Title: Tools for ecological network analysis (ena) in R
Diff between enaR versions 2.7 dated 2014-06-11 and 2.8 dated 2014-11-01
Description: Functions for the analysis of ecological networks
Author: M.K. Lau, S.R. Borrett, D.E. Hines, P. Sing
Maintainer: Matthew K. Lau
enaR-2.7/enaR/inst/doc/enaR-vignette.R |only
enaR-2.7/enaR/inst/doc/enaR-vignette.Rnw |only
enaR-2.7/enaR/vignettes/ecology.bst |only
enaR-2.7/enaR/vignettes/enaR-vignette.Rnw |only
enaR-2.7/enaR/vignettes/srb.bib |only
enaR-2.7/enaR/vignettes/srbbib_abb.bib |only
enaR-2.7/enaR/vignettes/srbbib_long.bib |only
enaR-2.8/enaR/DESCRIPTION | 17 +--
enaR-2.8/enaR/MD5 | 114 +++++++++++-----------
enaR-2.8/enaR/NAMESPACE | 10 -
enaR-2.8/enaR/R/TES.R | 14 +-
enaR-2.8/enaR/R/TET.R | 14 +-
enaR-2.8/enaR/R/as.extended.R | 27 ++---
enaR-2.8/enaR/R/bal.R | 24 ++--
enaR-2.8/enaR/R/balance.R | 33 +++---
enaR-2.8/enaR/R/bcratio.R | 16 +--
enaR-2.8/enaR/R/cycliv.R |only
enaR-2.8/enaR/R/eigenCentrality.R | 14 +-
enaR-2.8/enaR/R/enaAll.R | 12 +-
enaR-2.8/enaR/R/enaAscendency.R | 79 ++++++++++++---
enaR-2.8/enaR/R/enaControl.R | 48 ++++++---
enaR-2.8/enaR/R/enaCycle.R |only
enaR-2.8/enaR/R/enaEnviron.R | 56 +++++------
enaR-2.8/enaR/R/enaFlow.R | 51 ++++------
enaR-2.8/enaR/R/enaMTI.R | 40 +++----
enaR-2.8/enaR/R/enaStorage.R | 56 +++++------
enaR-2.8/enaR/R/enaStructure.R | 18 +--
enaR-2.8/enaR/R/enaTroAgg.R |only
enaR-2.8/enaR/R/enaUtility.R | 50 ++++-----
enaR-2.8/enaR/R/environCentrality.R | 14 +-
enaR-2.8/enaR/R/findPathLength.R | 33 ++----
enaR-2.8/enaR/R/force.balance.R | 14 +-
enaR-2.8/enaR/R/get.ns.R | 18 +--
enaR-2.8/enaR/R/get.orient.R | 12 +-
enaR-2.8/enaR/R/mExp.R | 14 +-
enaR-2.8/enaR/R/netOrder.R |only
enaR-2.8/enaR/R/pack.R | 38 +++----
enaR-2.8/enaR/R/read.enam.R | 20 +--
enaR-2.8/enaR/R/read.nea.R | 22 ++--
enaR-2.8/enaR/R/read.scor.R | 126 +++++++++++--------------
enaR-2.8/enaR/R/read.wand.R | 16 +--
enaR-2.8/enaR/R/scc.R | 10 -
enaR-2.8/enaR/R/scifix.R | 14 +-
enaR-2.8/enaR/R/set.orient.R | 12 +-
enaR-2.8/enaR/R/ssCheck.R | 30 ++---
enaR-2.8/enaR/R/structure.statistics.R | 10 -
enaR-2.8/enaR/R/unpack.R | 14 +-
enaR-2.8/enaR/R/write.nea.R | 14 +-
enaR-2.8/enaR/build/vignette.rds |binary
enaR-2.8/enaR/data/bgcModels.rda |binary
enaR-2.8/enaR/data/enaModelInfo.rda |binary
enaR-2.8/enaR/data/enaModels.rda |binary
enaR-2.8/enaR/data/oyster.rda |binary
enaR-2.8/enaR/data/troModels.rda |binary
enaR-2.8/enaR/inst/doc/enaR-vignette.pdf |binary
enaR-2.8/enaR/inst/doc/enaR-vignette.pdf.asis |only
enaR-2.8/enaR/man/bal.Rd | 2
enaR-2.8/enaR/man/cycliv.Rd |only
enaR-2.8/enaR/man/enaAscendency.Rd | 9 +
enaR-2.8/enaR/man/enaControl.Rd | 19 +++
enaR-2.8/enaR/man/enaCycle.Rd |only
enaR-2.8/enaR/man/enaTroAgg.Rd |only
enaR-2.8/enaR/man/m.list.Rd |only
enaR-2.8/enaR/man/netOrder.Rd |only
enaR-2.8/enaR/man/read.scor.Rd | 5
enaR-2.8/enaR/man/write.nea.Rd | 2
enaR-2.8/enaR/vignettes/enaR-vignette.pdf.asis |only
67 files changed, 618 insertions(+), 543 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Diff between dbmss versions 2.1.1 dated 2014-05-13 and 2.1.2 dated 2014-11-01
Description: This package allows simple computation of a full set of spatial statistic functions of distance, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). It relies on spatstat for core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon
dbmss-2.1.1/dbmss/inst/CITATION |only
dbmss-2.1.1/dbmss/vignettes/figure |only
dbmss-2.1.1/dbmss/vignettes/framed.sty |only
dbmss-2.1.2/dbmss/DESCRIPTION | 10 +-
dbmss-2.1.2/dbmss/MD5 | 60 ++++++--------
dbmss-2.1.2/dbmss/NEWS | 15 +++
dbmss-2.1.2/dbmss/R/FillEnveloppe.R | 2
dbmss-2.1.2/dbmss/R/KEnvelope.R | 2
dbmss-2.1.2/dbmss/R/KdEnvelope.R | 5 -
dbmss-2.1.2/dbmss/R/Kdhat.R | 129 +++++++++++++++++++++----------
dbmss-2.1.2/dbmss/R/Khat.R | 2
dbmss-2.1.2/dbmss/R/RcppExports.R | 4
dbmss-2.1.2/dbmss/R/m_Envelope.R |only
dbmss-2.1.2/dbmss/R/m_hat.R |only
dbmss-2.1.2/dbmss/build/vignette.rds |binary
dbmss-2.1.2/dbmss/inst/doc/dbmss.R | 43 +++-------
dbmss-2.1.2/dbmss/inst/doc/dbmss.Rnw | 69 ++++++++++------
dbmss-2.1.2/dbmss/inst/doc/dbmss.pdf |binary
dbmss-2.1.2/dbmss/man/KEnvelope.Rd | 6 -
dbmss-2.1.2/dbmss/man/KdEnvelope.Rd | 16 +++
dbmss-2.1.2/dbmss/man/Kdhat.Rd | 15 ++-
dbmss-2.1.2/dbmss/man/Khat.Rd | 4
dbmss-2.1.2/dbmss/man/Ktest.Rd | 2
dbmss-2.1.2/dbmss/man/Mhat.Rd | 2
dbmss-2.1.2/dbmss/man/Rcpp.Rd | 2
dbmss-2.1.2/dbmss/man/dbmss-package.Rd | 8 -
dbmss-2.1.2/dbmss/man/m_Envelope.Rd |only
dbmss-2.1.2/dbmss/man/m_hat.Rd |only
dbmss-2.1.2/dbmss/man/rRandomLocation.Rd | 2
dbmss-2.1.2/dbmss/src/CountNbd.cpp | 81 ++++++++++++++++++-
dbmss-2.1.2/dbmss/src/RcppExports.cpp | 18 ++++
dbmss-2.1.2/dbmss/vignettes/dbmss.Rnw | 69 ++++++++++------
dbmss-2.1.2/dbmss/vignettes/dbmss.bib | 35 ++++++--
33 files changed, 413 insertions(+), 188 deletions(-)
Title: Mean and variance modeling of count data
Diff between CountsEPPM versions 1.0 dated 2013-05-01 and 2.0 dated 2014-11-01
Description: Modeling under- and over-dispersed count data using extended Poisson process models (EPPM)
Author: David M Smith, Malcolm J Faddy
Maintainer: David M. Smith
DESCRIPTION | 13
MD5 | 70 ++-
NAMESPACE | 3
R/CountsEPPM.R | 705 +++++++++++++++++++++++++++-------------
R/CountsEPPM.distribution.R | 49 +-
R/CountsEPPM.summary.R | 52 ++
R/EPPMprob.R | 6
R/F.Regression.Counts.R | 64 ---
R/Faddyprob.general.R | 31 +
R/Faddyprob.limiting.R | 9
R/LL.Regression.Counts.R |only
R/LRTruncation.R | 38 +-
R/Model.Counts.R | 10
R/Model.Faddy.R | 30 +
R/Model.FaddyJMV.general.R | 137 ++++---
R/Model.FaddyJMV.limiting.R | 51 +-
data/Luningetal.litters.rda |binary
data/Titanic.survivors.case.rda |only
data/Williams.litters.rda |binary
data/ceriodaphnia.group.rda |binary
data/herons.group.rda |binary
data/takeover.bids.case.rda |only
man/CountsEPPM-package.Rd | 18 -
man/CountsEPPM.Rd | 50 +-
man/CountsEPPM.distribution.Rd | 15
man/F.Regression.Counts.Rd | 30 -
man/Faddyprob.general.Rd | 9
man/Faddyprob.limiting.Rd | 8
man/LL.Regression.Counts.Rd |only
man/Luningetal.litters.Rd | 9
man/Model.Counts.Rd | 34 -
man/Model.Faddy.Rd | 39 +-
man/Model.FaddyJMV.general.Rd | 32 -
man/Model.FaddyJMV.limiting.Rd | 15
man/Titanic.survivors.case.Rd |only
man/Williams.litters.Rd | 9
man/ceriodaphnia.group.Rd | 13
man/herons.group.Rd | 8
man/takeover.bids.case.Rd |only
39 files changed, 947 insertions(+), 610 deletions(-)
Title: Extensions for Exponential Random Graph Models (ERGM)
Diff between xergm versions 1.1 dated 2014-08-07 and 1.3 dated 2014-11-01
Description: Temporal exponential random graph models (TERGM) by bootstrapped pseudolikelihood ("btergm") and MCMC MLE ("mtergm") and (temporal) network autocorrelation models ("tnam").
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [aut],
Bruce A. Desmarais [aut]
Maintainer: Philip Leifeld
xergm-1.1/xergm/R/behavior.R |only
xergm-1.3/xergm/DESCRIPTION | 14 ++--
xergm-1.3/xergm/MD5 | 30 ++++-----
xergm-1.3/xergm/NAMESPACE | 3
xergm-1.3/xergm/R/btergm.R | 9 +-
xergm-1.3/xergm/R/gof.R | 4 -
xergm-1.3/xergm/R/interpretation.R | 9 --
xergm-1.3/xergm/R/mtergm.R |only
xergm-1.3/xergm/R/preprocess.R | 19 +++--
xergm-1.3/xergm/R/tnam.R | 115 +++++++++++++++++++++++++++++++++++
xergm-1.3/xergm/inst/doc/btergm.Rnw | 2
xergm-1.3/xergm/inst/doc/btergm.pdf |binary
xergm-1.3/xergm/man/btergm.Rd | 23 ++++++-
xergm-1.3/xergm/man/preprocess.Rd | 2
xergm-1.3/xergm/man/tnam-terms.Rd | 27 +++++++-
xergm-1.3/xergm/man/tnam.Rd | 2
xergm-1.3/xergm/vignettes/btergm.Rnw | 2
17 files changed, 212 insertions(+), 49 deletions(-)
Title: Distributions, Statistics and Tests derived from Random Matrix
Theory
Diff between RMTstat versions 0.2 dated 2009-10-14 and 0.3 dated 2014-11-01
Description:
Functions for working with the Tracy-Widom laws and other distributions
related to the eigenvalues of large Wishart matrices.
The tables for computing the Tracy-Widom densities and distribution
functions were computed by Momar Dieng's MATLAB package "RMLab"
(formerly available on his homepage at
http://math.arizona.edu/~momar/research.htm ).
This package is part of a collaboration between Iain Johnstone,
Zongming Ma, Patrick Perry, and Morteza Shahram. It will soon be
replaced by a package with more accuracy and built-in support for
relevant statistical tests.
Author: Iain M. Johnstone, Zongming Ma, Patrick O. Perry and Morteza Shahram.
Maintainer: Patrick O. Perry
DESCRIPTION | 40 +++++++++++++++++++---------------------
LICENSE | 31 +++----------------------------
MD5 |only
R/WishartMax.R | 7 ++++---
4 files changed, 26 insertions(+), 52 deletions(-)
Title: Fitting Single and Mixture of Generalised Lambda Distributions
(RS and FMKL) using Various Methods
Diff between GLDEX versions 2.0.0.0 dated 2014-03-06 and 2.0.0.1 dated 2014-11-01
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
R/gl.check.lambda.alt.R | 4 +++-
README |only
man/GLDEX.package.Rd | 6 +++---
5 files changed, 14 insertions(+), 11 deletions(-)
Title: Extended and enhanced Hierarchical Logistic Regression models
(so-called Huisman-Olff-Fresco models).
Diff between eHOF versions 1.5 dated 2014-09-27 and 1.5.4 dated 2014-11-01
Description: Hierarchical logistic species response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen
eHOF-1.5.4/eHOF/DESCRIPTION | 10 +-
eHOF-1.5.4/eHOF/MD5 | 35 +++-----
eHOF-1.5.4/eHOF/R/HOF.default.r | 19 +++-
eHOF-1.5.4/eHOF/R/Para.deriv.r | 20 +++--
eHOF-1.5.4/eHOF/R/Para.niche.r | 144 +++++++++++++++++++------------------
eHOF-1.5.4/eHOF/R/Para.opt.r | 40 ++++++----
eHOF-1.5.4/eHOF/R/Para.r | 29 +++++++
eHOF-1.5.4/eHOF/R/pick.model.r | 46 +++++++----
eHOF-1.5.4/eHOF/R/plot.HOF.list.r | 24 +++---
eHOF-1.5.4/eHOF/R/plot.HOF.r | 33 +++-----
eHOF-1.5.4/eHOF/R/print.HOF.list.r | 6 -
eHOF-1.5.4/eHOF/R/print.HOF.r | 27 +++---
eHOF-1.5.4/eHOF/R/zzz.r | 2
eHOF-1.5.4/eHOF/inst/ChangeLog | 6 +
eHOF-1.5.4/eHOF/man/HOF.Rd | 12 +--
eHOF-1.5/eHOF/R/Para.HOF.r |only
eHOF-1.5/eHOF/vignettes/figure |only
17 files changed, 262 insertions(+), 191 deletions(-)
Title: Functions to access vegetation databases (Turboveg) and prepare
vegetation data especially its taxonomy for analysis
Diff between vegdata versions 0.6-6 dated 2014-01-24 and 0.6-7 dated 2014-11-01
Description: Handling of vegetation data from Turboveg, VegetWeb and ESVeg Exports. Taxonomic harmonization of data with appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL").
Author: Florian Jansen
Maintainer: Florian Jansen
vegdata-0.6-6/vegdata/R/compRefl.r |only
vegdata-0.6-6/vegdata/tests |only
vegdata-0.6-7/vegdata/DESCRIPTION | 10
vegdata-0.6-7/vegdata/MD5 | 46 +--
vegdata-0.6-7/vegdata/R/child.r | 6
vegdata-0.6-7/vegdata/R/reflist.r | 5
vegdata-0.6-7/vegdata/R/syntab.r | 30 +-
vegdata-0.6-7/vegdata/R/tax.r | 21 -
vegdata-0.6-7/vegdata/R/tax_add.r | 4
vegdata-0.6-7/vegdata/R/tv.compRefl.r |only
vegdata-0.6-7/vegdata/R/tv.home.r | 13
vegdata-0.6-7/vegdata/R/tv.site.r | 32 +-
vegdata-0.6-7/vegdata/R/tv.traits.r | 2
vegdata-0.6-7/vegdata/R/tv.veg.r | 3
vegdata-0.6-7/vegdata/R/tv.write.r | 27 +
vegdata-0.6-7/vegdata/build/vignette.rds |binary
vegdata-0.6-7/vegdata/inst/ChangeLog | 6
vegdata-0.6-7/vegdata/inst/doc/vegdata.R | 164 +++---------
vegdata-0.6-7/vegdata/inst/doc/vegdata.Rnw | 70 -----
vegdata-0.6-7/vegdata/inst/doc/vegdata.pdf |binary
vegdata-0.6-7/vegdata/inst/tvdata/Species/TaxrefExample.zip |only
vegdata-0.6-7/vegdata/man/tax.Rd | 2
vegdata-0.6-7/vegdata/man/taxval.Rd | 2
vegdata-0.6-7/vegdata/man/tv.site.Rd | 5
vegdata-0.6-7/vegdata/man/tv.write.Rd | 4
vegdata-0.6-7/vegdata/vignettes/vegdata.Rnw | 70 -----
26 files changed, 167 insertions(+), 355 deletions(-)
Title: K-Adaptive Partitioning for Survival data
Diff between kaps versions 1.0-0 dated 2014-03-19 and 1.0.2 dated 2014-11-01
Description: This package provides some routines to conduct the K-adaptive parititioning (kaps) algorithm for survival data. A function kaps is an implementation version of our algorithm.
Author: Soo-Heang Eo [aut, cre],
Seung-Mo Hong [ctb],
HyungJun Cho [aut]
Maintainer: Soo-Heang Eo
kaps-1.0-0/kaps/R/kaps.boot.R |only
kaps-1.0-0/kaps/man/kaps-class.Rd |only
kaps-1.0.2/kaps/DESCRIPTION | 30 ++++-----
kaps-1.0.2/kaps/MD5 | 36 +++++------
kaps-1.0.2/kaps/NAMESPACE | 8 --
kaps-1.0.2/kaps/R/accessaries.R | 115 +++++++++++++++++-------------------
kaps-1.0.2/kaps/R/kaps.fit.R | 23 ++++---
kaps-1.0.2/kaps/data/toy.rda |binary
kaps-1.0.2/kaps/inst/NEWS.Rd | 13 +++-
kaps-1.0.2/kaps/man/count.mindat.Rd | 2
kaps-1.0.2/kaps/man/kaps-classes.Rd |only
kaps-1.0.2/kaps/man/kaps-package.Rd | 10 +--
kaps-1.0.2/kaps/man/kaps.Rd | 16 ++---
kaps-1.0.2/kaps/man/kaps.control.Rd | 28 ++++----
kaps-1.0.2/kaps/man/kapsNews.Rd |only
kaps-1.0.2/kaps/man/km.curve.Rd | 7 --
kaps-1.0.2/kaps/man/plot.Rd | 18 +++--
kaps-1.0.2/kaps/man/print.Rd | 1
kaps-1.0.2/kaps/man/show.Rd | 2
kaps-1.0.2/kaps/man/summary.Rd | 6 -
kaps-1.0.2/kaps/man/toy.Rd | 11 +--
21 files changed, 166 insertions(+), 160 deletions(-)