Title: Species Distribution Modelling
Description: An extensible R framework for developing species distribution
models using individual and community-based approaches, generate ensembles of
models, evaluate the models, and predict species potential distributions in
space and time.
Author: Babak Naimi, Miguel B. Araujo
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between sdm versions 1.0-10 dated 2016-04-07 and 1.0-25 dated 2016-07-15
sdm-1.0-10/sdm/inst/external/model.sdm.rds |only sdm-1.0-25/sdm/DESCRIPTION | 14 +-- sdm-1.0-25/sdm/MD5 | 70 ++++++++++------- sdm-1.0-25/sdm/NAMESPACE | 6 - sdm-1.0-25/sdm/R/AAAClasses.R | 59 ++++++++++++++- sdm-1.0-25/sdm/R/calibration.R |only sdm-1.0-25/sdm/R/density.R |only sdm-1.0-25/sdm/R/evaluates.R | 61 +++++++++++---- sdm-1.0-25/sdm/R/gui.R |only sdm-1.0-25/sdm/R/isntallAll.R | 6 - sdm-1.0-25/sdm/R/plot.R | 114 +++++++++++++++++++++++++++-- sdm-1.0-25/sdm/R/roc.R | 25 +++--- sdm-1.0-25/sdm/R/sdmData.R | 25 +++++- sdm-1.0-25/sdm/R/show.R | 17 +++- sdm-1.0-25/sdm/R/varImp.R |only sdm-1.0-25/sdm/build/vignette.rds |binary sdm-1.0-25/sdm/inst/doc/quick_sdm.html | 65 ++++++++-------- sdm-1.0-25/sdm/inst/external/model.sdm |only sdm-1.0-25/sdm/inst/shinyApps |only sdm-1.0-25/sdm/man/add.Rd | 2 sdm-1.0-25/sdm/man/as.data.frame.Rd | 2 sdm-1.0-25/sdm/man/boxplot.Rd |only sdm-1.0-25/sdm/man/calibration.Rd |only sdm-1.0-25/sdm/man/density.Rd |only sdm-1.0-25/sdm/man/evaluates.Rd | 45 ++++++++++- sdm-1.0-25/sdm/man/extractIndex.Rd | 2 sdm-1.0-25/sdm/man/featuresFrame-class.Rd | 2 sdm-1.0-25/sdm/man/getModelInfo.Rd | 2 sdm-1.0-25/sdm/man/gui.Rd |only sdm-1.0-25/sdm/man/installAll.Rd | 2 sdm-1.0-25/sdm/man/names.Rd | 2 sdm-1.0-25/sdm/man/predict.Rd | 2 sdm-1.0-25/sdm/man/read.sdm.Rd | 2 sdm-1.0-25/sdm/man/roc.Rd | 2 sdm-1.0-25/sdm/man/sdm.Rd | 2 sdm-1.0-25/sdm/man/sdmData.Rd | 2 sdm-1.0-25/sdm/man/sdmModel-class.Rd | 2 sdm-1.0-25/sdm/man/sdmSetting.Rd | 2 sdm-1.0-25/sdm/man/subset.Rd | 2 sdm-1.0-25/sdm/man/varImportance.Rd |only 40 files changed, 422 insertions(+), 115 deletions(-)
Title: Daily Streamflow Trend and Change Point Screening
Description: Screens daily streamflow time series for temporal trends and
change-points. This package has been primarily developed for assessing
the quality of daily streamflow time series. It also contains tools for
plotting and calculating many different streamflow metrics. The package can be
used to produce summary screening plots showing change-points and significant
temporal trends for high flow, low flow, and/or baseflow statistics, or it can
be used to perform more detailed hydrological time series analyses. The
package was designed for screening daily streamflow time series from Water
Survey Canada and the United States Geological Survey but will also work
with streamflow time series from many other agencies.
Author: Jennifer Dierauer [aut, cre],
Paul Whitfield [aut]
Maintainer: Jennifer Dierauer <jen.r.brand@gmail.com>
Diff between FlowScreen versions 1.2 dated 2016-06-22 and 1.2.1 dated 2016-07-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/read.flows.R | 2 +- R/screen.cpts.R | 16 +++++++++++----- man/read.flows.Rd | 2 +- 5 files changed, 20 insertions(+), 14 deletions(-)
Title: T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
Description: A "pure R" implementation of the t-SNE algorithm.
Author: Justin Donaldson <jdonaldson@gmail.com>
Maintainer: Justin Donaldson <jdonaldson@gmail.com>
Diff between tsne versions 0.1-2 dated 2012-05-02 and 0.1-3 dated 2016-07-15
DESCRIPTION | 13 ++++++++----- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS | 3 ++- R/tsne.R | 27 ++++++++++----------------- man/tsne-package.Rd | 2 +- man/tsne.Rd | 10 ++++++---- 7 files changed, 34 insertions(+), 34 deletions(-)
Title: Tools for Multiple Imputation in Multilevel Modeling
Description: Provides tools for multiple imputation of missing data in multilevel
modeling. Includes a user-friendly interface to the packages 'pan' and 'jomo',
and several functions for visualization, data management and the analysis
of multiply imputed data sets.
Author: Simon Grund [aut,cre], Alexander Robitzsch [aut], Oliver Luedtke [aut]
Maintainer: Simon Grund <grund@ipn.uni-kiel.de>
Diff between mitml versions 0.3-2 dated 2016-05-30 and 0.3-3 dated 2016-07-15
DESCRIPTION | 8 - MD5 | 30 ++-- NEWS | 21 +++ R/internal-convergence.R | 6 R/internal-model.R | 140 ++++++++++++++++++++- R/jomoImpute.R | 250 +++++++++++++++++++++++++++++--------- R/panImpute.R | 18 ++ R/plot.mitml.R | 303 ++++++++++++++++++++++++++++++++++++++--------- R/print.mitml.R | 19 ++ R/print.mitml.summary.R | 53 +++++--- R/summary.mitml.R | 237 +++++++++++++++++++----------------- data/leadership.rda |only man/jomoImpute.Rd | 109 +++++++--------- man/justice.Rd | 2 man/leadership.Rd |only man/panImpute.Rd | 7 - man/plot.mitml.Rd | 7 - 17 files changed, 857 insertions(+), 353 deletions(-)
Title: Spatial Analysis of Phenotypic, Genotypic and Environmental Data
Description: Geostatistical tools for analyzing spatial patterns in
population biology. Easy integration of information from multiple sources
with "ecogen" objects.
Author: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Maintainer: Leandro Roser <learoser@gmail.com>
Diff between EcoGenetics versions 1.2.0-2 dated 2015-07-11 and 1.2.0-3 dated 2016-07-15
EcoGenetics-1.2.0-2/EcoGenetics/NEWS |only EcoGenetics-1.2.0-2/EcoGenetics/man/aue.diamond.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.2symmetric.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.dlatlon2distm.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.undimmattg.Rd |only EcoGenetics-1.2.0-3/EcoGenetics/DESCRIPTION | 23 EcoGenetics-1.2.0-3/EcoGenetics/MD5 | 366 ++-- EcoGenetics-1.2.0-3/EcoGenetics/NAMESPACE | 24 EcoGenetics-1.2.0-3/EcoGenetics/R/ZZZ.R | 5 EcoGenetics-1.2.0-3/EcoGenetics/R/accesors.R | 198 -- EcoGenetics-1.2.0-3/EcoGenetics/R/auxiliar.R | 340 ++- EcoGenetics-1.2.0-3/EcoGenetics/R/classes.R | 57 EcoGenetics-1.2.0-3/EcoGenetics/R/deprecated.R | 18 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.2spagedi.R | 198 +- EcoGenetics-1.2.0-3/EcoGenetics/R/eco.NDVI.post.R | 4 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.alfreq.R | 91 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.cormantel.R | 170 - EcoGenetics-1.2.0-3/EcoGenetics/R/eco.correlog.R | 95 - EcoGenetics-1.2.0-3/EcoGenetics/R/eco.detrend.R | 55 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.forestplot.R | 267 +- EcoGenetics-1.2.0-3/EcoGenetics/R/eco.format.R | 24 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.genepop2df.R | 6 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.gsa.R | 56 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.kin.loiselle.R | 2 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.lagweight.R | 491 ++--- EcoGenetics-1.2.0-3/EcoGenetics/R/eco.lmtree.R | 12 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.lsa.R | 911 ++++++---- EcoGenetics-1.2.0-3/EcoGenetics/R/eco.malecot.R | 304 +-- EcoGenetics-1.2.0-3/EcoGenetics/R/eco.mantel.R | 98 - EcoGenetics-1.2.0-3/EcoGenetics/R/eco.merge.R | 74 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.pairtest.R | 219 +- EcoGenetics-1.2.0-3/EcoGenetics/R/eco.post.geneland.R | 2 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.rankplot.R | 518 ++--- EcoGenetics-1.2.0-3/EcoGenetics/R/eco.rasterplot.R |only EcoGenetics-1.2.0-3/EcoGenetics/R/eco.rbind.R | 106 - EcoGenetics-1.2.0-3/EcoGenetics/R/eco.slide.con.R |only EcoGenetics-1.2.0-3/EcoGenetics/R/eco.slide.matrix.R |only EcoGenetics-1.2.0-3/EcoGenetics/R/eco.subset.R | 113 - EcoGenetics-1.2.0-3/EcoGenetics/R/eco.theilsen.R | 4 EcoGenetics-1.2.0-3/EcoGenetics/R/eco.variogram.R | 152 - EcoGenetics-1.2.0-3/EcoGenetics/R/eco.weight.R | 326 ++- EcoGenetics-1.2.0-3/EcoGenetics/R/ecogen.1OF5.definition.R | 2 EcoGenetics-1.2.0-3/EcoGenetics/R/ecogen.2OF5.constructor.R | 47 EcoGenetics-1.2.0-3/EcoGenetics/R/ecogen.3OF5.basic.methods.R | 192 +- EcoGenetics-1.2.0-3/EcoGenetics/R/ecogen.4OF5.brackets.R | 63 EcoGenetics-1.2.0-3/EcoGenetics/R/ecogen.5OF5.get&set.R | 55 EcoGenetics-1.2.0-3/EcoGenetics/R/int.break.R | 409 ++-- EcoGenetics-1.2.0-3/EcoGenetics/R/int.convert.R | 9 EcoGenetics-1.2.0-3/EcoGenetics/R/int.crosscor.R | 3 EcoGenetics-1.2.0-3/EcoGenetics/R/int.genind.R | 28 EcoGenetics-1.2.0-3/EcoGenetics/R/int.jackknife.R | 36 EcoGenetics-1.2.0-3/EcoGenetics/R/int.joincount.R | 8 EcoGenetics-1.2.0-3/EcoGenetics/R/int.kin.loiselle.R | 84 EcoGenetics-1.2.0-3/EcoGenetics/R/int.mantel.R | 6 EcoGenetics-1.2.0-3/EcoGenetics/R/int.multitable.R | 76 EcoGenetics-1.2.0-3/EcoGenetics/R/int.random.test.R | 415 ++-- EcoGenetics-1.2.0-3/EcoGenetics/R/miscellaneous.R | 63 EcoGenetics-1.2.0-3/EcoGenetics/R/plot.generic.R |only EcoGenetics-1.2.0-3/EcoGenetics/R/plot.methods.R | 671 ++++--- EcoGenetics-1.2.0-3/EcoGenetics/R/roxygen.auxiliar.R |only EcoGenetics-1.2.0-3/EcoGenetics/R/show_summary.methods.R | 334 ++- EcoGenetics-1.2.0-3/EcoGenetics/data/sokal1986.RData |only EcoGenetics-1.2.0-3/EcoGenetics/man/EcoGenetics-accessors.Rd | 251 +- EcoGenetics-1.2.0-3/EcoGenetics/man/EcoGenetics-package.Rd | 51 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.access.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.ad2wg.Rd |only EcoGenetics-1.2.0-3/EcoGenetics/man/aue.circle.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.circle.w.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.df2image.Rd |only EcoGenetics-1.2.0-3/EcoGenetics/man/aue.ellipse.Rd |only EcoGenetics-1.2.0-3/EcoGenetics/man/aue.filter.Rd | 32 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.fqal.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.genlab.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.geom.dist.Rd |only EcoGenetics-1.2.0-3/EcoGenetics/man/aue.image2df.Rd | 11 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.is.poly.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.phenosimil.Rd |only EcoGenetics-1.2.0-3/EcoGenetics/man/aue.point.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.rescale.Rd | 19 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.rm.nonpoly.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.rmspaces.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.rotate.Rd |only EcoGenetics-1.2.0-3/EcoGenetics/man/aue.seqlist.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.sort.Rd | 24 EcoGenetics-1.2.0-3/EcoGenetics/man/aue.square.Rd | 8 EcoGenetics-1.2.0-3/EcoGenetics/man/coordinates.Rd | 6 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.2geneland.Rd | 8 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.2genepop.Rd | 6 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.2gstudio.Rd | 8 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.2hierfstat.Rd | 8 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.2spagedi.Rd | 24 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.IBD-class.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.IBD-methods.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.IBD.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.NDVI.Rd | 33 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.NDVI.post.Rd | 33 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.Rd | 4 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.alfreq.Rd | 12 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.association.Rd | 12 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.autol-methods.Rd | 13 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.cbind.Rd | 14 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.clear.Rd | 6 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.convert.Rd | 20 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.cormantel.Rd | 38 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.correlog-class.Rd | 2 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.correlog-methods.Rd | 14 EcoGenetics-1.2.0-3/EcoGenetics/man/eco.correlog.Rd | 124 - 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Title: Functions to Embed Video in HTML
Description: A set of functions for generating HTML to
embed hosted video in your R Markdown documents or Shiny apps.
Author: Ian Lyttle [aut, cre, cph]
Maintainer: Ian Lyttle <ian.lyttle@schneider-electric.com>
Diff between vembedr versions 0.1.0 dated 2016-05-27 and 0.1.1 dated 2016-07-15
vembedr-0.1.0/vembedr/tests/testthat/test-secs.R |only vembedr-0.1.1/vembedr/DESCRIPTION | 8 vembedr-0.1.1/vembedr/MD5 | 43 +- vembedr-0.1.1/vembedr/NAMESPACE | 11 vembedr-0.1.1/vembedr/NEWS.md | 17 + vembedr-0.1.1/vembedr/R/embed.R | 80 +++++ vembedr-0.1.1/vembedr/R/helper.R | 29 + vembedr-0.1.1/vembedr/R/pipe.R |only vembedr-0.1.1/vembedr/R/rickroll.R | 11 vembedr-0.1.1/vembedr/R/use_start_time.R |only vembedr-0.1.1/vembedr/R/vembedr.R | 7 vembedr-0.1.1/vembedr/README.md | 148 +++++++--- vembedr-0.1.1/vembedr/build/vignette.rds |binary vembedr-0.1.1/vembedr/inst/doc/embed.R | 37 +- vembedr-0.1.1/vembedr/inst/doc/embed.Rmd | 135 ++++++--- vembedr-0.1.1/vembedr/inst/doc/embed.html | 126 +++++--- vembedr-0.1.1/vembedr/man/embed.Rd | 23 + vembedr-0.1.1/vembedr/man/hms.Rd |only vembedr-0.1.1/vembedr/man/pipe.Rd |only vembedr-0.1.1/vembedr/man/rickroll.Rd | 4 vembedr-0.1.1/vembedr/man/secs.Rd | 2 vembedr-0.1.1/vembedr/man/use_start_time.Rd |only vembedr-0.1.1/vembedr/man/vembedr.Rd | 7 vembedr-0.1.1/vembedr/tests/testthat/test-deprecate-allow_full_screen.R |only vembedr-0.1.1/vembedr/tests/testthat/test-secs-hms.R |only vembedr-0.1.1/vembedr/tests/testthat/test-use_start_time.R |only vembedr-0.1.1/vembedr/vignettes/embed.Rmd | 135 ++++++--- 27 files changed, 606 insertions(+), 217 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability
to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally,
'ggtern' has implemented several NEW geometries which are unavailable to the
standard 'ggplot2' release. For further examples and documentation, please
proceed to the 'ggtern' website.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 2.1.2 dated 2016-07-05 and 2.1.3 dated 2016-07-15
DESCRIPTION | 9 MD5 | 38 +- NAMESPACE | 2 NEWS | 14 R/annotation-tern.R |only R/coord-tern.R | 617 +++++++++++++++++++++++++------------------ R/geom-interpolate-tern.R | 7 R/geom-mask.R | 88 +++++- R/onLoad.R | 31 +- R/plot-build.R | 7 R/stat-interpolate-tern.R | 59 +--- R/theme-bordersontop.R | 8 R/theme-defaults.R | 592 +++++++++++++++++++---------------------- R/theme-elements.R | 38 +- R/theme-novar-tern.R | 1 R/utilities.R | 16 - build/partial.rdb |binary man/annotate.Rd |only man/geom_interpolate_tern.Rd | 19 - man/ggtern_themes.Rd | 33 +- man/undocumented.Rd | 4 21 files changed, 885 insertions(+), 698 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis of spectral data obtained via nuclear magnetic resonance (NMR), infrared (IR) or Raman spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette covering typical operations is available.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpec versions 4.3.17 dated 2016-03-24 and 4.3.34 dated 2016-07-15
DESCRIPTION | 8 +++---- MD5 | 21 ++++++++++-------- NAMESPACE | 3 +- NEWS | 19 +++++++++++++++++ R/files2SpectraObject.R | 49 ++++++++++++++++++++------------------------ R/matrix2SpectraObject.R |only R/readJDX.R | 29 +++++++++++++++----------- R/readJEOLascii.R |only R/removeSample.R | 2 - inst/doc/ChemoSpec.pdf |binary man/files2SpectraObject.Rd | 28 +++++++++++++++---------- man/matrix2SpectraObject.Rd |only man/plotSpectraJS.Rd | 3 ++ 13 files changed, 98 insertions(+), 64 deletions(-)
Title: Cox Model for Case-Cohort Data with Stratified
Subcohort-Selection
Description: Contains a function, also called 'cchs', that calculates Estimator III of Borgan et al (2000), <DOI:10.1023/A:1009661900674>. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.
Author: E. Jones
Maintainer: E. Jones <r-cchs@outlook.com>
Diff between cchs versions 0.2.0 dated 2016-01-26 and 0.3.0 dated 2016-07-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 12 +++++++----- R/cchs-class.R | 25 +++++++++++++++++++++++++ R/cchs.R | 8 ++------ data/cchsData.rda |binary man/cchs.Rd | 2 ++ 7 files changed, 47 insertions(+), 22 deletions(-)
Title: Procedures to Generate Patterns under Computerized Adaptive
Testing
Description: Generation of response patterns under dichotomous and polytomous computerized adaptive testing (CAT) framework.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis <david.magis@ulg.ac.be>
Diff between catR versions 3.8 dated 2016-06-13 and 3.9 dated 2016-07-15
DESCRIPTION | 8 - MD5 | 22 ++--- NEWS | 28 ++++++ R/genPattern.R | 32 ++++--- R/nextItem.R | 129 +++++++++++++++++------------- R/randomCAT.R | 77 ++++++++++-------- R/simulateRespondents.R | 200 +++++++++++++++++++++++++++--------------------- R/startItems.R | 42 ++++++---- R/testList.R | 42 +++++----- man/nextItem.Rd | 8 + man/randomCAT.Rd | 19 ++-- man/startItems.Rd | 7 + 12 files changed, 365 insertions(+), 249 deletions(-)
Title: Response Time Distributions
Description: Provides response time distributions (density/PDF, distribution
function/CDF, quantile function, and random generation): (a) Ratcliff diffusion
model based on C code by Andreas and Jochen Voss and (b) linear ballistic
accumulator (LBA) with different distributions underlying the drift rate.
Author: Henrik Singmann [aut, cre],
Scott Brown [aut],
Matthew Gretton [aut],
Andrew Heathcote [aut],
Andreas Voss [ctb],
Jochen Voss [ctb],
Andrew Terry [ctb]
Maintainer: Henrik Singmann <singmann+rtdists@gmail.com>
Diff between rtdists versions 0.6-5 dated 2016-07-05 and 0.6-6 dated 2016-07-15
DESCRIPTION | 17 ++++++----- MD5 | 14 ++++----- NEWS | 5 +++ R/diffusion.R | 55 ++++++++++++++++++++------------------ R/rtdists-package.R | 4 +- man/Diffusion.Rd | 43 ++++++++++++++++++++++++++++-- man/rtdists-package.Rd | 4 +- tests/testthat/test-diffusion.R | 57 +++++++++++++++++++++++++++++++++++++--- 8 files changed, 148 insertions(+), 51 deletions(-)
Title: Relationship Inference for DNA Mixtures
Description: Makes relationship inference involving DNA mixtures with unknown profiles.
Author: Navreet Kaur, Thore Egeland, Guro Dorum
Maintainer: Guro Dorum <guro.dorum@gmail.com>
Diff between relMix versions 1.0 dated 2015-12-09 and 1.1 dated 2016-07-15
relMix-1.0/relMix/R/extRelMix.R |only relMix-1.0/relMix/R/generate.R |only relMix-1.0/relMix/build |only relMix-1.0/relMix/man/extRelMix.Rd |only relMix-1.0/relMix/man/generate.Rd |only relMix-1.0/relMix/man/relMix-package.Rd |only relMix-1.1/relMix/DESCRIPTION | 19 +- relMix-1.1/relMix/MD5 | 30 ++-- relMix-1.1/relMix/NAMESPACE | 6 relMix-1.1/relMix/R/allGenos.R |only relMix-1.1/relMix/R/allGenosRel.R |only relMix-1.1/relMix/R/createDatamatrix.R |only relMix-1.1/relMix/R/generateMix.R |only relMix-1.1/relMix/R/globals.R | 9 - relMix-1.1/relMix/R/mixLikDrop.R |only relMix-1.1/relMix/R/relMix.R | 99 ++++++++++--- relMix-1.1/relMix/R/relMixGUI.R |only relMix-1.1/relMix/data/db2.RData |only relMix-1.1/relMix/man/allGenos.Rd |only relMix-1.1/relMix/man/allGenosRel.Rd |only relMix-1.1/relMix/man/createDatamatrix.Rd |only relMix-1.1/relMix/man/db2.Rd |only relMix-1.1/relMix/man/generateMix.Rd |only relMix-1.1/relMix/man/mixLikDrop.Rd |only relMix-1.1/relMix/man/relMix.Rd | 219 +++++++++++++++++------------- relMix-1.1/relMix/man/relMixGUI.Rd |only 26 files changed, 247 insertions(+), 135 deletions(-)
Title: Reproducible Retrieval of Pew Research Center Datasets
Description: Reproducible, programmatic retrieval of survey datasets from the
Pew Research Center.
Author: Frederick Solt [aut, cre],
Eric Persson [ctb]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Diff between pewdata versions 0.1.0 dated 2016-05-12 and 0.1.1 dated 2016-07-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 3 +++ R/pew_download.R | 2 +- README.md | 7 +++++-- build/vignette.rds |binary inst/doc/pewdata-vignette.html | 4 ++-- 7 files changed, 21 insertions(+), 15 deletions(-)
Title: Simplify Analysis and Annotation of Human Microarray Datasets
Description: Utilises GRanges, data.frame or IRanges objects. Integrates gene annotation for ImmunoChip (or your custom chip) with function calls. Intuitive wrappers for annotation lookup (gene lists, exon ranges, etc) and conversion (e.g, between build 36 and 37 coordinates). Conversion between ensembl and HGNC gene ids, chip ids to rs-ids for SNP-arrays. Retrieval of chromosome and position for gene, band or SNP-ids, or reverse lookup. Simulation functions for ranges objects.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper <njcooper@gmx.co.uk>
Diff between humarray versions 1.0.0 dated 2016-03-03 and 1.0.2 dated 2016-07-15
humarray-1.0.0/humarray/man/toGenomeOrder-methods.Rd |only humarray-1.0.2/humarray/DESCRIPTION | 17 - humarray-1.0.2/humarray/MD5 | 13 - humarray-1.0.2/humarray/NAMESPACE | 42 +-- humarray-1.0.2/humarray/R/humarray.R | 223 ++++++++++++++----- humarray-1.0.2/humarray/man/chrSelect.Rd | 2 humarray-1.0.2/humarray/man/humarray-internal.Rd | 4 humarray-1.0.2/humarray/man/humarray-package.Rd | 4 8 files changed, 210 insertions(+), 95 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 1.5.1 dated 2016-06-01 and 1.5.2 dated 2016-07-15
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/BAT.R | 27 ++++++++++++++++----------- 3 files changed, 22 insertions(+), 17 deletions(-)
Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (<http://www.synbiosys.alterra.nl/turboveg/>) and other sources (<http://www.vegetweb.de>). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", <http://www.botanik.uni-greifswald.de/GermanSL.html>).
Author: Florian Jansen <jansen@uni-greifswald.de>
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between vegdata versions 0.8.9 dated 2016-03-14 and 0.9 dated 2016-07-15
vegdata-0.8.9/vegdata/R/tv.biblio.r |only vegdata-0.8.9/vegdata/R/tv.metainfo.r |only vegdata-0.9/vegdata/DESCRIPTION | 6 +- vegdata-0.9/vegdata/MD5 | 38 +++++++-------- vegdata-0.9/vegdata/R/comb.species.r | 2 vegdata-0.9/vegdata/R/internal.r | 46 ++++++++---------- vegdata-0.9/vegdata/R/tax_add.r | 11 +++- vegdata-0.9/vegdata/R/taxval.r | 5 +- vegdata-0.9/vegdata/R/tv.home.r | 75 ++++++++++++++++++++++++++++++ vegdata-0.9/vegdata/R/tv.obs.r | 6 +- vegdata-0.9/vegdata/R/tv.site.r | 18 ++++--- vegdata-0.9/vegdata/R/tv.write.r | 15 +++--- vegdata-0.9/vegdata/R/vegetweb.r | 19 ++++--- vegdata-0.9/vegdata/build/vignette.rds |binary vegdata-0.9/vegdata/inst/ChangeLog | 5 ++ vegdata-0.9/vegdata/inst/doc/vegdata.R | 4 - vegdata-0.9/vegdata/inst/doc/vegdata.Rnw | 6 +- vegdata-0.9/vegdata/man/taxval.Rd | 2 vegdata-0.9/vegdata/man/tv.write.Rd | 6 +- vegdata-0.9/vegdata/man/vegetweb.Rd | 7 +- vegdata-0.9/vegdata/vignettes/vegdata.Rnw | 6 +- 21 files changed, 186 insertions(+), 91 deletions(-)
Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while
controlling false discovery rate for RNA-seq experimental design. Our
procedure depends on the Voom method proposed for RNA-seq data analysis
by Law et al. (2014) <DOI:10.1186/gb-2014-15-2-r29> and the sample size
calculation method proposed for microarray experiments by Liu and Hwang
(2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of functions
that calculates appropriate sample sizes for two-sample t-test for RNA-seq
experiments with fixed or varied set of parameters. The outputs also contain a
plot of power versus sample size, a table of power at different sample sizes,
and a table of critical test values at different sample sizes.
To install this package, please use
'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'.
Author: Ran Bi [aut, cre],
Peng Liu [aut],
Tim Triche [ctb]
Maintainer: Ran Bi <biran@iastate.edu>
Diff between ssizeRNA versions 1.2.4 dated 2016-02-11 and 1.2.6 dated 2016-07-15
DESCRIPTION | 17 +++++++++-------- MD5 | 26 +++++++++++++------------- NAMESPACE | 15 ++------------- R/check.power.R | 3 +-- R/sim.counts.R | 1 + R/ssize.twoSampVaryDelta.R | 3 +-- R/ssizeRNA_single.R | 3 +-- R/ssizeRNA_vary.R | 3 +-- build/vignette.rds |binary inst/NEWS.txt | 6 ++++++ inst/doc/ssizeRNA.Rnw | 24 +++++++++++++++++++++--- inst/doc/ssizeRNA.pdf |binary vignettes/ssizeRNA.Rnw | 24 +++++++++++++++++++++--- vignettes/ssizeRNA_ref.bib | 43 ++++++++++++++++++++++++------------------- 14 files changed, 101 insertions(+), 67 deletions(-)
Title: Phylogenetic Clustering (Phyloclustering)
Description: Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) provides a
convenient implementation of phyloclustering for DNA and SNP data,
capable of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It is
designed in C for performance, interfaced with R for visualization,
and incorporates other popular open source programs including
ms (Hudson 2002), seq-gen (Rambaut and Grassly 1997),
Hap-Clustering (Tzeng 2005) and PAML baseml (Yang 1997, 2007), for
simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.
Author: Wei-Chen Chen [aut, cre],
Karin Dorman [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between phyclust versions 0.1-16 dated 2015-12-04 and 0.1-17 dated 2016-07-15
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- R/f_file_phylip.r | 6 +++++- README.md |only inst/doc/phyclust-guide.pdf |binary vignettes/phyclust-include/01-introduction.tex | 2 +- 7 files changed, 19 insertions(+), 11 deletions(-)
Title: Programming with Big Data -- Interface to MPI
Description: An efficient interface to MPI by utilizing S4
classes and methods with a focus on Single Program/Multiple Data ('SPMD')
parallel programming style, which is intended for batch parallel
execution.
Author: Wei-Chen Chen [aut, cre],
George Ostrouchov [aut],
Drew Schmidt [aut],
Pragneshkumar Patel [aut],
Hao Yu [aut],
Christian Heckendorf [ctb] (FreeBSD),
Brian Ripley [ctb] (Windows HPC Pack 2012),
R Core team [ctb] (some functions are modified from the base packages)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdMPI versions 0.3-1 dated 2016-01-21 and 0.3-2 dated 2016-07-15
ChangeLog | 6 + DESCRIPTION | 12 +-- MD5 | 41 ++++++------- NAMESPACE | 5 + R/222_export_env.r | 12 +-- R/comm_stopifnot.r |only R/spmd_allreduce.r | 28 +++++---- R/spmd_allreduce_obj.r | 68 ++++++++++++++-------- R/spmd_reduce.r | 39 ++++++++---- R/spmd_reduce_obj.r | 79 +++++++++++++++----------- README.md | 3 demo/allreduce.r | 12 +++ demo/reduce.r | 13 ++++ inst/doc/pbdMPI-guide.pdf |binary man/aa_allreduce-method.Rd | 6 + man/aa_reduce-method.Rd | 6 + man/xx_comm_stop_warning.Rd | 16 ++++- man/zz_spmd_internal.Rd | 2 src/Makevars.win | 60 ++++++++++--------- vignettes/pbdMPI-include/01-introduction.tex | 2 vignettes/pbdMPI-include/03-faq.tex | 58 +++++++++++++++++++ vignettes/pbdMPI-include/04-windows_msmpi.tex | 59 +++++++++++++++++-- 22 files changed, 374 insertions(+), 153 deletions(-)
Title: Data.frame-Like Operations on Sparse and Dense Matrix Objects
Description: Implements data manipulation methods such as cast, aggregate, and merge/join for Matrix and matrix-like objects.
Author: Craig Varrichio <canthony427@gmail.com>
Maintainer: Craig Varrichio <canthony427@gmail.com>
Diff between Matrix.utils versions 0.9.1 dated 2016-06-16 and 0.9.2 dated 2016-07-15
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/Matrix.utils.R | 1 - 3 files changed, 5 insertions(+), 6 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger <michael.schweinberger@rice.edu> [aut, cre], Mark S. Handcock <handcock@ucla.edu> [ctb], Pamela Luna <pamela.luna@rice.edu> [ctb]
Maintainer: Michael Schweinberger <michael.schweinberger@rice.edu>
Diff between hergm versions 2.4-0 dated 2016-07-03 and 2.5-0 dated 2016-07-15
DESCRIPTION | 8 ++++---- MD5 | 27 ++++++++++++++------------- NAMESPACE | 10 ++++++---- R/hergm.gof.R | 11 ++++++----- R/hergm.mcmc.diagnostics.R | 10 ++++++++-- R/hergm.plot.R | 3 ++- R/hergm.postprocess.R | 10 ++++++++++ R/hergm.preprocess.R | 2 ++ R/hergm.simulate.R | 12 +++--------- R/hergm.summary.R | 18 +++++++++++------- R/hergm.terms.R | 4 ++-- man/hergm-internal.Rd | 2 -- man/hergm.mcmc.diagnostics.Rd | 6 +++++- man/hergm.postprocess.Rd |only src/h_ergm.c | 3 +++ 15 files changed, 76 insertions(+), 50 deletions(-)
Title: Download, Clean and Generate New Variables from GSOD Data
Description: Download, clean, reformat and create new variables from the
USA National Climatic Data Center (NCDC) Global Surface Summary of the Day
(GSOD) weather stations data,
<https://data.noaa.gov/dataset/global-surface-summary-of-the-day-gsod>.
The function, get_GSOD(), retrieves data from the GSOD ftp site and
reformats it from United States Customary System (USCS) units to
International System of Units (SI). Stations are individually checked for
number of missing days, as defined by the user, to assure data quality.
Stations with too many missing observations are omitted from final file.
Stations with missing latitude or longitude or values for both of 0 are
omitted. Also omitted are stations with a latitude of < -90 or > 90 or
longitude of < - 180 or > 180. Output is returned as a comma-separated
values (CSV) file written to disk in a location selected by the user, which
summarises each year by station and includes new variables: actual vapor
pressure, saturation vapor pressure and relative humidity, calculated
from the original GSOD data. The resulting files can be as large as 500mb
depending on the user's stringency for missing data and geographic area of
interest. Be sure to have sufficient RAM and disk space as well as a
reasonably fast internet connection to use this package to perform this
operation. However, for much smaller and more manageable data sets, an
individual country of interest may be selected as well as only stations
falling between -60/60 degrees latitude for agroclimatology work or
individual stations if the station ID is known. The resulting files include
station data (e.g., station name, country, latitude, longitude, elevation)
for use in a geographic information system (GIS). The function was largely
based on T. Hengl's 'getGSOD.R' script, available from
<http://spatial-analyst.net/book/system/files/getGSOD.R> with enhancements
to be cross-platform, faster and more flexible. For information on the
original data from NCDC, please see the GSOD readme.txt file available from,
<http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre],
Tomislav Hengl [ctb],
Andy Nelson [ctb],
Kay Sumfleth [ctb]
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between GSODR versions 0.1.8.1 dated 2016-07-07 and 0.1.9 dated 2016-07-15
DESCRIPTION | 19 +-- MD5 | 20 ++- NAMESPACE | 2 NEWS.md | 49 ++++++-- R/data.R | 78 +++++++++----- R/get_GSOD.R | 234 +++++++++++++++++++++++++----------------- README.md | 275 ++++++++++++++++++++++++++++++-------------------- data/country_list.rda |only data/stations.rda |binary man/country_list.Rd |only man/get_GSOD.Rd | 70 ++++++------ man/stations.Rd | 42 ++++--- 12 files changed, 478 insertions(+), 311 deletions(-)
Title: Functional Data Analysis and Empirical Dynamics
Description: Provides implementation of various methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this package is Functional Principal Component Analysis (FPCA), a key technique for functional data analysis, for sparsely or densely sampled random trajectories and time courses, via the Principal Analysis by Conditional Estimation (PACE) algorithm or numerical integration. PACE is useful for the analysis of data that have been generated by a sample of underlying (but usually not fully observed) random trajectories. It does not rely on pre-smoothing of trajectories, which is problematic if functional data are sparsely sampled. PACE provides options for functional regression and correlation, for Longitudinal Data Analysis, the analysis of stochastic processes from samples of realized trajectories, and for the analysis of underlying dynamics. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Xiongtao Dai,
Pantelis Z. Hadjipantelis,
Hao Ji,
Hans-Georg Mueller,
Jane-Ling Wang
Maintainer: Pantelis Z. Hadjipantelis <pantelis@ucdavis.edu>
Diff between fdapace versions 0.2.0 dated 2016-06-18 and 0.2.5 dated 2016-07-15
fdapace-0.2.0/fdapace/man/plot.FPCA.Rd |only fdapace-0.2.0/fdapace/vignettes/DerivativesFlies.pdf |only fdapace-0.2.0/fdapace/vignettes/DerivativesFliesInspect.pdf |only fdapace-0.2.0/fdapace/vignettes/DiagPlotSparse.pdf |only fdapace-0.2.0/fdapace/vignettes/DiagnoFlies.pdf |only fdapace-0.2.0/fdapace/vignettes/DiagnoSimu.pdf |only fdapace-0.2.0/fdapace/vignettes/DifferentBandwidths.pdf |only fdapace-0.2.0/fdapace/vignettes/OutliersFlies.pdf |only fdapace-0.2.0/fdapace/vignettes/PathFlies.pdf |only fdapace-0.2.0/fdapace/vignettes/fdapaceVignetteKnitr-concordance.tex |only fdapace-0.2.5/fdapace/DESCRIPTION | 11 fdapace-0.2.5/fdapace/MD5 | 111 ++++------ fdapace-0.2.5/fdapace/NAMESPACE | 1 fdapace-0.2.5/fdapace/NEWS | 11 fdapace-0.2.5/fdapace/R/BinRawCov.R | 10 fdapace-0.2.5/fdapace/R/CheckAndCreateCOPoptions.R | 2 fdapace-0.2.5/fdapace/R/CreateBWPlot.R | 4 fdapace-0.2.5/fdapace/R/CreateCovPlot.R | 35 ++- fdapace-0.2.5/fdapace/R/CreateDesignPlot.R | 19 - fdapace-0.2.5/fdapace/R/CreateDiagnosticsPlot.R | 35 ++- fdapace-0.2.5/fdapace/R/CreateFuncBoxPlot.R | 16 - fdapace-0.2.5/fdapace/R/CreateModeOfVarPlot.R | 18 + fdapace-0.2.5/fdapace/R/CreateOutliersPlot.R | 2 fdapace-0.2.5/fdapace/R/CreatePathPlot.R | 20 + fdapace-0.2.5/fdapace/R/FCReg.R | 8 fdapace-0.2.5/fdapace/R/FPCA.R | 6 fdapace-0.2.5/fdapace/R/GCVLwls2DV2.R | 2 fdapace-0.2.5/fdapace/R/GetBinNum.R | 6 fdapace-0.2.5/fdapace/R/GetCrCovYX.R | 43 ++- fdapace-0.2.5/fdapace/R/GetCrCovYX_old.R |only fdapace-0.2.5/fdapace/R/GetCrCovYZ.R | 7 fdapace-0.2.5/fdapace/R/GetEigenAnalysisResults.R | 2 fdapace-0.2.5/fdapace/R/GetLogLik.R | 18 - fdapace-0.2.5/fdapace/R/GetRawCrCovFuncFunc.R | 5 fdapace-0.2.5/fdapace/R/Lwls2D.R | 3 fdapace-0.2.5/fdapace/R/MakeFPCAInputs.R | 3 fdapace-0.2.5/fdapace/R/MakeGPFunctionalData.R | 42 ++- fdapace-0.2.5/fdapace/R/SelectK.R | 34 ++- fdapace-0.2.5/fdapace/R/SetOptions.R | 16 - fdapace-0.2.5/fdapace/R/SetSVDOptions.R | 4 fdapace-0.2.5/fdapace/R/SubsetFPCA.R | 14 - fdapace-0.2.5/fdapace/R/fitted.FPCA.R | 30 +- fdapace-0.2.5/fdapace/R/plot.FPCA.R | 4 fdapace-0.2.5/fdapace/R/print.FPCA.R | 8 fdapace-0.2.5/fdapace/R/print.FSVD.R | 8 fdapace-0.2.5/fdapace/build/vignette.rds |binary fdapace-0.2.5/fdapace/inst/doc/fdapaceVignetteKnitr.R | 27 +- fdapace-0.2.5/fdapace/inst/doc/fdapaceVignetteKnitr.Rnw | 37 ++- fdapace-0.2.5/fdapace/inst/doc/fdapaceVignetteKnitr.pdf |binary fdapace-0.2.5/fdapace/man/CreateDesignPlot.Rd | 6 fdapace-0.2.5/fdapace/man/CreateDiagnosticsPlot.Rd | 24 +- fdapace-0.2.5/fdapace/man/CreateFuncBoxPlot.Rd | 2 fdapace-0.2.5/fdapace/man/CreateModeOfVarPlot.Rd | 7 fdapace-0.2.5/fdapace/man/CreatePathPlot.Rd | 8 fdapace-0.2.5/fdapace/man/FCReg.Rd | 5 fdapace-0.2.5/fdapace/man/FPCA.Rd | 2 fdapace-0.2.5/fdapace/man/GetCrCovYX.Rd | 8 fdapace-0.2.5/fdapace/man/GetCrCovYZ.Rd | 6 fdapace-0.2.5/fdapace/man/MakeGPFunctionalData.Rd | 19 + fdapace-0.2.5/fdapace/man/SelectK.Rd | 7 fdapace-0.2.5/fdapace/man/fitted.FPCA.Rd | 7 fdapace-0.2.5/fdapace/vignettes/fdapaceVignetteKnitr.Rnw | 37 ++- 62 files changed, 482 insertions(+), 278 deletions(-)
Title: Tools for Building R Formats
Description: Builds format strings that can be used with strptime() and sprintf().
Author: Brandon Taylor [aut, cre]
Maintainer: Brandon Taylor <brandon.taylor221@gmail.com>
Diff between easyformatr versions 0.1.1 dated 2016-04-12 and 0.1.2 dated 2016-07-15
DESCRIPTION | 13 LICENSE | 4 MD5 | 56 +- NAMESPACE | 38 - NEWS.md | 4 R/easyformatr.R | 232 ++++----- R/numbers.R | 162 +++--- R/times.R | 294 ++++++------ R/tools.R | 322 ++++++------- README.md | 148 +++--- build/vignette.rds |binary inst/doc/easyformatr.R | 151 +++--- inst/doc/easyformatr.Rmd | 337 +++++++------- inst/doc/easyformatr.html | 873 ++++++++++++++++++------------------- man/easy_format.Rd | 50 +- man/easy_format_.Rd | 40 - man/filter_info.Rd | 44 - man/filter_info_.Rd | 36 - man/format_info.Rd | 30 - man/name_value_to_list.Rd | 30 - man/parse_binding_errors.Rd | 30 - man/paste_NA_omit.Rd | 38 - man/paste_NA_poison.Rd | 38 - man/remove_NA_columns.Rd | 36 - man/remove_single_value_columns.Rd | 36 - man/string_table.Rd | 34 - tests/testthat.R | 8 tests/testthat/test.R | 366 +++++++-------- vignettes/easyformatr.Rmd | 342 +++++++------- 29 files changed, 1910 insertions(+), 1882 deletions(-)
Title: Individual-Based, Spatially-Explicit Simulation and Analysis of
Multi-State Movements in River Networks 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 fill the gap of softwares simulating
spatially-explicit trajectories of species constrained to linear, dendritic habitats
(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. Thus, the user will be able
to use the package to simulate movements either in homogeneous landscapes, heterogeneous
landscapes (e.g. semi-aquatic animal in a riverscape), 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 null models to test e.g. for species site fidelity and other movement ecology
hypotheses, or to build predictive, mechanistic movement models, among other things. 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. This is the first released
experimental version; do test before using in production.
Author: Lorenzo Quaglietta [aut],
Miguel Porto [aut, cre],
Erida Gjini [ctb]
Maintainer: Miguel Porto <mpbertolo@gmail.com>
Diff between SiMRiv versions 0.9 dated 2016-07-12 and 0.9.1 dated 2016-07-15
SiMRiv-0.9.1/SiMRiv/DESCRIPTION | 12 +++----- SiMRiv-0.9.1/SiMRiv/MD5 | 11 +++----- SiMRiv-0.9.1/SiMRiv/man/simulate.Rd | 6 ++-- SiMRiv-0.9.1/SiMRiv/src/Makevars |only SiMRiv-0.9.1/SiMRiv/src/SiMRiv.h | 4 ++ SiMRiv-0.9.1/SiMRiv/src/simulate.c | 49 ++++++++++++++++++++++++------------ SiMRiv-0.9/SiMRiv/src/rand32.c |only SiMRiv-0.9/SiMRiv/src/rand32.h |only 8 files changed, 49 insertions(+), 33 deletions(-)