Trying to apply depth() to NULL?

[mbojan]

While estimating

fit <- ergm(
  net ~ nodefactor("season", levels = TRUE) + nodematch("div"),
  constraints = ~ blockdiag("season"),
  reference = ~ Poisson,
  response = "weight",
  verbose = TRUE,
  control = control.ergm(
    parallel = 7
  )
)

with CRAN versions of packages I'm getting:

(...)
Bridge sampling finished. Collating...
Note: Null model likelihood calculation is not implemented for valued ERGMs at this time.  This
means that all likelihood-based inference (LRT, Analysis of Deviance, AIC, BIC, etc.) is only
valid between models with the same reference distribution and constraints.
This model was fit using MCMC.  To examine model diagnostics and check for degeneracy, use the
mcmc.diagnostics() function.
Warning message:
In UseMethod("depth") :
  no applicable method for 'depth' applied to an object of class "NULL"

I'm filing it here although I'm not yet sure of seriousness of this nor if it belongs to ergm or here. The model took quite a while to converge so I will report back with more detailed debugging info.

EDIT: session info proper:

## - Session info ---------------------------------------------------------------
##  setting  value                       
##  version  R version 4.1.1 (2021-08-10)
##  os       Windows 10 x64              
##  system   x86_64, mingw32             
##  ui       RTerm                       
##  language (EN)                        
##  collate  Polish_Poland.1250          
##  ctype    Polish_Poland.1250          
##  tz       Europe/Warsaw               
##  date     2021-10-13                  
## 
## - Packages -------------------------------------------------------------------
##  package        * version      date       lib source        
##  assertthat       0.2.1        2019-03-21 [1] CRAN (R 4.1.0)
##  box              1.1.0        2021-09-13 [1] CRAN (R 4.1.1)
##  cachem           1.0.6        2021-08-19 [1] CRAN (R 4.1.1)
##  cli              3.0.1        2021-07-17 [1] CRAN (R 4.1.0)
##  coda             0.19-4       2020-09-30 [1] CRAN (R 4.1.0)
##  colorspace       2.0-2        2021-06-24 [1] CRAN (R 4.1.0)
##  crayon           1.4.1        2021-02-08 [1] CRAN (R 4.1.0)
##  DBI              1.1.1        2021-01-15 [1] CRAN (R 4.1.0)
##  DEoptimR         1.0-9        2021-05-24 [1] CRAN (R 4.1.0)
##  digest           0.6.28       2021-09-23 [1] CRAN (R 4.1.1)
##  dplyr            1.0.7        2021-06-18 [1] CRAN (R 4.1.0)
##  ellipsis         0.3.2        2021-04-29 [1] CRAN (R 4.1.0)
##  ergm           * 4.1.2        2021-07-27 [1] CRAN (R 4.1.0)
##  ergm.count     * 4.0-1408     2021-10-09 [1] local         
##  evaluate         0.14         2019-05-28 [1] CRAN (R 4.1.0)
##  fansi            0.5.0        2021-05-25 [1] CRAN (R 4.1.0)
##  farver           2.1.0        2021-02-28 [1] CRAN (R 4.1.0)
##  fastmap          1.1.0        2021-01-25 [1] CRAN (R 4.1.0)
##  generics         0.1.0        2020-10-31 [1] CRAN (R 4.1.0)
##  ggplot2        * 3.3.5        2021-06-25 [1] CRAN (R 4.1.0)
##  glue             1.4.2        2020-08-27 [1] CRAN (R 4.1.0)
##  gtable           0.3.0        2019-03-25 [1] CRAN (R 4.1.0)
##  highr            0.9          2021-04-16 [1] CRAN (R 4.1.0)
##  htmltools        0.5.2        2021-08-25 [1] CRAN (R 4.1.1)
##  igraph           1.2.6        2020-10-06 [1] CRAN (R 4.1.0)
##  intergraph       2.0-2        2016-12-05 [1] CRAN (R 4.1.0)
##  knitr            1.36         2021-09-29 [1] CRAN (R 4.1.1)
##  labeling         0.4.2        2020-10-20 [1] CRAN (R 4.1.0)
##  lattice          0.20-45      2021-09-22 [2] CRAN (R 4.1.1)
##  lifecycle        1.0.1        2021-09-24 [1] CRAN (R 4.1.1)
##  lpSolveAPI       5.5.2.0-17.7 2020-06-14 [1] CRAN (R 4.1.0)
##  magrittr         2.0.1        2020-11-17 [1] CRAN (R 4.1.0)
##  MASS             7.3-54       2021-05-03 [1] CRAN (R 4.1.0)
##  Matrix           1.3-4        2021-06-01 [2] CRAN (R 4.1.1)
##  memoise          2.0.0        2021-01-26 [1] CRAN (R 4.1.0)
##  munsell          0.5.0        2018-06-12 [1] CRAN (R 4.1.0)
##  network        * 1.17.1       2021-06-14 [1] CRAN (R 4.1.0)
##  pillar           1.6.3        2021-09-26 [1] CRAN (R 4.1.1)
##  pkgconfig        2.0.3        2019-09-22 [1] CRAN (R 4.1.0)
##  purrr            0.3.4        2020-04-17 [1] CRAN (R 4.1.0)
##  R6               2.5.1        2021-08-19 [1] CRAN (R 4.1.1)
##  rlang            0.4.11       2021-04-30 [1] CRAN (R 4.1.0)
##  rle              0.9.2        2020-09-25 [1] CRAN (R 4.1.0)
##  rmarkdown        2.11         2021-09-14 [1] CRAN (R 4.1.1)
##  robustbase       0.93-9       2021-09-27 [1] CRAN (R 4.1.1)
##  rstudioapi       0.13         2020-11-12 [1] CRAN (R 4.1.0)
##  scales           1.1.1        2020-05-11 [1] CRAN (R 4.1.0)
##  sessioninfo      1.1.1        2018-11-05 [1] CRAN (R 4.1.0)
##  statnet.common   4.5.0        2021-06-05 [1] CRAN (R 4.1.0)
##  stringi          1.7.4        2021-08-25 [1] CRAN (R 4.1.1)
##  stringr          1.4.0        2019-02-10 [1] CRAN (R 4.1.0)
##  tibble           3.1.5        2021-09-30 [1] CRAN (R 4.1.0)
##  tidyselect       1.1.1        2021-04-30 [1] CRAN (R 4.1.0)
##  trust            0.1-8        2020-01-10 [1] CRAN (R 4.1.0)
##  utf8             1.2.2        2021-07-24 [1] CRAN (R 4.1.0)
##  vctrs            0.3.8        2021-04-29 [1] CRAN (R 4.1.0)
##  withr            2.4.2        2021-04-18 [1] CRAN (R 4.1.0)
##  xfun             0.26         2021-09-14 [1] CRAN (R 4.1.1)
##  yaml             2.2.1        2020-02-01 [1] CRAN (R 4.1.0)
## 
## [1] F:/michal/R/library/x86_64-w64-mingw32/4.1
## [2] F:/michal/Programs/R-4.1.1/library

[krivit]

Can you please add a traceback?

[mbojan]

It's a warning so for traceback I'd need to re-run with options(warn=2). As it took a looong time, I'll try limiting iterations and see if it pops-up.

[krivit]

Hey, just checking: is this still an issue?

[mbojan]

Forgot about it... Will report back.