Running examples in ‘prettyglm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pretty_coefficients
> ### Title: pretty_coefficients
> ### Aliases: pretty_coefficients
> 
> ### ** Examples
> 
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(prettyglm)
> data('titanic')
> columns_to_factor <- c('Pclass',
+                        'Sex',
+                        'Cabin',
+                        'Embarked',
+                        'Cabintype',
+                        'Survived')
> meanage <- base::mean(titanic$Age, na.rm=TRUE)
> 
> titanic  <- titanic  %>%
+  dplyr::mutate_at(columns_to_factor, list(~factor(.))) %>%
+  dplyr::mutate(Age =base::ifelse(is.na(Age)==TRUE,meanage,Age)) %>%
+  dplyr::mutate(Age_0_25 = prettyglm::splineit(Age,0,25),
+                Age_25_50 = prettyglm::splineit(Age,25,50),
+                Age_50_120 = prettyglm::splineit(Age,50,120)) %>%
+  dplyr::mutate(Fare_0_250 = prettyglm::splineit(Fare,0,250),
+                Fare_250_600 = prettyglm::splineit(Fare,250,600))
> 
> # A simple example
> survival_model <- stats::glm(Survived ~
+                               Pclass +
+                               Sex +
+                               Age +
+                               Fare +
+                               Embarked +
+                               SibSp +
+                               Parch +
+                               Cabintype,
+                              data = titanic,
+                              family = binomial(link = 'logit'))
> pretty_coefficients(survival_model)
<table class="table" style="margin-left: auto; margin-right: auto;border-bottom: 0;">
 <thead>
  <tr>
   <th style="text-align:left;"> Variable </th>
   <th style="text-align:left;"> Level </th>
   <th style="text-align:left;"> Importance </th>
   <th style="text-align:right;"> Estimate </th>
   <th style="text-align:right;"> Std.error </th>
   <th style="text-align:right;"> P.Value </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> (Intercept) </td>
   <td style="text-align:left;"> (Intercept) </td>
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</td>
   <td style="text-align:right;"> 4.3534863 </td>
   <td style="text-align:right;"> 0.7100919 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #black !important;">0</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Pclass </td>
   <td style="text-align:left;"> 1 </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> 0.0000000 </td>
   <td style="text-align:right;"> 0.0000000 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #black !important;">NA</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Pclass </td>
   <td style="text-align:left;"> 2 </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> -0.2405205 </td>
   <td style="text-align:right;"> 0.4370773 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.58212</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Pclass </td>
   <td style="text-align:left;"> 3 </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> -1.3950560 </td>
   <td style="text-align:right;"> 0.4373004 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #black !important;">0.00142</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Sex </td>
   <td style="text-align:left;"> female </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> 0.0000000 </td>
   <td style="text-align:right;"> 0.0000000 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #black !important;">NA</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Sex </td>
   <td style="text-align:left;"> male </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> -2.7372606 </td>
   <td style="text-align:right;"> 0.2062126 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #black !important;">0</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Age </td>
   <td style="text-align:left;"> Age </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> -0.0412313 </td>
   <td style="text-align:right;"> 0.0081457 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #black !important;">0</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Fare </td>
   <td style="text-align:left;"> Fare </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> 0.0029675 </td>
   <td style="text-align:right;"> 0.0027001 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.27175</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Embarked </td>
   <td style="text-align:left;"> C </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> 0.0000000 </td>
   <td style="text-align:right;"> 0.0000000 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #black !important;">NA</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Embarked </td>
   <td style="text-align:left;"> Q </td>
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</td>
   <td style="text-align:right;"> -0.0783606 </td>
   <td style="text-align:right;"> 0.3862992 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.83925</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Embarked </td>
   <td style="text-align:left;"> S </td>
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   <td style="text-align:right;"> -0.5118226 </td>
   <td style="text-align:right;"> 0.2463878 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #black !important;">0.03777</span> </td>
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  <tr>
   <td style="text-align:left;"> SibSp </td>
   <td style="text-align:left;"> SibSp </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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   <td style="text-align:right;"> -0.3251949 </td>
   <td style="text-align:right;"> 0.1112076 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #black !important;">0.00345</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Parch </td>
   <td style="text-align:left;"> Parch </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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   <td style="text-align:right;"> -0.1115613 </td>
   <td style="text-align:right;"> 0.1208131 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.35579</span> </td>
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  <tr>
   <td style="text-align:left;"> Cabintype </td>
   <td style="text-align:left;"> A </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> 0.0000000 </td>
   <td style="text-align:right;"> 0.0000000 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #black !important;">NA</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Cabintype </td>
   <td style="text-align:left;"> B </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> -0.0252365 </td>
   <td style="text-align:right;"> 0.7183014 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.97197</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Cabintype </td>
   <td style="text-align:left;"> C </td>
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</td>
   <td style="text-align:right;"> -0.5019796 </td>
   <td style="text-align:right;"> 0.6626204 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.44871</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Cabintype </td>
   <td style="text-align:left;"> D </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> 0.4769107 </td>
   <td style="text-align:right;"> 0.7344476 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.51611</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Cabintype </td>
   <td style="text-align:left;"> E </td>
   <td style="text-align:left;">  <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" class="svglite" width="48.00pt" height="12.00pt" viewbox="0 0 48.00 12.00"><defs><style type="text/css">
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</td>
   <td style="text-align:right;"> 0.9884183 </td>
   <td style="text-align:right;"> 0.7381810 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.18057</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Cabintype </td>
   <td style="text-align:left;"> F </td>
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</td>
   <td style="text-align:right;"> 0.2948757 </td>
   <td style="text-align:right;"> 0.9803112 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.76357</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Cabintype </td>
   <td style="text-align:left;"> G </td>
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</td>
   <td style="text-align:right;"> -1.5773340 </td>
   <td style="text-align:right;"> 1.2574952 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.20972</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Cabintype </td>
   <td style="text-align:left;"> Missing </td>
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</td>
   <td style="text-align:right;"> -0.9127259 </td>
   <td style="text-align:right;"> 0.6723476 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.17462</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Cabintype </td>
   <td style="text-align:left;"> T </td>
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   <td style="text-align:right;"> -12.9204077 </td>
   <td style="text-align:right;"> 535.4114701 </td>
   <td style="text-align:right;"> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #F08080 !important;">0.98075</span> </td>
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</tbody>
<tfoot><tr><td style="padding: 0; " colspan="100%">
<span style="font-style: italic;text-decoration: underline;">Goodness-of-Fit:</span> <sup></sup>  AIC: 800.4 , Devience : 764.4 , Null Devience:  1182.8</td></tr></tfoot>
</table>> 
> # A more complicated example with a spline and different importance method
> survival_model3 <- stats::glm(Survived ~
+                                         Pclass +
+                                         Age_0_25 +
+                                         Age_25_50 +
+                                         Age_50_120 +
+                                         Sex:Fare_0_250 +
+                                         Sex:Fare_250_600 +
+                                         Embarked +
+                                         SibSp +
+                                         Parch +
+                                         Cabintype,
+                               data = titanic,
+                               family = binomial(link = 'logit'))
> pretty_coefficients(survival_model3,
+                     relativity_transform = 'exp(estimate)-1',
+                     spline_seperator = '_',
+                     vimethod = 'permute',
+                     target = 'Survived',
+                     metric = 'auc',
+                     pred_wrapper = predict.glm,
+                     reference_class = 0)
Error: Training data cannot be extracted from fitted model object. Please supply the raw training data using the `train` argument.
Execution halted