Forum: open-discussion

Requesting help regarding Biomod2 [ Reply ]
By: Kasuni Pitawala on 2022-12-22 18:48

I am new to RStudio, and I am carrying out my research on determining the species distribution of paddy using 19 bioclimatic variables.

Mentioned below are the codes I ran upto now,

## load the required packages
library(biomod2)
library(ggplot2)
library(gridExtra)
library(raster)
library(rasterVis)

## read data ----
Paddy_GPS <- read.csv('D:/Kasuni Research/SDM/Data/Paddy_GPS/GPS_Presence_csv.csv')
summary(Paddy_GPS)

HBCV <-
raster::stack(
c(
HBCV1 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv1.asc',
HBCV2 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv2.asc',
HBCV3 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv3.asc',
HBCV4 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv4.asc',
HBCV5 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv5.asc',
HBCV6 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv6.asc',
HBCV7 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv7.asc',
HBCV8 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv8.asc',
HBCV9 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv9.asc',
HBCV10 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv10.asc',
HBCV11 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv11.asc',
HBCV12 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv12.asc',
HBCV13 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv13.asc',
HBCV14 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv14.asc',
HBCV15 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv15.asc',
HBCV16 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv16.asc',
HBCV17 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv17.asc',
HBCV18 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv18.asc',
HBCV19 = 'D:/Kasuni Research/SDM/Data/HBCV/hbcv19.asc'
)
)

HBCV

rm(Paddy_GPS)

rm(Paddy_data)

rm(Paddy_opt)

## format the data ----
Paddy_data <-
BIOMOD_FormatingData(
resp.var = Paddy_GPS['Paddy'],
resp.xy = Paddy_GPS[, c('Long', 'Lat')],
expl.var = HBCV,
resp.name = "Paddy",
PA.nb.rep = 2,
PA.nb.absences = 25,
PA.strategy = 'random'
)

## formatted object summary
Paddy_data

## plot of selected pseudo-absences
plot(Paddy_data)

## define individual models options ----
Paddy_opt <-
BIOMOD_ModelingOptions(
GLM = NULL,
GBM = NULL,
SRE = NULL,
MAXENT.Phillips = NULL,
MARS = NULL,
FDA = NULL,
CTA = NULL,
ANN = NULL,
RF = NULL
)

## run the individual models ----
Paddy_models <-
BIOMOD_Modeling(
data = Paddy_data,
models = c("GLM", "GBM", "SRE", "MAXENT.Phillips", "MARS", "FDA", "CTA", "ANN", "RF"),
models.options = Paddy_opt,
NbRunEval = 70,
DataSplit = 80,
VarImport = 10,
modeling.id = "1"
)

However, when I ran the individual models (BIOMOD_Modeling), I got the error mentioned below,

Error in BIOMOD_Modeling(data = Paddy_data, models = c("GLM", "GBM", "SRE", :
argument 1 matches multiple formal arguments

May I please know how I can resolve this issue?