Title: Chemical Thermodynamics and Activity Diagrams
Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
and low-temperature geochemistry. The features include calculation of the standard molal
thermodynamic properties and chemical affinities of reactions involving minerals and/or
biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous
species; amino acid group additivity for the standard molal thermodynamic properties of
neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state
for aqueous species; construction of equilibrium activity diagrams as a function of
temperature, pressure, and chemical activities or fugacities of basis species.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.0.7 dated 2015-11-19 and 1.0.8 dated 2016-05-28
DESCRIPTION | 8 +++--- MD5 | 47 +++++++++++++++++++-------------------- R/EOSregress.R | 32 ++++++++++++++------------ R/examples.R | 11 +++++---- R/hkf.R | 30 ++++++++++++++---------- R/makeup.R | 19 +++++++++------ R/subcrt.R | 6 ++-- R/util.misc.R | 4 +-- build/vignette.rds |binary data/OBIGT.csv | 1 data/refs.csv | 7 +++-- demo/00Index | 3 +- demo/dehydration.R |only inst/CITATION | 2 - inst/NEWS | 33 ++++++++++++++++++++++++++- inst/doc/anintro.pdf |binary inst/doc/equilibrium.pdf |binary inst/doc/hotspring.pdf |binary inst/doc/wjd.R | 2 - inst/doc/wjd.pdf |binary inst/extdata/thermo/OBIGT-2.csv | 5 ++++ man/EOSregress.Rd | 8 ++++-- man/examples.Rd | 4 ++- man/subcrt.Rd | 7 +++-- tests/testthat/test-EOSregress.R | 20 ++++++++-------- 25 files changed, 156 insertions(+), 93 deletions(-)
Title: Large-Scale Bayesian Variable Selection Using Variational
Methods
Description: Fast algorithms for fitting Bayesian variable selection models and computing Bayes factors, in which the outcome (or response variable) is modeled using a linear regression or a logistic regression. The algorithms are based on the variational approximations described in "Scalable variational inference for Bayesian variable selection in regression, and its accuracy in genetic association studies" (P. Carbonetto & M. Stephens, 2012, <DOI:10.1214/12-BA703>). This software has been applied to large data sets with over a million variables and thousands of samples.
Author: Peter Carbonetto, Matthew Stephens
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between varbvs versions 1.0 dated 2012-04-10 and 2.0.0 dated 2016-05-28
varbvs-1.0/varbvs/R/createdata.R |only varbvs-1.0/varbvs/R/densities.R |only varbvs-1.0/varbvs/R/grid.R |only varbvs-1.0/varbvs/R/miscellaneous.R |only varbvs-1.0/varbvs/R/varbvsbinoptimize.R |only varbvs-1.0/varbvs/R/varbvsoptimize.R |only varbvs-1.0/varbvs/R/varbvsupdate.R |only varbvs-1.0/varbvs/R/varlb.R |only varbvs-1.0/varbvs/R/varsimbvs.R |only varbvs-1.0/varbvs/demo |only varbvs-1.0/varbvs/man/create.data.Rd |only varbvs-1.0/varbvs/man/create.snps.Rd |only varbvs-1.0/varbvs/man/grid3d.Rd |only varbvs-1.0/varbvs/man/updatestats.Rd |only varbvs-1.0/varbvs/man/varbvsbinoptimize.Rd |only varbvs-1.0/varbvs/man/varbvsoptimize.Rd |only varbvs-1.0/varbvs/man/varsimbvs.Rd |only varbvs-1.0/varbvs/src/sigmoid.c |only varbvs-1.0/varbvs/src/sigmoid.h |only varbvs-1.0/varbvs/src/varbvsbin.c |only varbvs-1.0/varbvs/src/varbvsbin.h |only varbvs-1.0/varbvs/src/varbvsbinupdateR.c |only varbvs-1.0/varbvs/src/varbvsupdateR.c |only varbvs-1.0/varbvs/src/vectorops.c |only varbvs-1.0/varbvs/src/vectorops.h |only varbvs-2.0.0/varbvs/DESCRIPTION | 32 ++--- varbvs-2.0.0/varbvs/MD5 | 82 ++++++++------ varbvs-2.0.0/varbvs/NAMESPACE | 33 ++++-- varbvs-2.0.0/varbvs/R/bayesfactor.R |only varbvs-2.0.0/varbvs/R/misc.R |only varbvs-2.0.0/varbvs/R/plot.varbvs.R |only varbvs-2.0.0/varbvs/R/predict.varbvs.R |only varbvs-2.0.0/varbvs/R/summary.varbvs.R |only varbvs-2.0.0/varbvs/R/varbvs.R |only varbvs-2.0.0/varbvs/R/varbvsbin.R |only varbvs-2.0.0/varbvs/R/varbvsbinupdate.R | 137 ++++++++++++------------- varbvs-2.0.0/varbvs/R/varbvsbinz.R |only varbvs-2.0.0/varbvs/R/varbvsbinzupdate.R |only varbvs-2.0.0/varbvs/R/varbvscoefcred.R |only varbvs-2.0.0/varbvs/R/varbvsindep.R |only varbvs-2.0.0/varbvs/R/varbvsnorm.R |only varbvs-2.0.0/varbvs/R/varbvsnormupdate.R |only varbvs-2.0.0/varbvs/R/varbvspve.R |only varbvs-2.0.0/varbvs/data |only varbvs-2.0.0/varbvs/man/bayesfactor.Rd |only varbvs-2.0.0/varbvs/man/cred.Rd |only varbvs-2.0.0/varbvs/man/cytokine.Rd |only varbvs-2.0.0/varbvs/man/leukemia.Rd |only varbvs-2.0.0/varbvs/man/normalizelogweights.Rd |only varbvs-2.0.0/varbvs/man/plot.varbvs.Rd |only varbvs-2.0.0/varbvs/man/predict.varbvs.Rd |only varbvs-2.0.0/varbvs/man/rand.Rd |only varbvs-2.0.0/varbvs/man/summary.varbvs.Rd |only varbvs-2.0.0/varbvs/man/varbvs-internal.Rd |only varbvs-2.0.0/varbvs/man/varbvs-package.Rd | 60 ++++------ varbvs-2.0.0/varbvs/man/varbvs.Rd |only varbvs-2.0.0/varbvs/man/varbvscoefcred.Rd |only varbvs-2.0.0/varbvs/man/varbvsindep.Rd |only varbvs-2.0.0/varbvs/src/diagsq.c |only varbvs-2.0.0/varbvs/src/diagsq.h |only varbvs-2.0.0/varbvs/src/diagsqr.c |only varbvs-2.0.0/varbvs/src/misc.c |only varbvs-2.0.0/varbvs/src/misc.h |only varbvs-2.0.0/varbvs/src/types.h | 8 - varbvs-2.0.0/varbvs/src/varbvs.c | 70 ++++++++++-- varbvs-2.0.0/varbvs/src/varbvs.h | 45 +++++++- varbvs-2.0.0/varbvs/src/varbvsr.c |only varbvs-2.0.0/varbvs/vignettes |only 68 files changed, 286 insertions(+), 181 deletions(-)
Title: Interpreting Time Series and Autocorrelated Data Using GAMMs
Description: GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999)
as implemented in the R package 'mgcv' (Wood, S.N., 2006; 2011) is a nonlinear
regression analysis which is particularly useful for time course data such as
EEG, pupil dilation, gaze data (eye tracking), and articulography recordings,
but also for behavioral data such as reaction times and response data. As time
course measures are sensitive to autocorrelation problems, GAMMs implements
methods to reduce the autocorrelation problems. This package includes functions
for the evaluation of GAMM models (e.g., model comparisons, determining regions
of significance, inspection of autocorrelational structure in residuals)
and interpreting of GAMMs (e.g., visualization of complex interactions, and
contrasts).
Author: Jacolien van Rij [aut, cre],
Martijn Wieling [aut],
R. Harald Baayen [aut],
Hedderik van Rijn [ctb]
Maintainer: Jacolien van Rij <vanrij.jacolien@gmail.com>
Diff between itsadug versions 2.0 dated 2016-03-20 and 2.1 dated 2016-05-28
itsadug-2.0/itsadug/man/addInterval.Rd |only itsadug-2.0/itsadug/man/add_bars.Rd |only itsadug-2.0/itsadug/man/alpha.Rd |only itsadug-2.0/itsadug/man/alphaPalette.Rd |only itsadug-2.0/itsadug/man/check_normaldist.Rd |only itsadug-2.0/itsadug/man/color_contour.Rd |only itsadug-2.0/itsadug/man/dotplot_error.Rd |only itsadug-2.0/itsadug/man/drawArrows.Rd |only itsadug-2.0/itsadug/man/emptyPlot.Rd |only itsadug-2.0/itsadug/man/errorBars.Rd |only itsadug-2.0/itsadug/man/fill_area.Rd |only itsadug-2.0/itsadug/man/findAbsMin.Rd |only itsadug-2.0/itsadug/man/find_n_neighbors.Rd |only itsadug-2.0/itsadug/man/getCoords.Rd |only itsadug-2.0/itsadug/man/getDec.Rd |only itsadug-2.0/itsadug/man/getFigCoords.Rd |only itsadug-2.0/itsadug/man/getProps.Rd |only itsadug-2.0/itsadug/man/getRange.Rd |only itsadug-2.0/itsadug/man/gradientLegend.Rd |only itsadug-2.0/itsadug/man/group_sort.Rd |only itsadug-2.0/itsadug/man/list2str.Rd |only itsadug-2.0/itsadug/man/marginDensityPlot.Rd |only itsadug-2.0/itsadug/man/move_n_point.Rd |only itsadug-2.0/itsadug/man/plot_error.Rd |only itsadug-2.0/itsadug/man/plot_image.Rd |only itsadug-2.0/itsadug/man/plotsurface.Rd |only itsadug-2.0/itsadug/man/se.Rd |only itsadug-2.1/itsadug/DESCRIPTION | 12 itsadug-2.1/itsadug/MD5 | 81 itsadug-2.1/itsadug/NAMESPACE | 28 itsadug-2.1/itsadug/R/acf.R | 33 itsadug-2.1/itsadug/R/eval.R | 49 itsadug-2.1/itsadug/R/inspect.R | 146 - itsadug-2.1/itsadug/R/itsadug.R | 2 itsadug-2.1/itsadug/R/pca.R | 2 itsadug-2.1/itsadug/R/plot.R | 2566 ---------------------- itsadug-2.1/itsadug/R/predict.R | 6 itsadug-2.1/itsadug/R/test.R | 18 itsadug-2.1/itsadug/R/util.R | 291 -- itsadug-2.1/itsadug/build/vignette.rds |binary itsadug-2.1/itsadug/inst/NEWS | 26 itsadug-2.1/itsadug/inst/doc/acf.html | 41 itsadug-2.1/itsadug/inst/doc/inspect.html | 157 - itsadug-2.1/itsadug/inst/doc/test.html | 19 itsadug-2.1/itsadug/man/convertNonAlphanumeric.Rd | 8 itsadug-2.1/itsadug/man/diff_terms.Rd | 8 itsadug-2.1/itsadug/man/fadeRug.Rd | 12 itsadug-2.1/itsadug/man/find_difference.Rd | 8 itsadug-2.1/itsadug/man/missing_est.Rd | 10 itsadug-2.1/itsadug/man/plot_smooth.Rd | 14 itsadug-2.1/itsadug/man/print_summary.Rd | 10 itsadug-2.1/itsadug/man/rug_model.Rd | 13 itsadug-2.1/itsadug/man/start_event.Rd | 10 itsadug-2.1/itsadug/man/summary_data.Rd | 10 itsadug-2.1/itsadug/man/timeBins.Rd | 10 55 files changed, 371 insertions(+), 3219 deletions(-)
Title: Assemble Data Frames from HTML Tables
Description: HTML tables are a valuable data source but extracting and recasting
these data into a useful format can be tedious. This package allows to collect
structured information from HTML tables. It is similar to readHTMLTable()
of the XML package but provides three major advantages. First, the function
automatically expands row and column spans in the header and body cells.
Second, users are given more control over the identification of header and body
rows which will end up in the R table, including semantic header information
that appear throughout the body. Third, the function preprocesses table code,
corrects common types of malformations, removes unneeded parts and so helps to
alleviate the need for tedious post-processing.
Author: Christian Rubba [aut, cre]
Maintainer: Christian Rubba <christian.rubba@gmail.com>
Diff between htmltab versions 0.6.0 dated 2015-07-22 and 0.7.0 dated 2016-05-28
htmltab-0.6.0/htmltab/README.md |only htmltab-0.7.0/htmltab/DESCRIPTION | 26 +- htmltab-0.7.0/htmltab/LICENSE | 2 htmltab-0.7.0/htmltab/MD5 | 59 +++-- htmltab-0.7.0/htmltab/NAMESPACE | 2 htmltab-0.7.0/htmltab/NEWS | 23 + htmltab-0.7.0/htmltab/R/body.R | 17 + htmltab-0.7.0/htmltab/R/colnames.R | 7 htmltab-0.7.0/htmltab/R/header.R | 19 + htmltab-0.7.0/htmltab/R/htmltab.R | 65 +++-- htmltab-0.7.0/htmltab/R/identify_rows.R | 9 htmltab-0.7.0/htmltab/R/inbody_header.R | 1 htmltab-0.7.0/htmltab/R/setup_and_checks.R | 112 +++++++-- htmltab-0.7.0/htmltab/R/utils.R | 6 htmltab-0.7.0/htmltab/build/vignette.rds |binary htmltab-0.7.0/htmltab/inst/doc/htmltab.R | 9 htmltab-0.7.0/htmltab/inst/doc/htmltab.Rmd | 15 - htmltab-0.7.0/htmltab/inst/doc/htmltab.html | 175 +++++++-------- htmltab-0.7.0/htmltab/man/check_type.Rd |only htmltab-0.7.0/htmltab/man/create_inbody.Rd |only htmltab-0.7.0/htmltab/man/eval_body.Rd |only htmltab-0.7.0/htmltab/man/eval_header.Rd |only htmltab-0.7.0/htmltab/man/get_body_xpath.Rd |only htmltab-0.7.0/htmltab/man/get_cell_element.Rd |only htmltab-0.7.0/htmltab/man/get_head_xpath.Rd |only htmltab-0.7.0/htmltab/man/get_header_elements.Rd |only htmltab-0.7.0/htmltab/man/get_span.Rd |only htmltab-0.7.0/htmltab/man/get_trindex.Rd |only htmltab-0.7.0/htmltab/man/htmltab.Rd | 25 +- htmltab-0.7.0/htmltab/man/identify_elements.Rd |only htmltab-0.7.0/htmltab/man/normalize_tr.Rd |only htmltab-0.7.0/htmltab/man/num_xpath.Rd | 2 htmltab-0.7.0/htmltab/man/rm_empty_cols.Rd |only htmltab-0.7.0/htmltab/man/rm_empty_rows.Rd |only htmltab-0.7.0/htmltab/man/rm_nuisance.Rd |only htmltab-0.7.0/htmltab/man/select_tab.Rd |only htmltab-0.7.0/htmltab/tests/testthat/test_expand_spans.R | 1 htmltab-0.7.0/htmltab/tests/testthat/test_inputs.R | 6 htmltab-0.7.0/htmltab/vignettes/htmltab.Rmd | 15 - 39 files changed, 369 insertions(+), 227 deletions(-)
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell, <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@umich.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>
Diff between rdrobust versions 0.90 dated 2016-05-08 and 0.91 dated 2016-05-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/functions.R | 2 +- R/rdbwselect.R | 12 ++++++------ R/rdrobust.R | 12 ++++++------ 5 files changed, 21 insertions(+), 21 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), analise de multiplos fatores (MFA), para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.7 dated 2016-04-14 and 1.8 dated 2016-05-28
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- R/CoefVar.R |only R/NormData.R | 16 ++++++++++------ R/Plot.MFA.R | 4 ++-- man/CoefVar.Rd |only man/MVar.pt-package.Rd | 4 ++-- 7 files changed, 24 insertions(+), 18 deletions(-)