Title: Time Indexes and Time Indexed Series
Diff between tis versions 1.23 dated 2013-01-08 and 1.27 dated 2014-10-18
Description: Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.
Author: Jeff Hallman
Maintainer: Jeff Hallman
tis-1.23/tis/COPYRIGHTS |only
tis-1.27/tis/DESCRIPTION | 6
tis-1.27/tis/MD5 | 53 ++++---
tis-1.27/tis/NAMESPACE | 12 -
tis-1.27/tis/NEWS | 29 ++++
tis-1.27/tis/R/barplot.tis.R | 8 -
tis-1.27/tis/R/barplot2.R | 216 +++++++++++++++---------------
tis-1.27/tis/R/capitalize.R |only
tis-1.27/tis/R/holidays.R | 5
tis-1.27/tis/R/inferTi.R | 8 -
tis-1.27/tis/R/nber.R | 93 +-----------
tis-1.27/tis/R/nberShade.ggplot.R | 8 -
tis-1.27/tis/R/ti.R | 7
tis-1.27/tis/R/tier.R | 6
tis-1.27/tis/R/tisFromCsv.R | 15 +-
tis-1.27/tis/R/tisPlot.R | 55 ++++---
tis-1.27/tis/R/ymdShade.R |only
tis-1.27/tis/R/zooStuff.R | 4
tis-1.27/tis/inst |only
tis-1.27/tis/man/barplot.tis.Rd | 14 -
tis-1.27/tis/man/barplot2.Rd |only
tis-1.27/tis/man/capitalize.Rd |only
tis-1.27/tis/man/holidays.Rd | 3
tis-1.27/tis/man/nberShade.Rd | 53 +------
tis-1.27/tis/man/nberShade.ggplot.Rd | 2
tis-1.27/tis/man/setDefaultFrequencies.Rd | 2
tis-1.27/tis/man/tis-package.Rd | 2
tis-1.27/tis/man/tisFromCsv.Rd | 16 +-
tis-1.27/tis/man/tisLegend.Rd | 3
tis-1.27/tis/man/tisPlot.Rd | 37 +++--
tis-1.27/tis/man/ymdShade.Rd |only
31 files changed, 309 insertions(+), 348 deletions(-)
Title: Pathwise Calibrated Sparse Shooting Algorithm
Diff between picasso versions 0.2.0 dated 2014-10-06 and 0.3.0 dated 2014-10-18
Description: Implement a new family of efficient algorithms, called PathwIse CalibrAted Sparse Shooting AlgOrithm, for a variety of sparse learning problems, including Sparse Linear Regression, Sparse Logistic Regression, Sparse Column Inverse Operator and Sparse Multivariate Regression. Different types of active set identification schemes are implemented, such as cyclic search, greedy search, stochastic search and proximal gradient search. Besides, the package provides the choices between convex (L1 norm) and non-convex (MCP and SCAD) regularizations. Moreover, group regularization, such as group Lasso, group MCP and group SCAD, are also implemented for Sparse Linear Regression, Sparse Logistic Regression and Sparse Multivariate Regression.
Author: Xingguo Li, Tuo Zhao and Han Liu
Maintainer: Xingguo Li
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/picasso.scio.R | 2 +-
man/picasso-package.Rd | 4 ++--
4 files changed, 10 insertions(+), 10 deletions(-)
More information about multispatialCCM at CRAN
Permanent link
Title: Family of Lasso Regression
Diff between flare versions 1.4.0 dated 2014-07-09 and 1.5.0 dated 2014-10-18
Description: The package "flare" provides the implementation of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear model. We adopt the alternating direction method of multipliers and convert the original optimization problem into a sequential L1 penalized least square minimization problem, which can be efficiently solved by linearization algorithm. A multi-stage screening approach is adopted for further acceleration. Besides the sparse linear model estimation, we also provide the extension of these Lasso variants to sparse Gaussian graphical model estimation including TIGER and CLIME using either L1 or adaptive penalty. Missing values can be tolerated for Dantzig selector and CLIME. The computation is memory-optimized using the sparse matrix output.
Author: Xingguo Li, Tuo Zhao, Lie Wang, Xiaoming Yuan and Han Liu
Maintainer: Xingguo Li
DESCRIPTION | 11 +++++------
MD5 | 42 +++++++++++++++++++++---------------------
NAMESPACE | 2 +-
R/slim.R | 2 +-
R/sugm.clime.ladm.scr.R | 3 ---
R/sugm.tiger.ladm.scr.R | 1 -
build/vignette.rds |binary
man/flare-package.Rd | 4 ++--
man/slim.Rd | 4 ++--
man/sugm.Rd | 6 +++---
man/sugm.generator.Rd | 2 +-
man/sugm.plot.Rd | 2 +-
man/sugm.roc.Rd | 2 +-
man/sugm.select.Rd | 6 +++---
src/SFGen.c | 18 +++++++++++-------
src/euc_proj.c | 2 +-
src/mymath.c | 10 +++++-----
src/slim_lasso_ladm_scr.c | 7 ++++---
src/slim_lq_ladm_scr_btr.c | 2 +-
src/slim_sqrt_ladm_scr.c | 4 ++--
src/sugm_clime_ladm_scr.c | 4 ++--
src/sugm_tiger_ladm_scr.c | 10 +++++-----
22 files changed, 72 insertions(+), 72 deletions(-)
Title: Fast and versatile argument checks
Diff between checkmate versions 1.4 dated 2014-09-03 and 1.5.0 dated 2014-10-18
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang
Maintainer: Michel Lang
checkmate-1.4/checkmate/src/assertions.c |only
checkmate-1.4/checkmate/src/assertions.h |only
checkmate-1.5.0/checkmate/DESCRIPTION | 6
checkmate-1.5.0/checkmate/MD5 | 113 +++---
checkmate-1.5.0/checkmate/NAMESPACE | 11
checkmate-1.5.0/checkmate/NEWS | 8
checkmate-1.5.0/checkmate/R/anyInfinite.r |only
checkmate-1.5.0/checkmate/R/checkNamed.r | 2
checkmate-1.5.0/checkmate/R/checkNames.r |only
checkmate-1.5.0/checkmate/R/checkPercentage.r |only
checkmate-1.5.0/checkmate/man/anyInfinite.Rd |only
checkmate-1.5.0/checkmate/man/anyMissing.Rd | 2
checkmate-1.5.0/checkmate/man/asInteger.Rd | 8
checkmate-1.5.0/checkmate/man/assert.Rd | 2
checkmate-1.5.0/checkmate/man/checkAccess.Rd | 10
checkmate-1.5.0/checkmate/man/checkArray.Rd | 10
checkmate-1.5.0/checkmate/man/checkAtomic.Rd | 10
checkmate-1.5.0/checkmate/man/checkAtomicVector.Rd | 10
checkmate-1.5.0/checkmate/man/checkCharacter.Rd | 18
checkmate-1.5.0/checkmate/man/checkChoice.Rd | 8
checkmate-1.5.0/checkmate/man/checkClass.Rd | 10
checkmate-1.5.0/checkmate/man/checkComplex.Rd | 10
checkmate-1.5.0/checkmate/man/checkCount.Rd | 13
checkmate-1.5.0/checkmate/man/checkDataFrame.Rd | 26 -
checkmate-1.5.0/checkmate/man/checkDirectory.Rd | 10
checkmate-1.5.0/checkmate/man/checkEnvironment.Rd | 10
checkmate-1.5.0/checkmate/man/checkFactor.Rd | 10
checkmate-1.5.0/checkmate/man/checkFile.Rd | 10
checkmate-1.5.0/checkmate/man/checkFlag.Rd | 11
checkmate-1.5.0/checkmate/man/checkFunction.Rd | 10
checkmate-1.5.0/checkmate/man/checkInt.Rd | 13
checkmate-1.5.0/checkmate/man/checkInteger.Rd | 10
checkmate-1.5.0/checkmate/man/checkIntegerish.Rd | 10
checkmate-1.5.0/checkmate/man/checkList.Rd | 16
checkmate-1.5.0/checkmate/man/checkLogical.Rd | 10
checkmate-1.5.0/checkmate/man/checkMatrix.Rd | 10
checkmate-1.5.0/checkmate/man/checkNamed.Rd | 12
checkmate-1.5.0/checkmate/man/checkNames.Rd |only
checkmate-1.5.0/checkmate/man/checkNull.Rd | 2
checkmate-1.5.0/checkmate/man/checkNumber.Rd | 13
checkmate-1.5.0/checkmate/man/checkNumeric.Rd | 10
checkmate-1.5.0/checkmate/man/checkPathForOutput.Rd | 10
checkmate-1.5.0/checkmate/man/checkPercentage.Rd |only
checkmate-1.5.0/checkmate/man/checkScalar.Rd | 13
checkmate-1.5.0/checkmate/man/checkScalarNA.Rd | 6
checkmate-1.5.0/checkmate/man/checkSetEqual.Rd | 10
checkmate-1.5.0/checkmate/man/checkString.Rd | 13
checkmate-1.5.0/checkmate/man/checkSubset.Rd | 10
checkmate-1.5.0/checkmate/man/checkVector.Rd | 10
checkmate-1.5.0/checkmate/man/checkmate.Rd | 2
checkmate-1.5.0/checkmate/man/qassert.Rd | 2
checkmate-1.5.0/checkmate/man/qassertr.Rd | 2
checkmate-1.5.0/checkmate/src/any_infinite.c |only
checkmate-1.5.0/checkmate/src/any_infinite.h |only
checkmate-1.5.0/checkmate/src/any_missing.c | 12
checkmate-1.5.0/checkmate/src/as_type.c |only
checkmate-1.5.0/checkmate/src/as_type.h |only
checkmate-1.5.0/checkmate/src/bounds.c | 8
checkmate-1.5.0/checkmate/src/checks.c | 185 ++++------
checkmate-1.5.0/checkmate/src/checks.h | 1
checkmate-1.5.0/checkmate/tests/testthat/test_anyInfinite.r |only
checkmate-1.5.0/checkmate/tests/testthat/test_checkMatrix.r | 2
checkmate-1.5.0/checkmate/tests/testthat/test_checkNames.r |only
checkmate-1.5.0/checkmate/tests/testthat/test_checkNumeric.r | 1
checkmate-1.5.0/checkmate/tests/testthat/test_checkPercentage.r |only
65 files changed, 390 insertions(+), 341 deletions(-)
Title: Read, Write and Edit XLSX Files.
Diff between openxlsx versions 2.0.15 dated 2014-07-27 and 2.2.1 dated 2014-10-18
Description: Simplifies the creation of XLSX files by providing a
high level interface to writing, styling and editing worksheets. Through
the use of Rcpp, read/write times are comparable to the xlsx and XLConnect
packages with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre],
Luca Braglia [ctb]
Maintainer: Alexander Walker
openxlsx-2.0.15/openxlsx/inst/doc/Formatting.Rnw |only
openxlsx-2.0.15/openxlsx/inst/doc/Formatting.pdf |only
openxlsx-2.0.15/openxlsx/man/orderCellRef.Rd |only
openxlsx-2.0.15/openxlsx/vignettes/Formatting.Rnw |only
openxlsx-2.2.1/openxlsx/DESCRIPTION | 12
openxlsx-2.2.1/openxlsx/MD5 | 76
openxlsx-2.2.1/openxlsx/NAMESPACE | 4
openxlsx-2.2.1/openxlsx/NEWS | 50
openxlsx-2.2.1/openxlsx/R/RcppExports.R | 28
openxlsx-2.2.1/openxlsx/R/WorkbookClass.R | 831 +++-
openxlsx-2.2.1/openxlsx/R/baseXML.R | 398 --
openxlsx-2.2.1/openxlsx/R/borderFunctions.R | 6
openxlsx-2.2.1/openxlsx/R/helperFunctions.R | 100
openxlsx-2.2.1/openxlsx/R/loadWorkbook.R | 133
openxlsx-2.2.1/openxlsx/R/openxlsx.R | 5
openxlsx-2.2.1/openxlsx/R/readWorkbook.R | 71
openxlsx-2.2.1/openxlsx/R/wrappers.R | 3889 +++++++++++----------
openxlsx-2.2.1/openxlsx/R/writeData.R | 27
openxlsx-2.2.1/openxlsx/R/writeDataTable.R | 91
openxlsx-2.2.1/openxlsx/R/writexlsx.R | 217 -
openxlsx-2.2.1/openxlsx/build/vignette.rds |binary
openxlsx-2.2.1/openxlsx/inst/doc/Introduction.Rnw | 71
openxlsx-2.2.1/openxlsx/inst/doc/Introduction.pdf |binary
openxlsx-2.2.1/openxlsx/inst/doc/formatting.Rnw |only
openxlsx-2.2.1/openxlsx/inst/doc/formatting.pdf |only
openxlsx-2.2.1/openxlsx/man/addFilter.Rd |only
openxlsx-2.2.1/openxlsx/man/addWorksheet.Rd | 68
openxlsx-2.2.1/openxlsx/man/conditionalFormat.Rd | 17
openxlsx-2.2.1/openxlsx/man/convertToDateTime.Rd | 6
openxlsx-2.2.1/openxlsx/man/createStyle.Rd | 9
openxlsx-2.2.1/openxlsx/man/openxlsx.Rd | 4
openxlsx-2.2.1/openxlsx/man/pageSetup.Rd | 7
openxlsx-2.2.1/openxlsx/man/read.xlsx.Rd | 6
openxlsx-2.2.1/openxlsx/man/readWorkbook.Rd | 4
openxlsx-2.2.1/openxlsx/man/removeFilter.Rd |only
openxlsx-2.2.1/openxlsx/man/setColWidths.Rd | 20
openxlsx-2.2.1/openxlsx/man/setHeaderFooter.Rd |only
openxlsx-2.2.1/openxlsx/man/write.xlsx.Rd | 35
openxlsx-2.2.1/openxlsx/man/writeData.Rd | 9
openxlsx-2.2.1/openxlsx/man/writeDataTable.Rd | 18
openxlsx-2.2.1/openxlsx/src/RcppExports.cpp | 93
openxlsx-2.2.1/openxlsx/src/cppFunctions.cpp | 474 +-
openxlsx-2.2.1/openxlsx/vignettes/Introduction.Rnw | 71
openxlsx-2.2.1/openxlsx/vignettes/formatting.Rnw |only
44 files changed, 4313 insertions(+), 2537 deletions(-)
Title: raster: Geographic data analysis and modeling
Diff between raster versions 2.3-10 dated 2014-10-16 and 2.3-12 dated 2014-10-18
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans
ChangeLog | 2 +-
DESCRIPTION | 12 ++++++------
MD5 | 18 +++++++++---------
R/erase.R | 2 +-
R/intersect_sp.R | 2 +-
R/rowMinMax.R | 15 +++++++++++----
inst/doc/Raster.pdf |binary
inst/doc/functions.pdf |binary
inst/doc/rasterfile.pdf |binary
man/predict.Rd | 2 +-
10 files changed, 30 insertions(+), 23 deletions(-)
Title: Stochastic Profiling using Maximum Likelihood Estimation
Diff between stochprofML versions 1.1 dated 2014-05-22 and 1.2 dated 2014-10-18
Description: This is an R package accompanying the paper "Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles" by Sameer S Bajikar, Christiane Fuchs, Andreas Roller, Fabian J Theis and Kevin A Janes (PNAS 2014, 111(5), E626-635). In this paper, we measure expression profiles from small heterogeneous populations of cells, where each cell is assumed to be from a mixture of lognormal distributions. We perform maximum likelihood estimation in order to infer the mixture ratio and the parameters of these lognormal distributions from the cumulated expression measurements.
Author: Christiane Fuchs
Maintainer: Christiane Fuchs
DESCRIPTION | 8 ++++----
MD5 | 25 +++++++++++++++----------
NAMESPACE | 3 ++-
R/analyze.sod2.R | 4 +++-
R/stochasticProfilingData.R |only
R/stochasticProfilingML.R |only
R/stochprof.logit.R | 2 +-
R/stochprofML-internal.R |only
data/sod2.rda |binary
data/toycluster.EXPLN.rda |binary
data/toycluster.LNLN.rda |binary
data/toycluster.rLNLN.rda |binary
man/generate.toydata.Rd | 6 +++++-
man/stochasticProfilingData.Rd |only
man/stochasticProfilingML.Rd |only
man/stochprofML-package.Rd | 19 ++++++++++++++-----
16 files changed, 44 insertions(+), 23 deletions(-)
Title: Ecological and biogeographical null model tests for comparing
rarefaction curves
Diff between rareNMtests versions 1.0 dated 2014-06-06 and 1.1 dated 2014-10-18
Description: Randomization tests for the statistical comparison of \emph{i} = two or more individual-based, sample-based or coverage-based rarefaction curves. The ecological null hypothesis is that the \emph{i} samples were all drawn randomly from a single assemblage, with (necessarily) a single underlying species abundance distribution. The biogeographic null hypothesis is that the \emph{i} samples were all drawn from different assemblages that, nonetheless, share similar species richness and species abundance distributions
Author: Luis Cayuela and Nicholas J. Gotelli
Maintainer: Luis Cayuela
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/BiogTest.individual.R | 9 +++++----
R/BiogTest.sample.R | 21 ++++++++++++++-------
R/EcoTest.sample.R | 1 +
5 files changed, 28 insertions(+), 19 deletions(-)