A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment
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...
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ftdatacite:10.6084/m9.figshare.1538626.v2 2023-05-15T17:22:01+02:00 A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment Rittenhouse, Matthew 2016 https://dx.doi.org/10.6084/m9.figshare.1538626.v2 https://figshare.com/articles/dataset/A_Model_For_Sea_Lice_Lepeophtheirus_salmonis_Dynamics_In_A_Seasonally_Changing_Environment/1538626/2 unknown figshare https://dx.doi.org/10.6084/m9.figshare.1538626 Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 CC-BY Parasitology Ecology FOS Biological sciences dataset Dataset 2016 ftdatacite https://doi.org/10.6084/m9.figshare.1538626.v2 https://doi.org/10.6084/m9.figshare.1538626 2021-11-05T12:55:41Z 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 R e (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") Dataset Newfoundland DataCite Metadata Store (German National Library of Science and Technology) Albright ENVELOPE(155.100,155.100,-82.817,-82.817) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Parasitology Ecology FOS Biological sciences |
spellingShingle |
Parasitology Ecology FOS Biological sciences Rittenhouse, Matthew A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment |
topic_facet |
Parasitology Ecology FOS Biological sciences |
description |
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 R e (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") |
format |
Dataset |
author |
Rittenhouse, Matthew |
author_facet |
Rittenhouse, Matthew |
author_sort |
Rittenhouse, Matthew |
title |
A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment |
title_short |
A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment |
title_full |
A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment |
title_fullStr |
A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment |
title_full_unstemmed |
A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment |
title_sort |
model for sea lice (lepeophtheirus salmonis) dynamics in a seasonally changing environment |
publisher |
figshare |
publishDate |
2016 |
url |
https://dx.doi.org/10.6084/m9.figshare.1538626.v2 https://figshare.com/articles/dataset/A_Model_For_Sea_Lice_Lepeophtheirus_salmonis_Dynamics_In_A_Seasonally_Changing_Environment/1538626/2 |
long_lat |
ENVELOPE(155.100,155.100,-82.817,-82.817) |
geographic |
Albright |
geographic_facet |
Albright |
genre |
Newfoundland |
genre_facet |
Newfoundland |
op_relation |
https://dx.doi.org/10.6084/m9.figshare.1538626 |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.1538626.v2 https://doi.org/10.6084/m9.figshare.1538626 |
_version_ |
1766108256211566592 |