Hi there,
I am trying to conduct a goodness of fit test using the mb.gof.test from the unmarked package. It gives me the following error:
Error in hist.mat[j, ] <- ifelse(strip.hist == "1", preds.p.not.na[j, :
number of items to replace is not a multiple of replacement length
my code is as follows
#########################################################################################################
## Canis Mesomelas Survey Template
## Richard Carkeek
## Zoology Honours Project 2020
#########################################################################################################
setwd()
#########################################################################################################
## Relative abundance indeces
RAI_N_L <- read.csv("RAI_N_L2.csv", header = T, sep = ";", dec = ".")
View(RAI_N_L)
#########################################################################################################
## Scale Data
RAI_N_L[,1:11] <- scale(RAI_N_L[,1:11], center = TRUE, scale = TRUE)
DFRAI_N_L <- data.frame(RAI_N_L)
View(DFRAI_N_L)
#########################################################################################################
## Spearmans Correlation
corL = cor(DFRAI_N_L, method = "spearman")
View(corL)
#########################################################################################################
## Remove correlated variables
# med + large prey
# megaherb
# med pred
# Human
DFRAI_N_L[,c(3, 4, 5, 7)] <- NULL
DFRAI_N_L[,6] <- NULL
#########################################################################################################
## Replace Standardized values with words for habitat and road (Potentially Camera traps as well)
DFRAI_N_L[,6] <- data.frame ("Habitat"=c ("BS",
"GL",
"ST",
"BT",
"FP",
"ST",
"ST",
"GL",
"GL",
"GL",
"BT",
"GL",
"GL"))
DFRAI_N_L[,7] <- data.frame ("Road"=c ("Path",
"Path",
"Road",
"Road",
"Road",
"Path",
"Road",
"Road",
"Road",
"Road",
"Path",
"Road",
"Path"))
DFRAI_N_L[,1] <- data.frame ("CT" = c ("L1",
"L3",
"L4",
"L5",
"L6",
"L7",
"L8",
"L9",
"L10",
"L11",
"L12",
"L13",
"L14"))
#########################################################################################################
## Import Dection Data (Collapsed Intervals)
## 4 Day interval
D4L <- read.csv("4DL.csv", header = T, sep = ";", dec = ".")
View(D4L)
#########################################################################################################
## Detection tests (Unmarked and AIC)
## Unmarked Frame 4 Days
umfL4 <- unmarkedFrameOccu(y = D4L, siteCovs = DFRAI_N_L)
umfL4
fmL4 <- occu(~1~ Small_Prey + Small_Pred + Large_Pred + Habitat + Road, data = umfL4)
fmL4
#########################################################################################################
## This all works fine
#########################################################################################################
## This is the line of code for the goodness of fit test which produces the error
RL4 <- mb.gof.test(fmL4, plot.hist = TRUE, nsim = 1000)
RL4
## The Error
> RL4 <- mb.gof.test(fmL4, plot.hist = TRUE, nsim = 1000)
Error in hist.mat[j, ] <- ifelse(strip.hist == "1", preds.p.not.na[j, :
number of items to replace is not a multiple of replacement length
Any advice or help will be greatly appreciated, Thanks!