Title: Structural Time Series Models
Diff between stsm versions 1.3 dated 2014-05-30 and 1.4 dated 2014-07-27
Description: This package provides algorithms to fit
structural time series models by maximum likelihood.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle
stsm-1.3/stsm/inst/CHANGES |only
stsm-1.4/stsm/DESCRIPTION | 8
stsm-1.4/stsm/MD5 | 64 +++--
stsm-1.4/stsm/R/logLik.R | 4
stsm-1.4/stsm/R/maxclik-fd-scoring.R | 13 -
stsm-1.4/stsm/R/maxlik-fd-optim.R | 142 ++++--------
stsm-1.4/stsm/R/maxlik-fd-scoring.R | 142 ++++--------
stsm-1.4/stsm/R/maxlik-td-optim.R | 111 ++-------
stsm-1.4/stsm/R/maxlik-td-scoring.R | 140 ++++--------
stsm-1.4/stsm/R/mcloglik-fd.R | 8
stsm-1.4/stsm/R/methods-stsmFit.R | 65 ++++-
stsm-1.4/stsm/R/methods-vcov-confint.R | 21 +
stsm-1.4/stsm/R/mloglik-fd.R | 193 +++++++++++++----
stsm-1.4/stsm/R/mloglik-td.R | 125 +++++++----
stsm-1.4/stsm/R/stsmFit.R | 16 +
stsm-1.4/stsm/inst/NEWS |only
stsm-1.4/stsm/inst/README |only
stsm-1.4/stsm/inst/doc |only
stsm-1.4/stsm/inst/sims/datagen-llm.R | 7
stsm-1.4/stsm/inst/sims/datagen-llmseas.R | 11
stsm-1.4/stsm/inst/sims/sim-llm-mcl-fd.R | 58 -----
stsm-1.4/stsm/inst/sims/sim-llm-ml-fd.R | 13 -
stsm-1.4/stsm/inst/sims/sim-llm-ml-td.R | 9
stsm-1.4/stsm/inst/sims/sim-llmseas-mcl-fd.R | 23 +-
stsm-1.4/stsm/inst/sims/sim-llmseas-ml-fd.R | 15 -
stsm-1.4/stsm/inst/sims/sim-llmseas-ml-td.R | 83 -------
stsm-1.4/stsm/inst/sims/test-derivatives-mcloglik-fd.R | 1
stsm-1.4/stsm/inst/sims/test-derivatives-mloglik-fd.R | 59 -----
stsm-1.4/stsm/man/maxlik-fd.Rd | 23 --
stsm-1.4/stsm/man/maxlik-td.Rd | 17 -
stsm-1.4/stsm/man/methods-stsmFit.Rd | 15 +
stsm-1.4/stsm/man/mloglik-fd.Rd | 45 +++
stsm-1.4/stsm/man/mloglik-td.Rd | 15 -
33 files changed, 695 insertions(+), 751 deletions(-)
Title: Useful R code for the Estimation of Migration
Diff between migest versions 1.5 dated 2014-03-27 and 1.6 dated 2014-07-27
Description: The migest package contains a collection of R functions that are useful to estimate migration when there is missing data. Included is the ffs routine to estimate migration flows from stock data, as well as various other functions to indirectly estimate flows where marginal totals are known. Functions are illustrated with dummy data.
Author: Guy J. Abel
Maintainer: Guy J. Abel
DESCRIPTION | 8 -
MD5 | 28 ++---
R/ffs.R | 23 +++-
R/ipf2.R | 5
R/ipf3.R | 5
R/ipf3.qi.R | 4
R/migest-internal.R | 251 ++++++++++++++++++++++++--------------------------
data/rc9.fund.rda |binary
demo/cfplot_nat.R | 6 -
demo/cfplot_reg.R | 6 -
man/cm2.Rd | 2
man/cm3.Rd | 4
man/ffs.Rd | 11 +-
man/ipf2.Rd | 3
man/migest-package.Rd | 2
15 files changed, 198 insertions(+), 160 deletions(-)
Title: A multi-platform GUI for drawing customizable graphs in R
Diff between GrapheR versions 1.9-83 dated 2014-06-28 and 1.9-84 dated 2014-07-27
Description: GrapheR is a multi-platform user interface for drawing highly customizable graphs in R. It aims to be a valuable help to quickly draw publishable graphs without any knowledge of R commands. Six kinds of graph are available: histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter plot.
Author: Maxime Hervé
Maintainer: Maxime Hervé
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 8 +++++++-
R/zzzz.R | 2 +-
inst/CITATION | 6 ++----
man/GrapheR-package.Rd | 10 +++++-----
6 files changed, 24 insertions(+), 20 deletions(-)
Title: file-based access to large matrices stored on HDD in binary
format
Diff between DatABEL versions 0.9-4 dated 2013-03-12 and 0.9-4.1 dated 2014-07-27
Description: a package providing an interface to the C++ FILEVECTOR
library facilitating analysis of large (giga- to tera-bytes)
matrices; matrix storage is organized in a way that either
columns or rows are quickly accessible; primarily aimed to
support genome-wide association analyses e.g. using GenABEL,
MixABEL and ProbABEL
Author: Yurii Aulchenko, Stepan Yakovenko, Erik Roos, Marcel Kempenaar
Maintainer: Yurii Aulchenko
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
R/zzz.R | 6 ++++--
man/apply2dfo.Rd | 6 ++++--
man/text2databel.Rd | 8 ++++----
src/CastUtils.cpp | 7 ++++---
6 files changed, 24 insertions(+), 19 deletions(-)
Title: an R package for genetic analysis of populations with mixed
reproduction
Diff between poppr versions 1.1.0 dated 2014-07-24 and 1.1.1 dated 2014-07-27
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar
Maintainer: Zhian N. Kamvar
DESCRIPTION | 8
MD5 | 62 ++--
NEWS | 7
R/amova.r | 2
R/distances.r | 20 -
R/internal.r | 6
R/poppr.R | 16 -
inst/doc/algo.Rnw | 4
inst/doc/algo.pdf |binary
inst/doc/poppr_manual.R | 4
inst/doc/poppr_manual.Rnw | 9
inst/doc/poppr_manual.pdf |binary
man/Pinf.Rd | 2
man/genetic_distance.Rd | 20 -
man/monpop.Rd | 4
man/poppr-package.Rd | 16 -
man/poppr.amova.Rd | 2
src/poppr_distance.c | 470 ++++++++++++++------------------
tests/testthat/test-values.R | 4
vignettes/algo.Rnw | 4
vignettes/figure/Aeut_MLG_Ahena.pdf |binary
vignettes/figure/Aeut_MLG_black.pdf |binary
vignettes/figure/Aeut_MLG_title.pdf |binary
vignettes/figure/bd_histogram.pdf |binary
vignettes/figure/ex_data_picture.pdf |binary
vignettes/figure/initializing_poppr.pdf |binary
vignettes/figure/mlgbarplot.pdf |binary
vignettes/figure/mlgrareplot.pdf |binary
vignettes/figure/subnor.pdf |binary
vignettes/figure/unnamed-chunk-3.pdf |binary
vignettes/poppr_manual-concordance.tex | 4
vignettes/poppr_manual.Rnw | 9
32 files changed, 314 insertions(+), 359 deletions(-)
Title: .xlsx reading, writing and editing.
Diff between openxlsx versions 2.0.1 dated 2014-05-29 and 2.0.15 dated 2014-07-27
Description: This package 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-2.0.1/openxlsx/inst/doc/Examples.Rnw |only
openxlsx-2.0.1/openxlsx/inst/doc/Examples.pdf |only
openxlsx-2.0.1/openxlsx/vignettes/Examples.Rnw |only
openxlsx-2.0.15/openxlsx/DESCRIPTION | 8
openxlsx-2.0.15/openxlsx/MD5 | 82
openxlsx-2.0.15/openxlsx/NAMESPACE | 3
openxlsx-2.0.15/openxlsx/NEWS | 43
openxlsx-2.0.15/openxlsx/R/RcppExports.R | 20
openxlsx-2.0.15/openxlsx/R/StyleClass.R | 10
openxlsx-2.0.15/openxlsx/R/WorkbookClass.R | 750 ++--
openxlsx-2.0.15/openxlsx/R/baseXML.R | 7
openxlsx-2.0.15/openxlsx/R/borderFunctions.R | 701 +++-
openxlsx-2.0.15/openxlsx/R/helperFunctions.R | 381 ++
openxlsx-2.0.15/openxlsx/R/loadWorkbook.R | 317 -
openxlsx-2.0.15/openxlsx/R/openXL.R | 3
openxlsx-2.0.15/openxlsx/R/openxlsx.R |only
openxlsx-2.0.15/openxlsx/R/readWorkbook.R | 27
openxlsx-2.0.15/openxlsx/R/wrappers.R | 3421 ++++++++++----------
openxlsx-2.0.15/openxlsx/R/writeData.R | 262 -
openxlsx-2.0.15/openxlsx/R/writeDataTable.R | 87
openxlsx-2.0.15/openxlsx/R/writexlsx.R | 92
openxlsx-2.0.15/openxlsx/build/vignette.rds |binary
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/inst/doc/Introduction.Rnw |only
openxlsx-2.0.15/openxlsx/inst/doc/Introduction.pdf |only
openxlsx-2.0.15/openxlsx/inst/readTest.xlsx |binary
openxlsx-2.0.15/openxlsx/man/conditionalFormat.Rd | 73
openxlsx-2.0.15/openxlsx/man/convertToDate.Rd | 1
openxlsx-2.0.15/openxlsx/man/convertToDateTime.Rd |only
openxlsx-2.0.15/openxlsx/man/createStyle.Rd | 2
openxlsx-2.0.15/openxlsx/man/createWorkbook.Rd | 2
openxlsx-2.0.15/openxlsx/man/insertPlot.Rd | 8
openxlsx-2.0.15/openxlsx/man/loadWorkbook.Rd | 2
openxlsx-2.0.15/openxlsx/man/names.Rd |only
openxlsx-2.0.15/openxlsx/man/openxlsx.Rd |only
openxlsx-2.0.15/openxlsx/man/renameWorksheet.Rd | 16
openxlsx-2.0.15/openxlsx/man/setColWidths.Rd | 3
openxlsx-2.0.15/openxlsx/man/sheets.Rd | 12
openxlsx-2.0.15/openxlsx/man/showGridLines.Rd | 2
openxlsx-2.0.15/openxlsx/man/worksheetOrder.Rd | 4
openxlsx-2.0.15/openxlsx/man/write.xlsx.Rd | 14
openxlsx-2.0.15/openxlsx/man/writeData.Rd | 93
openxlsx-2.0.15/openxlsx/man/writeDataTable.Rd | 8
openxlsx-2.0.15/openxlsx/src/RcppExports.cpp | 84
openxlsx-2.0.15/openxlsx/src/cppFunctions.cpp | 1109 ++----
openxlsx-2.0.15/openxlsx/vignettes/Formatting.Rnw |only
openxlsx-2.0.15/openxlsx/vignettes/Introduction.Rnw |only
openxlsx-2.0.15/openxlsx/vignettes/tableStyles.PNG |only
49 files changed, 4128 insertions(+), 3519 deletions(-)
Title: Kalman Filter, Smoother and Disturbance Smoother
Diff between KFKSDS versions 1.4 dated 2014-06-15 and 1.5 dated 2014-07-27
Description: Naive implementation of the Kalman filter, smoother and disturbance
smoother for state space models. An interface to other implementations of the
filter that are available in other packages is also provided.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle
KFKSDS-1.4/KFKSDS/inst/CHANGES |only
KFKSDS-1.5/KFKSDS/DESCRIPTION | 8 -
KFKSDS-1.5/KFKSDS/MD5 | 15 +--
KFKSDS-1.5/KFKSDS/R/KF.R | 113 ++++++++++++++++++--------
KFKSDS-1.5/KFKSDS/inst/NEWS |only
KFKSDS-1.5/KFKSDS/inst/tests/DS-derivatives.R | 2
KFKSDS-1.5/KFKSDS/inst/tests/KF-deriv-xreg.R |only
KFKSDS-1.5/KFKSDS/man/KF.Rd | 23 ++++-
KFKSDS-1.5/KFKSDS/man/predict-stsmSS.Rd | 3
KFKSDS-1.5/KFKSDS/src/KF-deriv.cpp | 89 +++++++++++++++-----
10 files changed, 183 insertions(+), 70 deletions(-)
Title: Hierarchical Climate Regionalization: An Improved Hierarchical
Clustering in R for Climate Regionalization
Diff between HiClimR versions 1.1.1 dated 2014-07-14 and 1.1.2 dated 2014-07-27
Description: HiClimR package modifies and improves hierarchical clustering in R
('hclust' function in 'stats' library), for climate regionalization. It adds a new
clustering method (called, regional linkage) to the set of available methods together
with several features including regridding, coarsening spatial resolution, geographic
masking, data thresholds, detrending and standardization preprocessing, faster correlation
function, hybrid hierarchical clustering, and cluster validation.
Badr et. al (2014) describes the regionalization algorithms and data processing tools
included in the package and presents a demonstration application in which the package
is used to regionalize Africa on the basis of interannual precipitation variability.
It is applicable to any correlation-based clustering.
Author: Hamada S. Badr [aut, cre],
Benjamin F. Zaitchik [aut],
Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr
Changelog | 23 +++++++++++++++++------
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
R/HiClimR.R | 11 +++++++++--
R/coarseR.R | 5 +++--
R/fastCor.R | 5 +++--
R/geogMask.R | 5 +++--
R/grid2D.R | 5 +++--
R/minSigCor.R | 5 +++--
R/validClimR.R | 5 +++--
inst/CITATION | 8 ++++----
src/HiClimR.f90 | 3 ++-
12 files changed, 65 insertions(+), 40 deletions(-)