Title: Phylogeographic Analysis of Island Colonization Events
Description: Estimation of the number of colonization events between islands of the same archipelago for a species. It uses rarefaction curves to control for both field and genetic sample sizes as it was described in Coello et al. (2022) <doi:10.1111/jbi.14341>.
Author: Alberto J. Coello [aut, cre] ,
Mario Fernandez-Mazuecos [aut] ,
Ruben H. Heleno [aut] ,
Pablo Vargas [aut]
Maintainer: Alberto J. Coello <albjcoello@gmail.com>
Diff between PAICE versions 1.0.1 dated 2023-11-13 and 1.0.2 dated 2024-07-15
PAICE-1.0.1/PAICE/R/PAICE.R |only PAICE-1.0.2/PAICE/DESCRIPTION | 10 +++++----- PAICE-1.0.2/PAICE/MD5 | 16 ++++++++-------- PAICE-1.0.2/PAICE/R/PAiCE.R |only PAICE-1.0.2/PAICE/R/print.colonization.R | 2 +- PAICE-1.0.2/PAICE/R/print.maxCol.R | 4 ++-- PAICE-1.0.2/PAICE/R/zzz.R | 2 +- PAICE-1.0.2/PAICE/data/CmonsData.RData |binary PAICE-1.0.2/PAICE/data/CmonsNetwork.RData |binary PAICE-1.0.2/PAICE/data/CmonsRare.RData |binary 10 files changed, 17 insertions(+), 17 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb, cph],
David Bryant [ctb, cph],
Ya-Mei Chang [ctb, cph],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.2-3 dated 2024-02-29 and 3.3-1 dated 2024-07-15
spatstat.random-3.2-3/spatstat.random/R/indefinteg.R |only spatstat.random-3.2-3/spatstat.random/man/indefinteg.Rd |only spatstat.random-3.3-1/spatstat.random/DESCRIPTION | 17 - spatstat.random-3.3-1/spatstat.random/MD5 | 115 ++++------ spatstat.random-3.3-1/spatstat.random/NAMESPACE | 3 spatstat.random-3.3-1/spatstat.random/NEWS | 37 +++ spatstat.random-3.3-1/spatstat.random/R/clusterinfo.R | 6 spatstat.random-3.3-1/spatstat.random/R/rPerfect.R | 38 +-- spatstat.random-3.3-1/spatstat.random/R/rags.R | 4 spatstat.random-3.3-1/spatstat.random/R/random.R | 4 spatstat.random-3.3-1/spatstat.random/R/randomNS.R | 6 spatstat.random-3.3-1/spatstat.random/R/randomcircembed.R | 8 spatstat.random-3.3-1/spatstat.random/R/rcauchy.R | 10 spatstat.random-3.3-1/spatstat.random/R/rmatclust.R | 14 - spatstat.random-3.3-1/spatstat.random/R/rmhmodel.R | 110 ++++----- spatstat.random-3.3-1/spatstat.random/R/rthomas.R | 10 spatstat.random-3.3-1/spatstat.random/inst/doc/packagesizes.txt | 2 spatstat.random-3.3-1/spatstat.random/inst/info |only spatstat.random-3.3-1/spatstat.random/man/Window.rmhmodel.Rd | 12 - spatstat.random-3.3-1/spatstat.random/man/as.owin.rmhmodel.Rd | 14 - spatstat.random-3.3-1/spatstat.random/man/domain.rmhmodel.Rd | 4 spatstat.random-3.3-1/spatstat.random/man/expand.owin.Rd | 10 spatstat.random-3.3-1/spatstat.random/man/is.stationary.Rd | 2 spatstat.random-3.3-1/spatstat.random/man/rGaussPoisson.Rd | 8 spatstat.random-3.3-1/spatstat.random/man/rMaternI.Rd | 10 spatstat.random-3.3-1/spatstat.random/man/rMaternII.Rd | 10 spatstat.random-3.3-1/spatstat.random/man/rMosaicField.Rd | 2 spatstat.random-3.3-1/spatstat.random/man/rPoissonCluster.Rd | 6 spatstat.random-3.3-1/spatstat.random/man/rSSI.Rd | 2 spatstat.random-3.3-1/spatstat.random/man/rStrauss.Rd | 2 spatstat.random-3.3-1/spatstat.random/man/rcell.Rd | 2 spatstat.random-3.3-1/spatstat.random/man/rclusterBKBC.Rd | 4 spatstat.random-3.3-1/spatstat.random/man/rlabel.Rd | 6 spatstat.random-3.3-1/spatstat.random/man/rmh.default.Rd | 10 spatstat.random-3.3-1/spatstat.random/man/rmhcontrol.Rd | 8 spatstat.random-3.3-1/spatstat.random/man/rmhexpand.Rd | 8 spatstat.random-3.3-1/spatstat.random/man/rmhmodel.default.Rd | 4 spatstat.random-3.3-1/spatstat.random/man/rmhstart.Rd | 2 spatstat.random-3.3-1/spatstat.random/man/rmpoint.Rd | 7 spatstat.random-3.3-1/spatstat.random/man/rmpoispp.Rd | 9 spatstat.random-3.3-1/spatstat.random/man/rnoise.Rd | 10 spatstat.random-3.3-1/spatstat.random/man/rpoint.Rd | 9 spatstat.random-3.3-1/spatstat.random/man/rpoisline.Rd | 4 spatstat.random-3.3-1/spatstat.random/man/rpoislinetess.Rd | 10 spatstat.random-3.3-1/spatstat.random/man/rpoispp.Rd | 11 spatstat.random-3.3-1/spatstat.random/man/rpoispp3.Rd | 12 - spatstat.random-3.3-1/spatstat.random/man/rpoisppOnLines.Rd | 4 spatstat.random-3.3-1/spatstat.random/man/rpoisppx.Rd | 12 - spatstat.random-3.3-1/spatstat.random/man/rshift.Rd | 10 spatstat.random-3.3-1/spatstat.random/man/rshift.ppp.Rd | 4 spatstat.random-3.3-1/spatstat.random/man/rshift.splitppp.Rd | 2 spatstat.random-3.3-1/spatstat.random/man/rstrat.Rd | 18 - spatstat.random-3.3-1/spatstat.random/man/rthinclumps.Rd | 10 spatstat.random-3.3-1/spatstat.random/man/runifdisc.Rd | 14 - spatstat.random-3.3-1/spatstat.random/man/runifpoint.Rd | 12 - spatstat.random-3.3-1/spatstat.random/man/runifpoint3.Rd | 12 - spatstat.random-3.3-1/spatstat.random/man/runifpointOnLines.Rd | 6 spatstat.random-3.3-1/spatstat.random/man/runifpointx.Rd | 12 - spatstat.random-3.3-1/spatstat.random/man/spatstat.random-internal.Rd | 1 spatstat.random-3.3-1/spatstat.random/src/Perfect.cc | 5 60 files changed, 359 insertions(+), 345 deletions(-)
More information about spatstat.random at CRAN
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Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.2-11 dated 2024-03-22 and 3.3-1 dated 2024-07-15
DESCRIPTION | 19 +-- MD5 | 251 ++++++++++++++++++++--------------------- NAMESPACE | 5 NEWS | 45 +++++++ R/evidence.R | 4 R/logistic.R | 11 + R/measures.R | 6 R/mpl.R | 13 +- R/ppm.R | 7 - R/predict.ppm.R | 56 +++------ R/response.R | 2 R/slrm.R | 28 +++- R/sysdata.rda |binary inst/doc/packagesizes.txt | 1 inst/info |only man/AreaInter.Rd | 4 man/DiggleGatesStibbard.Rd | 2 man/Extract.influence.ppm.Rd | 2 man/Extract.leverage.ppm.Rd | 6 man/Gcom.Rd | 10 - man/Gres.Rd | 4 man/Kcom.Rd | 10 - man/Kmodel.Rd | 9 - man/Kmodel.kppm.Rd | 2 man/Kmodel.ppm.Rd | 2 man/Kres.Rd | 4 man/MultiHard.Rd | 2 man/Smooth.msr.Rd | 4 man/Window.ppm.Rd | 12 - man/addvar.Rd | 4 man/anova.ppm.Rd | 4 man/as.fv.kppm.Rd | 6 man/as.layered.msr.Rd | 6 man/as.owin.ppm.Rd | 8 - man/auc.Rd | 6 man/berman.test.Rd | 8 - man/cauchy.estK.Rd | 12 - man/cauchy.estpcf.Rd | 14 +- man/cdf.test.Rd | 10 - man/cdf.test.mppm.Rd | 14 +- man/closepaircounts.Rd | 2 man/clusterfit.Rd | 8 - man/clusterkernel.kppm.Rd | 2 man/clusterradius.kppm.Rd | 2 man/compareFit.Rd | 4 man/data.ppm.Rd | 2 man/detpointprocfamilyfun.Rd | 4 man/dfbetas.ppm.Rd | 2 man/diagnose.ppm.Rd | 2 man/domain.ppm.Rd | 4 man/dppm.Rd | 16 +- man/dummy.ppm.Rd | 2 man/effectfun.Rd | 2 man/emend.ppm.Rd | 2 man/emend.slrm.Rd | 2 man/envelope.Rd | 60 ++++----- man/fitted.slrm.Rd | 36 +++++ man/formula.ppm.Rd | 2 man/harmonise.msr.Rd | 4 man/improve.kppm.Rd | 2 man/influence.ppm.Rd | 5 man/intensity.ppm.Rd | 6 man/intensity.slrm.Rd | 4 man/is.marked.ppm.Rd | 4 man/is.multitype.ppm.Rd | 4 man/is.stationary.ppm.Rd | 10 - man/kppm.Rd | 26 ++-- man/leverage.ppm.Rd | 7 - man/lgcp.estK.Rd | 6 man/lgcp.estpcf.Rd | 8 - man/logLik.ppm.Rd | 2 man/matclust.estK.Rd | 10 - man/matclust.estpcf.Rd | 12 - man/methods.fii.Rd | 4 man/mincontrast.Rd | 4 man/model.images.Rd | 12 - man/mppm.Rd | 10 - man/msr.Rd | 2 man/panel.contour.Rd | 10 - man/parres.Rd | 4 man/plot.dppm.Rd | 5 man/plot.influence.ppm.Rd | 2 man/plot.kppm.Rd | 11 - man/plot.leverage.ppm.Rd | 16 +- man/plot.mppm.Rd | 6 man/plot.msr.Rd | 16 +- man/plot.plotppm.Rd | 7 - man/plot.ppm.Rd | 6 man/plot.rppm.Rd | 6 man/plot.slrm.Rd | 4 man/ppm.Rd | 6 man/ppm.object.Rd | 26 ++-- man/ppm.ppp.Rd | 45 ++++--- man/predict.mppm.Rd | 4 man/predict.ppm.Rd | 8 - man/predict.slrm.Rd | 2 man/psst.Rd | 4 man/psstA.Rd | 8 - man/psstG.Rd | 4 man/qqplot.ppm.Rd | 18 +- man/quad.ppm.Rd | 4 man/quadrat.test.Rd | 18 +- man/quadrat.test.mppm.Rd | 4 man/reach.Rd | 2 man/relrisk.ppm.Rd | 8 - man/residuals.ppm.Rd | 4 man/rhohat.Rd | 10 - man/rmh.ppm.Rd | 54 ++++---- man/rmhmodel.ppm.Rd | 20 +-- man/roc.Rd | 6 man/simulate.dppm.Rd | 2 man/simulate.kppm.Rd | 20 +-- man/simulate.ppm.Rd | 10 - man/simulate.slrm.Rd | 7 - man/slrm.Rd | 2 man/spatstat.model-internal.Rd | 10 + man/spatstat.model-package.Rd | 5 man/split.msr.Rd | 8 - man/thomas.estK.Rd | 10 - man/thomas.estpcf.Rd | 14 +- man/unitname.Rd | 10 - man/unstack.msr.Rd | 2 man/varcount.Rd | 2 man/vargamma.estK.Rd | 12 - man/vargamma.estpcf.Rd | 14 +- man/vcov.ppm.Rd | 2 tests/testsP2.R | 9 + 127 files changed, 759 insertions(+), 637 deletions(-)
More information about spatstat.model at CRAN
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Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.1-5 dated 2024-03-25 and 3.2-1 dated 2024-07-15
DESCRIPTION | 18 +-- MD5 | 179 ++++++++++++++++----------------- NAMESPACE | 18 +++ NEWS | 36 ++++++ R/density.lpp.R | 2 R/densityfunlpp.R | 4 R/evaluateNetCovariate.R |only R/evidencelppm.R | 206 +++++++++++++++++++++++++++++++++++++- R/exactlppm.R |only R/linnet.R | 10 + R/linnetsurgery.R | 82 +++++++++------ R/lpp.R | 5 R/relrisk.lpp.R | 6 - inst/doc/packagesizes.txt | 2 inst/info |only man/Extract.linim.Rd | 6 + man/Extract.lpp.Rd | 2 man/Replace.linim.Rd | 6 - man/Smooth.lpp.Rd | 4 man/affine.linnet.Rd | 22 ++-- man/affine.lpp.Rd | 22 ++-- man/as.linim.Rd | 8 - man/as.linnet.psp.Rd | 4 man/auc.lpp.Rd | 4 man/berman.test.lpp.Rd | 4 man/bw.lppl.Rd | 4 man/cdf.test.lpp.Rd | 4 man/chop.linnet.Rd | 6 - man/clickjoin.Rd | 4 man/clicklpp.Rd | 8 - man/crossdist.lpp.Rd | 10 - man/crossing.linnet.Rd | 2 man/data.lppm.Rd | 2 man/delaunayNetwork.Rd | 10 - man/density.lpp.Rd | 4 man/densityEqualSplit.Rd | 6 - man/densityHeat.lpp.Rd | 8 - man/densityQuick.lpp.Rd | 6 - man/densityVoronoi.lpp.Rd | 4 man/diameter.linnet.Rd | 6 - man/distfun.lpp.Rd | 2 man/distmap.lpp.Rd | 4 man/envelope.lpp.Rd | 8 - man/eval.linim.Rd | 2 man/fitted.lppm.Rd | 12 -- man/heatkernelapprox.Rd | 2 man/integral.linim.Rd | 2 man/intensity.lpp.Rd | 9 - man/linearK.Rd | 2 man/linearKEuclidInhom.Rd | 4 man/linearKcross.Rd | 4 man/linearKcross.inhom.Rd | 4 man/linearKdot.Rd | 6 - man/linearKdot.inhom.Rd | 4 man/linearKinhom.Rd | 4 man/linearmarkconnect.Rd | 6 - man/linearmarkequal.Rd | 4 man/linearpcfEuclidInhom.Rd | 4 man/linearpcfcross.Rd | 6 - man/linearpcfcross.inhom.Rd | 6 - man/linearpcfdot.Rd | 8 - man/linearpcfdot.inhom.Rd | 8 - man/linearpcfinhom.Rd | 4 man/lineartileindex.Rd | 2 man/linim.Rd | 2 man/lpp.Rd | 4 man/lppm.Rd | 8 - man/mean.linim.Rd | 6 - man/methods.linfun.Rd | 4 man/methods.linim.Rd | 8 - man/methods.linnet.Rd | 44 ++++---- man/model.frame.lppm.Rd | 2 man/nnfun.lpp.Rd | 2 man/pairs.linim.Rd | 2 man/plot.linim.Rd | 14 +- man/plot.linnet.Rd | 4 man/plot.lintess.Rd | 8 - man/plot.lpp.Rd | 16 +- man/points.lpp.Rd | 2 man/predict.lppm.Rd | 2 man/rThomaslpp.Rd | 2 man/rcelllpp.Rd | 2 man/relrisk.lpp.Rd | 4 man/roc.lpp.Rd | 2 man/rpoislpp.Rd | 8 - man/runiflpp.Rd | 2 man/spatstat.linnet-deprecated.Rd | 1 man/spatstat.linnet-internal.Rd | 23 ++++ man/spatstat.linnet-package.Rd | 9 + man/superimpose.lpp.Rd | 4 man/thinNetwork.Rd | 9 + tests/testsL.R | 9 + 92 files changed, 692 insertions(+), 362 deletions(-)
More information about spatstat.linnet at CRAN
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Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oehlschlaegel [ctb, cph],
Suman Rakshit [ctb], [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.2-9 dated 2024-02-28 and 3.3-2 dated 2024-07-15
spatstat.geom-3.2-9/spatstat.geom/R/breakpts.R |only spatstat.geom-3.2-9/spatstat.geom/R/ewcdf.R |only spatstat.geom-3.2-9/spatstat.geom/R/hotrod.R |only spatstat.geom-3.2-9/spatstat.geom/R/integral.R |only spatstat.geom-3.2-9/spatstat.geom/R/transformquantiles.R |only spatstat.geom-3.2-9/spatstat.geom/R/uniquemap.R |only spatstat.geom-3.2-9/spatstat.geom/R/unnormdensity.R |only spatstat.geom-3.2-9/spatstat.geom/R/weightedStats.R |only spatstat.geom-3.2-9/spatstat.geom/man/ewcdf.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/hotrod.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/integral.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/integral.density.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/mean.ewcdf.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/quantile.ewcdf.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/quantilefun.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/rounding.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/transformquantiles.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/uniquemap.default.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/unnormdensity.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/weighted.median.Rd |only spatstat.geom-3.2-9/spatstat.geom/man/whist.Rd |only spatstat.geom-3.2-9/spatstat.geom/src/hotrod.c |only spatstat.geom-3.2-9/spatstat.geom/src/tabnum.c |only spatstat.geom-3.2-9/spatstat.geom/src/whist.c |only spatstat.geom-3.3-2/spatstat.geom/DESCRIPTION | 14 spatstat.geom-3.3-2/spatstat.geom/MD5 | 203 +-- spatstat.geom-3.3-2/spatstat.geom/NAMESPACE | 56 spatstat.geom-3.3-2/spatstat.geom/NEWS | 143 ++ spatstat.geom-3.3-2/spatstat.geom/R/affine.R | 9 spatstat.geom-3.3-2/spatstat.geom/R/colourtables.R | 28 spatstat.geom-3.3-2/spatstat.geom/R/diagram.R | 32 spatstat.geom-3.3-2/spatstat.geom/R/plot.owin.R | 21 spatstat.geom-3.3-2/spatstat.geom/R/plot.ppp.R | 622 +++++----- spatstat.geom-3.3-2/spatstat.geom/R/ppp.R | 18 spatstat.geom-3.3-2/spatstat.geom/R/ppx.R | 4 spatstat.geom-3.3-2/spatstat.geom/R/psp.R | 38 spatstat.geom-3.3-2/spatstat.geom/R/randombasic.R | 6 spatstat.geom-3.3-2/spatstat.geom/R/round.R | 30 spatstat.geom-3.3-2/spatstat.geom/R/simplepanel.R | 22 spatstat.geom-3.3-2/spatstat.geom/R/solist.R | 8 spatstat.geom-3.3-2/spatstat.geom/R/symbolmap.R | 112 + spatstat.geom-3.3-2/spatstat.geom/R/tess.R | 4 spatstat.geom-3.3-2/spatstat.geom/R/unique.ppp.R | 22 spatstat.geom-3.3-2/spatstat.geom/R/uniquemap.ppp.R |only spatstat.geom-3.3-2/spatstat.geom/inst/doc/packagesizes.txt | 2 spatstat.geom-3.3-2/spatstat.geom/inst/info |only spatstat.geom-3.3-2/spatstat.geom/man/Window.tess.Rd | 12 spatstat.geom-3.3-2/spatstat.geom/man/affine.im.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/affine.owin.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/as.im.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/as.matrix.owin.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/as.polygonal.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/bdist.pixels.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/boundingcircle.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/bufftess.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/closing.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/commonGrid.Rd | 6 spatstat.geom-3.3-2/spatstat.geom/man/connected.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/connected.tess.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/covering.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/default.symbolmap.Rd |only spatstat.geom-3.3-2/spatstat.geom/man/default.symbolmap.ppp.Rd |only spatstat.geom-3.3-2/spatstat.geom/man/deltametric.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/dilation.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/disc.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/discretise.Rd | 8 spatstat.geom-3.3-2/spatstat.geom/man/discs.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/distmap.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/distmap.owin.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/distmap.ppp.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/distmap.psp.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/domain.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/ellipse.Rd | 6 spatstat.geom-3.3-2/spatstat.geom/man/erosion.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/fardist.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/framedist.pixels.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/gridweights.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/integral.im.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/intensity.quadratcount.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/intersect.owin.Rd | 6 spatstat.geom-3.3-2/spatstat.geom/man/intersect.tess.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/is.subset.owin.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/layout.boxes.Rd | 24 spatstat.geom-3.3-2/spatstat.geom/man/nearest.raster.point.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/nnmap.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/nnmark.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/opening.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/owin.object.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/owin2mask.Rd | 10 spatstat.geom-3.3-2/spatstat.geom/man/pixelcentres.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/pixellate.owin.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/pixellate.ppp.Rd | 6 spatstat.geom-3.3-2/spatstat.geom/man/pixellate.psp.Rd | 8 spatstat.geom-3.3-2/spatstat.geom/man/pixelquad.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/plot.colourmap.Rd | 20 spatstat.geom-3.3-2/spatstat.geom/man/plot.owin.Rd | 10 spatstat.geom-3.3-2/spatstat.geom/man/plot.ppp.Rd | 17 spatstat.geom-3.3-2/spatstat.geom/man/plot.tess.Rd | 14 spatstat.geom-3.3-2/spatstat.geom/man/plot.texturemap.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/project2set.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/psp2mask.Rd | 8 spatstat.geom-3.3-2/spatstat.geom/man/quantilefun.im.Rd | 7 spatstat.geom-3.3-2/spatstat.geom/man/raster.x.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/rotate.owin.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/round.ppp.Rd | 5 spatstat.geom-3.3-2/spatstat.geom/man/rounding.ppp.Rd |only spatstat.geom-3.3-2/spatstat.geom/man/setcov.Rd | 2 spatstat.geom-3.3-2/spatstat.geom/man/spatstat.geom-deprecated.Rd | 1 spatstat.geom-3.3-2/spatstat.geom/man/spatstat.geom-internal.Rd | 69 - spatstat.geom-3.3-2/spatstat.geom/man/spatstat.geom-package.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/summary.distfun.Rd | 4 spatstat.geom-3.3-2/spatstat.geom/man/uniquemap.ppp.Rd | 9 spatstat.geom-3.3-2/spatstat.geom/src/init.c | 4 spatstat.geom-3.3-2/spatstat.geom/src/proto.h | 4 spatstat.geom-3.3-2/spatstat.geom/tests/testsD.R | 23 spatstat.geom-3.3-2/spatstat.geom/tests/testsS.R | 13 spatstat.geom-3.3-2/spatstat.geom/tests/testsUtoZ.R | 25 117 files changed, 1048 insertions(+), 785 deletions(-)
Title: Exploratory Data Analysis for the 'spatstat' Family
Description: Functionality for exploratory data analysis and nonparametric analysis of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Warick Brown [cph],
Achmad Choiruddin [ctb],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb, cph],
Julian Gi [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.explore versions 3.2-7 dated 2024-03-21 and 3.3-1 dated 2024-07-15
spatstat.explore-3.2-7/spatstat.explore/R/bw.abram.R |only spatstat.explore-3.2-7/spatstat.explore/R/densityAdaptiveKernel.R |only spatstat.explore-3.2-7/spatstat.explore/R/kernels.R |only spatstat.explore-3.2-7/spatstat.explore/R/kmrs.R |only spatstat.explore-3.2-7/spatstat.explore/R/quantiledensity.R |only spatstat.explore-3.2-7/spatstat.explore/R/stieltjes.R |only spatstat.explore-3.2-7/spatstat.explore/man/CDF.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/bw.abram.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/densityAdaptiveKernel.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/dkernel.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/kaplan.meier.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/kernel.factor.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/kernel.moment.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/kernel.squint.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/km.rs.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/quantile.density.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/reduced.sample.Rd |only spatstat.explore-3.2-7/spatstat.explore/man/stieltjes.Rd |only spatstat.explore-3.3-1/spatstat.explore/DESCRIPTION | 20 spatstat.explore-3.3-1/spatstat.explore/MD5 | 280 ++++------ spatstat.explore-3.3-1/spatstat.explore/NAMESPACE | 26 spatstat.explore-3.3-1/spatstat.explore/NEWS | 62 ++ spatstat.explore-3.3-1/spatstat.explore/R/Kinhom.R | 6 spatstat.explore-3.3-1/spatstat.explore/R/bw.abram.ppp.R |only spatstat.explore-3.3-1/spatstat.explore/R/bw.ppl.R | 5 spatstat.explore-3.3-1/spatstat.explore/R/densityAdaptiveKernel.ppp.R |only spatstat.explore-3.3-1/spatstat.explore/R/edgeTrans.R | 6 spatstat.explore-3.3-1/spatstat.explore/R/evidence.R | 31 - spatstat.explore-3.3-1/spatstat.explore/R/fv.R | 39 + spatstat.explore-3.3-1/spatstat.explore/R/smooth.ppp.R | 5 spatstat.explore-3.3-1/spatstat.explore/R/spatialQuantile.R | 2 spatstat.explore-3.3-1/spatstat.explore/R/sysdata.rda |binary spatstat.explore-3.3-1/spatstat.explore/inst/doc/packagesizes.txt | 1 spatstat.explore-3.3-1/spatstat.explore/inst/info |only spatstat.explore-3.3-1/spatstat.explore/man/Emark.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/F3est.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/Fest.Rd | 14 spatstat.explore-3.3-1/spatstat.explore/man/Finhom.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/FmultiInhom.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/G3est.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Gcross.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Gdot.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Gest.Rd | 22 spatstat.explore-3.3-1/spatstat.explore/man/Gfox.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Ginhom.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/Gmulti.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/GmultiInhom.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/Hest.Rd | 6 spatstat.explore-3.3-1/spatstat.explore/man/Iest.Rd | 6 spatstat.explore-3.3-1/spatstat.explore/man/Jcross.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Jdot.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Jest.Rd | 12 spatstat.explore-3.3-1/spatstat.explore/man/Jinhom.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Jmulti.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/K3est.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Kcross.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Kcross.inhom.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Kdot.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Kdot.inhom.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Kest.Rd | 10 spatstat.explore-3.3-1/spatstat.explore/man/Kest.fft.Rd | 8 spatstat.explore-3.3-1/spatstat.explore/man/Kinhom.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Kmark.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Kmeasure.Rd | 14 spatstat.explore-3.3-1/spatstat.explore/man/Kmulti.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Kmulti.inhom.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Kscaled.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Ksector.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Lest.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Linhom.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Smooth.ppp.Rd | 10 spatstat.explore-3.3-1/spatstat.explore/man/Smoothfun.ppp.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/Tstat.Rd | 7 spatstat.explore-3.3-1/spatstat.explore/man/Window.quadrattest.Rd | 12 spatstat.explore-3.3-1/spatstat.explore/man/adaptive.density.Rd | 26 spatstat.explore-3.3-1/spatstat.explore/man/allstats.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/as.owin.quadrattest.Rd | 8 spatstat.explore-3.3-1/spatstat.explore/man/as.tess.Rd | 5 spatstat.explore-3.3-1/spatstat.explore/man/auc.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/berman.test.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/bind.fv.Rd | 39 + spatstat.explore-3.3-1/spatstat.explore/man/blur.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/bw.CvL.adaptive.Rd | 6 spatstat.explore-3.3-1/spatstat.explore/man/bw.abram.ppp.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/bw.frac.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/cdf.test.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/clarkevans.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/clusterset.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/compatible.fasp.Rd | 9 spatstat.explore-3.3-1/spatstat.explore/man/compatible.fv.Rd | 5 spatstat.explore-3.3-1/spatstat.explore/man/density.ppp.Rd | 14 spatstat.explore-3.3-1/spatstat.explore/man/density.psp.Rd | 8 spatstat.explore-3.3-1/spatstat.explore/man/density.splitppp.Rd | 8 spatstat.explore-3.3-1/spatstat.explore/man/densityAdaptiveKernel.ppp.Rd |only spatstat.explore-3.3-1/spatstat.explore/man/densityAdaptiveKernel.splitppp.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/densityVoronoi.Rd | 8 spatstat.explore-3.3-1/spatstat.explore/man/densityfun.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/distcdf.Rd | 14 spatstat.explore-3.3-1/spatstat.explore/man/domain.quadrattest.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/edge.Trans.Rd | 8 spatstat.explore-3.3-1/spatstat.explore/man/envelope.Rd | 12 spatstat.explore-3.3-1/spatstat.explore/man/envelope.pp3.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/fryplot.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/harmonise.fv.Rd | 10 spatstat.explore-3.3-1/spatstat.explore/man/hopskel.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/hotbox.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/idw.Rd | 15 spatstat.explore-3.3-1/spatstat.explore/man/integral.fv.Rd | 6 spatstat.explore-3.3-1/spatstat.explore/man/laslett.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/markconnect.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/markcorr.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/markcrosscorr.Rd | 12 spatstat.explore-3.3-1/spatstat.explore/man/markmarkscatter.Rd | 6 spatstat.explore-3.3-1/spatstat.explore/man/marktable.Rd | 8 spatstat.explore-3.3-1/spatstat.explore/man/markvario.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/methods.ssf.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/miplot.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/nnclean.Rd | 6 spatstat.explore-3.3-1/spatstat.explore/man/nncorr.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/nndensity.Rd | 10 spatstat.explore-3.3-1/spatstat.explore/man/pairMean.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/pairs.im.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/panel.contour.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/pcf.ppp.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/pcf3est.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/pcfinhom.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/plot.fv.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/plot.laslett.Rd | 14 spatstat.explore-3.3-1/spatstat.explore/man/plot.quadrattest.Rd | 11 spatstat.explore-3.3-1/spatstat.explore/man/plot.scan.test.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/pool.anylist.Rd | 12 spatstat.explore-3.3-1/spatstat.explore/man/quadrat.test.Rd | 12 spatstat.explore-3.3-1/spatstat.explore/man/quadrat.test.splitppp.Rd | 6 spatstat.explore-3.3-1/spatstat.explore/man/radcumint.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/rat.Rd | 6 spatstat.explore-3.3-1/spatstat.explore/man/rectcontact.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/man/relrisk.ppp.Rd | 10 spatstat.explore-3.3-1/spatstat.explore/man/rhohat.Rd | 6 spatstat.explore-3.3-1/spatstat.explore/man/roc.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/rotmean.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/scan.test.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/scanLRTS.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/segregation.test.Rd | 6 spatstat.explore-3.3-1/spatstat.explore/man/spatcov.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/spatialcdf.Rd | 8 spatstat.explore-3.3-1/spatstat.explore/man/spatstat.explore-deprecated.Rd | 3 spatstat.explore-3.3-1/spatstat.explore/man/spatstat.explore-internal.Rd | 9 spatstat.explore-3.3-1/spatstat.explore/man/spatstat.explore-package.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/stienen.Rd | 17 spatstat.explore-3.3-1/spatstat.explore/man/transect.im.Rd | 2 spatstat.explore-3.3-1/spatstat.explore/man/varblock.Rd | 4 spatstat.explore-3.3-1/spatstat.explore/tests/testsNtoO.R | 17 152 files changed, 598 insertions(+), 568 deletions(-)
More information about spatstat.explore at CRAN
Permanent link
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.0-8 dated 2024-03-26 and 3.1-1 dated 2024-07-15
DESCRIPTION | 18 ++--- MD5 | 49 +++++++------ NAMESPACE | 1 NEWS | 29 ++++++++ R/news.R | 11 ++- build/vignette.rds |binary inst/doc/bugfixes.Rnw | 26 ++++++- inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 1 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/spatstatKnetsize.txt | 2 inst/doc/spatstatguisize.txt | 2 inst/doc/spatstatlocalsize.txt | 3 inst/doc/updates.R | 22 ++++-- inst/doc/updates.Rnw | 146 +++++++++++++++++++++++++++++++++-------- inst/doc/updates.pdf |binary inst/info |only man/spatstat-internal.Rd | 1 man/spatstat-package.Rd | 2 man/spatstat.family.Rd | 1 vignettes/bugfixes.Rnw | 26 ++++++- vignettes/updates.Rnw | 146 +++++++++++++++++++++++++++++++++-------- 26 files changed, 386 insertions(+), 100 deletions(-)
Title: Comparing and Visualizing Differences Between Surveys
Description: Easily analyze and visualize differences between samples (e.g., benchmark comparisons, nonresponse comparisons in surveys) on three levels. The comparisons can be univariate, bivariate or multivariate. On univariate level the variables of interest of a survey and a comparison survey (i.e. benchmark) are compared, by calculating one of several difference measures (e.g., relative difference in mean), and an average difference between the surveys. On bivariate level a function can calculate significant differences in correlations for the surveys. And on multivariate levels a function can calculate significant differences in model coefficients between the surveys of comparison. All of those differences can be easily plotted and outputted as a table. For more detailed information on the methods and example use see Rohr, B., Silber, H., & Felderer, B. (2024). „Comparing the Accuracy of Univariate, Bivariate, and Multivariate Estimates across Probability and Non-Probability Surveys with [...truncated...]
Author: Bjoern Rohr [aut, cre, cph],
Barbara Felderer [aut]
Maintainer: Bjoern Rohr <bjoern.rohr@gesis.org>
Diff between sampcompR versions 0.2.0 dated 2024-07-12 and 0.2.1 dated 2024-07-15
DESCRIPTION | 13 - MD5 | 13 - NAMESPACE | 2 NEWS.md | 11 + R/Output_Tables.R | 378 ++++++++++++++++++++++++++++++++++++++++++++++ README.md | 6 man/biv_per_variable.Rd |only man/figures/logo.png |only man/multi_per_variable.Rd |only 9 files changed, 409 insertions(+), 14 deletions(-)
Title: Lining Up Two Sets of Measurements
Description: Tools for detecting and correcting sample mix-ups between two sets
of measurements, such as between gene expression data on two tissues.
Broman et al. (2015) <doi:10.1534/g3.115.019778>.
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between lineup versions 0.42 dated 2022-07-10 and 0.44 dated 2024-07-15
DESCRIPTION | 10 - MD5 | 26 +-- NEWS.md | 10 + R/calc.locallod.R | 4 README.md | 3 build/vignette.rds |binary data/expr1.rda |binary data/expr2.rda |binary data/f2cross.rda |binary data/genepos.rda |binary data/pmap.rda |binary inst/CITATION | 16 +- inst/doc/lineup.html | 359 ++++++++++++++++----------------------------------- man/calc.locallod.Rd | 4 14 files changed, 157 insertions(+), 275 deletions(-)
Title: Structured Learning in Time-Dependent Cox Models
Description: Efficient procedures for fitting and cross-validating the structurally-regularized time-dependent Cox models.
Author: Yi Lian [aut, cre],
Guanbo Wang [aut],
Archer Y. Yang [aut],
Mireille E. Schnitzer [aut],
Robert W. Platt [aut],
Rui Wang [aut],
Marc Dorais [aut],
Sylvie Perreault [aut],
Julien Mairal [ctb],
Yuansi Chen [ctb]
Maintainer: Yi Lian <yi.lian@mail.mcgill.ca>
Diff between sox versions 1.1 dated 2023-12-11 and 1.2 dated 2024-07-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ inst/include/dictLearn/dicts.h | 2 +- inst/include/linalg/linalg.h | 4 ++-- inst/include/prox/fista.h | 24 ++++++++++++------------ man/sox-package.Rd | 1 - tests/testthat/test-sox.R | 1 + 7 files changed, 27 insertions(+), 27 deletions(-)
Title: Common Computational Operations Working with RefSeq Entries
(GenBank)
Description: Fetches NCBI data (RefSeq <https://www.ncbi.nlm.nih.gov/refseq/> database) and provides an environment to
extract information at the level of gene, mRNA or protein accessions.
Author: Jose V. Die [aut, cre] ,
Lluis Revilla Sancho [ctb]
Maintainer: Jose V. Die <jose.die@uco.es>
Diff between refseqR versions 1.0.2 dated 2024-05-22 and 1.1.2 dated 2024-07-15
refseqR-1.0.2/refseqR/R/refseq_XMfromXP.R |only refseqR-1.0.2/refseqR/R/refseq_XPfromXM.R |only refseqR-1.0.2/refseqR/R/refseq_XPlength.R |only refseqR-1.0.2/refseqR/R/refseq_fromXM.R |only refseqR-1.0.2/refseqR/R/refseq_geneSymbol.R |only refseqR-1.0.2/refseqR/R/refseq_mol_wt.R |only refseqR-1.0.2/refseqR/man/refseq_XMfromXP.Rd |only refseqR-1.0.2/refseqR/man/refseq_XPfromXM.Rd |only refseqR-1.0.2/refseqR/man/refseq_XPlength.Rd |only refseqR-1.0.2/refseqR/man/refseq_fromXM.Rd |only refseqR-1.0.2/refseqR/man/refseq_geneSymbol.Rd |only refseqR-1.0.2/refseqR/man/refseq_mol_wt.Rd |only refseqR-1.1.2/refseqR/DESCRIPTION | 6 - refseqR-1.1.2/refseqR/LICENSE | 2 refseqR-1.1.2/refseqR/MD5 | 65 +++++++------ refseqR-1.1.2/refseqR/NAMESPACE | 13 +- refseqR-1.1.2/refseqR/R/extract_feats.R |only refseqR-1.1.2/refseqR/R/refseqR.R | 2 refseqR-1.1.2/refseqR/R/refseq_AA_length.R |only refseqR-1.1.2/refseqR/R/refseq_AA_mol_wt.R |only refseqR-1.1.2/refseqR/R/refseq_AAseq.R | 22 ++-- refseqR-1.1.2/refseqR/R/refseq_CDScoords.R | 24 ++--- refseqR-1.1.2/refseqR/R/refseq_CDSseq.R | 18 ++- refseqR-1.1.2/refseqR/R/refseq_GeneID.R |only refseqR-1.1.2/refseqR/R/refseq_description.R | 24 ++--- refseqR-1.1.2/refseqR/R/refseq_fromGene.R | 109 +++++++++++++---------- refseqR-1.1.2/refseqR/R/refseq_mRNA2protein.R |only refseqR-1.1.2/refseqR/R/refseq_mRNAfeat.R |only refseqR-1.1.2/refseqR/R/refseq_protein2mRNA.R |only refseqR-1.1.2/refseqR/README.md |only refseqR-1.1.2/refseqR/inst/doc/refseqR.R | 38 ++++---- refseqR-1.1.2/refseqR/inst/doc/refseqR.Rmd | 82 ++++++++--------- refseqR-1.1.2/refseqR/inst/doc/refseqR.html | 76 ++++++++-------- refseqR-1.1.2/refseqR/man/extract_from_xm.Rd |only refseqR-1.1.2/refseqR/man/refseqR.Rd | 2 refseqR-1.1.2/refseqR/man/refseq_AA_length.Rd |only refseqR-1.1.2/refseqR/man/refseq_AA_mol_wt.Rd |only refseqR-1.1.2/refseqR/man/refseq_AAseq.Rd | 12 +- refseqR-1.1.2/refseqR/man/refseq_CDScoords.Rd | 18 ++- refseqR-1.1.2/refseqR/man/refseq_CDSseq.Rd | 12 +- refseqR-1.1.2/refseqR/man/refseq_GeneID.Rd |only refseqR-1.1.2/refseqR/man/refseq_description.Rd | 20 ++-- refseqR-1.1.2/refseqR/man/refseq_fromGene.Rd | 22 ++-- refseqR-1.1.2/refseqR/man/refseq_mRNA2protein.Rd |only refseqR-1.1.2/refseqR/man/refseq_mRNAfeat.Rd |only refseqR-1.1.2/refseqR/man/refseq_protein2mRNA.Rd |only refseqR-1.1.2/refseqR/vignettes/refseqR.Rmd | 82 ++++++++--------- 47 files changed, 342 insertions(+), 307 deletions(-)
Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data
Analysis Tools
Description: Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Author: Jan-Philipp Quast [aut, cre] ,
Dina Schuster [aut] ,
ETH Zurich [cph, fnd]
Maintainer: Jan-Philipp Quast <quast@imsb.biol.ethz.ch>
Diff between protti versions 0.8.0 dated 2024-03-28 and 0.9.0 dated 2024-07-15
DESCRIPTION | 6 MD5 | 74 +++---- NEWS.md | 24 ++ R/analyse_functional_network.R | 123 +++++++++---- R/calculate_go_enrichment.R | 69 ++++--- R/calculate_protein_abundance.R | 6 R/calculate_sequence_coverage.R | 1 R/fetch_alphafold_aligned_error.R | 23 +- R/fetch_alphafold_prediction.R | 13 + R/fetch_chebi.R | 10 - R/fetch_mobidb.R | 13 + R/fetch_quickgo.R | 33 +++ R/fetch_uniprot.R | 48 +++-- R/fetch_uniprot_proteome.R | 18 + R/find_peptide.R | 8 R/find_peptide_in_structure.R | 2 R/qc_cvs.R | 23 +- R/try_query.R | 42 ++-- inst/doc/data_analysis_dose_response_workflow.R | 7 inst/doc/data_analysis_dose_response_workflow.Rmd | 15 + inst/doc/data_analysis_dose_response_workflow.html | 61 ++++-- inst/doc/data_analysis_single_dose_treatment_workflow.html | 4 inst/doc/input_preparation_workflow.html | 4 inst/doc/protein_structure_workflow.html | 4 inst/doc/quality_control_workflow.html | 4 man/analyse_functional_network.Rd | 4 man/calculate_go_enrichment.Rd | 11 + man/calculate_protein_abundance.Rd | 5 man/fetch_alphafold_aligned_error.Rd | 10 - man/fetch_alphafold_prediction.Rd | 4 man/fetch_mobidb.Rd | 14 + man/fetch_quickgo.Rd | 8 man/fetch_uniprot.Rd | 7 man/fetch_uniprot_proteome.Rd | 14 + man/qc_cvs.Rd | 2 man/try_query.Rd | 2 tests/testthat/test-structure_functions.R | 2 vignettes/data_analysis_dose_response_workflow.Rmd | 15 + 38 files changed, 523 insertions(+), 210 deletions(-)
Title: Parallel Partitioning-Around-Medoids (PAM) for Big Sets of Data
Description: Application of the Partitioning-Around-Medoids (PAM) clustering algorithm described in Schubert, E. and Rousseeuw, P.J.:
"Fast and eager k-medoids clustering: O(k) runtime improvement of the PAM, CLARA, and CLARANS algorithms." Information Systems,
vol. 101, p. 101804, (2021). <doi:10.1016/j.is.2021.101804>.
It uses a binary format for storing and retrieval of matrices developed for the 'jmatrix' package but the functionality of 'jmatrix'
is included here, so you do not need to install it. Also, it is used by package 'scellpam', so if you have installed it, you do not need
to install this package.
PAM can be applied to sets of data whose dissimilarity matrix can be very big. It has been tested with up to 100.000 points.
It does this with the help of the code developed for other package, 'jmatrix', which allows the matrix not to be loaded in 'R' memory (which
would force it to be of double type) but it gets from disk, which allows using float (or even smaller data types). Moreover [...truncated...]
Author: Juan Domingo [aut, cre] ,
Guillermo Ayala [ctb] ,
Spanish Ministry of Science and Innovation, MCIN/AEI
<doi:10.13039/501100011033> [fnd]
Maintainer: Juan Domingo <Juan.Domingo@uv.es>
Diff between parallelpam versions 1.4.2 dated 2024-07-01 and 1.4.3 dated 2024-07-15
DESCRIPTION | 8 +- MD5 | 10 +- NEWS | 4 + inst/doc/jmatrixpp.html | 148 ++++++++++++++++++++++---------------------- inst/doc/parallelpam.html | 148 ++++++++++++++++++++++---------------------- inst/include/sparsematrix.h | 4 - 6 files changed, 165 insertions(+), 157 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface from within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating time spent and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.1.1 dated 2024-07-03 and 0.1.2 dated 2024-07-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 +++++- tests/testthat/test_NMsim.R | 2 ++ 4 files changed, 13 insertions(+), 7 deletions(-)
Title: Generating Features for a Cohort
Description: An R interface for generating features for a cohort using data in the Common Data Model. Features can be constructed using default or custom made feature definitions. Furthermore it's possible to aggregate features and get the summary statistics.
Author: Martijn Schuemie [aut],
Marc Suchard [aut],
Patrick Ryan [aut],
Jenna Reps [aut],
Anthony Sena [aut],
Ger Inberg [aut, cre],
Observational Health Data Science and Informatics [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between FeatureExtraction versions 3.5.2 dated 2024-05-01 and 3.6.0 dated 2024-07-15
FeatureExtraction-3.5.2/FeatureExtraction/inst/java/featureExtraction-3.5.0-SNAPSHOT.jar |only FeatureExtraction-3.6.0/FeatureExtraction/DESCRIPTION | 10 FeatureExtraction-3.6.0/FeatureExtraction/MD5 | 69 +-- FeatureExtraction-3.6.0/FeatureExtraction/NEWS.md | 12 FeatureExtraction-3.6.0/FeatureExtraction/R/CovariateData.R | 2 FeatureExtraction-3.6.0/FeatureExtraction/R/DefaultCovariateSettings.R | 46 +- FeatureExtraction-3.6.0/FeatureExtraction/R/DefaultTemporalCovariateSettings.R | 14 FeatureExtraction-3.6.0/FeatureExtraction/R/GetCovariates.R | 6 FeatureExtraction-3.6.0/FeatureExtraction/R/GetDefaultCovariates.R | 11 FeatureExtraction-3.6.0/FeatureExtraction/R/Normalization.R | 4 FeatureExtraction-3.6.0/FeatureExtraction/inst/csv/PrespecAnalyses.csv | 222 +++++----- FeatureExtraction-3.6.0/FeatureExtraction/inst/csv/PrespecTemporalAnalyses.csv | 86 +-- FeatureExtraction-3.6.0/FeatureExtraction/inst/csv/jarChecksum.txt | 2 FeatureExtraction-3.6.0/FeatureExtraction/inst/doc/CreatingCovariatesBasedOnOtherCohorts.pdf |binary FeatureExtraction-3.6.0/FeatureExtraction/inst/doc/CreatingCovariatesUsingCohortAttributes.pdf |binary FeatureExtraction-3.6.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuilders.R | 3 FeatureExtraction-3.6.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuilders.Rmd | 5 FeatureExtraction-3.6.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuilders.pdf |binary FeatureExtraction-3.6.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuildersKorean.pdf |binary FeatureExtraction-3.6.0/FeatureExtraction/inst/doc/UsingFeatureExtraction.pdf |binary FeatureExtraction-3.6.0/FeatureExtraction/inst/doc/UsingFeatureExtractionKorean.pdf |binary FeatureExtraction-3.6.0/FeatureExtraction/inst/java/FeatureExtraction.jar |only FeatureExtraction-3.6.0/FeatureExtraction/inst/sql/sql_server/CreateCovAnalysisRefTables.sql | 4 FeatureExtraction-3.6.0/FeatureExtraction/inst/sql/sql_server/MeasObsValueAsConcept.sql |only FeatureExtraction-3.6.0/FeatureExtraction/java/org/ohdsi/featureExtraction/FeatureExtraction.java | 2 FeatureExtraction-3.6.0/FeatureExtraction/man/createCovariateSettings.Rd | 50 ++ FeatureExtraction-3.6.0/FeatureExtraction/man/createTemporalCovariateSettings.Rd | 16 FeatureExtraction-3.6.0/FeatureExtraction/man/getDbCovariateData.Rd | 8 FeatureExtraction-3.6.0/FeatureExtraction/tests/testBigQuery.R |only FeatureExtraction-3.6.0/FeatureExtraction/tests/testOracle.R | 4 FeatureExtraction-3.6.0/FeatureExtraction/tests/testPostgres.R | 4 FeatureExtraction-3.6.0/FeatureExtraction/tests/testRedshift.R | 4 FeatureExtraction-3.6.0/FeatureExtraction/tests/testSnowflake.R |only FeatureExtraction-3.6.0/FeatureExtraction/tests/testSpark.R |only FeatureExtraction-3.6.0/FeatureExtraction/tests/testSqlServer.R | 4 FeatureExtraction-3.6.0/FeatureExtraction/tests/testthat/setup.R | 111 +++-- FeatureExtraction-3.6.0/FeatureExtraction/tests/testthat/test-PostcoordConcepts.R |only FeatureExtraction-3.6.0/FeatureExtraction/tests/testthat/test-query-no-fail.R | 20 FeatureExtraction-3.6.0/FeatureExtraction/vignettes/CreatingCustomCovariateBuilders.Rmd | 5 39 files changed, 481 insertions(+), 243 deletions(-)
More information about FeatureExtraction at CRAN
Permanent link
Title: Physics-Informed Spatial and Functional Data Analysis
Description: An implementation of regression models with partial differential regularizations, making use of the Finite Element Method. The models efficiently handle data distributed over irregularly shaped domains and can comply with various conditions at the boundaries of the domain. A priori information about the spatial structure of the phenomenon under study can be incorporated in the model via the differential regularization. See Sangalli, L. M. (2021) <doi:10.1111/insr.12444> "Spatial Regression With Partial Differential Equation Regularisation" for an overview. The release 1.1-9 requires R (>= 4.2.0) to be installed on windows machines.
Author: Eleonora Arnone [aut, cre],
Aldo Clemente [aut],
Laura M. Sangalli [aut],
Eardi Lila [aut],
Jim Ramsay [aut],
Luca Formaggia [aut],
Giovanni Ardenghi [ctb],
Blerta Begu [ctb],
Michele Cavazzutti [ctb],
Alessandra Colli [ctb],
Alberto Colombo [ctb],
L [...truncated...]
Maintainer: Eleonora Arnone <eleonora.arnone@polimi.it>
Diff between fdaPDE versions 1.1-18 dated 2024-05-30 and 1.1-19 dated 2024-07-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/Lambda_Optimization/Include/Lambda_Optimizer.h | 6 +++--- src/Regression/Include/Mixed_FE_Regression_imp.h | 18 +++++++++--------- 4 files changed, 19 insertions(+), 19 deletions(-)
Title: Covariance Regression with Random Forests
Description: Covariance Regression with Random Forests (CovRegRF) is a
random forest method for estimating the covariance matrix of a
multivariate response given a set of covariates. Random forest trees
are built with a new splitting rule which is designed to maximize the
distance between the sample covariance matrix estimates of the child
nodes. The method is described in Alakus et al. (2023)
<doi:10.1186/s12859-023-05377-y>. 'CovRegRF' uses 'randomForestSRC' package
(Ishwaran and Kogalur, 2022)
<https://cran.r-project.org/package=randomForestSRC> by freezing at the
version 3.1.0. The custom splitting rule feature is utilised to apply the
proposed splitting rule. The 'randomForestSRC' package implements 'OpenMP'
by default, contingent upon the support provided by the target architecture
and operating system. In this package, 'LAPACK' and 'BLAS' libraries are
used for matrix decompositions.
Author: Cansu Alakus [aut, cre],
Denis Larocque [aut],
Aurelie Labbe [aut],
Hemant Ishwaran [ctb] ,
Udaya B. Kogalur [ctb] ,
Intel Corporation [cph] ,
Keita Teranishi [ctb]
Maintainer: Cansu Alakus <cansu.alakus@hec.ca>
Diff between CovRegRF versions 2.0.0 dated 2024-02-13 and 2.0.1 dated 2024-07-15
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 3 +++ configure | 18 +++++++++--------- configure.ac | 2 +- src/randomForestSRC.c | 12 ++++++------ 6 files changed, 27 insertions(+), 24 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-13 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-02 0.4.2
2021-01-06 0.4.1
2020-11-23 0.4.0
Title: Easily Build Command Line Applications
Description: Run simple 'R' scripts as command line applications, with
automatic robust and convenient support for command line arguments.
This package provides 'Rapp', an alternative 'R' front-end similar to
'Rscript', that enables this.
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between Rapp versions 0.1.0 dated 2023-03-20 and 0.2.0 dated 2024-07-15
DESCRIPTION | 10 ++-- MD5 | 28 +++++++------ NAMESPACE | 4 + NEWS.md |only R/app.R | 8 +-- R/args.R | 91 ++++++++++++++++++++++++++++++++++++------- R/utils.R | 24 +++++++++++ R/yaml.R | 13 +++--- README.md | 39 ++++++++++++------ inst/examples/flip-coin.R | 6 +- inst/examples/magic-8-ball.R | 10 +++- inst/examples/unique.R | 15 +++++-- man/figures |only man/run.Rd | 2 tests/testthat/test-basics.R | 2 15 files changed, 189 insertions(+), 63 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between performance versions 0.12.0 dated 2024-06-08 and 0.12.1 dated 2024-07-15
performance-0.12.0/performance/tests/testthat/test-logLik.R |only performance-0.12.1/performance/DESCRIPTION | 31 +- performance-0.12.1/performance/MD5 | 76 ++--- performance-0.12.1/performance/NAMESPACE | 4 performance-0.12.1/performance/NEWS.md | 61 +++- performance-0.12.1/performance/R/check_distribution.R | 14 - performance-0.12.1/performance/R/check_homogeneity.R | 8 performance-0.12.1/performance/R/check_multimodal.R | 24 - performance-0.12.1/performance/R/check_predictions.R | 12 performance-0.12.1/performance/R/helpers.R | 2 performance-0.12.1/performance/R/icc.R | 108 +++++--- performance-0.12.1/performance/R/performance_rmse.R | 133 ++++++++-- performance-0.12.1/performance/R/r2.R | 35 ++ performance-0.12.1/performance/R/r2_bayes.R | 91 ++++-- performance-0.12.1/performance/R/r2_ferarri.R |only performance-0.12.1/performance/R/r2_mcfadden.R | 7 performance-0.12.1/performance/R/r2_nakagawa.R | 86 +++++- performance-0.12.1/performance/README.md | 47 +-- performance-0.12.1/performance/build/partial.rdb |binary performance-0.12.1/performance/inst/WORDLIST | 5 performance-0.12.1/performance/man/figures/unnamed-chunk-14-1.png |binary performance-0.12.1/performance/man/figures/unnamed-chunk-20-1.png |binary performance-0.12.1/performance/man/icc.Rd | 102 ++++++- performance-0.12.1/performance/man/performance_mae.Rd | 4 performance-0.12.1/performance/man/performance_mse.Rd | 4 performance-0.12.1/performance/man/performance_rmse.Rd | 44 +++ performance-0.12.1/performance/man/r2.Rd | 13 performance-0.12.1/performance/man/r2_bayes.Rd | 45 ++- performance-0.12.1/performance/man/r2_ferrari.Rd |only performance-0.12.1/performance/man/r2_nakagawa.Rd | 99 ++++++- performance-0.12.1/performance/tests/testthat/_snaps/check_distribution.md | 40 +-- performance-0.12.1/performance/tests/testthat/test-check_model.R | 10 performance-0.12.1/performance/tests/testthat/test-check_predictions.R | 15 + performance-0.12.1/performance/tests/testthat/test-helpers.R | 2 performance-0.12.1/performance/tests/testthat/test-icc.R | 20 - performance-0.12.1/performance/tests/testthat/test-model_performance.bayesian.R | 27 +- performance-0.12.1/performance/tests/testthat/test-model_performance.merMod.R | 2 performance-0.12.1/performance/tests/testthat/test-r2_bayes.R | 14 + performance-0.12.1/performance/tests/testthat/test-r2_ferrari.R |only performance-0.12.1/performance/tests/testthat/test-r2_nakagawa.R | 1 performance-0.12.1/performance/tests/testthat/test-rmse.R | 25 + 41 files changed, 882 insertions(+), 329 deletions(-)
Title: Animal Dominance Hierarchies by Elo Rating
Description: Provides functions to quantify animal dominance hierarchies. The major focus is on Elo rating and its ability to deal with temporal dynamics in dominance interaction sequences. For static data, David's score and de Vries' I&SI are also implemented. In addition, the package provides functions to assess transitivity, linearity and stability of dominance networks. See Neumann et al (2011) <doi:10.1016/j.anbehav.2011.07.016> for an introduction.
Author: Christof Neumann [aut, cre] ,
Lars Kulik [aut]
Maintainer: Christof Neumann <christofneumann1@gmail.com>
Diff between EloRating versions 0.46.11 dated 2020-03-12 and 0.46.18 dated 2024-07-15
EloRating-0.46.11/EloRating/R/elo.seq.R |only EloRating-0.46.18/EloRating/DESCRIPTION | 10 EloRating-0.46.18/EloRating/MD5 | 278 EloRating-0.46.18/EloRating/NAMESPACE | 174 EloRating-0.46.18/EloRating/R/CBI.R | 266 EloRating-0.46.18/EloRating/R/DCindex.R | 60 EloRating-0.46.18/EloRating/R/DS.R | 128 EloRating-0.46.18/EloRating/R/ISI-diffmat.R | 46 EloRating-0.46.18/EloRating/R/ISI-incon.R | 45 EloRating-0.46.18/EloRating/R/ISI-incontable.R | 109 EloRating-0.46.18/EloRating/R/ISI-sincon.R | 55 EloRating-0.46.18/EloRating/R/ISI.R | 422 - EloRating-0.46.18/EloRating/R/ISIranks.R | 90 EloRating-0.46.18/EloRating/R/RcppExports.R | 32 EloRating-0.46.18/EloRating/R/adv-data.R | 34 EloRating-0.46.18/EloRating/R/adv2-data.R | 36 EloRating-0.46.18/EloRating/R/advpres-data.R | 36 EloRating-0.46.18/EloRating/R/baboons-data.R | 38 EloRating-0.46.18/EloRating/R/bonobo-data.R | 36 EloRating-0.46.18/EloRating/R/coresidence.R | 258 EloRating-0.46.18/EloRating/R/correctly_predicted.R | 308 - EloRating-0.46.18/EloRating/R/creatematrix.R | 309 - EloRating-0.46.18/EloRating/R/createstartvalues.R | 160 EloRating-0.46.18/EloRating/R/devries98-data.R | 34 EloRating-0.46.18/EloRating/R/dommats-data.R | 48 EloRating-0.46.18/EloRating/R/dyadic_dom.R | 96 EloRating-0.46.18/EloRating/R/dyadic_reversals.R | 200 EloRating-0.46.18/EloRating/R/e.single.R | 160 EloRating-0.46.18/EloRating/R/elo.seq.r |only EloRating-0.46.18/EloRating/R/elo.seq_old.r | 1065 +-- EloRating-0.46.18/EloRating/R/eloplot.r | 360 - EloRating-0.46.18/EloRating/R/extract_elo.R | 318 - EloRating-0.46.18/EloRating/R/h.index.R | 232 EloRating-0.46.18/EloRating/R/heatmapplot.R | 244 EloRating-0.46.18/EloRating/R/individuals.r | 164 EloRating-0.46.18/EloRating/R/lastdaypresent.R | 127 EloRating-0.46.18/EloRating/R/likelo.R | 208 EloRating-0.46.18/EloRating/R/mat2seq.R | 70 EloRating-0.46.18/EloRating/R/optimizek.R | 276 EloRating-0.46.18/EloRating/R/optistart.R | 164 EloRating-0.46.18/EloRating/R/presence_summary.R | 158 EloRating-0.46.18/EloRating/R/print.elo.R | 40 EloRating-0.46.18/EloRating/R/print.seqchecknopres.r | 54 EloRating-0.46.18/EloRating/R/print.sequencecheck.r | 146 EloRating-0.46.18/EloRating/R/prunk.R | 214 EloRating-0.46.18/EloRating/R/randomelo.R | 186 EloRating-0.46.18/EloRating/R/randomeloextract.R | 96 EloRating-0.46.18/EloRating/R/randomsequence.R | 368 - EloRating-0.46.18/EloRating/R/scale_elo.R | 54 EloRating-0.46.18/EloRating/R/seqcheck.R | 608 +- EloRating-0.46.18/EloRating/R/simple_dom.R | 118 EloRating-0.46.18/EloRating/R/stab_elo.R | 104 EloRating-0.46.18/EloRating/R/steepness.R | 104 EloRating-0.46.18/EloRating/R/summary.elo.R | 58 EloRating-0.46.18/EloRating/R/traj_elo.r | 144 EloRating-0.46.18/EloRating/R/transitivity.R | 240 EloRating-0.46.18/EloRating/R/winprob.r | 192 EloRating-0.46.18/EloRating/R/z_helpers.R |only EloRating-0.46.18/EloRating/README.md | 50 EloRating-0.46.18/EloRating/build/partial.rdb |binary EloRating-0.46.18/EloRating/build/vignette.rds |binary EloRating-0.46.18/EloRating/inst/NEWS.Rd | 274 EloRating-0.46.18/EloRating/inst/REFERENCES.bib | 734 +- EloRating-0.46.18/EloRating/inst/doc/EloRating_tutorial.R | 1841 +++--- EloRating-0.46.18/EloRating/inst/doc/EloRating_tutorial.Rmd | 2784 ++++------ EloRating-0.46.18/EloRating/inst/doc/EloRating_tutorial.pdf |binary EloRating-0.46.18/EloRating/inst/ex-parasites.txt | 94 EloRating-0.46.18/EloRating/inst/ex-sequence.txt | 502 - EloRating-0.46.18/EloRating/man/CBI.Rd | 198 EloRating-0.46.18/EloRating/man/DCindex.Rd | 66 EloRating-0.46.18/EloRating/man/DS.Rd | 70 EloRating-0.46.18/EloRating/man/EloRating-package.Rd | 58 EloRating-0.46.18/EloRating/man/ISI.Rd | 106 EloRating-0.46.18/EloRating/man/ISIranks.Rd | 76 EloRating-0.46.18/EloRating/man/adv.Rd | 44 EloRating-0.46.18/EloRating/man/adv2.Rd | 44 EloRating-0.46.18/EloRating/man/advpres.Rd | 44 EloRating-0.46.18/EloRating/man/baboons1.Rd | 64 EloRating-0.46.18/EloRating/man/bonobos.Rd | 44 EloRating-0.46.18/EloRating/man/coresidence.Rd | 118 EloRating-0.46.18/EloRating/man/correctly_predicted.Rd | 262 EloRating-0.46.18/EloRating/man/creatematrix.Rd | 147 EloRating-0.46.18/EloRating/man/createstartvalues.Rd | 116 EloRating-0.46.18/EloRating/man/devries98.Rd | 44 EloRating-0.46.18/EloRating/man/dommats.Rd | 62 EloRating-0.46.18/EloRating/man/dot-diffmat.Rd | 56 EloRating-0.46.18/EloRating/man/dot-elo.seq_old.Rd | 168 EloRating-0.46.18/EloRating/man/dot-incon.Rd | 56 EloRating-0.46.18/EloRating/man/dot-sincon.Rd | 62 EloRating-0.46.18/EloRating/man/dyadic_dom.Rd | 54 EloRating-0.46.18/EloRating/man/dyadic_reversals.Rd | 88 EloRating-0.46.18/EloRating/man/e.single.Rd | 94 EloRating-0.46.18/EloRating/man/elo.seq.Rd | 288 - EloRating-0.46.18/EloRating/man/eloplot.Rd | 96 EloRating-0.46.18/EloRating/man/extract_elo.Rd | 148 EloRating-0.46.18/EloRating/man/h.index.Rd | 70 EloRating-0.46.18/EloRating/man/heatmapplot.Rd | 130 EloRating-0.46.18/EloRating/man/incontable.Rd | 56 EloRating-0.46.18/EloRating/man/individuals.Rd | 112 EloRating-0.46.18/EloRating/man/lastdaypresent.Rd | 69 EloRating-0.46.18/EloRating/man/likelo.Rd | 112 EloRating-0.46.18/EloRating/man/mat2seq.Rd | 64 EloRating-0.46.18/EloRating/man/optimizek.Rd | 148 EloRating-0.46.18/EloRating/man/optistart.Rd | 114 EloRating-0.46.18/EloRating/man/presence_summary.Rd | 64 EloRating-0.46.18/EloRating/man/print.elo.Rd | 48 EloRating-0.46.18/EloRating/man/print.seqchecknopres.Rd | 46 EloRating-0.46.18/EloRating/man/print.sequencecheck.Rd | 50 EloRating-0.46.18/EloRating/man/prunk.Rd | 58 EloRating-0.46.18/EloRating/man/randomelo.Rd | 104 EloRating-0.46.18/EloRating/man/randomeloextract.Rd | 72 EloRating-0.46.18/EloRating/man/randomsequence.Rd | 108 EloRating-0.46.18/EloRating/man/scale_elo.Rd | 60 EloRating-0.46.18/EloRating/man/seqcheck.Rd | 216 EloRating-0.46.18/EloRating/man/simple_dom.Rd | 70 EloRating-0.46.18/EloRating/man/stab_elo.Rd | 100 EloRating-0.46.18/EloRating/man/steepness.Rd | 76 EloRating-0.46.18/EloRating/man/summary.elo.Rd | 52 EloRating-0.46.18/EloRating/man/traj_elo.Rd | 98 EloRating-0.46.18/EloRating/man/transitivity.Rd | 60 EloRating-0.46.18/EloRating/man/winprob.Rd | 170 EloRating-0.46.18/EloRating/src/Makevars.win | 2 EloRating-0.46.18/EloRating/src/RcppExports.cpp | 5 EloRating-0.46.18/EloRating/tests/testthat.R | 8 EloRating-0.46.18/EloRating/tests/testthat/test-ISI.R | 88 EloRating-0.46.18/EloRating/tests/testthat/test-correctly_predicted.R | 64 EloRating-0.46.18/EloRating/tests/testthat/test-dyadic_dom.R | 44 EloRating-0.46.18/EloRating/tests/testthat/test-dyadic_reversals.R | 36 EloRating-0.46.18/EloRating/tests/testthat/test-elo.R |only EloRating-0.46.18/EloRating/tests/testthat/test_DS.R | 26 EloRating-0.46.18/EloRating/tests/testthat/test_comparisontooldversion.R | 162 EloRating-0.46.18/EloRating/tests/testthat/test_conversions.R | 52 EloRating-0.46.18/EloRating/tests/testthat/test_customelo.R | 102 EloRating-0.46.18/EloRating/tests/testthat/test_customelopresence.R | 240 EloRating-0.46.18/EloRating/tests/testthat/test_e.single.R | 8 EloRating-0.46.18/EloRating/tests/testthat/test_extract_elo.R | 102 EloRating-0.46.18/EloRating/tests/testthat/test_fastelo.R | 78 EloRating-0.46.18/EloRating/tests/testthat/test_mat2seq.R | 32 EloRating-0.46.18/EloRating/tests/testthat/test_misc.R |only EloRating-0.46.18/EloRating/tests/testthat/test_optimizek.R | 56 EloRating-0.46.18/EloRating/tests/testthat/test_seqcheck.R |only EloRating-0.46.18/EloRating/tests/testthat/test_transitivity.R | 66 EloRating-0.46.18/EloRating/vignettes/EloRating_tutorial.Rmd | 2784 ++++------ 143 files changed, 12397 insertions(+), 12417 deletions(-)
Title: Consistency in the Analytic Hierarchy Process
Description: A Swiss Army knife of utility functions for users of the Analytic
Hierarchy Process (AHP) which will help you to assess the consistency of a
PCM as well as to improve its consistency ratio, to compute the sensitivity
of a PCM, create a logical (as distinct from a random PCM) from preferences
provided for the alternatives, and a function that helps evaluate the actual
consistency of a PCM based on objective, fair bench marking. The various
functions in the toolkit additionally provide the flexibility to users to
specify only the upper triangular comparison ratios of the PCM in order to
performs its assigned task.
Author: Amarnath Bose [aut, cre]
Maintainer: Amarnath Bose <amarnath.bose@gmail.com>
Diff between AHPtools versions 0.2.1 dated 2023-11-02 and 0.3.0 dated 2024-07-15
DESCRIPTION | 16 ++--- MD5 | 25 +++++--- NAMESPACE | 4 + NEWS.md | 4 + R/AHPtools-package.R |only R/AHPtools.R | 117 +++++++++++++++++++++++++++++++++++++++++ R/logitModel.R |only build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 15 +++-- inst/doc/AHPtools.R | 2 inst/doc/AHPtools.html | 4 - man/AHPtools-package.Rd |only man/consEval.Rd |only man/logitModel.Rd |only tests/testthat/test-AHPtools.R | 29 +++++++++- 16 files changed, 187 insertions(+), 29 deletions(-)
Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression
models with missing values in covariates or the dependent
variable using maximum likelihood or Bayesian estimation
(Ibrahim et al., 2005; <doi:10.1198/016214504000001844>;
Luedtke, Robitzsch, & West, 2020a, 2020b;
<doi:10.1080/00273171.2019.1640104><doi:10.1037/met0000233>).
The regression model can be nonlinear (e.g., interaction
effects, quadratic effects or B-spline functions).
Multilevel models with missing data in predictors are
available for Bayesian estimation. Substantive-model compatible
multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between mdmb versions 1.8-7 dated 2023-02-28 and 1.9-22 dated 2024-07-15
DESCRIPTION | 8 MD5 | 202 +++++++++++------------ R/RcppExports.R | 2 R/bct_regression.R | 4 R/dbct_scaled.R | 6 R/dyjt_scaled.R | 10 - R/eval_prior_list.R | 6 R/eval_prior_list_gradient_log.R | 17 - R/eval_prior_list_sumlog.R | 10 - R/fit_bct_scaled.R | 4 R/fit_mdmb_distribution.R | 44 ++--- R/fit_mdmb_distribution_extract_results.R | 4 R/fit_mdmb_distribution_logLik_extract.R | 8 R/fit_mdmb_distribution_summary.R | 28 +-- R/fit_mdmb_distribution_summary_table.R | 4 R/fit_oprobit.R | 4 R/fit_t_scaled.R | 4 R/fit_yjt_scaled.R | 4 R/frm2datlist.R | 8 R/frm_append_list.R | 4 R/frm_check_predictor_matrix.R | 10 - R/frm_define_model_R_function.R | 52 ++--- R/frm_descriptives_variables.R | 11 - R/frm_em.R | 21 +- R/frm_em_avcov.R | 43 ++-- R/frm_em_calc_likelihood.R | 28 +-- R/frm_em_calc_likelihood_estimate_model.R | 10 - R/frm_em_ic.R | 6 R/frm_em_linreg_density_extend_args.R | 4 R/frm_em_summary_print_nodes.R | 14 - R/frm_fb.R | 18 +- R/frm_fb_descriptives_variables.R | 15 - R/frm_fb_init_imputations.R | 17 - R/frm_fb_initial_parameters.R | 31 +-- R/frm_fb_initial_parameters_se_sd_proposal.R | 4 R/frm_fb_mh_refresh_imputed_values.R | 8 R/frm_fb_mh_refresh_parameters.R | 15 - R/frm_fb_partable.R | 39 ++-- R/frm_fb_sample_imputed_values.R | 20 +- R/frm_fb_sample_imputed_values_eval_likelihood.R | 6 R/frm_fb_sample_imputed_values_proposal.R | 20 +- R/frm_fb_sample_parameter_step.R | 4 R/frm_fb_sample_parameters.R | 16 - R/frm_fb_sample_parameters_df_squeeze.R | 4 R/frm_fb_verbose_iterations.R | 16 - R/frm_fb_verbose_mh_refresh.R | 6 R/frm_formula_character.R | 6 R/frm_formula_extract_terms.R | 7 R/frm_linreg_density.R | 6 R/frm_linreg_sample_parameters.R | 6 R/frm_mdmb_regression_density.R | 15 - R/frm_mlreg_density.R | 6 R/frm_mlreg_wrapper_ml_mcmc.R | 7 R/frm_modify_parameter_labels.R | 16 - R/frm_oprobit_density.R | 4 R/frm_partable_thresholds.R | 8 R/frm_prepare_data_em.R | 13 - R/frm_prepare_data_fb.R | 18 +- R/frm_prepare_data_include_latent_data.R | 22 -- R/frm_prepare_model_nodes_weights.R | 38 ++-- R/frm_prepare_models.R | 12 - R/frm_prepare_models_design_matrices.R | 11 - R/frm_prepare_models_sigma_fixed.R | 4 R/frm_proposal_refresh_helper.R | 4 R/logLik_extract_ic.R | 8 R/logistic_regression.R | 6 R/mdmb_extract_coef.R | 4 R/mdmb_ginv.R | 4 R/mdmb_optim.R | 6 R/mdmb_optim_control.R | 10 - R/mdmb_regression.R | 66 +++---- R/mdmb_regression_R2.R | 16 - R/mdmb_regression_est_df_description.R | 6 R/mdmb_regression_extract_parameters.R | 6 R/mdmb_regression_loglike_case.R | 10 - R/mdmb_regression_loglike_logpost.R | 6 R/mdmb_regression_oprobit_density.R | 8 R/mdmb_regression_optim_oprobit_grad.R | 4 R/mdmb_regression_predict.R | 16 - R/mdmb_regression_predict_yjt_bct.R | 6 R/mdmb_regression_proc_control_optim_fct.R | 5 R/mdmb_regression_summary.R | 92 +++++----- R/mdmb_regression_summary_table.R | 4 R/mdmb_sample_missings.R | 4 R/mdmb_summary_print_computation_time.R | 6 R/offset_values_extract.R | 6 R/oprobit_regression.R | 6 R/plot.frm_fb.R | 22 +- R/summary.frm_em.R | 74 ++++---- R/summary.frm_fb.R | 56 +++--- R/yjt_regression.R | 4 build/partial.rdb |binary data/data.mb01.rda |binary data/data.mb02.rda |binary data/data.mb03.rda |binary data/data.mb04.rda |binary data/data.mb05.rda |binary inst/CITATION | 3 inst/NEWS | 10 + man/data.mb.Rd | 4 man/frm.Rd | 5 src/RcppExports.cpp | 2 102 files changed, 738 insertions(+), 769 deletions(-)
Title: Quality Control for RNA-Seq Data
Description: Functions for semi-automated quality control of bulk RNA-seq data.
Author: Frederik Ziebell [cre],
Frederik Ziebell [aut] ,
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Frederik Ziebell <f_ziebell@web.de>
Diff between RNAseqQC versions 0.2.0 dated 2024-07-01 and 0.2.1 dated 2024-07-15
DESCRIPTION | 6 ++-- MD5 | 12 ++++----- NEWS.md | 3 ++ R/pca.R | 22 +++++++++------- README.md | 5 +++ inst/doc/introduction.html | 60 ++++++++++++++++++++++----------------------- man/all_numeric.Rd | 6 ++-- 7 files changed, 63 insertions(+), 51 deletions(-)
Title: Construct Process Maps Using Event Data
Description: Visualize event logs using directed graphs, i.e. process maps. Part of the 'bupaR' framework.
Author: Gert Janssenswillen [aut, cre],
Gerard van Hulzen [ctb],
Benoît Depaire [ctb],
Felix Mannhardt [ctb],
Thijs Beuving [ctb],
urvikalia [ctb],
Hasselt University [cph]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between processmapR versions 0.5.3 dated 2023-04-06 and 0.5.4 dated 2024-07-15
DESCRIPTION | 17 ++--- MD5 | 73 +++++++++++++++++----- NAMESPACE | 1 R/dotted_chart.R | 4 - R/dotted_chart_helpers.R | 2 R/layout.R | 2 R/process_map.R | 150 ++++++++++++++++++++-------------------------- R/processmapR.R | 1 R/render_map.R | 100 ++++++++++++++++++++++++++++++ R/trace_explorer.R | 2 R/utils_animateR.R |only README.md | 7 +- inst/doc/processmapr.html | 4 - inst/htmlwidgets |only man/dotted_chart.Rd | 4 - man/layout_pm.Rd | 2 man/lined_chart.Rd | 4 - man/process_map.Rd | 6 - man/trace_explorer.Rd | 4 - 19 files changed, 252 insertions(+), 131 deletions(-)
Title: Feature Stores for the 'diseasy' Framework
Description: Simple feature stores and tools for creating personalised feature stores.
'diseasystore' powers feature stores which can automatically link and aggregate features to a given stratification
level. These feature stores are automatically time-versioned (powered by the 'SCDB' package) and allows you to easily
and dynamically compute features as part of your continuous integration.
Author: Rasmus Skytte Randloev [aut, cre]
,
Marcus Munch Gruenewald [ctb] ,
Kaare Graesboell [rev] ,
Kasper Schou Telkamp [rev] ,
Lasse Engbo Christiansen [rev]
,
Sofia Myrup Otero [rev],
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between diseasystore versions 0.2.1 dated 2024-04-22 and 0.2.2 dated 2024-07-15
DESCRIPTION | 8 MD5 | 26 +-- NEWS.md | 166 ++++++++++---------- R/0_R6_utils.R | 2 R/0_linters.R | 12 - R/grapes-.-grapes.R | 20 +- build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/diseasystore-ecdc-respiratory-viruses.html | 4 inst/doc/diseasystore-google-covid-19.html | 4 inst/doc/diseasystore.html | 124 +++++++------- tests/testthat/helper-setup.R | 2 tests/testthat/test-grapes-.-grapes.R | 35 ++++ tests/testthat/test-truncate_interlace.R | 43 +++-- 14 files changed, 264 insertions(+), 189 deletions(-)
Title: Some Latent Variable Models
Description: Includes some procedures for latent variable modeling with a
particular focus on multilevel data.
The 'LAM' package contains mean and covariance structure modelling
for multivariate normally distributed data (mlnormal(); Longford, 1987;
<doi:10.1093/biomet/74.4.817>), a general Metropolis-Hastings algorithm
(amh(); Roberts & Rosenthal, 2001, <doi:10.1214/ss/1015346320>) and
penalized maximum likelihood estimation (pmle(); Cole, Chu & Greenland,
2014; <doi:10.1093/aje/kwt245>).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between LAM versions 0.6-19 dated 2022-05-18 and 0.7-22 dated 2024-07-15
DESCRIPTION | 8 - MD5 | 136 ++++++++++++++-------------- R/RcppExports.R | 2 R/amh.R | 50 +++++----- R/amh_compare_estimators.R | 16 +-- R/amh_eval_priors.R | 4 R/amh_ic.R | 8 - R/amh_init_acceptance_parameters.R | 4 R/amh_proposal_refresh.R | 15 +-- R/amh_sampling.R | 20 ++-- R/clpm_to_ctm.R | 8 - R/clpm_to_ctm_drift_to_paths.R | 4 R/clpm_to_ctm_paths_to_drift.R | 4 R/confint.amh.R | 15 +-- R/confint.mlnormal.R | 14 +- R/confint.pmle.R | 12 +- R/logLik_lam.R | 8 - R/loglike_mvnorm_NA_pattern.R | 10 +- R/loglike_mvnorm_NA_pattern_R.R | 4 R/loglike_mvnorm_R.R | 6 - R/mlnormal.R | 31 +++--- R/mlnormal_check_matrix_list_difference.R | 7 - R/mlnormal_create_disp.R | 6 - R/mlnormal_equal_list_matrices.R | 4 R/mlnormal_eval_penalty_update_theta.R | 7 - R/mlnormal_eval_priors.R | 4 R/mlnormal_fill_matrix_from_list.R | 16 +-- R/mlnormal_fit_function_ml.R | 7 - R/mlnormal_ic.R | 7 - R/mlnormal_information_matrix_reml.R | 26 ++--- R/mlnormal_matrix2list.R | 13 +- R/mlnormal_postproc_eval_posterior.R | 4 R/mlnormal_postproc_parameters.R | 35 +++---- R/mlnormal_proc.R | 57 +++++------ R/mlnormal_proc_variance_shortcut.R | 20 ++-- R/mlnormal_proc_variance_shortcut_XY_R.R | 21 ++-- R/mlnormal_proc_variance_shortcut_Z_R.R | 44 ++++----- R/mlnormal_proc_variance_shortcut_Z_Rcpp.R | 26 ++--- R/mlnormal_process_prior.R | 20 ++-- R/mlnormal_update_V_R.R | 14 +- R/mlnormal_update_beta.R | 7 - R/mlnormal_update_beta_XVX_R.R | 49 ++++------ R/mlnormal_update_beta_iterations_penalty.R | 5 - R/mlnormal_update_control_list.R | 4 R/mlnormal_update_ml_derivative_V.R | 29 ++--- R/mlnormal_update_theta_ml.R | 59 +++++------- R/mlnormal_verbose_f0.R | 4 R/mlnormal_verbose_f1.R | 4 R/mlnormal_verbose_f2.R | 18 +-- R/plot.amh.R | 67 +++++++------ R/pmle.R | 30 +++--- R/pmle_eval_posterior.R | 4 R/pmle_eval_prior.R | 4 R/pmle_ic.R | 8 - R/pmle_prior_extract_density.R | 24 ++-- R/pmle_process_prior.R | 23 ++-- R/print.mlnormal.R | 47 ++++----- R/suff_stat_NA_pattern.R | 10 +- R/summary.amh.R | 108 +++++++++++----------- R/summary.mlnormal.R | 84 ++++++++--------- R/summary.pmle.R | 76 ++++++++------- R/zzz.R | 8 - README.md | 5 - build/partial.rdb |binary data/data.HT12.rda |binary inst/CITATION | 7 - inst/NEWS | 9 + man/mlnormal.Rd | 4 src/RcppExports.cpp | 2 69 files changed, 707 insertions(+), 709 deletions(-)
Title: Linters for 'box' Modules
Description: Static code analysis of 'box' modules.
The package enhances code quality by providing linters that check for common issues,
enforce best practices, and ensure consistent coding standards.
Author: Ricardo Rodrigo Basa [aut, cre],
Jakub Nowicki [aut],
Appsilon Sp. z o.o. [cph]
Maintainer: Ricardo Rodrigo Basa <opensource+rodrigo@appsilon.com>
Diff between box.linters versions 0.9.1 dated 2024-06-04 and 0.10.0 dated 2024-07-15
DESCRIPTION | 14 +-- MD5 | 57 ++++++++++----- NAMESPACE | 4 + NEWS.md | 10 ++ R/box_alphabetical_calls_linter.R | 16 ++-- R/box_mod_fun_exists_linter.R | 6 + R/box_module_usage_helper_functions.R | 17 ++++ R/box_package_usage_helper_functions.R | 31 +++++++- R/box_unused_attached_mod_linter.R | 8 +- R/box_unused_attached_mod_obj_linter.R | 6 + R/namespaced_function_calls.R |only R/style_box_use.R |only R/style_ts_queries.R |only R/zzz.R | 2 inst/WORDLIST | 2 man/namespaced_function_calls.Rd |only man/style_box_use_dir.Rd |only man/style_box_use_file.Rd |only man/style_box_use_text.Rd |only tests/testthat/mod/path/relative |only tests/testthat/styled |only tests/testthat/test-box_alphabetical_calls_linter.R | 14 +-- tests/testthat/test-box_mod_fun_exists_linter.R | 31 ++++++++ tests/testthat/test-box_module_usage_halper_functions.R | 42 +++++++++++ tests/testthat/test-box_package_usage_helper_functions.R | 50 +++++++++++++ tests/testthat/test-box_unused_attached_mod_linter.R | 29 +++++++ tests/testthat/test-box_unused_attached_mod_obj_linter.R | 35 +++++++++ tests/testthat/test-namespaced_function_calls.R |only tests/testthat/test-style_box_use.R |only tests/testthat/test-zzz.R | 3 tests/testthat/to_style |only 31 files changed, 327 insertions(+), 50 deletions(-)
Title: General to Specific Modeling and Indicator Saturation in 2SLS
Models
Description: Provides facilities of general to specific model selection for
exogenous regressors in 2SLS models. Furthermore, indicator saturation
methods can be used to detect outliers and structural breaks in the sample.
Author: Kurle Jonas [aut, cre]
Maintainer: Kurle Jonas <mail@jonaskurle.com>
Diff between ivgets versions 0.1.1 dated 2022-10-17 and 0.1.2 dated 2024-07-15
ivgets-0.1.1/ivgets/R/ivgets.R |only ivgets-0.1.2/ivgets/DESCRIPTION | 10 ivgets-0.1.2/ivgets/MD5 | 44 - ivgets-0.1.2/ivgets/NEWS.md | 20 ivgets-0.1.2/ivgets/R/data.R | 176 ++-- ivgets-0.1.2/ivgets/R/getsiv.R | 2 ivgets-0.1.2/ivgets/R/ivgets-package.R |only ivgets-0.1.2/ivgets/README.md | 79 -- ivgets-0.1.2/ivgets/build/vignette.rds |binary ivgets-0.1.2/ivgets/inst/doc/GETS-IV.R | 2 ivgets-0.1.2/ivgets/inst/doc/GETS-IV.Rmd | 38 - ivgets-0.1.2/ivgets/inst/doc/GETS-IV.html | 146 ++- ivgets-0.1.2/ivgets/man/extract_variables.Rd | 46 - ivgets-0.1.2/ivgets/man/factory_indicators.Rd | 54 - ivgets-0.1.2/ivgets/man/gets.ivreg.Rd | 200 ++--- ivgets-0.1.2/ivgets/man/ivDiag.Rd | 80 +- ivgets-0.1.2/ivgets/man/ivgets-package.Rd | 33 ivgets-0.1.2/ivgets/man/ivgets.Rd | 2 ivgets-0.1.2/ivgets/man/new_formula.Rd | 82 +- ivgets-0.1.2/ivgets/tests/testthat.R | 8 ivgets-0.1.2/ivgets/tests/testthat/test-additional.R | 594 ++++++++-------- ivgets-0.1.2/ivgets/tests/testthat/test-getsiv.R | 470 ++++++------ ivgets-0.1.2/ivgets/tests/testthat/test-getsiv_nosnap.R | 436 +++++------ ivgets-0.1.2/ivgets/vignettes/GETS-IV.Rmd | 38 - 24 files changed, 1269 insertions(+), 1291 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The [...truncated...]
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.32.9 dated 2024-05-29 and 2.32.10 dated 2024-07-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/stanmath.html | 6 +++--- inst/include/src/stan/model/model_base_crtp.hpp | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to assist in key steps involved in any data
analysis workflow: (1) wrangling the raw data to get it in the needed form,
(2) applying preprocessing steps and statistical transformations, and
(3) compute statistical summaries of data properties and distributions.
It is also the data wrangling backend for packages in 'easystats' ecosystem.
References: Patil et al. (2022) <doi:10.21105/joss.04684>.
Author: Indrajeet Patil [aut] ,
Etienne Bacher [aut, cre] ,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [ctb] ,
Thomas J. Faulkenberry [rev],
Robert Garrett [rev]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between datawizard versions 0.12.0 dated 2024-07-11 and 0.12.1 dated 2024-07-15
DESCRIPTION | 14 ++-- MD5 | 10 +-- NEWS.md | 5 + inst/doc/tidyverse_translation.R | 6 +- inst/doc/tidyverse_translation.Rmd | 107 ++++++++++++++++++------------------ vignettes/tidyverse_translation.Rmd | 107 ++++++++++++++++++------------------ 6 files changed, 131 insertions(+), 118 deletions(-)
Title: Exemplar Data Sets for Student Growth Percentiles (SGP) Analyses
Description: Data sets utilized by the 'SGP' package as exemplars for users to conduct their own student growth percentiles (SGP) analyses.
Author: Damian W. Betebenner [aut, cre],
Adam R. Van Iwaarden [aut],
Ben Domingue [aut]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between SGPdata versions 27.0-0.0 dated 2023-10-18 and 28.0-0.0 dated 2024-07-15
DESCRIPTION | 8 ++-- MD5 | 23 ++++++------ R/zzz.R | 2 - build/vignette.rds |binary data/sgpData.rda |binary data/sgpData_LONG.rda |binary inst/CITATION | 10 ++--- inst/NEWS | 4 ++ inst/doc/SGPdata.html | 60 +++++++++++++++++--------------- man/SGPdata-package.Rd | 4 +- man/sgpData.Rd | 4 +- vignettes/releases/SGPdata-27.0-0.0.Rmd | 13 ++++-- vignettes/releases/SGPdata-28.0-0.0.Rmd |only 13 files changed, 72 insertions(+), 56 deletions(-)