Comments (4)
That is... frustrating. I didn't realise there would be such matrices in the data. I can sort of see why in exceptional cases like these it might be necessary to relax the rules of the class, though. What I would suggest doing instead is that we migrate this check to functions in Rage
which assume a nonnegative matrix so that whilst the data may be included in com(p)adre and pass the checks of the ´class, that they can't be in calculations whose assumptions they violate (this is the approach I've taken in popdemo
)
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I can take care of coding this in the CompadreM
class file. I've assigned myself the task
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I've removed the need for matrices to be nonnegative... hopefully now the current databases will work as CompadreM objects @levisc8
We'll need to be careful about making sure to check for nonnegativity in other functions in Rcompadre, Rage and popdemo. For popdemo I've been thinking about writing a checking function that runs through common culprits which can then be run at the start of each functions with arguments to select or deselect the components to check against. Maybe this would be a good idea for Rcompadre and Rage also...
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@iainmstott I've tested the new version and it seems to work. I definitely agree that we need to be mindful of implementing those checks in Rage
and popdemo
though.
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Related Issues (20)
- Add a function to output a Matlab compatible data file
- Function to load local com(p)adre .Rdata files HOT 3
- Change name of matrixClass to MatrixClass for consistency HOT 4
- Check that Rcompadre works well with the old database versions HOT 1
- Add method for droplevels
- Add function to create CompadreDB object from matrices and metadata. HOT 2
- Write vignette to illustrate `cdb_build_cdb` functionality HOT 1
- cdb_rbind - allow binding of COMPADRE objects with different metadata.
- mat_to_string fails when whole matrix is NA HOT 1
- filter error when compiling vignette. Error in storage.mode(x) <- "double" :
- Improve vignette to illustrate cdb_build_cdb functionality
- Add argument to cdb_fetch to automatically add error flag columns HOT 1
- Add vignette with NO piping HOT 1
- Add unit tests to cdb_build_cdb
- Standardize case convention on database column names HOT 1
- add methods for CompadreDB objects or supress helper text HOT 2
- suggestion for additional calculations across matrices: mat_sd and mat_median HOT 2
- 2 small taxonomic inconsistencies for crocodiles and turtles? HOT 1
- cdb_rbind improvement
- popbio should be popdemo HOT 1
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