Title: A simple logging system for R, based on log4j.
Diff between log4r versions 0.1-4 dated 2012-03-01 and 0.2 dated 2014-09-29
Description: logr4 provides an object-oriented logging system that uses an API
roughly equivalent to log4j and its related variants.
Author: John Myles White [aut, cph],
Kenton White [ctb],
Kirill Müller [ctb, cre]
Maintainer: Kirill Müller
log4r-0.1-4/log4r/.gitignore |only
log4r-0.1-4/log4r/ChangeLog |only
log4r-0.1-4/log4r/R/constants.R |only
log4r-0.1-4/log4r/R/level.R |only
log4r-0.1-4/log4r/R/level_-.R |only
log4r-0.1-4/log4r/R/level_-.logger.R |only
log4r-0.1-4/log4r/R/logfile.R |only
log4r-0.1-4/log4r/R/logfile_-.R |only
log4r-0.1-4/log4r/R/logfile_-.logger.R |only
log4r-0.1-4/log4r/R/logformat.R |only
log4r-0.1-4/log4r/R/logformat_-.R |only
log4r-0.1-4/log4r/R/logformat_-.logger.R |only
log4r-0.1-4/log4r/README.markdown |only
log4r-0.1-4/log4r/build_package.sh |only
log4r-0.1-4/log4r/man/debug.Rd |only
log4r-0.1-4/log4r/man/error.Rd |only
log4r-0.1-4/log4r/man/fatal.Rd |only
log4r-0.1-4/log4r/man/info.Rd |only
log4r-0.1-4/log4r/man/level.logger.Rd |only
log4r-0.1-4/log4r/man/level_-.logger.Rd |only
log4r-0.1-4/log4r/man/logfile_-.logger.Rd |only
log4r-0.1-4/log4r/man/logformat.logger.Rd |only
log4r-0.1-4/log4r/man/logformat_-.logger.Rd |only
log4r-0.1-4/log4r/man/verbosity.Rd |only
log4r-0.1-4/log4r/man/warn.Rd |only
log4r-0.1-4/log4r/tests/1.R |only
log4r-0.1-4/log4r/tests/2.R |only
log4r-0.1-4/log4r/upload.sh |only
log4r-0.2/log4r/DESCRIPTION | 24 +++++++---
log4r-0.2/log4r/MD5 | 63 ++++++++++------------------
log4r-0.2/log4r/NAMESPACE | 44 ++++++++++++-------
log4r-0.2/log4r/R/create.logger.R | 23 ++++++++--
log4r-0.2/log4r/R/level.logger.R | 53 +++++++++++++++++++++--
log4r-0.2/log4r/R/log4r-package.R |only
log4r-0.2/log4r/R/logfile.logger.R | 47 +++++++++++++++++++-
log4r-0.2/log4r/R/logformat.logger.R | 37 ++++++++++++++++
log4r-0.2/log4r/R/logfuncs.R | 51 +++++++++++++++++++---
log4r-0.2/log4r/R/loglevel.R |only
log4r-0.2/log4r/R/write.message.R | 5 ++
log4r-0.2/log4r/build |only
log4r-0.2/log4r/inst |only
log4r-0.2/log4r/man/create.logger.Rd | 35 ++++++++-------
log4r-0.2/log4r/man/level.Rd |only
log4r-0.2/log4r/man/levellog.Rd |only
log4r-0.2/log4r/man/log4r-package.Rd | 41 ++++++++++--------
log4r-0.2/log4r/man/logfile.Rd | 33 +++++++++-----
log4r-0.2/log4r/man/logformat.Rd |only
log4r-0.2/log4r/man/loglevel.Rd |only
log4r-0.2/log4r/man/write.message.Rd | 20 ++++----
log4r-0.2/log4r/tests/run-all.R |only
log4r-0.2/log4r/tests/testthat |only
51 files changed, 336 insertions(+), 140 deletions(-)
Title: Apply Gaussian Process in Functional data analysis
Diff between GPFDA versions 2.1 dated 2014-05-29 and 2.2 dated 2014-09-29
Description: Use functional regression as the mean structure and Gaussian Process as the covariance structure.
Author: Jian Qing Shi, Yafeng Cheng
Maintainer: Yafeng Cheng
GPFDA-2.1/GPFDA/R/gp.functions4.R |only
GPFDA-2.1/GPFDA/R/gpfr.functions4.R |only
GPFDA-2.2/GPFDA/DESCRIPTION | 10 -
GPFDA-2.2/GPFDA/MD5 | 34 ++--
GPFDA-2.2/GPFDA/NAMESPACE | 18 +-
GPFDA-2.2/GPFDA/R/gp.functions5.R |only
GPFDA-2.2/GPFDA/R/gpfr.functions5.R |only
GPFDA-2.2/GPFDA/demo/co2.R | 30 ++-
GPFDA-2.2/GPFDA/demo/gpfr.R | 160 ++++++++++--------
GPFDA-2.2/GPFDA/demo/gpr_ex1.R | 9 -
GPFDA-2.2/GPFDA/demo/gpr_ex2.R | 9 -
GPFDA-2.2/GPFDA/man/co2.Rd | 3
GPFDA-2.2/GPFDA/man/cov.linear.Rd | 23 +-
GPFDA-2.2/GPFDA/man/cov.pow.ex.Rd | 23 +-
GPFDA-2.2/GPFDA/man/cov.rat.qu.Rd | 23 +-
GPFDA-2.2/GPFDA/man/gpfr.Rd | 306 ++++++++++++++++++------------------
GPFDA-2.2/GPFDA/man/gpfrpred.Rd | 239 ++++++++++++++--------------
GPFDA-2.2/GPFDA/man/gppredict.Rd | 19 +-
GPFDA-2.2/GPFDA/man/gpr.Rd | 15 +
GPFDA-2.2/GPFDA/man/plot.gpfr.Rd |only
GPFDA-2.2/GPFDA/man/plot.gpr.Rd |only
21 files changed, 488 insertions(+), 433 deletions(-)
Title: Wrapper package for design of experiments functionality
Diff between DoE.wrapper versions 0.8-9 dated 2013-09-13 and 0.8-10 dated 2014-09-29
Description: This package creates various kinds of designs for
(industrial) experiments. It uses, and sometimes enhances,
design generation routines from other packages.
So far, response surface designs from package rsm, latin hypercube
samples from packages lhs and DiceDesign, and
D-optimal designs from package AlgDesign have been implemented.
Author: Ulrike Groemping [aut, cre],
Lenth Russ [ctb]
Maintainer: Ulrike Groemping
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
inst/NEWS | 5 +++++
man/Dopt.design.Rd | 5 +++--
tests/bbd.test.Rout.save | 28 ++++++++++++++--------------
5 files changed, 30 insertions(+), 24 deletions(-)
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Diff between DoE.base versions 0.26-2 dated 2014-08-16 and 0.26-3 dated 2014-09-29
Description: This package creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides some utility functions used also by other DoE packages.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping
DESCRIPTION | 8 ++++----
MD5 | 12 +++++++-----
NAMESPACE | 2 +-
R/planor2design.r |only
R/sysdata.rda |binary
inst/NEWS | 5 +++++
man/halfnormal.Rd | 8 ++++----
man/planor2design.Rd |only
8 files changed, 21 insertions(+), 14 deletions(-)
Title: The ScottKnott Clustering Algorithm
Diff between ScottKnott versions 1.2-4 dated 2013-11-28 and 1.2-5 dated 2014-09-29
Description: Division of an ANOVA experiment treatment means into
homogeneous distinct groups using the clustering method of
Scott & Knott
Author: Enio Jelihovschi
Maintainer: Ivan Bezerra Allaman
ChangeLog | 102 ++---
DESCRIPTION | 10
INDEX | 42 +-
MD5 | 39 +-
NAMESPACE | 20 -
R/MaxValue.R | 246 ++++++-------
R/SK.R | 10
R/SK.aov.R | 132 +++----
R/SK.default.R | 94 ++---
R/m.inf.1a.R | 50 +-
R/m.inf.1b.R | 50 +-
R/m.inf.2a.R | 58 +--
R/m.inf.2b.R | 58 +--
R/m.inf.3a.R | 66 +--
R/m.inf.3b.R | 66 +--
R/plot.SK.R | 220 +++++------
R/summary.SK.R | 78 ++--
README.md |only
demo/00Index | 14
inst/CITATION | 47 +-
man/ScottKnott-package.Rd | 844 +++++++++++++++++++++++-----------------------
21 files changed, 1129 insertions(+), 1117 deletions(-)
Title: Modular Leaf Ordering Methods for Dendrogram Nodes
Diff between dendsort versions 0.3.1 dated 2014-09-27 and 0.3.2 dated 2014-09-29
Description: This package includes functions to optimize ordering of nodes in a dendrogram,
without affecting the meaning of the dendrogram. A dendrogram can be sorted based
on the average distance of subtrees, or based on the smallest distance value.
These sorting methods improve readability and interpretability of tree structure,
especially for tasks such as comparison of different distance measures or linkage
types and identification of tight clusters and outliers. As a result, it also
introduces more meaningful reordering for a coupled heatmap visualization.
Author: Ryo Sakai
Maintainer: Ryo Sakai
DESCRIPTION | 10 +++----
MD5 | 34 +++++++++++++-------------
R/cal_length.R | 2 -
R/cal_node_limit.R | 2 -
R/cal_total_length.R | 2 -
R/dendsort-package.R | 4 +--
R/sort_average.R | 2 -
R/sort_average_r.R | 2 -
R/sort_smallest.R | 2 -
R/sort_smallest_r.R | 2 -
man/cal_length.Rd | 2 -
man/cal_node_limit.Rd | 2 -
man/cal_total_length.Rd | 2 -
man/dendsort-package.Rd | 62 ++++++++----------------------------------------
man/sort_average.Rd | 2 -
man/sort_average_r.Rd | 2 -
man/sort_smallest.Rd | 2 -
man/sort_smallest_r.Rd | 2 -
18 files changed, 49 insertions(+), 89 deletions(-)
Title: Predict Presence of Signal Peptides
Diff between signal.hsmm versions 1.0 dated 2014-08-07 and 1.1 dated 2014-09-29
Description: Predicts presence of signal peptides in eukaryotic protein using
hidden semi-Markov models. The implemented algorithm can be accessed both
from command line and GUI.
Author: Michal Burdukiewicz [cre, aut],
Piotr Sobczyk [aut]
Maintainer: Michal Burdukiewicz
signal.hsmm-1.0/signal.hsmm/R/durationViterbi.R |only
signal.hsmm-1.1/signal.hsmm/DESCRIPTION | 18
signal.hsmm-1.1/signal.hsmm/MD5 | 68 +
signal.hsmm-1.1/signal.hsmm/NAMESPACE | 31
signal.hsmm-1.1/signal.hsmm/R/datasets.R | 55 -
signal.hsmm-1.1/signal.hsmm/R/degenerate.R | 56 -
signal.hsmm-1.1/signal.hsmm/R/duration_viterbi.R |only
signal.hsmm-1.1/signal.hsmm/R/find_nhc.R | 135 +--
signal.hsmm-1.1/signal.hsmm/R/hsmm_pred.R | 200 ++---
signal.hsmm-1.1/signal.hsmm/R/hsmm_pred_list.R | 92 +-
signal.hsmm-1.1/signal.hsmm/R/is_protein.R |only
signal.hsmm-1.1/signal.hsmm/R/read_txt.R | 74 +-
signal.hsmm-1.1/signal.hsmm/R/read_uniprot.R | 241 +++---
signal.hsmm-1.1/signal.hsmm/R/run_signal.hsmm.R | 346 +++++-----
signal.hsmm-1.1/signal.hsmm/R/signal.hsmm.R | 48 -
signal.hsmm-1.1/signal.hsmm/README.md |only
signal.hsmm-1.1/signal.hsmm/data/aaaggregation.rda |binary
signal.hsmm-1.1/signal.hsmm/inst/signal_gui/prots.txt |only
signal.hsmm-1.1/signal.hsmm/inst/signal_gui/readme.md |only
signal.hsmm-1.1/signal.hsmm/inst/signal_gui/server.R | 278 ++++----
signal.hsmm-1.1/signal.hsmm/inst/signal_gui/signalhsmm_report.Rmd | 25
signal.hsmm-1.1/signal.hsmm/inst/signal_gui/ui.R | 42 -
signal.hsmm-1.1/signal.hsmm/man/aaaggregation.Rd | 30
signal.hsmm-1.1/signal.hsmm/man/benchmark_dat.Rd | 50 -
signal.hsmm-1.1/signal.hsmm/man/degenerate.Rd | 56 -
signal.hsmm-1.1/signal.hsmm/man/duration_viterbi.Rd |only
signal.hsmm-1.1/signal.hsmm/man/find_nhc.Rd | 66 -
signal.hsmm-1.1/signal.hsmm/man/gui_signal.hsmm.Rd | 47 -
signal.hsmm-1.1/signal.hsmm/man/hsmm_pred.Rd | 44 -
signal.hsmm-1.1/signal.hsmm/man/hsmm_pred_list.Rd | 28
signal.hsmm-1.1/signal.hsmm/man/is_protein.Rd |only
signal.hsmm-1.1/signal.hsmm/man/plot.hsmm_pred.Rd | 46 -
signal.hsmm-1.1/signal.hsmm/man/pred2df.Rd | 38 -
signal.hsmm-1.1/signal.hsmm/man/read_txt.Rd | 45 -
signal.hsmm-1.1/signal.hsmm/man/read_uniprot.Rd | 43 -
signal.hsmm-1.1/signal.hsmm/man/run_signal.hsmm.Rd | 114 +--
signal.hsmm-1.1/signal.hsmm/man/signal.hsmm.Rd | 58 -
signal.hsmm-1.1/signal.hsmm/man/summary.hsmm_pred.Rd | 42 -
signal.hsmm-1.1/signal.hsmm/man/summary.hsmm_pred_list.Rd | 44 -
39 files changed, 1265 insertions(+), 1195 deletions(-)
Title: Pretty scientific plotting with minor-tick and log minor-tick
support
Diff between magicaxis versions 1.9 dated 2014-07-16 and 1.9.3 dated 2014-09-29
Description: Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
Author: Aaron Robotham
Maintainer: Aaron Robotham
DESCRIPTION | 8 ++---
MD5 | 24 +++++++--------
NEWS | 18 ++++++++++-
R/magaxis.R | 2 -
R/magbar.R | 3 -
R/magcon.R | 11 +++++-
R/magerr.R | 75 ++++++++++++++++++++++++++++++-----------------
R/magmap.R | 15 +++++----
R/magplot.R | 18 ++++++++---
man/magerr.Rd | 28 +++++++++++++----
man/magicaxis-package.Rd | 4 +-
man/magmap.Rd | 41 +++++++++++++++++++------
man/magplot.Rd | 16 ++++++++--
13 files changed, 181 insertions(+), 82 deletions(-)
Title: Estimation and tests of hierarchical F-statistics
Diff between hierfstat versions 0.04-10 dated 2013-04-10 and 0.04-14 dated 2014-09-29
Description: This R package allows the estimation of hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions are also given to test via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G -see Goudet etal (Genetics, 1996, 144(4): 1933-1940)
Author: Jerome Goudet
Maintainer: Jerome Goudet
CHANGES | 11 +++++++
DESCRIPTION | 16 +++-------
MD5 | 32 +++++++++++----------
NAMESPACE | 29 +++++++++++++------
R/beta.R | 6 ++--
R/misc.R | 65 +++++++++++++++++++++++++-------------------
R/simgenot.R | 72 +++++++++++++++++++++++++++----------------------
R/varcomp.R |only
R/writeped.R |only
data/gtrunchier.rda |binary
inst/doc/hierfstat.pdf |binary
man/betai.rd | 5 ++-
man/boot.ppfis.rd | 8 ++---
man/boot.ppfst.rd | 4 +-
man/indpca.rd | 3 +-
man/pcoa.rd | 3 +-
man/sim.genot.rd | 14 ++++-----
man/write.struct.rd | 6 +---
18 files changed, 157 insertions(+), 117 deletions(-)
Title: Basic HTTP Request
Diff between httpRequest versions 0.0.9 dated 2012-12-04 and 0.0.10 dated 2014-09-29
Description: HTTP Request protocols. Implements the GET, POST and multipart POST request.
Author: Eryk Witold Wolski, Andreas Westfeld
Maintainer: Andreas Westfeld
DESCRIPTION | 12 +++---
MD5 | 6 +--
R/httpRequest.R | 92 ++++++++++++++++++++++--------------------------
man/simplePostToHost.Rd | 21 +++++++---
4 files changed, 67 insertions(+), 64 deletions(-)
Title: Functions for Drawing Gapped Cluster Heatmap with ggplot2
Diff between gapmap versions 0.0.1 dated 2014-09-11 and 0.0.2 dated 2014-09-29
Description: The gap encodes the distance between clusters and improves
interpretation of cluster heatmaps. The gaps can be of the same
distance based on a height threshold to cut the dendrogram. Another
option is to vary the size of gaps based on the distance between
clusters.
Author: Ryo Sakai
Maintainer: Ryo Sakai
DESCRIPTION | 10 +++----
MD5 | 22 ++++++++--------
R/gap_dendrogram.R | 2 -
R/gapmap.R | 6 ++--
inst/doc/simple_example.R | 21 ++++++++-------
inst/doc/simple_example.Rmd | 22 ++++++++--------
inst/doc/simple_example.html | 22 ++++++++--------
inst/doc/tcga_example.R | 25 ++++++++++++++++--
inst/doc/tcga_example.Rmd | 47 +++++++++++++++++++++++++++++-----
inst/doc/tcga_example.html | 59 +++++++++++++++++++++++++++++++++++++------
vignettes/simple_example.Rmd | 22 ++++++++--------
vignettes/tcga_example.Rmd | 47 +++++++++++++++++++++++++++++-----
12 files changed, 220 insertions(+), 85 deletions(-)
Title: Analysis of Feedback in Time Series
Diff between FeedbackTS versions 1.1 dated 2014-07-03 and 1.2 dated 2014-09-29
Description: Analysis of fragmented time directionality to investigate feedback in time series. Tools provided by the package allow the analysis of feedback for a single time series and the analysis of feedback for a set of time series collected across a spatial domain.
Author: Samuel Soubeyrand, Cindy E. Morris, E. Keith Bigg
Maintainer: Samuel Soubeyrand
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
NAMESPACE | 1 +
man/FeedbackTS-package.Rd | 4 ++--
man/KDD-class.Rd | 20 ++++++++++++--------
man/KDD.yearly.average-class.Rd | 6 +++---
man/KT.output-class.Rd | 10 +++++-----
7 files changed, 34 insertions(+), 29 deletions(-)
Title: Efficient Estimation of Covariance and (Partial) Correlation
Diff between corpcor versions 1.6.6 dated 2013-05-15 and 1.6.7 dated 2014-09-29
Description: This package implements a James-Stein-type shrinkage estimator for
the covariance matrix, with separate shrinkage for variances and correlations.
The details of the method are explained in Sch\"afer and Strimmer (2005) and
Opgen-Rhein and Strimmer (2007). The approach is both computationally as well
as statistically very efficient, it is applicable to "small n, large p" data,
and always returns a positive definite and well-conditioned covariance matrix.
In addition to inferring the covariance matrix the package also provides
shrinkage estimators for partial correlations and partial variances.
The inverse of the covariance and correlation matrix
can be efficiently computed, as well as any arbitrary power of the
shrinkage correlation matrix. Furthermore, functions are available for fast
singular value decomposition, for computing the pseudoinverse, and for
checking the rank and positive definiteness of a matrix.
Author: Juliane Sch\"afer, Rainer Opgen-Rhein, Verena Zuber, Miika Ahdesm\"aki,
A. Pedro Duarte Silva, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 45 +++++++++++++++++++++------------------------
MD5 | 4 ++--
NEWS | 7 +++++++
3 files changed, 30 insertions(+), 26 deletions(-)
Title: An R-package for estimating absolute protein quantities from
label-free LC-MS/MS proteomics data
Diff between aLFQ versions 1.3.1 dated 2014-02-27 and 1.3.2 dated 2014-09-29
Description: Determination of absolute protein quantities is necessary for multiple applications, such as mechanistic modeling of biological systems. Quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics can measure relative protein abundance on a system-wide scale. To estimate absolute quantitative information using these relative abundance measurements requires additional information such as heavy-labeled references of known concentration. Multiple methods have been using different references and strategies; some are easily available whereas others require more effort on the users end. Hence, we believe the field might benefit from making some of these methods available under an automated framework, which also facilitates validation of the chosen strategy. We have implemented the most commonly used absolute label-free protein abundance estimation methods for LC-MS/MS modes quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, we used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. Our open-source software is written in the statistical programming language R and validated and demonstrated on a synthetic sample.
Author: aLFQ: George Rosenberger, Hannes Roest, Christina Ludwig. AAindex: Barry Grant.
Maintainer: George Rosenberger
DESCRIPTION | 13 +++++++------
MD5 | 17 +++++++++--------
NAMESPACE | 9 ++++++++-
R/ALF.R | 1 -
R/APEX.R | 7 +------
R/AbsoluteQuantification.R | 2 --
R/ProteinInference.R | 3 +--
inst/CITATION |only
man/aLFQ.package.Rd | 8 ++++----
tests/Examples/aLFQ-Ex.Rout.save | 30 +++---------------------------
10 files changed, 33 insertions(+), 57 deletions(-)
Title: The YUIMA Project package for SDEs
Diff between yuima versions 1.0.30 dated 2014-09-17 and 1.0.36 dated 2014-09-29
Description: Simulation and Inference for Stochastic Differential Equations
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus
DESCRIPTION | 8 +-
MD5 | 29 ++++++----
NAMESPACE | 9 ++-
NEWS | 3 -
R/AllClasses.R | 6 +-
R/qmle.R | 104 ++++++++++++++++++++++++++++++--------
R/rng.R | 13 +++-
R/setPoisson.R |only
R/sim.euler.R | 123 ++++++++++++++++++++++++++++++++-------------
R/simCP.R |only
R/simulate.R | 18 ++++--
R/yuima.R | 12 ++--
R/yuima.model.R | 111 +++++++++++++++++++++++++++-------------
man/rconst.Rd |only
man/setModel.Rd | 2
man/setPoisson.Rd |only
man/simulate.Rd | 34 +++++++-----
man/yuima.poisson-class.Rd |only
18 files changed, 336 insertions(+), 136 deletions(-)
Title: Functions for soil texture plot, classification and
transformation
Diff between soiltexture versions 1.2.13 dated 2014-01-14 and 1.2.19 dated 2014-09-29
Description: "The Soil Texture Wizard" is a set of R functions designed to produce
texture triangles (also called texture plots, texture diagrams, texture ternary plots),
classify and transform soil textures data. These functions virtually allows to plot any
soil texture triangle / classification into any triangle geometry (isosceles,
right-angled triangles, etc.). This set of function is expected to be useful to people
using soil textures data from different soil texture classification or different particle
size systems. Several texture triangles are predefined: USDA; FAO (which is also the
triangle for the soil map of Europe); Aisne (France); GEPPA (France); German triangles
"Bodenkundliche Kartieranleitung 1994", "SEA 1974" and "TGL 1985"; Soil
Survey of England and Wales; Australian triangle; Belgian triangle; Canadian triangle;
ISSS triangle; Romanian triangle; Polish triangle.
Author: Julien MOEYS
Maintainer: Julien MOEYS
soiltexture-1.2.13/soiltexture/inst/polish_language.r |only
soiltexture-1.2.13/soiltexture/inst/polish_language_ANSI.r |only
soiltexture-1.2.13/soiltexture/inst/polish_triangle.r |only
soiltexture-1.2.13/soiltexture/inst/polish_triangle_ANSI.r |only
soiltexture-1.2.19/soiltexture/DESCRIPTION | 12
soiltexture-1.2.19/soiltexture/MD5 | 36
soiltexture-1.2.19/soiltexture/NEWS | 189 ++--
soiltexture-1.2.19/soiltexture/R/onAttach.R | 49 -
soiltexture-1.2.19/soiltexture/R/soiltexture.R | 140 +++
soiltexture-1.2.19/soiltexture/R/soiltextureInfo.R |only
soiltexture-1.2.19/soiltexture/build/vignette.rds |binary
soiltexture-1.2.19/soiltexture/inst/SVN_VERSION |only
soiltexture-1.2.19/soiltexture/inst/doc/soiltexture_vignette.R | 236 +++--
soiltexture-1.2.19/soiltexture/inst/doc/soiltexture_vignette.Rnw | 85 +
soiltexture-1.2.19/soiltexture/inst/doc/soiltexture_vignette.pdf |binary
soiltexture-1.2.19/soiltexture/inst/languages.rds |only
soiltexture-1.2.19/soiltexture/inst/triangles.rds |only
soiltexture-1.2.19/soiltexture/man/TT.plot.Rd | 34
soiltexture-1.2.19/soiltexture/man/soiltexture-package.Rd | 8
soiltexture-1.2.19/soiltexture/man/soiltextureInfo.Rd |only
soiltexture-1.2.19/soiltexture/tests/TT.plot.R | 34
soiltexture-1.2.19/soiltexture/tests/soiltextureInfo.R |only
soiltexture-1.2.19/soiltexture/vignettes/soiltexture_vignette.Rnw | 85 +
soiltexture-1.2.19/soiltexture/vignettes/soiltexture_vignette.bib | 428 +++++-----
24 files changed, 872 insertions(+), 464 deletions(-)
Title: Applied Latent Semantic Analysis (LSA) functions
Diff between LSAfun versions 0.3.1 dated 2014-07-07 and 0.3.2 dated 2014-09-29
Description: This package provides functions that allow for convenient working
with Latent Semantic Analysis. For actually building an LSA space, use the
package 'lsa'.
Author: Fritz Guenther [aut, cre]
Maintainer: Fritz Guenther
ChangeLog | 11 +++++++++++
DESCRIPTION | 8 ++++----
MD5 | 28 ++++++++++++++--------------
NAMESPACE | 2 ++
R/MultipleChoice.r | 13 +++++++++----
R/choose.target.r | 1 +
R/costring.r | 7 +++++++
R/multicostring.r | 7 +++++++
R/neighbors.r | 1 +
R/plot_neighbors.r | 5 +++--
R/plot_wordlist.r | 7 ++++---
data/syntest.rda |binary
man/MultipleChoice.Rd | 4 ++--
man/plot_neighbors.Rd | 6 ++++--
man/plot_wordlist.Rd | 4 +++-
15 files changed, 72 insertions(+), 32 deletions(-)
Title: Tools for extracting dendrogram and tree diagram plot data for
use with ggplot2
Diff between ggdendro versions 0.1-14 dated 2013-09-03 and 0.1-15 dated 2014-09-29
Description: This is a set of tools for dendrograms and
tree plots using ggplot2. The ggplot2 philosophy is to
clearly separate data from the presentation.
Unfortunately the plot method for dendrograms plots
directly to a plot device without exposing the data.
The ggdendro package resolves this by making available
functions that extract the dendrogram plot data.
Author: Andrie de Vries [aut, cre],
Brian D. Ripley [aut] (author of package tree)
Maintainer: Andrie de Vries
ggdendro-0.1-14/ggdendro/inst/doc/ggdendro-dendro1.pdf |only
ggdendro-0.1-14/ggdendro/inst/doc/ggdendro-dendro2.pdf |only
ggdendro-0.1-14/ggdendro/inst/doc/ggdendro-dendro3.pdf |only
ggdendro-0.1-14/ggdendro/inst/doc/ggdendro-dendrogram.pdf |only
ggdendro-0.1-14/ggdendro/inst/doc/ggdendro-rpart1.pdf |only
ggdendro-0.1-14/ggdendro/inst/doc/ggdendro-tree1.pdf |only
ggdendro-0.1-14/ggdendro/inst/doc/ggdendro.Rnw |only
ggdendro-0.1-14/ggdendro/inst/doc/ggdendro.pdf |only
ggdendro-0.1-14/ggdendro/inst/tests |only
ggdendro-0.1-14/ggdendro/vignettes/ggdendro.Rnw |only
ggdendro-0.1-15/ggdendro/DESCRIPTION | 25 ++--
ggdendro-0.1-15/ggdendro/MD5 | 64 ++++------
ggdendro-0.1-15/ggdendro/NAMESPACE | 8 -
ggdendro-0.1-15/ggdendro/NEWS | 12 +
ggdendro-0.1-15/ggdendro/R/dendrogram.R | 7 -
ggdendro-0.1-15/ggdendro/build |only
ggdendro-0.1-15/ggdendro/inst/doc/ggdendro.R |only
ggdendro-0.1-15/ggdendro/inst/doc/ggdendro.Rmd |only
ggdendro-0.1-15/ggdendro/inst/doc/ggdendro.html |only
ggdendro-0.1-15/ggdendro/man/as.dendro.Rd | 18 +-
ggdendro-0.1-15/ggdendro/man/dendro_data.Rd | 47 +++----
ggdendro-0.1-15/ggdendro/man/dendro_data.dendrogram.Rd | 37 ++---
ggdendro-0.1-15/ggdendro/man/dendro_data.rpart.Rd | 87 ++++----------
ggdendro-0.1-15/ggdendro/man/dendro_data.tree.Rd | 46 ++-----
ggdendro-0.1-15/ggdendro/man/dendrogram_data.Rd | 31 ++--
ggdendro-0.1-15/ggdendro/man/get_data_tree_leaf_labels.Rd | 19 +--
ggdendro-0.1-15/ggdendro/man/ggdendro-package.Rd | 61 ++++-----
ggdendro-0.1-15/ggdendro/man/ggdendrogram.Rd | 31 ++--
ggdendro-0.1-15/ggdendro/man/is.dendro.Rd | 10 -
ggdendro-0.1-15/ggdendro/man/labels.rpart.Rd | 23 +--
ggdendro-0.1-15/ggdendro/man/rpart_labels.Rd | 27 ++--
ggdendro-0.1-15/ggdendro/man/rpart_segments.Rd | 15 +-
ggdendro-0.1-15/ggdendro/man/rpartco.Rd | 9 -
ggdendro-0.1-15/ggdendro/man/segment.Rd | 15 +-
ggdendro-0.1-15/ggdendro/man/theme_dendro.Rd | 8 -
ggdendro-0.1-15/ggdendro/man/tree_labels.Rd | 21 +--
ggdendro-0.1-15/ggdendro/man/tree_segments.Rd | 19 +--
ggdendro-0.1-15/ggdendro/man/treeco.Rd | 9 -
ggdendro-0.1-15/ggdendro/tests |only
ggdendro-0.1-15/ggdendro/vignettes/ggdendro.Rmd |only
40 files changed, 292 insertions(+), 357 deletions(-)
Title: Social Relations Analyses with roles ("Family SRM")
Diff between fSRM versions 0.3.5 dated 2014-05-13 and 0.6 dated 2014-09-29
Description: The package computes Social Relations Analysis with roles ("Family
SRM"), using a structural equation modeling approach. Groups ranging from
three members up to an unlimited number of members are supported and the
mean structure can be computed. Means and variances can be compared between
different groups of families and between roles.
Author: Felix Schönbrodt, Lara Stas, Tom Loeys
Maintainer: Felix Schönbrodt
fSRM-0.3.5/fSRM/R/buildSRMSyntaxLatent.R |only
fSRM-0.3.5/fSRM/man/buildSRMSyntaxLatent.Rd |only
fSRM-0.6/fSRM/DESCRIPTION | 13
fSRM-0.6/fSRM/MD5 | 59
fSRM-0.6/fSRM/NAMESPACE | 14
fSRM-0.6/fSRM/R/buildSRMSyntax.R |only
fSRM-0.6/fSRM/R/clinical-data.R |only
fSRM-0.6/fSRM/R/equalMeans.R | 14
fSRM-0.6/fSRM/R/fSRM.R | 91
fSRM-0.6/fSRM/R/generics.R | 78
fSRM-0.6/fSRM/R/helpers.R | 40
fSRM-0.6/fSRM/R/import.R | 12
fSRM-0.6/fSRM/R/merge.rec.R | 3
fSRM-0.6/fSRM/R/percTable.R | 4
fSRM-0.6/fSRM/R/plots.R |only
fSRM-0.6/fSRM/R/print.fSRM.R | 215
fSRM-0.6/fSRM/R/two.groups-data.R | 19
fSRM-0.6/fSRM/R/varComp.R | 4
fSRM-0.6/fSRM/data/clinical.tab |only
fSRM-0.6/fSRM/data/clinical.wide.tab |only
fSRM-0.6/fSRM/data/two.groups.tab | 6556 +++++++++++++---------------
fSRM-0.6/fSRM/data/two.groups.wide.tab |only
fSRM-0.6/fSRM/inst/NEWS.Rd | 30
fSRM-0.6/fSRM/man/buildSRMSyntax.Rd |only
fSRM-0.6/fSRM/man/clinical.Rd |only
fSRM-0.6/fSRM/man/equalMeans.Rd | 9
fSRM-0.6/fSRM/man/fSRM.Rd | 129
fSRM-0.6/fSRM/man/four.person.Rd | 39
fSRM-0.6/fSRM/man/import.Rd | 47
fSRM-0.6/fSRM/man/mod.Rd | 6
fSRM-0.6/fSRM/man/plot.fSRM.Rd |only
fSRM-0.6/fSRM/man/predict.fSRM.Rd | 9
fSRM-0.6/fSRM/man/three.person.Rd | 48
fSRM-0.6/fSRM/man/two.groups.Rd | 34
fSRM-0.6/fSRM/man/two.indicators.Rd | 18
fSRM-0.6/fSRM/man/update.fSRM.Rd | 7
36 files changed, 3813 insertions(+), 3685 deletions(-)
Title: Automated caret feature selection
Diff between fscaret versions 0.8.5.7 dated 2014-08-28 and 0.8.6.2 dated 2014-09-29
Description: Automated feature selection using variety of models
provided by caret package
Author: Jakub Szlek
Maintainer: Jakub Szlek
DESCRIPTION | 22 ++++----
MD5 | 29 ++++++----
NAMESPACE | 3 -
R/classVarImp.R |only
R/fscaret.R | 96 ++++++++++++++++++++++++++++++++++-
R/funcClass.all.R |only
R/funcReg.all.R | 121 ++++++++++++++++++++++++++++++++++++++++++---
R/regVarImp.R | 126 ++++++++++++++++++++++++++++++++---------------
build/vignette.rds |binary
data/funcClassPred.RData |only
data/funcRegPred.RData |binary
inst/NEWS.Rd | 23 ++++++++
inst/doc/fscaret.Rnw | 43 ++++++++++------
inst/doc/fscaret.pdf |binary
man/classVarImp.Rd |only
man/fscaret-package.Rd | 4 -
man/funcClass.all.Rd |only
vignettes/fscaret.Rnw | 14 ++++-
18 files changed, 387 insertions(+), 94 deletions(-)
Title: Fixed Size Subset Sum Solution
Diff between FLSSS versions 1.0 dated 2014-05-29 and 2.0 dated 2014-09-29
Description: Solve an approximate Subset Sum Problem by introducing a recursive
compression algorithm
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu
FLSSS-1.0/FLSSS/R/the_FLSSS.R |only
FLSSS-1.0/FLSSS/man/FLSSS.Rd |only
FLSSS-1.0/FLSSS/src/FLSSS.cpp |only
FLSSS-2.0/FLSSS/DESCRIPTION | 12 ++++++------
FLSSS-2.0/FLSSS/MD5 | 8 ++++----
FLSSS-2.0/FLSSS/R/FLSSS_20140929.r |only
FLSSS-2.0/FLSSS/man/FLSSS-package.Rd |only
FLSSS-2.0/FLSSS/src/FLSSS_20140929.cpp |only
8 files changed, 10 insertions(+), 10 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.11.2 dated 2014-06-08 and 0.11.3 dated 2014-09-29
Description: The Rcpp package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about Rcpp is provided by several vignettes included in this package, via the
Rcpp Gallery site at http://gallery.rcpp.org, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Douglas Bates, and John Chambers
Maintainer: Dirk Eddelbuettel
Rcpp-0.11.2/inst/include/Rcpp/macros/preprocessor_generated.h |only
Rcpp-0.11.3/ChangeLog | 227
Rcpp-0.11.3/DESCRIPTION | 62
Rcpp-0.11.3/MD5 | 185
Rcpp-0.11.3/R/Attributes.R | 16
Rcpp-0.11.3/R/Rcpp.package.skeleton.R | 59
Rcpp-0.11.3/R/unit.tests.R | 10
Rcpp-0.11.3/build/Rcpp.pdf |only
Rcpp-0.11.3/build/vignette.rds |binary
Rcpp-0.11.3/cleanup | 1
Rcpp-0.11.3/inst/NEWS.Rd | 70
Rcpp-0.11.3/inst/THANKS | 1
Rcpp-0.11.3/inst/doc/Rcpp-FAQ.R | 32
Rcpp-0.11.3/inst/doc/Rcpp-FAQ.Rnw | 81
Rcpp-0.11.3/inst/doc/Rcpp-FAQ.pdf |binary
Rcpp-0.11.3/inst/doc/Rcpp-attributes.pdf |binary
Rcpp-0.11.3/inst/doc/Rcpp-extending.pdf |binary
Rcpp-0.11.3/inst/doc/Rcpp-introduction.pdf |binary
Rcpp-0.11.3/inst/doc/Rcpp-modules.pdf |binary
Rcpp-0.11.3/inst/doc/Rcpp-package.pdf |binary
Rcpp-0.11.3/inst/doc/Rcpp-quickref.pdf |binary
Rcpp-0.11.3/inst/doc/Rcpp-sugar.pdf |binary
Rcpp-0.11.3/inst/doc/Rcpp-unitTests.R | 12
Rcpp-0.11.3/inst/doc/Rcpp-unitTests.Rnw | 12
Rcpp-0.11.3/inst/doc/Rcpp-unitTests.pdf |binary
Rcpp-0.11.3/inst/include/Rcpp/Benchmark/Timer.h | 30
Rcpp-0.11.3/inst/include/Rcpp/Date.h | 4
Rcpp-0.11.3/inst/include/Rcpp/Environment.h | 12
Rcpp-0.11.3/inst/include/Rcpp/InternalFunction.h | 18
Rcpp-0.11.3/inst/include/Rcpp/InternalFunctionWithStdFunction.h |only
Rcpp-0.11.3/inst/include/Rcpp/Language.h | 24
Rcpp-0.11.3/inst/include/Rcpp/api/meat/meat.h | 2
Rcpp-0.11.3/inst/include/Rcpp/api/meat/proxy.h |only
Rcpp-0.11.3/inst/include/Rcpp/config.h | 2
Rcpp-0.11.3/inst/include/Rcpp/generated/InternalFunctionWithStdFunction_call.h |only
Rcpp-0.11.3/inst/include/Rcpp/generated/InternalFunction__ctors.h | 601
Rcpp-0.11.3/inst/include/Rcpp/macros/macros.h | 1
Rcpp-0.11.3/inst/include/Rcpp/module/CppFunction.h | 29
Rcpp-0.11.3/inst/include/Rcpp/module/Module_generated_CppFunction.h |23941 ++++----
Rcpp-0.11.3/inst/include/Rcpp/module/Module_generated_CppMethod.h |27778 ++++------
Rcpp-0.11.3/inst/include/Rcpp/module/Module_generated_Pointer_CppMethod.h | 9489 +--
Rcpp-0.11.3/inst/include/Rcpp/module/Module_generated_Pointer_method.h | 1653
Rcpp-0.11.3/inst/include/Rcpp/module/Module_generated_function.h | 1659
Rcpp-0.11.3/inst/include/Rcpp/module/Module_generated_get_signature.h | 6218 +-
Rcpp-0.11.3/inst/include/Rcpp/module/Module_generated_method.h | 3700 -
Rcpp-0.11.3/inst/include/Rcpp/module/get_return_type.h | 12
Rcpp-0.11.3/inst/include/Rcpp/platform/compiler.h | 13
Rcpp-0.11.3/inst/include/Rcpp/proxy/AttributeProxy.h | 21
Rcpp-0.11.3/inst/include/Rcpp/proxy/Binding.h | 15
Rcpp-0.11.3/inst/include/Rcpp/proxy/DottedPairProxy.h | 20
Rcpp-0.11.3/inst/include/Rcpp/proxy/FieldProxy.h | 24
Rcpp-0.11.3/inst/include/Rcpp/proxy/NamesProxy.h | 13
Rcpp-0.11.3/inst/include/Rcpp/proxy/SlotProxy.h | 9
Rcpp-0.11.3/inst/include/Rcpp/proxy/TagProxy.h | 21
Rcpp-0.11.3/inst/include/Rcpp/proxy/proxy.h | 8
Rcpp-0.11.3/inst/include/Rcpp/sugar/block/SugarBlock_1.h | 8
Rcpp-0.11.3/inst/include/Rcpp/sugar/block/SugarBlock_2.h | 24
Rcpp-0.11.3/inst/include/Rcpp/sugar/block/SugarBlock_3.h | 26
Rcpp-0.11.3/inst/include/Rcpp/sugar/block/SugarMath.h | 30
Rcpp-0.11.3/inst/include/Rcpp/sugar/functions/complex.h | 10
Rcpp-0.11.3/inst/include/Rcpp/sugar/functions/ifelse.h | 4
Rcpp-0.11.3/inst/include/Rcpp/vector/DimNameProxy.h |only
Rcpp-0.11.3/inst/include/Rcpp/vector/ListOf.h | 2
Rcpp-0.11.3/inst/include/Rcpp/vector/Matrix.h | 15
Rcpp-0.11.3/inst/include/Rcpp/vector/Vector.h | 14
Rcpp-0.11.3/inst/include/Rcpp/vector/no_init.h | 38
Rcpp-0.11.3/inst/include/Rcpp/vector/proxy.h | 6
Rcpp-0.11.3/inst/skeleton/Rcpp_modules_examples.Rd |only
Rcpp-0.11.3/inst/unitTests/cpp/InternalFunction.cpp |only
Rcpp-0.11.3/inst/unitTests/cpp/InternalFunctionCPP11.cpp |only
Rcpp-0.11.3/inst/unitTests/cpp/Matrix.cpp | 20
Rcpp-0.11.3/inst/unitTests/cpp/Module.cpp | 159
Rcpp-0.11.3/inst/unitTests/cpp/wrap.cpp | 29
Rcpp-0.11.3/inst/unitTests/runit.InternalFunction.R |only
Rcpp-0.11.3/inst/unitTests/runit.InternalFunctionCPP11.R |only
Rcpp-0.11.3/inst/unitTests/runit.Matrix.R | 19
Rcpp-0.11.3/inst/unitTests/runit.Rcpp.package.skeleton.R | 24
Rcpp-0.11.3/inst/unitTests/runit.environments.R | 36
Rcpp-0.11.3/inst/unitTests/runit.wrap.R | 4
Rcpp-0.11.3/inst/unitTests/testRcppClass/DESCRIPTION | 6
Rcpp-0.11.3/inst/unitTests/testRcppClass/NAMESPACE | 4
Rcpp-0.11.3/inst/unitTests/testRcppClass/R/load.R | 12
Rcpp-0.11.3/inst/unitTests/testRcppClass/R/rcpp_hello_world.R | 2
Rcpp-0.11.3/inst/unitTests/testRcppClass/man/Rcpp_class_examples.Rd |only
Rcpp-0.11.3/inst/unitTests/testRcppClass/src/stdVector.cpp | 10
Rcpp-0.11.3/inst/unitTests/testRcppModule/DESCRIPTION | 4
Rcpp-0.11.3/inst/unitTests/testRcppModule/NAMESPACE | 2
Rcpp-0.11.3/inst/unitTests/testRcppModule/R/rcpp_hello_world.R | 2
Rcpp-0.11.3/inst/unitTests/testRcppModule/R/zzz.R | 15
Rcpp-0.11.3/inst/unitTests/testRcppModule/man/Rcpp_modules_examples.Rd |only
Rcpp-0.11.3/man/Rcpp.package.skeleton.Rd | 8
Rcpp-0.11.3/man/sourceCpp.Rd | 11
Rcpp-0.11.3/src/Module.cpp | 2
Rcpp-0.11.3/src/Rcpp_init.cpp | 1
Rcpp-0.11.3/src/api.cpp | 23
Rcpp-0.11.3/src/attributes.cpp | 2
Rcpp-0.11.3/src/internal.h | 1
Rcpp-0.11.3/vignettes/Rcpp-FAQ.Rnw | 81
Rcpp-0.11.3/vignettes/Rcpp-unitTests.Rnw | 12
100 files changed, 38471 insertions(+), 38283 deletions(-)
Title: Solve systems of non linear equations
Diff between nleqslv versions 2.4 dated 2014-08-09 and 2.5 dated 2014-09-29
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 | 10 +++++-----
NEWS | 12 ++++++++++--
man/nleqslv-package.Rd | 12 ++++++------
man/nleqslv.Rd | 2 ++
src/nwclsh.f | 22 +++++++++++++++-------
6 files changed, 42 insertions(+), 24 deletions(-)
Title: R Commander Plug-in for the EZR (Easy R) Package
Diff between RcmdrPlugin.EZR versions 1.25 dated 2014-08-19 and 1.26 dated 2014-09-29
More information about RcmdrPlugin.EZR at CRAN
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN-10: 4498109007), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda
DESCRIPTION | 8
MD5 | 18
NEWS | 8
R/EZR.R | 1134 ++++++++++++++++------------
inst/CHANGES | 8
inst/etc/menus.txt | 27
inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.EZR.mo |binary
man/EZR.Rd | 5
man/EZR.dialogs.Rd | 1
po/R-RcmdrPlugin.EZR.po | 383 +++++++--
10 files changed, 1031 insertions(+), 561 deletions(-)
Permanent link
Title: Toolkit of helper functions to pre-process amplification data
Diff between chipPCR versions 0.0.8-1 dated 2014-08-26 and 0.0.8-3 dated 2014-09-29
Description: The chipPCR package is a toolkit of functions to pre-process
amplification curve data. Amplification data can be obtained from
conventional PCR reactions or isothermal amplification reactions. The
package contains functions to normalize and baseline amplification curves,
a routine to detect the start of an amplification reaction, several
smoothers for amplification data, a function to distinguish positive and
negative amplification reactions and a function to determine the
amplification efficiency. The smoothers are based on LOWESS, moving
average, cubic splines, Savitzky-Golay and others. In addition the first
approximate approximate derivative maximum (FDM) and second approximate
derivative maximum (SDM) can be calculated by a 5-point-stencil as
quantification points from real-time amplification curves. chipPCR contains
data sets of experimental nucleic acid amplification systems including the
VideoScan HCU and a capillary convective PCR (ccPCR) system. The
amplification data were generated by helicase dependent amplification (HDA)
or polymerase chain reaction (PCR) under various temperature conditions. As
detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis
probes (TaqMan) were used. The latest source code is available via:
https://github.com/michbur/chipPCR
Author: Stefan Roediger [cre, aut],
Michal Burdukiewicz [aut]
Maintainer: Stefan Roediger
chipPCR-0.0.8-1/chipPCR/README |only
chipPCR-0.0.8-3/chipPCR/CHANGELOG | 16
chipPCR-0.0.8-3/chipPCR/DESCRIPTION | 23
chipPCR-0.0.8-3/chipPCR/MD5 | 133
chipPCR-0.0.8-3/chipPCR/R/AmpSim.R | 9
chipPCR-0.0.8-3/chipPCR/R/CPP.R | 24
chipPCR-0.0.8-3/chipPCR/R/MFIaggr.R | 2
chipPCR-0.0.8-3/chipPCR/R/check.method.R |only
chipPCR-0.0.8-3/chipPCR/R/classes.R | 3
chipPCR-0.0.8-3/chipPCR/R/humanrater.R | 9
chipPCR-0.0.8-3/chipPCR/R/lm.coefs.R | 15
chipPCR-0.0.8-3/chipPCR/R/normalizer.R | 18
chipPCR-0.0.8-3/chipPCR/R/plotCurves.R | 134
chipPCR-0.0.8-3/chipPCR/R/smoother.R | 14
chipPCR-0.0.8-3/chipPCR/README.md |only
chipPCR-0.0.8-3/chipPCR/build/vignette.rds |binary
chipPCR-0.0.8-3/chipPCR/data/C126EG595.rda |binary
chipPCR-0.0.8-3/chipPCR/data/C126EG685.rda |binary
chipPCR-0.0.8-3/chipPCR/data/C127EGHP.rda |binary
chipPCR-0.0.8-3/chipPCR/data/C17.rda |binary
chipPCR-0.0.8-3/chipPCR/data/C54.rda |binary
chipPCR-0.0.8-3/chipPCR/data/C60.amp.rda |binary
chipPCR-0.0.8-3/chipPCR/data/C60.melt.rda |binary
chipPCR-0.0.8-3/chipPCR/data/C67.rda |binary
chipPCR-0.0.8-3/chipPCR/data/C81.rda |binary
chipPCR-0.0.8-3/chipPCR/data/C85.rda |binary
chipPCR-0.0.8-3/chipPCR/data/CD74.rda |binary
chipPCR-0.0.8-3/chipPCR/data/CD75.rda |binary
chipPCR-0.0.8-3/chipPCR/data/Eff1000.rda |binary
chipPCR-0.0.8-3/chipPCR/data/Eff625.rda |binary
chipPCR-0.0.8-3/chipPCR/data/Eff750.rda |binary
chipPCR-0.0.8-3/chipPCR/data/Eff875.rda |binary
chipPCR-0.0.8-3/chipPCR/data/VIMCFX96_60.rda |binary
chipPCR-0.0.8-3/chipPCR/data/VIMCFX96_69.rda |binary
chipPCR-0.0.8-3/chipPCR/data/VIMCFX96_meltcurve.rda |binary
chipPCR-0.0.8-3/chipPCR/data/VIMiQ5_595.rda |binary
chipPCR-0.0.8-3/chipPCR/data/VIMiQ5_685.rda |binary
chipPCR-0.0.8-3/chipPCR/data/VIMiQ5_melt.rda |binary
chipPCR-0.0.8-3/chipPCR/data/capillaryPCR.rda |binary
chipPCR-0.0.8-3/chipPCR/inst/AmpSim.gui/readme.md |only
chipPCR-0.0.8-3/chipPCR/inst/AmpSim.gui/server.R | 13
chipPCR-0.0.8-3/chipPCR/inst/AmpSim.gui/ui.R | 53
chipPCR-0.0.8-3/chipPCR/inst/MFIaggr.gui/readme.md |only
chipPCR-0.0.8-3/chipPCR/inst/MFIaggr.gui/refMFI_report.Rmd | 3
chipPCR-0.0.8-3/chipPCR/inst/MFIaggr.gui/server.R | 88
chipPCR-0.0.8-3/chipPCR/inst/MFIaggr.gui/ui.R | 16
chipPCR-0.0.8-3/chipPCR/inst/doc/chipPCR.R | 1009 ++--
chipPCR-0.0.8-3/chipPCR/inst/doc/chipPCR.Rnw | 2661 +++++++-----
chipPCR-0.0.8-3/chipPCR/inst/doc/chipPCR.pdf |binary
chipPCR-0.0.8-3/chipPCR/man/AmpSim.Rd | 2
chipPCR-0.0.8-3/chipPCR/man/AmpSim.gui.Rd | 2
chipPCR-0.0.8-3/chipPCR/man/C17.Rd | 4
chipPCR-0.0.8-3/chipPCR/man/C67.Rd | 4
chipPCR-0.0.8-3/chipPCR/man/CD75.Rd | 2
chipPCR-0.0.8-3/chipPCR/man/CPP.Rd | 6
chipPCR-0.0.8-3/chipPCR/man/MFIaggr.Rd | 11
chipPCR-0.0.8-3/chipPCR/man/capillaryPCR.Rd | 2
chipPCR-0.0.8-3/chipPCR/man/chipPCR-package.Rd | 4
chipPCR-0.0.8-3/chipPCR/man/chipPCR.datasets.Rd | 4
chipPCR-0.0.8-3/chipPCR/man/der-class.Rd | 2
chipPCR-0.0.8-3/chipPCR/man/humanrater.Rd | 7
chipPCR-0.0.8-3/chipPCR/man/lm.coefs.Rd | 12
chipPCR-0.0.8-3/chipPCR/man/normalizer.Rd | 6
chipPCR-0.0.8-3/chipPCR/man/plotCurves.Rd | 26
chipPCR-0.0.8-3/chipPCR/man/th.cyc.Rd | 5
chipPCR-0.0.8-3/chipPCR/vignettes/MFIaggr_gui.png |only
chipPCR-0.0.8-3/chipPCR/vignettes/browser.png |only
chipPCR-0.0.8-3/chipPCR/vignettes/chipPCR.Rnw | 2661 +++++++-----
chipPCR-0.0.8-3/chipPCR/vignettes/fixNA_test1.png |only
chipPCR-0.0.8-3/chipPCR/vignettes/humanrater.png |only
chipPCR-0.0.8-3/chipPCR/vignettes/logo.pdf |only
chipPCR-0.0.8-3/chipPCR/vignettes/logo.png |only
chipPCR-0.0.8-3/chipPCR/vignettes/roediger-burdukiewicz.bib | 372 +
73 files changed, 4739 insertions(+), 2636 deletions(-)