Error in goodness of fit test using unmarked

[Rich2210]

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!

[nirgrahamuk]

Hi!

To help us help you, could you please prepare a reproducible example (reprex) illustrating your issue?

You provided code, but not the data that would be required to reproduce your issue.

Please have a look at this guide, to see how to create a reprex:

FAQ: How to do a minimal reproducible example ( reprex ) for beginners

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…