Title: Tidy Model Visualisation for Generalised Additive Models
Description: Provides functions for visualising generalised
additive models and getting predicted values using tidy tools from the 'tidyverse' packages.
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between tidymv versions 2.2.0 dated 2019-06-17 and 3.0.0 dated 2020-04-24
tidymv-2.2.0/tidymv/man/plot_difference.Rd |only tidymv-3.0.0/tidymv/DESCRIPTION | 12 tidymv-3.0.0/tidymv/MD5 | 44 +- tidymv-3.0.0/tidymv/NEWS.md | 9 tidymv-3.0.0/tidymv/R/plotting.R | 80 ---- tidymv-3.0.0/tidymv/R/tidymv-defunct.R | 4 tidymv-3.0.0/tidymv/R/utils.R | 2 tidymv-3.0.0/tidymv/README.md | 7 tidymv-3.0.0/tidymv/build/vignette.rds |binary tidymv-3.0.0/tidymv/inst/doc/plot-smooths.R | 43 -- tidymv-3.0.0/tidymv/inst/doc/plot-smooths.Rmd | 33 - tidymv-3.0.0/tidymv/inst/doc/plot-smooths.html | 247 ++++++------ tidymv-3.0.0/tidymv/inst/doc/predict-gam.R | 26 - tidymv-3.0.0/tidymv/inst/doc/predict-gam.html | 405 ++++++++++----------- tidymv-3.0.0/tidymv/man/geom_smooth_ci.Rd | 3 tidymv-3.0.0/tidymv/man/get_gam_predictions.Rd | 18 tidymv-3.0.0/tidymv/man/inter_df.Rd | 6 tidymv-3.0.0/tidymv/man/plot_difference-defunct.Rd |only tidymv-3.0.0/tidymv/man/plot_smooths.Rd | 19 tidymv-3.0.0/tidymv/man/pois_df.Rd | 6 tidymv-3.0.0/tidymv/man/predict_gam.Rd | 3 tidymv-3.0.0/tidymv/man/tidymv-defunct.Rd | 13 tidymv-3.0.0/tidymv/man/tidymv.Rd | 1 tidymv-3.0.0/tidymv/vignettes/plot-smooths.Rmd | 33 - 24 files changed, 464 insertions(+), 550 deletions(-)
Title: R Interface to 'Apache Tika'
Description: Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
Author: Sasha Goodman [aut, cre],
The Apache Software Foundation [aut, cph],
Julia Silge [rev] (Reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/191),
David Gohel [rev] (Reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/191)
Maintainer: Sasha Goodman <goodmansasha@gmail.com>
Diff between rtika versions 1.23 dated 2019-12-12 and 1.24.1 dated 2020-04-24
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------ NEWS.md | 7 +++++ R/install_tika.R | 8 +++--- R/tika.R | 14 +++++----- R/zzz.R | 2 - build/vignette.rds |binary inst/doc/rtika_introduction.html | 50 +++++++++++++++++++-------------------- man/install_tika.Rd | 8 +++--- 9 files changed, 60 insertions(+), 53 deletions(-)
Title: Rank Preserving Structural Failure Time Models
Description: Implements methods described by the paper Robins and Tsiatis (1991) <DOI:10.1080/03610929108830654>. These use g-estimation to estimate the causal effect of a treatment in a two-armed randomised control trial where non-compliance exists and is measured, under an assumption of an accelerated failure time model and no unmeasured confounders.
Author: Simon Bond [aut, cre] (primary author of code, secondary author of
vignette),
Annabel Allison [aut] (primary author of vignette, secondary author of
code)
Maintainer: Simon Bond <simon.bond@addenbrookes.nhs.uk>
Diff between rpsftm versions 1.2.6 dated 2019-11-11 and 1.2.7 dated 2020-04-24
DESCRIPTION | 12 MD5 | 82 - NAMESPACE | 2 NEWS.md | 4 R/cox.zph.R | 54 R/est_eqn.R | 80 - R/extract_z.R | 118 - R/plot.rpsftm.R | 78 - R/rand.R | 70 - R/rpsftm.R | 694 +++++----- R/terms.inner.R | 58 R/uniroot_all.R |only R/untreated.R | 96 - README.md | 114 - inst/doc/rpsftm_vignette.R | 2 inst/doc/rpsftm_vignette.Rmd | 592 ++++---- inst/doc/rpsftm_vignette.html | 283 ++-- man/cox.zph.Rd | 52 man/est_eqn.Rd | 81 - man/extract_z.Rd | 90 - man/immdef.Rd | 60 man/plot.rpsftm.Rd | 78 - man/print.rand.Rd | 50 man/print.rpsftm.Rd | 44 man/print.rpsftm.coxph.Rd | 39 man/print.rpsftm.summary.coxph.Rd | 48 man/print.rpsftm.summary.survreg.Rd | 39 man/print.rpsftm.survreg.Rd | 34 man/rand.Rd | 66 man/residuals.rpsftm.Rd | 50 man/rpsftm-package.Rd | 50 man/rpsftm.Rd | 210 +-- man/summary.rpsftm.Rd | 44 man/survfit.rpsftm.Rd | 50 man/terms.inner.Rd | 38 man/uniroot_all.Rd |only man/untreated.Rd | 70 - tests/testthat/test_errors.R | 526 +++---- vignettes/rpsftm_vignette.Rmd | 592 ++++---- vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-12-1.png |binary vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-5-1.png |binary vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-7-1.png |binary vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-9-1.png |binary 43 files changed, 2335 insertions(+), 2315 deletions(-)
Title: Analysis of RD Designs with Multiple Cutoffs or Scores
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. The 'rdmulti' package provides tools to analyze RD designs with multiple cutoffs or scores: rdmc() estimates pooled and cutoff specific effects for multi-cutoff designs, rdmcplot() draws RD plots for multi-cutoff designs and rdms() estimates effects in cumulative cutoffs or multi-score designs. See Cattaneo, Titiunik and Vazquez-Bare (2020) <https://sites.google.com/site/rdpackages/rdmulti/Cattaneo-Titiunik-VazquezBare_2020_Stata.pdf> for further methodological details.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@econ.ucsb.edu>
Diff between rdmulti versions 0.4 dated 2020-01-13 and 0.5 dated 2020-04-24
DESCRIPTION | 12 - MD5 | 20 +- NAMESPACE | 38 ++-- R/rdmc.R | 389 ++++++++++++++++++++++++++----------------------- R/rdmcplot.R | 322 ++++++++++++++++++++++++++-------------- R/rdms.R | 348 +++++++++++++++++++++++-------------------- R/rdmulti_package.R | 7 man/rdmc.Rd | 260 +++++++++++++++++++------------- man/rdmcplot.Rd | 208 ++++++++++++++++---------- man/rdms.Rd | 259 +++++++++++++++++++------------- man/rdmulti-package.Rd | 54 +++--- 11 files changed, 1126 insertions(+), 791 deletions(-)
Title: Nonlinear Regression for Agricultural Applications
Description: Additional nonlinear regression functions using self-start (SS) algorithms. One of the functions is the Beta growth function proposed by Yin et al. (2003) <doi:10.1093/aob/mcg029>. There are several other functions with breakpoints (e.g. linear-plateau, plateau-linear, exponential-plateau, plateau-exponential, quadratic-plateau, plateau-quadratic and bilinear), a non-rectangular hyperbola and a bell-shaped curve. Twenty one (21) new self-start (SS) functions in total. This package also supports the publication 'Nonlinear regression Models and applications in agricultural research' by Archontoulis and Miguez (2015) <doi:10.2134/agronj2012.0506>, a book chapter with similar material <doi:10.2134/appliedstatistics.2016.0003.c15> and a publication by Oddi et. al. (2019) in Ecology and Evolution <doi:10.1002/ece3.5543>. The function 'nlsLMList' uses nlsLM for fitting, but it is otherwise almost identical to 'nlme::nlsList'.In addition, this release of the package provides functions for conducting simulation for 'nlme' and 'gnls' objects as well as bootstrapping. These functions are intended to work with the modeling framework of the 'nlme' package. It also provides four vignettes with extended examples.
Author: Fernando Miguez [aut, cre] (<https://orcid.org/0000-0002-4627-8329>),
José Pinheiro [ctb, cph] (author of nlme::nlsList, nlme::predict.gnls,
nlme::predict.nlme),
Douglas Bates [ctb, cph] (author of nlme::nlsList, nlme::predict.gnls,
nlme::predict.nlme),
R-core [ctb, cph]
Maintainer: Fernando Miguez <femiguez@iastate.edu>
Diff between nlraa versions 0.53 dated 2020-01-13 and 0.65 dated 2020-04-24
DESCRIPTION | 24 ++++--- MD5 | 59 +++++++++++++------ NAMESPACE | 10 +++ R/SSexplin.R |only R/SSlogis5.R |only R/SSnrh.R | 4 - R/SStrlin.R |only R/boot_nlme.R |only R/data-doc.R | 6 - R/simulate_gnls.R |only R/simulate_nlme.R |only R/simulate_nlme_one.R |only README.md | 5 + build/vignette.rds |binary inst/doc/Bootstrapping.R |only inst/doc/Bootstrapping.Rmd |only inst/doc/Bootstrapping.html |only inst/doc/nlraa-AgronJ-paper.R | 2 inst/doc/nlraa-AgronJ-paper.Rmd | 6 + inst/doc/nlraa-AgronJ-paper.html | 16 ++--- inst/doc/nlraa-Oddi-LFMC.html | 4 - inst/doc/nlraa.R | 5 - inst/doc/nlraa.Rmd | 39 +++++++++++- inst/doc/nlraa.html | 51 ++++++++++++---- man/SSexplin.Rd |only man/SSlogis5.Rd |only man/SSnrh.Rd | 4 - man/SStrlin.Rd |only man/boot_nlme.Rd |only man/nlraa.env.Rd |only man/simulate_gnls.Rd |only man/simulate_nlme.Rd |only man/simulate_nlme_one.Rd |only man/sm.Rd | 5 - tests/test_boot_nlme.R |only tests/test_sim_boot_lfmc.R |only tests/test_simulate_gnls.R |only tests/test_simulate_nlme.R |only tests/tests_SSother.R | 119 +++++++++++++++++++++++++++++++++++++++ vignettes/Bootstrapping.Rmd |only vignettes/nlraa-AgronJ-paper.Rmd | 6 + vignettes/nlraa.Rmd | 39 +++++++++++- 42 files changed, 331 insertions(+), 73 deletions(-)
Title: Download Data from the International House Price Database
Description: Web scraping the <https://www.dallasfed.org> for
up-to-date data on international house prices and exuberance
indicators. Download data in tidy format.
Author: Kostas Vasilopoulos [aut, cre]
Maintainer: Kostas Vasilopoulos <k.vasilopoulo@gmail.com>
Diff between ihpdr versions 1.1.0 dated 2019-10-15 and 1.2.0 dated 2020-04-24
DESCRIPTION | 28 +++++---- MD5 | 27 +++++---- NAMESPACE | 3 + NEWS.md | 12 +++- R/get.R | 103 +++++++++++++++++++++--------------- R/tf.R |only README.md | 31 +++++----- inst/CITATION |only inst/WORDLIST | 1 man/figures/README-exuber-ind-1.png |binary man/figures/README-rhpi-1.png |binary man/ihpd_browse.Rd | 44 +++++++-------- man/ihpd_get.Rd | 15 ++++- man/ihpd_release_dates.Rd | 6 ++ tests/testthat/helper.R |only tests/testthat/test-get.R | 15 +++++ 16 files changed, 178 insertions(+), 107 deletions(-)
Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of 'TraMineR'.
Author: Gilbert Ritschard [aut, cre, ths, cph]
(<https://orcid.org/0000-0001-7776-0903>),
Matthias Studer [aut] (<https://orcid.org/0000-0002-6269-1412>),
Reto Buergin [aut],
Alexis Gabadinho [ctb],
Pierre-Alexandre Fonta [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineRextras versions 0.4.7 dated 2020-03-02 and 0.6.0 dated 2020-04-24
DESCRIPTION | 13 ++--- MD5 | 22 ++++---- NAMESPACE | 8 ++- R/seqCompare.R |only R/seqemlt.R | 7 +- R/seqgranularity.R | 124 ++++++++++++++++++++++++++++++++++++-------------- R/seqplot-rf.R | 42 ++++++++++++---- inst/NEWS | 20 +++++++- inst/NEWS.Rd | 30 ++++++++++++ man/seqCompare.Rd |only man/seqemlt.Rd | 2 man/seqgranularity.Rd | 15 ++++-- man/seqplot-rf.Rd | 7 +- 13 files changed, 214 insertions(+), 76 deletions(-)
More information about TraMineRextras at CRAN
Permanent link
Title: ROC Curve Inference with and without Covariates
Description: Estimates the pooled (unadjusted) Receiver Operating Characteristic (ROC) curve, the covariate-adjusted ROC (AROC) curve, and the covariate-specific/conditional ROC (cROC) curve by different methods, both Bayesian and frequentist. Also, it provides functions to obtain ROC-based optimal cutpoints utilizing several criteria. Based on Erkanli, A. et al. (2006) <doi:10.1002/sim.2496>; Faraggi, D. (2003) <doi:10.1111/1467-9884.00350>; Gu, J. et al. (2008) <doi:10.1002/sim.3366>; Inacio de Carvalho, V. et al. (2013) <doi:10.1214/13-BA825>; Inacio de Carvalho, V., and Rodriguez-Alvarez, M.X. (2018) <arXiv:1806.00473>; Janes, H., and Pepe, M.S. (2009) <doi:10.1093/biomet/asp002>; Pepe, M.S. (1998) <https://www.jstor.org/stable/2534001?seq=1>; Rodriguez-Alvarez, M.X. et al. (2011a) <doi:10.1016/j.csda.2010.07.018>; Rodriguez-Alvarez, M.X. et al. (2011a) <doi:10.1007/s11222-010-9184-1>. Please see Rodriguez-Alvarez, M.X. and Inacio, V. (20208) <arXiv:2003.13111> for more details.
Author: Maria Xose Rodriguez-Alvarez [aut, cre]
(<https://orcid.org/0000-0002-1329-9238>),
Vanda Inacio [aut] (<https://orcid.org/0000-0001-8084-1616>)
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@bcamath.org>
Diff between ROCnReg versions 1.0 dated 2020-03-19 and 1.0-1 dated 2020-04-24
DESCRIPTION | 10 - MD5 | 164 ++++++++++++++--------------- NEWS |only R/AROC.bnp.R | 95 ++++++++-------- R/AROC.kernel.R | 22 +-- R/AROC.sp.R | 60 +++------- R/bddp.R | 40 +++---- R/cROC.bnp.R | 145 +++++++++++++++---------- R/cROC.kernel.R | 22 +-- R/cROC.sp.R | 92 ++++++---------- R/compute.threshold.AROC.R | 4 R/compute.threshold.FPF.AROC.bnp.R | 4 R/compute.threshold.FPF.AROC.kernel.R | 4 R/compute.threshold.FPF.AROC.sp.R | 4 R/compute.threshold.FPF.cROC.bnp.R | 4 R/compute.threshold.FPF.cROC.kernel.R | 4 R/compute.threshold.FPF.cROC.sp.R | 4 R/compute.threshold.FPF.pooledROC.BB.R | 4 R/compute.threshold.FPF.pooledROC.dpm.R | 4 R/compute.threshold.FPF.pooledROC.emp.R | 4 R/compute.threshold.FPF.pooledROC.kernel.R | 4 R/compute.threshold.YI.AROC.bnp.R | 4 R/compute.threshold.YI.AROC.kernel.R | 6 - R/compute.threshold.YI.AROC.sp.R | 6 - R/compute.threshold.YI.cROC.bnp.R | 4 R/compute.threshold.YI.cROC.kernel.R | 8 - R/compute.threshold.YI.cROC.sp.R | 8 - R/compute.threshold.YI.pooledROC.BB.R | 4 R/compute.threshold.YI.pooledROC.dpm.R | 4 R/compute.threshold.YI.pooledROC.emp.R | 4 R/compute.threshold.YI.pooledROC.kernel.R | 4 R/compute.threshold.cROC.R | 4 R/compute.threshold.pooledROC.R | 4 R/ls.function.R |only R/plot.AROC.R | 2 R/plot.pooledROC.R | 2 R/pooledROC.BB.R | 8 - R/pooledROC.dpm.R | 8 - R/pooledROC.emp.R | 8 - R/pooledROC.kernel.R | 8 - R/predictive.checks.AROC.bnp.R | 6 - R/predictive.checks.cROC.bnp.R | 8 - R/predictive.checks.helper.R | 8 - R/print.AROC.R | 2 R/print.cROC.R | 2 R/print.pooledROC.R | 2 R/print.summary.AROC.R | 11 + R/print.summary.cROC.R | 27 ++-- R/regnth.R | 18 +-- R/summary.AROC.R | 30 ++--- R/summary.cROC.R | 35 +++--- R/summary.pooledROC.R | 10 - build/partial.rdb |binary man/AROC.bnp.Rd | 42 +++---- man/AROC.kernel.Rd | 18 +-- man/AROC.sp.Rd | 28 ++-- man/ROCnReg-package.Rd | 8 - man/cROC.bnp.Rd | 44 +++---- man/cROC.kernel.Rd | 18 +-- man/cROC.sp.Rd | 30 ++--- man/compute.threshold.AROC.Rd | 12 +- man/compute.threshold.cROC.Rd | 18 +-- man/compute.threshold.pooledROC.Rd | 16 +- man/densitycontrol.Rd | 12 +- man/densitycontrol.aroc.Rd | 10 - man/endosyn.Rd | 2 man/mcmccontrol.Rd | 14 +- man/pauccontrol.Rd | 16 +- man/plot.AROC.Rd | 16 +- man/plot.cROC.Rd | 20 +-- man/plot.pooledROC.Rd | 12 +- man/pooledROC.BB.Rd | 12 +- man/pooledROC.dpm.Rd | 14 +- man/pooledROC.emp.Rd | 12 +- man/pooledROC.kernel.Rd | 18 +-- man/predictive.checks.Rd | 16 +- man/print.AROC.Rd | 14 +- man/print.cROC.Rd | 16 +- man/print.pooledROC.Rd | 8 - man/priorcontrol.bnp.Rd | 8 - man/psa.Rd | 12 +- man/summary.AROC.Rd | 12 +- man/summary.cROC.Rd | 17 +-- man/summary.pooledROC.Rd | 8 - 84 files changed, 723 insertions(+), 729 deletions(-)
Title: Draws Overview of Outliers (O3) Plots
Description: Potential outliers are identified for all combinations of a dataset's variables. O3 plots are described in Unwin(2019) <doi:10.1080/10618600.2019.1575226>. The available methods are HDoutliers() from the package 'HDoutliers', FastPCS() from the package 'FastPCS', mvBACON() from 'robustX', adjOutlyingness() from 'robustbase', DectectDeviatingCells() from 'cellWise', covMcd() from 'robustbase'.
Author: Antony Unwin
Maintainer: Antony Unwin <unwin@math.uni-augsburg.de>
Diff between OutliersO3 versions 0.6.2 dated 2019-03-23 and 0.6.3 dated 2020-04-24
DESCRIPTION | 8 MD5 | 52 ++-- NEWS | 5 R/O3plotM.R | 7 R/O3plotT.R | 5 README.md | 66 +++-- build/vignette.rds |binary inst/doc/DrawingO3plots.R | 12 inst/doc/DrawingO3plots.Rmd | 20 - inst/doc/DrawingO3plots.html | 360 +++++++++++++++++++++++------ inst/doc/MultTolLevels.R | 12 inst/doc/MultTolLevels.Rmd | 2 inst/doc/MultTolLevels.html | 347 ++++++++++++++++++++++------ inst/doc/PCPsO3.R | 6 inst/doc/PCPsO3.Rmd | 6 inst/doc/PCPsO3.html | 383 +++++++++++++++++++++++-------- inst/doc/xtraO3methods.R | 2 inst/doc/xtraO3methods.html | 295 ++++++++++++++++++++--- man/Election2005.Rd | 1 man/O3plotM.Rd | 2 man/O3plotT.Rd | 2 man/O3prep.Rd | 6 man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary vignettes/DrawingO3plots.Rmd | 20 - vignettes/MultTolLevels.Rmd | 2 vignettes/PCPsO3.Rmd | 6 27 files changed, 1249 insertions(+), 378 deletions(-)
Title: False Discovery Rate Procedures Under Discrete and Heterogeneous
Null Distributions
Description: It is known that current false discovery rate (FDR) procedures can be very conservative when applied to multiple testing in the discrete paradigm where p-values (and test statistics) have discrete and heterogeneous null distributions. This package implements more powerful weighted or adaptive FDR procedures for FDR control and estimation in the discrete paradigm. The package takes in the original data set rather than just the p-values in order to carry out the adjustments for discreteness and heterogeneity of p-value distributions. The package implements methods for two types of test statistics and their p-values: (a) binomial test on if two independent Poisson distributions have the same means, (b) Fisher's exact test on if the conditional distribution is the same as the marginal distribution for two binomial distributions, or on if two independent binomial distributions have the same probabilities of success.
Author: Xiongzhi Chen and Rebecca W. Doerge <rwdoerge@andrew.cmu.edu>
Maintainer: Xiongzhi Chen <xiongzhi.chen@wsu.edu>
Diff between fdrDiscreteNull versions 1.3 dated 2018-01-05 and 1.4 dated 2020-04-24
DESCRIPTION | 8 MD5 | 19 - NAMESPACE | 2 R/BHplus.r |only R/BHplus_mod.r |only R/Generalized_FDR_Estimators.r | 2 R/MultipleTesting_HeteroDist.r | 140 +++++----- R/MultipleTesting_HeteroDist_ModFuncs.r | 448 +++++++++++++++----------------- data/hivdata.RData |only man/BHPlusTwoSide.Rd |only man/GeneralizedEstimatorsGrouped.Rd | 47 +-- man/GeneralizedFDREstimators.Rd | 19 - man/hivdata.Rd |only 13 files changed, 333 insertions(+), 352 deletions(-)
More information about fdrDiscreteNull at CRAN
Permanent link
Title: Procedures for Ecological Assessment of Surface Waters
Description: Functions for evaluating and visualizing
ecological assessment procedures for surface waters
containing physical, chemical and biological assessments
in the form of value functions.
Author: Nele Schuwirth <nele.schuwirth@eawag.ch> and Peter Reichert <peter.reichert@eawag.ch>
with contributions by Simone Langhans and Christian Michel
Maintainer: Nele Schuwirth <nele.schuwirth@eawag.ch>
Diff between ecoval versions 1.2.6 dated 2020-03-20 and 1.2.7 dated 2020-04-24
DESCRIPTION | 8 +- MD5 | 22 ++--- NAMESPACE | 3 R/msk.macrophytes.2017.prepare.data.R | 134 +++++++++++++++++++--------------- data/ecoval_data.RData |binary inst/NEWS | 8 ++ man/ecoval-package.Rd | 4 - man/figures/lakemorphol2016.pdf |binary man/figures/lakemorphol2016French.pdf |binary man/figures/lakemorphol2016German.pdf |binary man/msk.invertebrates.2010.create.Rd | 2 man/val.invertebrates.create.Rd | 2 12 files changed, 106 insertions(+), 77 deletions(-)
Title: Recursive Partitioning for Longitudinal Data and Right Censored
Data Using Baseline Covariates
Description: Constructs tree for continuous longitudinal data and survival data using baseline covariates as partitioning variables according to the 'LongCART' and 'SurvCART' algorithm, respectively.
Author: Madan G Kundu
Maintainer: Madan G Kundu <madan_g.kundu@yahoo.com>
Diff between LongCART versions 1.1 dated 2020-04-02 and 2.0 dated 2020-04-24
DESCRIPTION | 16 ++++++++-------- MD5 | 23 +++++++++++++++++------ NAMESPACE | 14 ++++++++++++++ R/StabCat_surv.R |only R/StabCont_surv.R |only R/SurvCART.R |only R/plot_n_text_nouse.R | 2 +- data/GBSG2.rda |only man/GBSG2.Rd |only man/KMPlot.SurvCART.Rd |only man/LongCART.Rd | 14 ++++++++------ man/StabCat.surv.Rd |only man/StabCont.surv.Rd |only man/SurvCART.Rd |only man/plot.SurvCART.Rd |only man/plotLongCART.Rd | 14 +++++++------- man/text.SurvCART.Rd |only man/textLongCART.Rd | 16 ++++++++-------- 18 files changed, 63 insertions(+), 36 deletions(-)
Title: Model-Free Functional Chi-Squared and Exact Tests
Description: Statistical hypothesis testing methods for
inferring model-free functional dependency using asymptotic
chi-squared or exact distributions. Functional test
statistics are asymmetric and functionally optimal, unique
from other related statistics. Tests in this package reveal
evidence for causality based on the
causality-by-functionality principle. They include
asymptotic functional chi-squared tests
(Zhang & Song 2013) <arXiv:1311.2707> and an exact
functional test (Zhong & Song 2019)
<doi:10.1109/TCBB.2018.2809743>. The normalized functional
chi-squared test was used by Best Performer 'NMSUSongLab'
in HPN-DREAM (DREAM8) Breast Cancer Network Inference
Challenges (Hill et al 2016) <doi:10.1038/nmeth.3773>. A
function index (Zhong & Song 2019)
<doi:10.1186/s12920-019-0565-9> (Kumar et al 2018)
<doi:10.1109/BIBM.2018.8621502> derived from the
functional test statistic offers a new effect size measure
for the strength of functional dependency, a better
alternative to conditional entropy in many aspects. For
continuous data, these tests offer an advantage over
regression analysis when a parametric functional form
cannot be assumed; for categorical data, they provide a
novel means to assess directional dependency not possible
with symmetrical Pearson's chi-squared or Fisher's exact
tests.
Author: Yang Zhang [aut],
Hua Zhong [aut] (<https://orcid.org/0000-0003-1962-2603>),
Hien Nguyen [aut] (<https://orcid.org/0000-0002-7237-4752>),
Ruby Sharma [aut],
Sajal Kumar [aut] (<https://orcid.org/0000-0003-0930-1582>),
Joe Song [aut, cre] (<https://orcid.org/0000-0002-6883-6547>)
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.4.9.2 dated 2020-03-14 and 2.5.0 dated 2020-04-24
DESCRIPTION | 13 +- MD5 | 32 +++--- NAMESPACE | 2 NEWS | 82 +++++++++++---- R/simulate_tables.R | 52 +++++---- README.md | 3 build/partial.rdb |binary inst/CITATION | 78 ++++++++++++-- inst/REFERENCES.bib | 214 +++++++++++++++++++++-------------------- man/EFT.Rd | 11 -- man/FunChisq-deprecated.Rd | 2 man/FunChisq-package.Rd | 52 --------- man/cond.fun.chisq.test.Rd | 13 +- man/fun.chisq.test.Rd | 35 ------ man/noise_model.Rd | 3 man/simulate_tables.Rd | 47 ++++----- tests/testthat/test_simulate.R | 29 ++--- 17 files changed, 350 insertions(+), 318 deletions(-)
Title: A 'dplyr' Interface for Crunch
Description: In order to facilitate analysis of datasets hosted on the Crunch
data platform <http://crunch.io/>, the 'crplyr' package implements 'dplyr'
methods on top of the Crunch backend. The usual methods 'select', 'filter',
'group_by', 'summarize', and 'collect' are implemented in such a way as to
perform as much computation on the server and pull as little data locally
as possible.
Author: Greg Freedman Ellis [aut, cre],
Jonathan Keane [aut],
Neal Richardson [aut],
Mike Malecki [aut],
Gordon Shotwell [aut]
Maintainer: Greg Freedman Ellis <greg@crunch.io>
Diff between crplyr versions 0.3.3 dated 2020-01-14 and 0.3.4 dated 2020-04-24
crplyr-0.3.3/crplyr/man/as_tibble.CrunchCube.Rd |only crplyr-0.3.4/crplyr/DESCRIPTION | 22 crplyr-0.3.4/crplyr/MD5 | 86 - crplyr-0.3.4/crplyr/NAMESPACE | 41 crplyr-0.3.4/crplyr/NEWS.md | 7 crplyr-0.3.4/crplyr/R/as-tibble.R | 34 crplyr-0.3.4/crplyr/R/collect.R | 2 crplyr-0.3.4/crplyr/R/compat-lazyeval.R |only crplyr-0.3.4/crplyr/R/filter.R | 50 crplyr-0.3.4/crplyr/R/group-by.R | 101 + crplyr-0.3.4/crplyr/R/plotting.R | 15 crplyr-0.3.4/crplyr/R/select.R | 6 crplyr-0.3.4/crplyr/R/summarize.R | 37 crplyr-0.3.4/crplyr/README.md | 2 crplyr-0.3.4/crplyr/build/vignette.rds |binary crplyr-0.3.4/crplyr/inst/doc/plotting.Rmd | 4 crplyr-0.3.4/crplyr/inst/doc/plotting.html | 626 +++++----- crplyr-0.3.4/crplyr/man/as_cr_tibble.Rd |only crplyr-0.3.4/crplyr/man/filter.Rd | 8 crplyr-0.3.4/crplyr/man/filter_.CrunchDataset.Rd |only crplyr-0.3.4/crplyr/man/group_by.Rd | 4 crplyr-0.3.4/crplyr/man/select.Rd | 2 crplyr-0.3.4/crplyr/man/summarize.Rd | 5 crplyr-0.3.4/crplyr/tests/figs/autoplot/cat-cat-bar.svg | 4 crplyr-0.3.4/crplyr/tests/figs/autoplot/cat-cat-prop-bar.svg | 4 crplyr-0.3.4/crplyr/tests/figs/autoplot/cat-cat-prop-tile.svg | 20 crplyr-0.3.4/crplyr/tests/figs/autoplot/cat-cat-tile.svg | 26 crplyr-0.3.4/crplyr/tests/figs/autoplot/cat-x-mr-x-mr-bar.svg | 16 crplyr-0.3.4/crplyr/tests/figs/autoplot/cat-x-mr-x-mr-tile.svg | 20 crplyr-0.3.4/crplyr/tests/figs/autoplot/catarray-x-cat-bar.svg | 28 crplyr-0.3.4/crplyr/tests/figs/autoplot/catarray-x-cat-tile.svg | 38 crplyr-0.3.4/crplyr/tests/figs/autoplot/catarray-x-cat-x-cat-bar.svg | 540 ++++---- crplyr-0.3.4/crplyr/tests/figs/autoplot/catarray-x-cat-x-cat-tile.svg | 20 crplyr-0.3.4/crplyr/tests/figs/autoplot/catarray-x-mr-bar.svg | 54 crplyr-0.3.4/crplyr/tests/figs/autoplot/catarray-x-mr-tile.svg | 20 crplyr-0.3.4/crplyr/tests/figs/autoplot/univariate-bar.svg | 2 crplyr-0.3.4/crplyr/tests/figs/autoplot/univariate-tile.svg | 38 crplyr-0.3.4/crplyr/tests/testthat/test-as-tibble.R | 23 crplyr-0.3.4/crplyr/tests/testthat/test-filter.R | 19 crplyr-0.3.4/crplyr/tests/testthat/test-group-by.R | 20 crplyr-0.3.4/crplyr/tests/testthat/test-mutate.R | 2 crplyr-0.3.4/crplyr/tests/testthat/test-plots-vdiff.R | 5 crplyr-0.3.4/crplyr/tests/testthat/test-select.R | 10 crplyr-0.3.4/crplyr/tests/testthat/test-summarize.R | 6 crplyr-0.3.4/crplyr/tests/testthat/test-tbl_crunch_cube.R | 14 crplyr-0.3.4/crplyr/vignettes/plotting.Rmd | 4 46 files changed, 1159 insertions(+), 826 deletions(-)
Title: Product Concordance
Description: A set of utilities for matching products in different
classification codes used in international trade
research. It supports concordance between the Harmonized
System (HS0, HS1, HS2, HS3, HS4, HS5, HS combined), the Standard
International Trade Classification (SITC1, SITC2, SITC3, SITC4),
the North American Industry Classification System (NAICS combined),
as well as the Broad Economic Categories (BEC), the International
Standard of Industrial Classification (ISIC), and the Standard Industrial
Classification (SIC). It also provides code nomenclature/descriptions
look-up, Rauch classification look-up (via concordance to SITC2), and
trade elasticity look-up (via concordance to HS0 or SITC3
codes).
Author: Steven Liao [aut, cre],
In Song Kim [aut],
Sayumi Miyano [aut],
Feng Zhu [aut]
Maintainer: Steven Liao <steven.liao@ucr.edu>
Diff between concordance versions 1.6 dated 2016-01-11 and 2.0.0 dated 2020-04-24
concordance-1.6/concordance/R/concord_test.R |only concordance-1.6/concordance/R/desc.R |only concordance-1.6/concordance/R/extend_concord.R |only concordance-1.6/concordance/R/proddiff.R |only concordance-1.6/concordance/R/rauch.R |only concordance-1.6/concordance/R/sigma.R |only concordance-1.6/concordance/R/sigma2.R |only concordance-1.6/concordance/data/BWsigma.rda |only concordance-1.6/concordance/data/codedesc.rda |only concordance-1.6/concordance/data/concord_data.rda |only concordance-1.6/concordance/data/rauch.rda |only concordance-1.6/concordance/data/sigmatab.rda |only concordance-1.6/concordance/data/sitc2_rauch.rda |only concordance-1.6/concordance/man/BWsigma.Rd |only concordance-1.6/concordance/man/Rauch.Rd |only concordance-1.6/concordance/man/code_lengths.Rd |only concordance-1.6/concordance/man/codedesc.Rd |only concordance-1.6/concordance/man/concord_data.Rd |only concordance-1.6/concordance/man/concord_long.Rd |only concordance-1.6/concordance/man/concord_test.Rd 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concordance-2.0.0/concordance/R/concord_hs_sitc.R |only concordance-2.0.0/concordance/R/concord_sitc.R |only concordance-2.0.0/concordance/R/concord_sitc_naics.R |only concordance-2.0.0/concordance/R/data.R |only concordance-2.0.0/concordance/R/get_desc.R |only concordance-2.0.0/concordance/R/get_proddiff.R |only concordance-2.0.0/concordance/R/get_sigma.R |only concordance-2.0.0/concordance/README.md |only concordance-2.0.0/concordance/data/bec_desc.RData |only concordance-2.0.0/concordance/data/datalist |only concordance-2.0.0/concordance/data/hs0_desc.RData |only concordance-2.0.0/concordance/data/hs0_naics.RData |only concordance-2.0.0/concordance/data/hs0_sitc1.RData |only concordance-2.0.0/concordance/data/hs0_sitc2.RData |only concordance-2.0.0/concordance/data/hs0_sitc3.RData |only concordance-2.0.0/concordance/data/hs0_sitc4.RData |only concordance-2.0.0/concordance/data/hs1_desc.RData |only concordance-2.0.0/concordance/data/hs1_hs0.RData |only concordance-2.0.0/concordance/data/hs1_naics.RData |only concordance-2.0.0/concordance/data/hs1_sitc1.RData |only concordance-2.0.0/concordance/data/hs1_sitc2.RData |only concordance-2.0.0/concordance/data/hs1_sitc3.RData |only concordance-2.0.0/concordance/data/hs1_sitc4.RData |only concordance-2.0.0/concordance/data/hs2_desc.RData |only concordance-2.0.0/concordance/data/hs2_hs0.RData |only concordance-2.0.0/concordance/data/hs2_hs1.RData |only concordance-2.0.0/concordance/data/hs2_naics.RData |only concordance-2.0.0/concordance/data/hs2_sitc1.RData |only concordance-2.0.0/concordance/data/hs2_sitc2.RData |only concordance-2.0.0/concordance/data/hs2_sitc3.RData |only concordance-2.0.0/concordance/data/hs2_sitc4.RData |only concordance-2.0.0/concordance/data/hs3_desc.RData |only concordance-2.0.0/concordance/data/hs3_hs0.RData |only concordance-2.0.0/concordance/data/hs3_hs1.RData |only concordance-2.0.0/concordance/data/hs3_hs2.RData |only concordance-2.0.0/concordance/data/hs3_naics.RData |only concordance-2.0.0/concordance/data/hs3_sitc1.RData |only concordance-2.0.0/concordance/data/hs3_sitc2.RData |only concordance-2.0.0/concordance/data/hs3_sitc3.RData |only concordance-2.0.0/concordance/data/hs3_sitc4.RData |only concordance-2.0.0/concordance/data/hs4_desc.RData |only concordance-2.0.0/concordance/data/hs4_hs0.RData |only concordance-2.0.0/concordance/data/hs4_hs1.RData |only concordance-2.0.0/concordance/data/hs4_hs2.RData |only concordance-2.0.0/concordance/data/hs4_hs3.RData |only concordance-2.0.0/concordance/data/hs4_naics.RData |only concordance-2.0.0/concordance/data/hs4_sitc1.RData |only concordance-2.0.0/concordance/data/hs4_sitc2.RData |only concordance-2.0.0/concordance/data/hs4_sitc3.RData |only concordance-2.0.0/concordance/data/hs4_sitc4.RData |only concordance-2.0.0/concordance/data/hs5_desc.RData |only concordance-2.0.0/concordance/data/hs5_hs0.RData |only concordance-2.0.0/concordance/data/hs5_hs1.RData |only concordance-2.0.0/concordance/data/hs5_hs2.RData |only concordance-2.0.0/concordance/data/hs5_hs3.RData |only concordance-2.0.0/concordance/data/hs5_hs4.RData |only concordance-2.0.0/concordance/data/hs5_naics.RData |only concordance-2.0.0/concordance/data/hs5_sitc1.RData |only concordance-2.0.0/concordance/data/hs5_sitc2.RData |only concordance-2.0.0/concordance/data/hs5_sitc3.RData |only concordance-2.0.0/concordance/data/hs5_sitc4.RData |only concordance-2.0.0/concordance/data/hs_desc.RData |only concordance-2.0.0/concordance/data/hs_naics.RData |only concordance-2.0.0/concordance/data/hs_sitc1.RData |only concordance-2.0.0/concordance/data/hs_sitc2.RData |only concordance-2.0.0/concordance/data/hs_sitc3.RData |only concordance-2.0.0/concordance/data/hs_sitc4.RData |only concordance-2.0.0/concordance/data/isic2_desc.RData |only concordance-2.0.0/concordance/data/isic3_desc.RData |only concordance-2.0.0/concordance/data/isic4_desc.RData |only concordance-2.0.0/concordance/data/naics2002_desc.RData |only concordance-2.0.0/concordance/data/naics2007_desc.RData |only concordance-2.0.0/concordance/data/naics2012_desc.RData |only concordance-2.0.0/concordance/data/naics2017_desc.RData |only concordance-2.0.0/concordance/data/sigma_hs0.RData |only concordance-2.0.0/concordance/data/sigma_sitc3.RData |only concordance-2.0.0/concordance/data/sitc1_desc.RData |only concordance-2.0.0/concordance/data/sitc1_naics.RData |only concordance-2.0.0/concordance/data/sitc2_desc.RData |only concordance-2.0.0/concordance/data/sitc2_naics.RData |only concordance-2.0.0/concordance/data/sitc2_rauch.RData |only concordance-2.0.0/concordance/data/sitc2_sitc1.RData |only concordance-2.0.0/concordance/data/sitc3_desc.RData |only concordance-2.0.0/concordance/data/sitc3_naics.RData |only concordance-2.0.0/concordance/data/sitc3_sitc1.RData |only concordance-2.0.0/concordance/data/sitc3_sitc2.RData |only concordance-2.0.0/concordance/data/sitc4_desc.RData |only concordance-2.0.0/concordance/data/sitc4_naics.RData |only concordance-2.0.0/concordance/data/sitc4_sitc1.RData |only concordance-2.0.0/concordance/data/sitc4_sitc2.RData |only concordance-2.0.0/concordance/data/sitc4_sitc3.RData |only concordance-2.0.0/concordance/man/bec_desc.Rd |only concordance-2.0.0/concordance/man/concord.Rd | 131 ++++----- concordance-2.0.0/concordance/man/concord_hs.Rd |only concordance-2.0.0/concordance/man/concord_hs_naics.Rd |only concordance-2.0.0/concordance/man/concord_hs_sitc.Rd |only concordance-2.0.0/concordance/man/concord_sitc.Rd |only concordance-2.0.0/concordance/man/concord_sitc_naics.Rd |only concordance-2.0.0/concordance/man/get_desc.Rd |only concordance-2.0.0/concordance/man/get_proddiff.Rd |only concordance-2.0.0/concordance/man/get_sigma.Rd |only concordance-2.0.0/concordance/man/hs0_desc.Rd |only 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Title: Generates Aoristic Probability Distributions
Description: It can sometimes be difficult to ascertain when some events (such as property crime)
occur because the victim is not present when the crime happens. As a result, police databases often
record a 'start' (or 'from') date and time, and an 'end' (or 'to') date and time. The time span between
these date/times can be minutes, hours, or sometimes days, hence the term 'Aoristic'.
Aoristic is one of the past tenses in Greek and represents an uncertain occurrence in time.
For events with a location describes with either a latitude/longitude, or X,Y coordinate pair,
and a start and end date/time, this package generates an aoristic data frame with aoristic weighted
probability values for each hour of the week, for each observation. Outputs include an aoristic data frame, as well as summary graphs and displays.
For more information see:
Ratcliffe, JH (2002) Aoristic signatures and the temporal analysis of high volume crime patterns,
Journal of Quantitative Criminology. 18 (1): 23-43.
Note: This package replaces an original 'aoristic' package (version 0.6) by George Kikuchi that has been discontinued with his permission.
Author: Jerry Ratcliffe
Maintainer: Jerry Ratcliffe <jhr@temple.edu>
Diff between aoristic versions 0.6 dated 2015-01-10 and 1.0.0 dated 2020-04-24
aoristic-0.6/aoristic/R/aoristic-package.R |only aoristic-0.6/aoristic/R/aoristic.all.graph.R |only aoristic-0.6/aoristic/R/aoristic.density.R |only aoristic-0.6/aoristic/R/aoristic.grid.R |only aoristic-0.6/aoristic/R/aoristic.shp.R |only aoristic-0.6/aoristic/R/aoristic.spdf.R |only aoristic-0.6/aoristic/data/aoristic.rda |only aoristic-0.6/aoristic/demo |only aoristic-0.6/aoristic/inst |only aoristic-0.6/aoristic/man/aoristic-package.Rd |only aoristic-0.6/aoristic/man/aoristic.Rd |only aoristic-1.0.0/aoristic/DESCRIPTION | 56 ++--- aoristic-1.0.0/aoristic/MD5 | 56 ++--- aoristic-1.0.0/aoristic/NAMESPACE | 35 --- aoristic-1.0.0/aoristic/R/aoristic.datacheck.R |only aoristic-1.0.0/aoristic/R/aoristic.df.R | 240 ++++++++++++++++------ aoristic-1.0.0/aoristic/R/aoristic.graph.R |only aoristic-1.0.0/aoristic/R/aoristic.map.R |only aoristic-1.0.0/aoristic/R/aoristic.ref.R |only aoristic-1.0.0/aoristic/R/aoristic.summary.R |only aoristic-1.0.0/aoristic/R/data.R |only aoristic-1.0.0/aoristic/R/defunct.R |only aoristic-1.0.0/aoristic/README.md | 232 +++++++++++++++++++++ aoristic-1.0.0/aoristic/data/NYburg.rda |only aoristic-1.0.0/aoristic/data/dcburglaries.rda |only aoristic-1.0.0/aoristic/data/dcburgsum.rda |only aoristic-1.0.0/aoristic/man/CouncilDistrict.Rd | 31 +- aoristic-1.0.0/aoristic/man/NYburg.Rd |only aoristic-1.0.0/aoristic/man/aoristic.all.graph.Rd | 64 ++--- aoristic-1.0.0/aoristic/man/aoristic.datacheck.Rd |only aoristic-1.0.0/aoristic/man/aoristic.density.Rd | 51 +--- aoristic-1.0.0/aoristic/man/aoristic.df.Rd | 40 ++- aoristic-1.0.0/aoristic/man/aoristic.graph.Rd |only aoristic-1.0.0/aoristic/man/aoristic.grid.Rd | 46 +--- aoristic-1.0.0/aoristic/man/aoristic.map.Rd |only aoristic-1.0.0/aoristic/man/aoristic.ref.Rd |only aoristic-1.0.0/aoristic/man/aoristic.shp.Rd | 46 +--- aoristic-1.0.0/aoristic/man/aoristic.spdf.Rd | 49 +--- aoristic-1.0.0/aoristic/man/aoristic.summary.Rd |only aoristic-1.0.0/aoristic/man/arlington.Rd | 31 +- aoristic-1.0.0/aoristic/man/dcburglaries.Rd |only aoristic-1.0.0/aoristic/man/dcburgsum.Rd |only aoristic-1.0.0/aoristic/man/figures |only 43 files changed, 600 insertions(+), 377 deletions(-)
Title: Alternative Meta-Analysis Methods
Description: Provides alternative statistical methods for meta-analysis, including new heterogeneity tests and measures that are robust to outliers; measures, tests, and visualization tools for publication bias; meta-analysis methods for synthesizing proportions; models for multivariate meta-analysis, etc.
Author: Lifeng Lin [aut, cre] (<https://orcid.org/0000-0002-3562-9816>),
Haitao Chu [aut] (<https://orcid.org/0000-0003-0932-598X>)
Maintainer: Lifeng Lin <linl@stat.fsu.edu>
Diff between altmeta versions 2.3 dated 2020-01-26 and 3.0 dated 2020-04-24
DESCRIPTION | 14 +++--- MD5 | 89 +++++++++++++++++++++++++++++++++++--------- NAMESPACE | 9 ++-- R/check.counts.R |only R/find.counts.R |only R/hypergeometric.R |only R/maprop.glmm.R |only R/maprop.twostep.R |only R/pb.as.rank.R |only R/pb.as.reg.R |only R/pb.as.reg.het.R |only R/pb.count.R |only R/pb.hybrid.binary.R |only R/pb.hybrid.generic.R |only R/pb.inv.n.R |only R/pb.inv.sqrt.n.R |only R/pb.n.R |only R/pb.rank.R |only R/pb.reg.R |only R/pb.reg.het.R |only R/pb.score.R |only R/pb.skew.R |only R/pb.skew.het.R |only R/pb.smoothed.R |only R/pb.smoothed.het.R |only R/pb.trimfill.R |only R/ssfunnel.R |only R/ssfunnel.lor.R |only R/ssfunnel.lrr.R |only R/ssfunnel.md.R |only R/ssfunnel.rd.R |only R/ssfunnel.smd.R |only build |only data/dat.annane.rda |only data/dat.barlow.rda |only data/dat.beck17.rda |only data/dat.butters.rda |only data/dat.chor.rda |only data/dat.kaner.rda |only data/dat.paige.rda |only data/dat.plourde.rda |only data/dat.whiting.rda |only data/dat.williams.rda |only man/dat.aex.Rd | 6 +- man/dat.annane.Rd |only man/dat.barlow.Rd |only man/dat.beck17.Rd |only man/dat.butters.Rd |only man/dat.chor.Rd |only man/dat.fib.Rd | 10 ++-- man/dat.ha.Rd | 8 +-- man/dat.hipfrac.Rd | 8 +-- man/dat.kaner.Rd |only man/dat.lcj.Rd | 8 +-- man/dat.paige.Rd |only man/dat.plourde.Rd |only man/dat.pte.Rd | 8 +-- man/dat.slf.Rd | 8 +-- man/dat.whiting.Rd |only man/dat.williams.Rd |only man/maprop.glmm.Rd |only man/maprop.twostep.Rd |only man/metahet.Rd | 19 ++++----- man/metaoutliers.Rd | 13 +++--- man/metapb.Rd | 13 +++--- man/mvma.Rd | 13 +++--- man/mvma.bayesian.Rd | 37 +++++++++--------- man/mvma.hybrid.Rd | 21 ++++++---- man/mvma.hybrid.bayesian.Rd | 35 +++++++++-------- man/pb.hybrid.binary.Rd |only man/pb.hybrid.generic.Rd |only man/plot.metaoutliers.Rd | 14 ++++-- man/ssfunnel.Rd |only 73 files changed, 207 insertions(+), 126 deletions(-)
More information about ItemResponseTrees at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-20 1.3.3
2019-06-14 1.3.1
2018-08-13 1.1.1
2018-04-01 1.0.2
2018-03-29 1.0.0
2017-07-25 0.9.3
2017-07-17 0.9.2
2017-03-12 0.8.1
2017-02-13 0.7.2
Title: Semi-Automatic Analysis of Sound Correspondences
Description: A set of tools that can be used in computer-aided analysis of
sound correspondences between languages, plus several helper functions.
Analytic functions range from purely qualitative analysis, through
statistic methods yielding qualitative results, to an entirely
quantitative approach.
Author: Kamil Stachowski [aut, cre]
Maintainer: Kamil Stachowski <kamil.stachowski@gmail.com>
Diff between soundcorrs versions 0.1.0 dated 2020-01-22 and 0.1.1 dated 2020-04-24
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS |only R/soundcorrs.R | 34 +++++++++++++++++++++++++++------- build/vignette.rds |binary inst/doc/soundcorrs.R | 2 +- inst/doc/soundcorrs.Rmd | 4 ++-- inst/doc/soundcorrs.html | 28 +++++++++++++--------------- inst/extdata/trans-ipa.tsv | 2 ++ vignettes/soundcorrs.Rmd | 4 ++-- 10 files changed, 59 insertions(+), 38 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory models can be estimated with quadrature (EM)
or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modeling
item and person covariates. Finally, latent class models such as the DINA,
DINO, multidimensional latent class, and several other discrete latent
variable models, including mixture and zero-inflated response models,
are supported.
Author: Phil Chalmers [aut, cre] (<https://orcid.org/0000-0001-5332-2810>),
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.31 dated 2019-09-14 and 1.32 dated 2020-04-24
mirt-1.31/mirt/R/LoadPars.R |only mirt-1.31/mirt/R/PrepData.R |only mirt-1.31/mirt/R/SE.methods.R |only mirt-1.31/mirt/R/calcLogLik.R |only mirt-1.31/mirt/R/model.elements.R |only mirt-1.32/mirt/DESCRIPTION | 10 - mirt-1.32/mirt/MD5 | 170 ++++++++++----------- mirt-1.32/mirt/NEWS.md | 54 ++++++ mirt-1.32/mirt/R/02-item_methods.R | 50 ++++-- mirt-1.32/mirt/R/03-estimation.R | 59 ++++--- mirt-1.32/mirt/R/04-PrepData.R |only mirt-1.32/mirt/R/05-model.elements.R |only mirt-1.32/mirt/R/06-LoadPars.R |only mirt-1.32/mirt/R/07-calcLogLik.R |only mirt-1.32/mirt/R/08-SE.methods.R |only mirt-1.32/mirt/R/DIF.R | 47 +++-- mirt-1.32/mirt/R/DRF.R | 26 ++- mirt-1.32/mirt/R/Discrete-methods.R | 2 mirt-1.32/mirt/R/EMstep.group.R | 40 +++- mirt-1.32/mirt/R/EMstep.utils.R | 28 +-- mirt-1.32/mirt/R/MHRM.group.R | 8 mirt-1.32/mirt/R/MHRM.utils.R | 42 ++--- mirt-1.32/mirt/R/PLCI.mirt.R | 3 mirt-1.32/mirt/R/SingleGroup-methods.R | 25 +-- mirt-1.32/mirt/R/bfactor.R | 7 mirt-1.32/mirt/R/boot.LR.R | 4 mirt-1.32/mirt/R/createGroup.R | 13 + mirt-1.32/mirt/R/extract.group.R | 12 + mirt-1.32/mirt/R/extract.mirt.R | 6 mirt-1.32/mirt/R/fscores.internal.R | 56 ++++-- mirt-1.32/mirt/R/itemfit.R | 65 ++------ mirt-1.32/mirt/R/lagrange.R | 8 mirt-1.32/mirt/R/marginal_rxx.R | 2 mirt-1.32/mirt/R/mdirt.R | 1 mirt-1.32/mirt/R/mirt.R | 51 +++--- mirt-1.32/mirt/R/mirt.model.R | 4 mirt-1.32/mirt/R/mirtCluster.R | 12 + mirt-1.32/mirt/R/mixedmirt.R | 7 mirt-1.32/mirt/R/multipleGroup.R | 22 +- mirt-1.32/mirt/R/personfit.R | 61 ++----- mirt-1.32/mirt/R/utils.R | 41 ++++- mirt-1.32/mirt/build/partial.rdb |binary mirt-1.32/mirt/build/vignette.rds |binary mirt-1.32/mirt/man/DIF.Rd | 24 ++ mirt-1.32/mirt/man/DRF.Rd | 32 ++- mirt-1.32/mirt/man/DTF.Rd | 14 + mirt-1.32/mirt/man/M2.Rd | 16 + mirt-1.32/mirt/man/PLCI.mirt.Rd | 15 + mirt-1.32/mirt/man/SIBTEST.Rd | 22 ++ mirt-1.32/mirt/man/anova-method.Rd | 3 mirt-1.32/mirt/man/areainfo.Rd | 11 - mirt-1.32/mirt/man/bfactor.Rd | 11 + mirt-1.32/mirt/man/coef-method.Rd | 18 +- mirt-1.32/mirt/man/createGroup.Rd | 22 ++ mirt-1.32/mirt/man/createItem.Rd | 17 +- mirt-1.32/mirt/man/draw_parameters.Rd | 9 - mirt-1.32/mirt/man/empirical_ES.Rd | 18 +- mirt-1.32/mirt/man/empirical_plot.Rd | 19 +- mirt-1.32/mirt/man/estfun.AllModelClass.Rd | 7 mirt-1.32/mirt/man/expected.test.Rd | 10 - mirt-1.32/mirt/man/extract.mirt.Rd | 4 mirt-1.32/mirt/man/fscores.Rd | 39 +++- mirt-1.32/mirt/man/itemGAM.Rd | 24 ++ mirt-1.32/mirt/man/itemfit.Rd | 38 +++- mirt-1.32/mirt/man/iteminfo.Rd | 3 mirt-1.32/mirt/man/itemplot.Rd | 26 ++- mirt-1.32/mirt/man/mdirt.Rd | 25 ++- mirt-1.32/mirt/man/mirt.Rd | 98 ++++++++---- mirt-1.32/mirt/man/mirt.model.Rd | 28 ++- mirt-1.32/mirt/man/mirtCluster.Rd | 12 + mirt-1.32/mirt/man/mixedmirt.Rd | 41 +++-- mirt-1.32/mirt/man/multipleGroup.Rd | 26 ++- mirt-1.32/mirt/man/numerical_deriv.Rd | 10 - mirt-1.32/mirt/man/personfit.Rd | 4 mirt-1.32/mirt/man/plot-method.Rd | 33 ++-- mirt-1.32/mirt/man/residuals-method.Rd | 25 ++- mirt-1.32/mirt/man/simdata.Rd | 26 ++- mirt-1.32/mirt/man/summary-method.Rd | 10 - mirt-1.32/mirt/man/testinfo.Rd | 10 - mirt-1.32/mirt/src/Estep.cpp | 31 +++ mirt-1.32/mirt/src/Makevars | 3 mirt-1.32/mirt/src/Makevars.win | 3 mirt-1.32/mirt/src/ggum_derivs.cpp | 1 mirt-1.32/mirt/src/traceLinePts.cpp | 9 - mirt-1.32/mirt/tests/tests/test-01-mirtOne.R | 10 - mirt-1.32/mirt/tests/tests/test-02-mirtTwo.R | 20 +- mirt-1.32/mirt/tests/tests/test-03-bfactor.R | 8 mirt-1.32/mirt/tests/tests/test-04-multipleGroup.R | 8 mirt-1.32/mirt/tests/tests/test-07-mixedmirt.R | 11 - mirt-1.32/mirt/tests/tests/test-11-discrete.R | 3 mirt-1.32/mirt/tests/tests/test-16-DCIRT.R | 14 - 91 files changed, 1194 insertions(+), 613 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-17 1.0.12
2019-10-01 1.0.11
2019-09-26 1.0.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-04 1.7.7
2019-11-06 1.7.5
2019-10-10 1.7.4
2018-04-09 1.7.2
2018-02-05 1.7.0
2017-08-29 1.6.3
2017-08-14 1.6.2
2016-05-20 1.5.0
2015-11-27 1.4.6
2015-08-26 1.4.0
2015-07-16 1.3.2
2015-07-07 1.3.1
2015-05-21 1.2.4
2015-03-25 1.2.1
2015-03-23 1.2.0
2015-02-21 1.1.3
2015-01-05 1.1.1
2014-09-17 1.0.0
2014-04-09 0.9.4
2014-02-27 0.9.3
2014-01-30 0.9.2
2013-11-23 0.9.0
Title: Header-Only C++ Mathematical Optimization Library for
'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library
(by the 'MLPACK' team) that provides a simple set of abstractions for writing an
objective function to optimize. Provided within are various standard and
cutting-edge optimizers that include full-batch gradient descent techniques,
small-batch techniques, gradient-free optimizers, and constrained optimization.
The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library
and pairs the appropriate header files from 'armadillo' through the
'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor
'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under
3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2,
'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under
the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under
similar terms. Note that 'Ensmallen' requires a compiler that supports
'C++11' and 'Armadillo' 8.400 or later.
Author: James Joseph Balamuta [aut, cre, cph]
(<https://orcid.org/0000-0003-2826-8458>),
Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between RcppEnsmallen versions 0.2.11.3.1 dated 2020-02-20 and 0.2.12.1.1 dated 2020-04-24
ChangeLog | 9 + DESCRIPTION | 6 MD5 | 28 ++-- NEWS.md | 115 +++++++++-------- build/vignette.rds |binary inst/doc/using-rcppensmallen.html | 20 +- inst/include/ensmallen_bits/callbacks/progress_bar.hpp | 26 +-- inst/include/ensmallen_bits/cmaes/cmaes_impl.hpp | 7 - inst/include/ensmallen_bits/ens_version.hpp | 6 inst/include/ensmallen_bits/function/arma_traits.hpp | 25 +++ inst/include/ensmallen_bits/sa/sa.hpp | 9 + inst/include/ensmallen_bits/sa/sa_impl.hpp | 2 inst/include/ensmallen_bits/sdp/primal_dual.hpp | 79 ----------- inst/include/ensmallen_bits/sdp/primal_dual_impl.hpp | 94 +------------ inst/include/ensmallen_bits/utility/arma_traits.hpp | 21 +++ 15 files changed, 179 insertions(+), 268 deletions(-)
Title: 'MGMS2' for Polymicrobial Samples
Description: A glycolipid mass spectrometry technology has the potential to accurately identify individual bacterial species from polymicrobial samples. To develop bacterial identification algorithms (e.g. machine learning) using this glycolipid technology, it is necessary to generate a large number of various in-silico polymicrobial mass spectra that are similar to real mass spectra. 'MGMS2' (Membrane Glycolipid Mass Spectrum Simulator) generates such in-silico mass spectra, considering errors in m/z (mass-to-charge ratio) and variances of intensity values, occasions of missing signature ions, and noise peaks. It estimates summary statistics of monomicrobial mass spectra for each strain or species and simulates polymicrobial glycolipid mass spectra using the summary statistics of monomicrobial mass spectra. References: Ryu, S.Y., Wendt, G.A., Chandler, C.E., Ernst, R.K. and Goodlett, D.R. (2019) <doi:10.1021/acs.analchem.9b03340> "Model-based Spectral Library Approach for Bacterial Identification via Membrane Glycolipids." Gibb, S. and Strimmer, K. (2012) <doi:10.1093/bioinformatics/bts447> "MALDIquant: a versatile R package for the analysis of mass spectrometry data."
Author: So Young Ryu [aut] (<https://orcid.org/0000-0003-2347-7015>),
George Wendt [cre] (<https://orcid.org/0000-0003-3608-9601>)
Maintainer: George Wendt <gwendt@unr.edu>
Diff between MGMS2 versions 1.0.1 dated 2020-01-09 and 1.0.2 dated 2020-04-24
MGMS2-1.0.1/MGMS2/R/SpecFunctions_Final3.R |only MGMS2-1.0.2/MGMS2/DESCRIPTION | 6 +- MGMS2-1.0.2/MGMS2/MD5 | 29 +++++++------- MGMS2-1.0.2/MGMS2/NAMESPACE | 1 MGMS2-1.0.2/MGMS2/R/SpecFunctions.R |only MGMS2-1.0.2/MGMS2/man/characterize_peak.Rd |only MGMS2-1.0.2/MGMS2/man/create_insilico_mixture_template.Rd | 2 MGMS2-1.0.2/MGMS2/man/filtermass.Rd | 2 MGMS2-1.0.2/MGMS2/man/gather_summary.Rd | 2 MGMS2-1.0.2/MGMS2/man/gather_summary_file.Rd | 2 MGMS2-1.0.2/MGMS2/man/preprocessMS.Rd | 2 MGMS2-1.0.2/MGMS2/man/process_monospectra.Rd | 2 MGMS2-1.0.2/MGMS2/man/simulate_ind_spec_single.Rd | 2 MGMS2-1.0.2/MGMS2/man/simulate_many_poly_spectra.Rd | 2 MGMS2-1.0.2/MGMS2/man/simulate_poly_spectra.Rd | 2 MGMS2-1.0.2/MGMS2/man/summarize_monospectra.Rd | 2 MGMS2-1.0.2/MGMS2/man/summary_mono.Rd | 2 17 files changed, 30 insertions(+), 28 deletions(-)
Title: GEV Conditional Density Estimation Network
Description: Implements a flexible nonlinear modelling framework for nonstationary generalized extreme value analysis in hydroclimatology following Cannon (2010) <doi:10.1002/hyp.7506>.
Author: Alex J. Cannon [aut, cre] (<https://orcid.org/0000-0002-8025-3790>)
Maintainer: Alex J. Cannon <alex.cannon@canada.ca>
Diff between GEVcdn versions 1.1.6 dated 2017-12-04 and 1.1.6-2 dated 2020-04-24
DESCRIPTION | 14 ++++++++------ MD5 | 10 ++++++---- NAMESPACE | 5 ----- R/gev.R |only R/gevcdn.reshape.R | 1 - man/GEVcdn-package.Rd | 14 +++++++------- man/gev.Rd |only 7 files changed, 21 insertions(+), 23 deletions(-)
Title: Gaussian Process Based Design and Analysis for the Active
Subspace Method
Description: The active subspace method is a sensitivity analysis technique that finds important linear combinations of input variables for a simulator. This package provides functions allowing estimation of the active subspace without gradient information using Gaussian processes as well as sequential experimental design tools to minimize the amount of data required to do so. Implements Wycoff et al. (2019) <arXiv:1907.11572>.
Author: Nathan Wycoff, Mickael Binois
Maintainer: Nathan Wycoff <nathw95@vt.edu>
Diff between activegp versions 1.0.3 dated 2020-04-06 and 1.0.4 dated 2020-04-24
DESCRIPTION | 6 MD5 | 4 src/kernelexps.cpp | 510 ++++++++++++++++++++++++++--------------------------- 3 files changed, 260 insertions(+), 260 deletions(-)