Title: Explorer of World Population Prospects
Description: Explore data in the 'wpp2015' (or 2012, 2010) package using a 'shiny' interface.
Author: Hana Sevcikova <hanas@uw.edu>
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wppExplorer versions 1.8-1 dated 2016-04-23 and 1.9-0 dated 2016-08-12
ChangeLog | 12 ++++++++- DESCRIPTION | 12 ++++----- MD5 | 18 ++++++------- NAMESPACE | 2 - R/global.R | 5 ++- R/wpp.R | 7 +++-- inst/explore/README.html | 2 - inst/explore/server.R | 58 ++++++++++++++++++++++++++++++++++++--------- inst/explore/ui.R | 4 ++- man/wppExplorer-package.Rd | 4 +-- 10 files changed, 87 insertions(+), 37 deletions(-)
Title: Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms
Description: Algorithms for accelerating the convergence of slow,
monotone sequences from smooth, contraction mapping such as the
EM algorithm. It can be used to accelerate any smooth, linearly
convergent acceleration scheme. A tutorial style introduction
to this package is available in a vignette on the CRAN download
page or, when the package is loaded in an R session, with
vignette("SQUAREM").
Author: Ravi Varadhan
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between SQUAREM versions 2014.8-1 dated 2014-08-28 and 2016.8-1 dated 2016-08-12
DESCRIPTION | 14 MD5 | 13 NAMESPACE | 7 NEWS | 6 build |only inst/doc/SQUAREM.Rnw | 933 +++++++++++++++++++++++++++++++++++++++----------- inst/doc/SQUAREM.pdf |binary vignettes/SQUAREM.Rnw | 933 +++++++++++++++++++++++++++++++++++++++----------- 8 files changed, 1483 insertions(+), 423 deletions(-)
Title: River Network Distance Computation and Applications
Description: Reads river network shape files and computes network distances.
Also included are a variety of computation and graphical tools designed
for fisheries telemetry research, such as minimum home range, kernel density
estimation, and clustering analysis using empirical k-functions with
a bootstrap envelope. Tools are also provided for editing the river
networks, meaning there is no reliance on external software.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matt.tyers@alaska.gov>
Diff between riverdist versions 0.12.0 dated 2016-07-05 and 0.12.2 dated 2016-08-12
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 16 ++++++++++++---- R/apps_of_direction.R | 12 ------------ R/detectbraiding.R | 2 +- R/segs_direction.R | 4 ++-- R/shortestroute_cleanup.R | 2 +- README.md | 2 +- man/riverdist-package.Rd | 4 ++-- 9 files changed, 33 insertions(+), 37 deletions(-)
Title: Rank Correlations
Description: Computes rank correlations and their p-values with various options for tied ranks.
Author: Amerise I. L. <ilaria.amerise@unical.it>, Marozzi M. <marco.marozzi@unical.it>, Tarsitano A. <agostino.tarsitano@unical.it>
Maintainer: Ilaria Lucrezia Amerise <ilaria.amerise@unical.it>
Diff between pvrank versions 1.1 dated 2016-02-24 and 1.1.1 dated 2016-08-12
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/comprank.R | 9 +++++---- R/qrank.R | 24 ++++++++++++------------ R/rankcor.R | 2 +- R/ranktes.R | 34 ++++++++++++++++++---------------- man/GGFR.Rd | 2 +- man/comprank.Rd | 32 +++++++++++++++++--------------- man/qrank.Rd | 6 +++--- man/rankor.Rd | 12 ++++++------ man/ranktes.Rd | 20 ++++++++++---------- 11 files changed, 86 insertions(+), 81 deletions(-)
Title: Simulation from Endpoint-Conditioned Continuous Time Markov
Chains
Description: Draw sample paths for endpoint-conditioned continuous time Markov chains via modified rejection sampling or uniformization.
Author: Jon Fintzi [aut, cre]
Maintainer: Jon Fintzi <fintzij@uw.edu>
Diff between ECctmc versions 0.2.1 dated 2016-07-01 and 0.2.2 dated 2016-08-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/ECctmc_vignette.Rmd | 2 +- inst/doc/ECctmc_vignette.html | 4 ++-- src/simulation_functions.cpp | 6 +++--- vignettes/ECctmc_vignette.Rmd | 2 +- 7 files changed, 17 insertions(+), 17 deletions(-)
Title: Design and Analysis of Mixture Experiments
Description: Functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.
Author: John Lawson [aut, cre],
Cameron Willden [aut],
Greg Piepel [ctb]
Maintainer: John Lawson <lawson@byu.edu>
Diff between mixexp versions 1.2.4 dated 2016-08-11 and 1.2.5 dated 2016-08-12
DESCRIPTION | 12 ++++++------ MD5 | 3 ++- inst |only 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Computes and Compares Species Richnesses
Description: Computes rarefaction curves, cumulated and mean species
richness. Compares these estimates by means of randomization
tests.
Author: Jean-Pierre Rossi
Maintainer: Jean-Pierre Rossi <jean-pierre.rossi@supagro.inra.fr>
Diff between rich versions 0.3 dated 2012-11-21 and 1.0.1 dated 2016-08-12
DESCRIPTION | 22 +++++++---- MD5 | 56 +++++++++++++++------------- NAMESPACE | 9 ++++ R/c2m.R | 108 ++++++++++++++++++++++++++----------------------------- R/rarc.R | 25 ++++++++---- R/raref.R | 4 +- R/raref2.R | 4 +- R/rich.R | 1 R/zzz.R | 14 ++----- build |only data/Tomicus.rda |binary data/ea.rda |binary data/ef.rda |binary data/efea.rda |binary data/efeb.rda |binary inst/doc |only man/Tomicus.Rd | 4 +- man/c2cv.Rd | 9 +--- man/c2m.Rd | 58 +++++++++++++++++++---------- man/ea.Rd | 2 - man/ef.Rd | 2 - man/efea.Rd | 2 - man/efeb.Rd | 2 - man/rarc.Rd | 45 +++++++++++++--------- man/raref.Rd | 9 ++-- man/raref2.Rd | 6 +-- man/rich.Rd | 7 ++- man/shared.Rd | 4 -- vignettes |only 29 files changed, 215 insertions(+), 178 deletions(-)
Title: Multivariate Distance Matrix Regression
Description: Allows a user to conduct multivariate distance matrix regression using analytic p-values and compute measures of effect size.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>
Diff between MDMR versions 0.4.1 dated 2016-08-05 and 0.4.2 dated 2016-08-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/mdmr.R | 13 ++++++++++--- inst/doc/mdmr-vignette.html | 4 ++-- 4 files changed, 19 insertions(+), 12 deletions(-)
Title: Ridge Estimation of Precision Matrices from High-Dimensional
Data
Description: Proper L2-penalized ML estimators for the
precision matrix as well as supporting functions to employ these estimators
in a graphical modeling setting.
Author: Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]
Maintainer: Carel F.W. Peeters <cf.peeters@vumc.nl>
Diff between rags2ridges versions 2.0 dated 2015-10-15 and 2.1 dated 2016-08-12
DESCRIPTION | 7 MD5 | 64 ++--- R/RcppExports.R | 8 R/rags2ridges.R | 460 +++++++++++++++++++++++++++++++++++---- R/rags2ridgesMisc.R | 67 +++++ README.md | 38 ++- inst/CITATION | 15 - inst/NEWS.Rd | 67 +++++ inst/RAGS.png |only man/CNplot.Rd |only man/GGMblockNullPenalty.Rd | 5 man/GGMblockTest.Rd | 2 man/GGMpathStats.Rd | 7 man/Ugraph.Rd | 84 ++++--- man/armaRidgeP.Rd | 8 man/conditionNumberPlot.Rd | 37 --- man/covML.Rd | 13 - man/covMLknown.Rd | 4 man/default.target.Rd | 9 man/edgeHeat.Rd | 2 man/fullMontyS.Rd | 5 man/fused.test.Rd | 2 man/is.Xlist.Rd | 5 man/loss.Rd | 7 man/optPenalty.LOOCV.Rd | 25 +- man/optPenalty.LOOCVauto.Rd | 32 ++ man/optPenalty.aLOOCV.Rd | 33 ++ man/print.optPenaltyFusedGrid.Rd | 6 man/rags2ridges-package.Rd | 8 man/ridgeP.Rd | 7 man/ridgePathS.Rd | 2 man/sparsify.Rd | 2 src/RcppExports.cpp | 26 ++ src/rags2ridges.cpp | 48 +++- 34 files changed, 889 insertions(+), 216 deletions(-)
Title: One Rule Machine Learning Classification Algorithm with
Enhancements
Description: Implements the One Rule (OneR) Machine Learning classification algorithm with enhancements for sophisticated handling of numeric data and missing values together with extensive diagnostic functions. It is useful as a baseline for machine learning models and the rules are often helpful heuristics.
Author: Holger von Jouanne-Diedrich
Maintainer: Holger von Jouanne-Diedrich <holger.jouanne-diedrich@h-ab.de>
Diff between OneR versions 1.3 dated 2016-07-22 and 2.0 dated 2016-08-12
DESCRIPTION | 13 +++-- MD5 | 40 +++++++++------ NEWS | 27 ++++++++++ R/OneR.R | 131 ++++++++++++++++++++++++++++++---------------------- R/OneR_data.R |only R/OneR_internal.R | 68 +++++++++++++++++--------- R/OneR_main.R | 22 +++++++- README.md | 6 -- build |only data |only inst |only man/OneR.Rd | 5 + man/bin.Rd | 6 +- man/breastcancer.Rd |only man/eval_model.Rd | 2 man/is.OneR.Rd | 2 man/maxlevels.Rd | 3 - man/optbin.Rd | 11 ++-- man/plot.OneR.Rd | 2 man/predict.OneR.Rd | 16 ++++-- man/print.OneR.Rd | 2 man/summary.OneR.Rd | 2 vignettes |only 23 files changed, 233 insertions(+), 125 deletions(-)
Title: Multivariate Functional Principal Component Analysis for Data
Observed on Different Dimensional Domains
Description: Calculate a multivariate functional principal component analysis
for data observed on different dimensional domains. The estimation algorithm
relies on univariate basis expansions for each element of the multivariate
functional data. Multivariate and univariate functional data objects are
represented by S4 classes for this type of data implemented in the package
'funData'.
Author: Clara Happ [aut, cre]
Maintainer: Clara Happ <clara.happ@stat.uni-muenchen.de>
Diff between MFPCA versions 1.0 dated 2016-07-22 and 1.0-1 dated 2016-08-12
MFPCA-1.0-1/MFPCA/DESCRIPTION | 6 +++--- MFPCA-1.0-1/MFPCA/MD5 | 8 ++++---- MFPCA-1.0-1/MFPCA/inst |only MFPCA-1.0-1/MFPCA/tests/testthat/test_univDecomp.R | 4 ++-- MFPCA-1.0-1/MFPCA/tests/testthat/test_univExpansion.R | 9 +++++++-- MFPCA-1.0/MFPCA/configure |only 6 files changed, 16 insertions(+), 11 deletions(-)
Title: Bi-Level Optimization of Metabolic Network Models
Description: Initial metabolic networks often inaccurately predict in-silico growth or non-growth if compared to in-vivo data. This package refines metabolic network models by making networks changes (i.e., removing, adding, changing reversibility of reactions; adding and removing biomass metabolites) and simultaneously matching sets of experimental growth and non-growth data (e.g., KO-mutants, mutants grown under different media conditions,...)
Author: Daniel Hartleb
Maintainer: Daniel Hartleb <daniel.hartleb@hhu.de>
Diff between GlobalFit versions 1.1 dated 2016-03-31 and 1.2 dated 2016-08-12
DESCRIPTION | 8 - MD5 | 30 ++--- R/FastGlobalFit.R | 22 +-- R/FastGlobalFit_MULT_BIOM.R |only R/GlobalFit.R | 16 -- R/GlobalFit_methods.R | 107 +++++++++++++----- build/partial.rdb |binary data/example_net1.rda |binary data/example_net2.rda |binary data/example_net3.rda |binary man/GlobalFit-package.Rd | 93 ++++++++------- man/bilevel_optimize.Rd | 142 ++++++++++++++---------- man/example_net1.Rd | 2 man/example_net2.Rd | 2 man/sysBiolAlg_FastGlobalFit-class.Rd | 12 -- man/sysBiolAlg_FastGlobalFit_MULT_BIOM-class.Rd |only man/sysBiolAlg_GlobalFit-class.Rd | 12 -- 17 files changed, 257 insertions(+), 189 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photographs, computes record databases and detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station) and can visualise activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <niedballa@izw-berlin.de>
Diff between camtrapR versions 0.99.3 dated 2016-08-01 and 0.99.4 dated 2016-08-12
DESCRIPTION | 8 - MD5 | 21 +-- NEWS | 19 ++- R/onAttach.R |only R/spatialDetectionHistory.R | 142 ++++++++++++---------- R/variousOtherHelperFunctions.R | 29 ++++ inst/doc/DataExploration.html | 14 +- inst/doc/DataExtraction.html | 164 +++++++++++++------------- inst/doc/ImageOrganisation.html | 56 ++++---- inst/doc/SpeciesIndividualIdentification.html | 92 +++++++------- man/recordTableIndividual.Rd | 13 -- man/spatialDetectionHistory.Rd | 40 +++--- 12 files changed, 331 insertions(+), 267 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-04 1.0.0
Title: Easily Tidy Data with `spread()` and `gather()` Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.5.1 dated 2016-06-14 and 0.6.0 dated 2016-08-12
tidyr-0.5.1/tidyr/data/table4.rdata |only tidyr-0.5.1/tidyr/data/table6.rdata |only tidyr-0.5.1/tidyr/man/population.Rd |only tidyr-0.6.0/tidyr/DESCRIPTION | 6 tidyr-0.6.0/tidyr/MD5 | 49 ++++--- tidyr-0.6.0/tidyr/NAMESPACE | 7 + tidyr-0.6.0/tidyr/NEWS.md | 23 +++ tidyr-0.6.0/tidyr/R/data.R | 61 +++++---- tidyr-0.6.0/tidyr/R/drop_na.r |only tidyr-0.6.0/tidyr/R/expand.R | 44 +++++- tidyr-0.6.0/tidyr/R/seq.R | 4 tidyr-0.6.0/tidyr/R/unnest.R | 2 tidyr-0.6.0/tidyr/R/utils.R | 13 -- tidyr-0.6.0/tidyr/README.md | 2 tidyr-0.6.0/tidyr/data/table2.rdata |binary tidyr-0.6.0/tidyr/data/table3.rdata |binary tidyr-0.6.0/tidyr/data/table4a.rdata |only tidyr-0.6.0/tidyr/data/table4b.rdata |only tidyr-0.6.0/tidyr/data/table5.rdata |binary tidyr-0.6.0/tidyr/inst/doc/tidy-data.html | 156 ++++++++++-------------- tidyr-0.6.0/tidyr/man/complete.Rd | 8 - tidyr-0.6.0/tidyr/man/drop_na.Rd |only tidyr-0.6.0/tidyr/man/drop_na_.Rd |only tidyr-0.6.0/tidyr/man/expand.Rd | 18 ++ tidyr-0.6.0/tidyr/man/extract_numeric.Rd | 13 -- tidyr-0.6.0/tidyr/man/table1.Rd | 23 ++- tidyr-0.6.0/tidyr/man/unnest.Rd | 2 tidyr-0.6.0/tidyr/man/who.Rd | 26 ++-- tidyr-0.6.0/tidyr/tests/testthat/test-drop_na.R |only tidyr-0.6.0/tidyr/tests/testthat/test-expand.R | 9 + 30 files changed, 277 insertions(+), 189 deletions(-)
Title: Mid-Domain Effect and Species Richness Patterns
Description: Generates expected values of species richness, with continuous or
scattered ranges, for data across one or two dimensions.
Author: Aniruddha Marathe, ATREE, Bangalore
Maintainer: Aniruddha Marathe <aniruddha.pravin.marathe@gmail.com>
Diff between rangemodelR versions 1.0 dated 2016-02-09 and 1.0.1 dated 2016-08-12
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++++---------- NAMESPACE | 2 ++ R/rangemod1d.R |only R/rangemod2d.R |only R/rangemod_2d.R | 13 ++++++++----- R/rangemodelR-package.R | 2 +- R/rangemodel_1d.R | 14 +++++++++----- data/shp.rda |binary data/spmat.rda |binary man/rangemod.1d.Rd | 6 +++++- man/rangemod.2d.Rd | 9 ++++++--- man/rangemod1d.Rd |only man/rangemod2d.Rd |only man/rangemodelR-package.Rd | 2 +- 15 files changed, 51 insertions(+), 31 deletions(-)
Title: Extract Text and Data from PDF Documents
Description: Utilities based on libpoppler for extracting text,
fonts, attachments and metadata from a pdf file. Also implements
rendering of PDF to bitmaps on supported platforms.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between pdftools versions 0.3 dated 2016-04-08 and 0.4 dated 2016-08-12
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 5 +++++ R/tools.R | 10 +++++----- configure | 4 ++-- man/pdftools.Rd | 10 +++++----- src/Makevars.win | 12 ++++++++---- tools/winlibs.R | 6 +++--- 8 files changed, 38 insertions(+), 29 deletions(-)
Title: Calculate and Plot Decision Curves
Description: Decision curves are a useful tool to evaluate the population impact
of adopting a risk prediction instrument into clinical practice. Given one or more
instruments (risk models) that predict the probability of a binary outcome, this
package calculates and plots decision curves, which display estimates of the
standardized net benefit by the probability threshold used to categorize observations
as 'high risk.' Curves can be estimated using data from an observational cohort, or
from case-control studies when an estimate of the population outcome prevalence
is available. Confidence intervals calculated using the bootstrap can be displayed and
a wrapper function to calculate cross-validated curves using k-fold cross-validation is
also provided.
Author: Marshall Brown
Maintainer: Marshall Brown <mdbrown@fredhutch.org>
Diff between DecisionCurve versions 1.1 dated 2016-01-13 and 1.3 dated 2016-08-12
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- NEWS |only R/cv_decision_curve.R | 2 +- R/decision_curve.R | 6 +++++- R/plot_functions_sub.R | 15 +++++++++++---- README.md | 29 +++++++++++++++++++++++------ inst/notes/tutorial.Rmd | 12 +++++++++++- inst/notes/tutorial.html |only man/decision_curve.Rd | 2 +- 10 files changed, 65 insertions(+), 25 deletions(-)