Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-03 0.2
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions from Heng Li
<lh3@live.co.uk> (Heng Li wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 4.7 dated 2015-08-18 and 4.9 dated 2015-09-16
ChangeLog | 5 ++++ DESCRIPTION | 8 +++---- MD5 | 29 +++++++++++++++------------ NAMESPACE | 5 ++++ R/genMakefile.R | 48 ++++++++++++++++++++++++++++++++++++++++++--- R/seqminer.R | 12 ++++------- man/addJob.Rd |only man/isTabixRange.Rd |only man/newJob.Rd |only man/newWorkflow.Rd |only man/rvmeta.writeCovData.Rd | 2 - man/writeWorkflow.Rd |only src/bcf_index.c | 3 ++ src/bedidx.c | 3 ++ src/knetfile.c | 4 +++ src/rvMetaLoader.cpp | 7 ++++-- src/tabix_index.c | 3 ++ src/vcf.c | 3 ++ 18 files changed, 103 insertions(+), 29 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, shared objects, vignettes, or function documentation. It is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo and (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.7.0 dated 2015-07-16 and 2.8.0 dated 2015-09-16
StanHeaders-2.7.0/StanHeaders/inst/include/src/stan/interface |only StanHeaders-2.8.0/StanHeaders/DESCRIPTION | 10 StanHeaders-2.8.0/StanHeaders/MD5 | 292 ++--- StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/interface_callbacks |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/array_var_context.hpp | 4 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/json/json_parser.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/mcmc_writer.hpp | 80 - StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/reader.hpp | 9 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/stan_csv_reader.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/ast.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/function_signatures.h | 8 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/generator.hpp | 548 ++++++---- StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar_def.hpp | 24 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar_def.hpp | 53 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar_def.hpp | 41 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/rethrow_located.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/model/prob_grad.hpp | 17 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/model/util.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/optimization/bfgs.hpp | 159 +- StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/optimization/bfgs_linesearch.hpp | 61 - StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/optimization/bfgs_update.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/optimization/lbfgs_update.hpp | 20 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/optimization/newton.hpp | 16 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt.hpp | 14 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_delta.hpp | 10 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_engaged.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_gamma.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_init_buffer.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_kappa.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_t0.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_term_buffer.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_window.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_bfgs.hpp | 42 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_data.hpp | 13 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_data_file.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_dense_e.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_diag_e.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_diagnose.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_diagnostic_file.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_engine.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_fail.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_fixed_param.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_history_size.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_hmc.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_id.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_init.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_init_alpha.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_int_time.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_iter.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_lbfgs.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_max_depth.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_method.hpp | 10 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_metric.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_newton.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_num_samples.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_num_warmup.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_nuts.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_optimize.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_optimize_algo.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_output.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_output_file.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_random.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_refresh.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_rwm.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_sample.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_sample_algo.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_save_iterations.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_save_warmup.hpp | 10 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_seed.hpp | 10 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_static.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_stepsize.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_stepsize_jitter.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_test.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_test_grad_eps.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_test_grad_err.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_test_gradient.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_thin.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_tolerance.hpp | 18 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_unit_e.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/argument.hpp | 20 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/argument_parser.hpp | 54 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/argument_probe.hpp | 20 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/categorical_argument.hpp | 25 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/list_argument.hpp | 59 - StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/singleton_argument.hpp | 25 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/unvalued_argument.hpp | 19 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/valued_argument.hpp | 23 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/init_nuts.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/init_static_hmc.hpp | 7 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/init_windowed_adapt.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/initialize_state.hpp | 39 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/io/write_error_msg.hpp | 19 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/io/write_iteration.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/io/write_stan.hpp | 14 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/mcmc/print_progress.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/mcmc/run_markov_chain.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/mcmc/sample.hpp | 13 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/mcmc/warmup.hpp | 9 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/optimization/do_bfgs_optimize.hpp | 16 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/variational/advi.hpp | 89 + StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/variational/base_family.hpp | 20 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/variational/families/normal_fullrank.hpp | 56 - StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/variational/families/normal_meanfield.hpp | 46 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/version.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math.hpp | 9 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/quad_form_sym.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/trace_quad_form.hpp | 44 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_Phi.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/arr/meta/container_view.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_definite.hpp | 55 - StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/assign.hpp | 45 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_decompose.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cols.hpp | 14 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_constrain.hpp | 1 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_u.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_v.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_w.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_matrix_times_vector.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_to_dense_matrix.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_u_to_z.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rank.hpp | 35 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rows.hpp | 14 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/size.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/meta/container_view.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_log.hpp | 8 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_Phi.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/scal/meta/container_view.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/scal/meta/is_constant_struct.hpp | 1 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_cdf.hpp | 79 - StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/scal/prob/wiener_log.hpp | 16 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/mat/fun/cholesky_decompose.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/acosh.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/asinh.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/atanh.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/cbrt.hpp | 6 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/erf.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/erfc.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/expm1.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/fma.hpp | 7 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_Phi.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m_exp.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log_diff_exp.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/owens_t.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/trunc.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/version.hpp | 2 145 files changed, 1647 insertions(+), 1403 deletions(-)
Title: JavaScript Charts API Tool
Description: API for using 'AmCharts' Library. Based on the 'htmlwidgets'
package, it provides a global architecture to generate 'JavaScript' source
code for charts. Most of classes in the library have their equivalent in R
with S4 classes; for those classes, not all properties have been referenced
but can easily be added in the constructors. Complex properties (e.g.
'JavaScript' object) can be passed as named list. See examples at <http://
dataknowledge.github.io/rAmCharts/>. and <http://www.amcharts.com/> for more
information about the library. The package includes the free version of 'AmCharts'
Library. Its only limitation is that a small link to the web site will be
displayed in your charts. If you enjoy this library, do not hesitate to refer
to this page <http://www.amcharts.com/online-store/> to purchase a licence,
and thus support its creators and get a period of Priority Support. See also
<http://www.amcharts.com/about/> for more information about 'AmCharts' company.
Author: Jeffery Petit [aut, cre],
Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory
htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/),
Benoit Thieurmel [aut, ctb],
DataKnowledge [ctb] (See official web site at http://www.datak.fr)
Maintainer: Jeffery Petit <jeff@datak.fr>
Diff between rAmCharts versions 1.1 dated 2015-09-16 and 1.1.1 dated 2015-09-16
DESCRIPTION | 31 +++++++++++++++++++++---------- MD5 | 4 +++- inst/NOTICE.Rmd |only inst/NOTICE.pdf |only 4 files changed, 24 insertions(+), 11 deletions(-)
Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.0 dated 2014-08-25 and 1.1 dated 2015-09-16
DESCRIPTION | 10 ++-- MD5 | 18 ++++--- NAMESPACE | 3 + R/aov.P.R |only R/functions.R | 68 ----------------------------- R/higgins.fisher.kruskal.test.R |only R/mood.median.test.R |only R/tukey.kruskal.test.R |only man/aov.P.Rd | 10 ++-- man/higgins.fisher.kruskal.test.Rd | 12 ++--- man/tukey.kruskal.test.Rd | 8 +-- src/aovp.f90 | 84 +++++++++++++++---------------------- 12 files changed, 70 insertions(+), 143 deletions(-)
Title: Multiple Factor Analysis (MFA)
Description: Performs Multiple Factor Analysis method for quantitative, categorical, frequency and mixed data, in addition to generating a lot of graphics, also has other useful functions.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MFAg versions 1.1 dated 2015-08-29 and 1.2 dated 2015-09-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/MFA.Rd | 26 +++++++++++++------------- man/MFAg-package.Rd | 4 ++-- man/Plot.MFA.Rd | 36 ++++++++++++++++++------------------ 5 files changed, 41 insertions(+), 41 deletions(-)
Title: Nomograms for High-Dimensional Cox Models
Description: Build nomograms for high-dimensional Cox models, with support for model validation and calibration.
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <nanx@uchicago.edu>
Maintainer: Nan Xiao <nanx@uchicago.edu>
Diff between hdnom versions 1.2 dated 2015-08-27 and 2.0 dated 2015-09-16
hdnom-1.2/hdnom/man/glmnet.calibrate.internal.true.Rd |only hdnom-2.0/hdnom/DESCRIPTION | 10 hdnom-2.0/hdnom/MD5 | 61 - hdnom-2.0/hdnom/NAMESPACE | 10 hdnom-2.0/hdnom/NEWS.md | 12 hdnom-2.0/hdnom/R/hdnom.calibrate.R | 838 ++++++++++++--- hdnom-2.0/hdnom/R/hdnom.models.R | 471 ++++++++ hdnom-2.0/hdnom/R/hdnom.nomogram.R | 303 ++++- hdnom-2.0/hdnom/R/hdnom.validate.R | 573 ++++++++-- hdnom-2.0/hdnom/README.md | 6 hdnom-2.0/hdnom/TODO | 4 hdnom-2.0/hdnom/inst/doc/hdnom.R | 6 hdnom-2.0/hdnom/inst/doc/hdnom.Rmd | 31 hdnom-2.0/hdnom/inst/doc/hdnom.html | 68 + hdnom-2.0/hdnom/man/glmnet.basesurv.Rd | 2 hdnom-2.0/hdnom/man/glmnet.calibrate.internal.pred.Rd | 4 hdnom-2.0/hdnom/man/hdcox.aenet.Rd | 3 hdnom-2.0/hdnom/man/hdcox.alasso.Rd | 3 hdnom-2.0/hdnom/man/hdcox.enet.Rd | 3 hdnom-2.0/hdnom/man/hdcox.flasso.Rd |only hdnom-2.0/hdnom/man/hdcox.lasso.Rd | 3 hdnom-2.0/hdnom/man/hdcox.mcp.Rd |only hdnom-2.0/hdnom/man/hdcox.mnet.Rd |only hdnom-2.0/hdnom/man/hdcox.scad.Rd |only hdnom-2.0/hdnom/man/hdcox.snet.Rd |only hdnom-2.0/hdnom/man/hdnom.calibrate.Rd | 40 hdnom-2.0/hdnom/man/hdnom.calibrate.internal.true.Rd |only hdnom-2.0/hdnom/man/hdnom.nomogram.Rd | 22 hdnom-2.0/hdnom/man/hdnom.validate.Rd | 38 hdnom-2.0/hdnom/man/ncvreg.basesurv.Rd |only hdnom-2.0/hdnom/man/ncvreg.calibrate.internal.pred.Rd |only hdnom-2.0/hdnom/man/ncvreg.survcurve.Rd |only hdnom-2.0/hdnom/man/ncvreg.tune.gamma.Rd |only hdnom-2.0/hdnom/man/ncvreg.tune.gamma.alpha.Rd |only hdnom-2.0/hdnom/man/ncvreg.validate.internal.Rd |only hdnom-2.0/hdnom/man/penalized.basesurv.Rd |only hdnom-2.0/hdnom/man/penalized.calibrate.internal.pred.Rd |only hdnom-2.0/hdnom/man/penalized.survcurve.Rd |only hdnom-2.0/hdnom/man/penalized.validate.internal.Rd |only hdnom-2.0/hdnom/vignettes/hdnom.Rmd | 31 40 files changed, 2138 insertions(+), 404 deletions(-)
Title: An Algorithm to Infer Relatedness
Description: Inference of relatedness coefficients from a bi-allelic genotype matrix using a Maximum Likelihood estimation.
Author: Fabien Laporte
Maintainer: Fabien Laporte <fabien.laporte@moulon.inra.fr>
Diff between Relatedness versions 1.0 dated 2015-09-15 and 1.1 dated 2015-09-16
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/RelCoef.R | 12 ++++++++---- man/RelCoef.Rd | 2 +- man/Relatedness-package.Rd | 2 +- 5 files changed, 17 insertions(+), 13 deletions(-)
Title: Distance Based Ranking Models
Description: Implements distance based probability models for ranking data.
The supported distance metrics include Kendall distance, Spearman distance, Footrule distance, Hamming distance,
and Weighted-tau distance and geo-Weighted Kendall distance.
Mixture models are also supported.
Author: Zhaozhi Qian
Maintainer: Zhaozhi Qian <qianzhaozhi@connect.hku.hk>
Diff between rankdist versions 1.1.0 dated 2015-08-19 and 1.1.1 dated 2015-09-16
DESCRIPTION | 10 ++++---- MD5 | 26 ++++++++++----------- R/class.R | 39 +++++++++++++++++++++----------- R/rankdist.R | 5 +++- man/RankControl-class.Rd | 2 - man/RankControlCayley-class.Rd | 3 ++ man/RankControlFootrule-class.Rd | 3 ++ man/RankControlHamming-class.Rd | 3 ++ man/RankControlKendall-class.Rd | 2 - man/RankControlPhiComponent-class.Rd | 2 - man/RankControlSpearman-class.Rd | 3 ++ man/RankControlWeightedKendall-class.Rd | 2 + man/RankControlWtau-class.Rd | 8 ++++++ src/utils.cpp | 2 - 14 files changed, 71 insertions(+), 39 deletions(-)
Title: Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
Description: Exploratory data analysis and manipulation functions for
multi-label data sets along with an interactive Shiny application to ease their
use.
Author: David Charte [cre],
Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@outlook.com>
Diff between mldr versions 0.2.33 dated 2015-07-18 and 0.2.51 dated 2015-09-16
DESCRIPTION | 8 +++--- MD5 | 18 ++++++------- R/graphics.R | 72 +++++++++++++++++++++++++++++++++--------------------- R/measures.R | 3 ++ R/read.arff.R | 2 - data/birds.rda |binary data/emotions.rda |binary data/genbase.rda |binary inst/doc/mldr.pdf |binary man/plot.mldr.Rd | 13 ++++++--- 10 files changed, 71 insertions(+), 45 deletions(-)
Title: Thermoluminescence Glow Curve Deconvolution
Description: Deconvolving first-order and general-order thermoluminescence glow
curves using a modified Levenberg-Marquardt algorithm. It provides the
possibility of setting constraints or fixing any of parameters. It offers
an interactive way to initialize parameters by clicking with a mouse on a
plot at positions where peak maxima should be located. The optimal estimate
is obtained by "Try-and-error". It also provides routines for simulating
first-, second-, and general-order glow peaks (or glow curves).
Author: Jun Peng [aut, cre], Jorge More [ctb], Burton Garbow [ctb], Kenneth Hillstrom [ctb], John Burkardt [ctb], Linda R. Petzold [ctb], Alan C. Hindmarsh [ctb], R. Woodrow Setzer [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>
Diff between tgcd versions 1.5 dated 2015-08-05 and 1.7 dated 2015-09-16
tgcd-1.5/tgcd/src/BulirschStoer.f90 |only tgcd-1.5/tgcd/src/inverse.f90 |only tgcd-1.5/tgcd/src/numHess.f90 |only tgcd-1.7/tgcd/DESCRIPTION | 23 ++- tgcd-1.7/tgcd/MD5 | 25 ++- tgcd-1.7/tgcd/NAMESPACE | 3 tgcd-1.7/tgcd/R/simPeak.R | 182 ++++++++++++++++++++-------- tgcd-1.7/tgcd/R/simqOTOR.R |only tgcd-1.7/tgcd/R/tgcd.R | 227 +++++++++++++++++++++++++++--------- tgcd-1.7/tgcd/man/Refglow.Rd | 2 tgcd-1.7/tgcd/man/simPeak.Rd | 101 +++++++++------- tgcd-1.7/tgcd/man/simqOTOR.Rd |only tgcd-1.7/tgcd/man/tgcd.Rd | 89 +++++++------- tgcd-1.7/tgcd/src/lsoda.f |only tgcd-1.7/tgcd/src/qeOTOR.f90 |only tgcd-1.7/tgcd/src/simPeak.f90 |only tgcd-1.7/tgcd/src/tgcd.f90 | 66 +++------- tgcd-1.7/tgcd/src/tgcd1.f90 |only 18 files changed, 458 insertions(+), 260 deletions(-)
More information about TestingSimilarity at CRAN
Permanent link
Title: Reads Mass Spectrometry Data in mzXML Format
Description: Functions for reading mass spectrometry data in mzXML format.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between readMzXmlData versions 2.8 dated 2014-09-28 and 2.8.1 dated 2015-09-16
DESCRIPTION | 10 +++++----- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 3 ++- NEWS | 3 +++ R/base64-functions.R | 12 ++++++------ R/package.R | 5 +++-- man/attributeTimeToDouble.Rd | 3 ++- man/attributeToDouble.Rd | 3 ++- man/attributeToString.Rd | 3 ++- man/base64-decode.Rd | 3 ++- man/grepNumeric.Rd | 3 ++- man/grepSubString.Rd | 3 ++- man/mzXmlHandlers.Rd | 3 ++- man/parseMzXml.Rd | 3 ++- man/readMzXmlData-defunct.Rd | 3 ++- man/readMzXmlData-package.Rd | 7 ++++--- man/readMzXmlDir.Rd | 3 ++- man/readMzXmlFile-internal.Rd | 3 ++- man/readMzXmlFile.Rd | 3 ++- man/revfregexpr.Rd | 3 ++- 20 files changed, 68 insertions(+), 49 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) and other
two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive
features, namely baseline subtraction methods such as
morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak
alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb [aut, cre],
Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.12 dated 2015-06-11 and 1.13 dated 2015-09-16
MALDIquant-1.12/MALDIquant/R/calculateLabelPositions-methods.R |only MALDIquant-1.13/MALDIquant/DESCRIPTION | 23 ++-- MALDIquant-1.13/MALDIquant/MD5 | 49 ++++---- MALDIquant-1.13/MALDIquant/NAMESPACE | 32 +++++ MALDIquant-1.13/MALDIquant/NEWS | 43 +++++++ MALDIquant-1.13/MALDIquant/R/AllGenerics.R | 19 --- MALDIquant-1.13/MALDIquant/R/Deprecated.R | 56 ---------- MALDIquant-1.13/MALDIquant/R/calculateLabelPositions-functions.R |only MALDIquant-1.13/MALDIquant/R/calibrateIntensity-functions.R | 52 ++++++++- MALDIquant-1.13/MALDIquant/R/calibrateIntensity-methods.R | 32 ++--- MALDIquant-1.13/MALDIquant/R/msiSlices-functions.R | 2 MALDIquant-1.13/MALDIquant/R/plotMsiSlice-functions.R | 2 MALDIquant-1.13/MALDIquant/R/plotMsiSlice-methods.R | 2 MALDIquant-1.13/MALDIquant/build/vignette.rds |binary MALDIquant-1.13/MALDIquant/inst/doc/MALDIquant-intro.pdf |binary MALDIquant-1.13/MALDIquant/man/MALDIquant-defunct.Rd | 3 MALDIquant-1.13/MALDIquant/man/MALDIquant-deprecated.Rd | 23 +--- MALDIquant-1.13/MALDIquant/man/MALDIquant-package.Rd | 15 +- MALDIquant-1.13/MALDIquant/man/MALDIquant-parallel.Rd | 35 +++++- MALDIquant-1.13/MALDIquant/man/alignSpectra-functions.Rd | 2 MALDIquant-1.13/MALDIquant/man/binPeaks-functions.Rd | 2 MALDIquant-1.13/MALDIquant/man/calibrateIntensity-methods.Rd | 15 +- MALDIquant-1.13/MALDIquant/man/determineWarpingFunctions-functions.Rd | 2 MALDIquant-1.13/MALDIquant/man/referencePeaks-functions.Rd | 2 MALDIquant-1.13/MALDIquant/tests/testthat/test_alignSpectra-functions.R |only MALDIquant-1.13/MALDIquant/tests/testthat/test_calibrateIntensity-methods.R | 15 ++ MALDIquant-1.13/MALDIquant/tests/testthat/test_plotMsiSlice-functions.R | 8 - 27 files changed, 261 insertions(+), 173 deletions(-)
Title: Fused Lasso Latent Feature Model
Description: Fits the Fused Lasso Latent Feature model, which is used for modeling multi-sample aCGH data to identify regions of copy number variation (CNV). Produces a set of features that describe the patterns of CNV and a set of weights that describe the composition of each sample. Also provides functions for choosing the optimal tuning parameters and the appropriate number of features, and for estimating the false discovery rate.
Author: Gen Nowak [aut, cre],
Trevor Hastie [aut],
Jonathan R. Pollack [aut],
Robert Tibshirani [aut],
Nicholas Johnson [aut]
Maintainer: Gen Nowak <gen.nowak@gmail.com>
Diff between FLLat versions 1.1 dated 2014-01-06 and 1.2 dated 2015-09-16
DESCRIPTION | 12 +-- MD5 | 48 ++++++------ NAMESPACE | 9 +- NEWS | 13 +++ R/CheckPars.R | 8 +- R/FLLat.FDR.R | 18 ++-- R/FLLat.R | 1 R/plot.FDR.R | 6 + R/plot.FLLat.R | 10 +- R/plot.PVE.R | 6 + R/predict.FLLat.R |only build/vignette.rds |binary inst/doc/FLLat_tutorial.R | 23 ++++-- inst/doc/FLLat_tutorial.pdf |binary inst/doc/FLLat_tutorial.rnw | 163 ++++++++++++++++++++++++++++--------------- man/FLLat.BIC.Rd | 43 +++++------ man/FLLat.FDR.Rd | 38 ++++------ man/FLLat.PVE.Rd | 66 ++++++++--------- man/FLLat.Rd | 75 ++++++++++--------- man/plot.FLLat.Rd | 57 +++++++-------- man/predict.FLLat.Rd |only man/simaCGH.Rd | 15 +++ src/Lat_L2.cpp | 59 ++++++++++++++- src/gen_lat_func.cpp | 6 + src/gen_lat_func.h | 4 - vignettes/FLLat_tutorial.rnw | 163 ++++++++++++++++++++++++++++--------------- 26 files changed, 522 insertions(+), 321 deletions(-)
Title: Penalized Likelihood Factor Analysis via Nonconvex Penalty
Description: An R package "fanc" computes the penalized maximum
likelihood estimates of factor loadings and unique variances
for various tuning parameters. The pathwise coordinate descent
along with EM algorithm is used. This package also includes a
new graphical tool which outputs path diagram, goodness-of-fit
indices and model selection criteria for each regularization
parameter. The user can change the regularization parameter by
manipulating scrollbars, which is helpful to find a suitable
value of regularization parameter.
Author: Kei Hirose, Michio Yamamoto, Haruhisa Nagata
Maintainer: Kei Hirose <mail@keihirose.com>
Diff between fanc versions 1.23 dated 2015-03-27 and 1.25 dated 2015-09-16
DESCRIPTION | 8 MD5 | 8 NAMESPACE | 4 R/fanc.R | 3 src/fanc.c | 2449 +++++++++++++++++++++++++++++------------------------------- 5 files changed, 1239 insertions(+), 1233 deletions(-)
Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial, Gaussian or Poisson. The spatial autocorrelation is modelled by a set of random effects, which are assigned a conditional autoregressive (CAR) prior distribution. A number of different CAR priors are available for the random effects, and full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development is supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayes versions 4.2 dated 2015-06-30 and 4.3 dated 2015-09-16
DESCRIPTION | 8 MD5 | 66 +- R/RcppExports.R | 28 - R/binomial.bymCAR.R | 44 + R/binomial.dissimilarityCAR.R | 46 +- R/binomial.iarCAR.R | 42 + R/binomial.independent.R | 42 + R/binomial.lerouxCAR.R | 908 ++++++++++++++++++++--------------------- R/binomial.localisedCAR.R | 5 R/gaussian.dissimilarityCAR.R | 53 +- R/gaussian.iarCAR.R | 54 +- R/gaussian.lerouxCAR.R | 46 +- R/poisson.bymCAR.R | 38 + R/poisson.dissimilarityCAR.R | 37 + R/poisson.iarCAR.R | 32 - R/poisson.independent.R | 36 + R/poisson.lerouxCAR.R | 41 + R/poisson.localisedCAR.R | 7 R/poisson.localisedCARagg.R | 7 R/print.carbayes.R | 18 build/vignette.rds |binary inst/doc/CARBayesvignette.Rnw | 16 inst/doc/CARBayesvignette.pdf |binary man/CARBayes-package.Rd | 7 man/S.CARbym.Rd | 8 man/S.CARdissimilarity.Rd | 8 man/S.CARiar.Rd | 8 man/S.CARleroux.Rd | 8 man/S.CARlocalised.Rd | 9 man/S.independent.Rd | 8 src/CARBayes.cpp | 44 - src/RcppExports.cpp | 49 +- vignettes/CARBayesvignette.Rnw | 16 vignettes/jss996.bib | 4 34 files changed, 991 insertions(+), 752 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-8 dated 2015-08-11 and 0.2-10 dated 2015-09-16
arulesSequences-0.2-10/arulesSequences/CHANGELOG | 22 + arulesSequences-0.2-10/arulesSequences/DESCRIPTION | 8 arulesSequences-0.2-10/arulesSequences/MD5 | 45 +- arulesSequences-0.2-10/arulesSequences/NAMESPACE | 5 arulesSequences-0.2-10/arulesSequences/R/02sequences.R | 81 ++-- arulesSequences-0.2-10/arulesSequences/R/03rules.R | 8 arulesSequences-0.2-10/arulesSequences/R/04parameter.R | 4 arulesSequences-0.2-10/arulesSequences/R/05read_write.R | 90 +++- arulesSequences-0.2-10/arulesSequences/R/10timed.R | 74 ++-- arulesSequences-0.2-10/arulesSequences/R/20support.R | 185 ++++++---- arulesSequences-0.2-10/arulesSequences/R/native.R | 3 arulesSequences-0.2-10/arulesSequences/data/zaki.rda |binary arulesSequences-0.2-10/arulesSequences/man/SPparameter-class.Rd | 2 arulesSequences-0.2-10/arulesSequences/man/cspade.Rd | 45 +- arulesSequences-0.2-10/arulesSequences/man/read_baskets.Rd | 29 + arulesSequences-0.2-10/arulesSequences/man/sequences-class.Rd | 1 arulesSequences-0.2-10/arulesSequences/man/support-methods.Rd | 46 +- arulesSequences-0.2-10/arulesSequences/src/cSPADE/sequence.cc | 2 arulesSequences-0.2-10/arulesSequences/src/idlists.c |only arulesSequences-0.2-10/arulesSequences/src/makebin.c | 15 arulesSequences-0.2-10/arulesSequences/tests/idlists.R |only arulesSequences-0.2-10/arulesSequences/tests/idlists.Rout.save |only arulesSequences-0.2-10/arulesSequences/tests/zaki.R | 10 arulesSequences-0.2-10/arulesSequences/tests/zaki.Rout.save | 34 + arulesSequences-0.2-8/arulesSequences/R/arules.R |only arulesSequences-0.2-8/arulesSequences/src/ptree.c |only 26 files changed, 458 insertions(+), 251 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.19.4 dated 2015-09-15 and 0.19.6 dated 2015-09-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/export_functions.r | 47 ++++++++++++++++++++++++++++++++++------------- inst/doc/sdcTable.pdf |binary 4 files changed, 40 insertions(+), 19 deletions(-)
Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org' archives.
Functions allow searching by many parameters, including 'taxonomic' names,
places, and dates. In addition, there is an interface for conducting spatially
delimited searches, and another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rvertnet versions 0.3.0 dated 2015-06-26 and 0.3.4 dated 2015-09-16
DESCRIPTION | 9 +++--- MD5 | 36 +++++++++++++++------------ NAMESPACE | 15 +++++++++-- R/rvertnet-package.R | 7 +++++ R/searchbyterm.R | 48 +++++++++++++++--------------------- R/vert_id.R |only R/vertmap.R | 4 ++- R/vertsearch.R | 6 ++-- R/vertsummary.R | 4 +-- R/yyy.R | 3 ++ R/zzz.R | 28 +++++++++++---------- README.md | 1 build/vignette.rds |binary man/searchbyterm.Rd | 20 +++++---------- man/vert_id.Rd |only man/vertsearch.Rd | 6 ++-- man/vertsummary.Rd | 4 +-- tests/testthat/test-searchbyterm.R | 6 ++-- tests/testthat/test-spatialsearch.R | 6 ++-- tests/testthat/test-vertmap.R |only tests/testthat/test-vertsummary.R |only 21 files changed, 109 insertions(+), 94 deletions(-)
Title: Interface to the Search 'API' for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based
search 'API' (http://api.plos.org/) provided by the Public
Library of Science journals to search their articles.
Functions are included for searching for articles, retrieving
articles, making plots, doing 'faceted' searches,
'highlight' searches, and viewing results of 'highlighted'
searches in a browser.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rplos versions 0.5.2 dated 2015-08-05 and 0.5.4 dated 2015-09-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 7 +++++++ build/vignette.rds |binary tests/testthat/test-fulltext.R | 2 +- 5 files changed, 16 insertions(+), 9 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances. Also included are tools to plot compositional data on ternary diagrams, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 0.3 dated 2015-08-13 and 0.5 dated 2015-09-16
provenance-0.3/provenance/man/KS.dist.Rd |only provenance-0.3/provenance/man/SH.dist.Rd |only provenance-0.3/provenance/man/dist.Rd |only provenance-0.3/provenance/man/getKDE.Rd |only provenance-0.3/provenance/man/getKDEs.Rd |only provenance-0.3/provenance/man/getMDS.Rd |only provenance-0.3/provenance/man/getPCA.Rd |only provenance-0.3/provenance/man/plot.DZdata.Rd |only provenance-0.3/provenance/man/plot.HMdata.Rd |only provenance-0.3/provenance/man/read.DZdata.Rd |only provenance-0.3/provenance/man/read.HMdata.Rd |only provenance-0.3/provenance/man/subset.Rd |only provenance-0.3/provenance/man/ternaryplot.Rd |only provenance-0.5/provenance/DESCRIPTION | 10 provenance-0.5/provenance/MD5 | 82 - provenance-0.5/provenance/NAMESPACE | 58 provenance-0.5/provenance/R/botev.R |only provenance-0.5/provenance/R/documentation.R |only provenance-0.5/provenance/R/kde.R |only provenance-0.5/provenance/R/minsorting.R |only provenance-0.5/provenance/R/plot.R |only provenance-0.5/provenance/R/provenance.R | 1259 ++++------------- provenance-0.5/provenance/R/sircombe.R |only provenance-0.5/provenance/R/srd.R |only provenance-0.5/provenance/data |only provenance-0.5/provenance/inst/HM.csv | 34 provenance-0.5/provenance/inst/PT.csv | 34 provenance-0.5/provenance/inst/PTHM.csv |only provenance-0.5/provenance/inst/densities.csv |only provenance-0.5/provenance/inst/endmembers.csv |only provenance-0.5/provenance/man/KDE.Rd |only provenance-0.5/provenance/man/KDEs.Rd |only provenance-0.5/provenance/man/KS.diss.Rd |only provenance-0.5/provenance/man/MDS.Rd |only provenance-0.5/provenance/man/Namib.Rd |only provenance-0.5/provenance/man/PCA.Rd |only provenance-0.5/provenance/man/SH.diss.Rd |only provenance-0.5/provenance/man/amalgamate.Rd |only provenance-0.5/provenance/man/botev.Rd | 4 provenance-0.5/provenance/man/bray.diss.Rd |only provenance-0.5/provenance/man/clr.Rd | 21 provenance-0.5/provenance/man/densities.Rd |only provenance-0.5/provenance/man/diss.Rd |only provenance-0.5/provenance/man/endmembers.Rd |only provenance-0.5/provenance/man/get.n.Rd | 4 provenance-0.5/provenance/man/indscal.Rd | 9 provenance-0.5/provenance/man/minsorting.Rd |only provenance-0.5/provenance/man/plot.GPA.Rd | 10 provenance-0.5/provenance/man/plot.INDSCAL.Rd | 10 provenance-0.5/provenance/man/plot.KDE.Rd | 14 provenance-0.5/provenance/man/plot.MDS.Rd | 9 provenance-0.5/provenance/man/plot.PCA.Rd | 10 provenance-0.5/provenance/man/plot.compositional.Rd |only provenance-0.5/provenance/man/plot.distributional.Rd |only provenance-0.5/provenance/man/plot.minsorting.Rd |only provenance-0.5/provenance/man/plot.ternary.Rd |only provenance-0.5/provenance/man/procrustes.Rd | 9 provenance-0.5/provenance/man/read.compositional.Rd |only provenance-0.5/provenance/man/read.densities.Rd |only provenance-0.5/provenance/man/read.distributional.Rd |only provenance-0.5/provenance/man/restore.Rd |only provenance-0.5/provenance/man/subset.compositional.Rd |only provenance-0.5/provenance/man/subset.distributional.Rd |only provenance-0.5/provenance/man/summaryplot.Rd | 19 provenance-0.5/provenance/man/ternary.Rd |only 65 files changed, 553 insertions(+), 1043 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between PRIMsrc versions 0.5.9 dated 2015-09-08 and 0.6.0 dated 2015-09-16
PRIMsrc-0.5.9/PRIMsrc/inst/doc/PRIMsrc_0.5.9.pdf |only PRIMsrc-0.6.0/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.6.0/PRIMsrc/MD5 | 16 - PRIMsrc-0.6.0/PRIMsrc/R/PRIMsrc.internal.r | 54 +++--- PRIMsrc-0.6.0/PRIMsrc/R/PRIMsrc.r | 191 +++++++++-------------- PRIMsrc-0.6.0/PRIMsrc/inst/NEWS | 39 +++- PRIMsrc-0.6.0/PRIMsrc/inst/doc/PRIMsrc_0.6.0.pdf |only PRIMsrc-0.6.0/PRIMsrc/man/plot_boxtrace.Rd | 4 PRIMsrc-0.6.0/PRIMsrc/man/plot_boxtraj.Rd | 4 PRIMsrc-0.6.0/PRIMsrc/man/sbh.Rd | 22 +- 10 files changed, 159 insertions(+), 179 deletions(-)
Title: Evaluation of Diversity in Nucleotide Libraries
Description: Evaluation of diversity in peptide libraries, including NNN, NNB,
NNK/S, and 20/20 schemes. Custom encoding schemes can also be defined.
Metrics for evaluation include expected coverage, relative efficiency, and
the functional diversity of the library. Peptide-level inclusion
probabilities are computable for both the native and custom encoding
schemes.
Author: Heike Hofmann [aut],
Eric Hare [aut, cre],
GGobi Foundation [aut]
Maintainer: Eric Hare <erichare@iastate.edu>
Diff between peptider versions 0.2 dated 2015-04-11 and 0.2.2 dated 2015-09-16
DESCRIPTION | 8 +++--- MD5 | 54 ++++++++++++++++++++++---------------------- NAMESPACE | 5 +++- R/peptider.r | 7 +++++ R/tabulate.r | 1 man/BLOSUM80.Rd | 2 - man/codons.Rd | 2 - man/coverage.Rd | 2 - man/detect.Rd | 2 - man/diversity.Rd | 2 - man/efficiency.Rd | 2 - man/encodingReduce.Rd | 2 - man/genNeighbors.Rd | 2 - man/genNeighbors_reduced.Rd | 2 - man/generateCustom.Rd | 2 - man/generateCustomLib.Rd | 2 - man/generateCustomNei.Rd | 2 - man/generateCustomProbs.Rd | 2 - man/getChoices.Rd | 2 - man/getCounts.Rd | 2 - man/getNeighbors.Rd | 2 - man/getNofNeighbors.Rd | 2 - man/libBuild.Rd | 2 - man/libscheme.Rd | 2 - man/makowski.Rd | 2 - man/ppeptide.Rd | 2 - man/scheme.Rd | 2 - man/schemes.Rd | 2 - 28 files changed, 66 insertions(+), 55 deletions(-)
Title: Statistics and Metrics for Seismic Data
Description: Classes and functions for metrics calculation as part of the
'IRIS DMC MUSTANG' project. The functionality in this package
builds upon the base classes of the 'IrisSeismic' package.
Metrics include basic statistics as well as higher level
'health' metrics that can help identify problematic seismometers.
Author: Jonathan Callahan [aut, cre],
Rob Casey [aut],
Mary Templeton [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between IRISMustangMetrics versions 1.0.0 dated 2015-08-02 and 1.0.1 dated 2015-09-16
IRISMustangMetrics-1.0.0/IRISMustangMetrics/R/PSDMetrics.R |only IRISMustangMetrics-1.0.0/IRISMustangMetrics/R/crossCorrelationMetrics.R |only IRISMustangMetrics-1.0.0/IRISMustangMetrics/R/transferFunctionMetrics.R |only IRISMustangMetrics-1.0.0/IRISMustangMetrics/man/PSDMetrics.Rd |only IRISMustangMetrics-1.0.0/IRISMustangMetrics/man/crossCorrelationMetrics.Rd |only IRISMustangMetrics-1.0.0/IRISMustangMetrics/man/transferFunctionMetrics.Rd |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/DESCRIPTION | 12 +++--- IRISMustangMetrics-1.0.1/IRISMustangMetrics/MD5 | 18 +++++----- IRISMustangMetrics-1.0.1/IRISMustangMetrics/NAMESPACE | 6 +-- IRISMustangMetrics-1.0.1/IRISMustangMetrics/R/PSDMetric.R |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/R/correlationMetric.R | 8 +--- IRISMustangMetrics-1.0.1/IRISMustangMetrics/R/crossCorrelationMetric.R |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/R/transferFunctionMetric.R |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/man/PSDMetric.Rd |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/man/crossCorrelationMetric.Rd |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/man/transferFunctionMetric.Rd |only 16 files changed, 21 insertions(+), 23 deletions(-)
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Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation or the graphical lasso,
and both methods can be further accelerated by the lossy
screening rule preselecting the neighborhood of each variable
by correlation thresholding. We target on high-dimensional data
analysis usually d >> n, and the computation is
memory-optimized using the sparse matrix output. We also
provide a computationally efficient approach, correlation
thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stability approach for
regularization selection (2) rotation information criterion (3)
extended Bayesian information criterion which is only available
for the graphical lasso.
Author: Tuo Zhao, Xingguo Li, Han Liu, Kathryn Roeder, John Lafferty, Larry
Wasserman
Maintainer: Tuo Zhao <tzhao5@jhu.edu>
Diff between huge versions 1.2.6 dated 2014-02-28 and 1.2.7 dated 2015-09-16
DESCRIPTION | 14 +++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 8 ++++++-- R/huge.generator.R | 2 +- build/vignette.rds |binary man/huge-package.Rd | 6 +++--- man/huge.Rd | 24 ++++++++++++------------ man/huge.select.Rd | 4 ++-- src/SFGen.c | 18 +++++++++++------- 9 files changed, 50 insertions(+), 42 deletions(-)
Title: Create and Manipulate Discrete Random Variables
Description: Create, manipulate, transform, and simulate from discrete random
variables. The syntax is modeled after that which is used in mathematical
statistics and probability courses, but with powerful support for more
advanced probability calculations. This includes the creation of joint
random variables, and the derivation and manipulation of their conditional
and marginal distributions.
Author: Andreas Buja [aut],
Eric Hare [aut, cre],
Heike Hofmann [aut]
Maintainer: Eric Hare <erichare@iastate.edu>
Diff between discreteRV versions 1.2.1 dated 2015-05-03 and 1.2.2 dated 2015-09-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 10 ++++++++++ R/discreteRV-Probabilities.r | 14 ++++++++++++++ R/discreteRV-Simulations.r | 1 + build/vignette.rds |binary inst/doc/discreteRV.html | 14 +++++++------- 7 files changed, 41 insertions(+), 16 deletions(-)
Title: Desirability Functions for Ranking, Selecting, and Integrating
Data
Description: Functions for (1) ranking, selecting, and prioritising genes,
proteins, and metabolites from high dimensional biology experiments, (2)
multivariate hit calling in high content screens, and (3) combining data
from diverse sources.
Author: Stanley E. Lazic
Maintainer: Stanley E. Lazic <stan.lazic@cantab.net>
Diff between desiR versions 1.0 dated 2015-06-16 and 1.1 dated 2015-09-16
DESCRIPTION | 16 +++++++++------- MD5 | 35 ++++++++++++++++++----------------- NAMESPACE | 1 + R/d.central.R | 9 +++++---- R/d.ends.R | 7 ++++--- R/d.high.R | 6 +++--- R/d.low.R | 6 +++--- R/des.line.R | 40 +++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/Gene_ranking.R | 14 +++++++------- inst/doc/Gene_ranking.Rmd | 22 ++++++++++------------ inst/doc/Gene_ranking.pdf |binary man/d.central.Rd | 9 +++++---- man/d.ends.Rd | 7 ++++--- man/d.high.Rd | 6 +++--- man/d.low.Rd | 6 +++--- man/des.line.Rd | 14 ++++++++++---- vignettes/Gene_ranking.Rmd | 22 ++++++++++------------ vignettes/Gene_ranking.html |only 19 files changed, 120 insertions(+), 100 deletions(-)
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Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by
Bold Systems for genetic barcode data. Functions include methods for
searching by sequences by taxonomic names, ids, collectors, and
institutions; as well as a function for searching for specimens, and
downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 0.2.6 dated 2015-04-18 and 0.3.0 dated 2015-09-16
DESCRIPTION | 13 LICENSE | 4 MD5 | 39 +- NAMESPACE | 3 NEWS | 11 R/bold-package.R | 39 +- R/bold_seq.R | 2 R/bold_seqspec.R | 4 R/bold_specimens.R | 8 README.md | 48 +-- build/vignette.rds |binary inst/doc/bold_vignette.Rmd | 440 +++++++++++++++++++++++++++++++ inst/doc/bold_vignette.html | 493 +++++++++++++++++------------------ man/bold-package.Rd | 29 +- man/bold_seq.Rd | 2 man/bold_seqspec.Rd | 4 man/bold_specimens.Rd | 6 man/sequences.Rd | 9 tests/test-all.R |only tests/testthat/test-bold_specimens.R | 2 vignettes/bold_vignette.Rmd | 440 +++++++++++++++++++++++++++++++ 21 files changed, 1248 insertions(+), 348 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL.
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.1-5 dated 2015-02-10 and 1.2-5 dated 2015-09-16
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