Title: Functions for Hierarchical Bayesian Estimation: A Flexible
Approach
Description: Functions for estimating models using a Hierarchical Bayesian (HB) framework. The flexibility comes in allowing the user to specify the likelihood function directly instead of assuming predetermined model structures. Types of models that can be estimated with this code include the family of discrete choice models (Multinomial Logit, Mixed Logit, Nested Logit, Error Components Logit and Latent Class) as well ordered response models like ordered probit and ordered logit. In addition, the package allows for flexibility in specifying parameters as either fixed (non-varying across individuals) or random with continuous distributions. Parameter distributions supported include normal, positive/negative log-normal, positive/negative censored normal, and the Johnson SB distribution. Kenneth Train's Matlab and Gauss code for doing Hierarchical Bayesian estimation has served as the basis for a few of the functions included in this package. These Matlab/Gauss functions have been rewritten to be optimized within R. Considerable code has been added to increase the flexibility and usability of the code base. Train's original Gauss and Matlab code can be found here: http://elsa.berkeley.edu/Software/abstracts/train1006mxlhb.html See Train's chapter on HB in Discrete Choice with Simulation here: http://elsa.berkeley.edu/books/choice2.html; and his paper on using HB with non-normal distributions here: http://eml.berkeley.edu//~train/trainsonnier.pdf.
Author: Jeff Dumont [aut, cre],
Jeff Keller [aut],
Chase Carpenter [ctb]
Maintainer: Jeff Dumont <Jeff.Dumont@rsginc.com>
Diff between RSGHB versions 1.0.2 dated 2014-05-30 and 1.1.0 dated 2015-06-08
RSGHB-1.0.2/RSGHB/R/plotA.R |only RSGHB-1.0.2/RSGHB/R/plotF.R |only RSGHB-1.0.2/RSGHB/R/plotLog.R |only RSGHB-1.0.2/RSGHB/R/writeLog.R |only RSGHB-1.0.2/RSGHB/data/Example1_F.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_A.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_B.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_Bsd.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_C.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_Csd.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_D.txt.gz |only RSGHB-1.0.2/RSGHB/data/datalist |only RSGHB-1.0.2/RSGHB/man/Example1_F.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_A.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_B.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_Bsd.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_C.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_Csd.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_D.Rd |only RSGHB-1.0.2/RSGHB/man/RSGHB-internal.Rd |only RSGHB-1.0.2/RSGHB/man/plotA.Rd |only RSGHB-1.0.2/RSGHB/man/plotC.Rd |only RSGHB-1.0.2/RSGHB/man/plotF.Rd |only RSGHB-1.0.2/RSGHB/man/plotLog.Rd |only RSGHB-1.0.2/RSGHB/man/vech.Rd |only RSGHB-1.0.2/RSGHB/man/xpnd.Rd |only RSGHB-1.0.2/RSGHB/tools |only RSGHB-1.0.2/RSGHB/vignettes/MNL_logPlot1.png |only RSGHB-1.0.2/RSGHB/vignettes/MNL_logPlot2.png |only RSGHB-1.0.2/RSGHB/vignettes/MNL_markovChains2.png |only RSGHB-1.0.2/RSGHB/vignettes/RSGHB_HowTo.synctex.gz |only RSGHB-1.0.2/RSGHB/vignettes/RSGHB_HowTo.tex |only RSGHB-1.0.2/RSGHB/vignettes/figure |only RSGHB-1.0.2/RSGHB/vignettes/framed.sty |only RSGHB-1.1.0/RSGHB/DESCRIPTION | 28 RSGHB-1.1.0/RSGHB/MD5 | 78 -- RSGHB-1.1.0/RSGHB/NAMESPACE | 19 RSGHB-1.1.0/RSGHB/NEWS |only RSGHB-1.1.0/RSGHB/R/checkModel.R | 160 ++-- RSGHB-1.1.0/RSGHB/R/doHB.R | 240 +++--- RSGHB-1.1.0/RSGHB/R/hb.R | 162 +--- RSGHB-1.1.0/RSGHB/R/methods.R |only RSGHB-1.1.0/RSGHB/R/nextD.R | 15 RSGHB-1.1.0/RSGHB/R/nextDind.R | 8 RSGHB-1.1.0/RSGHB/R/onLoad.R |only RSGHB-1.1.0/RSGHB/R/plotC.R | 15 RSGHB-1.1.0/RSGHB/R/progreport.R |only RSGHB-1.1.0/RSGHB/R/writeModel.R |only RSGHB-1.1.0/RSGHB/build/vignette.rds |binary RSGHB-1.1.0/RSGHB/inst/doc/RSGHB_HowTo.R | 350 ++++----- RSGHB-1.1.0/RSGHB/inst/doc/RSGHB_HowTo.pdf |binary RSGHB-1.1.0/RSGHB/inst/doc/RSGHB_HowTo.rnw | 573 ++++++---------- RSGHB-1.1.0/RSGHB/man/doHB.Rd | 182 ++--- RSGHB-1.1.0/RSGHB/man/plot.Rd |only RSGHB-1.1.0/RSGHB/man/writeModel.Rd |only RSGHB-1.1.0/RSGHB/vignettes/MMNL_MarkovChains.png |only RSGHB-1.1.0/RSGHB/vignettes/MNL_markovChains.png |binary RSGHB-1.1.0/RSGHB/vignettes/RSGHB_HowTo-concordance.tex | 5 RSGHB-1.1.0/RSGHB/vignettes/RSGHB_HowTo.rnw | 573 ++++++---------- 59 files changed, 1020 insertions(+), 1388 deletions(-)
Title: Bayesian Non- and Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 1.0.2 dated 2015-01-02 and 1.0.3 dated 2015-06-08
ChangeLog | 14 ++- DESCRIPTION | 12 +-- MD5 | 18 ++-- R/bnpglm.R | 64 ++++++++++------ man/BNSP-package.Rd | 4 - man/bnpglm.Rd | 138 +++++++++++++++++++++++++----------- src/OneResLtnt.c | 191 ++++++++++++++++++++++++++++++++++++++------------ src/other.functions.h | 39 +++++++++- src/pdfs.h | 77 +++++++++++++++++++- src/sampling.h | 24 ++++++ 10 files changed, 449 insertions(+), 132 deletions(-)
Title: Plant Root System Architecture Analysis Using DART and RSML
Files
Description: Analysis of complex plant root system architectures (RSA) using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) DART: a software to analyse root system architecture and development from captured images, Plant and Soil, 326, 261--273), and RSA data encoded with the Root System Markup Language (RSML) (Lobet et al (2015) Root System Markup Language: Toward a Unified Root Architecture Description Language, Plant Physiology, 167, 617--627).
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory <Benjamin.Delory@ulg.ac.be>
Diff between archiDART versions 1.0 dated 2014-12-05 and 1.1 dated 2015-06-08
DESCRIPTION | 15 +- MD5 | 31 ++--- NAMESPACE | 3 R/archidraw.R | 95 ++++++++++++--- R/archigrow.R | 10 - R/architect.R | 235 ++++++++++++++++++++++++++++----------- R/latdist.R | 157 ++++++++++++++++++++++---- R/rsmlToDART.R |only R/trajectory.R | 322 +++++++++++++++++++++++++++++++++++------------------- man/archidraw.Rd | 49 ++++---- man/archigrow.Rd | 30 ++--- man/architect.Rd | 52 +++++--- man/ch7lie.Rd | 3 man/ch7rac.Rd | 7 - man/ch7tps.Rd | 12 +- man/latdist.Rd | 39 +++--- man/trajectory.Rd | 51 ++++---- 17 files changed, 757 insertions(+), 354 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer <Valentin.Wimmer@kws.com>
Diff between synbreed versions 0.11-4 dated 2015-05-27 and 0.11-8 dated 2015-06-08
DESCRIPTION | 12 +- MD5 | 8 - R/codeGeno.r | 273 +++++++++++++++++++++++++++-------------------------- R/create.gpData.r | 4 R/read.write.vcf.r | 2 5 files changed, 156 insertions(+), 143 deletions(-)
Title: Smoothing for Stream Network Data
Description: Fits flexible additive models to data on stream networks, taking account of flow-connectivity of the network. Models are fitted using penalised least squares.
Author: Alastair Rushworth
Maintainer: Alastair Rushworth <alastair.rushworth@strath.ac.uk>
Diff between smnet versions 1.0 dated 2014-12-09 and 2.0 dated 2015-06-08
smnet-1.0/smnet/R/plot_continuous.R |only smnet-1.0/smnet/R/simulateNetwork.R |only smnet-1.0/smnet/man/simulateNetwork.Rd |only smnet-2.0/smnet/DESCRIPTION | 16 +- smnet-2.0/smnet/MD5 | 62 +++++----- smnet-2.0/smnet/NAMESPACE | 11 - smnet-2.0/smnet/R/adjacency_to_shreve.R |only smnet-2.0/smnet/R/check_additive_weight.R |only smnet-2.0/smnet/R/check_weight.R |only smnet-2.0/smnet/R/get_adjacency.R | 40 +++--- smnet-2.0/smnet/R/get_crit.R | 53 ++------ smnet-2.0/smnet/R/get_crit_exact.R | 36 ++---- smnet-2.0/smnet/R/get_lm_fit.R | 32 +++-- smnet-2.0/smnet/R/get_max_df.R |only smnet-2.0/smnet/R/get_model_objects.R | 51 ++++++-- smnet-2.0/smnet/R/get_optimal_smooth.R | 179 +++++++++++++++--------------- smnet-2.0/smnet/R/get_penalty.R | 4 smnet-2.0/smnet/R/is.wholenumber.R |only smnet-2.0/smnet/R/network.R | 4 smnet-2.0/smnet/R/plot.smnet.R | 84 ++++++-------- smnet-2.0/smnet/R/plot_cov.R | 143 +++++++++++------------ smnet-2.0/smnet/R/plot_full.R |only smnet-2.0/smnet/R/plot_node.R | 123 +++++++++++++++----- smnet-2.0/smnet/R/plot_segments.R |only smnet-2.0/smnet/R/predict.smnet.R | 13 -- smnet-2.0/smnet/R/predictSSNobject.R | 73 +++++------- smnet-2.0/smnet/R/re_map_rid.R |only smnet-2.0/smnet/R/show_weights.R |only smnet-2.0/smnet/R/smnet.R | 155 +++++++++++++++++-------- smnet-2.0/smnet/R/summary.smnet.R | 82 +++++-------- smnet-2.0/smnet/inst |only smnet-2.0/smnet/man/get_adjacency.Rd | 129 +++++++++++++-------- smnet-2.0/smnet/man/m.Rd | 129 +++++++++++++-------- smnet-2.0/smnet/man/network.Rd | 133 +++++++++++++--------- smnet-2.0/smnet/man/plot.smnet.Rd | 139 ++++++++++++++--------- smnet-2.0/smnet/man/predict.smnet.Rd | 140 +++++++++++++---------- smnet-2.0/smnet/man/show_weights.Rd |only smnet-2.0/smnet/man/smnet.Rd | 155 ++++++++++++++++--------- smnet-2.0/smnet/man/summary.smnet.Rd | 129 +++++++++++++-------- 39 files changed, 1208 insertions(+), 907 deletions(-)
Title: Interface to the Global Biodiversity Information Facility 'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.8.0 dated 2015-03-09 and 0.8.4 dated 2015-06-08
rgbif-0.8.0/rgbif/inst/vign/figure/densitylist2.png |only rgbif-0.8.0/rgbif/inst/vign/figure/gbifmap1.png |only rgbif-0.8.0/rgbif/inst/vign/figure/occurrencelist_many.png |only rgbif-0.8.0/rgbif/man/ldfast.Rd |only rgbif-0.8.0/rgbif/vignettes/figure |only rgbif-0.8.4/rgbif/DESCRIPTION | 23 rgbif-0.8.4/rgbif/MD5 | 258 ++++---- rgbif-0.8.4/rgbif/NAMESPACE | 23 rgbif-0.8.4/rgbif/NEWS | 42 + rgbif-0.8.4/rgbif/R/check_wkt.r | 26 rgbif-0.8.4/rgbif/R/count_facet.r | 43 - rgbif-0.8.4/rgbif/R/dataset_metrics.r | 13 rgbif-0.8.4/rgbif/R/dataset_search.r | 2 rgbif-0.8.4/rgbif/R/dataset_suggest.r | 2 rgbif-0.8.4/rgbif/R/elevation.r | 45 - rgbif-0.8.4/rgbif/R/enumeration.R |only rgbif-0.8.4/rgbif/R/gbif_names.R | 4 rgbif-0.8.4/rgbif/R/gbif_photos.r | 14 rgbif-0.8.4/rgbif/R/gbifmap.r | 54 - rgbif-0.8.4/rgbif/R/name_backbone.r | 2 rgbif-0.8.4/rgbif/R/name_lookup.r | 54 + rgbif-0.8.4/rgbif/R/name_suggest.r | 4 rgbif-0.8.4/rgbif/R/name_usage.r | 2 rgbif-0.8.4/rgbif/R/nodes.r | 25 rgbif-0.8.4/rgbif/R/occ_count.r | 11 rgbif-0.8.4/rgbif/R/occ_get.r | 63 +- rgbif-0.8.4/rgbif/R/occ_issues.r | 56 - rgbif-0.8.4/rgbif/R/occ_metadata.r | 1 rgbif-0.8.4/rgbif/R/occ_search.r | 119 +-- rgbif-0.8.4/rgbif/R/on_load.R |only rgbif-0.8.4/rgbif/R/parsenames.R | 2 rgbif-0.8.4/rgbif/R/plyr_fxns.R |only rgbif-0.8.4/rgbif/R/read_wkt.R |only rgbif-0.8.4/rgbif/R/zzz.r | 207 +++--- rgbif-0.8.4/rgbif/README.md | 2 rgbif-0.8.4/rgbif/build/vignette.rds |binary rgbif-0.8.4/rgbif/inst/doc/issues_vignette.Rmd | 166 ++--- rgbif-0.8.4/rgbif/inst/doc/issues_vignette.html | 166 ++--- rgbif-0.8.4/rgbif/inst/doc/rgbif_vignette.html | 398 ++++++------- rgbif-0.8.4/rgbif/inst/js |only rgbif-0.8.4/rgbif/inst/vign/figure/gbifmap1-1.png |binary rgbif-0.8.4/rgbif/inst/vign/issues_vignette.md | 166 ++--- rgbif-0.8.4/rgbif/inst/vign/rgbif_vignette.Rmd | 8 rgbif-0.8.4/rgbif/inst/vign/rgbif_vignette.md | 396 ++++++------ rgbif-0.8.4/rgbif/man/blanktheme.Rd | 2 rgbif-0.8.4/rgbif/man/check_wkt.Rd | 2 rgbif-0.8.4/rgbif/man/commas_to_periods.Rd | 2 rgbif-0.8.4/rgbif/man/count_facet.Rd | 2 rgbif-0.8.4/rgbif/man/create_gist.Rd | 2 rgbif-0.8.4/rgbif/man/dataset_metrics.Rd | 6 rgbif-0.8.4/rgbif/man/dataset_search.Rd | 2 rgbif-0.8.4/rgbif/man/dataset_suggest.Rd | 2 rgbif-0.8.4/rgbif/man/datasetparser.Rd | 2 rgbif-0.8.4/rgbif/man/datasets.Rd | 2 rgbif-0.8.4/rgbif/man/density_spplist.Rd | 2 rgbif-0.8.4/rgbif/man/densitylist.Rd | 2 rgbif-0.8.4/rgbif/man/elevation.Rd | 22 rgbif-0.8.4/rgbif/man/enumeration.Rd |only rgbif-0.8.4/rgbif/man/gbif_bbox2wkt.Rd | 8 rgbif-0.8.4/rgbif/man/gbif_capwords.Rd | 2 rgbif-0.8.4/rgbif/man/gbif_issues.Rd | 2 rgbif-0.8.4/rgbif/man/gbif_names.Rd | 2 rgbif-0.8.4/rgbif/man/gbif_photos.Rd | 2 rgbif-0.8.4/rgbif/man/gbifdata.Rd | 2 rgbif-0.8.4/rgbif/man/gbifmap.Rd | 10 rgbif-0.8.4/rgbif/man/gbifmap_dens.Rd | 2 rgbif-0.8.4/rgbif/man/gbifmap_list.Rd | 2 rgbif-0.8.4/rgbif/man/gbifparser.Rd | 2 rgbif-0.8.4/rgbif/man/gbifparser_verbatim.Rd | 2 rgbif-0.8.4/rgbif/man/get_credentials.Rd | 2 rgbif-0.8.4/rgbif/man/gist.Rd | 2 rgbif-0.8.4/rgbif/man/installations.Rd | 2 rgbif-0.8.4/rgbif/man/isocodes.Rd | 2 rgbif-0.8.4/rgbif/man/name_backbone.Rd | 2 rgbif-0.8.4/rgbif/man/name_lookup.Rd | 11 rgbif-0.8.4/rgbif/man/name_suggest.Rd | 2 rgbif-0.8.4/rgbif/man/name_usage.Rd | 2 rgbif-0.8.4/rgbif/man/namelkupparser.Rd | 2 rgbif-0.8.4/rgbif/man/networks.Rd | 2 rgbif-0.8.4/rgbif/man/nodes.Rd | 23 rgbif-0.8.4/rgbif/man/occ_count.Rd | 9 rgbif-0.8.4/rgbif/man/occ_fields.Rd | 2 rgbif-0.8.4/rgbif/man/occ_get.Rd | 14 rgbif-0.8.4/rgbif/man/occ_issues.Rd | 12 rgbif-0.8.4/rgbif/man/occ_issues_lookup.Rd | 2 rgbif-0.8.4/rgbif/man/occ_metadata.Rd | 2 rgbif-0.8.4/rgbif/man/occ_search.Rd | 29 rgbif-0.8.4/rgbif/man/occurrencecount.Rd | 2 rgbif-0.8.4/rgbif/man/occurrencedensity.Rd | 2 rgbif-0.8.4/rgbif/man/occurrenceget.Rd | 2 rgbif-0.8.4/rgbif/man/occurrencelist.Rd | 2 rgbif-0.8.4/rgbif/man/occurrencelist_all.Rd | 2 rgbif-0.8.4/rgbif/man/occurrencelist_many.Rd | 2 rgbif-0.8.4/rgbif/man/organizations.Rd | 2 rgbif-0.8.4/rgbif/man/parsenames.Rd | 2 rgbif-0.8.4/rgbif/man/parseresults.Rd | 2 rgbif-0.8.4/rgbif/man/pipe.Rd | 2 rgbif-0.8.4/rgbif/man/providers.Rd | 2 rgbif-0.8.4/rgbif/man/read_wkt.Rd |only rgbif-0.8.4/rgbif/man/resources.Rd | 2 rgbif-0.8.4/rgbif/man/rgb_country_codes.Rd | 2 rgbif-0.8.4/rgbif/man/rgbif-defunct.Rd | 2 rgbif-0.8.4/rgbif/man/rgbif-package.Rd | 2 rgbif-0.8.4/rgbif/man/stylegeojson.Rd | 2 rgbif-0.8.4/rgbif/man/suggestfields.Rd | 2 rgbif-0.8.4/rgbif/man/taxoncount.Rd | 2 rgbif-0.8.4/rgbif/man/taxonget.Rd | 2 rgbif-0.8.4/rgbif/man/taxonsearch.Rd | 2 rgbif-0.8.4/rgbif/man/taxrank.Rd | 2 rgbif-0.8.4/rgbif/man/togeojson.Rd | 2 rgbif-0.8.4/rgbif/man/type_sum.Rd | 2 rgbif-0.8.4/rgbif/man/typestatus.Rd | 2 rgbif-0.8.4/rgbif/tests/test-all.R |only rgbif-0.8.4/rgbif/tests/testthat/test-count_facet.r | 29 rgbif-0.8.4/rgbif/tests/testthat/test-country_codes.r | 6 rgbif-0.8.4/rgbif/tests/testthat/test-dataset_metrics.r | 20 rgbif-0.8.4/rgbif/tests/testthat/test-dataset_search.r | 36 - rgbif-0.8.4/rgbif/tests/testthat/test-dataset_suggest.r | 14 rgbif-0.8.4/rgbif/tests/testthat/test-datasets.r | 36 - rgbif-0.8.4/rgbif/tests/testthat/test-enumeration.r |only rgbif-0.8.4/rgbif/tests/testthat/test-gbifmap.r | 25 rgbif-0.8.4/rgbif/tests/testthat/test-installations.r | 37 - rgbif-0.8.4/rgbif/tests/testthat/test-name_backbone.r | 9 rgbif-0.8.4/rgbif/tests/testthat/test-name_lookup.r | 35 - rgbif-0.8.4/rgbif/tests/testthat/test-name_suggest.r | 19 rgbif-0.8.4/rgbif/tests/testthat/test-name_usage.r | 18 rgbif-0.8.4/rgbif/tests/testthat/test-nodes.r | 19 rgbif-0.8.4/rgbif/tests/testthat/test-occ_count.r | 25 rgbif-0.8.4/rgbif/tests/testthat/test-occ_get.r | 24 rgbif-0.8.4/rgbif/tests/testthat/test-occ_metadata.r | 32 - rgbif-0.8.4/rgbif/tests/testthat/test-occ_search.r | 91 +- rgbif-0.8.4/rgbif/tests/testthat/test-organizations.r | 13 rgbif-0.8.4/rgbif/tests/testthat/test-parsenames.r | 20 rgbif-0.8.4/rgbif/vignettes/issues_vignette.Rmd | 166 ++--- rgbif-0.8.4/rgbif/vignettes/rgbif_vignette.Rmd | 396 ++++++------ 135 files changed, 1921 insertions(+), 1802 deletions(-)
Title: Reverse Ecology Analysis on Microbiome
Description: An implementation of the reverse ecology framework. Reverse ecology
refers to the use of genomics to study ecology with no a priori assumptions
about the organism(s) under consideration, linking organisms to their
environment. It allows researchers to reconstruct the metabolic networks and
study the ecology of poorly characterized microbial species from their
genomic information, and has substantial potentials for microbial community
ecological analysis.
Author: Yang Cao, Fei Li
Maintainer: Yang Cao <yiluheihei@gmail.com>
Diff between RevEcoR versions 0.99.1 dated 2015-06-04 and 0.99.2 dated 2015-06-08
DESCRIPTION | 15 ++--- MD5 | 28 +++++---- NAMESPACE | 5 - R/AllClasses.R | 3 - R/RevEcoR.R | 5 - R/getOrgMetabolicData.R | 21 +++++-- R/getSeedSets.R | 3 - R/reconsructGsMN.R | 5 - README.md | 37 ++++++------ data/RefDbcache.rda |only inst/doc/RevEcoR.R | 14 ++-- inst/doc/RevEcoR.Rmd | 120 +++++++++++++++++++----------------------- inst/doc/RevEcoR.html | 137 ++++++++++++++++++++---------------------------- man/RefDbcache.Rd |only man/reconstructGsMN.Rd | 4 - vignettes/RevEcoR.Rmd | 120 +++++++++++++++++++----------------------- 16 files changed, 244 insertions(+), 273 deletions(-)
Title: A Collection of Small Text Corpora of Interesting Data
Description: A collection of small text corpora of interesting data.
It contains all data sets from https://github.com/dariusk/corpora.
Some examples:
names of animals: birds, dinosaurs, dogs; foods: beer categories,
pizza toppings; geography: English towns, rivers, oceans;
humans: authors, US presidents, occupations; science: elements,
planets; words: adjectives, verbs, proverbs, US president quotes.
Author: Darius Kazemi, Matthew Rothenberg, Karl Swedberg, Matthew Hokanson,
Nathan Lachenmyer, Aaron Marriner, Mark Sample, Casey Kolderup,
Nathaniel Mitchell, Daniel D. Beck, Mike Nowak, Ryan Freebern,
Ross Barclay, Ross Binden, Justin Alford, Cole Willsea,
Andrew Gorman, Javier Arce, Patrick Rodriguez,
Liam Cooke, Will Hankinson, K. Adam White, Garrett Miller, Zac Moody,
Jordan Killpack, Brian Jones, Greg Borenstein, Noah Swartz, Nathan Black,
Russell Horton, Mark Wunsch, Kay Belardinelli, Colin Mitchell,
Michael Dewberry, Joe Mahoney
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rcorpora versions 1.0.1 dated 2015-04-07 and 1.1.0 dated 2015-06-08
DESCRIPTION | 6 MD5 | 44 NAMESPACE | 2 build/rcorpora.pdf |binary inst/NEWS.md |only inst/README.markdown |only inst/corpora/README.md | 1 inst/corpora/data/animals/dinosaurs.json | 3189 ++++++---------- inst/corpora/data/architecture |only inst/corpora/data/art |only inst/corpora/data/corporations/fortune500.json |only inst/corpora/data/foods/breads_and_pastries.json |only inst/corpora/data/foods/condiments.json |only inst/corpora/data/foods/curds.json |only inst/corpora/data/games/street_fighter_ii.json |only inst/corpora/data/governments/uk_political_parties.json |only inst/corpora/data/humans/moods.json |only inst/corpora/data/materials |only inst/corpora/data/music |only inst/corpora/data/mythology |only inst/corpora/data/objects/objects.json | 453 ++ inst/corpora/data/technology/appliances.json |only man/categories.Rd | 2 man/corpora.Rd | 2 24 files changed, 1877 insertions(+), 1822 deletions(-)
Title: Methods for Causal Inference with Interference
Description: Provides methods for estimating causal effects in the presence of interference. Currently it implements the IPW estimators proposed by E.J. Tchetgen Tchetgen and T.J. Vanderweele in "On causal inference in the presence of interference" (Statistical Methods in Medical Research, 21(1) 55-75).
Author: Bradley Saul
Maintainer: Bradley Saul <saulb@live.unc.edu>
Diff between inferference versions 0.4.61 dated 2015-03-09 and 0.4.62 dated 2015-06-08
DESCRIPTION | 10 MD5 | 43 NAMESPACE | 2 R/effect_calc.R | 2 R/interference.R | 6 R/ipw_interference.R | 2 README.md |only build/vignette.rds |binary inst/doc/inferference_intro.R | 4 inst/doc/inferference_intro.Rmd | 8 inst/doc/inferference_intro.html |23054 --------------------------------------- inst/doc/inferference_plots.html | 4 man/direct_effect.Rd | 2 man/indirect_effect.Rd | 2 man/inferference.Rd | 2 man/interference.Rd | 8 man/logit_integrand.Rd | 2 man/overall_effect.Rd | 2 man/print.interference.Rd | 2 man/total_effect.Rd | 2 man/vaccinesim.Rd | 2 man/voters.Rd | 2 vignettes/inferference_intro.Rmd | 8 23 files changed, 215 insertions(+), 22954 deletions(-)
Title: Hartigan's Dip Test Statistic for Unimodality - Corrected
Description: Compute Hartigan's dip test statistic for unimodality /
multimodality and provide a test with simulation based p-values, where
the original public code has been corrected.
Author: Martin Maechler (originally from Fortran and S-plus by Dario Ringach, NYU.edu)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between diptest versions 0.75-6 dated 2014-11-25 and 0.75-7 dated 2015-06-08
DESCRIPTION | 13 +++++++------ MD5 | 21 +++++++++++---------- R/dip.R | 3 +-- build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/diptest-issues.R | 2 +- man/dip.Rd | 9 +++++++-- man/dip.test.Rd | 4 ++-- man/qDiptab.Rd | 3 ++- tests/ex1.Rout.save | 12 ++++++------ tests/sim1.Rout.save | 16 ++++++++-------- vignettes/diptest-issues.Rnw | 16 ++++++++-------- 12 files changed, 53 insertions(+), 46 deletions(-)
Title: Ferguson-Klass Type Algorithm for Posterior Normalized Random
Measures
Description: Modeling mixtures with normalized random measures by a Ferguson-Klass type algorithm for posterior normalized random measures.
Author: Ernesto Barrios, Antonio Lijoi, Luis E. Nieto-Barajas and Igor Prünster. R implementation by Ernesto Barrios and Luis E. Nieto-Barajas.
Maintainer: Ernesto Barrios <ebarrios@itam.mx>
Diff between BNPdensity versions 2013.8 dated 2013-07-31 and 2015.5 dated 2015-06-08
DESCRIPTION | 18 - MD5 | 74 +++---- R/MixNRMI1.R | 164 ++++++++--------- R/MixNRMI2.R | 170 ++++++++--------- R/Mv.R | 24 +- R/MvInv.R | 35 ++- R/comp1.R | 48 ++--- R/comp2.R | 60 +++--- R/cpo.R | 14 - R/dk.R | 84 ++++---- R/fcondXA.R | 22 +- R/fcondXA2.R | 22 +- R/fcondYXA.R | 24 +- R/fcondYZXA.R | 32 +-- R/gs3.R | 40 ++-- R/gs4.R | 40 ++-- R/gs5.R | 40 ++-- R/gsHP.R | 78 ++++---- R/gsYZstar.R | 86 ++++---- R/p0.R | 62 +++--- R/rfystar.R | 28 +- R/rfyzstar.R | 34 +-- R/rk.R | 86 ++++---- data/Enzyme1.out.rda |binary data/Enzyme2.out.rda |binary data/Galaxy1.out.rda |binary data/Galaxy2.out.rda |binary data/acidity.rda |binary data/enzyme.rda |binary data/galaxy.rda |binary man/BNPdensity-package.Rd | 109 +++++------ man/Enzyme1.out.Rd | 39 +--- man/Enzyme2.out.Rd | 41 ++-- man/Galaxy1.out.Rd | 39 +--- man/Galaxy2.out.Rd | 41 ++-- man/MixNRMI1.Rd | 441 +++++++++++++++++++++++----------------------- man/MixNRMI2.Rd | 423 +++++++++++++++++++++----------------------- man/MvInv.Rd | 66 +++--- 38 files changed, 1245 insertions(+), 1239 deletions(-)