Title: Bayesian State-Space Models for Animal Movement
Description: Tools to fit Bayesian state-space models to animal tracking data. Models are provided for location
filtering, location filtering and behavioural state estimation, and their hierarchical versions.
The models are primarily intended for fitting to ARGOS satellite tracking data but options exist to fit
to other tracking data types. For Global Positioning System data, consider the 'moveHMM' package.
Simplified Markov Chain Monte Carlo convergence diagnostic plotting is provided but users are encouraged
to explore tools available in packages such as 'coda' and 'boa'.
Author: Ian Jonsen [aut, cre],
Sophie Bestley [ctb],
Simon Wotherspoon [ctb],
Michael Sumner [ctb],
Joanna Mills Flemming [ctb]
Maintainer: Ian Jonsen <ian.jonsen@mq.edu.au>
Diff between bsam versions 1.1.1 dated 2016-11-17 and 1.1.2 dated 2017-06-30
DESCRIPTION | 19 ++++++++++++------- MD5 | 48 ++++++++++++++++++++++++------------------------ NAMESPACE | 2 ++ NEWS.md | 5 ++++- R/bsam-package.R | 2 +- R/dat4jags.R | 8 ++++---- R/fit_ssm.R | 11 ++++++++--- R/hssm.R | 17 ++++++++++------- R/ssm.R | 2 ++ README.md | 2 ++ inst/jags/hDCRW.txt | 2 +- inst/jags/hDCRWS.txt | 2 +- man/bsam-deprecated.Rd | 3 +-- man/bsam-package.Rd | 15 +++++++-------- man/dat4jags.Rd | 1 - man/diag_ssm.Rd | 1 - man/ellie.Rd | 1 - man/fit_ssm.Rd | 16 +++++++++------- man/get_summary.Rd | 1 - man/hssm.Rd | 1 - man/map_ssm.Rd | 1 - man/plot_fit.Rd | 1 - man/simulate.Rd | 1 - man/ssm.Rd | 1 - man/tpar.Rd | 1 - 25 files changed, 88 insertions(+), 76 deletions(-)
Title: R Interface for H2O Sparkling Water
Description: An extension package for 'sparklyr' that provides an R interface to
H2O Sparkling Water machine learning library (see <https://github.com/h2oai/sparkling-water> for more information).
Author: JJ Allaire [aut],
Erin LeDell [aut],
Michal Malohlava [aut],
Navdeep Gill [aut, cre],
Jakub Hava [aut],
RStudio [cph],
H2O.ai [cph]
Maintainer: Navdeep Gill <navdeep@h2o.ai>
Diff between rsparkling versions 0.2.0 dated 2017-03-17 and 0.2.1 dated 2017-06-30
DESCRIPTION | 6 +++--- MD5 | 21 +++++++++++++++++---- R/install_h2o.R | 24 ++++++++++++------------ R/package.R | 21 +++++++++++---------- inst/examples/h2ologs |only inst/examples/log4j.spark.log |only inst/examples/log4j.spark.log.2017-05-08 |only inst/examples/log4j.spark.log.2017-05-09 |only inst/examples/nycflights13.R | 9 ++++++--- 9 files changed, 49 insertions(+), 32 deletions(-)
Title: A Package for Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data, in
particular representation, manipulation and simulation of multistate
data - the Lexis suite of functions, which includes interfaces to
'mstate', 'etm' and 'cmprsk' packages.
Also contains functions for Age-Period-Cohort and Lee-Carter
modeling and a function for interval censored data and some useful
functions for tabulation and plotting, as well as a number of
epidemiological data sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.15 dated 2017-05-30 and 2.16 dated 2017-06-30
CHANGES | 8 +++++++- DESCRIPTION | 12 ++++++------ MD5 | 26 ++++++++++++++------------ NAMESPACE | 5 ++++- R/addCov.Lexis.R |only R/lexis.R | 3 +++ inst/doc/Follow-up.pdf |binary inst/doc/simLexis.pdf |binary inst/doc/yll.pdf |binary man/LCa.fit.Rd | 5 ++--- man/Lexis.Rd | 2 ++ man/addCov.Lexis.Rd |only man/cutLexis.Rd | 1 + man/splitLexis.Rd | 6 +++++- man/transform.Lexis.Rd | 12 +++++++++++- 15 files changed, 55 insertions(+), 25 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal maximum likelihood estimation of uni- and
multidimensional item response models (Rasch, 2PL, 3PL,
Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models)
and joint maximum likelihood estimation for models
from the Rasch family.
Latent regression models and plausible value imputation are
also supported.
Author:
Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between TAM versions 2.3-18 dated 2017-06-25 and 2.4-9 dated 2017-06-30
DESCRIPTION | 8 MD5 | 22 +- NAMESPACE | 1 R/RcppExports.R | 16 + R/tam.mml.wle2.R | 216 +++++++++++++++-------- R/tam.pv.R | 29 +-- R/tam_pv_draw_pv_normal_approximation_multidim.R |only R/tam_pv_sampling_theta.R | 6 inst/NEWS | 23 ++ man/tam.wle.Rd | 4 src/RcppExports.cpp | 49 +++++ src/init.c | 72 ++++--- src/tam_pv_multivariate_normal_approximation.cpp |only 13 files changed, 313 insertions(+), 133 deletions(-)
Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra.
Differences with other sparse matrix packages are:
(1) we only support (essentially) one sparse matrix format,
(2) based on transparent and simple structure(s),
(3) tailored for MCMC calculations within G(M)RF.
(4) and it is fast and scalable (with the extension package spam64).
Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb], Daniel Gerber [ctb], Kaspar Moesinger [ctb]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam versions 1.4-0 dated 2016-08-30 and 2.1-0 dated 2017-06-30
spam-1.4-0/spam/R/image_spam.R |only spam-1.4-0/spam/R/makeprec.R |only spam-1.4-0/spam/tests/constructors.R |only spam-1.4-0/spam/tests/covmat.R |only spam-1.4-0/spam/tests/crossprod.R |only spam-1.4-0/spam/tests/diff.R |only spam-1.4-0/spam/tests/dim.R |only spam-1.4-0/spam/tests/displays.R |only spam-1.4-0/spam/tests/dist.R |only spam-1.4-0/spam/tests/foreign.R |only spam-1.4-0/spam/tests/helper.R |only spam-1.4-0/spam/tests/kronecker.R |only spam-1.4-0/spam/tests/math.R |only spam-1.4-0/spam/tests/mle.R |only spam-1.4-0/spam/tests/norm.R |only spam-1.4-0/spam/tests/ops.R |only spam-1.4-0/spam/tests/overall.R |only spam-1.4-0/spam/tests/permutation.R |only spam-1.4-0/spam/tests/rowcolstats.R |only spam-1.4-0/spam/tests/solve.R |only spam-1.4-0/spam/tests/spamlist.R |only spam-1.4-0/spam/tests/subsetting.R |only spam-1.4-0/spam/tests/xybind.R |only spam-2.1-0/spam/ChangeLog | 1372 ++++++++++ spam-2.1-0/spam/DESCRIPTION | 35 spam-2.1-0/spam/MD5 | 309 +- spam-2.1-0/spam/NAMESPACE | 18 spam-2.1-0/spam/R/apply.R | 38 spam-2.1-0/spam/R/constructors.R | 18 spam-2.1-0/spam/R/covmat.R | 32 spam-2.1-0/spam/R/definitions.R | 1856 +++++++++----- spam-2.1-0/spam/R/deprecated.R |only spam-2.1-0/spam/R/diff.R | 12 spam-2.1-0/spam/R/dim.R | 134 - spam-2.1-0/spam/R/dist.R | 123 spam-2.1-0/spam/R/foreign.R | 116 spam-2.1-0/spam/R/helper.R | 95 spam-2.1-0/spam/R/kronecker.R | 151 - spam-2.1-0/spam/R/math.R | 403 ++- spam-2.1-0/spam/R/mle.R | 18 spam-2.1-0/spam/R/norm.R | 18 spam-2.1-0/spam/R/permutation.R | 216 + spam-2.1-0/spam/R/plotting.R | 26 spam-2.1-0/spam/R/precmat.R | 70 spam-2.1-0/spam/R/profile.R | 167 - spam-2.1-0/spam/R/rep_len_long.R |only spam-2.1-0/spam/R/rmvnorm.R | 12 spam-2.1-0/spam/R/rowcolstats.R | 126 spam-2.1-0/spam/R/s3only.R | 12 spam-2.1-0/spam/R/s4coerce.R | 19 spam-2.1-0/spam/R/spam_solve.R | 879 ++++-- spam-2.1-0/spam/R/spamlist.R | 203 + spam-2.1-0/spam/R/subset.R | 469 ++- spam-2.1-0/spam/R/summary.R |only spam-2.1-0/spam/R/tailhead.R | 13 spam-2.1-0/spam/R/tcrossprod.R | 24 spam-2.1-0/spam/R/toepliz.R | 154 - spam-2.1-0/spam/R/xybind.R | 113 spam-2.1-0/spam/build/vignette.rds |binary spam-2.1-0/spam/demo/article-jss-example1.R | 2 spam-2.1-0/spam/demo/article-jss-example2.R | 2 spam-2.1-0/spam/demo/article-jss.R | 16 spam-2.1-0/spam/demo/cholesky.R | 16 spam-2.1-0/spam/demo/jss10-example1.R | 2 spam-2.1-0/spam/demo/jss15-BYM.R | 2 spam-2.1-0/spam/demo/jss15-Leroux.R | 2 spam-2.1-0/spam/demo/spam.R | 2 spam-2.1-0/spam/inst/NEWS | 27 spam-2.1-0/spam/man/Oral.Rd | 3 spam-2.1-0/spam/man/UScounties.Rd | 3 spam-2.1-0/spam/man/USprecip.Rd | 3 spam-2.1-0/spam/man/adjacency.Rd | 3 spam-2.1-0/spam/man/allequal.Rd | 3 spam-2.1-0/spam/man/apply.Rd | 3 spam-2.1-0/spam/man/bandwidth.Rd | 3 spam-2.1-0/spam/man/bdiag.Rd | 3 spam-2.1-0/spam/man/chol.Rd | 16 spam-2.1-0/spam/man/circulant.Rd | 7 spam-2.1-0/spam/man/cleanup.Rd | 5 spam-2.1-0/spam/man/coerce.Rd | 3 spam-2.1-0/spam/man/coercion.Rd | 7 spam-2.1-0/spam/man/complexity.Rd | 3 spam-2.1-0/spam/man/constructors.Rd | 3 spam-2.1-0/spam/man/cov.Rd | 21 spam-2.1-0/spam/man/crossprod.Rd | 11 spam-2.1-0/spam/man/det.Rd | 3 spam-2.1-0/spam/man/diag.Rd | 7 spam-2.1-0/spam/man/diff.Rd | 3 spam-2.1-0/spam/man/dim.Rd | 3 spam-2.1-0/spam/man/display.Rd | 19 spam-2.1-0/spam/man/foreign.Rd | 3 spam-2.1-0/spam/man/germany.Rd | 3 spam-2.1-0/spam/man/germanydata.Rd | 3 spam-2.1-0/spam/man/grid_trace2.Rd | 3 spam-2.1-0/spam/man/grid_zoom.Rd | 3 spam-2.1-0/spam/man/headtail.Rd | 3 spam-2.1-0/spam/man/history.spam.Rd | 3 spam-2.1-0/spam/man/image.Rd | 11 spam-2.1-0/spam/man/import.Rd | 5 spam-2.1-0/spam/man/isSymmetric.Rd | 3 spam-2.1-0/spam/man/kronecker.Rd | 6 spam-2.1-0/spam/man/landkreis.Rd | 3 spam-2.1-0/spam/man/lu.tri.Rd | 7 spam-2.1-0/spam/man/makeprec.Rd | 7 spam-2.1-0/spam/man/math.Rd | 7 spam-2.1-0/spam/man/math2.Rd | 3 spam-2.1-0/spam/man/methods.Rd | 3 spam-2.1-0/spam/man/mle.Rd | 3 spam-2.1-0/spam/man/nearestdist.Rd | 3 spam-2.1-0/spam/man/operations.Rd | 5 spam-2.1-0/spam/man/options.Rd | 109 spam-2.1-0/spam/man/ordering.Rd | 3 spam-2.1-0/spam/man/pad.Rd | 5 spam-2.1-0/spam/man/permutation.Rd | 5 spam-2.1-0/spam/man/powerboost.Rd | 3 spam-2.1-0/spam/man/precmat.Rd | 5 spam-2.1-0/spam/man/print.Rd | 9 spam-2.1-0/spam/man/rdist.Rd | 3 spam-2.1-0/spam/man/rmvnorm.Rd | 3 spam-2.1-0/spam/man/rmvnorm.const.Rd | 3 spam-2.1-0/spam/man/rowcolstats.Rd | 3 spam-2.1-0/spam/man/s3only.Rd | 3 spam-2.1-0/spam/man/solve.Rd | 7 spam-2.1-0/spam/man/spam-class.Rd | 10 spam-2.1-0/spam/man/spam-deprecated.Rd | 11 spam-2.1-0/spam/man/spam-package.Rd | 3 spam-2.1-0/spam/man/spam.chol.NgPeyton-class.Rd | 3 spam-2.1-0/spam/man/spam.creation.Rd | 26 spam-2.1-0/spam/man/spam.internal.Rd | 3 spam-2.1-0/spam/man/summary.Rd | 10 spam-2.1-0/spam/man/todo.Rd | 3 spam-2.1-0/spam/man/toeplitz.Rd | 7 spam-2.1-0/spam/man/triplet.Rd | 3 spam-2.1-0/spam/man/validate_spam.Rd |only spam-2.1-0/spam/man/version.Rd | 3 spam-2.1-0/spam/man/xybind.Rd | 12 spam-2.1-0/spam/src/Makevars |only spam-2.1-0/spam/src/bckslvmodified.f | 4 spam-2.1-0/spam/src/cholmodified.f | 494 +-- spam-2.1-0/spam/src/dist.f | 1 spam-2.1-0/spam/src/fromsparsekit.f | 51 spam-2.1-0/spam/src/init.c |only spam-2.1-0/spam/src/kronecker.f | 2 spam-2.1-0/spam/src/rep_len_long.c |only spam-2.1-0/spam/src/spamown.f | 23 spam-2.1-0/spam/src/spamown2.f | 3 spam-2.1-0/spam/src/xybind.f | 2 spam-2.1-0/spam/tests/demo_article-jss-example1.R | 2 spam-2.1-0/spam/tests/demo_article-jss-example1.Rout.save |only spam-2.1-0/spam/tests/demo_article-jss-example2.R | 2 spam-2.1-0/spam/tests/demo_article-jss-example2.Rout.save |only spam-2.1-0/spam/tests/demo_article-jss.R | 14 spam-2.1-0/spam/tests/demo_article-jss.Rout.save |only spam-2.1-0/spam/tests/demo_cholesky.R | 16 spam-2.1-0/spam/tests/demo_cholesky.Rout.save |only spam-2.1-0/spam/tests/demo_jss15-BYM.R | 2 spam-2.1-0/spam/tests/demo_jss15-BYM.Rout.save |only spam-2.1-0/spam/tests/demo_jss15-Leroux.R | 2 spam-2.1-0/spam/tests/demo_jss15-Leroux.Rout.save |only spam-2.1-0/spam/tests/demo_spam.R | 2 spam-2.1-0/spam/tests/demo_spam.Rout.save |only spam-2.1-0/spam/tests/demo_timing.Rout.save |only spam-2.1-0/spam/tests/jss_areal_counts.R | 2 spam-2.1-0/spam/tests/jss_areal_counts.Rout.save |only spam-2.1-0/spam/tests/testthat |only spam-2.1-0/spam/tests/testthat.R |only spam-2.1-0/spam/tests/testthat.Rout.save |only 167 files changed, 6008 insertions(+), 2413 deletions(-)
Title: R Interface to a 'PostGIS' Database
Description: Provides an interface between R and
'PostGIS'-enabled 'PostgreSQL' databases to transparently transfer
spatial data. Both vector (points, lines, polygons) and raster
data are supported in read and write modes. Also provides
convenience functions to execute common procedures in
'PostgreSQL/PostGIS'.
Author: Mathieu Basille [aut],
David Bucklin [aut, cre]
Maintainer: David Bucklin <david.bucklin@gmail.com>
Diff between rpostgis versions 1.2.1 dated 2017-05-07 and 1.3.0 dated 2017-06-30
rpostgis-1.2.1/rpostgis/R/data.R |only rpostgis-1.2.1/rpostgis/data |only rpostgis-1.2.1/rpostgis/man/roe_gps_data.Rd |only rpostgis-1.3.0/rpostgis/DESCRIPTION | 12 - rpostgis-1.3.0/rpostgis/MD5 | 76 ++++---- rpostgis-1.3.0/rpostgis/NAMESPACE | 11 + rpostgis-1.3.0/rpostgis/NEWS | 67 +++++++ rpostgis-1.3.0/rpostgis/R/all_db_wrapper_fns.R | 42 ++-- rpostgis-1.3.0/rpostgis/R/dbUtils_notExported.R | 73 +++++++- rpostgis-1.3.0/rpostgis/R/dbWriteDataFrame.R | 71 ++++++-- rpostgis-1.3.0/rpostgis/R/pgGetBoundary.R | 36 ++-- rpostgis-1.3.0/rpostgis/R/pgGetGeom.R | 137 ++++++++++----- rpostgis-1.3.0/rpostgis/R/pgGetRast.R | 211 ++++++++++++++++++------ rpostgis-1.3.0/rpostgis/R/pgInsert.R | 24 ++ rpostgis-1.3.0/rpostgis/R/pgInsertize.R | 15 + rpostgis-1.3.0/rpostgis/R/pgListGeom.R | 61 ++++-- rpostgis-1.3.0/rpostgis/R/pgMakePts.R | 8 rpostgis-1.3.0/rpostgis/R/pgPostGIS.R | 4 rpostgis-1.3.0/rpostgis/R/pgSRID.R | 2 rpostgis-1.3.0/rpostgis/R/pgWriteRast.R | 74 +++++--- rpostgis-1.3.0/rpostgis/R/rpostgis-package.R | 2 rpostgis-1.3.0/rpostgis/man/dbGetDefs.Rd |only rpostgis-1.3.0/rpostgis/man/dbTableInfo.Rd | 2 rpostgis-1.3.0/rpostgis/man/dbTableNameFix.Rd | 2 rpostgis-1.3.0/rpostgis/man/dbWriteDataFrame.Rd | 2 rpostgis-1.3.0/rpostgis/man/pgCheckGeom.Rd | 6 rpostgis-1.3.0/rpostgis/man/pgGetBoundary.Rd | 8 rpostgis-1.3.0/rpostgis/man/pgGetGeom.Rd | 23 ++ rpostgis-1.3.0/rpostgis/man/pgGetLines.Rd | 2 rpostgis-1.3.0/rpostgis/man/pgGetPolys.Rd | 2 rpostgis-1.3.0/rpostgis/man/pgGetPts.Rd | 2 rpostgis-1.3.0/rpostgis/man/pgGetRast.Rd | 23 +- rpostgis-1.3.0/rpostgis/man/pgGetSRID.Rd |only rpostgis-1.3.0/rpostgis/man/pgInsert.Rd | 19 +- rpostgis-1.3.0/rpostgis/man/pgInsertizeGeom.Rd | 6 rpostgis-1.3.0/rpostgis/man/pgListGeom.Rd | 23 +- rpostgis-1.3.0/rpostgis/man/pgPostGIS.Rd | 2 rpostgis-1.3.0/rpostgis/man/pgSRID.Rd | 2 rpostgis-1.3.0/rpostgis/man/pgWriteRast.Rd | 20 +- rpostgis-1.3.0/rpostgis/man/rpostgis.Rd | 2 40 files changed, 756 insertions(+), 316 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone and Ryan Kyle.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 0.9-82 dated 2017-04-07 and 0.9-87 dated 2017-06-30
DESCRIPTION | 10 MD5 | 20 R/epi.2by2.R | 4859 +++++++++++++++++++++++++------------------------- R/epi.ccsize.R | 119 + R/epi.conf.R | 7 R/epi.equivb.R | 68 man/epi.2by2.Rd | 75 man/epi.ccsize.Rd | 85 man/epi.cohortsize.Rd | 2 man/epi.conf.Rd | 5 man/epi.meansize.Rd | 6 11 files changed, 2734 insertions(+), 2522 deletions(-)
Title: Implementation of a Generic Adaptive Monte Carlo Markov Chain
Sampler
Description: Enables sampling from arbitrary distributions if the log density is known up to a constant; a common situation in the context of Bayesian inference. The implemented sampling algorithm was proposed by Vihola (2012) <DOI:10.1007/s11222-011-9269-5> and achieves often a high efficiency by tuning the proposal distributions to a user defined acceptance rate.
Author: Andreas Scheidegger, <andreas.scheidegger@eawag.ch>, <scheidegger.a@gmail.com>
Maintainer: Andreas Scheidegger <andreas.scheidegger@eawag.ch>
Diff between adaptMCMC versions 1.1 dated 2012-06-22 and 1.2 dated 2017-06-30
DESCRIPTION | 23 - MD5 | 16 - NAMESPACE | 12 R/Adaptive_MCMC.R | 541 ++++++++++++++++++++++++--------------------- man/MCMC.Rd | 350 ++++++++++++++++------------- man/MCMC.add.samples.Rd | 142 +++++------ man/MCMC.parallel.Rd | 208 ++++++++--------- man/convert.to.coda.Rd | 136 +++++------ man/genericMCMC-package.Rd | 95 +++---- 9 files changed, 801 insertions(+), 722 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for Bayesian estimation of
antigen-driven selection in immunoglobulin (Ig) sequences, providing an
intuitive means of analyzing selection by quantifying the degree of
selective pressure. Also provides tools to profile mutations in Ig
sequences, build models of somatic hypermutation (SHM) in Ig sequences,
and make model-dependent distance comparisons of Ig repertoires.
Author: Mohamed Uduman [aut],
Gur Yaari [aut],
Namita Gupta [aut],
Jason Vander Heiden [aut, cre],
Ang Cui [ctb],
Susanna Marquez [ctb],
Julian Zhou [ctb],
Nima Nouri [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between shazam versions 0.1.7 dated 2017-05-14 and 0.1.8 dated 2017-06-30
DESCRIPTION | 16 MD5 | 108 - NAMESPACE | 9 NEWS.md | 41 R/Baseline.R | 220 +- R/Core.R | 25 R/DistToNearest.R | 710 +++++++-- R/MutationDefinitions.R | 18 R/MutationProfiling.R | 2577 ++++++++++++++++++++++++++--------- R/Shazam.R | 8 R/Shmulate.R | 2 R/TargetingModels.R | 54 R/sysdata.rda |binary data/CHARGE_MUTATIONS.rda |binary data/HYDROPATHY_MUTATIONS.rda |binary data/POLARITY_MUTATIONS.rda |binary data/VOLUME_MUTATIONS.rda |binary inst/doc/Baseline-Vignette.R | 38 inst/doc/Baseline-Vignette.Rmd | 58 inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.R | 4 inst/doc/DistToNearest-Vignette.Rmd | 37 inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Mutation-Vignette.R | 12 inst/doc/Mutation-Vignette.Rmd | 14 inst/doc/Mutation-Vignette.pdf |binary inst/doc/Targeting-Vignette.pdf |binary man/GmmThreshold-class.Rd | 31 man/calcBaseline.Rd | 33 man/calcExpectedMutations.Rd | 12 man/calcObservedMutations.Rd | 196 +- man/collapseClones.Rd | 364 ++++ man/createMutabilityMatrix.Rd | 6 man/createSubstitutionMatrix.Rd | 6 man/createTargetingModel.Rd | 6 man/distToNearest.Rd | 4 man/editBaseline.Rd | 13 man/expectedMutations.Rd | 8 man/extendMutabilityMatrix.Rd | 2 man/findThreshold.Rd | 77 - man/getBaselineStats.Rd | 11 man/groupBaseline.Rd | 22 man/minNumSeqMutationsTune.Rd | 3 man/observedMutations.Rd | 49 man/plotBaselineDensity.Rd | 15 man/plotBaselineSummary.Rd | 10 man/plotDensityThreshold.Rd | 2 man/plotGmmThreshold.Rd | 4 man/slideWindowTune.Rd | 4 man/slideWindowTunePlot.Rd | 2 man/summarizeBaseline.Rd | 15 man/testBaseline.Rd | 9 vignettes/Baseline-Vignette.Rmd | 58 vignettes/DistToNearest-Vignette.Rmd | 37 vignettes/Mutation-Vignette.Rmd | 14 55 files changed, 3696 insertions(+), 1268 deletions(-)
Title: Capture-Mark-Recapture Analysis using Multiple Non-Invasive
Marks
Description: Traditional and spatial capture-mark-recapture analysis with
multiple non-invasive marks. The models implemented in 'multimark' combine
encounter history data arising from two different non-invasive ``marks'',
such as images of left-sided and right-sided pelage patterns of bilaterally
asymmetrical species, to estimate abundance and related demographic
parameters while accounting for imperfect detection. Bayesian models are
specified using simple formulae and fitted using Markov chain Monte Carlo.
Addressing deficiencies in currently available software, 'multimark' also
provides a user-friendly interface for performing Bayesian multimodel
inference using non-spatial or spatial capture-recapture data consisting of a single
conventional mark or multiple non-invasive marks.
Author: Brett T. McClintock [aut, cre],
Acho Arnold [ctb, cph] (C original matrix library,
https://github.com/najela/matrix.h),
Barry Brown [ctb] (Fortran original ranlib library),
James Lovato [ctb] (Fortran original ranlib library),
John Burkardt [ctb] (C original ranlib library,
http://people.sc.fsu.edu/~jburkardt/c_src/ranlib),
Cleve Moler [ctb] (C original linpack library,
http://www.kkant.net/geist/ranlib/),
Arjun Gopalaswamy [ctb] (modified snippets of R package SPACECAP code)
Maintainer: Brett T. McClintock <brett.mcclintock@noaa.gov>
Diff between multimark versions 2.0.0 dated 2016-09-02 and 2.0.1 dated 2017-06-30
DESCRIPTION | 10 +++--- MD5 | 67 +++++++++++++++++++++-------------------- NEWS | 15 ++++++++- R/CJS.R | 4 +- R/Closed.R | 4 +- R/ClosedSCR.R | 23 ++++++++------ R/multimark_functions.R | 56 +++++++++++++++++++++++++++++++++- data/bobcatSCR.RData |only man/bobcat.Rd | 1 man/bobcatSCR.Rd |only man/getdensityClosedSCR.Rd | 7 +--- man/getprobsCJS.Rd | 7 +--- man/getprobsClosed.Rd | 7 +--- man/getprobsClosedSCR.Rd | 10 +++--- man/markCJS.Rd | 7 +--- man/markClosed.Rd | 7 +--- man/markClosedSCR.Rd | 9 ++--- man/multimarkCJS.Rd | 7 +--- man/multimarkClosed.Rd | 7 +--- man/multimarkClosedSCR.Rd | 11 +++--- man/multimarkSCRsetup-class.Rd | 9 +++-- man/multimarksetup-class.Rd | 9 +++-- man/multimodelCJS.Rd | 11 +++--- man/multimodelClosed.Rd | 11 +++--- man/multimodelClosedSCR.Rd | 17 ++++------ man/plotSpatialData.Rd | 1 man/processdata.Rd | 7 +--- man/processdataSCR.Rd | 9 ++--- man/simdataCJS.Rd | 7 +--- man/simdataClosed.Rd | 7 +--- man/simdataClosedSCR.Rd | 7 +--- man/tiger.Rd | 3 - src/Closed.c | 2 - src/ClosedSCR.c | 2 - src/ProbitCJS.c | 2 - src/multimark_init.c |only 36 files changed, 209 insertions(+), 154 deletions(-)
Title: Rainforest Plots and Visual Funnel Plot Inference for
Meta-Analysis
Description: Creates rainforest plots (proposed by Schild & Voracek, 2015
<doi:10.1002/jrsm.1125>), a variant and enhancement of the classic forest plot
for meta-analysis. In addition, functionalities for visual funnel plot inference are provided.
In the near future, the 'metaviz' package will be extended by further,
established as well as novel, plotting options for visualizing meta-analytic data.
Author: Michael Kossmeier [cre, aut],
Ulrich S. Tran [aut],
Martin Voracek [aut]
Maintainer: Michael Kossmeier <michael.kossmeier@univie.ac.at>
Diff between metaviz versions 0.1.0 dated 2017-02-06 and 0.1.1 dated 2017-06-30
DESCRIPTION | 27 +++++++++++++++------------ MD5 | 31 ++++++++++++++++++------------- NAMESPACE | 2 ++ R/brainvol.R |only R/funnelinf.R |only R/mozart.R | 2 +- R/rainforest.R | 8 ++++---- build/vignette.rds |binary data/brainvol.rda |only inst/doc/metaviz.R | 4 ++-- inst/doc/metaviz.Rmd | 6 +++--- inst/doc/metaviz.html | 24 +++++++++++++----------- man/brainvol.Rd |only man/funnelinf.Rd |only man/mozart.Rd | 3 +-- man/rainforest.Rd | 23 +++++++++++------------ man/rem_effect.Rd | 1 - man/rem_err.Rd | 1 - vignettes/metaviz.Rmd | 6 +++--- 19 files changed, 73 insertions(+), 65 deletions(-)
Title: Hierarchical Algorithm for Post-Hoc Testing
Description: A set of tools to support results of post-hoc testing and enable to extract hierarchical structure of factors. Work on this package was financially supported by the 'NCN Opus grant 2016/21/B/ST6/02176'.
Author: Agnieszka Sitko [aut, cre],
Przemyslaw Biecek [aut, ths]
Maintainer: Agnieszka Sitko <ag.agnieszka.sitko@gmail.com>
Diff between factorMerger versions 0.3 dated 2017-06-25 and 0.3.1 dated 2017-06-30
DESCRIPTION | 12 MD5 | 74 ++-- NAMESPACE | 4 R/factorManipulation.R | 15 R/factorMergerClasses.R | 83 +++-- R/factorMergerHelper.R | 98 +++--- R/sampleGeneration.R | 12 R/statisticCalc.R | 15 R/visualizations.R | 305 +++++++++++++------ R/visualizationsCalc.R | 45 +- R/zzz.R | 5 build/vignette.rds |binary inst/doc/brca.R | 8 inst/doc/brca.Rmd | 12 inst/doc/brca.html | 19 - inst/doc/factorMerger.R | 2 inst/doc/factorMerger.Rmd | 6 inst/doc/factorMerger.html | 603 +++++++++++++++++--------------------- inst/doc/pisa2012.R | 24 - inst/doc/pisa2012.Rmd | 26 - inst/doc/pisa2012.html | 115 +------ man/cutTree.Rd | 15 man/generateMultivariateSample.Rd | 3 man/getOptimalPartition.Rd | 15 man/getOptimalPartitionDf.Rd | 15 man/groupsStats.Rd | 3 man/mergeFactors.Rd | 8 man/mergingHistory.Rd | 15 man/plotBoxplot.Rd | 4 man/plotHeatmap.Rd | 4 man/plotMeansAndConfInt.Rd | 4 man/plotProfile.Rd | 4 man/plotProportion.Rd | 4 man/plotSurvival.Rd | 4 man/print.factorMerger.Rd | 6 vignettes/brca.Rmd | 12 vignettes/factorMerger.Rmd | 6 vignettes/pisa2012.Rmd | 26 - 38 files changed, 869 insertions(+), 762 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Development, simulation testing, and implementation of management
procedures for data-limited fisheries
(see Carruthers et al (2014) <doi:10.1016/j.fishres.2013.12.014>).
Author: Tom Carruthers [aut, cre],
Adrian Hordyk [aut]
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 4.2 dated 2017-06-02 and 4.3.1 dated 2017-06-30
DESCRIPTION | 8 MD5 | 95 +-- NAMESPACE | 10 R/Blow_funcs.R | 25 R/ChooseEffort.r | 49 - R/ChooseMort.R |only R/ChooseSelect.r | 3 R/DLMtool-package.R | 13 R/DataObj.r | 6 R/DefineClasses.r | 831 +++++++++++++------------- R/GetMoreData.R | 12 R/MSEObj.r | 20 R/MiscFuns.r | 35 - R/MiscInt.r | 22 R/Output.r | 7 R/RcppExports.R | 6 R/SS2DLM.R | 2 R/SampleCpars.R |only R/SampleFleetPars.r |only R/SampleImpPars.R |only R/SampleObsPars.R |only R/SampleStockPars.R |only R/cpars.R | 2 R/plotFleet.r | 374 ++---------- R/plotOM.R | 2 R/plotObsImp.R | 42 - R/plotStock.r | 299 ++++----- R/runMSE.r | 1513 ++++++++++++++++++------------------------------- R/runMSE_old.R |only R/runMSErobust.r | 46 - R/userguide.R |only man/Blow_opt.Rd | 2 man/ChooseMort.Rd |only man/DLMtool-package.Rd | 17 man/Data-class.Rd | 2 man/OM-class.Rd | 9 man/Obs-class.Rd | 2 man/SampleCpars.Rd |only man/SampleFleetPars.Rd |only man/SampleImpPars.Rd |only man/SampleObsPars.Rd |only man/SampleStockPars.Rd |only man/Stock-class.Rd | 6 man/doprojPI_cpp.Rd | 4 man/getBlow.Rd | 6 man/getFMSY2.Rd | 6 man/getFref2.Rd | 8 man/getq2.Rd | 12 man/hist2.Rd |only man/plotStock.Rd | 6 man/runMSE.Rd | 2 man/runMSE_old.Rd |only man/userguide.Rd |only src/RcppExports.cpp | 16 src/doprojPI_cpp.cpp | 19 src/optQ_cpp.cpp | 84 +- src/projOpt_cpp.cpp | 95 +-- 57 files changed, 1577 insertions(+), 2141 deletions(-)
Title: Builds Trees by Sampling Variables in Groups
Description: Random Forest-like tree ensemble that works with groups of predictor variables. When building a tree, a number of variables is taken randomly from each group separately, thus ensuring that it considers variables from each group for the splits. Useful when rows contain information about different things (e.g. user information and product information) and it's not sensible to make a prediction with information from only one group of variables, or when there are far more variables from one group than the other and it's desired to have groups appear evenly on trees.
Trees are grown using the C5.0 algorithm rather than the usual CART algorithm. Supports parallelization (multithreaded), missing values in predictors, and categorical variables (without doing One-Hot encoding in the processing). Can also be used to create a regular (non-stratified) Random Forest-like model, but made up of C5.0 trees and with some additional control options.
As it's built with C5.0 trees, it works only for classification (not for regression).
Author: David Cortes <david.cortes.rivera@gmail.com>
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between StratifiedRF versions 0.1.1 dated 2017-06-21 and 0.2.2 dated 2017-06-30
DESCRIPTION | 15 - MD5 | 16 - NAMESPACE | 2 R/rf_c50.R | 426 +++++++++++++++++++++++++++++++------------ man/predict.stratified_rf.Rd | 16 + man/print.stratified_rf.Rd | 2 man/stratified_rf.Rd | 39 ++- man/summary.stratified_rf.Rd | 7 man/varimp_stratified_rf.Rd | 8 9 files changed, 384 insertions(+), 147 deletions(-)
Title: Taxometric Analysis
Description: We provide functions to perform taxometric analyses. This package contains 42 functions, but only 5 should be called directly by users. CheckData() should be run prior to any taxometric analysis to ensure that the data are appropriate for taxometric analysis. RunTaxometrics() performs taxometric analyses for a sample of data. RunCCFIProfile() performs a series of taxometric analyses to generate a CCFI profile. CreateData() generates a sample of categorical or dimensional data. ClassifyCases() assigns cases to groups using the base-rate classification method.
Author: John Ruscio <ruscio@tcnj.edu> and Shirley Wang <wangs7@tcnj.edu>
Maintainer: John Ruscio <ruscio@tcnj.edu>
Diff between RTaxometrics versions 2.1 dated 2017-06-29 and 2.2 dated 2017-06-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/CalculateMAMBAC.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Risk Regression Models and Prediction Scores for Survival
Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis.
Risk regression models for survival endpoints also in the presence of competing
risks are fitted using binomial regression based on a time sequence of binary
event status variables. A formula interface for the Fine-Gray regression model
and an interface for the combination of cause-specific Cox regression models.
A toolbox for assessing and comparing performance of risk predictions (risk
markers and risk prediction models). Prediction performance is measured by the
Brier score and the area under the ROC curve for binary possibly time-dependent
outcome. Inverse probability of censoring weighting and pseudo values are used
to deal with right censored data. Lists of risk markers and lists of risk models
are assessed simultaneously. Cross-validation repeatedly splits the data, trains
the risk prediction models on one part of each split and then summarizes and
compares the performance across splits.
Author: Thomas Alexander Gerds, Thomas Harder Scheike, Paul Blanche, Brice
Ozenne
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 1.3.7 dated 2017-03-12 and 1.4.3 dated 2017-06-30
riskRegression-1.3.7/riskRegression/R/plot.predictCSC.R |only riskRegression-1.3.7/riskRegression/R/qplot.predictCSC.R |only riskRegression-1.3.7/riskRegression/R/qplot.predictCox.R |only riskRegression-1.3.7/riskRegression/R/qplotAUC.R |only riskRegression-1.3.7/riskRegression/inst |only riskRegression-1.3.7/riskRegression/man/IClambda2hazard.Rd |only riskRegression-1.3.7/riskRegression/man/plot.predictCSC.Rd |only riskRegression-1.3.7/riskRegression/man/qplot.predictCSC.Rd |only riskRegression-1.3.7/riskRegression/man/qplot.predictCox.Rd |only riskRegression-1.3.7/riskRegression/man/qplotAUC.Rd |only riskRegression-1.3.7/riskRegression/man/seCSC.Rd |only riskRegression-1.3.7/riskRegression/man/seRobustCox.Rd |only riskRegression-1.3.7/riskRegression/tests/test-predictCoxSE.R |only riskRegression-1.3.7/riskRegression/tests/test-predictRisk.R |only riskRegression-1.3.7/riskRegression/tests/test-predictRiskIID.R |only riskRegression-1.4.3/riskRegression/DESCRIPTION | 43 riskRegression-1.4.3/riskRegression/MD5 | 244 +-- riskRegression-1.4.3/riskRegression/NAMESPACE | 52 riskRegression-1.4.3/riskRegression/R/CSC.R | 25 riskRegression-1.4.3/riskRegression/R/RcppExports.R | 94 + riskRegression-1.4.3/riskRegression/R/Score.R | 199 +- riskRegression-1.4.3/riskRegression/R/as.data.table.predictCSC.R | 60 riskRegression-1.4.3/riskRegression/R/as.data.table.predictCox.R | 69 riskRegression-1.4.3/riskRegression/R/ate.R | 722 +++++----- riskRegression-1.4.3/riskRegression/R/autoplot.ate.R |only riskRegression-1.4.3/riskRegression/R/autoplot.predictCSC.R |only riskRegression-1.4.3/riskRegression/R/autoplot.predictCox.R |only riskRegression-1.4.3/riskRegression/R/boxplot.Score.R | 134 - riskRegression-1.4.3/riskRegression/R/calcSeCSC.R |only riskRegression-1.4.3/riskRegression/R/calcSeCox.R |only riskRegression-1.4.3/riskRegression/R/coef.CauseSpecificCox.R |only riskRegression-1.4.3/riskRegression/R/confBandCox.R |only riskRegression-1.4.3/riskRegression/R/getComparisons.R | 4 riskRegression-1.4.3/riskRegression/R/getCoxInfo.R | 44 riskRegression-1.4.3/riskRegression/R/getInfluenceCurve.R | 2 riskRegression-1.4.3/riskRegression/R/iidCox.R | 292 ++-- riskRegression-1.4.3/riskRegression/R/influenceTest.R |only riskRegression-1.4.3/riskRegression/R/plot.riskRegression.R | 2 riskRegression-1.4.3/riskRegression/R/plotAUC.R | 188 -- riskRegression-1.4.3/riskRegression/R/plotBrier.R | 4 riskRegression-1.4.3/riskRegression/R/plotCalibration.R | 9 riskRegression-1.4.3/riskRegression/R/plotROC.R | 8 riskRegression-1.4.3/riskRegression/R/plotRisk.R |only riskRegression-1.4.3/riskRegression/R/predict.CauseSpecificCox.R | 419 ++--- riskRegression-1.4.3/riskRegression/R/predictCox.R | 427 ++--- riskRegression-1.4.3/riskRegression/R/print.ate.R | 19 riskRegression-1.4.3/riskRegression/R/print.predictCSC.R | 4 riskRegression-1.4.3/riskRegression/R/print.predictCox.R | 14 riskRegression-1.4.3/riskRegression/R/riskQuantile.R | 27 riskRegression-1.4.3/riskRegression/R/riskRegression-package.R | 5 riskRegression-1.4.3/riskRegression/R/riskRegression.R | 2 riskRegression-1.4.3/riskRegression/R/summary.riskRegression.R | 3 riskRegression-1.4.3/riskRegression/man/CSC.Rd | 14 riskRegression-1.4.3/riskRegression/man/CoxBaseEstimator.Rd | 1 riskRegression-1.4.3/riskRegression/man/CoxCenter.Rd | 3 riskRegression-1.4.3/riskRegression/man/CoxDesign.Rd | 1 riskRegression-1.4.3/riskRegression/man/CoxFormula.Rd | 3 riskRegression-1.4.3/riskRegression/man/CoxLP.Rd | 3 riskRegression-1.4.3/riskRegression/man/CoxN.Rd | 3 riskRegression-1.4.3/riskRegression/man/CoxSpecialStrata.Rd | 1 riskRegression-1.4.3/riskRegression/man/CoxStrata.Rd | 9 riskRegression-1.4.3/riskRegression/man/CoxVarCov.Rd | 3 riskRegression-1.4.3/riskRegression/man/CoxVariableName.Rd | 1 riskRegression-1.4.3/riskRegression/man/FGR.Rd | 7 riskRegression-1.4.3/riskRegression/man/IFlambda2hazard.Rd |only riskRegression-1.4.3/riskRegression/man/Melanoma.Rd | 3 riskRegression-1.4.3/riskRegression/man/Score.list.Rd | 19 riskRegression-1.4.3/riskRegression/man/SurvResponseVar.Rd | 1 riskRegression-1.4.3/riskRegression/man/as.data.table.predictCSC.Rd | 1 riskRegression-1.4.3/riskRegression/man/as.data.table.predictCox.Rd | 1 riskRegression-1.4.3/riskRegression/man/ate.Rd | 56 riskRegression-1.4.3/riskRegression/man/autoplot.ate.Rd |only riskRegression-1.4.3/riskRegression/man/autoplot.predictCSC.Rd |only riskRegression-1.4.3/riskRegression/man/autoplot.predictCox.Rd |only riskRegression-1.4.3/riskRegression/man/boxplot.Score.Rd | 19 riskRegression-1.4.3/riskRegression/man/calcSeCSC.Rd |only riskRegression-1.4.3/riskRegression/man/calcSeCox.Rd |only riskRegression-1.4.3/riskRegression/man/coef.CauseSpecificCox.Rd |only riskRegression-1.4.3/riskRegression/man/coef.riskRegression.Rd | 1 riskRegression-1.4.3/riskRegression/man/colCenter_cpp.Rd | 1 riskRegression-1.4.3/riskRegression/man/colCumSum.Rd | 1 riskRegression-1.4.3/riskRegression/man/colMultiply_cpp.Rd | 1 riskRegression-1.4.3/riskRegression/man/colScale_cpp.Rd | 1 riskRegression-1.4.3/riskRegression/man/colSumsCrossprod.Rd | 1 riskRegression-1.4.3/riskRegression/man/confBandCox.Rd |only riskRegression-1.4.3/riskRegression/man/extractStrata.Rd | 1 riskRegression-1.4.3/riskRegression/man/findP1.Rd | 1 riskRegression-1.4.3/riskRegression/man/iid.Rd | 36 riskRegression-1.4.3/riskRegression/man/influenceTest.Rd |only riskRegression-1.4.3/riskRegression/man/ipcw.Rd | 7 riskRegression-1.4.3/riskRegression/man/model.matrix.phreg.Rd | 1 riskRegression-1.4.3/riskRegression/man/penalizedS3.Rd | 1 riskRegression-1.4.3/riskRegression/man/plot.riskRegression.Rd | 3 riskRegression-1.4.3/riskRegression/man/plotAUC.Rd | 54 riskRegression-1.4.3/riskRegression/man/plotBrier.Rd | 1 riskRegression-1.4.3/riskRegression/man/plotCalibration.Rd | 1 riskRegression-1.4.3/riskRegression/man/plotEffects.Rd | 1 riskRegression-1.4.3/riskRegression/man/plotROC.Rd | 1 riskRegression-1.4.3/riskRegression/man/plotRisk.Rd |only riskRegression-1.4.3/riskRegression/man/predict.CauseSpecificCox.Rd | 35 riskRegression-1.4.3/riskRegression/man/predict.FGR.Rd | 1 riskRegression-1.4.3/riskRegression/man/predict.riskRegression.Rd | 11 riskRegression-1.4.3/riskRegression/man/predictCox.Rd | 36 riskRegression-1.4.3/riskRegression/man/predictRisk.Rd | 27 riskRegression-1.4.3/riskRegression/man/print.CauseSpecificCox.Rd | 1 riskRegression-1.4.3/riskRegression/man/print.FGR.Rd | 1 riskRegression-1.4.3/riskRegression/man/print.Score.Rd | 1 riskRegression-1.4.3/riskRegression/man/print.ate.Rd | 1 riskRegression-1.4.3/riskRegression/man/print.predictCSC.Rd | 1 riskRegression-1.4.3/riskRegression/man/print.predictCox.Rd | 1 riskRegression-1.4.3/riskRegression/man/print.riskRegression.Rd | 1 riskRegression-1.4.3/riskRegression/man/print.subjectWeights.Rd | 1 riskRegression-1.4.3/riskRegression/man/riskRegression.Rd | 13 riskRegression-1.4.3/riskRegression/man/rowCenter_cpp.Rd | 1 riskRegression-1.4.3/riskRegression/man/rowCumSum.Rd | 1 riskRegression-1.4.3/riskRegression/man/rowMultiply_cpp.Rd | 1 riskRegression-1.4.3/riskRegression/man/rowScale_cpp.Rd | 1 riskRegression-1.4.3/riskRegression/man/rowSumsCrossprod.Rd | 1 riskRegression-1.4.3/riskRegression/man/sampleData.Rd | 7 riskRegression-1.4.3/riskRegression/man/selectJump.Rd | 9 riskRegression-1.4.3/riskRegression/man/simMelanoma.Rd | 1 riskRegression-1.4.3/riskRegression/man/sliceMultiply_cpp.Rd |only riskRegression-1.4.3/riskRegression/man/sliceScale_cpp.Rd |only riskRegression-1.4.3/riskRegression/man/subjectWeights.Rd | 7 riskRegression-1.4.3/riskRegression/man/summary.FGR.Rd | 1 riskRegression-1.4.3/riskRegression/man/summary.riskRegression.Rd | 1 riskRegression-1.4.3/riskRegression/src/RcppExports.cpp | 190 ++ riskRegression-1.4.3/riskRegression/src/calcSeHazardCif.cpp |only riskRegression-1.4.3/riskRegression/src/confBand.cpp |only riskRegression-1.4.3/riskRegression/src/declareRoutines.c | 50 riskRegression-1.4.3/riskRegression/src/iid.cpp | 152 +- riskRegression-1.4.3/riskRegression/src/predictCIF.cpp | 71 riskRegression-1.4.3/riskRegression/src/sweepCenterScale.cpp | 58 riskRegression-1.4.3/riskRegression/tests/test-BrierScore.R | 18 riskRegression-1.4.3/riskRegression/tests/test-ate.R | 16 riskRegression-1.4.3/riskRegression/tests/test-boxplotScore.R | 16 riskRegression-1.4.3/riskRegression/tests/test-confidenceBand_vs_timereg.R |only riskRegression-1.4.3/riskRegression/tests/test-iidCox.R |only riskRegression-1.4.3/riskRegression/tests/test-phreg.R | 7 riskRegression-1.4.3/riskRegression/tests/test-predictCSC_vs_mstate.R |only riskRegression-1.4.3/riskRegression/tests/test-predictCox-CSC-Risk_internal.R |only riskRegression-1.4.3/riskRegression/tests/test-predictCox_vs_timereg.R |only riskRegression-1.4.3/riskRegression/tests/test-score.R | 144 + riskRegression-1.4.3/riskRegression/tests/testScore.org | 26 144 files changed, 2432 insertions(+), 1856 deletions(-)
More information about riskRegression at CRAN
Permanent link
Title: Easy Spatial Microsimulation (Raking) in R
Description: Functions for performing spatial microsimulation ('raking')
in R.
Author: Phil Mike Jones [aut, cre],
Robin Lovelace [aut] (Many functions are based on code by Robin
Lovelace and Morgane Dumont),
Morgane Dumont [aut] (Many functions are based on code by Robin
Lovelace and Morgane Dumont),
Andrew Smith [ctb]
Maintainer: Phil Mike Jones <philmikejones@gmail.com>
Diff between rakeR versions 0.1.2 dated 2016-11-14 and 0.2.0 dated 2017-06-30
rakeR-0.1.2/rakeR/tests/book_wt.csv |only rakeR-0.2.0/rakeR/DESCRIPTION | 20 - rakeR-0.2.0/rakeR/MD5 | 37 +- rakeR-0.2.0/rakeR/NAMESPACE | 2 rakeR-0.2.0/rakeR/NEWS.md | 22 + rakeR-0.2.0/rakeR/R/prep_functions.R | 2 rakeR-0.2.0/rakeR/R/rake_functions.R | 378 ++++++++++++++++----- rakeR-0.2.0/rakeR/README.md | 156 +++++++- rakeR-0.2.0/rakeR/man/check_constraint.Rd | 3 rakeR-0.2.0/rakeR/man/check_ind.Rd | 1 rakeR-0.2.0/rakeR/man/extract.Rd |only rakeR-0.2.0/rakeR/man/extract_weights.Rd |only rakeR-0.2.0/rakeR/man/integerise.Rd | 34 + rakeR-0.2.0/rakeR/man/rake.Rd | 29 + rakeR-0.2.0/rakeR/man/simulate.Rd | 41 -- rakeR-0.2.0/rakeR/man/weight.Rd | 16 rakeR-0.2.0/rakeR/tests/testthat/test_check_ind.R | 2 rakeR-0.2.0/rakeR/tests/testthat/test_extract.R |only rakeR-0.2.0/rakeR/tests/testthat/test_integerise.R | 41 -- rakeR-0.2.0/rakeR/tests/testthat/test_rake.R |only rakeR-0.2.0/rakeR/tests/testthat/test_simulate.R | 37 -- rakeR-0.2.0/rakeR/tests/testthat/test_weight.R | 65 --- 22 files changed, 555 insertions(+), 331 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>
Diff between PAFit versions 1.0.0.0 dated 2017-06-14 and 1.0.0.1 dated 2017-06-30
PAFit-1.0.0.0/PAFit/R/Generate_BA.R |only PAFit-1.0.0.1/PAFit/DESCRIPTION | 8 +- PAFit-1.0.0.1/PAFit/MD5 | 54 ++++++++++++------- PAFit-1.0.0.1/PAFit/NAMESPACE | 5 - PAFit-1.0.0.1/PAFit/R/PAFit.R | 24 ++++---- PAFit-1.0.0.1/PAFit/R/generate_BA.R |only PAFit-1.0.0.1/PAFit/R/get_statistics.R | 2 PAFit-1.0.0.1/PAFit/R/prep_simulate_true_net.R |only PAFit-1.0.0.1/PAFit/R/print.CV_Result.R | 4 - PAFit-1.0.0.1/PAFit/R/summary.CV_Result.R | 4 - PAFit-1.0.0.1/PAFit/inst/NEWS.Rd | 8 ++ PAFit-1.0.0.1/PAFit/inst/doc/Tutorial.pdf |binary PAFit-1.0.0.1/PAFit/man/PAFit-package.Rd | 17 ----- PAFit-1.0.0.1/PAFit/man/joint_estimate.rd | 2 PAFit-1.0.0.1/PAFit/man/only_A_estimate.rd | 2 PAFit-1.0.0.1/PAFit/man/only_F_estimate.rd | 2 PAFit-1.0.0.1/PAFit/man/plot.Full_PAFit_result.Rd | 4 - PAFit-1.0.0.1/PAFit/man/plot.PAFit_net.Rd | 2 PAFit-1.0.0.1/PAFit/man/plot.PAFit_result.rd |only PAFit-1.0.0.1/PAFit/man/plot.PA_result.rd | 3 - PAFit-1.0.0.1/PAFit/man/print.CV_Result.rd |only PAFit-1.0.0.1/PAFit/man/print.CV_data.rd |only PAFit-1.0.0.1/PAFit/man/print.Full_PAFit_result.Rd |only PAFit-1.0.0.1/PAFit/man/print.PAFit_data.rd |only PAFit-1.0.0.1/PAFit/man/print.PAFit_net.rd |only PAFit-1.0.0.1/PAFit/man/print.PAFit_result.rd |only PAFit-1.0.0.1/PAFit/man/print.PA_result.rd |only PAFit-1.0.0.1/PAFit/man/summary.CV_Data.rd |only PAFit-1.0.0.1/PAFit/man/summary.CV_Result.rd |only PAFit-1.0.0.1/PAFit/man/summary.Full_PAFit_result.Rd |only PAFit-1.0.0.1/PAFit/man/summary.PAFit_data.rd |only PAFit-1.0.0.1/PAFit/man/summary.PAFit_net.rd |only PAFit-1.0.0.1/PAFit/man/summary.PAFit_result.rd |only PAFit-1.0.0.1/PAFit/man/summary.PA_result.rd |only PAFit-1.0.0.1/PAFit/src/Makevars.win | 2 PAFit-1.0.0.1/PAFit/tests/loop_joint_estimate.R | 4 - PAFit-1.0.0.1/PAFit/tests/test_joint_estimate.R | 4 - 37 files changed, 78 insertions(+), 73 deletions(-)
Title: Bibtex Parser
Description: Utility to parse a bibtex file.
Author: Romain Francois [aut, cre],
Kurt Hornik [ctb],
Michael Koohafkan [ctb],
Mathew W. McLean [ctb]
Maintainer: Romain Francois <romain@r-enthusiasts.com>
Diff between bibtex versions 0.4.0 dated 2014-12-31 and 0.4.2 dated 2017-06-30
DESCRIPTION | 31 - MD5 | 32 - NAMESPACE | 22 R/bibtex.R | 299 +++++++--- README.md |only inst/bib/badFormat.bib |only inst/bib/base.bib | 302 +++++----- inst/bib/datasets.bib | 306 +++++----- inst/bib/grDevices.bib | 156 ++--- inst/bib/graphics.bib | 186 +++--- inst/bib/stats.bib | 1452 ++++++++++++++++++++++++------------------------- inst/clean-bibtex.R |only inst/grammar/biblex.l | 69 +- man/do_read_bib.Rd |only man/read.bib.Rd | 78 +- man/write.bib.Rd | 56 - src/biblex.c | 69 +- src/init.c |only tests |only 19 files changed, 1608 insertions(+), 1450 deletions(-)
Title: R Wrapper for Java Implementation of BiBit
Description: A simple R wrapper for the Java BiBit algorithm from "A
biclustering algorithm for extracting bit-patterns from binary datasets"
from Domingo et al. (2011) <DOI:10.1093/bioinformatics/btr464>. An simple adaption for the BiBit algorithm which allows noise in the biclusters is also introduced as well as a function to guide the algorithm towards given (sub)patterns. Further, a workflow to derive noisy biclusters from discoverd larger column patterns is included as well.
Author: De Troyer Ewoud
Maintainer: De Troyer Ewoud <ewoud.detroyer@uhasselt.be>
Diff between BiBitR versions 0.3.0 dated 2017-06-29 and 0.3.1 dated 2017-06-30
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/utilities.R | 2 +- R/workflowfunction.R | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Get EC2 Instance Metadata
Description: Retrieve Amazon EC2 instance metadata from within the running instance.
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between aws.ec2metadata versions 0.1.1 dated 2016-12-20 and 0.1.2 dated 2017-06-30
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 4 ++++ R/aws.ec2metadata-package.R | 19 ++++++++++++++++--- README.md | 3 ++- man/ec2metadata.Rd | 16 ++++++++++------ 7 files changed, 44 insertions(+), 21 deletions(-)
More information about aws.ec2metadata at CRAN
Permanent link
Title: Automatic Item Generator
Description: A collection of Automatic Item Generators used mainly for
psychological research. This package can generate linear syllogistic reasoning,
arithmetic and 2D/3D/Double 3D spatial reasoning items. It is recommended for research
purpose only.
Author: Bao Sheng Loe (Aiden) [aut, cre, cph],
David Condon [ctb, cph],
Francis Smart [ctb, cph]
Maintainer: Bao Sheng Loe (Aiden) <bsl28@cam.ac.uk>
Diff between AIG versions 0.1.6 dated 2017-06-01 and 0.1.7 dated 2017-06-30
DESCRIPTION | 15 +++++++++++---- MD5 | 14 +++++++------- R/MR3d.R | 2 +- R/MR3d2.R | 2 +- R/MRtwoD.R | 2 +- man/spatial2d.Rd | 2 +- man/spatial3d.Rd | 2 +- man/spatial3dDouble.Rd | 2 +- 8 files changed, 24 insertions(+), 17 deletions(-)
Title: Import Articles from 'LexisNexis' Using the 'tm' Text Mining
Framework
Description: Provides a 'tm' Source to create corpora from
articles exported from the 'LexisNexis' content provider as
HTML files. It is able to read both text content and meta-data
information (including source, date, title, author and pages).
Note that the file format is highly unstable: there is no warranty
that this package will work for your corpus, and you may have
to adjust the code to adapt it to your particular format.
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between tm.plugin.lexisnexis versions 1.3 dated 2016-06-29 and 1.3.1 dated 2017-06-30
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS | 3 +++ R/readLexisNexisHTML.R | 2 +- 4 files changed, 13 insertions(+), 10 deletions(-)
More information about tm.plugin.lexisnexis at CRAN
Permanent link
Title: An R Package for Spatial Smoothing
Description: Group of functions for spatial smoothing using cubic splines and variogram maximum likelihood estimation. Also allow the inclusion of linear parametric terms and change-points for segmented smoothing splines models.
Author: Mario A. Martínez Araya [aut,cre] and Jianxin Pan [ths]
Maintainer: Mario A. Martínez Araya <mma@mariomartinezaraya.com>
Diff between scpm versions 1.0-1 dated 2017-06-28 and 1.0-2 dated 2017-06-30
scpm-1.0-1/scpm/R/scpm_1.0-1.R |only scpm-1.0-2/scpm/DESCRIPTION | 12 ++++++++---- scpm-1.0-2/scpm/MD5 | 8 ++++---- scpm-1.0-2/scpm/NAMESPACE | 1 + scpm-1.0-2/scpm/R/scpm_1.0-2.R |only scpm-1.0-2/scpm/man/scpm-package.Rd | 6 +++--- 6 files changed, 16 insertions(+), 11 deletions(-)
Title: JavaScript Charts Tool
Description: Provides an R interface for using 'AmCharts' Library. Based on 'htmlwidgets', it
provides a global architecture to generate 'JavaScript' source code for charts.
Most of classes in the library have their equivalent in R with S4 classes;
for those classes, not all properties have been referenced but can easily be
added in the constructors. Complex properties (e.g. 'JavaScript' object) can
be passed as named list. See examples at
<http://datastorm-open.github.io/introduction_ramcharts/>
and <http://www.amcharts.com/> for more information
about the library. The package includes the free version of 'AmCharts'
Library. Its only limitation is a small link to the web site displayed on
your charts. If you enjoy this library, do not hesitate to refer to this
page <http://www.amcharts.com/online-store/> to purchase a licence, and thus
support its creators and get a period of Priority Support. See also
<http://www.amcharts.com/about/> for more information about 'AmCharts' company.
Author: Jeffery Petit [aut, cre],
Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory
htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/),
Benoit Thieurmel [aut, ctb],
Elena Salette [aut, ctb],
Titouan Robert [aut, ctb]
Maintainer: Jeffery Petit <jeffery.petit@datastorm.fr>
Diff between rAmCharts versions 2.1.3 dated 2017-01-18 and 2.1.5 dated 2017-06-30
DESCRIPTION | 33 ++-- MD5 | 254 +++++++++++++++++----------------- NAMESPACE | 9 - R/base_data.R | 13 + R/chart_amBoxplot.R | 103 ++++++++++--- R/chart_amDataset.R | 31 +--- R/chart_amPlot.R | 110 ++++++++++---- R/chart_amTimeSeries.R | 171 +++++++++++++++------- R/class_AmStockChart.R | 14 + R/shiny_modules_export.R | 4 R/shiny_modules_timeSeries.R |only R/union_AmCharts.R | 59 +++++++ R/utils_amOptions.R | 3 data/data_stock_2.rda |binary data/data_stock_3.rda |only inst/conf.yaml | 23 ++- inst/htmlwidgets/ramcharts_base.js | 48 ++++++ inst/modules |only inst/shiny/server.R | 4 inst/shiny/src/hist |only inst/shiny/src/menu/menu.R | 8 + inst/shiny/src/stock/amstock_server.R | 105 +++++++++++++- inst/shiny/src/stock/amstock_ui.R | 175 +++++++++++++++++++++++ inst/shiny/src/stock/stock_ui.R | 1 inst/shiny/ui.R | 4 man/AmBalloon.Rd | 3 man/AmChart-class.Rd | 2 man/AmGraph.Rd | 3 man/AmLegend-class.Rd | 2 man/AmObject-class.Rd | 2 man/AmStockChart-class.Rd | 10 - man/AmStockChart.Rd | 28 ++- man/AxisBase-class.Rd | 2 man/CategoryAxis-class.Rd | 2 man/ChartCursor-class.Rd | 2 man/ChartScrollbar-class.Rd | 2 man/DataSet-class.Rd | 2 man/DataSet.Rd | 11 - man/DataSetSelector-class.Rd | 2 man/DataSetSelector.Rd | 3 man/GaugeArrow-class.Rd | 2 man/GaugeArrow.Rd | 6 man/GaugeAxis-class.Rd | 2 man/GaugeAxis.Rd | 7 man/GaugeBand-class.Rd | 2 man/GaugeBand.Rd | 3 man/Guide-class.Rd | 2 man/Label-class.Rd | 2 man/Label.Rd | 1 man/PeriodSelector-class.Rd | 2 man/StockEvent-class.Rd | 2 man/StockPanel-class.Rd | 2 man/Title-class.Rd | 2 man/Title.Rd | 7 man/TrendLine-class.Rd | 2 man/TrendLine.Rd | 11 - man/ValueAxis-class.Rd | 2 man/add_dataloader_dependency.Rd | 1 man/add_export_dependency.Rd | 1 man/add_responsive_dependency.Rd | 1 man/add_theme_dependency.Rd | 1 man/amAngularGauge.Rd | 1 man/amBarplot.Rd | 1 man/amBoxplot.Rd | 16 +- man/amBullet.Rd | 1 man/amCandlestick.Rd | 1 man/amChartsOutput.Rd | 1 man/amFloatingBar.Rd | 1 man/amFunnel.Rd | 1 man/amHist.Rd | 1 man/amLines.Rd | 7 man/amMekko.Rd | 1 man/amOHLC.Rd | 1 man/amOptions.Rd | 1 man/amPie.Rd | 1 man/amPlot.Rd | 29 ++- man/amRadar.Rd | 1 man/amSolidGauge.Rd | 1 man/amStockMultiSet.Rd | 32 +--- man/amTimeSeries.Rd | 46 ++++-- man/amWaterfall.Rd | 1 man/amWind.Rd | 1 man/amcharts-setters.Rd | 1 man/api.Rd | 1 man/controlShinyPlot.Rd | 1 man/data_AirPassengers.Rd | 1 man/data_bar.Rd | 1 man/data_candleStick1.Rd | 1 man/data_candleStick2.Rd | 1 man/data_fbar.Rd | 1 man/data_funnel.Rd | 1 man/data_gantt.Rd | 1 man/data_gbar.Rd | 1 man/data_gdp.Rd | 1 man/data_mekko.Rd | 1 man/data_pie.Rd | 1 man/data_radar.Rd | 1 man/data_stock1.Rd | 1 man/data_stock_2.Rd | 1 man/data_stock_3.Rd |only man/data_waterfall.Rd | 1 man/data_wind.Rd | 1 man/getCurrentStockData.Rd |only man/getTransformTS.Rd |only man/initialize-AmChart.Rd | 60 ++++---- man/initialize-AmLegend.Rd | 3 man/initialize-AxisBase.Rd | 1 man/initialize-CategoryAxis.Rd | 3 man/initialize-ChartCursor.Rd | 6 man/initialize-ChartScrollbar.Rd | 8 - man/initialize-Guide.Rd | 3 man/initialize-PeriodSelector.Rd | 5 man/initialize-StockEvent.Rd | 6 man/initialize-StockPanel.Rd | 10 - man/initialize-ValueAxis.Rd | 3 man/listProperties-AmObject.Rd | 1 man/methods-AmObject.Rd | 1 man/plot.AmChart.Rd | 1 man/print-AmObject-method.Rd | 1 man/rAmCharts-shinymodules-ts.Rd |only man/rAmCharts-shinymodules.Rd | 9 - man/renderAmCharts.Rd | 1 man/runExamples.Rd | 1 man/shared-generics.Rd | 7 man/show-AmChart-method.Rd | 1 man/show-AmObject-method.Rd | 1 man/show-AmStockChart-method.Rd | 1 man/stockGraph.Rd | 1 man/stockLegend.Rd | 1 tests/testthat/test_getAggregateTS.R |only 130 files changed, 1095 insertions(+), 514 deletions(-)
Title: Bespoke Images of 'OpenStreetMap' Data
Description: Bespoke images of 'OpenStreetMap' ('OSM') data and data
visualisation using 'OSM' objects.
Author: Mark Padgham [aut, cre],
Finkelstein Noam [ctb, cph] (Author of included stub.R code),
Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmplotr versions 0.2.3 dated 2016-07-13 and 0.3.0 dated 2017-06-30
osmplotr-0.2.3/osmplotr/R/extract-highway.R |only osmplotr-0.3.0/osmplotr/DESCRIPTION | 34 osmplotr-0.3.0/osmplotr/MD5 | 119 - osmplotr-0.3.0/osmplotr/NAMESPACE | 31 osmplotr-0.3.0/osmplotr/NEWS | 21 osmplotr-0.3.0/osmplotr/R/add-axes.R | 229 +- osmplotr-0.3.0/osmplotr/R/add-colourbar.R | 291 +- osmplotr-0.3.0/osmplotr/R/add-osm-groups.R | 1008 +++++----- osmplotr-0.3.0/osmplotr/R/add-osm-objects.R | 223 +- osmplotr-0.3.0/osmplotr/R/add-osm-surface.R | 538 ++--- osmplotr-0.3.0/osmplotr/R/adjust-colours.R | 100 osmplotr-0.3.0/osmplotr/R/check-fns.R |only osmplotr-0.3.0/osmplotr/R/colour-mat.R | 124 - osmplotr-0.3.0/osmplotr/R/connect-highways.R | 539 ++--- osmplotr-0.3.0/osmplotr/R/extract-highways.R | 276 -- osmplotr-0.3.0/osmplotr/R/extract-osm-objects.R | 281 +- osmplotr-0.3.0/osmplotr/R/get-bbox.R | 3 osmplotr-0.3.0/osmplotr/R/get-highway-cycle.R | 374 +-- osmplotr-0.3.0/osmplotr/R/make-osm-map.R | 140 - osmplotr-0.3.0/osmplotr/R/order-lines.R | 264 -- osmplotr-0.3.0/osmplotr/R/osm-basemap.R | 83 osmplotr-0.3.0/osmplotr/R/osm-structures.R | 218 +- osmplotr-0.3.0/osmplotr/R/osmplotr.R | 61 osmplotr-0.3.0/osmplotr/R/print-osm-map.R | 62 osmplotr-0.3.0/osmplotr/R/zzz.R |only osmplotr-0.3.0/osmplotr/build/vignette.rds |binary osmplotr-0.3.0/osmplotr/data/london.rda |binary osmplotr-0.3.0/osmplotr/inst/doc/basic-maps.R | 392 ++- osmplotr-0.3.0/osmplotr/inst/doc/basic-maps.Rmd | 605 +++--- osmplotr-0.3.0/osmplotr/inst/doc/basic-maps.html | 673 ++++-- osmplotr-0.3.0/osmplotr/inst/doc/data-maps.R | 775 ++++--- osmplotr-0.3.0/osmplotr/inst/doc/data-maps.Rmd | 840 ++++---- osmplotr-0.3.0/osmplotr/inst/doc/data-maps.html | 725 ++++--- osmplotr-0.3.0/osmplotr/inst/extdata |only osmplotr-0.3.0/osmplotr/man/add_axes.Rd | 9 osmplotr-0.3.0/osmplotr/man/add_colourbar.Rd | 32 osmplotr-0.3.0/osmplotr/man/add_osm_groups.Rd | 48 osmplotr-0.3.0/osmplotr/man/add_osm_objects.Rd | 31 osmplotr-0.3.0/osmplotr/man/add_osm_surface.Rd | 55 osmplotr-0.3.0/osmplotr/man/adjust_colours.Rd | 19 osmplotr-0.3.0/osmplotr/man/colour_mat.Rd | 13 osmplotr-0.3.0/osmplotr/man/connect_highways.Rd | 20 osmplotr-0.3.0/osmplotr/man/extract_osm_objects.Rd | 46 osmplotr-0.3.0/osmplotr/man/get_bbox.Rd | 1 osmplotr-0.3.0/osmplotr/man/london.Rd | 47 osmplotr-0.3.0/osmplotr/man/make_osm_map.Rd | 12 osmplotr-0.3.0/osmplotr/man/osm_basemap.Rd | 5 osmplotr-0.3.0/osmplotr/man/osm_structures.Rd | 7 osmplotr-0.3.0/osmplotr/man/print_osm_map.Rd | 12 osmplotr-0.3.0/osmplotr/tests/stub.R |only osmplotr-0.3.0/osmplotr/tests/testthat/test-add-axes.R | 50 osmplotr-0.3.0/osmplotr/tests/testthat/test-add-colourbar.R | 105 - osmplotr-0.3.0/osmplotr/tests/testthat/test-add-groups.R | 161 - osmplotr-0.3.0/osmplotr/tests/testthat/test-add-objects.R | 88 osmplotr-0.3.0/osmplotr/tests/testthat/test-add-surface.R | 69 osmplotr-0.3.0/osmplotr/tests/testthat/test-adjust-colours.R | 25 osmplotr-0.3.0/osmplotr/tests/testthat/test-colourmat.R | 46 osmplotr-0.3.0/osmplotr/tests/testthat/test-connect-highways.R | 97 osmplotr-0.3.0/osmplotr/tests/testthat/test-extract-objects.R | 79 osmplotr-0.3.0/osmplotr/tests/testthat/test-make-osmmap.R |only osmplotr-0.3.0/osmplotr/tests/testthat/test-osm-basemap.R | 16 osmplotr-0.3.0/osmplotr/tests/testthat/test-print-map.R |only osmplotr-0.3.0/osmplotr/vignettes/basic-maps.Rmd | 605 +++--- osmplotr-0.3.0/osmplotr/vignettes/data-maps.Rmd | 840 ++++---- 64 files changed, 6163 insertions(+), 5404 deletions(-)
Title: Inference in Randomized Controlled Trials with Death and
Missingness
Description: In randomized studies involving severely ill patients, functional
outcomes are often unobserved due to missed clinic visits, premature
withdrawal or death. It is well known that if these unobserved functional
outcomes are not handled properly, biased treatment comparisons can be
produced. In this package, we implement a procedure for comparing treatments
that is based on the composite endpoint of both the functional outcome and
survival. The procedure was proposed in Wang et al. (2016) <doi:10.1111/biom.12594>.
It considers missing data imputation with a sensitivity
analysis strategy to handle the unobserved functional outcomes not due to
death.
Author: Chenguang Wang [aut, cre],
Andrew Leroux [aut, cre],
Elizabeth Colantuoni [aut],
Daniel O Scharfstein [aut],
Trustees of Columbia University [cph] (tools/make_cpp.R, R/stanmodels.R)
Maintainer: Chenguang Wang <cwang68@jhmi.edu>
Diff between idem versions 2.0 dated 2017-04-23 and 2.2 dated 2017-06-30
DESCRIPTION | 10 MD5 | 52 R/idem_analysis.R | 88 - R/idem_tools.R | 23 R/idem_visualize.R | 4 build/vignette.rds |binary inst/doc/vignette.html | 3216 +++++++++++++++++++++++----------------------- inst/shiny/composite_ui.R | 2 man/abc.Rd | 1 man/idem-package.Rd | 4 man/idem-parameters.Rd | 1 man/imBs.Rd | 6 man/imChkPars.Rd | 1 man/imEstimate.Rd | 6 man/imFitModel.Rd | 1 man/imImpAll.Rd | 1 man/imImpSingle.Rd | 1 man/imMisTable.Rd | 1 man/imNeedImp.Rd | 1 man/imPlotCompleters.Rd | 1 man/imPlotComposite.Rd | 1 man/imPlotContour.Rd | 1 man/imPlotImputed.Rd | 1 man/imPlotMisPattern.Rd | 1 man/imPlotSurv.Rd | 1 man/imShiny.Rd | 1 man/imTest.Rd | 1 27 files changed, 1750 insertions(+), 1677 deletions(-)
Title: Apply Two Fuzzy Numbers on a Monotone Function
Description: One can easily draw the membership function of f(x,y) by package 'FuzzyNumbers.Ext.2' in which f(.,.) is supposed monotone and x and y are two fuzzy numbers. This work is possible using function f2apply() which is an extension of function fapply() from Package 'FuzzyNumbers' for two-variable monotone functions. Moreover, the ability of computing the core, support and alpha-cuts of the result is added to the Version 2.0.
Author: Abbas Parchami (Department of Statistics, Faculty of Mathematics and Computer, Shahid Bahonar University of Kerman, Kerman, Iran)
Maintainer: Abbas Parchami <parchami@uk.ac.ir>
Diff between FuzzyNumbers.Ext.2 versions 1.0 dated 2017-03-18 and 2.0 dated 2017-06-30
DESCRIPTION | 10 +++--- MD5 | 8 ++--- R/f2apply.R | 11 ++++++- build/partial.rdb |binary man/f2apply.Rd | 78 +++++++++++++++++++++++++++++++++++++++--------------- 5 files changed, 76 insertions(+), 31 deletions(-)
More information about FuzzyNumbers.Ext.2 at CRAN
Permanent link
Title: Bayesian Dose-Finding Designs using Pharmacokinetics(PK) for
Phase I Clinical Trials
Description: Statistical methods involving PK measures are provided, in the dose allocation
process during a Phase I clinical trials. These methods enter pharmacokinetics
(PK) in the dose finding designs in different ways, including covariates models,
dependent variable or hierarchical models.
This package provides functions to generate data from several scenarios and functions
to run simulations which their objective is to determine the maximum tolerated dose (MTD).
Author: Artemis Toumazi <artemis.toumazi@inserm.fr>, Moreno Ursino <moreno.ursino@inserm.fr>
and Sarah Zohar <sarah.zohar@inserm.fr>
Maintainer: Artemis Toumazi <artemis.toumazi@inserm.fr>
Diff between dfpk versions 3.3.0 dated 2017-06-29 and 3.3.1 dated 2017-06-30
DESCRIPTION | 8 +-- MD5 | 24 ++++----- R/S4_classes.R | 87 ++++++++++++++++----------------- R/nextDose.R | 36 +++++++------ R/sim.data.R | 6 +- man/dose-class.Rd | 18 +++--- man/dosefinding-class.Rd | 36 ++++++------- man/nextDose.Rd | 32 ++++++------ man/nsim.Rd | 54 ++++++++++---------- man/plot-dosefinding-missing-method.Rd | 6 +- man/scen-class.Rd | 30 +++++------ man/show-methods.Rd | 6 +- man/sim.data.Rd | 29 +++++------ 13 files changed, 189 insertions(+), 183 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-22 1.1.2
2017-04-19 1.1
Title: Robust Trimmed Clustering
Description: Provides functions for robust trimmed clustering. The methods are described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>, Fritz et al. (2012) <doi:10.18637/jss.v047.i12> and others.
Author: Agustin Mayo Iscar, Luis Angel Garcia Escudero, Heinrich Fritz
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between tclust versions 1.2-3 dated 2014-10-20 and 1.2-7 dated 2017-06-30
ChangeLog | 31 + DESCRIPTION | 10 MD5 | 33 - NAMESPACE | 18 R/R_restr.eigen.R | 78 +-- R/tclust.R | 62 +- R/tkmeans.C.R | 25 - build/vignette.rds |binary inst/doc/tclust.pdf |binary man/DiscrFact.Rd | 5 man/discr_coords.Rd | 5 src/R_meal.h | 5 src/R_package.cpp | 4 src/R_package.h | 5 src/smat.base.h | 9 src/tclust_init.c |only tests/ttclust.R | 27 - tests/ttclust.Rout.save | 1174 +++++++++++++++++++++++------------------------- 18 files changed, 765 insertions(+), 726 deletions(-)
Title: Opasnet Modelling Environment Utility Functions
Description: Contains tools for open assessment and modelling in Opasnet,
a wiki-based web site and workspace for societal decision making
(see <http://en.opasnet.org/w/Main_Page> for more information).
The core principle of the workspace is maximal openness and modularity.
Variables are defined on public wiki pages using wiki inputs/tables,
databases and R code. This package provides the functionality to download and use these
variables. It also contains health impact assessment tools such as
spatial methods for exposure modelling.
Author: Teemu Rintala, Einari Happonen, Jouni Tuomisto
Maintainer: Teemu Rintala <teemu.rintala.a@gmail.com>
Diff between OpasnetUtils versions 1.2.0 dated 2015-06-03 and 1.3 dated 2017-06-30
CHANGELOG | 16 ++- DESCRIPTION | 10 +- MD5 | 42 +++++---- NAMESPACE | 7 + R/CheckDecisions.r | 62 +++++++++----- R/CheckMarginals.r | 36 +++++--- R/CollapseMarginal.r | 4 R/ComputeDependencies.r | 8 - R/EvalOutput.r | 6 + R/Fetch.r | 4 R/ORBind.r | 6 - R/OVariable.r | 195 +++++++++++++++++++++++++++++++++++++++++---- R/Oapply.r | 20 ++++ R/objects.R | 26 +++++- R/odag.R |only R/odebug.R | 84 +++++++++++++------ R/unkeep.R | 18 ++-- man/Check.Rd | 8 + man/ComputeDependencies.Rd | 5 - man/objects.Rd | 9 +- man/odag.Rd |only man/orbind.Rd | 8 + man/ovariable-class.Rd | 31 +++++-- 23 files changed, 454 insertions(+), 151 deletions(-)
Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al.
(2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed
using both regional and local information. Functional Rarity combines both
the functional aspect of rarity as well as the extent aspect of rarity.
Author: Matthias Grenié [aut, cre],
Pierre Denelle [aut],
Caroline Tucker [aut]
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>
Diff between funrar versions 1.1.1 dated 2017-06-27 and 1.2.0 dated 2017-06-30
funrar-1.1.1/funrar/man/rarity_dimensions.Rd |only funrar-1.2.0/funrar/DESCRIPTION | 6 funrar-1.2.0/funrar/MD5 | 98 - funrar-1.2.0/funrar/NAMESPACE | 49 funrar-1.2.0/funrar/NEWS.md | 60 funrar-1.2.0/funrar/R/check_functions.R | 504 ++--- funrar-1.2.0/funrar/R/compute_dist_matrix.R | 184 - funrar-1.2.0/funrar/R/distinctiveness.R | 551 ++--- funrar-1.2.0/funrar/R/funrar.R | 226 +- funrar-1.2.0/funrar/R/make_relative.R | 180 - funrar-1.2.0/funrar/R/rarity_dimensions.R | 229 +- funrar-1.2.0/funrar/R/restrictedness.R | 274 +- funrar-1.2.0/funrar/R/scarcity.R | 336 +-- funrar-1.2.0/funrar/R/stack_matrix.R | 312 +-- funrar-1.2.0/funrar/R/uniqueness.R | 290 +-- funrar-1.2.0/funrar/README.md | 88 funrar-1.2.0/funrar/build/vignette.rds |binary funrar-1.2.0/funrar/inst/doc/rarity_indices.R | 324 +-- funrar-1.2.0/funrar/inst/doc/rarity_indices.Rmd | 700 +++---- funrar-1.2.0/funrar/inst/doc/rarity_indices.html | 1138 ++++++------ funrar-1.2.0/funrar/inst/doc/sparse_matrices.R | 186 - funrar-1.2.0/funrar/inst/doc/sparse_matrices.Rmd | 320 +-- funrar-1.2.0/funrar/inst/doc/sparse_matrices.html | 464 ++-- funrar-1.2.0/funrar/man/combination_trait_dist.Rd |only funrar-1.2.0/funrar/man/compute_dist_matrix.Rd | 146 - funrar-1.2.0/funrar/man/distinctiveness.Rd | 158 - funrar-1.2.0/funrar/man/distinctiveness_com.Rd | 92 funrar-1.2.0/funrar/man/distinctiveness_dimensions.Rd |only funrar-1.2.0/funrar/man/distinctiveness_stack.Rd | 126 - funrar-1.2.0/funrar/man/funrar.Rd | 90 funrar-1.2.0/funrar/man/funrar_stack.Rd | 98 - funrar-1.2.0/funrar/man/is_relative.Rd | 76 funrar-1.2.0/funrar/man/make_relative.Rd | 54 funrar-1.2.0/funrar/man/matrix_to_stack.Rd | 92 funrar-1.2.0/funrar/man/restrictedness.Rd | 110 - funrar-1.2.0/funrar/man/restrictedness_stack.Rd | 88 funrar-1.2.0/funrar/man/scarcity.Rd | 102 - funrar-1.2.0/funrar/man/scarcity_com.Rd | 82 funrar-1.2.0/funrar/man/scarcity_stack.Rd | 102 - funrar-1.2.0/funrar/man/stack_to_matrix.Rd | 84 funrar-1.2.0/funrar/man/uniqueness.Rd | 128 - funrar-1.2.0/funrar/man/uniqueness_dimensions.Rd |only funrar-1.2.0/funrar/man/uniqueness_stack.Rd | 100 - funrar-1.2.0/funrar/tests/testthat.R | 8 funrar-1.2.0/funrar/tests/testthat/test-check_functions.R | 350 +-- funrar-1.2.0/funrar/tests/testthat/test-dist_matrix.R | 290 +-- funrar-1.2.0/funrar/tests/testthat/test-rarity_dimensions.R | 239 +- funrar-1.2.0/funrar/tests/testthat/test-rarity_indices.R | 616 +++--- funrar-1.2.0/funrar/tests/testthat/test-rel_abund.R | 166 - funrar-1.2.0/funrar/tests/testthat/test-tidy_matrix.R | 318 +-- funrar-1.2.0/funrar/vignettes/rarity_indices.Rmd | 700 +++---- funrar-1.2.0/funrar/vignettes/sparse_matrices.Rmd | 320 +-- 52 files changed, 5671 insertions(+), 5583 deletions(-)