Title: Robust Estimation for Compositional Data.
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
Diff between robCompositions versions 1.5.0 dated 2011-05-06 and 1.6.0 dated 2012-05-15
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 robCompositions-1.5.0/robCompositions/inst/doc/ternary.pdf |only 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(-)
More information about robCompositions at CRAN
Permanent link
Title: Mixed Effects Cox Models.
Description: Cox proportional hazards models containing Gaussian random
effects, also known as frailty models.
Author: Terry Therneau
Maintainer: Terry Therneau
Diff between coxme versions 2.2-2 dated 2012-04-27 and 2.2-3 dated 2012-05-15
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.
Description: Bayes Clustering Package
Author: Gopal, V. and Fuentes, C. and Casella, G.
Maintainer: Gopal, V.
Diff between bayesclust versions 3.0 dated 2010-03-13 and 3.1 dated 2012-05-15
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
Description: Functions for statistical analysis, prediction and control
of time series.
Author: The Institute of Statistical Mathematics
Maintainer: The Institute of Statistical Mathematics
Diff between timsac versions 1.2.6 dated 2012-03-05 and 1.2.7 dated 2012-05-15
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
Description: graphic extensions for categorical data
Author: Alexander Pilhoefer
Maintainer: Alexander Pilhoefer
Diff between extracat versions 1.4-0 dated 2011-08-30 and 1.5-0 dated 2012-05-15
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
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
Diff between secr versions 2.3.1 dated 2011-12-20 and 2.3.2 dated 2012-05-15
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
Description: An R client for the Redis persistent key-value database
available from http://redis.io.
Author: B. W. Lewis
Maintainer: B. W. Lewis
Diff between rredis versions 1.6.3 dated 2011-10-23 and 1.6.6 dated 2012-05-15
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
Description: A programmatic interface to fishbase.org.
Author: Carl Boettiger [aut, cre], Duncan Temple Lang [aut], Peter C.
Wainwright [aut]
Maintainer: Carl Boettiger,
Diff between rfishbase versions 0.0-8 dated 2012-04-03 and 0.0-9 dated 2012-05-15
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
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
Diff between RcppSMC versions 0.1.0 dated 2012-03-22 and 0.1.1 dated 2012-05-15
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
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
Diff between pomp versions 0.42-1 dated 2012-05-03 and 0.42-4 dated 2012-05-15
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
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
Diff between planar versions 1.2 dated 2012-03-05 and 1.2.1 dated 2012-05-15
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
Description: Functions to fit and test the phenology of species based
on counts.
Author: Marc Girondot
Maintainer: Marc Girondot
Diff between phenology versions 3.29 dated 2012-04-11 and 3.31 dated 2012-05-15
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
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
Diff between maps versions 2.2-5 dated 2012-01-15 and 2.2-6 dated 2012-05-15
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
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
Diff between fda versions 2.2.7 dated 2011-08-30 and 2.2.8 dated 2012-05-15
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(-)