Title: Generic Functions for Cross Validation
Diff between crossval versions 1.0.0 dated 2014-03-31 and 1.0.1 dated 2014-04-24
Description: This package contains generic functions for performing
cross validation and for computing diagnostic errors.
Author: Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
NEWS | 10 ++++++++++
R/diagnosticErrors.R | 4 ++--
man/crossval.Rd | 41 ++++++++++++++++++++++++++++++++++++++++-
5 files changed, 61 insertions(+), 12 deletions(-)
Title: Weibull Regression for a Right-Censored Endpoint with
Interval-Censored Covariate
Diff between SurvRegCensCov versions 1.2 dated 2014-04-07 and 1.3 dated 2014-04-24
More information about SurvRegCensCov at CRAN
Description: The main function of this package allows estimation of a Weibull Regression for a right-censored endpoint, one interval-censored covariate, and an arbitrary number of non-censored covariates. Additional functions allow to switch between different parametrizations of Weibull regression used by different R functions, inference for the mean difference of two arbitrarily censored Normal samples, and estimation of canonical parameters from censored samples for several distributional assumptions.
Author: Stanislas Hubeaux
Maintainer: Stanislas Hubeaux
DESCRIPTION | 14 -
MD5 | 40 +++--
NAMESPACE | 6
NEWS | 11 +
R/NormalMeanDiffCens.R | 4
R/ParamSampleCens.R | 2
R/SurvRegCens.R | 299 +++++++++++++++++++++++++-----------------
R/coef.src.r |only
R/logLik.src.r |only
R/print.src.r |only
R/summary.src.r |only
build/vignette.rds |binary
data/larynx.rda |binary
inst/doc/weibull.pdf |binary
man/ConvertWeibull.Rd | 2
man/NormalMeanDiffCens.Rd | 28 ---
man/ParamSampleCens.Rd | 29 +---
man/SurvRegCens.Rd | 103 +++++++-------
man/SurvRegCensCov-package.Rd | 8 -
man/censorContVar.Rd | 6
man/coef.src.Rd |only
man/larynx.Rd | 3
man/logLik.src.Rd |only
man/print.src.Rd |only
man/summary.src.Rd |only
25 files changed, 304 insertions(+), 251 deletions(-)
Permanent link
Title: Calculate textures from grey-level co-occurrence matrices
(GLCMs) in R
Diff between glcm versions 0.2 dated 2014-02-17 and 0.3.1 dated 2014-04-24
Description: Enables calculation of image textures derived from grey-level
co-occurrence matrices (GLCMs) in R. The texture calculation is coded in
C++ to optimize computation time.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff
glcm-0.2/glcm/data/glcm_test_raster.RData |only
glcm-0.2/glcm/data/glcm_test_raster_ENVI_textures.RData |only
glcm-0.2/glcm/inst |only
glcm-0.2/glcm/man/glcm_test_raster.Rd |only
glcm-0.2/glcm/man/glcm_test_raster_ENVI_textures.Rd |only
glcm-0.3.1/glcm/DESCRIPTION | 14 ++--
glcm-0.3.1/glcm/MD5 | 34 ++++++-----
glcm-0.3.1/glcm/NAMESPACE | 1
glcm-0.3.1/glcm/NEWS | 25 ++++++++
glcm-0.3.1/glcm/R/glcm-package.R | 49 ++++++++++++----
glcm-0.3.1/glcm/R/glcm.R | 48 +++++++--------
glcm-0.3.1/glcm/data/L5TSR_1986.RData |binary
glcm-0.3.1/glcm/data/expected_textures_3x3_1x1.RData |only
glcm-0.3.1/glcm/data/expected_textures_5x3_n1xn2.RData |only
glcm-0.3.1/glcm/data/expected_textures_5x7_2x3.RData |only
glcm-0.3.1/glcm/data/test_raster.RData |only
glcm-0.3.1/glcm/man/L5TSR_1986.Rd | 3
glcm-0.3.1/glcm/man/expected_textures_3x3_1x1.Rd |only
glcm-0.3.1/glcm/man/expected_textures_5x3_n1xn2.Rd |only
glcm-0.3.1/glcm/man/expected_textures_5x7_2x3.Rd |only
glcm-0.3.1/glcm/man/glcm.Rd | 27 +++++---
glcm-0.3.1/glcm/man/test_raster.Rd |only
glcm-0.3.1/glcm/src/calc_texture.cpp | 36 ++++++++---
glcm-0.3.1/glcm/tests/test-all.R | 3
glcm-0.3.1/glcm/tests/testthat |only
25 files changed, 158 insertions(+), 82 deletions(-)
Title: Weather Forecast Verification Utilities.
Diff between verification versions 1.37 dated 2014-04-02 and 1.38 dated 2014-04-24
Description: This package contains utilities for verification of
discrete,continuous, probabilistic forecasts and forecast
expressed as parametric distributions.
Author: NCAR - Research Applications Laboratory
Maintainer: Eric Gilleland
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/discrimination.plot.R | 2 +-
man/discrimination.plot.Rd | 2 +-
4 files changed, 8 insertions(+), 8 deletions(-)
Title: Stratigraphic Tree Analysis for Palaeontology
Diff between strap versions 1.0 dated 2014-03-31 and 1.1 dated 2014-04-24
Description: Functions for the stratigraphic analysis of phylogenetic trees.
Author: Mark A. Bell
Maintainer: Mark A. Bell
DESCRIPTION | 8
MD5 | 18
R/DatePhylo.R | 17
R/StratPhyloCongruence.R | 1224 ++++++++++++++++++++++----------------------
R/geoscalePhylo.R | 406 +++++++++-----
data/UKzones.RData |only
man/DatePhylo.Rd | 10
man/StratPhyloCongruence.Rd | 8
man/UKzones.Rd |only
man/geoscalePhylo.Rd | 56 +-
man/strap-package.Rd | 68 +-
11 files changed, 997 insertions(+), 818 deletions(-)
Title: Basic Robust Statistics
Diff between robustbase versions 0.90-2 dated 2014-02-04 and 0.91-0 dated 2014-04-24
Description: "Essential" Robust Statistics. The goal is to provide
tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by Maronna, Martin and Yohai; Wiley 2006.
Author: Original code by many authors, notably
Peter Rousseeuw and Christophe Croux, see file 'Copyrights';
Valentin Todorov
Maintainer: Martin Maechler
ChangeLog | 10 +-
DESCRIPTION | 10 +-
MD5 | 139 ++++++++++++++---------------
R/lmrob.MM.R | 105 ++++++++++++---------
R/lmrob.R | 1
R/ltsReg.R | 19 ++-
R/nlregrob.R | 19 +--
R/nlrob.R | 17 +--
R/qnsn.R | 1
TODO | 6 -
build/vignette.rds |binary
inst/doc/aggr_results.Rdata |binary
inst/doc/asymptotic.max.bias.Rdata |binary
inst/doc/estimating.functions.R | 7 +
inst/doc/lmrob_simulation.R | 110 +++++++---------------
inst/doc/lmrob_simulation.Rnw | 112 +++++++++--------------
inst/doc/lmrob_simulation.pdf |binary
inst/doc/psi_functions.pdf |binary
inst/doc/simulation.init.R |only
inst/xtraR/ex-funs.R | 19 ++-
man/M.psi.Rd | 10 +-
man/Qn.Rd | 7 -
man/lmrob.Rd | 19 +--
man/lmrob.S.Rd | 2
man/lmrob.control.Rd | 2
man/scaleTau2.Rd | 16 +++
man/summary.lmrob.Rd | 13 ++
src/init.c | 2
src/rfltsreg.f | 19 +--
tests/NAcoef.R | 3
tests/NAcoef.Rout.save | 46 ++-------
tests/Rsquared.R | 51 ++++++----
tests/Rsquared.Rout.save | 99 +++++++-------------
tests/lmrob-methods.Rout.save | 34 +++----
tests/lmrob-psifns.Rout.save | 92 +++++++++----------
tests/m-s-estimator.R | 13 +-
tests/nlregrob-tst.R | 14 +-
tests/nlrob-tst.R | 4
tests/weights.R | 12 ++
tests/weights.Rout.save | 44 ++++++---
vignettes/lmrob_simulation.Rnw | 112 +++++++++--------------
vignettes/plot-fig-AdB2-1.pdf |binary
vignettes/plot-fig-Mscale-all.pdf |binary
vignettes/plot-fig-Mscale.pdf |binary
vignettes/plot-fig-cpr.pdf |binary
vignettes/plot-fig-efficiency-all.pdf |binary
vignettes/plot-fig-efficiency.pdf |binary
vignettes/plot-fig-emp-level.pdf |binary
vignettes/plot-fig-example-design.pdf |binary
vignettes/plot-fig-lqq-level.pdf |binary
vignettes/plot-fig-max-asymptotic-bias.pdf |binary
vignettes/plot-fig-meanscale.pdf |binary
vignettes/plot-fig-power-1-0_2.pdf |binary
vignettes/plot-fig-power-1-0_4.pdf |binary
vignettes/plot-fig-power-1-0_6.pdf |binary
vignettes/plot-fig-power-1-0_8.pdf |binary
vignettes/plot-fig-power-1-1.pdf |binary
vignettes/plot-fig-pred-points.pdf |binary
vignettes/plot-fig-psi-functions.pdf |binary
vignettes/plot-fig-qscale-all.pdf |binary
vignettes/plot-fig-qscale.pdf |binary
vignettes/plot-fig-sdAdB2-1.pdf |binary
vignettes/plot-fig-sdscale-1.pdf |binary
vignettes/plot-fig-sdscale-all.pdf |binary
vignettes/psi-GGW.pdf |binary
vignettes/psi-Hampel.pdf |binary
vignettes/psi-Huber.pdf |binary
vignettes/psi-LQQ.pdf |binary
vignettes/psi-Welsh.pdf |binary
vignettes/psi-bisquare.pdf |binary
vignettes/psi-optimal.pdf |binary
71 files changed, 573 insertions(+), 616 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Diff between mvMORPH versions 1.0.1 dated 2014-02-07 and 1.0.2 dated 2014-04-24
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel
DESCRIPTION | 6 +++---
MD5 | 20 +++++++++++---------
NAMESPACE | 2 +-
R/fun.r | 1 +
R/mvOUC.r | 10 ++++++----
R/mvSHIFT.r | 35 ++++++++++++++++++++++++-----------
man/mvOU.Rd | 6 +++---
man/mvSHIFT.rd | 8 ++++----
src/covar-matrix-simmap.c | 2 ++
src/mvmorph-covar-mat.c |only
src/mvmorph-covar-ou.c |only
src/weight-matrix-simmap.c | 7 ++++---
12 files changed, 59 insertions(+), 38 deletions(-)
Title: Multiple Imputation for interval censored data regression
Diff between MIICD versions 1.0 dated 2014-04-23 and 1.1 dated 2014-04-24
Description: Applies the Pan's (2000) multiple imputation approach to Cox or Fine and Gray regression for interval censored data.
Author: Marc Delord
Maintainer: Marc Delord
MIICD-1.0/MIICD/data/cml.rda |only
MIICD-1.0/MIICD/man/cml.Rd |only
MIICD-1.1/MIICD/DESCRIPTION | 6 +++---
MIICD-1.1/MIICD/MD5 | 8 +++-----
MIICD-1.1/MIICD/man/MIICD-package.Rd | 12 +++++-------
MIICD-1.1/MIICD/man/MIICD.crreg.Rd | 10 +---------
6 files changed, 12 insertions(+), 24 deletions(-)
Title: Evidence Combination in R
Diff between EvCombR versions 0.1-1 dated 2014-01-23 and 0.1-2 dated 2014-04-24
Description: Package for combining pieces of evidence
Author: Alexander Karlsson
Maintainer: Alexander Karlsson
DESCRIPTION | 8 -
MD5 | 37 ++++----
NAMESPACE | 1
R/EvCombR.R | 202 ++++++++++++++++++++++++++++++++-----------------
inst/CITATION | 4
inst/NEWS.Rd | 47 ++++++-----
man/EvCombR-package.Rd | 4
man/credal-class.Rd | 4
man/credal-methods.Rd | 6 -
man/credal.Rd | 12 +-
man/focal_-.Rd | 2
man/lower-methods.Rd | 15 +++
man/lower.Rd | 7 +
man/mass-class.Rd | 12 +-
man/upper-methods.Rd | 9 ++
man/upper.Rd | 11 +-
man/z[-methods.Rd | 10 +-
man/z[[-methods.Rd | 6 -
man/z[[_--methods.Rd |only
man/z[_--methods.Rd | 8 -
20 files changed, 256 insertions(+), 149 deletions(-)
Title: Analysis of habitat selection by animals
Diff between adehabitat versions 1.8.12 dated 2013-01-11 and 1.8.13 dated 2014-04-24
Description: A collection of tools for the analysis of habitat selection by animals
Author: Clement Calenge, contributions from Mathieu Basille, Stephane Dray and Scott Fortmann-Roe
Maintainer: Clement Calenge
adehabitat-1.8.12/adehabitat/CONTENTS |only
adehabitat-1.8.12/adehabitat/R/NNCH.r |only
adehabitat-1.8.12/adehabitat/R/print.NNCH.r |only
adehabitat-1.8.12/adehabitat/man/NNCH.Rd |only
adehabitat-1.8.12/adehabitat/man/NNCH.area.Rd |only
adehabitat-1.8.12/adehabitat/man/NNCH.select.Rd |only
adehabitat-1.8.13/adehabitat/DESCRIPTION | 19 ++++-----
adehabitat-1.8.13/adehabitat/MD5 | 42 +++++++++-------------
adehabitat-1.8.13/adehabitat/NAMESPACE | 6 ---
adehabitat-1.8.13/adehabitat/R/ararea.r | 16 +++++---
adehabitat-1.8.13/adehabitat/R/area2spol.r | 4 --
adehabitat-1.8.13/adehabitat/R/asc2spixdf.r | 4 --
adehabitat-1.8.13/adehabitat/R/clusthr.r | 28 +++++++++++---
adehabitat-1.8.13/adehabitat/R/debut.r | 11 +++--
adehabitat-1.8.13/adehabitat/R/explore.kasc.r | 3 -
adehabitat-1.8.13/adehabitat/R/kasc2spixdf.r | 2 -
adehabitat-1.8.13/adehabitat/R/kver2spol.r | 2 -
adehabitat-1.8.13/adehabitat/R/mcp.area.r | 14 +++++--
adehabitat-1.8.13/adehabitat/R/spixdf2kasc.r | 2 -
adehabitat-1.8.13/adehabitat/R/spol2area.r | 2 -
adehabitat-1.8.13/adehabitat/R/trajdyn.r | 2 -
adehabitat-1.8.13/adehabitat/man/clusthr.Rd | 3 -
adehabitat-1.8.13/adehabitat/man/kerneloverlap.Rd | 7 ++-
adehabitat-1.8.13/adehabitat/man/mcp.Rd | 9 +---
adehabitat-1.8.13/adehabitat/man/perarea.Rd | 6 ---
25 files changed, 86 insertions(+), 96 deletions(-)
Title: Spatial Oblique Decision Tree
Diff between SPODT versions 0.8.2 dated 2014-01-31 and 0.9 dated 2014-04-24
Description: SPODT is a spatial partitioning method based on oblique decision trees, in order to classify study area into zones of different risks, determining their boundaries
Author: Jean Gaudart, Nathalie Graffeo, Guillaume Barbet, Bernard Fichet, Roch Giorgi (Aix-Marseille University)
Maintainer: Jean Gaudart
SPODT-0.8.2/SPODT/R/OLD_spodt.R |only
SPODT-0.8.2/SPODT/R/recursif.carte.R |only
SPODT-0.8.2/SPODT/R/spodt.map.R |only
SPODT-0.8.2/SPODT/man/spodt.map.Rd |only
SPODT-0.8.2/SPODT/tests |only
SPODT-0.9/SPODT/DESCRIPTION | 10 +-
SPODT-0.9/SPODT/MD5 | 67 ++++++-------
SPODT-0.9/SPODT/NAMESPACE | 8 -
SPODT-0.9/SPODT/R/base.d2.R |only
SPODT-0.9/SPODT/R/classe.spodt.r | 4
SPODT-0.9/SPODT/R/is.in.R |only
SPODT-0.9/SPODT/R/recurs.d2.r |only
SPODT-0.9/SPODT/R/recursif.carte.sp.R |only
SPODT-0.9/SPODT/R/rm.dupl.R |only
SPODT-0.9/SPODT/R/sp1.R | 11 +-
SPODT-0.9/SPODT/R/spodt.R | 149 +++----------------------------
SPODT-0.9/SPODT/R/spodt.fct.R |only
SPODT-0.9/SPODT/R/spodtSpatialLines.R |only
SPODT-0.9/SPODT/R/test.spodt.R | 116 +++++++++++-------------
SPODT-0.9/SPODT/man/SPODT-package.Rd | 35 +++++--
SPODT-0.9/SPODT/man/dataBALL0.Rd | 10 +-
SPODT-0.9/SPODT/man/dataBALL0_5.Rd | 11 +-
SPODT-0.9/SPODT/man/dataBALL1_5.Rd | 11 +-
SPODT-0.9/SPODT/man/dataBALL2.Rd | 11 +-
SPODT-0.9/SPODT/man/dataCOV.Rd | 16 +--
SPODT-0.9/SPODT/man/dataMALARIA.Rd | 24 +++-
SPODT-0.9/SPODT/man/dataSQUARE0.Rd | 12 +-
SPODT-0.9/SPODT/man/dataSQUARE0_5.Rd | 10 +-
SPODT-0.9/SPODT/man/dataSQUARE1_5.Rd | 10 +-
SPODT-0.9/SPODT/man/dataSQUARE2.Rd | 10 +-
SPODT-0.9/SPODT/man/dataV0.Rd | 12 +-
SPODT-0.9/SPODT/man/dataV0_5.Rd | 13 +-
SPODT-0.9/SPODT/man/dataV1_5.Rd | 13 +-
SPODT-0.9/SPODT/man/dataV2.Rd | 13 +-
SPODT-0.9/SPODT/man/spodt-class.Rd | 7 -
SPODT-0.9/SPODT/man/spodt.Rd | 33 ++++--
SPODT-0.9/SPODT/man/spodt.tree.Rd | 21 +++-
SPODT-0.9/SPODT/man/spodtSpatialLines.Rd |only
SPODT-0.9/SPODT/man/test.spodt.Rd | 41 ++++----
39 files changed, 337 insertions(+), 341 deletions(-)
Title: rpubchem - Interface to the PubChem Collection
Diff between rpubchem versions 1.5.0.1 dated 2014-03-11 and 1.5.0.2 dated 2014-04-24
Description: Access PubChem data (compounds, substance, assays).
Structural information is provided in the form of SMILES
strings. This package only provides access to a subset of the
precalculated data stored by PubChem. Bio-assay data can be
accessed to obtain descriptions as well as the actual data. It
is also possible to search for assay ID's by keyword. Currently
the main limitation is that only 1000 molecules can be
downloaded at a time from the PubChem servers
Author: Rajarshi Guha
Maintainer: Rajarshi Guha
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/getassay.R | 13 +++++++++----
3 files changed, 15 insertions(+), 10 deletions(-)
Title: Toolkit of helper functions to pre-process amplification data
Diff between chipPCR versions 0.0.5 dated 2013-12-11 and 0.0.6 dated 2014-04-24
Description: The chipPCR package is a toolkit of helper functions to pre-process amplification data. Amplification data can be obtained from classical PCR reactions or isothermal amplification reactions. The package contains functions to normalize amplification, a simple routine to detect the start of an amplification reaction and several smoothers for amplification data. The smoothers are based on LOWESS, moving average, cubic splines, Savitzky-Golay and others. In addition contains the chipPCR package data sets of experimental nucleic acid amplification systems including the VideoScan HCU and a capillary convective PCR system. The amplification data were generated by helicase dependent amplification (HDA) or polymerase chain reaction (PCR) under various temperature conditions. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.
Author: Stefan Roediger, Michal Burdukiewicz
Maintainer: Stefan Roediger
CHANGELOG |only
DESCRIPTION | 12 +--
MD5 | 90 +++++++++++++++---------
NAMESPACE | 1
R/AmpSim.R | 9 +-
R/CPP.R | 4 -
R/amptester.R | 6 -
R/bg.max.R | 15 ++--
R/fixNA.R | 4 -
R/inder.R | 12 ++-
R/smoother.R | 6 -
data/C126EG595.rda |only
data/C126EG685.rda |only
data/C127EGHP.rda |only
data/C17.rda |binary
data/C67.rda |binary
data/C81.rda |binary
data/C85.rda |binary
data/CD74.rda |binary
data/CD75.rda |binary
data/Eff1000.rda |only
data/Eff625.rda |only
data/Eff750.rda |only
data/Eff875.rda |only
data/VIMCFX96_60.rda |only
data/VIMCFX96_69.rda |only
data/VIMCFX96_meltcurve.rda |only
data/VIMiQ5_595.rda |only
data/VIMiQ5_685.rda |only
data/VIMiQ5_melt.rda |only
data/capillaryPCR.rda |binary
data/datalist |only
man/AmpSim.Rd | 45 ++++++------
man/C126EG595.Rd |only
man/C126EG685.Rd |only
man/C127EGHP.Rd |only
man/C17.Rd | 48 +++++++-----
man/C67.Rd | 46 ++++++------
man/C81.Rd | 42 ++++++-----
man/C85.Rd | 130 ++++++++++++++++++++++++++++++----
man/CD74.Rd | 117 +++++++++++++++++++++++--------
man/CD75.Rd | 42 ++++++-----
man/CPP.Rd | 46 ++++++------
man/Eff1000.Rd |only
man/Eff625.Rd |only
man/Eff750.Rd |only
man/Eff875.Rd |only
man/VIMCFX96_60.Rd |only
man/VIMCFX96_69.Rd |only
man/VIMCFX96_meltcurve.Rd |only
man/VIMiQ5_595.Rd |only
man/VIMiQ5_685.Rd |only
man/VIMiQ5_melt.Rd |only
man/amptester.Rd | 101 ++++++++++++++-------------
man/bg.max.Rd | 56 ++++++++-------
man/capillaryPCR.Rd | 164 ++++++++++++++++++++++++++++++++++++++------
man/chipPCR-package.Rd | 51 +++++++------
man/fixNA.Rd | 61 ++++++++++------
man/inder.Rd | 64 +++++++++++------
man/smoother.Rd | 131 ++++++++++++++++++++---------------
60 files changed, 866 insertions(+), 437 deletions(-)
Title: R package to compute the FastRCS outlyingness index.
Diff between FastRCS versions 0.0.2 dated 2014-02-19 and 0.0.3 dated 2014-04-24
Description: The FastRCS outlyingness index is an algorithm for finding outliers for the linear regression model.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/FastRCS.R | 2 +-
src/FastRCS.cpp | 22 +++++++++++++---------
src/Makevars | 1 +
5 files changed, 22 insertions(+), 17 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Diff between arm versions 1.6-10 dated 2013-11-18 and 1.7-02 dated 2014-04-24
Description: R functions for processing lm, glm, svy.glm, merMod and polr outputs.
Author: Andrew Gelman [aut],
Yu-Sung Su [aut, cre],
Masanao Yajima [ctb],
Jennifer Hill [ctb],
Maria Grazia Pittau [ctb],
Jouni Kerman [ctb],
Tian Zheng [ctb],
Vicent Dorie [ctb]
Maintainer: Yu-Sung Su
CHANGELOG | 152 ++++++++++++------------
DESCRIPTION | 28 ++--
MD5 | 12 -
R/bayesglm.R | 370 +++++++++++++++++++++++++++++------------------------------
R/fitted.R | 14 --
R/simmer.R | 5
man/sim.Rd | 2
7 files changed, 294 insertions(+), 289 deletions(-)
Title: R package to compute the FastPCS outlyingness index.
Diff between FastPCS versions 0.0.8 dated 2014-02-15 and 0.0.9 dated 2014-04-24
Description: The FastPCS outlyingness index is an algorithm for finding outliers for the multivariate elliptical model.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
man/FastPCS-package.Rd | 12 ++++++------
src/FastPCS.cpp | 28 +++++++++++++++++-----------
src/Makevars | 4 +++-
5 files changed, 34 insertions(+), 26 deletions(-)
Title: Multivariate Permutation Tests
Diff between flip versions 2.4.1 dated 2014-04-14 and 2.4.2 dated 2014-04-24
Description: It implements many univariate and multivariate permutation (and rotation) tests. Allowed tests: the t one and two samples, ANOVA, linear models, Chi Squared test, rank tests (i.e. Wilcoxon, Mann-Whitney, Kruskal-Wallis), Sign test and McNemar. Test on Linear Models are performed also in presence of covariates (i.e. nuisance parameters). The permutation and the rotation methods to get the null distribution of the test statistics are available. It also implements methods for multiplicity control such as Westfall-Young minP procedure and Closed Testing (Marcus, 1976) and k-FWER. Moreover, it allows to test for fixed effects in mixed effects models.
Author: Livio Finos, with contributions by Dario Basso, Aldo Solari, Jelle Goeman and Marco Rinaldo. Special thanks are due to Ivan Marin-Franch and Fredrik Nilsson for the debugging and the good questions.
Maintainer: Livio Finos
ChangeLog | 8 ++++----
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
man/flip.Rd | 9 +++++----
man/permutationSpace.Rd | 2 ++
5 files changed, 19 insertions(+), 16 deletions(-)
Title: Analysis of Factorial Experiments
Diff between afex versions 0.8-94 dated 2014-02-23 and 0.9-109 dated 2014-04-24
Description: Provides convenience functions for analyzing factorial experiments
using ANOVA or mixed-models. ez.glm() and aov.car() allow convenient
calculation of between, within (i.e., repeated-measures), or mixed
between-within (i.e., split-plot) ANOVAs for data in the long format (i.e.,
one observation per row) wrapping car::Anova() (aggregating more then one
observation per individual and cell of the design), per default returning a
print ready ANOVA table. Function mixed() fits a mixed model using
lme4::lmer() and computes p-values for all effects in the model using
either the Kenward-Roger approximation of degrees of freedom (LMM only),
parametric bootstrap (LMMs and GLMMs) or likelihood ratio tests (LMMs and
GLMMs). afex uses type 3 sums of squares as default (imitating commercial
statistical software) and sets the default contrasts to contr.sum.
Furthermore, compare.2.vectors() conveniently compares two vectors using a
variety of tests.
Author: Henrik Singmann [aut, cre],
Ben Bolker [ctb],
Søren Højsgaard [ctb],
Ulrich Halekoh [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb]
Maintainer: Henrik Singmann
DESCRIPTION | 65 +++++-----
MD5 | 59 +++++----
NAMESPACE | 10 +
NEWS | 44 +++++++
R/afex-package.R | 14 +-
R/aov.car.R | 82 ++++++++++---
R/compare.2.vectors.R | 4
R/md_12.1-data.R | 23 +++
R/md_16.1-data.R | 2
R/md_16.4-data.R | 3
R/mixed.R | 291 ++++++++++++++++++++++-------------------------
R/nice.anova.R | 3
R/obk.long-data.R | 2
R/round_ps.R | 2
data/md_12.1.rda |binary
data/md_16.1.rda |binary
data/md_16.4.rda |binary
data/obk.long.rda |binary
man/afex-package.Rd | 13 --
man/aov.car.Rd | 85 ++++++++-----
man/compare.2.vectors.Rd | 1
man/md_12.1.Rd | 23 +--
man/md_16.1.Rd | 1
man/md_16.4.Rd | 1
man/mixed.Rd | 236 +++++++++++++++++++++++---------------
man/nice.anova.Rd | 1
man/obk.long.Rd | 1
man/round_ps.Rd | 1
tests |only
29 files changed, 584 insertions(+), 383 deletions(-)
Title: Efficient and accurate P-value computation for Position Weight
Matrices.
Diff between TFMPvalue versions 0.0.2 dated 2014-03-31 and 0.0.3 dated 2014-04-24
Description: TFMPvalue provides the accurate calculation of P-value with score threshold for Position Weight Matrices, or the score with given P-value. This package is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
Author: Ge Tan
Maintainer: Ge Tan
DESCRIPTION | 8 ++---
MD5 | 12 ++++----
src/Matrix.cpp | 74 +++++++++++++++++++++++++++---------------------------
src/Matrix.h | 51 +++++++++++++++++++++----------------
src/TFMMain.cpp | 28 ++++++++++----------
src/TFMpvalue.cpp | 68 ++++++++++++++++++++++++-------------------------
src/TFMpvalue.h | 4 +-
7 files changed, 126 insertions(+), 119 deletions(-)
Title: Interface between R and GGobi
Diff between rggobi versions 2.1.19 dated 2012-07-12 and 2.1.20 dated 2014-04-24
Description: The rggobi package provides a command-line interface to GGobi, an
interactive and dynamic graphics package. Rggobi complements GGobi's
graphical user interface, providing a way to fluidly transition between
analysis and exploration, as well as automating common tasks.
Author: Duncan Temple Lang
Maintainer: Hadley Wickham
rggobi-2.1.19/rggobi/.gitignore |only
rggobi-2.1.19/rggobi/aclocal.m4 |only
rggobi-2.1.19/rggobi/load.r |only
rggobi-2.1.19/rggobi/src/Makevars |only
rggobi-2.1.19/rggobi/start.r |only
rggobi-2.1.19/rggobi/test |only
rggobi-2.1.20/rggobi/DESCRIPTION | 33 ++--
rggobi-2.1.20/rggobi/LICENSE |only
rggobi-2.1.20/rggobi/MD5 | 41 ++----
rggobi-2.1.20/rggobi/NAMESPACE | 1
rggobi-2.1.20/rggobi/NEWS | 9 +
rggobi-2.1.20/rggobi/R/datasets.r | 94 +++++++-------
rggobi-2.1.20/rggobi/R/edges.r | 48 +++----
rggobi-2.1.20/rggobi/R/longitudinal.r | 33 ++--
rggobi-2.1.20/rggobi/R/zzz.r | 25 +--
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rggobi-2.1.20/rggobi/cleanup |only
rggobi-2.1.20/rggobi/man/ggobi-display-save-picture-bw.rd | 3
rggobi-2.1.20/rggobi/man/ggobi-set-data-frame-vy.rd | 3
rggobi-2.1.20/rggobi/src/data.c | 16 +-
rggobi-2.1.20/rggobi/src/ggobi.c | 25 ---
rggobi-2.1.20/rggobi/src/utils.c | 2
22 files changed, 150 insertions(+), 183 deletions(-)
Title: Gaussian, Poisson, and Binomial Hierarchical Modeling
Diff between Rgbp versions 1.0.5 dated 2014-03-01 and 1.0.6 dated 2014-04-24
Description: Rgbp is an R package that utilizes approximate Bayesian machinery to provide a method of estimating two-level hierarchical models for Gaussian, Poisson, and Binomial data in a fast and computationally efficient manner. The main products of this package are point and interval estimates for the true parameters, whose good frequency properties can be validated via its repeated sampling procedure called frequency method checking. It is found that such Bayesian-frequentist reconciliation allows Rgbp to have attributes desirable both sides of the aisle, working well in small samples and yielding good coverage probabilities for its interval estimates.
Author: Joseph Kelly, Hyungsuk Tak, and Carl Morris
Maintainer: Joseph Kelly
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/coverage.R | 23 ++++++++++++-----------
R/gbp.R | 45 +++++++++++++++++++++++++++------------------
4 files changed, 46 insertions(+), 36 deletions(-)
Title: Interface to the Global Biodiversity Information Facility API
Diff between rgbif versions 0.6.0 dated 2014-04-17 and 0.6.2 dated 2014-04-24
Description: A programmatic interface to the
Web Service methods provided by the Global
Biodiversity Information Facility.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain
rgbif-0.6.0/rgbif/R/gist.r |only
rgbif-0.6.0/rgbif/R/stylegeojson.r |only
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rgbif-0.6.2/rgbif/DESCRIPTION | 12
rgbif-0.6.2/rgbif/MD5 | 121 +--
rgbif-0.6.2/rgbif/NEWS | 16
rgbif-0.6.2/rgbif/R/count_facet.r | 19
rgbif-0.6.2/rgbif/R/dataset_metrics.r | 18
rgbif-0.6.2/rgbif/R/deprecated.r | 322 +++++++++-
rgbif-0.6.2/rgbif/R/elevation.r | 12
rgbif-0.6.2/rgbif/R/gbifmap.r | 13
rgbif-0.6.2/rgbif/R/globals.r | 2
rgbif-0.6.2/rgbif/R/installations.r | 1
rgbif-0.6.2/rgbif/R/name_lookup.r | 2
rgbif-0.6.2/rgbif/R/occ_get.r | 25
rgbif-0.6.2/rgbif/R/occ_metadata.r | 8
rgbif-0.6.2/rgbif/R/occ_search.r | 4
rgbif-0.6.2/rgbif/R/rgbif-package.r | 8
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rgbif-0.6.2/rgbif/inst/vign/rgbif_vignette.md | 95 +--
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rgbif-0.6.2/rgbif/man/dataset_metrics.Rd | 12
rgbif-0.6.2/rgbif/man/density_spplist-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/densitylist-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/elevation.Rd | 9
rgbif-0.6.2/rgbif/man/gbifdata-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/gbifmap.Rd | 2
rgbif-0.6.2/rgbif/man/gbifmap_dens-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/gbifmap_list-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/gbifparser_verbatim.Rd | 6
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rgbif-0.6.2/rgbif/man/installations.Rd | 1
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rgbif-0.6.2/rgbif/man/occ_get.Rd | 22
rgbif-0.6.2/rgbif/man/occ_metadata.Rd | 3
rgbif-0.6.2/rgbif/man/occ_search.Rd | 4
rgbif-0.6.2/rgbif/man/occurrencecount-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/occurrenceget-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/occurrencelist-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/occurrencelist_all-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/occurrencelist_many-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/providers-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/resources-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/rgbif-deprecated.Rd | 9
rgbif-0.6.2/rgbif/man/stylegeojson-deprecated.Rd |only
rgbif-0.6.2/rgbif/man/taxoncount-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/taxonget-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/taxonsearch-deprecated.Rd | 2
rgbif-0.6.2/rgbif/man/togeojson-deprecated.Rd |only
rgbif-0.6.2/rgbif/tests/testthat/test-datasets.r | 2
rgbif-0.6.2/rgbif/tests/testthat/test-gbifmap.r |only
rgbif-0.6.2/rgbif/tests/testthat/test-occ_get.r | 17
rgbif-0.6.2/rgbif/vignettes/figure/gbifmap1.png |binary
rgbif-0.6.2/rgbif/vignettes/rgbif_vignette.Rmd | 95 +--
rgbif-0.6.2/rgbif/vignettes/rgbif_vignette.html | 505 +++++++++++-----
rgbif-0.6.2/rgbif/vignettes/rgbif_vignette.md | 95 +--
rgbif-0.6.2/rgbif/vignettes/rgbif_vignette_oldapi.html | 341 ++++++++--
71 files changed, 1351 insertions(+), 572 deletions(-)
Title: Dictionaries and word lists for the qdap package.
Diff between qdapDictionaries versions 0.0.3 dated 2014-03-17 and 0.0.4 dated 2014-04-24
More information about qdapDictionaries at CRAN
Description: This package is a collection of dictionaries and word lists for
use with the qdap package.
Author: Tyler Rinker
Maintainer: Tyler Rinker
DESCRIPTION | 6 +-
MD5 | 88 ++++++++++++++++++++++-----------------
NEWS | 11 ++++
R/qdapDictionaries-package.R | 92 ++++++++++++++++++++++++++++++++++++++---
README.md | 2
data/BuckleySaltonSWL.rda |binary
data/DICTIONARY.rda |binary
data/Dolch.rda |binary
data/Fry_1000.rda |binary
data/Leveled_Dolch.rda |binary
data/NAMES.rda |binary
data/NAMES_LIST.rda |binary
data/NAMES_SEX.rda |binary
data/OnixTxtRetToolkitSWL1.rda |binary
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data/Top100Words.rda |binary
data/Top200Words.rda |binary
data/Top25Words.rda |binary
data/abbreviations.rda |binary
data/action.verbs.rda |binary
data/adverb.rda |binary
data/amplification.words.rda |binary
data/contractions.rda |binary
data/datalist | 6 ++
data/deamplification.words.rda |binary
data/emoticon.rda |binary
data/env.pol.rda |binary
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data/interjections.rda |binary
data/labMT.rda |binary
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inst/CITATION | 4 -
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man/NAMES_LIST.Rd | 2
man/NAMES_SEX.Rd | 2
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man/power.words.Rd |only
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51 files changed, 163 insertions(+), 52 deletions(-)
Permanent link
Title: Bootstrapped Basis Regression with Oracle Model Selection
Diff between polywog versions 0.3-0 dated 2013-01-09 and 0.4-0 dated 2014-04-24
Description: Routines for flexible functional form estimation via basis
regression, with model selection via the adaptive LASSO or SCAD to prevent
overfitting.
Author: Brenton Kenkel and Curtis S. Signorino
Maintainer: Brenton Kenkel
polywog-0.3-0/polywog/NEWS |only
polywog-0.3-0/polywog/R/fitters.r |only
polywog-0.3-0/polywog/R/fn_cv.r |only
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polywog-0.3-0/polywog/man/rawpoly.Rd |only
polywog-0.4-0/polywog/DESCRIPTION | 24
polywog-0.4-0/polywog/MD5 | 85 +-
polywog-0.4-0/polywog/NAMESPACE | 17
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polywog-0.4-0/polywog/man/polywog.Rd | 316 ++++---
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