tests/testthat/testNlmixr.R

In tdmore-dev/tdmore: In silico evaluation of precision dosing

library(tdmore)
library(nlmixr)
library(ggplot2)
library(testthat)

# Load the default tdmore
tdmore <- getModel("default")

regimen <- data.frame(
  TIME=seq(0, 1)*24,
  AMT=5 #5mg
)
covariates = c(WT=70)

# Default tdmore plot
plot(tdmore, regimen, covariates=covariates)

# Create the observed and covariates dataframe
observed <- data.frame(TIME=c(2), CONC=c(0.040))

# Compute PRED
pred <- tdmore %>% estimate(regimen = regimen, covariates=covariates)
expect_equal(pred$res, c(ECL=0.0, EV1=0.0))

# Compute IPRED
ipred <- tdmore %>% estimate(observed = observed, regimen = regimen, covariates = covariates)
expect_equal(round(ipred$res, digits=4), c(ECL=0.0336, EV1=0.1175))

# Plot IPRED
p1 <- plot(ipred, newdata=data.frame(TIME=seq(0, 48, by=0.1), CONC=NA))

# Find dose example and test
observed <- data.frame(TIME=c(2,26), CONC=c(0.040, 0.0675))
covariates <- data.frame(TIME=c(0), WT=c(70))

# Compute new IPRED
ipred <- tdmore %>% estimate(observed = observed, regimen = regimen, covariates = covariates)

# Plot IPRED
p2 <- plot(ipred, newdata=data.frame(TIME=seq(0, 48, by=0.1), CONC=NA))

# Find dose test
D <- findDose(ipred, regimen=regimen, target=data.frame(TIME=35, CONC=0.0395))
expect_equal(round(D$dose, digits=2), 5.84)

plot(p1)
plot(p2)