Title: Flexible Modeling of Count Processes
Description: A toolkit for flexible modeling of count processes where data (over- or under-) dispersion exists.
Estimations can be obtained under two data constructs where one has:
(1) data on number of events in an s-unit time interval, or (2) only wait-time data.
This package is supplementary to the work set forth in Zhu et al. (2016) <doi:10.1080/00031305.2016.1234976>.
Author: Li Zhu [aut],
Kimberly Sellers [aut],
Darcy Morris [aut],
Galit Shmueli [aut],
Diag Davenport [aut, cre]
Maintainer: Diag Davenport <diag.davenport@gmail.com>
Diff between cmpprocess versions 1.0 dated 2017-03-12 and 1.1 dated 2020-01-13
cmpprocess-1.0/cmpprocess/man/cmpproc.Rd |only cmpprocess-1.1/cmpprocess/DESCRIPTION | 6 cmpprocess-1.1/cmpprocess/MD5 | 22 - cmpprocess-1.1/cmpprocess/NAMESPACE | 14 cmpprocess-1.1/cmpprocess/R/cmpproc.r | 397 ++++++++++++++-------------- cmpprocess-1.1/cmpprocess/R/cmpprocwt.r | 80 ++--- cmpprocess-1.1/cmpprocess/R/data.R | 98 +++--- cmpprocess-1.1/cmpprocess/man/CMPProc.Rd |only cmpprocess-1.1/cmpprocess/man/cmpprocwt.Rd | 52 +-- cmpprocess-1.1/cmpprocess/man/fetalcount.Rd | 40 +- cmpprocess-1.1/cmpprocess/man/fetalwait.Rd | 34 +- cmpprocess-1.1/cmpprocess/man/floodcount.Rd | 44 +-- cmpprocess-1.1/cmpprocess/man/floodwait.Rd | 40 +- 13 files changed, 416 insertions(+), 411 deletions(-)
Title: Yield Per Recruit
Description: An implementation of equilibrium-based yield per recruit methods.
Yield per recruit methods can used to estimate the optimal yield for a fish population
as described by Walters and Martell (2004) <isbn:0-691-11544-3>.
The yield can be based on the number of fish caught (or harvested) or
biomass caught for all fish or just large (trophy) individuals.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ypr versions 0.3.1 dated 2019-04-26 and 0.4.0 dated 2020-01-13
ypr-0.3.1/ypr/R/check.R |only ypr-0.3.1/ypr/R/print.R |only ypr-0.3.1/ypr/man/ypr_inst2inter.Rd |only ypr-0.3.1/ypr/man/ypr_inter2inst.Rd |only ypr-0.3.1/ypr/man/ypr_schedule.Rd |only ypr-0.3.1/ypr/man/ypr_tabulate_sr.ypr_population.Rd |only ypr-0.3.1/ypr/man/ypr_tabulate_sr.ypr_populations.Rd |only ypr-0.3.1/ypr/man/ypr_tabulate_yield.ypr_population.Rd |only ypr-0.3.1/ypr/man/ypr_tabulate_yield.ypr_populations.Rd |only ypr-0.3.1/ypr/man/ypr_tabulate_yields.ypr_population.Rd |only ypr-0.3.1/ypr/man/ypr_tabulate_yields.ypr_populations.Rd |only ypr-0.4.0/ypr/DESCRIPTION | 25 - ypr-0.4.0/ypr/MD5 | 195 ++++----- ypr-0.4.0/ypr/NAMESPACE | 27 + ypr-0.4.0/ypr/NEWS.md | 57 ++ ypr-0.4.0/ypr/R/as-ypr-population.R |only ypr-0.4.0/ypr/R/as-ypr-populations.R |only ypr-0.4.0/ypr/R/base.R |only ypr-0.4.0/ypr/R/chk-parameters.R |only ypr-0.4.0/ypr/R/chk.R |only ypr-0.4.0/ypr/R/data.R | 25 - ypr-0.4.0/ypr/R/deprecated.R |only ypr-0.4.0/ypr/R/exploitation.R | 11 ypr-0.4.0/ypr/R/internal.R | 33 - ypr-0.4.0/ypr/R/namespace.R | 5 ypr-0.4.0/ypr/R/optimise.R | 25 - ypr-0.4.0/ypr/R/params.R |only ypr-0.4.0/ypr/R/plot.R | 262 ++++++------ ypr-0.4.0/ypr/R/population.R | 180 +++++--- ypr-0.4.0/ypr/R/report.R | 79 ++- ypr-0.4.0/ypr/R/schedule.R | 47 +- ypr-0.4.0/ypr/R/sr.R | 33 - ypr-0.4.0/ypr/R/sysdata.rda |binary ypr-0.4.0/ypr/R/tabulate.R | 325 +++++++-------- ypr-0.4.0/ypr/R/utils.R | 69 ++- ypr-0.4.0/ypr/R/yield.R | 30 - ypr-0.4.0/ypr/R/yields.R | 25 - ypr-0.4.0/ypr/R/zzz.R | 3 ypr-0.4.0/ypr/README.md | 110 ++--- ypr-0.4.0/ypr/build/vignette.rds |binary ypr-0.4.0/ypr/data/adams_bt_03.rda |binary ypr-0.4.0/ypr/data/chilliwack_bt_05.rda |binary ypr-0.4.0/ypr/data/kootenay_bt_13.rda |binary ypr-0.4.0/ypr/data/kootenay_rb.rda |binary ypr-0.4.0/ypr/data/kootenay_rb_13.rda |binary ypr-0.4.0/ypr/data/quesnel_bt.rda |binary ypr-0.4.0/ypr/data/quesnel_lt.rda |binary ypr-0.4.0/ypr/data/quesnel_rb.rda |binary ypr-0.4.0/ypr/inst/doc/ypr.R | 48 +- ypr-0.4.0/ypr/inst/doc/ypr.Rmd | 34 + ypr-0.4.0/ypr/inst/doc/ypr.html | 318 +++++++++++--- ypr-0.4.0/ypr/man/adams_bt_03.Rd | 2 ypr-0.4.0/ypr/man/as_ypr_population.Rd |only ypr-0.4.0/ypr/man/as_ypr_populations.Rd |only ypr-0.4.0/ypr/man/chilliwack_bt_05.Rd | 9 ypr-0.4.0/ypr/man/figures/README-unnamed-chunk-1-1.png |binary ypr-0.4.0/ypr/man/figures/README-unnamed-chunk-2-1.png |binary ypr-0.4.0/ypr/man/figures/README-unnamed-chunk-3-1.png |binary ypr-0.4.0/ypr/man/figures/README-unnamed-chunk-4-1.png |binary ypr-0.4.0/ypr/man/figures/README-unnamed-chunk-5-1.png |binary ypr-0.4.0/ypr/man/kootenay_bt_13.Rd | 2 ypr-0.4.0/ypr/man/kootenay_rb.Rd | 2 ypr-0.4.0/ypr/man/kootenay_rb_13.Rd | 4 ypr-0.4.0/ypr/man/params.Rd |only ypr-0.4.0/ypr/man/plot.ypr_population.Rd | 6 ypr-0.4.0/ypr/man/quesnel_bt.Rd | 2 ypr-0.4.0/ypr/man/quesnel_lt.Rd | 2 ypr-0.4.0/ypr/man/quesnel_rb.Rd | 2 ypr-0.4.0/ypr/man/ypr-package.Rd | 12 ypr-0.4.0/ypr/man/ypr_age_at_length.Rd |only ypr-0.4.0/ypr/man/ypr_detabulate_parameters.Rd | 8 ypr-0.4.0/ypr/man/ypr_exploitation.Rd | 6 ypr-0.4.0/ypr/man/ypr_length_at_age.Rd |only ypr-0.4.0/ypr/man/ypr_optimize.Rd | 10 ypr-0.4.0/ypr/man/ypr_plot_biomass.Rd |only ypr-0.4.0/ypr/man/ypr_plot_fish.Rd | 18 ypr-0.4.0/ypr/man/ypr_plot_schedule.Rd | 4 ypr-0.4.0/ypr/man/ypr_plot_sr.Rd | 21 ypr-0.4.0/ypr/man/ypr_plot_yield.Rd | 2 ypr-0.4.0/ypr/man/ypr_plot_yield.ypr_population.Rd | 26 - ypr-0.4.0/ypr/man/ypr_plot_yield.ypr_populations.Rd | 30 - ypr-0.4.0/ypr/man/ypr_population.Rd | 62 ++ ypr-0.4.0/ypr/man/ypr_population_names.Rd |only ypr-0.4.0/ypr/man/ypr_population_update.Rd | 20 ypr-0.4.0/ypr/man/ypr_populations.Rd | 10 ypr-0.4.0/ypr/man/ypr_populations_expand.Rd |only ypr-0.4.0/ypr/man/ypr_populations_update.Rd |only ypr-0.4.0/ypr/man/ypr_report.Rd | 25 - ypr-0.4.0/ypr/man/ypr_sr.Rd | 20 ypr-0.4.0/ypr/man/ypr_tabulate_biomass.Rd |only ypr-0.4.0/ypr/man/ypr_tabulate_fish.Rd | 14 ypr-0.4.0/ypr/man/ypr_tabulate_parameters.Rd | 16 ypr-0.4.0/ypr/man/ypr_tabulate_schedule.Rd |only ypr-0.4.0/ypr/man/ypr_tabulate_sr.Rd | 51 ++ ypr-0.4.0/ypr/man/ypr_tabulate_yield.Rd | 48 ++ ypr-0.4.0/ypr/man/ypr_tabulate_yields.Rd | 48 ++ ypr-0.4.0/ypr/man/ypr_yield.Rd | 10 ypr-0.4.0/ypr/man/ypr_yields.Rd | 19 ypr-0.4.0/ypr/tests/testthat/test-aaa-deprecated.R |only ypr-0.4.0/ypr/tests/testthat/test-as-ypr-population.R |only ypr-0.4.0/ypr/tests/testthat/test-as-ypr-populations.R |only ypr-0.4.0/ypr/tests/testthat/test-base.R |only ypr-0.4.0/ypr/tests/testthat/test-data.R | 44 +- ypr-0.4.0/ypr/tests/testthat/test-internal.R | 7 ypr-0.4.0/ypr/tests/testthat/test-optimize.R | 4 ypr-0.4.0/ypr/tests/testthat/test-plot.R | 16 ypr-0.4.0/ypr/tests/testthat/test-population.R | 129 +++++ ypr-0.4.0/ypr/tests/testthat/test-report.R | 2 ypr-0.4.0/ypr/tests/testthat/test-schedule.R | 46 +- ypr-0.4.0/ypr/tests/testthat/test-sr.R | 18 ypr-0.4.0/ypr/tests/testthat/test-tabulate.R | 189 +++++--- ypr-0.4.0/ypr/tests/testthat/test-utils.R | 97 ++++ ypr-0.4.0/ypr/tests/testthat/test-yield.R | 29 - ypr-0.4.0/ypr/tests/testthat/test-yields.R | 2 ypr-0.4.0/ypr/vignettes/ypr.Rmd | 34 + 115 files changed, 2082 insertions(+), 1012 deletions(-)
Title: Graphical Displays for Subgroup Analysis in Clinical Trials
Description: Provides functions for obtaining a variety of
graphical displays that may be useful in the subgroup analysis setting.
An example with a prostate cancer dataset is provided.
The graphical techniques considered include level plots, mosaic plots,
contour plots, bar charts, Venn diagrams, tree plots, forest plots,
Galbraith plots, L'Abbé plots, the subpopulation treatment effect pattern
plot, alluvial plots, circle plots and UpSet plots.
Author: Nicolas Ballarini [aut, cre],
Yi-Da Chiu [aut],
Jake Conway [ctb],
Nils Gehlenborg [ctb],
Michal Bojanowski [ctb],
Robin Edwards [ctb]
Maintainer: Nicolas Ballarini <nicoballarini@gmail.com>
Diff between SubgrPlots versions 0.1.0 dated 2018-07-10 and 0.1.2 dated 2020-01-13
SubgrPlots-0.1.0/SubgrPlots/inst/paper |only SubgrPlots-0.1.2/SubgrPlots/DESCRIPTION | 19 SubgrPlots-0.1.2/SubgrPlots/MD5 | 173 -- SubgrPlots-0.1.2/SubgrPlots/NAMESPACE | 6 SubgrPlots-0.1.2/SubgrPlots/R/01-level-plot-function-new.r | 70 - SubgrPlots-0.1.2/SubgrPlots/R/02-contour-plot-function.r | 144 +- SubgrPlots-0.1.2/SubgrPlots/R/02-contour-plot-localreg.r | 31 SubgrPlots-0.1.2/SubgrPlots/R/03-venn-diagram-function-areaprop.r | 65 - SubgrPlots-0.1.2/SubgrPlots/R/03-venn-diagram-function-fill.r | 77 - SubgrPlots-0.1.2/SubgrPlots/R/03-venn-diagram-function.r | 603 +++++----- SubgrPlots-0.1.2/SubgrPlots/R/04-bar-chart-function-new.r | 70 - SubgrPlots-0.1.2/SubgrPlots/R/05-forest-plot-function.r | 156 +- SubgrPlots-0.1.2/SubgrPlots/R/06-tree-plot-function.r | 81 - SubgrPlots-0.1.2/SubgrPlots/R/07-ggradial-plot-function.r |only SubgrPlots-0.1.2/SubgrPlots/R/07-radial-plot-function.r | 159 +- SubgrPlots-0.1.2/SubgrPlots/R/08-labbe-plot-function.r | 74 - SubgrPlots-0.1.2/SubgrPlots/R/09-ggstepp-plot-function.r |only SubgrPlots-0.1.2/SubgrPlots/R/09-stepp-plot-function.r | 32 SubgrPlots-0.1.2/SubgrPlots/R/13-e-plt-dis-msr.r | 2 SubgrPlots-0.1.2/SubgrPlots/R/13-f-alt-plt-dis-msr.r | 2 SubgrPlots-0.1.2/SubgrPlots/R/23-MainBar_legend_t.r | 4 SubgrPlots-0.1.2/SubgrPlots/R/23-SizeBar2.r | 2 SubgrPlots-0.1.2/SubgrPlots/R/23-subgroupset.r | 2 SubgrPlots-0.1.2/SubgrPlots/R/23-subgroupset_transposed.r | 1 SubgrPlots-0.1.2/SubgrPlots/R/24-mosaic-plot-function.r | 68 - SubgrPlots-0.1.2/SubgrPlots/R/26-circular-plot-function.r | 15 SubgrPlots-0.1.2/SubgrPlots/R/30-nightingale_rose.R |only SubgrPlots-0.1.2/SubgrPlots/build |only SubgrPlots-0.1.2/SubgrPlots/inst/doc |only SubgrPlots-0.1.2/SubgrPlots/man/ggplot_radial.Rd |only SubgrPlots-0.1.2/SubgrPlots/man/ggplot_radial2.Rd |only SubgrPlots-0.1.2/SubgrPlots/man/ggplot_stepp.Rd |only SubgrPlots-0.1.2/SubgrPlots/man/plot_alluvial.Rd | 25 SubgrPlots-0.1.2/SubgrPlots/man/plot_barchart.Rd | 19 SubgrPlots-0.1.2/SubgrPlots/man/plot_circle.Rd | 32 SubgrPlots-0.1.2/SubgrPlots/man/plot_circle2.Rd | 33 SubgrPlots-0.1.2/SubgrPlots/man/plot_contour.Rd | 33 SubgrPlots-0.1.2/SubgrPlots/man/plot_contour_localreg.Rd | 29 SubgrPlots-0.1.2/SubgrPlots/man/plot_dissimilarity.Rd | 12 SubgrPlots-0.1.2/SubgrPlots/man/plot_dissimilarity_alternative.Rd | 12 SubgrPlots-0.1.2/SubgrPlots/man/plot_forest.Rd | 34 SubgrPlots-0.1.2/SubgrPlots/man/plot_labbe.Rd | 23 SubgrPlots-0.1.2/SubgrPlots/man/plot_level.Rd | 28 SubgrPlots-0.1.2/SubgrPlots/man/plot_matrix_overlap.Rd | 10 SubgrPlots-0.1.2/SubgrPlots/man/plot_mosaic.Rd | 40 SubgrPlots-0.1.2/SubgrPlots/man/plot_network.Rd | 10 SubgrPlots-0.1.2/SubgrPlots/man/plot_nightingale.Rd |only SubgrPlots-0.1.2/SubgrPlots/man/plot_nightingale_effect.Rd |only SubgrPlots-0.1.2/SubgrPlots/man/plot_overlap.Rd | 10 SubgrPlots-0.1.2/SubgrPlots/man/plot_overlap2.Rd | 10 SubgrPlots-0.1.2/SubgrPlots/man/plot_overlap_alternative.Rd | 11 SubgrPlots-0.1.2/SubgrPlots/man/plot_radial.Rd | 19 SubgrPlots-0.1.2/SubgrPlots/man/plot_radial2.Rd | 34 SubgrPlots-0.1.2/SubgrPlots/man/plot_stepp.Rd | 24 SubgrPlots-0.1.2/SubgrPlots/man/plot_tree.Rd | 20 SubgrPlots-0.1.2/SubgrPlots/man/plot_venn.Rd | 40 SubgrPlots-0.1.2/SubgrPlots/man/prca.Rd | 1 SubgrPlots-0.1.2/SubgrPlots/man/subgroupset.Rd | 65 - SubgrPlots-0.1.2/SubgrPlots/vignettes |only 59 files changed, 1450 insertions(+), 980 deletions(-)
Title: Analyzing Diagnostic Observer Performance Studies
Description: Implements software for assessing medical imaging systems, radiologists or computer aided detection algorithms.
Models of observer performance are implemented, including the binormal model (BM), the contaminated binormal model (CBM), the
correlated contaminated binormal model (CORCBM), and the radiological search model (RSM). The software and applications are
described in a book - Chakraborty DP: Observer Performance Methods for Diagnostic Imaging - Foundations, Modeling, and
Applications with R-Based Examples. Taylor-Francis LLC; 2017 - and its vignettes <https://dpc10ster.github.io/RJafroc/>.
Observer performance data collection paradigms are the receiver operating characteristic (ROC) and its location specific
extensions, primarily free-response ROC (FROC) and the location ROC (LROC). ROC data consists of single ratings per images.
A rating is the perceived confidence level that the image is that of a diseased patient. FROC data consists of a variable
number (including zero) of mark-rating pairs per image, where a mark is the location of a clinically reportable suspicious region
and the rating is the corresponding confidence level that it is a real lesion. LROC data consists of a rating and a forced
localization of the most suspicious region on every image. RJafroc supersedes the Windows version of JAFROC software
V4.2.1, <http://www.devchakraborty.com>:. Package functions are organized as follows. Data file related function names are
preceded by Df, curve fitting functions by Fit, included data sets by dataset, plotting functions by
Plot, significance testing functions by St, sample size related functions by Ss, data simulation functions
by Simulate and utility functions by Util. Implemented are figures of merit (FOMs) for quantifying performance,
functions for visualizing empirical operating characteristics: e.g., ROC, FROC, alternative FROC (AFROC) and weighted AFROC
(wAFROC) curves. Four maximum likelihood curve-fitting algorithms are implemented: the binormal model (BM), the contaminated
binormal model (CBM), the correlated contaminated binormal model (CORCBM) and the radiological search model (RSM). Unlike the
binormal model, CBM, CORCBM and RSM predict "proper" ROC curves that do not cross the chance diagonal. RSM fitting additionally
yields measures of search and lesion-classification performances. Search performance is the ability to find lesions while
avoiding finding non-lesions. Lesion-classification performance is the ability to correctly classify found lesions from found
non-lesions. For fully crossed study designs significance testing of reader-averaged FOM differences between modalities is
implemented via both Dorfman-Berbaum-Metz and the Obuchowski-Rockette methods, including Hillis' extensions. Also implemented are
single treatment analyses, which allow comparison of performance of a group of radiologists to a specified value, or comparison
to CAD to a group of radiologists interpreting the same cases. Crossed-modality analysis is implemented wherein there are two crossed
treatment factors and the desire is to determined performance in each treatment factor averaged over all levels of the other factor.
Sample size estimation tools are provided for ROC and FROC studies; these use estimates of the relevant variances from a pilot study
to predict required numbers of readers and cases in a pivotal study to achieve a desired power. Utility and data file manipulation
functions allow data to be read in any of the currently used input formats, including Excel, and the results of the analysis can be
viewed in text or Excel output files. The methods are illustrated with several included datasets from the author's international
collaborations. This version corrects a few bugs noticed by users and extends the Excel file input format for
greater flexibility in handling non-crossed datasets and the sample size routines have been rewritten for ease of use.
Author: Dev Chakraborty [cre, aut, cph],
Peter Philips [aut],
Xuetong Zhai [aut],
Lucy D'Agostino McGowan [ctb],
Alejandro RodriguezRuiz [ctb]
Maintainer: Dev Chakraborty <dpc10ster@gmail.com>
Diff between RJafroc versions 1.2.0 dated 2019-07-31 and 1.3.1 dated 2020-01-13
RJafroc-1.2.0/RJafroc/R/SsFROCPowerGivenJK.R |only RJafroc-1.2.0/RJafroc/R/UtilLesionDistribution.R |only RJafroc-1.2.0/RJafroc/R/UtilLesionWeights.R |only RJafroc-1.2.0/RJafroc/R/genericPlotLROC.R |only RJafroc-1.2.0/RJafroc/R/genericPlotROC.R |only RJafroc-1.2.0/RJafroc/build |only RJafroc-1.2.0/RJafroc/inst/doc |only RJafroc-1.2.0/RJafroc/inst/extdata/includedCrossedModalitiesData.xlsx |only RJafroc-1.2.0/RJafroc/inst/extdata/includedFrocData.xlsx |only RJafroc-1.2.0/RJafroc/inst/extdata/includedRocData.csv |only RJafroc-1.2.0/RJafroc/inst/extdata/includedRocData.imrmc |only RJafroc-1.2.0/RJafroc/inst/extdata/includedRocData.lrc |only RJafroc-1.2.0/RJafroc/inst/extdata/includedRocData.txt |only RJafroc-1.2.0/RJafroc/inst/extdata/includedRocData.xlsx |only RJafroc-1.2.0/RJafroc/inst/extdata/includedRoiData.xlsx |only RJafroc-1.2.0/RJafroc/man/UtilLesionDistribution.Rd |only RJafroc-1.2.0/RJafroc/man/UtilLesionWeights.Rd |only RJafroc-1.2.0/RJafroc/src/CorCBMFuncs.cpp |only RJafroc-1.2.0/RJafroc/tests |only RJafroc-1.2.0/RJafroc/vignettes |only RJafroc-1.3.1/RJafroc/DESCRIPTION | 76 RJafroc-1.3.1/RJafroc/MD5 | 418 -- RJafroc-1.3.1/RJafroc/NAMESPACE | 15 RJafroc-1.3.1/RJafroc/NEWS.md | 192 - RJafroc-1.3.1/RJafroc/R/ChisqrGoodnessOfFit.R | 8 RJafroc-1.3.1/RJafroc/R/Compare3ProperRocFits.R | 2 RJafroc-1.3.1/RJafroc/R/Df2RJafrocDataset.R | 66 RJafroc-1.3.1/RJafroc/R/DfBinDataset.R | 6 RJafroc-1.3.1/RJafroc/R/DfFroc2Afroc.R | 2 RJafroc-1.3.1/RJafroc/R/DfFroc2Lroc.R |only RJafroc-1.3.1/RJafroc/R/DfFroc2Roc.R | 20 RJafroc-1.3.1/RJafroc/R/DfLroc2Froc.R |only RJafroc-1.3.1/RJafroc/R/DfLroc2Roc.R | 56 RJafroc-1.3.1/RJafroc/R/DfReadCrossedModalities.R | 44 RJafroc-1.3.1/RJafroc/R/DfReadDataFile.R | 1230 +++++++ RJafroc-1.3.1/RJafroc/R/DfReadLrocDataFile.R | 4 RJafroc-1.3.1/RJafroc/R/DfSaveDataFile.R | 16 RJafroc-1.3.1/RJafroc/R/FitBinormalRoc.R | 2 RJafroc-1.3.1/RJafroc/R/FitRsmRoc.R | 32 RJafroc-1.3.1/RJafroc/R/PlotEmpiricalOperatingCharacteristics.R | 682 +++- RJafroc-1.3.1/RJafroc/R/PlotRsmOperatingCharacteristics.R | 226 - RJafroc-1.3.1/RJafroc/R/RcppExports.R | 24 RJafroc-1.3.1/RJafroc/R/ReadOrDbmMrmc.R | 8 RJafroc-1.3.1/RJafroc/R/SimulateFrocDataset.R | 21 RJafroc-1.3.1/RJafroc/R/SimulateLrocDataset.R |only RJafroc-1.3.1/RJafroc/R/SimulateRocDataset.R | 5 RJafroc-1.3.1/RJafroc/R/SimulateRoiDataset.R | 2 RJafroc-1.3.1/RJafroc/R/SsFrocNhRsmModel.R |only RJafroc-1.3.1/RJafroc/R/SsPowerGivenJK.R | 272 + RJafroc-1.3.1/RJafroc/R/SsPowerTable.R | 129 RJafroc-1.3.1/RJafroc/R/SsSampleSizeKGivenJ.R | 235 + RJafroc-1.3.1/RJafroc/R/StDBMHAnalysis.R |only RJafroc-1.3.1/RJafroc/R/StORHAnalysis.R |only RJafroc-1.3.1/RJafroc/R/StOldCode.R |only RJafroc-1.3.1/RJafroc/R/StSignificanceTesting.R | 1623 ++-------- RJafroc-1.3.1/RJafroc/R/StSignificanceTestingCadVsRadiologists.R | 719 ++-- RJafroc-1.3.1/RJafroc/R/StSignificanceTestingCrossedModalities.R | 44 RJafroc-1.3.1/RJafroc/R/StSignificanceTestingSingleFixedFactor.R | 31 RJafroc-1.3.1/RJafroc/R/StSingleTreatmentRandomReader.R |only RJafroc-1.3.1/RJafroc/R/UtilDBM2ORVarComp.R |only RJafroc-1.3.1/RJafroc/R/UtilFigureOfMerit.R | 55 RJafroc-1.3.1/RJafroc/R/UtilLesionDistr.R |only RJafroc-1.3.1/RJafroc/R/UtilLesionWeightsDistr.R |only RJafroc-1.3.1/RJafroc/R/UtilMeanSquares.R | 40 RJafroc-1.3.1/RJafroc/R/UtilOutputReport.R | 149 RJafroc-1.3.1/RJafroc/R/UtilPseudoValues.R | 94 RJafroc-1.3.1/RJafroc/R/UtilVarComponentsOR.R |only RJafroc-1.3.1/RJafroc/R/datasets.R | 90 RJafroc-1.3.1/RJafroc/R/gpfMyFOM.R | 78 RJafroc-1.3.1/RJafroc/R/isValidDataset.R | 8 RJafroc-1.3.1/RJafroc/data/dataset01.RData |binary RJafroc-1.3.1/RJafroc/data/dataset02.RData |binary RJafroc-1.3.1/RJafroc/data/dataset03.RData |binary RJafroc-1.3.1/RJafroc/data/dataset04.RData |binary RJafroc-1.3.1/RJafroc/data/dataset05.RData |binary RJafroc-1.3.1/RJafroc/data/dataset06.RData |binary RJafroc-1.3.1/RJafroc/data/dataset07.RData |binary RJafroc-1.3.1/RJafroc/data/dataset08.RData |binary RJafroc-1.3.1/RJafroc/data/dataset09.RData |binary RJafroc-1.3.1/RJafroc/data/dataset10.RData |binary RJafroc-1.3.1/RJafroc/data/dataset11.RData |binary RJafroc-1.3.1/RJafroc/data/dataset12.RData |binary RJafroc-1.3.1/RJafroc/data/dataset13.RData |binary RJafroc-1.3.1/RJafroc/data/dataset14.RData |binary RJafroc-1.3.1/RJafroc/data/datasetBinned123.RData |binary RJafroc-1.3.1/RJafroc/data/datasetBinned124.RData |binary RJafroc-1.3.1/RJafroc/data/datasetBinned125.RData |binary RJafroc-1.3.1/RJafroc/data/datasetCadLroc.RData |binary RJafroc-1.3.1/RJafroc/data/datasetCadSimuFroc.RData |only RJafroc-1.3.1/RJafroc/data/datasetCrossedModality.RData |binary RJafroc-1.3.1/RJafroc/data/datasetDegenerate.RData |binary RJafroc-1.3.1/RJafroc/data/datasetROI.RData |binary RJafroc-1.3.1/RJafroc/inst/extdata/CrossedModalitiesData.xlsx |only RJafroc-1.3.1/RJafroc/inst/extdata/FrocData.xlsx |only RJafroc-1.3.1/RJafroc/inst/extdata/RocData.csv |only RJafroc-1.3.1/RJafroc/inst/extdata/RocData.imrmc |only RJafroc-1.3.1/RJafroc/inst/extdata/RocData.lrc |only RJafroc-1.3.1/RJafroc/inst/extdata/RocData.txt |only RJafroc-1.3.1/RJafroc/inst/extdata/RocData.xlsx |only RJafroc-1.3.1/RJafroc/inst/extdata/RoiData.xlsx |only RJafroc-1.3.1/RJafroc/inst/extdata/toyFiles |only RJafroc-1.3.1/RJafroc/man/ChisqrGoodnessOfFit.Rd | 8 RJafroc-1.3.1/RJafroc/man/Compare3ProperRocFits.Rd | 9 RJafroc-1.3.1/RJafroc/man/Df2RJafrocDataset.Rd | 16 RJafroc-1.3.1/RJafroc/man/DfBinDataset.Rd | 10 RJafroc-1.3.1/RJafroc/man/DfCreateCorCbmDataset.Rd | 15 RJafroc-1.3.1/RJafroc/man/DfFroc2Afroc.Rd | 2 RJafroc-1.3.1/RJafroc/man/DfFroc2Lroc.Rd |only RJafroc-1.3.1/RJafroc/man/DfFroc2Roc.Rd | 12 RJafroc-1.3.1/RJafroc/man/DfLroc2Froc.Rd |only RJafroc-1.3.1/RJafroc/man/DfLroc2Roc.Rd | 13 RJafroc-1.3.1/RJafroc/man/DfReadCrossedModalities.Rd | 8 RJafroc-1.3.1/RJafroc/man/DfReadDataFile.Rd | 40 RJafroc-1.3.1/RJafroc/man/DfReadLrocDataFile.Rd | 2 RJafroc-1.3.1/RJafroc/man/DfSaveDataFile.Rd | 8 RJafroc-1.3.1/RJafroc/man/FitBinormalRoc.Rd | 2 RJafroc-1.3.1/RJafroc/man/FitRsmRoc.Rd | 26 RJafroc-1.3.1/RJafroc/man/PlotEmpiricalOperatingCharacteristics.Rd | 99 RJafroc-1.3.1/RJafroc/man/PlotRsmOperatingCharacteristics.Rd | 79 RJafroc-1.3.1/RJafroc/man/RJafroc-package.Rd | 51 RJafroc-1.3.1/RJafroc/man/SimulateCorCbmDataset.Rd | 15 RJafroc-1.3.1/RJafroc/man/SimulateFrocDataset.Rd | 11 RJafroc-1.3.1/RJafroc/man/SimulateLrocDataset.Rd |only RJafroc-1.3.1/RJafroc/man/SimulateRocDataset.Rd | 5 RJafroc-1.3.1/RJafroc/man/SsFrocNhRsmModel.Rd |only RJafroc-1.3.1/RJafroc/man/SsPowerGivenJK.Rd | 57 RJafroc-1.3.1/RJafroc/man/SsPowerGivenJKDbmVarComp.Rd |only RJafroc-1.3.1/RJafroc/man/SsPowerGivenJKOrVarComp.Rd |only RJafroc-1.3.1/RJafroc/man/SsPowerTable.Rd | 31 RJafroc-1.3.1/RJafroc/man/SsSampleSizeKGivenJ.Rd | 73 RJafroc-1.3.1/RJafroc/man/StSignificanceTesting.Rd | 166 - RJafroc-1.3.1/RJafroc/man/StSignificanceTestingCadVsRadiologists.Rd | 191 - RJafroc-1.3.1/RJafroc/man/StSignificanceTestingCrossedModalities.Rd | 11 RJafroc-1.3.1/RJafroc/man/StSignificanceTestingSingleFixedFactor.Rd | 18 RJafroc-1.3.1/RJafroc/man/StSingleTreatmentRandomReader.Rd |only RJafroc-1.3.1/RJafroc/man/UtilFigureOfMerit.Rd | 11 RJafroc-1.3.1/RJafroc/man/UtilLesionDistr.Rd |only RJafroc-1.3.1/RJafroc/man/UtilLesionWeightsDistr.Rd |only RJafroc-1.3.1/RJafroc/man/UtilMeanSquares.Rd | 7 RJafroc-1.3.1/RJafroc/man/UtilOutputReport.Rd | 52 RJafroc-1.3.1/RJafroc/man/UtilPseudoValues.Rd | 18 RJafroc-1.3.1/RJafroc/man/UtilVarComponentsDBM.Rd |only RJafroc-1.3.1/RJafroc/man/UtilVarComponentsOR.Rd |only RJafroc-1.3.1/RJafroc/man/dataset01.Rd | 2 RJafroc-1.3.1/RJafroc/man/dataset02.Rd | 4 RJafroc-1.3.1/RJafroc/man/dataset03.Rd | 10 RJafroc-1.3.1/RJafroc/man/dataset04.Rd | 7 RJafroc-1.3.1/RJafroc/man/dataset05.Rd | 2 RJafroc-1.3.1/RJafroc/man/dataset06.Rd | 2 RJafroc-1.3.1/RJafroc/man/dataset07.Rd | 2 RJafroc-1.3.1/RJafroc/man/dataset08.Rd | 4 RJafroc-1.3.1/RJafroc/man/dataset09.Rd | 4 RJafroc-1.3.1/RJafroc/man/dataset10.Rd | 4 RJafroc-1.3.1/RJafroc/man/dataset11.Rd | 2 RJafroc-1.3.1/RJafroc/man/dataset12.Rd | 2 RJafroc-1.3.1/RJafroc/man/dataset13.Rd | 2 RJafroc-1.3.1/RJafroc/man/dataset14.Rd | 2 RJafroc-1.3.1/RJafroc/man/datasetBinned123.Rd | 2 RJafroc-1.3.1/RJafroc/man/datasetBinned124.Rd | 2 RJafroc-1.3.1/RJafroc/man/datasetBinned125.Rd | 2 RJafroc-1.3.1/RJafroc/man/datasetCadLroc.Rd | 2 RJafroc-1.3.1/RJafroc/man/datasetCadSimuFroc.Rd |only RJafroc-1.3.1/RJafroc/man/datasetCrossedModality.Rd | 2 RJafroc-1.3.1/RJafroc/man/datasetDegenerate.Rd | 2 RJafroc-1.3.1/RJafroc/man/datasetROI.Rd | 2 RJafroc-1.3.1/RJafroc/src/CommonFuncs.h | 4 RJafroc-1.3.1/RJafroc/src/MyFOM.cpp | 10 RJafroc-1.3.1/RJafroc/src/RcppExports.cpp | 72 RJafroc-1.3.1/RJafroc/src/RsmFuncs.cpp | 106 169 files changed, 4712 insertions(+), 3333 deletions(-)
Title: High Precision Timing of R Expressions
Description: Tools to accurately benchmark and analyze execution times for R expressions.
Author: Jim Hester [aut, cre],
Drew Schmidt [ctb] (read_proc_file implementation)
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between bench versions 1.1.0 dated 2020-01-09 and 1.1.1 dated 2020-01-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/mark.R | 18 ++++++------------ tests/testthat/test-mark.R | 17 ++++++++--------- 5 files changed, 26 insertions(+), 28 deletions(-)
Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like
'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
https://github.com/mandreyel/ [cph] (mio library),
R Core Team [ctb] (localtime.c code adapted from R),
Jukka Jylänki [cph] (grisu3 implementation),
Mikkel Jørgensen [cph] (grisu3 implementation),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between vroom versions 1.0.2 dated 2019-06-28 and 1.2.0 dated 2020-01-13
vroom-1.0.2/vroom/inst/bench/all_character-benchmark.R |only vroom-1.0.2/vroom/inst/bench/all_character-times.tsv |only vroom-1.0.2/vroom/inst/bench/all_numeric-benchmark.R |only vroom-1.0.2/vroom/inst/bench/all_numeric-times.tsv |only vroom-1.0.2/vroom/inst/bench/fwf-benchmark.R |only vroom-1.0.2/vroom/inst/bench/fwf-times.tsv |only vroom-1.0.2/vroom/inst/bench/sessioninfo.tsv |only vroom-1.0.2/vroom/inst/bench/taxi-benchmark.R |only vroom-1.0.2/vroom/inst/bench/taxi-times.tsv |only vroom-1.0.2/vroom/inst/bench/taxi_multiple-benchmark.R |only vroom-1.0.2/vroom/inst/bench/taxi_multiple-times.tsv |only vroom-1.0.2/vroom/inst/bench/taxi_writing-benchmark.R |only vroom-1.0.2/vroom/inst/bench/taxi_writing-times.tsv |only vroom-1.2.0/vroom/DESCRIPTION | 18 vroom-1.2.0/vroom/MD5 | 327 +++- vroom-1.2.0/vroom/NAMESPACE | 8 vroom-1.2.0/vroom/NEWS.md | 72 + vroom-1.2.0/vroom/R/RcppExports.R | 14 vroom-1.2.0/vroom/R/altrep.R | 2 vroom-1.2.0/vroom/R/col_types.R | 70 vroom-1.2.0/vroom/R/generator.R | 2 vroom-1.2.0/vroom/R/path.R | 32 vroom-1.2.0/vroom/R/utils.R | 2 vroom-1.2.0/vroom/R/vroom-package.R | 1 vroom-1.2.0/vroom/R/vroom.R | 156 +- vroom-1.2.0/vroom/R/vroom_fwf.R | 18 vroom-1.2.0/vroom/R/vroom_lines.R | 14 vroom-1.2.0/vroom/R/vroom_write.R | 10 vroom-1.2.0/vroom/README.md | 74 - vroom-1.2.0/vroom/build/vignette.rds |binary vroom-1.2.0/vroom/build/vroom.pdf |only vroom-1.2.0/vroom/inst/WORDLIST | 12 vroom-1.2.0/vroom/inst/bench/GNUmakefile |only vroom-1.2.0/vroom/inst/bench/README.md |only vroom-1.2.0/vroom/inst/bench/all_character-long |only vroom-1.2.0/vroom/inst/bench/all_character-long.tsv |only vroom-1.2.0/vroom/inst/bench/all_character-wide |only vroom-1.2.0/vroom/inst/bench/all_character-wide.tsv |only vroom-1.2.0/vroom/inst/bench/all_numeric-long |only vroom-1.2.0/vroom/inst/bench/all_numeric-long.tsv |only vroom-1.2.0/vroom/inst/bench/all_numeric-wide |only vroom-1.2.0/vroom/inst/bench/all_numeric-wide.tsv |only vroom-1.2.0/vroom/inst/bench/fwf |only vroom-1.2.0/vroom/inst/bench/fwf.tsv |only vroom-1.2.0/vroom/inst/bench/run-bench-fwf.R |only vroom-1.2.0/vroom/inst/bench/run-bench.R |only vroom-1.2.0/vroom/inst/bench/session_info.R |only vroom-1.2.0/vroom/inst/bench/session_info.tsv |only vroom-1.2.0/vroom/inst/bench/summarise-benchmarks.R |only vroom-1.2.0/vroom/inst/bench/taxi |only vroom-1.2.0/vroom/inst/bench/taxi.tsv |only vroom-1.2.0/vroom/inst/bench/taxi_multiple |only vroom-1.2.0/vroom/inst/bench/taxi_multiple.tsv |only vroom-1.2.0/vroom/inst/bench/taxi_writing |only vroom-1.2.0/vroom/inst/bench/taxi_writing.tsv |only vroom-1.2.0/vroom/inst/doc/benchmarks.R | 135 + vroom-1.2.0/vroom/inst/doc/benchmarks.Rmd | 179 +- vroom-1.2.0/vroom/inst/doc/benchmarks.html | 1208 +++++++++++------ vroom-1.2.0/vroom/inst/doc/vroom.R | 77 - vroom-1.2.0/vroom/inst/doc/vroom.Rmd | 146 +- vroom-1.2.0/vroom/inst/doc/vroom.html | 602 ++++---- vroom-1.2.0/vroom/man/cols.Rd | 16 vroom-1.2.0/vroom/man/date_names.Rd | 3 vroom-1.2.0/vroom/man/figures |only vroom-1.2.0/vroom/man/gen_tbl.Rd | 17 vroom-1.2.0/vroom/man/generators.Rd | 36 vroom-1.2.0/vroom/man/guess_type.Rd | 10 vroom-1.2.0/vroom/man/locale.Rd | 14 vroom-1.2.0/vroom/man/reexports.Rd | 2 vroom-1.2.0/vroom/man/vroom-package.Rd | 6 vroom-1.2.0/vroom/man/vroom.Rd | 62 vroom-1.2.0/vroom/man/vroom_altrep.Rd |only vroom-1.2.0/vroom/man/vroom_altrep_opts.Rd | 36 vroom-1.2.0/vroom/man/vroom_format.Rd | 19 vroom-1.2.0/vroom/man/vroom_fwf.Rd | 51 vroom-1.2.0/vroom/man/vroom_lines.Rd | 21 vroom-1.2.0/vroom/man/vroom_str.Rd | 2 vroom-1.2.0/vroom/man/vroom_write.Rd | 28 vroom-1.2.0/vroom/src/DateTimeParser.h | 25 vroom-1.2.0/vroom/src/RcppExports.cpp | 35 vroom-1.2.0/vroom/src/altrep.cc | 16 vroom-1.2.0/vroom/src/collectors.h | 52 vroom-1.2.0/vroom/src/columns.h | 20 vroom-1.2.0/vroom/src/connection.h | 11 vroom-1.2.0/vroom/src/delimited_index.cc | 6 vroom-1.2.0/vroom/src/delimited_index.h | 3 vroom-1.2.0/vroom/src/delimited_index_connection.cc | 12 vroom-1.2.0/vroom/src/fixed_width_index.h | 25 vroom-1.2.0/vroom/src/fixed_width_index_connection.cc | 4 vroom-1.2.0/vroom/src/guess_type.cc | 42 vroom-1.2.0/vroom/src/index.h | 1 vroom-1.2.0/vroom/src/index_collection.cc | 14 vroom-1.2.0/vroom/src/index_collection.h | 2 vroom-1.2.0/vroom/src/multi_progress.h | 6 vroom-1.2.0/vroom/src/r_utils.h | 21 vroom-1.2.0/vroom/src/utils.h | 2 vroom-1.2.0/vroom/src/vroom.cc | 13 vroom-1.2.0/vroom/src/vroom.h | 3 vroom-1.2.0/vroom/src/vroom_big_int.cc |only vroom-1.2.0/vroom/src/vroom_big_int.h |only vroom-1.2.0/vroom/src/vroom_date.cc | 2 vroom-1.2.0/vroom/src/vroom_date.h | 2 vroom-1.2.0/vroom/src/vroom_dbl.cc | 10 vroom-1.2.0/vroom/src/vroom_dttm.cc | 2 vroom-1.2.0/vroom/src/vroom_dttm.h | 2 vroom-1.2.0/vroom/src/vroom_fct.cc | 6 vroom-1.2.0/vroom/src/vroom_fwf.cc | 13 vroom-1.2.0/vroom/src/vroom_time.cc | 2 vroom-1.2.0/vroom/src/vroom_time.h | 2 vroom-1.2.0/vroom/tests/testthat.R | 6 vroom-1.2.0/vroom/tests/testthat/fwf-trailing-crlf.txt |only vroom-1.2.0/vroom/tests/testthat/helper.R | 23 vroom-1.2.0/vroom/tests/testthat/test-big-int.R |only vroom-1.2.0/vroom/tests/testthat/test-chr.R | 6 vroom-1.2.0/vroom/tests/testthat/test-col_types.R | 7 vroom-1.2.0/vroom/tests/testthat/test-connection.R | 17 vroom-1.2.0/vroom/tests/testthat/test-datetime.R | 254 +-- vroom-1.2.0/vroom/tests/testthat/test-dbl.R |only vroom-1.2.0/vroom/tests/testthat/test-factor.R | 12 vroom-1.2.0/vroom/tests/testthat/test-int.R | 10 vroom-1.2.0/vroom/tests/testthat/test-path.R | 8 vroom-1.2.0/vroom/tests/testthat/test-select.R | 13 vroom-1.2.0/vroom/tests/testthat/test-vroom.R | 80 - vroom-1.2.0/vroom/tests/testthat/test-vroom_fwf.R | 86 + vroom-1.2.0/vroom/tests/testthat/test-vroom_write.R | 30 vroom-1.2.0/vroom/vignettes/benchmarks.Rmd | 179 +- vroom-1.2.0/vroom/vignettes/vroom.Rmd | 146 +- 127 files changed, 3055 insertions(+), 1678 deletions(-)
Title: Text to Speech
Description: Unifies different text to speech engines, such as
Google, Microsoft, and Amazon. Text synthesis can be done
in any engine with a simple switch of an argument denoting
the service requested.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between text2speech versions 0.2.5 dated 2019-06-24 and 0.2.9 dated 2020-01-13
DESCRIPTION | 14 MD5 | 39 NAMESPACE | 3 NEWS.md | 13 R/pcm_to_wav.R |only R/tts_auth.R | 13 R/tts_backend.R | 62 + R/tts_speak_engine.R |only R/tts_voices.R | 50 + R/utils-pipe.R | 2 inst/doc/listing_voices.R | 20 inst/doc/listing_voices.Rmd | 8 inst/doc/listing_voices.html | 1804 ++++++++++--------------------------------- inst/extdata |only man/pcm_to_wav.Rd |only man/pipe.Rd | 2 man/tts.Rd | 67 + man/tts_auth.Rd | 15 man/tts_bind_wav.Rd | 4 man/tts_speak_engine.Rd |only man/tts_voices.Rd | 12 tests/testthat/test-voices.R | 19 vignettes/listing_voices.Rmd | 8 23 files changed, 702 insertions(+), 1453 deletions(-)
Title: An Integrated Framework for Textual Sentiment Time Series
Aggregation and Prediction
Description: Optimized prediction based on textual sentiment, accounting for the intrinsic challenge that sentiment can be computed and pooled across texts and time in various ways. See Ardia et al. (2019) <doi:10.2139/ssrn.3067734>.
Author: Samuel Borms [aut, cre] (<https://orcid.org/0000-0001-9533-1870>),
David Ardia [aut] (<https://orcid.org/0000-0003-2823-782X>),
Keven Bluteau [aut] (<https://orcid.org/0000-0003-2990-4807>),
Kris Boudt [aut] (<https://orcid.org/0000-0002-1000-5142>),
Jeroen Van Pelt [ctb],
Andres Algaba [ctb]
Maintainer: Samuel Borms <samuel.borms@unine.ch>
Diff between sentometrics versions 0.7.6 dated 2019-11-01 and 0.8.0 dated 2020-01-13
DESCRIPTION | 8 MD5 | 134 ++++++------ NAMESPACE | 4 NEWS.md | 49 ++-- R/deprecated.R | 2 R/sentiment_engines.R | 11 R/sentocorpus.R | 35 ++- R/sentolexicons.R | 3 R/sentomeasures_main.R | 56 +++-- R/sentomeasures_measures_xyz.R | 30 -- R/sentomeasures_methods.R | 32 ++ R/sentomodel.R | 13 - R/utils.R | 3 README.md | 2 inst/CITATION | 2 man/add_features.Rd | 163 +++++++------- man/aggregate.sentiment.Rd | 128 ++++++----- man/aggregate.sento_measures.Rd | 209 +++++++++--------- man/as.data.table.sento_measures.Rd | 83 +++---- man/as.sentiment.Rd | 124 +++++------ man/as.sento_corpus.Rd | 142 ++++++------ man/attributions.Rd | 114 +++++----- man/compute_sentiment.Rd | 309 ++++++++++++++-------------- man/corpus_summarize.Rd | 94 ++++---- man/ctr_agg.Rd | 257 ++++++++++++----------- man/ctr_model.Rd | 246 +++++++++++----------- man/data-defunct.Rd | 32 +- man/diff.sento_measures.Rd | 86 +++---- man/epu.Rd | 76 +++--- man/get_dates.Rd | 40 +-- man/get_dimensions.Rd | 40 +-- man/get_hows.Rd | 46 ++-- man/get_loss_data.Rd | 149 ++++++------- man/list_lexicons.Rd | 128 +++++------ man/list_valence_shifters.Rd | 70 +++--- man/measures_fill.Rd | 112 +++++----- man/measures_update.Rd | 84 +++---- man/merge.sentiment.Rd | 126 +++++------ man/nmeasures.Rd | 38 +-- man/nobs.sento_measures.Rd | 44 +-- man/peakdates.Rd | 108 ++++----- man/peakdocs.Rd | 108 ++++----- man/plot.attributions.Rd | 64 ++--- man/plot.sento_measures.Rd | 102 ++++----- man/plot.sento_modelIter.Rd | 56 ++--- man/predict.sento_model.Rd | 73 +++--- man/scale.sento_measures.Rd | 122 +++++------ man/sento_corpus.Rd | 168 +++++++-------- man/sento_lexicons.Rd | 148 ++++++------- man/sento_measures.Rd | 130 +++++------ man/sento_model.Rd | 292 +++++++++++++------------- man/sentometrics-defunct.Rd | 209 +++++++----------- man/sentometrics-deprecated.Rd | 24 +- man/sentometrics-package.Rd | 134 ++++++------ man/subset.sento_measures.Rd | 147 ++++++------- man/usnews.Rd | 72 +++--- man/weights_almon.Rd | 69 +++--- man/weights_beta.Rd | 80 +++---- man/weights_exponential.Rd | 62 ++--- src/SentimentScorerBigrams.h | 4 src/SentimentScorerClusters.h | 4 src/SentimentScorerOnegrams.h | 2 src/SentimentScorerSentences.h | 2 src/utils.h | 69 +++--- tests/testthat/test_aggregation.R | 16 - tests/testthat/test_corpus_building.R | 23 +- tests/testthat/test_modelling.R | 4 tests/testthat/test_sentiment_computation.R | 35 ++- 68 files changed, 2874 insertions(+), 2777 deletions(-)
Title: Routines for Block Diagonal Symmetric Matrices
Description: This is a special case of sparse matrices, used by coxme.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau@mayo.edu>
Diff between bdsmatrix versions 1.3-3 dated 2017-12-21 and 1.3-4 dated 2020-01-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/bdsmatrix.reconcile.R | 2 +- inst/NEWS.Rd | 6 ++++++ 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Interactive Interpretation of Linear Regression Models
Description: Interactive visualization of effects, response functions
and marginal effects for different kinds of regression models. In this version
linear regression models, generalized linear models, generalized additive
models and linear mixed-effects models are supported.
Major features are the interactive approach and the handling of the effects of categorical covariates:
if two or more factors are used as covariates every combination of the levels of each
factor is treated separately. The automatic calculation of
marginal effects and a number of possibilities to customize the graphical output
are useful features as well.
Author: Martin Meermeyer
Maintainer: Martin Meermeyer <m.meermeyer@gmail.com>
Diff between LinRegInteractive versions 0.3-1 dated 2015-04-23 and 0.3-2 dated 2020-01-13
LinRegInteractive-0.3-1/LinRegInteractive/build |only LinRegInteractive-0.3-1/LinRegInteractive/inst/doc/LinRegInteractive.R |only LinRegInteractive-0.3-1/LinRegInteractive/inst/doc/LinRegInteractive.Rnw |only LinRegInteractive-0.3-1/LinRegInteractive/inst/doc/vignettegraphics.zip |only LinRegInteractive-0.3-1/LinRegInteractive/vignettes/LinRegInteractive.tex |only LinRegInteractive-0.3-1/LinRegInteractive/vignettes/vignettegraphics.zip |only LinRegInteractive-0.3-2/LinRegInteractive/DESCRIPTION | 10 LinRegInteractive-0.3-2/LinRegInteractive/MD5 | 33 - LinRegInteractive-0.3-2/LinRegInteractive/NAMESPACE | 4 LinRegInteractive-0.3-2/LinRegInteractive/R/LinRegInteractive_functions.R | 221 +++++----- LinRegInteractive-0.3-2/LinRegInteractive/inst/doc/LinRegInteractive.pdf |binary LinRegInteractive-0.3-2/LinRegInteractive/inst/doc/VignetteAux.zip |only LinRegInteractive-0.3-2/LinRegInteractive/man/LinRegInteractive-package.Rd | 8 LinRegInteractive-0.3-2/LinRegInteractive/man/creditdata.Rd | 4 LinRegInteractive-0.3-2/LinRegInteractive/man/fxInteractive.Rd | 14 LinRegInteractive-0.3-2/LinRegInteractive/man/fxInteractive.glm.Rd | 4 LinRegInteractive-0.3-2/LinRegInteractive/man/fxInteractive.lm.Rd | 2 LinRegInteractive-0.3-2/LinRegInteractive/man/fxInteractive.lme.Rd | 6 LinRegInteractive-0.3-2/LinRegInteractive/man/munichrent03.Rd | 7 LinRegInteractive-0.3-2/LinRegInteractive/vignettes/LinRegInteractive.Rnw | 15 LinRegInteractive-0.3-2/LinRegInteractive/vignettes/LinRegInteractive.bib | 56 +- 21 files changed, 197 insertions(+), 187 deletions(-)
More information about LinRegInteractive at CRAN
Permanent link
Title: Comparing Multiple Survival Functions with Crossing Hazards
Description: Computing the one-sided/two-sided integrated/maximally selected EL statistics for simultaneous testing, the one-sided/two-sided EL tests for pointwise testing, and an initial test that precedes one-sided testing to exclude the possibility of crossings or alternative orderings among the survival functions.
Author: Hsin-wen Chang [aut, cre] <hwchang@stat.sinica.edu.tw>
Maintainer: Guo-You Lan <jj6020770416jj@gmail.com>
Diff between survELtest versions 2.0.0 dated 2020-01-08 and 2.0.1 dated 2020-01-13
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms
Description: Algorithms for accelerating the convergence of slow,
monotone sequences from smooth, contraction mapping such as the
EM algorithm. It can be used to accelerate any smooth, linearly
convergent acceleration scheme. A tutorial style introduction
to this package is available in a vignette on the CRAN download
page or, when the package is loaded in an R session, with
vignette("SQUAREM").
Author: Ravi Varadhan
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between SQUAREM versions 2017.10-1 dated 2017-10-07 and 2020.1 dated 2020-01-13
DESCRIPTION | 8 MD5 | 16 NEWS | 2 R/squarem.R | 36 - build/vignette.rds |binary inst/doc/SQUAREM.Rnw | 933 +++++++++++---------------------------------------- inst/doc/SQUAREM.pdf |binary man/fpiter.Rd | 4 man/squarem.Rd | 20 - 9 files changed, 255 insertions(+), 764 deletions(-)
Title: Simulate Joint Distribution
Description: Simulate multivariate correlated data given nonparametric marginals and their covariance structure characterized by a Pearson or Spearman correlation matrix. The simulator engages the problem from a purely computational perspective. It assumes no statistical models such as copulas or parametric distributions, and can approximate the target correlations regardless of theoretical feasibility. The algorithm integrates and advances the Iman-Conover (1982) approach <doi:10.1080/03610918208812265> and the Ruscio-Kaczetow iteration (2008) <doi:10.1080/00273170802285693>. Package functions are carefully implemented in C++ for squeezing computing speed, suitable for large input in a manycore environment. Precision of the approximation and computing speed both outperform various CRAN packages to date by substantial margins. Benchmarks are detailed in function examples. A simple heuristic algorithm is additionally designed to optimize the joint distribution in the post-simulation stage. This heuristic demonstrated not only strong capability of cost reduction, but also good potential of achieving the same level of precision of approximation without the enhanced Iman-Conover-Ruscio-Kaczetow. The package contains a copy of Permuted Congruential Generator from <http://www.pcg-random.org>.
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>
Diff between SimJoint versions 0.3.4 dated 2020-01-10 and 0.3.5 dated 2020-01-13
DESCRIPTION | 6 +-- MD5 | 24 ++++++------- inst/NEWS.Rd | 9 ++++- src/decor.cpp | 2 + src/hpp/LHSsorted.hpp | 2 + src/hpp/dnyTasking.hpp | 2 + src/jointSimulation.cpp | 2 + src/lhsPMF.cpp | 2 + src/pcg/parallelSeeds.hpp | 2 + src/pcg/pcg_extras.hpp | 1 src/pcg/pcg_random.hpp | 79 +++++++++++++++++++++++----------------------- src/pcg/pcg_uint128.hpp | 1 src/pcg/toSeed.hpp | 1 13 files changed, 78 insertions(+), 55 deletions(-)
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Diff between RaceID versions 0.1.6 dated 2019-11-21 and 0.1.7 dated 2020-01-13
DESCRIPTION | 8 +++--- MD5 | 12 +++++----- R/VarID_functions.R | 52 +++++++++++++++++++++++++++++++++++--------- inst/doc/RaceID.R | 10 ++++---- inst/doc/RaceID.Rmd | 19 ++++++++-------- inst/doc/RaceID.html | 59 +++++++++++++++++++++++++-------------------------- vignettes/RaceID.Rmd | 19 ++++++++-------- 7 files changed, 106 insertions(+), 73 deletions(-)
Title: Neyman-Pearson (NP) Classification Algorithms and NP Receiver
Operating Characteristic (NP-ROC) Curves
Description: In many binary classification applications, such as disease
diagnosis and spam detection, practitioners commonly face the need to limit
type I error (i.e., the conditional probability of misclassifying a class 0
observation as class 1) so that it remains below a desired threshold. To address
this need, the Neyman-Pearson (NP) classification paradigm is a natural choice;
it minimizes type II error (i.e., the conditional probability of misclassifying
a class 1 observation as class 0) while enforcing an upper bound, alpha, on the
type I error. Although the NP paradigm has a century-long history in hypothesis
testing, it has not been well recognized and implemented in classification
schemes. Common practices that directly limit the empirical type I error to
no more than alpha do not satisfy the type I error control objective because
the resulting classifiers are still likely to have type I errors much larger
than alpha. As a result, the NP paradigm has not been properly implemented
for many classification scenarios in practice. In this work, we develop the
first umbrella algorithm that implements the NP paradigm for all scoring-type
classification methods, including popular methods such as logistic regression,
support vector machines and random forests. Powered by this umbrella algorithm,
we propose a novel graphical tool for NP classification methods: NP receiver
operating characteristic (NP-ROC) bands, motivated by the popular receiver
operating characteristic (ROC) curves. NP-ROC bands will help choose in a data
adaptive way and compare different NP classifiers.
Author: Yang Feng [aut, cre],
Jessica Li [aut],
Xin Tong [aut],
Ye Tian [ctb]
Maintainer: Yang Feng <yangfengstat@gmail.com>
Diff between nproc versions 2.1.4 dated 2018-11-16 and 2.1.5 dated 2020-01-13
DESCRIPTION | 19 - MD5 | 14 - R/npfuns.R | 606 +++++++++++++++++++++++----------------------- build/vignette.rds |binary man/npc.Rd | 9 man/nproc.Rd | 6 man/rocCV.Rd | 6 vignettes/nproc-demo.html | 258 ++----------------- 8 files changed, 368 insertions(+), 550 deletions(-)
Title: Factor Adjusted Robust Multiple Testing
Description: Performs robust multiple testing for means in the presence of known and unknown latent factors.
It implements a series of adaptive Huber methods combined with fast data-drive tuning schemes to estimate model parameters and construct test statistics that are robust against heavy-tailed and/or asymetric error distributions.
Extensions to two-sample simultaneous mean comparison problems are also included.
As by-products, this package also contains functions that compute adaptive Huber mean and covariance matrix estimators that are of independent interest.
Author: Xiaoou Pan, Yuan Ke and Wen-Xin Zhou
Maintainer: Xiaoou Pan <xip024@ucsd.edu>
Diff between FarmTest versions 1.0.3 dated 2018-05-29 and 2.0.0 dated 2020-01-13
FarmTest-1.0.3/FarmTest/R/FarmTest-package.r |only FarmTest-1.0.3/FarmTest/R/load.R |only FarmTest-1.0.3/FarmTest/build |only FarmTest-1.0.3/FarmTest/inst |only FarmTest-1.0.3/FarmTest/man/farm.FDR.Rd |only FarmTest-1.0.3/FarmTest/man/farm.scree.Rd |only FarmTest-1.0.3/FarmTest/man/plot.farm.scree.Rd |only FarmTest-1.0.3/FarmTest/man/print.farm.scree.Rd |only FarmTest-1.0.3/FarmTest/src/Cfunctions.cpp |only FarmTest-1.0.3/FarmTest/vignettes |only FarmTest-2.0.0/FarmTest/DESCRIPTION | 34 +- FarmTest-2.0.0/FarmTest/MD5 | 50 +-- FarmTest-2.0.0/FarmTest/NAMESPACE | 18 - FarmTest-2.0.0/FarmTest/R/FarmTest.R |only FarmTest-2.0.0/FarmTest/R/RcppExports.R | 235 +++++++++++----- FarmTest-2.0.0/FarmTest/README.md |only FarmTest-2.0.0/FarmTest/man/FarmTest.Rd | 33 +- FarmTest-2.0.0/FarmTest/man/farm.cov.Rd | 43 +- FarmTest-2.0.0/FarmTest/man/farm.fdr.Rd |only FarmTest-2.0.0/FarmTest/man/farm.mean.Rd | 41 +- FarmTest-2.0.0/FarmTest/man/farm.test.Rd | 154 +++++----- FarmTest-2.0.0/FarmTest/man/farmTestFac.Rd |only FarmTest-2.0.0/FarmTest/man/farmTestFacBoot.Rd |only FarmTest-2.0.0/FarmTest/man/farmTestTwo.Rd |only FarmTest-2.0.0/FarmTest/man/farmTestTwoFac.Rd |only FarmTest-2.0.0/FarmTest/man/farmTestTwoFacBoot.Rd |only FarmTest-2.0.0/FarmTest/man/getRej.Rd |only FarmTest-2.0.0/FarmTest/man/huberCov.Rd |only FarmTest-2.0.0/FarmTest/man/huberMean.Rd |only FarmTest-2.0.0/FarmTest/man/print.farm.test.Rd | 38 -- FarmTest-2.0.0/FarmTest/man/rmTest.Rd |only FarmTest-2.0.0/FarmTest/man/rmTestBoot.Rd |only FarmTest-2.0.0/FarmTest/man/rmTestTwo.Rd |only FarmTest-2.0.0/FarmTest/man/rmTestTwoBoot.Rd |only FarmTest-2.0.0/FarmTest/src/FarmTest.cpp |only FarmTest-2.0.0/FarmTest/src/Makevars | 4 FarmTest-2.0.0/FarmTest/src/Makevars.win | 4 FarmTest-2.0.0/FarmTest/src/RcppExports.cpp | 316 +++++++++------------- 38 files changed, 490 insertions(+), 480 deletions(-)
Title: Tools to Deal with Raster Maps
Description: A collection of tools to deal with raster maps.
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge <clement.calenge@ofb.gouv.fr>
Diff between adehabitatMA versions 0.3.13 dated 2019-04-07 and 0.3.14 dated 2020-01-13
adehabitatMA-0.3.13/adehabitatMA/build |only adehabitatMA-0.3.13/adehabitatMA/inst/doc/adehabitatMA.R |only adehabitatMA-0.3.13/adehabitatMA/inst/doc/adehabitatMA.Rnw |only adehabitatMA-0.3.14/adehabitatMA/DESCRIPTION | 10 +-- adehabitatMA-0.3.14/adehabitatMA/MD5 | 37 +++++-------- adehabitatMA-0.3.14/adehabitatMA/inst/doc/adehabitatMA.pdf |binary adehabitatMA-0.3.14/adehabitatMA/man/adeoptions.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/ascgen.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/buffer.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/count.points.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/distfacmap.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/explore.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/getcontour.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/join.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/kasc2spixdf.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/labcon.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/lowres.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/mimage.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/morphology.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/perarea.Rd | 2 adehabitatMA-0.3.14/adehabitatMA/man/subsetmap.Rd | 2 21 files changed, 37 insertions(+), 40 deletions(-)
Title: Analysis of Habitat Selection by Animals
Description: A collection of tools for the analysis of habitat selection.
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge <clement.calenge@ofb.gouv.fr>
Diff between adehabitatHS versions 0.3.14 dated 2019-04-07 and 0.3.15 dated 2020-01-13
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- man/canomi.Rd | 2 +- man/compana.Rd | 2 +- man/domain.Rd | 2 +- man/dunnfa.Rd | 2 +- man/eisera.Rd | 2 +- man/engen2008II.Rd | 2 +- man/gnesfa.Rd | 2 +- man/kselect.Rd | 2 +- man/madifa.Rd | 2 +- man/mahasuhab.Rd | 2 +- man/niche.test.Rd | 2 +- man/rand.kselect.Rd | 2 +- man/randtest.enfa.Rd | 2 +- man/scatterniche.Rd | 2 +- man/wi.Rd | 2 +- 17 files changed, 36 insertions(+), 36 deletions(-)
Title: Analysis of RD Designs with Multiple Cutoffs or Scores
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. The 'rdmulti' package provides tools to analyze RD designs with multiple cutoffs or scores: rdmc() estimates pooled and cutoff specific effects for multi-cutoff designs, rdmcplot() draws RD plots for multi-cutoff designs and rdms() estimates effects in cumulative cutoffs or multi-score designs. See Cattaneo, Titiunik and Vazquez-Bare (2019) <https://sites.google.com/site/rdpackages/rdmulti/Cattaneo-Titiunik-VazquezBare_2019_rdmulti.pdf> for further methodological details.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@econ.ucsb.edu>
Diff between rdmulti versions 0.3 dated 2019-10-29 and 0.4 dated 2020-01-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/rdmc.R | 14 +++++++------- R/rdmcplot.R | 2 +- R/rdms.R | 8 ++++---- R/rdmulti_package.R | 2 +- 6 files changed, 21 insertions(+), 21 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>),
Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>),
David Wilson [ctb],
Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>),
John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>)
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 0.11.0 dated 2019-10-11 and 0.11.1 dated 2020-01-13
AlphaSimR-0.11.0/AlphaSimR/man/pullMultipleSnpGeno.Rd |only AlphaSimR-0.11.0/AlphaSimR/man/pullMultipleSnpHaplo.Rd |only AlphaSimR-0.11.1/AlphaSimR/DESCRIPTION | 10 AlphaSimR-0.11.1/AlphaSimR/MD5 | 124 ++-- AlphaSimR-0.11.1/AlphaSimR/NAMESPACE | 5 AlphaSimR-0.11.1/AlphaSimR/NEWS | 14 AlphaSimR-0.11.1/AlphaSimR/R/Class-Pop.R | 75 ++ AlphaSimR-0.11.1/AlphaSimR/R/Class-SimParam.R | 35 - AlphaSimR-0.11.1/AlphaSimR/R/RcppExports.R | 8 AlphaSimR-0.11.1/AlphaSimR/R/crossing.R | 52 + AlphaSimR-0.11.1/AlphaSimR/R/founderPop.R | 10 AlphaSimR-0.11.1/AlphaSimR/R/mergePops.R | 5 AlphaSimR-0.11.1/AlphaSimR/R/misc.R | 48 + AlphaSimR-0.11.1/AlphaSimR/R/polyploids.R |only AlphaSimR-0.11.1/AlphaSimR/R/pullGeno.R | 266 ++++----- AlphaSimR-0.11.1/AlphaSimR/build/vignette.rds |binary AlphaSimR-0.11.1/AlphaSimR/inst/doc/intro.R | 20 AlphaSimR-0.11.1/AlphaSimR/inst/doc/intro.html | 9 AlphaSimR-0.11.1/AlphaSimR/inst/doc/traits.pdf |binary AlphaSimR-0.11.1/AlphaSimR/man/AlphaSimR.Rd | 1 AlphaSimR-0.11.1/AlphaSimR/man/MapPop-class.Rd | 2 AlphaSimR-0.11.1/AlphaSimR/man/RRBLUP.Rd | 13 AlphaSimR-0.11.1/AlphaSimR/man/RRBLUP2.Rd | 18 AlphaSimR-0.11.1/AlphaSimR/man/RRBLUP_D.Rd | 14 AlphaSimR-0.11.1/AlphaSimR/man/RRBLUP_D2.Rd | 19 AlphaSimR-0.11.1/AlphaSimR/man/RRBLUP_GCA.Rd | 14 AlphaSimR-0.11.1/AlphaSimR/man/RRBLUP_GCA2.Rd | 20 AlphaSimR-0.11.1/AlphaSimR/man/RRBLUP_SCA.Rd | 14 AlphaSimR-0.11.1/AlphaSimR/man/RRBLUP_SCA2.Rd | 21 AlphaSimR-0.11.1/AlphaSimR/man/SimParam.Rd | 472 ++++++++++++++++- AlphaSimR-0.11.1/AlphaSimR/man/SimParam_addSnpChip.Rd | 9 AlphaSimR-0.11.1/AlphaSimR/man/cChr.Rd |only AlphaSimR-0.11.1/AlphaSimR/man/doubleGenome.Rd |only AlphaSimR-0.11.1/AlphaSimR/man/editGenomeTopQtl.Rd | 3 AlphaSimR-0.11.1/AlphaSimR/man/fastRRBLUP.Rd | 15 AlphaSimR-0.11.1/AlphaSimR/man/hybridCross.Rd | 9 AlphaSimR-0.11.1/AlphaSimR/man/makeDH.Rd | 9 AlphaSimR-0.11.1/AlphaSimR/man/newPop.Rd | 11 AlphaSimR-0.11.1/AlphaSimR/man/pedigreeCross.Rd | 15 AlphaSimR-0.11.1/AlphaSimR/man/pullIbdHaplo.Rd | 9 AlphaSimR-0.11.1/AlphaSimR/man/pullQtlGeno.Rd | 55 + AlphaSimR-0.11.1/AlphaSimR/man/pullQtlHaplo.Rd | 87 +++ AlphaSimR-0.11.1/AlphaSimR/man/pullSnpHaplo.Rd | 3 AlphaSimR-0.11.1/AlphaSimR/man/quickHaplo.Rd | 3 AlphaSimR-0.11.1/AlphaSimR/man/randCross.Rd | 11 AlphaSimR-0.11.1/AlphaSimR/man/randCross2.Rd | 14 AlphaSimR-0.11.1/AlphaSimR/man/reduceGenome.Rd |only AlphaSimR-0.11.1/AlphaSimR/man/runMacs.Rd | 15 AlphaSimR-0.11.1/AlphaSimR/man/runMacs2.Rd | 21 AlphaSimR-0.11.1/AlphaSimR/man/sampleHaplo.Rd | 3 AlphaSimR-0.11.1/AlphaSimR/man/selectCross.Rd | 17 AlphaSimR-0.11.1/AlphaSimR/man/selectFam.Rd | 16 AlphaSimR-0.11.1/AlphaSimR/man/selectInd.Rd | 15 AlphaSimR-0.11.1/AlphaSimR/man/selectOP.Rd | 16 AlphaSimR-0.11.1/AlphaSimR/man/selectWithinFam.Rd | 16 AlphaSimR-0.11.1/AlphaSimR/man/self.Rd | 3 AlphaSimR-0.11.1/AlphaSimR/man/setEBV.Rd | 10 AlphaSimR-0.11.1/AlphaSimR/man/setPheno.Rd | 11 AlphaSimR-0.11.1/AlphaSimR/man/setPhenoGCA.Rd | 15 AlphaSimR-0.11.1/AlphaSimR/man/usefulness.Rd | 11 AlphaSimR-0.11.1/AlphaSimR/man/writePlink.Rd | 43 + AlphaSimR-0.11.1/AlphaSimR/man/writeRecords.Rd | 11 AlphaSimR-0.11.1/AlphaSimR/src/RcppExports.cpp | 32 - AlphaSimR-0.11.1/AlphaSimR/src/init.c | 84 +-- AlphaSimR-0.11.1/AlphaSimR/src/meiosis.cpp | 120 ++++ AlphaSimR-0.11.1/AlphaSimR/src/plink.cpp | 64 +- 66 files changed, 1604 insertions(+), 461 deletions(-)
Title: Load Census TIGER/Line Shapefiles
Description: Download TIGER/Line shapefiles from the United States Census Bureau
(<https://www.census.gov/geo/maps-data/data/tiger-line.html>) and load into R as 'SpatialDataFrame' or 'sf' objects.
Author: Kyle Walker [aut, cre],
Bob Rudis [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>
Diff between tigris versions 0.8.2 dated 2019-06-12 and 0.9.1 dated 2020-01-13
DESCRIPTION | 10 +- MD5 | 108 ++++++++++++++--------------- NEWS | 4 - R/enumeration_units.R | 54 +++++++------- R/helpers.R | 2 R/landmarks.R | 14 +-- R/legislative.R | 5 - R/metro_areas.R | 30 ++++---- R/national.R | 12 +-- R/native.R | 30 ++++---- R/places.R | 6 - R/pumas.R | 6 - R/states.R | 6 - R/transportation.R | 30 ++++---- R/water.R | 27 ++++--- README.md | 74 +++++++++---------- data/fips_codes.rda |binary man/address_ranges.Rd | 12 +-- man/alaska_native_regional_corporations.Rd | 13 +-- man/area_water.Rd | 9 +- man/block_groups.Rd | 20 +++-- man/blocks.Rd | 20 +++-- man/coastline.Rd | 7 + man/combined_statistical_areas.Rd | 15 ++-- man/congressional_districts.Rd | 10 +- man/core_based_statistical_areas.Rd | 15 ++-- man/counties.Rd | 22 +++-- man/county_subdivisions.Rd | 34 +++++---- man/divisions.Rd | 7 + man/geo_join.Rd | 3 man/landmarks.Rd | 4 - man/linear_water.Rd | 9 +- man/metro_divisions.Rd | 12 +-- man/military.Rd | 6 - man/nation.Rd | 7 + man/native_areas.Rd | 13 +-- man/new_england.Rd | 12 +-- man/places.Rd | 19 +++-- man/primary_roads.Rd | 12 +-- man/primary_secondary_roads.Rd | 12 +-- man/pumas.Rd | 19 +++-- man/rails.Rd | 13 +-- man/regions.Rd | 7 + man/roads.Rd | 13 +-- man/school_districts.Rd | 19 +++-- man/state_legislative_districts.Rd | 16 +++- man/states.Rd | 19 +++-- man/tigris.Rd | 1 man/tracts.Rd | 19 +++-- man/tribal_block_groups.Rd | 13 +-- man/tribal_census_tracts.Rd | 13 +-- man/tribal_subdivisions_national.Rd | 13 +-- man/urban_areas.Rd | 12 +-- man/voting_districts.Rd | 5 - man/zctas.Rd | 22 +++-- 55 files changed, 499 insertions(+), 416 deletions(-)
Title: Rapid Calculation of Model Metrics
Description: Collection of metrics for evaluating models written in C++ using 'Rcpp'. Popular metrics include area under the curve, log loss, root mean square error, etc.
Author: Tyler Hunt [aut, cre]
Maintainer: Tyler Hunt <thunt@snapfinance.com>
Diff between ModelMetrics versions 1.2.2 dated 2018-11-03 and 1.2.2.1 dated 2020-01-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/ModelMetrics.R | 4 ++-- data/testDF.rda |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-29 2.1.2
2018-06-28 2.1.1
2017-08-18 2.1.0
2016-08-29 2.0.1
2016-05-27 2.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-08 0.7-11
Title: A Suite of Convergence Acceleration Schemes for EM, MM and Other
Fixed-Point Algorithms
Description: Algorithms for accelerating the convergence of slow,
monotone sequences from smooth, contraction mapping such as the
EM and MM algorithms. It can be used to accelerate any smooth,
linearly convergent acceleration scheme. A tutorial style
introduction to this package is available in a vignette on the
CRAN download page or, when the package is loaded in an R
session, with vignette("turboEM").
Author: Jennifer F. Bobb [aut],
Ravi Varadhan [aut, cre],
Hui Zhao [ctb]
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between turboEM versions 2018.1 dated 2018-05-06 and 2020.1 dated 2020-01-13
DESCRIPTION | 6 MD5 | 12 - NEWS | 6 R/turboem.R | 53 +++---- build/vignette.rds |binary inst/doc/turboEM.pdf |binary man/turboem.Rd | 379 +++++++++++++++++++++++++-------------------------- 7 files changed, 231 insertions(+), 225 deletions(-)
Title: Tools for Post-Processing Class Probability Estimates
Description: Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations.
Author: Max Kuhn [aut],
Davis Vaughan [aut, cre],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between probably versions 0.0.3 dated 2019-07-07 and 0.0.4 dated 2020-01-13
DESCRIPTION | 11 + MD5 | 25 ++-- NEWS.md | 6 + inst/doc/equivocal-zones.R | 14 +- inst/doc/equivocal-zones.html | 10 + inst/doc/where-to-use.R | 29 ++--- inst/doc/where-to-use.Rmd | 1 inst/doc/where-to-use.html | 215 +++++++++++++++++++-------------------- man/append_class_pred.Rd | 10 + man/make_class_pred.Rd | 12 +- man/threshold_perf.Rd | 3 tests/testthat/output |only tests/testthat/test-class-pred.R | 8 + vignettes/where-to-use.Rmd | 1 14 files changed, 187 insertions(+), 158 deletions(-)
More information about optimalThreshold at CRAN
Permanent link
Title: Interface to the California Data Exchange Center
Description: Connect to the California Data Exchange Center (CDEC)
Web Service <http://cdec.water.ca.gov/>. 'CDEC' provides a centralized
database to store, process, and exchange real-time hydrologic information
gathered by various cooperators throughout California. The 'CDEC' Web Service
<http://cdec.water.ca.gov/dynamicapp/wsSensorData> provides a data download
service for accessing historical records.
Author: Michael Koohafkan [aut, cre]
Maintainer: Michael Koohafkan <michael.koohafkan@gmail.com>
Diff between cder versions 0.2-0 dated 2019-08-07 and 0.2-1 dated 2020-01-13
DESCRIPTION | 14 +-- MD5 | 33 ++++----- NAMESPACE | 2 NEWS.md |only R/query.r | 20 ++--- inst/doc/quickstart.html | 168 ++++++++++++++++++++++------------------------- inst/doc/quickstart.rmd | 89 +++++++++++------------- man/Deprecated.Rd | 44 ++++++------ man/basic_query.Rd | 34 ++++----- man/cdec-search.Rd | 64 ++++++++--------- man/cdec_meta.Rd | 30 ++++---- man/cdec_query.Rd | 78 ++++++++++----------- man/cdec_query_group.Rd | 70 +++++++++---------- man/cder.Rd | 66 +++++++++--------- man/cder_handle.Rd | 22 +++--- man/group.spec.Rd | 26 +++---- man/station.spec.Rd | 26 +++---- vignettes/quickstart.rmd | 89 +++++++++++------------- 18 files changed, 425 insertions(+), 450 deletions(-)
Title: Null Model Analysis for Ecological Networks
Description: Tools for using null models to analyse ecological
networks (e.g. food webs, flower-visitation networks, seed-dispersal
networks) and detect resource preferences or non-random interactions among
network nodes. Tools are provided to run null models, test for and plot
preferences, plot and analyse bipartite networks, and export null model
results in a form compatible with other network analysis packages. The
underlying null model was developed by Agusti et al. (2003) Molecular
Ecology <doi:10.1046/j.1365-294X.2003.02014.x> and the full application to
ecological networks by Vaughan et al. (2018) econullnetr: an R package
using null models to analyse the structure of ecological networks and
identify resource selection. Methods in Ecology & Evolution,
<doi.org/10.1111/2041-210X.12907>.
Author: Ian Vaughan
Maintainer: Ian Vaughan <vaughanip@cardiff.ac.uk>
Diff between econullnetr versions 0.1.0.1 dated 2019-06-09 and 0.2.0 dated 2020-01-13
econullnetr-0.1.0.1/econullnetr/tests/testthat/gl_test |only econullnetr-0.1.0.1/econullnetr/tests/testthat/nl_test |only econullnetr-0.1.0.1/econullnetr/tests/testthat/sl_test |only econullnetr-0.2.0/econullnetr/DESCRIPTION | 19 econullnetr-0.2.0/econullnetr/MD5 | 142 - econullnetr-0.2.0/econullnetr/NAMESPACE | 3 econullnetr-0.2.0/econullnetr/NEWS.md | 9 econullnetr-0.2.0/econullnetr/R/WelshStreams.R | 15 econullnetr-0.2.0/econullnetr/R/WelshStreams_fl.R | 7 econullnetr-0.2.0/econullnetr/R/WelshStreams_order.R | 7 econullnetr-0.2.0/econullnetr/R/WelshStreams_prey.R | 7 econullnetr-0.2.0/econullnetr/R/bipartite_stats.R | 22 econullnetr-0.2.0/econullnetr/R/econullnetr.R | 6 econullnetr-0.2.0/econullnetr/R/expanding_interaction_matrix.R |only econullnetr-0.2.0/econullnetr/R/generate_edgelist.R | 56 econullnetr-0.2.0/econullnetr/R/null_model.R | 31 econullnetr-0.2.0/econullnetr/R/plot_bipartite.R | 8 econullnetr-0.2.0/econullnetr/R/plot_preferences.R | 8 econullnetr-0.2.0/econullnetr/R/test_interactions.R | 22 econullnetr-0.2.0/econullnetr/README.md | 57 econullnetr-0.2.0/econullnetr/build/vignette.rds |binary econullnetr-0.2.0/econullnetr/data/Broadstone.fl.rda |binary econullnetr-0.2.0/econullnetr/data/Broadstone.nodes.rda |binary econullnetr-0.2.0/econullnetr/data/Broadstone.prey.rda |binary econullnetr-0.2.0/econullnetr/data/Broadstone.rda |binary econullnetr-0.2.0/econullnetr/data/Silene.plants.rda |binary econullnetr-0.2.0/econullnetr/data/Silene.rda |binary econullnetr-0.2.0/econullnetr/data/WelshStreams.fl.rda |binary econullnetr-0.2.0/econullnetr/data/WelshStreams.order.rda |binary econullnetr-0.2.0/econullnetr/data/WelshStreams.prey.rda |binary econullnetr-0.2.0/econullnetr/data/WelshStreams.rda |binary econullnetr-0.2.0/econullnetr/inst/doc/econullnetr-intro.R | 342 -- econullnetr-0.2.0/econullnetr/inst/doc/econullnetr-intro.Rmd | 189 - econullnetr-0.2.0/econullnetr/inst/doc/econullnetr-intro.html | 1324 ++++------ econullnetr-0.2.0/econullnetr/inst/testdata/expand_matrix_test.csv |only econullnetr-0.2.0/econullnetr/inst/testdata/expanded_matrix.csv |only econullnetr-0.2.0/econullnetr/man/Broadstone.Rd | 81 econullnetr-0.2.0/econullnetr/man/Broadstone.fl.Rd | 59 econullnetr-0.2.0/econullnetr/man/Broadstone.nodes.Rd | 47 econullnetr-0.2.0/econullnetr/man/Broadstone.prey.Rd | 47 econullnetr-0.2.0/econullnetr/man/Silene.Rd | 61 econullnetr-0.2.0/econullnetr/man/Silene.plants.Rd | 49 econullnetr-0.2.0/econullnetr/man/WelshStreams.Rd | 86 econullnetr-0.2.0/econullnetr/man/WelshStreams.fl.Rd | 62 econullnetr-0.2.0/econullnetr/man/WelshStreams.order.Rd | 58 econullnetr-0.2.0/econullnetr/man/WelshStreams.prey.Rd | 52 econullnetr-0.2.0/econullnetr/man/bipartite_stats.Rd | 297 +- econullnetr-0.2.0/econullnetr/man/econullnetr.Rd | 38 econullnetr-0.2.0/econullnetr/man/expand_matrix.Rd |only econullnetr-0.2.0/econullnetr/man/generate_edgelist.Rd | 195 - econullnetr-0.2.0/econullnetr/man/generate_null_net.Rd | 403 +-- econullnetr-0.2.0/econullnetr/man/plot_bipartite.Rd | 149 - econullnetr-0.2.0/econullnetr/man/plot_preferences.Rd | 240 - econullnetr-0.2.0/econullnetr/man/test_interactions.Rd | 181 - econullnetr-0.2.0/econullnetr/tests/figs/deps.txt | 8 econullnetr-0.2.0/econullnetr/tests/figs/plot-bipartite/plot-bipartite-consumer-no-interactions.svg | 132 econullnetr-0.2.0/econullnetr/tests/figs/plot-bipartite/plot-bipartite-unused-resource-zero-abund.svg | 146 - econullnetr-0.2.0/econullnetr/tests/figs/plot-bipartite/plot-bipartite-unused-resource.svg | 146 - econullnetr-0.2.0/econullnetr/tests/figs/plot-bipartite/plot-bipartite-v1-0-90.svg | 82 econullnetr-0.2.0/econullnetr/tests/figs/plot-bipartite/plot-bipartite-v1-0-95.svg | 82 econullnetr-0.2.0/econullnetr/tests/figs/plot-bipartite/plot-bipartite-v1-0-99.svg | 82 econullnetr-0.2.0/econullnetr/tests/figs/plot-bipartite/plot-bipartite-v2-0-95.svg | 82 econullnetr-0.2.0/econullnetr/tests/figs/plot-bipartite/plot-bipartite-v3-0-95.svg | 82 econullnetr-0.2.0/econullnetr/tests/figs/plot-preferences/plot-pref-bars-b-ses.svg | 149 - econullnetr-0.2.0/econullnetr/tests/figs/plot-preferences/plot-prefs-bars-a-0-95.svg | 197 - econullnetr-0.2.0/econullnetr/tests/figs/plot-preferences/plot-prefs-bars-a-ses.svg | 157 - econullnetr-0.2.0/econullnetr/tests/figs/plot-preferences/plot-prefs-bars-b-0-95.svg | 197 - econullnetr-0.2.0/econullnetr/tests/figs/plot-preferences/plot-prefs-dots-a-0-95.svg | 116 econullnetr-0.2.0/econullnetr/tests/figs/plot-preferences/plot-prefs-dots-a-ses.svg | 156 - econullnetr-0.2.0/econullnetr/tests/figs/plot-preferences/plot-prefs-dots-b-0-95.svg | 102 econullnetr-0.2.0/econullnetr/tests/figs/plot-preferences/plot-prefs-dots-b-ses.svg | 152 - econullnetr-0.2.0/econullnetr/tests/testthat.R | 2 econullnetr-0.2.0/econullnetr/tests/testthat/test_bipartite_stats.R | 115 econullnetr-0.2.0/econullnetr/tests/testthat/test_expand_matrix.R |only econullnetr-0.2.0/econullnetr/tests/testthat/test_test_interactions.R | 2 econullnetr-0.2.0/econullnetr/vignettes/econullnetr-intro.Rmd | 189 - 76 files changed, 3261 insertions(+), 3494 deletions(-)
Title: Exploratory Data Analysis System
Description: Performs an exploratory data analysis through a 'shiny' interface. It includes basic methods such as the mean, median, mode, normality test, among others. It also includes clustering techniques such as Principal Components Analysis, Hierarchical Clustering and the K-Means Method.
Author: Oldemar Rodriguez R. with contributions from Diego Jimenez A. and Andres Navarro D.
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between discoveR versions 1.1.0 dated 2019-03-03 and 1.2.4 dated 2020-01-13
DESCRIPTION | 6 - MD5 | 12 +- inst/application/global.R | 145 +++++++++++++++++++++++++---------- inst/application/server.R | 54 ++++++++----- inst/application/ui.R | 32 +++++-- inst/application/www/diccionario.csv | 1 inst/application/www/translation.bin |binary 7 files changed, 173 insertions(+), 77 deletions(-)
Title: Tools: moving window statistics, GIF, Base64, ROC AUC, etc
Description: Contains several basic utility functions including: moving
(rolling, running) window statistic functions, read/write for
GIF and ENVI binary files, fast calculation of AUC, LogitBoost
classifier, base64 encoder/decoder, round-off-error-free sum
and cumsum, etc.
Author: Jarek Tuszynski <jaroslaw.w.tuszynski@saic.com>
Maintainer: ORPHANED
Diff between caTools versions 1.17.1.3 dated 2019-11-30 and 1.17.1.4 dated 2020-01-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- man/caTools-package.Rd | 1 + 3 files changed, 6 insertions(+), 5 deletions(-)
Title: Rarefaction Tool Kit
Description: Rarefy data, calculate diversity and plot the results.
Author: Paul Saary, Falk Hildebrand
Maintainer: Paul Saary <rtk@paulsaary.de>
Diff between rtk versions 0.2.5.7 dated 2018-12-08 and 0.2.5.8 dated 2020-01-13
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + R/collectorscurve.R | 12 ++++++------ R/rarefaction.R | 16 ++++++++-------- R/rarefaction.plots.R | 9 ++++----- build/partial.rdb |binary man/plot.rarefaction.Rd | 2 +- src/ClStr2Mat.cpp | 8 ++++---- src/Matrix.cpp | 2 +- src/RRare.cpp | 2 +- src/Rwrapper.cpp | 2 +- 12 files changed, 43 insertions(+), 43 deletions(-)
Title: Common Public Health Statistics and their Confidence Intervals
Description: Functions to calculate commonly used public health statistics and
their confidence intervals using methods approved for use in the production
of Public Health England indicators such as those presented via Fingertips
(<http://fingertips.phe.org.uk/>). It provides functions for the generation
of proportions, crude rates, means, directly standardised rates, indirectly
standardised rates, standardised mortality ratios, slope and relative index
of inequality and life expectancy.
Statistical methods are referenced in the following publications.
Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>.
Dobson et al (1991) <doi:10.1002/sim.4780100317>.
Armitage P, Berry G (2002) <doi:10.1002/9780470773666>.
Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>.
Altman DG et al (2000, ISBN: 978-0-727-91375-3).
Chiang CL. (1968, ISBN: 978-0-882-75200-6).
Newell C. (1994, ISBN: 978-0-898-62451-9).
Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>.
Silcocks PBS et al (2001) <doi:10.1136/jech.55.1.38>.
Low and Low (2004) <doi:10.1093/pubmed/fdh175>.
Author: Anderson Georgina [aut, cre],
Fox Sebastian [ctb],
Francis Matthew [ctb],
Fryers Paul [ctb],
Clegg Emma [ctb]
Maintainer: Anderson Georgina <georgina.anderson@phe.gov.uk>
Diff between PHEindicatormethods versions 1.1.5 dated 2019-09-11 and 1.2.0 dated 2020-01-13
DESCRIPTION | 10 MD5 | 116 +-- NAMESPACE | 3 NEWS.md | 17 R/DSR.R | 191 +++-- R/ISR.R | 145 ++-- R/LifeExpectancy.R | 61 + R/Means.R | 133 ++-- R/PHEindicatormethods.R | 7 R/Proportions.R | 128 ++- R/Quantiles.R | 97 +- R/Rates.R | 136 ++-- R/SII_function.R | 57 + R/SMR.R | 128 ++- R/sysdata.rda |binary R/utils.R | 16 build/vignette.rds |binary data/DSR_data.rda |binary data/LE_data.rda |binary data/esp2013.rda |binary data/prevalence_data.rda |binary inst/doc/DSR-vignette.R | 2 inst/doc/DSR-vignette.html | 141 ++-- inst/doc/Introduction_to_PHEindicatormethods.R | 2 inst/doc/Introduction_to_PHEindicatormethods.html | 728 ++++++++++------------ inst/doc/WorkedExamples_phe_sii.R | 10 inst/doc/WorkedExamples_phe_sii.html | 163 ++-- man/DSR_data.Rd | 34 - man/FindXValues.Rd | 34 - man/LE_data.Rd | 34 - man/PHEindicatormethods.Rd | 21 man/SimulationFunc.Rd | 109 +-- man/byars_lower.Rd | 75 +- man/byars_upper.Rd | 71 +- man/esp2013.Rd | 70 +- man/na.zero.Rd | 26 man/phe_dsr.Rd | 183 +++-- man/phe_isr.Rd | 199 +++--- man/phe_life_expectancy.Rd | 320 +++++---- man/phe_mean.Rd | 108 +-- man/phe_proportion.Rd | 152 ++-- man/phe_quantile.Rd | 160 ++-- man/phe_rate.Rd | 142 ++-- man/phe_sii.Rd | 313 ++++----- man/phe_smr.Rd | 194 +++-- man/prevalence_data.Rd | 34 - man/wilson_lower.Rd | 77 +- man/wilson_upper.Rd | 77 +- tests/testthat/testDSRs.R | 69 +- tests/testthat/testISRs.R | 66 + tests/testthat/testMeans.R | 57 + tests/testthat/testProportions.R | 88 ++ tests/testthat/testQuantiles.R | 30 tests/testthat/testRates.R | 91 ++ tests/testthat/testSMRs.R | 86 ++ tests/testthat/testdata_DSR_ISR_SMR.xlsx |binary tests/testthat/testdata_Mean.xlsx |binary tests/testthat/testdata_Proportion.xlsx |binary tests/testthat/testdata_Rate.xlsx |binary 59 files changed, 2990 insertions(+), 2221 deletions(-)
More information about PHEindicatormethods at CRAN
Permanent link
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph] (<https://orcid.org/0000-0002-6269-1412>),
Nicolas Müller [aut],
Reto Bürgin [aut],
Pierre-Alexandre Fonta [aut],
Gilbert Ritschard [aut, cre, cph]
(<https://orcid.org/0000-0001-7776-0903>)
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 2.0-13 dated 2019-11-19 and 2.0-14 dated 2020-01-13
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS | 18 ++++++++++++------ R/stslist.freq-methods.R | 4 ++-- build/vignette.rds |binary data/ex1.rda |binary data/ex2.rda |binary data/famform.rda |binary inst/NEWS.Rd | 12 +++++++++++- inst/doc/TraMineR-state-sequence.pdf |binary man/TraMineR-package.Rd | 2 +- man/seqtab.Rd | 1 + 12 files changed, 42 insertions(+), 25 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft Sql Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', and 'SQLite'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.6.2 dated 2019-06-24 and 1.6.3 dated 2020-01-13
DESCRIPTION | 10 +- MD5 | 60 ++++++++-------- NAMESPACE | 2 NEWS.md | 25 ++++++ build/vignette.rds |binary inst/csv/replacementPatterns.csv | 29 +++++--- inst/doc/UsingSqlRender.pdf |binary inst/java/SqlRender.jar |binary java/org/ohdsi/sql/BigQueryTranslate.java | 21 ++++- java/org/ohdsi/sql/SqlRender.java | 16 ++++ java/org/ohdsi/sql/SqlTranslate.java | 7 + java/org/ohdsi/sql/StringUtils.java | 81 ++++++++++++++++++++++ man/SqlRender.Rd | 17 ++-- man/camelCaseToSnakeCase.Rd | 42 +++++------ man/createRWrapperForSql.Rd | 76 +++++++++++---------- man/launchSqlRenderDeveloper.Rd | 36 +++++----- man/loadRenderTranslateSql.Rd | 98 ++++++++++++++------------- man/readSql.Rd | 48 ++++++------- man/render.Rd | 98 +++++++++++++-------------- man/renderSql.Rd | 48 ++++++------- man/renderSqlFile.Rd | 71 +++++++++---------- man/snakeCaseToCamelCase.Rd | 42 +++++------ man/splitSql.Rd | 50 ++++++------- man/translate.Rd | 64 ++++++++--------- man/translateSingleStatement.Rd | 65 ++++++++---------- man/translateSql.Rd | 48 ++++++------- man/translateSqlFile.Rd | 68 ++++++++++-------- man/writeSql.Rd | 48 ++++++------- tests/testthat/test-renderSql.R | 5 + tests/testthat/test-translate-sqlite.R | 21 ++++- tests/testthat/test-translateSql.R | 108 +++++++++++++++++++++++++----- 31 files changed, 776 insertions(+), 528 deletions(-)
Title: Spatial Coverage Sampling and Random Sampling from Compact
Geographical Strata
Description: Spatial coverage sampling and random sampling from compact
geographical strata created by k-means. See Walvoort et al. (2010)
<doi:10.1016/j.cageo.2010.04.005> for details.
Author: Dennis Walvoort [aut, cre, cph],
Dick Brus [aut, cph],
Jaap de Gruijter [aut, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between spcosa versions 0.3-8 dated 2018-03-30 and 0.3-9 dated 2020-01-13
DESCRIPTION | 11 MD5 | 17 R/method_stratify-SpatialPixels.R | 2 R/onLoad.R | 5 README.md |only build/spcosa.pdf |binary build/vignette.rds |binary inst/NEWS.Rd | 326 - inst/doc/spcosa.R | 814 +-- inst/doc/spcosa.html |10073 +++++++++++++++++++------------------- 10 files changed, 5652 insertions(+), 5596 deletions(-)
Title: Interactive Studio with Explanations for ML Predictive Models
Description: Automate explanation of machine learning predictive models.
This package generates advanced interactive and animated model explanations in the form
of a serverless HTML site. It combines 'R' with 'D3.js' to produce plots and descriptions
for various local and global explanations. Tools for model exploration unite with
tools for EDA (Exploratory Data Analysis) to give a broad overview of the model behaviour.
'modelStudio' is a fast and condensed way to get all the answers without much effort.
Break down your model and look into its ingredients with only a few lines of code.
Author: Hubert Baniecki [aut, cre] (<https://orcid.org/0000-0001-6661-5364>),
Przemyslaw Biecek [aut] (<https://orcid.org/0000-0001-8423-1823>)
Maintainer: Hubert Baniecki <hbaniecki@gmail.com>
Diff between modelStudio versions 0.1.9 dated 2019-11-03 and 0.2.0 dated 2020-01-13
DESCRIPTION | 15 MD5 | 39 +- NAMESPACE | 3 NEWS.md | 21 + R/modelStudio.R | 166 ++++++-- R/modelStudioOptions.R | 27 + R/prepare.R | 284 +++++++++++++- inst/CITATION |only inst/WORDLIST |only inst/d3js/generatePlots.js | 587 ++++++++++++++++++++++++++++--- inst/d3js/generateTooltipHtml.js | 6 inst/d3js/modelStudio.js | 50 ++ inst/doc/vignette_modelStudio.Rmd | 2 inst/doc/vignette_modelStudio.html | 12 man/figures/logo.png |binary man/modelStudio.Rd | 274 ++++++++------ man/modelStudioOptions.Rd | 170 ++++---- tests/spelling.R |only tests/testthat/test_modelStudio.R | 49 +- tests/testthat/test_modelStudioOptions.R | 2 tests/testthat/test_objects.R | 24 - vignettes/vignette_modelStudio.Rmd | 2 22 files changed, 1328 insertions(+), 405 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-13 1.0.0
Title: Extract Text from Rich Text Format (RTF) Documents
Description: Wraps the 'unrtf' utility to extract text from RTF files. Supports
document conversion to HTML, LaTeX or plain text. Output in HTML is recommended
because 'unrtf' has limited support for converting between character encodings.
Author: Jeroen Ooms [aut, cre],
Free Software Foundation, Inc [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between unrtf versions 1.3 dated 2018-11-08 and 1.4 dated 2020-01-13
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NEWS | 3 +++ src/libunrtf/my_iconv.c | 10 ++++++++-- 4 files changed, 20 insertions(+), 10 deletions(-)
Title: Multistage Allocation
Description: Multivariate optimal allocation for different domains in one and two stages stratified sample design. R2BEAT extends the Neyman (1934) <doi:10.2307/2342192> – Tschuprow (1923) allocation method to the case of several variables, adopting a generalization of the Bethel’s proposal (1989). R2BEAT develops this methodology but, moreover, it allows to determine the sample allocation in the multivariate and multi-domains case of estimates for two-stage stratified samples.
Author: Stefano Falorsi <stfalors@istat.it>, Andrea Fasulo <fasulo@istat.it>, Alessio Guandalini <alessio.guandalini@istat.it>, Daniela Pagliuca <pagliuca@istat.it>, Marco Dionisio Terribili <terribili@istat.it>
Maintainer: Andrea Fasulo <fasulo@istat.it>
Diff between R2BEAT versions 1.0.0 dated 2019-07-18 and 1.0.1 dated 2020-01-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- data/beat.example.rda |binary man/beth2.Rd | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Highly Optimized Protocol Buffer Serializers
Description: Pure C++ implementations for reading and writing several common data
formats based on Google protocol-buffers. Currently supports 'rexp.proto' for
serialized R objects, 'geobuf.proto' for binary geojson, and 'mvt.proto' for
vector tiles. This package uses the auto-generated C++ code by protobuf-compiler,
hence the entire serialization is optimized at compile time. The 'RProtoBuf'
package on the other hand uses the protobuf runtime library to provide a general-
purpose toolkit for reading and writing arbitrary protocol-buffer data in R.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between protolite versions 2.0 dated 2019-10-10 and 2.1 dated 2020-01-13
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 14 +++++++------- NEWS | 4 ++++ cleanup | 2 +- configure | 14 +++++++++----- src/geobuf.cpp | 4 ++++ src/serialize.cpp | 4 ++++ 8 files changed, 33 insertions(+), 17 deletions(-)
Title: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility
Description: The goal of checkpoint is to solve the problem of package
reproducibility in R. Specifically, checkpoint allows you to install packages
as they existed on CRAN on a specific snapshot date as if you had a CRAN time
machine. To achieve reproducibility, the checkpoint() function installs the
packages required or called by your project and scripts to a local library
exactly as they existed at the specified point in time. Only those packages
are available to your project, thereby avoiding any package updates that came
later and may have altered your results. In this way, anyone using checkpoint's
checkpoint() can ensure the reproducibility of your scripts or projects at any
time. To create the snapshot archives, once a day (at midnight UTC) Microsoft
refreshes the Austria CRAN mirror on the "Microsoft R Archived Network"
server (<https://mran.microsoft.com/>). Immediately after completion
of the rsync mirror process, the process takes a snapshot, thus creating the
archive. Snapshot archives exist starting from 2014-09-17.
Author: Hong Ooi [aut, cre],
Andrie de Vries [aut],
Microsoft [aut, cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between checkpoint versions 0.4.7 dated 2019-09-08 and 0.4.8 dated 2020-01-13
DESCRIPTION | 12 +- MD5 | 20 ++-- NEWS.md | 6 + R/checkpoint.R | 7 + inst/doc/checkpoint.R | 16 +-- inst/doc/checkpoint.Rmd | 4 inst/doc/checkpoint.html | 120 +++++++++++++------------ inst/doc/managing-checkpoint-archives.R | 26 ++--- inst/doc/managing-checkpoint-archives.html | 134 ++++++++++++++--------------- man/checkpoint.Rd | 4 vignettes/checkpoint.Rmd | 4 11 files changed, 185 insertions(+), 168 deletions(-)
Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brüggemann [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.11 dated 2019-11-12 and 0.12 dated 2020-01-13
DESCRIPTION | 8 +- MD5 | 37 +++++---- NAMESPACE | 1 NEWS.md | 4 + R/command.R | 2 R/io.R | 4 - R/revcheck.R | 4 - R/string.R | 20 +++++ README.md | 2 build/vignette.rds |binary inst/doc/xfun.Rmd | 2 inst/doc/xfun.html | 168 ++++++++++++++++++++++++--------------------- man/pkg_attach.Rd | 6 + man/raw_string.Rd | 2 man/rename_seq.Rd | 9 +- man/rev_check.Rd | 11 ++ man/split_lines.Rd |only man/upload_ftp.Rd | 7 + tests/testit/test-string.R | 12 +++ vignettes/xfun.Rmd | 2 20 files changed, 187 insertions(+), 114 deletions(-)
Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires
the detection of trends and change-points.
This package includes tests for trend detection
(Cox-Stuart Trend Test, Mann-Kendall Trend Test,
(correlated) Hirsch-Slack Test,
partial Mann-Kendall Trend Test, multivariate (multisite)
Mann-Kendall Trend Test, (Seasonal) Sen's slope,
partial Pearson and Spearman correlation trend test),
change-point detection (Lanzante's test procedures,
Pettitt's test, Buishand Range Test,
Buishand U Test, Standard Normal Homogeinity Test),
detection of non-randomness (Wallis-Moore Phase Frequency Test,
Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test)
and the two sample Robust Rank-Order Distributional Test.
Author: Thorsten Pohlert [aut, cre] (<https://orcid.org/0000-0003-3855-3025>)
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between trend versions 1.1.1 dated 2018-07-30 and 1.1.2 dated 2020-01-13
trend-1.1.1/trend/src/Makevars |only trend-1.1.1/trend/src/trend.h |only trend-1.1.2/trend/DESCRIPTION | 18 ++++++----- trend-1.1.2/trend/MD5 | 24 ++++++-------- trend-1.1.2/trend/R/mult.mk.test.R | 2 - trend-1.1.2/trend/R/summary.smk.test.R | 1 trend-1.1.2/trend/build/vignette.rds |binary trend-1.1.2/trend/inst/NEWS.Rd | 8 ++++ trend-1.1.2/trend/inst/doc/trend.pdf |binary trend-1.1.2/trend/man/bartels.test.Rd | 4 -- trend-1.1.2/trend/man/mk.test.Rd | 3 - trend-1.1.2/trend/man/rrod.test.Rd | 3 - trend-1.1.2/trend/man/smk.test.Rd | 7 +--- trend-1.1.2/trend/src/init.c | 53 ++++++++++++--------------------- 14 files changed, 57 insertions(+), 66 deletions(-)
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are
cumulative probability distributions which are fitted to
toxicity concentrations for different species as described by
Posthuma et al. (2001) <isbn:9781566705783>.
The ssdtools package uses Maximum Likelihood to fit distributions
such as the log-normal, gamma, burr Type-III, log-logistic,
log-Gumbel, Gompertz and Weibull.
The user can provide custom distributions.
Multiple distributions can be averaged using Information Criteria.
Confidence intervals on hazard concentrations and proportions are produced by
parametric bootstrapping.
Author: Joe Thorley [aut, cre, ctr] (<https://orcid.org/0000-0002-7683-4592>),
Carl Schwarz [aut, ctr],
Angeline Tillmanns [ctb],
Ali Azizishirazi [ctb],
Rebecca Fisher [ctb],
David Fox [ctb],
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Andy Teucher [ctb],
Emilie Doussantousse [ctb],
Stephanie Hazlitt [ctb],
Nan-Hung Hsieh [ctb],
Sergio Ibarra Espinosa [ctb],
Province of British Columbia [cph]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 0.0.3 dated 2018-11-25 and 0.1.0 dated 2020-01-13
ssdtools-0.0.3/ssdtools/R/llog.R |only ssdtools-0.0.3/ssdtools/R/sys.R |only ssdtools-0.0.3/ssdtools/inst/doc/ssdtools-manual.R |only ssdtools-0.0.3/ssdtools/inst/doc/ssdtools-manual.Rmd |only ssdtools-0.0.3/ssdtools/inst/doc/ssdtools-manual.html |only ssdtools-0.0.3/ssdtools/man/autoplot.fitdistcens.Rd |only ssdtools-0.0.3/ssdtools/man/autoplot.fitdists.Rd |only ssdtools-0.0.3/ssdtools/man/autoplot.fitdistscens.Rd |only ssdtools-0.0.3/ssdtools/man/llog.Rd |only ssdtools-0.0.3/ssdtools/man/ssd_cfplot.Rd |only ssdtools-0.0.3/ssdtools/tests/testthat/test-llog.R |only ssdtools-0.0.3/ssdtools/vignettes/ssdtools-manual.Rmd |only ssdtools-0.1.0/ssdtools/DESCRIPTION | 55 - ssdtools-0.1.0/ssdtools/MD5 | 228 ++-- ssdtools-0.1.0/ssdtools/NAMESPACE | 52 - ssdtools-0.1.0/ssdtools/NEWS.md | 39 ssdtools-0.1.0/ssdtools/R/autoplot.R |only ssdtools-0.1.0/ssdtools/R/boot.R |only ssdtools-0.1.0/ssdtools/R/burrIII2.R |only ssdtools-0.1.0/ssdtools/R/burrIII3.R |only ssdtools-0.1.0/ssdtools/R/cis.R |only ssdtools-0.1.0/ssdtools/R/coef.R | 14 ssdtools-0.1.0/ssdtools/R/data.R | 4 ssdtools-0.1.0/ssdtools/R/deprecated.R |only ssdtools-0.1.0/ssdtools/R/exposure.R |only ssdtools-0.1.0/ssdtools/R/fit.R | 115 +- ssdtools-0.1.0/ssdtools/R/gamma.R |only ssdtools-0.1.0/ssdtools/R/ggplot.R |only ssdtools-0.1.0/ssdtools/R/ggproto.R |only ssdtools-0.1.0/ssdtools/R/gof.R | 76 + ssdtools-0.1.0/ssdtools/R/gompertz.R | 62 - ssdtools-0.1.0/ssdtools/R/hc.R | 212 +++- ssdtools-0.1.0/ssdtools/R/hp.R |only ssdtools-0.1.0/ssdtools/R/internal.R | 29 ssdtools-0.1.0/ssdtools/R/is.R |only ssdtools-0.1.0/ssdtools/R/lgumbel.R | 63 - ssdtools-0.1.0/ssdtools/R/llogis.R |only ssdtools-0.1.0/ssdtools/R/match-moments.R |only ssdtools-0.1.0/ssdtools/R/namespace.R | 4 ssdtools-0.1.0/ssdtools/R/nobs.R |only ssdtools-0.1.0/ssdtools/R/npars.R |only ssdtools-0.1.0/ssdtools/R/params.R |only ssdtools-0.1.0/ssdtools/R/pareto.R | 63 - ssdtools-0.1.0/ssdtools/R/plot-cdf.R |only ssdtools-0.1.0/ssdtools/R/plot-cf.R |only ssdtools-0.1.0/ssdtools/R/plot.R | 483 ---------- ssdtools-0.1.0/ssdtools/R/predict.R | 131 -- ssdtools-0.1.0/ssdtools/R/print.R |only ssdtools-0.1.0/ssdtools/R/release.R |only ssdtools-0.1.0/ssdtools/R/ssd-plot.R |only ssdtools-0.1.0/ssdtools/R/ssdtools-package.R | 14 ssdtools-0.1.0/ssdtools/R/subset.R | 30 ssdtools-0.1.0/ssdtools/R/utils.R | 132 -- ssdtools-0.1.0/ssdtools/R/weibull.R |only ssdtools-0.1.0/ssdtools/R/zzz.R | 4 ssdtools-0.1.0/ssdtools/README.md | 122 +- ssdtools-0.1.0/ssdtools/build/vignette.rds |binary ssdtools-0.1.0/ssdtools/data/boron_data.rda |binary ssdtools-0.1.0/ssdtools/data/boron_dists.rda |binary ssdtools-0.1.0/ssdtools/data/boron_hc5.rda |binary ssdtools-0.1.0/ssdtools/data/boron_lnorm.rda |binary ssdtools-0.1.0/ssdtools/data/boron_pred.rda |binary ssdtools-0.1.0/ssdtools/data/ccme_data.rda |binary ssdtools-0.1.0/ssdtools/data/fluazinam_dists.rda |binary ssdtools-0.1.0/ssdtools/data/fluazinam_lnorm.rda |binary ssdtools-0.1.0/ssdtools/data/fluazinam_pred.rda |binary ssdtools-0.1.0/ssdtools/demo/ssdtools.R | 50 - ssdtools-0.1.0/ssdtools/inst/CITATION |only ssdtools-0.1.0/ssdtools/inst/doc/distributions.R |only ssdtools-0.1.0/ssdtools/inst/doc/distributions.Rmd |only ssdtools-0.1.0/ssdtools/inst/doc/distributions.html |only ssdtools-0.1.0/ssdtools/inst/doc/exposure-plots.R |only ssdtools-0.1.0/ssdtools/inst/doc/exposure-plots.Rmd |only ssdtools-0.1.0/ssdtools/inst/doc/exposure-plots.html |only ssdtools-0.1.0/ssdtools/inst/doc/faqs.R |only ssdtools-0.1.0/ssdtools/inst/doc/faqs.Rmd |only ssdtools-0.1.0/ssdtools/inst/doc/faqs.html |only ssdtools-0.1.0/ssdtools/inst/doc/small-sample-bias-ref.R |only ssdtools-0.1.0/ssdtools/inst/doc/small-sample-bias-ref.Rmd |only ssdtools-0.1.0/ssdtools/inst/doc/small-sample-bias-ref.html |only ssdtools-0.1.0/ssdtools/inst/doc/small-sample-bias.pdf |only ssdtools-0.1.0/ssdtools/inst/doc/small-sample-bias.pdf.asis |only ssdtools-0.1.0/ssdtools/inst/doc/ssdtools.R |only ssdtools-0.1.0/ssdtools/inst/doc/ssdtools.Rmd |only ssdtools-0.1.0/ssdtools/inst/doc/ssdtools.html |only ssdtools-0.1.0/ssdtools/man/autoplot.fitdist.Rd | 37 ssdtools-0.1.0/ssdtools/man/boron_dists.Rd | 2 ssdtools-0.1.0/ssdtools/man/boron_hc5.Rd | 1 ssdtools-0.1.0/ssdtools/man/boron_pred.Rd | 1 ssdtools-0.1.0/ssdtools/man/burrIII2.Rd |only ssdtools-0.1.0/ssdtools/man/burrIII3.Rd |only ssdtools-0.1.0/ssdtools/man/figures/README-unnamed-chunk-10-1.png |binary ssdtools-0.1.0/ssdtools/man/figures/README-unnamed-chunk-5-1.png |binary ssdtools-0.1.0/ssdtools/man/fluazinam_dists.Rd | 2 ssdtools-0.1.0/ssdtools/man/fluazinam_pred.Rd | 1 ssdtools-0.1.0/ssdtools/man/gamma.Rd |only ssdtools-0.1.0/ssdtools/man/geom_hcintersect.Rd | 26 ssdtools-0.1.0/ssdtools/man/geom_ssd.Rd | 30 ssdtools-0.1.0/ssdtools/man/geom_xribbon.Rd | 30 ssdtools-0.1.0/ssdtools/man/gompertz.Rd | 41 ssdtools-0.1.0/ssdtools/man/is.fitdist.Rd | 4 ssdtools-0.1.0/ssdtools/man/is.fitdistcens.Rd | 4 ssdtools-0.1.0/ssdtools/man/is.fitdists.Rd | 4 ssdtools-0.1.0/ssdtools/man/is.fitdistscens.Rd | 4 ssdtools-0.1.0/ssdtools/man/lgumbel.Rd | 40 ssdtools-0.1.0/ssdtools/man/llogis.Rd |only ssdtools-0.1.0/ssdtools/man/nobs.fitdist.Rd | 2 ssdtools-0.1.0/ssdtools/man/nobs.fitdistcens.Rd | 4 ssdtools-0.1.0/ssdtools/man/npars.Rd | 4 ssdtools-0.1.0/ssdtools/man/params.Rd |only ssdtools-0.1.0/ssdtools/man/pareto.Rd | 42 ssdtools-0.1.0/ssdtools/man/predict.fitdist.Rd | 24 ssdtools-0.1.0/ssdtools/man/predict.fitdistcens.Rd | 26 ssdtools-0.1.0/ssdtools/man/predict.fitdists.Rd | 36 ssdtools-0.1.0/ssdtools/man/predict.fitdistscens.Rd | 36 ssdtools-0.1.0/ssdtools/man/ssd_exposure.Rd |only ssdtools-0.1.0/ssdtools/man/ssd_fit_dists.Rd | 23 ssdtools-0.1.0/ssdtools/man/ssd_gof.Rd | 15 ssdtools-0.1.0/ssdtools/man/ssd_hc.Rd | 108 +- ssdtools-0.1.0/ssdtools/man/ssd_hp.Rd |only ssdtools-0.1.0/ssdtools/man/ssd_match_moments.Rd |only ssdtools-0.1.0/ssdtools/man/ssd_plot.Rd | 26 ssdtools-0.1.0/ssdtools/man/ssd_plot_cdf.Rd |only ssdtools-0.1.0/ssdtools/man/ssd_plot_cf.Rd |only ssdtools-0.1.0/ssdtools/man/ssdtools-ggproto.Rd | 2 ssdtools-0.1.0/ssdtools/man/ssdtools-package.Rd | 31 ssdtools-0.1.0/ssdtools/man/stat_ssd.Rd | 30 ssdtools-0.1.0/ssdtools/man/subset.fitdists.Rd | 6 ssdtools-0.1.0/ssdtools/man/weibull.Rd |only ssdtools-0.1.0/ssdtools/tests/testthat/test-aaa-deprecated.R |only ssdtools-0.1.0/ssdtools/tests/testthat/test-burrIII2.R |only ssdtools-0.1.0/ssdtools/tests/testthat/test-burrrIII3.R |only ssdtools-0.1.0/ssdtools/tests/testthat/test-data.R | 19 ssdtools-0.1.0/ssdtools/tests/testthat/test-exposure.R |only ssdtools-0.1.0/ssdtools/tests/testthat/test-fit.R | 77 + ssdtools-0.1.0/ssdtools/tests/testthat/test-gof.R | 25 ssdtools-0.1.0/ssdtools/tests/testthat/test-gompertz.R |only ssdtools-0.1.0/ssdtools/tests/testthat/test-hc.R | 177 +++ ssdtools-0.1.0/ssdtools/tests/testthat/test-hp.R |only ssdtools-0.1.0/ssdtools/tests/testthat/test-lgumbel.R | 68 + ssdtools-0.1.0/ssdtools/tests/testthat/test-llogis.R |only ssdtools-0.1.0/ssdtools/tests/testthat/test-match-moments.R |only ssdtools-0.1.0/ssdtools/tests/testthat/test-pareto.R |only ssdtools-0.1.0/ssdtools/tests/testthat/test-plot.R | 74 + ssdtools-0.1.0/ssdtools/tests/testthat/test-predict.R | 81 + ssdtools-0.1.0/ssdtools/tests/testthat/test-schwarz-tillmans.R |only ssdtools-0.1.0/ssdtools/tests/testthat/test-subset.R | 2 ssdtools-0.1.0/ssdtools/tests/testthat/test-utils.R | 18 ssdtools-0.1.0/ssdtools/vignettes/distributions.Rmd |only ssdtools-0.1.0/ssdtools/vignettes/exposure-plots.Rmd |only ssdtools-0.1.0/ssdtools/vignettes/faqs.Rmd |only ssdtools-0.1.0/ssdtools/vignettes/references.bib | 18 ssdtools-0.1.0/ssdtools/vignettes/small-sample-bias-ref.Rmd |only ssdtools-0.1.0/ssdtools/vignettes/small-sample-bias.pdf.asis |only ssdtools-0.1.0/ssdtools/vignettes/ssdtools.Rmd |only 155 files changed, 1795 insertions(+), 1388 deletions(-)
Title: Gamma and Exponential Generalized Linear Models with Elastic Net
Penalty
Description: Implements the fast iterative shrinkage-thresholding algorithm
(FISTA) algorithm to fit a Gamma distribution with an elastic net
penalty as described in Chen, Arakvin and Martin (2018)
<arxiv:1804.07780>. An implementation for the case of the
exponential distribution is also available, with details available
in Chen and Martin (2018) <https://papers.ssrn.com/abstract_id=3085672>.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Xin Chen <chenx26@uw.edu>,
Daniel Hanson <hansondj@uw.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPEGLMEN versions 1.0 dated 2019-09-07 and 1.0.1 dated 2020-01-13
RPEGLMEN-1.0.1/RPEGLMEN/DESCRIPTION | 10 RPEGLMEN-1.0.1/RPEGLMEN/MD5 | 24 - RPEGLMEN-1.0.1/RPEGLMEN/NAMESPACE | 9 RPEGLMEN-1.0.1/RPEGLMEN/NEWS.md |only RPEGLMEN-1.0.1/RPEGLMEN/R/glmGammaNet.R | 11 RPEGLMEN-1.0.1/RPEGLMEN/R/glmnet_exp.R | 8 RPEGLMEN-1.0.1/RPEGLMEN/build/vignette.rds |binary RPEGLMEN-1.0.1/RPEGLMEN/cleanup | 2 RPEGLMEN-1.0.1/RPEGLMEN/configure.ac | 19 RPEGLMEN-1.0.1/RPEGLMEN/inst/doc/RPEGLMENVignette.pdf.asis | 2 RPEGLMEN-1.0.1/RPEGLMEN/man/fit.glmGammaNet.Rd | 232 ++++++------ RPEGLMEN-1.0.1/RPEGLMEN/man/glmnet_exp.Rd | 221 ++++++----- RPEGLMEN-1.0.1/RPEGLMEN/vignettes/RPEGLMENVignette.pdf.asis | 2 RPEGLMEN-1.0/RPEGLMEN/NEWS |only 14 files changed, 290 insertions(+), 250 deletions(-)
Title: Quickly View Data Frames in 'Excel', Build Folder Paths and
Create Date Vectors
Description: Contains several useful navigation helper functions, including easily building
folder paths, quick viewing dataframes in 'Excel', creating date vectors and changing the
console prompt to reflect time.
Author: Nico Katzke [aut, cre]
Maintainer: Nico Katzke <nfkatzke@gmail.com>
Diff between rmsfuns versions 0.0.0.2 dated 2017-10-16 and 0.0.0.3 dated 2020-01-13
rmsfuns-0.0.0.2/rmsfuns/README.md |only rmsfuns-0.0.0.3/rmsfuns/DESCRIPTION | 17 - rmsfuns-0.0.0.3/rmsfuns/MD5 | 21 - rmsfuns-0.0.0.3/rmsfuns/NAMESPACE | 6 rmsfuns-0.0.0.3/rmsfuns/R/Safe_Return.portfolio.R |only rmsfuns-0.0.0.3/rmsfuns/R/ViewXL.R | 4 rmsfuns-0.0.0.3/rmsfuns/R/load_pkg.R | 1 rmsfuns-0.0.0.3/rmsfuns/build/vignette.rds |binary rmsfuns-0.0.0.3/rmsfuns/inst/doc/rmsfuns.Rmd | 27 ++ rmsfuns-0.0.0.3/rmsfuns/inst/doc/rmsfuns.html | 222 ++++++++++++++++++- rmsfuns-0.0.0.3/rmsfuns/man/Safe_Return.portfolio.Rd |only rmsfuns-0.0.0.3/rmsfuns/man/ViewXL.Rd | 2 rmsfuns-0.0.0.3/rmsfuns/vignettes/rmsfuns.Rmd | 27 ++ 13 files changed, 301 insertions(+), 26 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.0-3 dated 2019-06-23 and 1.0-4 dated 2020-01-13
mlt.docreg-1.0-3/mlt.docreg/tests/GBSG2.Rout.save |only mlt.docreg-1.0-4/mlt.docreg/DESCRIPTION | 8 mlt.docreg-1.0-4/mlt.docreg/MD5 | 31 - mlt.docreg-1.0-4/mlt.docreg/build/vignette.rds |binary mlt.docreg-1.0-4/mlt.docreg/inst/NEWS.Rd | 6 mlt.docreg-1.0-4/mlt.docreg/inst/doc/mlt.R | 271 ++++++------ mlt.docreg-1.0-4/mlt.docreg/inst/doc/mlt.Rnw | 312 +++++++------- mlt.docreg-1.0-4/mlt.docreg/inst/doc/mlt.pdf |binary mlt.docreg-1.0-4/mlt.docreg/tests/GBSG2.R | 1 mlt.docreg-1.0-4/mlt.docreg/tests/faithful.R | 1 mlt.docreg-1.0-4/mlt.docreg/tests/faithful.Rout.save | 45 +- mlt.docreg-1.0-4/mlt.docreg/tests/timedep_covar.R | 4 mlt.docreg-1.0-4/mlt.docreg/tests/timedep_covar.Rout.save | 14 mlt.docreg-1.0-4/mlt.docreg/tests/udist-Ex.R | 2 mlt.docreg-1.0-4/mlt.docreg/tests/udist-Ex.Rout.save | 10 mlt.docreg-1.0-4/mlt.docreg/vignettes/mlt.Rnw | 312 +++++++------- mlt.docreg-1.0-4/mlt.docreg/vignettes/mlt.bib | 251 +++++++++-- 17 files changed, 768 insertions(+), 500 deletions(-)
Title: Generalized Berk-Jones Test for Set-Based Inference in Genetic
Association Studies
Description: Offers the Generalized Berk-Jones (GBJ) test for set-based inference in genetic
association studies. The GBJ is designed as an alternative to tests such as Berk-Jones (BJ),
Higher Criticism (HC), Generalized Higher Criticism (GHC), Minimum p-value (minP), and Sequence
Kernel Association Test (SKAT). All of these other methods (except for SKAT) are also implemented
in this package, and we additionally provide an omnibus test (OMNI) which integrates information from each of the tests.
The GBJ has been shown to outperform other tests in genetic association studies when signals
are correlated and moderately sparse. Please see the vignette for a quickstart guide or the paper at
<doi:10.1080/01621459.2019.1660170> for full details.
Author: Ryan Sun [aut, cre]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
Diff between GBJ versions 0.5.2 dated 2018-06-27 and 0.5.3 dated 2020-01-13
DESCRIPTION | 14 +++---- MD5 | 64 ++++++++++++++++++------------------ R/calc_score_stats.R | 5 +- R/data.R | 4 +- R/score_stats_only.R | 4 +- build/vignette.rds |binary inst/doc/GBJ_tutorial.R | 10 ++--- inst/doc/GBJ_tutorial.Rmd | 2 - inst/doc/GBJ_tutorial.html | 59 ++++++++++++++++++++++++--------- man/BJ.Rd | 1 man/FGFR2.Rd | 1 man/GBJ.Rd | 1 man/GBJ_objective.Rd | 1 man/GBJ_pvalue.Rd | 1 man/GHC.Rd | 1 man/GHC_objective.Rd | 1 man/HC.Rd | 1 man/OMNI_individual.Rd | 1 man/OMNI_ss.Rd | 1 man/calc_score_stats.Rd | 2 - man/calc_var_nonzero_mu.Rd | 1 man/ebb_loglik.Rd | 1 man/estimate_ss_cor.Rd | 1 man/gbr_pcs.Rd | 1 man/herm_poly_diff_t.Rd | 1 man/minP.Rd | 1 man/parse_input.Rd | 1 man/qnorm_mu.Rd | 1 man/score_stats_only.Rd | 1 man/surv.Rd | 1 tests/testthat/test_omnibus.R | 8 ++-- tests/testthat/test_variance_calc.R | 2 - vignettes/GBJ_tutorial.Rmd | 2 - 33 files changed, 103 insertions(+), 93 deletions(-)
Title: Routines for Performing Empirical Calibration of Observational
Study Estimates
Description: Routines for performing empirical calibration of observational
study estimates. By using a set of negative control hypotheses we can
estimate the empirical null distribution of a particular observational
study setup. This empirical null distribution can be used to compute a
calibrated p-value, which reflects the probability of observing an
estimated effect size when the null hypothesis is true taking both random
and systematic error into account. A similar approach can be used to
calibrate confidence intervals, using both negative and positive controls.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between EmpiricalCalibration versions 2.0.0 dated 2019-07-08 and 2.0.1 dated 2020-01-13
DESCRIPTION | 10 +- MD5 | 82 +++++++++---------- NAMESPACE | 2 NEWS.md | 11 ++ R/ConfidenceIntervalCalibration.R | 12 +- R/Data.R | 2 R/EmpiricalCalibration.R | 2 R/EmpiricalCalibrationUsingAsymptotics.R | 2 R/EmpiricalCalibrationUsingMcmc.R | 2 R/EmpiricalCalibrationUsingPLikelihood.R | 2 R/Evaluation.R | 2 R/Plots.R | 2 R/Simulation.R | 2 build/vignette.rds |binary inst/doc/EmpiricalCiCalibrationVignette.pdf |binary inst/doc/EmpiricalPCalibrationVignette.pdf |binary man/EmpiricalCalibration.Rd | 1 man/calibrateConfidenceInterval.Rd | 76 +++++++++--------- man/calibrateP.Rd | 118 ++++++++++++++-------------- man/caseControl.Rd | 70 ++++++++-------- man/cohortMethod.Rd | 86 ++++++++++---------- man/computeTraditionalCi.Rd | 62 +++++++------- man/computeTraditionalP.Rd | 56 ++++++------- man/convertNullToErrorModel.Rd | 86 ++++++++++---------- man/evaluateCiCalibration.Rd | 9 +- man/fitMcmcNull.Rd | 80 +++++++++--------- man/fitNull.Rd | 72 ++++++++--------- man/fitSystematicErrorModel.Rd | 9 +- man/grahamReplication.Rd | 90 ++++++++++----------- man/plotCalibration.Rd | 10 +- man/plotCalibrationEffect.Rd | 16 ++- man/plotCiCalibration.Rd | 14 ++- man/plotCiCalibrationEffect.Rd | 12 ++ man/plotCiCoverage.Rd | 15 ++- man/plotErrorModel.Rd | 10 +- man/plotExpectedType1Error.Rd | 15 ++- man/plotForest.Rd | 10 +- man/plotMcmcTrace.Rd | 58 ++++++------- man/plotTrueAndObserved.Rd | 10 +- man/sccs.Rd | 72 ++++++++--------- man/simulateControls.Rd | 9 +- man/southworthReplication.Rd | 76 +++++++++--------- 42 files changed, 683 insertions(+), 592 deletions(-)
More information about EmpiricalCalibration at CRAN
Permanent link
Title: Analysis of Dramatic Texts
Description: Analysis of preprocessed dramatic texts, with respect to literary research.
The package provides functions to analyze and visualize information about characters,
stage directions, the dramatic structure and the text itself.
The dramatic texts are expected to be in CSV format, which can be installed from within
the package, sample texts are provided. The package and the reasoning behind it are described in
Reiter et al. (2017) <doi:10.18420/in2017_119>.
Author: Nils Reiter <nils.reiter@ims.uni-stuttgart.de>
Maintainer: Nils Reiter <nils.reiter@ims.uni-stuttgart.de>
Diff between DramaAnalysis versions 3.0.0 dated 2019-07-10 and 3.0.1 dated 2020-01-13
DESCRIPTION | 15 ++- MD5 | 85 +++++++++++----------- NAMESPACE | 5 + NEWS.md | 14 +++ R/data.R | 2 R/figures.R | 2 R/load.R | 8 +- R/loadTEI.R | 123 +++++++++++++++++++++++++------- R/personnelExchange.R | 9 +- R/plots.R | 62 ++++++++++++++++ R/presence.R | 27 +++++-- R/text.R | 2 R/utteranceStatistics.R | 2 README.md | 1 man/barplot.QDCharacterStatistics.Rd | 11 ++ man/characterStatistics.Rd | 8 +- man/configuration.Rd | 8 +- man/correlationAnalysis.Rd | 3 man/data.Rd | 2 man/dictionaryHandling.Rd | 10 +- man/dictionaryStatistics.Rd | 31 +++++--- man/dramaNames.Rd | 3 man/filterCharacters.Rd | 8 +- man/frequencyTable.Rd | 20 +++-- man/frequencytable2.Rd | 11 ++ man/installCollectionData.Rd | 9 +- man/installData.Rd | 12 ++- man/isolateCharacterSpeech.Rd | 13 ++- man/keyness.Rd | 11 ++ man/loadAllInstalledIds.Rd | 6 + man/loadCharacters.Rd | 7 + man/loadDramaTEI.Rd | 12 ++- man/loadText.Rd | 9 +- man/newCollection.Rd | 12 ++- man/personnelExchange.Rd | 7 - man/plot.QDHamming.Rd |only man/plot.QDUtteranceStatistics.Rd | 3 man/plotSpiderWebs.Rd | 16 +++- man/report.Rd | 9 +- man/setup.Rd | 22 +++-- man/utteranceStatistics.Rd | 2 tests/testthat/example_tei.xml |only tests/testthat/test-loadDramaTEI.R |only tests/testthat/test-personnelExchange.R | 6 + tests/testthat/test-presence.R | 10 +- 45 files changed, 458 insertions(+), 180 deletions(-)
Title: Optimal Design Emulators via Point Processes
Description: Implements the Determinantal point process (DPP) based optimal design
emulator described in Pratola, Lin and Craigmile (2018) <arXiv:1804.02089> for
Gaussian process regression models. See <http://www.matthewpratola.com/software>
for more information and examples.
Author: Matthew T. Pratola <mpratola@stat.osu.edu> [aut, cre, cph]
Maintainer: Matthew T. Pratola <mpratola@stat.osu.edu>
Diff between demu versions 0.2.0 dated 2018-07-28 and 0.3.0 dated 2020-01-13
DESCRIPTION | 8 ++-- MD5 | 23 ++++++----- NAMESPACE | 2 - R/simdpp.r | 70 ++++++++++++++++++++++++++---------- build/partial.rdb |binary man/demu-package.Rd | 2 - man/sim.dpp.modal.fast.seq.Rd |only man/sim.dpp.modal.np.Rd | 2 - man/sim.dpp.modal.nystrom.Rd | 7 ++- man/sim.dpp.modal.nystrom.kmeans.Rd | 13 +++--- src/Makevars | 3 + src/Makevars.win | 3 + src/dpparmadillo.cpp | 37 +++++++++++++------ 13 files changed, 113 insertions(+), 57 deletions(-)
Title: Casualty Actuarial Society Individual Claim Simulator
Description: It is an open source insurance claim simulation engine sponsored
by the Casualty Actuarial Society. It generates individual insurance claims
including open claims, reopened claims, incurred but not reported claims
and future claims. It also includes claim data fitting functions to help set
simulation assumptions. It is useful for claim level reserving analysis.
Parodi (2013) <https://www.actuaries.org.uk/documents/triangle-free-reserving-non-traditional-framework-estimating-reserves-and-reserve-uncertainty>.
Author: Robert Bear [aut],
Kailan Shang [aut, cre],
Hai You [aut],
Brian Fannin [ctb]
Maintainer: Kailan Shang <klshang81@gmail.com>
Diff between cascsim versions 0.3 dated 2019-06-04 and 0.4 dated 2020-01-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/Common.R | 8 ++++---- build/vignette.rds |binary inst/doc/cascsim.Rmd | 2 +- vignettes/cascsim.Rmd | 2 +- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: C5.0 Decision Trees and Rule-Based Models
Description: C5.0 decision trees and rule-based models for pattern recognition that extend the work of Quinlan (1993, ISBN:1-55860-238-0).
Author: Max Kuhn [aut, cre],
Steve Weston [ctb],
Mark Culp [ctb],
Nathan Coulter [ctb],
Ross Quinlan [aut] (Author of imported C code),
RuleQuest Research [cph] (Copyright holder of imported C code),
Rulequest Research Pty Ltd. [cph] (Copyright holder of imported C code)
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between C50 versions 0.1.2 dated 2018-05-22 and 0.1.3 dated 2020-01-13
C50-0.1.2/C50/R/churn.R |only C50-0.1.2/C50/data |only C50-0.1.2/C50/man/churn.Rd |only C50-0.1.3/C50/DESCRIPTION | 13 C50-0.1.3/C50/MD5 | 42 +- C50-0.1.3/C50/NEWS.md |only C50-0.1.3/C50/R/C5.0.R | 195 ++++++------ C50-0.1.3/C50/R/as.party.C5.0.R | 17 - C50-0.1.3/C50/R/predict.C5.0.R | 57 +-- C50-0.1.3/C50/build/vignette.rds |binary C50-0.1.3/C50/inst/doc/C5.0.R | 24 - C50-0.1.3/C50/inst/doc/C5.0.Rmd | 8 C50-0.1.3/C50/inst/doc/C5.0.html | 305 +++++++++++--------- C50-0.1.3/C50/inst/doc/Class_Probability_Calcs.R | 6 C50-0.1.3/C50/inst/doc/Class_Probability_Calcs.html | 150 ++++++--- C50-0.1.3/C50/man/C5.0.Rd | 23 - C50-0.1.3/C50/man/C5.0Control.Rd | 25 + C50-0.1.3/C50/man/C5imp.Rd | 5 C50-0.1.3/C50/man/predict.C5.0.Rd | 20 - C50-0.1.3/C50/man/summary.C5.0.Rd | 5 C50-0.1.3/C50/src/extern.h | 2 C50-0.1.3/C50/src/hash.c | 2 C50-0.1.3/C50/src/rulebasedmodels.c | 16 - C50-0.1.3/C50/vignettes/C5.0.Rmd | 8 24 files changed, 526 insertions(+), 397 deletions(-)
Title: Markov Beta and Gamma Processes for Modeling Hazard Rates
Description: Computes the hazard rate estimate as described by Nieto-Barajas and Walker (2002), Nieto-Barajas (2003) and Nieto-Barajas, L. E., & Yin, G. (2008).
Author: L. E. Nieto-Barajas, J. A. Garcia Bueno and E.A. Morones Ishikawa
Maintainer: Emilio Akira Morones Ishikawa <emiliomorones@gmail.com>
Diff between BGPhazard versions 1.2.3 dated 2016-02-11 and 2.0.0 dated 2020-01-13
BGPhazard-1.2.3/BGPhazard/R/BePrC.R |only BGPhazard-1.2.3/BGPhazard/R/BePrU.R |only BGPhazard-1.2.3/BGPhazard/R/BeTao.R |only BGPhazard-1.2.3/BGPhazard/R/CGaN.R |only BGPhazard-1.2.3/BGPhazard/R/CGaPred.R |only BGPhazard-1.2.3/BGPhazard/R/CLambdaSumm.R |only BGPhazard-1.2.3/BGPhazard/R/Cftheta.R |only BGPhazard-1.2.3/BGPhazard/R/GaNM.R |only BGPhazard-1.2.3/BGPhazard/R/GaPrU.R |only BGPhazard-1.2.3/BGPhazard/R/GaTao.R |only BGPhazard-1.2.3/BGPhazard/R/GaUpdU.R |only BGPhazard-1.2.3/BGPhazard/R/PlotTheta.R |only BGPhazard-1.2.3/BGPhazard/man/BGPhazard-package.Rd |only BGPhazard-1.2.3/BGPhazard/man/BeNM.Rd |only BGPhazard-1.2.3/BGPhazard/man/BePrC.Rd |only BGPhazard-1.2.3/BGPhazard/man/BePrU.Rd |only BGPhazard-1.2.3/BGPhazard/man/BeTao.Rd |only BGPhazard-1.2.3/BGPhazard/man/BeUpdC.Rd |only BGPhazard-1.2.3/BGPhazard/man/BeUpdU.Rd |only BGPhazard-1.2.3/BGPhazard/man/CGaM.Rd |only BGPhazard-1.2.3/BGPhazard/man/CGaN.Rd |only BGPhazard-1.2.3/BGPhazard/man/CGaPred.Rd |only BGPhazard-1.2.3/BGPhazard/man/CLambdaSumm.Rd |only BGPhazard-1.2.3/BGPhazard/man/CUpdTheta.Rd |only BGPhazard-1.2.3/BGPhazard/man/Cftheta.Rd |only BGPhazard-1.2.3/BGPhazard/man/GaNM.Rd |only BGPhazard-1.2.3/BGPhazard/man/GaPrU.Rd |only BGPhazard-1.2.3/BGPhazard/man/GaTao.Rd |only BGPhazard-1.2.3/BGPhazard/man/GaUpdC.Rd |only BGPhazard-1.2.3/BGPhazard/man/GaUpdU.Rd |only BGPhazard-1.2.3/BGPhazard/man/LambdaSumm.Rd |only BGPhazard-1.2.3/BGPhazard/man/PiSumm.Rd |only BGPhazard-1.2.3/BGPhazard/man/PlotTheta.Rd |only BGPhazard-1.2.3/BGPhazard/man/UpdLambda.Rd |only BGPhazard-1.2.3/BGPhazard/man/UpdPi.Rd |only BGPhazard-1.2.3/BGPhazard/vignettes/BGPhazard-concordance.tex |only BGPhazard-1.2.3/BGPhazard/vignettes/BGPhazard.tex |only BGPhazard-2.0.0/BGPhazard/DESCRIPTION | 21 BGPhazard-2.0.0/BGPhazard/MD5 | 142 +- BGPhazard-2.0.0/BGPhazard/NAMESPACE | 41 BGPhazard-2.0.0/BGPhazard/R/BGPHazard-package.R |only BGPhazard-2.0.0/BGPhazard/R/BeMRes.R | 336 +++--- BGPhazard-2.0.0/BGPhazard/R/BeNM.R | 32 BGPhazard-2.0.0/BGPhazard/R/BePlotDiag.R | 168 ++- BGPhazard-2.0.0/BGPhazard/R/BePloth.R | 268 ++--- BGPhazard-2.0.0/BGPhazard/R/BeUpdC.R | 31 BGPhazard-2.0.0/BGPhazard/R/BeUpdU.R | 39 BGPhazard-2.0.0/BGPhazard/R/CCuLambdaSumm.R |only BGPhazard-2.0.0/BGPhazard/R/CCuMRes.R |only BGPhazard-2.0.0/BGPhazard/R/CCuPlotDiag.R |only BGPhazard-2.0.0/BGPhazard/R/CCuPloth.R |only BGPhazard-2.0.0/BGPhazard/R/CCuUpdDelta.R |only BGPhazard-2.0.0/BGPhazard/R/CCuUpdTheta.R |only BGPhazard-2.0.0/BGPhazard/R/CCuUpdZ.R |only BGPhazard-2.0.0/BGPhazard/R/CCuW.R |only BGPhazard-2.0.0/BGPhazard/R/CGaLambdaSumm.R |only BGPhazard-2.0.0/BGPhazard/R/CGaM.R | 34 BGPhazard-2.0.0/BGPhazard/R/CGaMRes.R | 496 +++++----- BGPhazard-2.0.0/BGPhazard/R/CGaPlotDiag.R | 172 ++- BGPhazard-2.0.0/BGPhazard/R/CGaPloth.R | 301 +++--- BGPhazard-2.0.0/BGPhazard/R/CUpdTheta.R | 39 BGPhazard-2.0.0/BGPhazard/R/CuLambdaSumm.R |only BGPhazard-2.0.0/BGPhazard/R/CuMRes.R |only BGPhazard-2.0.0/BGPhazard/R/CuPlotDiag.R |only BGPhazard-2.0.0/BGPhazard/R/CuPloth.R |only BGPhazard-2.0.0/BGPhazard/R/CuUpdLambda.R |only BGPhazard-2.0.0/BGPhazard/R/CuUpdZ.R |only BGPhazard-2.0.0/BGPhazard/R/GaMRes.R | 406 ++++---- BGPhazard-2.0.0/BGPhazard/R/GaPlotDiag.R | 159 ++- BGPhazard-2.0.0/BGPhazard/R/GaPloth.R | 283 ++--- BGPhazard-2.0.0/BGPhazard/R/GaUpdC.R | 39 BGPhazard-2.0.0/BGPhazard/R/LambdaSumm.R | 63 - BGPhazard-2.0.0/BGPhazard/R/NM.R |only BGPhazard-2.0.0/BGPhazard/R/PiSumm.R | 67 - BGPhazard-2.0.0/BGPhazard/R/Tao.R |only BGPhazard-2.0.0/BGPhazard/R/UpdLambda.R | 37 BGPhazard-2.0.0/BGPhazard/R/UpdPi.R | 35 BGPhazard-2.0.0/BGPhazard/R/UpdU.R |only BGPhazard-2.0.0/BGPhazard/R/cpo.R |only BGPhazard-2.0.0/BGPhazard/R/extract.R |only BGPhazard-2.0.0/BGPhazard/build/vignette.rds |binary BGPhazard-2.0.0/BGPhazard/data/BMTKleinbook.rda |only BGPhazard-2.0.0/BGPhazard/data/crm3.rda |only BGPhazard-2.0.0/BGPhazard/inst/doc/BGPhazard.R | 285 ++--- BGPhazard-2.0.0/BGPhazard/inst/doc/BGPhazard.pdf |binary BGPhazard-2.0.0/BGPhazard/man/BGPHazard.Rd |only BGPhazard-2.0.0/BGPhazard/man/BMTKLeinbook.Rd |only BGPhazard-2.0.0/BGPhazard/man/BeMRes.Rd | 163 +-- BGPhazard-2.0.0/BGPhazard/man/BePlotDiag.Rd | 109 +- BGPhazard-2.0.0/BGPhazard/man/BePloth.Rd | 138 +- BGPhazard-2.0.0/BGPhazard/man/CCuMRes.Rd |only BGPhazard-2.0.0/BGPhazard/man/CCuPlotDiag.Rd |only BGPhazard-2.0.0/BGPhazard/man/CCuPloth.Rd |only BGPhazard-2.0.0/BGPhazard/man/CGaMRes.Rd | 219 ++-- BGPhazard-2.0.0/BGPhazard/man/CGaPlotDiag.Rd | 97 + BGPhazard-2.0.0/BGPhazard/man/CGaPloth.Rd | 152 +-- BGPhazard-2.0.0/BGPhazard/man/CuMRes.Rd |only BGPhazard-2.0.0/BGPhazard/man/CuPlotDiag.Rd |only BGPhazard-2.0.0/BGPhazard/man/CuPloth.Rd |only BGPhazard-2.0.0/BGPhazard/man/GaMRes.Rd | 170 +-- BGPhazard-2.0.0/BGPhazard/man/GaPlotDiag.Rd | 108 +- BGPhazard-2.0.0/BGPhazard/man/GaPloth.Rd | 145 +- BGPhazard-2.0.0/BGPhazard/man/cpo.Rd |only BGPhazard-2.0.0/BGPhazard/man/crm3.Rd |only BGPhazard-2.0.0/BGPhazard/man/gehan.Rd | 81 - BGPhazard-2.0.0/BGPhazard/man/leukemiaFZ.Rd | 79 - BGPhazard-2.0.0/BGPhazard/man/psych.Rd | 87 - 107 files changed, 2724 insertions(+), 2318 deletions(-)
Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference
procedures aimed particularly at categorical data. Special
emphasis is given to highly extensible grid graphics. The
package was package was originally inspired by the book
"Visualizing Categorical Data" by Michael Friendly and is
now the main support package for a new book,
"Discrete Data Analysis with R" by Michael Friendly and
David Meyer (2015).
Author: David Meyer [aut, cre],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>),
Kurt Hornik [aut],
Florian Gerber [ctb],
Michael Friendly [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between vcd versions 1.4-4 dated 2017-12-06 and 1.4-5 dated 2020-01-13
DESCRIPTION | 6 ++-- MD5 | 50 ++++++++++++++++++++--------------------- R/strucplot.R | 5 +++- R/tile.R | 5 +++- build/vignette.rds |binary data/Butterfly.rda |binary data/Employment.rda |binary data/Federalist.rda |binary data/HorseKicks.rda |binary data/Hospital.rda |binary data/Lifeboats.rda |binary data/MSPatients.rda |binary data/PreSex.rda |binary data/RepVict.rda |binary data/Rochdale.rda |binary data/Saxony.rda |binary data/Suicide.rda |binary data/UKSoccer.rda |binary data/WeldonDice.rda |binary data/WomenQueue.rda |binary inst/NEWS.Rd | 7 +++++ inst/doc/residual-shadings.pdf |binary inst/doc/strucplot.pdf |binary man/agreementplot.Rd | 2 - man/shadings.Rd | 4 +-- vignettes/vcd.bib | 2 - 26 files changed, 47 insertions(+), 34 deletions(-)
Title: I/O Operations with Sparse Matrices
Description: Fast 'SVMlight' reader and writer.
'SVMlight' is most commonly used format for storing
sparse matrices (possibly with some target variable) on disk.
For additional information about 'SVMlight' format see <http://svmlight.joachims.org/>.
Author: Dmitriy Selivanov [aut, cre],
Felix Riedel [aut]
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>
Diff between sparsio versions 1.0.0 dated 2017-06-28 and 1.0.1 dated 2020-01-13
DESCRIPTION | 10 ++++---- MD5 | 17 +++++++------ NAMESPACE | 2 - R/RcppExports.R | 4 +-- R/sparsio.R | 2 - README.md | 40 +++++++++++++++++++------------- src/RcppExports.cpp | 8 +++--- src/read_svmlight.cpp | 9 ++++--- tests/testthat/test-empty-rows.svmlight |only tests/testthat/test-read.R | 21 +++++++++++++++- 10 files changed, 70 insertions(+), 43 deletions(-)
Title: Calculate the NLTT Statistic
Description: Provides functions to calculate the normalised Lineage-Through-
Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures
the difference between two Lineage-Through-Time curves, where each curve is
normalised both in time and in number of lineages.
Author: Thijs Janzen [aut, cre],
Richel Bilderbeek [aut]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between nLTT versions 1.4.1 dated 2019-05-18 and 1.4.3 dated 2020-01-13
DESCRIPTION | 11 ++--- MD5 | 51 ++++++++++++------------ R/get_nltt_values.R | 7 ++- R/nLTTDiff.R | 49 +++++++++++++++++------ inst/doc/get_nltt_values.R | 72 +++++++++++++++++----------------- inst/doc/get_nltt_values.html | 31 +++++++------- inst/doc/nltt_diff.R | 16 +++---- inst/doc/nltt_diff.html | 10 +++- inst/doc/nltts_plot.R | 24 +++++------ inst/doc/nltts_plot.html | 10 +++- inst/doc/stretch_nltt_matrix.R | 36 ++++++++--------- inst/doc/stretch_nltt_matrix.html | 10 +++- inst/doc/trees_with_root_edge.R | 16 +++---- inst/doc/trees_with_root_edge.html | 10 +++- inst/doc/walkthrough.R | 38 ++++++++--------- inst/doc/walkthrough.html | 10 +++- man/get_nltt_values.Rd | 9 +++- man/nLTT-package.Rd | 3 - man/nLTTstat.Rd | 5 +- man/nLTTstat_exact.Rd | 6 ++ man/nltt_diff.Rd | 6 ++ man/nltt_diff_exact.Rd | 5 +- man/nltts_diff.Rd | 6 ++ tests/testthat/Rplots.pdf |binary tests/testthat/test-get_nltt_values.R | 32 +++++++++------ tests/testthat/test-log_transform.R |only tests/testthat/test-nLTTstat.R | 2 27 files changed, 279 insertions(+), 196 deletions(-)
Title: A Class for Vectors of 1-Bit Booleans
Description: True boolean datatype (no NAs),
coercion from and to logicals, integers and integer subscripts;
fast boolean operators and fast summary statistics.
With 'bit' vectors you can store true binary booleans {FALSE,TRUE} at the
expense of 1 bit only, on a 32 bit architecture this means factor 32 less
RAM and ~ factor 32 more speed on boolean operations. Due to overhead of
R calls, actual speed gain depends on the size of the vector: expect gains
for vectors of size > 10000 elements. Even for one-time boolean operations
it can pay-off to convert to bit, the pay-off is obvious, when such
components are used more than once.
Reading from and writing to bit is approximately as fast as accessing
standard logicals - mostly due to R's time for memory allocation. The package
allows to work with pre-allocated memory for return values by calling .Call()
directly: when evaluating the speed of C-access with pre-allocated vector
memory, coping from bit to logical requires only 70% of the time for copying
from logical to logical; and copying from logical to bit comes at a
performance penalty of 150%. the package now contains further classes for
representing logical selections: 'bitwhich' for very skewed selections and
'ri' for selecting ranges of values for chunked processing. All three index
classes can be used for subsetting 'ff' objects (ff-2.1-0 and higher).
Author: Jens Oehlschlägel [aut, cre],
Brian Ripley [ctb]
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Diff between bit versions 1.1-14 dated 2018-05-29 and 1.1-15 dated 2020-01-13
DESCRIPTION | 18 ++++++++------ MD5 | 9 ++++--- NEWS | 19 ++++++++++++++- R/bit.R | 75 +++++++++++++++++++++++++++++------------------------------- src/bit.c | 22 +++++++++++------ src/init.c |only 6 files changed, 84 insertions(+), 59 deletions(-)
Title: 'AWS S3' Client Package
Description: A simple client package for the Amazon Web Services ('AWS') Simple
Storage Service ('S3') 'REST' 'API' <https://aws.amazon.com/s3/>.
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>),
Boettiger Carl [ctb],
Andrew Martin [ctb],
Mark Thompson [ctb],
Tyler Hunt [ctb],
Steven Akins [ctb],
Bao Nguyen [ctb],
Thierry Onkelinx [ctb]
Maintainer: ORPHANED
Diff between aws.s3 versions 0.3.12 dated 2018-05-25 and 0.3.12.1 dated 2020-01-13
DESCRIPTION | 10 ++++++---- MD5 | 2 +- 2 files changed, 7 insertions(+), 5 deletions(-)
Title: Client for AWS Polly
Description: A client for AWS Polly <http://aws.amazon.com/documentation/polly>, a speech synthesis service.
Author: Thomas J. Leeper [aut, cre]
Maintainer: ORPHANED
Diff between aws.polly versions 0.1.2 dated 2016-12-08 and 0.1.2.1 dated 2020-01-13
DESCRIPTION | 10 ++++++---- MD5 | 2 +- 2 files changed, 7 insertions(+), 5 deletions(-)
Title: Easily Improve the User Experience of Your Shiny Apps in Seconds
Description: Perform common useful JavaScript operations in Shiny apps that will
greatly improve your apps without having to know any JavaScript. Examples
include: hiding an element, disabling an input, resetting an input back to
its original value, delaying code execution by a few seconds, and many more
useful functions for both the end user and the developer. 'shinyjs' can also
be used to easily call your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 1.0 dated 2018-01-08 and 1.1 dated 2020-01-13
DESCRIPTION | 8 - MD5 | 60 +++++----- NEWS.md | 17 ++ R/jsFunc-aaa.R | 6 - R/jsFunc-classFuncs.R | 14 +- R/jsFunc-click.R | 6 - R/jsFunc-html.R | 6 - R/jsFunc-stateFuncs.R | 17 +- R/jsFunc-visibilityFuncs.R | 14 +- R/onevent.R | 65 +++++++--- R/runcode.R | 34 +++-- R/useShinyjs.R | 11 + README.md | 4 build/vignette.rds |binary inst/doc/shinyjs-example.html | 199 ++++++++++++++++++++++++++++++++- inst/doc/shinyjs-extend.html | 209 +++++++++++++++++++++++++++++++++-- inst/doc/shinyjs-usage.Rmd | 14 +- inst/doc/shinyjs-usage.html | 213 +++++++++++++++++++++++++++++++++--- inst/doc/shinyjs.Rmd | 4 inst/doc/shinyjs.html | 211 +++++++++++++++++++++++++++++++++-- inst/srcjs/shinyjs-default-funcs.js | 75 +++++++----- man/classFuncs.Rd | 17 +- man/click.Rd | 5 man/html.Rd | 6 - man/onevent.Rd | 44 +++++-- man/runcode.Rd | 13 +- man/stateFuncs.Rd | 13 +- man/useShinyjs.Rd | 15 ++ man/visibilityFuncs.Rd | 21 ++- vignettes/shinyjs-usage.Rmd | 14 +- vignettes/shinyjs.Rmd | 4 31 files changed, 1119 insertions(+), 220 deletions(-)
Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from
the book "Quantitative Risk Management: Concepts, Techniques and Tools".
Furthermore, new developments and auxiliary functions for Quantitative
Risk Management practice.
Author: Marius Hofert [aut, cre],
Kurt Hornik [aut],
Alexander J. McNeil [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrmtools versions 0.0-11 dated 2019-12-03 and 0.0-12 dated 2020-01-13
DESCRIPTION | 10 - MD5 | 46 +++-- NAMESPACE | 8 - R/Black_Scholes.R | 72 ++++++--- R/alloc.R |only R/returns.R | 149 +++++++++++-------- R/risk_measures.R | 35 +++- TODO | 3 inst/doc/ARMA_GARCH_VaR.R | 3 inst/doc/ARMA_GARCH_VaR.Rmd | 3 inst/doc/ARMA_GARCH_VaR.html | 9 - inst/doc/VaR_bounds.R | 108 ++++++------- inst/doc/VaR_bounds.Rmd | 9 - inst/doc/VaR_bounds.html | 264 ++++++++++++++++------------------ inst/doc/geometric_risk_measures.R | 12 - inst/doc/geometric_risk_measures.Rmd | 12 - inst/doc/geometric_risk_measures.html | 22 +- man/Black_Scholes.Rd | 14 + man/alloc.Rd |only man/returns.Rd | 11 + man/risk_measures.Rd | 29 ++- man/tests.Rd | 2 vignettes/ARMA_GARCH_VaR.Rmd | 3 vignettes/VaR_bounds.Rmd | 9 - vignettes/geometric_risk_measures.Rmd | 12 - 25 files changed, 480 insertions(+), 365 deletions(-)
Title: Multivariate Normal Variance Mixtures
Description: Functions for working with multivariate normal variance mixture
distributions (evaluation of distribution functions and densities,
random number generation and parameter estimation), including
Student's t distribution for non-integer degrees of freedom.
Author: Marius Hofert [aut, cre],
Erik Hintz [aut],
Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between nvmix versions 0.0-2 dated 2019-11-13 and 0.0-3 dated 2020-01-13
nvmix-0.0-2/nvmix/R/get.set.parameters.R |only nvmix-0.0-2/nvmix/man/get.set.parameters.Rd |only nvmix-0.0-2/nvmix/man/qqplot.maha.Rd |only nvmix-0.0-3/nvmix/DESCRIPTION | 18 nvmix-0.0-3/nvmix/MD5 | 65 nvmix-0.0-3/nvmix/NAMESPACE | 17 nvmix-0.0-3/nvmix/R/Norm.R | 35 nvmix-0.0-3/nvmix/R/Student.R | 43 nvmix-0.0-3/nvmix/R/copula.R | 136 - nvmix-0.0-3/nvmix/R/dnvmix.R | 1376 ++++++------- nvmix-0.0-3/nvmix/R/fitnvmix.R | 1515 +++++++------- nvmix-0.0-3/nvmix/R/gammamix.R | 676 +++--- nvmix-0.0-3/nvmix/R/get_set_param.R |only nvmix-0.0-3/nvmix/R/graphics.R |only nvmix-0.0-3/nvmix/R/pnvmix.R | 1655 ++++++++-------- nvmix-0.0-3/nvmix/R/qnvmix.R | 373 +-- nvmix-0.0-3/nvmix/R/riskmeasures.R |only nvmix-0.0-3/nvmix/R/rnvmix.R | 348 +-- nvmix-0.0-3/nvmix/build/vignette.rds |binary nvmix-0.0-3/nvmix/data/numerical_experiments_data.RData |binary nvmix-0.0-3/nvmix/demo/numerical_experiments.R | 28 nvmix-0.0-3/nvmix/inst/doc/nvmix_functionality.R | 2 nvmix-0.0-3/nvmix/inst/doc/nvmix_functionality.Rmd | 25 nvmix-0.0-3/nvmix/inst/doc/nvmix_functionality.html | 59 nvmix-0.0-3/nvmix/inst/doc/nvmix_riskmeasures.R |only nvmix-0.0-3/nvmix/inst/doc/nvmix_riskmeasures.Rmd |only nvmix-0.0-3/nvmix/inst/doc/nvmix_riskmeasures.html |only nvmix-0.0-3/nvmix/man/copula.Rd | 75 nvmix-0.0-3/nvmix/man/dnvmix.Rd | 99 nvmix-0.0-3/nvmix/man/fitnvmix.Rd | 171 + nvmix-0.0-3/nvmix/man/gammamix.Rd | 96 nvmix-0.0-3/nvmix/man/get_set_param.Rd |only nvmix-0.0-3/nvmix/man/numerical_experiments_data.Rd | 57 nvmix-0.0-3/nvmix/man/pnvmix.Rd | 107 - nvmix-0.0-3/nvmix/man/qnvmix.rd | 145 - nvmix-0.0-3/nvmix/man/qqplot_maha.Rd |only nvmix-0.0-3/nvmix/man/riskmeasures.Rd |only nvmix-0.0-3/nvmix/man/rnvmix.Rd | 31 nvmix-0.0-3/nvmix/vignettes/nvmix_functionality.Rmd | 25 nvmix-0.0-3/nvmix/vignettes/nvmix_riskmeasures.Rmd |only 40 files changed, 3619 insertions(+), 3558 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-01 0.1.2
Title: Easy Access for West Java Data
Description: Interface to browse, list, and fetch data about West Java.
Author: Muhammad Aswan Syahputra [aut, cre]
Maintainer: Muhammad Aswan Syahputra <muhammadaswansyahputra@gmail.com>
Diff between jabr versions 0.1.1 dated 2019-12-15 and 0.1.2 dated 2020-01-13
DESCRIPTION | 9 +-- MD5 | 22 ++++--- NAMESPACE | 2 R/jabr_basemap.R | 2 R/jabr_fetch.R | 8 +- R/jabr_fetch_group.R |only R/jabr_list_dataset.R | 24 ++++---- R/utils.R | 1 README.md | 139 +++++++++++++++++++++++++++++++++++++++--------- man/jabr-package.Rd | 3 - man/jabr_basemap.Rd | 2 man/jabr_fetch.Rd | 2 man/jabr_fetch_group.Rd |only 13 files changed, 155 insertions(+), 59 deletions(-)
Title: Robust Data Analysis Through Monitoring and Dynamic
Visualization
Description: Provides interface to the 'MATLAB' toolbox 'Flexible Statistical Data Analysis
(FSDA)' which is a comprehensive and computationally efficient
software package for robust statistics in regression, multivariate
and categorical data analysis. The current R version implements tools
for regression: (forward search, S- and MM-estimation, least trimmed
squares (LTS) and least median of squares (LMS)), for multivariate analysis
(forward search, S- and MM-estimation), for cluster analysis and cluster-wise regression.
The distinctive feature of our package is the possibility of
monitoring the statistics of interest as function of breakdown point,
efficiency or subset size, depending on the estimator. This is
accompanied by a rich set of graphical features, such as dynamic
brushing, linking, particularly useful for exploratory data analysis.
Author: Valentin Todorov [aut, cre] (<https://orcid.org/0000-0003-4215-0245>),
Emmanuele Sordini [aut],
Aldo Corbellini [ctb],
Francesca Torti [ctb],
Marco Riani [ctb],
Domenico Perrotta [ctb],
Andrea Cerioli [ctb]
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between fsdaR versions 0.4-6 dated 2019-03-14 and 0.4-8 dated 2020-01-13
fsdaR-0.4-6/fsdaR/R/s3objecsdoc.R |only fsdaR-0.4-8/fsdaR/ChangeLog | 5 +++ fsdaR-0.4-8/fsdaR/DESCRIPTION | 26 +++++++++-------- fsdaR-0.4-8/fsdaR/MD5 | 34 +++++++++++----------- fsdaR-0.4-8/fsdaR/NAMESPACE | 11 ++----- fsdaR-0.4-8/fsdaR/R/corfwdplot.R | 37 ++++++++++++++++++++++-- fsdaR-0.4-8/fsdaR/R/datadoc.R | 2 - fsdaR-0.4-8/fsdaR/R/fsreg.R | 42 ++++------------------------ fsdaR-0.4-8/fsdaR/R/s3objectsdoc.R |only fsdaR-0.4-8/fsdaR/R/tclust.R | 2 - fsdaR-0.4-8/fsdaR/inst/work/Bug-examples.R | 4 +- fsdaR-0.4-8/fsdaR/man/corfwdplot.Rd | 18 ++++++++++++ fsdaR-0.4-8/fsdaR/man/emilia2001.Rd | 2 - fsdaR-0.4-8/fsdaR/man/loyalty.Rd | 2 - fsdaR-0.4-8/fsdaR/man/tclusteda.object.Rd | 2 - fsdaR-0.4-8/fsdaR/man/tclustfsda.Rd | 2 - fsdaR-0.4-8/fsdaR/man/tclustfsda.object.Rd | 2 - fsdaR-0.4-8/fsdaR/man/tclustic.object.Rd | 2 - fsdaR-0.4-8/fsdaR/man/tclusticsol.object.Rd | 2 - 19 files changed, 109 insertions(+), 86 deletions(-)
Title: Analysis and Visualization of Droplet Digital PCR in R and on
the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR
(ddPCR) data in R. This is the first non-proprietary software for analyzing
two-channel ddPCR data. An interactive tool was also created and is available
online to facilitate this analysis for anyone who is not comfortable with
using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ddpcr versions 1.11 dated 2019-01-03 and 1.12 dated 2020-01-13
ddpcr-1.11/ddpcr/man/PNPP_EXPERIMENT.Rd |only ddpcr-1.12/ddpcr/DESCRIPTION | 8 ddpcr-1.12/ddpcr/MD5 | 344 +++++----- ddpcr-1.12/ddpcr/NEWS.md | 6 ddpcr-1.12/ddpcr/R/plate-print.R | 12 ddpcr-1.12/ddpcr/R/utils.R | 21 ddpcr-1.12/ddpcr/README.md | 202 ++--- ddpcr-1.12/ddpcr/build/vignette.rds |binary ddpcr-1.12/ddpcr/inst/doc/algorithm.html | 31 ddpcr-1.12/ddpcr/inst/doc/extend.html | 295 ++++---- ddpcr-1.12/ddpcr/inst/doc/overview.Rmd | 9 ddpcr-1.12/ddpcr/inst/doc/overview.html | 276 ++++---- ddpcr-1.12/ddpcr/inst/doc/technical_details.html | 13 ddpcr-1.12/ddpcr/inst/vignette_files/overview_files/figure-markdown_strict/crosshairresults-1.png |binary ddpcr-1.12/ddpcr/inst/vignette_files/overview_files/figure-markdown_strict/plotcrosshair-1.png |binary ddpcr-1.12/ddpcr/inst/vignette_files/overview_files/figure-markdown_strict/plotparams-1.png |binary ddpcr-1.12/ddpcr/inst/vignette_files/overview_files/figure-markdown_strict/plotparams-2.png |binary ddpcr-1.12/ddpcr/inst/vignette_files/overview_files/figure-markdown_strict/plotraw-1.png |binary ddpcr-1.12/ddpcr/inst/vignette_files/overview_files/figure-markdown_strict/plotsimple-1.png |binary ddpcr-1.12/ddpcr/inst/vignette_files/overview_files/figure-markdown_strict/pnppplot-1.png |binary ddpcr-1.12/ddpcr/inst/vignette_files/overview_files/figure-markdown_strict/quickstart-1.png |binary ddpcr-1.12/ddpcr/inst/vignette_files/overview_files/figure-markdown_strict/quickstart-2.png |binary ddpcr-1.12/ddpcr/man/WELL_ID_REGEX.Rd | 1 ddpcr-1.12/ddpcr/man/analysis_complete.Rd | 1 ddpcr-1.12/ddpcr/man/analyze.Rd | 1 ddpcr-1.12/ddpcr/man/bind_df_ends.Rd | 1 ddpcr-1.12/ddpcr/man/calc_negative_freq_simple.Rd | 1 ddpcr-1.12/ddpcr/man/calculate_concentration.Rd | 1 ddpcr-1.12/ddpcr/man/calculate_concentration_single.Rd | 1 ddpcr-1.12/ddpcr/man/calculate_neg_freq_single.Rd | 1 ddpcr-1.12/ddpcr/man/calculate_negative_freqs.Rd | 1 ddpcr-1.12/ddpcr/man/capitalize.Rd | 1 ddpcr-1.12/ddpcr/man/cat0.Rd | 1 ddpcr-1.12/ddpcr/man/check_step.Rd | 3 ddpcr-1.12/ddpcr/man/classify_droplets.Rd | 1 ddpcr-1.12/ddpcr/man/classify_droplets.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/classify_droplets_single.Rd | 1 ddpcr-1.12/ddpcr/man/classify_droplets_single.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/classify_thresholds.Rd | 1 ddpcr-1.12/ddpcr/man/cluster.Rd | 1 ddpcr-1.12/ddpcr/man/cluster_name.Rd | 1 ddpcr-1.12/ddpcr/man/clusters.Rd | 1 ddpcr-1.12/ddpcr/man/col_to_num.Rd | 1 ddpcr-1.12/ddpcr/man/custom_thresholds.Rd | 1 ddpcr-1.12/ddpcr/man/ddpcr.Rd | 1 ddpcr-1.12/ddpcr/man/ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/define_clusters.Rd | 1 ddpcr-1.12/ddpcr/man/define_clusters.custom_thresholds.Rd | 1 ddpcr-1.12/ddpcr/man/define_clusters.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/define_clusters.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/define_params.Rd | 1 ddpcr-1.12/ddpcr/man/define_params.custom_thresholds.Rd | 1 ddpcr-1.12/ddpcr/man/define_params.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/define_params.fam_positive_pnpp.Rd | 1 ddpcr-1.12/ddpcr/man/define_params.hex_positive_pnpp.Rd | 1 ddpcr-1.12/ddpcr/man/define_params.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/define_params.wildtype_mutant_pnpp.Rd | 1 ddpcr-1.12/ddpcr/man/define_steps.Rd | 1 ddpcr-1.12/ddpcr/man/define_steps.custom_thresholds.Rd | 1 ddpcr-1.12/ddpcr/man/define_steps.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/define_steps.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/diff.point2d.Rd | 1 ddpcr-1.12/ddpcr/man/err_msg.Rd | 1 ddpcr-1.12/ddpcr/man/fam_positive_pnpp.Rd | 1 ddpcr-1.12/ddpcr/man/get_col.Rd | 1 ddpcr-1.12/ddpcr/man/get_empty_cutoff.Rd | 1 ddpcr-1.12/ddpcr/man/get_empty_cutoff.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/get_empty_cutoff.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/get_filled_border.Rd | 1 ddpcr-1.12/ddpcr/man/get_filled_drops.Rd | 1 ddpcr-1.12/ddpcr/man/get_outlier_cutoff.Rd | 1 ddpcr-1.12/ddpcr/man/get_outlier_cutoff.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/get_row.Rd | 1 ddpcr-1.12/ddpcr/man/get_single_well.Rd | 1 ddpcr-1.12/ddpcr/man/get_wells_btwn.Rd | 1 ddpcr-1.12/ddpcr/man/grapes-btwn-grapes.Rd | 1 ddpcr-1.12/ddpcr/man/grapes-greater-than-grapes.Rd | 1 ddpcr-1.12/ddpcr/man/has_signif_negative_cluster.Rd | 1 ddpcr-1.12/ddpcr/man/has_step.Rd | 1 ddpcr-1.12/ddpcr/man/hex_positive_pnpp.Rd | 1 ddpcr-1.12/ddpcr/man/is_dir.Rd | 1 ddpcr-1.12/ddpcr/man/is_dirty.Rd | 1 ddpcr-1.12/ddpcr/man/is_empty_plate.Rd | 1 ddpcr-1.12/ddpcr/man/is_file.Rd | 1 ddpcr-1.12/ddpcr/man/is_range.Rd | 1 ddpcr-1.12/ddpcr/man/is_well_success.Rd | 1 ddpcr-1.12/ddpcr/man/is_well_success.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/is_well_success.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/launch.Rd | 1 ddpcr-1.12/ddpcr/man/load_plate.Rd | 1 ddpcr-1.12/ddpcr/man/local_maxima.Rd | 1 ddpcr-1.12/ddpcr/man/local_minima.Rd | 1 ddpcr-1.12/ddpcr/man/lol_to_df.Rd | 1 ddpcr-1.12/ddpcr/man/mark_clusters.Rd | 1 ddpcr-1.12/ddpcr/man/merge_dfs_overwrite_col.Rd | 1 ddpcr-1.12/ddpcr/man/meta_var_name.Rd | 1 ddpcr-1.12/ddpcr/man/move_back.Rd | 1 ddpcr-1.12/ddpcr/man/move_front.Rd | 1 ddpcr-1.12/ddpcr/man/msg.Rd | 1 ddpcr-1.12/ddpcr/man/name.Rd | 1 ddpcr-1.12/ddpcr/man/named_vec_to_df.Rd | 1 ddpcr-1.12/ddpcr/man/new_plate.Rd | 2 ddpcr-1.12/ddpcr/man/next_step.Rd | 1 ddpcr-1.12/ddpcr/man/normalize_to_rds.Rd | 1 ddpcr-1.12/ddpcr/man/num_to_col.Rd | 1 ddpcr-1.12/ddpcr/man/num_to_row.Rd | 1 ddpcr-1.12/ddpcr/man/other_dim.Rd | 1 ddpcr-1.12/ddpcr/man/params.Rd | 1 ddpcr-1.12/ddpcr/man/parent_plate_type.Rd | 1 ddpcr-1.12/ddpcr/man/parent_plate_type.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/parent_plate_type.default.Rd | 1 ddpcr-1.12/ddpcr/man/parent_plate_type.fam_positive_pnpp.Rd | 1 ddpcr-1.12/ddpcr/man/parent_plate_type.hex_positive_pnpp.Rd | 1 ddpcr-1.12/ddpcr/man/parent_plate_type.wildtype_mutant_pnpp.Rd | 1 ddpcr-1.12/ddpcr/man/plate_data-set.Rd | 1 ddpcr-1.12/ddpcr/man/plate_data.Rd | 3 ddpcr-1.12/ddpcr/man/plate_meta-set.Rd | 1 ddpcr-1.12/ddpcr/man/plate_meta.Rd | 7 ddpcr-1.12/ddpcr/man/plate_types.Rd | 1 ddpcr-1.12/ddpcr/man/plot.custom_thresholds.Rd | 1 ddpcr-1.12/ddpcr/man/plot.ddpcr_plate.Rd | 24 ddpcr-1.12/ddpcr/man/plot.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/plot.wildtype_mutant_pnpp.Rd | 1 ddpcr-1.12/ddpcr/man/pnpp_experiment.Rd |only ddpcr-1.12/ddpcr/man/point2d.Rd | 1 ddpcr-1.12/ddpcr/man/positive_dim.Rd | 1 ddpcr-1.12/ddpcr/man/positive_dim_var.Rd | 1 ddpcr-1.12/ddpcr/man/positive_name.Rd | 5 ddpcr-1.12/ddpcr/man/print.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/quiet.Rd | 1 ddpcr-1.12/ddpcr/man/range_list_to_vec.Rd | 1 ddpcr-1.12/ddpcr/man/range_to_endpoints.Rd | 1 ddpcr-1.12/ddpcr/man/range_to_seq.Rd | 1 ddpcr-1.12/ddpcr/man/reclassify_droplets.Rd | 1 ddpcr-1.12/ddpcr/man/reclassify_droplets.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/reclassify_droplets_single.Rd | 1 ddpcr-1.12/ddpcr/man/reclassify_droplets_single.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/remove_empty.Rd | 1 ddpcr-1.12/ddpcr/man/remove_empty.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/remove_empty.pnpp_experiment.Rd | 1 ddpcr-1.12/ddpcr/man/remove_failures.Rd | 1 ddpcr-1.12/ddpcr/man/remove_failures.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/remove_outliers.Rd | 1 ddpcr-1.12/ddpcr/man/remove_outliers.ddpcr_plate.Rd | 1 ddpcr-1.12/ddpcr/man/reset.Rd | 1 ddpcr-1.12/ddpcr/man/row_to_num.Rd | 1 ddpcr-1.12/ddpcr/man/sample_data.Rd | 3 ddpcr-1.12/ddpcr/man/save_plate.Rd | 1 ddpcr-1.12/ddpcr/man/set_default_params.Rd | 1 ddpcr-1.12/ddpcr/man/status.Rd | 3 ddpcr-1.12/ddpcr/man/step.Rd | 1 ddpcr-1.12/ddpcr/man/step_begin.Rd | 1 ddpcr-1.12/ddpcr/man/step_end.Rd | 1 ddpcr-1.12/ddpcr/man/step_name.Rd | 1 ddpcr-1.12/ddpcr/man/steps.Rd | 1 ddpcr-1.12/ddpcr/man/subset.ddpcr_plate.Rd | 5 ddpcr-1.12/ddpcr/man/thresholds.Rd | 3 ddpcr-1.12/ddpcr/man/type.Rd | 5 ddpcr-1.12/ddpcr/man/unanalyzed_clusters.Rd | 1 ddpcr-1.12/ddpcr/man/variable_dim.Rd | 1 ddpcr-1.12/ddpcr/man/variable_dim_var.Rd | 1 ddpcr-1.12/ddpcr/man/warn_msg.Rd | 1 ddpcr-1.12/ddpcr/man/well_info.Rd | 1 ddpcr-1.12/ddpcr/man/wells_mutant.Rd | 1 ddpcr-1.12/ddpcr/man/wells_negative.Rd | 1 ddpcr-1.12/ddpcr/man/wells_positive.Rd | 1 ddpcr-1.12/ddpcr/man/wells_success.Rd | 3 ddpcr-1.12/ddpcr/man/wells_used.Rd | 1 ddpcr-1.12/ddpcr/man/wells_wildtype.Rd | 1 ddpcr-1.12/ddpcr/man/wildtype_mutant_pnpp.Rd | 1 ddpcr-1.12/ddpcr/man/x_threshold.Rd | 1 ddpcr-1.12/ddpcr/man/x_var.Rd | 3 ddpcr-1.12/ddpcr/man/y_threshold.Rd | 1 ddpcr-1.12/ddpcr/vignettes/overview.Rmd | 9 174 files changed, 665 insertions(+), 767 deletions(-)