Title: IRT Item-Person Map with 'ConQuest' Integration
Description: A powerful yet simple graphical tool available in the field of psychometrics is the Wright Map (also known as item maps or item-person maps), which presents the location of both respondents and items on the same scale. Wright Maps are commonly used to present the results of dichotomous or polytomous item response models. The 'WrightMap' package provides functions to create these plots from item parameters and person estimates stored as R objects. Although the package can be used in conjunction with any software used to estimate the IRT model (e.g. 'TAM', 'mirt', 'eRm' or 'IRToys' in 'R', or 'Stata', 'Mplus', etc.), 'WrightMap' features special integration with 'ConQuest' to facilitate reading and plotting its output directly.The 'wrightMap' function creates Wright Maps based on person estimates and item parameters produced by an item response analysis. The 'CQmodel' function reads output files created using 'ConQuest' software and creates a set of data frames for easy data manipulation, bundled in a 'CQmodel' object. The 'wrightMap' function can take a 'CQmodel' object as input or it can be used to create Wright Maps directly from data frames of person and item parameters.
Author: David Torres Irribarra & Rebecca Freund
Maintainer: David Torres Irribarra <dti@berkeley.edu>
Diff between WrightMap versions 1.2 dated 2016-03-18 and 1.2.1 dated 2016-03-23
DESCRIPTION | 10 +++++----- MD5 | 30 ++++++++++++++++-------------- NEWS | 2 ++ R/CQmodel.R | 46 +++++++++++++++------------------------------- R/itemClassic.R | 13 ++++++++----- R/itemHist.R | 12 ++++++------ R/itemModern.R | 9 +++++---- R/personDens.R | 13 +++++++------ R/personHist.R | 33 +++++++++++++-------------------- R/plotCI.R | 2 +- R/wrightMap.R | 32 ++++++++++++++++++++------------ README.md | 6 ++---- inst/extdata/ex7a.eap |only inst/extdata/ex7a.shw |only man/WrightMap-package.Rd | 3 +++ man/plotCI.Rd | 2 +- man/wrightMap.Rd | 1 + 17 files changed, 105 insertions(+), 109 deletions(-)
Title: Variance Component Analysis
Description: ANOVA-type estimation (prediction) of random effects in linear mixed models is implemented, following
Searle et al. (1991, ANOVA for unbalanced data). For better performance the SWEEP-Operator is implemented
for generating the ANOVA Type-1 error sum of squares. Restricted Maximum Likelihood (REML) estimation is
also available making use of the 'lme4' package.
The primary objective of this package is to perform Variance Component Analyses (VCA).
This is a special type of analysis frequently used in verifying the precision performance of diagnostics.
The Satterthwaite approximation of the total degrees of freedom and for individual variance components is
implemented for models fitted by ANOVA as well as for models fitted by REML. These are used in the Chi-Squared
tests against a claimed value, and in the respective confidence intervals.
Satterthwaite's approximation of denominator degrees of freedom in t-/F-tests of fixed effects are also
available. For models fitted by (REML) the variance-covariance matrix of the variance components is approximated
by the method pointed out in Giesbrecht & Burns (1985), which is required for applying the Satterthwaite approximation
of the degrees of freedom. For models fitted by ANOVA the method pointed out in Searle et al. (1991) employing quadratic
forms generating ANOVA sum of squares is also available.
There are several functions for extracting, random effects, fixed effects, variance-covariance
matrices of random and fixed effects. Residuals (marginal, conditional) can be extracted as raw, standardized
and studentized residuals.
Additionally, plotting methods for residuals and random effects and a variability chart are available. The latter
is useful for visualizing the variability in sub-classes emerging from the experimental design.
Author: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VCA versions 1.2.1 dated 2015-11-24 and 1.3 dated 2016-03-23
DESCRIPTION | 27 MD5 | 66 NAMESPACE | 6 R/plot.R | 990 +++++----- R/vca.R | 3346 +++++++++++++++++++++++++----------- data/ReproData1.RData |only inst/ChangeLog.txt | 23 inst/UnitTests/runit.VCAinference.R | 204 +- inst/UnitTests/runit.anovaMM.R | 2 inst/UnitTests/runit.anovaVCA.R | 360 +-- inst/UnitTests/runit.misc.R | 315 +++ inst/UnitTests/runit.remlMM.R |only inst/UnitTests/runit.remlVCA.R |only man/ReproData1.Rd |only man/Solve.Rd | 4 man/Trace.Rd | 4 man/VCA-Package.Rd | 54 man/VCAinference.Rd | 15 man/anovaDF.Rd | 24 man/anovaMM.Rd | 10 man/anovaVCA.Rd | 16 man/check4MKL.Rd |only man/coef.VCA.Rd | 4 man/getGB.Rd |only man/getV.Rd | 4 man/lmerG.Rd |only man/lmerMatrices.Rd |only man/lmerSummary.Rd |only man/load_if_installed.Rd |only man/lsmMat.Rd | 6 man/ranef.VCA.Rd | 4 man/remlMM.Rd |only man/remlVCA.Rd |only man/residuals.VCA.Rd | 4 man/test.fixef.Rd | 40 man/test.lsmeans.Rd | 37 man/varPlot.Rd | 3 man/vcov.VCA.Rd | 4 man/vcovFixed.Rd | 8 man/vcovVC.Rd | 12 40 files changed, 3779 insertions(+), 1813 deletions(-)
Title: Big Data in-Database Analytics with Teradata Aster
Description: A consistent set of tools to perform in-database analytics
on Teradata Aster Big Data Discovery Platform. toaster (a.k.a 'to Aster')
embraces simple 2-step approach: compute in Aster - visualize and analyze
in R. Its `compute` functions use combination of SQL and
SQL/MR functions running in Aster database - highly scalable parallel
and distributed analytical platform. Then `create` functions visualize
results with boxplots, scatterplots, histograms, heatmaps, word clouds,
maps, or slope graphs. Advanced options such as faceting, coloring,
labeling, and others are supported with most functions.
Author: Gregory Kanevsky [aut, cre],
Nick Switanek [aut]
Maintainer: Gregory Kanevsky <gregory.kanevsky@teradata.com>
Diff between toaster versions 0.4.2 dated 2016-01-22 and 0.5.1 dated 2016-03-23
DESCRIPTION | 17 - MD5 | 47 ++-- NAMESPACE | 11 + NEWS | 32 +++ R/computeGraph.R |only R/computeTfIdf.R | 11 - R/maps.R | 2 R/misc.R | 58 +++++ R/showData.R | 2 R/showGraph.R |only R/toaster.R | 3 R/utils.R | 295 +++++++++++++++++++--------- man/computeEgoGraph.Rd |only man/computeGraph.Rd |only man/computeGraphHistogram.Rd |only man/computeGraphMetric.Rd |only man/createMap.Rd | 3 man/getNullCounts.Rd | 16 + man/getTableSummary.Rd | 3 man/getWindowFunction.Rd |only man/isTable.Rd | 23 +- man/makeFromClause.Rd |only man/showData.Rd | 2 man/showGraph.Rd |only man/toaGraph.Rd |only tests/testthat/test-computeEgoGraph.R |only tests/testthat/test-computeGraph.R |only tests/testthat/test-computeGraphHistogram.R |only tests/testthat/test-computeGraphMetric.R |only tests/testthat/test-computeHistogram.R | 3 tests/testthat/test-showGraph.R |only tests/testthat/test-utils.R | 39 +++ 32 files changed, 430 insertions(+), 137 deletions(-)
Title: R Client for the eBird Database of Bird Observations
Description: A programmatic client for the eBird database, including functions
for searching for bird observations by geographic location (latitude,
longitude), eBird hotspots, location identifiers, by notable sightings, by
region, and by taxonomic name.
Author: Rafael Maia [aut],
Scott Chamberlain [aut],
Andy Teucher [aut],
Sebastian Pardo [aut, cre]
Maintainer: Sebastian Pardo <sebpardo@gmail.com>
Diff between rebird versions 0.2 dated 2015-07-09 and 0.3.0 dated 2016-03-23
DESCRIPTION | 25 +++---- LICENSE | 2 MD5 | 43 ++++++------- NAMESPACE | 2 NEWS.md |only R/ebirdregioncheck.R | 7 -- R/getlatlng.R | 4 - R/nearestobs.R | 4 - R/zzz.R | 18 ++--- README.md | 125 ++++++++++++++++++++------------------- build/vignette.rds |binary man/ebirdfreq.Rd | 33 ++++------ man/ebirdgeo.Rd | 4 - man/ebirdhotspot.Rd | 2 man/ebirdloc.Rd | 22 +++--- man/ebirdnotable.Rd | 2 man/ebirdregion.Rd | 2 man/ebirdregioncheck.Rd | 2 man/ebirdtaxonomy.Rd | 16 ++-- man/getlatlng.Rd | 2 man/nearestobs.Rd | 6 - man/rebird-package.Rd | 8 +- tests/testthat/test-nearestobs.R | 4 - 23 files changed, 169 insertions(+), 164 deletions(-)
Title: Multivariate Distance Matrix Regression
Description: Allows a user to conduct multivariate distance matrix regression using analytic p-values and compute measures of effect size.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>
Diff between MDMR versions 0.3.0 dated 2016-02-03 and 0.3.3 dated 2016-03-23
DESCRIPTION | 8 MD5 | 10 - R/mdmr.R | 388 +++++++++++++++++++++++++------------------- inst/doc/mdmr-vignette.html | 231 ++++++++++++++------------ man/delta.Rd | 31 ++- man/summary.mdmr.Rd | 2 6 files changed, 391 insertions(+), 279 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
using Pareto smoothed importance sampling (PSIS), a new procedure for
regularizing importance weights. As a byproduct of the calculations, we also
obtain approximate standard errors for estimated predictive errors and for
the comparison of predictive errors between models. We also compute the
widely applicable information criterion (WAIC).
Author: Aki Vehtari [aut],
Andrew Gelman [aut],
Jonah Gabry [cre, aut],
Juho Piironen [ctb],
Ben Goodrich [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 0.1.5 dated 2016-02-12 and 0.1.6 dated 2016-03-23
DESCRIPTION | 16 ++++++++-------- MD5 | 34 +++++++++++++++++----------------- R/compare.R | 11 +++++------ R/extract_log_lik.R | 5 +++-- R/helpers.R | 31 +++++++++++++++++++++---------- R/loo.R | 6 ++++-- R/print.R | 15 +++++++++------ R/psislw.R | 9 ++++++--- R/waic.R | 6 ++++-- R/zzz.R | 8 ++++---- build/vignette.rds |binary inst/CITATION | 4 ++-- inst/doc/Example.R | 5 +++-- inst/doc/Example.Rmd | 5 +++-- inst/doc/Example.html | 18 ++++++++++-------- man/compare.Rd | 4 ++-- tests/testthat/test_compare.R | 15 ++++++--------- vignettes/Example.Rmd | 5 +++-- 18 files changed, 110 insertions(+), 87 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.7 dated 2016-01-09 and 1.2.0 dated 2016-03-23
gdm-1.1.7/gdm/vignettes/gdmVignette.Rmd |only gdm-1.1.7/gdm/vignettes/gdmVignette.bib |only gdm-1.2.0/gdm/DESCRIPTION | 12 gdm-1.2.0/gdm/MD5 | 25 gdm-1.2.0/gdm/NAMESPACE | 12 gdm-1.2.0/gdm/R/GDM_Table_Funcs.R | 942 +++++++++++++++++++++++---- gdm-1.2.0/gdm/build/vignette.rds |binary gdm-1.2.0/gdm/data/gdm.RData |binary gdm-1.2.0/gdm/inst/doc/gdmVignette.pdf |binary gdm-1.2.0/gdm/man/formatsitepair.Rd | 37 - gdm-1.2.0/gdm/man/gd.varImp.Rd |only gdm-1.2.0/gdm/man/permutateSitePair.Rd |only gdm-1.2.0/gdm/man/permutateVarSitePair.Rd |only gdm-1.2.0/gdm/man/plot.gdm.Rd | 130 +-- gdm-1.2.0/gdm/man/plotUncertainty.Rd |only gdm-1.2.0/gdm/man/removeSitesFromSitePair.Rd |only gdm-1.2.0/gdm/src/Gdmlib.cpp | 44 - 17 files changed, 954 insertions(+), 248 deletions(-)
Title: Direction Analysis for Pathways and Kinases
Description: Direction analysis is a set of tools designed to identify
combinatorial effects of multiple treatments and/or perturbations on pathways
and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics
data.
Author: Pengyi Yang & Ellis Patrick
Maintainer: Pengyi Yang <yangpy7@gmail.com>
Diff between directPA versions 1.2 dated 2015-06-18 and 1.3 dated 2016-03-23
directPA-1.2/directPA/R/directEnrichPlot2d.R |only directPA-1.2/directPA/man/directEnrichPlot2d.Rd |only directPA-1.3/directPA/DESCRIPTION | 14 ++- directPA-1.3/directPA/MD5 | 27 +++--- directPA-1.3/directPA/NAMESPACE | 8 +- directPA-1.3/directPA/R/directPA.R | 95 ++++++++++-------------- directPA-1.3/directPA/R/geneStats.R | 2 directPA-1.3/directPA/R/kinasePA.R |only directPA-1.3/directPA/R/perturbPlot2d.R |only directPA-1.3/directPA/README.md |only directPA-1.3/directPA/man/directExplorer2d.Rd | 15 ++- directPA-1.3/directPA/man/directPA.Rd | 82 +++++++------------- directPA-1.3/directPA/man/geneStats.Rd | 11 +- directPA-1.3/directPA/man/kinasePA.Rd |only directPA-1.3/directPA/man/pathwayStats.Rd | 13 +-- directPA-1.3/directPA/man/perturbPlot2d.Rd |only directPA-1.3/directPA/man/rotate2d.Rd | 3 directPA-1.3/directPA/man/rotate3d.Rd | 3 18 files changed, 128 insertions(+), 145 deletions(-)
Title: Three-Way Data Analysis Through Densities
Description: The three-way data consists of a set of variables measured on several groups of individuals. To each group is associated an estimated probability density function. The package provides functional methods (principal component analysis, multidimensional scaling, discriminant analysis...) for such probability densities.
Author: Rachid Boumaza, Pierre Santagostini, Smail Yousfi, Sabine Demotes-Mainard
Maintainer: Rachid Boumaza <rachid.boumaza@agrocampus-ouest.fr>
Diff between dad versions 1.0.2 dated 2015-11-05 and 1.1.0 dated 2016-03-23
DESCRIPTION | 10 +- MD5 | 34 ++++--- R/append.df2fh.R |only R/fdiscd.misclass.R | 7 - R/fdiscd.predict.R | 7 - R/folderh.R | 204 +++++++++++++++++++++++++++++++---------------- R/folderh2df.R | 2 R/folderh2folder.R | 4 R/plot.fmdsd.R | 2 R/plot.fpcad.R | 4 data/roseflowers.rda |binary data/roseleaves.rda |only man/append.df2folderh.Rd |only man/folderh.Rd | 78 ++++++++--------- man/folderh2df.Rd | 8 - man/folderh2folder.Rd | 8 - man/plot.fmdsd.Rd | 5 - man/plot.fpcad.Rd | 5 - man/roseflowers.Rd | 2 man/roseleaves.Rd |only 20 files changed, 229 insertions(+), 151 deletions(-)
Title: Interface to Bold Systems 'API'
Description: A programmatic interface to the Web Service methods provided by
Bold Systems for genetic 'barcode' data. Functions include methods for
searching by sequences by taxonomic names, ids, collectors, and
institutions; as well as a function for searching for specimens, and
downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 0.3.0 dated 2015-09-16 and 0.3.4 dated 2016-03-23
bold-0.3.0/bold/NEWS |only bold-0.3.4/bold/DESCRIPTION | 17 +++---- bold-0.3.4/bold/LICENSE | 2 bold-0.3.4/bold/MD5 | 54 +++++++++++------------ bold-0.3.4/bold/NAMESPACE | 15 +++--- bold-0.3.4/bold/NEWS.md |only bold-0.3.4/bold/R/bold-package.R | 2 bold-0.3.4/bold/R/bold_identify.R | 33 +++++++------- bold-0.3.4/bold/R/bold_seq.R | 6 +- bold-0.3.4/bold/R/bold_seqspec.R | 50 +++++++++++++++------ bold-0.3.4/bold/R/bold_specimens.R | 12 +++-- bold-0.3.4/bold/R/bold_tax_id.R | 19 +++++--- bold-0.3.4/bold/R/bold_tax_name.R | 10 ++-- bold-0.3.4/bold/R/bold_trace.R | 24 +++++++--- bold-0.3.4/bold/R/zzz.R | 47 +++++++++++--------- bold-0.3.4/bold/README.md | 64 +++++++++++++++------------- bold-0.3.4/bold/build/vignette.rds |binary bold-0.3.4/bold/inst/doc/bold_vignette.Rmd | 2 bold-0.3.4/bold/inst/doc/bold_vignette.html | 2 bold-0.3.4/bold/man/bold-package.Rd | 12 ++--- bold-0.3.4/bold/man/bold_identify.Rd | 2 bold-0.3.4/bold/man/bold_seq.Rd | 14 +++--- bold-0.3.4/bold/man/bold_seqspec.Rd | 25 +++++++--- bold-0.3.4/bold/man/bold_specimens.Rd | 16 +++---- bold-0.3.4/bold/man/bold_tax_id.Rd | 2 bold-0.3.4/bold/man/bold_tax_name.Rd | 2 bold-0.3.4/bold/man/bold_trace.Rd | 32 +++++++------- bold-0.3.4/bold/man/sequences.Rd | 6 +- bold-0.3.4/bold/vignettes/bold_vignette.Rmd | 2 29 files changed, 272 insertions(+), 200 deletions(-)