Title: Calculate and Plot Decision Curve
Description: Diagnostic and prognostic models are typically evaluated with
measures of accuracy that do not address clinical consequences.
Decision-analytic techniques allow assessment of clinical outcomes but
often require collection of additional information and may be cumbersome to
apply to models that yield a continuous result.
Decision curve analysis is a suitable method for evaluating
alternative diagnostic and prognostic strategies that has advantages over
other commonly used measures and techniques.
This method was described by Andrew J. Vickers (2006) <doi:10.1177/0272989X06295361>.
Author: Jing Zhang [aut, cre],
Zhi Jin [aut]
Maintainer: Jing Zhang <zj391120@163.com>
Diff between ggDCA versions 1.0 dated 2020-08-24 and 1.1 dated 2020-09-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/dca.cph.R | 5 +++-- 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Functions to Inline C, C++, Fortran Function Calls from R
Description: Functionality to dynamically define R functions and S4 methods
with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling
conventions.
Author: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel,
Romain Francois, Karline Soetaert
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between inline versions 0.3.15 dated 2018-05-18 and 0.3.16 dated 2020-09-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/cfunction.R | 14 ++++++++------ README.md | 29 +++++++++++++++++++---------- build/partial.rdb |binary inst/NEWS.Rd | 9 +++++++++ 7 files changed, 47 insertions(+), 27 deletions(-)
Title: 'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest
Neighbors
Description: 'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This
package provides a minimal R interface by relying on the 'Rcpp' package. See
<https://github.com/nmslib/hnswlib> for more on 'hnswlib'. 'hnswlib' is
released under Version 2.0 of the Apache License.
Author: James Melville [aut, cre],
Aaron Lun [ctb],
Samuel Granjeaud [ctb],
Dmitriy Selivanov [ctb],
Yuxing Liao [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between RcppHNSW versions 0.2.0 dated 2019-09-20 and 0.3.0 dated 2020-09-06
RcppHNSW-0.2.0/RcppHNSW/R/DONTCHECKMEIN.R |only RcppHNSW-0.2.0/RcppHNSW/R/progress.R |only RcppHNSW-0.3.0/RcppHNSW/DESCRIPTION | 19 RcppHNSW-0.3.0/RcppHNSW/MD5 | 39 RcppHNSW-0.3.0/RcppHNSW/NEWS.md | 26 RcppHNSW-0.3.0/RcppHNSW/R/hnsw.R | 143 + RcppHNSW-0.3.0/RcppHNSW/R/rcpphnsw-package.R | 2 RcppHNSW-0.3.0/RcppHNSW/R/util.R | 19 RcppHNSW-0.3.0/RcppHNSW/inst/include/RcppPerpendicular |only RcppHNSW-0.3.0/RcppHNSW/inst/include/bruteforce.h | 59 RcppHNSW-0.3.0/RcppHNSW/inst/include/hnswalg.h | 1316 +++++++------- RcppHNSW-0.3.0/RcppHNSW/inst/include/hnswlib.h | 76 RcppHNSW-0.3.0/RcppHNSW/man/RcppHnsw-package.Rd | 2 RcppHNSW-0.3.0/RcppHNSW/man/hnsw_build.Rd | 28 RcppHNSW-0.3.0/RcppHNSW/man/hnsw_knn.Rd | 32 RcppHNSW-0.3.0/RcppHNSW/man/hnsw_search.Rd | 27 RcppHNSW-0.3.0/RcppHNSW/src/hnsw.cpp | 437 +++- RcppHNSW-0.3.0/RcppHNSW/tests/testthat/helper_data.R | 20 RcppHNSW-0.3.0/RcppHNSW/tests/testthat/test_add_get_all.R | 2 RcppHNSW-0.3.0/RcppHNSW/tests/testthat/test_cosine.R | 8 RcppHNSW-0.3.0/RcppHNSW/tests/testthat/test_get_knn.R | 3 RcppHNSW-0.3.0/RcppHNSW/tests/testthat/test_parallel.R |only RcppHNSW-0.3.0/RcppHNSW/tests/testthat/test_verbose.R |only 23 files changed, 1328 insertions(+), 930 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut, cre],
Adam Banker [aut],
Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>
Diff between paws.common versions 0.3.3 dated 2020-07-19 and 0.3.4 dated 2020-09-06
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 7 +++++++ R/custom_s3.R | 1 + R/jsonutil.R | 2 +- R/url.R | 16 +++++++++++----- R/xmlutil.R | 4 ++-- tests/testthat/test_custom_s3.R | 36 ++++++++++++++++++++++++++++++++++++ tests/testthat/test_url.R |only 9 files changed, 69 insertions(+), 18 deletions(-)
Title: Miscellaneous 3D Plots
Description: A collection of miscellaneous 3d plots, including
isosurfaces.
Author: Dai Feng and Luke Tierney
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between misc3d versions 0.8-4 dated 2013-01-25 and 0.9-0 dated 2020-09-06
DESCRIPTION | 10 ++++++---- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 10 ++++++++-- R/contour3d.R | 10 +++++++--- R/export.R | 12 ++++++------ R/image3d.R | 6 +++--- R/loadRGL.R | 2 +- R/render.R | 16 ++++++++-------- R/slices3d.R | 10 +++++----- R/triangles.R | 10 +++++----- demo/lighting.R | 2 +- demo/teapot.R | 2 +- inst/CITATION | 4 ++-- man/contour3d.Rd | 4 ++-- man/exportScene.Rd | 5 +++-- man/teapot.Rd | 8 +++++--- 16 files changed, 78 insertions(+), 63 deletions(-)
Title: Ensemble Tool for Predictions from Species Distribution Models
Description: A tool which allows users to create and evaluate ensembles
of species distribution model (SDM) predictions.
Functionality is offered through R functions or a GUI (R Shiny app).
This tool can assist users in identifying spatial uncertainties and
making informed conservation and management decisions. The package is
further described in Woodman et al (2019) <doi:10.1111/2041-210X.13283>.
Author: Sam Woodman [aut, cre] (<https://orcid.org/0000-0001-6071-8186>)
Maintainer: Sam Woodman <sam.woodman@noaa.gov>
Diff between eSDM versions 0.3.4 dated 2020-04-26 and 0.3.5 dated 2020-09-06
DESCRIPTION | 14 MD5 | 204 NAMESPACE | 98 NEWS.md | 91 R/data.R | 136 R/eSDM-internal.R | 250 - R/ensemble_create.R | 406 - R/ensemble_rescale.R | 318 - R/evaluation_metrics.R | 4 R/model_abundance.R | 118 R/overlay_sdm.R | 476 +- R/pts2poly_centroids.R | 164 R/pts2poly_vertices.R | 122 build/vignette.rds |binary inst/CITATION | 40 inst/doc/example-analysis.R | 858 ++-- inst/doc/example-analysis.Rmd | 1096 ++--- inst/doc/example-analysis.html | 2117 +++++----- inst/eSDM_vignette_helper.R | 414 - inst/extdata/README.txt | 90 inst/extdata/Shapefiles/Study_Area_CCE.shp.xml | 4 inst/extdata/Table3.csv | 22 inst/shiny/app.R | 536 +- inst/shiny/server_1_loadModels/server_1_loadModels.R | 222 - inst/shiny/server_1_loadModels/server_1_loadModels_create_local.R | 186 inst/shiny/server_1_loadModels/server_1_loadModels_csv.R | 550 +- inst/shiny/server_1_loadModels/server_1_loadModels_funcs.R | 300 - inst/shiny/server_1_loadModels/server_1_loadModels_raster.R | 268 - inst/shiny/server_1_loadModels/server_1_loadModels_renderUI.R | 684 +-- inst/shiny/server_1_loadModels/server_1_loadModels_shpgdb.R | 448 +- inst/shiny/server_1_loadModels/server_1_loadModels_shpgdb_create_local.R | 124 inst/shiny/server_2_overlay/server_2_overlay.R | 170 inst/shiny/server_2_overlay/server_2_overlay_funcs.R | 28 inst/shiny/server_2_overlay/server_2_overlay_loadPoly_csv.R | 214 - inst/shiny/server_2_overlay/server_2_overlay_loadPoly_provided.R | 42 inst/shiny/server_2_overlay/server_2_overlay_loadPoly_shpgdb.R | 284 - inst/shiny/server_2_overlay/server_2_overlay_overlayModels.R | 765 +-- inst/shiny/server_2_overlay/server_2_overlay_overlayModels_base.R | 688 +-- inst/shiny/server_2_overlay/server_2_overlay_renderUI.R | 142 inst/shiny/server_3_createEns/server_3_createEns.R | 302 - inst/shiny/server_3_createEns/server_3_createEns_create.R | 692 +-- inst/shiny/server_3_createEns/server_3_createEns_create_regexc.R | 908 ++-- inst/shiny/server_3_createEns/server_3_createEns_create_weighted.R | 382 - inst/shiny/server_3_createEns/server_3_createEns_renderUI.R | 688 +-- inst/shiny/server_4_evalMetrics/server_4_evalMetrics.R | 460 +- inst/shiny/server_4_evalMetrics/server_4_evalMetrics_funcs.R | 278 - inst/shiny/server_4_evalMetrics/server_4_evalMetrics_loadData.R | 636 +-- inst/shiny/server_4_evalMetrics/server_4_evalMetrics_renderUI.R | 360 - inst/shiny/server_5_prettyPlot/server_5_prettyPlot.R | 412 - inst/shiny/server_5_prettyPlot/server_5_prettyPlot_addobj.R | 612 +- inst/shiny/server_5_prettyPlot/server_5_prettyPlot_addobj_renderUI.R | 472 +- inst/shiny/server_5_prettyPlot/server_5_prettyPlot_addobj_update.R | 550 +- inst/shiny/server_5_prettyPlot/server_5_prettyPlot_download.R | 262 - inst/shiny/server_5_prettyPlot/server_5_prettyPlot_funcs.R | 254 - inst/shiny/server_5_prettyPlot/server_5_prettyPlot_plot.R | 550 +- inst/shiny/server_5_prettyPlot/server_5_prettyPlot_prep.R | 762 +-- inst/shiny/server_5_prettyPlot/server_5_prettyPlot_renderUI.R | 886 ++-- inst/shiny/server_5_prettyPlot/server_5_prettyPlot_toplot.R | 482 +- inst/shiny/server_5_prettyPlot/server_5_prettyPlot_update.R | 1054 ++-- inst/shiny/server_5_prettyPlot/server_5_prettyPlot_update_renderUI.R | 1048 ++-- inst/shiny/server_6_export/server_6_export.R | 522 +- inst/shiny/server_6_export/server_6_export_renderUI.R | 238 - inst/shiny/server_other/server_checks.R | 432 +- inst/shiny/server_other/server_funcs.R | 1006 ++-- inst/shiny/server_other/server_funcs_preview360.R | 610 +- inst/shiny/server_other/server_plots.R | 570 +- inst/shiny/server_other/server_plots_download.R | 470 +- inst/shiny/server_other/server_plots_funcs.R | 1228 ++--- inst/shiny/server_other/server_reactiveValues.R | 308 - inst/shiny/server_other/server_render.R | 1092 ++--- inst/shiny/server_other/server_roadmap_download.R | 144 inst/shiny/server_other/server_tables.R | 172 inst/shiny/server_other/server_workspace.R | 392 - inst/shiny/ui_files/ui_0_roadmap.R | 348 - inst/shiny/ui_files/ui_1_loadModels.R | 532 +- inst/shiny/ui_files/ui_2_overlay.R | 568 +- inst/shiny/ui_files/ui_3_createEns.R | 870 ++-- inst/shiny/ui_files/ui_4_evalMetrics.R | 508 +- inst/shiny/ui_files/ui_5_prettyPlot.R | 1050 ++-- inst/shiny/ui_files/ui_6_export.R | 284 - inst/shiny/ui_files/ui_7_manual.R | 54 inst/shiny/ui_files/ui_common.R | 530 +- inst/shiny/ui_files/ui_funcs.R | 160 inst/shiny/www/eSDM_manual.pdf |binary man/eSDM-package.Rd | 68 man/eSDM_GUI.Rd | 38 man/ensemble_create.Rd | 144 man/ensemble_rescale.Rd | 124 man/evaluation_metrics.Rd | 90 man/gshhg.l.L16.Rd | 40 man/model_abundance.Rd | 84 man/overlay_sdm.Rd | 106 man/preds.Rd | 106 man/pts2poly_centroids.Rd | 118 man/pts2poly_vertices.Rd | 92 man/validation.data.Rd | 44 tests/testthat.R | 8 tests/testthat/test-ensemble.R | 168 tests/testthat/test-internals.R | 76 tests/testthat/test-model_abundance.R | 54 tests/testthat/test-overlay_sdm.R | 60 tests/testthat/test-pts2poly.R | 80 vignettes/example-analysis.Rmd | 1096 ++--- 103 files changed, 19735 insertions(+), 19692 deletions(-)