inst/maintenance/unit/test-pkmodel.R

In mrgsolve/mrgsolvetk: Simulation Tool Kit for mrgsolve

# Copyright (C) 2013 - 2017  Metrum Research Group, LLC
#
# This file is part of mrgsolve.
#
# mrgsolve is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# mrgsolve is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with mrgsolve.  If not, see <http://www.gnu.org/licenses/>.

library(testthat)
library(mrgsolve)
library(dplyr)
Sys.setenv(R_TESTS="")
options("mrgsolve_mread_quiet"=TRUE)

project <- file.path(system.file(package="mrgsolve"), "models")
tmp <- tempdir()

context("Compare PKMODEL with equivalent ODEs.")

ode <- mrgsolve:::house() %>% param(CL=1,VC=20,KA=1.1)


code2 <- '
$PARAM CL=1, V=20, KA=1.1
$CMT CENT
$PKMODEL ncmt=1
'
pred2 <- mcode("test13.2", code2)


# 
# test_that("ADVAN2 same as ODE - initial condition", {
#   out1 <- ode  %>% init(GUT=1000) %>% 
#     Req(GUT,CENT) %>% mrgsim(end=24,delta=0.1 ,digits=5)
# 
#   expect_equal(out1$CENT,out2$CENT)
#   expect_equal(names(out1),names(out2))
# })
# 
# 
# test_that("ADVAN2 same as ODE - GUT,bolus,addl", {
#   e <- ev(amt=100,ii=48,addl=4)
#   out1 <- ode  %>% ev(e) %>% 
#     Req(GUT,CENT) %>% mrgsim(end=264,delta=0.1 ,digits=5)
#   out2 <- pred %>% ev(e) %>% 
#     Req(GUT,CENT) %>% mrgsim(end=264,delta=0.1,digits=5)
#   
#   expect_equal(out1$CENT,out2$CENT)
# })
# 
# 
# 
# test_that("ADVAN2 same as ODE - GUT,infus,addl", {
#   e <- ev(amt=1000,rate=50,ii=48,addl=4,cmt=2)
#   out1 <- ode  %>% ev(e) %>% 
#     Req(CENT) %>% mrgsim(end=264,delta=0.1 ,digits=5,hmax=0.1,atol=1E-12,rtol=1E-12)
#   out2 <- pred %>% ev(e) %>% 
#     Req(CENT) %>% mrgsim(end=264,delta=0.1,digits=5)
#   
#   expect_equal(out1$CENT,out2$CENT)
# })
# 

test_that("ADVAN2 same as ODE - CENT,infus,addl", {
  e <- ev(amt=1000,rate=50,ii=48,addl=4,cmt=2)
  out1 <- ode  %>% ev(e) %>% 
    Req(CENT) %>% mrgsim(end=264,delta=0.1 ,digits=5,hmax=0.1,atol=1E-12,rtol=1E-12)
  # out2 <- pred %>% ev(e) %>% 
  #   Req(CENT) %>% mrgsim(end=264,delta=0.1,digits=5)
  e2 <- ev(amt=1000,rate=50,ii=48,addl=4,cmt=1)
  out3 <- pred2 %>% ev(e2) %>% 
    Req(CENT) %>% mrgsim(end=264,delta=0.1,digits=5)
  
#  expect_equal(out1$CENT,out2$CENT)
  expect_equal(out1$CENT,out3$CENT)
})


# test_that("ADVAN2 same as ODE - CENT,infus,ss,addl", {
#   e <- ev(amt=1000,rate=50,ii=48,addl=4,cmt=2,ss=1)
#   out1 <- ode  %>% ev(e) %>% 
#     Req(CENT) %>% mrgsim(end=264,delta=0.1 ,digits=5,hmax=0.1,atol=1E-12,rtol=1E-12)
#   out2 <- pred %>% ev(e) %>% 
#     Req(CENT) %>% mrgsim(end=264,delta=0.1,digits=5)
#   expect_equal(out1$CENT,out2$CENT)
# })


# 
# test_that("ADVAN2 same as ODE - GUT,bolus,ss,addl", {
#   e <- ev(amt=1000,ii=12,addl=16,cmt=1,ss=1)
#   out1 <- ode  %>% ev(e) %>% 
#     Req(CENT) %>% mrgsim(end=264,delta=0.1 ,digits=5,
#                          hmax=0.1,atol=1E-12,rtol=1E-12)
#   out2 <- pred %>% ev(e) %>% 
#     Req(CENT) %>% mrgsim(end=264,delta=0.1,digits=5)
#   
#   expect_equal(out1$CENT,out2$CENT)
# })
# 


project <- file.path(system.file(package="mrgsolve"), "models")

ode_code <- '
$PARAM CL=1, VC=20, Q=4, KA=1.1, VP=300
$CMT GUT CENT PER
$ODE
dxdt_GUT = -KA*GUT;
dxdt_CENT = KA*GUT - CENT*(CL+Q)/VC + PER*Q/VP;
dxdt_PER = CENT*Q/VC - PER*Q/VP;
'


pred_code <- '
$PARAM CL=1, VC=20, KA=1.1, Q=4, VP=300
$CMT GUT CENT PER
$ADVAN4
$MAIN
pred_CL = CL;
pred_V2 = VC;
pred_KA = KA;
pred_Q = Q;
pred_V3 = VP;
'
pred2 <- '
$PARAM CL=1, V1=20, KA=1.1, Q=4, V2=300
$CMT CENT PER
$PKMODEL ncmt=2
'

ode <- mcode("test13_3",ode_code) 
#pred <- mread(code=pred_code, model="test13.4", project=tmp)
pred2 <- mcode("test13_5",pred2)


# 
# test_that("ADVAN4 same as ODE - initial condition", {
#   out1 <- ode  %>% init(GUT=1000) %>% 
#     Req(GUT,CENT) %>% mrgsim(end=24,delta=0.1 ,digits=5)
#   out2 <- pred %>% init(GUT=1000) %>% 
#     Req(GUT,CENT) %>% mrgsim(end=24,delta=0.1,digits=5)
#   
#   
#   expect_equal(out1$CENT,out2$CENT)
#   expect_equal(names(out1),names(out2))
# })


# test_that("ADVAN4 same as ODE - GUT,bolus,addl", {
#   e <- ev(amt=100,ii=48,addl=4)
#   out1 <- ode  %>% ev(e) %>% 
#     Req(GUT,CENT,PER) %>% mrgsim(end=264,delta=0.1 ,digits=5)
#   out2 <- pred %>% ev(e) %>% 
#     Req(GUT,CENT,PER) %>% mrgsim(end=264,delta=0.1,digits=5)
#   
#   expect_equal(out1$CENT,out2$CENT)
#   expect_equal(out1$PER,out2$PER)
# })
# 


# test_that("ADVAN4 same as ODE - GUT,infus,addl", {
#   e <- ev(amt=1000,rate=50,ii=48,addl=4)
#   out1 <- ode  %>% ev(e) %>% 
#     Req(CENT,PER) %>% mrgsim(end=264,delta=0.1 ,digits=5,hmax=0.1,atol=1E-12,rtol=1E-12)
#   out2 <- pred %>% ev(e) %>% 
#     Req(CENT,PER) %>% mrgsim(end=264,delta=0.1,digits=5)
#   
#   expect_equal(out1$CENT,out2$CENT)
#   expect_equal(out1$PER,out2$PER)
# })

test_that("ADVAN4 same as ODE - CENT,infus,addl", {
  
  e <- ev(amt=1000,rate=50,ii=48,addl=4,cmt=2)
  out1 <- ode  %>% ev(e) %>% 
    Req(CENT,PER) %>% mrgsim(end=264,delta=0.1 ,digits=5,hmax=0.1,atol=1E-12,rtol=1E-12)
  # out2 <- pred %>% ev(e) %>% 
  #   Req(CENT,PER) %>% mrgsim(end=264,delta=0.1,digits=5)
  
  e <- ev(amt=1000,rate=50,ii=48,addl=4,cmt=1)
  out3 <- pred2 %>% ev(e) %>% 
    Req(CENT,PER) %>% mrgsim(end=264,delta=0.1,digits=5)
  
#  expect_equal(out1$CENT,out2$CENT)
 # expect_equal(out1$PER,out2$PER)
  
  expect_equal(out1$CENT,out3$CENT)
  expect_equal(out1$PER,out3$PER)
})

# 
# test_that("ADVAN4 same as ODE - CENT,infus,ss,addl", {
#   e <- ev(amt=1000,rate=50,ii=48,addl=4,cmt=2,ss=1)
#   out1 <- ode  %>% ev(e) %>% 
#     Req(CENT,PER) %>% mrgsim(end=264,delta=0.1 ,digits=5,hmax=0.1,atol=1E-12,rtol=1E-12)
#   out2 <- pred %>% ev(e) %>% 
#     Req(CENT,PER) %>% mrgsim(end=264,delta=0.1,digits=5)
#   
#   expect_equal(out1$CENT,out2$CENT)
#   expect_equal(out1$PER,out2$PER)
# })



# test_that("ADVAN4 same as ODE - GUT,bolus,ss,addl", {
#   e <- ev(amt=100,ii=12,addl=16,cmt=1,ss=1)
#   out1<- ode  %>% ev(e) %>% 
#     Req(CENT,PER) %>% mrgsim(end=264,delta=0.1 ,digits=5,
#                              hmax=0.1,atol=1E-12,rtol=1E-12)
#   out2 <- pred %>% ev(e) %>% 
#     Req(CENT,PER) %>% mrgsim(end=264,delta=0.1,digits=5)
#   
#   
#   expect_equal(out1$CENT,out2$CENT)
#   expect_equal(out1$PER,out2$PER)
# })
# 

# context("Check $CMT/$INIT specification with ADVAN2/4")
# test_that("No compartments generates error", {
#   expect_error(mod <- mread(code="$ADVAN2", model="a2error1",tmp))
#   expect_error(mod <- mread(code="$ADVAN4", model="a2error2",tmp))
# })
# 
# test_that("Incorrect number of compartments causes error", {
#   expect_error(mod <- mread(code="$ADVAN2\n$CMT A", model="a2error3",tmp))
#   expect_error(mod <- mread(code="$ADVAN4\n$CMT A B C D", model="a2error4",tmp))
# })
# 
# test_that("Correct number of compartments causes no error", {
#   expect_is(mread(code="$ADVAN2\n$CMT A B", model="a2error5",tmp),"mrgmod")
#   expect_is(mread(code="$ADVAN4\n$CMT A B C", model="a2error6",tmp),"mrgmod")
# })
# 
# 
# 
#