In OhdsiReportGenerator: Observational Health Data Sciences and Informatics Report Generator

Visualizations

The following visualizations will can be viewed per model:

modelEvaluation <- data.frame(rbind(
    c("ROC Plot", "The ROC plot plots the sensitivity against 1-specificity on the test set. The plot shows how well the model is able to discriminate between the people with the outcome and those without. The dashed diagonal line is the performance of a model that randomly assigns predictions. The higher the area under the ROC plot the better the discrimination of the model."),
    c("Calibration Plot", "The calibration plot shows how close the predicted risk is to the observed risk. The diagonal dashed line thus indicates a perfectly calibrated model. The ten (or fewer) dots represent the mean predicted values for each quantile plotted against the observed fraction of people in that quantile who had the outcome (observed fraction). The straight black line is the linear regression using these 10 plotted quantile mean predicted vs observed fraction points. The two blue straight lines represented the 95% lower and upper confidence intervals of the slope of the fitted line."),
    c("Smooth Calibration Plot", "Similar to the traditional calibration shown above the Smooth Calibration plot shows the relationship between predicted and observed risk. the major difference is that the smooth fit allows for a more fine grained examination of this. Whereas the traditional plot will be heavily influenced by the areas with the highest density of data the smooth plot will provide the same information for this region as well as a more accurate interpretation of areas with lower density. the plot also contains information on the distribution of the outcomes relative to predicted risk.  However the increased information game comes at a computational cost. It is recommended to use the traditional plot for examination and then to produce the smooth plot for final versions."),
    c("Prediction Distribution Plots", "The preference distribution plots are the preference score distributions corresponding to i) people in the test set with the outcome (red) and ii) people in the test set without the outcome (blue)."),
    c("Box Plots", "The prediction distribution boxplots are box plots for the predicted risks of the people in the test set with the outcome (class 1: blue) and without the outcome (class 0: red)."),
    c("Test-Train Similarity Plot", "The test-train similarity is presented by plotting the mean covariate values in the train set against those in the test set for people with and without the outcome."),
    c("Variable Scatter Plot", "The variable scatter plot shows the mean covariate value for the people with the outcome against the mean covariate value for the people without the outcome. The size and color of the dots correspond to the importance of the covariates in the trained model (size of beta) and its direction (sign of beta with green meaning positive and red meaning negative), respectively."),
    c("Precision Recall Plot", "The precision-recall curve is valuable for dataset with a high imbalance between the size of the positive and negative class. It shows the tradeoff between precision and recall for different threshold. High precision relates to a low false positive rate, and high recall relates to a low false negative rate. High scores for both show that the classifier is returning accurate results (high precision), as well as returning a majority of all positive results (high recall). A high area under the curve represents both high recall and high precision."),
    c("Demographic Summary Plot", "This plot shows for females and males the expected and observed risk in different age groups together with a confidence area.")
  ))
  names(modelEvaluation) <- c("Plot","Description")
  row.names(modelEvaluation) <- NULL
  data <- modelEvaluation[order(modelEvaluation$Plot),]
  knitr::kable(x = data, caption = 'Standard Plots')

OhdsiReportGenerator documentation built on April 12, 2025, 2:09 a.m.