Title: Streamline Bioacoustic Analysis
Description: Offers three overarching categories of functions to obtain bird vocalization recordings from the web, manage sound files, and facilitate (bio)acoustic analysis in R.
Author: Marcelo Araya-Salas, Grace Smith Vidaurre, Hua Zhong
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between warbleR versions 1.0.2 dated 2015-07-27 and 1.0.3 dated 2015-09-09
warbleR-1.0.2/warbleR/R/Arre.aura-data.R |only warbleR-1.0.2/warbleR/R/Phae.cuvi-data.R |only warbleR-1.0.2/warbleR/data/Arre.aura.rda |only warbleR-1.0.2/warbleR/data/Phae.cuvi.rda |only warbleR-1.0.2/warbleR/data/datalist |only warbleR-1.0.2/warbleR/man/Arre.aura.Rd |only warbleR-1.0.2/warbleR/man/Phae.cuvi.Rd |only warbleR-1.0.3/warbleR/DESCRIPTION | 12 - warbleR-1.0.3/warbleR/MD5 | 65 +++++--- warbleR-1.0.3/warbleR/R/autodetec.R | 211 ++++++++++++++++++----------- warbleR-1.0.3/warbleR/R/lspec.R | 14 - warbleR-1.0.3/warbleR/R/manualoc.df-data.R | 4 warbleR-1.0.3/warbleR/R/querxc.R | 28 +++ warbleR-1.0.3/warbleR/R/sig2noise.R | 8 - warbleR-1.0.3/warbleR/R/snrspecs.R | 33 ++-- warbleR-1.0.3/warbleR/R/specreator.R | 22 +-- warbleR-1.0.3/warbleR/R/trackfreqs.R | 62 ++++---- warbleR-1.0.3/warbleR/R/warbleR-package.R | 2 warbleR-1.0.3/warbleR/build |only warbleR-1.0.3/warbleR/data/manualoc.df.rda |binary warbleR-1.0.3/warbleR/inst/CITATION | 4 warbleR-1.0.3/warbleR/inst/doc |only warbleR-1.0.3/warbleR/man/lspec.Rd | 7 warbleR-1.0.3/warbleR/man/manualoc.df.Rd | 4 warbleR-1.0.3/warbleR/man/querxc.Rd | 10 + warbleR-1.0.3/warbleR/man/sig2noise.Rd | 8 - warbleR-1.0.3/warbleR/man/snrspecs.Rd | 12 - warbleR-1.0.3/warbleR/man/specreator.Rd | 15 -- warbleR-1.0.3/warbleR/man/trackfreqs.Rd | 31 +--- warbleR-1.0.3/warbleR/man/warbleR.Rd | 12 - warbleR-1.0.3/warbleR/vignettes |only 31 files changed, 328 insertions(+), 236 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item functioning and modelling item and person
covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.10 dated 2015-06-15 and 1.13 dated 2015-09-09
mirt-1.10/mirt/R/read.mirt.R |only mirt-1.10/mirt/src/dgroup.c |only mirt-1.13/mirt/DESCRIPTION | 12 mirt-1.13/mirt/MD5 | 106 +++--- mirt-1.13/mirt/NAMESPACE | 7 mirt-1.13/mirt/NEWS | 24 + mirt-1.13/mirt/R/02-item_methods.R | 94 +---- mirt-1.13/mirt/R/03-estimation.R | 44 +- mirt-1.13/mirt/R/DTF.R | 6 mirt-1.13/mirt/R/Discrete-methods.R | 17 - mirt-1.13/mirt/R/EMstep.group.R | 10 mirt-1.13/mirt/R/EMstep.utils.R | 43 ++ mirt-1.13/mirt/R/LoadPars.R | 2 mirt-1.13/mirt/R/M2.R | 5 mirt-1.13/mirt/R/MHRM.group.R | 61 +-- mirt-1.13/mirt/R/MultipleGroup-methods.R | 80 +++- mirt-1.13/mirt/R/PLCI.mirt.R | 2 mirt-1.13/mirt/R/SE.methods.R | 54 ++- mirt-1.13/mirt/R/SingleGroup-methods.R | 154 ++++++--- mirt-1.13/mirt/R/boot.mirt.R | 22 - mirt-1.13/mirt/R/fscores.internal.R | 30 + mirt-1.13/mirt/R/imputeMissing.R | 39 -- mirt-1.13/mirt/R/itemGAM.R | 25 + mirt-1.13/mirt/R/itemfit.R | 74 +++- mirt-1.13/mirt/R/iteminfo.R | 11 mirt-1.13/mirt/R/itemplot.R | 32 + mirt-1.13/mirt/R/itemplot.internal.R | 38 +- mirt-1.13/mirt/R/key2binary.R | 25 + mirt-1.13/mirt/R/marginal_rxx.R | 4 mirt-1.13/mirt/R/mirt-package.R | 6 mirt-1.13/mirt/R/mirt.R | 17 - mirt-1.13/mirt/R/mixedmirt.R | 11 mirt-1.13/mirt/R/simdata.R | 68 +++- mirt-1.13/mirt/R/utils.R | 113 ++++--- mirt-1.13/mirt/build/vignette.rds |binary mirt-1.13/mirt/man/DTF.Rd | 4 mirt-1.13/mirt/man/boot.mirt.Rd | 7 mirt-1.13/mirt/man/coef-method.Rd | 2 mirt-1.13/mirt/man/imputeMissing.Rd | 11 mirt-1.13/mirt/man/itemGAM.Rd | 11 mirt-1.13/mirt/man/itemfit.Rd | 16 mirt-1.13/mirt/man/itemplot.Rd | 32 + mirt-1.13/mirt/man/key2binary.Rd | 16 mirt-1.13/mirt/man/marginal_rxx.Rd | 1 mirt-1.13/mirt/man/mirt.Rd | 17 - mirt-1.13/mirt/man/mixedmirt.Rd | 11 mirt-1.13/mirt/man/plot-method.Rd | 26 - mirt-1.13/mirt/man/simdata.Rd | 36 ++ mirt-1.13/mirt/src/Misc.h | 2 mirt-1.13/mirt/src/dpars.cpp | 337 ++++++++++++++++++++- mirt-1.13/mirt/tests/tests/test-02-mirtTwo.R | 2 mirt-1.13/mirt/tests/tests/test-04-multipleGroup.R | 4 mirt-1.13/mirt/tests/tests/test-05-confmirtOne.R | 12 mirt-1.13/mirt/tests/tests/test-06-confmirtTwo.R | 6 mirt-1.13/mirt/tests/tests/test-07-mixedmirt.R | 32 - 55 files changed, 1284 insertions(+), 537 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 1.0 dated 2015-03-27 and 1.1.1 dated 2015-09-09
DESCRIPTION | 6 MD5 | 30 NAMESPACE | 3 R/GDM_Table_Funcs.R | 2810 ++++++++++++++++++++++++++------------------------ data/gdm.RData |binary inst/doc |only man/createsitepair.Rd | 4 man/formatsitepair.Rd | 2 man/gdm-package.Rd | 8 man/gdm.Rd | 4 man/gdm.transform.Rd | 51 man/gdmDissim.Rd | 2 man/isplineExtract.Rd | 8 man/plot.gdm.Rd | 2 man/predict.gdm.Rd | 44 man/stackedVars.Rd | 2 16 files changed, 1599 insertions(+), 1377 deletions(-)
Title: Implements ACME Estimator of Bird and Bat Mortality by Wind
Turbines
Description: Implementation of estimator ACME, described in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran Mortality at Wind
Turbines (submitted). Unlike most other models, this estimator
supports decreasing-hazard Weibull model for persistence;
decreasing search proficiency as carcasses age; variable
bleed-through at successive searches; and interval mortality
estimates. The package provides, based on search data, functions
for estimating the mortality inflation factor in Frequentist and
Bayesian settings.
Author: Robert Wolpert [aut, cre],
Jacob Coleman [aut]
Maintainer: Robert Wolpert <wolpert@stat.duke.edu>
Diff between acmeR versions 1.0.0 dated 2015-07-24 and 1.1.0 dated 2015-09-09
acmeR-1.0.0/acmeR/man/ObjPost.Rd |only acmeR-1.1.0/acmeR/DESCRIPTION | 29 +++--- acmeR-1.1.0/acmeR/MD5 | 27 +++--- acmeR-1.1.0/acmeR/NAMESPACE | 3 acmeR-1.1.0/acmeR/R/acme_post.R | 148 +++++++++++++++++++++------------- acmeR-1.1.0/acmeR/R/acme_summary.R | 16 ++- acmeR-1.1.0/acmeR/R/acme_table.R |only acmeR-1.1.0/acmeR/R/read_data.R | 47 ++++++++-- acmeR-1.1.0/acmeR/R/sysdata.rda |binary acmeR-1.1.0/acmeR/build |only acmeR-1.1.0/acmeR/data/altamont.rda |binary acmeR-1.1.0/acmeR/inst |only acmeR-1.1.0/acmeR/man/acme.post.Rd |only acmeR-1.1.0/acmeR/man/acme.summary.Rd | 4 acmeR-1.1.0/acmeR/man/acme.table.Rd |only acmeR-1.1.0/acmeR/man/read.data.Rd | 4 acmeR-1.1.0/acmeR/vignettes |only 17 files changed, 175 insertions(+), 103 deletions(-)
Title: Seasonal/Sequential (Instants/Durations, Even or not) Time
Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>
Diff between timetools versions 1.7.0 dated 2015-06-17 and 1.7.2 dated 2015-09-09
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 6 ++++-- R/TimeInstantDataFrame.R | 6 +++--- R/TimeIntervalDataFrame.R | 2 +- README | 4 ++++ man/timetools-package.Rd | 4 ++-- 7 files changed, 26 insertions(+), 20 deletions(-)
Title: Parallel Line Assays
Description: Parallel Line Assays: Completely randomized design,
Randomized Block design, and Latin squares design.
Balanced data are fitted as described in the Ph.Eur.
In the presence of missing values complete data analysis can be
performed (with computation of Fieller's confidence intervals for
the estimated potency), or imputation of values can be applied.
The package contains a script such that a pdf-document with a
report of an analysis of an assay can be produced from an input file
with data of the assay. Here no knowledge of R is needed by the user.
Author: Jens Henrik Badsberg
Maintainer: Jens Henrik Badsberg <pla2015@badsberg.eu>
Diff between pla versions 0.1 dated 2015-08-18 and 0.2 dated 2015-09-09
DESCRIPTION | 8 - MD5 | 163 ++++++++++++++++++++++++++++++++++++--- NAMESPACE | 2 R/methodsData.R | 85 ++++++++++++-------- data |only inst/scripts/Makefile |only inst/scripts/R/xtables.bak.R |only inst/vignettes |only man/AgarDiffusionAssay.Rd |only man/Corticotrophin.Rd |only man/Diphteria.Rd |only man/Erythromycin.Rd |only man/Erythropoietin.Rd |only man/FactorIX.Rd |only man/HeparinSodium.Rd |only man/HepatitisB.Rd |only man/HepatitisBvaccine.Rd |only man/HumanHepatitis.Rd |only man/IPV.Rd |only man/Nystatin.Rd |only man/Turbidimetric.Rd |only man/Vancomycin.Rd |only man/Work |only man/assayTable2frame.Rd | 8 + man/data2assayFrame.Rd | 19 ++++ man/pheur325.Rd | 2 man/pla-package.Rd | 87 +++++++++++++++++++-- man/pla.Rd | 2 man/pla.fit.Rd | 21 ++++- man/pla.plots.Rd | 28 ++++++ man/potency.Rd | 2 man/readAssayTable.Rd | 176 ++++++++++++++++++++++++++++++++++++++++++- 32 files changed, 537 insertions(+), 66 deletions(-)
Title: Orthogonal Nonlinear Least-Squares Regression
Description: Orthogonal Nonlinear Least-Squares Regression using Levenberg-Marquardt Minimization.
Author: Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
Maintainer: Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
Diff between onls versions 0.1-0 dated 2015-01-17 and 0.1-1 dated 2015-09-09
onls-0.1-0/onls/inst/onls-vignette.pdf |only onls-0.1-1/onls/DESCRIPTION | 10 +++++----- onls-0.1-1/onls/MD5 | 24 ++++++++++++++---------- onls-0.1-1/onls/NAMESPACE | 7 +++++++ onls-0.1-1/onls/NEWS | 7 ++++++- onls-0.1-1/onls/build |only onls-0.1-1/onls/inst/doc |only onls-0.1-1/onls/man/check_o.Rd | 2 +- onls-0.1-1/onls/man/deviance_o.Rd | 2 +- onls-0.1-1/onls/man/onls.Rd | 2 +- onls-0.1-1/onls/man/plot.onls.Rd | 4 ++-- onls-0.1-1/onls/man/print.onls.Rd | 2 +- onls-0.1-1/onls/man/summary.onls.Rd | 2 +- onls-0.1-1/onls/vignettes |only 14 files changed, 39 insertions(+), 23 deletions(-)
Title: Inference of Species Associations from Co-Occurrence Data
Description: Infers species associations from community matrices. Uses local and (optional) regional-scale co-occurrence data by comparing observed partial correlation coefficients between species to those estimated from regional species distributions. Extends Gaussian graphical models to a null modeling framework. Provides interface to a variety of inverse covariance matrix estimation methods.
Author: Benjamin Blonder, Naia Morueta-Holme
Maintainer: Benjamin Blonder <bblonder@gmail.com>
Diff between netassoc versions 0.4.7 dated 2015-06-24 and 0.6.0 dated 2015-09-09
netassoc-0.4.7/netassoc/R/netassoc.R |only netassoc-0.4.7/netassoc/man/makenetwork.Rd |only netassoc-0.6.0/netassoc/DESCRIPTION | 11 ++++++----- netassoc-0.6.0/netassoc/MD5 | 17 +++++++++++------ netassoc-0.6.0/netassoc/NAMESPACE | 13 +++++++++++-- netassoc-0.6.0/netassoc/R/generate_nul_resample.R |only netassoc-0.6.0/netassoc/R/make_netassoc_network.R |only netassoc-0.6.0/netassoc/R/partial_correlation.R |only netassoc-0.6.0/netassoc/R/plot.R |only netassoc-0.6.0/netassoc/man/make_netassoc_network.Rd |only netassoc-0.6.0/netassoc/man/netassoc-package.Rd | 4 ++-- netassoc-0.6.0/netassoc/man/partial_correlation.Rd |only netassoc-0.6.0/netassoc/man/plot_netassoc_matrix.Rd |only netassoc-0.6.0/netassoc/man/plot_netassoc_network.Rd | 8 ++++++-- 14 files changed, 36 insertions(+), 17 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.3 dated 2015-08-21 and 1.4 dated 2015-09-09
DESCRIPTION | 14 +++++++------- MD5 | 38 +++++++++++++++++++------------------- R/CA.R | 23 +++++++++++++++++------ man/Biplot.Rd | 2 +- man/CA.Rd | 41 +++++++++++++++++++++++++---------------- man/DataFreq.Rd | 4 ++-- man/DataMix.Rd | 8 ++++---- man/DataQuali.Rd | 6 +++--- man/DataQuan.Rd | 6 +++--- man/Data_Cafes.Rd | 6 +++--- man/Data_Individuos.Rd | 6 +++--- man/GSVD.Rd | 18 +++++++++--------- man/IM.Rd | 16 ++++++++-------- man/MFA.Rd | 42 +++++++++++++++++++++--------------------- man/MVar.pt-package.Rd | 12 ++++++------ man/NormData.Rd | 12 ++++++------ man/PCA.Rd | 24 ++++++++++++------------ man/Plot.CA.Rd | 14 +++++++------- man/Plot.MFA.Rd | 32 ++++++++++++++++---------------- man/Plot.PCA.Rd | 14 +++++++------- 20 files changed, 179 insertions(+), 159 deletions(-)
Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Description: Implements nonparametric hypothesis tests to check isotropy and symmetry properties for two-dimensional spatial data.
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>
Diff between spTest versions 0.1.1 dated 2015-07-24 and 0.2.0 dated 2015-09-09
spTest-0.1.1/spTest/inst/CITATION |only spTest-0.2.0/spTest/DESCRIPTION | 16 +++---- spTest-0.2.0/spTest/MD5 | 62 ++++++++++++++++++++++++------ spTest-0.2.0/spTest/R/Data_Description.R |only spTest-0.2.0/spTest/R/GuanTestGrid.R | 53 ++++++++++++++----------- spTest-0.2.0/spTest/R/GuanTestUnif.R | 10 +++- spTest-0.2.0/spTest/R/GuanTestUnif_help.R | 4 - spTest-0.2.0/spTest/R/LuTest.R | 2 spTest-0.2.0/spTest/R/LuTest_help.R | 2 spTest-0.2.0/spTest/R/MaityTest.R | 9 +++- spTest-0.2.0/spTest/R/MaityTest_help.R | 4 - spTest-0.2.0/spTest/build |only spTest-0.2.0/spTest/data |only spTest-0.2.0/spTest/inst/doc |only spTest-0.2.0/spTest/man/GuanTestGrid.Rd | 24 +++++------ spTest-0.2.0/spTest/man/GuanTestUnif.Rd | 4 - spTest-0.2.0/spTest/man/WRFG.Rd |only spTest-0.2.0/spTest/vignettes |only 18 files changed, 125 insertions(+), 65 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators; confront
data with them and analyze or visualize the results. The package supports
rules that are per-field, in-record, cross-record or cross-dataset. Rules
can be automatically analyzed for rule type and connectivity.
Author: Mark van der Loo [cre, aut],
Edwin de Jonge [aut],
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 0.1.2 dated 2015-09-01 and 0.1.3 dated 2015-09-09
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- R/compare.R | 2 +- inst/doc/intro.R | 7 +++++++ inst/doc/intro.Rmd | 12 +++++++----- inst/doc/intro.html | 36 +++++++++++++++++++++++++----------- inst/doc/rule-files.Rmd | 2 +- inst/doc/rule-files.html | 2 +- vignettes/intro.Rmd | 12 +++++++----- vignettes/rule-files.Rmd | 2 +- vignettes/rule-tour.Rmd |only vignettes/rule-tour.html |only 12 files changed, 65 insertions(+), 38 deletions(-)
Title: Package for Calculation of ARMSS, Local MSSS and Global MSSS
Description: Calculates ARMSS (age related multiple sclerosis severity), and both local and global MSSS (multiple sclerosis severity score).
Author: Helga Westerlind, Ali Manouchehrinia
Maintainer: Helga Westerlind <Helga.Westerlind@ki.se>
Diff between ms.sev versions 1.0.1 dated 2015-08-31 and 1.0.2 dated 2015-09-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ms_sev.R | 9 +++++---- 3 files changed, 11 insertions(+), 10 deletions(-)
Title: Multivariable Fractional Polynomials
Description: Fractional polynomials are used to represent curvature in regression models. A key reference is Royston and Altman, 1994.
Author: original by Gareth Ambler <gareth@stats.ucl.ac.uk>, modified by Axel Benner <benner@dkfz.de>
Maintainer: Stephan Luecke <s.luecke@dkfz.de>
Diff between mfp versions 1.5.1 dated 2015-02-04 and 1.5.2 dated 2015-09-09
mfp-1.5.1/mfp/ChangeLog |only mfp-1.5.2/mfp/DESCRIPTION | 8 +- mfp-1.5.2/mfp/MD5 | 18 ++-- mfp-1.5.2/mfp/NAMESPACE | 13 +-- mfp-1.5.2/mfp/NEWS |only mfp-1.5.2/mfp/build/vignette.rds |binary mfp-1.5.2/mfp/data/bodyfat.rda |binary mfp-1.5.2/mfp/inst/doc/mfp_vignette.R | 120 +++++++++++++++---------------- mfp-1.5.2/mfp/inst/doc/mfp_vignette.Rnw | 2 mfp-1.5.2/mfp/inst/doc/mfp_vignette.pdf |binary mfp-1.5.2/mfp/vignettes/mfp_vignette.Rnw | 2 11 files changed, 82 insertions(+), 81 deletions(-)
Title: Discrete Laplace Mixture Inference using the EM Algorithm
Description: Make inference in a mixture of discrete Laplace distributions using the EM algorithm. This can e.g. be used for modelling the distribution of Y chromosomal haplotypes as described in [1, 2] (refer to the URL section).
Author: Mikkel Meyer Andersen and Poul Svante Eriksen
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between disclapmix versions 1.6.1 dated 2015-06-12 and 1.6.2 dated 2015-09-09
disclapmix-1.6.1/disclapmix/man/haplotype_diversity.Rd |only disclapmix-1.6.1/disclapmix/man/happrobsum.Rd |only disclapmix-1.6.2/disclapmix/DESCRIPTION | 12 disclapmix-1.6.2/disclapmix/MD5 | 45 disclapmix-1.6.2/disclapmix/NAMESPACE | 7 disclapmix-1.6.2/disclapmix/NEWS | 5 disclapmix-1.6.2/disclapmix/R/RcppExports.R | 28 disclapmix-1.6.2/disclapmix/R/helper.R | 143 -- disclapmix-1.6.2/disclapmix/R/proto_functions.R |only disclapmix-1.6.2/disclapmix/man/clusterdist.Rd | 2 disclapmix-1.6.2/disclapmix/man/clusterprob.Rd | 2 disclapmix-1.6.2/disclapmix/man/contributor_pairs.Rd | 2 disclapmix-1.6.2/disclapmix/man/disclapmix-package.Rd | 2 disclapmix-1.6.2/disclapmix/man/disclapmix.Rd | 2 disclapmix-1.6.2/disclapmix/man/disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/man/generate_mixture.Rd | 2 disclapmix-1.6.2/disclapmix/man/plot.disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/man/predict.disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/man/print.disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/man/rank_contributor_pairs.Rd | 2 disclapmix-1.6.2/disclapmix/man/simulate.disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/man/summary.disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/src/RcppExports.cpp | 378 +++--- disclapmix-1.6.2/disclapmix/src/happrobsum.cpp | 804 +++++++++++++- disclapmix-1.6.2/disclapmix/src/helper.cpp | 34 25 files changed, 1120 insertions(+), 362 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.8.2-1 dated 2015-08-18 and 0.8.4-2 dated 2015-09-09
quanteda-0.8.2-1/quanteda/man/bigrams.Rd |only quanteda-0.8.4-2/quanteda/DESCRIPTION | 10 quanteda-0.8.4-2/quanteda/MD5 | 71 +- quanteda-0.8.4-2/quanteda/NAMESPACE | 11 quanteda-0.8.4-2/quanteda/NEWS | 37 + quanteda-0.8.4-2/quanteda/R/collocations.R | 2 quanteda-0.8.4-2/quanteda/R/corpus.R | 24 quanteda-0.8.4-2/quanteda/R/dfm-classes.R | 16 quanteda-0.8.4-2/quanteda/R/dfm-main.R | 47 - quanteda-0.8.4-2/quanteda/R/dictionaries.R | 4 quanteda-0.8.4-2/quanteda/R/encoding.R | 4 quanteda-0.8.4-2/quanteda/R/ngrams.R | 346 ++++++++++---- quanteda-0.8.4-2/quanteda/R/stopwords.R | 21 quanteda-0.8.4-2/quanteda/R/textfile.R | 73 +- quanteda-0.8.4-2/quanteda/R/textmodel-generics.R | 2 quanteda-0.8.4-2/quanteda/R/toLower.R | 4 quanteda-0.8.4-2/quanteda/R/tokenize.R | 61 +- quanteda-0.8.4-2/quanteda/R/wordstem.R | 21 quanteda-0.8.4-2/quanteda/build/vignette.rds |binary quanteda-0.8.4-2/quanteda/inst/doc/development-plans.Rmd | 3 quanteda-0.8.4-2/quanteda/inst/doc/development-plans.html | 1 quanteda-0.8.4-2/quanteda/inst/doc/quickstart.R | 4 quanteda-0.8.4-2/quanteda/inst/doc/quickstart.Rmd | 4 quanteda-0.8.4-2/quanteda/inst/doc/quickstart.html | 78 +-- quanteda-0.8.4-2/quanteda/man/collocations.Rd | 2 quanteda-0.8.4-2/quanteda/man/corpus.Rd | 10 quanteda-0.8.4-2/quanteda/man/dfm.Rd | 41 - quanteda-0.8.4-2/quanteda/man/dictionary.Rd | 4 quanteda-0.8.4-2/quanteda/man/encoding.Rd | 4 quanteda-0.8.4-2/quanteda/man/ngrams.Rd | 79 ++- quanteda-0.8.4-2/quanteda/man/selectFeatures.Rd | 4 quanteda-0.8.4-2/quanteda/man/textfile.Rd | 45 - quanteda-0.8.4-2/quanteda/man/textmodel.Rd | 2 quanteda-0.8.4-2/quanteda/man/toLower.Rd | 3 quanteda-0.8.4-2/quanteda/man/tokenize.Rd | 34 + quanteda-0.8.4-2/quanteda/vignettes/development-plans.Rmd | 3 quanteda-0.8.4-2/quanteda/vignettes/quickstart.Rmd | 4 37 files changed, 667 insertions(+), 412 deletions(-)
Title: Psychometric Mixture Models
Description: Psychometric mixture models based on 'flexmix' infrastructure. At the moment Rasch mixture models
with different parameterizations of the score distribution (saturated vs. mean/variance specification)
and Bradley-Terry mixture models are implemented. Both mixture models can be estimated with or without
concomitant variables. See vignette('raschmix', package = 'psychomix') for details on the Rasch mixture
models.
Author: Hannah Frick [aut, cre],
Carolin Strobl [aut],
Friedrich Leisch [aut],
Achim Zeileis [aut]
Maintainer: Hannah Frick <h.frick@ucl.ac.uk>
Diff between psychomix versions 1.1-2 dated 2015-05-05 and 1.1-3 dated 2015-09-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ NEWS | 5 +++++ build/vignette.rds |binary inst/doc/raschmix.pdf |binary inst/doc/scores.pdf |binary man/btmix.Rd | 1 + tests/Examples/psychomix-Ex.Rout.save | 6 +++--- 9 files changed, 23 insertions(+), 15 deletions(-)
Title: Mesh Generation and Surface Tesselation
Description: Makes the qhull library (www.qhull.org)
available in R, in a similar manner as in Octave and MATLAB. Qhull
computes convex hulls, Delaunay triangulations, halfspace
intersections about a point, Voronoi diagrams, furthest-site
Delaunay triangulations, and furthest-site Voronoi diagrams. It
runs in 2-d, 3-d, 4-d, and higher dimensions. It implements the
Quickhull algorithm for computing the convex hull. Qhull does not
support constrained Delaunay triangulations, or mesh generation of
non-convex objects, but the package does include some R functions
that allow for this. Currently the package only gives access to
Delaunay triangulation and convex hull computation.
Author: C. B. Barber [cph],
Kai Habel [cph, aut],
Raoul Grasman [cph, aut],
Robert B. Gramacy [cph, aut],
Andreas Stahel [cph, aut],
David C. Sterratt [cph, aut, cre]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between geometry versions 0.3-5 dated 2014-11-08 and 0.3-6 dated 2015-09-09
DESCRIPTION | 18 +++++------ MD5 | 76 ++++++++++++++++++++++++------------------------- NAMESPACE | 6 +++ NEWS | 23 ++++++++++++++ R/convhulln.R | 8 +++-- R/delaunayn.R | 13 ++++---- R/distmesh2d.R | 6 +-- R/distmeshnd.R | 8 ++--- R/mesh.dcircle.R | 2 - R/mesh.drectangle.R | 2 - R/mesh.dsphere.R | 2 - R/surf.tri.R | 24 +++++++-------- R/tetramesh.R | 9 ++--- R/trimesh.R | 1 inst/doc/index.html | 25 ++-------------- man/Unique.Rd | 3 + man/bary2cart.Rd | 3 + man/cart2bary.Rd | 3 + man/convhulln.Rd | 3 + man/delaunayn.Rd | 8 ++--- man/distmesh2d.Rd | 5 +-- man/distmeshnd.Rd | 5 +-- man/dot.Rd | 3 + man/entry.value.Rd | 3 + man/extprod3d.Rd | 3 + man/matmax.Rd | 3 + man/mesh.dcircle.Rd | 5 +-- man/mesh.diff.Rd | 3 + man/mesh.drectangle.Rd | 5 +-- man/mesh.dsphere.Rd | 5 +-- man/mesh.hunif.Rd | 3 + man/polyarea.Rd | 3 + man/surf.tri.Rd | 27 ++++++++--------- man/tetramesh.Rd | 10 +++--- man/trimesh.Rd | 3 + man/tsearch.Rd | 3 + man/tsearchn.Rd | 3 + src/Rconvhulln.c | 4 +- src/Rdelaunayn.c | 4 +- 39 files changed, 186 insertions(+), 157 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 0.6-2 dated 2015-04-19 and 0.7 dated 2015-09-09
DESCRIPTION | 32 +++- MD5 | 117 +++++++++++------- NAMESPACE | 16 ++ NEWS | 35 +++++ R/blobbogram.R | 15 +- R/code.R | 2 R/deviance.R |only R/inits.R | 121 +++++++++++------- R/likelihoods.R |only R/ll-helper.counts.R |only R/ll.binom.cloglog.R | 41 ++++-- R/ll.binom.log.R |only R/ll.binom.logit.R | 42 ++++-- R/ll.call.R | 8 - R/ll.normal.identity.R | 31 +++- R/ll.poisson.log.R | 54 +++++++- R/minimum.diameter.spanning.tree.R | 8 - R/mtc.model.R | 13 +- R/mtc.model.consistency.R | 4 R/mtc.model.nodesplit.R | 20 ++- R/mtc.model.ume.R | 32 ++++ R/mtc.model.use.R | 8 - R/mtc.network.R | 119 +----------------- R/mtc.network.xml.R |only R/mtc.result.R | 35 +++-- R/mtc.run.R | 135 ++++----------------- R/relative.effect.R | 2 R/relative.effect.table.R |only data |only inst/gemtc.releffect.likelihood.r2.txt | 6 inst/gemtc.releffect.likelihood.rm.txt | 3 man/depression.Rd |only man/gemtc-package.Rd | 17 +- man/ll.call.Rd | 1 man/mtc.hy.prior.Rd | 9 - man/mtc.model.Rd | 14 +- man/mtc.network.Rd | 44 +----- man/mtc.network.xml.Rd |only man/mtc.nodesplit.Rd | 6 man/mtc.run.Rd | 22 ++- man/parkinson.Rd |only man/rank.probability.Rd | 4 man/relative.effect.Rd | 9 - man/relative.effect.table.Rd |only man/smoking.Rd |only man/thrombolytic.Rd |only tests/data/riskratio.data.txt |only tests/data/riskratio.summaries.txt |only tests/data/rr-pairwise.csv |only tests/testthat/helper-regress.R | 32 +++- tests/testthat/helper-validate.R | 10 - tests/testthat/test-regress-anohe.R | 6 tests/testthat/test-regress-models.R | 8 - tests/testthat/test-unit-ll.R | 4 tests/testthat/test-unit-ll.binom.log.R |only tests/testthat/test-unit-ll.binom.logit.R |only tests/testthat/test-unit-ll.poisson.log.R |only tests/testthat/test-unit-mtc.model.consistency.R |only tests/testthat/test-unit-mtc.model.graph.R | 2 tests/testthat/test-unit-mtc.model.nodesplit.R |only tests/testthat/test-unit-mtc.model.ume.R | 16 ++ tests/testthat/test-unit-mtc.model.use.R |only tests/testthat/test-unit-mtc.model_inits.R | 31 ++++ tests/testthat/test-unit-relative.effect.R | 2 tests/testthat/test-unit-relative.effect.table.R |only tests/testthat/test-validate-cipriani-efficacy.R | 3 tests/testthat/test-validate-luades-smoking.R | 3 tests/testthat/test-validate-luades-thrombolytic.R | 3 tests/testthat/test-validate-parkinson.R | 3 tests/testthat/test-validate-riskratio.R |only 70 files changed, 656 insertions(+), 492 deletions(-)
Title: Generate High-Resolution Venn and Euler Plots
Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Author: Hanbo Chen
Maintainer: Paul Boutros <Paul.Boutros@oicr.on.ca>
Diff between VennDiagram versions 1.6.9 dated 2014-09-24 and 1.6.15 dated 2015-09-09
VennDiagram-1.6.15/VennDiagram/DESCRIPTION | 13 VennDiagram-1.6.15/VennDiagram/MD5 | 114 - VennDiagram-1.6.15/VennDiagram/NAMESPACE | 32 VennDiagram-1.6.15/VennDiagram/NEWS | 43 VennDiagram-1.6.15/VennDiagram/R/draw.pairwise.venn.R | 227 ++ VennDiagram-1.6.15/VennDiagram/R/draw.quad.venn.R | 157 +- VennDiagram-1.6.15/VennDiagram/R/draw.quintuple.venn.R | 189 +- VennDiagram-1.6.15/VennDiagram/R/draw.single.venn.R | 65 VennDiagram-1.6.15/VennDiagram/R/draw.sp.case.R | 56 VennDiagram-1.6.15/VennDiagram/R/draw.sp.case.preprocess.R |only VennDiagram-1.6.15/VennDiagram/R/draw.sp.case.scaled.R |only VennDiagram-1.6.15/VennDiagram/R/draw.triple.venn.R | 189 +- VennDiagram-1.6.15/VennDiagram/R/ellipse.R | 9 VennDiagram-1.6.15/VennDiagram/R/flip.venn.R | 3 VennDiagram-1.6.15/VennDiagram/R/partitionText.R |only VennDiagram-1.6.15/VennDiagram/R/rotate.sp.R | 71 VennDiagram-1.6.15/VennDiagram/R/venn.diagram.R | 760 +++++++--- VennDiagram-1.6.15/VennDiagram/TODO | 5 VennDiagram-1.6.15/VennDiagram/data |only VennDiagram-1.6.15/VennDiagram/inst |only VennDiagram-1.6.15/VennDiagram/man/calculate.overlap.Rd |only VennDiagram-1.6.15/VennDiagram/man/draw.pairwise.venn.Rd | 32 VennDiagram-1.6.15/VennDiagram/man/draw.quad.venn.Rd | 28 VennDiagram-1.6.15/VennDiagram/man/draw.quintuple.venn.Rd | 31 VennDiagram-1.6.15/VennDiagram/man/draw.sp.case.preprocess.Rd |only VennDiagram-1.6.15/VennDiagram/man/draw.sp.case.scaled.Rd |only VennDiagram-1.6.15/VennDiagram/man/draw.triple.venn.Rd | 34 VennDiagram-1.6.15/VennDiagram/man/get.venn.partitions.Rd |only VennDiagram-1.6.15/VennDiagram/man/make.truth.table.Rd |only VennDiagram-1.6.15/VennDiagram/man/venn.diagram.Rd | 21 VennDiagram-1.6.15/VennDiagram/man/venn.plot.Rd |only VennDiagram-1.6.15/VennDiagram/tests |only VennDiagram-1.6.9/VennDiagram/R/draw.001.R |only VennDiagram-1.6.9/VennDiagram/R/draw.010.R |only VennDiagram-1.6.9/VennDiagram/R/draw.011A.R |only VennDiagram-1.6.9/VennDiagram/R/draw.011O.R |only VennDiagram-1.6.9/VennDiagram/R/draw.012AA.R |only VennDiagram-1.6.9/VennDiagram/R/draw.021AA.R |only VennDiagram-1.6.9/VennDiagram/R/draw.022AAAO.R |only VennDiagram-1.6.9/VennDiagram/R/draw.022AAOO.R |only VennDiagram-1.6.9/VennDiagram/R/draw.023.R |only VennDiagram-1.6.9/VennDiagram/R/draw.032.R |only VennDiagram-1.6.9/VennDiagram/R/draw.033.R |only VennDiagram-1.6.9/VennDiagram/R/draw.100.R |only VennDiagram-1.6.9/VennDiagram/R/draw.110.R |only VennDiagram-1.6.9/VennDiagram/R/draw.111A.R |only VennDiagram-1.6.9/VennDiagram/R/draw.112AA.R |only VennDiagram-1.6.9/VennDiagram/R/draw.120.R |only VennDiagram-1.6.9/VennDiagram/R/draw.121AO.R |only VennDiagram-1.6.9/VennDiagram/R/draw.122AAOO.R |only VennDiagram-1.6.9/VennDiagram/R/draw.130.R |only VennDiagram-1.6.9/VennDiagram/man/draw.001.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.010.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.011A.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.011O.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.012AA.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.021AA.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.022AAAO.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.022AAOO.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.023.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.032.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.033.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.100.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.110.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.111A.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.112AA.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.120.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.121AO.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.122AAOO.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.130.Rd |only 70 files changed, 1455 insertions(+), 624 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.2-0 dated 2015-09-07 and 1.2-1 dated 2015-09-09
DESCRIPTION | 8 +-- MD5 | 18 +++--- inst/NEWS | 3 + inst/doc/stream.R | 112 +++++++++++++++++++++--------------------- inst/doc/stream.Rnw | 64 +++++++++++++----------- inst/doc/stream.pdf |binary inst/doc/stream_extension.pdf |binary inst/tests/test-DSC.R | 13 ++++ inst/tests/test-DSD.R | 1 vignettes/stream.Rnw | 64 +++++++++++++----------- 10 files changed, 155 insertions(+), 128 deletions(-)
Title: Create Dashboards with 'Shiny'
Description: Create dashboards with 'Shiny'. This package provides
a theme on top of 'Shiny', making it easy to create attractive dashboards.
Author: Winston Chang [aut, cre],
RStudio [cph],
Almasaeed Studio [ctb, cph] (AdminLTE theme for Bootstrap),
Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinydashboard versions 0.5.0 dated 2015-06-16 and 0.5.1 dated 2015-09-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 18 +++++++++++++++++- R/dashboardSidebar.R | 4 ++++ R/deps.R | 2 +- R/tabs.R | 2 ++ R/utils.R | 8 ++++++++ inst/shinydashboard.css | 25 +++++++++++++------------ 8 files changed, 56 insertions(+), 25 deletions(-)
More information about shinydashboard at CRAN
Permanent link
Title: Adaptive Builder for Formatted Strings
Description: Provides a set of functions to facilitate building formatted strings
under various replacement rules: C-style formatting, variable-based formatting,
and number-based formatting. C-style formatting is basically identical to built-in
function 'sprintf'. Variable-based formatting allows users to put variable names
in a formatted string which will be replaced by variable values. Number-based
formatting allows users to use index numbers to represent the corresponding
argument value to appear in the string.
Author: Kun Ren <ken@renkun.me>
Maintainer: Kun Ren <ken@renkun.me>
Diff between rprintf versions 0.1-2 dated 2014-08-15 and 0.2.1 dated 2015-09-09
rprintf-0.1-2/rprintf/inst |only rprintf-0.2.1/rprintf/DESCRIPTION | 22 ++++---- rprintf-0.2.1/rprintf/MD5 | 30 +++++----- rprintf-0.2.1/rprintf/NAMESPACE | 4 + rprintf-0.2.1/rprintf/NEWS | 4 + rprintf-0.2.1/rprintf/R/internal.R | 23 ++++---- rprintf-0.2.1/rprintf/R/rprintf.R | 55 +++++++++----------- rprintf-0.2.1/rprintf/R/rprintn.R | 36 ++++++++----- rprintf-0.2.1/rprintf/R/rprintv.R | 35 ++++++++---- rprintf-0.2.1/rprintf/README.md | 6 +- rprintf-0.2.1/rprintf/man/rprintf.Rd | 43 ++++++++------- rprintf-0.2.1/rprintf/man/rprintn.Rd | 13 ++-- rprintf-0.2.1/rprintf/man/rprintv.Rd | 11 ++-- rprintf-0.2.1/rprintf/tests/testthat/test-rprintf.R | 18 +++--- rprintf-0.2.1/rprintf/tests/testthat/test-rprintn.R | 26 ++++----- rprintf-0.2.1/rprintf/tests/testthat/test-rprintv.R | 24 ++++---- 16 files changed, 190 insertions(+), 160 deletions(-)
Title: A Toolbox for Non-Tabular Data Manipulation
Description: Provides a set of functions for data manipulation with
list objects, including mapping, filtering, grouping, sorting,
updating, searching, and other useful functions. Most functions
are designed to be pipeline friendly so that data processing with
lists can be chained.
Author: Kun Ren <ken@renkun.me>
Maintainer: Kun Ren <ken@renkun.me>
Diff between rlist versions 0.4.2.3 dated 2015-07-09 and 0.4.5.1 dated 2015-09-09
DESCRIPTION | 8 +++---- MD5 | 40 +++++++++++++++++------------------ NEWS | 5 +++- R/internal.R | 48 +++++++++++++++++++------------------------ R/lambda.R | 9 ++++---- R/list.all.R | 14 +++++++----- R/list.clean.R | 2 - R/list.count.R | 3 -- R/list.first.R | 14 ++++-------- R/list.flatten.R | 20 +++++++++++++---- R/list.map.R | 10 ++++---- R/list.order.R | 3 -- R/list.search.R | 12 ++++------ R/list.skip.R | 4 +-- R/list.take.R | 4 +-- R/utils.R | 10 +++----- README.md | 5 +++- man/list.clean.Rd | 2 - man/list.flatten.Rd | 16 +++++++++++++- tests/testthat/test-basic.R | 19 ++++++++++++++++- tests/testthat/test-search.R | 2 + 21 files changed, 144 insertions(+), 106 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to http://www.fishbase.org, re-written based on an accompanying 'RESTful' API.
Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more.
This package also supports experimental access to http://www.sealifebase.org data, which contains nearly
200,000 species records for all types of aquatic life not covered by 'FishBase.'
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Duncan Temple Lang [aut],
Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@ropensci.org>
Diff between rfishbase versions 2.0.2 dated 2015-09-01 and 2.0.3 dated 2015-09-09
DESCRIPTION | 6 +- MD5 | 92 +++++++++++++++++++------------------- NEWS | 6 ++ R/common_names.R | 6 +- R/distribution.R | 12 ++-- R/docs.R | 2 R/morpho_physio.R | 10 ++-- R/population_dynamics.R | 10 ++-- R/reproduction.R | 8 +-- R/species.R | 2 R/species_list.R | 2 R/synonyms.R | 2 R/trophic_ecology.R | 12 ++-- man/common_names.Rd | 2 man/common_to_sci.Rd | 2 man/diet.Rd | 2 man/distribution.Rd | 2 man/docs.Rd | 2 man/ecology.Rd | 2 man/ecosystem.Rd | 2 man/faoareas.Rd | 2 man/fecundity.Rd | 2 man/fooditems.Rd | 2 man/introductions.Rd | 2 man/length_freq.Rd | 2 man/length_length.Rd | 2 man/length_weight.Rd | 2 man/maturity.Rd | 2 man/morphology.Rd | 2 man/morphometrics.Rd | 2 man/occurrence.Rd | 2 man/oxygen.Rd | 2 man/popchar.Rd | 2 man/popgrowth.Rd | 2 man/popqb.Rd | 2 man/predators.Rd | 2 man/ration.Rd | 2 man/reproduction.Rd | 2 man/sci_to_common.Rd | 2 man/spawning.Rd | 2 man/species.Rd | 2 man/species_list.Rd | 2 man/speed.Rd | 2 man/stocks.Rd | 2 man/swimming.Rd | 2 man/synonyms.Rd | 2 tests/testthat/helper_rfishbase.R | 18 +++---- 47 files changed, 129 insertions(+), 125 deletions(-)
Title: Quantile Regression Forests
Description: Quantile Regression Forests is a tree-based ensemble
method for estimation of conditional quantiles. It is
particularly well suited for high-dimensional data. Predictor
variables of mixed classes can be handled. The package is
dependent on the package randomForests, written by Andy Liaw.
Author: Nicolai Meinshausen, Lukas Schiesser
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between quantregForest versions 1.0 dated 2015-06-03 and 1.1 dated 2015-09-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/quantregForest.pdf |binary src/findweightsinbagfast.c | 8 ++++---- src/findweightsinbagfastimp.c | 8 ++++---- 6 files changed, 17 insertions(+), 17 deletions(-)
More information about quantregForest at CRAN
Permanent link
Title: Parametric Network Enrichment Analysis
Description: Collection of functions for Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Diff between pnea versions 1.0.1 dated 2015-08-29 and 1.1.0 dated 2015-09-09
pnea-1.0.1/pnea/man/plot.pneac.Rd |only pnea-1.0.1/pnea/man/print.pneac.Rd |only pnea-1.0.1/pnea/man/summary.pneac.Rd |only pnea-1.1.0/pnea/DESCRIPTION | 10 +- pnea-1.1.0/pnea/MD5 | 21 ++-- pnea-1.1.0/pnea/NAMESPACE | 6 - pnea-1.1.0/pnea/R/pnea.R | 149 ++++++++++++++++++++++------------- pnea-1.1.0/pnea/build/partial.rdb |binary pnea-1.1.0/pnea/data |only pnea-1.1.0/pnea/man/plot.pnea.Rd |only pnea-1.1.0/pnea/man/pnea-package.Rd | 4 pnea-1.1.0/pnea/man/pnea.Rd | 72 ++++++++++++---- pnea-1.1.0/pnea/man/print.pnea.Rd |only pnea-1.1.0/pnea/man/summary.pnea.Rd |only pnea-1.1.0/pnea/man/yeast.Rd |only 15 files changed, 169 insertions(+), 93 deletions(-)
Title: Fast Spatial Ancestry via Flexible Allele Frequency Surfaces
Description: Used primarily for estimates of allele frequency surfaces from point estimates.
It can also place individuals of unknown origin back onto the geographic map with great accuracy.
Additionally, it can place admixed individuals by estimating contributing fractions at each
location on a map. Lastly, it can rank SNPs by their ability to differentiate populations.
See "Fast Spatial Ancestry via Flexible Allele Frequency Surfaces" (John Michael Ranola, John
Novembre, Kenneth Lange) in Bioinformatics 2014 for more info.
Author: John Michael O Ranola, John Novembre, and Kenneth Lange
Maintainer: John Michael O. Ranola <ranolaj@uw.edu>
Diff between OriGen versions 1.3 dated 2015-08-28 and 1.3.1 dated 2015-09-09
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- man/FitAdmixedModelFindUnknowns.Rd | 2 ++ man/OriGen-package.Rd | 23 +++++++++++++++-------- man/PlotAdmixedSurface.Rd | 2 ++ src/OriGen.f90 | 10 +++++----- 6 files changed, 34 insertions(+), 23 deletions(-)
Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh (2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller (2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al. (2008, <doi:10.1214/07-AOS517>); Jiang et al. (2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre],
Samuel Mueller [aut],
Alan Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>
Diff between mplot versions 0.6.2 dated 2015-06-10 and 0.7.1 dated 2015-09-09
DESCRIPTION | 14 - MD5 | 36 ++-- NAMESPACE | 2 NEWS | 22 ++ R/Qm.R | 8 R/af.R | 204 ++++++++++++------------- R/bglmnet.R | 245 +++++++++++++++--------------- R/glmfence.R | 30 +-- R/lmfence.R | 34 ++-- R/mplot-package.R | 145 ++++++++--------- R/mplot.R | 121 +++++++------- R/qrange.R | 30 +-- R/vis.R | 423 ++++++++++++++++++++++++++-------------------------- README.md | 43 ++++- inst/CITATION | 26 ++- man/bglmnet.Rd |only man/plot.af.Rd | 6 man/plot.bglmnet.Rd |only man/plot.vis.Rd | 4 man/vis.Rd | 9 - 20 files changed, 746 insertions(+), 656 deletions(-)
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and use the utility
methods to traverse the tree in various orders. Aggregate, cumulate, print, convert to and from data.frame,
and apply functions to your tree data. Useful for decision trees, machine learning, finance, conversion
from and to JSON, and many other applications.
Author: Christoph Glur
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between data.tree versions 0.2.0-3 dated 2015-09-07 and 0.2.1 dated 2015-09-09
data.tree-0.2.0-3/data.tree/inst/extdata/useR15.yaml |only data.tree-0.2.1/data.tree/DESCRIPTION | 12 data.tree-0.2.1/data.tree/MD5 | 178 data.tree-0.2.1/data.tree/NAMESPACE | 104 data.tree-0.2.1/data.tree/NEWS | 154 data.tree-0.2.1/data.tree/R/data.tree.R | 194 data.tree-0.2.1/data.tree/R/data_doc.R | 72 data.tree-0.2.1/data.tree/R/node.R | 694 +- data.tree-0.2.1/data.tree/R/node_actives.R | 152 data.tree-0.2.1/data.tree/R/node_conversion.R | 142 data.tree-0.2.1/data.tree/R/node_conversion_ape.R | 260 data.tree-0.2.1/data.tree/R/node_conversion_dataframe.R | 670 +- data.tree-0.2.1/data.tree/R/node_conversion_dendrogram.R | 258 data.tree-0.2.1/data.tree/R/node_conversion_igraph.R | 82 data.tree-0.2.1/data.tree/R/node_conversion_list.R | 408 - data.tree-0.2.1/data.tree/R/node_methods.R | 932 +-- data.tree-0.2.1/data.tree/R/node_methods_sideeffect.R | 228 data.tree-0.2.1/data.tree/R/node_methods_traversal.R | 460 - data.tree-0.2.1/data.tree/R/util.R | 410 - data.tree-0.2.1/data.tree/README.md | 58 data.tree-0.2.1/data.tree/build/vignette.rds |binary data.tree-0.2.1/data.tree/data/acme.rda |binary data.tree-0.2.1/data.tree/data/mushroom.rda |binary data.tree-0.2.1/data.tree/inst/doc/applications.R | 1542 ++--- data.tree-0.2.1/data.tree/inst/doc/applications.Rmd | 2566 ++++----- data.tree-0.2.1/data.tree/inst/doc/applications.html | 2677 ++++------ data.tree-0.2.1/data.tree/inst/doc/data.tree.R | 819 +-- data.tree-0.2.1/data.tree/inst/doc/data.tree.Rmd | 1850 +++--- data.tree-0.2.1/data.tree/inst/doc/data.tree.html | 2359 ++++---- data.tree-0.2.1/data.tree/inst/extdata/flare.json |only data.tree-0.2.1/data.tree/inst/extdata/jennylind.yaml | 60 data.tree-0.2.1/data.tree/inst/extdata/portfolio.csv | 58 data.tree-0.2.1/data.tree/inst/extdata/useR15.csv | 254 data.tree-0.2.1/data.tree/man/Aggregate.Rd | 126 data.tree-0.2.1/data.tree/man/AreNamesUnique.Rd | 54 data.tree-0.2.1/data.tree/man/Climb.Rd | 78 data.tree-0.2.1/data.tree/man/ClimbByAttribute.Rd | 68 data.tree-0.2.1/data.tree/man/Clone.Rd | 66 data.tree-0.2.1/data.tree/man/CreateRandomTree.Rd | 38 data.tree-0.2.1/data.tree/man/CreateRegularTree.Rd | 38 data.tree-0.2.1/data.tree/man/Cumulate.Rd | 72 data.tree-0.2.1/data.tree/man/DefaultPlotHeight.Rd | 50 data.tree-0.2.1/data.tree/man/Do.Rd | 40 data.tree-0.2.1/data.tree/man/FormatFixedDecimal.Rd | 48 data.tree-0.2.1/data.tree/man/FormatPercent.Rd | 62 data.tree-0.2.1/data.tree/man/Get.Rd | 128 data.tree-0.2.1/data.tree/man/GetAttribute.Rd | 70 data.tree-0.2.1/data.tree/man/GetPhyloNr.Rd | 68 data.tree-0.2.1/data.tree/man/NODE_RESERVED_NAMES_CONST.Rd | 36 data.tree-0.2.1/data.tree/man/Node.Rd | 148 data.tree-0.2.1/data.tree/man/Prune.Rd | 56 data.tree-0.2.1/data.tree/man/Revert.Rd | 50 data.tree-0.2.1/data.tree/man/Set.Rd | 76 data.tree-0.2.1/data.tree/man/SetFormat.Rd | 80 data.tree-0.2.1/data.tree/man/Sort.Rd | 86 data.tree-0.2.1/data.tree/man/ToNewick.Rd | 62 data.tree-0.2.1/data.tree/man/Traverse.Rd | 54 data.tree-0.2.1/data.tree/man/acme.Rd | 42 data.tree-0.2.1/data.tree/man/as.Node.Rd | 52 data.tree-0.2.1/data.tree/man/as.Node.data.frame.Rd | 180 data.tree-0.2.1/data.tree/man/as.Node.dendrogram.Rd | 84 data.tree-0.2.1/data.tree/man/as.Node.list.Rd | 180 data.tree-0.2.1/data.tree/man/as.Node.phylo.Rd | 86 data.tree-0.2.1/data.tree/man/as.data.frame.Node.Rd | 164 data.tree-0.2.1/data.tree/man/as.dendrogram.Node.Rd | 84 data.tree-0.2.1/data.tree/man/as.igraph.Node.Rd | 82 data.tree-0.2.1/data.tree/man/as.list.Node.Rd | 96 data.tree-0.2.1/data.tree/man/as.phylo.Node.Rd | 58 data.tree-0.2.1/data.tree/man/averageBranchingFactor.Rd | 30 data.tree-0.2.1/data.tree/man/data.tree.Rd | 228 data.tree-0.2.1/data.tree/man/isLeaf.Rd | 36 data.tree-0.2.1/data.tree/man/isNotLeaf.Rd | 36 data.tree-0.2.1/data.tree/man/isNotRoot.Rd | 36 data.tree-0.2.1/data.tree/man/isRoot.Rd | 36 data.tree-0.2.1/data.tree/man/mushroom.Rd | 50 data.tree-0.2.1/data.tree/man/print.Node.Rd | 68 data.tree-0.2.1/data.tree/tests/testthat.R | 6 data.tree-0.2.1/data.tree/tests/testthat/test-treeConstruction.R | 118 data.tree-0.2.1/data.tree/tests/testthat/test-treeConversion.R | 272 - data.tree-0.2.1/data.tree/tests/testthat/test-treeConversionApe.R | 202 data.tree-0.2.1/data.tree/tests/testthat/test-treeConversionDataFrame.R | 260 data.tree-0.2.1/data.tree/tests/testthat/test-treeConversionDendrogram.R | 40 data.tree-0.2.1/data.tree/tests/testthat/test-treeConversionigraph.R | 44 data.tree-0.2.1/data.tree/tests/testthat/test-treeDocu.R | 10 data.tree-0.2.1/data.tree/tests/testthat/test-treeMethods.R | 1270 ++-- data.tree-0.2.1/data.tree/tests/testthat/test-treeMethodsSideEffect.R | 114 data.tree-0.2.1/data.tree/tests/testthat/test-util.R | 88 data.tree-0.2.1/data.tree/vignettes/applications.Rmd | 2566 ++++----- data.tree-0.2.1/data.tree/vignettes/applications.banner.html | 28 data.tree-0.2.1/data.tree/vignettes/data.tree.Rmd | 1850 +++--- data.tree-0.2.1/data.tree/vignettes/intro.banner.html | 32 91 files changed, 13922 insertions(+), 13913 deletions(-)
Title: Change Point Regression
Description: Change point regression models are also called two-phase regression, break-point regression, split-point regression structural change models and threshold regression models. Hypothesis testing in change point logistic regression with or without interaction terms. Several options are provided for testing in models with interaction, including a maximum of likelihood ratios test that determines p-value through Monte Carlo. Estimation under change point model is also included, but less developed at this point.
Author: Youyi Fong
Maintainer: Youyi Fong <yfong@fhcrc.org>
Diff between chngpt versions 2014.12-2 dated 2014-12-05 and 2015.9-5 dated 2015-09-09
chngpt-2014.12-2/chngpt/R/sim.sigmoid.R |only chngpt-2014.12-2/chngpt/man/sim.sigmoid.Rd |only chngpt-2015.9-5/chngpt/ChangeLog | 6 chngpt-2015.9-5/chngpt/DESCRIPTION | 12 chngpt-2015.9-5/chngpt/MD5 | 25 chngpt-2015.9-5/chngpt/NAMESPACE | 18 chngpt-2015.9-5/chngpt/R/chngpt.test.2.R |only chngpt-2015.9-5/chngpt/R/chngpt.test.R | 512 ++++---------- chngpt-2015.9-5/chngpt/R/chngptm.R | 371 ++++++---- chngpt-2015.9-5/chngpt/R/sim.chngpt.R |only chngpt-2015.9-5/chngpt/inst/unitTests/runit.chngpt.test.R | 68 + chngpt-2015.9-5/chngpt/inst/unitTests/runit.chngptm.R | 81 +- chngpt-2015.9-5/chngpt/man/chngpt.Rd | 2 chngpt-2015.9-5/chngpt/man/chngpt.test.Rd | 40 - chngpt-2015.9-5/chngpt/man/chngptm.Rd | 55 + chngpt-2015.9-5/chngpt/man/sim.chngpt.Rd |only 16 files changed, 615 insertions(+), 575 deletions(-)
Title: High Dimensional Factor Analysis and Confounder Adjusted Testing
and Estimation
Description: Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing.
Author: Jingshu Wang [aut],
Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@stanford.edu>
Diff between cate versions 1.0.2 dated 2015-09-08 and 1.0.3 dated 2015-09-09
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/cate-vignette.R | 3 +-- inst/doc/cate-vignette.Rnw | 25 ++++++++++++++++++++++--- inst/doc/cate-vignette.pdf |binary vignettes/cate-vignette.Rnw | 25 ++++++++++++++++++++++--- 7 files changed, 56 insertions(+), 19 deletions(-)