I have the following variables I am inputting into biomod model:
myResp=
structure(list(occ = c(NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, 1, 1, 1,
NA_real_, 1, 1, 1, 1, 1, 1,
N1, 1)), row.names = c(NA, 20L), class = "data.frame")
ENV<-
structure(list(SST = c(7.59180453767379, 7.73509759058555, 7.84841126371175,
7.93174555705239, 8.07323373736193, 8.27287580464035, 8.60783228824536,
9.07810318817695, 9.55298856149117, 10.032488408188, 10.7857288212205,
11.8127098005886, 12.6318128572156, 13.2430379911015, 13.5948196913426,
13.6871579579388, 13.9124653160572, 14.2707417656978, 14.9238792363554,
15.8718777280301), SSS = c(34.0450506702065, 34.0508728072047,
34.0571919595202, 34.0640081271529, 34.0731531754136, 34.0846271043022,
34.0977436259389, 34.1125027403235, 34.132830452919, 34.1587267637253,
34.2435973445574, 34.3874421954155, 34.5183364008864, 34.6362799609701,
34.6962110688289, 34.6981297244628, 34.7175911421577, 34.7545953219136,
34.8712614620725, 35.0675895626346), SO2 = c(0.299824322961892,
0.299422515447562, 0.299219067511149, 0.299213979152652, 0.298692794353701,
0.297655513114296, 0.2957078315046, 0.292849749524612, 0.289952534728218,
0.287016187115417, 0.282462434495877, 0.276291276869597, 0.271238694060594,
0.267304686068868, 0.265136273610794, 0.264733456686372, 0.263699139289868,
0.262033321421283, 0.258719810688247, 0.253758607090761), NPP = c(3.85156376257745e-07,
3.96088458405608e-07, 4.11107894580006e-07, 4.30214684780938e-07,
4.4703424908014e-07, 4.61566587477609e-07, 4.77750944139858e-07,
4.95587319066885e-07, 5.13265392578418e-07, 5.30785164674456e-07,
5.50156834773034e-07, 5.71380402874152e-07, 5.84950195207471e-07,
5.90866211772993e-07, 5.98413147197737e-07, 6.07591001481704e-07,
6.22490969298673e-07, 6.43113050648643e-07, 6.34808436525414e-07,
5.97577126928983e-07), MLD = c(108.645480087648, 104.108556013554,
98.3433291949332, 92.578102376312, 86.8128755576909, 81.6714904400887,
77.1539470235055, 72.6364036069223, 68.1188601903391, 65.1494404875645,
63.7281444985984, 62.3068485096323, 60.8855525206661, 59.9668972487703,
59.5508826939446, 59.1348681391189, 58.7188535842932, 59.1232465262892,
60.3480469651069, 61.5728474039246), SIC = c(0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names = c(NA,
20L), class = "data.frame")
resp.xy=
structure(list(X = c(-179.75, -179.75, -179.75, -179.75, -179.75,
-179.75, -179.75, -179.75, -179.75, -179.75, -179.75, -179.75,
-179.75, -179.75, -179.75, -179.75, -179.75, -179.75, -179.75,
-179.75), Y = c(-52.25, -51.75, -51.25, -50.75, -50.25, -49.75,
-49.25, -48.75, -48.25, -47.75, -47.25, -46.75, -46.25, -45.75,
-45.25, -44.75, -44.25, -43.75, -43.25, -42.75)), row.names = c(NA,
20L), class = "data.frame")
But I get the following error
library(biomod2)
BIOMOD_FormatingData(
resp.var = SpatialPointsDataFrame(resp.xy, myResp, proj4string = CRS("+proj=longlat +datum=WGS84")),
expl.var = SpatialPointsDataFrame(resp.xy, ENV, proj4string = CRS("+proj=longlat +datum=WGS84")),
resp.name = 'Species',
eval.resp.var = NULL,
eval.expl.var = NULL,
eval.resp.xy = NULL,
PA.nb.rep = 1,
PA.nb.absences = 3,
PA.strategy = "random",
PA.dist.min = 0,
PA.dist.max = NULL,
PA.sre.quant = 0.025,
PA.user.table = NULL,
na.rm = TRUE
)
I get the error: rror in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘BIOMOD.formated.data’ for signature ‘"list", "data.frame"’ which I do not understand , I provide no lists, only SpatialPointsDataFrame object as listed in the documentation
my biomod2 version 4.0 ( but I tried previous versions too), sp version is 1.4.7 ( I am on Windows 10) and using R version 4.2.0 ( but the same error was on previous version)
for version bimod 3.5.1 - there is a bug- so the only way to make it work is convert env variables to ratser :
stack_raster <- function(ENV, resp.xy ) {
r <- stack()
for (col in 1:ncol(ENV)) {
ENV_col <- rasterFromXYZ(cbind(resp.xy, ENV[, col]), digits = 5 )
r <- stack(r , ENV_col)
}
names(r) = colnames(ENV)
return(r)
}
r <- stack_raster(ENV, resp.xy)
r
myBiomodData <- BIOMOD_FormatingData(
resp.var = myResp,
expl.var = r,
resp.xy = resp.xy ,
resp.name = 'Swordfish',
eval.resp.var = NULL,
eval.expl.var = NULL,
eval.resp.xy = NULL,
PA.nb.rep = 1,
PA.nb.absences = 100,
PA.strategy = "random",
PA.dist.min = 0,
PA.dist.max = NULL,
PA.sre.quant = 0.025,
na.rm = TRUE
)
If updated to version 4.0 ( but you will need to update all function names and argument names , the following code will work :
myBiomodData <- BIOMOD_FormatingData(
resp.var = SpatialPointsDataFrame(resp.xy, myResp,, proj4string = CRS("+proj=longlat +datum=WGS84")),
expl.var = SpatialPointsDataFrame(resp.xy, ENV, proj4string = CRS("+proj=longlat +datum=WGS84")),
resp.name = as.character(gsub("[()]", "", metainfo$AcceptedSciName)),
PA.nb.rep = 2,
PA.nb.absences = nb,
PA.strategy = 'random'
)