Augment data with information from a(n) clm object

Augment accepts a model object and a dataset and adds information about each observation in the dataset. Most commonly, this includes predicted values in the .fitted column, residuals in the .resid column, and standard errors for the fitted values in a .se.fit column. New columns always begin with a . prefix to avoid overwriting columns in the original dataset.

Users may pass data to augment via either the data argument or the newdata argument. If the user passes data to the data argument, it must be exactly the data that was used to fit the model object. Pass datasets to newdata to augment data that was not used during model fitting. This still requires that at least all predictor variable columns used to fit the model are present. If the original outcome variable used to fit the model is not included in newdata, then no .resid column will be included in the output.

Augment will often behave differently depending on whether data or newdata is given. This is because there is often information associated with training observations (such as influences or related) measures that is not meaningfully defined for new observations.

For convenience, many augment methods provide default data arguments, so that augment(fit) will return the augmented training data. In these cases, augment tries to reconstruct the original data based on the model object with varying degrees of success.

The augmented dataset is always returned as a tibble::tibble with the same number of rows as the passed dataset. This means that the passed data must be coercible to a tibble. If a predictor enters the model as part of a matrix of covariates, such as when the model formula uses splines::ns(), stats::poly(), or survival::Surv(), it is represented as a matrix column.

We are in the process of defining behaviors for models fit with various na.action arguments, but make no guarantees about behavior when data is missing at this time.

Usage

# S3 method for class 'clm'
augment(
  x,
  data = model.frame(x),
  newdata = NULL,
  type.predict = c("prob", "class"),
  ...
)

Arguments

x

A clm object returned from ordinal::clm().

data

A base::data.frame or tibble::tibble() containing the original data that was used to produce the object x. Defaults to stats::model.frame(x) so that augment(my_fit) returns the augmented original data. Do not pass new data to the data argument. Augment will report information such as influence and cooks distance for data passed to the data argument. These measures are only defined for the original training data.

newdata

A base::data.frame() or tibble::tibble() containing all the original predictors used to create x. Defaults to NULL, indicating that nothing has been passed to newdata. If newdata is specified, the data argument will be ignored.

type.predict

Which type of prediction to compute, either "prob" or "class", passed to ordinal::predict.clm(). Defaults to "prob".

...

Additional arguments. Not used. Needed to match generic signature only. Cautionary note: Misspelled arguments will be absorbed in ..., where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass conf.lvel = 0.9, all computation will proceed using conf.level = 0.95. Two exceptions here are:

tidy() methods will warn when supplied an exponentiate argument if it will be ignored.
augment() methods will warn when supplied a newdata argument if it will be ignored.

Examples


# load libraries for models and data
library(ordinal)
#> 
#> Attaching package: ‘ordinal’
#> The following object is masked from ‘package:dplyr’:
#> 
#>     slice

# fit model
fit <- clm(rating ~ temp * contact, data = wine)

# summarize model fit with tidiers
tidy(fit)
#> # A tibble: 7 × 6
#>   term                estimate std.error statistic  p.value coef.type
#>   <chr>                  <dbl>     <dbl>     <dbl>    <dbl> <chr>    
#> 1 1|2                   -1.41      0.545    -2.59  9.66e- 3 intercept
#> 2 2|3                    1.14      0.510     2.24  2.48e- 2 intercept
#> 3 3|4                    3.38      0.638     5.29  1.21e- 7 intercept
#> 4 4|5                    4.94      0.751     6.58  4.66e-11 intercept
#> 5 tempwarm               2.32      0.701     3.31  9.28e- 4 location 
#> 6 contactyes             1.35      0.660     2.04  4.13e- 2 location 
#> 7 tempwarm:contactyes    0.360     0.924     0.389 6.97e- 1 location 
tidy(fit, conf.int = TRUE, conf.level = 0.9)
#> # A tibble: 7 × 8
#>   term  estimate std.error statistic  p.value conf.low conf.high coef.type
#>   <chr>    <dbl>     <dbl>     <dbl>    <dbl>    <dbl>     <dbl> <chr>    
#> 1 1|2     -1.41      0.545    -2.59  9.66e- 3   NA         NA    intercept
#> 2 2|3      1.14      0.510     2.24  2.48e- 2   NA         NA    intercept
#> 3 3|4      3.38      0.638     5.29  1.21e- 7   NA         NA    intercept
#> 4 4|5      4.94      0.751     6.58  4.66e-11   NA         NA    intercept
#> 5 temp…    2.32      0.701     3.31  9.28e- 4    1.20       3.52 location 
#> 6 cont…    1.35      0.660     2.04  4.13e- 2    0.284      2.47 location 
#> 7 temp…    0.360     0.924     0.389 6.97e- 1   -1.17       1.89 location 
tidy(fit, conf.int = TRUE, conf.type = "Wald", exponentiate = TRUE)
#> # A tibble: 7 × 8
#>   term  estimate std.error statistic  p.value conf.low conf.high coef.type
#>   <chr>    <dbl>     <dbl>     <dbl>    <dbl>    <dbl>     <dbl> <chr>    
#> 1 1|2      0.244     0.545    -2.59  9.66e- 3   0.0837     0.710 intercept
#> 2 2|3      3.14      0.510     2.24  2.48e- 2   1.16       8.52  intercept
#> 3 3|4     29.3       0.638     5.29  1.21e- 7   8.38     102.    intercept
#> 4 4|5    140.        0.751     6.58  4.66e-11  32.1      610.    intercept
#> 5 temp…   10.2       0.701     3.31  9.28e- 4   2.58      40.2   location 
#> 6 cont…    3.85      0.660     2.04  4.13e- 2   1.05      14.0   location 
#> 7 temp…    1.43      0.924     0.389 6.97e- 1   0.234      8.76  location 

glance(fit)
#> # A tibble: 1 × 6
#>     edf   AIC   BIC logLik   df.residual  nobs
#>   <int> <dbl> <dbl> <logLik>       <dbl> <dbl>
#> 1     7  187.  203. -86.4162          65    72
augment(fit, type.predict = "prob")
#> # A tibble: 72 × 4
#>    rating temp  contact .fitted
#>    <ord>  <fct> <fct>     <dbl>
#>  1 2      cold  no       0.562 
#>  2 3      cold  no       0.209 
#>  3 3      cold  yes      0.435 
#>  4 4      cold  yes      0.0894
#>  5 4      warm  no       0.190 
#>  6 4      warm  no       0.190 
#>  7 5      warm  yes      0.286 
#>  8 5      warm  yes      0.286 
#>  9 1      cold  no       0.196 
#> 10 2      cold  no       0.562 
#> # ℹ 62 more rows
augment(fit, type.predict = "class")
#> # A tibble: 72 × 4
#>    rating temp  contact .fitted
#>    <ord>  <fct> <fct>   <fct>  
#>  1 2      cold  no      2      
#>  2 3      cold  no      2      
#>  3 3      cold  yes     3      
#>  4 4      cold  yes     3      
#>  5 4      warm  no      3      
#>  6 4      warm  no      3      
#>  7 5      warm  yes     4      
#>  8 5      warm  yes     4      
#>  9 1      cold  no      2      
#> 10 2      cold  no      2      
#> # ℹ 62 more rows

# ...and again with another model specification
fit2 <- clm(rating ~ temp, nominal = ~contact, data = wine)

tidy(fit2)
#> # A tibble: 9 × 6
#>   term            estimate std.error statistic      p.value coef.type
#>   <chr>              <dbl>     <dbl>     <dbl>        <dbl> <chr>    
#> 1 1|2.(Intercept)    -1.32     0.562     -2.35 0.0186       intercept
#> 2 2|3.(Intercept)     1.25     0.475      2.63 0.00866      intercept
#> 3 3|4.(Intercept)     3.55     0.656      5.41 0.0000000625 intercept
#> 4 4|5.(Intercept)     4.66     0.860      5.42 0.0000000608 intercept
#> 5 1|2.contactyes     -1.62     1.16      -1.39 0.164        intercept
#> 6 2|3.contactyes     -1.51     0.591     -2.56 0.0105       intercept
#> 7 3|4.contactyes     -1.67     0.649     -2.58 0.00985      intercept
#> 8 4|5.contactyes     -1.05     0.897     -1.17 0.241        intercept
#> 9 tempwarm            2.52     0.535      4.71 0.00000250   location 
glance(fit2)
#> # A tibble: 1 × 6
#>     edf   AIC   BIC logLik    df.residual  nobs
#>   <int> <dbl> <dbl> <logLik>        <dbl> <dbl>
#> 1     9  190.  211. -86.20855          63    72

Augment data with information from a(n) clm object

Usage

Arguments

See also

Examples