Error with model-averaged phylolm object

[MarcRieraDominguez]

Hi! Congratulations on the great package! I've com across an error when trying to plot predictions from model-averaged phylolm objects. While ggpredict will plot a phylolm model just fine, it won't plot a model-averaged one. For completion, I show that the error message also appears with model.avg(fit = FALSE).
Cant his be fixed?

Note that the order in which you install the packages is potentially important: this reprex won't work if you load phylolm after MuMIn, I think due to differences in the logLik method. I'll notify the developpers of phylolm of such behaviour.

library(caper)
#> Loading required package: ape
#> Loading required package: MASS
#> Loading required package: mvtnorm
library(ggeffects)
#> Warning: package 'ggeffects' was built under R version 4.2.3
library(phylolm)
library(MuMIn)
#> Warning: package 'MuMIn' was built under R version 4.2.3
#> Registered S3 methods overwritten by 'MuMIn':
#>   method         from   
#>   nobs.pgls      caper  
#>   nobs.phylolm   phylolm
#>   logLik.phylolm phylolm

## Create data
data(shorebird)
summary(shorebird.data)
#>    Species              M.Mass           F.Mass         Egg.Mass    
#>  Length:71          Min.   : 20.30   Min.   : 22.2   Min.   : 5.80  
#>  Class :character   1st Qu.: 54.45   1st Qu.: 62.0   1st Qu.: 9.85  
#>  Mode  :character   Median :108.30   Median :117.0   Median :16.50  
#>                     Mean   :173.95   Mean   :197.3   Mean   :22.45  
#>                     3rd Qu.:181.25   3rd Qu.:243.3   3rd Qu.:29.20  
#>                     Max.   :740.30   Max.   :788.0   Max.   :76.00  
#>     Cl.size      Mat.syst
#>  Min.   :1.700   MO:54   
#>  1st Qu.:3.700   PA:15   
#>  Median :3.900   PG: 2   
#>  Mean   :3.658           
#>  3rd Qu.:4.000           
#>  Max.   :4.100

summary(shorebird.tree)
#> 
#> Phylogenetic tree: shorebird.tree 
#> 
#>   Number of tips: 71 
#>   Number of nodes: 62 
#>   Branch lengths:
#>     mean: 10.12843 
#>     variance: 84.77508 
#>     distribution summary:
#>    Min. 1st Qu.  Median 3rd Qu.    Max. 
#>   0.435   3.483   7.400  13.762  52.100 
#>   No root edge.
#>   First ten tip labels: Catoptrophorus_semipalmatus 
#>                         Tringa_ochropus
#>                         Tringa_stagnatilis
#>                         Tringa_flavipes
#>                         Tringa_nebularia
#>                         Tringa_totanus
#>                         Tringa_erythropus
#>                         Tringa_melanoleuca
#>                         Tringa_glareola
#>                         Steganopus_tricolor
#>   No node labels.


## Fit model
mod <- phylolm::phylolm(Egg.Mass ~ M.Mass + F.Mass, data = shorebird.data, phy = shorebird.tree, model = "lambda")


## Model average
options(na.action = "na.fail")
mod.d <- MuMIn::dredge(mod, rank = "AICc")
#> Fixed term is "(Intercept)"
mod.avg.fit <- MuMIn::model.avg(mod.d, revised.var = TRUE, fit = TRUE)
mod.avg.no.fit <- MuMIn::model.avg(mod.d, revised.var = TRUE, fit = FALSE)


## Compare coefficients
cbind(coef(mod), confint(mod))
#>                               2.5 %     97.5 %
#> (Intercept)  6.41712259 -0.93856939 13.7728146
#> M.Mass      -0.01096584 -0.07074487  0.0488132
#> F.Mass       0.08434847  0.03085706  0.1378399

cbind(coef(mod.avg.fit, full = TRUE), confint(mod.avg.fit, full = TRUE))
#>                                2.5 %      97.5 %
#> (Intercept)  6.437285624 -0.79029863 13.66486988
#> F.Mass       0.076339943  0.04345065  0.10922924
#> M.Mass      -0.001736286 -0.03770974  0.03423716
cbind(coef(mod.avg.no.fit, full = TRUE), confint(mod.avg.no.fit, full = TRUE))
#>                                2.5 %      97.5 %
#> (Intercept)  6.437285624 -0.79029863 13.66486988
#> F.Mass       0.076339943  0.04345065  0.10922924
#> M.Mass      -0.001736286 -0.03770974  0.03423716


plot( ggeffects::ggpredict(mod, terms = c("M.Mass")) )

plot( ggeffects::ggpredict(mod.avg.fit, terms = c("M.Mass")) )
#> Warning: Could not access model information.
#> Warning: Could not access model information.
#> Error in !is.null(model_info) && model_info$is_trial: invalid 'y' type in 'x && y'


plot( ggeffects::ggpredict(mod.avg.no.fit, terms = c("M.Mass")) )
#> Warning: Can't calculate covariance matrix. Please use 'fit = TRUE' in
#>   'model.avg()'.
#> Warning: Can't retrieve data. Please use `fit = TRUE` in `model.avg()`.

#> Warning: Can't retrieve data. Please use `fit = TRUE` in `model.avg()`.
#> Warning: Can't calculate covariance matrix. Please use 'fit = TRUE' in
#>   'model.avg()'.
#> Error in !is.null(model_info) && model_info$is_trial: invalid 'y' type in 'x && y'


sessionInfo()
#> R version 4.2.0 (2022-04-22 ucrt)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 22000)
#> 
#> Matrix products: default
#> 
#> locale:
#> [1] LC_COLLATE=Spanish_Spain.utf8  LC_CTYPE=Spanish_Spain.utf8   
#> [3] LC_MONETARY=Spanish_Spain.utf8 LC_NUMERIC=C                  
#> [5] LC_TIME=Spanish_Spain.utf8    
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] MuMIn_1.47.5      phylolm_2.6.2     ggeffects_1.3.1.5 caper_1.0.1      
#> [5] mvtnorm_1.1-3     MASS_7.3-57       ape_5.6-2        
#> 
#> loaded via a namespace (and not attached):
#>  [1] tidyselect_1.2.0   sjlabelled_1.2.0   xfun_0.40          listenv_0.8.0     
#>  [5] haven_2.5.0        lattice_0.20-45    snakecase_0.11.0   generics_0.1.2    
#>  [9] colorspace_2.0-3   vctrs_0.6.3        htmltools_0.5.6    stats4_4.2.0      
#> [13] yaml_2.3.5         utf8_1.2.2         rlang_1.1.1        pillar_1.9.0      
#> [17] glue_1.6.2         withr_2.5.0        lifecycle_1.0.3    stringr_1.5.0     
#> [21] munsell_0.5.0      gtable_0.3.0       future_1.25.0      codetools_0.2-18  
#> [25] evaluate_0.15      labeling_0.4.2     knitr_1.39         forcats_0.5.1     
#> [29] fastmap_1.1.0      datawizard_0.7.0   parallel_4.2.0     fansi_1.0.3       
#> [33] highr_0.9          Rcpp_1.0.10        scales_1.2.1       farver_2.1.0      
#> [37] parallelly_1.31.1  fs_1.5.2           ggplot2_3.4.0      hms_1.1.1         
#> [41] digest_0.6.29      stringi_1.7.6      dplyr_1.1.2        insight_0.19.5    
#> [45] grid_4.2.0         cli_3.6.1          tools_4.2.0        magrittr_2.0.3    
#> [49] tibble_3.2.1       future.apply_1.9.0 pkgconfig_2.0.3    ellipsis_0.3.2    
#> [53] Matrix_1.4-1       reprex_2.0.2       rmarkdown_2.14     rstudioapi_0.13   
#> [57] R6_2.5.1           globals_0.15.0     nlme_3.1-157       compiler_4.2.0

^{Created on 2023-10-09 with reprex v2.0.2}

[strengejacke]

Thanks! This issue will be fixed once this PR is merged:
easystats/insight#975

library(caper)
#> Loading required package: ape
#> Loading required package: MASS
#> Loading required package: mvtnorm
library(ggeffects)
library(phylolm)
library(MuMIn)
#> Registered S3 methods overwritten by 'MuMIn':
#>   method         from   
#>   nobs.pgls      caper  
#>   nobs.phylolm   phylolm
#>   logLik.phylolm phylolm
## Create data
data(shorebird)
## Fit model
mod <- phylolm::phylolm(Egg.Mass ~ M.Mass + F.Mass, data = shorebird.data, phy = shorebird.tree, model = "lambda")

## Model average
options(na.action = "na.fail")
mod.d <- MuMIn::dredge(mod, rank = "AICc")
#> Fixed term is "(Intercept)"
mod.avg.fit <- MuMIn::model.avg(mod.d, revised.var = TRUE, fit = TRUE)
mod.avg.no.fit <- MuMIn::model.avg(mod.d, revised.var = TRUE, fit = FALSE)

ggeffects::ggpredict(mod.avg.fit, terms = c("M.Mass"))
#> # Predicted values of Egg.Mass
#> 
#> M.Mass | Predicted |       95% CI
#> ---------------------------------
#>      0 |     19.38 | 10.69, 28.08
#>    100 |     19.21 | 12.05, 26.38
#>    200 |     19.04 | 11.76, 26.31
#>    300 |     18.86 |  9.90, 27.83
#>    350 |     18.78 |  8.59, 28.96
#>    450 |     18.60 |  5.56, 31.64
#>    550 |     18.43 |  2.24, 34.62
#>    750 |     18.08 | -4.81, 40.98
#> 
#> Adjusted for:
#> * F.Mass = 169.60
#> 
#> Not all rows are shown in the output. Use `print(..., n = Inf)` to show
#>   all rows.
ggeffects::ggpredict(mod.avg.no.fit, terms = c("M.Mass"))
#> Warning: Can't access model information. Please use 'fit = TRUE' in
#>   'model.avg()'.
#> Warning: Can't access model information. Please use 'fit = TRUE' in
#>   'model.avg()'.
#> Warning: Can't retrieve data. Please use `fit = TRUE` in `model.avg()`.
#> Warning: Can't retrieve data. Please use `fit = TRUE` in `model.avg()`.
#> Warning: Can't access model information. Please use 'fit = TRUE' in
#>   'model.avg()'.
#> Error in names(datlist) <- names(focal_terms): 'names' attribute [1] must be the same length as the vector [0]

^{Created on 2024-11-26 with reprex v2.1.1}