Title: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Description: Provides tools for importing and working with bibliographic
references. It greatly enhances the 'bibentry' class by providing a class
'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8'
encoding, and can be easily searched by any field, by date ranges, and by
various formats for name lists (author by last names, translator by full names,
etc.). Entries can be updated, combined, sorted, printed in a number of styles,
and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and
converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and
'Zotero' are provided for importing references and references can be created
from locally stored 'PDF' files using 'Poppler'. Includes functions for citing
and generating a bibliography with hyperlinks for documents prepared with
'RMarkdown' or 'RHTML'.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean <mathew.w.mclean@gmail.com>
Diff between RefManageR versions 0.14.12 dated 2017-07-04 and 0.14.20 dated 2017-08-17
.Rinstignore |only DESCRIPTION | 12 +- MD5 | 86 +++++++++---------- NAMESPACE | 3 R/02BibOptions.R | 8 + R/04InternalFunctions.R | 139 ++++++++++++++++-------------- R/BibEntryAddOp.R | 5 - R/GetBibEntryWithDOI.R | 16 ++- R/GetDOIs.R | 11 +- R/ReadCrossRef.R | 60 ++++++++----- R/ReadGS.R | 2 R/ReadPDFs.R | 9 +- R/ReadPubMed.R | 31 ++---- R/head.BibEntry.R | 8 + R/rmdCite.R | 180 ++++++++++++++++++++++++---------------- R/toBibtex.R | 140 ++++++++++++++++++------------- README.md | 17 ++- inst/CITATION | 11 ++ inst/NEWS.md | 19 ++++ inst/Rhtml/TestAuthorYear.Rhtml | 10 +- inst/Rhtml/TestHtml.Rhtml | 7 - inst/doc/120_status.svg |only inst/doc/TestHtml.R | 10 -- inst/doc/TestHtml.Rhtml | 19 ++-- inst/doc/TestHtml.html | 31 ++---- inst/doc/TestRmd.R | 4 inst/doc/TestRmd.Rmd | 5 + inst/doc/TestRmd.html | 15 +-- inst/doc/manual.pdf |binary inst/doc/ropensci_footer.png |only man/BibOptions.Rd | 8 + man/Cite.Rd | 7 + man/GetBibEntryWithDOI.Rd | 2 man/GetDOIs.Rd | 2 man/GetPubMedByID.Rd | 2 man/GetPubMedRelated.Rd | 2 man/LookupPubMedID.Rd | 4 man/ReadCrossRef.Rd | 5 - man/ReadGS.Rd | 2 man/ReadPDFs.Rd | 6 + man/ReadPubMed.Rd | 4 man/head.BibEntry.Rd | 7 + tests/testthat/test-methods.R | 12 ++ tests/testthat/test-pubmed.R | 2 vignettes/TestHtml.Rhtml | 19 ++-- vignettes/TestRmd.Rmd | 5 + 46 files changed, 559 insertions(+), 388 deletions(-)
Title: Analysis of the 'Elements of Metacommunity Structure'
Description: Functions to analyze coherence, boundary clumping, and turnover
following the pattern-based metacommunity analysis of Leibold and Mikkelson
2002 <doi:10.1034/j.1600-0706.2002.970210.x>. The package also includes
functions to visualize ecological networks, and to calculate modularity
as a replacement to boundary clumping.
Author: Tad Dallas
Maintainer: Tad Dallas <tdallas@ucdavis.edu>
Diff between metacom versions 1.4.6 dated 2017-03-29 and 1.4.7 dated 2017-08-17
DESCRIPTION | 15 +++++++-------- MD5 | 20 +++++++++++++------- R/BoundaryClump.R | 43 ++++++++++++++++++++++++------------------- R/Imagine.R | 2 +- R/Metacommunity.R | 4 ++-- R/Turnover.R | 43 +++++++++++++++++++++++-------------------- man/BoundaryClump.Rd | 6 +++++- man/Turnover.Rd | 6 +++++- tests |only 9 files changed, 80 insertions(+), 59 deletions(-)
Title: Miscellaneous Functions for the USGS INL Project Office
Description: A collection of functions for creating high-level graphics,
performing raster-based analysis, processing MODFLOW-based models, etc.
Used to support packages and scripts written by researchers at the
United States Geological Survey (USGS)
Idaho National Laboratory (INL) Project Office.
Author: Jason C. Fisher [aut, cre]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between inlmisc versions 0.3.1 dated 2017-08-14 and 0.3.2 dated 2017-08-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/RecreateLibrary.R | 43 ++++++++++++++++++++++--------------------- man/RecreateLibrary.Rd | 7 ++++--- 5 files changed, 40 insertions(+), 32 deletions(-)
Title: Generalized Additive Models for Bivariate Conditional Dependence
Structures and Vine Copulas
Description: Implementation of various inference and simulation tools to
apply generalized additive models to bivariate dependence structures and
non-simplified vine copulas.
Author: Thomas Nagler [aut],
Thibault Vatter [aut, cre]
Maintainer: Thibault Vatter <thibault.vatter@gmail.com>
Diff between gamCopula versions 0.0-3 dated 2017-08-14 and 0.0-4 dated 2017-08-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 12 ++++++++++++ R/gamBiCopFit.R | 19 ++++++++++--------- R/gamBiCopSelect.R | 11 +++++++++-- man/gamCopula-package.Rd | 6 +++--- 6 files changed, 43 insertions(+), 23 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as?publication-ready univariate or bivariate tables?in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures?to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics?(mean, median, frequencies, incidences, etc.). Perform the appropriate tests?(t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data?(Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana, Joan Vila, H\'ector Sanz, Gavin Lucas, Judith Pe\~nafiel and David Gim\'enez
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 3.2.4 dated 2017-03-14 and 3.3 dated 2017-08-17
DESCRIPTION | 12 - MD5 | 29 +- R/compare.i.R | 4 R/compareGroups.default.R | 7 R/createTable.R | 26 ++ R/export2html.R | 16 - R/export2md.R | 4 build/vignette.rds |binary inst/app/log |only inst/app/server.R | 4 inst/doc/changelog | 5 inst/doc/compareGroups_vignette.html | 156 +++++++-------- man/compareGroups-internal.Rd | 2 man/compareGroups-package.Rd | 4 man/compareGroups.Rd | 4 man/createTable.Rd | 355 +++++++++++++++++------------------ 16 files changed, 338 insertions(+), 290 deletions(-)
Title: Individual-Based, Spatially-Explicit Simulation and Analysis of
Multi-State Movements in River Networks, Homogeneous, and
Heterogeneous Landscapes
Description: Provides functions to generate and analyze individual-based spatially-explicit
simulations of multi-state movements in heterogeneous landscapes, based on "resistance"
rasters. Although originally conceived and designed to simulate spatially-explicit trajectories
of species constrained to linear habitats or dendritic ecological networks (e.g., river networks), the simulation
algorithm is built to be highly flexible and can be applied to any (aquatic, semi-aquatic or
terrestrial) organism, independently on the landscape in which it moves. Thus, the user will be able to use the package
to simulate movements either in homogeneous landscapes, heterogeneous landscapes (e.g. semi-aquatic animal moving
mainly along rivers but also using the matrix), or even in highly contrasted landscapes
(e.g. fish in a river network). The algorithm and its input parameters are the same for all
cases, so that results are comparable. Simulated trajectories can then be used as mechanistic
null models to test e.g. for species site fidelity and other 'Movement Ecology' hypotheses
(Nathan et al. 2008, <DOI:10.1073/pnas.0800375105>), or for other predictive purposes.
The package should thus be relevant to explore a broad spectrum of ecological phenomena, such as those at the interface
of animal behaviour, landscape, spatial and movement ecology, disease and invasive species spread, and population dynamics.
Author: Lorenzo Quaglietta [aut],
Miguel Porto [aut, cre],
Erida Gjini [ctb]
Maintainer: Miguel Porto <mpbertolo@gmail.com>
Diff between SiMRiv versions 1.0.0 dated 2017-07-27 and 1.0.1 dated 2017-08-17
SiMRiv-1.0.0/SiMRiv/vignettes/fullpage.sty |only SiMRiv-1.0.1/SiMRiv/DESCRIPTION | 26 +- SiMRiv-1.0.1/SiMRiv/MD5 | 31 +-- SiMRiv-1.0.1/SiMRiv/R/SiMRiv.r | 9 SiMRiv-1.0.1/SiMRiv/R/estimation.r | 285 +++++++++++++++++++---------- SiMRiv-1.0.1/SiMRiv/R/internal.r | 16 - SiMRiv-1.0.1/SiMRiv/build/partial.rdb |binary SiMRiv-1.0.1/SiMRiv/inst/doc/SiMRiv.Rnw | 30 +-- SiMRiv-1.0.1/SiMRiv/inst/doc/SiMRiv.pdf |binary SiMRiv-1.0.1/SiMRiv/man/SiMRiv-package.Rd | 6 SiMRiv-1.0.1/SiMRiv/man/adjustModel.Rd | 59 +++--- SiMRiv-1.0.1/SiMRiv/man/generationPlot.Rd | 8 SiMRiv-1.0.1/SiMRiv/man/simulate.Rd | 2 SiMRiv-1.0.1/SiMRiv/man/species.Rd | 3 SiMRiv-1.0.1/SiMRiv/man/speciesModel.Rd | 20 +- SiMRiv-1.0.1/SiMRiv/src/simulate.c | 29 +- SiMRiv-1.0.1/SiMRiv/vignettes/SiMRiv.Rnw | 30 +-- 17 files changed, 342 insertions(+), 212 deletions(-)
Title: Tools for Polyploid Microsatellite Analysis
Description: A collection of tools to handle microsatellite data of
any ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes. It can import and export data in
ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi',
'POPDIST', 'STRand', and binary presence/absence formats. It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account. These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R. Allelic diversity
statistics and Polymorphic Information Content are also available. polysat can
assist the user in estimating the ploidy of samples, and it can estimate allele
frequencies in populations, calculate pairwise or global differentiation statistics
based on those frequencies, and export allele frequencies to 'SPAGeDi' and 'adegenet'.
Functions are also included for assigning alleles to isoloci in cases where one pair
of microsatellite primers amplifies alleles from two or more independently
segregating isoloci. polysat is described by Clark and Jasieniuk (2011)
<doi:10.1111/j.1755-0998.2011.02985.x> and Clark and Schreier (2016)
<doi:10.1111/1755-0998.12639>.
Author: Lindsay V. Clark [aut, cre]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Diff between polysat versions 1.7-1 dated 2017-07-23 and 1.7-2 dated 2017-08-17
DESCRIPTION | 12 - MD5 | 28 +-- NEWS | 7 R/population_stats.R | 6 inst/doc/allopolyVignette.pdf |binary inst/doc/polysattutorial.pdf |binary inst/extdata/STRandExample.txt | 18 +- man/alleleDiversity.Rd | 148 ++++++++++----------- man/catalanAlleles.Rd | 288 ++++++++++++++++++++--------------------- man/mergeAlleleAssignments.Rd | 164 +++++++++++------------ man/pld.Rd | 206 ++++++++++++++--------------- man/ploidysuper-class.Rd | 146 ++++++++++---------- man/read.STRand.Rd | 174 ++++++++++++------------ man/reformatPloidies.Rd | 224 +++++++++++++++---------------- vignettes/STRandExample.txt | 18 +- 15 files changed, 725 insertions(+), 714 deletions(-)
Title: Fuzzy Linear Programming
Description: Provides methods to solve Fuzzy Linear Programming Problems with
fuzzy constraints (following different approaches proposed by
Verdegay, Zimmermann, Werners and Tanaka), fuzzy costs, and fuzzy
technological matrix.
Author: Carlos A. Rabelo [aut, cre],
Pablo J. Villacorta [ctb]
Maintainer: Carlos A. Rabelo <carabelo@gmail.com>
Diff between FuzzyLP versions 0.1-4 dated 2017-06-25 and 0.1-5 dated 2017-08-17
DESCRIPTION | 10 ++++++---- MD5 | 7 +++++-- build |only inst/doc/FuzzyLP.pdf |binary inst/doc/FuzzyLP.pdf.asis |only vignettes |only 6 files changed, 11 insertions(+), 6 deletions(-)
Title: Tools for the Bayesian Discount Prior Function
Description: Functions for data augmentation using the
Bayesian discount prior function for 1 arm and 2 arm clinical trials.
Author: Shawn Balcome [cre],
Donnie Musgrove [aut],
Tarek Haddad [aut],
Christopher Jackson [ctb] (For the ppexp R code that was ported to
C++.)
Maintainer: Shawn Balcome <sbalcome@mdic.org>
Diff between bayesDP versions 1.2.1 dated 2017-08-01 and 1.2.2 dated 2017-08-17
DESCRIPTION | 8 MD5 | 28 - R/RcppExports.R | 22 build/vignette.rds |binary inst/doc/bdpbinomial-vignette.R | 142 ++--- inst/doc/bdpbinomial-vignette.Rmd | 27 inst/doc/bdpbinomial-vignette.html | 718 ++++++++++++++++---------- inst/doc/bdpnormal-vignette.R | 162 +++-- inst/doc/bdpnormal-vignette.Rmd | 20 inst/doc/bdpnormal-vignette.html | 758 +++++++++++++++++---------- inst/doc/bdpsurvival-vignette.R | 230 ++++---- inst/doc/bdpsurvival-vignette.Rmd | 51 + inst/doc/bdpsurvival-vignette.html | 1002 ++++++++++++++++++++++--------------- src/RcppExports.cpp | 4 src/bayesDP-init.c | 22 15 files changed, 1934 insertions(+), 1260 deletions(-)
Title: Statistical Models for Word Frequency Distributions
Description: Statistical models and utilities for the analysis of word frequency distributions.
The utilities include functions for loading, manipulating and visualizing word frequency
data and vocabulary growth curves. The package also implements several statistical
models for the distribution of word frequencies in a population. (The name of this package
derives from the most famous word frequency distribution, Zipf's law.)
Author: Stefan Evert <stefan.evert@fau.de>, Marco Baroni <marco.baroni@unitn.it>
Maintainer: Stefan Evert <stefan.evert@fau.de>
Diff between zipfR versions 0.6-6 dated 2012-04-03 and 0.6-10 dated 2017-08-17
zipfR-0.6-10/zipfR/DESCRIPTION | 32 +-- zipfR-0.6-10/zipfR/MD5 | 110 +++++------ zipfR-0.6-10/zipfR/NAMESPACE | 7 zipfR-0.6-10/zipfR/NEWS |only zipfR-0.6-10/zipfR/R/auto_gzfile.R | 10 - zipfR-0.6-10/zipfR/R/lnre_bootstrap.R | 5 zipfR-0.6-10/zipfR/R/read_tfl.R | 4 zipfR-0.6-10/zipfR/R/spc.R | 2 zipfR-0.6-10/zipfR/R/write_tfl.R | 4 zipfR-0.6-10/zipfR/R/zipfR_par.R | 2 zipfR-0.6-10/zipfR/R/zipfR_plotutils.R | 75 +++++-- zipfR-0.6-10/zipfR/TODO |only zipfR-0.6-10/zipfR/build |only zipfR-0.6-10/zipfR/data/Brown.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/Brown.spc.rda |binary zipfR-0.6-10/zipfR/data/Brown.tfl.rda |binary zipfR-0.6-10/zipfR/data/Brown100k.spc.rda |binary zipfR-0.6-10/zipfR/data/BrownAdj.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/BrownAdj.spc.rda |binary zipfR-0.6-10/zipfR/data/BrownImag.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/BrownImag.spc.rda |binary zipfR-0.6-10/zipfR/data/BrownInform.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/BrownInform.spc.rda |binary zipfR-0.6-10/zipfR/data/BrownNoun.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/BrownNoun.spc.rda |binary zipfR-0.6-10/zipfR/data/BrownVer.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/BrownVer.spc.rda |binary zipfR-0.6-10/zipfR/data/Dickens.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/Dickens.spc.rda |binary zipfR-0.6-10/zipfR/data/DickensGreatExpectations.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/DickensGreatExpectations.spc.rda |binary zipfR-0.6-10/zipfR/data/DickensOliverTwist.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/DickensOliverTwist.spc.rda |binary zipfR-0.6-10/zipfR/data/DickensOurMutualFriend.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/DickensOurMutualFriend.spc.rda |binary zipfR-0.6-10/zipfR/data/ItaRi.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/ItaRi.spc.rda |binary zipfR-0.6-10/zipfR/data/ItaUltra.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/ItaUltra.spc.rda |binary zipfR-0.6-10/zipfR/data/TigerNP.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/TigerNP.spc.rda |binary zipfR-0.6-10/zipfR/data/TigerNP.tfl.rda |binary zipfR-0.6-10/zipfR/data/TigerPP.emp.vgc.rda |binary zipfR-0.6-10/zipfR/data/TigerPP.spc.rda |binary zipfR-0.6-10/zipfR/data/TigerPP.tfl.rda |binary zipfR-0.6-10/zipfR/inst/CITATION | 2 zipfR-0.6-10/zipfR/inst/doc/zipfr-tutorial.R |only zipfR-0.6-10/zipfR/inst/doc/zipfr-tutorial.Rnw |only zipfR-0.6-10/zipfR/inst/doc/zipfr-tutorial.pdf |binary zipfR-0.6-10/zipfR/man/Tiger.Rd | 38 +-- zipfR-0.6-10/zipfR/man/lnre_bootstrap.Rd | 7 zipfR-0.6-10/zipfR/man/lnre_fzm.Rd | 2 zipfR-0.6-10/zipfR/man/lnre_zm.Rd | 2 zipfR-0.6-10/zipfR/man/plot_spc.Rd | 27 +- zipfR-0.6-10/zipfR/man/read_write_tfl.Rd | 6 zipfR-0.6-10/zipfR/man/zipfR_package.Rd | 45 ++-- zipfR-0.6-10/zipfR/man/zipfR_plotutils.Rd | 63 ++++-- zipfR-0.6-10/zipfR/vignettes |only zipfR-0.6-6/zipfR/CHANGES |only zipfR-0.6-6/zipfR/inst/doc/index.html |only 60 files changed, 249 insertions(+), 194 deletions(-)
Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Description: Start an HTTP server in R to serve static files, or dynamic
documents that can be converted to HTML files (e.g., R Markdown) under a
given directory.
Author: Yihui Xie [aut, cre],
Carson Sievert [ctb],
Jesse Anderson [ctb],
Ramnath Vaidyanathan [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between servr versions 0.6 dated 2017-05-12 and 0.7 dated 2017-08-17
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS | 12 ++++++++++++ R/static.R | 23 ++++++++++++++++------- R/utils.R | 6 +++++- README.md | 2 +- man/httd.Rd | 5 ++++- man/server_config.Rd | 4 ++-- 9 files changed, 53 insertions(+), 24 deletions(-)
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability
and/or uncertain theta0.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability and/or uncertain theta0.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits (EMA recommended) based on simulations.
Contains also functions scABEL.ad() and sampleN.scABEL.ad() to iteratively
adjust alpha in order to maintain the overall consumer risk in ABEL studies
and adapt the sample size for the loss in power.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
Contains further functions power.HVNTID() and sampleN.HVNTID() to calculate
power and sample size for the BE decision via the FDA procedure for
highly variable NTID's (see FDA Dabigatran / rivaroxaban guidances)
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / sample size estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.4-5 dated 2017-05-20 and 1.4-6 dated 2017-08-17
DESCRIPTION | 9 ++--- MD5 | 60 ++++++++++++++++++----------------- NAMESPACE | 2 + NEWS | 12 +++++++ R/CVwRfromU.R |only R/SampleSize.R | 1 R/expSampleSize.R | 7 ---- R/expSampleSize_noninf.R | 7 ---- R/exppower.R | 7 ---- R/exppower_noninf.R | 7 ---- R/power.R | 43 ++++++++++++++----------- R/power_HVNTID.R | 4 +- R/power_RSABE.R | 8 +++- R/power_RSABE_NTID.R | 4 +- R/power_scABEL1.R | 4 +- R/power_scABEL2.R | 4 +- R/power_scABEL_0.R | 4 +- R/power_scABEL_lo.R | 4 +- build/partial.rdb |binary inst/doc/Expected_Power_for_TOST.pdf |binary man/CVwRfromU.Rd |only man/data_2x2.Rd | 27 +++++++++------ man/data_2x2x3.Rd | 29 +++++++++------- man/data_2x4x4.Rd | 29 +++++++++------- man/data_parallel.Rd | 38 ++++++++++++---------- man/exppower.TOST.Rd | 17 +++------ man/exppower.noninf.Rd | 21 ++++-------- man/expsampleN.TOST.Rd | 36 ++++----------------- man/expsampleN.noninf.Rd | 38 +++++++++++++++------- man/pa.NTIDFDA.Rd | 15 +++++++- man/power.noninf.Rd | 5 +- man/sampleN.noninf.Rd | 4 +- 32 files changed, 236 insertions(+), 210 deletions(-)
Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R.
The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange
with R. This provides a reliable and scalable foundation for statistical services or
building R web applications. The OpenCPU server runs either as a single-user development
server within the interactive R session, or as a multi-user Linux stack based on Apache2.
The entire system is fully open source and permissively licensed. The OpenCPU website
has detailed documentation and example apps.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between opencpu versions 2.0.3 dated 2017-06-25 and 2.0.4 dated 2017-08-17
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS | 10 ++++++++++ R/config.R | 6 ++++-- R/email.R | 4 ++-- R/httpget_webhook.R | 4 ++-- R/log.R | 4 +++- R/request.R | 4 ++-- R/serve.R | 23 ++++++++--------------- R/start.R | 41 ++++++++++++++++++++++++++++------------- R/utils.R | 6 ++++++ build/vignette.rds |binary inst/config/defaults.conf | 3 ++- inst/doc/opencpu-paper.pdf |binary 14 files changed, 83 insertions(+), 54 deletions(-)
Title: Omics Data Integration Project
Description: Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.
Author: Kim-Anh Le Cao, Florian Rohart, Ignacio Gonzalez, Sebastien Dejean with key contributors Benoit Gautier, Francois Bartolo
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <kimanh.lecao@unimelb.edu.au>
Diff between mixOmics versions 6.1.3 dated 2017-05-11 and 6.2.0 dated 2017-08-17
DESCRIPTION | 8 - MD5 | 207 ++++++++++++++++++++-------------------- NEWS | 18 +++ R/AUC_ROC.R | 36 +++++- R/LOGOCV.R | 24 +++- R/internal_mint.block.R | 2 R/internal_mint.block_helpers.R | 6 - R/internal_predict.DA.R | 1 R/internal_wrapper.mint.R | 30 +++++ R/perf.R | 24 +++- R/perf.diablo.R | 48 ++++++++- R/perf.mint.splsda.R | 27 ++++- R/plotIndiv.mint.R | 2 R/plotIndiv.sgcca.R | 3 R/plotVar.R | 12 +- R/pls.R | 4 R/plsda.R | 4 R/spls.R | 4 R/splsda.R | 4 R/t.test.process.R |only R/tune.R | 9 - R/tune.block.splsda.R | 27 ++++- R/tune.mint.splsda.R | 24 +++- R/tune.multilevel.R | 3 R/tune.splsda.R | 29 ----- man/Koren.16S.Rd | 4 man/auroc.Rd | 11 +- man/background.predict.Rd | 8 - man/block.pls.Rd | 7 - man/block.plsda.Rd | 15 +- man/block.spls.Rd | 7 - man/block.splsda.Rd | 16 +-- man/breast.TCGA.Rd | 2 man/breast.tumors.Rd | 2 man/cim.Rd | 2 man/cimDiablo.Rd | 3 man/circosPlot.Rd | 3 man/colors.Rd | 2 man/diverse.16S.Rd | 4 man/estim.regul.Rd | 2 man/explained_variance.Rd | 2 man/get.confusion_matrix.Rd | 5 man/image.estim.regul.Rd | 2 man/image.tune.rcc.Rd | 2 man/imgCor.Rd | 2 man/ipca.Rd | 2 man/linnerud.Rd | 2 man/liver.toxicity.Rd | 2 man/logratio.transfo.Rd | 2 man/mat.rank.Rd | 2 man/mint.block.pls.Rd | 6 - man/mint.block.plsda.Rd | 8 - man/mint.block.spls.Rd | 6 - man/mint.block.splsda.Rd | 7 - man/mint.pca.Rd | 2 man/mint.pls.Rd | 6 - man/mint.plsda.Rd | 9 - man/mint.spls.Rd | 6 - man/mint.splsda.Rd | 9 - man/mixOmics.Rd | 52 +++++++--- man/multidrug.Rd | 2 man/nearZeroVar.Rd | 2 man/network.Rd | 14 +- man/nipals.Rd | 2 man/nutrimouse.Rd | 2 man/pca.Rd | 6 - man/pcatune.Rd | 2 man/perf.Rd | 93 ++++++++++++++--- man/plot.perf.Rd | 13 ++ man/plot.rcc.Rd | 2 man/plot.tune.Rd | 2 man/plotArrow.Rd | 4 man/plotContrib.Rd | 2 man/plotDiablo.Rd | 2 man/plotIndiv.Rd | 2 man/plotLoadings.Rd | 2 man/plotVar.Rd | 8 - man/pls.Rd | 19 ++- man/plsda.Rd | 12 +- man/predict.Rd | 20 ++- man/print.methods.Rd | 2 man/rcc.Rd | 2 man/selectVar.Rd | 2 man/sipca.Rd | 2 man/spca.Rd | 2 man/spls.Rd | 19 ++- man/splsda.Rd | 13 +- man/srbct.Rd | 2 man/stemcells.Rd | 2 man/study_split.Rd | 2 man/summary.Rd | 2 man/tune.Rd | 46 +++++++- man/tune.block.splsda.Rd | 68 +++---------- man/tune.mint.splsda.Rd | 38 ++++--- man/tune.multilevel.Rd | 15 +- man/tune.pca.Rd | 2 man/tune.rcc.Rd | 2 man/tune.splsda.Rd | 52 ++-------- man/vac18.Rd | 2 man/vac18.simulated.Rd | 2 man/vip.Rd | 2 man/withinVariation.Rd | 2 man/wrapper.rgcca.Rd | 2 man/wrapper.sgcca.Rd | 5 man/yeast.Rd | 2 105 files changed, 805 insertions(+), 474 deletions(-)
Title: Mini Charts for Interactive Maps
Description: Add and modify small charts on an interactive map created with
package 'leaflet'. These charts can be used to represent at same time multiple
variables on a single map.
Author: Francois Guillem [aut, cre],
Jalal-Edine ZAWAM [ctb],
RTE [cph]
Maintainer: Francois Guillem <francois.guillem@rte-france.com>
Diff between leaflet.minicharts versions 0.5.0 dated 2017-07-10 and 0.5.1 dated 2017-08-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 5 +++++ inst/doc/introduction.html | 28 ++++++++++++++-------------- inst/leaflet.minicharts.min.js | 22 +++++++++++----------- 5 files changed, 37 insertions(+), 32 deletions(-)
More information about leaflet.minicharts at CRAN
Permanent link
Title: Programmatic Interface to the Web Service Methods Provided by UC
Berkeley's Natural History Data
Description: The ecoengine ('ecoengine';
<https://ecoengine.berkeley.edu/>). provides access to more than 5 million georeferenced
specimen records from the University of California, Berkeley's Natural History
Museums.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>
Diff between ecoengine versions 1.10.0 dated 2016-05-24 and 1.11.0 dated 2017-08-17
ecoengine-1.10.0/ecoengine/inst/Using_ecoengine_cache |only ecoengine-1.10.0/ecoengine/inst/cache |only ecoengine-1.11.0/ecoengine/DESCRIPTION | 18 ecoengine-1.11.0/ecoengine/MD5 | 229 -- ecoengine-1.11.0/ecoengine/NAMESPACE | 1 ecoengine-1.11.0/ecoengine/NEWS | 5 ecoengine-1.11.0/ecoengine/R/ee_checklists.R | 2 ecoengine-1.11.0/ecoengine/R/ee_observations.R | 8 ecoengine-1.11.0/ecoengine/R/ee_photos.R | 6 ecoengine-1.11.0/ecoengine/README.md | 33 ecoengine-1.11.0/ecoengine/inst/Using_ecoengine.Rmd | 6 ecoengine-1.11.0/ecoengine/inst/Using_ecoengine.html |only ecoengine-1.11.0/ecoengine/inst/Using_ecoengine.md | 1544 +++++++++--------- ecoengine-1.11.0/ecoengine/man/california_counties.Rd | 1 ecoengine-1.11.0/ecoengine/man/checklist_details.Rd | 1 ecoengine-1.11.0/ecoengine/man/ecoengine.Rd | 1 ecoengine-1.11.0/ecoengine/man/ee_about.Rd | 1 ecoengine-1.11.0/ecoengine/man/ee_cbind.Rd | 1 ecoengine-1.11.0/ecoengine/man/ee_checklists.Rd | 3 ecoengine-1.11.0/ecoengine/man/ee_footprints.Rd | 1 ecoengine-1.11.0/ecoengine/man/ee_observations.Rd | 3 ecoengine-1.11.0/ecoengine/man/ee_pages.Rd | 1 ecoengine-1.11.0/ecoengine/man/ee_paginator.Rd | 1 ecoengine-1.11.0/ecoengine/man/ee_photos.Rd | 3 ecoengine-1.11.0/ecoengine/man/ee_search.Rd | 1 ecoengine-1.11.0/ecoengine/man/ee_search_obs.Rd | 1 ecoengine-1.11.0/ecoengine/man/ee_sources.Rd | 1 ecoengine-1.11.0/ecoengine/man/full_sensor_list.Rd | 1 ecoengine-1.11.0/ecoengine/man/print.ecoengine.Rd | 1 ecoengine-1.11.0/ecoengine/man/view_photos.Rd | 1 30 files changed, 869 insertions(+), 1006 deletions(-)
Title: Plot and Manipulate Multigraphs
Description: Functions to plot and manipulate multigraphs, signed, weighted multigraphs, and bipartite graphs with different layout options.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multigraph versions 0.60 dated 2017-05-04 and 0.71 dated 2017-08-17
DESCRIPTION | 12 - MD5 | 26 ++-- R/bmgraph.R | 149 +++++++++++++++--------- R/frcd.R | 21 +-- R/mbnd.R | 138 ++++++++++++++-------- R/multigraph.R | 282 ++++++++++++++++++++++++++++++++++------------ R/nrm.R | 2 R/stsm.R | 83 +++++++++---- man/bmgraph.Rd | 51 +++++--- man/conc.Rd | 13 +- man/frcd.Rd | 13 +- man/multigraph-package.Rd | 6 man/multigraph.Rd | 42 +++++- man/stsm.Rd | 13 +- 14 files changed, 586 insertions(+), 265 deletions(-)
Title: World Population Prospects 2017
Description: Provides data from the United Nation's World Population Prospects 2017.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wpp2017 versions 1.0-1 dated 2017-06-29 and 1.1-0 dated 2017-08-17
ChangeLog | 4 DESCRIPTION | 8 MD5 | 12 data/mxF.txt |10604 ++++++++++++++++++++++++------------------------- data/mxM.txt |10604 ++++++++++++++++++++++++------------------------- man/ASMR.Rd | 8 man/wpp2017-package.Rd | 4 7 files changed, 10627 insertions(+), 10617 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.7.900.2.0 dated 2017-06-04 and 0.7.960.1.0 dated 2017-08-17
.aspell |only ChangeLog | 163 + DESCRIPTION | 14 MD5 | 129 - NAMESPACE | 3 R/SciPy2R.R |only R/unit.test.R | 14 build/vignette.rds |binary configure | 28 configure.ac | 10 inst/AUTHORS |only inst/COPYRIGHTS |only inst/NEWS.Rd | 57 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/RcppArmadilloAs.h | 518 ++++ inst/include/RcppArmadilloConfig.h | 8 inst/include/RcppArmadilloWrap.h | 25 inst/include/armadillo | 3 inst/include/armadillo_bits/Cube_bones.hpp | 21 inst/include/armadillo_bits/Cube_meat.hpp | 77 inst/include/armadillo_bits/Mat_bones.hpp | 2 inst/include/armadillo_bits/Mat_meat.hpp | 2 inst/include/armadillo_bits/SpMat_meat.hpp | 3 inst/include/armadillo_bits/arma_config.hpp | 7 inst/include/armadillo_bits/arma_rng.hpp | 127 + inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/auxlib_meat.hpp | 1 inst/include/armadillo_bits/compiler_setup.hpp | 29 inst/include/armadillo_bits/config.hpp | 8 inst/include/armadillo_bits/config.hpp.cmake | 8 inst/include/armadillo_bits/debug.hpp | 1 inst/include/armadillo_bits/eglue_core_meat.hpp | 53 inst/include/armadillo_bits/eop_core_meat.hpp | 53 inst/include/armadillo_bits/fn_accu.hpp | 402 ++- inst/include/armadillo_bits/fn_det.hpp | 2 inst/include/armadillo_bits/fn_inv.hpp | 10 inst/include/armadillo_bits/fn_misc.hpp | 2 inst/include/armadillo_bits/fn_reshape.hpp | 42 inst/include/armadillo_bits/fn_solve.hpp | 8 inst/include/armadillo_bits/fn_sort.hpp | 4 inst/include/armadillo_bits/fn_sort_index.hpp | 4 inst/include/armadillo_bits/fn_strans.hpp | 15 inst/include/armadillo_bits/fn_trans.hpp | 28 inst/include/armadillo_bits/fn_trimat.hpp | 70 inst/include/armadillo_bits/glue_atan2_meat.hpp | 87 inst/include/armadillo_bits/gmm_diag_bones.hpp | 72 inst/include/armadillo_bits/gmm_diag_meat.hpp | 1112 +++++++--- inst/include/armadillo_bits/gmm_full_bones.hpp |only inst/include/armadillo_bits/gmm_full_meat.hpp |only inst/include/armadillo_bits/gmm_misc_bones.hpp | 72 inst/include/armadillo_bits/gmm_misc_meat.hpp | 128 - inst/include/armadillo_bits/mp_misc.hpp |only inst/include/armadillo_bits/newarp_GenEigsSolver_meat.hpp | 5 inst/include/armadillo_bits/newarp_UpperHessenbergEigen_meat.hpp | 9 inst/include/armadillo_bits/op_sum_bones.hpp | 6 inst/include/armadillo_bits/op_sum_meat.hpp | 193 + inst/include/armadillo_bits/op_trimat_bones.hpp | 26 inst/include/armadillo_bits/op_trimat_meat.hpp | 182 + inst/include/armadillo_bits/operator_cube_minus.hpp | 16 inst/include/armadillo_bits/operator_minus.hpp | 14 inst/include/armadillo_bits/subview_meat.hpp | 2 inst/unitTests/cpp/any_as_vec.cpp |only inst/unitTests/cpp/armadillo.cpp | 6 inst/unitTests/cpp/colrow_as_vec.cpp |only inst/unitTests/cpp/sparse.cpp | 5 inst/unitTests/runit.RcppArmadillo.R | 13 inst/unitTests/runit.scipy2r.R |only inst/unitTests/runit.sparse.R | 18 inst/unitTests/runit.sparseConversion.R |only tests/doRUnit.R | 50 vignettes/RcppArmadillo-sparseMatrix.Rnw |only 72 files changed, 3006 insertions(+), 967 deletions(-)
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 0.1-5 dated 2017-06-08 and 0.1-6 dated 2017-08-17
wru-0.1-5/wru/R/State.FIPS.R |only wru-0.1-5/wru/R/pid.R |only wru-0.1-5/wru/man/State.FIPS.Rd |only wru-0.1-5/wru/man/pid.Rd |only wru-0.1-5/wru/man/surnames.Rd |only wru-0.1-6/wru/ChangeLog | 1 wru-0.1-6/wru/DESCRIPTION | 20 ++--- wru-0.1-6/wru/MD5 | 42 +++++------ wru-0.1-6/wru/R/census_geo_api.R | 42 ++++++----- wru-0.1-6/wru/R/census_helper.R | 126 ++++++++++++++++++---------------- wru-0.1-6/wru/R/get_census_data.R | 37 +++++---- wru-0.1-6/wru/R/merge_surnames.R | 3 wru-0.1-6/wru/R/predict_race.R | 56 +++++++++------ wru-0.1-6/wru/R/surnames2010.R | 4 - wru-0.1-6/wru/R/voters.R | 1 wru-0.1-6/wru/README.md | 75 +++++++++++--------- wru-0.1-6/wru/data/datalist | 2 wru-0.1-6/wru/data/surnames2010.RData |binary wru-0.1-6/wru/data/voters.RData |binary wru-0.1-6/wru/man/census_geo_api.Rd | 6 - wru-0.1-6/wru/man/census_helper.Rd | 7 + wru-0.1-6/wru/man/get_census_data.Rd | 7 + wru-0.1-6/wru/man/predict_race.Rd | 21 +++-- wru-0.1-6/wru/man/surnames2010.Rd |only wru-0.1-6/wru/man/voters.Rd | 1 25 files changed, 250 insertions(+), 201 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
should be familiar to experienced R users. Provides a wrapper for several
topic models that take similarly-formatted input and give similarly-formatted
output. Has additional functionality for analyzing and diagnostics for
topic models.
Author: Thomas Jones [aut, cre],
William Doane [ctb]
Maintainer: Thomas Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 2.0.5 dated 2017-04-07 and 2.0.6 dated 2017-08-17
textmineR-2.0.5/textmineR/src/textmineR_init.cpp |only textmineR-2.0.6/textmineR/DESCRIPTION | 15 ++++++----- textmineR-2.0.6/textmineR/MD5 | 13 ++++----- textmineR-2.0.6/textmineR/NAMESPACE | 2 - textmineR-2.0.6/textmineR/R/CreateTcm.R | 8 +++--- textmineR-2.0.6/textmineR/R/RcppExports.R | 14 +++++----- textmineR-2.0.6/textmineR/R/TmParallelApply.R | 1 textmineR-2.0.6/textmineR/src/RcppExports.cpp | 30 +++++++++++++++++------ 8 files changed, 50 insertions(+), 33 deletions(-)
Title: Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
Description: Bayesian reconstruction of disease outbreaks using epidemiological
and genetic information.
Author: Thibaut Jombart <thibautjombart@gmail.com>, Anne Cori, Joel Hellewell
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between outbreaker versions 1.1-7 dated 2015-12-07 and 1.1-8 dated 2017-08-17
DESCRIPTION | 11 +++++------ MD5 | 28 +++++++++++++++------------- NAMESPACE | 2 +- R/package.R | 2 +- R/simOutbreak.R | 7 +++++-- cleanup |only man/get.mu.Rd | 1 - man/outbreaker.Rd | 14 ++++++++------ man/outbreaker.package.Rd | 1 - man/plot.Rd | 7 ++++--- man/repro.Rd | 5 +++-- man/selectChains.Rd | 1 - man/simOutbreak.Rd | 21 ++++++++++++++------- man/simulated-outbreak-dataset.Rd | 3 +-- man/tTree.Rd | 12 +++++++----- src/outbreaker_init.c |only 16 files changed, 64 insertions(+), 51 deletions(-)
Title: A Tool for Automating Download and Preprocessing of MODIS Land
Products Data
Description: Allows automating the creation of time series of rasters derived
from MODIS Satellite Land Products data. It performs several typical
preprocessing steps such as download, mosaicking, reprojection and resize
of data acquired on a specified time period. All processing parameters
can be set using a user-friendly GUI. Users can select which layers of
the original MODIS HDF files they want to process, which additional
Quality Indicators should be extracted from aggregated MODIS Quality
Assurance layers and, in the case of Surface Reflectance products
, which Spectral Indexes should be computed from the original reflectance
bands. For each output layer, outputs are saved as single-band raster
files corresponding to each available acquisition date. Virtual files
allowing access to the entire time series as a single file are also created.
Command-line execution exploiting a previously saved processing options
file is also possible, allowing to automatically update time series
related to a MODIS product whenever a new image is available.
Author: Lorenzo Busetto [aut, cre],
Luigi Ranghetti [aut]
Maintainer: Lorenzo Busetto <lbusett@gmail.com>
Diff between MODIStsp versions 1.3.3 dated 2017-08-12 and 1.3.3.1 dated 2017-08-17
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 13 +++++++++++++ R/MODIStsp.R | 1 + R/MODIStsp_process_indexes.R | 8 ++++---- R/MODIStsp_vrt_create.R | 8 ++++---- build/vignette.rds |binary inst/doc/MODIStsp.Rmd | 2 +- inst/doc/MODIStsp.pdf |binary vignettes/MODIStsp.Rmd | 2 +- 11 files changed, 38 insertions(+), 23 deletions(-)
Title: Performing Multivariate Dose-Response Meta-Analysis
Description: It consists of a collection of
functions to estimate dose-response relations from summarized dose-response
data and to combine them according to principles of (multivariate)
random-effects model.
Author: Alessio Crippa
Maintainer: Alessio Crippa <alessio.crippa@ki.se>
Diff between dosresmeta versions 1.3.3 dated 2016-08-08 and 2.0.0 dated 2017-08-17
dosresmeta-1.3.3/dosresmeta/R/coef.dosresmeta.R |only dosresmeta-1.3.3/dosresmeta/R/grl.R |only dosresmeta-1.3.3/dosresmeta/R/hamling.R |only dosresmeta-1.3.3/dosresmeta/R/predict.dosresmeta.R |only dosresmeta-1.3.3/dosresmeta/R/summary.dosresmeta.R |only dosresmeta-2.0.0/dosresmeta/DESCRIPTION | 22 dosresmeta-2.0.0/dosresmeta/MD5 | 88 + dosresmeta-2.0.0/dosresmeta/NAMESPACE | 27 dosresmeta-2.0.0/dosresmeta/R/additional.R |only dosresmeta-2.0.0/dosresmeta/R/covariance.R |only dosresmeta-2.0.0/dosresmeta/R/dataset.R |only dosresmeta-2.0.0/dosresmeta/R/dosresmeta-package.R | 219 +--- dosresmeta-2.0.0/dosresmeta/R/dosresmeta.R | 963 +++++++++++++----- dosresmeta-2.0.0/dosresmeta/R/methods.R |only dosresmeta-2.0.0/dosresmeta/R/undocumented.R |only dosresmeta-2.0.0/dosresmeta/data/alcohol_esoph.rda |only dosresmeta-2.0.0/dosresmeta/data/alcohol_lc.rda |only dosresmeta-2.0.0/dosresmeta/data/ari.rda |only dosresmeta-2.0.0/dosresmeta/data/bmi_rc.rda |only dosresmeta-2.0.0/dosresmeta/data/ci_ex.rda |only dosresmeta-2.0.0/dosresmeta/data/coffee_cancer.rda |only dosresmeta-2.0.0/dosresmeta/data/coffee_cvd.rda |only dosresmeta-2.0.0/dosresmeta/data/coffee_mort.rda |only dosresmeta-2.0.0/dosresmeta/data/coffee_stroke.rda |only dosresmeta-2.0.0/dosresmeta/data/fish_ra.rda |only dosresmeta-2.0.0/dosresmeta/data/ir_ex.rda |only dosresmeta-2.0.0/dosresmeta/data/milk_mort.rda |only dosresmeta-2.0.0/dosresmeta/data/milk_ov.rda |only dosresmeta-2.0.0/dosresmeta/data/oc_breast.rda |only dosresmeta-2.0.0/dosresmeta/data/process_bc.rda |only dosresmeta-2.0.0/dosresmeta/data/red_bc.rda |only dosresmeta-2.0.0/dosresmeta/data/sim_os.rda |only dosresmeta-2.0.0/dosresmeta/inst/CITATION | 2 dosresmeta-2.0.0/dosresmeta/man/alcohol_crc.Rd | 19 dosresmeta-2.0.0/dosresmeta/man/alcohol_cvd.Rd | 22 dosresmeta-2.0.0/dosresmeta/man/alcohol_esoph.Rd |only dosresmeta-2.0.0/dosresmeta/man/alcohol_lc.Rd |only dosresmeta-2.0.0/dosresmeta/man/ari.Rd |only dosresmeta-2.0.0/dosresmeta/man/blup.dosresmeta.Rd |only dosresmeta-2.0.0/dosresmeta/man/bmi_rc.Rd |only dosresmeta-2.0.0/dosresmeta/man/cc_ex.Rd | 20 dosresmeta-2.0.0/dosresmeta/man/ci_ex.Rd |only dosresmeta-2.0.0/dosresmeta/man/coef.dosresmeta.Rd | 21 dosresmeta-2.0.0/dosresmeta/man/coffee_cancer.Rd |only dosresmeta-2.0.0/dosresmeta/man/coffee_cvd.Rd |only dosresmeta-2.0.0/dosresmeta/man/coffee_mort.Rd |only dosresmeta-2.0.0/dosresmeta/man/coffee_stroke.Rd |only dosresmeta-2.0.0/dosresmeta/man/covar.logrr.Rd |only dosresmeta-2.0.0/dosresmeta/man/covar.smd.Rd |only dosresmeta-2.0.0/dosresmeta/man/dosresmeta-package.Rd | 110 +- dosresmeta-2.0.0/dosresmeta/man/dosresmeta.Rd | 164 +-- dosresmeta-2.0.0/dosresmeta/man/dosresmeta.control.Rd |only dosresmeta-2.0.0/dosresmeta/man/dosresmeta.fixed.Rd |only dosresmeta-2.0.0/dosresmeta/man/dosresmeta.ml.Rd |only dosresmeta-2.0.0/dosresmeta/man/dosresmetaObject.Rd |only dosresmeta-2.0.0/dosresmeta/man/fish_ra.Rd |only dosresmeta-2.0.0/dosresmeta/man/fracpol.Rd |only dosresmeta-2.0.0/dosresmeta/man/gof.Rd |only dosresmeta-2.0.0/dosresmeta/man/grl.Rd | 78 - dosresmeta-2.0.0/dosresmeta/man/hamling.Rd | 85 - dosresmeta-2.0.0/dosresmeta/man/ir_ex.Rd |only dosresmeta-2.0.0/dosresmeta/man/logLik.dosresmeta.Rd |only dosresmeta-2.0.0/dosresmeta/man/milk_mort.Rd |only dosresmeta-2.0.0/dosresmeta/man/milk_ov.Rd |only dosresmeta-2.0.0/dosresmeta/man/mlprof.fun.Rd |only dosresmeta-2.0.0/dosresmeta/man/oc_breast.Rd |only dosresmeta-2.0.0/dosresmeta/man/predict.dosresmeta.Rd | 97 + dosresmeta-2.0.0/dosresmeta/man/process_bc.Rd |only dosresmeta-2.0.0/dosresmeta/man/qtest.dosresmeta.Rd |only dosresmeta-2.0.0/dosresmeta/man/red_bc.Rd |only dosresmeta-2.0.0/dosresmeta/man/sim_os.Rd |only dosresmeta-2.0.0/dosresmeta/man/summary.dosresmeta.Rd | 37 dosresmeta-2.0.0/dosresmeta/man/vpc.Rd |only dosresmeta-2.0.0/dosresmeta/man/waldtest.Rd |only 74 files changed, 1305 insertions(+), 669 deletions(-)
Title: Download and Aggregate Data from Public Hire Bicycle Systems
Description: Download and aggregate data from all public hire bicycle systems
which provide open data, currently including 'Santander' Cycles in London,
U.K., and from the U.S.A., 'citibike' in New York City NY, 'Divvy' in
Chicago IL, 'Capital Bikeshare' in Washington DC, 'Hubway' in Boston MA, and
'Metro' in Los Angeles LA.
Author: Mark Padgham [aut, cre],
Richard Ellison [aut],
Bea Hernández [rev] (Bea reviewed the package for ropensci, see
https://github.com/ropensci/onboarding/issues/116),
Elaine McVey [rev] (Elaine reviewed the package for ropensci, see
https://github.com/ropensci/onboarding/issues/116),
SQLite Consortium [ctb] (Authors of included SQLite code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between bikedata versions 0.0.3 dated 2017-07-14 and 0.0.4 dated 2017-08-17
DESCRIPTION | 24 MD5 | 55 - NAMESPACE | 13 R/RcppExports.R | 12 R/bikedata-package.R | 5 R/database-stats.R | 130 ++- R/stations.R | 9 R/store-bikedata.R | 97 ++ R/tripmat.R | 32 R/utils.R | 6 build/vignette.rds |binary inst/doc/bikedata.R | 3 inst/doc/bikedata.Rmd | 21 inst/doc/bikedata.html | 1283 +++++++++++++++++++++++++-------------- man/bike_daily_trips.Rd | 5 man/bike_datelimits.Rd | 3 man/bike_db_totals.Rd | 23 man/bike_demographic_data.Rd | 25 man/bike_rm_db.Rd | 3 man/bike_stations.Rd | 3 man/bike_summary_stats.Rd | 3 man/bike_tripmat.Rd | 3 man/index_bikedata_db.Rd |only man/store_bikedata.Rd | 9 src/RcppExports.cpp | 12 src/bikedata_init.c | 24 src/read-city-files.h | 6 tests/testthat/test-store-data.R | 6 vignettes/bikedata.Rmd | 21 29 files changed, 1205 insertions(+), 631 deletions(-)
Title: Geometric Shadow Calculations
Description: Functions for calculating (1) shadow heights; (2) shadow footprint on ground polygons; and (3) Sky View Factor values. Inputs include a polygonal layer of obstacle outlines along with their heights, sun azimuth and sun elevation. The package also provides functions for related preliminary calculations: breaking polygons into line segments, finding segment azimuth, shifting segments by azimuth and distance, and constructing the footprint of a line of sight between an observer and the sun.
Author: Michael Dorman [aut, cre],
Evyatar Erell [ctb],
Itai Kloog [ctb],
Adi Vulkan [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between shadow versions 0.3.3 dated 2017-06-14 and 0.3.5 dated 2017-08-17
DESCRIPTION | 6 +-- MD5 | 26 ++++++------- NEWS.md | 8 +++- R/SVF.R | 32 +++++++++++++++- R/SVFPnt.R | 82 ++++++++++++++++++++++++++++++++----------- R/checkInputs.R | 12 +++++- R/ray.R | 4 +- R/shadow.R | 21 +++++++---- R/shadowHeight.R | 85 ++++++++++++++++++++++++++++++++++++++------- build/vignette.rds |binary inst/doc/introduction.html | 10 ++--- man/SVF.Rd | 23 +++++++++++- man/shadow.Rd | 21 +++++++---- man/shadowHeight.Rd | 14 +++++-- 14 files changed, 265 insertions(+), 79 deletions(-)
Title: Multivariate Synthetic Control Method Using Time Series
Description: Multivariate Synthetic Control Method Using Time Series.
Three generalizations of the synthetic control method (which has already an
implementation in package 'Synth') are implemented: first, 'MSCMT' allows
for using multiple outcome variables, second, time series can be supplied as
economic predictors, and third, a well-defined cross-validation approach can be used.
Much effort has been taken to make the implementation as stable as possible
(including edge cases) without losing computational efficiency.
Author: Martin Becker [aut, cre],
Stefan Klößner [aut],
Karline Soetaert [com],
LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between MSCMT versions 1.2.0 dated 2017-01-30 and 1.3.0 dated 2017-08-17
DESCRIPTION | 24 +- MD5 | 75 ++++---- NAMESPACE | 10 + NEWS | 24 ++ R/Helpers.r | 349 +++++++++++++++++++++++++++++++++-------- R/MSCMT-package.r | 21 +- R/ModularOptimization.r | 18 ++ R/atomOpt.r | 56 ++++-- R/determine_v.r | 316 ++++++++++++++++++++++++------------- R/ggplot.r | 60 ++++--- R/improveSynth.r | 44 +++++ R/mscmt.r | 125 ++++++++++++-- R/multiOpt.r | 92 +++++++--- R/prepare.r | 14 + R/zzz.r | 2 build/partial.rdb |only build/vignette.rds |binary inst/REFERENCES.bib |only inst/doc/CheckingSynth.Rmd | 5 inst/doc/CheckingSynth.html | 38 ++-- inst/doc/UsingTimeSeries.Rmd | 9 - inst/doc/UsingTimeSeries.html | 25 ++ inst/doc/WorkingWithMSCMT.Rmd | 8 inst/doc/WorkingWithMSCMT.html | 66 ++++--- man/MSCMTfunction.Rd | 56 +++++- man/MSCMTpackage.Rd | 20 +- man/compare.Rd | 1 man/did.Rd | 1 man/ggplot.mscmt.Rd | 8 man/improveSynth.Rd | 1 man/listFromLong.Rd | 1 man/macros |only man/plot.mscmt.Rd | 1 man/ppratio.Rd | 1 man/print.mscmt.Rd | 1 man/pvalue.Rd | 1 src/MSCMT.c | 1 vignettes/CheckingSynth.Rmd | 5 vignettes/UsingTimeSeries.Rmd | 9 - vignettes/WorkingWithMSCMT.Rmd | 8 40 files changed, 1099 insertions(+), 397 deletions(-)