Title: A Simple Approach to Scale Gene Expression Data Derived from
Different Platforms for Integrated Analyses
Description: Simple method for comparison of gene
expression generated across different experiments, and on
different platforms; that does not require global
renormalization, and is not restricted to comparison of
identical probes. YuGene works on a range of microarray dataset
distributions, such as between manufacturers. The resulting
output allows direct comparisons of gene expression between
experiments and experimental platforms.
Author: Kim-Anh Le Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A. Wells
Maintainer: Florian Rohart <f.rohart@uq.edu.au>
Diff between YuGene versions 1.1.5 dated 2015-11-19 and 1.1.6 dated 2018-05-16
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- build |only man/YuGene-package.Rd | 31 +++++++++++-------------------- 4 files changed, 18 insertions(+), 26 deletions(-)
Title: Finding Multiple-Objective Optimal Designs for the 4-Parameter
Logistic Model
Description: Provide tools for finding multiple-objective optimal designs for
estimating the shape of dose-response, the ED50 (the dose producing an effect
midway between the expected responses at the extreme doses) and the MED (the
minimum effective dose level) for the 2,3,4-parameter logistic models and for
evaluating its efficiencies for the three objectives. The acronym VNM stands
for V-algorithm using Newton Raphson method to search multiple-objective
optimal design.
Author: Seung Won Hyun, Weng Kee Wong, and Yarong Yang
Maintainer: Yarong Yang <yarongyang78@gmail.com>
Diff between VNM versions 6.1 dated 2018-02-15 and 7.1 dated 2018-05-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/OPT-class.Rd | 2 +- man/PAR-class.Rd | 2 +- man/SW-class.Rd | 2 +- man/VNM-package.Rd | 2 +- 6 files changed, 13 insertions(+), 13 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of vine copula models.
The package includes tools for parameter estimation, model selection,
simulation, goodness-of-fit tests, and visualization. Tools for estimation,
selection and exploratory data analysis of bivariate copula models are also
provided.
Author: Ulf Schepsmeier [aut],
Jakob Stoeber [aut],
Eike Christian Brechmann [aut],
Benedikt Graeler [aut],
Thomas Nagler [aut, cre],
Tobias Erhardt [aut],
Carlos Almeida [ctb],
Aleksey Min [ctb, ths],
Claudia Czado [ctb, ths],
Mathias Hofmann [ctb],
Matthias Killiches [ctb],
Harry Joe [ctb],
Thibault Vatter [ctb]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between VineCopula versions 2.1.4 dated 2018-02-11 and 2.1.5 dated 2018-05-16
DESCRIPTION | 6 ++--- MD5 | 17 +++++++-------- NEWS.md | 29 +++++++++++++++++-------- R/BiCopEst.R | 4 +-- R/RVinePIT.R | 4 --- R/RVineSeqEst.R | 2 - R/VineCopula-package.R | 25 +++++++--------------- build |only man/VineCopula-package.Rd | 26 ++++++----------------- src/tools.c | 52 ++++++++++++++++++++++++---------------------- 10 files changed, 78 insertions(+), 87 deletions(-)
Title: Basic Functions for Pre-Processing Microarrays
Description: Provides classes to pre-process microarray gene
expression data as part of the OOMPA collection of packages
described at <http://oompa.r-forge.r-project.org/>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between PreProcess versions 3.1.4 dated 2017-07-13 and 3.1.5 dated 2018-05-16
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 7 +++++++ R/b03-channel-type.R | 12 ++++++------ R/b04-channel.R | 10 +++++----- R/b05-processor.R | 8 ++++---- R/b06-pipeline.R | 6 +++--- R/b07-complete-channel.R | 8 ++++---- build/vignette.rds |binary inst/doc/oompa-prep.pdf |binary 10 files changed, 42 insertions(+), 35 deletions(-)
Title: Maximum Likelihood Estimation of DNA Methylation and
Hydroxymethylation Proportions
Description: Maximum likelihood estimates (MLE) of the proportions
of 5-mC and 5-hmC in the DNA using information from BS-conversion,
TAB-conversion, and oxBS-conversion methods. One can use information from all three methods
or any combination of two of them. Estimates are based on Binomial model by
Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and
Kiihl et al. (2018, to appear).
Author: Samara Kiihl [aut, cre],
Maria Jose Martinez-Garrido [aut],
Arce Domingo-Relloso [aut],
Jose Bermudez [aut],
Maria Tellez-Plaza [aut]
Maintainer: Samara Kiihl <samara@ime.unicamp.br>
Diff between MLML2R versions 0.2.0 dated 2018-02-21 and 0.2.1 dated 2018-05-16
DESCRIPTION | 6 - MD5 | 20 ++-- build/vignette.rds |binary inst/doc/vignette.R | 116 +++++++++++++++++++++------ inst/doc/vignette.Rmd | 180 ++++++++++++++++++++++++++++++++++-------- inst/doc/vignette.pdf |binary vignettes/Real1_estimates.pdf |binary vignettes/Real2_estimates.pdf |only vignettes/True_parameters.pdf |binary vignettes/refs.bib | 13 +++ vignettes/vignette.Rmd | 180 ++++++++++++++++++++++++++++++++++-------- vignettes/vignette.html |only 12 files changed, 417 insertions(+), 98 deletions(-)
Title: Bootstrap Subsamplings of Sparse Partial Least Squares -
Discriminant Analysis for Classification and Signature
Identification
Description: Applicable to any classification problem with more than 2 classes. It relies on bootstrap subsamplings of sPLS-DA and provides tools to select the most stable variables (defined as the ones consistently selected over the bootstrap subsamplings) and to predict the class of test samples.
Author: Florian Rohart [aut, cre], Kim-Anh Le Cao [boss], Christine Wells [boss]
Maintainer: Florian Rohart <florian.rohart@gmail.com>
Diff between bootsPLS versions 1.1.1 dated 2017-12-17 and 1.1.2 dated 2018-05-16
DESCRIPTION | 6 +++--- MD5 | 5 +++-- build |only man/bootsPLS-package.Rd | 29 ++++++++++------------------- 4 files changed, 16 insertions(+), 24 deletions(-)
Title: Inverse Compliance Score Weighting
Description: Provides the necessary tools to estimate average treatment effects with an instrumental variable by re-weighting observations using a model of compliance.
Author: Peter M. Aronow <peter.aronow@yale.edu>, Dean Eckles <icsw@deaneckles.com> and Kyle Peyton <kyle.peyton@yale.edu>
Maintainer: Kyle Peyton <kyle.peyton@yale.edu>
Diff between icsw versions 0.9 dated 2015-07-07 and 1.0.0 dated 2018-05-16
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- man/FoxDebate.Rd | 2 +- man/compliance.score.Rd | 10 +++++----- man/icsw-package.Rd | 4 ++-- man/icsw.tsls.Rd | 2 +- 6 files changed, 19 insertions(+), 18 deletions(-)
Title: Omnibus Test for Genetic Association Analysis using the Rank
Normal Transformation
Description: Implementation of genetic association tests using the rank based inverse normal transformation (INT). The primary contribution is an omnibus test, which synthesizes two complementary INT-based approaches. In simulations against phenotypes with skewed and heavy tailed residuals, the omnibus test provided valid inference in the absence of genetic effects. When genetic effects were present, the omnibus test provided power comparable to the more efficient of the component methods. Under these settings, standard linear regression variously failed to control the type I error in the absence of genetic effects, and was underpowered in the presence of genetic effects.
Author: Zachary McCaw [aut, cre]
Maintainer: Zachary McCaw <zmccaw@g.harvard.edu>
Diff between RNOmni versions 0.3.0 dated 2018-04-18 and 0.4.0 dated 2018-05-16
RNOmni-0.3.0/RNOmni/man/IINT0.Rd |only RNOmni-0.3.0/RNOmni/man/fastMvp.Rd |only RNOmni-0.3.0/RNOmni/man/incP.Rd |only RNOmni-0.3.0/RNOmni/man/matQF.Rd |only RNOmni-0.3.0/RNOmni/man/vecQF.Rd |only RNOmni-0.4.0/RNOmni/DESCRIPTION | 10 RNOmni-0.4.0/RNOmni/MD5 | 49 +-- RNOmni-0.4.0/RNOmni/NAMESPACE | 15 - RNOmni-0.4.0/RNOmni/R/BasicTest.R |only RNOmni-0.4.0/RNOmni/R/DirectMethod.R |only RNOmni-0.4.0/RNOmni/R/IndirectMethod.R |only RNOmni-0.4.0/RNOmni/R/InputCheck.R | 4 RNOmni-0.4.0/RNOmni/R/RankNormal.R | 459 +++++-------------------------- RNOmni-0.4.0/RNOmni/R/RcppExports.R | 48 +-- RNOmni-0.4.0/RNOmni/inst/doc/RNOmni.Rmd | 10 RNOmni-0.4.0/RNOmni/inst/doc/RNOmni.html | 36 +- RNOmni-0.4.0/RNOmni/man/AvgCorr.Rd | 13 RNOmni-0.4.0/RNOmni/man/BAT.Rd | 16 - RNOmni-0.4.0/RNOmni/man/BootCorr.Rd | 15 - RNOmni-0.4.0/RNOmni/man/DINT.Rd | 16 - RNOmni-0.4.0/RNOmni/man/IINT.Rd | 22 - RNOmni-0.4.0/RNOmni/man/OmniP.Rd | 13 RNOmni-0.4.0/RNOmni/man/RNOmni.Rd | 19 - RNOmni-0.4.0/RNOmni/man/Resid.Rd |only RNOmni-0.4.0/RNOmni/man/fastQF.Rd |only RNOmni-0.4.0/RNOmni/man/olsB.Rd |only RNOmni-0.4.0/RNOmni/man/rankNormal.Rd | 2 RNOmni-0.4.0/RNOmni/src/MatrixOps.cpp | 51 +-- RNOmni-0.4.0/RNOmni/src/RNOmni.cpp | 1 RNOmni-0.4.0/RNOmni/src/RcppExports.cpp | 60 +--- RNOmni-0.4.0/RNOmni/vignettes/RNOmni.Rmd | 10 31 files changed, 278 insertions(+), 591 deletions(-)
Title: Modeling Phylogenetic Signals using Eigenvector Maps
Description: Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Author: Guillaume Guenard, with contribution from Pierre Legendre
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>
Diff between MPSEM versions 0.3-3 dated 2017-09-25 and 0.3-4 dated 2018-05-16
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ build/partial.rdb |only build/vignette.rds |binary inst/doc/MPSEM.Rnw | 2 +- inst/doc/MPSEM.pdf |binary man/MPSEM-package.Rd | 34 ++++++++++++++++++---------------- vignettes/MPSEM.Rnw | 2 +- 8 files changed, 31 insertions(+), 28 deletions(-)
Title: Selecting Attributes
Description: Functions for selecting attributes from a given dataset. Attribute
subset selection is the process of identifying and removing as much of the
irrelevant and redundant information as possible.
Author: Piotr Romanski, Lars Kotthoff
Maintainer: Lars Kotthoff <larsko@uwyo.edu>
Diff between FSelector versions 0.21 dated 2016-06-30 and 0.31 dated 2018-05-16
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/selector.oneR.R | 2 +- man/FSelector-package.Rd | 8 ++++---- man/best.first.search.Rd | 2 +- 5 files changed, 15 insertions(+), 15 deletions(-)
Title: An Algorithm for Reducing Errors-in-Variable Bias in Simple
Linear Regression
Description: Performs a compact genetic algorithm search to reduce errors-in-variables bias in linear regression. The algorithm estimates the regression parameters with lower biases and higher variances but mean-square errors (MSEs) are reduced.
Author: Mehmet Hakan Satman (PhD), Erkin Diyarbakirlioglu (PhD)
Maintainer: Mehmet Hakan Satman <mhsatman@istanbul.edu.tr>
Diff between eive versions 2.1 dated 2014-07-05 and 2.3 dated 2018-05-16
DESCRIPTION | 14 +++++++------- MD5 | 6 ++++-- NAMESPACE | 4 +++- inst |only src/registerDynamicSymbol.c |only 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Edge Detection and Clustering in Images
Description: Detection of edge points in images based on the difference
of two asymmetric M-kernel estimators. Linear and circular
regression clustering based on redescending M-estimators.
Detection of linear edges in images.
Author: Tim Garlipp <TimGarlipp@gmx.de>
Maintainer: Dominik Kirchhoff <dominik.kirchhoff@tu-dortmund.de>
Diff between edci versions 1.1-2 dated 2016-08-24 and 1.1-3 dated 2018-05-16
DESCRIPTION | 8 +++--- MD5 | 5 ++- src/init.c |only src/oregMclust.cc | 72 +++++++++++++++++++++++++++--------------------------- 4 files changed, 43 insertions(+), 42 deletions(-)
Title: CBA Classifier for R
Description: Provides implementations of a classifier based on the
"Classification Based on Associations" (CBA). It can be used for building
classification models from association rules. Rules are pruned in the order of
precedence given by the sort criteria and a default rule is added. The final
classifier labels provided instances. CBA was originally proposed by Liu,
B. Hsu, W. and Ma, Y. Integrating Classification and Association Rule
Mining. Proceedings KDD-98, New York, 27-31 August. AAAI. pp80-86 (1998, ISBN:1-57735-070-7).
Author: Jaroslav Kuchar [aut, cre],
Tomas Kliegr [ctb]
Maintainer: Jaroslav Kuchar <jaroslav.kuchar@gmail.com>
Diff between rCBA versions 0.4.1 dated 2018-05-09 and 0.4.2 dated 2018-05-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 8 ++++++++ R/init.R | 8 ++++---- 4 files changed, 18 insertions(+), 10 deletions(-)
Title: Scores Features for Feature Selection
Description: For each feature, a score is computed that can be useful
for feature selection. Several random subsets are sampled from
the input data and for each random subset, various linear
models are fitted using lars method. A score is assigned to
each feature based on the tendency of LASSO in including that
feature in the models.Finally, the average score and the models
are returned as the output. The features with relatively low
scores are recommended to be ignored because they can lead to
overfitting of the model to the training data. Moreover, for
each random subset, the best set of features in terms of global
error is returned. They are useful for applying Bolasso, the
alternative feature selection method that recommends the
intersection of features subsets.
Author: Habil Zare
Maintainer: Habil Zare <zare@txstate.edu>
Diff between FeaLect versions 1.10 dated 2015-05-12 and 1.12 dated 2018-05-16
DESCRIPTION | 8 +-- MD5 | 20 ++++---- NAMESPACE | 4 + build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only inst/doc/FeaLect_feature_scorer.R | 3 - inst/doc/FeaLect_feature_scorer.Rnw | 5 +- inst/doc/FeaLect_feature_scorer.pdf |binary man/FeaLect-package.Rd | 80 +++++++++++++---------------------- vignettes/FeaLect_feature_scorer.Rnw | 5 +- vignettes/overfitting.bib | 13 +++-- 12 files changed, 66 insertions(+), 72 deletions(-)
Title: Multiscale Codependence Analysis
Description: Computation of Multiscale Codependence Analysis and spatial eigenvector maps, as an additional feature.
Author: Guillaume Guenard and Pierre Legendre, Bertrand Pages
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>
Diff between codep versions 0.8-1 dated 2018-04-16 and 0.9-1 dated 2018-05-16
DESCRIPTION | 8 +++--- MD5 | 9 +++--- R/eigenmap.R | 8 +++++- build |only man/codep-package.Rd | 66 +++++++++++++++++++++++++++++++++++++++++---------- man/eigenmap.Rd | 60 ++++++++++++++++++++++++++++------------------ 6 files changed, 107 insertions(+), 44 deletions(-)
Title: A Computational Tool for Astrochronology
Description: Routines for astrochronologic testing, astronomical time scale construction, and time series analysis. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Author: Stephen Meyers [aut,cre], Alberto Malinverno [ctb], Linda Hinnov [ctb], Vincent Moron [ctb]
Maintainer: Stephen Meyers <smeyers@geology.wisc.edu>
Diff between astrochron versions 0.7 dated 2017-06-14 and 0.8 dated 2018-05-16
astrochron-0.7/astrochron/R/FUNCTION-autoPlot_v9.R |only astrochron-0.7/astrochron/R/FUNCTION-delPts_v6.R |only astrochron-0.7/astrochron/R/FUNCTION-eha_v21a.R |only astrochron-0.7/astrochron/R/FUNCTION-getData.R |only astrochron-0.7/astrochron/R/FUNCTION-hilbert_v15.R |only astrochron-0.7/astrochron/R/FUNCTION-idPts_v10.R |only astrochron-0.7/astrochron/R/FUNCTION-linterp_v9.R |only astrochron-0.7/astrochron/R/FUNCTION-lowspec_v20.R |only astrochron-0.7/astrochron/R/FUNCTION-mtmAR_v7.R |only astrochron-0.7/astrochron/R/FUNCTION-mtmML96_v14a.R |only astrochron-0.7/astrochron/R/FUNCTION-mtm_v18a.R |only astrochron-0.7/astrochron/R/FUNCTION-mwCor_v5.R |only astrochron-0.7/astrochron/R/FUNCTION-mwStats_v4.R |only astrochron-0.7/astrochron/R/FUNCTION-periodogram_v13.R |only astrochron-0.7/astrochron/R/FUNCTION-plotEha_v4.R |only astrochron-0.7/astrochron/R/FUNCTION-readMatrix_v7.R |only astrochron-0.7/astrochron/R/FUNCTION-read_v28a.R |only astrochron-0.7/astrochron/R/FUNCTION-sedrate2time_v2.R |only astrochron-0.7/astrochron/R/FUNCTION-slideCor_v6.R |only astrochron-0.7/astrochron/R/FUNCTION-taner_v7.R |only astrochron-0.7/astrochron/R/FUNCTION-timeOptPlot.R |only astrochron-0.7/astrochron/R/FUNCTION-timeOptSim_v7c.R |only astrochron-0.7/astrochron/R/FUNCTION-timeOpt_v9.R |only astrochron-0.7/astrochron/R/FUNCTION-tune_v7b.R |only astrochron-0.8/astrochron/DESCRIPTION | 13 - astrochron-0.8/astrochron/MD5 | 164 ++++++++------- astrochron-0.8/astrochron/NAMESPACE | 25 ++ astrochron-0.8/astrochron/NEWS |only astrochron-0.8/astrochron/R/FUNCTION-autoPlot_v10.R |only astrochron-0.8/astrochron/R/FUNCTION-calcPeriods_v3.R |only astrochron-0.8/astrochron/R/FUNCTION-confAdjust_v8.R |only astrochron-0.8/astrochron/R/FUNCTION-delPts_v7.R |only astrochron-0.8/astrochron/R/FUNCTION-eTimeOptTrack_v2.R |only astrochron-0.8/astrochron/R/FUNCTION-eTimeOpt_v6.R |only astrochron-0.8/astrochron/R/FUNCTION-eha_v21b.R |only astrochron-0.8/astrochron/R/FUNCTION-getData_v3.R |only astrochron-0.8/astrochron/R/FUNCTION-hilbert_v16.R |only astrochron-0.8/astrochron/R/FUNCTION-idPts_v11.R |only astrochron-0.8/astrochron/R/FUNCTION-linterp_v10.R |only astrochron-0.8/astrochron/R/FUNCTION-lowspec_v20b.R |only astrochron-0.8/astrochron/R/FUNCTION-makeNoise_v3.R |only astrochron-0.8/astrochron/R/FUNCTION-mtmAR_v7a.R |only astrochron-0.8/astrochron/R/FUNCTION-mtmML96_v14b.R |only astrochron-0.8/astrochron/R/FUNCTION-mtmPL_v6.R |only astrochron-0.8/astrochron/R/FUNCTION-mtm_v18b.R |only astrochron-0.8/astrochron/R/FUNCTION-multiTest_v8.R |only astrochron-0.8/astrochron/R/FUNCTION-mwCor_v6.R |only astrochron-0.8/astrochron/R/FUNCTION-mwStats_v5.R |only astrochron-0.8/astrochron/R/FUNCTION-periodogram_v15.R |only astrochron-0.8/astrochron/R/FUNCTION-plotEha_v5.R |only astrochron-0.8/astrochron/R/FUNCTION-pwrLawFit_v4.R |only astrochron-0.8/astrochron/R/FUNCTION-pwrLaw_v4.R |only astrochron-0.8/astrochron/R/FUNCTION-readMatrix_v9.R |only astrochron-0.8/astrochron/R/FUNCTION-read_v30.R |only astrochron-0.8/astrochron/R/FUNCTION-sedrate2time_v3.R |only astrochron-0.8/astrochron/R/FUNCTION-slideCor_v8.R |only astrochron-0.8/astrochron/R/FUNCTION-taner_v8.R |only astrochron-0.8/astrochron/R/FUNCTION-testBackground_v8.R |only astrochron-0.8/astrochron/R/FUNCTION-timeOptMCMC.R |only astrochron-0.8/astrochron/R/FUNCTION-timeOptPlot_v5.R |only astrochron-0.8/astrochron/R/FUNCTION-timeOptSim_v8b.R |only astrochron-0.8/astrochron/R/FUNCTION-timeOpt_v14.R |only astrochron-0.8/astrochron/R/FUNCTION-tracePeak.R |only astrochron-0.8/astrochron/R/FUNCTION-trackPeak.R |only astrochron-0.8/astrochron/R/FUNCTION-tune_v8.R |only astrochron-0.8/astrochron/R/startupMessage.R |only astrochron-0.8/astrochron/man/ar1.Rd | 2 astrochron-0.8/astrochron/man/asm.Rd | 2 astrochron-0.8/astrochron/man/astrochron-package.Rd | 4 astrochron-0.8/astrochron/man/autoPlot.Rd | 17 - astrochron-0.8/astrochron/man/bandpass.Rd | 2 astrochron-0.8/astrochron/man/calcPeriods.Rd |only astrochron-0.8/astrochron/man/cb.Rd | 2 astrochron-0.8/astrochron/man/confAdjust.Rd |only astrochron-0.8/astrochron/man/cycles.Rd | 2 astrochron-0.8/astrochron/man/delPts.Rd | 7 astrochron-0.8/astrochron/man/eTimeOpt.Rd |only astrochron-0.8/astrochron/man/eTimeOptTrack.Rd |only astrochron-0.8/astrochron/man/eha.Rd | 2 astrochron-0.8/astrochron/man/etp.Rd | 2 astrochron-0.8/astrochron/man/getData.Rd | 2 astrochron-0.8/astrochron/man/hilbert.Rd | 5 astrochron-0.8/astrochron/man/idPts.Rd | 4 astrochron-0.8/astrochron/man/integratePower.Rd | 2 astrochron-0.8/astrochron/man/linterp.Rd | 3 astrochron-0.8/astrochron/man/lowpass.Rd | 2 astrochron-0.8/astrochron/man/lowspec.Rd | 8 astrochron-0.8/astrochron/man/makeNoise.Rd |only astrochron-0.8/astrochron/man/mtm.Rd | 4 astrochron-0.8/astrochron/man/mtmAR.Rd | 5 astrochron-0.8/astrochron/man/mtmML96.Rd | 10 astrochron-0.8/astrochron/man/mtmPL.Rd |only astrochron-0.8/astrochron/man/multiTest.Rd |only astrochron-0.8/astrochron/man/mwCor.Rd | 4 astrochron-0.8/astrochron/man/mwStats.Rd | 8 astrochron-0.8/astrochron/man/mwin.Rd | 4 astrochron-0.8/astrochron/man/peak.Rd | 2 astrochron-0.8/astrochron/man/periodogram.Rd | 17 - astrochron-0.8/astrochron/man/plotEha.Rd | 2 astrochron-0.8/astrochron/man/pwrLaw.Rd |only astrochron-0.8/astrochron/man/pwrLawFit.Rd |only astrochron-0.8/astrochron/man/rankSeries.Rd | 2 astrochron-0.8/astrochron/man/read.Rd | 5 astrochron-0.8/astrochron/man/readMatrix.Rd | 5 astrochron-0.8/astrochron/man/sedRamp.Rd | 2 astrochron-0.8/astrochron/man/sedrate2time.Rd | 3 astrochron-0.8/astrochron/man/slideCor.Rd | 5 astrochron-0.8/astrochron/man/surrogateCor.Rd | 2 astrochron-0.8/astrochron/man/surrogates.Rd | 5 astrochron-0.8/astrochron/man/taner.Rd | 5 astrochron-0.8/astrochron/man/testBackground.Rd |only astrochron-0.8/astrochron/man/timeOpt.Rd | 12 - astrochron-0.8/astrochron/man/timeOptMCMC.Rd |only astrochron-0.8/astrochron/man/timeOptPlot.Rd | 10 astrochron-0.8/astrochron/man/timeOptSim.Rd | 48 +++- astrochron-0.8/astrochron/man/tones.Rd | 2 astrochron-0.8/astrochron/man/tracePeak.Rd |only astrochron-0.8/astrochron/man/trackPeak.Rd |only astrochron-0.8/astrochron/man/trough.Rd | 2 astrochron-0.8/astrochron/man/tune.Rd | 3 astrochron-0.8/astrochron/man/xplot.Rd | 6 121 files changed, 240 insertions(+), 203 deletions(-)
Title: Power Analysis Tools for Multilevel Randomized Experiments
Description: R version of PowerUp! <https://www.causalevaluation.org/>. Includes tools to calculate statistical power, minimum detectable effect size, and minimum required sample size for various multilevel randomized experiments with continuous outcomes.
Author: Metin Bulus [aut, cre, trl],
Nianbo Dong [aut],
Benjamin Kelcey [aut],
Jessaca Spybrook [aut]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between PowerUpR versions 0.2.3 dated 2018-02-16 and 1.0.0 dated 2018-05-16
PowerUpR-0.2.3/PowerUpR/inst/doc/cross_checks.R |only PowerUpR-0.2.3/PowerUpR/inst/doc/cross_checks.Rmd |only PowerUpR-0.2.3/PowerUpR/inst/doc/cross_checks.html |only PowerUpR-0.2.3/PowerUpR/vignettes/cross_checks.Rmd |only PowerUpR-1.0.0/PowerUpR/DESCRIPTION | 16 PowerUpR-1.0.0/PowerUpR/MD5 | 96 - PowerUpR-1.0.0/PowerUpR/NAMESPACE | 24 PowerUpR-1.0.0/PowerUpR/NEWS.md | 23 PowerUpR-1.0.0/PowerUpR/R/bcra3f2.R | 15 PowerUpR-1.0.0/PowerUpR/R/bcra3r2.R | 15 PowerUpR-1.0.0/PowerUpR/R/bcra4f3.R | 15 PowerUpR-1.0.0/PowerUpR/R/bcra4r2.R | 15 PowerUpR-1.0.0/PowerUpR/R/bcra4r3.R | 15 PowerUpR-1.0.0/PowerUpR/R/bira2c1.R | 15 PowerUpR-1.0.0/PowerUpR/R/bira2f1.R | 15 PowerUpR-1.0.0/PowerUpR/R/bira2r1.R | 15 PowerUpR-1.0.0/PowerUpR/R/bira3r1.R | 15 PowerUpR-1.0.0/PowerUpR/R/bira4r1.R | 15 PowerUpR-1.0.0/PowerUpR/R/conv.R | 86 - PowerUpR-1.0.0/PowerUpR/R/cra2r2.R | 695 +++++++++- PowerUpR-1.0.0/PowerUpR/R/cra3r3.R | 495 ++++++- PowerUpR-1.0.0/PowerUpR/R/cra4r4.R | 15 PowerUpR-1.0.0/PowerUpR/R/depdef.R | 1 PowerUpR-1.0.0/PowerUpR/R/error.R | 183 +- PowerUpR-1.0.0/PowerUpR/R/ira1r1.R | 15 PowerUpR-1.0.0/PowerUpR/R/plot.R | 95 - PowerUpR-1.0.0/PowerUpR/R/utils.R | 178 ++ PowerUpR-1.0.0/PowerUpR/README.md | 85 - PowerUpR-1.0.0/PowerUpR/build/vignette.rds |binary PowerUpR-1.0.0/PowerUpR/inst/CITATION | 15 PowerUpR-1.0.0/PowerUpR/inst/doc/three_level_cluster_randomized_trial.R | 1 PowerUpR-1.0.0/PowerUpR/inst/doc/three_level_cluster_randomized_trial.Rmd | 7 PowerUpR-1.0.0/PowerUpR/inst/doc/three_level_cluster_randomized_trial.html | 48 PowerUpR-1.0.0/PowerUpR/man/PowerUpR-package.Rd | 8 PowerUpR-1.0.0/PowerUpR/man/bcra3f2.Rd | 13 PowerUpR-1.0.0/PowerUpR/man/bcra3r2.Rd | 15 PowerUpR-1.0.0/PowerUpR/man/bcra4f3.Rd | 15 PowerUpR-1.0.0/PowerUpR/man/bcra4r2.Rd | 17 PowerUpR-1.0.0/PowerUpR/man/bcra4r3.Rd | 17 PowerUpR-1.0.0/PowerUpR/man/bira2c1.Rd | 11 PowerUpR-1.0.0/PowerUpR/man/bira2f1.Rd | 11 PowerUpR-1.0.0/PowerUpR/man/bira2r1.Rd | 13 PowerUpR-1.0.0/PowerUpR/man/bira3r1.Rd | 15 PowerUpR-1.0.0/PowerUpR/man/bira4r1.Rd | 17 PowerUpR-1.0.0/PowerUpR/man/conv.Rd | 4 PowerUpR-1.0.0/PowerUpR/man/cra2r2.Rd | 153 ++ PowerUpR-1.0.0/PowerUpR/man/cra3r3.Rd | 122 + PowerUpR-1.0.0/PowerUpR/man/cra4r4.Rd | 17 PowerUpR-1.0.0/PowerUpR/man/ira1r1.Rd | 11 PowerUpR-1.0.0/PowerUpR/man/plot.Rd | 21 PowerUpR-1.0.0/PowerUpR/vignettes/three_level_cluster_randomized_trial.Rmd | 7 51 files changed, 2114 insertions(+), 601 deletions(-)
Title: Relevant Component Analysis for Supervised Distance Metric
Learning
Description: Relevant Component Analysis (RCA) tries to find a linear
transformation of the feature space such that the effect of irrelevant
variability is reduced in the transformed space.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>)
Maintainer: Nan Xiao <me@nanx.me>
Diff between RECA versions 1.5 dated 2018-04-20 and 1.6 dated 2018-05-16
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/RECA-package.R | 5 +++-- R/rca.R | 4 ++++ man/RECA-package.Rd | 5 +++-- man/rca.Rd | 4 ++++ 6 files changed, 22 insertions(+), 12 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InSilicoVA versions 1.1.5 dated 2017-11-19 and 1.2.0 dated 2018-05-16
InSilicoVA-1.1.5/InSilicoVA/java/Insilico/src/InsilicoSampler.java |only InSilicoVA-1.1.5/InSilicoVA/java/Insilico/src/MathUtil.java |only InSilicoVA-1.1.5/InSilicoVA/java/Insilico/src/ProgressBar.java |only InSilicoVA-1.1.5/InSilicoVA/java/Insilico/src/ProgressPopup.java |only InSilicoVA-1.2.0/InSilicoVA/DESCRIPTION | 10 InSilicoVA-1.2.0/InSilicoVA/MD5 | 44 - InSilicoVA-1.2.0/InSilicoVA/NAMESPACE | 53 - InSilicoVA-1.2.0/InSilicoVA/R/indivplot.r | 2 InSilicoVA-1.2.0/InSilicoVA/R/insilico_core.r | 345 ++++++++-- InSilicoVA-1.2.0/InSilicoVA/R/insilico_standard.r | 31 InSilicoVA-1.2.0/InSilicoVA/R/insilico_train.r | 8 InSilicoVA-1.2.0/InSilicoVA/R/phy_debias.r | 1 InSilicoVA-1.2.0/InSilicoVA/R/plot.r | 2 InSilicoVA-1.2.0/InSilicoVA/R/print_insilico.r | 33 InSilicoVA-1.2.0/InSilicoVA/R/print_insilico_summary.r | 38 + InSilicoVA-1.2.0/InSilicoVA/R/report.r | 4 InSilicoVA-1.2.0/InSilicoVA/inst/NEWS.rd | 10 InSilicoVA-1.2.0/InSilicoVA/java/Insilico/src/sampler |only InSilicoVA-1.2.0/InSilicoVA/java/Insilico/src/utils |only InSilicoVA-1.2.0/InSilicoVA/man/csmf.diag.Rd | 40 - InSilicoVA-1.2.0/InSilicoVA/man/insilico.Rd | 116 +-- InSilicoVA-1.2.0/InSilicoVA/man/insilico.fit.Rd | 34 InSilicoVA-1.2.0/InSilicoVA/man/insilico.train.Rd | 6 InSilicoVA-1.2.0/InSilicoVA/man/print.insilico.Rd |only InSilicoVA-1.2.0/InSilicoVA/man/print.insilico_summary.Rd |only InSilicoVA-1.2.0/InSilicoVA/man/summary.insilico.Rd | 1 26 files changed, 578 insertions(+), 200 deletions(-)
Title: Process Biogas Data and Predict Biogas Production
Description: High- and low-level functions for processing biogas data and predicting biogas production. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas quantity can be converted between volume, mass, and moles. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, or gravimetric methods for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Biogas quantity and composition can be predicted from substrate composition and additional, optional data. Lastly, inoculum and substrate mass can be determined for planning BMP experiments.
Author: Sasha D. Hafner [aut, cre],
Charlotte Rennuit [aut],
Jin Mi Triolo [ctb],
Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <sasha.hafner@eng.au.dk>
Diff between biogas versions 1.10.2 dated 2018-05-02 and 1.10.3 dated 2018-05-16
biogas-1.10.2/biogas/R/startup.R |only biogas-1.10.2/biogas/man/biogas-package.Rd |only biogas-1.10.3/biogas/ChangeLog | 9 +++++++++ biogas-1.10.3/biogas/DESCRIPTION | 8 ++++---- biogas-1.10.3/biogas/MD5 | 12 +++++------- biogas-1.10.3/biogas/NEWS | 7 +++++++ biogas-1.10.3/biogas/inst/doc/biogas_quick_start.pdf |binary biogas-1.10.3/biogas/inst/doc/predBg_function.pdf |binary 8 files changed, 25 insertions(+), 11 deletions(-)
Title: Statistical Patterns in Genomic Sequences
Description: A collection of statistical hypothesis tests and other
techniques for identifying certain spatial relationships/phenomena in
DNA sequences. In particular, it provides tests and graphical methods for determining
whether or not DNA sequences comply with Chargaff's second parity rule
or exhibit purine-pyrimidine parity. In addition, there are functions for
efficiently simulating discrete state space Markov chains and testing
arbitrary symbolic sequences of symbols for the presence of first-order
Markovianness.
Also, it has functions for counting words/k-mers (and cylinder patterns) in
arbitrary symbolic sequences. Functions which take a DNA sequence as input
can handle sequences stored as SeqFastadna objects from the 'seqinr' package.
Author: Andrew Hart [aut, cre],
Servet Martínez [aut],
Universidad de Chile [cph],
INRIA-Chile [cph]
Maintainer: Andrew Hart <ahart@dim.uchile.cl>
Diff between spgs versions 1.0-1 dated 2017-07-21 and 1.0-2 dated 2018-05-16
DESCRIPTION | 13 ++++++++----- MD5 | 7 ++++--- build |only inst/NEWS.Rd | 11 ++++++++++- man/spgs-package.Rd | 9 ++++----- 5 files changed, 26 insertions(+), 14 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 0.47.5 dated 2018-03-26 and 0.49.0 dated 2018-05-16
DESCRIPTION | 10 MD5 | 52 +- NEWS | 32 + R/RcppExports.R | 102 ++--- R/eval_design.R | 33 - R/eval_design_custom_mc.R | 19 R/eval_design_mc.R | 30 - R/eval_design_survival_mc.R | 19 R/gen_anticoef.R | 2 R/gen_design.R | 46 +- R/reduceRunMatrix.R | 12 R/skprGUI.R | 30 - inst/shiny/skprGUI/server.R | 126 +++--- src/AOptimality.cpp | 9 src/DOptimality.cpp | 12 src/DOptimalityBlocked.cpp | 12 src/IOptimality.cpp | 9 src/RcppExports.cpp | 80 ++-- src/calcAliasTrace.cpp | 11 src/calculateAOptimalityPseudo.cpp | 9 src/calculateDEfficiency.cpp | 9 src/covarianceMatrix.cpp | 9 src/covarianceMatrixPseudo.cpp | 9 src/genOptimalDesign.cpp | 707 +++++++++++++++++++------------------ src/genPseudoInverse.cpp | 8 tests/testthat/Rplots.pdf |binary tests/testthat/testExampleCode.R | 22 - 27 files changed, 730 insertions(+), 689 deletions(-)
Title: A Data-Centered Data Flow Manager
Description: A data manager meant to avoid manual storage/retrieval of
data to/from the file system. It builds one (or more) centralized
repository where R objects are stored with rich annotations,
including corresponding code chunks, and easily searched and
retrieved.
Author: Francesco Napolitano <franapoli@gmail.com>
Maintainer: Francesco Napolitano <franapoli@gmail.com>
Diff between repo versions 2.1.2 dated 2017-11-27 and 2.1.3 dated 2018-05-16
DESCRIPTION | 8 +- MD5 | 28 ++++----- NEWS.md | 26 ++++++++ R/repo_private.R | 61 ++++++++++---------- R/repo_public.R | 136 +++++++++++++++++++--------------------------- README.md | 1 build/vignette.rds |binary inst/doc/index.R | 23 +++++-- inst/doc/index.Rmd | 23 +++++-- inst/doc/index.html | 114 ++++++++++++++++++++------------------ man/repo_lazydo.Rd | 59 +++++++++++-------- man/repo_stash.Rd | 6 -- man/repo_stashclear.Rd | 3 - tests/testthat/testrepo.R | 51 +++++++++++++++++ vignettes/index.Rmd | 23 +++++-- 15 files changed, 328 insertions(+), 234 deletions(-)
Title: R Commander Plug-in for MPA Statistics
Description: Extends R Commander with a unified menu of new and pre-existing
statistical functions related to public management and policy analysis
statistics. Functions and menus have been renamed according to the
usage in PMGT 630 in the Master of Public Administration program at
Brigham Young University.
Author: Andrew Heiss, Richard Payne, Christa Schank, Jessica Reese
Maintainer: Andrew Heiss <andrew@andrewheiss.com>
Diff between RcmdrPlugin.MPAStats versions 1.2.1 dated 2016-05-13 and 1.2.2 dated 2018-05-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/RcmdrPlugin.MPAStats-package.Rd | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
More information about RcmdrPlugin.MPAStats at CRAN
Permanent link
Title: Automated Method for Verbal Autopsy
Description: Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between openVA versions 1.0.3 dated 2017-01-07 and 1.0.4 dated 2018-05-16
DESCRIPTION | 10 - MD5 | 36 ++-- NAMESPACE | 30 +-- R/CSMF.r | 48 +++++- R/ConvertData.r | 372 ++++++++++++++++++++++++++++++++++++++++++++++- R/VAmain.r | 82 ++++++++-- R/stackplot.r | 4 inst/NEWS.Rd | 7 man/ConvertData.Rd | 9 - man/ConvertData.phmrc.Rd | 7 man/codeVA.Rd | 29 ++- man/getCSMF.Rd | 18 +- man/getCSMF_accuracy.Rd | 5 man/getIndivProb.Rd | 6 man/getPHMRC_url.Rd | 4 man/getTopCOD.Rd | 8 - man/interVA.train.Rd | 7 man/plotVA.Rd | 9 - man/stackplotVA.Rd | 13 - 19 files changed, 585 insertions(+), 119 deletions(-)
Title: Estimation of Multinormal Mixture Distribution
Description: Fit multivariate mixture of normal distribution using
covariance structure.
Author: Charles-Edouard Giguere
Maintainer: Charles-Edouard Giguere <ce.giguere@gmail.com>
Diff between mmeln versions 1.2 dated 2015-09-25 and 1.3 dated 2018-05-16
ChangeLog | 15 +- DESCRIPTION | 10 - MD5 | 11 - R/mmeln.R | 374 +++++++++++++++++++++++++-------------------------- R/post.R | 106 +++++++------- build |only man/mmeln-package.Rd | 22 +-- 7 files changed, 271 insertions(+), 267 deletions(-)
Title: Time Delay Estimation for Stochastic Time Series of
Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, and Aneta Siemiginowska
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between timedelay versions 1.0.7 dated 2017-05-27 and 1.0.8 dated 2018-05-16
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 +- R/bayesian.R | 5 ++--- man/bayesian.Rd | 1 - man/timedelay-package.Rd | 7 ++----- 6 files changed, 15 insertions(+), 20 deletions(-)
Title: Simulation Parameter Analysis R Toolkit ApplicatioN: 'spartan'
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. 'spartan', first described in our 2013 publication in PLoS Computational Biology, provided code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 added support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions. Version 3.0 offers significant additional functionality that permits the creation of emulations of simulation results, derived using the same sampling techniques in the global sensitivity analysis techniques, and the generation of combinations of these machine learning algorithms to one create one predictive tool, more commonly known as an ensemble model. Version 3.0 also improved the standard of the graphs produced in the original sensitivity analysis techniques, and introduced a polar plot to examine parameter sensitivity.
Author: Kieran Alden [cre, aut],
Mark Read [aut],
Paul Andrews [aut],
Jason Cosgrove [aut],
Mark Coles [aut],
Jon Timmis [aut]
Maintainer: Kieran Alden <kieran.alden@gmail.com>
Diff between spartan versions 3.0.0 dated 2017-09-06 and 3.0.1 dated 2018-05-16
spartan-3.0.0/spartan/R/robustness_utilities.R |only spartan-3.0.0/spartan/man/lhc_countSignificantParametersOverTime.Rd |only spartan-3.0.0/spartan/man/lhc_graphPRCCForMultipleTimepoints.Rd |only spartan-3.0.0/spartan/man/oat_countResponsesOfDesiredValue.Rd |only spartan-3.0.1/spartan/DESCRIPTION | 12 spartan-3.0.1/spartan/MD5 | 444 ++- spartan-3.0.1/spartan/NAMESPACE | 181 - spartan-3.0.1/spartan/NEWS.md |only spartan-3.0.1/spartan/R/abc_utilities.R | 3 spartan-3.0.1/spartan/R/aleatory_analysis.R | 753 +++-- spartan-3.0.1/spartan/R/aleatory_analysis_plotting.R | 146 - spartan-3.0.1/spartan/R/atest_utilities.R | 23 spartan-3.0.1/spartan/R/datadoc.R | 52 spartan-3.0.1/spartan/R/efast_analysis.R | 658 ++--- spartan-3.0.1/spartan/R/efast_analysis_netlogo.R | 30 spartan-3.0.1/spartan/R/efast_plotting.R | 4 spartan-3.0.1/spartan/R/efast_sampling.R | 272 +- spartan-3.0.1/spartan/R/efast_sampling_netlogo.R | 381 -- spartan-3.0.1/spartan/R/efast_utilities.R | 2 spartan-3.0.1/spartan/R/emulation_evolution.R | 6 spartan-3.0.1/spartan/R/emulation_generation.R | 2 spartan-3.0.1/spartan/R/emulation_plotting.R | 22 spartan-3.0.1/spartan/R/emulation_sensitivity_analysis.R | 42 spartan-3.0.1/spartan/R/emulation_utilities.R | 2 spartan-3.0.1/spartan/R/ensemble_generation.R | 20 spartan-3.0.1/spartan/R/lhc_analysis.R | 675 +++-- spartan-3.0.1/spartan/R/lhc_analysis_netlogo.R | 131 - spartan-3.0.1/spartan/R/lhc_plotting.R | 395 +-- spartan-3.0.1/spartan/R/lhc_prcc_utilities.R | 81 spartan-3.0.1/spartan/R/lhc_preprocess.R | 11 spartan-3.0.1/spartan/R/lhc_sampling.R | 146 - spartan-3.0.1/spartan/R/lhc_sampling_netlogo.R | 209 - spartan-3.0.1/spartan/R/method_argument_check.R |only spartan-3.0.1/spartan/R/netlogo_sampling_utilities.R |only spartan-3.0.1/spartan/R/neural_network_utilities.R | 704 ++--- spartan-3.0.1/spartan/R/robustness_analysis.R | 801 +++--- spartan-3.0.1/spartan/R/robustness_analysis_netlogo.R | 99 spartan-3.0.1/spartan/R/robustness_plotting.R | 18 spartan-3.0.1/spartan/R/robustness_sampling.R | 153 + spartan-3.0.1/spartan/R/spartan_utilities.R | 370 +- spartan-3.0.1/spartan/README.md |only spartan-3.0.1/spartan/build/vignette.rds |binary spartan-3.0.1/spartan/data/a_test_results.rda |only spartan-3.0.1/spartan/data/exemplar_sim_output.rda |only spartan-3.0.1/spartan/inst/doc/emulation_ensembles.R | 551 ++-- spartan-3.0.1/spartan/inst/doc/emulation_ensembles.Rmd | 763 ++--- spartan-3.0.1/spartan/inst/doc/emulation_ensembles.html | 1005 ++++--- spartan-3.0.1/spartan/inst/doc/netlogo.R | 477 +-- spartan-3.0.1/spartan/inst/doc/netlogo.Rmd | 5 spartan-3.0.1/spartan/inst/doc/netlogo.html | 949 ++++--- spartan-3.0.1/spartan/inst/doc/sensitivity_analysis.R | 610 ++-- spartan-3.0.1/spartan/inst/doc/sensitivity_analysis.Rmd | 14 spartan-3.0.1/spartan/inst/doc/sensitivity_analysis.html | 1302 +++++----- spartan-3.0.1/spartan/man/a_test_results.Rd |only spartan-3.0.1/spartan/man/aa_getATestResults.Rd | 96 spartan-3.0.1/spartan/man/aa_getATestResults_overTime.Rd |only spartan-3.0.1/spartan/man/aa_graphATestsForSampleSize.Rd | 54 spartan-3.0.1/spartan/man/aa_graphSampleSizeSummary.Rd | 88 spartan-3.0.1/spartan/man/aa_sampleSizeSummary.Rd | 76 spartan-3.0.1/spartan/man/aa_sampleSizeSummary_overTime.Rd |only spartan-3.0.1/spartan/man/aa_summariseReplicateRuns.Rd | 93 spartan-3.0.1/spartan/man/aa_summariseReplicateRuns_overTime.Rd |only spartan-3.0.1/spartan/man/add_parameter_value_to_file.Rd |only spartan-3.0.1/spartan/man/analysenetwork_structures.Rd | 68 spartan-3.0.1/spartan/man/append_time_to_argument.Rd |only spartan-3.0.1/spartan/man/atest.Rd | 34 spartan-3.0.1/spartan/man/build_performance_statistics.Rd | 62 spartan-3.0.1/spartan/man/calculate_atest_score.Rd |only spartan-3.0.1/spartan/man/calculate_fold_MSE.Rd | 46 spartan-3.0.1/spartan/man/calculate_medians_for_all_measures.Rd |only spartan-3.0.1/spartan/man/calculate_prcc_for_all_measures.Rd |only spartan-3.0.1/spartan/man/calculate_prccs_all_parameters.Rd |only spartan-3.0.1/spartan/man/calculate_weights_for_ensemble_model.Rd | 58 spartan-3.0.1/spartan/man/check_acceptable_model_type.Rd | 36 spartan-3.0.1/spartan/man/check_argument_positive_int.Rd |only spartan-3.0.1/spartan/man/check_boolean.Rd |only spartan-3.0.1/spartan/man/check_column_ranges.Rd |only spartan-3.0.1/spartan/man/check_confidence_interval.Rd |only spartan-3.0.1/spartan/man/check_consistency_result_type.Rd |only spartan-3.0.1/spartan/man/check_double_value_in_range.Rd |only spartan-3.0.1/spartan/man/check_file_exist.Rd |only spartan-3.0.1/spartan/man/check_file_exists.Rd |only spartan-3.0.1/spartan/man/check_file_extension.Rd | 24 spartan-3.0.1/spartan/man/check_filepath_exists.Rd |only spartan-3.0.1/spartan/man/check_function_dependent_paramvals.Rd |only spartan-3.0.1/spartan/man/check_global_param_sampling_args.Rd |only spartan-3.0.1/spartan/man/check_graph_output_type.Rd |only spartan-3.0.1/spartan/man/check_input_args.Rd |only spartan-3.0.1/spartan/man/check_lengths_parameters_ranges.Rd |only spartan-3.0.1/spartan/man/check_lhs_algorithm.Rd |only spartan-3.0.1/spartan/man/check_list_all_integers.Rd |only spartan-3.0.1/spartan/man/check_nested_filepaths.Rd |only spartan-3.0.1/spartan/man/check_netlogo_parameters_and_values.Rd |only spartan-3.0.1/spartan/man/check_numeric_list_values.Rd |only spartan-3.0.1/spartan/man/check_package_installed.Rd |only spartan-3.0.1/spartan/man/check_parameters_and_ranges.Rd |only spartan-3.0.1/spartan/man/check_paramvals_length_equals_parameter_length.Rd |only spartan-3.0.1/spartan/man/check_robustness_parameter_and_ranges_lengths.Rd |only spartan-3.0.1/spartan/man/check_robustness_paramvals_contains_baseline.Rd |only spartan-3.0.1/spartan/man/check_robustness_range_contains_baseline.Rd |only spartan-3.0.1/spartan/man/check_robustness_range_or_values.Rd |only spartan-3.0.1/spartan/man/check_robustness_sampling_args.Rd |only spartan-3.0.1/spartan/man/check_text.Rd |only spartan-3.0.1/spartan/man/check_text_list.Rd |only spartan-3.0.1/spartan/man/close_and_write_netlogo_file.Rd |only spartan-3.0.1/spartan/man/compare_all_values_of_parameter_to_baseline.Rd |only spartan-3.0.1/spartan/man/construct_result_filename.Rd |only spartan-3.0.1/spartan/man/createAndEvaluateFolds.Rd | 86 spartan-3.0.1/spartan/man/createTrainingFold.Rd | 56 spartan-3.0.1/spartan/man/create_abc_settings_object.Rd | 72 spartan-3.0.1/spartan/man/create_ensemble.Rd | 96 spartan-3.0.1/spartan/man/create_neural_network.Rd | 64 spartan-3.0.1/spartan/man/createtest_fold.Rd | 50 spartan-3.0.1/spartan/man/denormalise_dataset.Rd | 42 spartan-3.0.1/spartan/man/determine_optimal_neural_network_structure.Rd | 58 spartan-3.0.1/spartan/man/efast_cvmethod.Rd | 62 spartan-3.0.1/spartan/man/efast_generate_medians_for_all_parameter_subsets.Rd | 138 - spartan-3.0.1/spartan/man/efast_generate_medians_for_all_parameter_subsets_overTime.Rd |only spartan-3.0.1/spartan/man/efast_generate_sample.Rd | 100 spartan-3.0.1/spartan/man/efast_generate_sample_netlogo.Rd | 98 spartan-3.0.1/spartan/man/efast_get_overall_medians.Rd | 111 spartan-3.0.1/spartan/man/efast_get_overall_medians_overTime.Rd |only spartan-3.0.1/spartan/man/efast_graph_Results.Rd | 66 spartan-3.0.1/spartan/man/efast_netlogo_get_overall_medians.Rd | 72 spartan-3.0.1/spartan/man/efast_netlogo_run_Analysis.Rd | 102 spartan-3.0.1/spartan/man/efast_parameterdist.Rd | 46 spartan-3.0.1/spartan/man/efast_process_netlogo_result.Rd | 84 spartan-3.0.1/spartan/man/efast_run_Analysis.Rd | 130 spartan-3.0.1/spartan/man/efast_run_Analysis_overTime.Rd |only spartan-3.0.1/spartan/man/efast_sd.Rd | 24 spartan-3.0.1/spartan/man/efast_setfreq.Rd | 24 spartan-3.0.1/spartan/man/efast_ttest.Rd | 26 spartan-3.0.1/spartan/man/emulate_efast_sampled_parameters.Rd | 76 spartan-3.0.1/spartan/man/emulate_lhc_sampled_parameters.Rd | 92 spartan-3.0.1/spartan/man/emulated_lhc_values.Rd | 54 spartan-3.0.1/spartan/man/emulation_algorithm_settings.Rd | 136 - spartan-3.0.1/spartan/man/emulator_parameter_evolution.Rd | 72 spartan-3.0.1/spartan/man/emulator_predictions.Rd | 72 spartan-3.0.1/spartan/man/ensemble_abc_wrapper.Rd | 50 spartan-3.0.1/spartan/man/execute_checks.Rd |only spartan-3.0.1/spartan/man/exemplar_sim_output.Rd |only spartan-3.0.1/spartan/man/extract_predictions_from_result_list.Rd | 44 spartan-3.0.1/spartan/man/format_efast_result_for_output.Rd |only spartan-3.0.1/spartan/man/generate_a_test_results_header.Rd |only spartan-3.0.1/spartan/man/generate_a_test_score.Rd |only spartan-3.0.1/spartan/man/generate_efast_parameter_sets.Rd |only spartan-3.0.1/spartan/man/generate_emulator_model.Rd | 74 spartan-3.0.1/spartan/man/generate_emulators_and_ensemble.Rd | 132 - spartan-3.0.1/spartan/man/generate_ensemble_from_existing_emulations.Rd | 110 spartan-3.0.1/spartan/man/generate_ensemble_training_set.Rd | 68 spartan-3.0.1/spartan/man/generate_headers_for_atest_file.Rd |only spartan-3.0.1/spartan/man/generate_list_of_checks.Rd |only spartan-3.0.1/spartan/man/generate_medians_for_param_set.Rd |only spartan-3.0.1/spartan/man/generate_model_formula.Rd | 40 spartan-3.0.1/spartan/man/generate_parameter_table.Rd |only spartan-3.0.1/spartan/man/generate_prcc_results_header.Rd |only spartan-3.0.1/spartan/man/generate_predictions_from_emulator.Rd | 56 spartan-3.0.1/spartan/man/generate_requested_emulations.Rd | 148 - spartan-3.0.1/spartan/man/generate_sensitivity_indices.Rd |only spartan-3.0.1/spartan/man/generate_summary_stats_for_all_param_sets.Rd |only spartan-3.0.1/spartan/man/getMediansSubset.Rd | 76 spartan-3.0.1/spartan/man/get_argument_correct_case.Rd |only spartan-3.0.1/spartan/man/get_correct_file_path_for_function.Rd |only spartan-3.0.1/spartan/man/get_file_and_object_argument_names.Rd |only spartan-3.0.1/spartan/man/get_max_and_median_atest_scores.Rd |only spartan-3.0.1/spartan/man/get_median_results_for_all_measures.Rd |only spartan-3.0.1/spartan/man/get_medians_for_size_subsets.Rd |only spartan-3.0.1/spartan/man/graph_Posteriors_All_Parameters.Rd | 52 spartan-3.0.1/spartan/man/graph_sample_size_results.Rd |only spartan-3.0.1/spartan/man/import_model_result.Rd |only spartan-3.0.1/spartan/man/initialise_netlogo_xml_file.Rd |only spartan-3.0.1/spartan/man/join_strings.Rd | 40 spartan-3.0.1/spartan/man/join_strings_nospace.Rd | 36 spartan-3.0.1/spartan/man/join_strings_space.Rd | 36 spartan-3.0.1/spartan/man/kfoldCrossValidation.Rd | 62 spartan-3.0.1/spartan/man/lhc_calculatePRCCForMultipleTimepoints.Rd | 52 spartan-3.0.1/spartan/man/lhc_constructcoeff_dataset.Rd | 24 spartan-3.0.1/spartan/man/lhc_generateLHCSummary.Rd | 109 spartan-3.0.1/spartan/man/lhc_generateLHCSummary_overTime.Rd |only spartan-3.0.1/spartan/man/lhc_generatePRCoEffs.Rd | 88 spartan-3.0.1/spartan/man/lhc_generatePRCoEffs_overTime.Rd |only spartan-3.0.1/spartan/man/lhc_generateTimepointFiles.Rd | 58 spartan-3.0.1/spartan/man/lhc_generate_lhc_sample.Rd | 97 spartan-3.0.1/spartan/man/lhc_generate_lhc_sample_netlogo.Rd | 76 spartan-3.0.1/spartan/man/lhc_generate_netlogo_PRCoEffs.Rd | 56 spartan-3.0.1/spartan/man/lhc_graphMeasuresForParameterChange.Rd | 102 spartan-3.0.1/spartan/man/lhc_graphMeasuresForParameterChange_overTime.Rd |only spartan-3.0.1/spartan/man/lhc_netlogo_graphMeasuresForParameterChange.Rd | 84 spartan-3.0.1/spartan/man/lhc_plotCoEfficients.Rd | 66 spartan-3.0.1/spartan/man/lhc_polarplot.Rd | 70 spartan-3.0.1/spartan/man/lhc_process_netlogo_result.Rd | 74 spartan-3.0.1/spartan/man/lhc_process_sample_run_subsets.Rd | 154 - spartan-3.0.1/spartan/man/lhc_process_sample_run_subsets_overTime.Rd |only spartan-3.0.1/spartan/man/make_extension.Rd | 40 spartan-3.0.1/spartan/man/make_filename.Rd | 36 spartan-3.0.1/spartan/man/make_graph_title.Rd |only spartan-3.0.1/spartan/man/make_lhc_plot.Rd |only spartan-3.0.1/spartan/man/make_path.Rd | 36 spartan-3.0.1/spartan/man/meanSquaredError.Rd | 40 spartan-3.0.1/spartan/man/normaliseATest.Rd | 34 spartan-3.0.1/spartan/man/normalise_dataset.Rd | 52 spartan-3.0.1/spartan/man/nsga2_set_user_params.Rd | 78 spartan-3.0.1/spartan/man/num.decimals.Rd | 34 spartan-3.0.1/spartan/man/oat_csv_result_file_analysis.Rd | 97 spartan-3.0.1/spartan/man/oat_csv_result_file_analysis_overTime.Rd |only spartan-3.0.1/spartan/man/oat_generate_netlogo_behaviour_space_XML.Rd | 68 spartan-3.0.1/spartan/man/oat_graphATestsForSampleSize.Rd | 78 spartan-3.0.1/spartan/man/oat_parameter_sampling.Rd | 76 spartan-3.0.1/spartan/man/oat_plotResultDistribution.Rd | 82 spartan-3.0.1/spartan/man/oat_processParamSubsets.Rd | 113 spartan-3.0.1/spartan/man/oat_processParamSubsets_overTime.Rd |only spartan-3.0.1/spartan/man/oat_process_netlogo_result.Rd | 84 spartan-3.0.1/spartan/man/output_ggplot_graph.Rd |only spartan-3.0.1/spartan/man/output_param_sets_per_curve.Rd |only spartan-3.0.1/spartan/man/partition_dataset.Rd | 103 spartan-3.0.1/spartan/man/pcor.mat.Rd | 24 spartan-3.0.1/spartan/man/pcor.rec.Rd | 24 spartan-3.0.1/spartan/man/pcor.test.Rd | 24 spartan-3.0.1/spartan/man/perform_aTest_for_all_sim_measures.Rd | 48 spartan-3.0.1/spartan/man/plotATestsFromTimepointFiles.Rd | 68 spartan-3.0.1/spartan/man/plotPRCCSFromTimepointFiles.Rd | 76 spartan-3.0.1/spartan/man/plot_compare_sim_observed_to_model_prediction.Rd | 56 spartan-3.0.1/spartan/man/ploteFASTSiFromTimepointFiles.Rd | 54 spartan-3.0.1/spartan/man/prepare_parameter_value_list.Rd | 56 spartan-3.0.1/spartan/man/process_netlogo_parameter_range_info.Rd |only spartan-3.0.1/spartan/man/process_parameter_value_if_exists.Rd |only spartan-3.0.1/spartan/man/produce_accuracy_plots_all_measures.Rd | 50 spartan-3.0.1/spartan/man/produce_accuracy_plots_single_measure.Rd | 48 spartan-3.0.1/spartan/man/produce_atest_score_summary.Rd |only spartan-3.0.1/spartan/man/produce_summary_for_all_values_of_parameter.Rd |only spartan-3.0.1/spartan/man/rSquared.Rd | 40 spartan-3.0.1/spartan/man/read_all_curve_results.Rd |only spartan-3.0.1/spartan/man/read_from_csv.Rd |only spartan-3.0.1/spartan/man/read_model_result_file.Rd |only spartan-3.0.1/spartan/man/read_simulation_results.Rd |only spartan-3.0.1/spartan/man/retrieve_results_for_comparison_result_set.Rd |only spartan-3.0.1/spartan/man/sample_parameter_space.Rd |only spartan-3.0.1/spartan/man/scale_lhc_sample.Rd |only spartan-3.0.1/spartan/man/screen_nsga2_parameters.Rd | 84 spartan-3.0.1/spartan/man/selectSuitableStructure.Rd | 40 spartan-3.0.1/spartan/man/set.nsga_sensitivity_params.Rd | 64 spartan-3.0.1/spartan/man/sim_data_for_emulation.Rd | 60 spartan-3.0.1/spartan/man/summarise_lhc_sweep_responses.Rd |only spartan-3.0.1/spartan/man/summarise_replicate_runs.Rd |only spartan-3.0.1/spartan/man/tutorial_consistency_set.Rd | 54 spartan-3.0.1/spartan/man/updateErrorForStructure.Rd | 46 spartan-3.0.1/spartan/man/use_ensemble_to_generate_predictions.Rd | 64 spartan-3.0.1/spartan/man/visualise_data_distribution.Rd | 44 spartan-3.0.1/spartan/man/weight_emulator_predictions_by_ensemble.Rd | 58 spartan-3.0.1/spartan/man/write_data_to_csv.Rd |only spartan-3.0.1/spartan/tests |only spartan-3.0.1/spartan/vignettes/emulation_ensembles.Rmd | 763 ++--- spartan-3.0.1/spartan/vignettes/netlogo.Rmd | 5 spartan-3.0.1/spartan/vignettes/sensitivity_analysis.Rmd | 14 254 files changed, 10757 insertions(+), 9660 deletions(-)
Title: Functions for Epidemiological Analysis using Population Data
Description: Enables computation of epidemiological statistics, including those
where counts or mortality rates of the reference population are used.
Currently supported: excess hazard models, rates, mean survival times,
relative survival, and standardized incidence and mortality ratios
(SIRs/SMRs), all of which can be easily adjusted for by covariates such as
age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi')
and other computations achieved using 'data.table'.
Author: Joonas Miettinen [aut, cre],
Matti Rantanen [aut],
Karri Seppa [ctb]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>
Diff between popEpi versions 0.4.4 dated 2017-11-14 and 0.4.5 dated 2018-05-16
popEpi-0.4.4/popEpi/tests/testthat/test_splitting_randomly.R |only popEpi-0.4.5/popEpi/DESCRIPTION | 20 popEpi-0.4.5/popEpi/MD5 | 264 popEpi-0.4.5/popEpi/NAMESPACE | 176 popEpi-0.4.5/popEpi/NEWS.md | 274 popEpi-0.4.5/popEpi/R/S3_definitions.R | 2946 +++++----- popEpi-0.4.5/popEpi/R/aggregating.R | 1232 ++-- popEpi-0.4.5/popEpi/R/data_document.R | 348 - popEpi-0.4.5/popEpi/R/direct_adjusting.R | 314 - popEpi-0.4.5/popEpi/R/evaluation.R | 1914 +++--- popEpi-0.4.5/popEpi/R/flexyargs.R | 332 - popEpi-0.4.5/popEpi/R/fractional_years.R | 300 - popEpi-0.4.5/popEpi/R/incidence_rates.R | 689 +- popEpi-0.4.5/popEpi/R/incidence_rates_utils.R | 266 popEpi-0.4.5/popEpi/R/lexpand.R | 1880 +++--- popEpi-0.4.5/popEpi/R/lexpand2.R | 278 popEpi-0.4.5/popEpi/R/lifetime_function.R | 564 - popEpi-0.4.5/popEpi/R/ltable.R | 502 - popEpi-0.4.5/popEpi/R/mean_survival.R | 1326 ++-- popEpi-0.4.5/popEpi/R/popEpi_package.r | 60 popEpi-0.4.5/popEpi/R/pophaz.R | 136 popEpi-0.4.5/popEpi/R/prevalence.R | 282 popEpi-0.4.5/popEpi/R/relative_poisson.R | 1220 ++-- popEpi-0.4.5/popEpi/R/relative_poisson_net_survival.R | 352 - popEpi-0.4.5/popEpi/R/sir.R | 2900 ++++----- popEpi-0.4.5/popEpi/R/sir_utils.R | 226 popEpi-0.4.5/popEpi/R/splitLexisDT.R | 602 +- popEpi-0.4.5/popEpi/R/splitMulti.R | 538 - popEpi-0.4.5/popEpi/R/splitting_utility_functions.R | 2852 ++++----- popEpi-0.4.5/popEpi/R/startup_message.R | 85 popEpi-0.4.5/popEpi/R/survival_aggregated.R | 1780 +++--- popEpi-0.4.5/popEpi/R/survival_lexis.R | 1188 ++-- popEpi-0.4.5/popEpi/R/survival_utility_functions.R | 1276 ++-- popEpi-0.4.5/popEpi/R/utility_functions.R | 2872 ++++----- popEpi-0.4.5/popEpi/R/weighted_table.R | 1326 ++-- popEpi-0.4.5/popEpi/README.md | 378 - popEpi-0.4.5/popEpi/build/vignette.rds |binary popEpi-0.4.5/popEpi/inst/doc/sir.R | 128 popEpi-0.4.5/popEpi/inst/doc/sir.Rmd | 318 - popEpi-0.4.5/popEpi/inst/doc/sir.html | 600 +- popEpi-0.4.5/popEpi/inst/doc/survtab_examples.R | 340 - popEpi-0.4.5/popEpi/inst/doc/survtab_examples.Rmd | 592 +- popEpi-0.4.5/popEpi/inst/doc/survtab_examples.html | 822 +- popEpi-0.4.5/popEpi/man/ICSS.Rd | 72 popEpi-0.4.5/popEpi/man/Lexis_fpa.Rd | 164 popEpi-0.4.5/popEpi/man/RPL.Rd | 42 popEpi-0.4.5/popEpi/man/adjust.Rd | 48 popEpi-0.4.5/popEpi/man/aggre.Rd | 370 - popEpi-0.4.5/popEpi/man/all_names_present.Rd | 62 popEpi-0.4.5/popEpi/man/as.Date.yrs.Rd | 84 popEpi-0.4.5/popEpi/man/as.aggre.Rd | 152 popEpi-0.4.5/popEpi/man/as.data.frame.ratetable.Rd | 66 popEpi-0.4.5/popEpi/man/as.data.table.ratetable.Rd | 68 popEpi-0.4.5/popEpi/man/cast_simple.Rd | 100 popEpi-0.4.5/popEpi/man/cut_bound.Rd | 56 popEpi-0.4.5/popEpi/man/direct_standardization.Rd | 308 - popEpi-0.4.5/popEpi/man/fac2num.Rd | 74 popEpi-0.4.5/popEpi/man/flexible_argument.Rd | 334 - popEpi-0.4.5/popEpi/man/get.yrs.Rd | 156 popEpi-0.4.5/popEpi/man/is.Date.Rd | 82 popEpi-0.4.5/popEpi/man/is_leap_year.Rd | 56 popEpi-0.4.5/popEpi/man/lexpand.Rd | 736 +- popEpi-0.4.5/popEpi/man/lines.sirspline.Rd | 84 popEpi-0.4.5/popEpi/man/lines.survmean.Rd | 70 popEpi-0.4.5/popEpi/man/lines.survtab.Rd | 120 popEpi-0.4.5/popEpi/man/longDF2ratetable.Rd | 60 popEpi-0.4.5/popEpi/man/lower_bound.Rd | 36 popEpi-0.4.5/popEpi/man/ltable.Rd | 290 popEpi-0.4.5/popEpi/man/makeWeightsDT.Rd | 306 - popEpi-0.4.5/popEpi/man/meanpop_fi.Rd | 58 popEpi-0.4.5/popEpi/man/na2zero.Rd | 54 popEpi-0.4.5/popEpi/man/plot.rate.Rd | 66 popEpi-0.4.5/popEpi/man/plot.sir.Rd | 140 popEpi-0.4.5/popEpi/man/plot.sirspline.Rd | 92 popEpi-0.4.5/popEpi/man/plot.survmean.Rd | 76 popEpi-0.4.5/popEpi/man/plot.survtab.Rd | 126 popEpi-0.4.5/popEpi/man/poisson.ci.Rd | 52 popEpi-0.4.5/popEpi/man/popEpi.Rd | 68 popEpi-0.4.5/popEpi/man/pophaz.Rd | 114 popEpi-0.4.5/popEpi/man/popmort.Rd | 56 popEpi-0.4.5/popEpi/man/prepExpo.Rd | 210 popEpi-0.4.5/popEpi/man/print.aggre.Rd | 54 popEpi-0.4.5/popEpi/man/print.rate.Rd | 48 popEpi-0.4.5/popEpi/man/print.survtab.Rd | 66 popEpi-0.4.5/popEpi/man/rate.Rd | 212 popEpi-0.4.5/popEpi/man/rate_ratio.Rd | 140 popEpi-0.4.5/popEpi/man/relpois.Rd | 234 popEpi-0.4.5/popEpi/man/relpois_ag.Rd | 188 popEpi-0.4.5/popEpi/man/robust_values.Rd | 90 popEpi-0.4.5/popEpi/man/rpcurve.Rd | 142 popEpi-0.4.5/popEpi/man/setaggre.Rd | 104 popEpi-0.4.5/popEpi/man/setclass.Rd | 54 popEpi-0.4.5/popEpi/man/setcolsnull.Rd | 64 popEpi-0.4.5/popEpi/man/sibr.Rd | 76 popEpi-0.4.5/popEpi/man/sir.Rd | 388 - 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popEpi-0.4.5/popEpi/tests/testthat/test_survtab_usage.R | 960 +-- popEpi-0.4.5/popEpi/tests/testthat/test_utils.R | 834 +- popEpi-0.4.5/popEpi/tests/testthat/test_weighter.R | 278 popEpi-0.4.5/popEpi/vignettes/sir.Rmd | 318 - popEpi-0.4.5/popEpi/vignettes/survtab_examples.Rmd | 592 +- 134 files changed, 26881 insertions(+), 26789 deletions(-)
Title: Functions and Datasets to Accompany Hollander, Wolfe, and
Chicken - Nonparametric Statistical Methods, Third Edition
Description: Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Author: Grant Schneider, Eric Chicken, Rachel Becvarik
Maintainer: Grant Schneider <schneider.393@osu.edu>
Diff between NSM3 versions 1.11 dated 2018-02-25 and 1.12 dated 2018-05-16
NSM3-1.11/NSM3/man/NSM3-package.Rd |only NSM3-1.12/NSM3/DESCRIPTION | 8 ++++---- NSM3-1.12/NSM3/MD5 | 3 +-- 3 files changed, 5 insertions(+), 6 deletions(-)
Title: Get WHO Tuberculosis Data
Description: Facilitates easy import of analysis ready World Health Organisation Tuberculosis data and provides plotting functions for exploratory data analysis.
Author: Sam Abbott [aut, cre] (<https://orcid.org/0000-0001-8057-8037>)
Maintainer: Sam Abbott <contact@samabbott.co.uk>
Diff between getTBinR versions 0.5.3 dated 2018-03-10 and 0.5.4 dated 2018-05-16
DESCRIPTION | 19 ++-- MD5 | 72 ++++++++++------- NAMESPACE | 19 ++++ NEWS.md | 30 +++++-- R/get_tb_burden.R | 64 +++++++++++++-- R/map_tb_burden.R | 62 ++++++++++---- R/summarise_tb_burden.R |only README.md | 32 +++++-- build/vignette.rds |binary inst/doc/case_fatality_rate.Rmd | 2 inst/doc/case_fatality_rate.html | 86 +++++++++++--------- inst/doc/case_study_global_trends.Rmd | 2 inst/doc/case_study_global_trends.html | 19 ++-- inst/doc/intro.html | 109 ++++++++++++++++---------- man/figure/map-tb-incidence-eur-1.png |binary man/figure/plot-tb-incidence-eur-1.png |binary man/figure/plot-tb-incidence-eur-per-1.png |binary man/figure/plot-tb-incidence-uk-1.png |binary man/getTBinR-package.Rd | 2 man/get_tb_burden.Rd | 15 ++- man/map_tb_burden.Rd | 8 + man/plot_tb_burden.Rd | 2 man/plot_tb_burden_overview.Rd | 2 man/prepare_df_plot.Rd | 2 man/summarise_tb_burden.Rd |only tests/test-files |only tests/testthat/test-get_data.R | 4 tests/testthat/test-get_tb_burden.R | 25 +++++ tests/testthat/test-map_tb_burden.R | 28 ++++++ tests/testthat/test-plot_tb_burden.R | 6 + tests/testthat/test-plot_tb_burden_overview.R | 4 tests/testthat/test-prepare_df_plot.R | 5 - tests/testthat/test-summarise_tb_burden.R |only vignettes/case_fatality_rate.Rmd | 2 vignettes/case_study_global_trends.Rmd | 2 35 files changed, 429 insertions(+), 194 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-22 0.3-9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-25 0.15
2014-07-09 0.11
2013-12-10 0.9-4
Title: Statistical Disclosure Control Methods for Anonymization of
Microdata and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files. In
addition, various risk estimation methods are included. Note that the package
includes a graphical user interface that allows to use various methods of this
package.
Author: Matthias Templ [aut, cre],
Bernhard Meindl [aut],
Alexander Kowarik [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 5.2.0 dated 2018-04-13 and 5.3.0 dated 2018-05-16
DESCRIPTION | 8 MD5 | 54 ++-- NEWS | 11 R/GUIfunctions.R | 2 R/freqCalc.r | 4 R/riskyCells.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/CASCrefmicrodata.rda |binary data/EIA.rda |binary data/Tarragona.rda |binary data/casc1.rda |binary data/francdat.rda |binary data/free1.rda |binary data/microData.rda |binary data/testdata.RData |binary data/testdata2.RData |binary inst/doc/sdcMicro.Rmd | 4 inst/doc/sdcMicro.html | 192 ----------------- inst/doc/sdc_guidelines.pdf |binary inst/shiny/sdcApp/controllers/reactive_expressions.R | 2 inst/shiny/sdcApp/controllers/ui_export_data.R | 10 inst/shiny/sdcApp/controllers/ui_setup_sdc.R | 15 - inst/shiny/sdcApp/controllers/ui_sidebar_problemInfo.R | 3 inst/shiny/sdcApp/server.R | 1 man/riskyCells.Rd | 2 vignettes/sdcApp.R |only vignettes/sdcApp.html |only vignettes/sdcMicro.Rmd | 4 29 files changed, 86 insertions(+), 228 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on undirected graphical models for accomplishing three important and interrelated goals in genetics: (1) linkage map construction, (2) reconstructing intra- and inter-chromosomal conditional interactions (linkage disequilibrium) networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-phenotype-environment interactions network. For this purpose, we use conditional (in)dependence relationships between variables. The netgwas package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The package is implemented the recent developments in Behrouzi and Wit (2017) <arXiv:1710.00894> and Behrouzi and Wit (2017) <arXiv:1710.01063>.
NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between netgwas versions 0.1.4.2 dated 2018-04-06 and 1.5.0 dated 2018-05-16
DESCRIPTION | 13 +++--- MD5 | 5 +- inst |only man/netgwas-package.Rd | 101 +++++++++++++++++++++++++++---------------------- 4 files changed, 66 insertions(+), 53 deletions(-)
Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analysis functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/> including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: OECD <http://www.oecd.org/>, including PISA, TALIS, PIAAC; and IEA <http://www.iea.nl/>, including TIMSS, TIMSS Advanced, PIRLS, ICCS, ICILS, and CivEd.
Author: Paul Bailey [aut, cre], Ren C'deBaca [ctb], Ahmad Emad [aut], Huade Huo [aut], Michael Lee [aut], Yuqi Liao [aut], Trang Nguyen [aut], Qingshu Xie [aut], Jiao Yu [aut], Ting Zhang [aut]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between EdSurvey versions 1.0.6 dated 2017-05-04 and 2.0.3 dated 2018-05-16
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Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
The package is described in Calabrese & Fleming (2016) <doi:10.1111/2041-210X.12559> and its methods are based on those introduced in
Fleming et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2016) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
and
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc],
Rogério C. de Paula [dtc],
Thomas Akre [dtc],
Jonathan Drescher-Lehman [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.4.1 dated 2017-08-30 and 0.5.0 dated 2018-05-16
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Title: Geometric Shadow Calculations
Description: Functions for calculating: (1) shadow height, (2) logical shadow flag, (3) shadow footprint, (4) Sky View Factor and (5) radiation load. Basic required inputs include a polygonal layer of obstacle outlines along with their heights (i.e. "extruded polygons"), sun azimuth and sun elevation. The package also provides functions for related preliminary calculations: breaking polygons into line segments, determining azimuth of line segments, shifting segments by azimuth and distance, constructing the footprint of a line-of-sight between an observer and the sun, and creating a 3D grid covering the surface area of extruded polygons.
Author: Michael Dorman [aut, cre],
Evyatar Erell [ctb],
Itai Kloog [ctb],
Adi Vulkan [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between shadow versions 0.5.0 dated 2018-03-06 and 0.5.3 dated 2018-05-16
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Title: Growth Charts via Regression Quantiles
Description: Fits non-crossing regression quantiles as a function of linear covariates and multiple smooth terms via B-splines with L1-norm difference penalties. See Muggeo, Sciandra, Tomasello and Calvo (2013) <doi:10.1007/s10651-012-0232-1> and <doi:10.13140/RG.2.2.12924.85122> for some code example.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between quantregGrowth versions 0.4-0 dated 2018-03-06 and 0.4-1 dated 2018-05-16
DESCRIPTION | 10 ++-- MD5 | 16 +++--- NAMESPACE | 4 - NEWS | 12 ++++- R/gcrq.R | 28 +++++++++++- R/plot.gcrq.R | 97 +++++++++++++++++++++++++++++++++++------- man/gcrq.Rd | 2 man/plot.gcrq.Rd | 21 ++++++--- man/quantregGrowth-package.Rd | 6 +- 9 files changed, 153 insertions(+), 43 deletions(-)
More information about quantregGrowth at CRAN
Permanent link
Title: The Poisson Binomial Distribution
Description: Implementation of both the exact and approximation methods for computing the cdf of the Poisson binomial distribution. It also provides the pmf, quantile function, and random number generation for the Poisson binomial distribution.
Author: Yili Hong
Maintainer: Yili Hong <yilihong@vt.edu>
Diff between poibin versions 1.2 dated 2013-02-14 and 1.3 dated 2018-05-16
DESCRIPTION | 14 ++++++-------- MD5 | 10 ++++++---- NAMESPACE | 3 ++- build |only man/poibin-package.Rd | 25 ++++++++----------------- man/ppoibin.Rd | 2 +- src/poibin_init.c |only 7 files changed, 23 insertions(+), 31 deletions(-)
Title: Downloads, Unpacks and Tidies Legislative Data from the
Brazilian Federal Senate and Chamber of Deputies
Description: Downloads and tidies data from the Brazilian Federal Senate and
Chamber of Deputies Application Programming Interfaces available at <http://
legis.senado.gov.br/dadosabertos/> and <http://www.camara.leg.br/SitCamaraWS/>
respectively.
Author: Robert McDonnell [aut, cre],
Guilherme Jardim Duarte [aut],
Danilo Freire [aut],
Julio Trecenti [aut]
Maintainer: Robert McDonnell <mcdonnell.robert5@gmail.com>
Diff between congressbr versions 0.1.1 dated 2017-06-20 and 0.1.2 dated 2018-05-16
congressbr-0.1.1/congressbr/data/senate_nominal_votes.rda |only congressbr-0.1.1/congressbr/man/senate_nominal_votes.Rd |only congressbr-0.1.2/congressbr/DESCRIPTION | 30 congressbr-0.1.2/congressbr/MD5 | 67 - congressbr-0.1.2/congressbr/NEWS.md | 4 congressbr-0.1.2/congressbr/R/cham_nominal_votes.R |only congressbr-0.1.2/congressbr/R/cham_votes.R | 10 congressbr-0.1.2/congressbr/R/sen_agenda.R | 8 congressbr-0.1.2/congressbr/R/sen_bill_search.R | 5 congressbr-0.1.2/congressbr/R/sen_bills.R | 62 - congressbr-0.1.2/congressbr/R/sen_bills_various.R | 87 + congressbr-0.1.2/congressbr/R/sen_budget.R | 2 congressbr-0.1.2/congressbr/R/sen_coalition_info.R | 2 congressbr-0.1.2/congressbr/R/sen_coalitions.R | 6 congressbr-0.1.2/congressbr/R/sen_commission_list.R | 8 congressbr-0.1.2/congressbr/R/sen_nominal_votes.R | 6 congressbr-0.1.2/congressbr/R/sen_plenary.R | 16 congressbr-0.1.2/congressbr/R/sen_senator.R | 12 congressbr-0.1.2/congressbr/R/sen_senator_details.R | 12 congressbr-0.1.2/congressbr/R/sen_senator_list.R | 6 congressbr-0.1.2/congressbr/R/sen_sponsor_list.R | 4 congressbr-0.1.2/congressbr/R/sen_various.R | 10 congressbr-0.1.2/congressbr/R/sen_votes.R | 4 congressbr-0.1.2/congressbr/R/util.R | 2 congressbr-0.1.2/congressbr/R/vote_to_rollcall.R | 45 congressbr-0.1.2/congressbr/README.md | 208 +++- congressbr-0.1.2/congressbr/build/vignette.rds |binary congressbr-0.1.2/congressbr/data/cham_nominal_votes.rda |only congressbr-0.1.2/congressbr/data/sen_nominal_votes.rda |only congressbr-0.1.2/congressbr/inst/doc/chamber.html | 506 +++++++--- congressbr-0.1.2/congressbr/inst/doc/senate.R | 18 congressbr-0.1.2/congressbr/inst/doc/senate.Rmd | 22 congressbr-0.1.2/congressbr/inst/doc/senate.html | 646 +++++++++----- congressbr-0.1.2/congressbr/man/cham_nominal_votes.Rd |only congressbr-0.1.2/congressbr/man/sen_bills.Rd | 6 congressbr-0.1.2/congressbr/man/sen_nominal_votes.Rd |only congressbr-0.1.2/congressbr/man/vote_to_rollcall.Rd | 24 congressbr-0.1.2/congressbr/vignettes/senate.Rmd | 22 38 files changed, 1173 insertions(+), 687 deletions(-)
Title: 'TK' Widget Tools for 'rgl'
Description: Provides 'TK' widget tools for the 'rgl' package.
Author: Duncan Murdoch/Ming Chen
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between tkrgl versions 0.7 dated 2011-11-27 and 0.8 dated 2018-05-16
DESCRIPTION | 16 ++++---- MD5 | 13 +++--- NAMESPACE | 4 ++ build |only man/par3dsave.Rd | 91 +++++++++++++++++++++++----------------------- man/spin3d.Rd | 55 ++++++++++++++-------------- man/spinControl.Rd | 100 ++++++++++++++++++++++++++------------------------- man/tkrgl-package.Rd | 70 +++++++++++++---------------------- 8 files changed, 172 insertions(+), 177 deletions(-)
Title: Japanese Map Data and Functions
Description: Digital map data of Japan for choropleth mapping, including a circle cartogram.
Author: Susumu Tanimura [aut, cre]
Maintainer: Susumu Tanimura <aruminat@gmail.com>
Diff between NipponMap versions 0.1 dated 2017-11-29 and 0.2 dated 2018-05-16
ChangeLog | 10 ++++++ DESCRIPTION | 8 ++--- MD5 | 11 ++++--- R/JapanPrefMap.R | 4 ++ build |only man/JapanPrefMap.Rd | 5 ++- man/NipponMap-package.Rd | 68 ++++++++++++++++++++++++++--------------------- 7 files changed, 64 insertions(+), 42 deletions(-)
Title: Japanese Utility Functions and Data
Description: Japan-specific data is sometimes too unhandy for R users to manage. The utility functions and data in this package disencumber us from such an unnecessary burden.
Author: Susumu Tanimura <aruminat@gmail.com> [aut, cre],
Hironobu Takahashi [cph],
Hajime Baba [cph],
Takatsugu Nokubi [cph]
Maintainer: Susumu Tanimura <aruminat@gmail.com>
Diff between Nippon versions 0.7 dated 2018-05-06 and 0.7.1 dated 2018-05-16
ChangeLog | 3 ++ DESCRIPTION | 8 +++--- MD5 | 7 +++--- build |only man/Nippon-package.Rd | 58 +++++++++++++++++++++++++++----------------------- 5 files changed, 43 insertions(+), 33 deletions(-)
Title: Lightning Fast Serialization of Data Frames for R
Description: Multithreaded serialization of compressed data frames using the
'fst' format. The 'fst' format allows for random access of stored data and
compression with the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD
compression library is owned by Facebook Inc.
Author: Mark Klik [aut, cre, cph],
Yann Collet [ctb, cph] (Yann Collet is author of the bundled LZ4 and
ZSTD code and copyright holder of LZ4),
Facebook, Inc. [cph] (Bundled ZSTD code)
Maintainer: Mark Klik <markklik@gmail.com>
Diff between fst versions 0.8.4 dated 2018-01-25 and 0.8.6 dated 2018-05-16
fst-0.8.4/fst/src/fstcore/LZ4/lz4.cpp |only fst-0.8.6/fst/DESCRIPTION | 10 fst-0.8.6/fst/MD5 | 141 fst-0.8.6/fst/NAMESPACE | 2 fst-0.8.6/fst/R/RcppExports.R | 4 fst-0.8.6/fst/R/fst.R | 48 fst-0.8.6/fst/R/fst_table.R | 149 fst-0.8.6/fst/R/onAttach.R | 29 fst-0.8.6/fst/R/openmp.R | 24 fst-0.8.6/fst/R/package.R | 40 fst-0.8.6/fst/R/type_dependencies.R |only fst-0.8.6/fst/man/fst.Rd | 10 fst-0.8.6/fst/man/threads_fst.Rd | 16 fst-0.8.6/fst/man/write_fst.Rd | 20 fst-0.8.6/fst/src/RcppExports.cpp | 10 fst-0.8.6/fst/src/flex_store.cpp | 2 fst-0.8.6/fst/src/fst_blockrunner_char.h | 12 fst-0.8.6/fst/src/fst_column.h | 33 fst-0.8.6/fst/src/fstcore/LZ4/lz4.c |only fst-0.8.6/fst/src/fstcore/LZ4/lz4.h | 294 - fst-0.8.6/fst/src/fstcore/LZ4/xxhash.c | 2 fst-0.8.6/fst/src/fstcore/ZSTD/common/bitstream.h | 4 fst-0.8.6/fst/src/fstcore/ZSTD/common/compiler.h | 25 fst-0.8.6/fst/src/fstcore/ZSTD/common/cpu.h |only fst-0.8.6/fst/src/fstcore/ZSTD/common/error_private.c | 1 fst-0.8.6/fst/src/fstcore/ZSTD/common/fse.h | 2 fst-0.8.6/fst/src/fstcore/ZSTD/common/fse_decompress.c | 4 fst-0.8.6/fst/src/fstcore/ZSTD/common/huf.h | 203 fst-0.8.6/fst/src/fstcore/ZSTD/common/mem.h | 39 fst-0.8.6/fst/src/fstcore/ZSTD/common/pool.c | 66 fst-0.8.6/fst/src/fstcore/ZSTD/common/pool.h | 27 fst-0.8.6/fst/src/fstcore/ZSTD/common/threading.h | 24 fst-0.8.6/fst/src/fstcore/ZSTD/common/zstd_common.c | 14 fst-0.8.6/fst/src/fstcore/ZSTD/common/zstd_errors.h | 23 fst-0.8.6/fst/src/fstcore/ZSTD/common/zstd_internal.h | 229 fst-0.8.6/fst/src/fstcore/ZSTD/compress/fse_compress.c | 30 fst-0.8.6/fst/src/fstcore/ZSTD/compress/huf_compress.c | 222 fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_compress.c | 2064 ++++--- fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_compress_internal.h |only fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_double_fast.c | 141 fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_double_fast.h | 18 fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_fast.c | 159 fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_fast.h | 19 fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_lazy.c | 625 +- fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_lazy.h | 48 fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_ldm.c | 680 +- fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_ldm.h | 94 fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_opt.c | 1354 ++-- fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstd_opt.h | 24 fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstdmt_compress.c | 1626 ++++- fst-0.8.6/fst/src/fstcore/ZSTD/compress/zstdmt_compress.h | 54 fst-0.8.6/fst/src/fstcore/ZSTD/decompress/huf_decompress.c | 680 +- fst-0.8.6/fst/src/fstcore/ZSTD/decompress/zstd_decompress.c | 1274 ++-- fst-0.8.6/fst/src/fstcore/ZSTD/dictBuilder/cover.c | 19 fst-0.8.6/fst/src/fstcore/ZSTD/dictBuilder/divsufsort.c | 2744 +++++----- fst-0.8.6/fst/src/fstcore/ZSTD/dictBuilder/zdict.c | 135 fst-0.8.6/fst/src/fstcore/ZSTD/dictBuilder/zdict.h | 87 fst-0.8.6/fst/src/fstcore/ZSTD/zstd.h | 549 +- fst-0.8.6/fst/src/fstcore/compression/compression.cpp | 4 fst-0.8.6/fst/src/fstcore/interface/fststore.cpp | 4 fst-0.8.6/fst/src/fstcore/interface/ifstcolumn.h | 6 fst-0.8.6/fst/src/fstcore/interface/openmphelper.cpp | 58 fst-0.8.6/fst/src/fstcore/interface/openmphelper.h | 53 fst-0.8.6/fst/src/init.c | 31 fst-0.8.6/fst/src/openmp.cpp | 72 fst-0.8.6/fst/src/openmp.h | 30 fst-0.8.6/fst/tests/testthat/1.fst |only fst-0.8.6/fst/tests/testthat/FactorStore/data1.fst |binary fst-0.8.6/fst/tests/testthat/datasets/enc.fst |only fst-0.8.6/fst/tests/testthat/encoding.fst |only fst-0.8.6/fst/tests/testthat/some_fst_file.fst |only fst-0.8.6/fst/tests/testthat/test_encoding.R | 13 fst-0.8.6/fst/tests/testthat/test_factor.R | 1 fst-0.8.6/fst/tests/testthat/test_fst_table.R | 100 fst-0.8.6/fst/tests/testthat/test_omp.R | 45 fst-0.8.6/fst/tests/testthat/test_roundtrip.R | 10 76 files changed, 8515 insertions(+), 6065 deletions(-)
Title: Calculates the Bidimensional Regression Between Two 2D
Configurations
Description: Calculates the bidimensional regression between two 2D configurations following the approach by Tobler (1965).
Author: Claus-Christian Carbon [aut],
Alexander (Sasha) Pastukhov [cre, ctb]
Maintainer: Alexander (Sasha) Pastukhov <pastukhov.alexander@gmail.com>
Diff between BiDimRegression versions 1.0.6 dated 2014-03-22 and 2.0.0 dated 2018-05-16
BiDimRegression-1.0.6/BiDimRegression/R/print.BiDimRegression.R |only BiDimRegression-1.0.6/BiDimRegression/R/print.summary.BiDimRegression.R |only BiDimRegression-1.0.6/BiDimRegression/R/summary.BiDimRegression.R |only BiDimRegression-1.0.6/BiDimRegression/THANKS |only BiDimRegression-1.0.6/BiDimRegression/man/BiDimRegression-package.Rd |only BiDimRegression-1.0.6/BiDimRegression/man/print.BiDimRegression.Rd |only BiDimRegression-1.0.6/BiDimRegression/man/print.summary.BiDimRegression.Rd |only BiDimRegression-1.0.6/BiDimRegression/man/summary.BiDimRegression.Rd |only BiDimRegression-2.0.0/BiDimRegression/DESCRIPTION | 36 BiDimRegression-2.0.0/BiDimRegression/MD5 | 40 BiDimRegression-2.0.0/BiDimRegression/NAMESPACE | 22 BiDimRegression-2.0.0/BiDimRegression/NEWS.md |only BiDimRegression-2.0.0/BiDimRegression/R/BiDimRegression.R | 414 ++++++---- BiDimRegression-2.0.0/BiDimRegression/R/bidimensional.R |only BiDimRegression-2.0.0/BiDimRegression/R/data.R |only BiDimRegression-2.0.0/BiDimRegression/README.md |only BiDimRegression-2.0.0/BiDimRegression/build |only BiDimRegression-2.0.0/BiDimRegression/data/EyegazeData.rda |only BiDimRegression-2.0.0/BiDimRegression/inst |only BiDimRegression-2.0.0/BiDimRegression/man/BiDimRegression.Rd | 80 + BiDimRegression-2.0.0/BiDimRegression/man/EyegazeData.Rd |only BiDimRegression-2.0.0/BiDimRegression/man/anova.lm2.Rd |only BiDimRegression-2.0.0/BiDimRegression/man/lm2.Rd |only BiDimRegression-2.0.0/BiDimRegression/man/lm2affine.Rd |only BiDimRegression-2.0.0/BiDimRegression/man/lm2euclidean.Rd |only BiDimRegression-2.0.0/BiDimRegression/man/lm2fit.Rd |only BiDimRegression-2.0.0/BiDimRegression/man/lm2projective.Rd |only BiDimRegression-2.0.0/BiDimRegression/man/predict.lm2.Rd |only BiDimRegression-2.0.0/BiDimRegression/man/summary.lm2.Rd |only BiDimRegression-2.0.0/BiDimRegression/tests |only BiDimRegression-2.0.0/BiDimRegression/vignettes |only 31 files changed, 379 insertions(+), 213 deletions(-)
More information about BiDimRegression at CRAN
Permanent link
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Diff between mvSLOUCH versions 1.3.3 dated 2017-06-18 and 1.3.4 dated 2018-05-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/mvSLOUCH-package.Rd | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Generalized Least Squares with Measurement Error
Description: Performs linear regression with correlated predictors, responses and correlated measurement errors in predictors and responses, correcting for biased caused by these.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Diff between GLSME versions 1.0.3 dated 2015-07-20 and 1.0.4 dated 2018-05-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/GLSME-package.Rd | 7 ++++--- man/GLSME.Rd | 3 ++- man/GLSME.predict.Rd | 3 ++- 5 files changed, 16 insertions(+), 13 deletions(-)
Title: The Multiplicative Multinomial Distribution
Description: Various utilities for the Multiplicative Multinomial distribution.
Author: Robin K. S. Hankin and P. M. E. Altham
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between MM versions 1.6-2 dated 2013-01-21 and 1.6-5 dated 2018-05-16
DESCRIPTION | 18 +++++++++--------- MD5 | 26 ++++++++++++++------------ NAMESPACE | 14 ++++++++++++++ R/MM.R | 1 - build |only data/danaher.rda |binary data/pollen.rda |binary data/powell.rda |binary data/skellam.rda |binary data/sweets.rda |binary data/voting.rda |binary data/wilson.rda |binary inst/doc/Gianfranco.R |only inst/doc/Gianfranco.pdf |binary man/Lindsey.Rd | 1 + 15 files changed, 38 insertions(+), 22 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-22 1.3.4
2017-12-17 1.3.3
2017-08-28 1.2.3
2017-06-01 1.2.1
2017-06-01 1.2.2
2017-05-27 1.2.0
2016-11-18 1.1.0
2016-10-10 1.0.0
Title: Efficient and Accurate P-Value Computation for Position Weight
Matrices
Description: In putative Transcription Factor Binding Sites (TFBSs)
identification from sequence/alignments,
we are interested in the significance of certain match score.
TFMPvalue provides the accurate calculation of P-value with
score threshold for Position Weight Matrices,
or the score with given P-value.
It is an interface to code originally made available by
Helene Touzet and Jean-Stephane Varre, 2007,
Algorithms Mol Biol:2, 15.
Touzet and Varre (2007) <DOI:10.1186/1748-7188-2-15>.
Author: Ge Tan <ge_tan@live.com>
Maintainer: Ge Tan <ge_tan@live.com>
Diff between TFMPvalue versions 0.0.6 dated 2015-11-29 and 0.0.8 dated 2018-05-16
DESCRIPTION | 16 +++++++++------- MD5 | 7 +++++-- src/Makevars |only src/Makevars.win |only src/Matrix.h | 2 +- src/TFMPvalue_init.c |only 6 files changed, 15 insertions(+), 10 deletions(-)
Title: Bayesian Genomic Linear Models Applied to GE Genome Selection
Description: Application of genome prediction for a continuous variable, focused
on genotype by environment (GE) genomic selection models (GS). It consists a group of functions
that help to create regression kernels for some GE genomic models proposed by JarquÃn et al. (2014) <doi:10.1007/s00122-013-2243-1>
and Lopez-Cruz et al. (2015) <doi:10.1534/g3.114.016097>. Also, it computes genomic predictions based on Bayesian approaches.
The prediction function uses an orthogonal transformation of the data and specific priors
present by Cuevas et al. (2014) <doi:10.1534/g3.114.013094>.
Author: Italo Granato [aut, cre],
Luna-Vázquez Francisco J. [aut],
Cuevas Jaime [aut]
Maintainer: Italo Granato <italo.granato@gmail.com>
Diff between BGGE versions 0.6.2 dated 2018-05-10 and 0.6.3 dated 2018-05-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/getK.R | 4 ++++ 3 files changed, 10 insertions(+), 6 deletions(-)
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut, cre],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>),
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifeng Geng [aut],
Yutian Li [aut],
XGBoost contributors [cph] (base XGBoost implementation)
Maintainer: Tong He <hetong007@gmail.com>
Diff between xgboost versions 0.6.4.1 dated 2018-01-23 and 0.71.1 dated 2018-05-16
xgboost-0.6.4.1/xgboost/src/src/common/thread_local.h |only xgboost-0.71.1/xgboost/DESCRIPTION | 58 xgboost-0.71.1/xgboost/MD5 | 320 ++- xgboost-0.71.1/xgboost/NAMESPACE | 10 xgboost-0.71.1/xgboost/R/callbacks.R | 249 ++ xgboost-0.71.1/xgboost/R/utils.R | 59 xgboost-0.71.1/xgboost/R/xgb.Booster.R | 389 ++-- xgboost-0.71.1/xgboost/R/xgb.DMatrix.R | 106 - xgboost-0.71.1/xgboost/R/xgb.DMatrix.save.R | 6 xgboost-0.71.1/xgboost/R/xgb.create.features.R | 2 xgboost-0.71.1/xgboost/R/xgb.cv.R | 34 xgboost-0.71.1/xgboost/R/xgb.dump.R | 40 xgboost-0.71.1/xgboost/R/xgb.importance.R | 190 +- xgboost-0.71.1/xgboost/R/xgb.load.R | 23 xgboost-0.71.1/xgboost/R/xgb.model.dt.tree.R | 112 - xgboost-0.71.1/xgboost/R/xgb.plot.deepness.R | 16 xgboost-0.71.1/xgboost/R/xgb.plot.importance.R | 10 xgboost-0.71.1/xgboost/R/xgb.plot.multi.trees.R | 166 + xgboost-0.71.1/xgboost/R/xgb.plot.shap.R |only xgboost-0.71.1/xgboost/R/xgb.plot.tree.R | 140 + xgboost-0.71.1/xgboost/R/xgb.save.R | 29 xgboost-0.71.1/xgboost/R/xgb.save.raw.R | 2 xgboost-0.71.1/xgboost/R/xgb.train.R | 94 - 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xgboost-0.71.1/xgboost/src/src/common/random.h | 4 xgboost-0.71.1/xgboost/src/src/common/row_set.h |only xgboost-0.71.1/xgboost/src/src/common/timer.h |only xgboost-0.71.1/xgboost/src/src/data/data.cc | 118 - xgboost-0.71.1/xgboost/src/src/data/simple_csr_source.cc | 21 xgboost-0.71.1/xgboost/src/src/data/simple_csr_source.h | 6 xgboost-0.71.1/xgboost/src/src/data/simple_dmatrix.cc | 104 - xgboost-0.71.1/xgboost/src/src/data/simple_dmatrix.h | 28 xgboost-0.71.1/xgboost/src/src/data/sparse_batch_page.h | 21 xgboost-0.71.1/xgboost/src/src/data/sparse_page_dmatrix.cc | 67 xgboost-0.71.1/xgboost/src/src/data/sparse_page_dmatrix.h | 31 xgboost-0.71.1/xgboost/src/src/data/sparse_page_raw_format.cc | 5 xgboost-0.71.1/xgboost/src/src/data/sparse_page_source.cc | 34 xgboost-0.71.1/xgboost/src/src/data/sparse_page_source.h | 2 xgboost-0.71.1/xgboost/src/src/data/sparse_page_writer.cc | 12 xgboost-0.71.1/xgboost/src/src/gbm/gblinear.cc | 453 ++--- xgboost-0.71.1/xgboost/src/src/gbm/gblinear_model.h |only xgboost-0.71.1/xgboost/src/src/gbm/gbm.cc | 1 xgboost-0.71.1/xgboost/src/src/gbm/gbtree.cc | 716 +++----- xgboost-0.71.1/xgboost/src/src/gbm/gbtree_model.h |only xgboost-0.71.1/xgboost/src/src/learner.cc | 401 ++-- xgboost-0.71.1/xgboost/src/src/linear |only xgboost-0.71.1/xgboost/src/src/metric/elementwise_metric.cc | 12 xgboost-0.71.1/xgboost/src/src/metric/multiclass_metric.cc | 16 xgboost-0.71.1/xgboost/src/src/metric/rank_metric.cc | 248 ++ xgboost-0.71.1/xgboost/src/src/objective/multiclass_obj.cc | 35 xgboost-0.71.1/xgboost/src/src/objective/objective.cc | 6 xgboost-0.71.1/xgboost/src/src/objective/rank_obj.cc | 75 xgboost-0.71.1/xgboost/src/src/objective/regression_loss.h |only xgboost-0.71.1/xgboost/src/src/objective/regression_obj.cc | 315 ++- xgboost-0.71.1/xgboost/src/src/objective/regression_obj_gpu.cu |only xgboost-0.71.1/xgboost/src/src/predictor |only xgboost-0.71.1/xgboost/src/src/tree/fast_hist_param.h |only xgboost-0.71.1/xgboost/src/src/tree/param.h | 209 +- xgboost-0.71.1/xgboost/src/src/tree/tree_model.cc | 113 - xgboost-0.71.1/xgboost/src/src/tree/tree_updater.cc | 7 xgboost-0.71.1/xgboost/src/src/tree/updater_basemaker-inl.h | 168 - xgboost-0.71.1/xgboost/src/src/tree/updater_colmaker.cc | 625 +++---- xgboost-0.71.1/xgboost/src/src/tree/updater_fast_hist.cc |only xgboost-0.71.1/xgboost/src/src/tree/updater_gpu.cu |only xgboost-0.71.1/xgboost/src/src/tree/updater_gpu_common.cuh |only xgboost-0.71.1/xgboost/src/src/tree/updater_gpu_hist.cu |only xgboost-0.71.1/xgboost/src/src/tree/updater_histmaker.cc | 549 +++--- xgboost-0.71.1/xgboost/src/src/tree/updater_prune.cc | 42 xgboost-0.71.1/xgboost/src/src/tree/updater_refresh.cc | 83 xgboost-0.71.1/xgboost/src/src/tree/updater_skmaker.cc | 236 +- xgboost-0.71.1/xgboost/src/src/tree/updater_sync.cc | 10 xgboost-0.71.1/xgboost/src/xgboost_R.cc | 13 xgboost-0.71.1/xgboost/tests/testthat/test_basic.R | 54 xgboost-0.71.1/xgboost/tests/testthat/test_callbacks.R | 53 xgboost-0.71.1/xgboost/tests/testthat/test_dmatrix.R | 25 xgboost-0.71.1/xgboost/tests/testthat/test_glm.R | 41 xgboost-0.71.1/xgboost/tests/testthat/test_helpers.R | 187 +- xgboost-0.71.1/xgboost/tests/testthat/test_monotone.R | 4 xgboost-0.71.1/xgboost/tests/testthat/test_update.R | 39 xgboost-0.71.1/xgboost/vignettes/discoverYourData.Rmd | 13 175 files changed, 7038 insertions(+), 4807 deletions(-)
Title: Estimating Regulatory Scores and Identifying ATAC-STARR Data
Description: An algorithm for identifying high-resolution driver elements for datasets from a high-definition reporter assay library. Xinchen Wang, Liang He, Sarah Goggin, Alham Saadat, Li Wang, Melina Claussnitzer, Manolis Kellis (2017) <doi:10.1101/193136>.
Author: Liang He
Maintainer: Liang He <lianghe@mit.edu>
Diff between sharpr2 versions 1.0.0.0 dated 2017-11-07 and 1.1.1.0 dated 2018-05-16
DESCRIPTION | 18 +++++++------- MD5 | 18 +++++++------- NAMESPACE | 4 ++- R/sharpr2.r | 12 ++++++++- R/sharpr2_local.r | 49 ++++++++++++++++++++++++++++------------ R/sharpr2_local_r.r | 60 +++++++++++++++++++++++++++++++++++-------------- data/hidra_ex.rda |binary man/hidra_ex.Rd | 2 - man/sharpr2-package.Rd | 8 +++--- man/sharpr2.Rd | 6 +++- 10 files changed, 119 insertions(+), 58 deletions(-)
Title: Polygon Clipping
Description: R port of Angus Johnson's open source library Clipper. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. Computes Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.
Author: Angus Johnson [aut] (C++ original,
http://www.angusj.com/delphi/clipper.php),
Adrian Baddeley [aut, trl, cre],
Brian D. Ripley [ctb],
Elliott Sales de Andrade [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between polyclip versions 1.8-3 dated 2018-05-11 and 1.8-7 dated 2018-05-16
DESCRIPTION | 14 ++++++++------ MD5 | 10 +++++----- configure | 20 ++++++++++---------- configure.ac | 4 ++-- src/clipper.h | 10 ++++++++++ src/interface.cpp | 2 +- 6 files changed, 36 insertions(+), 24 deletions(-)
Title: Markov-Switching GARCH Models
Description: Fit (by Maximum Likelihood or MCMC/Bayesian), simulate, and forecast various Markov-Switching GARCH models as described in Ardia et al. (2017) <https://ssrn.com/abstract=2845809>.
Author: David Ardia [aut],
Keven Bluteau [aut, cre],
Kris Boudt [ctb],
Leopoldo Catania [aut],
Alexios Ghalanos [ctb],
Brian Peterson [ctb],
Denis-Alexandre Trottier [aut]
Maintainer: Keven Bluteau <Keven.Bluteau@unine.ch>
Diff between MSGARCH versions 2.1 dated 2018-02-26 and 2.3 dated 2018-05-16
DESCRIPTION | 11 +++++++---- MD5 | 14 +++++++------- NEWS | 8 ++++++++ R/Inference.R | 4 ++-- R/Utils.R | 2 +- THANKS | 1 + inst/CITATION | 10 ++++++++-- man/MSGARCH-package.Rd | 1 + 8 files changed, 35 insertions(+), 16 deletions(-)
Title: Chordalysis R Package
Description: Learning the structure of graphical models from datasets with thousands of variables.
More information about the research papers detailing the theory behind Chordalysis is available at
<http://www.francois-petitjean.com/Research> (KDD 2016, SDM 2015, ICDM 2014, ICDM 2013).
The R package development site is <https://github.com/HerrmannM/Monash-ChoR>.
Author: François Petitjean [aut],
Matthieu Herrmann [aut, com, cre],
Christoph Bergmeir [ctb]
Maintainer: Matthieu Herrmann <matthieu.herrmann@monash.edu>
Diff between ChoR versions 0.0-3 dated 2017-10-12 and 0.0-4 dated 2018-05-16
DESCRIPTION | 10 +++++----- MD5 | 15 +++++++++------ R/onLoad.R | 9 ++++++++- inst/examples/script.R | 46 ++++++++++------------------------------------ inst/extdata |only inst/java/choR.jar |binary java/choR.jar |binary man/ChoR.Rd | 46 ++++++++++------------------------------------ 8 files changed, 42 insertions(+), 84 deletions(-)
Title: Irucka Embry's Miscellaneous Functions
Description: A collection of Irucka Embry's miscellaneous functions
(Engineering Economics, Civil & Environmental/Water Resources Engineering,
Geometry, Statistics, GNU Octave length functions, Trigonometric functions
in degrees, etc.).
Author: Irucka Embry [aut, cre], Felix Andrews [aut, ctb] (zoo code), Hans
Werner Borchers [aut, ctb] (pracma code), Samit Basu [aut, ctb]
(FreeMat code), David Bateman [aut, ctb] (GNU Octave code), Rik Wehbring
[aut, ctb] (GNU Octave code)
Maintainer: Irucka Embry <iembry@ecoccs.com>
Diff between iemisc versions 0.9.6 dated 2016-10-17 and 0.9.7 dated 2018-05-16
iemisc-0.9.6/iemisc/R/concr_mix_normal_strength.R |only iemisc-0.9.6/iemisc/man/concr_mix_normal_strength.Rd |only iemisc-0.9.7/iemisc/DESCRIPTION | 24 iemisc-0.9.7/iemisc/MD5 | 158 ++-- iemisc-0.9.7/iemisc/NAMESPACE | 10 iemisc-0.9.7/iemisc/NEWS.md | 57 + iemisc-0.9.7/iemisc/R/Manningcirc.R | 28 iemisc-0.9.7/iemisc/R/Manningpara.R | 44 - iemisc-0.9.7/iemisc/R/Manningrect.R | 36 - iemisc-0.9.7/iemisc/R/Manningtrap.R | 53 - iemisc-0.9.7/iemisc/R/Manningtri.R | 36 - iemisc-0.9.7/iemisc/R/PgivenG.R | 2 iemisc-0.9.7/iemisc/R/benefitcost.R | 26 iemisc-0.9.7/iemisc/R/iemisc.R | 10 iemisc-0.9.7/iemisc/R/size.R | 4 iemisc-0.9.7/iemisc/README.md | 6 iemisc-0.9.7/iemisc/build/vignette.rds |binary iemisc-0.9.7/iemisc/inst/CITATION | 8 iemisc-0.9.7/iemisc/inst/doc/Open-Channel-Flow_Examples_Geometric_Shapes.R | 15 iemisc-0.9.7/iemisc/inst/doc/Open-Channel-Flow_Examples_Geometric_Shapes.Rmd | 15 iemisc-0.9.7/iemisc/inst/doc/Open-Channel-Flow_Examples_Geometric_Shapes.html | 351 +++++----- iemisc-0.9.7/iemisc/man/AgivenF.Rd | 4 iemisc-0.9.7/iemisc/man/AgivenFcont.Rd | 1 iemisc-0.9.7/iemisc/man/AgivenG.Rd | 1 iemisc-0.9.7/iemisc/man/AgivenP.Rd | 4 iemisc-0.9.7/iemisc/man/AgivenPcont.Rd | 1 iemisc-0.9.7/iemisc/man/CompIntPaid.Rd | 1 iemisc-0.9.7/iemisc/man/EffInt.Rd | 1 iemisc-0.9.7/iemisc/man/FgivenA.Rd | 4 iemisc-0.9.7/iemisc/man/FgivenAcont.Rd | 1 iemisc-0.9.7/iemisc/man/FgivenP.Rd | 4 iemisc-0.9.7/iemisc/man/FgivenPcont.Rd | 1 iemisc-0.9.7/iemisc/man/Manningcirc.Rd | 10 iemisc-0.9.7/iemisc/man/Manningpara.Rd | 7 iemisc-0.9.7/iemisc/man/Manningrect.Rd | 7 iemisc-0.9.7/iemisc/man/Manningtrap.Rd | 22 iemisc-0.9.7/iemisc/man/Manningtri.Rd | 7 iemisc-0.9.7/iemisc/man/PgivenA.Rd | 4 iemisc-0.9.7/iemisc/man/PgivenA1.Rd | 1 iemisc-0.9.7/iemisc/man/PgivenAcont.Rd | 1 iemisc-0.9.7/iemisc/man/PgivenF.Rd | 4 iemisc-0.9.7/iemisc/man/PgivenFcont.Rd | 1 iemisc-0.9.7/iemisc/man/PgivenFivary.Rd | 1 iemisc-0.9.7/iemisc/man/PgivenG.Rd | 3 iemisc-0.9.7/iemisc/man/SimpIntPaid.Rd | 1 iemisc-0.9.7/iemisc/man/acosd.Rd | 7 iemisc-0.9.7/iemisc/man/acotd.Rd | 7 iemisc-0.9.7/iemisc/man/acscd.Rd | 7 iemisc-0.9.7/iemisc/man/approxerror.Rd | 1 iemisc-0.9.7/iemisc/man/asecd.Rd | 7 iemisc-0.9.7/iemisc/man/asind.Rd | 7 iemisc-0.9.7/iemisc/man/atan2d.Rd | 7 iemisc-0.9.7/iemisc/man/atand.Rd | 7 iemisc-0.9.7/iemisc/man/benefitcost.Rd | 19 iemisc-0.9.7/iemisc/man/cosd.Rd | 7 iemisc-0.9.7/iemisc/man/cotd.Rd | 7 iemisc-0.9.7/iemisc/man/cscd.Rd | 7 iemisc-0.9.7/iemisc/man/cv.Rd | 1 iemisc-0.9.7/iemisc/man/iemisc.Rd | 4 iemisc-0.9.7/iemisc/man/igivenPFn.Rd | 1 iemisc-0.9.7/iemisc/man/length_octave.Rd | 7 iemisc-0.9.7/iemisc/man/n.Rd | 1 iemisc-0.9.7/iemisc/man/na.interp1.Rd | 7 iemisc-0.9.7/iemisc/man/nc1.Rd | 1 iemisc-0.9.7/iemisc/man/nc2.Rd | 1 iemisc-0.9.7/iemisc/man/nc3.Rd | 1 iemisc-0.9.7/iemisc/man/nc4.Rd | 1 iemisc-0.9.7/iemisc/man/ngivenPFi.Rd | 1 iemisc-0.9.7/iemisc/man/numel.Rd | 7 iemisc-0.9.7/iemisc/man/ranges.Rd | 1 iemisc-0.9.7/iemisc/man/relerror.Rd | 1 iemisc-0.9.7/iemisc/man/righttri.Rd | 1 iemisc-0.9.7/iemisc/man/rms.Rd | 1 iemisc-0.9.7/iemisc/man/secd.Rd | 7 iemisc-0.9.7/iemisc/man/sgm.Rd | 1 iemisc-0.9.7/iemisc/man/shm.Rd | 1 iemisc-0.9.7/iemisc/man/sind.Rd | 7 iemisc-0.9.7/iemisc/man/size.Rd | 11 iemisc-0.9.7/iemisc/man/tand.Rd | 7 iemisc-0.9.7/iemisc/man/volsphere.Rd | 1 iemisc-0.9.7/iemisc/vignettes/Open-Channel-Flow_Examples_Geometric_Shapes.Rmd | 15 81 files changed, 643 insertions(+), 509 deletions(-)
Title: An Interface to DATASUS System
Description: It allows the user to retrieve the data from the systems of
DATASUS (SUS IT department related to the Brazilian Ministry of Health,
see <http://datasus.saude.gov.br/informacoes-de-saude/tabnet/> for more
information) much in the same way that is done in the online portal.
For now the package allows access to the SINASC and SIM's (ICD-10)
systems, that is, the 'EstatÃsticas Vitais'.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>
Diff between datasus versions 0.4.0 dated 2017-07-25 and 0.4.1 dated 2018-05-16
DESCRIPTION | 6 MD5 | 46 NEWS.md | 4 R/sim_evita10_bruf.R | 906 +++++++-------- R/sim_evita10_mun.R | 1314 +++++++++++----------- R/sim_evita10_uf.R | 1046 ++++++++--------- R/sim_evitb10_bruf.R | 968 ++++++++-------- R/sim_evitb10_mun.R | 1374 +++++++++++------------ R/sim_evitb10_uf.R | 1102 +++++++++--------- R/sim_inf10_bruf.R | 1632 +++++++++++++-------------- R/sim_inf10_mun.R | 2026 +++++++++++++++++----------------- R/sim_inf10_uf.R | 1698 ++++++++++++++-------------- R/sim_obt10_bruf.R | 1160 +++++++++---------- R/sim_obt10_mun.R | 1574 +++++++++++++------------- R/sim_obt10_uf.R | 1304 ++++++++++----------- R/sinasc_nv_bruf.R | 1244 ++++++++++---------- R/sinasc_nv_mun.R | 1660 +++++++++++++-------------- R/sinasc_nv_uf.R | 2 README.md | 72 - build/vignette.rds |binary inst/doc/Introduction_to_datasus.R | 4 inst/doc/Introduction_to_datasus.Rmd | 4 inst/doc/Introduction_to_datasus.html | 51 vignettes/Introduction_to_datasus.Rmd | 4 24 files changed, 9602 insertions(+), 9599 deletions(-)