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

• Main Author: Rittenhouse, Matthew
• Format: Dataset
• Language: unknown
• Published: figshare 2015
• Subjects: Parasitology; Ecology; FOS Biological sciences; Albright; Newfoundland
• Online Access: https://dx.doi.org/10.6084/m9.figshare.1538626.v1; https://figshare.com/articles/dataset/A_Model_For_Sea_Lice_Lepeophtheirus_salmonis_Dynamics_In_A_Seasonally_Changing_Environment/1538626/1

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 R0(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")