changed, 354 insertions(+), 176 deletions(-)
Title: Dynamic Hazard Models using State Space Models
Description: Contains functions that lets you fit dynamic hazard models with binary
outcomes using state space models. The methods are originally described in
Fahrmeir (1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir (1994)
<doi:10.1093/biomet/81.2.317>. The functions also provide an extension hereof where the
Extended Kalman filter is replaced by an Unscented Kalman filter. Models are
fitted with the regular coxph() like formula.
Author: Benjamin Christoffersen [cre, aut],
Alan Miller [cph],
Anthony Williams [cph],
Boost developers [cph],
R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between dynamichazard versions 0.3.0 dated 2017-06-07 and 0.3.1 dated 2017-06-08
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- inst/doc/Bootstrap_illustration.pdf |binary inst/doc/Comparing_methods_for_logistic_models.pdf |binary inst/doc/Diagnostics.pdf |binary inst/doc/Sim_study_with_logit.pdf |binary inst/doc/ddhazard.pdf |binary src/ddhazard_UKF_solver.cpp | 7 ++++++- 8 files changed, 16 insertions(+), 11 deletions(-)
Title: Building Augmented Data to Run Multi-State Models with 'msm'
Package
Description: A fast and general method for restructuring classical longitudinal data into
augmented ones. The reason for this is to facilitate the modeling of longitudinal data under
a multi-state framework using the 'msm' package.
Author: Francesco Grossetti [aut, cre]
Maintainer: Francesco Grossetti <francesco.grossetti@unibocconi.it>
Diff between msmtools versions 1.2 dated 2016-06-21 and 1.3 dated 2017-06-08
msmtools-1.2/msmtools/inst/doc/msmtools.pdf |only msmtools-1.3/msmtools/DESCRIPTION | 14 msmtools-1.3/msmtools/MD5 | 38 - msmtools-1.3/msmtools/NAMESPACE | 1 msmtools-1.3/msmtools/NEWS.md | 130 ++++- msmtools-1.3/msmtools/R/augment.R | 558 +++++++++++++------------ msmtools-1.3/msmtools/R/msmtools.R | 3 msmtools-1.3/msmtools/R/polish.R |only msmtools-1.3/msmtools/R/prevplot.R | 192 +++++--- msmtools-1.3/msmtools/R/survplot.R | 249 ++++++----- msmtools-1.3/msmtools/README.md | 69 ++- msmtools-1.3/msmtools/build/vignette.rds |binary msmtools-1.3/msmtools/inst/doc/msmtools.Rmd | 539 +++++++++++++----------- msmtools-1.3/msmtools/inst/doc/msmtools.html |only msmtools-1.3/msmtools/man/augment.Rd | 267 ++++++----- msmtools-1.3/msmtools/man/hosp.Rd | 1 msmtools-1.3/msmtools/man/msmtools.Rd | 4 msmtools-1.3/msmtools/man/polish.Rd |only msmtools-1.3/msmtools/man/prevplot.Rd | 126 +++-- msmtools-1.3/msmtools/man/survplot.Rd | 240 +++++----- msmtools-1.3/msmtools/vignettes/msmtools.Rmd | 539 +++++++++++++----------- msmtools-1.3/msmtools/vignettes/references.bib | 14 22 files changed, 1702 insertions(+), 1282 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-07 0.9.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-06 0.0.1
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg.
Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 3.1.1 dated 2016-07-27 and 3.2.0 dated 2017-06-08
DESCRIPTION | 8 +-- MD5 | 71 ++++++++++++++++++----------------- NAMESPACE | 4 + R/db.r | 103 +++++++++++++++++++++++++++------------------------ R/iso.r | 6 +- R/map.r | 36 ++++++++++++++--- R/mapclip.r |only R/misc.r | 11 ++--- R/polygon.r | 15 +++---- R/read.sp.R | 16 ++++--- R/smooth.r | 6 +- README.md | 8 ++- configure | 32 ++++++++++----- configure.ac | 2 data/county.fips.rda |binary data/state.fips.rda |binary data/us.cities.rda |binary inst/NEWS.Rd | 23 +++++++++++ inst/README.md | 2 man/county.fips.Rd | 2 man/identify.map.Rd | 2 man/internal2.Rd | 4 + man/map.Rd | 25 ++++++++---- man/map.cities.Rd | 4 - man/map.where.Rd | 7 +-- man/ozone.Rd | 15 ++++++- man/state.fips.Rd | 4 - man/world.Rd | 3 + man/world2.Rd | 18 ++++---- src/Makefile.in | 56 ++++++++++++++------------- src/Makefile.win | 62 +++++++++++++----------------- src/init.c |only src/italy.name | 16 +++---- src/map.h | 14 ------ src/mapclip.c |only src/mapget.c | 49 +++++++++++++----------- src/thin.c | 2 src/world.name | 6 +- 38 files changed, 365 insertions(+), 267 deletions(-)
Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P
Minka, transition to Plan 9 codebase by Roger Bivand.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between mapproj versions 1.2-4 dated 2015-08-03 and 1.2-5 dated 2017-06-08
DESCRIPTION | 8 - MD5 | 13 +- NAMESPACE | 2 R/mapproj.r | 240 +++++++++++++++++++++++++++--------------------------- man/mapproject.Rd | 2 src/cuts.c | 2 src/init.c |only src/lune.c | 2 8 files changed, 135 insertions(+), 134 deletions(-)
Title: Extension to 'ggplot2'
Description: The R package 'ggplot2' is a plotting system based on the grammar of graphics.
'GGally' extends 'ggplot2' by adding several functions
to reduce the complexity of combining geometric objects with transformed data.
Some of these functions include a pairwise plot matrix, a two group pairwise plot
matrix, a parallel coordinates plot, a survival plot, and several functions to
plot networks.
Author: Barret Schloerke [aut, cre] (author for ggpairs, ggduo, ggnostic, ggts,
ggfacet, and ggally_*. Contributor for all functions.),
Jason Crowley [aut] (ggparcoord),
Di Cook [aut, ths] (ggscatmat, gglyph),
Heike Hofmann [ths],
Hadley Wickham [ths],
Francois Briatte [aut] (ggcorr, ggnet, ggnet2),
Moritz Marbach [aut] (ggnet, ggnet2),
Edwin Thoen [aut] (ggsurv),
Amos Elberg [aut] (ggnetworkmap),
Joseph Larmarange [aut] (ggcoef)
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between GGally versions 1.3.0 dated 2016-11-13 and 1.3.1 dated 2017-06-08
DESCRIPTION | 8 - MD5 | 208 ++++++++++++++++++------------------- NAMESPACE | 1 NEWS.md | 28 ++++ R/data-psychademic.R |only R/gg-plots.R | 6 - R/ggmatrix.R | 3 R/ggmatrix_gtable.R | 8 - R/ggmatrix_gtable_helpers.R | 8 - R/ggmatrix_legend.R | 2 R/ggmatrix_print.R | 2 R/ggnostic.R | 18 +-- R/ggpairs.R | 147 ++++++++++---------------- R/ggpairs_add.R | 26 ++++ R/ggpairs_getput.R | 2 R/ggpairs_internal_plots.R | 10 - R/ggsurv.R | 4 build/vignette.rds |binary data/psychademic.rda |only inst/doc/docs.Rmd | 52 ++++----- man/add_and_overwrite_aes.Rd | 1 man/add_ref_boxes.Rd | 1 man/add_ref_lines.Rd | 1 man/australia_PISA2012.Rd | 1 man/brew_colors.Rd | 1 man/broomify.Rd | 1 man/column_is_character.Rd | 1 man/find_plot_type.Rd | 1 man/flea.Rd | 1 man/fn_switch.Rd | 3 man/getPlot.Rd | 5 man/get_x_axis_labels.Rd | 1 man/gg-add.Rd | 5 man/ggally_barDiag.Rd | 3 man/ggally_blank.Rd | 1 man/ggally_box.Rd | 1 man/ggally_cor.Rd | 3 man/ggally_density.Rd | 1 man/ggally_densityDiag.Rd | 1 man/ggally_denstrip.Rd | 1 man/ggally_diagAxis.Rd | 1 man/ggally_dot.Rd | 1 man/ggally_dot_and_box.Rd | 1 man/ggally_facetbar.Rd | 3 man/ggally_facetdensity.Rd | 1 man/ggally_facetdensitystrip.Rd | 1 man/ggally_facethist.Rd | 1 man/ggally_na.Rd | 1 man/ggally_nostic_cooksd.Rd | 1 man/ggally_nostic_hat.Rd | 1 man/ggally_nostic_line.Rd | 3 man/ggally_nostic_resid.Rd | 3 man/ggally_nostic_se_fit.Rd | 1 man/ggally_nostic_sigma.Rd | 1 man/ggally_nostic_std_resid.Rd | 1 man/ggally_points.Rd | 1 man/ggally_ratio.Rd | 1 man/ggally_smooth.Rd | 3 man/ggally_text.Rd | 1 man/ggcoef.Rd | 1 man/ggcorr.Rd | 9 - man/ggduo.Rd | 140 +++++++++--------------- man/ggfacet.Rd | 1 man/gglegend.Rd | 3 man/ggmatrix.Rd | 8 - man/ggmatrix_gtable.Rd | 7 - man/ggnet.Rd | 9 - man/ggnet2.Rd | 9 - man/ggnetworkmap.Rd | 1 man/ggnostic.Rd | 10 - man/ggpairs.Rd | 19 +-- man/ggparcoord.Rd | 1 man/ggscatmat.Rd | 1 man/ggsurv.Rd | 1 man/ggts.Rd | 1 man/glyphplot.Rd | 3 man/glyphs.Rd | 1 man/grab_legend.Rd | 1 man/happy.Rd | 1 man/is_blank_plot.Rd | 1 man/is_date.Rd | 1 man/lowertriangle.Rd | 1 man/mapping_color_to_fill.Rd | 1 man/model_terms.Rd | 7 - man/nasa.Rd | 1 man/pigs.Rd | 1 man/plot_types.Rd | 1 man/plotting_data_type.Rd | 1 man/print.ggmatrix.Rd | 3 man/print_if_interactive.Rd | 1 man/psychademic.Rd |only man/putPlot.Rd | 3 man/require_pkgs.Rd | 1 man/rescale01.Rd | 4 man/scag_order.Rd | 1 man/scatmat.Rd | 1 man/singleClassOrder.Rd | 1 man/skewness.Rd | 1 man/str.ggmatrix.Rd | 1 man/twitter_spambots.Rd | 1 man/uppertriangle.Rd | 1 man/v1_ggmatrix_theme.Rd |only man/wrap.Rd | 9 - tests/testthat/test-ggmatrix_add.R | 26 ++++ tests/testthat/test-ggsurv.R | 9 - vignettes/docs.Rmd | 52 ++++----- vignettes/rd_index.yaml | 1 107 files changed, 444 insertions(+), 508 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Antigoni Kaliontzopoulou, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 3.0.3 dated 2016-09-09 and 3.0.4 dated 2017-06-08
geomorph-3.0.3/geomorph/R/coords.subset.R |only geomorph-3.0.4/geomorph/DESCRIPTION | 10 geomorph-3.0.4/geomorph/MD5 | 312 ++-- geomorph-3.0.4/geomorph/NAMESPACE | 1 geomorph-3.0.4/geomorph/NEWS | 27 geomorph-3.0.4/geomorph/R/advanced.procD.lm.r | 182 +- geomorph-3.0.4/geomorph/R/arrayspecs.r | 59 geomorph-3.0.4/geomorph/R/bilat.symmetry.r | 14 geomorph-3.0.4/geomorph/R/compare.evol.rates.r | 62 geomorph-3.0.4/geomorph/R/compare.multi.evol.rates.r | 18 geomorph-3.0.4/geomorph/R/compare.pls.r | 39 geomorph-3.0.4/geomorph/R/coords.subset.r |only geomorph-3.0.4/geomorph/R/define.modules.r | 2 geomorph-3.0.4/geomorph/R/define.sliders.r | 13 geomorph-3.0.4/geomorph/R/digit.curves.r | 44 geomorph-3.0.4/geomorph/R/digitize2d.r | 10 geomorph-3.0.4/geomorph/R/digitsurface.r | 1 geomorph-3.0.4/geomorph/R/estimate.missing.r | 2 geomorph-3.0.4/geomorph/R/findMeanSpec.r | 4 geomorph-3.0.4/geomorph/R/fixed.angle.r | 2 geomorph-3.0.4/geomorph/R/geomorph.support.code.r | 947 ++++++++----- geomorph-3.0.4/geomorph/R/geomorph.utils.r | 359 ++-- geomorph-3.0.4/geomorph/R/gpagen.r | 44 geomorph-3.0.4/geomorph/R/integration.test.r | 55 geomorph-3.0.4/geomorph/R/interlmkdist.r |only geomorph-3.0.4/geomorph/R/modularity.test.r | 8 geomorph-3.0.4/geomorph/R/morphol.disparity.r | 113 + geomorph-3.0.4/geomorph/R/nested.update.r | 61 geomorph-3.0.4/geomorph/R/phylo.integration.r | 45 geomorph-3.0.4/geomorph/R/plotAllSpecimens.r | 8 geomorph-3.0.4/geomorph/R/plotGMPhyloMorphoSpace.r | 15 geomorph-3.0.4/geomorph/R/plotOutliers.r | 2 geomorph-3.0.4/geomorph/R/plotRefToTarget.r | 14 geomorph-3.0.4/geomorph/R/plotTangentSpace.r | 25 geomorph-3.0.4/geomorph/R/procD.allometry.r | 151 +- geomorph-3.0.4/geomorph/R/procD.lm.r | 209 ++ geomorph-3.0.4/geomorph/R/procD.pgls.r | 197 ++ geomorph-3.0.4/geomorph/R/read.morphologika.r | 85 - geomorph-3.0.4/geomorph/R/read.ply.r | 2 geomorph-3.0.4/geomorph/R/readland.nts.r | 34 geomorph-3.0.4/geomorph/R/readland.tps.r | 37 geomorph-3.0.4/geomorph/R/readmulti.nts.r | 33 geomorph-3.0.4/geomorph/R/shape.predictor.r | 20 geomorph-3.0.4/geomorph/R/trajectory.analysis.r | 58 geomorph-3.0.4/geomorph/R/two.b.pls.r | 52 geomorph-3.0.4/geomorph/R/two.d.array.r | 23 geomorph-3.0.4/geomorph/R/warpRefMesh.r | 1 geomorph-3.0.4/geomorph/R/writeland.tps.r | 4 geomorph-3.0.4/geomorph/README.md | 11 geomorph-3.0.4/geomorph/man/advanced.procD.lm.Rd | 58 geomorph-3.0.4/geomorph/man/arrayspecs.Rd | 22 geomorph-3.0.4/geomorph/man/bilat.symmetry.Rd | 11 geomorph-3.0.4/geomorph/man/buildtemplate.Rd | 7 geomorph-3.0.4/geomorph/man/compare.evol.rates.Rd | 58 geomorph-3.0.4/geomorph/man/compare.modular.partitions.Rd | 1 geomorph-3.0.4/geomorph/man/compare.multi.evol.rates.Rd | 19 geomorph-3.0.4/geomorph/man/compare.pls.Rd | 45 geomorph-3.0.4/geomorph/man/coords.subset.Rd | 9 geomorph-3.0.4/geomorph/man/define.links.Rd | 7 geomorph-3.0.4/geomorph/man/define.modules.Rd | 9 geomorph-3.0.4/geomorph/man/define.sliders.Rd | 12 geomorph-3.0.4/geomorph/man/digit.curves.Rd | 23 geomorph-3.0.4/geomorph/man/digit.fixed.Rd | 7 geomorph-3.0.4/geomorph/man/digitize2d.Rd | 3 geomorph-3.0.4/geomorph/man/digitsurface.Rd | 7 geomorph-3.0.4/geomorph/man/editTemplate.Rd | 1 geomorph-3.0.4/geomorph/man/estimate.missing.Rd | 7 geomorph-3.0.4/geomorph/man/findMeanSpec.Rd | 9 geomorph-3.0.4/geomorph/man/fixed.angle.Rd | 9 geomorph-3.0.4/geomorph/man/geomorph-package.Rd | 6 geomorph-3.0.4/geomorph/man/geomorph.data.frame.Rd | 1 geomorph-3.0.4/geomorph/man/globalIntegration.Rd | 7 geomorph-3.0.4/geomorph/man/gpagen.Rd | 9 geomorph-3.0.4/geomorph/man/gridPar.Rd | 7 geomorph-3.0.4/geomorph/man/hummingbirds.Rd | 7 geomorph-3.0.4/geomorph/man/integration.test.Rd | 49 geomorph-3.0.4/geomorph/man/interlmkdist.Rd |only geomorph-3.0.4/geomorph/man/larvalTails.Rd | 7 geomorph-3.0.4/geomorph/man/modularity.test.Rd | 7 geomorph-3.0.4/geomorph/man/morphol.disparity.Rd | 44 geomorph-3.0.4/geomorph/man/morphol.integr.Rd | 1 geomorph-3.0.4/geomorph/man/mosquito.Rd | 1 geomorph-3.0.4/geomorph/man/motionpaths.Rd | 7 geomorph-3.0.4/geomorph/man/mshape.Rd | 9 geomorph-3.0.4/geomorph/man/nested.update.Rd | 27 geomorph-3.0.4/geomorph/man/phylo.integration.Rd | 39 geomorph-3.0.4/geomorph/man/phylo.modularity.Rd | 7 geomorph-3.0.4/geomorph/man/phylo.pls.Rd | 1 geomorph-3.0.4/geomorph/man/physignal.Rd | 7 geomorph-3.0.4/geomorph/man/plethShapeFood.Rd | 7 geomorph-3.0.4/geomorph/man/plethodon.Rd | 7 geomorph-3.0.4/geomorph/man/plethspecies.Rd | 7 geomorph-3.0.4/geomorph/man/plot.CR.Rd | 3 geomorph-3.0.4/geomorph/man/plot.CR.phylo.Rd | 3 geomorph-3.0.4/geomorph/man/plot.advanced.procD.lm.Rd | 9 geomorph-3.0.4/geomorph/man/plot.bilat.symmetry.Rd | 1 geomorph-3.0.4/geomorph/man/plot.evolrate.Rd | 1 geomorph-3.0.4/geomorph/man/plot.gpagen.Rd | 5 geomorph-3.0.4/geomorph/man/plot.physignal.Rd | 3 geomorph-3.0.4/geomorph/man/plot.pls.Rd | 1 geomorph-3.0.4/geomorph/man/plot.procD.allometry.Rd | 7 geomorph-3.0.4/geomorph/man/plot.procD.lm.Rd | 30 geomorph-3.0.4/geomorph/man/plot.trajectory.analysis.Rd | 3 geomorph-3.0.4/geomorph/man/plotAllSpecimens.Rd | 3 geomorph-3.0.4/geomorph/man/plotAllometry.Rd | 1 geomorph-3.0.4/geomorph/man/plotGMPhyloMorphoSpace.Rd | 11 geomorph-3.0.4/geomorph/man/plotOutliers.Rd | 9 geomorph-3.0.4/geomorph/man/plotRefToTarget.Rd | 7 geomorph-3.0.4/geomorph/man/plotTangentSpace.Rd | 11 geomorph-3.0.4/geomorph/man/plotspec.Rd | 7 geomorph-3.0.4/geomorph/man/print.CR.Rd | 3 geomorph-3.0.4/geomorph/man/print.CR.phylo.Rd | 3 geomorph-3.0.4/geomorph/man/print.advanced.procD.lm.Rd | 3 geomorph-3.0.4/geomorph/man/print.bilat.symmetry.Rd | 3 geomorph-3.0.4/geomorph/man/print.compare.pls.Rd | 1 geomorph-3.0.4/geomorph/man/print.evolrate.Rd | 1 geomorph-3.0.4/geomorph/man/print.evolrate1.Rd | 1 geomorph-3.0.4/geomorph/man/print.gpagen.Rd | 3 geomorph-3.0.4/geomorph/man/print.morphol.disparity.Rd | 3 geomorph-3.0.4/geomorph/man/print.physignal.Rd | 3 geomorph-3.0.4/geomorph/man/print.plotTangentSpace.Rd | 1 geomorph-3.0.4/geomorph/man/print.pls.Rd | 3 geomorph-3.0.4/geomorph/man/print.procD.allometry.Rd | 3 geomorph-3.0.4/geomorph/man/print.procD.lm.Rd | 1 geomorph-3.0.4/geomorph/man/print.trajectory.analysis.Rd | 1 geomorph-3.0.4/geomorph/man/procD.allometry.Rd | 45 geomorph-3.0.4/geomorph/man/procD.lm.Rd | 95 + geomorph-3.0.4/geomorph/man/procD.pgls.Rd | 58 geomorph-3.0.4/geomorph/man/pupfish.Rd | 7 geomorph-3.0.4/geomorph/man/ratland.Rd | 7 geomorph-3.0.4/geomorph/man/read.morphologika.Rd | 24 geomorph-3.0.4/geomorph/man/read.ply.Rd | 1 geomorph-3.0.4/geomorph/man/readland.nts.Rd | 31 geomorph-3.0.4/geomorph/man/readland.tps.Rd | 9 geomorph-3.0.4/geomorph/man/readmulti.nts.Rd | 33 geomorph-3.0.4/geomorph/man/scallopPLY.Rd | 7 geomorph-3.0.4/geomorph/man/scallops.Rd | 7 geomorph-3.0.4/geomorph/man/shape.predictor.Rd | 19 geomorph-3.0.4/geomorph/man/summary.CR.Rd | 3 geomorph-3.0.4/geomorph/man/summary.CR.phylo.Rd | 3 geomorph-3.0.4/geomorph/man/summary.advanced.procD.lm.Rd | 3 geomorph-3.0.4/geomorph/man/summary.bilat.symmetry.Rd | 1 geomorph-3.0.4/geomorph/man/summary.compare.pls.Rd | 1 geomorph-3.0.4/geomorph/man/summary.evolrate.Rd | 1 geomorph-3.0.4/geomorph/man/summary.evolrate1.Rd | 1 geomorph-3.0.4/geomorph/man/summary.gpagen.Rd | 3 geomorph-3.0.4/geomorph/man/summary.morphol.disparity.Rd | 3 geomorph-3.0.4/geomorph/man/summary.physignal.Rd | 3 geomorph-3.0.4/geomorph/man/summary.plotTangentSpace.Rd | 1 geomorph-3.0.4/geomorph/man/summary.pls.Rd | 3 geomorph-3.0.4/geomorph/man/summary.procD.allometry.Rd | 3 geomorph-3.0.4/geomorph/man/summary.procD.lm.Rd | 3 geomorph-3.0.4/geomorph/man/summary.trajectory.analysis.Rd | 1 geomorph-3.0.4/geomorph/man/trajectory.analysis.Rd | 31 geomorph-3.0.4/geomorph/man/two.b.pls.Rd | 45 geomorph-3.0.4/geomorph/man/two.d.array.Rd | 19 geomorph-3.0.4/geomorph/man/warpRefMesh.Rd | 7 geomorph-3.0.4/geomorph/man/warpRefOutline.Rd | 7 geomorph-3.0.4/geomorph/man/writeland.tps.Rd | 5 159 files changed, 2988 insertions(+), 1653 deletions(-)
Title: Zelig Ecological Inference Models
Description: Add-on package for Zelig 5. Enables the use of a variety of
ecological inference models.
Author: Christopher Gandrud [cre],
James Honaker [aut]
Maintainer: Christopher Gandrud <zelig.zee@gmail.com>
Diff between ZeligEI versions 0.1-1 dated 2017-05-22 and 0.1-2 dated 2017-06-08
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS.md | 5 +++++ R/model-ei.R | 4 ++-- tests/testthat/test-zelig-core.R |only 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Zelig Choice Models
Description: Add-on package for Zelig 5. Enables the use of a variety of logit
and probit regressions.
Author: Christine. Choirat [aut],
Christopher Gandrud [aut, cre],
James Honaker [aut],
Kosuke Imai [aut],
Gary King [aut],
Olivia Lau [aut]
Maintainer: Christopher Gandrud <zelig.zee@gmail.com>
Diff between ZeligChoice versions 0.9-5 dated 2017-05-10 and 0.9-6 dated 2017-06-08
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/model-bbinchoice.R | 5 ++++- R/model-obinchoice.R | 22 ++++++++++++---------- R/model-ologit.R | 7 +++---- tests/testthat/test-mlogit.R | 16 +++++++++++++++- 7 files changed, 54 insertions(+), 28 deletions(-)
Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical work-flow--procedures and algorithms that may be
essential to one user's application but which the original package
developer did not use in their own research and might not themselves
support. These include bootstrapping, jackknifing, and re-weighting of data.
In particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine Choirat [aut],
Christopher Gandrud [aut, cre],
James Honaker [aut],
Kosuke Imai [aut],
Gary King [aut],
Olivia Lau [aut],
IQSS Harvard University [cph]
Maintainer: Christopher Gandrud <zelig.zee@gmail.com>
Diff between Zelig versions 5.1-1 dated 2017-05-11 and 5.1-2 dated 2017-06-08
DESCRIPTION | 8 +- MD5 | 75 ++++++++++++----------- NEWS.md | 41 ++++++++++++- R/assertions.R | 20 ++++++ R/interface.R | 87 +++++++++++++++++++++++++-- R/model-ivreg.R | 4 - R/model-logit.R | 24 +++++++ R/model-normal-survey.R | 2 R/model-survey.R | 23 ++++++- R/model-zelig.R | 75 +++++++++++++---------- R/utils.R | 44 ++++++++++--- R/wrappers.R | 30 ++++++++- README.md | 104 +++++++++++++++++++++------------ man/Zelig-ivreg-class.Rd | 4 - man/Zelig-logit-class.Rd | 5 + man/coalition2.Rd | 62 +++++++++---------- man/figures/example_plot_ci_plot-1.png |binary man/figures/example_plot_graph-1.png |binary man/friendship.Rd | 56 ++++++++--------- man/get_pvalue.Rd |only man/get_se.Rd |only man/homerun.Rd | 50 +++++++-------- man/is_zeligei.Rd |only man/model_lookup_df.Rd |only man/to_zelig.Rd |only man/voteincome.Rd | 52 ++++++++-------- man/zelig_qi_to_df.Rd | 12 +-- tests/testthat.R | 4 - tests/testthat/test-gamma.R | 22 ++++++ tests/testthat/test-interface.R | 8 ++ tests/testthat/test-logit.R | 24 +++++++ tests/testthat/test-logitbayes.R | 6 - tests/testthat/test-ls.R | 13 ++++ tests/testthat/test-normalsurvey.R | 14 +++- tests/testthat/test-poisson.R | 11 +++ tests/testthat/test-probit.R | 29 ++++++++- tests/testthat/test-survey.R | 97 ++++++++++++++++-------------- tests/testthat/test-utils.R | 8 -- tests/testthat/test-weights.R | 5 - tests/testthat/test-wrappers.R | 5 - tests/testthat/test-zelig.R | 2 41 files changed, 700 insertions(+), 326 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of
linear or logistic regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge.
Author: Patrick Breheny [aut, cre], Yaohui Zeng [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 3.1-0 dated 2017-05-18 and 3.1-1 dated 2017-06-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 5 +++++ R/cv.grpreg.R | 39 ++++++++++++++++++++++----------------- R/reorderGroups.R | 12 +++++------- inst/doc/penalties.pdf |binary inst/doc/quick-start.pdf |binary inst/tests/extra-features.R | 10 +++++++++- 8 files changed, 52 insertions(+), 36 deletions(-)
Title: Generalized Correlations and Initial Causal Path
Description: Since causal paths from data are important for all sciences, the
package provides sophisticated functions. The idea is simply
that if X causes Y (path: X to Y) then non-deterministic variation in X
is more "original or independent" than similar variation in Y. We compare
two flipped kernel regressions: X=f(Y, Z) and Y=g(X,Z), where Z are control
variables. Our first two criteria compare absolute gradients (Cr1) and
absolute residuals (Cr2), both quantified by stochastic dominance of four
orders (SD1 to SD4). Our third criterion (Cr3) expects X to be better able
to predict Y than the other way around using generalized partial correlation
If |r*(x|y)|> |r*(y|x)| it suggests that y is more likely
the "kernel cause" of x. The usual partial correlations are generalized for
the asymmetric matrix of r*'s developed here.
Partial correlations help asses effect of x on y after removing the effect of a
set of variables.
The package provides additional tools for causal assessment,
for printing the causal directions in a clear, comprehensive compact summary form,
for matrix algebra, for "outlier detection", and for numerical integration by the
trapezoidal rule, stochastic dominance, etc.
The package has functions for bootstrap-based statistical inference and one
for a heuristic t-test.
Author: Prof. H. D. Vinod, Fordham University, NY.
Maintainer: H. D. Vinod <vinod@fordham.edu>
Diff between generalCorr versions 1.0.3 dated 2016-06-28 and 1.0.4 dated 2017-06-08
DESCRIPTION | 34 ++- MD5 | 159 +++++++++-------- NAMESPACE | 2 R/EuroCrime.R | 4 R/Panel2Lag.R | 4 R/PanelLag.R | 4 R/abs_stdres.R | 6 R/allPairs.R | 6 R/bigfp.R | 4 R/bootPairs.R | 85 ++++++--- R/causeSummary.R |only R/cofactor.R | 4 R/comp_portfo2.R | 4 R/generalCorrInfo.R | 19 +- R/get0outliers.R | 4 R/gmcmtx0.R | 4 R/gmcmtxZ.R | 5 R/gmcxy_np.R | 4 R/kern.R | 13 - R/kern_ctrl.R | 11 - R/mag.R | 2 R/mag_ctrl.R | 4 R/naTriplet.R | 40 ++-- R/napair.R | 7 R/parcorSilent.R | 6 R/parcor_ijk.R | 4 R/parcor_ridg.R | 9 - R/pcause.R | 14 - R/rstar.R | 4 R/silentPairs.R | 283 ++++++++++++++++---------------- R/some0Pairs.R | 16 - R/someCPairs.R | 8 R/someMagPairs.R | 2 R/somePairs.R | 3 R/sort_matrix.R | 2 build/vignette.rds |binary inst/doc/generalCorr-vignette.pdf |binary inst/doc/generalCorr-vignette.pdf.asis | 1 man/EuroCrime.Rd | 3 man/Panel2Lag.Rd | 9 - man/PanelLag.Rd | 3 man/abs_res.Rd | 1 man/abs_stdapd.Rd | 1 man/abs_stdapdC.Rd | 7 man/abs_stdres.Rd | 11 - man/abs_stdresC.Rd | 7 man/allPairs.Rd | 9 - man/bigfp.Rd | 9 - man/bootPairs.Rd | 59 ++++-- man/causeSummary.Rd |only man/cofactor.Rd | 4 man/comp_portfo2.Rd | 3 man/generalCorrInfo.Rd | 16 + man/get0outliers.Rd | 5 man/gmcmtx0.Rd | 9 - man/gmcmtxZ.Rd | 9 - man/gmcxy_np.Rd | 9 - man/heurist.Rd | 1 man/kern.Rd | 19 +- man/kern_ctrl.Rd | 12 - man/mag.Rd | 9 - man/mag_ctrl.Rd | 11 - man/minor.Rd | 1 man/naTriplet.Rd | 9 - man/napair.Rd | 1 man/parcorSilent.Rd | 11 - man/parcor_ijk.Rd | 3 man/parcor_ridg.Rd | 14 - man/pcause.Rd | 9 - man/prelec2.Rd | 7 man/rstar.Rd | 9 - man/silentPairs.Rd | 64 ++++--- man/some0Pairs.Rd | 21 +- man/someCPairs.Rd | 15 - man/someMagPairs.Rd | 9 - man/somePairs.Rd | 10 - man/sort_matrix.Rd | 3 man/stdz_xy.Rd | 1 man/stochdom2.Rd | 7 man/wtdpapb.Rd | 7 vignettes/generalCorr-vignette.pdf.asis | 1 vignettes/generalCorr-vignette2.pdf |only 82 files changed, 647 insertions(+), 562 deletions(-)