20231215 - probability nomogram

10-Prediction.Rmd

@@ -3688,7 +3688,7 @@ The probability of having the condition if the person has a positive test on Tes
 ### Probability Nomogram {#nomogram}
 
 The [`petersenlab`](https://github.com/DevPsyLab/petersenlab) package [@R-petersenlab] contains the `nomogrammer()` function that creates a probability nomogram plot, adapted from https://github.com/achekroud/nomogrammer.\index{petersenlab package}\index{probability!nomogram}
-In Figure \@ref(nomogramPlot), the probability nomogram is generated using the [base rate](#pretestProbability) of the condition and the [sensitivity](#sensitivity) and [specificity](#specificity) of the test at a given cutoff.\index{petersenlab package}\index{probability!nomogram}
+In Figure \@ref(fig:nomogramPlot), the probability nomogram is generated using the [base rate](#pretestProbability) of the condition and the [sensitivity](#sensitivity) and [specificity](#specificity) of the test at a given cutoff.\index{petersenlab package}\index{probability!nomogram}\index{base rate}\index{sensitivity}\index{specificity}\index{cutoff}
 
 ```{r nomogramPlot, fig.align = "center", fig.cap = "Probability Nomogram."}
 nomogrammer(
@@ -3698,9 +3698,9 @@ nomogrammer(
 )
 ```
 
-The blue line indicates the [posterior probability](#posttestProbability) of the condition given a positive test.\index{petersenlab package}\index{probability!nomogram}
-The pink line indicates the [posterior probability](#posttestProbability) of the condition given a negative test.\index{petersenlab package}\index{probability!nomogram}
-One can also generate the probability nomogram from the [base rate](#pretestProbability), [positive likelihood ratio](#positiveLikelihoodRatio), and [negative likelihood ratio](#negativeLikelihoodRatio) at a given cutoff:\index{petersenlab package}\index{probability!nomogram}
+The blue line indicates the [posterior probability](#posttestProbability) of the condition given a positive test.\index{petersenlab package}\index{probability!nomogram}\index{probability!posttest}
+The pink line indicates the [posterior probability](#posttestProbability) of the condition given a negative test.\index{petersenlab package}\index{probability!nomogram}\index{probability!posttest}
+One can also generate the probability nomogram from the [base rate](#pretestProbability), [positive likelihood ratio](#positiveLikelihoodRatio), and [negative likelihood ratio](#negativeLikelihoodRatio) at a given cutoff:\index{petersenlab package}\index{probability!nomogram}\index{positive likelihood ratio}\index{negative likelihood ratio}\index{cutoff}
 
 ```{r, eval = FALSE}
 nomogrammer(