Title: Interface to the 'HDF5' Library
Description: S4 Interface to the 'HDF5' library supporting fast storage and
retrieval of R-objects like vectors, matrices and arrays to binary files in
a language independent format. The 'HDF5' format can therefore be used as
an alternative to R's save/load mechanism. Since h5 is able to access only
subsets of stored data it can also handle data sets which do not fit into
memory.
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau <mario.annau@gmail.com>
Diff between h5 versions 0.9.3 dated 2015-08-11 and 0.9.4 dated 2015-10-12
DESCRIPTION | 16 +-- MD5 | 47 ++++---- NAMESPACE | 2 R/CommonFG.R | 28 +++++ R/H5File.R | 99 +++++++++++++++--- R/H5Group.R | 6 - R/H5Location-Attribute.R | 14 +- R/RcppExports.R | 12 +- inst/NEWS.Rd | 13 ++ inst/test-f32.h5 |only inst/test-f32.py |only man/CommonFG.Rd | 8 + man/H5File.Rd | 96 +++++++++++++++--- src/Attribute.cpp | 56 +++++++++- src/Attribute.h | 4 src/Dataset.cpp | 9 - src/Group.cpp | 29 +---- src/Group.h | 3 src/Helpers.cpp | 192 +++++++++++++++++++----------------- src/RcppExports.cpp | 31 +++++ tests/testthat/test-Attribute.R | 44 ++++++++ tests/testthat/test-DataSet-IO-NA.R |only tests/testthat/test-DataSet.R | 17 +++ tests/testthat/test-H5File.R | 16 +++ tests/testthat/test-H5Group.R | 69 ++++++++++++ tests/testthat/test-vlen.R | 47 ++++++++ 26 files changed, 660 insertions(+), 198 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 <nick@ggtern.com>
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 1.0.6.0 dated 2015-08-03 and 1.0.6.1 dated 2015-10-12
DESCRIPTION | 10 +- MD5 | 53 ++++++------ NEWS | 10 ++ R/coord-tern.R | 39 ++------- R/data.R | 8 + R/geom-confidence.R | 59 +++++++------- R/gg-internal.R | 1 R/ggtern-build.R | 1 R/onLoad.R | 4 R/scales.R | 26 ++++-- R/stat-interpolate-tern.R | 10 ++ R/tern-render.R | 59 ++++++++------ R/theme-defaults.R | 180 +++++++++++++++++++++++++------------------- R/theme-elements.R | 5 - R/theme-noarrows.R | 4 R/utilities.R | 37 ++++++++- README.md | 3 build/partial.rdb |binary data/Feldspar.RData |binary man/coord_tern.Rd | 5 - man/data_Feldspar.Rd | 11 +- man/getBreaks.Rd |only man/scale_TLR_continuous.Rd | 26 +++--- man/theme_custom.Rd | 9 +- man/theme_elements.Rd | 1 man/theme_gray.Rd | 1 man/theme_rgbw.Rd | 4 man/themeshowhidearrows.Rd | 4 28 files changed, 335 insertions(+), 235 deletions(-)
Title: Modified Variance Estimators for Generalized Estimating
Equations
Description: Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance.
Author: Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>
Diff between geesmv versions 1.2 dated 2015-08-28 and 1.3 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GEE.var.mbn.R | 2 +- man/GEE.var.mbn.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves
Description: Implements a very fast C++ algorithm to quickly bootstrap
receiver operating characteristics (ROC) curves and derived performance metrics, including the area under the
curve (AUC) as well as the true and false positive rate. The analysis of paired
receiver operating curves is supported as well, so that a comparison of two predictors is possible.
You can also plot the results and calculate confidence intervals.
Currently the calculation of 100000 bootstrap replicates for 500 observations
takes about one second.
Author: Erik Peter [aut, cre]
Maintainer: Erik Peter <jerikpeter@googlemail.com>
Diff between fbroc versions 0.3.0 dated 2015-10-08 and 0.3.1 dated 2015-10-12
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/fbroc.methods.R | 6 ++++-- man/plot.fbroc.roc.Rd | 2 ++ 4 files changed, 14 insertions(+), 10 deletions(-)
Title: A Toolbox for Multivariate Meta-Analysis
Description: A toolbox for meta-analysis. This package includes a collection of functions for (1) implementing robust multivariate meta-analysis of continuous or binary outcomes; and (2) testing and correcting of publication bias in multivariate meta-analysis settings.
Author: Yong Chen, Chuan Hong, Haitao Chu
Maintainer: Yong Chen <ychen.upenn@gmail.com>
Diff between xmeta versions 1.0 dated 2015-10-02 and 1.0-1 dated 2015-10-12
DESCRIPTION | 16 ++++++++-------- MD5 | 8 +++++--- NAMESPACE | 2 +- R/galaxy.R |only man/galaxy.Rd |only man/xmeta-package.Rd | 3 ++- 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian
framework using JAGS. Includes methods to assess heterogeneity and
inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef <g.h.m.van.valkenhoef@rug.nl>
Diff between gemtc versions 0.7 dated 2015-09-09 and 0.7-1 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 7 +++++++ inst/gemtc.randomeffects.txt | 2 +- 4 files changed, 15 insertions(+), 8 deletions(-)
More information about batteryreduction at CRAN
Permanent link
Title: Barnard's Unconditional Test
Description: Barnard's unconditional test for 2x2 contingency tables.
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Diff between Barnard versions 1.4 dated 2015-10-09 and 1.5 dated 2015-10-12
DESCRIPTION | 9 ++++---- MD5 | 6 ++--- R/barnardw.test.R | 57 ++++++++++++++++++++++++++++++--------------------- man/barnardw.test.Rd | 26 +++++++++++------------ 4 files changed, 55 insertions(+), 43 deletions(-)
Title: Bayesian Network Feature Finder
Description: Provides a full package of posterior inference, model comparison, and graphical illustration of model fitting. A parallel computing algorithm for the Markov chain Monte Carlo (MCMC) based posterior inference and an Expectation-Maximization (EM) based algorithm for posterior approximation are are developed, both of which greatly reduce the computational time for model inference.
Author: Zhou Lan, Yize Zhao, Jian Kang, Tianwei Yu
Maintainer: Zhou Lan <zlan6@gatech.edu>
Diff between BANFF versions 0.3 dated 2015-02-16 and 1.0 dated 2015-10-12
BANFF-0.3/BANFF/R/All_functions.R |only BANFF-0.3/BANFF/R/main.R |only BANFF-1.0/BANFF/DESCRIPTION | 9 +-- BANFF-1.0/BANFF/MD5 | 43 ++++++++++++++- BANFF-1.0/BANFF/NAMESPACE | 74 ++++++++++++++------------- BANFF-1.0/BANFF/R/DPM.HODC.R |only BANFF-1.0/BANFF/R/DPdensitycluster.R |only BANFF-1.0/BANFF/R/EM.HODC.R |only BANFF-1.0/BANFF/R/Generating_Zi.R |only BANFF-1.0/BANFF/R/Gibbsfortheta.R |only BANFF-1.0/BANFF/R/Grid.Adjmatrix.Transfer.R |only BANFF-1.0/BANFF/R/HODCMclust.R |only BANFF-1.0/BANFF/R/HyperPara.Select.R |only BANFF-1.0/BANFF/R/Initial_mu_var.R |only BANFF-1.0/BANFF/R/Innerfunc.R |only BANFF-1.0/BANFF/R/Inte_Distance.R |only BANFF-1.0/BANFF/R/Iteration3_DPdensity.R |only BANFF-1.0/BANFF/R/Iteration3_DPdensity_Par.R |only BANFF-1.0/BANFF/R/Iteration3_Mclust.R |only BANFF-1.0/BANFF/R/Kmeans.R |only BANFF-1.0/BANFF/R/LikelihoodHistory.R |only BANFF-1.0/BANFF/R/Mixture.R |only BANFF-1.0/BANFF/R/Model.R |only BANFF-1.0/BANFF/R/Networks.Fast.R |only BANFF-1.0/BANFF/R/Networks.STD.R |only BANFF-1.0/BANFF/R/Parameter_Define.R |only BANFF-1.0/BANFF/R/Pi_rho_gen.R |only BANFF-1.0/BANFF/R/Pi_rho_selecting.R |only BANFF-1.0/BANFF/R/Plot.Subnetwork.R |only BANFF-1.0/BANFF/R/Step1_1_Update_gi_zi.R |only BANFF-1.0/BANFF/R/Step1_2_Check.R |only BANFF-1.0/BANFF/R/Step_2_Update_mu_var.R |only BANFF-1.0/BANFF/R/Step_3_switch_the_label.R |only BANFF-1.0/BANFF/R/Subnetwork.Select.R |only BANFF-1.0/BANFF/R/SummaryAccuracy.R |only BANFF-1.0/BANFF/R/TPR.R |only BANFF-1.0/BANFF/R/Transfer.R |only BANFF-1.0/BANFF/R/biGaussian.R |only BANFF-1.0/BANFF/R/plot.Networks.Fast.R |only BANFF-1.0/BANFF/R/plot.Networks.STD.R |only BANFF-1.0/BANFF/R/summary.Networks.Fast.R |only BANFF-1.0/BANFF/R/summary.Networks.STD.R |only 42 files changed, 83 insertions(+), 43 deletions(-)
Title: Variable Selection Using Random Forests
Description: Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Author: Robin Genuer [aut, cre],
Jean-Michel Poggi [aut],
Christine Tuleau-Malot [aut]
Maintainer: Robin Genuer <Robin.Genuer@isped.u-bordeaux2.fr>
Diff between VSURF versions 1.0.0 dated 2015-05-15 and 1.0.1 dated 2015-10-12
DESCRIPTION | 9 +++++---- MD5 | 26 +++++++++++++++----------- NAMESPACE | 14 +++++++++++++- NEWS | 9 ++++++++- R/VSURF.R | 16 ++++++++-------- R/VSURF_interp.R | 18 +++++++----------- R/VSURF_pred.R | 2 +- R/VSURF_thres.R | 27 ++++++++++++--------------- R/plot.VSURF.R | 1 + man/VSURF.Rd | 6 +++--- man/VSURF_interp.Rd | 4 ++-- man/VSURF_thres.Rd | 5 +++-- tests |only 13 files changed, 78 insertions(+), 59 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, PCA and correlation matrices, cluster analyses, scatter plots, Likert scales, effects plots of regression models (including interaction terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.8.3 dated 2015-08-26 and 1.8.4 dated 2015-10-12
DESCRIPTION | 8 MD5 | 58 NAMESPACE | 1 NEWS | 1290 +++++++------- R/helpfunctions.R | 1555 ++++++++--------- R/sjPlotAnova.R | 2 R/sjPlotFrequencies.R | 14 R/sjPlotGLME.R | 4231 +++++++++++++++++++++++------------------------ R/sjPlotInteractions.R | 2967 ++++++++++++++++---------------- R/sjPlotLinreg.R | 9 R/sjPlotLinregMultiple.R | 6 R/sjPlotPCA.R | 2 R/sjTabCorr.R | 1020 +++++------ R/sjTabDataFrame.R | 3 R/sjTabFrequencies.R | 2 R/sjTabItemAnalysis.R | 13 R/sjTabLinReg.R | 3062 +++++++++++++++++----------------- R/sjTabOdds.R | 2720 +++++++++++++++--------------- R/sjTabPCA.R | 1188 ++++++------- R/sjTabSPSS.R | 792 ++++---- R/sjTabStackFrq.R | 1038 +++++------ README.md | 36 man/sjPlot-package.Rd | 102 - man/sjp.glmer.Rd | 7 man/sjp.int.Rd | 783 ++++---- man/sjp.lm.Rd | 496 ++--- man/sjp.lmer.Rd | 7 man/sjt.glmer.Rd | 17 man/sjt.lmer.Rd | 17 man/view_df.Rd | 26 30 files changed, 10817 insertions(+), 10655 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended for people coming from other statistical software packages like 'SPSS', and/or who are new to R), supporting following common tasks:
1) Reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this includes easy ways to get and set label attributes, to convert labelled vectors into factors (and vice versa), or to deal with multiple declared missing values etc.
2) Data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values.
3) Convenient functions to perform frequently used statistical tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.1 dated 2015-08-26 and 1.2 dated 2015-10-12
DESCRIPTION | 11 - MD5 | 34 +-- NAMESPACE | 1 NEWS | 12 + R/as_labelled.R | 2 R/converge_ok.R |only R/reliab_test.R | 8 R/set_na.R | 461 ++++++++++++++++++++++++-------------------------- R/to_na.R | 136 +++++++------- R/weight.R | 8 README.md | 136 +++++--------- man/as_labelled.Rd | 2 man/converge_ok.Rd |only man/mean_n.Rd | 144 +++++++-------- man/sjmisc-package.Rd | 4 man/std_beta.Rd | 128 ++++++------- man/to_na.Rd | 2 man/weight.Rd | 10 - man/weight2.Rd | 4 19 files changed, 549 insertions(+), 554 deletions(-)
Title: Interface Between GRASS 7 Geographical Information System and R
Description: Interpreted interface between GRASS 7 geographical
information system and R, based on starting R from within the GRASS GIS
environment, or running free-standing R in a temporary GRASS location;
the package provides facilities for using all GRASS commands from the
R command line. This package may not be used for GRASS 6, for which
spgrass6 should be used.
Author: Roger Bivand [cre, aut],
Rainer Krug [ctb],
Markus Neteler [ctb],
Sebastian Jeworutzki [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass7 versions 0.1-2 dated 2015-08-23 and 0.1-3 dated 2015-10-12
ChangeLog | 1066 ---------------------------------------------------------- DESCRIPTION | 8 MD5 | 6 R/vect_link.R | 91 ++-- 4 files changed, 52 insertions(+), 1119 deletions(-)
Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (mosaic-web.org) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel Kaplan
<kaplan@macalester.edu>, Nicholas Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaic versions 0.11 dated 2015-09-10 and 0.12 dated 2015-10-12
DESCRIPTION | 8 MD5 | 146 ++- NAMESPACE | 31 R/Clustering.R | 3 R/aggregatingAux.R | 10 R/aggregatingMeta.R | 21 R/cdist.R | 70 + R/do.R | 370 ++++++---- R/dotPlot.R | 5 R/dpqrdist.R | 32 R/favstats.R | 5 R/frequencyPolygon.R | 2 R/groupwiseModels.R |only R/integrateODE.R | 1 R/makeFun.R | 6 R/maps2.R | 9 R/mm.R | 148 ---- R/mosaic-package.R | 2 R/mplot.R | 44 - R/plotModel.R | 195 +++-- R/resample.R | 57 - R/statTally.R | 4 R/xpnorm.R | 38 - build/vignette.rds |binary inst/doc/GraphicsWithMosaic.html | 38 - inst/doc/LessVolume-MoreCreativity.Rmd | 6 inst/doc/LessVolume-MoreCreativity.html | 14 inst/doc/MinimalR.pdf |binary inst/doc/Resampling.R | 2 inst/doc/Resampling.Rnw | 2 inst/doc/Resampling.pdf |binary inst/doc/mosaic-resources.html | 4 inst/doc/plotModel-vignette.R |only inst/doc/plotModel-vignette.Rmd |only inst/doc/plotModel-vignette.html |only man/MSPE.Rd |only man/aggregating.Rd | 3 man/cdist.Rd | 23 man/cull_for_do.Rd |only man/do.Rd | 5 man/dotPlot.Rd | 2 man/freqpolygon.Rd | 2 man/gwm.Rd |only man/makeFun.Rd | 4 man/mm.Rd | 51 - man/mosaic-internal.Rd | 7 man/mplot.Rd | 12 man/nicenames.Rd | 4 man/plotModel.Rd | 9 man/pqrdata2.Rd | 15 man/qdist.Rd | 16 man/resample.Rd | 2 tests/testthat/test-aggregating.R | 11 tests/testthat/test-do.R |only tests/testthat/test-groupwiseModels.R | 34 vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-3.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-3.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-8-2.png |binary vignettes/LessVolume-MoreCreativity.Rmd | 6 vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-50-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-51-1.png |binary vignettes/Resampling.Rnw | 2 vignettes/plotModel-vignette.Rmd |only vignettes/plotModel-vignette_files |only 68 files changed, 785 insertions(+), 696 deletions(-)
Title: Preference Rating for Visual Stimuli Based on Elo Ratings
Description: Allows calculating global scores for characteristics of visual stimuli. Stimuli are presented as sequence of pairwise comparisons ('contests'), during each of which a rater expresses preference for one stimulus over the other. The algorithm for calculating global scores is based on Elo rating, which updates individual scores after each single pairwise contest. Elo rating is widely used to rank chess players according to their performance. Its core feature is that dyadic contests with expected outcomes lead to smaller changes of participants' scores than outcomes that were unexpected. As such, Elo rating is an efficient tool to rate individual stimuli when a large number of such stimuli are paired against each other in the context of experiments where the goal is to rank stimuli according to some characteristic of interest.
Author: Christof Neumann
Maintainer: Christof Neumann <christofneumann1@gmail.com>
Diff between EloChoice versions 0.28 dated 2015-10-11 and 0.29 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- inst/NEWS.Rd | 6 ++++++ inst/doc/tutorial.Rnw | 2 +- inst/doc/tutorial.pdf |binary man/EloChoice-package.Rd | 4 ++-- src/eloint.cpp | 41 +++++++++++++++++------------------------ vignettes/tutorial.Rnw | 2 +- 8 files changed, 38 insertions(+), 39 deletions(-)
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Author: Marc Girondot <marc.girondot@u-psud.fr>
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between embryogrowth versions 6.0 dated 2015-04-15 and 6.1 dated 2015-10-12
embryogrowth-6.0/embryogrowth/R/fonctionfit.R |only embryogrowth-6.1/embryogrowth/DESCRIPTION | 12 embryogrowth-6.1/embryogrowth/MD5 | 202 - embryogrowth-6.1/embryogrowth/NAMESPACE | 9 embryogrowth-6.1/embryogrowth/NEWS | 32 embryogrowth-6.1/embryogrowth/R/ChangeSSM.R | 8 embryogrowth-6.1/embryogrowth/R/Exponential.R | 2 embryogrowth-6.1/embryogrowth/R/FormatNests.R | 40 embryogrowth-6.1/embryogrowth/R/GRTRN_MHmcmc.R | 32 embryogrowth-6.1/embryogrowth/R/GenerateTest.R | 3 embryogrowth-6.1/embryogrowth/R/Gompertz.R | 2 embryogrowth-6.1/embryogrowth/R/Linear.R | 2 embryogrowth-6.1/embryogrowth/R/MovingIncubation.R | 337 -- embryogrowth-6.1/embryogrowth/R/SSM.R | 6 embryogrowth-6.1/embryogrowth/R/STRN_MHmcmc.R | 19 embryogrowth-6.1/embryogrowth/R/STRN_fit.R | 2 embryogrowth-6.1/embryogrowth/R/TRN_MHmcmc_p.R | 22 embryogrowth-6.1/embryogrowth/R/TSP.list.R |only embryogrowth-6.1/embryogrowth/R/embryogrowth-package.R | 12 embryogrowth-6.1/embryogrowth/R/fonctionMCMC.R | 6 embryogrowth-6.1/embryogrowth/R/gradientRichardson.R | 2 embryogrowth-6.1/embryogrowth/R/hessianRichardson.R | 2 embryogrowth-6.1/embryogrowth/R/hist.Nests.R | 6 embryogrowth-6.1/embryogrowth/R/hist.NestsResult.R | 7 embryogrowth-6.1/embryogrowth/R/info.nests.R | 952 +++++-- embryogrowth-6.1/embryogrowth/R/likelihoodR.R | 10 embryogrowth-6.1/embryogrowth/R/modelTSD.R | 5 embryogrowth-6.1/embryogrowth/R/plot.NestsResult.R | 1275 +--------- embryogrowth-6.1/embryogrowth/R/plot.tsd.R | 4 embryogrowth-6.1/embryogrowth/R/plotR.R | 14 embryogrowth-6.1/embryogrowth/R/plotR_hist.R | 36 embryogrowth-6.1/embryogrowth/R/plot_transition.R | 4 embryogrowth-6.1/embryogrowth/R/resultNest_4p.R | 2 embryogrowth-6.1/embryogrowth/R/resultNest_4p_weight.R | 2 embryogrowth-6.1/embryogrowth/R/resultNest_6p.R | 2 embryogrowth-6.1/embryogrowth/R/resultNest_newp.R | 8 embryogrowth-6.1/embryogrowth/R/result_mcmc_4p.R | 4 embryogrowth-6.1/embryogrowth/R/result_mcmc_4p_weight.R | 9 embryogrowth-6.1/embryogrowth/R/result_mcmc_6p.R | 2 embryogrowth-6.1/embryogrowth/R/result_mcmc_newp.R | 21 embryogrowth-6.1/embryogrowth/R/searchR.R | 138 - embryogrowth-6.1/embryogrowth/R/summary.Nests.R | 4 embryogrowth-6.1/embryogrowth/R/tempConst.R | 2 embryogrowth-6.1/embryogrowth/R/tsd.R | 47 embryogrowth-6.1/embryogrowth/R/tsd_MHmcmc.R | 12 embryogrowth-6.1/embryogrowth/R/tsd_MHmcmc_p.R | 11 embryogrowth-6.1/embryogrowth/R/weightmaxentropy.R | 10 embryogrowth-6.1/embryogrowth/data/STSRE_TSD.rda |binary embryogrowth-6.1/embryogrowth/data/TSP.list.rda |only embryogrowth-6.1/embryogrowth/data/resultNest_4p.rda |binary embryogrowth-6.1/embryogrowth/data/resultNest_6p.rda |binary embryogrowth-6.1/embryogrowth/data/resultNest_newp.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_4p.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_4p_weight.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_6p.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_newp.rda |binary embryogrowth-6.1/embryogrowth/man/ChangeSSM.Rd | 10 embryogrowth-6.1/embryogrowth/man/FormatNests.Rd | 2 embryogrowth-6.1/embryogrowth/man/GRTRN_MHmcmc.Rd | 32 embryogrowth-6.1/embryogrowth/man/GenerateAnchor.Rd | 2 embryogrowth-6.1/embryogrowth/man/GenerateConstInc.Rd | 2 embryogrowth-6.1/embryogrowth/man/GenerateTest.Rd | 2 embryogrowth-6.1/embryogrowth/man/MovingIncubation.Rd | 43 embryogrowth-6.1/embryogrowth/man/STRN.Rd | 2 embryogrowth-6.1/embryogrowth/man/STRN_MHmcmc.Rd | 9 embryogrowth-6.1/embryogrowth/man/STSRE_NestingArea.Rd | 2 embryogrowth-6.1/embryogrowth/man/STSRE_TSD.Rd | 8 embryogrowth-6.1/embryogrowth/man/TRN_MHmcmc_p.Rd | 8 embryogrowth-6.1/embryogrowth/man/TSP.list.Rd |only embryogrowth-6.1/embryogrowth/man/TestParallel.Rd | 2 embryogrowth-6.1/embryogrowth/man/dydt.Gompertz.Rd | 4 embryogrowth-6.1/embryogrowth/man/dydt.exponential.Rd | 4 embryogrowth-6.1/embryogrowth/man/dydt.linear.Rd | 4 embryogrowth-6.1/embryogrowth/man/embryogrowth-package.Rd | 14 embryogrowth-6.1/embryogrowth/man/hist.Nests.Rd | 2 embryogrowth-6.1/embryogrowth/man/hist.NestsResult.Rd | 2 embryogrowth-6.1/embryogrowth/man/info.nests.Rd | 86 embryogrowth-6.1/embryogrowth/man/likelihoodR.Rd | 2 embryogrowth-6.1/embryogrowth/man/logLik.NestsResult.Rd | 2 embryogrowth-6.1/embryogrowth/man/logLik.tsd.Rd | 2 embryogrowth-6.1/embryogrowth/man/nest.Rd | 2 embryogrowth-6.1/embryogrowth/man/plot.NestsResult.Rd | 105 embryogrowth-6.1/embryogrowth/man/plot.tsd.Rd | 2 embryogrowth-6.1/embryogrowth/man/plotR.Rd | 6 embryogrowth-6.1/embryogrowth/man/plotR_hist.Rd | 2 embryogrowth-6.1/embryogrowth/man/plot_transition.Rd | 4 embryogrowth-6.1/embryogrowth/man/predict.tsd.Rd | 6 embryogrowth-6.1/embryogrowth/man/resultNest_4p.Rd | 4 embryogrowth-6.1/embryogrowth/man/resultNest_4p_transition.Rd | 2 embryogrowth-6.1/embryogrowth/man/resultNest_4p_weight.Rd | 4 embryogrowth-6.1/embryogrowth/man/resultNest_6p.Rd | 4 embryogrowth-6.1/embryogrowth/man/resultNest_newp.Rd | 10 embryogrowth-6.1/embryogrowth/man/result_mcmc_4p.Rd | 6 embryogrowth-6.1/embryogrowth/man/result_mcmc_4p_weight.Rd | 11 embryogrowth-6.1/embryogrowth/man/result_mcmc_6p.Rd | 4 embryogrowth-6.1/embryogrowth/man/result_mcmc_newp.Rd | 23 embryogrowth-6.1/embryogrowth/man/searchR.Rd | 47 embryogrowth-6.1/embryogrowth/man/summary.Nests.Rd | 6 embryogrowth-6.1/embryogrowth/man/switch.transition.Rd | 2 embryogrowth-6.1/embryogrowth/man/tempConst.Rd | 4 embryogrowth-6.1/embryogrowth/man/tsd.Rd | 16 embryogrowth-6.1/embryogrowth/man/tsd_MHmcmc.Rd | 6 embryogrowth-6.1/embryogrowth/man/tsd_MHmcmc_p.Rd | 6 embryogrowth-6.1/embryogrowth/man/weightmaxentropy.Rd | 4 104 files changed, 1694 insertions(+), 2177 deletions(-)
Title: Tools for Retrieval and Storage of Functional Genomics Data
Description: Package for the systematic retrieval and storage of
functional genomics data via a MySQL database.
Author: Umesh K. Nandal <u.k.nandal@amc.uva.nl> and Perry D. Moerland
<p.d.moerland@amc.uva.nl>
Maintainer: Umesh Nandal <u.k.nandal@amc.uva.nl>
Diff between compendiumdb versions 1.0.2 dated 2015-10-03 and 1.0.3 dated 2015-10-12
DESCRIPTION | 10 +++++----- INSTALL | 2 +- MD5 | 12 ++++++------ inst/doc/compendiumdb.pdf |binary man/compendiumdb-package.Rd | 4 ++-- man/downloadGEOdata.Rd | 2 +- man/loadDatabaseSchema.Rd | 2 +- 7 files changed, 16 insertions(+), 16 deletions(-)
Title: IP Address Geolocation
Description: Connectors to online and offline sources for taking IP addresses and geolocating them to country, city, timezone and other geographic ranges. For individual connectors, see the package index.
Author: Oliver Keyes [aut, cre], Drew Schmidt [aut], David Robinson [ctb], Maxmind, Inc. [cph], Pascal Gloor [cph]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between rgeolocate versions 0.4.1 dated 2015-07-25 and 0.5.0 dated 2015-10-12
rgeolocate-0.4.1/rgeolocate/R/freegeoip.R |only rgeolocate-0.4.1/rgeolocate/man/freegeoip.Rd |only rgeolocate-0.4.1/rgeolocate/tests/testthat/test_freegeoip.R |only rgeolocate-0.5.0/rgeolocate/DESCRIPTION | 12 rgeolocate-0.5.0/rgeolocate/MD5 | 49 - rgeolocate-0.5.0/rgeolocate/NAMESPACE | 1 rgeolocate-0.5.0/rgeolocate/NEWS | 13 rgeolocate-0.5.0/rgeolocate/R/maxmind.R | 17 rgeolocate-0.5.0/rgeolocate/R/telize.R | 2 rgeolocate-0.5.0/rgeolocate/README.md | 5 rgeolocate-0.5.0/rgeolocate/build/vignette.rds |binary rgeolocate-0.5.0/rgeolocate/configure | 29 - rgeolocate-0.5.0/rgeolocate/configure.ac | 14 rgeolocate-0.5.0/rgeolocate/inst/doc/Introduction_to_rgeolocate.Rmd | 2 rgeolocate-0.5.0/rgeolocate/inst/doc/Introduction_to_rgeolocate.html | 276 ++-------- rgeolocate-0.5.0/rgeolocate/inst/extdata/GeoIP2-Anonymous-IP-Test.mmdb |only rgeolocate-0.5.0/rgeolocate/inst/extdata/GeoIP2-City-Test.mmdb |only rgeolocate-0.5.0/rgeolocate/inst/extdata/GeoIP2-Precision-City-Test.mmdb |only rgeolocate-0.5.0/rgeolocate/man/maxmind.Rd | 15 rgeolocate-0.5.0/rgeolocate/man/telize.Rd | 2 rgeolocate-0.5.0/rgeolocate/src/Makevars.win | 2 rgeolocate-0.5.0/rgeolocate/src/config.h.in | 6 rgeolocate-0.5.0/rgeolocate/src/maxmind.cpp | 71 ++ rgeolocate-0.5.0/rgeolocate/src/maxmind.h | 4 rgeolocate-0.5.0/rgeolocate/src/maxminddb_config.h | 25 rgeolocate-0.5.0/rgeolocate/tests/testthat/test_ip_api.R | 13 rgeolocate-0.5.0/rgeolocate/tests/testthat/test_maxmind.R | 35 + rgeolocate-0.5.0/rgeolocate/vignettes/Introduction_to_rgeolocate.Rmd | 2 rgeolocate-0.5.0/rgeolocate/vignettes/Introduction_to_rgeolocate.md |only 29 files changed, 239 insertions(+), 356 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: Provides an interface to kernel routines from the FCNN C++ library.
FCNN is based on a completely new Artificial Neural Network
representation that offers unmatched efficiency, modularity,
and extensibility. FCNN4R provides standard teaching
(backpropagation, Rprop, simulated annealing) and pruning algorithms
(minimum magnitude, Optimal Brain Surgeon), but it is first
and foremost an efficient computational engine. Users can easily
implement their algorithms by taking advantage of fast gradient
computing routines, as well as network reconstruction functionality
(removing weights and redundant neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.4.1 dated 2015-08-26 and 0.5.0 dated 2015-10-12
DESCRIPTION | 29 ++++------ MD5 | 39 +++++++------ NAMESPACE | 3 + R/mlp_gteach.R |only R/mlp_net.R | 97 +++++++++++++++++++++------------- R/mlp_plot.R | 41 ++++++++------ R/mlp_teach.R | 6 +- man/FCNN4R-package.Rd | 50 ++++++++++------- man/mlp_export_C.Rd | 10 +-- man/mlp_net-combining-two-networks.Rd | 6 +- man/mlp_net-export-import.Rd | 8 +- man/mlp_net.Rd | 6 +- man/mlp_teach_bp.Rd | 2 man/mlp_teach_grprop.Rd |only man/mlp_teach_rprop.Rd | 4 - man/mlp_teach_sa.Rd |only src/fcnn/export.cpp | 6 +- src/fcnn/level1.h | 42 ++++++++------ src/fcnn/level3.cpp | 3 - src/fcnn/struct.cpp | 48 ++++++++++++---- src/fcnn/utils.cpp | 12 ++++ src/fcnn/utils.h | 4 + 22 files changed, 253 insertions(+), 163 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: An easily accessible continuous (and discrete) time dynamic
modelling package for panel and time series data, reliant upon the OpenMx.
package (http://openmx.psyc.virginia.edu/) for computation. Most
dynamic modelling approaches to longitudinal data rely on the assumption
that time intervals between observations are consistent. When this
assumption is adhered to, the data gathering process is necessarily limited
to a specific schedule, and when broken, the resulting parameter estimates
may be biased and reduced in power. Continuous time models are
conceptually similar to vector autoregressive models (thus also the latent
change models popularised in a structural equation modelling context),
however by explicitly including the length of time between observations,
continuous time models are freed from the assumption that measurement
intervals are consistent. This allows: data to be gathered irregularly;
the elimination of noise and bias due to varying measurement intervals;
parsimonious structures for complex dynamics.
The application of such a model in this SEM framework allows full-information
maximum-likelihood estimates for both N = 1 and N > 1 cases, multiple
measured indicators per latent process, and the flexibility to incorporate
additional elements, including individual heterogeneity in the latent
process and manifest intercepts, and time dependent and independent
exogenous covariates. Furthermore, due to the SEM implementation we are
able to estimate a random effects model where the impact of time dependent
and time independent predictors can be assessed simultaneously, but without
the classic problems of random effects models assuming no covariance
between unit level effects and predictors.
Author: Manuel Voelkle [aut, cph] (Original development of continuous time
model specification within OpenMx, advisor for further development),
Han Oud [aut, cph] (Original development of continuous time model
specification within OpenMx),
Charles Driver [aut, cre, cph] (Further development of continuous time
model specification within OpenMx, package development,
documentation and maintenance)
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>
Diff between ctsem versions 1.1.1 dated 2015-08-10 and 1.1.3 dated 2015-10-12
DESCRIPTION | 12 MD5 | 63 - NAMESPACE | 4 R/ctCI.R |only R/ctDeintervalise.R | 12 R/ctFit.R | 807 ++++++++++++------ R/ctGenerate.R | 30 R/ctLabel.R | 1 R/ctModel.R | 4 R/ctMultigroupFit.R | 31 R/ctPSMfit.R |only R/ctsem.R | 5 R/plot.ctsemFit.R | 247 ++++- R/summary.ctsemFit.R | 424 ++++++--- build/vignette.rds |binary data/ctExample1.rda |binary data/ctExample1TIpred.rda |binary inst/doc/ctsem.R | 296 ++++-- inst/doc/ctsem.pdf |binary inst/doc/ctsem.rnw | 640 +++++++++----- man/ctCI.Rd |only man/ctFit.Rd | 75 + man/ctGenerate.Rd | 22 man/ctModel.Rd | 3 man/ctMultigroupFit.Rd | 14 man/ctPSMfit.Rd |only man/ctsem.Rd | 5 man/plot.ctsemFit.Rd | 17 man/plot.ctsemMultigroupFit.Rd |only man/summary.ctsemFit.Rd | 16 man/summary.ctsemMultigroupFit.Rd |only vignettes/ctsem.rnw | 640 +++++++++----- vignettes/ctsem_paper_source.zip |only vignettes/pathdiagramtwoprocessbasic.pdf |binary vignettes/pathdiagramtwoprocessfull2.pdf |binary vignettes/references.bib | 1343 +++++++++++++++++-------------- 36 files changed, 2996 insertions(+), 1715 deletions(-)
Title: Get Hourly Meteorological Data from Global Stations
Description: Selectively acquire hourly meteorological data from stations located all over the world.
Author: Richard Iannone [aut, cre]
Maintainer: Richard Iannone <riannone@me.com>
Diff between stationaRy versions 0.3 dated 2015-06-23 and 0.4 dated 2015-10-12
DESCRIPTION | 14 MD5 | 32 NAMESPACE | 13 R/get_isd_station_data.R | 2211 ++++++++++++++++++++++++++++++++++++++++++-- R/get_isd_stations.R | 79 + R/map_isd_stations.R |only R/select_isd_station.R | 45 README.md | 246 +++- inst/000000-00000-2015.gz |only inst/999999-63897-2013.gz |only inst/999999-63897-2014.gz |only inst/999999-63897-2015.gz |only inst/stations.rda |binary inst/stations_map.png |only man/get_isd_station_data.Rd | 104 +- man/get_isd_stations.Rd | 37 man/map_isd_stations.Rd |only man/select_isd_station.Rd | 11 tests |only 19 files changed, 2569 insertions(+), 223 deletions(-)
Title: Integration of One-Dimensional Functions with Double Exponential
Formulas
Description: Numerical quadrature of functions of one variable over a finite or infinite interval
with double exponential formulas.
Author: Hiroyuki Okamura
Maintainer: Hiroyuki Okamura <okamu@rel.hiroshima-u.ac.jp>
Diff between deformula versions 0.1.0 dated 2015-10-09 and 0.1.1 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/deformula-package.Rd | 4 ++-- src/R_deformula.cpp | 4 ++-- src/deformula.cpp | 3 ++- src/include/deformula.hpp | 7 +++++-- 6 files changed, 20 insertions(+), 16 deletions(-)
Title: Edit, Run and Evaluate APSIM Simulations Easily Using R
Description: The Agricultural Production Systems sIMulator (APSIM) is a widely
used simulator of agricultural systems. This package includes
functions to create, edit and run APSIM simulations from R. It
also includes functions to visualize the results of an APSIM simulation
and perform sensitivity/uncertainty analysis of APSIM either via functions
in the sensitivity package or by novel emulator-based functions.
For more on APSIM including download instructions go to
\url{www.apsim.info}.
Author: Bryan Stanfill
Maintainer: Bryan Stanfill <bstanfill2003@gmail.com>
Diff between apsimr versions 1.1 dated 2015-07-29 and 1.2 dated 2015-10-12
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS | 9 +++++++++ R/runAPSIM.R | 6 +++--- R/visualize.R | 9 +++++++-- build/vignette.rds |binary inst/doc/apsimr-basics.pdf |binary man/apsimr-package.Rd | 6 +++--- 8 files changed, 34 insertions(+), 20 deletions(-)