Katherine Scranton, Jonas Knape, Perry de Valpine. 2014. An approximate Bayesian computation approach to parameter estimation in a stochastic stage-structured population model. Ecology 95:1418–1428. http://dx.doi.org/10.1890/13-1065.1

Supplement

C++ code and R script files for summary statistics, distance metrics, population simulation, and sequential Monte Carlo algorithm used for parameter estimation of a stochastic stage-structured population model.
Ecological Archives E095-122-S1.

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Authors
File list (downloads)
Description

Author(s)

Katherine Scranton
University of California, Berkeley
Department of Environmental Science, Policy, and Management
137 Mulford Hal #3114, Berkeley, CA 94720
E-mail: katherine.scranton@yale.edu

Jonas Knape
University of California, Berkeley
Department of Environmental Science, Policy, and Management
137 Mulford Hal #3114, Berkeley, CA 94720

Perry de Valpine
University of California, Berkeley
Department of Environmental Science, Policy, and Management
137 Mulford Hal #3114, Berkeley, CA 94720

File list

distanceCode.R (MD5: 263965622e4839af0d19193c0cf32195)

obsDataC.R (MD5: 0347a95c067dddee0cf34fe286b7ca9c)

popSimCodeC_E.R (MD5: 531aafb2d51a23449756138cd8ea994a)

simCohortVec.so (MD5: 3ebd32ff70131efa625f378c59e1e46a)

SMCcode_E.R (MD5: d7819abf935cec9b4d6f17962eb4fd78)

execSMC_C_E.R (MD5: c2583fd6716ac06fb377f75f0fd10e4b)

Description

We provide functions to compute distances using all candidate summary statistics and distance metrics in distanceCode.R.

obsDataC.R is a data file that was used as our "observed" data set.

We simulated many data sets using popSimCodeC_E.R. This source file contains both an R function to simulate a data set and an interface to call C++ code simCohortVec.co to simulate a data set.

The actual ABC SMC algorithm is coded in a function in SMCcode_E.R.