calibmsm - Calibration Plots for the Transition Probabilities from Multistate Models

Assess the calibration of an existing (i.e. previously developed) multistate model through calibration plots. Calibration is assessed using one of three methods. 1) Calibration methods for binary logistic regression models applied at a fixed time point in conjunction with inverse probability of censoring weights. 2) Calibration methods for multinomial logistic regression models applied at a fixed time point in conjunction with inverse probability of censoring weights. 3) Pseudo-values estimated using the Aalen-Johansen estimator of observed risk. All methods are applied in conjunction with landmarking when required. These calibration plots evaluate the calibration (in a validation cohort of interest) of the transition probabilities estimated from an existing multistate model. While package development has focused on multistate models, calibration plots can be produced for any model which utilises information post baseline to update predictions (e.g. dynamic models); competing risks models; or standard single outcome survival models, where predictions can be made at any landmark time. Please see Pate et al. (2024) <doi:10.1002/sim.10094> and Pate et al. (2024) <https://alexpate30.github.io/calibmsm/articles/Overview.html>.

Last updated 3 months ago

5.48 score 2 stars 9 scripts 215 downloads

rcprd - Extraction and Management of Clinical Practice Research Datalink Data

Simplify the process of extracting and processing Clinical Practice Research Datalink (CPRD) data in order to build datasets ready for statistical analysis. This process is difficult in 'R', as the raw data is very large and cannot be read into the R workspace. 'rcprd' utilises 'RSQLite' to create 'SQLite' databases which are stored on the hard disk. These are then queried to extract the required information for a cohort of interest, and create datasets ready for statistical analysis. The processes follow closely that from the 'rEHR' package, see Springate et al., (2017) <doi:10.1371/journal.pone.0171784>.

Last updated 3 months ago

5.45 score 2 stars 5 scripts 595 downloads