Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported. There is a also support for vector data operations such as intersections. See the manual and tutorials on <https://rspatial.org/> to get started.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ctb],
Duncan Golicher [ctb],
Josh Gray [ctb],
Jonathan A. Greenberg [ctb],
Paul Hiemstra [ctb],
Institute for Mathematics Applied Geosciences [cph],
Charles Karney [ctb],
Matteo Mattiuzzi [ctb],
Steven Mosher [ctb],
Jakub Nowosad [ctb],
Edzer Pebesma [ctb],
Oscar Perpinan Lamigueiro [ctb],
Etienne B. Racine [ctb],
Barry Rowlingson [ctb],
Ashton Shortridge [ctb],
Bill Venables [ctb],
Rafael Wueest [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 3.0-2 dated 2019-08-22 and 3.0-7 dated 2019-09-24
ChangeLog | 8 + DESCRIPTION | 8 - MD5 | 184 +++++++++++++++++----------------- NAMESPACE | 2 R/AAgeneric_functions.R | 19 ++- R/as.character.R | 4 R/barplot.R | 4 R/bbox.R | 4 R/boxplot.R | 4 R/cellFromPolygon.R | 2 R/clump.R | 4 R/cropSpatial.R | 52 ++++----- R/cut.R | 4 R/extent.R | 6 - R/intersect.R | 4 R/intersect_sp.R | 6 - R/ncell.R | 4 R/netCDFtoRasterCD.R | 3 R/predict.R | 10 + R/projection.R | 26 ++-- R/rasterizePolygons.R | 2 R/resample.R | 6 - R/rotate.R | 5 R/sampleRegular.R | 6 - R/subset.R | 4 R/terrain.R | 246 +++++++++++++++++++++++----------------------- R/transpose.R | 5 R/union.R | 4 R/union_sp.R | 4 R/values.R | 10 - inst/doc/Raster.pdf |binary inst/doc/functions.pdf |binary inst/doc/rasterfile.pdf |binary man/Arith-methods.Rd | 2 man/Logic-methods.Rd | 2 man/as.data.frame.Rd | 2 man/as.logical-methods.Rd | 2 man/as.matrix.Rd | 2 man/as.raster.Rd | 2 man/atan2.Rd | 4 man/autocor.Rd | 2 man/boxplot.Rd | 6 - man/brick.Rd | 2 man/buffer.Rd | 2 man/calc.Rd | 2 man/cellStats.Rd | 2 man/cellsFromExtent.Rd | 2 man/clearValues.Rd | 2 man/clump.Rd | 2 man/cluster.Rd | 2 man/cover.Rd | 2 man/crop.Rd | 2 man/crosstab.Rd | 2 man/cut.Rd | 2 man/direction.Rd | 2 man/disaggregate.Rd | 2 man/distance.Rd | 2 man/drawExtent.Rd | 2 man/extend.Rd | 2 man/extractIndex.Rd | 2 man/factor.Rd | 4 man/flip.Rd | 4 man/focal.Rd | 2 man/freq.Rd | 2 man/getValuesFocal.Rd | 2 man/headtail.Rd | 2 man/init.Rd | 2 man/mask.Rd | 4 man/match.Rd | 2 man/merge.Rd | 4 man/mosaic.Rd | 6 - man/names.Rd | 2 man/nlayers.Rd | 2 man/plot.Rd | 4 man/quantile.Rd | 2 man/rasterToPoints.Rd | 2 man/rasterToPolygons.Rd | 2 man/rasterize.Rd | 4 man/reclassify.Rd | 7 - man/replacement.Rd | 2 man/resample.Rd | 2 man/rotate.Rd | 2 man/round.Rd | 2 man/sampleStratified.Rd | 2 man/select.Rd | 2 man/setValues.Rd | 2 man/stackSelect.Rd | 2 man/strech.Rd | 2 man/subs.Rd | 2 man/terrain.Rd | 3 man/transpose.Rd | 2 man/which.Rd | 2 man/zonal.Rd | 4 93 files changed, 371 insertions(+), 429 deletions(-)
Title: Model-Free Functional Chi-Squared and Exact Tests
Description: Statistical hypothesis testing methods for
inferring model-free functional dependency using asymptotic
chi-squared or exact distributions. Functional test
statistics are asymmetric and functionally optimal, unique
from other related statistics. Tests in this package reveal
evidence for causality based on the
causality-by-functionality principle. They include
asymptotic functional chi-squared tests
('Zhang & Song' 2013) <arXiv:1311.2707> and an exact
functional test ('Zhong & Song' 2019)
<doi:10.1109/TCBB.2018.2809743>. The normalized functional
chi-squared test was used by Best Performer 'NMSUSongLab'
in HPN-DREAM (DREAM8) Breast Cancer Network Inference
Challenges ('Hill et al' 2016) <doi:10.1038/nmeth.3773>. A
function index ('Zhong & Song' in press) ('Kumar et al' 2018)
<doi:10.1109/BIBM.2018.8621502> derived from the
functional test statistic offers a new effect size measure
for the strength of functional dependency, a better
alternative to conditional entropy in many aspects. For
continuous data, these tests offer an advantage over
regression analysis when a parametric functional form
cannot be assumed; for categorical data, they provide a
novel means to assess directional dependency not possible
with symmetrical Pearson's chi-squared or Fisher's exact
tests.
Author: Yang Zhang [aut],
Hua Zhong [aut] (<https://orcid.org/0000-0003-1962-2603>),
Hien Nguyen [aut] (<https://orcid.org/0000-0002-7237-4752>),
Ruby Sharma [aut],
Sajal Kumar [aut],
Joe Song [aut, cre] (<https://orcid.org/0000-0002-6883-6547>)
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.4.8-1 dated 2019-09-08 and 2.4.9.1 dated 2019-09-24
DESCRIPTION | 13 - MD5 | 36 +-- NEWS | 16 + README.md | 6 build/vignette.rds |binary inst/doc/exact.fun.test.html | 8 inst/doc/fun.chisq.test.html | 4 inst/doc/patterns.html | 22 +- man/FunChisq-package.Rd | 2 src/EFTNetwork.cpp | 8 src/EFT_DP.cpp | 64 ++---- src/EFT_DP.h | 11 - src/EFT_DQP.cpp | 450 ++++++++++++++++++++----------------------- src/EFT_DQP.h | 19 - src/EFT_QP.cpp | 14 - src/Node.cpp | 82 ++++--- src/Node.h | 54 ++--- src/trimTable.cpp |only src/trimTable.h |only tests/testthat/test_EFT.R | 38 +++ 20 files changed, 445 insertions(+), 402 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-06 1.5
2019-03-27 1.4
2016-04-03 1.1
2015-10-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-22 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-24 1.0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-04 2.1.1
Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data
transformation tasks like recoding, dichotomizing or grouping variables,
setting and replacing missing values. The data transformation functions
also support labelled data, and all integrate seamlessly into a
'tidyverse'-workflow.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Iago Giné-Vázquez [ctb],
Alexander Bartel [ctb] (<https://orcid.org/0000-0002-1280-6138>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 2.8.1 dated 2019-06-17 and 2.8.2 dated 2019-09-24
DESCRIPTION | 23 +++-- MD5 | 85 +++++++++---------- NAMESPACE | 7 + NEWS.md | 25 +++++ R/S3-methods.R | 15 +-- R/add_columns.R | 4 R/de_mean.R | 2 R/descr.R | 32 ++++++- R/find_var.R | 15 ++- R/frq.R | 176 ++++++++++++++++++++++++++++++++-------- R/helpfunctions.R | 48 ++++++++++ R/is_empty.R | 16 ++- R/merge_df.R | 11 ++ R/merge_imputations.R | 4 R/rec.R | 62 ++++++-------- R/str_start_end.R | 2 R/tidy_values.R | 13 ++ R/to_label.R | 2 R/var_labels.R | 34 +++++-- R/word_wrap.R | 20 ++-- R/zzz.R | 6 - README.md | 8 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/design_philosophy.Rmd | 2 inst/doc/design_philosophy.html | 12 +- inst/doc/exploringdatasets.html | 59 +++++++------ inst/doc/recodingvariables.html | 140 ++++++++++++++++--------------- man/add_columns.Rd | 4 man/add_rows.Rd | 2 man/descr.Rd | 22 ++++- man/find_var.Rd | 10 +- man/frq.Rd | 55 +++++++++++- man/is_empty.Rd | 13 ++ man/merge_imputations.Rd | 4 man/str_start.Rd | 6 - man/tidy_values.Rd | 11 +- man/to_character.Rd | 2 man/var_rename.Rd | 21 +++- man/word_wrap.Rd | 5 - tests/testthat/test-frq.R | 102 +++++++++++++++++++++++ tests/testthat/test-rec.R | 26 +++++ tests/testthat/test-word_wrap.R |only vignettes/design_philosophy.Rmd | 2 44 files changed, 799 insertions(+), 309 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between devtools versions 2.2.0 dated 2019-09-07 and 2.2.1 dated 2019-09-24
DESCRIPTION | 18 ++-- MD5 | 44 ++++++------ NAMESPACE | 2 NEWS.md | 42 ++++++++++- R/check-win.R | 2 R/check.R | 2 R/document.R | 13 ++- R/install.R | 15 +++- R/release.R | 15 ---- R/reload.R | 2 R/remotes.R | 11 ++- R/revdep.R | 2 R/test.R | 6 + R/utils.R | 2 R/vignette-r.R | 2 R/zzz.R | 5 - README.md | 14 +-- inst/WORDLIST | 155 ++++++++++++++++++++++++++++++++++++++----- inst/doc/dependencies.Rmd | 4 - inst/doc/dependencies.html | 8 +- man/check_win.Rd | 2 tests/spelling.R |only tests/testthat/test-reload.R |only vignettes/dependencies.Rmd | 4 - 24 files changed, 271 insertions(+), 99 deletions(-)
Title: Social Mixing Matrices for Infectious Disease Modelling
Description: Provides methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.
Author: Sebastian Funk [aut, cre]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between socialmixr versions 0.1.4 dated 2019-07-24 and 0.1.5 dated 2019-09-24
DESCRIPTION | 8 +++---- MD5 | 23 +++++++++++---------- NEWS.md | 4 +++ R/get_survey.r | 10 --------- TODO |only inst/doc/introduction.R | 4 +-- inst/doc/introduction.Rmd | 4 +-- inst/doc/introduction.html | 45 ++++++++---------------------------------- man/get_survey.Rd | 2 - man/survey_countries.Rd | 2 - tests/testthat/test-matrix.r | 1 tests/testthat/test-surveys.r | 1 vignettes/introduction.Rmd | 4 +-- 13 files changed, 38 insertions(+), 70 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly
configurable drop-in replacements for base url() and download.file() with
better performance, support for encryption (https, ftps), gzip compression,
authentication, and other 'libcurl' goodies. The core of the package implements a
framework for performing fully customized requests where data can be processed
either in memory, on disk, or streaming via the callback or connection
interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly
web client see the 'httr' package which builds on this package with http
specific tools and logic.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between curl versions 4.1 dated 2019-09-16 and 4.2 dated 2019-09-24
DESCRIPTION | 6 ++-- MD5 | 20 +++++++------- NEWS | 4 ++ inst/doc/intro.html | 61 +++++++++++++++++++++---------------------- inst/doc/windows.html | 42 ++++++++++++++--------------- src/handle.c | 26 +++++++++--------- src/init.c | 3 -- src/multi.c | 11 +++---- src/ssl.c | 10 ------- src/utils.c | 30 +++++++++++++++++++-- tests/testthat/test-handle.R | 21 +++++++++++--- 11 files changed, 132 insertions(+), 102 deletions(-)
Title: Density Estimation by Life Time Distributions
Description: It plots densities by using asymmetrical kernels which belong to
life time distributions and calculate its related MSE. For details see Chen (2000),
Jin and Kawczak (2003) and Salha et al. (2014) <doi:10.12988/pms.2014.4616>.
Author: Javaria Ahmad Khan, Atif Akbar.
Maintainer: Javaria Ahmad Khan <jakhan0@yahoo.com>
Diff between DELTD versions 1.2.1 dated 2019-09-23 and 1.3.1 dated 2019-09-24
DESCRIPTION | 6 ++-- MD5 | 6 ++-- R/DELTD.R | 84 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ man/dencomb.Rd | 4 ++ 4 files changed, 93 insertions(+), 7 deletions(-)
Title: Ace Editor Bindings for Shiny
Description: Ace editor bindings to enable a rich text editing environment
within Shiny.
Author: Vincent Nijs [aut, cre],
Forest Fang [aut],
Trestle Technology, LLC [aut],
Jeff Allen [aut],
Institut de Radioprotection et de Surete Nucleaire [cph],
Ajax.org B.V. [ctb, cph] (Ace)
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between shinyAce versions 0.4.0 dated 2019-07-09 and 0.4.1 dated 2019-09-24
DESCRIPTION | 11 MD5 | 75 +++++- NAMESPACE | 10 NEWS.md | 5 R/aaa.R | 13 - R/ace-annotate.R |only R/ace-autocomplete.R | 276 +++++++++++++++++++++++-- R/ace-editor.R | 180 ++++++++-------- R/ace-tooltips.R |only R/get-ace-modes.R | 8 R/get-ace-themes.R | 8 R/init.R | 7 R/shinyAce-options.R |only R/update-ace-editor.R | 15 - R/utils.R |only README.md | 2 inst/examples/05-hotkeys/rsconnect |only inst/examples/06-autocomplete/rsconnect |only inst/examples/07-autocomplete-combine/server.R | 22 + inst/examples/08-resize/rsconnect |only inst/examples/09-selectionId/rsconnect |only inst/examples/12-tooltips |only inst/examples/13-modules-with-tooltips |only inst/www/shinyAce.css | 17 + inst/www/shinyAce.js | 219 ++++++++++++++++--- man/aceAnnotate.Rd |only man/aceAutocomplete.Rd | 36 ++- man/aceEditor.Rd | 104 ++++----- man/aceTooltip.Rd |only man/build_tooltip_fields.Rd |only man/dot-fname_regex.Rd |only man/dot-tools.Rd |only man/dot-utils.Rd |only man/get_arg_help.Rd |only man/get_desc_help.Rd |only man/get_help_file.Rd |only man/get_usage_help.Rd |only man/is.empty.Rd | 1 man/meta_obj.Rd |only man/meta_pkg.Rd |only man/r_completions_function_call_metadata.Rd |only man/r_completions_general_metadata.Rd |only man/r_completions_metadata.Rd |only man/rd_2_html.Rd |only man/re_capture.Rd |only man/shinyAce-options.Rd |only man/shinyAce_debug.Rd |only man/tooltip_html.Rd |only tests/test-all.R | 2 tests/testthat/test-shinyAce.R | 6 tests/testthat/test-tooltips.R |only 51 files changed, 755 insertions(+), 262 deletions(-)
Title: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS
Tool
Description: A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can
(1) effectively process large data,
(2) rapidly evaluate population structure,
(3) efficiently estimate variance components several algorithms,
(4) implement parallel-accelerated association tests of markers three methods,
(5) globally efficient design on GWAS process computing,
(6) enhance visualization of related information.
'rMVP' contains three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jianming Yu (2006) <DOI:10.1038/ng1702>)
and FarmCPU (Xiaolei Liu (2016) <doi:10.1371/journal.pgen.1005767>); variance components estimation methods EMMAX
(Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>,
R implementation from 'GAPIT2': You Tang and Xiaolei Liu (2016) <DOI:10.1371/journal.pone.0107684> and
'SUPER': Qishan Wang and Feng Tian (2014) <DOI:10.1371/journal.pone.0107684>), and HE regression
(Xiang Zhou (2017) <DOI:10.1214/17-AOAS1052>).
Author: Lilin Yin [aut],
Haohao Zhang [aut],
Zhenshuang Tang [aut],
Jingya Xu [aut],
Dong Yin [aut],
Zhiwu Zhang [aut],
Xiaohui Yuan [aut],
Mengjin Zhu [aut],
Shuhong Zhao [aut],
Xinyun Li [aut],
Qishan Wang [ctb],
Feng Tian [ctb],
Hyunmin Kang [ctb],
Xiang Zhou [ctb],
Xiaolei Liu [cre, aut, cph]
Maintainer: Xiaolei Liu <xiaoleiliu@mail.hzau.edu.cn>
Diff between rMVP versions 0.99.15 dated 2019-08-30 and 0.99.16 dated 2019-09-24
rMVP-0.99.15/rMVP/inst/extdata/02_bfile/mvp |only rMVP-0.99.15/rMVP/inst/extdata/03_hapmap/mvp.diploid.hmp.txt |only rMVP-0.99.15/rMVP/inst/extdata/06_mvp-impute/mvp.imp.map |only rMVP-0.99.15/rMVP/inst/extdata/07_other/mvp.map |only rMVP-0.99.16/rMVP/DESCRIPTION | 8 rMVP-0.99.16/rMVP/MD5 | 82 rMVP-0.99.16/rMVP/NAMESPACE | 1 rMVP-0.99.16/rMVP/R/MVP.Data.r | 46 rMVP-0.99.16/rMVP/R/MVP.FarmCPU.r | 14 rMVP-0.99.16/rMVP/R/MVP.GLM.r | 5 rMVP-0.99.16/rMVP/R/MVP.Logging.R | 4 rMVP-0.99.16/rMVP/R/MVP.MLM.r | 3 rMVP-0.99.16/rMVP/R/MVP.Report.r | 3453 +++++----- rMVP-0.99.16/rMVP/R/MVP.r | 50 rMVP-0.99.16/rMVP/inst/extdata/01_vcf/mvp.vcf | 3205 --------- rMVP-0.99.16/rMVP/inst/extdata/02_bfile/mvp.bed |binary rMVP-0.99.16/rMVP/inst/extdata/02_bfile/mvp.bim | 3000 -------- rMVP-0.99.16/rMVP/inst/extdata/02_bfile/mvp.fam | 291 rMVP-0.99.16/rMVP/inst/extdata/03_hapmap/mvp.hmp.txt | 3194 --------- rMVP-0.99.16/rMVP/inst/extdata/04_numeric/mvp.map |only rMVP-0.99.16/rMVP/inst/extdata/04_numeric/mvp.num | 3193 --------- rMVP-0.99.16/rMVP/inst/extdata/05_mvp/mvp.geno.bin |binary rMVP-0.99.16/rMVP/inst/extdata/05_mvp/mvp.geno.desc | 6 rMVP-0.99.16/rMVP/inst/extdata/05_mvp/mvp.geno.ind | 271 rMVP-0.99.16/rMVP/inst/extdata/05_mvp/mvp.geno.map | 3194 --------- rMVP-0.99.16/rMVP/inst/extdata/06_mvp-impute/mvp.imp.geno.bin |binary rMVP-0.99.16/rMVP/inst/extdata/06_mvp-impute/mvp.imp.geno.desc | 6 rMVP-0.99.16/rMVP/inst/extdata/06_mvp-impute/mvp.imp.geno.ind | 271 rMVP-0.99.16/rMVP/inst/extdata/06_mvp-impute/mvp.imp.geno.map |only rMVP-0.99.16/rMVP/inst/extdata/07_other/mvp.phe | 271 rMVP-0.99.16/rMVP/man/MVP.Data.Bfile2MVP.Rd | 4 rMVP-0.99.16/rMVP/man/MVP.Data.Hapmap2MVP.Rd | 4 rMVP-0.99.16/rMVP/man/MVP.Data.Kin.Rd | 2 rMVP-0.99.16/rMVP/man/MVP.Data.MVP2Bfile.Rd | 2 rMVP-0.99.16/rMVP/man/MVP.Data.Map.Rd | 6 rMVP-0.99.16/rMVP/man/MVP.Data.Numeric2MVP.Rd | 4 rMVP-0.99.16/rMVP/man/MVP.Data.PC.Rd | 2 rMVP-0.99.16/rMVP/man/MVP.Data.Pheno.Rd | 2 rMVP-0.99.16/rMVP/man/MVP.Data.Rd | 4 rMVP-0.99.16/rMVP/man/MVP.Data.VCF2MVP.Rd | 2 rMVP-0.99.16/rMVP/man/MVP.Data.impute.Rd | 2 rMVP-0.99.16/rMVP/man/MVP.FarmCPU.Rd | 2 rMVP-0.99.16/rMVP/man/MVP.Rd | 2 rMVP-0.99.16/rMVP/man/MVP.Report.Rd | 131 rMVP-0.99.16/rMVP/src/data_converter.cpp | 11 45 files changed, 2566 insertions(+), 18182 deletions(-)
Title: Robust Model-Based Clustering
Description: Performs robust cluster analysis allowing for outliers and noise that cannot be fitted by any cluster. The data are modelled by a mixture of Gaussian distributions and a noise component, which is an improper uniform distribution covering the whole Euclidean space. Parameters are estimated by (pseudo) maximum likelihood. This is fitted by a EM-type algorithm. See Coretto and Hennig (2016) <doi:10.1080/01621459.2015.1100996>, and Coretto and Hennig (2017) <http://jmlr.org/papers/v18/16-382.html>.
Author: Pietro Coretto [aut, cre],
Christian Hennig [aut]
Maintainer: Pietro Coretto <pcoretto@unisa.it>
Diff between otrimle versions 1.2 dated 2019-09-23 and 1.3 dated 2019-09-24
ChangeLog | 21 +++++++++++++++------ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- man/InitClust.Rd | 8 ++++---- man/otrimle.Rd | 8 ++++---- man/plot.otrimle.Rd | 13 +++++++------ man/plot.rimle.Rd | 8 ++++---- man/rimle.Rd | 9 +++++---- 8 files changed, 50 insertions(+), 39 deletions(-)
Title: Accurate Timing Functions
Description: Provides infrastructure to accurately measure and compare
the execution time of R expressions.
Author: Olaf Mersmann [aut],
Claudia Beleites [ctb],
Rainer Hurling [ctb],
Ari Friedman [ctb],
Joshua M. Ulrich [cre]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between microbenchmark versions 1.4-6 dated 2018-10-18 and 1.4-7 dated 2019-09-24
microbenchmark-1.4-6/microbenchmark/inst/tests |only microbenchmark-1.4-6/microbenchmark/tests/runtests.R |only microbenchmark-1.4-7/microbenchmark/DESCRIPTION | 8 +- microbenchmark-1.4-7/microbenchmark/MD5 | 22 ++++---- microbenchmark-1.4-7/microbenchmark/R/autoplot.R | 1 microbenchmark-1.4-7/microbenchmark/R/boxplot.R | 3 - microbenchmark-1.4-7/microbenchmark/R/microbenchmark.R | 27 +++++++--- microbenchmark-1.4-7/microbenchmark/R/microtiming_precision.R | 1 microbenchmark-1.4-7/microbenchmark/R/nanotime.R | 2 microbenchmark-1.4-7/microbenchmark/R/print.R | 1 microbenchmark-1.4-7/microbenchmark/R/summary.R | 2 microbenchmark-1.4-7/microbenchmark/inst/unitTests |only microbenchmark-1.4-7/microbenchmark/man/microbenchmark.Rd | 14 ++++- microbenchmark-1.4-7/microbenchmark/tests/doRUnit.R |only 14 files changed, 49 insertions(+), 32 deletions(-)
More information about microbenchmark at CRAN
Permanent link
Title: Data-Limited Methods Toolkit
Description: Development, simulation testing, and implementation of management
procedures for data-limited fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Tom Carruthers [aut, cre],
Adrian Hordyk [aut],
M. Bryan [ctb],
HF. Geremont [ctb],
C. Grandin [ctb],
W. Harford [ctb],
Q. Huynh [ctb],
C. Walters [ctb]
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 5.3.1 dated 2019-04-29 and 5.4.0 dated 2019-09-24
DLMtool-5.3.1/DLMtool/data/Generic_Fleet.RData |only DLMtool-5.3.1/DLMtool/data/Generic_Obs.RData |only DLMtool-5.3.1/DLMtool/man/DOM.Rd |only DLMtool-5.4.0/DLMtool/DESCRIPTION | 18 DLMtool-5.4.0/DLMtool/MD5 | 381 +- DLMtool-5.4.0/DLMtool/NAMESPACE | 11 DLMtool-5.4.0/DLMtool/NEWS.md | 24 DLMtool-5.4.0/DLMtool/R/Blow_funcs.R | 18 DLMtool-5.4.0/DLMtool/R/Data2csv.R | 141 DLMtool-5.4.0/DLMtool/R/Data_Functions.R | 1776 +++++++++- DLMtool-5.4.0/DLMtool/R/Data_make_update.R | 128 DLMtool-5.4.0/DLMtool/R/DefineClasses.r | 617 ++- DLMtool-5.4.0/DLMtool/R/Fease_Functions.R | 5 DLMtool-5.4.0/DLMtool/R/MPs_Input.R | 17 DLMtool-5.4.0/DLMtool/R/MPs_Output.R | 163 DLMtool-5.4.0/DLMtool/R/MPs_Reference.R | 1 DLMtool-5.4.0/DLMtool/R/MSE_Plotting.R | 61 DLMtool-5.4.0/DLMtool/R/MSE_Plotting_PMs.R | 14 DLMtool-5.4.0/DLMtool/R/MSE_functions.R | 312 + DLMtool-5.4.0/DLMtool/R/MSYplotDev.R |only DLMtool-5.4.0/DLMtool/R/Misc_Exported.R | 102 DLMtool-5.4.0/DLMtool/R/Misc_Internal.R | 262 - DLMtool-5.4.0/DLMtool/R/OM_Plotting.R | 622 ++- DLMtool-5.4.0/DLMtool/R/OM_functions.R | 14 DLMtool-5.4.0/DLMtool/R/OM_init_doc.R | 127 DLMtool-5.4.0/DLMtool/R/OMts_dev.R |only DLMtool-5.4.0/DLMtool/R/PMobjects.R | 33 DLMtool-5.4.0/DLMtool/R/RcppExports.R | 9 DLMtool-5.4.0/DLMtool/R/SampleOM.R | 86 DLMtool-5.4.0/DLMtool/R/Turing.R | 19 DLMtool-5.4.0/DLMtool/R/aaImportFrom.R | 2 DLMtool-5.4.0/DLMtool/R/popdyn.R | 237 - DLMtool-5.4.0/DLMtool/R/popdynDEVELOP.R |only DLMtool-5.4.0/DLMtool/R/runMSE.r | 505 +- DLMtool-5.4.0/DLMtool/R/sysdata.rda |binary DLMtool-5.4.0/DLMtool/data/Albacore.RData |binary DLMtool-5.4.0/DLMtool/data/Atlantic_mackerel.RData |binary DLMtool-5.4.0/DLMtool/data/Blue_shark.RData |binary DLMtool-5.4.0/DLMtool/data/Bluefin_tuna.RData |binary DLMtool-5.4.0/DLMtool/data/Bluefin_tuna_WAtl.RData |binary DLMtool-5.4.0/DLMtool/data/Butterfish.RData |binary DLMtool-5.4.0/DLMtool/data/China_rockfish.RData |binary DLMtool-5.4.0/DLMtool/data/Cobia.RData |binary DLMtool-5.4.0/DLMtool/data/DataDescription.RData |binary DLMtool-5.4.0/DLMtool/data/DecE_Dom.RData |binary DLMtool-5.4.0/DLMtool/data/DecE_HDom.RData |binary DLMtool-5.4.0/DLMtool/data/DecE_NDom.RData |binary DLMtool-5.4.0/DLMtool/data/Example_datafile.RData |binary DLMtool-5.4.0/DLMtool/data/FlatE_Dom.RData |binary DLMtool-5.4.0/DLMtool/data/FlatE_HDom.RData |binary DLMtool-5.4.0/DLMtool/data/FlatE_NDom.RData |binary DLMtool-5.4.0/DLMtool/data/FleetDescription.RData |binary DLMtool-5.4.0/DLMtool/data/Generic_DecE.RData |binary DLMtool-5.4.0/DLMtool/data/Generic_FlatE.RData |binary DLMtool-5.4.0/DLMtool/data/Generic_IncE.RData |binary DLMtool-5.4.0/DLMtool/data/Generic_fleet.RData |only DLMtool-5.4.0/DLMtool/data/Generic_obs.RData |only DLMtool-5.4.0/DLMtool/data/Gulf_blue_tilefish.RData |binary DLMtool-5.4.0/DLMtool/data/Herring.RData |binary DLMtool-5.4.0/DLMtool/data/ImpDescription.RData |binary DLMtool-5.4.0/DLMtool/data/Imprecise_Biased.RData |binary DLMtool-5.4.0/DLMtool/data/Imprecise_Unbiased.RData |binary DLMtool-5.4.0/DLMtool/data/IncE_HDom.RData |binary DLMtool-5.4.0/DLMtool/data/IncE_NDom.RData |binary DLMtool-5.4.0/DLMtool/data/LHdatabase.RData |binary DLMtool-5.4.0/DLMtool/data/Low_Effort_Non_Target.RData |binary DLMtool-5.4.0/DLMtool/data/MSEDescription.RData |binary DLMtool-5.4.0/DLMtool/data/Mackerel.RData |binary DLMtool-5.4.0/DLMtool/data/OMDescription.RData |binary DLMtool-5.4.0/DLMtool/data/ObsDescription.RData |binary DLMtool-5.4.0/DLMtool/data/Overages.RData |binary DLMtool-5.4.0/DLMtool/data/Perfect_Imp.RData |binary DLMtool-5.4.0/DLMtool/data/Perfect_Info.RData |binary DLMtool-5.4.0/DLMtool/data/Porgy.RData |binary DLMtool-5.4.0/DLMtool/data/Precise_Biased.RData |binary DLMtool-5.4.0/DLMtool/data/Precise_Unbiased.RData |binary DLMtool-5.4.0/DLMtool/data/Red_snapper.RData |binary DLMtool-5.4.0/DLMtool/data/ReqData.RData |binary DLMtool-5.4.0/DLMtool/data/Rockfish.RData |binary DLMtool-5.4.0/DLMtool/data/SimulatedData.RData |binary DLMtool-5.4.0/DLMtool/data/Simulation_1.RData |binary DLMtool-5.4.0/DLMtool/data/Snapper.RData |binary DLMtool-5.4.0/DLMtool/data/Sole.RData |binary DLMtool-5.4.0/DLMtool/data/StockDescription.RData |binary DLMtool-5.4.0/DLMtool/data/Target_All_Fish.RData |binary DLMtool-5.4.0/DLMtool/data/Targeting_Small_Fish.RData |binary DLMtool-5.4.0/DLMtool/data/Toothfish.RData |binary DLMtool-5.4.0/DLMtool/data/datalist | 4 DLMtool-5.4.0/DLMtool/data/ourReefFish.RData |binary DLMtool-5.4.0/DLMtool/data/testOM.RData |binary DLMtool-5.4.0/DLMtool/data/tiny.RData |binary DLMtool-5.4.0/DLMtool/inst/Cobia.csv | 54 DLMtool-5.4.0/DLMtool/inst/Data.csv | 166 DLMtool-5.4.0/DLMtool/inst/Data.xlsx |binary DLMtool-5.4.0/DLMtool/inst/Data_Example.csv |only DLMtool-5.4.0/DLMtool/inst/Data_Example.md |only DLMtool-5.4.0/DLMtool/inst/Data_Example.xlsx |only DLMtool-5.4.0/DLMtool/inst/PLimitTable.Rmd | 5 DLMtool-5.4.0/DLMtool/inst/PObjTable.Rmd | 5 DLMtool-5.4.0/DLMtool/inst/Rmd |only DLMtool-5.4.0/DLMtool/inst/Simulation_1.csv | 2 DLMtool-5.4.0/DLMtool/inst/ourReefFish.csv | 6 DLMtool-5.4.0/DLMtool/man/AvC.Rd | 4 DLMtool-5.4.0/DLMtool/man/AvC_MLL.Rd | 4 DLMtool-5.4.0/DLMtool/man/BK.Rd | 4 DLMtool-5.4.0/DLMtool/man/Blow_opt.Rd | 4 DLMtool-5.4.0/DLMtool/man/CC1.Rd | 11 DLMtool-5.4.0/DLMtool/man/CalcMPDynamics.Rd | 17 DLMtool-5.4.0/DLMtool/man/CompSRA.Rd | 4 DLMtool-5.4.0/DLMtool/man/DBSRA.Rd | 4 DLMtool-5.4.0/DLMtool/man/DCAC.Rd | 4 DLMtool-5.4.0/DLMtool/man/DD.Rd | 4 DLMtool-5.4.0/DLMtool/man/DDe.Rd | 4 DLMtool-5.4.0/DLMtool/man/DTe40.Rd | 4 DLMtool-5.4.0/DLMtool/man/Data-class.Rd | 172 DLMtool-5.4.0/DLMtool/man/DataDescription.Rd | 2 DLMtool-5.4.0/DLMtool/man/DataInit.Rd | 17 DLMtool-5.4.0/DLMtool/man/Dom.Rd |only DLMtool-5.4.0/DLMtool/man/DynF.Rd | 4 DLMtool-5.4.0/DLMtool/man/EtargetLopt.Rd | 4 DLMtool-5.4.0/DLMtool/man/FMSYref.Rd | 4 DLMtool-5.4.0/DLMtool/man/Fadapt.Rd | 4 DLMtool-5.4.0/DLMtool/man/Fdem.Rd | 4 DLMtool-5.4.0/DLMtool/man/Fratio.Rd | 4 DLMtool-5.4.0/DLMtool/man/GB_CC.Rd | 4 DLMtool-5.4.0/DLMtool/man/GB_slope.Rd | 4 DLMtool-5.4.0/DLMtool/man/GB_target.Rd | 4 DLMtool-5.4.0/DLMtool/man/Gcontrol.Rd | 4 DLMtool-5.4.0/DLMtool/man/ICI.Rd | 4 DLMtool-5.4.0/DLMtool/man/IT5.Rd | 4 DLMtool-5.4.0/DLMtool/man/ITM.Rd | 4 DLMtool-5.4.0/DLMtool/man/ITe5.Rd | 4 DLMtool-5.4.0/DLMtool/man/Iratio.Rd | 4 DLMtool-5.4.0/DLMtool/man/Islope1.Rd | 4 DLMtool-5.4.0/DLMtool/man/Itarget1.Rd | 4 DLMtool-5.4.0/DLMtool/man/Itarget1_MPA.Rd | 4 DLMtool-5.4.0/DLMtool/man/ItargetE1.Rd | 4 DLMtool-5.4.0/DLMtool/man/LBSPR.Rd | 8 DLMtool-5.4.0/DLMtool/man/Lratio_BHI.Rd | 4 DLMtool-5.4.0/DLMtool/man/LstepCC1.Rd | 4 DLMtool-5.4.0/DLMtool/man/LstepCE1.Rd | 4 DLMtool-5.4.0/DLMtool/man/Ltarget1.Rd | 4 DLMtool-5.4.0/DLMtool/man/LtargetE1.Rd | 4 DLMtool-5.4.0/DLMtool/man/MCD.Rd | 4 DLMtool-5.4.0/DLMtool/man/MRreal.Rd | 4 DLMtool-5.4.0/DLMtool/man/MSEDescription.Rd | 2 DLMtool-5.4.0/DLMtool/man/MSYCalcs.Rd | 4 DLMtool-5.4.0/DLMtool/man/OM-class.Rd | 4 DLMtool-5.4.0/DLMtool/man/OMexample.Rd | 4 DLMtool-5.4.0/DLMtool/man/Obs-class.Rd | 4 DLMtool-5.4.0/DLMtool/man/PerformanceMetric.Rd | 7 DLMtool-5.4.0/DLMtool/man/Pplot2.Rd | 12 DLMtool-5.4.0/DLMtool/man/Rcontrol.Rd | 4 DLMtool-5.4.0/DLMtool/man/Replace.Rd | 2 DLMtool-5.4.0/DLMtool/man/Report.Rd |only DLMtool-5.4.0/DLMtool/man/ReqData.Rd | 2 DLMtool-5.4.0/DLMtool/man/Required.Rd | 3 DLMtool-5.4.0/DLMtool/man/SBT1.Rd | 4 DLMtool-5.4.0/DLMtool/man/SPMSY.Rd | 4 DLMtool-5.4.0/DLMtool/man/SPSRA.Rd | 4 DLMtool-5.4.0/DLMtool/man/SPmod.Rd | 4 DLMtool-5.4.0/DLMtool/man/SPslope.Rd | 4 DLMtool-5.4.0/DLMtool/man/SampleImpPars.Rd | 2 DLMtool-5.4.0/DLMtool/man/TradePlot.Rd | 8 DLMtool-5.4.0/DLMtool/man/XL2Data.Rd | 8 DLMtool-5.4.0/DLMtool/man/YPR.Rd | 4 DLMtool-5.4.0/DLMtool/man/curE.Rd | 4 DLMtool-5.4.0/DLMtool/man/getBlow.Rd | 5 DLMtool-5.4.0/DLMtool/man/getFref3.Rd | 8 DLMtool-5.4.0/DLMtool/man/getq3.Rd | 4 DLMtool-5.4.0/DLMtool/man/join_plots.Rd | 4 DLMtool-5.4.0/DLMtool/man/matlenlim.Rd | 4 DLMtool-5.4.0/DLMtool/man/optMSY.Rd | 6 DLMtool-5.4.0/DLMtool/man/optMSY_eq.Rd | 4 DLMtool-5.4.0/DLMtool/man/optQ.Rd | 4 DLMtool-5.4.0/DLMtool/man/plot-OM.Rd | 6 DLMtool-5.4.0/DLMtool/man/plot.Stock.Rd |only DLMtool-5.4.0/DLMtool/man/plotM.Rd | 2 DLMtool-5.4.0/DLMtool/man/plotMPA.Rd | 2 DLMtool-5.4.0/DLMtool/man/popdynCPP.Rd | 4 DLMtool-5.4.0/DLMtool/man/popdynOneTScpp.Rd | 2 DLMtool-5.4.0/DLMtool/man/runMSE.Rd | 11 DLMtool-5.4.0/DLMtool/src/RcppExports.cpp | 18 DLMtool-5.4.0/DLMtool/src/popddynCPP.cpp | 42 DLMtool-5.4.0/DLMtool/tests/manual/test-code/test-Data2csv.R | 8 DLMtool-5.4.0/DLMtool/tests/manual/test-code/test-Import_Data.R | 8 DLMtool-5.4.0/DLMtool/tests/manual/test-code/test-MSE_Plotting.R | 1 DLMtool-5.4.0/DLMtool/tests/manual/test-code/test-MSE_functions.R | 6 DLMtool-5.4.0/DLMtool/tests/manual/test-code/test-OM_Plotting.R | 20 DLMtool-5.4.0/DLMtool/tests/manual/test-code/test-RealIndices.R | 224 - DLMtool-5.4.0/DLMtool/tests/manual/test-code/test-slotDescription.R | 2 191 files changed, 4812 insertions(+), 1995 deletions(-)
Title: Statistically Validated Networks
Description: Determines networks of significant synchronization between the discrete states of nodes; see Tumminello et al <doi:10.1371/journal.pone.0017994>.
Author: Damien Challet
Maintainer: Damien Challet <damien.challet@gmail.com>
Diff between SVN versions 1.0 dated 2019-04-10 and 1.0.1 dated 2019-09-24
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- man/SVN-package.Rd | 3 ++- 3 files changed, 10 insertions(+), 9 deletions(-)
Title: Identify Sudden Gains in Longitudinal Data
Description: Identify sudden gains based on the three criteria outlined by Tang and DeRubeis (1999) <doi:10.1037/0022-006X.67.6.894> to a selection of repeated measures. Sudden losses, defined as the opposite of sudden gains can also be identified. Two different datasets can be created, one including all sudden gains/losses and one including one selected sudden gain/loss for each case. It can extract scores around sudden gains/losses. It can plot the average change around sudden gains/losses and trajectories of individual cases.
Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>),
Graham M Thew [ctb] (<https://orcid.org/0000-0003-2851-1315>),
Richard Stott [ctb] (<https://orcid.org/0000-0003-2533-5504>),
Anke Ehlers [ctb, ths] (<https://orcid.org/0000-0002-8742-0192>)
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>
Diff between suddengains versions 0.3.0 dated 2019-08-20 and 0.3.1 dated 2019-09-24
DESCRIPTION | 8 MD5 | 12 NEWS.md | 5 R/create_bysg.R | 2 R/define_crit1_cutoff.R | 3 R/extract_values.R | 15 - inst/doc/suddengains-tutorial.html | 466 +++++++++++++++++++------------------ 7 files changed, 266 insertions(+), 245 deletions(-)
Title: View 3D Raster Cubes Interactively
Description: Creates a 3D data cube view of a RasterStack/Brick, typically a
collection/array of RasterLayers (along z-axis) with the same geographical
extent (x and y dimensions) and resolution, provided by package 'raster'.
Slices through each dimension (x/y/z), freely adjustable in location,
are mapped to the visible sides of the cube. The cube can be freely rotated.
Zooming and panning can be used to focus on different areas of the cube.
Author: Tim Appelhans [cre, aut],
Stefan Woellauer [aut],
three.js authors [ctb, cph] (three.js library)
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between cubeview versions 0.1.0 dated 2019-03-15 and 0.2.0 dated 2019-09-24
cubeview-0.1.0/cubeview/man/cubeView.Rd |only cubeview-0.2.0/cubeview/DESCRIPTION | 22 cubeview-0.2.0/cubeview/LICENSE | 4 cubeview-0.2.0/cubeview/MD5 | 40 cubeview-0.2.0/cubeview/NAMESPACE | 51 cubeview-0.2.0/cubeview/NEWS | 10 cubeview-0.2.0/cubeview/NEWS.md | 10 cubeview-0.2.0/cubeview/R/color.R | 37 cubeview-0.2.0/cubeview/R/cubeView.R | 713 ++- cubeview-0.2.0/cubeview/R/legend.R | 8 cubeview-0.2.0/cubeview/README.md | 5 cubeview-0.2.0/cubeview/inst/htmlwidgets/cubeView.js | 53 cubeview-0.2.0/cubeview/inst/htmlwidgets/cubeView.yaml | 16 cubeview-0.2.0/cubeview/inst/htmlwidgets/lib/OrbitControls-r108 |only cubeview-0.2.0/cubeview/inst/htmlwidgets/lib/TrackballControls-r74/LICENSE | 42 cubeview-0.2.0/cubeview/inst/htmlwidgets/lib/TrackballControls-r74/TrackballControls.min.js | 2 cubeview-0.2.0/cubeview/inst/htmlwidgets/lib/cubeView_style/cubeView.css | 42 cubeview-0.2.0/cubeview/inst/htmlwidgets/lib/three.js-r108 |only cubeview-0.2.0/cubeview/inst/htmlwidgets/lib/three.js-r74/LICENSE | 42 cubeview-0.2.0/cubeview/inst/htmlwidgets/lib/three.js-r74/three.min.js | 1916 +++++----- cubeview-0.2.0/cubeview/man/cubeViewOutput.Rd | 100 cubeview-0.2.0/cubeview/man/cubeview.Rd |only 22 files changed, 1630 insertions(+), 1483 deletions(-)
Title: Model Audit - Verification, Validation, and Error Analysis
Description: Provides an easy to use unified interface for creating validation plots for any model.
The 'auditor' helps to avoid repetitive work consisting of writing code needed to create residual plots.
This visualizations allow to asses and compare the goodness of fit, performance, and similarity of models.
Author: Alicja Gosiewska [aut, cre] (<https://orcid.org/0000-0001-6563-5742>),
Przemyslaw Biecek [aut, ths] (<https://orcid.org/0000-0001-8423-1823>),
Hubert Baniecki [aut],
Tomasz Mikołajczyk [aut],
Michal Burdukiewicz [ctb],
Szymon Maksymiuk [ctb]
Maintainer: Alicja Gosiewska <alicjagosiewska@gmail.com>
Diff between auditor versions 1.0.0 dated 2019-08-31 and 1.1.0 dated 2019-09-24
auditor-1.0.0/auditor/man/check_object.Rd |only auditor-1.0.0/auditor/man/drwhy_geom_point.Rd |only auditor-1.0.0/auditor/man/drwhy_geom_smooth.Rd |only auditor-1.0.0/auditor/man/make_dataframe.Rd |only auditor-1.0.0/auditor/man/prepare_object.Rd |only auditor-1.0.0/auditor/man/theme_drwhy.Rd |only auditor-1.1.0/auditor/DESCRIPTION | 12 auditor-1.1.0/auditor/MD5 | 103 +-- auditor-1.1.0/auditor/NAMESPACE | 14 auditor-1.1.0/auditor/NEWS.md | 6 auditor-1.1.0/auditor/R/plot_prediction.R | 6 auditor-1.1.0/auditor/R/plot_radar.R | 28 auditor-1.1.0/auditor/R/plot_residual_density.R | 32 - auditor-1.1.0/auditor/R/plot_support_function.R | 20 auditor-1.1.0/auditor/R/print.R | 27 auditor-1.1.0/auditor/R/score.R | 24 auditor-1.1.0/auditor/R/score_F1.R |only auditor-1.1.0/auditor/R/score_acc.R |only auditor-1.1.0/auditor/R/score_auc.R | 40 + auditor-1.1.0/auditor/R/score_mae.R | 2 auditor-1.1.0/auditor/R/score_mse.R | 4 auditor-1.1.0/auditor/R/score_precision.R |only auditor-1.1.0/auditor/R/score_rec.R | 2 auditor-1.1.0/auditor/R/score_recall.R |only auditor-1.1.0/auditor/R/score_rroc.R | 2 auditor-1.1.0/auditor/R/score_specificity.R |only auditor-1.1.0/auditor/R/scores_support_functions.R |only auditor-1.1.0/auditor/R/theme_drwhy.R | 29 auditor-1.1.0/auditor/build/vignette.rds |binary auditor-1.1.0/auditor/inst/doc/model_evaluation_audit.R | 6 auditor-1.1.0/auditor/inst/doc/model_evaluation_audit.Rmd | 53 - auditor-1.1.0/auditor/inst/doc/model_evaluation_audit.html | 72 -- auditor-1.1.0/auditor/inst/doc/model_fit_audit.R | 26 auditor-1.1.0/auditor/inst/doc/model_fit_audit.Rmd | 95 +-- auditor-1.1.0/auditor/inst/doc/model_fit_audit.html | 104 +-- auditor-1.1.0/auditor/inst/doc/model_performance_audit.R | 13 auditor-1.1.0/auditor/inst/doc/model_performance_audit.Rmd | 67 -- auditor-1.1.0/auditor/inst/doc/model_performance_audit.html | 117 +-- auditor-1.1.0/auditor/inst/doc/model_residuals_audit.R | 91 +- auditor-1.1.0/auditor/inst/doc/model_residuals_audit.Rmd | 274 ++++---- auditor-1.1.0/auditor/inst/doc/model_residuals_audit.html | 307 ++++------ auditor-1.1.0/auditor/inst/doc/observation_influence_audit.R | 10 auditor-1.1.0/auditor/inst/doc/observation_influence_audit.Rmd | 75 -- auditor-1.1.0/auditor/inst/doc/observation_influence_audit.html | 90 -- auditor-1.1.0/auditor/man/figures |only auditor-1.1.0/auditor/man/plot_prediction.Rd | 4 auditor-1.1.0/auditor/man/plot_radar.Rd | 11 auditor-1.1.0/auditor/man/print.auditor_score.Rd |only auditor-1.1.0/auditor/man/score.Rd | 8 auditor-1.1.0/auditor/man/score_acc.Rd |only auditor-1.1.0/auditor/man/score_f1.Rd |only auditor-1.1.0/auditor/man/score_one_minus_acc.Rd |only auditor-1.1.0/auditor/man/score_one_minus_auc.Rd |only auditor-1.1.0/auditor/man/score_one_minus_f1.Rd |only auditor-1.1.0/auditor/man/score_one_minus_precision.Rd |only auditor-1.1.0/auditor/man/score_one_minus_recall.Rd |only auditor-1.1.0/auditor/man/score_one_minus_specificity.Rd |only auditor-1.1.0/auditor/man/score_precision.Rd |only auditor-1.1.0/auditor/man/score_recall.Rd |only auditor-1.1.0/auditor/man/score_specificity.Rd |only auditor-1.1.0/auditor/vignettes/model_evaluation_audit.Rmd | 53 - auditor-1.1.0/auditor/vignettes/model_fit_audit.Rmd | 95 +-- auditor-1.1.0/auditor/vignettes/model_performance_audit.Rmd | 67 -- auditor-1.1.0/auditor/vignettes/model_residuals_audit.Rmd | 274 ++++---- auditor-1.1.0/auditor/vignettes/observation_influence_audit.Rmd | 75 -- 65 files changed, 1074 insertions(+), 1264 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongphamthe@gmail.com>
Diff between PAFit versions 1.0.1.2 dated 2019-04-11 and 1.0.1.4 dated 2019-09-24
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/get_statistics.R | 2 ++ build/vignette.rds |binary inst/doc/Tutorial.pdf |binary man/PAFit-package.Rd | 10 +++++----- man/generate_BA.rd | 2 +- man/generate_BB.rd | 2 +- man/generate_net.Rd | 4 ++-- man/graph_from_file.rd | 5 +++-- man/graph_to_file.rd | 2 +- man/joint_estimate.rd | 2 +- man/only_A_estimate.rd | 4 ++-- man/only_F_estimate.rd | 2 +- tests/test_graph_from_file.R | 16 ++++++++-------- tests/test_graph_to_file.R | 6 +++--- 16 files changed, 49 insertions(+), 46 deletions(-)
Title: Multi-SNP Mediation Intersection-Union Test
Description: Testing the mediation effect of multiple SNPs on an outcome through a mediator.
Author: Wujuan Zhong
Maintainer: Wujuan Zhong <zhongwujuan@gmail.com>
Diff between SMUT versions 1.0.1 dated 2019-04-08 and 1.1 dated 2019-09-24
DESCRIPTION | 6 +++--- MD5 | 14 +++++++++----- NAMESPACE | 2 +- R/GSMUT.R |only R/Generalized_Testing_coefficient_of_mediator.R |only man/GSMUT.Rd |only man/Generalized_Testing_coefficient_of_mediator.Rd |only man/SMUT.Rd | 4 ++++ man/Testing_coefficient_of_mediator.Rd | 2 +- man/eigenMapMatMult.Rd | 2 +- 10 files changed, 19 insertions(+), 11 deletions(-)
Title: Bayesian 4 Parameter Item Response Model
Description: Estimate Barton & Lord's (1981) <doi:10.1002/j.2333-8504.1981.tb01255.x>
four parameter IRT model with lower and upper asymptotes using Bayesian
formulation described by Culpepper (2016) <doi:10.1007/s11336-015-9477-6>.
Author: Steven Andrew Culpepper [aut, cre, cph]
(<https://orcid.org/0000-0003-4226-6176>)
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between fourPNO versions 1.0.5 dated 2019-01-22 and 1.1.0 dated 2019-09-24
fourPNO-1.0.5/fourPNO/R/fourPNO-internal.R |only fourPNO-1.1.0/fourPNO/DESCRIPTION | 18 - fourPNO-1.1.0/fourPNO/MD5 | 18 - fourPNO-1.1.0/fourPNO/NAMESPACE | 4 fourPNO-1.1.0/fourPNO/NEWS.md | 10 fourPNO-1.1.0/fourPNO/R/RcppExports.R | 302 +++++++++++++-------------- fourPNO-1.1.0/fourPNO/R/fourPNO-package.R |only fourPNO-1.1.0/fourPNO/man/Gibbs_2PNO.Rd | 25 +- fourPNO-1.1.0/fourPNO/man/Gibbs_4PNO.Rd | 13 - fourPNO-1.1.0/fourPNO/man/fourPNO-package.Rd | 3 fourPNO-1.1.0/fourPNO/src/fourpno_101315.cpp | 89 +++---- 11 files changed, 247 insertions(+), 235 deletions(-)