pcountOpen goodness-of-fit help

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parker....@gmail.com

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Aug 15, 2022, 12:44:06 PMAug 15
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Hi all, 
First thanks to everyone who takes the time to respond to messages in this group. It's really a great resource! 

I am running a larger pcountOpen model (~1100 sites, 22 primary periods, 12 visits). I am attempting to run a goodness-of-fit test on a cluster computer using AICcmodavg's Nmix.gof.test. When I run the test with a lower number of simulations (1000), it runs but I get a NaN value for chat. I'm moving forward on the assumption (or hope) that that is a problem of not enough simulations and not lack of fit. However, when I attempt to increase the number of simulations to 5k (and I plan to run 10k) I get this error: 

"Error in socketAccept(socket = socket, blocking = TRUE, open = "a+b",  :
  all connections are in use"

My current request from the cluster is 32 cores on a single node with 650GB of memory. So I'm hoping someone with more experience with cluster computers and parboot might:

  1. Have a suggestion for best practices for running Nmix.gof.test() on a cluster. So that might look like is it better to run this (or any) GOF test with more nodes, cores, memory etc. Any insight would be appreciated.  
  2. Know what is going on with that socket error? 
The summary output of my unmarkedFramePCO object is below. The NAs are mostly structural placeholders for when there were fewer than 12 visits per year. Though some of the yearly site covariates do not yet have data for the final year. I'm currently trying to run the goodness-of-fit test on the model below rather than a global or set of sub-global models. 

Thanks! 
Kevin 

system.time(go.spei90d_july_p_HOR <-
              pcountOpen(
                lambda = ~HOR,
                gamma  = ~gm_spei90d_p,
                omega  = ~HOR,
                p      = ~Season,
                umf_bre,
                K=68,
                #se= FALSE,
                #starts = inits,
                dynamics = "gompertz"
              ))
 


unmarkedFrame Object

1181 sites
Maximum number of observations per site: 264
Mean number of observations per site: 4.84
Number of primary survey periods: 22
Number of secondary survey periods: 12
Sites with at least one detection: 1165

Tabulation of y observations:
     0      1      2      3      4      5      6      7      8      9     10     11     12
   659   3036    868    393    248    122     87     61     46     41     17     20     23
    13     14     15     16     17     18     19     20     21     22     23     24     25
    12     11      7      3      5      7      3      3      8      4      6      2      2
    26     27     28     29     30     32     36     39     40     45     46     48   <NA>
     2      2      1      2      1      2      1      2      1      1      1      1                306073

Site-level covariates:
   bd_result           HOR                      nndist                      DuPont                 private      
 Min.   :0.0000      Min.   :0.0000      Min.   :   0.637       Min.   :0.0000       Min.   :0.0000  
 1st Qu.:0.0000   1st Qu.:0.0000     1st Qu.:  20.028   1st Qu.:0.0000      1st Qu.:0.0000  
 Median :0.0000  Median :0.0000   Median :  45.360   Median :1.0000   Median :0.0000  
 Mean   :0.1611    Mean   :0.1016    Mean   : 134.210   Mean   :0.5868    Mean   :0.2049  
 3rd Qu.:0.0000    3rd Qu.:0.0000    3rd Qu.: 113.463   3rd Qu.:1.0000    3rd Qu.:0.0000  
 Max.   :2.0000    Max.   :1.0000       Max.   :5657.168   Max.   :1.0000    Max.   :1.0000  
 NA's   :1032                                                                          

Observation-level covariates:
     J_date             Season      
 Min.   : 17.0        Spring:  1437  
 1st Qu.:150.0     Summer:  1683  
 Median :252.0    Fall  :  2242  
 Mean   :221.7     Winter:   349  
 3rd Qu.:293.0     NA's  :306073  
 Max.   :365.0                  
 NA's   :306073                  

Yearly-site-level covariates:
   pdsi_aug_c.V1    pdsi_july_c.V1    pdsi_july_p.V1     pdsi_aug_p.V1    tmax_july_c.V1  
 Min.   :-1.5937      Min.   :-1.8284      Min.   :-1.7713      Min.   :-1.5210   Min.   :-3.5197  
 1st Qu.:-0.6979    1st Qu.:-0.8107    1st Qu.:-0.7508     1st Qu.:-0.7416   1st Qu.:-0.6595  
 Median :-0.3033   Median :-0.2126   Median :-0.3480   Median :-0.3297   Median :-0.0424 
 Mean   : 0.0000    Mean   : 0.0000     Mean   : 0.0000    Mean   : 0.0000   Mean   : 0.0000  
 3rd Qu.: 0.7735    3rd Qu.: 0.7218     3rd Qu.: 0.7560    3rd Qu.: 0.7105   3rd Qu.: 0.6465  
 Max.   : 2.3190     Max.   : 2.2126      Max.   : 2.2808      Max.   : 2.3878   Max.   : 4.3779  
 NA's   :1181          NA's   :1181           NA's   :1181           NA's   :1181      NA's   :1181    

 
  tmax_july_p.V1     tmax_aug_c.V1     tmax_aug_p.V1     tmin_dec_c.V1     tmin_jan_c.V1  
 Min.   :-3.5319   Min.   :-3.0506   Min.   :-3.0741   Min.   :-2.9035   Min.   :-2.8460  
 1st Qu.:-0.6651   1st Qu.:-0.7425   1st Qu.:-0.7123   1st Qu.:-0.7157   1st Qu.:-0.7050  
 Median :-0.0246   Median : 0.0027   Median :-0.0181   Median : 0.2886   Median :-0.1785 
 Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000  
 3rd Qu.: 0.6432   3rd Qu.: 0.5299   3rd Qu.: 0.5656   3rd Qu.: 0.5742   3rd Qu.: 0.7016  
 Max.   : 4.3646   Max.   : 4.3156   Max.   : 4.1261   Max.   : 2.7258   Max.   : 2.3145  
 NA's   :1181      NA's   :1181      NA's   :1181      NA's   :1181      NA's   :1181    
 
   tmin_dec_p.V1     tmin_jan_p.V1    gm_spei180d        gm_spei1y         gm_spei2y      
 Min.   :-2.9317   Min.   :-2.8940   Min.   :-2.0900   Min.   :-2.0900   Min.   :-2.09000  
 1st Qu.:-0.7325   1st Qu.:-0.6990   1st Qu.:-0.7100   1st Qu.:-0.6200   1st Qu.:-0.80000  
 Median : 0.2771   Median :-0.1593   Median :-0.3200   Median :-0.1000   Median:0.03000 
 Mean   : 0.0000   Mean   : 0.0000   Mean   :-0.0443   Mean   : 0.1445   Mean   : 0.09956  
 3rd Qu.: 0.5642   3rd Qu.: 0.7392   3rd Qu.: 0.5400   3rd Qu.: 1.1300   3rd Qu.: 0.80000  
 Max.   : 2.7270   Max.   : 2.3966   Max.   : 2.0900   Max.   : 2.0900   Max.   : 2.09000  
 NA's   :1181      NA's   :1181          
                                                  
  gm_spei30d_p       gm_spei90d_p    
 Min.   :-2.09000   Min.   :-2.09000  
 1st Qu.:-0.54000   1st Qu.:-0.62000  
 Median :-0.17000   Median :-0.03000  
 Mean   :-0.01057   Mean   : 0.07694  
 3rd Qu.: 0.63000   3rd Qu.: 1.13000  
 Max.   : 2.09000   Max.   : 2.09000  

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