==1785496== Memcheck, a memory error detector ==1785496== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1785496== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1785496== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R --vanilla ==1785496== R Under development (unstable) (2022-03-20 r81945) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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. Natural language support but running in an English locale 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. > pkgname <- "FlywayNet" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('FlywayNet') > > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("estimate_migration_ABC") > ### * estimate_migration_ABC > > flush(stderr()); flush(stdout()) > > ### Name: estimate_migration_ABC > ### Title: Estimates migration parameters using an ABC method. > ### Aliases: estimate_migration_ABC > > ### ** Examples > > migr <- generate_toy_migration() > # Argument nb_simul just provide to reduce running time > estimated_migr <- estimate_migration_ABC( migr, nb_simul = 30 ) [1] " ------ Lenormand et al. (2012)'s algorithm ------" ==1785496== Invalid read of size 8 ==1785496== at 0x173C2EFD: simulate_trajectories(Rcpp::Matrix<14, Rcpp::PreserveStorage>&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, int) (packages/tests-vg/FlywayNet/src/generate_trajectories_C.cpp:119) ==1785496== by 0x173C3958: generate_trajectories_C(Rcpp::Vector<19, Rcpp::PreserveStorage>, Rcpp::Nullable >, Rcpp::Nullable) (packages/tests-vg/FlywayNet/src/generate_trajectories_C.cpp:36) ==1785496== by 0x173AA585: _FlywayNet_generate_trajectories_C (packages/tests-vg/FlywayNet/src/RcppExports.cpp:65) ==1785496== by 0x49E90F: R_doDotCall (svn/R-devel/src/main/dotcode.c:607) ==1785496== by 0x49EE5B: do_dotcall (svn/R-devel/src/main/dotcode.c:1284) ==1785496== by 0x4D638B: bcEval (svn/R-devel/src/main/eval.c:7136) ==1785496== by 0x4F070F: Rf_eval (svn/R-devel/src/main/eval.c:748) ==1785496== by 0x4F206D: R_execClosure (svn/R-devel/src/main/eval.c:1918) ==1785496== by 0x4F2DC2: Rf_applyClosure (svn/R-devel/src/main/eval.c:1844) ==1785496== by 0x4E197D: bcEval (svn/R-devel/src/main/eval.c:7104) ==1785496== by 0x4F070F: Rf_eval (svn/R-devel/src/main/eval.c:748) ==1785496== by 0x4F206D: R_execClosure (svn/R-devel/src/main/eval.c:1918) ==1785496== Address 0x1ef205d0 is 32 bytes before a block of size 288 in arena "client" ==1785496== [1] "step 1 completed" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:05 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:03 | |========== | 20% Time elapsed: 00:00:01 Estimated time remaining: 00:00:04 | |============= | 27% Time elapsed: 00:00:01 Estimated time remaining: 00:00:03 | |================= | 33% Time elapsed: 00:00:01 Estimated time remaining: 00:00:03 | |==================== | 40% Time elapsed: 00:00:01 Estimated time remaining: 00:00:02 | |======================= | 47% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |=========================== | 53% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |================================= | 67% Time elapsed: 00:00:02 Estimated time remaining: 00:00:01 | |===================================== | 73% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 2 completed - p_acc = 0.6" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |======================= | 47% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |=========================== | 53% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |================================= | 67% Time elapsed: 00:00:02 Estimated time remaining: 00:00:01 | |===================================== | 73% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 3 completed - p_acc = 0.333333333333333" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======================= | 47% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |=========================== | 53% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |================================= | 67% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 4 completed - p_acc = 0.4" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======================= | 47% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |=========================== | 53% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 5 completed - p_acc = 0.466666666666667" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 6 completed - p_acc = 0.666666666666667" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:03 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |======================= | 47% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |=========================== | 53% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 7 completed - p_acc = 1" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 8 completed - p_acc = 0.466666666666667" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 9 completed - p_acc = 0.933333333333333" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 10 completed - p_acc = 0.666666666666667" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 11 completed - p_acc = 0.8" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 12 completed - p_acc = 0.6" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 13 completed - p_acc = 0.933333333333333" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 14 completed - p_acc = 0.6" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 15 completed - p_acc = 0.266666666666667" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 16 completed - p_acc = 0.4" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 17 completed - p_acc = 0.266666666666667" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 18 completed - p_acc = 0.466666666666667" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 19 completed - p_acc = 0.2" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 20 completed - p_acc = 0.4" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 21 completed - p_acc = 0.0666666666666667" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 22 completed - p_acc = 0.2" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 23 completed - p_acc = 0.133333333333333" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 24 completed - p_acc = 0.133333333333333" | | | 0% | |=== | 7% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======= | 13% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============= | 27% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================= | 33% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================= | 47% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |=========================== | 53% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |================================= | 67% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |===================================== | 73% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=========================================== | 87% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=============================================== | 93% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:01 [1] "step 25 completed - p_acc = 0" > print( estimated_migr$estimation_method$output$transition_law_param ) [,1] [,2] [,3] [,4] [,5] [1,] 0 0.9 0.0000000 0.0000000 0.0 [2,] 0 0.0 0.5544109 0.2455891 0.0 [3,] 0 0.0 0.0000000 0.0000000 0.8 [4,] 0 0.0 0.0000000 0.0000000 0.9 [5,] 0 0.0 0.0000000 0.0000000 0.0 > estimated_migr <- estimate_migration_ABC( migr, nb_simul = 40 , sojourn_domain = c(2,4), + estimate_sojourns = c(TRUE, TRUE, TRUE, FALSE, FALSE)) [1] " ------ Lenormand et al. (2012)'s algorithm ------" [1] "step 1 completed" | | | 0% | |== | 5% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |===== | 10% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======== | 15% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============ | 25% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |=============== | 30% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================== | 35% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |====================== | 45% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========================= | 50% Time elapsed: 00:00:00 Estimated time remaining: 00:00:00 | |============================ | 55% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================ | 65% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=================================== | 70% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |====================================== | 75% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |========================================== | 85% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |============================================= | 90% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================================ | 95% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 2 completed - p_acc = 0.7" | | | 0% | |== | 5% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |===== | 10% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======== | 15% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============ | 25% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |=============== | 30% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================== | 35% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |====================== | 45% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |========================= | 50% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================ | 55% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================ | 65% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=================================== | 70% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |====================================== | 75% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |========================================== | 85% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |============================================= | 90% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |================================================ | 95% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 3 completed - p_acc = 0.55" | | | 0% | |== | 5% Time elapsed: 00:00:00 Estimated time remaining: 00:00:03 | |===== | 10% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |======== | 15% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |============ | 25% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |=============== | 30% Time elapsed: 00:00:01 Estimated time remaining: 00:00:02 | |================== | 35% Time elapsed: 00:00:01 Estimated time remaining: 00:00:02 | |==================== | 40% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |====================== | 45% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |========================= | 50% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================ | 55% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |================================ | 65% Time elapsed: 00:00:02 Estimated time remaining: 00:00:01 | |=================================== | 70% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |====================================== | 75% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |========================================== | 85% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |============================================= | 90% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |================================================ | 95% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 4 completed - p_acc = 0.25" | | | 0% | |== | 5% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |===== | 10% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======== | 15% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |============ | 25% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |=============== | 30% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================== | 35% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |====================== | 45% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |========================= | 50% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================ | 55% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |================================ | 65% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=================================== | 70% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |====================================== | 75% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |========================================== | 85% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |============================================= | 90% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |================================================ | 95% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 5 completed - p_acc = 0.6" | | | 0% | |== | 5% Time elapsed: 00:00:00 Estimated time remaining: 00:00:02 | |===== | 10% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======== | 15% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============ | 25% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |=============== | 30% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================== | 35% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |====================== | 45% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========================= | 50% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================ | 55% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================ | 65% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=================================== | 70% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |====================================== | 75% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |========================================== | 85% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |============================================= | 90% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================================ | 95% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 6 completed - p_acc = 0.25" | | | 0% | |== | 5% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |===== | 10% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======== | 15% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============ | 25% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |=============== | 30% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================== | 35% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |====================== | 45% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========================= | 50% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================ | 55% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================ | 65% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=================================== | 70% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |====================================== | 75% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |========================================== | 85% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |============================================= | 90% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |================================================ | 95% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 7 completed - p_acc = 0.4" | | | 0% | |== | 5% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |===== | 10% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |======== | 15% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========== | 20% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |============ | 25% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |=============== | 30% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |================== | 35% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |==================== | 40% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |====================== | 45% Time elapsed: 00:00:00 Estimated time remaining: 00:00:01 | |========================= | 50% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================ | 55% Time elapsed: 00:00:01 Estimated time remaining: 00:00:01 | |============================== | 60% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |================================ | 65% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |=================================== | 70% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |====================================== | 75% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |======================================== | 80% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |========================================== | 85% Time elapsed: 00:00:01 Estimated time remaining: 00:00:00 | |============================================= | 90% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |================================================ | 95% Time elapsed: 00:00:02 Estimated time remaining: 00:00:00 | |==================================================| 100% Completed in 00:00:02 [1] "step 8 completed - p_acc = 0.05" > print( estimated_migr$estimation_method$output$transition_law_param ) [,1] [,2] [,3] [,4] [,5] [1,] 0 0.9 0.0000000 0.0000000 0.0 [2,] 0 0.0 0.4828525 0.3171475 0.0 [3,] 0 0.0 0.0000000 0.0000000 0.8 [4,] 0 0.0 0.0000000 0.0000000 0.9 [5,] 0 0.0 0.0000000 0.0000000 0.0 > > > > cleanEx() > nameEx("estimate_migration_MCEM") > ### * estimate_migration_MCEM > > flush(stderr()); flush(stdout()) > > ### Name: estimate_migration_MCEM > ### Title: Estimates migration parameters using an MCEM method. > ### Aliases: estimate_migration_MCEM > > ### ** Examples > > migr <- generate_toy_migration() > estimated_migr <- estimate_migration_MCEM( migr ) -------------- ITER EM MH 1 ==1785496== Invalid read of size 8 ==1785496== at 0x173C2EFD: simulate_trajectories(Rcpp::Matrix<14, Rcpp::PreserveStorage>&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, int) (packages/tests-vg/FlywayNet/src/generate_trajectories_C.cpp:119) ==1785496== by 0x173B9655: estimate_migration_MCEM_C(Rcpp::Vector<19, Rcpp::PreserveStorage>, Rcpp::Nullable, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable) (packages/tests-vg/FlywayNet/src/estimate_migration_MCEM_C.cpp:262) ==1785496== by 0x173AA1A3: _FlywayNet_estimate_migration_MCEM_C (packages/tests-vg/FlywayNet/src/RcppExports.cpp:36) ==1785496== by 0x49E6BD: R_doDotCall (svn/R-devel/src/main/dotcode.c:686) ==1785496== by 0x49EE5B: do_dotcall (svn/R-devel/src/main/dotcode.c:1284) ==1785496== by 0x4D638B: bcEval (svn/R-devel/src/main/eval.c:7136) ==1785496== by 0x4F070F: Rf_eval (svn/R-devel/src/main/eval.c:748) ==1785496== by 0x4F206D: R_execClosure (svn/R-devel/src/main/eval.c:1918) ==1785496== by 0x4F2DC2: Rf_applyClosure (svn/R-devel/src/main/eval.c:1844) ==1785496== by 0x4E197D: bcEval (svn/R-devel/src/main/eval.c:7104) ==1785496== by 0x4F070F: Rf_eval (svn/R-devel/src/main/eval.c:748) ==1785496== by 0x4F206D: R_execClosure (svn/R-devel/src/main/eval.c:1918) ==1785496== Address 0x1d52e768 is 24 bytes before a block of size 288 alloc'd ==1785496== at 0x484086F: malloc (/builddir/build/BUILD/valgrind-3.18.1/coregrind/m_replacemalloc/vg_replace_malloc.c:381) ==1785496== by 0x52EAC4: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2838) ==1785496== by 0x173BCFB9: Rcpp::Vector<14, Rcpp::PreserveStorage>::Vector(Rcpp::Dimension const&) (R-devel/site-library/Rcpp/include/Rcpp/vector/Vector.h:135) ==1785496== by 0x173C2AB9: Matrix (R-devel/site-library/Rcpp/include/Rcpp/vector/Matrix.h:60) ==1785496== by 0x173C2AB9: simulate_trajectories(Rcpp::Matrix<14, Rcpp::PreserveStorage>&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, int) (packages/tests-vg/FlywayNet/src/generate_trajectories_C.cpp:82) ==1785496== by 0x173B9655: estimate_migration_MCEM_C(Rcpp::Vector<19, Rcpp::PreserveStorage>, Rcpp::Nullable, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable) (packages/tests-vg/FlywayNet/src/estimate_migration_MCEM_C.cpp:262) ==1785496== by 0x173AA1A3: _FlywayNet_estimate_migration_MCEM_C (packages/tests-vg/FlywayNet/src/RcppExports.cpp:36) ==1785496== by 0x49E6BD: R_doDotCall (svn/R-devel/src/main/dotcode.c:686) ==1785496== by 0x49EE5B: do_dotcall (svn/R-devel/src/main/dotcode.c:1284) ==1785496== by 0x4D638B: bcEval (svn/R-devel/src/main/eval.c:7136) ==1785496== by 0x4F070F: Rf_eval (svn/R-devel/src/main/eval.c:748) ==1785496== by 0x4F206D: R_execClosure (svn/R-devel/src/main/eval.c:1918) ==1785496== by 0x4F2DC2: Rf_applyClosure (svn/R-devel/src/main/eval.c:1844) ==1785496== ==1785496== Invalid read of size 8 ==1785496== at 0x173C2EFD: simulate_trajectories(Rcpp::Matrix<14, Rcpp::PreserveStorage>&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, int) (packages/tests-vg/FlywayNet/src/generate_trajectories_C.cpp:119) ==1785496== by 0x173B1654: resimulate_trajectories(Rcpp::Matrix<14, Rcpp::PreserveStorage>&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, int, double) (packages/tests-vg/FlywayNet/src/birdnet_mcem_mh.cpp:33) ==1785496== by 0x173B9AB3: estimate_migration_MCEM_C(Rcpp::Vector<19, Rcpp::PreserveStorage>, Rcpp::Nullable, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable, Rcpp::Nullable) (packages/tests-vg/FlywayNet/src/estimate_migration_MCEM_C.cpp:274) ==1785496== by 0x173AA1A3: _FlywayNet_estimate_migration_MCEM_C (packages/tests-vg/FlywayNet/src/RcppExports.cpp:36) ==1785496== by 0x49E6BD: R_doDotCall (svn/R-devel/src/main/dotcode.c:686) ==1785496== by 0x49EE5B: do_dotcall (svn/R-devel/src/main/dotcode.c:1284) ==1785496== by 0x4D638B: bcEval (svn/R-devel/src/main/eval.c:7136) ==1785496== by 0x4F070F: Rf_eval (svn/R-devel/src/main/eval.c:748) ==1785496== by 0x4F206D: R_execClosure (svn/R-devel/src/main/eval.c:1918) ==1785496== by 0x4F2DC2: Rf_applyClosure (svn/R-devel/src/main/eval.c:1844) ==1785496== by 0x4E197D: bcEval (svn/R-devel/src/main/eval.c:7104) ==1785496== by 0x4F070F: Rf_eval (svn/R-devel/src/main/eval.c:748) ==1785496== Address 0x1bcc2710 is 32 bytes before a block of size 336 in arena "client" ==1785496== -------------- ITER EM MH 2 -------------- ITER EM MH 3 -------------- ITER EM MH 4 -------------- ITER EM MH 5 -------------- ITER EM MH 6 -------------- ITER EM MH 7 -------------- ITER EM MH 8 -------------- ITER EM MH 9 -------------- ITER EM MH 10 > print( estimated_migr$estimation_method$output$transition_law_param ) [,1] [,2] [,3] [,4] [,5] [1,] 0 0.9 0.0000000 0.0000000 0.0 [2,] 0 0.0 0.5915957 0.2084043 0.0 [3,] 0 0.0 0.0000000 0.0000000 0.8 [4,] 0 0.0 0.0000000 0.0000000 0.9 [5,] 0 0.0 0.0000000 0.0000000 0.0 > estimated_migr <- estimate_migration_MCEM( migr, sojourn_domain = c(2,4), itermax = 15, + estimate_sojourns = c(TRUE, TRUE, TRUE, FALSE, FALSE)) -------------- ITER EM MH 1 -------------- ITER EM MH 2 -------------- ITER EM MH 3 -------------- ITER EM MH 4 -------------- ITER EM MH 5 -------------- ITER EM MH 6 -------------- ITER EM MH 7 -------------- ITER EM MH 8 -------------- ITER EM MH 9 -------------- ITER EM MH 10 -------------- ITER EM MH 11 -------------- ITER EM MH 12 -------------- ITER EM MH 13 -------------- ITER EM MH 14 -------------- ITER EM MH 15 > print( estimated_migr$estimation_method$output$transition_law_param ) [,1] [,2] [,3] [,4] [,5] [1,] 0 0.9 0.0000000 0.0000000 0.0 [2,] 0 0.0 0.5507607 0.2492393 0.0 [3,] 0 0.0 0.0000000 0.0000000 0.8 [4,] 0 0.0 0.0000000 0.0000000 0.9 [5,] 0 0.0 0.0000000 0.0000000 0.0 > > > > cleanEx() > nameEx("estimate_migration_from_trajectories") > ### * estimate_migration_from_trajectories > > flush(stderr()); flush(stdout()) > > ### Name: estimate_migration_from_trajectories > ### Title: Estimates migration parameters using trajectories. > ### Aliases: estimate_migration_from_trajectories > > ### ** Examples > > migr <- generate_toy_migration() > traj <- generate_trajectories( migr ) > estimated_migr <- estimate_migration_from_trajectories( migr, traj ) > print( estimated_migr$estimation_method$output$transition_law_param ) [,1] [,2] [,3] [,4] [,5] [1,] 0 0.9 0.0000000 0.0000000 0.0 [2,] 0 0.0 0.5684211 0.2315789 0.0 [3,] 0 0.0 0.0000000 0.0000000 0.8 [4,] 0 0.0 0.0000000 0.0000000 0.9 [5,] 0 0.0 0.0000000 0.0000000 0.0 > > > > cleanEx() > nameEx("generate_modified_migration") > ### * generate_modified_migration > > flush(stderr()); flush(stdout()) > > ### Name: generate_modified_migration > ### Title: Return a modified migration according generative parameters. > ### Aliases: generate_modified_migration > > ### ** Examples > > migr <- generate_random_migration() > mod_migr <- generate_modified_migration(migr, transition_mode = "unif") > > > > cleanEx() > nameEx("generate_observedcounts") > ### * generate_observedcounts > > flush(stderr()); flush(stdout()) > > ### Name: generate_observedcounts > ### Title: Generate observed counts from the set of bird trajectories. > ### Aliases: generate_observedcounts > > ### ** Examples > > migr <- generate_toy_migration() > traj <- generate_trajectories( migr ) > obs <- generate_observedcounts( migr, traj ) > > > > cleanEx() > nameEx("generate_random_migration") > ### * generate_random_migration > > flush(stderr()); flush(stdout()) > > ### Name: generate_random_migration > ### Title: Generate a migration structure with a random structure. > ### Aliases: generate_random_migration > > ### ** Examples > > migr = generate_random_migration() > > > > cleanEx() > nameEx("generate_toy_migration") > ### * generate_toy_migration > > flush(stderr()); flush(stdout()) > > ### Name: generate_toy_migration > ### Title: Generate a toy migration structure with 5 sites. > ### Aliases: generate_toy_migration > > ### ** Examples > > toy_migration <- generate_toy_migration() > > > > cleanEx() > nameEx("generate_trajectories") > ### * generate_trajectories > > flush(stderr()); flush(stdout()) > > ### Name: generate_trajectories > ### Title: Generate trajectories of birds. > ### Aliases: generate_trajectories > > ### ** Examples > > migr <- generate_toy_migration() > traj <- generate_trajectories( migr ) > > > > cleanEx() > nameEx("get_counts") > ### * get_counts > > flush(stderr()); flush(stdout()) > > ### Name: get_counts > ### Title: Count birds on each site at each time step from given set of > ### trajectories. > ### Aliases: get_counts > > ### ** Examples > > migr <- generate_toy_migration() > traj <- generate_trajectories( migr ) > get_counts( migr, traj ) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [1,] 100 96 82 56 30 16 9 5 3 0 0 0 0 0 [2,] 0 0 4 16 40 64 73 71 59 45 38 25 15 9 [3,] 0 0 0 0 0 0 1 4 6 14 21 26 24 25 [4,] 0 0 0 0 0 0 0 0 0 2 6 11 13 14 [5,] 0 0 0 0 0 0 0 0 0 0 2 2 5 7 [6,] 0 0 2 4 5 7 8 10 14 15 16 19 24 28 [7,] 0 4 12 24 25 13 9 10 18 24 17 17 19 17 [,15] [,16] [,17] [,18] [,19] [,20] [,21] [1,] 0 0 0 0 0 0 0 [2,] 6 2 0 0 0 0 0 [3,] 16 10 9 8 6 3 2 [4,] 15 11 11 10 9 7 2 [5,] 13 19 27 34 32 31 30 [6,] 33 38 40 42 50 52 57 [7,] 17 20 13 6 3 7 9 > > > > cleanEx() > nameEx("get_freeparametersvalue") > ### * get_freeparametersvalue > > flush(stderr()); flush(stdout()) > > ### Name: get_freeparametersvalue > ### Title: Extract free parameter values from a migration structure. > ### Aliases: get_freeparametersvalue > > ### ** Examples > > migr <- generate_toy_migration() > get_freeparametersvalue(migr) site1_to_site2 soj_departure soj_site1 soj_site2 soj_site3 0.55 3.00 4.00 2.00 4.00 > > > > cleanEx() > nameEx("get_observation_probability") > ### * get_observation_probability > > flush(stderr()); flush(stdout()) > > ### Name: get_observation_probability > ### Title: Computes the probability of observations given the birds count > ### from trajectories. > ### Aliases: get_observation_probability > > ### ** Examples > > migr <- generate_toy_migration() > traj <- generate_trajectories( migr ) > get_observation_probability( migr$observation, get_counts( migr, traj ), use_log = FALSE) [1] 8.027823e-312 > > > > cleanEx() > nameEx("get_paramlikelihood") > ### * get_paramlikelihood > > flush(stderr()); flush(stdout()) > > ### Name: get_paramlikelihood > ### Title: Computes, by simulation, the log-likelihood of parameters > ### Aliases: get_paramlikelihood > > ### ** Examples > > migr <- generate_toy_migration() > get_paramlikelihood( migr, migr$observation) [1] -534.7684 > > > > cleanEx() > nameEx("new_migration") > ### * new_migration > > flush(stderr()); flush(stdout()) > > ### Name: new_migration > ### Title: Initialize a migration structure. > ### Aliases: new_migration > > ### ** Examples > > migr <- new_migration( + site_name = c("s1", "s2", "s3"), + flight_duration = matrix(c(0, 1, 2, 0, 0, 1, 0, 0, 0), ncol = 3, byrow = TRUE), + initial_state = c(10, 0, 0), + horizon = 5, + death_probability = c(0.05, 0.1, 1), + observation = matrix(c(9, 0, 0, 8, 0, 0, 2, 4, 1, 0, 0, 7), ncol = 3, byrow = TRUE) + ) > > > > cleanEx() > nameEx("plot.migration") > ### * plot.migration > > flush(stderr()); flush(stdout()) > > ### Name: plot.migration > ### Title: Plot a migration network from transition probabilities and mean > ### sojourn time parameters. > ### Aliases: plot.migration > > ### ** Examples > > migr <- generate_toy_migration() > plot( migr ) IGRAPH 9683c5f DNW- 5 5 -- + attr: name (v/c), TRUE (v/c), weight (e/n) + edges from 9683c5f (vertex names): [1] departure->site1 site1 ->site2 site1 ->site3 site2 ->arrival [5] site3 ->arrival > > > > cleanEx() > nameEx("plot_observedcounts") > ### * plot_observedcounts > > flush(stderr()); flush(stdout()) > > ### Name: plot_observedcounts > ### Title: Barplot observed counts at different sites and time steps. > ### Aliases: plot_observedcounts > > ### ** Examples > > migr <- generate_toy_migration() > traj <- generate_trajectories( migr ) > obs <- generate_observedcounts( migr, traj ) > plot_observedcounts( migr, obs ) > > > > cleanEx() > nameEx("plot_trajectories") > ### * plot_trajectories > > flush(stderr()); flush(stdout()) > > ### Name: plot_trajectories > ### Title: Barplot of birds counts par site and per time step, given bird > ### trajectories. > ### Aliases: plot_trajectories > > ### ** Examples > > migr <- generate_toy_migration() > traj <- generate_trajectories( migr ) > counts <- plot_trajectories( migr, traj ) > > > > cleanEx() > nameEx("read_migration") > ### * read_migration > > flush(stderr()); flush(stdout()) > > ### Name: read_migration > ### Title: Read a migration structure in a text file. > ### Aliases: read_migration > > ### ** Examples > > migr <- generate_toy_migration() > write_migration( migr, "toy_migration.txt") > read_migration("toy_migration.txt") $site_name [1] "departure" "site1" "site2" "site3" "arrival" $link_knowledge [,1] [,2] [,3] [,4] [,5] [1,] FALSE TRUE FALSE FALSE FALSE [2,] FALSE FALSE TRUE TRUE FALSE [3,] FALSE FALSE FALSE FALSE TRUE [4,] FALSE FALSE FALSE FALSE TRUE [5,] FALSE FALSE FALSE FALSE FALSE $flight_duration [,1] [,2] [,3] [,4] [,5] [1,] 0 1 0 0 0 [2,] 0 0 1 2 0 [3,] 0 0 0 0 2 [4,] 0 0 0 0 1 [5,] 0 0 0 0 0 $initial_state [1] 100 0 0 0 0 $horizon [1] 20 $death_probability [1] 0.1 0.2 0.2 0.1 1.0 $transition_law_type [1] "multinomial" $transition_law_param [,1] [,2] [,3] [,4] [,5] [1,] 0 0.9 0.00 0.00 0.0 [2,] 0 0.0 0.55 0.25 0.0 [3,] 0 0.0 0.00 0.00 0.8 [4,] 0 0.0 0.00 0.00 0.9 [5,] 0 0.0 0.00 0.00 0.0 $sojourn_law_type [1] "Poisson" $sojourn_law_param [,1] [,2] [,3] [,4] [,5] [1,] 3 4 2 4 5 $observation_law_type [1] "Poisson" $observation_law_param NULL $observation [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [1,] NA 91 58 30 11 6 2 2 0 0 NA NA NA NA [2,] NA 3 18 49 51 45 46 33 20 12 11 5 7 6 [3,] NA 0 0 0 3 12 20 5 8 22 7 4 2 5 [4,] NA 0 0 0 0 1 1 0 11 9 4 5 7 7 [5,] NA 0 0 0 0 0 0 0 0 16 25 15 37 39 [6,] NA NA NA NA NA NA NA NA NA NA NA NA NA NA [7,] NA NA NA NA NA NA NA NA NA NA NA NA NA NA [,15] [,16] [,17] [,18] [,19] [,20] [,21] [1,] NA NA NA NA NA NA NA [2,] 3 0 0 NA NA NA NA [3,] 2 0 0 1 2 1 0 [4,] 10 8 4 1 2 0 0 [5,] 44 49 41 49 47 58 52 [6,] NA NA NA NA NA NA NA [7,] NA NA NA NA NA NA NA attr(,"class") [1] "migration" > unlink("toy_migration.txt") # delete the file to pass package check > > > > cleanEx() > nameEx("reestimate_migration_from_MCEMruns") > ### * reestimate_migration_from_MCEMruns > > flush(stderr()); flush(stdout()) > > ### Name: reestimate_migration_from_MCEMruns > ### Title: Estimates migration parameters from multiple MCEM runs > ### Aliases: reestimate_migration_from_MCEMruns > > ### ** Examples > > migr1 <- generate_toy_migration() > estimated_migr1 <- estimate_migration_MCEM(migr1, MC_algo="MH", + log_transitions = TRUE, + log_sojourns = TRUE, + log_loglikelihood = TRUE) -------------- ITER EM MH 1 -------------- ITER EM MH 2 -------------- ITER EM MH 3 -------------- ITER EM MH 4 -------------- ITER EM MH 5 -------------- ITER EM MH 6 -------------- ITER EM MH 7 -------------- ITER EM MH 8 -------------- ITER EM MH 9 -------------- ITER EM MH 10 > migr2 <- generate_modified_migration(migr1, + sojourn_mode=c(rep("unif", 4), "no"), + sojourn_domain=c(1,5), + transition_mode="unif") > estimated_migr2 <- estimate_migration_MCEM(migr2, MC_algo="MH", + log_transitions = TRUE, + log_sojourns = TRUE, + log_loglikelihood = TRUE) -------------- ITER EM MH 1 -------------- ITER EM MH 2 -------------- ITER EM MH 3 -------------- ITER EM MH 4 -------------- ITER EM MH 5 -------------- ITER EM MH 6 -------------- ITER EM MH 7 -------------- ITER EM MH 8 -------------- ITER EM MH 9 -------------- ITER EM MH 10 > estimated_migr = reestimate_migration_from_MCEMruns(list(estimated_migr1, estimated_migr2)) > print( estimated_migr$estimation_method$output$transition_law_param ) [,1] [,2] [,3] [,4] [,5] [1,] 0 0.9 0.0000000 0.0000000 0.0 [2,] 0 0.0 0.5759831 0.2240169 0.0 [3,] 0 0.0 0.0000000 0.0000000 0.8 [4,] 0 0.0 0.0000000 0.0000000 0.9 [5,] 0 0.0 0.0000000 0.0000000 0.0 > > > > cleanEx() > nameEx("set_freeparametersvalue") > ### * set_freeparametersvalue > > flush(stderr()); flush(stdout()) > > ### Name: set_freeparametersvalue > ### Title: Assign free parameter values to a migration structure. > ### Aliases: set_freeparametersvalue > > ### ** Examples > > migr <- generate_toy_migration() > param <- get_freeparametersvalue(migr) # just for example purpose, should be different values > set_freeparametersvalue(migr, param) $site_name [1] "departure" "site1" "site2" "site3" "arrival" $link_knowledge [,1] [,2] [,3] [,4] [,5] [1,] FALSE TRUE FALSE FALSE FALSE [2,] FALSE FALSE TRUE TRUE FALSE [3,] FALSE FALSE FALSE FALSE TRUE [4,] FALSE FALSE FALSE FALSE TRUE [5,] FALSE FALSE FALSE FALSE FALSE $flight_duration [,1] [,2] [,3] [,4] [,5] [1,] 0 1 0 0 0 [2,] 0 0 1 2 0 [3,] 0 0 0 0 2 [4,] 0 0 0 0 1 [5,] 0 0 0 0 0 $initial_state [1] 100 0 0 0 0 $horizon [1] 20 $death_probability [1] 0.1 0.2 0.2 0.1 1.0 $transition_law_type [1] "multinomial" $transition_law_param [,1] [,2] [,3] [,4] [,5] [1,] 0 0.9 0.00 0.00 0.0 [2,] 0 0.0 0.55 0.25 0.0 [3,] 0 0.0 0.00 0.00 0.8 [4,] 0 0.0 0.00 0.00 0.9 [5,] 0 0.0 0.00 0.00 0.0 $sojourn_law_type [1] "Poisson" $sojourn_law_param [1] 3 4 2 4 5 $observation_law_type [1] "Poisson" $observation_law_param NULL $observation [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [1,] NA 91 58 30 11 6 2 2 0 0 NA NA NA NA [2,] NA 3 18 49 51 45 46 33 20 12 11 5 7 6 [3,] NA 0 0 0 3 12 20 5 8 22 7 4 2 5 [4,] NA 0 0 0 0 1 1 0 11 9 4 5 7 7 [5,] NA 0 0 0 0 0 0 0 0 16 25 15 37 39 [6,] NA NA NA NA NA NA NA NA NA NA NA NA NA NA [7,] NA NA NA NA NA NA NA NA NA NA NA NA NA NA [,15] [,16] [,17] [,18] [,19] [,20] [,21] [1,] NA NA NA NA NA NA NA [2,] 3 0 0 NA NA NA NA [3,] 2 0 0 1 2 1 0 [4,] 10 8 4 1 2 0 0 [5,] 44 49 41 49 47 58 52 [6,] NA NA NA NA NA NA NA [7,] NA NA NA NA NA NA NA attr(,"class") [1] "migration" > > > > cleanEx() > nameEx("validate_migration") > ### * validate_migration > > flush(stderr()); flush(stdout()) > > ### Name: validate_migration > ### Title: Check a migration structure. > ### Aliases: validate_migration > > ### ** Examples > > migr <- generate_toy_migration() > msg <- validate_migration( migr ) > > > > cleanEx() > nameEx("write_migration") > ### * write_migration > > flush(stderr()); flush(stdout()) > > ### Name: write_migration > ### Title: Write a migration structure in a text file. > ### Aliases: write_migration > > ### ** Examples > > migr <- generate_toy_migration() > write_migration( migr, "toy_migration.txt" ) > unlink("toy_migration.txt") # delete the file to pass package check > > > > ### *