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Title: Model selection and multimodel inference based on (Q)AIC(c)
Diff between AICcmodavg versions 1.25 dated 2012-08-16 and 1.26 dated 2012-08-30
Description: This package includes functions to create model selection
tables based on Akaike's information criterion (AIC) and the
second-order AIC (AICc), as well as their quasi-likelihood
counterparts (QAIC, QAICc). Tables are printed with delta AIC
and Akaike weights. The package also features functions to
conduct classic model averaging (multimodel inference) for a
given parameter of interest and predicted values, as well as a
shrinkage version of model averaging parameter estimates.
Other handy functions enable the computation of relative
variable importance, evidence ratios, and confidence sets for
the best model. The present version works with Cox regression
('coxph' class), linear models ('lm' class), generalized linear
models ('glm' class), linear models fit by generalized least
squares ('gls' class), linear mixed models ('lme' class),
generalized linear mixed models ('mer' class), multinomial and
ordinal logistic regressions ('multinom', 'polr', 'clm', and
'clmm' classes), robust regression models ('rlm' class), and
nonlinear models ('nls' class). The package also supports
various models incorporating detection probabilities such as
single-season occupancy models ('unmarkedFitOccu' class),
multiple-season occupancy models ('unmarkedFitColExt' class),
single-season heterogeneity models ('unmarkedFitOccuRN' class),
single-season and multiple-season N-mixture models for repeated
counts ('unmarkedFitPCount' and 'unmarkedFitPCO' classes,
respectively), and distance sampling models ('unmarkedFitDS'
and 'unmarkedFitGDS' classes).
Author: Marc J. Mazerolle
Maintainer: Marc J. Mazerolle
DESCRIPTION | 16 +-
MD5 | 57 +++++----
R/AICc.R | 20 +++
R/AICc.clm.R |only
R/AICc.clmm.R |only
R/AICc.rlm.R |only
R/aictab.R | 26 +++-
R/aictab.clm.R |only
R/aictab.clmm.R |only
R/aictab.rlm.R |only
R/importance.R | 18 ++
R/modavg.R | 32 ++++-
R/modavg.clm.R |only
R/modavg.clmm.R |only
R/modavg.effect.r | 13 +-
R/modavg.effect.rlm.r |only
R/modavg.rlm.R |only
R/modavg.shrink.R | 29 ++++
R/modavg.shrink.clm.R |only
R/modavg.shrink.clmm.R |only
R/modavg.shrink.rlm.R |only
R/modavg.unmarked.R | 28 +++-
R/modavgpred.R | 284 ++++++++++++++++++++++++++++++++--------------
R/predictSE.gls.r | 14 +-
R/predictSE.lme.r | 13 +-
R/predictSE.mer.r | 48 +++++--
inst/NEWS | 13 ++
man/AICc.Rd | 37 ++++-
man/AICcmodavg-package.Rd | 25 ++--
man/aictab.Rd | 47 ++++---
man/modavg.Rd | 35 ++++-
man/modavg.effect.Rd | 35 +++--
man/modavg.shrink.Rd | 51 +++++---
man/modavgpred.Rd | 25 ++--
man/predictSE.gls.Rd | 4
man/predictSE.mer.Rd | 15 +-
36 files changed, 641 insertions(+), 244 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-20 dated 2012-08-01 and 7.3-21 dated 2012-08-30
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Kurt Hornik
[trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial
port ca 1998), David Firth [ctb]
Maintainer: Brian Ripley
DESCRIPTION | 10 ++++-----
MD5 | 8 +++----
R/mvrnorm.R | 8 ++++---
inst/NEWS | 5 +++-
man/mvrnorm.Rd | 59 +++++++++++++++++++++++----------------------------------
5 files changed, 42 insertions(+), 48 deletions(-)
Title: Flexible procedures for clustering
Diff between fpc versions 2.0-3 dated 2010-11-19 and 2.1-4 dated 2012-08-30
Description: Various methods for clustering and cluster validation.
Fixed point clustering. Linear regression clustering.
Clustering by merging Gaussian mixture components. Symmetric
and asymmetric discriminant projections for visualisation of
the separation of groupings. Cluster validation statistics for
distance based clustering including corrected Rand index.
Cluster-wise cluster stability assessment. Methods for
estimation of the number of clusters: Calinski-Harabasz,
Tibshirani and Walther's prediction strength, Fang and Wang's
bootstrap stability. Gaussian/multinomial mixture fitting for
mixed continuous/categorical variables. Variable-wise
statistics for cluster interpretation. DBSCAN clustering.
Interface functions for many clustering methods implemented in
R, including estimating the number of clusters with kmeans, pam
and clara. Modality diagnosis for Gaussian mixtures. For an
overview see package?fpc.
Author: Christian Hennig
Maintainer: Christian Hennig
fpc-2.0-3/fpc/data/tonedata.txt |only
fpc-2.0-3/fpc/man/dip.pvalue.Rd |only
fpc-2.1-4/fpc/DESCRIPTION | 34 -
fpc-2.1-4/fpc/MD5 |only
fpc-2.1-4/fpc/NAMESPACE |only
fpc-2.1-4/fpc/R/addclustermethods.R | 254 +++++++----
fpc-2.1-4/fpc/R/clusterboot.R | 412 ++++++++++-------
fpc-2.1-4/fpc/R/dbscan.R | 2
fpc-2.1-4/fpc/R/fpc.R | 20
fpc-2.1-4/fpc/R/lcmixed.R | 22
fpc-2.1-4/fpc/R/localshape.R |only
fpc-2.1-4/fpc/R/mergenormals.R | 99 +---
fpc-2.1-4/fpc/data/tonedata.txt.gz |only
fpc-2.1-4/fpc/man/adcoord.Rd | 2
fpc-2.1-4/fpc/man/ancoord.Rd | 2
fpc-2.1-4/fpc/man/awcoord.Rd | 2
fpc-2.1-4/fpc/man/batcoord.Rd | 2
fpc-2.1-4/fpc/man/bhattacharyya.dist.Rd | 2
fpc-2.1-4/fpc/man/bhattacharyya.matrix.Rd | 2
fpc-2.1-4/fpc/man/calinhara.Rd | 4
fpc-2.1-4/fpc/man/can.Rd | 2
fpc-2.1-4/fpc/man/cat2bin.Rd | 2
fpc-2.1-4/fpc/man/classifdist.Rd |only
fpc-2.1-4/fpc/man/clucols.Rd | 2
fpc-2.1-4/fpc/man/clujaccard.Rd | 2
fpc-2.1-4/fpc/man/clusexpect.Rd | 2
fpc-2.1-4/fpc/man/cluster.stats.Rd | 85 +++
fpc-2.1-4/fpc/man/cluster.varstats.Rd | 2
fpc-2.1-4/fpc/man/clusterboot.Rd | 13
fpc-2.1-4/fpc/man/cmahal.Rd | 2
fpc-2.1-4/fpc/man/concomp.Rd | 2
fpc-2.1-4/fpc/man/confusion.Rd | 2
fpc-2.1-4/fpc/man/cov.wml.Rd | 2
fpc-2.1-4/fpc/man/cweight.Rd | 2
fpc-2.1-4/fpc/man/dbscan.Rd | 10
fpc-2.1-4/fpc/man/dipp.tantrum.Rd | 6
fpc-2.1-4/fpc/man/diptest.multi.Rd | 4
fpc-2.1-4/fpc/man/discrcoord.Rd | 2
fpc-2.1-4/fpc/man/discrete.recode.Rd | 2
fpc-2.1-4/fpc/man/discrproj.Rd | 2
fpc-2.1-4/fpc/man/distancefactor.Rd | 6
fpc-2.1-4/fpc/man/distcritmulti.Rd |only
fpc-2.1-4/fpc/man/dridgeline.Rd | 2
fpc-2.1-4/fpc/man/dudahart2.Rd | 2
fpc-2.1-4/fpc/man/extract.mixturepars.Rd | 2
fpc-2.1-4/fpc/man/fixmahal.Rd | 2
fpc-2.1-4/fpc/man/fixreg.Rd | 2
fpc-2.1-4/fpc/man/flexmixedruns.Rd | 6
fpc-2.1-4/fpc/man/fpc-package.Rd | 28 -
fpc-2.1-4/fpc/man/fpclusters.Rd | 2
fpc-2.1-4/fpc/man/itnumber.Rd | 2
fpc-2.1-4/fpc/man/jittervar.Rd | 2
fpc-2.1-4/fpc/man/kmeansCBI.Rd | 54 +-
fpc-2.1-4/fpc/man/kmeansruns.Rd | 4
fpc-2.1-4/fpc/man/lcmixed.Rd | 6
fpc-2.1-4/fpc/man/localshape.Rd |only
fpc-2.1-4/fpc/man/mahalanodisc.Rd | 2
fpc-2.1-4/fpc/man/mahalanofix.Rd | 2
fpc-2.1-4/fpc/man/mahalconf.Rd | 2
fpc-2.1-4/fpc/man/mergenormals.Rd | 4
fpc-2.1-4/fpc/man/mergeparameters.Rd | 2
fpc-2.1-4/fpc/man/minsize.Rd | 2
fpc-2.1-4/fpc/man/mixdens.Rd | 2
fpc-2.1-4/fpc/man/mixpredictive.Rd | 2
fpc-2.1-4/fpc/man/mvdcoord.Rd | 2
fpc-2.1-4/fpc/man/ncoord.Rd | 2
fpc-2.1-4/fpc/man/nselectboot.Rd |only
fpc-2.1-4/fpc/man/pamk.Rd | 35 +
fpc-2.1-4/fpc/man/piridge.Rd | 2
fpc-2.1-4/fpc/man/piridge.zeroes.Rd | 2
fpc-2.1-4/fpc/man/plotcluster.Rd | 2
fpc-2.1-4/fpc/man/prediction.strength.Rd | 57 +-
fpc-2.1-4/fpc/man/rFace.Rd | 2
fpc-2.1-4/fpc/man/randcmatrix.Rd | 2
fpc-2.1-4/fpc/man/randconf.Rd | 2
fpc-2.1-4/fpc/man/regmix.Rd | 8
fpc-2.1-4/fpc/man/ridgeline.Rd | 2
fpc-2.1-4/fpc/man/ridgeline.diagnosis.Rd | 2
fpc-2.1-4/fpc/man/simmatrix.Rd | 2
fpc-2.1-4/fpc/man/solvecov.Rd | 2
fpc-2.1-4/fpc/man/sseg.Rd | 2
fpc-2.1-4/fpc/man/tdecomp.Rd | 2
fpc-2.1-4/fpc/man/unimodal.ind.Rd | 2
fpc-2.1-4/fpc/man/weightplots.Rd | 2
fpc-2.1-4/fpc/man/wfu.Rd | 2
fpc-2.1-4/fpc/man/zmisclassification.matrix.Rd | 2
fpc-2.1-4/fpc/tests/Examples/fpc-Ex.Rout.save | 577 +++++++++++++++----------
fpc-2.1-4/fpc/tests/fpctests.R | 16
fpc-2.1-4/fpc/tests/fpctests.Rout.save | 236 +++++++---
89 files changed, 1345 insertions(+), 763 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Diff between rgdal versions 0.7-16 dated 2012-08-20 and 0.7-18 dated 2012-08-30
Description: Provides bindings to Frank Warmerdam's Geospatial Data
Abstraction Library (GDAL) (>= 1.6.0) and access to
projection/transformation operations from the PROJ.4 library.
The GDAL and PROJ.4 libraries are external to the package, and,
when installing the package from source, must be correctly
installed first. Both GDAL raster and OGR vector map data can
be imported into R, and GDAL raster data and OGR vector data
exported. Use is made of classes defined in the sp package.
Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and
Expat) are provided on CRAN.
Author: Timothy H. Keitt
Maintainer: Roger Bivand
ChangeLog | 26 ++++++++++++++++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 18 ++++++++++--------
R/project.R | 16 ++++++++--------
inst/ChangeLog | 26 ++++++++++++++++++++++++++
man/project.Rd | 2 +-
man/spTransform-methods.Rd | 26 +++++++++++++++++++++++++-
src/init.c | 2 +-
src/projectit.cpp | 4 ++--
tests/test_proj.R |only
tests/test_proj.Rout.save |only
11 files changed, 103 insertions(+), 25 deletions(-)
Title: Benchmarking routine for R
Diff between rbenchmark versions 0.3.1 dated 2012-08-13 and 1.0.0 dated 2012-08-30
Description: rbenchmark is inspired by the Perl module Benchmark, and
is intended to facilitate benchmarking of arbitrary R code. The
library consists of just one function, benchmark, which is a
simple wrapper around system.time. Given a specification of
the benchmarking process (counts of replications, evaluation
environment) and an arbitrary number of expressions, benchmark
evaluates each of the expressions in the specified environment,
replicating the evaluation as many times as specified, and
returning the results conveniently wrapped into a data frame.
Author: Wacek Kusnierczyk
Maintainer: Wacek Kusnierczyk
ChangeLog | 42 +++++++++++++++++
DESCRIPTION | 14 +++--
MD5 | 12 ++--
R/benchmark.R | 30 ++++++------
demo/benchmark.R | 54 +++++++++++-----------
man/benchmark-package.Rd | 52 ++++++++++++++++++---
man/benchmark.Rd | 115 ++++++++++++++++++++++++-----------------------
7 files changed, 206 insertions(+), 113 deletions(-)
Title: Functions for extreme value distributions
Diff between evd versions 2.2-7 dated 2012-07-31 and 2.3-0 dated 2012-08-30
Description: Extends simulation, distribution, quantile and density
functions to univariate and multivariate parametric extreme
value distributions, and provides fitting functions which
calculate maximum likelihood estimates for univariate and
bivariate maxima models, and for univariate and bivariate
threshold models.
Author: Alec Stephenson. Function fbvpot by Chris Ferro.
Maintainer: Alec Stephenson
evd-2.2-7/evd/demo |only
evd-2.2-7/evd/inst/demos.txt |only
evd-2.3-0/evd/DESCRIPTION | 8 +-
evd-2.3-0/evd/MD5 | 50 ++++++-------
evd-2.3-0/evd/NAMESPACE | 10 +-
evd-2.3-0/evd/R/bvfit.R | 5 -
evd-2.3-0/evd/R/bvpot.R | 44 ++++++-----
evd-2.3-0/evd/R/mdiag.R | 2
evd-2.3-0/evd/R/pmdiag.R | 87 ++++++++++++++++++++++-
evd-2.3-0/evd/inst/CHANGES | 12 +++
evd-2.3-0/evd/inst/README | 12 +--
evd-2.3-0/evd/inst/doc/Multivariate_Extremes.Rnw |only
evd-2.3-0/evd/inst/doc/Multivariate_Extremes.pdf |only
evd-2.3-0/evd/man/abvnonpar.Rd | 13 ++-
evd-2.3-0/evd/man/bvtcplot.Rd |only
evd-2.3-0/evd/man/clusters.Rd | 1
evd-2.3-0/evd/man/confint.evd.Rd | 1
evd-2.3-0/evd/man/evind.test.Rd |only
evd-2.3-0/evd/man/evmc.Rd | 2
evd-2.3-0/evd/man/exi.Rd | 1
evd-2.3-0/evd/man/fbvpot.Rd | 34 +++++++-
evd-2.3-0/evd/man/hbvevd.Rd | 4 -
evd-2.3-0/evd/man/marma.Rd | 9 +-
evd-2.3-0/evd/man/mrlplot.Rd | 1
evd-2.3-0/evd/man/plot.bvpot.Rd | 2
evd-2.3-0/evd/man/tcplot.Rd | 1
evd-2.3-0/evd/src/bvpot.c | 58 +++++++--------
evd-2.3-0/evd/src/header.h | 12 +--
evd-2.3-0/evd/vignettes |only
29 files changed, 248 insertions(+), 121 deletions(-)
Title: Event History Analysis
Diff between eha versions 2.0-7 dated 2012-01-05 and 2.1-2 dated 2012-08-30
Description: Event history analysis: Sampling of risk sets in Cox
regression, selections in the Lexis diagram, bootstrapping.
Parametric proportional hazards fitting with left truncation
and right censoring for common families of distributions,
piecewise constant hazards, and discrete models. AFT regression
for left truncated and right censored data. Binary and Poisson
regression for clustered data, fixed and random effects with
bootstrapping.
Author: Göran Broström
Maintainer: Göran Broström
ChangeLog | 18 +++++++++++
DESCRIPTION | 24 +++++++-------
MD5 | 45 ++++++++++++++-------------
R/aftreg.R | 19 +++++++++--
R/glmmML.R | 32 +++++++++++--------
R/glmmML.fit.R | 78 +++++++++++++++++++++++++-----------------------
R/ltx.R | 20 +++++++++++-
R/poisgam.R |only
R/print.aftreg.R | 8 +++-
data/fert.rda |binary
data/infants.rda |binary
data/logrye.rda |binary
data/male.mortality.rda |binary
data/mort.rda |binary
data/oldmort.rda |binary
data/scania.rda |binary
data/swe07.rda |binary
inst/doc/glmmML.pdf |binary
inst/doc/parametric.pdf |binary
man/aftreg.Rd | 16 +++++++--
man/glmmML.Rd | 6 ++-
man/glmmboot.Rd | 2 -
man/glmmbootFit.Rd | 2 -
src/aftregGomp.c | 8 +++-
24 files changed, 176 insertions(+), 102 deletions(-)
Title: Infer a time-varying DBN network from time series data.
Diff between ARTIVA versions 1.1 dated 2012-07-02 and 1.2 dated 2012-08-30
Description: This package generates Reversible Jump MCMC (RJ-MCMC)
sampling for approximating the posterior distribution of a time
varying regulatory network, under the Auto Regressive TIme
VArying (ARTIVA) model (for a detailed description of the
algorithm, see Lebre et al. BMC Systems Biology, 2010).
Starting from time-course gene expression measurements for a
gene of interest (referred to as "target gene") and a set of
genes (referred to as "parent genes") which may explain the
expression of the target gene, the ARTIVA procedure identifies
temporal segments for which a set of interactions occur between
the "parent genes" and the "target gene". The time points that
delimit the different temporal segments are referred to as
changepoints (CP).
Author: S. Lebre and G. Lelandais.
Maintainer: S. Lebre
DESCRIPTION | 10 +--
MD5 | 33 +++++-----
R/ARTIVAnet.R | 4 -
R/ARTIVAsubnet.R | 5 -
R/ARTIVAsubnetAnalysis.R | 2
R/PlotFunction.R | 2
R/geneNetworkSummary.R | 53 ++++++++++-------
R/plotSegmentModel.postDist.R | 2
R/traceGeneProfiles.R | 4 -
R/traceNetworks.R | 128 ++++++++++++++++++++++++++++++++++++------
man/ARTIVA-internal.Rd | 1
man/ARTIVAnet.Rd | 2
man/ARTIVAsubnet.Rd | 2
man/ARTIVAsubnetAnalysis.Rd | 2
man/geneNetworkSummary.Rd |only
man/traceGeneProfiles.Rd | 6 -
man/traceNetworks.Rd | 18 ++---
man/yeast.Rd | 2
18 files changed, 190 insertions(+), 86 deletions(-)
Title: Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
Diff between SNPRelate versions 0.9.6 dated 2012-07-22 and 0.9.7 dated 2012-08-30
Description: A High-performance computing toolset for relatedness and
principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
SNPRelate-0.9.6/SNPRelate/inst/doc/A_Tutorial_for_the_R_Package_SNPRelate.pdf |only
SNPRelate-0.9.6/SNPRelate/man/snpgdsPosition.Rd |only
SNPRelate-0.9.7/SNPRelate/DESCRIPTION | 14
SNPRelate-0.9.7/SNPRelate/MD5 | 52 +-
SNPRelate-0.9.7/SNPRelate/NEWS |only
SNPRelate-0.9.7/SNPRelate/R/main.r | 198 +++++-----
SNPRelate-0.9.7/SNPRelate/inst/doc/SNPRelateTutorial.Rnw |only
SNPRelate-0.9.7/SNPRelate/inst/doc/SNPRelateTutorial.pdf |only
SNPRelate-0.9.7/SNPRelate/inst/unitTests |only
SNPRelate-0.9.7/SNPRelate/man/SNPRelate-package.Rd | 14
SNPRelate-0.9.7/SNPRelate/man/snpgdsCombineGeno.Rd | 9
SNPRelate-0.9.7/SNPRelate/man/snpgdsGDS2BED.Rd | 2
SNPRelate-0.9.7/SNPRelate/man/snpgdsIBDMoM.Rd | 1
SNPRelate-0.9.7/SNPRelate/man/snpgdsLDMat.Rd | 41 +-
SNPRelate-0.9.7/SNPRelate/man/snpgdsLDpair.Rd | 20 -
SNPRelate-0.9.7/SNPRelate/man/snpgdsLDpruning.Rd | 7
SNPRelate-0.9.7/SNPRelate/man/snpgdsSummary.Rd | 2
SNPRelate-0.9.7/SNPRelate/man/snpgdsVCF2GDS.Rd | 3
SNPRelate-0.9.7/SNPRelate/src/CoreDEF.h | 35 +
SNPRelate-0.9.7/SNPRelate/src/Makevars | 2
SNPRelate-0.9.7/SNPRelate/src/Makevars.win | 2
SNPRelate-0.9.7/SNPRelate/src/dType.h | 21 -
SNPRelate-0.9.7/SNPRelate/src/dVect.cpp | 20 -
SNPRelate-0.9.7/SNPRelate/src/genLD.cpp | 48 +-
SNPRelate-0.9.7/SNPRelate/src/main.cpp | 18
SNPRelate-0.9.7/SNPRelate/tests |only
SNPRelate-0.9.7/SNPRelate/vignettes |only
27 files changed, 315 insertions(+), 194 deletions(-)
Title: Multivariate Autoregressive State-Space Modeling
Diff between MARSS versions 3.1 dated 2012-07-13 and 3.2 dated 2012-08-30
Description: The MARSS package provides maximum-likelihood parameter
estimation for constrained and unconstrained linear
multivariate autoregressive state-space (MARSS) models fit to
multivariate time-series data. Fitting is primarily via an
Expectation-Maximization (EM) algorithm, although fitting via
the BFGS algorithm (using the optim function) is also provided.
MARSS models are a class of dynamic linear model (DLM) and
vector autoregressive model (VAR) model. Functions are
provided for parametric and innovations bootstrapping, Kalman
filtering and smoothing, bootstrap model selection criteria
(AICb), confidences intervals via the Hessian approximation and
via bootstrapping and calculation of auxiliary residuals for
detecting outliers and shocks. The user guide shows examples
of using MARSS for parameter estimation for a variety of
applications, model selection, dynamic factor analysis, outlier
and shock detection, and addition of covariates. Type
RShowDoc("UserGuide", package="MARSS") at the R command line to
open the MARSS user guide. Online workshops (lecture material)
at http://faculty.washington.edu/eeholmes/workshops.shtml
Author: Eli Holmes, Eric Ward, and Kellie Wills, NOAA, Seattle, USA
Maintainer: Eli Holmes
MARSS-3.1/MARSS/inst/doc/.Rinstignore |only
MARSS-3.1/MARSS/man/MARSS.dfa.Rd |only
MARSS-3.1/MARSS/man/allowed.rd |only
MARSS-3.2/MARSS/.Rinstignore |only
MARSS-3.2/MARSS/DESCRIPTION | 12 -
MARSS-3.2/MARSS/MD5 | 42 ++---
MARSS-3.2/MARSS/NEWS | 88 +----------
MARSS-3.2/MARSS/R/MARSSinits.R | 2
MARSS-3.2/MARSS/R/MARSSkemcheck.r | 2
MARSS-3.2/MARSS/R/MARSSmcinit.R | 2
MARSS-3.2/MARSS/data/isleRoyal.rda |binary
MARSS-3.2/MARSS/inst/doc/Case_study_2.R | 23 +-
MARSS-3.2/MARSS/inst/doc/Case_study_3.R | 5
MARSS-3.2/MARSS/inst/doc/Case_study_4.R | 214 +++++++++++++++++----------
MARSS-3.2/MARSS/inst/doc/Case_study_7.R | 89 +++++++----
MARSS-3.2/MARSS/inst/doc/Case_study_8.R | 94 ++++++-----
MARSS-3.2/MARSS/inst/doc/Covariates.R |only
MARSS-3.2/MARSS/inst/doc/EMDerivation.pdf |binary
MARSS-3.2/MARSS/inst/doc/Manual.bib | 9 +
MARSS-3.2/MARSS/inst/doc/Manual.pdf |binary
MARSS-3.2/MARSS/inst/doc/Quick_Start.pdf |binary
MARSS-3.2/MARSS/inst/doc/README_vers_3.0.pdf |binary
MARSS-3.2/MARSS/inst/doc/UserGuide.pdf |binary
MARSS-3.2/MARSS/man/MARSS.dfa.rd |only
MARSS-3.2/MARSS/man/allowed.Rd |only
MARSS-3.2/MARSS/man/graywhales.Rd | 6
MARSS-3.2/MARSS/man/isleRoyal.rd |only
27 files changed, 310 insertions(+), 278 deletions(-)