Supplement 1. Data and Matlab code.
plankton_mort.m (MD5: 30d22d4b051b03454fdf54ab8e585bef )
sim_fun.m (MD5: 33e12a378a5af32d0f131a695460dde0)
Larv_data.mat (MD5: 0a4e8d0d0b6e737025ebd1a58816f305)
Larval_abundance_data.csv (MD5: 0db6c2fafab998c67d23d551d1509790)
plankton_mort.m is Matlab code that calculates mortality rates using the modified VLT method described in the text. It can use the Larv_data.mat data set supplied here or a user-supplied data set. Comments in the header of the file describe inputs, outputs, and other details for usage.
sim_fun.m is Matlab code that simulates the log-likelihood of the ratio of two negative binomial-distributed variables, as described in Appendix B. It is called by plankton_mort.m and does not need to be manipulated by the user, unless the user wishes to experiment with alternative simulation approaches.
Larv_data.mat is the data set used in this paper, formatted as a Matlab data file. It contains the structure file larv, which is just a structure version of the data set in Larval_abundance_data.csv, as well as the structure file larv_dur, which contains the stage durations of each species, the cell array SpeciesNames listing the names of species in the data set, and the vector Days listing the sampling days (1 to 65) on which sampling occurred.
Larval_abundance_data.csv is the planktonic larval abundance data used in the paper. It contains data from plankton trawls made in June–July 2005 offshore of Bodega Marine Laboratory, California, USA. It contains the following columns:
Date: date of sampling (month/day/year)
Spp: organisms identified to lowest taxonomic level possible
StageGroup: developmental stage of that taxon (early/mid/late/PL) (PL = postlarval)
Day: day of sampling (1–65, bidaily)
Rep: replicate trawl made on a given date
Density/100 m3: abundance of that taxon and stage per 100 m3 volume of water