Examples

Attach packages

library(cvms)
library(groupdata2) # fold() partition()
library(knitr) # kable()
library(dplyr) # %>% arrange()
library(ggplot2)

Load data

The dataset participant.scores comes with cvms.

data <- participant.scores

Fold data

Create a grouping factor for subsetting of folds using groupdata2::fold(). Order the dataset by the folds.

# Set seed for reproducibility
set.seed(7)

# Fold data 
data <- fold(data, k = 4,
             cat_col = 'diagnosis',
             id_col = 'participant') %>% 
  arrange(.folds)

# Show first 15 rows of data
data %>% head(15) %>% kable()

participant	age	diagnosis	score	session	.folds
9	34	0	33	1	1
9	34	0	53	2	1
9	34	0	66	3	1
8	21	1	16	1	1
8	21	1	32	2	1
8	21	1	44	3	1
2	23	0	24	1	2
2	23	0	40	2	2
2	23	0	67	3	2
1	20	1	10	1	2
1	20	1	24	2	2
1	20	1	45	3	2
6	31	1	14	1	2
6	31	1	25	2	2
6	31	1	30	3	2

Cross-validate a single model

Gaussian

CV1 <- cross_validate(data, "score~diagnosis",
                      fold_cols = '.folds',
                      family = 'gaussian',
                      REML = FALSE)

# Show results
CV1
#> # A tibble: 1 x 20
#>    RMSE   MAE   r2m   r2c   AIC  AICc   BIC Predictions Results Coefficients
#>   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <list>      <list>  <list>      
#> 1  16.4  13.8 0.271 0.271  195.  196.  198. <tibble [3… <tibbl… <tibble [8 …
#> # … with 10 more variables: Folds <int>, `Fold Columns` <int>, `Convergence
#> #   Warnings` <int>, `Singular Fit Messages` <int>, `Other Warnings` <int>,
#> #   `Warnings and Messages` <list>, Family <chr>, Link <chr>, Dependent <chr>,
#> #   Fixed <chr>

# Let's take a closer look at the different parts of the output 

# Results metrics
CV1 %>% select_metrics() %>% kable()

RMSE	MAE	r2m	r2c	AIC	AICc	BIC	Dependent	Fixed
16.35261	13.75772	0.270991	0.270991	194.6218	195.9276	197.9556	score	diagnosis


# Nested predictions 
# Note that [[1]] picks predictions for the first row
CV1$Predictions[[1]] %>% head() %>% kable()

Fold Column	Fold	Target	Prediction
.folds	1	33	51.00000
.folds	1	53	51.00000
.folds	1	66	51.00000
.folds	1	16	30.66667
.folds	1	32	30.66667
.folds	1	44	30.66667


# Nested results from the different folds
CV1$Results[[1]] %>% kable()

Fold Column	Fold	RMSE	MAE	r2m	r2c	AIC	AICc	BIC
.folds	1	12.56760	10.72222	0.2439198	0.2439198	209.9622	211.1622	213.4963
.folds	2	16.60767	14.77778	0.2525524	0.2525524	182.8739	184.2857	186.0075
.folds	3	15.97355	12.87037	0.2306104	0.2306104	207.9074	209.1074	211.4416
.folds	4	20.26162	16.66049	0.3568816	0.3568816	177.7436	179.1554	180.8772


# Nested model coefficients
# Note that you have the full p-values, 
# but kable() only shows a certain number of digits
CV1$Coefficients[[1]] %>% kable()

term	estimate	std.error	statistic	p.value	Fold	Fold Column
(Intercept)	51.00000	5.901264	8.642216	0.0000000	1	.folds
diagnosis	-20.33333	7.464574	-2.723978	0.0123925	1	.folds
(Intercept)	53.33333	5.718886	9.325826	0.0000000	2	.folds
diagnosis	-19.66667	7.565375	-2.599563	0.0176016	2	.folds
(Intercept)	49.77778	5.653977	8.804030	0.0000000	3	.folds
diagnosis	-18.77778	7.151778	-2.625610	0.0154426	3	.folds
(Intercept)	49.55556	5.061304	9.791065	0.0000000	4	.folds
diagnosis	-22.30556	6.695476	-3.331437	0.0035077	4	.folds


# Additional information about the model
# and the training process
CV1 %>% select(11:17) %>% kable()

Folds	Fold Columns	Convergence Warnings	Singular Fit Messages	Other Warnings	Warnings and Messages	Family
4	1	0	0	0	list(`Fold Column` = character(0), Fold = integer(0), Type = character(0), Message = character(0))	gaussian

Binomial

CV2 <- cross_validate(data, "diagnosis~score",
                      fold_cols = '.folds',
                      family = 'binomial')
#> Registered S3 methods overwritten by 'survival':
#>   method       from 
#>   nobs.coxph   MuMIn
#>   nobs.survreg MuMIn

# Show results
CV2
#> # A tibble: 1 x 28
#>   `Balanced Accur…    F1 Sensitivity Specificity `Pos Pred Value`
#>              <dbl> <dbl>       <dbl>       <dbl>            <dbl>
#> 1            0.736 0.821       0.889       0.583            0.762
#> # … with 23 more variables: `Neg Pred Value` <dbl>, AUC <dbl>, `Lower
#> #   CI` <dbl>, `Upper CI` <dbl>, Kappa <dbl>, MCC <dbl>, `Detection
#> #   Rate` <dbl>, `Detection Prevalence` <dbl>, Prevalence <dbl>,
#> #   Predictions <list>, ROC <list>, `Confusion Matrix` <list>,
#> #   Coefficients <list>, Folds <int>, `Fold Columns` <int>, `Convergence
#> #   Warnings` <int>, `Singular Fit Messages` <int>, `Other Warnings` <int>,
#> #   `Warnings and Messages` <list>, Family <chr>, Link <chr>, Dependent <chr>,
#> #   Fixed <chr>

# Let's take a closer look at the different parts of the output 
# We won't repeat the parts too similar to those in Gaussian

# Results metrics
CV2 %>% select(1:9) %>% kable()

Balanced Accuracy	F1	Sensitivity	Specificity	Pos Pred Value	Neg Pred Value	AUC	Lower CI	Upper CI
0.7361111	0.8205128	0.8888889	0.5833333	0.7619048	0.7777778	0.7685185	0.5962701	0.9407669

CV2 %>% select(10:14) %>% kable()

Kappa	MCC	Detection Rate	Detection Prevalence	Prevalence
0.4927536	0.5048268	0.5333333	0.7	0.6


# ROC curve info
CV2$ROC[[1]] %>% head() %>% kable()

Sensitivities	Specificities
1.0000000	0.0000000
1.0000000	0.0833333
0.9444444	0.0833333
0.9444444	0.1666667
0.9444444	0.2500000
0.8888889	0.2500000


# Confusion matrix
CV2$`Confusion Matrix`[[1]] %>% kable()

Fold Column	Prediction	Target	Pos_0	Pos_1	N
.folds	0	0	TP	TN	7
.folds	1	0	FN	FP	5
.folds	0	1	FP	FN	2
.folds	1	1	TN	TP	16

Cross-validate multiple models

Create model formulas

models <- c("score~diagnosis", "score~age")
mixed_models <- c("score~diagnosis+(1|session)", "score~age+(1|session)")

Cross-validate fixed effects models

CV3 <- cross_validate(data, models,
                      fold_cols = '.folds',
                      family = 'gaussian',
                      REML = FALSE)

# Show results
CV3
#> # A tibble: 2 x 20
#>    RMSE   MAE    r2m    r2c   AIC  AICc   BIC Predictions Results Coefficients
#>   <dbl> <dbl>  <dbl>  <dbl> <dbl> <dbl> <dbl> <list>      <list>  <list>      
#> 1  16.4  13.8 0.271  0.271   195.  196.  198. <tibble [3… <tibbl… <tibble [8 …
#> 2  22.4  18.9 0.0338 0.0338  201.  202.  204. <tibble [3… <tibbl… <tibble [8 …
#> # … with 10 more variables: Folds <int>, `Fold Columns` <int>, `Convergence
#> #   Warnings` <int>, `Singular Fit Messages` <int>, `Other Warnings` <int>,
#> #   `Warnings and Messages` <list>, Family <chr>, Link <chr>, Dependent <chr>,
#> #   Fixed <chr>

Cross-validate mixed effects models

CV4 <- cross_validate(data, mixed_models,
                      fold_cols = '.folds',
                      family = 'gaussian',
                      REML = FALSE)

# Show results
CV4
#> # A tibble: 2 x 21
#>    RMSE   MAE    r2m   r2c   AIC  AICc   BIC Predictions Results Coefficients
#>   <dbl> <dbl>  <dbl> <dbl> <dbl> <dbl> <dbl> <list>      <list>  <list>      
#> 1  7.95  6.41 0.290  0.811  176.  178.  180. <tibble [3… <tibbl… <tibble [8 …
#> 2 17.5  16.2  0.0366 0.526  194.  196.  198. <tibble [3… <tibbl… <tibble [8 …
#> # … with 11 more variables: Folds <int>, `Fold Columns` <int>, `Convergence
#> #   Warnings` <int>, `Singular Fit Messages` <int>, `Other Warnings` <int>,
#> #   `Warnings and Messages` <list>, Family <chr>, Link <chr>, Dependent <chr>,
#> #   Fixed <chr>, Random <chr>

Repeated cross-validation

Let’s first add some extra fold columns. We will use the num_fold_cols argument to add 3 unique fold columns. We tell fold() to keep the existing fold column and simply add three extra columns. We could also choose to remove the existing fold column, if for instance we were changing the number of folds (k). Note, that the original fold column will be renamed to “.folds_1”.

# Set seed for reproducibility
set.seed(2)

# Fold data 
data <- fold(data, k = 4,
             cat_col = 'diagnosis',
             id_col = 'participant',
             num_fold_cols = 3,
             handle_existing_fold_cols = "keep")

# Show first 15 rows of data
data %>% head(10) %>% kable()

participant	age	score	session	.folds_1	.folds_2	.folds_3	.folds_4
10	32	29	1	4	4	3	1
10	32	55	2	4	4	3	1
10	32	81	3	4	4	3	1
2	23	24	1	2	3	1	2
2	23	40	2	2	3	1	2
2	23	67	3	2	3	1	2
4	21	35	1	3	2	4	4
4	21	50	2	3	2	4	4
4	21	78	3	3	2	4	4
9	34	33	1	1	1	2	3

CV5 <- cross_validate(data, "diagnosis ~ score",
                      fold_cols = paste0(".folds_", 1:4),
                      family = 'binomial',
                      REML = FALSE)

# Show results
CV5
#> # A tibble: 1 x 29
#>   `Balanced Accur…    F1 Sensitivity Specificity `Pos Pred Value`
#>              <dbl> <dbl>       <dbl>       <dbl>            <dbl>
#> 1            0.729 0.813       0.875       0.583            0.759
#> # … with 24 more variables: `Neg Pred Value` <dbl>, AUC <dbl>, `Lower
#> #   CI` <dbl>, `Upper CI` <dbl>, Kappa <dbl>, MCC <dbl>, `Detection
#> #   Rate` <dbl>, `Detection Prevalence` <dbl>, Prevalence <dbl>,
#> #   Predictions <list>, ROC <list>, Results <list>, `Confusion Matrix` <list>,
#> #   Coefficients <list>, Folds <int>, `Fold Columns` <int>, `Convergence
#> #   Warnings` <int>, `Singular Fit Messages` <int>, `Other Warnings` <int>,
#> #   `Warnings and Messages` <list>, Family <chr>, Link <chr>, Dependent <chr>,
#> #   Fixed <chr>

# The binomial output now has a nested 'Results' tibble
# Let's see a subset of the columns
CV5$Results[[1]] %>% select(1:8) %>%  kable()

Fold Column	Balanced Accuracy	F1	Sensitivity	Specificity	Pos Pred Value	Neg Pred Value	AUC
.folds_1	0.7361111	0.8205128	0.8888889	0.5833333	0.7619048	0.7777778	0.7685185
.folds_2	0.7361111	0.8205128	0.8888889	0.5833333	0.7619048	0.7777778	0.7777778
.folds_3	0.7083333	0.7894737	0.8333333	0.5833333	0.7500000	0.7000000	0.7476852
.folds_4	0.7361111	0.8205128	0.8888889	0.5833333	0.7619048	0.7777778	0.7662037

Cross-validating custom model functions

cross_validate_fn() works with regression (gaussian), binary classification (binomial), and multiclass classification (multinomial).

SVM

Let’s cross-validate a support-vector machine using the svm() function from the e1071 package. First, we will create a model function. You can do anything you want in it, as long as it takes the arguments train_data and formula and returns the fitted model object.

# Create model function
#
# train_data : tibble with the training data
# formula : a formula object

svm_model_fn <- function(train_data, formula){
  
  # Note that `formula` must be specified first
  # when calling svm(), otherwise it fails
  e1071::svm(formula = formula,
             data = train_data, 
             kernel = "linear",
             type = "C-classification")
}

For the svm() function, the default predict function and settings within cross_validate_fn() works, so we don’t have to specify a predict function. In many cases, it’s probably safer to supply a predict function anyway, so you’re sure everything is correct. We will see how in the naive Bayes example below, but first, let’s cross-validate the model function. Note, that some of the arguments have changed names (models -> formulas, family -> type).

# Cross-validate svm_model_fn
CV6 <- cross_validate_fn(data = data,
                         model_fn = svm_model_fn,
                         formulas = c("diagnosis~score", "diagnosis~age"),
                         fold_cols = '.folds_1', 
                         type = 'binomial')

CV6
#> # A tibble: 2 x 26
#>   `Balanced Accur…    F1 Sensitivity Specificity `Pos Pred Value`
#>              <dbl> <dbl>       <dbl>       <dbl>            <dbl>
#> 1            0.694 0.80        0.889         0.5            0.727
#> 2            0.417 0.667       0.833         0              0.556
#> # … with 21 more variables: `Neg Pred Value` <dbl>, AUC <dbl>, `Lower
#> #   CI` <dbl>, `Upper CI` <dbl>, Kappa <dbl>, MCC <dbl>, `Detection
#> #   Rate` <dbl>, `Detection Prevalence` <dbl>, Prevalence <dbl>,
#> #   Predictions <list>, ROC <list>, `Confusion Matrix` <list>,
#> #   Coefficients <list>, Folds <int>, `Fold Columns` <int>, `Convergence
#> #   Warnings` <int>, `Other Warnings` <int>, `Warnings and Messages` <list>,
#> #   Family <chr>, Dependent <chr>, Fixed <chr>

Naive Bayes

The naive Bayes classifier requires us to supply a predict function, so we will go through that next. First, let’s create the model function.

# Create model function
#
# train_data : tibble with the training data
# formula : a formula object

nb_model_fn <- function(train_data, formula){
  e1071::naiveBayes(formula = formula, 
                    data = train_data)
}

Now, we will create a predict function. This will usually wrap stats::predict() and just make sure, the predictions have the correct format. When type is binomial, the predictions should be a vector, or a one-column matrix / data frame, with the probabilities of the second class (alphabetically). That is, if we have the classes 0 and 1, it should be the probabilities of the observations being in class 1. The help file, ?cross_validate_fn, describes the formats for the other types (gaussian and multinomial).

The predict function should take the arguments test_data, model, and formula. You do not need to use the formula within your function.

# Create predict function
#
# test_data : tibble with the test data
# model : fitted model object
# formula : a formula object
nb_predict_fn <- function(test_data, model, formula){
    stats::predict(object = model, newdata = test_data, 
                   type = "raw", allow.new.levels = TRUE)[,2]
  }

With both functions specified, we are ready to cross-validate our naive Bayes classifier.

CV7 <- cross_validate_fn(data,
                         model_fn = nb_model_fn,
                         formulas = c("diagnosis~score", "diagnosis~age"),
                         type = 'binomial',
                         predict_fn = nb_predict_fn,
                         fold_cols = '.folds_1')

CV7
#> # A tibble: 2 x 26
#>   `Balanced Accur…    F1 Sensitivity Specificity `Pos Pred Value`
#>              <dbl> <dbl>       <dbl>       <dbl>            <dbl>
#> 1            0.736 0.821       0.889       0.583            0.762
#> 2            0.25  0.462       0.5         0                0.429
#> # … with 21 more variables: `Neg Pred Value` <dbl>, AUC <dbl>, `Lower
#> #   CI` <dbl>, `Upper CI` <dbl>, Kappa <dbl>, MCC <dbl>, `Detection
#> #   Rate` <dbl>, `Detection Prevalence` <dbl>, Prevalence <dbl>,
#> #   Predictions <list>, ROC <list>, `Confusion Matrix` <list>,
#> #   Coefficients <list>, Folds <int>, `Fold Columns` <int>, `Convergence
#> #   Warnings` <int>, `Other Warnings` <int>, `Warnings and Messages` <list>,
#> #   Family <chr>, Dependent <chr>, Fixed <chr>

Evaluating predictions

Evaluate predictions from a model trained outside cvms. Works with regression (gaussian), binary classification (binomial), and multiclass classification (multinomial). The following is an example of multinomial evaluation.

Multinomial

Create a dataset with 3 predictors and a target column. Partition it with groupdata2::partition() to create a training set and a validation set. multiclass_probability_tibble() is a simple helper function for generating random tibbles.

# Set seed
set.seed(1)

# Create class names
class_names <- paste0("class_", 1:4)

# Create random dataset with 100 observations 
# Partition into training set (75%) and test set (25%)
multiclass_partitions <- multiclass_probability_tibble(
  num_classes = 3, # Here, number of predictors
  num_observations = 100,
  apply_softmax = FALSE,
  FUN = rnorm,
  class_name = "predictor_") %>%
  dplyr::mutate(class = sample(
    class_names,
    size = 100,
    replace = TRUE)) %>%
  partition(p = 0.75,
            cat_col = "class")

# Extract partitions
multiclass_train_set <- multiclass_partitions[[1]]
multiclass_test_set <- multiclass_partitions[[2]]

multiclass_test_set
#> # A tibble: 26 x 4
#>    predictor_1 predictor_2 predictor_3 class  
#>          <dbl>       <dbl>       <dbl> <chr>  
#>  1      1.60         0.158     -0.331  class_1
#>  2     -1.99        -0.180     -0.341  class_1
#>  3      0.418       -0.324      0.263  class_1
#>  4      0.398        0.450      0.136  class_1
#>  5      0.0743       1.03      -1.32   class_1
#>  6      0.738        0.910      0.541  class_2
#>  7      0.576        0.384     -0.0134 class_2
#>  8     -0.305        1.68       0.510  class_2
#>  9     -0.0449      -0.393      1.52   class_2
#> 10      0.557       -0.464     -0.879  class_2
#> # … with 16 more rows

Train multinomial model using the nnet package and get the predicted probabilities.

# Train multinomial model
multiclass_model <- nnet::multinom(
   "class ~ predictor_1 + predictor_2 + predictor_3",
   data = multiclass_train_set)
#> # weights:  20 (12 variable)
#> initial  value 102.585783 
#> iter  10 value 98.124010
#> final  value 98.114250 
#> converged

# Predict the targets in the test set
predictions <- predict(multiclass_model, 
                       multiclass_test_set,
                       type = "probs") %>%
  dplyr::as_tibble()

# Add the targets
predictions[["target"]] <- multiclass_test_set[["class"]]

head(predictions, 10)
#> # A tibble: 10 x 5
#>    class_1 class_2 class_3 class_4 target 
#>      <dbl>   <dbl>   <dbl>   <dbl> <chr>  
#>  1   0.243   0.214   0.304   0.239 class_1
#>  2   0.136   0.371   0.234   0.259 class_1
#>  3   0.230   0.276   0.264   0.230 class_1
#>  4   0.194   0.218   0.262   0.326 class_1
#>  5   0.144   0.215   0.302   0.339 class_1
#>  6   0.186   0.166   0.241   0.407 class_2
#>  7   0.201   0.222   0.272   0.305 class_2
#>  8   0.117   0.131   0.195   0.557 class_2
#>  9   0.237   0.264   0.215   0.284 class_2
#> 10   0.216   0.310   0.303   0.171 class_2

Perform the evaluation. This will create one-vs-all binomial evaluations and summarize the results.

# Evaluate predictions
ev <- evaluate(data = predictions,
               target_col = "target",
               prediction_cols = class_names,
               type = "multinomial")

ev
#> # A tibble: 1 x 18
#>   `Overall Accura… `Balanced Accur…    F1 Sensitivity Specificity
#>              <dbl>            <dbl> <dbl>       <dbl>       <dbl>
#> 1            0.154            0.427   NaN       0.143       0.712
#> # … with 13 more variables: `Pos Pred Value` <dbl>, `Neg Pred Value` <dbl>,
#> #   AUC <dbl>, `Lower CI` <dbl>, `Upper CI` <dbl>, Kappa <dbl>, MCC <dbl>,
#> #   `Detection Rate` <dbl>, `Detection Prevalence` <dbl>, Prevalence <dbl>,
#> #   `Class Level Results` <list>, Predictions <list>, `Confusion Matrix` <list>

The class level results (i.e., the one-vs-all evaluations) are also included, and would usually be reported alongside the above results.

ev$`Class Level Results`
#> [[1]]
#> # A tibble: 4 x 18
#>   Class `Balanced Accur…      F1 Sensitivity Specificity `Pos Pred Value`
#>   <chr>            <dbl>   <dbl>       <dbl>       <dbl>            <dbl>
#> 1 clas…            0.476 NaN           0           0.952            0    
#> 2 clas…            0.380   0.211       0.286       0.474            0.167
#> 3 clas…            0.474 NaN           0           0.947            0    
#> 4 clas…            0.380   0.211       0.286       0.474            0.167
#> # … with 12 more variables: `Neg Pred Value` <dbl>, AUC <dbl>, `Lower
#> #   CI` <dbl>, `Upper CI` <dbl>, Kappa <dbl>, MCC <dbl>, `Detection
#> #   Rate` <dbl>, `Detection Prevalence` <dbl>, Prevalence <dbl>, Support <int>,
#> #   ROC <list>, `Confusion Matrix` <list>

Baseline evaluations

Create baseline evaluations of a test set.

Gaussian

Approach: The baseline model (y ~ 1), where 1 is simply the intercept (i.e. mean of y), is fitted on n random subsets of the training set and evaluated on the test set. We also perform an evaluation of the model fitted on the entire training set.

Start by partitioning the dataset.

# Set seed for reproducibility
set.seed(1)

# Partition the dataset 
partitions <- groupdata2::partition(participant.scores,
                                    p = 0.7,
                                    cat_col = 'diagnosis',
                                    id_col = 'participant',
                                    list_out = TRUE)
train_set <- partitions[[1]]
test_set <- partitions[[2]]

Create the baseline evaluations:

baseline(test_data = test_set, train_data = train_set,
         n = 100, dependent_col = "score", family = "gaussian")
#> $summarized_metrics
#> # A tibble: 9 x 9
#>   Measure   RMSE    MAE   r2m   r2c   AIC  AICc   BIC `Training Rows`
#>   <chr>    <dbl>  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>           <dbl>
#> 1 Mean     19.7  15.8       0     0  87.0  89.5  87.4            9.63
#> 2 Median   19.2  15.5       0     0  83.3  85.3  83.7            9   
#> 3 SD        1.05  0.759     0     0  28.9  27.6  29.6            3.22
#> 4 IQR       1.16  0.264     0     0  45.9  44.3  47.0            5   
#> 5 Max      24.1  19.4       0     0 137.  138.  138.            15   
#> 6 Min      18.9  15.5       0     0  42.0  48.0  41.2            5   
#> 7 NAs       0     0         0     0   0     0     0              0   
#> 8 INFs      0     0         0     0   0     0     0              0   
#> 9 All_rows 19.1  15.5       0     0 161.  162.  163.            18   
#> 
#> $random_evaluations
#> # A tibble: 100 x 13
#>     RMSE   MAE   r2m   r2c   AIC  AICc   BIC Predictions Coefficients
#>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <list>      <list>      
#>  1  20.0  16.3     0     0  72.5  74.9  72.7 <tibble [1… <tibble [1 …
#>  2  19.0  15.5     0     0 137.  138.  138.  <tibble [1… <tibble [1 …
#>  3  20.2  15.7     0     0  61.3  64.3  61.2 <tibble [1… <tibble [1 …
#>  4  20.0  15.7     0     0  97.7  99.2  98.5 <tibble [1… <tibble [1 …
#>  5  19.3  15.6     0     0  73.3  75.7  73.5 <tibble [1… <tibble [1 …
#>  6  20.4  15.9     0     0  44.4  50.4  43.6 <tibble [1… <tibble [1 …
#>  7  19.0  15.5     0     0 118.  120.  119.  <tibble [1… <tibble [1 …
#>  8  19.4  15.5     0     0  93.3  95.1  94.0 <tibble [1… <tibble [1 …
#>  9  20.7  16.2     0     0  71.2  73.6  71.3 <tibble [1… <tibble [1 …
#> 10  20.8  17.1     0     0  43.7  49.7  42.9 <tibble [1… <tibble [1 …
#> # … with 90 more rows, and 4 more variables: `Training Rows` <int>,
#> #   Family <chr>, Dependent <chr>, Fixed <chr>

Binomial

Approach: n random sets of predictions are evaluated against the dependent variable in the test set. We also evaluate a set of all 0s and a set of all 1s.

Create the baseline evaluations:

baseline(test_data = test_set, n = 100, 
         dependent_col = "diagnosis", family = "binomial")
#> $summarized_metrics
#> # A tibble: 10 x 15
#>    Measure `Balanced Accur…     F1 Sensitivity Specificity `Pos Pred Value`
#>    <chr>              <dbl>  <dbl>       <dbl>       <dbl>            <dbl>
#>  1 Mean               0.502  0.495       0.478       0.525            0.498
#>  2 Median             0.5    0.5         0.5         0.5              0.500
#>  3 SD                 0.147  0.159       0.215       0.210            0.194
#>  4 IQR                0.167  0.252       0.333       0.333            0.200
#>  5 Max                0.833  0.833       0.833       1                1    
#>  6 Min                0.167  0.182       0           0                0    
#>  7 NAs                0      4           0           0                0    
#>  8 INFs               0      0           0           0                0    
#>  9 All_0              0.5   NA           0           1              NaN    
#> 10 All_1              0.5    0.667       1           0                0.5  
#> # … with 9 more variables: `Neg Pred Value` <dbl>, AUC <dbl>, `Lower CI` <dbl>,
#> #   `Upper CI` <dbl>, Kappa <dbl>, MCC <dbl>, `Detection Rate` <dbl>,
#> #   `Detection Prevalence` <dbl>, Prevalence <dbl>
#> 
#> $random_evaluations
#> # A tibble: 100 x 19
#>    `Balanced Accur…    F1 Sensitivity Specificity `Pos Pred Value`
#>               <dbl> <dbl>       <dbl>       <dbl>            <dbl>
#>  1            0.417 0.364       0.333       0.5              0.4  
#>  2            0.5   0.5         0.5         0.5              0.5  
#>  3            0.417 0.364       0.333       0.5              0.4  
#>  4            0.667 0.6         0.5         0.833            0.75 
#>  5            0.583 0.667       0.833       0.333            0.556
#>  6            0.667 0.6         0.5         0.833            0.75 
#>  7            0.25  0.308       0.333       0.167            0.286
#>  8            0.5   0.4         0.333       0.667            0.500
#>  9            0.25  0.182       0.167       0.333            0.20 
#> 10            0.417 0.222       0.167       0.667            0.333
#> # … with 90 more rows, and 14 more variables: `Neg Pred Value` <dbl>,
#> #   AUC <dbl>, `Lower CI` <dbl>, `Upper CI` <dbl>, Kappa <dbl>, MCC <dbl>,
#> #   `Detection Rate` <dbl>, `Detection Prevalence` <dbl>, Prevalence <dbl>,
#> #   Predictions <list>, ROC <list>, `Confusion Matrix` <list>, Family <chr>,
#> #   Dependent <chr>

Multinomial

Approach: Creates one-vs-all (binomial) baseline evaluations for n sets of random predictions against the dependent variable, along with sets of “all class x,y,z,…” predictions.

Create the baseline evaluations:

multiclass_baseline <- baseline(
  test_data = multiclass_test_set, n = 100,
  dependent_col = "class", family = "multinomial")

# Summarized metrics
multiclass_baseline$summarized_metrics
#> # A tibble: 12 x 16
#>    Measure `Overall Accura… `Balanced Accur…      F1 Sensitivity Specificity
#>    <chr>              <dbl>            <dbl>   <dbl>       <dbl>       <dbl>
#>  1 Mean              0.250            0.501   0.283       0.252       0.750 
#>  2 Median            0.231            0.494   0.280       0.243       0.746 
#>  3 SD                0.0841           0.0567  0.0737      0.0853      0.0284
#>  4 IQR               0.115            0.0795  0.0920      0.121       0.0385
#>  5 Max               0.538            0.786   0.667       1           1     
#>  6 Min               0.0769           0.262   0.111       0           0.474 
#>  7 NAs              NA                0      61           0           0     
#>  8 INFs             NA                0       0           0           0     
#>  9 All_cl…           0.192            0.5    NA           0.25        0.75  
#> 10 All_cl…           0.269            0.5    NA           0.25        0.75  
#> 11 All_cl…           0.269            0.5    NA           0.25        0.75  
#> 12 All_cl…           0.269            0.5    NA           0.25        0.75  
#> # … with 10 more variables: `Pos Pred Value` <dbl>, `Neg Pred Value` <dbl>,
#> #   AUC <dbl>, `Lower CI` <dbl>, `Upper CI` <dbl>, Kappa <dbl>, MCC <dbl>,
#> #   `Detection Rate` <dbl>, `Detection Prevalence` <dbl>, Prevalence <dbl>

# Summarized class level results for class 1
multiclass_baseline$summarized_class_level_results %>% 
  dplyr::filter(Class == "class_1") %>%
  tidyr::unnest(Results)
#> # A tibble: 10 x 16
#>    Class Measure `Balanced Accur…     F1 Sensitivity Specificity
#>    <chr> <chr>              <dbl>  <dbl>       <dbl>       <dbl>
#>  1 clas… Mean               0.514  0.284       0.28       0.748 
#>  2 clas… Median             0.529  0.286       0.2        0.762 
#>  3 clas… SD                 0.102  0.106       0.191      0.0979
#>  4 clas… IQR                0.124  0.182       0.2        0.0952
#>  5 clas… Max                0.786  0.526       1          0.952 
#>  6 clas… Min                0.262  0.125       0          0.524 
#>  7 clas… NAs                0     18           0          0     
#>  8 clas… INFs               0      0           0          0     
#>  9 clas… All_0              0.5   NA           0          1     
#> 10 clas… All_1              0.5    0.323       1          0     
#> # … with 10 more variables: `Pos Pred Value` <dbl>, `Neg Pred Value` <dbl>,
#> #   AUC <dbl>, `Lower CI` <dbl>, `Upper CI` <dbl>, Kappa <dbl>, MCC <dbl>,
#> #   `Detection Rate` <dbl>, `Detection Prevalence` <dbl>, Prevalence <dbl>

# Random evaluations
# Note, that the class level results for each repetition
# is available as well
multiclass_baseline$random_evaluations
#> # A tibble: 100 x 21
#>    Repetition `Overall Accura… `Balanced Accur…      F1 Sensitivity Specificity
#>         <dbl>            <dbl>            <dbl>   <dbl>       <dbl>       <dbl>
#>  1          1            0.154            0.445 NaN           0.171       0.719
#>  2          2            0.269            0.518 NaN           0.279       0.758
#>  3          3            0.192            0.460   0.195       0.193       0.727
#>  4          4            0.385            0.591   0.380       0.386       0.797
#>  5          5            0.154            0.430 NaN           0.143       0.717
#>  6          6            0.154            0.438 NaN           0.157       0.718
#>  7          7            0.154            0.445 NaN           0.171       0.719
#>  8          8            0.346            0.574   0.341       0.364       0.784
#>  9          9            0.308            0.541   0.315       0.314       0.767
#> 10         10            0.308            0.536   0.322       0.3         0.772
#> # … with 90 more rows, and 15 more variables: `Pos Pred Value` <dbl>, `Neg Pred
#> #   Value` <dbl>, AUC <dbl>, `Lower CI` <dbl>, `Upper CI` <dbl>, Kappa <dbl>,
#> #   MCC <dbl>, `Detection Rate` <dbl>, `Detection Prevalence` <dbl>,
#> #   Prevalence <dbl>, Predictions <list>, `Confusion Matrix` <list>, `Class
#> #   Level Results` <list>, Family <chr>, Dependent <chr>

Plot results

There are currently a small set of plots for quick visualization of the results. It is supposed to be easy to extract the needed information to create your own plots. If you lack access to any information or have other requests or ideas, feel free to open an issue.

Gaussian

cv_plot(CV1, type = "RMSE") +
  theme_bw()

cv_plot(CV1, type = "r2") +
  theme_bw()

cv_plot(CV1, type = "IC") +
  theme_bw()

cv_plot(CV1, type = "coefficients") +
  theme_bw()

Binomial

cv_plot(CV2, type = "ROC") +
  theme_bw()

Generate model formulas

Instead of manually typing all possible model formulas for a set of fixed effects (including the possible interactions), combine_predictors() can do it for you (with some constraints).

When including interactions, >200k formulas have been precomputed for up to 8 fixed effects, with a maximum interaction size of 3, and a maximum of 5 fixed effects per formula. It’s possible to further limit the generated formulas.

We can also append a random effects structure to the generated formulas.

combine_predictors(dependent = "y",
                   fixed_effects = c("a","b","c"),
                   random_effects = "(1|d)")
#>  [1] "y ~ a + (1|d)"                     "y ~ b + (1|d)"                    
#>  [3] "y ~ c + (1|d)"                     "y ~ a * b + (1|d)"                
#>  [5] "y ~ a * c + (1|d)"                 "y ~ a + b + (1|d)"                
#>  [7] "y ~ a + c + (1|d)"                 "y ~ b * c + (1|d)"                
#>  [9] "y ~ b + c + (1|d)"                 "y ~ a * b * c + (1|d)"            
#> [11] "y ~ a * b + c + (1|d)"             "y ~ a * c + b + (1|d)"            
#> [13] "y ~ a + b * c + (1|d)"             "y ~ a + b + c + (1|d)"            
#> [15] "y ~ a * b + a * c + (1|d)"         "y ~ a * b + b * c + (1|d)"        
#> [17] "y ~ a * c + b * c + (1|d)"         "y ~ a * b + a * c + b * c + (1|d)"

If two or more fixed effects should not be in the same formula, like an effect and its log-transformed version, we can provide them as sublists.

combine_predictors(dependent = "y",
                   fixed_effects = list("a", list("b","log_b")),
                   random_effects = "(1|d)")
#> [1] "y ~ a + (1|d)"         "y ~ b + (1|d)"         "y ~ log_b + (1|d)"    
#> [4] "y ~ a * b + (1|d)"     "y ~ a * log_b + (1|d)" "y ~ a + b + (1|d)"    
#> [7] "y ~ a + log_b + (1|d)"

Introduction to cvms

Ludvig Renbo Olsen

2019-12-01

Main functions

The difference between `cross_validate()` and `cross_validate_fn()`

Examples

Attach packages

Load data

Fold data

Cross-validate a single model

Gaussian

Binomial

Cross-validate multiple models

Create model formulas

Cross-validate fixed effects models

Cross-validate mixed effects models

Repeated cross-validation

Cross-validating custom model functions

SVM

Naive Bayes

Evaluating predictions

Multinomial

Baseline evaluations

Gaussian

Binomial

Multinomial

Plot results

Gaussian

Binomial

Generate model formulas

participant	age	diagnosis	score	session	.folds
9	34	0	33	1	1
9	34	0	53	2	1
9	34	0	66	3	1
8	21	1	16	1	1
8	21	1	32	2	1
8	21	1	44	3	1
2	23	0	24	1	2
2	23	0	40	2	2
2	23	0	67	3	2
1	20	1	10	1	2
1	20	1	24	2	2
1	20	1	45	3	2
6	31	1	14	1	2
6	31	1	25	2	2
6	31	1	30	3	2

participant	age	score	session	.folds_1	.folds_2	.folds_3	.folds_4
10	32	29	1	4	4	3	1
10	32	55	2	4	4	3	1
10	32	81	3	4	4	3	1
2	23	24	1	2	3	1	2
2	23	40	2	2	3	1	2
2	23	67	3	2	3	1	2
4	21	35	1	3	2	4	4
4	21	50	2	3	2	4	4
4	21	78	3	3	2	4	4
9	34	33	1	1	1	2	3

participant	age	diagnosis	score	session	.folds
9	34	0	33	1	1
9	34	0	53	2	1
9	34	0	66	3	1
8	21	1	16	1	1
8	21	1	32	2	1
8	21	1	44	3	1
2	23	0	24	1	2
2	23	0	40	2	2
2	23	0	67	3	2
1	20	1	10	1	2
1	20	1	24	2	2
1	20	1	45	3	2
6	31	1	14	1	2
6	31	1	25	2	2
6	31	1	30	3	2

participant	age	score	session	.folds_1	.folds_2	.folds_3	.folds_4
10	32	29	1	4	4	3	1
10	32	55	2	4	4	3	1
10	32	81	3	4	4	3	1
2	23	24	1	2	3	1	2
2	23	40	2	2	3	1	2
2	23	67	3	2	3	1	2
4	21	35	1	3	2	4	4
4	21	50	2	3	2	4	4
4	21	78	3	3	2	4	4
9	34	33	1	1	1	2	3

Introduction to cvms

Ludvig Renbo Olsen

2019-12-01

Main functions

The difference between cross_validate() and cross_validate_fn()

Examples

Attach packages

Load data

Fold data

Cross-validate a single model

Gaussian

Binomial

Cross-validate multiple models

Create model formulas

Cross-validate fixed effects models

Cross-validate mixed effects models

Repeated cross-validation

Cross-validating custom model functions

SVM

Naive Bayes

Evaluating predictions

Multinomial

Baseline evaluations

Gaussian

Binomial

Multinomial

Plot results

Gaussian

Binomial

Generate model formulas

The difference between `cross_validate()` and `cross_validate_fn()`

participant	age	diagnosis	score	session	.folds
9	34	0	33	1	1
9	34	0	53	2	1
9	34	0	66	3	1
8	21	1	16	1	1
8	21	1	32	2	1
8	21	1	44	3	1
2	23	0	24	1	2
2	23	0	40	2	2
2	23	0	67	3	2
1	20	1	10	1	2
1	20	1	24	2	2
1	20	1	45	3	2
6	31	1	14	1	2
6	31	1	25	2	2
6	31	1	30	3	2

participant	age	score	session	.folds_1	.folds_2	.folds_3	.folds_4
10	32	29	1	4	4	3	1
10	32	55	2	4	4	3	1
10	32	81	3	4	4	3	1
2	23	24	1	2	3	1	2
2	23	40	2	2	3	1	2
2	23	67	3	2	3	1	2
4	21	35	1	3	2	4	4
4	21	50	2	3	2	4	4
4	21	78	3	3	2	4	4
9	34	33	1	1	1	2	3