Title: Reads Mass Spectrometry Data in mzXML Format
Diff between readMzXmlData versions 2.7 dated 2013-07-03 and 2.8 dated 2014-09-28
Description: Functions for reading mass spectrometry data in mzXML format.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb
readMzXmlData-2.7/readMzXmlData/R/mqReadMzXml-functions.R |only
readMzXmlData-2.7/readMzXmlData/man/mqReadMzXml.Rd |only
readMzXmlData-2.8/readMzXmlData/DESCRIPTION | 20 +--
readMzXmlData-2.8/readMzXmlData/MD5 | 41 +++---
readMzXmlData-2.8/readMzXmlData/NAMESPACE | 3
readMzXmlData-2.8/readMzXmlData/NEWS | 5
readMzXmlData-2.8/readMzXmlData/R/package.R | 24 ++-
readMzXmlData-2.8/readMzXmlData/R/readMzXmlDir-functions.R | 3
readMzXmlData-2.8/readMzXmlData/R/readMzXmlFile-functions.R | 27 ++--
readMzXmlData-2.8/readMzXmlData/man/attributeTimeToDouble.Rd | 25 +--
readMzXmlData-2.8/readMzXmlData/man/attributeToDouble.Rd | 24 +--
readMzXmlData-2.8/readMzXmlData/man/attributeToString.Rd | 25 +--
readMzXmlData-2.8/readMzXmlData/man/base64-decode.Rd | 33 ++---
readMzXmlData-2.8/readMzXmlData/man/grepNumeric.Rd | 31 ++--
readMzXmlData-2.8/readMzXmlData/man/grepSubString.Rd | 16 +-
readMzXmlData-2.8/readMzXmlData/man/mzXmlHandlers.Rd | 18 +-
readMzXmlData-2.8/readMzXmlData/man/parseMzXml.Rd | 13 +-
readMzXmlData-2.8/readMzXmlData/man/readMzXmlData-defunct.Rd |only
readMzXmlData-2.8/readMzXmlData/man/readMzXmlData-package.Rd | 39 ++----
readMzXmlData-2.8/readMzXmlData/man/readMzXmlDir.Rd | 64 +++++-----
readMzXmlData-2.8/readMzXmlData/man/readMzXmlFile-internal.Rd | 22 +--
readMzXmlData-2.8/readMzXmlData/man/readMzXmlFile.Rd | 38 +++--
readMzXmlData-2.8/readMzXmlData/man/revfregexpr.Rd | 16 +-
23 files changed, 247 insertions(+), 240 deletions(-)
Title: Local Average Response Functions for Instrumental Variable
Estimation of Treatment Effects
Diff between LARF versions 1.1 dated 2013-09-12 and 1.2 dated 2014-09-28
Description: Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.
Author: Weihua An and Xuefu Wang, Indiana University Bloomington
Maintainer: Weihua An
DESCRIPTION | 14 -
MD5 | 18 -
R/larf.R | 478 ++++++++++++++++++++++++++++++++++------------------
man/c401k.Rd | 6
man/larf.Rd | 80 +++++---
man/larf.fit.Rd | 62 +-----
man/larf.predict.Rd | 36 ---
man/print.larf.Rd | 11 -
man/summary.larf.Rd | 24 --
man/vcov.larf.Rd | 7
10 files changed, 417 insertions(+), 319 deletions(-)
Title: ExPANdS
Diff between expands versions 1.4 dated 2014-03-02 and 1.5 dated 2014-09-28
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (ExPANdS) characterizes coexisting subpopulations in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model amplifies the statistical power to detect coexisting genotypes, by exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results. Updates include: (1) Additional optional parameter "min_CellFreq" provided for function runExPANdS, specifying the minimum cellular prevalence of mutations to be included for subpopulation predictions.(2) Filtered loci with high-level amplifications, according to max_PM setting. This reduces unnecessary processing time, as assignment of mutations within amplified regions to subpopulations is not successful. (3) Additional function "buildMultiSamplePhylo" available, which integrates the subpopulations predicted in multiple, geographically distinct tumor samples into one common phylogeny.
Author: Noemi Andor
Maintainer: Noemi Andor
DESCRIPTION | 11
MD5 | 59 ++--
R/assignMutations.R | 4
R/assignQuantityToSP.R | 121 +++++----
R/buildMultiSamplePhylo.R |only
R/buildPhylo.R | 2
R/cellfrequency_pdf.R | 2
R/clusterCellFrequencies.R | 54 ++--
R/computeCellFrequencyDistributions.R | 4
R/plotSPs.R | 176 ++++++-------
R/runExPANdS.R | 406 ++++++++++++++++---------------
build |only
inst/doc/expands.R |only
inst/doc/expands.Rnw | 47 +++
inst/doc/expands.pdf |binary
java |only
man/assignMutations.Rd | 7
man/assignQuantityToMutation.Rd | 2
man/assignQuantityToSP.Rd | 12
man/buildMultiSamplePhylo.Rd |only
man/buildPhylo.Rd | 2
man/cellfrequency_pdf.Rd | 9
man/clusterCellFrequencies.Rd | 15 -
man/computeCellFrequencyDistributions.Rd | 9
man/plotSPs.Rd | 4
man/roi.Rd | 2
man/runExPANdS.Rd | 32 +-
man/snv.Rd | 2
vignettes/ID_MRD_001_metKidney.cbs |only
vignettes/ID_MRD_001_metKidney.sps |only
vignettes/ID_MRD_001_metLung.cbs |only
vignettes/ID_MRD_001_metLung.sps |only
vignettes/ID_MRD_001_primPancreas.cbs |only
vignettes/ID_MRD_001_primPancreas.sps |only
vignettes/expands.Rnw | 49 +++
vignettes/expands.bib | 3
36 files changed, 587 insertions(+), 447 deletions(-)
Title: Handling of Swedish Identity Numbers
Diff between sweidnumbr versions 0.1.1 dated 2014-09-06 and 0.2 dated 2014-09-28
Description: Structural handling of identity numbers used in the Swedish
administration such as personal identity numbers ('personnummer') and
organizational identity numbers ('organisationsnummer').
Author: Mans Magnusson
Maintainer: Mans Magnusson
sweidnumbr-0.1.1/sweidnumbr/inst/tests/test-pin_format.R |only
sweidnumbr-0.1.1/sweidnumbr/man/pin_format.Rd |only
sweidnumbr-0.2/sweidnumbr/DESCRIPTION | 8
sweidnumbr-0.2/sweidnumbr/MD5 | 69 +++--
sweidnumbr-0.2/sweidnumbr/NAMESPACE | 7
sweidnumbr-0.2/sweidnumbr/R/pin.R | 154 +++++++++----
sweidnumbr-0.2/sweidnumbr/R/pin_internal.R | 22 +
sweidnumbr-0.2/sweidnumbr/R/pin_methods.R |only
sweidnumbr-0.2/sweidnumbr/R/sweidnumbr.R | 5
sweidnumbr-0.2/sweidnumbr/README.md | 26 ++
sweidnumbr-0.2/sweidnumbr/build/vignette.rds |binary
sweidnumbr-0.2/sweidnumbr/inst/doc/sweidnumbr.R | 9
sweidnumbr-0.2/sweidnumbr/inst/tests/test-as.pin.R |only
sweidnumbr-0.2/sweidnumbr/inst/tests/test-is.pin.R | 5
sweidnumbr-0.2/sweidnumbr/inst/tests/test-pin_age.R | 20 +
sweidnumbr-0.2/sweidnumbr/inst/tests/test-pin_birthplace.R | 8
sweidnumbr-0.2/sweidnumbr/inst/tests/test-pin_convert.R | 13 -
sweidnumbr-0.2/sweidnumbr/inst/tests/test-pin_sex.R | 8
sweidnumbr-0.2/sweidnumbr/inst/tests/test-pin_to_date.R |only
sweidnumbr-0.2/sweidnumbr/man/as.pin.Rd |only
sweidnumbr-0.2/sweidnumbr/man/is.oin.Rd | 2
sweidnumbr-0.2/sweidnumbr/man/is.pin.Rd | 10
sweidnumbr-0.2/sweidnumbr/man/luhn_algo.Rd | 2
sweidnumbr-0.2/sweidnumbr/man/oin_ctrl.Rd | 2
sweidnumbr-0.2/sweidnumbr/man/oin_group.Rd | 2
sweidnumbr-0.2/sweidnumbr/man/oin_group_element.Rd | 2
sweidnumbr-0.2/sweidnumbr/man/pin_add_zero.Rd | 2
sweidnumbr-0.2/sweidnumbr/man/pin_age.Rd | 16 +
sweidnumbr-0.2/sweidnumbr/man/pin_birthplace.Rd | 4
sweidnumbr-0.2/sweidnumbr/man/pin_birthplace_internal.Rd | 4
sweidnumbr-0.2/sweidnumbr/man/pin_century.Rd | 2
sweidnumbr-0.2/sweidnumbr/man/pin_convert.Rd | 6
sweidnumbr-0.2/sweidnumbr/man/pin_coordn.Rd | 4
sweidnumbr-0.2/sweidnumbr/man/pin_coordn_correct.Rd | 4
sweidnumbr-0.2/sweidnumbr/man/pin_ctrl.Rd | 4
sweidnumbr-0.2/sweidnumbr/man/pin_sex.Rd | 6
sweidnumbr-0.2/sweidnumbr/man/pin_to_date.Rd |only
sweidnumbr-0.2/sweidnumbr/man/sweidnumbr.Rd | 4
sweidnumbr-0.2/sweidnumbr/vignettes/sweidnumbr.Rmd | 16 +
39 files changed, 295 insertions(+), 151 deletions(-)
Title: Fetch economic and financial time series data from public
sources
Diff between pdfetch versions 0.1.5 dated 2014-08-10 and 0.1.6 dated 2014-09-28
Description: A package for downloading economic and financial time series from
public sources.
Author: Abiel Reinhart
Maintainer: Abiel Reinhart
DESCRIPTION | 10 +--
MD5 | 35 +++++------
NAMESPACE | 3
NEWS | 7 ++
R/help.R | 2
R/pdfetch.R | 136 ++++++++++++++++++++++++++++++++++++--------
README.md | 1
inst/tests/test-pdfetch.R | 15 +++-
man/pdfetch_BLS.Rd | 5 +
man/pdfetch_BOE.Rd | 5 +
man/pdfetch_ECB.Rd | 5 +
man/pdfetch_EIA.Rd |only
man/pdfetch_EUROSTAT.Rd | 7 +-
man/pdfetch_EUROSTAT_DSD.Rd | 5 +
man/pdfetch_FRED.Rd | 5 +
man/pdfetch_INSEE.Rd | 5 +
man/pdfetch_ONS.Rd | 9 +-
man/pdfetch_WB.Rd | 5 +
man/pdfetch_YAHOO.Rd | 9 ++
19 files changed, 204 insertions(+), 65 deletions(-)
Title: Accurate Timing Functions
Diff between microbenchmark versions 1.3-0 dated 2013-02-20 and 1.4-2 dated 2014-09-28
More information about microbenchmark at CRAN
Description: Provides infrastructure to accurately measure and compare
the execution time of R expressions.
Author: Olaf Mersmann [aut, cre],
Claudia Beleites [ctb],
Rainer Hurling [ctb],
Ari Friedman [ctb]
Maintainer: Olaf Mersmann
microbenchmark-1.3-0/microbenchmark/ChangeLog |only
microbenchmark-1.4-2/microbenchmark/DESCRIPTION | 29 -
microbenchmark-1.4-2/microbenchmark/LICENSE |only
microbenchmark-1.4-2/microbenchmark/MD5 | 59 +-
microbenchmark-1.4-2/microbenchmark/NAMESPACE | 23 -
microbenchmark-1.4-2/microbenchmark/R/autoplot.R | 60 +-
microbenchmark-1.4-2/microbenchmark/R/boxplot.R | 30 -
microbenchmark-1.4-2/microbenchmark/R/internal.R | 106 ++---
microbenchmark-1.4-2/microbenchmark/R/microbenchmark.R | 209 ++++++----
microbenchmark-1.4-2/microbenchmark/R/microtiming_precision.R | 30 -
microbenchmark-1.4-2/microbenchmark/R/nanotime.R |only
microbenchmark-1.4-2/microbenchmark/R/print.R | 63 ++-
microbenchmark-1.4-2/microbenchmark/R/summary.R | 65 +--
microbenchmark-1.4-2/microbenchmark/inst |only
microbenchmark-1.4-2/microbenchmark/man/autoplot.microbenchmark.Rd | 23 -
microbenchmark-1.4-2/microbenchmark/man/boxplot.microbenchmark.Rd | 20
microbenchmark-1.4-2/microbenchmark/man/coalesce.Rd | 15
microbenchmark-1.4-2/microbenchmark/man/convert_to_unit.Rd | 41 +
microbenchmark-1.4-2/microbenchmark/man/find_prefix.Rd | 30 -
microbenchmark-1.4-2/microbenchmark/man/get_nanotime.Rd |only
microbenchmark-1.4-2/microbenchmark/man/microbenchmark.Rd | 151 ++++---
microbenchmark-1.4-2/microbenchmark/man/microtiming_precision.Rd | 26 -
microbenchmark-1.4-2/microbenchmark/man/print.microbenchmark.Rd | 53 +-
microbenchmark-1.4-2/microbenchmark/man/summary.microbenchmark.Rd | 32 -
microbenchmark-1.4-2/microbenchmark/src/Makevars | 2
microbenchmark-1.4-2/microbenchmark/src/Makevars.win |only
microbenchmark-1.4-2/microbenchmark/src/do_nothing.c |only
microbenchmark-1.4-2/microbenchmark/src/do_nothing.h |only
microbenchmark-1.4-2/microbenchmark/src/nanotimer.c | 181 ++++----
microbenchmark-1.4-2/microbenchmark/src/nanotimer_gettime.h | 4
microbenchmark-1.4-2/microbenchmark/src/nanotimer_macosx.h | 2
microbenchmark-1.4-2/microbenchmark/src/nanotimer_rtposix.h | 18
microbenchmark-1.4-2/microbenchmark/src/nanotimer_windows.h | 4
microbenchmark-1.4-2/microbenchmark/tools |only
34 files changed, 742 insertions(+), 534 deletions(-)
Permanent link
Title: Maximum Entropy Bootstrap for Time Series
Diff between meboot versions 1.4-3 dated 2014-03-26 and 1.4-5 dated 2014-09-28
Description: This package performs maximum entropy density based
dependent data bootstrap. An algorithm is provided to create a
population of time series (ensemble) without assuming
stationarity. The reference paper (Vinod, H.D., 2004) explains
how the algorithm satisfies the ergodic theorem and the central
limit theorem.
Author: Hrishikesh D. Vinod
Maintainer: Javier López-de-Lacalle
meboot-1.4-3/meboot/R/slider.mts.R |only
meboot-1.4-3/meboot/man/slider.mts.Rd |only
meboot-1.4-5/meboot/DESCRIPTION | 14 +++++++-------
meboot-1.4-5/meboot/MD5 | 16 +++++++---------
meboot-1.4-5/meboot/NAMESPACE | 2 +-
meboot-1.4-5/meboot/R/expand.sd.R | 29 +++++++++++++++++++++++------
meboot-1.4-5/meboot/R/flexMeboot.R | 4 ++--
meboot-1.4-5/meboot/R/meboot.R | 2 +-
meboot-1.4-5/meboot/inst/doc/meboot.pdf |binary
meboot-1.4-5/meboot/man/meboot.Rd | 2 --
10 files changed, 41 insertions(+), 28 deletions(-)
Title: Tools for Two-Dimensional Monte-Carlo Simulations
Diff between mc2d versions 0.1-14 dated 2013-10-16 and 0.1-15 dated 2014-09-28
Description: Various distributions and utilities to ease the use of R to build and study Two-Dimensional Monte-Carlo simulations
Author: Regis Pouillot [aut, cre],
Marie-Laure Delignette-Muller [ctb],
Jean-Baptiste Denis [ctb]
Maintainer: Regis Pouillot
DESCRIPTION | 12 ++++++------
MD5 | 10 +++++-----
R/mcstoc.R | 40 +++++++++++++++++++++++++---------------
build/vignette.rds |binary
data/ec.rda |binary
inst/NEWS | 7 +++++++
6 files changed, 43 insertions(+), 26 deletions(-)
Title: Add Standardized Regression Coefficients to lm-Objects
Diff between lm.beta versions 1.0 dated 2014-07-20 and 1.5 dated 2014-09-28
Description: Adds standardized regression coefficients to objects created by lm. Also extends the S3 methods print, summary and coef with additional boolean argument standardized.
Author: Stefan Behrendt [aut, cre]
Maintainer: Stefan Behrendt
DESCRIPTION | 15 ++++++++-------
MD5 | 21 +++++++++++----------
NEWS |only
R/coef.lm.beta.R | 4 ++--
R/lm.beta.R | 4 +---
R/print.lm.beta.R | 6 +++---
R/summary.lm.beta.R | 2 +-
man/coef.lm.beta.Rd | 10 ++++++----
man/lm.beta-package.Rd | 26 ++++++++++++++++++--------
man/lm.beta.Rd | 26 ++++++++++++++++++--------
man/print.lm.beta.Rd | 10 ++++++----
man/summary.lm.beta.Rd | 12 +++++++-----
12 files changed, 81 insertions(+), 55 deletions(-)
Title: Planning and Analyzing Dose Finding experiments
Diff between DoseFinding versions 0.9-11 dated 2014-02-11 and 0.9-12 dated 2014-09-28
Description: The DoseFinding package provides functions for the design and analysis
of dose-finding experiments (with focus on pharmaceutical Phase
II clinical trials). It provides functions for: multiple contrast
tests, fitting non-linear dose-response models (using Bayesian and
non-Bayesian estimation), calculating optimal designs and an
implementation of the MCPMod methodology.
Author: Bjoern Bornkamp, Jose Pinheiro, Frank Bretz
Maintainer: Bjoern Bornkamp
ChangeLog | 10 +++++++
DESCRIPTION | 12 ++++----
MD5 | 52 +++++++++++++++++++-------------------
R/Mods.R | 6 ++--
R/bFitMod.R | 4 ++
R/optContr.R | 9 ++++--
R/optDesign.R | 13 +++++----
R/planMod.R | 4 +-
data/glycobrom.rda |binary
man/DoseFinding-package.Rd | 10 +++----
man/MCPMod.Rd | 6 ++--
man/MCTtest.Rd | 8 ++---
man/bFitMod.Rd | 61 +++++++++++++++++++++++++++++++++++++++++++--
man/fitMod.Rd | 6 ++--
man/glycobrom.Rd | 27 +++++++++++++++++++
man/neurodeg.Rd | 8 ++---
man/optContr.Rd | 6 ++--
tests/testgFit.R | 4 --
tests/testplanMod.R | 1
tests/testsDesign.R | 14 +++++++++-
tests/testsFitting.R | 2 -
tests/testsMCPMod.R | 3 --
tests/testsMCT.R | 6 ++--
tests/testsoptContr.R | 6 ++--
tests/testsplotDRMod.R | 2 -
tests/testssampSize.R | 2 -
tests/testssamplMod.R | 3 --
27 files changed, 199 insertions(+), 86 deletions(-)
Title: Hot Deck Imputation Methods for Missing Data.
Diff between HotDeckImputation versions 0.1.0 dated 2013-08-12 and 1.0.0 dated 2014-09-28
More information about HotDeckImputation at CRAN
Description: This package provides hot deck imputation methods to resolve missing data.
Author: Dieter William Joenssen [aut, cre, cph]
Maintainer: Dieter William Joenssen
DESCRIPTION | 17 ++--
MD5 | 26 ++++---
NAMESPACE | 4 -
NEWS | 5 +
R/HotDeckImputation.R | 134 ++++++++++++++++++++++++++-------------
R/SeqentialHotDeck.R |only
R/zzz.R |only
man/HotDeckImputation-package.Rd | 18 ++++-
man/impute.CPS_SEQ_HD.Rd |only
man/impute.NN_HD.Rd | 26 ++++---
man/impute.SEQ_HD.Rd |only
man/impute.mean.Rd | 10 +-
man/match.d_r_odd.Rd |only
man/match.d_r_vam.Rd | 2
man/reweight.data.Rd | 12 +--
src/Distmatrix.c | 67 +------------------
src/seq_HD.c |only
17 files changed, 171 insertions(+), 150 deletions(-)
Permanent link