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psc

The goal of psc is to compare a dataset of observations against a parametric model

Installation

You can install the development version of psc from GitHub with:

# install.packages("devtools")
devtools::install_github("richJJackson/psc")

Example

This is a basic example which shows you how to solve a common problem:

library(psc)
#> Loading required package: survival
#> Loading required package: ggplot2
library(survival)
## basic example code

### Load model
data("surv.mod")

### Load Data
data("data")
#> Warning in data("data"): data set 'data' not found

### Use 'pscfit' to compare
surv.psc <- pscfit(surv.mod,data)
#> Warning in pscData_match(CFM$cov_class, CFM$cov_lev, DCcov): vi specified as a character in the model, consider respecifying
#>                 as a factor to ensure categories match between CFM and DC
#> Warning in pscData_match(CFM$cov_class, CFM$cov_lev, DCcov): allmets specified as a character in the model, consider respecifying
#>                 as a factor to ensure categories match between CFM and DC

You can use standard commands for getting a summary of your analysis…

summary(surv.psc)
#> Counterfactual Model (CFM): 
#> A model of class 'flexsurvreg' 
#>  Fit with 3 internal knots
#> 
#> CFM Formula: 
#> Surv(time, cen) ~ vi/age60 + ecog + allmets + logafp + alb + 
#>     logcreat + logast + aet
#> <environment: 0x116b6fd60>
#> 
#> CFM Summary: 
#> Expected response for the outcome under the CFM:
#>      S      lo      hi  
#>  9.694   9.094  11.013  
#> 
#> Observed outcome from the Data Cohort:
#>          [,1] 
#> median   6.366
#> 0.95LCL  5.436
#> 0.95UCL  9.094
#> 
#> MCMC Fit: 
#> Posterior Distribution obtaine with fit summary:
#>       variable     rhat         ess_bulk     ess_tail     mcse_mean  
#> [1,]  beta_1       1.001575     1157.117     1022.026     0.002900963
#> 
#> Summary: 
#> Posterior Distribution for beta:Call:
#>  CFM model + beta
#> 
#> Coefficients:
#>            variable    mean        sd          median      q5        
#> posterior  beta_1      0.3707433   0.09903147  0.3708735   0.2103505 
#>            q95       
#> posterior  0.5420673

… and to see a plot of what you have done

#>            variable    mean        sd          median      q5        
#> posterior  beta_1      0.3707433   0.09903147  0.3708735   0.2103505 
#>            q95       
#> posterior  0.5420673
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the ggpubr package.
#>   Please report the issue at <https://github.com/kassambara/ggpubr/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Ignoring unknown labels:
#> • colour : "Strata"

In that case, don’t forget to commit and push the resulting figure files, so they display on GitHub and CRAN.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.