Title: Stratified Medicine
Description: A toolkit for stratified medicine, subgroup identification, and precision medicine.
Current tools include (1) filtering models (reduce covariate space), (2) patient-level estimate
models (counterfactual patient-level quantities, for example the individual treatment effect),
(3) subgroup identification models (find subsets of patients with similar treatment effects),
and (4) parameter estimation and inference (for the overall population and discovered subgroups).
These tools can directly feed into stratified medicine algorithms including PRISM
(patient response identifiers for stratified medicine; Jemielita and Mehrotra 2019 (in progress)).
PRISM is a flexible and general framework which accepts user-created models/functions. This
package is in beta and will be continually updated.
Author: Thomas Jemielita [aut, cre]
Maintainer: Thomas Jemielita <thomasjemielita@gmail.com>
Diff between StratifiedMedicine versions 0.1.3 dated 2019-09-04 and 0.2.0 dated 2019-10-13
StratifiedMedicine-0.1.3/StratifiedMedicine/man/predict.ple_bart.Rd |only StratifiedMedicine-0.1.3/StratifiedMedicine/man/predict.ple_causal_forest.Rd |only StratifiedMedicine-0.1.3/StratifiedMedicine/man/predict.ple_glmnet.Rd |only StratifiedMedicine-0.1.3/StratifiedMedicine/man/predict.ple_ranger.Rd |only StratifiedMedicine-0.1.3/StratifiedMedicine/man/predict.submod_ctree.Rd |only StratifiedMedicine-0.1.3/StratifiedMedicine/man/predict.submod_lmtree.Rd |only StratifiedMedicine-0.1.3/StratifiedMedicine/man/predict.submod_otr.Rd |only StratifiedMedicine-0.1.3/StratifiedMedicine/man/predict.submod_rpart.Rd |only StratifiedMedicine-0.1.3/StratifiedMedicine/man/predict.submod_weibull.Rd |only StratifiedMedicine-0.2.0/StratifiedMedicine/DESCRIPTION | 13 StratifiedMedicine-0.2.0/StratifiedMedicine/MD5 | 114 +- StratifiedMedicine-0.2.0/StratifiedMedicine/NAMESPACE | 12 StratifiedMedicine-0.2.0/StratifiedMedicine/R/PRISM.R | 92 + StratifiedMedicine-0.2.0/StratifiedMedicine/R/PRISM_resamp.R | 277 ++--- StratifiedMedicine-0.2.0/StratifiedMedicine/R/PRISM_train.R | 61 - StratifiedMedicine-0.2.0/StratifiedMedicine/R/generate_subgrp_data.R | 16 StratifiedMedicine-0.2.0/StratifiedMedicine/R/model_template.R |only StratifiedMedicine-0.2.0/StratifiedMedicine/R/param_cox.R | 49 - StratifiedMedicine-0.2.0/StratifiedMedicine/R/param_rmst.R | 58 - StratifiedMedicine-0.2.0/StratifiedMedicine/R/ple_bart.R | 101 -- StratifiedMedicine-0.2.0/StratifiedMedicine/R/ple_causal_forest.R | 107 -- StratifiedMedicine-0.2.0/StratifiedMedicine/R/ple_glmnet.R | 89 - StratifiedMedicine-0.2.0/StratifiedMedicine/R/ple_ranger.R | 198 +--- StratifiedMedicine-0.2.0/StratifiedMedicine/R/ple_train.R | 12 StratifiedMedicine-0.2.0/StratifiedMedicine/R/plot.R | 182 +++ StratifiedMedicine-0.2.0/StratifiedMedicine/R/submod_ctree.R | 71 - StratifiedMedicine-0.2.0/StratifiedMedicine/R/submod_lmtree.R | 74 - StratifiedMedicine-0.2.0/StratifiedMedicine/R/submod_otr.R | 74 - StratifiedMedicine-0.2.0/StratifiedMedicine/R/submod_rpart.R | 70 - StratifiedMedicine-0.2.0/StratifiedMedicine/R/submod_train.R | 13 StratifiedMedicine-0.2.0/StratifiedMedicine/R/submod_weibull.R | 94 - StratifiedMedicine-0.2.0/StratifiedMedicine/R/utils.R | 271 +++++ StratifiedMedicine-0.2.0/StratifiedMedicine/README.md | 61 - StratifiedMedicine-0.2.0/StratifiedMedicine/build/vignette.rds |binary StratifiedMedicine-0.2.0/StratifiedMedicine/inst/doc/SM_PRISM.R | 207 +--- StratifiedMedicine-0.2.0/StratifiedMedicine/inst/doc/SM_PRISM.Rmd | 269 +---- StratifiedMedicine-0.2.0/StratifiedMedicine/inst/doc/SM_PRISM.html | 471 ++++------ StratifiedMedicine-0.2.0/StratifiedMedicine/inst/doc/SM_User_Models.R |only StratifiedMedicine-0.2.0/StratifiedMedicine/inst/doc/SM_User_Models.Rmd |only StratifiedMedicine-0.2.0/StratifiedMedicine/inst/doc/SM_User_Models.html |only StratifiedMedicine-0.2.0/StratifiedMedicine/man/PRISM.Rd | 42 StratifiedMedicine-0.2.0/StratifiedMedicine/man/PRISM_resamp.Rd | 16 StratifiedMedicine-0.2.0/StratifiedMedicine/man/figures/README-example-1.png |binary StratifiedMedicine-0.2.0/StratifiedMedicine/man/figures/README-example-2.png |binary StratifiedMedicine-0.2.0/StratifiedMedicine/man/figures/README-example-3.png |binary StratifiedMedicine-0.2.0/StratifiedMedicine/man/figures/README-example-4.png |binary StratifiedMedicine-0.2.0/StratifiedMedicine/man/figures/README-example-5.png |binary StratifiedMedicine-0.2.0/StratifiedMedicine/man/figures/README-example-6.png |binary StratifiedMedicine-0.2.0/StratifiedMedicine/man/generate_subgrp_data.Rd | 6 StratifiedMedicine-0.2.0/StratifiedMedicine/man/model_template.Rd |only StratifiedMedicine-0.2.0/StratifiedMedicine/man/param_cox.Rd | 6 StratifiedMedicine-0.2.0/StratifiedMedicine/man/ple_bart.Rd | 2 StratifiedMedicine-0.2.0/StratifiedMedicine/man/ple_causal_forest.Rd | 2 StratifiedMedicine-0.2.0/StratifiedMedicine/man/ple_glmnet.Rd | 3 StratifiedMedicine-0.2.0/StratifiedMedicine/man/ple_ranger.Rd | 2 StratifiedMedicine-0.2.0/StratifiedMedicine/man/ple_train.Rd | 2 StratifiedMedicine-0.2.0/StratifiedMedicine/man/plot.PRISM.Rd | 13 StratifiedMedicine-0.2.0/StratifiedMedicine/man/predict.PRISM.Rd | 6 StratifiedMedicine-0.2.0/StratifiedMedicine/man/predict.ple_train.Rd | 4 StratifiedMedicine-0.2.0/StratifiedMedicine/man/predict.submod_train.Rd | 1 StratifiedMedicine-0.2.0/StratifiedMedicine/man/submod_train.Rd | 2 StratifiedMedicine-0.2.0/StratifiedMedicine/tests |only StratifiedMedicine-0.2.0/StratifiedMedicine/vignettes/SM_PRISM.Rmd | 269 +---- StratifiedMedicine-0.2.0/StratifiedMedicine/vignettes/SM_User_Models.Rmd |only 64 files changed, 1540 insertions(+), 1892 deletions(-)
More information about StratifiedMedicine at CRAN
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Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with triangle splines without additivity assumptions. See Liao X, Meyer MC (2019)<doi: 10.18637/jss.v089.i05> for more details.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <liaoxiyue2011@gmail.com>
Diff between cgam versions 1.14 dated 2019-05-01 and 1.15 dated 2019-10-13
ChangeLog | 5 DESCRIPTION | 10 MD5 | 12 NAMESPACE | 9 R/cgam.R | 4157 ++++++++++++++++++++++++++++++++++++++---------------- R/cgamm.R | 870 +++++++++++ data/COforest.rda |only man/COforest.Rd |only 8 files changed, 3844 insertions(+), 1219 deletions(-)
Title: Continuous Time Distance-Based and Network-Based Individual
Level Models for Epidemics
Description: Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks.
Author: Waleed Almutiry [aut, cre],
Rob Deardon [aut, ths],
Vineetha Warriyar K. V. [ctb]
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>
Diff between EpiILMCT versions 1.1.3 dated 2019-04-17 and 1.1.4 dated 2019-10-13
EpiILMCT-1.1.3/EpiILMCT/src/mcmcsinr.f95 |only EpiILMCT-1.1.3/EpiILMCT/src/mcmcsir.f95 |only EpiILMCT-1.1.3/EpiILMCT/tests/testthat |only EpiILMCT-1.1.3/EpiILMCT/tests/testthat.R |only EpiILMCT-1.1.4/EpiILMCT/DESCRIPTION | 23 EpiILMCT-1.1.4/EpiILMCT/MD5 | 72 EpiILMCT-1.1.4/EpiILMCT/NAMESPACE | 4 EpiILMCT-1.1.4/EpiILMCT/R/datgen.r | 15 EpiILMCT-1.1.4/EpiILMCT/R/epictmcmc.r | 2731 +++------------------ EpiILMCT-1.1.4/EpiILMCT/R/epictmcmcsinr.r |only EpiILMCT-1.1.4/EpiILMCT/R/epictmcmcsir.r |only EpiILMCT-1.1.4/EpiILMCT/R/epiplot.r | 290 +- EpiILMCT-1.1.4/EpiILMCT/R/loglikelihoodepiILM.r | 4 EpiILMCT-1.1.4/EpiILMCT/R/netdis.r | 2 EpiILMCT-1.1.4/EpiILMCT/data/NetworkData.RData |binary EpiILMCT-1.1.4/EpiILMCT/man/NetworkData.Rd | 3 EpiILMCT-1.1.4/EpiILMCT/man/NetworkDataSINR.Rd | 17 EpiILMCT-1.1.4/EpiILMCT/man/SpatialData.Rd | 5 EpiILMCT-1.1.4/EpiILMCT/man/SpatialNetData.Rd | 5 EpiILMCT-1.1.4/EpiILMCT/man/as.datagen.Rd | 8 EpiILMCT-1.1.4/EpiILMCT/man/contactnet.Rd | 28 EpiILMCT-1.1.4/EpiILMCT/man/datagen.Rd | 30 EpiILMCT-1.1.4/EpiILMCT/man/epictmcmc.Rd | 70 EpiILMCT-1.1.4/EpiILMCT/man/plot.contactnet.Rd | 2 EpiILMCT-1.1.4/EpiILMCT/man/plot.datagen.Rd | 2 EpiILMCT-1.1.4/EpiILMCT/man/plot.epictmcmc.Rd | 7 EpiILMCT-1.1.4/EpiILMCT/man/print.epictmcmc.Rd | 2 EpiILMCT-1.1.4/EpiILMCT/man/tswv.Rd | 6 EpiILMCT-1.1.4/EpiILMCT/src/datsim.f95 | 8 EpiILMCT-1.1.4/EpiILMCT/src/datsimsinr.f95 | 12 EpiILMCT-1.1.4/EpiILMCT/src/freginf.c | 126 EpiILMCT-1.1.4/EpiILMCT/src/loglikeoisinr.f95 | 8 EpiILMCT-1.1.4/EpiILMCT/src/loglikepi.f95 | 8 EpiILMCT-1.1.4/EpiILMCT/src/mcmcsinr2.f95 | 38 EpiILMCT-1.1.4/EpiILMCT/src/mcmcsir2.f95 | 323 +- EpiILMCT-1.1.4/EpiILMCT/tests/as.datagen.R |only EpiILMCT-1.1.4/EpiILMCT/tests/as.datagen.Rout.save |only EpiILMCT-1.1.4/EpiILMCT/tests/contactnet.R |only EpiILMCT-1.1.4/EpiILMCT/tests/contactnet.Rout.save |only EpiILMCT-1.1.4/EpiILMCT/tests/datagen.R |only EpiILMCT-1.1.4/EpiILMCT/tests/datagen.Rout.save |only EpiILMCT-1.1.4/EpiILMCT/tests/epictmcmc.R |only EpiILMCT-1.1.4/EpiILMCT/tests/epictmcmc.Rout.save |only 43 files changed, 1048 insertions(+), 2801 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 1.6.1 dated 2019-10-04 and 1.6.3 dated 2019-10-13
DESCRIPTION | 8 - MD5 | 67 +++++++------ NEWS.md | 9 + R/armRatioCI.R | 5 - R/asymmetry.R | 13 +- R/asymmetryA2.R | 6 + R/checkNameChrDfMarks.R | 12 +- R/fixChrNameDupDF.R |only R/plotIdiograms.R | 31 +++++- R/robert.R | 2 README.md | 2 data/bigdfChrSizeHolo.rda |binary data/bigdfOfChrSize.rda |binary inst/doc/AplotIdiogramsVig.R | 32 +++--- inst/doc/AplotIdiogramsVig.Rmd | 30 +++--- inst/doc/AplotIdiogramsVig.html | 180 ++++++++++++++++++++++++++++++------ inst/doc/BplotIdiogramsHoloVig.R | 33 ++++-- inst/doc/BplotIdiogramsHoloVig.Rmd | 36 ++++--- inst/doc/BplotIdiogramsHoloVig.html | 85 +++++++++-------- inst/doc/CgroupsVig.html | 8 + inst/doc/DphylogenyVig.R | 4 inst/doc/DphylogenyVig.Rmd | 11 +- inst/doc/DphylogenyVig.html | 10 +- inst/doc/EhumanVig.html | 6 + inst/doc/index.html | 12 +- man/armRatioCI.Rd | 7 + man/asymmetry.Rd | 16 ++- man/asymmetryA2.Rd | 9 + man/fixChrNameDupDF.Rd |only man/plotIdiograms.Rd | 2 man/robert.Rd | 2 vignettes/AplotIdiogramsVig.Rmd | 30 +++--- vignettes/BplotIdiogramsHoloVig.Rmd | 36 ++++--- vignettes/DphylogenyVig.Rmd | 11 +- vignettes/bigdfOfChrSize.png |only vignettes/mystyle.css | 8 + 36 files changed, 503 insertions(+), 220 deletions(-)
Title: Wrap R Tools for Debugging and Parametric Programming
Description: Tools for writing and debugging R code. Provides:
'%.>%' dot-pipe (an 'S3' configurable pipe),
'let()'
(converts non-standard evaluation interfaces to parametric standard
evaluation interfaces, inspired by 'gtools:strmacro()' and 'base::bquote()'),
'build_frame()'/'draw_frame()' ('data.frame' example tools),
'qc()' (quoting concatenate),
':=' (named map builder),
and more.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 1.9.1 dated 2019-10-06 and 1.9.2 dated 2019-10-13
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 4 ++++ R/cf.R | 7 ++++--- R/mapvars.R | 6 ++++-- inst/doc/CornerCases.html | 4 ++-- inst/doc/DebugFnW.html | 6 +++--- inst/doc/FrameTools.html | 4 ++-- inst/doc/Function_Objects.html | 4 ++-- inst/doc/Named_Arguments.html | 4 ++-- inst/doc/QuotingConcatinate.html | 4 ++-- inst/doc/SubstitutionModes.html | 4 ++-- inst/doc/bquote.html | 6 +++--- inst/doc/dot_pipe.html | 4 ++-- inst/doc/lambda.html | 4 ++-- inst/doc/let.html | 4 ++-- inst/doc/named_map_builder.html | 4 ++-- inst/doc/wrapr_applicable.html | 4 ++-- 18 files changed, 61 insertions(+), 54 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data, geostatistics, and spatial statistics. The major methods
include cubic, and thin plate splines, Kriging, and compactly supported
covariance functions for large data sets. The splines and Kriging methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by restricted maximum likelihood. For Kriging
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. There are also many useful functions for plotting
and working with spatial data as images. This package also contains
an implementation of sparse matrix methods for large spatial data
sets and currently requires the sparse matrix (spam) package. Use
help(fields) to get started and for an overview. The fields source
code is deliberately commented and provides useful explanations of
numerical details as a companion to the manual pages. The commented
source code can be viewed by expanding source code version
and looking in the R subdirectory. The reference for fields can be generated
by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development
of this package was supported in part by the National Science Foundation Grant
1417857 and the National Center for Atmospheric Research. See the Fields URL
for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut],
Florian Gerber [aut],
Matthew Iverson [aut],
University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 9.8-6 dated 2019-08-19 and 9.9 dated 2019-10-13
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 20 ++++++++++++-------- R/RdistEarth.R |only R/envelopePlot.R |only R/fields.mkpoly.R | 2 +- man/CO.Rd | 13 ++++--------- man/RCMexample.Rd | 2 +- man/RMprecip.Rd | 11 +++++------ man/envelopePlot.Rd |only man/rdist.earth.Rd | 18 ++++++++++++++---- src/RdistEarth.c |only tests/mKrig.MLE.test.R | 2 +- tests/mKrig.MLE.test.Rout.save | 24 +++--------------------- 13 files changed, 56 insertions(+), 60 deletions(-)
Title: Pattern-Based Zoneless Method for Analysis and Visualization of
Racial Topography
Description: Implements a computational framework for a pattern-based,
zoneless analysis, and visualization of (ethno)racial topography. It is a reimagined
approach for analyzing residential segregation and racial diversity based on
the concept of 'landscape’ used in the domain of landscape ecology.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Anna Dmowska [aut],
Tomasz Stepinski [aut]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between raceland versions 1.0.0 dated 2019-09-04 and 1.0.3 dated 2019-10-13
raceland-1.0.0/raceland/vignettes/raceland-intro.html |only raceland-1.0.3/raceland/DESCRIPTION | 10 - raceland-1.0.3/raceland/MD5 | 37 ++--- raceland-1.0.3/raceland/R/calculate_metrics.R | 11 + raceland-1.0.3/raceland/R/create_grid.R | 4 raceland-1.0.3/raceland/README.md | 26 ++- raceland-1.0.3/raceland/build/vignette.rds |binary raceland-1.0.3/raceland/inst/doc/raceland-intro1.R | 3 raceland-1.0.3/raceland/inst/doc/raceland-intro1.Rmd | 3 raceland-1.0.3/raceland/inst/doc/raceland-intro1.html | 67 +++++----- raceland-1.0.3/raceland/inst/doc/raceland-intro2.Rmd | 2 raceland-1.0.3/raceland/inst/doc/raceland-intro2.html | 60 ++++---- raceland-1.0.3/raceland/inst/doc/raceland-intro3.html | 10 + raceland-1.0.3/raceland/man/figures/README-unnamed-chunk-4-1.png |binary raceland-1.0.3/raceland/man/figures/README-unnamed-chunk-5-1.png |binary raceland-1.0.3/raceland/man/figures/README-unnamed-chunk-6-1.png |binary raceland-1.0.3/raceland/man/raceland-package.Rd | 8 + raceland-1.0.3/raceland/src/it_metrics.cpp | 2 raceland-1.0.3/raceland/vignettes/raceland-intro1.Rmd | 3 raceland-1.0.3/raceland/vignettes/raceland-intro2.Rmd | 2 20 files changed, 138 insertions(+), 110 deletions(-)
Title: The 'noweb' System for R
Description: The noweb system for source code, implemented in R.
Author: Terry Therneau
Maintainer: Terry Therneau <terry.therneau@mayo.edu>
Diff between noweb versions 1.0-4 dated 2013-03-27 and 1.1-2 dated 2019-10-13
noweb-1.0-4/noweb/inst/doc/noweb.R |only noweb-1.0-4/noweb/inst/doc/nowebsource.pdf |only noweb-1.0-4/noweb/inst/include/noweb.sty.orig |only noweb-1.0-4/noweb/man/nwread.Rd |only noweb-1.0-4/noweb/vignettes/noweb.sty |only noweb-1.1-2/noweb/DESCRIPTION | 11 - noweb-1.1-2/noweb/MD5 | 36 +--- noweb-1.1-2/noweb/NAMESPACE | 1 noweb-1.1-2/noweb/R/noweb.R | 163 ++++++++++--------- noweb-1.1-2/noweb/R/zzz.R | 5 noweb-1.1-2/noweb/build |only noweb-1.1-2/noweb/data/noweb.rda |binary noweb-1.1-2/noweb/inst/NEWS.Rd | 26 +-- noweb-1.1-2/noweb/inst/doc/noweb.Rnw | 52 +++--- noweb-1.1-2/noweb/inst/doc/noweb.pdf |binary noweb-1.1-2/noweb/inst/include/noweb.sty | 2 noweb-1.1-2/noweb/man/notangle.Rd | 9 - noweb-1.1-2/noweb/man/noweave.Rd | 10 - noweb-1.1-2/noweb/man/noweb.Rd | 8 noweb-1.1-2/noweb/noweb/noweave.Rnw | 218 +++++++++++++------------- noweb-1.1-2/noweb/noweb/nowebsource.Rnw | 66 +++++-- noweb-1.1-2/noweb/vignettes/noweb.Rnw | 52 +++--- 22 files changed, 365 insertions(+), 294 deletions(-)
Title: Generalized Linear Mixed Model Analysis via Expectation
Propagation
Description: Approximate frequentist inference for generalized linear mixed model analysis with expectation propagation used to circumvent the need for multivariate integration. In this version, the random effects can be any reasonable dimension. However, only probit mixed models with one level of nesting are supported. The methodology is described in Hall, Johnstone, Ormerod, Wand and Yu (2018) <arXiv:1805.08423v1>.
Author: Matt P. Wand [aut, cre],
James C.F. Yu [aut]
Maintainer: Matt P. Wand <matt.wand@uts.edu.au>
Diff between glmmEP versions 1.0-2 dated 2019-09-16 and 1.0-3 dated 2019-10-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/doc/manual.pdf |binary src/asn.f | 4 ++-- src/cpbt.f | 8 ++++---- src/epllk.f | 4 ++-- src/init.c | 4 ++-- 7 files changed, 20 insertions(+), 20 deletions(-)
Title: RDF Library Bindings in R
Description: Provides methods to parse, query and serialize information
stored in the Resource Description Framework (RDF). RDF is described at <http://www.w3.org/TR/rdf-primer>.
This package supports RDF by implementing an R interface to the Redland RDF C library,
described at <http://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph
consisting of Statements composed of Subject, Predicate, and Object Nodes.
Author: Matthew B. Jones [aut, cre],
Peter Slaughter [aut],
Jeroen Ooms [aut],
Carl Boettiger [aut],
Scott Chamberlain [aut],
David Beckett [cph],
University of Bristol [cph],
Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between redland versions 1.0.17-10 dated 2018-07-20 and 1.0.17-11 dated 2019-10-13
redland-1.0.17-10/redland/man/getNextResult.Rd |only redland-1.0.17-10/redland/man/librdf_node_to_string.Rd |only redland-1.0.17-10/redland/man/librdf_parser_guess_name.Rd |only redland-1.0.17-10/redland/man/librdf_query_results_to_file.Rd |only redland-1.0.17-10/redland/man/librdf_query_results_to_string.Rd |only redland-1.0.17-10/redland/man/librdf_statement_to_string.Rd |only redland-1.0.17-10/redland/man/librdf_stream_get_context.Rd |only redland-1.0.17-11/redland/DESCRIPTION | 10 redland-1.0.17-11/redland/MD5 | 73 +-- redland-1.0.17-11/redland/NAMESPACE | 7 redland-1.0.17-11/redland/NEWS | 8 redland-1.0.17-11/redland/R/Query.R | 9 redland-1.0.17-11/redland/R/QueryResults.R | 86 --- redland-1.0.17-11/redland/R/mergeNamespace_roclet.R | 25 - redland-1.0.17-11/redland/R/redland-package.R | 8 redland-1.0.17-11/redland/R/redland.R | 90 --- redland-1.0.17-11/redland/README.md | 4 redland-1.0.17-11/redland/build/vignette.rds |binary redland-1.0.17-11/redland/inst/WORDLIST | 63 +- redland-1.0.17-11/redland/inst/doc/redland_overview.R | 5 redland-1.0.17-11/redland/inst/doc/redland_overview.Rmd | 8 redland-1.0.17-11/redland/inst/doc/redland_overview.html | 69 ++ redland-1.0.17-11/redland/man/Node-initialize.Rd | 4 redland-1.0.17-11/redland/man/Query-class.Rd | 5 redland-1.0.17-11/redland/man/Query-initialize.Rd | 4 redland-1.0.17-11/redland/man/QueryResults-class.Rd | 25 - redland-1.0.17-11/redland/man/Statement-initialize.Rd | 7 redland-1.0.17-11/redland/man/Storage-initialize.Rd | 4 redland-1.0.17-11/redland/man/freeQuery.Rd | 4 redland-1.0.17-11/redland/man/freeQueryResults.Rd | 23 redland-1.0.17-11/redland/man/redland.Rd | 8 redland-1.0.17-11/redland/man/roclet_output.roclet_mergeNamespace.Rd | 4 redland-1.0.17-11/redland/man/roclet_process.roclet_mergeNamespace.Rd | 8 redland-1.0.17-11/redland/man/serializeToCharacter.Rd | 4 redland-1.0.17-11/redland/man/serializeToFile.Rd | 4 redland-1.0.17-11/redland/man/setNameSpace.Rd | 4 redland-1.0.17-11/redland/man/writeResults.Rd | 3 redland-1.0.17-11/redland/src/redland.c | 240 ---------- redland-1.0.17-11/redland/tests/testthat/test.Query.R | 193 +------- redland-1.0.17-11/redland/tests/testthat/test.redland_base.R | 26 - redland-1.0.17-11/redland/vignettes/redland_overview.Rmd | 8 41 files changed, 249 insertions(+), 794 deletions(-)
Title: Fit Interpretable Models and Explain Blackbox Machine Learning
Description: Machine Learning package for training interpretable models and explaining blackbox systems. Historically, the most intelligible models were not very accurate, and the most accurate models were not intelligible. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and intelligibility. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut],
Harsha Nori [aut],
Paul Koch [aut],
Rich Caruana [aut, cre],
Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>
Diff between interpret versions 0.1.21 dated 2019-10-10 and 0.1.22 dated 2019-10-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ src/Makevars | 11 +++++++---- src/core/EbmInternal.h | 1 + src/core/SegmentedTensor.h | 2 +- src/core/Training.cpp | 4 ++-- src/core/inc/ebmcore.h | 32 ++++++++++++++++---------------- 7 files changed, 37 insertions(+), 33 deletions(-)
Title: Clustering Method Based on Local
Description: We developed the clues R package to provide functions
for automatically estimating the number of clusters and
getting the final cluster partition without any input
parameter except the stopping rule for convergence.
The package also provides functions to
evaluate and compare the performances of partitions of a data
set both numerically and graphically.
Author: Fang Chang [aut, ctb],
Weiliang Qiu [aut, cre],
Vincent Carey [aut, ctb],
Ruben H. Zamar [aut, ctb],
Ross Lazarus [aut, ctb],
Xiaogang Wang [aut, ctb]
Maintainer: Weiliang Qiu <weiliang.qiu@gmail.com>
Diff between clues versions 0.5.9 dated 2016-10-14 and 0.6.1 dated 2019-10-13
DESCRIPTION | 24 ++++++++++++------------ MD5 | 11 ++++++----- NAMESPACE | 2 +- NEWS | 5 +++++ src/adjustedRand.c | 1 + src/chooseK.f95 | 10 +++++----- src/registerDynamicSymbol.c |only 7 files changed, 30 insertions(+), 23 deletions(-)
Title: Targeted Maximum Likelihood Estimation
Description: Targeted maximum likelihood estimation of point treatment effects (Targeted Maximum Likelihood Learning, The International Journal of Biostatistics, 2(1), 2006. This version automatically estimates the additive treatment effect among the treated (ATT) and among the controls (ATC). The tmle() function calculates the adjusted marginal difference in mean outcome associated with a binary point treatment, for continuous or binary outcomes. Relative risk and odds ratio estimates are also reported for binary outcomes. Missingness in the outcome is allowed, but not in treatment assignment or baseline covariate values. The population mean is calculated when there is missingness, and no variation in the treatment assignment. The tmleMSM() function estimates the parameters of a marginal structural model for a binary point treatment effect. Effect estimation stratified by a binary mediating variable is also available. An ID argument can be used to identify repeated measures. Default settings call 'SuperLearner' to estimate the Q and g portions of the likelihood, unless values or a user-supplied regression function are passed in as arguments.
Author: Susan Gruber [aut, cre],
Mark van der Laan [aut],
Chris Kennedy [ctr]
Maintainer: Susan Gruber <sgruber@cal.berkeley.edu>
Diff between tmle versions 1.3.0-2 dated 2019-02-20 and 1.4.0 dated 2019-10-13
DESCRIPTION | 21 + MD5 | 33 +- NAMESPACE | 6 NEWS | 20 + R/tmle.R | 579 ++++++++++++++++++++++++++++++++----------------- R/zzz.R | 2 man/calcParameters.Rd | 2 man/calcSigma.Rd | 2 man/estimateG.Rd | 8 man/estimateQ.Rd | 11 man/oneStepATT.Rd | 2 man/summary.tmle.Rd | 5 man/summary.tmleMSM.Rd | 2 man/tmle-package.Rd | 6 man/tmle.Rd | 54 ++-- man/tmle.Sl.dbarts2.Rd |only man/tmleMSM.Rd | 37 +-- man/tmleNews.Rd | 2 18 files changed, 510 insertions(+), 282 deletions(-)
Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: MCMC algorithms & processing functions for non- and semi-parametric models: 1. Dirichlet process mixtures & 2. spike-slab for multivariate (and univariate) regression, with nonparametric models for the means, the variances and the correlation matrix.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 2.1.0 dated 2019-05-24 and 2.1.1 dated 2019-10-13
DESCRIPTION | 10 MD5 | 27 - R/bnpMulti.R | 1103 ++++++++++++++++++++++------------------------------ R/mvrm.R | 26 - R/plot.R |only man/BNSP-package.Rd | 6 man/mvrm.Rd | 19 man/plot.mvrm.Rd | 9 src/BayesMult.c | 77 +-- src/BayesMultG.c | 65 +-- src/BayesMultGV.c | 63 +- src/mathm.h | 49 ++ src/mvrmGAM.c | 144 +++--- src/pdfs.h | 1 src/spec.BCM.h | 303 +++++++++++++- 15 files changed, 1052 insertions(+), 850 deletions(-)
Title: Wizardry Code Offensive Programming Test Generation
Description: Allows to generate automatically 'testthat' code files from offensive
programming test cases. Generated test files are complete and ready to run.
Using 'wyz.code.testthat' you will earn a lot of time, reduce the number of
errors in test case production, be able to test immediately generated files
without any need to view or modify them, and enter a zero time latency between
code implementation and industrial testing. As with 'testthat', you may
complete provided test cases according to your needs to push testing further,
but this need is nearly void when using 'wyz.code.offensiveProgramming'.
Refer to chapter 9 of Offensive Programming Book, Fabien GELINEAU (2019,
ISBN:979-10-699-4075-8), to learn about details and get value from this package.
Author: Fabien Gelineau <neonira@gmail.com>
Maintainer: Fabien Gelineau <neonira@gmail.com>
Diff between wyz.code.testthat versions 1.1.6 dated 2019-08-28 and 1.1.9 dated 2019-10-13
wyz.code.testthat-1.1.6/wyz.code.testthat/R/guardExecution.R |only wyz.code.testthat-1.1.9/wyz.code.testthat/DESCRIPTION | 8 - wyz.code.testthat-1.1.9/wyz.code.testthat/MD5 | 30 ++- wyz.code.testthat-1.1.9/wyz.code.testthat/NAMESPACE | 4 wyz.code.testthat-1.1.9/wyz.code.testthat/R/outOfPackage.R | 11 + wyz.code.testthat-1.1.9/wyz.code.testthat/R/reifyObject.R | 18 -- wyz.code.testthat-1.1.9/wyz.code.testthat/build/partial.rdb |binary wyz.code.testthat-1.1.9/wyz.code.testthat/build/vignette.rds |binary wyz.code.testthat-1.1.9/wyz.code.testthat/inst/doc/wyz.code.testthat.html | 4 wyz.code.testthat-1.1.9/wyz.code.testthat/man/generateAllUnitTestsFromObject.Rd | 2 wyz.code.testthat-1.1.9/wyz.code.testthat/tests/testthat.R | 6 wyz.code.testthat-1.1.9/wyz.code.testthat/tests/testthat/test_gautfo.R | 8 - wyz.code.testthat-1.1.9/wyz.code.testthat/tests/testthat/test_reifyObject.R | 79 ++-------- wyz.code.testthat-1.1.9/wyz.code.testthat/tests/testthat/tests |only 14 files changed, 69 insertions(+), 101 deletions(-)
More information about wyz.code.testthat at CRAN
Permanent link
More information about wyz.code.metaTesting at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-24 0.1.1
2018-02-28 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-18 0.3.1
2019-04-11 0.3.0
2019-01-24 0.2.2
2018-12-11 0.2.1
2018-09-26 0.2.0
2018-06-10 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-25 1.1.4
2019-03-20 1.1.2
2018-05-18 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-21 0.2
2016-07-18 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-09 1.1.2
2018-10-10 1.1.0
2018-07-20 1.0.0
Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport
data and non-motorized modes. Enables common transport planning tasks including:
downloading and cleaning transport datasets; creating geographic "desire lines"
from origin-destination (OD) data; route assignment, locally and via
interfaces to routing services such as <http://cyclestreets.net/>;
calculation of route segment attributes such as bearing and aggregate flow;
and 'travel watershed' analysis.
See Lovelace and Ellison (2018) <doi:10.32614/RJ-2018-053>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Richard Ellison [aut],
Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>),
Barry Rowlingson [ctb] (Author of overline),
Nick Bearman [ctb] (Co-author of gclip),
Nikolai Berkoff [ctb] (Co-author of line2route),
Scott Chamberlain [rev] (Scott reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/10),
Mark Padgham [ctb],
Andrea Gilardi [ctb] (<https://orcid.org/0000-0002-9424-7439>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.3.1 dated 2019-09-17 and 0.4.0 dated 2019-10-13
stplanr-0.3.1/stplanr/R/load-stats19.R |only stplanr-0.3.1/stplanr/man/dl_stats19.Rd |only stplanr-0.3.1/stplanr/man/figures/logo.png |only stplanr-0.3.1/stplanr/man/format_stats19_ac.Rd |only stplanr-0.3.1/stplanr/man/format_stats19_ca.Rd |only stplanr-0.3.1/stplanr/man/format_stats19_ve.Rd |only stplanr-0.3.1/stplanr/man/line_to_points.Rd |only stplanr-0.3.1/stplanr/man/read_stats19_ac.Rd |only stplanr-0.3.1/stplanr/man/read_stats19_ca.Rd |only stplanr-0.3.1/stplanr/man/read_stats19_ve.Rd |only stplanr-0.4.0/stplanr/DESCRIPTION | 13 stplanr-0.4.0/stplanr/MD5 | 141 ++-- stplanr-0.4.0/stplanr/NAMESPACE | 21 stplanr-0.4.0/stplanr/NEWS.md | 21 stplanr-0.4.0/stplanr/R/SpatialLinesNetwork.R | 35 - stplanr-0.4.0/stplanr/R/data.R | 36 + stplanr-0.4.0/stplanr/R/depreciated.R | 2 stplanr-0.4.0/stplanr/R/linefuns.R | 1 stplanr-0.4.0/stplanr/R/node-funs.R |only stplanr-0.4.0/stplanr/R/od-funs.R | 79 +- stplanr-0.4.0/stplanr/R/rnet-clean.R |only stplanr-0.4.0/stplanr/R/route.R | 155 ++--- stplanr-0.4.0/stplanr/R/stplanr-package.R | 3 stplanr-0.4.0/stplanr/README.md | 12 stplanr-0.4.0/stplanr/data/rnet_cycleway_intersection.rda |only stplanr-0.4.0/stplanr/data/rnet_overpass.rda |only stplanr-0.4.0/stplanr/data/rnet_roundabout.rda |only stplanr-0.4.0/stplanr/inst/doc/stplanr-od.R | 147 ++-- stplanr-0.4.0/stplanr/inst/doc/stplanr-od.Rmd | 172 ++--- stplanr-0.4.0/stplanr/inst/doc/stplanr-od.html | 130 ++-- stplanr-0.4.0/stplanr/inst/doc/stplanr-paper.R | 58 + stplanr-0.4.0/stplanr/inst/doc/stplanr-paper.Rmd | 58 + stplanr-0.4.0/stplanr/inst/doc/stplanr-paper.html | 55 - stplanr-0.4.0/stplanr/inst/doc/stplanr-route-nets.R | 152 +++- stplanr-0.4.0/stplanr/inst/doc/stplanr-route-nets.Rmd | 190 ++++-- stplanr-0.4.0/stplanr/inst/doc/stplanr-route-nets.html | 85 ++ stplanr-0.4.0/stplanr/inst/doc/stplanr-routing.R | 35 + stplanr-0.4.0/stplanr/inst/doc/stplanr-routing.Rmd | 62 +- stplanr-0.4.0/stplanr/inst/doc/stplanr-routing.html | 25 stplanr-0.4.0/stplanr/inst/doc/stplanr.R | 49 - stplanr-0.4.0/stplanr/inst/doc/stplanr.Rmd | 49 - stplanr-0.4.0/stplanr/inst/doc/stplanr.html | 97 +-- stplanr-0.4.0/stplanr/inst/stplanr-logo-vector-only.svg | 307 +++++----- stplanr-0.4.0/stplanr/man/angle_diff.Rd | 15 stplanr-0.4.0/stplanr/man/figures/README-plot1-1.png |binary stplanr-0.4.0/stplanr/man/figures/README-unnamed-chunk-6-1.png |binary stplanr-0.4.0/stplanr/man/figures/stplanr.png |binary stplanr-0.4.0/stplanr/man/geo_toptail.Rd | 15 stplanr-0.4.0/stplanr/man/is_linepoint.Rd | 15 stplanr-0.4.0/stplanr/man/line2df.Rd | 15 stplanr-0.4.0/stplanr/man/line2points.Rd |only stplanr-0.4.0/stplanr/man/line_bearing.Rd | 15 stplanr-0.4.0/stplanr/man/line_match.Rd | 15 stplanr-0.4.0/stplanr/man/line_midpoint.Rd | 15 stplanr-0.4.0/stplanr/man/line_sample.Rd | 15 stplanr-0.4.0/stplanr/man/line_segment.Rd | 15 stplanr-0.4.0/stplanr/man/line_via.Rd | 15 stplanr-0.4.0/stplanr/man/mats2line.Rd | 15 stplanr-0.4.0/stplanr/man/n_sample_length.Rd | 15 stplanr-0.4.0/stplanr/man/n_vertices.Rd | 15 stplanr-0.4.0/stplanr/man/onewaygeo.Rd | 15 stplanr-0.4.0/stplanr/man/onewayid.Rd | 15 stplanr-0.4.0/stplanr/man/points2line.Rd | 15 stplanr-0.4.0/stplanr/man/rnet_add_node.Rd |only stplanr-0.4.0/stplanr/man/rnet_breakup_vertices.Rd |only stplanr-0.4.0/stplanr/man/rnet_cycleway_intersection.Rd |only stplanr-0.4.0/stplanr/man/rnet_get_nodes.Rd |only stplanr-0.4.0/stplanr/man/rnet_overpass.Rd |only stplanr-0.4.0/stplanr/man/rnet_roundabout.Rd |only stplanr-0.4.0/stplanr/man/route.Rd | 7 stplanr-0.4.0/stplanr/man/route_dodgr.Rd | 24 stplanr-0.4.0/stplanr/man/route_nearest_point.Rd |only stplanr-0.4.0/stplanr/man/route_split.Rd |only stplanr-0.4.0/stplanr/man/route_split_id.Rd |only stplanr-0.4.0/stplanr/man/sln_add_node.Rd |only stplanr-0.4.0/stplanr/man/sln_clean_graph.Rd |only stplanr-0.4.0/stplanr/man/stplanr-deprecated.Rd | 5 stplanr-0.4.0/stplanr/man/toptail_buff.Rd | 15 stplanr-0.4.0/stplanr/man/toptailgs.Rd | 15 stplanr-0.4.0/stplanr/man/update_line_geometry.Rd | 16 stplanr-0.4.0/stplanr/vignettes/stplanr-od.Rmd | 172 ++--- stplanr-0.4.0/stplanr/vignettes/stplanr-paper.Rmd | 58 + stplanr-0.4.0/stplanr/vignettes/stplanr-route-nets.Rmd | 190 ++++-- stplanr-0.4.0/stplanr/vignettes/stplanr-routing.Rmd | 62 +- stplanr-0.4.0/stplanr/vignettes/stplanr.Rmd | 49 - 85 files changed, 1862 insertions(+), 1181 deletions(-)
Title: Shed Light on Black Box Machine Learning Models
Description: Shed light on black box machine learning models by
the help of model performance, permutation variable importance (Fisher
et al. (2018) <arxiv:1801.01489>), ICE profiles, partial dependence
(Friedman J. H. (2001) <doi:10.1214/aos/1013203451>), accumulated
local effects (Apley D. W. (2016) <arXiv:1612.08468>), further effects
plots, and variable contribution breakdown for single observations
(Gosiewska and Biecek (2019) <arxiv:1903.11420>). All tools are
implemented to work with case weights and allow for stratified
analysis. Furthermore, multiple flashlights can be combined and
analyzed together.
Author: Michael Mayer [aut, cre, cph]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between flashlight versions 0.2.0 dated 2019-09-18 and 0.3.0 dated 2019-10-13
DESCRIPTION | 11 MD5 | 50 +- NAMESPACE | 1 NEWS.md | 24 + R/ale_profile.R |only R/grouped_stats.R | 12 R/light_effects.R | 31 + R/light_ice.R | 30 + R/light_importance.R | 4 R/light_profile.R | 80 ++-- R/plot_light_effects.R | 13 R/plot_light_ice.R | 5 R/plot_light_profile.R | 6 README.md | 14 inst/doc/flashlight.R | 75 +++- inst/doc/flashlight.Rmd | 131 +++++-- inst/doc/flashlight.html | 837 +++++++++++++++++++++++++--------------------- man/ale_profile.Rd |only man/grouped_stats.Rd | 5 man/light_effects.Rd | 23 - man/light_ice.Rd | 16 man/light_importance.Rd | 4 man/light_profile.Rd | 50 +- man/plot.light_effects.Rd | 10 man/plot.light_ice.Rd | 5 man/plot.light_profile.Rd | 6 vignettes/flashlight.Rmd | 131 +++++-- 27 files changed, 1000 insertions(+), 574 deletions(-)
Title: Methods Used in the Economic Complexity Literature
Description: A wrapper of different indices and networks commonly used in
Economic Complexity to explore bipartite relations such as countries and their
exported products. These methods are also useful for different kind of
relations such as countries and their spoken languages.
The functions within this package correspond to code implementations of the
equations described in Hausmann, et al. (2005) <doi:10.3386/w11905>,
Hausmann, et al. (2014) <doi:10.7551/mitpress/9647.001.0001>, and
Mariani, et al. (2015) <doi:10.1140/epjb/e2015-60298-7>.
Author: Mauricio Vargas [aut, cre, cph]
(<https://orcid.org/0000-0003-1017-7574>),
Carlo Bottai [ctb] (improved the eigenvalues calculation),
Diego Kozlowski [ctb] (provided initial RCA and proximity functions he
used for his thesis),
Mark Padgham [rev] (compared PRODY equations from different articles),
Nico Pintar [rev] (suggested improvements to special cases in
eigenvalues calculation),
The World Bank [dtc],
Open Trade Statistics [dtc]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>
Diff between economiccomplexity versions 0.2.2 dated 2019-09-17 and 0.2.3 dated 2019-10-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/proximity.R | 10 ++++++++-- build/partial.rdb |binary inst/doc/basic-usage.html | 4 ++-- 5 files changed, 17 insertions(+), 11 deletions(-)
More information about economiccomplexity at CRAN
Permanent link
Title: Analysis of the 'Elements of Metacommunity Structure'
Description: Functions to analyze coherence, boundary clumping, and turnover
following the pattern-based metacommunity analysis of Leibold and Mikkelson
2002 <doi:10.1034/j.1600-0706.2002.970210.x>. The package also includes
functions to visualize ecological networks, and to calculate modularity
as a replacement to boundary clumping.
Author: Tad Dallas [aut, cre],
Tom Pulliam [ctb]
Maintainer: Tad Dallas <tad.a.dallas@gmail.com>
Diff between metacom versions 1.5.1 dated 2018-08-17 and 1.5.2 dated 2019-10-13
metacom-1.5.1/metacom/R/Modularity.R |only metacom-1.5.1/metacom/man/Modularity.Rd |only metacom-1.5.1/metacom/tests/testthat/test-Modularity.R |only metacom-1.5.2/metacom/DESCRIPTION | 8 +-- metacom-1.5.2/metacom/MD5 | 29 ++++++-------- metacom-1.5.2/metacom/NAMESPACE | 1 metacom-1.5.2/metacom/NEWS.md | 6 ++ metacom-1.5.2/metacom/R/Coherence.R | 4 - metacom-1.5.2/metacom/R/Metacommunity.R | 2 metacom-1.5.2/metacom/R/Turnover.R | 4 - metacom-1.5.2/metacom/data/TestMatrices.rda |binary metacom-1.5.2/metacom/man/Coherence.Rd | 5 +- metacom-1.5.2/metacom/man/Metacommunity.Rd | 6 +- metacom-1.5.2/metacom/man/Turnover.Rd | 6 +- metacom-1.5.2/metacom/tests/testthat/test-BoundaryClump.R | 10 ++++ metacom-1.5.2/metacom/tests/testthat/test-Coherence.R | 11 +++++ metacom-1.5.2/metacom/tests/testthat/test-Turnover.R | 10 ++++ 17 files changed, 68 insertions(+), 34 deletions(-)