Title: Generates Expectations for 'testthat' Unit Testing
Description: Helps systematize and ease the process of
building unit tests with the 'testthat' package by providing
tools for generating expectations.
Author: Ludvig Renbo Olsen [aut, cre],
R. Mark Sharp [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between xpectr versions 0.3.0 dated 2020-03-31 and 0.4.0 dated 2020-06-18
DESCRIPTION | 14 +- MD5 | 117 ++++++++++---------- NAMESPACE | 1 NEWS.md | 20 +++ R/addin_utils.R | 5 R/assert_collection_addin.R | 4 R/create_expectations.R | 21 ++- R/do_if.R | 32 ++--- R/dput_addins.R | 4 R/element_descriptors.R | 12 +- R/gxs_function.R | 47 ++++++-- R/gxs_selection.R | 43 ++++--- R/helpers.R | 35 +++++ R/initialize_gxs_function_addin.R | 11 + R/initialize_test_that_addin.R | 4 R/navigateTestFileAddin.R | 4 R/prepare_insertion.R | 6 - R/sample.R | 22 +-- R/set_test_seed.R | 10 - R/side_effects.R | 53 +++++---- R/simplified_formals.R | 6 - R/string_utils.R | 7 + R/strip.R | 29 ++++ R/strip_side_effect_messages.R | 15 +- R/suppress_mw.R | 8 - R/testthat_addins.R | 36 ++++-- R/wrap_string_addin.R | 11 + README.md | 3 build/xpectr.pdf |binary inst/doc/readme.R | 3 inst/doc/readme.Rmd | 3 inst/doc/readme.html | 13 +- inst/rstudio/addins.dcf | 7 + man/assertCollectionAddin.Rd | 4 man/capture_parse_eval_side_effects.Rd | 31 ++++- man/capture_side_effects.Rd | 37 ++++-- man/dputSelectedAddin.Rd | 4 man/element_classes.Rd | 4 man/element_lengths.Rd | 4 man/element_types.Rd | 4 man/gxs_function.Rd | 47 +++++--- man/gxs_selection.Rd | 38 ++++-- man/initializeGXSFunctionAddin.Rd | 8 - man/initializeTestthatAddin.Rd | 4 man/insertExpectationsAddin.Rd | 41 +++++-- man/navigateTestFileAddin.Rd | 4 man/num_total_elements.Rd | 4 man/prepare_insertion.Rd | 6 - man/set_test_seed.Rd | 10 - man/simplified_formals.Rd | 6 - man/smpl.Rd | 22 +-- man/stop_if.Rd | 14 +- man/strip.Rd | 9 + man/strip_msg.Rd | 20 ++- man/suppress_mw.Rd | 8 - man/wrapStringAddin.Rd | 8 - tests/testthat/test_capture_side_effects.R |only tests/testthat/test_initialize_gxs_function_addin.R | 27 ++-- tests/testthat/test_strip.R | 3 vignettes/readme.Rmd | 3 60 files changed, 634 insertions(+), 342 deletions(-)
Title: Text Plots
Description: Visualise complex relations in texts. This is done by providing functionalities for displaying
text co-occurrence networks, text correlation networks, dependency relationships as well as text clustering.
Feel free to join the effort of providing interesting text visualisations.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Sacha Epskamp [ctb, cph] (code in R/matrix_reduction.R adapted from the
qgraph package version 1.4.0 which is GPL-2 licensed),
Ingo Feinerer and Kurt Hornik [ctb, cph] (partial code in
R/textplot_corlines.R adapted from the tm package version 0.4 which
is GPL-2 licensed)
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between textplot versions 0.1.2 dated 2020-05-23 and 0.1.3 dated 2020-06-18
DESCRIPTION | 9 - MD5 | 40 +++---- NEWS.md | 4 R/textplot_bar.R | 1 R/textplot_biterms.R | 44 +++++++- R/textplot_cooccurrence.R | 10 + R/textplot_corglasso.R | 11 ++ R/textplot_corlines.R | 18 +++ R/textplot_dependencies.R | 13 ++ inst/doc/textplot-examples.R | 165 +++++++------------------------- inst/doc/textplot-examples.Rnw | 122 ++++++++++------------- inst/doc/textplot-examples.pdf |binary man/example_btm.Rd | 9 + man/plot.BTM.Rd | 13 ++ man/textplot_bitermclusters.Rd | 12 ++ man/textplot_cooccurrence.Rd | 10 + man/textplot_correlation_glasso.Rd | 11 ++ man/textplot_correlation_lines.Rd | 10 + man/textplot_correlation_lines_attrs.Rd | 8 + man/textplot_dependencyparser.Rd | 13 ++ vignettes/textplot-examples.Rnw | 122 ++++++++++------------- 21 files changed, 351 insertions(+), 294 deletions(-)
Title: Calculate Power and Sample Size for Two Sample Mean Tests
Description: Power calculations are a critical component of any research study to determine the
minimum sample size necessary to detect differences between multiple groups. Here we
present an 'R' package, 'PASSED', that performs power and sample size calculations for
the test of two-sample means or ratios with data following beta,
gamma (Chang et al. (2011), <doi:10.1007/s00180-010-0209-1>), normal,
Poisson (Gu et al. (2008), <doi:10.1002/bimj.200710403>), binomial, geometric, and
negative binomial (Zhu and Lakkis (2014), <doi:10.1002/sim.5947>) distributions.
Author: Jinpu Li [aut, cre],
Ryan Knigge [aut],
Emily Leary [aut]
Maintainer: Jinpu Li <lijinp@health.missouri.edu>
Diff between PASSED versions 1.0-1 dated 2020-05-13 and 1.0-2 dated 2020-06-18
DESCRIPTION | 10 +-- MD5 | 20 +++--- NAMESPACE | 2 R/power_Binomial.R | 104 ++++++++++++++++++++++---------- R/power_Gamma.R | 1 R/power_Normal.R | 159 +++++++++++++++++++++++++++++++++----------------- R/power_Poisson.R | 3 man/power_Binomial.Rd | 3 man/power_Gamma.Rd | 1 man/power_Normal.Rd | 3 man/power_Poisson.Rd | 3 11 files changed, 206 insertions(+), 103 deletions(-)
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create
readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed
models. Currently supported are linear and generalized linear (mixed) models from 'lme4'
(classes 'lmerMod', 'glmerMod'), 'glmmTMB' and 'spaMM', generalized additive models ('gam' from
'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model
classes. Moreover, externally created simulations, e.g. posterior predictive simulations
from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well.
The resulting residuals are standardized to values between 0 and 1 and can be interpreted
as intuitively as residuals from a linear regression. The package also provides a number of
plot and test functions for typical model misspecification problems, such as
over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (<https://orcid.org/0000-0002-6255-9059>)
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between DHARMa versions 0.3.1 dated 2020-05-12 and 0.3.2.0 dated 2020-06-18
DESCRIPTION | 8 MD5 | 36 +-- NEWS | 8 R/plots.R | 30 +-- R/simulateResiduals.R | 4 R/tests.R | 67 +++--- inst/doc/DHARMa.Rmd | 4 inst/doc/DHARMa.html | 388 +++++++++++++++++++-------------------- inst/examples/createDharmaHelp.R | 81 -------- inst/examples/testOutliersHelp.R |only man/createDHARMa.Rd | 81 -------- man/plot.DHARMa.Rd | 8 man/plotResiduals.Rd | 13 - man/plotSimulatedResiduals.Rd | 2 man/simulateResiduals.Rd | 4 man/testDispersion.Rd | 4 man/testOutliers.Rd | 71 ++----- tests/testthat/Rplots.pdf |only tests/testthat/testTests.R | 135 +++++++------ vignettes/DHARMa.Rmd | 4 20 files changed, 400 insertions(+), 548 deletions(-)
Title: Pipe-Friendly Framework for Basic Statistical Tests
Description: Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy,
for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses.
The output of each test is automatically transformed into a tidy data frame to facilitate visualization.
Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.
Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs
(repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs.
It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and
'Cramer V' for the association between categorical variables.
The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between rstatix versions 0.5.0 dated 2020-04-28 and 0.6.0 dated 2020-06-18
DESCRIPTION | 16 +++++------ MD5 | 46 ++++++++++++++++++--------------- NAMESPACE | 3 +- NEWS.md | 14 ++++++++++ R/anova_summary.R | 9 ++++++ R/anova_test.R | 5 ++- R/emmeans_test.R | 16 ++++++++--- R/get_pvalue_position.R | 61 ++++++++++++++++++++++++++++----------------- R/get_summary_stats.R | 2 - R/p_value.R | 1 R/reexports.R | 14 ++-------- R/tukey_hsd.R | 11 ++++++++ R/utils-manova.R |only R/utils-pipe.R |only R/wilcox_test.R | 45 ++++++++++++++++++++++++++------- README.md | 33 +++++++++++++++++------- inst/WORDLIST | 6 ++++ man/Manova.Rd |only man/anova_summary.Rd | 9 ++++++ man/cohens_d.Rd | 5 +-- man/fisher_test.Rd | 6 +++- man/get_pvalue_position.Rd | 37 +++++++++++++++++---------- man/pipe.Rd |only man/reexports.Rd | 8 +---- man/wilcox_effsize.Rd | 8 ++--- man/wilcox_test.Rd | 37 ++++++++++++++++++++++----- 26 files changed, 272 insertions(+), 120 deletions(-)
Title: Lightweight and Feature Complete Unit Testing Framework
Description: Provides a lightweight (zero-dependency) and easy to use
unit testing framework. Main features: install tests with
the package. Test results are treated as data that can be stored and
manipulated. Test files are R scripts interspersed with test commands, that
can be programmed over. Fully automated build-install-test sequence for
packages. Skip tests when not run locally (e.g. on CRAN). Flexible and
configurable output printing. Compare computed output with output stored
with the package. Run tests in parallel. Extensible by other packages.
Report side effects.
Author: Mark van der Loo [aut, cre] (<https://orcid.org/0000-0002-9807-4686>)
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between tinytest versions 1.2.1 dated 2020-05-18 and 1.2.2 dated 2020-06-18
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS | 5 +++++ R/expectations.R | 8 +++++--- R/tinytest.R | 35 ++++++++++++++++++++++++++--------- build/vignette.rds |binary inst/doc/tinytest_examples.pdf |binary inst/doc/using_tinytest.pdf |binary man/build_install_test.Rd | 11 +++++++++++ man/run_test_dir.Rd | 6 +++--- man/run_test_file.Rd | 2 +- man/test_package.Rd | 4 ++-- man/using.Rd | 2 +- 13 files changed, 69 insertions(+), 34 deletions(-)
Title: Perform Inference on Algorithm-Agnostic Variable Importance
Description: Calculate point estimates of and valid confidence intervals for
nonparametric, algorithm-agnostic variable importance measures in high and low dimensions,
using flexible estimators of the underlying regression functions. For more information
about the methods, please see Williamson et al. (Biometrics, 2020), Williamson et al. (arXiv, 2020+) <arXiv:2004.03683>, and Williamson and Feng (ICML, 2020) <arXiv:>.
Author: Brian D. Williamson [aut, cre]
(<https://orcid.org/0000-0002-7024-548X>),
Noah Simon [aut] (<https://orcid.org/0000-0002-8985-2474>),
Marco Carone [aut] (<https://orcid.org/0000-0003-2106-0953>)
Maintainer: Brian D. Williamson <brianw26@uw.edu>
Diff between vimp versions 2.0.2 dated 2020-04-27 and 2.1.0 dated 2020-06-18
vimp-2.0.2/vimp/R/vimp.R |only vimp-2.1.0/vimp/DESCRIPTION | 13 vimp-2.1.0/vimp/MD5 | 48 vimp-2.1.0/vimp/NAMESPACE | 6 vimp-2.1.0/vimp/NEWS.md |only vimp-2.1.0/vimp/R/cv_vim.R | 35 vimp-2.1.0/vimp/R/sample_subsets.R |only vimp-2.1.0/vimp/R/sp_vim.R |only vimp-2.1.0/vimp/R/spvim_ics.R |only vimp-2.1.0/vimp/R/spvim_se.R |only vimp-2.1.0/vimp/R/utils.R |only vimp-2.1.0/vimp/R/vim.R | 29 vimp-2.1.0/vimp/R/vimp-package.R |only vimp-2.1.0/vimp/inst/doc/introduction_to_vimp.R | 2 vimp-2.1.0/vimp/inst/doc/introduction_to_vimp.Rmd | 37 vimp-2.1.0/vimp/inst/doc/introduction_to_vimp.html | 881 ++++++++------ vimp-2.1.0/vimp/man/cv_vim.Rd | 17 vimp-2.1.0/vimp/man/figures |only vimp-2.1.0/vimp/man/sample_subsets.Rd |only vimp-2.1.0/vimp/man/sp_vim.Rd |only vimp-2.1.0/vimp/man/spvim_ics.Rd |only vimp-2.1.0/vimp/man/spvim_se.Rd |only vimp-2.1.0/vimp/man/vim.Rd | 11 vimp-2.1.0/vimp/man/vimp.Rd | 56 vimp-2.1.0/vimp/tests/testthat/test-average_vim.R | 2 vimp-2.1.0/vimp/tests/testthat/test-binary_outcomes.R | 17 vimp-2.1.0/vimp/tests/testthat/test-continuous_outcomes.R | 7 vimp-2.1.0/vimp/tests/testthat/test-cv_vim.R | 2 vimp-2.1.0/vimp/tests/testthat/test-merge_vim.R | 2 vimp-2.1.0/vimp/tests/testthat/test-sp_vim.R |only vimp-2.1.0/vimp/tests/testthat/test-vim.R | 17 vimp-2.1.0/vimp/vignettes/introduction_to_vimp.Rmd | 37 32 files changed, 772 insertions(+), 447 deletions(-)
Title: Time Aware Tibbles
Description: Built on top of the 'tibble' package, 'tibbletime' is an extension
that allows for the creation of time aware tibbles. Some immediate
advantages of this include: the ability to perform time-based subsetting
on tibbles, quickly summarising and aggregating results by time periods,
and creating columns that can be used as 'dplyr' time-based groups.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between tibbletime versions 0.1.4 dated 2020-05-26 and 0.1.5 dated 2020-06-18
DESCRIPTION | 8 +- MD5 | 30 ++++--- NAMESPACE | 1 NEWS.md | 9 ++ R/coercion.R | 23 +----- R/compat-dplyr.R | 1 build/vignette.rds |binary inst/doc/TT-01-time-based-filtering.html | 4 - inst/doc/TT-02-changing-time-periods.html | 4 - inst/doc/TT-03-rollify-for-rolling-analysis.html | 14 +-- inst/doc/TT-04-use-with-dplyr.html | 88 +++++++++++------------ man/ceiling_index.Rd | 6 - man/floor_index.Rd | 6 - man/reexports.Rd | 2 man/rollify.Rd | 2 tests/testthat/test-coercion.R |only tests/testthat/test_compat-dplyr.R |only 17 files changed, 98 insertions(+), 100 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The
package should add new functionality to R such as the possibility to
manipulate 'NeXML' objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Hilmar Lapp [aut] (<https://orcid.org/0000-0001-9107-0714>),
Kseniia Shumelchyk [aut],
Rutger Vos [aut] (<https://orcid.org/0000-0001-9254-7318>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.4.4 dated 2020-05-10 and 2.4.5 dated 2020-06-18
RNeXML-2.4.4/RNeXML/tests/testthat/Rplots.pdf |only RNeXML-2.4.5/RNeXML/DESCRIPTION | 8 RNeXML-2.4.5/RNeXML/MD5 | 39 ++-- RNeXML-2.4.5/RNeXML/NEWS.md | 2 RNeXML-2.4.5/RNeXML/R/S4-utils.R | 46 ++-- RNeXML-2.4.5/RNeXML/R/constructors.R | 6 RNeXML-2.4.5/RNeXML/R/nexml_read.R | 6 RNeXML-2.4.5/RNeXML/build/vignette.rds |binary RNeXML-2.4.5/RNeXML/inst/WORDLIST | 8 RNeXML-2.4.5/RNeXML/inst/doc/S4.html | 56 +++--- RNeXML-2.4.5/RNeXML/inst/doc/intro.html | 110 ++++++----- RNeXML-2.4.5/RNeXML/inst/doc/metadata.html | 146 +++++++-------- RNeXML-2.4.5/RNeXML/inst/doc/simmap.html | 76 ++++---- RNeXML-2.4.5/RNeXML/inst/doc/sparql.html | 196 ++++++++++----------- RNeXML-2.4.5/RNeXML/man/New.Rd | 6 RNeXML-2.4.5/RNeXML/man/dot-callGeneric.Rd | 6 RNeXML-2.4.5/RNeXML/man/dot-methodWithNext.Rd | 12 - RNeXML-2.4.5/RNeXML/man/dot-sigLabel.Rd | 4 RNeXML-2.4.5/RNeXML/man/findNextMethod.Rd | 16 - RNeXML-2.4.5/RNeXML/man/nexml_read.Rd | 6 RNeXML-2.4.5/RNeXML/tests/testthat/test_01_utils.R | 8 21 files changed, 383 insertions(+), 374 deletions(-)
Title: Creating and Working with Pedigrees and Marker Data
Description: A lightweight, but comprehensive collection of tools for creating,
manipulating and visualising pedigrees and genetic marker data. Pedigrees
can be read from text files or created on the fly with built-in functions.
A range of utilities enable modifications like adding or removing individuals,
breaking loops, and merging pedigrees. Pedigree plots are produced by wrapping
the plotting functionality of the 'kinship2' package.
Author: Magnus Dehli Vigeland [aut, cre]
(<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedtools versions 0.9.3 dated 2020-03-21 and 0.9.4 dated 2020-06-18
pedtools-0.9.3/pedtools/man/deprecated.Rd |only pedtools-0.9.4/pedtools/DESCRIPTION | 6 pedtools-0.9.4/pedtools/MD5 | 114 ++-- pedtools-0.9.4/pedtools/NAMESPACE | 13 pedtools-0.9.4/pedtools/NEWS.md | 31 + pedtools-0.9.4/pedtools/R/deprecated.R | 94 --- pedtools-0.9.4/pedtools/R/getMap.R | 30 + pedtools-0.9.4/pedtools/R/marker.R | 72 ++ pedtools-0.9.4/pedtools/R/marker_accessors.R | 22 pedtools-0.9.4/pedtools/R/marker_allelematrix.R | 10 pedtools-0.9.4/pedtools/R/marker_attach.R | 41 - pedtools-0.9.4/pedtools/R/marker_database.R | 26 + pedtools-0.9.4/pedtools/R/marker_locusattributes.R | 8 pedtools-0.9.4/pedtools/R/marker_print.R | 4 pedtools-0.9.4/pedtools/R/marker_select.R | 19 pedtools-0.9.4/pedtools/R/marker_transfer.R | 2 pedtools-0.9.4/pedtools/R/mendelianCheck.R | 4 pedtools-0.9.4/pedtools/R/ped_accessors.R | 85 +++ pedtools-0.9.4/pedtools/R/ped_basic.R | 12 pedtools-0.9.4/pedtools/R/ped_complex.R | 46 + pedtools-0.9.4/pedtools/R/ped_convert.R | 25 - pedtools-0.9.4/pedtools/R/ped_internal.R | 15 pedtools-0.9.4/pedtools/R/ped_loops.R | 10 pedtools-0.9.4/pedtools/R/ped_modify.R | 8 pedtools-0.9.4/pedtools/R/ped_plot.R | 245 +++++----- pedtools-0.9.4/pedtools/R/ped_subgroups.R | 66 ++ pedtools-0.9.4/pedtools/R/ped_utils.R | 35 - pedtools-0.9.4/pedtools/R/randomPed.R | 2 pedtools-0.9.4/pedtools/R/readPed.R | 17 pedtools-0.9.4/pedtools/R/utils.R | 4 pedtools-0.9.4/pedtools/R/writePed.R | 186 ++++--- pedtools-0.9.4/pedtools/build/vignette.rds |binary pedtools-0.9.4/pedtools/inst/WORDLIST | 7 pedtools-0.9.4/pedtools/inst/doc/pedtools.R | 46 + pedtools-0.9.4/pedtools/inst/doc/pedtools.Rmd | 46 + pedtools-0.9.4/pedtools/inst/doc/pedtools.html | 196 ++++---- pedtools-0.9.4/pedtools/man/as.data.frame.ped.Rd | 2 pedtools-0.9.4/pedtools/man/as.ped.Rd | 2 pedtools-0.9.4/pedtools/man/freqDatabase.Rd | 8 pedtools-0.9.4/pedtools/man/getSex.Rd | 42 + pedtools-0.9.4/pedtools/man/locusAttributes.Rd | 4 pedtools-0.9.4/pedtools/man/marker.Rd | 27 - pedtools-0.9.4/pedtools/man/marker_attach.Rd | 10 pedtools-0.9.4/pedtools/man/marker_select.Rd | 7 pedtools-0.9.4/pedtools/man/ped_internal.Rd | 13 pedtools-0.9.4/pedtools/man/ped_subgroups.Rd | 34 - pedtools-0.9.4/pedtools/man/plot.ped.Rd | 56 +- pedtools-0.9.4/pedtools/man/plotPedList.Rd | 25 - pedtools-0.9.4/pedtools/man/readPed.Rd | 2 pedtools-0.9.4/pedtools/man/writePed.Rd | 41 + pedtools-0.9.4/pedtools/tests/testthat/test-founder-inbreeding.R | 4 pedtools-0.9.4/pedtools/tests/testthat/test-marker-creation.R | 9 pedtools-0.9.4/pedtools/tests/testthat/test-marker-select.R |only pedtools-0.9.4/pedtools/tests/testthat/test-ped-modifications.R | 24 pedtools-0.9.4/pedtools/tests/testthat/test-ped-read.R | 2 pedtools-0.9.4/pedtools/tests/testthat/test-ped-relatives.R | 27 + pedtools-0.9.4/pedtools/tests/testthat/test-ped-write.R |only pedtools-0.9.4/pedtools/tests/testthat/test-plots.R |only pedtools-0.9.4/pedtools/tests/testthat/test-singleton.R | 7 pedtools-0.9.4/pedtools/vignettes/pedtools.Rmd | 46 + 60 files changed, 1131 insertions(+), 808 deletions(-)
Title: An Image Processing Toolkit
Description: Incorporates functions for image preprocessing, filtering and image recognition. The package takes advantage of 'RcppArmadillo' to speed up computationally intensive functions. The histogram of oriented gradients descriptor is a modification of the 'findHOGFeatures' function of the 'SimpleCV' computer vision platform, the average_hash(), dhash() and phash() functions are based on the 'ImageHash' python library. The Gabor Feature Extraction functions are based on 'Matlab' code of the paper, "CloudID: Trustworthy cloud-based and cross-enterprise biometric identification" by M. Haghighat, S. Zonouz, M. Abdel-Mottaleb, Expert Systems with Applications, vol. 42, no. 21, pp. 7905-7916, 2015, <doi:10.1016/j.eswa.2015.06.025>. The 'SLIC' and 'SLICO' superpixel algorithms were explained in detail in (i) "SLIC Superpixels Compared to State-of-the-art Superpixel Methods", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 34, num. 11, p. 2274-2282, May 2012, <doi:10.1109/TPAMI.2012.120> and (ii) "SLIC Superpixels", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, EPFL Technical Report no. 149300, June 2010.
Author: Lampros Mouselimis [aut, cre],
Sight Machine [cph] (findHOGFeatures function of the SimpleCV computer
vision platform),
Johannes Buchner [cph] (average_hash, dhash and phash functions of the
ImageHash python library),
Mohammad Haghighat [cph] (Gabor Feature Extraction),
Radhakrishna Achanta [cph] (Author of the C++ code of the SLIC and
SLICO algorithms (for commercial use please contact the author))
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between OpenImageR versions 1.1.6 dated 2019-12-01 and 1.1.7 dated 2020-06-18
DESCRIPTION | 10 MD5 | 79 +- NAMESPACE | 3 NEWS.md | 10 R/RcppExports.R | 4 R/open_image_rscript.R | 460 ++++++------- R/superpixels.R | 233 ++++++ build/vignette.rds |binary inst/doc/Gabor_Feature_Extraction.html | 499 +++++++------- inst/doc/Image_segmentation_superpixels_clustering.Rmd | 8 inst/doc/Image_segmentation_superpixels_clustering.html | 525 +++++++-------- inst/doc/The_OpenImageR_package.R | 72 +- inst/doc/The_OpenImageR_package.html | 558 +++++++--------- inst/include/OpenImageRheader.h | 71 ++ man/Augmentation.Rd | 26 man/GaborFeatureExtract.Rd | 270 ++++++- man/HOG_apply.Rd | 10 man/List_2_Array.Rd | 2 man/MinMaxObject.Rd | 4 man/NormalizeObject.Rd | 4 man/RGB_to_Lab.Rd | 2 man/average_hash.Rd | 3 man/delationErosion.Rd | 2 man/down_sample_image.Rd | 9 man/edge_detection.Rd | 13 man/hash_apply.Rd | 14 man/invariant_hash.Rd | 16 man/padding.Rd |only man/phash.Rd | 9 man/rotateImage.Rd | 3 man/superpixel_bbox.Rd |only man/superpixel_bbox_subset.Rd |only man/superpixels.Rd | 17 man/switch_filter.Rd | 10 man/switch_hashing.Rd | 13 man/switch_invariant.Rd | 3 man/translation.Rd | 2 src/RcppExports.cpp | 14 src/extract_inst_folder_headers.cpp | 14 src/init.c | 2 tests/testthat/test-superpixels.R | 149 +++- vignettes/Image_segmentation_superpixels_clustering.Rmd | 8 42 files changed, 1918 insertions(+), 1233 deletions(-)
Title: Lists of Numeric Atomic Objects
Description: Create and manipulate numeric list (nlist) objects.
An nlist is an S3 list of uniquely named numeric atomic (natomic) objects.
An natomic object is an integer or double vector, matrix or array.
An nlists object is a S3 class list of nlist objects with the
same names, dimensionalities and typeofs.
Numeric list objects are of interest because they are the raw data inputs
for analytic engines such as 'JAGS', 'STAN' and 'TMB'.
Numeric lists objects, which are useful for storing multiple realizations of
of simulated data sets, can be converted to
coda::mcmc and coda::mcmc.list objects.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between nlist versions 0.1.0 dated 2020-01-24 and 0.1.1 dated 2020-06-18
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 12 +++++++++++- NEWS.md | 4 ++++ R/namespace.R | 4 +++- R/nchains.R | 4 ++-- R/pars.R | 17 +++++++++++++++++ README.md | 36 +++++++++++++++--------------------- man/nchains.Rd | 4 ++-- tests/testthat/test-as-term.R | 24 +++++++++--------------- 10 files changed, 77 insertions(+), 56 deletions(-)
Title: Framework for Unified Estimation in Lognormal Models
Description: Lognormal models have broad applications in various research areas such as economics, actuarial science, biology, environmental science and psychology. The estimation problem in lognormal models has been extensively studied. This R package 'fuel' implements thirty-nine existing and newly proposed estimators. See Zhang, F., and Gou, J. (2020), A unified framework for estimation in lognormal models, Technical report.
Author: Jiangtao Gou and Fengqing (Zoe) Zhang
Maintainer: Jiangtao Gou <gouRpackage@gmail.com>
Diff between fuel versions 1.1.0 dated 2020-06-16 and 1.2.0 dated 2020-06-18
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- R/LN1060.R | 2 ++ R/LN1158.R |only R/lognormalest.R | 12 ++++++++++-- R/lognormalmean.R | 6 ++++-- R/lognormalmedian.R | 6 ++++-- R/lognormalsd.R | 6 ++++-- man/lognormalest.Rd | 6 ++++-- man/lognormalmean.Rd | 6 ++++-- man/lognormalmedian.Rd | 6 ++++-- man/lognormalsd.Rd | 6 ++++-- 12 files changed, 56 insertions(+), 31 deletions(-)
Title: Create Interactive Graphs with 'Echarts JavaScript' Version 4
Description: Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes
36 chart types, themes, 'Shiny' proxies and animations.
Author: John Coene [aut, cre, cph]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between echarts4r versions 0.2.3 dated 2019-07-18 and 0.3.2 dated 2020-06-18
echarts4r-0.2.3/echarts4r/R/pipes.R |only echarts4r-0.2.3/echarts4r/inst/htmlwidgets/lib/echarts-4.3.2 |only echarts4r-0.3.2/echarts4r/DESCRIPTION | 22 echarts4r-0.3.2/echarts4r/MD5 | 359 +- echarts4r-0.3.2/echarts4r/NAMESPACE | 99 echarts4r-0.3.2/echarts4r/NEWS.md | 49 echarts4r-0.3.2/echarts4r/R/add.R | 1384 ++++++++++- echarts4r-0.3.2/echarts4r/R/add_.R | 130 - echarts4r-0.3.2/echarts4r/R/append.R | 86 echarts4r-0.3.2/echarts4r/R/button.R | 2 echarts4r-0.3.2/echarts4r/R/echarts4r.R | 136 - echarts4r-0.3.2/echarts4r/R/geo.R | 27 echarts4r-0.3.2/echarts4r/R/grid.R | 118 echarts4r-0.3.2/echarts4r/R/helpers.R | 2 echarts4r-0.3.2/echarts4r/R/leaflet.R | 25 echarts4r-0.3.2/echarts4r/R/loading.R | 6 echarts4r-0.3.2/echarts4r/R/map.R | 97 echarts4r-0.3.2/echarts4r/R/mark.R | 31 echarts4r-0.3.2/echarts4r/R/nesting.R | 2 echarts4r-0.3.2/echarts4r/R/opts.R | 29 echarts4r-0.3.2/echarts4r/R/plugins.R | 34 echarts4r-0.3.2/echarts4r/R/proxies.R | 60 echarts4r-0.3.2/echarts4r/R/themes.R | 109 echarts4r-0.3.2/echarts4r/R/timeline.R | 35 echarts4r-0.3.2/echarts4r/R/utils-exports.R |only echarts4r-0.3.2/echarts4r/R/utils-pipe.R |only echarts4r-0.3.2/echarts4r/R/utils.R | 81 echarts4r-0.3.2/echarts4r/R/zzz.R | 5 echarts4r-0.3.2/echarts4r/README.md | 28 echarts4r-0.3.2/echarts4r/inst/htmlwidgets/echarts4r.js | 123 echarts4r-0.3.2/echarts4r/inst/htmlwidgets/echarts4r.yaml | 39 echarts4r-0.3.2/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0 |only echarts4r-0.3.2/echarts4r/inst/tutorials |only echarts4r-0.3.2/echarts4r/man/angle_axis.Rd | 3 echarts4r-0.3.2/echarts4r/man/append.Rd | 24 echarts4r-0.3.2/echarts4r/man/axis.Rd | 46 echarts4r-0.3.2/echarts4r/man/axis3d.Rd | 3 echarts4r-0.3.2/echarts4r/man/band.Rd | 29 echarts4r-0.3.2/echarts4r/man/callbacks.Rd | 3 echarts4r-0.3.2/echarts4r/man/connections.Rd | 13 echarts4r-0.3.2/echarts4r/man/e-tooltip.Rd | 42 echarts4r-0.3.2/echarts4r/man/e_add.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_animation.Rd | 17 echarts4r-0.3.2/echarts4r/man/e_area.Rd | 29 echarts4r-0.3.2/echarts4r/man/e_aria.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_axis_labels.Rd |only echarts4r-0.3.2/echarts4r/man/e_axis_pointer.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_axis_stagger.Rd |only echarts4r-0.3.2/echarts4r/man/e_bar.Rd | 29 echarts4r-0.3.2/echarts4r/man/e_bar_3d.Rd | 29 echarts4r-0.3.2/echarts4r/man/e_boxplot.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_brush.Rd | 16 echarts4r-0.3.2/echarts4r/man/e_button.Rd | 5 echarts4r-0.3.2/echarts4r/man/e_calendar.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_candle.Rd | 19 echarts4r-0.3.2/echarts4r/man/e_capture.Rd | 8 echarts4r-0.3.2/echarts4r/man/e_cloud.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_color.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_color_range.Rd | 18 echarts4r-0.3.2/echarts4r/man/e_correlations.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_datazoom.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_dispatch_action_p.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_draft.Rd | 6 echarts4r-0.3.2/echarts4r/man/e_draw_p.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_execute.Rd |only echarts4r-0.3.2/echarts4r/man/e_facet.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_flip_coords.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_flow_gl.Rd | 31 echarts4r-0.3.2/echarts4r/man/e_funnel.Rd | 24 echarts4r-0.3.2/echarts4r/man/e_gauge.Rd | 5 echarts4r-0.3.2/echarts4r/man/e_geo.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_geo_3d.Rd | 17 echarts4r-0.3.2/echarts4r/man/e_get_data.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_globe.Rd | 6 echarts4r-0.3.2/echarts4r/man/e_grid.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_grid_3d.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_heatmap.Rd | 33 echarts4r-0.3.2/echarts4r/man/e_hide_grid_lines.Rd |only echarts4r-0.3.2/echarts4r/man/e_labels.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_legend.Rd | 6 echarts4r-0.3.2/echarts4r/man/e_line.Rd | 29 echarts4r-0.3.2/echarts4r/man/e_lines.Rd | 39 echarts4r-0.3.2/echarts4r/man/e_lines_gl.Rd | 6 echarts4r-0.3.2/echarts4r/man/e_liquid.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_list.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_map_register.Rd | 21 echarts4r-0.3.2/echarts4r/man/e_modularity.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_parallel.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_pictorial.Rd | 29 echarts4r-0.3.2/echarts4r/man/e_pie.Rd | 9 echarts4r-0.3.2/echarts4r/man/e_polar.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_radar.Rd | 35 echarts4r-0.3.2/echarts4r/man/e_radar_opts.Rd | 18 echarts4r-0.3.2/echarts4r/man/e_remove.Rd |only echarts4r-0.3.2/echarts4r/man/e_resize.Rd |only echarts4r-0.3.2/echarts4r/man/e_restore.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_river.Rd | 9 echarts4r-0.3.2/echarts4r/man/e_sankey.Rd | 27 echarts4r-0.3.2/echarts4r/man/e_scatter_3d.Rd | 36 echarts4r-0.3.2/echarts4r/man/e_scatter_gl.Rd | 27 echarts4r-0.3.2/echarts4r/man/e_single_axis.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_step.Rd | 35 echarts4r-0.3.2/echarts4r/man/e_sunburst.Rd | 20 echarts4r-0.3.2/echarts4r/man/e_surface.Rd | 6 echarts4r-0.3.2/echarts4r/man/e_text_style.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_title.Rd | 6 echarts4r-0.3.2/echarts4r/man/e_tree.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_treemap.Rd | 18 echarts4r-0.3.2/echarts4r/man/e_utc.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_visual_map.Rd | 23 echarts4r-0.3.2/echarts4r/man/e_visual_map_range.Rd | 3 echarts4r-0.3.2/echarts4r/man/e_zoom.Rd | 3 echarts4r-0.3.2/echarts4r/man/echarts4r-shiny.Rd | 33 echarts4r-0.3.2/echarts4r/man/echartsNJSON.Rd | 5 echarts4r-0.3.2/echarts4r/man/errorbar.Rd | 29 echarts4r-0.3.2/echarts4r/man/figures |only echarts4r-0.3.2/echarts4r/man/formatters.Rd | 3 echarts4r-0.3.2/echarts4r/man/graph.Rd | 22 echarts4r-0.3.2/echarts4r/man/graph_action.Rd | 3 echarts4r-0.3.2/echarts4r/man/graphic.Rd | 3 echarts4r-0.3.2/echarts4r/man/highlight_action.Rd | 3 echarts4r-0.3.2/echarts4r/man/highlight_proxy.Rd | 3 echarts4r-0.3.2/echarts4r/man/histogram.Rd | 55 echarts4r-0.3.2/echarts4r/man/init.Rd | 54 echarts4r-0.3.2/echarts4r/man/leaflet.Rd | 10 echarts4r-0.3.2/echarts4r/man/legend_action.Rd | 3 echarts4r-0.3.2/echarts4r/man/line3D.Rd | 64 echarts4r-0.3.2/echarts4r/man/loading.Rd | 21 echarts4r-0.3.2/echarts4r/man/map.Rd | 60 echarts4r-0.3.2/echarts4r/man/map_actions.Rd | 3 echarts4r-0.3.2/echarts4r/man/mapbox.Rd | 3 echarts4r-0.3.2/echarts4r/man/mark.Rd | 42 echarts4r-0.3.2/echarts4r/man/node_adjacency.Rd | 9 echarts4r-0.3.2/echarts4r/man/pie_action.Rd | 3 echarts4r-0.3.2/echarts4r/man/pipe.Rd |only echarts4r-0.3.2/echarts4r/man/radius_axis.Rd | 3 echarts4r-0.3.2/echarts4r/man/reexports.Rd | 8 echarts4r-0.3.2/echarts4r/man/scatter.Rd | 103 echarts4r-0.3.2/echarts4r/man/smooth.Rd | 38 echarts4r-0.3.2/echarts4r/man/theme.Rd | 64 echarts4r-0.3.2/echarts4r/man/timeline-opts.Rd | 14 echarts4r-0.3.2/echarts4r/man/toolbox.Rd | 3 echarts4r-0.3.2/echarts4r/man/tooltip_action.Rd | 3 echarts4r-0.3.2/echarts4r/man/tooltip_proxy.Rd | 3 144 files changed, 3889 insertions(+), 843 deletions(-)
Title: Multivariate Tools for Compositional Data Analysis
Description: Provides functions for multivariate analysis with compositional data. Includes a function for doing compositional canonical correlation analysis. This analysis requires two data matrices of compositions, which can be adequately transformed and used as entries in a specialized program for canonical correlation analysis, that is able to deal with singular covariance matrices. The methodology is described in Graffelman et al. (2017) <doi:10.1101/144584>. A function for log-ratio principal component analysis with condition number computations has been added to the package.
Author: Jan Graffelman <jan.graffelman@upc.edu>
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between ToolsForCoDa versions 1.0.2 dated 2017-11-13 and 1.0.5 dated 2020-06-18
DESCRIPTION | 12 ++-- MD5 | 26 ++++++---- NAMESPACE | 5 +- R/largest.kappas.R |only R/lrpca.R |only build/vignette.rds |binary data/bentonites.rda |only inst/CITATION | 25 ++++------ inst/doc/ToolsForCoDa.R | 76 +++++++++++++++++++++--------- inst/doc/ToolsForCoDa.Rnw | 82 ++++++++++++++++++++++++++------- inst/doc/ToolsForCoDa.pdf |binary man/bentonites.Rd |only man/largest.kappas.Rd |only man/lrpca.Rd |only vignettes/ToolsForCoDa-018.pdf |only vignettes/ToolsForCoDa-concordance.tex |only vignettes/ToolsForCoDa.Rnw | 82 ++++++++++++++++++++++++++------- vignettes/ToolsForCoDa.bib | 23 ++++++--- 18 files changed, 241 insertions(+), 90 deletions(-)
Title: Spatial Survey Design and Analysis
Description: These functions provide procedures for selecting sites for spatial
surveys using spatially balanced algorithms applied to discrete points,
linear networks, or polygons. The probability survey designs available
include independent random samples, stratified random samples, and unequal
probability random samples (categorical or probability proportional to
size). Design-based estimation based on the results from surveys is
available for estimating totals, means, quantiles, CDFs, and linear models.
The analyses rely on package survey for most results. Variance estimation
options include a local neighborhood variance estimator that is appropriate
for spatially-balanced survey designs. A reference for the survey design
portion of the package is: D. L. Stevens, Jr. and A. R. Olsen (2004),
"Spatially-balanced sampling of natural resources.", Journal of the American
Statistical Association 99(465): 262-278, <DOI:10.1198/016214504000000250>.
Additional helpful references for this package are A. R. Olsen, T. M.
Kincaid, and Q. Payton (2012) and T. M. Kincaid and A. R. Olsen (2012), both
of which are chapters in the book "Design and Analysis of Long-Term
Ecological Monitoring Studies" (R. A. Gitzen, J. J. Millspaugh, A. B.
Cooper, and D. S. Licht (eds.), Cambridge University Press, New York,
<Online ISBN:9781139022422>).
Author: Tom Kincaid [aut],
Tony Olsen [aut],
Marc Weber [aut, cre],
Don Stevens [ctb],
Christian Platt [ctb],
Denis White [ctb],
Richard Remington [ctb]
Maintainer: Marc Weber <Weber.Marc@epa.gov>
Diff between spsurvey versions 4.1.2 dated 2020-04-01 and 4.1.3 dated 2020-06-18
DESCRIPTION | 12 MD5 | 128 ++++--- NEWS.md | 8 R/attrisk.var.R | 31 - R/catvar.prop.R | 12 R/catvar.size.R | 12 R/cdfvar.prop.R | 12 R/cdfvar.size.prop.R | 12 R/cdfvar.size.total.R | 12 R/cdfvar.test.R | 12 R/cdfvar.total.R | 12 R/changevar.mean.R | 11 R/changevar.prop.R | 11 R/changevar.size.R | 11 R/grts.R | 24 + R/grtsarea.R | 6 R/grtslin.R | 5 R/grtspts.R | 2 R/relrisk.var.R | 30 - build/vignette.rds |binary inst/doc/Area_Analysis.R | 71 ++-- inst/doc/Area_Analysis.Rmd | 1 inst/doc/Area_Analysis.html | 459 ++++++++++++--------------- inst/doc/Area_Design.R | 59 +-- inst/doc/Area_Design.Rmd | 9 inst/doc/Area_Design.html | 680 +++++++++++++++++++--------------------- inst/doc/CDF_Analysis.R | 35 +- inst/doc/CDF_Analysis.Rmd | 1 inst/doc/CDF_Analysis.html | 245 +++++++------- inst/doc/CDF_Deconvolution.R | 24 - inst/doc/CDF_Deconvolution.html | 300 ++++++++--------- inst/doc/CHANGES.pdf |binary inst/doc/Change_Analysis.R | 31 - inst/doc/Change_Analysis.Rmd | 1 inst/doc/Change_Analysis.html | 514 +++++++++++++++--------------- inst/doc/Finite_Analysis.R | 73 ++-- inst/doc/Finite_Analysis.Rmd | 1 inst/doc/Finite_Analysis.html | 637 ++++++++++++++++++------------------- inst/doc/Finite_Design.R | 53 +-- inst/doc/Finite_Design.Rmd | 1 inst/doc/Finite_Design.html | 479 ++++++++++++++-------------- inst/doc/Linear_Analysis.R | 72 ++-- inst/doc/Linear_Analysis.html | 530 +++++++++++++++---------------- inst/doc/Linear_Design.R | 59 +-- inst/doc/Linear_Design.Rmd | 9 inst/doc/Linear_Design.html | 677 ++++++++++++++++++++------------------- inst/doc/Risk_Analysis.R | 33 + inst/doc/Risk_Analysis.Rmd | 1 inst/doc/Risk_Analysis.html | 493 +++++++++++++---------------- tests/testthat/ButteCreek.dbf |only tests/testthat/ButteCreek.prj |only tests/testthat/ButteCreek.shp |only tests/testthat/ButteCreek.shx |only tests/testthat/NHDPoint.dbf |only tests/testthat/NHDPoint.prj |only tests/testthat/NHDPoint.shp |only tests/testthat/NHDPoint.shx |only tests/testthat/reg1_lakes.dbf |only tests/testthat/reg1_lakes.prj |only tests/testthat/reg1_lakes.shp |only tests/testthat/reg1_lakes.shx |only tests/testthat/test-frames.R | 6 tests/testthat/test-grts.R | 6 vignettes/Area_Analysis.Rmd | 1 vignettes/Area_Design.Rmd | 9 vignettes/CDF_Analysis.Rmd | 1 vignettes/Change_Analysis.Rmd | 1 vignettes/Finite_Analysis.Rmd | 1 vignettes/Finite_Design.Rmd | 1 vignettes/Linear_Design.Rmd | 9 vignettes/Risk_Analysis.Rmd | 1 71 files changed, 2900 insertions(+), 3047 deletions(-)
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>.
Author: Stefan Widgren [aut, cre] (<https://orcid.org/0000-0001-5745-2284>),
Robin Eriksson [aut] (<https://orcid.org/0000-0002-4291-712X>),
Stefan Engblom [aut] (<https://orcid.org/0000-0002-3614-1732>),
Pavol Bauer [aut] (<https://orcid.org/0000-0003-4328-7171>),
Thomas Rosendal [ctb] (<https://orcid.org/0000-0002-6576-9668>),
Attractive Chaos [cph] (Author of 'kvec.h'.)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 7.0.0 dated 2020-05-23 and 7.0.1 dated 2020-06-18
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 18 ++++++++++++++++++ R/C-generator.R | 4 +--- R/run.R | 2 +- README.md | 3 ++- inst/doc/SimInf.pdf |binary src/solvers/SimInf_solver.c | 2 +- tests/mparse.R | 10 ++++++---- 9 files changed, 40 insertions(+), 21 deletions(-)
Title: Test Shiny Apps
Description: For automated testing of Shiny applications, using a headless
browser, driven through 'WebDriver'.
Author: Winston Chang [aut, cre],
Gábor Csárdi [aut],
RStudio [cph, fnd],
Mango Solutions [cph, ccp]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinytest versions 1.3.1 dated 2019-05-06 and 1.4.0 dated 2020-06-18
shinytest-1.3.1/shinytest/tests/testthat/apps/006-tabsets |only shinytest-1.4.0/shinytest/DESCRIPTION | 18 - shinytest-1.4.0/shinytest/MD5 | 106 +++--- shinytest-1.4.0/shinytest/NAMESPACE | 1 shinytest-1.4.0/shinytest/NEWS.md | 21 + shinytest-1.4.0/shinytest/R/app-get-all-values.R | 1 shinytest-1.4.0/shinytest/R/migrate-shinytest-dir.R |only shinytest-1.4.0/shinytest/R/recorder.R | 10 shinytest-1.4.0/shinytest/R/session.R | 6 shinytest-1.4.0/shinytest/R/shiny-driver.R | 99 +++++ shinytest-1.4.0/shinytest/R/snapshot.R | 81 +++- shinytest-1.4.0/shinytest/R/test-app.R | 170 ++++++++-- shinytest-1.4.0/shinytest/R/utils.R | 47 ++ shinytest-1.4.0/shinytest/R/view-diff.R | 70 ++-- shinytest-1.4.0/shinytest/R/widget-get-value.R | 1 shinytest-1.4.0/shinytest/README.md | 19 - shinytest-1.4.0/shinytest/inst/diffviewerapp/app.R | 17 - shinytest-1.4.0/shinytest/inst/js/shiny-tracer.js | 69 ++-- shinytest-1.4.0/shinytest/inst/recorder/app.R | 17 - shinytest-1.4.0/shinytest/man/ShinyDriver.Rd | 112 +++--- shinytest-1.4.0/shinytest/man/Widget.Rd | 24 - shinytest-1.4.0/shinytest/man/dependenciesInstalled.Rd | 2 shinytest-1.4.0/shinytest/man/diffviewer_widget.Rd | 3 shinytest-1.4.0/shinytest/man/expectUpdate.Rd | 9 shinytest-1.4.0/shinytest/man/installDependencies.Rd | 4 shinytest-1.4.0/shinytest/man/migrateShinytestDir.Rd |only shinytest-1.4.0/shinytest/man/recordTest.Rd | 12 shinytest-1.4.0/shinytest/man/shinytest.Rd | 1 shinytest-1.4.0/shinytest/man/snapshotCompare.Rd | 17 - shinytest-1.4.0/shinytest/man/testApp.Rd | 20 - shinytest-1.4.0/shinytest/man/textTestDiff.Rd | 6 shinytest-1.4.0/shinytest/man/viewTestDiff.Rd | 15 shinytest-1.4.0/shinytest/man/viewTestDiffWidget.Rd | 6 shinytest-1.4.0/shinytest/tests/testthat/apps/006-tabsets-id/DESCRIPTION | 1 shinytest-1.4.0/shinytest/tests/testthat/apps/050-kmeans-example/DESCRIPTION | 1 shinytest-1.4.0/shinytest/tests/testthat/example_test_dirs |only shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/001.json | 3 shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/002.json | 3 shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/003.json | 3 shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/004.json | 3 shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/005.json | 4 shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/041-dynamic-ui/tests/mytest-expected/006.json | 4 shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/app-waitForValue |only shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/rmd-prerendered/tests/mytest-expected/001.json | 5 shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/rmd-prerendered/tests/mytest-expected/002.json | 5 shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/rmd/tests/mytest-expected/001.json | 21 + shinytest-1.4.0/shinytest/tests/testthat/recorded_tests/rmd/tests/mytest-expected/002.json | 21 + shinytest-1.4.0/shinytest/tests/testthat/test-find-tests.R |only shinytest-1.4.0/shinytest/tests/testthat/test-list-widgets.R | 2 shinytest-1.4.0/shinytest/tests/testthat/test-recorded-tests.R | 12 50 files changed, 772 insertions(+), 300 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 2.7-2 dated 2020-04-02 and 2.7-4 dated 2020-06-18
openair-2.7-2/openair/man/importAQE.Rd |only openair-2.7-2/openair/man/importSAQN.Rd |only openair-2.7-2/openair/man/importWAQN.Rd |only openair-2.7-4/openair/DESCRIPTION | 14 +- openair-2.7-4/openair/MD5 | 45 +++--- openair-2.7-4/openair/NAMESPACE | 3 openair-2.7-4/openair/R/TheilSen.R | 2 openair-2.7-4/openair/R/corPlot.R | 192 +++++++++++++--------------- openair-2.7-4/openair/R/cutData.R | 8 - openair-2.7-4/openair/R/getMeta.R | 125 +++++++++++------- openair-2.7-4/openair/R/importAQE.R | 171 +------------------------ openair-2.7-4/openair/R/importAURN.R | 218 +++++--------------------------- openair-2.7-4/openair/R/importNI.R |only openair-2.7-4/openair/R/importSAQN.R | 213 +------------------------------ openair-2.7-4/openair/R/importUKAQ.R |only openair-2.7-4/openair/R/importWAQN.R | 173 +------------------------ openair-2.7-4/openair/R/polarPlot.R | 116 ++++++++++++++--- openair-2.7-4/openair/R/timeProp.R | 6 openair-2.7-4/openair/R/utilities.R | 2 openair-2.7-4/openair/R/windRose.R | 6 openair-2.7-4/openair/R/zzz.R | 4 openair-2.7-4/openair/man/TheilSen.Rd | 2 openair-2.7-4/openair/man/corPlot.Rd | 181 ++++++++++++-------------- openair-2.7-4/openair/man/importAURN.Rd | 128 +++++++++++++----- openair-2.7-4/openair/man/importMeta.Rd | 57 ++++---- openair-2.7-4/openair/man/polarPlot.Rd | 24 ++- 26 files changed, 602 insertions(+), 1088 deletions(-)
Title: Recurrence Risk Assessment Tool
Description: Functions to estimate the risk of recurrence using disease-specific survival data. Mariotto AB, Zou Z, Zhang F, et al (2018) <doi:10.1158/1055-9965.EPI-17-1129>.
Author: Fanni Zhang <fannizhang@gmail.com>
Maintainer: Fanni Zhang <fannizhang@gmail.com>
Diff between RecurRisk versions 1.0 dated 2020-05-16 and 1.0.1 dated 2020-06-18
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- build/partial.rdb |binary man/RecurRisk-package.Rd | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Breast Cancer Risk Assessment
Description: Functions provide risk projections of invasive breast cancer based on Gail model according to National Cancer Institute's Breast Cancer Risk Assessment Tool algorithm for specified race/ethnic groups and age intervals.
Author: Fanni Zhang <fannizhang@gmail.com>
Maintainer: Fanni Zhang <fannizhang@gmail.com>
Diff between BCRA versions 2.1 dated 2018-10-30 and 2.1.1 dated 2020-06-18
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- man/BCRA-package.Rd | 4 ++-- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] (<https://orcid.org/0000-0003-4967-3831>),
Trustees of Columbia University [cph] (src/init.cpp, tools/make_cc.R,
R/stanmodels.R)
Maintainer: Kenta Yoshida <6.kurabupasu@gmail.com>
Diff between rstanemax versions 0.1.1 dated 2019-11-19 and 0.1.2 dated 2020-06-18
rstanemax-0.1.1/rstanemax/man/pipe.Rd |only rstanemax-0.1.2/rstanemax/DESCRIPTION | 8 rstanemax-0.1.2/rstanemax/LICENSE | 1348 +++++----- rstanemax-0.1.2/rstanemax/MD5 | 75 rstanemax-0.1.2/rstanemax/NAMESPACE | 32 rstanemax-0.1.2/rstanemax/NEWS.md | 37 rstanemax-0.1.2/rstanemax/R/create_model_frame.R | 222 - rstanemax-0.1.2/rstanemax/R/posterior_predict.R | 379 +- rstanemax-0.1.2/rstanemax/R/rstanemax-package.R | 34 rstanemax-0.1.2/rstanemax/R/set_prior.R | 152 - rstanemax-0.1.2/rstanemax/R/stan_emax.R | 349 +- rstanemax-0.1.2/rstanemax/R/stanemax-methods.R | 324 +- rstanemax-0.1.2/rstanemax/R/stanmodels.R | 74 rstanemax-0.1.2/rstanemax/R/utils.R | 18 rstanemax-0.1.2/rstanemax/R/yyy.R | 104 rstanemax-0.1.2/rstanemax/R/zzz.R | 8 rstanemax-0.1.2/rstanemax/README.md | 278 +- rstanemax-0.1.2/rstanemax/build/vignette.rds |binary rstanemax-0.1.2/rstanemax/inst/doc/emaxmodel.R | 227 - rstanemax-0.1.2/rstanemax/inst/doc/emaxmodel.Rmd | 382 +- rstanemax-0.1.2/rstanemax/inst/doc/emaxmodel.html | 857 ++++-- rstanemax-0.1.2/rstanemax/man/exposure.response.sample.Rd | 8 rstanemax-0.1.2/rstanemax/man/exposure.response.sample.test.Rd | 8 rstanemax-0.1.2/rstanemax/man/figures/README-unnamed-chunk-3-1.png |binary rstanemax-0.1.2/rstanemax/man/posterior_predict.Rd | 13 rstanemax-0.1.2/rstanemax/man/reexports.Rd |only rstanemax-0.1.2/rstanemax/man/rstanemax-package.Rd | 2 rstanemax-0.1.2/rstanemax/man/stan_emax.Rd | 22 rstanemax-0.1.2/rstanemax/man/stanemax-methods.Rd | 10 rstanemax-0.1.2/rstanemax/src/stan_files/chunks/license.stan | 28 rstanemax-0.1.2/rstanemax/src/stan_files/emax.stan | 186 - rstanemax-0.1.2/rstanemax/tests/spelling.R | 6 rstanemax-0.1.2/rstanemax/tests/testthat.R | 9 rstanemax-0.1.2/rstanemax/tests/testthat/Rplots.pdf |only rstanemax-0.1.2/rstanemax/tests/testthat/test-create_model_frame.R | 58 rstanemax-0.1.2/rstanemax/tests/testthat/test-posterior_predict.R | 194 - rstanemax-0.1.2/rstanemax/tests/testthat/test-set_prior.R | 160 - rstanemax-0.1.2/rstanemax/tests/testthat/test-stan_emax.R | 147 - rstanemax-0.1.2/rstanemax/tools/make_cc.R | 96 rstanemax-0.1.2/rstanemax/vignettes/emaxmodel.Rmd | 382 +- 40 files changed, 3337 insertions(+), 2900 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut, cre],
Hadley Wickham [aut],
lexicalunit [cph] (nanodbc library),
Google Inc. [cph] (cctz library),
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between odbc versions 1.2.2 dated 2020-01-10 and 1.2.3 dated 2020-06-18
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 8 ++++++++ R/DataTypes.R | 37 ++++++++++++++++++++++++++++++++----- R/Driver.R | 6 +++--- R/Table.R | 6 +++--- README.md | 2 +- build/odbc.pdf |binary man/dbConnect-OdbcDriver-method.Rd | 8 ++++---- src/Makevars.in | 2 +- src/Makevars.win | 2 +- src/odbc_result.cpp | 4 ++-- tests/testthat.R | 2 +- tests/testthat/test-MySQL.R | 9 +-------- tests/testthat/test-PostgreSQL.R | 5 +---- tests/testthat/test-SQLServer.R | 12 +----------- tests/testthat/test-SQLite.R | 6 +----- 17 files changed, 81 insertions(+), 70 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>),
Andrew Dunning [ctb] (<https://orcid.org/0000-0003-0464-5036>),
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Barret Schloerke [ctb],
Christophe Dervieux [ctb],
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Jeff Allen [ctb],
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>),
Malcolm Barrett [ctb],
Rob Hyndman [ctb],
Romain Lesur [ctb],
Roy Storey [ctb],
Ruben Arslan [ctb],
Sergio Oller [ctb],
RStudio, PBC [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs),
Benct Philip Jonsson [ctb, cph] (pagebreak lua filter),
Albert Krewinkel [ctb, cph] (pagebreak lua filter)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.2 dated 2020-05-31 and 2.3 dated 2020-06-18
DESCRIPTION | 8 ++-- MD5 | 53 ++++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 18 ++++++++++ R/html_dependencies.R | 12 +++++++ R/html_document.R | 12 +++++-- R/html_vignette.R | 2 + R/knit_print.R | 6 ++- R/output_format.R | 8 ++++ R/pandoc.R | 9 ++++- R/publish_site.R |only R/render.R | 30 +++++++++++++++-- build/vignette.rds |binary inst/doc/lua-filters.html | 16 +++++++++ inst/doc/pandoc.html | 16 +++++++++ inst/doc/rmarkdown.html | 16 +++++++++ inst/rmd/h/accessibility |only inst/rmd/h/navigation-1.1/codefolding.js | 2 - inst/rmd/ioslides/default.html | 2 - man/output_format.Rd | 8 ++++ man/publish_site.Rd |only tests/testthat.R | 3 - tests/testthat/test-formats.R | 6 --- tests/testthat/test-ioslides.R | 4 -- tests/testthat/test-notebook.R | 5 -- tests/testthat/test-params.R | 8 ---- tests/testthat/test-resources.R | 30 ----------------- tests/testthat/test-site.R | 3 - tests/testthat/test-vignette.R | 7 +++- 29 files changed, 184 insertions(+), 101 deletions(-)
Title: Access Databases from the Federal Statistical Office of Germany
Description: Retrieve and import data from different databases of the Federal Statistical Office of Germany (DESTATIS) using their SOAP XML web service <https://www-genesis.destatis.de/>.
Author: Moritz Marbach <moritz.marbach@gess.ethz.ch> [aut, cre]
Maintainer: Moritz Marbach <moritz.marbach@gess.ethz.ch>
Diff between wiesbaden versions 1.2.2 dated 2020-02-15 and 1.2.3 dated 2020-06-18
DESCRIPTION | 12 ++++----- MD5 | 20 +++++++-------- NEWS.md | 7 ++++- R/retrieve_data.R | 12 +++++++-- R/retrieve_valuelabel.R | 4 +-- build/vignette.rds |binary inst/doc/using-wiesbaden.R | 5 +++ inst/doc/using-wiesbaden.Rmd | 7 +++++ inst/doc/using-wiesbaden.html | 54 +++++++++++++++++------------------------- man/retrieve_data.Rd | 10 ++++++- vignettes/using-wiesbaden.Rmd | 7 +++++ 11 files changed, 82 insertions(+), 56 deletions(-)
Title: Functions for Forest Biometrics
Description: Functions for different purposes related to forest biometrics, including illustrative graphics, numerical computation, modeling height-diameter relationships, prediction of tree volumes, modelling of diameter distributions and estimation off stand density using ITD. Several empirical datasets are also included.
Author: Lauri Mehtatalo and Kasper Kansanen
Maintainer: Lauri Mehtatalo <lauri.mehtatalo@uef.fi>
Diff between lmfor versions 1.4 dated 2019-10-22 and 1.5 dated 2020-06-18
DESCRIPTION | 12 ++-- MD5 | 74 +++++++++++++++----------- NAMESPACE | 17 +++--- R/dd.R |only R/lmfor.R | 135 ------------------------------------------------ R/recweib2.R |only build |only data/BrkRes.RData |only data/plants.RData |only data/thefdata.RData |only data/thinning.RData |only man/BrkRes.Rd |only man/HDmodels.Rd | 8 +- man/HTest.Rd | 11 +-- man/HTest_cps.Rd | 23 ++++---- man/ImputeHeights.Rd | 6 +- man/NR.Rd | 2 man/NRnum.Rd | 2 man/afterthin.Rd | 7 +- man/alsTree.Rd | 7 ++ man/circle.Rd | 2 man/ddcomp.Rd | 4 - man/fithd.Rd | 8 -- man/foto.Rd | 5 + man/ips.Rd | 5 + man/linesplot.Rd | 11 +-- man/lmfor-package.Rd | 18 +++--- man/logit-logistic.Rd |only man/mywhiskers.Rd | 5 + man/patti.Rd | 7 +- man/percentile-based.Rd |only man/plants.Rd |only man/plants2.Rd | 5 + man/plot.hdmod.Rd | 2 man/predvol.Rd | 4 - man/qqplotHD.Rd | 2 man/qtree.Rd |only man/recweib.Rd | 50 ++++++++++++----- man/scaleDMean.Rd | 40 ++++++++------ man/spati.Rd | 5 + man/spati2.Rd | 5 + man/stumplift.Rd | 9 ++- man/thefdata.Rd |only man/thinning.Rd |only man/updown.Rd | 2 45 files changed, 214 insertions(+), 279 deletions(-)
Title: Fetch Data from 'National Stock Exchange (India)'
Description: Fetch data related to stocks, index, futures & options from the
'NSE (National Stock Exchange, India)'. This package is community maintained
and is not officially supported by 'NSE'. The accuracy of data is only as
correct as provided on <https://www.nseindia.com>.
Author: Lokesh Kumar [aut],
Aravind Hebbali [aut, cre],
Lionel Pinto [ctb]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between nse2r versions 0.1.1 dated 2020-01-08 and 0.1.2 dated 2020-06-18
DESCRIPTION | 14 MD5 | 32 - NEWS.md | 13 R/nse-shiny-app.R | 1 R/nse-stock.R | 8 R/nse-utils.R | 14 README.md | 1113 ++++++++++++++++++++++++++++------- inst/application/logic/logic_binom.R | 2 man/nse2r.Rd | 1 tests |only 10 files changed, 949 insertions(+), 249 deletions(-)
Title: A Quick Way to Map U.S. Rates and Data of U.S. States, Counties,
Census Tracts, or Seer Registries using 2000 and 2010 U.S.
Census Boundaries
Description: Provides an easy way to map seer registry area rate data on a U.S. map.
The U.S. data may be mapped at the state or state/county.
U.S. Seer registry data may be mapped at the Seer registry area, Seer Registry
area/county or Seer Registry area/county/census tract level. The function uses
a calculated default categorization breakpoint list for 5 categories,
when not breakpoint list is provided or the number of categories is specified
by the user. A user provided break point list is limited to containing 5 values.
The number of calculated categories may be from 3 to 11. The user provide the p-value
for each area and request hatching over any areas with a p-value > 0.05.
Other types of comparisons can be specified. If states or
state/counties are used, the area identifier is the U.S. FIPS codes for states and
counties, 2 digits and 5 digits respectfully. If the data is for U.S. Seer Registry
areas, the Seer Registry area identifier used to link the data to the geographical
area is a Seer Registry area abbreviation. See documentation for the list of
acceptable Seer Registry area names and abbreviations. The state boundaries are
overlaid all rate maps. The package contains the boundary data for state, county,
Seer Registry areas, and census tracts for counties within a Seer registry area.
The package support boundary data from the 2000 and 2010 U.S. Census.
The SeerMapper package version contains the U.S. Census 2000 and 2010 boundary data
for the regional, state, Seer Registry, and county levels. Six supplement packages
contain the census tract boundary data.
Copyrighted 2014, 2015, 2016, 2017, 2018 and 2019 by Pearson and Pickle.
Author: Jim Pearson <jbpearson353@gmail.com>
Maintainer: Fanni Zhang <zhangf@imsweb.com>
Diff between SeerMapper versions 1.2.2 dated 2020-06-08 and 1.2.3 dated 2020-06-18
DESCRIPTION | 10 MD5 | 20 R/SeerMapper.R | 8 data/co99_d00.rda |binary data/hs99_d00.rda |binary data/rg99_d00.rda |binary data/sa99_d00.rda |binary data/st99_d00.rda |binary inst/doc/NEWS | 72 man/SeerMapper-package.Rd | 38 man/SeerMapper.Rd | 5170 ++++++++++++++++++++++------------------------ 11 files changed, 2654 insertions(+), 2664 deletions(-)
Title: Mixture Models with Heterogeneous and (Partially) Missing Data
Description: Mixture Composer <https://github.com/modal-inria/MixtComp> is a project to build mixture models with
heterogeneous data sets and partially missing data management.
It includes models for real, categorical, counting, functional and ranking data.
This package contains the minimal R interface of the C++ 'MixtComp' library.
Author: Vincent Kubicki [aut],
Christophe Biernacki [aut],
Quentin Grimonprez [aut, cre],
Serge Iovleff [ctb],
Matthieu Marbac-Lourdelle [ctb],
Étienne Goffinet [ctb],
Patrick Wieschollek [ctb] (for CppOptimizationLibrary),
Tobias Wood [ctb] (for CppOptimizationLibrary)
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>
Diff between RMixtCompIO versions 4.0.2 dated 2019-12-16 and 4.0.5 dated 2020-06-18
DESCRIPTION | 10 - MD5 | 49 ++++---- NEWS | 6 + R/GENDATA_functionalGenerator.R | 31 +---- R/RMixtCompIO-package.R | 2 R/rmcMultiRun.R | 42 +++++++ man/RMixtCompIO-package.Rd | 2 man/rmcMultiRun.Rd | 6 - src/lib/Composer/MixtureComposer.cpp | 23 +++- src/lib/Composer/MixtureComposer.h | 53 +++------ src/lib/Composer/ZClassInd.cpp | 40 +++++++ src/lib/Composer/ZClassInd.h | 17 +-- src/lib/LinAlg/Maths.h | 4 src/lib/Mixture/Rank/RankMixture.h | 33 ++++++ src/lib/Mixture/Simple/Gaussian/Gaussian.cpp | 2 src/lib/Mixture/Simple/NegativeBinomial/NegativeBinomial.cpp | 2 src/lib/Mixture/Simple/SimpleMixture.h | 60 ++++++++++- src/lib/Mixture/Simple/Weibull/Weibull.cpp | 2 src/lib/Run/Learn.h | 2 src/lib/Run/Predict.h | 2 src/lib/Statistic/NormalStatistic.cpp | 2 src/lib/Strategy/SEMStrategy.h | 2 src/lib/Various/Constants.cpp | 5 src/lib/Various/Constants.h | 2 tests/testthat/test.index.R |only tests/testthat/test.run.R | 16 +- 26 files changed, 290 insertions(+), 125 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented wing2015() for
segment_snags()),
Bourdon Jean-François [ctb] (Contributed to Roussel2020() for
track_sensor()),
Gatziolis Demetrios [ctb] (Implemented Gatziolis2019() for
track_sensor())
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 3.0.0 dated 2020-06-08 and 3.0.1 dated 2020-06-18
DESCRIPTION | 10 - MD5 | 156 ++++++++++++------------ NEWS.md | 11 + R/Class-LAS.R | 4 R/add_attribute.R | 6 R/algorithm-dec.R | 2 R/algorithm-trk.R | 2 R/catalog_apply.R | 8 - R/catalog_intersect.R | 2 R/catalog_makecluster.R | 2 R/catalog_retile.R | 6 R/catalog_select.R | 4 R/clip_roi.R | 2 R/cloud_metrics.R | 20 +-- R/deprecated.R | 24 +-- R/filter_poi.R | 8 - R/grid_metrics.R | 8 - R/grid_terrain.R | 2 R/hexbin_metrics.R | 2 R/io_readLAS.R | 14 +- R/io_readLAScatalog.R | 6 R/io_readMSLAS.R | 2 R/io_writeLAS.R | 2 R/merge_spatial.R | 1 R/methods-LAS.R | 2 R/normalize_height.R | 4 R/normalize_intensity.R | 2 R/plot.R | 6 R/plot.s3.R | 15 -- R/projection.R | 6 R/tree_metrics.R | 2 R/utils_catalog_options.R | 4 R/utils_colors.R | 1 R/utils_metrics.R | 14 +- R/utils_threads.R | 2 build/vignette.rds |binary inst/doc/lidR-LAScatalog-engine.html | 6 inst/doc/lidR-computation-speed-LAScatalog.html | 2 man/LAD.Rd | 4 man/LAS-class.Rd | 6 man/Roussel2020.Rd | 2 man/VCI.Rd | 2 man/add_attribute.Rd | 6 man/catalog_apply.Rd | 8 - man/catalog_intersect.Rd | 2 man/catalog_makechunks.Rd | 2 man/catalog_options_tools.Rd | 4 man/catalog_retile.Rd | 6 man/catalog_select.Rd | 4 man/clip.Rd | 2 man/cloud_metrics.Rd | 20 +-- man/deprecated.Rd | 24 +-- man/entropy.Rd | 4 man/filter_poi.Rd | 4 man/filters.Rd | 4 man/gap_fraction_profile.Rd | 2 man/grid_metrics.Rd | 8 - man/hexbin_metrics.Rd | 2 man/lidrpalettes.Rd | 3 man/normalize_height.Rd | 2 man/normalize_intensity.Rd | 2 man/plot.Rd | 6 man/plot.lasmetrics3d.Rd | 10 - man/plot_3d.Rd | 6 man/random.Rd | 2 man/readLAS.Rd | 6 man/readLAScatalog.Rd | 6 man/readLASheader.Rd | 2 man/readMSLAS.Rd | 2 man/set_lidr_threads.Rd | 2 man/stdmetrics.Rd | 2 man/tree_metrics.Rd | 2 man/writeLAS.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-grid_terrain.R | 4 tests/testthat/test-lascheck.R | 2 tests/testthat/test-lasmergespatial.R | 1 tests/testthat/test-lastrees.R | 7 - tests/testthat/test-tree_hulls.R | 12 + 79 files changed, 288 insertions(+), 279 deletions(-)
Title: Feature Set Enrichment Analysis for Metabolomics and
Transcriptomics
Description: Methods and feature set definitions for feature or gene set
enrichment analysis in transcriptional and metabolic profiling data.
Package includes tests for enrichment based on ranked lists of features,
functions for visualisation and multivariate functional analysis.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between tmod versions 0.40 dated 2018-11-29 and 0.44 dated 2020-06-18
tmod-0.40/tmod/R/userguide.R |only tmod-0.40/tmod/inst/doc/tmod.R |only tmod-0.40/tmod/inst/doc/tmod.rmd |only tmod-0.40/tmod/inst/doc/tmod_user_manual.pdf |only tmod-0.40/tmod/inst/tmod_user_manual.pdf |only tmod-0.40/tmod/man/tmodUserGuide.Rd |only tmod-0.40/tmod/vignettes/bibliography.bib |only tmod-0.40/tmod/vignettes/tmod.rmd |only tmod-0.44/tmod/ChangeLog | 18 tmod-0.44/tmod/DESCRIPTION | 17 tmod-0.44/tmod/MD5 | 89 ++-- tmod-0.44/tmod/NAMESPACE | 15 tmod-0.44/tmod/R/Egambia.R | 34 - tmod-0.44/tmod/R/classes.R | 44 ++ tmod-0.44/tmod/R/importexport.R | 113 ++++++ tmod-0.44/tmod/R/lem.R |only tmod-0.44/tmod/R/limma.R | 4 tmod-0.44/tmod/R/modstats.R | 123 ++++++ tmod-0.44/tmod/R/multivariate.R | 181 ++++++--- tmod-0.44/tmod/R/panelplots.R | 343 ++++++++++-------- tmod-0.44/tmod/R/statisticaltests.R | 46 +- tmod-0.44/tmod/R/tmod-package.R | 2 tmod-0.44/tmod/R/tmodSummary.R |only tmod-0.44/tmod/R/visualizations.R | 506 +++++++++++++++++++++++++-- tmod-0.44/tmod/README.md |only tmod-0.44/tmod/build/vignette.rds |binary tmod-0.44/tmod/inst/doc/tmod.pdf |binary tmod-0.44/tmod/inst/doc/tmod.pdf.asis |only tmod-0.44/tmod/man/Egambia.Rd | 36 - tmod-0.44/tmod/man/evidencePlot.Rd | 43 +- tmod-0.44/tmod/man/extract-methods.Rd | 3 tmod-0.44/tmod/man/getGenes.Rd | 3 tmod-0.44/tmod/man/makeTmodFromDataFrame.Rd |only tmod-0.44/tmod/man/modCorPlot.Rd |only tmod-0.44/tmod/man/modGroups.Rd |only tmod-0.44/tmod/man/modOverlaps.Rd |only tmod-0.44/tmod/man/pcaplot.Rd | 23 + tmod-0.44/tmod/man/pvalEffectPlot.Rd | 28 + tmod-0.44/tmod/man/showGene.Rd | 13 tmod-0.44/tmod/man/tmod2DataFrame.Rd |only tmod-0.44/tmod/man/tmodAUC.Rd | 13 tmod-0.44/tmod/man/tmodDecideTests.Rd | 13 tmod-0.44/tmod/man/tmodImportMSigDB.Rd | 13 tmod-0.44/tmod/man/tmodLEA.Rd |only tmod-0.44/tmod/man/tmodLEASummary.Rd |only tmod-0.44/tmod/man/tmodLimmaDecideTests.Rd | 13 tmod-0.44/tmod/man/tmodLimmaTest.Rd | 12 tmod-0.44/tmod/man/tmodLimmaTopTable.Rd | 9 tmod-0.44/tmod/man/tmodPCA.Rd | 24 + tmod-0.44/tmod/man/tmodPal.Rd | 2 tmod-0.44/tmod/man/tmodPanelPlot.Rd | 54 ++ tmod-0.44/tmod/man/tmodSummary.Rd | 23 + tmod-0.44/tmod/man/tmodTagcloud.Rd | 23 + tmod-0.44/tmod/man/tmodUtest.Rd | 119 ++++-- tmod-0.44/tmod/man/upset.Rd |only tmod-0.44/tmod/vignettes/.install_extras |only tmod-0.44/tmod/vignettes/tmod.pdf.asis |only 57 files changed, 1558 insertions(+), 444 deletions(-)
Title: Conversion of R Regression Output to LaTeX or HTML Tables
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented. (If the Zelig package, which this package enhances, cannot be found on CRAN, you can find it at <https://github.com/IQSS/Zelig>.)
Author: Philip Leifeld [aut, cre],
Claudia Zucca [ctb]
Maintainer: Philip Leifeld <philip.leifeld@essex.ac.uk>
Diff between texreg versions 1.37.4 dated 2020-06-15 and 1.37.5 dated 2020-06-18
texreg-1.37.4/texreg/tests/files/huxtablereg.RDS |only texreg-1.37.5/texreg/DESCRIPTION | 12 ++--- texreg-1.37.5/texreg/MD5 | 17 +++----- texreg-1.37.5/texreg/R/extract.R | 2 texreg-1.37.5/texreg/R/texreg.R | 6 +- texreg-1.37.5/texreg/inst/doc/texreg.pdf |binary texreg-1.37.5/texreg/tests/testthat/test-extract.R | 17 ++++++++ texreg-1.37.5/texreg/tests/testthat/test-huxtablereg.R | 7 +-- texreg-1.37.5/texreg/tests/testthat/test-plotreg.R | 2 texreg-1.37.5/texreg/tests/testthat/test-texreg.R | 36 +++++++++++++++++ 10 files changed, 77 insertions(+), 22 deletions(-)
Title: Solve for Leaf Temperature Using Energy Balance
Description: Implements models of leaf temperature using energy balance. It uses units to ensure that parameters are properly specified and transformed before calculations. It allows separate lower and upper surface conductances to heat and water vapour, so sensible and latent heat loss are calculated for each surface separately as in Foster and Smith (1986) <doi:10.1111/j.1365-3040.1986.tb02108.x>. It's straightforward to model leaf temperature over environmental gradients such as light, air temperature, humidity, and wind. It can also model leaf temperature over trait gradients such as leaf size or stomatal conductance. Other references are Monteith and Unsworth (2013, ISBN:9780123869104), Nobel (2009, ISBN:9780123741431), and Okajima et al. (2012) <doi:10.1007/s11284-011-0905-5>.
Author: Chris Muir [aut, cre] (<https://orcid.org/0000-0003-2555-3878>)
Maintainer: Chris Muir <cdmuir@hawaii.edu>
Diff between tealeaves versions 1.0.3 dated 2020-06-13 and 1.0.5 dated 2020-06-18
DESCRIPTION | 17 +++---- MD5 | 28 ++++++----- NEWS.md | 12 +++++ R/constants.R | 16 +++--- R/enviro-par.R | 56 +++++++++++------------ R/leaf-par.R | 2 R/make_parameters.R | 71 +++++++++++++++++------------- R/parameter_names.R | 26 ++++++++++ R/tleaves.R | 43 ++++++++++++++++-- README.md | 6 -- build/vignette.rds |binary inst/doc/parameter-functions.html | 8 +-- inst/doc/tealeaves-intermediate.html | 4 - inst/doc/tealeaves-introduction.html | 26 +--------- tests/testthat/test-parameter-functions.R |only tests/testthat/test-tleaves-crossing.R |only 16 files changed, 189 insertions(+), 126 deletions(-)
Title: Supplemental U.S. 2000 Census Tract Boundaries for 13 Western
States without Seer Registries for 'SeerMapper'
Description: Provides supplemental 2000 census tract boundaries for the 13 states
without Seer Registries that are west of the Mississippi river
for use with the 'SeerMapper' package.
The data contained in this
package is derived from U.S. 2000 Census data and is in the public domain.
Updated to Alber Equal Area projection.
Author: Jim Pearson <jbpearson353@gmail.com> with data provided by U.S. Census Bureau
Maintainer: Fanni Zhang <zhangf@imsweb.com>
Diff between SeerMapperWest versions 1.2.2 dated 2020-05-21 and 1.2.3 dated 2020-06-18
DESCRIPTION | 10 +- MD5 | 6 - inst/NEWS | 34 +++++---- man/SeerMapperWest-package.Rd | 152 +++++++++++++++++++++--------------------- 4 files changed, 103 insertions(+), 99 deletions(-)
More information about SeerMapperWest at CRAN
Permanent link
Title: Supplemental U.S. 2000 Census Tract Boundaries for 19 States
with Seer Registries for 'SeerMapper'
Description: Provides supplemental 2000 census tract boundaries for the 19 states
containing Seer Registries for use with the 'SeerMapper' package.
The data contained in this
package is derived from U.S. Census data and is in the public domain.
Author: Jim Pearson <jbpearson353@gmail.com> with data provided by U.S. Census Bureau
Maintainer: Fanni Zhang <zhangf@imsweb.com>
Diff between SeerMapperRegs versions 1.2.2 dated 2020-05-21 and 1.2.3 dated 2020-06-18
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/NEWS | 31 ++++++++++++++++--------------- man/SeerMapperRegs-package.Rd | 10 +++++----- 4 files changed, 29 insertions(+), 28 deletions(-)
More information about SeerMapperRegs at CRAN
Permanent link
Title: Supplemental U.S. 2000 Census Tract Boundaries for 20 Eastern
States, District and Territory without Seer Registries for
'SeerMapper'
Description: Provides supplemental 2000 census tract boundaries for the 20 states, district and territory
without Seer Registries that are east of the Mississippi river
for use with the 'SeerMapper' package.
The data contained in this
package is derived from U.S. Census data and is in the public domain.
Author: Jim Pearson <jbpearson353@gmail.com> with data provided by U.S. Census Bureau
Maintainer: Fanni Zhang <zhangf@imsweb.com>
Diff between SeerMapperEast versions 1.2.2 dated 2020-05-21 and 1.2.3 dated 2020-06-18
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/NEWS | 33 ++++++++++++++++++--------------- man/SeerMapperEast-package.Rd | 12 ++++++------ 4 files changed, 32 insertions(+), 29 deletions(-)
More information about SeerMapperEast at CRAN
Permanent link
Title: Supplemental U.S. 2010 Census Tract Boundaries for 13 Western
States without Seer Registries for 'SeerMapper'
Description: Provides supplemental 2010 census tract boundaries for the 13 states
without Seer Registries that are west of the Mississippi river
for use with the 'SeerMapper' package.
The data contained in this
package is derived from U.S. 2010 Census data and is in public domain.
Author: Jim Pearson <jbpearson353@gmail.com> with data provided by U.S. Census Bureau
Maintainer: Fanni Zhang <zhangf@imsweb.com>
Diff between SeerMapper2010West versions 1.2.2 dated 2020-05-21 and 1.2.3 dated 2020-06-18
DESCRIPTION | 10 +- MD5 | 6 - inst/NEWS | 35 +++++--- man/SeerMapper2010West-package.Rd | 149 ++++++++++++++++++-------------------- 4 files changed, 102 insertions(+), 98 deletions(-)
More information about SeerMapper2010West at CRAN
Permanent link
Title: Supplemental U.S. 2010 Census Tract Boundaries for 19 States
with Seer Registries for 'SeerMapper'
Description: Provides supplemental 2010 census tract boundaries of the 19 states
containing Seer Registries for use with the 'SeerMapper' package.
The data contained in this
package is derived from U.S. 2010 Census data and is in public domain.
Author: Jim Pearson <jbpearson353@gmail.com> with data provided by U.S. Census Bureau
Maintainer: Fanni Zhang <zhangf@imsweb.com>
Diff between SeerMapper2010Regs versions 1.2.2 dated 2020-05-21 and 1.2.3 dated 2020-06-18
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/NEWS | 32 +++++++++++++++++--------------- man/SeerMapper2010Regs-package.Rd | 10 +++++----- 4 files changed, 30 insertions(+), 28 deletions(-)
More information about SeerMapper2010Regs at CRAN
Permanent link
Title: Supplemental U.S. 2010 Census Tract Boundaries for 20 Eastern
States (including DC and PR) without Registries for
'SeerMapper'
Description: Provides supplemental 2010 census tract boundary package for 20 states
without Seer Registries that are east of the Mississippi river
for use with the 'SeerMapper' package.
The data contained in this
package is derived from U.S. Census data and is in public domain.
Author: Jim Pearson <jbpearson353@gmail.com> with data provided by U.S. Census Bureau
Maintainer: Fanni Zhang <zhangf@imsweb.com>
Diff between SeerMapper2010East versions 1.2.2 dated 2020-05-21 and 1.2.3 dated 2020-06-18
DESCRIPTION | 13 ++++++------ MD5 | 6 ++--- inst/NEWS | 40 +++++++++++++++++++++----------------- man/SeerMapper2010East-package.Rd | 10 ++++----- 4 files changed, 38 insertions(+), 31 deletions(-)
More information about SeerMapper2010East at CRAN
Permanent link
Title: Reproducible Reports in Psychology
Description: Helper functions for producing reports in Psychology (Reproducible Research). Provides required formatted strings (APA style) for use in 'Knitr'/'Latex' integration within *.Rnw files.
Author: Ian G Mackenzie
Maintainer: Ian G Mackenzie <ian.mackenzie@uni-tuebingen.de>
Diff between psychReport versions 0.7 dated 2019-08-29 and 1.1.0 dated 2020-06-18
psychReport-0.7/psychReport/R/addDataDF.R |only psychReport-0.7/psychReport/R/aovDispMeans.R |only psychReport-0.7/psychReport/R/aovDispTable.R |only psychReport-0.7/psychReport/R/aovEffectSize.R |only psychReport-0.7/psychReport/R/aovJackknifeAdjustment.R |only psychReport-0.7/psychReport/R/aovRoundDigits.R |only psychReport-0.7/psychReport/R/aovSphericityAdjustment.R |only psychReport-0.7/psychReport/R/aovTable.R |only psychReport-0.7/psychReport/R/ciStrT.R |only psychReport-0.7/psychReport/R/createDF.R |only psychReport-0.7/psychReport/R/dat.R |only psychReport-0.7/psychReport/R/effectsizeValueString.R |only psychReport-0.7/psychReport/R/errDist.R |only psychReport-0.7/psychReport/R/exampleRnwFiles.R |only psychReport-0.7/psychReport/R/fValueString.R |only psychReport-0.7/psychReport/R/mathString.R |only psychReport-0.7/psychReport/R/meanStrAov.R |only psychReport-0.7/psychReport/R/meanStrT.R |only psychReport-0.7/psychReport/R/numValueString.R |only psychReport-0.7/psychReport/R/pValueString.R |only psychReport-0.7/psychReport/R/pValueSummary.R |only psychReport-0.7/psychReport/R/printAovMeans.R |only psychReport-0.7/psychReport/R/printTable.R |only psychReport-0.7/psychReport/R/requiredPackages.R |only psychReport-0.7/psychReport/R/rtDist.R |only psychReport-0.7/psychReport/R/sphericityValueString.R |only psychReport-0.7/psychReport/R/statStrAov.R |only psychReport-0.7/psychReport/R/statStrT.R |only psychReport-0.7/psychReport/R/tValueString.R |only psychReport-0.7/psychReport/data |only psychReport-0.7/psychReport/man/dat.Rd |only psychReport-0.7/psychReport/man/exampleRnwFiles.Rd |only psychReport-0.7/psychReport/tests/testthat/test-exampleRnwFiles.R |only psychReport-1.1.0/psychReport/DESCRIPTION | 13 psychReport-1.1.0/psychReport/MD5 | 155 ++++------ psychReport-1.1.0/psychReport/NAMESPACE | 3 psychReport-1.1.0/psychReport/R/anova.R |only psychReport-1.1.0/psychReport/R/psychReportData.R |only psychReport-1.1.0/psychReport/R/ttest.R |only psychReport-1.1.0/psychReport/R/utils.R |only psychReport-1.1.0/psychReport/man/addDataDF.Rd | 59 ++- psychReport-1.1.0/psychReport/man/aovDispMeans.Rd | 20 - psychReport-1.1.0/psychReport/man/aovDispTable.Rd | 20 - psychReport-1.1.0/psychReport/man/aovEffectSize.Rd | 45 +- psychReport-1.1.0/psychReport/man/aovJackknifeAdjustment.Rd | 41 +- psychReport-1.1.0/psychReport/man/aovRoundDigits.Rd | 34 -- psychReport-1.1.0/psychReport/man/aovSphericityAdjustment.Rd | 27 - psychReport-1.1.0/psychReport/man/aovTable.Rd | 65 +--- psychReport-1.1.0/psychReport/man/aovTidyTable.Rd |only psychReport-1.1.0/psychReport/man/ciStrT.Rd | 11 psychReport-1.1.0/psychReport/man/createDF.Rd | 26 - psychReport-1.1.0/psychReport/man/effectsizeValueString.Rd | 46 +- psychReport-1.1.0/psychReport/man/errDist.Rd | 2 psychReport-1.1.0/psychReport/man/fValueString.Rd | 39 -- psychReport-1.1.0/psychReport/man/mathString.Rd | 6 psychReport-1.1.0/psychReport/man/meanStrAov.Rd | 39 +- psychReport-1.1.0/psychReport/man/meanStrT.Rd | 10 psychReport-1.1.0/psychReport/man/numValueString.Rd | 2 psychReport-1.1.0/psychReport/man/pValueString.Rd | 8 psychReport-1.1.0/psychReport/man/pValueSummary.Rd | 12 psychReport-1.1.0/psychReport/man/printAovMeans.Rd | 27 - psychReport-1.1.0/psychReport/man/printTable.Rd | 25 - psychReport-1.1.0/psychReport/man/psychReport-package.Rd | 2 psychReport-1.1.0/psychReport/man/requiredPackages.Rd | 18 - psychReport-1.1.0/psychReport/man/rtDist.Rd | 6 psychReport-1.1.0/psychReport/man/sphericityValueString.Rd | 32 -- psychReport-1.1.0/psychReport/man/statStrAov.Rd | 43 +- psychReport-1.1.0/psychReport/man/statStrT.Rd | 15 psychReport-1.1.0/psychReport/man/tValueString.Rd | 14 psychReport-1.1.0/psychReport/tests/testthat.R | 2 psychReport-1.1.0/psychReport/tests/testthat/test-addDataDF.R | 48 +-- psychReport-1.1.0/psychReport/tests/testthat/test-aovDispMeans.R | 23 - psychReport-1.1.0/psychReport/tests/testthat/test-aovDispTable.R | 23 - psychReport-1.1.0/psychReport/tests/testthat/test-aovEffectSize.R | 39 -- psychReport-1.1.0/psychReport/tests/testthat/test-aovJackknifeAdjustment.R | 19 - psychReport-1.1.0/psychReport/tests/testthat/test-aovRoundDigits.R | 34 +- psychReport-1.1.0/psychReport/tests/testthat/test-aovSphericityAdjustment.R | 22 - psychReport-1.1.0/psychReport/tests/testthat/test-aovTable.R | 51 +-- psychReport-1.1.0/psychReport/tests/testthat/test-aovTidyTable.R |only psychReport-1.1.0/psychReport/tests/testthat/test-ciStrT.R | 6 psychReport-1.1.0/psychReport/tests/testthat/test-createDF.R | 24 - psychReport-1.1.0/psychReport/tests/testthat/test-effectsizeValueString.R | 37 +- psychReport-1.1.0/psychReport/tests/testthat/test-errDist.R | 22 - psychReport-1.1.0/psychReport/tests/testthat/test-fValueString.R | 32 +- psychReport-1.1.0/psychReport/tests/testthat/test-mathString.R | 10 psychReport-1.1.0/psychReport/tests/testthat/test-meanStrAov.R | 26 + psychReport-1.1.0/psychReport/tests/testthat/test-meanStrT.R | 10 psychReport-1.1.0/psychReport/tests/testthat/test-numValueString.R | 12 psychReport-1.1.0/psychReport/tests/testthat/test-pValueString.R | 18 - psychReport-1.1.0/psychReport/tests/testthat/test-pValueSummary.R | 14 psychReport-1.1.0/psychReport/tests/testthat/test-printAovMeans.R | 25 + psychReport-1.1.0/psychReport/tests/testthat/test-printTable.R | 19 - psychReport-1.1.0/psychReport/tests/testthat/test-requiredPackages.R | 4 psychReport-1.1.0/psychReport/tests/testthat/test-rtDist.R | 12 psychReport-1.1.0/psychReport/tests/testthat/test-sphericityValueString.R | 16 - psychReport-1.1.0/psychReport/tests/testthat/test-statStrAov.R | 29 + psychReport-1.1.0/psychReport/tests/testthat/test-statStrT.R | 2 psychReport-1.1.0/psychReport/tests/testthat/test-tValueString.R | 7 98 files changed, 718 insertions(+), 733 deletions(-)
Title: Summarizes Provenance Related to Inputs and Outputs of a Script
or Console Commands
Description: Reads the provenance collected by the 'rdt' or
'rdtLite' packages, or other tools providing compatible PROV JSON output
created by the execution of a script, and provides a human-readable
summary identifying the input and output files, the script used
(if any), errors and warnings produced, and the environment in
which it was executed. It can also optionally package all the
files into a zip file. The exact format of the JSON created by
'rdt' and 'rdtLite' is described in
<https://github.com/End-to-end-provenance/ExtendedProvJson>.
More information about 'rdtLite' and associated tools is available
at <https://github.com/End-to-end-provenance/> and Barbara Lerner,
Emery Boose, and Luis Perez (2018), Using Introspection to Collect
Provenance in R, Informatics, <doi: 10.3390/informatics5010012>.
Author: Barbara Lerner [cre],
Emery Boose [aut]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Diff between provSummarizeR versions 1.3 dated 2019-12-06 and 1.4 dated 2020-06-18
DESCRIPTION | 12 +++--- MD5 | 24 ++++++------ NEWS.md | 16 ++++---- R/provSummarizeR.R | 32 +++++++++++++++- README.md | 12 ++++-- inst/testdata/console.json | 50 +++++++++++++------------- inst/testdata/files.json | 66 +++++++++++++++++------------------ inst/testdata/prov.json | 66 +++++++++++++++++------------------ inst/testsummaries/console.expected | 37 ++++++++++--------- inst/testsummaries/files.expected | 47 +++++++++++++----------- inst/testsummaries/prov.expected | 49 +++++++++++++------------ inst/testsummaries/warnings.expected | 5 ++ man/summarize.Rd | 6 ++- 13 files changed, 234 insertions(+), 188 deletions(-)
More information about provSummarizeR at CRAN
Permanent link
Title: Maximum Diversity Weighting
Description: Dimension-reduction methods aim at defining a score that maximizes signal diversity. Three approaches, tree weight, maximum entropy weights, and maximum variance weights are provided. These methods are described in He and Fong (2019) <DOI:10.1002/sim.8212>.
Author: Zonglin He [aut],
Youyi Fong [cre]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between mdw versions 2017.12-03 dated 2017-12-04 and 2020.6-17 dated 2020-06-18
ChangeLog | 7 + DESCRIPTION | 23 +++-- MD5 | 32 +++++--- NAMESPACE | 29 ++++--- R/entropy.weight.R | 101 ++++++++++++++++++------- R/get.bw.R |only R/non-normal_categrical_data_generation.R |only R/tree_weight.R |only R/var.weight.R | 118 ++++++++++++++++++++---------- build |only inst/doc |only inst/unitTests/runit.weight.R | 25 +++++- man/asym.v.e.Rd | 52 ++++++------- man/asym.v.v.Rd | 46 +++++------ man/entropy.weight.Rd | 51 +++++++----- man/get.bw.Rd |only man/mdw.Rd |only man/pca.weight.Rd | 42 +++++----- man/tree.weight.Rd |only man/var.weight.Rd | 50 +++++++----- vignettes |only 21 files changed, 355 insertions(+), 221 deletions(-)
Title: Frechet Random Forests
Description: Random forests are a statistical learning method widely used in many areas of scientific research essentially for its ability to learn complex relationships between input and output variables and also its capacity to handle high-dimensional data. However, current random forests approaches are not flexible enough to handle longitudinal data, shapes and images. In this package, we introduce Fréchet trees and Fréchet random forests, which allow to manage data for which input and output can either curves, scalars, factors, shapes or images. To this end, a new way of splitting the nodes of trees is introduced and the prediction procedures of trees and forests are generalized.
Author: Louis Capitaine [aut, cre]
Maintainer: Louis Capitaine <louis.capitaine@u-bordeaux.fr>
Diff between FrechForest versions 0.8.1 dated 2019-12-04 and 0.9 dated 2020-06-18
FrechForest-0.8.1/FrechForest/R/FrechetPckg-package.R |only FrechForest-0.8.1/FrechForest/R/frechetpc.R |only FrechForest-0.8.1/FrechForest/man/DataGenCurves.Rd |only FrechForest-0.8.1/FrechForest/man/ERimpurity_split.Rd |only FrechForest-0.8.1/FrechForest/man/FrechForest-package.Rd |only FrechForest-0.8.1/FrechForest/man/FrechTree.Rd |only FrechForest-0.8.1/FrechForest/man/Frechforest.Rd |only FrechForest-0.8.1/FrechForest/man/Huberts.Rd |only FrechForest-0.8.1/FrechForest/man/TreeShapeCV.Rd |only FrechForest-0.8.1/FrechForest/man/curve.reduc.times.Rd |only FrechForest-0.8.1/FrechForest/man/elagageHuberts.Rd |only FrechForest-0.8.1/FrechForest/man/permutation.Rd |only FrechForest-0.8.1/FrechForest/man/predict.FrechTree.Rd |only FrechForest-0.8.1/FrechForest/man/predict.Frechforest.Rd |only FrechForest-0.8.1/FrechForest/man/rf_shape.Rd |only FrechForest-0.8.1/FrechForest/tests/testthat/test-that.R |only FrechForest-0.9/FrechForest/DESCRIPTION | 16 +- FrechForest-0.9/FrechForest/MD5 | 60 ++++----- FrechForest-0.9/FrechForest/NAMESPACE | 30 ++-- FrechForest-0.9/FrechForest/R/FrechForest.R |only FrechForest-0.9/FrechForest/man/Curve.reduc.times.Rd |only FrechForest-0.9/FrechForest/man/ERvar_split.Rd | 30 ++-- FrechForest-0.9/FrechForest/man/Fact.partitions.Rd |only FrechForest-0.9/FrechForest/man/FrechForest.Rd |only FrechForest-0.9/FrechForest/man/FrechetTree.Rd |only FrechForest-0.9/FrechForest/man/OOB.rfshape.Rd | 41 ++---- FrechForest-0.9/FrechForest/man/OOB.tree.Rd | 41 ++---- FrechForest-0.9/FrechForest/man/Rtmax.Rd | 66 +++++----- FrechForest-0.9/FrechForest/man/Tmax.Rd | 55 ++++---- FrechForest-0.9/FrechForest/man/branche.Rd | 32 ++-- FrechForest-0.9/FrechForest/man/elagage.Rd | 30 ++-- FrechForest-0.9/FrechForest/man/impurity.Rd | 36 ++--- FrechForest-0.9/FrechForest/man/impurity_split.Rd | 38 ++--- FrechForest-0.9/FrechForest/man/noeuds_deg.Rd | 30 ++-- FrechForest-0.9/FrechForest/man/ordonne.Rd | 34 ++--- FrechForest-0.9/FrechForest/man/permutation_courbes.Rd |only FrechForest-0.9/FrechForest/man/permutation_shapes.Rd |only FrechForest-0.9/FrechForest/man/pred.FT.Rd | 56 ++++---- FrechForest-0.9/FrechForest/man/predict.FrechForest.Rd |only FrechForest-0.9/FrechForest/man/read.Xarg.Rd |only FrechForest-0.9/FrechForest/man/rf_shape_para.Rd | 51 ++----- FrechForest-0.9/FrechForest/man/var_split.Rd | 40 ++---- FrechForest-0.9/FrechForest/tests/testthat.R | 8 - FrechForest-0.9/FrechForest/tests/testthat/test-FrechForest.R |only 44 files changed, 326 insertions(+), 368 deletions(-)
Title: Fit Continuous-Time State-Space and Latent Variable Models for
Quality Control of Argos Satellite (and Other) Telemetry Data
and for Estimating Movement Behaviour
Description: Fits continuous-time random walk and correlated random walk state-space models for quality control animal tracking data ('Argos', processed light-level 'geolocation', 'GPS'). Template Model Builder ('TMB') is used for fast estimation. The 'Argos' data can be: (older) least squares-based locations; (newer) Kalman filter-based locations with error ellipse information; or a mixture of both. The models estimate two sets of location states corresponding to: 1) each observation, which are (usually) irregularly timed; and 2) user-specified time intervals (regular or irregular). Latent variable models are provided to estimate move persistence along tracks as an index of behaviour. 'Jonsen I', 'McMahon CR', 'Patterson TA', 'Auger-Méthé M', 'Harcourt R', 'Hindell MA', 'Bestley S' (2019) Movement responses to environment: fast inference of variation among southern elephant seals with a mixed effects model. Ecology 100:e02566 <doi:10.1002/ecy.2566>.
Author: Ian Jonsen [aut, cre, cph],
Toby Patterson [aut, ctb]
Maintainer: Ian Jonsen <ian.jonsen@mq.edu.au>
Diff between foieGras versions 0.4.0 dated 2019-10-07 and 0.6-7 dated 2020-06-18
foieGras-0.4.0/foieGras/inst/doc/foiegras-basics.R |only foieGras-0.4.0/foieGras/inst/doc/foiegras-basics.Rmd |only foieGras-0.4.0/foieGras/inst/doc/foiegras-basics.html |only foieGras-0.4.0/foieGras/src/TMB/sub/ssm.hpp |only foieGras-0.4.0/foieGras/vignettes/foiegras-basics.Rmd |only foieGras-0.6-7/foieGras/DESCRIPTION | 34 - foieGras-0.6-7/foieGras/MD5 | 104 ++--- foieGras-0.6-7/foieGras/NAMESPACE | 17 foieGras-0.6-7/foieGras/NEWS.md | 14 foieGras-0.6-7/foieGras/R/emf.R | 26 - foieGras-0.6-7/foieGras/R/fit_mpm.R | 66 +-- foieGras-0.6-7/foieGras/R/fit_ssm.R | 164 ++++---- foieGras-0.6-7/foieGras/R/fmap.R | 22 - foieGras-0.6-7/foieGras/R/foieGras-package.R | 27 - foieGras-0.6-7/foieGras/R/grab.R | 26 - foieGras-0.6-7/foieGras/R/join.R | 21 - foieGras-0.6-7/foieGras/R/mpmf.R | 99 +++-- foieGras-0.6-7/foieGras/R/osar.r | 10 foieGras-0.6-7/foieGras/R/plot.fG_osar.R | 13 foieGras-0.6-7/foieGras/R/plot.fG_ssm.R | 18 foieGras-0.6-7/foieGras/R/prefilter.R | 136 +++---- foieGras-0.6-7/foieGras/R/print.ssm.R | 8 foieGras-0.6-7/foieGras/R/sfilter.R | 302 +++++++++------- foieGras-0.6-7/foieGras/README.md | 3 foieGras-0.6-7/foieGras/build/vignette.rds |binary foieGras-0.6-7/foieGras/data/fmpm.RData |binary foieGras-0.6-7/foieGras/data/fssm.RData |binary foieGras-0.6-7/foieGras/inst/doc/basics.R |only foieGras-0.6-7/foieGras/inst/doc/basics.Rmd |only foieGras-0.6-7/foieGras/inst/doc/basics.html |only foieGras-0.6-7/foieGras/man/ellie.Rd | 4 foieGras-0.6-7/foieGras/man/ellies.Rd | 4 foieGras-0.6-7/foieGras/man/emf.Rd | 19 - foieGras-0.6-7/foieGras/man/fit_mpm.Rd | 10 foieGras-0.6-7/foieGras/man/fit_ssm.Rd | 108 +++-- foieGras-0.6-7/foieGras/man/fmap.Rd | 17 foieGras-0.6-7/foieGras/man/fmpm.Rd | 4 foieGras-0.6-7/foieGras/man/foieGras-package.Rd | 8 foieGras-0.6-7/foieGras/man/fssm.Rd | 4 foieGras-0.6-7/foieGras/man/grab.Rd | 14 foieGras-0.6-7/foieGras/man/join.Rd | 8 foieGras-0.6-7/foieGras/man/mpmf.Rd | 12 foieGras-0.6-7/foieGras/man/osar.Rd | 4 foieGras-0.6-7/foieGras/man/plot.fG_osar.Rd | 9 foieGras-0.6-7/foieGras/man/plot.fG_ssm.Rd | 7 foieGras-0.6-7/foieGras/man/prefilter.Rd | 26 - foieGras-0.6-7/foieGras/man/print.ssm.Rd | 5 foieGras-0.6-7/foieGras/man/sfilter.Rd | 28 + foieGras-0.6-7/foieGras/src/TMB/sub/crw.hpp |only foieGras-0.6-7/foieGras/src/TMB/sub/joint_mpm.hpp | 35 + foieGras-0.6-7/foieGras/src/TMB/sub/mpm.hpp | 47 +- foieGras-0.6-7/foieGras/src/TMB/sub/rw.hpp |only foieGras-0.6-7/foieGras/src/foieGras.cpp | 9 foieGras-0.6-7/foieGras/tests/testthat/test-emf.R |only foieGras-0.6-7/foieGras/tests/testthat/test-fit_mpm.R | 12 foieGras-0.6-7/foieGras/tests/testthat/test-fit_ssm.R | 60 +-- foieGras-0.6-7/foieGras/tests/testthat/test-osar.R | 19 - foieGras-0.6-7/foieGras/tests/testthat/test-prefilter.R | 12 foieGras-0.6-7/foieGras/vignettes/basics.Rmd |only 59 files changed, 937 insertions(+), 658 deletions(-)
Title: Fast Fixed-Effects Estimations
Description: Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial.
The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://wwwen.uni.lu/content/download/110162/1299525/file/2018_13>.
Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
Author: Laurent Berge [aut, cre]
Maintainer: Laurent Berge <laurent.berge@uni.lu>
Diff between fixest versions 0.5.0 dated 2020-06-10 and 0.5.1 dated 2020-06-18
fixest-0.5.0/fixest/inst/NEWS.Rd |only fixest-0.5.0/fixest/src/omp_utilities.cpp |only fixest-0.5.1/fixest/DESCRIPTION | 6 fixest-0.5.1/fixest/MD5 | 64 - fixest-0.5.1/fixest/NEWS.md | 27 fixest-0.5.1/fixest/R/ESTIMATION_FUNS.R | 18 fixest-0.5.1/fixest/R/Lagging.R | 8 fixest-0.5.1/fixest/R/Methods.R | 6 fixest-0.5.1/fixest/R/MiscFuns.R | 241 ++++-- fixest-0.5.1/fixest/R/RcppExports.R | 28 fixest-0.5.1/fixest/R/coefplot.R | 2 fixest-0.5.1/fixest/R/fixest.R | 2 fixest-0.5.1/fixest/README.md | 2 fixest-0.5.1/fixest/inst/doc/fixest_walkthrough.html | 55 - fixest-0.5.1/fixest/man/coef.fixest.Rd | 2 fixest-0.5.1/fixest/man/coefplot.Rd | 2 fixest-0.5.1/fixest/man/deviance.fixest.Rd | 2 fixest-0.5.1/fixest/man/etable.Rd | 26 fixest-0.5.1/fixest/man/feNmlm.Rd | 6 fixest-0.5.1/fixest/man/feglm.Rd | 13 fixest-0.5.1/fixest/man/femlm.Rd | 11 fixest-0.5.1/fixest/man/feols.Rd | 6 fixest-0.5.1/fixest/man/fixef_reexported.Rd | 2 fixest-0.5.1/fixest/man/fixest-package.Rd | 2 fixest-0.5.1/fixest/man/panel.Rd | 6 fixest-0.5.1/fixest/man/setFixest_dict.Rd | 2 fixest-0.5.1/fixest/man/setFixest_fml.Rd | 2 fixest-0.5.1/fixest/man/sigma.fixest.Rd | 2 fixest-0.5.1/fixest/man/sub-.fixest_panel.Rd | 2 fixest-0.5.1/fixest/man/weights.fixest.Rd | 2 fixest-0.5.1/fixest/src/RcppExports.cpp | 95 -- fixest-0.5.1/fixest/src/lm_related.cpp | 746 ++++++------------- fixest-0.5.1/fixest/src/misc_funs.cpp | 231 ----- fixest-0.5.1/fixest/src/parallel_funs.cpp | 7 34 files changed, 573 insertions(+), 1053 deletions(-)
Title: Continuous Norming
Description: Conventional methods for producing standard scores in psychometrics or biometrics
are often plagued with "jumps" or "gaps" (i.e., discontinuities) in norm tables and low
confidence for assessing extreme scores. The continuous norming method introduced by A.
Lenhard et al. (2016, <doi:10.1177/1073191116656437>; 2019, <doi:10.1371/journal.pone.0222279>) and generates continuous test norm
scores on the basis of the raw data from standardization samples, without requiring
assumptions about the distribution of the raw data: Norm scores are directly established
from raw data by modeling the latter ones as a function of both percentile scores and an
explanatory variable (e.g., age). The method minimizes bias arising from sampling and
measurement error, while handling marked deviations from normality, addressing bottom
or ceiling effects and capturing almost all of the variance in the original norm data
sample. An online demonstration is available via <https://cnorm.shinyapps.io/cNORM/>.
Author: Wolfgang Lenhard [cre, aut] (<https://orcid.org/0000-0002-8184-6889>),
Alexandra Lenhard [aut],
Sebastian Gary [aut]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 1.2.2 dated 2019-09-19 and 1.2.3 dated 2020-06-18
DESCRIPTION | 18 +- MD5 | 112 +++++++++--------- NAMESPACE | 2 NEWS.md | 18 ++ R/data.R | 36 +++++ R/modelling.R | 30 +++- R/plot.R | 90 ++++++++------ R/predict.R | 73 ++++++++--- R/preparation.R | 12 + R/roots.R | 20 ++- README.md | 4 TODO |only build/vignette.rds |binary data/epm.rda |only inst/CITATION | 16 ++ inst/doc/cNORM-Demo.R | 26 ++-- inst/doc/cNORM-Demo.html | 71 +++++------ inst/shiny/server.R | 10 - inst/shiny/ui.R | 23 ++- inst/shiny/www/introduction.html | 4 man/CDC.Rd | 74 ++++++----- man/bestModel.Rd | 233 +++++++++++++++++++------------------ man/boxcox.Rd | 120 +++++++++---------- man/cNORM.Rd | 241 +++++++++++++++++++-------------------- man/calcPolyInL.Rd | 46 +++---- man/calcPolyInLBase.Rd |only man/checkConsistency.Rd | 155 +++++++++++++------------ man/cnorm.cv.Rd | 172 ++++++++++++++------------- man/computePowers.Rd | 126 ++++++++++---------- man/derivationTable.Rd | 84 +++++++------ man/derive.Rd | 60 ++++----- man/elfe.Rd | 80 ++++++------ man/epm.Rd |only man/getNormCurve.Rd | 92 ++++++++------ man/life.Rd | 98 ++++++++------- man/mortality.Rd | 90 +++++++------- man/normTable.Rd | 123 ++++++++++--------- man/plotBoxCox.Rd | 99 ++++++++-------- man/plotDensity.Rd | 85 +++++++------ man/plotDerivative.Rd | 110 +++++++++-------- man/plotNorm.Rd | 81 ++++++------- man/plotNormCurves.Rd | 129 +++++++++++--------- man/plotPercentileSeries.Rd | 105 +++++++++------- man/plotPercentiles.Rd | 151 +++++++++++++----------- man/plotRaw.Rd | 64 +++++----- man/plotSubset.Rd | 80 ++++++------ man/ppvt.Rd | 102 ++++++++-------- man/predictNorm.Rd | 93 ++++++++------- man/predictNormBC.Rd | 98 +++++++-------- man/predictRaw.Rd | 106 +++++++++-------- man/predictRawBC.Rd | 100 ++++++++-------- man/prepareData.Rd | 121 ++++++++++--------- man/printSubset.Rd | 46 +++---- man/rangeCheck.Rd | 76 ++++++------ man/rankByGroup.Rd | 171 ++++++++++++++------------- man/rankBySlidingWindow.Rd | 204 +++++++++++++++++---------------- man/rawTable.Rd | 111 +++++++++-------- man/regressionFunction.Rd | 56 ++++----- man/simulateRasch.Rd | 148 ++++++++++++----------- 59 files changed, 2520 insertions(+), 2175 deletions(-)
Title: Modern Psychometrics with R
Description: Supplementary materials and datasets for the book "Modern Psychometrics With R" (Mair, 2018, Springer useR! series).
Author: Patrick Mair [aut, cre]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between MPsychoR versions 0.10-7 dated 2018-05-26 and 0.10-8 dated 2020-06-18
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/Privacy.Rd | 12 +++++++----- 3 files changed, 13 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-07 0.2.1
2019-08-24 0.2.0
2019-06-05 0.1.3
2018-11-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-15 0.2.8
2018-03-13 0.2.7
Title: Parametric Survival Simulation with Parameter Uncertainty
Description: Perform survival simulation with parametric survival model generated from 'survreg' function in 'survival' package.
In each simulation coefficients are resampled from variance-covariance matrix of parameter estimates to
capture uncertainty in model parameters.
Prediction intervals of Kaplan-Meier estimates and hazard ratio of treatment effect can be further calculated using simulated survival data.
Author: Kenta Yoshida [aut, cre] (<https://orcid.org/0000-0003-4967-3831>),
Laurent Claret [aut]
Maintainer: Kenta Yoshida <6.kurabupasu@gmail.com>
Diff between survParamSim versions 0.1.1 dated 2020-05-12 and 0.1.2 dated 2020-06-18
DESCRIPTION | 8 MD5 | 38 +-- NEWS.md | 9 R/calc_hr_pi.R | 30 +- R/calc_km_pi.R | 29 +- R/extract_pi.R | 7 R/extract_raw_sim.R | 9 R/surv_param_sim_resample.R | 15 - build/vignette.rds |binary inst/doc/survParamSim.html | 304 +++++++++++++------------- man/calc_hr_pi.Rd | 6 man/calc_km_pi.Rd | 6 man/extractpi.Rd | 5 man/extractrawsim.Rd | 9 man/plot_hr_pi.Rd | 2 man/plot_km_pi.Rd | 4 man/survparamsim.Rd | 48 ++-- tests/testthat.R | 1 tests/testthat/test-extract_raw_sim.R | 2 tests/testthat/test-surv_param_sim_resample.R | 16 + 20 files changed, 297 insertions(+), 251 deletions(-)
Title: Robust Generalized Linear Models (GLM) using Mixtures
Description: Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between robmixglm versions 1.0-4 dated 2020-04-17 and 1.1-0 dated 2020-06-18
robmixglm-1.0-4/robmixglm/R/negbinom.fit.robmixglm.R |only robmixglm-1.1-0/robmixglm/DESCRIPTION | 11 robmixglm-1.1-0/robmixglm/MD5 | 78 +-- robmixglm-1.1-0/robmixglm/NAMESPACE | 17 robmixglm-1.1-0/robmixglm/R/RcppExports.R | 4 robmixglm-1.1-0/robmixglm/R/binomial.fit.robmixglm.R | 58 +- robmixglm-1.1-0/robmixglm/R/coef.robmixglm.R | 2 robmixglm-1.1-0/robmixglm/R/fit.robmixglm.R | 14 robmixglm-1.1-0/robmixglm/R/fitted.robmixglm.R | 4 robmixglm-1.1-0/robmixglm/R/gamma.fit.robmixglm.R | 56 +- robmixglm-1.1-0/robmixglm/R/gaussian.fit.robmixglm.R | 307 ++++++++------- robmixglm-1.1-0/robmixglm/R/globals.R | 4 robmixglm-1.1-0/robmixglm/R/myoptim.R | 14 robmixglm-1.1-0/robmixglm/R/nbinom.fit.robmixglm.R |only robmixglm-1.1-0/robmixglm/R/outlierTest.robmixglm.R | 196 ++++----- robmixglm-1.1-0/robmixglm/R/poisson.fit.robmixglm.R | 59 +- robmixglm-1.1-0/robmixglm/R/predict.robmixglm.R |only robmixglm-1.1-0/robmixglm/R/residuals.robmixglm.R | 28 - robmixglm-1.1-0/robmixglm/R/robmixglm.R | 39 + robmixglm-1.1-0/robmixglm/R/summary.robmixglm.R | 2 robmixglm-1.1-0/robmixglm/R/truncpoisson.fit.robmixglm.R | 56 +- robmixglm-1.1-0/robmixglm/build/vignette.rds |binary robmixglm-1.1-0/robmixglm/inst/NEWS | 10 robmixglm-1.1-0/robmixglm/man/AIC.Rd | 6 robmixglm-1.1-0/robmixglm/man/BIC.Rd | 7 robmixglm-1.1-0/robmixglm/man/coef.robmixglm.Rd | 7 robmixglm-1.1-0/robmixglm/man/diabdata.Rd | 18 robmixglm-1.1-0/robmixglm/man/extractAIC.Rd | 10 robmixglm-1.1-0/robmixglm/man/fitted.robmixglm.Rd | 9 robmixglm-1.1-0/robmixglm/man/hospcosts.Rd | 19 robmixglm-1.1-0/robmixglm/man/logLik.Rd | 7 robmixglm-1.1-0/robmixglm/man/outlierProbs.robmixglm.Rd | 5 robmixglm-1.1-0/robmixglm/man/outlierTest.robmixglm.Rd | 9 robmixglm-1.1-0/robmixglm/man/plot.outlierProbs.Rd | 9 robmixglm-1.1-0/robmixglm/man/predict.robmixglm.Rd |only robmixglm-1.1-0/robmixglm/man/print.outlierTest.Rd | 6 robmixglm-1.1-0/robmixglm/man/residuals.Rd | 9 robmixglm-1.1-0/robmixglm/man/robmixglm-package.Rd | 54 +- robmixglm-1.1-0/robmixglm/man/robmixglm.Rd | 30 - robmixglm-1.1-0/robmixglm/man/summary.robmixglm.Rd | 7 robmixglm-1.1-0/robmixglm/src/RcppExports.cpp | 10 robmixglm-1.1-0/robmixglm/src/fit.robmixglm.cpp | 2 42 files changed, 650 insertions(+), 533 deletions(-)
Title: Calculate Solutions to the Kelvin Differential Equation using
Bessel Functions
Description: Uses Bessel functions to calculate the
fundamental and complementary analytic solutions to the
Kelvin differential equation.
Author: Andrew J Barbour
Maintainer: Andrew J Barbour <andy.barbour@gmail.com>
Diff between kelvin versions 2.0-0 dated 2015-09-19 and 2.0-2 dated 2020-06-18
DESCRIPTION | 18 - MD5 | 24 +- NAMESPACE | 2 R/Beir.R | 8 R/Keir.R | 8 build/vignette.rds |binary inst/NEWS.Rd | 8 inst/doc/Curves.R | 6 inst/doc/Curves.html | 536 +++++++++++++++++++++++++++------------------ man/Beir.Rd | 23 + man/Keir.Rd | 34 +- man/kelvin-package.Rd | 27 +- tests/testthat/test-Beir.R | 2 13 files changed, 416 insertions(+), 280 deletions(-)
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@essex.ac.uk>
Diff between btergm versions 1.9.7 dated 2020-04-07 and 1.9.9 dated 2020-06-18
DESCRIPTION | 8 +++--- MD5 | 22 ++++++++--------- R/gofmethods.R | 31 ++++++++++++++++++++++++ R/gofstatistics.R | 10 +++---- R/interpretation.R | 54 +++++++++++++++++++++++++++++++------------ man/btergm-class.Rd | 2 - man/btergm.Rd | 4 +-- man/getformula.Rd | 2 - man/gofmethods.Rd | 2 - man/simulate.btergm.Rd | 8 +++--- tests/testthat/test-btergm.R | 1 tests/testthat/test-gof.R | 31 +++++++++++++++++++++++- 12 files changed, 130 insertions(+), 45 deletions(-)