Title: The Iterative Signature Algorithm
Diff between isa2 versions 0.3.3 dated 2013-09-24 and 0.3.4 dated 2015-04-08
Description: The ISA is a biclustering algorithm that finds modules
in an input matrix. A module or bicluster is a block of the
reordered input matrix.
Author: Gabor Csardi
Maintainer: Gabor Csardi
DESCRIPTION | 14 ++++++-----
MD5 | 16 ++++++------
NAMESPACE | 3 ++
R/biclust.R | 2 -
R/isa3.R | 52 ++++++++++++++++++++++-------------------
R/viz.R | 2 -
inst/doc/ISA_parallel.pdf |binary
inst/doc/ISA_tutorial.pdf |binary
inst/doc/ISA_tutorial.vignette | 1
9 files changed, 50 insertions(+), 40 deletions(-)
Title: Import SPSS, Stata and SAS Files
Diff between haven versions 0.1.1 dated 2015-03-03 and 0.2.0 dated 2015-04-08
Description: Import foreign statistical formats into R via the embedded
ReadStat C library (https://github.com/WizardMac/ReadStat). Package includes
preliminary support for writing Stata and SPSS formats.
Author: Hadley Wickham [aut, cre],
Evan Miller [aut, cph] (Author of included ReadStat code),
RStudio [cph]
Maintainer: Hadley Wickham
haven-0.1.1/haven/src/DfBuilder.cpp |only
haven-0.2.0/haven/DESCRIPTION | 6
haven-0.2.0/haven/MD5 | 75 ++--
haven-0.2.0/haven/NAMESPACE | 1
haven-0.2.0/haven/R/RcppExports.R | 12
haven-0.2.0/haven/R/as_factor.R | 3
haven-0.2.0/haven/R/haven.R | 31 +
haven-0.2.0/haven/R/hhmm.R | 10
haven-0.2.0/haven/R/labelled.R | 17
haven-0.2.0/haven/README.md | 6
haven-0.2.0/haven/build/vignette.rds |binary
haven-0.2.0/haven/inst/doc/datetimes.html | 4
haven-0.2.0/haven/man/as_factor.Rd | 3
haven-0.2.0/haven/man/labelled.Rd | 2
haven-0.2.0/haven/man/read_dta.Rd | 18 -
haven-0.2.0/haven/man/read_spss.Rd | 12
haven-0.2.0/haven/src/DfReader.cpp |only
haven-0.2.0/haven/src/DfWriter.cpp | 19 -
haven-0.2.0/haven/src/RcppExports.cpp | 16
haven-0.2.0/haven/src/readstat.h | 5
haven-0.2.0/haven/src/readstat_dta.c | 2
haven-0.2.0/haven/src/readstat_dta.h | 4
haven-0.2.0/haven/src/readstat_dta_read.c | 37 ++
haven-0.2.0/haven/src/readstat_dta_write.c | 2
haven-0.2.0/haven/src/readstat_io.c | 14
haven-0.2.0/haven/src/readstat_io.h | 2
haven-0.2.0/haven/src/readstat_parser.c | 5
haven-0.2.0/haven/src/readstat_por.c | 71 ++-
haven-0.2.0/haven/src/readstat_por_parse.c | 97 ++---
haven-0.2.0/haven/src/readstat_por_parse.h | 2
haven-0.2.0/haven/src/readstat_sas.c | 54 ++-
haven-0.2.0/haven/src/readstat_sav.c | 2
haven-0.2.0/haven/src/readstat_sav.h | 4
haven-0.2.0/haven/src/readstat_sav_parse.c | 14
haven-0.2.0/haven/src/readstat_sav_read.c | 373 ++++++++++++++++-----
haven-0.2.0/haven/src/readstat_sav_write.c | 15
haven-0.2.0/haven/tests/testthat/test-labelled.R |only
haven-0.2.0/haven/tests/testthat/test-read-sas.R | 7
haven-0.2.0/haven/tests/testthat/test-read-sav.R | 11
haven-0.2.0/haven/tests/testthat/test-read-stata.R |only
haven-0.2.0/haven/tests/testthat/types.dta |only
41 files changed, 679 insertions(+), 277 deletions(-)
Title: Define Truthy and Falsy Values
Diff between falsy versions 1.0 dated 2014-08-27 and 1.0.1 dated 2015-04-08
Description: A value is falsy if it is NULL, FALSE, the empty string,
zero, or an empty vector or list. Other values are truthy. The new
%&&% and %||% operators work with falsy and truthy values and
can be used for concise conditional execution.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi
DESCRIPTION | 14 +++++++-------
LICENSE | 2 +-
MD5 | 27 ++++++++++++++-------------
NAMESPACE | 2 +-
R/falsy-package.r | 14 --------------
man/FALSY.Rd | 3 ++-
man/Falsy-package.Rd | 3 ++-
man/TRUTHY.Rd | 3 ++-
man/and.Rd | 3 ++-
man/is_falsy.Rd | 3 ++-
man/is_truthy.Rd | 3 ++-
man/nay.Rd | 3 ++-
man/or.Rd | 12 ++----------
man/try_quietly.Rd | 8 ++------
vignettes |only
15 files changed, 41 insertions(+), 59 deletions(-)
Title: Colored Terminal Output
Diff between crayon versions 1.1.0 dated 2014-10-15 and 1.2.0 dated 2015-04-08
Description: Colored terminal output on
terminals that support ANSI color and highlight codes.
ANSI color support is automatically detected.
Colors and highlighting can be combined and nested. New styles
can also be created easily. This package was inspired by the chalk
JavaScript project.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi
crayon-1.1.0/crayon/README.md |only
crayon-1.2.0/crayon/DESCRIPTION | 15 ++--
crayon-1.2.0/crayon/LICENSE | 2
crayon-1.2.0/crayon/MD5 | 43 ++++++-----
crayon-1.2.0/crayon/NAMESPACE | 6 +
crayon-1.2.0/crayon/R/machinery.r | 4 +
crayon-1.2.0/crayon/R/string_operations.r |only
crayon-1.2.0/crayon/R/utils.r | 70 +++++++++++++++++++
crayon-1.2.0/crayon/man/chr.Rd | 3
crayon-1.2.0/crayon/man/col_nchar.Rd |only
crayon-1.2.0/crayon/man/col_strsplit.Rd |only
crayon-1.2.0/crayon/man/col_substr.Rd |only
crayon-1.2.0/crayon/man/col_substring.Rd |only
crayon-1.2.0/crayon/man/combine_styles.Rd | 3
crayon-1.2.0/crayon/man/concat.Rd | 3
crayon-1.2.0/crayon/man/crayon.Rd | 3
crayon-1.2.0/crayon/man/drop_style.Rd | 3
crayon-1.2.0/crayon/man/has_color.Rd | 3
crayon-1.2.0/crayon/man/has_style.Rd | 3
crayon-1.2.0/crayon/man/make_style.Rd | 3
crayon-1.2.0/crayon/man/num_colors.Rd | 3
crayon-1.2.0/crayon/man/show_ansi_colors.Rd | 3
crayon-1.2.0/crayon/man/strip_style.Rd | 3
crayon-1.2.0/crayon/man/style.Rd | 3
crayon-1.2.0/crayon/man/styles.Rd | 3
crayon-1.2.0/crayon/tests/testthat/test-operations.R |only
26 files changed, 138 insertions(+), 41 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data in R
Diff between hsdar versions 0.1.1 dated 2015-03-25 and 0.1.2 dated 2015-04-08
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using PROSPECT and PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [ctb],
Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert
hsdar-0.1.1/hsdar/man/add2speclib.Rd |only
hsdar-0.1.2/hsdar/DESCRIPTION | 10 -
hsdar-0.1.2/hsdar/MD5 | 97 +++++++--------
hsdar-0.1.2/hsdar/R/AAAClasses.R | 6
hsdar-0.1.2/hsdar/R/HyperSpecRaster_methods.R | 28 ++--
hsdar-0.1.2/hsdar/R/rastermeta.R |only
hsdar-0.1.2/hsdar/R/speclib.R | 22 ++-
hsdar-0.1.2/hsdar/R/unmix.R | 8 -
hsdar-0.1.2/hsdar/R/vegindex.R | 18 +-
hsdar-0.1.2/hsdar/data/endmember_spectra.RData |binary
hsdar-0.1.2/hsdar/data/spectral_data.RData |binary
hsdar-0.1.2/hsdar/inst/doc/References.pdf |binary
hsdar-0.1.2/hsdar/man/Clman-class.Rd | 3
hsdar-0.1.2/hsdar/man/DistMat3D-class.Rd | 3
hsdar-0.1.2/hsdar/man/DistMat3D-methods.Rd | 2
hsdar-0.1.2/hsdar/man/HyperSpecRaster.Rd | 3
hsdar-0.1.2/hsdar/man/Nri-class.Rd | 9 -
hsdar-0.1.2/hsdar/man/Specfeat-class.Rd | 3
hsdar-0.1.2/hsdar/man/Speclib-class.Rd | 3
hsdar-0.1.2/hsdar/man/addcp.Rd | 8 -
hsdar-0.1.2/hsdar/man/applyDistMat3D.Rd | 6
hsdar-0.1.2/hsdar/man/applySpeclib.Rd | 2
hsdar-0.1.2/hsdar/man/bandnames.Rd | 4
hsdar-0.1.2/hsdar/man/bdri.Rd | 6
hsdar-0.1.2/hsdar/man/checkhull.Rd | 2
hsdar-0.1.2/hsdar/man/cor.test.normalized.ratio.index.Rd | 4
hsdar-0.1.2/hsdar/man/cut.specfeat.Rd | 2
hsdar-0.1.2/hsdar/man/define.features.Rd | 6
hsdar-0.1.2/hsdar/man/deletecp.Rd | 4
hsdar-0.1.2/hsdar/man/dist_speclib.Rd | 4
hsdar-0.1.2/hsdar/man/feature_properties.Rd | 22 ++-
hsdar-0.1.2/hsdar/man/figures |only
hsdar-0.1.2/hsdar/man/getNRI.Rd | 2
hsdar-0.1.2/hsdar/man/getcp.Rd | 2
hsdar-0.1.2/hsdar/man/glm.normalized.ratio.index.Rd | 23 +--
hsdar-0.1.2/hsdar/man/hsdar-package.Rd | 5
hsdar-0.1.2/hsdar/man/merge_speclib.Rd |only
hsdar-0.1.2/hsdar/man/plot.glm.normalized.ratio.index.Rd | 33 +----
hsdar-0.1.2/hsdar/man/plot.specfeat.Rd | 4
hsdar-0.1.2/hsdar/man/plot.speclib.Rd | 2
hsdar-0.1.2/hsdar/man/rastermeta.Rd |only
hsdar-0.1.2/hsdar/man/rededge.Rd | 6
hsdar-0.1.2/hsdar/man/response_functions.Rd | 6
hsdar-0.1.2/hsdar/man/smooth_speclib.Rd | 2
hsdar-0.1.2/hsdar/man/specfeat.Rd | 4
hsdar-0.1.2/hsdar/man/speclib.Rd | 7 -
hsdar-0.1.2/hsdar/man/spectra.Rd | 2
hsdar-0.1.2/hsdar/man/subset_speclib.Rd | 8 -
hsdar-0.1.2/hsdar/man/t.test.nri.Rd | 2
hsdar-0.1.2/hsdar/man/transform.Rd | 2
hsdar-0.1.2/hsdar/man/vegindex.Rd | 2
51 files changed, 218 insertions(+), 179 deletions(-)
Title: An Improved Heatmap Package
Diff between heatmap3 versions 1.0.7 dated 2014-08-29 and 1.1.1 dated 2015-04-08
Description: An improved heatmap package. Completely
compatible with the original R function heatmap,
and provides more powerful and convenient features.
Author: Shilin Zhao, Yan Guo, Quanhu Sheng, Yu Shyr
Maintainer: Shilin Zhao
heatmap3-1.0.7/heatmap3/vignettes/cache/setting_3fb270dc41facb42653a4ae883076b21.RData |only
heatmap3-1.0.7/heatmap3/vignettes/cache/setting_3fb270dc41facb42653a4ae883076b21.rdb |only
heatmap3-1.0.7/heatmap3/vignettes/cache/setting_3fb270dc41facb42653a4ae883076b21.rdx |only
heatmap3-1.1.1/heatmap3/DESCRIPTION | 16 -
heatmap3-1.1.1/heatmap3/MD5 | 32 +-
heatmap3-1.1.1/heatmap3/NAMESPACE | 2
heatmap3-1.1.1/heatmap3/NEWS | 12
heatmap3-1.1.1/heatmap3/R/heatmap3.R | 39 ++-
heatmap3-1.1.1/heatmap3/build/vignette.rds |binary
heatmap3-1.1.1/heatmap3/inst/doc/vignette.R | 16 -
heatmap3-1.1.1/heatmap3/inst/doc/vignette.Rnw | 4
heatmap3-1.1.1/heatmap3/inst/doc/vignette.pdf |binary
heatmap3-1.1.1/heatmap3/man/colByValue.Rd | 6
heatmap3-1.1.1/heatmap3/man/heatmap3.Rd | 122 +++++-----
heatmap3-1.1.1/heatmap3/man/showAnn.Rd | 2
heatmap3-1.1.1/heatmap3/man/showLegend.Rd | 10
heatmap3-1.1.1/heatmap3/vignettes/cache/setting_6613d1170cc2b09af00f80888ca7726a.RData |only
heatmap3-1.1.1/heatmap3/vignettes/cache/setting_6613d1170cc2b09af00f80888ca7726a.rdb |only
heatmap3-1.1.1/heatmap3/vignettes/cache/setting_6613d1170cc2b09af00f80888ca7726a.rdx |only
heatmap3-1.1.1/heatmap3/vignettes/vignette.Rnw | 4
20 files changed, 149 insertions(+), 116 deletions(-)
Title: Analyze Dose-Volume Histograms and Check Constraints
Diff between DVHmetrics versions 0.1 dated 2015-01-29 and 0.2 dated 2015-04-08
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files,
calculate DVH metrics, gEUD, NTCP, TCP, show DVH diagrams,
check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger
parseDVH.R | 118 +++-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.1/DVHmetrics/R/dvhConvert.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.1/DVHmetrics/R/shine.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.1/DVHmetrics/man/harmoConstrDVH.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.1/DVHmetrics/man/shine.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/DESCRIPTION | 12
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/MD5 | 115 ++--
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/NAMESPACE | 47 +
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/checkConstraint.R | 135 +++--
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/convertDVH.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/dvhDistance.R | 59 +-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/getBED.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/getDMEAN.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/getEUD.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/getMetric.R | 257 ++++------
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/getNTCP.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/loessSelSpan.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/parseCadplan.R | 18
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/parseEclipse.R | 35 +
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/parseMasterplan.R | 41 -
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/parseMetric.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/parsePinnacleDVH.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/readConstraint.R | 7
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/readDVH.R | 73 ++
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/runGUI.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/showConstraint.R | 29 -
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/showDVH.R | 31 -
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/smoothDVH.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/unix/parseDVH.R | 88 ++-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/build/vignette.rds |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/data/dataConstr.rda |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/data/dataMZ.rda |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/ChangeLog |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/DVHnotebooks |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/DVHshiny/ABOUT.md |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/DVHshiny/helper.R | 16
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/DVHshiny/server.R | 229 +++++++-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/DVHshiny/ui.R | 202 ++++---
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHmetrics.R | 19
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHmetrics.Rnw | 80 ++-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHmetrics.pdf |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHshiny.R | 2
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHshiny.Rnw | 6
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHshiny.pdf |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/DVHmetrics-package.Rd | 9
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/checkConstraint.Rd | 30 -
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/convertDVH.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/dataConstr.Rd | 2
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getBED.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getDMEAN.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getEQD2.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getEUD.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getIsoEffD.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getMetric.Rd | 51 +
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getNTCP.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getTCP.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/mergeDVH.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/print.Rd | 1
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/readDVH.Rd | 32 +
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/runGUI.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/saveConstraint.Rd | 1
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/saveDVH.Rd | 1
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/saveMetric.Rd | 1
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/showDVH.Rd | 1
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/DVHmetrics.Rnw | 80 ++-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/DVHshiny.Rnw | 6
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/appCheckConstr.jpg |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/appFileOpen.jpg |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/appMetrics.jpg |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/appShowConstr.jpg |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/appShowDVH.jpg |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/lit.bib | 100 +++
72 files changed, 1380 insertions(+), 554 deletions(-)
Title: Wegener Center Climate Uncertainty Explorer
Diff between wux versions 1.2-3 dated 2015-02-06 and 2.0-0 dated 2015-04-08
Description: Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary 'NetCDF' format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global Circulation Models, as the 'CMIP5' simulations, can be read in the same way as Regional Climate Models, as e.g. the 'CORDEX' or 'ENSEMBLES' simulations. The package has been developed at the 'Wegener Center for Climate and Global Change' at the University of Graz, Austria.
Author: Thomas Mendlik [aut, cre], Georg Heinrich [aut], Armin Leuprecht [aut], Andreas Gobiet [ths]
Maintainer: Thomas Mendlik
wux-1.2-3/wux/man/AnnualCycleplotWux.Rd |only
wux-1.2-3/wux/man/AnovaBarplotWux.Rd |only
wux-1.2-3/wux/man/AnovaReconstructIterative.Rd |only
wux-1.2-3/wux/man/AnovaReconstructIterativeCC.Rd |only
wux-1.2-3/wux/man/AnovaReconstructLES.Rd |only
wux-1.2-3/wux/man/HistplotWux.Rd |only
wux-1.2-3/wux/man/ScatterplotWux.Rd |only
wux-1.2-3/wux/man/WuxAnova.Rd |only
wux-1.2-3/wux/man/summaryWux.Rd |only
wux-2.0-0/wux/DESCRIPTION | 12 -
wux-2.0-0/wux/MD5 | 79 +++++-----
wux-2.0-0/wux/NAMESPACE | 27 ++-
wux-2.0-0/wux/R/AnovaReconstruct.R | 32 +++-
wux-2.0-0/wux/R/CMIP5toModelinput.R |only
wux-2.0-0/wux/R/PlotFunctions.R | 44 +++--
wux-2.0-0/wux/R/models2wux.R | 36 ++--
wux-2.0-0/wux/R/models2wuxGetAggregatedSpatioTemporalData.R | 30 ++--
wux-2.0-0/wux/R/models2wuxSubregions.R | 28 +++
wux-2.0-0/wux/R/plotit.R | 89 ++++++++----
wux-2.0-0/wux/R/read.wux.table.R | 14 +
wux-2.0-0/wux/R/summaryWux.R | 22 +-
wux-2.0-0/wux/data/CMIP5_example_changesignal.rda |only
wux-2.0-0/wux/data/alpinesummer.csv.gz |only
wux-2.0-0/wux/data/cmip3_2050.rda |only
wux-2.0-0/wux/data/cmip3_2100.rda |only
wux-2.0-0/wux/data/cmip5_2050.rda |only
wux-2.0-0/wux/data/datalist | 1
wux-2.0-0/wux/data/ensembles.rda |only
wux-2.0-0/wux/data/ensembles_gcms.rda |only
wux-2.0-0/wux/data/modelinput_test.rda |binary
wux-2.0-0/wux/data/userinput_CMIP5_changesignal.rda |binary
wux-2.0-0/wux/data/userinput_CMIP5_timeseries.rda |binary
wux-2.0-0/wux/exec/CMIP5_downloader.py | 2
wux-2.0-0/wux/exec/cmip5_to_wux_modeldict.py |only
wux-2.0-0/wux/man/CMIP5toModelinput.Rd |only
wux-2.0-0/wux/man/alpinesummer.Rd |only
wux-2.0-0/wux/man/aovWux.Rd |only
wux-2.0-0/wux/man/cmip3_2050.Rd | 4
wux-2.0-0/wux/man/cmip3_2100.Rd | 4
wux-2.0-0/wux/man/cmip5_2050.Rd | 4
wux-2.0-0/wux/man/cmip5_2100.Rd | 4
wux-2.0-0/wux/man/ensembles.Rd | 8 -
wux-2.0-0/wux/man/ensembles_gcms.Rd | 4
wux-2.0-0/wux/man/hist.wux.df.Rd |only
wux-2.0-0/wux/man/models2wux.Rd | 66 ++++++--
wux-2.0-0/wux/man/plot.wux.aov.Rd |only
wux-2.0-0/wux/man/plot.wux.df.Rd |only
wux-2.0-0/wux/man/plotAnnualCycle.Rd |only
wux-2.0-0/wux/man/read.wux.table.Rd | 8 -
wux-2.0-0/wux/man/reconstruct.Rd |only
wux-2.0-0/wux/man/summary.wux.df.Rd |only
wux-2.0-0/wux/man/userinput_CMIP5_changesignal.Rd | 4
wux-2.0-0/wux/man/userinput_CMIP5_timeseries.Rd | 2
wux-2.0-0/wux/man/wux-package.Rd | 43 +++--
54 files changed, 373 insertions(+), 194 deletions(-)
Title: Functions to Compute Chemical Reaction Similarity
Diff between RxnSim versions 1.0 dated 2015-03-12 and 1.0.1 dated 2015-04-08
Description: Methods to compute chemical similarity between two or more reactions and molecules. Allows masking of chemical substructures for weighted similarity computations. Uses packages 'rCDK' and 'fingerprint' for cheminformatics functionality.
Author: Varun Giri [aut, cre]
Maintainer: Varun Giri
RxnSim-1.0.1/RxnSim/CHANGELOG |only
RxnSim-1.0.1/RxnSim/DESCRIPTION | 12 +-
RxnSim-1.0.1/RxnSim/MD5 | 20 ++--
RxnSim-1.0.1/RxnSim/NAMESPACE | 3
RxnSim-1.0.1/RxnSim/NEWS |only
RxnSim-1.0.1/RxnSim/R/RxnSim.R | 59 ++++++++-----
RxnSim-1.0.1/RxnSim/R/RxnSimHelper.R | 118 ++++++++++++++++++++-------
RxnSim-1.0.1/RxnSim/R/RxnSimMask.R | 18 ++--
RxnSim-1.0.1/RxnSim/inst/DB/RheaData_v60.txt |only
RxnSim-1.0.1/RxnSim/man/rs.compute.Rd | 2
RxnSim-1.0.1/RxnSim/man/rs.makeDB.Rd | 8 +
RxnSim-1.0.1/RxnSim/man/rs.mask.Rd | 8 +
RxnSim-1.0/RxnSim/inst/DB/RheaData_v59.txt |only
13 files changed, 168 insertions(+), 80 deletions(-)
Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files
Diff between RDML versions 0.8-2 dated 2015-04-07 and 0.8-3 dated 2015-04-08
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) format files and transforms to the appropriate
formats of the 'qpcR' and 'chipPCR' packages.
Author: Konstantin A. Blagodatskikh [cre, aut],
Stefan Roediger [aut],
Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh
CHANGELOG | 3 +++
DESCRIPTION | 10 +++++-----
MD5 | 32 ++++++++++++++++----------------
NAMESPACE | 1 -
R/RDML.AsDendrogram.R | 10 +++++++---
R/RDML.AsTable.R | 4 ++--
R/RDML.GetFData.R | 6 +++---
R/RDML.R | 2 +-
R/RDML.SetFData.R | 6 +++---
R/RDML.init.R | 3 +--
R/names.RDML.R | 4 ++--
man/RDML.class.Rd | 4 ++--
man/asdendrogram-method.Rd | 4 ++--
man/astable-method.Rd | 4 ++--
man/getfdata-method.Rd | 6 +++---
man/names.RDML.Rd | 4 ++--
man/setfdata-method.Rd | 6 +++---
17 files changed, 57 insertions(+), 52 deletions(-)
Title: Density Estimation with a Penalized Mixture Approach
Diff between pendensity versions 0.2.7 dated 2014-02-25 and 0.2.8 dated 2015-04-08
Description: Estimation of univariate (conditional) densities using penalized B-splines with automatic selection of optimal smoothing parameter.
Author: Christian Schellhase
Maintainer: Christian Schellhase
DESCRIPTION | 10 +++++-----
MD5 | 13 +++++++------
NAMESPACE | 4 +++-
R/new.beta.val.R | 9 +--------
R/pendensity.R | 4 ++--
build |only
man/pendensity-package.Rd | 4 ++--
man/pendensity.Rd | 2 +-
8 files changed, 21 insertions(+), 25 deletions(-)
Title: A Toolkit for Recursive Partytioning
Diff between partykit versions 1.0-0 dated 2015-02-21 and 1.0-1 dated 2015-04-08
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources (rpart, RWeka, PMML) yielding objects that share
functionality for print/plot/predict methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree) and model-based
recursive partitioning (mob) from the party package are provided based
on the new infrastructure.
Author: Torsten Hothorn [aut, cre],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 15 ++++-----
MD5 | 50 +++++++++++++++---------------
R/as.party.R | 4 ++
R/glmtree.R | 23 +++++++++++--
R/lmtree.R | 23 +++++++++++--
R/plot.R | 24 +++++++++-----
build/vignette.rds |binary
data/HuntingSpiders.rda |only
inst/NEWS.Rd | 28 ++++++++++++++++
inst/doc/constparty.pdf |binary
inst/doc/ctree.R | 35 +++++++++------------
inst/doc/ctree.Rnw | 76 +++++++++++++++++++++++-----------------------
inst/doc/ctree.pdf |binary
inst/doc/mob.pdf |binary
inst/doc/partykit.pdf |binary
man/HuntingSpiders.Rd |only
man/WeatherPlay.Rd | 2 -
man/cforest.Rd | 69 +++++++++++++++++++++--------------------
man/ctree.Rd | 36 +++++++++++----------
man/glmtree.Rd | 11 +++---
man/lmtree.Rd | 11 +++---
man/mob.Rd | 6 +--
man/panelfunctions.Rd | 5 +--
man/party-plot.Rd | 4 +-
vignettes/ctree.Rnw | 76 +++++++++++++++++++++++-----------------------
vignettes/ctree.Rout.save | 60 +++++++++++++++++-------------------
vignettes/party.bib | 2 -
27 files changed, 316 insertions(+), 244 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Diff between glmnet versions 1.9-8 dated 2014-05-24 and 2.0-1 dated 2015-04-08
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.
Author: Jerome Friedman, Trevor Hastie, Noah Simon, Rob Tibshirani
Maintainer: Trevor Hastie
ChangeLog | 5 +
DESCRIPTION | 17 ++--
MD5 | 43 +++++++-----
NAMESPACE | 8 ++
R/cv.coxnet.R | 96 +++++++++++++++------------
R/cv.elnet.R | 84 +++++++++++++----------
R/cv.fishnet.R | 105 ++++++++++++++++-------------
R/cv.glmnet.R | 144 +++++++++++++++++++++++++---------------
R/cv.lognet.R | 162 ++++++++++++++++++++++++----------------------
R/cv.mrelnet.R | 8 +-
R/cv.multnet.R | 133 +++++++++++++++++++------------------
R/lognet.R | 15 +++-
R/predict.multnet.R | 2
build/vignette.rds |binary
data |only
inst/doc/Coxnet.pdf |binary
inst/doc/glmnet_beta.R |only
inst/doc/glmnet_beta.Rmd |only
inst/doc/glmnet_beta.html |only
man/beta_CVX.Rd |only
man/glmnet.Rd | 7 +
vignettes/glmnet_beta.Rmd |only
22 files changed, 479 insertions(+), 350 deletions(-)
Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Diff between rSPACE versions 1.1.0 dated 2015-02-28 and 1.1.1 dated 2015-04-08
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
NAMESPACE | 2 ++
R/Create_Landscapes.r | 3 ++-
R/Test_Samples.r | 3 ++-
data/WolverineHabitat.rda |binary
6 files changed, 14 insertions(+), 10 deletions(-)
Title: Analysis of Binary Character Evolution
Diff between corHMM versions 1.15 dated 2014-09-18 and 1.16 dated 2015-04-08
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 14 +++---
MD5 | 10 ++--
NAMESPACE | 2
R/ancRECON.R | 4 -
R/corHMM.R | 117 ++++++++++++++++++++++++++++++----------------------------
man/corHMM.Rd | 7 +--
6 files changed, 79 insertions(+), 75 deletions(-)
Title: Model-Based Clustering of Categorical Sequences
Diff between ClickClust versions 1.1.3 dated 2014-11-24 and 1.1.4 dated 2015-04-08
Description: Clustering categorical sequences by means of finite mixtures with Markov model components is the main utility of ClickClust. The package also allows detecting blocks of equivalent states by forward and backward state selection procedures.
Author: Volodymyr Melnykov [aut, cre]
Maintainer: Volodymyr Melnykov
ClickClust-1.1.3/ClickClust/demo/sec3.1_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.2_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.2_ex2.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.3_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.4_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.4_ex2.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.5_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.6_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.6_ex2.R |only
ClickClust-1.1.4/ClickClust/DESCRIPTION | 14
ClickClust-1.1.4/ClickClust/MD5 | 57 ++--
ClickClust-1.1.4/ClickClust/NEWS | 6
ClickClust-1.1.4/ClickClust/R/libClickClust.R | 93 +++---
ClickClust-1.1.4/ClickClust/R/libGraphics.R | 239 ++++++++++++-----
ClickClust-1.1.4/ClickClust/data |only
ClickClust-1.1.4/ClickClust/demo/00Index | 24 -
ClickClust-1.1.4/ClickClust/demo/BackwardSelection.R |only
ClickClust-1.1.4/ClickClust/demo/ClickPlot1.R |only
ClickClust-1.1.4/ClickClust/demo/ClickPlot2.R |only
ClickClust-1.1.4/ClickClust/demo/ConfidenceIntervals.R |only
ClickClust-1.1.4/ClickClust/demo/DataSimulation.R |only
ClickClust-1.1.4/ClickClust/demo/EMalgorithm1.R |only
ClickClust-1.1.4/ClickClust/demo/EMalgorithm2.R |only
ClickClust-1.1.4/ClickClust/demo/ForwardSelection.R |only
ClickClust-1.1.4/ClickClust/demo/ReadData.R |only
ClickClust-1.1.4/ClickClust/demo/StatePrediction.R |only
ClickClust-1.1.4/ClickClust/demo/demoClickClust.R | 2
ClickClust-1.1.4/ClickClust/demo/msnbc323.R |only
ClickClust-1.1.4/ClickClust/demo/utility.R | 7
ClickClust-1.1.4/ClickClust/man/B3.Rd |only
ClickClust-1.1.4/ClickClust/man/BackwardSearch.Rd | 5
ClickClust-1.1.4/ClickClust/man/C.Rd |only
ClickClust-1.1.4/ClickClust/man/ClickClust-package.Rd | 2
ClickClust-1.1.4/ClickClust/man/ClickClust.Rd | 2
ClickClust-1.1.4/ClickClust/man/ClickPlot.Rd | 22 +
ClickClust-1.1.4/ClickClust/man/ForwardSearch.Rd | 5
ClickClust-1.1.4/ClickClust/man/Predict.Rd | 2
ClickClust-1.1.4/ClickClust/man/ReadData.Rd | 11
ClickClust-1.1.4/ClickClust/man/VarEst.Rd | 2
ClickClust-1.1.4/ClickClust/man/msnbc323.Rd |only
ClickClust-1.1.4/ClickClust/man/synth.Rd |only
41 files changed, 318 insertions(+), 175 deletions(-)
Title: Generative Models for Complex Networks with Conditionally
Independent Dyadic Structure
Diff between CIDnetworks versions 0.8.0 dated 2015-03-11 and 0.8.1 dated 2015-04-08
Description: Generative models for complex networks with conditionally independent dyadic structure. Now supports directed arcs!
Author: Samrachana Adhikari [aut],
Beau Dabbs [cre, aut],
Brian Junker [aut],
Mauricio Sadinle [aut],
Tracy Sweet [aut],
A.C. Thomas [aut]
Maintainer: Beau Dabbs
DESCRIPTION | 8 +--
MD5 | 21 ++++----
NAMESPACE | 1
R/CID-external.R | 45 ++++++++++++++++-
R/CID-gibbs.R | 133 +++++++++++++++++++++++++++++++++++++++++-----------
R/COV-reference.R | 85 +++++++++++++++++++++++++--------
R/SBM-reference.R | 2
R/plotting-pieces.R | 8 +--
data/Advice.RData |only
man/CID-data.Rd | 13 ++++-
man/CID-gibbs.Rd | 4 -
man/CID-master.Rd | 3 -
12 files changed, 252 insertions(+), 71 deletions(-)