In AndySouth/resistanceGame: prototyping an insecticide resistance management computer game

This document is automtically created by querying the live copies of the game config google docs. We can use it for testing and balancing outside of the game.

#### load required packages
library(googlesheets)
library(readr)
library(resistanceGame)
library(dplyr)
library(ggplot2)

#eval et to false to not query gdocs

url_locations <- "https://docs.google.com/spreadsheets/d/1w6vZvxqX3FgtkmM8mUSvB67reekKz148LoQY2OT012M/"
url_resistances <- "https://docs.google.com/spreadsheets/d/1f9omxuMru95xBkmR0hLhrM88tvnxvJjsEXIiDjJOgL4"
url_interventions <- "https://docs.google.com/spreadsheets/d/1SVyZZTR6tmDHRr0hLAyn3UYS6n0x9vuu1YEKJ4M8MIs"
url_vectors <- "https://docs.google.com/spreadsheets/d/10urCBTuW-_E7i1alJOfqXF3r2jglrAQGBsvOGo7k1sA"

#reading location config file from googledocs
gd <- gs_url(url_locations)
locations <- gs_read(gd)

gd <- gs_url(url_resistances)
resistances <- gs_read(gd)

gd <- gs_url(url_interventions)
interventions <- gs_read(gd)

gd <- gs_url(url_vectors)
vectors <- gs_read(gd)


#cut first 2 rows which have junk in
locations <- as.data.frame( locations[-c(1:2),] )
#cut columns after 9 which contain non useful stuff
locations <- locations[,c(1:9)] 
#cut rows with NULL & NA in Vector ID column
locations <- locations[ -which(is.na(locations["Vector IDs"]) | locations["Vector IDs"]=='NULL'), ] 

#rename columns to more useful
colnames(locations)[colnames(locations)=="Location ID"] <- "loc_id"
colnames(locations)[colnames(locations)=="Vector\nEmergences"] <- "emergences"
colnames(locations)[colnames(locations)=="Vector IDs"] <- "vec_ids"
colnames(locations)[colnames(locations)=="Vector Resistance\nIDs (*)"] <- "vec_res_ids"
colnames(locations)[colnames(locations)=="Vector\nPopulations (*)"] <- "vec_abund"
colnames(locations)[colnames(locations)=="Vector Resistance\nFrequencies (*)"] <- "vec_res_freqs"
colnames(locations)[colnames(locations)=="Vector Resistance\nIntensities (*)"] <- "vec_res_ints"

colnames(vectors)[colnames(vectors)=="Vector ID"] <- "vec_id"
colnames(vectors)[colnames(vectors)=="Name"] <- "name"
colnames(vectors)[colnames(vectors)=="Survival Rate"] <- "survival"
colnames(vectors)[colnames(vectors)=="Infection Rate"] <- "infection"

#save example edited data to the package
devtools::use_data(locations, overwrite=TRUE)
devtools::use_data(resistances, overwrite=TRUE)
devtools::use_data(interventions, overwrite=TRUE)
devtools::use_data(vectors, overwrite=TRUE)

#create a composite dataframe of vectors at locations for later use
vecbyloc <- vecbyloc_from_gdocs()
devtools::use_data(vecbyloc, overwrite=TRUE)

Emergence patterns by location and vector over 12 months.

#locations should be got from saved ver. in package
#data(locations)

plot_config_gdocs_emergences()

Expected abundance patterns in absence of interventions over 3 years.

  #for each vecloc combination
  for (i in 1:nrow(vecbyloc))
  {
      #expanding the emergence string
      tmp5 <- expand_season(vecbyloc$emer_string[i], return_tstep = 'weeks')

      #run sim & just plot pop
      plot_sim_pop( run_sim(num_tsteps=144,
                    emergence=tmp5, survival=vecbyloc$survival[i]),
         title=paste0(vecbyloc$id[i]," survival:",vecbyloc$survival[i]), axis_x=TRUE, leg_pos='topleft')
  }

Expected abundance and resistance under one example scenario of intervention, insecticide_kill (0.9) & resistance

  #for each vecloc combination
  for (i in 1:nrow(vecbyloc))
  {
      #expanding the emergence string
      tmp5 <- expand_season(vecbyloc$emer_string[i], return_tstep = 'weeks')

      #run sim
      l_config2 <- config_plan(read_config(), t_strt=c(12*4, 24*4), t_stop=c(18*4,30*4),
                          control_id=c('irs_pyr'))
      plot_sim( run_sim(num_tsteps=144, emergence=tmp5, survival=vecbyloc$survival[i],
                   l_config=l_config2,
                   insecticide_kill=0.9, resist_freq_start = 0.05, resist_mech='metabolic',
                   resist_incr=0.1, resist_decr = 0.02),           
                   plot_emergence=TRUE, title=paste0(vecbyloc$id[i]), leg_pos='topleft' )

  }

AndySouth/resistanceGame documentation built on May 5, 2019, 6:01 a.m.