Title: Optimal Binning for Scoring Modeling
Description: It categorizes a numeric variable into bins mapped to a binary target variable for its ulterior usage in scoring modeling. Its purpose is to automate the time consuming process of selecting the right cut points, quickly calculate metrics such as Weight of Evidence and Information Value; and also document SQL codes, tables, and plots used throughout the development stage. The package also allows users to establish their own cut points for numeric characteristics and run the analysis for categorical variables.
Author: Herman Jopia
Maintainer: Herman Jopia <hjopia@gmail.com>
Diff between smbinning versions 0.1 dated 2015-02-15 and 0.2 dated 2015-06-13
DESCRIPTION | 10 MD5 | 12 - R/smbinning.R | 503 +++++++++++++++++++++++++++++++++++++++++++++--- man/smbinning.Rd | 13 - man/smbinning.custom.Rd |only man/smbinning.factor.Rd |only man/smbinning.gen.Rd | 2 man/smbinning.plot.Rd | 2 8 files changed, 500 insertions(+), 42 deletions(-)
Title: Periodogram Peaks in Correlated Time Series
Description: Calculates the periodogram of a time series, maximum-likelihood fits an Ornstein-Uhlenbeck state space (OUSS) null model and evaluates the statistical significance of periodogram peaks against the OUSS null hypothesis. The OUSS is a parsimonious model for stochastically fluctuating variables with linear stabilizing forces, subject to uncorrelated measurement errors. Contrary to the classical white noise null model for detecting cyclicity, the OUSS model can account for temporal correlations typically occurring in ecological and geological time series.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@math.ubc.ca>
Diff between peacots versions 1.1 dated 2014-10-29 and 1.2 dated 2015-06-13
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/runExample.R | 6 +++--- inst/CITATION | 5 ++++- man/evaluate.pm.Rd | 2 +- man/evaluate.pm.wn.Rd | 2 +- man/generate_ouss.Rd | 2 +- man/peacots-package.Rd | 6 +++--- man/plotReport.Rd | 2 +- man/ps_ouss.Rd | 2 +- man/ps_ouss_asymptotic.Rd | 2 +- man/runExample.Rd | 2 +- man/significanceOfLocalPeak.Rd | 2 +- 13 files changed, 34 insertions(+), 31 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann+mptinr@gmail.com>
Diff between MPTinR versions 1.8.0 dated 2015-04-30 and 1.9.2 dated 2015-06-13
DESCRIPTION | 12 ++++++------ MD5 | 17 ++++++++++++----- NEWS | 21 +++++++++++++++++++++ R/fit.mptinr.R | 2 +- R/select.mpt.R | 2 +- build |only inst/CITATION | 9 ++++++--- inst/doc |only vignettes |only 9 files changed, 47 insertions(+), 16 deletions(-)
Title: Bayesian Linear Mixed-Effects Models
Description: Maximum a posteriori estimation for linear and generalized
linear mixed-effects models in a Bayesian setting. Extends
'lme4' by Douglas Bates, Martin Maechler, Ben Bolker, and Steve Walker.
Author: Vincent Dorie <vjd4@nyu.edu>
Maintainer: Vincent Dorie <vjd4@nyu.edu>
Diff between blme versions 1.0-3 dated 2015-05-30 and 1.0-4 dated 2015-06-13
DESCRIPTION | 14 - MD5 | 14 - NAMESPACE | 4 R/blmer.R | 457 +++++++++++++++++++++-------------------- R/devFun.R | 43 ++- README.md | 4 man/blmer.Rd | 3 tests/testthat/test-10-refit.R | 79 +++---- 8 files changed, 333 insertions(+), 285 deletions(-)
Title: Easily Play Notification Sounds on any Platform
Description: The sole function of this package is beep(), with the purpose to
make it easy to play notification sounds on whatever platform you are on.
It is intended to be useful, for example, if you are running a long analysis
in the background and want to know when it is ready.
Author: Rasmus Bååth <rasmus.baath@gmail.com>
Maintainer: Rasmus Bååth <rasmus.baath@gmail.com>
Diff between beepr versions 1.1 dated 2014-06-26 and 1.2 dated 2015-06-13
DESCRIPTION | 12 ++++---- MD5 | 17 ++++++------ NAMESPACE | 2 - NEWS | 12 ++++++++ R/beepr.R | 49 +++++++++++++++++++++++++----------- README.md | 13 ++++++++- inst/sounds/microwave_ping_mono.wav |binary inst/sounds/sword.wav |only man/beep.Rd | 19 ++++++++----- man/beepr.Rd | 3 +- 10 files changed, 86 insertions(+), 41 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Taxonomic information from around the web. This package
interacts with a suite of web 'APIs' for taxonomic tasks, such
as verifying species names, getting taxonomic hierarchies,
and verifying name spelling.
Author: Scott Chamberlain [aut, cre],
Eduard Szoecs [aut],
Zachary Foster [aut],
Carl Boettiger [aut],
Karthik Ram [aut],
Ignasi Bartomeus [aut],
John Baumgartner [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.5.2 dated 2014-12-19 and 0.6.0 dated 2015-06-13
taxize-0.5.2/taxize/data/apg_genera.RData |only taxize-0.5.2/taxize/data/datalist |only taxize-0.5.2/taxize/inst/vign/cache/taxname_f6bfd7efb6327a4d98fe2ce6978a484a.RData |only taxize-0.5.2/taxize/inst/vign/cache/taxname_f6bfd7efb6327a4d98fe2ce6978a484a.rdb |only taxize-0.5.2/taxize/inst/vign/cache/taxname_f6bfd7efb6327a4d98fe2ce6978a484a.rdx |only taxize-0.5.2/taxize/man/apg_genera.Rd |only taxize-0.5.2/taxize/man/eol_invasive-deprecated.Rd |only taxize-0.5.2/taxize/man/gisd_invasive-deprecated.Rd |only taxize-0.5.2/taxize/man/nbn_classifcation.Rd |only taxize-0.5.2/taxize/man/ncbi_getbyid-deprecated.Rd |only taxize-0.5.2/taxize/man/ncbi_getbyname-deprecated.Rd |only taxize-0.5.2/taxize/man/ncbi_search-deprecated.Rd |only taxize-0.5.2/taxize/tests/testthat/test-eol_invasive.R |only taxize-0.5.2/taxize/tests/testthat/test-gisd_isinvasive.R |only taxize-0.5.2/taxize/tests/testthat/test-ncbi_getbyid.R |only taxize-0.5.2/taxize/tests/testthat/test-ncbi_getbyname.R |only taxize-0.5.2/taxize/tests/testthat/test-ncbi_search.R |only taxize-0.6.0/taxize/DESCRIPTION | 41 taxize-0.6.0/taxize/LICENSE | 4 taxize-0.6.0/taxize/MD5 | 553 +++++----- taxize-0.6.0/taxize/NAMESPACE | 12 taxize-0.6.0/taxize/NEWS | 58 + taxize-0.6.0/taxize/R/apg.R |only taxize-0.6.0/taxize/R/apg_lookup.R | 33 taxize-0.6.0/taxize/R/children.R | 23 taxize-0.6.0/taxize/R/class2tree.R | 77 + taxize-0.6.0/taxize/R/classification.R | 94 - taxize-0.6.0/taxize/R/col_children.R | 14 taxize-0.6.0/taxize/R/col_classification.R | 21 taxize-0.6.0/taxize/R/col_downstream.R | 26 taxize-0.6.0/taxize/R/col_search.R | 114 +- taxize-0.6.0/taxize/R/comm2sci.R | 33 taxize-0.6.0/taxize/R/downstream.R | 18 taxize-0.6.0/taxize/R/eol_dataobjects.R | 38 taxize-0.6.0/taxize/R/eol_hierarchy.R | 4 taxize-0.6.0/taxize/R/eol_invasive.R | 160 +- taxize-0.6.0/taxize/R/eol_pages.R | 31 taxize-0.6.0/taxize/R/eol_search.R | 24 taxize-0.6.0/taxize/R/eol_utiils.R |only taxize-0.6.0/taxize/R/genbank2uid.R | 39 taxize-0.6.0/taxize/R/get_boldid.R | 143 +- taxize-0.6.0/taxize/R/get_colid.R | 133 +- taxize-0.6.0/taxize/R/get_eolid.R | 97 - taxize-0.6.0/taxize/R/get_gbifid.R | 170 ++- taxize-0.6.0/taxize/R/get_ids.R | 13 taxize-0.6.0/taxize/R/get_nbnid.R | 5 taxize-0.6.0/taxize/R/get_tpsid.R | 116 +- taxize-0.6.0/taxize/R/get_tsn.R | 24 taxize-0.6.0/taxize/R/get_ubioid.R | 165 ++ taxize-0.6.0/taxize/R/get_uid.R | 162 ++ taxize-0.6.0/taxize/R/gisd_isinvasive.R | 68 - taxize-0.6.0/taxize/R/gnr_datasources.R | 7 taxize-0.6.0/taxize/R/gnr_resolve.R | 66 - taxize-0.6.0/taxize/R/itis.R | 366 ++---- taxize-0.6.0/taxize/R/itis_acceptname.R | 12 taxize-0.6.0/taxize/R/itis_native.R | 8 taxize-0.6.0/taxize/R/itis_terms.R | 16 taxize-0.6.0/taxize/R/names_list.r | 2 taxize-0.6.0/taxize/R/nbn_classification.R | 8 taxize-0.6.0/taxize/R/nbn_search.R | 2 taxize-0.6.0/taxize/R/ncbi_children.R | 38 taxize-0.6.0/taxize/R/ncbi_get_taxon_summary.R | 11 taxize-0.6.0/taxize/R/ncbi_getbyid.R | 63 - taxize-0.6.0/taxize/R/ncbi_getbyname.R | 232 ++-- taxize-0.6.0/taxize/R/ncbi_search.R | 316 ++--- taxize-0.6.0/taxize/R/phylomatic_format.R | 24 taxize-0.6.0/taxize/R/phylomatic_tree.R | 4 taxize-0.6.0/taxize/R/ping.R | 7 taxize-0.6.0/taxize/R/rankagg.R | 4 taxize-0.6.0/taxize/R/rename.R |only taxize-0.6.0/taxize/R/resolve.R | 12 taxize-0.6.0/taxize/R/sci2comm.R | 6 taxize-0.6.0/taxize/R/synonyms.R | 155 ++ taxize-0.6.0/taxize/R/tax_agg.R | 16 taxize-0.6.0/taxize/R/taxize-package.R | 95 + taxize-0.6.0/taxize/R/taxize_cite.R | 263 ++++ taxize-0.6.0/taxize/R/tnrs.R | 22 taxize-0.6.0/taxize/R/tp_accnames.R | 19 taxize-0.6.0/taxize/R/tp_classification.R | 6 taxize-0.6.0/taxize/R/tp_dist.R | 17 taxize-0.6.0/taxize/R/tp_refs.R | 9 taxize-0.6.0/taxize/R/tp_search.R | 20 taxize-0.6.0/taxize/R/tp_summary.R | 10 taxize-0.6.0/taxize/R/tp_synonyms.R | 23 taxize-0.6.0/taxize/R/tpl_families.r | 21 taxize-0.6.0/taxize/R/tpl_get.r | 54 taxize-0.6.0/taxize/R/tpl_search.r | 29 taxize-0.6.0/taxize/R/ubio_search.R | 26 taxize-0.6.0/taxize/R/upstream.R | 16 taxize-0.6.0/taxize/R/vascan_search.r | 5 taxize-0.6.0/taxize/R/zzz.R | 37 taxize-0.6.0/taxize/README.md | 107 - taxize-0.6.0/taxize/build/vignette.rds |binary taxize-0.6.0/taxize/data/theplantlist.RData |binary taxize-0.6.0/taxize/inst/doc/taxize_infotable.Rmd | 1 taxize-0.6.0/taxize/inst/doc/taxize_infotable.html | 1 taxize-0.6.0/taxize/inst/doc/taxize_vignette.Rmd | 252 +--- taxize-0.6.0/taxize/inst/doc/taxize_vignette.html | 239 +--- taxize-0.6.0/taxize/inst/vign/cache/__packages | 14 taxize-0.6.0/taxize/inst/vign/cache/taxname_0f3fcc7119f159af267de7a029f64f5e.RData |only taxize-0.6.0/taxize/inst/vign/cache/taxname_0f3fcc7119f159af267de7a029f64f5e.rdb |only taxize-0.6.0/taxize/inst/vign/cache/taxname_0f3fcc7119f159af267de7a029f64f5e.rdx |only taxize-0.6.0/taxize/inst/vign/cache/tnrs_c39c1e0c556437f6b37ba3c369e8be54.RData |only taxize-0.6.0/taxize/inst/vign/cache/tnrs_c39c1e0c556437f6b37ba3c369e8be54.rdb |only taxize-0.6.0/taxize/inst/vign/cache/tnrs_c39c1e0c556437f6b37ba3c369e8be54.rdx |only taxize-0.6.0/taxize/inst/vign/taxize_infotable.Rmd | 1 taxize-0.6.0/taxize/inst/vign/taxize_infotable.md | 1 taxize-0.6.0/taxize/inst/vign/taxize_vignette.Rmd | 24 taxize-0.6.0/taxize/inst/vign/taxize_vignette.md | 252 +--- taxize-0.6.0/taxize/man/apg.Rd |only taxize-0.6.0/taxize/man/apg_families.Rd | 20 taxize-0.6.0/taxize/man/apg_lookup.Rd | 25 taxize-0.6.0/taxize/man/apg_orders.Rd | 19 taxize-0.6.0/taxize/man/bold_search.Rd | 2 taxize-0.6.0/taxize/man/children.Rd | 22 taxize-0.6.0/taxize/man/class2tree.Rd | 4 taxize-0.6.0/taxize/man/classification.Rd | 20 taxize-0.6.0/taxize/man/col_children.Rd | 6 taxize-0.6.0/taxize/man/col_classification-defunct.Rd | 24 taxize-0.6.0/taxize/man/col_downstream.Rd | 7 taxize-0.6.0/taxize/man/col_search.Rd | 9 taxize-0.6.0/taxize/man/comm2sci.Rd | 9 taxize-0.6.0/taxize/man/downstream.Rd | 17 taxize-0.6.0/taxize/man/eol_dataobjects.Rd | 27 taxize-0.6.0/taxize/man/eol_hierarchy-defunct.Rd | 8 taxize-0.6.0/taxize/man/eol_invasive-defunct.Rd |only taxize-0.6.0/taxize/man/eol_pages.Rd | 8 taxize-0.6.0/taxize/man/eol_search.Rd | 6 taxize-0.6.0/taxize/man/gbif_name_usage.Rd | 2 taxize-0.6.0/taxize/man/gbif_parse.Rd | 2 taxize-0.6.0/taxize/man/genbank2uid.Rd | 2 taxize-0.6.0/taxize/man/get_boldid.Rd | 52 taxize-0.6.0/taxize/man/get_colid.Rd | 57 - taxize-0.6.0/taxize/man/get_eolid.Rd | 2 taxize-0.6.0/taxize/man/get_gbifid.Rd | 57 - taxize-0.6.0/taxize/man/get_genes-deprecated.Rd | 2 taxize-0.6.0/taxize/man/get_genes_avail-deprecated.Rd | 2 taxize-0.6.0/taxize/man/get_ids.Rd | 7 taxize-0.6.0/taxize/man/get_nbnid.Rd | 7 taxize-0.6.0/taxize/man/get_seqs-deprecated.Rd | 2 taxize-0.6.0/taxize/man/get_tpsid.Rd | 41 taxize-0.6.0/taxize/man/get_tsn.Rd | 26 taxize-0.6.0/taxize/man/get_ubioid.Rd | 47 taxize-0.6.0/taxize/man/get_uid.Rd | 55 taxize-0.6.0/taxize/man/getacceptednamesfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getanymatchcount.Rd | 2 taxize-0.6.0/taxize/man/getcommentdetailfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getcommonnamesfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getcoremetadatafromtsn.Rd | 2 taxize-0.6.0/taxize/man/getcoveragefromtsn.Rd | 2 taxize-0.6.0/taxize/man/getcredibilityratingfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getcredibilityratings.Rd | 2 taxize-0.6.0/taxize/man/getcurrencyfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getdatedatafromtsn.Rd | 2 taxize-0.6.0/taxize/man/getdescription.Rd | 2 taxize-0.6.0/taxize/man/getexpertsfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getfullhierarchyfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getfullrecordfromlsid.Rd | 2 taxize-0.6.0/taxize/man/getfullrecordfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getgeographicdivisionsfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getgeographicvalues.Rd | 2 taxize-0.6.0/taxize/man/getglobalspeciescompletenessfromtsn.Rd | 2 taxize-0.6.0/taxize/man/gethierarchydownfromtsn.Rd | 2 taxize-0.6.0/taxize/man/gethierarchyupfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getitisterms.Rd | 2 taxize-0.6.0/taxize/man/getitistermsfromcommonname.Rd | 2 taxize-0.6.0/taxize/man/getitistermsfromscientificname.Rd | 2 taxize-0.6.0/taxize/man/getjurisdictionaloriginfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getjurisdictionoriginvalues.Rd | 2 taxize-0.6.0/taxize/man/getjurisdictionvalues.Rd | 2 taxize-0.6.0/taxize/man/getkey.Rd | 2 taxize-0.6.0/taxize/man/getkingdomnamefromtsn.Rd | 2 taxize-0.6.0/taxize/man/getkingdomnames.Rd | 2 taxize-0.6.0/taxize/man/getlastchangedate.Rd | 2 taxize-0.6.0/taxize/man/getlsidfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getothersourcesfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getparenttsnfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getpublicationsfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getranknames.Rd | 2 taxize-0.6.0/taxize/man/getrecordfromlsid.Rd | 2 taxize-0.6.0/taxize/man/getreviewyearfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getscientificnamefromtsn.Rd | 2 taxize-0.6.0/taxize/man/getsynonymnamesfromtsn.Rd | 2 taxize-0.6.0/taxize/man/gettaxonauthorshipfromtsn.Rd | 2 taxize-0.6.0/taxize/man/gettaxonomicranknamefromtsn.Rd | 2 taxize-0.6.0/taxize/man/gettaxonomicusagefromtsn.Rd | 2 taxize-0.6.0/taxize/man/gettsnbyvernacularlanguage.Rd | 2 taxize-0.6.0/taxize/man/gettsnfromlsid.Rd | 2 taxize-0.6.0/taxize/man/getunacceptabilityreasonfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getvernacularlanguages.Rd | 2 taxize-0.6.0/taxize/man/gisd_invasive-defunct.Rd |only taxize-0.6.0/taxize/man/gni_details.Rd | 2 taxize-0.6.0/taxize/man/gni_parse.Rd | 2 taxize-0.6.0/taxize/man/gni_search.Rd | 2 taxize-0.6.0/taxize/man/gnr_datasources.Rd | 4 taxize-0.6.0/taxize/man/gnr_resolve.Rd | 6 taxize-0.6.0/taxize/man/ifelsedata.Rd | 2 taxize-0.6.0/taxize/man/iplant_resolve.Rd | 2 taxize-0.6.0/taxize/man/ipni_search.Rd | 2 taxize-0.6.0/taxize/man/itis-api.Rd | 2 taxize-0.6.0/taxize/man/itis_acceptname.Rd | 2 taxize-0.6.0/taxize/man/itis_downstream.Rd | 2 taxize-0.6.0/taxize/man/itis_getrecord.Rd | 2 taxize-0.6.0/taxize/man/itis_hierarchy.Rd | 2 taxize-0.6.0/taxize/man/itis_kingdomnames.Rd | 2 taxize-0.6.0/taxize/man/itis_lsid.Rd | 2 taxize-0.6.0/taxize/man/itis_name-deprecated.Rd | 2 taxize-0.6.0/taxize/man/itis_native.Rd | 2 taxize-0.6.0/taxize/man/itis_refs.Rd | 2 taxize-0.6.0/taxize/man/itis_searchcommon.Rd | 2 taxize-0.6.0/taxize/man/itis_taxrank.Rd | 2 taxize-0.6.0/taxize/man/itis_terms.Rd | 2 taxize-0.6.0/taxize/man/iucn_getname.Rd | 2 taxize-0.6.0/taxize/man/iucn_status.Rd | 2 taxize-0.6.0/taxize/man/iucn_summary.Rd | 2 taxize-0.6.0/taxize/man/names_list.Rd | 2 taxize-0.6.0/taxize/man/nbn_classification.Rd |only taxize-0.6.0/taxize/man/nbn_search.Rd | 4 taxize-0.6.0/taxize/man/nbn_synonyms.Rd | 2 taxize-0.6.0/taxize/man/ncbi_children.Rd | 16 taxize-0.6.0/taxize/man/ncbi_get_taxon_summary.Rd | 10 taxize-0.6.0/taxize/man/ncbi_getbyid-defunct.Rd |only taxize-0.6.0/taxize/man/ncbi_getbyname-defunct.Rd |only taxize-0.6.0/taxize/man/ncbi_search-defunct.Rd |only taxize-0.6.0/taxize/man/phylomatic_format.Rd | 2 taxize-0.6.0/taxize/man/phylomatic_tree-deprecated.Rd | 6 taxize-0.6.0/taxize/man/ping.Rd | 7 taxize-0.6.0/taxize/man/plantGenusNames.Rd | 12 taxize-0.6.0/taxize/man/plantNames.Rd | 13 taxize-0.6.0/taxize/man/plantminer.Rd | 2 taxize-0.6.0/taxize/man/rank_ref.Rd | 2 taxize-0.6.0/taxize/man/rankagg.Rd | 3 taxize-0.6.0/taxize/man/resolve.Rd | 6 taxize-0.6.0/taxize/man/sci2comm.Rd | 8 taxize-0.6.0/taxize/man/scrapenames.Rd | 2 taxize-0.6.0/taxize/man/searchbycommonname.Rd | 2 taxize-0.6.0/taxize/man/searchbycommonnamebeginswith.Rd | 2 taxize-0.6.0/taxize/man/searchbycommonnameendswith.Rd | 2 taxize-0.6.0/taxize/man/searchbyscientificname.Rd | 2 taxize-0.6.0/taxize/man/searchforanymatch.Rd | 2 taxize-0.6.0/taxize/man/searchforanymatchpaged.Rd | 2 taxize-0.6.0/taxize/man/status_codes.Rd | 2 taxize-0.6.0/taxize/man/synonyms.Rd | 49 taxize-0.6.0/taxize/man/tax_agg.Rd | 3 taxize-0.6.0/taxize/man/tax_name.Rd | 2 taxize-0.6.0/taxize/man/tax_rank.Rd | 2 taxize-0.6.0/taxize/man/taxize-defunct.Rd | 7 taxize-0.6.0/taxize/man/taxize-deprecated.Rd | 21 taxize-0.6.0/taxize/man/taxize-package.Rd | 2 taxize-0.6.0/taxize/man/taxize_capwords.Rd | 2 taxize-0.6.0/taxize/man/taxize_cite.Rd | 12 taxize-0.6.0/taxize/man/taxize_ldfast.Rd | 2 taxize-0.6.0/taxize/man/theplantlist.Rd | 17 taxize-0.6.0/taxize/man/tnrs.Rd | 9 taxize-0.6.0/taxize/man/tnrs_sources.Rd | 2 taxize-0.6.0/taxize/man/tp_acceptednames-deprecated.Rd | 2 taxize-0.6.0/taxize/man/tp_accnames.Rd | 6 taxize-0.6.0/taxize/man/tp_classification-defunct.Rd | 9 taxize-0.6.0/taxize/man/tp_dist.Rd | 6 taxize-0.6.0/taxize/man/tp_namedistributions-deprecated.Rd | 2 taxize-0.6.0/taxize/man/tp_namereferences-deprecated.Rd | 2 taxize-0.6.0/taxize/man/tp_refs.Rd | 6 taxize-0.6.0/taxize/man/tp_search.Rd | 6 taxize-0.6.0/taxize/man/tp_summary.Rd | 6 taxize-0.6.0/taxize/man/tp_synonyms.Rd | 6 taxize-0.6.0/taxize/man/tpl_families.Rd | 4 taxize-0.6.0/taxize/man/tpl_get.Rd | 27 taxize-0.6.0/taxize/man/tpl_search-defunct.Rd | 15 taxize-0.6.0/taxize/man/ubio_classification.Rd | 2 taxize-0.6.0/taxize/man/ubio_classification_search.Rd | 2 taxize-0.6.0/taxize/man/ubio_id.Rd | 2 taxize-0.6.0/taxize/man/ubio_search.Rd | 6 taxize-0.6.0/taxize/man/ubio_synonyms.Rd | 2 taxize-0.6.0/taxize/man/upstream.Rd | 15 taxize-0.6.0/taxize/man/vascan_search.Rd | 7 taxize-0.6.0/taxize/tests/testthat/test-apgscraping.R |only taxize-0.6.0/taxize/tests/testthat/test-class2tree.R | 19 taxize-0.6.0/taxize/tests/testthat/test-classification.R | 6 taxize-0.6.0/taxize/tests/testthat/test-col_children.R | 16 taxize-0.6.0/taxize/tests/testthat/test-col_downstream.R | 11 taxize-0.6.0/taxize/tests/testthat/test-eol_dataobjects.R | 5 taxize-0.6.0/taxize/tests/testthat/test-get_ids.R | 14 taxize-0.6.0/taxize/tests/testthat/test-gnr_datasources.R | 20 taxize-0.6.0/taxize/tests/testthat/test-itis_downstream.R | 4 taxize-0.6.0/taxize/tests/testthat/test-names_list.R | 8 taxize-0.6.0/taxize/tests/testthat/test-phylomatic_tree.R | 12 taxize-0.6.0/taxize/tests/testthat/test-rankagg.R |only taxize-0.6.0/taxize/tests/testthat/test-sci2comm.R | 4 taxize-0.6.0/taxize/tests/testthat/test-synonyms.R | 6 taxize-0.6.0/taxize/tests/testthat/test-tax_agg.R | 4 taxize-0.6.0/taxize/tests/testthat/test-tnrs.R | 8 taxize-0.6.0/taxize/tests/testthat/test-tp_dist.R | 2 taxize-0.6.0/taxize/tests/testthat/test-vascan_search.r | 6 taxize-0.6.0/taxize/vignettes/taxize_infotable.Rmd | 1 taxize-0.6.0/taxize/vignettes/taxize_vignette.Rmd | 252 +--- 295 files changed, 3985 insertions(+), 2981 deletions(-)
Title: Phylogenetic Comparative Methods for Function-Valued and Other
High-Dimensional Traits
Description: Tools for studying the evolution of function-valued traits (as well as other high-dimensional traits) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit http://www.phylocurve.org for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between phylocurve versions 1.1.0 dated 2015-05-11 and 1.2.0 dated 2015-06-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/phylocurve.R | 14 +++++++------- man/phylocurve-package.Rd | 4 ++-- 4 files changed, 16 insertions(+), 16 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Diff between nodiv versions 1.0.3 dated 2015-03-26 and 1.0.4 dated 2015-06-13
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/Add_to_data_object.R | 13 ++++++++----- R/General_figure_functions.R | 10 ++++++++-- R/Methods_for_data_objects.R | 33 +++++++++++++++++++++++++-------- R/Methods_for_result_objects.R | 4 +++- R/Prepare_data.R | 4 ++-- man/Nspecies.Rd | 10 ++++++++-- man/nodiv-package.Rd | 6 +++--- 9 files changed, 70 insertions(+), 36 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.6.1 dated 2015-05-07 and 0.7 dated 2015-06-13
rmarkdown-0.6.1/rmarkdown/inst/rmd/beamer |only rmarkdown-0.7/rmarkdown/DESCRIPTION | 8 - rmarkdown-0.7/rmarkdown/MD5 | 38 +++--- rmarkdown-0.7/rmarkdown/NEWS | 22 +++ rmarkdown-0.7/rmarkdown/R/beamer_presentation.R | 10 + rmarkdown-0.7/rmarkdown/R/html_dependencies.R | 19 +++ rmarkdown-0.7/rmarkdown/R/html_document_base.R | 9 + rmarkdown-0.7/rmarkdown/R/html_fragment.R | 27 +++- rmarkdown-0.7/rmarkdown/R/html_resources.R | 57 ++++++++++ rmarkdown-0.7/rmarkdown/R/output_format.R | 15 ++ rmarkdown-0.7/rmarkdown/R/pandoc.R | 5 rmarkdown-0.7/rmarkdown/R/pdf_document.R | 57 ++++++++-- rmarkdown-0.7/rmarkdown/R/render.R | 46 ++++++-- rmarkdown-0.7/rmarkdown/inst/rmarkdown/templates/html_vignette/skeleton/skeleton.Rmd | 2 rmarkdown-0.7/rmarkdown/inst/rmd/latex/default-1.14.tex |only rmarkdown-0.7/rmarkdown/man/beamer_presentation.Rd | 7 - rmarkdown-0.7/rmarkdown/man/html_fragment.Rd | 17 +- rmarkdown-0.7/rmarkdown/man/output_format.Rd | 12 +- rmarkdown-0.7/rmarkdown/tests/testthat/resources/empty.bib |only rmarkdown-0.7/rmarkdown/tests/testthat/resources/empty.csl |only rmarkdown-0.7/rmarkdown/tests/testthat/resources/pdf.Rmd |only rmarkdown-0.7/rmarkdown/tests/testthat/resources/period.Rmd |only rmarkdown-0.7/rmarkdown/tests/testthat/test-resources.R | 33 +++++ 23 files changed, 320 insertions(+), 64 deletions(-)
Title: Tools for Polyploid Microsatellite Analysis
Description: A collection of tools to handle microsatellite data of
any ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes. It can import and export data in
ABI GeneMapper, Structure, ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi,
POPDIST, STRand, and binary presence/absence formats. It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account. These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R. Allelic diversity
statistics are also available. polysat can assist the user in estimating the
ploidy of samples, and it can estimate allele frequencies in
populations, calculate pairwise Fst values based on those frequencies, and
export allele frequencies to SPAGeDi and adegenet. Functions are also
included for assigning alleles to isoloci in cases where one pair of
microsatellite primers amplifies alleles from two or more independently
segregating isoloci.
Author: Lindsay V. Clark [aut, cre]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Diff between polysat versions 1.3-3 dated 2014-09-22 and 1.4-0 dated 2015-06-13
DESCRIPTION | 24 +++-- MD5 | 49 ++++++---- NAMESPACE | 3 NEWS | 22 ++++ R/allopolyploidy.R |only R/dataimport.R | 6 + R/individual_distance.R | 36 ++----- build/vignette.rds |binary data/AllopolyTutorialData.RData |only data/FCRinfo.txt.gz |binary inst/CITATION | 19 ++-- inst/doc/allopolyVignette.R |only inst/doc/allopolyVignette.Rnw |only inst/doc/allopolyVignette.pdf |only inst/doc/polysattutorial.Rnw | 96 ++++++++++++--------- inst/doc/polysattutorial.pdf |binary man/AllopolyTutorialData.Rd |only man/FCRinfo.Rd | 6 + man/alleleCorrelations.Rd |only man/catalanAlleles.Rd |only man/mergeAlleleAssignments.Rd |only man/read.GeneMapper.Rd | 2 man/read.SPAGeDi.Rd | 2 man/recodeAllopoly.Rd |only man/simAllopoly.Rd |only man/testgenotypes.Rd | 6 + man/write.GeneMapper.Rd | 2 man/write.SPAGeDi.Rd | 2 man/write.freq.SPAGeDi.Rd | 2 vignettes/allopolyVignette.Rnw |only vignettes/polysattutorial.Rnw | 96 ++++++++++++--------- vignettes/vignettebuild/AllopolyTutorialDist.RData |only 32 files changed, 233 insertions(+), 140 deletions(-)
Title: Create Simple Packages Which Do not Upset R Package Checks
Description: Provides a function kitten() which creates cute little
packages which pass R package checks. This sets it apart from
package.skeleton() which it calls, and which leaves imperfect files
behind. As this is not exactly helpful for beginners, kitten() offers
an alternative.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between pkgKitten versions 0.1.2 dated 2014-09-11 and 0.1.3 dated 2015-06-13
ChangeLog | 30 ++++++++++++++++++++++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 1 + R/pkgKitten.R | 37 ++++++++++++++++++++++++++----------- README.md | 4 ++-- inst/NEWS.Rd | 15 +++++++++++++-- man/kitten.Rd | 18 ++++++++++-------- man/playWithPerPackageHelpPage.Rd | 3 ++- 9 files changed, 99 insertions(+), 38 deletions(-)
Title: Using R to Install Stuff (Such As: R, Rtools, RStudio, Git, and
More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.15.17 dated 2015-06-03 and 0.16.0 dated 2015-06-13
ChangeLog | 53 +++++++ DESCRIPTION | 11 - MD5 | 186 +++++++++++++-------------- NAMESPACE | 2 NEWS | 12 + R/install.R | 12 + R/updateR.R | 22 ++- R/zzz.R | 3 README.md | 4 man/R_version_in_a_folder.Rd | 20 +- man/add.installr.GUI.Rd | 8 - man/add_load_installr_on_startup_menu.Rd | 5 man/add_remove_installr_from_startup_menu.Rd | 5 man/add_to_.First_in_Rprofile.site.Rd | 16 +- man/ask.user.for.a.row.Rd | 34 +--- man/ask.user.yn.question.Rd | 18 -- man/barplot_package_users_per_day.Rd | 30 +--- man/browse.latest.R.NEWS.Rd | 11 - man/check.for.updates.R.Rd | 25 +-- man/check.integer.Rd | 10 - man/checkMD5sums2.Rd | 23 +-- man/copy.packages.between.libraries.Rd | 47 ++---- man/cranometer.Rd | 50 +++---- man/create.global.library.Rd | 10 - man/download_RStudio_CRAN_data.Rd | 50 ++----- man/fetch_tag_from_Rd.Rd | 18 +- man/file.name.from.url.Rd | 15 -- man/format_RStudio_CRAN_data.Rd | 18 +- man/freegeoip.Rd | 21 +-- man/get.installed.R.folders.Rd | 27 +-- man/get_Rscript_PID.Rd | 15 -- man/get_pid.Rd | 25 +-- man/get_tasklist.Rd | 15 -- man/install.7zip.Rd | 47 +++--- man/install.CMake.Rd | 26 +-- man/install.Cygwin.Rd | 18 +- man/install.FFmpeg.Rd | 29 +--- man/install.GitHub.Rd | 20 +- man/install.GraphicsMagick.Rd | 26 +-- man/install.ImageMagick.Rd | 26 +-- man/install.LaTeX2RTF.Rd | 24 +-- man/install.LyX.Rd | 37 +---- man/install.MikTeX.Rd | 29 +--- man/install.R.Rd | 39 +---- man/install.RStudio.Rd | 20 +- man/install.Rdevel.Rd | 17 +- man/install.Rtools.Rd | 46 +----- man/install.SWFTools.Rd | 27 +-- man/install.Texmaker.Rd | 22 +-- man/install.URL.Rd | 38 +---- man/install.git.Rd | 18 +- man/install.notepadpp.Rd | 32 +--- man/install.npptor.Rd | 31 +--- man/install.packages.zip.Rd | 27 +-- man/install.pandoc.Rd | 30 +--- man/installr.Rd | 26 +-- man/is.RStudio.Rd | 13 - man/is.Rgui.Rd | 13 - man/is.empty.Rd | 15 +- man/is.exe.installed.Rd | 10 - man/is.windows.Rd | 17 -- man/is_in_.First_in_Rprofile.site.Rd | 10 - man/kill_all_Rscript_s.Rd | 31 +--- man/kill_pid.Rd | 31 +--- man/kill_process.Rd | 34 ++-- man/lineplot_package_downloads.Rd | 25 +-- man/load_installr_on_startup.Rd | 5 man/most_downloaded_packages.Rd | 19 +- man/myip.Rd | 8 - man/os.hibernate.Rd | 29 +--- man/os.lock.Rd | 25 +-- man/os.manage.Rd | 29 +--- man/os.restart.Rd | 25 +-- man/os.shutdown.Rd | 36 +---- man/os.sleep.Rd | 32 +--- man/package_authors.Rd | 33 ++-- man/pkgDNLs_worldmapcolor.Rd | 24 +-- man/read_RStudio_CRAN_data.Rd | 38 ++--- man/remove.installr.GUI.Rd | 5 man/remove_from_.First_in_Rprofile.site.Rd | 16 +- man/rename_r_to_R.Rd | 32 ++-- man/require2.Rd | 20 -- man/restart_RGui.Rd | 4 man/rm_installr_from_startup.Rd | 5 man/source.https.Rd | 28 +--- man/system.PATH.Rd | 8 - man/turn.number.version.Rd | 9 - man/turn.version.to.number.Rd | 9 - man/turn.version.to.number1.Rd | 8 - man/uninstall.R.Rd | 20 +- man/uninstall.packages.Rd | 23 +-- man/up_folder.Rd | 12 - man/updateR.Rd | 132 +++++-------------- man/xlsx2csv.Rd | 15 -- 94 files changed, 921 insertions(+), 1403 deletions(-)
Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymized data the user often encounters heaped data, i.e. data which are rounded (to a possibly different
degree of coarseness). While this is mostly a minor problem in parametric density estimation the bias can be very large
for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional
parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods. Varying rounding probabilities (depending on the true value) and asymmetric rounding is estimable as well. Additionally, bivariate non-parametric density estimation for rounded data is supported.
Author: Marcus Gross
Maintainer: Marcus Gross <marcus.gross@fu-berlin.de>
Diff between Kernelheaping versions 0.5 dated 2015-04-27 and 0.9 dated 2015-06-13
Kernelheaping-0.5/Kernelheaping/data/students.R |only Kernelheaping-0.5/Kernelheaping/man/Rprx.Rd |only Kernelheaping-0.9/Kernelheaping/DESCRIPTION | 19 Kernelheaping-0.9/Kernelheaping/MD5 | 31 - Kernelheaping-0.9/Kernelheaping/NAMESPACE | 8 Kernelheaping-0.9/Kernelheaping/R/Kernelheaping.R | 17 Kernelheaping-0.9/Kernelheaping/R/functions.R | 303 ++++++++-- Kernelheaping-0.9/Kernelheaping/data/students.rda |only Kernelheaping-0.9/Kernelheaping/man/Kernelheaping.Rd | 17 Kernelheaping-0.9/Kernelheaping/man/createSim.Kernelheaping.Rd | 2 Kernelheaping-0.9/Kernelheaping/man/dbivr.Rd |only Kernelheaping-0.9/Kernelheaping/man/dheaping.Rd | 9 Kernelheaping-0.9/Kernelheaping/man/plot.Kernelheaping.Rd | 2 Kernelheaping-0.9/Kernelheaping/man/plot.bivrounding.Rd |only Kernelheaping-0.9/Kernelheaping/man/sim.Kernelheaping.Rd | 4 Kernelheaping-0.9/Kernelheaping/man/simSummary.Kernelheaping.Rd | 2 Kernelheaping-0.9/Kernelheaping/man/students.Rd | 2 Kernelheaping-0.9/Kernelheaping/man/summary.Kernelheaping.Rd | 2 Kernelheaping-0.9/Kernelheaping/man/tracePlots.Rd | 2 19 files changed, 320 insertions(+), 100 deletions(-)