Electronic resources to PhD thesis of Simon Aeschbacher

Contact: Simon Aeschbacher, Department of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, 1090 Vienna, Austria
E-mail | Website | Phone: +43(0)1 4277 50773

Chapter 4
Census sizes (PDF)
Transfer events (PDF)
Driver scripts for ABC
Worker scripts for ABC

Chapter 4

Supporting files

Supporting file 1: Census population sizes of Alpine ibex (Capra ibex) demes in the Swiss Alps. Download PDF (87 KB)

Supporting file 2: Numbers of Alpine ibex (Capra ibex) transferred between demes by humans. Download PDF (55 KB)

Driver scripts used on cluster for ABC

Download zipped archive (6.3 KB) of the files described in the table below. Go to top of page.

File name	Type	Description	Remark
driver_p2_simul.sh	bash script	Array job script for parallel simulation of the ibex scenario with SPoCS. Used to generate the ABC simulations.	Before launching SPoCS.jar, it launches createPriors_set02.R to sample input values from the prior distributions. After launching SPoCS.jar, it launches collectSumStats.R; paths and arguments may need to be adjusted.
driver_p2_merge_param_sst.sh	bash script	Merges summary statistics and parameters to one file. Removes duplicate entries in parameter files that arose due to simulations that failed and had to be redone.	Launches rm_duplicates.sh; paths may need to be adjusted.
driver_p2_subsetsstparam.sh	bash script	Extracts from the merged summary statistics and parameters those of interest for later steps, and establishes what simulations are close to the putative target.	Launches extractColsParam.R, extractColsSst.R, obtainCloseSimulations_p2.R; paths and arguments may need to be adjusted.
driver_p2_sstchoice_global.sh	bash script	Array job script for global choice of summary statistics.	Launches chooseSstPLS_p2.R, chooseSstLGB_p2.R, chooseSstL1B_p2.R and chooseSstL2B_p2.R; paths and arguments may need to be adjusted.
driver_p2_sstchoice_pls_local.sh	bash script	Array job script for local choice of summary statistics via partial least squares (PLS) regression.	Launches chooseSstPLS_local_p2.R; paths and arguments may need to be adjusted.
driver_p2_sstchoice_lgb_local.sh	bash script	Array job script for local choice of summary statistics via boosting with the logistic loss (LogitBoosting).	Launches chooseSstLGB_local_p2.R; paths and arguments may need to be adjusted.
driver_p2_sstchoice_l1b_local.sh	bash script	Array job script for local choice of summary statistics via boosting with the L1-loss.	Launches chooseSstL1B_local_p2.R; paths and arguments may need to be adjusted.
driver_p2_sstchoice_l2b_local.sh	bash script	Array job script for local choice of summary statistics via boosting with the L2-loss.	Launches chooseSstL2B_local_p2.R; paths and arguments may need to be adjusted.
driver_p2_abc_allsst.sh	bash script	Array job script for ABC with all summary statistics.	Launches abcAllSst_p2.R; paths and arguments may need to be adjusted.
driver_p2_abc_[v1]_local.sh	bash script	Array job script for ABC with summary statistics chosen locally by the method denoted by v1. v1 is one of 'pls', 'lgb', 'l1b' or 'l2b'.	Launches abcLocal[v1]_p2.R, where v1 is the place holder for the respective method.; paths and arguments may need to be adjusted.
driver_p2_abc_[v1]_global.sh	bash script	Array job script for ABC with summary statistics chosen globally by the method denoted by v1. v1 is one of 'pls', 'lgb', 'l1b' or 'l2b'.	Launches abcGlobal[v1]_p2.R, where v1 is the place holder for the respective method; paths and arguments may need to be adjusted.
driver_p1_abc_l2b_local_nonfocal.sh	bash script	Array job script for ABC with summary statistics chosen locally by the method l2b. Here, only the parameters that were originally not of interest in chapter 3, namely the migration rates, are analyzed here. The goal is to see if there is implicit prior coming in from chapter 3.	Launches abcLocalL2B_nonfocal.R; paths and arguments may need to be adjusted.
driver_zeromig_simul.sh	bash script	Array job script for paralel simulation of the ibex scenario with SPoCS. Used to generate the ABC simulations under the model without migration (nomig).	Before launching SPoCS.jar, it launches createPriors_zeromig.R to sample input values from the prior distributions (all migration rates are equal to zero here!). After launching SPoCS.jar, it launches collectSumStats.R; paths and arguments may need to be adjusted.
driver_zeromig_subsetsstparam.sh	bash script	Does some file manipulation and extracts parameters and summary statistics of interest. This is for the model without migration (nomig).	Launches extractColsParam.R, extractColsSst.R; paths and arguments may need to be adjusted.
driver_zeromig_merge_param_sst.sh	bash script	Merges summary statistics and parameters to one file. Removes duplicate entries in parameter files that arose due to simulations that failed and had to be redone. This is for the model without migration (nomig).	Launches rm_duplicates.sh; paths may need to be adjusted.
driver_modelcomp_abc_l2b_global.sh	bash script	Array job script for ABC with summary statistics chosen globally by the method l2b. ABC is done here for comparison of the model with migration (mig) versus the one without (nomig).	Launches abcGlobalL2B_modelcomp.R; paths and arguments may need to be adjusted.

Download zipped archive (6.3 KB) of the files described in the table above. Go to top of page.

Worker scripts used on cluster for ABC

Download zipped archive (24 KB) of the files described in the table below. Go to top of page.

File name	Type	Description	Remark
createPriors_set02.R	R script	Samples parameter values from respective prior distributions and stores the values in files that later serve as input files to the ABC simulations.	Launched by driver_p2_simul.sh; paths and arguments may need to be adjusted.
collectSumStats.R	R script	Collects summary statistics generated in multiple simulations by SPoCS, omitting those which are not needed.	Launched by driver_p2_simul.sh; paths and arguments may need to be adjusted.
rm_duplicates.sh	bash script	Removes duplicate lines with same run ID from prior files. Such lines exist because SPoCS is relaunched whenever the simulation fails. The last line from those lines with the same run ID is taken.	Launched by driver_p2_merge_param_sst.sh; paths and arguments may need to be adjusted.
extractColsParam.R	R script	Extracts the desired columns from the prior parameter values; this is to make further steps more efficient, getting rid of data that are not needed.	Launched by driver_p2_subsetsstparam.sh; paths and arguments may need to be adjusted.
extractColsSst.R	R script	Extracts the desired candidate summary statistics from the files with all summary statistics.	Launched by driver_p2_subsetsstparam.sh; paths and arguments may need to be adjusted.
obtainCloseSimulations_p2.R	R script	Determines which simulations are close to the putative truth.	Launched by driver_p2_sst.sh; paths and arguments may need to be adjusted.
chooseSstPLS_p2.R	R script	Chooses summary statistics globally via partial least squares (PLS) regression .	Launched by driver_p2_sstchoice_global.sh; paths and arguments may need to be adjusted.
chooseSstLGB_p2.R	R script	Chooses summary statistics globally via boosting with the logistic loss (LogitBoosting).	Launched by driver_p2_sstchoice_global.sh; paths and arguments may need to be adjusted.
chooseSstL1B_p2.R	R script	Chooses summary statistics globally via boosting with the L1-loss.	Launched by driver_p2_sstchoice_global.sh; paths and arguments may need to be adjusted.
chooseSstL2B_p2.R	R script	Chooses summary statistics globally via boosting with the L2-loss.	Launched by driver_p2_sstchoice_global.sh; paths and arguments may need to be adjusted.
chooseSstPLS_local_p2.R	R script	Chooses summary statistics locally via partial least squares (PLS) regression .	Launched by driver_p2_sstchoice_pls_local.sh; paths and arguments may need to be adjusted.
chooseSstLGB_local_p2.R	R script	Chooses summary statistics locally via boosting with the logistic loss (LogitBoosting).	Launched by driver_p2_sstchoice_lgb_local.sh; paths and arguments may need to be adjusted.
chooseSstL1B_local_p2.R	R script	Chooses summary statistics locally via boosting with the L1-loss.	Launched by driver_p2_sstchoice_l1b_local.sh; paths and arguments may need to be adjusted.
chooseSstL2B_local_p2.R	R script	Chooses summary statistics locally via boosting with the L2-loss.	Launched by driver_p2_sstchoice_l2b_local.sh; paths and arguments may need to be adjusted.
abcAllSst_p2.R	R script	Performs ABC with all summary statistics.	Launched by driver_p2_abc_allsst.sh; paths and arguments may need to be adjusted.
abcLocal[v1]_p2.R	R script	Performs ABC with summary statistics chosen locally by the method denoted by v1. v1 is one of 'PLS', 'LGB', 'L1B' or 'L2B'.	Launched by driver_p2_abc_[v1]_local.sh; paths and arguments may need to be adjusted.
abcGlobal[v1]_p2.R	R script	Performs ABC with summary statistics chosen globally by the method denoted by v1. v1 is one of 'PLS', 'LGB', 'L1B' or 'L2B'.	Launched by driver_p2_abc_[v1]_global.sh; paths and arguments may need to be adjusted.
abcGlobalL2B_nonfocal.R	R script	Performs ABC with summary statistics chosen globally by the method l2b. Here, only the parameters that were originally not of interest in chapter 3, namely the migration rates, are analyzed here..	Launched by driver_p2_abc_[v1]_global.sh; paths and arguments may need to be adjusted.
createPriors_zeromig.R	R script	Samples parameter values from respective prior distributions, but with migration rates set to zero (nomig model) and stores the values in files that later serve as input files to the ABC simulations.	Launched by driver_zeromig_simul.sh; paths and arguments may need to be adjusted.
abcGlobalL2B_modelcomp.R	R script	Performs ABC with summary statistics chosen globally by the method l2b. It does ABC for comparison between the migration (mig) and the non-migration (nomig) model.	Launched by driver_modelcomp_abc_l2b_global.sh; paths and arguments may need to be adjusted.

Download zipped archive (24 KB) of the files described in the table above. Go to top of page.