Title: Unpivot Complex and Irregular Data Layouts
Description: Tools for converting data from complex or irregular layouts to a
columnar structure. For example, tables with multilevel column or row
headers, or spreadsheets. Header and data cells are selected by their
contents and position, as well as formatting and comments where available,
and are associated with one other by their proximity in given directions.
Functions for data frames and HTML tables are provided.
Author: Duncan Garmonsway [aut, cre]
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>
Diff between unpivotr versions 0.5.0 dated 2019-01-02 and 0.5.1 dated 2019-03-30
DESCRIPTION | 8 - MD5 | 60 +++---- NEWS.md | 5 R/as_cells.R | 93 +++++++---- R/behead.R | 84 ++++++---- R/enhead.R | 93 +++++++---- R/isolate_sentinels.R | 28 ++- R/justify.R | 4 R/merge.R | 36 +++- R/pack.R | 64 ++++---- R/partition.R | 18 +- R/rectify.R | 29 ++- R/spatter.R | 45 +++-- R/unpivotr.R | 2 R/utils.R | 83 +++++----- build/vignette.rds |binary inst/doc/compass-directions.html | 33 +++- inst/doc/html.html | 33 +++- inst/doc/small-multiples.html | 33 +++- tests/testthat/test-as_cells.R | 90 ++++++----- tests/testthat/test-behead.R | 110 +++++++------- tests/testthat/test-concatenate.R | 142 ++++++++++++------ tests/testthat/test-enhead.R | 217 +++++++++++++++------------ tests/testthat/test-isolate_sentinels.R | 26 +-- tests/testthat/test-justify.R | 10 - tests/testthat/test-merge.R | 78 ++++----- tests/testthat/test-pack.R | 66 +++++--- tests/testthat/test-partition.R | 111 +++++++++----- tests/testthat/test-rectify.R | 250 ++++++++++++++++++-------------- tests/testthat/test-spatter.R | 175 ++++++++++++++-------- tests/testthat/test-tidy_table.R | 89 ++++++----- 31 files changed, 1278 insertions(+), 837 deletions(-)
Title: Weighted Mixed-Effects Models Using Multilevel Pseudo Maximum
Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Author: Paul Bailey, Claire Kelley, Trang Nguyen, Huade Huo.
Maintainer: Claire Kelley <ckelley@air.org>
Diff between WeMix versions 2.2.1 dated 2019-03-14 and 3.0.0 dated 2019-03-30
WeMix-2.2.1/WeMix/R/RcppExports.R |only WeMix-2.2.1/WeMix/inst/doc/WeightedMixedModels.R |only WeMix-2.2.1/WeMix/inst/doc/WeightedMixedModels.Rmd |only WeMix-2.2.1/WeMix/inst/doc/WeightedMixedModels.pdf |only WeMix-2.2.1/WeMix/man/calc_lin_lnl_quad_fast.Rd |only WeMix-2.2.1/WeMix/src |only WeMix-2.2.1/WeMix/tests/testthat/Examples.smcl |only WeMix-2.2.1/WeMix/vignettes/WeightedMixedModels.Rmd |only WeMix-3.0.0/WeMix/DESCRIPTION | 17 WeMix-3.0.0/WeMix/MD5 | 48 WeMix-3.0.0/WeMix/NAMESPACE | 19 WeMix-3.0.0/WeMix/R/adaptiveQuad.R | 506 +++++-- WeMix-3.0.0/WeMix/R/analyticSolve.R |only WeMix-3.0.0/WeMix/R/drv.R | 1 WeMix-3.0.0/WeMix/R/helpers.R | 305 ++++ WeMix-3.0.0/WeMix/R/lnl.R | 66 WeMix-3.0.0/WeMix/R/weMix-package.R | 32 WeMix-3.0.0/WeMix/R/zzz.R |only WeMix-3.0.0/WeMix/build/vignette.rds |binary WeMix-3.0.0/WeMix/inst/NEWS.Rd | 15 WeMix-3.0.0/WeMix/inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.R |only WeMix-3.0.0/WeMix/inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.Rmd |only WeMix-3.0.0/WeMix/inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.pdf |only WeMix-3.0.0/WeMix/inst/doc/Weighted_Linear_Mixed_Effects_Models.Rmd |only WeMix-3.0.0/WeMix/inst/doc/Weighted_Linear_Mixed_Effects_Models.pdf |only WeMix-3.0.0/WeMix/man/WeMix-package.Rd | 35 WeMix-3.0.0/WeMix/man/analyticSolve.Rd |only WeMix-3.0.0/WeMix/man/devG.Rd |only WeMix-3.0.0/WeMix/man/makeSandwich.Rd |only WeMix-3.0.0/WeMix/man/mix.Rd | 132 + WeMix-3.0.0/WeMix/man/waldTest.Rd |only WeMix-3.0.0/WeMix/tests/testthat/test-0-main.R | 687 ++++++++-- WeMix-3.0.0/WeMix/vignettes/Introduction_to_Mixed_Effects_Models_With_WeMix.Rmd |only WeMix-3.0.0/WeMix/vignettes/Weighted_Linear_Mixed_Effects_Models.Rmd |only 34 files changed, 1460 insertions(+), 403 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre],
Ruth Keogh [aut]
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>
Diff between smcfcs versions 1.3.1 dated 2018-10-10 and 1.4.0 dated 2019-03-30
DESCRIPTION | 9 - MD5 | 28 ++-- R/smcfcs.r | 224 ++++++++++++++++++++++++--------- build/vignette.rds |binary inst/doc/smcfcs-vignette.Rmd | 6 inst/doc/smcfcs-vignette.html | 39 ++++- inst/doc/smcfcs_coverror-vignette.R |only inst/doc/smcfcs_coverror-vignette.Rmd |only inst/doc/smcfcs_coverror-vignette.html |only man/smcfcs.Rd | 22 ++- man/smcfcs.casecohort.Rd | 12 + man/smcfcs.nestedcc.Rd | 12 + tests/testthat/test_coxph.r | 1 tests/testthat/test_errorchecks.R | 141 +++++++++++++++++++- tests/testthat/test_measerror.r |only tests/testthat/test_weibull.r |only vignettes/smcfcs-vignette.Rmd | 6 vignettes/smcfcs_coverror-vignette.Rmd |only 18 files changed, 393 insertions(+), 107 deletions(-)
Title: Construct Reproducible Analytic Data Sets as R Packages
Description: A framework to help construct R data packages in a
reproducible manner. Potentially time consuming processing of
raw data sets into analysis ready data sets is done in a reproducible
manner and decoupled from the usual R CMD build process so that
data sets can be processed into R objects in the data package and
the data package can then be shared, built, and installed by others
without the need to repeat computationally costly data processing.
The package maintains data provenance by turning the data processing
scripts into package vignettes, as well as enforcing documentation
and version checking of included data objects. Data packages can be
version controlled in github, and used to share data for manuscripts,
collaboration and general reproducibility.
Author: Greg Finak [aut, cre, cph],
Paul Obrecht [ctb],
Ellis Hughes [ctb],
Kara Woo [rev] (Kara reviewed the package for ropensci, see
<https://github.com/ropensci/onboarding/issues/230>),
William Landau [rev] (William reviewed the package for ropensci, see
<https://github.com/ropensci/onboarding/issues/230>)
Maintainer: Greg Finak <gfinak@fredhutch.org>
Diff between DataPackageR versions 0.15.6 dated 2019-03-13 and 0.15.7 dated 2019-03-30
DESCRIPTION | 6 MD5 | 31 - NEWS.md | 6 R/skeleton.R | 15 inst/doc/YAML_CONFIG.html | 93 ++--- inst/doc/usingDataPackageR.R | 2 inst/doc/usingDataPackageR.Rmd | 2 inst/doc/usingDataPackageR.html | 401 +++++++++++------------ inst/extdata/Logfiles |only tests/testthat/test-conditional-build.R | 2 tests/testthat/test-data-version.R | 4 tests/testthat/test-document.R | 1 tests/testthat/test-edge-cases.R | 2 tests/testthat/test-project-path.R | 2 tests/testthat/test-r-processing.R | 1 tests/testthat/test-skeleton-data-dependencies.R | 1 vignettes/usingDataPackageR.Rmd | 2 17 files changed, 300 insertions(+), 271 deletions(-)
Title: Download Mexico City Pollution, Wind, and Temperature Data
Description: Tools for downloading hourly averages, daily maximums and minimums from each of the
pollution, wind, and temperature measuring stations or geographic zones in the Mexico City
metro area. The package also includes the locations of each of the stations and zones. See
<http://aire.cdmx.gob.mx/> for more information.
Author: Diego Valle-Jones [aut, cre]
Maintainer: Diego Valle-Jones <diego@diegovalle.net>
Diff between aire.zmvm versions 0.8.1 dated 2019-02-06 and 0.8.2 dated 2019-03-30
DESCRIPTION | 6 ++-- MD5 | 36 +++++++++++++-------------- NEWS.md | 10 +++++++ R/aire.zmvm-deprecated.R | 2 - R/download_archives.R | 30 +++++++--------------- R/get_station_imeca.R | 10 +++---- R/idw360.R | 5 ++- data/stations.RData |binary man/idw360.Rd | 5 ++- tests/testthat/test_convert_to_imeca.R | 1 tests/testthat/test_convert_to_index.R | 2 + tests/testthat/test_download_archives.R | 2 + tests/testthat/test_get_latest.R | 10 ++++++- tests/testthat/test_get_station_data.R | 2 + tests/testthat/test_get_station_imeca.R | 2 + tests/testthat/test_get_station_month_data.R | 2 + tests/testthat/test_get_zone_imeca.R | 1 tests/testthat/test_idw360.R | 1 tests/testthat/test_utils.R | 2 + 19 files changed, 77 insertions(+), 52 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and R maintainer until
2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 2.43-3 dated 2018-11-26 and 2.44-1 dated 2019-03-30
survival-2.43-3/survival/R/survfitKM.S |only survival-2.43-3/survival/R/survreg.fit.S |only survival-2.43-3/survival/data/genfan.rda |only survival-2.43-3/survival/man/genfan.Rd |only survival-2.43-3/survival/man/survConcordance.Rd |only survival-2.43-3/survival/noweb/coxph2.Rnw |only survival-2.43-3/survival/noweb/survconcordance.Rnw |only survival-2.43-3/survival/tests/data.capacitor |only survival-2.43-3/survival/tests/data.cracks |only survival-2.43-3/survival/tests/data.valve |only survival-2.43-3/survival/tests/r_capacitor.R |only survival-2.43-3/survival/tests/r_capacitor.Rout.save |only survival-2.43-3/survival/vignettes/temp.r |only survival-2.44-1/survival/DESCRIPTION | 8 survival-2.44-1/survival/MD5 | 226 +- survival-2.44-1/survival/NAMESPACE | 15 survival-2.44-1/survival/R/agreg.fit.R | 15 survival-2.44-1/survival/R/concordance.R | 10 survival-2.44-1/survival/R/coxph.R | 20 survival-2.44-1/survival/R/coxph.fit.R | 16 survival-2.44-1/survival/R/finegray.R | 18 survival-2.44-1/survival/R/parsecovar.R |only survival-2.44-1/survival/R/plot.survfit.R | 304 +- survival-2.44-1/survival/R/print.summary.coxph.S | 6 survival-2.44-1/survival/R/pyears.R | 51 survival-2.44-1/survival/R/residuals.survreg.R | 8 survival-2.44-1/survival/R/survConcordance.R | 2 survival-2.44-1/survival/R/survConcordance.fit.R | 1 survival-2.44-1/survival/R/survfit.R | 61 survival-2.44-1/survival/R/survfit.coxph.R | 3 survival-2.44-1/survival/R/survfit23.R |only survival-2.44-1/survival/R/survfitCI.R | 87 survival-2.44-1/survival/R/survfitKM.R |only survival-2.44-1/survival/R/survfitTurnbull.S | 8 survival-2.44-1/survival/R/survfitms.R | 63 survival-2.44-1/survival/R/survreg.fit.R |only survival-2.44-1/survival/build/vignette.rds |binary survival-2.44-1/survival/data/reliability.rda |only survival-2.44-1/survival/inst/NEWS.Rd | 51 survival-2.44-1/survival/inst/doc/adjcurve.pdf |binary survival-2.44-1/survival/inst/doc/compete.pdf |binary survival-2.44-1/survival/inst/doc/concordance.R | 11 survival-2.44-1/survival/inst/doc/concordance.Rnw | 78 survival-2.44-1/survival/inst/doc/concordance.pdf |binary survival-2.44-1/survival/inst/doc/multi.R | 4 survival-2.44-1/survival/inst/doc/multi.Rnw | 4 survival-2.44-1/survival/inst/doc/multi.pdf |binary survival-2.44-1/survival/inst/doc/population.pdf |binary survival-2.44-1/survival/inst/doc/splines.pdf |binary survival-2.44-1/survival/inst/doc/survival.R |only survival-2.44-1/survival/inst/doc/survival.Rnw |only survival-2.44-1/survival/inst/doc/survival.pdf |only survival-2.44-1/survival/inst/doc/tests.pdf |binary survival-2.44-1/survival/inst/doc/tiedtimes.pdf |binary survival-2.44-1/survival/inst/doc/timedep.pdf |binary survival-2.44-1/survival/inst/doc/validate.pdf |binary survival-2.44-1/survival/man/Surv.Rd | 22 survival-2.44-1/survival/man/concordance.Rd | 8 survival-2.44-1/survival/man/concordancefit.Rd |only survival-2.44-1/survival/man/coxph.control.Rd | 37 survival-2.44-1/survival/man/figures |only survival-2.44-1/survival/man/finegray.Rd | 3 survival-2.44-1/survival/man/lines.survfit.Rd | 6 survival-2.44-1/survival/man/lung.Rd | 12 survival-2.44-1/survival/man/plot.survfit.Rd | 21 survival-2.44-1/survival/man/reliability.Rd |only survival-2.44-1/survival/man/summary.coxph.Rd | 51 survival-2.44-1/survival/man/survConcordance-deprecated.Rd |only survival-2.44-1/survival/man/survfit.formula.Rd | 165 - survival-2.44-1/survival/man/survival-internal.Rd | 17 survival-2.44-1/survival/man/transplant.Rd | 25 survival-2.44-1/survival/noweb/Makefile | 11 survival-2.44-1/survival/noweb/agreg.Rnw | 120 - survival-2.44-1/survival/noweb/concordance.Rnw | 14 survival-2.44-1/survival/noweb/coxph.Rnw | 22 survival-2.44-1/survival/noweb/coxsurv.Rnw | 3 survival-2.44-1/survival/noweb/finegray.Rnw | 10 survival-2.44-1/survival/noweb/msurv.nw | 14 survival-2.44-1/survival/noweb/parse.Rnw | 4 survival-2.44-1/survival/noweb/plot.Rnw | 178 - survival-2.44-1/survival/noweb/pyears.Rnw | 51 survival-2.44-1/survival/noweb/residuals.survreg.Rnw | 8 survival-2.44-1/survival/noweb/survConcordance.Rnw |only survival-2.44-1/survival/noweb/survfit.Rnw | 66 survival-2.44-1/survival/noweb/survfitCI.Rnw | 87 survival-2.44-1/survival/noweb/survfitKM.Rnw | 1405 +++++++++---- survival-2.44-1/survival/noweb/survfitKM.Rnw.orig |only survival-2.44-1/survival/noweb/survfitms.Rnw | 47 survival-2.44-1/survival/src/agfit4.c | 370 ++- survival-2.44-1/survival/src/agfit5.c | 3 survival-2.44-1/survival/src/coxfit5.c | 3 survival-2.44-1/survival/src/coxfit6.c | 466 +--- survival-2.44-1/survival/src/init.c | 1 survival-2.44-1/survival/src/norisk.c | 1 survival-2.44-1/survival/src/survfitci.c | 12 survival-2.44-1/survival/src/survfitkm.c |only survival-2.44-1/survival/src/survproto.h | 8 survival-2.44-1/survival/tests/bladder.Rout.save | 7 survival-2.44-1/survival/tests/book1.R | 21 survival-2.44-1/survival/tests/book1.Rout.save | 33 survival-2.44-1/survival/tests/book3.R | 1 survival-2.44-1/survival/tests/book3.Rout.save | 10 survival-2.44-1/survival/tests/book5.Rout.save | 7 survival-2.44-1/survival/tests/book6.Rout.save | 7 survival-2.44-1/survival/tests/cancer.Rout.save | 11 survival-2.44-1/survival/tests/concordance.R | 74 survival-2.44-1/survival/tests/concordance.Rout.save | 83 survival-2.44-1/survival/tests/doweight.Rout.save | 8 survival-2.44-1/survival/tests/finegray.R | 4 survival-2.44-1/survival/tests/finegray.Rout.save | 13 survival-2.44-1/survival/tests/infcox.Rout.save | 11 survival-2.44-1/survival/tests/jasa.Rout.save | 8 survival-2.44-1/survival/tests/ovarian.Rout.save | 7 survival-2.44-1/survival/tests/r_resid.Rout.save | 8 survival-2.44-1/survival/tests/r_sas.R | 65 survival-2.44-1/survival/tests/r_sas.Rout.save | 216 - survival-2.44-1/survival/tests/r_tdist.R | 41 survival-2.44-1/survival/tests/r_tdist.Rout.save | 190 - survival-2.44-1/survival/tests/survfit1.R |only survival-2.44-1/survival/tests/survfit1.Rout.save |only survival-2.44-1/survival/tests/survfit2.R | 2 survival-2.44-1/survival/tests/survfit2.Rout.save | 12 survival-2.44-1/survival/tests/survreg1.R |only survival-2.44-1/survival/tests/survtest.R | 14 survival-2.44-1/survival/tests/survtest.Rout.save | 25 survival-2.44-1/survival/tests/testci2.R | 2 survival-2.44-1/survival/tests/testci2.Rout.save | 8 survival-2.44-1/survival/vignettes/concordance.Rnw | 78 survival-2.44-1/survival/vignettes/multi.Rnw | 4 survival-2.44-1/survival/vignettes/survival.Rnw |only 130 files changed, 3126 insertions(+), 2185 deletions(-)
Title: Post Processing of (Half-)Hourly Eddy-Covariance Measurements
Description: Standard and extensible Eddy-Covariance data post-processing
(Wutzler et al. (2018) <doi:10.5194/bg-15-5015-2018>)
includes
uStar-filtering, gap-filling, and flux-partitioning.
The Eddy-Covariance (EC) micrometeorological technique quantifies continuous
exchange fluxes of gases, energy, and momentum between an ecosystem and the atmosphere.
It is important for understanding ecosystem dynamics and upscaling exchange fluxes.
(Aubinet et al. (2012) <doi:10.1007/978-94-007-2351-1>).
This package inputs pre-processed (half-)hourly data and supports further processing.
First, a quality-check and filtering is performed based on the relationship between
measured flux and friction
velocity (uStar) to discard biased data
(Papale et al. (2006) <doi:10.5194/bg-3-571-2006>).
Second, gaps in the data are filled based on information from environmental conditions
(Reichstein et al. (2005) <doi:10.1111/j.1365-2486.2005.001002.x>).
Third, the net flux of carbon dioxide is partitioned
into its gross fluxes in and out of the ecosystem by night-time
based and day-time based approaches
(Lasslop et al. (2010) <doi:10.1111/j.1365-2486.2009.02041.x>).
Author: Department for Biogeochemical Integration at MPI-BGC, Jena, Germany
[cph],
Thomas Wutzler [aut, cre],
Markus Reichstein [aut],
Antje Maria Moffat [aut, trl],
Olaf Menzer [ctb],
Mirco Migliavacca [aut],
Kerstin Sickel [ctb, trl],
Ladislav Šigut [ctb]
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between REddyProc versions 1.1.5 dated 2018-05-17 and 1.2 dated 2019-03-30
REddyProc-1.1.5/REddyProc/inst/doc/useCase.md |only REddyProc-1.1.5/REddyProc/man/fCalcSunPosition.Rd |only REddyProc-1.2/REddyProc/DESCRIPTION | 17 REddyProc-1.2/REddyProc/MD5 | 221 - REddyProc-1.2/REddyProc/NAMESPACE | 22 REddyProc-1.2/REddyProc/NEWS.md | 82 REddyProc-1.2/REddyProc/R/DataFunctions.R | 534 ++- REddyProc-1.2/REddyProc/R/EddyGapfilling.R | 1326 ++++--- REddyProc-1.2/REddyProc/R/EddyPartitioning.R | 1148 ++++-- REddyProc-1.2/REddyProc/R/EddyPlotting.R | 1407 ++++---- REddyProc-1.2/REddyProc/R/EddyUStarFilterChangePointDetection.R | 34 REddyProc-1.2/REddyProc/R/EddyUStarFilterDP.R | 585 ++- REddyProc-1.2/REddyProc/R/Example.R | 20 REddyProc-1.2/REddyProc/R/FileHandling.R | 127 REddyProc-1.2/REddyProc/R/FileHandlingFormats.R | 3 REddyProc-1.2/REddyProc/R/GeoFunctions.R | 555 +-- REddyProc-1.2/REddyProc/R/LRC_base.R | 130 REddyProc-1.2/REddyProc/R/PartitioningLasslop10.R | 235 - REddyProc-1.2/REddyProc/R/PartitioningLasslop10Nighttime.R | 786 ++-- REddyProc-1.2/REddyProc/R/aEddy.R | 441 +- REddyProc-1.2/REddyProc/R/imports.R | 23 REddyProc-1.2/REddyProc/R/variableNames.R | 3 REddyProc-1.2/REddyProc/R/zzzDebugCode.R | 44 REddyProc-1.2/REddyProc/build/vignette.rds |binary REddyProc-1.2/REddyProc/inst/doc/DEGebExample.R | 204 - REddyProc-1.2/REddyProc/inst/doc/DEGebExample.Rmd | 159 REddyProc-1.2/REddyProc/inst/doc/DEGebExample.html | 876 ++--- REddyProc-1.2/REddyProc/inst/doc/aggUncertainty.Rmd |only REddyProc-1.2/REddyProc/inst/doc/aggUncertainty.html |only REddyProc-1.2/REddyProc/inst/doc/bigleaf.Rmd |only REddyProc-1.2/REddyProc/inst/doc/bigleaf.html |only REddyProc-1.2/REddyProc/inst/doc/gapFilling.R | 189 - REddyProc-1.2/REddyProc/inst/doc/gapFilling.Rmd | 75 REddyProc-1.2/REddyProc/inst/doc/gapFilling.html | 597 +-- REddyProc-1.2/REddyProc/inst/doc/uStarCases.R | 161 REddyProc-1.2/REddyProc/inst/doc/uStarCases.Rmd | 122 REddyProc-1.2/REddyProc/inst/doc/uStarCases.html | 733 ++-- REddyProc-1.2/REddyProc/inst/doc/useCase.Rmd | 176 - REddyProc-1.2/REddyProc/inst/doc/useCase.html | 447 +- REddyProc-1.2/REddyProc/inst/genData/REddyProc-package.Rd | 26 REddyProc-1.2/REddyProc/inst/genData/pipe.Rd |only REddyProc-1.2/REddyProc/inst/genData/sEddyProc-class.Rd | 4 REddyProc-1.2/REddyProc/man/BerkeleyJulianDateToPOSIXct.Rd | 3 REddyProc-1.2/REddyProc/man/POSIXctToBerkeleyJulianDate.Rd | 2 REddyProc-1.2/REddyProc/man/REddyProc-package.Rd | 26 REddyProc-1.2/REddyProc/man/fCalcAVPfromVMFandPress.Rd | 9 REddyProc-1.2/REddyProc/man/fCalcETfromLE.Rd | 9 REddyProc-1.2/REddyProc/man/fCalcExtRadiation.Rd | 7 REddyProc-1.2/REddyProc/man/fCalcPotRadiation.Rd | 33 REddyProc-1.2/REddyProc/man/fCalcRHfromAVPandTair.Rd | 5 REddyProc-1.2/REddyProc/man/fCalcSVPfromTair.Rd | 5 REddyProc-1.2/REddyProc/man/fCalcVPDfromRHandTair.Rd | 9 REddyProc-1.2/REddyProc/man/fCheckHHTimeSeries.Rd | 21 REddyProc-1.2/REddyProc/man/fConvertCtoK.Rd | 5 REddyProc-1.2/REddyProc/man/fConvertGlobalToVisible.Rd | 6 REddyProc-1.2/REddyProc/man/fConvertKtoC.Rd | 5 REddyProc-1.2/REddyProc/man/fConvertTimeToPosix.Rd | 56 REddyProc-1.2/REddyProc/man/fConvertVisibleWm2toPhotons.Rd | 6 REddyProc-1.2/REddyProc/man/fLloydTaylor.Rd | 29 REddyProc-1.2/REddyProc/man/fLoadTXTIntoDataframe.Rd | 19 REddyProc-1.2/REddyProc/man/fWriteDataframeToFile.Rd | 20 REddyProc-1.2/REddyProc/man/filterLongRuns.Rd |only REddyProc-1.2/REddyProc/man/filterLongRunsInVector.Rd |only REddyProc-1.2/REddyProc/man/partGLControl.Rd | 7 REddyProc-1.2/REddyProc/man/partGLExtractStandardData.Rd | 78 REddyProc-1.2/REddyProc/man/partitionNEEGL.Rd | 32 REddyProc-1.2/REddyProc/man/pipe.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc-class.Rd | 4 REddyProc-1.2/REddyProc/man/sEddyProc_initialize.Rd | 72 REddyProc-1.2/REddyProc/man/sEddyProc_sApplyUStarScen.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sCalcPotRadiation.Rd | 8 REddyProc-1.2/REddyProc/man/sEddyProc_sEstUstarThold.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sEstUstarThreshold.Rd | 7 REddyProc-1.2/REddyProc/man/sEddyProc_sEstUstarThresholdDistribution.Rd | 68 REddyProc-1.2/REddyProc/man/sEddyProc_sEstimateUstarScenarios.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sExportData.Rd | 2 REddyProc-1.2/REddyProc/man/sEddyProc_sExportResults.Rd | 5 REddyProc-1.2/REddyProc/man/sEddyProc_sFillInit.Rd | 19 REddyProc-1.2/REddyProc/man/sEddyProc_sFillLUT.Rd | 2 REddyProc-1.2/REddyProc/man/sEddyProc_sFillMDC.Rd | 2 REddyProc-1.2/REddyProc/man/sEddyProc_sGLFluxPartition.Rd | 32 REddyProc-1.2/REddyProc/man/sEddyProc_sGLFluxPartitionUStarScens.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sGetData.Rd | 2 REddyProc-1.2/REddyProc/man/sEddyProc_sGetEstimatedUstarThresholdDistribution.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sGetUstarScenarios.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sMDSGapFill.Rd | 100 REddyProc-1.2/REddyProc/man/sEddyProc_sMDSGapFillAfterUStarDistr.Rd | 49 REddyProc-1.2/REddyProc/man/sEddyProc_sMDSGapFillAfterUstar.Rd | 56 REddyProc-1.2/REddyProc/man/sEddyProc_sMDSGapFillUStarScens.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sMRFluxPartition.Rd | 133 REddyProc-1.2/REddyProc/man/sEddyProc_sMRFluxPartitionUStarScens.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sPlotDailySums.Rd | 34 REddyProc-1.2/REddyProc/man/sEddyProc_sPlotDailySumsY.Rd | 52 REddyProc-1.2/REddyProc/man/sEddyProc_sPlotDiurnalCycle.Rd | 33 REddyProc-1.2/REddyProc/man/sEddyProc_sPlotFingerprint.Rd | 24 REddyProc-1.2/REddyProc/man/sEddyProc_sPlotFingerprintY.Rd | 47 REddyProc-1.2/REddyProc/man/sEddyProc_sPlotHHFluxes.Rd | 31 REddyProc-1.2/REddyProc/man/sEddyProc_sPlotHHFluxesY.Rd | 28 REddyProc-1.2/REddyProc/man/sEddyProc_sPlotNEEVersusUStarForSeason.Rd | 15 REddyProc-1.2/REddyProc/man/sEddyProc_sSetLocationInfo.Rd | 18 REddyProc-1.2/REddyProc/man/sEddyProc_sSetUStarSeasons.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sSetUstarScenarios.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sTKFluxPartition.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_sTKFluxPartitionUStarScens.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_useAnnualUStarThresholds.Rd |only REddyProc-1.2/REddyProc/man/sEddyProc_useSeaonsalUStarThresholds.Rd |only REddyProc-1.2/REddyProc/man/usEstUstarThreshold.Rd | 28 REddyProc-1.2/REddyProc/man/usEstUstarThresholdSingleFw1Binned.Rd | 4 REddyProc-1.2/REddyProc/man/usEstUstarThresholdSingleFw2Binned.Rd | 6 REddyProc-1.2/REddyProc/man/usGetAnnualSeasonUStarMap.Rd | 3 REddyProc-1.2/REddyProc/man/usGetYearOfSeason.Rd | 4 REddyProc-1.2/REddyProc/tests/testthat/test_UStarFilter.R | 110 REddyProc-1.2/REddyProc/tests/testthat/test_fConvertTimeToPosix.R | 140 REddyProc-1.2/REddyProc/tests/testthat/test_gapfilling.R |only REddyProc-1.2/REddyProc/tests/testthat/test_geoFunctions.R | 50 REddyProc-1.2/REddyProc/tests/testthat/test_partGL.R | 1693 +++++----- REddyProc-1.2/REddyProc/tests/testthat/test_plotFingerprint.R |only REddyProc-1.2/REddyProc/tests/testthat/test_sEddyProc.R | 298 + REddyProc-1.2/REddyProc/tests/testthat/test_sEddyProc_Partitioning.R | 101 REddyProc-1.2/REddyProc/tests/testthat/test_uStarProc.R |only REddyProc-1.2/REddyProc/vignettes/DEGebExample.Rmd | 159 REddyProc-1.2/REddyProc/vignettes/aggUncertainty.Rmd |only REddyProc-1.2/REddyProc/vignettes/bigleaf.Rmd |only REddyProc-1.2/REddyProc/vignettes/gapFilling.Rmd | 75 REddyProc-1.2/REddyProc/vignettes/uStarCases.Rmd | 122 REddyProc-1.2/REddyProc/vignettes/useCase.Rmd | 176 - 126 files changed, 9098 insertions(+), 6618 deletions(-)
Title: Partial Orders in Socio-Economics
Description: Implements tools for the analysis of partially ordered data, with a particular focus on the evaluation of multidimensional systems of indicators and on the analysis of poverty. References, Fattore M. (2016) <doi:10.1007/s11205-015-1059-6> Fattore M., Arcagni A. (2016) <doi:10.1007/s11205-016-1501-4> Arcagni A. (2017) <doi:10.1007/978-3-319-45421-4_19>.
Author: Alberto Arcagni [aut, cre],
Marco Fattore [aut]
Maintainer: Alberto Arcagni <alberto.arcagni@unimib.it>
Diff between parsec versions 1.2.1 dated 2018-11-02 and 1.2.2 dated 2019-03-30
DESCRIPTION | 12 ++++++------ MD5 | 20 +++++++++++--------- NAMESPACE | 4 ++-- R/FOD.wprof.R | 15 +++++++++++++-- R/MRP.R |only R/evaluation.R | 13 ++++++++----- R/plot.average_ranks.R | 5 +++-- R/validate.partialorder.incidence.R | 3 ++- man/FOD.Rd | 6 +++++- man/MRP.Rd |only man/evaluation.Rd | 12 ++++++------ man/plot.average_ranks.Rd | 2 +- 12 files changed, 57 insertions(+), 35 deletions(-)
Title: Fluid Data Transformations
Description: Supplies higher-order coordinatized data specification and fluid transform operators that include pivot and anti-pivot as special cases.
The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 .
This package introduces the idea of control table specification of data transforms (later also adapted from 'cdata' by 'tidyr').
Works on in-memory data or on remote data using 'rquery' and 'SQL' database interfaces.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between cdata versions 1.0.7 dated 2019-03-23 and 1.0.8 dated 2019-03-30
cdata-1.0.7/cdata/man/checkColsFormUniqueKeys.Rd |only cdata-1.0.8/cdata/DESCRIPTION | 17 cdata-1.0.8/cdata/MD5 | 107 ++-- cdata-1.0.8/cdata/NAMESPACE | 17 cdata-1.0.8/cdata/NEWS.md | 5 cdata-1.0.8/cdata/R/DefOps.R | 5 cdata-1.0.8/cdata/R/GeneralTransform.R | 24 - cdata-1.0.8/cdata/R/LocalOps.R | 95 +--- cdata-1.0.8/cdata/R/RowsColsQ.R | 89 +-- cdata-1.0.8/cdata/R/RowsColumns.R | 139 ------ cdata-1.0.8/cdata/R/check_keying.R |only cdata-1.0.8/cdata/R/checks.R |only cdata-1.0.8/cdata/R/draw_framec.R |only cdata-1.0.8/cdata/R/opspec.R |only cdata-1.0.8/cdata/R/package.R | 7 cdata-1.0.8/cdata/R/relops.R | 37 + cdata-1.0.8/cdata/R/run_cdata_tests.R | 8 cdata-1.0.8/cdata/README.md | 147 +++++- cdata-1.0.8/cdata/build/vignette.rds |binary cdata-1.0.8/cdata/inst/doc/blocksrecs.R | 6 cdata-1.0.8/cdata/inst/doc/blocksrecs.Rmd | 6 cdata-1.0.8/cdata/inst/doc/blocksrecs.html | 431 ++++++++++++++----- cdata-1.0.8/cdata/inst/doc/cdata.R | 3 cdata-1.0.8/cdata/inst/doc/cdata.Rmd | 6 cdata-1.0.8/cdata/inst/doc/cdata.html | 351 ++++++++++++--- cdata-1.0.8/cdata/inst/doc/control_table_keys.R | 10 cdata-1.0.8/cdata/inst/doc/control_table_keys.Rmd | 12 cdata-1.0.8/cdata/inst/doc/control_table_keys.html | 374 +++++++++++++--- cdata-1.0.8/cdata/inst/doc/design.R | 6 cdata-1.0.8/cdata/inst/doc/design.Rmd | 6 cdata-1.0.8/cdata/inst/doc/design.html | 381 +++++++++++++--- cdata-1.0.8/cdata/inst/doc/general_transform.R | 19 cdata-1.0.8/cdata/inst/doc/general_transform.Rmd | 19 cdata-1.0.8/cdata/inst/doc/general_transform.html | 471 +++++++++++++++------ cdata-1.0.8/cdata/inst/doc/operators.R |only cdata-1.0.8/cdata/inst/doc/operators.Rmd |only cdata-1.0.8/cdata/inst/doc/operators.html |only cdata-1.0.8/cdata/inst/unit_tests/test_check.R | 2 cdata-1.0.8/cdata/inst/unit_tests/test_checks_2.R | 76 ++- cdata-1.0.8/cdata/inst/unit_tests/test_dates.R |only cdata-1.0.8/cdata/inst/unit_tests/test_operators.R |only cdata-1.0.8/cdata/man/blocks_to_rowrecs.Rd | 4 cdata-1.0.8/cdata/man/blocks_to_rowrecs_q.Rd | 7 cdata-1.0.8/cdata/man/blocks_to_rowrecs_spec.Rd |only cdata-1.0.8/cdata/man/build_pivot_control_q.Rd | 1 cdata-1.0.8/cdata/man/cdata.Rd | 7 cdata-1.0.8/cdata/man/convert_records.Rd | 52 -- cdata-1.0.8/cdata/man/get_transform_details.Rd |only cdata-1.0.8/cdata/man/grapes-slash-slash-grapes.Rd |only cdata-1.0.8/cdata/man/grapes-times-times-grapes.Rd |only cdata-1.0.8/cdata/man/pivot_to_rowrecs.Rd | 2 cdata-1.0.8/cdata/man/qlook.Rd | 1 cdata-1.0.8/cdata/man/rowrecs_to_blocks_q.Rd | 7 cdata-1.0.8/cdata/man/rowrecs_to_blocks_spec.Rd |only cdata-1.0.8/cdata/man/rows_are_uniquely_keyed.Rd |only cdata-1.0.8/cdata/man/run_cdata_tests.Rd | 9 cdata-1.0.8/cdata/man/unpivot_to_blocks.Rd | 12 cdata-1.0.8/cdata/vignettes/blocksrecs.Rmd | 6 cdata-1.0.8/cdata/vignettes/cdata.Rmd | 6 cdata-1.0.8/cdata/vignettes/control_table_keys.Rmd | 12 cdata-1.0.8/cdata/vignettes/design.Rmd | 6 cdata-1.0.8/cdata/vignettes/general_transform.Rmd | 19 cdata-1.0.8/cdata/vignettes/operators.Rmd |only 63 files changed, 2025 insertions(+), 1002 deletions(-)
Title: Sound Analysis and Synthesis
Description: Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.
Author: Jerome Sueur <sueur@mnhn.fr> [cre, au], Thierry Aubin [au],
Caroline Simonis [au], Laurent Lellouch [main ctrb],
Ethan C. Brown [ctrb], Marion Depraetere [ctrb],
Camille Desjonqueres [ctrb], Francois Fabianek [ctrb],
Amandine Gasc [ctrb], Eric Kasten [ctrb], Stefanie LaZerte [ctrb], Jonathan Lees [ctrb],
Jean Marchal [ctrb], Andre Mikulec [ctrb], Sandrine Pavoine [ctrb], David Pinaud [ctrb], Alicia Stotz [ctrb],
Luis J. Villanueva-Rivera [ctrb], Zev Ross [ctrb],
Carl G. Witthoft [ctrb], Hristo Zhivomirov [ctrb].
Maintainer: Jerome Sueur <sueur@mnhn.fr>
Diff between seewave versions 2.1.0 dated 2018-03-02 and 2.1.3 dated 2019-03-30
seewave-2.1.0/seewave/man/stft.ext.Rd |only seewave-2.1.0/seewave/src |only seewave-2.1.3/seewave/DESCRIPTION | 12 seewave-2.1.3/seewave/MD5 | 71 - seewave-2.1.3/seewave/NAMESPACE | 1 seewave-2.1.3/seewave/NEWS | 26 seewave-2.1.3/seewave/R/seewave.r | 1195 ++++++++++--------- seewave-2.1.3/seewave/R/zzz.r | 2 seewave-2.1.3/seewave/build/vignette.rds |binary seewave-2.1.3/seewave/inst/CITATION | 2 seewave-2.1.3/seewave/inst/doc/seewave_IO.pdf |binary seewave-2.1.3/seewave/inst/doc/seewave_analysis.pdf |binary seewave-2.1.3/seewave/inst/doc/seewave_analysis.rnw | 3 seewave-2.1.3/seewave/man/ACI.Rd | 2 seewave-2.1.3/seewave/man/NDSI.Rd | 7 seewave-2.1.3/seewave/man/dBweight.Rd | 7 seewave-2.1.3/seewave/man/diffenv.Rd | 3 seewave-2.1.3/seewave/man/diffspec.Rd | 1 seewave-2.1.3/seewave/man/diffwave.Rd | 1 seewave-2.1.3/seewave/man/dynspec.Rd | 2 seewave-2.1.3/seewave/man/env.Rd | 9 seewave-2.1.3/seewave/man/listen.Rd | 8 seewave-2.1.3/seewave/man/lts.Rd |only seewave-2.1.3/seewave/man/meanspec.Rd | 2 seewave-2.1.3/seewave/man/oscillo.Rd | 7 seewave-2.1.3/seewave/man/oscilloST.Rd | 4 seewave-2.1.3/seewave/man/seewave.package.Rd | 21 seewave-2.1.3/seewave/man/sh.Rd | 2 seewave-2.1.3/seewave/man/sox.Rd | 115 + seewave-2.1.3/seewave/man/spec.Rd | 2 seewave-2.1.3/seewave/man/spectro.Rd | 10 seewave-2.1.3/seewave/man/spectro3D.Rd | 4 seewave-2.1.3/seewave/man/timer.Rd | 29 seewave-2.1.3/seewave/man/wf.Rd | 2 seewave-2.1.3/seewave/vignettes/seewave_analysis.rnw | 3 35 files changed, 892 insertions(+), 661 deletions(-)
Title: Artificial Neural Networks for Anomaly Detection
Description: Training of neural networks for classification and regression tasks
using mini-batch gradient descent. Special features include a function for
training autoencoders, which can be used to detect anomalies, and some
related plotting functions. Multiple activation functions are supported,
including tanh, relu, step and ramp. For the use of the step and ramp
activation functions in detecting anomalies using autoencoders, see
Hawkins et al. (2002) <doi:10.1007/3-540-46145-0_17>. Furthermore,
several loss functions are supported, including robust ones such as Huber
and pseudo-Huber loss, as well as L1 and L2 regularization. The possible
options for optimization algorithms are RMSprop, Adam and SGD with momentum.
The package contains a vectorized C++ implementation that facilitates
fast training through mini-batch learning.
Author: Bart Lammers
Maintainer: Bart Lammers <bart.f.lammers@gmail.com>
Diff between ANN2 versions 2.3 dated 2019-03-20 and 2.3.1 dated 2019-03-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test-cpp.R | 1 + 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Interface to Praat
Description: Read, write and manipulate 'Praat' TextGrid, PitchTier, Pitch, IntensityTier, Formant, and Collection files <http://www.fon.hum.uva.nl/praat/>.
Author: Tomas Boril [aut, cre]
Maintainer: Tomas Boril <borilt@gmail.com>
Diff between rPraat versions 1.2.0 dated 2018-12-08 and 1.2.0-1 dated 2019-03-30
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/it.R | 8 ++++---- R/pt.R | 8 ++++---- R/rpraat.R | 2 +- R/tg.R | 4 ++-- README.md | 38 +++++++++++++++++++++----------------- 8 files changed, 47 insertions(+), 39 deletions(-)
Title: Dynamical Systems Approach to Infectious Disease Epidemiology
Description: A collection of 'shiny' apps that allow for the simulation and
exploration of various infectious disease transmission dynamics scenarios.
The purpose of the package is to help individuals learn
about infectious disease epidemiology from a dynamical systems perspective.
All apps include explanations of the underlying models and instructions on
what to do with the models.
Author: Andreas Handel [aut, cre] (<https://orcid.org/0000-0002-4622-1146>),
Isaac Chun-Hai Fung [ctb],
Spencer Hall [ctb],
Ben Listyg [ctb],
Brian McKay [ctb],
John Rossow [ctb],
Sina Solaimanpour [ctb],
Henok Woldu [ctb]
Maintainer: Andreas Handel <ahandel@uga.edu>
Diff between DSAIDE versions 0.7.0 dated 2018-08-06 and 0.8.0 dated 2019-03-30
DSAIDE-0.7.0/DSAIDE/R/dsaideapps.R |only DSAIDE-0.7.0/DSAIDE/R/generate_plots.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_directtransmission.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_environmentaltransmission.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_evolution.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_heterogeneity.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_idcharacteristics.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_idcontrol.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_idpatterns.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_introduction.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_multipathogen.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_reproductivenumber.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_stochastic_SEIR.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_stochastic_SIR.R |only DSAIDE-0.7.0/DSAIDE/R/simulate_vectortransmission.R |only DSAIDE-0.7.0/DSAIDE/inst/docsfordevelopers/newappfiles |only DSAIDE-0.7.0/DSAIDE/inst/media |only DSAIDE-0.7.0/DSAIDE/inst/shinyapps |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/generate_documentation.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_directtransmission.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_environmentaltransmission.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_evolution.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_heterogeneity.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_idcharacteristics.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_idcontrol.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_idpatterns.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_introduction.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_multipathogen.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_reproductivenumber.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_stochastic_SEIR.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_stochastic_SIR.R |only DSAIDE-0.7.0/DSAIDE/inst/simulatorfunctions/simulate_vectortransmission.R |only DSAIDE-0.7.0/DSAIDE/man/dsaideapps.Rd |only DSAIDE-0.7.0/DSAIDE/man/generate_plots.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_directtransmission.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_environmentaltransmission.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_evolution.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_heterogeneity.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_idcharacteristics.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_idcontrol.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_idpatterns.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_introduction.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_multipathogen.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_reproductivenumber.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_stochastic_SEIR.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_stochastic_SIR.Rd |only DSAIDE-0.7.0/DSAIDE/man/simulate_vectortransmission.Rd |only DSAIDE-0.7.0/DSAIDE/tests/testthat/test-dsaideapps.R |only DSAIDE-0.7.0/DSAIDE/tests/testthat/test-generate_plots.R |only DSAIDE-0.8.0/DSAIDE/DESCRIPTION | 25 DSAIDE-0.8.0/DSAIDE/MD5 | 293 +- DSAIDE-0.8.0/DSAIDE/NAMESPACE | 43 DSAIDE-0.8.0/DSAIDE/NEWS.md | 25 DSAIDE-0.8.0/DSAIDE/R/dsaidemenu.R | 37 DSAIDE-0.8.0/DSAIDE/R/generate_documentation.R | 26 DSAIDE-0.8.0/DSAIDE/R/generate_fctcall.R |only DSAIDE-0.8.0/DSAIDE/R/generate_ggplot.R |only DSAIDE-0.8.0/DSAIDE/R/generate_plotly.R |only DSAIDE-0.8.0/DSAIDE/R/generate_shinyinput.R |only DSAIDE-0.8.0/DSAIDE/R/generate_text.R | 64 DSAIDE-0.8.0/DSAIDE/R/run_model.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_directtransmission_ode.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_environmentaltransmission_ode.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_evolution_stochastic.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_heterogeneity_ode.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_idcharacteristics_ode.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_idcontrol_ode.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_idpatterns_ode.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_modelexploration_sir.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_multipathogen_ode.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_reproductivenumber_ode.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_seir_stochastic.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_sir_discrete.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_sir_ode.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_sirdemographic_ode.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_sirdemographic_stochastic.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_usanalysis_sir.R |only DSAIDE-0.8.0/DSAIDE/R/simulate_vectortransmission_ode.R |only DSAIDE-0.8.0/DSAIDE/build/vignette.rds |binary DSAIDE-0.8.0/DSAIDE/inst/DSAIDE |only DSAIDE-0.8.0/DSAIDE/inst/appinformation |only DSAIDE-0.8.0/DSAIDE/inst/doc/DSAIDE.R | 58 DSAIDE-0.8.0/DSAIDE/inst/doc/DSAIDE.Rmd | 150 - DSAIDE-0.8.0/DSAIDE/inst/doc/DSAIDE.html | 293 +- DSAIDE-0.8.0/DSAIDE/inst/docsfordevelopers/documentation.md | 50 DSAIDE-0.8.0/DSAIDE/inst/epirecipes |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_directtransmission_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_environmentaltransmission_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_evolution_stochastic.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_heterogeneity_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_idcharacteristics_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_idcontrol_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_idpatterns_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_modelexploration_sir.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_multipathogen_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_reproductivenumber_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_seir_stochastic.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_sir_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_sirdemographic_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_sirdemographic_stochastic.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_usanalysis_sir.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulate_vectortransmission_ode.R |only DSAIDE-0.8.0/DSAIDE/inst/simulatorfunctions/simulatorfunctions.zip |only DSAIDE-0.8.0/DSAIDE/man/dsaidemenu.Rd | 4 DSAIDE-0.8.0/DSAIDE/man/generate_documentation.Rd | 13 DSAIDE-0.8.0/DSAIDE/man/generate_fctcall.Rd |only DSAIDE-0.8.0/DSAIDE/man/generate_ggplot.Rd |only DSAIDE-0.8.0/DSAIDE/man/generate_plotly.Rd |only DSAIDE-0.8.0/DSAIDE/man/generate_shinyinput.Rd |only DSAIDE-0.8.0/DSAIDE/man/generate_text.Rd | 14 DSAIDE-0.8.0/DSAIDE/man/run_model.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_directtransmission_ode.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_environmentaltransmission_ode.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_evolution_stochastic.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_heterogeneity_ode.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_idcharacteristics_ode.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_idcontrol_ode.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_idpatterns_ode.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_modelexploration_sir.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_multipathogen_ode.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_reproductivenumber_ode.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_seir_stochastic.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_sir_discrete.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_sir_ode.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_sirdemographic_ode.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_sirdemographic_stochastic.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_usanalysis_sir.Rd |only DSAIDE-0.8.0/DSAIDE/man/simulate_vectortransmission_ode.Rd |only DSAIDE-0.8.0/DSAIDE/tests/testthat/Rplots.pdf |binary DSAIDE-0.8.0/DSAIDE/tests/testthat/test-generate_documentation.R |only DSAIDE-0.8.0/DSAIDE/tests/testthat/test-generate_ggplot.R |only DSAIDE-0.8.0/DSAIDE/tests/testthat/test-generate_plotly.R |only DSAIDE-0.8.0/DSAIDE/tests/testthat/test-generate_shinyinput.R |only DSAIDE-0.8.0/DSAIDE/tests/testthat/test-generate_text.R | 2 DSAIDE-0.8.0/DSAIDE/tests/testthat/test-generate_usplot.R |only DSAIDE-0.8.0/DSAIDE/tests/testthat/test-modelexploration.R |only DSAIDE-0.8.0/DSAIDE/tests/testthat/test-run_model.R |only DSAIDE-0.8.0/DSAIDE/vignettes/DSAIDE.Rmd | 150 - DSAIDE-0.8.0/DSAIDE/vignettes/mysimulator.R | 118 DSAIDE-0.8.0/DSAIDE/vignettes/vignetterefs.bib | 1356 ++++------ 140 files changed, 1264 insertions(+), 1457 deletions(-)