calCurvPlot {ClinicalUtilityRecal} | R Documentation |

## Calibration Curve Plot

### Description

Flexible function for plotting the calibration curve for a risk score and different recalibrations of a risk score. Histograms of risk score and recalibrated risk scores can be plotted using argument "hist==TRUE". Dotted guidelines for the risk threshold R are plotted and clinically releavant risk region [R_l, R_u] are plotted to help gauge calibration in clinically relevants.

### Usage

```
calCurvPlot(y,p,p.std=NULL,p.recal=NULL,
stdPlot=FALSE, recalPlot=FALSE,
xlim=c(0,1),ylim=c(0,1),
label="Original Risk Score",
label2 = "Standard Recalibrated Risk Score",
label3 = "Weighted/Constrained Recalibrated Risk Score",
legendLab = c("Orig.", "Std.", "Wt."),
mainTitle="Calibration of Risk Score",
hist=TRUE,ylimHist = c(0,0.5),
r,rl = -Inf, ru = Inf)
```

### Arguments

`y` |
Vector of binary outcomes, with 1 indicating event (case) and 0 indicating no event (controls) |

`p` |
Vector of risk score values |

`p.std` |
Vector of risk score values after standard logistic recalibration |

`p.recal` |
Vector of risk score values after weighted/contratined logistic recalibration |

`stdPlot` |
If TRUE plot calibration curve for standard logistic recalibrated risk score |

`recalPlot` |
If TRUE plot calibration curve for weighted/contratined recalibrated risk score |

`xlim` |
Limits for x-axis |

`ylim` |
Limits for y-axis |

`label` |
Label for x-axis corresponding to p vector |

`label2` |
Label for x-axis corresponding to p.std vector |

`label3` |
Label for x-axis corresponding to p.recal vector |

`legendLab` |
Label for legend |

`mainTitle` |
Main title for plot |

`hist` |
If true plot distribution of risk scores along with calibration curve |

`ylimHist` |
Limits for y-axis of histogram |

`r` |
Clinically relevant risk threshold used indicated with dotted line |

`rl` |
Lower bound of clinically relevant region indicated with dotted-dashed line |

`ru` |
Upper bound of clinically relevant region indicated with dotted-dashed line |

### Value

Prints calibration plot of risk model p, and optional histogram of risk score

### Author(s)

Anu Mishra

### References

Mishra, A. (2019). Methods for Risk Markers that Incorporate Clinical Utility (Doctoral dissertation). (Available Upon Request)

### Examples

```
## Not run:
data("fakeData")
### get standard recalibrated risk score
stdRecal.res <- stdRecal(y = fakeData$y,p = fakeData$p)
p.std <- stdRecal.res$p.std
### Select tuning parameter lamba using 5-fold cross-validation repeated 25 times
grid <- RAWgrid(r = 0.3,rl = -Inf,ru = Inf,p = fakeData$p,y = fakeData$y,
cvParm = "lambda",rl.raw = 0.25,ru.raw = 0.35)
repCV <- cvRepWtTuning(y = fakeData$y,p = fakeData$p,rl = -Inf,ru = Inf,r = 0.3,
kFold = 5,cvRep = 25,cvParm = "lambda",tuneSeq = grid,stdErrRule = TRUE)
## Implement weighted logistic recalibration
wtRecal.res <- wtRecal(y = fakeData$y,p = fakeData$p,r = 0.3,rl = -Inf,ru = Inf,
lambda = repCV$cv.lambda,delta=1)
p.recal <- wtRecal.res$p.wt
### Calibration curve of only original risk score with histogram
calCurvPlot(y=fakeData$y,p=fakeData$p,p.std=NULL,p.recal=NULL,
stdPlot=FALSE, recalPlot=FALSE,
xlim=c(0,1),ylim=c(0,1),
label="Original Risk Score",
label2 = "Standard Recalibrated Risk Score",
label3 = "Weighted/Constrained Recalibrated Risk Score",
legendLab = c("Orig.", "Std.", "Wt."),
mainTitle="Calibration of Risk Score",
hist=TRUE,ylimHist = c(0,0.5),
r=0.3,rl = -Inf, ru = Inf)
### Calibration curve of only original, standard and weighted recalibrated risk score
calCurvPlot(fakeData$y,p=fakeData$p,p.std=p.std,p.recal=p.recal,
stdPlot=TRUE, recalPlot=TRUE,
xlim=c(0,1),ylim=c(0,1),
label="Original Risk Score",
label2 = "Standard Recalibrated Risk Score",
label3 = "Weighted/Constrained Recalibrated Risk Score",
legendLab = c("Orig.", "Std.", "Wt."),
mainTitle="Calibration of Risk Score",
hist=TRUE,ylimHist = c(0,0.5),
r=0.3,rl = -Inf, ru = Inf)
## End(Not run)
```

*ClinicalUtilityRecal*version 0.1.0 Index]