############################################################################################## # --- CODE OF THE MODEL TO ASSESS THE ROLE OF DENS IN THE SPREAD, INVASION AND PERSISTENCE---# # --- OF SARCOPTIC MANGE IN THE SAN JOAQUIN FOX POPULATION LOCATED IN BAKERSFIELD, CA -------# # --- SPECIFICALLY THIS SCRIPT RUNS THE MODEL AND PRODUCES OUTPUT IN YOUR R ENVIRONMENT -----# ############################################################################################## # Author:Diego Montecino-Latorre # dmontecino@ucdavis.edu # Details of the model are published in the journal "Epidemics" January 2019 ###################### #--- load library ---# ###################### # the RCurl is not installed, installed and load it, otherwise just load it if (!require('RCurl')) install.packages('RCurl'); library('RCurl') # to run script from github #just dealing with a bug closeAllConnections() # this is needed to prevent a bug when calling objects through the url function ################################ # Define paramters of interest # ################################ epidemic=TRUE # Do you want to model an epidemic or an endemic scenario num.iterations=2 # number of iterations per scenario years_simulate=2 # number of year each scenario is simulated show.year.finished = TRUE # do you want to print the week just finished show.week.of.the.year.finished = TRUE # do you want to print the year just finished show.iteration.finished = TRUE # do you want to print the iteration just finished # Disease parameters # pSocial in Table 2. prob.trans.foxes.contact.fam.min = 0.15 # the minimum value of the weekly trasnmission probability of sarcoptic mange due to social contact among foxes of the same family prob.trans.foxes.contact.fam.max = 0.3 # the maximum value of the weekly trasnmission probability of sarcoptic mange due to social contact among foxes of the same family # pMate in Table 2. prob.trans.foxes.mating.min = 0.9 # the minimum value of the weekly trasnmission probability of sarcoptic mange to the mating pair prob.trans.foxes.mating.max = 1 # the maximum value of the weekly trasnmission probability of sarcoptic mange to the mating pair # pNurse in Table 2. prob.trans.pups.nursing.inf.female.min = 0.95 # the minimum value of the weekly trasnmission probability of sarcoptic mange to nursing pups from the lactating mother (dominant female) prob.trans.pups.nursing.inf.female.max = 1 # the maximum value of the weekly trasnmission probability of sarcoptic mange to nursing pups from the lactating mother (dominant female) #pShare in Table 2. prob.trans.foxes.share.den.min = 0.4 # the minimum value of the weekly trasnmission probability of sarcoptic mange due to foxes sharing a den prob.trans.foxes.share.den.max = 0.7 # the maximum value of the weekly trasnmission probability of sarcoptic mange due to foxes sharing a den #pDenfox in Table 2. prob.trans.den.to.foxes.min = 0.3 # the minimum value of the weekly trasnmission probability of sarcoptic mange from an infested den to a susceptible fix using it prob.trans.den.to.foxes.max = 0.6 # the maximum value of the weekly trasnmission probability of sarcoptic mange from an infested den to a susceptible fix using it # Weeks survival Sarcoptes scabiei off-host within den # Modify them to create the different sub experiments # for details about these parameters see section 2.4 of the manuscript weeks.s.scabiei.surv.cold.open = 1 # number of weeks S. scabiei can survive off-host within dens located in ‘Open’, ‘Transition’, ‘Industrial’, and ‘Linear’ land types during the cold season weeks.s.scabiei.surv.cold.residential = 3 # number of weeks S. scabiei can survive off-host within dens located in ‘Residential’, ‘Commercial’, and ‘Manicured’ land types during the cold season weeks.s.scabiei.surv.cold.sump = 2 # number of weeks S. scabiei can survive off-host within dens located in "Water catchment basins" during the cold season weeks.s.scabiei.surv.warm.open = 0.1 # number of weeks S. scabiei can survive off-host within dens located in ‘Open’, ‘Transition’, ‘Industrial’, and ‘Linear’ land types during the warm season weeks.s.scabiei.surv.warm.residential = 3 # number of weeks S. scabiei can survive off-host within dens located in ‘Residential’, ‘Commercial’, and ‘Manicured’ land types during the warm season weeks.s.scabiei.surv.warm.sump = 1 # number of weeks S. scabiei can survive off-host within dens located in "Water catchment basins" during the warm season ################# # RUN THE MODEL # ################# # Script to set up the model eval(parse(text = getURL("https://raw.githubusercontent.com/dmontecino/SJKF_Model/master/Setup_model_script.R", ssl.verifypeer = FALSE))) # This code loads the data needed to run the model such as the home ranges per iteration, # and the dens per iteration. These files are directly loaded as temp files from google drive # The code also loads the parameters not associates with disease transmission but with the naturla history of the san joaquin kit fox # It also creates objects to save the output from the model as well as objects with time periods # load the home ranges # # modify the "your_path/all_home_ranges_per_iteration.RDS" to the location of the all_home_ranges_per_iteration.RDS in your computer # go to the README if you do not know where to download this file from. all_home_ranges=readRDS("/Your_path/all_home_ranges_per_iteration.RDS") # The model script eval(parse(text = getURL("https://raw.githubusercontent.com/dmontecino/SJKF_Model/master/Natural_history_script.R", ssl.verifypeer = FALSE))) # the object output contains the data created by the model ##----------------------------------## # Asess the output (e.g., the number of infested foxes) matplot(t(output$N), type="l", ylim=c(0,400))