Title: Multivariate Adaptive Shrinkage
Description: Implements the multivariate adaptive shrinkage (mash)
method of Urbut et al (2019) <DOI:10.1038/s41588-018-0268-8> for
estimating and testing large numbers of effects in many conditions
(or many outcomes). Mash takes an empirical Bayes approach to
testing and effect estimation; it estimates patterns of similarity
among conditions, then exploits these patterns to improve accuracy
of the effect estimates. The core linear algebra is implemented in
C++ for fast model fitting and posterior computation.
Author: Matthew Stephens [aut],
Sarah Urbut [aut],
Gao Wang [aut],
Yuxin Zou [aut],
Yunqi Yang [ctb],
Sam Roweis [cph],
David Hogg [cph],
Jo Bovy [cph],
Peter Carbonetto [aut, cre]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between mashr versions 0.2.38 dated 2020-06-19 and 0.2.50 dated 2021-05-23
mashr-0.2.38/mashr/inst/doc/intro_mashnobaseline.R |only mashr-0.2.38/mashr/inst/doc/intro_mashnobaseline.Rmd |only mashr-0.2.38/mashr/inst/doc/intro_mashnobaseline.html |only mashr-0.2.38/mashr/vignettes/intro_mashnobaseline.Rmd |only mashr-0.2.50/mashr/DESCRIPTION | 22 - mashr-0.2.50/mashr/MD5 | 87 +++--- mashr-0.2.50/mashr/NAMESPACE | 2 mashr-0.2.50/mashr/R/RcppExports.R | 4 mashr-0.2.50/mashr/R/data2cov.R | 81 +++++ mashr-0.2.50/mashr/R/ed.R | 67 ++-- mashr-0.2.50/mashr/R/mash.R | 31 +- mashr-0.2.50/mashr/R/matrix_utils.R | 10 mashr-0.2.50/mashr/R/posterior.R | 8 mashr-0.2.50/mashr/R/set_data.R | 24 + mashr-0.2.50/mashr/README.md | 92 ++---- mashr-0.2.50/mashr/build/vignette.rds |binary mashr-0.2.50/mashr/inst/doc/eQTL_outline.Rmd | 14 - mashr-0.2.50/mashr/inst/doc/eQTL_outline.html | 34 +- mashr-0.2.50/mashr/inst/doc/flash_mash.R |only mashr-0.2.50/mashr/inst/doc/flash_mash.Rmd |only mashr-0.2.50/mashr/inst/doc/flash_mash.html |only mashr-0.2.50/mashr/inst/doc/intro_correlations.html | 16 - mashr-0.2.50/mashr/inst/doc/intro_mash.Rmd | 6 mashr-0.2.50/mashr/inst/doc/intro_mash.html | 32 +- mashr-0.2.50/mashr/inst/doc/intro_mash_dd.html | 12 mashr-0.2.50/mashr/inst/doc/intro_mashbaselinemean.R |only mashr-0.2.50/mashr/inst/doc/intro_mashbaselinemean.Rmd |only mashr-0.2.50/mashr/inst/doc/intro_mashbaselinemean.html |only mashr-0.2.50/mashr/inst/doc/intro_mashcommonbaseline.Rmd | 29 +- mashr-0.2.50/mashr/inst/doc/intro_mashcommonbaseline.html | 26 - mashr-0.2.50/mashr/inst/doc/mash_sampling.html | 18 - mashr-0.2.50/mashr/inst/doc/simulate_noncanon.html | 12 mashr-0.2.50/mashr/inst/misc/uncrustify_default.cfg | 1 mashr-0.2.50/mashr/man/compute_posterior_matrices.Rd | 5 mashr-0.2.50/mashr/man/cov_ed.Rd | 4 mashr-0.2.50/mashr/man/cov_flash.Rd |only mashr-0.2.50/mashr/man/mash.Rd | 13 mashr-0.2.50/mashr/src/Makevars.in | 1 mashr-0.2.50/mashr/src/RcppExports.cpp | 68 +++- mashr-0.2.50/mashr/src/extreme_deconvolution.cpp | 31 -- mashr-0.2.50/mashr/src/mash.cpp | 119 ++++---- mashr-0.2.50/mashr/src/mash.h | 191 +++++--------- mashr-0.2.50/mashr/tests/testthat/ExDeconDemo_c.log |only mashr-0.2.50/mashr/tests/testthat/ExDeconDemo_loglike.log |only mashr-0.2.50/mashr/tests/testthat/test_ash.R | 4 mashr-0.2.50/mashr/tests/testthat/test_estimate_cor.R | 6 mashr-0.2.50/mashr/tests/testthat/test_getfunctions.R | 3 mashr-0.2.50/mashr/vignettes/eQTL_outline.Rmd | 14 - mashr-0.2.50/mashr/vignettes/flash_mash.Rmd |only mashr-0.2.50/mashr/vignettes/intro_mash.Rmd | 6 mashr-0.2.50/mashr/vignettes/intro_mashbaselinemean.Rmd |only mashr-0.2.50/mashr/vignettes/intro_mashcommonbaseline.Rmd | 29 +- 52 files changed, 600 insertions(+), 522 deletions(-)
Title: Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Description: Implements the basic elements of the multi-model
inference paradigm for up to twenty species-area relationship models (SAR), using simple
R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>.
The package is scalable and users can easily create their own model and data objects. Additional
SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] (<https://orcid.org/0000-0002-7624-244X>),
Francois Guilhaumon [aut] (<https://orcid.org/0000-0003-4707-8932>),
Kevin Cazelles [rev] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between sars versions 1.3.3 dated 2021-03-08 and 1.3.4 dated 2021-05-23
DESCRIPTION | 6 - MD5 | 138 +++++++++++++++---------------- NEWS.md | 13 ++ R/class_plot.R | 5 - R/obs_shape.R | 18 ++-- R/optim.R | 105 +++++++++++++++++------ R/sar_asymp.R | 14 ++- R/sar_average.R | 94 ++++++++++++++------- R/sar_betap.R | 14 ++- R/sar_chapman.R | 14 ++- R/sar_conf_int.R | 12 +- R/sar_epm1.R | 14 ++- R/sar_epm2.R | 14 ++- R/sar_gompertz.R | 14 ++- R/sar_heleg.R | 14 ++- R/sar_koba.R | 14 ++- R/sar_linear.R | 15 ++- R/sar_loga.R | 14 ++- R/sar_logistic.R | 14 ++- R/sar_mmf.R | 14 ++- R/sar_monod.R | 14 ++- R/sar_negexpo.R | 14 ++- R/sar_p1.R | 14 ++- R/sar_p2.R | 14 ++- R/sar_power.R | 18 +++- R/sar_powerR.R | 14 ++- R/sar_ratio.R | 14 ++- R/sar_threshold.R | 18 +++- R/sar_weibull3.R | 14 ++- R/sar_weibull4.R | 14 ++- README.md | 2 inst/doc/sars-r-package.html | 73 ++++------------ inst/model_factory.R | 30 +++++- man/figures/README-unnamed-chunk-5-1.png |binary man/plot.sars.Rd | 3 man/sar_asymp.Rd | 6 + man/sar_average.Rd | 10 +- man/sar_betap.Rd | 6 + man/sar_chapman.Rd | 6 + man/sar_epm1.Rd | 6 + man/sar_epm2.Rd | 6 + man/sar_gompertz.Rd | 6 + man/sar_heleg.Rd | 6 + man/sar_koba.Rd | 6 + man/sar_linear.Rd | 4 man/sar_loga.Rd | 6 + man/sar_logistic.Rd | 6 + man/sar_mmf.Rd | 6 + man/sar_monod.Rd | 6 + man/sar_multi.Rd | 8 + man/sar_negexpo.Rd | 6 + man/sar_p1.Rd | 6 + man/sar_p2.Rd | 6 + man/sar_power.Rd | 10 ++ man/sar_powerR.Rd | 6 + man/sar_pred.Rd | 3 man/sar_ratio.Rd | 6 + man/sar_weibull3.Rd | 6 + man/sar_weibull4.Rd | 6 + tests/testthat.R | 8 + tests/testthat/test_convergence.R | 3 tests/testthat/test_crit_method.R | 48 +++++----- tests/testthat/test_grid_start.R | 8 - tests/testthat/test_indiv_CIs.R |only tests/testthat/test_logistic.R | 1 tests/testthat/test_monod.R | 3 tests/testthat/test_p2.R | 1 tests/testthat/test_pred.R | 9 +- tests/testthat/test_thresholds.R | 58 ++++++------- tests/testthat/test_warnings.R |only tests/testthat/test_weibull3.R | 2 71 files changed, 733 insertions(+), 373 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Armadillo requires a C++11 compiler.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.10.4.0.0 dated 2021-04-13 and 0.10.5.0.0 dated 2021-05-23
RcppArmadillo-0.10.4.0.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp.cmake |only RcppArmadillo-0.10.5.0.0/RcppArmadillo/ChangeLog | 42 RcppArmadillo-0.10.5.0.0/RcppArmadillo/DESCRIPTION | 11 RcppArmadillo-0.10.5.0.0/RcppArmadillo/MD5 | 251 ++--- RcppArmadillo-0.10.5.0.0/RcppArmadillo/build/partial.rdb |binary RcppArmadillo-0.10.5.0.0/RcppArmadillo/build/vignette.rds |binary RcppArmadillo-0.10.5.0.0/RcppArmadillo/configure | 18 RcppArmadillo-0.10.5.0.0/RcppArmadillo/configure.ac | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/NEWS.Rd | 28 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/doc/RcppArmadillo-sparseMatrix.pdf |binary RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp | 9 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp | 103 ++ RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp | 5 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp | 159 ++- RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp | 5 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 155 ++- RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp | 9 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp | 103 ++ RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_bones.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp | 54 + RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_bones.hpp | 5 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_col_list_meat.hpp | 8 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_meat.hpp | 64 + RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/arma_config.hpp | 8 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/arma_forward.hpp | 5 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_meat.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/arma_rng.hpp | 292 +++--- RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_bones.hpp | 13 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_meat.hpp | 71 + RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp | 64 - RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp | 9 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/def_superlu.hpp | 8 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/diagview_bones.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/diagview_meat.hpp | 32 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/field_meat.hpp | 40 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_as_scalar.hpp | 66 - RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_chi2rnd.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_clamp.hpp | 68 - RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_conv_to.hpp | 28 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_eps.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_find.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_interp1.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_join.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_misc.hpp | 12 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_normalise.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_randg.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_randi.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_size.hpp | 66 + RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_svds.hpp | 8 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_sylvester.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_symmat.hpp | 16 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_trimat_ind.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/glue_affmul_meat.hpp | 10 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/glue_conv_meat.hpp | 14 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/glue_intersect_meat.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/glue_join_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/glue_mixed_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/glue_polyfit_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/glue_quantile_meat.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/glue_times_meat.hpp | 10 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/gmm_diag_meat.hpp | 28 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/gmm_full_meat.hpp | 36 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/hdf5_misc.hpp | 28 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/mul_gemm.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/mul_herk.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/mul_syrk.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/newarp_DoubleShiftQR_meat.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/newarp_GenEigsSolver_meat.hpp | 23 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/newarp_SparseGenRealShiftSolve_meat.hpp | 11 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/newarp_SymEigsSolver_meat.hpp | 33 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/newarp_UpperHessenbergEigen_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/newarp_UpperHessenbergQR_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_clamp_bones.hpp | 29 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_clamp_meat.hpp | 464 ++++++++-- RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_diagmat_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_find_meat.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_find_unique_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_hist_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_htrans_meat.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_index_max_meat.hpp | 8 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_index_min_meat.hpp | 8 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_inv_meat.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_logmat_meat.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_nonzeros_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_norm_meat.hpp | 8 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_pinv_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_princomp_meat.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_sqrtmat_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_strans_meat.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_sum_bones.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_sum_meat.hpp | 209 ---- RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_symmat_bones.hpp | 30 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_symmat_meat.hpp | 248 +++-- RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_trimat_bones.hpp | 1 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_trimat_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_unique_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_vectorise_meat.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/op_wishrnd_meat.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/operator_div.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/operator_times.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/sp_auxlib_meat.hpp | 20 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spdiagview_bones.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spdiagview_meat.hpp | 81 + RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spglue_join_meat.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spglue_kron_meat.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spglue_merge_meat.hpp | 29 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_max_meat.hpp | 26 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_mean_meat.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_min_meat.hpp | 30 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_meat.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_normalise_meat.hpp | 8 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_repmat_meat.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_reverse_meat.hpp | 6 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_sum_meat.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/subview_bones.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_bones.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_each_meat.hpp | 16 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_meat.hpp | 36 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/subview_each_meat.hpp | 12 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem1_bones.hpp | 4 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem1_meat.hpp | 32 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem2_bones.hpp | 2 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem2_meat.hpp | 16 RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/subview_meat.hpp | 52 - RcppArmadillo-0.10.5.0.0/RcppArmadillo/inst/include/armadillo_bits/translate_superlu.hpp | 14 127 files changed, 2368 insertions(+), 1233 deletions(-)
Title: Parse and Manipulate Research Patient Data Registry ('RPDR')
Text Queries
Description: Functions to load Research Patient Data Registry ('RPDR') text queries from Partners Healthcare institutions into R.
The package also provides helper functions to manipulate data and execute common procedures
such as finding the closest radiological exams considering a given timepoint. 'parseRPDR' currently supports
txt sources: "mrn", "con", "dem", "enc", "rdt", "lab", "med", "dia", "rfv", "prc",
"car", "dis", "end", "hnp", "opn", "pat", "prg", "pul", "rad" and "vis".
All functionalities are parallelized for fast and efficient analyses.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <mkolossvary@mgh.harvard.edu>
Diff between parseRPDR versions 0.1.0 dated 2021-05-10 and 0.1.1 dated 2021-05-23
DESCRIPTION | 12 ++-- MD5 | 60 +++++++++++----------- NAMESPACE | 2 NEWS.md | 12 ++++ R/convert_dia.R | 4 - R/convert_enc.R | 2 R/convert_med.R | 2 R/convert_prc.R |only R/convert_rfv.R | 5 - R/load_all.R | 17 +++++- R/load_base.R | 4 - R/load_dia.R | 4 - R/load_enc.R | 4 - R/load_med.R | 2 R/load_notes.R | 2 R/load_prc.R |only R/load_rdt.R | 2 R/load_rfv.R | 2 README.md | 22 +++++--- inst/doc/Using_parseRPDR.R | 7 ++ inst/doc/Using_parseRPDR.Rmd | 19 +++++-- inst/doc/Using_parseRPDR.html | 114 ++++++++++++++++++++++-------------------- man/convert_dia.Rd | 2 man/convert_prc.Rd |only man/load_all.Rd | 8 +- man/load_base.Rd | 4 + man/load_dia.Rd | 4 - man/load_enc.Rd | 4 - man/load_med.Rd | 2 man/load_prc.Rd |only man/load_rdt.Rd | 2 man/load_rfv.Rd | 2 vignettes/Using_parseRPDR.Rmd | 19 +++++-- 33 files changed, 208 insertions(+), 137 deletions(-)
Title: Function that Creates a Heat Map from Hybridization Data
Description: Using hybrid data, this package created a vividly colored hybrid heat map.
The input is two files which are auto-selected.
The first file has three columns, the first two for pairs of species,
with the third column for the hybrid experiment code (an integer).
The second file is a list of code and their descriptions in two
columns. The output is a figure showing the hybrid heat map with a color legend.
Author: Matthew Cserhati
Maintainer: Matthew Cserhati <csmatyi@protonmail.com>
Diff between hybridogram versions 0.3.0 dated 2021-05-18 and 0.3.2 dated 2021-05-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/hybridogram.R | 20 +++++++------------- man/hybridogram.Rd | 6 +++--- 4 files changed, 17 insertions(+), 23 deletions(-)
Title: Decomposition of Bulk Expression with Single-Cell Sequencing
Description: Provides tools to accurately estimate cell type abundances
from heterogeneous bulk expression. A reference-based method utilizes
single-cell information to generate a signature matrix and transformation
of bulk expression for accurate regression based estimates. A marker-based
method utilizes known cell-specific marker genes to measure relative
abundances across samples.
For more details, see Jew and Alvarez et al (2019) <doi:10.1101/669911>.
Author: Brandon Jew [aut, cre],
Marcus Alvarez [aut]
Maintainer: Brandon Jew <brandon.jew@ucla.edu>
Diff between BisqueRNA versions 1.0.4 dated 2020-07-18 and 1.0.5 dated 2021-05-23
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- R/reference_based.R | 5 ++++- tests/testthat/test_ref_based.R | 3 ++- tests/testthat/test_utils.R | 12 ++++++------ 5 files changed, 21 insertions(+), 16 deletions(-)
Title: Semi-Supervised Classification, Regression and Clustering
Methods
Description: Providing a collection of techniques for semi-supervised
classification, regression and clustering. In semi-supervised problem, both labeled and unlabeled
data are used to train a classifier. The package includes a collection of
semi-supervised learning techniques: self-training, co-training, democratic,
decision tree, random forest, 'S3VM' ... etc, with a fairly intuitive interface
that is easy to use.
Author: Francisco Jesús Palomares Alabarce [aut, cre]
(<https://orcid.org/0000-0002-0499-7034>),
José Manuel Benítez [ctb] (<https://orcid.org/0000-0002-2346-0793>),
Isaac Triguero [ctb] (<https://orcid.org/0000-0002-0150-0651>),
Christoph Bergmeir [ctb] (<https://orcid.org/0000-0002-3665-9021>),
Mabel González [ctb] (<https://orcid.org/0000-0003-0152-444X>)
Maintainer: Francisco Jesús Palomares Alabarce <fpalomares@correo.ugr.es>
Diff between SSLR versions 0.9.3.1 dated 2021-01-10 and 0.9.3.2 dated 2021-05-23
DESCRIPTION | 6 MD5 | 26 NAMESPACE | 200 ++--- NEWS.md | 10 build/vignette.rds |binary inst/doc/classification.html | 396 ++-------- inst/doc/clustering.html | 252 ------ inst/doc/fit.html | 264 +----- inst/doc/introduction.html | 236 ----- inst/doc/models.html | 183 ---- inst/doc/regression.html | 310 +------ tests/testthat/test-EMLeastSquaresClassifierSSLR.R | 37 tests/testthat/test-EntropyRegularizedLogisticRegressionSSLR.R | 35 tests/testthat/test-USMLeastSquaresClassifierSSLR.R | 35 14 files changed, 413 insertions(+), 1577 deletions(-)
Title: Query Random User Data from the Random User Generator API
Description: Generate random user data from the Random User Generator API.
For more information, see <https://randomuser.me/>.
Author: Mohamed El Fodil Ihaddaden
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between radous versions 0.1.2 dated 2021-01-18 and 0.1.3 dated 2021-05-23
DESCRIPTION | 7 +++---- MD5 | 6 +++--- R/get_data.R | 2 +- tests/testthat/test-test_get_data.R | 6 +++--- 4 files changed, 10 insertions(+), 11 deletions(-)
Title: Selection of Statistically Similar Research Groups
Description: Select statistically similar research groups by backward selection using various robust algorithms, including a heuristic based on linear discriminant analysis, multiple heuristics based on the test statistic, and parallelized exhaustive search.
Author: Kyle Gorman [aut, cre],
Géza Kiss [aut]
Maintainer: Kyle Gorman <kylebgorman@gmail.com>
Diff between ldamatch versions 1.0.1 dated 2016-06-27 and 1.0.2 dated 2021-05-23
ldamatch-1.0.1/ldamatch/R/search_heuristic1.R |only ldamatch-1.0.1/ldamatch/man/search_heuristic1.Rd |only ldamatch-1.0.1/ldamatch/tests/testthat/test-compare_ldamatch_outputs.R |only ldamatch-1.0.2/ldamatch/DESCRIPTION | 22 ldamatch-1.0.2/ldamatch/MD5 | 121 - ldamatch-1.0.2/ldamatch/NAMESPACE | 8 ldamatch-1.0.2/ldamatch/R/estimate_exhaustive.R | 97 - ldamatch-1.0.2/ldamatch/R/evaluation.R | 111 + ldamatch-1.0.2/ldamatch/R/globals.R | 14 ldamatch-1.0.2/ldamatch/R/halting_tests.R | 26 ldamatch-1.0.2/ldamatch/R/helpers.R | 380 ++++ ldamatch-1.0.2/ldamatch/R/ldamatch.R | 242 +-- ldamatch-1.0.2/ldamatch/R/search_exhaustive.R | 93 - ldamatch-1.0.2/ldamatch/R/search_heuristic2.R | 44 ldamatch-1.0.2/ldamatch/R/search_heuristic3.R | 331 +--- ldamatch-1.0.2/ldamatch/R/search_heuristic4.R | 216 +- ldamatch-1.0.2/ldamatch/R/search_heuristic_with_lookahead.R |only ldamatch-1.0.2/ldamatch/R/search_random.R | 40 ldamatch-1.0.2/ldamatch/build/vignette.rds |binary ldamatch-1.0.2/ldamatch/inst/doc/ldamatch-demos.R | 45 ldamatch-1.0.2/ldamatch/inst/doc/ldamatch-demos.Rmd | 27 ldamatch-1.0.2/ldamatch/inst/doc/ldamatch-demos.html | 787 ++++++---- ldamatch-1.0.2/ldamatch/man/U_halt.Rd | 1 ldamatch-1.0.2/ldamatch/man/ad_halt.Rd | 1 ldamatch-1.0.2/ldamatch/man/calc_metrics.Rd | 19 ldamatch-1.0.2/ldamatch/man/calc_p_value.Rd | 1 ldamatch-1.0.2/ldamatch/man/compare_ldamatch_outputs.Rd | 23 ldamatch-1.0.2/ldamatch/man/create_halting_test.Rd | 3 ldamatch-1.0.2/ldamatch/man/dot-U_crit.Rd |only ldamatch-1.0.2/ldamatch/man/dot-ad_crit.Rd |only ldamatch-1.0.2/ldamatch/man/dot-apply_crit.Rd |only ldamatch-1.0.2/ldamatch/man/dot-apply_crit_to_condition_pairs.Rd |only ldamatch-1.0.2/ldamatch/man/dot-calc_multipliers.Rd |only ldamatch-1.0.2/ldamatch/man/dot-calc_p_thresh_ratio.Rd |only ldamatch-1.0.2/ldamatch/man/dot-calc_subject_balance_divergence.Rd |only ldamatch-1.0.2/ldamatch/man/dot-check_subspaces_for_group_size_setup.Rd |only ldamatch-1.0.2/ldamatch/man/dot-choose_best_subjects.Rd |only ldamatch-1.0.2/ldamatch/man/dot-choose_best_test_statistic.Rd |only ldamatch-1.0.2/ldamatch/man/dot-choose_most_frequently_chosen_subject_from_subject_tuples.Rd |only ldamatch-1.0.2/ldamatch/man/dot-choose_subject_with_best_p_value_from_subject_tuples.Rd |only ldamatch-1.0.2/ldamatch/man/dot-combine_sets.Rd |only ldamatch-1.0.2/ldamatch/man/dot-create_Cartesian_iterable.Rd |only ldamatch-1.0.2/ldamatch/man/dot-decrease_group_sizes.Rd |only ldamatch-1.0.2/ldamatch/man/dot-f_crit.Rd |only ldamatch-1.0.2/ldamatch/man/dot-flip_ind.Rd |only ldamatch-1.0.2/ldamatch/man/dot-foreach.Rd |only ldamatch-1.0.2/ldamatch/man/dot-get_halting_test.Rd |only ldamatch-1.0.2/ldamatch/man/dot-get_human_readable.Rd |only ldamatch-1.0.2/ldamatch/man/dot-get_if_args_are_missing.Rd |only ldamatch-1.0.2/ldamatch/man/dot-internally_compare_ldamatch_outputs.Rd |only ldamatch-1.0.2/ldamatch/man/dot-ks_crit.Rd |only ldamatch-1.0.2/ldamatch/man/dot-l_crit.Rd |only ldamatch-1.0.2/ldamatch/man/dot-normalize_max_removed_per_cond.Rd |only ldamatch-1.0.2/ldamatch/man/dot-normalize_props.Rd |only ldamatch-1.0.2/ldamatch/man/dot-recycle.Rd |only ldamatch-1.0.2/ldamatch/man/dot-search_heuristic_with_lookahead.Rd |only ldamatch-1.0.2/ldamatch/man/dot-sort_group_sizes.Rd |only ldamatch-1.0.2/ldamatch/man/dot-t_crit.Rd |only ldamatch-1.0.2/ldamatch/man/dot-tolerance.Rd |only ldamatch-1.0.2/ldamatch/man/dot-unique_list.Rd |only ldamatch-1.0.2/ldamatch/man/dot-vector_list_to_string.Rd |only ldamatch-1.0.2/ldamatch/man/dot-warn_about_extra_params.Rd |only ldamatch-1.0.2/ldamatch/man/estimate_exhaustive.Rd | 35 ldamatch-1.0.2/ldamatch/man/f_halt.Rd | 1 ldamatch-1.0.2/ldamatch/man/get_param.Rd | 5 ldamatch-1.0.2/ldamatch/man/ks_halt.Rd | 1 ldamatch-1.0.2/ldamatch/man/l_halt.Rd | 1 ldamatch-1.0.2/ldamatch/man/ldamatch.Rd | 2 ldamatch-1.0.2/ldamatch/man/match_groups.Rd | 71 ldamatch-1.0.2/ldamatch/man/matching_methods.Rd |only ldamatch-1.0.2/ldamatch/man/nondeterministic_matching_methods.Rd |only ldamatch-1.0.2/ldamatch/man/parallelized_matching_methods.Rd |only ldamatch-1.0.2/ldamatch/man/search_exhaustive.Rd | 25 ldamatch-1.0.2/ldamatch/man/search_heuristic2.Rd | 38 ldamatch-1.0.2/ldamatch/man/search_heuristic3.Rd | 57 ldamatch-1.0.2/ldamatch/man/search_heuristic4.Rd | 57 ldamatch-1.0.2/ldamatch/man/search_random.Rd | 32 ldamatch-1.0.2/ldamatch/man/set_param.Rd | 9 ldamatch-1.0.2/ldamatch/man/t_halt.Rd | 1 ldamatch-1.0.2/ldamatch/man/wilks_halt.Rd | 1 ldamatch-1.0.2/ldamatch/tests/testthat/test-ldamatch.R | 113 - ldamatch-1.0.2/ldamatch/vignettes/ldamatch-demos.Rmd | 27 82 files changed, 1970 insertions(+), 1158 deletions(-)
Title: High Dimensional Survival Data Analysis with Markov Chain Monte
Carlo
Description: High dimensional survival data analysis with Markov Chain Monte Carlo(MCMC).
Currently support frailty data analysis. Allows for Weibull and
Exponential distribution. Includes function for interval censored data.
Author: Atanu Bhattacharjee [aut, cre, ctb],
Akash Pawar [aut, ctb]
Maintainer: Atanu Bhattacharjee <atanustat@gmail.com>
Diff between SurviMChd versions 0.1.0 dated 2021-03-23 and 0.1.1 dated 2021-05-23
DESCRIPTION | 12 +-- MD5 | 40 +++++----- NAMESPACE | 6 - R/fraidm.R | 69 +++++++++--------- R/fraidpm.R | 122 ++++++++++++++++---------------- R/frairand.R | 115 ++++++++++++++++-------------- R/mcsurv.R | 10 +- R/survMC.R | 197 ++++++++++++++++++++++++----------------------------- R/survMCmulti.R |only R/survexpMC.R | 142 +++++++++++++++++++------------------- R/survintMC.R | 25 ++++-- R/survweibMC.R | 43 ++++------- data/mcsurv.rda |binary man/fraidm.Rd | 13 +-- man/fraidpm.Rd | 16 ++-- man/frairand.Rd | 16 ++-- man/mcsurv.Rd | 10 +- man/survMC.Rd | 16 ++-- man/survMCmulti.Rd |only man/survexpMC.Rd | 2 man/survintMC.Rd | 4 - man/survweibMC.Rd | 2 22 files changed, 431 insertions(+), 429 deletions(-)
Title: Seasonal Generalized Space Time Autoregressive (S-GSTAR) Model
Description: A set of function that implements for seasonal multivariate time series analysis based on Seasonal Generalized Space
Time Autoregressive with Seemingly Unrelated Regression (S-GSTAR-SUR) Model by Setiawan(2016)<https://www.researchgate.net/publication/316517889_S-GSTAR-SUR_model_for_seasonal_spatio_temporal_data_forecasting>.
Author: M. Yoga Satria Utama [aut, cre],
Ernawati Pasaribu [aut]
Maintainer: M. Yoga Satria Utama <221709801@stis.ac.id>
Diff between sgstar versions 0.1.1 dated 2021-01-28 and 0.1.2 dated 2021-05-23
DESCRIPTION | 8 ++-- MD5 | 10 ++--- NAMESPACE | 3 + R/plot_sgstar.R | 2 - R/predict_sgstar.R | 3 + R/sgstar.R | 97 +++++++++++++++++++++++++++++++++++++---------------- 6 files changed, 82 insertions(+), 41 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
<doi:10.1111/j.1538-4632.1995.tb00912.x>,
'saddlepoint' approximations ('Tiefelsdorf' 2002)
<doi:10.1111/j.1538-4632.2002.tb01084.x> and exact tests
for global and local 'Moran's I' ('Bivand et al.' 2009)
<doi:10.1016/j.csda.2008.07.021> and 'LOSH' local indicators
of spatial heteroscedasticity ('Ord' and 'Getis')
<doi:10.1007/s00168-011-0492-y>. The implementation of most of
the measures is described in 'Bivand' and 'Wong' (2018)
<doi:10.1007/s11749-018-0599-x>.
'spdep' >= 1.1-1 corresponds to 'spatialreg' >= 1.1-1, in which the model
fitting functions are deprecated and pass through to 'spatialreg', but
will mask those in 'spatialreg'. From versions 1.2-1, the functions will
be made defunct in 'spdep'.
For now 'spatialreg' only has functions from 'spdep', where they are shown
as deprecated. 'spatialreg' only loads the namespace of 'spdep'; if you
attach 'spdep', the same functions in the other package will be masked.
Some feed through adequately, others do not.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Angela Li [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Abhirup Mallik [ctb, trl],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Jeff Sauer [ctb],
Michael Tiefelsdorf [ctb],
René Westerholt [ctb],
Levi Wolf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.1-7 dated 2021-04-03 and 1.1-8 dated 2021-05-23
DESCRIPTION | 14 +++++++++----- MD5 | 38 ++++++++++++++++++++------------------ NAMESPACE | 3 +-- NEWS.md | 12 +++++++++++- R/cellneighbours.R | 14 +++++++++++++- R/localmoran.R | 37 +++++++++++++++++++++++++------------ R/poly2nb.R | 5 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/CO69.html | 16 ++++++++-------- inst/doc/nb.html | 19 ++++++++++--------- inst/doc/nb_igraph.html | 8 ++++---- inst/doc/nb_sf.html | 20 ++++++++++---------- inst/doc/sids.R | 7 ++++++- inst/doc/sids.Rmd | 7 ++++++- inst/doc/sids.html | 47 ++++++++++++++++++++++++++--------------------- inst/tinytest |only man/cell2nb.Rd | 44 +++++++++++++++++++++++++------------------- man/localmoran.Rd | 9 ++++++--- tests |only vignettes/sids.Rmd | 7 ++++++- 21 files changed, 189 insertions(+), 118 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Monte Carlo
Expectation Maximization, and some other tools. The nimbleFunction system makes
it easy to do things like implement new MCMC samplers from R, customize the
assignment of samplers to different parts of a model from R, and compile the
new samplers automatically via C++ alongside the samplers 'NIMBLE' provides.
'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New
distributions and functions can be added, including as calls to external
compiled code. Although most people think of MCMC as the main goal of the
'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing
arbitrary other kinds of model-generic algorithms as well. A full User Manual is
available at <https://r-nimble.org>.
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] (Bayesian nonparametrics system),
Abel Rodrìguez [aut] (Bayesian nonparametrics system),
Duncan Temple Lang [aut] (packaging configuration),
Sally Paganin [aut] (reversible jump MCMC),
Jagadish Babu [ctb] (code for the compilation system for an early
version of NIMBLE),
Lauren Ponisio [ctb] (contributions to the cross-validation code),
Peter Sujan [ctb] (multivariate t distribution code)
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.11.0 dated 2021-04-17 and 0.11.1 dated 2021-05-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/MCMC_samplers.R | 11 +++++++++-- inst/NEWS | 12 ++++++++++++ man/samplers.Rd | 12 +++++++++++- tests/testthat/test-mcmc.R | 36 ++++++++++++++++++++++++++++++++++++ 6 files changed, 77 insertions(+), 12 deletions(-)
Title: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines,
shortest path computation, bagged clustering, naive Bayes
classifier, generalized k-nearest neighbour ...
Author: David Meyer [aut, cre],
Evgenia Dimitriadou [aut, cph],
Kurt Hornik [aut],
Andreas Weingessel [aut],
Friedrich Leisch [aut],
Chih-Chung Chang [ctb, cph] (libsvm C++-code),
Chih-Chen Lin [ctb, cph] (libsvm C++-code)
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between e1071 versions 1.7-6 dated 2021-03-18 and 1.7-7 dated 2021-05-23
DESCRIPTION | 6 +-- MD5 | 14 ++++---- R/cshell.R | 78 +++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/NEWS.Rd | 6 +++ inst/doc/svmdoc.pdf |binary inst/doc/svminternals.pdf |binary man/cshell.Rd | 15 ++------ 8 files changed, 61 insertions(+), 58 deletions(-)
Title: Call 'BEAST2'
Description: 'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAST2' is a command-line tool.
This package provides a way to call 'BEAST2'
from an 'R' function call.
Author: Richèl J.C. Bilderbeek [aut, cre]
(<https://orcid.org/0000-0003-1107-7049>),
Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci,
see https://github.com/ropensci/onboarding/issues/209),
David Winter [rev] (David reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/209),
Jason Griffiths [ctb] (<https://orcid.org/0000-0002-1667-8233>),
Thijs Janzen [ctb]
Maintainer: Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>
Diff between beastier versions 2.2.1 dated 2020-10-30 and 2.4 dated 2021-05-23
beastier-2.2.1/beastier/R/beast2_internal_filenames_to_table.R |only beastier-2.2.1/beastier/R/check_beast2_internal_filenames.R |only beastier-2.2.1/beastier/R/create_beast2_internal_filenames.R |only beastier-2.2.1/beastier/R/print_beast2_internal_filenames.R |only beastier-2.2.1/beastier/R/update_beastier.R |only beastier-2.2.1/beastier/man/beast2_internal_filenames_to_table.Rd |only beastier-2.2.1/beastier/man/check_beast2_internal_filenames.Rd |only beastier-2.2.1/beastier/man/check_beast2_internal_filenames_data_types.Rd |only beastier-2.2.1/beastier/man/check_beast2_internal_filenames_filenames_differ.Rd |only beastier-2.2.1/beastier/man/check_beast2_internal_filenames_names.Rd |only beastier-2.2.1/beastier/man/create_beast2_internal_filenames.Rd |only beastier-2.2.1/beastier/man/print_beast2_internal_filenames.Rd |only beastier-2.2.1/beastier/man/update_beastier.Rd |only beastier-2.4/beastier/DESCRIPTION | 17 beastier-2.4/beastier/MD5 | 137 ++-- beastier-2.4/beastier/NAMESPACE | 22 beastier-2.4/beastier/R/add_quotes_if_has_spaces.R |only beastier-2.4/beastier/R/are_beast2_input_lines.R | 2 beastier-2.4/beastier/R/are_identical_alignments.R | 4 beastier-2.4/beastier/R/beastier_report.R | 10 beastier-2.4/beastier/R/check_beast2.R | 4 beastier-2.4/beastier/R/check_beast2_options_do_not_overwrite_existing_files.R | 11 beastier-2.4/beastier/R/check_can_create_dir_for_state_output_file.R |only beastier-2.4/beastier/R/check_can_create_screenlog_file.R |only beastier-2.4/beastier/R/check_can_create_state_output_file.R |only beastier-2.4/beastier/R/check_can_create_tracelog_file.R |only beastier-2.4/beastier/R/check_can_create_treelog_file.R |only beastier-2.4/beastier/R/check_input_filename.R | 48 + beastier-2.4/beastier/R/continue_beast2.R |only beastier-2.4/beastier/R/create_beast2_continue_cmd_from_options.R |only beastier-2.4/beastier/R/create_beast2_run_cmd.R | 55 - beastier-2.4/beastier/R/create_beast2_run_cmd_from_options.R |only beastier-2.4/beastier/R/create_beast2_validate_cmd.R | 14 beastier-2.4/beastier/R/create_beast2_version_cmd.R | 2 beastier-2.4/beastier/R/create_random_alignment.R | 4 beastier-2.4/beastier/R/create_random_fasta.R | 4 beastier-2.4/beastier/R/create_random_phylogeny.R | 2 beastier-2.4/beastier/R/create_temp_input_filename.R | 2 beastier-2.4/beastier/R/create_temp_state_filename.R | 13 beastier-2.4/beastier/R/default_params_doc.R | 4 beastier-2.4/beastier/R/get_beast2_example_filename.R | 2 beastier-2.4/beastier/R/get_beast2_example_filenames.R | 6 beastier-2.4/beastier/R/get_beast2_version.R | 2 beastier-2.4/beastier/R/get_default_beast2_folder.R | 2 beastier-2.4/beastier/R/get_default_java_path.R | 2 beastier-2.4/beastier/R/gives_beast2_warning.R | 4 beastier-2.4/beastier/R/install_beast2.R | 68 -- beastier-2.4/beastier/R/is_beast2_input_file.R | 12 beastier-2.4/beastier/R/is_beast2_installed.R | 2 beastier-2.4/beastier/R/is_bin_path.R | 2 beastier-2.4/beastier/R/is_on_ci.R | 8 beastier-2.4/beastier/R/run_beast2_from_options.R | 72 -- beastier-2.4/beastier/R/uninstall_beast2.R | 37 - beastier-2.4/beastier/R/upgrade_beast2.R | 22 beastier-2.4/beastier/build/vignette.rds |binary beastier-2.4/beastier/inst/WORDLIST | 5 beastier-2.4/beastier/inst/doc/demo.R | 4 beastier-2.4/beastier/inst/doc/demo.Rmd | 12 beastier-2.4/beastier/inst/doc/demo.html | 300 ++++------ beastier-2.4/beastier/man/add_quotes_if_has_spaces.Rd |only beastier-2.4/beastier/man/check_beast2.Rd | 2 beastier-2.4/beastier/man/check_beast2_options_do_not_overwrite_existing_files.Rd | 9 beastier-2.4/beastier/man/check_can_create_dir_for_state_output_file.Rd |only beastier-2.4/beastier/man/check_can_create_screenlog_file.Rd |only beastier-2.4/beastier/man/check_can_create_state_output_file.Rd |only beastier-2.4/beastier/man/check_can_create_tracelog_file.Rd |only beastier-2.4/beastier/man/check_can_create_treelog_file.Rd |only beastier-2.4/beastier/man/check_input_filename_validity.Rd |only beastier-2.4/beastier/man/continue_beast2.Rd |only beastier-2.4/beastier/man/create_beast2_continue_cmd_from_options.Rd |only beastier-2.4/beastier/man/create_beast2_run_cmd.Rd | 6 beastier-2.4/beastier/man/create_beast2_run_cmd_from_options.Rd |only beastier-2.4/beastier/man/create_random_alignment.Rd |only beastier-2.4/beastier/man/create_random_fasta.Rd |only beastier-2.4/beastier/man/create_random_phylogeny.Rd |only beastier-2.4/beastier/man/default_params_doc.Rd | 5 beastier-2.4/beastier/man/figures/GitHubActions.png |only beastier-2.4/beastier/man/get_default_beast2_folder.Rd | 2 beastier-2.4/beastier/man/gives_beast2_warning.Rd | 2 beastier-2.4/beastier/man/install_beast2.Rd | 10 beastier-2.4/beastier/man/is_beast2_installed.Rd | 2 beastier-2.4/beastier/man/is_on_appveyor.Rd | 2 beastier-2.4/beastier/man/is_on_ci.Rd | 2 beastier-2.4/beastier/man/is_on_travis.Rd | 4 beastier-2.4/beastier/man/is_win_bin_path.Rd |only beastier-2.4/beastier/man/uninstall_beast2.Rd | 9 beastier-2.4/beastier/man/upgrade_beast2.Rd | 4 beastier-2.4/beastier/vignettes/demo.Rmd | 12 88 files changed, 436 insertions(+), 552 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-27 0.4.7
2021-02-21 0.4.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-01 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-03 0.1.0
Title: Tabulate Descriptive Statistics in Multiple Formats
Description: Creates a table of descriptive statistics
for factor and numeric columns in a data frame. Displays
these by groups, if any. Highly customizable, with support
for 'html' and 'pdf' provided by 'kableExtra'. Respects
original column order, column labels, and factor level order.
See ?tablet.data.frame and vignettes.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between tablet versions 0.2.7 dated 2021-02-26 and 0.2.9 dated 2021-05-23
DESCRIPTION | 14 ++++++++------ MD5 | 21 ++++++++++++++++----- NAMESPACE | 1 + R/mesa.R |only build/vignette.rds |binary inst/doc/tablet-introduction-html.html | 4 ++-- inst/doc/tablet-introduction-pdf.pdf |binary inst/shiny-examples |only man/mesa.Rd |only 9 files changed, 27 insertions(+), 13 deletions(-)
Title: Create Useful Summaries of the Portal Data
Description: Download and generate summaries for the rodent,
plant, ant, and weather data from the Portal Project. Portal is a
long-term (and ongoing) experimental monitoring site in the Chihuahua
desert. The raw data files can be found at
<https://github.com/weecology/portaldata>.
Author: Glenda M. Yenni [aut, cre] (<https://orcid.org/0000-0001-6969-1848>),
Hao Ye [aut] (<https://orcid.org/0000-0002-8630-1458>),
Erica M. Christensen [aut] (<https://orcid.org/0000-0002-5635-2502>),
Juniper L. Simonis [aut] (<https://orcid.org/0000-0001-9798-0460>),
Ellen K. Bledsoe [aut] (<https://orcid.org/0000-0002-3629-7235>),
Renata M. Diaz [aut] (<https://orcid.org/0000-0003-0803-4734>),
Shawn D. Taylor [aut] (<https://orcid.org/0000-0002-6178-6903>),
Ethan P, White [aut] (<https://orcid.org/0000-0001-6728-7745>),
S.K. Morgan Ernest [aut] (<https://orcid.org/0000-0002-6026-8530>),
Weecology [cph]
Maintainer: Glenda M. Yenni <glenda@weecology.org>
Diff between portalr versions 0.3.7 dated 2021-01-27 and 0.3.8 dated 2021-05-23
DESCRIPTION | 7 - MD5 | 52 ++++++------ NAMESPACE | 1 R/download_data.R | 7 - R/load_data.R | 22 ----- R/process_rodent_data.R | 20 +++- R/season_function.R | 5 - R/summarize_individual_rodents.R | 3 R/summarize_plants.R | 4 R/summarize_rodents.R | 31 +++---- README.md | 108 +++++++++++-------------- build/vignette.rds |binary inst/doc/portal_researcher_examples.Rmd | 2 inst/doc/portal_researcher_examples.html | 15 ++- inst/doc/rodent-abundance-demo.Rmd | 4 inst/doc/rodent-abundance-demo.html | 25 +++-- man/add_seasons.Rd | 6 - man/download_observations.Rd | 7 - man/load_datafile.Rd | 5 - man/load_rodent_data.Rd | 14 --- man/summarize_plant_data.Rd | 5 - man/summarize_rodent_data.Rd | 19 +--- tests/testthat/test-03-summarize-rodents.R | 19 ++++ tests/testthat/test-05-individual-stake-data.R | 10 +- tests/testthat/test-99-regression.R | 9 ++ vignettes/portal_researcher_examples.Rmd | 2 vignettes/rodent-abundance-demo.Rmd | 4 27 files changed, 189 insertions(+), 217 deletions(-)
Title: R Interface for the 'H2O' Scalable Machine Learning Platform
Description: R interface for 'H2O', the scalable open source machine learning
platform that offers parallelized implementations of many supervised and
unsupervised machine learning algorithms such as Generalized Linear
Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests,
Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes,
Generalized Additive Models (GAM), Cox Proportional Hazards, K-Means, PCA,
Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
Author: Erin LeDell [aut, cre],
Navdeep Gill [aut],
Spencer Aiello [aut],
Anqi Fu [aut],
Arno Candel [aut],
Cliff Click [aut],
Tom Kraljevic [aut],
Tomas Nykodym [aut],
Patrick Aboyoun [aut],
Michal Kurka [aut],
Michal Malohlava [aut],
Ludi Rehak [ctb],
Eric Eckstrand [ctb],
Brandon Hill [ctb],
Sebastian Vidrio [ctb],
Surekha Jadhawani [ctb],
Amy Wang [ctb],
Raymond Peck [ctb],
Wendy Wong [ctb],
Jan Gorecki [ctb],
Matt Dowle [ctb],
Yuan Tang [ctb],
Lauren DiPerna [ctb],
Tomas Fryda [ctb],
H2O.ai [cph, fnd]
Maintainer: Erin LeDell <erin@h2o.ai>
Diff between h2o versions 3.32.1.2 dated 2021-05-06 and 3.32.1.3 dated 2021-05-23
DESCRIPTION | 8 +++---- MD5 | 18 +++++++-------- NAMESPACE | 1 R/connection.R | 28 +++++------------------- R/explain.R | 34 ----------------------------- R/models.R | 15 +++++++++++-- R/zzz.R | 56 +++++++++++++++++++++++++++++++++++++++++++++++++ inst/buildnum.txt | 2 - man/h2o-package.Rd | 4 +-- man/h2o.performance.Rd | 6 ++++- 10 files changed, 97 insertions(+), 75 deletions(-)
Title: A Small Collection of Fish Population Datasets
Description: A collection of four datasets
based around the population dynamics of migratory fish. Datasets
contain both basic size information on a per fish basis, as well as
otolith data that contains a per day record of fish growth history.
All data in this package was collected by the author, from
2015-2016, in the Wellington region of New Zealand.
Author: Conor Neilson [aut, cre]
Maintainer: Conor Neilson <condwanaland@gmail.com>
Diff between fishdata versions 0.1.3 dated 2018-02-13 and 1.0.1 dated 2021-05-23
fishdata-0.1.3/fishdata/R/adult_growths.R |only fishdata-0.1.3/fishdata/R/adult_morphologies.R |only fishdata-0.1.3/fishdata/R/juvenile_growths.R |only fishdata-0.1.3/fishdata/R/juvenile_morphologies.R |only fishdata-0.1.3/fishdata/data/adult_growths.rda |only fishdata-0.1.3/fishdata/data/adult_morphologies.rda |only fishdata-0.1.3/fishdata/data/juvenile_growths.rda |only fishdata-0.1.3/fishdata/data/juvenile_morphologies.rda |only fishdata-0.1.3/fishdata/inst/doc/Using_fishdata.R |only fishdata-0.1.3/fishdata/inst/doc/Using_fishdata.Rmd |only fishdata-0.1.3/fishdata/inst/doc/Using_fishdata.html |only fishdata-0.1.3/fishdata/man/adult_growths.Rd |only fishdata-0.1.3/fishdata/man/adult_morphologies.Rd |only fishdata-0.1.3/fishdata/man/juvenile_growths.Rd |only fishdata-0.1.3/fishdata/man/juvenile_morphologies.Rd |only fishdata-0.1.3/fishdata/vignettes/Using_fishdata.Rmd |only fishdata-1.0.1/fishdata/DESCRIPTION | 11 ++- fishdata-1.0.1/fishdata/MD5 | 48 +++++++++------- fishdata-1.0.1/fishdata/NAMESPACE | 3 - fishdata-1.0.1/fishdata/R/adult_growth.R |only fishdata-1.0.1/fishdata/R/adult_metrics.R |only fishdata-1.0.1/fishdata/R/adults.R |only fishdata-1.0.1/fishdata/R/juvenile_growth.R |only fishdata-1.0.1/fishdata/R/juvenile_metrics.R |only fishdata-1.0.1/fishdata/R/juveniles.R |only fishdata-1.0.1/fishdata/build/vignette.rds |binary fishdata-1.0.1/fishdata/data/adult_growth.rda |only fishdata-1.0.1/fishdata/data/adult_metrics.rda |only fishdata-1.0.1/fishdata/data/adults.rda |only fishdata-1.0.1/fishdata/data/juvenile_growth.rda |only fishdata-1.0.1/fishdata/data/juvenile_metrics.rda |only fishdata-1.0.1/fishdata/data/juveniles.rda |only fishdata-1.0.1/fishdata/inst/doc/Data-Model.R |only fishdata-1.0.1/fishdata/inst/doc/Data-Model.Rmd |only fishdata-1.0.1/fishdata/inst/doc/Data-Model.html |only fishdata-1.0.1/fishdata/inst/doc/fishdata-examples.R |only fishdata-1.0.1/fishdata/inst/doc/fishdata-examples.Rmd |only fishdata-1.0.1/fishdata/inst/doc/fishdata-examples.html |only fishdata-1.0.1/fishdata/man/adult_growth.Rd |only fishdata-1.0.1/fishdata/man/adult_metrics.Rd |only fishdata-1.0.1/fishdata/man/adults.Rd |only fishdata-1.0.1/fishdata/man/juvenile_growth.Rd |only fishdata-1.0.1/fishdata/man/juvenile_metrics.Rd |only fishdata-1.0.1/fishdata/man/juveniles.Rd |only fishdata-1.0.1/fishdata/vignettes/Data-Model.Rmd |only fishdata-1.0.1/fishdata/vignettes/fishdata-examples.Rmd |only 46 files changed, 37 insertions(+), 25 deletions(-)
Title: 'BEAUti' from R
Description: 'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAUti 2' (which is part of 'BEAST2') is a GUI tool
that allows users to specify the many possible setups
and generates the XML file 'BEAST2' needs to run.
This package provides a way to create 'BEAST2' input
files without active user input, but using
R function calls instead.
Author: Richèl J.C. Bilderbeek [aut, cre]
(<https://orcid.org/0000-0003-1107-7049>),
Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci,
see https://github.com/ropensci/onboarding/issues/209),
David Winter [rev] (David reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/209),
Paul Van Els [ctb] (<https://orcid.org/0000-0002-9499-8873>),
Raphael Scherrer [ctb] (<https://orcid.org/0000-0002-1447-7630>),
Yacine B. Chehida [ctb] (<https://orcid.org/0000-0001-7269-9082>),
Katharine S. Walter [ctb] (<https://orcid.org/0000-0003-0065-2204>),
Gary Napier [ctb] (<https://orcid.org/0000-0002-1077-0055>),
Jason Griffiths [ctb] (<https://orcid.org/0000-0002-1667-8233>),
Thijs Janzen [ctb] (<https://orcid.org/0000-0002-4162-1140>),
Jana Riederer [ctb] (<https://orcid.org/0000-0001-6951-9984>)
Maintainer: Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>
Diff between beautier versions 2.5.2 dated 2021-05-22 and 2.6 dated 2021-05-23
DESCRIPTION | 6 MD5 | 172 +++++----- NAMESPACE | 1 R/beautier.R | 3 R/create_beast2_input_file.R | 4 R/create_beast2_input_file_from_model.R | 4 R/create_clock_model.R | 124 +++---- R/create_distr.R | 214 ++++++------ R/create_gamma_site_model.R | 18 - R/create_inference_model.R | 4 R/create_mcmc.R | 4 R/create_mcmc_nested_sampling.R | 28 - R/create_param.R | 486 ++++++++++++++--------------- R/create_site_model.R | 55 +-- R/create_temp_screenlog_filename.R | 3 R/create_temp_tracelog_filename.R | 3 R/create_temp_treelog_filename.R | 3 R/create_test_inference_model.R | 3 R/create_test_mcmc.R | 3 R/create_test_ns_mcmc.R | 6 R/create_tree_prior.R | 169 +++++----- R/get_beautier_tempfilename.R |only R/get_remove_hex_fun.R | 3 R/get_test_filenames.R | 14 inst/WORDLIST | 2 inst/doc/demo.R | 5 inst/doc/demo.Rmd | 9 inst/doc/demo.html | 9 inst/doc/inference_models.R | 6 inst/doc/inference_models.Rmd | 7 inst/doc/inference_models.html | 15 man/beautier.Rd | 3 man/create_alpha_param.Rd | 30 - man/create_bd_tree_prior.Rd | 36 +- man/create_beast2_input_file.Rd | 4 man/create_beast2_input_file_from_model.Rd | 4 man/create_beta_distr.Rd | 18 - man/create_beta_param.Rd | 30 - man/create_cbs_tree_prior.Rd | 16 man/create_ccp_tree_prior.Rd | 16 man/create_cep_tree_prior.Rd | 16 man/create_clock_model.Rd | 32 - man/create_clock_rate_param.Rd | 30 - man/create_distr.Rd | 20 - man/create_exp_distr.Rd | 18 - man/create_gamma_distr.Rd | 28 - man/create_gamma_site_model.Rd | 18 - man/create_gtr_site_model.Rd | 30 - man/create_hky_site_model.Rd | 5 man/create_inference_model.Rd | 4 man/create_inv_gamma_distr.Rd | 18 - man/create_jc69_site_model.Rd | 4 man/create_lambda_param.Rd | 30 - man/create_laplace_distr.Rd | 18 - man/create_log_normal_distr.Rd | 18 - man/create_m_param.Rd | 30 - man/create_mcmc.Rd | 4 man/create_mean_param.Rd | 30 - man/create_mu_param.Rd | 30 - man/create_normal_distr.Rd | 18 - man/create_ns_mcmc.Rd | 28 - man/create_one_div_x_distr.Rd | 18 - man/create_param.Rd | 30 - man/create_poisson_distr.Rd | 18 - man/create_rate_ac_param.Rd | 22 - man/create_rate_ag_param.Rd | 22 - man/create_rate_at_param.Rd | 22 - man/create_rate_cg_param.Rd | 22 - man/create_rate_ct_param.Rd | 22 - man/create_rate_gt_param.Rd | 22 - man/create_rln_clock_model.Rd | 36 +- man/create_s_param.Rd | 30 - man/create_scale_param.Rd | 30 - man/create_sigma_param.Rd | 30 - man/create_site_model.Rd | 12 man/create_strict_clock_model.Rd | 42 +- man/create_test_inference_model.Rd | 3 man/create_test_mcmc.Rd | 3 man/create_test_ns_mcmc.Rd | 6 man/create_tn93_site_model.Rd | 4 man/create_tree_prior.Rd | 70 ++-- man/create_uniform_distr.Rd | 18 - man/create_yule_tree_prior.Rd | 3 man/get_beautier_tempfilename.Rd |only man/get_fasta_filename.Rd | 14 man/get_remove_hex_fun.Rd | 3 vignettes/demo.Rmd | 9 vignettes/inference_models.Rmd | 7 88 files changed, 1283 insertions(+), 1204 deletions(-)