README.md

In mrgsolve/mrgsim: Scripted simulation with 'mrgsolve'

Scripted simulation runs with mrgsolve

library(mrgsim)
library(mrgsolve)
library(dplyr)

Load a model

mod <- mread("popex", modlib())

param(mod)

. 
.  Model parameters (N=4):
.  name value . name value
.  TVCL 1     | TVV  24   
.  TVKA 0.5   | WT   70

Load a scripted simulation run

run <- load_run("inst/yaml/foo.yaml")

Simulate

out <- sim_run(mod,run)

runtime

.    user  system elapsed 
.   0.499   0.014   0.515

dim(out)

. [1] 109850      5

out %>%
  group_by(arm) %>% 
  filter(time==4032) %>%
  summarise(Mean = mean(DV), Min = min(DV), Max = max(DV), N=n())

. # A tibble: 3 x 5
.     arm      Mean        Min       Max     N
.   <chr>     <dbl>      <dbl>     <dbl> <int>
. 1  arm1  7.014079 0.11433253  78.11614   250
. 2  arm2  3.492472 0.09303598  22.02542   250
. 3  arm3 17.942659 0.65358606 112.13541   150

The simulation run specification

  name: Simulation 1

  endpoints: [DV,CP,RESP]

  output_file: saved.RDS

  model: irm1

  project: /Users/kyleb/Rlibs/mrgsolve/models

  covariate:
    WT:   {distribution: rlnorm,  meanlog: 4.3 , sdlog: 0.5, by: ID, lb: 40, ub: 140}
    SEX:  {distribution: rbinomial, p: 0.5}
    AGE1: {distribution: runif, min: 21, max: 42, as: AGE}
    AGE2: {distribution: runif, min: 12, max: 27, as: AGE}

  covset:
    cov1: [WT,SEX,AGE1]
    cov2: [WT,SEX,AGE2]

  period:
    a: {amt: 100, ii: 24, addl: 83}
    b: {amt: 200, ii: 24, addl: 83}
    c: {amt: 500, ii: 24, addl: 168}

  sequence:
    s1: [a, b]
    s2: [a, a]
    s3: [c]

  sample:
    des1: {end: 4032, delta: 24, add: [0]}

  arm:
    arm1: {nid: 250, sequence: s1, covset: cov1}
    arm2: {nid: 250, sequence: s2, covset: cov2}
    arm3: {nid: 150, sequence: c,  covset: cov1}

  objects:
    - "Sigma <- diag(c(1,1))"
    - "mu <- log(c(2,20))"

Run specification for pediatric / adult pk

  name: Pediatrics and adults, same dose

  endpoints: [DV]

  output_file: saved.RDS

  model: popex

  covariate:
    WT1:   {distribution: rlnorm,  meanlog: 4.3 , sdlog: 0.5, by: ID, lb: 50, ub: 120, as: WT}
    WT2:   {distribution: rlnorm,  meanlog: 3.6 , sdlog: 0.5, by: ID, lb: 25, ub: 80,  as: WT}

  covset:
    cov1: [WT1]
    cov2: [WT2]

  period:
    dose100: {amt: 100, ii: 24, addl: 168}

  sample:
    des1: {end: 4032, delta: 24, add: [0]}

  arm:
    adult:     {nid: 250, sequence: dose100, covset: cov1}
    pediatric: {nid: 250, sequence: dose100, covset: cov2}

Run specification details

The run has arms

arms(run)

. # A tibble: 3 x 9
.     nid sequence covset sample   arm covsetn sequencen samplen  armn
.   <int>    <chr>  <chr>  <chr> <chr>   <int>     <int>   <int> <int>
. 1   250       s1   cov1   des1  arm1       1         1       1     1
. 2   250       s2   cov2   des1  arm2       2         2       1     2
. 3   150        c   cov1   des1  arm3       1         6       1     3

treatment sequences

sequences(run)

. # A tibble: 6 x 2
.   sequence periods
.      <chr>   <chr>
. 1       s1     a,b
. 2       s2     a,a
. 3       s3       c
. 4        a       a
. 5        b       b
. 6        c       c

treatment periods

run$periods

. $s1
. Events:
.   time cmt amt ii addl evid
. 1    0   1 100 24   83    1
. 2 2016   1 200 24   83    1
. 
. $s2
. Events:
.   time cmt amt ii addl evid
. 1    0   1 100 24   83    1
. 2 2016   1 100 24   83    1
. 
. $s3
. Events:
.   time cmt amt ii addl evid
. 1    0   1 500 24  168    1
. 
. $a
. Events:
.   time cmt amt ii addl evid
. 1    0   1 100 24   83    1
. 
. $b
. Events:
.   time cmt amt ii addl evid
. 1    0   1 200 24   83    1
. 
. $c
. Events:
.   time cmt amt ii addl evid
. 1    0   1 500 24  168    1

covariate sets

covsets(run)

. $cov1
.  Formulae                             
.    WT~rlnorm(meanlog=4.3,sdlog=0.5)|ID
.    SEX~rbinomial(p=0.5)               
.    AGE~runif(min=21,max=42)           
. 
. $cov2
.  Formulae                             
.    WT~rlnorm(meanlog=4.3,sdlog=0.5)|ID
.    SEX~rbinomial(p=0.5)               
.    AGE~runif(min=12,max=27)

sampling times

run$designs

. $des1
. start:  0  end:    4032  delta:  24  offset: 0  min:    0   max:    4032

mrgsolve/mrgsim documentation built on May 30, 2019, 8:07 p.m.