Title: Treatment Effect eXplorer for Microbial Ecology eXperiments
(using Sequence Counts)
Description: Analysis and visualization of community dynamics in microbial
ecology experiments (that use sequence count data) using the
truncated Poisson lognormal distribution.
Author: Scott Olesen
Maintainer: Scott Olesen <swo@mit.edu>
Diff between texmexseq versions 0.1 dated 2015-03-11 and 0.2 dated 2016-05-26
texmexseq-0.1/texmexseq/R/experiment.R |only texmexseq-0.1/texmexseq/demo/build-from-vectors.R |only texmexseq-0.1/texmexseq/demo/interpret-data.R |only texmexseq-0.1/texmexseq/demo/load-from-tables.R |only texmexseq-0.1/texmexseq/inst/extdata/pairs.dat |only texmexseq-0.1/texmexseq/inst/extdata/quads.dat |only texmexseq-0.1/texmexseq/man/experiment.Rd |only texmexseq-0.1/texmexseq/man/pair.Rd |only texmexseq-0.1/texmexseq/man/sample.Rd |only texmexseq-0.2/texmexseq/DESCRIPTION | 9 texmexseq-0.2/texmexseq/MD5 | 35 +- texmexseq-0.2/texmexseq/NAMESPACE | 8 texmexseq-0.2/texmexseq/R/session.R | 265 +++++++--------------- texmexseq-0.2/texmexseq/R/texmexseq.R | 61 ++--- texmexseq-0.2/texmexseq/README.md |only texmexseq-0.2/texmexseq/demo/00Index | 4 texmexseq-0.2/texmexseq/demo/demo.R |only texmexseq-0.2/texmexseq/man/dpoilog.Rd | 2 texmexseq-0.2/texmexseq/man/poilogMLE.Rd | 20 - texmexseq-0.2/texmexseq/man/ppplot.Rd |only texmexseq-0.2/texmexseq/man/quad-table.Rd |only texmexseq-0.2/texmexseq/man/texmex-fit.Rd |only texmexseq-0.2/texmexseq/man/z-transform-sample.Rd |only texmexseq-0.2/texmexseq/tests |only 24 files changed, 158 insertions(+), 246 deletions(-)
Title: Spatial Stochastic Frontier Models
Description: A set of tools for estimation of various spatial specifications of
stochastic frontier models.
Author: Dmitry Pavlyuk <Dmitry.V.Pavlyuk@gmail.com>
Maintainer: Dmitry Pavlyuk <Dmitry.V.Pavlyuk@gmail.com>
Diff between spfrontier versions 0.1.12 dated 2014-12-21 and 0.2.3 dated 2016-05-26
spfrontier-0.1.12/spfrontier/R/spfrontier_test.R |only spfrontier-0.2.3/spfrontier/DESCRIPTION | 22 ++- spfrontier-0.2.3/spfrontier/MD5 | 39 +++--- spfrontier-0.2.3/spfrontier/NAMESPACE | 9 + spfrontier-0.2.3/spfrontier/NEWS | 8 + spfrontier-0.2.3/spfrontier/R/classes.R | 20 ++- spfrontier-0.2.3/spfrontier/R/spfrontier.R | 49 +++++--- spfrontier-0.2.3/spfrontier/R/spfrontier_mle.R | 29 +++- spfrontier-0.2.3/spfrontier/R/test_ezsim.R | 2 spfrontier-0.2.3/spfrontier/R/util_misc.R | 3 spfrontier-0.2.3/spfrontier/R/util_mle.R | 93 ++++++++++------ spfrontier-0.2.3/spfrontier/data/airports.greece.rda |binary spfrontier-0.2.3/spfrontier/data/airports.rda |binary spfrontier-0.2.3/spfrontier/man/ModelEstimates-class.Rd | 6 - spfrontier-0.2.3/spfrontier/man/data-airports-greece.Rd | 6 - spfrontier-0.2.3/spfrontier/man/data-airports.Rd | 4 spfrontier-0.2.3/spfrontier/man/logLikelihood.Rd | 8 - spfrontier-0.2.3/spfrontier/man/simulation.Rd | 20 +-- spfrontier-0.2.3/spfrontier/man/spfrontier-package.Rd | 2 spfrontier-0.2.3/spfrontier/man/spfrontier.Rd | 16 +- spfrontier-0.2.3/spfrontier/man/util-misc.Rd | 12 +- 21 files changed, 215 insertions(+), 133 deletions(-)
Title: Probabilistic Suffix Trees and Variable Length Markov Chains
Description: Provides a framework for analysing state sequences with probabilistic suffix trees (PST), the construction that stores variable length Markov chains (VLMC). Besides functions for learning and optimizing VLMC models, the PST library includes many additional tools to analyse sequence data with these models: visualization tools, functions for sequence prediction and artificial sequences generation, as well as for context and pattern mining. The package is specifically adapted to the field of social sciences by allowing to learn VLMC models from sets of individual sequences possibly containing missing values, and by accounting for case weights. The library also allows to compute probabilistic divergence between two models, and to fit segmented VLMC, where sub-models fitted to distinct strata of the learning sample are stored in a single PST. This software results from research work executed within the framework of the Swiss National Centre of Competence in Research LIVES, which is financed by the Swiss National Science Foundation. The authors are grateful to the Swiss National Science Foundation for its financial support.
Author: Alexis Gabadinho [aut, cre, cph]
Maintainer: Alexis Gabadinho <alexis.gabadinho@unige.ch>
Diff between PST versions 0.86 dated 2015-02-18 and 0.88 dated 2016-05-26
DESCRIPTION | 12 ++++++------ MD5 | 15 ++++++++------- NAMESPACE | 4 ++++ R/gain.R | 2 +- R/pqplot.R | 4 ++-- R/seqgbar.R |only data/SRH.RData |binary data/s1.rda |binary man/cmine.Rd | 1 + 9 files changed, 22 insertions(+), 16 deletions(-)
Title: Clustering High-Throughput Transcriptome Sequencing (HTS) Data
Description: A Poisson mixture model is implemented to cluster genes from high-
throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is
performed using either the EM or CEM algorithm, and the slope heuristics are
used for model selection (i.e., to choose the number of clusters).
Author: Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis-
Rabusseau
Maintainer: Andrea Rau <andrea.rau@jouy.inra.fr>
Diff between HTSCluster versions 2.0.4 dated 2014-08-26 and 2.0.8 dated 2016-05-26
HTSCluster-2.0.4/HTSCluster/R/zzz.R |only HTSCluster-2.0.4/HTSCluster/man/logLikePoisMixDiff.Rd |only HTSCluster-2.0.8/HTSCluster/DESCRIPTION | 22 +- HTSCluster-2.0.8/HTSCluster/MD5 | 56 ++--- HTSCluster-2.0.8/HTSCluster/NAMESPACE | 20 +- HTSCluster-2.0.8/HTSCluster/R/HTSCluster-internal.R | 19 -- HTSCluster-2.0.8/HTSCluster/R/PoisMixClus.R | 94 +++++----- HTSCluster-2.0.8/HTSCluster/R/PoisMixClusWrapper.R | 78 ++++---- HTSCluster-2.0.8/HTSCluster/R/PoisMixMean.R | 6 HTSCluster-2.0.8/HTSCluster/R/emInit.R | 33 --- HTSCluster-2.0.8/HTSCluster/R/kmeanInit.R | 57 ++---- HTSCluster-2.0.8/HTSCluster/R/logLikePoisMix.R |only HTSCluster-2.0.8/HTSCluster/R/logLikePoisMixDiff.R | 7 HTSCluster-2.0.8/HTSCluster/R/probaPost.R | 6 HTSCluster-2.0.8/HTSCluster/R/probaPostInit.R | 61 ++---- HTSCluster-2.0.8/HTSCluster/R/splitEMInit.R | 11 - HTSCluster-2.0.8/HTSCluster/R/summary.HTSCluster.R | 2 HTSCluster-2.0.8/HTSCluster/build/vignette.rds |binary HTSCluster-2.0.8/HTSCluster/inst/CITATION | 22 +- HTSCluster-2.0.8/HTSCluster/inst/NEWS | 29 +++ HTSCluster-2.0.8/HTSCluster/inst/doc/HTSCluster.pdf |binary HTSCluster-2.0.8/HTSCluster/inst/doc/HTSClusterUsersGuide.pdf |binary HTSCluster-2.0.8/HTSCluster/man/HTSCluster-package.Rd | 29 +-- HTSCluster-2.0.8/HTSCluster/man/Init.Rd | 44 ++-- HTSCluster-2.0.8/HTSCluster/man/PoisMixClus.Rd | 91 +++++---- HTSCluster-2.0.8/HTSCluster/man/PoisMixMean.Rd | 5 HTSCluster-2.0.8/HTSCluster/man/highDimensionARI.Rd | 2 HTSCluster-2.0.8/HTSCluster/man/logLikePoisMix.Rd |only HTSCluster-2.0.8/HTSCluster/man/plot.HTSCluster.Rd | 7 HTSCluster-2.0.8/HTSCluster/man/probaPost.Rd | 4 HTSCluster-2.0.8/HTSCluster/man/summary.HTSCluster.Rd | 6 31 files changed, 348 insertions(+), 363 deletions(-)
Title: Building Diversity Models from Multiple Species Occupancy Models
Description: Predictions of alpha diversity are fitted from presence data, first abundance is modeled from occupancy models and then, several diversity indices are calculated and finally GLM models are used to predict diversity in different environments and select priority areas.
Author: Derek Corcoran [aut, cre],
Dylan Kesler [aut],
Nicole Michel [ctb],
Mike Meredith [ctb]
Maintainer: Derek Corcoran <derek.corcoran.barrios@gmail.com>
Diff between DiversityOccupancy versions 1.0.3 dated 2016-05-12 and 1.0.4 dated 2016-05-26
DESCRIPTION | 14 ++--- MD5 | 12 ++-- NAMESPACE | 2 R/DiversityOccu.R | 125 +++++++++++++++------------------------------- inst/doc/my-vignette.html | 4 - man/batchoccu.Rd | 7 -- man/diversityoccu.Rd | 8 +- 7 files changed, 63 insertions(+), 109 deletions(-)
More information about DiversityOccupancy at CRAN
Permanent link
Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data.
Functions are provided to rapidly read from and write to VCF files.
Once VCF data is read into R a parser function extracts matrices of data.
This information can then be used for quality control or other purposes.
Additional functions provide visualization of genomic data.
Once processing is complete data may be written to a VCF file (*.vcf.gz).
It also may be converted into other popular R objects (e.g., genlight, DNAbin).
VcfR provides a link between VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut],
Niklaus J. Grunwald [aut],
Eric C. Anderson [ctb],
David J. Winter [ctb]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>
Diff between vcfR versions 1.0.0 dated 2016-02-22 and 1.1.0 dated 2016-05-26
vcfR-1.0.0/vcfR/R/chromR_methods.R |only vcfR-1.0.0/vcfR/R/vcfR_methods.R |only vcfR-1.0.0/vcfR/man/chromR_methods.Rd |only vcfR-1.0.0/vcfR/man/vcfR-methods.Rd |only vcfR-1.0.0/vcfR/tests/testthat/test_chromo.R |only vcfR-1.1.0/vcfR/DESCRIPTION | 35 +- vcfR-1.1.0/vcfR/MD5 | 161 +++++----- vcfR-1.1.0/vcfR/NAMESPACE | 19 - vcfR-1.1.0/vcfR/R/AllClass.R | 112 +++--- vcfR-1.1.0/vcfR/R/RcppExports.R | 46 ++ vcfR-1.1.0/vcfR/R/addID.R |only vcfR-1.1.0/vcfR/R/chromR-method.R |only vcfR-1.1.0/vcfR/R/chromR_to_vcfR.R | 19 - vcfR-1.1.0/vcfR/R/chromo_plot.R | 86 +++-- vcfR-1.1.0/vcfR/R/create_chromR.R | 26 + vcfR-1.1.0/vcfR/R/drplot.R | 4 vcfR-1.1.0/vcfR/R/genotype_matrix_functions.R | 11 vcfR-1.1.0/vcfR/R/heatmap_bp.R | 4 vcfR-1.1.0/vcfR/R/io_vcfR.R | 49 ++- vcfR-1.1.0/vcfR/R/is_het.R |only vcfR-1.1.0/vcfR/R/maf.R |only vcfR-1.1.0/vcfR/R/vcfR-method.R |only vcfR-1.1.0/vcfR/R/vcfR.R | 6 vcfR-1.1.0/vcfR/R/vcfR2DNAbin.R | 51 --- vcfR-1.1.0/vcfR/R/vcfR_conversion.R | 31 + vcfR-1.1.0/vcfR/R/vcfR_test.R |only vcfR-1.1.0/vcfR/R/vcfR_to_tidy_functions.R |only vcfR-1.1.0/vcfR/README.md | 66 +++- vcfR-1.1.0/vcfR/build/vignette.rds |binary vcfR-1.1.0/vcfR/data/vcfR_test.RData |only vcfR-1.1.0/vcfR/inst/CITATION | 37 +- vcfR-1.1.0/vcfR/inst/doc/converting_data.R | 10 vcfR-1.1.0/vcfR/inst/doc/converting_data.Rmd | 2 vcfR-1.1.0/vcfR/inst/doc/converting_data.html | 43 +- vcfR-1.1.0/vcfR/inst/doc/filtering_data.html | 25 - vcfR-1.1.0/vcfR/inst/doc/intro_to_vcfR.R | 12 vcfR-1.1.0/vcfR/inst/doc/intro_to_vcfR.Rmd | 33 -- vcfR-1.1.0/vcfR/inst/doc/intro_to_vcfR.html | 37 -- vcfR-1.1.0/vcfR/inst/doc/ranking_data.html | 27 - vcfR-1.1.0/vcfR/inst/doc/sequence_coverage.html | 17 - vcfR-1.1.0/vcfR/inst/doc/vcf_data.html | 17 - vcfR-1.1.0/vcfR/inst/doc/visualization_1.html | 31 - vcfR-1.1.0/vcfR/inst/doc/visualization_2.html | 17 - vcfR-1.1.0/vcfR/man/AD_frequency.Rd |only vcfR-1.1.0/vcfR/man/addID.Rd |only vcfR-1.1.0/vcfR/man/chromR-class.Rd | 9 vcfR-1.1.0/vcfR/man/chromR-method.Rd |only vcfR-1.1.0/vcfR/man/chromR_functions.Rd | 2 vcfR-1.1.0/vcfR/man/chrom_to_vcfR.Rd | 6 vcfR-1.1.0/vcfR/man/chromo_plot.Rd | 7 vcfR-1.1.0/vcfR/man/create_chromR.Rd | 15 vcfR-1.1.0/vcfR/man/drplot.Rd | 8 vcfR-1.1.0/vcfR/man/extract_gt.Rd | 4 vcfR-1.1.0/vcfR/man/fasta_output.Rd | 4 vcfR-1.1.0/vcfR/man/genotype_matrix.Rd | 9 vcfR-1.1.0/vcfR/man/heatmap_bp.Rd | 4 vcfR-1.1.0/vcfR/man/io_vcfR.Rd | 32 + vcfR-1.1.0/vcfR/man/is_het.Rd |only vcfR-1.1.0/vcfR/man/maf.Rd |only vcfR-1.1.0/vcfR/man/pipe.Rd |only vcfR-1.1.0/vcfR/man/proc_chromR.Rd | 2 vcfR-1.1.0/vcfR/man/query_gt.Rd | 4 vcfR-1.1.0/vcfR/man/ranking.Rd | 2 vcfR-1.1.0/vcfR/man/summary_tables.Rd | 6 vcfR-1.1.0/vcfR/man/vcfR-class.Rd | 9 vcfR-1.1.0/vcfR/man/vcfR-method.Rd |only vcfR-1.1.0/vcfR/man/vcfR.Rd | 6 vcfR-1.1.0/vcfR/man/vcfR2DNAbin.Rd | 2 vcfR-1.1.0/vcfR/man/vcfR_conversion.Rd | 17 - vcfR-1.1.0/vcfR/man/vcfR_example.Rd | 6 vcfR-1.1.0/vcfR/man/vcfR_test.Rd |only vcfR-1.1.0/vcfR/man/vcfR_to_tidy_conversion.Rd |only vcfR-1.1.0/vcfR/man/windowing.Rd | 2 vcfR-1.1.0/vcfR/src/RcppExports.cpp | 14 vcfR-1.1.0/vcfR/src/ad_frequency.cpp |only vcfR-1.1.0/vcfR/src/extractGT2NM.cpp | 67 +++- vcfR-1.1.0/vcfR/src/vcf_io.cpp | 44 +- vcfR-1.1.0/vcfR/tests/testthat.R | 30 + vcfR-1.1.0/vcfR/tests/testthat/test_1_vcf.R | 146 ++++++++- vcfR-1.1.0/vcfR/tests/testthat/test_2_chromR.R | 84 +++++ vcfR-1.1.0/vcfR/tests/testthat/test_3_extract_gt.R | 118 ++++++- vcfR-1.1.0/vcfR/tests/testthat/test_4_vcfR2DNAbin.R | 14 vcfR-1.1.0/vcfR/tests/testthat/test_ad_frequency.R |only vcfR-1.1.0/vcfR/tests/testthat/test_addID.R |only vcfR-1.1.0/vcfR/tests/testthat/test_chromR_method.R |only vcfR-1.1.0/vcfR/tests/testthat/test_chromo_plot.R |only vcfR-1.1.0/vcfR/tests/testthat/test_conversion.R | 1 vcfR-1.1.0/vcfR/tests/testthat/test_drplot.R | 122 +++++-- vcfR-1.1.0/vcfR/tests/testthat/test_genotype_matrix_functions.R |only vcfR-1.1.0/vcfR/tests/testthat/test_heatmapbp.R | 18 - vcfR-1.1.0/vcfR/tests/testthat/test_io.R | 45 ++ vcfR-1.1.0/vcfR/tests/testthat/test_is_het.R |only vcfR-1.1.0/vcfR/tests/testthat/test_maf.R |only vcfR-1.1.0/vcfR/tests/testthat/test_vcfRtidy.R |only vcfR-1.1.0/vcfR/vignettes/converting_data.Rmd | 17 - vcfR-1.1.0/vcfR/vignettes/sequence_coverage.Rmd | 13 vcfR-1.1.0/vcfR/vignettes/vcf_data.Rmd | 6 97 files changed, 1328 insertions(+), 601 deletions(-)
Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding as implemented in this package consists in
the estimation of the joint size-shape-orientation distribution of spheroidal
shaped particles based on the same measured quantities of corresponding planar
section profiles. A single trivariate discretized version of the (stereological)
integral equation in the case of prolate and oblate spheroids is solved
numerically by the EM algorithm. The estimation of diameter distribution of
spheres from planar sections (Wicksell's corpuscle problem) is also implemented.
Further, the package provides routines for the simulation of a Poisson germ-
grain process with either spheroids, spherocylinders or spheres as grains together
with functions for planar sections. For the purpose of exact simulation a bivariate size-shape
distribution is implemented.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>
Diff between unfoldr versions 0.5.1 dated 2016-05-04 and 0.5.5 dated 2016-05-26
DESCRIPTION | 14 - MD5 | 53 ++-- NAMESPACE | 13 - R/cylinder.R |only R/sphere.R | 16 - R/spheroid.R | 96 +++++++ R/unfolding.R | 4 inst/examples/coeffarray.R | 2 inst/examples/cylinder.R |only man/cylinders3d.Rd |only man/setupSpheroidSystem.Rd | 2 man/simCylinderSystem.Rd |only man/simSphereSystem.Rd | 5 man/simSpheroidSystem.Rd | 4 man/spheroids3d.Rd |only man/updateIntersections.Rd | 10 src/GeometricPrimitives.cpp | 542 +++++++++++++++++++++++++++++++++++++------- src/GeometricPrimitives.h | 526 +++++++++++++++++++++++++++++++++++++++++- src/Intersector.cpp | 232 ++++++++++++++++++ src/Intersector.h | 236 ++++++++++++++++++- src/SimCylinder.cpp |only src/SimCylinder.h |only src/SimEllipsoid.cpp | 166 ++++--------- src/SimEllipsoid.h | 22 - src/SimSphere.cpp | 90 +++++-- src/SimSphere.h | 8 src/Utils.cpp | 123 +++++++++ src/Utils.h | 25 +- src/Vector.h | 7 src/unfold.cpp | 66 ----- src/unfold.h | 4 31 files changed, 1872 insertions(+), 394 deletions(-)
Title: Utilities for Quantiles
Description: This is a collection of functions for unconditional and conditional quantiles. These include methods for transformation-based quantile regression, quantile-based measures of location, scale and shape, methods for quantiles of discrete variables, quantile-based multiple imputation, and restricted quantile regression.
Author: Marco Geraci
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>
Diff between Qtools versions 1.0 dated 2016-02-04 and 1.1 dated 2016-05-26
DESCRIPTION | 10 MD5 | 49 - NAMESPACE | 10 NEWS | 11 R/Qtools.R | 1591 +++++++++++++++++++++++++-------------------- inst/doc/Qtools.pdf |binary man/GOFTest.Rd | 3 man/Qtools-internal.Rd | 8 man/Qtools-package.Rd | 6 man/ao.Rd | 4 man/confint.midquantile.Rd |only man/maref.rqt.Rd | 61 - man/midquantile.Rd | 38 - man/plot.midquantile.Rd |only man/plot.qlss.Rd | 17 man/predict.qlss.Rd |only man/predict.rq.counts.Rd | 10 man/predict.rqt.Rd | 9 man/print.midquantile.Rd |only man/print.qlss.Rd |only man/print.rrq.Rd | 2 man/qlss.Rd | 75 +- man/rq.bin.Rd | 2 man/rq.counts.Rd | 45 - man/rqbinControl.Rd | 10 man/sparsity.rqt.Rd | 6 man/summary.rqt.Rd | 8 man/tsrq.Rd | 172 ++-- 28 files changed, 1219 insertions(+), 928 deletions(-)
Title: R Interface to 'FOAAS'
Description: R access to the 'FOAAS' (F... Off As A Service) web service is provided.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between rfoaas versions 0.1.8 dated 2015-10-24 and 0.1.9 dated 2016-05-26
ChangeLog | 35 ++++++++++++++++++++++++++++++++++- DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 3 +++ R/foaas.R | 21 ++++++++++++++++++--- README.md | 4 ++-- man/rfoaas-package.Rd | 24 ++++++++++++++++++++---- tests/runTestsAgainstFOAAS.R | 13 +++++++++++-- 8 files changed, 101 insertions(+), 25 deletions(-)
Title: Incidence Estimation Tools
Description: Tools for estimating incidence from biomarker data in cross-
sectional surveys and for calibrating tests for recent infection.
Author: Alex Welte [aut],
Eduard Grebe [cre, aut],
Avery McIntosh [aut],
Petra Bäumler [aut],
Reshma Kassanjee [ctb],
Hilmarie Brand [ctb],
Cari Van Schalkwyk [ctb],
Yuruo Li [ctb],
Simon Daniel [ctb],
Stefano Ongarello [ctb],
Yusuke Asai [ctb]
Maintainer: Eduard Grebe <eduardgrebe@sun.ac.za>
Diff between inctools versions 1.0.3 dated 2016-05-18 and 1.0.5 dated 2016-05-26
DESCRIPTION | 10 ++++++---- MD5 | 20 ++++++++++---------- R/calibration_mdri.R | 19 ++++++++++++++----- R/incidence.R | 6 +++--- R/power.R | 1 - inst/doc/EstimatingIncidence.html | 4 ++-- inst/doc/Introduction.Rmd | 1 + inst/doc/TestCalibration.html | 12 ++++++------ man/incpower.Rd | 1 - man/incprops.Rd | 6 ++++-- vignettes/Introduction.Rmd | 1 + 11 files changed, 47 insertions(+), 34 deletions(-)
Title: Imputation Methods for Multivariate Multinomial Data
Description: Implements imputation methods using EM and Data Augmentation for
multinomial data following the work of Schafer 1997 <ISBN: 978-0-412-04061-0>.
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>
Diff between imputeMulti versions 0.4.5 dated 2016-05-05 and 0.4.6 dated 2016-05-26
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/multinomial_data_aug.R | 22 +++++++++++++--------- R/multinomial_em.R | 18 +++++++++++------- man/multinomial_data_aug.Rd | 6 +++--- man/multinomial_em.Rd | 2 +- src/utilities_rcpp.cpp | 5 +++-- 7 files changed, 40 insertions(+), 31 deletions(-)
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@fhi.no>
Diff between Haplin versions 6.0 dated 2016-05-25 and 6.0.1 dated 2016-05-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/hapPower.R | 4 ++-- R/haplin.R | 2 +- inst/doc/Haplin_data_format.pdf |binary inst/doc/Haplin_power.pdf |binary 6 files changed, 12 insertions(+), 12 deletions(-)
Title: Spatial Ecology Miscellaneous Methods
Description: Colection of R functions and data sets for the support of spatial ecology analyses with a focus on pre-, core and post- modelling analyses of species distribution, niche quantification and community assembly., written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) & Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland.
Author: Olivier Broennimann [aut],
Valeria Di Cola [cre, aut],
Blaise Petitpierre [ctb],
Frank Breiner [ctb],
Manuela D`Amen [ctb],
Christophe Randin [ctb],
Robin Engler [ctb],
Wim Hordijk [ctb],
Julien Pottier [ctb],
Mirko Di Febbraro [ctb],
Loic Pellissier [ctb],
Dorothea Pio [ctb],
Ruben Garcia Mateo [ctb],
Anne Dubuis [ctb],
Daniel Scherrer [ctb],
Luigi Maiorano [ctb],
Achilleas Psomas [ctb],
Charlotte Ndiribe [ctb],
Nicolas Salamin [ctb],
Niklaus Zimmermann [ctb],
Antoine Guisan [aut]
Maintainer: Valeria Di Cola <valeria.dicola@unil.ch>
Diff between ecospat versions 1.1 dated 2015-03-06 and 2.0 dated 2016-05-26
ecospat-1.1/ecospat/R/ecospat.SSDMeval.R |only ecospat-1.1/ecospat/man/ecospat.SSDMeval.Rd |only ecospat-1.1/ecospat/man/ecospat.cv.gam.Rd |only ecospat-1.1/ecospat/man/ecospat.fun.arrows.Rd |only ecospat-2.0/ecospat/DESCRIPTION | 85 +- ecospat-2.0/ecospat/MD5 | 92 +- ecospat-2.0/ecospat/NAMESPACE | 50 + ecospat-2.0/ecospat/NEWS |only ecospat-2.0/ecospat/R/ecospat.CommunityEval.R |only ecospat-2.0/ecospat/R/ecospat.ESM.R |only ecospat-2.0/ecospat/R/ecospat.SESAM.prr.R |only ecospat-2.0/ecospat/R/ecospat.adj.D2.R |only ecospat-2.0/ecospat/R/ecospat.cor.panel.R |only ecospat-2.0/ecospat/R/ecospat.cv.R | 576 +++++++------- ecospat-2.0/ecospat/R/ecospat.eval.R |only ecospat-2.0/ecospat/R/ecospat.exdet.r |only ecospat-2.0/ecospat/R/ecospat.nichedynamic.R | 104 ++ ecospat-2.0/ecospat/R/ecospat.nicheoverlap.R | 194 ++-- ecospat-2.0/ecospat/data/datalist |only ecospat-2.0/ecospat/data/ecospat.testNiche.inv.txt.gz |only ecospat-2.0/ecospat/data/ecospat.testNiche.nat.txt.gz |only ecospat-2.0/ecospat/inst/doc/ecospat.pdf |binary ecospat-2.0/ecospat/man/ecospat-package.Rd | 52 - ecospat-2.0/ecospat/man/ecospat.CommunityEval.Rd |only ecospat-2.0/ecospat/man/ecospat.ESM.EnsembleModeling.Rd |only ecospat-2.0/ecospat/man/ecospat.ESM.EnsembleProjection.Rd |only ecospat-2.0/ecospat/man/ecospat.ESM.Modeling.Rd |only ecospat-2.0/ecospat/man/ecospat.ESM.Projection.Rd |only ecospat-2.0/ecospat/man/ecospat.Epred.Rd | 2 ecospat-2.0/ecospat/man/ecospat.SESAM.prr.Rd |only ecospat-2.0/ecospat/man/ecospat.adj.D2.Rd |only ecospat-2.0/ecospat/man/ecospat.boyce.Rd | 4 ecospat-2.0/ecospat/man/ecospat.calculate.pd.Rd | 4 ecospat-2.0/ecospat/man/ecospat.caleval.Rd | 4 ecospat-2.0/ecospat/man/ecospat.co_occurrences.Rd | 2 ecospat-2.0/ecospat/man/ecospat.cohen.kappa.Rd |only ecospat-2.0/ecospat/man/ecospat.cons_Cscore.Rd | 14 ecospat-2.0/ecospat/man/ecospat.cor.plot.Rd |only ecospat-2.0/ecospat/man/ecospat.cv.gbm.Rd | 2 ecospat-2.0/ecospat/man/ecospat.cv.glm.Rd | 2 ecospat-2.0/ecospat/man/ecospat.cv.rf.Rd | 2 ecospat-2.0/ecospat/man/ecospat.exdet.Rd |only ecospat-2.0/ecospat/man/ecospat.grid.clim.dyn.Rd | 42 - ecospat-2.0/ecospat/man/ecospat.max.kappa.Rd |only ecospat-2.0/ecospat/man/ecospat.max.tss.Rd |only ecospat-2.0/ecospat/man/ecospat.mess.Rd | 6 ecospat-2.0/ecospat/man/ecospat.meva.table.Rd |only ecospat-2.0/ecospat/man/ecospat.migclim.Rd | 22 ecospat-2.0/ecospat/man/ecospat.mpa.Rd |only ecospat-2.0/ecospat/man/ecospat.niche.similarity.test.Rd | 7 ecospat-2.0/ecospat/man/ecospat.occ.desaggregation.Rd | 6 ecospat-2.0/ecospat/man/ecospat.plot.kappa.Rd |only ecospat-2.0/ecospat/man/ecospat.plot.mess.Rd | 6 ecospat-2.0/ecospat/man/ecospat.plot.niche.dyn.Rd | 5 ecospat-2.0/ecospat/man/ecospat.plot.tss.Rd |only ecospat-2.0/ecospat/man/ecospat.rand.pseudoabsences.Rd | 6 ecospat-2.0/ecospat/man/ecospat.sample.envar.Rd | 10 ecospat-2.0/ecospat/man/ecospat.shift.centroids.Rd |only ecospat-2.0/ecospat/man/ecospat.testData.Rd | 15 ecospat-2.0/ecospat/man/ecospat.testNiche.Rd | 2 ecospat-2.0/ecospat/man/ecospat.testNiche.inv.Rd |only ecospat-2.0/ecospat/man/ecospat.testNiche.nat.Rd |only ecospat-2.0/ecospat/man/ecospat.testTree.Rd | 6 ecospat-2.0/ecospat/man/ecospat.varpart.Rd | 2 64 files changed, 776 insertions(+), 548 deletions(-)
Title: Data Driven Smooth Tests
Description: Smooth testing of goodness of fit. These tests are data
driven (alternative hypothesis is dynamically selected based on data). In this
package you will find various tests for exponent, Gaussian, Gumbel and uniform
distribution.
Author: Przemyslaw Biecek (R code), Teresa Ledwina (support,
descriptions)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between ddst versions 1.03 dated 2012-08-19 and 1.4 dated 2016-05-26
ddst-1.03/ddst/data |only ddst-1.4/ddst/DESCRIPTION | 19 ddst-1.4/ddst/MD5 | 40 ddst-1.4/ddst/NAMESPACE | 9 ddst-1.4/ddst/R/ddst.IIC.R | 12 ddst-1.4/ddst/R/ddst.base.cos.R | 14 ddst-1.4/ddst/R/ddst.base.legendre.R | 10 ddst-1.4/ddst/R/ddst.exp.Nk.R | 26 ddst-1.4/ddst/R/ddst.exp.test.R | 1712 ++++++++++---------- ddst-1.4/ddst/R/ddst.extr.Nk.R | 40 ddst-1.4/ddst/R/ddst.extr.test.R | 1852 +++++++++++----------- ddst-1.4/ddst/R/ddst.norm.Nk.R | 40 ddst-1.4/ddst/R/ddst.norm.test.R | 2750 ++++++++++++++++----------------- ddst-1.4/ddst/R/ddst.phi.R | 10 ddst-1.4/ddst/R/ddst.uniform.Nk.R | 20 ddst-1.4/ddst/R/ddst.uniform.test.R | 64 ddst-1.4/ddst/R/zzz.R |only ddst-1.4/ddst/man/ddst-package.Rd | 300 +-- ddst-1.4/ddst/man/ddst.exp.test.Rd | 141 - ddst-1.4/ddst/man/ddst.extr.test.Rd | 153 - ddst-1.4/ddst/man/ddst.norm.test.Rd | 158 - ddst-1.4/ddst/man/ddst.uniform.test.Rd | 140 - 22 files changed, 3771 insertions(+), 3739 deletions(-)
Title: Statistical Methods for Climate Sciences
Description: Absolute homogeneity tests SNHT absolute 1-breaks, 1-break,
SD different from 1, 2-breaks, Buishand, Pettitt, von Neumann ratio and
ratio-rank, Worsley, and Craddock, Relative homogeneity tests SNHT
absolute 1-breaks, 1-break SD different from 1, 2-breaks, Peterson
and Easterling, and Vincent, Differences in scale between two groups Siegel–Tukey,
Create reference time series mean, weights/correlation, finding outliers Grubbs,
ESD, MAD, Tietjen Moore, Hampel, etc.
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama <rxprtgama@gmail.com>
Diff between climtrends versions 1.0.5 dated 2015-09-20 and 1.0.6 dated 2016-05-26
DESCRIPTION | 10 +++--- MD5 | 28 +++++++++-------- data/Buishand.Critical.Values.rda |binary data/Cumulative.Deviations.Test.Critical.Values.rda |only data/Pettitt.Critical.Values.rda |binary data/Rank.Von.Neumann.Ratio.Test.Critical.Values.rda |binary data/SNHT.Critical.Values.Alexandersson1997.rda |binary data/SNHT.Critical.Values.rda |binary data/SNHT.TwoDifferentSDs.Critical.Values.rda |binary data/SNHT.TwoShifts.Critical.Values.rda |binary data/Von.Neumann.Ratio.Test.Critical.Values.rda |binary data/Worsley.Likelihood.Ratio.Test.Critical.Values.rda |binary data/annual.precipitation.totals.Madison.rda |binary data/yearly.average.temperature.Turin.Milan.rda |binary man/Cumulative.Deviations.Test.Critical.Values.Rd |only man/Worsley.Likelihood.Ratio.Test.Critical.Values.Rd | 4 +- 16 files changed, 22 insertions(+), 20 deletions(-)
Title: Analyze Time Series
Description: Main function of package is helped to analyze time series, peculiar is fuzzy time series. The package can calculate AIC value of common time series models and propose the best models according AIC values. To fuzzy time series by "Chen", "Sing", "Heuristic" and "Chen-Hsu" models, also can fuzzy and forecast time series by Abbasov-Mamedova model.
Author: Tran Thi Ngoc Han <tranthingochan01011994@gmail.com>_ Doan Hai Nghi <Hainghi1426262609121094@gmail.com> _ Mai Thi Hong Diem <maidiemks@gmail.com> _ Nguyen Thi Diem My <myntdhg@gmail.com> _ Hong Viet Minh <hongvietminh@gmail.com> _ Vo Van Tai <vvtai@ctu.edu.vn>
Maintainer: Hong Viet Minh <hongvietminh@gmail.com>
Diff between AnalyzeTS versions 1.8 dated 2016-04-04 and 1.9 dated 2016-05-26
AnalyzeTS-1.8/AnalyzeTS/R/base.ts.R |only AnalyzeTS-1.8/AnalyzeTS/man/base.ts.Rd |only AnalyzeTS-1.9/AnalyzeTS/DESCRIPTION | 10 AnalyzeTS-1.9/AnalyzeTS/MD5 | 28 - AnalyzeTS-1.9/AnalyzeTS/R/Abbasov.Cs2.R |only AnalyzeTS-1.9/AnalyzeTS/R/Abbasov.Cs3.R |only AnalyzeTS-1.9/AnalyzeTS/R/ChenHsu.bin.R |only AnalyzeTS-1.9/AnalyzeTS/R/av.res.R | 12 AnalyzeTS-1.9/AnalyzeTS/R/fuzzy.ts1.R | 195 ++------ AnalyzeTS-1.9/AnalyzeTS/R/fuzzy.ts2.R | 504 ++++++++++++----------- AnalyzeTS-1.9/AnalyzeTS/R/fuzzy.ts3.R |only AnalyzeTS-1.9/AnalyzeTS/build/partial.rdb |binary AnalyzeTS-1.9/AnalyzeTS/man/Abbasov.Cs2.Rd |only AnalyzeTS-1.9/AnalyzeTS/man/Abbasov.Cs3.Rd |only AnalyzeTS-1.9/AnalyzeTS/man/AnalyzeTS-package.Rd | 24 - AnalyzeTS-1.9/AnalyzeTS/man/CMA.Rd | 4 AnalyzeTS-1.9/AnalyzeTS/man/ChenHsu.bin.Rd |only AnalyzeTS-1.9/AnalyzeTS/man/fuzzy.ts1.Rd | 23 - AnalyzeTS-1.9/AnalyzeTS/man/fuzzy.ts2.Rd | 55 +- AnalyzeTS-1.9/AnalyzeTS/man/fuzzy.ts3.Rd |only 20 files changed, 405 insertions(+), 450 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-02-25 0.9.3
Title: Replication Interval Functions
Description: A common problem faced by journal reviewers and authors is the question of
whether the results of a replication study are consistent with the original
published study. One solution to this problem is to examine the effect size
from the original study and generate the range of effect sizes that could
reasonably be obtained (due to random sampling) in a replication attempt
(i.e., calculate a replication interval). If a replication effect size falls
outside the replication interval, then that effect likely did not occur
due to the effects of sampling error alone. Alternatively, if a replication
effect size falls within the replication interval, then the replication
effect could have reasonably occurred due to the effects of sampling error
alone. This package has functions that calculate the replication interval for
the correlation (i.e., r), standardized mean difference (i.e., d-value), and mean.
The calculations used in version 2.0.0 and onward differ from past calculations
due to feedback during the journal review process. The new calculations allow
for a more precise interpretation of the replication interval.
Author: David Stanley
Maintainer: David Stanley <dstanley@uoguelph.ca>
Diff between replicationInterval versions 1.0.0 dated 2015-07-07 and 2.0.1 dated 2016-05-26
DESCRIPTION | 42 +-- LICENSE |only MD5 | 21 + NAMESPACE | 19 + R/correlationFunctions.R |only R/dValueFunctions.R |only R/meanFunctions.R |only R/replicationInterval.R | 441 ++----------------------------------- R/utilityFunctions.R |only man/replicationInterval-package.Rd | 47 ++- man/ri.d.Rd | 22 - man/ri.d.demo.Rd |only man/ri.m.Rd |only man/ri.m.demo.Rd |only man/ri.r.Rd | 24 -- man/ri.r.demo.Rd |only 16 files changed, 130 insertions(+), 486 deletions(-)
More information about replicationInterval at CRAN
Permanent link
Title: Download, Clean and Generate New Variables from GSOD Data
Description: Download, clean, reformat and create new variables from the
USA National Climatic Data Center (NCDC) Global Surface Summary of the Day
(GSOD) weather stations data,
<https://data.noaa.gov/dataset/global-surface-summary-of-the-day-gsod>.
The function, get_GSOD(), retrieves data from the GSOD ftp site and
reformats it from United States Customary System (USCS) units to
International System of Units (SI), also for convenience elevation is
converted from decimetres to metres. Stations are individually checked for
number of missing days, as defined by the user, to assure data quality.
Stations with too many missing observations are omitted from final file.
Stations with missing latitude or longitude or values for both of 0 are
omitted. Also omitted are stations with a latitude of < -90 or > 90 or
longitude of < - 180 or > 180. Output is returned as a comma-separated
values (CSV) file written to disk in a location selected by the user, which
summarises each year by station and includes new variables: actual vapor
pressure, saturation vapor pressure and relative humidity are calculated
from the original GSOD data. The resulting files can be as large as 500mb
depending on the user's stringency for missing data and geographic area of
interest. Be sure to have sufficient RAM and disk space as well as a
reasonably fast internet connection to use this package to perform this
operation. However, for much smaller and more manageable data sets, an
individual country of interest may be selected as well as only stations
falling between -60/60 degrees latitude for agroclimatology work or
individual stations if the station ID is known. The resulting files include
station data (e.g., station name, country, latitude, longitude, elevation)
for use in a geographic information system (GIS). The function was largely
based on T. Hengl's 'getGSOD.R' script, available from
<http://spatial-analyst.net/book/system/files/getGSOD.R> with enhancements
to be more cross-platform, faster and more flexible. See the GSOD readme.txt
<http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre],
Tomislav Hengl [ctb],
Andy Nelson [ctb],
Kay Sumfleth [ctb]
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between GSODR versions 0.1.5 dated 2016-05-16 and 0.1.6 dated 2016-05-26
DESCRIPTION | 70 +++++++++++----------- MD5 | 13 ++-- NEWS.md | 7 ++ R/data.R |only R/get_GSOD.R | 173 ++++++++++++++++++++++++++------------------------------ README.md | 145 ++++++++++++++++++++++++++++++++++++++++++---- data |only man/get_GSOD.Rd | 72 +++++++++++++---------- man/stations.Rd |only 9 files changed, 304 insertions(+), 176 deletions(-)
Title: Forecasting Time Series by Theta Models
Description: Routines for forecasting univariate time series using Theta Models. Contains several cross-validation routines.
Author: Jose Augusto Fiorucci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fiorucci <jafiorucci@gmail.com>
Diff between forecTheta versions 2.1 dated 2016-03-07 and 2.2 dated 2016-05-26
ChangeLog | 11 ++ DESCRIPTION | 10 +- MD5 | 14 +-- NAMESPACE | 6 - R/forecastFunctions.R | 201 +++++++++++++++++++++++++++++++++++----------- man/forecTheta-package.Rd | 11 +- man/plot.thetaModel.Rd | 6 + man/thetaModels.Rd | 49 +++++++---- 8 files changed, 225 insertions(+), 83 deletions(-)
Title: Elliptic Functions
Description:
A suite of elliptic and related functions including Weierstrass and
Jacobi forms. Also includes various tools for manipulating and
visualizing complex functions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between elliptic versions 1.3-5 dated 2014-11-05 and 1.3-7 dated 2016-05-26
DESCRIPTION | 8 +++---- MD5 | 28 ++++++++++++++------------- NAMESPACE | 4 +++ build/vignette.rds |binary inst/CITATION | 7 ++---- inst/doc/ellipticpaper.pdf |binary inst/doc/residuetheorem.R | 4 +-- inst/doc/residuetheorem.Rnw | 41 +++++++++++++++++++++++++--------------- inst/doc/residuetheorem.pdf |binary man/congruence.Rd | 10 ++++----- man/farey.Rd | 2 - man/half.periods.Rd | 2 - man/parameters.Rd | 4 +-- vignettes/residuetheorem.Rnw | 41 +++++++++++++++++++++++++--------------- vignettes/semicircular_path.pdf |only vignettes/semicircular_path.svg |only 16 files changed, 89 insertions(+), 62 deletions(-)
Title: The Davies Quantile Function
Description: Various utilities for the Davies distribution.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between Davies versions 1.1-8 dated 2012-11-07 and 1.1-9 dated 2016-05-26
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 3 +++ data/ozturk.rda |binary data/x00m700p4.rda |binary man/davies.moment.Rd | 8 ++++++-- 6 files changed, 20 insertions(+), 13 deletions(-)
Title: Continued Fractions
Description: Various utilities for evaluating continued fractions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between contfrac versions 1.1-9 dated 2013-01-21 and 1.1-10 dated 2016-05-26
contfrac-1.1-10/contfrac/DESCRIPTION | 11 ++++++----- contfrac-1.1-10/contfrac/MD5 | 11 +++++------ contfrac-1.1-10/contfrac/man/CF.Rd | 4 ++-- contfrac-1.1-10/contfrac/man/as_cf.Rd | 6 +++--- contfrac-1.1-10/contfrac/man/contfrac-package.Rd | 8 ++++++++ contfrac-1.1-10/contfrac/man/convergents.Rd | 2 +- contfrac-1.1-9/contfrac/inst |only 7 files changed, 25 insertions(+), 17 deletions(-)