Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currently it works with GFS, MeteoGalicia, NAM, and RAP.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>
Diff between meteoForecast versions 0.52 dated 2018-04-04 and 0.53 dated 2018-11-19
DESCRIPTION | 7 +++---- MD5 | 12 ++++++------ R/composeURL.R | 10 ++++++---- man/getPoint.Rd | 2 +- man/getRaster.Rd | 14 +++++++------- man/meteo-package.Rd | 7 +++---- man/vars.Rd | 6 +++--- 7 files changed, 29 insertions(+), 29 deletions(-)
Title: Google Citation Parser
Description: Scrapes Google Citation pages and creates data frames of
citations over time.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between gcite versions 0.9.2 dated 2018-02-02 and 0.9.3 dated 2018-11-19
DESCRIPTION | 19 ++++++++++++------- MD5 | 18 +++++++++--------- NEWS.md | 7 ++++++- R/gcite_citation_page.R | 7 +++++++ README.md | 17 ++++++++++++----- man/gcite.Rd | 3 ++- man/gcite_author_info.Rd | 4 ++-- man/gcite_citation_page.Rd | 18 ++++++++++-------- man/gcite_paper_df.Rd | 3 ++- man/gcite_username.Rd | 3 ++- 10 files changed, 64 insertions(+), 35 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis.
This includes meta-analysis, (robust) prior derivation
from historical data, operating characteristics
and analysis (1 and 2 sample cases).
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Trustees of Columbia University [cph] (src/init.cpp, tools/make_cc.R,
R/stanmodels.R, src/Makevars, src/Makevars.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.3-6 dated 2018-11-15 and 1.3-7 dated 2018-11-19
DESCRIPTION | 11 ++++---- MD5 | 36 +++++++++++++++-------------- NAMESPACE | 8 +++--- R/RBesT-package.R | 3 +- R/mixbeta.R | 2 + R/mixgamma.R | 2 + R/mixnorm.R | 1 inst/NEWS | 4 +++ inst/doc/PoS_codata.html | 41 ++++++++++++++++----------------- inst/doc/PoS_interim.html | 40 ++++++++++++++++---------------- inst/doc/RBesT.pdf |binary inst/doc/customizing_plots.html | 46 ++++++++++++++++++------------------- inst/doc/introduction.html | 46 ++++++++++++++++++------------------- inst/doc/introduction_normal.html | 46 ++++++++++++++++++------------------- inst/doc/robustMAP.html | 47 +++++++++++++++++++------------------- inst/doc/variances_MAP.html | 47 +++++++++++++++++++------------------- src/Makevars | 2 - src/Makevars.win | 2 - tools/build.sh |only tools/build_ref_pdf.sh |only 20 files changed, 200 insertions(+), 184 deletions(-)
Title: Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids
Description: Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids. The genotype
probabilities, or genotypes sampled from those probabilties, can then be exported
for downstream analysis. 'polyRAD' is described by Clark et al. (2018)
<doi:10.1101/380899>.
Author: Lindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>),
U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Diff between polyRAD versions 0.5-0 dated 2018-08-02 and 1.0 dated 2018-11-19
polyRAD-0.5-0/polyRAD/src/AlleleProbExp.cpp |only polyRAD-1.0/polyRAD/DESCRIPTION | 10 polyRAD-1.0/polyRAD/MD5 | 62 - polyRAD-1.0/polyRAD/NAMESPACE | 15 polyRAD-1.0/polyRAD/NEWS |only polyRAD-1.0/polyRAD/R/RcppExports.R | 8 polyRAD-1.0/polyRAD/R/calculations.R | 7 polyRAD-1.0/polyRAD/R/classes_methods.R | 200 ++++- polyRAD-1.0/polyRAD/R/data_export.R | 21 polyRAD-1.0/polyRAD/R/data_import.R | 159 ++++ polyRAD-1.0/polyRAD/R/overdispersion.R |only polyRAD-1.0/polyRAD/R/pipelines.R | 29 polyRAD-1.0/polyRAD/data/Msi01genes.RData |binary polyRAD-1.0/polyRAD/data/exampleRAD.RData |binary polyRAD-1.0/polyRAD/data/exampleRAD_mapping.RData |binary polyRAD-1.0/polyRAD/inst/doc/polyRADtutorial.R | 58 + polyRAD-1.0/polyRAD/inst/doc/polyRADtutorial.Rmd | 127 ++- polyRAD-1.0/polyRAD/inst/doc/polyRADtutorial.html | 574 +++++++-------- polyRAD-1.0/polyRAD/inst/extdata/exampleTASSEL_SAM.txt |only polyRAD-1.0/polyRAD/inst/extdata/example_TagTaxaDist.txt |only polyRAD-1.0/polyRAD/man/AddGenotypeLikelihood.Rd | 22 polyRAD-1.0/polyRAD/man/AddGenotypePriorProb_Even.Rd |only polyRAD-1.0/polyRAD/man/ExportGAPIT.Rd | 39 - polyRAD-1.0/polyRAD/man/GetWeightedMeanGenotypes.Rd | 5 polyRAD-1.0/polyRAD/man/IterateHWE.Rd | 18 polyRAD-1.0/polyRAD/man/PipelineMapping2Parents.Rd | 14 polyRAD-1.0/polyRAD/man/RADdata.Rd | 11 polyRAD-1.0/polyRAD/man/SubsetByLocus.Rd | 33 polyRAD-1.0/polyRAD/man/TestOverdispersion.Rd |only polyRAD-1.0/polyRAD/man/VCF2RADdata.Rd | 2 polyRAD-1.0/polyRAD/man/readHMC.Rd | 3 polyRAD-1.0/polyRAD/man/readStacks.Rd | 2 polyRAD-1.0/polyRAD/man/readTASSELGBSv2.Rd |only polyRAD-1.0/polyRAD/man/readTagDigger.Rd | 3 polyRAD-1.0/polyRAD/src/RcppExports.cpp | 21 polyRAD-1.0/polyRAD/vignettes/polyRADtutorial.Rmd | 127 ++- 36 files changed, 1067 insertions(+), 503 deletions(-)
More information about LindleyPowerSeries at CRAN
Permanent link
Title: Elementary Epidemiological Functions for Epidemiology and
Biostatistics
Description: Contains elementary tools for analysis of
common epidemiological problems, ranging from sample size
estimation, through 2x2 contingency table analysis and basic
measures of agreement (kappa, sensitivity/specificity).
Appropriate print and summary statements are also written to
facilitate interpretation wherever possible. Source code is commented throughout to facilitate modification. The target audience includes advanced undergraduate and graduate students
in epidemiology or biostatistics courses, and clinical researchers.
Author: Michael A Rotondi <mrotondi@yorku.ca>
Maintainer: Michael A Rotondi <mrotondi@yorku.ca>
Diff between epibasix versions 1.3 dated 2012-11-15 and 1.5 dated 2018-11-19
DESCRIPTION | 18 ++++++++---------- MD5 | 26 +++++++++++++------------- NAMESPACE | 26 ++++++++++++++++++++++++++ R/epi2x2.R | 4 ++-- man/corXY.Rd | 2 +- man/diffDetect.Rd | 2 +- man/epi2x2.Rd | 2 +- man/epiKappa.Rd | 2 +- man/epiTTest.Rd | 2 +- man/mcNemar.Rd | 2 +- man/n4means.Rd | 2 +- man/n4props.Rd | 6 ++++-- man/sensSpec.Rd | 2 +- man/univar.Rd | 2 +- 14 files changed, 62 insertions(+), 36 deletions(-)
Title: Mixed-Effect Models, Particularly Spatial Models
Description: Inference based on mixed-effect models, including generalized linear mixed models with spatial correlations and models with non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a generalized linear mixed model. Various approximations of likelihood or restricted likelihood are implemented, in particular h-likelihood (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) and Laplace approximation.
Author: François Rousset [aut, cre, cph]
(<https://orcid.org/0000-0003-4670-0371>),
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut] (<https://orcid.org/0000-0003-0637-2959>),
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 2.5.0 dated 2018-09-28 and 2.5.11 dated 2018-11-19
DESCRIPTION | 8 MD5 | 96 +++++------ NAMESPACE | 5 R/GLM.fit.R | 4 R/HLCor_body.R | 25 ++ R/HLFactorList.R | 2 R/HLfit_Internals.R | 82 +++------ R/HLfit_body.R | 8 R/HLframes.R | 138 ++++++++++------ R/MakeCovEst.R | 2 R/Matern_family.R | 3 R/bloc_lambda.R | 10 - R/calc_LRT.R | 4 R/corrHLfit-internals.R | 2 R/corrHLfit_body.R | 6 R/corrMM.LRT.R | 4 R/corrPars.R | 9 - R/correlationFns.R | 14 + R/cov_new_fix.R | 32 ++- R/dispGammaGLM.R | 19 -- R/extractors.R | 119 ++++++++++++-- R/fitme_body.R | 41 +++- R/fitmecorrHLfit_body_internals.R | 8 R/geo_info.R | 5 R/locoptim.R | 19 +- R/merge_parlist.R | 2 R/predict.R | 39 ++-- R/predictor.R | 7 R/preprocess.R | 52 +++--- R/save.R | 10 - R/spaMM.data.R | 2 R/spaMM_boot.R | 8 R/spaMM_error.R | 21 +- R/step_HLfit.R | 4 R/summary.HL.R | 322 ++++++++++++++++++++------------------ R/update.HL.R | 4 R/utils.R | 9 - build/partial.rdb |binary inst/NEWS.Rd | 28 +++ man/HLfit.Rd | 13 - man/corr_family.Rd | 2 man/extractors.Rd | 27 +-- man/fixed.Rd | 4 man/get_matrix.Rd |only man/get_ranPars.Rd | 16 + man/spaMM-internal.Rd | 2 man/spaMM_boot.Rd | 2 man/vcov.Rd |only tests/testthat/test-CAR.R | 2 tests/testthat/test-predVar.R | 20 ++ 50 files changed, 772 insertions(+), 489 deletions(-)
Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
Description: Provides automated downloading, parsing, cleaning, unit conversion
and formatting of Global Surface Summary of the Day ('GSOD') weather data
from the from the USA National Centers for Environmental Information
('NCEI') for use in R. Units are converted from from United States
Customary System ('USCS') units to International System of Units ('SI').
Stations may be individually checked for number of missing days defined by
the user, where stations with too many missing observations are omitted.
Only stations with valid reported latitude and longitude values are
permitted in the final data. Additional useful elements, saturation vapour
pressure ('es'), actual vapour pressure ('ea') and relative humidity are
calculated from the original data and included in the final data set. The
resulting data include station identification information, state, country,
latitude, longitude, elevation, weather observations and associated flags.
Additional data are included with this R package: a list of elevation values
for stations between -60 and 60 degrees latitude derived from the Shuttle
Radar Topography Measuring Mission ('SRTM'). For information on the 'GSOD'
data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from,
<http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Tomislav Hengl [aut] (<https://orcid.org/0000-0002-9921-5129>),
Andrew Nelson [aut] (<https://orcid.org/0000-0002-7249-3778>),
Hugh Parsonage [cph, ctb] (<https://orcid.org/0000-0003-4055-0835>),
Bob Rudis [cph, ctb] (<https://orcid.org/0000-0001-5670-2640>),
Gwenael Giboire [ctb] (Several bug reports in early versions and
testing feedback),
Łukasz Pawlik [ctb] (Reported bug in windspeed conversion calculation),
Ross Darnell [ctb] (Reported bug in 'Windows OS' versions causing
'GSOD' data untarring to fail)
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between GSODR versions 1.2.3 dated 2018-10-11 and 1.3.0 dated 2018-11-19
DESCRIPTION | 14 - MD5 | 34 +- NEWS.md | 9 R/get_GSOD.R | 62 +++-- R/get_inventory.R | 2 R/internal_functions.R | 15 + R/reformat_GSOD.R | 18 - README.md | 70 +++--- build/vignette.rds |binary inst/doc/GSODR.R | 4 inst/doc/GSODR.Rmd | 17 + inst/doc/GSODR.html | 473 ++++++++++++++++++++--------------------- inst/extdata/country_list.rda |binary inst/extdata/isd_history.rda |binary man/get_GSOD.Rd | 29 ++ man/reformat_GSOD.Rd | 13 - tests/testthat/test-get_GSOD.R | 2 vignettes/GSODR.Rmd | 17 + 18 files changed, 436 insertions(+), 343 deletions(-)
Title: Scopus Database 'API' Interface
Description: Uses Elsevier 'Scopus' API
<https://dev.elsevier.com/sc_apis.html> to download
information about authors and their citations.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between rscopus versions 0.6.1 dated 2018-10-22 and 0.6.3 dated 2018-11-19
DESCRIPTION | 8 +-- MD5 | 12 ++--- NAMESPACE | 1 NEWS.md | 5 ++ R/author_df.R | 3 + R/citation_retrieval.R | 107 +++++++++++++++++++++++++++++++++++++++------- man/citation_retrieval.Rd | 23 ++++++++- 7 files changed, 131 insertions(+), 28 deletions(-)
Title: R Client for the Microsoft Cognitive Services 'Text-to-Speech'
REST API
Description: R Client for the Microsoft Cognitive Services
'Text-to-Speech' REST API, including voice synthesis. A valid account
must be registered at the Microsoft Cognitive Services website
<https://www.microsoft.com/cognitive-services/> in order to
obtain a (free) API key. Without an API key, this package will not
work properly.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between mscstts versions 0.3.0 dated 2018-08-16 and 0.4.0 dated 2018-11-19
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 2 ++ NEWS.md | 6 +++++- R/ms_synthesize.R | 35 +++++++++++++++++++++++++---------- R/show.token.R | 6 ++++++ man/ms_synthesize.Rd | 9 ++++++++- man/print.token.Rd | 3 +++ 8 files changed, 59 insertions(+), 22 deletions(-)
Title: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from
Functional MRI of the Brain ('FMRIB')
Description: Wrapper functions that interface with 'FSL'
<http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging'
software, using system commands. The goal is to be able to interface with 'FSL'
completely in R, where you pass R objects of class 'nifti', implemented by
package 'oro.nifti', and the function executes an 'FSL' command and returns an R
object of class 'nifti' if desired.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between fslr versions 2.17.3 dated 2018-02-02 and 2.22.0 dated 2018-11-19
DESCRIPTION | 18 +++---- MD5 | 107 +++++++++++++++++++++++++--------------------- NAMESPACE | 25 ++++++++++ NEWS.md | 12 +++++ R/applytopup.R |only R/enforce_form.R |only R/fast.R | 73 +++++++++++++++++++++++++++---- R/fsl_cluster.R |only R/fsl_read_xfm.R |only R/fsl_resample.R |only R/fsl_smoothest.R |only R/fslfill2.R | 34 +++++++------- R/fslhd.R | 33 ++++++++++++-- R/fslrandn.R | 2 R/fslview.R | 52 +++++++++++++++++++++- R/mid_sagittal_align.R | 10 ++-- R/probtrackx.R | 2 R/rpi_orient.R | 81 ++++++++++++++++++++++++---------- R/topup.R | 6 ++ R/zzz.R |only build/vignette.rds |binary inst/doc/dti_data.Rmd | 2 inst/doc/dti_data.html | 66 +++++++++++++--------------- inst/doc/fslr.html | 30 ++++++------ man/applytopup.Rd |only man/dtifit.Rd | 6 +- man/eddy_correct.Rd | 3 - man/enforce_form.Rd |only man/fast.Rd | 21 ++++++++- man/fnirt.Rd | 4 - man/fnirt_with_affine.Rd | 7 +-- man/fsl_biascorrect.Rd | 5 +- man/fsl_cluster.Rd |only man/fsl_resample.Rd |only man/fsl_smoothest.Rd |only man/fslbet.Rd | 4 - man/fslchfiletype.Rd | 5 +- man/fslcmd.Rd | 7 ++- man/fsldilate.Rd | 3 - man/fsldir.Rd | 1 man/fslepi_reg.Rd | 8 ++- man/fslmerge.Rd | 5 +- man/fslrandn.Rd | 2 man/fslreorient2std.Rd | 4 - man/fslrobustfov.Rd | 5 +- man/fslroi.Rd | 7 +-- man/fslslicetimer.Rd | 8 ++- man/fslsmooth.Rd | 7 +-- man/fslsplit.Rd | 5 +- man/fslswapdim.Rd | 3 - man/fslthresh.Rd | 3 - man/fslview.Rd | 7 +++ man/fslview.help.Rd | 1 man/get.fsloutput.Rd | 2 man/probtrackx.Rd | 28 ++++++------ man/read_xfm.Rd |only man/reverse_rpi_orient.Rd | 4 - man/rpi_orient.Rd | 6 ++ man/topup.Rd | 11 ++-- man/xfibres.Rd | 9 ++- vignettes/dti_data.Rmd | 2 61 files changed, 508 insertions(+), 238 deletions(-)
Title: Time Series Analysis and Computational Finance
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre],
Blake LeBaron [ctb] (BDS test code)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tseries versions 0.10-45 dated 2018-06-04 and 0.10-46 dated 2018-11-19
ChangeLog | 11 +++++++++++ DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- R/test.R | 4 ++-- README | 6 +++--- data/NelPlo.rda |binary data/USeconomic.rda |binary data/bev.rda |binary data/camp.rda |binary data/ice.river.rda |binary data/nino.rda |binary data/tcm.rda |binary data/tcmd.rda |binary man/kpss.test.Rd | 4 ++-- 14 files changed, 34 insertions(+), 23 deletions(-)
Title: Simulating the Evolution of Biological Sequences
Description: A coalescent simulator that allows the rapid simulation of
biological sequences under neutral models of evolution. Different to other
coalescent based simulations, it has an optional approximation parameter that
allows for high accuracy while maintaining a linear run time cost for long
sequences. It is optimized for simulating massive data sets as produced by Next-
Generation Sequencing technologies for up to several thousand sequences.
Author: Paul Staab [aut, cre, cph],
Zhu Sha [aut, cph],
Dirk Metzler [aut, cph, ths],
Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between scrm versions 1.7.2-4 dated 2018-06-30 and 1.7.3-1 dated 2018-11-19
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 14 ++++++++++++++ README.md | 7 +------ build/vignette.rds |binary inst/doc/scrm-Arguments.Rmd | 9 ++++++--- inst/doc/scrm-Arguments.html | 12 +++++++----- inst/doc/scrm-TreesForApe.html | 4 ++-- src/scrm/forest.cc | 40 +++++++++++++++------------------------- src/scrm/model.cc | 26 ++++++++++++-------------- src/scrm/model.h | 18 +++++++++++------- src/scrm/param.cc | 18 ++++++++++++++++-- vignettes/scrm-Arguments.Rmd | 9 ++++++--- 13 files changed, 106 insertions(+), 83 deletions(-)
Title: A 'ggplot2'-Plot of Composition of Solvency II SCR: SF and IM
Description: An implementation of 'ggplot2'-methods to present the composition of Solvency II Solvency Capital Requirement (SCR) as a series of concentric circle-parts.
Solvency II (Solvency 2) is European insurance legislation, coming in force by the delegated acts of October 10, 2014.
<https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=OJ%3AL%3A2015%3A012%3ATOC>.
Additional files, defining the structure of the Standard Formula (SF) method of the SCR-calculation are provided.
The structure files can be adopted for localization or for insurance companies who use Internal Models (IM).
Options are available for combining smaller components, horizontal and vertical scaling, rotation, and plotting only some circle-parts.
With outlines and connectors several SCR-compositions can be compared, for example in ORSA-scenarios (Own Risk and Solvency Assessment).
Author: Marco van Zanden [aut, cre]
Maintainer: Marco van Zanden <git@vanzanden.nl>
Diff between ggsolvencyii versions 0.1.0 dated 2018-10-28 and 0.1.1 dated 2018-11-19
ggsolvencyii-0.1.0/ggsolvencyii/inst/doc/geom_sii_riskconnection.R |only ggsolvencyii-0.1.0/ggsolvencyii/inst/doc/geom_sii_riskconnection.Rmd |only ggsolvencyii-0.1.0/ggsolvencyii/inst/doc/geom_sii_riskconnection.html |only ggsolvencyii-0.1.0/ggsolvencyii/inst/doc/geom_sii_riskoutline.R |only ggsolvencyii-0.1.0/ggsolvencyii/inst/doc/geom_sii_riskoutline.Rmd |only ggsolvencyii-0.1.0/ggsolvencyii/inst/doc/geom_sii_riskoutline.html |only ggsolvencyii-0.1.0/ggsolvencyii/inst/doc/geom_sii_risksurface.R |only ggsolvencyii-0.1.0/ggsolvencyii/inst/doc/geom_sii_risksurface.Rmd |only ggsolvencyii-0.1.0/ggsolvencyii/inst/doc/geom_sii_risksurface.html |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_add_ind_show.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_circlepoints.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_computegroup.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_constructionplotdetails.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_cornerpoints.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_determinelevels.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_geomsiidatatopoints.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_levelonedescription.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_maxscrvalue.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_polygonpoints.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_rotation.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_setupdata_connection.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_setupdata_outline.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_setupdata_surfaces.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_sqXP.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_sqYP.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_sqdegseq.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_squareconversion.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_squareddegrees.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_squarepoints.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_structure_data_integration.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_structure_expansion.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/fn_transform_plotdetails.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/man/sii_debug.Rd |only ggsolvencyii-0.1.0/ggsolvencyii/vignettes/geom_sii_riskconnection.Rmd |only ggsolvencyii-0.1.0/ggsolvencyii/vignettes/geom_sii_riskoutline.Rmd |only ggsolvencyii-0.1.0/ggsolvencyii/vignettes/geom_sii_risksurface.Rmd |only ggsolvencyii-0.1.1/ggsolvencyii/DESCRIPTION | 12 ggsolvencyii-0.1.1/ggsolvencyii/MD5 | 155 ++-- ggsolvencyii-0.1.1/ggsolvencyii/NAMESPACE | 7 ggsolvencyii-0.1.1/ggsolvencyii/NEWS.md | 23 ggsolvencyii-0.1.1/ggsolvencyii/R/101_geomandstat.R | 82 +- ggsolvencyii-0.1.1/ggsolvencyii/R/111_setupparams.R | 93 +- ggsolvencyii-0.1.1/ggsolvencyii/R/121_setupdata_risksurface.R | 119 +-- ggsolvencyii-0.1.1/ggsolvencyii/R/122_setupdata_riskoutline.R | 23 ggsolvencyii-0.1.1/ggsolvencyii/R/123_setupdata_riskconnection.R | 26 ggsolvencyii-0.1.1/ggsolvencyii/R/131_computegroup.R | 101 +- ggsolvencyii-0.1.1/ggsolvencyii/R/136_computegroup_subA.R | 134 ++- ggsolvencyii-0.1.1/ggsolvencyii/R/137_computegroup_subB.R | 126 +-- ggsolvencyii-0.1.1/ggsolvencyii/R/200_ggsolvencyii_debug.R | 20 ggsolvencyii-0.1.1/ggsolvencyii/R/data.R | 20 ggsolvencyii-0.1.1/ggsolvencyii/R/zzz.R | 4 ggsolvencyii-0.1.1/ggsolvencyii/README.md | 53 - 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Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for
quantitative text analysis in R. Provides functionality for corpus management,
creating and manipulating tokens and ngrams, exploring keywords in context,
forming and manipulating sparse matrices
of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and
distances, applying content dictionaries, applying supervised and unsupervised machine learning,
visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph]
(<https://orcid.org/0000-0002-0797-564X>),
Kohei Watanabe [aut] (<https://orcid.org/0000-0001-6519-5265>),
Haiyan Wang [aut] (<https://orcid.org/0000-0003-4992-4311>),
Paul Nulty [aut] (<https://orcid.org/0000-0002-7214-4666>),
Adam Obeng [aut] (<https://orcid.org/0000-0002-2906-4775>),
Stefan Müller [aut] (<https://orcid.org/0000-0002-6315-4125>),
Akitaka Matsuo [aut] (<https://orcid.org/0000-0002-3323-6330>),
Patrick O. Perry [aut] (<https://orcid.org/0000-0001-7460-127X>),
Jouni Kuha [aut] (<https://orcid.org/0000-0002-1156-8465>),
Benjamin Lauderdale [aut] (<https://orcid.org/0000-0003-3090-0969>),
William Lowe [aut] (<https://orcid.org/0000-0002-1549-6163>),
Christian Müller [ctb],
Lori Young [dtc] (Lexicoder Sentiment Dictionary 2015),
Stuart Soroka [dtc] (Lexicoder Sentiment Dictionary 2015),
Ian Fellows [cph] (authored wordcloud C source code (modified)),
European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 1.3.13 dated 2018-11-01 and 1.3.14 dated 2018-11-19
DESCRIPTION | 8 - MD5 | 49 ++++--- NEWS.md | 12 + R/dfm-print.R | 49 +++++++ R/textstat_keyness.R | 9 + R/textstat_lexdiv.R | 111 +++++++++++------ R/textstat_simil.R | 51 ++++++-- R/textstat_simil_old.R | 27 ---- inst/doc/quickstart.R | 6 inst/doc/quickstart.Rmd | 6 inst/doc/quickstart.html | 191 ++++++++++++++---------------- man/as.matrix.simil.Rd | 17 +- man/format_sparsity.Rd |only man/quanteda-package.Rd | 2 man/textstat_lexdiv.Rd | 73 ++++++----- man/textstat_proxy.Rd | 4 man/textstat_simil.Rd | 10 - tests/cheatsheet/quanteda-cheatsheet.pdf |binary tests/cheatsheet/quanteda-cheatsheet.pptx |binary tests/data/corpora/needles_eye_ch3.txt |only tests/data/corpora/stjohn_latin.csv |only tests/testthat/test-dfm.R | 30 ++++ tests/testthat/test-textstat_keyness.R | 48 +++++++ tests/testthat/test-textstat_lexdiv.R | 73 +++++++++++ tests/testthat/test-textstat_proxy.R | 11 - tests/testthat/test-textstat_simil.R | 27 ++++ vignettes/quickstart.Rmd | 6 27 files changed, 565 insertions(+), 255 deletions(-)
Title: R Interface to 'TensorFlow'
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>,
an open source software library for numerical computation using data
flow graphs. Nodes in the graph represent mathematical operations,
while the graph edges represent the multidimensional data arrays
(tensors) communicated between them. The flexible architecture allows
you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop,
server, or mobile device with a single 'API'. 'TensorFlow' was originally
developed by researchers and engineers working on the Google Brain Team
within Google's Machine Intelligence research organization for the
purposes of conducting machine learning and deep neural networks research,
but the system is general enough to be applicable in a wide variety
of other domains as well.
Author: JJ Allaire [aut, cre],
RStudio [cph, fnd],
Yuan Tang [aut, cph] (<https://orcid.org/0000-0001-5243-233X>),
Dirk Eddelbuettel [ctb, cph],
Nick Golding [ctb, cph],
Tomasz Kalinowski [ctb, cph],
Google Inc. [ctb, cph] (Examples and Tutorials)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between tensorflow versions 1.9 dated 2018-08-07 and 1.10 dated 2018-11-19
DESCRIPTION | 8 +++--- MD5 | 17 +++++++------- NAMESPACE | 5 ++++ R/generics.R | 39 +++++++++++++++++++++++++++++++--- R/install.R | 9 ++++++- man/install_tensorflow.Rd | 3 +- man/reexports.Rd | 15 ------------- man/tensorboard.Rd | 4 +-- man/use_session_with_seed.Rd | 4 +-- tests/testthat/test-generic-methods.R |only 10 files changed, 68 insertions(+), 36 deletions(-)
Title: Simulation Parameter Analysis R Toolkit ApplicatioN: 'spartan'
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. 'spartan', first described in our 2013 publication in PLoS Computational Biology, provided code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 added support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions. Version 3.0 offers significant additional functionality that permits the creation of emulations of simulation results, derived using the same sampling techniques in the global sensitivity analysis techniques, and the generation of combinations of these machine learning algorithms to one create one predictive tool, more commonly known as an ensemble model. Version 3.0 also improved the standard of the graphs produced in the original sensitivity analysis techniques, and introduced a polar plot to examine parameter sensitivity.
Author: Kieran Alden [cre, aut],
Mark Read [aut],
Paul Andrews [aut],
Jason Cosgrove [aut],
Mark Coles [aut],
Jon Timmis [aut]
Maintainer: Kieran Alden <kieran.alden@gmail.com>
Diff between spartan versions 3.0.1 dated 2018-05-16 and 3.0.2 dated 2018-11-19
DESCRIPTION | 8 MD5 | 500 +-- NAMESPACE | 184 - NEWS.md | 48 R/abc_utilities.R | 56 R/efast_analysis.R | 150 + R/efast_plotting.R | 70 R/efast_sampling.R | 27 R/efast_utilities.R | 2 R/emulation_generation.R | 37 R/emulation_plotting.R | 34 R/emulation_sensitivity_analysis.R | 124 R/emulation_utilities.R | 88 R/ensemble_generation.R | 44 R/ensemble_utilities.R | 42 R/lhc_analysis.R | 94 R/lhc_plotting.R | 241 + R/lhc_prcc_utilities.R | 2 R/lhc_sampling.R | 14 R/method_argument_check.R | 32 R/netlogo_sampling_utilities.R | 7 R/robustness_analysis.R | 1004 ++++--- R/robustness_plotting.R | 151 - R/robustness_sampling.R | 32 R/spartan_utilities.R | 217 + build/vignette.rds |binary inst/doc/emulation_ensembles.R | 556 ++-- inst/doc/emulation_ensembles.Rmd | 768 ++--- inst/doc/emulation_ensembles.html | 1010 +++---- inst/doc/netlogo.R | 478 +-- inst/doc/netlogo.Rmd | 2 inst/doc/netlogo.html | 950 ++----- inst/doc/sensitivity_analysis.R | 618 ++-- inst/doc/sensitivity_analysis.html | 1310 ++++------ man/a_test_results.Rd | 50 man/aa_getATestResults.Rd | 99 man/aa_getATestResults_overTime.Rd | 74 man/aa_graphATestsForSampleSize.Rd | 54 man/aa_graphSampleSizeSummary.Rd | 88 man/aa_sampleSizeSummary.Rd | 78 man/aa_sampleSizeSummary_overTime.Rd | 65 man/aa_summariseReplicateRuns.Rd | 98 man/aa_summariseReplicateRuns_overTime.Rd | 73 man/add_parameter_value_to_file.Rd | 56 man/analysenetwork_structures.Rd | 68 man/append_time_to_argument.Rd | 42 man/atest.Rd | 34 man/build_curve_results_from_r_object.Rd |only man/build_performance_statistics.Rd | 62 man/calculate_atest_score.Rd | 56 man/calculate_fold_MSE.Rd | 46 man/calculate_medians_for_all_measures.Rd | 48 man/calculate_prcc_for_all_measures.Rd | 60 man/calculate_prccs_all_parameters.Rd | 50 man/calculate_weights_for_ensemble_model.Rd | 59 man/check_acceptable_model_type.Rd | 36 man/check_argument_positive_int.Rd | 38 man/check_boolean.Rd | 38 man/check_column_ranges.Rd | 44 man/check_confidence_interval.Rd | 46 man/check_consistency_result_type.Rd | 42 man/check_double_value_in_range.Rd | 46 man/check_file_exist.Rd | 38 man/check_file_exists.Rd | 34 man/check_file_extension.Rd | 24 man/check_filepath_exists.Rd | 38 man/check_function_dependent_paramvals.Rd | 38 man/check_global_param_sampling_args.Rd | 38 man/check_graph_output_type.Rd | 38 man/check_input_args.Rd | 38 man/check_lengths_parameters_ranges.Rd | 34 man/check_lhs_algorithm.Rd | 38 man/check_list_all_integers.Rd | 38 man/check_nested_filepaths.Rd | 38 man/check_netlogo_parameters_and_values.Rd | 40 man/check_numeric_list_values.Rd | 42 man/check_package_installed.Rd | 34 man/check_parameters_and_ranges.Rd | 44 man/check_paramvals_length_equals_parameter_length.Rd | 36 man/check_robustness_parameter_and_ranges_lengths.Rd | 40 man/check_robustness_paramvals_contains_baseline.Rd | 38 man/check_robustness_range_contains_baseline.Rd | 38 man/check_robustness_range_or_values.Rd | 40 man/check_robustness_sampling_args.Rd | 42 man/check_text.Rd | 38 man/check_text_list.Rd | 38 man/close_and_write_netlogo_file.Rd | 32 man/compare_all_values_of_parameter_to_baseline.Rd | 70 man/construct_result_filename.Rd | 42 man/createAndEvaluateFolds.Rd | 86 man/createTrainingFold.Rd | 56 man/create_abc_settings_object.Rd | 79 man/create_ensemble.Rd | 98 man/create_neural_network.Rd | 64 man/createtest_fold.Rd | 51 man/dataset_precheck.Rd |only man/denormalise_dataset.Rd | 42 man/determine_optimal_neural_network_structure.Rd | 58 man/efast_cvmethod.Rd | 62 man/efast_generate_medians_for_all_parameter_subsets.Rd | 142 - 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man/generate_ensemble_from_existing_emulations.Rd | 112 man/generate_ensemble_training_set.Rd | 68 man/generate_headers_for_atest_file.Rd | 34 man/generate_list_of_checks.Rd | 38 man/generate_medians_for_param_set.Rd | 74 man/generate_model_formula.Rd | 40 man/generate_parameter_table.Rd | 46 man/generate_prcc_results_header.Rd | 34 man/generate_predictions_from_emulator.Rd | 56 man/generate_requested_emulations.Rd | 150 - man/generate_sensitivity_indices.Rd | 62 man/generate_summary_stats_for_all_param_sets.Rd | 80 man/getMediansSubset.Rd | 76 man/get_argument_correct_case.Rd | 42 man/get_correct_file_path_for_function.Rd | 40 man/get_file_and_object_argument_names.Rd | 40 man/get_max_and_median_atest_scores.Rd | 43 man/get_median_results_for_all_measures.Rd | 38 man/get_medians_for_size_subsets.Rd | 65 man/graph_Posteriors_All_Parameters.Rd | 54 man/graph_sample_size_results.Rd | 50 man/import_model_result.Rd | 52 man/initialise_netlogo_xml_file.Rd | 61 man/join_strings.Rd | 40 man/join_strings_nospace.Rd | 36 man/join_strings_space.Rd | 36 man/kfoldCrossValidation.Rd | 62 man/lhc_calculatePRCCForMultipleTimepoints.Rd | 52 man/lhc_constructcoeff_dataset.Rd | 24 man/lhc_generateLHCSummary.Rd | 116 man/lhc_generateLHCSummary_overTime.Rd | 92 man/lhc_generatePRCoEffs.Rd | 103 man/lhc_generatePRCoEffs_db_link.Rd |only man/lhc_generatePRCoEffs_overTime.Rd | 74 man/lhc_generateTimepointFiles.Rd | 58 man/lhc_generate_lhc_sample.Rd | 111 man/lhc_generate_lhc_sample_netlogo.Rd | 76 man/lhc_generate_netlogo_PRCoEffs.Rd | 56 man/lhc_graphMeasuresForParameterChange.Rd | 111 man/lhc_graphMeasuresForParameterChange_from_db.Rd |only man/lhc_graphMeasuresForParameterChange_overTime.Rd | 96 man/lhc_netlogo_graphMeasuresForParameterChange.Rd | 84 man/lhc_plotCoEfficients.Rd | 66 man/lhc_polarplot.Rd | 70 man/lhc_process_netlogo_result.Rd | 74 man/lhc_process_sample_run_subsets.Rd | 160 - 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tests/testthat/test_evolution.R | 157 - tests/testthat/test_input_argument.R | 1059 ++++---- tests/testthat/test_lhc_sampling.R | 4 tests/testthat/test_lhc_sampling_netlogo.R | 91 tests/testthat/test_neural_network_utilities.R | 505 +-- tests/testthat/test_robustness_analysis.R | 73 tests/testthat/test_robustness_sampling.R | 2 tests/testthat/test_spartan_utilities.R | 31 vignettes/emulation_ensembles.Rmd | 768 ++--- vignettes/netlogo.Rmd | 2 254 files changed, 12587 insertions(+), 12363 deletions(-)
Title: Extra Recipes for Encoding Categorical Predictors
Description: Factor predictors can be converted to one or more numeric representations using simple generalized linear models <arXiv:1611.09477> or nonlinear models <arXiv:1604.06737>. All encoding methods are supervised.
Author: Max Kuhn [aut, cre],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between embed versions 0.0.1 dated 2018-09-14 and 0.0.2 dated 2018-11-19
DESCRIPTION | 12 ++--- MD5 | 32 ++++++++------- NAMESPACE | 8 +++ NEWS.md | 11 +++++ R/bayes.R | 44 ++++++++++++--------- R/glm.R | 37 ++++++++++-------- R/lme.R | 40 +++++++++++-------- R/reexports.R |only R/tf.R | 80 ++++++++++++++++++++++----------------- man/reexports.Rd |only man/step_embed.Rd | 38 +++++++++--------- man/step_lencode_bayes.Rd | 9 ++-- man/step_lencode_glm.Rd | 11 ++--- man/step_lencode_mixed.Rd | 8 +-- tests/testthat/test_mixed.R | 18 ++++---- tests/testthat/test_no_pooling.R | 18 ++++---- tests/testthat/test_pooling.R | 19 ++++----- tests/testthat/test_tf.R | 18 ++++---- 18 files changed, 228 insertions(+), 175 deletions(-)
Title: Quantile-Quantile Plot with Several Gaussian Simulations
Description: Plots a QQ-Norm Plot with several Gaussian simulations.
Author: Matthias Salvisberg
Maintainer: Matthias Salvisberg <matthias.salvisberg@gmail.com>
Diff between StMoSim versions 3.1 dated 2018-11-14 and 3.1.1 dated 2018-11-19
DESCRIPTION | 17 +++--- MD5 | 16 ++--- NAMESPACE | 3 - R/StMoSim.R | 15 ++++- R/qqnormSim.R | 147 +++++++++++++++++++++++++++++++++++++++++++++++-------- man/StMoSim.Rd | 15 ++++- man/qqnormSim.Rd | 88 +++++++++++++++++++++++++++++--- src/Makevars | 1 src/Makevars.win | 4 + 9 files changed, 255 insertions(+), 51 deletions(-)
Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analysis functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: OECD <http://www.oecd.org/>, including PISA, TALIS, PIAAC, and IEA <http://www.iea.nl/>, including TIMSS, TIMSS Advanced, PIRLS, ICCS, ICILS, and CivEd.
Author: Paul Bailey [aut, cre], Ren C'deBaca [ctb], Ahmad Emad [aut], Huade Huo [aut], Michael Lee [aut], Yuqi Liao [aut], Alex Lishinski [aut], Trang Nguyen [aut], Qingshu Xie [aut], Jiao Yu [aut], Ting Zhang [aut]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between EdSurvey versions 2.2.1 dated 2018-11-19 and 2.2.2 dated 2018-11-19
DESCRIPTION | 8 +-- MD5 | 14 ++--- man/examples/percentile.R | 2 man/percentile.Rd | 2 tests/Examples/edsurvey-Ex.Rout.save | 90 ++++++++++++----------------------- tests/testthat/test-0-main.R | 3 - tests/testthat/test-2-esdfl.R | 29 ++--------- tests/testthat/test-mvrlm.R | 6 +- 8 files changed, 58 insertions(+), 96 deletions(-)
Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a common interface for model fitting, prediction, performance assessment, and presentation of results. Supports predictive modeling of numerical, categorical, and censored time-to-event outcomes and resample (bootstrap and cross-validation) estimation of model performance.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 0.1-1 dated 2018-10-14 and 0.2.0 dated 2018-11-19
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Title: Partitioning of Individual Autozygosity into Multiple
Homozygous-by-Descent Classes
Description: Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to
estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes
with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct
for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the
segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the
parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity
probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017)
<doi:10.1111/mec.14324>.
Author: Tom Druet, Naveen Kumar Kadri, Amandine Bertrand and Mathieu Gautier
Maintainer: Tom Druet <tom.druet@uliege.be>
Diff between RZooRoH versions 0.2.1 dated 2018-11-15 and 0.2.2 dated 2018-11-19
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Title: Simple Colour Manipulation
Description: Functions for easily manipulating colours, creating colour scales and calculating colour distances.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between shades versions 1.2.0 dated 2018-04-26 and 1.3.0 dated 2018-11-19
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Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analysis functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: OECD <http://www.oecd.org/>, including PISA, TALIS, PIAAC, and IEA <http://www.iea.nl/>, including TIMSS, TIMSS Advanced, PIRLS, ICCS, ICILS, and CivEd.
Author: Paul Bailey [aut, cre], Ren C'deBaca [ctb], Ahmad Emad [aut], Huade Huo [aut], Michael Lee [aut], Yuqi Liao [aut], Alex Lishinski [aut], Trang Nguyen [aut], Qingshu Xie [aut], Jiao Yu [aut], Ting Zhang [aut]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between EdSurvey versions 2.0.3 dated 2018-05-16 and 2.2.1 dated 2018-11-19
EdSurvey-2.0.3/EdSurvey/tests/testthat/REF-0-main.R |only EdSurvey-2.0.3/EdSurvey/tests/testthat/REF-1-lesdf.R |only EdSurvey-2.0.3/EdSurvey/tests/testthat/REF-2-esdfl.R |only EdSurvey-2.0.3/EdSurvey/tests/testthat/lm10.rds |only EdSurvey-2.0.3/EdSurvey/tests/testthat/lm1f.rds |only EdSurvey-2.2.1/EdSurvey/DESCRIPTION | 26 EdSurvey-2.2.1/EdSurvey/MD5 | 316 EdSurvey-2.2.1/EdSurvey/NAMESPACE | 56 EdSurvey-2.2.1/EdSurvey/R/DoFCorrection.R | 22 EdSurvey-2.2.1/EdSurvey/R/achievementLevels.R | 137 EdSurvey-2.2.1/EdSurvey/R/all.R | 2 EdSurvey-2.2.1/EdSurvey/R/cacheMetaReqUpdate.R | 20 EdSurvey-2.2.1/EdSurvey/R/cbind.light.edsurvey.data.frame.R | 2 EdSurvey-2.2.1/EdSurvey/R/checkDataClass.R | 8 EdSurvey-2.2.1/EdSurvey/R/contourPlot.R | 6 EdSurvey-2.2.1/EdSurvey/R/cor.sdf.R | 50 EdSurvey-2.2.1/EdSurvey/R/dim.edsurvey.data.frame.R | 2 EdSurvey-2.2.1/EdSurvey/R/downloadECLS_K.R |only EdSurvey-2.2.1/EdSurvey/R/downloadICCS.R | 46 EdSurvey-2.2.1/EdSurvey/R/downloadICILS.R | 46 EdSurvey-2.2.1/EdSurvey/R/downloadPIAAC.R | 44 EdSurvey-2.2.1/EdSurvey/R/downloadPIRLS.R | 91 EdSurvey-2.2.1/EdSurvey/R/downloadPISA.R | 119 EdSurvey-2.2.1/EdSurvey/R/downloadTALIS.R | 34 EdSurvey-2.2.1/EdSurvey/R/downloadTIMSS.R | 66 EdSurvey-2.2.1/EdSurvey/R/downloadTIMSSAdv.R | 78 EdSurvey-2.2.1/EdSurvey/R/download_ePIRLS.R |only EdSurvey-2.2.1/EdSurvey/R/edsurvey-package.R | 12 EdSurvey-2.2.1/EdSurvey/R/edsurvey.data.frame.R | 243 EdSurvey-2.2.1/EdSurvey/R/edsurvey.data.frame.list.R | 8 EdSurvey-2.2.1/EdSurvey/R/edsurveyTable.R | 716 EdSurvey-2.2.1/EdSurvey/R/edsurveyTable2pdf.R | 11 EdSurvey-2.2.1/EdSurvey/R/gap.R | 230 EdSurvey-2.2.1/EdSurvey/R/getAttributes.R | 4 EdSurvey-2.2.1/EdSurvey/R/getData.R | 167 EdSurvey-2.2.1/EdSurvey/R/glm.sdf.R | 244 EdSurvey-2.2.1/EdSurvey/R/itterateESDFL.R | 4 EdSurvey-2.2.1/EdSurvey/R/levelsSDF.R | 145 EdSurvey-2.2.1/EdSurvey/R/lm.sdf.R | 507 EdSurvey-2.2.1/EdSurvey/R/merge.light.edsurvey.data.frame.R | 2 EdSurvey-2.2.1/EdSurvey/R/mixed.sdf.R |only EdSurvey-2.2.1/EdSurvey/R/mvrlm.sdf.R |only EdSurvey-2.2.1/EdSurvey/R/percentile.R | 93 EdSurvey-2.2.1/EdSurvey/R/print.edsurvey.data.frame.R | 19 EdSurvey-2.2.1/EdSurvey/R/rbind.light.edsurvey.data.frame.R | 2 EdSurvey-2.2.1/EdSurvey/R/readECLS_K1998.R |only EdSurvey-2.2.1/EdSurvey/R/readECLS_K2011.R |only EdSurvey-2.2.1/EdSurvey/R/readICCS.R | 163 EdSurvey-2.2.1/EdSurvey/R/readICILS.R | 75 EdSurvey-2.2.1/EdSurvey/R/readNAEP.r | 4 EdSurvey-2.2.1/EdSurvey/R/readPIAAC.R | 49 EdSurvey-2.2.1/EdSurvey/R/readPIRLS.R | 638 EdSurvey-2.2.1/EdSurvey/R/readPISA.R | 614 EdSurvey-2.2.1/EdSurvey/R/readTALIS.R | 355 EdSurvey-2.2.1/EdSurvey/R/readTIMSS.R | 213 EdSurvey-2.2.1/EdSurvey/R/readTIMSSAdv.R | 81 EdSurvey-2.2.1/EdSurvey/R/read_ePIRLS.R |only EdSurvey-2.2.1/EdSurvey/R/rebindAttributes.R |only EdSurvey-2.2.1/EdSurvey/R/recode.sdf.R | 20 EdSurvey-2.2.1/EdSurvey/R/rename.sdf.R | 64 EdSurvey-2.2.1/EdSurvey/R/searchSDF.R | 57 EdSurvey-2.2.1/EdSurvey/R/setAttributes.R | 6 EdSurvey-2.2.1/EdSurvey/R/showCodebook.R | 24 EdSurvey-2.2.1/EdSurvey/R/showCutPoints.R | 2 EdSurvey-2.2.1/EdSurvey/R/showPlausibleValues.R | 4 EdSurvey-2.2.1/EdSurvey/R/showWeights.R | 2 EdSurvey-2.2.1/EdSurvey/R/subset.edsurvey.data.frame.R | 7 EdSurvey-2.2.1/EdSurvey/R/subset.edsurvey.data.frame.list.R | 2 EdSurvey-2.2.1/EdSurvey/R/subset.light.edsurvey.data.frame.R | 2 EdSurvey-2.2.1/EdSurvey/R/summary2.R |only EdSurvey-2.2.1/EdSurvey/R/utilities.R |only EdSurvey-2.2.1/EdSurvey/R/varEstToCov.R | 34 EdSurvey-2.2.1/EdSurvey/R/waldTest.R |only EdSurvey-2.2.1/EdSurvey/R/zzz.R | 1 EdSurvey-2.2.1/EdSurvey/build/vignette.rds |binary EdSurvey-2.2.1/EdSurvey/inst/NEWS.Rd | 51 EdSurvey-2.2.1/EdSurvey/inst/doc/introduction.Rmd | 14 EdSurvey-2.2.1/EdSurvey/inst/doc/introduction.html | 484 EdSurvey-2.2.1/EdSurvey/inst/mapproj |only EdSurvey-2.2.1/EdSurvey/man/DoFCorrection.Rd | 6 EdSurvey-2.2.1/EdSurvey/man/EdSurvey-package.Rd | 12 EdSurvey-2.2.1/EdSurvey/man/achievementLevels.Rd | 40 EdSurvey-2.2.1/EdSurvey/man/bind-methods.Rd | 2 EdSurvey-2.2.1/EdSurvey/man/contourPlot.Rd | 4 EdSurvey-2.2.1/EdSurvey/man/cor.sdf.Rd | 23 EdSurvey-2.2.1/EdSurvey/man/downloadCivEDICCS.Rd | 12 EdSurvey-2.2.1/EdSurvey/man/downloadECLS_K.Rd |only EdSurvey-2.2.1/EdSurvey/man/downloadICILS.Rd | 10 EdSurvey-2.2.1/EdSurvey/man/downloadPIAAC.Rd | 21 EdSurvey-2.2.1/EdSurvey/man/downloadPIRLS.Rd | 32 EdSurvey-2.2.1/EdSurvey/man/downloadPISA.Rd | 48 EdSurvey-2.2.1/EdSurvey/man/downloadTALIS.Rd | 13 EdSurvey-2.2.1/EdSurvey/man/downloadTIMSS.Rd | 20 EdSurvey-2.2.1/EdSurvey/man/downloadTIMSSAdv.Rd | 28 EdSurvey-2.2.1/EdSurvey/man/download_ePIRLS.Rd |only EdSurvey-2.2.1/EdSurvey/man/edsurvey-class.Rd |only EdSurvey-2.2.1/EdSurvey/man/edsurvey.data.frame.list.Rd | 8 EdSurvey-2.2.1/EdSurvey/man/edsurveyTable.Rd | 30 EdSurvey-2.2.1/EdSurvey/man/edsurveyTable2pdf.Rd | 11 EdSurvey-2.2.1/EdSurvey/man/examples/cor.sdf.R | 8 EdSurvey-2.2.1/EdSurvey/man/examples/downloadECLS_K.R |only EdSurvey-2.2.1/EdSurvey/man/examples/downloadICCS.R |only EdSurvey-2.2.1/EdSurvey/man/examples/downloadICILS.R |only EdSurvey-2.2.1/EdSurvey/man/examples/downloadPIAAC.R |only EdSurvey-2.2.1/EdSurvey/man/examples/downloadPIRLS.R | 14 EdSurvey-2.2.1/EdSurvey/man/examples/downloadPISA.R |only EdSurvey-2.2.1/EdSurvey/man/examples/downloadTALIS.R |only EdSurvey-2.2.1/EdSurvey/man/examples/downloadTIMSS.R | 4 EdSurvey-2.2.1/EdSurvey/man/examples/downloadTIMSSAdv.R | 14 EdSurvey-2.2.1/EdSurvey/man/examples/download_ePIRLS.R |only EdSurvey-2.2.1/EdSurvey/man/examples/edsurveyTable2pdf.R | 1 EdSurvey-2.2.1/EdSurvey/man/examples/glm.sdf.R | 2 EdSurvey-2.2.1/EdSurvey/man/examples/merge.light.edsurvey.data.frame.R | 5 EdSurvey-2.2.1/EdSurvey/man/examples/mixed.sdf.R |only EdSurvey-2.2.1/EdSurvey/man/examples/mvrlm.sdf.R |only EdSurvey-2.2.1/EdSurvey/man/examples/oddsRatio.R |only EdSurvey-2.2.1/EdSurvey/man/examples/readECLS_K1998.R |only EdSurvey-2.2.1/EdSurvey/man/examples/readECLS_K2011.R |only EdSurvey-2.2.1/EdSurvey/man/examples/read_ePIRLS.R |only EdSurvey-2.2.1/EdSurvey/man/examples/rebindAttributes.R |only EdSurvey-2.2.1/EdSurvey/man/examples/recode.sdf.R | 10 EdSurvey-2.2.1/EdSurvey/man/examples/summary2.R |only EdSurvey-2.2.1/EdSurvey/man/examples/waldTest.R |only EdSurvey-2.2.1/EdSurvey/man/gap.Rd | 67 EdSurvey-2.2.1/EdSurvey/man/getData.Rd | 10 EdSurvey-2.2.1/EdSurvey/man/glm.sdf.Rd | 31 EdSurvey-2.2.1/EdSurvey/man/lm.sdf.Rd | 48 EdSurvey-2.2.1/EdSurvey/man/merge.Rd | 7 EdSurvey-2.2.1/EdSurvey/man/mixed.sdf.Rd |only EdSurvey-2.2.1/EdSurvey/man/mvrlm.sdf.Rd |only EdSurvey-2.2.1/EdSurvey/man/oddsRatio.Rd |only EdSurvey-2.2.1/EdSurvey/man/percentile.Rd | 25 EdSurvey-2.2.1/EdSurvey/man/print.achievementLevels.Rd | 10 EdSurvey-2.2.1/EdSurvey/man/printGap.Rd | 5 EdSurvey-2.2.1/EdSurvey/man/readCivEDICCS.Rd | 6 EdSurvey-2.2.1/EdSurvey/man/readECLS_K1998.Rd |only EdSurvey-2.2.1/EdSurvey/man/readECLS_K2011.Rd |only EdSurvey-2.2.1/EdSurvey/man/readICILS.Rd | 4 EdSurvey-2.2.1/EdSurvey/man/readNAEP.Rd | 2 EdSurvey-2.2.1/EdSurvey/man/readPIAAC.Rd | 4 EdSurvey-2.2.1/EdSurvey/man/readPIRLS.Rd | 4 EdSurvey-2.2.1/EdSurvey/man/readPISA.Rd | 8 EdSurvey-2.2.1/EdSurvey/man/readTALIS.Rd | 8 EdSurvey-2.2.1/EdSurvey/man/readTIMSS.Rd | 7 EdSurvey-2.2.1/EdSurvey/man/readTIMSSAdv.Rd | 4 EdSurvey-2.2.1/EdSurvey/man/read_ePIRLS.Rd |only EdSurvey-2.2.1/EdSurvey/man/rebindAttributes.Rd |only EdSurvey-2.2.1/EdSurvey/man/recode.sdf.Rd | 12 EdSurvey-2.2.1/EdSurvey/man/rename.sdf.Rd | 2 EdSurvey-2.2.1/EdSurvey/man/searchSDF.Rd | 6 EdSurvey-2.2.1/EdSurvey/man/showCodebook.Rd | 6 EdSurvey-2.2.1/EdSurvey/man/showCutPoints.Rd | 2 EdSurvey-2.2.1/EdSurvey/man/showPlausibleValues.Rd | 2 EdSurvey-2.2.1/EdSurvey/man/showWeights.Rd | 2 EdSurvey-2.2.1/EdSurvey/man/subset.Rd | 2 EdSurvey-2.2.1/EdSurvey/man/summary2.Rd |only EdSurvey-2.2.1/EdSurvey/man/updatePlausibleValue.Rd | 2 EdSurvey-2.2.1/EdSurvey/man/varEstToCov.Rd | 21 EdSurvey-2.2.1/EdSurvey/man/waldTest.Rd |only 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EdSurvey-2.2.1/EdSurvey/tests/testthat/test-3-TIMSS.R |only EdSurvey-2.2.1/EdSurvey/tests/testthat/test-4-pisa.R |only EdSurvey-2.2.1/EdSurvey/tests/testthat/test-5-piaac.R |only EdSurvey-2.2.1/EdSurvey/tests/testthat/test-6-ECLS_K.R |only EdSurvey-2.2.1/EdSurvey/tests/testthat/test-mixed.R |only EdSurvey-2.2.1/EdSurvey/tests/testthat/test-mvrlm.R |only EdSurvey-2.2.1/EdSurvey/tests/testthat/waldtestChisq.rds |only EdSurvey-2.2.1/EdSurvey/tests/testthat/waldtestF.rds |only EdSurvey-2.2.1/EdSurvey/tests/testthat_tests.R | 1 EdSurvey-2.2.1/EdSurvey/vignettes/introduction.Rmd | 14 186 files changed, 10748 insertions(+), 7678 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: Dylan Beaudette [cre],
Jay Skovlin [aut],
Stephen Roecker [aut]
Maintainer: Dylan Beaudette <dylan.beaudette@ca.usda.gov>
Diff between soilDB versions 2.0-1 dated 2018-01-23 and 2.3 dated 2018-11-19
soilDB-2.0-1/soilDB/data/gSSURGO.chunk.rda |only soilDB-2.0-1/soilDB/man/gSSURGO.chunk.Rd |only soilDB-2.3/soilDB/.Rinstignore | 6 soilDB-2.3/soilDB/DESCRIPTION | 20 soilDB-2.3/soilDB/MD5 | 127 +- soilDB-2.3/soilDB/NAMESPACE | 5 soilDB-2.3/soilDB/NEWS | 42 soilDB-2.3/soilDB/R/AAAA.R | 19 soilDB-2.3/soilDB/R/KSSL_VG_model.R | 86 - soilDB-2.3/soilDB/R/OSDquery.R |only soilDB-2.3/soilDB/R/SDA-spatial.R |only soilDB-2.3/soilDB/R/SDA_query.R | 162 --- soilDB-2.3/soilDB/R/STR.R |only soilDB-2.3/soilDB/R/fetchHenry.R | 734 ++++++-------- soilDB-2.3/soilDB/R/fetchNASIS_components.R | 11 soilDB-2.3/soilDB/R/fetchNASIS_pedons.R | 50 soilDB-2.3/soilDB/R/fetchOSD.R | 120 +- soilDB-2.3/soilDB/R/fetchSCAN.R | 654 ++++++------ soilDB-2.3/soilDB/R/fetchVegdata.R |only soilDB-2.3/soilDB/R/get_colors_from_NASIS_db.R | 2 soilDB-2.3/soilDB/R/get_component_data_from_NASIS_db.R | 192 +++ soilDB-2.3/soilDB/R/get_component_from_LIMS.R | 98 + soilDB-2.3/soilDB/R/get_component_from_SDA.R | 183 +++ soilDB-2.3/soilDB/R/get_cosoilmoist_from_LIMS.R | 8 soilDB-2.3/soilDB/R/get_cosoilmoist_from_NASIS.R | 2 soilDB-2.3/soilDB/R/get_cosoilmoist_from_SDA.R | 2 soilDB-2.3/soilDB/R/get_extended_data_from_NASIS_db.R | 9 soilDB-2.3/soilDB/R/get_hz_data_from_NASIS_db.R | 2 soilDB-2.3/soilDB/R/get_lablayer_data_from_NASIS_db.R | 2 soilDB-2.3/soilDB/R/get_labpedon_data_from_NASIS_db.R | 2 soilDB-2.3/soilDB/R/get_phlabresults_data_from_NASIS_db.R | 2 soilDB-2.3/soilDB/R/get_projectmapunit_from_NASIS.R | 11 soilDB-2.3/soilDB/R/get_site_data_from_NASIS_db.R | 9 soilDB-2.3/soilDB/R/get_soilseries_from_NASIS.R |only soilDB-2.3/soilDB/R/get_text_notes_from_NASIS_db.R | 18 soilDB-2.3/soilDB/R/get_veg_data_from_NASIS_db.R | 140 +- soilDB-2.3/soilDB/R/get_vegplot_data_from_NASIS_db.R | 422 +++++++- soilDB-2.3/soilDB/R/mix_and_clean_colors.R | 2 soilDB-2.3/soilDB/R/parseWebReport.R | 9 soilDB-2.3/soilDB/R/siblings.R |only soilDB-2.3/soilDB/R/simplfyFragmentData.R | 96 + soilDB-2.3/soilDB/R/simplifyColorData.R | 180 +-- soilDB-2.3/soilDB/R/uncode.R | 2 soilDB-2.3/soilDB/R/utils.R | 234 ++++ soilDB-2.3/soilDB/data/SCAN_SNOTEL_metadata.rda |only soilDB-2.3/soilDB/data/mineralKing.rda |only soilDB-2.3/soilDB/data/state_FIPS_codes.rda |only soilDB-2.3/soilDB/data/us_ss_timeline.rda |only soilDB-2.3/soilDB/man/KSSL_VG_model.Rd | 108 +- soilDB-2.3/soilDB/man/OSDquery.Rd |only soilDB-2.3/soilDB/man/SCAN_SNOTEL_metadata.Rd |only soilDB-2.3/soilDB/man/SDA_query_features.Rd | 1 soilDB-2.3/soilDB/man/STRplot.Rd |only soilDB-2.3/soilDB/man/estimateSTR.Rd |only soilDB-2.3/soilDB/man/fetchHenry.Rd | 3 soilDB-2.3/soilDB/man/fetchKSSL.Rd | 4 soilDB-2.3/soilDB/man/fetchLIMS_component.Rd | 65 - soilDB-2.3/soilDB/man/fetchNASIS.Rd | 21 soilDB-2.3/soilDB/man/fetchOSD.Rd | 48 soilDB-2.3/soilDB/man/fetchSCAN.Rd | 17 soilDB-2.3/soilDB/man/fetchSDA_component.Rd | 48 soilDB-2.3/soilDB/man/get_soilseries_from_NASIS.Rd |only soilDB-2.3/soilDB/man/get_text_notes_from_NASIS_db.Rd | 3 soilDB-2.3/soilDB/man/get_veg_data_from_NASIS_db.Rd | 62 - soilDB-2.3/soilDB/man/loafercreek.Rd | 2 soilDB-2.3/soilDB/man/parseWebReport.Rd | 54 - soilDB-2.3/soilDB/man/siblings.Rd |only soilDB-2.3/soilDB/man/simplfyFragmentData.Rd | 9 soilDB-2.3/soilDB/man/simplifyColorData.Rd | 72 - soilDB-2.3/soilDB/man/us_ss_timeline.Rd |only soilDB-2.3/soilDB/tests |only 71 files changed, 2601 insertions(+), 1579 deletions(-)
Title: Preprocessing Tools to Create Design Matrices
Description: An extensible framework to create and preprocess
design matrices. Recipes consist of one or more data manipulation
and analysis "steps". Statistical parameters for the steps can
be estimated from an initial data set and then applied to
other data sets. The resulting design matrices can then be used
as inputs into statistical or machine learning models.
Author: Max Kuhn [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between recipes versions 0.1.3 dated 2018-06-16 and 0.1.4 dated 2018-11-19
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280 files changed, 5094 insertions(+), 3216 deletions(-)
Title: Calculating Proportionality Between Vectors of Compositional
Data
Description: The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, correlation lacks validity when
applied to relative data, including count data generated by next-generation
sequencing. This package implements several metrics for proportionality, including
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
implements several metrics for differential proportionality. Unlike correlation,
these measures give the same result for both relative and absolute data.
Author: Thomas Quinn [aut, cre],
David Lovell [aut],
Ionas Erb [aut],
Anders Bilgrau [ctb],
Greg Gloor [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between propr versions 4.0.0 dated 2018-07-25 and 4.1.1 dated 2018-11-19
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Title: Estimate Pollinator Body Size and Co-Varying Ecological Traits
Description: Tools to estimate pollinator body size and co-varying traits. This package contains novel Bayesian predictive models of pollinator body size (for bees and hoverflies) as well as preexisting predictive models for pollinator body size (currently implemented for ants, bees, butterflies, flies, moths and wasps) as well as bee tongue length and foraging distance, total field nectar loads and wing loading. An additional GitHub repository <https://github.com/liamkendall/pollimetrydata> provides model objects to use the bodysize function internally. All models are described in Kendall et al (2018) <doi:10.1101/397604>.
Author: Liam Kendall [aut, cre],
Ignasi Bartomeus [aut],
Louis Sutter [ctb]
Maintainer: Liam Kendall <liam.k.kendall@gmail.com>
Diff between pollimetry versions 1.0.0 dated 2018-09-11 and 1.0.1 dated 2018-11-19
DESCRIPTION | 12 +++--- MD5 | 20 ++++++---- NAMESPACE | 2 + R/bodysize.R | 30 +++++++++++++--- R/headwidthsize.R | 78 +++++++++++++++++++++--------------------- R/nectarload.R |only R/wingloading.R |only README.md | 5 ++ data/pollimetry_dataset.rdata |binary man/bodysize.Rd | 2 - man/headwidthsize.Rd | 2 - man/nectarload.Rd |only man/wingloading.Rd |only 13 files changed, 90 insertions(+), 61 deletions(-)
Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. This package includes functions to improve spatial-temporal modelling tasks using 'caret'. It prepares data for Leave-Location-Out and Leave-Time-Out cross-validation which are target-oriented validation strategies for spatial-temporal models. To decrease overfitting and improve model performances, the package implements a forward feature selection that selects suitable predictor variables in view to their contribution to the target-oriented performance.
Author: Hanna Meyer [cre, aut],
Chris Reudenbach [ctb],
Marvin Ludwig [ctb],
Thomas Nauss [ctb]
Maintainer: Hanna Meyer <hanna.meyer@geo.uni-marburg.de>
Diff between CAST versions 0.3.0 dated 2018-10-11 and 0.3.1 dated 2018-11-19
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 3 +++ NEWS.md | 8 ++++++++ R/CAST-package.R | 1 + R/CreateSpacetimeFolds.R | 29 +++++++++++++++++++++-------- R/ffs.R | 4 ++-- R/plot_ffs.R | 41 ++++++++++++++++++++++++++++++++++++----- inst/doc/CAST-intro.html | 8 ++++---- man/plot_ffs.Rd | 18 +++++++++--------- 10 files changed, 97 insertions(+), 41 deletions(-)
Title: Variable Selection for Gaussian Model-Based Clustering
Description: Variable selection for Gaussian model-based clustering as implemented in the 'mclust' package. The methodology allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting 'mclust' models. By default the algorithm uses a sequential search, but parallelisation is also available.
Author: Nema Dean [aut] (<https://orcid.org/0000-0002-5080-2517>),
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between clustvarsel versions 2.3.2 dated 2018-04-09 and 2.3.3 dated 2018-11-19
DESCRIPTION | 21 +++++++++------ MD5 | 18 ++++++------- R/clustvarsel.R | 24 ++++++++++++------ R/clvarselgrbkw.R | 15 +++++++++-- build/vignette.rds |binary inst/NEWS | 5 +++ inst/doc/clustvarsel.Rmd | 51 ++++++++++++++++++++++++++------------ inst/doc/clustvarsel.html | 61 ++++++++++++++++++++++++++++++++-------------- man/clustvarsel.Rd | 12 +++++---- vignettes/clustvarsel.Rmd | 51 ++++++++++++++++++++++++++------------ 10 files changed, 175 insertions(+), 83 deletions(-)
Title: Tools for Parsing, Manipulating, and Graphing Taxonomic
Abundance Data
Description: A set of tools for parsing, manipulating, and graphing data
classified by a hierarchy (e.g. a taxonomy).
Author: Zachary Foster [aut, cre],
Niklaus Grunwald [ths],
Rob Gilmore [ctb]
Maintainer: ORPHANED
Diff between metacoder versions 0.3.0 dated 2018-08-28 and 0.3.0.1 dated 2018-11-19
DESCRIPTION | 22 +++++++++++++--------- MD5 | 2 +- 2 files changed, 14 insertions(+), 10 deletions(-)
Title: Color Calculations with Emphasis on Spectral Data
Description: Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners.
Build complex systems from simpler parts using a spectral product algebra. For light sources,
compute CCT and CRI. For object colors, compute optimal colors and Logvinenko coordinates.
Work with the standard CIE illuminants and color matching functions, and read spectra from
text files, including CGATS files. Estimate a spectrum from its response. A user guide and 8 vignettes are included.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between colorSpec versions 0.7-3 dated 2018-04-02 and 0.7-5 dated 2018-11-19
DESCRIPTION | 14 MD5 | 109 - NAMESPACE | 10 NEWS.md | 6 R/colorSpec.CCT.R | 144 +- R/colorSpec.comp.R | 110 + R/colorSpec.daylight.R | 8 R/colorSpec.invert.R |only R/colorSpec.ops.R | 14 R/colorSpec.optimal.R | 53 R/colorSpec.plot.R | 40 R/events.R |only R/interp.R | 4 R/logging.R | 12 R/squashing.R |only R/utils.R | 109 - build/vignette.rds |binary inst/CITATION | 24 inst/doc/blueflame.pdf |binary inst/doc/blueflame.rnw | 8 inst/doc/colorSpec-guide.Rmd | 11 inst/doc/colorSpec-guide.html | 90 - inst/doc/emulation.pdf |binary inst/doc/emulation.rnw | 32 inst/doc/gallery.pdf |binary inst/doc/gallery.rnw | 23 inst/doc/inversion.pdf |only inst/doc/inversion.rnw |only inst/doc/lens-aging.pdf |binary inst/doc/lens-aging.rnw | 12 inst/doc/optimals.pdf |binary inst/doc/optimals.rnw | 4 inst/doc/phenolred.Rmd | 9 inst/doc/phenolred.html | 27 inst/doc/photoncounting.html | 24 man/calibrate.Rd | 13 man/colorSpec-package.Rd | 12 man/colorSpec.Rd | 2 man/computeADL.Rd | 11 man/computeCCT.Rd | 48 man/invert.Rd |only man/lightSpectra.Rd | 7 man/materialSpectra.Rd | 122 + man/multiply.Rd | 27 man/plotOptimals.Rd | 2 man/probeOptimalColors.Rd | 10 man/resample.Rd | 21 tests/test-invert.R |only vignettes/CIExy1931_AdobeRGB_vs_sRGB.jpg |binary vignettes/MacbethCC.txt |only vignettes/bibliography.bib | 2059 ++++++++++++++++--------------- vignettes/blueflame.rnw | 8 vignettes/colorSpec-guide.Rmd | 11 vignettes/emulation.rnw | 32 vignettes/gallery.rnw | 23 vignettes/inversion.rnw |only vignettes/invert-help.R |only vignettes/lens-aging.rnw | 12 vignettes/optimals.rnw | 4 vignettes/phenolred.Rmd | 9 vignettes/right-inverse.txt |only 61 files changed, 1935 insertions(+), 1395 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 3.1.7 dated 2018-10-04 and 3.1.8 dated 2018-11-19
secr-3.1.7/secr/R/join.R |only secr-3.1.8/secr/DESCRIPTION | 8 - secr-3.1.8/secr/MD5 | 40 ++--- secr-3.1.8/secr/NAMESPACE | 49 ++---- secr-3.1.8/secr/NEWS | 16 ++ secr-3.1.8/secr/R/ClosedN.R | 1 secr-3.1.8/secr/R/clone.R | 17 +- secr-3.1.8/secr/R/make.mask.R | 6 secr-3.1.8/secr/R/methods.R | 4 secr-3.1.8/secr/R/model.average.R | 2 secr-3.1.8/secr/R/secrloglik.R | 2 secr-3.1.8/secr/R/sim.capthist.R | 1 secr-3.1.8/secr/R/sim.secr.R | 29 ++- secr-3.1.8/secr/R/summary.secr.R |only secr-3.1.8/secr/R/trap.builder.R | 24 ++- secr-3.1.8/secr/inst/doc/secr-datainput.pdf |binary secr-3.1.8/secr/inst/doc/secr-overview.pdf |binary secr-3.1.8/secr/man/make.systematic.Rd | 14 + secr-3.1.8/secr/man/print.secr.Rd | 47 +++++- secr-3.1.8/secr/man/secr-package.Rd | 4 secr-3.1.8/secr/man/smooths.Rd | 2 secr-3.1.8/secr/src/secr.c | 207 ++++++++++++++-------------- 22 files changed, 281 insertions(+), 192 deletions(-)
Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut], Peter Hurford [aut]
Maintainer: Peter Hurford <api-maintainer@datarobot.com>
Diff between datarobot versions 2.9.0 dated 2018-09-11 and 2.10.0 dated 2018-11-19
datarobot-2.10.0/datarobot/DESCRIPTION | 8 datarobot-2.10.0/datarobot/MD5 | 131 ++++------ datarobot-2.10.0/datarobot/NAMESPACE | 13 datarobot-2.10.0/datarobot/NEWS | 20 + datarobot-2.10.0/datarobot/R/Blueprints.R | 23 - datarobot-2.10.0/datarobot/R/Enums.R | 7 datarobot-2.10.0/datarobot/R/Features.R | 5 datarobot-2.10.0/datarobot/R/GetPredictions.R | 4 datarobot-2.10.0/datarobot/R/Models.R | 20 - datarobot-2.10.0/datarobot/R/Partitions.R | 60 +++- datarobot-2.10.0/datarobot/R/StartAutopilot.R | 10 datarobot-2.10.0/datarobot/R/asDataFrame.R | 2 datarobot-2.10.0/datarobot/build/vignette.rds |binary datarobot-2.10.0/datarobot/inst/doc/AdvancedVignette.R | 70 +++-- datarobot-2.10.0/datarobot/inst/doc/AdvancedVignette.Rmd | 70 +++-- datarobot-2.10.0/datarobot/inst/doc/AdvancedVignette.html | 40 +-- datarobot-2.10.0/datarobot/inst/doc/ComparingSubsets.R | 101 +++---- datarobot-2.10.0/datarobot/inst/doc/ComparingSubsets.Rmd | 106 ++++---- datarobot-2.10.0/datarobot/inst/doc/ComparingSubsets.html | 27 +- datarobot-2.10.0/datarobot/inst/doc/DatetimePartitionedProjects.R | 27 +- datarobot-2.10.0/datarobot/inst/doc/DatetimePartitionedProjects.Rmd | 27 +- datarobot-2.10.0/datarobot/inst/doc/DatetimePartitionedProjects.html | 27 +- datarobot-2.10.0/datarobot/inst/doc/IntroductionToDataRobot.R | 5 datarobot-2.10.0/datarobot/inst/doc/IntroductionToDataRobot.Rmd | 5 datarobot-2.10.0/datarobot/inst/doc/PartialDependence.R | 73 ++--- datarobot-2.10.0/datarobot/inst/doc/PartialDependence.Rmd | 73 ++--- datarobot-2.10.0/datarobot/inst/doc/PartialDependence.html | 48 +-- datarobot-2.10.0/datarobot/inst/doc/ReasonCodeVignette.R | 34 +- datarobot-2.10.0/datarobot/inst/doc/ReasonCodeVignette.Rmd | 34 +- datarobot-2.10.0/datarobot/inst/doc/ReasonCodeVignette.html | 24 + datarobot-2.10.0/datarobot/inst/doc/TimeSeries.R | 4 datarobot-2.10.0/datarobot/inst/doc/TimeSeries.Rmd | 8 datarobot-2.10.0/datarobot/inst/doc/TimeSeries.html | 4 datarobot-2.10.0/datarobot/inst/doc/VariableImportance.R | 77 ++--- datarobot-2.10.0/datarobot/inst/doc/VariableImportance.Rmd | 77 ++--- datarobot-2.10.0/datarobot/inst/doc/VariableImportance.html | 47 +-- datarobot-2.10.0/datarobot/man/CreateDatetimePartitionSpecification.Rd | 24 + datarobot-2.10.0/datarobot/man/CreateGroupPartition.Rd | 6 datarobot-2.10.0/datarobot/man/DeletePredictJob.Rd | 2 datarobot-2.10.0/datarobot/man/GenerateDatetimePartition.Rd | 6 datarobot-2.10.0/datarobot/man/GetBlueprintDocumentation.Rd | 2 datarobot-2.10.0/datarobot/man/GetFeatureInfo.Rd | 4 datarobot-2.10.0/datarobot/man/GetPredictions.Rd | 4 datarobot-2.10.0/datarobot/man/SetTarget.Rd | 6 datarobot-2.10.0/datarobot/tests/testthat/test-CreateGroupPartition.R | 11 datarobot-2.10.0/datarobot/tests/testthat/test-StartAutopilot.R | 6 datarobot-2.10.0/datarobot/vignettes/AdvancedVignette.Rmd | 70 +++-- datarobot-2.10.0/datarobot/vignettes/ComparingSubsets.Rmd | 106 ++++---- datarobot-2.10.0/datarobot/vignettes/DatetimePartitionedProjects.Rmd | 27 +- datarobot-2.10.0/datarobot/vignettes/IntroductionToDataRobot.Rmd | 5 datarobot-2.10.0/datarobot/vignettes/PartialDependence.Rmd | 73 ++--- datarobot-2.10.0/datarobot/vignettes/ReasonCodeVignette.Rmd | 34 +- datarobot-2.10.0/datarobot/vignettes/TimeSeries.Rmd | 8 datarobot-2.10.0/datarobot/vignettes/VariableImportance.Rmd | 77 ++--- datarobot-2.9.0/datarobot/R/ModelDeployment.R |only datarobot-2.9.0/datarobot/R/RequestPredictions.R |only datarobot-2.9.0/datarobot/man/GetAllModels.Rd |only datarobot-2.9.0/datarobot/man/GetBlueprintDocuments.Rd |only datarobot-2.9.0/datarobot/man/GetModelDeployment.Rd |only datarobot-2.9.0/datarobot/man/GetModelDeploymentActionLog.Rd |only datarobot-2.9.0/datarobot/man/GetModelDeploymentServiceStatistics.Rd |only datarobot-2.9.0/datarobot/man/GetModelObject.Rd |only datarobot-2.9.0/datarobot/man/GetRecommendedBlueprints.Rd |only datarobot-2.9.0/datarobot/man/ListModelDeployments.Rd |only datarobot-2.9.0/datarobot/man/ModelDeploymentStatus.Rd |only datarobot-2.9.0/datarobot/man/RequestModelDeployment.Rd |only datarobot-2.9.0/datarobot/man/RequestPredictions.Rd |only datarobot-2.9.0/datarobot/man/UpdateModelDeployment.Rd |only datarobot-2.9.0/datarobot/man/summary.dataRobotModelDeploymentsList.Rd |only datarobot-2.9.0/datarobot/vignettes/ModelDeployments.Rmd |only datarobot-2.9.0/datarobot/vignettes/actionLog.rds |only datarobot-2.9.0/datarobot/vignettes/getModelDeployment.rds |only datarobot-2.9.0/datarobot/vignettes/listModelDeployments.rds |only datarobot-2.9.0/datarobot/vignettes/listModelDeploymentsLimit2.rds |only datarobot-2.9.0/datarobot/vignettes/listModelDeploymentsLimit2OrderByLabel.rds |only datarobot-2.9.0/datarobot/vignettes/listModelDeploymentsOffset2.rds |only datarobot-2.9.0/datarobot/vignettes/listModelDeploymentsQuery.rds |only datarobot-2.9.0/datarobot/vignettes/serverHealth.rds |only datarobot-2.9.0/datarobot/vignettes/updatedModelDeployment.rds |only 79 files changed, 930 insertions(+), 852 deletions(-)