Deriving Goodness of Fit and c-hat from OccuMS

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Benjamin Becker

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Jul 21, 2022, 8:22:53 PMJul 21
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Dear List,

Is there any guidance for calculating c-hat and goodness of fit from an occuMS() model? I see that parboot() does not support the condbinom parameterization and when I run the multinom parameterization I get: 

> parboot(mod04b_stacked_fit)
Error in sample.int(length(x), size, replace, prob) :
  NA in probability vector


The model object works fine with predict(), SSE(), plot(), and gives reasonable errors, plots, and parameter results, but not ranef().

> ranef(mod04b_stacked_fit)
Mean Mode      2.5% 97.5%
[1,] NA   integer,0 NA   NA  
[2,] NA   integer,0 NA   NA  
[3,] NA   integer,0 NA   NA

Thanks for any guidance.

-Ben


Ken Kellner

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Jul 21, 2022, 8:30:21 PMJul 21
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Hi Ben,

parboot and ranef work for me with the example code in the occuMS help file. Do you have missing values in your y-matrix and/or covariates? I suspect these may not be being handled properly.

Ken

On Thu, Jul 21, 2022 at 05:07:43PM -0700, Benjamin Becker wrote:
> Dear List,
>
> Is there any guidance for calculating *c-hat *and *goodness of fit *from an
> *occuMS()* model? I see that parboot() does not support the condbinom
> parameterization and when I run the multinom parameterization I get:
>
> > parboot(mod04b_stacked_fit)
> Error in sample.int(length(x), size, replace, prob) :
> NA in probability vector
>
> The model object works fine with predict(), SSE(), plot(), and gives
> reasonable errors, plots, and parameter results, but not ranef().
>
> > ranef(mod04b_stacked_fit)
> Mean Mode 2.5% 97.5%
> [1,] NA integer,0 NA NA
> [2,] NA integer,0 NA NA
> [3,] NA integer,0 NA NA
>
> Thanks for any guidance.
>
> -Ben
>
>
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Benjamin Becker

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Jul 25, 2022, 10:57:49 PMJul 25
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Thanks so much Ken - You are correct that we have lots of NAs in both the  y-matrix and covariates since we have different numbers of visits for each site and year.  Collapsing/pooling surveys to biweekly or monthly sample periods doesn't help since not all sites are visited each year, and some sites only visited a few times early in the year to establish occupancy, but not revisited later in season if no occupancy.  (problem of highly unbalanced sampling design).

We currently have a survey level covariate for pre-nestling or post-nestling period based on date (0/1).Would it be acceptable to add a third factor level of "not visited" (so (0/1/2) which would remove all NAs from the covariates (but we would still would have NAs in the y's)?

Thanks,

-Ben



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Ken Kellner

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Jul 26, 2022, 8:25:19 AMJul 26
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Hi Ben,

unmarked should handle the NAs itself. I was able to find the problem with ranef but I can't replicate your issue with parboot. Can you email me your model object (mod04b) as an .Rdata or .Rds file off-list (to con...@kenkellner.com) so I can take a closer look at it?

Ken

On Mon, Jul 25, 2022 at 07:57:30PM -0700, Benjamin Becker wrote:
> Thanks so much Ken - You are correct that we have lots of NAs in both the
> y-matrix and covariates since we have different numbers of visits for each
> site and year. Collapsing/pooling surveys to biweekly or monthly sample
> periods doesn't help since not all sites are visited each year, and some
> sites only visited a few times early in the year to establish
> occupancy, but not revisited later in season if no occupancy. (problem of
> highly unbalanced sampling design).
>
> We currently have a survey level covariate for *pre-nestling* or
> *post-nestling* period based on date (0/1).Would it be acceptable to add
> To view this discussion on the web visit https://groups.google.com/d/msgid/unmarked/CADm2a3pA8Tf0apfL6-9rEJEJgoiKJqKt7kODpzxchhiBQdkWWg%40mail.gmail.com.

Ken Kellner

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Jul 26, 2022, 8:58:54 AMJul 26
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I think I figured it out. Can you try the attached patch to see if it helps?

library(unmarked)
source("occuMS_patch.R")

#...your code
> To view this discussion on the web visit https://groups.google.com/d/msgid/unmarked/Yt/dK1W0sfCCYQfs%40COYOTE.
occuMS_patch.R

Benjamin Becker

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Jul 26, 2022, 5:36:48 PMJul 26
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Ken, 

This patch worked for both ranef() and parboot().

Thanks so much !

-Ben

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