Title: Lightweight Access to the 'Geospatial Data Abstraction Library'
('GDAL')
Description: Provides low-level access to 'GDAL' functionality for R packages. The aim is to minimize
the level of interpretation put on the 'GDAL' facilities, to enable direct use of it for a variety of purposes.
'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats
that presents a single raster abstract data model and single vector abstract data model to the calling application
for all supported formats <http://gdal.org/>. Other available packages 'rgdal' and 'sf' also provide access to
the 'GDAL' library, but neither can be used for these lower level tasks, and both do many other tasks.
Author: Michael Sumner [aut, cre] (<https://orcid.org/0000-0002-2471-7511>),
Simon Wotherspoon [ctb] (figured out the mechanism for the resampling
algorithm),
Mark Padgham [ctb] (helped get started :)),
Edzer Pebesma [ctb] (wrote allocate_attribute, copied here from sf),
Roger Bivand [ctb] (wrote configure.ac, copied here from rgdal),
Jim Hester [ctb] (wrote CollectorList.h, copied here from fs package),
Timothy Keitt [ctb] (wrote GetPointsInternal copied here from rgdal2
package),
Jeroen Ooms [ctb] (tweaked build process),
Dale Maschette [ctb] (created the hex logo)
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between vapour versions 0.3.0 dated 2019-09-18 and 0.4.0 dated 2019-09-27
vapour-0.3.0/vapour/src/gdal_warper.cpp |only vapour-0.4.0/vapour/DESCRIPTION | 6 vapour-0.4.0/vapour/MD5 | 63 - vapour-0.4.0/vapour/NAMESPACE | 1 vapour-0.4.0/vapour/NEWS.md | 28 vapour-0.4.0/vapour/R/RcppExports.R | 8 vapour-0.4.0/vapour/R/raster-info.R | 2 vapour-0.4.0/vapour/R/raster-input.R | 102 + vapour-0.4.0/vapour/R/vapour-helpers.R | 16 vapour-0.4.0/vapour/R/vapour-package.R | 10 vapour-0.4.0/vapour/README.md | 78 + vapour-0.4.0/vapour/configure | 520 ---------- vapour-0.4.0/vapour/configure.ac | 371 ------- vapour-0.4.0/vapour/data/tas_wkt.rda |only vapour-0.4.0/vapour/inst/WORDLIST | 6 vapour-0.4.0/vapour/inst/doc/vapour.R | 2 vapour-0.4.0/vapour/inst/doc/vapour.Rmd | 5 vapour-0.4.0/vapour/inst/doc/vapour.html | 65 - vapour-0.4.0/vapour/inst/docker |only vapour-0.4.0/vapour/man/tas_wkt.Rd |only vapour-0.4.0/vapour/man/vapour_raster_info.Rd | 2 vapour-0.4.0/vapour/man/vapour_read_raster.Rd | 9 vapour-0.4.0/vapour/man/vapour_srs_wkt.Rd |only vapour-0.4.0/vapour/src/RcppExports.cpp | 27 vapour-0.4.0/vapour/src/init.c | 6 vapour-0.4.0/vapour/src/raster_warp.cpp |only vapour-0.4.0/vapour/src/rasterio.cpp | 5 vapour-0.4.0/vapour/src/sds_io.cpp | 1 vapour-0.4.0/vapour/src/srs.cpp |only vapour-0.4.0/vapour/src/vapour.cpp | 2 vapour-0.4.0/vapour/tests/testthat.R | 2 vapour-0.4.0/vapour/tests/testthat/test-features.R | 34 vapour-0.4.0/vapour/tests/testthat/test-helpers.R | 8 vapour-0.4.0/vapour/tests/testthat/test-raster-info.R | 25 vapour-0.4.0/vapour/tests/testthat/test-rasterio-resampling.R | 5 vapour-0.4.0/vapour/vignettes/vapour.Rmd | 5 36 files changed, 414 insertions(+), 1000 deletions(-)
Title: Tidy Statistical Inference
Description: The objective of this package is to perform inference using an expressive statistical grammar that coheres with the tidy design framework.
Author: Andrew Bray [aut, cre],
Chester Ismay [aut],
Evgeni Chasnovski [aut],
Ben Baumer [aut],
Mine Cetinkaya-Rundel [aut],
Ted Laderas [ctb],
Nick Solomon [ctb],
Johanna Hardin [ctb],
Albert Y. Kim [ctb],
Neal Fultz [ctb],
Doug Friedman [ctb],
Richie Cotton [ctb],
Brian Fannin [ctb]
Maintainer: Andrew Bray <abray@reed.edu>
Diff between infer versions 0.4.0.1 dated 2019-04-22 and 0.5.0 dated 2019-09-27
DESCRIPTION | 16 MD5 | 137 ++ NAMESPACE | 3 NEWS.md |only R/calculate.R | 6 R/generate.R | 21 R/hypothesize.R | 99 -- R/infer.R | 2 R/shade_confidence_interval.R |only R/shade_p_value.R |only R/specify.R | 180 +-- R/utils.R | 139 +- R/visualize.R | 273 ----- R/wrappers.R | 283 ++++- build/vignette.rds |binary inst/doc/chisq_test.R | 44 inst/doc/chisq_test.Rmd | 105 +- inst/doc/chisq_test.html | 541 ++++++++--- inst/doc/flights_examples.R | 4 inst/doc/flights_examples.Rmd | 4 inst/doc/flights_examples.html | 829 ++++++++++------- inst/doc/mtcars_examples.html | 903 +++++++++++------- inst/doc/observed_stat_examples.html | 1163 ++++++++++++++---------- inst/doc/two_sample_t.html | 456 ++++++--- man/chisq_stat.Rd | 10 man/chisq_test.Rd | 10 man/generate.Rd | 6 man/hypothesize.Rd | 14 man/shade_confidence_interval.Rd | 2 man/shade_p_value.Rd | 24 man/t_stat.Rd | 26 man/t_test.Rd | 13 tests/figs |only tests/testthat.R | 4 tests/testthat/helper-data.R | 17 tests/testthat/test-calculate.R | 22 tests/testthat/test-generate.R | 1 tests/testthat/test-hypothesize.R | 123 ++ tests/testthat/test-rep_sample_n.R | 2 tests/testthat/test-shade_confidence_interval.R |only tests/testthat/test-shade_p_value.R |only tests/testthat/test-utils.R | 11 tests/testthat/test-visualize.R | 532 +++++----- tests/testthat/test-wrappers.R | 127 +- vignettes/chisq_test.Rmd | 105 +- vignettes/flights_examples.Rmd | 4 46 files changed, 3915 insertions(+), 2346 deletions(-)
Title: Area-Proportional Euler and Venn Diagrams with Ellipses
Description: Generate area-proportional Euler diagrams
using numerical optimization. An Euler diagram is a generalization of a Venn
diagram, relaxing the criterion that all interactions need to be
represented. Diagrams may be fit with ellipses and circles via
a wide range of inputs and can be visualized in numerous ways.
Author: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>),
A. Jonathan R. Godfrey [ctb],
Peter Gustafsson [ctb],
David H. Eberly [ctb] (geometric algorithms),
Emanuel Huber [ctb] (root solver code),
Kamil Slowikowski [ctb, cph] (modified code from ggrepel)
Maintainer: Johan Larsson <mail@larssonjohan.com>
Diff between eulerr versions 5.1.0 dated 2019-02-04 and 6.0.0 dated 2019-09-27
DESCRIPTION | 13 MD5 | 64 ++-- NAMESPACE | 2 NEWS.md | 37 ++ R/RcppExports.R | 62 ++++ R/eulerr.R | 1 R/eulerr_options.R | 12 R/layout.R | 70 ++--- R/plot.euler.R | 471 +++++++++-------------------------- R/setup_geometry.R |only R/setup_grobs.R |only R/tag-grobs.R |only R/utils.R | 5 README.md | 24 + build/vignette.rds |binary inst/WORDLIST | 84 +++--- inst/doc/gallery.R |only inst/doc/gallery.Rmd |only inst/doc/gallery.html |only inst/doc/introduction.html | 53 ++- inst/doc/under-the-hood.Rmd | 2 inst/doc/under-the-hood.html | 39 +- inst/doc/venn-diagrams.html | 23 + inst/doc/visualization.html | 17 - man/eulerr-package.Rd | 1 man/eulerr_options.Rd | 8 man/figures/README-plot_method-1.png |binary man/makeContent.EulerTags.Rd |only man/plot.euler.Rd | 47 ++- man/setup_geometry.Rd | 18 - man/setup_grobs.Rd | 7 man/setup_tag.Rd |only src/RcppExports.cpp | 23 + src/label-repel.cpp |only tests/testthat.R | 6 tests/testthat/test-plotting.R | 23 + vignettes/gallery.Rmd |only vignettes/under-the-hood.Rmd | 2 38 files changed, 569 insertions(+), 545 deletions(-)
Title: Damped Anderson Acceleration with Epsilon Monotonicity for
Accelerating EM-Like Monotone Algorithms
Description: Implements the DAAREM method for accelerating the convergence of slow, monotone sequences from smooth, fixed-point iterations such as the EM algorithm. For further details about the DAAREM method. see Henderson, N.C. and Varadhan, R. (2018) <arXiv:1803.06673>.
Author: Nicholas Henderson [cre, aut],
Ravi Varadhan [aut]
Maintainer: Nicholas Henderson <nchender@umich.edu>
Diff between daarem versions 0.3 dated 2019-02-09 and 0.4 dated 2019-09-27
DESCRIPTION | 12 ++-- MD5 | 12 ++-- NAMESPACE | 3 - NEWS | 20 ++++--- R/daarem.R | 131 ++++-------------------------------------------- R/daarem_base_noobjfn.R |only R/daarem_base_objfn.R |only man/daarem.Rd | 17 ++++-- 8 files changed, 48 insertions(+), 147 deletions(-)
Title: Power Calculations for Assessing Correlates of Risk in Clinical
Efficacy Trials
Description: Calculates power for assessment of intermediate biomarker responses as correlates of risk in the active treatment group in clinical efficacy trials, as described in Gilbert, Janes, and Huang, Power/Sample Size Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials (2016, Statistics in Medicine). The methods differ from past approaches by accounting for the level of clinical treatment efficacy overall and in biomarker response subgroups, which enables the correlates of risk results to be interpreted in terms of potential correlates of efficacy/protection. The methods also account for inter-individual variability of the observed biomarker response that is not biologically relevant (e.g., due to technical measurement error of the laboratory assay used to measure the biomarker response), which is important because power to detect a specified correlate of risk effect size is heavily affected by the biomarker's measurement error. The methods can be used for a general binary clinical endpoint model with a univariate dichotomous, trichotomous, or continuous biomarker response measured in active treatment recipients at a fixed timepoint after randomization, with either case-cohort Bernoulli sampling or case-control without-replacement sampling of the biomarker (a baseline biomarker is handled as a trivial special case). In a specified two-group trial design, the computeN() function can initially be used for calculating additional requisite design parameters pertaining to the target population of active treatment recipients observed to be at risk at the biomarker sampling timepoint. Subsequently, the power calculation employs an inverse probability weighted logistic regression model fitted by the tps() function in the 'osDesign' package. Power results as well as the relationship between the correlate of risk effect size and treatment efficacy can be visualized using various plotting functions. To link power calculations for detecting a correlate of risk and a correlate of treatment efficacy, a baseline immunogenicity predictor (BIP) can be simulated according to a specified classification rule (for dichotomous or trichotomous BIPs) or correlation with the biomarker response (for continuous BIPs), then outputted along with biomarker response data under assignment to treatment, and clinical endpoint data for both treatment and placebo groups.
Author: Stephanie Wu [aut],
Michal Juraska [aut, cre],
Peter Gilbert [aut],
Yunda Huang [aut]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between CoRpower versions 1.0.2 dated 2019-06-19 and 1.0.3 dated 2019-09-27
DESCRIPTION | 6 - MD5 | 22 ++--- R/computePower.R | 42 +++++----- R/plotPowerCont.R | 103 ++++++++++++++++-------- R/plotPowerTri.R | 155 +++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/CoRpowerIntroduction.Rmd | 38 +++++---- inst/doc/CoRpowerIntroduction.html | 41 ++++++--- man/computePower.Rd | 16 +-- man/plotPowerCont.Rd | 24 +++-- man/plotPowerTri.Rd | 21 ++--- vignettes/CoRpowerIntroduction.Rmd | 38 +++++---- 12 files changed, 320 insertions(+), 186 deletions(-)
Title: Fit a GLM (or Cox Model) with a Combination of Lasso and Group
Lasso Regularization
Description: Fit a regularized generalized linear model via penalized
maximum likelihood. The model is fit for a path of values of
the penalty parameter. Fits linear, logistic and Cox models.
Author: Noah Simon, Jerome Friedman, Trevor Hastie, and Rob Tibshirani
Maintainer: Noah Simon <nrsimon@uw.edu>
Diff between SGL versions 1.2 dated 2018-12-21 and 1.3 dated 2019-09-27
DESCRIPTION | 8 +-- MD5 | 18 ++++---- NAMESPACE | 1 R/SGLmain.R | 112 +++++++++++++++++++++++++++++++---------------------- R/predictSGL.R | 23 +++++----- R/print.SGL.R |only R/zCoxCrossVal.R | 33 ++++++--------- R/zLinCrossVal.R | 24 ++++------- R/zlogitCrossVal.R | 36 +++++++---------- man/cvSGL.Rd | 11 +++-- man/print.SGL.Rd |only 11 files changed, 141 insertions(+), 125 deletions(-)
Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between languageserver versions 0.3.0 dated 2019-09-09 and 0.3.1 dated 2019-09-27
languageserver-0.3.0/languageserver/man/detect_closure.Rd |only languageserver-0.3.0/languageserver/man/detect_function.Rd |only languageserver-0.3.0/languageserver/man/detect_hover.Rd |only languageserver-0.3.0/languageserver/man/detect_token.Rd |only languageserver-0.3.0/languageserver/man/document_backward_search.Rd |only languageserver-0.3.0/languageserver/man/document_line.Rd |only languageserver-0.3.0/languageserver/man/getppid.Rd |only languageserver-0.3.1/languageserver/DESCRIPTION | 13 languageserver-0.3.1/languageserver/MD5 | 176 ++-- languageserver-0.3.1/languageserver/NEWS.md | 11 languageserver-0.3.1/languageserver/R/capabilities.R | 16 languageserver-0.3.1/languageserver/R/completion.R | 64 - languageserver-0.3.1/languageserver/R/definition.R | 80 - languageserver-0.3.1/languageserver/R/diagnostics.R | 8 languageserver-0.3.1/languageserver/R/document.R | 423 +++++----- languageserver-0.3.1/languageserver/R/formatting.R | 99 +- languageserver-0.3.1/languageserver/R/handlers-general.R | 10 languageserver-0.3.1/languageserver/R/handlers-langfeatures.R | 46 - languageserver-0.3.1/languageserver/R/handlers-textsync.R | 35 languageserver-0.3.1/languageserver/R/handlers-workspace.R | 10 languageserver-0.3.1/languageserver/R/hover.R | 15 languageserver-0.3.1/languageserver/R/languagebase.R |only languageserver-0.3.1/languageserver/R/languageclient.R | 100 -- languageserver-0.3.1/languageserver/R/languageserver.R | 119 -- languageserver-0.3.1/languageserver/R/log.R |only languageserver-0.3.1/languageserver/R/namespace.R |only languageserver-0.3.1/languageserver/R/protocol.R | 4 languageserver-0.3.1/languageserver/R/signature.R | 14 languageserver-0.3.1/languageserver/R/utils.R | 206 ++-- languageserver-0.3.1/languageserver/R/workspace.R | 72 - languageserver-0.3.1/languageserver/README.md | 18 languageserver-0.3.1/languageserver/man/Logger.Rd | 2 languageserver-0.3.1/languageserver/man/Namespace.Rd | 2 languageserver-0.3.1/languageserver/man/ServerCapabilities.Rd | 16 languageserver-0.3.1/languageserver/man/arg_completion.Rd | 6 languageserver-0.3.1/languageserver/man/become_orphan.Rd |only languageserver-0.3.1/languageserver/man/cancel_request.Rd | 2 languageserver-0.3.1/languageserver/man/check_scope.Rd | 2 languageserver-0.3.1/languageserver/man/code_lens_resolve.Rd | 2 languageserver-0.3.1/languageserver/man/code_point_to_unit.Rd |only languageserver-0.3.1/languageserver/man/completion_item_resolve.Rd | 2 languageserver-0.3.1/languageserver/man/content_backward_search.Rd |only languageserver-0.3.1/languageserver/man/document_link_resolve.Rd | 2 languageserver-0.3.1/languageserver/man/is_rmarkdown.Rd | 2 languageserver-0.3.1/languageserver/man/log_write.Rd | 2 languageserver-0.3.1/languageserver/man/ncodeunit.Rd |only languageserver-0.3.1/languageserver/man/on_exit.Rd | 2 languageserver-0.3.1/languageserver/man/on_initialize.Rd | 2 languageserver-0.3.1/languageserver/man/on_initialized.Rd | 2 languageserver-0.3.1/languageserver/man/on_shutdown.Rd | 2 languageserver-0.3.1/languageserver/man/path_from_uri.Rd | 2 languageserver-0.3.1/languageserver/man/style_file.Rd | 2 languageserver-0.3.1/languageserver/man/style_text.Rd | 8 languageserver-0.3.1/languageserver/man/text_document_code_action.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_code_lens.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_color_presentation.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_completion.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_definition.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_did_change.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_did_close.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_did_open.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_did_save.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_document_color.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_document_highlight.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_document_link.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_document_symbol.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_folding_range.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_formatting.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_hover.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_implementation.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_on_type_formatting.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_prepare_rename.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_range_formatting.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_references.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_rename.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_signature_help.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_type_definition.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_will_save.Rd | 2 languageserver-0.3.1/languageserver/man/text_document_will_save_wait_until.Rd | 2 languageserver-0.3.1/languageserver/man/to_string.Rd | 2 languageserver-0.3.1/languageserver/man/utf8_to_utf16_code_point.Rd |only languageserver-0.3.1/languageserver/man/workspace_completion.Rd | 15 languageserver-0.3.1/languageserver/man/workspace_did_change_configuration.Rd | 2 languageserver-0.3.1/languageserver/man/workspace_did_change_watched_files.Rd | 2 languageserver-0.3.1/languageserver/man/workspace_did_change_workspace_folder_params.Rd | 2 languageserver-0.3.1/languageserver/man/workspace_execute_command.Rd | 2 languageserver-0.3.1/languageserver/man/workspace_symbol.Rd | 2 languageserver-0.3.1/languageserver/src/document.c | 4 languageserver-0.3.1/languageserver/src/document.h | 2 languageserver-0.3.1/languageserver/src/languageserver.c | 15 languageserver-0.3.1/languageserver/tests/testthat/helper-utils.R | 147 +++ languageserver-0.3.1/languageserver/tests/testthat/test-codeunits.R |only languageserver-0.3.1/languageserver/tests/testthat/test-completion.R |only languageserver-0.3.1/languageserver/tests/testthat/test-definition.R | 152 +-- languageserver-0.3.1/languageserver/tests/testthat/test-formatting.R |only languageserver-0.3.1/languageserver/tests/testthat/test-hover.R |only languageserver-0.3.1/languageserver/tests/testthat/test-signature.R |only languageserver-0.3.1/languageserver/tests/testthat/test-stdio.R | 17 languageserver-0.3.1/languageserver/tests/testthat/test-symbol.R | 75 - 99 files changed, 1073 insertions(+), 1017 deletions(-)
More information about languageserver at CRAN
Permanent link
Title: An Automated Cleaning Tool for Semantic and Linguistic Data
Description: Implements several functions that automates the cleaning and spell-checking of text data. Also converges, finalizes, removes plurals and continuous strings, and puts text data in binary format for semantic network analysis. Uses the 'SemNetDictionaries' package to make the cleaning process more accurate, efficient, and reproducible.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNetCleaner versions 1.1.0 dated 2019-08-06 and 1.1.1 dated 2019-09-27
SemNetCleaner-1.1.0/SemNetCleaner/R/autoConverge.R |only SemNetCleaner-1.1.0/SemNetCleaner/R/autoDestr.R |only SemNetCleaner-1.1.0/SemNetCleaner/R/corr.chn.R |only SemNetCleaner-1.1.0/SemNetCleaner/R/equate.multi.R |only SemNetCleaner-1.1.0/SemNetCleaner/man/autoConverge.Rd |only SemNetCleaner-1.1.0/SemNetCleaner/man/autoDestr.Rd |only SemNetCleaner-1.1.0/SemNetCleaner/man/corr.chn.Rd |only SemNetCleaner-1.1.0/SemNetCleaner/man/equate.multi.Rd |only SemNetCleaner-1.1.1/SemNetCleaner/DESCRIPTION | 11 SemNetCleaner-1.1.1/SemNetCleaner/MD5 | 66 +-- SemNetCleaner-1.1.1/SemNetCleaner/NAMESPACE | 9 SemNetCleaner-1.1.1/SemNetCleaner/NEWS | 22 + SemNetCleaner-1.1.1/SemNetCleaner/R/bin2resp.R | 2 SemNetCleaner-1.1.1/SemNetCleaner/R/converge.R | 2 SemNetCleaner-1.1.1/SemNetCleaner/R/correct.changes.R |only SemNetCleaner-1.1.1/SemNetCleaner/R/destr.R | 2 SemNetCleaner-1.1.1/SemNetCleaner/R/dup.match.R | 6 SemNetCleaner-1.1.1/SemNetCleaner/R/equate.R | 85 ++-- SemNetCleaner-1.1.1/SemNetCleaner/R/finalize.R | 2 SemNetCleaner-1.1.1/SemNetCleaner/R/open.animals.R | 11 SemNetCleaner-1.1.1/SemNetCleaner/R/pluralize.R | 184 ++++++--- SemNetCleaner-1.1.1/SemNetCleaner/R/read.data.R |only SemNetCleaner-1.1.1/SemNetCleaner/R/singularize.R | 200 ++++++++-- SemNetCleaner-1.1.1/SemNetCleaner/R/spell.check.dictionary.R | 46 +- SemNetCleaner-1.1.1/SemNetCleaner/R/textcleaner.R | 11 SemNetCleaner-1.1.1/SemNetCleaner/data/open.animals.RData |binary SemNetCleaner-1.1.1/SemNetCleaner/inst/CITATION | 8 SemNetCleaner-1.1.1/SemNetCleaner/man/bin2resp.Rd | 2 SemNetCleaner-1.1.1/SemNetCleaner/man/converge.Rd | 2 SemNetCleaner-1.1.1/SemNetCleaner/man/correct.changes.Rd |only SemNetCleaner-1.1.1/SemNetCleaner/man/destr.Rd | 2 SemNetCleaner-1.1.1/SemNetCleaner/man/dup.match.Rd | 6 SemNetCleaner-1.1.1/SemNetCleaner/man/equate.Rd | 32 - SemNetCleaner-1.1.1/SemNetCleaner/man/finalize.Rd | 2 SemNetCleaner-1.1.1/SemNetCleaner/man/open.animals.Rd | 11 SemNetCleaner-1.1.1/SemNetCleaner/man/pluralize.Rd | 26 + SemNetCleaner-1.1.1/SemNetCleaner/man/read.data.Rd |only SemNetCleaner-1.1.1/SemNetCleaner/man/singularize.Rd | 44 ++ SemNetCleaner-1.1.1/SemNetCleaner/man/spell.check.dictionary.Rd | 2 SemNetCleaner-1.1.1/SemNetCleaner/man/textcleaner.Rd | 11 40 files changed, 568 insertions(+), 239 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre] (<https://orcid.org/0000-0001-7158-0653>),
Yves Rosseel [aut],
Ben Goodrich [aut],
Mauricio Garnier-Villarreal [ctb]
(<https://orcid.org/0000-0002-2951-6647>, R/ctr_bayes_fit.R),
Terrence D. Jorgensen [ctb] (<https://orcid.org/0000-0001-5111-6773>,
R/ctr_bayes_fit.R, R/ctr_ppmc.R),
Huub Hoofs [ctb] (R/ctr_bayes_fit.R),
Rens van de Schoot [ctb] (R/ctr_bayes_fit.R)
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.3-6 dated 2019-08-08 and 0.3-7 dated 2019-09-27
DESCRIPTION | 13 ++++--- MD5 | 27 ++++++++-------- NAMESPACE | 3 + NEWS | 14 ++++++++ R/blav_object_methods.R | 45 +++++++++++++-------------- R/blavaan.R | 21 +++++++----- R/postpred.R | 31 +----------------- R/stanmarg_data.R | 32 +++++++++++++++---- R/zzz.R | 2 - README.md | 14 +++++++- inst/testdata/sysdata.rda |binary man/plot.blavaan.Rd |only src/stan_files/stanmarg.stan | 40 +++++++++++++++++++----- tests/testthat/tests.blavaan.R | 14 +++++++- tests/testthat/tests.blavaanobject-methods.R | 25 +++++++++++++++ 15 files changed, 182 insertions(+), 99 deletions(-)
Title: Methods and Measures for Brain, Cognitive, and Psychometric
Network Analysis
Description: Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershogoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Author: Alexander Christensen [aut, cre],
Guido Previde Massara [ctb]
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Diff between NetworkToolbox versions 1.3.0 dated 2019-08-21 and 1.3.1 dated 2019-09-27
DESCRIPTION | 8 +++---- MD5 | 56 +++++++++++++++++++++++++------------------------- NEWS | 6 +++++ R/ECOplusMaST.R | 3 +- R/LoGo.R | 9 +++----- R/MaST.R | 14 ++++++------ R/TMFG.R | 20 ++++++++--------- R/betweenness.R | 2 - R/conn.R | 3 +- R/cpm.R | 2 - R/depend.R | 4 +-- R/edgerep.R | 6 +++-- R/impact.R | 3 +- R/node.redundant.R | 35 +++++++++++++++++++++++++------ R/smallworldness.R | 3 +- R/threshold.R | 4 +-- man/ECOplusMaST.Rd | 3 +- man/LoGo.Rd | 9 +++----- man/MaST.Rd | 14 ++++++------ man/TMFG.Rd | 16 +++++++------- man/betweenness.Rd | 2 - man/conn.Rd | 3 +- man/cpm.Rd | 2 - man/depend.Rd | 4 +-- man/edgerep.Rd | 6 +++-- man/impact.Rd | 3 +- man/node.redundant.Rd | 18 ++++++++++++---- man/smallworldness.Rd | 3 +- man/threshold.Rd | 4 +-- 29 files changed, 155 insertions(+), 110 deletions(-)
More information about NetworkToolbox at CRAN
Permanent link
Title: Functional Data Analysis and Empirical Dynamics
Description: A versatile package that provides implementation of various
methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this
package is Functional Principal Component Analysis (FPCA), a key technique for
functional data analysis, for sparsely or densely sampled random trajectories
and time courses, via the Principal Analysis by Conditional Estimation
(PACE) algorithm. This core algorithm yields covariance and mean functions,
eigenfunctions and principal component (scores), for both functional data and
derivatives, for both dense (functional) and sparse (longitudinal) sampling designs.
For sparse designs, it provides fitted continuous trajectories with confidence bands,
even for subjects with very few longitudinal observations. PACE is a viable and
flexible alternative to random effects modeling of longitudinal data. There is also a
Matlab version (PACE) that contains some methods not available on fdapace and vice
versa. Please cite our package if you use it (You may run the command
citation("fdapace") to get the citation format and bibtex entry).
References: Wang, J.L., Chiou, J., Müller, H.G. (2016) <doi:10.1146/annurev-statistics-041715-033624>;
Chen, K., Zhang, X., Petersen, A., Müller, H.G. (2017) <doi:10.1007/s12561-015-9137-5>.
Author: Yaqing Chen [aut, cre],
Cody Carroll [aut],
Xiongtao Dai [aut],
Jianing Fan [aut],
Pantelis Z. Hadjipantelis [aut],
Kyunghee Han [aut],
Hao Ji [aut],
Shu-Chin Lin [ctb],
Paromita Dubey [ctb],
Hans-Georg Mueller [cph, ths, aut],
Jane-Ling Wang [cph, ths, aut]
Maintainer: Yaqing Chen <yaqchen@ucdavis.edu>
Diff between fdapace versions 0.5.0 dated 2019-08-31 and 0.5.1 dated 2019-09-27
DESCRIPTION | 12 MD5 | 42 +-- NEWS | 6 R/ConvertSupport.R | 2 R/FCReg.R | 21 - R/FLM.R | 4 R/FPCA.R | 2 R/FPCquantile.R | 2 R/MakeGPFunctionalData.R | 2 R/MakeSparseGP.R | 2 R/SetOptions.R | 532 ++++++++++++++++++++++---------------------- R/fitted.FPCA.R | 2 inst/doc/fdapaceVig.Rmd | 2 inst/doc/fdapaceVig.html | 77 ------ man/ConvertSupport.Rd | 2 man/FLM.Rd | 4 man/FPCA.Rd | 2 man/FPCquantile.Rd | 2 man/MakeGPFunctionalData.Rd | 2 man/MakeSparseGP.Rd | 2 man/fitted.FPCA.Rd | 2 vignettes/fdapaceVig.Rmd | 2 22 files changed, 335 insertions(+), 391 deletions(-)
Title: Sequentially-Allocated Latent Structure Optimization
Description: Point estimation for partition distributions using the sequentially-allocated latent structure optimization (SALSO) method to minimize the expectation of the Binder loss or the lower bound of the expectation of the variation of information loss. The SALSO method was presented at the workshop "Bayesian Nonparametric Inference: Dependence Structures and their Applications" in Oaxaca, Mexico on December 6, 2017. See <https://www.birs.ca/events/2017/5-day-workshops/17w5060/schedule>.
Author: David B. Dahl
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.1.2 dated 2019-09-21 and 0.1.3 dated 2019-09-27
salso-0.1.2/salso/src/rustlib/dahl-randompartition.h |only salso-0.1.3/salso/DESCRIPTION | 10 +-- salso-0.1.3/salso/INSTALL | 14 ++-- salso-0.1.3/salso/MD5 | 49 ++++++++-------- salso-0.1.3/salso/NAMESPACE | 16 +++++ salso-0.1.3/salso/NEWS | 10 ++- salso-0.1.3/salso/R/bell.R | 57 +++++++++--------- salso-0.1.3/salso/R/confidence.R |only salso-0.1.3/salso/R/dlso.R |only salso-0.1.3/salso/R/enumerate.partitions.R | 46 +++++++-------- salso-0.1.3/salso/R/loss.R | 9 +- salso-0.1.3/salso/R/plot.salso.confidence.R |only salso-0.1.3/salso/R/psm.R | 9 +- salso-0.1.3/salso/R/salso.R | 49 ++++++++++++---- salso-0.1.3/salso/man/bell.Rd | 3 salso-0.1.3/salso/man/binder.Rd | 9 +- salso-0.1.3/salso/man/confidence.Rd |only salso-0.1.3/salso/man/dlso.Rd |only salso-0.1.3/salso/man/enumerate.partitions.Rd | 2 salso-0.1.3/salso/man/plot.salso.confidence.Rd |only salso-0.1.3/salso/man/psm.Rd | 9 +- salso-0.1.3/salso/man/salso.Rd | 47 ++++++++++++--- salso-0.1.3/salso/src/Makevars | 2 salso-0.1.3/salso/src/rustlib/Cargo.lock | 58 +++++++------------ salso-0.1.3/salso/src/rustlib/Cargo.toml | 1 salso-0.1.3/salso/src/rustlib/dahl-partition.h | 36 ----------- salso-0.1.3/salso/src/rustlib/src/lib.rs | 1 salso-0.1.3/salso/src/wrapper.c | 4 - salso-0.1.3/salso/tools/staticlib.R | 51 +++++++++++----- 29 files changed, 277 insertions(+), 215 deletions(-)
Title: Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of several karyotypes having a set of dataframes for chromosome data
and optionally mark data. Includes also a function to plot holocentrics and its marks supporting
micrometers and Mb. Marks can have square or dot form, its legend (label) can be drawn inline
or to the right of karyotypes. It is possible to calculate
chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x> ,
karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and
Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre],
Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>
Diff between idiogramFISH versions 1.2.1 dated 2019-09-17 and 1.5.1 dated 2019-09-27
idiogramFISH-1.2.1/idiogramFISH/vignettes/idiogramFISHcitations.bib |only idiogramFISH-1.5.1/idiogramFISH/DESCRIPTION | 16 idiogramFISH-1.5.1/idiogramFISH/MD5 | 118 + idiogramFISH-1.5.1/idiogramFISH/NEWS.md | 25 idiogramFISH-1.5.1/idiogramFISH/R/armRatioCI.R | 7 idiogramFISH-1.5.1/idiogramFISH/R/asymmetry.R | 1 idiogramFISH-1.5.1/idiogramFISH/R/cenmarkdata.R | 4 idiogramFISH-1.5.1/idiogramFISH/R/chrbasicdatamono.R | 4 idiogramFISH-1.5.1/idiogramFISH/R/dfMarkStyle.R | 3 idiogramFISH-1.5.1/idiogramFISH/R/markpos.R | 4 idiogramFISH-1.5.1/idiogramFISH/R/plotIdiograms.R | 372 +++--- idiogramFISH-1.5.1/idiogramFISH/R/plotIdiogramsHolo.R | 183 ++ idiogramFISH-1.5.1/idiogramFISH/R/plotlabelsright.R | 39 idiogramFISH-1.5.1/idiogramFISH/R/roundPlot.R | 6 idiogramFISH-1.5.1/idiogramFISH/README.md | 96 - idiogramFISH-1.5.1/idiogramFISH/build/vignette.rds |binary idiogramFISH-1.5.1/idiogramFISH/data/allCenMarksSample.rda |only idiogramFISH-1.5.1/idiogramFISH/data/allChrSizeSample.rda |only idiogramFISH-1.5.1/idiogramFISH/data/allMarksSample.rda |only idiogramFISH-1.5.1/idiogramFISH/data/mydfMaColor.rda |only idiogramFISH-1.5.1/idiogramFISH/inst/doc/groupsVig.R | 38 idiogramFISH-1.5.1/idiogramFISH/inst/doc/groupsVig.Rmd | 78 - idiogramFISH-1.5.1/idiogramFISH/inst/doc/groupsVig.html | 235 +++ idiogramFISH-1.5.1/idiogramFISH/inst/doc/humanVig.R | 53 idiogramFISH-1.5.1/idiogramFISH/inst/doc/humanVig.Rmd | 94 - idiogramFISH-1.5.1/idiogramFISH/inst/doc/humanVig.html | 618 ++++++---- idiogramFISH-1.5.1/idiogramFISH/inst/doc/index.R | 137 ++ idiogramFISH-1.5.1/idiogramFISH/inst/doc/index.Rmd | 215 ++- idiogramFISH-1.5.1/idiogramFISH/inst/doc/index.html | 432 ++++-- idiogramFISH-1.5.1/idiogramFISH/inst/doc/phylogenyVig.R |only idiogramFISH-1.5.1/idiogramFISH/inst/doc/phylogenyVig.Rmd |only idiogramFISH-1.5.1/idiogramFISH/inst/doc/phylogenyVig.html |only idiogramFISH-1.5.1/idiogramFISH/inst/doc/plotIdiogramsHoloVig.R | 66 + idiogramFISH-1.5.1/idiogramFISH/inst/doc/plotIdiogramsHoloVig.Rmd | 93 - idiogramFISH-1.5.1/idiogramFISH/inst/doc/plotIdiogramsHoloVig.html | 391 ++++-- idiogramFISH-1.5.1/idiogramFISH/inst/doc/plotIdiogramsVig.R | 77 + idiogramFISH-1.5.1/idiogramFISH/inst/doc/plotIdiogramsVig.Rmd | 102 - idiogramFISH-1.5.1/idiogramFISH/inst/doc/plotIdiogramsVig.html | 349 ++++- idiogramFISH-1.5.1/idiogramFISH/inst/extdata |only idiogramFISH-1.5.1/idiogramFISH/man/cenmarkdata.Rd | 5 idiogramFISH-1.5.1/idiogramFISH/man/chrbasicdatamono.Rd | 5 idiogramFISH-1.5.1/idiogramFISH/man/dfMarkStyle.Rd | 5 idiogramFISH-1.5.1/idiogramFISH/man/figures/README-example-1.png |binary idiogramFISH-1.5.1/idiogramFISH/man/figures/README-example2-1.png |binary idiogramFISH-1.5.1/idiogramFISH/man/idiogramFISH-package.Rd | 1 idiogramFISH-1.5.1/idiogramFISH/man/markpos.Rd | 5 idiogramFISH-1.5.1/idiogramFISH/man/plotIdiograms.Rd | 11 idiogramFISH-1.5.1/idiogramFISH/man/plotIdiogramsHolo.Rd | 11 idiogramFISH-1.5.1/idiogramFISH/man/plotlabelsright.Rd | 4 idiogramFISH-1.5.1/idiogramFISH/vignettes/all.minMod.css |only idiogramFISH-1.5.1/idiogramFISH/vignettes/allrefs.bib | 55 idiogramFISH-1.5.1/idiogramFISH/vignettes/bootstrap.min.js |only idiogramFISH-1.5.1/idiogramFISH/vignettes/bootstrap.minO.css |only idiogramFISH-1.5.1/idiogramFISH/vignettes/clipboard.min.js |only idiogramFISH-1.5.1/idiogramFISH/vignettes/firstplot2.png |only idiogramFISH-1.5.1/idiogramFISH/vignettes/fonts |only idiogramFISH-1.5.1/idiogramFISH/vignettes/groupsVig.Rmd | 78 - idiogramFISH-1.5.1/idiogramFISH/vignettes/humanVig.Rmd | 94 - idiogramFISH-1.5.1/idiogramFISH/vignettes/index.Rmd | 215 ++- idiogramFISH-1.5.1/idiogramFISH/vignettes/iqtree.bib |only idiogramFISH-1.5.1/idiogramFISH/vignettes/jquery.min.js |only idiogramFISH-1.5.1/idiogramFISH/vignettes/link.svg |only idiogramFISH-1.5.1/idiogramFISH/vignettes/mystyle.css |only idiogramFISH-1.5.1/idiogramFISH/vignettes/packages.bib |only idiogramFISH-1.5.1/idiogramFISH/vignettes/phylogenyVig.Rmd |only idiogramFISH-1.5.1/idiogramFISH/vignettes/plotIdiogramsHoloVig.Rmd | 93 - idiogramFISH-1.5.1/idiogramFISH/vignettes/plotIdiogramsVig.Rmd | 102 - idiogramFISH-1.5.1/idiogramFISH/vignettes/revbayes.bib |only idiogramFISH-1.5.1/idiogramFISH/vignettes/secondplot2.png |only 69 files changed, 2987 insertions(+), 1553 deletions(-)
Title: Dynamic Simulation and Testing for Single-Equation ARDL Models
Description: While autoregressive distributed lag (ARDL) models allow for extremely flexible dynamics, interpreting substantive significance of complex lag structures remains difficult. This package is designed to assist users in dynamically simulating and plotting the results of various ARDL models. It also contains post-estimation diagnostics, including a test for cointegration when estimating the error-correction variant of the autoregressive distributed lag model (Pesaran, Shin, and Smith 2001 <doi:10.1002/jae.616>).
Author: Soren Jordan [aut, cre, cph],
Andrew Q. Philips [aut]
Maintainer: Soren Jordan <sorenjordanpols@gmail.com>
Diff between dynamac versions 0.1.8 dated 2019-04-09 and 0.1.9 dated 2019-09-27
DESCRIPTION | 6 MD5 | 37 - NAMESPACE | 2 R/dynamac.R | 873 ++++++++++++++++++++++++++++++++--------- build/vignette.rds |binary inst/doc/dynamac-vignette.R | 31 + inst/doc/dynamac-vignette.Rmd | 82 ++- inst/doc/dynamac-vignette.html | 417 +++++++++++++------ inst/dynamac-manual.pdf |binary man/dshift.Rd | 6 man/dynardl.Rd | 63 +- man/dynardl.all.plots.Rd |only man/dynardl.auto.correlated.Rd | 16 man/dynardl.simulation.plot.Rd | 43 +- man/france.data.Rd | 2 man/ldshift.Rd | 6 man/lshift.Rd | 6 man/pssbounds.Rd | 13 man/summary.dynardl.Rd | 6 vignettes/dynamac-vignette.Rmd | 82 ++- 20 files changed, 1248 insertions(+), 443 deletions(-)
Title: Multivariate Normality Tests
Description: Performs multivariate normality tests and graphical approaches and
implements multivariate outlier detection and univariate normality of marginal
distributions through plots and tests, and performs multivariate Box-Cox transformation
(Korkmaz et al, (2014), <https://journal.r-project.org/archive/2014-2/korkmaz-goksuluk-zararsiz.pdf>).
Author: Selcuk Korkmaz [aut, cre],
Dincer Goksuluk [aut],
Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between MVN versions 5.7 dated 2019-03-18 and 5.8 dated 2019-09-27
MVN-5.7/MVN/vignettes/MVN-concordance.tex |only MVN-5.8/MVN/DESCRIPTION | 8 ++++---- MVN-5.8/MVN/MD5 | 17 ++++++++--------- MVN-5.8/MVN/R/mvn.R | 22 +++++++++++++++------- MVN-5.8/MVN/build/vignette.rds |binary MVN-5.8/MVN/inst/doc/MVN.R | 12 ++++++------ MVN-5.8/MVN/inst/doc/MVN.Rnw | 14 +++++++------- MVN-5.8/MVN/inst/doc/MVN.pdf |binary MVN-5.8/MVN/man/mvn.Rd | 12 ++++++------ MVN-5.8/MVN/vignettes/MVN.Rnw | 14 +++++++------- 10 files changed, 53 insertions(+), 46 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package helps to design cartographic representations such as proportional symbols, choropleth, typology, flows or discontinuities maps. It also offers several features that improve the graphic presentation of maps, for instance, map palettes, layout elements (scale, north arrow, title...), labels or legends. See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>),
Nicolas Lambert [aut],
Ian Fellows [cph] (no overlap algorithm for labels, from wordcloud
package)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between cartography versions 2.2.0 dated 2019-02-07 and 2.2.1 dated 2019-09-27
DESCRIPTION | 13 MD5 | 94 +- NEWS.md | 8 R/choroLayer.R | 6 R/discLayer.R | 4 R/dotDensityLayer.R | 9 R/getBorders.R | 7 R/getGridLayer.R | 161 ---- R/getLinkLayer.R | 6 R/getOuterBorders.R | 12 R/gradLinkLayer.R | 4 R/gradLinkTypoLayer.R | 6 R/labelLayer.R | 11 R/legends.R | 6 R/north.R | 86 +- R/propLinkLayer.R | 6 R/propSymbolsChoroLayer.R | 8 R/propSymbolsTypoLayer.R | 9 R/propTrianglesLayer.R | 8 R/smoothLayer.R | 10 R/typoLayer.R | 6 README.md | 29 build/vignette.rds |binary inst/doc/cartography.R | 6 inst/doc/cartography.Rmd | 6 inst/doc/cartography.html | 1468 +++++++++++++++++++----------------------- inst/doc/cheatsheet.html | 330 +++------ man/choroLayer.Rd | 6 man/discLayer.Rd | 4 man/dotDensityLayer.Rd | 9 man/getBorders.Rd | 7 man/getGridLayer.Rd | 2 man/getLinkLayer.Rd | 6 man/getOuterBorders.Rd | 4 man/gradLinkLayer.Rd | 4 man/gradLinkTypoLayer.Rd | 6 man/labelLayer.Rd | 13 man/north.Rd | 4 man/propLinkLayer.Rd | 6 man/propSymbolsChoroLayer.Rd | 8 man/propSymbolsTypoLayer.Rd | 9 man/propTrianglesLayer.Rd | 8 man/smoothLayer.Rd | 10 man/typoLayer.Rd | 6 tests/testthat/Rplots.pdf |binary tests/testthat/test_legends.R | 4 tests/testthat/test_north.R | 1 vignettes/cartography.Rmd | 6 48 files changed, 1103 insertions(+), 1339 deletions(-)
Title: Dictionaries for the 'SemNetCleaner' Package
Description: Implements dictionaries that can be used in the 'SemNetCleaner' package. Also includes several functions aimed at facilitating the text cleaning analysis in the 'SemNetCleaner' package. This package is designed to integrate and update word lists and dictionaries based on each user's individual needs by allowing users to store and save their own dictionaries. Dictionaries can be added to the 'SemNetDictionaries' package by submitting user-defined dictionaries to <https://github.com/AlexChristensen/SemNetDictionaries>.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNetDictionaries versions 0.1.3 dated 2019-08-05 and 0.1.4 dated 2019-09-27
DESCRIPTION | 8 +++---- MD5 | 22 ++++++++++---------- NEWS | 14 +++++++++++++ R/animals.dictionary.R | 4 +-- R/append.dictionary.R | 43 ++++++++++++---------------------------- R/find.dictionaries.R | 45 +++++++++++++++++++++++++++++------------- R/load.dictionaries.R | 2 - data/animals.dictionary.RData |binary data/jobs.moniker.RData |binary inst/CITATION | 8 +++---- man/animals.dictionary.Rd | 4 +-- man/append.dictionary.Rd | 8 ++++++- 12 files changed, 90 insertions(+), 68 deletions(-)
More information about SemNetDictionaries at CRAN
Permanent link
Title: Methods and Measures for Semantic Network Analysis
Description: Implements several functions for the analysis of semantic networks including partial node bootstrapping (Kenett, Anaki, & Faust, 2014 <doi:10.3389/fnhum.2014.00407>), random walk simulation (Kenett & Austerweil, 2016 <http://alab.psych.wisc.edu/papers/files/Kenett16CreativityRW.pdf>), and a function to compute global network measures. Significance tests and plotting features are also implemented.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>),
Yoed N. Kenett [aut, ctb] (<https://orcid.org/0000-0003-3872-7689>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNeT versions 1.0.0 dated 2019-08-05 and 1.1.1 dated 2019-09-27
DESCRIPTION | 8 - MD5 | 55 +++---- NAMESPACE | 4 NEWS | 17 ++ R/SemNeT.R | 4 R/compare.nets.R | 230 ++++++++++++++++++++++++------ R/convert2cytoscape.R | 2 R/org.plot.R | 35 +--- R/partboot.R | 215 +++++++++++----------------- R/partboot.one.test.R |only R/partboot.test.R | 353 +++++++++++++++++++---------------------------- R/plot.partboot.R | 43 ++--- R/randnet.test.R | 101 ++++++++----- R/randwalk.R | 4 R/semnetmeas.R | 25 ++- R/sim.fluency.R | 10 - R/similarity.R | 17 +- inst |only man/SemNeT-package.Rd | 4 man/compare.nets.Rd | 69 +++++++-- man/org.plot.Rd | 11 - man/partboot.Rd | 17 -- man/partboot.one.test.Rd |only man/partboot.test.Rd | 37 +++- man/plot.partboot.Rd | 6 man/randnet.test.Rd | 2 man/randwalk.Rd | 4 man/semnetmeas.Rd | 7 man/sim.fluency.Rd | 10 - man/similarity.Rd | 17 +- 30 files changed, 725 insertions(+), 582 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis with industrial strength.
Some features are
1) Use of CDISC SDTM terms
2) Automatic or manual slope selection
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between NonCompart versions 0.4.4 dated 2018-07-19 and 0.4.5 dated 2019-09-27
NonCompart-0.4.4/NonCompart/inst/doc/NonCompart-validation.pdf |only NonCompart-0.4.5/NonCompart/DESCRIPTION | 15 - NonCompart-0.4.5/NonCompart/MD5 | 13 - NonCompart-0.4.5/NonCompart/R/sNCA.R | 4 NonCompart-0.4.5/NonCompart/inst/NEWS.Rd | 5 NonCompart-0.4.5/NonCompart/inst/doc/NonCompart-manual.pdf |binary NonCompart-0.4.5/NonCompart/man/NonCompart-package.Rd | 2 NonCompart-0.4.5/NonCompart/tests/RptCfg.csv | 98 +++++----- 8 files changed, 70 insertions(+), 67 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Report
Description: Conduct a noncompartmental analysis with industrial strength.
Some features are
1) CDISC SDTM terms
2) Automatic or manual slope selection
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
5) Produce pdf, rtf, text report files.
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between ncar versions 0.4.1 dated 2018-07-19 and 0.4.2 dated 2019-09-27
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- inst/NEWS.Rd | 6 +++++- inst/doc/ncar-manual.pdf |binary man/ncar-package.Rd | 2 +- 5 files changed, 17 insertions(+), 13 deletions(-)
Title: Meta-Analysis of Diagnostic Accuracy
Description: Provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter & Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Holling et al. (2012) is also available. Standard methods like summary, plot and so on are provided.
Author: Philipp Doebler
Maintainer: Philipp Doebler <philipp.doebler@googlemail.com>
Diff between mada versions 0.5.8 dated 2017-10-09 and 0.5.9 dated 2019-09-27
DESCRIPTION | 13 +++++++---- MD5 | 22 +++++++++---------- build/vignette.rds |binary data/AuditC.rda |binary data/Dementia.rda |binary data/IAQ.rda |binary data/SAQ.rda |binary data/smoking.rda |binary inst/doc/mada.pdf |binary man/CIrho.Rd | 60 ++++++++++++++++++++++++++--------------------------- man/madad.Rd | 1 man/reitsma.Rd | 2 - 12 files changed, 49 insertions(+), 49 deletions(-)
Title: Simulate Temporally Autocorrelated Populations
Description: Temporally autocorrelated populations are correlated in their vital rates (growth, death, etc.) from year to year. It is very common for populations, whether they be bacteria, plants, or humans, to be temporally autocorrelated. This poses a challenge for stochastic population modeling, because a temporally correlated population will behave differently from an uncorrelated one.
This package provides tools for simulating populations with white noise (no temporal autocorrelation), red noise (positive temporal autocorrelation), and blue noise (negative temporal autocorrelation). The algebraic formulation for autocorrelated noise comes from Ruokolainen et al. (2009) <doi:10.1016/j.tree.2009.04.009>. Models for unstructured populations and for structured populations (matrix models) are available.
Author: Julia Pilowsky [aut, cre] (<https://orcid.org/0000-0002-6376-2585>)
Maintainer: Julia Pilowsky <jap2178@caa.columbia.edu>
Diff between colorednoise versions 1.0.4 dated 2019-01-23 and 1.0.5 dated 2019-09-27
DESCRIPTION | 10 - MD5 | 17 +-- NEWS.md | 4 R/simulate_populations.R | 4 README.md | 20 +-- build/vignette.rds |binary inst/doc/noise.html | 213 +++++++++++++++++++++------------------ man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/logo.png |only 10 files changed, 145 insertions(+), 123 deletions(-)
Title: NHS and Healthcare Related Data for Education and Training
Description: Free United Kingdom National Health Service (NHS) and other healthcare, or population health-related data for education and training purposes. This package currently contains a single simulated hospital dataset for teaching regression methods, with the addition of more datasets planned for future releases. This package exists to support skills development in the NHS-R community: <https://nhsrcommunity.com/>.
Author: Chris Mainey [aut, cre] (<https://orcid.org/0000-0002-3018-6171>),
Tom Jemmett [aut] (<https://orcid.org/0000-0002-6943-2990>),
NHS-R community [cph]
Maintainer: Chris Mainey <chris.mainey@uhb.nhs.uk>
Diff between NHSRdatasets versions 0.1.1 dated 2019-08-03 and 0.1.2 dated 2019-09-27
NHSRdatasets-0.1.1/NHSRdatasets/tests |only NHSRdatasets-0.1.2/NHSRdatasets/DESCRIPTION | 12 ++-- NHSRdatasets-0.1.2/NHSRdatasets/MD5 | 19 ++++--- NHSRdatasets-0.1.2/NHSRdatasets/NEWS.md | 7 ++ NHSRdatasets-0.1.2/NHSRdatasets/R/ae_attendances.R |only NHSRdatasets-0.1.2/NHSRdatasets/README.md | 29 +++++++---- NHSRdatasets-0.1.2/NHSRdatasets/build/vignette.rds |binary NHSRdatasets-0.1.2/NHSRdatasets/data/ae_attendances.RData |only NHSRdatasets-0.1.2/NHSRdatasets/inst/doc/LOS_model.html | 4 - NHSRdatasets-0.1.2/NHSRdatasets/inst/doc/ae_attendances.R |only NHSRdatasets-0.1.2/NHSRdatasets/inst/doc/ae_attendances.Rmd |only NHSRdatasets-0.1.2/NHSRdatasets/inst/doc/ae_attendances.html |only NHSRdatasets-0.1.2/NHSRdatasets/man/ae_attendances.Rd |only NHSRdatasets-0.1.2/NHSRdatasets/vignettes/ae_attendances.Rmd |only 14 files changed, 48 insertions(+), 23 deletions(-)
Title: Parse Data of 'R' Code as an 'XML' Tree
Description: Convert the output of 'utils::getParseData()' to an 'XML'
tree, that one can search via 'XPath', and easier to manipulate in
general.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between xmlparsedata versions 1.0.2 dated 2018-09-17 and 1.0.3 dated 2019-09-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/package.R | 6 +++++- tests/testthat/test.R | 15 ++++++++++++++- 5 files changed, 33 insertions(+), 9 deletions(-)
Title: Calculator of Understandability Metrics for BPMN
Description: Calculate several understandability metrics of BPMN models. BPMN stands for business process modelling notation and is a language for expressing business processes into business process diagrams. Examples of these understandability metrics are: average connector degree, maximum connector degree, sequentiality, cyclicity, diameter, depth, token split, control flow complexity, connector mismatch, connector heterogeneity, separability, structuredness and cross connectivity. See R documentation and paper on metric implementation included in this package for more information concerning the metrics.
Author: Jonas Lieben [aut],
Gert Janssenswillen [cre]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between understandBPMN versions 1.1.0 dated 2018-06-08 and 1.1.1 dated 2019-09-27
understandBPMN-1.1.0/understandBPMN/README.md |only understandBPMN-1.1.1/understandBPMN/DESCRIPTION | 17 understandBPMN-1.1.1/understandBPMN/LICENSE | 4 understandBPMN-1.1.1/understandBPMN/MD5 | 115 understandBPMN-1.1.1/understandBPMN/NAMESPACE | 96 understandBPMN-1.1.1/understandBPMN/NEWS.md | 10 understandBPMN-1.1.1/understandBPMN/R/Behavioral_profile.R | 2786 ++++---- understandBPMN-1.1.1/understandBPMN/R/Create_path_log.R | 1270 +-- understandBPMN-1.1.1/understandBPMN/R/RcppExports.R | 38 understandBPMN-1.1.1/understandBPMN/R/UnderstandBPMN.R | 46 understandBPMN-1.1.1/understandBPMN/R/helper.R | 1620 ++-- understandBPMN-1.1.1/understandBPMN/R/metrics.R | 3295 +++++----- understandBPMN-1.1.1/understandBPMN/inst/extdata/doc.txt | 4 understandBPMN-1.1.1/understandBPMN/man/activity_multiple_times_executed.Rd | 58 understandBPMN-1.1.1/understandBPMN/man/activity_names_repetitions.Rd | 48 understandBPMN-1.1.1/understandBPMN/man/avg_connector_degree.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/calculate_metrics.Rd | 66 understandBPMN-1.1.1/understandBPMN/man/coefficient_network_connectivity.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/cognitive_weight.Rd |only understandBPMN-1.1.1/understandBPMN/man/connectivity_level_between_pools.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/connector_heterogeneity.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/connector_mismatch.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/control_flow_complexity.Rd | 48 understandBPMN-1.1.1/understandBPMN/man/coupling_metric.Rd |only understandBPMN-1.1.1/understandBPMN/man/create_internal_doc.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/create_path_and_repetition_log.Rd | 68 understandBPMN-1.1.1/understandBPMN/man/cross_connectivity.Rd | 66 understandBPMN-1.1.1/understandBPMN/man/cyclicity.Rd | 61 understandBPMN-1.1.1/understandBPMN/man/cyclomatic_metric.Rd | 66 understandBPMN-1.1.1/understandBPMN/man/density_process_model.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/depth.Rd | 68 understandBPMN-1.1.1/understandBPMN/man/diameter.Rd | 62 understandBPMN-1.1.1/understandBPMN/man/direct_parallel_relations.Rd | 52 understandBPMN-1.1.1/understandBPMN/man/filtered_path_log_parallel.Rd | 51 understandBPMN-1.1.1/understandBPMN/man/max_connector_degree.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/n_data_objects.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/n_duplicate_tasks.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/n_empty_sequence_flows.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/n_message_flows.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/n_pools.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/n_swimlanes.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/separability.Rd | 65 understandBPMN-1.1.1/understandBPMN/man/sequentiality.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/size_process_model.Rd | 46 understandBPMN-1.1.1/understandBPMN/man/some_traces_without_activity.Rd | 54 understandBPMN-1.1.1/understandBPMN/man/structuredness.Rd | 74 understandBPMN-1.1.1/understandBPMN/man/task_names.Rd | 52 understandBPMN-1.1.1/understandBPMN/man/token_split.Rd | 48 understandBPMN-1.1.1/understandBPMN/man/traces_contain_relation.Rd | 106 understandBPMN-1.1.1/understandBPMN/man/understandBPMN.Rd | 20 understandBPMN-1.1.1/understandBPMN/tests/testthat.R | 8 understandBPMN-1.1.1/understandBPMN/tests/testthat/diagram_behavioral_profile.bpmn | 1044 +-- understandBPMN-1.1.1/understandBPMN/tests/testthat/paper_diagram.bpmn | 826 +- understandBPMN-1.1.1/understandBPMN/tests/testthat/paper_diagram_empty.bpmn | 14 understandBPMN-1.1.1/understandBPMN/tests/testthat/paper_diagram_event.bpmn | 32 understandBPMN-1.1.1/understandBPMN/tests/testthat/paper_diagram_modified.bpmn | 962 +- understandBPMN-1.1.1/understandBPMN/tests/testthat/paper_diagram_simple.bpmn | 124 understandBPMN-1.1.1/understandBPMN/tests/testthat/testHelper.R | 364 - understandBPMN-1.1.1/understandBPMN/tests/testthat/testMetrics.R | 542 - understandBPMN-1.1.1/understandBPMN/tests/testthat/testPathLog.R | 90 60 files changed, 7682 insertions(+), 7494 deletions(-)
More information about understandBPMN at CRAN
Permanent link
Title: Tree-Structured Clustering
Description: Tree-structured modelling of categorical predictors (Tutz and Berger (2018), <doi:10.1007/s11634-017-0298-6>) or measurement
units (Berger and Tutz (2018), <doi:10.1080/10618600.2017.1371030>).
Author: Moritz Berger
Maintainer: Moritz Berger <Moritz.Berger@imbie.uni-bonn.de>
Diff between structree versions 1.1.5 dated 2017-08-01 and 1.1.6 dated 2019-09-27
structree-1.1.5/structree/R/structree-internal.R |only structree-1.1.6/structree/DESCRIPTION | 14 +++++++------- structree-1.1.6/structree/MD5 | 15 +++++++-------- structree-1.1.6/structree/R/plot.structree.R | 10 +++++----- structree-1.1.6/structree/R/structree.R | 10 +++++----- structree-1.1.6/structree/build/vignette.rds |binary structree-1.1.6/structree/inst/doc/examples_fixed.pdf |binary structree-1.1.6/structree/man/plot.structree.Rd | 17 +++++++++-------- structree-1.1.6/structree/man/structree.Rd | 14 +++++++------- 9 files changed, 40 insertions(+), 40 deletions(-)
Title: Tools for Conducting and Analyzing Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct
respirometry experiments. Strong emphasis is on aquatic respirometry. Tools
focus on helping the researcher setup and conduct experiments. Functions for
analysis of resulting respirometry data are also provided. This package
provides tools for intermittent, flow-through, and closed respirometry
techniques.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between respirometry versions 1.0.0 dated 2019-05-27 and 1.0.1 dated 2019-09-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ R/import_firesting.R | 11 +++++++---- 4 files changed, 17 insertions(+), 11 deletions(-)
Title: Detection of Univariate Outliers
Description: Well known outlier detection techniques in the univariate case. Methods to deal with skewed distribution are included too. The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of historical data is implemented as well. When available, survey weights can be used in outliers detection.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio <mdo.statmatch@gmail.com>
Diff between univOutl versions 0.1-4 dated 2018-01-09 and 0.1-5 dated 2019-09-27
DESCRIPTION | 8 ++++---- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + NEWS | 4 ++++ R/HBmethod.R | 18 +++++++++++------- R/plot4ratios.R |only R/ratioSize.R | 6 +++--- man/HBmethod.Rd | 31 +++++++++++++++++++++---------- man/LocScaleB.Rd | 10 +++++----- man/boxB.Rd | 4 ++-- man/plot4ratios.Rd |only man/ratioSize.Rd | 11 ++++++----- man/univOutl-package.Rd | 4 ++-- 13 files changed, 71 insertions(+), 48 deletions(-)
Title: Optimal Stratification of Univariate Populations
Description: This implements the stratification of univariate populations under stratified sampling designs using the method of Khan et al. (2002) <doi:10.1177/0008068320020518>, Khan et al. (2008) (<http://www.statcan.gc.ca/pub/12-001-x/2008002/article/10761-eng.pdf>) and Khan et al. (2015) <doi:10.1080/02664763.2015.1018674>. It determines the Optimum Strata Boundaries (OSB) and Optimum Sample Sizes (OSS) for the study variable, y, using the best-fit frequency distribution of a survey variable (if data is available) or a hypothetical distribution (if data is not available). The method formulates the problem of determining the OSB as mathematical programming problem which is solved by using a dynamic programming technique. If a dataset of the population is available to the surveyor, the method estimates its best-fit distribution and determines the OSB and OSS under Neyman allocation directly. When the dataset is not available, stratification is made based on the assumption that the values of the study variable, y, are available as hypothetical realizations of proxy values of y from recent surveys. Thus, it requires certain distributional assumptions about the study variable. At present, it handles stratification for the populations where the study variable follows a continuous distribution, namely, Pareto, Triangular, Right-triangular, Weibull, Gamma, Exponential, Uniform, Normal, Log-normal and Cauchy distributions.
Author: Karuna G. Reddy [aut, cre],
M. G. M. Khan [aut]
Maintainer: Karuna G. Reddy <karuna.reddy@anu.edu.au>
Diff between stratifyR versions 1.0-1 dated 2018-04-12 and 1.0-2 dated 2019-09-27
stratifyR-1.0-1/stratifyR/R/data.res.R |only stratifyR-1.0-1/stratifyR/R/distr.res.R |only stratifyR-1.0-1/stratifyR/man/data.res.Rd |only stratifyR-1.0-1/stratifyR/man/distr.res.Rd |only stratifyR-1.0-2/stratifyR/DESCRIPTION | 15 stratifyR-1.0-2/stratifyR/MD5 | 68 +- stratifyR-1.0-2/stratifyR/NAMESPACE | 1 stratifyR-1.0-2/stratifyR/R/create.mat.R | 2 stratifyR-1.0-2/stratifyR/R/data.alloc.R | 13 stratifyR-1.0-2/stratifyR/R/data.optim.R | 13 stratifyR-1.0-2/stratifyR/R/data.root.R | 40 - stratifyR-1.0-2/stratifyR/R/distr.alloc.R | 57 +- stratifyR-1.0-2/stratifyR/R/distr.optim.R | 13 stratifyR-1.0-2/stratifyR/R/distr.root.R | 36 - stratifyR-1.0-2/stratifyR/R/get.dist.R | 7 stratifyR-1.0-2/stratifyR/R/minim.val.R | 6 stratifyR-1.0-2/stratifyR/R/realloc.R | 23 stratifyR-1.0-2/stratifyR/R/strata.data.R | 164 +++++- stratifyR-1.0-2/stratifyR/R/strata.distr.R | 109 +++- stratifyR-1.0-2/stratifyR/R/summary.strata.R |only stratifyR-1.0-2/stratifyR/build/vignette.rds |binary stratifyR-1.0-2/stratifyR/inst/doc/stratifyR-vignette.R | 68 +- stratifyR-1.0-2/stratifyR/inst/doc/stratifyR-vignette.Rmd | 102 ++- stratifyR-1.0-2/stratifyR/inst/doc/stratifyR-vignette.html | 338 +++++++------ stratifyR-1.0-2/stratifyR/man/data.alloc.Rd | 6 stratifyR-1.0-2/stratifyR/man/data.optim.Rd | 6 stratifyR-1.0-2/stratifyR/man/data.root.Rd | 10 stratifyR-1.0-2/stratifyR/man/distr.alloc.Rd | 6 stratifyR-1.0-2/stratifyR/man/distr.optim.Rd | 6 stratifyR-1.0-2/stratifyR/man/distr.root.Rd | 12 stratifyR-1.0-2/stratifyR/man/get.dist.Rd | 6 stratifyR-1.0-2/stratifyR/man/minim.val.Rd | 6 stratifyR-1.0-2/stratifyR/man/realloc.Rd | 9 stratifyR-1.0-2/stratifyR/man/strata.data.Rd | 48 + stratifyR-1.0-2/stratifyR/man/strata.distr.Rd | 47 + stratifyR-1.0-2/stratifyR/man/summary.strata.Rd |only stratifyR-1.0-2/stratifyR/vignettes/library.bib | 20 stratifyR-1.0-2/stratifyR/vignettes/stratifyR-vignette.Rmd | 102 ++- 38 files changed, 802 insertions(+), 557 deletions(-)
More information about SimDissolution at CRAN
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Title: Domain-Specific Language for Building PLS Structural Equation
Models
Description: A powerful, easy to write and easy to modify syntax for
specifying and estimating Partial Least Squares (PLS) path models allowing for the latest estimation methods
for Consistent PLS as per Dijkstra & Henseler (2015, MISQ 39(2): 297-316), adjusted interactions as per
Henseler & Chin (2010) <doi:10.1080/10705510903439003> and bootstrapping utilizing
parallel processing as per Hair et al. (2017, ISBN:978-1483377445).
Author: Soumya Ray [aut, ths],
Nicholas Danks [aut, cre],
Juan Manuel Velasquez Estrada [aut]
Maintainer: Nicholas Danks <nicholasdanks@hotmail.com>
Diff between seminr versions 0.7.0 dated 2019-05-07 and 1.0.0 dated 2019-09-27
seminr-0.7.0/seminr/R/bootstrap.R |only seminr-0.7.0/seminr/R/consistent.R |only seminr-0.7.0/seminr/R/constructs.R |only seminr-0.7.0/seminr/R/evaluation.R |only seminr-0.7.0/seminr/R/interactions.R |only seminr-0.7.0/seminr/R/metrics.R |only seminr-0.7.0/seminr/R/model.R |only seminr-0.7.0/seminr/R/model_extraction.R |only seminr-0.7.0/seminr/R/model_fit.R |only seminr-0.7.0/seminr/R/relationships.R |only seminr-0.7.0/seminr/R/reliability.R |only seminr-0.7.0/seminr/R/reporting.R |only seminr-0.7.0/seminr/R/simplePLS.R |only seminr-0.7.0/seminr/R/summary.R |only seminr-0.7.0/seminr/R/validity.R |only seminr-0.7.0/seminr/R/warnings.R |only seminr-0.7.0/seminr/man/SRMR.Rd |only seminr-0.7.0/seminr/man/interaction_ortho.Rd |only seminr-0.7.0/seminr/man/interaction_scaled.Rd |only seminr-0.7.0/seminr/man/interactions.Rd |only seminr-0.7.0/seminr/tests/fixtures/V_3_5_X/pvalues.csv |only seminr-0.7.0/seminr/tests/fixtures/V_3_5_X/tvalues.csv |only seminr-0.7.0/seminr/tests/fixtures/V_3_6_0/pvalues.csv |only seminr-0.7.0/seminr/tests/fixtures/V_3_6_0/tvalues.csv |only seminr-1.0.0/seminr/DESCRIPTION | 8 seminr-1.0.0/seminr/MD5 | 161 +-- seminr-1.0.0/seminr/NAMESPACE | 11 seminr-1.0.0/seminr/R/estimate_bootstrap.R |only seminr-1.0.0/seminr/R/estimate_metrics.R |only seminr-1.0.0/seminr/R/estimate_model.R |only seminr-1.0.0/seminr/R/estimate_simplePLS.R |only seminr-1.0.0/seminr/R/evaluate_effects.R |only seminr-1.0.0/seminr/R/evaluate_measurement_model.R |only seminr-1.0.0/seminr/R/evaluate_model.R |only seminr-1.0.0/seminr/R/evaluate_reliability.R |only seminr-1.0.0/seminr/R/evaluate_validity.R |only seminr-1.0.0/seminr/R/evaluate_warnings.R |only seminr-1.0.0/seminr/R/feature_consistent.R |only seminr-1.0.0/seminr/R/feature_higher_order.R |only seminr-1.0.0/seminr/R/library.R | 79 + seminr-1.0.0/seminr/R/plot_results.R |only seminr-1.0.0/seminr/R/report_descriptives.R |only seminr-1.0.0/seminr/R/report_measurement_model.R |only seminr-1.0.0/seminr/R/report_paths_and_intervals.R |only seminr-1.0.0/seminr/R/report_summary.R |only seminr-1.0.0/seminr/R/specify_constructs.R |only seminr-1.0.0/seminr/R/specify_interactions.R |only seminr-1.0.0/seminr/R/specify_relationships.R |only seminr-1.0.0/seminr/README.md | 98 + seminr-1.0.0/seminr/demo/00Index | 1 seminr-1.0.0/seminr/demo/seminr-contained.R | 10 seminr-1.0.0/seminr/demo/seminr-hoc.R |only seminr-1.0.0/seminr/demo/seminr-interaction.R | 58 - 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seminr-1.0.0/seminr/tests/testthat/test-validity.R | 6 seminr-1.0.0/seminr/vignettes/SEMinR.Rmd | 146 +- 123 files changed, 973 insertions(+), 567 deletions(-)
Title: Methods for Analysing Forensic Ancestry Informative Markers
Description: Evaluates likelihood ratio tests for alleged ancestry. Implements the methods of Tvedebrink et al (2018) <doi:10.1016/j.tpb.2017.12.004>.
Author: Torben Tvedebrink
Maintainer: Torben Tvedebrink <tvede@math.aau.dk>
Diff between genogeographer versions 0.1.8 dated 2018-03-14 and 0.1.19 dated 2019-09-27
DESCRIPTION | 10 - MD5 | 41 ++-- NAMESPACE | 28 ++ R/LR_table.R | 20 +- R/admixture.R |only R/app_helpers.R | 72 +++++-- R/dp_prep_helpers.R | 21 +- R/exponential_tilt.R | 166 +++++++++------- R/genogeo.R | 16 + R/genogeographer.R | 22 +- R/map_plot.R | 42 ++-- R/profile_AA_x0.R | 14 + R/random_AIMs_profile.R | 4 R/scores_pop.R | 1 R/server_fct.R | 354 +++++++++++++++++++++++++++--------- R/ui_fct.R | 10 - inst/deployable_app/LR_plot.R |only inst/deployable_app/aims_report.Rmd | 27 +- inst/deployable_app/app.R | 6 inst/deployable_app/miniCRAN.R | 18 + man/LR_table.Rd | 4 man/profile_admixture.Rd |only man/random_AIMs_profile.Rd | 4 23 files changed, 605 insertions(+), 275 deletions(-)
More information about genogeographer at CRAN
Permanent link
Title: A Fully Featured Logging Framework
Description: A flexible, feature-rich yet light-weight logging
framework based on 'R6' classes. It supports hierarchical loggers,
custom log levels, arbitrary data fields in log events, logging to
plaintext, 'JSON', (rotating) files, memory buffers, and databases, as
well as email and push notifications. For a full list of features with
examples please refer to the package vignette.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between lgr versions 0.3.2 dated 2019-08-20 and 0.3.3 dated 2019-09-27
DESCRIPTION | 6 - MD5 | 12 +-- NEWS.md | 7 ++ R/Logger.R | 103 ++++++++++++++++++++---------- R/get_logger.R | 8 -- build/vignette.rds |binary inst/doc/lgr.html | 177 +++++++++++++++++++++++++---------------------------- 7 files changed, 173 insertions(+), 140 deletions(-)
Title: Bayesian Additive Models for Location, Scale, and Shape (and
Beyond)
Description: Infrastructure for estimating probabilistic distributional regression models in a Bayesian framework.
The distribution parameters may capture location, scale, shape, etc. and every parameter may depend
on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model.
The conceptual and computational framework is introduced in Umlauf, Klein, Zeileis (2019)
<doi:10.1080/10618600.2017.1407325> and the R package in Umlauf, Klein, Simon, Zeileis (2019)
<arXiv:1909.11784>.
Author: Nikolaus Umlauf [aut, cre] (<https://orcid.org/0000-0003-2160-9803>),
Nadja Klein [aut],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>),
Meike Koehler [ctb],
Thorsten Simon [aut] (<https://orcid.org/0000-0002-3778-7738>),
Stanislaus Stadlmann [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between bamlss versions 1.0-2 dated 2019-07-30 and 1.1-0 dated 2019-09-27
DESCRIPTION | 30 ++-- MD5 | 71 ++++++----- NAMESPACE | 44 ++++--- NEWS.md | 23 +++ R/BAMLSS.R | 225 +++++++++++++++++++++++++++++------- R/GAMart.R | 11 + R/JM.R | 63 +++++----- R/data.R | 22 +++ R/families.R | 31 +++++ R/optimizers.R | 308 +++++++++++++++++++++++++++++++++++++++----------- R/stabsel.R | 17 +- R/survival.R | 16 +- R/vis.R | 54 +++++++- build |only data/Golf.rda |only inst/CITATION | 46 ++++--- inst/doc |only man/Crazy.Rd |only man/Golf.Rd |only man/Surv2.Rd | 4 man/bamlss-package.Rd | 10 + man/bamlss.Rd | 9 + man/bboost.Rd | 6 man/bfit.Rd | 10 - man/boost.Rd | 42 +++--- man/cox.mcmc.Rd | 14 +- man/cox.mode.Rd | 12 - man/cox.predict.Rd | 18 +- man/jm_bamlss.Rd | 51 +++----- man/lasso.Rd | 42 +++--- man/pathplot.Rd |only man/plot2d.Rd | 2 man/plotmap.Rd | 3 man/response_name.Rd |only man/simJM.Rd | 2 man/simSurv.Rd | 2 man/smooth_check.Rd |only man/surv.transform.Rd | 12 - vignettes |only 39 files changed, 838 insertions(+), 362 deletions(-)
Title: Subgroup Identification Based on Differential Effect Search
Description: Provides function to apply "Subgroup Identification based on Differential Effect Search" (SIDES) method proposed by Lipkovich et al. (2011) <doi:10.1002/sim.4289>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between SIDES versions 1.13 dated 2018-08-21 and 1.14 dated 2019-09-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/SIDES_MAIN.R | 2 +- man/SIDES-package.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut],
Romain Francois [aut, cph],
Kevin Ushey [aut, cre],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/),
RStudio [cph],
Intel [aut, cph] (Intel TBB library,
https://www.threadingbuildingblocks.org/),
Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 4.4.3 dated 2019-05-22 and 4.4.4 dated 2019-09-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/NEWS | 4 ++++ inst/include/RcppParallel/TinyThread.h | 12 ++++-------- src/Makevars.in | 4 ++-- tools/config/cleanup.R | 2 +- 6 files changed, 19 insertions(+), 19 deletions(-)
Title: Modelling Tools for Reproduction and Survival Data in
Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the
mathematical and statistical modelling of toxicity test data. They use advanced and
innovative methods for a valuable quantitative environmental risk assessment. See also
Delignette-Muller et al. (2017) <doi:10.1021/acs.est.6b05326>. and Baudrot et al. (2018) <doi:10.1021/acs.est.7b05464>.
Author: Virgile Baudrot [aut],
Sandrine Charles [aut],
Marie Laure Delignette-Muller [aut],
Wandrille Duchemin [ctb],
Benoit Goussen [ctb],
Guillaume Kon-Kam-King [ctb],
Christelle Lopes [ctb],
Philippe Ruiz [aut],
Alexander Singer [ctb],
Philippe Veber [aut]
Maintainer: Philippe Veber <philippe.veber@univ-lyon1.fr>
Diff between morse versions 3.2.4 dated 2019-06-21 and 3.2.5 dated 2019-09-27
DESCRIPTION | 6 MD5 | 55 +- R/LCx.survFit.R | 16 R/MFx.survFit.R | 16 R/likelihood.R |only R/plot.LCx.R | 6 R/plot.MFx.R | 6 R/plot.survFitCstExp.R | 12 R/plot.survFitPredict.R | 10 R/plot.survFitPredict_Nsurv.R | 8 R/plot.survFitTKTD.R | 12 R/plot.survFitTT.R | 12 R/plot.survFitVarExp.R | 12 R/plotDoseResponse.survDataCstExp.R | 10 build/vignette.rds |binary inst/doc/modelling.pdf |binary inst/doc/tutorial.R | 371 +++++++++++++++ inst/doc/tutorial.html | 773 +++++++++++++++++---------------- man/LCx.survFit.Rd | 10 man/MFx.survFit.Rd | 12 man/plot.LCx.Rd | 6 man/plot.MFx.Rd | 6 man/plot.survFitCstExp.Rd | 18 man/plot.survFitPredict.Rd | 14 man/plot.survFitPredict_Nsurv.Rd | 8 man/plot.survFitTKTD.Rd | 18 man/plot.survFitTT.Rd | 12 man/plot.survFitVarExp.Rd | 17 man/plotDoseResponse.survDataCstExp.Rd | 10 29 files changed, 930 insertions(+), 526 deletions(-)
Title: Encoding of Sequences Based on Frequency Matrix Chaos Game
Representation
Description: Sequences encoding by using the chaos game representation.
Löchel et al. (2019) <doi:10.1093/bioinformatics/btz493>.
Author: Dominik Eger and Hannah Franziska Löchel
Maintainer: Hannah Franziska Löchel <loechelh@mathematik.uni-marburg.de>
Diff between kaos versions 0.1.1 dated 2019-05-28 and 0.1.2 dated 2019-09-27
DESCRIPTION | 8 ++++---- MD5 | 4 +++- R/Message.R |only inst |only 4 files changed, 7 insertions(+), 5 deletions(-)
Title: Tools for Reading and Writing ISO/OGC Geographic Metadata
Description: Provides facilities to handle reading and writing of geographic metadata
defined with OGC/ISO 19115, 11119 and 19110 geographic information metadata standards,
and encoded using the ISO 19139 (XML) standard. It includes also a facility to check
the validity of ISO 19139 XML encoded metadata.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geometa versions 0.5-0 dated 2019-05-26 and 0.6-0 dated 2019-09-27
DESCRIPTION | 10 MD5 | 368 ++++--- NAMESPACE | 46 R/GMLAbstractCoordinateOperation.R | 8 R/GMLAbstractGML.R | 6 R/GMLAbstractGeneralConversion.R | 4 R/GMLAbstractGeneralOperationParameter.R | 4 R/GMLAbstractSingleOperation.R | 4 R/GMLAbstractTimeGeometricPrimitive.R | 1 R/GMLConventionalUnit.R | 6 R/GMLConversion.R | 8 R/GMLCoordinateSystemAxis.R | 10 R/GMLDerivedCRS.R | 6 R/GMLEnvelope.R | 4 R/GMLEnvelopeWithTimePeriod.R | 4 R/GMLGeneralGridAxis.R | 8 R/GMLGeodeticCRS.R | 10 R/GMLOperationMethod.R | 14 R/GMLOperationParameter.R | 4 R/GMLOperationParameterGroup.R | 8 R/GMLParameterValue.R | 4 R/GMLParameterValueGroup.R | 4 R/GMLProjectedCRS.R | 4 R/GMLTemporalCRS.R | 4 R/GMLTimeInstant.R | 2 R/GMLTimePeriod.R | 6 R/GMLUnitDefinition.R | 4 R/GMLVerticalCRS.R | 4 R/INSPIREMetadataValidator.R | 116 +- R/ISOAbstractObject.R | 98 + R/ISOBaseDecimal.R | 14 R/ISOCitation.R | 193 +++ R/ISOCodeListValue.R | 1 R/ISOCodelist.R | 21 R/ISODataFile.R |only R/ISODataQualityCompleteness.R | 12 R/ISODataQualityLogicalConsistency.R | 20 R/ISODataQualityPositionalAccuracy.R | 16 R/ISODataQualityTemporalAccuracy.R | 16 R/ISODataQualityThematicAccuracy.R | 16 R/ISODate.R | 7 R/ISOImageryAcquisitionInformation.R |only R/ISOImageryAlgorithm.R |only R/ISOImageryBand.R |only R/ISOImageryBandDefinition.R |only R/ISOImageryContext.R |only R/ISOImageryCoverageDescription.R |only R/ISOImageryCoverageResult.R |only R/ISOImageryEnvironmentalRecord.R |only R/ISOImageryEvent.R |only R/ISOImageryGCP.R |only R/ISOImageryGCPCollection.R |only R/ISOImageryGeolocationInformation.R |only R/ISOImageryGeometryType.R |only R/ISOImageryGeorectified.R |only R/ISOImageryGeoreferenceable.R |only R/ISOImageryImageDescription.R |only R/ISOImageryInstrument.R |only R/ISOImageryMetadata.R |only R/ISOImageryNominalResolution.R |only R/ISOImageryObjective.R |only R/ISOImageryObjectiveType.R |only R/ISOImageryOperation.R |only R/ISOImageryOperationType.R |only R/ISOImageryPlan.R |only R/ISOImageryPlatform.R |only R/ISOImageryPlatformPass.R |only R/ISOImageryPolarisationOrientation.R |only R/ISOImageryPriority.R |only R/ISOImageryProcessStep.R |only R/ISOImageryProcessStepReport.R |only R/ISOImageryProcessing.R |only R/ISOImageryRangeElementDescription.R |only R/ISOImageryRequestedDate.R |only R/ISOImageryRequirement.R |only R/ISOImagerySensorType.R |only R/ISOImagerySequence.R |only R/ISOImagerySource.R |only R/ISOImageryTransferFunctionType.R |only R/ISOImageryTrigger.R |only R/ISOImageryUsability.R |only R/ISOKeywords.R | 2 R/ISOMetadata.R | 6 R/ISOMetadataNamespace.R | 2 R/geometa.R | 4 R/geometa_mapping.R | 101 + R/profile.R | 2 R/readISO19139.R | 3 README.md | 6 inst/extdata/codelists/gmxCodelists.xml | 34 inst/extdata/coverage/geometa_coverage_inventory.csv | 82 - inst/extdata/coverage/geometa_coverage_summary.csv | 4 inst/extdata/examples/metadata.R |only inst/extdata/examples/metadata.xml | 330 ++++-- inst/extdata/mappings/geometa_mapping.csv | 4 inst/extdata/schemas/gmi/acquisitionInformation.xsd | 820 ++++++++-------- man/GMLAbstractCoordinateOperation.Rd | 8 man/GMLAbstractGML.Rd | 6 man/GMLAbstractGeneralConversion.Rd | 4 man/GMLAbstractGeneralOperationParameter.Rd | 4 man/GMLAbstractSingleOperation.Rd | 4 man/GMLConventionalUnit.Rd | 6 man/GMLConversion.Rd | 8 man/GMLCoordinateSystemAxis.Rd | 10 man/GMLDerivedCRS.Rd | 6 man/GMLEnvelope.Rd | 4 man/GMLEnvelopeWithTimePeriod.Rd | 4 man/GMLGeneralGridAxis.Rd | 8 man/GMLGeodeticCRS.Rd | 8 man/GMLOperationMethod.Rd | 14 man/GMLOperationParameter.Rd | 4 man/GMLOperationParameterGroup.Rd | 8 man/GMLParameterValue.Rd | 4 man/GMLParameterValueGroup.Rd | 4 man/GMLProjectedCRS.Rd | 4 man/GMLTemporalCRS.Rd | 4 man/GMLTimeInstant.Rd | 2 man/GMLTimePeriod.Rd | 6 man/GMLUnitDefinition.Rd | 4 man/GMLVerticalCRS.Rd | 4 man/INSPIREMetadataValidator.Rd | 6 man/ISOAbsoluteExternalPositionalAccuracy.Rd | 4 man/ISOAbstractCompleteness.Rd | 4 man/ISOAbstractLogicalConsistency.Rd | 4 man/ISOAbstractPositionalAccuracy.Rd | 4 man/ISOAbstractTemporalAccuracy.Rd | 4 man/ISOAbstractThematicAccuracy.Rd | 4 man/ISOAccuracyOfATimeMeasurement.Rd | 4 man/ISOCitation.Rd | 57 + man/ISOCompletenessCommission.Rd | 4 man/ISOCompletenessOmission.Rd | 4 man/ISOConceptualConsistency.Rd | 4 man/ISODataFile.Rd |only man/ISODate.Rd | 3 man/ISODomainConsistency.Rd | 4 man/ISOFormatConsistency.Rd | 4 man/ISOGriddedDataPositionalAccuracy.Rd | 4 man/ISOImageryAbstractGeolocationInformation.Rd |only man/ISOImageryAcquisitionInformation.Rd |only man/ISOImageryAlgorithm.Rd |only man/ISOImageryBand.Rd |only man/ISOImageryBandDefinition.Rd |only man/ISOImageryContext.Rd |only man/ISOImageryCoverageDescription.Rd |only man/ISOImageryCoverageResult.Rd |only man/ISOImageryEnvironmentalRecord.Rd |only man/ISOImageryEvent.Rd |only man/ISOImageryGCP.Rd |only man/ISOImageryGCPCollection.Rd |only man/ISOImageryGeometryType.Rd |only man/ISOImageryGeorectified.Rd |only man/ISOImageryGeoreferenceable.Rd |only man/ISOImageryImageDescription.Rd |only man/ISOImageryInstrument.Rd |only man/ISOImageryMetadata.Rd |only man/ISOImageryNominalResolution.Rd |only man/ISOImageryObjective.Rd |only man/ISOImageryObjectiveType.Rd |only man/ISOImageryOperation.Rd |only man/ISOImageryOperationType.Rd |only man/ISOImageryPlan.Rd |only man/ISOImageryPlatform.Rd |only man/ISOImageryPlatformPass.Rd |only man/ISOImageryPolarisationOrientation.Rd |only man/ISOImageryPriority.Rd |only man/ISOImageryProcessStep.Rd |only man/ISOImageryProcessStepReport.Rd |only man/ISOImageryProcessing.Rd |only man/ISOImageryRangeElementDescription.Rd |only man/ISOImageryRequestedDate.Rd |only man/ISOImageryRequirement.Rd |only man/ISOImagerySensorType.Rd |only man/ISOImagerySequence.Rd |only man/ISOImagerySource.Rd |only man/ISOImageryTransferFunctionType.Rd |only man/ISOImageryTrigger.Rd |only man/ISOImageryUsability.Rd |only man/ISOKeywords.Rd | 2 man/ISOMetadata.Rd | 6 man/ISONonQuantitativeAttributeAccuracy.Rd | 4 man/ISOQuantitativeAttributeAccuracy.Rd | 4 man/ISORelativeInternalPositionalAccuracy.Rd | 4 man/ISOTemporalConsistency.Rd | 4 man/ISOTemporalValidity.Rd | 4 man/ISOThematicClassificationCorrectness.Rd | 4 man/ISOTopologicalConsistency.Rd | 4 man/cacheISOClasses.Rd |only man/convert_metadata.Rd |only man/geometa.Rd | 4 man/getISOClasses.Rd |only man/getMappingFormats.Rd | 5 man/getMappings.Rd |only tests/testthat/test_ISOBaseBoolean.R | 2 tests/testthat/test_ISOBaseCharacterString.R | 2 tests/testthat/test_ISOBaseDate.R | 2 tests/testthat/test_ISOBaseDateTime.R | 2 tests/testthat/test_ISOBaseDecimal.R | 2 tests/testthat/test_ISOBaseInteger.R | 2 tests/testthat/test_ISOBaseReal.R | 2 tests/testthat/test_ISODataFile.R |only tests/testthat/test_ISODate.R | 5 tests/testthat/test_ISODefinitionReference.R | 2 tests/testthat/test_ISOFeatureCatalogue.R | 2 tests/testthat/test_ISOFeatureOperation.R | 1 tests/testthat/test_ISOFileName.R | 2 tests/testthat/test_ISOImageryAlgorithm.R |only tests/testthat/test_ISOImageryBand.R |only tests/testthat/test_ISOImageryCoverageDescription.R |only tests/testthat/test_ISOImageryEnvironmentalRecord.R |only tests/testthat/test_ISOImageryEvent.R |only tests/testthat/test_ISOImageryGCP.R |only tests/testthat/test_ISOImageryGCPCollection.R |only tests/testthat/test_ISOImageryGeorectified.R |only tests/testthat/test_ISOImageryGeoreferenceable.R |only tests/testthat/test_ISOImageryImageDescription.R |only tests/testthat/test_ISOImageryInstrument.R |only tests/testthat/test_ISOImageryMetadata.R |only tests/testthat/test_ISOImageryNominalResolution.R |only tests/testthat/test_ISOImageryObjective.R |only tests/testthat/test_ISOImageryPlan.R |only tests/testthat/test_ISOImageryPlatform.R |only tests/testthat/test_ISOImageryPlatformPass.R |only tests/testthat/test_ISOImageryProcessStep.R |only tests/testthat/test_ISOImageryProcessing.R |only tests/testthat/test_ISOImageryRangeElementDescription.R |only tests/testthat/test_ISOImageryRequestedDate.R |only tests/testthat/test_ISOImageryRequirement.R |only tests/testthat/test_ISOImagerySource.R |only tests/testthat/test_ISOImageryUsability.R |only tests/testthat/test_ISOKeywords.R | 3 tests/testthat/test_ISOLocaleContainer.R | 8 tests/testthat/test_ISOLocalisedCharacterString.R | 2 tests/testthat/test_ISOMeasure.R | 8 tests/testthat/test_ISOMedium.R | 6 tests/testthat/test_ISOMetadata.R | 2 tests/testthat/test_ISOMetadataExtensionInformation.R | 4 tests/testthat/test_ISOProcessStep.R | 2 tests/testthat/test_ISOPropertyType.R | 2 tests/testthat/test_ISOResponsibleParty.R | 2 tests/testthat/test_ISOUsage.R | 6 tests/testthat/test_geometa_mapping.R | 26 241 files changed, 1778 insertions(+), 1115 deletions(-)
Title: Statistical Modelling with Applications in Forestry
Description: Developed for the following tasks. I) Computing the probability density function, cumulative distribution function, random generation, and estimating the parameters of the eleven mixture models including mixture of Birnbaum-Saunders, BurrXII, Chen, F, Frechet, gamma, Gompertz, log-logistic, log-normal, Lomax, and Weibull. II) Point estimation of the parameters of two- and three-parameter Weibull distributions. In the case of two-parameter, twelve methods consist of generalized least square type 1, generalized least square type 2, L-moment, maximum likelihood, logarithmic moment, moment, percentile, rank correlation, least square, weighted maximum likelihood, U-statistic, weighted least square are used and investigated methods for the three-parameter case are: maximum likelihood, modified moment type 1, modified moment type 2, modified moment type 3, modified maximum likelihood type 1, modified maximum likelihood type 2, modified maximum likelihood type 3, modified maximum likelihood type 4, moment, maximum product spacing, T-L moment, and weighted maximum likelihood. III) The Bayesian estimators of the three-parameter Weibull distribution developed by Green et al. (1994) <doi:10.2307/2533217>. IV) Estimating parameters of the three-parameter Weibull distribution fitted to grouped data using three methods including approximated maximum likelihood, expectation maximization, and maximum likelihood. V) Estimating the parameters of the gamma, log-normal, and Weibull mixture models fitted to the grouped data through the EM algorithm. VI) Estimating parameters of the non-linear growth curve fitted to the height-diameter observations.
Author: Mahdi Teimouri
Maintainer: Mahdi Teimouri <teimouri@aut.ac.ir>
Diff between ForestFit versions 0.4 dated 2019-09-11 and 0.4.1 dated 2019-09-27
DESCRIPTION | 10 - MD5 | 12 +- R/ForestFit.R | 269 +++++++++++++++++++++++-------------------------- man/dmixture.Rd | 3 man/fitWeibull.Rd | 6 - man/fitbayesWeibull.Rd | 6 - man/pmixture.Rd | 3 7 files changed, 156 insertions(+), 153 deletions(-)
Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>),
Bradley Jones [ctb],
Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidytree versions 0.2.7 dated 2019-09-12 and 0.2.8 dated 2019-09-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/ancestor.R | 9 ++++++++- R/offspring.R | 5 +++-- inst/doc/tidytree.html | 4 ++-- 6 files changed, 25 insertions(+), 13 deletions(-)
Title: A Lightweight and Flexible Web Framework
Description: A very flexible framework for building server side logic in R. The
framework is unopinionated when it comes to how HTTP requests and WebSocket
messages are handled and supports all levels of app complexity; from serving
static content to full-blown dynamic web-apps. Fiery does not hold your hand
as much as e.g. the shiny package does, but instead sets you free to create
your web app the way you want.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>)
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between fiery versions 1.1.1 dated 2018-10-22 and 1.1.2 dated 2019-09-27
fiery-1.1.1/fiery/R/delay_doc.R |only fiery-1.1.1/fiery/R/event_doc.R |only fiery-1.1.1/fiery/R/plugin_doc.R |only fiery-1.1.1/fiery/man/delay_doc.Rd |only fiery-1.1.1/fiery/man/event_doc.Rd |only fiery-1.1.1/fiery/man/plugin_doc.Rd |only fiery-1.1.2/fiery/DESCRIPTION | 30 +++--- fiery-1.1.2/fiery/MD5 | 39 ++++---- fiery-1.1.2/fiery/NEWS.md | 9 + fiery-1.1.2/fiery/R/Fire.R | 17 +-- fiery-1.1.2/fiery/R/FutureStack.R | 4 fiery-1.1.2/fiery/R/aaa.R | 3 fiery-1.1.2/fiery/R/fiery-package.R | 12 -- fiery-1.1.2/fiery/README.md | 128 +++++++++++++++++++-------- fiery-1.1.2/fiery/build |only fiery-1.1.2/fiery/inst/doc |only fiery-1.1.2/fiery/man/Fire.Rd | 16 +-- fiery-1.1.2/fiery/man/fiery-package.Rd | 13 -- fiery-1.1.2/fiery/tests/testthat/test-Fire.R | 14 +- fiery-1.1.2/fiery/vignettes |only 20 files changed, 170 insertions(+), 115 deletions(-)
Title: Timescale-Specific Variance Ratio for Use in Community Ecology
Description: Tools for timescale decomposition of the classic variance ratio of community ecology. Tools are as described in Zhao et al (in prep), extending commonly used methods introduced by Peterson et al (1975) <doi: 10.2307/1936306>.
Author: Daniel C. Reuman [aut, cre],
Lei Zhao [aut],
Shaopeng Wang [aut]
Maintainer: Daniel C. Reuman <reuman@ku.edu>
Diff between tsvr versions 1.0.0 dated 2019-02-27 and 1.0.1 dated 2019-09-27
DESCRIPTION | 6 ++--- MD5 | 35 ++++++++++++++++--------------- R/cv2f.R | 29 ++++++++++++++----------- R/tsvreq.R | 2 - R/tsvreq_classic.R | 2 - R/vreq.R | 2 - R/vreq_methods.R | 5 ++-- R/vrf.R | 26 +++++++++++++---------- README.md |only inst/doc/tsvrvignette.Rmd | 2 - inst/doc/tsvrvignette.pdf |binary man/setget_methods.Rd | 5 ++++ man/tsvreq.Rd | 4 +++ man/tsvreq_classic.Rd | 2 - man/vreq.Rd | 4 +++ tests/testthat/tests_cv2f.R | 45 +++++++++++++++++++++++++++++++++++++++- tests/testthat/tests_vrf.R | 44 +++++++++++++++++++++++++++++++++++++++ vignettes/tsvrvignette.Rmd | 2 - vignettes/tsvrvignette_refs.bib | 2 + 19 files changed, 164 insertions(+), 53 deletions(-)
Title: Phylogenetic Clustering (Phyloclustering)
Description: Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) provides a
convenient implementation of phyloclustering for DNA and SNP data,
capable of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It is
designed in C for performance, interfaced with R for visualization,
and incorporates other popular open source programs including
ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>,
seq-gen (Rambaut and Grassly 1997)
<doi:10.1093/bioinformatics/13.3.235>,
Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and
PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>,
<doi:10.1093/molbev/msm088>,
for simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.
Author: Wei-Chen Chen [aut, cre],
Karin Dorman [aut],
Yan-Han Chen [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between phyclust versions 0.1-25 dated 2019-08-25 and 0.1-26 dated 2019-09-27
ChangeLog | 3 +++ DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- R/p_tool_star_tree.r | 2 +- 4 files changed, 14 insertions(+), 10 deletions(-)