Title: Access Vegetation Databases and Treat Taxonomy
Diff between vegdata versions 0.6-7 dated 2014-11-01 and 0.6.9 dated 2015-04-18
Description: Handling of vegetation data from Turboveg (http://www.synbiosys.alterra.nl/turboveg/) and other sources (http://www.vegetweb.de). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", http://www.botanik.uni-greifswald.de/GermanSL.html).
Author: Florian Jansen
Maintainer: Florian Jansen
vegdata-0.6-7/vegdata/vignettes/ecol_let.bst |only
vegdata-0.6.9/vegdata/DESCRIPTION | 17 +++----
vegdata-0.6.9/vegdata/MD5 | 57 +++++++++++-------------
vegdata-0.6.9/vegdata/NAMESPACE | 2
vegdata-0.6.9/vegdata/R/child.r | 12 ++---
vegdata-0.6.9/vegdata/R/internal.r | 13 ++++-
vegdata-0.6.9/vegdata/R/monotypic.r | 2
vegdata-0.6.9/vegdata/R/reflist.r | 11 ++--
vegdata-0.6.9/vegdata/R/syntab.r | 9 ++-
vegdata-0.6.9/vegdata/R/tax.r | 2
vegdata-0.6.9/vegdata/R/tax_add.r | 9 ++-
vegdata-0.6.9/vegdata/R/tv.biblio.r | 12 +++--
vegdata-0.6.9/vegdata/R/tv.coverperc.r | 15 +++---
vegdata-0.6.9/vegdata/R/tv.home.r | 11 ++--
vegdata-0.6.9/vegdata/R/tv.obs.r | 2
vegdata-0.6.9/vegdata/R/tv.site.r | 34 ++++++++------
vegdata-0.6.9/vegdata/R/tv.veg.r | 11 ++--
vegdata-0.6.9/vegdata/R/tv.write.r | 61 +++++++++++++++++++++++---
vegdata-0.6.9/vegdata/build/vignette.rds |binary
vegdata-0.6.9/vegdata/inst/ChangeLog | 5 ++
vegdata-0.6.9/vegdata/inst/doc/vegdata.R | 26 ++++++-----
vegdata-0.6.9/vegdata/inst/doc/vegdata.Rnw | 40 ++++++++++-------
vegdata-0.6.9/vegdata/inst/doc/vegdata.pdf |binary
vegdata-0.6.9/vegdata/man/tv.biblio.Rd | 4 +
vegdata-0.6.9/vegdata/man/tv.coverperc.Rd | 11 ++--
vegdata-0.6.9/vegdata/man/tv.site.Rd | 2
vegdata-0.6.9/vegdata/man/tv.veg.Rd | 2
vegdata-0.6.9/vegdata/man/tv.write.Rd | 4 +
vegdata-0.6.9/vegdata/man/vegdata-internal.Rd | 1
vegdata-0.6.9/vegdata/vignettes/vegdata.Rnw | 40 ++++++++++-------
30 files changed, 259 insertions(+), 156 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Diff between heplots versions 1.0-12 dated 2014-07-02 and 1.0-15 dated 2015-04-18
Description: Provides HE plot functions for visualizing hypothesis tests in multivariate linear models. They represents sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions).
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb]
Maintainer: Michael Friendly
DESCRIPTION | 12 +-
MD5 | 158 ++++++++++++++++----------------
NAMESPACE | 9 +
NEWS | 12 ++
R/arrow3d.R | 10 +-
R/cross3d.R | 6 -
R/ellipse3d.axes.R | 10 +-
R/heplot1d.R | 3
R/heplot3d.R | 48 +++++----
R/mark.H0.R | 4
build/vignette.rds |binary
data/Adopted.RData |binary
data/Bees.rda |binary
data/FootHead.rda |binary
data/Headache.RData |binary
data/Hernior.RData |binary
data/MockJury.RData |binary
data/NLSY.RData |binary
data/Oslo.RData |binary
data/Plastic.rda |binary
data/Pottery2.RData |binary
data/Probe1.RData |binary
data/Probe2.RData |binary
data/RatWeight.RData |binary
data/ReactTime.RData |binary
data/Rohwer.rda |binary
data/RootStock.rda |binary
data/Sake.RData |binary
data/Skulls.RData |binary
data/SocGrades.RData |binary
data/VocabGrowth.rda |binary
data/WeightLoss.RData |binary
data/schooldata.RData |binary
man/Oslo.Rd | 4
man/RatWeight.Rd | 2
man/Skulls.Rd | 3
man/heplot-package.Rd | 8 -
man/heplot.Rd | 4
man/robmlm.Rd | 7 -
vignettes/fig/plot-Ortho-fm1.pdf |binary
vignettes/fig/plot-Ortho-fm3.pdf |binary
vignettes/fig/plot-grades-can-class.pdf |binary
vignettes/fig/plot-grades-can-gpa.pdf |binary
vignettes/fig/plot-grades-can-sex.pdf |binary
vignettes/fig/plot-grades-pairs.pdf |binary
vignettes/fig/plot-hern-can-age.pdf |binary
vignettes/fig/plot-hern-can-build.pdf |binary
vignettes/fig/plot-hern-can-cardiac.pdf |binary
vignettes/fig/plot-hern-can-pstat.pdf |binary
vignettes/fig/plot-hern-pairs.pdf |binary
vignettes/fig/plot-jury-can1.pdf |binary
vignettes/fig/plot-jury-mod1-HE.pdf |binary
vignettes/fig/plot-jury-mod1-pairs.pdf |binary
vignettes/fig/plot-jury-mod2-HE.pdf |binary
vignettes/fig/plot-jury-mod3-eff.pdf |binary
vignettes/fig/plot-obk-HE1.pdf |binary
vignettes/fig/plot-obk-HE2.pdf |binary
vignettes/fig/plot-obk-HE3.pdf |binary
vignettes/fig/plot-obk2-HE1.pdf |binary
vignettes/fig/plot-obk2-HE2.pdf |binary
vignettes/fig/plot-ortho-HE.pdf |binary
vignettes/fig/plot-ortho-nonlin-HE.pdf |binary
vignettes/fig/plot-ortho-xyplot1.pdf |binary
vignettes/fig/plot-ortho-xyplot2.pdf |binary
vignettes/fig/plot-plastic2.pdf |binary
vignettes/fig/plot-rohwer-HE1.pdf |binary
vignettes/fig/plot-rohwer-HE2.pdf |binary
vignettes/fig/plot-rohwer-HE3.pdf |binary
vignettes/fig/plot-rohwer-HE4.pdf |binary
vignettes/fig/plot-skulls-HE-pairs.pdf |binary
vignettes/fig/plot-skulls-bwplot.pdf |binary
vignettes/fig/plot-skulls-can2.pdf |binary
vignettes/fig/plot-skulls4.pdf |binary
vignettes/fig/plot-voc1.pdf |binary
vignettes/fig/plot-voc4.pdf |binary
vignettes/fig/plot-voc8.pdf |binary
vignettes/fig/plot-wl-HE1.pdf |binary
vignettes/fig/plot-wl-HE2.pdf |binary
vignettes/fig/plot-wl-HE3.pdf |binary
vignettes/fig/plot-wl-means.pdf |binary
80 files changed, 163 insertions(+), 137 deletions(-)
Title: Extended HOF (Huisman-Olff-Fresco) Models
Diff between eHOF versions 1.5.7 dated 2015-01-14 and 1.5.8 dated 2015-04-18
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman eta l. 1993 JVS) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen
eHOF-1.5.7/eHOF/vignettes/figure |only
eHOF-1.5.8/eHOF/DESCRIPTION | 15 ++++------
eHOF-1.5.8/eHOF/MD5 | 52 ++++++++++++++-----------------------
eHOF-1.5.8/eHOF/NAMESPACE | 5 +++
eHOF-1.5.8/eHOF/R/Para.deriv.r | 4 --
eHOF-1.5.8/eHOF/R/Para.opt.r | 15 ++++------
eHOF-1.5.8/eHOF/R/Para.r | 2 -
eHOF-1.5.8/eHOF/R/autolayout.r | 10 ++-----
eHOF-1.5.8/eHOF/R/coef.HOF.r | 18 +++++++-----
eHOF-1.5.8/eHOF/R/pick.model.r | 2 -
eHOF-1.5.8/eHOF/R/plot.HOF.list.r | 10 ++++---
eHOF-1.5.8/eHOF/R/plot.HOF.r | 42 ++++++++++++-----------------
eHOF-1.5.8/eHOF/R/print.HOF.list.r | 2 -
eHOF-1.5.8/eHOF/R/zzz.r | 4 --
eHOF-1.5.8/eHOF/build/vignette.rds |binary
eHOF-1.5.8/eHOF/inst/ChangeLog | 7 ++--
eHOF-1.5.8/eHOF/inst/doc/eHOF.R | 23 ++--------------
eHOF-1.5.8/eHOF/inst/doc/eHOF.Rnw | 46 ++++----------------------------
eHOF-1.5.8/eHOF/inst/doc/eHOF.pdf |binary
eHOF-1.5.8/eHOF/man/HOF.Rd | 7 ++--
eHOF-1.5.8/eHOF/man/autolayout.Rd | 6 +---
eHOF-1.5.8/eHOF/vignettes/eHOF.Rnw | 46 ++++----------------------------
22 files changed, 107 insertions(+), 209 deletions(-)
Title: Pairwise Distance Estimation with TKF91 and TKF92 Model
Diff between TKF versions 0.0.3 dated 2015-02-10 and 0.0.8 dated 2015-04-18
Description: Pairwise evolutionary distance estimation between protein sequences with the TKF91 and TKF92 model, which consider all the possible paths of transforming from one sequence to another.
Author: Ge Tan
Maintainer: Ge Tan
DESCRIPTION | 11 ++++++-----
MD5 | 25 ++++++++++++++++---------
NAMESPACE | 12 +++++++++++-
R/MinSqTree.R |only
R/TKF91.R | 21 ++++++++++++++++++---
R/TKF92.R | 22 +++++++++++++++++++---
R/TKF92HG.R |only
inst/makePackage/TKF.txt | 29 ++++++++++++++++++++++++-----
inst/unitTests/test_TKF92HG.R |only
man/TKF91.Rd | 1 +
man/TKF92.Rd | 25 ++++++++++++-------------
man/TKF92HG.Rd |only
man/optim.phylo.wls.Rd |only
src/R_init_TKF.c | 9 +++++++++
src/TKF92.h | 2 +-
src/TKF92HG.c |only
src/TKF92HG.h |only
17 files changed, 117 insertions(+), 40 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-07 3.8.31-4
2014-07-04 3.8.31-3
2014-05-07 3.8.31-2
2013-03-29 3.8.31-1
2012-10-15 3.8.31-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-07 1.0.0
Title: Spatial Modeling on Stream Networks
Diff between SSN versions 1.1.4 dated 2014-11-03 and 1.1.5 dated 2015-04-18
Description: Geostatistical modeling for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including covariates, can be fit with ML or REML. Mapping and other graphical functions are included.
Author: Jay Ver Hoef and Erin Peterson
Maintainer: Jay Ver Hoef
DESCRIPTION | 8 +-
MD5 | 58 ++++++++--------
NAMESPACE | 19 ++++-
R/SSN-methods.R | 12 +++
R/additive.function.jay.R | 54 +++++++++++----
R/copyLSN2temp.R |only
R/createDistMat.R | 28 ++++++--
R/createSSN.R | 2
R/split.predictions.R | 12 +--
R/writeSSN.r | 96 +++++++++++++++++++++-------
build/vignette.rds |binary
data/mf04.rda |binary
data/mf04p.rda |binary
data/modelFits.rda |binary
inst/doc/STARS.pdf |binary
man/AIC.glmssn.Rd | 8 +-
man/BLUP.Rd | 6 +
man/BlockPredict.Rd | 50 +++++++-------
man/CrossValidationSSN.Rd | 6 +
man/CrossValidationStatsSSN.Rd | 8 +-
man/additive.function.Rd | 6 +
man/as.SpatialLines.SpatialStreamNetwork.rd | 11 ++-
man/copyLSN2temp.Rd |only
man/covparms.Rd | 9 ++
man/createDistMat.Rd | 9 +-
man/getPreds.Rd | 9 ++
man/getStreamDistMat.rd | 6 +
man/importPredpts.Rd | 7 +-
man/plot.glmssn.predict.Rd | 11 ++-
man/splitPredictions.Rd | 15 +---
man/writeSSN.Rd | 5 +
31 files changed, 302 insertions(+), 153 deletions(-)
Title: Functions to Analyze Single System Data
Diff between SSDforR versions 1.4.8 dated 2014-12-07 and 1.4.9 dated 2015-04-18
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach
DESCRIPTION | 10 +--
MD5 | 138 +++++++++++++++++++++++++-------------------------
man/ABWilcox.Rd | 2
man/ABanova.Rd | 4 -
man/ABarrow.Rd | 2
man/ABautoacf.Rd | 2
man/ABbinomial.Rd | 2
man/ABdescrip.Rd | 2
man/ABiqr.Rd | 2
man/ABlineD.Rd | 2
man/ABlines.Rd | 2
man/ABma.Rd | 2
man/ABregres.Rd | 2
man/ABrf2.Rd | 2
man/ABrobust.Rd | 2
man/ABtext.Rd | 2
man/ABtsplot.Rd | 2
man/ABttest.Rd | 2
man/Append.Rd | 2
man/Aregres.Rd | 2
man/Arimadiff.Rd | 2
man/Arimama.Rd | 2
man/Arobust.Rd | 2
man/Cchart.Rd | 2
man/Effectsize.Rd | 2
man/GABrf2.Rd | 2
man/GABttest.Rd | 2
man/Getcsv.Rd | 2
man/Gindex.Rd | 2
man/Gline.Rd | 2
man/Gmedian.Rd | 2
man/IQRbandgraph.Rd | 2
man/IQRlegend.Rd | 2
man/IQRline.Rd | 2
man/PANDlegend.Rd | 2
man/PEMabove.Rd | 2
man/PEMbelow.Rd | 2
man/PNDbelow.Rd | 2
man/Pchart.Rd | 2
man/Rchart.Rd | 2
man/Rchartsd.Rd | 2
man/SD1legend.Rd | 2
man/SD2legend.Rd | 2
man/SDAband.Rd | 2
man/SN.Rd | 2
man/SPClegend.Rd | 2
man/SPCline.Rd | 2
man/SSDforR.Rd | 2
man/Savecsv.Rd | 2
man/Trimline.Rd | 2
man/XRchart.Rd | 2
man/Xmrchart.Rd | 2
man/cdcabove.rd | 2
man/cdcbelow.rd | 2
man/diffchart.Rd | 2
man/insert.rd | 2
man/ird.rd | 2
man/listnames.rd | 2
man/meanabove.rd | 2
man/meanbelow.rd | 2
man/pandabove.rd | 2
man/pandbelow.rd | 2
man/pemlegend.rd | 2
man/regabove.Rd | 2
man/regbelow.Rd | 2
man/robregabove.Rd | 2
man/robregbelow.Rd | 2
man/robustCDCabove.Rd | 2
man/robustCDCbelow.Rd | 2
man/trimabove.Rd | 2
70 files changed, 143 insertions(+), 143 deletions(-)
Title: Calculate Species Richness and Extrapolation Metrics
Diff between sprex versions 1.0 dated 2015-02-24 and 1.1 dated 2015-04-18
Description: Calculate species richness functions for rarefaction and
extrapolation.
Author: Eric Archer
Maintainer: Eric Archer
DESCRIPTION | 8 ++---
MD5 | 60 +++++++++++++++++++++---------------------
R/ACE.R | 1
R/Chao1.R | 5 ++-
R/Swor1.R | 21 ++++++++++----
R/bootstrap.assemblage.R | 10 ++++---
R/discovery.curve.R | 49 ++++++++++++++++++++--------------
R/expand.freqs.R | 14 ++++++---
R/expected.num.species.R | 26 ++++++++++--------
R/f.stats.R | 8 +++--
R/f0.R | 29 ++++++++++----------
R/iChao1.R | 4 ++
R/jack1.R | 1
R/jack2.R | 1
R/num.samples.required.R | 28 +++++++++++--------
R/plot.discovery.curve.R | 24 ++++++++++------
R/sample.to.species.freq.R | 17 +++++++----
R/species.to.sample.freq.R | 11 ++++---
R/sprex-package.R | 13 ++++-----
man/bootstrap.assemblage.Rd | 9 +++---
man/discovery.curve.Rd | 42 ++++++++++++++++-------------
man/expand.freqs.Rd | 13 +++++----
man/expected.num.species.Rd | 25 +++++++++--------
man/f.stats.Rd | 7 ++--
man/f0.Rd | 29 ++++++++++----------
man/num.samples.required.Rd | 22 ++++++++-------
man/osa.old.growth.Rd | 4 +-
man/plot.discovery.curve.Rd | 16 ++++++-----
man/sample.to.species.freq.Rd | 15 +++++++---
man/species.to.sample.freq.Rd | 10 ++++---
man/sprex-package.Rd | 9 +++---
31 files changed, 307 insertions(+), 224 deletions(-)
Title: Miscellaneous Data Management Tools
Diff between sjmisc versions 1.0.0 dated 2015-03-22 and 1.0.1 dated 2015-04-18
Description: Collection of several utility functions for reading or writing data, recoding and labelling variables and some frequently used statistical tests.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke
DESCRIPTION | 10
MD5 | 105 +-
NAMESPACE | 87 +
NEWS | 45 -
R/sjImportSPSS.R | 2191 +++++++++++++++++++++++++-------------------------
R/sjRecode.R | 212 ++--
R/sjStatistics.R | 240 ++++-
README.md | 96 +-
man/chisq_gof.Rd | 68 -
man/cramer.Rd | 52 -
man/cronb.Rd | 50 -
man/cv.Rd | 66 -
man/dicho.Rd | 87 +
man/efc.Rd | 84 -
man/efc2.Rd | 50 -
man/efc3.Rd | 50 -
man/eta_sq.Rd | 94 +-
man/get_val_labels.Rd | 146 +--
man/get_var_labels.Rd | 160 +--
man/group_labels.Rd | 164 +--
man/group_str.Rd | 98 +-
man/group_var.Rd | 146 +--
man/is_crossed.Rd |only
man/is_nested.Rd |only
man/is_num_fac.Rd |only
man/levene_test.Rd | 46 -
man/mean_n.Rd | 80 -
man/mic.Rd | 80 -
man/mwu.Rd | 104 +-
man/phi.Rd | 52 -
man/read_sas.Rd | 68 -
man/read_spss.Rd | 150 +--
man/read_stata.Rd | 64 -
man/rec.Rd | 120 +-
man/recode_to.Rd | 112 +-
man/reliab_test.Rd | 164 +--
man/rmse.Rd | 54 -
man/set_na.Rd | 93 +-
man/set_val_labels.Rd | 136 +--
man/set_var_labels.Rd | 174 +--
man/sjmisc-package.Rd | 60 -
man/std_beta.Rd | 92 +-
man/std_e.Rd | 42
man/str_pos.Rd | 138 +--
man/table_values.Rd | 72 -
man/to_fac.Rd | 91 +-
man/to_label.Rd | 101 +-
man/to_sjPlot.Rd | 68 -
man/to_value.Rd | 102 +-
man/weight.Rd | 78 -
man/weight2.Rd | 90 +-
man/word_wrap.Rd | 56 -
man/write_spss.Rd | 62 -
man/write_stata.Rd | 54 -
tests |only
55 files changed, 3619 insertions(+), 3285 deletions(-)
Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Diff between MATA versions 0.2 dated 2015-01-08 and 0.3 dated 2015-04-18
Description: Calculates Model-Averaged Tail Area Wald (MATA-Wald) confidence
intervals, which are constructed using single-model estimators and model
weights.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek
DESCRIPTION | 14 +++++++-------
MD5 | 2 +-
2 files changed, 8 insertions(+), 8 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Diff between Luminescence versions 0.4.2 dated 2015-03-23 and 0.4.3 dated 2015-04-18
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Rachel K. Smedley [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer
DESCRIPTION | 10
MD5 | 78 -
NAMESPACE | 3
NEWS | 232 +++
R/Analyse_SAR.OSLdata.R | 415 +++---
R/RLum.Analysis-class.R | 801 ++++++-------
R/RisoeBINfileData-class.R | 198 +--
R/analyse_IRSAR.RF.R | 6
R/analyse_SAR.CWOSL.R | 20
R/calc_MinDose.R | 2
R/calc_OSLLxTxRatio.R | 282 ++--
R/calc_Statistics.R | 4
R/extract_IrradiationTimes.R | 186 ++-
R/fit_CWCurve.R | 744 ++++++------
R/plot_GrowthCurve.R | 2455 ++++++++++++++++++++--------------------
R/plot_Histogram.R | 1297 ++++++++++-----------
R/plot_RLum.Analysis.R | 309 +++--
R/plot_RLum.Data.Spectrum.R | 270 ++--
R/readBIN2R.R | 2013 ++++++++++++++++----------------
R/readXSYG2R.R | 13
R/writeR2BIN.R | 116 +
inst/CITATION | 6
inst/NEWS.Rd | 144 ++
man/Analyse_SAR.OSLdata.Rd | 93 -
man/Luminescence-package.Rd | 27
man/Risoe.BINfileData-class.Rd | 151 +-
man/analyse_IRSAR.RF.Rd | 2
man/analyse_SAR.CWOSL.Rd | 2
man/calc_MinDose.Rd | 2
man/calc_OSLLxTxRatio.Rd | 62 -
man/calc_Statistics.Rd | 2
man/extract_IrradiationTimes.Rd | 35
man/fit_CWCurve.Rd | 98 -
man/plot_GrowthCurve.Rd | 2
man/plot_Histogram.Rd | 9
man/plot_RLum.Analysis.Rd | 13
man/plot_RLum.Data.Spectrum.Rd | 55
man/readBIN2R.Rd | 7
man/readXSYG2R.Rd | 2
man/writeR2BIN.Rd | 14
40 files changed, 5543 insertions(+), 4637 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Diff between KFAS versions 1.0.4-1 dated 2014-06-06 and 1.1.0 dated 2015-04-18
Description: Functions for Kalman filtering, smoothing,
forecasting and simulation of multivariate exponential family state space
models with exact diffuse initialization and sequential processing.
Author: Jouni Helske
Maintainer: Jouni Helske
KFAS-1.0.4-1/KFAS/src/deviance.f95 |only
KFAS-1.0.4-1/KFAS/src/glogliku.f95 |only
KFAS-1.1.0/KFAS/ChangeLog | 50 -
KFAS-1.1.0/KFAS/DESCRIPTION | 19
KFAS-1.1.0/KFAS/MD5 | 202 ++--
KFAS-1.1.0/KFAS/NAMESPACE | 4
KFAS-1.1.0/KFAS/R/KFAS-package.R | 256 +++--
KFAS-1.1.0/KFAS/R/KFS.R | 985 ++++++++++-----------
KFAS-1.1.0/KFAS/R/SSMarima.R | 41
KFAS-1.1.0/KFAS/R/SSMcustom.R | 25
KFAS-1.1.0/KFAS/R/SSMcycle.R | 61 -
KFAS-1.1.0/KFAS/R/SSModel.R | 589 ++++++------
KFAS-1.1.0/KFAS/R/SSMregression.R | 360 +++----
KFAS-1.1.0/KFAS/R/SSMseasonal.R | 279 ++---
KFAS-1.1.0/KFAS/R/SSMtrend.R | 59 -
KFAS-1.1.0/KFAS/R/approxSSM.R | 160 ++-
KFAS-1.1.0/KFAS/R/artransform.R | 23
KFAS-1.1.0/KFAS/R/checkModel.R | 179 ++-
KFAS-1.1.0/KFAS/R/coef.KFS.R | 60 -
KFAS-1.1.0/KFAS/R/deviance.KFS.R | 19
KFAS-1.1.0/KFAS/R/extract.SSModel.R | 293 +++---
KFAS-1.1.0/KFAS/R/fitSSM.R | 189 ++--
KFAS-1.1.0/KFAS/R/fitted.KFS.R | 33
KFAS-1.1.0/KFAS/R/hatvalues.KFS.R | 60 -
KFAS-1.1.0/KFAS/R/importanceSSM.R | 259 ++---
KFAS-1.1.0/KFAS/R/initTheta.R |only
KFAS-1.1.0/KFAS/R/internalResids.R |only
KFAS-1.1.0/KFAS/R/interval.R | 159 +--
KFAS-1.1.0/KFAS/R/ldl.R | 9
KFAS-1.1.0/KFAS/R/logLik.SSModel.R | 294 +++---
KFAS-1.1.0/KFAS/R/mvInnovations.R |only
KFAS-1.1.0/KFAS/R/predict.SSModel.R | 368 +++----
KFAS-1.1.0/KFAS/R/print.objects.R | 144 +--
KFAS-1.1.0/KFAS/R/residuals.KFS.R | 209 ++--
KFAS-1.1.0/KFAS/R/rstandard.KFS.R | 238 +----
KFAS-1.1.0/KFAS/R/signals.R | 149 +--
KFAS-1.1.0/KFAS/R/simHelper.R |only
KFAS-1.1.0/KFAS/R/simulateSSM.R | 222 +---
KFAS-1.1.0/KFAS/R/subset.SSModel.R | 138 --
KFAS-1.1.0/KFAS/R/transformSSM.R | 279 +++--
KFAS-1.1.0/KFAS/README.md | 58 -
KFAS-1.1.0/KFAS/build |only
KFAS-1.1.0/KFAS/data/alcohol.rda |only
KFAS-1.1.0/KFAS/inst |only
KFAS-1.1.0/KFAS/man/Extract.SSModel.Rd | 79 -
KFAS-1.1.0/KFAS/man/GlobalTemp.Rd | 13
KFAS-1.1.0/KFAS/man/KFAS.Rd | 298 +++---
KFAS-1.1.0/KFAS/man/KFS.Rd | 347 +++----
KFAS-1.1.0/KFAS/man/SSModel.Rd | 303 +++---
KFAS-1.1.0/KFAS/man/alcohol.Rd |only
KFAS-1.1.0/KFAS/man/approxSSM.Rd | 105 +-
KFAS-1.1.0/KFAS/man/artransform.Rd | 22
KFAS-1.1.0/KFAS/man/boat.Rd | 8
KFAS-1.1.0/KFAS/man/checkModel.Rd | 40
KFAS-1.1.0/KFAS/man/coef.KFS.Rd | 38
KFAS-1.1.0/KFAS/man/deviance.KFS.Rd | 15
KFAS-1.1.0/KFAS/man/fitSSM.Rd | 90 +
KFAS-1.1.0/KFAS/man/fitted.KFS.Rd | 22
KFAS-1.1.0/KFAS/man/hatvalues.KFS.Rd | 30
KFAS-1.1.0/KFAS/man/importanceSSM.Rd | 96 +-
KFAS-1.1.0/KFAS/man/ldl.Rd | 16
KFAS-1.1.0/KFAS/man/logLik.SSModel.Rd | 108 +-
KFAS-1.1.0/KFAS/man/predict.SSModel.Rd | 129 +-
KFAS-1.1.0/KFAS/man/print.KFS.Rd | 14
KFAS-1.1.0/KFAS/man/print.SSModel.Rd | 6
KFAS-1.1.0/KFAS/man/residuals.KFS.Rd | 56 -
KFAS-1.1.0/KFAS/man/rstandard.KFS.Rd | 88 +
KFAS-1.1.0/KFAS/man/sexratio.Rd | 7
KFAS-1.1.0/KFAS/man/signal.Rd | 38
KFAS-1.1.0/KFAS/man/simulateSSM.Rd | 52 -
KFAS-1.1.0/KFAS/man/transformSSM.Rd | 48 -
KFAS-1.1.0/KFAS/src/Makevars | 2
KFAS-1.1.0/KFAS/src/Makevars.win |only
KFAS-1.1.0/KFAS/src/approx.f95 | 200 ++--
KFAS-1.1.0/KFAS/src/approxloop.f95 |only
KFAS-1.1.0/KFAS/src/artransform.f95 | 39
KFAS-1.1.0/KFAS/src/cdistwrap.c |only
KFAS-1.1.0/KFAS/src/covmeanw.f95 | 28
KFAS-1.1.0/KFAS/src/declarations.h | 12
KFAS-1.1.0/KFAS/src/filter1step.f95 |only
KFAS-1.1.0/KFAS/src/filter1stepnovar.f95 |only
KFAS-1.1.0/KFAS/src/filtersimfast.f95 | 111 --
KFAS-1.1.0/KFAS/src/gloglik.f95 | 179 +--
KFAS-1.1.0/KFAS/src/gsmoothall.f95 | 359 +++----
KFAS-1.1.0/KFAS/src/init.c | 11
KFAS-1.1.0/KFAS/src/isample.f95 | 57 -
KFAS-1.1.0/KFAS/src/isamplefilter.f95 | 95 +-
KFAS-1.1.0/KFAS/src/kfilter.f95 | 210 ----
KFAS-1.1.0/KFAS/src/kfstheta.f95 | 316 +-----
KFAS-1.1.0/KFAS/src/ldl.f95 | 5
KFAS-1.1.0/KFAS/src/ldlssm.f95 | 4
KFAS-1.1.0/KFAS/src/marginalxx.f95 |only
KFAS-1.1.0/KFAS/src/mvfilter.f95 |only
KFAS-1.1.0/KFAS/src/ngfilter.f95 | 27
KFAS-1.1.0/KFAS/src/ngloglik.f95 | 110 +-
KFAS-1.1.0/KFAS/src/ngsmooth.f95 | 26
KFAS-1.1.0/KFAS/src/predict.f95 | 5
KFAS-1.1.0/KFAS/src/ptheta.f95 |only
KFAS-1.1.0/KFAS/src/pytheta.f95 |only
KFAS-1.1.0/KFAS/src/simfilter.f95 | 69 -
KFAS-1.1.0/KFAS/src/simgaussian.f95 | 58 -
KFAS-1.1.0/KFAS/src/smoothonestep.f95 |only
KFAS-1.1.0/KFAS/src/smoothsim.f95 | 306 +-----
KFAS-1.1.0/KFAS/src/smoothsimfast.f95 | 267 +----
KFAS-1.1.0/KFAS/tests/testthat/testBasics.R | 7
KFAS-1.1.0/KFAS/tests/testthat/testGLM.R | 113 --
KFAS-1.1.0/KFAS/tests/testthat/testImportanceSSM.R |only
KFAS-1.1.0/KFAS/tests/testthat/testNumerical.R |only
KFAS-1.1.0/KFAS/tests/testthat/testPredict.R |only
KFAS-1.1.0/KFAS/tests/testthat/testSSMarima.R | 26
KFAS-1.1.0/KFAS/tests/testthat/testSimulateSSM.R |only
KFAS-1.1.0/KFAS/tests/testthat/testStruct.R | 40
KFAS-1.1.0/KFAS/vignettes |only
113 files changed, 5332 insertions(+), 5890 deletions(-)
Title: Tools for Checking Data Consistency
Diff between datacheck versions 1.0.4 dated 2014-09-23 and 1.2.2 dated 2015-04-18
Description: Functions to check variables against a
set of data quality rules. A rule file can be accompanied by look-up tables. In
addition, there are some convenience functions that may
serve as an example for defining clearer 'data rules'. An
HTML based user interface facilitates initial exploration of the
functionality.
Author: "Simon, Reinhard (CIP)"
Maintainer: "Simon, Reinhard (CIP)"
datacheck-1.0.4/datacheck/build |only
datacheck-1.0.4/datacheck/inst/doc/index.R |only
datacheck-1.2.2/datacheck/DESCRIPTION | 35
datacheck-1.2.2/datacheck/LICENSE |only
datacheck-1.2.2/datacheck/MD5 | 106
datacheck-1.2.2/datacheck/NAMESPACE | 20
datacheck-1.2.2/datacheck/NEWS | 27
datacheck-1.2.2/datacheck/R/datacheck.R | 963 +++-
datacheck-1.2.2/datacheck/README.md | 18
datacheck-1.2.2/datacheck/inst/doc/RN_1.0.4.md |only
datacheck-1.2.2/datacheck/inst/doc/RN_1.0.4.pdf |only
datacheck-1.2.2/datacheck/inst/doc/RN_1.1.0.md |only
datacheck-1.2.2/datacheck/inst/doc/RN_1.1.0.pdf |only
datacheck-1.2.2/datacheck/inst/doc/RN_1.2.2.md |only
datacheck-1.2.2/datacheck/inst/doc/RN_1.2.2.pdf |only
datacheck-1.2.2/datacheck/inst/doc/index.Rmd | 37
datacheck-1.2.2/datacheck/inst/doc/index.html | 2982 ++-----------
datacheck-1.2.2/datacheck/inst/examples/datadict_profile.R | 30
datacheck-1.2.2/datacheck/inst/examples/has_punct.R | 2
datacheck-1.2.2/datacheck/inst/examples/has_ruleErrors.R | 13
datacheck-1.2.2/datacheck/inst/examples/is_oneOf.R | 40
datacheck-1.2.2/datacheck/inst/examples/is_onlyLowers.R | 7
datacheck-1.2.2/datacheck/inst/examples/is_properName.R | 6
datacheck-1.2.2/datacheck/inst/examples/is_withinRange.R | 4
datacheck-1.2.2/datacheck/inst/examples/person_rules.R | 18
datacheck-1.2.2/datacheck/inst/examples/rules.R | 18
datacheck-1.2.2/datacheck/inst/examples/rules1.R | 12
datacheck-1.2.2/datacheck/inst/examples/rules2.R | 4
datacheck-1.2.2/datacheck/inst/examples/soil_rules.R | 59
datacheck-1.2.2/datacheck/inst/www/server.R | 22
datacheck-1.2.2/datacheck/inst/www/ui.R | 55
datacheck-1.2.2/datacheck/man/as.rules.Rd | 12
datacheck-1.2.2/datacheck/man/as_rules.Rd |only
datacheck-1.2.2/datacheck/man/datacheck-package.Rd | 9
datacheck-1.2.2/datacheck/man/datadict.profile.Rd | 39
datacheck-1.2.2/datacheck/man/datadict_profile.Rd |only
datacheck-1.2.2/datacheck/man/has.punct.Rd | 15
datacheck-1.2.2/datacheck/man/has.ruleErrors.Rd | 24
datacheck-1.2.2/datacheck/man/has_punct.Rd |only
datacheck-1.2.2/datacheck/man/has_rule_errors.Rd |only
datacheck-1.2.2/datacheck/man/heatmap.quality.Rd | 10
datacheck-1.2.2/datacheck/man/heatmap_quality.Rd |only
datacheck-1.2.2/datacheck/man/is.datadict.profile.Rd | 43
datacheck-1.2.2/datacheck/man/is.oneOf.Rd | 53
datacheck-1.2.2/datacheck/man/is.onlyLowers.Rd | 18
datacheck-1.2.2/datacheck/man/is.properName.Rd | 19
datacheck-1.2.2/datacheck/man/is.withinRange.Rd | 14
datacheck-1.2.2/datacheck/man/is_datadict_profile.Rd |only
datacheck-1.2.2/datacheck/man/is_one_of.Rd |only
datacheck-1.2.2/datacheck/man/is_only_lowers.Rd |only
datacheck-1.2.2/datacheck/man/is_proper_name.Rd |only
datacheck-1.2.2/datacheck/man/is_within_range.Rd |only
datacheck-1.2.2/datacheck/man/pkg.version.Rd | 6
datacheck-1.2.2/datacheck/man/pkg_version.Rd |only
datacheck-1.2.2/datacheck/man/prep4rep.Rd | 10
datacheck-1.2.2/datacheck/man/read.rules.Rd | 11
datacheck-1.2.2/datacheck/man/read_rules.Rd |only
datacheck-1.2.2/datacheck/man/ruleCoverage.Rd | 7
datacheck-1.2.2/datacheck/man/rule_coverage.Rd |only
datacheck-1.2.2/datacheck/man/runDatacheck.Rd | 6
datacheck-1.2.2/datacheck/man/run_datacheck.Rd |only
datacheck-1.2.2/datacheck/man/scoreSum.Rd | 7
datacheck-1.2.2/datacheck/man/score_sum.Rd |only
datacheck-1.2.2/datacheck/man/shortSummary.Rd | 8
datacheck-1.2.2/datacheck/man/short_summary.Rd |only
datacheck-1.2.2/datacheck/vignettes/index.Rmd | 34
datacheck-1.2.2/datacheck/vignettes/index.html |only
67 files changed, 1754 insertions(+), 3069 deletions(-)
Title: Diff, Patch and Merge for Data.frames
Diff between daff versions 0.1.2 dated 2015-02-24 and 0.1.4 dated 2015-04-18
Description: Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches.
Changes to data can be made visible by using render_diff. The V8 package is used to
wrap the 'daff.js' JavaScript library which is included in the package.
Author: Paul Fitzpatrick [aut] (JavaScript original,
http://paulfitz.github.io/daff/),
Edwin de Jonge [aut, cre] (R wrapper)
Maintainer: Edwin de Jonge
DESCRIPTION | 17 ++++++++---------
MD5 | 20 ++++++++++----------
NAMESPACE | 1 +
NEWS | 3 +++
R/TableView.R | 18 +++++++++---------
R/context.R | 2 +-
R/diff-data.R | 2 +-
R/merge-data.R | 6 +++---
R/patch-data.R | 2 +-
R/render-diff.R | 2 +-
README.md | 13 ++++++++-----
11 files changed, 46 insertions(+), 40 deletions(-)
Title: A Package for Coincidence Analysis (CNA)
Diff between cna versions 1.0-2 dated 2015-01-03 and 1.0-3 dated 2015-04-18
Description: Provides functions for performing Coincidence Analysis (CNA).
Author: Ambuehl, Mathias, Michael Baumgartner, Ruedi Epple, Alexis Kauffmann and Alrik Thiem
Maintainer: Alexis Kauffmann
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/cna_aux.r | 2 +-
inst/CITATION | 2 +-
inst/ChangeLog | 2 ++
man/cna.package.Rd | 4 ++--
6 files changed, 15 insertions(+), 13 deletions(-)
Title: Analysis and Visualisation of Ecological Communities
Diff between cheddar versions 0.1-626 dated 2014-08-28 and 0.1-629 dated 2015-04-18
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson
DESCRIPTION | 15 +--
LICENSE | 2
MD5 | 63 +++++++--------
NAMESPACE | 15 +++
R/community_MN.R | 6 -
R/community_trophic_links.R | 4
R/graph_nodes.R | 80 +++++++++++++++++++
build/vignette.rds |binary
inst/CITATION | 3
inst/doc/CheddarQuickstart.R | 18 ++--
inst/doc/CheddarQuickstart.Rnw | 6 +
inst/doc/CheddarQuickstart.pdf |binary
inst/doc/Collections.R | 104 ++++++++++++-------------
inst/doc/Collections.Rnw | 6 +
inst/doc/Collections.pdf |binary
inst/doc/Community.R | 166 ++++++++++++++++++++--------------------
inst/doc/Community.Rnw | 6 +
inst/doc/Community.pdf |binary
inst/doc/ImportExport.R | 36 ++++----
inst/doc/ImportExport.Rnw | 6 +
inst/doc/ImportExport.pdf |binary
inst/doc/PlotsAndStats.R | 138 ++++++++++++++++-----------------
inst/doc/PlotsAndStats.Rnw | 7 +
inst/doc/PlotsAndStats.pdf |binary
man/PlotCircularWeb.Rd | 3
man/PlotWagonWheel.Rd |only
man/TrophicLevels.Rd | 34 ++++----
man/cheddar.Rd | 4
vignettes/CheddarQuickstart.Rnw | 6 +
vignettes/Collections.Rnw | 6 +
vignettes/Community.Rnw | 6 +
vignettes/ImportExport.Rnw | 6 +
vignettes/PlotsAndStats.Rnw | 7 +
33 files changed, 448 insertions(+), 305 deletions(-)
Title: Interface to Bold Systems API
Diff between bold versions 0.2.0 dated 2014-08-20 and 0.2.6 dated 2015-04-18
Description: A programmatic interface to the Web Service methods provided by
Bold Systems for genetic barcode data. Functions include methods for
searching by sequences by taxonomic names, ids, collectors, and
institutions; as well as a function for searching for specimens, and
downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
DESCRIPTION | 10
MD5 | 50 ++--
NAMESPACE | 29 ++
NEWS | 16 +
R/bold_identify.R | 51 ++--
R/bold_seq.R | 24 --
R/bold_seqspec.R | 48 +---
R/bold_specimens.R | 39 +--
R/bold_tax_id.R | 49 ++--
R/bold_tax_name.R | 56 +----
R/bold_trace.R | 79 +++++--
R/zzz.R | 38 +++
README.md | 236 +++++++++-------------
build/vignette.rds |binary
inst/doc/bold_vignette.Rmd | 463 --------------------------------------------
inst/doc/bold_vignette.html | 268 +++++++++++++------------
man/bold-package.Rd | 3
man/bold_identify.Rd | 39 +--
man/bold_seq.Rd | 8
man/bold_seqspec.Rd | 11 -
man/bold_specimens.Rd | 7
man/bold_tax_id.Rd | 32 ++-
man/bold_tax_name.Rd | 16 +
man/bold_trace.Rd | 35 ++-
man/sequences.Rd | 3
vignettes/bold_vignette.Rmd | 463 --------------------------------------------
26 files changed, 629 insertions(+), 1444 deletions(-)