profile_SongEvo_methode.R
In SongEvo: An Individual-Based Model of Bird Song Evolution

# Example code for line profiling SongEvo
library(profvis)
# Reuse Basic tests for SongEvo correctness

library(SongEvo)
# glo.parms=glo.parms[ ! names(glo.parms) %in% "global.parms$learning.error.d" ]
reg.count=40

# Make starting population for prbo in 1969
local({
  data("song.data")
  starting.trait.obs <- subset(song.data, Population %in% "PRBO" & Year %in% 1969)$Trill.FBW
  
  # Generate additional individuals to reach number of territories for this vignette (40)
  starting.trait.gen <- rnorm(reg.count-length(starting.trait.obs), 
                              mean=mean(starting.trait.obs), sd=sd(starting.trait.obs))
  starting.trait <- c(starting.trait.obs, starting.trait.gen)
  
  # Build data frame of territory id, age, and song trait value (in this case trill bandwidth)
  init.inds <- data.frame(id = 1:reg.count, age = 2, trait = starting.trait,
                          row.names=paste0("A",formatC(1:reg.count, width=2, flag = "0")))
  
  # Generate lat long coordinates for center? of each territory
  init.inds$x1 <-  round(runif(reg.count, min=-122.481858, max=-122.447270), digits=8)
  init.inds$y1 <-  round(runif(reg.count, min=37.787768, max=37.805645), digits=8)
  init.inds
}) -> trill.prbo.1969

# Make starting population for Schooner in 1969
local({
  data("song.data")
  starting.trait.obs <- subset(song.data, Population %in% "Schooner" & Year %in% 1969)$Trill.FBW
  
  # Generate additional individuals to reach number of territories for this vignette (40)
  starting.trait.gen <- rnorm(reg.count-length(starting.trait.obs), 
                              mean=mean(starting.trait.obs), sd=sd(starting.trait.obs))
  starting.trait <- c(starting.trait.obs, starting.trait.gen)
  
  # Build data frame of territory id, age, and song trait value (in this case trill bandwidth)
  init.inds <- data.frame(id = 1:reg.count, age = 2, trait = starting.trait,
                          row.names=paste0("A",formatC(1:reg.count, width=2, flag = "0")))
  
  # Generate lat long coordinates for center? of each territory
  init.inds$x1 <-  round(runif(reg.count, min=-122.481858, max=-122.447270), digits=8)
  init.inds$y1 <-  round(runif(reg.count, min=37.787768, max=37.805645), digits=8)
  init.inds
}) -> trill.sb.1969

# Make starting population for Bear Valley in 1969
local({
  data("song.data")
  starting.trait.obs <- subset(song.data, Population %in% "Bear Valley" & Year %in% 1969)$Trill.FBW
  
  # Generate additional individuals to reach number of territories for this vignette (40)
  starting.trait.gen <- rnorm(reg.count-length(starting.trait.obs), 
                              mean=mean(starting.trait.obs), sd=sd(starting.trait.obs))
  starting.trait <- c(starting.trait.obs, starting.trait.gen)
  
  # Build data frame of territory id, age, and song trait value (in this case trill bandwidth)
  init.inds <- data.frame(id = 1:reg.count, age = 2, trait = starting.trait,
                          row.names=paste0("A",formatC(1:reg.count, width=2, flag = "0")))
  
  # Generate lat long coordinates for center? of each territory
  init.inds$x1 <-  round(runif(reg.count, min=-122.481858, max=-122.447270), digits=8)
  init.inds$y1 <-  round(runif(reg.count, min=37.787768, max=37.805645), digits=8)
  init.inds
}) -> trill.bear.1969

# n.territories = 40, 
# lifespan = 2.083333, 


# Default arguments:
fledge_counts=c(1, 1, 2, 1, 0, 2, 2, 2, 2, 1, 1, 2, 1, 
                1, 1, 1, 1, 1, 0, 2, 1, 2, 1, 2, 2, 2, 
                1, 1, 1, 2, 1, 1, 
                1, 2, 2, 1, 1, 2, 1, 1)

default.parms <- list(init.inds = NULL, iteration = 100, steps = NULL,  # years / timestep
                      timestep = 1, #steps in years by default
                      n.territories = reg.count, terr.turnover = 0.5, 
                      learning.method = "integrate", integrate.dist = 0.1, 
                      learning.error.d = 0, learning.error.sd = 430, 
                      mortality.a = 0.468, mortality.j = 0.5, lifespan = NA, 
                      phys.lim.min = 1559, phys.lim.max = 4364, 
                      male.fledge.n.mean = 1.35, male.fledge.n.sd = 0.5,
                      male.fledge.n = fledge_counts, disp.age = 2, 
                      disp.distance.mean = 110, disp.distance.sd = 100,
                      mate.comp = FALSE, prin = FALSE, all = TRUE)

str(default.parms)

# SongEvo args for prbo 1969
trill.prbo.test=list(parms=default.parms)
trill.prbo.test$parms$init.inds = trill.prbo.1969 
trill.prbo.test$parms$steps = 2005-1969

# SongEvo args for Schooner Bay 1969
trill.sb.test=list(parms=default.parms)
trill.sb.test$parms$init.inds = trill.sb.1969 
trill.sb.test$parms$steps = 2005-1969

# SongEvo args for Bear Valley 1969
trill.bear.test=list(parms=default.parms)
trill.bear.test$parms$init.inds = trill.bear.1969 
trill.bear.test$parms$steps = 2005-1969

str(trill.prbo.test)
str(trill.sb.test)
str(trill.bear.test)

# Execution tests
profvis::profvis({
trill.prbo.test$res=do.call(SongEvo,trill.prbo.test$parms)
})
profvis::profvis({
trill.sb.test$res=  do.call(SongEvo,trill.sb.test$parms)
})
profvis::profvis({
trill.bear.test$res=do.call(SongEvo,trill.bear.test$parms)
})
str(trill.prbo.test)
str(trill.sb.test)
str(trill.bear.test)