`run.MCDS` is confused when fitting a gamma key with covariate

[erex]

Jason Roberts is fitting a gamma with covariates. Minimum reproducible example with the golf tees (below) causes a spurious error to be written to the console:

Code:

library(mrds)
data(book.tee.data)
region <- book.tee.data$book.tee.region
egdata <- book.tee.data$book.tee.dataframe
#  reduce detections at small distances
reduced <- egdata[egdata$distance>0.3, ]
samples <- book.tee.data$book.tee.samples
obs <- book.tee.data$book.tee.obs
result <- ddf(dsmodel = ~mcds(key = "gamma",  formula = ~sex),
              data = reduced[reduced$observer==1, ], method = "ds",
              meta.data = list(width = 4))
summary(result)
plot(result, main="Gamma with sex as covariate")

Message

** Error: When covariates are present, only the half-normal or hazard-rate keys may be specified. **

This appears to be coming from run.MCDS that writes a command file to send to MCDS. This command file is incorrect when the gamma is used

Browse[1]> log.file
 [1] " This is mcds.exe version 7.4.0     "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
 [2] " OPTIONS;                                                                      "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
 [3] " DISTANCE=PERP /UNITS='Meters' /WIDTH=4;                                       "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
 [4] " TYPE=LINE;                                                                    "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
 [5] " OBJECT=SINGLE;                                                                "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
 [6] " PRINT=SUMMARY;                                                                "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
 [7] " SELECTION=SPECIFY;                                                            "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
 [8] " END;                                                                          "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
 [9] " DATA /STRUCTURE=FLAT;                                                         "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[10] " FIELDS=SMP_LABEL,SMP_EFFORT,DISTANCE,sex;                                     "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[11] " INFILE=C:\\Users\\erexs\\AppData\\Local\\Temp\\RtmpITJx3q\\data54cc42d45de4.txt /NOECHO;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               "
[12] " Data will be input from file - [...]TMPITJX3Q\\DATA54CC42D45DE4.TXT"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
[13] " END;                                                                          "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[14] " Dataset has been stored."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
[15] " ESTIMATE;                                                                     "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[16] " DETECTION=ALL;                                                                "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[17] " ESTIMATOR /KEY=NEXPON /COVARIATES=sex;                                        "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[18] " MONOTONE=NONE;                                                                "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[19] " DISTANCE /WIDTH=4 /LEFT=0;                                                    "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[20] " END;                                                                          "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[21] "** Error: When covariates are present, only the half-normal or hazard-rate keys may be specified. **" 

Note the negative exponential incorrectly gets specified and the error messages is appended to the log.file and subsequently printed to the console.

But the story continues:

I believe the code carries on (in ddf.ds) after failing to fit the model when using MCDS, to use the "R" optimiser, which succeeds in fitting the desired gamma-key model with a covariate.

Conclusion

A trap needs to be constructed such that MCDS is not called when trying to fit a gamma key with covariates

[LHMarshall]

MCDS options

CDS analyses

Note that the CDS call for a gamma distribution results in a negative exponential being fitted

MCDS analyses

This is what the user will see now if trying to run this

[LHMarshall]

@erex this issue is fixed on this branch https://github.com/DistanceDevelopment/mrds/tree/Issue-113 will merge and close once we have also resolved the gamma / negative exponential aspect.

Jason can hopfully install using

# First, ensure you have a copy of the `devtools` package:
if (!nzchar(system.file(package = "devtools"))) install.packages("devtools")

devtools::install_github("DistanceDevelopment/mrds", ref = "Issue-113" )

[erex]

My opinion about mrds issue 113 is that the negative exponential is NOT the right thing to do. I'm almost certain that the gamma was not in the minds of Dave and Jonah when they wrote that cascade of if-then-else statements

mrds/R/mcds_tools.R

Line 257 in 50d9c0c

cat("NEXPON", file=command.file.name, append=TRUE)

You'll see that NEXPON is the catch-all "ELSE", if you don't know what to do use the negative exponential. I don't think that's right

[LHMarshall]

@erex yes, although I was confused as to what the thinking was given that the negative exponential is never an option in mrds. I've created a validation function now so easy to add this any any other peculiarities that shouldn't be an option in the future.