R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 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(testthat) > library(o2geosocial) Registered S3 methods overwritten by 'o2geosocial': method from plot.outbreaker_chains outbreaker2 print.custom_likelihoods outbreaker2 print.custom_priors outbreaker2 print.outbreaker_chains outbreaker2 summary.outbreaker_chains outbreaker2 > > test_check("o2geosocial") ///// outbreaker custom likelihoods /// class: custom_likelihoods list number of items: 5 /// custom likelihoods set to NULL (default used) // $reporting NULL $timing_infections NULL $timing_sampling NULL $space NULL $age NULL ///// outbreaker custom likelihoods /// class: custom_likelihoods list number of items: 5 /// custom likelihoods // $reporting function(data, param, i) cpp_ll_reporting(data, param, i) $timing_infections function(data, param, i) cpp_ll_timing_infections(data, param, i) $timing_sampling function(data, param, i) cpp_ll_timing_sampling(data, param, i) $space function(data, config, param, i) cpp_ll_space(data, config, param, i) $age function(data, param, i) cpp_ll_age(data, param, i) ///// outbreaker results /// class: outbreaker_chains data.frame dimensions 21 rows, 22 columns ancestries not shown: alpha_2 - alpha_5 infection dates not shown: t_inf_1 - t_inf_5 intermediate generations not shown: kappa_1 - kappa_5 /// head // step post like prior a b pi alpha_1 1 1 -32.88389 -33.28774 0.4038415 0.7 0.1 0.9103669 NA 2 50 -39.51264 -38.91464 -0.5980045 0.7 0.1 0.8051902 2 3 100 -34.21771 -35.52312 1.3054073 0.7 0.1 0.9948269 2 ... /// tail // step post like prior a b pi alpha_1 19 900 -32.02185 -33.24110 1.2192534 0.7 0.1 0.9853492 5 20 950 -33.65435 -34.66317 1.0088272 0.7 0.1 0.9625783 2 21 1000 -35.73840 -36.49890 0.7604945 0.7 0.1 0.9363814 2 ///// outbreaker results /// class: outbreaker_chains data.frame dimensions 21 rows, 22 columns ancestries not shown: alpha_2 - alpha_5 infection dates not shown: t_inf_1 - t_inf_5 intermediate generations not shown: kappa_1 - kappa_5 /// head // step post like prior a b pi alpha_1 1 1 -32.88389 -33.28774 0.4038415 0.7 0.1 0.9103669 NA 2 50 -39.51264 -38.91464 -0.5980045 0.7 0.1 0.8051902 2 ... /// tail // step post like prior a b pi alpha_1 20 950 -33.65435 -34.66317 1.0088272 0.7 0.1 0.9625783 2 21 1000 -35.73840 -36.49890 0.7604945 0.7 0.1 0.9363814 2 ///// outbreaker results /// class: outbreaker_chains data.frame dimensions 21 rows, 22 columns ancestries not shown: alpha_1 - alpha_5 infection dates not shown: t_inf_1 - t_inf_5 intermediate generations not shown: kappa_1 - kappa_5 /// head // step post like prior 1 1 -32.88389 -33.28774 0.4038415 2 50 -39.51264 -38.91464 -0.5980045 3 100 -34.21771 -35.52312 1.3054073 ... /// tail // step post like prior 19 900 -32.02185 -33.24110 1.2192534 20 950 -33.65435 -34.66317 1.0088272 21 1000 -35.73840 -36.49890 0.7604945 /// head // 1 2 3 4 5 1 0 0 0 0 1 2 0 0 0 0 1 3 0 0 0 0 1 ... /// tail // 1 2 3 4 5 19 0 0 0 0 1 20 0 0 0 0 1 21 0 0 0 0 1 Biggest cluster: 5 Cluster not shown: 2 to 5 /// head // 1 2 1 0 0 2 0 0 3 0 0 ... /// tail // 1 2 19 0 0 20 0 0 21 0 0 /// head // 1 2 3 4 5 1 0 0 0 0 1 2 0 0 0 0 1 3 0 0 0 0 1 ... /// tail // 1 2 3 4 5 19 0 0 0 0 1 20 0 0 0 0 1 21 0 0 0 0 1 ///// outbreaker custom priors /// class: custom_priors list number of items: 3 /// custom priors set to NULL (default used) // $pi NULL $a NULL $b NULL ///// outbreaker custom priors /// class: custom_priors list number of items: 3 /// custom priors // $pi function(param){ return(dnorm(x = param$pi, mean = config$prior_pi[1], sd = config$prior_pi[2], log = T)) } $a function(param){ return(dnorm(x = param$a, mean = config$prior_a[1], sd = config$prior_a[2], log = T)) } $b function(param){ return(dnorm(x = param$b, mean = config$prior_b[1], sd = config$prior_b[2], log = T)) } [ FAIL 0 | WARN 3031 | SKIP 0 | PASS 197 ] [ FAIL 0 | WARN 3031 | SKIP 0 | PASS 197 ] > > proc.time() user system elapsed 18.03 0.85 18.87