Fail on ZI model

[mattansb]

Can't close easystats/effectsize#135 until this is resolved here.

I'm sure detective @strengejacke will figure this out soon enough (:

library(pscl)
#> Classes and Methods for R developed in the
#> Political Science Computational Laboratory
#> Department of Political Science
#> Stanford University
#> Simon Jackman
#> hurdle and zeroinfl functions by Achim Zeileis

data("bioChemists")
m <- zeroinfl(art ~ fem + mar * exp(kid5) + ment | kid5 + phd, data = bioChemists)
#> Warning in value[[3L]](cond): system is computationally singular: reciprocal
#> condition number = 1.40243e-18FALSE

parameters::model_parameters(m)
#> Error in match.arg(component): 'arg' must be NULL or a character vector

^{Created on 2020-09-25 by the reprex package (v0.3.0)}

[strengejacke]

I think, the source of this issue is in the pscl package:

library(pscl)
data("bioChemists")
m <- zeroinfl(art ~ fem + mar * exp(kid5) + ment | kid5 + phd, data = bioChemists)
#> Warning in value[[3L]](cond): system is computationally singular: reciprocal
#> condition number = 1.40243e-18FALSE

summary(m)
#> 
#> Call:
#> zeroinfl(formula = art ~ fem + mar * exp(kid5) + ment | kid5 + phd, data = bioChemists)
#> 
#> Pearson residuals:
#>     Min      1Q  Median      3Q     Max 
#> -1.4931 -0.9865 -0.3077  0.5162  7.0935 
#> 
#> Count model coefficients (poisson with log link):
#>                       Estimate Std. Error z value Pr(>|z|)
#> (Intercept)           0.614732         NA      NA       NA
#> femWomen             -0.222654         NA      NA       NA
#> marMarried            0.100129         NA      NA       NA
#> exp(kid5)            -0.049270         NA      NA       NA
#> ment                  0.020771         NA      NA       NA
#> marMarried:exp(kid5)  0.005204         NA      NA       NA
#> 
#> Zero-inflation model coefficients (binomial with logit link):
#>             Estimate Std. Error z value Pr(>|z|)
#> (Intercept) -0.91252         NA      NA       NA
#> kid5         0.04277         NA      NA       NA
#> phd         -0.25150         NA      NA       NA
#> 
#> Number of iterations in BFGS optimization: 15 
#> Log-likelihood: -1619 on 9 Df
coef(summary(m))
#> $count
#>                          Estimate Std. Error z value Pr(>|z|)
#> (Intercept)           0.614731515         NA      NA       NA
#> femWomen             -0.222653796         NA      NA       NA
#> marMarried            0.100128808         NA      NA       NA
#> exp(kid5)            -0.049270280         NA      NA       NA
#> ment                  0.020770936         NA      NA       NA
#> marMarried:exp(kid5)  0.005203873         NA      NA       NA
#> 
#> $zero
#>                Estimate Std. Error z value Pr(>|z|)
#> (Intercept) -0.91252297         NA      NA       NA
#> kid5         0.04277055         NA      NA       NA
#> phd         -0.25150110         NA      NA       NA

^{Created on 2020-09-26 by the reprex package (v0.3.0)}

this caused .compact_list() to fail (so we essentially have to revise this helper-function in all packages):
The code snippet any(i == "NULL") must be any(i == "NULL", na.rm = TRUE).

Now it works:

library(pscl)
data("bioChemists")
m <- zeroinfl(art ~ fem + mar * exp(kid5) + ment | kid5 + phd, data = bioChemists)
#> Warning in value[[3L]](cond): system is computationally singular: reciprocal
#> condition number = 1.40243e-18FALSE

cs <- coef(summary(m))
insight:::.compact_list(cs)
#> $count
#>                          Estimate Std. Error z value Pr(>|z|)
#> (Intercept)           0.614731515         NA      NA       NA
#> femWomen             -0.222653796         NA      NA       NA
#> marMarried            0.100128808         NA      NA       NA
#> exp(kid5)            -0.049270280         NA      NA       NA
#> ment                  0.020770936         NA      NA       NA
#> marMarried:exp(kid5)  0.005203873         NA      NA       NA
#> 
#> $zero
#>                Estimate Std. Error z value Pr(>|z|)
#> (Intercept) -0.91252297         NA      NA       NA
#> kid5         0.04277055         NA      NA       NA
#> phd         -0.25150110         NA      NA       NA

^{Created on 2020-09-26 by the reprex package (v0.3.0)}

But since only NA is returned, get_statistic() is no longer meaningful:

library(pscl)
#> Classes and Methods for R developed in the
#> Political Science Computational Laboratory
#> Department of Political Science
#> Stanford University
#> Simon Jackman
#> hurdle and zeroinfl functions by Achim Zeileis
data("bioChemists")
m <- zeroinfl(art ~ fem + mar * exp(kid5) + ment | kid5 + phd, data = bioChemists)
#> Warning in value[[3L]](cond): system is computationally singular: reciprocal
#> condition number = 1.40243e-18FALSE

insight::get_statistic(m)
#>                    Parameter Statistic     Component
#> 1          count_(Intercept)        NA   conditional
#> 2             count_femWomen        NA   conditional
#> 3           count_marMarried        NA   conditional
#> 4            count_exp(kid5)        NA   conditional
#> 5                 count_ment        NA   conditional
#> 6 count_marMarried:exp(kid5)        NA   conditional
#> 7           zero_(Intercept)        NA zero_inflated
#> 8                  zero_kid5        NA zero_inflated
#> 9                   zero_phd        NA zero_inflated

parameters::model_parameters(m)
#> # Fixed Effects component
#> 
#> Parameter                  | Log-Mean
#> -------------------------------------
#> (Intercept)                |     0.61
#> fem [Women]                |    -0.22
#> mar [Married]              |     0.10
#> kid5 [exp]                 |    -0.05
#> ment                       |     0.02
#> mar [Married] * kid5 [exp] | 5.20e-03
#> 
#> # Zero-Inflated component
#> 
#> Parameter   | Log-Odds
#> ----------------------
#> (Intercept) |    -0.91
#> kid5        |     0.04
#> phd         |    -0.25

^{Created on 2020-09-26 by the reprex package (v0.3.0)}

[strengejacke]

It's actually a problem of the model specification, this works:

library(pscl)
#> Classes and Methods for R developed in the
#> Political Science Computational Laboratory
#> Department of Political Science
#> Stanford University
#> Simon Jackman
#> hurdle and zeroinfl functions by Achim Zeileis
data("bioChemists")
m <- zeroinfl(art ~ fem + mar + kid5 + ment | kid5 + phd, data = bioChemists)

insight::get_statistic(m)
#>           Parameter  Statistic     Component
#> 1 count_(Intercept)  8.2629494   conditional
#> 2    count_femWomen -3.9098651   conditional
#> 3  count_marMarried  2.0713360   conditional
#> 4        count_kid5 -3.4315540   conditional
#> 5        count_ment 10.0539061   conditional
#> 6  zero_(Intercept) -2.1430201 zero_inflated
#> 7         zero_kid5  0.2138228 zero_inflated
#> 8          zero_phd -1.8425594 zero_inflated

parameters::model_parameters(m)
#> # Fixed Effects component
#> 
#> Parameter     | Log-Mean |       SE |         95% CI |     z |      p
#> ---------------------------------------------------------------------
#> (Intercept)   |     0.56 |     0.07 | [ 0.43,  0.69] |  8.26 | < .001
#> fem [Women]   |    -0.23 |     0.06 | [-0.34, -0.11] | -3.91 | < .001
#> mar [Married] |     0.14 |     0.07 | [ 0.01,  0.27] |  2.07 | 0.038 
#> kid5          |    -0.17 |     0.05 | [-0.26, -0.07] | -3.43 | < .001
#> ment          |     0.02 | 2.12e-03 | [ 0.02,  0.03] | 10.05 | < .001
#> 
#> # Zero-Inflated component
#> 
#> Parameter   | Log-Odds |   SE |         95% CI |     z |     p
#> --------------------------------------------------------------
#> (Intercept) |    -0.93 | 0.43 | [-1.78, -0.08] | -2.14 | 0.032
#> kid5        |     0.05 | 0.22 | [-0.38,  0.47] |  0.21 | 0.831
#> phd         |    -0.25 | 0.14 | [-0.51,  0.02] | -1.84 | 0.065

^{Created on 2020-09-26 by the reprex package (v0.3.0)}