Error in finding compute.link and related functions

posts related to the RMark library, which may not be of general interest to users of 'classic' MARK

Error in finding compute.link and related functions

Postby kefagan » Mon Nov 29, 2021 7:50 pm

Hello,

For context, I'm running a multi-scale occupancy model. My models perform as expected, and model outputs are consistent with those from other programs (e.g., Presence). Using the parameter estimates from my top model and the delta method, I have my estimates of standard error around cumulative probability of detection. I now need to estimate confidence intervals, which must be first calculated on the logit scale.

Here's my problem: At first glance, it seemed that RMark had a few options for giving me estimates and the VCV matrix on the logit scale (i.e., functions described in the package like 'compute.link' and 'compute.links.from.reals'). Unfortunately, these lead to the same error suggesting that the functions are not available (e.g., ' Error in compute.link(model = top.mod, design = dm, vcv = TRUE) : could not find function "compute.link" '). The 'real'-related equivalents of these functions (e.g., 'compute.real', 'get.real') work as expected.

Does anyone have insight on the availability of these functions? I do have the most recent versions of both MARK and RMARK (both of which I have uninstalled and reinstalled, just in case). Should I side-step the delta method altogether and instead use bootstrapping to generate my confidence intervals?

Thank you for your time.
kefagan
 
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Re: Error in finding compute.link and related functions

Postby jlaake » Mon Nov 29, 2021 7:56 pm

I'm not exactly sure what you are doing, but in a package some functions are exported and others are not. But you can always get to a function by typing pkg:::fct like RMark:::compute.link
jlaake
 
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Re: Error in finding compute.link and related functions

Postby kefagan » Wed Dec 08, 2021 4:55 pm

This worked perfectly. Thank you!
kefagan
 
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