Title: Causal Mediation Analysis Using Weighting Approach
Description: We implement causal mediation analysis using the methods proposed by Hong (2010) and Hong, Deutsch & Hill (2015) <doi:10.3102/1076998615583902>. It allows the estimation and hypothesis testing of causal mediation effects through ratio of mediator probability weights (RMPW). This strategy conveniently relaxes the assumption of no treatment-by-mediator interaction while greatly simplifying the outcome model specification without invoking strong distributional assumptions. We also implement a sensitivity analysis by extending the RMPW method to assess potential bias in the presence of omitted pretreatment or posttreatment covariates. The sensitivity strategy was proposed by Hong, Qin, and Yang (2018) <doi:10.3102/1076998615583902>.
Author: Xu Qin, Guanglei Hong, and Fan Yang
Maintainer: Xu Qin <xuqin@uchicago.edu>
Diff between rmpw versions 0.0.1 dated 2017-02-27 and 0.0.2 dated 2017-12-21
DESCRIPTION | 13 - MD5 | 12 - NAMESPACE | 9 + R/rmpw.R | 426 +++++++++++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary data/Riverside.rda |binary man/sensitivity.Rd |only man/sensitivity.plot.Rd |only 8 files changed, 448 insertions(+), 12 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 0.1.4 dated 2017-11-05 and 0.1.6 dated 2017-12-21
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NAMESPACE | 1 + NEWS.md | 10 ++++++++++ R/types.R | 41 +++++++++++++++++++++++++++++++++++++++++ build/vignette.rds |binary man/is_reference.Rd |only src/capture.c | 3 +-- 8 files changed, 63 insertions(+), 11 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis.
This includes meta-analysis, (robust) prior derivation
from historical data, operating characteristics
and analysis (1 and 2 sample cases).
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Trustees of Columbia University [cph] (src/init.cpp, tools/make_cpp.R,
R/stanmodels.R)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.2-3 dated 2017-08-21 and 1.3-1 dated 2017-12-21
RBesT-1.2-3/RBesT/R/oc1Sdecision.R |only RBesT-1.2-3/RBesT/R/oc2Sdecision.R |only RBesT-1.2-3/RBesT/man/dBetaBinomial.Rd |only RBesT-1.2-3/RBesT/man/oc1Sdecision.Rd |only RBesT-1.2-3/RBesT/man/oc2Sdecision.Rd |only RBesT-1.3-1/RBesT/DESCRIPTION | 17 RBesT-1.3-1/RBesT/MD5 | 107 +- RBesT-1.3-1/RBesT/NAMESPACE | 26 RBesT-1.3-1/RBesT/R/AS.R | 2 RBesT-1.3-1/RBesT/R/EM_bmm_mun.R | 3 RBesT-1.3-1/RBesT/R/RBesT-package.R | 5 RBesT-1.3-1/RBesT/R/RcppExports.R |only RBesT-1.3-1/RBesT/R/dBetaBinomial.R | 22 RBesT-1.3-1/RBesT/R/decision1S.R |only RBesT-1.3-1/RBesT/R/decision1S_boundary.R |only RBesT-1.3-1/RBesT/R/decision2S.R |only RBesT-1.3-1/RBesT/R/decision2S_boundary.R |only RBesT-1.3-1/RBesT/R/deprecation_message.R |only RBesT-1.3-1/RBesT/R/gMAP.R | 75 + RBesT-1.3-1/RBesT/R/integrate_logit_log.R |only RBesT-1.3-1/RBesT/R/log_colSum_exp.R | 4 RBesT-1.3-1/RBesT/R/mix.R | 45 - RBesT-1.3-1/RBesT/R/mixdiff.R | 40 RBesT-1.3-1/RBesT/R/oc1S.R | 289 +----- RBesT-1.3-1/RBesT/R/oc2S.R | 494 ++--------- RBesT-1.3-1/RBesT/R/pos1S.R |only RBesT-1.3-1/RBesT/R/pos2S.R |only RBesT-1.3-1/RBesT/inst/NEWS | 19 RBesT-1.3-1/RBesT/inst/doc/RBesT.pdf |binary RBesT-1.3-1/RBesT/inst/doc/customizing_plots.R | 8 RBesT-1.3-1/RBesT/inst/doc/customizing_plots.Rmd | 8 RBesT-1.3-1/RBesT/inst/doc/customizing_plots.html | 80 - RBesT-1.3-1/RBesT/inst/doc/introduction.R | 11 RBesT-1.3-1/RBesT/inst/doc/introduction.Rmd | 19 RBesT-1.3-1/RBesT/inst/doc/introduction.html | 101 +- RBesT-1.3-1/RBesT/inst/doc/introduction_normal.R | 2 RBesT-1.3-1/RBesT/inst/doc/introduction_normal.Rmd | 4 RBesT-1.3-1/RBesT/inst/doc/introduction_normal.html | 98 +- RBesT-1.3-1/RBesT/inst/doc/robustMAP.R | 2 RBesT-1.3-1/RBesT/inst/doc/robustMAP.Rmd | 2 RBesT-1.3-1/RBesT/inst/doc/robustMAP.html | 62 - RBesT-1.3-1/RBesT/inst/extra/run-oq.R | 2 RBesT-1.3-1/RBesT/man/AS.Rd | 2 RBesT-1.3-1/RBesT/man/RBesT-package.Rd | 5 RBesT-1.3-1/RBesT/man/decision1S.Rd |only RBesT-1.3-1/RBesT/man/decision1S_boundary.Rd |only RBesT-1.3-1/RBesT/man/decision2S.Rd |only RBesT-1.3-1/RBesT/man/decision2S_boundary.Rd |only RBesT-1.3-1/RBesT/man/integrate_density_log.Rd |only RBesT-1.3-1/RBesT/man/oc1S.Rd | 178 +--- RBesT-1.3-1/RBesT/man/oc2S.Rd | 145 +-- RBesT-1.3-1/RBesT/man/pBetaBinomial.Rd |only RBesT-1.3-1/RBesT/man/pos1S.Rd |only RBesT-1.3-1/RBesT/man/pos2S.Rd |only RBesT-1.3-1/RBesT/src/RcppExports.cpp | 31 RBesT-1.3-1/RBesT/src/beta_binomial.cpp |only RBesT-1.3-1/RBesT/src/include/models.hpp | 828 +++++++++----------- RBesT-1.3-1/RBesT/tests/testthat/test-gMAP.R | 24 RBesT-1.3-1/RBesT/tests/testthat/test-oc1S.R | 31 RBesT-1.3-1/RBesT/tests/testthat/test-oc2S.R | 73 + RBesT-1.3-1/RBesT/tests/testthat/test-pos1S.R |only RBesT-1.3-1/RBesT/tests/testthat/test-pos2S.R |only RBesT-1.3-1/RBesT/tests/testthat/test-preddist.R | 32 RBesT-1.3-1/RBesT/vignettes/customizing_plots.Rmd | 8 RBesT-1.3-1/RBesT/vignettes/introduction.Rmd | 19 RBesT-1.3-1/RBesT/vignettes/introduction_normal.Rmd | 4 RBesT-1.3-1/RBesT/vignettes/robustMAP.Rmd | 2 67 files changed, 1318 insertions(+), 1611 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut],
Martin Maechler [aut],
Ben Bolker [aut, cre],
Steven Walker [aut],
Rune Haubo Bojesen Christensen [ctb],
Henrik Singmann [ctb],
Bin Dai [ctb],
Fabian Scheipl [ctb],
Gabor Grothendieck [ctb],
Peter Green [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-14 dated 2017-09-27 and 1.1-15 dated 2017-12-21
DESCRIPTION | 9 +++- MD5 | 29 ++++++++------- NAMESPACE | 2 + R/lmer.R | 12 ++++-- R/modular.R | 3 + R/profile.R | 57 +++++++++++++++---------------- R/utilities.R | 5 +- inst/NEWS.Rd | 33 ++++++++++++++--- man/confint.merMod.Rd | 9 ++++ man/convergence.Rd | 3 + man/ranef.Rd | 8 ++-- tests/confint.R | 5 -- tests/testthat/test-doubleVertNotation.R | 6 +-- tests/testthat/test-methods.R | 19 ++++++++++ tests/testthat/test-methods.Rout |only tests/testthat/test-summary.R | 19 +++++++++- 16 files changed, 145 insertions(+), 74 deletions(-)
Title: Analysis of Covariance Operators
Description: Provides a variety of tools for the analysis of covariance operators including k-sample tests for equality and classification and clustering methods found in the works of Cabassi et al (2017) <doi:10.1214/17-EJS1347>, Kashlak et al (2017) <arXiv:1604.06310>, Pigoli et al (2014) <doi:10.1093/biomet/asu008>, and Panaretos et al (2010) <doi:10.1198/jasa.2010.tm09239>.
Author: Alessandra Cabassi [aut],
Adam B Kashlak [aut, cre],
Davide Pigoli [ctb]
Maintainer: Adam B Kashlak <kashlak@ualberta.ca>
Diff between fdcov versions 1.0.0 dated 2016-06-16 and 1.1.0 dated 2017-12-21
DESCRIPTION | 24 ++++++----- MD5 | 84 ++++++++++++++++++++++++++++++++-------- NAMESPACE | 3 + R/FWEmaxT.R | 1 R/classif_com.R | 2 R/cluster_com.R | 2 R/distNorm.R | 107 ++++++++++++++++++++++++--------------------------- R/fdcov.R | 47 ++++++++++++++-------- R/ksamp_asymp.R |only R/ksamp_com.R | 2 R/ksamp_perm.R | 10 ++++ R/ksamp_perm_plot.R | 2 build |only inst |only man/classify_com.Rd | 9 +--- man/cluster.com.Rd | 7 +-- man/fdcov-package.Rd | 52 +++++++++++++++++------- man/ksample.com.Rd | 7 +-- man/ksample.gauss.Rd |only man/ksample.perm.Rd | 14 ++++-- man/ksample.vstab.Rd |only man/perm.plot.Rd | 7 +-- vignettes |only 23 files changed, 238 insertions(+), 142 deletions(-)
Title: Sensitivity Analyses for Unmeasured Confounding in Observational
Studies and Meta-Analyses
Description: Conducts sensitivity analyses for unmeasured confounding for either an observational study or a meta-analysis of observational studies. For a single observational study, the package reports E-values, defined as the minimum strength of association on the risk ratio scale that an unmeasured confounder would need to have with both the treatment and the outcome to fully explain away a specific treatment-outcome association, conditional on the measured covariates. One can use one of the evalues.XX() functions to compute E-values for the relevant outcome types. Outcome types include risk ratios, odds ratio with common or rare outcomes, hazard ratios with common or rare outcomes, and standardized differences in outcomes. Optionally, one can use the bias_plot() function to plot the bias factor as a function of two sensitivity parameters. (See VanderWeele & Ding, 2017 [<http://annals.org/aim/article/2643434>] for details.) For a meta-analysis, use the function confounded_meta to compute point estimates and inference for: (1) the proportion of studies with true causal effect sizes more extreme than a specified threshold of scientific importance; and (2) the minimum bias factor and confounding strength required to reduce to less than a specified threshold the proportion of studies with true effect sizes of scientifically significant size. The functions sens_plot() and sens_table() create plots and tables for visualizing these meta-analysis metrics across a range of bias values, and scrape_meta helps scrape study-level data from a published forest plot or summary table to obtain the needed estimates when these are not reported. (See Mathur & VanderWeele [<https://osf.io/jkhfg/>] for details.) Most of the analyses available in this package can also be conducted using web-based graphical interfaces (for a single observational study: <https://mmathur.shinyapps.io/evalue/>; for a meta-analysis: <https://mmathur.shinyapps.io/meta_gui_2/>).
Author: Maya B. Mathur, Peng Ding, Tyler J. VanderWeele
Maintainer: Maya B. Mathur <mmathur@stanford.edu>
Diff between EValue versions 1.1.0 dated 2017-11-29 and 1.1.1 dated 2017-12-21
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
using Stan for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include non-linear and
smooth terms, auto-correlation structures, censored data, meta-analytic
standard errors, and quite a few more. In addition, all parameters of the
response distribution can be predicted in order to perform distributional
regression. Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs.
Model fit can easily be assessed and compared with posterior predictive
checks and leave-one-out cross-validation.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>
Diff between brms versions 2.0.0 dated 2017-12-15 and 2.0.1 dated 2017-12-21
DESCRIPTION | 12 +-- MD5 | 90 +++++++++++++-------------- NAMESPACE | 7 ++ R/brmsfit-helpers.R | 91 +++++++++------------------ R/brmsfit-methods.R | 39 ++++++----- R/brmsformula.R | 25 +++---- R/data-helpers.R | 109 ++++++++++++++++++--------------- R/extract_draws.R | 6 + R/families.R | 6 - R/fitted.R | 2 R/generics.R | 38 +++++++++-- R/linear_predictor.R | 3 R/loglik.R | 15 ++-- R/make_stancode.R | 3 R/marginal_effects-helpers.R | 2 R/marginal_smooths-helpers.R | 2 R/misc-methods.R | 31 +++++++++ R/predict.R | 4 - R/re-syntax-helpers.R | 32 +++------ R/rename.R | 7 -- R/stan-predictor.R | 12 +-- R/sysdata.rda |binary R/validate.R | 44 +++++++++---- build/vignette.rds |binary inst/NEWS.Rd | 24 +++++++ inst/doc/brms_blogposts.Rmd | 1 inst/doc/brms_blogposts.html | 5 - inst/doc/brms_distreg.html | 28 ++++---- inst/doc/brms_families.html | 4 - inst/doc/brms_monotonic.html | 32 ++++----- inst/doc/brms_multilevel.pdf |binary inst/doc/brms_multivariate.html | 108 ++++++++++++++++---------------- inst/doc/brms_nonlinear.html | 4 - inst/doc/brms_overview.pdf |binary inst/doc/brms_phylogenetics.html | 64 +++++++++---------- man/LOO.Rd | 8 +- man/WAIC.Rd | 2 man/bayes_factor.brmsfit.Rd | 15 ---- man/kfold.Rd | 4 - man/mixture.Rd | 6 - man/mvbrmsformula.Rd | 9 ++ man/posterior_summary.Rd |only man/posterior_table.Rd |only tests/testthat/tests.brmsfit-helpers.R | 5 - tests/testthat/tests.make_stancode.R | 4 - tests/testthat/tests.validate.R | 12 +-- vignettes/brms_blogposts.Rmd | 1 47 files changed, 504 insertions(+), 412 deletions(-)
Title: Routines for Block Diagonal Symmetric Matrices
Description: This is a special case of sparse matrices, used by coxme.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau@mayo.edu>
Diff between bdsmatrix versions 1.3-2 dated 2014-08-22 and 1.3-3 dated 2017-12-21
DESCRIPTION | 13 +++----- MD5 | 50 +++++++++++++++---------------- NAMESPACE | 3 + R/as.matrix.bdsmatrix.R | 2 - R/backsolve.R | 6 +-- R/bdsmatrix.R | 10 +++--- R/bdsmatrix.reconcile.R | 8 ++-- R/diag.bdsmatrix.R | 4 +- R/gchol.R | 2 - R/gchol.bdsmatrix.R | 16 ++++----- R/listbdsmatrix.R | 2 - R/multiply.bdsmatrix.R | 2 - R/solve.bdsmatrix.R | 6 +-- R/solve.gchol.R | 6 +-- R/solve.gchol.bdsmatrix.R | 17 ++++------ inst/NEWS.Rd | 7 ++++ src/R_init_bdsmatrix.c | 74 ++++++++++++++++++++++++++++++++++++---------- src/bdsmatrix.h | 47 +++++++++++++++++++++++------ src/bdsmatrix_prod2.c | 1 src/bdsmatrix_prod4.c | 1 src/chinv4.c | 1 src/chinv5.c | 1 src/cholesky4.c | 1 src/cholesky5.c | 1 src/chsolve4.c | 1 src/chsolve5.c | 1 26 files changed, 182 insertions(+), 101 deletions(-)
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre] (0000-0003-4198-9911),
David Meyer [aut],
Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between slam versions 0.1-40 dated 2016-12-01 and 0.1-42 dated 2017-12-21
DESCRIPTION | 13 +++++++------ MD5 | 41 ++++++++++++++++++++++------------------- NAMESPACE | 19 +------------------ R/abind.R | 4 ++-- R/foreign.R | 4 ++-- R/matrix.R | 4 ++-- R/reduce.R | 2 +- R/rollup.R | 2 +- R/subassign.R | 6 ++++++ inst |only man/matrix.Rd | 8 +++++++- po |only src/dll.c |only src/sparse.c | 20 ++++++++++---------- src/util.c | 3 ++- tests/extract.R | 4 ++-- tests/extract.Rout.save | 4 ++-- tests/ssa_valid.R | 2 +- tests/ssa_valid.Rout.save | 2 +- tests/subassign.R | 12 +++++++++--- tests/subassign.Rout.save | 20 ++++++++++++++------ tests/util.R | 42 +++++++++++++++++++++--------------------- tests/util.Rout.save | 42 +++++++++++++++++++++--------------------- 23 files changed, 134 insertions(+), 120 deletions(-)
Title: Collection of Information-Based Feature Selection Filters
Description: A collection of feature selection filters performing greedy optimisation of mutual information-based usefulness criteria, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <http://www.jmlr.org/papers/v13/brown12a.html>.
Implements, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <http://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa
Maintainer: Miron B. Kursa <M.Kursa@icm.edu.pl>
Diff between praznik versions 1.0.0 dated 2017-11-20 and 2.0.0 dated 2017-12-21
DESCRIPTION | 6 ++-- MD5 | 29 ++++++++++---------- NAMESPACE | 1 R/algorithms.R | 13 +++++++++ inst/NEWS | 5 +++ man/setOmpThreads.Rd |only src/Makevars | 4 +- src/cmim.h | 50 ++++++++++++++++++++++-------------- src/mi.h | 23 ++++++++++------ src/mim.h | 34 +++++++++++++++--------- src/mrmr.h | 38 ++++++++++++++++++--------- src/praznik.c | 2 + src/shared.h | 48 +++++++++++++++++++++++----------- src/side.h | 4 ++ src/xj.h | 61 +++++++++++++++++++++++++++----------------- tests/testthat/test-input.R | 7 +++++ 16 files changed, 215 insertions(+), 110 deletions(-)
Title: Response Transformations for Random Effect and Variance
Component Models
Description: Response transformations for overdispersed generalized linear
models and variance component models using nonparametric profile maximum
likelihood estimation. The main function is optim.boxcox().
Author: Amani Almohaimeed and Jochen Einbeck
Maintainer: Amani Almohaimeed <amani.almohaimeed@gmail.com>
Diff between boxcoxmix versions 0.14 dated 2017-10-09 and 0.15 dated 2017-12-21
boxcoxmix-0.14/boxcoxmix/vignettes/boxcoxmix-knitr.Rnw |only boxcoxmix-0.15/boxcoxmix/DESCRIPTION | 11 ++++++----- boxcoxmix-0.15/boxcoxmix/MD5 | 7 +++---- boxcoxmix-0.15/boxcoxmix/R/boxcoxmix-package.R | 2 +- boxcoxmix-0.15/boxcoxmix/man/boxcoxmix-package.Rd | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: 64-Bit Extension of the SPArse Matrix R Package 'spam'
Description: Provides the Fortran code of the R package 'spam'
with 64-bit integers. Loading this package together with the R package
'spam' enables the sparse matrix class "spam" to handle huge sparse matrices
with more than 2^31-1 non-zero elements.
Author: Reinhard Furrer [aut, cre],
Florian Gerber [ctb],
Daniel Gerber [ctb],
Kaspar Moesinger [ctb],
Youcef Saad [ctb] (SPARSEKIT
http://www-users.cs.umn.edu/~saad/software/SPARSKIT/),
Esmond G. Ng [ctb] (Fortran Cholesky routines),
Barry W. Peyton [ctb] (Fortran Cholesky routines),
Joseph W.H. Liu [ctb] (Fortran Cholesky routines),
Alan D. George [ctb] (Fortran Cholesky routines)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam64 versions 2.1-1 dated 2017-07-02 and 2.1-2 dated 2017-12-21
spam64-2.1-1/spam64/src/rep_len_long.c |only spam64-2.1-2/spam64/DESCRIPTION | 29 +++++--- spam64-2.1-2/spam64/MD5 | 12 +-- spam64-2.1-2/spam64/inst/CITATION | 52 ++++++++------- spam64-2.1-2/spam64/man/spam64-package.Rd | 103 ++++++++++++------------------ spam64-2.1-2/spam64/src/dist.f | 25 ++++--- spam64-2.1-2/spam64/src/init.c | 14 +++- spam64-2.1-2/spam64/src/rep_len64.c |only 8 files changed, 123 insertions(+), 112 deletions(-)
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <http://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and a vignette with recommendations for
developers.
Author: Jonah Gabry [aut, cre],
Ben Goodrich [aut],
Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between rstantools versions 1.3.0 dated 2017-08-02 and 1.4.0 dated 2017-12-21
DESCRIPTION | 12 +-- MD5 | 20 ++--- NEWS.md | 5 + R/rstan_package_skeleton.R | 91 +++++++++++++++------------ build/vignette.rds |binary inst/doc/developer-guidelines.R | 2 inst/doc/developer-guidelines.Rmd | 35 +++++----- inst/doc/developer-guidelines.html | 19 +++-- man/rstan_package_skeleton.Rd | 3 tests/testthat/test-rstan_package_skeleton.R | 5 - vignettes/developer-guidelines.Rmd | 35 +++++----- 11 files changed, 130 insertions(+), 97 deletions(-)
Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan'
package, which provides the R interface to the Stan C++ library for Bayesian
estimation. Users specify models via the customary R syntax with a formula and
data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut],
Imad Ali [ctb],
Sam Brilleman [ctb],
Trustees of Columbia University [cph],
Simon Wood [cph] (R/stan_gamm4.R),
R Core Deveopment Team [cph] (R/stan_aov.R),
Douglas Bates [cph] (R/pp_data.R),
Martin Maechler [cph] (R/pp_data.R),
Ben Bolker [cph] (R/pp_data.R),
Steve Walker [cph] (R/pp_data.R),
Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R),
William Venables [cph] (R/stan_polr.R),
Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstanarm versions 2.15.3 dated 2017-04-29 and 2.17.2 dated 2017-12-21
rstanarm-2.15.3/rstanarm/R/gamm4_to_glmer.R |only rstanarm-2.15.3/rstanarm/exec |only rstanarm-2.15.3/rstanarm/inst/chunks |only rstanarm-2.15.3/rstanarm/man/shinystan.Rd |only rstanarm-2.15.3/rstanarm/src/Modules.cpp |only rstanarm-2.15.3/rstanarm/src/include |only rstanarm-2.15.3/rstanarm/tools/make_cpp.R |only rstanarm-2.17.2/rstanarm/DESCRIPTION | 37 rstanarm-2.17.2/rstanarm/MD5 | 446 ++-- rstanarm-2.17.2/rstanarm/NAMESPACE | 57 rstanarm-2.17.2/rstanarm/R/adapt_delta.R | 2 rstanarm-2.17.2/rstanarm/R/bayes_R2.R |only rstanarm-2.17.2/rstanarm/R/data_block.R | 10 rstanarm-2.17.2/rstanarm/R/datasets.R | 33 rstanarm-2.17.2/rstanarm/R/example_jm.R |only rstanarm-2.17.2/rstanarm/R/example_model.R | 1 rstanarm-2.17.2/rstanarm/R/jm_data_block.R |only rstanarm-2.17.2/rstanarm/R/jm_make_assoc_parts.R |only rstanarm-2.17.2/rstanarm/R/jm_make_assoc_terms.R |only rstanarm-2.17.2/rstanarm/R/log_lik.R | 606 +++++- rstanarm-2.17.2/rstanarm/R/loo-prediction.R | 1 rstanarm-2.17.2/rstanarm/R/loo.R | 65 rstanarm-2.17.2/rstanarm/R/misc.R | 987 +++++++++- rstanarm-2.17.2/rstanarm/R/plots.R | 53 rstanarm-2.17.2/rstanarm/R/posterior_linpred.R | 25 rstanarm-2.17.2/rstanarm/R/posterior_predict.R | 163 + rstanarm-2.17.2/rstanarm/R/posterior_survfit.R |only rstanarm-2.17.2/rstanarm/R/posterior_traj.R |only rstanarm-2.17.2/rstanarm/R/pp_check.R | 49 rstanarm-2.17.2/rstanarm/R/pp_data.R | 317 ++- rstanarm-2.17.2/rstanarm/R/pp_validate.R | 2 rstanarm-2.17.2/rstanarm/R/predictive_error.R | 141 + rstanarm-2.17.2/rstanarm/R/print-and-summary.R | 400 +++- rstanarm-2.17.2/rstanarm/R/prior_summary.R | 164 + rstanarm-2.17.2/rstanarm/R/priors.R | 109 - 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Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Benjamin Risk, Ricardo Pita,
Antonio Mira, Pedro Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.5.6 dated 2017-07-08 and 1.0 dated 2017-12-21
MetaLandSim-0.5.6/MetaLandSim/inst/doc/MetaLandSim.pdf |only MetaLandSim-0.5.6/MetaLandSim/inst/doc/landscape_simulation.R |only MetaLandSim-0.5.6/MetaLandSim/inst/doc/landscape_simulation.Rnw |only MetaLandSim-0.5.6/MetaLandSim/inst/doc/landscape_simulation.pdf |only MetaLandSim-0.5.6/MetaLandSim/inst/doc/parametrization.R |only MetaLandSim-0.5.6/MetaLandSim/inst/doc/parametrization.Rnw |only MetaLandSim-0.5.6/MetaLandSim/inst/doc/parametrization.pdf |only MetaLandSim-0.5.6/MetaLandSim/inst/doc/range_expansion.R |only MetaLandSim-0.5.6/MetaLandSim/inst/doc/range_expansion.Rnw |only MetaLandSim-0.5.6/MetaLandSim/inst/doc/range_expansion.pdf |only MetaLandSim-0.5.6/MetaLandSim/vignettes/landscape_simulation.Rnw |only MetaLandSim-0.5.6/MetaLandSim/vignettes/parametrization.Rnw |only MetaLandSim-0.5.6/MetaLandSim/vignettes/range_expansion.Rnw |only MetaLandSim-1.0/MetaLandSim/DESCRIPTION | 15 +- MetaLandSim-1.0/MetaLandSim/MD5 | 61 ++++++---- MetaLandSim-1.0/MetaLandSim/NAMESPACE | 14 +- MetaLandSim-1.0/MetaLandSim/R/MetaLandSim.GUI.R | 4 MetaLandSim-1.0/MetaLandSim/R/accept.calculate.r |only MetaLandSim-1.0/MetaLandSim/R/acceptance.rate.r |only MetaLandSim-1.0/MetaLandSim/R/calcmode.r |only MetaLandSim-1.0/MetaLandSim/R/coda.create.r |only MetaLandSim-1.0/MetaLandSim/R/combine.chains.r |only MetaLandSim-1.0/MetaLandSim/R/decide.r |only MetaLandSim-1.0/MetaLandSim/R/ifm.missing.MCMC.R |only MetaLandSim-1.0/MetaLandSim/R/ifm.naive.MCMC.R |only MetaLandSim-1.0/MetaLandSim/R/ifm.robust.MCMC.R |only MetaLandSim-1.0/MetaLandSim/R/log.lik.data.z.r |only MetaLandSim-1.0/MetaLandSim/R/na.cnt.r |only MetaLandSim-1.0/MetaLandSim/R/prop.state.z.r |only MetaLandSim-1.0/MetaLandSim/R/prop.year.missing.r |only MetaLandSim-1.0/MetaLandSim/build/vignette.rds |binary MetaLandSim-1.0/MetaLandSim/data/simulatedifm.rda |only MetaLandSim-1.0/MetaLandSim/inst/doc/landscape_simulation-knitr.R |only MetaLandSim-1.0/MetaLandSim/inst/doc/landscape_simulation-knitr.Rnw |only MetaLandSim-1.0/MetaLandSim/inst/doc/landscape_simulation-knitr.pdf |only MetaLandSim-1.0/MetaLandSim/inst/doc/parameter_estimation-knitr.R |only MetaLandSim-1.0/MetaLandSim/inst/doc/parameter_estimation-knitr.Rnw |only MetaLandSim-1.0/MetaLandSim/inst/doc/parameter_estimation-knitr.pdf |only MetaLandSim-1.0/MetaLandSim/inst/doc/range_expansion-knitr.R |only MetaLandSim-1.0/MetaLandSim/inst/doc/range_expansion-knitr.Rnw |only MetaLandSim-1.0/MetaLandSim/inst/doc/range_expansion-knitr.pdf |only MetaLandSim-1.0/MetaLandSim/man/MetaLandSim-package.Rd | 15 +- MetaLandSim-1.0/MetaLandSim/man/accept.calculate.Rd |only MetaLandSim-1.0/MetaLandSim/man/calcmode.Rd |only MetaLandSim-1.0/MetaLandSim/man/coda.create.Rd |only MetaLandSim-1.0/MetaLandSim/man/combine.chains.Rd |only MetaLandSim-1.0/MetaLandSim/man/ifm.missing.MCMC.Rd |only MetaLandSim-1.0/MetaLandSim/man/ifm.naive.MCMC.Rd |only MetaLandSim-1.0/MetaLandSim/man/ifm.robust.MCMC.Rd |only MetaLandSim-1.0/MetaLandSim/man/simulatedifm.Rd |only MetaLandSim-1.0/MetaLandSim/vignettes/landscape_simulation-knitr.Rnw |only MetaLandSim-1.0/MetaLandSim/vignettes/parameter_estimation-knitr.Rnw |only MetaLandSim-1.0/MetaLandSim/vignettes/range_expansion-knitr.Rnw |only MetaLandSim-1.0/MetaLandSim/vignettes/rg1.png |binary MetaLandSim-1.0/MetaLandSim/vignettes/rg2.png |binary 55 files changed, 73 insertions(+), 36 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <http://canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut, cre],
Connie Brett [ctb]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.17.9 dated 2017-11-28 and 1.18.1 dated 2017-12-21
DESCRIPTION | 6 MD5 | 40 - NEWS.md | 4 R/canvasXpress.R | 13 build/vignette.rds |binary inst/doc/additional_examples.html | 518 +++++------------- inst/doc/getting_started.html | 503 +++++------------ inst/extdata/cX-networkbasic-edges.txt | 12 inst/extdata/cX-networkbasic-nodes.txt | 12 inst/extdata/cX-wpapoptosis-edges.txt |only inst/extdata/cX-wpapoptosis-nodes.txt |only inst/htmlwidgets/canvasXpress.js | 71 +- inst/htmlwidgets/canvasXpress.yaml | 2 inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 4 man/canvasXpress.Rd | 5 man/renderCanvasXpress.Rd | 9 tests/cX-function.R | 39 + tests/testthat/test--BASE.R | 9 tests/testthat/test-candlestick.R | 4 tests/testthat/test-heatmap.R | 1 tests/testthat/test-layout.R | 2 tests/testthat/test-network.R | 17 22 files changed, 476 insertions(+), 795 deletions(-)
Title: Taxonomic Information from 'Wikipedia'
Description: 'Taxonomic' information from 'Wikipedia', 'Wikicommons',
'Wikispecies', and 'Wikidata'. Functions included for getting
taxonomic information from each of the sources just listed, as
well performing taxonomic search.
Author: Scott Chamberlain [aut, cre],
Ethan Welty [aut]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Diff between wikitaxa versions 0.1.4 dated 2017-05-05 and 0.2.0 dated 2017-12-21
DESCRIPTION | 6 MD5 | 30 - NEWS.md | 14 R/wiki.R | 22 R/wikicommons.R | 41 + R/wikispecies.R | 3 R/zzz.R | 4 README.md | 129 ++--- build/vignette.rds |binary inst/doc/wikitaxa_vignette.html | 853 +++++++++++++++++++++++--------------- man/wt_data.Rd | 2 man/wt_wikicommons.Rd | 6 man/wt_wikispecies.Rd | 3 tests/testthat/test-wikicommons.R | 8 tests/testthat/test-wikipedia.R | 3 tests/testthat/test-wikispecies.R | 2 16 files changed, 686 insertions(+), 440 deletions(-)
Title: A Package to Generate Ternary Plots
Description: Plots ternary diagrams using the standard graphics functions.
An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.
Author: Martin R. Smith [aut, cre, cph] (0000-0001-5660-1727)
Maintainer: Martin R. Smith <martins@gmail.com>
Diff between Ternary versions 0.1.1 dated 2017-11-23 and 1.0.0 dated 2017-12-21
DESCRIPTION | 10 - MD5 | 39 ++--- NAMESPACE | 3 NEWS.md | 8 + R/ReleaseQuestions.R | 3 R/TernaryPlot.R | 297 +++++++++++++++++++++++++++++++----------- R/data.R | 9 - README.md | 4 build/partial.rdb |only build/vignette.rds |binary inst/doc/Using-Ternary.R | 25 ++- inst/doc/Using-Ternary.Rmd | 41 ++++- inst/doc/Using-Ternary.html | 39 ++++- man/AddToTernary.Rd | 7 man/TernaryCoords.Rd | 30 ++-- man/TernaryPlot.Rd | 83 ++++++++--- man/TernaryXRange.Rd |only man/cbPalette15.Rd | 9 - man/cbPalette8.Rd | 6 tests/Test-plots.Rmd |only tests/testthat/test-ternary.R | 11 - vignettes/Using-Ternary.Rmd | 41 ++++- 22 files changed, 497 insertions(+), 168 deletions(-)
Title: Plotting Methods for 'simmer'
Description: A set of plotting methods for 'simmer' trajectories and simulations.
Author: Iñaki Ucar [aut, cph, cre] (0000-0001-6403-5550),
Bart Smeets [aut, cph]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer.plot versions 0.1.11 dated 2017-10-24 and 0.1.12 dated 2017-12-21
simmer.plot-0.1.11/simmer.plot/R/plot_arrivals.R |only simmer.plot-0.1.11/simmer.plot/R/plot_attributes.R |only simmer.plot-0.1.11/simmer.plot/R/plot_resources.R |only simmer.plot-0.1.12/simmer.plot/DESCRIPTION | 13 +- simmer.plot-0.1.12/simmer.plot/MD5 | 47 +++++---- simmer.plot-0.1.12/simmer.plot/NAMESPACE | 6 + simmer.plot-0.1.12/simmer.plot/NEWS.md | 10 + simmer.plot-0.1.12/simmer.plot/R/plot.arrivals.R |only simmer.plot-0.1.12/simmer.plot/R/plot.attributes.R |only simmer.plot-0.1.12/simmer.plot/R/plot.resources.R |only simmer.plot-0.1.12/simmer.plot/R/plot.simmer.R | 52 ---------- simmer.plot-0.1.12/simmer.plot/R/plot.trajectory.R | 3 simmer.plot-0.1.12/simmer.plot/R/simmer.plot.R |only simmer.plot-0.1.12/simmer.plot/R/utils.R | 3 simmer.plot-0.1.12/simmer.plot/build/vignette.rds |binary simmer.plot-0.1.12/simmer.plot/inst/doc/plot.simmer.R | 10 + simmer.plot-0.1.12/simmer.plot/inst/doc/plot.simmer.Rmd | 14 +- simmer.plot-0.1.12/simmer.plot/inst/doc/plot.simmer.html | 26 ++--- simmer.plot-0.1.12/simmer.plot/inst/doc/plot.trajectory.html | 4 simmer.plot-0.1.12/simmer.plot/man/get_mon.Rd |only simmer.plot-0.1.12/simmer.plot/man/plot.mon.Rd |only simmer.plot-0.1.12/simmer.plot/man/plot.simmer.Rd | 47 --------- simmer.plot-0.1.12/simmer.plot/man/plot.trajectory.Rd | 2 simmer.plot-0.1.12/simmer.plot/man/simmer.plot.Rd |only simmer.plot-0.1.12/simmer.plot/tests/testthat/test-plot-arrivals.R | 25 +++- simmer.plot-0.1.12/simmer.plot/tests/testthat/test-plot-attributes.R | 25 +++- simmer.plot-0.1.12/simmer.plot/tests/testthat/test-plot-resources.R | 37 ++++--- simmer.plot-0.1.12/simmer.plot/tests/testthat/test-plot-simmer.R | 18 --- simmer.plot-0.1.12/simmer.plot/tests/testthat/test-plot-utils.R |only simmer.plot-0.1.12/simmer.plot/vignettes/plot.simmer.Rmd | 14 +- 30 files changed, 157 insertions(+), 199 deletions(-)
Title: Propagation of Uncertainty
Description: Propagation of uncertainty using higher-order Taylor expansion and Monte Carlo simulation.
Author: Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
Maintainer: Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
Diff between propagate versions 1.0-4 dated 2014-09-27 and 1.0-5 dated 2017-12-21
propagate-1.0-4/propagate/R/contribution.R |only propagate-1.0-4/propagate/man/contribution.Rd |only propagate-1.0-4/propagate/src/colVarsC.cpp |only propagate-1.0-4/propagate/src/rowVarsC.cpp |only propagate-1.0-5/propagate/DESCRIPTION | 8 propagate-1.0-5/propagate/MD5 | 68 ++-- propagate-1.0-5/propagate/NAMESPACE | 17 - propagate-1.0-5/propagate/NEWS | 13 propagate-1.0-5/propagate/R/WelchSatter.R | 20 - propagate-1.0-5/propagate/R/bigcor.R | 56 ++- propagate-1.0-5/propagate/R/cor2cov.R | 8 propagate-1.0-5/propagate/R/distr-densities.R | 56 +++ propagate-1.0-5/propagate/R/distr-samplers.R | 83 ++++- propagate-1.0-5/propagate/R/fitDistr.R | 86 +++-- propagate-1.0-5/propagate/R/makeDat.R | 4 propagate-1.0-5/propagate/R/matrixStats.R | 8 propagate-1.0-5/propagate/R/mixCov.R | 79 +---- propagate-1.0-5/propagate/R/predictNLS.R | 39 +- propagate-1.0-5/propagate/R/print.propagate.R | 6 propagate-1.0-5/propagate/R/propagate.R | 273 +++++++++--------- propagate-1.0-5/propagate/R/stochContr.R |only propagate-1.0-5/propagate/R/summary.propagate.R | 84 +++-- propagate-1.0-5/propagate/R/utils.R | 4 propagate-1.0-5/propagate/man/WelchSatter.Rd | 18 - propagate-1.0-5/propagate/man/bigcor.Rd | 21 + propagate-1.0-5/propagate/man/cor2cov.Rd | 2 propagate-1.0-5/propagate/man/fitDistr.Rd | 40 +- propagate-1.0-5/propagate/man/interval.Rd | 21 + propagate-1.0-5/propagate/man/mixCov.Rd | 35 -- propagate-1.0-5/propagate/man/moments.Rd | 2 propagate-1.0-5/propagate/man/numDerivs.Rd | 2 propagate-1.0-5/propagate/man/predictNLS.Rd | 50 +-- propagate-1.0-5/propagate/man/propagate.Rd | 203 +++++-------- propagate-1.0-5/propagate/man/rDistr.Rd | 13 propagate-1.0-5/propagate/man/stochContr.Rd |only propagate-1.0-5/propagate/man/summary.propagate.Rd | 17 - propagate-1.0-5/propagate/src/CcolVarsC.cpp |only propagate-1.0-5/propagate/src/CrowVarsC.cpp |only propagate-1.0-5/propagate/src/Makevars.win |only propagate-1.0-5/propagate/src/registerDynamicSymbol.c |only 40 files changed, 758 insertions(+), 578 deletions(-)
Title: Partially Balanced Incomplete Block Designs
Description: The PBIB designs are important type of incomplete block designs having wide area of their applications for example in agricultural experiments, in plant breeding, in sample surveys etc. This package constructs various series of PBIB designs and assists in checking all the necessary conditions of PBIB designs and the association scheme on which these designs are based on. It also assists in calculating the efficiencies of PBIB designs with any number of associate classes. The package also constructs Youden-m square designs which are Row-Column designs for the two-way elimination of heterogeneity. The incomplete columns of these Youden-m square designs constitute PBIB designs. With the present functionality, the package will be of immense importance for the researchers as it will help them to construct PBIB designs, to check if their PBIB designs and association scheme satisfy various necessary conditions for the existence, to calculate the efficiencies of PBIB designs based on any association scheme and to construct Youden-m square designs for the two-way elimination of heterogeneity. R. C. Bose and K. R. Nair (1939) <http://www.jstor.org/stable/40383923>.
Author: Parneet Kaur <parneet.nonu93@gmail.com>, Kush Sharma <kush.vashishtha@gmail.com>, Davinder Kumar Garg <dkgarg_stat@yahoo.co.in>
Maintainer: Kush Sharma <kush.vashishtha@gmail.com>
Diff between PBIBD versions 1.2 dated 2017-01-20 and 1.3 dated 2017-12-21
PBIBD-1.2/PBIBD/R/apbibd2.R |only PBIBD-1.2/PBIBD/R/apbibd3.R |only PBIBD-1.2/PBIBD/R/apbibd4.R |only PBIBD-1.2/PBIBD/R/apbibd5.R |only PBIBD-1.2/PBIBD/man/apbibd2.Rd |only PBIBD-1.2/PBIBD/man/apbibd3.Rd |only PBIBD-1.2/PBIBD/man/apbibd4.Rd |only PBIBD-1.2/PBIBD/man/apbibd5.Rd |only PBIBD-1.3/PBIBD/DESCRIPTION | 10 ++++---- PBIBD-1.3/PBIBD/MD5 | 43 ++++++++++++++++++++--------------- PBIBD-1.3/PBIBD/NAMESPACE | 12 ++++++--- PBIBD-1.3/PBIBD/R/PBIBD-internal.R |only PBIBD-1.3/PBIBD/R/circulant.R |only PBIBD-1.3/PBIBD/R/series3.R | 2 + PBIBD-1.3/PBIBD/R/series5.R |only PBIBD-1.3/PBIBD/R/series6.R |only PBIBD-1.3/PBIBD/R/verify.R |only PBIBD-1.3/PBIBD/R/ym1.R |only PBIBD-1.3/PBIBD/R/ym2.R |only PBIBD-1.3/PBIBD/R/ym3.R |only PBIBD-1.3/PBIBD/build/partial.rdb |binary PBIBD-1.3/PBIBD/man/PBIBD-package.Rd | 27 ++++++++++----------- PBIBD-1.3/PBIBD/man/apbibd.Rd | 13 ++++------ PBIBD-1.3/PBIBD/man/circulant.Rd |only PBIBD-1.3/PBIBD/man/series1.Rd | 15 ++++++------ PBIBD-1.3/PBIBD/man/series2.Rd | 15 ++++++------ PBIBD-1.3/PBIBD/man/series3.Rd | 11 ++++---- PBIBD-1.3/PBIBD/man/series4.Rd | 17 ++++++++----- PBIBD-1.3/PBIBD/man/series5.Rd |only PBIBD-1.3/PBIBD/man/series6.Rd |only PBIBD-1.3/PBIBD/man/verify.Rd |only PBIBD-1.3/PBIBD/man/ym1.Rd |only PBIBD-1.3/PBIBD/man/ym2.Rd |only PBIBD-1.3/PBIBD/man/ym3.Rd |only 34 files changed, 91 insertions(+), 74 deletions(-)
Title: Paired Data Analysis
Description: Many datasets and a set of graphics (based on ggplot2), statistics, effect sizes and hypothesis tests are provided for analysing paired data with S4 class.
Author: Stephane Champely <champely@univ-lyon1.fr>
Maintainer: Stephane Champely <champely@univ-lyon1.fr>
Diff between PairedData versions 1.0.1 dated 2013-04-19 and 1.1.0 dated 2017-12-21
PairedData-1.0.1/PairedData/man/bonettseier.var.test.Rd |only PairedData-1.0.1/PairedData/man/grambsch.var.test.Rd |only PairedData-1.0.1/PairedData/man/imam.var.test.Rd |only PairedData-1.0.1/PairedData/man/levene.var.test.Rd |only PairedData-1.0.1/PairedData/man/mcculloch.var.test.Rd |only PairedData-1.0.1/PairedData/man/sandvikolsson.var.test.Rd |only PairedData-1.0.1/PairedData/man/var.test.Rd |only PairedData-1.1.0/PairedData/DESCRIPTION | 15 -- PairedData-1.1.0/PairedData/MD5 | 36 ++--- PairedData-1.1.0/PairedData/NAMESPACE | 27 ++++ PairedData-1.1.0/PairedData/R/ClassP1.R | 4 PairedData-1.1.0/PairedData/R/global1.R | 91 +++++++------- PairedData-1.1.0/PairedData/man/BloodLead.Rd | 7 - PairedData-1.1.0/PairedData/man/Corn.Rd | 6 PairedData-1.1.0/PairedData/man/HorseBeginners.Rd | 8 - PairedData-1.1.0/PairedData/man/PairedData-package.Rd | 4 PairedData-1.1.0/PairedData/man/SkiExperts.Rd | 2 PairedData-1.1.0/PairedData/man/Tobacco.Rd | 4 PairedData-1.1.0/PairedData/man/Var.test.Rd |only PairedData-1.1.0/PairedData/man/bonettseier.Var.test.Rd |only PairedData-1.1.0/PairedData/man/grambsch.Var.test.Rd |only PairedData-1.1.0/PairedData/man/imam.Var.test.Rd |only PairedData-1.1.0/PairedData/man/levene.Var.test.Rd |only PairedData-1.1.0/PairedData/man/mcculloch.Var.test.Rd |only PairedData-1.1.0/PairedData/man/plot.Rd | 4 PairedData-1.1.0/PairedData/man/sandvikolsson.Var.test.Rd |only 26 files changed, 117 insertions(+), 91 deletions(-)
Title: A Fractal Time Series Modeling and Analysis Package
Description: Stochastic fractal and deterministic chaotic time series
analysis.
Author: William Constantine [cre, aut],
Donald Percival [aut]
Maintainer: William Constantine <wlbconstan@gmail.com>
Diff between fractal versions 2.0-1 dated 2016-05-20 and 2.0-4 dated 2017-12-21
DESCRIPTION | 8 MD5 | 14 - R/fra_hurst.R | 6 R/fra_stny.R | 4 man/determinism.Rd | 404 ++++++++++++++++++++++++------------------------- man/hurstBlock.Rd | 12 - man/infoDim.Rd | 360 +++++++++++++++++++++---------------------- man/localProjection.Rd | 208 ++++++++++++------------- 8 files changed, 513 insertions(+), 503 deletions(-)
Title: Plant Root System Architecture Analysis Using DART and RSML
Files
Description: Analysis of complex plant root system architectures (RSA) using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) "DART: a software to analyse root system architecture and development from captured images", Plant and Soil, <DOI:10.1007/s11104-009-0005-2>), and RSA data encoded with the Root System Markup Language (RSML) (Lobet et al (2015) "Root System Markup Language: toward a unified root architecture description language", Plant Physiology, <DOI:10.1104/pp.114.253625>). More information can be found in Delory et al (2016) "archiDART: an R package for the automated computation of plant root architectural traits", Plant and Soil, <DOI:10.1007/s11104-015-2673-4>.
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Guillaume Lobet, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory <Benjamin.Delory@leuphana.de>
Diff between archiDART versions 2.0 dated 2017-05-11 and 3.0 dated 2017-12-21
archiDART-2.0/archiDART/inst/doc/archiDART.pdf |only archiDART-2.0/archiDART/inst/doc/rsml.pdf |only archiDART-3.0/archiDART/DESCRIPTION | 12 archiDART-3.0/archiDART/MD5 | 39 archiDART-3.0/archiDART/NAMESPACE | 13 archiDART-3.0/archiDART/R/archidraw.R | 250 ++++- archiDART-3.0/archiDART/R/archigrow.R | 362 ++++++- archiDART-3.0/archiDART/R/architect.R | 570 +++++++++++- archiDART-3.0/archiDART/R/bottleneckdist.R |only archiDART-3.0/archiDART/R/dartToTable.R |only archiDART-3.0/archiDART/R/fitter.R |only archiDART-3.0/archiDART/R/latdist.R | 86 + archiDART-3.0/archiDART/R/perhomology.R |only archiDART-3.0/archiDART/R/plot.barcode.R |only archiDART-3.0/archiDART/R/rsmlToDART.R | 658 ++++++++------ archiDART-3.0/archiDART/R/rsmlToTable.R |only archiDART-3.0/archiDART/R/trajectory.R | 319 ++++++ archiDART-3.0/archiDART/inst/doc/RSML_PlantPhysiology.pdf |only archiDART-3.0/archiDART/inst/doc/archiDART_PlantSoil.pdf |only archiDART-3.0/archiDART/man/archidraw.Rd | 9 archiDART-3.0/archiDART/man/archigrow.Rd | 5 archiDART-3.0/archiDART/man/architect.Rd | 101 +- archiDART-3.0/archiDART/man/bottleneckdist.Rd |only archiDART-3.0/archiDART/man/dartToTable.Rd |only archiDART-3.0/archiDART/man/perhomology.Rd |only archiDART-3.0/archiDART/man/plot.barcode.Rd |only archiDART-3.0/archiDART/man/rsmlToTable.Rd |only archiDART-3.0/archiDART/man/trajectory.Rd | 54 - 28 files changed, 2053 insertions(+), 425 deletions(-)
Title: Topic Modelling
Description: Helps in initial processing like converting text to lower case, removing punctuation, numbers, stop words, stemming, sparsity control and term frequency inverse document frequency processing. Helps in recognizing domain or corpus specific stop words. Makes use of 'ldatunig' output to pick optimal number of topics for topic modelling. Helps in topic modelling the content.
Author: Krishna Harsha
Maintainer: Krishna Harsha <khkrishnaharsha123@gmail.com>
Diff between BullsEyeR versions 0.1.0 dated 2017-12-11 and 0.2.0 dated 2017-12-21
DESCRIPTION | 8 +-- MD5 | 8 +-- R/BullsEyeR.R | 123 +++---------------------------------------------------- man/BullsEye.Rd | 8 +-- man/BullsEyeR.Rd | 5 -- 5 files changed, 19 insertions(+), 133 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, and stats for plotting "light"
spectra with 'ggplot2', together with specializations of ggplot()
and plot() methods for spectral data stored in objects of the classes
defined in package 'photobiology' and a plot() method for objects of
class "waveband", also defined in package 'photobiology'.
Author: Pedro J. Aphalo [aut, cre],
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.2.2 dated 2017-08-31 and 0.2.3 dated 2017-12-21
DESCRIPTION | 18 +-- MD5 | 164 +++++++++++++++++---------------- NAMESPACE | 3 NEWS | 11 ++ R/axis-utils-cps-spct.R | 2 R/axis-utils-filter-spct.R | 14 +- R/axis-utils-raw-spct.R | 2 R/axis-utils-response-spct.R | 2 R/axis-utils-source-spct.R | 2 R/axis-utils_wlength.R | 2 R/build-plot-title.R | 8 + R/geom-spct.R | 8 - R/ggplot-methods.R | 18 +++ R/on-load.R |only R/plot-calibration-spct.R |only R/plot-cps-spct.R | 29 +++-- R/plot-filter-spct.R | 42 ++++++-- R/plot-raw-spct.R | 41 +++++--- R/plot-response-spct.R | 14 ++ R/plot-source-spct.r | 14 ++ R/plot-waveband.R | 27 ++--- R/stat-color.R | 2 R/stat-label-peaks.R | 6 - R/stat-peaks.R | 6 - R/stat-wb-box.R | 2 R/stat-wb-column.R | 2 R/stat-wb-contribution.R | 2 R/stat-wb-hbar.R | 2 R/stat-wb-irrad.R | 2 R/stat-wb-label.R | 2 R/stat-wb-mean.R | 2 R/stat-wb-relative.R | 2 R/stat-wb-sirrad.R | 2 R/stat-wb-total.R | 2 R/stat-wl-strip.R | 2 R/stat-wl-summary.R | 2 R/title-utils.R |only README.md | 8 + build/vignette.rds |binary inst/doc/userguide1-grammar.R | 14 +- inst/doc/userguide1-grammar.Rmd | 21 ++-- inst/doc/userguide1-grammar.html | 52 ++++++---- inst/doc/userguide2-plot-methods.R | 6 + inst/doc/userguide2-plot-methods.Rmd | 31 +++++- inst/doc/userguide2-plot-methods.html | 75 +++++++++++++-- man/A_internal_label.Rd | 8 - man/cal_plot.Rd |only man/geom_spct.Rd | 8 - man/ggplot.Rd | 4 man/ggtitle_spct.Rd |only man/plot.calibration_spct.Rd |only man/plot.cps_spct.Rd | 10 +- man/plot.filter_spct.Rd | 9 + man/plot.object_spct.Rd | 11 +- man/plot.raw_spct.Rd | 10 +- man/plot.reflector_spct.Rd | 9 + man/plot.response_spct.Rd | 10 +- man/plot.source_spct.Rd | 11 +- man/plot.waveband.Rd | 5 - man/scale_x_wl_continuous.Rd | 2 man/scale_y_A_internal_continuous.Rd | 2 man/scale_y_Rfr_specular_continuous.Rd | 2 man/scale_y_Tfr_internal_continuous.Rd | 2 man/scale_y_counts_continuous.Rd | 2 man/scale_y_cps_continuous.Rd | 2 man/scale_y_s.e.irrad_continuous.Rd | 2 man/scale_y_s.e.response_continuous.Rd | 2 man/stat_color.Rd | 2 man/stat_label_peaks.Rd | 6 - man/stat_peaks.Rd | 6 - man/stat_wb_box.Rd | 2 man/stat_wb_column.Rd | 2 man/stat_wb_contribution.Rd | 2 man/stat_wb_hbar.Rd | 2 man/stat_wb_irrad.Rd | 2 man/stat_wb_label.Rd | 2 man/stat_wb_mean.Rd | 2 man/stat_wb_relative.Rd | 2 man/stat_wb_sirrad.Rd | 2 man/stat_wb_total.Rd | 2 man/stat_wl_strip.Rd | 2 man/stat_wl_summary.Rd | 2 man/subtitle_spct.generic_spct.Rd | 3 man/title_spct.Rd | 3 vignettes/userguide1-grammar.Rmd | 21 ++-- vignettes/userguide2-plot-methods.Rmd | 31 +++++- 86 files changed, 575 insertions(+), 298 deletions(-)