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Perna canaliculus rundeb error #34

@jatalah

Description

@jatalah

Hi,

I am trying to run a DEB model for Perna canaliculus using the rundeb function, but I get the following error:


deb <- rundeb(
  species = species,
  ndays = ndays,
  div = div,
  Tbs = Tbs,
  clutchsize = clutchsize,
  Xs = Xs,
  mass.unit = mass.unit,
  length.unit = length.unit,
  start.stage = start.stage,
  E_sm = E_sm,
  plot = plot
)

NOTE: No length data in parameter estimation, assuming del.M of 0.2, predictions of physical lengths are suspect. 
Error in if (H < E_Hb) { : missing value where TRUE/FALSE needed

This is the code I am using, based on the tutorial here: https://mrke.github.io/NicheMapR/inst/doc/deb-model-tutorial


library(NicheMapR)
# Load saved data
load("C:/Users/javiera/OneDrive - Cawthron/Stats/others/allstat.Rda")

# Get all species names
allDEB.species <- unlist(labels(allStat$allStat))
allDEB.species <- allDEB.species[1:(length(allDEB.species) - 2)]

head(allDEB.species)
allDEB.species[str_detect(allDEB.species, "Perna.canaliculus")]

species <- "Perna.canaliculus"
species.slot <- which(allDEB.species == species)
par.names <- unlist(labels(allStat$allStat[[species.slot]]))

for (i in seq_along(par.names)) {
  assign(par.names[i], unlist(allStat$allStat[[species.slot]][i]))
}

# Model parameters
ndays <- 365 * 3
div <- 1
Tbs <- rep(25, ndays * div)
starvetime <- 0
X <- 100
Xs <- c(
  rep(X, ndays * div / 2),
  rep(0.000005, starvetime),
  rep(X, ndays * div / 2 - starvetime + 1)
)
E_sm <- 350
clutchsize <- 5
mass.unit <- "g"
length.unit <- "mm"
plot <- 1
start.stage <- 1

deb <- rundeb(
  species = species,
  ndays = ndays,
  div = div,
  Tbs = Tbs,
  clutchsize = clutchsize,
  Xs = Xs,
  mass.unit = mass.unit,
  length.unit = length.unit,
  start.stage = start.stage,
  E_sm = E_sm,
  plot = plot
)

Could you please advise what might be causing this error and whether I need to manually add certain species parameters for P. canaliculus?

Thanks,
Javier

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