Title: Robust Estimation for Compositional Data.
Diff between robCompositions versions 1.5.0 dated 2011-05-06 and 1.6.0 dated 2012-05-15
More information about robCompositions at CRAN
Description: The package includes methods for imputation of
compositional data including robust methods, methods to impute
rounded zeros, (robust) outlier detection for compositional
data, (robust) principal component analysis for compositional
data, (robust) factor analysis for compositional data, (robust)
discriminant analysis for compositional data (Fisher rule),
robust regression with compositional predictors and (robust)
Anderson-Darling normality tests for compositional data as well
as popular log-ratio transformations (alr, clr, ilr, and their
inverse transformations). In addition, visualisation and
diagnostic tools are implemented as well as high and low-level
plot functions for the ternary diagram.
Author: Matthias Templ, Karel Hron, Peter Filzmoser
Maintainer: Matthias Templ
robCompositions-1.5.0/robCompositions/R/drawMahal.R |only
robCompositions-1.5.0/robCompositions/inst/doc/.project |only
robCompositions-1.5.0/robCompositions/inst/doc/CoDaWork.sty |only
robCompositions-1.5.0/robCompositions/inst/doc/boxplot.pdf |only
robCompositions-1.5.0/robCompositions/inst/doc/ilr.pdf |only
robCompositions-1.5.0/robCompositions/inst/doc/logo.pdf |only
robCompositions-1.5.0/robCompositions/inst/doc/pca1.pdf |only
robCompositions-1.5.0/robCompositions/inst/doc/pcaOrig.pdf |only
robCompositions-1.5.0/robCompositions/inst/doc/plot-acomp.pdf |only
robCompositions-1.5.0/robCompositions/inst/doc/ref.bib |only
robCompositions-1.5.0/robCompositions/inst/doc/refPCS.bib |only
robCompositions-1.5.0/robCompositions/inst/doc/refPCSn.bib |only
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robCompositions-1.6.0/robCompositions/DESCRIPTION | 27
robCompositions-1.6.0/robCompositions/MD5 |only
robCompositions-1.6.0/robCompositions/NAMESPACE | 6
robCompositions-1.6.0/robCompositions/R/adtest.R | 12
robCompositions-1.6.0/robCompositions/R/daFisher.R | 2
robCompositions-1.6.0/robCompositions/R/ilrregression.R |only
robCompositions-1.6.0/robCompositions/R/impCoda.R | 4
robCompositions-1.6.0/robCompositions/R/impCoda2.R |only
robCompositions-1.6.0/robCompositions/R/impRZilr.R | 1
robCompositions-1.6.0/robCompositions/R/lmCoDaX.R |only
robCompositions-1.6.0/robCompositions/R/pcaCoDa.R | 13
robCompositions-1.6.0/robCompositions/R/plot.pcaCoDa.R | 1
robCompositions-1.6.0/robCompositions/R/robGUI.R | 1288 ++++++++--
robCompositions-1.6.0/robCompositions/R/robVariation.R | 3
robCompositions-1.6.0/robCompositions/R/robilrregression.R |only
robCompositions-1.6.0/robCompositions/R/summary.imp.R | 4
robCompositions-1.6.0/robCompositions/R/ternaryDiag.R | 165 +
robCompositions-1.6.0/robCompositions/R/ternaryDiagAbline.R |only
robCompositions-1.6.0/robCompositions/R/ternaryDiagEllipse.R |only
robCompositions-1.6.0/robCompositions/R/ternaryDiagLines.R |only
robCompositions-1.6.0/robCompositions/R/ternaryDiagPoints.R |only
robCompositions-1.6.0/robCompositions/R/utils.R |only
robCompositions-1.6.0/robCompositions/R/zzz.R | 10
robCompositions-1.6.0/robCompositions/data/expenditures.rda |binary
robCompositions-1.6.0/robCompositions/inst/CITATION | 31
robCompositions-1.6.0/robCompositions/inst/doc/imputation.pdf |binary
robCompositions-1.6.0/robCompositions/inst/doc/robCompostions-overview.pdf |binary
robCompositions-1.6.0/robCompositions/man/expenditures.Rd | 2
robCompositions-1.6.0/robCompositions/man/lmCoDaX.Rd |only
robCompositions-1.6.0/robCompositions/man/ternaryDiag.Rd | 22
robCompositions-1.6.0/robCompositions/man/ternaryDiagAbline.Rd |only
robCompositions-1.6.0/robCompositions/man/ternaryDiagEllipse.Rd |only
robCompositions-1.6.0/robCompositions/man/ternaryDiagPoints.Rd |only
robCompositions-1.6.0/robCompositions/tests/rz.R | 9
robCompositions-1.6.0/robCompositions/vignettes |only
48 files changed, 1328 insertions(+), 272 deletions(-)
Permanent link
Title: Mixed Effects Cox Models.
Diff between coxme versions 2.2-2 dated 2012-04-27 and 2.2-3 dated 2012-05-15
Description: Cox proportional hazards models containing Gaussian random
effects, also known as frailty models.
Author: Terry Therneau
Maintainer: Terry Therneau
DESCRIPTION | 14 +--
MD5 | 48 +++++++------
NAMESPACE | 1
R/anova.coxme.R |only
R/bdsmatrix.R |only
R/coxmeMlist.R | 2
R/lmekin.R | 150 +---------------------------------------
inst/NEWS.Rd | 20 +++++
inst/doc/coxme.Rnw | 1
inst/doc/coxme.pdf |binary
inst/doc/laplace.pdf |binary
inst/doc/lmekin.Rnw | 65 ++++++++++++-----
inst/doc/lmekin.pdf |binary
inst/doc/variance.Rnw | 2
inst/doc/variance.pdf |binary
man/anova.coxme.Rd |only
man/coxmeMlist.Rd | 2
noweb/Makefile | 17 ++++
noweb/all.nw | 177 +++++++++++++++++++++++++++++++++++-------------
noweb/bdsmatrix.Rnw | 131 ++++++++++++++++++++++++++---------
noweb/lmekin.Rnw | 41 +++++++----
noweb/varfun2.Rnw | 5 +
src/bds_dsc.c |only
tests/lmekin2.R |only
tests/lmekin2.Rout.save |only
vignettes/coxme.Rnw | 1
vignettes/lmekin.Rnw | 65 ++++++++++++-----
vignettes/variance.Rnw | 2
28 files changed, 436 insertions(+), 308 deletions(-)
Title: Tests/Searches for significant clusters in genetic data.
Diff between bayesclust versions 3.0 dated 2010-03-13 and 3.1 dated 2012-05-15
Description: Bayes Clustering Package
Author: Gopal, V. and Fuentes, C. and Casella, G.
Maintainer: Gopal, V.
DESCRIPTION | 8 ++++----
MD5 |only
inst |only
man/bayesclust-package.Rd | 4 ++++
4 files changed, 8 insertions(+), 4 deletions(-)
Title: TIMe Series Analysis and Control package
Diff between timsac versions 1.2.6 dated 2012-03-05 and 1.2.7 dated 2012-05-15
Description: Functions for statistical analysis, prediction and control
of time series.
Author: The Institute of Statistical Mathematics
Maintainer: The Institute of Statistical Mathematics
DESCRIPTION | 6
MD5 | 118 ++---
data/Airpolution.rda |binary
data/Amerikamaru.rda |binary
data/Blsallfood.rda |binary
data/Canadianlynx.rda |binary
data/LaborData.rda |binary
data/MYE1F.rda |binary
data/Powerplant.rda |binary
data/bispecData.rda |binary
data/locarData.rda |binary
data/nonstData.rda |binary
inst/doc/changes.txt | 8
inst/doc/timsac-manual.pdf |binary
src/armaf.f | 1
src/auspecf.f | 1
src/autarmf.f | 1
src/autcorf.f | 1
src/bayseaf.f | 5
src/bispecf.f | 1
src/blocarf.f | 1
src/blomarf.f | 1
src/bsubstf.f | 933 +++++----------------------------------------
src/canarmf.f | 3
src/canocaf.f | 1
src/comsub.f | 15
src/covgenf.f | 1
src/exsarf.f | 3
src/fftcorf.f | 1
src/fpeautf.f | 1
src/fpecf.f | 1
src/markovf.f | 1
src/mlocarf.f | 1
src/mlomarf.f | 3
src/mulbarf.f | 1
src/mulcorf.f | 1
src/mulfref.f | 1
src/mulmar.c | 15
src/mulmarf.f | 1
src/mulnosf.f | 1
src/mulrspf.f | 1
src/mulspef.f | 1
src/ngsmthf.f | 1
src/nonstf.f | 1
src/optdesf.f | 1
src/optsimf.f | 1
src/perarsf.f | 3
src/prdctrf.f | 1
src/raspecf.f | 1
src/sglfref.f | 1
src/simconf.f | 1
src/smoothf.f | 1
src/thirmof.f | 1
src/tvarf.f | 2
src/tvspcf.f | 1
src/tvvarf.f | 1
src/unibarf.f | 1
src/unimarf.f | 1
src/wnoisef.f | 1
src/xsarmaf.f | 1
60 files changed, 203 insertions(+), 948 deletions(-)
Title: Graphic Extensions for Categorical Data
Diff between extracat versions 1.4-0 dated 2011-08-30 and 1.5-0 dated 2012-05-15
Description: graphic extensions for categorical data
Author: Alexander Pilhoefer
Maintainer: Alexander Pilhoefer
extracat-1.4-0/extracat/R/irmb2.R |only
extracat-1.4-0/extracat/R/optile_skeleton.R |only
extracat-1.4-0/extracat/man/bloma.Rd |only
extracat-1.4-0/extracat/man/irmb.Rd |only
extracat-1.5-0/extracat/DESCRIPTION | 13
extracat-1.5-0/extracat/MD5 | 79
extracat-1.5-0/extracat/NAMESPACE | 13
extracat-1.5-0/extracat/R/arsim.R |only
extracat-1.5-0/extracat/R/boxplot2g.R |only
extracat-1.5-0/extracat/R/caclust.R |only
extracat-1.5-0/extracat/R/cpcp2.R | 2
extracat-1.5-0/extracat/R/dcov.R |only
extracat-1.5-0/extracat/R/fastRcrit.R |only
extracat-1.5-0/extracat/R/fechner.R |only
extracat-1.5-0/extracat/R/fluctuations.R | 427 +-
extracat-1.5-0/extracat/R/getsets.R | 74
extracat-1.5-0/extracat/R/hexpie.R |only
extracat-1.5-0/extracat/R/kendalls.R |only
extracat-1.5-0/extracat/R/newrmb5.R | 417 +-
extracat-1.5-0/extracat/R/optile_skeleton.r |only
extracat-1.5-0/extracat/R/rmbmat.R |only
extracat-1.5-0/extracat/data/.Rhistory |only
extracat-1.5-0/extracat/data/CPScluster.rda |binary
extracat-1.5-0/extracat/data/carcustomers.rda |binary
extracat-1.5-0/extracat/data/dmc.rda |binary
extracat-1.5-0/extracat/data/olives.rda |only
extracat-1.5-0/extracat/data/plants.rda |only
extracat-1.5-0/extracat/depr |only
extracat-1.5-0/extracat/man/arsim.Rd |only
extracat-1.5-0/extracat/man/boxplot2g.Rd |only
extracat-1.5-0/extracat/man/carcustomers.Rd | 156
extracat-1.5-0/extracat/man/cfluctile.Rd | 34
extracat-1.5-0/extracat/man/cpcp.Rd | 12
extracat-1.5-0/extracat/man/dcor.Rd |only
extracat-1.5-0/extracat/man/dmc.Rd | 5
extracat-1.5-0/extracat/man/extracat.Rd | 99
extracat-1.5-0/extracat/man/fluctile.Rd | 57
extracat-1.5-0/extracat/man/fluctile3d.Rd |only
extracat-1.5-0/extracat/man/hexpie.Rd |only
extracat-1.5-0/extracat/man/ihcrit.Rd |only
extracat-1.5-0/extracat/man/innerval.Rd |only
extracat-1.5-0/extracat/man/kendalls.Rd |only
extracat-1.5-0/extracat/man/listen.Rd | 103
extracat-1.5-0/extracat/man/olives.Rd |only
extracat-1.5-0/extracat/man/optile.Rd | 66
extracat-1.5-0/extracat/man/plants.Rd |only
extracat-1.5-0/extracat/man/quickfechner.Rd |only
extracat-1.5-0/extracat/man/regmax.Rd |only
extracat-1.5-0/extracat/man/resort.Rd | 120
extracat-1.5-0/extracat/man/rmb.Rd | 61
extracat-1.5-0/extracat/man/rmbmat.Rd |only
extracat-1.5-0/extracat/man/spread.Rd | 8
extracat-1.5-0/extracat/man/subtable.Rd | 7
extracat-1.5-0/extracat/man/subtree.Rd |only
extracat-1.5-0/extracat/man/tfluctile.Rd |only
extracat-1.5-0/extracat/man/untableSet.Rd | 15
extracat-1.5-0/extracat/src/optile.c | 4604 +++++++++++++++++---------
57 files changed, 4276 insertions(+), 2096 deletions(-)
Title: Spatially explicit capture-recapture
Diff between secr versions 2.3.1 dated 2011-12-20 and 2.3.2 dated 2012-05-15
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive
detectors, such as traps, or by searching polygons or
transects. Models incorporating distance-dependent detection
are fitted by maximizing the likelihood. Tools are included for
data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford
secr-2.3.1/secr/R/phi.designdata.R |only
secr-2.3.2/secr/DESCRIPTION | 17
secr-2.3.2/secr/MD5 | 153 ++--
secr-2.3.2/secr/NAMESPACE | 4
secr-2.3.2/secr/NEWS | 91 ++
secr-2.3.2/secr/R/D.designdata.R | 2
secr-2.3.2/secr/R/autoini.R | 13
secr-2.3.2/secr/R/empirical.R | 23
secr-2.3.2/secr/R/esa.R | 5
secr-2.3.2/secr/R/functions.R | 84 --
secr-2.3.2/secr/R/fxi.R | 9
secr-2.3.2/secr/R/join.R | 34
secr-2.3.2/secr/R/make.capthist.R | 86 +-
secr-2.3.2/secr/R/make.mask.R | 26
secr-2.3.2/secr/R/methods.R | 287 +++++--
secr-2.3.2/secr/R/model.average.R | 16
secr-2.3.2/secr/R/pdot.R | 2
secr-2.3.2/secr/R/plot.secr.R | 26
secr-2.3.2/secr/R/randomHabitat.r |only
secr-2.3.2/secr/R/read.traps.R | 5
secr-2.3.2/secr/R/reduce.capthist.R | 26
secr-2.3.2/secr/R/regionN.R | 23
secr-2.3.2/secr/R/secr.design.MS.R | 81 +-
secr-2.3.2/secr/R/secr.fit.R | 146 +--
secr-2.3.2/secr/R/sim.capthist.R | 52 -
secr-2.3.2/secr/R/sim.popn.R | 22
secr-2.3.2/secr/R/sim.secr.R | 17
secr-2.3.2/secr/R/trap.builder.R | 21
secr-2.3.2/secr/R/utility.R | 52 +
secr-2.3.2/secr/R/verify.R | 10
secr-2.3.2/secr/data/deermouse.RData |binary
secr-2.3.2/secr/data/hornedlizard.RData |binary
secr-2.3.2/secr/data/housemouse.RData |binary
secr-2.3.2/secr/data/ovenbird.RData |binary
secr-2.3.2/secr/data/ovensong.RData |binary
secr-2.3.2/secr/data/possum.RData |binary
secr-2.3.2/secr/data/secrdemo.RData |binary
secr-2.3.2/secr/data/skink.RData |binary
secr-2.3.2/secr/data/stoatDNA.RData |binary
secr-2.3.2/secr/inst/doc/secr-datainput.pdf |binary
secr-2.3.2/secr/inst/doc/secr-densitysurfaces.pdf |binary
secr-2.3.2/secr/inst/doc/secr-finitemixtures.pdf |binary
secr-2.3.2/secr/inst/doc/secr-manual.pdf |binary
secr-2.3.2/secr/inst/doc/secr-overview.pdf |binary
secr-2.3.2/secr/inst/doc/secr-polygondetectors.pdf |binary
secr-2.3.2/secr/inst/doc/secr-sound.pdf |binary
secr-2.3.2/secr/man/RMarkInput.Rd | 19
secr-2.3.2/secr/man/capthistfn.Rd | 7
secr-2.3.2/secr/man/derivedMS.Rd | 3
secr-2.3.2/secr/man/empirical.Rd | 26
secr-2.3.2/secr/man/expected.n.Rd | 4
secr-2.3.2/secr/man/hornedlizard.Rd | 2
secr-2.3.2/secr/man/make.capthist.Rd | 8
secr-2.3.2/secr/man/make.mask.Rd | 10
secr-2.3.2/secr/man/make.traps.Rd | 6
secr-2.3.2/secr/man/make.tri.Rd | 2
secr-2.3.2/secr/man/model.average.Rd | 3
secr-2.3.2/secr/man/ovenbird.Rd | 2
secr-2.3.2/secr/man/plot.traps.Rd | 21
secr-2.3.2/secr/man/pointsInPolygon.Rd | 16
secr-2.3.2/secr/man/possum.Rd | 29
secr-2.3.2/secr/man/print.secr.Rd | 4
secr-2.3.2/secr/man/randomHabitat.Rd |only
secr-2.3.2/secr/man/rbind.traps.Rd | 2
secr-2.3.2/secr/man/region.N.Rd | 39 -
secr-2.3.2/secr/man/secr-package.Rd | 7
secr-2.3.2/secr/man/secr.fit.Rd | 31
secr-2.3.2/secr/man/sim.popn.Rd | 18
secr-2.3.2/secr/man/subset.capthist.Rd | 13
secr-2.3.2/secr/man/suggest.buffer.Rd | 2
secr-2.3.2/secr/man/transformations.Rd | 6
secr-2.3.2/secr/man/trap.builder.Rd | 5
secr-2.3.2/secr/man/troubleshooting.Rd | 4
secr-2.3.2/secr/src/detectfn.c | 76 +-
secr-2.3.2/secr/src/secr.c | 779 ++++++++++-----------
secr-2.3.2/secr/src/secr.h | 75 --
secr-2.3.2/secr/src/simsecr.c | 90 +-
secr-2.3.2/secr/src/trapping.c | 93 +-
secr-2.3.2/secr/src/utils.c | 41 -
79 files changed, 1726 insertions(+), 1050 deletions(-)
Title: Redis client for R
Diff between rredis versions 1.6.3 dated 2011-10-23 and 1.6.6 dated 2012-05-15
Description: An R client for the Redis persistent key-value database
available from http://redis.io.
Author: B. W. Lewis
Maintainer: B. W. Lewis
DESCRIPTION | 13 ++++++-------
MD5 | 12 +++++++-----
NEWS | 7 +++++++
R/hashCMD.R | 29 ++++++++++++++++++++---------
R/redis-internal.R | 23 +++++++++++++++++++----
inst/doc/rredis.pdf |binary
man/redisCmd.Rd |only
man/redisHMGet.Rd |only
8 files changed, 59 insertions(+), 25 deletions(-)
Title: R Interface to FishBASE
Diff between rfishbase versions 0.0-8 dated 2012-04-03 and 0.0-9 dated 2012-05-15
Description: A programmatic interface to fishbase.org.
Author: Carl Boettiger [aut, cre], Duncan Temple Lang [aut], Peter C.
Wainwright [aut]
Maintainer: Carl Boettiger,
rfishbase-0.0-8/rfishbase/demo |only
rfishbase-0.0-8/rfishbase/man/tree.Rd |only
rfishbase-0.0-9/rfishbase/DESCRIPTION | 16 ++-
rfishbase-0.0-9/rfishbase/MD5 | 81 ++++++++++++----
rfishbase-0.0-9/rfishbase/NAMESPACE | 5 -
rfishbase-0.0-9/rfishbase/NEWS | 18 ++-
rfishbase-0.0-9/rfishbase/R/analysis.R | 115 +++++++++++++++---------
rfishbase-0.0-9/rfishbase/R/cacheFB.R | 30 ++++--
rfishbase-0.0-9/rfishbase/R/fishbase.R | 8 -
rfishbase-0.0-9/rfishbase/README.md | 46 +++++++--
rfishbase-0.0-9/rfishbase/data/datalist | 2
rfishbase-0.0-9/rfishbase/data/labridtree.rda |binary
rfishbase-0.0-9/rfishbase/inst |only
rfishbase-0.0-9/rfishbase/man/familySearch.Rd | 15 ---
rfishbase-0.0-9/rfishbase/man/findSpecies.Rd | 12 +-
rfishbase-0.0-9/rfishbase/man/fish.data.Rd | 4
rfishbase-0.0-9/rfishbase/man/fish_names.Rd | 18 ++-
rfishbase-0.0-9/rfishbase/man/getDepth.Rd | 9 +
rfishbase-0.0-9/rfishbase/man/getQuantTraits.Rd | 11 +-
rfishbase-0.0-9/rfishbase/man/getRefs.Rd |only
rfishbase-0.0-9/rfishbase/man/getSize.Rd | 10 +-
rfishbase-0.0-9/rfishbase/man/habitatSearch.Rd | 10 --
rfishbase-0.0-9/rfishbase/man/labridtree.Rd |only
rfishbase-0.0-9/rfishbase/man/loadCache.Rd | 9 -
rfishbase-0.0-9/rfishbase/man/updateCache.Rd | 12 +-
rfishbase-0.0-9/rfishbase/man/which_fish.Rd | 15 ++-
26 files changed, 287 insertions(+), 159 deletions(-)
Title: Rcpp bindings for Sequential Monte Carlo
Diff between RcppSMC versions 0.1.0 dated 2012-03-22 and 0.1.1 dated 2012-05-15
Description: This package provides R with access to the Sequential
Monte Carlo Template Classes by Johansen (Journal of
Statistical Software, 2009, v30, i6).
At present, two additional examples have been added, and the first
example from the JSS paper has been extended. Further
integration and extensions are planned.
Author: Dirk Eddelbuettel and Adam M. Johansen
Maintainer: Dirk Eddelbuettel
ChangeLog | 10 +++++++++-
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
inst/include/sampler.h | 2 +-
4 files changed, 17 insertions(+), 9 deletions(-)
Title: Statistical inference for partially observed Markov processes
Diff between pomp versions 0.42-1 dated 2012-05-03 and 0.42-4 dated 2012-05-15
Description: Inference methods for partially-observed Markov processes
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner,
Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael
Lavine, Daniel C. Reuman
Maintainer: Aaron A. King
DESCRIPTION | 10 -
MD5 | 56 +++----
R/builder.R | 8 -
R/dmeasure-pomp.R | 16 --
R/dprocess-pomp.R | 12 -
R/pomp-methods.R | 4
R/rmeasure-pomp.R | 17 +-
R/rprocess-pomp.R | 13 -
R/skeleton-pomp.R | 19 --
R/trajectory-pomp.R | 24 +--
data/bbs.rda |binary
data/blowflies.rda |binary
data/dacca.rda |binary
data/euler.sir.rda |binary
data/gillespie.sir.rda |binary
data/gompertz.rda |binary
data/ou2.rda |binary
data/ricker.rda |binary
data/rw2.rda |binary
data/verhulst.rda |binary
demo/sir.R | 267 ++++++++++++++++++++---------------
inst/ChangeLog | 44 +++++
inst/NEWS | 8 +
inst/doc/advanced_topics_in_pomp.pdf |binary
inst/doc/intro_to_pomp.pdf |binary
src/R_init_pomp.c | 2
src/trajectory.c | 67 ++++++--
tests/sir.R | 44 +++++
tests/sir.Rout.save | 58 ++++++-
29 files changed, 436 insertions(+), 233 deletions(-)
Title: Multilayer optics
Diff between planar versions 1.2 dated 2012-03-05 and 1.2.1 dated 2012-05-15
Description: Solves the electromagnetic problem of reflection and
transmission at a multilayer planar interface. Also computes
the decay rates for a dipolar emitter near a multilayer
structure.
Author: baptiste Auguie
Maintainer: baptiste Auguie
DESCRIPTION | 6 ++---
MD5 | 8 +++----
NEWS | 4 +++
R/planar-package.r | 6 +++--
demo/fluorescence_pattern.r | 48 +++++++++++++++++++++-----------------------
5 files changed, 38 insertions(+), 34 deletions(-)
Title: Tools to manage a parametric function that describes phenology
Diff between phenology versions 3.29 dated 2012-04-11 and 3.31 dated 2012-05-15
Description: Functions to fit and test the phenology of species based
on counts.
Author: Marc Girondot
Maintainer: Marc Girondot
DESCRIPTION | 19 ++---
MD5 | 72 +++++++++++--------
NAMESPACE | 7 +
NEWS | 14 +++
R/Likelihood_phenology.R | 18 ++--
R/Lnegbin.R | 31 ++++----
R/add_format.R | 72 ++++++++++++++++---
R/daily_count.R | 16 +++-
R/extract_result.R | 2
R/fit_phenology.R | 161 ++++++++++++++++++++++++++++++++++++++-----
R/format_par.R | 2
R/growlnotify.R | 2
R/map_phenology.R | 28 +++++--
R/par_init.R | 4 -
R/phenology.R | 11 +-
R/plot.phenology.R |only
R/plot.phenologymap.R |only
R/plot_phenology.R | 24 +++---
R/print.phenology.R |only
R/print.phenologymap.R |only
R/read_folder.R |only
R/shift_sinusoid.R | 2
R/summary.phenology.R |only
R/summary.phenologymap.R |only
data/map_Gratiot.rda |binary
data/result_Gratiot.rda |binary
data/result_Gratiot1.rda |binary
data/result_Gratiot2.rda |binary
data/result_Gratiot_Flat.rda |binary
man/add_format.Rd | 31 +++++---
man/extract_result.Rd | 2
man/fit_phenology.Rd | 16 ++--
man/growlnotify.Rd | 2
man/likelihood_phenology.Rd | 2
man/par_init.Rd | 2
man/plot.phenology.Rd |only
man/plot.phenologymap.Rd |only
man/plot_phenology.Rd | 11 +-
man/print.phenology.Rd |only
man/print.phenologymap.Rd |only
man/read_folder.Rd |only
man/shift_sinusoid.Rd | 2
man/summary.phenology.Rd |only
man/summary.phenologymap.Rd |only
44 files changed, 403 insertions(+), 150 deletions(-)
Title: Draw Geographical Maps
Diff between maps versions 2.2-5 dated 2012-01-15 and 2.2-6 dated 2012-05-15
Description: Display of maps. Projection code and larger maps are in
separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks. R
version by Ray Brownrigg
Maintainer: Ray Brownrigg
DESCRIPTION | 8
MD5 | 12
data/world.cities.rda |binary
man/map.cities.Rd | 11
src/county.gon | 2
src/county.gonstats | 2
src/county.name | 1379 ++++++++++++++++++++++++--------------------------
7 files changed, 705 insertions(+), 709 deletions(-)
Title: Functional Data Analysis
Diff between fda versions 2.2.7 dated 2011-08-30 and 2.2.8 dated 2012-05-15
Description: These functions were developed to support functional data
analysis as described in Ramsay, J. O. and Silverman, B. W.
(2005) Functional Data Analysis. New York: Springer. They were
ported from earlier versions in Matlab and S-PLUS. An
introduction appears in Ramsay, J. O., Hooker, Giles, and
Graves, Spencer (2009) Functional Data Analysis with R and
Matlab (Springer). The package includes data sets and script
files working many examples including all but one of the 76
figures in this latter book. The principal changes to version
2.2.8 are: 1. The use of sparse matrix representation for
spline basis functions and in function smooth.basis. 2. The
correction of a bug in function pca.fd. Analyses using the
earlier version should be redone.
Author: J. O. Ramsay
Maintainer: J. O. Ramsay
fda-2.2.7/fda/inst/scripts/CSTR/CSTR_demoMatlab-R.ppt |only
fda-2.2.7/fda/inst/scripts/CSTR/CSTRsmth.mat |only
fda-2.2.7/fda/inst/scripts/CSTR/Dres.csv |only
fda-2.2.7/fda/inst/scripts/CSTR/fda-in-matlab-and-r.ppt |only
fda-2.2.7/fda/man/expect.phi.Rd |only
fda-2.2.8/fda/DESCRIPTION | 34
fda-2.2.8/fda/MD5 | 324 +-
fda-2.2.8/fda/NAMESPACE | 5
fda-2.2.8/fda/R/AmpPhaseDecomp.R | 13
fda-2.2.8/fda/R/CSTRfn.R | 670 ++--
fda-2.2.8/fda/R/Data2fd.R | 8
fda-2.2.8/fda/R/TaylorSpline.R | 35
fda-2.2.8/fda/R/basisfd.R | 9
fda-2.2.8/fda/R/bsplineS.R | 15
fda-2.2.8/fda/R/bsplinepen.R | 12
fda-2.2.8/fda/R/create.bspline.basis.R | 22
fda-2.2.8/fda/R/create.monomial.basis.R | 4
fda-2.2.8/fda/R/density.fd.R | 269 -
fda-2.2.8/fda/R/deriv.fd.R | 9
fda-2.2.8/fda/R/eval.basis.R | 42
fda-2.2.8/fda/R/eval.bifd.R | 35
fda-2.2.8/fda/R/eval.fd.R | 50
fda-2.2.8/fda/R/eval.monfd.R | 76
fda-2.2.8/fda/R/eval.posfd.R | 17
fda-2.2.8/fda/R/evaldiag.bifd.R | 13
fda-2.2.8/fda/R/fRegress.CV.R | 20
fda-2.2.8/fda/R/fRegress.R | 25
fda-2.2.8/fda/R/fRegress.fdPar.R | 32
fda-2.2.8/fda/R/fRegress.numeric.R | 26
fda-2.2.8/fda/R/fRegress.stderr.R | 20
fda-2.2.8/fda/R/getbasismatrix.R | 41
fda-2.2.8/fda/R/inprod.R | 35
fda-2.2.8/fda/R/intensity.fd.R | 151 -
fda-2.2.8/fda/R/lambda2df.R | 14
fda-2.2.8/fda/R/landmarkreg.R | 49
fda-2.2.8/fda/R/monfn.R | 16
fda-2.2.8/fda/R/mongrad.R | 24
fda-2.2.8/fda/R/monhess.R | 21
fda-2.2.8/fda/R/pca.fd.R | 59
fda-2.2.8/fda/R/pda.fd.R | 1370 +++++-----
fda-2.2.8/fda/R/pda.overlay.r | 15
fda-2.2.8/fda/R/phaseplanePlot.R | 37
fda-2.2.8/fda/R/plot.basisfd.R | 5
fda-2.2.8/fda/R/plot.fd.R | 7
fda-2.2.8/fda/R/plot.pda.fd.R | 3
fda-2.2.8/fda/R/project.basis.R | 10
fda-2.2.8/fda/R/quadset.R | 9
fda-2.2.8/fda/R/register.fd.R | 116
fda-2.2.8/fda/R/smooth.basis.R | 268 +
fda-2.2.8/fda/R/smooth.basisPar.R | 13
fda-2.2.8/fda/R/smooth.bibasis.R | 13
fda-2.2.8/fda/R/smooth.monotone.R | 29
fda-2.2.8/fda/R/smooth.morph.R | 15
fda-2.2.8/fda/R/smooth.pos.R | 61
fda-2.2.8/fda/data/CanadianWeather.rda |binary
fda-2.2.8/fda/data/MontrealTemp.rda |binary
fda-2.2.8/fda/data/ReginaPrecip.rda |binary
fda-2.2.8/fda/data/StatSciChinese.rda |binary
fda-2.2.8/fda/data/daily.rda |binary
fda-2.2.8/fda/data/dateAccessories.rda |binary
fda-2.2.8/fda/data/gait.rda |binary
fda-2.2.8/fda/data/growth.rda |binary
fda-2.2.8/fda/data/handwrit.rda |binary
fda-2.2.8/fda/data/infantGrowth.rda |binary
fda-2.2.8/fda/data/landmark.reg.expData.rda |binary
fda-2.2.8/fda/data/lip.rda |binary
fda-2.2.8/fda/data/melanoma.rda |binary
fda-2.2.8/fda/data/nondurables.rda |binary
fda-2.2.8/fda/data/onechild.rda |binary
fda-2.2.8/fda/data/pinch.rda |binary
fda-2.2.8/fda/data/pinchraw.rda |binary
fda-2.2.8/fda/data/refinery.rda |binary
fda-2.2.8/fda/data/seabird.rda |binary
fda-2.2.8/fda/inst/Matlab/fdaM/@basis/basis.m | 93
fda-2.2.8/fda/inst/Matlab/fdaM/@basis/getbasismatrix.m | 14
fda-2.2.8/fda/inst/Matlab/fdaM/@basis/getbasispars.m |only
fda-2.2.8/fda/inst/Matlab/fdaM/@basis/getbasistype.m | 14
fda-2.2.8/fda/inst/Matlab/fdaM/@basis/getbasisvalues.m | 4
fda-2.2.8/fda/inst/Matlab/fdaM/@basis/plot.m | 32
fda-2.2.8/fda/inst/Matlab/fdaM/@basis/putbasisvalues.m | 27
fda-2.2.8/fda/inst/Matlab/fdaM/@bibasis/bibasis.m | 42
fda-2.2.8/fda/inst/Matlab/fdaM/@fd/fd.m | 26
fda-2.2.8/fda/inst/Matlab/fdaM/@fd/plot.m | 143 -
fda-2.2.8/fda/inst/Matlab/fdaM/@fdPar/fdPar.m | 40
fda-2.2.8/fda/inst/Matlab/fdaM/bsplineM.m | 31
fda-2.2.8/fda/inst/Matlab/fdaM/create_bspline_basis.m | 7
fda-2.2.8/fda/inst/Matlab/fdaM/create_constant_basis.m | 7
fda-2.2.8/fda/inst/Matlab/fdaM/create_default_basis.m | 20
fda-2.2.8/fda/inst/Matlab/fdaM/create_exponential_basis.m | 8
fda-2.2.8/fda/inst/Matlab/fdaM/create_fdVariance_basis.m | 12
fda-2.2.8/fda/inst/Matlab/fdaM/create_fd_basis.m | 8
fda-2.2.8/fda/inst/Matlab/fdaM/create_nspline_basis.m |only
fda-2.2.8/fda/inst/Matlab/fdaM/eval_FEM_fd.m | 20
fda-2.2.8/fda/inst/Matlab/fdaM/eval_basis.m | 8
fda-2.2.8/fda/inst/Matlab/fdaM/eval_fd.m | 34
fda-2.2.8/fda/inst/Matlab/fdaM/eval_fdVar_fd.m |only
fda-2.2.8/fda/inst/Matlab/fdaM/eval_penalty.m | 5
fda-2.2.8/fda/inst/Matlab/fdaM/examples/goodsindex/goodsindex.mat |only
fda-2.2.8/fda/inst/Matlab/fdaM/examples/goodsindex/nondurables.txt |only
fda-2.2.8/fda/inst/Matlab/fdaM/landmarkreg.m | 37
fda-2.2.8/fda/inst/Matlab/fdaM/mass.m | 4
fda-2.2.8/fda/inst/Matlab/fdaM/monhess.m | 24
fda-2.2.8/fda/inst/Matlab/fdaM/nsplineM.m |only
fda-2.2.8/fda/inst/Matlab/fdaM/nsplinepen.m |only
fda-2.2.8/fda/inst/Matlab/fdaM/pca_fd.m | 78
fda-2.2.8/fda/inst/Matlab/fdaM/plot_pca_fd.m | 4
fda-2.2.8/fda/inst/Matlab/fdaM/plotfit_fd.m | 58
fda-2.2.8/fda/inst/Matlab/fdaM/register_fd.m | 37
fda-2.2.8/fda/inst/Matlab/fdaM/section_fd.m |only
fda-2.2.8/fda/inst/Matlab/fdaM/sfdint.m | 4
fda-2.2.8/fda/inst/Matlab/fdaM/smooth_basis.m | 42
fda-2.2.8/fda/inst/Matlab/fdaM/smooth_monotone.m | 70
fda-2.2.8/fda/inst/Matlab/fdaM/tri2grid_fd.m | 4
fda-2.2.8/fda/inst/Matlab/fdaM/tricoefCal.m |only
fda-2.2.8/fda/inst/doc/FDAfuns.pdf |binary
fda-2.2.8/fda/inst/scripts/fdarm-ch01.R | 32
fda-2.2.8/fda/inst/scripts/fdarm-ch02.R | 16
fda-2.2.8/fda/inst/scripts/fdarm-ch04.R | 28
fda-2.2.8/fda/inst/scripts/fdarm-ch05.R | 22
fda-2.2.8/fda/inst/scripts/fdarm-ch07.R | 24
fda-2.2.8/fda/inst/scripts/fdarm-ch08.R | 23
fda-2.2.8/fda/man/AmpPhaseDecomp.Rd | 6
fda-2.2.8/fda/man/Data2fd.Rd | 611 ++--
fda-2.2.8/fda/man/MontrealTemp.Rd | 2
fda-2.2.8/fda/man/arithmetic.basisfd.Rd | 2
fda-2.2.8/fda/man/as.fd.Rd | 25
fda-2.2.8/fda/man/basisfd.product.Rd | 14
fda-2.2.8/fda/man/bsplineS.Rd | 134
fda-2.2.8/fda/man/bsplinepen.Rd | 120
fda-2.2.8/fda/man/create.bspline.basis.Rd | 498 +--
fda-2.2.8/fda/man/density.fd.Rd | 259 -
fda-2.2.8/fda/man/deriv.fd.Rd | 156 -
fda-2.2.8/fda/man/eval.basis.Rd | 256 -
fda-2.2.8/fda/man/eval.bifd.Rd | 129
fda-2.2.8/fda/man/eval.fd.Rd | 271 +
fda-2.2.8/fda/man/eval.monfd.Rd | 264 -
fda-2.2.8/fda/man/eval.posfd.Rd | 9
fda-2.2.8/fda/man/evaldiag.bifd.Rd | 92
fda-2.2.8/fda/man/fRegress.CV.Rd | 7
fda-2.2.8/fda/man/fRegress.Rd | 32
fda-2.2.8/fda/man/fRegress.stderr.Rd | 14
fda-2.2.8/fda/man/fd.Rd | 13
fda-2.2.8/fda/man/fda-internal.Rd | 15
fda-2.2.8/fda/man/fda-package.Rd | 21
fda-2.2.8/fda/man/getbasismatrix.Rd | 96
fda-2.2.8/fda/man/inprod.Rd | 204 -
fda-2.2.8/fda/man/intensity.fd.Rd | 248 -
fda-2.2.8/fda/man/lambda2df.Rd | 94
fda-2.2.8/fda/man/landmarkreg.Rd | 40
fda-2.2.8/fda/man/mean.fd.Rd | 12
fda-2.2.8/fda/man/monfn.Rd | 6
fda-2.2.8/fda/man/pda.fd.Rd | 778 ++---
fda-2.2.8/fda/man/pda.overlay.Rd | 134
fda-2.2.8/fda/man/phaseplanePlot.Rd | 194 -
fda-2.2.8/fda/man/plotfit.fd.Rd | 8
fda-2.2.8/fda/man/plotreg.fd.rd | 1
fda-2.2.8/fda/man/project.basis.Rd | 94
fda-2.2.8/fda/man/quadset.Rd | 178 -
fda-2.2.8/fda/man/register.fd.Rd | 12
fda-2.2.8/fda/man/smooth.basis.Rd | 456 +--
fda-2.2.8/fda/man/smooth.bibasis.Rd | 137 -
fda-2.2.8/fda/man/smooth.fd.Rd | 8
fda-2.2.8/fda/man/smooth.monotone.Rd | 6
fda-2.2.8/fda/man/smooth.pos.Rd | 204 -
fda-2.2.8/fda/man/sum.fd.Rd | 8
fda-2.2.8/fda/man/summary.Lfd.Rd | 4
fda-2.2.8/fda/man/summary.basisfd.Rd | 4
fda-2.2.8/fda/man/summary.bifd.Rd | 4
fda-2.2.8/fda/man/summary.fd.Rd | 4
fda-2.2.8/fda/man/summary.fdPar.Rd | 6
170 files changed, 5845 insertions(+), 5313 deletions(-)