Nothing
## -----------------------------------------------------------------------------
### Experimental temperatures and development rate for the eggs
expeTempEggs <- c(10.0, 10.0, 13.0, 15.0, 15.0, 15.5, 16.0, 16.0, 17.0, 20.0, 20.0,
25.0, 25.0, 30.0, 30.0, 35.0)
expeDevEggs <- c(0.031, 0.039, 0.072, 0.047, 0.059, 0.066, 0.083, 0.1, 0.1, 0.1, 0.143,
0.171, 0.2, 0.2, 0.18, 0.001)
dfDevEggs <- data.frame(expeTempEggs, expeDevEggs)
### Experimental temperatures and development rate for the larva
expeTempLarva <- c(10.0, 10.0, 10.0, 13.0, 15.0, 15.5, 15.5, 15.5, 17.0, 20.0, 25.0,
25.0, 30.0, 35.0)
expeDevLarva <- c(0.01, 0.014, 0.019, 0.034, 0.024, 0.029, 0.034, 0.039, 0.067, 0.05,
0.076, 0.056, 0.0003, 0.0002)
dfDevLarva <- data.frame(expeTempLarva, expeDevLarva)
### Experimental temperatures and development rate for the pupa
expeTempPupa <- c(10.0, 10.0, 10.0, 13.0, 15.0, 15.0, 15.5, 15.5, 16.0, 16.0, 17.0,
20.0, 20.0, 25.0, 25.0, 30.0, 35.0)
expeDevPupa <- c(0.001, 0.008, 0.012, 0.044, 0.017, 0.044, 0.039, 0.037, 0.034, 0.051, 0.051, 0.08, 0.092, 0.102, 0.073, 0.005, 0.0002)
dfDevPupa <- data.frame(expeTempPupa, expeDevPupa)
### Same dataset included in the package in the form of matrices
library("devRate")
data(exTropicalMoth)
str(exTropicalMoth[[1]])
## -----------------------------------------------------------------------------
devRateFind(orderSP = "Lepidoptera")
## -----------------------------------------------------------------------------
devRateFind(familySP = "Gelechiidae")
## -----------------------------------------------------------------------------
devRateFind(species = "Tecia solanivora")
## -----------------------------------------------------------------------------
devRateFind(species = "Symmetrischema tangolias")
devRateFind(species = "Phthorimaea operculella")
## -----------------------------------------------------------------------------
devRateInfo(eq = taylor_81)
devRateInfo(eq = lactin1_95)
## -----------------------------------------------------------------------------
taylor_81$startVal[taylor_81$startVal["genSp"] == "Symmetrischema tangolias",]
lactin1_95$startVal[lactin1_95$startVal["genSp"] == "Phthorimaea operculella",]
## ---- fig.width = 6, fig.height = 6-------------------------------------------
devRatePlotInfo (eq = taylor_81, sortBy = "ordersp",
ylim = c(0, 0.20), xlim = c(0, 50))
devRatePlotInfo (eq = lactin1_95, sortBy = "ordersp",
ylim = c(0, 1.00), xlim = c(0, 50))
## -----------------------------------------------------------------------------
### using the vectors from section "Organizing the dataset"
############################################################
### for the taylor_81 model
mEggs01 <- devRateModel(eq = taylor_81,
temp = expeTempEggs,
devRate = expeDevEggs,
startValues = list(Rm = 0.05, Tm = 30, To = 5))
mLarva01 <- devRateModel(eq = taylor_81,
temp = expeTempLarva,
devRate = expeDevLarva,
startValues = list(Rm = 0.05, Tm = 25, To = 10))
mPupa01 <- devRateModel(eq = taylor_81,
temp = expeTempPupa,
devRate = expeDevPupa,
startValues = list(Rm = 0.1, Tm = 30, To = 10))
### for the lactin1_95 model
mEggs01b <- devRateModel(eq = lactin1_95,
temp = expeTempEggs,
devRate = expeDevEggs,
startValues = list(aa = 0.177, Tmax = 36.586, deltaT = 5.631))
# mLarva01b <- devRateModel(eq = lactin1_95,
# temp = expeTempLarva,
# devRate = expeDevLarva,
# startValues = list(aa = 0.169, Tmax = 37.914, deltaT = 5.912))
### The algorithm has not found a solution after 50 iterations
### One possibility is to increase the maximum number of iterations
### using the "control" argument (see ?nls() for more details).
mLarva01b <- devRateModel(eq = lactin1_95,
temp = expeTempLarva,
devRate = expeDevLarva,
startValues = list(aa = 0.169, Tmax = 37.914, deltaT = 5.912),
control = list(maxiter = 500))
mPupa01b <- devRateModel(eq = lactin1_95,
temp = expeTempPupa,
devRate = expeDevPupa,
startValues = list(aa = 0.193, Tmax = 36.291, deltaT = 5.18),
control = list(maxiter = 500))
### using the data frames from section "Organizing the dataset"
############################################################
mEggs02 <- devRateModel(eq = taylor_81,
dfData = dfDevEggs,
startValues = list(Rm = 0.05, Tm = 30, To = 5))
mLarva02 <- devRateModel(eq = taylor_81,
dfData = dfDevLarva,
startValues = list(Rm = 0.05, Tm = 25, To = 10))
mPupa02 <- devRateModel(eq = taylor_81,
dfData = dfDevPupa,
startValues = list(Rm = 0.1, Tm = 30, To = 10))
### using the dataset included in the package (only for taylor_81 model)
############################################################
mEggs <- devRateModel(eq = taylor_81,
temp = exTropicalMoth$raw$eggs[,1],
devRate = exTropicalMoth$raw$eggs[,2],
startValues = list(Rm = 0.05, Tm = 30, To = 5))
mLarva <- devRateModel(eq = taylor_81,
temp = exTropicalMoth$raw$larva[,1],
devRate = exTropicalMoth$raw$larva[,2],
startValues = list(Rm = 0.05, Tm = 25, To = 10))
mPupa <- devRateModel(eq = taylor_81,
temp = exTropicalMoth$raw$pupa[,1],
devRate = exTropicalMoth$raw$pupa[,2],
startValues = list(Rm = 0.1, Tm = 30, To = 10))
## -----------------------------------------------------------------------------
resultNLS <- devRatePrint(myNLS = mLarva)
resultNLSb <- devRatePrint(myNLS = mLarva01b)
## ---- fig.width = 7, fig.height = 5-------------------------------------------
par(mfrow = c(1, 2), mar = c(4, 4, 0, 0))
devRatePlot(eq = taylor_81,
nlsDR = mEggs,
pch = 16, ylim = c(0, 0.2))
devRatePlot(eq = lactin1_95,
nlsDR = mEggs01b,
pch = 16, ylim = c(0, 0.2))
devRatePlot(eq = taylor_81,
nlsDR = mLarva,
pch = 16, ylim = c(0, 0.1))
devRatePlot(eq = lactin1_95,
nlsDR = mLarva01b,
pch = 16, ylim = c(0, 0.1))
devRatePlot(eq = taylor_81,
nlsDR = mPupa,
pch = 16, ylim = c(0, 0.15))
devRatePlot(eq = lactin1_95,
nlsDR = mPupa01b,
pch = 16, ylim = c(0, 0.15))
## -----------------------------------------------------------------------------
### Models for the larva life stage
c(AIC(mLarva), AIC(mLarva01b))
c(BIC(mLarva), BIC(mLarva01b))
c(logLik(mLarva), logLik(mLarva01b))
## -----------------------------------------------------------------------------
forecastTsolanivora <- devRateIBM(
tempTS = rnorm(n = 100, mean = 15, sd = 1),
timeStepTS = 1,
models = list(mEggs, mLarva, mPupa),
numInd = 50,
stocha = 0.015,
timeLayEggs = 1)
print(forecastTsolanivora)
## ---- fig.width = 6, fig.height = 6-------------------------------------------
devRateIBMPlot(ibm = forecastTsolanivora, typeG = "density")
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