diff --git a/vignettes/08-evaluationMetrics.Rmd b/vignettes/08-evaluationMetrics.Rmd new file mode 100644 index 0000000000000000000000000000000000000000..28891f40755b3dd9a983b51838f74b16f02cb515 --- /dev/null +++ b/vignettes/08-evaluationMetrics.Rmd @@ -0,0 +1,81 @@ +--- +title: "About evaluation metrics" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{About evaluation metrics} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + + +## Root Mean Square Error (RMSE) + +RMSE measures the average deviation between predicted values and actual values. It is calculated as follows: + +\[ \text{RMSE} = \sqrt{\frac{1}{n}\sum_{i=1}^{n}(y_i - \hat{y}_i)^2} \] + +## R-squared (R²) + +R² measures the proportion of the variance in the dependent variable that is predictable from the independent variable(s). It is calculated as follows: + +\[ R^2 = 1 - \frac{\sum_{i=1}^{n}(y_i - \hat{y}_i)^2}{\sum_{i=1}^{n}(y_i - \bar{y})^2} \] + +## Precision-Recall Area Under Curve (PR-AUC) + +PR-AUC measures the area under the precision-recall curve. It is often used in binary classification tasks where the class distribution is imbalanced. + +## Performance Ratio + +performance ratio is calculated as the ratio of PR-AUC to the PR-AUC of a random classifier (`pr_randm_AUC`). +It provides a measure of how well the model performs compared to a random baseline. + +\[ performanceRatio = \frac{PR_{AUC}}{PR_{randomAUC}} \] + + +## Receiver Operating Characteristic Area Under Curve (ROC AUC) + +ROC AUC measures the area under the receiver operating characteristic curve. It evaluates the classifier's ability to distinguish between classes. + +## Confusion Matrix + +| | Predicted Negative | Predicted Positive | +|:---------------:|:------------------:|:------------------:| +| Actual Negative | TN | FP | +| Actual Positive | FN | TP | + +## Accuracy + +Accuracy measures the proportion of correct predictions out of the total predictions made by the model. It is calculated as follows: + +\[ +\text{Accuracy} = \frac{\text{TP} + \text{TN}}{\text{TP} + \text{TN} + \text{FP} + \text{FN}} +\] + +## Specificity + +Specificity measures the proportion of true negatives out of all actual negatives. It is calculated as follows: + +\[ +\text{Specificity} = \frac{\text{TN}}{\text{TN} + \text{FP}} +\] + +## Recall (Sensitivity) + +Recall, also known as sensitivity, measures the proportion of true positives out of all actual positives. It indicates the model's ability to correctly identify positive instances. + +\[ \text{Recall} = \text{Sensitivity} = \frac{\text{TP}}{\text{TP} + \text{FN}} \] + +## Precision + +Precision measures the proportion of true positives out of all predicted positives. It indicates the model's ability to avoid false positives. + +\[ \text{Precision} = \frac{\text{TP}}{\text{TP} + \text{FP}} \] + + diff --git a/vignettes/09-FAQ.Rmd b/vignettes/09-FAQ.Rmd new file mode 100644 index 0000000000000000000000000000000000000000..d1575b1c67a747645f8ee41974a2c4917efd9bad --- /dev/null +++ b/vignettes/09-FAQ.Rmd @@ -0,0 +1,34 @@ +--- +title: "Frequently Asked Questions" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Frequently Asked Questions} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + + +## Why mu has no effect within simulation + +some element of response + +## Difference between norm_distrib = 'univariate' & = 'multivariate' + +some element of response + + +## Why use `transform = 'x+1'` with `prepareData2Fit()` + +some element of response. Zero Nightmare + + +## Why use `row_threshold = 10` with `prepareData2Fit()` + +some element of response