R Under development (unstable) (2023-08-30 r85030 ucrt) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(aphylo) Loading required package: ape > > # Just for testing > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + expect_output <- function(x, pattern) { + + ans <- paste(capture.output(eval(x)), collapse = "\n") + test <- grepl(pattern, ans) + + tinytest::tinytest( + result = test, + call = sys.call(sys.parent(1)), + diff = paste("Expected:", pattern, ". Returned:", ans) + ) + } + + expect_lt <- function(a,b) { + + tinytest::tinytest( + result = a < b, + call = sys.call(sys.parent(1)), + diff = paste("b - a = ", b - a) + ) + + } + + expect_length <- function(x,n) { + + tinytest::tinytest( + result = length(x) == n, + call = sys.call(sys.parent(1)), + diff = paste("length(x) = ", length(x), " but expected ", n) + ) + + } + + + tinytest::test_package("aphylo") + } test-aphylo-ape-info.r........ 0 tests test-aphylo-ape-info.r........ 0 tests test-aphylo-ape-info.r........ 0 tests test-aphylo-ape-info.r........ 0 tests test-aphylo-ape-info.r........ 0 tests test-aphylo-ape-info.r........ 1 tests OK test-aphylo-ape-info.r........ 2 tests OK test-aphylo-ape-info.r........ 3 tests OK test-aphylo-ape-info.r........ 4 tests OK test-aphylo-ape-info.r........ 5 tests OK test-aphylo-ape-info.r........ 6 tests OK test-aphylo-ape-info.r........ 7 tests OK test-aphylo-ape-info.r........ 8 tests OK test-aphylo-ape-info.r........ 9 tests OK test-aphylo-ape-info.r........ 10 tests OK test-aphylo-ape-info.r........ 11 tests OK test-aphylo-ape-info.r........ 12 tests OK test-aphylo-ape-info.r........ 13 tests OK test-aphylo-ape-info.r........ 14 tests OK test-aphylo-ape-info.r........ 15 tests OK test-aphylo-ape-info.r........ 16 tests OK test-aphylo-ape-info.r........ 17 tests OK test-aphylo-ape-info.r........ 18 tests OK 0.1s test-aphylo_from_data_frame.R. 0 tests test-aphylo_from_data_frame.R. 0 tests test-aphylo_from_data_frame.R. 0 tests test-aphylo_from_data_frame.R. 0 tests test-aphylo_from_data_frame.R. 0 tests test-aphylo_from_data_frame.R. 0 tests test-aphylo_from_data_frame.R. 0 tests test-aphylo_from_data_frame.R. 0 tests test-aphylo_from_data_frame.R. 0 tests test-aphylo_from_data_frame.R. 0 tests test-aphylo_from_data_frame.R. 1 tests OK test-aphylo_from_data_frame.R. 1 tests OK test-aphylo_from_data_frame.R. 1 tests OK test-aphylo_from_data_frame.R. 2 tests OK test-aphylo_from_data_frame.R. 3 tests OK test-aphylo_from_data_frame.R. 4 tests OK test-aphylo_from_data_frame.R. 4 tests OK test-aphylo_from_data_frame.R. 5 tests OK test-aphylo_from_data_frame.R. 5 tests OK test-aphylo_from_data_frame.R. 5 tests OK test-aphylo_from_data_frame.R. 5 tests OK test-aphylo_from_data_frame.R. 5 tests OK test-aphylo_from_data_frame.R. 6 tests OK 27ms test-auc.r.................... 0 tests test-auc.r.................... 0 tests test-auc.r.................... 0 tests test-auc.r.................... 0 tests test-auc.r.................... 0 tests test-auc.r.................... 0 tests test-auc.r.................... 1 tests OK 16ms test-balance.r................ 0 tests test-balance.r................ 0 tests test-balance.r................ 0 tests test-balance.r................ 1 tests OK test-balance.r................ 1 tests OK test-balance.r................ 2 tests OK test-balance.r................ 2 tests OK test-balance.r................ 3 tests OK test-balance.r................ 4 tests OK 4ms test-cv.R..................... 0 tests test-cv.R..................... 0 tests Convergence has been reached with 500 steps. avg Geweke's Z: -1.6070. (50 final count of samples). -------------------------------------------------------------------------------- Leave-one-out cross validation of aphylo model with 20 cases 1 done... 2 done... 3 done... 4 done... 5 done... 6 done... 7 done... 8 done... 9 done... 10 done... 11 done... 12 done... 13 done... 14 done... 15 done... 16 done... 17 done... 18 done... 19 done... 20 done... test-cv.R..................... 0 tests Convergence has been reached with 500 steps. avg Geweke's Z: -1.8159. (50 final count of samples). test-cv.R..................... 0 tests test-cv.R..................... 1 tests OK test-cv.R..................... 1 tests OK test-cv.R..................... 2 tests OK test-cv.R..................... 2 tests OK test-cv.R..................... 2 tests OK Convergence has been reached with 500 steps. avg Geweke's Z: 0.4760. (50 final count of samples). -------------------------------------------------------------------------------- Leave-one-out cross validation of aphylo model with 2 cases 1 done... 2 done... test-cv.R..................... 2 tests OK Convergence has been reached with 500 steps. avg Geweke's Z: 0.9530. (50 final count of samples). test-cv.R..................... 2 tests OK 3.3s test-data-management.r........ 0 tests test-data-management.r........ 0 tests test-data-management.r........ 0 tests test-data-management.r........ 0 tests test-data-management.r........ 1 tests OK test-data-management.r........ 2 tests OK test-data-management.r........ 3 tests OK test-data-management.r........ 4 tests OK test-data-management.r........ 5 tests OK test-data-management.r........ 5 tests OK test-data-management.r........ 5 tests OK test-data-management.r........ 5 tests OK test-data-management.r........ 5 tests OK test-data-management.r........ 6 tests OK 54ms test-formula.r................ 0 tests test-formula.r................ 0 tests test-formula.r................ 0 tests test-formula.r................ 0 tests test-formula.r................ 0 tests test-formula.r................ 0 tests test-formula.r................ 1 tests OK test-formula.r................ 2 tests OK test-formula.r................ 2 tests OK test-formula.r................ 2 tests OK test-formula.r................ 3 tests OK test-formula.r................ 3 tests OK test-formula.r................ 4 tests OK test-formula.r................ 5 tests OK test-formula.r................ 6 tests OK test-formula.r................ 7 tests OK test-formula.r................ 8 tests OK test-formula.r................ 8 tests OK test-formula.r................ 8 tests OK test-formula.r................ 8 tests OK test-formula.r................ 8 tests OK test-formula.r................ 9 tests OK test-formula.r................ 10 tests OK 0.2s test-impute_duplications.R.... 0 tests test-impute_duplications.R.... 0 tests test-impute_duplications.R.... 0 tests test-impute_duplications.R.... 0 tests test-impute_duplications.R.... 0 tests test-impute_duplications.R.... 0 tests test-impute_duplications.R.... 0 tests test-impute_duplications.R.... 1 tests OK 36ms test-indexing.R............... 0 tests test-indexing.R............... 0 tests test-indexing.R............... 1 tests OK test-indexing.R............... 2 tests OK test-indexing.R............... 3 tests OK test-indexing.R............... 4 tests OK test-indexing.R............... 5 tests OK test-indexing.R............... 6 tests OK test-indexing.R............... 7 tests OK test-indexing.R............... 8 tests OK test-indexing.R............... 8 tests OK 19ms test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 0 tests test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 1 tests OK test-loglikelihood.r.......... 2 tests OK test-loglikelihood.r.......... 2 tests OK test-loglikelihood.r.......... 2 tests OK test-loglikelihood.r.......... 2 tests OK test-loglikelihood.r.......... 2 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 3 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 4 tests OK test-loglikelihood.r.......... 5 tests OK test-loglikelihood.r.......... 5 tests OK test-loglikelihood.r.......... 5 tests OK test-loglikelihood.r.......... 6 tests OK 45ms test-panther.r................ 0 tests test-panther.r................ 0 tests test-panther.r................ 1 tests OK test-panther.r................ 2 tests OK 18ms test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 0 tests test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 1 tests OK test-parameter-estimates-and-formulas.r 2 tests OK 3.1s test-parameter-estimates.r.... 0 tests test-parameter-estimates.r.... 0 tests test-parameter-estimates.r.... 0 tests test-parameter-estimates.r.... 0 tests test-parameter-estimates.r.... 0 tests test-parameter-estimates.r.... 0 tests test-parameter-estimates.r.... 0 tests test-parameter-estimates.r.... 0 tests test-parameter-estimates.r.... 0 tests test-parameter-estimates.r.... 1 tests OK test-parameter-estimates.r.... 2 tests OK test-parameter-estimates.r.... 3 tests OK test-parameter-estimates.r.... 4 tests OK test-parameter-estimates.r.... 5 tests OK test-parameter-estimates.r.... 5 tests OK test-parameter-estimates.r.... 6 tests OK test-parameter-estimates.r.... 7 tests OK test-parameter-estimates.r.... 8 tests OK test-parameter-estimates.r.... 9 tests OK test-parameter-estimates.r.... 10 tests OK test-parameter-estimates.r.... 11 tests OK test-parameter-estimates.r.... 11 tests OK test-parameter-estimates.r.... 11 tests OK test-parameter-estimates.r.... 11 tests OK test-parameter-estimates.r.... 11 tests OK test-parameter-estimates.r.... 11 tests OK test-parameter-estimates.r.... 12 tests OK test-parameter-estimates.r.... 13 tests OK test-parameter-estimates.r.... 13 tests OK test-parameter-estimates.r.... 13 tests OK test-parameter-estimates.r.... 13 tests OK test-parameter-estimates.r.... 13 tests OK test-parameter-estimates.r.... 13 tests OK test-parameter-estimates.r.... 13 tests OK Convergence has been reached with 5000 steps. avg Geweke's Z: -0.2919. (400 final count of samples). test-parameter-estimates.r.... 13 tests OK Convergence has been reached with 5000 steps. Gelman-Rubin's R: 1.0076. (400 final count of samples). test-parameter-estimates.r.... 13 tests OK test-parameter-estimates.r.... 13 tests OK test-parameter-estimates.r.... 14 tests OK 10.8s test-plot_loglike.r........... 0 tests test-plot_loglike.r........... 0 tests test-plot_loglike.r........... 1 tests OK test-plot_loglike.r........... 1 tests OK test-plot_loglike.r........... 2 tests OK 0.1s test-predict.r................ 0 tests test-predict.r................ 0 tests test-predict.r................ 0 tests test-predict.r................ 0 tests test-predict.r................ 0 tests test-predict.r................ 0 tests test-predict.r................ 0 tests test-predict.r................ 0 tests test-predict.r................ 0 tests test-predict.r................ 0 tests test-predict.r................ 0 tests test-predict.r................ 1 tests OK test-predict.r................ 2 tests OK test-predict.r................ 2 tests OK test-predict.r................ 2 tests OK test-predict.r................ 2 tests OK test-predict.r................ 2 tests OK test-predict.r................ 3 tests OK test-predict.r................ 3 tests OK test-predict.r................ 3 tests OK test-predict.r................ 3 tests OK No convergence yet (steps count: 2000). Gelman-Rubin's R: 1.6654. Trying with the next bulk. No convergence reached after 2000 steps (200 final count of samples). test-predict.r................ 3 tests OK test-predict.r................ 3 tests OK test-predict.r................ 3 tests OK test-predict.r................ 4 tests OK test-predict.r................ 5 tests OK test-predict.r................ 5 tests OK test-predict.r................ 5 tests OK test-predict.r................ 5 tests OK test-predict.r................ 5 tests OK test-predict.r................ 5 tests OK test-predict.r................ 5 tests OK test-predict.r................ 5 tests OK test-predict.r................ 6 tests OK test-predict.r................ 7 tests OK test-predict.r................ 8 tests OK test-predict.r................ 8 tests OK test-predict.r................ 8 tests OK test-predict.r................ 8 tests OK test-predict.r................ 9 tests OK test-predict.r................ 9 tests OK test-predict.r................ 10 tests OK test-predict.r................ 10 tests OK test-predict.r................ 10 tests OK test-predict.r................ 10 tests OK test-predict.r................ 10 tests OK test-predict.r................ 10 tests OK test-predict.r................ 11 tests OK test-predict.r................ 11 tests OK test-predict.r................ 11 tests OK No convergence yet (steps count: 2000). Gelman-Rubin's R: 1.1898. Trying with the next bulk. No convergence reached after 2000 steps (200 final count of samples). test-predict.r................ 11 tests OK test-predict.r................ 11 tests OK test-predict.r................ 11 tests OK test-predict.r................ 11 tests OK test-predict.r................ 11 tests OK test-predict.r................ 11 tests OK test-predict.r................ 11 tests OK test-predict.r................ 12 tests OK test-predict.r................ 12 tests OK test-predict.r................ 12 tests OK test-predict.r................ 13 tests OK test-predict.r................ 14 tests OK test-predict.r................ 15 tests OK 3.7s test-pseq-reduce.r............ 0 tests test-pseq-reduce.r............ 0 tests test-pseq-reduce.r............ 0 tests test-pseq-reduce.r............ 0 tests test-pseq-reduce.r............ 0 tests Convergence has been reached with 1000 steps. avg Geweke's Z: 4.1968. (100 final count of samples). test-pseq-reduce.r............ 0 tests test-pseq-reduce.r............ 0 tests Convergence has been reached with 1000 steps. avg Geweke's Z: 4.1968. (100 final count of samples). test-pseq-reduce.r............ 0 tests test-pseq-reduce.r............ 1 tests OK test-pseq-reduce.r............ 1 tests OK Convergence has been reached with 1000 steps. avg Geweke's Z: 4.6070. (100 final count of samples). test-pseq-reduce.r............ 1 tests OK test-pseq-reduce.r............ 1 tests OK Convergence has been reached with 1000 steps. avg Geweke's Z: 4.6070. (100 final count of samples). test-pseq-reduce.r............ 1 tests OK test-pseq-reduce.r............ 2 tests OK 1.0s test-sim_phylo.r.............. 0 tests test-sim_phylo.r.............. 0 tests test-sim_phylo.r.............. 0 tests test-sim_phylo.r.............. 0 tests test-sim_phylo.r.............. 0 tests test-sim_phylo.r.............. 1 tests OK test-sim_phylo.r.............. 1 tests OK test-sim_phylo.r.............. 1 tests OK test-sim_phylo.r.............. 1 tests OK test-sim_phylo.r.............. 1 tests OK test-sim_phylo.r.............. 2 tests OK test-sim_phylo.r.............. 3 tests OK test-sim_phylo.r.............. 3 tests OK test-sim_phylo.r.............. 3 tests OK test-sim_phylo.r.............. 3 tests OK test-sim_phylo.r.............. 3 tests OK test-sim_phylo.r.............. 3 tests OK test-sim_phylo.r.............. 3 tests OK test-sim_phylo.r.............. 4 tests OK test-sim_phylo.r.............. 4 tests OK test-sim_phylo.r.............. 4 tests OK test-sim_phylo.r.............. 5 tests OK test-sim_phylo.r.............. 5 tests OK test-sim_phylo.r.............. 5 tests OK test-sim_phylo.r.............. 5 tests OK test-sim_phylo.r.............. 6 tests OK test-sim_phylo.r.............. 6 tests OK test-sim_phylo.r.............. 6 tests OK test-sim_phylo.r.............. 6 tests OK test-sim_phylo.r.............. 6 tests OK test-sim_phylo.r.............. 7 tests OK test-sim_phylo.r.............. 8 tests OK test-sim_phylo.r.............. 8 tests OK test-sim_phylo.r.............. 9 tests OK test-sim_phylo.r.............. 9 tests OK test-sim_phylo.r.............. 9 tests OK test-sim_phylo.r.............. 9 tests OK test-sim_phylo.r.............. 10 tests OK test-sim_phylo.r.............. 11 tests OK test-sim_phylo.r.............. 12 tests OK test-sim_phylo.r.............. 13 tests OK test-sim_phylo.r.............. 13 tests OK test-sim_phylo.r.............. 14 tests OK test-sim_phylo.r.............. 14 tests OK test-sim_phylo.r.............. 14 tests OK test-sim_phylo.r.............. 14 tests OK test-sim_phylo.r.............. 14 tests OK test-sim_phylo.r.............. 14 tests OK test-sim_phylo.r.............. 14 tests OK test-sim_phylo.r.............. 15 tests OK test-sim_phylo.r.............. 16 tests OK test-sim_phylo.r.............. 17 tests OK test-sim_phylo.r.............. 17 tests OK test-sim_phylo.r.............. 17 tests OK test-sim_phylo.r.............. 17 tests OK test-sim_phylo.r.............. 18 tests OK test-sim_phylo.r.............. 18 tests OK test-sim_phylo.r.............. 18 tests OK test-sim_phylo.r.............. 18 tests OK test-sim_phylo.r.............. 19 tests OK 4.5s All ok, 118 results (27.1s) Warning message: While using multiple chains, a single initial point has been passed via `initial`: c(0.9, 0.5, 0.1, 0.05, 0.5). The values will be recycled. Ideally you would want to start each chain from different locations. > > > > proc.time() user system elapsed 24.82 0.37 28.57