Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its
application to forecasting. The main scope of the package is in variables selection
and models specification for cases of time series data. This includes promotional
modelling, selection between different dynamic regressions with non-standard
distributions of errors, selection based on cross validation, solutions to the fat
regression model problem and more. Models developed in the package are tailored
specifically for forecasting purposes. So as a results there are several methods
that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between greybox versions 0.5.1 dated 2019-04-28 and 0.5.2 dated 2019-06-14
DESCRIPTION | 11 +- MD5 | 102 ++++++++++--------- NAMESPACE | 4 NEWS | 20 +++ R/alaplace.R | 2 R/alm.R | 220 +++++++++++++++++++++++++++++++++---------- R/association.R | 3 R/bcnorm.R |only R/cramer.R | 3 R/determination.R | 3 R/fnorm.R | 2 R/greybox-package.R | 6 + R/laplace.R | 2 R/lmCombine.R | 24 ++-- R/lmDynamic.R | 26 +++-- R/mcor.R | 3 R/methods.R | 40 +++++++ R/rmc.R | 134 +++++++++++++------------- R/ro.R | 24 ++-- R/spread.R | 3 R/stepwise.R | 20 +-- R/svet.R | 2 R/tableplot.R | 3 R/xregExpander.R | 15 +- R/xregMultiplier.R | 15 +- R/xregTransformer.R | 15 +- README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/alm.html | 200 ++++++++++++++++++++------------------- inst/doc/greybox.Rmd | 1 inst/doc/greybox.html | 5 inst/doc/maUsingGreybox.html | 4 inst/doc/ro.html | 22 ++-- man/alm.Rd | 9 + man/association.Rd | 3 man/bcnorm-distribution.Rd |only man/cramer.Rd | 3 man/determination.Rd | 3 man/greybox.Rd | 6 + man/lmCombine.Rd | 7 - man/lmDynamic.Rd | 7 - man/mcor.Rd | 3 man/rmc.Rd | 60 +++++------ man/ro.Rd | 11 +- man/spread.Rd | 3 man/stepwise.Rd | 11 +- man/tableplot.Rd | 3 man/xregExpander.Rd | 6 - man/xregMultiplier.Rd | 6 - man/xregTransformer.Rd | 6 - src/polyMult.cpp | 42 ++++++++ vignettes/greybox.Rmd | 1 53 files changed, 713 insertions(+), 412 deletions(-)
Title: Composite Grid Gaussian Processes
Description: Run computer experiments using the adaptive composite grid
algorithm with a Gaussian process model.
The algorithm works best when running an experiment that can evaluate thousands
of points from a deterministic computer simulation.
This package is an implementation of a forthcoming paper by Plumlee,
Erickson, Ankenman, et al. For a preprint of the paper,
contact the maintainer of this package.
Author: Collin Erickson [aut, cre],
Matthew Plumlee [aut]
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between CGGP versions 1.0.0 dated 2019-06-13 and 1.0.1 dated 2019-06-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/CGGP_create_fs.R | 2 +- inst/doc/CGGP.html | 26 +++++++++++++------------- man/CGGPcreate.Rd | 4 ++-- 6 files changed, 30 insertions(+), 24 deletions(-)
Title: A Stable Isotope Mixing Model
Description: Fits a stable isotope mixing model via 'JAGS' in R. The package allows for any number of isotopes or sources, as well as concentration dependencies. The methods on the papers Parnell et al 2010 <doi:10.1371/journal.pone.0009672>, and Parnell et al 2013 <doi:10.1002/env.2221>.
Author: Andrew Parnell
Maintainer: Andrew Parnell <andrew.parnell@mu.ie>
Diff between simmr versions 0.3 dated 2016-01-19 and 0.4.0 dated 2019-06-14
simmr-0.3/simmr/README.md |only simmr-0.3/simmr/build/partial.rdb |only simmr-0.3/simmr/man/simmr-package.Rd |only simmr-0.4.0/simmr/DESCRIPTION | 20 simmr-0.4.0/simmr/MD5 | 75 - simmr-0.4.0/simmr/NAMESPACE | 51 simmr-0.4.0/simmr/NEWS.md |only simmr-0.4.0/simmr/R/combine_sources.R | 171 ++ simmr-0.4.0/simmr/R/compare_groups.R | 194 ++ simmr-0.4.0/simmr/R/compare_sources.R | 117 + simmr-0.4.0/simmr/R/plot.simmr_input.R | 322 ++++ simmr-0.4.0/simmr/R/plot.simmr_output.R | 151 +- simmr-0.4.0/simmr/R/posterior_predictive.simmr_output.R |only simmr-0.4.0/simmr/R/print.simmr_input.R | 10 simmr-0.4.0/simmr/R/print.simmr_output.R | 11 simmr-0.4.0/simmr/R/prior_viz.simmr_output.R |only simmr-0.4.0/simmr/R/simmr.R |only simmr-0.4.0/simmr/R/simmr_elicit.R | 245 ++- simmr-0.4.0/simmr/R/simmr_load.R | 286 +++- simmr-0.4.0/simmr/R/simmr_mcmc.R | 450 ++++++ simmr-0.4.0/simmr/R/simmr_mcmc_tdf.R |only simmr-0.4.0/simmr/R/summary.simmr_output.R | 181 +- simmr-0.4.0/simmr/R/summary.simmr_output_tdf.R |only simmr-0.4.0/simmr/build/vignette.rds |binary simmr-0.4.0/simmr/inst/doc/quick_start.R |only simmr-0.4.0/simmr/inst/doc/quick_start.Rmd |only simmr-0.4.0/simmr/inst/doc/quick_start.html |only simmr-0.4.0/simmr/inst/doc/simmr.R | 103 + simmr-0.4.0/simmr/inst/doc/simmr.Rmd | 263 +++ simmr-0.4.0/simmr/inst/doc/simmr.html | 1087 +++++++++++----- simmr-0.4.0/simmr/inst/extdata |only simmr-0.4.0/simmr/man/combine_sources.Rd | 72 - simmr-0.4.0/simmr/man/compare_groups.Rd | 80 - simmr-0.4.0/simmr/man/compare_sources.Rd | 79 - simmr-0.4.0/simmr/man/plot.simmr_input.Rd | 107 - simmr-0.4.0/simmr/man/plot.simmr_output.Rd | 95 - simmr-0.4.0/simmr/man/posterior_predictive.Rd |only simmr-0.4.0/simmr/man/print.simmr_input.Rd |only simmr-0.4.0/simmr/man/print.simmr_output.Rd |only simmr-0.4.0/simmr/man/prior_viz.Rd |only simmr-0.4.0/simmr/man/simmr.Rd |only simmr-0.4.0/simmr/man/simmr_elicit.Rd | 95 - simmr-0.4.0/simmr/man/simmr_load.Rd | 130 + simmr-0.4.0/simmr/man/simmr_mcmc.Rd | 115 + simmr-0.4.0/simmr/man/simmr_mcmc_tdf.Rd |only simmr-0.4.0/simmr/man/summary.simmr_output.Rd | 85 - simmr-0.4.0/simmr/man/summary.simmr_output_tdf.Rd |only simmr-0.4.0/simmr/vignettes/quick_start.Rmd |only simmr-0.4.0/simmr/vignettes/simmr.Rmd | 263 +++ 49 files changed, 3684 insertions(+), 1174 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>),
Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>),
Jeff Farrell [ctb],
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb]
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>
Diff between Seurat versions 3.0.1 dated 2019-05-16 and 3.0.2 dated 2019-06-14
DESCRIPTION | 10 - MD5 | 55 +++--- NAMESPACE | 9 - NEWS.md | 20 ++ R/clustering.R | 37 +++- R/differential_expression.R | 27 +-- R/dimensional_reduction.R | 3 R/generics.R | 14 + R/integration.R | 13 + R/objects.R | 309 ++++++++++++++++++++++++++++++++++-- R/preprocessing.R | 136 ++++++++++++--- R/tree.R | 4 R/utilities.R | 77 +++----- R/visualization.R | 279 ++++++++++++++++++++++++-------- README.md | 2 man/AverageExpression.Rd | 18 +- man/BuildClusterTree.Rd | 5 man/DimPlot.Rd | 8 man/FeaturePlot.Rd | 14 + man/FindAllMarkers.Rd | 2 man/FindClusters.Rd | 13 + man/FindMarkers.Rd | 2 man/GetResidual.Rd |only man/MULTIseqDemux.Rd | 2 man/SCTransform.Rd | 6 man/as.CellDataSet.Rd |only man/as.Seurat.Rd | 14 + man/as.list.SeuratCommand.Rd |only man/merge.Seurat.Rd | 4 tests/testthat/test_preprocessing.R | 37 ++++ 30 files changed, 875 insertions(+), 245 deletions(-)
Title: Plant Photobiology Related Functions and Data
Description: Provides functions for quantifying visible (VIS) and ultraviolet
(UV) radiation in relation to the photoreceptors Phytochromes,
Cryptochromes, and UVR8 which are present in plants. It also includes data
sets on the optical properties of plants. Part of the 'r4photobiology'
suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyPlants versions 0.4.1 dated 2017-03-21 and 0.4.2 dated 2019-06-14
photobiologyPlants-0.4.1/photobiologyPlants/R/cry2-mspct.r |only photobiologyPlants-0.4.1/photobiologyPlants/data/UVR8.spct.rda |only photobiologyPlants-0.4.1/photobiologyPlants/data/cry.spct.rda |only photobiologyPlants-0.4.1/photobiologyPlants/inst/doc/dataplotsPlants.R |only photobiologyPlants-0.4.1/photobiologyPlants/inst/doc/dataplotsPlants.Rnw |only photobiologyPlants-0.4.1/photobiologyPlants/inst/doc/dataplotsPlants.pdf |only photobiologyPlants-0.4.1/photobiologyPlants/inst/doc/userguideplants.R |only photobiologyPlants-0.4.1/photobiologyPlants/inst/doc/userguideplants.Rnw |only photobiologyPlants-0.4.1/photobiologyPlants/inst/doc/userguideplants.pdf |only photobiologyPlants-0.4.1/photobiologyPlants/inst/staticdocs |only photobiologyPlants-0.4.1/photobiologyPlants/man/CRY2.mspct.Rd |only photobiologyPlants-0.4.1/photobiologyPlants/man/UVR8_Glasgow.spct.Rd |only photobiologyPlants-0.4.1/photobiologyPlants/man/phytochrome.spct.Rd |only photobiologyPlants-0.4.1/photobiologyPlants/vignettes/dataplotsPlants-concordance.tex |only photobiologyPlants-0.4.1/photobiologyPlants/vignettes/dataplotsPlants.Rnw |only photobiologyPlants-0.4.1/photobiologyPlants/vignettes/userguideplants-concordance.tex |only photobiologyPlants-0.4.1/photobiologyPlants/vignettes/userguideplants.Rnw |only photobiologyPlants-0.4.2/photobiologyPlants/DESCRIPTION | 28 - photobiologyPlants-0.4.2/photobiologyPlants/MD5 | 87 +++-- photobiologyPlants-0.4.2/photobiologyPlants/NEWS | 18 - photobiologyPlants-0.4.2/photobiologyPlants/R/McCree-photosynthesis-mspct.r | 8 photobiologyPlants-0.4.2/photobiologyPlants/R/Pfr-Ptot.r | 3 photobiologyPlants-0.4.2/photobiologyPlants/R/carotenoids-mspct.r |only photobiologyPlants-0.4.2/photobiologyPlants/R/chlorophylls-fluo-mspct.r |only photobiologyPlants-0.4.2/photobiologyPlants/R/chlorophylls-mspct.r |only photobiologyPlants-0.4.2/photobiologyPlants/R/crys-mspct.r |only photobiologyPlants-0.4.2/photobiologyPlants/R/photobiologyPlants.r | 14 photobiologyPlants-0.4.2/photobiologyPlants/R/phots-mspct.r |only photobiologyPlants-0.4.2/photobiologyPlants/R/phytochrome-data.r | 13 photobiologyPlants-0.4.2/photobiologyPlants/R/plant-optics-data.r | 2 photobiologyPlants-0.4.2/photobiologyPlants/R/uvr8-Glasgow-spct.r | 24 + photobiologyPlants-0.4.2/photobiologyPlants/R/ztls-mspct.r |only photobiologyPlants-0.4.2/photobiologyPlants/README.md | 156 +++++++++- photobiologyPlants-0.4.2/photobiologyPlants/build/vignette.rds |binary photobiologyPlants-0.4.2/photobiologyPlants/data/CRYs.mspct.rda |only photobiologyPlants-0.4.2/photobiologyPlants/data/McCree.rda |binary photobiologyPlants-0.4.2/photobiologyPlants/data/PHOTs.mspct.rda |only photobiologyPlants-0.4.2/photobiologyPlants/data/UVR8s.mspct.rda |only photobiologyPlants-0.4.2/photobiologyPlants/data/ZTLs.mspct.rda |only photobiologyPlants-0.4.2/photobiologyPlants/data/carotenoids-mspct.rda |only photobiologyPlants-0.4.2/photobiologyPlants/data/chlorophylls-fluorescence-mspct.rda |only photobiologyPlants-0.4.2/photobiologyPlants/data/chlorophylls-mspct.rda |only photobiologyPlants-0.4.2/photobiologyPlants/data/leaves.spct.rda |binary photobiologyPlants-0.4.2/photobiologyPlants/data/phytochrome.spct.rda |binary photobiologyPlants-0.4.2/photobiologyPlants/inst/CITATION |only photobiologyPlants-0.4.2/photobiologyPlants/inst/doc/user-guide.R |only photobiologyPlants-0.4.2/photobiologyPlants/inst/doc/user-guide.Rmd |only photobiologyPlants-0.4.2/photobiologyPlants/inst/doc/user-guide.html |only photobiologyPlants-0.4.2/photobiologyPlants/man/B_G.Rd | 3 photobiologyPlants-0.4.2/photobiologyPlants/man/Betula_ermanii.mspct.Rd | 2 photobiologyPlants-0.4.2/photobiologyPlants/man/CRYs.mspct.Rd |only photobiologyPlants-0.4.2/photobiologyPlants/man/McCree_photosynthesis.mspct.Rd | 5 photobiologyPlants-0.4.2/photobiologyPlants/man/PHOTs.mspct.Rd |only photobiologyPlants-0.4.2/photobiologyPlants/man/PHYs.mspct.Rd |only photobiologyPlants-0.4.2/photobiologyPlants/man/Pfr_Ptot.Rd | 4 photobiologyPlants-0.4.2/photobiologyPlants/man/R_FR.Rd | 3 photobiologyPlants-0.4.2/photobiologyPlants/man/UVA_PAR.Rd | 3 photobiologyPlants-0.4.2/photobiologyPlants/man/UVB_PAR.Rd | 3 photobiologyPlants-0.4.2/photobiologyPlants/man/UVR8s.mspct.Rd |only photobiologyPlants-0.4.2/photobiologyPlants/man/ZTLs.mspct.Rd |only photobiologyPlants-0.4.2/photobiologyPlants/man/carotenoids.mspct.Rd |only photobiologyPlants-0.4.2/photobiologyPlants/man/chlorophylls.mspct.Rd |only photobiologyPlants-0.4.2/photobiologyPlants/man/chlorophylls_fluorescence.mspct.Rd |only photobiologyPlants-0.4.2/photobiologyPlants/man/figures |only photobiologyPlants-0.4.2/photobiologyPlants/man/photobiologyPlants-package.Rd | 23 - photobiologyPlants-0.4.2/photobiologyPlants/vignettes/user-guide.Rmd |only 66 files changed, 302 insertions(+), 97 deletions(-)
More information about photobiologyPlants at CRAN
Permanent link
Title: Spectral Irradiance Data for Lamps
Description: Spectral emission data for some frequently used lamps excluding
led emitting diodes (LEDs) available as electronic components. Original
spectral irradiance data for incandescent-, LED- and discharge lamps are
included. They are complemented by data on the effect of temperature on
the emission by fluorescent tubes. Part of the 'r4photobiology' suite,
Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Lasse Ylianttila [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyLamps versions 0.4.2 dated 2018-02-26 and 0.4.3 dated 2019-06-14
photobiologyLamps-0.4.2/photobiologyLamps/R/lamp_brands.r |only photobiologyLamps-0.4.2/photobiologyLamps/R/maya.lamps.r |only photobiologyLamps-0.4.2/photobiologyLamps/R/on-load.R |only photobiologyLamps-0.4.3/photobiologyLamps/DESCRIPTION | 19 photobiologyLamps-0.4.3/photobiologyLamps/MD5 | 75 - photobiologyLamps-0.4.3/photobiologyLamps/NEWS | 16 photobiologyLamps-0.4.3/photobiologyLamps/R/lamp-brands.r |only photobiologyLamps-0.4.3/photobiologyLamps/R/ledsavers-mspct.r | 2 photobiologyLamps-0.4.3/photobiologyLamps/R/macam.r | 4 photobiologyLamps-0.4.3/photobiologyLamps/R/maya-lamps.r |only photobiologyLamps-0.4.3/photobiologyLamps/R/photobiologyLamps.r | 4 photobiologyLamps-0.4.3/photobiologyLamps/R/qp-uvb313-temp.r | 2 photobiologyLamps-0.4.3/photobiologyLamps/R/types.r | 3 photobiologyLamps-0.4.3/photobiologyLamps/R/uses.r |only photobiologyLamps-0.4.3/photobiologyLamps/README.md | 121 ++ photobiologyLamps-0.4.3/photobiologyLamps/build/vignette.rds |binary photobiologyLamps-0.4.3/photobiologyLamps/data/lamps-mspct.rda |binary photobiologyLamps-0.4.3/photobiologyLamps/data/ledsavers.rda |binary photobiologyLamps-0.4.3/photobiologyLamps/data/qp-uvb313-temp-mspct.rda |binary photobiologyLamps-0.4.3/photobiologyLamps/data/qp-uvb313-temp-spct.rda |binary photobiologyLamps-0.4.3/photobiologyLamps/inst/doc/user-guide.R | 3 photobiologyLamps-0.4.3/photobiologyLamps/inst/doc/user-guide.Rmd | 11 photobiologyLamps-0.4.3/photobiologyLamps/inst/doc/user-guide.html | 536 ++++++---- photobiologyLamps-0.4.3/photobiologyLamps/man/airam_lamps.Rd | 7 photobiologyLamps-0.4.3/photobiologyLamps/man/aputure_lamps.Rd | 7 photobiologyLamps-0.4.3/photobiologyLamps/man/figures |only photobiologyLamps-0.4.3/photobiologyLamps/man/fluence_lamps.Rd |only photobiologyLamps-0.4.3/photobiologyLamps/man/generic_lamps.Rd | 7 photobiologyLamps-0.4.3/photobiologyLamps/man/godox_lamps.Rd |only photobiologyLamps-0.4.3/photobiologyLamps/man/incandescent_lamps.Rd | 3 photobiologyLamps-0.4.3/photobiologyLamps/man/ledsavers.mspct.Rd | 2 photobiologyLamps-0.4.3/photobiologyLamps/man/macam_lamps.Rd | 4 photobiologyLamps-0.4.3/photobiologyLamps/man/oo_maya_lamps.Rd | 2 photobiologyLamps-0.4.3/photobiologyLamps/man/osram_lamps.Rd | 7 photobiologyLamps-0.4.3/photobiologyLamps/man/philips_lamps.Rd | 7 photobiologyLamps-0.4.3/photobiologyLamps/man/photobiologyLamps-package.Rd | 15 photobiologyLamps-0.4.3/photobiologyLamps/man/photography_lamps.Rd |only photobiologyLamps-0.4.3/photobiologyLamps/man/qp_uvb313_temp.spct.Rd | 2 photobiologyLamps-0.4.3/photobiologyLamps/man/qpanel_lamps.Rd | 7 photobiologyLamps-0.4.3/photobiologyLamps/man/sunwayfoto_lamps.Rd |only photobiologyLamps-0.4.3/photobiologyLamps/man/sylvania_lamps.Rd | 11 photobiologyLamps-0.4.3/photobiologyLamps/man/toshiba_lamps.Rd | 13 photobiologyLamps-0.4.3/photobiologyLamps/man/valoya_lamps.Rd | 15 photobiologyLamps-0.4.3/photobiologyLamps/vignettes/user-guide.Rmd | 11 44 files changed, 625 insertions(+), 291 deletions(-)
More information about photobiologyLamps at CRAN
Permanent link
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation (ODE) based
models typically employed in quantitative pharmacology and systems biology.
Author: Kyle T Baron [aut, cre] (<https://orcid.org/0000-0001-7252-5656>),
Alan C Hindmarsh [ctb],
Linda R Petzold [ctb],
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
odepack authors [cph],
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 0.9.0 dated 2019-01-23 and 0.9.1 dated 2019-06-14
DESCRIPTION | 28 - MD5 | 149 ++++--- NAMESPACE | 23 - R/Aaaa.R | 18 R/annot.R | 25 - R/chain.R | 19 R/class_build.R | 115 +++-- R/class_ev.R | 4 R/class_matlist.R | 35 + R/class_mrgmod.R | 57 ++ R/class_mrgsims.R | 2 R/class_numericlist.R | 22 - R/compile.R | 19 R/data_set.R | 2 R/env.R | 31 - R/events.R | 78 +-- R/funset.R | 6 R/handle_spec_block.R |only R/idata_set.R | 2 R/inven.R | 2 R/knobs.R | 7 R/model_include.R | 80 ++- R/modlib.R | 9 R/modspec.R | 769 +++++--------------------------------- R/mread.R | 347 +++++++++-------- R/mrgindata.R | 6 R/mrgsim_q.R | 81 ++-- R/mrgsims.R | 13 R/mrgsolve.R | 30 - R/package.R | 7 R/param.R | 4 R/print.R | 42 +- R/r_to_cpp.R |only R/render.R | 43 ++ R/utils.R | 290 +++++++------- inst/base/databox_cpp.h | 31 + inst/base/mrgsolv.h | 1 inst/models/popex.Rmd |only inst/models/popex.cpp | 6 inst/rmarkdown |only man/BLOCK_PARSE.Rd | 11 man/PKMODEL.Rd | 2 man/Req.Rd | 8 man/cvec.Rd | 7 man/ev_dplyr.Rd | 4 man/ev_seq.Rd | 6 man/modelparse.Rd | 4 man/mread.Rd | 5 man/mrgsim_q.Rd | 10 man/mrgsims.Rd | 4 man/mrgsims_dplyr.Rd | 4 man/mrgsolve_package.Rd | 8 man/reexports.Rd |only man/scrape_opts.Rd | 5 man/summary.mrgmod.Rd |only src/dataobject.cpp | 6 src/datarecord.cpp | 25 - src/housemodel-mread-header.h |only src/housemodel-mread-source.cpp | 82 ---- src/odeproblem.cpp | 3 src/opkda2_mrg.f | 662 -------------------------------- tests/testthat.R | 2 tests/testthat/test-data_set.R | 14 tests/testthat/test-ev.R | 14 tests/testthat/test-funset.R |only tests/testthat/test-init.R | 5 tests/testthat/test-knobs.R | 8 tests/testthat/test-matlist.R | 18 tests/testthat/test-modlib.R |only tests/testthat/test-modspec.R | 10 tests/testthat/test-mrgindata.R | 2 tests/testthat/test-mrgmod.R |only tests/testthat/test-mrgsim.R | 2 tests/testthat/test-mrgsim_q.R | 4 tests/testthat/test-mrgsims.R |only tests/testthat/test-numericlist.R |only tests/testthat/test-param.R | 6 tests/testthat/test-realize.R | 6 tests/testthat/test-tgrid.R |only tests/testthat/test-utils.R | 18 tests/testthat/test-workflow.R |only 81 files changed, 1209 insertions(+), 2159 deletions(-)
Title: Create Interactive Graphics Related to Clinical Trial Safety
Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the 'Shiny' application or create standalone 'htmlwidget' charts. Interactive charts are built using 'd3.js' and 'webcharts.js' 'JavaScript' libraries.
Author: Jeremy Wildfire [cre, aut],
Becca Krouse [aut],
Preston Burns [aut],
Xiao Ni [aut],
James Buchanan [aut],
Susan Duke [aut],
Rho Inc. [cph]
Maintainer: Jeremy Wildfire <jeremy_wildfire@rhoworld.com>
Diff between safetyGraphics versions 0.7.3 dated 2019-02-04 and 1.0.0 dated 2019-06-14
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More information about safetyGraphics at CRAN
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Title: Treatment Effects with Multiple Periods and Groups
Description: The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences models with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2018) <https://ssrn.com/abstract=3148250>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption, and plotting group-time average treatment effects.
Author: Brantly Callaway [aut, cre],
Pedro H.C. Sant'Anna [aut]
Maintainer: Brantly Callaway <brantly.callaway@temple.edu>
Diff between did versions 1.2.0 dated 2018-10-16 and 1.2.1 dated 2019-06-14
DESCRIPTION | 10 MD5 | 21 NEWS.md | 9 R/did.R | 2735 ++++++++++++++++++++++++------------------------ R/zzz.R | 2 build |only inst |only man/compute.aggte.Rd | 4 man/compute.mp.spatt.Rd | 4 man/mp.spatt.Rd | 4 man/mp.spatt.test.Rd | 4 vignettes |only 12 files changed, 1430 insertions(+), 1363 deletions(-)
Title: Powell Miscellaneous Functions for Teaching and Learning
Statistics
Description: Miscellaneous functions useful for teaching statistics as well as actually practicing the art. They typically are not “new” methods but rather wrappers around either base R or other packages.
Author: Chuck Powell [aut, cre] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Chuck Powell <ibecav@gmail.com>
Diff between CGPfunctions versions 0.5.2 dated 2019-03-22 and 0.5.7 dated 2019-06-14
DESCRIPTION | 19 - MD5 | 28 +- NAMESPACE | 3 NEWS.md | 12 - R/Plot2WayANOVA.R | 250 +++++++++++++++++------ R/newggslopegraph.R | 50 ++++ build/vignette.rds |binary inst/doc/Using-Plot2WayANOVA.R | 38 +++ inst/doc/Using-Plot2WayANOVA.Rmd | 258 +++++++++++++++++++++--- inst/doc/Using-Plot2WayANOVA.html | 381 +++++++++++++++++++++++++++--------- inst/doc/Using-PlotXTabs.html | 84 +++---- inst/doc/Using-newggslopegraph.html | 172 ++++++++-------- man/Plot2WayANOVA.Rd | 80 ++++++- man/newggslopegraph.Rd | 34 +++ vignettes/Using-Plot2WayANOVA.Rmd | 258 +++++++++++++++++++++--- 15 files changed, 1276 insertions(+), 391 deletions(-)
Title: Text to Speech
Description: Unifies different text to speech engines, such as
Google, Microsoft, and Amazon. Text synthesis can be done
in any engine with a simple switch of an argument denoting
the service requested.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between text2speech versions 0.2.3 dated 2019-05-16 and 0.2.4 dated 2019-06-14
DESCRIPTION | 6 MD5 | 12 NEWS.md | 3 R/tts_backend.R | 13 R/tts_synthesize.R | 8 inst/doc/listing_voices.html | 964 +++++++++++++++++++++++----------------- tests/testthat/test-translate.R | 5 7 files changed, 591 insertions(+), 420 deletions(-)
Title: Relational Query Generator for Data Manipulation at Scale
Description: A piped query generator based on Edgar F. Codd's relational
algebra, and on production experience using 'SQL' and 'dplyr' at big data
scale. The design represents an attempt to make 'SQL' more teachable by
denoting composition by a sequential pipeline notation instead of nested
queries or functions. The implementation delivers reliable high
performance data processing on large data systems such as 'Spark',
databases, and 'data.table'. Package features include: data processing trees
or pipelines as observable objects (able to report both columns
produced and columns used), optimized 'SQL' generation as an explicit
user visible table modeling step, plus explicit query reasoning and checking.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rquery versions 1.3.3 dated 2019-06-02 and 1.3.4 dated 2019-06-14
DESCRIPTION | 10 - MD5 | 128 +++++++++++----------- NAMESPACE | 1 NEWS.md | 6 + R/complete_design.R | 15 +- R/db_info.R | 100 +++++++++++++++++ R/db_ops.R | 176 ++++++++++++++++++++----------- R/drop_columns.R | 19 +-- R/extend.R | 7 - R/lookup_by_column.R | 10 + R/materialize.R | 41 ++++--- R/materialize_node.R | 10 + R/natural_join.R | 16 -- R/non_sql_node.R | 19 ++- R/null_replace.R | 8 - R/order_by.R | 4 R/order_expr.R | 4 R/pre_sql.R | 29 ++--- R/project.R | 31 ++--- R/quantile.R | 26 +++- R/rename.R | 4 R/rlook.R | 6 - R/rsummary.R | 56 ++++++--- R/select_columns.R | 12 -- R/select_rows.R | 4 R/set_indicator.R | 4 R/sql_node.R | 4 R/table_source.R | 7 - R/theta_join.R | 20 --- R/tokenize_for_sql.R | 4 R/union_all.R | 4 R/utils.R | 21 +++ README.md | 111 ++++--------------- build/vignette.rds |binary inst/doc/AssigmentPartitioner.html | 4 inst/doc/Parameterized_rquery.html | 4 inst/doc/PipeableSQL.html | 4 inst/doc/QueryGeneration.html | 4 inst/doc/R_mapping.R |only inst/doc/R_mapping.Rmd |only inst/doc/R_mapping.html |only inst/doc/rquery_intro.html | 26 ++-- inst/doc/rquery_substitution.Rmd | 1 inst/doc/rquery_substitution.html | 25 ++-- inst/doc/sql_quoting.html | 20 +-- inst/unit_tests/test_distinct.R |only man/expand_grid.Rd | 4 man/lookup_by_column.Rd | 4 man/materialize.Rd | 4 man/materialize_node.Rd | 7 + man/materialize_sql.Rd | 4 man/non_sql_node.Rd | 7 + man/pre_sql_to_query.Rd | 4 man/pre_sql_to_query.pre_sql_sub_expr.Rd | 5 man/pre_sql_to_query.pre_sql_token.Rd | 5 man/quantile_cols.Rd | 4 man/quantile_node.Rd | 5 man/rq_coltypes.Rd | 6 - man/rq_connection_tests.Rd | 1 man/rq_copy_to.Rd | 6 - man/rq_function_mappings.Rd |only man/rq_nrow.Rd | 6 - man/rq_remove_table.Rd | 6 - man/rq_table_exists.Rd | 6 - man/rstr.Rd | 8 + man/rsummary.Rd | 4 vignettes/R_mapping.Rmd |only vignettes/rquery_substitution.Rmd | 1 68 files changed, 651 insertions(+), 451 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates
graphics with details from statistical tests included in the plots
themselves. It is targeted primarily at behavioral sciences community
to provide a one-line code to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports only the most common types of
statistical tests: parametric, nonparametric, robust, and bayesian
versions of t-test/anova, correlation analyses, contingency table
analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, ctb]
(<https://orcid.org/0000-0003-1995-6531>),
Chuck Powell [aut, ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.0.10 dated 2019-03-17 and 0.0.11 dated 2019-06-14
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ggstatsplot-0.0.10/ggstatsplot/tests/testthat/test_subtitle_kw_nonparametric.R |only ggstatsplot-0.0.10/ggstatsplot/tests/testthat/test_subtitle_mann_nonparametric.R |only ggstatsplot-0.0.11/ggstatsplot/DESCRIPTION | 29 ggstatsplot-0.0.11/ggstatsplot/MD5 | 343 +-- ggstatsplot-0.0.11/ggstatsplot/NAMESPACE | 25 ggstatsplot-0.0.11/ggstatsplot/NEWS.md | 63 ggstatsplot-0.0.11/ggstatsplot/R/ggbarstats.R | 45 ggstatsplot-0.0.11/ggstatsplot/R/ggbetweenstats.R | 191 + ggstatsplot-0.0.11/ggstatsplot/R/ggcoefstats.R | 510 ++--- ggstatsplot-0.0.11/ggstatsplot/R/ggdotplotstats.R | 22 ggstatsplot-0.0.11/ggstatsplot/R/gghistostats.R | 47 ggstatsplot-0.0.11/ggstatsplot/R/ggpiestats.R | 47 ggstatsplot-0.0.11/ggstatsplot/R/ggscatterstats.R | 70 ggstatsplot-0.0.11/ggstatsplot/R/ggstatsplot-package.R | 9 ggstatsplot-0.0.11/ggstatsplot/R/ggwithinstats.R | 239 +- ggstatsplot-0.0.11/ggstatsplot/R/global_vars.R | 12 ggstatsplot-0.0.11/ggstatsplot/R/grouped_ggbarstats.R | 53 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Title: Bayesian Projection of Life Expectancy
Description: Making probabilistic projections of life expectancy for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-012-0193-x>.
Author: Hana Sevcikova, Adrian Raftery, Jennifer Chunn
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesLife versions 3.2-0 dated 2017-10-14 and 4.0-2 dated 2019-06-14
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man/e0.raftery.diag.Rd | 9 man/e0.trajectories.plot.Rd | 18 man/e0options.Rd |only man/get.e0.mcmc.Rd | 13 man/get.e0.parameter.traces.Rd | 22 man/get.e0.prediction.Rd | 12 man/get.thinned.e0.mcmc.Rd | 16 man/include.Rd | 16 man/joint.male.estimate.Rd | 10 man/joint.male.predict.Rd | 11 man/run.e0.mcmc.Rd | 110 man/run.e0.mcmc.extra.Rd | 16 man/summary-mcmc.Rd | 10 tests/test_functions.R | 52 769 files changed, 2204 insertions(+), 1910 deletions(-)
Title: Quantitative Fatty Acid Signature Analysis
Description: Accurate estimates of the diets of predators are required
in many areas of ecology, but for many species current methods are
imprecise, limited to the last meal, and often biased. The diversity
of fatty acids and their patterns in organisms, coupled with the
narrow limitations on their biosynthesis, properties of digestion in
monogastric animals, and the prevalence of large storage reservoirs of
lipid in many predators, led us to propose the use of quantitative
fatty acid signature analysis (QFASA) to study predator diets.
Author: Sara Iverson [aut],
Chris Field [aut],
Don Bowen [aut],
Wade Blanchard [aut],
Connie Stewart [aut, cph],
Shelley Lang [aut],
Justin Kamerman [cre, cph],
Hongchang Bao [ctb]
Maintainer: Justin Kamerman <justin@kaleco.net>
Diff between QFASA versions 1.0.2 dated 2016-10-29 and 1.0.3 dated 2019-06-14
QFASA-1.0.2/QFASA/inst/CITATION |only QFASA-1.0.2/QFASA/man/multiplot.Rd |only QFASA-1.0.3/QFASA/DESCRIPTION | 21 QFASA-1.0.3/QFASA/MD5 | 83 +- QFASA-1.0.3/QFASA/NAMESPACE | 11 QFASA-1.0.3/QFASA/NEWS.md | 11 QFASA-1.0.3/QFASA/R/Confidence_Interval_Beta_Distribution.R |only QFASA-1.0.3/QFASA/R/FAset.R | 3 QFASA-1.0.3/QFASA/R/Prey_Cluster.R |only QFASA-1.0.3/QFASA/R/prey.on.prey.R |only QFASA-1.0.3/QFASA/R/pseudo.pred.R |only QFASA-1.0.3/QFASA/R/qfasa.R | 325 ++++++---- QFASA-1.0.3/QFASA/build/vignette.rds |binary QFASA-1.0.3/QFASA/inst/doc/ModelingWorkflow.Rmd | 9 QFASA-1.0.3/QFASA/inst/doc/ModelingWorkflow.html | 386 +++++++++--- QFASA-1.0.3/QFASA/inst/doc/ParallelExecution.R |only QFASA-1.0.3/QFASA/inst/doc/ParallelExecution.Rmd |only QFASA-1.0.3/QFASA/inst/doc/ParallelExecution.html |only QFASA-1.0.3/QFASA/man/AIT.dist.Rd | 4 QFASA-1.0.3/QFASA/man/AIT.more.Rd | 9 QFASA-1.0.3/QFASA/man/AIT.obj.Rd | 5 QFASA-1.0.3/QFASA/man/CC.Rd | 1 QFASA-1.0.3/QFASA/man/CS.more.Rd | 11 QFASA-1.0.3/QFASA/man/CS.obj.Rd | 15 QFASA-1.0.3/QFASA/man/FAset.Rd | 7 QFASA-1.0.3/QFASA/man/KL.dist.Rd | 5 QFASA-1.0.3/QFASA/man/KL.more.Rd | 9 QFASA-1.0.3/QFASA/man/KL.obj.Rd | 9 QFASA-1.0.3/QFASA/man/MEANmeth.Rd | 1 QFASA-1.0.3/QFASA/man/QFASA.Rd | 1 QFASA-1.0.3/QFASA/man/QFASA.const.eqn.Rd | 9 QFASA-1.0.3/QFASA/man/Tstar.beta.Rd |only QFASA-1.0.3/QFASA/man/beta.meths.CI.Rd |only QFASA-1.0.3/QFASA/man/beta.pval.k.Rd |only QFASA-1.0.3/QFASA/man/bias.all.Rd |only QFASA-1.0.3/QFASA/man/bisect.beta.lim.Rd |only QFASA-1.0.3/QFASA/man/chisq.CA.Rd |only QFASA-1.0.3/QFASA/man/chisq.dist.Rd | 4 QFASA-1.0.3/QFASA/man/create.d.mat.Rd |only QFASA-1.0.3/QFASA/man/data.sim.beta.Rd |only QFASA-1.0.3/QFASA/man/gen.pseudo.seals.Rd |only QFASA-1.0.3/QFASA/man/mean.geometric.Rd | 1 QFASA-1.0.3/QFASA/man/p.QFASA.Rd | 25 QFASA-1.0.3/QFASA/man/p.beta.Rd |only QFASA-1.0.3/QFASA/man/predatorFAs.Rd | 1 QFASA-1.0.3/QFASA/man/prey.cluster.Rd |only QFASA-1.0.3/QFASA/man/prey.on.prey.Rd |only QFASA-1.0.3/QFASA/man/preyFAs.Rd | 1 QFASA-1.0.3/QFASA/man/pseudo.pred.Rd |only QFASA-1.0.3/QFASA/man/pseudo.seal.Rd |only QFASA-1.0.3/QFASA/man/split.prey.Rd |only QFASA-1.0.3/QFASA/man/testfordiff.ind.boot.Rd |only QFASA-1.0.3/QFASA/man/testfordiff.ind.boot.fun.Rd |only QFASA-1.0.3/QFASA/man/testfordiff.ind.pval.Rd |only QFASA-1.0.3/QFASA/man/uniroot.beta.Rd |only QFASA-1.0.3/QFASA/vignettes/ModelingWorkflow.Rmd | 9 QFASA-1.0.3/QFASA/vignettes/ParallelExecution.Rmd |only 57 files changed, 678 insertions(+), 298 deletions(-)
Title: Modified Versions of Mann Kendall and Spearman's Rho Trend Tests
Description: Power of non-parametric Mann-Kendall test and Spearman’s Rho test is highly influenced by serially correlated data. To address this issue, trend tests may be applied on the modified versions of the time series data by Block Bootstrapping (BBS), Prewhitening (PW) , Trend Free Prewhitening (TFPW), Bias Corrected Prewhitening and Variance Correction Approach by calculating effective sample size.
Mann, H. B. (1945).<doi:10.1017/CBO9781107415324.004>.
Kendall, M. (1975). Multivariate analysis. Charles Griffin&Company Ltd,.
sen, P. K. (1968).<doi:10.2307/2285891>.
Önöz, B., & Bayazit, M. (2012) <doi:10.1002/hyp.8438>.
Hamed, K. H. (2009).<doi:10.1016/j.jhydrol.2009.01.040>.
Yue, S., & Wang, C. Y. (2002) <doi:10.1029/2001WR000861>.
Yue, S., Pilon, P., Phinney, B., & Cavadias, G. (2002) <doi:10.1002/hyp.1095>.
Hamed, K. H., & Ramachandra Rao, A. (1998) <doi:10.1016/S0022-1694(97)00125-X>.
Yue, S., & Wang, C. Y. (2004) <doi:10.1023/B:WARM.0000043140.61082.60>.
Author: Sandeep Kumar Patakamuri [aut, cre],
Nicole O'Brien [aut, ctb]
Maintainer: Sandeep Kumar Patakamuri <sandeep.patakamuri@gmail.com>
Diff between modifiedmk versions 1.3.1 dated 2019-03-31 and 1.4.0 dated 2019-06-14
DESCRIPTION | 6 ++--- MD5 | 48 ++++++++++++++++++++++---------------------- R/bbsmk.R | 2 + R/bbssr.R | 4 ++- R/bcpw.R | 50 +++++++++++++++++++++------------------------- R/mkttest.R | 2 - R/mmkh.R | 2 - R/mmkh3.R | 4 +-- R/mmky.R | 2 - R/mmky1.R | 23 +++++++++++---------- R/pbmk.R | 38 ++++++++++++++++++++-------------- R/pwmk.R | 2 - R/spmr.R | 4 +-- R/tfpwmk.R | 4 +-- inst/doc/my-vignette.html | 15 +++++++++---- man/bbssr.Rd | 2 - man/bcpw.Rd | 16 +++++++------- man/mkttest.Rd | 2 - man/mmkh.Rd | 2 - man/mmkh3lag.Rd | 4 +-- man/mmky1lag.Rd | 4 +-- man/pbmk.Rd | 14 +++++++++--- man/pwmk.Rd | 2 - man/spear.Rd | 2 - man/tfpwmk.Rd | 4 +-- 25 files changed, 137 insertions(+), 121 deletions(-)
Title: Deploy 'TensorFlow' Models
Description: Tools to deploy 'TensorFlow' <https://www.tensorflow.org/> models across
multiple services. Currently, it provides a local server for testing 'cloudml'
compatible services.
Author: Javier Luraschi [aut, ctb],
Daniel Falbel [cre, ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between tfdeploy versions 0.6.0 dated 2019-02-05 and 0.6.1 dated 2019-06-14
tfdeploy-0.6.0/tfdeploy/tests/testthat/helper-cloudml.R |only tfdeploy-0.6.0/tfdeploy/tests/testthat/helper-initialize.R |only tfdeploy-0.6.0/tfdeploy/tests/testthat/models/keras-mnist |only tfdeploy-0.6.0/tfdeploy/tests/testthat/models/keras-multiple |only tfdeploy-0.6.0/tfdeploy/tests/testthat/models/tensorflow-multiple |only tfdeploy-0.6.0/tfdeploy/tests/testthat/models/tfestimators-example |only tfdeploy-0.6.0/tfdeploy/tests/testthat/models/tfestimators-example.R |only tfdeploy-0.6.0/tfdeploy/tests/testthat/models/tfestimators-mtcars |only tfdeploy-0.6.0/tfdeploy/tests/testthat/models/tfestimators-mtcars.tar |only tfdeploy-0.6.0/tfdeploy/tests/testthat/requests |only tfdeploy-0.6.0/tfdeploy/tests/testthat/test-predict-cloudml.R |only tfdeploy-0.6.0/tfdeploy/tests/testthat/test-predict-compare.R |only tfdeploy-0.6.0/tfdeploy/tests/testthat/test-predict-export.R |only tfdeploy-0.6.0/tfdeploy/tests/testthat/test-predict-serve.R |only tfdeploy-0.6.0/tfdeploy/tests/testthat/utils.R |only tfdeploy-0.6.1/tfdeploy/DESCRIPTION | 18 tfdeploy-0.6.1/tfdeploy/MD5 | 75 +-- tfdeploy-0.6.1/tfdeploy/R/load.R | 21 tfdeploy-0.6.1/tfdeploy/R/swagger.R | 7 tfdeploy-0.6.1/tfdeploy/R/utils.R | 7 tfdeploy-0.6.1/tfdeploy/build/vignette.rds |binary tfdeploy-0.6.1/tfdeploy/inst/doc/introduction.html | 229 +++++----- tfdeploy-0.6.1/tfdeploy/inst/doc/saved_models.html | 39 - tfdeploy-0.6.1/tfdeploy/man/load_savedmodel.Rd | 4 tfdeploy-0.6.1/tfdeploy/tests/testthat/data |only tfdeploy-0.6.1/tfdeploy/tests/testthat/helper-model-building.R |only tfdeploy-0.6.1/tfdeploy/tests/testthat/helper-serve.R | 31 - tfdeploy-0.6.1/tfdeploy/tests/testthat/helper-utils.R |only tfdeploy-0.6.1/tfdeploy/tests/testthat/model-building |only tfdeploy-0.6.1/tfdeploy/tests/testthat/models/keras-1.12.0 |only tfdeploy-0.6.1/tfdeploy/tests/testthat/models/keras-1.13.1 |only tfdeploy-0.6.1/tfdeploy/tests/testthat/models/keras-2.0.0-alpha0 |only tfdeploy-0.6.1/tfdeploy/tests/testthat/models/keras-multiple-1.13.1 |only tfdeploy-0.6.1/tfdeploy/tests/testthat/models/keras-multiple-2.0.0-alpha0 |only tfdeploy-0.6.1/tfdeploy/tests/testthat/models/tensorflow-1.12.0 |only tfdeploy-0.6.1/tfdeploy/tests/testthat/models/tensorflow-1.13.1 |only tfdeploy-0.6.1/tfdeploy/tests/testthat/test-serve.R | 53 +- 37 files changed, 259 insertions(+), 225 deletions(-)
Title: An R Package for Creating Ternary Plots
Description: Plots ternary diagrams using the standard graphics functions.
An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Ternary versions 1.1.0 dated 2019-04-15 and 1.1.1 dated 2019-06-14
DESCRIPTION | 8 +-- MD5 | 33 ++++++++-------- NAMESPACE | 3 + NEWS.md | 4 + R/Contours.R | 4 - R/TernaryPlot.R | 77 ++++++++++++++++++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Using-Ternary.R | 27 +++++++------ inst/doc/Using-Ternary.Rmd | 33 +++++++++------- inst/doc/Using-Ternary.html | 86 ++++++++++++++++++++++-------------------- man/AddToTernary.Rd | 36 +++++++++++------ man/CoordinatesToXY.Rd |only man/TernaryDensityContour.Rd | 24 +++++++++++ man/TernaryPlot.Rd | 5 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-ternary.R | 11 +++-- vignettes/Using-Ternary.Rmd | 33 +++++++++------- 18 files changed, 245 insertions(+), 139 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>),
Vector Exponential Smoothing (de Silva et al., 2010, <doi: 10.1177/1471082X0901000401>) in state space forms,
several simulation functions and intermittent demand state space models. It also allows dealing with
intermittent demand based on the iETS framework (Svetunkov & Boylan, 2017, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 2.5.0 dated 2019-04-25 and 2.5.1 dated 2019-06-14
DESCRIPTION | 21 - MD5 | 195 ++++++------ NAMESPACE | 2 NEWS | 23 + R/autoces.R | 47 +- R/autogum.R | 117 ++++--- R/automsarima.R | 101 +++--- R/autossarima.R | 103 +++--- R/ces.R | 86 ++--- R/cma.R | 79 ++-- R/depricator.R |only R/es.R | 181 ++++++----- R/gsi.R | 216 +++++++------ R/gum.R | 85 ++--- R/iss.R | 110 +++--- R/methods.R | 151 ++++----- R/msarima.R | 83 ++--- R/oes.R | 524 +++++++++++++++++++++++++-------- R/oesg.R | 99 +++--- R/simces.R | 2 R/simes.R | 2 R/simgum.R | 2 R/simsma.R | 2 R/simssarima.R | 4 R/simves.R | 3 R/sma.R | 67 ++-- R/smoothCombine.R | 102 +++--- R/ssarima.R | 88 +++-- R/ssfunctions.R | 666 +++++++++++++++++++++--------------------- R/ves.R | 100 +++--- R/viss.R | 48 +-- R/vmethods.R | 62 +-- R/vssFunctions.R | 152 ++++----- build/partial.rdb |binary inst/doc/ces.R | 8 inst/doc/ces.Rmd | 12 inst/doc/ces.html | 71 ++-- inst/doc/es.R | 13 inst/doc/es.Rmd | 23 - inst/doc/es.html | 199 ++++++------ inst/doc/gum.R | 2 inst/doc/gum.Rmd | 2 inst/doc/gum.html | 24 - inst/doc/oes.R | 2 inst/doc/oes.Rmd | 57 +-- inst/doc/oes.html | 186 +++++------ inst/doc/simulate.html | 76 ++-- inst/doc/sma.R | 2 inst/doc/sma.Rmd | 2 inst/doc/sma.html | 17 - inst/doc/smooth.Rmd | 6 inst/doc/smooth.html | 10 inst/doc/ssarima.R | 4 inst/doc/ssarima.Rmd | 4 inst/doc/ssarima.html | 60 +-- inst/doc/ves.Rmd | 2 inst/doc/ves.html | 10 man/auto.ces.Rd | 34 +- man/auto.gum.Rd | 50 +-- man/auto.msarima.Rd | 41 +- man/auto.ssarima.Rd | 41 +- man/ces.Rd | 55 +-- man/cma.Rd | 26 - man/es.Rd | 81 ++--- man/forecast.smooth.Rd | 16 - man/gsi.Rd | 37 +- man/gum.Rd | 69 ++-- man/iss.Rd | 2 man/msarima.Rd | 52 +-- man/oes.Rd | 37 +- man/oesg.Rd | 26 - man/pls.Rd | 2 man/sim.ces.Rd | 4 man/sim.es.Rd | 4 man/sim.gum.Rd | 6 man/sim.sma.Rd | 4 man/sim.ssarima.Rd | 4 man/sim.ves.Rd | 4 man/sma.Rd | 43 +- man/smooth.Rd | 2 man/smoothCombine.Rd | 58 +-- man/ssarima.Rd | 53 +-- man/ves.Rd | 39 +- man/viss.Rd | 12 src/ssGeneral.cpp | 5 src/ssOccurrence.cpp | 2 tests/testthat/test_ces.R | 4 tests/testthat/test_es.R | 6 tests/testthat/test_ges.R | 4 tests/testthat/test_ssarima.R | 4 tests/testthat/test_ves.R | 10 vignettes/ces.Rmd | 12 vignettes/es.Rmd | 23 - vignettes/gum.Rmd | 2 vignettes/oes.Rmd | 57 +-- vignettes/sma.Rmd | 2 vignettes/smooth.Rmd | 6 vignettes/ssarima.Rmd | 4 vignettes/ves.Rmd | 2 99 files changed, 2905 insertions(+), 2355 deletions(-)
Title: Reconstruct Animal Paths from Solar Geolocation Loggers Data
Description: Spatio-temporal locations of an animal are computed
from annotated data with a hidden Markov model via particle
filter algorithm. The package is relatively robust to varying
degrees of shading.
The hidden Markov model is described in Movement Ecology (Rakhimberdiev et al., 2015) <doi:10.1186/s40462-015-0062-5>,
general package description is in the Methods in Ecology and Evolution (Rakhimberdiev et al., 2017) <doi:10.1111/2041-210X.12765>
and package accuracy assessed in the Journal of Avian Biology (Rakhimberdiev et al. 2016) <doi:10.1111/jav.00891>.
Author: Eldar Rakhimberdiev [aut, cre],
Anatoly Saveliev [aut],
Julia Karagicheva [aut],
Simeon Lisovski [ctb]
Maintainer: Eldar Rakhimberdiev <e.rakhimberdiev@rug.nl>
Diff between FLightR versions 0.4.8 dated 2019-02-07 and 0.4.9 dated 2019-06-14
DESCRIPTION | 21 MD5 | 19 NAMESPACE | 1 R/data_preparation.R | 10 R/summary_functions.R | 42 README.md | 4 build/vignette.rds |binary inst/doc/FLightR_with_black-tailed_godwit_vignette_from_MEE_2017.Rmd | 8 inst/doc/FLightR_with_black-tailed_godwit_vignette_from_MEE_2017.html | 721 +++++----- man/FLightR2Movebank.Rd |only vignettes/FLightR_with_black-tailed_godwit_vignette_from_MEE_2017.Rmd | 8 11 files changed, 460 insertions(+), 374 deletions(-)
Title: R Interface to C API of COIN-or Clp
Description: R Interface to C API of COIN-OR Clp, depends on COIN-OR Clp Version >= 1.12.0.
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut],
C. Jonathan Fritzemeier [ctb]
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
Diff between clpAPI versions 1.2.9 dated 2018-09-24 and 1.2.11 dated 2019-06-14
DESCRIPTION | 10 - MD5 | 34 ++-- NAMESPACE | 6 R/clpAPI.R | 69 ++++++++ build/vignette.rds |binary cleanup | 4 configure | 350 ++++++++++++++++++++++++++++++++++++-------- configure.ac | 37 ++++ inst/NEWS.Rd | 18 ++ inst/c2r.map | 6 inst/doc/clpAPI.pdf |binary man/modifyCoefficientCLP.Rd |only man/setColNameCLP.Rd |only man/setRowNameCLP.Rd |only man/writeMPSCLP.Rd |only src/clpAPI.c | 106 ++++++++++++- src/clpAPI.h | 16 ++ src/clpR.h | 12 + src/config.h |only src/config.h.in |only src/init.c | 6 21 files changed, 583 insertions(+), 91 deletions(-)
Title: A Calculator for Single-Case Effect Sizes
Description: Provides R functions for calculating basic effect size indices for
single-case designs, including several non-overlap measures and parametric
effect size measures, and for estimating the gradual effects model developed
by Swan and Pustejovsky (2018) <DOI:10.1080/00273171.2018.1466681>.
Standard errors and confidence intervals (based on the assumption that the outcome
measurements are mutually independent) are provided for the subset of effect sizes
indices with known sampling distributions.
Author: James E. Pustejovsky [aut, cre],
Daniel M. Swan [aut]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Diff between SingleCaseES versions 0.4.1 dated 2019-01-06 and 0.4.2 dated 2019-06-14
DESCRIPTION | 13 MD5 | 62 NEWS.md | 9 R/SCD-effect-sizes.R | 144 - R/calculate-effect-sizes.R | 30 R/data-documentation.R |only R/gradual-effects-model.R | 3 R/parametric-measures.R | 2 build/vignette.rds |binary data/Wright2012.RData |only inst/WORDLIST | 5 inst/doc/Effect-size-definitions.Rmd | 1 inst/doc/Effect-size-definitions.html | 16 inst/doc/Using-SingleCaseES.R | 6 inst/doc/Using-SingleCaseES.Rmd | 17 inst/doc/Using-SingleCaseES.html | 1027 +++++------ inst/shiny-examples/SCD-effect-sizes/mappings.R | 15 inst/shiny-examples/SCD-effect-sizes/markdown/About.md | 6 inst/shiny-examples/SCD-effect-sizes/markdown/using_batch.md | 19 inst/shiny-examples/SCD-effect-sizes/server.R | 35 inst/shiny-examples/SCD-effect-sizes/ui.R | 30 man/McKissick.Rd | 2 man/Schmidt2007.Rd | 2 man/Schmidt2012.Rd | 2 man/Shogren.Rd | 2 man/Thorne.Rd | 2 man/Wright2012.Rd |only man/batch_calc_ES.Rd | 13 man/calc_ES.Rd | 8 tests/testthat/test-Pustejovsky-2015.R | 4 tests/testthat/test-Pustejovsky-2018-LRR.R | 2 tests/testthat/test-phase-selection.R |only vignettes/Effect-size-definitions.Rmd | 1 vignettes/Using-SingleCaseES.Rmd | 17 34 files changed, 737 insertions(+), 758 deletions(-)
Title: Interface to the 'Open Tree of Life' API
Description: An interface to the 'Open Tree of Life' API to retrieve
phylogenetic trees, information about studies used to assemble the synthetic
tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The
'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all
named species.
Author: Francois Michonneau [aut, cre]
(<https://orcid.org/0000-0002-9092-966X>),
Joseph Brown [aut] (<https://orcid.org/0000-0002-3835-8062>),
David Winter [aut] (<https://orcid.org/0000-0002-6165-0029>),
Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rotl versions 3.0.7 dated 2019-02-15 and 3.0.9 dated 2019-06-14
rotl-3.0.7/rotl/inst/doc/how-to-use-rotl.R |only rotl-3.0.7/rotl/inst/doc/how-to-use-rotl.Rmd |only rotl-3.0.7/rotl/inst/doc/how-to-use-rotl.html |only rotl-3.0.7/rotl/vignettes/how-to-use-rotl.Rmd |only rotl-3.0.9/rotl/DESCRIPTION | 6 rotl-3.0.9/rotl/MD5 | 28 +- rotl-3.0.9/rotl/NEWS.md | 4 rotl-3.0.9/rotl/R/api-studies.R | 11 rotl-3.0.9/rotl/README.md | 33 +- rotl-3.0.9/rotl/build/vignette.rds |binary rotl-3.0.9/rotl/inst/doc/data_mashups.html | 295 ++++++++++++++++------ rotl-3.0.9/rotl/inst/doc/meta-analysis.Rmd | 2 rotl-3.0.9/rotl/inst/doc/meta-analysis.html | 125 ++++----- rotl-3.0.9/rotl/inst/doc/rotl.R |only rotl-3.0.9/rotl/inst/doc/rotl.Rmd |only rotl-3.0.9/rotl/inst/doc/rotl.html |only rotl-3.0.9/rotl/tests/testthat/test-api-studies.R | 4 rotl-3.0.9/rotl/vignettes/meta-analysis.Rmd | 2 rotl-3.0.9/rotl/vignettes/rotl.Rmd |only 19 files changed, 337 insertions(+), 173 deletions(-)
Title: Handy File and String Manipulation
Description: This started out as a package for file and string manipulation.
Since then, the 'fs' and 'strex' packages emerged, offering functionality
previously given by this package (but it's done better in these new ones).
Those packages have hence almost pushed 'filesstrings' into extinction.
However, it still has a small number of unique, handy file manipulation
functions which can be seen in the vignette.
One example is a function to remove spaces from all file names in a
directory.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>),
Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between filesstrings versions 3.1.3 dated 2019-06-06 and 3.1.4 dated 2019-06-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 +++++++- build/partial.rdb |binary inst/doc/files.html | 4 ++-- tests/testthat/test_strings.R | 8 ++++---- 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Generation of ENVIREM Variables
Description: Generation of bioclimatic rasters that will be particularly
useful for species distribution modeling.
Author: Pascal O. Title, Jordan B. Bemmels
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between envirem versions 1.4 dated 2019-01-29 and 1.5 dated 2019-06-14
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/envirem-package.R | 6 +++--- R/generateRasters.R | 14 +++++++------- R/layerCreation.R | 30 +++++++++++++++--------------- R/pacificCentric.R | 2 +- R/topoWetnessIndex.R | 2 +- R/verifyFileStructure.R | 12 ++++++------ man/envirem.Rd | 6 +++--- man/generateRasters.Rd | 4 ++-- man/growingDegDays.Rd | 9 ++++----- man/topoWetnessIndex.Rd | 2 +- 12 files changed, 59 insertions(+), 60 deletions(-)
Title: Representation of DET Curve with Confidence Intervals
Description: Builds both ROC (Receiver Operating Characteristic) and DET (Detection Error Tradeoff) curves from a set of predictors, which are the
results of a binary classification system. The curves give a general vision of the performance of the classifier,
and are useful for comparing performance of different systems.
Author: García-Ródenas, Álvaro [aut, cre],
Franco, Manuel [aut],
Vivo, Juana-María [aut],
Fernández-Breis, Jesualdo T. [aut],
Font, Roberto [aut]
Maintainer: "García-Ródenas, Álvaro" <alvaro.garcia9@um.es>
Diff between DET versions 2.0.0 dated 2019-05-30 and 2.0.1 dated 2019-06-14
DESCRIPTION | 7 +++-- MD5 | 21 ++++++++++++----- NEWS.md | 10 ++++++++ R/detcurve.R | 59 +++++++++++++++++++++++++++++++++++-------------- R/ovarianCancer-data.R |only R/print.R | 3 ++ R/speaker-data.R |only data |only man/detc.CI.Rd | 19 ++++++++++++++- man/detc.Rd | 15 +++++++++--- man/ovarianCancer.Rd |only man/speaker.Rd |only 12 files changed, 104 insertions(+), 30 deletions(-)
Title: Visualize Data for Host and Viral Population from 'SMITIDstruct'
using HTMLwidgets
Description: Visualisation tools for 'SMITIDstruct' package.
Allow to visualize host timeline, transmission tree, index diversities
and variant graph using HTMLwidgets. It mainly using D3JS javascript framework.
Author: Jean-Francois Rey [aut, cre],
Julien Boge [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inra.fr>
Diff between SMITIDvisu versions 0.0.4 dated 2019-03-05 and 0.0.6 dated 2019-06-14
SMITIDvisu-0.0.4/SMITIDvisu/inst/htmlwidgets/lib/d3-4.12.2 |only SMITIDvisu-0.0.6/SMITIDvisu/DESCRIPTION | 20 + SMITIDvisu-0.0.6/SMITIDvisu/MD5 | 105 +++++++--- SMITIDvisu-0.0.6/SMITIDvisu/NAMESPACE | 7 SMITIDvisu-0.0.6/SMITIDvisu/R/SMITIDvisu.R | 7 SMITIDvisu-0.0.6/SMITIDvisu/R/data-format.R | 13 - SMITIDvisu-0.0.6/SMITIDvisu/R/df2geojson.R |only SMITIDvisu-0.0.6/SMITIDvisu/R/maptt.R |only SMITIDvisu-0.0.6/SMITIDvisu/R/timeLine.R | 5 SMITIDvisu-0.0.6/SMITIDvisu/R/tools.R |only SMITIDvisu-0.0.6/SMITIDvisu/R/transmissionTree.R | 6 SMITIDvisu-0.0.6/SMITIDvisu/R/transmissionTreeProxy.R |only SMITIDvisu-0.0.6/SMITIDvisu/data/hostline.rda |binary SMITIDvisu-0.0.6/SMITIDvisu/data/st.rda |binary SMITIDvisu-0.0.6/SMITIDvisu/data/transmissiontree.rda |binary SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/lib/d3-5.9.2 |only SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/lib/forcegraph.js | 2 SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/lib/iso8601-0.2 |only SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/lib/leaflet-1.4.0 |only SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/lib/maptt |only SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/lib/timeline.js | 3 SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/lib/timetree.js | 91 +++++++- SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/maptt.js |only SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/maptt.yaml |only SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/mstVariant.yaml | 4 SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/timeLine.yaml | 4 SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/transmissionTree.js | 37 +++ SMITIDvisu-0.0.6/SMITIDvisu/inst/htmlwidgets/transmissionTree.yaml | 4 SMITIDvisu-0.0.6/SMITIDvisu/man/SMITIDvisu-package.Rd | 6 SMITIDvisu-0.0.6/SMITIDvisu/man/SMITIDvisu-shiny.Rd | 10 SMITIDvisu-0.0.6/SMITIDvisu/man/createRainbowColors.Rd |only SMITIDvisu-0.0.6/SMITIDvisu/man/df2geojson.Rd |only SMITIDvisu-0.0.6/SMITIDvisu/man/maptt.Rd |only SMITIDvisu-0.0.6/SMITIDvisu/man/timeLine.Rd | 4 SMITIDvisu-0.0.6/SMITIDvisu/man/transmissionTree.Rd | 4 SMITIDvisu-0.0.6/SMITIDvisu/man/transmissionTreeProxy.Rd |only SMITIDvisu-0.0.6/SMITIDvisu/man/tt.edges.Rd | 11 - SMITIDvisu-0.0.6/SMITIDvisu/man/tt.events.Rd |only SMITIDvisu-0.0.6/SMITIDvisu/man/tt.nodes.Rd | 12 - SMITIDvisu-0.0.6/SMITIDvisu/man/updateTransmissionTree.Rd |only SMITIDvisu-0.0.6/SMITIDvisu/tests |only 41 files changed, 265 insertions(+), 90 deletions(-)
Title: Simulation Tools for Planning Vitamin D Studies
Description: Simulation tools for planning Vitamin D studies including
approximation of power. Individual vitamin D status
profiles are simulated, modelling population heterogeneity.
Individuals experience random exposures to infectious agents. Development of infection considers a heterogeneous treatment effect. This is incorporated into the power approximation.
Author: Rebecca Mangan [aut],
Jason Wyse [aut, cre],
Lina Zgaga [aut]
Maintainer: Jason Wyse <wyseja@tcd.ie>
Diff between SimVitD versions 0.1.0 dated 2019-05-03 and 0.1.1 dated 2019-06-14
SimVitD-0.1.0/SimVitD/inst/doc/SimVitD.ltx |only SimVitD-0.1.0/SimVitD/vignettes/SimVitD.ltx |only SimVitD-0.1.1/SimVitD/DESCRIPTION | 15 ++++++++------- SimVitD-0.1.1/SimVitD/MD5 | 17 +++++++++-------- SimVitD-0.1.1/SimVitD/R/power.calc.R | 8 ++++---- SimVitD-0.1.1/SimVitD/build/vignette.rds |binary SimVitD-0.1.1/SimVitD/inst/doc/SimVitD.R |only SimVitD-0.1.1/SimVitD/inst/doc/SimVitD.Rnw |only SimVitD-0.1.1/SimVitD/inst/doc/SimVitD.pdf |binary SimVitD-0.1.1/SimVitD/man/SimVitD-package.Rd | 4 ++-- SimVitD-0.1.1/SimVitD/man/power.calc.Rd | 4 +++- SimVitD-0.1.1/SimVitD/vignettes/SimVitD.Rnw |only 12 files changed, 26 insertions(+), 22 deletions(-)
Title: Pedigree Inference from SNPs
Description: Fast multi-generational pedigree inference from incomplete data on
hundreds of SNPs, including parentage assignment and sibship clustering.
See citation('sequoia') for more information.
Author: Jisca Huisman [aut, cre]
Maintainer: Jisca Huisman <jisca.huisman@gmail.com>
Diff between sequoia versions 1.1.1 dated 2018-08-13 and 1.3.1 dated 2019-06-14
sequoia-1.1.1/sequoia/man/MakeAgeprior.Rd |only sequoia-1.1.1/sequoia/man/SeqDup.Rd |only sequoia-1.3.1/sequoia/DESCRIPTION | 10 sequoia-1.3.1/sequoia/MD5 | 101 sequoia-1.3.1/sequoia/NAMESPACE | 27 sequoia-1.3.1/sequoia/NEWS |only sequoia-1.3.1/sequoia/R/CheckGeno.R |only sequoia-1.3.1/sequoia/R/ComparePeds.R | 37 sequoia-1.3.1/sequoia/R/ConfProb.R | 169 - sequoia-1.3.1/sequoia/R/Data_documentation.R | 48 sequoia-1.3.1/sequoia/R/GenoConvert.R | 439 ++- sequoia-1.3.1/sequoia/R/MkAgePrior.R | 717 ++++-- sequoia-1.3.1/sequoia/R/PairRelation.R |only sequoia-1.3.1/sequoia/R/Prepare.R | 74 sequoia-1.3.1/sequoia/R/SNPstats.R | 49 sequoia-1.3.1/sequoia/R/SeqListSummary.R |only sequoia-1.3.1/sequoia/R/Sequoia_F90wrappers.R | 677 +++-- sequoia-1.3.1/sequoia/R/Sequoia_Main.R | 226 + sequoia-1.3.1/sequoia/R/Simulate.R | 659 ++++- sequoia-1.3.1/sequoia/R/Utils.R | 90 sequoia-1.3.1/sequoia/R/Utils_hermaphrodites.R | 25 sequoia-1.3.1/sequoia/R/WriteToFiles.R | 46 sequoia-1.3.1/sequoia/build/vignette.rds |binary sequoia-1.3.1/sequoia/data/Inherit.RData |only sequoia-1.3.1/sequoia/data/LH_HSg5.txt | 2002 ++++++++-------- sequoia-1.3.1/sequoia/inst/doc/sequoia.R | 169 + sequoia-1.3.1/sequoia/inst/doc/sequoia.Rnw | 454 +++ sequoia-1.3.1/sequoia/inst/doc/sequoia.pdf |binary sequoia-1.3.1/sequoia/inst/extdata |only sequoia-1.3.1/sequoia/man/CheckGeno.Rd | 12 sequoia-1.3.1/sequoia/man/CheckLH.Rd |only sequoia-1.3.1/sequoia/man/DoErrors.Rd |only sequoia-1.3.1/sequoia/man/DyadCompare.Rd | 7 sequoia-1.3.1/sequoia/man/EstConf.Rd | 104 sequoia-1.3.1/sequoia/man/GenoConvert.Rd | 122 - sequoia-1.3.1/sequoia/man/GetMaybeRel.Rd |only sequoia-1.3.1/sequoia/man/GetRelCat.Rd |only sequoia-1.3.1/sequoia/man/Inherit.Rd |only sequoia-1.3.1/sequoia/man/LHConvert.Rd | 29 sequoia-1.3.1/sequoia/man/LH_HSg5.Rd | 14 sequoia-1.3.1/sequoia/man/MakeAgePrior.Rd |only sequoia-1.3.1/sequoia/man/MergeFill.Rd | 7 sequoia-1.3.1/sequoia/man/MkGenoErrors.Rd |only sequoia-1.3.1/sequoia/man/PedCompare.Rd | 26 sequoia-1.3.1/sequoia/man/Ped_HSg5.Rd | 8 sequoia-1.3.1/sequoia/man/PlotAgePrior.Rd |only sequoia-1.3.1/sequoia/man/SeqParSib.Rd | 10 sequoia-1.3.1/sequoia/man/SeqPrep.Rd | 18 sequoia-1.3.1/sequoia/man/SimGeno.Rd | 151 - sequoia-1.3.1/sequoia/man/SimGeno_example.Rd | 2 sequoia-1.3.1/sequoia/man/SnpStats.Rd | 16 sequoia-1.3.1/sequoia/man/SummarySeq.Rd |only sequoia-1.3.1/sequoia/man/WrapDup.Rd |only sequoia-1.3.1/sequoia/man/getGenerations.Rd |only sequoia-1.3.1/sequoia/man/orderLH.Rd | 2 sequoia-1.3.1/sequoia/man/plot.seq.Rd |only sequoia-1.3.1/sequoia/man/sequoia.Rd | 144 - sequoia-1.3.1/sequoia/man/writeSeq.Rd | 9 sequoia-1.3.1/sequoia/src/SimGenoErrors.f90 |only sequoia-1.3.1/sequoia/src/init.c | 89 sequoia-1.3.1/sequoia/src/sequoia.f90 | 2954 +++++++++++++++---------- sequoia-1.3.1/sequoia/vignettes/sequoia.Rnw | 454 +++ 62 files changed, 6598 insertions(+), 3599 deletions(-)
Title: R Interface to 'Bloomberg Data License'
Description: R interface to access prices and market data with the
'Bloomberg Data License' service from
<https://www.bloomberg.com/professional/product/data-license/>.
As a prerequisite, a valid Data License from 'Bloomberg' is needed
together with the corresponding SFTP credentials and whitelisting
of the IP from which accessing the service.
This software and its author are in no way affiliated,
endorsed, or approved by 'Bloomberg' or any of its affiliates.
'Bloomberg' is a registered trademark.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@hotmail.it>
Diff between RblDataLicense versions 0.1.2 dated 2019-03-15 and 0.2.0 dated 2019-06-14
DESCRIPTION | 32 +++++++----- MD5 | 20 +++---- NAMESPACE | 1 R/RblQuery.R | 68 ++++++++++++++++----------- R/core.R | 118 ++++++++++++++++++++++++++++++++++------------- README.md | 97 +++++++++++++++++++++++++++++++++++--- man/RblDownload.Rd | 21 ++++++-- man/RblParse.Rd | 27 ++++++++-- man/RblQuery.Rd | 38 +++++++++------ man/RblRequestBuilder.Rd | 26 +++++++--- man/RblUpload.Rd | 22 +++++++- 11 files changed, 343 insertions(+), 127 deletions(-)
More information about RblDataLicense at CRAN
Permanent link
Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits Poisson-Tweedie generalized linear mixed model.
Likelihood approximation based on adaptive Gauss Hermite quadrature rule.
Author: Mirko Signorelli [aut, cre],
Pietro Spitali [aut],
Roula Tsonaka [aut]
Maintainer: Mirko Signorelli <m.signorelli@lumc.nl>
Diff between ptmixed versions 0.0.4 dated 2019-05-26 and 0.1.2 dated 2019-06-14
ptmixed-0.0.4/ptmixed/inst/NEWS.txt |only ptmixed-0.1.2/ptmixed/DESCRIPTION | 8 - ptmixed-0.1.2/ptmixed/MD5 | 14 +- ptmixed-0.1.2/ptmixed/R/loglik.R | 14 +- ptmixed-0.1.2/ptmixed/R/ptmixed.R | 152 +++++++++++++++++++---------- ptmixed-0.1.2/ptmixed/R/summary.R | 2 ptmixed-0.1.2/ptmixed/inst/NEWS.Rmd |only ptmixed-0.1.2/ptmixed/man/loglik.pt.1re.Rd | 7 - ptmixed-0.1.2/ptmixed/man/ptmixed.Rd | 33 +++--- 9 files changed, 151 insertions(+), 79 deletions(-)
Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between GSED versions 2.1 dated 2019-06-14 and 2.2 dated 2019-06-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/GSED.R | 25 +++++++++++++++---------- man/GSED-package.Rd | 2 +- 4 files changed, 22 insertions(+), 17 deletions(-)
Title: Approximate Bayesian Computation via Random Forests
Description: Performs Approximate Bayesian Computation (ABC) model choice and parameter inference via random forests.
Pudlo P., Marin J.-M., Estoup A., Cornuet J.-M., Gautier M. and Robert C. P. (2016) <doi:10.1093/bioinformatics/btv684>.
Estoup A., Raynal L., Verdu P. and Marin J.-M. <http://journal-sfds.fr/article/view/709>.
Raynal L., Marin J.-M., Pudlo P., Ribatet M., Robert C. P. and Estoup A. (2019) <doi:10.1093/bioinformatics/bty867>.
Author: Jean-Michel Marin [aut, cre],
Louis Raynal [aut],
Pierre Pudlo [aut],
Christian P. Robert [ctb],
Arnaud Estoup [ctb]
Maintainer: Jean-Michel Marin <jean-michel.marin@umontpellier.fr>
Diff between abcrf versions 1.7.1 dated 2018-06-27 and 1.8 dated 2019-06-14
DESCRIPTION | 18 +- MD5 | 49 ++++--- NAMESPACE | 6 R/RcppExports.R | 20 ++- R/abcrf.R | 2 R/predict.abcrf.R | 287 +++++++++++++++++++++++----------------------- R/predict.regAbcrf.R | 160 +++++++++++++++++++++---- R/predictOOB.R | 283 ++++++++++++++++++++++++++++++--------------- R/regAbcrf.R | 10 - R/sampleTest.R |only man/abcrf.Rd | 8 - man/covRegAbcrf.Rd | 6 man/densityPlot.Rd | 6 man/err.abcrf.Rd | 4 man/err.regAbcrf.Rd | 6 man/plot.abcrf.Rd | 4 man/plot.regAbcrf.Rd | 6 man/predict.abcrf.Rd | 14 +- man/predict.regAbcrf.Rd | 30 +++- man/predictOOB.Rd | 21 +-- man/readRefTable.Rd | 5 man/regAbcrf.Rd | 6 man/snp.Rd | 2 src/RcppExports.cpp | 44 ++++++- src/computeNeighbours.cpp |only src/findweights.cpp | 12 - src/findweights_train.cpp |only 27 files changed, 639 insertions(+), 370 deletions(-)
Title: A Lightweight Template for Data Analysis Projects
Description: Creates useful files and folders for data
analysis projects and provides functions to manage data,
scripts and output files. Also provides a project
template for 'Rstudio'.
Author: Francois Guillem
Maintainer: Francois Guillem <guillem.francois@gmail.com>
Diff between tinyProject versions 0.6 dated 2019-06-11 and 0.6.1 dated 2019-06-14
tinyProject-0.6.1/tinyProject/DESCRIPTION | 7 tinyProject-0.6.1/tinyProject/MD5 | 51 +- tinyProject-0.6.1/tinyProject/NAMESPACE | 70 +-- tinyProject-0.6.1/tinyProject/NEWS.md | 23 - tinyProject-0.6.1/tinyProject/R/commandArgs.R | 102 ++--- tinyProject-0.6.1/tinyProject/R/library.R | 186 +++++----- tinyProject-0.6.1/tinyProject/R/project.R | 166 ++++---- tinyProject-0.6.1/tinyProject/R/requireVariable.R | 80 ++-- tinyProject-0.6.1/tinyProject/R/start.R | 98 ++--- tinyProject-0.6.1/tinyProject/R/zzz.R | 14 tinyProject-0.6.1/tinyProject/inst/Rprofile.brew | 37 + tinyProject-0.6.1/tinyProject/man/prInit.Rd | 128 +++--- tinyProject-0.6.1/tinyProject/man/prLibrary.Rd | 60 +-- tinyProject-0.6.1/tinyProject/man/prMoveData.Rd | 82 ++-- tinyProject-0.6.1/tinyProject/man/prMoveScript.Rd | 90 ++-- tinyProject-0.6.1/tinyProject/man/prOutput.Rd | 150 ++++---- tinyProject-0.6.1/tinyProject/man/prOutputDefaults.Rd | 94 ++--- tinyProject-0.6.1/tinyProject/man/prPath.Rd | 50 +- tinyProject-0.6.1/tinyProject/man/prSave.Rd | 124 +++--- tinyProject-0.6.1/tinyProject/man/prScript.Rd | 106 ++--- tinyProject-0.6.1/tinyProject/man/prSource.Rd | 78 ++-- tinyProject-0.6.1/tinyProject/man/prStart.Rd | 56 +-- tinyProject-0.6.1/tinyProject/man/prWriteTable.Rd | 82 ++-- tinyProject-0.6.1/tinyProject/man/requireVariable.Rd | 66 +-- tinyProject-0.6.1/tinyProject/tests/testthat/test-commandArgs.R | 82 ++-- tinyProject-0.6/tinyProject/inst/docker |only 26 files changed, 1045 insertions(+), 1037 deletions(-)
Title: Stacked Species Distribution Modelling
Description: Allows to map species richness and endemism based on stacked
species distribution models (SSDM). Individuals SDMs can be created using a
single or multiple algorithms (ensemble SDMs). For each species, an SDM can
yield a habitat suitability map, a binary map, a between-algorithm variance
map, and can assess variable importance, algorithm accuracy, and between-
algorithm correlation. Methods to stack individual SDMs include summing
individual probabilities and thresholding then summing. Thresholding can be
based on a specific evaluation metric or by drawing repeatedly from a Bernoulli
distribution. The SSDM package also provides a user-friendly interface.
Author: Sylvain Schmitt, Robin Pouteau, Dimitri Justeau, Florian de Boissieu, Philippe Birnbaum
Maintainer: Sylvain Schmitt <sylvain.m.schmitt@gmail.com>
Diff between SSDM versions 0.2.5 dated 2019-05-30 and 0.2.6 dated 2019-06-14
DESCRIPTION | 6 MD5 | 18 NEWS.md | 20 R/PA.select.R | 4 R/load_model.R | 16 R/project.R | 18 README.md | 2 build/vignette.rds |binary inst/doc/GUI.html | 1423 +++++++++++++++++++++++++++++++++++++++++++++++++-- inst/doc/SSDM.html | 1454 ++++++++++++++++++++++++++++++++++++++++++++++++++--- 10 files changed, 2808 insertions(+), 153 deletions(-)
Title: Data Structure and Manipulations Tool for Host and Viral
Population
Description: Statistical Methods for Inferring Transmissions of Infectious Diseases from deep sequencing data (SMITID).
It allow sequence-space-time host and viral population data storage, indexation and querying.
Author: Jean-Francois Rey [aut, cre]
Maintainer: Jean-Francois Rey <jean-francois.rey@inra.fr>
Diff between SMITIDstruct versions 0.0.4 dated 2019-03-05 and 0.0.5 dated 2019-06-14
DESCRIPTION | 10 +++---- MD5 | 22 ++++++++-------- NAMESPACE | 2 + R/Class-Host.R | 4 +- R/Methods-Host.R | 56 +++++++++++++++++++++++------------------ R/Methods-time.R | 5 ++- R/SMITIDstruct.R | 4 +- R/index.R | 58 ++++++++++++++++++++++++++++++++++++++++--- man/SMITIDstruct-package.Rd | 4 +- man/getInfosByHostAndTime.Rd |only man/isInCode.Rd |only man/loadTree.Rd | 4 ++ man/loadTreeDF.Rd | 6 ++-- 13 files changed, 121 insertions(+), 54 deletions(-)
Title: Tools to Support the Sheffield Elicitation Framework
Description: Implements various methods for eliciting a probability distribution
for a single parameter from an expert or a group of experts. The expert
provides a small number of probability judgements, corresponding
to points on his or her cumulative distribution function. A range of parametric
distributions can then be fitted and displayed, with feedback provided in the
form of fitted probabilities and percentiles. For multiple experts, a weighted
linear pool can be calculated. Also includes functions for eliciting beliefs
about population distributions, eliciting multivariate distributions using a
Gaussian copula, eliciting a Dirichlet distribution, and eliciting distributions
for variance parameters in a random effects meta-analysis model. R Shiny apps
for most of the methods are included.
Author: Jeremy Oakley
Maintainer: Jeremy Oakley <j.oakley@sheffield.ac.uk>
Diff between SHELF versions 1.5.0 dated 2019-03-26 and 1.6.0 dated 2019-06-14
DESCRIPTION | 11 MD5 | 59 +- NAMESPACE | 5 R/SHELF-package.R | 2 R/elicit.R | 250 +++++---- R/elicitBivariate.R | 4 R/elicitCopula.R | 26 R/elicitExtension.R |only R/elicitMultipleExperts.R | 422 +++++++++++++--- R/extensionScripts.R |only R/feedbackgroup.R | 6 R/feedbacksingle.R | 71 +- R/fitdist.R | 4 R/makeCDFPlot.R | 113 +++- R/makeSingleExpertPlot.R | 24 R/sampleFit.R | 18 build/vignette.rds |binary inst/NEWS.md | 16 inst/doc/Dirichlet-elicitation.pdf |binary inst/doc/Multivariate-normal-copula.R | 4 inst/doc/Multivariate-normal-copula.Rmd | 4 inst/doc/Multivariate-normal-copula.pdf |binary inst/doc/SHELF-overview.pdf |binary inst/shinyAppFiles/elicitationShinySummaryExtension.Rmd |only inst/shinyAppFiles/elicitationShinySummaryGroup.Rmd | 26 man/SHELF-package.Rd | 2 man/copulaSample.Rd | 2 man/elicitExtension.Rd |only man/makeCDFPlot.Rd |only man/plotConditionalDensities.Rd |only man/plotConditionalMedianFunction.Rd |only man/sampleMarginalFit.Rd |only tests/testthat/test-extension-method.R |only tests/testthat/test-fitting.R | 40 - vignettes/Multivariate-normal-copula.Rmd | 4 35 files changed, 788 insertions(+), 325 deletions(-)
Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor
(Pya and Wood, 2015) <doi:10.1007/s11222-013-9448-7>.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of gam()
in package 'mgcv' are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-3 dated 2018-09-25 and 1.2-4 dated 2019-06-14
ChangeLog | 14 DESCRIPTION | 8 MD5 | 49 - NAMESPACE | 2 R/bfgs.R | 204 +++++- R/bivar.smooth.const.R | 24 R/check.analytical.R | 5 R/estimate.scam.R | 38 - R/scam.r | 942 +++++++++++++++++++++++++++-- build/partial.rdb |binary man/bfgs_gcv.ubre.Rd | 27 man/check.analytical.Rd | 4 man/gcv.ubre_grad.Rd | 22 man/linear.functional.terms.Rd | 4 man/scam.Rd | 33 - man/scam.control.Rd |only man/scam.fit.Rd | 21 man/smooth.construct.tecvcv.smooth.spec.Rd | 8 man/smooth.construct.tecxcv.smooth.spec.Rd | 11 man/smooth.construct.tecxcx.smooth.spec.Rd | 7 man/smooth.construct.tedecv.smooth.spec.Rd | 7 man/smooth.construct.tedecx.smooth.spec.Rd | 16 man/smooth.construct.temicv.smooth.spec.Rd | 12 man/smooth.construct.temicx.smooth.spec.Rd | 13 man/smooth.construct.tescv.smooth.spec.Rd | 13 man/smooth.construct.tescx.smooth.spec.Rd | 17 26 files changed, 1290 insertions(+), 211 deletions(-)
Title: Generator of Experiments
Description: Generates experiments - simulating structured or experimental data as:
completely randomized design, randomized block design, latin square design,
factorial and split-plot experiments (Ferreira, 2008, ISBN:8587692526;
Naes et al., 2007 <doi:10.1002/qre.841>; Rencher et al., 2007, ISBN:9780471754985;
Montgomery, 2001, ISBN:0471316490).
Author: Ivan Bezerra Allaman <ivanalaman@gmail.com> and
José Cláudio Faria <joseclaudio.faria@gmail.com>
Maintainer: Ivan Bezerra Allaman <ivanalaman@gmail.com>
Diff between gexp versions 0.1-4 dated 2019-04-14 and 1.0-0 dated 2019-06-14
gexp-0.1-4/gexp/R/gexp.crd.R |only gexp-0.1-4/gexp/R/gexp.fe.R |only gexp-0.1-4/gexp/R/gexp.lsd.R |only gexp-0.1-4/gexp/R/gexp.rcbd.R |only gexp-0.1-4/gexp/R/gexp.spe.R |only gexp-0.1-4/gexp/R/plot.gexp.crd.R |only gexp-0.1-4/gexp/R/plot.gexp.fe.R |only gexp-0.1-4/gexp/R/plot.gexp.lsd.R |only gexp-0.1-4/gexp/R/plot.gexp.rcbd.R |only gexp-0.1-4/gexp/R/plot.gexp.spe.R |only gexp-1.0-0/gexp/ChangeLog | 16 gexp-1.0-0/gexp/DESCRIPTION | 13 gexp-1.0-0/gexp/MD5 | 72 gexp-1.0-0/gexp/NAMESPACE | 43 gexp-1.0-0/gexp/R/gexp.R | 3 gexp-1.0-0/gexp/R/gexp.default.R | 173 - gexp-1.0-0/gexp/R/gexp.fe_crd.R |only gexp-1.0-0/gexp/R/gexp.fe_lsd.R |only gexp-1.0-0/gexp/R/gexp.fe_rcbd.R |only gexp-1.0-0/gexp/R/gexp.simple_crd.R |only gexp-1.0-0/gexp/R/gexp.simple_lsd.R |only gexp-1.0-0/gexp/R/gexp.simple_rcbd.R |only gexp-1.0-0/gexp/R/gexp.spe_crd.R |only gexp-1.0-0/gexp/R/gexp.spe_lsd.R |only gexp-1.0-0/gexp/R/gexp.spe_rcbd.R |only gexp-1.0-0/gexp/R/latin.R | 53 gexp-1.0-0/gexp/R/makeContrasts.R |only gexp-1.0-0/gexp/R/makeInteraction.R |only gexp-1.0-0/gexp/R/makeTreatments.R |only gexp-1.0-0/gexp/R/makeXBeta.R |only gexp-1.0-0/gexp/R/mgsub.R | 29 gexp-1.0-0/gexp/R/plot.gexp.fe_crd.R |only gexp-1.0-0/gexp/R/plot.gexp.fe_lsd.R |only gexp-1.0-0/gexp/R/plot.gexp.fe_rcbd.R |only gexp-1.0-0/gexp/R/plot.gexp.simple_crd.R |only gexp-1.0-0/gexp/R/plot.gexp.simple_lsd.R |only gexp-1.0-0/gexp/R/plot.gexp.simple_rcbd.R |only gexp-1.0-0/gexp/R/plot.gexp.spe_crd.R |only gexp-1.0-0/gexp/R/plot.gexp.spe_lsd.R |only gexp-1.0-0/gexp/R/plot.gexp.spe_rcbd.R |only gexp-1.0-0/gexp/R/print.gexp.R | 60 gexp-1.0-0/gexp/R/summary.gexp.R | 22 gexp-1.0-0/gexp/build/vignette.rds |binary gexp-1.0-0/gexp/inst/doc/intro.R | 459 +- gexp-1.0-0/gexp/inst/doc/intro.Rmd | 192 - gexp-1.0-0/gexp/inst/doc/intro.html | 4606 ++++++++++++++---------------- gexp-1.0-0/gexp/man/gexp-internal.Rd | 10 gexp-1.0-0/gexp/man/gexp-package.Rd | 4 gexp-1.0-0/gexp/man/gexp.Rd | 1215 +++++-- gexp-1.0-0/gexp/man/plot.Rd | 508 +-- gexp-1.0-0/gexp/man/print.Rd | 287 - gexp-1.0-0/gexp/man/summary.Rd | 286 - gexp-1.0-0/gexp/vignettes/intro.Rmd | 192 - 53 files changed, 4142 insertions(+), 4101 deletions(-)
Title: Calculate Exposures, Assign Records to Intervals
Description: Creation of an exposure table with rows for policy-intervals from a table
with a unique policy number key and beginning and ending dates for each policy.
Methods for assigning supplemental data containing dates and policy numbers
to the corresponding interval from the created exposures table.
Author: Matthew Caseres [aut, cre]
Maintainer: Matthew Caseres <matthewcaseres@outlook.com>
Diff between expstudies versions 0.0.1 dated 2019-05-17 and 0.0.5 dated 2019-06-14
expstudies-0.0.1/expstudies/inst/doc/expstudies_intro.R |only expstudies-0.0.1/expstudies/inst/doc/expstudies_intro.Rmd |only expstudies-0.0.1/expstudies/inst/doc/expstudies_intro.html |only expstudies-0.0.1/expstudies/man/filter_trans.Rd |only expstudies-0.0.1/expstudies/vignettes/expstudies_intro.Rmd |only expstudies-0.0.5/expstudies/DESCRIPTION | 8 expstudies-0.0.5/expstudies/MD5 | 64 ++- expstudies-0.0.5/expstudies/NAMESPACE | 8 expstudies-0.0.5/expstudies/R/RcppExports.R | 17 expstudies-0.0.5/expstudies/R/data.R | 47 +- expstudies-0.0.5/expstudies/R/day_functions.R |only expstudies-0.0.5/expstudies/R/exposure_functions.R | 216 +++++++++-- expstudies-0.0.5/expstudies/R/expstudies-package.R | 8 expstudies-0.0.5/expstudies/R/transaction_functions.R | 39 - expstudies-0.0.5/expstudies/README.md |only expstudies-0.0.5/expstudies/build/vignette.rds |binary expstudies-0.0.5/expstudies/data/mortality_tables.rda |only expstudies-0.0.5/expstudies/inst/doc/creating_exposures.R |only expstudies-0.0.5/expstudies/inst/doc/creating_exposures.Rmd |only expstudies-0.0.5/expstudies/inst/doc/creating_exposures.html |only expstudies-0.0.5/expstudies/inst/doc/premium_pattern.R |only expstudies-0.0.5/expstudies/inst/doc/premium_pattern.Rmd |only expstudies-0.0.5/expstudies/inst/doc/premium_pattern.html |only expstudies-0.0.5/expstudies/inst/doc/rate_calculations.R |only expstudies-0.0.5/expstudies/inst/doc/rate_calculations.Rmd |only expstudies-0.0.5/expstudies/inst/doc/rate_calculations.html |only expstudies-0.0.5/expstudies/man/addDays.Rd |only expstudies-0.0.5/expstudies/man/addExposures.Rd | 9 expstudies-0.0.5/expstudies/man/addStart.Rd | 10 expstudies-0.0.5/expstudies/man/daySize.Rd |only expstudies-0.0.5/expstudies/man/expSize.Rd |only expstudies-0.0.5/expstudies/man/exposures.Rd | 30 - expstudies-0.0.5/expstudies/man/findStart.Rd |only expstudies-0.0.5/expstudies/man/makeDays.Rd |only expstudies-0.0.5/expstudies/man/makeRange.Rd | 45 +- expstudies-0.0.5/expstudies/man/mortality_tables.Rd |only expstudies-0.0.5/expstudies/man/records.Rd | 32 - expstudies-0.0.5/expstudies/man/trans.Rd | 32 - expstudies-0.0.5/expstudies/src/RcppExports.cpp | 15 expstudies-0.0.5/expstudies/src/findStart.cpp | 50 +- expstudies-0.0.5/expstudies/src/makeDays.cpp |only expstudies-0.0.5/expstudies/tests |only expstudies-0.0.5/expstudies/vignettes/creating_exposures.Rmd |only expstudies-0.0.5/expstudies/vignettes/premium_pattern.Rmd |only expstudies-0.0.5/expstudies/vignettes/rate_calculations.Rmd |only 45 files changed, 422 insertions(+), 208 deletions(-)
Title: Software Tools for the Statistical Analysis of Network Data
Description: Statnet is a collection of packages for statistical network analysis that are
designed to work together because they share common data representations and 'API'
design. They provide an integrated set of tools for the representation,
visualization, analysis, and simulation of many different forms of network data.
This package is designed to make it easy to install and load the
key 'statnet' packages in a single step. Learn more about 'statnet'
at <http://www.statnet.org>. Tutorials for many packages can be found
at <https://github.com/statnet/Workshops/wiki>. For an introduction to functions in this package,
type help(package='statnet').
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut] (<https://orcid.org/0000-0002-9101-3362>),
Skye Bender-deMoll [aut],
Martina Morris [aut, cre]
Maintainer: Martina Morris <morrism@uw.edu>
Diff between statnet versions 2018.10 dated 2018-10-22 and 2019.6 dated 2019-06-14
DESCRIPTION | 25 +++++++++++++------------ MD5 | 4 ++-- R/update_statnet.R | 5 ++++- 3 files changed, 19 insertions(+), 15 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code or function documentation. There is a shared object containing part of the 'CVODES' library, but it is not accessible from R. 'StanHeaders' is only useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut],
Trustees of Columbia University [cph],
Lawrence Livermore National Security [cph] (CVODES),
The Regents of the University of California [cph] (CVODES),
Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.18.1 dated 2019-01-28 and 2.18.1-10 dated 2019-06-14
StanHeaders-2.18.1-10/StanHeaders/DESCRIPTION | 11 StanHeaders-2.18.1-10/StanHeaders/MD5 | 1795 +-- StanHeaders-2.18.1-10/StanHeaders/build/vignette.rds |binary StanHeaders-2.18.1-10/StanHeaders/inst/CITATION | 6 StanHeaders-2.18.1-10/StanHeaders/inst/doc/sparselm_stan.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/doc/stanmath.R | 66 StanHeaders-2.18.1-10/StanHeaders/inst/doc/stanmath.Rmd | 364 StanHeaders-2.18.1-10/StanHeaders/inst/doc/stanmath.html | 684 - StanHeaders-2.18.1-10/StanHeaders/inst/include/cvodes/cvodes.h | 2003 --- StanHeaders-2.18.1-10/StanHeaders/inst/include/cvodes/cvodes_bandpre.h | 176 StanHeaders-2.18.1-10/StanHeaders/inst/include/cvodes/cvodes_bbdpre.h | 354 StanHeaders-2.18.1-10/StanHeaders/inst/include/cvodes/cvodes_diag.h | 124 StanHeaders-2.18.1-10/StanHeaders/inst/include/cvodes/cvodes_direct.h | 287 StanHeaders-2.18.1-10/StanHeaders/inst/include/cvodes/cvodes_ls.h |only StanHeaders-2.18.1-10/StanHeaders/inst/include/cvodes/cvodes_spils.h | 609 - StanHeaders-2.18.1-10/StanHeaders/inst/include/idas/idas.h | 2091 --- StanHeaders-2.18.1-10/StanHeaders/inst/include/idas/idas_bbdpre.h | 342 StanHeaders-2.18.1-10/StanHeaders/inst/include/idas/idas_direct.h | 282 StanHeaders-2.18.1-10/StanHeaders/inst/include/idas/idas_ls.h |only StanHeaders-2.18.1-10/StanHeaders/inst/include/idas/idas_spils.h | 585 - StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/cuda/ThreadPartitioning.hpp | 319 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/cuda/Vector.hpp | 225 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/cuda/VectorArrayKernels.cuh |only StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/cuda/VectorKernels.cuh | 283 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_cuda.h | 235 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_mpicuda.h |only StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_mpiraja.h |only StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_openmp.h | 244 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_openmpdev.h |only StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_parallel.h | 272 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_parhyp.h | 193 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_petsc.h | 193 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_pthreads.h | 281 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_raja.h | 222 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_serial.h | 240 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/nvector_trilinos.h |only StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/raja/Vector.hpp | 102 StanHeaders-2.18.1-10/StanHeaders/inst/include/nvector/trilinos |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/analyze |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/command/stanc_helper.hpp | 28 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/array_var_context.hpp | 40 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/ends_with.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/is_whitespace.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/json/json_data_handler.hpp | 18 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/json/json_parser.hpp | 29 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/program_reader.hpp | 512 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/reader.hpp | 2839 ++-- StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/stan_csv_reader.hpp | 48 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/starts_with.hpp | 28 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/trim_spaces.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/io/writer.hpp | 967 - StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast.hpp | 122 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_is_data_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_is_data_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_order_id_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_order_id_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_set_is_data_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_set_is_data_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_total_dims_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_total_dims_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_bounds_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_bounds_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_is_specialized_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_is_specialized_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_offset_multiplier_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_offset_multiplier_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_params_total_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_params_total_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/ends_with_def.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/expression_bare_type_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/expression_bare_type_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/generate_expression.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var_vis.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var_vis_def.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/has_prob_fun_suffix_def.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/has_rng_suffix_def.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var_vis.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var_vis_def.hpp | 207 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/indexed_type.hpp | 32 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/indexed_type_def.hpp | 124 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/infer_type_indexing.hpp | 33 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/infer_type_indexing_def.hpp | 55 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/is_assignable.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/is_assignable_def.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil_vis.hpp | 14 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil_vis_def.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/is_space.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/is_space_def.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/is_user_defined_def.hpp | 20 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/num_index_op_dims.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/num_index_op_dims_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/promote_primitive.hpp | 19 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/promote_primitive_def.hpp | 15 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_def.hpp | 25 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_vis.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_vis_def.hpp | 23 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/strip_ccdf_suffix_def.hpp | 26 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/strip_cdf_suffix_def.hpp | 24 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/strip_prob_fun_suffix_def.hpp | 28 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/var_occurs_vis.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/var_occurs_vis_def.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg1_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg1_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg2_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg2_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_name_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_name_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/write_bare_expr_type.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/write_bare_expr_type_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/write_block_var_type.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/write_block_var_type_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/write_expression_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/write_expression_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/write_idx_vis.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/fun/write_idx_vis_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/array_expr.hpp | 83 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/array_expr_def.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/assgn.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/assgn_def.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/binary_op.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/binary_op_def.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/block_var_decl.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/block_var_decl_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/conditional_op.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/conditional_op_def.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/double_literal.hpp | 67 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/double_literal_def.hpp | 14 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/expression.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/expression_def.hpp | 21 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/fun.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/function_decl_def.hpp | 20 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/function_decl_def_def.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/idx.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/idx_def.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/index_op.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/index_op_def.hpp | 27 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/index_op_sliced.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/int_literal.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/int_literal_def.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_1d.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_1d_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_ode.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/local_var_decl.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/local_var_decl_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/map_rect.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/map_rect_def.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/matrix_expr.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/offset_multiplier.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/offset_multiplier_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/printable.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/program.hpp | 22 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/program_def.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/range.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/row_vector_expr.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/sample_def.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/statements.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/statements_def.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/unary_op.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/unary_op_def.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/var_decl.hpp | 214 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/var_decl_def.hpp | 64 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/variable.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/node/variable_def.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signature_t.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signatures.hpp | 99 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signatures_def.hpp | 331 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/type |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/variable_map.hpp | 31 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast/variable_map_def.hpp | 18 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/ast_def.cpp | 108 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/function_signatures.h | 1752 +-- StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator.hpp | 81 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/expression_visgen.hpp | 115 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/fun_scalar_type.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_arg_decl.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_bare_type.hpp | 38 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_block_var.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_class_decl_end.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_constrained_param_names_method.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_constructor.hpp | 80 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_cpp.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_data_var_ctor.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_data_var_init.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_dims_method.hpp | 33 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_fun_inst_templ_params.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_function.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_function_body.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation_body.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_function_template_parameters.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_functor_arguments.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_indexed_expr.hpp | 58 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_initializer.hpp | 73 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_line_number.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_local_var_decl_inits.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_log_prob.hpp | 101 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_member_var_decls.hpp | 40 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_namespace_end.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_param_names_array.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_param_names_method.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_param_var.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_propto_default_function_body.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_read_transform_params.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_set_param_ranges.hpp | 26 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_transform_inits_method.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_typedefs.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_unconstrained_param_names_array.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_unconstrained_param_names_method.hpp | 18 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_block_var.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_context_size.hpp | 59 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_nonnegative.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_tparam_inits.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_var_decl.hpp | 69 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_var_dims.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_var_constructor.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_var_fill_define.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_write_array_method.hpp | 136 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/generate_write_block_var.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/get_block_var_dims.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/get_typedef_var_type.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/get_verbose_var_type.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/statement_visgen.hpp | 36 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_begin_all_dims_col_maj_loop.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_begin_all_dims_row_maj_loop.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_begin_array_dims_loop.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_begin_param_elements_loop.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_constraints_fn.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_end_loop.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_nested_resize_loop_begin.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_resize_var_idx.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_var_decl_arg.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_var_decl_type.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_var_idx_all_dims.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_var_idx_all_dims_msg.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/generator/write_var_idx_array_dims.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/bare_type_grammar.hpp | 22 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/bare_type_grammar_def.hpp | 39 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/block_var_decls_grammar.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/block_var_decls_grammar_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/block_var_decls_grammar_inst.cpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/common_adaptors_def.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/expression_grammar_def.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar_def.hpp | 18 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/indexes_grammar_def.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/local_var_decls_grammar.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/local_var_decls_grammar_def.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/local_var_decls_grammar_inst.cpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/program_grammar.hpp | 14 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/program_grammar_def.hpp | 21 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions.hpp | 1848 +-- StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions_def.cpp | 5818 ++++------ StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar_def.hpp | 34 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar_def.hpp | 51 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/var_decls_grammar.hpp | 161 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/var_decls_grammar_def.hpp | 431 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/grammars/var_decls_grammar_inst.cpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/lang/parser.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/mcmc/chains.hpp | 99 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/mcmc/sample.hpp | 14 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/model/model_header.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/optimization/bfgs.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/optimization/bfgs_linesearch.hpp | 25 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/services/experimental/advi/fullrank.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/services/experimental/advi/meanfield.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/services/sample/standalone_gqs.hpp | 200 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/variational/advi.hpp | 24 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/variational/base_family.hpp | 82 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/variational/families/normal_fullrank.hpp | 74 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/variational/families/normal_meanfield.hpp | 54 StanHeaders-2.18.1-10/StanHeaders/inst/include/src/stan/version.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/fwd/core/fvar.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/fwd/mat/fun/Eigen_NumTraits.hpp | 28 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/fwd/mat/fun/trace_quad_form.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/fwd/scal/fun/gamma_p.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/fwd/scal/fun/gamma_q.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_mix.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/fwd/scal/meta/ad_promotable.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/fwd/scal/meta/is_fvar.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/fwd/scal/meta/operands_and_partials.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/memory/stack_alloc.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/opencl |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/err/check_matching_sizes.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/err/check_nonzero_size.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/err/check_opencl.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/err/check_ordered.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/err/is_matching_size.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/err/is_nonzero_size.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/err/is_ordered.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/fun/sum.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/fun/value_of.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/fun/value_of_rec.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/functor/integrate_1d.hpp | 91 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/meta/as_scalar.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/meta/contains_std_vector.hpp | 21 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/meta/get.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/meta/is_constant_struct.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/arr/meta/length.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat.hpp | 31 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor_corr.hpp | 14 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_column_index.hpp | 15 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_consistent_size_mvt.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_consistent_sizes_mvt.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_corr_matrix.hpp | 21 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_cov_matrix.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_finite.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_ldlt_factor.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_lower_triangular.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_matching_dims.hpp | 25 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_multiplicable.hpp | 18 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_ordered.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_definite.hpp | 25 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_semidefinite.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_positive_ordered.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_range.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_row_index.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_simplex.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_spsd_matrix.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_square.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_std_vector_index.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_symmetric.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_unit_vector.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/check_vector.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_cholesky_factor.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_cholesky_factor_corr.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_column_index.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_corr_matrix.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_ldlt_factor.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_lower_triangular.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_mat_finite.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_matching_dims.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_pos_definite.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_square.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_symmetric.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/err/is_unit_vector.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/accumulator.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/add.hpp | 18 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/add_diag.hpp | 56 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/autocorrelation.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/cbrt.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_corr_constrain.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_decompose.hpp | 58 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/columns_dot_product.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_exp_quad.hpp | 180 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/cumulative_sum.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_post_multiply.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_pre_multiply.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/divide.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/divide_columns.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/dot_product.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/elt_divide.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/elt_multiply.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/erf.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/erfc.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/expm1.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_dot_prod_cov.hpp | 91 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_exp_quad_cov.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_exponential_cov.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_matern32_cov.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_matern52_cov.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/initialize.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/log_mix.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/log_softmax.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/log_sum_exp.hpp | 20 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/max.hpp | 15 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_ldlt.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/mean.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/min.hpp | 14 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/multiply.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/prod.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form_diag.hpp | 17 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form_sym.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/resize.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/rows_dot_product.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/softmax.hpp | 15 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_indices.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/subtract.hpp | 18 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/sum.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/tgamma.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_gen_inv_quad_form_ldlt.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_gen_quad_form.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_inv_quad_form_ldlt.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/value_of.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/fun/value_of_rec.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_concurrent.hpp | 33 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/functor/mpi_parallel_call.hpp | 21 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/meta/as_array_or_scalar.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/meta/as_column_vector_or_scalar.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/meta/as_scalar.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/meta/broadcast_array.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/meta/get.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/meta/is_constant_struct.hpp | 15 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/meta/is_vector_like.hpp | 21 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/meta/length.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/meta/operands_and_partials.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/meta/scalar_type.hpp | 39 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/bernoulli_logit_glm_log.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/bernoulli_logit_glm_lpmf.hpp | 171 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/gaussian_dlm_obs_lpdf.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_lpdf.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_lpdf.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_prec_lpdf.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_lpdf.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_lpmf.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_rng.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/neg_binomial_2_log_glm_log.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/neg_binomial_2_log_glm_lpmf.hpp | 254 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/normal_id_glm_log.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/normal_id_glm_lpdf.hpp | 212 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_lpmf.hpp | 282 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp | 159 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/mat/vectorize/apply_scalar_unary.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal.hpp | 25 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_2F1_converges.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_3F2_converges.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_bounded.hpp | 19 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_consistent_size.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_consistent_sizes.hpp | 22 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_finite.hpp | 20 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_greater.hpp | 21 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_greater_or_equal.hpp | 24 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_less.hpp | 20 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_less_or_equal.hpp | 23 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_nonnegative.hpp | 24 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_not_nan.hpp | 15 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive.hpp | 34 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive_finite.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/check_size_match.hpp | 25 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/domain_error.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/domain_error_vec.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/invalid_argument.hpp | 14 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/invalid_argument_vec.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/is_less_or_equal.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/is_not_nan.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/is_positive.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/is_scal_finite.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/is_size_match.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/out_of_range.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/err/system_error.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/Phi.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/acosh.hpp | 32 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/asinh.hpp | 15 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/atanh.hpp | 23 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/binomial_coefficient_log.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/cbrt.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/choose.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/constants.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/erf.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/erfc.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/exp.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/expm1.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_reg_inc_gamma.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_logit.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/is_inf.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/is_nan.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/lb_constrain.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/lbeta.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/lgamma.hpp | 9 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/lmgamma.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/locscale_constrain.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/locscale_free.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/log.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/log1p.hpp | 21 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/log_falling_factorial.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/log_rising_factorial.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/offset_multiplier_constrain.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/offset_multiplier_free.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/primitive_value.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/round.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/sqrt.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/sum.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/tgamma.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/trunc.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/fun/value_of.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/StdVectorBuilder.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/ad_promotable.hpp | 68 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/as_array_or_scalar.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/as_column_vector_or_scalar.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/as_scalar.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/broadcast_array.hpp | 17 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/conjunction.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_fvar.hpp | 22 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_nonconstant_struct.hpp | 23 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_std_vector.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_vector.hpp | 18 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/disjunction.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/include_summand.hpp | 34 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/is_constant.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/is_constant_struct.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/is_fvar.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/is_nonconstant_struct.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/is_var.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/is_var_or_arithmetic.hpp | 34 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/length.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/operands_and_partials.hpp | 23 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/partials_return_type.hpp | 41 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/return_type.hpp | 38 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/scalar_type_pre.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/meta/size_of.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_lpmf.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_rng.hpp | 51 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lccdf.hpp | 21 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lcdf.hpp | 19 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lpdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_ccdf_log.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_cdf_log.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_lccdf.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_lcdf.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_log.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_lpdf.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_rng.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_lpdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_cdf.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lccdf.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lcdf.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lpdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_lpdf.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_lpdf.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_cdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lccdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lcdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lpdf.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_lpdf.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_cdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lccdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lcdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lpdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lccdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lpdf.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_lpdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_lpdf.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_sufficient_lpdf.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_cdf.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lccdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lcdf.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lpdf.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_lpdf.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/std_normal_lpdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/prim/scal/prob/von_mises_lpdf.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/arr/fun/log_sum_exp.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/arr/functor/coupled_ode_system.hpp | 61 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/arr/functor/integrate_1d.hpp | 70 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/build_vari_array.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_addition.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_divide_equal.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_division.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_minus_equal.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_multiplication.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_multiply_equal.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_plus_equal.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_subtraction.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_unary_decrement.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_unary_increment.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/core/operator_unary_negative.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/cholesky_decompose.hpp | 291 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/columns_dot_product.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/columns_dot_self.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/cov_exp_quad.hpp | 138 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/determinant.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/dot_product.hpp | 25 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/dot_self.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/gp_exp_quad_cov.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/gp_periodic_cov.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/log_determinant_ldlt.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/log_softmax.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/log_sum_exp.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/matrix_exp_multiply.hpp | 390 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_ldlt.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_spd.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_tri.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/multiply.hpp | 19 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/multiply_lower_tri_self_transpose.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/ordered_constrain.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/quad_form.hpp | 25 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/quad_form_sym.hpp | 21 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/rows_dot_product.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/scale_matrix_exp_multiply.hpp | 19 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/sd.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/simplex_constrain.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/softmax.hpp | 101 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/squared_distance.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/tcrossprod.hpp | 4 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_gen_inv_quad_form_ldlt.hpp | 25 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_gen_quad_form.hpp | 32 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_inv_quad_form_ldlt.hpp | 26 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_quad_form.hpp | 18 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/unit_vector_constrain.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/fun/variance.hpp | 23 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/functor/adj_jac_apply.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_integrator.hpp | 12 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_ode_data.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_utils.hpp | 3 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/functor/idas_forward_system.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/functor/idas_integrator.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/functor/idas_system.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/mat/functor/integrate_dae.hpp |only StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/Phi.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/acos.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/acosh.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/asin.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/asinh.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/atan.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/atan2.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/atanh.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/bessel_first_kind.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/bessel_second_kind.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/binary_log_loss.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/cbrt.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/ceil.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/cos.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/cosh.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/digamma.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/erf.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/erfc.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/exp.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/exp2.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/expm1.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/fabs.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/fdim.hpp | 13 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/floor.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/fma.hpp | 18 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/fmod.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/gamma_p.hpp | 11 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/gamma_q.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/hypot.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/ibeta.hpp | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/inc_beta.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/inv.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_Phi.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_cloglog.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_logit.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_sqrt.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_square.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/lgamma.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/lmgamma.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log10.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m_exp.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log1p.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log1p_exp.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log2.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log_diff_exp.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log_falling_factorial.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log_inv_logit_diff.hpp | 22 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log_mix.hpp | 1 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log_rising_factorial.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/log_sum_exp.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/modified_bessel_first_kind.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/modified_bessel_second_kind.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/multiply_log.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/owens_t.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/pow.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/round.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/sin.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/sinh.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/sqrt.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/square.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/tan.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/tanh.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/tgamma.hpp | 8 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/fun/trunc.hpp | 6 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/meta/ad_promotable.hpp | 15 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/meta/is_var.hpp | 5 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/rev/scal/meta/operands_and_partials.hpp | 7 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan/math/version.hpp | 2 StanHeaders-2.18.1-10/StanHeaders/inst/include/stan_sundials_printf_override.hpp | 10 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_band.h | 61 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_config.h | 52 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_config.in | 23 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_dense.h | 65 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_direct.h | 117 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_fconfig.h |only StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_fconfig.in | 19 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_fnvector.h | 27 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_iterative.h | 328 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_klu_impl.h | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_lapack.h | 134 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_linearsolver.h | 366 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_math.h | 121 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_matrix.h | 178 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_mpi.h |only StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_mpi_types.h | 19 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_nonlinearsolver.h |only StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_nvector.h | 406 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_nvector_senswrapper.h |only StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_pcg.h | 56 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_sparse.h | 146 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_spbcgs.h | 32 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_spfgmr.h | 58 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_spgmr.h | 38 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_sptfqmr.h | 26 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_superlumt_impl.h | 16 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_types.h | 62 StanHeaders-2.18.1-10/StanHeaders/inst/include/sundials/sundials_version.h | 52 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_band.h | 68 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_dense.h | 78 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_klu.h | 135 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_lapackband.h | 71 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_lapackdense.h | 69 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_pcg.h | 159 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_spbcgs.h | 168 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_spfgmr.h | 187 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_spgmr.h | 191 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_sptfqmr.h | 163 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunlinsol/sunlinsol_superlumt.h | 92 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunmatrix/sunmatrix_band.h | 251 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunmatrix/sunmatrix_dense.h | 196 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunmatrix/sunmatrix_sparse.h | 258 StanHeaders-2.18.1-10/StanHeaders/inst/include/sunnonlinsol |only StanHeaders-2.18.1-10/StanHeaders/src/Makevars | 6 StanHeaders-2.18.1-10/StanHeaders/src/Makevars.win | 20 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/LICENSE | 77 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/NOTICE |only StanHeaders-2.18.1-10/StanHeaders/src/cvodes/README | 47 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodea.c | 369 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodea_io.c | 87 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes.c | 2448 +--- StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_bandpre.c | 182 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_bandpre_impl.h | 18 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_bbdpre.c | 234 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_bbdpre_impl.h | 18 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_diag.c | 16 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_diag_impl.h | 16 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_direct.c | 1145 - StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_impl.h | 141 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_io.c | 311 StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_ls.c |only StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_ls_impl.h |only StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_nls.c |only StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_nls_sim.c |only StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_nls_stg.c |only StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_nls_stg1.c |only StanHeaders-2.18.1-10/StanHeaders/src/cvodes/cvodes_spils.c | 2040 --- StanHeaders-2.18.1-10/StanHeaders/src/idas/LICENSE | 76 StanHeaders-2.18.1-10/StanHeaders/src/idas/NOTICE |only StanHeaders-2.18.1-10/StanHeaders/src/idas/README | 30 StanHeaders-2.18.1-10/StanHeaders/src/idas/idaa.c | 383 StanHeaders-2.18.1-10/StanHeaders/src/idas/idaa_io.c | 173 StanHeaders-2.18.1-10/StanHeaders/src/idas/idas.c | 1496 +- StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_bbdpre.c | 217 StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_bbdpre_impl.h | 18 StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_direct.c | 1205 -- StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_ic.c | 16 StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_impl.h | 106 StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_io.c | 184 StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_ls.c |only StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_ls_impl.h |only StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_nls.c |only StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_nls_sim.c |only StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_nls_stg.c |only StanHeaders-2.18.1-10/StanHeaders/src/idas/idas_spils.c | 2247 --- StanHeaders-2.18.1-10/StanHeaders/src/nvector |only StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_band.c | 16 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_dense.c | 16 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_direct.c | 16 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_iterative.c | 63 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_linearsolver.c | 18 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_math.c | 66 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_matrix.c | 18 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_mpi.c |only StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_nonlinearsolver.c |only StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_nvector.c | 280 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_nvector_senswrapper.c |only StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_pcg.c | 12 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_sparse.c | 28 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_spbcgs.c | 16 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_sptfqmr.c | 16 StanHeaders-2.18.1-10/StanHeaders/src/sundials/sundials_version.c | 16 StanHeaders-2.18.1-10/StanHeaders/src/sunlinsol |only 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StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/double_var_decl_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/expression_type_vis.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/expression_type_vis_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/int_var_decl.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/int_var_decl_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/matrix_var_decl.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/matrix_var_decl_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/nil.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/ordered_var_decl.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/ordered_var_decl_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/positive_ordered_var_decl.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/positive_ordered_var_decl_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/row_vector_var_decl.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/row_vector_var_decl_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/simplex_var_decl.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/simplex_var_decl_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/unit_vector_var_decl.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/unit_vector_var_decl_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/vector_var_decl.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/node/vector_var_decl_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/row_vector_type.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_arg_type.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_arg_type_def.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/vector_type.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/ast/void_type.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/constrained_param_names_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/dump_member_var_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/geneate_idx_user.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_array_var_type.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_eigen_index_expression.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_init_method.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_initialization.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_local_var_decls.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_local_var_inits.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_member_var_inits.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_type.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_positive.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_transformed_params.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_var_decls.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/generate_var_resizing.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/has_lb.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/has_lub.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/has_only_int_args.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/has_ub.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/init_local_var_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/init_vars_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/init_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/local_var_decl_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/local_var_init_nan_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/member_var_decl_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/set_param_ranges_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/to_string.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/unconstrained_param_names_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/validate_transformed_params_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/validate_var_decl_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/var_resizing_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/var_size_validating_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/write_array_vars_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/write_array_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/write_dims_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/src/stan/lang/generator/write_param_names_visgen.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/stan/math/gpu |only StanHeaders-2.18.1/StanHeaders/inst/include/stan/math/prim/arr/meta/is_std_vector.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/stan/math/prim/mat/fun/opencl_copy.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive_size.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/stan/math/prim/scal/meta/is_std_vector.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_isinf.hpp |only StanHeaders-2.18.1/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_isnan.hpp |only StanHeaders-2.18.1/StanHeaders/src/cvodes/CMakeLists.txt |only StanHeaders-2.18.1/StanHeaders/src/cvodes/cvodes_direct_impl.h |only StanHeaders-2.18.1/StanHeaders/src/cvodes/cvodes_spils_impl.h |only StanHeaders-2.18.1/StanHeaders/src/idas/CMakeLists.txt |only StanHeaders-2.18.1/StanHeaders/src/idas/idas_direct_impl.h |only StanHeaders-2.18.1/StanHeaders/src/idas/idas_spils_impl.h |only StanHeaders-2.18.1/StanHeaders/src/nvec_cuda |only StanHeaders-2.18.1/StanHeaders/src/nvec_openmp |only StanHeaders-2.18.1/StanHeaders/src/nvec_par |only StanHeaders-2.18.1/StanHeaders/src/nvec_parhyp |only StanHeaders-2.18.1/StanHeaders/src/nvec_petsc |only StanHeaders-2.18.1/StanHeaders/src/nvec_pthreads |only StanHeaders-2.18.1/StanHeaders/src/nvec_raja |only StanHeaders-2.18.1/StanHeaders/src/nvec_ser |only StanHeaders-2.18.1/StanHeaders/src/sundials/CMakeLists.txt |only StanHeaders-2.18.1/StanHeaders/src/sundials/LICENSE |only StanHeaders-2.18.1/StanHeaders/src/sundials/README |only StanHeaders-2.18.1/StanHeaders/src/sundials/sundials_spfgmr.c |only StanHeaders-2.18.1/StanHeaders/src/sundials/sundials_spgmr.c |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_band |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_dense |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_klu |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_lapackband |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_lapackdense |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_pcg |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_spbcgs |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_spfgmr |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_spgmr |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_sptfqmr |only StanHeaders-2.18.1/StanHeaders/src/sunlinsol_superlumt |only StanHeaders-2.18.1/StanHeaders/src/sunmat_band |only StanHeaders-2.18.1/StanHeaders/src/sunmat_dense |only StanHeaders-2.18.1/StanHeaders/src/sunmat_sparse |only StanHeaders-2.18.1/StanHeaders/vignettes/stan-functions.txt |only 930 files changed, 21863 insertions(+), 33925 deletions(-)
Title: 'sf'-Compatible Interface to 'Google Maps' APIs
Description: Interface to the 'Google Maps' APIs: (1) routing directions based on the 'Directions' API, returned as 'sf' objects, either as single feature per alternative route, or a single feature per segment per alternative route; (2) travel distance or time matrices based on the 'Distance Matrix' API; (3) geocoded locations based on the 'Geocode' API, returned as 'sf' objects, either points or bounds.
Author: Michael Dorman [aut, cre],
Tom Buckley [ctb],
Alex Dannenberg [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between mapsapi versions 0.4.0 dated 2019-04-06 and 0.4.1 dated 2019-06-14
DESCRIPTION | 8 +- MD5 | 10 +-- NEWS.md | 19 +++-- R/mp_get_points.R | 1 build/vignette.rds |binary inst/doc/intro.html | 171 ++++++++++++++++++++++++++++++---------------------- 6 files changed, 122 insertions(+), 87 deletions(-)
Title: Distance-Based K-Medoids
Description: Algorithms of distance-based k-medoids clustering:
simple and fast k-medoids, ranked k-medoids, and increasing number
of clusters in k-medoids. Calculate distances for mixed variable
data such as Gower, Podani, Wishart, Huang, Harikumar-PV, and
Ahmad-Dey. Cluster validations apply internal and relative
criteria. The internal criteria include silhouette index and
shadow values. The relative criterium applies bootstrap procedure
producing a heatmap with a flexible reordering matrix algorithm
such as ward, complete, or centroid linkages. The cluster result
can be plotted in a marked barplot or pca biplot.
Author: Weksi Budiaji
Maintainer: Weksi Budiaji <budiaji@untirta.ac.id>
Diff between kmed versions 0.2.0 dated 2019-01-02 and 0.3.0 dated 2019-06-14
kmed-0.2.0/kmed/inst/doc/kmedoid.R |only kmed-0.2.0/kmed/inst/doc/kmedoid.Rmd |only kmed-0.2.0/kmed/inst/doc/kmedoid.html |only kmed-0.2.0/kmed/vignettes/kmedoid.Rmd |only kmed-0.3.0/kmed/DESCRIPTION | 28 ++-- kmed-0.3.0/kmed/MD5 | 90 ++++++++------- kmed-0.3.0/kmed/NAMESPACE | 3 kmed-0.3.0/kmed/NEWS.md | 24 ++++ kmed-0.3.0/kmed/R/barplotnum.R | 45 +++++-- kmed-0.3.0/kmed/R/clustboot.R | 70 ++++++++--- kmed-0.3.0/kmed/R/clustheatmap.R | 46 ++++--- kmed-0.3.0/kmed/R/consensusmatrix.R | 83 +++++++++++--- kmed-0.3.0/kmed/R/cooccur.R | 159 +++++++++++++++++++-------- kmed-0.3.0/kmed/R/csv.R |only kmed-0.3.0/kmed/R/data.R | 133 ++++++++++++++++++++-- kmed-0.3.0/kmed/R/distNumeric.R | 68 ++++++++--- kmed-0.3.0/kmed/R/distmix.R | 193 ++++++++++++++++++++++++--------- kmed-0.3.0/kmed/R/fastkmed.R | 147 +++++++++++++++---------- kmed-0.3.0/kmed/R/inckmed.R |only kmed-0.3.0/kmed/R/matching.R | 43 ++++++- kmed-0.3.0/kmed/R/pcabiplot.R | 35 +++-- kmed-0.3.0/kmed/R/rankkmed.R | 60 ++++++---- kmed-0.3.0/kmed/R/shadow.R | 58 --------- kmed-0.3.0/kmed/R/sil.R |only kmed-0.3.0/kmed/R/silhoutte.R | 63 ---------- kmed-0.3.0/kmed/R/stepkmed.R | 47 +------- kmed-0.3.0/kmed/R/weightednum.R | 4 kmed-0.3.0/kmed/build/vignette.rds |binary kmed-0.3.0/kmed/data/clust5.rda |only kmed-0.3.0/kmed/data/heart.rda |only kmed-0.3.0/kmed/inst/doc/kmed.R |only kmed-0.3.0/kmed/inst/doc/kmed.Rmd |only kmed-0.3.0/kmed/inst/doc/kmed.html |only kmed-0.3.0/kmed/man/barplotnum.Rd | 37 +++++- kmed-0.3.0/kmed/man/clust4.Rd | 32 +++++ kmed-0.3.0/kmed/man/clust5.Rd |only kmed-0.3.0/kmed/man/clustboot.Rd | 69 +++++++++-- kmed-0.3.0/kmed/man/clustheatmap.Rd | 44 ++++--- kmed-0.3.0/kmed/man/consensusmatrix.Rd | 85 +++++++++++--- kmed-0.3.0/kmed/man/cooccur.Rd | 78 +++++++++++-- kmed-0.3.0/kmed/man/csv.Rd |only kmed-0.3.0/kmed/man/distNumeric.Rd | 49 ++++++-- kmed-0.3.0/kmed/man/distmix.Rd | 153 ++++++++++++++++++++------ kmed-0.3.0/kmed/man/fastkmed.Rd | 51 ++++++-- kmed-0.3.0/kmed/man/globalfood.Rd | 17 ++ kmed-0.3.0/kmed/man/heart.Rd |only kmed-0.3.0/kmed/man/inckmed.Rd |only kmed-0.3.0/kmed/man/matching.Rd | 44 ++++++- kmed-0.3.0/kmed/man/pcabiplot.Rd | 26 ++-- kmed-0.3.0/kmed/man/rankkmed.Rd | 46 +++++-- kmed-0.3.0/kmed/man/shadow.Rd | 31 ----- kmed-0.3.0/kmed/man/sil.Rd |only kmed-0.3.0/kmed/man/silhoutte.Rd | 30 ----- kmed-0.3.0/kmed/man/stepkmed.Rd | 32 ----- kmed-0.3.0/kmed/vignettes/kmed.Rmd |only 55 files changed, 1483 insertions(+), 740 deletions(-)
Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between GSED versions 2.0 dated 2018-11-26 and 2.1 dated 2019-06-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GSED.R | 2 +- man/GSED-package.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Differential Geometric Least Angle Regression
Description: Differential geometric least angle regression method for fitting sparse generalized linear models. In this version of the package, the user can fit models specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian family. Furthermore, several link functions can be used to model the relationship between the conditional expected value of the response variable and the linear predictor. The solution curve can be computed using an efficient predictor-corrector or a cyclic coordinate descent algorithm, as described in the paper linked to via the URL below.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between dglars versions 2.1.1 dated 2019-04-06 and 2.1.2 dated 2019-06-14
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/dglars-package.Rd | 6 +++--- man/dglars.Rd | 2 +- src/dglars.h | 12 ++++++------ 6 files changed, 22 insertions(+), 19 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.3.6 dated 2019-05-06 and 1.4.0 dated 2019-06-14
castor-1.3.6/castor/R/count_clades_over_time.R |only castor-1.3.6/castor/man/count_clades_over_time.Rd |only castor-1.3.6/castor/man/simulate_musse.Rd |only castor-1.4.0/castor/DESCRIPTION | 8 castor-1.4.0/castor/MD5 | 93 castor-1.4.0/castor/NAMESPACE | 11 castor-1.4.0/castor/R/RcppExports.R | 24 castor-1.4.0/castor/R/asr_max_parsimony.R | 2 castor-1.4.0/castor/R/auxiliary_routines.R | 88 castor-1.4.0/castor/R/collapse_monofurcations.R | 1 castor-1.4.0/castor/R/collapse_tree_at_resolution.R | 2 castor-1.4.0/castor/R/count_lineages_through_time.R |only castor-1.4.0/castor/R/find_farthest_tips.R | 2 castor-1.4.0/castor/R/fit_hbd_class_on_grid.R |only castor-1.4.0/castor/R/fit_hbd_model_on_grid.R |only castor-1.4.0/castor/R/fit_hbd_model_parametric.R |only castor-1.4.0/castor/R/fit_musse.R | 114 castor-1.4.0/castor/R/fit_tree_model.R | 12 castor-1.4.0/castor/R/generate_random_tree.R | 13 castor-1.4.0/castor/R/generate_tree_with_evolving_rates.R | 14 castor-1.4.0/castor/R/get_all_pairwise_distances.R |only castor-1.4.0/castor/R/get_subtree_at_node.R | 2 castor-1.4.0/castor/R/get_subtree_with_tips.R | 2 castor-1.4.0/castor/R/hsp_max_parsimony.R | 4 castor-1.4.0/castor/R/loglikelihood_hbd.R |only castor-1.4.0/castor/R/merge_short_edges.R | 2 castor-1.4.0/castor/R/multifurcations_to_bifurcations.R | 2 castor-1.4.0/castor/R/read_tree.R | 11 castor-1.4.0/castor/R/reconstruct_past_diversification.R | 4 castor-1.4.0/castor/R/reorder_tree_edges.R | 1 castor-1.4.0/castor/R/simulate_deterministic_hbd.R |only castor-1.4.0/castor/R/simulate_diversification_model.R | 12 castor-1.4.0/castor/R/simulate_dsse.R |only castor-1.4.0/castor/R/simulate_musse.R | 207 castor-1.4.0/castor/R/trim_tree_at_height.R | 1 castor-1.4.0/castor/man/count_lineages_through_time.Rd |only castor-1.4.0/castor/man/fit_hbd_class_on_grid.Rd |only castor-1.4.0/castor/man/fit_hbd_model_on_grid.Rd |only castor-1.4.0/castor/man/fit_hbd_model_parametric.Rd |only castor-1.4.0/castor/man/fit_musse.Rd | 10 castor-1.4.0/castor/man/fit_tree_model.Rd | 1 castor-1.4.0/castor/man/generate_random_tree.Rd | 2 castor-1.4.0/castor/man/generate_tree_with_evolving_rates.Rd | 18 castor-1.4.0/castor/man/get_all_pairwise_distances.Rd |only castor-1.4.0/castor/man/get_pairwise_distances.Rd | 5 castor-1.4.0/castor/man/loglikelihood_hbd.Rd |only castor-1.4.0/castor/man/read_tree.Rd | 8 castor-1.4.0/castor/man/reconstruct_past_diversification.Rd | 18 castor-1.4.0/castor/man/simulate_bm_model.Rd | 1 castor-1.4.0/castor/man/simulate_deterministic_hbd.Rd |only castor-1.4.0/castor/man/simulate_diversification_model.Rd | 45 castor-1.4.0/castor/man/simulate_dsse.Rd |only castor-1.4.0/castor/man/simulate_mk_model.Rd | 1 castor-1.4.0/castor/man/simulate_ou_model.Rd | 1 castor-1.4.0/castor/man/simulate_rou_model.Rd | 1 castor-1.4.0/castor/src/RcppExports.cpp | 101 castor-1.4.0/castor/src/phylogenetics_cpp_routines.cpp | 2453 +++++++++-- 57 files changed, 2683 insertions(+), 614 deletions(-)
Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Text mining for word processing and sentiment analysis using
'dplyr', 'ggplot2', and other tidy tools.
Author: Gabriela De Queiroz [ctb],
Emil Hvitfeldt [ctb],
Os Keyes [ctb] (<https://orcid.org/0000-0001-5196-609X>),
Kanishka Misra [ctb],
Tim Mastny [ctb],
Jeff Erickson [ctb],
David Robinson [aut],
Julia Silge [aut, cre] (<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between tidytext versions 0.2.0 dated 2018-10-17 and 0.2.1 dated 2019-06-14
DESCRIPTION | 15 ++-- MD5 | 89 +++++++++++++++-------------- NAMESPACE | 9 +- NEWS.md | 10 +++ R/bind_tf_idf.R | 4 - R/corpus_tidiers.R | 8 +- R/dictionary_tidiers.R | 4 - R/lda_tidiers.R | 8 +- R/mallet_tidiers.R | 2 R/reorder_within.R |only R/sentiments.R | 81 +++++++++++--------------- R/sparse_tidiers.R | 6 - R/stm_tidiers.R | 8 +- R/stop_words.R | 4 - R/unnest_tokens.R | 12 ++- README.md | 60 +++++++++---------- build/vignette.rds |binary data/sentiments.rda |binary inst/doc/tf_idf.html | 51 ++++++++++++---- inst/doc/tidying_casting.R | 1 inst/doc/tidying_casting.Rmd | 1 inst/doc/tidying_casting.html | 106 +++++++++++++++++++++-------------- inst/doc/tidytext.R | 8 +- inst/doc/tidytext.Rmd | 12 +-- inst/doc/tidytext.html | 95 +++++++++++++++++++------------ inst/doc/topic_modeling.R | 6 - inst/doc/topic_modeling.Rmd | 6 - inst/doc/topic_modeling.html | 69 +++++++++++++++------- man/deprecated-se.Rd | 4 - man/get_sentiments.Rd | 13 ++-- man/get_stopwords.Rd | 2 man/reexports.Rd | 2 man/reorder_within.Rd |only man/sentiments.Rd | 43 ++++---------- man/unnest_tokens.Rd | 8 +- tests/figs |only tests/testthat/test-corpus-tidiers.R | 2 tests/testthat/test-reorder-within.R |only tests/testthat/test-sentiments.R | 25 -------- tests/testthat/test-sparse-casters.R | 2 tests/testthat/test-stm-tidiers.R | 2 tests/testthat/test-tf-idf.R | 6 - tests/testthat/test-unnest-tokens.R | 36 +++++------ tools/README-unnamed-chunk-13-1.png |binary vignettes/tidying_casting.Rmd | 1 vignettes/tidytext.Rmd | 12 +-- vignettes/topic_modeling.Rmd | 6 - 47 files changed, 461 insertions(+), 378 deletions(-)
Title: Bayesian Exponential Smoothing Models with Trend Modifications
Description: An implementation of a number of Global Trend models for time series forecasting
that are Bayesian generalizations and extensions of some Exponential Smoothing models.
The main differences/additions include 1) nonlinear global trend, 2) Student-t error
distribution, and 3) a function for the error size, so heteroscedasticity. The methods
are particularly useful for short time series. When tested on the well-known M3 dataset,
they are able to outperform all classical time series algorithms. The models are fitted
with MCMC using the 'rstan' package.
Author: Slawek Smyl [aut],
Christoph Bergmeir [aut, cre],
Erwin Wibowo [aut],
To Wang Ng [aut],
Trustees of Columbia University [cph] (tools/make_cpp.R,
R/stanmodels.R)
Maintainer: Christoph Bergmeir <christoph.bergmeir@monash.edu>
Diff between Rlgt versions 0.1-2 dated 2019-02-22 and 0.1-3 dated 2019-06-14
ChangeLog | 4 + DESCRIPTION | 8 +- MD5 | 24 +++--- demo/00Index | 1 demo/GT_M3parallelDB.R | 147 ++++++++++++++++++++++++------------- demo/M4Hourly_parallelDB.R |only demo/basicDemos.R | 16 ++-- inst/doc/GT_models.Rmd | 22 +---- inst/doc/GT_models.html | 24 +----- inst/doc/gettingStarted.Rmd | 115 ++++++++++++---------------- inst/doc/gettingStarted.html | 129 +++++++++++++------------------- vignettes/GT_models.Rmd | 22 +---- vignettes/airPassengersNumeric.png |only vignettes/gettingStarted.Rmd | 115 ++++++++++++---------------- 14 files changed, 297 insertions(+), 330 deletions(-)