Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 2.1 dated 2016-11-15 and 2.2 dated 2017-12-15
cit-2.1/cit/R/C_CIT_V13.R |only cit-2.1/cit/src/citconlog2_v3.cpp |only cit-2.1/cit/src/citconlog2cvr_v3.cpp |only cit-2.1/cit/src/citconlog3_perm_v5.cpp |only cit-2.1/cit/src/citconlog3cvr_perm_v6.cpp |only cit-2.2/cit/DESCRIPTION | 8 ++++---- cit-2.2/cit/MD5 | 26 ++++++++++++++------------ cit-2.2/cit/R/C_CIT.R |only cit-2.2/cit/README.md |only cit-2.2/cit/man/cit-package.Rd | 4 ++-- cit-2.2/cit/man/cit.bp.Rd | 13 ++++++++++--- cit-2.2/cit/man/cit.cp.Rd | 13 ++++++++++--- cit-2.2/cit/man/fdr.cit.Rd | 5 ++++- cit-2.2/cit/src/Makevars | 1 + cit-2.2/cit/src/Makevars.win | 1 + cit-2.2/cit/src/cit_init.c |only cit-2.2/cit/src/citconlog2.cpp |only cit-2.2/cit/src/citconlog2cvr.cpp |only cit-2.2/cit/src/citconlog3_perm.cpp |only cit-2.2/cit/src/citconlog3cvr_perm.cpp |only 20 files changed, 46 insertions(+), 25 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <http://glottolog.org> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <http://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://ropensci.github.io/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and others.
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.0.9 dated 2017-11-30 and 1.0.10 dated 2017-12-15
lingtypology-1.0.10/lingtypology/DESCRIPTION | 6 lingtypology-1.0.10/lingtypology/MD5 | 56 +- lingtypology-1.0.10/lingtypology/NAMESPACE | 6 lingtypology-1.0.10/lingtypology/NEWS | 112 ++--- lingtypology-1.0.10/lingtypology/R/map.feature.R | 201 +++++++--- lingtypology-1.0.10/lingtypology/build/vignette.rds |binary lingtypology-1.0.10/lingtypology/data/abvd.RData |binary lingtypology-1.0.10/lingtypology/data/autotyp.RData |binary lingtypology-1.0.10/lingtypology/data/circassian.RData |binary lingtypology-1.0.10/lingtypology/data/countries.RData |binary lingtypology-1.0.10/lingtypology/data/ejective_and_n_consonants.RData |binary lingtypology-1.0.10/lingtypology/data/glottolog.modified.RData |binary lingtypology-1.0.10/lingtypology/data/glottolog.original.RData |binary lingtypology-1.0.10/lingtypology/data/wals.RData |binary lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_creating_maps.R |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_creating_maps.Rmd |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_creating_maps.html |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_db_API.R |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_db_API.Rmd |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_db_API.html |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_dplyr.R |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_dplyr.Rmd |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_dplyr.html |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_glottolog_functions.R |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_glottolog_functions.Rmd |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_glottolog_functions.html |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_intro.R |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_intro.Rmd |only lingtypology-1.0.10/lingtypology/inst/doc/lingtypology_intro.html |only lingtypology-1.0.10/lingtypology/inst/doc/manual/lingtypology.pdf |binary lingtypology-1.0.10/lingtypology/man/map.feature.Rd | 49 +- lingtypology-1.0.10/lingtypology/tests/testthat/test-mapfeature.R | 71 ++- lingtypology-1.0.10/lingtypology/vignettes/lingtypology_creating_maps.Rmd |only lingtypology-1.0.10/lingtypology/vignettes/lingtypology_db_API.Rmd |only lingtypology-1.0.10/lingtypology/vignettes/lingtypology_dplyr.Rmd |only lingtypology-1.0.10/lingtypology/vignettes/lingtypology_glottolog_functions.Rmd |only lingtypology-1.0.10/lingtypology/vignettes/lingtypology_intro.Rmd |only lingtypology-1.0.9/lingtypology/inst/doc/lingtypology.R |only lingtypology-1.0.9/lingtypology/inst/doc/lingtypology.Rmd |only lingtypology-1.0.9/lingtypology/inst/doc/lingtypology.html |only lingtypology-1.0.9/lingtypology/vignettes/lingtypology.Rmd |only 41 files changed, 346 insertions(+), 155 deletions(-)
Title: Store and Manage Arbitrarily Large Integers
Description: Multi-precission library that allows to store and manage arbitrarily big integers without
loss of precision. It includes a large list of tools to work with them, like:
- Arithmetic and logic operators
- Modular-arithmetic operators
- Computer Number Theory utilities
- Probabilistic primality tests
- Factorization algorithms
- Random generators of diferent types of integers.
Author: Javier Leiva Cuadrado
Maintainer: Javier Leiva Cuadrado <jleivacuadrado@gmail.com>
Diff between VeryLargeIntegers versions 0.1.4 dated 2017-09-27 and 0.1.5 dated 2017-12-15
DESCRIPTION | 6 +++--- MD5 | 38 +++++++++++++++++++------------------- R/Euler.R | 5 ++++- R/arithmeticlogic.R | 1 - R/binom.R | 7 ++++--- R/divisor.R | 7 +++++-- R/divp2.R | 18 ++++-------------- R/factorial.R | 5 ++++- R/factors.R | 3 ++- R/pi.R | 3 +-- R/primality.R | 5 ++++- R/primescount.R | 9 ++++++--- man/Euler.Rd | 4 +++- man/arithmeticlogic.Rd | 1 - man/binom.Rd | 6 +++--- man/divisor.Rd | 7 +++++-- man/divp2.Rd | 14 ++------------ man/factorial.Rd | 2 ++ man/primality.Rd | 2 ++ man/primescount.Rd | 2 ++ 20 files changed, 75 insertions(+), 70 deletions(-)
More information about VeryLargeIntegers at CRAN
Permanent link
Title: Read 'IPUMS' Extract Files
Description: An easy way to import census, survey and geographic data provided by 'IPUMS'
into R plus tools to help use the associated metadata to make analysis easier. 'IPUMS'
data describing 1.4 billion individuals drawn from over 750 censuses and surveys is
available free of charge from our website <https://ipums.org>.
Author: Greg Freedman Ellis [aut, cre],
Derek Burk [ctb],
Joe Grover [ctb],
Minnesota Population Center [cph]
Maintainer: Greg Freedman Ellis <gfellis@umn.edu>
Diff between ipumsr versions 0.1.0 dated 2017-11-13 and 0.1.1 dated 2017-12-15
ipumsr-0.1.0/ipumsr/man/figures/README-unnamed-chunk-7-1.png |only ipumsr-0.1.1/ipumsr/DESCRIPTION | 6 ipumsr-0.1.1/ipumsr/MD5 | 83 - ipumsr-0.1.1/ipumsr/NAMESPACE | 2 ipumsr-0.1.1/ipumsr/NEWS.md |only ipumsr-0.1.1/ipumsr/R/ddi_read.r | 34 ipumsr-0.1.1/ipumsr/R/ipums_info.r | 36 ipumsr-0.1.1/ipumsr/R/lbl_helpers.r | 89 - ipumsr-0.1.1/ipumsr/R/list_files.r | 6 ipumsr-0.1.1/ipumsr/R/micro_read.r | 38 ipumsr-0.1.1/ipumsr/R/nhgis_read.r | 38 ipumsr-0.1.1/ipumsr/R/shape_join.r | 37 ipumsr-0.1.1/ipumsr/R/shape_read.r | 309 +-- ipumsr-0.1.1/ipumsr/R/terra_read.r | 85 - ipumsr-0.1.1/ipumsr/R/utils.r | 70 ipumsr-0.1.1/ipumsr/README.md | 46 ipumsr-0.1.1/ipumsr/build/vignette.rds |binary ipumsr-0.1.1/ipumsr/inst/doc/ipums-cps.R | 230 +- ipumsr-0.1.1/ipumsr/inst/doc/ipums-cps.html | 747 +++++---- ipumsr-0.1.1/ipumsr/inst/doc/ipums-geography.R | 404 ++-- ipumsr-0.1.1/ipumsr/inst/doc/ipums-geography.Rmd | 2 ipumsr-0.1.1/ipumsr/inst/doc/ipums-geography.html | 745 +++++---- ipumsr-0.1.1/ipumsr/inst/doc/ipums-nhgis.R | 182 +- ipumsr-0.1.1/ipumsr/inst/doc/ipums-nhgis.html | 670 ++++---- ipumsr-0.1.1/ipumsr/inst/doc/ipums.html | 765 +++++---- ipumsr-0.1.1/ipumsr/inst/doc/value-labels.html | 900 ++++++----- ipumsr-0.1.1/ipumsr/man/figures/README-nhgis_map-1.png |only ipumsr-0.1.1/ipumsr/man/ipums_conditions.Rd | 6 ipumsr-0.1.1/ipumsr/man/lbl_add.Rd | 2 ipumsr-0.1.1/ipumsr/man/lbl_collapse.Rd | 5 ipumsr-0.1.1/ipumsr/man/lbl_na_if.Rd | 2 ipumsr-0.1.1/ipumsr/man/lbl_relabel.Rd | 3 ipumsr-0.1.1/ipumsr/man/read_ipums_sf.Rd | 3 ipumsr-0.1.1/ipumsr/man/read_nhgis.Rd | 5 ipumsr-0.1.1/ipumsr/man/read_terra_area.Rd | 10 ipumsr-0.1.1/ipumsr/man/read_terra_micro.Rd | 10 ipumsr-0.1.1/ipumsr/src/read_hier_list.cpp | 5 ipumsr-0.1.1/ipumsr/src/read_hier_long.cpp | 3 ipumsr-0.1.1/ipumsr/tests/testthat/test_lbls.r | 13 ipumsr-0.1.1/ipumsr/tests/testthat/test_micro.r | 21 ipumsr-0.1.1/ipumsr/tests/testthat/test_nhgis.r | 12 ipumsr-0.1.1/ipumsr/tests/testthat/test_select_style.r | 16 ipumsr-0.1.1/ipumsr/tests/testthat/test_shape_join.r | 17 ipumsr-0.1.1/ipumsr/vignettes/ipums-geography.Rmd | 2 44 files changed, 3279 insertions(+), 2380 deletions(-)
Title: Applied Statistical Time Series Analysis
Description: Included are data sets and scripts to accompany Time Series Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2017. <DOI:10.1007/978-3-319-52452-8>.
Author: David Stoffer
Maintainer: David Stoffer <stoffer@pitt.edu>
Diff between astsa versions 1.7 dated 2016-12-22 and 1.8 dated 2017-12-15
DESCRIPTION | 12 - MD5 | 186 ++++++++++--------- NAMESPACE | 7 R/ARMAtoAR.R |only R/EM0.R | 114 +++++------ R/EM1.R | 140 +++++++------- R/FDR.R | 58 +++--- R/Kfilter0.R | 108 +++++------ R/Kfilter1.R | 134 +++++++------- R/Kfilter2.R | 110 +++++------ R/Ksmooth0.R | 54 ++--- R/Ksmooth1.R | 56 ++--- R/Ksmooth2.R | 44 ++-- R/LagReg.R | 358 ++++++++++++++++++------------------- R/SigExtract.R | 236 ++++++++++++------------ R/acf1.R |only R/acf2.R | 86 ++++----- R/arma.spec.R | 70 +++---- R/ccf2.R |only R/lag1.plot.R | 60 +++--- R/lag2.plot.R | 64 +++--- R/sarima.R | 40 ++-- R/sarima.for.R | 138 +++++++------- R/stoch.reg.R | 200 ++++++++++---------- R/tsplot.R |only data/hor.rda |only man/ARMAtoAR.Rd |only man/EM0.Rd | 288 +++++++++++++++--------------- man/EM1.Rd | 310 ++++++++++++++++---------------- man/EQ5.Rd | 56 ++--- man/EQcount.Rd | 36 +-- man/EXP6.Rd | 56 ++--- man/FDR.Rd | 176 +++++++++--------- man/HCT.Rd | 56 ++--- man/Kfilter0.Rd | 264 +++++++++++++-------------- man/Kfilter1.Rd | 320 ++++++++++++++++----------------- man/Kfilter2.Rd | 308 ++++++++++++++++---------------- man/Ksmooth0.Rd | 228 +++++++++++------------ man/Ksmooth1.Rd | 328 +++++++++++++++++----------------- man/Ksmooth2.Rd | 312 ++++++++++++++++---------------- man/LagReg.Rd | 486 +++++++++++++++++++++++++-------------------------- man/PLT.Rd | 58 +++--- man/SVfilter.Rd | 238 ++++++++++++------------ man/SigExtract.Rd | 344 ++++++++++++++++++------------------ man/WBC.Rd | 56 ++--- man/acf1.Rd |only man/acf2.Rd | 173 +++++++++--------- man/ar1miss.Rd | 50 ++--- man/arf.Rd | 56 ++--- man/arma.spec.Rd | 220 +++++++++++------------ man/astsa-package.Rd | 58 +++--- man/beamd.Rd | 54 ++--- man/birth.Rd | 54 ++--- man/blood.Rd | 58 +++--- man/bnrf1ebv.Rd | 56 ++--- man/bnrf1hvs.Rd | 54 ++--- man/ccf2.Rd |only man/climhyd.Rd | 48 ++--- man/cmort.Rd | 56 ++--- man/econ5.Rd | 42 ++-- man/eqexp.Rd | 46 ++-- man/flu.Rd | 46 ++-- man/fmri.Rd | 48 ++--- man/fmri1.Rd | 58 +++--- man/gas.Rd | 46 ++-- man/gnp.Rd | 54 ++--- man/gtemp.Rd | 48 ++--- man/gtemp2.Rd | 48 ++--- man/hor.Rd |only man/jj.Rd | 44 ++-- man/lag1.plot.Rd | 166 ++++++++--------- man/lag2.plot.Rd | 174 +++++++++--------- man/lap.Rd | 82 ++++---- man/lead.Rd | 58 +++--- man/mvspec.Rd | 206 ++++++++++----------- man/nyse.Rd | 56 ++--- man/oil.Rd | 56 ++--- man/part.Rd | 60 +++--- man/prodn.Rd | 56 ++--- man/qinfl.Rd | 58 +++--- man/qintr.Rd | 56 ++--- man/rec.Rd | 48 ++--- man/sales.Rd | 56 ++--- man/salt.Rd | 58 +++--- man/saltemp.Rd | 58 +++--- man/sarima.Rd | 216 +++++++--------------- man/sarima.for.Rd | 222 ++++++++++------------- man/so2.Rd | 56 ++--- man/soi.Rd | 46 ++-- man/soiltemp.Rd | 54 ++--- man/sp500w.Rd | 30 +-- man/speech.Rd | 54 ++--- man/star.Rd | 62 +++--- man/stoch.reg.Rd | 324 +++++++++++++++++----------------- man/sunspotz.Rd | 60 +++--- man/tempr.Rd | 60 +++--- man/tsplot.Rd |only man/unemp.Rd | 58 +++--- man/varve.Rd | 56 ++--- 99 files changed, 5050 insertions(+), 5108 deletions(-)
Title: Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-8 dated 2017-08-09 and 1.7-10 dated 2017-12-15
ade4-1.7-10/ade4/ChangeLog | 236 +++++++++++++++++++++++++++- ade4-1.7-10/ade4/DESCRIPTION | 16 - ade4-1.7-10/ade4/MD5 | 153 +++++++++--------- ade4-1.7-10/ade4/NAMESPACE | 9 - ade4-1.7-10/ade4/R/EH.R | 2 ade4-1.7-10/ade4/R/ade4-deprecated.R |only ade4-1.7-10/ade4/R/bca.R |only ade4-1.7-10/ade4/R/bca.coinertia.R |only ade4-1.7-10/ade4/R/coinertia.R | 1 ade4-1.7-10/ade4/R/dagnelie.test.R |only ade4-1.7-10/ade4/R/dist.genet.R | 4 ade4-1.7-10/ade4/R/dudi.R | 1 ade4-1.7-10/ade4/R/dudi.pco.R | 1 ade4-1.7-10/ade4/R/fuzzygenet.R | 4 ade4-1.7-10/ade4/R/genet.R | 12 + ade4-1.7-10/ade4/R/mantel.randtest.R | 2 ade4-1.7-10/ade4/R/mantel.rtest.R | 4 ade4-1.7-10/ade4/R/mbpcaiv.R | 5 ade4-1.7-10/ade4/R/mbpls.R | 5 ade4-1.7-10/ade4/R/mcoa.R | 1 ade4-1.7-10/ade4/R/multiblock.R | 2 ade4-1.7-10/ade4/R/multispati.R | 4 ade4-1.7-10/ade4/R/nipals.R | 2 ade4-1.7-10/ade4/R/optimEH.R | 2 ade4-1.7-10/ade4/R/orisaved.R | 2 ade4-1.7-10/ade4/R/randEH.R | 2 ade4-1.7-10/ade4/R/randtest.R | 4 ade4-1.7-10/ade4/R/s.kde2d.R | 4 ade4-1.7-10/ade4/R/statis.R | 1 ade4-1.7-10/ade4/R/utilities.R | 6 ade4-1.7-10/ade4/R/wca.R |only ade4-1.7-10/ade4/R/wca.coinertia.R |only ade4-1.7-10/ade4/man/EH.Rd | 2 ade4-1.7-10/ade4/man/ade4-deprecated.Rd | 9 - ade4-1.7-10/ade4/man/area.plot.Rd | 50 ----- ade4-1.7-10/ade4/man/atya.Rd | 32 ++- ade4-1.7-10/ade4/man/avijons.Rd | 46 +++-- ade4-1.7-10/ade4/man/bca.Rd |only ade4-1.7-10/ade4/man/bca.coinertia.Rd |only ade4-1.7-10/ade4/man/buech.Rd | 56 ++++-- ade4-1.7-10/ade4/man/butterfly.Rd | 43 +++-- ade4-1.7-10/ade4/man/capitales.Rd | 30 ++- ade4-1.7-10/ade4/man/carni70.Rd | 45 ++--- ade4-1.7-10/ade4/man/dagnelie.test.Rd |only ade4-1.7-10/ade4/man/dist.genet.Rd | 2 ade4-1.7-10/ade4/man/elec88.Rd | 35 ++-- ade4-1.7-10/ade4/man/fuzzygenet.Rd | 2 ade4-1.7-10/ade4/man/genet.Rd | 2 ade4-1.7-10/ade4/man/ggtortoises.Rd | 50 +++-- ade4-1.7-10/ade4/man/gridrowcol.Rd | 2 ade4-1.7-10/ade4/man/irishdata.Rd | 45 +++-- ade4-1.7-10/ade4/man/julliot.Rd | 62 +++++-- ade4-1.7-10/ade4/man/jv73.Rd | 42 ++-- ade4-1.7-10/ade4/man/kcponds.Rd | 37 ++-- ade4-1.7-10/ade4/man/mafragh.Rd | 32 ++- ade4-1.7-10/ade4/man/mjrochet.Rd | 4 ade4-1.7-10/ade4/man/mld.Rd | 8 ade4-1.7-10/ade4/man/multispati.Rd | 4 ade4-1.7-10/ade4/man/multispati.randtest.Rd | 2 ade4-1.7-10/ade4/man/multispati.rtest.Rd | 2 ade4-1.7-10/ade4/man/neig.Rd | 9 - ade4-1.7-10/ade4/man/optimEH.Rd | 2 ade4-1.7-10/ade4/man/orisaved.Rd | 2 ade4-1.7-10/ade4/man/orthobasis.Rd | 8 ade4-1.7-10/ade4/man/palm.Rd | 5 ade4-1.7-10/ade4/man/randEH.Rd | 2 ade4-1.7-10/ade4/man/randtest.Rd | 3 ade4-1.7-10/ade4/man/sarcelles.Rd | 39 ++-- ade4-1.7-10/ade4/man/score.coa.Rd | 4 ade4-1.7-10/ade4/man/t3012.Rd | 29 ++- ade4-1.7-10/ade4/man/tintoodiel.Rd | 31 ++- ade4-1.7-10/ade4/man/ungulates.Rd | 13 - ade4-1.7-10/ade4/man/variance.phylog.Rd | 8 ade4-1.7-10/ade4/man/vegtf.Rd | 36 ++-- ade4-1.7-10/ade4/man/wca.Rd |only ade4-1.7-10/ade4/man/wca.coinertia.Rd |only ade4-1.7-10/ade4/man/withinpca.Rd | 2 ade4-1.7-10/ade4/man/zealand.Rd | 31 ++- ade4-1.7-8/ade4/R/between.R |only ade4-1.7-8/ade4/R/betweencoinertia.R |only ade4-1.7-8/ade4/R/orthogram.R |only ade4-1.7-8/ade4/R/within.R |only ade4-1.7-8/ade4/R/withincoinertia.R |only ade4-1.7-8/ade4/man/between.Rd |only ade4-1.7-8/ade4/man/betweencoinertia.Rd |only ade4-1.7-8/ade4/man/orthogram.Rd |only ade4-1.7-8/ade4/man/within.Rd |only ade4-1.7-8/ade4/man/withincoinertia.Rd |only 88 files changed, 903 insertions(+), 450 deletions(-)
Title: Helpers for Data Analysis and Presentation Focused on Undergrad
Psychology
Description: Contains functions for the easy display of statistical tests as well as
some convenience functions for data cleanup. It is meant to ease existing workflows
with packages like 'sjPlot', 'dplyr', and 'ggplot2'. The primary components are the functions
prefixed with 'tadaa_', which are built to work in an interactive environment, but also print
tidy markdown tables powered by 'pixiedust' for the creation of 'RMarkdown' reports.
Author: Lukas Burk [aut, cre],
Tobias Anton [aut],
Daniel Lüdecke [ctb]
Maintainer: Lukas Burk <lukas@quantenbrot.de>
Diff between tadaatoolbox versions 0.14.0 dated 2017-11-05 and 0.15.0 dated 2017-12-15
tadaatoolbox-0.14.0/tadaatoolbox/man/labels_to_factor.Rd |only tadaatoolbox-0.14.0/tadaatoolbox/man/likertize.Rd |only tadaatoolbox-0.14.0/tadaatoolbox/man/tadaatoolbox.Rd |only tadaatoolbox-0.15.0/tadaatoolbox/DESCRIPTION | 12 tadaatoolbox-0.15.0/tadaatoolbox/MD5 | 142 tadaatoolbox-0.15.0/tadaatoolbox/NAMESPACE | 6 tadaatoolbox-0.15.0/tadaatoolbox/NEWS.md | 17 tadaatoolbox-0.15.0/tadaatoolbox/R/cleanup_helpers.R | 36 tadaatoolbox-0.15.0/tadaatoolbox/R/confint.R | 16 tadaatoolbox-0.15.0/tadaatoolbox/R/data.R | 10 tadaatoolbox-0.15.0/tadaatoolbox/R/effect_size.R | 16 tadaatoolbox-0.15.0/tadaatoolbox/R/ggplot2_themes.R | 20 tadaatoolbox-0.15.0/tadaatoolbox/R/misc_stats.R | 16 tadaatoolbox-0.15.0/tadaatoolbox/R/nom_stats.R | 52 tadaatoolbox-0.15.0/tadaatoolbox/R/ord_stats.R | 47 tadaatoolbox-0.15.0/tadaatoolbox/R/recode_helpers.R | 57 tadaatoolbox-0.15.0/tadaatoolbox/R/tadaa_assumptions.R | 24 tadaatoolbox-0.15.0/tadaatoolbox/R/tadaa_chisq.R | 24 tadaatoolbox-0.15.0/tadaatoolbox/R/tadaa_omnibus.R | 48 tadaatoolbox-0.15.0/tadaatoolbox/R/tadaa_one_sample.R | 24 tadaatoolbox-0.15.0/tadaatoolbox/R/tadaa_pairwise_games_howell.R | 24 tadaatoolbox-0.15.0/tadaatoolbox/R/tadaa_pairwise_t.R | 46 tadaatoolbox-0.15.0/tadaatoolbox/R/tadaa_pairwise_tukey.R | 18 tadaatoolbox-0.15.0/tadaatoolbox/R/tadaa_plots.R | 58 tadaatoolbox-0.15.0/tadaatoolbox/R/tadaa_two_sample.R | 48 tadaatoolbox-0.15.0/tadaatoolbox/R/tadaatoolbox-package.r | 26 tadaatoolbox-0.15.0/tadaatoolbox/README.md | 5 tadaatoolbox-0.15.0/tadaatoolbox/build/vignette.rds |binary tadaatoolbox-0.15.0/tadaatoolbox/data/ngo.rda |binary tadaatoolbox-0.15.0/tadaatoolbox/inst/doc/overview.R | 1 tadaatoolbox-0.15.0/tadaatoolbox/inst/doc/overview.Rmd | 1 tadaatoolbox-0.15.0/tadaatoolbox/inst/doc/overview.html | 802 +--- tadaatoolbox-0.15.0/tadaatoolbox/inst/doc/test_output.R | 2 tadaatoolbox-0.15.0/tadaatoolbox/inst/doc/test_output.Rmd | 2 tadaatoolbox-0.15.0/tadaatoolbox/inst/doc/test_output.html | 1790 ++++------ tadaatoolbox-0.15.0/tadaatoolbox/man/delete_na.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/games_howell.Rd | 4 tadaatoolbox-0.15.0/tadaatoolbox/man/generate_recodes.Rd | 4 tadaatoolbox-0.15.0/tadaatoolbox/man/interval_labels.Rd | 4 tadaatoolbox-0.15.0/tadaatoolbox/man/mean_ci_t.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/modus.Rd | 4 tadaatoolbox-0.15.0/tadaatoolbox/man/ngo.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/nom_c.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/nom_chisqu.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/nom_lambda.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/nom_phi.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/nom_v.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/ord_gamma.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/ord_somers_d.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/ord_tau.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/pval_string.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/sidak_sd.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_aov.Rd | 6 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_balance.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_chisq.Rd | 10 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_int.Rd | 8 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_kruskal.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_levene.Rd | 4 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_mean_ci.Rd | 3 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_nom.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_normtest.Rd | 4 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_one_sample.Rd | 6 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_ord.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_pairwise_gh.Rd | 12 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_pairwise_t.Rd | 24 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_pairwise_tukey.Rd | 12 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_plot_tukey.Rd | 9 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_t.test.Rd | 18 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaa_wilcoxon.Rd | 4 tadaatoolbox-0.15.0/tadaatoolbox/man/tadaatoolbox-package.Rd |only tadaatoolbox-0.15.0/tadaatoolbox/man/theme_readthedown.Rd | 10 tadaatoolbox-0.15.0/tadaatoolbox/man/z.Rd | 2 tadaatoolbox-0.15.0/tadaatoolbox/vignettes/overview.Rmd | 1 tadaatoolbox-0.15.0/tadaatoolbox/vignettes/test_output.Rmd | 2 74 files changed, 1554 insertions(+), 2021 deletions(-)
Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least
Squares. The methods include filter methods, wrapper methods and embedded
methods. Both regression and classification is supported.
Author: Kristian Hovde Liland, Tahir Mehmood, Solve Sæbø
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between plsVarSel versions 0.9.3 dated 2017-11-22 and 0.9.4 dated 2017-12-15
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/BVE.R | 3 +++ R/GA.R | 2 ++ R/IPW.R | 3 +++ R/REP.R | 3 +++ R/SPA.R | 3 +++ R/UVE.R | 3 +++ R/filters.R | 7 +++++-- R/lda_from_pls.R | 4 ++-- R/shaving.R | 3 +++ man/lda_from_pls_cv.Rd | 4 ++-- 12 files changed, 44 insertions(+), 21 deletions(-)
Title: Optimum Contribution Selection and Population Genetics
Description: A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees.
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>
Diff between optiSel versions 1.0.0 dated 2017-08-15 and 2.0 dated 2017-12-15
optiSel-1.0.0/optiSel/R/getu.R |only optiSel-1.0.0/optiSel/R/kinwac.R |only optiSel-1.0.0/optiSel/man/kinwac.Rd |only optiSel-1.0.0/optiSel/src/optiSel_init.c |only optiSel-2.0/optiSel/DESCRIPTION | 14 optiSel-2.0/optiSel/MD5 | 127 +++-- optiSel-2.0/optiSel/NAMESPACE | 12 optiSel-2.0/optiSel/R/NPOdata.R |only optiSel-2.0/optiSel/R/NPOpop.R |only optiSel-2.0/optiSel/R/RcppExports.R | 24 - optiSel-2.0/optiSel/R/addClasses.R |only optiSel-2.0/optiSel/R/addContributions.R |only optiSel-2.0/optiSel/R/agecont.R |only optiSel-2.0/optiSel/R/bc4candes.R |only optiSel-2.0/optiSel/R/bounds4cand.R | 108 +--- optiSel-2.0/optiSel/R/candes.R | 401 +++-------------- optiSel-2.0/optiSel/R/characterizeBreeds.R |only optiSel-2.0/optiSel/R/characterizeClasses.R |only optiSel-2.0/optiSel/R/checkbc.R | 10 optiSel-2.0/optiSel/R/checkcon.R |only optiSel-2.0/optiSel/R/checkcont.R |only optiSel-2.0/optiSel/R/checkphen.R |only optiSel-2.0/optiSel/R/con2df.R | 40 + optiSel-2.0/optiSel/R/extractKinships.R |only optiSel-2.0/optiSel/R/f4cand.R | 29 + optiSel-2.0/optiSel/R/fun4Kin.R |only optiSel-2.0/optiSel/R/fun4KinatN.R |only optiSel-2.0/optiSel/R/getNe.R | 2 optiSel-2.0/optiSel/R/gettraits.R | 2 optiSel-2.0/optiSel/R/lc4cand.R | 74 +-- optiSel-2.0/optiSel/R/matings.R | 69 +- optiSel-2.0/optiSel/R/meankin.R |only optiSel-2.0/optiSel/R/noffspring.R | 66 +- optiSel-2.0/optiSel/R/opticont.R | 209 +++----- optiSel-2.0/optiSel/R/param4candes.R |only optiSel-2.0/optiSel/R/pedIBDatN.R | 21 optiSel-2.0/optiSel/R/prePed.R | 24 - optiSel-2.0/optiSel/R/printParam4candes.R |only optiSel-2.0/optiSel/R/qcrc4cand.R | 11 optiSel-2.0/optiSel/R/segIBDatN.R | 21 optiSel-2.0/optiSel/R/summary.candes.R | 25 - optiSel-2.0/optiSel/R/summary4opticont.R |only optiSel-2.0/optiSel/build/partial.rdb |binary optiSel-2.0/optiSel/build/vignette.rds |binary optiSel-2.0/optiSel/data/Cattle.rda |binary optiSel-2.0/optiSel/data/ExamplePed.rda |binary optiSel-2.0/optiSel/data/PedigWithErrors.rda |binary optiSel-2.0/optiSel/data/Phen.rda |binary optiSel-2.0/optiSel/data/map.rda |binary optiSel-2.0/optiSel/inst/doc/ocs-vignette.R | 153 ++++-- optiSel-2.0/optiSel/inst/doc/ocs-vignette.Rmd | 235 ++++++--- optiSel-2.0/optiSel/inst/doc/ocs-vignette.html | 588 ++++++++++++++----------- optiSel-2.0/optiSel/inst/doc/ped-vignette.R | 2 optiSel-2.0/optiSel/inst/doc/ped-vignette.Rmd | 2 optiSel-2.0/optiSel/inst/doc/ped-vignette.html | 136 ++--- optiSel-2.0/optiSel/inst/doc/seg-vignette.R | 6 optiSel-2.0/optiSel/inst/doc/seg-vignette.Rmd | 10 optiSel-2.0/optiSel/inst/doc/seg-vignette.html | 166 +++---- optiSel-2.0/optiSel/inst/extdata/Chr1.phased | 2 optiSel-2.0/optiSel/inst/extdata/Chr2.phased | 2 optiSel-2.0/optiSel/man/Cattle.Rd | 4 optiSel-2.0/optiSel/man/PedigWithErrors.Rd | 4 optiSel-2.0/optiSel/man/agecont.Rd |only optiSel-2.0/optiSel/man/candes.Rd | 101 +++- optiSel-2.0/optiSel/man/matings.Rd | 67 -- optiSel-2.0/optiSel/man/noffspring.Rd | 28 - optiSel-2.0/optiSel/man/optiSel-package.Rd | 4 optiSel-2.0/optiSel/man/opticomp.Rd | 24 - optiSel-2.0/optiSel/man/opticont.Rd | 276 +++++------ optiSel-2.0/optiSel/man/segIBDatN.Rd | 2 optiSel-2.0/optiSel/man/summary.candes.Rd | 2 optiSel-2.0/optiSel/src/Makevars.win | 5 optiSel-2.0/optiSel/src/RcppExports.cpp | 45 + optiSel-2.0/optiSel/vignettes/ocs-vignette.Rmd | 235 ++++++--- optiSel-2.0/optiSel/vignettes/ped-vignette.Rmd | 2 optiSel-2.0/optiSel/vignettes/seg-vignette.Rmd | 10 76 files changed, 1686 insertions(+), 1714 deletions(-)
Title: Genomic Mediation Analysis with Adaptive Confounding Adjustment
Description: Performs genomic mediation
analysis with adaptive confounding adjustment (GMAC) proposed by Yang et al. (2017) <doi:10.1101/078683>. It implements large scale
mediation analysis and adaptively selects potential confounding variables to
adjust for each mediation test from a pool of candidate confounders. The package
is tailored for but not limited to genomic mediation analysis (e.g., cis-gene
mediating trans-gene regulation pattern where an eQTL, its cis-linking gene
transcript, and its trans-gene transcript play the roles as treatment, mediator
and the outcome, respectively), restricting to scenarios with the presence of
cis-association (i.e., treatment-mediator association) and random eQTL (i.e.,
treatment).
Author: Fan Yang, Jiebiao Wang and Lin Chen
Maintainer: Fan Yang <yfcarolyn@gmail.com>
Diff between GMAC versions 2.0 dated 2017-10-31 and 3.0 dated 2017-12-15
DESCRIPTION | 10 +-- MD5 | 10 +-- NAMESPACE | 3 R/GMAC.R | 169 +++++++++++++++++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary man/gmac.Rd | 12 ++- 6 files changed, 185 insertions(+), 19 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Zachary Fisher [ctb],
Cara Arizmendi [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.3-1 dated 2017-10-27 and 0.3-2 dated 2017-12-15
DESCRIPTION | 8 ++-- MD5 | 24 ++++++------ NAMESPACE | 1 R/gimme-pkg.R | 2 - R/new_aggSEM.R | 14 +++---- R/new_funcs.R | 87 ++++++++++++++++++++++------------------------- R/new_gimme.R | 19 +++++----- R/new_indSEM.R | 2 - R/new_setup.R | 17 ++++----- R/print.aggSEMp.R | 20 +++++----- R/print.gimmep.R | 68 ++++++++++++++++++------------------ R/print.indSEMp.R | 42 +++++++++++----------- inst/extdata/sysdata.rda |binary 13 files changed, 151 insertions(+), 153 deletions(-)
Title: Extended Multiplicative Signal Correction
Description: Background correction of spectral like data. Handles variations in
scaling, polynomial baselines, interferents, constituents and replicate variation.
Parameters for corrections are stored for further analysis, and spectra are corrected
accordingly.
Author: Kristian Hovde Liland
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between EMSC versions 0.8.2 dated 2017-07-14 and 0.9.0 dated 2017-12-15
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- NAMESPACE | 1 + R/EMSC.R | 5 ++--- R/SavitzkyGolay.R |only man/SavitzkyGolay.Rd |only 6 files changed, 12 insertions(+), 10 deletions(-)
Title: Age-Depth Modelling using Bayesian Statistics
Description: Bacon is an approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011) <doi:10.1214/11-BA618>.
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [aut],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 2.3.1 dated 2017-12-14 and 2.3.1.1 dated 2017-12-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/Matrix.cpp | 2 +- src/hist2.cpp | 3 +++ 4 files changed, 11 insertions(+), 8 deletions(-)
Title: A Dirichlet Process Mixture Model for Clustering Longitudinal
Gene Expression Data
Description: Many clustering methods have been proposed, but
most of them cannot work for longitudinal gene expression data.
'BClustLonG' is a package that allows us to perform clustering analysis for
longitudinal gene expression data. It adopts a linear-mixed effects framework
to model the trajectory of genes over time, while clustering is jointly
conducted based on the regression coefficients obtained from all genes.
To account for the correlations among genes and alleviate the
high dimensionality challenges, factor analysis models are adopted
for the regression coefficients. The Dirichlet process prior distribution
is utilized for the means of the regression coefficients to induce clustering.
This package allows users to specify which variables to use for clustering
(intercepts or slopes or both) and whether a factor analysis model is desired.
More details about this method can be found in Jiehuan Sun, et al. (2017) <doi:10.1002/sim.7374>.
Author: Jiehuan Sun [aut, cre], Jose D. Herazo-Maya[aut], Naftali Kaminski[aut], Hongyu Zhao [aut], and Joshua L. Warren [aut],
Maintainer: Jiehuan Sun <jiehuan.sun@gmail.com>
Diff between BClustLonG versions 0.1.1 dated 2017-12-15 and 0.1.2 dated 2017-12-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/BClustLonG.pdf |binary src/sparseFactor.cpp | 6 ++++-- 4 files changed, 10 insertions(+), 8 deletions(-)
Title: A Collection of Functions Related to Item Response Theory (IRT)
Description: A collection of functions useful in learning and practicing IRT,
which can be combined into larger programs. Provides basic CTT analysis,
a simple common interface to the estimation of item
parameters in IRT models for binary responses with three different programs
(ICL, BILOG-MG, and ltm), ability estimation (MLE, BME, EAP, WLE, plausible
values), item and person fit statistics, scaling methods (MM, MS, Stocking-Lord,
and the complete Hebaera method), and a rich array of parametric and
non-parametric (kernel) plots. Estimates and plots Haberman's interaction model
when all items are dichotomously scored.
Author: Ivailo Partchev [aut, cre],
Gunter Maris [aut],
Tamaki Hattori [ctb]
Maintainer: Ivailo Partchev <partchev@gmail.com>
Diff between irtoys versions 0.2.0 dated 2016-10-10 and 0.2.1 dated 2017-12-15
DESCRIPTION | 17 +++--- MD5 | 119 +++++++++++++++++++++--------------------- NAMESPACE | 2 NEWS | 4 + R/ability.R | 12 ++-- R/estimate.R | 2 R/interaction.R | 6 +- R/irtoys-package.R | 6 +- R/itemfit.R | 4 - R/nonpar.R | 8 +- R/readin.R | 10 +-- R/scale.R | 2 R/tracelines.R | 24 ++++---- R/utils.R | 8 +- build/vignette.rds |binary inst/doc/irtoys-vignette.html | 24 ++++---- man/Scored.Rd | 1 man/Scored2pl.Rd | 1 man/Unscored.Rd | 1 man/ability.Rd | 7 +- man/api.Rd | 7 +- man/b1.Rd | 1 man/b2.Rd | 1 man/b3.Rd | 1 man/dpv.Rd | 7 +- man/eap.Rd | 7 +- man/erf.Rd | 1 man/est.Rd | 7 +- man/iif.Rd | 7 +- man/interactionModel.Rd | 7 +- man/irf.Rd | 7 +- man/irfPlot.Rd | 7 +- man/irtoys-package.Rd | 15 ++--- man/itf.Rd | 7 +- man/mlebme.Rd | 7 +- man/normal.qu.Rd | 7 +- man/npp.Rd | 7 +- man/plot.iif.Rd | 7 +- man/plot.imp.Rd | 7 +- man/plot.irf.Rd | 7 +- man/plot.tif.Rd | 7 +- man/plot.trf.Rd | 7 +- man/qrs.Rd | 7 +- man/read.ip.bilog.Rd | 1 man/read.ip.icl.Rd | 1 man/read.qu.icl.Rd | 7 +- man/read.resp.Rd | 7 +- man/rim.Rd | 7 +- man/sca.Rd | 7 +- man/sco.Rd | 1 man/scoreMetric.Rd | 1 man/scp.Rd | 7 +- man/sim.Rd | 1 man/tet.Rd | 7 +- man/tgf.Rd | 7 +- man/tia.Rd | 1 man/tif.Rd | 7 +- man/trf.Rd | 7 +- man/tsc.Rd | 7 +- man/wle.Rd | 7 +- src/packagename_init.c |only 61 files changed, 226 insertions(+), 260 deletions(-)
Title: Analysis of RNA Cytosine-5 Methylation
Description: Bisulfite-treated RNA non-conversion in a set of samples is
analysed as follows : each sample's non-conversion distribution is
identified to a Poisson distribution. P-values adjusted for multiple
testing are calculated in each sample. Combined non-conversion P-values
and standard errors are calculated on the intersection of the set of
samples. For further details, see C Legrand, F Tuorto, M Hartmann,
R Liebers, D Jakob, M Helm and F Lyko (2017) <doi:10.1101/gr.210666.116>.
Author: C Legrand
Maintainer: Carine Legrand <c.legrand@dkfz.de>
Diff between BisRNA versions 0.2.1 dated 2017-04-12 and 0.2.2 dated 2017-12-15
DESCRIPTION | 26 +++++++++++++------------- MD5 | 6 +++--- R/RNAmeth.poisson.par.R | 2 +- inst/CITATION | 10 +++++++--- 4 files changed, 24 insertions(+), 20 deletions(-)
Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
this package provides a parallel implementation of the Map function for high
performance computing systems managed by schedulers 'IBM Spectrum LSF'
(<http://www-03.ibm.com/systems/spectrum-computing/products/lsf/>),
'OpenLava' (<http://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
Engine' (<http://www.univa.com/>), 'Slurm' (<http://slurm.schedmd.com/>),
'TORQUE/PBS'
(<http://www.adaptivecomputing.com/products/open-source/torque/>), or
'Docker Swarm' (<https://docs.docker.com/swarm/>).
A multicore and socket mode allow the parallelization on a local machines,
and multiple machines can be hooked up via SSH to create a makeshift
cluster. Moreover, the package provides an abstraction mechanism to define
large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut] (0000-0001-9754-0393),
Bernd Bischl [aut],
Dirk Surmann [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between batchtools versions 0.9.7 dated 2017-11-15 and 0.9.8 dated 2017-12-15
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Title: Supervised Weight of Evidence Binning of Numeric Variables and
Factors
Description: Implements an automated binning of numeric variables and factors with
respect to a dichotomous target variable.
Two approaches are provided: An implementation of fine and coarse classing that
merges granular classes and levels step by step. And a tree-like approach that
iteratively segments the initial bins via binary splits. Both procedures merge,
respectively split, bins based on similar weight of evidence (WOE) values and
stop via an information value (IV) based criteria.
The package can be used with single variables or an entire data frame. It provides
flexible tools for exploring different binning solutions and for deploying them to
(new) data.
Author: Thilo Eichenberg
Maintainer: Thilo Eichenberg <te.r@gmx.net>
Diff between woeBinning versions 0.1.4 dated 2017-06-12 and 0.1.5 dated 2017-12-15
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/woe.tree.binning.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Simple Key Value Stores
Description: Creates and manages simple key-value stores. These can
use a variety of approaches for storing the data. This package
implements the base methods and support for file system, in-memory
and DBI-based database stores.
Author: Rich FitzJohn [aut, cre]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between storr versions 1.1.2 dated 2017-09-08 and 1.1.3 dated 2017-12-15
DESCRIPTION | 12 +- MD5 | 36 +++---- NEWS.md | 9 + R/driver_dbi.R | 185 ++++++++++++++++++++++++--------------- R/hash.R | 10 +- R/spec.R | 4 R/storr.R | 15 +++ README.md | 9 + inst/doc/external.html | 14 +- inst/doc/storr.Rmd | 4 inst/doc/storr.html | 17 +-- inst/spec/test-driver.R | 18 ++- man/storr.Rd | 48 +++++++++- man/storr_dbi.Rd | 7 + tests/testthat/test-driver-dbi.R | 71 ++++++++++++++ tests/testthat/test-hash.R | 12 +- tests/testthat/test-storr.R | 19 ++++ vignettes/src/storr.R | 4 vignettes/storr.Rmd | 4 19 files changed, 374 insertions(+), 124 deletions(-)
Title: Tests of Non-Nested Models
Description: Testing non-nested models via theory supplied by Vuong (1989) <DOI:10.2307/1912557>.
Includes tests of model distinguishability and of model fit that can be applied
to both nested and non-nested models. Also includes functionality to obtain
confidence intervals associated with AIC and BIC. This material is partially based on
work supported by the National Science Foundation under Grant Number SES-1061334.
Author: Edgar Merkle [aut, cre],
Dongjun You [aut],
Lennart Schneider [ctb],
Seongho Bae [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between nonnest2 versions 0.4-1 dated 2016-09-13 and 0.5 dated 2017-12-15
DESCRIPTION | 31 ++++++++---- MD5 | 24 ++++----- NAMESPACE | 3 + NEWS | 12 ++++ R/icci.R | 36 +++++++++----- R/llcont.R | 49 +++++++++++++++++--- R/vuongtest.R | 104 +++++++++++++++++++++++++++++++++++-------- build/vignette.rds |binary inst/doc/nonnest2.pdf |binary man/icci.Rd | 7 +- man/llcont.Rd | 6 +- man/vuongtest.Rd | 7 +- tests/testthat/test_llcont.R | 4 - 13 files changed, 212 insertions(+), 71 deletions(-)
Title: Evolutionary Learning of Globally Optimal Trees
Description: Commonly used classification and regression tree methods like the CART algorithm
are recursive partitioning methods that build the model in a forward stepwise search.
Although this approach is known to be an efficient heuristic, the results of recursive
tree methods are only locally optimal, as splits are chosen to maximize homogeneity at
the next step only. An alternative way to search over the parameter space of trees is
to use global optimization methods like evolutionary algorithms. The 'evtree' package
implements an evolutionary algorithm for learning globally optimal classification and
regression trees in R. CPU and memory-intensive tasks are fully computed in C++ while
the 'partykit' package is leveraged to represent the resulting trees in R, providing
unified infrastructure for summaries, visualizations, and predictions.
Author: Thomas Grubinger [aut, cre],
Achim Zeileis [aut] (0000-0003-0918-3766),
Karl-Peter Pfeiffer [aut]
Maintainer: Thomas Grubinger <Thomas.Grubinger@scch.at>
Diff between evtree versions 1.0-5 dated 2017-04-06 and 1.0-6 dated 2017-12-15
DESCRIPTION | 17 +++++++++-------- MD5 | 24 ++++++++++++------------ NEWS | 6 ++++++ build/vignette.rds |binary data/BBBClub.rda |binary data/ContraceptiveChoice.RData |binary data/GermanCredit.RData |binary data/MAGICGammaTelescope.RData |binary data/StatlogHeart.RData |binary inst/doc/evtree.pdf |binary man/BBBClub.Rd | 2 +- src/node.cpp | 12 ++++++------ tests/Examples/evtree-Ex.Rout.save | 2 +- 13 files changed, 35 insertions(+), 28 deletions(-)
Title: Non-Parametric Multiple Change-Point Analysis of Multivariate
Data
Description: Implements various procedures for finding
multiple change-points. Two methods make use of dynamic
programming and pruning, with no distributional
assumptions other than the existence of certain absolute
moments in one method. Hierarchical and exact search methods
are included. All methods return the set of estimated change-
points as well as other summary information.
Author: Nicholas A. James, Wenyu Zhang and David S. Matteson
Maintainer: Wenyu Zhang <wz258@cornell.edu>
Diff between ecp versions 3.0.0 dated 2016-09-27 and 3.1.0 dated 2017-12-15
DESCRIPTION | 13 MD5 | 25 NAMESPACE | 6 NEWS | 8 R/cp3o.R | 64 + R/energyChangePoint.R | 14 build/vignette.rds |binary man/e.agglo.Rd | 16 man/e.cp3o.Rd | 38 - man/e.cp3o_delta.Rd |only man/e.divisive.Rd | 5 man/ks.cp3o.Rd | 24 man/ks.cp3o_delta.Rd |only src/efast.cpp | 1662 +++++++++++++++++++++++++++++++++----------- src/registerDynamicSymbol.c |only 15 files changed, 1383 insertions(+), 492 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.5.1 dated 2017-07-28 and 4.6.0 dated 2017-12-15
DESCRIPTION | 12 MD5 | 67 +-- NEWS | 12 R/earth.R | 36 + R/earth.leaps.R | 2 build/partial.rdb |binary inst/doc/Auto.linpreds.example.pdf |only inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/earth.times.bat | 2 inst/slowtests/test.big.bat | 2 inst/slowtests/test.cv.bat | 2 inst/slowtests/test.earthc.c | 2 inst/slowtests/test.earthc.mak | 2 inst/slowtests/test.earthc.out.save | 4 inst/slowtests/test.earthmain.gcc.bat | 2 inst/slowtests/test.earthmain.gcc64.bat | 10 inst/slowtests/test.full.R | 170 +++++++++ inst/slowtests/test.full.Rout.save | 555 +++++++++++++++++++++++++++++- inst/slowtests/test.full.bat | 2 inst/slowtests/test.glm.bat | 2 inst/slowtests/test.incorrect.bat | 2 inst/slowtests/test.mods.bat | 2 inst/slowtests/test.plotd.bat | 2 inst/slowtests/test.pmethod.cv.bat | 2 inst/slowtests/test.varmod.bat | 2 inst/slowtests/test.varmod.mgcv.Rout.save | 2 inst/slowtests/test.varmod.mgcv.bat | 2 inst/slowtests/test.weights.Rout.save | 2 inst/slowtests/test.weights.bat | 2 man/earth.Rd | 32 + src/allowed.c | 6 src/earth.c | 46 +- src/earth.h | 4 src/rentries.c | 13 35 files changed, 892 insertions(+), 111 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
using Stan for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include non-linear and
smooth terms, auto-correlation structures, censored data, meta-analytic
standard errors, and quite a few more. In addition, all parameters of the
response distribution can be predicted in order to perform distributional
regression. Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs.
Model fit can easily be assessed and compared with posterior predictive
checks and leave-one-out cross-validation.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>
Diff between brms versions 1.10.2 dated 2017-10-20 and 2.0.0 dated 2017-12-15
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Title: Simulation of Dynamic Microbial Inactivation
Description: Prediction and adjustment to experimental data of microbial
inactivation. Several models available in the literature are implemented.
Author: Alberto Garre [aut, cre],
Pablo S. Fernandez [aut],
Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between bioinactivation versions 1.2.0 dated 2017-11-23 and 1.2.1 dated 2017-12-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/methods_s3_plot.R | 8 +++++++- inst/doc/inactivation.html | 4 ++-- 5 files changed, 22 insertions(+), 11 deletions(-)
More information about bioinactivation at CRAN
Permanent link
More information about quantregRanger at CRAN
Permanent link
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-8 dated 2017-04-11 and 1.0-9 dated 2017-12-15
adegraphics-1.0-8/adegraphics/tests/s1dclass.R |only adegraphics-1.0-8/adegraphics/tests/sarrow.R |only adegraphics-1.0-8/adegraphics/tests/sclass.R |only adegraphics-1.0-8/adegraphics/tests/scorcircle.R |only adegraphics-1.0-8/adegraphics/tests/sdensity.R |only adegraphics-1.0-8/adegraphics/tests/sdistri.R |only adegraphics-1.0-8/adegraphics/tests/shist.R |only adegraphics-1.0-8/adegraphics/tests/simage.R |only adegraphics-1.0-8/adegraphics/tests/slabel.R |only adegraphics-1.0-8/adegraphics/tests/slogo.R |only adegraphics-1.0-8/adegraphics/tests/smatch.R |only adegraphics-1.0-8/adegraphics/tests/straject.R |only adegraphics-1.0-8/adegraphics/tests/svalue.R |only adegraphics-1.0-8/adegraphics/tests/tdist.R |only adegraphics-1.0-8/adegraphics/tests/timage.R |only adegraphics-1.0-8/adegraphics/tests/tvalue.R |only adegraphics-1.0-9/adegraphics/DESCRIPTION | 16 adegraphics-1.0-9/adegraphics/MD5 | 143 ++- adegraphics-1.0-9/adegraphics/NAMESPACE | 4 adegraphics-1.0-9/adegraphics/R/ADEg.C1.R | 543 +++++++-------- adegraphics-1.0-9/adegraphics/R/ADEg.S1.R | 135 ++- adegraphics-1.0-9/adegraphics/R/ADEg.S2.R | 113 --- adegraphics-1.0-9/adegraphics/R/C1.density.R | 99 +- adegraphics-1.0-9/adegraphics/R/C1.gauss.R | 98 +- adegraphics-1.0-9/adegraphics/R/S1.boxplot.R | 16 adegraphics-1.0-9/adegraphics/R/S1.class.R | 38 - adegraphics-1.0-9/adegraphics/R/S2.arrow.R | 9 adegraphics-1.0-9/adegraphics/R/S2.class.R | 64 - adegraphics-1.0-9/adegraphics/R/S2.corcircle.R | 10 adegraphics-1.0-9/adegraphics/R/S2.density.R | 6 adegraphics-1.0-9/adegraphics/R/S2.distri.R | 17 adegraphics-1.0-9/adegraphics/R/S2.image.R | 18 adegraphics-1.0-9/adegraphics/R/S2.label.R | 2 adegraphics-1.0-9/adegraphics/R/S2.logo.R | 2 adegraphics-1.0-9/adegraphics/R/S2.match.R | 8 adegraphics-1.0-9/adegraphics/R/S2.traject.R | 25 adegraphics-1.0-9/adegraphics/R/S2.value.R | 318 ++++---- adegraphics-1.0-9/adegraphics/R/T.image.R | 168 ++-- adegraphics-1.0-9/adegraphics/R/T.value.R | 355 ++++----- adegraphics-1.0-9/adegraphics/R/Tr.class.R | 47 - adegraphics-1.0-9/adegraphics/R/Tr.label.R | 6 adegraphics-1.0-9/adegraphics/R/Tr.match.R | 5 adegraphics-1.0-9/adegraphics/R/Tr.traject.R | 21 adegraphics-1.0-9/adegraphics/R/addhist.R |only adegraphics-1.0-9/adegraphics/R/addline.R |only adegraphics-1.0-9/adegraphics/R/addpoint.R |only adegraphics-1.0-9/adegraphics/R/addsegment.R |only adegraphics-1.0-9/adegraphics/R/addtext.R | 42 - adegraphics-1.0-9/adegraphics/R/ade4-plot.R | 186 +++-- adegraphics-1.0-9/adegraphics/R/ade4-scatter.R | 456 ------------ adegraphics-1.0-9/adegraphics/R/ade4-score.R |only adegraphics-1.0-9/adegraphics/R/genericMethod.R | 3 adegraphics-1.0-9/adegraphics/R/panelfunctions.R | 10 adegraphics-1.0-9/adegraphics/R/utils.R | 23 adegraphics-1.0-9/adegraphics/build/vignette.rds |binary adegraphics-1.0-9/adegraphics/inst/doc/adegraphics.html | 16 adegraphics-1.0-9/adegraphics/man/addline.Rd |only adegraphics-1.0-9/adegraphics/man/addpoint.Rd |only adegraphics-1.0-9/adegraphics/man/addsegment.Rd |only adegraphics-1.0-9/adegraphics/man/addtext.Rd | 19 adegraphics-1.0-9/adegraphics/man/adeg.panel.Spatial.Rd | 15 adegraphics-1.0-9/adegraphics/man/adeg.panel.nb.Rd | 15 adegraphics-1.0-9/adegraphics/man/adegpar.Rd | 4 adegraphics-1.0-9/adegraphics/man/adegraphics-package.Rd | 4 adegraphics-1.0-9/adegraphics/man/cbindADEg.Rd | 3 adegraphics-1.0-9/adegraphics/man/insert.Rd | 5 adegraphics-1.0-9/adegraphics/man/plot.Rd | 6 adegraphics-1.0-9/adegraphics/man/plot.inertia.Rd |only adegraphics-1.0-9/adegraphics/man/s1d.density.Rd | 2 adegraphics-1.0-9/adegraphics/man/s1d.gauss.Rd | 2 adegraphics-1.0-9/adegraphics/tests/add.R | 171 ++++ adegraphics-1.0-9/adegraphics/tests/nbgraph.R | 14 adegraphics-1.0-9/adegraphics/tests/panelSpatial.R | 22 adegraphics-1.0-9/adegraphics/tests/parameter.R | 7 adegraphics-1.0-9/adegraphics/tests/s.arrow.R |only adegraphics-1.0-9/adegraphics/tests/s.class.R |only adegraphics-1.0-9/adegraphics/tests/s.corcircle.R |only adegraphics-1.0-9/adegraphics/tests/s.density.R |only adegraphics-1.0-9/adegraphics/tests/s.distri.R |only adegraphics-1.0-9/adegraphics/tests/s.image.R |only adegraphics-1.0-9/adegraphics/tests/s.label.R |only adegraphics-1.0-9/adegraphics/tests/s.logo.R |only adegraphics-1.0-9/adegraphics/tests/s.match.R |only adegraphics-1.0-9/adegraphics/tests/s.traject.R |only adegraphics-1.0-9/adegraphics/tests/s.value.R |only adegraphics-1.0-9/adegraphics/tests/s1d.boxplot.R | 7 adegraphics-1.0-9/adegraphics/tests/s1d.class.R |only adegraphics-1.0-9/adegraphics/tests/s1d.density.R | 37 - adegraphics-1.0-9/adegraphics/tests/s1d.distri.R | 8 adegraphics-1.0-9/adegraphics/tests/s1d.gauss.R | 21 adegraphics-1.0-9/adegraphics/tests/table.image.R |only adegraphics-1.0-9/adegraphics/tests/table.value.R |only 92 files changed, 1589 insertions(+), 1795 deletions(-)
Title: Efficient Designs for Discrete Choice Experiments
Description: Generates efficient designs for discrete choice experiments based on the multinomial logit model, and individually adapted designs for the mixed multinomial logit model. The generated designs can be presented on screen and choice data can be gathered using a shiny application. Crabbe M, Akinc D and Vandebroek M (2014) <doi:10.1016/j.trb.2013.11.008>.
Author: Frits Traets [aut, cre]
Maintainer: Frits Traets <frits.traets@kuleuven.be>
Diff between idefix versions 0.1.2 dated 2017-08-08 and 0.2.2 dated 2017-12-15
DESCRIPTION | 14 - MD5 | 19 + NAMESPACE | 4 R/data.R |only R/efficiency_algorithms.R | 15 - R/shiny_support.R | 513 +++++++++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary data |only inst/REFERENCES.bib | 34 --- man/Decode.Rd | 4 man/LoadData.Rd |only man/SurveyApp.Rd |only man/example_design.Rd |only 13 files changed, 554 insertions(+), 49 deletions(-)
Title: Antares Visualizations
Description: Visualize results generated by Antares, a powerful software
developed by RTE to simulate and study electric power systems
(more information about Antares here: <https://antares.rte-france.com>).
This package provides functions that create interactive charts to help
Antares users visually explore the results of their simulations.
Author: Jalal-Edine ZAWAM [aut, cre],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Baptiste SEGUINOT [ctb],
RTE [cph]
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>
Diff between antaresViz versions 0.11.2 dated 2017-12-05 and 0.12.0 dated 2017-12-15
DESCRIPTION | 26 MD5 | 126 +++- NAMESPACE | 23 NEWS | 256 ++++---- R/get_data_for_comp.R | 19 R/graph_utils.R |only R/h5_utils.R |only R/h5_utils_plot.R |only R/leafletDragPoints.R | 19 R/limitSizeGraph.R |only R/map.R | 539 ++++++++++++++--- R/map_helpers.R | 62 + R/map_layout.R | 545 ++++++++++++----- R/mod_XY.R |only R/mod_rpart.R |only R/plot.R | 721 ++++++++++++++++------- R/plot_XY.R |only R/plot_barplot.R | 12 R/plot_heatmap.R | 1 R/plot_stats.R | 61 + R/plot_thermal_group_capacities.R |only R/plot_ts.R | 41 + R/plot_utils.R |only R/runApp.R |only R/stack.R | 23 R/stack_exchanges.R | 277 +++++++- R/stack_map.R |only R/stack_prod.R | 377 ++++++++++-- R/zzz.R | 235 ++++--- README.md | 7 build |only inst/AntaresViz.xlsx |only inst/GraphicalCharter.csv | 58 - inst/application |only inst/color.csv |only inst/doc |only inst/htmlwidgets/leafletDragPoints.js | 81 +- inst/mapLayout |only inst/moduleDev |only inst/test_scripts |only man/exchangesStack.Rd | 57 + man/limitSizeGraph.Rd |only man/mapLayout.Rd | 14 man/modRpart.Rd |only man/modXY.Rd |only man/placeGeoPoints-shiny.Rd |only man/plotMap.Rd | 81 ++ man/plotMapLayout.Rd |only man/plotThermalGroupCapacities.Rd |only man/plotXY.Rd |only man/prodStack.Rd | 97 ++- man/runAppAntaresViz.Rd |only man/stackMap.Rd |only man/tsPlot.Rd | 177 ++++- tests/testthat/helper-init.R | 6 tests/testthat/test-exchangesStack.R |only tests/testthat/test-getTSData.R |only tests/testthat/test-get_data_for_comp.R | 1 tests/testthat/test-graphUtils.R |only tests/testthat/test-h5Request.R |only tests/testthat/test-map.R |only tests/testthat/test-plotThermalGroupCapacities.R |only tests/testthat/test-plotXY.R |only tests/testthat/test-prodStack.R |only tests/testthat/test-stackExchanges.R |only tests/testthat/test-ts_plot.R |only vignettes |only 67 files changed, 2994 insertions(+), 948 deletions(-)
Title: Functions Related to ICES Advice
Description: Functions that are related to the ICES advisory process.
Author: Arni Magnusson [aut, cre],
Anne Cooper [aut],
Colin Millar [ctb]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesAdvice versions 1.3-1 dated 2017-05-13 and 1.4-0 dated 2017-12-15
DESCRIPTION | 11 ++++++----- MD5 | 31 ++++++++++++++++++------------- NAMESPACE | 4 ++++ NEWS | 12 +++++++++++- R/Bpa.R | 6 +++--- R/DLS3.2.R | 4 ++-- R/Fpa.R | 6 +++--- R/icesAdvice-package.R | 11 +++++++++-- R/icesRound.R | 8 ++++---- R/icod.R |only R/mohn.R |only data |only man/Bpa.Rd | 6 +++--- man/DLS3.2.Rd | 4 ++-- man/Fpa.Rd | 6 +++--- man/icesAdvice-package.Rd | 8 ++++++++ man/icesRound.Rd | 7 +++---- man/icod.Rd |only man/mohn.Rd |only 19 files changed, 79 insertions(+), 45 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-24 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-07 2.2.2
Title: Europe SpatialPolygonsDataFrame Builder
Description: Build custom Europe SpatialPolygonsDataFrame, if you don't know what is a SpatialPolygonsDataFrame see SpatialPolygons() in 'sp', by example for mapLayout() in 'antaresViz'. Antares is a powerful software developed by RTE to simulate and study electric power systems (more information about 'Antares' here: <https://antares.rte-france.com>).
Author: Jalal-Edine ZAWAM [aut, cre],
Benoit Thieurmel [aut],
RTE [cph]
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>
Diff between spMaps versions 0.1 dated 2017-11-17 and 0.2 dated 2017-12-15
DESCRIPTION | 10 +++---- MD5 | 15 ++++++----- NAMESPACE | 2 + NEWS |only R/sysdata.rda |binary R/utils.R | 50 +++++++++++++++++++++++--------------- README.md | 2 - inst/dataset/build_save_data.R | 53 ++++++++++++++++++++++++++++++----------- man/spMaps.Rd | 12 +++++---- 9 files changed, 93 insertions(+), 51 deletions(-)
Title: Global Surface Summary of the Day (GSOD) Weather Data from R
Description: Provides automated downloading, parsing, cleaning, unit conversion
and formatting of Global Surface Summary of the Day (GSOD) weather data from
the from the USA National Centers for Environmental Information (NCEI) for
use in R. Units are converted from from United States Customary System
(USCS) units to International System of Units (SI). Stations may be
individually checked for number of missing days defined by the user, where
stations with too many missing observations are omitted. Only stations with
valid reported latitude and longitude values are permitted in the final
data. Additional useful elements, saturation vapour pressure (es), actual
vapour pressure (ea) and relative humidity are calculated from the original
data and included in the final data set. The resulting data include station
identification information, state, country, latitude, longitude, elevation,
weather observations and associated flags. Data may be automatically saved
to disk. File output may be returned as a comma-separated values (CSV) or
GeoPackage (GPKG) file. Additional data are included with this R package: a
list of elevation values for stations between -60 and 60 degrees latitude
derived from the Shuttle Radar Topography Measuring Mission (SRTM). For
information on the GSOD data from NCEI, please see the GSOD readme.txt file
available from, <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre] (0000-0002-0061-8359),
Tomislav Hengl [aut] (0000-0002-9921-5129),
Andrew Nelson [aut] (0000-0002-7249-3778),
Hugh Parsonage [cph, ctb] (0000-0003-4055-0835),
Bob Rudis [cph, ctb] (0000-0001-5670-2640)
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between GSODR versions 1.1.1 dated 2017-11-26 and 1.1.2 dated 2017-12-15
DESCRIPTION | 31 +- MD5 | 36 +- NEWS.md | 17 + R/GSODR-package.R | 2 R/get_GSOD.R | 10 R/reformat_GSOD.R | 2 R/zzz.R | 4 README.md | 12 build/vignette.rds |binary inst/doc/GSODR.Rmd | 2 inst/doc/GSODR.html | 275 +++++++++--------- inst/doc/Specified_stations_for_a_range_of_years.html | 12 inst/extdata/country_list.rda |binary inst/extdata/isd_history.rda |binary man/GSODR.Rd | 2 man/get_GSOD.Rd | 2 man/reformat_GSOD.Rd | 2 tests/testthat/test-get_GSOD.R | 6 vignettes/GSODR.Rmd | 2 19 files changed, 232 insertions(+), 185 deletions(-)
Title: Use and Explore CRU CL v. 2.0 Climatology Elements in R
Description: Provides functions that automate downloading and importing
University of East Anglia Climate Research Unit (CRU) CL v. 2.0 climatology
data into R, facilitates the calculation of minimum temperature and maximum
temperature and formats the data into a tidy data frame as a tibble or a
list of raster stack objects for use in an R session. CRU CL v. 2.0 data
are a gridded climatology of 1961-1990 monthly means released in 2002 and
cover all land areas (excluding Antarctica) at 10 arcminutes
(0.1666667 degree) resolution. For more information see the description of
the data provided by the University of East Anglia Climate Research Unit,
<https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
Author: Adam Sparks [aut, cre] (0000-0002-0061-8359)
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between getCRUCLdata versions 0.2.0 dated 2017-11-16 and 0.2.1 dated 2017-12-15
DESCRIPTION | 19 ++++++++++--------- MD5 | 6 +++--- NEWS.md | 8 ++++++++ build/vignette.rds |binary 4 files changed, 21 insertions(+), 12 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package enables extraction from seven datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; the Daymet gridded estimates of daily weather parameters
for North America, version 3, available from the Oak Ridge National Laboratory's
Distributed Active Archive Center (DAAC); the International Tree Ring Data Bank;
and the National Land Cover Database (NLCD).
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.4.7 dated 2017-11-20 and 2.5.0 dated 2017-12-15
FedData-2.4.7/FedData/data/tiles.rda |only FedData-2.4.7/FedData/man/tiles.Rd |only FedData-2.5.0/FedData/DESCRIPTION | 15 FedData-2.5.0/FedData/MD5 | 55 ++- FedData-2.5.0/FedData/NAMESPACE | 5 FedData-2.5.0/FedData/NEWS.md | 3 FedData-2.5.0/FedData/R/DAYMET_FUNCTIONS.R | 8 FedData-2.5.0/FedData/R/NED_FUNCTIONS.R | 10 FedData-2.5.0/FedData/R/NLCD_FUNCTIONS.R |only FedData-2.5.0/FedData/R/UTILITY_FUNCTIONS.R | 10 FedData-2.5.0/FedData/README.md | 179 +++++++--- FedData-2.5.0/FedData/data/daymet_tiles.rda |only FedData-2.5.0/FedData/data/nlcd_canopy_pam.rda |only FedData-2.5.0/FedData/data/nlcd_impervious_pam.rda |only FedData-2.5.0/FedData/data/nlcd_landcover_pam.rda |only FedData-2.5.0/FedData/data/nlcd_tiles.rda |only FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-10-1.png |binary FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-11-1.png |binary FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-12-1.png |binary FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-13-1.png |binary FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-14-1.png |only FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-14-2.png |only FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-14-3.png |only FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-14-4.png |only FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-14-5.png |only FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-14-6.png |only FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-6-1.png |binary FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-7-1.png |binary FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-8-1.png |binary FedData-2.5.0/FedData/inst/image/README-unnamed-chunk-9-1.png |binary FedData-2.5.0/FedData/man/daymet_tiles.Rd |only FedData-2.5.0/FedData/man/download_nlcd_tile.Rd |only FedData-2.5.0/FedData/man/get_ned.Rd | 6 FedData-2.5.0/FedData/man/get_nlcd.Rd |only FedData-2.5.0/FedData/man/get_nlcd_tile.Rd |only FedData-2.5.0/FedData/man/nlcd_canopy_pam.Rd |only FedData-2.5.0/FedData/man/nlcd_impervious_pam.Rd |only FedData-2.5.0/FedData/man/nlcd_landcover_pam.Rd |only FedData-2.5.0/FedData/man/nlcd_tiles.Rd |only FedData-2.5.0/FedData/tests/testthat/test.NLCD.R |only 40 files changed, 207 insertions(+), 84 deletions(-)
Title: Clusters of Effects Curves in Quantile Regression Models
Description: Clustering method to cluster both effects curves, through quantile regression coefficient modeling, and curves in functional data analysis. Sottile G. and Adelfio G. (2017) <https://iwsm2017.webhosting.rug.nl/IWSM_2017_V2.pdf>.
Author: Gianluca Sottile [aut, cre],
Giada Adelfio [aut]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between clustEff versions 0.1.0 dated 2017-09-26 and 0.1.2 dated 2017-12-15
DESCRIPTION | 14 +- MD5 | 13 +- NAMESPACE | 3 R/clustEff.R | 297 ++++++++++++++++++++++++++++++------------------ man/clustEff-package.Rd | 12 - man/clustEff.Rd | 44 +++---- man/distshape.Rd |only man/plot.clustEff.Rd | 10 - 8 files changed, 237 insertions(+), 156 deletions(-)
Title: Australian Government Bureau of Meteorology Data from R
Description: Provides functions to interface with Australian Government Bureau
of Meteorology (BoM) data, fetching data and returning a tidy data frame of
précis forecasts, current weather data from stations, agriculture
bulletin data, BoM 0900 or 1500 weather bulletins or a raster stack object
of satellite imagery from GeoTIFF files. Data (c) Australian Government
Bureau of Meteorology Creative Commons (CC) Attribution 3.0 licence or
Public Access Licence (PAL) as appropriate. See
<http://www.bom.gov.au/other/copyright.shtml> for further details.
Author: Adam Sparks [aut, cre] (0000-0002-0061-8359),
Mark Padgham [aut] (0000-0003-2172-5265),
Hugh Parsonage [aut] (0000-0003-4055-0835),
Keith Pembleton [aut] (0000-0002-1896-4516)
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between bomrang versions 0.1.0 dated 2017-12-04 and 0.1.1 dated 2017-12-15
DESCRIPTION | 22 - MD5 | 20 - NEWS.md | 42 ++- R/get_satellite_imagery.R | 2 README.md | 9 inst/doc/bomrang.html | 408 ++++++++++++++++++------------------ inst/doc/use_case.html | 250 +++++++++++----------- inst/extdata/AAC_codes.rda |binary inst/extdata/JSONurl_site_list.rda |binary inst/extdata/stations_site_list.rda |binary inst/vector |only man/figures/bomrang-hex.png |only 12 files changed, 395 insertions(+), 358 deletions(-)
Title: Sensitivity Analysis for Comparative Methods
Description: An implementation of sensitivity analysis for phylogenetic comparative
methods. The package is an umbrella of statistical and graphical methods that
estimate and report different types of uncertainty in PCM:
(i) Species Sampling uncertainty (sample size; influential species and clades).
(ii) Phylogenetic uncertainty (different topologies and/or branch lengths).
(iii) Data uncertainty (intraspecific variation and measurement error).
Author: Gustavo Paterno [cre, aut],
Gijsbert Werner [aut],
Caterina Penone [aut],
Pablo Martinez [ctb]
Maintainer: Gustavo Paterno <paternogbc@gmail.com>
Diff between sensiPhy versions 0.7.0 dated 2017-09-07 and 0.8.0 dated 2017-12-15
DESCRIPTION | 11 MD5 | 92 +++++-- NAMESPACE | 24 ++ NEWS.md | 45 +++ R/clade_Discrete.R |only R/clade_continuous.R |only R/clade_physig.R | 4 R/influ_Discrete.R |only R/influ_continuous.R |only R/influ_physig.R | 4 R/intra_clade_phylm.R | 2 R/intra_influ_phyglm.R | 2 R/intra_influ_phylm.R | 2 R/intra_physig.R | 4 R/print_methods.R | 17 + R/samp_Discrete.R |only R/samp_continuous.R |only R/samp_physig.R | 2 R/sensi_plot.R | 7 R/sensi_plot.sensiClade.R | 253 +++++++++++++++++++++ R/sensi_plot.sensiInflu.R | 181 +++++++++++++++ R/sensi_plot.sensiIntra.sensiTree.R | 180 +++++++++++++++ R/sensi_plot.sensiSamp.R | 383 +++++++++++++++++++++++++++++++++ R/sensi_plot.tree.bd.R |only R/sensi_plot.tree.physig.R | 2 R/summary_methods.R | 268 +++++++++++++++++++++++ R/tree_Discrete.R |only R/tree_bd.R |only R/tree_clade_phylm.R | 2 R/tree_continuous.R |only R/tree_physig.R | 6 R/tree_samp_phyglm.R | 2 R/tree_samp_phylm.R | 2 build |only inst |only man/clade_continuous.Rd |only man/clade_discrete.Rd |only man/influ_continuous.Rd |only man/influ_discrete.Rd |only man/intra_clade_phylm.Rd | 2 man/intra_influ_phyglm.Rd | 2 man/intra_influ_phylm.Rd | 2 man/samp_continuous.Rd |only man/samp_discrete.Rd |only man/sensi_plot.Rd | 7 man/sensi_plot.intra.physig.Rd | 2 man/sensi_plot.sensiClade.TraitEvol.Rd |only man/sensi_plot.sensiInflu.TraitEvol.Rd |only man/sensi_plot.sensiSamp.TraitEvol.Rd |only man/sensi_plot.sensiTree.TraitEvol.Rd |only man/sensi_plot.tree.bd.Rd |only man/tree_bd.Rd |only man/tree_clade_phylm.Rd | 2 man/tree_continuous.Rd |only man/tree_discrete.Rd |only man/tree_physig.Rd | 2 man/tree_samp_phyglm.Rd | 2 man/tree_samp_phylm.Rd | 2 vignettes |only 59 files changed, 1456 insertions(+), 62 deletions(-)
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application 'wallace' is a modular platform for reproducible modeling of species niches and distributions. 'wallace' guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
Author: Jamie M. Kass [aut, cre],
Bruno Vilela [aut],
Matthew E. Aiello-Lammens [aut],
Robert Muscarella [aut],
Cory Merow [aut],
Robert P. Anderson [aut]
Maintainer: Jamie M. Kass <jkass@gradcenter.cuny.edu>
Diff between wallace versions 1.0.1 dated 2017-11-29 and 1.0.2 dated 2017-12-15
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 6 +++++- R/wallace-package.R | 4 ++-- README.md | 2 +- inst/Rmd/text_intro.Rmd | 4 ++-- inst/Rmd/text_intro_tab.Rmd | 2 +- inst/Rmd/userReport.Rmd | 2 +- inst/shiny/modules/mod_c2_selectOccs.R | 8 ++++---- inst/shiny/modules/mod_c6_maxent.R | 6 ++++-- inst/shiny/modules/mod_c7_respPlots.R | 11 ++++++++--- inst/shiny/server.R | 7 +------ man/wallace-package.Rd | 7 +++---- 13 files changed, 47 insertions(+), 42 deletions(-)
Title: Tools for Combinatorics and Computational Mathematics
Description: Provides optimized functions implemented in C++ with 'Rcpp'
for solving problems in combinatorics and computational mathematics.
There is a combination function and a permutation function that are
both flexible as well as efficient with respect to speed and memory.
There are optional contraint arguments that when employed, generate
all combinations/permutations of a vector meeting a specific criteria
(E.g. finding all combinations such that the sum is less than a
bound). The generalized permutation function is also capable of
producing all permutations of multisets. Additionally, there are
various sieving functions that quickly generate essential components
for problems common in computational mathematics (E.g. number of
comprime elements, divisors, prime factorizations, and complete
factorizations for many numbers as well as primes in a range).
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 0.2.1 dated 2017-11-29 and 0.2.2 dated 2017-12-15
DESCRIPTION | 6 MD5 | 22 - NAMESPACE | 4 NEWS |only R/Combinatorics.R | 6 R/RcppExports.R | 4 README.md | 200 ++++++++- inst |only man/combinatoricsGeneral.Rd | 41 + src/CombPermUtility.cpp |only src/CombinatoricsContainer.cpp | 886 ++++++++++++++++++++++++----------------- src/ExpTableC.cpp |only src/Makevars |only src/RcppExports.cpp | 13 14 files changed, 779 insertions(+), 403 deletions(-)