More information about spectralGraphTopology at CRAN
Permanent link
Title: Import ASC Files from EyeLink Eye Trackers
Description: Imports plain-text ASC data files from EyeLink eye trackers
into (relatively) tidy data frames for analysis and visualization.
Author: Simon Barthelme <simon.barthelme@gipsa-lab.fr>
Maintainer: Austin Hurst <ajhurst@uwaterloo.ca>
Diff between eyelinker versions 0.1 dated 2016-04-21 and 0.2.0 dated 2019-09-22
eyelinker-0.1/eyelinker/NEWS |only eyelinker-0.2.0/eyelinker/DESCRIPTION | 29 eyelinker-0.2.0/eyelinker/LICENCE |only eyelinker-0.2.0/eyelinker/MD5 | 41 eyelinker-0.2.0/eyelinker/NAMESPACE | 20 eyelinker-0.2.0/eyelinker/NEWS.md |only eyelinker-0.2.0/eyelinker/R/eyelink_parser.R | 831 ++++++--- eyelinker-0.2.0/eyelinker/R/eyelinker.R | 26 eyelinker-0.2.0/eyelinker/R/utils.R | 98 - eyelinker-0.2.0/eyelinker/README.md | 53 eyelinker-0.2.0/eyelinker/build/vignette.rds |binary eyelinker-0.2.0/eyelinker/inst/doc/basics.R | 170 + eyelinker-0.2.0/eyelinker/inst/doc/basics.Rmd | 308 ++- eyelinker-0.2.0/eyelinker/inst/doc/basics.html | 860 ++++++---- eyelinker-0.2.0/eyelinker/inst/doc/format.R |only eyelinker-0.2.0/eyelinker/inst/doc/format.Rmd |only eyelinker-0.2.0/eyelinker/inst/doc/format.html |only eyelinker-0.2.0/eyelinker/man/eyelinker.Rd | 17 eyelinker-0.2.0/eyelinker/man/figures |only eyelinker-0.2.0/eyelinker/man/grapes-In-grapes.Rd | 18 eyelinker-0.2.0/eyelinker/man/read.asc.Rd | 66 eyelinker-0.2.0/eyelinker/man/whichInterval.Rd | 26 eyelinker-0.2.0/eyelinker/tests/testthat/test_examples.R | 39 eyelinker-0.2.0/eyelinker/tests/testthat/test_eyelink_parser.R |only eyelinker-0.2.0/eyelinker/vignettes/basics.Rmd | 308 ++- eyelinker-0.2.0/eyelinker/vignettes/format.Rmd |only 26 files changed, 1862 insertions(+), 1048 deletions(-)
Title: Data Modification and Analysis for Communication Research
Description: Provides convenience functions for common data
modification and analysis tasks in communication research. This
includes functions for univariate and bivariate data analysis, index
generation and reliability computation, and intercoder reliability
tests. All functions follow the style and syntax of the tidyverse, and
are construed to perform their computations on multiple variables at
once. Functions for univariate and bivariate data analysis comprise
summary statistics for continuous and categorical variables, as well
as several tests of bivariate association including effect sizes.
Functions for data modification comprise index generation and
automated reliability analysis of index variables. Functions for
intercoder reliability comprise tests of several intercoder
reliability estimates, including simple and mean pairwise percent
agreement, Krippendorff's Alpha (Krippendorff 2004, ISBN:
9780761915454), and various Kappa coefficients (Brennan & Prediger
1981 <doi: 10.1177/001316448104100307>; Cohen 1960 <doi:
10.1177/001316446002000104>; Fleiss 1971 <doi: 10.1037/h0031619>).
Author: Julian Unkel [aut, cre] (<https://orcid.org/0000-0001-9568-7041>)
Maintainer: Julian Unkel <julian.unkel@gmail.com>
Diff between tidycomm versions 0.0.1 dated 2019-09-19 and 0.1.0 dated 2019-09-22
tidycomm-0.0.1/tidycomm/inst/doc/bivariate.R |only tidycomm-0.0.1/tidycomm/inst/doc/bivariate.Rmd |only tidycomm-0.0.1/tidycomm/inst/doc/bivariate.html |only tidycomm-0.0.1/tidycomm/inst/doc/icr.R |only tidycomm-0.0.1/tidycomm/inst/doc/icr.Rmd |only tidycomm-0.0.1/tidycomm/inst/doc/icr.html |only tidycomm-0.0.1/tidycomm/inst/doc/reliability.R |only tidycomm-0.0.1/tidycomm/inst/doc/reliability.Rmd |only tidycomm-0.0.1/tidycomm/inst/doc/reliability.html |only tidycomm-0.0.1/tidycomm/inst/doc/univariate.R |only tidycomm-0.0.1/tidycomm/inst/doc/univariate.Rmd |only tidycomm-0.0.1/tidycomm/inst/doc/univariate.html |only tidycomm-0.0.1/tidycomm/man/check_equal.Rd |only tidycomm-0.0.1/tidycomm/man/cohens_d.Rd |only tidycomm-0.0.1/tidycomm/man/col_percs.Rd |only tidycomm-0.0.1/tidycomm/man/compute_aov.Rd |only tidycomm-0.0.1/tidycomm/man/compute_icr.Rd |only tidycomm-0.0.1/tidycomm/man/compute_reliability.Rd |only tidycomm-0.0.1/tidycomm/man/compute_t_test.Rd |only tidycomm-0.0.1/tidycomm/man/correlation_test.Rd |only tidycomm-0.0.1/tidycomm/man/count_value_in_unit.Rd |only tidycomm-0.0.1/tidycomm/man/cramer_V.Rd |only tidycomm-0.0.1/tidycomm/man/delta_sq.Rd |only tidycomm-0.0.1/tidycomm/man/grab_vars.Rd |only tidycomm-0.0.1/tidycomm/man/icr_agreement.Rd |only tidycomm-0.0.1/tidycomm/man/icr_brennan_prediger.Rd |only tidycomm-0.0.1/tidycomm/man/icr_cohens_kappa.Rd |only tidycomm-0.0.1/tidycomm/man/icr_fleiss_kappa.Rd |only tidycomm-0.0.1/tidycomm/man/icr_holstis_CR.Rd |only tidycomm-0.0.1/tidycomm/man/icr_kripp_alpha.Rd |only tidycomm-0.0.1/tidycomm/man/kalpha_denom.Rd |only tidycomm-0.0.1/tidycomm/man/kalpha_num_values.Rd |only tidycomm-0.0.1/tidycomm/man/kurtosis.Rd |only tidycomm-0.0.1/tidycomm/man/skewness.Rd |only tidycomm-0.0.1/tidycomm/man/unit_coder_matrix.Rd |only tidycomm-0.0.1/tidycomm/man/values_in_unit.Rd |only tidycomm-0.0.1/tidycomm/vignettes/bivariate.Rmd |only tidycomm-0.0.1/tidycomm/vignettes/icr.Rmd |only tidycomm-0.0.1/tidycomm/vignettes/reliability.Rmd |only tidycomm-0.0.1/tidycomm/vignettes/univariate.Rmd |only tidycomm-0.1.0/tidycomm/DESCRIPTION | 19 - tidycomm-0.1.0/tidycomm/MD5 | 110 +++------ tidycomm-0.1.0/tidycomm/R/categorical.R | 41 +-- tidycomm-0.1.0/tidycomm/R/correlation.R | 92 ++++--- tidycomm-0.1.0/tidycomm/R/describe.R | 33 +- tidycomm-0.1.0/tidycomm/R/icr.R | 55 +++- tidycomm-0.1.0/tidycomm/R/icr_agreement.R | 47 ++- tidycomm-0.1.0/tidycomm/R/icr_kappa.R | 81 +++--- tidycomm-0.1.0/tidycomm/R/icr_kripp_alpha.R | 126 +++++----- tidycomm-0.1.0/tidycomm/R/reliability.R | 165 +++++++------- tidycomm-0.1.0/tidycomm/R/ttest.R | 54 ++-- tidycomm-0.1.0/tidycomm/R/unianova.R | 24 +- tidycomm-0.1.0/tidycomm/R/utils-pipe.R | 22 - tidycomm-0.1.0/tidycomm/R/utils.R | 26 +- tidycomm-0.1.0/tidycomm/README.md | 8 tidycomm-0.1.0/tidycomm/build/vignette.rds |binary tidycomm-0.1.0/tidycomm/inst/doc/v01_univariate.R |only tidycomm-0.1.0/tidycomm/inst/doc/v01_univariate.Rmd |only tidycomm-0.1.0/tidycomm/inst/doc/v01_univariate.html |only tidycomm-0.1.0/tidycomm/inst/doc/v02_bivariate.R |only tidycomm-0.1.0/tidycomm/inst/doc/v02_bivariate.Rmd |only tidycomm-0.1.0/tidycomm/inst/doc/v02_bivariate.html |only tidycomm-0.1.0/tidycomm/inst/doc/v03_reliability.R |only tidycomm-0.1.0/tidycomm/inst/doc/v03_reliability.Rmd |only tidycomm-0.1.0/tidycomm/inst/doc/v03_reliability.html |only tidycomm-0.1.0/tidycomm/inst/doc/v04_icr.R |only tidycomm-0.1.0/tidycomm/inst/doc/v04_icr.Rmd |only tidycomm-0.1.0/tidycomm/inst/doc/v04_icr.html |only tidycomm-0.1.0/tidycomm/man/correlate.Rd | 3 tidycomm-0.1.0/tidycomm/man/crosstab.Rd | 5 tidycomm-0.1.0/tidycomm/man/get_reliability.Rd | 4 tidycomm-0.1.0/tidycomm/man/t_test.Rd | 4 tidycomm-0.1.0/tidycomm/man/tab_frequencies.Rd | 3 tidycomm-0.1.0/tidycomm/man/test_icr.Rd | 29 +- tidycomm-0.1.0/tidycomm/man/unianova.Rd | 3 tidycomm-0.1.0/tidycomm/tests/testthat.R | 8 tidycomm-0.1.0/tidycomm/tests/testthat/test-categorical.R | 76 +++--- tidycomm-0.1.0/tidycomm/tests/testthat/test-describe.R | 98 ++++---- tidycomm-0.1.0/tidycomm/tests/testthat/test-ttest.R | 108 ++++----- tidycomm-0.1.0/tidycomm/tests/testthat/test-unianova.R | 106 ++++---- tidycomm-0.1.0/tidycomm/vignettes/v01_univariate.Rmd |only tidycomm-0.1.0/tidycomm/vignettes/v02_bivariate.Rmd |only tidycomm-0.1.0/tidycomm/vignettes/v03_reliability.Rmd |only tidycomm-0.1.0/tidycomm/vignettes/v04_icr.Rmd |only 84 files changed, 708 insertions(+), 642 deletions(-)
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 2000 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 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.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Tilman Davies;
Yongtao Guan;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Greg McSwiggan;
Tuomas Rajala;
Suman Rakshit;
Dominic Schuhmacher;
Rasmus Waagepetersen;
and Hangsheng Wang.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
R. Arellano;
J. Astrom;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Brown;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
L. Cobo Sanchez;
J.-F. Coeurjolly;
K. Colyvas;
H. Commenges;
R. Constantine;
R. Corria Ainslie;
R. Cotton;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
M. Hesselbarth;
P. Hewson;
H. Heydarian;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
L. Kozmian-Ledward;
M. Kuhn;
J. Laake;
R.A. Lamb;
F. Lavancier;
T. Lawrence;
T. Lazauskas;
J. Lee;
G.P. Leser;
A. Li;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
I. Moncada;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Najari;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
T. Pollington;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud;
N. Read;
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
T.L. Silva;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
J. Sulavik;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
L. Torres;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
L. Yates;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.60-1 dated 2019-06-23 and 1.61-0 dated 2019-09-22
DESCRIPTION | 9 + MD5 | 190 ++++++++++++++++++++------------------ NAMESPACE | 13 ++ NEWS | 184 +++++++++++++++++++++++++++++++++++++ R/GJfox.R | 107 ++++++++++++++------- R/Hest.R | 5 - R/as.im.R | 28 +++-- R/blur.R | 14 +- R/bw.diggle.R | 12 -- R/bw.ppl.R | 102 ++++++++++++++++++-- R/bw.scott.R |only R/colourtables.R | 76 ++++++--------- R/density.lpp.R | 11 +- R/densitylppVoronoi.R | 31 +++++- R/effectfun.R | 11 +- R/envelope.R | 5 - R/envelopelpp.R | 8 - R/hyperframe.R | 31 +++++- R/hypersub.R | 30 +++--- R/images.R | 27 ++++- R/linfun.R | 7 + R/linim.R | 12 ++ R/lintess.R | 95 +++++++++++++------ R/localKcross.R | 103 +++++++++++++-------- R/lohboot.R | 6 - R/lpp.R | 12 +- R/lppm.R | 2 R/mppm.R | 20 ++-- R/pickoption.R | 6 - R/plot.anylist.R | 23 +++- R/plot.im.R | 10 +- R/pppmatch.R | 21 ++-- R/ppx.R | 10 +- R/quadrattest.R | 97 ++++++++++++++----- R/quickndirty.R |only R/rLGCP.R | 4 R/randomsets.R |only R/rhohat.R | 151 ++++++++++++++++++++++-------- R/solist.R | 4 R/sysdata.rda |binary R/tess.R | 175 ++++++++++++++++++++--------------- R/unstack.R | 6 - R/window.R | 8 + build/vignette.rds |binary inst/doc/Nickname.txt | 2 inst/doc/bugfixes.Rnw | 17 +++ inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 inst/doc/replicated.pdf |binary inst/doc/shapefiles.R | 40 ++++---- inst/doc/shapefiles.Rnw | 31 ++++++ inst/doc/shapefiles.pdf |binary inst/doc/updates.Rnw | 67 ++++++++++++- inst/doc/updates.pdf |binary man/Emark.Rd | 3 man/Gfox.Rd | 14 ++ man/Hest.Rd | 2 man/Replace.im.Rd | 45 +++++++-- man/anylist.Rd | 1 man/as.im.Rd | 26 +++++ man/bits.test.Rd | 5 - man/blur.Rd | 18 ++- man/bw.lppl.Rd |only man/bw.ppl.Rd | 21 +++- man/bw.scott.Rd | 80 +++++++++++++--- man/data.lppm.Rd |only man/data.ppm.Rd | 9 - man/density.lpp.Rd | 80 ++++++++++------ man/densityQuick.lpp.Rd |only man/dfbetas.ppm.Rd | 7 + man/dffit.ppm.Rd | 9 - man/influence.ppm.Rd | 7 + man/leverage.ppm.Rd | 7 + man/localKcross.inhom.Rd | 6 - man/plot.im.Rd | 21 +++- man/plot.linim.Rd | 4 man/plot.pppmatching.Rd |only man/ppm.object.Rd | 3 man/pppdist.Rd | 3 man/pppmatching.object.Rd | 5 - man/quadrat.test.Rd | 40 +++++--- man/rhohat.Rd | 225 +++++++++++++++++++++++++++++++++------------- man/rthin.Rd | 1 man/rthinclumps.Rd |only man/spatdim.Rd | 33 ++++-- man/spatstat-internal.Rd | 21 +++- man/spatstat-package.Rd | 34 +++++- man/tileindex.Rd | 5 + src/ripleypoly.h | 7 - tests/testsAtoD.R | 63 +++++++++++- tests/testsEtoF.R | 16 +++ tests/testsGtoK.R | 87 +++++++++++++++-- tests/testsLtoM.R | 78 ++++++++++++++- tests/testsNtoP.R | 28 +++++ tests/testsStoZ.R | 65 +++++++++++-- vignettes/bugfixes.Rnw | 17 +++ vignettes/shapefiles.Rnw | 31 ++++++ vignettes/updates.Rnw | 67 ++++++++++++- 100 files changed, 2245 insertions(+), 774 deletions(-)
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Diff between RaceID versions 0.1.4 dated 2019-09-20 and 0.1.5 dated 2019-09-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/RaceID.html | 4 ++-- src/VarID.cpp | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Stan Models for the Paired Comparison Factor Model
Description: Provides convenience functions and pre-programmed Stan models
related to the paired comparison factor model. Its purpose is to make fitting
paired comparison data using Stan easy.
Author: Joshua N. Pritikin [aut, cre] (<https://orcid.org/0000-0002-9862-5484>),
Daniel C. Furr [ctb],
Trustees of Columbia University [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between pcFactorStan versions 1.0.2 dated 2019-07-25 and 1.1.0 dated 2019-09-22
DESCRIPTION | 8 MD5 | 61 +-- NAMESPACE | 4 R/data.R |only R/fit.R | 80 ++++ R/generate.R | 178 ++++++++++ inst/doc/manual.R | 42 +- inst/doc/manual.Rmd | 121 ++++--- inst/doc/manual.html | 649 ++++++++------------------------------ man/filterGraph.Rd | 7 man/findModel.Rd | 6 man/generateCovItems.Rd | 35 +- man/generateFactorItems.Rd | 88 +++-- man/generateItem.Rd | 31 + man/generateSingleFactorItems.Rd |only man/itemModelExplorer.Rd | 21 - man/phyActFlowPropensity.Rd | 47 +- man/prepCleanData.Rd | 4 man/prepData.Rd | 4 man/prepFactorModel.Rd |only man/prepSingleFactorModel.Rd |only man/responseCurve.Rd | 21 - src/stan_files/factor.stan | 105 ++++-- src/stan_files/factor_ll.stan | 105 ++++-- tests/testthat/test-2generate.R | 32 + tests/testthat/test-3data.R | 99 +++++ tests/testthat/test-4likelihood.R | 11 tests/testthat/test-5loo.R | 17 tests/testthat/test-6explorer.R | 9 tests/testthat/test-7report.R | 1 tools/covr.R |only tools/genStan | 127 +++++-- tools/travis/install-linux | 2 vignettes/manual.Rmd | 121 ++++--- 34 files changed, 1204 insertions(+), 832 deletions(-)
Title: Extended Structural Equation Modelling
Description: Create structural equation models that can be manipulated programmatically.
Models may be specified with matrices or paths (LISREL or RAM)
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares.
equations, state space, and many others.
Support and advanced package binaries available at <http://openmx.ssri.psu.edu>.
The software is described in Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Association for Computing Machinery [cph],
Dieter Kraft [cph],
Stefan Wilhelm [cph],
Sarah Medland [cph],
Carl F. Falk [cph],
Matt Keller [cph],
Manjunath B G [cph],
The Regents of the University of California [cph],
Lester Ingber [cph],
Wong Shao Voon [cph],
Juan Palacios [cph],
Jiang Yang [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.13.2 dated 2019-05-26 and 2.14.11 dated 2019-09-22
OpenMx-2.13.2/OpenMx/CHANGES |only OpenMx-2.13.2/OpenMx/R/MxAlgebraTransform.R |only OpenMx-2.13.2/OpenMx/R/MxDiff.R |only OpenMx-2.13.2/OpenMx/R/MxRAMMetaData.R |only OpenMx-2.13.2/OpenMx/data/jointdata.txt.gz |only OpenMx-2.13.2/OpenMx/inst/models/nightly/FactorScores.R |only OpenMx-2.13.2/OpenMx/inst/models/nightly/LegacyMultipleGroupWLS.R |only OpenMx-2.13.2/OpenMx/inst/models/nightly/ModelIdentification.R |only OpenMx-2.13.2/OpenMx/inst/models/nightly/npdWarningWLS.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/ACELRTCI20160808.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/AlgebraComputePassing.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/ConstantSubstitution.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/DataErrorDetection.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/DefinitionTest2.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/GREML_Error_Detection.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/MatrixErrorDetection.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/Multilevel-GenData.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/MxBoundsTesting.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/dmvnorm.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/loadDataByCol.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/loadDataByRow.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/mxSave.R |only OpenMx-2.13.2/OpenMx/inst/models/passing/simplestCI.R |only OpenMx-2.13.2/OpenMx/man/MxRAMMetaData-class.Rd |only OpenMx-2.13.2/OpenMx/man/imxDiff.Rd |only OpenMx-2.13.2/OpenMx/src/bgen.cpp |only OpenMx-2.13.2/OpenMx/src/db_wrapper.cpp |only OpenMx-2.13.2/OpenMx/src/entropy_common.c |only OpenMx-2.13.2/OpenMx/src/fse_compress.c |only OpenMx-2.13.2/OpenMx/src/fse_decompress.c |only OpenMx-2.13.2/OpenMx/src/huf_compress.c |only OpenMx-2.13.2/OpenMx/src/huf_decompress.c |only OpenMx-2.13.2/OpenMx/src/include |only OpenMx-2.13.2/OpenMx/src/merge.cpp |only OpenMx-2.13.2/OpenMx/src/merge.h |only OpenMx-2.13.2/OpenMx/src/omxBuffer.h |only OpenMx-2.13.2/OpenMx/src/pgenlib_internal.cpp |only OpenMx-2.13.2/OpenMx/src/pgenlib_internal.h |only OpenMx-2.13.2/OpenMx/src/plink2_base.cc |only OpenMx-2.13.2/OpenMx/src/plink2_base.h |only OpenMx-2.13.2/OpenMx/src/sqlite3.c |only OpenMx-2.13.2/OpenMx/src/xxhash.c |only OpenMx-2.13.2/OpenMx/src/zbuff_compress.c |only OpenMx-2.13.2/OpenMx/src/zbuff_decompress.c |only OpenMx-2.13.2/OpenMx/src/zstd_common.c |only OpenMx-2.13.2/OpenMx/src/zstd_compress.c |only OpenMx-2.13.2/OpenMx/src/zstd_decompress.c |only OpenMx-2.14.11/OpenMx/DESCRIPTION | 38 OpenMx-2.14.11/OpenMx/MD5 | 451 +--- OpenMx-2.14.11/OpenMx/NAMESPACE | 1 OpenMx-2.14.11/OpenMx/NEWS.md | 1080 +++++++++ OpenMx-2.14.11/OpenMx/R/MxAlgebraConvert.R | 106 OpenMx-2.14.11/OpenMx/R/MxAlgebraObjective.R | 2 OpenMx-2.14.11/OpenMx/R/MxApply.R | 10 OpenMx-2.14.11/OpenMx/R/MxCommunication.R | 2 OpenMx-2.14.11/OpenMx/R/MxCompare.R | 155 - OpenMx-2.14.11/OpenMx/R/MxCompute.R | 139 - OpenMx-2.14.11/OpenMx/R/MxData.R | 26 OpenMx-2.14.11/OpenMx/R/MxDataWLS.R | 11 OpenMx-2.14.11/OpenMx/R/MxDependencies.R | 24 OpenMx-2.14.11/OpenMx/R/MxDetectCores.R | 2 OpenMx-2.14.11/OpenMx/R/MxErrorHandling.R | 9 OpenMx-2.14.11/OpenMx/R/MxEval.R | 19 OpenMx-2.14.11/OpenMx/R/MxExpectationLISREL.R | 8 OpenMx-2.14.11/OpenMx/R/MxExpectationMixture.R | 14 OpenMx-2.14.11/OpenMx/R/MxExpectationNormal.R | 201 + OpenMx-2.14.11/OpenMx/R/MxExpectationRAM.R | 21 OpenMx-2.14.11/OpenMx/R/MxExpectationStateSpace.R | 17 OpenMx-2.14.11/OpenMx/R/MxFactorScores.R | 4 OpenMx-2.14.11/OpenMx/R/MxFitFunctionWLS.R | 7 OpenMx-2.14.11/OpenMx/R/MxMLObjective.R | 3 OpenMx-2.14.11/OpenMx/R/MxMatrix.R | 4 OpenMx-2.14.11/OpenMx/R/MxNamespace.R | 27 OpenMx-2.14.11/OpenMx/R/MxRAMModel.R | 10 OpenMx-2.14.11/OpenMx/R/MxRAMtoML.R | 4 OpenMx-2.14.11/OpenMx/R/MxRObjective.R | 4 OpenMx-2.14.11/OpenMx/R/MxRestore.R | 207 + OpenMx-2.14.11/OpenMx/R/MxRowObjective.R | 4 OpenMx-2.14.11/OpenMx/R/MxRun.R | 2 OpenMx-2.14.11/OpenMx/R/MxSummary.R | 15 OpenMx-2.14.11/OpenMx/R/MxSwift.R | 2 OpenMx-2.14.11/OpenMx/R/MxUnitTesting.R | 282 -- OpenMx-2.14.11/OpenMx/R/MxVersion.R | 2 OpenMx-2.14.11/OpenMx/R/OriginalMx.R | 14 OpenMx-2.14.11/OpenMx/R/omxGetNPSOL.R | 5 OpenMx-2.14.11/OpenMx/R/sysdata.rda |binary OpenMx-2.14.11/OpenMx/R/zzz.R | 15 OpenMx-2.14.11/OpenMx/README.md | 3 OpenMx-2.14.11/OpenMx/configure | 69 OpenMx-2.14.11/OpenMx/data/jointdata.rda |only OpenMx-2.14.11/OpenMx/inst/CITATION | 4 OpenMx-2.14.11/OpenMx/inst/WORDLIST | 1 OpenMx-2.14.11/OpenMx/inst/models/nightly/InvalidComparisonDetection.R | 7 OpenMx-2.14.11/OpenMx/inst/models/nightly/Power1.R | 43 OpenMx-2.14.11/OpenMx/inst/models/nightly/Power2.R | 46 OpenMx-2.14.11/OpenMx/inst/models/nightly/ifa-ms.R | 6 OpenMx-2.14.11/OpenMx/inst/models/nightly/mxPowerDetail.R | 5 OpenMx-2.14.11/OpenMx/inst/models/nightly/startsTestMissing.R | 2 OpenMx-2.14.11/OpenMx/inst/models/passing/AnalyticConstraintJacobians--Eq_and_Ineq.R | 17 OpenMx-2.14.11/OpenMx/inst/models/passing/ContinuousOnlyWLSTest.R | 8 OpenMx-2.14.11/OpenMx/inst/models/passing/DefaultComputePlanTest.R | 11 OpenMx-2.14.11/OpenMx/inst/models/passing/DogChain.R | 6 OpenMx-2.14.11/OpenMx/inst/models/passing/GREML--minimal_test_model.R | 4 OpenMx-2.14.11/OpenMx/inst/models/passing/IntroSEM-BivariateRaw.R | 2 OpenMx-2.14.11/OpenMx/inst/models/passing/LISRELFactorRegression_Matrix.R | 2 OpenMx-2.14.11/OpenMx/inst/models/passing/MultipleGroupRAM.R | 32 OpenMx-2.14.11/OpenMx/inst/models/passing/NameParameterOverlap.R | 33 OpenMx-2.14.11/OpenMx/inst/models/passing/PowerError.R |only OpenMx-2.14.11/OpenMx/inst/models/passing/StateSpaceOsc.R | 2 OpenMx-2.14.11/OpenMx/inst/models/passing/SummaryCheck.R | 96 OpenMx-2.14.11/OpenMx/inst/models/passing/checkStandardizedLoadingsEtcetera.R | 4 OpenMx-2.14.11/OpenMx/inst/models/passing/defvaralgebra.R | 22 OpenMx-2.14.11/OpenMx/inst/models/passing/derivFilter.R | 18 OpenMx-2.14.11/OpenMx/inst/models/passing/exoPredWLS.R | 67 OpenMx-2.14.11/OpenMx/inst/models/passing/fm-example2-2.R | 8 OpenMx-2.14.11/OpenMx/inst/models/passing/ifa-drm-mg2.R | 5 OpenMx-2.14.11/OpenMx/inst/models/passing/ifa-lmp.R | 3 OpenMx-2.14.11/OpenMx/inst/models/passing/jointFactorWls.R | 4 OpenMx-2.14.11/OpenMx/inst/models/passing/xxm-3.R | 14 OpenMx-2.14.11/OpenMx/inst/tools/testModels.R | 2 OpenMx-2.14.11/OpenMx/man/MxMMI.Rd | 2 OpenMx-2.14.11/OpenMx/man/imxDataTypes.Rd | 2 OpenMx-2.14.11/OpenMx/man/imxOriginalMx.Rd | 17 OpenMx-2.14.11/OpenMx/man/imxReportProgress.Rd | 2 OpenMx-2.14.11/OpenMx/man/jointdata_data.Rd | 7 OpenMx-2.14.11/OpenMx/man/lazarsfeld_data.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxBootstrap.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxBootstrapEval.Rd | 48 OpenMx-2.14.11/OpenMx/man/mxBootstrapStdizeRAMpaths.Rd | 17 OpenMx-2.14.11/OpenMx/man/mxComputeCheckpoint.Rd | 43 OpenMx-2.14.11/OpenMx/man/mxComputeConfidenceInterval.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxComputeDefault.Rd | 6 OpenMx-2.14.11/OpenMx/man/mxComputeEM.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxComputeGradientDescent.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxComputeHessianQuality.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxComputeIterate.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxComputeLoadContext.Rd | 19 OpenMx-2.14.11/OpenMx/man/mxComputeLoadData.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxComputeLoadMatrix.Rd | 12 OpenMx-2.14.11/OpenMx/man/mxComputeLoop.Rd | 10 OpenMx-2.14.11/OpenMx/man/mxComputeNewtonRaphson.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxComputeNumericDeriv.Rd | 8 OpenMx-2.14.11/OpenMx/man/mxComputeOnce.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxComputeTryHard.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxData.Rd | 85 OpenMx-2.14.11/OpenMx/man/mxEval.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxExpectationStateSpace.Rd | 4 OpenMx-2.14.11/OpenMx/man/mxFitFunctionML.Rd | 6 OpenMx-2.14.11/OpenMx/man/mxGenerateData.Rd | 109 - OpenMx-2.14.11/OpenMx/man/mxLISRELObjective.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxOption.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxPath.Rd | 2 OpenMx-2.14.11/OpenMx/man/mxPower.Rd | 197 - OpenMx-2.14.11/OpenMx/man/mxRestore.Rd | 82 OpenMx-2.14.11/OpenMx/man/mxSave.Rd | 63 OpenMx-2.14.11/OpenMx/man/mxStandardizeRAMpaths.Rd | 2 OpenMx-2.14.11/OpenMx/man/omxCheckCloseEnough.Rd | 13 OpenMx-2.14.11/OpenMx/man/omxCheckEquals.Rd | 7 OpenMx-2.14.11/OpenMx/man/omxCheckError.Rd | 4 OpenMx-2.14.11/OpenMx/man/omxCheckIdentical.Rd | 7 OpenMx-2.14.11/OpenMx/man/omxCheckSetEquals.Rd | 7 OpenMx-2.14.11/OpenMx/man/omxCheckTrue.Rd | 2 OpenMx-2.14.11/OpenMx/man/omxCheckWarning.Rd | 7 OpenMx-2.14.11/OpenMx/man/omxCheckWithinPercentError.Rd | 2 OpenMx-2.14.11/OpenMx/man/omxDefaultComputePlan.Rd | 2 OpenMx-2.14.11/OpenMx/man/omxDetectCores.Rd | 3 OpenMx-2.14.11/OpenMx/man/omxGetNPSOL.Rd | 2 OpenMx-2.14.11/OpenMx/man/omxSaturatedModel.Rd | 2 OpenMx-2.14.11/OpenMx/man/omxSetParameters.Rd | 2 OpenMx-2.14.11/OpenMx/src/AlgebraFunctions.h | 442 ---- OpenMx-2.14.11/OpenMx/src/Compute.cpp | 1081 +++------- OpenMx-2.14.11/OpenMx/src/Compute.h | 34 OpenMx-2.14.11/OpenMx/src/ComputeGD.cpp | 40 OpenMx-2.14.11/OpenMx/src/ComputeNR.cpp | 15 OpenMx-2.14.11/OpenMx/src/Connectedness.h | 2 OpenMx-2.14.11/OpenMx/src/FellnerFitFunction.cpp | 2 OpenMx-2.14.11/OpenMx/src/LoadDataAPI.h |only OpenMx-2.14.11/OpenMx/src/Makevars.in | 47 OpenMx-2.14.11/OpenMx/src/Makevars.win | 4 OpenMx-2.14.11/OpenMx/src/MarkovFF.cpp | 2 OpenMx-2.14.11/OpenMx/src/RAMInternal.h | 28 OpenMx-2.14.11/OpenMx/src/asubnp.cpp | 29 OpenMx-2.14.11/OpenMx/src/ba81quad.h | 52 OpenMx-2.14.11/OpenMx/src/dmvnorm.cpp | 85 OpenMx-2.14.11/OpenMx/src/finiteDifferences.h | 6 OpenMx-2.14.11/OpenMx/src/glue.cpp | 11 OpenMx-2.14.11/OpenMx/src/matrix.cpp | 234 -- OpenMx-2.14.11/OpenMx/src/matrix.h | 82 OpenMx-2.14.11/OpenMx/src/nr.h | 4 OpenMx-2.14.11/OpenMx/src/omxAlgebra.h | 2 OpenMx-2.14.11/OpenMx/src/omxAlgebraFitFunction.cpp | 4 OpenMx-2.14.11/OpenMx/src/omxData.cpp | 43 OpenMx-2.14.11/OpenMx/src/omxData.h | 5 OpenMx-2.14.11/OpenMx/src/omxDefines.h | 8 OpenMx-2.14.11/OpenMx/src/omxExpectation.cpp | 4 OpenMx-2.14.11/OpenMx/src/omxExpectation.h | 3 OpenMx-2.14.11/OpenMx/src/omxExpectationBA81.cpp | 1 OpenMx-2.14.11/OpenMx/src/omxFIMLFitFunction.cpp | 10 OpenMx-2.14.11/OpenMx/src/omxFitFunction.cpp | 38 OpenMx-2.14.11/OpenMx/src/omxFitFunction.h | 3 OpenMx-2.14.11/OpenMx/src/omxFitFunctionBA81.cpp | 9 OpenMx-2.14.11/OpenMx/src/omxGREMLExpectation.h | 1 OpenMx-2.14.11/OpenMx/src/omxGREMLfitfunction.cpp | 11 OpenMx-2.14.11/OpenMx/src/omxHessianCalculation.cpp | 18 OpenMx-2.14.11/OpenMx/src/omxImportFrontendState.cpp | 6 OpenMx-2.14.11/OpenMx/src/omxMLFitFunction.cpp | 3 OpenMx-2.14.11/OpenMx/src/omxMatrix.cpp | 20 OpenMx-2.14.11/OpenMx/src/omxMatrix.h | 72 OpenMx-2.14.11/OpenMx/src/omxNLopt.cpp | 2 OpenMx-2.14.11/OpenMx/src/omxRAMExpectation.cpp | 21 OpenMx-2.14.11/OpenMx/src/omxSadmvnWrapper.h | 12 OpenMx-2.14.11/OpenMx/src/omxState.cpp | 32 OpenMx-2.14.11/OpenMx/src/omxState.h | 7 OpenMx-2.14.11/OpenMx/src/omxStateSpaceExpectation.cpp | 30 OpenMx-2.14.11/OpenMx/src/omxSymbolTable.cpp | 2 OpenMx-2.14.11/OpenMx/src/omxWLSFitFunction.cpp | 6 OpenMx-2.14.11/OpenMx/src/ssMLFit.cpp | 18 OpenMx-2.14.11/OpenMx/tests |only OpenMx-2.14.11/OpenMx/tools |only 219 files changed, 3756 insertions(+), 3159 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.0.0 dated 2019-08-19 and 1.0.1 dated 2019-09-22
DESCRIPTION | 8 - MD5 | 26 ++-- NEWS.md | 13 ++ R/FilePsInput.R | 49 ++++++++ R/FileRepeatedInput.R | 44 +++++++ R/FileSurveyInput.R | 42 +++++++ R/csvFileInput.R | 44 +++++++ R/jsBasicGadget.R | 57 ++++++++-- R/jsPropensityGadget.R | 54 ++++++++- R/jsRepeatedGadget.R | 56 ++++++++- R/jsSurveyGadget.R | 51 ++++++++ R/kaplan.R | 14 +- inst/doc/jsmodule.html | 4 tests/testthat/shinytest/basic/tests/basicTest-expected/001.json | 9 - 14 files changed, 420 insertions(+), 51 deletions(-)
Title: Solving Differential Equations (ODEs, SDEs, DDEs, DAEs)
Description: An interface to 'DifferentialEquations.jl' <http://docs.juliadiffeq.org/latest/> from the R programming language.
It has unique high performance methods for solving ordinary differential equations (ODE), stochastic differential equations (SDE),
delay differential equations (DDE), differential-algebraic equations (DAE), and more. Much of the functionality,
including features like adaptive time stepping in SDEs, are unique and allow for multiple orders of magnitude speedup over more common methods.
'diffeqr' attaches an R interface onto the package, allowing seamless use of this tooling by R users.
Author: Christopher Rackauckas [aut, cre]
Maintainer: Christopher Rackauckas <me@chrisrackauckas.com>
Diff between diffeqr versions 0.1.2 dated 2019-07-12 and 0.1.3 dated 2019-09-22
DESCRIPTION | 6 MD5 | 16 R/diffeqr.R | 853 +++++++++++++++++++++++----------------------- inst/doc/dae.html | 4 inst/doc/dde.html | 4 inst/doc/ode.html | 4 inst/doc/sde.html | 4 man/sde.solve.Rd | 5 tests/testthat/test_sde.R | 197 +++++----- 9 files changed, 557 insertions(+), 536 deletions(-)
Title: A Versatile Toolkit for Copy Number Variation Relationship Data
Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgeish, Yonghong Wang, Jack Zhu, Paul Meltzer
Maintainer: James Dalgleish <james.dalgleish@nih.gov>
Diff between CNVScope versions 2.7.0 dated 2019-07-23 and 2.7.2.5 dated 2019-09-22
DESCRIPTION | 10 LICENSE | 4 MD5 | 58 +-- NAMESPACE | 4 NEWS.md | 7 R/CNVScopeserver.R | 71 +++ R/calcCNVKernelProbDist.R | 294 +++++++-------- R/createChromosomalMatrixSet.R | 100 ++--- R/downsample_genomic_matrix.R | 104 ++--- R/formSampleMatrixFromRawGDCData.R | 142 +++++++ R/freadGDCfile.R | 142 +++---- R/getAnnotationMatrix.R | 220 +++++------ R/getAsymmetricBlockIndices.R | 350 +++++++++--------- R/getBlockAverageMatrixFromBreakpoints.R | 236 ++++++------ R/getInterchromosomalInteractivePlot.R | 146 +++---- R/rebinGenomicInteractions.R | 142 +++---- R/runCNVScopeShiny.R | 7 R/writeAsymmetricMeltedMatrixToDisk.R | 388 ++++++++++---------- R/writeMeltedChromosomalMatrixToDisk.R | 366 +++++++++---------- inst/doc/additonal_examples.Rmd | 580 +++++++++++++++---------------- inst/doc/additonal_examples.html | 1 inst/doc/create_input_matrix.R | 24 + inst/doc/create_input_matrix.Rmd | 200 +++++++--- inst/doc/create_input_matrix.html | 25 + inst/doc/power_analysis.Rmd | 110 ++--- inst/doc/power_analysis.html | 1 man/formSampleMatrixFromRawGDCData.Rd | 16 vignettes/additonal_examples.Rmd | 580 +++++++++++++++---------------- vignettes/create_input_matrix.Rmd | 200 +++++++--- vignettes/power_analysis.Rmd | 110 ++--- 30 files changed, 2522 insertions(+), 2116 deletions(-)
Title: Bayesian Structural Time Series
Description: Time series regression using dynamic linear models fit using
MCMC. See Scott and Varian (2014) <DOI:10.1504/IJMMNO.2014.059942>, among many
other sources.
Author: Steven L. Scott <steve.the.bayesian@gmail.com>
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between bsts versions 0.9.1 dated 2019-06-07 and 0.9.2 dated 2019-09-22
DESCRIPTION | 12 +-- MD5 | 37 +++++----- R/format.timestamps.R | 7 + R/mbsts.plots.R | 44 +++++++++++- R/predict.bsts.R | 64 +++++++++++++---- R/predict.mbsts.R | 20 ++--- inst/tests/testthat/test-dynamic-regression.R | 94 +++++++++++++++++++------ inst/tests/testthat/test-poisson.R | 26 +++++-- man/add.dynamic.regression.Rd | 4 + man/plot.mbsts.prediction.Rd |only src/Makevars | 8 +- src/create_shared_state_model.cpp | 95 -------------------------- src/create_shared_state_model.h | 11 --- src/create_state_model.cpp | 9 +- src/create_state_model.h | 20 +---- src/dynamic_intercept_model_manager.cc | 3 src/mbsts.cc | 2 src/model_manager.cc | 39 +++++++++- src/model_manager.h | 65 +++++++++++++---- src/multivariate_gaussian_model_manager.cc | 87 ++++++++++------------- 20 files changed, 374 insertions(+), 273 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Michael D. Wilson [aut] (<https://orcid.org/0000-0003-4143-7308>),
Paul-Christian Bürkner [rev],
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>),
Quentin F. Gronau [ctb] (<https://orcid.org/0000-0001-5510-6943>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between bayestestR versions 0.2.5 dated 2019-08-06 and 0.3.0 dated 2019-09-22
bayestestR-0.2.5/bayestestR/man/dot-reoder_rows.Rd |only bayestestR-0.3.0/bayestestR/DESCRIPTION | 25 bayestestR-0.3.0/bayestestR/MD5 | 211 +++---- bayestestR-0.3.0/bayestestR/NAMESPACE | 62 +- bayestestR-0.3.0/bayestestR/NEWS.md | 29 bayestestR-0.3.0/bayestestR/R/bayesfactor_inclusion.R | 18 bayestestR-0.3.0/bayestestR/R/bayesfactor_models.R | 50 + bayestestR-0.3.0/bayestestR/R/bayesfactor_parameters.R | 87 +- bayestestR-0.3.0/bayestestR/R/bayesfactor_restricted.R | 7 bayestestR-0.3.0/bayestestR/R/check_prior.R |only bayestestR-0.3.0/bayestestR/R/ci.R | 41 + bayestestR-0.3.0/bayestestR/R/contr.bayes.R |only bayestestR-0.3.0/bayestestR/R/convert_pd_to_p.R | 6 bayestestR-0.3.0/bayestestR/R/describe_posterior.R | 149 +++-- bayestestR-0.3.0/bayestestR/R/diagnostic_posterior.R | 3 bayestestR-0.3.0/bayestestR/R/distribution.R | 18 bayestestR-0.3.0/bayestestR/R/effective_sample.R | 37 + bayestestR-0.3.0/bayestestR/R/equivalence_test.R | 16 bayestestR-0.3.0/bayestestR/R/estimate_density.R | 2 bayestestR-0.3.0/bayestestR/R/eti.R | 55 + bayestestR-0.3.0/bayestestR/R/hdi.R | 57 + bayestestR-0.3.0/bayestestR/R/mcse.R | 20 bayestestR-0.3.0/bayestestR/R/p_direction.R | 57 + bayestestR-0.3.0/bayestestR/R/p_map.R | 49 + bayestestR-0.3.0/bayestestR/R/p_rope.R | 7 bayestestR-0.3.0/bayestestR/R/plot.R | 4 bayestestR-0.3.0/bayestestR/R/point_estimate.R | 63 +- bayestestR-0.3.0/bayestestR/R/print.bayesfactor_parameters.R | 4 bayestestR-0.3.0/bayestestR/R/print.ci.R | 70 -- bayestestR-0.3.0/bayestestR/R/print.describe_posterior.R |only bayestestR-0.3.0/bayestestR/R/print.p_direction.R | 20 bayestestR-0.3.0/bayestestR/R/print.p_map.R | 13 bayestestR-0.3.0/bayestestR/R/print.p_rope.R | 13 bayestestR-0.3.0/bayestestR/R/print.point_estimate.R |only bayestestR-0.3.0/bayestestR/R/print.rope.R | 2 bayestestR-0.3.0/bayestestR/R/reshape_ci.R | 2 bayestestR-0.3.0/bayestestR/R/rope.R | 162 +++-- bayestestR-0.3.0/bayestestR/R/rope_range.R | 59 + bayestestR-0.3.0/bayestestR/R/simulate_prior.R |only bayestestR-0.3.0/bayestestR/R/utils.R | 82 ++ bayestestR-0.3.0/bayestestR/R/utils_bayesfactor.R | 45 + bayestestR-0.3.0/bayestestR/R/utils_hdi_ci.R | 146 +--- bayestestR-0.3.0/bayestestR/R/utils_print_data_frame.R |only bayestestR-0.3.0/bayestestR/README.md | 62 -- bayestestR-0.3.0/bayestestR/build/partial.rdb |binary bayestestR-0.3.0/bayestestR/inst/CITATION | 23 bayestestR-0.3.0/bayestestR/inst/doc/bayes_factors.R | 95 +++ bayestestR-0.3.0/bayestestR/inst/doc/bayes_factors.Rmd | 177 +++++ bayestestR-0.3.0/bayestestR/inst/doc/bayes_factors.html | 297 +++++++--- bayestestR-0.3.0/bayestestR/inst/doc/bayestestR.Rmd | 5 bayestestR-0.3.0/bayestestR/inst/doc/bayestestR.html | 20 bayestestR-0.3.0/bayestestR/inst/doc/credible_interval.Rmd | 4 bayestestR-0.3.0/bayestestR/inst/doc/credible_interval.html | 9 bayestestR-0.3.0/bayestestR/inst/doc/example1.Rmd | 2 bayestestR-0.3.0/bayestestR/inst/doc/example1.html | 23 bayestestR-0.3.0/bayestestR/inst/doc/example2.Rmd | 2 bayestestR-0.3.0/bayestestR/inst/doc/example2.html | 29 bayestestR-0.3.0/bayestestR/inst/doc/example3.Rmd | 2 bayestestR-0.3.0/bayestestR/inst/doc/example3.html | 2 bayestestR-0.3.0/bayestestR/inst/doc/guidelines.Rmd | 7 bayestestR-0.3.0/bayestestR/inst/doc/guidelines.html | 7 bayestestR-0.3.0/bayestestR/inst/doc/indicesEstimationComparison.Rmd | 2 bayestestR-0.3.0/bayestestR/inst/doc/indicesEstimationComparison.html | 2 bayestestR-0.3.0/bayestestR/inst/doc/indicesExistenceComparison.Rmd | 7 bayestestR-0.3.0/bayestestR/inst/doc/indicesExistenceComparison.html | 7 bayestestR-0.3.0/bayestestR/inst/doc/probability_of_direction.Rmd | 7 bayestestR-0.3.0/bayestestR/inst/doc/probability_of_direction.html | 9 bayestestR-0.3.0/bayestestR/inst/doc/region_of_practical_equivalence.Rmd | 2 bayestestR-0.3.0/bayestestR/inst/doc/region_of_practical_equivalence.html | 6 bayestestR-0.3.0/bayestestR/man/bayesfactor_models.Rd | 6 bayestestR-0.3.0/bayestestR/man/bayesfactor_parameters.Rd | 14 bayestestR-0.3.0/bayestestR/man/bayesfactor_restricted.Rd | 4 bayestestR-0.3.0/bayestestR/man/check_prior.Rd |only bayestestR-0.3.0/bayestestR/man/ci.Rd | 28 bayestestR-0.3.0/bayestestR/man/contr.bayes.Rd |only bayestestR-0.3.0/bayestestR/man/describe_posterior.Rd | 16 bayestestR-0.3.0/bayestestR/man/distribution.Rd | 8 bayestestR-0.3.0/bayestestR/man/effective_sample.Rd | 4 bayestestR-0.3.0/bayestestR/man/eti.Rd | 11 bayestestR-0.3.0/bayestestR/man/figures/unnamed-chunk-12-1.png |only bayestestR-0.3.0/bayestestR/man/figures/unnamed-chunk-14-1.png |only bayestestR-0.3.0/bayestestR/man/figures/unnamed-chunk-16-1.png |only bayestestR-0.3.0/bayestestR/man/figures/unnamed-chunk-5-1.png |only bayestestR-0.3.0/bayestestR/man/figures/unnamed-chunk-7-1.png |only bayestestR-0.3.0/bayestestR/man/figures/unnamed-chunk-9-1.png |only bayestestR-0.3.0/bayestestR/man/hdi.Rd | 13 bayestestR-0.3.0/bayestestR/man/mcse.Rd | 5 bayestestR-0.3.0/bayestestR/man/p_direction.Rd | 3 bayestestR-0.3.0/bayestestR/man/rope.Rd | 4 bayestestR-0.3.0/bayestestR/man/simulate_prior.Rd |only bayestestR-0.3.0/bayestestR/tests/testthat/test-bayesfactor_models.R | 2 bayestestR-0.3.0/bayestestR/tests/testthat/test-bayesfactor_parameters.R | 4 bayestestR-0.3.0/bayestestR/tests/testthat/test-brms.R | 4 bayestestR-0.3.0/bayestestR/tests/testthat/test-ci.R | 38 + bayestestR-0.3.0/bayestestR/tests/testthat/test-density_at.R | 4 bayestestR-0.3.0/bayestestR/tests/testthat/test-describe_posterior.R | 29 bayestestR-0.3.0/bayestestR/tests/testthat/test-hdi.R | 42 + bayestestR-0.3.0/bayestestR/tests/testthat/test-map_estimate.R | 28 bayestestR-0.3.0/bayestestR/tests/testthat/test-p_direction.R | 25 bayestestR-0.3.0/bayestestR/tests/testthat/test-p_map.R | 33 - bayestestR-0.3.0/bayestestR/tests/testthat/test-point_estimate.R |only bayestestR-0.3.0/bayestestR/tests/testthat/test-rope.R | 26 bayestestR-0.3.0/bayestestR/tests/testthat/test-rstanarm.R | 2 bayestestR-0.3.0/bayestestR/vignettes/bayes_factors.Rmd | 177 +++++ bayestestR-0.3.0/bayestestR/vignettes/bayestestR.Rmd | 5 bayestestR-0.3.0/bayestestR/vignettes/bibliography.bib | 39 - bayestestR-0.3.0/bayestestR/vignettes/credible_interval.Rmd | 4 bayestestR-0.3.0/bayestestR/vignettes/example1.Rmd | 2 bayestestR-0.3.0/bayestestR/vignettes/example2.Rmd | 2 bayestestR-0.3.0/bayestestR/vignettes/example3.Rmd | 2 bayestestR-0.3.0/bayestestR/vignettes/guidelines.Rmd | 7 bayestestR-0.3.0/bayestestR/vignettes/indicesEstimationComparison.Rmd | 2 bayestestR-0.3.0/bayestestR/vignettes/indicesExistenceComparison.Rmd | 7 bayestestR-0.3.0/bayestestR/vignettes/probability_of_direction.Rmd | 7 bayestestR-0.3.0/bayestestR/vignettes/region_of_practical_equivalence.Rmd | 2 115 files changed, 2220 insertions(+), 888 deletions(-)
Title: Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Description: Hydrological modelling tools developed at Irstea-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>),
Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>),
Guillaume Thirel [aut] (<https://orcid.org/0000-0002-1444-1830>),
Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>),
Claude Michel [aut, ths],
Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>),
François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>,
'Parameter estimation' vignettes),
Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>),
Nicolas Le Moine [ctb],
Thibaut Mathevet [ctb],
Safouane Mouelhi [ctb],
Ludovic Oudin [ctb] (<https://orcid.org/0000-0002-3712-0933>),
Raji Pushpalatha [ctb],
Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@irstea.fr>
Diff between airGR versions 1.3.2.23 dated 2019-06-21 and 1.3.2.42 dated 2019-09-22
airGR-1.3.2.23/airGR/NEWS |only airGR-1.3.2.42/airGR/DESCRIPTION | 9 airGR-1.3.2.42/airGR/MD5 | 34 - airGR-1.3.2.42/airGR/NEWS.md |only airGR-1.3.2.42/airGR/R/CreateIniStates.R | 7 airGR-1.3.2.42/airGR/R/RunModel_CemaNeige.R | 6 airGR-1.3.2.42/airGR/R/RunModel_CemaNeigeGR4H.R | 4 airGR-1.3.2.42/airGR/R/RunModel_CemaNeigeGR4J.R | 4 airGR-1.3.2.42/airGR/R/RunModel_CemaNeigeGR5J.R | 4 airGR-1.3.2.42/airGR/R/RunModel_CemaNeigeGR6J.R | 4 airGR-1.3.2.42/airGR/README.md |only airGR-1.3.2.42/airGR/data/L0123001.rda |binary airGR-1.3.2.42/airGR/data/X0310010.rda |binary airGR-1.3.2.42/airGR/inst/doc/V01_get_started.html | 6 airGR-1.3.2.42/airGR/inst/doc/V04_cemaneige_hysteresis.R | 263 +++++----- airGR-1.3.2.42/airGR/inst/doc/V04_cemaneige_hysteresis.Rmd | 23 airGR-1.3.2.42/airGR/inst/doc/V04_cemaneige_hysteresis.html | 48 - airGR-1.3.2.42/airGR/inst/vignettesData/vignetteCNHysteresis.rda |only airGR-1.3.2.42/airGR/src/frun_cemaneige.f | 4 airGR-1.3.2.42/airGR/vignettes/V04_cemaneige_hysteresis.Rmd | 23 20 files changed, 204 insertions(+), 235 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Alvaro Florez Poveda, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 1.2 dated 2019-02-06 and 1.3 dated 2019-09-22
DESCRIPTION | 10 MD5 | 17 NAMESPACE | 37 -- NEWS | 4 R/FixedDiscrDiscrIT.R | 840 +++++++++++++++++++++++----------------------- R/ISTE.ContCont.R |only R/Sim.Data.MTS.R | 168 ++++----- R/Single.Trial.RE.AA.R | 4 man/ISTE.ContCont.Rd |only man/plot.ISTE.ContCont.Rd |only man/summary.gen.Rd | 2 11 files changed, 543 insertions(+), 539 deletions(-)
Title: Bayesian Regression with Time-Varying Coefficients
Description: Bayesian dynamic regression models where the regression
coefficients can vary over time as random walks.
Gaussian, Poisson, and binomial observations are supported.
The Markov chain Monte Carlo computations are done using
Hamiltonian Monte Carlo provided by Stan, using a state space representation
of the model in order to marginalise over the coefficients for efficient sampling.
For non-Gaussian models, walker uses the importance sampling type estimators based on
approximate marginal MCMC as in Vihola, Helske, Franks (2017, <arXiv:1609.02541>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between walker versions 0.2.5 dated 2019-03-04 and 0.3.0 dated 2019-09-22
DESCRIPTION | 10 MD5 | 96 NAMESPACE | 110 R/RcppExports.R | 22 R/fitted.R | 140 - R/plot_coefs.R | 122 R/plot_fit.R | 36 R/plot_predict.R | 154 - R/pp_check.R | 42 R/predict.R | 188 - R/print_fit.R | 22 R/rw.R | 178 - R/stanmodels.R | 84 R/walker.R | 1070 ++++---- R/walker_rw1.R | 494 +-- R/zzz.R | 14 README.md | 104 build/vignette.rds |binary cleanup.win | 18 exec/rw1_model.stan | 286 +- exec/rw1_model_naive.stan | 88 exec/rw_glm_model.stan | 406 +-- exec/walker_glm.stan | 426 +-- exec/walker_lm.stan | 284 +- inst/CITATION | 42 inst/chunks/common_functions.stan | 498 +-- inst/chunks/license.stan | 28 inst/doc/walker.R | 134 - inst/doc/walker.Rmd | 346 +- inst/doc/walker.html | 938 ++++--- man/coef.walker_fit.Rd | 48 man/fitted.walker_fit.Rd | 42 man/plot_coefs.Rd | 52 man/plot_fit.Rd | 40 man/plot_predict.Rd | 100 man/pp_check.walker_fit.Rd | 34 man/predict.walker_fit.Rd | 68 man/print.walker_fit.Rd | 32 man/rw1.Rd | 50 man/rw2.Rd | 56 man/walker.Rd | 228 - man/walker_glm.Rd | 228 - man/walker_rw1.Rd | 224 - src/include/models.hpp | 4864 ++++++++++++++++++-------------------- tests/test_all.R | 4 tests/testthat/tests.R | 50 tools/make_cpp.R | 94 vignettes/walker.Rmd | 346 +- vignettes/walker.bib | 146 - 49 files changed, 6656 insertions(+), 6430 deletions(-)
Title: Advanced Tables for Markdown/HTML
Description: Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While allowing
advanced layout, the underlying css-structure is simple in order to maximize
compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package
also contains a few text formatting functions that help outputting text
compatible with HTML/LaTeX.
Author: Max Gordon [aut, cre],
Stephen Gragg [aut],
Peter Konings [aut]
Maintainer: Max Gordon <max@gforge.se>
Diff between htmlTable versions 1.13.1 dated 2019-01-07 and 1.13.2 dated 2019-09-22
DESCRIPTION | 8 MD5 | 36 - R/htmlTable_helpers.R | 18 build/vignette.rds |binary inst/doc/general.html | 561 ++++++++++++++++-------- inst/doc/tables.html | 779 ++++++++++++++++++++-------------- inst/doc/tidyHtmlTable.html | 359 ++++++++++++--- man/prAddCells.Rd | 4 man/prAddSemicolon2StrEnd.Rd | 4 man/prEscapeHtml.Rd | 4 man/prGetCgroupHeader.Rd | 4 man/prGetRowlabelPos.Rd | 4 man/prGetStyle.Rd | 4 man/prPrepareAlign.Rd | 4 man/prPrepareCgroup.Rd | 4 man/prTblNo.Rd | 4 tests/testthat/test-htmlTable.R | 3 tests/testthat/test-htmlTable_dates.R | 2 tests/visual_tests/htmlTable_vtests.R | 20 19 files changed, 1191 insertions(+), 631 deletions(-)
Title: Fitting Frailty Models with the EM Algorithm
Description: Contains functions for fitting shared frailty models with a semi-parametric
baseline hazard with the Expectation-Maximization algorithm. Supported data formats
include clustered failures with left truncation and recurrent events in gap-time
or Andersen-Gill format. Several frailty distributions, such as the the gamma, positive stable
and the Power Variance Family are supported.
Author: Theodor Adrian Balan, Hein Putter
Maintainer: Theodor Adrian Balan <hello@tbalan.com>
Diff between frailtyEM versions 1.0.0 dated 2019-07-30 and 1.0.1 dated 2019-09-22
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/autoplot.emfrail.R | 5 ++++- R/emfrail.R | 34 +++++++++++++++++++++++++++++----- R/plot.emfrail.R | 3 +++ R/predict.emfrail.R | 12 +++++++----- inst/doc/frailtyEM_manual.pdf |binary man/autoplot.emfrail.Rd | 4 +++- man/plot.emfrail.Rd | 4 +++- man/predict.emfrail.Rd | 4 +++- 12 files changed, 72 insertions(+), 29 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-03 0.1.1
2019-05-08 0.1.0
Title: Private Configuration for 'R' Packages
Description: Set configuration options on a per-package basis.
Options set by a given package only apply to that package,
other packages are unaffected.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between pkgconfig versions 2.0.2 dated 2018-08-16 and 2.0.3 dated 2019-09-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/NEWS.markdown | 4 ++++ inst/README.Rmd | 8 +++----- inst/README.markdown | 8 +++----- tests/testthat.R | 3 ++- 6 files changed, 20 insertions(+), 19 deletions(-)
Title: Call R from R
Description: It is sometimes useful to perform a computation in a
separate R process, without affecting the current R process at all.
This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between callr versions 3.3.1 dated 2019-07-18 and 3.3.2 dated 2019-09-22
DESCRIPTION | 10 MD5 | 24 +- NEWS.md | 4 build/vignette.rds |binary inst/doc/Task-queue-with-callr.R | 33 +- inst/doc/Task-queue-with-callr.Rmd | 205 ++++-------------- inst/doc/Task-queue-with-callr.html | 404 ++++++++++++++++++------------------ tests/testthat.R | 6 tests/testthat/test-error.R | 3 tests/testthat/test-messages.R | 1 tests/testthat/test-r-session.R | 8 vignettes/Task-queue-with-callr.Rmd | 205 ++++-------------- vignettes/taskq.R | 3 13 files changed, 366 insertions(+), 540 deletions(-)
Title: Multivariate Ordinal Regression Models
Description: A flexible framework for fitting multivariate
ordinal regression models with composite likelihood methods.
Author: Rainer Hirk [aut, cre],
Kurt Hornik [aut],
Laura Vana [aut],
Alan Genz [ctb] (Fortran Code)
Maintainer: Rainer Hirk <rhirk@wu.ac.at>
Diff between mvord versions 0.3.5 dated 2019-03-06 and 0.3.6 dated 2019-09-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ R/utilities.R | 13 +++++++------ inst/doc/vignette_mvord.pdf |binary inst/doc/vignette_mvord2.html | 37 +++++++++++++++++++++++++++++++++---- 6 files changed, 52 insertions(+), 19 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models
Description: Hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger <michael.schweinberger@rice.edu> [aut, cre], Mark S. Handcock <handcock@ucla.edu> [aut], Sergii Babkin <babkin.sergii@gmail.com> [aut], Jonathan Stewart <jonathan.stewart@rice.edu> [aut], Duy Vu <duy.vu@unimelb.edu.au> [aut], Pamela Luna <pamela.luna@rice.edu> [ctb]
Maintainer: Michael Schweinberger <michael.schweinberger@rice.edu>
Diff between hergm versions 4.1-3 dated 2019-05-25 and 4.1-4 dated 2019-09-22
hergm-4.1-3/hergm/R/auxiliary_functions.r |only hergm-4.1-3/hergm/R/helper_functions.R |only hergm-4.1-4/hergm/DESCRIPTION | 8 - hergm-4.1-4/hergm/MD5 | 20 +-- hergm-4.1-4/hergm/R/helper.functions.R |only hergm-4.1-4/hergm/R/hergm.auxiliary.functions.R |only hergm-4.1-4/hergm/R/hergm.mcmc.R | 11 + hergm-4.1-4/hergm/R/hergm.mcmc.diagnostics.R | 147 ++++++++++++------------ hergm-4.1-4/hergm/R/hergm.multiple.R | 2 hergm-4.1-4/hergm/R/hergm.print.R | 63 +++++----- hergm-4.1-4/hergm/man/hergm.Rd | 14 +- hergm-4.1-4/hergm/src/MCMC.c | 5 hergm-4.1-4/hergm/src/h_ergm.c | 12 + 13 files changed, 157 insertions(+), 125 deletions(-)
Title: Dominance Analysis
Description: Dominance analysis is a method that allows to compare the
relative importance of predictors in multiple regression models:
ordinary least squares, generalized linear models,
hierarchical linear models and dynamic linear models. The main principles and methods of
dominance analysis are described in
Budescu, D. V. (1993) <doi:10.1037/0033-2909.114.3.542> and
Azen, R., & Budescu, D. V. (2003) <doi:10.1037/1082-989X.8.2.129>
for ordinary least squares regression. Subsequently, the extensions
for multivariate regression, logistic regression and
hierarchical linear models were described in
Azen, R., & Budescu, D. V. (2006) <doi:10.3102/10769986031002157>,
Azen, R., & Traxel, N. (2009) <doi:10.3102/1076998609332754> and
Luo, W., & Azen, R. (2013) <doi:10.3102/1076998612458319>,
respectively.
Author: Claudio Bustos Navarrete [aut, cre]
(<https://orcid.org/0000-0003-3478-9858>),
Filipa Coutinho Soares [aut] (<https://orcid.org/0000-0002-7579-2538>)
Maintainer: Claudio Bustos Navarrete <clbustos@gmail.com>
Diff between dominanceanalysis versions 1.0.0 dated 2019-01-30 and 1.2.0 dated 2019-09-22
DESCRIPTION | 23 MD5 | 102 +- NAMESPACE | 3 NEWS.md | 14 R/averageContribution.r | 9 R/bootAverageDominanceAnalysis.r | 9 R/bootDominanceAnalysis.r | 9 R/contributionByLevel.r | 4 R/daFitFunctions.r | 33 R/daRawResults.r | 2 R/daSubmodels.r | 3 R/daUtils.r | 18 R/dominanceAnalysis.r | 39 R/dominanceBriefing.r |only R/dominanceMatrix.r | 9 R/getFits.r | 5 R/mlmWithCov.r | 13 R/rankUsingMatrix.r | 4 R/summary.bootAverageDominanceAnalysis.r | 1 R/summary.bootDominanceAnalysis.r | 5 R/summary.dominanceAnalysis.r | 13 README.md | 574 +++++++------ build/vignette.rds |binary inst/WORDLIST | 8 inst/doc/da-logistic-regression.R | 13 inst/doc/da-logistic-regression.Rmd | 19 inst/doc/da-logistic-regression.html | 782 +++++++++++------- inst/extdata/bootavemodpres100.rds |binary inst/extdata/bootmodpres100.rds |binary man/averageContribution.Rd | 1 man/bootAverageDominanceAnalysis.Rd | 4 man/bootDominanceAnalysis.Rd | 6 man/contributionByLevel.Rd | 1 man/da.dynlm.fit.Rd |only man/da.glm.fit.Rd | 4 man/da.lm.fit.Rd | 4 man/da.lmWithCov.fit.Rd | 5 man/da.lmerMod.fit.Rd | 5 man/da.mlmWithCov.fit.Rd | 5 man/dominanceAnalysis.Rd | 1 man/dominanceBriefing.Rd |only man/dominanceMatrix.Rd | 3 man/getFits.Rd | 1 man/mlmWithCov.Rd | 13 man/rankUsingMatrix.Rd | 8 man/replaceTermsInString.Rd |only tests/testthat/test-daAverageBootstrap.R | 16 tests/testthat/test-daBootstrap.R | 23 tests/testthat/test-dominance-analysis-on-empty-set.R |only tests/testthat/test-dominanceanalysis-with-dynlm.R |only tests/testthat/test-glm-with-esoph-example.R |only tests/testthat/test-list-terms.R |only tests/testthat/test-lmWithCovsMlm.R | 18 tests/testthat/test-named-terms.R |only tests/testthat/test-replace-terms-in-string.R |only tests/testthat/test-retrieve-functions.R | 14 vignettes/da-logistic-regression.Rmd | 19 57 files changed, 1196 insertions(+), 669 deletions(-)
More information about dominanceanalysis at CRAN
Permanent link