Title: Additional Matrix Functionality
Description: Additional matrix functionality for R including: (1) wrappers
for the base matrix function that allows matrices to be created from character
strings and lists (the former is especially useful for creating block
matrices), (ii) better default printing of large matrices, and (iii) a number
of convenience functions for users more familiar with other scientific
languages like Julia, Matlab/Octave, or Python+NumPy.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between ramify versions 0.2.0 dated 2015-04-13 and 0.3.0 dated 2015-06-07
ramify-0.2.0/ramify/man/as.mat.Rd |only ramify-0.2.0/ramify/man/print.mat.Rd |only ramify-0.3.0/ramify/DESCRIPTION | 12 ramify-0.3.0/ramify/MD5 | 75 ++- ramify-0.3.0/ramify/NAMESPACE | 68 +-- ramify-0.3.0/ramify/NEWS | 12 ramify-0.3.0/ramify/R/bmat.R | 16 ramify-0.3.0/ramify/R/convenience.R | 370 ++++++++++++------ ramify-0.3.0/ramify/R/dmat.R | 8 ramify-0.3.0/ramify/R/mat.R | 190 +-------- ramify-0.3.0/ramify/R/pprint.R |only ramify-0.3.0/ramify/R/ramify.R | 2 ramify-0.3.0/ramify/R/utils.R | 21 - ramify-0.3.0/ramify/R/zzz.R | 7 ramify-0.3.0/ramify/README.md | 18 ramify-0.3.0/ramify/man/add_dots.Rd | 2 ramify-0.3.0/ramify/man/argmax.Rd | 2 ramify-0.3.0/ramify/man/atleast_2d.Rd |only ramify-0.3.0/ramify/man/bmat.Rd | 12 ramify-0.3.0/ramify/man/desc_mat.Rd | 2 ramify-0.3.0/ramify/man/dmat.Rd | 4 ramify-0.3.0/ramify/man/eye.Rd | 5 ramify-0.3.0/ramify/man/fill.Rd | 22 - ramify-0.3.0/ramify/man/flatten.Rd | 6 ramify-0.3.0/ramify/man/hcat.Rd | 7 ramify-0.3.0/ramify/man/inv.Rd | 6 ramify-0.3.0/ramify/man/is.tril.Rd |only ramify-0.3.0/ramify/man/is.triu.Rd |only ramify-0.3.0/ramify/man/linspace.Rd | 4 ramify-0.3.0/ramify/man/logspace.Rd | 2 ramify-0.3.0/ramify/man/mat.Rd | 13 ramify-0.3.0/ramify/man/meshgrid.Rd |only ramify-0.3.0/ramify/man/pprint.Rd |only ramify-0.3.0/ramify/man/ramify.Rd | 4 ramify-0.3.0/ramify/man/rand.Rd | 14 ramify-0.3.0/ramify/man/randi.Rd | 12 ramify-0.3.0/ramify/man/randn.Rd | 14 ramify-0.3.0/ramify/man/resize.Rd | 5 ramify-0.3.0/ramify/man/size.Rd | 9 ramify-0.3.0/ramify/man/tr.Rd |only ramify-0.3.0/ramify/man/tri.Rd |only ramify-0.3.0/ramify/man/tril.Rd |only ramify-0.3.0/ramify/man/triu.Rd |only ramify-0.3.0/ramify/tests/testthat/test-convenience.R |only ramify-0.3.0/ramify/tests/testthat/test-mat.R | 46 -- 45 files changed, 501 insertions(+), 489 deletions(-)
Title: Data Analysis in Ecology
Description: Miscellaneous functions for data analysis in ecology, with special emphasis on spatial data.
Author: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Maintainer: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Diff between pgirmess versions 1.6.1 dated 2015-06-06 and 1.6.2 dated 2015-06-07
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/QGIS2sp.R | 1 - man/PermTest.rd | 9 +++++---- man/QGIS2sp.Rd | 13 +++++-------- man/gps2gpx.rd | 1 + man/readVista.rd | 5 ++++- man/rmls.rd | 4 +--- man/uploadGPS.rd | 1 + 9 files changed, 30 insertions(+), 30 deletions(-)
Title: Introductory Statistics with R
Description: Data sets and scripts for text examples and exercises in
P. Dalgaard (2008), `Introductory Statistics with R', 2nd ed., Springer Verlag, ISBN 978-0387790534.
Author: Peter Dalgaard
Maintainer: Peter Dalgaard <pd.mes@cbs.dk>
Diff between ISwR versions 2.0-6 dated 2012-03-22 and 2.0-7 dated 2015-06-07
DESCRIPTION | 14 - MD5 | 6 tests/allexercises.Rout.save | 410 ++++++++++++++++----------------- tests/allscripts.Rout.save | 534 +++++++++++++++++++++---------------------- 4 files changed, 487 insertions(+), 477 deletions(-)
Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut],
Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between boot versions 1.3-15 dated 2015-02-11 and 1.3-16 dated 2015-06-07
ChangeLog | 6 +++++- DESCRIPTION | 8 ++++---- MD5 | 6 +++--- tests/Examples/boot-Ex.Rout.save | 19 +++++++++---------- 4 files changed, 21 insertions(+), 18 deletions(-)
Title: Visual Data Mining Tools for R
Description: This provides web-based visual data-mining tools by adding
interactive functions to 'ggplot2' graphics. Brushing and linking between the
multiple plots is one of the main feature of this package. Currently
scatter plots, histograms, parallel coordinate plots and choropleth maps are
supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>
Diff between vdmR versions 0.1.0 dated 2014-09-20 and 0.1.1 dated 2015-06-07
vdmR-0.1.0/vdmR/inst/tests/vdmR-test.R |only vdmR-0.1.1/vdmR/DESCRIPTION | 14 ++++---- vdmR-0.1.1/vdmR/MD5 | 38 +++++++++++----------- vdmR-0.1.1/vdmR/NAMESPACE | 2 - vdmR-0.1.1/vdmR/R/misc.R | 6 +-- vdmR-0.1.1/vdmR/R/vcmap.R | 5 ++ vdmR-0.1.1/vdmR/R/vhist.R | 15 ++++---- vdmR-0.1.1/vdmR/R/vlaunch.R | 50 ++++++++++++++++------------- vdmR-0.1.1/vdmR/R/vpcp.R | 7 +++- vdmR-0.1.1/vdmR/R/vscat.R | 10 ++++- vdmR-0.1.1/vdmR/build/vignette.rds |binary vdmR-0.1.1/vdmR/inst/doc/vdmR-vignette.pdf |binary vdmR-0.1.1/vdmR/inst/tests/test-vdmR.R |only vdmR-0.1.1/vdmR/man/kw2011.Rd | 3 + vdmR-0.1.1/vdmR/man/vcmap.Rd | 3 + vdmR-0.1.1/vdmR/man/vdmR-package.Rd | 3 + vdmR-0.1.1/vdmR/man/vhist.Rd | 3 + vdmR-0.1.1/vdmR/man/vlaunch.Rd | 3 + vdmR-0.1.1/vdmR/man/vpcp.Rd | 3 + vdmR-0.1.1/vdmR/man/vscat.Rd | 3 + vdmR-0.1.1/vdmR/man/vsfuk2012.Rd | 3 + 21 files changed, 99 insertions(+), 72 deletions(-)
Title: Tools Inspired by Stata to Manipulate Tabular Data
Description: A set of tools to explore data.frames (summarize,
tabulate, xtile, pctile, binscatter) and work with panel data (elapsed
quarters/month, lead/lag, fill in rows of values, rolling functions).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>
Diff between statar versions 0.2 dated 2015-06-03 and 0.3.0 dated 2015-06-07
statar-0.2/statar/R/demean.R |only statar-0.2/statar/R/floor_date.R |only statar-0.2/statar/R/vars.R |only statar-0.2/statar/man/demean.Rd |only statar-0.2/statar/man/floor_date.Rd |only statar-0.2/statar/man/graph.Rd |only statar-0.2/statar/man/vars.Rd |only statar-0.3.0/statar/DESCRIPTION | 23 statar-0.3.0/statar/MD5 | 82 +-- statar-0.3.0/statar/NAMESPACE | 48 +- statar-0.3.0/statar/R/count_combinations.R | 72 +-- statar-0.3.0/statar/R/elapsed_dates.R | 4 statar-0.3.0/statar/R/find_duplicates.R | 20 statar-0.3.0/statar/R/fuzzy_join.R | 172 +++---- statar-0.3.0/statar/R/graph.R | 251 ---------- statar-0.3.0/statar/R/group.R |only statar-0.3.0/statar/R/join.R | 16 statar-0.3.0/statar/R/pctile.R |only statar-0.3.0/statar/R/stat_binmean.R |only statar-0.3.0/statar/R/statar.R | 39 + statar-0.3.0/statar/R/sum_up.R | 41 - statar-0.3.0/statar/R/tab.R | 58 +- statar-0.3.0/statar/R/utils.R | 508 +++++++++++++++------- statar-0.3.0/statar/R/xtile.R | 53 -- statar-0.3.0/statar/README.md | 26 + statar-0.3.0/statar/build/vignette.rds |binary statar-0.3.0/statar/inst/doc/macros.html | 242 +--------- statar-0.3.0/statar/inst/doc/merge-records.html | 296 +++--------- statar-0.3.0/statar/inst/doc/panel-data.html | 364 +++++---------- statar-0.3.0/statar/inst/doc/summary.Rmd | 73 --- statar-0.3.0/statar/inst/doc/summary.html | 398 +++-------------- statar-0.3.0/statar/inst/doc/vector.Rmd | 12 statar-0.3.0/statar/inst/doc/vector.html | 254 +++-------- statar-0.3.0/statar/man/compute_distance.Rd | 13 statar-0.3.0/statar/man/count_combinations.Rd | 11 statar-0.3.0/statar/man/find_duplicates.Rd | 6 statar-0.3.0/statar/man/fuzzy_join.Rd | 34 - statar-0.3.0/statar/man/group.Rd |only statar-0.3.0/statar/man/join.Rd | 10 statar-0.3.0/statar/man/pctile.Rd |only statar-0.3.0/statar/man/stat_binmean.Rd |only statar-0.3.0/statar/man/tab.Rd | 10 statar-0.3.0/statar/man/xtile.Rd | 4 statar-0.3.0/statar/tests/testthat/test_elapsed.R | 3 statar-0.3.0/statar/vignettes/output_2_0.png |binary statar-0.3.0/statar/vignettes/output_3_0.png |binary statar-0.3.0/statar/vignettes/output_4_0.png |only statar-0.3.0/statar/vignettes/summary.Rmd | 73 --- statar-0.3.0/statar/vignettes/vector.Rmd | 12 49 files changed, 1161 insertions(+), 2067 deletions(-)
Title: Simulating the Evolution of Biological Sequences
Description: A coalescent simulator that allows the rapid simulation of
biological sequences under neutral models of evolution. Different to
other coalescent based simulations, it has an optional approximation
parameter that allows for high accuracy while maintaining a linear run time
cost for long sequences. It is optimized for simulating massive data sets as
produced by Next-Generation Sequencing technologies for up to several thousand
sequences.
Author: Paul Staab [aut, cre, cph],
Zhu Sha [aut, cph],
Dirk Metzler [aut, cph, ths],
Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between scrm versions 1.5.0-1 dated 2015-04-11 and 1.6.0-2 dated 2015-06-07
DESCRIPTION | 22 MD5 | 60 +- NAMESPACE | 2 NEWS | 25 - README.md | 25 - build/vignette.rds |binary inst/CITATION | 11 inst/doc/scrm-Arguments.Rmd | 9 inst/doc/scrm-Arguments.html | 12 inst/doc/scrm-TreesForApe.R | 2 inst/doc/scrm-TreesForApe.html | 4 man/scrm-package.Rd | 2 man/scrm.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 src/scrm/forest.cc | 110 ++-- src/scrm/forest.h | 56 +- src/scrm/model.cc | 539 ++++++++++------------- src/scrm/model.h | 181 +++---- src/scrm/node.cc | 10 src/scrm/node.h | 22 src/scrm/param.cc | 187 +++---- src/scrm/param.h | 86 +-- src/scrm/summary_statistics/frequency_spectrum.h | 4 src/scrm/summary_statistics/newick_tree.cc | 41 - src/scrm/summary_statistics/newick_tree.h | 88 +-- src/scrm/summary_statistics/oriented_forest.cc | 2 src/scrm/summary_statistics/oriented_forest.h | 59 +- src/scrmr.cpp | 5 src/summary_statistics.cpp | 36 - vignettes/scrm-Arguments.Rmd | 9 31 files changed, 798 insertions(+), 817 deletions(-)
Title: Functions for Time Series Analysis
Description: Includes non-parametric estimators and tests for time series analysis. The functions allow to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
Author: Vyacheslav Lyubchich <lyubchic@cbl.umces.edu>;
Yulia R. Gel <ygl@utdallas.edu>;
Xingyu Wang <x263wang@uwaterloo.ca>
Maintainer: Vyacheslav Lyubchich <lyubchic@cbl.umces.edu>
Diff between funtimes versions 1.0 dated 2015-01-27 and 1.1 dated 2015-06-07
DESCRIPTION | 8 ++--- MD5 | 8 ++--- R/sync.test.R | 86 ++++++++++++++++++++++++++++++------------------------- R/wavk.test.R | 2 - man/sync.test.Rd | 7 ++-- 5 files changed, 61 insertions(+), 50 deletions(-)
Title: Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves
Description: Implements a very fast C++ algorithm to quickly bootstrap
receiver operating characteristics (ROC) curves and derived performance metrics, including the area under the
curve (AUC) as well as the true and false positive rate.
You can also plot the results and calculate confidence intervals.
Currently the calculation of 100000 bootstrap replicates for 500 observations
takes about one second.
Author: Erik Peter [aut, cre]
Maintainer: Erik Peter <jerikpeter@googlemail.com>
Diff between fbroc versions 0.2.0 dated 2015-06-05 and 0.2.1 dated 2015-06-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/fbroc.methods.R | 2 +- src/roc.cpp | 12 ++++++------ 4 files changed, 14 insertions(+), 14 deletions(-)
Title: Conditional Maximum Likelihood for Quadratic Exponential Models
for Binary Panel Data
Description: Estimation, based on conditional maximum likelihood, of the quadratic exponential model proposed by Bartolucci, F. & Nigro, V. (2010, Econometrica) and of a simplified and a modified version of this model. The quadratic exponential model is suitable for the analysis of binary longitudinal data when state dependence (further to the effect of the covariates and a time-fixed individual intercept) has to be taken into account. Therefore, this is an alternative to the dynamic logit model having the advantage of easily allowing conditional inference in order to eliminate the individual intercepts and then getting consistent estimates of the parameters of main interest (for the covariates and the lagged response). The simplified version of this model does not distinguish, as the original model does, between the last time occasion and the previous occasions. The modified version formulates in a different way the interaction terms and it may be used to test in a easy way state dependence as shown in Bartolucci, F., Nigro, V. & Pigini, C. (2013, Econometric Reviews). The package also includes estimation of the dynamic logit model by a pseudo conditional estimator based on the quadratic exponential model, as proposed by Bartolucci, F. & Nigro, V. (2012, Journal of Econometrics).
Author: Francesco Bartolucci (University of Perugia), Claudia Pigini (University of Perugia)
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between cquad versions 1.0 dated 2015-01-05 and 1.1 dated 2015-06-07
cquad-1.0/cquad/data/PSID.RData |only cquad-1.0/cquad/man/PSID.Rd |only cquad-1.1/cquad/DESCRIPTION | 14 +++++++------- cquad-1.1/cquad/MD5 | 26 +++++++++++++------------- cquad-1.1/cquad/NAMESPACE | 5 +++++ cquad-1.1/cquad/R/cquad_pseudo.R | 5 +++-- cquad-1.1/cquad/data/data_sim.RData |only cquad-1.1/cquad/man/cquad-package.Rd | 18 +++++++++--------- cquad-1.1/cquad/man/cquad_basic.Rd | 10 +++++----- cquad-1.1/cquad/man/cquad_equ.Rd | 10 +++++----- cquad-1.1/cquad/man/cquad_ext.Rd | 10 +++++----- cquad-1.1/cquad/man/cquad_pseudo.Rd | 13 +++++-------- cquad-1.1/cquad/man/data_sim.Rd |only cquad-1.1/cquad/man/print.cquad.Rd | 2 +- cquad-1.1/cquad/man/sim_panel_logit.Rd | 4 ++-- cquad-1.1/cquad/man/summary.cquad.Rd | 2 +- 16 files changed, 61 insertions(+), 58 deletions(-)