Title: R Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI). GloBI provides
access to spatial-temporal species interaction records from
sources all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction data set.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen <jhpoelen@xs4all.nl>
Diff between rglobi versions 0.2.13 dated 2018-02-28 and 0.2.14 dated 2018-03-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 9 +++++++++ build/vignette.rds |binary tests/testthat/test-globi.R | 5 +---- 5 files changed, 18 insertions(+), 12 deletions(-)
Title: Calling Copy Number Alterations in Amplicon Sequencing Data
Description: Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls. Budczies (2016 Mar 15) <doi:10.18632/oncotarget.7451>.
Author: Jan Budczies, Eva Romanovsky
Maintainer: Jan Budczies <jan.budczies@charite.de>
Diff between ioncopy versions 2.1.0 dated 2018-03-14 and 2.1.1 dated 2018-03-23
DESCRIPTION | 8 +++--- MD5 | 6 ++-- inst/doc/Ioncopy_manual.pdf |binary man/ioncopy-package.Rd | 54 +++++++++++++++++++++++--------------------- 4 files changed, 36 insertions(+), 32 deletions(-)
Title: The Essential Histogram
Description: Provide an optimal histogram, in the sense of probability density estimation and features detection, by means of multiscale variational inference. For details see Li, Munk, Sieling and Walther (2016) <arXiv:1612.07216>.
Author: Housen Li [aut, cre],
Hannes Sieling [aut]
Maintainer: Housen Li <housen.li@outlook.com>
Diff between essHist versions 1.0.1 dated 2018-02-05 and 1.1.0 dated 2018-03-23
DESCRIPTION | 8 ++-- MD5 | 31 +++++++++--------- NAMESPACE | 2 - R/RcppExports.R | 4 +- R/checkHistogram.R | 77 ++++++++++++++++++++++----------------------- R/main.R | 47 +++++++++++++++++++-------- R/mixtureDistribution.R | 14 ++++---- build/partial.rdb |binary inst |only man/checkHistogram.Rd | 27 +++++++++++++-- man/essHist-package.Rd | 2 - man/essHistogram.Rd | 16 +++++---- man/mixnorm.Rd | 3 - man/msQuantile.Rd | 21 ++++++++---- src/RcppExports.cpp | 9 ++--- src/multiscaleQuantile.cpp | 14 ++------ src/stepHistogram.cpp | 14 -------- 17 files changed, 162 insertions(+), 127 deletions(-)
Title: Dynamically Generates Documentation from a 'Swagger' Compliant
API
Description: A collection of 'HTML', 'JavaScript', and 'CSS' assets that
dynamically generate beautiful documentation from a 'Swagger' compliant API:
<https://swagger.io/specification/>.
Author: Javier Luraschi [aut, cre],
RStudio [cph],
SmartBear Software [aut, cph]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between swagger versions 3.4.0 dated 2017-10-27 and 3.9.2 dated 2018-03-23
DESCRIPTION | 6 - MD5 | 11 +- NEWS.md |only inst/dist/swagger-ui-bundle.js | 114 ++++++++++++++++++++++++++---- inst/dist/swagger-ui-standalone-preset.js | 16 +++- inst/dist/swagger-ui.css | 3 inst/dist/swagger-ui.js | 10 ++ 7 files changed, 131 insertions(+), 29 deletions(-)
Title: Estimation of Transition Probabilities for the Illness-Death
Model
Description: Estimation of transition probabilities for the illness-death model. Both the Aalen-Johansen estimator for a Markov model and a novel non-Markovian estimator by de Una-Alvarez and Meira-Machado (2015) <doi:10.1111/biom.12288>, see also Balboa and de Una-Alvarez (2018) <doi:10.18637/jss.v083.i10>, are included.
Author: Vanesa Balboa-Barreiro, Jacobo de Una-Alvarez <jacobo@uvigo.es>
and Luis Meira-Machado <lmachado@math.uminho.pt>
Maintainer: Vanesa Balboa-Barreiro <vanesa.balboa@uvigo.es>
Diff between TP.idm versions 1.3 dated 2018-02-20 and 1.4 dated 2018-03-23
DESCRIPTION | 8 - MD5 | 26 +-- R/TP.idm-internal.R | 251 +++++++++++++++++++------------------- R/TPidm.R | 204 +++++++++++++++---------------- R/ci.AJ.R | 192 ++++++++++++++--------------- R/fun.AJ.R | 176 +++++++++++++------------- R/plot.TPidm.R | 182 +++++++++++++-------------- R/prep.data.AJ.R | 320 ++++++++++++++++++++++++------------------------- R/prep.data.event.AJ.R | 46 +++---- R/print.TPidm.R | 108 ++++++++-------- R/test.nm.R | 76 +++++------ R/var.AJ.R | 146 +++++++++++----------- R/var.NM.R | 12 - build/partial.rdb |binary 14 files changed, 874 insertions(+), 873 deletions(-)
Title: Create n-Dimensional, Quasi-Proportional Venn Diagrams
Description: Provides an interface for the nVenn algorithm
(Perez-Silva et al. 2018) <DOI:10.1093/bioinformatics/bty109>. This algorithm works for any number of sets,
and usually yields pleasing and informative Venn diagrams with proportionality information.
However, representing more than six sets takes a long time and is hard to interpret, unless many of the
regions are empty. If you cannot make sense of the result, you may want to consider 'UpSetR'
<https://cran.r-project.org/package=UpSetR/README.html>.
Author: Victor Quesada [aut, cre, cph]
Maintainer: Victor Quesada <quesadavictor@uniovi.es>
Diff between nVennR versions 0.1.4 dated 2018-03-21 and 0.1.5 dated 2018-03-23
DESCRIPTION | 9 ++++----- MD5 | 4 ++-- src/topol.cpp | 34 ++++++++++++++++++---------------- 3 files changed, 24 insertions(+), 23 deletions(-)
Title: A Method to Search for Differentially Expressed Genes and to
Detect Recurrent Chromosomal Copy Number Aberrations
Description: A fold change rank based method is presented to search for genes with changing
expression and to detect recurrent chromosomal copy number aberrations. This
method may be useful for high-throughput biological data (micro-array, sequencing, ...).
Probabilities are associated with genes or probes in the data set and there is no
problem of multiple tests when using this method. For array-based comparative genomic
hybridization data, segmentation results are obtained by merging the significant
probes detected.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele <doulaye@igbmc.fr>
Diff between fcros versions 1.5.5 dated 2017-11-16 and 1.5.6 dated 2018-03-23
DESCRIPTION | 9 ++++----- MD5 | 32 ++++++++++++++++---------------- man/chrMerge.rd | 4 ++-- man/chrPlot.rd | 4 ++-- man/chrPlot2.rd | 4 ++-- man/chrSegment.rd | 4 ++-- man/dataSummary.rd | 4 ++-- man/fc2Calc.rd | 4 ++-- man/fcros-package.Rd | 8 ++++---- man/fcrosMod.Rd | 4 ++-- man/moyStdCalc.rd | 4 ++-- man/pfco.rd | 4 ++-- man/pfcoMod.rd | 4 ++-- man/rankReads.Rd | 3 ++- man/rmatTrim.rd | 4 ++-- man/tcnReads.Rd | 3 ++- man/tprobaCalc.rd | 4 ++-- 17 files changed, 52 insertions(+), 51 deletions(-)
Title: Downloads Box Office Information for Given Dates
Description: Download daily box office information (how much each movie earned
in theaters) using data from either Box Office Mojo (<http://www.boxofficemojo.com/>) or
The Numbers (<http://www.the-numbers.com/>).
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between boxoffice versions 1.0.1 dated 2018-02-10 and 1.1.0 dated 2018-03-23
DESCRIPTION | 11 ++++------ MD5 | 26 ++++++++++++------------- NEWS.md | 7 ++++++ R/main_function.R | 37 ++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/Using-boxoffice.Rmd | 4 ++- inst/doc/Using-boxoffice.html | 32 ++++++++++++++++--------------- man/boxoffice.Rd | 5 ++-- tests/testthat/test-column-names.R | 8 +++---- tests/testthat/test-column-types.R | 8 +++---- tests/testthat/test-column-values.R | 23 +++++++++++----------- tests/testthat/test-dimmensions.R | 8 +++---- tests/testthat/test-errors-silent.R | 17 ++++++++++------ vignettes/Using-boxoffice.Rmd | 4 ++- 14 files changed, 111 insertions(+), 79 deletions(-)
Title: Constrained Triangulation for Simple Features
Description: Build a constrained Delaunay triangulation from simple features
objects, applying constraints based on input line segments, and triangle
properties including maximum area, minimum internal angle. The triangulation code
in 'RTriangle' uses the method of Cheng, Dey and Shewchuk (2012, ISBN:9781584887300).
For a low-dependency alternative with low-quality path-based constrained
triangulation see <https://CRAN.R-project.org/package=decido>.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between sfdct versions 0.0.5 dated 2018-01-05 and 0.0.6 dated 2018-03-23
DESCRIPTION | 13 ++++++++----- MD5 | 11 ++++++----- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/sfdct.html | 8 ++++---- inst/examples/topology_overlay.R |only tests/testthat/test-prepair-benchmarks.R | 25 +++++++++++++------------ 7 files changed, 35 insertions(+), 26 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>;
- league table with network meta-analysis results;
- additive network meta-analysis for combinations of treatments;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>.
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 0.9-7 dated 2017-12-05 and 0.9-8 dated 2018-03-23
netmeta-0.9-7/netmeta/R/netcomb.netmeta.R |only netmeta-0.9-8/netmeta/DESCRIPTION | 8 netmeta-0.9-8/netmeta/MD5 | 78 ++--- netmeta-0.9-8/netmeta/NAMESPACE | 8 netmeta-0.9-8/netmeta/NEWS | 141 +++++++++ netmeta-0.9-8/netmeta/R/bySummary.R |only netmeta-0.9-8/netmeta/R/compmatch.R |only netmeta-0.9-8/netmeta/R/compsplit.R |only netmeta-0.9-8/netmeta/R/createB.R | 4 netmeta-0.9-8/netmeta/R/createC.R | 79 ++--- netmeta-0.9-8/netmeta/R/discomb.R |only netmeta-0.9-8/netmeta/R/netcomb.R | 221 ++++++++++++++ netmeta-0.9-8/netmeta/R/netconnection.R | 13 netmeta-0.9-8/netmeta/R/netgraph.R | 374 ++++++++++++++++++++---- netmeta-0.9-8/netmeta/R/netleague.R | 203 +++++++++---- netmeta-0.9-8/netmeta/R/netmatrix.R |only netmeta-0.9-8/netmeta/R/netmeta-internal.R | 3 netmeta-0.9-8/netmeta/R/netmeta.R | 257 ++++++++++++++-- netmeta-0.9-8/netmeta/R/netsplit.R | 56 ++- netmeta-0.9-8/netmeta/R/nma.additive.R | 73 +++- netmeta-0.9-8/netmeta/R/nma.krahn.R | 24 - netmeta-0.9-8/netmeta/R/nma.ruecker.R | 20 - netmeta-0.9-8/netmeta/R/pairwise.R | 366 +++++++++++++++++------ netmeta-0.9-8/netmeta/R/prcombs.R | 5 netmeta-0.9-8/netmeta/R/prepare.R | 3 netmeta-0.9-8/netmeta/R/print.netcomb.R | 10 netmeta-0.9-8/netmeta/R/print.netconnection.R | 32 +- netmeta-0.9-8/netmeta/R/print.netmeta.R | 4 netmeta-0.9-8/netmeta/R/print.netsplit.R | 43 +- netmeta-0.9-8/netmeta/R/print.summary.netcomb.R | 84 ++++- netmeta-0.9-8/netmeta/R/print.summary.netmeta.R | 29 - netmeta-0.9-8/netmeta/man/discomb.Rd |only netmeta-0.9-8/netmeta/man/netcomb.Rd | 75 ++-- netmeta-0.9-8/netmeta/man/netconnection.Rd | 16 - netmeta-0.9-8/netmeta/man/netgraph.Rd | 45 ++ netmeta-0.9-8/netmeta/man/netleague.Rd | 63 +++- netmeta-0.9-8/netmeta/man/netmatrix.Rd |only netmeta-0.9-8/netmeta/man/netmeta-package.Rd | 3 netmeta-0.9-8/netmeta/man/netmeta.Rd | 36 +- netmeta-0.9-8/netmeta/man/netposet.Rd | 2 netmeta-0.9-8/netmeta/man/netsplit.Rd | 5 netmeta-0.9-8/netmeta/man/pairwise.Rd | 107 +++--- netmeta-0.9-8/netmeta/man/print.netcomb.Rd | 8 netmeta-0.9-8/netmeta/man/smokingcessation.Rd | 4 44 files changed, 1935 insertions(+), 567 deletions(-)
More information about MetabolomicsBasics at CRAN
Permanent link
Title: Fast Multivariate Log-Concave Density Estimation
Description: A fast solver for the maximum likelihood estimator (MLE) of a
multivariate log-concave probability function. Given a sample X, it estimates
a non-parametric density function whose logarithm is a concave function. Many
well-known parametric densities belong to that class, among them the normal
density, the uniform density, the exponential distribution and many more. This
package provides functions for the estimation of a log-concave density and
a mixture of log-concave densities in multiple dimensions. While being similar
to the package LogConcDEAD, fmlogcondens provides much fast run times for
large samples (>= 250 points). As a reference see Fabian Rathke, Christoph
Schnörr (2015), <doi:10.1515/auom-2015-0053>.
Author: Fabian Rathke [aut, cre],
Christoph Schnörr [aut],
Giovanni Garberoglio [cph]
Maintainer: Fabian Rathke <frathke@gmail.com>
Diff between fmlogcondens versions 1.0.1 dated 2018-03-20 and 1.0.2 dated 2018-03-23
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ R/fmlcd.R | 2 +- inst/doc/documentation.Rmd | 2 +- inst/doc/documentation.html | 40 ++++++++++++++++++++-------------------- man/correctIntegral.Rd | 4 ++-- man/fmlcd.Rd | 2 +- man/paramFitGammaOne.Rd | 8 +++++--- src/bfgsFullC.c | 6 +++--- src/util.c | 6 +++++- vignettes/documentation.Rmd | 2 +- 12 files changed, 59 insertions(+), 47 deletions(-)
Title: Automated Cleaning of Occurrence Records from Biological
Collections
Description: Automated cleaning of geographic species occurrence records by automated flagging of problems common to biodiversity data from biological collections. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. See <https://github.com/azizka/CoordinateCleaner/wiki> for more details and tutorials.
Author: Alexander Zizka [aut, cre],
Daniele Silvestro [ctb]
Maintainer: Alexander Zizka <alexander.zizka@bioenv.gu.se>
Diff between CoordinateCleaner versions 1.0-6 dated 2018-02-27 and 1.0-7 dated 2018-03-23
DESCRIPTION | 9 MD5 | 83 +++---- R/CleanCoordinates.R | 338 +++++++++++++++---------------- R/CleanCoordinatesDS.R | 225 ++++++++++---------- R/CleanCoordinatesFOS.R | 434 ++++++++++++++++++---------------------- R/WritePyRate.R | 305 ++++++++++++++-------------- R/cc_cap.R | 82 +++---- R/cc_cen.R | 97 ++++---- R/cc_coun.R | 81 +++---- R/cc_dupl.R | 43 +-- R/cc_equ.R | 53 ++-- R/cc_gbif.R | 47 ++-- R/cc_inst.R | 78 +++---- R/cc_outl.R | 163 +++++++-------- R/cc_sea.R | 67 +++--- R/cc_urb.R | 77 +++---- R/cc_val.R | 59 ++--- R/cc_zero.R | 59 ++--- R/dc_ddmm.R | 191 ++++++++--------- R/dc_round.R | 411 ++++++++++++++++++------------------- R/internal_CleanCoordinatesDS.R | 272 +++++++++++++------------ R/internal_WritePyRate.R | 15 - R/methods.spatialvalid.R | 182 +++++++--------- R/tc_equal.R | 61 ++--- R/tc_outl.R | 413 +++++++++++++++++++------------------- R/tc_range.R | 281 ++++++++++++------------- build/partial.rdb |binary man/CleanCoordinates.Rd | 12 - man/CleanCoordinatesFOS.Rd | 12 - man/cc_dupl.Rd | 2 man/cc_equ.Rd | 2 man/cc_outl.Rd | 2 man/cc_urb.Rd | 2 man/cc_val.Rd | 3 man/cc_zero.Rd | 2 man/dc_ddmm.Rd | 2 man/dc_round.Rd | 2 man/plot.spatialvalid.Rd | 2 man/tc_equal.Rd | 2 man/tc_outl.Rd | 2 man/tc_range.Rd | 2 tests |only 42 files changed, 2068 insertions(+), 2107 deletions(-)
More information about CoordinateCleaner at CRAN
Permanent link
More information about ZIBBSeqDiscovery at CRAN
Permanent link
Title: Lining Up Two Sets of Measurements
Description: Tools for detecting and correcting sample mix-ups between two sets
of measurements, such as between gene expression data on two tissues.
Author: Karl W Broman <kbroman@biostat.wisc.edu>
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between lineup versions 0.37-6 dated 2015-07-28 and 0.37-10 dated 2018-03-23
lineup-0.37-10/lineup/ChangeLog | 18 ++ lineup-0.37-10/lineup/DESCRIPTION | 11 - lineup-0.37-10/lineup/MD5 | 107 +++++++------- lineup-0.37-10/lineup/NAMESPACE | 4 lineup-0.37-10/lineup/R/corbetw2mat.R | 2 lineup-0.37-10/lineup/R/distee.R | 8 - lineup-0.37-10/lineup/R/disteg.R | 2 lineup-0.37-10/lineup/R/fscale.R | 2 lineup-0.37-10/lineup/R/plot.lineupdist.R | 4 lineup-0.37-10/lineup/R/plot2dist.R | 14 - lineup-0.37-10/lineup/R/subset.lineupdist.R | 10 - lineup-0.37-10/lineup/R/summary.lineupdist.R | 4 lineup-0.37-10/lineup/README.md |only lineup-0.37-10/lineup/build/vignette.rds |binary lineup-0.37-10/lineup/data/expr1.rda |binary lineup-0.37-10/lineup/data/expr2.rda |binary lineup-0.37-10/lineup/data/f2cross.rda |binary lineup-0.37-10/lineup/data/genepos.rda |binary lineup-0.37-10/lineup/data/pmap.rda |binary lineup-0.37-10/lineup/inst/LICENSE.md |only lineup-0.37-10/lineup/inst/doc/lineup.Rmd | 4 lineup-0.37-10/lineup/inst/doc/lineup.html | 144 +++++++++++--------- lineup-0.37-10/lineup/man/calc.locallod.Rd | 10 - lineup-0.37-10/lineup/man/combinedist.Rd | 14 - lineup-0.37-10/lineup/man/corbetw2mat.Rd | 11 - lineup-0.37-10/lineup/man/distee.Rd | 13 - lineup-0.37-10/lineup/man/disteg.Rd | 10 - lineup-0.37-10/lineup/man/expr-data.Rd | 3 lineup-0.37-10/lineup/man/f2cross.Rd | 3 lineup-0.37-10/lineup/man/find.gene.pseudomarker.Rd | 10 - lineup-0.37-10/lineup/man/findCommonID.Rd | 11 - lineup-0.37-10/lineup/man/fscale.Rd | 11 - lineup-0.37-10/lineup/man/genepos.Rd | 3 lineup-0.37-10/lineup/man/lineupversion.Rd | 7 lineup-0.37-10/lineup/man/omitdiag.Rd | 10 - lineup-0.37-10/lineup/man/plot.lineupdist.Rd | 14 - lineup-0.37-10/lineup/man/plot2dist.Rd | 16 +- lineup-0.37-10/lineup/man/plotEGclass.Rd | 10 - lineup-0.37-10/lineup/man/pmap.Rd | 3 lineup-0.37-10/lineup/man/pulldiag.Rd | 10 - lineup-0.37-10/lineup/man/subset.lineupdist.Rd | 17 +- lineup-0.37-10/lineup/man/summary.lineupdist.Rd | 12 - lineup-0.37-10/lineup/src/R_init.c |only lineup-0.37-10/lineup/src/R_init.h |only lineup-0.37-10/lineup/src/corbetw2mat.c | 2 lineup-0.37-10/lineup/src/corbetw2mat.h | 2 lineup-0.37-10/lineup/src/fscale.c | 2 lineup-0.37-10/lineup/src/fscale.h | 16 +- lineup-0.37-10/lineup/src/propmismatch.c | 2 lineup-0.37-10/lineup/src/propmismatch.h | 2 lineup-0.37-10/lineup/src/rmsd.c | 2 lineup-0.37-10/lineup/src/rmsd.h | 2 lineup-0.37-10/lineup/src/util.c | 2 lineup-0.37-10/lineup/src/util.h | 16 +- lineup-0.37-10/lineup/vignettes/lineup.Rmd | 4 lineup-0.37-6/lineup/NEWS |only lineup-0.37-6/lineup/inst/LICENSE.txt |only lineup-0.37-6/lineup/inst/TODO.txt |only 58 files changed, 310 insertions(+), 274 deletions(-)
Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling for both dichotomous and polytomous responses. Various cognitive diagnosis models can be estimated, include the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7>, the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070>, and many other models they subsume. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.
Author: Wenchao Ma [aut, cre, cph],
Jimmy de la Torre [aut, cph],
Miguel Sorrel [ctb]
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>
Diff between GDINA versions 1.4.2 dated 2017-04-13 and 2.0 dated 2018-03-23
GDINA-1.4.2/GDINA/R/HOsupplement.R |only GDINA-1.4.2/GDINA/R/M.R |only GDINA-1.4.2/GDINA/R/M.mono.R |only GDINA-1.4.2/GDINA/R/Msupplement.R |only GDINA-1.4.2/GDINA/R/extract.GDINA.R |only GDINA-1.4.2/GDINA/R/extract.Qval.R |only GDINA-1.4.2/GDINA/R/extract.itemfit.R |only GDINA-1.4.2/GDINA/R/extract.modelcomp.R |only GDINA-1.4.2/GDINA/R/extract.simGDINA.R |only GDINA-1.4.2/GDINA/R/hoparm.R |only GDINA-1.4.2/GDINA/R/zzz.R |only GDINA-1.4.2/GDINA/man/hoparm.Rd |only GDINA-1.4.2/GDINA/man/rowCount.Rd |only GDINA-1.4.2/GDINA/src/Rljs.cpp |only GDINA-1.4.2/GDINA/src/designM.cpp |only GDINA-1.4.2/GDINA/src/init.c |only GDINA-1.4.2/GDINA/src/uP.cpp |only GDINA-2.0/GDINA/DESCRIPTION | 49 GDINA-2.0/GDINA/MD5 | 200 +-- GDINA-2.0/GDINA/NAMESPACE | 29 GDINA-2.0/GDINA/NEWS.md | 9 GDINA-2.0/GDINA/R/CA.R |only GDINA-2.0/GDINA/R/CR.R | 7 GDINA-2.0/GDINA/R/Est.R |only GDINA-2.0/GDINA/R/ExportedFuncs.R | 185 ++- GDINA-2.0/GDINA/R/GDI.R | 157 +-- GDINA-2.0/GDINA/R/GDINA-package.R | 29 GDINA-2.0/GDINA/R/GDINA.R | 989 +++++++------------ GDINA-2.0/GDINA/R/HO.R | 302 +++-- GDINA-2.0/GDINA/R/M2.R |only GDINA-2.0/GDINA/R/Mstep.R | 457 +++++++- GDINA-2.0/GDINA/R/RcppExports.R | 206 +++ GDINA-2.0/GDINA/R/anova.GDINA.R | 60 - GDINA-2.0/GDINA/R/att.struc.R | 4 GDINA-2.0/GDINA/R/autoGDINA.R | 124 -- GDINA-2.0/GDINA/R/bootSE.R |only GDINA-2.0/GDINA/R/coef.R |only GDINA-2.0/GDINA/R/designmatrix.R | 94 + GDINA-2.0/GDINA/R/dif.R | 175 +-- GDINA-2.0/GDINA/R/ecpe.R | 8 GDINA-2.0/GDINA/R/extract.R |only GDINA-2.0/GDINA/R/frac20.R | 3 GDINA-2.0/GDINA/R/heatplot.itemfit.R | 11 GDINA-2.0/GDINA/R/initials.R | 63 - GDINA-2.0/GDINA/R/itemfit.R | 28 GDINA-2.0/GDINA/R/itemparm.GDINA.R | 51 GDINA-2.0/GDINA/R/modelcomp.R | 431 +++++--- GDINA-2.0/GDINA/R/monocheck.R | 2 GDINA-2.0/GDINA/R/personparm.GDINA.R | 113 +- GDINA-2.0/GDINA/R/plotIRF.GDINA.R | 96 - GDINA-2.0/GDINA/R/plotPVAF.Qval.R | 26 GDINA-2.0/GDINA/R/print.GDINA.R | 118 +- GDINA-2.0/GDINA/R/s3GDINA.R | 34 GDINA-2.0/GDINA/R/score.R | 115 -- GDINA-2.0/GDINA/R/sim10GDINA.R | 8 GDINA-2.0/GDINA/R/sim20seqGDINA.R | 11 GDINA-2.0/GDINA/R/sim21seqDINA.R | 8 GDINA-2.0/GDINA/R/sim30DINA.R | 8 GDINA-2.0/GDINA/R/sim30GDINA.R | 8 GDINA-2.0/GDINA/R/sim30pGDINA.R | 8 GDINA-2.0/GDINA/R/simGDINA.R | 254 +++- GDINA-2.0/GDINA/R/startGDINA.R | 1 GDINA-2.0/GDINA/R/structuralparm.R |only GDINA-2.0/GDINA/R/summary.GDINA.R | 20 GDINA-2.0/GDINA/R/utils.R | 468 +++----- GDINA-2.0/GDINA/inst/CITATION | 8 GDINA-2.0/GDINA/inst/shiny/server.R | 84 + GDINA-2.0/GDINA/inst/shiny/ui.R | 89 + GDINA-2.0/GDINA/man/CA.Rd |only GDINA-2.0/GDINA/man/ClassRate.Rd | 3 GDINA-2.0/GDINA/man/GDINA-package.Rd | 30 GDINA-2.0/GDINA/man/GDINA.Rd | 651 ++++++++---- GDINA-2.0/GDINA/man/LC2LG.Rd | 2 GDINA-2.0/GDINA/man/Qval.Rd | 8 GDINA-2.0/GDINA/man/att.structure.Rd | 2 GDINA-2.0/GDINA/man/attributepattern.Rd | 15 GDINA-2.0/GDINA/man/autoGDINA.Rd | 60 - GDINA-2.0/GDINA/man/bootSE.Rd |only GDINA-2.0/GDINA/man/designmatrix.Rd | 38 GDINA-2.0/GDINA/man/dif.Rd | 48 GDINA-2.0/GDINA/man/ecpe.Rd | 8 GDINA-2.0/GDINA/man/extract.Rd | 68 - GDINA-2.0/GDINA/man/frac20.Rd | 3 GDINA-2.0/GDINA/man/heatplot.Rd | 10 GDINA-2.0/GDINA/man/indlogLik.Rd | 13 GDINA-2.0/GDINA/man/indlogPost.Rd | 12 GDINA-2.0/GDINA/man/internal_GDINA.Rd |only GDINA-2.0/GDINA/man/itemfit.Rd | 8 GDINA-2.0/GDINA/man/itemparm.Rd | 41 GDINA-2.0/GDINA/man/mesaplot.Rd | 9 GDINA-2.0/GDINA/man/modelcomp.Rd | 114 +- GDINA-2.0/GDINA/man/modelfit.Rd |only GDINA-2.0/GDINA/man/npar.Rd | 10 GDINA-2.0/GDINA/man/personparm.Rd | 28 GDINA-2.0/GDINA/man/plotIRF.Rd | 4 GDINA-2.0/GDINA/man/score.Rd | 11 GDINA-2.0/GDINA/man/sim10GDINA.Rd | 8 GDINA-2.0/GDINA/man/sim20seqGDINA.Rd | 10 GDINA-2.0/GDINA/man/sim21seqDINA.Rd | 8 GDINA-2.0/GDINA/man/sim30DINA.Rd | 8 GDINA-2.0/GDINA/man/sim30GDINA.Rd | 8 GDINA-2.0/GDINA/man/sim30pGDINA.Rd | 8 GDINA-2.0/GDINA/man/simGDINA.Rd | 166 ++- GDINA-2.0/GDINA/man/startGDINA.Rd | 3 GDINA-2.0/GDINA/src/Lik.cpp | 313 ++++-- GDINA-2.0/GDINA/src/LouisC.cpp |only GDINA-2.0/GDINA/src/Makevars.win | 7 GDINA-2.0/GDINA/src/Mord.cpp |only GDINA-2.0/GDINA/src/Mstep.cpp |only GDINA-2.0/GDINA/src/NgRg.cpp | 7 GDINA-2.0/GDINA/src/RcppExports.cpp | 599 ++++++++++- GDINA-2.0/GDINA/src/SE.cpp |only GDINA-2.0/GDINA/src/sequP.cpp | 3 GDINA-2.0/GDINA/src/util.cpp |only GDINA-2.0/GDINA/tests/testthat/test-Qval.R |only GDINA-2.0/GDINA/tests/testthat/test-basic.R |only GDINA-2.0/GDINA/tests/testthat/test-likelihood.R | 193 +-- GDINA-2.0/GDINA/tests/testthat/test-scorefunctions.R | 6 GDINA-2.0/GDINA/tests/testthat/text-GDINAextract.R |only 119 files changed, 4753 insertions(+), 2940 deletions(-)
Title: Individual Tree Crowns Segmentation
Description: Three methods for Individual Tree Crowns (ITCs) delineation on remote sensing data: one is based on LiDAR data in x,y,z format and one on imagery data in raster format.
Author: Michele Dalponte
Maintainer: Michele Dalponte <michele.dalponte@fmach.it>
Diff between itcSegment versions 0.7 dated 2018-03-06 and 0.8 dated 2018-03-23
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/itcLiDARallo.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: A GUI for the UNU.RAN Random Variate Generators
Description: A GUI (Graphical User Interface) for the UNU.RAN random variate
generators. Thus it allows to build non-uniform random number
generators interactively for quite arbitrary distributions.
In addition, R code for the required calls from package Runuran can
be displayed and stored for later use. Some basic analysis like
goodness-of-fit tests can be performed.
Author: Josef Leydold
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between RunuranGUI versions 0.2 dated 2018-01-26 and 0.3 dated 2018-03-23
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS | 7 +++++++ R/common.R | 11 +++-------- R/stage1.R | 3 +-- R/stage2.R | 6 ++---- R/stage3.R | 10 +++++----- man/RunuranGUI-package.Rd | 2 +- 8 files changed, 31 insertions(+), 32 deletions(-)
Title: Tutorial Analysis of Some Agricultural Experiments
Description: Example software for the analysis of data from designed
experiments, especially agricultural crop experiments. The basics
of the analysis of designed experiments are discussed
using real examples from agricultural field trials.
A range of statistical methods using a range
of R statistical packages are exemplified . The experimental
data is made available as separate data sets for each example
and the R analysis code is made available as example code.
The example code can be readily extended, as required.
Author: R. N. Edmondson and H.P. Piepho
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between agriTutorial versions 0.1.2 dated 2018-02-06 and 0.1.3 dated 2018-03-23
DESCRIPTION | 12 +- MD5 | 16 +-- R/agriTutorial-package.R | 2 R/example3.R | 10 +- R/example4.R | 220 ++++++++++++++++++++++++++++++----------------- build/vignette.rds |binary man/agriTutorial.Rd | 2 man/example3.Rd | 10 +- man/example4.Rd | 216 +++++++++++++++++++++++++++++----------------- 9 files changed, 310 insertions(+), 178 deletions(-)
Title: Functions Related to ICES Advice
Description: Functions that are related to the ICES advisory process.
Author: Arni Magnusson [aut, cre],
Anne Cooper [aut],
Colin Millar [ctb]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesAdvice versions 1.4-0 dated 2017-12-15 and 1.4-1 dated 2018-03-23
icesAdvice-1.4-0/icesAdvice/R/icod.R |only icesAdvice-1.4-0/icesAdvice/data/icod.rda |only icesAdvice-1.4-0/icesAdvice/man/icod.Rd |only icesAdvice-1.4-1/icesAdvice/DESCRIPTION | 8 ++--- icesAdvice-1.4-1/icesAdvice/MD5 | 18 ++++++------ icesAdvice-1.4-1/icesAdvice/NEWS | 8 +++++ icesAdvice-1.4-1/icesAdvice/R/icesAdvice-package.R | 2 - icesAdvice-1.4-1/icesAdvice/R/mohn.R | 26 +++++++++++------- icesAdvice-1.4-1/icesAdvice/R/shake.R |only icesAdvice-1.4-1/icesAdvice/data/shake.rda |only icesAdvice-1.4-1/icesAdvice/man/icesAdvice-package.Rd | 2 - icesAdvice-1.4-1/icesAdvice/man/mohn.Rd | 26 +++++++++++------- icesAdvice-1.4-1/icesAdvice/man/shake.Rd |only 13 files changed, 55 insertions(+), 35 deletions(-)
Title: Analysis of Functional and Phylogenetic Patterns in
Metacommunities
Description: Analysis of metacommunities based on functional traits and
phylogeny of the community components. The functions that are offered here
implement for the R environment methods that have been available in the
SYNCSA application written in C++ (by Valerio Pillar, available at <http://
ecoqua.ecologia.ufrgs.br/ecoqua/SYNCSA.html>).
Author: Vanderlei Julio Debastiani
Maintainer: Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>
Diff between SYNCSA versions 1.3.2 dated 2014-02-07 and 1.3.3 dated 2018-03-23
SYNCSA-1.3.2/SYNCSA/man/SYNCSA-package.Rd |only SYNCSA-1.3.2/SYNCSA/man/cor.matrix.partial.Rd |only SYNCSA-1.3.3/SYNCSA/DESCRIPTION | 25 - SYNCSA-1.3.3/SYNCSA/MD5 | 81 ++- SYNCSA-1.3.3/SYNCSA/NAMESPACE | 64 ++ SYNCSA-1.3.3/SYNCSA/R/ProgressBAR.R | 27 - SYNCSA-1.3.3/SYNCSA/R/belonging.R | 46 + SYNCSA-1.3.3/SYNCSA/R/cent.norm.R | 22 SYNCSA-1.3.3/SYNCSA/R/cor.mantel.R |only SYNCSA-1.3.3/SYNCSA/R/cor.matrix.R | 167 +++++- SYNCSA-1.3.3/SYNCSA/R/cor.matrix.partial.R | 143 ++++- SYNCSA-1.3.3/SYNCSA/R/cor.procrustes.R |only SYNCSA-1.3.3/SYNCSA/R/matrix.p.R | 66 ++ SYNCSA-1.3.3/SYNCSA/R/matrix.t.R | 101 +++- SYNCSA-1.3.3/SYNCSA/R/matrix.x.R | 138 ++++- SYNCSA-1.3.3/SYNCSA/R/optimal.R | 395 ++++++++++++---- SYNCSA-1.3.3/SYNCSA/R/organize.syncsa.R | 305 +++++++++--- SYNCSA-1.3.3/SYNCSA/R/part.cor.R |only SYNCSA-1.3.3/SYNCSA/R/pca.R |only SYNCSA-1.3.3/SYNCSA/R/permut.row.matrix.R | 40 + SYNCSA-1.3.3/SYNCSA/R/permut.vector.R |only SYNCSA-1.3.3/SYNCSA/R/plot.pcasyncsa.R |only SYNCSA-1.3.3/SYNCSA/R/print.optimal.R |only SYNCSA-1.3.3/SYNCSA/R/print.syncsa.R |only SYNCSA-1.3.3/SYNCSA/R/pro.matrix.R |only SYNCSA-1.3.3/SYNCSA/R/pro.matrix.partial.R |only SYNCSA-1.3.3/SYNCSA/R/procrustes.partial.R |only SYNCSA-1.3.3/SYNCSA/R/procrustes.syncsa.R |only SYNCSA-1.3.3/SYNCSA/R/rao.diversity.R | 225 ++++++--- SYNCSA-1.3.3/SYNCSA/R/startup.R |only SYNCSA-1.3.3/SYNCSA/R/syncsa.R | 635 ++++++++++++++++++++++---- SYNCSA-1.3.3/SYNCSA/R/var.dummy.R |only SYNCSA-1.3.3/SYNCSA/R/var.type.R |only SYNCSA-1.3.3/SYNCSA/data/ADRS.rda |only SYNCSA-1.3.3/SYNCSA/man/ADRS.Rd |only SYNCSA-1.3.3/SYNCSA/man/ProgressBAR.Rd | 19 SYNCSA-1.3.3/SYNCSA/man/belonging.Rd | 50 +- SYNCSA-1.3.3/SYNCSA/man/cent.norm.Rd | 21 SYNCSA-1.3.3/SYNCSA/man/cor.matrix.Rd | 174 +++++-- SYNCSA-1.3.3/SYNCSA/man/flona.Rd | 3 SYNCSA-1.3.3/SYNCSA/man/matrix.p.Rd | 66 +- SYNCSA-1.3.3/SYNCSA/man/matrix.t.Rd | 81 ++- SYNCSA-1.3.3/SYNCSA/man/matrix.x.Rd | 93 ++- SYNCSA-1.3.3/SYNCSA/man/optimal.Rd | 156 ++++-- SYNCSA-1.3.3/SYNCSA/man/organize.syncsa.Rd | 98 ++-- SYNCSA-1.3.3/SYNCSA/man/part.cor.Rd |only SYNCSA-1.3.3/SYNCSA/man/pca.Rd |only SYNCSA-1.3.3/SYNCSA/man/permut.row.matrix.Rd | 25 - SYNCSA-1.3.3/SYNCSA/man/permut.vector.Rd |only SYNCSA-1.3.3/SYNCSA/man/procrustes.syncsa.Rd |only SYNCSA-1.3.3/SYNCSA/man/rao.diversity.Rd | 124 +++-- SYNCSA-1.3.3/SYNCSA/man/syncsa.Rd | 414 +++++++++++++--- SYNCSA-1.3.3/SYNCSA/man/var.dummy.Rd |only SYNCSA-1.3.3/SYNCSA/man/var.type.Rd |only 54 files changed, 2915 insertions(+), 889 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
Author: Rahul Satija [aut],
Andrew Butler [aut],
Paul Hoffman [aut, cre],
Jeff Farrell [ctb],
Shiwei Zheng [ctb],
Christoph Hafemeister [ctb],
Patrick Roelli [ctb]
Maintainer: Paul Hoffman <seuratpackage@gmail.com>
Diff between Seurat versions 2.2.1 dated 2018-02-14 and 2.3.0 dated 2018-03-23
DESCRIPTION | 17 +- MD5 | 117 +++++++------- NAMESPACE | 18 ++ NEWS.md | 17 +- R/RcppExports.R | 12 + R/cluster_determination.R | 44 +++-- R/cluster_determination_internal.R | 60 ++----- R/differential_expression.R | 112 +++++++++---- R/dimensional_reduction.R | 29 ++- R/dimensional_reduction_internal.R | 132 +++++++++++++++ R/interaction.R | 299 +++++++++++++++++++++++++++++------- R/jackstraw.R | 100 ++++++++---- R/multi_modal.R | 233 +++++++++++++++++++++++++++- R/plotting.R | 181 ++++++++++++++++----- R/plotting_internal.R | 92 ++++++++--- R/plotting_utilities.R | 39 ++++ R/preprocessing.R | 29 +++ R/preprocessing_internal.R | 60 +++++-- R/printing_utilities.R | 14 - R/snn.R | 156 +++++------------- R/spatial.R | 18 +- R/utilities.R | 2 R/utilities_internal.R | 17 ++ README.md | 14 + man/AddSamples.Rd | 4 man/AugmentPlot.Rd |only man/BuildSNN.Rd | 28 ++- man/CellPlot.Rd | 3 man/CombineIdent.Rd |only man/DESeq2DETest.Rd | 7 man/DimHeatmap.Rd | 12 - man/DimPlot.Rd | 13 + man/FastWhichCells.Rd | 3 man/FeaturePlot.Rd | 4 man/FindAllMarkers.Rd | 8 man/FindAllMarkersNode.Rd | 8 man/FindClusters.Rd | 18 +- man/FindMarkers.Rd | 11 - man/FindVariableGenes.Rd | 13 + man/GenePlot.Rd | 7 man/HTODemux.Rd |only man/JackStraw.Rd | 20 +- man/MASTDETest.Rd | 7 man/RenameIdent.Rd | 3 man/ReorderIdent.Rd | 15 + man/RunTSNE.Rd | 12 + man/ScaleData.Rd | 7 man/SetAllIdent.Rd | 5 man/SetAssayData.Rd | 4 man/SplitObject.Rd |only man/StashIdent.Rd | 6 man/SubsetByPredicate.Rd |only man/SubsetData.Rd | 13 + man/TransferIdent.Rd |only man/WhichCells.Rd | 8 man/WilcoxDETest.Rd | 7 src/RcppExports.cpp | 41 ++++ src/data_manipulation.cpp | 15 + src/data_manipulation.h | 7 src/snn.cpp |only src/snn.h |only tests/testthat/test_interaction.R |only tests/testthat/test_preprocessing.R | 18 ++ tests/testthat/test_seurat_object.R | 14 + 64 files changed, 1617 insertions(+), 536 deletions(-)
Title: Bayesian Mixture Models for Marker Dosage in Autopolyploids
Description: Fits Bayesian mixture models to estimate marker dosage for dominant markers in autopolyploids using JAGS (1.0 or greater) as outlined in Baker et al "Bayesian estimation of marker dosage in sugarcane and other autopolyploids" (2010, <doi:10.1007/s00122-010-1283-z>). May be used in conjunction with polySegratio for simulation studies and comparison with standard methods.
Author: Peter Baker [aut, cre]
Maintainer: Peter Baker <p.baker1@uq.edu.au>
Diff between polySegratioMM versions 0.6-3 dated 2014-03-06 and 0.6-4 dated 2018-03-23
DESCRIPTION | 23 ++++++++-------- MD5 | 29 ++++++++++---------- NAMESPACE | 5 +++ R/plotTheoretical.R | 2 - README.md |only build/vignette.rds |binary inst/CITATION | 47 ++++++++++++++++------------------ inst/doc/polySegratioMM-overview.R | 38 +++++++++++++-------------- inst/doc/polySegratioMM-overview.Rnw | 9 +++--- inst/doc/polySegratioMM-overview.pdf |binary man/polySegratioMM-package.Rd | 9 ++---- vignettes/polySegratioMM-overview.Rnw | 9 +++--- vignettes/tmp/tmp-006.pdf |binary vignettes/tmp/tmp-009.pdf |binary vignettes/tmp/tmp-016.pdf |binary vignettes/tmp/tmp-017.pdf |binary 16 files changed, 89 insertions(+), 82 deletions(-)
More information about polySegratioMM at CRAN
Permanent link
Title: Analysis of Metabolomics Data
Description: Metabolomics data are inevitably subject to a component of unwanted
variation, due to factors such as batch effects, matrix effects, and confounding
biological variation. This package is a collection of functions designed to
implement, assess, and choose a suitable normalization method
for a given metabolomics study (De Livera et al (2015) <doi:10.1021/ac502439y>).
Author: Alysha M De Livera, Gavriel Olshansky
Maintainer: Alysha M De Livera <alyshad@unimelb.edu.au>
Diff between NormalizeMets versions 0.24 dated 2018-02-22 and 0.25 dated 2018-03-23
NormalizeMets-0.24/NormalizeMets/inst/doc/interactiveRlaPlot.html |only NormalizeMets-0.25/NormalizeMets/DESCRIPTION | 8 NormalizeMets-0.25/NormalizeMets/MD5 | 79 NormalizeMets-0.25/NormalizeMets/NAMESPACE | 52 NormalizeMets-0.25/NormalizeMets/R/ColList.R | 36 NormalizeMets-0.25/NormalizeMets/R/ComparePcaPlots.R | 797 ++++--- NormalizeMets-0.25/NormalizeMets/R/CompareVolcanoPlots.r | 2 NormalizeMets-0.25/NormalizeMets/R/Dendrogram.r | 2 NormalizeMets-0.25/NormalizeMets/R/GenerateReport.R | 12 NormalizeMets-0.25/NormalizeMets/R/RlaPlots.r | 66 NormalizeMets-0.25/NormalizeMets/R/SvmFit.R | 4 NormalizeMets-0.25/NormalizeMets/inst/doc/NormalizeMets_vignette.html | 42 NormalizeMets-0.25/NormalizeMets/inst/rmd/General_Report_Template.Rmd | 1037 +++++----- NormalizeMets-0.25/NormalizeMets/man/ComparePcaPlots.Rd | 128 - NormalizeMets-0.25/NormalizeMets/man/ComparePvalHist.Rd | 180 - NormalizeMets-0.25/NormalizeMets/man/CompareRlaPlots.Rd | 116 - NormalizeMets-0.25/NormalizeMets/man/CompareVolcanoPlots.Rd | 228 +- NormalizeMets-0.25/NormalizeMets/man/ContrastMatrix.Rd | 62 NormalizeMets-0.25/NormalizeMets/man/Corr.Rd | 104 - NormalizeMets-0.25/NormalizeMets/man/Dendrogram.Rd | 146 - NormalizeMets-0.25/NormalizeMets/man/GenerateReport.Rd | 156 - NormalizeMets-0.25/NormalizeMets/man/HeatMap.Rd | 184 - NormalizeMets-0.25/NormalizeMets/man/LinearModelFit.Rd | 322 +-- NormalizeMets-0.25/NormalizeMets/man/LogTransform.Rd | 86 NormalizeMets-0.25/NormalizeMets/man/MissingValues.Rd | 148 - NormalizeMets-0.25/NormalizeMets/man/NormCombined.Rd | 158 - NormalizeMets-0.25/NormalizeMets/man/NormQcmets.Rd | 316 +-- NormalizeMets-0.25/NormalizeMets/man/NormQcsamples.Rd | 144 - NormalizeMets-0.25/NormalizeMets/man/NormScaling.Rd | 154 - NormalizeMets-0.25/NormalizeMets/man/NormalizeMets-package.Rd | 52 NormalizeMets-0.25/NormalizeMets/man/PcaPlots.Rd | 194 - NormalizeMets-0.25/NormalizeMets/man/RlaPlots.Rd | 185 - NormalizeMets-0.25/NormalizeMets/man/SvmFit.Rd | 144 - NormalizeMets-0.25/NormalizeMets/man/ToInputdata.Rd | 56 NormalizeMets-0.25/NormalizeMets/man/VennPlot.Rd | 170 - NormalizeMets-0.25/NormalizeMets/man/VolcanoPlot.Rd | 220 +- NormalizeMets-0.25/NormalizeMets/man/alldatacheck.Rd | 52 NormalizeMets-0.25/NormalizeMets/man/dataview.Rd | 52 NormalizeMets-0.25/NormalizeMets/man/editcolnames.Rd | 38 NormalizeMets-0.25/NormalizeMets/man/metgroupCheck.Rd | 48 NormalizeMets-0.25/NormalizeMets/man/multiplot.Rd | 62 41 files changed, 3105 insertions(+), 2937 deletions(-)
Title: Principal Coordinates of Phylogenetic Structure
Description: Set of functions for analysis of Principal Coordinates of Phylogenetic Structure (PCPS).
Author: Vanderlei Julio Debastiani
Maintainer: Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>
Diff between PCPS versions 1.0.3 dated 2016-04-05 and 1.0.4 dated 2018-03-23
PCPS-1.0.3/PCPS/R/scores.pcoasig.R |only PCPS-1.0.3/PCPS/R/scores.pcps.R |only PCPS-1.0.4/PCPS/DESCRIPTION | 16 - PCPS-1.0.4/PCPS/MD5 | 53 ++--- PCPS-1.0.4/PCPS/NAMESPACE | 15 + PCPS-1.0.4/PCPS/R/define.clade.R | 83 ++++---- PCPS-1.0.4/PCPS/R/matrix.p.sig.R | 144 ++++++++++---- PCPS-1.0.4/PCPS/R/pcoa.sig.R | 303 +++++++++++++------------------ PCPS-1.0.4/PCPS/R/pcpc.curve.calc.R |only PCPS-1.0.4/PCPS/R/pcps.R | 84 +++----- PCPS-1.0.4/PCPS/R/pcps.curve.R | 166 +++++++++------- PCPS-1.0.4/PCPS/R/pcps.sig.R | 218 ++++++++++++---------- PCPS-1.0.4/PCPS/R/plot.pcps.R | 27 +- PCPS-1.0.4/PCPS/R/plot.pcpscurve.R | 20 +- PCPS-1.0.4/PCPS/R/print.pcoasig.R | 6 PCPS-1.0.4/PCPS/R/print.pcps.R | 4 PCPS-1.0.4/PCPS/R/print.pcpscurve.R | 8 PCPS-1.0.4/PCPS/R/print.summarypcoasig.R |only PCPS-1.0.4/PCPS/R/print.summarypcps.R |only PCPS-1.0.4/PCPS/R/self.belonging.R | 16 - PCPS-1.0.4/PCPS/R/summary.pcoasig.R | 24 +- PCPS-1.0.4/PCPS/R/summary.pcps.R | 25 +- PCPS-1.0.4/PCPS/R/summary.pcpscurve.R | 71 ++----- PCPS-1.0.4/PCPS/R/wcmdscale.org.R |only PCPS-1.0.4/PCPS/man/define.clade.Rd | 9 PCPS-1.0.4/PCPS/man/pcoa.sig.Rd | 62 +++--- PCPS-1.0.4/PCPS/man/pcps.Rd | 57 +++-- PCPS-1.0.4/PCPS/man/pcps.curve.Rd | 59 ++++-- PCPS-1.0.4/PCPS/man/pcps.sig.Rd | 35 ++- PCPS-1.0.4/PCPS/man/self.belonging.Rd | 13 - PCPS-1.0.4/PCPS/man/wcmdscale.org.Rd |only 31 files changed, 809 insertions(+), 709 deletions(-)