Error in ectorun(ecto) : NA/NaN/Inf in foreign function call (arg 4)
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Maya Viiala
Aug 4, 2025, 2:30:03 AM8/4/25
to NicheMapR
Hello,
I'm trying to run this code:
ecto<-ectotherm(DEB=1,
pantmax = pantmax,
pct_mouth = pct_mouth,
pct_eyes = pct_eyes,
pct_cond = pct_cond,
fluid = fluid,
Ww_g = Ww_g,
stages = stages,
S_instar = S_instar,
s_j = s.j,
metab_mode = metab_mode,
k_EV = k.EV,
kap_V = kap.V,
soilnode = soilnode,
E_sm = E.sm,
X = X,
p_Xm = p.Xm,
pct_H_X = pct_H_X,
pct_H_N = pct_H_N,
pct_H_R = pct_H_R,
pct_H_P = pct_H_P,
pct_H_death = pct_H_death,
K_egg = K_egg,
PE = abs(micro$PE[seq(1, 19, 2)])*-1,
#K_skin = 0,
spec_hyd_egg = spec_hyd_egg,
psi_egg = psi_egg,
pct_cond_egg = pct_cond_egg,
gutfill = gutfill,
raindrink = raindrink,
viviparous=viviparous,
clutchsize=clutchsize,
z.mult=z.mult,
shape=shape,
alpha_max=alpha_max,
alpha_min=alpha_min,
T_F_min=T_F_min,
T_F_max=T_F_max,
T_B_min=T_B_min,
T_RB_min=T_RB_min,
T_pref=T_pref,
CT_max=CT_max,
CT_min=CT_min,
diurn=diurn,
nocturn=nocturn,
crepus=crepus,
shade_seek=shade_seek,
burrow=burrow,
climb=climb,
mindepth=mindepth,
maxdepth=maxdepth,
pct_wet=pct_wet,
z=z*z.mult,
del_M=del.M,
kap_X=kap.X,
v=v/24,
kap=kap,
p_M=p.M/24,
E_G=E.G,
kap_R=kap.R,
k_J=k.J/24,
E_Hb=E.Hb*z.mult^3,
E_Hj=E.Hj*z.mult^3,
E_Hp=E.Hp*z.mult^3,
E_He=E.He*z.mult^3,
h_a=h.a/(24^2),
s_G=s.G,
T_REF=T.ref,
T_A=T.A,
T_AL=T.AL,
T_AH=T.AH,
T_L=T.L,
T_H=T.H,
E_0=E.0*z.mult^4,
f=f,
d_V=d.V,
d_E=d.E,
d_Egg=d.E,
mu_X=mu.X,
mu_E=mu.E,
mu_V=mu.V,
mu_P=mu.P,
kap_X_P=kap.P,
n_X=c(n.CX,n.HX,n.OX,n.NX),
n_E=c(n.CE,n.HE,n.OE,n.NE),
n_V=c(n.CV,n.HV,n.OV,n.NV),
n_P=c(n.CP,n.HP,n.OP,n.NP),
n_M_nitro=c(n.CN,n.HN,n.ON,n.NN),
L_b=L.b,
V_init=V_init,
E_init=E_init,
E_H_init=E_H_init,
stage=stage,
photostart = photostart,
photofinish = photofinish,
starvemode = starvemode,
nyears = 1,
minshades = rep(micro$minshade[-(1:180)], each = 24),
maxshades = rep(micro$maxshade[-(1:180)], each = 24),
metout = micro$metout[-(1:(24*180)), ],
shadmet = micro$shadmet[-(1:(24*180)), ],
soil = micro$soil[-(1:(24*180)), ],
shadsoil = micro$shadsoil[-(1:(24*180)), ],
soilmoist = micro$soilmoist[-(1:(24*180)), ],
shadmoist = micro$shadmoist[-(1:(24*180)), ],
humid = micro$humid[-(1:(24*180)), ],
shadhumid = micro$shadhumid[-(1:(24*180)), ],
soilpot = micro$soilpot[-(1:(24*180)), ],
shadpot = micro$shadpot[-(1:(24*180)), ],
tcond = micro$tcond[-(1:(24*180)), ],
shadtcond = micro$shadtcond[-(1:(24*180)), ],
rainfall = micro$RAINFALL[-(1:180)],
rainhr = rep(-1,nrow(micro$metout[-(1:(24*180)), ])),
preshr = rep(101325 * ((1 - (0.0065 * as.numeric(micro$elev) / 288)) ^ (1/0.190284)), nrow(micro$metout[-(1:(24*180)), ]))
)
pantmax = pantmax,
pct_mouth = pct_mouth,
pct_eyes = pct_eyes,
pct_cond = pct_cond,
fluid = fluid,
Ww_g = Ww_g,
stages = stages,
S_instar = S_instar,
s_j = s.j,
metab_mode = metab_mode,
k_EV = k.EV,
kap_V = kap.V,
soilnode = soilnode,
E_sm = E.sm,
X = X,
p_Xm = p.Xm,
pct_H_X = pct_H_X,
pct_H_N = pct_H_N,
pct_H_R = pct_H_R,
pct_H_P = pct_H_P,
pct_H_death = pct_H_death,
K_egg = K_egg,
PE = abs(micro$PE[seq(1, 19, 2)])*-1,
#K_skin = 0,
spec_hyd_egg = spec_hyd_egg,
psi_egg = psi_egg,
pct_cond_egg = pct_cond_egg,
gutfill = gutfill,
raindrink = raindrink,
viviparous=viviparous,
clutchsize=clutchsize,
z.mult=z.mult,
shape=shape,
alpha_max=alpha_max,
alpha_min=alpha_min,
T_F_min=T_F_min,
T_F_max=T_F_max,
T_B_min=T_B_min,
T_RB_min=T_RB_min,
T_pref=T_pref,
CT_max=CT_max,
CT_min=CT_min,
diurn=diurn,
nocturn=nocturn,
crepus=crepus,
shade_seek=shade_seek,
burrow=burrow,
climb=climb,
mindepth=mindepth,
maxdepth=maxdepth,
pct_wet=pct_wet,
z=z*z.mult,
del_M=del.M,
kap_X=kap.X,
v=v/24,
kap=kap,
p_M=p.M/24,
E_G=E.G,
kap_R=kap.R,
k_J=k.J/24,
E_Hb=E.Hb*z.mult^3,
E_Hj=E.Hj*z.mult^3,
E_Hp=E.Hp*z.mult^3,
E_He=E.He*z.mult^3,
h_a=h.a/(24^2),
s_G=s.G,
T_REF=T.ref,
T_A=T.A,
T_AL=T.AL,
T_AH=T.AH,
T_L=T.L,
T_H=T.H,
E_0=E.0*z.mult^4,
f=f,
d_V=d.V,
d_E=d.E,
d_Egg=d.E,
mu_X=mu.X,
mu_E=mu.E,
mu_V=mu.V,
mu_P=mu.P,
kap_X_P=kap.P,
n_X=c(n.CX,n.HX,n.OX,n.NX),
n_E=c(n.CE,n.HE,n.OE,n.NE),
n_V=c(n.CV,n.HV,n.OV,n.NV),
n_P=c(n.CP,n.HP,n.OP,n.NP),
n_M_nitro=c(n.CN,n.HN,n.ON,n.NN),
L_b=L.b,
V_init=V_init,
E_init=E_init,
E_H_init=E_H_init,
stage=stage,
photostart = photostart,
photofinish = photofinish,
starvemode = starvemode,
nyears = 1,
minshades = rep(micro$minshade[-(1:180)], each = 24),
maxshades = rep(micro$maxshade[-(1:180)], each = 24),
metout = micro$metout[-(1:(24*180)), ],
shadmet = micro$shadmet[-(1:(24*180)), ],
soil = micro$soil[-(1:(24*180)), ],
shadsoil = micro$shadsoil[-(1:(24*180)), ],
soilmoist = micro$soilmoist[-(1:(24*180)), ],
shadmoist = micro$shadmoist[-(1:(24*180)), ],
humid = micro$humid[-(1:(24*180)), ],
shadhumid = micro$shadhumid[-(1:(24*180)), ],
soilpot = micro$soilpot[-(1:(24*180)), ],
shadpot = micro$shadpot[-(1:(24*180)), ],
tcond = micro$tcond[-(1:(24*180)), ],
shadtcond = micro$shadtcond[-(1:(24*180)), ],
rainfall = micro$RAINFALL[-(1:180)],
rainhr = rep(-1,nrow(micro$metout[-(1:(24*180)), ])),
preshr = rep(101325 * ((1 - (0.0065 * as.numeric(micro$elev) / 288)) ^ (1/0.190284)), nrow(micro$metout[-(1:(24*180)), ]))
)
but keep getting this error message: Error in ectorun(ecto) : NA/NaN/Inf in foreign function call (arg 4)
I've tried reinstalling NicheMapR, but that didn't work. In micro$metout and micro$shadmet, the column 'POOLDEP' returns all NaNs. I also get NaNs in other outputs (soilpot, shadpot etc.,). The microclimate model runs with no issues. I'm a bit stuck on how to fix this.
Thanks,
Maya
NicheMapR
Aug 4, 2025, 2:36:35 AM8/4/25
to NicheMapR
Hi Maya,
Yes it’s to do with something going wrong in the microclimate simulation. There shouldn’t be NaNs in the output. I'll have to see the code you’re using to simulate the microclimate. Are you running the Shiny app and then modifying the code?
All the best,
Mike
Maya Viiala
Aug 4, 2025, 2:40:08 AM8/4/25
to NicheMapR
Hi Mike,
Thanks re. rocks.
I am using the shiny apps then modifying the code from there? Is that what's causing the problem?
This is my microclimate code:
dstart <- "31/12/1979"
dfinish <- "31/12/2024"
minshade <- 0
maxshade <- 30
Thcond <- 2.5
SpecHeat <- 870
Density <- 2.56
BulkDensity <- 2.56
windfac <- 1
REFL <- 0.2
cap <- 0
SLE <- 0.95
warm <- 0
Usrhyt <- 0.01
clearsky <- 0
lon <- 117.32987
lat <- -32.54115997
cat('downloading DEM via package elevatr \n')
dem <- microclima::get_dem(r = NA, lat = lat, lon = lon, resolution = 5, zmin = -20, xdims = 100, ydims = 100)
if(FALSE){
elev <- raster::extract(dem, c(lon, lat))[1]
xy <- data.frame(x = lon, y = lat)
sp::coordinates(xy) = ~x + y
sp::proj4string(xy) = "+init=epsg:4326"
xy <- as.data.frame(sp::spTransform(xy, raster::crs(dem)))
slope <- raster::terrain(dem, unit = "degrees")
slope <- raster::extract(slope, xy)
aspect <- raster::terrain(dem, opt = "aspect", unit = "degrees")
aspect <- raster::extract(aspect, xy)
ha36 <- 0
for (i in 0:35) {
har <- microclima::horizonangle(dem, i * 10, raster::res(dem)[1])
ha36[i + 1] <- atan(raster::extract(har, xy)) * (180/pi)
}
hori <- spline(x = ha36, n = 24, method = 'periodic')$y
hori[hori < 0] <- 0
hori[hori > 90] <- 90
}else{
slope <- 0
aspect <- 0
hori<- c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
ha36 <- spline(x = hori, n = 36, method = 'periodic')$y
ha36[ha36 < 0] <- 0
ha36[ha36 > 90] <- 90
elev <- NA
}
rainmult = 1
DEP=c(0, 2.5, 5, 10, 15, 20, 30, 50, 100, 200)
claypan = FALSE
if(claypan){
soilpro <- matrix(data = 0, nrow = 6, ncol = 5)
colnames(soilpro) <- c("depth", "blkdens", "clay", "silt", "sand")
soilpro[, 1] <- c(2.5, 7.5, 22.5, 45, 80, 150)
soilpro[, 2] <- 1.4 # bulk density (Mg/m3)
soilpro[, 3] <- 90 # % clay
soilpro[, 4] <- 0 # % silit
soilpro[, 5] <- 10 # % sand
soil.hydro <- pedotransfer(soilpro = as.data.frame(soilpro), DEP = DEP)
PE <- soil.hydro$PE
BB <- soil.hydro$BB
BD <- soil.hydro$BD
KS <- soil.hydro$KS
BulkDensity <- BD[seq(1, 19, 2)] * 1000 #rep(1360,10) # soil bulk density (kg/m3)
DD = rep(Density, 19)
}else{
PE = rep(1.1, 19)
KS = rep(0.0037, 19)
BB = rep(4.5, 19)
BD = rep(BulkDensity, 19)
DD = rep(Density, 19)
}
soilgrids <- 0
ERR <- 1
tz <- tz_lookup_coords(lat, lon, method = "fast")
dataset <- 'SILO'
if(dataset == 'SILO'){
micro <- micro_silo(dem = dem, SLE = SLE, ERR = ERR, Thcond = Thcond, SpecHeat = SpecHeat, dstart = dstart, dfinish = dfinish, Usrhyt = Usrhyt, soilgrids = soilgrids,
windfac = windfac, slope = slope, aspect = aspect, REFL = REFL,
hori = hori, minshade = minshade,
maxshade = maxshade, loc = c(lon, lat), runshade = 1,
run.gads = 1, snowmodel = 0, BulkDensity = BulkDensity, Density = Density,
cap = cap, warm = warm,
email = "maya....@outlook.com", PE = PE, BB = BB, KS = KS, BD = BD, DD = DD)
while(min(micro$metout[,1]) == 0 & ERR <= 3){
cat("model crashed, trying a higher error tolerance \n")
ERR <- ERR + 0.5
micro <- micro_silo(dem = dem, SLE = SLE, ERR = ERR, Thcond = Thcond, SpecHeat = SpecHeat, dstart = dstart, dfinish = dfinish, Usrhyt = Usrhyt, soilgrids = soilgrids,
windfac = windfac, slope = slope, aspect = aspect, REFL = REFL,
hori = hori, minshade = minshade,
maxshade = maxshade, loc = c(lon, lat), runshade = 1,
run.gads = 1, snowmodel = 0, BulkDensity = BulkDensity, Density = Density,
cap = cap, warm = warm,
email = "maya....@outlook.com", PE = PE, BB = BB, KS = KS, BD = BD, DD = DD)
}
}else{
micro <- micro_micro.in(ERR = ERR, soilgrids = soilgrids, dstart = dstart, dfinish = dfinish,
Usrhyt = Usrhyt, slope = slope, aspect = aspect, REFL = REFL,
hori = hori, minshade = minshade, maxshade = maxshade,
loc = c(lon, lat), runshade = 1, run.gads = 1, snowmodel = 0,
BulkDensity = BulkDensity, cap = cap, elev = elev,
Density = Density, Thcond = Thcond, SpecHeat = SpecHeat,
windfac = windfac, PE = PE, BB = BB, KS = KS, BD = BD, DD = DD)
while(min(micro$metout[,1]) == 0 & ERR <= 3){
cat("model crashed, trying a higher error tolerance \n")
ERR <- ERR + 0.5
micro <- micro_micro.in(ERR = ERR, soilgrids = soilgrids, dstart = dstart, dfinish = dfinish,
Usrhyt = Usrhyt, slope = slope, aspect = aspect, REFL = REFL,
hori = hori, minshade = minshade, maxshade = maxshade,
loc = c(lon, lat), runshade = 1, run.gads = 1, snowmodel = 0,
BulkDensity = BulkDensity, cap = cap, elev = elev,
Density = Density, Thcond = Thcond, SpecHeat = SpecHeat,
windfac = windfac, PE = PE, BB = BB, KS = KS, BD = BD, DD = DD)
}
}
dfinish <- "31/12/2024"
minshade <- 0
maxshade <- 30
Thcond <- 2.5
SpecHeat <- 870
Density <- 2.56
BulkDensity <- 2.56
windfac <- 1
REFL <- 0.2
cap <- 0
SLE <- 0.95
warm <- 0
Usrhyt <- 0.01
clearsky <- 0
lon <- 117.32987
lat <- -32.54115997
cat('downloading DEM via package elevatr \n')
dem <- microclima::get_dem(r = NA, lat = lat, lon = lon, resolution = 5, zmin = -20, xdims = 100, ydims = 100)
if(FALSE){
elev <- raster::extract(dem, c(lon, lat))[1]
xy <- data.frame(x = lon, y = lat)
sp::coordinates(xy) = ~x + y
sp::proj4string(xy) = "+init=epsg:4326"
xy <- as.data.frame(sp::spTransform(xy, raster::crs(dem)))
slope <- raster::terrain(dem, unit = "degrees")
slope <- raster::extract(slope, xy)
aspect <- raster::terrain(dem, opt = "aspect", unit = "degrees")
aspect <- raster::extract(aspect, xy)
ha36 <- 0
for (i in 0:35) {
har <- microclima::horizonangle(dem, i * 10, raster::res(dem)[1])
ha36[i + 1] <- atan(raster::extract(har, xy)) * (180/pi)
}
hori <- spline(x = ha36, n = 24, method = 'periodic')$y
hori[hori < 0] <- 0
hori[hori > 90] <- 90
}else{
slope <- 0
aspect <- 0
hori<- c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
ha36 <- spline(x = hori, n = 36, method = 'periodic')$y
ha36[ha36 < 0] <- 0
ha36[ha36 > 90] <- 90
elev <- NA
}
rainmult = 1
DEP=c(0, 2.5, 5, 10, 15, 20, 30, 50, 100, 200)
claypan = FALSE
if(claypan){
soilpro <- matrix(data = 0, nrow = 6, ncol = 5)
colnames(soilpro) <- c("depth", "blkdens", "clay", "silt", "sand")
soilpro[, 1] <- c(2.5, 7.5, 22.5, 45, 80, 150)
soilpro[, 2] <- 1.4 # bulk density (Mg/m3)
soilpro[, 3] <- 90 # % clay
soilpro[, 4] <- 0 # % silit
soilpro[, 5] <- 10 # % sand
soil.hydro <- pedotransfer(soilpro = as.data.frame(soilpro), DEP = DEP)
PE <- soil.hydro$PE
BB <- soil.hydro$BB
BD <- soil.hydro$BD
KS <- soil.hydro$KS
BulkDensity <- BD[seq(1, 19, 2)] * 1000 #rep(1360,10) # soil bulk density (kg/m3)
DD = rep(Density, 19)
}else{
PE = rep(1.1, 19)
KS = rep(0.0037, 19)
BB = rep(4.5, 19)
BD = rep(BulkDensity, 19)
DD = rep(Density, 19)
}
soilgrids <- 0
ERR <- 1
tz <- tz_lookup_coords(lat, lon, method = "fast")
dataset <- 'SILO'
if(dataset == 'SILO'){
micro <- micro_silo(dem = dem, SLE = SLE, ERR = ERR, Thcond = Thcond, SpecHeat = SpecHeat, dstart = dstart, dfinish = dfinish, Usrhyt = Usrhyt, soilgrids = soilgrids,
windfac = windfac, slope = slope, aspect = aspect, REFL = REFL,
hori = hori, minshade = minshade,
maxshade = maxshade, loc = c(lon, lat), runshade = 1,
run.gads = 1, snowmodel = 0, BulkDensity = BulkDensity, Density = Density,
cap = cap, warm = warm,
email = "maya....@outlook.com", PE = PE, BB = BB, KS = KS, BD = BD, DD = DD)
while(min(micro$metout[,1]) == 0 & ERR <= 3){
cat("model crashed, trying a higher error tolerance \n")
ERR <- ERR + 0.5
micro <- micro_silo(dem = dem, SLE = SLE, ERR = ERR, Thcond = Thcond, SpecHeat = SpecHeat, dstart = dstart, dfinish = dfinish, Usrhyt = Usrhyt, soilgrids = soilgrids,
windfac = windfac, slope = slope, aspect = aspect, REFL = REFL,
hori = hori, minshade = minshade,
maxshade = maxshade, loc = c(lon, lat), runshade = 1,
run.gads = 1, snowmodel = 0, BulkDensity = BulkDensity, Density = Density,
cap = cap, warm = warm,
email = "maya....@outlook.com", PE = PE, BB = BB, KS = KS, BD = BD, DD = DD)
}
}else{
micro <- micro_micro.in(ERR = ERR, soilgrids = soilgrids, dstart = dstart, dfinish = dfinish,
Usrhyt = Usrhyt, slope = slope, aspect = aspect, REFL = REFL,
hori = hori, minshade = minshade, maxshade = maxshade,
loc = c(lon, lat), runshade = 1, run.gads = 1, snowmodel = 0,
BulkDensity = BulkDensity, cap = cap, elev = elev,
Density = Density, Thcond = Thcond, SpecHeat = SpecHeat,
windfac = windfac, PE = PE, BB = BB, KS = KS, BD = BD, DD = DD)
while(min(micro$metout[,1]) == 0 & ERR <= 3){
cat("model crashed, trying a higher error tolerance \n")
ERR <- ERR + 0.5
micro <- micro_micro.in(ERR = ERR, soilgrids = soilgrids, dstart = dstart, dfinish = dfinish,
Usrhyt = Usrhyt, slope = slope, aspect = aspect, REFL = REFL,
hori = hori, minshade = minshade, maxshade = maxshade,
loc = c(lon, lat), runshade = 1, run.gads = 1, snowmodel = 0,
BulkDensity = BulkDensity, cap = cap, elev = elev,
Density = Density, Thcond = Thcond, SpecHeat = SpecHeat,
windfac = windfac, PE = PE, BB = BB, KS = KS, BD = BD, DD = DD)
}
}
apologies for the mass of text.
Thanks,
Maya
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