A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment

2016-03-30T15:17:40Z (GMT) by Matthew Rittenhouse

Updated March 30th, 2016

This project contains R code to replicate the results of our modelling research on sea lice.

The file, Marty_Data.csv, is a .csv conversion of data from Marty et al. (2010), DOI: 10.1073/pnas.1009573108. The file, RittenhouseEtAl_eggviability, fits a linear model to salinity and egg viability data from Johnson & Albright (1991). The file, RittenhouseEtAl_ModelDynamics.R produces figure 2 and figure 3 of our manuscript. The file, RittenhouseEtAl_SensitivityAnalysis.R, produces our sensitivity analysis results and figure 5 of our manuscript. The file, RittenhouseEtAl_SiteEnvironment, fits sinusoidal models to temperature and salinity data from British Columbia (Marty_Data.csv) and Newfoundland (not included), and finds the the 5th, 50th, and 95th percentiles of the temperature and salinity data at these two sites. The file, RittenhouseEtAl_R0t, finds Re(t) for the two sites as well as mortality rates and maturation times. The file, RittenhouseEtAl_CaseStudyFigure creates figure 4 of the main text.

For legal reasons, we unfortunately can not include data from our Newfoundland case study site. As such, errors will be returned on the RittenhouseEtAl_SiteEnvironment.R and RittenhouseEtAl_CaseStudyFigure.R files. The information for the British Columbia site, as well as panels A, B, and C of figure 5 are still able to be replicated without this data.

The files, RittenhouseEtAl_SiteEnvironment.R and RittenhouseEtAl.R0t.R should be run before RittenhouseEtAl_CaseStudyFigure.R. The files are meant to be placed in the same file and run in the following order and manner:

rm(list = ls()) # clear workspace

setwd() # Set this to folder's location

source("RittenhouseEtAl_eggviability.R")

 

rm(list = ls()) # clear workspace

setwd() # Set this to folder's location

source("RittenhouseEtAl_ModelDynamics.R")

 

rm(list = ls()) # clear workspace

setwd() # Set this to folder's location

source("RittenhouseEtAl_SensitivityAnalysis.R")

 

rm(list = ls()) # clear workspace

setwd() # Set this to folder's location

source("RittenhouseEtAl_SiteEnvironment.R")

 

rm(list = ls()) # clear workspace

setwd() # Set this to folder's location

source("RittenhouseEtAl_R0t.R")

 

rm(list = ls()) # clear workspace

setwd() # Set this to folder's location

source("RittenhouseEtAl_CaseStudyFigure.R")