Pink bands not in the right place in the check.mono plot (mrds function)

[LHMarshall]

Note check.mono is actually in mrds

Len commented:

• I can't make sense of the plot that come from calling check.mono(hn2$ddf, plot = TRUE) in that I expect the pink bar at the top to show where one of the constraints is broken, but it looks pink everywhere. I suspect there is a bug in the chpply function, which is defined within check.mono but I have not looked into it. I can raise as a separate issue if that's helpful.

Originally posted by @lenthomas in #186

MRE

The following code uses these duiker data: DaytimeDistances.txt

DuikerCameraTraps <- read.csv(file="DaytimeDistances.txt", header=TRUE, sep="\t")
DuikerCameraTraps$Area <- DuikerCameraTraps$Area / (1000*1000)
DuikerCameraTraps$object <- NA
DuikerCameraTraps$object[!is.na(DuikerCameraTraps$distance)] <- 1:sum(!is.na(DuikerCameraTraps$distance))

library(Distance)
trunc.list <- list(left = 2, right = 15)
mybreaks <- c(seq(2, 8, 1), 10, 12, 15)
conversion <- convert_units("meter", NULL, "square kilometer")
hn2 <- ds(DuikerCameraTraps, transect = "point", key = "hn", 
          adjustment = "cos",
          nadj=2, convert_units = conversion,
          monotonicity = "none",
          cutpoints = mybreaks, truncation = trunc.list)
plot(hn2)

check.mono(hn2$ddf, n.pts=10, plot = TRUE) # gives TRUE

[lenthomas]

Thanks @LHMarshall.

I note that the call to check.mono returns FALSE not TRUE, and that's the correct thing in this case where monotonicity is broken.

Looking at the plot, I think I understand what the it is doing, and I think all that is needed is some additional documentation. (Also this could probably be confirmed by looking at the code, which I have not done.)

I think there are 3 red boxes here, overlain. The top one, from 1-1.3 on the y-axis and 1-15 on the x-axis seems to show the area where estimated probability of detection is more than one. The second one from 0-1.3 on the y-axis and 1-5.5 on the x-axis shows the distnaces where weak monotonicity is broken. The third one, from 0-1.3 on the y-axis and 1-7 is where strict monotonicity is broken. This can be confirmed by adding strict = FALSE to the call to check.mono, above - this box then disappears.

One separate minor issue is the warning that In rug(x) : some values will be clipped. This is probably because of the left truncation, and hopefully could be fixed relatively easily?