Title: Random Forests for Survival, Regression and Classification
(RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes. Now extended to include multivariate and unsupervised forests.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.0.0 dated 2015-12-07 and 2.0.5 dated 2015-12-24
randomForestSRC-2.0.0/randomForestSRC/man/impute.Rd |only randomForestSRC-2.0.5/randomForestSRC/DESCRIPTION | 8 randomForestSRC-2.0.5/randomForestSRC/MD5 | 62 - randomForestSRC-2.0.5/randomForestSRC/NAMESPACE | 1 randomForestSRC-2.0.5/randomForestSRC/R/data.utilities.R | 80 + randomForestSRC-2.0.5/randomForestSRC/R/factor.utilities.R | 8 randomForestSRC-2.0.5/randomForestSRC/R/find.interaction.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/generic.impute.rfsrc.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/generic.predict.rfsrc.R | 130 +-- randomForestSRC-2.0.5/randomForestSRC/R/impute.rfsrc.R | 5 randomForestSRC-2.0.5/randomForestSRC/R/max.subtree.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/plot.competing.risk.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/plot.rfsrc.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/plot.survival.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/plot.variable.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/predict.rfsrc.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/print.rfsrc.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/rf2rfz.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/rfsrc.R | 121 +- randomForestSRC-2.0.5/randomForestSRC/R/rfsrc.news.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/rfsrcSyn.R | 16 randomForestSRC-2.0.5/randomForestSRC/R/stat.split.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/utilities.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/var.select.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/vimp.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/zzz.R | 2 randomForestSRC-2.0.5/randomForestSRC/configure.ac | 2 randomForestSRC-2.0.5/randomForestSRC/inst/NEWS | 13 randomForestSRC-2.0.5/randomForestSRC/inst/doc/rsf-Rnews.pdf |binary randomForestSRC-2.0.5/randomForestSRC/man/impute.rfsrc.Rd |only randomForestSRC-2.0.5/randomForestSRC/man/rfsrc.Rd | 40 randomForestSRC-2.0.5/randomForestSRC/src/randomForestSRC.c | 426 ++++------ randomForestSRC-2.0.5/randomForestSRC/src/randomForestSRC.h | 2 33 files changed, 496 insertions(+), 450 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Visualization of Spatial and Spatio-Temporal Objects in Google
Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>
Diff between plotKML versions 0.5-3 dated 2015-07-09 and 0.5-4 dated 2015-12-24
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/AAAA.R | 3 ++- R/layer.Raster.R | 3 ++- R/layer.RasterBrick.R | 3 ++- R/layer.SpatialPixels.R | 3 ++- R/legend.whitening.R | 4 ++-- R/plotKML.GDALobj.R | 3 ++- build/vignette.rds |binary inst/doc/jss1079.pdf |binary man/eberg.Rd | 2 +- man/layer.Raster.Rd | 7 ++++--- man/layer.RasterBrick.Rd | 3 ++- man/layer.SpatialPixels.Rd | 7 ++++--- man/legend.whitening.Rd | 3 ++- 15 files changed, 43 insertions(+), 34 deletions(-)
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,
Robert R. Junker <Robert.Junker@sbg.ac.at>,
Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,
Arne Bathke <Arne.Bathke@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Diff between dynRB versions 0.4 dated 2015-08-11 and 0.5 dated 2015-12-24
dynRB-0.4/dynRB/R/funclist1.R |only dynRB-0.4/dynRB/R/funclist2.R |only dynRB-0.4/dynRB/R/funclist3.R |only dynRB-0.4/dynRB/man/funclist1.Rd |only dynRB-0.4/dynRB/man/funclist2.Rd |only dynRB-0.4/dynRB/man/funclist3.Rd |only dynRB-0.5/dynRB/DESCRIPTION | 7 ++++--- dynRB-0.5/dynRB/MD5 | 30 ++++++++++++++++-------------- dynRB-0.5/dynRB/NAMESPACE | 3 ++- dynRB-0.5/dynRB/R/dynRB-internal.R |only dynRB-0.5/dynRB/R/dynRB_Pn.R | 29 ++++++++++++----------------- dynRB-0.5/dynRB/R/dynRB_VPa.R | 13 ++++--------- dynRB-0.5/dynRB/R/dynRB_Vn.R | 9 ++------- dynRB-0.5/dynRB/R/overview.R | 8 ++------ dynRB-0.5/dynRB/inst |only dynRB-0.5/dynRB/man/dynRB-package.Rd | 4 ++-- dynRB-0.5/dynRB/man/overview.Rd | 2 +- dynRB-0.5/dynRB/tests |only 18 files changed, 45 insertions(+), 60 deletions(-)
Title: Tools for Easily Combining and Cleaning Data Sets
Description: Tools for combining and cleaning data sets, particularly
with grouped and time series data.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between DataCombine versions 0.2.9 dated 2015-02-11 and 0.2.18 dated 2015-12-24
DESCRIPTION | 13 - MD5 | 64 +++--- NAMESPACE | 11 + NEWS | 42 ++++ R/DropNA.R | 80 ++++---- R/FillIn.R | 8 R/PercChange.R | 95 ++++++++- R/internals.R | 1 R/slide.R | 507 ++++++++++++++++++++++++++--------------------------- R/utils.R | 107 +++++++---- README.md | 14 - man/CountSpell.Rd | 8 man/DropNA.Rd | 3 man/FillDown.Rd | 6 man/FillIn.Rd | 3 man/FindDups.Rd |only man/FindReplace.Rd | 3 man/InsertRow.Rd | 3 man/MoveFront.Rd | 3 man/NaVar.Rd | 3 man/PercChange.Rd | 6 man/SpreadDummy.Rd | 3 man/StartEnd.Rd | 9 man/TimeExpand.Rd | 9 man/TimeFill.Rd | 3 man/VarDrop.Rd | 3 man/change.Rd |only man/dMerge.Rd | 2 man/grepl.sub.Rd | 8 man/rmExcept.Rd | 3 man/shift.Rd | 2 man/shiftMA.Rd | 2 man/slide.Rd | 13 - man/slideMA.Rd | 11 - 34 files changed, 617 insertions(+), 431 deletions(-)
Title: Affinity Propagation Clustering
Description: The 'apcluster' package implements Frey's and Dueck's
Affinity Propagation clustering in R. The algorithms are
largely analogous to the 'Matlab' code published by Frey and
Dueck. The package further provides leveraged affinity
propagation and an algorithm for exemplar-based agglomerative
clustering that can also be used to join clusters obtained
from affinity propagation. Various plotting functions are
available for analyzing clustering results.
Author: Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas Kothmeier
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Diff between apcluster versions 1.4.1 dated 2014-12-09 and 1.4.2 dated 2015-12-24
apcluster-1.4.1/apcluster/data |only apcluster-1.4.2/apcluster/DESCRIPTION | 17 apcluster-1.4.2/apcluster/MD5 | 30 - apcluster-1.4.2/apcluster/NAMESPACE | 9 apcluster-1.4.2/apcluster/NEWS | 10 apcluster-1.4.2/apcluster/R/apcluster-methods.R | 20 apcluster-1.4.2/apcluster/R/apclusterL-methods.R | 19 apcluster-1.4.2/apcluster/R/coerce-methods.R | 2 apcluster-1.4.2/apcluster/R/heatmap-methods.R | 2 apcluster-1.4.2/apcluster/build/vignette.rds |binary apcluster-1.4.2/apcluster/inst/doc/apcluster.R | 471 ++++----------------- apcluster-1.4.2/apcluster/inst/doc/apcluster.Rnw | 173 ++++--- apcluster-1.4.2/apcluster/inst/doc/apcluster.pdf |binary apcluster-1.4.2/apcluster/inst/examples |only apcluster-1.4.2/apcluster/man/ch22Promoters.Rd | 27 - apcluster-1.4.2/apcluster/src/apclusterSparseC.cpp | 2 apcluster-1.4.2/apcluster/vignettes/apcluster.Rnw | 173 ++++--- 17 files changed, 395 insertions(+), 560 deletions(-)
Title: Exact Goodness-of-Fit Test for Multinomial Data with Fixed
Probabilities
Description: Tests whether a set of counts fit a given expected ratio. For
example, a genetic cross might be expected to produce four types in the
relative frequencies of 9:3:3:1. To see whether a set of observed counts
fits this expectation, one can examine all possible outcomes with xmulti() or a
random sample of them with xmonte() and find the probability of an observation
deviating from the expectation by at least as much as the observed. As a
measure of deviation from the expected, one can use the log-likelihood
ratio, the multinomial probability, or the classic chi-square statistic. A
histogram of the test statistic can also be plotted and compared with the
asymptotic curve.
Author: Bill Engels <wrengels@wisc.edu>
Maintainer: Bill Engels <wrengels@wisc.edu>
Diff between XNomial versions 1.0.1 dated 2014-02-08 and 1.0.4 dated 2015-12-24
DESCRIPTION | 16 - MD5 | 23 +- NAMESPACE | 9 R/xmonte.R | 5 R/xmulti.R | 15 + build/vignette.rds |binary inst/doc/XNomial.R | 16 - inst/doc/XNomial.Rmd | 32 +-- inst/doc/XNomial.html | 516 ++++++++++++++++---------------------------------- man/xmonte.Rd | 99 +++------ man/xmulti.Rd | 97 +++------ vignettes/XNomial.Rmd | 32 +-- vignettes/XNomial.md |only 13 files changed, 316 insertions(+), 544 deletions(-)
Title: Fisheries Stock Assessment Simulation Testing with Stock
Synthesis
Description: The ss3sim package develops a framework for fisheries stock
assessment simulation testing with Stock Synthesis 3 (SS3).
Author: Sean Anderson [aut, cre],
Cole Monnahan [aut],
Kelli Johnson [aut],
Kotaro Ono [aut],
Juan Valero [aut],
Curry Cunningham [aut],
Allan Hicks [aut],
Felipe Hurtado-Ferro [aut],
Peter Kuriyama [aut],
Roberto Licandeo [aut],
Carey McGilliard [aut],
Melissa Muradian [ctb],
Merrill Rudd [aut],
Christine Stawitz [aut],
Cody Szuwalski [aut],
Ian Taylor [aut],
Katyana Vert-pre [aut],
Athol Whitten [aut]
Maintainer: Sean Anderson <sean@seananderson.ca>
Diff between ss3sim versions 0.8.2 dated 2014-03-09 and 0.9.0 dated 2015-12-24
ss3sim-0.8.2/ss3sim/R/change_agecomp.r |only ss3sim-0.8.2/ss3sim/R/change_index.r |only ss3sim-0.8.2/ss3sim/R/change_lcomp.r |only ss3sim-0.8.2/ss3sim/inst/doc/ss3sim-vignette.R |only ss3sim-0.8.2/ss3sim/inst/doc/ss3sim-vignette.Rnw |only ss3sim-0.8.2/ss3sim/inst/doc/ss3sim-vignette.pdf |only ss3sim-0.8.2/ss3sim/inst/extdata/eg-cases/R0-cod.txt |only ss3sim-0.8.2/ss3sim/inst/extdata/eg-cases/R1-cod.txt |only ss3sim-0.8.2/ss3sim/inst/extdata/eg-cases/lcomp100-cod.txt |only ss3sim-0.8.2/ss3sim/inst/extdata/models/fla-em |only ss3sim-0.8.2/ss3sim/inst/extdata/models/fla-om |only ss3sim-0.8.2/ss3sim/inst/extdata/models/sar-em |only ss3sim-0.8.2/ss3sim/inst/extdata/models/sar-om |only ss3sim-0.8.2/ss3sim/inst/ss3-tests |only ss3sim-0.8.2/ss3sim/inst/tests |only ss3sim-0.8.2/ss3sim/man/figures |only ss3sim-0.8.2/ss3sim/man/is_f.Rd |only ss3sim-0.8.2/ss3sim/vignettes/README.md |only ss3sim-0.8.2/ss3sim/vignettes/file-structure.pdf |only ss3sim-0.8.2/ss3sim/vignettes/github.css |only ss3sim-0.8.2/ss3sim/vignettes/knit |only ss3sim-0.8.2/ss3sim/vignettes/solarized-light.css |only ss3sim-0.8.2/ss3sim/vignettes/ss3sim-vignette.Rnw |only ss3sim-0.9.0/ss3sim/DESCRIPTION | 31 ss3sim-0.9.0/ss3sim/LICENSE | 9 ss3sim-0.9.0/ss3sim/MD5 | 304 +- ss3sim-0.9.0/ss3sim/NAMESPACE | 70 ss3sim-0.9.0/ss3sim/R/add_nulls.R |only ss3sim-0.9.0/ss3sim/R/bias_ss3.r | 38 ss3sim-0.9.0/ss3sim/R/calculate_re.R |only ss3sim-0.9.0/ss3sim/R/case-parsing.r | 98 ss3sim-0.9.0/ss3sim/R/case-write.R |only ss3sim-0.9.0/ss3sim/R/change_data.r |only ss3sim-0.9.0/ss3sim/R/change_e.r | 235 +- ss3sim-0.9.0/ss3sim/R/change_em_binning.r |only ss3sim-0.9.0/ss3sim/R/change_f.r | 45 ss3sim-0.9.0/ss3sim/R/change_fltname.r |only ss3sim-0.9.0/ss3sim/R/change_lcomp_constant.R |only ss3sim-0.9.0/ss3sim/R/change_maturity.R |only ss3sim-0.9.0/ss3sim/R/change_rec_devs.r | 31 ss3sim-0.9.0/ss3sim/R/change_retro.r | 16 ss3sim-0.9.0/ss3sim/R/change_tail_compression.R |only ss3sim-0.9.0/ss3sim/R/change_tv.r | 64 ss3sim-0.9.0/ss3sim/R/change_year.R |only ss3sim-0.9.0/ss3sim/R/clean_data.r |only ss3sim-0.9.0/ss3sim/R/copy_ss3models.r | 57 ss3sim-0.9.0/ss3sim/R/create_argfiles.r | 20 ss3sim-0.9.0/ss3sim/R/expand_scenarios.r | 4 ss3sim-0.9.0/ss3sim/R/extract_expected_data.r | 17 ss3sim-0.9.0/ss3sim/R/fill_across.r |only ss3sim-0.9.0/ss3sim/R/get-results.r | 560 +++- ss3sim-0.9.0/ss3sim/R/get_bin.R |only ss3sim-0.9.0/ss3sim/R/get_bin_info.r |only ss3sim-0.9.0/ss3sim/R/growth_estimation.R |only ss3sim-0.9.0/ss3sim/R/make_dummy_data.r |only ss3sim-0.9.0/ss3sim/R/plot_functions.R |only ss3sim-0.9.0/ss3sim/R/profile_fmsy.r |only ss3sim-0.9.0/ss3sim/R/run_bias_ss3.r | 14 ss3sim-0.9.0/ss3sim/R/run_ss3model.r | 69 ss3sim-0.9.0/ss3sim/R/run_ss3sim.r | 183 + ss3sim-0.9.0/ss3sim/R/sample_agecomp.R |only ss3sim-0.9.0/ss3sim/R/sample_calcomp.R |only ss3sim-0.9.0/ss3sim/R/sample_index.r |only ss3sim-0.9.0/ss3sim/R/sample_lcomp.R |only ss3sim-0.9.0/ss3sim/R/sample_mlacomp.R |only ss3sim-0.9.0/ss3sim/R/sample_wtatage.R |only ss3sim-0.9.0/ss3sim/R/setup_parallel.r | 17 ss3sim-0.9.0/ss3sim/R/ss3sim.r | 28 ss3sim-0.9.0/ss3sim/R/ss3sim_base.r | 484 ++-- ss3sim-0.9.0/ss3sim/R/standardize_bounds.R |only ss3sim-0.9.0/ss3sim/R/verify_input.r | 1 ss3sim-0.9.0/ss3sim/README.md | 87 ss3sim-0.9.0/ss3sim/build/vignette.rds |binary ss3sim-0.9.0/ss3sim/data/scalar_dat.rda |binary ss3sim-0.9.0/ss3sim/data/ts_dat.rda |binary ss3sim-0.9.0/ss3sim/inst/CITATION | 27 ss3sim-0.9.0/ss3sim/inst/doc/introduction.R |only ss3sim-0.9.0/ss3sim/inst/doc/introduction.Rmd |only ss3sim-0.9.0/ss3sim/inst/doc/introduction.html |only ss3sim-0.9.0/ss3sim/inst/doc/making-functions.Rmd |only ss3sim-0.9.0/ss3sim/inst/doc/making-functions.html |only ss3sim-0.9.0/ss3sim/inst/doc/making-models.Rmd |only ss3sim-0.9.0/ss3sim/inst/doc/making-models.html |only ss3sim-0.9.0/ss3sim/inst/doc/modifying-models.Rmd |only ss3sim-0.9.0/ss3sim/inst/doc/modifying-models.html |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/agecomp0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/agecomp2-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/data0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/index0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/index2-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/lcomp0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/lcomp1-cod.txt | 1 ss3sim-0.9.0/ss3sim/inst/extdata/cases/lcomp1-fla.txt | 1 ss3sim-0.9.0/ss3sim/inst/extdata/cases/lcomp1-sar.txt | 1 ss3sim-0.9.0/ss3sim/inst/extdata/cases/lcomp2-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/F0-cod.txt | 11 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/agecomp0-cod.txt | 9 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/agecomp1-cod.txt | 9 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/agecomp100-cod.txt | 9 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/index0-cod.txt | 4 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/index1-cod.txt | 2 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/index100-cod.txt | 2 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/lcomp0-cod.txt | 9 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/lcomp1-cod.txt | 9 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/retro0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/retro1-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/tail_compression0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/tail_compression1-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-em/codEM.ctl | 176 - ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-em/forecast.ss | 92 ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-em/starter.ss | 21 ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-om/codOM.ctl | 406 ++- ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-om/codOM.dat | 1163 +++++----- ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-om/forecast.ss | 92 ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-om/ss3.par | 248 +- ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-om/starter.ss | 21 ss3sim-0.9.0/ss3sim/inst/extdata/output |only ss3sim-0.9.0/ss3sim/man/add_nulls.Rd |only ss3sim-0.9.0/ss3sim/man/bias_ss3.Rd | 50 ss3sim-0.9.0/ss3sim/man/calculate_data_units.Rd |only ss3sim-0.9.0/ss3sim/man/calculate_re.Rd |only ss3sim-0.9.0/ss3sim/man/calculate_runtime.Rd | 22 ss3sim-0.9.0/ss3sim/man/case_comp.Rd |only ss3sim-0.9.0/ss3sim/man/case_deparse.Rd |only ss3sim-0.9.0/ss3sim/man/case_fishing.Rd |only ss3sim-0.9.0/ss3sim/man/case_index.Rd |only ss3sim-0.9.0/ss3sim/man/case_tv.Rd |only ss3sim-0.9.0/ss3sim/man/change_agecomp.Rd | 127 - ss3sim-0.9.0/ss3sim/man/change_data.Rd |only ss3sim-0.9.0/ss3sim/man/change_e.Rd | 196 - ss3sim-0.9.0/ss3sim/man/change_em_binning.Rd |only ss3sim-0.9.0/ss3sim/man/change_f.Rd | 59 ss3sim-0.9.0/ss3sim/man/change_fltname.Rd |only ss3sim-0.9.0/ss3sim/man/change_index.Rd | 87 ss3sim-0.9.0/ss3sim/man/change_lcomp.Rd | 126 - ss3sim-0.9.0/ss3sim/man/change_lcomp_constant.Rd |only ss3sim-0.9.0/ss3sim/man/change_maturity.Rd |only ss3sim-0.9.0/ss3sim/man/change_rec_devs.Rd | 28 ss3sim-0.9.0/ss3sim/man/change_retro.Rd | 45 ss3sim-0.9.0/ss3sim/man/change_tail_compression.Rd |only ss3sim-0.9.0/ss3sim/man/change_tv.Rd | 154 - ss3sim-0.9.0/ss3sim/man/change_year.Rd |only ss3sim-0.9.0/ss3sim/man/check_data.Rd |only ss3sim-0.9.0/ss3sim/man/clean_data.Rd |only ss3sim-0.9.0/ss3sim/man/cleanup_ss3.Rd | 13 ss3sim-0.9.0/ss3sim/man/copy_ss3models.Rd | 51 ss3sim-0.9.0/ss3sim/man/create_argfiles.Rd | 77 ss3sim-0.9.0/ss3sim/man/expand_scenarios.Rd | 14 ss3sim-0.9.0/ss3sim/man/extract_expected_data.Rd | 14 ss3sim-0.9.0/ss3sim/man/facet_form.Rd |only ss3sim-0.9.0/ss3sim/man/fill_across.Rd |only ss3sim-0.9.0/ss3sim/man/get_args.Rd | 8 ss3sim-0.9.0/ss3sim/man/get_bin.Rd |only ss3sim-0.9.0/ss3sim/man/get_bin_info.Rd |only ss3sim-0.9.0/ss3sim/man/get_caseargs.Rd | 133 - ss3sim-0.9.0/ss3sim/man/get_caseval.Rd | 12 ss3sim-0.9.0/ss3sim/man/get_fish600_casefolder.Rd | 7 ss3sim-0.9.0/ss3sim/man/get_model_folder.Rd | 21 ss3sim-0.9.0/ss3sim/man/get_nll_components.Rd |only ss3sim-0.9.0/ss3sim/man/get_recdevs.Rd | 18 ss3sim-0.9.0/ss3sim/man/get_results_all.Rd | 115 ss3sim-0.9.0/ss3sim/man/get_results_derived.Rd |only ss3sim-0.9.0/ss3sim/man/get_results_scalar.Rd | 20 ss3sim-0.9.0/ss3sim/man/get_results_scenario.Rd | 48 ss3sim-0.9.0/ss3sim/man/get_results_timeseries.Rd | 18 ss3sim-0.9.0/ss3sim/man/get_sigmar.Rd | 11 ss3sim-0.9.0/ss3sim/man/id_scenarios.Rd |only ss3sim-0.9.0/ss3sim/man/pastef.Rd | 4 ss3sim-0.9.0/ss3sim/man/plot_scalar_boxplot.Rd |only ss3sim-0.9.0/ss3sim/man/plot_scalar_points.Rd |only ss3sim-0.9.0/ss3sim/man/plot_ts_boxplot.Rd |only ss3sim-0.9.0/ss3sim/man/plot_ts_lines.Rd |only ss3sim-0.9.0/ss3sim/man/plot_ts_points.Rd |only ss3sim-0.9.0/ss3sim/man/profile_fmsy.Rd |only ss3sim-0.9.0/ss3sim/man/rename_ss3_files.Rd |only ss3sim-0.9.0/ss3sim/man/run_bias_ss3.Rd | 76 ss3sim-0.9.0/ss3sim/man/run_ss3model.Rd | 101 ss3sim-0.9.0/ss3sim/man/run_ss3sim.Rd | 218 - ss3sim-0.9.0/ss3sim/man/sample_agecomp.Rd |only ss3sim-0.9.0/ss3sim/man/sample_calcomp.Rd |only ss3sim-0.9.0/ss3sim/man/sample_index.Rd |only ss3sim-0.9.0/ss3sim/man/sample_lcomp.Rd |only ss3sim-0.9.0/ss3sim/man/sample_mlacomp.Rd |only ss3sim-0.9.0/ss3sim/man/sample_wtatage.Rd |only ss3sim-0.9.0/ss3sim/man/sanitize_admb_options.Rd | 10 ss3sim-0.9.0/ss3sim/man/scalar_dat.Rd | 2 ss3sim-0.9.0/ss3sim/man/setup_parallel.Rd | 2 ss3sim-0.9.0/ss3sim/man/ss3sim.Rd | 150 - ss3sim-0.9.0/ss3sim/man/ss3sim_base.Rd | 294 +- ss3sim-0.9.0/ss3sim/man/standardize_bounds.Rd |only ss3sim-0.9.0/ss3sim/man/substr_r.Rd | 7 ss3sim-0.9.0/ss3sim/man/ts_dat.Rd | 2 ss3sim-0.9.0/ss3sim/man/vbgf_func.Rd |only ss3sim-0.9.0/ss3sim/man/verify_input.Rd | 30 ss3sim-0.9.0/ss3sim/man/verify_plot_arguments.Rd |only ss3sim-0.9.0/ss3sim/vignettes/cjfas.csl |only ss3sim-0.9.0/ss3sim/vignettes/filestructure.png |only ss3sim-0.9.0/ss3sim/vignettes/introduction.Rmd |only ss3sim-0.9.0/ss3sim/vignettes/making-functions.Rmd |only ss3sim-0.9.0/ss3sim/vignettes/making-models.Rmd |only ss3sim-0.9.0/ss3sim/vignettes/modifying-models.Rmd |only ss3sim-0.9.0/ss3sim/vignettes/refs.bib | 146 + 202 files changed, 4046 insertions(+), 3265 deletions(-)
Title: Automated Schema on Read
Description: Provides schema-on-read tools including a single function call (e.g., schemaOnRead('filename')) that reads text ('TXT'), comma separated value ('CSV'), raster image ('BMP', 'PNG', 'GIF', 'TIFF', and 'JPG'), R data ('RDS'), HDF5 ('H5'), NetCDF ('CS'), spreadsheet ('XLS', 'XLSX', 'ODS', and 'DIF'), Weka Attribute-Relation File Format ('ARFF'), Epi Info ('REC'), SPSS ('SAV'), Systat ('SYS'), and Stata ('DTA') files. It also recursively reads folders (e.g., schemaOnRead('folder')), returning a nested list of the contained elements.
Author: Michael North [aut, cre]
Maintainer: Michael North <north@anl.gov>
Diff between SchemaOnRead versions 1.0.1 dated 2015-11-03 and 1.0.2 dated 2015-12-24
SchemaOnRead-1.0.1/SchemaOnRead/man/schemaOnReadDefaultProcessors.Rd |only SchemaOnRead-1.0.1/SchemaOnRead/man/schemaOnReadSimpleProcessors.Rd |only SchemaOnRead-1.0.2/SchemaOnRead/DESCRIPTION | 16 SchemaOnRead-1.0.2/SchemaOnRead/MD5 | 93 - SchemaOnRead-1.0.2/SchemaOnRead/NAMESPACE | 77 - SchemaOnRead-1.0.2/SchemaOnRead/NEWS.md | 17 SchemaOnRead-1.0.2/SchemaOnRead/R/CheckExtensions.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/DefaultProcessors.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessARFFFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessBitmapFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessCSVFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessDBFFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessDIFFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessDefaultFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessDirectory.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessEPIINFOFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessGIFFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessHTMLFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessNetCDFandHDF5.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessODSFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessPajekFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessRDSFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessSASFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessSPSSFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessStataFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessSystatFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessTIFFFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessTextFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessXLSandXLSXFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessXMLFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/SchemaOnRead.R | 700 ---------- SchemaOnRead-1.0.2/SchemaOnRead/R/SimpleProcessors.R |only SchemaOnRead-1.0.2/SchemaOnRead/README.md | 4 SchemaOnRead-1.0.2/SchemaOnRead/inst/Data.xyz |only SchemaOnRead-1.0.2/SchemaOnRead/inst/doc/vignettes.Rmd | 101 - SchemaOnRead-1.0.2/SchemaOnRead/inst/doc/vignettes.html | 248 --- SchemaOnRead-1.0.2/SchemaOnRead/inst/extdata/dir1/Data2.xls |binary SchemaOnRead-1.0.2/SchemaOnRead/man/checkExtensions.Rd |only SchemaOnRead-1.0.2/SchemaOnRead/man/defaultProcessors.Rd |only SchemaOnRead-1.0.2/SchemaOnRead/man/schemaOnRead.Rd | 8 SchemaOnRead-1.0.2/SchemaOnRead/man/simpleProcessors.Rd |only SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat.R | 6 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.01.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.02.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.03.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.04.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.05.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.06.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.07.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.08.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.09.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.10.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.11.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.12.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.13.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.14.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.15.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.16.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.17.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.18.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.19.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.20.R | 39 SchemaOnRead-1.0.2/SchemaOnRead/vignettes/vignettes.Rmd | 101 - 63 files changed, 361 insertions(+), 1238 deletions(-)
Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI
data. It is best suited to data from a Freesurfer analysis (cortical
thickness, volumes, local gyrification index, surface area), but also works
with e.g., tractography data from FSL. It contains a graphical user
interface for graph visualization and data exploration.
Author: Christopher G. Watson <cgwatson@bu.edu>
Maintainer: Christopher G. Watson <cgwatson@bu.edu>
Diff between brainGraph versions 0.48.0 dated 2015-12-09 and 0.55.0 dated 2015-12-24
DESCRIPTION | 13 +- MD5 | 161 +++++++++++++++++++------------------ NAMESPACE | 10 +- R/assign_lobes.R | 17 ++- R/boot_global.R | 68 +++++++-------- R/brainGraph_init.R | 44 +++++++++- R/centr_lev.R | 3 R/check_resid.R | 2 R/choose_edges.R | 8 - R/corr_matrix.R | 12 +- R/count_homologous.R | 7 + R/count_interlobar.R | 19 ++-- R/dti_create_mats.R | 9 +- R/edge_asymmetry.R | 39 +++++--- R/get_resid.R | 88 ++++++++++++++------ R/graph_contract_brain.R | 5 - R/graph_efficiency.R | 39 ++++++-- R/individ_contrib.R |only R/part_coeff.R | 22 +++-- R/permute_group.R | 21 ++-- R/plot_boot.R |only R/plot_corr_mat.R | 4 R/plot_perm_diffs.R | 4 R/plot_rich_norm.R |only R/rich_club_coeff.R | 3 R/rich_club_norm.R | 3 R/rich_core.R | 6 + R/robustness.R | 8 - R/set_brainGraph_attributes.R | 5 - R/sim_rand_graph_par.R | 6 - R/small_world.R | 9 -- R/spatial_dist.R | 8 + R/vertex_attr_dt.R | 33 ++----- R/vulnerability.R | 3 R/within_module_degree_z_score.R | 3 man/aop.Rd |only man/assign_lobes.Rd | 9 +- man/boot_global.Rd | 23 ++--- man/brainGraph_init.Rd | 3 man/centr_lev.Rd | 2 man/check.resid.Rd | 4 man/choose.edges.Rd | 2 man/color.edges.Rd | 2 man/color.vertices.Rd | 2 man/corr.matrix.Rd | 2 man/count_homologous.Rd | 2 man/count_interlobar.Rd | 9 -- man/dti_create_mats.Rd | 9 +- man/edge_asymmetry.Rd | 2 man/get.resid.Rd | 31 ++++--- man/graph.contract.brain.Rd | 2 man/graph.efficiency.Rd | 8 + man/graph_attr_dt.Rd | 2 man/graph_neighborhood_multiple.Rd | 2 man/group.graph.diffs.Rd | 2 man/loo.Rd |only man/part.coeff.Rd | 2 man/permute.group.Rd | 11 -- man/permute.vertex.Rd | 2 man/plot_boot.Rd |only man/plot_brainGraph.Rd | 2 man/plot_brainGraph_gui.Rd | 2 man/plot_brainGraph_list.Rd | 2 man/plot_brainGraph_mni.Rd | 2 man/plot_corr_mat.Rd | 2 man/plot_group_means.Rd | 2 man/plot_perm_diffs.Rd | 6 - man/plot_rich_norm.Rd |only man/plot_vertex_measures.Rd | 2 man/rich.club.coeff.Rd | 2 man/rich.club.norm.Rd | 2 man/rich.core.Rd | 2 man/robustness.Rd | 2 man/rotation.Rd | 2 man/set.brainGraph.attributes.Rd | 2 man/sim.rand.graph.clust.Rd | 2 man/sim.rand.graph.par.Rd | 2 man/small.world.Rd | 2 man/spatial.dist.Rd | 2 man/update_brainGraph_gui.Rd | 2 man/vec.transform.Rd | 2 man/vertex_attr_dt.Rd | 2 man/vulnerability.Rd | 2 man/within_module_deg_z_score.Rd | 2 man/write.brainnet.Rd | 2 85 files changed, 505 insertions(+), 362 deletions(-)