The goal of censlm is to simplify fitting censored linear models and using them to draw plausible imputed values for censored observations.
You can install the development version of censlm like so:
remotes::install_github("mikmart/censlm")Fit a censored linear model to left-censored data with clm(), then
draw random values for censored observations from the fitted
distribution with imputed():
library(censlm)
#> Loading required package: survival
set.seed(42)
# Simulate left-censored log-normal CRP observations
crp <- rlnorm(10000, 1.355, 1.450)
lloq <- 3
obs <- replace(crp, crp < lloq, lloq)
crpdf <- data.frame(crp, lloq, obs)
# Fit censored linear model and extract (random) imputations
fit <- clm(log(obs) ~ 1, left = log(lloq))
imp <- exp(imputed(fit))
summary(fit)
#>
#> Call:
#> survreg(formula = Surv(log(obs), log(obs) > log(lloq), type = "left") ~
#> 1, dist = "gaussian")
#> Value Std. Error z p
#> (Intercept) 1.3421 0.0168 79.8 <2e-16
#> Log(scale) 0.3749 0.0103 36.3 <2e-16
#>
#> Scale= 1.45
#>
#> Gaussian distribution
#> Loglik(model)= -13460.2 Loglik(intercept only)= -13460.2
#> Number of Newton-Raphson Iterations: 4
#> n= 10000
summary(cbind(crpdf, imp))
#> crp lloq obs imp
#> Min. : 0.011 Min. :3 Min. : 3.000 Min. : 0.0056
#> 1st Qu.: 1.418 1st Qu.:3 1st Qu.: 3.000 1st Qu.: 1.4200
#> Median : 3.842 Median :3 Median : 3.842 Median : 3.8418
#> Mean : 11.158 Mean :3 Mean : 11.883 Mean : 11.1576
#> 3rd Qu.: 10.139 3rd Qu.:3 3rd Qu.: 10.139 3rd Qu.: 10.1394
#> Max. :2060.559 Max. :3 Max. :2060.559 Max. :2060.5585