Title: Multiple Sequence Alignment
Diff between muscle versions 3.8.31-2 dated 2014-05-07 and 3.8.31-3 dated 2014-07-04
Description: MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.
Author: Algorithm by Robert C. Edgar. R port by Alex T. Kalinka.
Maintainer: Alex T. Kalinka
DESCRIPTION | 6 +++---
MD5 | 11 ++++++-----
R/muscle_main.R | 17 +++++++++++++++++
man/XStringSet2fasta.Rd |only
src/clustset.h | 4 ++--
src/globalslinux.cpp | 2 +-
src/handle_fasta.cpp | 6 +++---
7 files changed, 32 insertions(+), 14 deletions(-)
Title: Dynamic slicing
Diff between dslice versions 1.0 dated 2014-07-01 and 1.0.2 dated 2014-07-04
Description: Dynamic slicing is a method designed for dependency detection between a categorical variable and a continuous variable. It could be applied for non-parametric hypothesis testing and gene set enrichment analysis.
Author: Chao Ye and Bo Jiang
Maintainer: Chao Ye
DESCRIPTION | 6 ++--
MD5 | 14 ++++-----
src/ds_1.cpp | 10 +++----
src/ds_eqp_1.cpp | 10 +++----
src/ds_eqp_k.cpp | 22 +++++++--------
src/ds_k.cpp | 6 ++--
src/dslice_eqp_k.cpp | 72 +++++++++++++++++++++++++--------------------------
src/dslice_k.cpp | 46 ++++++++++++++++----------------
8 files changed, 93 insertions(+), 93 deletions(-)
Title: Analyze shot group data
Diff between shotGroups versions 0.4 dated 2014-03-03 and 0.5 dated 2014-07-04
Description: Analyzes shooting data with respect to group shape,
precision, and accuracy. This includes graphical methods,
descriptive statistics, and inference tests using standard,
but also nonparametric and robust statistical methods. Works
with files exported by OnTarget PC and OnTarget TDS or with
custom data files in text format with a similar structure.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger
DESCRIPTION | 8 -
MD5 | 81 ++++++++--------
NAMESPACE | 4
R/compareGroups.R | 209 ++++++++++++++++++++++++++++++++++++++++++
R/draw.R | 2
R/drawGroup.R | 2
R/getCEP.R | 25 ++---
R/getHitProb.R | 15 +--
R/getMOA.R | 72 ++++++++++----
R/groupShape.R | 206 ++++++++++++++++++++++++++++++++++++++++--
R/groupSpread.R | 224 ++++++++++++++++++++++++++++++++++++++++++++--
R/grubbs.R | 2
R/hoyt.R | 75 ++++++++-------
R/mvnEll.R | 119 +++++++++++++++++++-----
R/rayleigh.R | 3
R/simRingCount.R | 8 +
R/unitConversion.R | 8 -
build/vignette.rds |binary
data/DF300BLK.rda |binary
data/DF300BLKhl.rda |binary
data/DFcciHV.rda |binary
data/DFcm.rda |binary
data/DFinch.rda |binary
data/DFlistCm.rda |binary
data/DFsavage.rda |binary
data/DFscar17.rda |binary
data/DFtalon.rda |binary
data/targets.rda |binary
inst/ChangeLog | 24 ++++
inst/doc/shotGroups.R | 50 +++-------
inst/doc/shotGroups.Rnw | 41 ++++++--
inst/doc/shotGroups.pdf |binary
man/fromMOA.Rd | 5 -
man/getCEP.Rd | 8 -
man/getDistance.Rd |only
man/getMOA.Rd | 5 -
man/hoyt.Rd | 2
man/mvnEll.Rd | 16 ++-
man/shotGroups-package.Rd | 4
man/targets.Rd | 2
vignettes/lit.bib | 41 +++++++-
vignettes/shotGroups.Rnw | 41 ++++++--
42 files changed, 1053 insertions(+), 249 deletions(-)
Title: A toolset for working with lists
Diff between rlist versions 0.1 dated 2014-06-27 and 0.2.1 dated 2014-07-04
Description: A toolset for working with lists as dataset,
including filtering, mapping, grouping, sorting, updating, and
many other functions, which allow functional programming
style applied in list operations.
Author: Kun Ren
Maintainer: Kun Ren
DESCRIPTION | 10 -
MD5 | 207 +++++++++++++++-----------
NAMESPACE | 9 +
NEWS | 16 +-
R/functions.R | 52 ++++++
R/internal.R |only
R/list.all.R | 8 -
R/list.any.R | 8 -
R/list.append.R | 11 -
R/list.cases.R | 12 -
R/list.cbind.R | 6
R/list.class.R | 22 --
R/list.clean.R |only
R/list.count.R | 8 -
R/list.do.R |only
R/list.exclude.R | 13 -
R/list.filter.R | 12 -
R/list.find.R | 15 -
R/list.findi.R | 30 ---
R/list.group.R | 30 ---
R/list.if.R | 25 ---
R/list.insert.R | 6
R/list.iter.R | 22 --
R/list.join.R |only
R/list.load.R | 4
R/list.map.R | 44 ++---
R/list.match.R | 8 -
R/list.order.R | 12 -
R/list.parse.R |only
R/list.prepend.R | 10 -
R/list.rbind.R | 6
R/list.remove.R | 16 +-
R/list.reverse.R | 6
R/list.sample.R | 8 -
R/list.save.R | 24 ---
R/list.select.R | 34 ----
R/list.serialize.R | 3
R/list.skip.R | 6
R/list.skipWhile.R | 45 ++---
R/list.sort.R | 10 -
R/list.take.R | 6
R/list.takeWhile.R | 45 ++---
R/list.ungroup.R | 9 -
R/list.update.R | 36 ----
R/list.which.R | 8 -
R/rlist.R |only
R/subset.list.R | 51 ++----
README.md | 292 ++++++--------------------------------
build/vignette.rds |binary
inst/doc/filtering.R |only
inst/doc/filtering.html |only
inst/doc/grouping.R |only
inst/doc/grouping.html |only
inst/doc/introduction.R | 5
inst/doc/introduction.html | 232 +++++++++++++++---------------
inst/doc/io.R |only
inst/doc/io.html |only
inst/doc/joining.R |only
inst/doc/joining.html |only
inst/doc/lambda.R |only
inst/doc/lambda.html |only
inst/doc/mapping.R |only
inst/doc/mapping.html |only
inst/doc/sorting.R |only
inst/doc/sorting.html |only
inst/doc/updating.R |only
inst/doc/updating.html |only
man/list.all.Rd | 6
man/list.any.Rd | 6
man/list.append.Rd | 8 -
man/list.cases.Rd | 4
man/list.cbind.Rd | 4
man/list.class.Rd | 11 -
man/list.clean.Rd |only
man/list.count.Rd | 6
man/list.do.Rd |only
man/list.exclude.Rd | 9 -
man/list.filter.Rd | 8 -
man/list.find.Rd | 10 -
man/list.findi.Rd | 4
man/list.group.Rd | 8 -
man/list.if.Rd | 6
man/list.insert.Rd | 4
man/list.iter.Rd | 4
man/list.join.Rd |only
man/list.map.Rd | 8 -
man/list.mapv.Rd |only
man/list.match.Rd | 6
man/list.order.Rd | 4
man/list.parse.Rd |only
man/list.prepend.Rd | 8 -
man/list.rbind.Rd | 4
man/list.remove.Rd | 4
man/list.reverse.Rd | 4
man/list.sample.Rd | 4
man/list.save.Rd | 3
man/list.select.Rd | 4
man/list.serialize.Rd | 2
man/list.skip.Rd | 4
man/list.skipWhile.Rd | 8 -
man/list.sort.Rd | 4
man/list.take.Rd | 4
man/list.takeWhile.Rd | 8 -
man/list.ungroup.Rd | 6
man/list.update.Rd | 12 -
man/list.which.Rd | 6
man/rlist.Rd |only
man/subset.list.Rd | 9 -
tests/testthat/test-basic.R | 25 ++-
tests/testthat/test-list.class.R | 1
tests/testthat/test-list.filter.R | 2
tests/testthat/test-list.find.R | 1
tests/testthat/test-list.group.R | 2
tests/testthat/test-list.join.R |only
tests/testthat/test-list.map.R | 18 ++
tests/testthat/test-list.select.R | 2
tests/testthat/test-list.sort.R | 6
tests/testthat/test-list.update.R | 1
tests/testthat/test-subset.list.R | 4
119 files changed, 725 insertions(+), 989 deletions(-)
Title: PopGen: A simple way to analyse and visualize population genetic
data
Diff between PopGenReport versions 1.8 dated 2014-03-03 and 2.0 dated 2014-07-04
Description: This package provides an easy way to analyse population genetic data
Author: Aaron Adamack & Bernd Gruber
Maintainer: Bernd Gruber
DESCRIPTION | 12 +--
MD5 | 48 ++++++------
NAMESPACE | 16 ++--
R/genleastcost.r | 116 +++++++++++++++++++++---------
R/landgenreport.r | 25 ++++--
R/lgrMMRR.r |only
R/wassermann.r | 45 +++++++++--
inst/CITATION |only
inst/doc/PopGenReportIntroduction.R | 27 ------
inst/doc/PopGenReportIntroduction.pdf |binary
inst/doc/PopGenReportIntroduction.rnw | 3
inst/doc/Tutorial_landgenreport.pdf |only
inst/extdata/nancycoords.csv |only
inst/swchunks/header.snw | 2
inst/swchunks/pmantel.snw | 84 +++++++++++++--------
inst/swchunks/required.snw | 1
man/PopGenReport-package.Rd | 6 -
man/fric.raster.Rd | 1
man/genleastcost.Rd | 35 +++++----
man/landgenreport.Rd | 44 ++++++-----
man/lgrMMRR.Rd |only
man/wassermann.Rd | 24 +++---
vignettes/PopGenReportIntroduction.rnw | 3
vignettes/figures/PopGenReport_bilby.pdf |binary
vignettes/figures/PopGenReport_counts.pdf |binary
vignettes/figures/createpdfs.R | 13 +++
vignettes/figures/platy-map.pdf |only
vignettes/figures/tiger-map.pdf |binary
28 files changed, 314 insertions(+), 191 deletions(-)
Title: Solve systems of non linear equations
Diff between nleqslv versions 2.2 dated 2014-06-04 and 2.3 dated 2014-07-04
Description: Solve a system of non linear equations using a Broyden or a Newton method
with a choice of global strategies such as line search and trust region.
There are options for using a numerical or user supplied Jacobian and
for specifying that a numerical Jacobian is banded.
Author: Berend Hasselman
Maintainer: Berend Hasselman
DESCRIPTION | 8 -
MD5 | 30 ++---
NEWS | 25 +++-
man/zznleqslv-iterationreport.Rd | 30 +++--
src/nwbrdn.f | 47 ++++----
src/nwclsh.f | 44 +++----
src/nwddlg.f | 19 +--
src/nwglsh.f | 16 --
src/nwnleq.f | 5
src/nwnwtn.f | 14 +-
src/nwout.c | 218 +++++++++++++++++++--------------------
src/nwpdlg.f | 19 +--
src/nwpure.f | 14 --
src/nwqlsh.f | 16 --
src/nwtrup.f | 15 --
src/nwutil.f | 15 +-
16 files changed, 249 insertions(+), 286 deletions(-)