Title: Plotting ggplot2 Graphics in an XKCD Style
Description: Plotting ggplot2 graphs using the XKCD style.
Author: Emilio Torres-Manzanera
Maintainer: Emilio Torres-Manzanera <torres@uniovi.es>
Diff between xkcd versions 0.0.4 dated 2014-12-15 and 0.0.5 dated 2016-01-13
xkcd-0.0.4/xkcd/vignettes/xkcd-intro-008.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-011.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-012.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-015.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-016.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-017.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-018.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-021.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-022.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-CaritasSpain.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-angles.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-facetcity.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-facetvs.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-motherday.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-twoman.png |only xkcd-0.0.5/xkcd/DESCRIPTION | 17 ++-- xkcd-0.0.5/xkcd/MD5 | 71 +++++++----------- xkcd-0.0.5/xkcd/NAMESPACE | 3 xkcd-0.0.5/xkcd/NEWS | 51 +----------- xkcd-0.0.5/xkcd/R/xkcdaxis.R | 5 - xkcd-0.0.5/xkcd/R/xkcdline.R | 9 +- xkcd-0.0.5/xkcd/build/vignette.rds |binary xkcd-0.0.5/xkcd/inst/doc/xkcd-intro.R | 14 --- xkcd-0.0.5/xkcd/inst/doc/xkcd-intro.Rnw | 24 +----- xkcd-0.0.5/xkcd/inst/doc/xkcd-intro.pdf |binary xkcd-0.0.5/xkcd/man/theme_xkcd.Rd | 3 xkcd-0.0.5/xkcd/man/xkcd-package.Rd | 3 xkcd-0.0.5/xkcd/man/xkcdaxis.Rd | 3 xkcd-0.0.5/xkcd/man/xkcdline.Rd | 3 xkcd-0.0.5/xkcd/man/xkcdman.Rd | 3 xkcd-0.0.5/xkcd/man/xkcdrect.Rd | 3 xkcd-0.0.5/xkcd/vignettes/gr1.pdf |binary xkcd-0.0.5/xkcd/vignettes/gr1.png |binary xkcd-0.0.5/xkcd/vignettes/graxis.png |binary xkcd-0.0.5/xkcd/vignettes/grbar.png |binary xkcd-0.0.5/xkcd/vignettes/grcaritas.png |binary xkcd-0.0.5/xkcd/vignettes/grfonts.png |binary xkcd-0.0.5/xkcd/vignettes/grhelp.png |binary xkcd-0.0.5/xkcd/vignettes/grhomosapiens.png |binary xkcd-0.0.5/xkcd/vignettes/grmotherday.png |binary xkcd-0.0.5/xkcd/vignettes/grnofonts.png |binary xkcd-0.0.5/xkcd/vignettes/grsevan.png |binary xkcd-0.0.5/xkcd/vignettes/grstickfigure.png |binary xkcd-0.0.5/xkcd/vignettes/xkcd-intro.Rnw | 24 +----- 44 files changed, 77 insertions(+), 159 deletions(-)
Title: Twitter Collector and Export to 'SQLite', 'postGIS' and 'GIS'
Format
Description: This is an improved implementation of the package 'StreamR' to capture tweets and store it into a SQLite and 'postGIS' data base. The package simplifies the configuration task to capture tweets and facilitates its store into a 'PostGIS' database. Also exports tweets to 'GIS' format.
Author: Pau Aragó
Maintainer: Pau Aragó <parago@uji.es>
Diff between tweet2r versions 0.3 dated 2015-12-28 and 0.4.1 dated 2016-01-13
ChangeLog | 11 +++++++++++ DESCRIPTION | 14 ++++++-------- MD5 | 17 +++++++++-------- NAMESPACE | 2 +- R/t2gis.R | 16 +++++++++++----- R/t2pgis.R | 4 +++- R/t2sqlite.R | 2 +- R/tweet2r.R | 7 ++----- README.md |only man/tweet2r.Rd | 2 +- 10 files changed, 45 insertions(+), 30 deletions(-)
Title: Range Ancestral State Estimation for Phylogeography and
Comparative Analyses
Description: The rase package primarily implements the Range Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P., Jetz, W., & Crawford, F. W. (2015). Historical Biogeography Using Species Geographical Ranges. Systematic biology, 64(6), 1059-1073. It also includes Bayesian inference of ancestral states under a Brownian Motion model of character evolution and Maximum Likelihood estimation of rase for n-dimensional data. Visualizing functions in 3D are implemented using the rgl package.
Author: Ignacio Quintero [aut, cre],
Forrest W. Crawford [aut],
Petr Keil [aut]
Maintainer: Ignacio Quintero <ignacio.quintero@yale.edu>
Diff between rase versions 0.2-21 dated 2015-11-09 and 0.2-22 dated 2016-01-13
rase-0.2-21/rase/man/random_rase3d.Rd |only rase-0.2-22/rase/DESCRIPTION | 12 +++---- rase-0.2-22/rase/MD5 | 15 ++++----- rase-0.2-22/rase/NAMESPACE | 5 --- rase-0.2-22/rase/R/rase_source.r | 50 --------------------------------- rase-0.2-22/rase/README.md | 19 ++++++------ rase-0.2-22/rase/man/bm_ase.Rd | 2 - rase-0.2-22/rase/man/point.like.bm.Rd | 2 - rase-0.2-22/rase/man/ranges.like.bm.Rd | 2 - 9 files changed, 27 insertions(+), 80 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH
pubkey parsers. Supports RSA, DSA and NIST curves P-256, P-384 and P-521.
Cryptographic signatures can either be created and verified manually or via x509
certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA
for asymmetric (public key) encryption. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.8 dated 2015-12-14 and 0.9 dated 2016-01-13
openssl-0.8/openssl/inst/doc/intro.Rmd |only openssl-0.8/openssl/inst/doc/intro.html |only openssl-0.9/openssl/DESCRIPTION | 8 +-- openssl-0.9/openssl/LICENSE | 2 openssl-0.9/openssl/MD5 | 27 +++++------ openssl-0.9/openssl/NEWS | 4 + openssl-0.9/openssl/R/cert.R | 6 -- openssl-0.9/openssl/R/hash.R | 5 -- openssl-0.9/openssl/inst/doc/bignum.html | 54 +++++++++++------------ openssl-0.9/openssl/inst/doc/crypto_hashing.html | 27 ++++++----- openssl-0.9/openssl/inst/doc/secure_rng.html | 32 ++++++------- openssl-0.9/openssl/man/certificates.Rd | 2 openssl-0.9/openssl/man/hash.Rd | 5 -- openssl-0.9/openssl/src/Makevars.win | 7 +- openssl-0.9/openssl/src/ssl.c | 44 +++++++++++------- openssl-0.9/openssl/src/win32 |only 16 files changed, 119 insertions(+), 104 deletions(-)
Title: Functions for Optimal Non-Bipartite Matching
Description: Perform non-bipartite matching and matched randomization. A
"bipartite" matching utilizes two separate groups, e.g. smokers being
matched to nonsmokers or cases being matched to controls. A "non-bipartite"
matching creates mates from one big group, e.g. 100 hospitals being
randomized for a two-arm cluster randomized trial or 5000 children who
have been exposed to various levels of secondhand smoke and are being
paired to form a greater exposure vs. lesser exposure comparison. At the
core of a non-bipartite matching is a N x N distance matrix for N potential
mates. The distance between two units expresses a measure of similarity or
quality as mates (the lower the better). The 'gendistance()' and
'distancematrix()' functions assist in creating this. The 'nonbimatch()'
function creates the matching that minimizes the total sum of distances
between mates; hence, it is referred to as an "optimal" matching. The
'assign.grp()' function aids in performing a matched randomization. Note
bipartite matching can be performed using the prevent option in
'gendistance()'.
Author: Cole Beck [aut, cre], Bo Lu [aut], Robert Greevy [aut]
Maintainer: Cole Beck <cole.beck@vanderbilt.edu>
Diff between nbpMatching versions 1.4.5 dated 2015-05-14 and 1.5.0 dated 2016-01-13
DESCRIPTION | 12 ++++------ MD5 | 20 ++++++++-------- NAMESPACE | 2 + R/distancematrix.R | 45 ++++++++++++++++++-------------------- R/gendistance.R | 27 ++++++++++++---------- R/make.phantoms.R | 8 +++--- R/nbpmatching-package.R | 12 ++++++++++ R/nonbimatch.R | 25 ++++++++++++++++----- man/gendistance.Rd | 17 ++++++++++---- man/make.phantoms.Rd | 4 +-- tests/testthat/test-gendistance.R | 2 - 11 files changed, 104 insertions(+), 70 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, and orientation patch count for teeth using scans of enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Julia M. Winchester [aut, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 0.2 dated 2015-12-11 and 0.3 dated 2016-01-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/DNE.R | 23 +++++++++++++---------- R/DNE3d.R | 2 +- R/compute_energy_per_face.R | 2 +- build/molaR.pdf |binary man/DNE.Rd | 11 +++++++---- vignettes/molaR_vignette.Rmd | 11 +++++++---- 8 files changed, 39 insertions(+), 30 deletions(-)
Title: Zoo of Geometric Objects
Description: Geometric objects defined in geozoo can be simulated or displayed in the R package tourr.
Author: Barret Schloerke [aut, cre],
Di Cook [ths],
Hadley Wickham [ths]
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between geozoo versions 0.4.3 dated 2014-01-03 and 0.5.0 dated 2016-01-13
geozoo-0.4.3/geozoo/R/cross.polytope.r |only geozoo-0.4.3/geozoo/R/cube.r |only geozoo-0.4.3/geozoo/R/mobius.r |only geozoo-0.4.3/geozoo/R/parametric.r |only geozoo-0.4.3/geozoo/R/print.r |only geozoo-0.4.3/geozoo/R/simplex.r |only geozoo-0.4.3/geozoo/R/sphere.r |only geozoo-0.4.3/geozoo/R/torus.r |only geozoo-0.4.3/geozoo/R/xml.r |only geozoo-0.5.0/geozoo/DESCRIPTION | 36 ++++++---- geozoo-0.5.0/geozoo/MD5 | 79 ++++++++++++----------- geozoo-0.5.0/geozoo/NAMESPACE | 6 + geozoo-0.5.0/geozoo/NEWS | 22 +++++- geozoo-0.5.0/geozoo/R/cross.polytope.R |only geozoo-0.5.0/geozoo/R/cube.R |only geozoo-0.5.0/geozoo/R/geozoo.R |only geozoo-0.5.0/geozoo/R/mobius.R |only geozoo-0.5.0/geozoo/R/parametric.R |only geozoo-0.5.0/geozoo/R/print.R |only geozoo-0.5.0/geozoo/R/simplex.R |only geozoo-0.5.0/geozoo/R/sphere.R |only geozoo-0.5.0/geozoo/R/torus.R |only geozoo-0.5.0/geozoo/R/xml.R |only geozoo-0.5.0/geozoo/README.md |only geozoo-0.5.0/geozoo/man/boy.surface.Rd | 13 ++- geozoo-0.5.0/geozoo/man/conic.spiral.Rd | 25 ++++--- geozoo-0.5.0/geozoo/man/conic.spiral.nautilus.Rd | 26 ++++--- geozoo-0.5.0/geozoo/man/cross.cap.Rd | 17 ++-- geozoo-0.5.0/geozoo/man/cross.polytope.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/cube.dotline.Rd | 17 ++-- geozoo-0.5.0/geozoo/man/cube.face.Rd | 17 ++-- geozoo-0.5.0/geozoo/man/cube.iterate.Rd | 17 ++-- geozoo-0.5.0/geozoo/man/cube.solid.grid.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/cube.solid.random.Rd | 19 +++-- geozoo-0.5.0/geozoo/man/dini.surface.Rd | 21 +++--- geozoo-0.5.0/geozoo/man/ellipsoid.Rd | 23 +++--- geozoo-0.5.0/geozoo/man/enneper.surface.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/klein.fig.eight.Rd | 21 +++--- geozoo-0.5.0/geozoo/man/mobius.Rd | 16 ++-- geozoo-0.5.0/geozoo/man/mobius.experiment.Rd | 16 ++-- geozoo-0.5.0/geozoo/man/print.geozoo.Rd | 14 ++-- geozoo-0.5.0/geozoo/man/print.geozooNoScale.Rd |only geozoo-0.5.0/geozoo/man/roman.surface.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/simplex.Rd | 17 ++-- geozoo-0.5.0/geozoo/man/sphere.hollow.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/sphere.solid.grid.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/sphere.solid.random.Rd | 19 +++-- geozoo-0.5.0/geozoo/man/torus.Rd | 21 +++--- geozoo-0.5.0/geozoo/man/torus.flat.Rd | 19 +++-- geozoo-0.5.0/geozoo/man/write.xml.Rd | 16 ++-- geozoo-0.5.0/geozoo/tests |only 51 files changed, 357 insertions(+), 260 deletions(-)
Title: Methods for Reading dChip Files
Description: Functions for reading DCP and CDF.bin files generated by the dChip software.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between dChipIO versions 0.1.4 dated 2016-01-12 and 0.1.5 dated 2016-01-13
DESCRIPTION | 8 +++--- MD5 | 19 ++++++++-------- NEWS | 8 ++++++ R/readCdfBin.R | 29 ++++++++++++++---------- R/readCdfBinHeader.R | 39 ++++++++++++--------------------- R/readDcp.R | 51 +++++++++++++++++++------------------------ R/readDcpHeader.R | 56 +++++++++++++++++++---------------------------- R/readDcpRectangle.R | 6 +++-- R/utils.R |only man/readCdfBin.Rd | 48 ++++++++++++++++++++-------------------- man/readDcp.Rd | 60 +++++++++++++++++++++++++-------------------------- 11 files changed, 158 insertions(+), 166 deletions(-)
Title: Wegener Center Climate Uncertainty Explorer
Description: Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary 'NetCDF' format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global Circulation Models, as the 'CMIP5' simulations, can be read in the same way as Regional Climate Models, as e.g. the 'CORDEX' or 'ENSEMBLES' simulations. The package has been developed at the 'Wegener Center for Climate and Global Change' at the University of Graz, Austria.
Author: Thomas Mendlik [aut, cre], Georg Heinrich [aut], Armin Leuprecht [aut], Andreas Gobiet [ths]
Maintainer: Thomas Mendlik <thomas.mendlik@uni-graz.at>
Diff between wux versions 2.1-1 dated 2015-09-17 and 2.2-0 dated 2016-01-13
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- R/InitModelDictionary.R | 4 ++-- R/ReadGridFile.R | 20 +++++++++++++------- R/ReadNetCdf.R | 26 +++++++++++++++++--------- R/ReadNetCdfTimeData.R | 18 ++++++++++++------ R/landmask.R | 12 +++++++++--- R/models2wuxAggregateTemporal.R | 19 ++++++++++++++----- R/models2wuxGetFilenames.R | 4 ++-- R/models2wuxGetParameterShortName.R | 17 ++++++++++++++--- 11 files changed, 98 insertions(+), 52 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-05 0.4
2014-12-29 0.3
2014-05-18 0.2
2014-01-05 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-13 0.14.8
2016-01-07 0.14.7
Title: Tools for Semantic Vector Spaces
Description: Various tools for semantic vector spaces, such as
correspondence analysis (simple, multiple and discriminant), latent
semantic analysis, probabilistic latent semantic analysis, non-negative
matrix factorization, latent class analysis and EM clustering. Furthermore,
there are specialized distance measures, plotting functions and some helper
functions.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between svs versions 1.0.3 dated 2015-10-18 and 1.1.0 dated 2016-01-13
DESCRIPTION | 13 - MD5 | 36 ++-- NAMESPACE | 6 R/svs.r | 349 ++++++++++++++++++++++++++++++++++++--------- man/MI.Rd |only man/cd_plot.Rd | 7 man/centers_ca.Rd | 10 + man/dist_chisquare.Rd | 6 man/dist_cosine.Rd | 6 man/dist_wrt.Rd | 6 man/dist_wrt_centers.Rd | 10 + man/fast_E_M.Rd | 3 man/fast_lca.Rd |only man/fast_mca.Rd | 2 man/fast_psa.Rd | 5 man/freq_ca.Rd | 5 man/outerec.Rd |only man/pc_plot.Rd | 6 man/pmi.Rd |only man/svs-package.Rd | 11 + man/weighting_functions.Rd | 18 +- 21 files changed, 398 insertions(+), 101 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended
for people coming from other statistical software packages like 'SPSS', and/
or who are new to R), supporting following common tasks: 1) Reading and writing
data between R and other statistical software packages like 'SPSS', 'SAS' or
'Stata' and working with labelled data; this includes easy ways to get and set
label attributes, to convert labelled vectors into factors (and vice versa),
or to deal with multiple declared missing values etc. 2) Data transformation
tasks like recoding, dichotomizing or grouping variables, setting and replacing
missing values. 3) Convenient functions to perform frequently used statistical
tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.3 dated 2015-11-23 and 1.4 dated 2016-01-13
DESCRIPTION | 8 - MD5 | 38 +++-- NAMESPACE | 4 NEWS | 14 ++ R/efc.R | 64 ++++----- R/is_empty.R | 90 ++++++++----- R/overdisp.R |only R/std_b.R | 3 R/to_dummy.R |only R/to_value.R | 195 +++++++++++++++--------------- README.md | 20 +-- man/efc.Rd | 71 +++++----- man/get_label.Rd | 160 ++++++++++++------------ man/get_labels.Rd | 324 +++++++++++++++++++++++++------------------------- man/is_empty.Rd | 94 +++++++------- man/overdisp.Rd |only man/set_label.Rd | 228 +++++++++++++++++------------------ man/set_labels.Rd | 292 ++++++++++++++++++++++----------------------- man/sjmisc-package.Rd | 4 man/to_dummy.Rd |only man/to_factor.Rd | 208 ++++++++++++++++---------------- man/to_value.Rd | 3 22 files changed, 933 insertions(+), 887 deletions(-)
Title: Similarity Regression Functions
Description: Functions for performing Bayesian `similarity regression',
specialised for modelling the association between a HPO-encoded phenotype
and binary genotype. A `no association' model is compared with one in which
the log odds of having a rare genotype is linked to the semantic similarity
between patient phenotype and a latent characteristic phenotype. The method
estimates the probability of an association together with an HPO-coded phenotype
characteristic of the disease.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between SimReg versions 1.2 dated 2015-09-15 and 1.3 dated 2016-01-13
SimReg-1.2/SimReg/R/imports.R |only SimReg-1.2/SimReg/man/as.row.leaves.Rd |only SimReg-1.2/SimReg/man/get.term.term.matrix.Rd |only SimReg-1.2/SimReg/man/get.two.term.marginals.Rd |only SimReg-1.2/SimReg/man/hpo.plot.marginal.freqs.Rd |only SimReg-1.2/SimReg/man/leaf.term.pair.marginal.matrix.Rd |only SimReg-1.2/SimReg/man/sim.reg.Rd |only SimReg-1.2/SimReg/man/sim.reg.full.summary.Rd |only SimReg-1.2/SimReg/man/sim.reg.summary.Rd |only SimReg-1.2/SimReg/man/single.term.marginals.plot.Rd |only SimReg-1.2/SimReg/man/two.term.marginals.plot.Rd |only SimReg-1.3/SimReg/DESCRIPTION | 25 SimReg-1.3/SimReg/MD5 | 46 - SimReg-1.3/SimReg/NAMESPACE | 58 + SimReg-1.3/SimReg/R/functions.R | 145 +++- SimReg-1.3/SimReg/R/plots.R | 521 +++++----------- SimReg-1.3/SimReg/R/simReg.R | 231 +++---- SimReg-1.3/SimReg/build |only SimReg-1.3/SimReg/inst |only SimReg-1.3/SimReg/man/SimReg-package.Rd | 28 SimReg-1.3/SimReg/man/as_row_leaves.Rd |only SimReg-1.3/SimReg/man/full_names.Rd |only SimReg-1.3/SimReg/man/log_odds_trace.Rd |only SimReg-1.3/SimReg/man/phi_plot.Rd |only SimReg-1.3/SimReg/man/prune_sim_mat.Rd |only SimReg-1.3/SimReg/man/sim_reg.Rd |only SimReg-1.3/SimReg/man/sim_reg_summary.Rd |only SimReg-1.3/SimReg/man/term_marginals.Rd |only SimReg-1.3/SimReg/man/term_marginals_from_phi_vec.Rd |only SimReg-1.3/SimReg/man/term_pair_marginals.Rd |only SimReg-1.3/SimReg/man/term_pair_marginals_plot.Rd |only SimReg-1.3/SimReg/src/DeltaLikelihood.cpp | 4 SimReg-1.3/SimReg/src/RcppExports.cpp | 11 SimReg-1.3/SimReg/src/RcppExports.h | 16 SimReg-1.3/SimReg/vignettes |only 35 files changed, 511 insertions(+), 574 deletions(-)
Title: Sample Size Computations Controlling the Type-II Generalized
Family-Wise Error Rate
Description: The significance of mean difference tests in clinical trials is established if at least r null hypotheses are rejected among m that are simultaneously tested. This package enables one to compute necessary sample sizes for single-step (Bonferroni) and step-wise procedures (Holm and Hochberg). These three procedures control the q-generalized family-wise error rate (probability of making at least q false rejections). Sample size is computed (for these single-step and step-wise procedures) in a such a way that the r-power (probability of rejecting at least r false null hypotheses, i.e. at least r significant endpoints among m) is above some given threshold, in the context of tests of difference of means for two groups of continuous endpoints (variables). Various types of structure of correlation are considered. It is also possible to analyse data (i.e., actually test difference in means) when these are available. The case r equals 1 is treated in separate functions that were used in Lafaye de Micheaux et al. (2014) <doi:10.1080/10543406.2013.860156>.
Author: Pierre Lafaye de Micheaux, Benoit Liquet and Jeremie Riou
Maintainer: Pierre Lafaye de Micheaux <lafaye@dms.umontreal.ca>
Diff between rPowerSampleSize versions 1.0 dated 2015-11-28 and 1.0.1 dated 2016-01-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/indivne.rm.ssc.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
More information about rPowerSampleSize at CRAN
Permanent link
Title: Hierarchical Modeling and Frequency Method Checking on
Overdispersed Gaussian, Poisson, and Binomial Data
Description: We utilize approximate Bayesian machinery to fit two-level conjugate hierarchical models on overdispersed Gaussian, Poisson, and Binomial data and evaluates whether the resulting approximate Bayesian interval estimates for random effects meet the nominal confidence levels via frequency coverage evaluation. The data that Rgbp assumes comprise observed sufficient statistic for each random effect, such as an average or a proportion of each group, without population-level data. The approximate Bayesian tool equipped with the adjustment for density maximization produces approximate point and interval estimates for model parameters including second-level variance component, regression coefficients, and random effect. For the Binomial data, the package provides an option to produce posterior samples of all the model parameters via the acceptance-rejection method. The package provides a quick way to evaluate coverage rates of the resultant Bayesian interval estimates for random effects via a parametric bootstrapping, which we call frequency method checking.
Author: Joseph Kelly, Hyungsuk Tak, and Carl Morris
Maintainer: Joseph Kelly <josephkelly@post.harvard.edu>
Diff between Rgbp versions 1.1.0 dated 2015-08-04 and 1.1.1 dated 2016-01-13
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ R/br.R | 27 +++++++++---------- R/coverage.R | 78 +++++++++++++++++++++++++++---------------------------- R/gbp.R | 12 ++++---- R/gr.R | 14 ++++----- R/pr.R | 18 ++++++------ man/coverage.Rd | 2 - man/gbp.Rd | 12 ++++---- man/print.gbp.Rd | 4 +- 10 files changed, 96 insertions(+), 95 deletions(-)
Title: Hydrology and Climate Forecasting
Description: Focuses on data processing and visualization in hydrology and
climate forecasting. Main function includes data extraction, data downscaling, data
resampling, gap filler of precipitation, bias correction of forecasting data, flexible
time series plot, and spatial map generation. It is a good pre-processing and
post-processing tool for hydrological and hydraulic modellers.
Author: Yuanchao Xu [aut, cre]
Maintainer: Yuanchao Xu <xuyuanchao37@gmail.com>
Diff between hyfo versions 1.3.4 dated 2015-12-05 and 1.3.6 dated 2016-01-13
DESCRIPTION | 10 +- MD5 | 42 +++++----- NAMESPACE | 2 NEWS | 23 +++++- R/array_dimension.R | 4 - R/biasCorrect(generic).R | 4 - R/getEnsemble.R | 3 R/getPreciBar(generic).R | 4 - R/getSpatialMap.R | 2 R/multi-biasCorrect(generic).R | 4 - R/ncdf.R | 157 +++++++++++++++++++++++++---------------- R/startup.R | 2 README.md | 16 ++++ inst/doc/hyfo.pdf |binary man/downscaleNcdf.Rd | 5 - man/getFrcEnsem.Rd | 3 man/getNcdfVar.Rd | 5 - man/getPreciBar.Rd | 2 man/getPreciBar_comb.Rd | 2 man/getSpatialMap_comb.Rd | 2 man/loadNcdf.Rd | 5 - man/writeNcdf.Rd | 12 +-- 22 files changed, 189 insertions(+), 120 deletions(-)
Title: Functional Clustering Algorithms
Description: Unified framework to cluster functional data according to one of seven models. All models are based on the projection of the curves onto a basis. The main function funcit() calls wrapper functions for the existing algorithms, so that input parameters are the same. A list is returned with each entry representing the same or extended output for the corresponding method. Method specific as well as general visualization tools are available.
Author: Christina Yassouridis [aut, cre],
Dominik Ernst [ctb],
Madison Giacofci [ctb],
Sophie Lambert-Lacroix [ctb],
Guillemette Marot [ctb],
Franck Picard [ctb],
Nicoleta Serban [ctb],
Huijing Jiang [ctb],
Gareth James [ctb],
Catherine Sugar [ctb],
Hans-Georg Mueller [ctb],
Jie Peng [ctb],
Chiou Jeng-Min [ctb],
Pai-Ling Li [ctb]
Maintainer: Christina Yassouridis <c_ya02@yahoo.de>
Diff between funcy versions 0.8.3 dated 2015-10-19 and 0.8.4 dated 2016-01-13
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NEWS.md | 43 ++++++++++++++++++++-------- R/plot.R | 6 ++- R/plotFSCM.R | 79 ++++++++++++++++++++++++++++++---------------------- R/xecute.R | 3 - src/la/clapack.h | 4 +- src/la/uselapack.cc | 2 + 8 files changed, 98 insertions(+), 61 deletions(-)
Title: Doubly Robust Generalized Estimating Equations
Description: Fit restricted mean models for the conditional association
between an exposure and an outcome, given covariates. Three methods
are implemented: O-estimation, where a nuisance model for the
association between the covariates and the outcome is used;
E-estimation where a nuisance model for the association
between the covariates and the exposure is used, and doubly robust (DR)
estimation where both nuisance models are used. In DR-estimation,
the estimates will be consistent when at least one of the nuisance
models is correctly specified, not necessarily both.
Author: Johan Zetterqvist <johan.zetterqvist@ki.se> , Arvid Sjölander <arvid.sjolander@ki.se> with contributions from Alexander Ploner.
Maintainer: Johan Zetterqvist <johan.zetterqvist@ki.se>
Diff between drgee versions 1.1.3 dated 2015-06-12 and 1.1.4 dated 2016-01-13
drgee-1.1.3/drgee/R/clogitRes.R |only drgee-1.1.4/drgee/DESCRIPTION | 13 drgee-1.1.4/drgee/MD5 | 50 - drgee-1.1.4/drgee/NAMESPACE | 9 drgee-1.1.4/drgee/NEWS | 120 ++- drgee-1.1.4/drgee/R/condit.R |only drgee-1.1.4/drgee/R/drFit.R | 34 - drgee-1.1.4/drgee/R/dreFit.R | 529 ++++++++-------- drgee-1.1.4/drgee/R/dreFitCond.R | 44 - drgee-1.1.4/drgee/R/drgee.R | 330 +++++----- drgee-1.1.4/drgee/R/drgeeData.R | 1060 ++++++++++++++++----------------- drgee-1.1.4/drgee/R/eFit.R | 67 -- drgee-1.1.4/drgee/R/findRoots.R | 43 - drgee-1.1.4/drgee/R/gee.R | 272 ++++---- drgee-1.1.4/drgee/R/geeFit.R | 93 +- drgee-1.1.4/drgee/R/geeFitCond.R | 171 ++--- drgee-1.1.4/drgee/R/oFit.R | 82 +- drgee-1.1.4/drgee/R/robVcov.R | 67 +- drgee-1.1.4/drgee/inst/CITATION | 47 + drgee-1.1.4/drgee/man/drgee-package.Rd | 88 +- drgee-1.1.4/drgee/man/drgee.Rd | 617 +++++++++---------- drgee-1.1.4/drgee/man/drgeeData.Rd | 313 ++++----- drgee-1.1.4/drgee/man/findRoots.Rd | 110 +-- drgee-1.1.4/drgee/man/gee.Rd | 208 +++--- drgee-1.1.4/drgee/man/robVcov.Rd | 98 +-- drgee-1.1.4/drgee/src |only 26 files changed, 2273 insertions(+), 2192 deletions(-)
Title: Profile Output Processing Tools for R
Description: Tools for examining Rprof profile output.
Author: Luke Tierney and Riad Jarjour
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between proftools versions 0.99-0 dated 2016-01-05 and 0.99-2 dated 2016-01-13
proftools-0.99-0/proftools/vignettes/Rprof.cg |only proftools-0.99-0/proftools/vignettes/proftools.R |only proftools-0.99-0/proftools/vignettes/proftools.pdf |only proftools-0.99-0/proftools/vignettes/proftools.tex |only proftools-0.99-2/proftools/DESCRIPTION | 9 +++++---- proftools-0.99-2/proftools/MD5 | 13 +++++++------ proftools-0.99-2/proftools/build |only proftools-0.99-2/proftools/inst/doc |only proftools-0.99-2/proftools/man/annotateSource.Rd | 2 +- proftools-0.99-2/proftools/vignettes/jsslogo.jpg |only 10 files changed, 13 insertions(+), 11 deletions(-)
Title: Statistical Matching
Description: Integration of two data sources referred to the same target population which share a number of common variables (aka data fusion). Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio <madorazi@istat.it>
Diff between StatMatch versions 1.2.3 dated 2015-01-29 and 1.2.4 dated 2016-01-13
StatMatch-1.2.3/StatMatch/R/Frechet.bounds.cat.R |only StatMatch-1.2.3/StatMatch/R/RANDwNND.hotdeck.r |only StatMatch-1.2.4/StatMatch/DESCRIPTION | 8 StatMatch-1.2.4/StatMatch/MD5 | 34 - StatMatch-1.2.4/StatMatch/NAMESPACE | 5 StatMatch-1.2.4/StatMatch/NEWS | 8 StatMatch-1.2.4/StatMatch/R/Fbwidths.by.x.R | 121 ++-- StatMatch-1.2.4/StatMatch/R/Frechet.bounds.cat.2.R |only StatMatch-1.2.4/StatMatch/R/RANDwNND.hotdeck.R |only StatMatch-1.2.4/StatMatch/R/comb.samples.R | 285 +++++----- StatMatch-1.2.4/StatMatch/R/pBayes.R |only StatMatch-1.2.4/StatMatch/build/vignette.rds |binary StatMatch-1.2.4/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.R | 78 +- StatMatch-1.2.4/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.Rnw | 105 +-- StatMatch-1.2.4/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.pdf |binary StatMatch-1.2.4/StatMatch/man/Fbwidths.by.x.Rd | 29 - StatMatch-1.2.4/StatMatch/man/Frechet.bounds.cat.Rd | 8 StatMatch-1.2.4/StatMatch/man/comb.samples.Rd | 6 StatMatch-1.2.4/StatMatch/man/pBayes.Rd |only StatMatch-1.2.4/StatMatch/man/pw.assoc.Rd | 4 StatMatch-1.2.4/StatMatch/vignettes/Statistical_Matching_with_StatMatch.Rnw | 105 +-- 21 files changed, 450 insertions(+), 346 deletions(-)
Title: Sensitivity Indices with Dependent Inputs
Description: Sensitivity indices with dependent correlated inputs, using a
method based on PLS regression.
Author: A. Bouvier [aut], J.-P. Gauchi [aut, cre], E. Volatier [ctb]
Maintainer: Annie Bouvier <annie.bouvier@jouy.inra.fr>
Diff between sivipm versions 1.1-2 dated 2015-10-28 and 1.1-3 dated 2016-01-13
DESCRIPTION | 8 +- MD5 | 52 +++++++++---------- NAMESPACE | 5 + NEWS | 12 ++++ R/allmono.R | 2 R/class-sivip.R | 35 +++++++++--- R/factorsplit.R | 2 R/fastregpls2.R | 7 +- R/polynome.R | 2 R/regpls2.R | 24 +++++--- R/sivipm.R | 60 ++++++++++++++------- R/vect2poly.R | 2 inst/doc/Vignette.pdf |binary man/sivip-class.Rd | 15 ++--- man/sivipboot.Rd | 2 man/sivipm.Rd | 33 +++++------- src/bouclen.c | 24 ++++++++ tests/exX18Y14.R | 4 - tests/exX18Y14.Rout.save | 38 +++++++++---- tests/exX18Y2.R | 8 +- tests/exX18Y2.Rout.save | 123 ++++++++++++++++++++++++--------------------- tests/exXY180.R | 2 tests/exXY180.Rout.save | 22 +++++--- tests/excornell0.R | 14 ++--- tests/excornell0.Rout.save | 102 +++++++++++++++++++++---------------- tests/excornell1.R | 10 ++- tests/excornell1.Rout.save | 62 +++++++++++++++++++--- 27 files changed, 424 insertions(+), 246 deletions(-)
Title: Optimal Stratification of Sampling Frames for Multipurpose
Sampling Surveys
Description: In the field of stratified sampling design, this package
offers an approach for the determination of the best
stratification of a sampling frame, the one that ensures the
minimum sample cost under the condition to satisfy precision
constraints in a multivariate and multidomain case. This
approach is based on the use of the genetic algorithm: each
solution (i.e. a particular partition in strata of the sampling
frame) is considered as an individual in a population; the
fitness of all individuals is evaluated applying the
Bethel-Chromy algorithm to calculate the sampling size
satisfying precision constraints on the target estimates.
Functions in the package allows to: (a) analyse the obtained
results of the optimisation step; (b) assign the new strata
labels to the sampling frame; (c) select a sample from the new
frame accordingly to the best allocation.
Functions for the execution of the genetic algorithm are a modified
version of the functions in the 'genalg' package.
Author: Giulio Barcaroli, Daniela Pagliuca, Egon Willighagen,
Diego Zardetto
Maintainer: Giulio Barcaroli <barcarol@istat.it>
Diff between SamplingStrata versions 1.0-4 dated 2015-08-25 and 1.1 dated 2016-01-13
DESCRIPTION | 13 ++-- MD5 | 31 ++++++----- NAMESPACE | 3 - NEWS | 14 +++++ R/buildStrataDF.R | 7 +- R/optimizeStrata.R | 67 ++++++++++++++++-------- R/plotSamprate.R |only R/rbgaV2.R | 17 +++++- R/recode.R |only R/strataGenalg.R | 8 +- build/vignette.rds |binary inst/doc/SamplingStrataVignette.R | 93 +++++++++++++++++++++++++++++++++ inst/doc/SamplingStrataVignette.Rnw | 97 +++++++++++++++++++++++++++++++++-- inst/doc/SamplingStrataVignette.pdf |binary inst/doc/tuneParameters.pdf |binary man/plotSamprate.Rd |only man/swissmunicipalities.Rd | 4 - vignettes/SamplingStrataVignette.Rnw | 97 +++++++++++++++++++++++++++++++++-- 18 files changed, 389 insertions(+), 62 deletions(-)
More information about SamplingStrata at CRAN
Permanent link
Title: Plotting Multi-Dimensional Data
Description: Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between plot3D versions 1.0-2 dated 2014-11-07 and 1.1 dated 2016-01-13
DESCRIPTION | 16 ++++---- MD5 | 94 +++++++++++++++++++++++++-------------------------- NAMESPACE | 1 R/Contour.R | 1 R/Image.R | 90 +++++++++++++++++++++++++++++++++--------------- R/arrows3D.R | 25 +++++++------ R/box3D.R | 65 +++++++++++++++++++++-------------- R/colorlegend.R | 43 +++++++++++++++++------ R/contour3D.R | 5 +- R/functions.R | 37 ++++++++++++-------- R/hist3D.R | 81 ++++++++++++++++++++++++++++++++++--------- R/image3D.R | 8 ++-- R/isosurf3D.R | 24 ++++++++----- R/paintit.R | 81 ++++++++++++++++++++++++++----------------- R/persp3D.R | 41 +++++++++++++--------- R/persp3Db.R | 4 +- R/plot.struct.R | 20 +++------- R/plot2D.R | 25 +++++++------ R/poly3D.R | 41 ++++++++++++++-------- R/polygon3D.R | 22 +++++++---- R/ribbon3D.R | 28 +++++++++------ R/scatter.R | 16 +++++--- R/scatter3D.R | 19 +++++++--- R/segments3D.R | 18 +++++---- R/slice3D.R | 24 +++++++++---- R/slicecont3D.R | 21 +++++++---- R/sphere.R | 20 +++++++--- R/surf3D.R | 20 ++++++---- R/text3D.R | 28 +++++++++------ R/voxel3D.R | 11 +++-- build/vignette.rds |binary data/Hypsometry.rda |binary data/Oxsat.rda |binary inst/doc/plot3D.R | 90 ++++++++++++++++++++++++++++++++++++++++++++++++ inst/doc/plot3D.rnw | 72 +++++++++++++++++++++++++++++++++++++++ man/Image.Rd | 29 +++++++++++++-- man/Oxsat.Rd | 2 - man/arrows3D.Rd | 48 ++++++++++++++------------ man/colorkey.Rd | 8 +++- man/colors.Rd | 2 - man/image3D.Rd | 13 ++++--- man/persp3D.Rd | 33 +++++++++++------ man/plot3D.Rd | 2 - man/plotdev.Rd | 11 ++++- man/scatter.Rd | 30 ++++++++++------ man/slice3D.Rd | 14 ++++--- man/surf3D.Rd | 15 +++++--- vignettes/plot3D.rnw | 72 +++++++++++++++++++++++++++++++++++++++ 48 files changed, 952 insertions(+), 418 deletions(-)
Title: Helper Functions for QCA in R
Description: Helper functions for Qualitative Comparative Analysis: evaluate and
plot Boolean formulae on fuzzy set score data, apply Boolean operations, compute
consistency and coverage measures.
Author: Jirka Lewandowski <jirka.lewandowski@wzb.eu> [aut, cre]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between QCAtools versions 0.1 dated 2015-01-07 and 0.2.1 dated 2016-01-13
DESCRIPTION | 18 +++++++++++------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 26 ++++++++++++++------------ R/QCAtools-package.r | 6 +++++- R/boolean.R | 4 ++-- R/xyplot.R | 7 ++++--- README.md | 4 ++-- man/QCAtools.Rd | 2 +- man/boolean.Rd | 3 ++- man/consistency.Rd | 8 +++++--- man/evaluate_dnf.Rd | 5 +++-- man/format_dnf.Rd | 2 +- man/formula_to_function.Rd | 3 ++- man/plot.qca.Rd | 5 +++-- man/xyplot.Rd | 5 +++-- 15 files changed, 72 insertions(+), 54 deletions(-)
More information about ontologySimilarity at CRAN
Permanent link
Title: An R Package for Multiple Break-Point Detection via the
Cross-Entropy Method
Description: Implements the Cross-Entropy (CE) method, which is a model based stochastic optimization technique to estimate both the number and their corresponding locations of break-points in continuous and discrete measurements (Priyadarshana and Sofronov (2015), Priyadarshana and Sofronov (2012a), Priyadarshana and Sofronov (2012b)).
Author: Priyadarshana W.J.R.M. and Georgy Sofronov
Maintainer: Priyadarshana W.J.R.M. <mjayawardana@swin.edu.au>
Diff between breakpoint versions 1.1 dated 2014-12-21 and 1.2 dated 2016-01-13
breakpoint-1.1/breakpoint/R/CE.Normal.R |only breakpoint-1.1/breakpoint/R/ce.4betaNB.R |only breakpoint-1.1/breakpoint/R/ce.simNormalNB.R |only breakpoint-1.1/breakpoint/man/CE.Normal.Rd |only breakpoint-1.2/breakpoint/DESCRIPTION | 22 +- breakpoint-1.2/breakpoint/MD5 | 89 ++++++-- breakpoint-1.2/breakpoint/NAMESPACE | 5 breakpoint-1.2/breakpoint/NEWS |only breakpoint-1.2/breakpoint/R/AIC.MeanNormal.R |only breakpoint-1.2/breakpoint/R/AIC.MeanVarNormal.R |only breakpoint-1.2/breakpoint/R/AICnb.R |only breakpoint-1.2/breakpoint/R/AICzinb.R |only breakpoint-1.2/breakpoint/R/BIC.MeanNormal.R |only breakpoint-1.2/breakpoint/R/BIC.MeanVarNormal.R |only breakpoint-1.2/breakpoint/R/CE.NB.Init.R |only breakpoint-1.2/breakpoint/R/CE.NB.R | 131 ++++++++---- breakpoint-1.2/breakpoint/R/CE.Normal.Init.Mean.R |only breakpoint-1.2/breakpoint/R/CE.Normal.Init.MeanVar.R |only breakpoint-1.2/breakpoint/R/CE.Normal.Mean.R |only breakpoint-1.2/breakpoint/R/CE.Normal.MeanVar.R |only breakpoint-1.2/breakpoint/R/CE.ZINB.Init.R |only breakpoint-1.2/breakpoint/R/CE.ZINB.R | 131 ++++++++---- breakpoint-1.2/breakpoint/R/betaIntEst.R |only breakpoint-1.2/breakpoint/R/breakpoint-internal.R |only breakpoint-1.2/breakpoint/R/ce.4betaNB.AIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.4betaNB.AIC.R |only breakpoint-1.2/breakpoint/R/ce.4betaNB.BIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.4betaNB.BIC.R |only breakpoint-1.2/breakpoint/R/ce.4betaZINB.AIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.4betaZINB.AIC.R |only breakpoint-1.2/breakpoint/R/ce.4betaZINB.BIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.4betaZINB.BIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.Init.Mean.AIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.Init.Mean.BIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.Init.MeanVar.AIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.Init.MeanVar.BIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.Init.mBIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.MeanAIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.MeanBIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.MeanVar.AIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.MeanVar.BIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.R | 7 breakpoint-1.2/breakpoint/R/ce.simNormalNB.AIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.simNormalNB.AIC.R |only breakpoint-1.2/breakpoint/R/ce.simNormalNB.BIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.simNormalNB.BIC.R |only breakpoint-1.2/breakpoint/R/ce.simNormalZINB.AIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.simNormalZINB.AIC.R |only breakpoint-1.2/breakpoint/R/ce.simNormalZINB.BIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.simNormalZINB.BIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.Init.Mean.AIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.Init.Mean.BIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.Init.MeanVar.AIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.Init.MeanVar.BIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.Init.mBIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.MeanAIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.MeanBIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.MeanVar.AIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.MeanVar.BIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.R | 9 breakpoint-1.2/breakpoint/R/llhood.MeanNormal.R |only breakpoint-1.2/breakpoint/R/llhood.MeanVarNormal.R |only breakpoint-1.2/breakpoint/R/loglik.MeanNormal.R |only breakpoint-1.2/breakpoint/R/loglik.MeanVarNormal.R |only breakpoint-1.2/breakpoint/R/profilePlot.R | 3 breakpoint-1.2/breakpoint/data/ch1.GM03563.rda |binary breakpoint-1.2/breakpoint/man/CE.NB.Init.Rd |only breakpoint-1.2/breakpoint/man/CE.NB.Rd | 49 ++-- breakpoint-1.2/breakpoint/man/CE.Normal.Init.Mean.Rd |only breakpoint-1.2/breakpoint/man/CE.Normal.Init.MeanVar.Rd |only breakpoint-1.2/breakpoint/man/CE.Normal.Mean.Rd |only breakpoint-1.2/breakpoint/man/CE.Normal.MeanVar.Rd |only breakpoint-1.2/breakpoint/man/CE.ZINB.Init.Rd |only breakpoint-1.2/breakpoint/man/CE.ZINB.Rd | 38 ++- breakpoint-1.2/breakpoint/man/breakpoint-package.Rd | 19 - breakpoint-1.2/breakpoint/man/ch1.GM03563.Rd | 6 breakpoint-1.2/breakpoint/man/profilePlot.Rd | 16 - 77 files changed, 365 insertions(+), 160 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-29 0.1.1
2015-04-02 0.1.0
Title: Using GPUs in Statistical Genomics
Description: Can be used to carry out
permutation resampling inference in the context of RNA
microarray studies.
Author: Ivo D. Shterev, Sin-Ho Jung, Stephen L. George and Kouros Owzar
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>
Diff between permGPU versions 0.14.7 dated 2016-01-07 and 0.14.8 dated 2016-01-13
DESCRIPTION | 12 +++++++----- MD5 | 10 +++++----- NEWS | 4 ++++ man/permGPU-package.Rd | 5 +++-- man/permgpu.Rd | 4 ++-- man/scoregpu.Rd | 4 ++-- 6 files changed, 23 insertions(+), 16 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of a joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Multivariate joint frailty models for two types of recurrent events and a terminal event.
7) Joint models for longitudinal data and a terminal event.
8) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available. Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.8.2 dated 2015-12-08 and 2.8.3 dated 2016-01-13
DESCRIPTION | 8 +++---- MD5 | 26 ++++++++++++---------- NEWS | 6 +++++ R/epoce.R | 3 +- R/prediction.R | 2 - R/print.trivPenal.R | 2 - man/frailtyPenal.Rd | 2 - man/frailtypack-package.Rd | 6 ++--- man/num.id.Rd | 17 +++++++-------- src/aresidusMartingale.f90 | 51 +++++++++++++++++++++++---------------------- src/epoce.f90 |only src/epoce_log.f90 |only src/epoce_long.f90 | 8 +++---- src/joint_longi.f90 | 18 +++++++-------- src/prediction_tri.f90 | 12 +++++----- 15 files changed, 87 insertions(+), 74 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon, Bruno Herault
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between entropart versions 1.4-3 dated 2015-12-06 and 1.4-4 dated 2016-01-13
DESCRIPTION | 11 ++-- MD5 | 44 ++++++++-------- NAMESPACE | 1 NEWS | 16 +++++ R/AbdFreqCount.R | 4 - R/CommunityProfile.R | 4 - R/Coverage.R | 2 R/DivEst.R | 10 ++- R/DivPart.R | 3 - R/DivProfile.R | 121 +++++++++++++++++++++++++++++++++++++++++---- R/Shannon.R | 18 +++--- R/SpeciesDistribution.R | 4 - R/Tsallis.R | 19 ++----- R/rCommunity.R | 6 -- build/vignette.rds |binary inst/doc/entropart.R | 2 inst/doc/entropart.Rnw | 6 +- inst/doc/entropart.pdf |binary man/DivEst.Rd | 4 - man/DivProfile.Rd | 29 +++++++++- man/SpeciesDistribution.Rd | 4 - vignettes/entropart.Rnw | 6 +- vignettes/entropart.bib | 10 +++ 23 files changed, 238 insertions(+), 86 deletions(-)
Title: Generate Cofeature Matrices
Description: Generate cofeature (feature by sample) matrices. The package
utilizes ggplot2::geom_tile() to generate the matrix allowing for easy
additions from the base matrix.
Author: Fong Chun Chan [aut, cre]
Maintainer: Fong Chun Chan <fongchunchan@gmail.com>
Diff between cofeatureR versions 1.0.0 dated 2015-12-23 and 1.0.1 dated 2016-01-13
DESCRIPTION | 10 ++--- MD5 | 6 +-- R/plot_cofeature_mat.R | 9 ++--- README.md | 87 ++++++++++++++++++++++++++++++++++++++----------- 4 files changed, 81 insertions(+), 31 deletions(-)
Title: A MediaWiki API Wrapper
Description: A wrapper for the MediaWiki API, aimed particularly at the
Wikimedia 'production' wikis, such as Wikipedia. It can be used to retrieve
page text, information about users or the history of pages, and elements of
the category tree.
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between WikipediR versions 1.2.0 dated 2015-05-17 and 1.3.0 dated 2016-01-13
DESCRIPTION | 12 +++++++----- MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 3 ++- NEWS | 9 +++++++++ R/categories.R | 7 +++++-- R/metadata.R | 7 +++++-- R/query.R | 13 +++++++------ README.md | 6 ++++-- build/vignette.rds |binary man/categories_in_page.Rd | 3 ++- man/page_backlinks.Rd | 2 +- man/page_content.Rd | 2 +- man/page_external_links.Rd | 2 +- man/page_info.Rd | 3 ++- man/page_links.Rd | 7 +++++-- man/pages_in_category.Rd | 18 +++++++++++------- man/query.Rd | 2 +- man/random_page.Rd | 2 +- man/recent_changes.Rd | 2 +- man/revision_content.Rd | 3 ++- man/revision_diff.Rd | 3 ++- man/user_contributions.Rd | 6 ++++-- man/user_information.Rd | 2 +- 23 files changed, 96 insertions(+), 62 deletions(-)
Title: Access and Plot CanVec and CanVec+ Data for Rapid Basemap
Creation in Canada
Description: Provides an interface to the National Topographic System (NTS), which is
the way in which a number of freely available Canadian datasets
are organized. CanVec and CanVec+ datasets, which include all data used
to create Canadian topographic maps, are two such datasets that are useful
in creating vector-based maps for locations across Canada. This packages searches
CanVec data by location, plots it using pretty defaults, and exports it to
human-readable shapefiles for use in another GIS.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rcanvec versions 0.1.3 dated 2015-10-18 and 0.1.4 dated 2016-01-13
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/nts.R | 4 +++- README.md |only man/rcanvec-package.Rd | 9 +-------- 5 files changed, 12 insertions(+), 16 deletions(-)
Title: Body Mass Estimation Equations for Vertebrates
Description: Estimation equations are from a variety of sources but are, in general, based on regressions between skeletal measurements (e.g., femoral circumference) and body mass in living taxa.
Author: Nicolas E. Campione
Maintainer: Nicolas E. Campione <nicolas.campione@geo.uu.se>
Diff between MASSTIMATE versions 1.2 dated 2014-05-19 and 1.3 dated 2016-01-13
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ NAMESPACE | 1 + R/QE.R | 27 +++++++++++++++++++++++---- R/bipeds.R | 20 ++++++++++++++++++-- R/cQE.R | 22 ++++++++++++++++++++-- R/quadrupeds.R | 30 +++++++++++++++++++++++++----- README.md |only man/MASSTIMATE-package.Rd | 12 +++++++----- man/QE.Rd | 30 +++++++++++++++++++++--------- man/bipeds.Rd | 19 ++++++++++++------- man/cQE.Rd | 39 ++++++++++++++++++++++++--------------- man/dinosbip.Rd | 4 ++-- man/quadrupeds.Rd | 15 ++++++++++----- 14 files changed, 180 insertions(+), 72 deletions(-)
Title: R Interface to 'lp_solve' Version 5.5.2.0
Description: The lpSolveAPI package provides an R interface to 'lp_solve',
a Mixed Integer Linear Programming (MILP) solver with support for pure
linear, (mixed) integer/binary, semi-continuous and special ordered sets
(SOS) models.
Author: lp_solve <http://lpsolve.sourceforge.net/>,
Kjell Konis <kjell.konis@me.com>.
Maintainer: Kjell Konis <kjell.konis@me.com>
Diff between lpSolveAPI versions 5.5.2.0-14 dated 2014-11-12 and 5.5.2.0-17 dated 2016-01-13
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- NAMESPACE | 21 ++++++++++++++++----- R/lp.control.q | 4 ++-- 4 files changed, 29 insertions(+), 18 deletions(-)