Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.18 dated 2020-12-15 and 0.0.19 dated 2021-07-30
ChangeLog | 10 ++++++++++ DESCRIPTION | 11 +++++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/UsingAnnoyInCcppWrapper.pdf |binary 6 files changed, 28 insertions(+), 9 deletions(-)
Title: Bounding Omitted Variable Bias Using Auxiliary Data
Description: Functions to implement a Hwang(2021) <doi:10.2139/ssrn.3866876> estimator, which bounds an omitted variable bias using auxiliary data.
Author: Yujung Hwang [aut, cre] (<https://orcid.org/0000-0002-8136-8987>)
Maintainer: Yujung Hwang <yujungghwang@gmail.com>
Diff between bndovb versions 1.0 dated 2021-06-21 and 1.1 dated 2021-07-30
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/bndovbme.R | 35 +++++++++++++++++++++++++++-------- build/partial.rdb |binary inst/doc/bndovb.html | 14 +++++++------- 5 files changed, 41 insertions(+), 22 deletions(-)
Title: Create Beautiful, Simple Personal Websites
Description: A collection of R Markdown templates for creating simple and easy
to personalize single page websites.
Author: Sean Kross [aut, cre] (<https://orcid.org/0000-0001-5215-0316>)
Maintainer: Sean Kross <sean@seankross.com>
Diff between postcards versions 0.2.0 dated 2021-01-06 and 0.2.1 dated 2021-07-30
DESCRIPTION | 9 +--- MD5 | 34 +++++++++------ NAMESPACE | 1 NEWS.md | 4 + R/create.R | 11 ++-- R/postcards.R | 8 +++ README.md | 60 +++++++++++++++++++++++++-- inst/img/sigridur.jpg |only inst/pandoc_templates/solana.html |only inst/rmarkdown/templates/solana |only inst/rstudio/templates/project/postcards.dcf | 2 man/create_postcard.Rd | 3 - man/figures/solana-preview.png |only man/figures/trestles-preview.png |binary man/jolla.Rd | 5 +- man/jolla_blue.Rd | 5 +- man/onofre.Rd | 5 +- man/solana.Rd |only man/trestles.Rd | 5 +- tests/testthat/test-postcards.R | 1 20 files changed, 120 insertions(+), 33 deletions(-)
Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods dedicated to sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2018) <doi:10.1214/18-STS646>, the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation and overimputation for 'mice'.
Author: Vincent Audigier [aut, cre] (CNAM MSDMA team),
Matthieu Resche-Rigon [aut] (INSERM ECSTRA team)
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between micemd versions 1.6.0 dated 2019-07-09 and 1.7.0 dated 2021-07-30
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/mice.impute.2l.glm.bin.R | 7 +++---- R/mice.impute.2l.glm.norm.R | 4 ++-- R/mice.impute.2l.glm.pois.R | 7 +++---- R/overimpute.R | 10 +++++----- man/mice.par.Rd | 2 +- man/overimpute.Rd | 2 +- 8 files changed, 26 insertions(+), 28 deletions(-)
Title: Download Air Quality and Meteorological Information of Chile
Description: Download air quality and meteorological information of Chile from the National Air Quality System (S.I.N.C.A.)<https://sinca.mma.gob.cl/> dependent on the Ministry of the Environment and the Meteorological Directorate of Chile (D.M.C.)<http://www.meteochile.gob.cl/> dependent on the Directorate General of Civil Aeronautics.
Author: Francisco Catalan Meyer [aut, cre]
(<https://orcid.org/0000-0003-3506-5376>),
Manuel Leiva [aut] (<https://orcid.org/0000-0001-8891-0399>),
Richard Toro [aut]
Maintainer: Francisco Catalan Meyer <francisco.catalan@ug.uchile.cl>
Diff between AtmChile versions 0.1.1 dated 2021-07-13 and 0.1.2 dated 2021-07-30
DESCRIPTION | 6 +-- MD5 | 10 +++--- R/ChileAirQuality.R | 74 ++++++++++++------------------------------------ R/ChileClimateData.R | 8 ++--- man/ChileAirQuality.Rd | 2 - man/ChileClimateData.Rd | 6 +-- 6 files changed, 35 insertions(+), 71 deletions(-)
Title: Distance Sampling Survey Design
Description: Creates survey designs for distance sampling surveys. These
designs can be assessed for various effort and coverage statistics.
Once the user is satisfied with the design characteristics they can
generate a set of transects to use in their distance sampling survey.
Many of the designs implemented in this R package were first made
available in our 'Distance' for Windows software and are detailed in
Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008,
ISBN-13: 978-0199225873). Find out more about estimating animal/plant
abundance with distance sampling at <http://distancesampling.org/>.
Author: Laura Marshall [aut, cre],
Rexstad Eric [ctb]
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between dssd versions 0.2.2 dated 2021-02-25 and 0.3.0 dated 2021-07-30
dssd-0.2.2/dssd/inst/extdata/TrackExample.prj |only dssd-0.2.2/dssd/tests/testthat/test-SegmentedDesign.r |only dssd-0.2.2/dssd/tests/testthat/test-UserInput.r |only dssd-0.2.2/dssd/tests/testthat/test-xdonttest.R |only dssd-0.3.0/dssd/DESCRIPTION | 38 - dssd-0.3.0/dssd/MD5 | 66 +- dssd-0.3.0/dssd/NAMESPACE | 12 dssd-0.3.0/dssd/NEWS | 18 dssd-0.3.0/dssd/R/Class.Constructors.R | 100 +-- dssd-0.3.0/dssd/R/Line.Transect.Design.R | 4 dssd-0.3.0/dssd/R/Point.Transect.Design.R | 3 dssd-0.3.0/dssd/R/Region.R | 262 +++----- dssd-0.3.0/dssd/R/calculate.effort.R |only dssd-0.3.0/dssd/R/calculate.trackline.segl.R | 3 dssd-0.3.0/dssd/R/check.design.R |only dssd-0.3.0/dssd/R/check.line.design.R | 393 +++++++----- dssd-0.3.0/dssd/R/check.point.design.R | 254 ++++--- dssd-0.3.0/dssd/R/dssd-package.R | 2 dssd-0.3.0/dssd/README.md |only dssd-0.3.0/dssd/build/vignette.rds |binary dssd-0.3.0/dssd/inst/doc/GettingStarted.R | 12 dssd-0.3.0/dssd/inst/doc/GettingStarted.Rmd | 21 dssd-0.3.0/dssd/inst/doc/GettingStarted.html | 338 +++------- dssd-0.3.0/dssd/inst/doc/MultiStrataVignette.R | 10 dssd-0.3.0/dssd/inst/doc/MultiStrataVignette.Rmd | 14 dssd-0.3.0/dssd/inst/doc/MultiStrataVignette.html | 484 +++++---------- dssd-0.3.0/dssd/man/Line.Transect.Design-class.Rd | 2 dssd-0.3.0/dssd/man/calculate.effort.Rd |only dssd-0.3.0/dssd/man/dssd-package.Rd | 2 dssd-0.3.0/dssd/man/make.coverage.Rd | 16 dssd-0.3.0/dssd/man/make.design.Rd | 48 + dssd-0.3.0/dssd/man/plot.Region-methods.Rd | 48 + dssd-0.3.0/dssd/tests/test-that.R | 2 dssd-0.3.0/dssd/tests/testthat/test-check_CalcEffort.R |only dssd-0.3.0/dssd/tests/testthat/test-check_DesignParams.R |only dssd-0.3.0/dssd/tests/testthat/test-check_Designs.R |only dssd-0.3.0/dssd/tests/testthat/test-check_SegDesign.R |only dssd-0.3.0/dssd/tests/testthat/test-check_UserInput.R |only dssd-0.3.0/dssd/tests/testthat/test-x_seed_tests.R |only dssd-0.3.0/dssd/vignettes/GettingStarted.Rmd | 21 dssd-0.3.0/dssd/vignettes/MultiStrataVignette.Rmd | 14 41 files changed, 1077 insertions(+), 1110 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from
National Water Information System (NWIS) <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>.
Both EPA and USGS water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>),
Robert Hirsch [aut] (<https://orcid.org/0000-0002-4534-075X>),
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Carr [ctb],
David Watkins [aut] (<https://orcid.org/0000-0002-7544-0700>),
David Blodgett [ctb],
Mike Johnson [aut] (<https://orcid.org/0000-0002-5288-8350>)
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.8 dated 2021-06-26 and 2.7.9 dated 2021-07-30
dataRetrieval-2.7.8/dataRetrieval/vignettes/QW_changes_cache |only dataRetrieval-2.7.8/dataRetrieval/vignettes/atascadero-creek-nldi.png |only dataRetrieval-2.7.8/dataRetrieval/vignettes/ucsb.png |only dataRetrieval-2.7.9/dataRetrieval/DESCRIPTION | 8 dataRetrieval-2.7.9/dataRetrieval/MD5 | 55 -- dataRetrieval-2.7.9/dataRetrieval/NEWS | 6 dataRetrieval-2.7.9/dataRetrieval/R/findNLDI.R | 274 +++++----- dataRetrieval-2.7.9/dataRetrieval/R/getWebServiceData.R | 7 dataRetrieval-2.7.9/dataRetrieval/R/importRDB1.r | 27 dataRetrieval-2.7.9/dataRetrieval/R/readNWISdata.r | 15 dataRetrieval-2.7.9/dataRetrieval/R/readNWISqw.r | 24 dataRetrieval-2.7.9/dataRetrieval/R/whatNWISData.r | 7 dataRetrieval-2.7.9/dataRetrieval/build/vignette.rds |binary dataRetrieval-2.7.9/dataRetrieval/inst/CITATION | 2 dataRetrieval-2.7.9/dataRetrieval/inst/doc/dataRetrieval.html | 2 dataRetrieval-2.7.9/dataRetrieval/inst/doc/qwdata_changes.R |only dataRetrieval-2.7.9/dataRetrieval/inst/doc/qwdata_changes.Rmd |only dataRetrieval-2.7.9/dataRetrieval/inst/doc/qwdata_changes.html |only dataRetrieval-2.7.9/dataRetrieval/man/findNLDI.Rd | 6 dataRetrieval-2.7.9/dataRetrieval/man/readNWISdata.Rd | 4 dataRetrieval-2.7.9/dataRetrieval/man/readNWISqw.Rd | 21 dataRetrieval-2.7.9/dataRetrieval/tests/testthat/tests_general.R | 13 dataRetrieval-2.7.9/dataRetrieval/tests/testthat/tests_nldi.R | 2 dataRetrieval-2.7.9/dataRetrieval/tests/testthat/tests_userFriendly_fxns.R | 53 - dataRetrieval-2.7.9/dataRetrieval/vignettes/nwisData.rds |only dataRetrieval-2.7.9/dataRetrieval/vignettes/qwdata_changes.Rmd |only dataRetrieval-2.7.9/dataRetrieval/vignettes/wqpData.rds |only 27 files changed, 253 insertions(+), 273 deletions(-)
Title: Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Description: Provides functions for forest analysis using airborne laser scanning (LiDAR remote sensing) data: tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation and mapping with the area-based approach. It includes complementary steps for forest mapping: co-registration of field plots with LiDAR data (Monnet and Mermin (2014) <doi:10.3390/f5092307>); extraction of both physical (gaps, edges, trees) and statistical features from LiDAR data useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>); model calibration with ground reference, and maps export.
Author: Jean-Matthieu Monnet [aut, cre],
Pascal Obstétar [ctb]
Maintainer: Jean-Matthieu Monnet <jean-matthieu.monnet@inrae.fr>
Diff between lidaRtRee versions 3.0.2 dated 2021-04-10 and 3.1.0 dated 2021-07-30
lidaRtRee-3.0.2/lidaRtRee/R/chmchablais3-data.R |only lidaRtRee-3.0.2/lidaRtRee/R/gap.detection.R |only lidaRtRee-3.0.2/lidaRtRee/R/laschablais3-data.R |only lidaRtRee-3.0.2/lidaRtRee/R/optical.metrics.R |only lidaRtRee-3.0.2/lidaRtRee/R/quatremontagnes-data.R |only lidaRtRee-3.0.2/lidaRtRee/R/raster.metrics.R |only lidaRtRee-3.0.2/lidaRtRee/R/tree.detection.R |only lidaRtRee-3.0.2/lidaRtRee/R/tree.match.R |only lidaRtRee-3.0.2/lidaRtRee/R/tree.metrics.R |only lidaRtRee-3.0.2/lidaRtRee/R/treeinventorychablais3-data.R |only lidaRtRee-3.0.2/lidaRtRee/data/chmchablais3.rda |only lidaRtRee-3.0.2/lidaRtRee/data/laschablais3.rda |only lidaRtRee-3.0.2/lidaRtRee/data/quatremontagnes.rda |only lidaRtRee-3.0.2/lidaRtRee/data/treeinventorychablais3.rda |only lidaRtRee-3.0.2/lidaRtRee/man/ABAinference.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/ABAmodel.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/ABAmodelCombineStrata.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/ABAmodelMetrics.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/ABAmodelPlot.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/ABApredict.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/AddVegetationIndices.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/BoxcoxTr.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/chmchablais3.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/cleanRaster.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/cloudMetrics.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/cloudTreeMetrics.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/createDisk.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/demFiltering.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/edgeDetection.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/gapDetection.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/heightRegression.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/histDetection.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/histStack.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/iBoxcoxTr.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/iBoxcoxTrBiasCor.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/laschablais3.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/lmaCheck.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/maximaDetection.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/maximaSelection.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/plot2Dmatched.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/plotTreeInventory.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/points2terrainStats.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/quatremontagnes.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rasterChullMask.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rasterLocalmax.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rasterMetrics.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rasterXYMask.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rasterZonalStats.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rastersMovingCor.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/segAdjust.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/speciesColor.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/stdTreeMetrics.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/treeExtraction.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/treeMatching.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/treeSegmentation.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/treeinventorychablais3.Rd |only lidaRtRee-3.1.0/lidaRtRee/DESCRIPTION | 18 lidaRtRee-3.1.0/lidaRtRee/MD5 | 159 - lidaRtRee-3.1.0/lidaRtRee/NAMESPACE | 78 lidaRtRee-3.1.0/lidaRtRee/R/aba.R | 1342 +++++++----- lidaRtRee-3.1.0/lidaRtRee/R/chm_chablais3-data.R |only lidaRtRee-3.1.0/lidaRtRee/R/common.R | 668 +++-- lidaRtRee-3.1.0/lidaRtRee/R/coregistration.R | 479 ++-- lidaRtRee-3.1.0/lidaRtRee/R/gap_detection.R |only lidaRtRee-3.1.0/lidaRtRee/R/las_chablais3-data.R |only lidaRtRee-3.1.0/lidaRtRee/R/metrics.R | 496 ++-- lidaRtRee-3.1.0/lidaRtRee/R/optical_metrics.R |only lidaRtRee-3.1.0/lidaRtRee/R/quatre_montagnes-data.R |only lidaRtRee-3.1.0/lidaRtRee/R/raster_metrics.R |only lidaRtRee-3.1.0/lidaRtRee/R/tree_detection.R |only lidaRtRee-3.1.0/lidaRtRee/R/tree_inventory_chablais3-data.R |only lidaRtRee-3.1.0/lidaRtRee/R/tree_match.R |only lidaRtRee-3.1.0/lidaRtRee/R/tree_metrics.R |only lidaRtRee-3.1.0/lidaRtRee/build/partial.rdb |binary lidaRtRee-3.1.0/lidaRtRee/data/chm_chablais3.rda |only lidaRtRee-3.1.0/lidaRtRee/data/las_chablais3.rda |only lidaRtRee-3.1.0/lidaRtRee/data/quatre_montagnes.rda |only lidaRtRee-3.1.0/lidaRtRee/data/tree_inventory_chablais3.rda |only lidaRtRee-3.1.0/lidaRtRee/man/aba_build_model.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/aba_combine_strata.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/aba_inference.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/aba_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/aba_plot.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/aba_predict.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/add_vegetation_indices.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/boxcox_itr.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/boxcox_itr_bias_cor.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/boxcox_tr.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/chm_chablais3.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/cimg2Raster.Rd | 25 lidaRtRee-3.1.0/lidaRtRee/man/circle2Raster.Rd | 3 lidaRtRee-3.1.0/lidaRtRee/man/clean_raster.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/clouds_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/clouds_tree_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/coregistration.Rd | 61 lidaRtRee-3.1.0/lidaRtRee/man/create_disk.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/dem_filtering.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/edge_detection.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/ellipses4Crown.Rd | 25 lidaRtRee-3.1.0/lidaRtRee/man/gap_detection.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/height_regression.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/hist_detection.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/hist_stack.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/las_chablais3.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/lma_check.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/maxima_detection.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/maxima_selection.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/plot_matched.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/plot_tree_inventory.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/pointList2SPDF.Rd | 23 lidaRtRee-3.1.0/lidaRtRee/man/points2DSM.Rd | 11 lidaRtRee-3.1.0/lidaRtRee/man/points2DTM.Rd | 18 lidaRtRee-3.1.0/lidaRtRee/man/polar2Projected.Rd | 38 lidaRtRee-3.1.0/lidaRtRee/man/quatre_montagnes.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/raster2Cimg.Rd | 24 lidaRtRee-3.1.0/lidaRtRee/man/raster_chull_mask.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/raster_local_max.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/raster_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/raster_xy_mask.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/raster_zonal_stats.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/rasters2Cor.Rd | 45 lidaRtRee-3.1.0/lidaRtRee/man/rasters_moving_cor.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/seg_adjust.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/segmentation.Rd | 42 lidaRtRee-3.1.0/lidaRtRee/man/species_color.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/std_tree_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/terrain_points_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/tree_extraction.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/tree_inventory_chablais3.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/tree_matching.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/tree_segmentation.Rd |only lidaRtRee-3.1.0/lidaRtRee/tests |only 132 files changed, 2022 insertions(+), 1533 deletions(-)
Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. We also provide functions for sample size determination and estimation of diagnostic accuracy measures. We also include graphical tools. The statistical methodology used here can be found in Perez-Jaume et al (2017) <doi:10.18637/jss.v082.i04>.
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.8.3 dated 2020-09-28 and 2.9.0 dated 2021-07-30
ThresholdROC-2.8.3/ThresholdROC/data/AD.txt |only ThresholdROC-2.8.3/ThresholdROC/data/chemo.txt |only ThresholdROC-2.9.0/ThresholdROC/DESCRIPTION | 14 ThresholdROC-2.9.0/ThresholdROC/MD5 | 20 ThresholdROC-2.9.0/ThresholdROC/NAMESPACE | 5 ThresholdROC-2.9.0/ThresholdROC/R/ThresholdROC-2states.R | 282 +++++++++++- ThresholdROC-2.9.0/ThresholdROC/data/AD.txt.gz |only ThresholdROC-2.9.0/ThresholdROC/data/chemo.txt.gz |only ThresholdROC-2.9.0/ThresholdROC/man/SS.Rd | 9 ThresholdROC-2.9.0/ThresholdROC/man/ThresholdROC-package.Rd | 4 ThresholdROC-2.9.0/ThresholdROC/man/plotCostROC.Rd | 2 ThresholdROC-2.9.0/ThresholdROC/man/thres2.Rd | 27 + ThresholdROC-2.9.0/ThresholdROC/man/thresTH2.Rd | 7 13 files changed, 319 insertions(+), 51 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: This is a set of functions to retrieve information about GIMMS
NDVI3g files currently available online; download (and re-arrange, in the
case of NDVI3g.v0) the half-monthly data sets; import downloaded files from
ENVI binary (NDVI3g.v0) or NetCDF format (NDVI3g.v1) directly into R based
on the widespread 'raster' package; conduct quality control; and generate
monthly composites (e.g., maximum values) from the half-monthly input data.
As a special gimmick, a method is included to conveniently apply the
Mann-Kendall trend test upon 'Raster*' images, optionally featuring
trend-free pre-whitening to account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between gimms versions 1.2.0 dated 2021-04-16 and 1.2.1 dated 2021-07-30
DESCRIPTION | 7 -- MD5 | 30 ++++----- NEWS.md | 11 +++ R/gimmsControls.R | 16 +++- R/significantTau.R | 4 - R/updateInventory.R | 127 +++++++++++++++++++++++++++++++++++++-- README.md | 6 + build/partial.rdb |binary data/bale3g.v1.rda |binary data/kili3g.v0.rda |binary inst/extdata/poles.html |only inst/tinytest/test-getPolesFTP.R |only inst/tinytest/tests.R | 8 ++ man/downloadGimms.Rd | 6 - man/gimms-package.Rd | 20 +++--- man/significantTau.Rd | 4 - man/updateInventory.Rd | 18 ++--- 17 files changed, 206 insertions(+), 51 deletions(-)
Title: Explore the Innards of 'ggplot2' Objects
Description: Extensions to 'ggplot2' providing low-level debug tools: statistics
and geometries echoing their data argument. Layer manipulation: deletion,
insertion, extraction and reordering of layers. Deletion of unused variables
from the data object embedded in "ggplot" objects.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between gginnards versions 0.1.0 dated 2021-05-27 and 0.1.0-1 dated 2021-07-30
DESCRIPTION | 14 ++-- MD5 | 40 +++++------ NEWS.md | 7 ++ R/data-manip.R | 14 ++-- R/geom-debug.R | 19 +++-- R/layer-manip.R | 58 ++++++++-------- README.md | 6 - inst/doc/user-guide-1.html | 6 - inst/doc/user-guide-2.R | 10 +- inst/doc/user-guide-2.Rmd | 14 ++-- inst/doc/user-guide-2.html | 106 +++++++++++++++++-------------- man/delete_layers.Rd | 56 ++++++++-------- man/drop_vars.Rd | 12 ++- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-6-2.png |binary man/geom_debug.Rd | 10 +- man/geom_null.Rd | 9 +- man/gginnards-package.Rd | 2 vignettes/user-guide-2.Rmd | 14 ++-- 21 files changed, 223 insertions(+), 174 deletions(-)
Title: Adoption Probability, Triers and Users Rate of a New Product
Description: Calculate users prevalence of a product based on the prevalence of triers in the population. The measurement of triers is relatively easy. It is just a question of whether a person tried a product even once in his life or not. On the other hand, The measurement of people who also adopt it as part of their life is more complicated since adopting an innovative product is a subjective view of the individual. Mickey Kislev and Shira Kislev developed a formula to calculate the prevalence of a product's users to overcome this difficulty. The current package assists in calculating the users prevalence of a product based on the prevalence of triers in the population. See for: Kislev, M. M., and S. Kislev (2020) <doi:10.5539/ijms.v12n4p63>.
Author: Mickey Kislev [cre],
Shira Kislev [aut]
Maintainer: Mickey Kislev <mickeykislev@researchgap.ac>
Diff between ADP versions 0.1.3 dated 2021-07-28 and 0.1.5 dated 2021-07-30
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/ADP.R | 14 ++++++-------- man/ADP.Rd | 2 +- man/adp.t.Rd | 2 +- man/adp.u.Rd | 2 +- man/ptriers.Rd | 2 +- man/pusers.Rd | 4 ++-- 8 files changed, 24 insertions(+), 26 deletions(-)
Title: An R Package to Retrieve, Analyze and Visualize Air Traffic Data
Description: Provides functionalities and data structures to retrieve, analyze and visualize aviation
data. It includes a client interface to the 'OpenSky' API <https://opensky-network.org>. It allows
retrieval of flight information, as well as aircraft state vectors.
Author: Rafael Ayala, Daniel Ayala, David Ruiz, Aleix Sellés, Lara Sellés Vidal
Maintainer: Rafael Ayala <rafael.ayala@oist.jp>
Diff between openSkies versions 1.1.1 dated 2021-04-17 and 1.1.2 dated 2021-07-30
DESCRIPTION | 10 - MD5 | 21 +- NAMESPACE | 1 NEWS | 4 R/openSkies_classDefinitions.R | 8 + R/openSkies_formatResponseFunctions.R | 2 R/openSkies_getStateVectorsFunctions.R | 50 ++++++ R/openSkies_otherSupportFunctions.R | 31 +++ build/vignette.rds |binary inst/doc/openSkies.html | 262 +++++++++++++++------------------ man/getIntervalFlights.Rd | 2 man/getIntervalStateVectors.Rd |only 12 files changed, 233 insertions(+), 158 deletions(-)
Title: Simulate Expression Data from 'igraph' Networks
Description: Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix derived from a graph structure in 'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' structures rather than sigma matrices as input. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression. For example methods to infer biological pathways and gene regulatory networks from gene expression data can be tested on simulated datasets using this framework. This also allows for pathway structures to be considered as a confounding variable when simulating gene expression data to test the performance of genomic analyses.
Author: S. Thomas Kelly [aut, cre],
Michael A. Black [aut, ths],
Robrecht Cannoodt [ctb],
Jason Cory Brunson [ctb]
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>
Diff between graphsim versions 1.0.1 dated 2020-07-17 and 1.0.2 dated 2021-07-30
graphsim-1.0.1/graphsim/inst/doc/plots_directed.html |only graphsim-1.0.1/graphsim/inst/doc/plots_directed.html.asis |only graphsim-1.0.1/graphsim/vignettes/plots_directed.html.asis |only graphsim-1.0.2/graphsim/DESCRIPTION | 17 graphsim-1.0.2/graphsim/MD5 | 27 graphsim-1.0.2/graphsim/NEWS.md | 8 graphsim-1.0.2/graphsim/R/graphsim-package.R | 7 graphsim-1.0.2/graphsim/R/plot_directed.R | 1 graphsim-1.0.2/graphsim/README.md | 13 graphsim-1.0.2/graphsim/build/partial.rdb |only graphsim-1.0.2/graphsim/build/vignette.rds |binary graphsim-1.0.2/graphsim/inst/CITATION | 2 graphsim-1.0.2/graphsim/inst/doc/simulate_expression.html | 1711 ++++++------- graphsim-1.0.2/graphsim/man/graphsim-package.Rd | 7 graphsim-1.0.2/graphsim/vignettes/import_reactome.html |only graphsim-1.0.2/graphsim/vignettes/plots_directed.Rmd | 3 graphsim-1.0.2/graphsim/vignettes/simulate_expression.Rmd | 22 17 files changed, 923 insertions(+), 895 deletions(-)
Title: Collective Matrix Factorization for Recommender Systems
Description: Collective matrix factorization (a.k.a. multi-view or multi-way factorization,
Singh, Gordon, (2008) <doi:10.1145/1401890.1401969>) tries to approximate a matrix 'X' as the
product of two low-dimensional matrices aided with secondary information matrices about rows
and/or columns of 'X' which are also factorized using the same latent components.
The intended usage is for recommender systems, dimensionality reduction, and missing value imputation.
Implements extensions of the original model (Cortes, (2018) <arXiv:1809.00366>) and can produce
different factorizations such as the weighted 'implicit-feedback' model (Hu, Koren, Volinsky,
(2008) <doi:10.1109/ICDM.2008.22>), the 'weighted-lambda-regularization' model,
(Zhou, Wilkinson, Schreiber, Pan, (2008) <doi:10.1007/978-3-540-68880-8_32>),
or the enhanced model with 'implicit features' (Rendle, Zhang,
Koren, (2019) <arXiv:1905.01395>), with or without side information. Can use gradient-based
procedures or alternating-least squares procedures (Koren, Bell, Volinsky, (2009)
<doi:10.1109/MC.2009.263>), with either a Cholesky solver, a faster conjugate gradient solver
(Takacs, Pilaszy, Tikk, (2011) <doi:10.1145/2043932.2043987>), or a non-negative
coordinate descent solver (Franc, Hlavac, Navara, (2005) <doi:10.1007/11556121_50>),
providing efficient methods for sparse and dense data, and mixtures thereof.
Supports L1 and L2 regularization in the main models,
offers alternative most-popular and content-based models, and implements functionality
for cold-start recommendations and imputation of 2D data.
Author: David Cortes [aut, cre, cph],
Jorge Nocedal [cph] (Copyright holder of included LBFGS library),
Naoaki Okazaki [cph] (Copyright holder of included LBFGS library),
David Blackman [cph] (Copyright holder of original Xoshiro code),
Sebastiano Vigna [cph] (Copyright holder of original Xoshiro code)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between cmfrec versions 3.2.1 dated 2021-07-29 and 3.2.2 dated 2021-07-30
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/helpers.c | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Machine Learning Time Series Forecasting
Description: Compute both static and recursive time series forecasts of machine learning models.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between iForecast versions 1.0.2 dated 2021-02-21 and 1.0.3 dated 2021-07-30
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- R/rollingWindows.R |only man/iForecast.Rd | 2 +- man/rollingWindows.Rd |only man/ttsCaret.Rd | 6 +++--- 6 files changed, 13 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-10 1.2
2020-02-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-17 1.4
2019-11-22 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-16 1.0
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre],
Matt Dennis [ctb],
Antoine Bichat [ctb] (<https://orcid.org/0000-0001-6599-7081>),
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>
Diff between emayili versions 0.4.12 dated 2021-07-13 and 0.4.15 dated 2021-07-30
DESCRIPTION | 13 ++++--------- MD5 | 24 ++++++++++++------------ NEWS.md | 17 ++++++++++++++++- R/attachment.R | 4 ++-- R/body.R | 12 +++++++++++- R/server.R | 4 +++- README.md | 8 ++++---- man/attachment.Rd | 11 +++++++++-- man/html.Rd | 6 +++++- tests/testthat/setup-files.R | 9 +++++++-- tests/testthat/teardown-files.R | 2 +- tests/testthat/test-body.R | 9 +++++++++ tests/testthat/test-server.R | 2 +- 13 files changed, 84 insertions(+), 37 deletions(-)
Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading,
analyzing and visualizing datasets from UCSC Xena
(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public
databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Yi Xiong [aut] (<https://orcid.org/0000-0002-4370-9824>),
Longfei Zhao [aut] (<https://orcid.org/0000-0002-6277-0137>),
Kai Gu [aut] (<https://orcid.org/0000-0002-0177-0774>),
Yin Li [aut],
Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaShiny versions 1.1.0 dated 2021-07-16 and 1.1.1 dated 2021-07-30
DESCRIPTION | 6 MD5 | 288 NAMESPACE | 150 NEWS.md | 41 R/GeomSplitViolin.R | 110 R/analyze_gene_drug_response.R | 908 R/ccle.R | 288 R/data.R | 244 R/ezcor.R | 870 R/get_pancan_value.R | 758 R/get_pcawg_value.R | 254 R/globalVariables.R | 34 R/load_data.R | 134 R/ope_pancan_value.R | 122 R/query_custom_value.R | 20 R/query_toil_value_df.R | 122 R/query_value.R | 392 R/run.R | 50 R/tcga_surv.R | 412 R/utils-pipe.R | 36 R/utils.R | 116 R/vis_analyze_gene_drug_response.R | 224 R/vis_ccle_value.R | 332 R/vis_identifier.R | 748 R/vis_pancan_value.R | 2588 - R/vis_pcawg_value.R | 928 R/xenashiny.R | 18 R/zzz.R |only README.md | 534 build/vignette.rds |binary inst/doc/api.R | 108 inst/doc/api.Rmd | 254 inst/doc/api.html | 898 inst/extdata/ccle_drug_response_extend.rda |only inst/modules_apps/app.R | 38 inst/modules_apps/simple_module_from_rstudio.R | 66 inst/modules_apps/xx_modules.R | 98 inst/shinyapp/App.R | 670 inst/shinyapp/modules/combo-single-gene-pan-cancer-analysis.R | 124 inst/shinyapp/modules/home-pancan-search.R | 178 inst/shinyapp/modules/modules-ccle-gene-drug-respose-df.R | 352 inst/shinyapp/modules/modules-ccle-gene-drug-target.R | 358 inst/shinyapp/modules/modules-ccle-genecor.R | 516 inst/shinyapp/modules/modules-ccle-search.R | 328 inst/shinyapp/modules/modules-file-upload.R | 238 inst/shinyapp/modules/modules-ga-group-comparison.R | 1496 inst/shinyapp/modules/modules-ga-matrix-correlation.R | 778 inst/shinyapp/modules/modules-ga-scatter-correlation.R | 762 inst/shinyapp/modules/modules-ga-surv-analysis.R | 1420 inst/shinyapp/modules/modules-pancan-anatomy.R | 340 inst/shinyapp/modules/modules-pancan-genecor.R | 498 inst/shinyapp/modules/modules-pancan-immune.R | 352 inst/shinyapp/modules/modules-pancan-radar.R | 402 inst/shinyapp/modules/modules-pancan-search-cancer.R | 380 inst/shinyapp/modules/modules-pancan-search.R | 378 inst/shinyapp/modules/modules-pancan-til.R | 376 inst/shinyapp/modules/modules-pancan-unicox.R | 350 inst/shinyapp/modules/modules-pcawg-genecor.R | 590 inst/shinyapp/modules/modules-pcawg-search.R | 432 inst/shinyapp/modules/modules-pcawg-survival-analysis.R | 692 inst/shinyapp/modules/modules-pcawg-unicox.R | 384 inst/shinyapp/modules/modules-survival-analysis.R | 792 inst/shinyapp/server/general-analysis.R | 384 inst/shinyapp/server/global.R | 32 inst/shinyapp/server/home.R | 170 inst/shinyapp/server/modules.R | 36 inst/shinyapp/server/repository.R | 832 inst/shinyapp/shiny-doc/citation.md | 83 inst/shinyapp/shiny-doc/terms.md | 324 inst/shinyapp/shiny-doc/usage.md | 324 inst/shinyapp/ui/chooser.R | 94 inst/shinyapp/ui/developers.R | 244 inst/shinyapp/ui/footer.R | 32 inst/shinyapp/ui/general-analysis.R | 187 inst/shinyapp/ui/global.R | 22 inst/shinyapp/ui/help.R | 64 inst/shinyapp/ui/home.R | 284 inst/shinyapp/ui/pancan-analysis.R | 156 inst/shinyapp/ui/repository.R | 238 inst/shinyapp/www/bootstrap4.css | 704 inst/shinyapp/www/chooser-binding.js | 168 inst/shinyapp/www/css/bootstrap-grid.css | 4098 +- inst/shinyapp/www/css/bootstrap-grid.min.css | 12 inst/shinyapp/www/css/bootstrap-reboot.css | 658 inst/shinyapp/www/css/bootstrap-reboot.min.css | 14 inst/shinyapp/www/css/bootstrap.css |17948 +++++----- inst/shinyapp/www/css/bootstrap.min.css | 12 inst/shinyapp/www/js/bootstrap.bundle.js |12656 +++---- inst/shinyapp/www/js/bootstrap.bundle.min.js | 12 inst/shinyapp/www/js/bootstrap.js | 7788 ++-- inst/shinyapp/www/js/bootstrap.min.js | 12 man/TCGA.organ.Rd | 30 man/UCSCXenaShiny.Rd | 18 man/analyze_gene_drug_response_asso.Rd | 74 man/analyze_gene_drug_response_diff.Rd | 130 man/app_run.Rd | 48 man/available_hosts.Rd | 34 man/ccle_absolute.Rd | 36 man/ccle_info.Rd | 36 man/ezcor.Rd | 98 man/ezcor_batch.Rd | 104 man/ezcor_partial_cor.Rd | 98 man/get_pancan_value.Rd | 298 man/keep_cat_cols.Rd | 44 man/load_data.Rd | 82 man/pcawg_info.Rd | 36 man/pcawg_purity.Rd | 36 man/pipe.Rd | 24 man/query_molecule_value.Rd | 76 man/query_pancan_value.Rd | 120 man/query_toil_value_df.Rd | 68 man/tcga_clinical.Rd | 36 man/tcga_genome_instability.Rd | 36 man/tcga_gtex.Rd | 30 man/tcga_purity.Rd | 36 man/tcga_subtypes.Rd | 36 man/tcga_surv.Rd | 36 man/tcga_surv_analysis.Rd | 154 man/tcga_tmb.Rd | 36 man/toil_info.Rd | 36 man/vis_ccle_gene_cor.Rd | 108 man/vis_ccle_tpm.Rd | 44 man/vis_gene_TIL_cor.Rd | 74 man/vis_gene_cor.Rd | 84 man/vis_gene_cor_cancer.Rd | 96 man/vis_gene_drug_response_asso.Rd | 52 man/vis_gene_drug_response_diff.Rd | 70 man/vis_gene_immune_cor.Rd | 72 man/vis_gene_msi_cor.Rd | 66 man/vis_gene_stemness_cor.Rd | 66 man/vis_gene_tmb_cor.Rd | 66 man/vis_identifier_cor.Rd | 136 man/vis_identifier_grp_comparison.Rd | 210 man/vis_identifier_grp_surv.Rd | 144 man/vis_identifier_multi_cor.Rd | 146 man/vis_pancan_anatomy.Rd | 62 man/vis_pcawg_dist.Rd | 102 man/vis_pcawg_gene_cor.Rd | 120 man/vis_pcawg_unicox_tree.Rd | 74 man/vis_toil_TvsN.Rd | 110 man/vis_toil_TvsN_cancer.Rd | 92 man/vis_unicox_tree.Rd | 74 tests/testthat.R | 8 tests/testthat/test-run_app.R | 2 tests/testthat/test-vis_pancan_value.R | 10 vignettes/api.Rmd | 254 146 files changed, 38638 insertions(+), 38593 deletions(-)
Title: Raw Data Quality Control Tool for LC-MS System
Description: Assess LC–MS system performance by visualizing instrument log files and monitoring raw quality control samples within a project.
Author: Yonghui Dong
Maintainer: Yonghui Dong <yonghui.dong@gmail.com>
Diff between RawHummus versions 0.1.0 dated 2021-07-19 and 0.1.5 dated 2021-07-30
DESCRIPTION | 11 MD5 | 25 - NAMESPACE | 3 R/runGui.R | 39 - README.md |only inst/shiny/Gui/Report.Rmd | 329 +++++++++++---- inst/shiny/Gui/logo.png |only inst/shiny/Gui/mds/landing.md | 64 +- inst/shiny/Gui/rsconnect/shinyapps.io/dong/RawHummus.dcf | 6 inst/shiny/Gui/server-convert.R | 101 ++-- inst/shiny/Gui/server-evaluate.R | 4 inst/shiny/Gui/server.R | 6 inst/shiny/Gui/style.css |only inst/shiny/Gui/ui-tab-evaluate.R | 2 inst/shiny/Gui/ui.R | 119 ++--- 15 files changed, 445 insertions(+), 264 deletions(-)
Title: Creates Log Files
Description: Contains functions to help create log files. The
package aims to overcome the difficulty of the base R sink() command. The
log_print() function will print to both the console and the file log,
without interfering in other write operations.
Author: David Bosak [aut, cre]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between logr versions 1.2.4 dated 2021-06-16 and 1.2.5 dated 2021-07-30
DESCRIPTION | 10 - MD5 | 36 +++-- NAMESPACE | 2 NEWS.md | 20 +-- R/logr.R | 203 ++++++++++++++++++++++++------- R/unicode.R |only README.md | 2 build/vignette.rds |binary inst/doc/logr-globals.R | 8 + inst/doc/logr-globals.Rmd | 19 ++ inst/doc/logr-globals.html | 6 inst/doc/logr-put.Rmd | 2 inst/doc/logr-put.html | 2 man/log_path.Rd |only man/log_status.Rd |only tests/testthat/log |only tests/testthat/test-logr.R | 294 +++++++++++++++++++++++++++++++++++++++++++++ vignettes/logr-globals.Rmd | 19 ++ vignettes/logr-put.Rmd | 2 19 files changed, 549 insertions(+), 76 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp, Mathew Jay, Charles Reynard, Allison Cheung and Nagendra Singanallur.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.31 dated 2021-07-19 and 2.0.33 dated 2021-07-30
DESCRIPTION | 10 MD5 | 71 +- NEWS | 20 R/epi.bohning.R | 12 R/epi.descriptives.R | 117 ++-- R/epi.ssclus1estb.R | 5 R/epi.ssclus1estc.R | 6 R/epi.ssclus2estb.R | 7 R/epi.ssclus2estc.R | 4 R/epi.sssimpleestb.R | 5 R/epi.sssimpleestc.R | 4 R/epi.ssstrataestb.R | 5 R/epi.ssstrataestc.R | 4 inst/doc/epiR_RSurveillance.html | 4 inst/doc/epiR_descriptive.html | 48 - inst/doc/epiR_measures_of_association.R | 51 + inst/doc/epiR_measures_of_association.Rmd | 139 ++++- inst/doc/epiR_measures_of_association.html | 690 ++++++++++++++++++++++--- inst/doc/epiR_sample_size.R | 22 inst/doc/epiR_sample_size.Rmd | 24 inst/doc/epiR_sample_size.html | 28 - inst/doc/epiR_surveillance.html | 4 man/epi.descriptives.Rd | 27 man/epi.edr.Rd | 2 man/epi.ssclus1estb.Rd | 14 man/epi.ssclus1estc.Rd | 10 man/epi.ssclus2estb.Rd | 10 man/epi.ssclus2estc.Rd | 10 man/epi.sssimpleestb.Rd | 36 + man/epi.sssimpleestc.Rd | 17 man/epi.ssstrataestb.Rd | 12 man/epi.ssstrataestc.Rd | 11 vignettes/attributable_fraction.png |only vignettes/attributable_risk.png |only vignettes/epiR_measures_of_association.Rmd | 139 ++++- vignettes/epiR_sample_size.Rmd | 24 vignettes/population_attributable_fraction.png |only vignettes/population_attributable_risk.png |only vignettes/risk_ratio.png |only 39 files changed, 1269 insertions(+), 323 deletions(-)
Title: Minimal R/Shiny Interface to JavaScript Library 'ECharts'
Description: The goal is to deliver the full functionality of 'ECharts' with minimal overhead. 'ECharts' is based on data structures and 'echarty' users build R lists for these same data structures. One to three 'echarty' commands are usually sufficient to produce any chart.
Author: Larry Helgason [aut, cre, cph],
John Coene [aut, cph]
Maintainer: Larry Helgason <larry@helgasoft.com>
Diff between echarty versions 0.2.0 dated 2021-06-13 and 0.3.1 dated 2021-07-30
echarty-0.2.0/echarty/man/ec.timegrp.Rd |only echarty-0.3.1/echarty/DESCRIPTION | 8 echarty-0.3.1/echarty/MD5 | 34 echarty-0.3.1/echarty/NAMESPACE | 2 echarty-0.3.1/echarty/NEWS.md | 63 + echarty-0.3.1/echarty/R/echarty.R | 599 ++++++++++------ echarty-0.3.1/echarty/R/examples.R | 167 +--- echarty-0.3.1/echarty/demo/eshiny.R | 797 +++++++++++----------- echarty-0.3.1/echarty/inst/htmlwidgets/echarty.js | 85 +- echarty-0.3.1/echarty/inst/js/echarts.min.js | 4 echarty-0.3.1/echarty/inst/js/renderers.js | 4 echarty-0.3.1/echarty/man/ec.clmn.Rd |only echarty-0.3.1/echarty/man/ec.data.Rd | 5 echarty-0.3.1/echarty/man/ec.examples.Rd | 167 +--- echarty-0.3.1/echarty/man/ec.init.Rd | 71 + echarty-0.3.1/echarty/man/ec.inspect.Rd | 6 echarty-0.3.1/echarty/man/ec.plugjs.Rd | 8 echarty-0.3.1/echarty/man/ecr.band.Rd | 50 - echarty-0.3.1/echarty/man/ecr.ebars.Rd | 33 19 files changed, 1155 insertions(+), 948 deletions(-)
Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation.
Data diagnostics provides information and visualization of missing values and outliers and
unique and negative values to help you understand the distribution and quality of your data.
Data exploration provides information and visualization of the descriptive statistics of
univariate variables, normality tests and outliers, correlation of two variables, and
relationship between target variable and predictor. Data transformation supports binning
for categorizing continuous variables, imputates missing values and outliers, resolving skewness.
And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
Diff between dlookr versions 0.4.5 dated 2021-05-29 and 0.5.0 dated 2021-07-30
dlookr-0.4.5/dlookr/inst/fonts/LiberationSansNarrow/LiberationSansNarrow-Bold.ttf |only dlookr-0.4.5/dlookr/inst/fonts/LiberationSansNarrow/LiberationSansNarrow-BoldItalic.ttf |only dlookr-0.4.5/dlookr/inst/fonts/LiberationSansNarrow/LiberationSansNarrow-Italic.ttf |only dlookr-0.4.5/dlookr/vignettes/img/diag_intro_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/diag_outlier_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/diagn_agenda_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/diagn_title_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_agenda_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_anova_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_intro_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_lm_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_normality_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_title_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/trans_agenda_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/trans_content_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/trans_title_pdf.png |only dlookr-0.5.0/dlookr/DESCRIPTION | 18 dlookr-0.5.0/dlookr/MD5 | 155 +- dlookr-0.5.0/dlookr/NAMESPACE | 50 dlookr-0.5.0/dlookr/NEWS | 57 dlookr-0.5.0/dlookr/R/EDA.R | 7 dlookr-0.5.0/dlookr/R/aggregate.R | 277 ++++ dlookr-0.5.0/dlookr/R/binning.R | 49 dlookr-0.5.0/dlookr/R/compare.R | 14 dlookr-0.5.0/dlookr/R/correlate.R | 84 - dlookr-0.5.0/dlookr/R/diagnose.R | 22 dlookr-0.5.0/dlookr/R/discribe.R | 181 --- dlookr-0.5.0/dlookr/R/dlookr.R | 9 dlookr-0.5.0/dlookr/R/dlookr_templ_html.R |only dlookr-0.5.0/dlookr/R/dlookr_templ_paged.R |only dlookr-0.5.0/dlookr/R/html_diagnose.R |only dlookr-0.5.0/dlookr/R/html_eda.R |only dlookr-0.5.0/dlookr/R/html_transformation.R |only dlookr-0.5.0/dlookr/R/missing.R | 7 dlookr-0.5.0/dlookr/R/overview.R | 250 +++- dlookr-0.5.0/dlookr/R/paged.R |only dlookr-0.5.0/dlookr/R/report.R |only dlookr-0.5.0/dlookr/R/report_tbl_dbi.R |only dlookr-0.5.0/dlookr/R/tbl_dbi.R | 30 dlookr-0.5.0/dlookr/R/transform.R | 9 dlookr-0.5.0/dlookr/R/utils.R | 217 +++ dlookr-0.5.0/dlookr/inst/doc/EDA.R | 136 -- dlookr-0.5.0/dlookr/inst/doc/EDA.Rmd | 289 ++--- dlookr-0.5.0/dlookr/inst/doc/EDA.html | 413 ++++--- dlookr-0.5.0/dlookr/inst/doc/diagonosis.R | 92 - dlookr-0.5.0/dlookr/inst/doc/diagonosis.Rmd | 240 ++-- dlookr-0.5.0/dlookr/inst/doc/diagonosis.html | 573 ++++++---- dlookr-0.5.0/dlookr/inst/doc/introduce.Rmd | 9 dlookr-0.5.0/dlookr/inst/doc/introduce.html | 54 dlookr-0.5.0/dlookr/inst/doc/transformation.R | 33 dlookr-0.5.0/dlookr/inst/doc/transformation.Rmd | 163 ++ dlookr-0.5.0/dlookr/inst/doc/transformation.html | 271 +++- dlookr-0.5.0/dlookr/inst/report/R_logo_html.svg |only dlookr-0.5.0/dlookr/inst/report/cover1.jpg |only dlookr-0.5.0/dlookr/inst/report/cover2.jpg |only dlookr-0.5.0/dlookr/inst/report/cover3.jpg |only dlookr-0.5.0/dlookr/inst/report/diagnosis_paged_temp.Rmd |only dlookr-0.5.0/dlookr/inst/report/diagnosis_temp.Rmd |only dlookr-0.5.0/dlookr/inst/report/dlookr.svg |only dlookr-0.5.0/dlookr/inst/report/dlookr_html.svg |only dlookr-0.5.0/dlookr/inst/report/eda_paged_temp.Rmd |only dlookr-0.5.0/dlookr/inst/report/eda_temp.Rmd |only dlookr-0.5.0/dlookr/inst/report/header_temp.html |only dlookr-0.5.0/dlookr/inst/report/transformation_paged_temp.Rmd |only dlookr-0.5.0/dlookr/inst/report/transformation_temp.Rmd |only dlookr-0.5.0/dlookr/inst/resources |only dlookr-0.5.0/dlookr/man/describe.data.frame.Rd | 12 dlookr-0.5.0/dlookr/man/describe.tbl_dbi.Rd | 18 dlookr-0.5.0/dlookr/man/diagnose_category.data.frame.Rd | 6 dlookr-0.5.0/dlookr/man/diagnose_paged_report.data.frame.Rd |only dlookr-0.5.0/dlookr/man/diagnose_paged_report.tbl_dbi.Rd |only dlookr-0.5.0/dlookr/man/diagnose_web_report.data.frame.Rd |only dlookr-0.5.0/dlookr/man/diagnose_web_report.tbl_dbi.Rd |only dlookr-0.5.0/dlookr/man/dlookr_orange_paged.Rd |only dlookr-0.5.0/dlookr/man/dlookr_templ_html.Rd |only dlookr-0.5.0/dlookr/man/eda_paged_report.data.frame.Rd |only dlookr-0.5.0/dlookr/man/eda_paged_report.tbl_dbi.Rd |only dlookr-0.5.0/dlookr/man/eda_web_report.data.frame.Rd |only dlookr-0.5.0/dlookr/man/eda_web_report.tbl_dbi.Rd |only dlookr-0.5.0/dlookr/man/find_class.Rd | 7 dlookr-0.5.0/dlookr/man/overview.Rd | 15 dlookr-0.5.0/dlookr/man/plot.optimal_bins.Rd | 8 dlookr-0.5.0/dlookr/man/plot_box_numeric.data.frame.Rd | 6 dlookr-0.5.0/dlookr/man/plot_hist_numeric.data.frame.Rd |only dlookr-0.5.0/dlookr/man/plot_na_pareto.Rd | 4 dlookr-0.5.0/dlookr/man/summary.overview.Rd | 5 dlookr-0.5.0/dlookr/man/transformation_paged_report.Rd |only dlookr-0.5.0/dlookr/man/transformation_web_report.Rd |only dlookr-0.5.0/dlookr/vignettes/EDA.Rmd | 289 ++--- dlookr-0.5.0/dlookr/vignettes/diagonosis.Rmd | 240 ++-- dlookr-0.5.0/dlookr/vignettes/img/diag_paged_content.jpg |only dlookr-0.5.0/dlookr/vignettes/img/diag_paged_cover.jpg |only dlookr-0.5.0/dlookr/vignettes/img/diag_web_content.jpg |only dlookr-0.5.0/dlookr/vignettes/img/diag_web_title.jpg |only dlookr-0.5.0/dlookr/vignettes/img/eda_paged_content.jpg |only dlookr-0.5.0/dlookr/vignettes/img/eda_paged_cover.jpg |only dlookr-0.5.0/dlookr/vignettes/img/eda_web_title.jpg |only dlookr-0.5.0/dlookr/vignettes/img/transformation_paged_content.jpg |only dlookr-0.5.0/dlookr/vignettes/img/transformation_paged_cover.jpg |only dlookr-0.5.0/dlookr/vignettes/img/transformation_web_title.jpg |only dlookr-0.5.0/dlookr/vignettes/introduce.Rmd | 9 dlookr-0.5.0/dlookr/vignettes/transformation.Rmd | 163 ++ 102 files changed, 3022 insertions(+), 1469 deletions(-)