In jmaspons/LHR: Tools for Life History Modeling

knitr::opts_chunk$set(echo=FALSE)

library(LHR)
library(microbenchmark)

discretePop

tf<- 5
N0<- c(N1s=5, N1b=5, N1bF=5, N2s=5, N2b=5, N2bF=5)
params<- list(b1=2, b2=2,   broods=2, PbF1=.4, PbF2=.4,  a1=.3,ab1=.25,sa1=.25,j1=.1,
              a2=.3,ab2=.25,sa2=.20,j2=.1, AFR=1, K=500, Pb1=1, Pb2=1, c1=1, c2=1, cF=1,
              P1s=.5, P1b=.5, P1sa=.5, P1j=.5)
replicates<- 1000

benchmarkRep<- microbenchmark(r100=discreteABMSim(N0=N0, params=params, tf=tf, replicates=100, Ntf=TRUE),
                              r1000=discreteABMSim(N0=N0, params=params, tf=tf, replicates=1000, Ntf=TRUE),
                              r10000=discreteABMSim(N0=N0, params=params, tf=tf, replicates=10000, Ntf=TRUE),
                              r100000=discreteABMSim(N0=N0, params=params, tf=tf, replicates=100000, Ntf=TRUE), times=10)

boxplot(benchmarkRep)
ggplot2::autoplot(benchmarkRep)

profvisRep<- profvis::profvis({
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=100, Ntf=TRUE)
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=1000, Ntf=TRUE)
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=10000, Ntf=TRUE)
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=100000, Ntf=TRUE)
})

profvisRep

profvisNtf<- profvis::profvis({
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=replicates, Ntf=TRUE)
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=replicates, Ntf=FALSE)
})

profvisNtf

ABM

tf<- 5
N0<- c(N1s=5, N1b=5, N1bF=5, N2s=5, N2b=5, N2bF=5)
params<- list(b1=2, b2=2,   broods=2, PbF1=.4, PbF2=.4,  a1=.3,ab1=.25,sa1=.25,j1=.1,
              a2=.3,ab2=.25,sa2=.20,j2=.1, AFR=1, K=500, Pb1=1, Pb2=1, c1=1, c2=1, cF=1,
              P1s=.5, P1b=.5, P1sa=.5, P1j=.5)
replicates<- 1000

benchmarkRep<- microbenchmark(r100=discreteABMSim(N0=N0, params=params, tf=tf, replicates=100, Ntf=TRUE),
                              r1000=discreteABMSim(N0=N0, params=params, tf=tf, replicates=1000, Ntf=TRUE),
                              r10000=discreteABMSim(N0=N0, params=params, tf=tf, replicates=10000, Ntf=TRUE),
                              r100000=discreteABMSim(N0=N0, params=params, tf=tf, replicates=100000, Ntf=TRUE), times=10)

boxplot(benchmarkRep)
ggplot2::autoplot(benchmarkRep)

profvisRep<- profvis::profvis({
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=100, Ntf=TRUE)
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=1000, Ntf=TRUE)
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=10000, Ntf=TRUE)
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=100000, Ntf=TRUE)
})

profvisRep

profvisNtf<- profvis::profvis({
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=replicates, Ntf=TRUE)
  discreteABMSim(N0=N0, params=params, tf=tf, replicates=replicates, Ntf=FALSE)
})

profvisNtf

ABM numericDistri

lh<- LH(method="LH axes", lambda=1.05)
env<- Env(seasonAmplitude=0, varJ=0, varA=0, breedFail=.5)

N0<- c(N1s=0, N1b=1, N1bF=0, N2s=0, N2b=1, N2bF=0)
N0<- lapply(seq(1, 20, by=2), function(x) N0 * x)
names(N0)<- paste0("N", sapply(N0, sum))

sim<- Sim.numericDistriABM(transitionsFunc=LHR:::transitionABM.LH_Beh_DIST, tf=2, maxN=10000, N0=N0)

patchScenario<- getPatchScenario(behavior="skip")

pars<- getParamsCombination.LHEnv_2patchBeh(lh=lh, env=env, patchScenario=patchScenario)
pars<- pars[pars$broods < 2, ]
model<- Model(sim=sim, pars=pars)

# model<- Model(lh=lh, env=env, sim=sim)
# model<- model[model$habDiff == "nestPredHab2" & model$behavior == "learnExploreBreed", ]

params<- S3Part(model)[1,]


N0<- c(N1s=0, N1b=1, N1bF=0, N2s=0, N2b=1, N2bF=0)
N0<- lapply(seq(1, 20, by=4), function(x) N0 * x)
names(N0)<- paste0("N", sapply(N0, sum))

expr<- lapply(names(N0), function(x){
  parse(text=paste0(x, "=numericDistriABMSim(N0=N0[['", x, "']], params=params, tf=5, Ntf=TRUE, maxN=1e30)"))
})
names(expr)<- names(N0)
tf<- 3
benchmarkN0<- microbenchmark(
  N1=numericDistriABMSim(N0=N0[[1]], params=params, tf=tf, Ntf=TRUE, maxN=1e10),
  N2=numericDistriABMSim(N0=N0[[2]], params=params, tf=tf, Ntf=TRUE, maxN=1e10),
  N3=numericDistriABMSim(N0=N0[[3]], params=params, tf=tf, Ntf=TRUE, maxN=1e10),
  N4=numericDistriABMSim(N0=N0[[4]], params=params, tf=tf, Ntf=TRUE, maxN=1e10),
  # N5=numericDistriABMSim(N0=N0[[5]], params=params, tf=5, Ntf=TRUE, maxN=1e30),
  # N6=numericDistriABMSim(N0=N0[[6]], params=params, tf=5, Ntf=TRUE, maxN=1e30),
  # N7=numericDistriABMSim(N0=N0[[7]], params=params, tf=5, Ntf=TRUE, maxN=1e30),
  times=5)

# benchmarkN0<- microbenchmark(list=expr, times=10) ## No differences on time


tf<- seq(3, 20, by=4)
expr<- lapply(tf, function(x){
  parse(text=paste0("numericDistriABMSim(N0=N0[[2]], params=params, tf=", x, ", Ntf=TRUE, maxN=1e30)"))
})
names(expr)<- tf

# benchmarkTf<- microbenchmark(list=expr, times=10)

benchmarkTf<- microbenchmark(
  tf1=numericDistriABMSim(N0=N0[[2]], params=params, tf=tf[1], Ntf=TRUE, maxN=1e30),
  tf2=numericDistriABMSim(N0=N0[[2]], params=params, tf=tf[2], Ntf=TRUE, maxN=1e30),
  tf3=numericDistriABMSim(N0=N0[[2]], params=params, tf=tf[3], Ntf=TRUE, maxN=1e30),
  tf4=numericDistriABMSim(N0=N0[[2]], params=params, tf=tf[4], Ntf=TRUE, maxN=1e30),
  # tf5=numericDistriABMSim(N0=N0[[2]], params=params, tf=tf[5], Ntf=TRUE, maxN=1e30),
  # tf6=numericDistriABMSim(N0=N0[[2]], params=params, tf=tf[6], Ntf=TRUE, maxN=1e30),
  # tf7=numericDistriABMSim(N0=N0[[2]], params=params, tf=tf[7], Ntf=TRUE, maxN=1e30),
  times=5)

# boxplot(benchmarkN0)
ggplot2::autoplot(benchmarkN0)
names(N0)

# boxplot(benchmarkTf)
ggplot2::autoplot(benchmarkTf)
tf

tf<- 3
profvisNtf<- profvis::profvis({
  numericDistriABMSim(N0=N0[[2]], params=params, tf=tf, Ntf=TRUE)
  numericDistriABMSim(N0=N0[[2]], params=params, tf=tf, Ntf=FALSE)
})

profvisNtf

profvisN0<- profvis::profvis({
  numericDistriABMSim(N0=N0[[1]], params=params, tf=tf, Ntf=TRUE)
  numericDistriABMSim(N0=N0[[2]], params=params, tf=tf, Ntf=TRUE)
  numericDistriABMSim(N0=N0[[3]], params=params, tf=tf, Ntf=TRUE)
  numericDistriABMSim(N0=N0[[4]], params=params, tf=tf, Ntf=TRUE)
})

profvisN0

profvisTf<- profvis::profvis({
  numericDistriABMSim(N0=N0[[2]], params=params, tf=2, Ntf=TRUE)
  numericDistriABMSim(N0=N0[[2]], params=params, tf=4, Ntf=TRUE)
  numericDistriABMSim(N0=N0[[2]], params=params, tf=6, Ntf=TRUE)
  numericDistriABMSim(N0=N0[[2]], params=params, tf=8, Ntf=TRUE)
})

profvisTf