Title: Generation of Virtual Species Distributions
Description: Provides a framework for generating virtual species distributions,
a procedure increasingly used in ecology to improve species distribution models.
This package integrates the existing methodological approaches with the
objective of generating virtual species distributions with increased
ecological realism.
Author: Boris Leroy, Christine N. Meynard, Celine Bellard and Franck Courchamp
Maintainer: Boris Leroy <leroy.boris@gmail.com>
Diff between virtualspecies versions 1.0 dated 2014-09-25 and 1.1 dated 2015-05-15
DESCRIPTION | 10 +-- MD5 | 53 +++++++++-------- NAMESPACE | 4 - R/formatFunctions.R | 5 + R/generateRandomSp.R | 20 +++++- R/generateSpFromFun.R | 129 ++++++++++++++++-------------------------- R/generateSpFromPCA.R | 53 ++++++----------- R/genericfunctions.R | 14 +--- R/limitDistribution.R | 7 -- R/sp.env.functions.R | 121 +++++++++++++++++++++++++++++++++++++++ R/thermalFunctionDraft.R |only R/virtualspecies-package.R | 7 +- README.md |only inst |only man/betaFun.Rd |only man/convertToPA.Rd | 3 man/custnorm.Rd |only man/formatFunctions.Rd | 5 - man/generateRandomSp.Rd | 23 ++++++- man/generateSpFromFun.Rd | 34 +++++------ man/generateSpFromPCA.Rd | 37 +++++------- man/limitDistribution.Rd | 10 --- man/linearFun.Rd | 3 man/logisticFun.Rd | 3 man/plotResponse.Rd | 3 man/quadraticFun.Rd | 3 man/removeCollinearity.Rd | 3 man/sampleOccurrences.Rd | 3 man/synchroniseNA.Rd | 3 man/virtualspecies-package.Rd | 10 +-- 30 files changed, 341 insertions(+), 225 deletions(-)
More information about virtualspecies at CRAN
Permanent link
Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to the Concorde TSP solver and its implementation of the
Chained-Lin-Kernighan heuristic. Concorde
itself is not included in the package and has to be obtained separately
from http://www.math.uwaterloo.ca/tsp/concorde.html.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between TSP versions 1.1-0 dated 2015-03-15 and 1.1-1 dated 2015-05-15
TSP-1.1-0/TSP/inst/tests/TSPLIB.R |only TSP-1.1-0/TSP/inst/tests/solve_TSP.R |only TSP-1.1-1/TSP/DESCRIPTION | 9 +++--- TSP-1.1-1/TSP/MD5 | 24 +++++++++--------- TSP-1.1-1/TSP/build/vignette.rds |binary TSP-1.1-1/TSP/data/USCA312.rda |binary TSP-1.1-1/TSP/data/USCA312_map.rda |binary TSP-1.1-1/TSP/data/USCA50.rda |binary TSP-1.1-1/TSP/inst/NEWS | 4 +++ TSP-1.1-1/TSP/inst/doc/TSP.pdf |binary TSP-1.1-1/TSP/inst/tests/test-TSPLIB.R |only TSP-1.1-1/TSP/inst/tests/test-solve_TSP.R |only TSP-1.1-1/TSP/src/insertion_cost.c | 28 +++++++++++---------- TSP-1.1-1/TSP/src/tour_length.c | 31 +++++++++++++---------- TSP-1.1-1/TSP/src/two_opt.c | 39 +++++++++++++----------------- 15 files changed, 71 insertions(+), 64 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.0.0 dated 2015-01-28 and 1.1.0 dated 2015-05-15
stochvol-1.0.0/stochvol/R/wrapper.R |only stochvol-1.1.0/stochvol/DESCRIPTION | 8 stochvol-1.1.0/stochvol/MD5 | 73 +- stochvol-1.1.0/stochvol/NEWS | 34 + stochvol-1.1.0/stochvol/R/plotting.R |only stochvol-1.1.0/stochvol/R/simulation.R | 37 - stochvol-1.1.0/stochvol/R/utilities_svdraws.R | 324 +----------- stochvol-1.1.0/stochvol/R/wrappers.R |only stochvol-1.1.0/stochvol/build/vignette.rds |binary stochvol-1.1.0/stochvol/data/exrates.RData |binary stochvol-1.1.0/stochvol/inst/CITATION | 15 stochvol-1.1.0/stochvol/inst/doc/article.R | 39 - stochvol-1.1.0/stochvol/inst/doc/article.Rnw | 19 stochvol-1.1.0/stochvol/inst/doc/article.pdf |binary stochvol-1.1.0/stochvol/inst/doc/heavytails.R |only stochvol-1.1.0/stochvol/inst/doc/heavytails.Rnw |only stochvol-1.1.0/stochvol/inst/doc/heavytails.pdf |only stochvol-1.1.0/stochvol/inst/include/update.h | 6 stochvol-1.1.0/stochvol/man/extractors.Rd | 2 stochvol-1.1.0/stochvol/man/logret.Rd | 2 stochvol-1.1.0/stochvol/man/paradensplot.Rd | 7 stochvol-1.1.0/stochvol/man/paratraceplot.Rd | 6 stochvol-1.1.0/stochvol/man/plot.svdraws.Rd | 4 stochvol-1.1.0/stochvol/man/stochvol-package.Rd | 2 stochvol-1.1.0/stochvol/man/svsample.Rd | 15 stochvol-1.1.0/stochvol/man/svsample2.Rd | 10 stochvol-1.1.0/stochvol/man/svsim.Rd | 13 stochvol-1.1.0/stochvol/man/updatesummary.Rd | 2 stochvol-1.1.0/stochvol/man/volplot.Rd | 6 stochvol-1.1.0/stochvol/src/Makevars.win | 10 stochvol-1.1.0/stochvol/src/densities.h | 18 stochvol-1.1.0/stochvol/src/progutils.cpp | 43 + stochvol-1.1.0/stochvol/src/progutils.h | 23 stochvol-1.1.0/stochvol/src/sampler.cpp | 133 ++-- stochvol-1.1.0/stochvol/src/sampler.h | 2 stochvol-1.1.0/stochvol/vignettes/Makefile | 10 stochvol-1.1.0/stochvol/vignettes/article.Rnw | 19 stochvol-1.1.0/stochvol/vignettes/extrafig/predlik_terr.pdf |only stochvol-1.1.0/stochvol/vignettes/heavytails.Rnw |only stochvol-1.1.0/stochvol/vignettes/heavytails.tex |only stochvol-1.1.0/stochvol/vignettes/macros.tex | 6 stochvol-1.1.0/stochvol/vignettes/mybib.bib | 123 ++++ 42 files changed, 519 insertions(+), 492 deletions(-)
Title: Bi-Directional Interface Between R and Scala with Callbacks
Description: The Scala interpreter is embedded in R and callbacks to R from the embedded interpreter are supported. Conversely, the R interpreter is embedded in Scala. Scala versions 2.10 and 2.11 are supported.
Author: David B. Dahl [aut, cre],
Scala developers [ctb] (see http://scala-lang.org/)
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 1.0.4 dated 2015-03-24 and 1.0.6 dated 2015-05-15
rscala-1.0.4/rscala/inst/java/rscala_2.10-1.0.4.jar |only rscala-1.0.4/rscala/inst/java/rscala_2.11-1.0.4.jar |only rscala-1.0.4/rscala/java/rscala_2.10-1.0.4-sources.jar |only rscala-1.0.4/rscala/java/rscala_2.11-1.0.4-sources.jar |only rscala-1.0.6/rscala/DESCRIPTION | 11 rscala-1.0.6/rscala/MD5 | 38 + rscala-1.0.6/rscala/NAMESPACE | 7 rscala-1.0.6/rscala/NEWS | 30 + rscala-1.0.6/rscala/R/common.R | 5 rscala-1.0.6/rscala/R/globals.R |only rscala-1.0.6/rscala/R/rServer.R | 64 ++- rscala-1.0.6/rscala/R/scalaInterpreter.R | 327 +++++++++++------ rscala-1.0.6/rscala/R/zzz.R | 7 rscala-1.0.6/rscala/README |only rscala-1.0.6/rscala/inst/bin |only rscala-1.0.6/rscala/inst/doc |only rscala-1.0.6/rscala/inst/java/rscala_2.10-1.0.6.jar |only rscala-1.0.6/rscala/inst/java/rscala_2.11-1.0.6.jar |only rscala-1.0.6/rscala/java/rscala_2.10-1.0.6-sources.jar |only rscala-1.0.6/rscala/java/rscala_2.11-1.0.6-sources.jar |only rscala-1.0.6/rscala/man/close.Rd | 2 rscala-1.0.6/rscala/man/constructor.Rd | 59 +-- rscala-1.0.6/rscala/man/eval.Rd | 33 - rscala-1.0.6/rscala/man/print.Rd | 2 rscala-1.0.6/rscala/man/settings.Rd | 2 rscala-1.0.6/rscala/man/strintrpl.Rd | 4 26 files changed, 403 insertions(+), 188 deletions(-)
Title: Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Description: Implements TRACDS (Temporal Relationships
between Clusters for Data Streams), a generalization of
Extensible Markov Model (EMM). TRACDS adds a temporal or order model
to data stream clustering by superimposing a dynamically adapting
Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN
data stream clustering). Development of this
package was supported in part by NSF IIS-0948893 and R21HG005912 from
the National Human Genome Research Institute.
Author: Michael Hahsler [aut, cre, cph],
Margaret H. Dunham [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between rEMM versions 1.0-8 dated 2014-01-14 and 1.0-9 dated 2015-05-15
rEMM-1.0-8/rEMM/inst/tests/EMM.R |only rEMM-1.0-8/rEMM/inst/tests/remove.R |only rEMM-1.0-8/rEMM/tests/EMM.R |only rEMM-1.0-8/rEMM/tests/EMM.Rout.save |only rEMM-1.0-8/rEMM/tests/remove.R |only rEMM-1.0-9/rEMM/DESCRIPTION | 29 +++++++++++-------------- rEMM-1.0-9/rEMM/MD5 | 35 ++++++++++++++----------------- rEMM-1.0-9/rEMM/NAMESPACE | 19 ++++++++-------- rEMM-1.0-9/rEMM/R/AAA.R | 3 ++ rEMM-1.0-9/rEMM/R/SimpleMC.R | 4 +-- rEMM-1.0-9/rEMM/R/ellipse.R | 2 - rEMM-1.0-9/rEMM/R/graph.R | 2 - rEMM-1.0-9/rEMM/R/plot.R | 9 ++++--- rEMM-1.0-9/rEMM/build/vignette.rds |binary rEMM-1.0-9/rEMM/data/16S.rda |binary rEMM-1.0-9/rEMM/data/Derwent.rda |binary rEMM-1.0-9/rEMM/data/EMMTraffic.rda |binary rEMM-1.0-9/rEMM/data/EMMsim.rda |binary rEMM-1.0-9/rEMM/inst/NEWS | 6 ++++- rEMM-1.0-9/rEMM/inst/doc/rEMM.pdf |binary rEMM-1.0-9/rEMM/inst/tests/test-EMM.R |only rEMM-1.0-9/rEMM/inst/tests/test-remove.R |only 22 files changed, 56 insertions(+), 53 deletions(-)
Title: Analysis of Queueing Networks and Models
Description: It provides versatile tools for analysis of birth and death based Markovian Queueing Models
and Single and Multiclass Product-Form Queueing Networks.
It implements M/M/1, M/M/c, M/M/Infinite, M/M/1/K, M/M/c/K, M/M/c/c, M/M/1/K/K, M/M/c/K/K, M/M/c/K/m, M/M/Infinite/K/K,
Multiple Channel Open Jackson Networks, Multiple Channel Closed Jackson Networks,
Single Channel Multiple Class Open Networks, Single Channel Multiple Class Closed Networks
and Single Channel Multiple Class Mixed Networks.
Also it provides a B-Erlang, C-Erlang and Engset calculators.
This work is dedicated to the memory of D. Sixto Rios Insua.
Author: Pedro Canadilla
Maintainer: Pedro Canadilla <pedro.canadilla@gmail.com>
Diff between queueing versions 0.2.4 dated 2015-04-12 and 0.2.5 dated 2015-05-15
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/queueing.R | 2 +- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Calculating Effective Sizes Based on Known Demographic
Parameters of a Population
Description: Effective population sizes (often abbreviated as "Neff") are essential in biodiversity monitoring and conservation. For the first time, calculating effective sizes with data obtained within less than a generation but considering demographic parameters is possible. This individual based model uses demographic parameters of a population to calculate annual effective sizes and effective population sizes (per generation). A defined number of alleles and loci will be used to simulate the genotypes of the individuals. Stepwise mutation rates can be included. Variations in life history parameters (sex ratio, sex-specific survival, recruitment rate, reproductive skew) are possible. These results will help managers to define existing populations as viable or not.
Author: Annegret Grimm, Bernd Gruber & Klaus Henle
Maintainer: Annegret Grimm <annegret.grimm@ufz.de>
Diff between NEff versions 1.0 dated 2013-09-10 and 1.1 dated 2015-05-15
DESCRIPTION | 14 - MD5 | 8 R/population.R | 466 ++++++++++++++++++++++++++++++++++++++++++++-------- man/NEff-package.Rd | 18 +- man/population.Rd | 65 ++++--- 5 files changed, 469 insertions(+), 102 deletions(-)
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the 'FME' package.
Please note that no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9-34 dated 2014-11-21 and 0.9-35 dated 2015-05-15
mkin-0.9-34/mkin/inst/unitTests |only mkin-0.9-34/mkin/tests/doRUnit.R |only mkin-0.9-35/mkin/DESCRIPTION | 17 - mkin-0.9-35/mkin/MD5 | 84 +++++--- mkin-0.9-35/mkin/NAMESPACE | 3 mkin-0.9-35/mkin/NEWS |only mkin-0.9-35/mkin/R/ilr.R | 2 mkin-0.9-35/mkin/R/mkin_long_to_wide.R | 2 mkin-0.9-35/mkin/R/mkin_wide_to_long.R | 2 mkin-0.9-35/mkin/R/mkinfit.R | 13 + mkin-0.9-35/mkin/R/mkinparplot.R | 15 - mkin-0.9-35/mkin/README.md | 11 - mkin-0.9-35/mkin/build/vignette.rds |binary mkin-0.9-35/mkin/data/FOCUS_2006_DFOP_ref_A_to_B.rda |binary mkin-0.9-35/mkin/data/FOCUS_2006_FOMC_ref_A_to_F.rda |binary mkin-0.9-35/mkin/data/FOCUS_2006_HS_ref_A_to_F.rda |binary mkin-0.9-35/mkin/data/FOCUS_2006_SFO_ref_A_to_F.rda |binary mkin-0.9-35/mkin/data/FOCUS_2006_datasets.RData |binary mkin-0.9-35/mkin/data/mccall81_245T.RData |binary mkin-0.9-35/mkin/data/schaefer07_complex_case.RData |binary mkin-0.9-35/mkin/data/synthetic_data_for_UBA_2014.RData |only mkin-0.9-35/mkin/inst/doc/FOCUS_L.html | 165 ++++++++-------- mkin-0.9-35/mkin/inst/doc/FOCUS_Z.pdf |binary mkin-0.9-35/mkin/inst/doc/mkin.pdf |binary mkin-0.9-35/mkin/man/schaefer07_complex_case.Rd | 2 mkin-0.9-35/mkin/man/synthetic_data_for_UBA.Rd |only mkin-0.9-35/mkin/tests/testthat |only mkin-0.9-35/mkin/tests/testthat.R |only mkin-0.9-35/mkin/vignettes/compiled_models_cache |only 29 files changed, 186 insertions(+), 130 deletions(-)
Title: Belief Function Implementation
Description: Some basic functions to implement belief functions including: transformation between belief functions using the method introduced by Philippe Smets (arXiv:1304.1122 [cs.AI]), evidence combination, evidence discounting, decision-making, and constructing masses. Currently, thirteen combination rules and five decision rules are supported. It can also be used to generate different types of random masses when working on belief combination and conflict management.
Author: Kuang Zhou <kzhoumath@163.com>; Arnaud Martin
<arnaud.martin@univ-rennes1.fr>
Maintainer: Kuang Zhou <kzhoumath@163.com>
Diff between ibelief versions 1.0 dated 2014-10-07 and 1.1 dated 2015-05-15
ibelief-1.0/ibelief/R/BayesianMass.r |only ibelief-1.0/ibelief/R/ConflictPCR6.r |only ibelief-1.0/ibelief/R/ConflictTable.r |only ibelief-1.0/ibelief/R/DST.r |only ibelief-1.0/ibelief/R/DST_fmt_functions.r |only ibelief-1.0/ibelief/R/PCR6.r |only ibelief-1.0/ibelief/R/RandomMass.r |only ibelief-1.0/ibelief/R/dec2bin.r |only ibelief-1.0/ibelief/R/decisionDST.r |only ibelief-1.0/ibelief/R/discounting.r |only ibelief-1.1/ibelief/DESCRIPTION | 11 ++-- ibelief-1.1/ibelief/MD5 | 30 +++++++----- ibelief-1.1/ibelief/NAMESPACE | 71 +++++++++++++++--------------- ibelief-1.1/ibelief/NEWS |only ibelief-1.1/ibelief/R/BayesianMass.R |only ibelief-1.1/ibelief/R/ConflictPCR6.R |only ibelief-1.1/ibelief/R/ConflictTable.R |only ibelief-1.1/ibelief/R/DST.R |only ibelief-1.1/ibelief/R/DST_fmt_functions.R |only ibelief-1.1/ibelief/R/LCRule.R |only ibelief-1.1/ibelief/R/PCR6.R |only ibelief-1.1/ibelief/R/RandomMass.R |only ibelief-1.1/ibelief/R/dec2bin.R |only ibelief-1.1/ibelief/R/decisionDST.R |only ibelief-1.1/ibelief/R/discounting.R |only ibelief-1.1/ibelief/README.md |only ibelief-1.1/ibelief/man/LCRule.Rd |only ibelief-1.1/ibelief/man/discounting.Rd | 58 ++++++++++++------------ 28 files changed, 87 insertions(+), 83 deletions(-)
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@fhi.no>
Diff between Haplin versions 5.3 dated 2013-05-23 and 5.5 dated 2015-05-15
Haplin-5.3/Haplin/R/f.batch.R |only Haplin-5.3/Haplin/R/f.load.R |only Haplin-5.3/Haplin/R/f.save.R |only Haplin-5.3/Haplin/R/loadData.R |only Haplin-5.3/Haplin/R/saveData.R |only Haplin-5.5/Haplin/DESCRIPTION | 31 +-- Haplin-5.5/Haplin/MD5 | 86 +++++---- Haplin-5.5/Haplin/NAMESPACE | 47 ++--- Haplin-5.5/Haplin/R/cbindFiles.R |only Haplin-5.5/Haplin/R/coef.haptable.R | 1 Haplin-5.5/Haplin/R/convertPed.R | 64 ++++--- Haplin-5.5/Haplin/R/f.EM.missing.R | 10 - Haplin-5.5/Haplin/R/f.HWE.R | 2 Haplin-5.5/Haplin/R/f.check.pars.R | 23 -- Haplin-5.5/Haplin/R/f.coefnames.R |only Haplin-5.5/Haplin/R/f.data.R | 2 Haplin-5.5/Haplin/R/f.debug.pvalues.R |only Haplin-5.5/Haplin/R/f.get.data.R | 24 -- Haplin-5.5/Haplin/R/f.plot.effects.R | 17 + Haplin-5.5/Haplin/R/f.pos.match.R | 2 Haplin-5.5/Haplin/R/f.post.chisq.R | 2 Haplin-5.5/Haplin/R/f.post.diff.R | 34 ++- Haplin-5.5/Haplin/R/f.post.poo.diff.R |only Haplin-5.5/Haplin/R/f.posttest.R | 29 +-- Haplin-5.5/Haplin/R/f.posttest.score.R | 4 Haplin-5.5/Haplin/R/f.prep.reference.R | 12 + Haplin-5.5/Haplin/R/f.prob.R |only Haplin-5.5/Haplin/R/f.rand.geno.R |only Haplin-5.5/Haplin/R/f.sim.R |only Haplin-5.5/Haplin/R/f.suest.R | 9 - Haplin-5.5/Haplin/R/haplin.R | 2 Haplin-5.5/Haplin/R/haplinSlide.R | 22 +- Haplin-5.5/Haplin/R/lineByLine.R | 79 ++++---- Haplin-5.5/Haplin/R/plot.haplin.R | 17 + Haplin-5.5/Haplin/R/plot.haptable.R | 3 Haplin-5.5/Haplin/R/postTest.R | 110 +++++------- Haplin-5.5/Haplin/R/prepPed.R | 22 +- Haplin-5.5/Haplin/R/print.suest.R | 15 - Haplin-5.5/Haplin/R/print.summary.tri.glm.R | 2 Haplin-5.5/Haplin/R/rbindFiles.R |only Haplin-5.5/Haplin/R/snpPos.R | 18 -- Haplin-5.5/Haplin/R/snpPower.R |only Haplin-5.5/Haplin/R/snpSampleSize.R |only Haplin-5.5/Haplin/R/summary.tri.glm.R | 69 +++++-- Haplin-5.5/Haplin/R/toDataFrame.R | 2 Haplin-5.5/Haplin/R/uniqueID.R |only Haplin-5.5/Haplin/inst/doc/Haplin_data_format.pdf |binary Haplin-5.5/Haplin/man/cbindFiles.Rd |only Haplin-5.5/Haplin/man/convertPed.Rd | 197 +++++++++++----------- Haplin-5.5/Haplin/man/haplin.Rd | 6 Haplin-5.5/Haplin/man/lineByLine.Rd | 157 +++++++++-------- Haplin-5.5/Haplin/man/rbindFiles.Rd |only Haplin-5.5/Haplin/man/snpPower.Rd |only Haplin-5.5/Haplin/man/snpSampleSize.Rd |only 54 files changed, 589 insertions(+), 531 deletions(-)
Title: Fast Calculation of the Likelihood of a Stochastic Survival
Model
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the fast calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert <carlo.albert@eawag.ch> and Sören Vogel <soeren.vogel@posteo.ch>
Maintainer: Sören Vogel <soeren.vogel@posteo.ch>
Diff between GUTS versions 0.9.1 dated 2015-05-06 and 0.9.3 dated 2015-05-15
DESCRIPTION | 15 ++++++---- MD5 | 12 ++++---- R/GUTS.R | 17 ++++++++++-- data/diazinon.rda |binary man/GUTS-package.Rd | 2 - man/GUTS.Rd | 55 ++++++++++++++++++++-------------------- src/guts_calc_loglikelihood.cpp | 21 +-------------- 7 files changed, 61 insertions(+), 61 deletions(-)
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at> and Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Diff between dynRB versions 0.1 dated 2015-05-06 and 0.2 dated 2015-05-15
dynRB-0.1/dynRB/R/dynRB_Qn.R |only dynRB-0.1/dynRB/R/dynRB_Qnc.R |only dynRB-0.1/dynRB/R/dynRB_SQa.R |only dynRB-0.1/dynRB/R/dynRB_SQac.R |only dynRB-0.1/dynRB/R/dynRB_Sn.R |only dynRB-0.1/dynRB/R/dynRB_Snc.R |only dynRB-0.1/dynRB/man/dynRB_Qn.Rd |only dynRB-0.1/dynRB/man/dynRB_Qnc.Rd |only dynRB-0.1/dynRB/man/dynRB_SQa.Rd |only dynRB-0.1/dynRB/man/dynRB_SQac.Rd |only dynRB-0.1/dynRB/man/dynRB_Sn.Rd |only dynRB-0.1/dynRB/man/dynRB_Snc.Rd |only dynRB-0.2/dynRB/DESCRIPTION | 6 +++--- dynRB-0.2/dynRB/MD5 | 28 ++++++++++++++-------------- dynRB-0.2/dynRB/R/dynRB_Pn.R |only dynRB-0.2/dynRB/R/dynRB_Pnc.R |only dynRB-0.2/dynRB/R/dynRB_VPa.R |only dynRB-0.2/dynRB/R/dynRB_VPac.R |only dynRB-0.2/dynRB/R/dynRB_Vn.R |only dynRB-0.2/dynRB/R/dynRB_Vnc.R |only dynRB-0.2/dynRB/man/dynRB-package.Rd | 7 ++++--- dynRB-0.2/dynRB/man/dynRB_Pn.Rd |only dynRB-0.2/dynRB/man/dynRB_Pnc.Rd |only dynRB-0.2/dynRB/man/dynRB_VPa.Rd |only dynRB-0.2/dynRB/man/dynRB_VPac.Rd |only dynRB-0.2/dynRB/man/dynRB_Vn.Rd |only dynRB-0.2/dynRB/man/dynRB_Vnc.Rd |only 27 files changed, 21 insertions(+), 20 deletions(-)
Title: Node Harvest for Regression and Classification
Description: Node harvest is a simple interpretable tree-like estimator for high-dimensional regression and classification. A few nodes are selected from an initially large ensemble of nodes, each associated with a positive weight. New observations can fall into one or several nodes and predictions are the weighted average response across all these groups. The package offers visualization of the estimator. Predictions can return the nodes a new observation fell into, along with the mean response of training observations in each node, offering a simple explanation of the prediction.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between nodeHarvest versions 0.6 dated 2013-11-28 and 0.7-1 dated 2015-05-15
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/nodeHarvest.R | 24 ++++++++++++++---------- 3 files changed, 21 insertions(+), 17 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 0.8.2 dated 2014-05-12 and 1.0.0 dated 2015-05-15
VSURF-0.8.2/VSURF/R/VSURF.interp.R |only VSURF-0.8.2/VSURF/R/VSURF.pred.R |only VSURF-0.8.2/VSURF/R/VSURF.thres.R |only VSURF-0.8.2/VSURF/man/VSURF.interp.Rd |only VSURF-0.8.2/VSURF/man/VSURF.pred.Rd |only VSURF-0.8.2/VSURF/man/VSURF.thres.Rd |only VSURF-1.0.0/VSURF/DESCRIPTION | 22 +- VSURF-1.0.0/VSURF/MD5 | 44 ++-- VSURF-1.0.0/VSURF/NAMESPACE | 64 +++--- VSURF-1.0.0/VSURF/NEWS | 31 ++- VSURF-1.0.0/VSURF/R/VSURF.R | 265 +++++++++----------------- VSURF-1.0.0/VSURF/R/VSURF_interp.R |only VSURF-1.0.0/VSURF/R/VSURF_pred.R |only VSURF-1.0.0/VSURF/R/VSURF_thres.R |only VSURF-1.0.0/VSURF/R/plot.VSURF.R | 332 ++++++++++++++++----------------- VSURF-1.0.0/VSURF/R/predict.VSURF.R |only VSURF-1.0.0/VSURF/R/print.VSURF.R | 7 VSURF-1.0.0/VSURF/R/summary.VSURF.R | 11 - VSURF-1.0.0/VSURF/R/toys.R | 4 VSURF-1.0.0/VSURF/R/tune.R | 113 +++++------ VSURF-1.0.0/VSURF/man/VSURF.Rd | 108 ++++++---- VSURF-1.0.0/VSURF/man/VSURF_interp.Rd |only VSURF-1.0.0/VSURF/man/VSURF_pred.Rd |only VSURF-1.0.0/VSURF/man/VSURF_thres.Rd |only VSURF-1.0.0/VSURF/man/plot.VSURF.Rd | 89 +++++--- VSURF-1.0.0/VSURF/man/predict.VSURF.Rd |only VSURF-1.0.0/VSURF/man/print.VSURF.Rd | 7 VSURF-1.0.0/VSURF/man/summary.VSURF.Rd | 11 - VSURF-1.0.0/VSURF/man/toys.Rd | 7 VSURF-1.0.0/VSURF/man/tune.Rd | 43 ++-- 30 files changed, 568 insertions(+), 590 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Jeff Enos, Claus Ekstrom, Martin Elff, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.10 dated 2015-03-21 and 0.99.11 dated 2015-05-15
DescTools-0.99.10/DescTools/R/PlotFct.R |only DescTools-0.99.10/DescTools/R/Rev.data.frame.R |only DescTools-0.99.10/DescTools/R/SaveAs.R |only DescTools-0.99.10/DescTools/R/fastPOSIXct.R |only DescTools-0.99.10/DescTools/man/PlotFct.Rd |only DescTools-0.99.10/DescTools/man/SaveAs.Rd |only DescTools-0.99.10/DescTools/man/fastPOSIXct.Rd |only DescTools-0.99.10/DescTools/src/tparse.c |only DescTools-0.99.11/DescTools/DESCRIPTION | 16 DescTools-0.99.11/DescTools/MD5 | 257 +++--- DescTools-0.99.11/DescTools/NAMESPACE | 25 DescTools-0.99.11/DescTools/NEWS | 49 + DescTools-0.99.11/DescTools/R/AddMonths.R | 2 DescTools-0.99.11/DescTools/R/Agree.R | 18 DescTools-0.99.11/DescTools/R/Atkinson.R | 2 DescTools-0.99.11/DescTools/R/BoxCoxLambda.R | 2 DescTools-0.99.11/DescTools/R/ChooseColorDlg.R | 5 DescTools-0.99.11/DescTools/R/CohenD.R | 12 DescTools-0.99.11/DescTools/R/CohenKappa.R | 2 DescTools-0.99.11/DescTools/R/ColorLegend.R | 6 DescTools-0.99.11/DescTools/R/Conf.R |only DescTools-0.99.11/DescTools/R/Conf.default.R |only DescTools-0.99.11/DescTools/R/Conf.glm.R |only DescTools-0.99.11/DescTools/R/Conf.matrix.R |only DescTools-0.99.11/DescTools/R/Conf.multinom.R |only DescTools-0.99.11/DescTools/R/Conf.randomForest.R |only DescTools-0.99.11/DescTools/R/Conf.regr.R |only DescTools-0.99.11/DescTools/R/Conf.rpart.R |only DescTools-0.99.11/DescTools/R/Conf.svm.R |only DescTools-0.99.11/DescTools/R/Conf.table.R |only DescTools-0.99.11/DescTools/R/CorPolychor.R |only DescTools-0.99.11/DescTools/R/Desc.table.R | 21 DescTools-0.99.11/DescTools/R/DescTools-internal.R | 489 ++++++++---- DescTools-0.99.11/DescTools/R/DescWrd.default.R | 4 DescTools-0.99.11/DescTools/R/DunnTest.default.R | 1 DescTools-0.99.11/DescTools/R/Format.default.R | 54 + DescTools-0.99.11/DescTools/R/Freq.R | 74 - DescTools-0.99.11/DescTools/R/GTest.R |only DescTools-0.99.11/DescTools/R/Gini.R | 2 DescTools-0.99.11/DescTools/R/Herfindahl.R | 2 DescTools-0.99.11/DescTools/R/HodgesLehmann.R | 3 DescTools-0.99.11/DescTools/R/HuberM.R | 190 ++-- DescTools-0.99.11/DescTools/R/ImportDlg.R | 4 DescTools-0.99.11/DescTools/R/ImportFileDlg.R |only DescTools-0.99.11/DescTools/R/KendallTauB.R | 53 + DescTools-0.99.11/DescTools/R/Kurt.R | 4 DescTools-0.99.11/DescTools/R/Lc.default.R | 2 DescTools-0.99.11/DescTools/R/MarginTable.R | 2 DescTools-0.99.11/DescTools/R/MoveAvg.R | 31 DescTools-0.99.11/DescTools/R/NemenyiTest.R |only DescTools-0.99.11/DescTools/R/NemenyiTest.default.R |only DescTools-0.99.11/DescTools/R/NemenyiTest.formula.R |only DescTools-0.99.11/DescTools/R/OrderMixed.R | 1 DescTools-0.99.11/DescTools/R/ParseSASDatalines.R | 21 DescTools-0.99.11/DescTools/R/PasswordDlg.R | 70 - DescTools-0.99.11/DescTools/R/PercTable.table.R | 7 DescTools-0.99.11/DescTools/R/PlotCirc.R | 6 DescTools-0.99.11/DescTools/R/PlotDesc.Date.R | 6 DescTools-0.99.11/DescTools/R/PlotDesc.matrix.R |only DescTools-0.99.11/DescTools/R/PlotDot.R |only DescTools-0.99.11/DescTools/R/PlotFaces.R | 45 - DescTools-0.99.11/DescTools/R/PlotFun.R |only DescTools-0.99.11/DescTools/R/PlotLinesA.R |only DescTools-0.99.11/DescTools/R/PlotPar.R | 11 DescTools-0.99.11/DescTools/R/PlotRCol.R | 5 DescTools-0.99.11/DescTools/R/PostHocTest.matrix.R | 16 DescTools-0.99.11/DescTools/R/Rev.matrix.R | 9 DescTools-0.99.11/DescTools/R/Rev.table.R | 14 DescTools-0.99.11/DescTools/R/Rosenbluth.R | 2 DescTools-0.99.11/DescTools/R/SampleTwins.R | 8 DescTools-0.99.11/DescTools/R/SaveAsDlg.R |only DescTools-0.99.11/DescTools/R/Sens.R |only DescTools-0.99.11/DescTools/R/Skew.R | 4 DescTools-0.99.11/DescTools/R/Spec.R |only DescTools-0.99.11/DescTools/R/SplitPath.R |only DescTools-0.99.11/DescTools/R/Stamp.R | 4 DescTools-0.99.11/DescTools/R/StrChop.R | 1 DescTools-0.99.11/DescTools/R/Strata.R | 289 +------ DescTools-0.99.11/DescTools/R/ToLong.R | 3 DescTools-0.99.11/DescTools/R/TukeyBiweight.R | 2 DescTools-0.99.11/DescTools/R/WrdTable.ftable.R |only DescTools-0.99.11/DescTools/R/as.matrix.xtabs.R |only DescTools-0.99.11/DescTools/R/plot.Conf.R |only DescTools-0.99.11/DescTools/R/power.chisq.test.R |only DescTools-0.99.11/DescTools/R/print.Conf.R |only DescTools-0.99.11/DescTools/R/print.CorPolychor.R |only DescTools-0.99.11/DescTools/R/print.DunnTest.R | 2 DescTools-0.99.11/DescTools/R/print.Freq.R | 5 DescTools-0.99.11/DescTools/build/vignette.rds |binary DescTools-0.99.11/DescTools/data/day.abb.rda |binary DescTools-0.99.11/DescTools/data/day.name.rda |binary DescTools-0.99.11/DescTools/data/hblue.rda |binary DescTools-0.99.11/DescTools/data/hecru.rda |binary DescTools-0.99.11/DescTools/data/hgreen.rda |binary DescTools-0.99.11/DescTools/data/horange.rda |binary DescTools-0.99.11/DescTools/data/hred.rda |binary DescTools-0.99.11/DescTools/data/hyellow.rda |binary DescTools-0.99.11/DescTools/data/wdConst.rda |binary DescTools-0.99.11/DescTools/inst/CITATION | 1 DescTools-0.99.11/DescTools/inst/doc/DescTools.pdf |binary DescTools-0.99.11/DescTools/inst/doc/DescToolsCompanion.pdf |binary DescTools-0.99.11/DescTools/inst/extdata/R.ico |only DescTools-0.99.11/DescTools/man/AddMonths.Rd | 4 DescTools-0.99.11/DescTools/man/Agree.Rd | 7 DescTools-0.99.11/DescTools/man/AllDuplicated.Rd | 9 DescTools-0.99.11/DescTools/man/Between.Rd | 4 DescTools-0.99.11/DescTools/man/BreslowDayTest.Rd | 22 DescTools-0.99.11/DescTools/man/CoefVar.Rd | 3 DescTools-0.99.11/DescTools/man/CohenD.Rd | 4 DescTools-0.99.11/DescTools/man/CohenKappa.Rd | 7 DescTools-0.99.11/DescTools/man/ColorLegend.Rd | 4 DescTools-0.99.11/DescTools/man/Conf.Rd |only DescTools-0.99.11/DescTools/man/CorPolychor.Rd |only DescTools-0.99.11/DescTools/man/Desc.table.Rd | 8 DescTools-0.99.11/DescTools/man/DescTools-package.Rd | 46 - DescTools-0.99.11/DescTools/man/ErrBars.Rd | 13 DescTools-0.99.11/DescTools/man/Explore.Rd | 4 DescTools-0.99.11/DescTools/man/FindColor.Rd | 45 - DescTools-0.99.11/DescTools/man/FisherZ.Rd | 2 DescTools-0.99.11/DescTools/man/Format.Rd | 9 DescTools-0.99.11/DescTools/man/Freq.Rd | 26 DescTools-0.99.11/DescTools/man/GTest.Rd |only DescTools-0.99.11/DescTools/man/GetNewWrd.Rd | 5 DescTools-0.99.11/DescTools/man/Gini.Rd | 45 - DescTools-0.99.11/DescTools/man/HuberM.Rd | 88 -- DescTools-0.99.11/DescTools/man/ImportFileDlg.Rd |only DescTools-0.99.11/DescTools/man/Lambda.Rd | 5 DescTools-0.99.11/DescTools/man/Logit.Rd | 112 +- DescTools-0.99.11/DescTools/man/MeanAD.Rd | 4 DescTools-0.99.11/DescTools/man/MoveAvg.Rd | 44 - DescTools-0.99.11/DescTools/man/NemenyiTest.Rd |only DescTools-0.99.11/DescTools/man/OddsRatio.Rd | 41 - DescTools-0.99.11/DescTools/man/ParseSASDatalines.Rd | 36 DescTools-0.99.11/DescTools/man/PlotACF.Rd | 4 DescTools-0.99.11/DescTools/man/PlotDesc.Rd | 4 DescTools-0.99.11/DescTools/man/PlotDot.Rd |only DescTools-0.99.11/DescTools/man/PlotFaces.Rd | 4 DescTools-0.99.11/DescTools/man/PlotFun.Rd |only DescTools-0.99.11/DescTools/man/PlotLinesA.Rd |only DescTools-0.99.11/DescTools/man/Rev.Rd | 26 DescTools-0.99.11/DescTools/man/SampleTwins.Rd | 6 DescTools-0.99.11/DescTools/man/SaveAsDlg.Rd |only DescTools-0.99.11/DescTools/man/Skew.Rd | 43 - DescTools-0.99.11/DescTools/man/SplitPath.Rd |only DescTools-0.99.11/DescTools/man/Stamp.Rd | 3 DescTools-0.99.11/DescTools/man/StrRight.Rd | 2 DescTools-0.99.11/DescTools/man/StrTrunc.Rd | 4 DescTools-0.99.11/DescTools/man/Strata.Rd | 31 DescTools-0.99.11/DescTools/man/StuartMaxwellTest.Rd | 6 DescTools-0.99.11/DescTools/man/StuartTauC.Rd | 14 DescTools-0.99.11/DescTools/man/ToWide.Rd | 2 DescTools-0.99.11/DescTools/man/VarCI.Rd | 3 DescTools-0.99.11/DescTools/man/WrdTable.Rd | 3 DescTools-0.99.11/DescTools/man/as.matrix.Rd |only DescTools-0.99.11/DescTools/man/power.chisq.test.Rd |only 155 files changed, 1486 insertions(+), 1130 deletions(-)
Title: Fishery Stock Assessment by Generalized Depletion Models
Description: Based on fishery Catch Dynamics instead of fish Population Dynamics (hence CatDyn) and using high-frequency or medium-frequency catch in biomass or numbers, fishing nominal effort, and mean fish body weight by time step, from one or two fishing fleets, estimate stock abundance, natural mortality rate, and fishing operational parameters. It includes methods for data organization, plotting standard exploratory and analytical plots, predictions, for 77 types of models of increasing complexity, and 56 likelihood models for the data.
Author: Ruben H. Roa-Ureta
Maintainer: Ruben H. Roa-Ureta <ruben.roa.ureta@mail.com>
Diff between CatDyn versions 1.0-6 dated 2015-01-18 and 1.1-0 dated 2015-05-15
CatDyn-1.0-6/CatDyn/inst |only CatDyn-1.1-0/CatDyn/DESCRIPTION | 10 CatDyn-1.1-0/CatDyn/MD5 | 47 CatDyn-1.1-0/CatDyn/R/CatDyn-internal.R |74133 +----------------------------- CatDyn-1.1-0/CatDyn/R/CatDynFit.R |24905 ++-------- CatDyn-1.1-0/CatDyn/R/CatDynPred.R | 640 CatDyn-1.1-0/CatDyn/R/CatDynSum.R | 187 CatDyn-1.1-0/CatDyn/R/catdynexp_1.R | 3776 - CatDyn-1.1-0/CatDyn/R/plot.CatDynExp.R | 6 CatDyn-1.1-0/CatDyn/R/plot.CatDynMod.R | 6 CatDyn-1.1-0/CatDyn/data/gayhake.rda |binary CatDyn-1.1-0/CatDyn/data/lolgahi.rda |binary CatDyn-1.1-0/CatDyn/data/twelver.rda |binary CatDyn-1.1-0/CatDyn/man/CatDyn-package.Rd | 47 CatDyn-1.1-0/CatDyn/man/CatDynCor.Rd | 13 CatDyn-1.1-0/CatDyn/man/CatDynExp.Rd | 3 CatDyn-1.1-0/CatDyn/man/CatDynFit.Rd | 347 CatDyn-1.1-0/CatDyn/man/CatDynPred.Rd | 16 CatDyn-1.1-0/CatDyn/man/CatDynSum.Rd | 15 CatDyn-1.1-0/CatDyn/man/as.CatDynData.Rd | 88 CatDyn-1.1-0/CatDyn/man/catdyn.Rd | 2 CatDyn-1.1-0/CatDyn/man/catdynexp_1.Rd | 61 CatDyn-1.1-0/CatDyn/man/deltamethod.Rd | 20 CatDyn-1.1-0/CatDyn/man/plot.CatDynExp.Rd | 15 CatDyn-1.1-0/CatDyn/man/plot.CatDynMod.Rd | 24 25 files changed, 11897 insertions(+), 92464 deletions(-)
Title: Robust Structural Equation Modeling with Missing Data and
Auxiliary Variables
Description: A robust procedure is implemented to estimate means and covariance matrix of multiple variables with missing data using Huber weight and then to estimate a structural equation model.
Author: Ke-Hai Yuan and Zhiyong Zhang
Maintainer: Zhiyong Zhang <zhiyongzhang@nd.edu>
Diff between rsem versions 0.4.5 dated 2013-07-17 and 0.4.6 dated 2015-05-15
DESCRIPTION | 10 ++++---- MD5 | 8 ++++-- NAMESPACE | 4 ++- R/lav_fun.R |only R/rsem.R | 62 +++++++++++++++++++++++++++++++++++++++++------------ man/rsem.lavaan.Rd |only 6 files changed, 61 insertions(+), 23 deletions(-)
Title: Analyzing RNA Sequencing Count Tables Using Quasi-Likelihood
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with 'QL', 'QLShrink' and 'QLSpline' methods (Lund, Nettleton, McCarthy, and Smyth, 2012).
Author: Steve Lund [aut],
Long Qu [aut, cre, ctb],
Ian Marschner [aut] (The author of glm2::glm.fit2, which was modified
slightly leading to glm.fit3 in this package.),
R Core Team [aut] (The author of stats::glm.fit, which was modified
slightly leading to glm.fit3 in this package.)
Maintainer: Long Qu <long.qu@wright.edu>
Diff between QuasiSeq versions 1.0-7 dated 2015-05-13 and 1.0-8 dated 2015-05-15
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- src/Makevars | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Build Panel Data Sets from PSID Raw Data
Description: Makes it easy to build panel data in wide format from PSID
delivered raw data. Deals with data downloaded and pre-processed by Stata or SAS,
or can optionally download directly from the PSID server using the SAScii package.
`psidR` takes care of merging data from each wave onto a cross-period index file,
so that individuals can be followed over time. The user must specify which years
they are interested in, and the PSID variable names (e.g. ER21003) for each year
(they differ in each year). There are different panel data designs and
sample subsetting criteria implemented ("SRC", "SEO", "immigrant" and "latino"
samples).
Author: Florian Oswald
Maintainer: Florian Oswald <florian.oswald@gmail.com>
Diff between psidR versions 1.2 dated 2013-09-10 and 1.3 dated 2015-05-15
DESCRIPTION | 19 +-- MD5 | 25 ++-- NAMESPACE | 5 NEWS | 14 ++ R/build.panel.r | 275 ++++++++++++++++++++++++++++------------------------- R/makeids.r | 93 +++++++++++++++++ R/psidR-package.r | 4 man/build.panel.Rd | 188 +++++++++++------------------------- man/get.psid.Rd | 17 +-- man/make.char.Rd | 11 +- man/makeids.Rd | 14 -- man/psidR.Rd | 17 +-- man/testPSID.Rd |only tests |only 14 files changed, 375 insertions(+), 307 deletions(-)
Title: Projection Pursuit Classification Tree Visualization
Description: Tools for exploring projection pursuit classification tree using LDA,
Lr or PDA projection pursuit index.
Author: Eun-Kyung Lee
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Diff between PPtreeViz versions 1.0.1 dated 2015-05-08 and 1.0.3 dated 2015-05-15
DESCRIPTION | 8 ++--- MD5 | 26 ++++++++--------- R/LDAopt.R | 15 ++++------ R/PDAopt.R | 20 +++++-------- R/PPclassNodeViz.R | 72 +++++++++++++++++++++++++++++++------------------ R/PPclassify.R | 8 ++--- R/PPoptViz.R | 57 ++++++++++++++++++++++++-------------- R/PPtreeClass.R | 2 - R/plotPPtreeclass.R | 7 +--- R/printPPtreeclass.R | 18 ++++-------- man/PP.classify.Rd | 5 +-- man/PPclassNode.Viz.Rd | 8 +++-- man/PPopt.Viz.Rd | 2 - src/PPoptimize.cpp | 16 ++++------ 14 files changed, 141 insertions(+), 123 deletions(-)
Title: Obtain Alpha-Outlier Regions for Well-Known Probability
Distributions
Description: Given the parameters of a distribution, the package uses the concept of alpha-outliers by Davies and Gather (1993) to flag outliers in a data set. See Davies, L.; Gather, U. (1993): The identification of multiple outliers, JASA, 88 423, 782-792, doi: 10.1080/01621459.1993.10476339 for details.
Author: Andre Rehage, Sonja Kuhnt
Maintainer: Andre Rehage <rehage@statistik.tu-dortmund.de>
Diff between alphaOutlier versions 1.0.0 dated 2015-05-07 and 1.0.1 dated 2015-05-15
DESCRIPTION | 8 +++--- MD5 | 60 ++++++++++++++++++++++++++-------------------------- NEWS | 11 +++++++-- R/aout.binom.R | 6 ++--- R/aout.cg.R | 21 ++++++------------ R/aout.chisq.R | 6 ++--- R/aout.conttab.R | 30 ++++++++++++++------------ R/aout.exp.R | 8 +++--- R/aout.gandh.R | 6 ++--- R/aout.hyper.R | 6 ++--- R/aout.laplace.R | 6 ++--- R/aout.logis.R | 6 ++--- R/aout.mvnorm.R | 6 ++--- R/aout.nbinom.R | 6 ++--- R/aout.norm.R | 6 ++--- R/aout.pareto.R | 6 ++--- R/aout.pois.R | 6 ++--- R/aout.weibull.R | 8 +++--- man/aout.cg.Rd | 2 - man/aout.chisq.Rd | 2 - man/aout.conttab.Rd | 2 - man/aout.exp.Rd | 4 +-- man/aout.gandh.Rd | 2 - man/aout.hyper.Rd | 2 - man/aout.laplace.Rd | 2 - man/aout.mvnorm.Rd | 2 - man/aout.nbinom.Rd | 2 - man/aout.norm.Rd | 2 - man/aout.pareto.Rd | 2 - man/aout.pois.Rd | 2 - man/aout.weibull.Rd | 2 - 31 files changed, 123 insertions(+), 117 deletions(-)