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neither tidy nor glance methods work for gee objects #708

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IndrajeetPatil opened this issue May 28, 2019 · 4 comments
Closed

neither tidy nor glance methods work for gee objects #708

IndrajeetPatil opened this issue May 28, 2019 · 4 comments
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@dgrtwo
Labels
beginner-friendly bug an unexpected problem or unintended behavior

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@IndrajeetPatil
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Objects of class gee are not supported but because it also inherits glm class, I guess that's the tidier that gets picked up.

# setup
set.seed(123)
library(MASS)
library(gee)
data(OME)

# model
fm <-
  gee(
    cbind(Correct, Trials - Correct) ~ Loud + Age + OME,
    id = ID,
    data = OME,
    family = binomial,
    corstr = "exchangeable"
  )
#> Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
#> running glm to get initial regression estimate
#> (Intercept)        Loud         Age     OMEhigh      OMElow 
#> -5.90984676  0.15516993  0.01876291 -0.07569691 -0.31660542

# class of object
class(fm)
#> [1] "gee" "glm"

# summary
summary(fm)
#> 
#>  GEE:  GENERALIZED LINEAR MODELS FOR DEPENDENT DATA
#>  gee S-function, version 4.13 modified 98/01/27 (1998) 
#> 
#> Model:
#>  Link:                      Logit 
#>  Variance to Mean Relation: Binomial 
#>  Correlation Structure:     Exchangeable 
#> 
#> Call:
#> gee(formula = cbind(Correct, Trials - Correct) ~ Loud + Age + 
#>     OME, id = ID, data = OME, family = binomial, corstr = "exchangeable")
#> 
#> Summary of Residuals:
#>        Min         1Q     Median         3Q        Max 
#> -0.9585811  0.5507230  2.0414189  3.1210663 12.0241951 
#> 
#> 
#> Coefficients:
#>                Estimate  Naive S.E.     Naive z Robust S.E.    Robust z
#> (Intercept) -5.90100336 0.336455218 -17.5387482 0.231463368 -25.4943295
#> Loud         0.15507565 0.007513314  20.6401142 0.005321880  29.1392592
#> Age          0.01851319 0.003561640   5.1979385 0.003305525   5.6006793
#> OMEhigh     -0.04183516 0.160288285  -0.2609995 0.152182352  -0.2749015
#> OMElow      -0.28563252 0.131496124  -2.1721745 0.117510247  -2.4307031
#> 
#> Estimated Scale Parameter:  1.250466
#> Number of Iterations:  4
#> 
#> Working Correlation
#>              [,1]        [,2]        [,3]        [,4]        [,5]
#>  [1,]  1.00000000 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [2,] -0.02344803  1.00000000 -0.02344803 -0.02344803 -0.02344803
#>  [3,] -0.02344803 -0.02344803  1.00000000 -0.02344803 -0.02344803
#>  [4,] -0.02344803 -0.02344803 -0.02344803  1.00000000 -0.02344803
#>  [5,] -0.02344803 -0.02344803 -0.02344803 -0.02344803  1.00000000
#>  [6,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [7,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [8,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [9,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [10,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [11,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [12,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [13,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [14,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [15,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [16,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [17,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [18,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [19,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [20,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [21,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [22,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [23,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [24,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [25,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [26,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [27,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [28,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [29,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [30,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>              [,6]        [,7]        [,8]        [,9]       [,10]
#>  [1,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [2,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [3,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [4,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [5,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [6,]  1.00000000 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [7,] -0.02344803  1.00000000 -0.02344803 -0.02344803 -0.02344803
#>  [8,] -0.02344803 -0.02344803  1.00000000 -0.02344803 -0.02344803
#>  [9,] -0.02344803 -0.02344803 -0.02344803  1.00000000 -0.02344803
#> [10,] -0.02344803 -0.02344803 -0.02344803 -0.02344803  1.00000000
#> [11,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [12,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [13,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [14,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [15,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [16,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [17,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [18,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [19,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [20,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [21,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [22,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [23,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [24,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [25,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [26,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [27,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [28,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [29,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [30,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>             [,11]       [,12]       [,13]       [,14]       [,15]
#>  [1,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [2,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [3,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [4,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [5,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [6,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [7,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [8,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [9,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [10,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [11,]  1.00000000 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [12,] -0.02344803  1.00000000 -0.02344803 -0.02344803 -0.02344803
#> [13,] -0.02344803 -0.02344803  1.00000000 -0.02344803 -0.02344803
#> [14,] -0.02344803 -0.02344803 -0.02344803  1.00000000 -0.02344803
#> [15,] -0.02344803 -0.02344803 -0.02344803 -0.02344803  1.00000000
#> [16,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [17,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [18,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [19,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [20,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [21,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [22,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [23,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [24,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [25,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [26,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [27,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [28,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [29,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [30,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>             [,16]       [,17]       [,18]       [,19]       [,20]
#>  [1,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [2,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [3,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [4,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [5,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [6,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [7,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [8,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [9,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [10,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [11,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [12,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [13,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [14,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [15,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [16,]  1.00000000 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [17,] -0.02344803  1.00000000 -0.02344803 -0.02344803 -0.02344803
#> [18,] -0.02344803 -0.02344803  1.00000000 -0.02344803 -0.02344803
#> [19,] -0.02344803 -0.02344803 -0.02344803  1.00000000 -0.02344803
#> [20,] -0.02344803 -0.02344803 -0.02344803 -0.02344803  1.00000000
#> [21,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [22,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [23,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [24,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [25,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [26,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [27,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [28,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [29,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [30,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>             [,21]       [,22]       [,23]       [,24]       [,25]
#>  [1,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [2,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [3,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [4,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [5,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [6,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [7,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [8,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [9,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [10,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [11,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [12,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [13,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [14,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [15,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [16,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [17,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [18,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [19,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [20,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [21,]  1.00000000 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [22,] -0.02344803  1.00000000 -0.02344803 -0.02344803 -0.02344803
#> [23,] -0.02344803 -0.02344803  1.00000000 -0.02344803 -0.02344803
#> [24,] -0.02344803 -0.02344803 -0.02344803  1.00000000 -0.02344803
#> [25,] -0.02344803 -0.02344803 -0.02344803 -0.02344803  1.00000000
#> [26,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [27,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [28,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [29,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [30,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>             [,26]       [,27]       [,28]       [,29]       [,30]
#>  [1,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [2,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [3,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [4,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [5,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [6,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [7,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [8,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#>  [9,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [10,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [11,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [12,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [13,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [14,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [15,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [16,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [17,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [18,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [19,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [20,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [21,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [22,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [23,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [24,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [25,] -0.02344803 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [26,]  1.00000000 -0.02344803 -0.02344803 -0.02344803 -0.02344803
#> [27,] -0.02344803  1.00000000 -0.02344803 -0.02344803 -0.02344803
#> [28,] -0.02344803 -0.02344803  1.00000000 -0.02344803 -0.02344803
#> [29,] -0.02344803 -0.02344803 -0.02344803  1.00000000 -0.02344803
#> [30,] -0.02344803 -0.02344803 -0.02344803 -0.02344803  1.00000000

# tidy output
broom::tidy(fm)
#> Column 6 must be named.
#> Use .name_repair to specify repair.

# glance
broom::glance(fm)
#> All columns in a tibble must be 1d or 2d objects:
#> * Column `null.deviance` is NULL
#> * Column `df.null` is NULL
#> * Column `deviance` is NULL
#> * Column `df.residual` is NULL

Created on 2019-05-28 by the reprex package (v0.3.0)

Session info 
devtools::session_info()
#> - Session info ----------------------------------------------------------
#>  setting  value                                    
#>  version  R version 3.6.0 alpha (2019-03-29 r76300)
#>  os       Windows 10 x64                           
#>  system   x86_64, mingw32                          
#>  ui       RTerm                                    
#>  language (EN)                                     
#>  collate  English_United States.1252               
#>  ctype    English_United States.1252               
#>  tz       America/New_York                         
#>  date     2019-05-28                               
#> 
#> - Packages --------------------------------------------------------------
#>  package     * version    date       lib source                         
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#>  backports     1.1.4      2019-04-10 [1] CRAN (R 3.6.0)                 
#>  broom         0.5.2.9001 2019-04-09 [1] local                          
#>  callr         3.2.0      2019-03-15 [1] CRAN (R 3.6.0)                 
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#>  desc          1.2.0      2019-04-03 [1] Github (r-lib/desc@c860e7b)    
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#>  fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                 
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#> 
#> [1] C:/Users/inp099/Documents/R/win-library/3.6
#> [2] C:/Program Files/R/R-3.6.0alpha/library
@alexpghayes
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The short term solution is:

#' @export
tidy.gee <- tidy.default

and analogous methods for glance() and augment(). The long term solution is proper tidiers.

@alexpghayes alexpghayes added beginner-friendly bug an unexpected problem or unintended behavior labels Aug 7, 2019
@alexpghayes
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@jyuu This could be a six liner or you could write new tidiers from scratch

alexpghayes added a commit that referenced this issue Aug 13, 2019
@alexpghayes
Block glm tidiers for gee objects. Fixes #708.
ce212e7
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Closed in #742

@simonpcouch simonpcouch mentioned this issue Dec 3, 2020
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github-actions bot commented Mar 9, 2021

This issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with a reprex: https://reprex.tidyverse.org) and link to this issue.

@github-actions github-actions bot locked and limited conversation to collaborators Mar 9, 2021
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