Title: High-Speed Processing of VCF, FASTA and Alignment Data
Description: Provides very fast access to whole genome, population scale variation data
from VCF files and sequence data from FASTA-formatted files.
It also reads in alignments from FASTA, Phylip, MAF and other file formats.
Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data
from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
Author: Ulrich Wittelsbuerger [aut, cre], Heng Li [ctb], Bob Handsaker [ctb]
Maintainer: Ulrich Wittelsbuerger <ulrich.wittelsbuerger@uni-duesseldorf.de>
Diff between WhopGenome versions 0.9.2 dated 2015-02-20 and 0.9.3 dated 2015-09-08
DESCRIPTION | 15 ++++++--------- MD5 | 8 ++++---- NAMESPACE | 3 +++ src/Makevars | 15 ++++++++++++++- src/tabix/razf.c | 2 +- 5 files changed, 28 insertions(+), 15 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Lei Huang [aut, cre],
Fabian Scheipl [aut],
Jeff Goldsmith [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip Reiss [aut],
Yakuan Chen [ctb],
Sonja Greven [ctb],
Lan Huo [ctb],
Madan Gopal Kundu [ctb],
Julia Wrobel [ctb]
Maintainer: Lei Huang <huangracer@gmail.com>
Diff between refund versions 0.1-12 dated 2015-08-06 and 0.1-13 dated 2015-09-08
DESCRIPTION |only MD5 |only NAMESPACE | 7 ++++++- R |only data/DTI.RData |only data/DTI2.RData |only data/PEER.Sim.RData |binary data/Q.RData |only data/datalist |only data/sofa.RData |only man |only 11 files changed, 6 insertions(+), 1 deletion(-)
Title: Tools for Survey Statistics in Educational Assessment
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply imputed datasets and
nested multiply imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE [aut], Alexander Robitzsch [ctb,cre],
Konrad Oberwimmer [ctb]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between BIFIEsurvey versions 1.3-0 dated 2015-07-10 and 1.4-0 dated 2015-09-08
DESCRIPTION | 12 ++-- MD5 | 56 +++++++++--------- R/BIFIE.by.R | 26 +++++++- R/BIFIE.correl.R | 36 ++++++++++-- R/BIFIE.crosstab.R | 32 ++++++++++ R/BIFIE.data.jack.R | 7 +- R/BIFIE.ecdf.R | 29 ++++++++- R/BIFIE.freq.R | 39 ++++++++++--- R/BIFIE.hist.R | 21 ++++++- R/BIFIE.linreg.R | 26 ++++++++ R/BIFIE.logistreg.R | 24 +++++++- R/BIFIE.pathmodel.R | 33 +++++++++-- R/BIFIE.twolevelreg.R | 2 R/BIFIE.univar.R | 107 ++++++++++++++++++++++++++++++------ R/BIFIE_NMI_inference_parameters.R | 9 ++- R/BIFIE_multiple_groupings_helper.R |only R/BIFIE_table_multiple_groupings.R |only inst/NEWS | 23 +++++++ man/BIFIE.by.Rd | 2 man/BIFIE.correl.Rd | 4 - man/BIFIE.crosstab.Rd | 2 man/BIFIE.freq.Rd | 7 ++ man/BIFIE.hist.Rd | 6 +- man/BIFIE.linreg.Rd | 4 - man/BIFIE.logistreg.Rd | 4 - man/BIFIE.pathmodel.Rd | 9 ++- man/BIFIE.univar.Rd | 6 +- man/BIFIEsurvey-package.Rd | 5 + man/bifietable.Rd | 7 +- man/save.BIFIEdata.Rd | 18 +++--- 30 files changed, 449 insertions(+), 107 deletions(-)
Title: Anonymize Data Containing Personally Identifiable Information
Description: Allows users to quickly and easily anonymize data containing
Personally Identifiable Information (PII) through convenience functions.
Author: Paul Hendricks [aut, cre]
Maintainer: Paul Hendricks <paul.hendricks.2013@owu.edu>
Diff between anonymizer versions 0.1.0 dated 2015-08-25 and 0.2.0 dated 2015-09-08
DESCRIPTION | 6 +- MD5 | 28 +++++---- NAMESPACE | 2 R/anonymize.R | 23 +++++--- R/anonymizer.R | 3 - R/hash.R |only R/salt.R | 24 +++++++- R/unsalt.R |only README.md | 114 +++++++++++++++++++++------------------- man/anonymize.Rd | 23 ++++++-- man/anonymizer.Rd | 3 - man/hash.Rd |only man/salt.Rd | 23 +++++++- man/unsalt.Rd |only tests/testthat/test-anonymize.R | 3 - tests/testthat/test-hash.R |only tests/testthat/test-salt.R | 5 + tests/testthat/test-unsalt.R |only 18 files changed, 163 insertions(+), 94 deletions(-)
Title: Simulates Correlated Multinomial Responses
Description: Simulates correlated multinomial responses by utilizing threshold approaches under a cumulative link model, a continuation ratio model or a baseline-category logit marginal model specification.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between SimCorMultRes versions 1.3.0 dated 2015-01-08 and 1.3.1 dated 2015-09-08
DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ NAMESPACE | 3 ++- build/vignette.rds |binary inst/NEWS | 4 ++++ inst/doc/SCMRvin.pdf |binary man/SimCorMultRes-package.Rd | 4 ++-- 7 files changed, 21 insertions(+), 15 deletions(-)
Title: Shrinkage Covariance Matrix Estimators
Description: Provides nonparametric Steinian shrinkage estimators of the covariance matrix that are suitable in high dimensional settings, that is when the number of variables is larger than the sample size.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between ShrinkCovMat versions 1.1.0 dated 2015-01-08 and 1.1.1 dated 2015-09-08
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/NEWS | 3 +++ man/ShrinkCovMat-package.Rd | 2 +- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: GEE Solver for Correlated Nominal or Ordinal Multinomial
Responses
Description: GEE solver for correlated nominal or ordinal multinomial responses using a local odds ratios parameterization.
Author: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between multgee versions 1.5.1 dated 2015-03-11 and 1.5.2 dated 2015-09-08
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 3 ++- build/vignette.rds |binary inst/NEWS | 4 ++++ inst/doc/multgee.Rnw | 10 +++++----- inst/doc/multgee.pdf |binary man/multgee-package.Rd | 2 +- vignettes/multgee.Rnw | 10 +++++----- 9 files changed, 32 insertions(+), 26 deletions(-)
Title: Regression Models with Breakpoints/Changepoints Estimation
Description: Given a regression model, segmented `updates' the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 0.5-1.1 dated 2015-02-18 and 0.5-1.2 dated 2015-09-08
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 13 +++++++++++++ NEWS | 8 ++++++++ R/broken.line.r | 1 + R/lines.segmented.R | 2 +- R/segmented.Arima.r | 13 ++++++++++--- R/segmented.default.r | 14 +++++++++++--- R/segmented.glm.R | 12 +++++++++--- R/segmented.lm.R | 15 +++++++++++---- R/slope.R | 2 +- data/down.rda |binary data/plant.rda |binary data/stagnant.rda |binary man/segmented-package.Rd | 4 ++-- man/segmented.Rd | 9 +++++---- 16 files changed, 91 insertions(+), 40 deletions(-)
Title: Static R Code Analysis
Description: Checks adherence to a given style, syntax errors and possible
semantic issues. Supports on the fly checking of R code edited with Emacs,
Vim and Sublime Text.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between lintr versions 0.3.1 dated 2015-09-03 and 0.3.2 dated 2015-09-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/spaces_left_parentheses_linter.R | 3 ++- README.md | 1 + tests/testthat/test-methods.R | 8 ++++---- tests/testthat/test-spaces_left_parentheses_linter.R | 10 ++++++++++ 6 files changed, 25 insertions(+), 13 deletions(-)
Title: Analyze and Gaussianize Heavy-Tailed, Skewed Data
Description: Lambert W x F distributions are a generalized framework to analyze
skewed, heavy-tailed data. They are based on an input/output system, where
the input random variable (RV) X ~ F, and the output Y is a non-linearly
transformed version of X with similar properties, but slightly skewed and/or
heavy-tailed. This transformed RV Y has a Lambert W x F distribution.
This package contains functions to model and analyze skewed, heavy-tailed
data the Lambert Way: simulate random samples, estimate parameters, compute
quantiles, and plot/print results nicely. Probably the most important
function is 'Gaussianize', which works similarly to 'scale', but actually
makes the data Gaussian. A do-it-yourself toolkit allows users to define
their own Lambert W x 'MyFavoriteDistribution' and use it in their analysis
right away.
Author: Georg M. Goerg <im@gmge.org>
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between LambertW versions 0.5.1 dated 2015-04-28 and 0.6.0 dated 2015-09-08
LambertW-0.5.1/LambertW/R/H.R |only LambertW-0.5.1/LambertW/man/H.Rd |only LambertW-0.6.0/LambertW/DESCRIPTION | 12 - LambertW-0.6.0/LambertW/MD5 | 135 ++++++++++--------- LambertW-0.6.0/LambertW/NAMESPACE | 11 + LambertW-0.6.0/LambertW/NEWS | 61 ++++++++ LambertW-0.6.0/LambertW/R/0_LambertW-utils.R | 3 LambertW-0.6.0/LambertW/R/0_W.R | 90 +++++++----- LambertW-0.6.0/LambertW/R/0_loglik-LambertW-utils.R | 4 LambertW-0.6.0/LambertW/R/Gaussianize.R | 12 - LambertW-0.6.0/LambertW/R/IGMM.R | 28 ++- LambertW-0.6.0/LambertW/R/LambertW-package.R | 6 LambertW-0.6.0/LambertW/R/MLE_LambertW.R | 32 +++- LambertW-0.6.0/LambertW/R/check_beta.R | 4 LambertW-0.6.0/LambertW/R/create_LambertW_input.R | 24 ++- LambertW-0.6.0/LambertW/R/create_LambertW_output.R | 9 - LambertW-0.6.0/LambertW/R/dLambertW.R | 39 +++-- LambertW-0.6.0/LambertW/R/datasets.R | 1 LambertW-0.6.0/LambertW/R/delta_GMM.R | 41 +++++ LambertW-0.6.0/LambertW/R/delta_Taylor.R | 10 - LambertW-0.6.0/LambertW/R/deprecated_functions.R | 11 + LambertW-0.6.0/LambertW/R/deriv_W.R | 43 +++++- LambertW-0.6.0/LambertW/R/deriv_W_gamma.R | 3 LambertW-0.6.0/LambertW/R/estimate_beta.R | 8 - LambertW-0.6.0/LambertW/R/gamma_GMM.R | 6 LambertW-0.6.0/LambertW/R/gamma_Taylor.R | 5 LambertW-0.6.0/LambertW/R/get_distname_family.R | 15 +- LambertW-0.6.0/LambertW/R/get_gamma_bounds.R | 2 LambertW-0.6.0/LambertW/R/get_initial_tau.R | 3 LambertW-0.6.0/LambertW/R/get_initial_theta.R | 7 LambertW-0.6.0/LambertW/R/get_input.R | 5 LambertW-0.6.0/LambertW/R/get_output.R | 21 +- LambertW-0.6.0/LambertW/R/get_support.R | 46 ++++-- LambertW-0.6.0/LambertW/R/log_W.R | 8 - LambertW-0.6.0/LambertW/R/loglik_LambertW.R | 14 - LambertW-0.6.0/LambertW/R/loglik_penalty.R | 18 +- LambertW-0.6.0/LambertW/R/lp_norm.R | 5 LambertW-0.6.0/LambertW/R/normalize_by_tau.R |only LambertW-0.6.0/LambertW/R/pLambertW.R | 59 ++++---- LambertW-0.6.0/LambertW/R/p_m1.R | 1 LambertW-0.6.0/LambertW/R/plot.LambertW_fit.R | 60 ++++---- LambertW-0.6.0/LambertW/R/private_functions.R |only LambertW-0.6.0/LambertW/R/qLambertW.R | 121 ++++++++--------- LambertW-0.6.0/LambertW/R/rLambertW.R | 5 LambertW-0.6.0/LambertW/R/summary.LambertW_fit.R | 11 - LambertW-0.6.0/LambertW/R/test_normality.R | 14 - LambertW-0.6.0/LambertW/R/test_symmetry.R | 28 ++- LambertW-0.6.0/LambertW/R/xexp.R |only LambertW-0.6.0/LambertW/man/Gaussianize.Rd | 9 - LambertW-0.6.0/LambertW/man/LambertW-package.Rd | 2 LambertW-0.6.0/LambertW/man/LambertW-toolkit.Rd | 11 + LambertW-0.6.0/LambertW/man/LambertW-utils.Rd | 13 + LambertW-0.6.0/LambertW/man/W.Rd | 42 ++--- LambertW-0.6.0/LambertW/man/delta_GMM.Rd | 2 LambertW-0.6.0/LambertW/man/deprecated-functions.Rd | 3 LambertW-0.6.0/LambertW/man/distname-utils.Rd | 9 - LambertW-0.6.0/LambertW/man/get_output.Rd | 8 - LambertW-0.6.0/LambertW/man/get_support.Rd | 10 + LambertW-0.6.0/LambertW/man/loglik-LambertW-utils.Rd | 11 - LambertW-0.6.0/LambertW/man/tau-utils.Rd | 19 ++ LambertW-0.6.0/LambertW/man/test_symmetry.Rd | 6 LambertW-0.6.0/LambertW/man/xexp.Rd |only LambertW-0.6.0/LambertW/tests |only 63 files changed, 733 insertions(+), 453 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon, Bruno Herault
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between entropart versions 1.3.2 dated 2015-09-05 and 1.3.3 dated 2015-09-08
DESCRIPTION | 8 ++++---- MD5 | 46 +++++++++++++++++++++++----------------------- NEWS | 4 ++-- R/Diversity.R | 2 +- R/Dqz.R | 2 +- R/Hqz.R | 2 +- R/HqzBeta.R | 2 +- R/Hurlbert.R | 2 +- R/HurlbertD.R | 2 +- R/PhyloBetaEntropy.R | 2 +- R/PhyloDiversity.R | 2 +- R/PhyloEntropy.R | 2 +- R/Rao.R | 2 +- R/Richness.R | 2 +- R/Shannon.R | 2 +- R/ShannonBeta.R | 2 +- R/Simpson.R | 2 +- R/SimpsonBeta.R | 2 +- R/SpeciesDistribution.R | 32 +++++++++++++++++++++++++++++--- R/Tsallis.R | 2 +- R/TsallisBeta.R | 2 +- R/rCommunity.R | 2 +- inst/doc/entropart.pdf |binary man/entropart-package.Rd | 4 ++-- 24 files changed, 78 insertions(+), 52 deletions(-)
Title: Evaluation of Modeling without Information Leakage
Description: A toolbox for designing and evaluating predictive models with
resampling methods. The aim of this package is to provide a simple and
efficient general framework for working with any type of prediction
problem, be it classification, regression or survival analysis, that is
easy to extend and adapt to your specific setting. Some commonly used
methods for classification, regression and survival analysis are included.
Author: Christofer Backlin [aut, cre],
Mats Gustafsson [aut]
Maintainer: Christofer Backlin <emil@christofer.backlin.se>
Diff between emil versions 2.1.1 dated 2015-07-09 and 2.2.2 dated 2015-09-08
DESCRIPTION | 16 - MD5 | 56 ++++-- NAMESPACE | 42 ++++ NEWS.md |only R/RcppExports.R |only R/RcppWrappers.r |only R/error-functions.r | 15 + R/helpers.r | 163 ++++++++++++++++++ R/imputation.r |only R/learning-curve.r | 8 R/modeling.r | 1 R/preprocessing.r | 328 ++++++++++++++------------------------ R/randomForest.r | 6 R/resampling.r | 33 +++ R/reshape-result.r | 51 +++-- R/roc-curve.r | 8 man/factor_to_logical.Rd |only man/has_na.Rd |only man/impute.Rd | 2 man/is_constant.Rd |only man/mode.Rd |only man/na_index.Rd | 11 + man/pipe.Rd |only man/pre_factor_to_logical.Rd |only man/pre_impute.Rd | 2 man/pre_impute_df.Rd |only man/pre_impute_knn.Rd | 2 man/pre_log_message.Rd |only man/pre_process.Rd | 9 - man/select.Rd | 4 man/trivial_error_rate.Rd |only man/validate_data.Rd |only src |only tests/testthat/test-cppfunction.r |only tests/testthat/test-helpers.r | 37 +++- tests/testthat/test-preprocess.r | 37 ++++ 36 files changed, 553 insertions(+), 278 deletions(-)
Title: Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach
Description: Compute the median ranking according the Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete.
Author: Antonio D'Ambrosio <antdambr@unina.it>, Sonia Amodio <sonia.amodio@unina.it>
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>
Diff between ConsRank versions 0.0.1 dated 2015-08-01 and 1.0.0 dated 2015-09-08
DESCRIPTION | 8 +-- MD5 | 25 +++++----- R/ALL.r | 116 +++++++++++++++++++++++++++++++++++++++++------- data/USAranks.rda |only man/BBFULL.Rd |only man/BBconsensus.Rd | 8 ++- man/BBconsensus2.Rd | 5 +- man/ConsRank-package.Rd | 11 ++-- man/EMCons.Rd | 4 + man/FASTcons.Rd | 7 ++ man/Penalty.Rd | 2 man/QuickCons.Rd | 7 ++ man/USAranks.Rd |only man/branches.Rd | 5 +- man/findbranches.Rd | 5 +- 15 files changed, 157 insertions(+), 46 deletions(-)
Title: Clustering of Variables Around Latent Variables
Description: Functions for the clustering of variables around Latent Variables. Each cluster of variables, which may be defined as a local or directional cluster, is associated with a latent variable.
External variables measured on the same observations or/and additional information on the variables can be taken into account.
Author: Evelyne Vigneau, Mingkun Chen
Maintainer: Evelyne Vigneau <evelyne.vigneau@oniris-nantes.fr>
Diff between ClustVarLV versions 1.4.0 dated 2015-06-02 and 1.4.1 dated 2015-09-08
ClustVarLV-1.4.0/ClustVarLV/R/descrip_gp.R |only ClustVarLV-1.4.0/ClustVarLV/R/summary_clv.R |only ClustVarLV-1.4.0/ClustVarLV/man/summary_clv.Rd |only ClustVarLV-1.4.1/ClustVarLV/DESCRIPTION | 8 +- ClustVarLV-1.4.1/ClustVarLV/MD5 | 27 ++++------ ClustVarLV-1.4.1/ClustVarLV/NAMESPACE | 5 + ClustVarLV-1.4.1/ClustVarLV/R/summary.clv.R |only ClustVarLV-1.4.1/ClustVarLV/build/vignette.rds |binary ClustVarLV-1.4.1/ClustVarLV/data/AUPA_psycho.rda |binary ClustVarLV-1.4.1/ClustVarLV/data/apples_sh.rda |binary ClustVarLV-1.4.1/ClustVarLV/data/authen_NMR.rda |binary ClustVarLV-1.4.1/ClustVarLV/inst/doc/Getting_started_with_ClustVarLV.R | 2 ClustVarLV-1.4.1/ClustVarLV/inst/doc/Getting_started_with_ClustVarLV.Rmd | 6 +- ClustVarLV-1.4.1/ClustVarLV/inst/doc/Getting_started_with_ClustVarLV.pdf |binary ClustVarLV-1.4.1/ClustVarLV/man/summary.clv.Rd |only ClustVarLV-1.4.1/ClustVarLV/vignettes/Getting_started_with_ClustVarLV.Rmd | 6 +- ClustVarLV-1.4.1/ClustVarLV/vignettes/Getting_started_with_ClustVarLV.html | 8 +- 17 files changed, 31 insertions(+), 31 deletions(-)
Title: Tools for Handling and Scrapping Instant Weather Forecast Feeds
Description: Handle instant weather forecasts and geographical information. It combines multiple sources of information to obtain instant weather forecasts.
Author: Stan Yip [aut, cre]
Maintainer: Stan Yip <stanyip101@gmail.com>
Diff between weatherr versions 0.1.1 dated 2015-08-26 and 0.1.2 dated 2015-09-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ggele.R | 2 +- man/ggele.Rd | 2 ++ man/locationforecast.Rd | 2 ++ man/weatherr-package.Rd | 4 ++-- 6 files changed, 16 insertions(+), 12 deletions(-)
Title: Patient Rule Induction Method (PRIM)
Description: Patient Rule Induction Method (PRIM) for bump hunting in high-dimensional data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between prim versions 1.0.15 dated 2014-11-04 and 1.0.16 dated 2015-09-08
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 11 ++++++++--- build/vignette.rds |binary inst/doc/prim-2d.pdf |binary inst/doc/prim-3d.pdf |binary 6 files changed, 19 insertions(+), 14 deletions(-)
Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Description: Calculate comorbidities, Charlson scores, perform fast and accurate
validation, conversion, manipulation, filtering and comparison of ICD-9-CM
(clinical modification) codes. ICD-9 codes appear numeric but leading and
trailing zeroes, and both decimal and non-decimal "short" format codes
exist. The package enables a work flow from raw lists of ICD-9 codes from
hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Any
other mapping of codes, such as ICD-10, to comorbidities can be used.
Author: Jack O. Wasey [aut, cre, cph],
William Murphy [ctb]
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between icd9 versions 1.2.1 dated 2015-09-04 and 1.2.2 dated 2015-09-08
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- configure.ac | 12 +++++++++++- inst/doc/introduction.html | 4 ++-- src/comorbid.cpp | 4 ++-- src/local.h | 4 ++-- src/util.cpp | 6 +++--- tools/r-base-ubsan-gcc |only tools/r-devel-ubsan-clang/Dockerfile | 3 +++ 9 files changed, 36 insertions(+), 21 deletions(-)
Title: Local Inferential Feature Significance for Multivariate Kernel
Density Estimation
Description: Local inferential feature significance for multivariate kernel density estimation.
Author: Tarn Duong <tarn.duong@gmail.com> & Matt Wand <Matt.Wand@uts.edu.au>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between feature versions 1.2.11 dated 2014-11-04 and 1.2.12 dated 2015-09-08
DESCRIPTION | 15 ++++++++------- MD5 | 12 ++++++------ NAMESPACE | 16 +++++++--------- build/vignette.rds |binary data/earthquake.RData |binary inst/doc/feature.pdf |binary man/SiZer.Rd | 2 +- 7 files changed, 22 insertions(+), 23 deletions(-)
Title: Composite Indicators Functions
Description: Contains several functions to enhance approaches to the Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps.
Author: Francesco Vidoli, Elisa Fusco
Maintainer: Francesco Vidoli <fvidoli@gmail.com>
Diff between Compind versions 1.0 dated 2014-09-24 and 1.1 dated 2015-09-08
DESCRIPTION | 16 ++++++---------- MD5 | 21 ++++++++++++--------- NAMESPACE | 1 + R/ci_bod.R | 8 ++++++-- R/ci_factor.R | 27 +++++++++++++++++++-------- R/ci_mean_min.R |only man/ci_bod.Rd | 5 +++++ man/ci_factor.Rd | 9 +++++++-- man/ci_mean_min.Rd |only man/ci_mpi.Rd | 4 ++-- man/ci_rbod.Rd | 2 +- man/normalise_ci.Rd | 2 +- vignettes |only 13 files changed, 60 insertions(+), 35 deletions(-)
Title: Birnbaum-Saunders Model Based on Skew-Normal Distribution
Description: It provides the density, distribution function, quantile function, random number generator, reliability function, failure rate, likelihood function,
moments and EM algorithm for Maximum Likelihood estimators, also empirical quantile and generated envelope for a given sample, all this for the three parameter
Birnbaum-Saunders model based on Skew-Normal Distribution.
Additionally, it provides the random number generator for the mixture of Birnbaum-Saunders model based on Skew-Normal distribution.
Author: Rocio Paola Maehara <rmaeharaa@gmail.com> and Luis Benites Sanchez <lbenitesanchez@gmail.com>
Maintainer: Rocio Paola Maehara <rmaeharaa@gmail.com>
Diff between bssn versions 0.5 dated 2015-08-11 and 0.6 dated 2015-09-08
bssn-0.5/bssn/R/initial.R |only bssn-0.6/bssn/DESCRIPTION | 16 ++--- bssn-0.6/bssn/MD5 | 19 +++--- bssn-0.6/bssn/NAMESPACE | 4 + bssn-0.6/bssn/R/EMbssn.R | 7 +- bssn-0.6/bssn/R/algEMbssn.R | 81 +++++++++++++++++++-------- bssn-0.6/bssn/R/functions.R | 110 ++++++++++++++++++++------------------ bssn-0.6/bssn/man/EMbssn.Rd | 10 ++- bssn-0.6/bssn/man/bssn-package.Rd | 12 ++-- bssn-0.6/bssn/man/bssn.Rd | 38 ++++++++++--- bssn-0.6/bssn/man/momentsbssn.Rd | 2 11 files changed, 182 insertions(+), 117 deletions(-)
Title: Easily Tidy Data with `spread()` and `gather()` Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.2.0 dated 2014-12-05 and 0.3.0 dated 2015-09-08
DESCRIPTION | 27 MD5 | 98 +- NAMESPACE | 23 R/RcppExports.R |only R/complete.R |only R/expand.R | 80 +- R/extract.R | 36 - R/fill.R |only R/gather.R | 113 +++ R/nest.R |only R/replace_na.R |only R/separate.R | 87 +- R/spread.R | 23 R/unite.R | 2 R/unnest.R | 135 ++-- R/utils.R | 21 README.md | 4 build/vignette.rds |binary inst/doc/tidy-data.R | 6 inst/doc/tidy-data.Rmd | 22 inst/doc/tidy-data.html | 1077 +++++++++++++------------------- man/complete.Rd |only man/complete_.Rd |only man/expand.Rd | 62 + man/expand_.Rd | 3 man/extract.Rd | 13 man/extract_.Rd | 3 man/extract_numeric.Rd | 3 man/fill.Rd |only man/fill_.Rd |only man/gather.Rd | 19 man/gather_.Rd | 3 man/nest.Rd |only man/nest_.Rd |only man/pipe.Rd |only man/replace_na.Rd |only man/separate.Rd | 33 man/separate_.Rd | 22 man/seq_range.Rd | 3 man/spread.Rd | 10 man/spread_.Rd | 10 man/unite.Rd | 5 man/unite_.Rd | 3 man/unnest.Rd | 50 + man/unnest_.Rd | 7 src |only tests/testthat/test-complete.R |only tests/testthat/test-expand.R |only tests/testthat/test-extract.R | 13 tests/testthat/test-fill.R |only tests/testthat/test-gather.R | 92 ++ tests/testthat/test-matrixToDataFrame.R |only tests/testthat/test-nest.R |only tests/testthat/test-replace_na.R |only tests/testthat/test-separate.R | 54 + tests/testthat/test-spread.R | 20 tests/testthat/test-unite.R |only tests/testthat/test-unnest.R |only vignettes/tidy-data.Rmd | 22 59 files changed, 1270 insertions(+), 934 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Josh O'Brien [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.1-1 dated 2015-06-05 and 1.2-0 dated 2015-09-08
sp-1.1-1/sp/man/nowrapSpatialLines.Rd |only sp-1.2-0/sp/ChangeLog | 177 +++++++++++++++++++ sp-1.2-0/sp/DESCRIPTION | 17 + sp-1.2-0/sp/MD5 | 88 +++++---- sp-1.2-0/sp/NAMESPACE | 39 +++- sp-1.2-0/sp/R/Class-SpatialMultiPoints.R |only sp-1.2-0/sp/R/Class-SpatialMultiPointsDataFrame.R |only sp-1.2-0/sp/R/Class-SpatialPoints.R | 3 sp-1.2-0/sp/R/Spatial-methods.R | 41 +++- sp-1.2-0/sp/R/SpatialMultiPoints-methods.R |only sp-1.2-0/sp/R/SpatialMultiPointsDataFrame-methods.R |only sp-1.2-0/sp/R/SpatialPolygons-displayMethods.R | 4 sp-1.2-0/sp/R/aggregate.R | 28 +-- sp-1.2-0/sp/R/over.R | 24 ++ sp-1.2-0/sp/R/recenter.R | 100 ---------- sp-1.2-0/sp/R/spplot.R | 15 + sp-1.2-0/sp/build/vignette.rds |binary sp-1.2-0/sp/demo/00Index | 2 sp-1.2-0/sp/demo/depend.R | 8 sp-1.2-0/sp/demo/meuse.R | 2 sp-1.2-0/sp/demo/mp.R |only sp-1.2-0/sp/demo/webmap.R |only sp-1.2-0/sp/inst/ChangeLog | 177 +++++++++++++++++++ sp-1.2-0/sp/inst/NEWS.Rd |only sp-1.2-0/sp/inst/doc/csdacm.pdf |binary sp-1.2-0/sp/inst/doc/intro_sp.pdf |binary sp-1.2-0/sp/inst/doc/over.R | 83 ++++++++ sp-1.2-0/sp/inst/doc/over.Rnw | 115 ++++++++++++ sp-1.2-0/sp/inst/doc/over.pdf |binary sp-1.2-0/sp/inst/include/sp.h | 2 sp-1.2-0/sp/man/00sp.Rd | 2 sp-1.2-0/sp/man/CRS-class.Rd | 2 sp-1.2-0/sp/man/SpatialMultiPoints-class.Rd |only sp-1.2-0/sp/man/SpatialMultiPoints.Rd |only sp-1.2-0/sp/man/SpatialMultiPointsDataFrame-class.Rd |only sp-1.2-0/sp/man/SpatialPoints-class.Rd | 2 sp-1.2-0/sp/man/addattr.Rd | 1 sp-1.2-0/sp/man/aggregate.Rd | 8 sp-1.2-0/sp/man/coordinates-methods.Rd | 1 sp-1.2-0/sp/man/coordnames-methods.Rd | 2 sp-1.2-0/sp/man/geometry-methods.Rd | 2 sp-1.2-0/sp/man/over.Rd | 26 ++ sp-1.2-0/sp/man/spplot.Rd | 3 sp-1.2-0/sp/src/sp.h | 2 sp-1.2-0/sp/tests/fail1.Rout.save | 11 - sp-1.2-0/sp/tests/mp.R |only sp-1.2-0/sp/tests/mp.Rout.save |only sp-1.2-0/sp/tests/over.R |only sp-1.2-0/sp/tests/over.Rout.save | 57 +++--- sp-1.2-0/sp/tests/over2.R |only sp-1.2-0/sp/tests/over2.Rout.save |only sp-1.2-0/sp/tests/pass1.Rout.save | 57 ++---- sp-1.2-0/sp/vignettes/over.Rnw | 115 ++++++++++++ 53 files changed, 964 insertions(+), 252 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Joe Cheng [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.4-18 dated 2015-08-15 and 2.4-20 dated 2015-09-08
DESCRIPTION | 15 MD5 | 18 - R/cropSpatial.R | 2 R/shift.R | 7 build/vignette.rds |binary inst/doc/Raster.R | 732 ++++++++++++++++++++++++------------------------ inst/doc/Raster.pdf |binary inst/doc/functions.R | 686 ++++++++++++++++++++++---------------------- inst/doc/functions.pdf |binary inst/doc/rasterfile.pdf |binary 10 files changed, 728 insertions(+), 732 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 1.0.1 dated 2015-08-27 and 1.0.2 dated 2015-09-08
DESCRIPTION | 10 ++++++---- MD5 | 24 ++++++++++++++++-------- R/cate.R | 30 ++++++++++++++++-------------- R/datasets.R |only R/factor_functions.R | 28 ++++++++++++++-------------- build |only data |only inst |only man/EigenDiff.Rd | 4 ++-- man/cate.Rd | 8 ++++---- man/est.confounder.num.Rd | 32 ++++++++++++++++---------------- man/factor.analysis.Rd | 2 +- man/gender.sm.Rd |only man/wrapper.Rd | 2 +- vignettes |only 15 files changed, 76 insertions(+), 64 deletions(-)
Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such
as calculating spectral indices, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut],
Ned Horning [aut]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>
Diff between RStoolbox versions 0.1.0 dated 2015-09-05 and 0.1.1 dated 2015-09-08
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 4 ++++ README.md | 7 ++++++- src/classQA.cpp | 2 +- 5 files changed, 20 insertions(+), 11 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between PRIMsrc versions 0.5.8 dated 2015-08-29 and 0.5.9 dated 2015-09-08
PRIMsrc-0.5.8/PRIMsrc/inst/doc/Abstract_JCB2015.pdf |only PRIMsrc-0.5.8/PRIMsrc/inst/doc/PRIMsrc_0.5.8.pdf |only PRIMsrc-0.5.8/PRIMsrc/man/plot_scatter.Rd |only PRIMsrc-0.5.9/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.5.9/PRIMsrc/MD5 | 34 +- PRIMsrc-0.5.9/PRIMsrc/NAMESPACE | 28 - PRIMsrc-0.5.9/PRIMsrc/R/PRIMsrc.internal.r | 1 PRIMsrc-0.5.9/PRIMsrc/R/PRIMsrc.r | 339 ++++++++++---------- PRIMsrc-0.5.9/PRIMsrc/inst/CITATION | 214 ++++++------ PRIMsrc-0.5.9/PRIMsrc/inst/NEWS | 26 - PRIMsrc-0.5.9/PRIMsrc/inst/doc/Abstract.JCB2016.pdf |only PRIMsrc-0.5.9/PRIMsrc/inst/doc/PRIMsrc_0.5.9.pdf |only PRIMsrc-0.5.9/PRIMsrc/man/PrimSRC-package.Rd | 19 - PRIMsrc-0.5.9/PRIMsrc/man/plot.Rd |only PRIMsrc-0.5.9/PRIMsrc/man/plot_boxtrace.Rd | 2 PRIMsrc-0.5.9/PRIMsrc/man/plot_boxtraj.Rd | 2 PRIMsrc-0.5.9/PRIMsrc/man/plot_profile.Rd | 2 PRIMsrc-0.5.9/PRIMsrc/man/predict.Rd | 2 PRIMsrc-0.5.9/PRIMsrc/man/print.Rd | 2 PRIMsrc-0.5.9/PRIMsrc/man/sbh.Rd | 4 PRIMsrc-0.5.9/PRIMsrc/man/summary.Rd | 2 21 files changed, 352 insertions(+), 333 deletions(-)
Title: Gene Set Uncertainty in Enrichment Analysis
Description: Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets.
Author: Florian Schmid, Christoph Müssel, Johann M. Kraus, Hans A. Kestler
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>
Diff between GiANT versions 1.0 dated 2015-08-06 and 1.1 dated 2015-09-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/analysis.R | 2 +- R/hist.R | 4 ++-- build/vignette.rds |binary inst/doc/giant_package_vignette.pdf |binary man/parseGmt.Rd | 8 -------- 7 files changed, 13 insertions(+), 21 deletions(-)
Title: Create Dendrograms and Tree Diagrams Using 'ggplot2'
Description: This is a set of tools for dendrograms and
tree plots using 'ggplot2'. The 'ggplot2' philosophy is to
clearly separate data from the presentation.
Unfortunately the plot method for dendrograms plots
directly to a plot device without exposing the data.
The 'ggdendro' package resolves this by making available
functions that extract the dendrogram plot data. The package
provides implementations for tree, rpart, as well as diana and agnes
cluster diagrams.
Author: Andrie de Vries [aut, cre],
Brian D. Ripley [aut] (author of package tree)
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between ggdendro versions 0.1-15 dated 2014-09-29 and 0.1-17 dated 2015-09-08
ggdendro-0.1-15/ggdendro/man/dendro_data.dendrogram.Rd |only ggdendro-0.1-17/ggdendro/DESCRIPTION | 25 +- ggdendro-0.1-17/ggdendro/MD5 | 86 ++++--- ggdendro-0.1-17/ggdendro/NAMESPACE | 22 + ggdendro-0.1-17/ggdendro/NEWS | 19 + ggdendro-0.1-17/ggdendro/R/dendro_data.R | 23 - ggdendro-0.1-17/ggdendro/R/dendro_rpart.R | 20 - ggdendro-0.1-17/ggdendro/R/dendro_tree.R | 23 - ggdendro-0.1-17/ggdendro/R/dendrogram.R | 69 ++--- ggdendro-0.1-17/ggdendro/R/ggdendro-package.R | 31 +- ggdendro-0.1-17/ggdendro/R/ggdendrogram.R | 74 ++---- ggdendro-0.1-17/ggdendro/R/rpart.R | 14 - ggdendro-0.1-17/ggdendro/build/vignette.rds |binary ggdendro-0.1-17/ggdendro/inst/doc/ggdendro.R | 70 +++--- ggdendro-0.1-17/ggdendro/inst/doc/ggdendro.Rmd | 98 +++++--- ggdendro-0.1-17/ggdendro/inst/doc/ggdendro.html | 116 ++++++---- ggdendro-0.1-17/ggdendro/inst/examples |only ggdendro-0.1-17/ggdendro/man/as.dendro.Rd | 3 ggdendro-0.1-17/ggdendro/man/dendro_data.Rd | 103 ++++++++ ggdendro-0.1-17/ggdendro/man/dendro_data.rpart.Rd | 27 +- ggdendro-0.1-17/ggdendro/man/dendro_data.tree.Rd | 45 ++- ggdendro-0.1-17/ggdendro/man/dendrogram_data.Rd | 19 + ggdendro-0.1-17/ggdendro/man/get_data_tree_leaf_labels.Rd | 3 ggdendro-0.1-17/ggdendro/man/ggdendro-package.Rd | 24 +- ggdendro-0.1-17/ggdendro/man/ggdendrogram.Rd | 13 - ggdendro-0.1-17/ggdendro/man/is.dendro.Rd | 5 ggdendro-0.1-17/ggdendro/man/labels.rpart.Rd | 7 ggdendro-0.1-17/ggdendro/man/rpart_labels.Rd | 12 - ggdendro-0.1-17/ggdendro/man/rpart_segments.Rd | 7 ggdendro-0.1-17/ggdendro/man/rpartco.Rd | 3 ggdendro-0.1-17/ggdendro/man/segment.Rd | 3 ggdendro-0.1-17/ggdendro/man/theme_dendro.Rd | 3 ggdendro-0.1-17/ggdendro/man/tree_labels.Rd | 3 ggdendro-0.1-17/ggdendro/man/tree_segments.Rd | 3 ggdendro-0.1-17/ggdendro/man/treeco.Rd | 3 ggdendro-0.1-17/ggdendro/tests/testthat/Rplots.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots1.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots2.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots3.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots4.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots5.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots6.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/test-1-dendrogram.R | 100 -------- ggdendro-0.1-17/ggdendro/tests/testthat/test-2-hclust.R |only ggdendro-0.1-17/ggdendro/tests/testthat/test-3-rpart.R |only ggdendro-0.1-17/ggdendro/tests/testthat/test-3-tree.R |only ggdendro-0.1-17/ggdendro/tests/testthat/test-4-clusterplots.R |only ggdendro-0.1-17/ggdendro/tests/testthat/test-6-ggdendrogram.R |only ggdendro-0.1-17/ggdendro/vignettes/ggdendro.Rmd | 102 +++++--- 49 files changed, 655 insertions(+), 523 deletions(-)