Title: Semantic Annotation and Discoverability System for R-Based
Artifacts
Description: Automatically annotates R-based artifacts
with relevant descriptive and provenance-related
and provides a backend-agnostic storage and
discoverability system for organizing, retrieving, and
interrogating such artifacts.
Author: Gabriel Becker [aut, cre],
Sara Moore [aut]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between trackr versions 0.10.2 dated 2018-08-29 and 0.10.5 dated 2018-11-06
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/Extending-trackr.pdf |binary inst/doc/index.html | 42 +++++++++++++++++++++--------------------- 5 files changed, 31 insertions(+), 31 deletions(-)
Title: Parametric Frailty Models
Description: Fits Parametric Frailty Models by maximum marginal likelihood.
Possible baseline hazards:
exponential, Weibull, inverse Weibull (Fréchet),
Gompertz, lognormal, log-skew-normal, and loglogistic.
Possible Frailty distributions:
gamma, positive stable, inverse Gaussian and lognormal.
Author: Federico Rotolo [aut, cre],
Marco Munda [aut],
Andrea Callegaro [ctb]
Maintainer: Federico Rotolo <federico.rotolo@innate-pharma.fr>
Diff between parfm versions 2.7.5 dated 2017-04-29 and 2.7.6 dated 2018-11-06
DESCRIPTION | 17 +- MD5 | 80 ++++++------ NEWS | 9 - R/Omega.R | 60 ++++----- R/anova.parfm.R | 232 ++++++++++++++++++------------------ R/ci.parfm.R | 62 ++++----- R/logLik.parfm.R | 42 +++--- R/plot.parfm.R | 192 ++++++++++++++--------------- R/print.predict.parfm.R | 68 +++++----- R/tau.R | 76 +++++------ README.md |only build/partial.rdb |binary build/vignette.rds |binary data/asthma.RData |binary data/culling.RData |binary data/datalist | 16 +- data/diagnosis.RData |binary data/ecf.RData |binary data/insem.RData |binary data/insemtvc.RData |binary data/mastitis.RData |binary data/reconstitution.RData |binary inst/doc/parfm.pdf |binary man/asthma.Rd | 3 man/insemtvc.Rd | 140 ++++++++++----------- man/parfm.Rd | 3 tests/asthma.R | 30 ++-- tests/culling.R | 20 +-- tests/insem.R | 20 +-- tests/mastitis.R | 100 +++++++-------- tests/select.parfm.R | 16 +- vignettes/graphs/R.example.R | 122 +++++++++--------- vignettes/multirow.sty |only vignettes/tex/02.1_Gamma.tex | 92 +++++++------- vignettes/tex/02.2_PS.tex | 104 ++++++++-------- vignettes/tex/02.3_IG.tex | 144 +++++++++++----------- vignettes/tex/04_sexample.tex | 36 ++--- vignettes/tex/99.1_derLTIG.tex | 146 +++++++++++----------- vignettes/tex/99.2_condEfrailty.tex | 56 ++++---- vignettes/tex/99.3_condIG.tex | 50 +++---- vignettes/tex/99.3_condIG2.tex | 50 +++---- vignettes/tex/99.4_kidney.tex | 64 ++++----- 42 files changed, 1020 insertions(+), 1030 deletions(-)
Title: Maximum Likelihood Shrinkage via Generalized Ridge or Least
Angle Regression
Description: Identify and display TRACEs for a specified shrinkage path and determine
the extent of shrinkage most likely, under normal distribution theory, to produce an
optimal reduction in MSE Risk in estimates of regression (beta) coefficients. Alternative
estimates are also provided when ill-conditioned (nearly multicollinear) models yield
OLS estimates with "wrong" numerical signs.
Author: Bob Obenchain
Maintainer: Bob Obenchain <wizbob@att.net>
Diff between RXshrink versions 1.0-9 dated 2018-04-08 and 1.1 dated 2018-11-06
DESCRIPTION | 12 +++++++----- MD5 | 36 +++++++++++++++++++----------------- NAMESPACE | 5 ++++- R/RXsigns.R |only data/haldport.rda |binary data/longley2.rda |binary data/mpg.rda |binary demo/longley2.R | 7 ++++++- man/RXlarlso.Rd | 3 +-- man/RXridge.Rd | 5 ++--- man/RXshrink-package.Rd | 22 ++++++++++++++-------- man/RXsigns.Rd |only man/RXtrisk.Rd | 2 +- man/RXtsimu.Rd | 7 +++---- man/RXuclars.Rd | 2 +- man/plot.RXlarlso.Rd | 3 +-- man/plot.RXridge.Rd | 3 +-- man/plot.RXtrisk.Rd | 3 +-- man/plot.RXtsimu.Rd | 3 +-- man/plot.RXuclars.Rd | 3 +-- 20 files changed, 63 insertions(+), 53 deletions(-)
Title: Data for "R Graphics Cookbook"
Description: Data sets used in the book "R Graphics Cookbook" by Winston
Chang, published by O'Reilly Media.
Author: Winston Chang
Maintainer: Winston Chang <winston@stdout.org>
Diff between gcookbook versions 1.0 dated 2012-11-30 and 2.0 dated 2018-11-06
DESCRIPTION | 14 +++++----- MD5 | 64 ++++++++++++++++++++++++------------------------ NAMESPACE | 2 + R/gcookbook.r | 34 ++++++++++++++++++------- data/aapl.rda |binary data/cabbage_exp.rda |binary data/datalist | 1 data/heightweight.rda |binary data/tg.rda |only data/tophitters2001.rda |binary man/aapl.Rd | 16 ++++++++---- man/anthoming.Rd | 37 +++++++++++++++------------ man/cabbage_exp.Rd | 19 +++++++------- man/climate.Rd | 35 ++++++++++++++------------ man/corneas.Rd | 27 +++++++++++--------- man/countries.Rd | 28 +++++++++++++-------- man/drunk.Rd | 18 +++++++------ man/gcookbook.Rd | 10 +++---- man/heightweight.Rd | 23 ++++++++++++----- man/isabel.Rd | 36 ++++++++++++++++----------- man/madmen.Rd | 34 ++++++++++++++----------- man/madmen2.Rd | 38 +++++++++++++++------------- man/marathon.Rd | 20 +++++++++------ man/pg_mean.Rd | 20 ++++++++------- man/plum.Rd | 38 +++++++++++++++------------- man/plum_wide.Rd | 38 +++++++++++++++------------- man/simpledat.Rd | 14 ++++++---- man/simpledat_long.Rd | 14 ++++++---- man/tg.Rd |only man/tophitters2001.Rd | 59 ++++++++++++++++++++++++++++---------------- man/uspopage.Rd | 23 ++++++++++------- man/uspopchange.Rd | 23 +++++++++++------ man/wind.Rd | 33 ++++++++++++++---------- man/worldpop.Rd | 15 ++++++++--- 34 files changed, 434 insertions(+), 299 deletions(-)
Title: Basic Statistical Functions for Package 'ff'
Description: Extends the out of memory vectors of 'ff' with
statistical functions and other utilities to ease their usage.
Author: Edwin de Jonge, Jan Wijffels, Jan van der Laan
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between ffbase versions 0.12.5 dated 2018-09-24 and 0.12.7 dated 2018-11-06
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/auxilary.R | 4 ++-- R/compact.R | 2 +- R/ffdfdply.R | 1 + R/rev_ff.R | 2 +- man/bigglm.ffdf.Rd | 3 +++ man/ffdfdply.Rd | 4 ++-- man/merge.ffdf.Rd | 5 ++--- tests/testthat/testmerge.R | 4 +++- tests/testthat/testsops.R | 18 +++++++++--------- 11 files changed, 37 insertions(+), 32 deletions(-)
Title: Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Sets
Description: Principled methods for the imputation of zeros, left-censored and missing data in
compositional data sets.
Author: Javier Palarea-Albaladejo and Josep Antoni Martin-Fernandez
Maintainer: Javier Palarea-Albaladejo <javier.palarea@bioss.ac.uk>
Diff between zCompositions versions 1.1.1-1 dated 2018-10-27 and 1.1.2 dated 2018-11-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++-- R/lrEM.R | 6 +++--- README.md | 2 +- man/lrEM.Rd | 16 +++++++++------- man/zCompositions-package.Rd | 4 ++-- 7 files changed, 28 insertions(+), 25 deletions(-)
Title: Data Analysis of Liquid-Liquid Systems
Description: Analyses experimental data from liquid-liquid phase diagrams and
provide a simple way to obtain its parameters and a simplified report. Designed
initially to analyse Aqueous Two-Phases Systems, the package will include (every
other update) new functions in order to comprise useful tools in liquid-liquid
analysis.
Author: Diego F Coelho <diegofcoelho@gmail.com>
Maintainer: Diego F Coelho <diegofcoelho@gmail.com>
Diff between LLSR versions 0.0.2.1 dated 2018-08-22 and 0.0.2.2 dated 2018-11-06
LLSR-0.0.2.1/LLSR/R/Multiplot.R |only LLSR-0.0.2.2/LLSR/DESCRIPTION | 13 - LLSR-0.0.2.2/LLSR/MD5 | 57 +++-- LLSR-0.0.2.2/LLSR/NAMESPACE | 8 LLSR-0.0.2.2/LLSR/R/AQSys.R | 223 ++++++--------------- LLSR-0.0.2.2/LLSR/R/AQSys.err.R | 5 LLSR-0.0.2.2/LLSR/R/AQSys.gsnchk.R | 36 +-- LLSR-0.0.2.2/LLSR/R/AQSys.mathDesc.R | 25 ++ LLSR-0.0.2.2/LLSR/R/AQSys.mrchk.R | 35 +-- LLSR-0.0.2.2/LLSR/R/AQSys.mrgsn.R | 1 LLSR-0.0.2.2/LLSR/R/AQSysCurve.R | 202 +++++++++++-------- LLSR-0.0.2.2/LLSR/R/AQSysDB.R | 253 ++++++++++-------------- LLSR-0.0.2.2/LLSR/R/AQSysEval.R |only LLSR-0.0.2.2/LLSR/R/AQSysFormulas.R | 131 +++++++----- LLSR-0.0.2.2/LLSR/R/AQSysPlot.R |only LLSR-0.0.2.2/LLSR/R/AQSysUtils.R | 260 ++++++++++++++++++++++++- LLSR-0.0.2.2/LLSR/R/CorporateColours.R |only LLSR-0.0.2.2/LLSR/R/LLSRUtils.R | 117 +++++++++++ LLSR-0.0.2.2/LLSR/R/LLSRxy.R | 31 ++ LLSR-0.0.2.2/LLSR/man/AQSys.Rd | 18 - LLSR-0.0.2.2/LLSR/man/AQSys.crpt.Rd | 6 LLSR-0.0.2.2/LLSR/man/AQSys.gsnchk.Rd | 10 LLSR-0.0.2.2/LLSR/man/AQSys.plot.Rd | 40 +-- LLSR-0.0.2.2/LLSR/man/AQSys.tielines.Rd | 6 LLSR-0.0.2.2/LLSR/man/AQSysCurve.Rd | 34 +-- LLSR-0.0.2.2/LLSR/man/AQSysDB.Rd | 6 LLSR-0.0.2.2/LLSR/man/AQSysEval.Rd |only LLSR-0.0.2.2/LLSR/man/AQSysList.Rd | 5 LLSR-0.0.2.2/LLSR/man/AQSysPlot.Rd |only LLSR-0.0.2.2/LLSR/man/LLSRxy.Rd | 8 LLSR-0.0.2.2/LLSR/man/llsr_cols.Rd |only LLSR-0.0.2.2/LLSR/man/scale_color_llsr.Rd |only LLSR-0.0.2.2/LLSR/man/scale_fill_llsr.Rd |only LLSR-0.0.2.2/LLSR/tests/testthat/testMainFns.R | 12 - 34 files changed, 952 insertions(+), 590 deletions(-)
Title: A Bunch of Structure and Sequence Analysis
Description: Reads and plots phylogenetic placements.
Author: Pierre Lefeuvre
Maintainer: Pierre Lefeuvre <pierre.lefeuvre@cirad.fr>
Diff between BoSSA versions 3.5 dated 2018-09-25 and 3.6 dated 2018-11-06
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- build/partial.rdb |binary inst/doc/bossa-analysis.html | 20 ++++++++++---------- inst/doc/bossa-refpkg.R | 21 ++++++++++++--------- inst/doc/bossa-refpkg.Rmd | 21 ++++++++++++--------- inst/doc/bossa-refpkg.html | 35 +++++++++++++++++++---------------- inst/doc/bossa-tree.html | 8 ++++---- vignettes/bossa-refpkg.Rmd | 21 ++++++++++++--------- 9 files changed, 81 insertions(+), 69 deletions(-)
Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'.
Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions,
conditioned scatter plot with marginal densities,
box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between WVPlots versions 1.0.5 dated 2018-10-22 and 1.0.6 dated 2018-11-06
DESCRIPTION | 10 +++++----- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/GainCurve.R | 15 +++------------ R/LiftCurve.R |only README.md | 8 +++++--- inst/doc/WVPlots_concept.html | 6 +++--- inst/doc/WVPlots_examples.html | 6 +++--- man/GainCurvePlot.Rd | 4 ---- man/GainCurvePlotC.Rd | 2 -- man/GainCurvePlotWithNotation.Rd | 4 ---- man/LiftCurvePlot.Rd |only 13 files changed, 36 insertions(+), 46 deletions(-)
Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression
models with missing values in covariates or the dependent
variable using maximum likelihood or Bayesian estimation
(Ibrahim et al., 2005; <doi:10.1198/016214504000001844>).
The regression model can be nonlinear (e.g., interaction
effects, quadratic effects or B-spline functions).
Multilevel models with missing data in predictors are
available for Bayesian estimation. Substantive-model compatible
multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between mdmb versions 0.11-7 dated 2018-10-16 and 1.0-18 dated 2018-11-06
DESCRIPTION | 12 ++--- MD5 | 63 +++++++++++++++--------------- NAMESPACE | 3 - R/RcppExports.R | 2 R/frm_define_model_R_function.R | 8 ++- R/frm_descriptives_variables.R | 10 ++-- R/frm_em.R | 12 ++--- R/frm_em_calc_likelihood.R | 9 ++-- R/frm_em_calc_likelihood_estimate_model.R | 3 - R/frm_fb.R | 15 +++---- R/frm_fb_init_imputations.R | 8 ++- R/frm_fb_init_matrices_saved_parameters.R | 7 ++- R/frm_fb_initial_parameters.R | 7 +-- R/frm_fb_sample_imputed_values.R | 7 ++- R/frm_fb_sample_parameter_step.R | 2 R/frm_fb_sample_parameters.R | 4 - R/frm_linreg_density.R | 28 ++++++++++--- R/frm_linreg_sample_parameters.R | 24 ++++++++--- R/frm_mdmb_regression_density.R | 6 +- R/frm_prepare_models_sigma_fixed.R | 6 +- R/mdmb_regression.R | 6 +- R/mdmb_weighted_sd.R |only R/mdmb_weighted_var.R |only R/summary.frm_em.R | 4 - R/summary.frm_fb.R | 13 ++---- R/zzz.R | 11 ++++- README.md | 2 build |only inst/NEWS | 20 ++++++++- man/frm.Rd | 5 -- man/mdmb-package.Rd | 31 +++++--------- src/RcppExports.cpp | 2 src/mdmb_rcpp_linreg.cpp | 12 ++--- src/mdmb_rcpp_linreg.h | 2 34 files changed, 203 insertions(+), 141 deletions(-)
Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data
transformation tasks like recoding, dichotomizing or grouping variables,
setting and replacing missing values. The data transformation functions
also support labelled data, and all integrate seamlessly into a
'tidyverse'-workflow.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 2.7.5 dated 2018-09-13 and 2.7.6 dated 2018-11-06
DESCRIPTION | 8 MD5 | 32 +- NEWS.md | 7 R/add_cases.R | 26 + R/descr.R | 2 R/frq.R | 20 - R/move_column.R | 14 R/replace_na.R | 5 R/select_helpers.R | 27 - README.md | 2 build/partial.rdb |binary inst/doc/design_philosophy.html | 634 +++++++++++++--------------------------- inst/doc/exploringdatasets.html | 538 ++++++++++----------------------- man/add_variables.Rd | 12 man/frq.Rd | 10 man/replace_na.Rd | 5 tests/testthat/test-add_case.R | 7 17 files changed, 467 insertions(+), 882 deletions(-)
Title: Themes for Shiny
Description: Themes for use with Shiny. Includes several Bootstrap themes
from <http://bootswatch.com/>, which are packaged for use with Shiny
applications.
Author: Winston Chang [aut, cre],
RStudio [cph],
Thomas Park [ctb, cph] (Bootswatch themes),
Lukasz Dziedzic [ctb, cph] (Lato font),
Nathan Willis [ctb, cph] (News Cycle font),
Google Corporation [ctb, cph] (Open Sans and Roboto fonts),
Matt McInerney [ctb, cph] (Raleway font),
Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font),
Canonical Ltd [ctb, cph] (Ubuntu font)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinythemes versions 1.1.1 dated 2016-10-12 and 1.1.2 dated 2018-11-06
DESCRIPTION | 9 +- MD5 | 60 +++++++++---------- NEWS.md | 7 +- R/shinythemes-package.r | 32 +++++----- README.md | 32 +++++----- inst/shinythemes/fonts/Lato_300.ttf |binary inst/shinythemes/fonts/Lato_400.ttf |binary inst/shinythemes/fonts/Lato_400italic.ttf |binary inst/shinythemes/fonts/Lato_700.ttf |binary inst/shinythemes/fonts/News_Cycle_400.ttf |binary inst/shinythemes/fonts/News_Cycle_700.ttf |binary inst/shinythemes/fonts/Open_Sans_300.ttf |binary inst/shinythemes/fonts/Open_Sans_300italic.ttf |binary inst/shinythemes/fonts/Open_Sans_400.ttf |binary inst/shinythemes/fonts/Open_Sans_400italic.ttf |binary inst/shinythemes/fonts/Open_Sans_700.ttf |binary inst/shinythemes/fonts/Open_Sans_700italic.ttf |binary inst/shinythemes/fonts/README.md | 4 - inst/shinythemes/fonts/Raleway_400.ttf |binary inst/shinythemes/fonts/Raleway_700.ttf |binary inst/shinythemes/fonts/Roboto_300.ttf |only inst/shinythemes/fonts/Roboto_400.ttf |binary inst/shinythemes/fonts/Roboto_500.ttf |only inst/shinythemes/fonts/Roboto_700.ttf |binary inst/shinythemes/fonts/Source_Sans_Pro_300.ttf |binary inst/shinythemes/fonts/Source_Sans_Pro_400.ttf |binary inst/shinythemes/fonts/Source_Sans_Pro_400italic.ttf |binary inst/shinythemes/fonts/Source_Sans_Pro_700.ttf |binary inst/shinythemes/fonts/Ubuntu_400.ttf |binary man/shinytheme.Rd | 1 man/shinythemes.Rd | 33 +++++----- man/themeSelector.Rd | 1 32 files changed, 92 insertions(+), 87 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.
Author: Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut],
Daniel Caetano [aut]
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.8.8 dated 2018-10-19 and 1.8.9 dated 2018-11-06
DESCRIPTION | 8 - MD5 | 42 ++++---- R/fgeohisse.R | 71 ++++++++----- R/geohisse.R | 113 +++++++++++++--------- R/getModelAveEqFreqs.R | 168 ++++++++++++++++++++++++++++++--- R/hisse.R | 198 +++++++++++++++++++++------------------ R/hisseLikelihood.R | 5 R/hisseNull4.R | 30 +++-- R/muhisse.R | 55 ++++++---- inst/doc/MuHiSSE-vignette.R | 28 ++++- inst/doc/MuHiSSE-vignette.Rmd | 40 ++++++- inst/doc/MuHiSSE-vignette.pdf |binary man/GeoHiSSE.Rd | 22 +++- man/MuHiSSE.Rd | 26 ++++- man/fGeoHiSSE.Rd | 22 +++- man/hisse.Rd | 22 ++++ man/hisseNull4.Rd | 20 +++ man/makeHiSSELikelihood.Rd | 2 man/modelAveEqFreqs.Rd | 11 -- tests/testthat/test_likelihood.R | 48 ++++----- vignettes/MuHiSSE-vignette.Rmd | 40 ++++++- vignettes/MuHiSSE-vignette.html | 41 ++++++-- 22 files changed, 709 insertions(+), 303 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling
for dichotomous and polytomous item responses. This package enables the estimation of
the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>),
the multiple group (polytomous) GDINA model (de la Torre, 2011,
<doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009,
<doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008,
<doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992,
<doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis
(Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>).
See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02>
for further details on estimation and the package structure.
For tutorials on how to use the CDM package see
George and Robitzsch (2015, <doi:10.20982/tqmp.11.3.p189>) as well as
Ravand and Robitzsch (2015).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 6.6-5 dated 2018-09-30 and 7.0-12 dated 2018-11-06
CDM-6.6-5/CDM/R/summary.IRT.RMSD_print_statistics.R |only CDM-7.0-12/CDM/DESCRIPTION | 8 CDM-7.0-12/CDM/MD5 | 166 +++++++++---------- CDM-7.0-12/CDM/NAMESPACE | 1 CDM-7.0-12/CDM/R/IRT_RMSD_summary_print_statistics.R |only CDM-7.0-12/CDM/R/RcppExports.R | 2 CDM-7.0-12/CDM/R/cat_paste.R |only CDM-7.0-12/CDM/R/gdina_mstep_item_uls.R | 4 CDM-7.0-12/CDM/R/mcdina.simul.R | 6 CDM-7.0-12/CDM/R/print.summary.din.R | 10 - CDM-7.0-12/CDM/R/reglca.R | 8 CDM-7.0-12/CDM/R/reglca_fit_probabilities.R | 9 - CDM-7.0-12/CDM/R/reglca_mstep_item_parameters.R | 9 - CDM-7.0-12/CDM/R/reglca_threshold_parameter.R | 8 CDM-7.0-12/CDM/R/reglca_update_parameter.R | 17 + CDM-7.0-12/CDM/R/rrum.param.R | 4 CDM-7.0-12/CDM/R/sim.gdina.R | 20 +- CDM-7.0-12/CDM/R/sim.gdina.prepare.R | 2 CDM-7.0-12/CDM/R/skill.cor.R | 53 +++--- CDM-7.0-12/CDM/R/summary.IRT.RMSD.R | 10 - CDM-7.0-12/CDM/R/summary.gdm.R | 47 ++--- CDM-7.0-12/CDM/R/summary.mcdina.R | 10 - CDM-7.0-12/CDM/R/summary.slca.R | 3 CDM-7.0-12/CDM/R/zzz.R | 10 + CDM-7.0-12/CDM/README.md | 2 CDM-7.0-12/CDM/build |only CDM-7.0-12/CDM/data/data.Students.rda |binary CDM-7.0-12/CDM/data/data.cdm01.rda |binary CDM-7.0-12/CDM/data/data.cdm02.rda |binary CDM-7.0-12/CDM/data/data.cdm03.rda |binary CDM-7.0-12/CDM/data/data.cdm04.rda |binary CDM-7.0-12/CDM/data/data.cdm05.rda |binary CDM-7.0-12/CDM/data/data.cdm06.rda |binary CDM-7.0-12/CDM/data/data.cdm07.rda |binary CDM-7.0-12/CDM/data/data.cdm08.rda |binary CDM-7.0-12/CDM/data/data.dcm.rda |binary CDM-7.0-12/CDM/data/data.dtmr.rda |binary CDM-7.0-12/CDM/data/data.ecpe.rda |binary CDM-7.0-12/CDM/data/data.fraction1.rda |binary CDM-7.0-12/CDM/data/data.fraction2.rda |binary CDM-7.0-12/CDM/data/data.fraction3.rda |binary CDM-7.0-12/CDM/data/data.fraction4.rda |binary CDM-7.0-12/CDM/data/data.fraction5.rda |binary CDM-7.0-12/CDM/data/data.hr.rda |binary CDM-7.0-12/CDM/data/data.jang.rda |binary CDM-7.0-12/CDM/data/data.melab.rda |binary CDM-7.0-12/CDM/data/data.mg.rda |binary CDM-7.0-12/CDM/data/data.pgdina.rda |binary CDM-7.0-12/CDM/data/data.pisa00R.cc.rda |binary CDM-7.0-12/CDM/data/data.pisa00R.ct.rda |binary CDM-7.0-12/CDM/data/data.sda6.rda |binary CDM-7.0-12/CDM/data/data.timss03.G8.su.rda |binary CDM-7.0-12/CDM/data/data.timss07.G4.Qdomains.rda |binary CDM-7.0-12/CDM/data/data.timss07.G4.lee.rda |binary CDM-7.0-12/CDM/data/data.timss07.G4.py.rda |binary CDM-7.0-12/CDM/data/data.timss11.G4.AUT.part.rda |binary CDM-7.0-12/CDM/data/data.timss11.G4.AUT.rda |binary CDM-7.0-12/CDM/data/data.timss11.G4.sa.rda |binary CDM-7.0-12/CDM/data/fraction.subtraction.data.rda |binary CDM-7.0-12/CDM/data/fraction.subtraction.qmatrix.rda |binary CDM-7.0-12/CDM/data/sim.dina.rda |binary CDM-7.0-12/CDM/data/sim.dino.rda |binary CDM-7.0-12/CDM/data/sim.qmatrix.rda |binary CDM-7.0-12/CDM/inst/NEWS | 11 + CDM-7.0-12/CDM/man/CDM-package.Rd | 26 -- CDM-7.0-12/CDM/man/CDM-utilities.Rd | 10 - CDM-7.0-12/CDM/man/data.cdm.Rd | 2 CDM-7.0-12/CDM/man/data.timss07.G4.lee.Rd | 10 - CDM-7.0-12/CDM/man/din.Rd | 2 CDM-7.0-12/CDM/man/din.deterministic.Rd | 4 CDM-7.0-12/CDM/man/din.validate.qmatrix.Rd | 10 - CDM-7.0-12/CDM/man/discrim.index.Rd | 10 - CDM-7.0-12/CDM/man/gdina.Rd | 2 CDM-7.0-12/CDM/man/gdina.dif.Rd | 2 CDM-7.0-12/CDM/man/gdina.wald.Rd | 2 CDM-7.0-12/CDM/man/gdm.Rd | 4 CDM-7.0-12/CDM/man/modelfit.cor.Rd | 2 CDM-7.0-12/CDM/man/numerical_Hessian.Rd | 2 CDM-7.0-12/CDM/man/reglca.Rd | 5 CDM-7.0-12/CDM/man/skillspace.approximation.Rd | 4 CDM-7.0-12/CDM/man/skillspace.hierarchy.Rd | 2 CDM-7.0-12/CDM/man/slca.Rd | 2 CDM-7.0-12/CDM/src/Makevars | 2 CDM-7.0-12/CDM/src/Makevars.win | 2 CDM-7.0-12/CDM/src/RcppExports.cpp | 2 CDM-7.0-12/CDM/src/init.c | 2 86 files changed, 278 insertions(+), 251 deletions(-)
Title: Making Optimal Matching Size-Scalable Using Optimal Calipers
Description: Implements optimal matching with near-fine balance in large observational studies with the use of optimal calipers to get a sparse network. The caliper is optimal in the sense that it is as small as possible such that a matching exists. The main functions in the 'bigmatch' package are optcal() to find the optimal caliper, optconstant() to find the optimal number of nearest neighbors and nfmatch() to find a near-fine balance match with a caliper and a restriction on number of nearest neighbors.
Glover, F. (1967). <DOI:10.1002/nav.3800140304>.
Lipski, W., Jr, and Preparata, F. P. (1981). <DOI:10.1007/BF00264533>.
Rosenbaum, P.R. (1989). <DOI:10.1080/01621459.1989.10478868>.
Yang, D., Small, D. S., Silber, J. H., and Rosenbaum, P. R. (2012). <DOI:10.1111/j.1541-0420.2011.01691.x>.
Author: Ruoqi Yu
Maintainer: Ruoqi Yu <ruoqiyu@wharton.upenn.edu>
Diff between bigmatch versions 0.4.1 dated 2018-10-23 and 0.5.1 dated 2018-11-06
DESCRIPTION | 8 ++--- MD5 | 12 ++++---- NAMESPACE | 7 ++-- R/nfmatch.R | 10 +----- R/optcal.R | 37 +++++++++++++------------ R/optconstant.R | 51 ++++++++++++++++++++--------------- R/smahal.R | 81 ++++++++++++++++++++++++++++++++++++++++++++++---------- 7 files changed, 132 insertions(+), 74 deletions(-)
Title: Hidden Markov Models for Life Sequences and Other Multivariate,
Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture
hidden Markov models for social sequence data and other categorical time series.
Also some more restricted versions of these type of models are available: Markov
models, mixture Markov models, and latent class models. The package supports
models for one or multiple subjects with one or multiple parallel sequences
(channels). External covariates can be added to explain cluster membership in
mixture models. The package provides functions for evaluating and comparing
models, as well as functions for easy plotting of multichannel sequence data and
hidden Markov models. Models are estimated using maximum likelihood via the EM
algorithm and/or direct numerical maximization with analytical gradients. All
main algorithms are written in C++ with support for parallel computation.
Author: Jouni Helske, Satu Helske
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between seqHMM versions 1.0.8-1 dated 2018-05-10 and 1.0.9 dated 2018-11-06
DESCRIPTION | 10 MD5 | 42 NEWS | 9 R/fit_model.R | 2000 +++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/seqHMM.pdf | 54 - inst/doc/seqHMM_algorithms.pdf |binary inst/doc/seqHMM_estimation.pdf |binary inst/doc/seqHMM_visualization.pdf |binary man/build_lcm.Rd | 4 man/build_mmm.Rd | 4 man/fit_model.Rd | 11 man/gridplot.Rd | 9 man/mssplot.Rd | 14 man/plot.hmm.Rd | 15 man/plot.mhmm.Rd | 13 man/seqHMM-deprecated.Rd | 24 man/ssp.Rd | 11 man/ssplot.Rd | 11 man/summary.mhmm.Rd | 4 src/Makevars | 2 src/internalBackward.cpp | 4 22 files changed, 1130 insertions(+), 1111 deletions(-)
Title: Simulating and Conducting Phase 123 Trials
Description: Contains three simulation functions for implementing the entire Phase 123 trial and the separate Eff-Tox and Phase 3 portions of the trial, which may be beneficial for use on clusters. The functions AssignEffTox() and RandomizeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() determines the optimal dose to continue with during Phase 3. The functions ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival for the agent doses and control and ReturnOCS() gives the operating characteristics of the design.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <achapp@lsuhsc.edu>
Diff between Phase123 versions 1.8 dated 2018-10-26 and 1.9 dated 2018-11-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/SimPhase3.R | 16 ++++++++-------- 3 files changed, 13 insertions(+), 13 deletions(-)
Title: Probabilities for Bivariate Normal Distribution
Description: Computes probabilities of the bivariate normal distribution
in a vectorized R function (Drezner & Wesolowsky, 1990,
<doi:10.1080/00949659008811236>).
Author: Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>)
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between pbv versions 0.1-17 dated 2018-10-30 and 0.2-16 dated 2018-11-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/RcppExports.R | 2 +- build/partial.rdb |binary inst/NEWS | 16 ++++++++++++++-- man/pbvnorm.Rd | 26 ++++++++++++++------------ src/RcppExports.cpp | 2 +- 7 files changed, 40 insertions(+), 26 deletions(-)
Title: Modified Versions of Mann Kendall and Spearman's Rho Trend Tests
Description: Power of non-parametric Mann-Kendall test and Spearman’s Rho test is highly influenced by serially correlated data. To address this issue, trend tests may applied on the modified versions of the time series data by Block Bootstrapping (BBS), Prewhitening (PW) , Trend Free Prewhitening (TFPW), Bias Corrected Prewhitening and Variance Correction Approach by calculating effective sample size.
Mann, H. B. (1945).<doi:10.1017/CBO9781107415324.004>.
Kendall, M. (1975). Multivariate analysis. Charles Griffin&Company Ltd,.
sen, P. K. (1968).<doi:10.2307/2285891>.
Önöz, B., & Bayazit, M. (2012) <doi:10.1002/hyp.8438>.
Hamed, K. H. (2009).<doi:10.1016/j.jhydrol.2009.01.040>.
Yue, S., & Wang, C. Y. (2002) <doi:10.1029/2001WR000861>.
Yue, S., Pilon, P., Phinney, B., & Cavadias, G. (2002) <doi:10.1002/hyp.1095>.
Hamed, K. H., & Ramachandra Rao, A. (1998) <doi:10.1016/S0022-1694(97)00125-X>.
Yue, S., & Wang, C. Y. (2004) <doi:10.1023/B:WARM.0000043140.61082.60>.
Author: Sandeep Kumar Patakamuri [aut, cre],
Nicole O'Brien [aut, ctb]
Maintainer: Sandeep Kumar Patakamuri <sandeep.patakamuri@gmail.com>
Diff between modifiedmk versions 1.1.0 dated 2018-06-20 and 1.2.0 dated 2018-11-06
DESCRIPTION | 22 ++++++++++++--------- MD5 | 48 +++++++++++++++++++++++----------------------- NAMESPACE | 3 ++ R/bbsmk.R | 6 ++--- R/bbssr.R | 4 +-- R/bcpw.R |only R/mkttest.R | 4 +-- R/mmkh.R | 8 +++---- R/mmkh3.R | 8 +++---- R/mmky.R | 6 ++--- R/mmky1.R | 6 ++--- R/pwmk.R | 10 +++++---- R/spmr.R | 2 - R/tfpwmk.R | 11 +++++++--- inst/doc/my-vignette.html | 2 - man/bbsmK.Rd | 6 ++--- man/bbssr.Rd | 4 +-- man/bcpw.Rd |only man/mkttest.Rd | 4 +-- man/mmkh.Rd | 8 +++---- man/mmkh3lag.Rd | 8 +++---- man/mmky.Rd | 6 ++--- man/mmky1lag.Rd | 6 ++--- man/pwmk.Rd | 10 +++++---- man/spear.Rd | 2 - man/tfpwmk.Rd | 10 ++++++--- 26 files changed, 113 insertions(+), 91 deletions(-)
Title: Bayesian Measurement Models for Analyzing Endorsement
Experiments
Description: Fit the hierarchical and non-hierarchical Bayesian measurement models proposed by Bullock, Imai, and Shapiro (2011) <DOI:10.1093/pan/mpr031> to analyze endorsement experiments. Endorsement experiments are a survey methodology for eliciting truthful responses to sensitive questions. This methodology is helpful when measuring support for socially sensitive political actors such as militant groups. The model is fitted with a Markov chain Monte Carlo algorithm and produces the output containing draws from the posterior distribution.
Author: Yuki Shiraito [aut, cre],
Kosuke Imai [aut],
Bryn Rosenfeld [ctb]
Maintainer: Yuki Shiraito <shiraito@umich.edu>
Diff between endorse versions 1.6.0 dated 2017-06-25 and 1.6.1 dated 2018-11-06
ChangeLog | 1 + DESCRIPTION | 20 +++++++++++--------- MD5 | 14 +++++++------- man/GeoCount.Rd | 6 +----- man/GeoId.Rd | 6 +----- man/endorse.Rd | 6 +----- man/endorse.plot.Rd | 10 +++------- man/predict.endorse.Rd | 3 +-- 8 files changed, 26 insertions(+), 40 deletions(-)
Title: Climate and Ecological Niche Factor Analysis
Description: Tools for climate- and ecological-niche factor analysis of spatial data, including methods for visualization of spatial variability of species sensitivity, exposure, and vulnerability to climate change. Processing of large files and parallel methods are supported. Ecological-niche factor analysis is described in Hirzel et al. (2002) <doi:10.2307/3071784> and Basille et al. (2008) <doi:10.1016/j.ecolmodel.2007.09.006>.
Author: D. Scott Rinnan
Maintainer: D. Scott Rinnan <scott.rinnan@yale.edu>
Diff between CENFA versions 0.1.0 dated 2018-02-06 and 1.0.0 dated 2018-11-06
DESCRIPTION | 26 +-- MD5 | 100 ++++++------- NAMESPACE | 41 ----- NEWS.md |only R/CENFA.R | 12 - R/GLcenfa.R | 27 +-- R/GLdeparture.R | 60 +++++-- R/calc.R | 4 R/cnfa-class.R | 15 + R/cnfa.R | 174 +++++++++++++++------- R/covij.R | 2 R/departure.R | 47 +++--- R/enfa-class.R | 11 - R/enfa.R | 130 ++++++++++------ R/exposure_map.R | 12 - R/names.R | 6 R/overlay.R |only R/parCov.R | 69 ++++---- R/parScale.R | 52 +++--- R/predict.R |only R/scatter.R | 18 +- R/sensitivity_map.R | 12 + R/slots.R | 9 + R/stretchPlot.R | 9 - R/vulnerability.R | 41 +++-- R/vulnerability_map.R | 2 README.md | 223 ++++++++++++++++++----------- build/vignette.rds |binary inst/doc/CENFA-vignette.R | 4 inst/doc/CENFA-vignette.Rmd | 14 - inst/doc/CENFA-vignette.html | 78 ++++------ man/CENFA-package.Rd | 7 man/GLcenfa.Rd | 21 +- man/GLdeparture.Rd | 22 ++ man/cnfa-class.Rd | 4 man/cnfa.Rd | 36 ++-- man/departure.Rd | 15 + man/enfa-class.Rd | 2 man/enfa.Rd | 35 ++-- man/figures/README-QUGA-plot-1.png |binary man/figures/README-exposure-map-1.png |binary man/figures/README-scatter-1.png |binary man/figures/README-sensitivity-map-1.png |binary man/figures/README-stretchPlot-1.png |binary man/figures/README-vulnerability-map-1.png |binary man/parCov.Rd | 14 + man/parScale.Rd | 14 + man/predict.Rd |only man/scatter.Rd | 3 man/slot-access.Rd | 8 - man/vulnerability.Rd | 10 - man/vulnerability_map.Rd | 2 vignettes/CENFA-vignette.Rmd | 14 - 53 files changed, 835 insertions(+), 570 deletions(-)
Title: Multi-Data-Driven Sparse PLS Robust to Missing Samples
Description: Allows to build Multi-Data-Driven Sparse PLS models. Multi-blocks with
high-dimensional settings are particularly sensible to this.
Author: Hadrien Lorenzo [aut, cre]
Maintainer: Hadrien Lorenzo <hadrien.lorenzo.2015@gmail.com>
Diff between ddsPLS versions 1.0.1 dated 2018-10-12 and 1.0.2 dated 2018-11-06
DESCRIPTION | 6 - MD5 | 29 ++++---- R/mddsPLS.R | 32 +++----- R/perf_mddsPLS.R | 45 ++++++++---- R/plot.perf_mddsPLS.R | 52 +++++++------- R/predict.mddsPLS.R | 42 ++++++----- build/partial.rdb |binary inst/doc/ddsPLS.R | 113 +++++++++++++++++++++++++------ inst/doc/ddsPLS.Rmd | 148 ++++++++++++++++++++++++++++++++++++----- inst/doc/ddsPLS.html | 165 ++++++++++++++++++++++++++++++++++------------ man/MddsPLS_core.Rd | 2 man/perf_mddsPLS.Rd | 2 vignettes/bib.bib | 9 ++ vignettes/cla_R.png |only vignettes/ddsPLS.Rmd | 148 ++++++++++++++++++++++++++++++++++++----- vignettes/reg_R.png |only vignettes/reg_R_multi.png |only 17 files changed, 604 insertions(+), 189 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on 'Windows',
'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gábor Csárdi [aut, cre],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between ps versions 1.2.0 dated 2018-10-16 and 1.2.1 dated 2018-11-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/ps.pdf |binary src/linux.c | 4 ++-- tests/testthat/test-common.R | 2 +- 6 files changed, 15 insertions(+), 11 deletions(-)
Title: Genotype Quality Control with 'PLINK'
Description: Genotyping arrays enable the direct measurement of an individuals
genotype at thousands of markers. 'plinkQC' facilitates genotype quality
control for genetic association studies as described by Anderson and
colleagues (2010) <doi:10.1038/nprot.2010.116>. It makes 'PLINK' basic
statistics (e.g. missing genotyping rates per individual, allele frequencies
per genetic marker) and relationship functions accessible from 'R' and
generates a per-individual and per-marker quality control report.
Individuals and markers that fail the quality control can subsequently be
removed to generate a new, clean dataset. Removal of individuals based on
relationship status is optimised to retain as many individuals as possible
in the study.
Author: Hannah Meyer [aut, cre] (<https://orcid.org/0000-0003-4564-0899>)
Maintainer: Hannah Meyer <hannah@ebi.ac.uk>
Diff between plinkQC versions 0.1.0 dated 2018-11-04 and 0.1.1 dated 2018-11-06
plinkQC-0.1.0/plinkQC/inst/extdata |only plinkQC-0.1.0/plinkQC/vignettes/Rplot.pdf |only plinkQC-0.1.1/plinkQC/DESCRIPTION | 6 plinkQC-0.1.1/plinkQC/MD5 | 97 +++---- plinkQC-0.1.1/plinkQC/NEWS.md | 11 plinkQC-0.1.1/plinkQC/R/applyQC.R | 2 plinkQC-0.1.1/plinkQC/R/individualQC.R | 184 ++++++++------- plinkQC-0.1.1/plinkQC/R/markerQC.R | 19 - plinkQC-0.1.1/plinkQC/README.md | 8 plinkQC-0.1.1/plinkQC/inst/doc/AncestryCheck.R | 32 +- plinkQC-0.1.1/plinkQC/inst/doc/AncestryCheck.Rmd | 8 plinkQC-0.1.1/plinkQC/inst/doc/AncestryCheck.pdf |binary plinkQC-0.1.1/plinkQC/inst/doc/Genomes1000.Rmd | 4 plinkQC-0.1.1/plinkQC/inst/doc/Genomes1000.pdf |binary plinkQC-0.1.1/plinkQC/inst/doc/HapMap.Rmd | 4 plinkQC-0.1.1/plinkQC/inst/doc/HapMap.pdf |binary plinkQC-0.1.1/plinkQC/inst/doc/plinkQC.pdf |binary plinkQC-0.1.1/plinkQC/man/check_ancestry.Rd | 17 - plinkQC-0.1.1/plinkQC/man/check_het_and_miss.Rd | 11 plinkQC-0.1.1/plinkQC/man/check_hwe.Rd | 3 plinkQC-0.1.1/plinkQC/man/check_maf.Rd | 5 plinkQC-0.1.1/plinkQC/man/check_relatedness.Rd | 11 plinkQC-0.1.1/plinkQC/man/check_sex.Rd | 11 plinkQC-0.1.1/plinkQC/man/check_snp_missingness.Rd | 3 plinkQC-0.1.1/plinkQC/man/cleanData.Rd | 2 plinkQC-0.1.1/plinkQC/man/evaluate_check_ancestry.Rd | 20 - plinkQC-0.1.1/plinkQC/man/evaluate_check_het_and_miss.Rd | 5 plinkQC-0.1.1/plinkQC/man/evaluate_check_relatedness.Rd | 5 plinkQC-0.1.1/plinkQC/man/evaluate_check_sex.Rd | 7 plinkQC-0.1.1/plinkQC/man/overviewPerIndividualQC.Rd | 3 plinkQC-0.1.1/plinkQC/man/overviewPerMarkerQC.Rd | 7 plinkQC-0.1.1/plinkQC/man/perIndividualQC.Rd | 11 plinkQC-0.1.1/plinkQC/man/perMarkerQC.Rd | 3 plinkQC-0.1.1/plinkQC/man/run_check_ancestry.Rd | 5 plinkQC-0.1.1/plinkQC/man/run_check_heterozygosity.Rd | 5 plinkQC-0.1.1/plinkQC/man/run_check_missingness.Rd | 5 plinkQC-0.1.1/plinkQC/man/run_check_relatedness.Rd | 13 - plinkQC-0.1.1/plinkQC/man/run_check_sex.Rd | 5 plinkQC-0.1.1/plinkQC/tests/testthat/test-individualQC.R | 143 +++++++++++ plinkQC-0.1.1/plinkQC/vignettes/AncestryCheck.Rmd | 8 plinkQC-0.1.1/plinkQC/vignettes/Genomes1000.Rmd | 4 plinkQC-0.1.1/plinkQC/vignettes/Genomes1000.md |only plinkQC-0.1.1/plinkQC/vignettes/HapMap.Rmd | 4 plinkQC-0.1.1/plinkQC/vignettes/HapMap.md |only 44 files changed, 426 insertions(+), 265 deletions(-)
Title: Classes and Methods for 'GRANBase'
Description: Provides the classes and methods for GRANRepository
objects that are used within the 'GRAN' build framework for R packages.
This is primarily used by the 'GRANBase' package and repositories
that are created by it.
Author: Gabriel Becker[aut,cre], Dinakar Kulkarni [aut,ctb]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between GRANCore versions 0.2.2 dated 2018-05-09 and 0.2.3 dated 2018-11-06
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between estimatr versions 0.12 dated 2018-09-15 and 0.14 dated 2018-11-06
estimatr-0.12/estimatr/man/tidy.Rd |only estimatr-0.12/estimatr/tests/testthat/helper-rm-call.R |only estimatr-0.14/estimatr/DESCRIPTION | 21 estimatr-0.14/estimatr/MD5 | 44 estimatr-0.14/estimatr/NAMESPACE | 8 estimatr-0.14/estimatr/NEWS.md | 4 estimatr-0.14/estimatr/R/S3_tidy.R | 152 - estimatr-0.14/estimatr/R/zzz.R | 13 estimatr-0.14/estimatr/man/difference_in_means.Rd | 4 estimatr-0.14/estimatr/man/estimatr_tidiers.Rd |only estimatr-0.14/estimatr/man/extract.lm_robust.Rd | 14 estimatr-0.14/estimatr/man/horvitz_thompson.Rd | 7 estimatr-0.14/estimatr/man/lm_lin.Rd | 5 estimatr-0.14/estimatr/man/lm_robust_fit.Rd | 8 estimatr-0.14/estimatr/man/reexports.Rd |only estimatr-0.14/estimatr/tests/testthat/helper-return-cleaners.R |only estimatr-0.14/estimatr/tests/testthat/helper-se-types.R |only estimatr-0.14/estimatr/tests/testthat/test-horvitz-thompson.R | 8 estimatr-0.14/estimatr/tests/testthat/test-iv-robust-fes.R | 391 --- estimatr-0.14/estimatr/tests/testthat/test-iv-robust.R | 188 - estimatr-0.14/estimatr/tests/testthat/test-lm-cluster.R | 182 - estimatr-0.14/estimatr/tests/testthat/test-lm-robust-fes.R | 1076 ++-------- estimatr-0.14/estimatr/tests/testthat/test-lm-robust.R | 286 -- estimatr-0.14/estimatr/tests/testthat/test-replicate-HT-middleton.R | 6 estimatr-0.14/estimatr/tests/testthat/test-s3-methods.R | 13 estimatr-0.14/estimatr/tests/testthat/test-starprep.R | 618 +---- 26 files changed, 924 insertions(+), 2124 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp and Mathew Jay.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 0.9-97 dated 2018-08-22 and 0.9-99 dated 2018-11-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 8 ++++++++ R/epi.prev.R | 23 +++++++++++++++++++---- man/epi.prev.Rd | 26 ++++++++++++++++---------- 5 files changed, 51 insertions(+), 22 deletions(-)
Title: Disciplined Convex Optimization
Description: An object-oriented modeling language for disciplined convex
programming (DCP). It allows the user to formulate convex optimization problems
in a natural way following mathematical convention and DCP rules. The system
analyzes the problem, verifies its convexity, converts it into a canonical form,
and hands it off to an appropriate solver to obtain the solution.
Author: Anqi Fu [aut, cre],
Balasubramanian Narasimhan [aut],
Steven Diamond [aut],
John Miller [aut],
Stephen Boyd [ctb],
Paul Kunsberg Rosenfield [ctb]
Maintainer: Anqi Fu <anqif@stanford.edu>
Diff between CVXR versions 0.99 dated 2018-05-26 and 0.99-2 dated 2018-11-06
DESCRIPTION | 8 - MD5 | 199 ++++++++++++++++++------------- NEWS.md | 12 + R/mosek-solver.R | 6 README.md | 18 +- build/vignette.rds |binary inst/doc/cvxr_intro.html | 4 inst/python/gurobiglue.py | 13 +- man/Abs-class.Rd | 4 man/AffineProd-class.Rd | 1 man/Atom-class.Rd | 3 man/Bool-class.Rd | 1 man/BoolConstr-class.Rd | 1 man/CallbackParam-class.Rd | 1 man/Constant-class.Rd | 1 man/Conv-class.Rd | 4 man/CumSum-class.Rd | 1 man/DiagMat-class.Rd | 1 man/DiagVec-class.Rd | 1 man/ECOS-class.Rd | 1 man/ECOS_BB-class.Rd | 5 man/Entr-class.Rd | 4 man/EqConstraint-class.Rd | 1 man/Exp-class.Rd | 4 man/ExpCone-class.Rd | 4 man/GLPK-class.Rd | 1 man/GUROBI-class.Rd | 5 man/GeoMean-class.Rd | 1 man/HStack-class.Rd | 1 man/Huber-class.Rd | 1 man/Index-class.Rd | 1 man/Int-class.Rd | 1 man/IntConstr-class.Rd | 1 man/KLDiv-class.Rd | 1 man/Kron-class.Rd | 4 man/LPSOLVE-class.Rd | 5 man/LambdaMax-class.Rd | 1 man/LeqConstraint-class.Rd | 1 man/Log-class.Rd | 4 man/Log1p-class.Rd | 1 man/LogDet-class.Rd | 1 man/LogSumExp-class.Rd | 1 man/Logistic-class.Rd | 1 man/MOSEK-class.Rd | 1 man/MatrixFrac-class.Rd | 1 man/MaxElemwise-class.Rd | 1 man/MaxEntries-class.Rd | 1 man/Maximize-class.Rd | 1 man/Minimize-class.Rd | 1 man/MulElemwise-class.Rd | 1 man/NonNegative-class.Rd | 1 man/NonlinearConstraint-class.Rd | 1 man/NormNuc-class.Rd | 1 man/PSDConstraint-class.Rd | 1 man/Parameter-class.Rd | 1 man/Pnorm-class.Rd | 1 man/Power-class.Rd | 1 man/Problem-class.Rd | 1 man/QuadOverLin-class.Rd | 1 man/Rdict-class.Rd | 1 man/Rdictdefault-class.Rd | 1 man/Reshape-class.Rd | 1 man/SCS-class.Rd | 1 man/SDP-class.Rd | 1 man/SOC-class.Rd | 1 man/SOCAxis-class.Rd | 4 man/SemidefUpperTri-class.Rd | 1 man/SigmaMax-class.Rd | 1 man/SizeMetrics-class.Rd | 1 man/Solver-class.Rd | 4 man/Solver-solve.Rd | 4 man/SolverStats-class.Rd | 1 man/Sqrt-class.Rd | 4 man/Square-class.Rd | 1 man/SumEntries-class.Rd | 1 man/SumLargest-class.Rd | 1 man/SymmetricUpperTri-class.Rd | 1 man/Trace-class.Rd | 1 man/UpperTri-class.Rd | 1 man/VStack-class.Rd | 1 man/Variable-class.Rd | 1 man/canonicalize.Rd | 1 man/dot-LinOpVector__new.Rd |only man/dot-LinOpVector__push_back.Rd |only man/dot-LinOp__args_push_back.Rd |only man/dot-LinOp__get_dense_data.Rd |only man/dot-LinOp__get_id.Rd |only man/dot-LinOp__get_size.Rd |only man/dot-LinOp__get_slice.Rd |only man/dot-LinOp__get_sparse.Rd |only man/dot-LinOp__get_sparse_data.Rd |only man/dot-LinOp__get_type.Rd |only man/dot-LinOp__new.Rd |only man/dot-LinOp__set_dense_data.Rd |only man/dot-LinOp__set_size.Rd |only man/dot-LinOp__set_slice.Rd |only man/dot-LinOp__set_sparse.Rd |only man/dot-LinOp__set_sparse_data.Rd |only man/dot-LinOp__set_type.Rd |only man/dot-LinOp__size_push_back.Rd |only man/dot-LinOp__slice_push_back.Rd |only man/dot-LinOp_at_index.Rd |only man/dot-ProblemData__get_I.Rd |only man/dot-ProblemData__get_J.Rd |only man/dot-ProblemData__get_V.Rd |only man/dot-ProblemData__get_const_to_row.Rd |only man/dot-ProblemData__get_const_vec.Rd |only man/dot-ProblemData__get_id_to_col.Rd |only man/dot-ProblemData__new.Rd |only man/dot-ProblemData__set_I.Rd |only man/dot-ProblemData__set_J.Rd |only man/dot-ProblemData__set_V.Rd |only man/dot-ProblemData__set_const_to_row.Rd |only man/dot-ProblemData__set_const_vec.Rd |only man/dot-ProblemData__set_id_to_col.Rd |only man/dot-build_matrix_0.Rd |only man/dot-build_matrix_1.Rd |only man/kronecker.Rd | 8 - 118 files changed, 194 insertions(+), 195 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-25 0.1.2
2015-12-07 0.1.0
Title: Discrete Choice (Binary, Poisson and Ordered) Models with Random
Parameters
Description: An implementation of simulated maximum likelihood method for the
estimation of Binary (Probit and Logit), Ordered (Probit and Logit) and
Poisson models with random parameters for cross-sectional and longitudinal
data.
Author: Mauricio Sarrias <msarrias86@gmail.com>
Maintainer: Mauricio Sarrias <msarrias86@gmail.com>
Diff between Rchoice versions 0.3-1 dated 2016-10-17 and 0.3-1.1 dated 2018-11-06
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 6 ++++++ data/Articles.rda |binary data/Attitudes.rda |binary data/Health.rda |binary data/Workmroz.rda |binary 7 files changed, 15 insertions(+), 9 deletions(-)
Title: An R 'Pandoc' Writer
Description: Contains some functions catching all messages, 'stdout' and other
useful information while evaluating R code and other helpers to return user
specified text elements (like: header, paragraph, table, image, lists etc.)
in 'pandoc' markdown or several type of R objects similarly automatically
transformed to markdown format. Also capable of exporting/converting (the
resulting) complex 'pandoc' documents to e.g. HTML, 'PDF', 'docx' or 'odt'. This
latter reporting feature is supported in brew syntax or with a custom reference
class with a smarty caching 'backend'.
Author: Gergely Daróczi [aut, cre] (<https://orcid.org/0000-0003-3149-8537>),
Roman Tsegelskyi [aut]
Maintainer: Gergely Daróczi <daroczig@rapporter.net>
Diff between pander versions 0.6.2 dated 2018-07-08 and 0.6.3 dated 2018-11-06
DESCRIPTION | 27 - MD5 | 66 +- NEWS | 14 R/S3.R | 7 R/helpers.R | 12 R/options.R | 2 R/pandoc.R | 40 + README.md | 6 build/vignette.rds |binary inst/README.brew | 6 inst/doc/evals.html | 887 +++++++++++++++++---------------- inst/doc/knitr.html | 1125 ++++++++++++++++++++++++++---------------- inst/doc/pander.html | 881 +++++++++++++++++--------------- inst/doc/pandoc_table.Rmd | 2 inst/doc/pandoc_table.html | 1151 ++++++++++++++++++++++--------------------- inst/tests/test-convert.R | 7 man/Pandoc.brew.Rd | 4 man/evals.Rd | 6 man/pander.Arima.Rd | 3 man/pander.cph.Rd | 3 man/pander.formula.Rd | 6 man/pander.lm.Rd | 4 man/pander.microbenchmark.Rd | 4 man/pander.ols.Rd | 3 man/pander.orm.Rd | 3 man/pander.summary.lm.Rd | 6 man/panderOptions.Rd | 2 man/pandoc.date.return.Rd | 4 man/pandoc.formula.return.Rd | 4 man/pandoc.list.return.Rd | 4 man/pandoc.table.return.Rd | 4 man/set.alignment.Rd | 3 man/splitLine.Rd | 2 vignettes/pandoc_table.Rmd | 2 34 files changed, 2399 insertions(+), 1901 deletions(-)
Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct
full and abridge life tables given various input indices. A mortality
law is a parametric function that describes the dying-out process of
individuals in a population during a significant portion of their
life spans. For a comprehensive review of the most important mortality
laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>.
An elegant function for downloading data from Human Mortality
Database <https://www.mortality.org> is provided as well.
Author: Marius D. Pascariu [aut, cre, cph]
(<https://orcid.org/0000-0002-2568-6489>),
Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>
Diff between MortalityLaws versions 1.6.0 dated 2018-08-31 and 1.7.0 dated 2018-11-06
MortalityLaws-1.6.0/MortalityLaws/man/makehambeard.Rd |only MortalityLaws-1.7.0/MortalityLaws/DESCRIPTION | 8 MortalityLaws-1.7.0/MortalityLaws/MD5 | 72 - MortalityLaws-1.7.0/MortalityLaws/NAMESPACE | 4 MortalityLaws-1.7.0/MortalityLaws/NEWS | 4 MortalityLaws-1.7.0/MortalityLaws/R/LifeTable.R | 1 MortalityLaws-1.7.0/MortalityLaws/R/MortalityLaw_models.R | 474 +++++----- MortalityLaws-1.7.0/MortalityLaws/R/availableLaws.R | 67 - MortalityLaws-1.7.0/MortalityLaws/R/readHMD.R | 222 +++- MortalityLaws-1.7.0/MortalityLaws/README.md | 1 MortalityLaws-1.7.0/MortalityLaws/inst/doc/Installation.pdf |binary MortalityLaws-1.7.0/MortalityLaws/inst/doc/Intro.pdf |binary MortalityLaws-1.7.0/MortalityLaws/man/HP.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/ReadHMD.Rd | 43 MortalityLaws-1.7.0/MortalityLaws/man/ReadHMD.core.Rd | 28 MortalityLaws-1.7.0/MortalityLaws/man/availableLaws.Rd | 5 MortalityLaws-1.7.0/MortalityLaws/man/beard.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/beard_makeham.Rd |only MortalityLaws-1.7.0/MortalityLaws/man/carriere1.Rd | 2 MortalityLaws-1.7.0/MortalityLaws/man/carriere2.Rd | 2 MortalityLaws-1.7.0/MortalityLaws/man/gompertz.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/kannisto.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/kannisto_makeham.Rd |only MortalityLaws-1.7.0/MortalityLaws/man/kostaki.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/makeham.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/martinelle.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/opperman.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/perks.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/print.ReadHMD.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/rogersplanck.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/siler.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/strehler_mildvan.Rd |only MortalityLaws-1.7.0/MortalityLaws/man/thiele.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/vandermaen.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/vandermaen2.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/man/weibull.Rd | 2 MortalityLaws-1.7.0/MortalityLaws/man/wittstein.Rd | 4 MortalityLaws-1.7.0/MortalityLaws/tests/testthat/test_MortalityLaws2.R | 35 MortalityLaws-1.7.0/MortalityLaws/tests/testthat/test_ReadHMD.R | 57 + 39 files changed, 667 insertions(+), 424 deletions(-)
Title: Multinomial Logit Models with Random Parameters
Description: An implementation of maximum simulated likelihood method for the
estimation of multinomial logit models with random coefficients.
Specifically, it allows estimating models with continuous heterogeneity
such as the mixed multinomial logit and the generalized multinomial logit.
It also allows estimating models with discrete heterogeneity such as the
latent class and the mixed-mixed multinomial logit model.
Author: Mauricio Sarrias [aut, cre],
Ricardo Daziano [aut],
Yves Croissant [ctb]
Maintainer: Mauricio Sarrias <msarrias86@gmail.com>
Diff between gmnl versions 1.1-3 dated 2017-07-09 and 1.1-3.1 dated 2018-11-06
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 4 ++++ 3 files changed, 10 insertions(+), 6 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability
to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally,
'ggtern' has implemented several NEW geometries which are unavailable to the
standard 'ggplot2' release. For further examples and documentation, please
proceed to the 'ggtern' website.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 3.0.0 dated 2018-08-22 and 3.0.0.1 dated 2018-11-06
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/utilities-help.R | 2 +- build/partial.rdb |binary data/Feldspar.RData |binary data/FeldsparRaster.RData |binary data/Fragments.RData |binary data/SkyeLava.RData |binary data/USDA.RData |binary data/WhiteCells.RData |binary 10 files changed, 14 insertions(+), 14 deletions(-)
Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Author: Maxime Hervé
Maintainer: Maxime Hervé <maxime.herve@univ-rennes1.fr>
Diff between RVAideMemoire versions 0.9-69-3 dated 2018-05-14 and 0.9-70 dated 2018-11-06
RVAideMemoire-0.9-69-3/RVAideMemoire/R/dunn.test.R |only RVAideMemoire-0.9-69-3/RVAideMemoire/R/pairwise.to.groups.R |only RVAideMemoire-0.9-69-3/RVAideMemoire/man/dunn.test.Rd |only RVAideMemoire-0.9-69-3/RVAideMemoire/man/pairwise.to.groups.Rd |only RVAideMemoire-0.9-70/RVAideMemoire/DESCRIPTION | 18 +- RVAideMemoire-0.9-70/RVAideMemoire/MD5 | 78 ++++------ RVAideMemoire-0.9-70/RVAideMemoire/NAMESPACE | 30 --- RVAideMemoire-0.9-70/RVAideMemoire/NEWS | 5 RVAideMemoire-0.9-70/RVAideMemoire/R/Anova.clm.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/CDA.cv.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/CDA.test.R | 4 RVAideMemoire-0.9-70/RVAideMemoire/R/CvM.test.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/MVA.cmv.R | 4 RVAideMemoire-0.9-70/RVAideMemoire/R/MVA.cor.R | 8 - RVAideMemoire-0.9-70/RVAideMemoire/R/MVA.cv.R | 4 RVAideMemoire-0.9-70/RVAideMemoire/R/MVA.scoreplot.R | 6 RVAideMemoire-0.9-70/RVAideMemoire/R/PLSDA.VIP.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/adonis.II.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/bootstrap.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/byf.hist.R | 10 - RVAideMemoire-0.9-70/RVAideMemoire/R/byf.mqqnorm.R | 4 RVAideMemoire-0.9-70/RVAideMemoire/R/byf.qqnorm.R | 7 RVAideMemoire-0.9-70/RVAideMemoire/R/cox.resid.R | 10 - RVAideMemoire-0.9-70/RVAideMemoire/R/cramer.test.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/deprecated.R | 16 +- RVAideMemoire-0.9-70/RVAideMemoire/R/dhist.R | 8 - RVAideMemoire-0.9-70/RVAideMemoire/R/mqqnorm.R | 4 RVAideMemoire-0.9-70/RVAideMemoire/R/multtest.gp.R | 4 RVAideMemoire-0.9-70/RVAideMemoire/R/overdisp.glmer.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/pcor.test.R | 4 RVAideMemoire-0.9-70/RVAideMemoire/R/plotresid.R | 5 RVAideMemoire-0.9-70/RVAideMemoire/R/predict.coadisc.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/prop.multinom.test.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/scat.cr.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/spearman.ci.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/to.dudi.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/wald.ptheo.test.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/R/zzz.R | 2 RVAideMemoire-0.9-70/RVAideMemoire/man/CDA.test.Rd | 2 RVAideMemoire-0.9-70/RVAideMemoire/man/PLSDA.VIP.Rd | 10 - RVAideMemoire-0.9-70/RVAideMemoire/man/RVAideMemoire-package.Rd | 4 RVAideMemoire-0.9-70/RVAideMemoire/man/deprecated.Rd | 14 + 42 files changed, 153 insertions(+), 136 deletions(-)
Title: Low-Level Support for Provenance Capture Between in-Memory R
Objects
Description: A suite of classes and methods which provide low-level support for modeling provenance between in-memory R objects. This is an infrastructure package and is not intended to be used directly by end-users.
Author: Gabriel Becker
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between roprov versions 0.1.1 dated 2018-08-16 and 0.1.2 dated 2018-11-06
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Tools for Making and Combining Functions
Description: Provides a suite of function-building tools centered around a
(forward) composition operator, %>>>%, which extends the semantics of the
'magrittr' %>% operator and supports 'tidyverse' quasiquotation. It enables
you to construct composite functions that can be inspected and transformed as
list-like objects. In conjunction with %>>>%, a compact function constructor,
fn(), and a function that performs partial application, partial(), are also
provided. Both support quasiquotation.
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>
Diff between gestalt versions 0.1.4 dated 2018-08-02 and 0.1.5 dated 2018-11-06
DESCRIPTION | 10 MD5 | 17 NAMESPACE | 1 R/context.R | 33 - R/partial.R | 6 R/utils.R | 48 +- inst/NEWS |only inst/doc/gestalt.html | 795 +++++++++++++++++++++--------------------- man/context.Rd | 22 - tests/testthat/test-context.R | 8 10 files changed, 486 insertions(+), 454 deletions(-)
Title: Data Files and Functions Accompanying the Book "Bayesian Data
Analysis in Ecology using R, BUGS and Stan"
Description: Data files and functions accompanying the book Korner-Nievergelt, Roth, von Felten, Guelat, Almasi, Korner-Nievergelt (2015) "Bayesian Data Analysis in Ecology using R, BUGS and Stan", Elsevier, New York.
Author: Fraenzi Korner-Nievergelt, Tobias Roth, Stefanie von Felten, Jerome Guelat, Bettina Almasi, Pius Korner-Nievergelt
Maintainer: Fraenzi Korner-Nievergelt <fraenzi.korner@oikostat.ch>
Diff between blmeco versions 1.1 dated 2015-08-22 and 1.2 dated 2018-11-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/WAIC.R | 7 ++++--- man/compareqqnorm.Rd | 3 ++- man/dispersion_glmer.Rd | 15 ++++++++++++--- 5 files changed, 26 insertions(+), 15 deletions(-)
Title: Toolkit for Electroencephalography Data
Description: Analysis and visualization tools for electroencephalography (EEG) data. Includes functions for (i) plotting EEG data, (ii) filtering EEG data, (iii) smoothing EEG data; (iv) frequency domain (Fourier) analysis of EEG data, (v) Independent Component Analysis of EEG data, and (vi) simulating event-related potential EEG data.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between eegkit versions 1.0-3 dated 2018-05-24 and 1.0-4 dated 2018-11-06
ChangeLog | 25 +++++++++++++++++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 34 ++++++++++++++++++++-------------- NAMESPACE | 2 +- R/eegcap.R | 14 ++++++++------ R/eegcap2d.R |only R/eegfilter.R |only R/eegpsd.R |only R/eegtime.R | 9 +++++---- R/eegtimemc.R | 13 ++++++++++--- build/partial.rdb |binary data/eegcoord.rda |binary data/eegdense.rda |binary data/eeghead.rda |binary data/eegmesh.rda |binary man/eegcap.Rd | 10 +++++++--- man/eegcap2d.Rd |only man/eegfft.Rd | 3 --- man/eegfilter.Rd |only man/eegpsd.Rd |only man/eegtime.Rd | 9 ++++++++- 21 files changed, 90 insertions(+), 41 deletions(-)
Title: Powerful and Reliable Tools for Running System Commands in R
Description: Drop-in replacements for the base system2() function with fine control
and consistent behavior across platforms. Supports clean interruption, timeout,
background tasks, and streaming STDIN / STDOUT / STDERR over binary or text
connections. Arguments on Windows automatically get encoded and quoted to work on different
locales. On Unix platforms the package also provides functions for evaluating
expressions inside a temporary fork. Such evaluations have no side effects on the
main R process, and support reliable interrupts and timeouts. This provides the
basis for a sandboxing mechanism.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between sys versions 1.6 dated 2018-07-24 and 2.0 dated 2018-11-06
DESCRIPTION | 24 +++++---- MD5 | 36 ++++++++------ NAMESPACE | 4 + NEWS | 10 +++ R/callr.R |only R/exec.R | 47 +++++++++++++----- R/quote.R |only configure | 16 +++--- inst/WORDLIST | 4 + inst/utf8.txt |only man/exec.Rd | 25 +++++++-- man/exec_r.Rd |only man/quote.Rd |only src/exec.c | 18 ++++--- src/fork.c | 2 src/init.c | 2 src/win32/exec.c | 104 +++++++++++++++++++++++++++++------------ tests/testthat/test-encoding.R |only tests/testthat/test-error.R | 2 tests/testthat/test-forking.R | 1 tests/testthat/test-quote.R |only tests/testthat/test-stdin.R |only tests/testthat/test-stdout.R | 2 23 files changed, 209 insertions(+), 88 deletions(-)
Title: Statistical Methods for the Item Count Technique and List
Experiment
Description: Allows researchers to conduct multivariate
statistical analyses of survey data with list experiments. This
survey methodology is also known as the item count technique or
the unmatched count technique and is an alternative to the commonly
used randomized response method. The package implements the methods
developed by Imai (2011) <doi:10.1198/jasa.2011.ap10415>,
Blair and Imai (2012) <doi:10.1093/pan/mpr048>,
Blair, Imai, and Lyall (2013) <doi:10.1111/ajps.12086>,
Imai, Park, and Greene (2014) <doi:10.1093/pan/mpu017>,
Aronow, Coppock, Crawford, and Green (2015) <doi:10.1093/jssam/smu023>,
Chou, Imai, and Rosenfeld (2017) <doi:10.1177/0049124117729711>, and
Blair, Chou, and Imai (2018) <https://imai.fas.harvard.edu/research/files/listerror.pdf>.
This includes a Bayesian MCMC implementation of regression for the
standard and multiple sensitive item list experiment designs and a
random effects setup, a Bayesian MCMC hierarchical regression model
with up to three hierarchical groups, the combined list experiment
and endorsement experiment regression model, a joint model of the
list experiment that enables the analysis of the list experiment as
a predictor in outcome regression models, a method for combining
list experiments with direct questions, and methods for diagnosing and
adjusting for response error. In addition, the package implements the
statistical test that is designed to detect certain failures of list
experiments, and a placebo test for the list experiment using data from
direct questions.
Author: Graeme Blair [aut, cre],
Winston Chou [aut],
Kosuke Imai [aut],
Bethany Park [ctb],
Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between list versions 8.3 dated 2016-12-30 and 9.0 dated 2018-11-06
list-8.3/list/R/bayesglm.R |only list-9.0/list/ChangeLog | 1 list-9.0/list/DESCRIPTION | 41 list-9.0/list/MD5 | 73 list-9.0/list/NAMESPACE | 6 list-9.0/list/R/combinedListDirect.R | 39 list-9.0/list/R/comp.listEndorse.R | 38 list-9.0/list/R/ict.hausman.test.R |only list-9.0/list/R/ict.test.R | 55 list-9.0/list/R/ictreg.R | 2724 ++++++++++++++++++++++++--- list-9.0/list/R/ictreg.joint.R | 270 ++ list-9.0/list/R/ictregBayes.R | 483 ++++ list-9.0/list/R/ictregBayesHier.R | 385 +++ list-9.0/list/R/list-package.R |only list-9.0/list/README.md | 8 list-9.0/list/build/vignette.rds |binary list-9.0/list/inst/doc/combined-list.html | 560 +++-- list-9.0/list/man/affirm.Rd | 57 list-9.0/list/man/combinedListDirect.Rd | 40 list-9.0/list/man/combinedListExps.Rd | 6 list-9.0/list/man/comp.listEndorse.Rd | 84 list-9.0/list/man/ict.hausman.test.Rd |only list-9.0/list/man/ict.test.Rd | 84 list-9.0/list/man/ictreg.Rd | 380 ++- list-9.0/list/man/ictreg.joint.Rd | 105 - list-9.0/list/man/ictregBayes.Rd | 333 ++- list-9.0/list/man/ictregBayesHier.Rd | 367 ++- list-9.0/list/man/mexico.Rd | 103 - list-9.0/list/man/mis.Rd | 85 list-9.0/list/man/multi.Rd | 64 list-9.0/list/man/plot.predict.ictreg.Rd | 112 - list-9.0/list/man/predict.ictreg.Rd | 143 - list-9.0/list/man/predict.ictreg.joint.Rd | 184 + list-9.0/list/man/predict.ictregBayes.Rd | 145 - list-9.0/list/man/predict.ictregBayesHier.Rd | 120 - list-9.0/list/man/race.Rd | 57 list-9.0/list/man/summary.ictreg.Rd | 95 list-9.0/list/src/init.c |only list-9.0/list/tests/testthat/Rplots.pdf |binary list-9.0/list/tests/testthat/test-ictreg.R | 15 40 files changed, 5838 insertions(+), 1424 deletions(-)
Title: Randomized Singular Value Decomposition
Description: Low-rank matrix decompositions are fundamental tools and widely used for data
analysis, dimension reduction, and data compression. Classically, highly accurate
deterministic matrix algorithms are used for this task. However, the emergence of
large-scale data has severely challenged our computational ability to analyze big data.
The concept of randomness has been demonstrated as an effective strategy to quickly produce
approximate answers to familiar problems such as the singular value decomposition (SVD).
The rsvd package provides several randomized matrix algorithms such as the randomized
singular value decomposition (rsvd), randomized principal component analysis (rpca),
randomized robust principal component analysis (rrpca), randomized interpolative
decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot
functions are provided. The methods are discussed in detail by Erichson et al. (2016) <arXiv:1608.02148>.
Author: N. Benjamin Erichson [aut, cre]
Maintainer: N. Benjamin Erichson <erichson@uw.edu>
Diff between rsvd versions 0.9 dated 2017-12-08 and 1.0.0 dated 2018-11-06
DESCRIPTION | 17 +++++++------- MD5 | 45 +++++++++++++++++++-------------------- NAMESPACE | 3 ++ R/ggcorplot.R | 4 +-- R/rpca.R | 3 -- R/rrpca.R | 4 +-- R/rsvd.R | 4 --- R/wrapper_function.R | 3 ++ inst |only man/ggbiplot.Rd | 5 ++-- man/ggcorplot.Rd | 5 ++-- man/rid.Rd | 4 +-- man/rpca.Rd | 4 +-- man/rrpca.Rd | 2 - man/rsvd.Rd | 24 ++++++++++++++++++++ tests/testthat/test_cur.R | 1 tests/testthat/test_dependency.R | 1 tests/testthat/test_id.R | 1 tests/testthat/test_rcur.R | 1 tests/testthat/test_rid.R | 1 tests/testthat/test_rpca.R | 1 tests/testthat/test_rqb.R | 1 tests/testthat/test_rrpca.R | 1 tests/testthat/test_rsvd.R | 19 +++++++++++++++- 24 files changed, 105 insertions(+), 49 deletions(-)
Title: Flexible Tools for Multiple Imputation
Description: Provides a set of tools that can be used across 'data.frame' and
'imputationList' objects.
Author: James Conigrave
Maintainer: James Conigrave <james.conigrave@gmail.com>
Diff between Conigrave versions 0.4.1 dated 2018-08-09 and 0.4.2 dated 2018-11-06
Conigrave-0.4.1/Conigrave/man/correlatrix.Rd |only Conigrave-0.4.2/Conigrave/DESCRIPTION | 14 Conigrave-0.4.2/Conigrave/MD5 | 15 Conigrave-0.4.2/Conigrave/NAMESPACE | 2 Conigrave-0.4.2/Conigrave/R/Interaction.plot.R | 11 Conigrave-0.4.2/Conigrave/R/check_names.R | 15 Conigrave-0.4.2/Conigrave/R/correlatrix.R | 612 +++++++++++++------------ Conigrave-0.4.2/Conigrave/R/find_similar.R |only Conigrave-0.4.2/Conigrave/README.md |only Conigrave-0.4.2/Conigrave/man/ctrx.Rd |only Conigrave-0.4.2/Conigrave/man/find_similar.Rd |only 11 files changed, 365 insertions(+), 304 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.3.1 dated 2018-07-03 and 0.3.2 dated 2018-11-06
ChangeLog | 56 ++ DESCRIPTION | 8 MD5 | 27 - R/assertions.R | 8 README.md | 2 build/partial.rdb |binary cleanup | 3 inst/NEWS.Rd | 15 inst/doc |only man/anytime-package.Rd | 14 man/anytime.Rd | 2 src/anytime.cpp | 11 tests/allFormats.R | 121 ++-- tests/bulkTest.R | 1221 ++++++++++++++++++++++++------------------------- tests/simpleTests.R | 182 ++++--- 15 files changed, 890 insertions(+), 780 deletions(-)