title: Edit: Set dispersion parameter in pooled dataset (mids object)
body: <p>EDIT 2 27/7: I figured out that I must get the correct output if I set the dispersion parameter to 0.64.</p>
  
  <p>I tried doing this with</p>
  
  <pre><code>summary(fit, dispersion = 0.64) 
  </code></pre>
  
  <p>but this doesn't work. Probably because it is an imputed dataset with pooled estimates. It does work in a dataset without imputation. Does anyone know how to rewrite this line so it will work in the pooled dataset?</p>
  
  <hr>
  
  <p>EDIT 26/7: I have managed to find the solution to this in the sample data:</p>
  
  <pre><code>gamma.shape(fit)
  summary(fit, dispersion = gamma.dispersion(fit))
  summary(fit, dispersion=1/gamma.shape(fit)$alpha)
  </code></pre>
  
  <p>The final line reproduces similar S.E.'s and p-values as SPSS. However, when I try to use the same method in the pooled dataset, it doesn't work. This is the error I get:</p>
  
  <pre><code> gamma.shape(fit)
  Error in -y : invalid argument to unary operator
  &gt; gamma.shape(pool(fit))
  Error in UseMethod("gamma.shape") : 
   no applicable method for 'gamma.shape' applied to an object of class 
  "c('mipo', 'data.frame')"
  &gt; 
  </code></pre>
  
  <p>Any clues on how to solve this?</p>
  
  <hr>
  
  <p>I am experiencing some difficulties with R. I previously posted a question here which brought me further, but also led to a different question:</p>
  
  <p>Is it possible to change the scale parameter method in R? I am performing a GLM with gamma log-link, but the estimated S.E.'s, confidence intervals and p-values differ between R and SPSS. I would like to replicate the exact SPSS findings in R, and I can't figure out how.</p>
  
  <p>My original dataset is an imputed dataset (mids object, created with the MICE package). For simplification, I have created a sample dataset with less data:</p>
  
  <p>## Sample data</p>
  
  <pre><code>F &lt;- structure(list(HbA1c = c(69, 75, 62, 96, NA, 86, 44, 49, NA, 63, 43, 75, 48, 56, 79, 78, 67, 66, 75, 67, 65, 66, 34, 62, 79, 60, 91, 51, 84, 72, 65, NA, NA, 62, 61, 69, 63, NA, 85, 38, 42, 80, 59, 96, 59, 49, 62, 98, 71, 78, 50, 43, 44, 69, 56, 38, 59, 74, 115, 69, 67, 51, NA, 107, 71, 86, 78, 41, 60, 59, 74, 73, 49, 34, 71, 57, 55, 74, 67, 61, 48, 59, 70, NA, 55, 72, 69, 82, 40, 58, NA, 53, 46, 69, 60, 39, 76, 69, 61, 86, 58, 63, 66, 103, 73, 54, 59, 46, 58, 70, 57, 53, 49, 53, 58, 71, 60, 76, 64, 97, 60, 49, 53, 44, 53, 73, 59, 75, 61, 55, 68, 56, 51, 91, 92, 76, 51, 55, 61, 83, 52, 62, 71, 75, 54, 64, 90, 65, NA, 69, 70, 70, 59, 62, 60, 63, 58, 58, 63, 60, 49, 62, 95, 42, 99, 67, 117, 68, 55, 55, 70, 60, 61, 91, 33, 89, 60, 47, 62, 72, 40, 88, 59, 56, 57, 59, 74, 41, 53, 76, 48, 73, 65, 96, 58, 55, 67, 45, 45, 69, 72, 44, 59, 43, 90, 69, 69, 71, 93, 42, 87, 54, 83, 60, 48, NA, 53, 56, 57, 77, 63, NA, 63, 60, 68, 51, 48, 65, 61, 79, 63, 62, 53, 67, 53, 53, 63, 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37, 37, 74, 53, 36, 60, 33, 35, 26, 44, 78, 22, 26, 77, 62, 121, 51, 28, 68, 63, 43, 64, 81, 120, 95, 98, 23, 11, 21, 10, 7, 41, 7, 33, 6, 40, 20, 2, 31, 23, 23, 13, 68, 9, 8, 41, 19, 27, 29, 46, NA, 35, 16, 12, 9, 14, 20, 7, 2, 4, 6, 6, 6, 4, 9, 6, 8, 9, 12, 9, 7, 8, 12, 11, 11, 14, 12, 14, 12, 16, 15, 22, 23, 19, 11, 12, 13, 17, 18, 19, 27, 15, 9, 17, 18, 19, 17, 19, 12, 16, 54, 21, 30, 23, 25, 24, 37, 35, 27, 47, 22, 27, 27, 30, 32, 32, 31, 39, 28, 36, 54, 50, 45, 42, 88, 56, 63, 82, 60, 70, 139, 122, 71, 130, 84, 33, 111, 111, 246, 157, 54, 24, 41, 22, 7, 33, 15, 9, 6, 16, 67, 3, 22, 48, 15, 57, 25, 48, 74, 40, 25, 18, 21, 3, 6, 7, 7, 14, 9, 11, 16, 14, 14, 14, 28, 18, 22, 21, 26, 39, 24, 22, 18, 22, 19, 19, 45, 15, 13, 22, 31, 29, 46, 37, 23, 35, 68, 39, 51, 35, 50, 80, 69, 51, 41, 90, 43, 32, 48, 34, 53, 25, 66, 39, 83, 70, 237, 81, 126, 95, 170, 35, 94, 8), etndich = c(1, 2, 1, 2, 1, 2, 1, 1, NA, 1, 1, 1, 1, 1, NA, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 2, 2, 1, 1, 2, 1, 1, 2, 1, 1, 2, 2, NA, 2, 1, NA, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, NA, 1, 2, 1, 2, 1, 1, 1, 1, 2, 1, 1, 1, 2, 1, 2, NA, 2, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 2, 1, 1, 1, 2, 1, 1, NA, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 2, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 1, 1, 1, 1, NA, 2, 1, 1, 1, 1, 1, 2, 1, 1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 2, 1, 1, 2, 1, 1, 1, 1, 2, 1, 1, 2, 2, 1, 2, 1, 1, 1, 1, 1, 2, 1, 2, 2, 1, 1, 1, 1, NA, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 2, 1, 2, 2, 1, 1, 2, 1, 1, 2, NA, 1, 2, 2, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 2, 1, NA, NA, 2, 1, 2, 1, 2, 1, 1, 1, 2, 1, 2, 2, 1, 1, 2, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, NA, 2, 1, 1, 1, 1, NA, 1, 1, 2, 1, 1, 1, 2, 1, NA, 1, 1, 1, 1, 1, 1, 1, NA, NA, 2, 1, 1, 2, 2, NA, 2, NA, 2, 2, 1, NA, 1, NA, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, NA, 1, 1, NA, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 1, 1, 2, 2), Leeftijd = c(26, 69, 67, 38, 29, 50, 29, 23, 52, 39, 50, 29, 36, 52, 43, 53, 47, 33, 52, 55, 43, 64, 35, 24, 51, 39, 50, 51, 46, 51, 30, 32, 28, 25, 52, 48, 60, 31, 61, 47, 46, 56, 38, 72, 88, 34, 56, 27, 27, 56, 52, 49, 34, 25, 22, 60, 61, 42, 45, 51, 42, 61, 69, 57, 35, 50, 42, 50, 51, 46, 28, 34, 52, 33, 30, 64, 65, 35, 31, 57, 75, 43, 46, 35, 65, 29, 29, 75, 49, 31, 57, 29, 40, 75, 30, 34, 58, 47, 37, 43, 34, 47, 46, 42, 49, 57, 46, 36, 51, 80, 45, 47, 48, 23, 51, 53, 44, 64, 44, 33, 40, 42, 29, 60, 28, 47, 47, 39, 25, 41, 39, 27, 57, 66, 42, 22, 59, 27, 43, 53, 65, 52, 41, 50, 55, 29, 55, 39, 41, 25, 74, 68, 55, 29, 77, 45, 18, 34, 49, 74, 44, 33, 48, 82, 61, 54, 46, 30, 33, 65, 51, 44, 50, 57, 27, 56, 85, 52, 31, 62, 62, 34, 48, 28, 28, 63, 30, 40, 44, 37, 73, 70, 39, 59, 56, 61, 40, 43, 33, 58, 44, 62, 26, 72, 67, 59, 48, 37, 52, 37, 57, 53, 59, 44, 71, 81, 33, 61, 50, 33, 48, 50, 63, 46, 60, 58, 40, 63, 39, 71, 38, 40, 56, 36, 52, 61, 83, 59, 43, 69, 50, 57, 38, 50, 27, 43, 46, 30, 50, 34, 68, 53, 48, 84, 41, 57, 61, 72, 27, 80, 71, 69, 61, 43, 67, 60, 58, 67, 72, 40, 79, 52, 80, 33, 25, 80, 67, 56, 66, 54, 50, 65, 39, 36, 69, 39, 34, 41, 36, 61, 33, 42, 43, 45, 48, 67, 69, 66, 37, 28, 64, 65, 68, 62, 84, 82, 59, 61, 74, 52, 41, 30, 33, 55, 55, 26, 53, 33, 64, 65, 74, 67, 70, 58, 51, 62, 67, 52, 40, 57, 57, 57, 59, 56, 61, 58, 45, 63, 61, 50, 70, 32, 50, 74, 70, 49, 42, 71, 51, 67, 46, 45, 75, 54, 75, 45, 46, 64, 60, 55, 61, 65, 68, 71, 43, 78, 53, 63, 85, 75, 66, 67, 54, 63, 68, 84, 58, 72, 70, 58, 29, 63, 83, 64, 75, 59, 76, 61, 62, 65, 61, 72, 20, 43, 67, 33, 62, 63, 51, 34, 68, 68, 60, 67, 44, 64, 69, 53, 69, 47, 41, 38, 57, 71, 70, 68, 25, 60, 71, 48, 64, 62, 72, 60, 45, 67, 59, 73, 27, 64, 66, 57, 72, 71, 77, 58, 56, 65, 74, 44, 22, 63, 42, 80, 52, 66, 60, 56, 54, 42, 68, 57, 37)), .Names = c("HbA1c", "BMI", "Comorb", "PAIDhoog", "PHQhoog", "totaalhealthcareutilization", "etndich", "Leeftijd"), row.names = c(NA, -453L), variable.labels = structure(c("HbA1c", "BMI level", "", "", "", "", "", ""), .Names = c("HbA1c", "BMI", "Comorb", "PAIDhoog", "PHQhoog", "totaalhealthcareutilization", "etndich", "Leeftijd")), codepage = 65001L, class = "data.frame")
  </code></pre>
  
  <p>When I perform a GLM, the R output is as follows:</p>
  
  <pre><code>fit &lt;- glm(formula = totaalhealthcareutilization ~ PAIDhoog + PHQhoog +
      Comorb + Leeftijd + etndich, family = Gamma(link = log),
      data = df)
  
  summary(fit)
  #
  #Call:
  #glm(formula = totaalhealthcareutilization ~ PAIDhoog + PHQhoog +
  #    Comorb + Leeftijd + etndich, family = Gamma(link = log),
  #    data = df)
  #
  #Deviance Residuals:
  #    Min       1Q   Median       3Q      Max
  #-2.1297  -0.7231  -0.3018   0.2075   3.1365
  #
  #Coefficients:
  #             Estimate Std. Error t value Pr(&gt;|t|)
  #(Intercept)  3.638751   0.267741  13.591  &lt; 2e-16 ***
  #PAIDhoog0   -0.201881   0.131777  -1.532   0.1264
  #PHQhoog0    -0.126989   0.157416  -0.807   0.4203
  #Comorbgeen  -0.638842   0.144459  -4.422 1.28e-05 ***
  #Comorb1     -0.348187   0.158484  -2.197   0.0286 *
  #Leeftijd     0.007311   0.003534   2.069   0.0392 *
  #etndich1    -0.151836   0.118872  -1.277   0.2023
  #---
  #Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
  #
  #(Dispersion parameter for Gamma family taken to be 0.9432289)
  #
  #    Null deviance: 286.49  on 381  degrees of freedom
  #Residual deviance: 243.01  on 375  degrees of freedom
  #  (71 observations deleted due to missingness)
  #AIC: 3156
  #
  #Number of Fisher Scoring iterations: 6
  </code></pre>
  
  <p>And the SPSS output:</p>
  
  <pre><code>Parameter Estimates                         
  Parameter   B   Std. Error  95% Wald Confidence Interval           Hypothesis Test      
          Lower   Upper   Wald Chi-Square df  Sig.
  (Intercept) 3,639   ,2177   3,212   4,065   279,350 1   ,000
  [PAIDhoog=0]    -,202   ,1056   -,409   ,005    3,657   1   ,056
   [PAIDhoog=1]   0a  .   .   .   .   .   .
  [PHQhoog=0] -,127   ,1260   -,374   ,120    1,015   1   ,314
  [PHQhoog=1] 0a  .   .   .   .   .   .
  [Comorb=1]  -,639   ,1148   -,864   -,414   30,940  1   ,000
  [Comorb=2]  -,348   ,1250   -,593   -,103   7,758   1   ,005
  [Comorb=3]  0a  .   .   .   .   .   .
  [etndich=1,00]  -,152   ,0936   -,335   ,032    2,633   1   ,105
  [etndich=2,00]  0a  .   .   .   .   .   .
  Leeftijd    ,007    ,0028   ,002    ,013    6,599   1   ,010
  (Scale) ,581b   ,0387   ,510    ,662            
  Dependent Variable: totaalhealthcareutilization
  Model: (Intercept), PAIDhoog, PHQhoog, Comorb, etndich, Leeftijd                            
  a Set to zero because this parameter is redundant.                          
  b Maximum likelihood estimate.                       
  </code></pre>
  
  <p>If I change the 'scale parameter method' in SPSS to 'Pearson Chi-Square', the exact R results are reproduced. However, I want to do the exact same thing with the SPSS results in R. Is it possible to change the scale parameter method in R?</p>
  
  <p>If any more information is necessary, please let me know.      </p>