10.5281/zenodo.56574
State-space integral projection models
This is the code described in White et al., Ecological Applications (2016) Fitting state-space integral projection models to time series data. All code is written for Matlab.
There are two runme files that are the primary wrappers for all the code.
runme_IPM_mockdata.m calls all of the necessary files for running the simulated blue rockfish data fits reported in the manuscript. The simulated data is actually generated by rockfish_mockdata.m
runme_IPM.m calls all of the necessary files for fitting the IPM to the Pt Lobos rockfish datasets.
The original PISCO data (for the selected species and sites) is in directory PISCO_data_2015 The fits to those data are in runs_for_publication_pre2007_July2015
The simulated data used in the manuscript is in mockdata_May2015 The fits to those simulated data are in mockdata_fits_June2015
The data from Rick Starr's hook & line survey data used to generate the observation ogive is in Starr_hookline_survey_data
Post-processing and figure-generating code includes: gridsize_figs.m mockdata_plots.m postproc_pisco_rockfish_fit.m