Nesting levels in rxode2

Nesting in rxode2

More than one level of nesting is possible in rxode2; In this example we will be using the following uncertainties and sources of variability:

Level	Variable	Matrix specified	Integrated Matrix
Model uncertainty	NA	`thetaMat`	`thetaMat`
Investigator	`inv.Cl`, `inv.Ka`	`omega`	`theta`
Subject	`eta.Cl`, `eta.Ka`	`omega`	`omega`
Eye	`eye.Cl`, `eye.Ka`	`omega`	`omega`
Occasion	`iov.Cl`, `occ.Ka`	`omega`	`omega`
Unexplained Concentration	`prop.sd`	`sigma`	`sigma`
Unexplained Effect	`add.sd`	`sigma`	`sigma`

Event table

This event table contains nesting variables:

inv: investigator id
id: subject id
eye: eye id (left or right)
occ: occasion

library(rxode2)

#> rxode2 2.1.3.9000 using 2 threads (see ?getRxThreads)
#>   no cache: create with `rxCreateCache()`

library(dplyr)

#> 
#> Attaching package: 'dplyr'

#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag

#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

et(amountUnits="mg", timeUnits="hours") %>%
  et(amt=10000, addl=9,ii=12,cmt="depot") %>%
  et(time=120, amt=2000, addl=4, ii=14, cmt="depot") %>%
  et(seq(0, 240, by=4)) %>% # Assumes sampling when there is no dosing information
  et(seq(0, 240, by=4) + 0.1) %>% ## adds 0.1 for separate eye
  et(id=1:20) %>%
  ## Add an occasion per dose
  mutate(occ=cumsum(!is.na(amt))) %>%
  mutate(occ=ifelse(occ == 0, 1, occ)) %>%
  mutate(occ=2- occ %% 2) %>%
  mutate(eye=ifelse(round(time) == time, 1, 2)) %>%
  mutate(inv=ifelse(id < 10, 1, 2)) %>% as_tibble ->
  ev

rxode2 model

This creates the rxode2 model with multi-level nesting. Note the variables inv.Cl, inv.Ka, eta.Cl etc; You only need one variable for each level of nesting.

mod <- rxode2({
  ## Clearance with individuals
  eff(0) = 1
  C2 = centr/V2*(1+prop.sd)
  C3 = peri/V3
  CL =  TCl*exp(eta.Cl + eye.Cl + iov.Cl + inv.Cl)
  KA = TKA * exp(eta.Ka + eye.Ka + iov.Cl + inv.Ka)
  d/dt(depot) =-KA*depot
  d/dt(centr) = KA*depot - CL*C2 - Q*C2 + Q*C3
  d/dt(peri)  =                    Q*C2 - Q*C3
  d/dt(eff)  = Kin - Kout*(1-C2/(EC50+C2))*eff
  ef0 = eff + add.sd
})

#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’

Uncertainty in Model parameters

theta <- c("TKA"=0.294, "TCl"=18.6, "V2"=40.2,
           "Q"=10.5, "V3"=297, "Kin"=1, "Kout"=1, "EC50"=200)

## Creating covariance matrix
tmp <- matrix(rnorm(8^2), 8, 8)
tMat <- tcrossprod(tmp, tmp) / (8 ^ 2)
dimnames(tMat) <- list(names(theta), names(theta))

tMat

#>               TKA           TCl           V2            Q           V3
#> TKA   0.173571236 -0.1003204607  0.038185010 -0.004108928 -0.095032973
#> TCl  -0.100320461  0.2195710868 -0.043849095  0.013295549 -0.007477895
#> V2    0.038185010 -0.0438490948  0.129784612 -0.017270432 -0.038004762
#> Q    -0.004108928  0.0132955493 -0.017270432  0.022145634  0.020376451
#> V3   -0.095032973 -0.0074778948 -0.038004762  0.020376451  0.165568340
#> Kin  -0.040867119 -0.0492597458 -0.003056722 -0.033468634 -0.003021883
#> Kout  0.035469225  0.0275087955  0.033725901  0.027668205  0.005497301
#> EC50  0.026158042  0.0009434711  0.039426946 -0.036283167 -0.093134292
#>               Kin         Kout          EC50
#> TKA  -0.040867119  0.035469225  0.0261580416
#> TCl  -0.049259746  0.027508796  0.0009434711
#> V2   -0.003056722  0.033725901  0.0394269465
#> Q    -0.033468634  0.027668205 -0.0362831667
#> V3   -0.003021883  0.005497301 -0.0931342922
#> Kin   0.226735493 -0.083447793  0.0659884544
#> Kout -0.083447793  0.117195570 -0.0291684598
#> EC50  0.065988454 -0.029168460  0.0928611407

Nesting Variability

To specify multiple levels of nesting, you can specify it as a nested lotri matrix; When using this approach you use the condition operator | to specify what variable nesting occurs on; For the Bayesian simulation we need to specify how much information we have for each parameter; For rxode2 this is the nu parameter.

In this case: - id, nu=100 or the model came from 100 subjects - eye, nu=200 or the model came from 200 eyes - occ, nu=200 or the model came from 200 occasions - inv, nu=10 or the model came from 10 investigators

To specify this in lotri you can use | var(nu=X), or:

omega <- lotri(lotri(eta.Cl ~ 0.1,
                     eta.Ka ~ 0.1) | id(nu=100),
               lotri(eye.Cl ~ 0.05,
                     eye.Ka ~ 0.05) | eye(nu=200),
               lotri(iov.Cl ~ 0.01,
                     iov.Ka ~ 0.01) | occ(nu=200),
               lotri(inv.Cl ~ 0.02,
                     inv.Ka ~ 0.02) | inv(nu=10))
omega

#> $id
#>        eta.Cl eta.Ka
#> eta.Cl    0.1    0.0
#> eta.Ka    0.0    0.1
#> 
#> $eye
#>        eye.Cl eye.Ka
#> eye.Cl   0.05   0.00
#> eye.Ka   0.00   0.05
#> 
#> $occ
#>        iov.Cl iov.Ka
#> iov.Cl   0.01   0.00
#> iov.Ka   0.00   0.01
#> 
#> $inv
#>        inv.Cl inv.Ka
#> inv.Cl   0.02   0.00
#> inv.Ka   0.00   0.02
#> 
#> Properties: nu

Unexplained variability

The last piece of variability to specify is the unexplained variability

sigma <- lotri(prop.sd ~ .25,
               add.sd~ 0.125)

Solving the problem

s <- rxSolve(mod, theta, ev,
             thetaMat=tMat, omega=omega,
             sigma=sigma, sigmaDf=400,
             nStud=400)

#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’

#> unhandled error message: EE:[lsoda] 70000 steps taken before reaching tout
#>  @(lsoda.c:754

#> Warning: some ID(s) could not solve the ODEs correctly; These values are
#> replaced with 'NA'

print(s)

#> -- Solved rxode2 object --
#> -- Parameters ($params): --
#> # A tibble: 8,000 x 24
#>    sim.id id    `inv.Cl(inv==1)` `inv.Cl(inv==2)` `inv.Ka(inv==1)`
#>     <int> <fct>            <dbl>            <dbl>            <dbl>
#>  1      1 1              0.00900           -0.117            0.312
#>  2      1 2              0.00900           -0.117            0.312
#>  3      1 3              0.00900           -0.117            0.312
#>  4      1 4              0.00900           -0.117            0.312
#>  5      1 5              0.00900           -0.117            0.312
#>  6      1 6              0.00900           -0.117            0.312
#>  7      1 7              0.00900           -0.117            0.312
#>  8      1 8              0.00900           -0.117            0.312
#>  9      1 9              0.00900           -0.117            0.312
#> 10      1 10             0.00900           -0.117            0.312
#> # i 7,990 more rows
#> # i 19 more variables: `inv.Ka(inv==2)` <dbl>, `eye.Cl(eye==1)` <dbl>,
#> #   `eye.Cl(eye==2)` <dbl>, `eye.Ka(eye==1)` <dbl>, `eye.Ka(eye==2)` <dbl>,
#> #   `iov.Cl(occ==1)` <dbl>, `iov.Cl(occ==2)` <dbl>, `iov.Ka(occ==1)` <dbl>,
#> #   `iov.Ka(occ==2)` <dbl>, V2 <dbl>, V3 <dbl>, TCl <dbl>, eta.Cl <dbl>,
#> #   TKA <dbl>, eta.Ka <dbl>, Q <dbl>, Kin <dbl>, Kout <dbl>, EC50 <dbl>
#> -- Initial Conditions ($inits): --
#> depot centr  peri   eff 
#>     0     0     0     1 
#> 
#> Simulation with uncertainty in:
#> * parameters ($thetaMat for changes)
#> * omega matrix ($omegaList)
#> 
#> -- First part of data (object): --
#> # A tibble: 976,000 x 21
#>   sim.id    id time  inv.Cl inv.Ka  eye.Cl  eye.Ka iov.Cl iov.Ka    C2     C3
#>    <int> <int>  [h]   <dbl>  <dbl>   <dbl>   <dbl>  <dbl>  <dbl> <dbl>  <dbl>
#> 1      1     1  0   0.00900  0.312 -0.330  -0.0547 0.0370  0.139  0    0     
#> 2      1     1  0.1 0.00900  0.312  0.0792  0.185  0.0370  0.139  8.04 0.0108
#> 3      1     1  4   0.00900  0.312 -0.330  -0.0547 0.0370  0.139 55.4  5.58  
#> 4      1     1  4.1 0.00900  0.312  0.0792  0.185  0.0370  0.139 23.2  5.69  
#> 5      1     1  8   0.00900  0.312 -0.330  -0.0547 0.0370  0.139 19.6  7.95  
#> 6      1     1  8.1 0.00900  0.312  0.0792  0.185  0.0370  0.139 20.0  7.97  
#> # i 975,994 more rows
#> # i 10 more variables: CL <dbl>, KA <dbl>, ef0 <dbl>, depot <dbl>, centr <dbl>,
#> #   peri <dbl>, eff <dbl>, occ <fct>, eye <fct>, inv <fct>

There are multiple investigators in a study; Each investigator has a number of individuals enrolled at their site. rxode2 automatically determines the number of investigators and then will simulate an effect for each investigator. With the output, inv.Cl(inv==1) will be the inv.Cl for investigator 1, inv.Cl(inv==2) will be the inv.Cl for investigator 2, etc.

inv.Cl(inv==1), inv.Cl(inv==2), etc will be simulated for each study and then combined to form the between investigator variability. In equation form these represent the following:

inv.Cl = (inv == 1) * `inv.Cl(inv==1)` + (inv == 2) * `inv.Cl(inv==2)`

If you look at the simulated parameters you can see inv.Cl(inv==1) and inv.Cl(inv==2) are in the s$params; They are the same for each study:

print(head(s$params))

#>   sim.id id inv.Cl(inv==1) inv.Cl(inv==2) inv.Ka(inv==1) inv.Ka(inv==2)
#> 1      1  1    0.008995575     -0.1165083      0.3118205   -0.001926179
#> 2      1  2    0.008995575     -0.1165083      0.3118205   -0.001926179
#> 3      1  3    0.008995575     -0.1165083      0.3118205   -0.001926179
#> 4      1  4    0.008995575     -0.1165083      0.3118205   -0.001926179
#> 5      1  5    0.008995575     -0.1165083      0.3118205   -0.001926179
#> 6      1  6    0.008995575     -0.1165083      0.3118205   -0.001926179
#>   eye.Cl(eye==1) eye.Cl(eye==2) eye.Ka(eye==1) eye.Ka(eye==2) iov.Cl(occ==1)
#> 1    -0.33023666    0.079190835    -0.05471051     0.18487157    0.037021761
#> 2    -0.42211135   -0.006773841    -0.15399939     0.22463048   -0.007762485
#> 3    -0.05128596    0.123504458     0.18243012     0.13361259   -0.168921159
#> 4    -0.06360621    0.340443016     0.65606292     0.04807945    0.157027939
#> 5     0.08009126   -0.027627640     0.06662396    -0.05838949   -0.226341946
#> 6    -0.11937190    0.090540884    -0.17320340     0.02039840   -0.211648032
#>   iov.Cl(occ==2) iov.Ka(occ==1) iov.Ka(occ==2)       V2       V3      TCl
#> 1    -0.19726803     0.13932112    0.088763868 40.26476 296.4748 19.25043
#> 2     0.04555116     0.07716277    0.049148937 40.26476 296.4748 19.25043
#> 3     0.17916513     0.08347085   -0.002990168 40.26476 296.4748 19.25043
#> 4    -0.13444417     0.24736740   -0.077647794 40.26476 296.4748 19.25043
#> 5     0.02049190    -0.09568733    0.054658457 40.26476 296.4748 19.25043
#> 6     0.12619350    -0.01547841    0.040206608 40.26476 296.4748 19.25043
#>        eta.Cl       TKA      eta.Ka        Q       Kin     Kout     EC50
#> 1  0.09788109 0.2354877 -0.21526790 10.43157 0.9256189 1.044937 200.3679
#> 2  0.33302598 0.2354877 -0.01028112 10.43157 0.9256189 1.044937 200.3679
#> 3  0.08504325 0.2354877  0.37253705 10.43157 0.9256189 1.044937 200.3679
#> 4  0.16521678 0.2354877 -0.01859974 10.43157 0.9256189 1.044937 200.3679
#> 5  0.53131380 0.2354877 -0.37109644 10.43157 0.9256189 1.044937 200.3679
#> 6 -0.30786713 0.2354877  0.14897588 10.43157 0.9256189 1.044937 200.3679

print(head(s$params %>% filter(sim.id == 2)))

#>   sim.id id inv.Cl(inv==1) inv.Cl(inv==2) inv.Ka(inv==1) inv.Ka(inv==2)
#> 1      2  1    -0.07227613    -0.01884171     0.07620864    -0.01962499
#> 2      2  2    -0.07227613    -0.01884171     0.07620864    -0.01962499
#> 3      2  3    -0.07227613    -0.01884171     0.07620864    -0.01962499
#> 4      2  4    -0.07227613    -0.01884171     0.07620864    -0.01962499
#> 5      2  5    -0.07227613    -0.01884171     0.07620864    -0.01962499
#> 6      2  6    -0.07227613    -0.01884171     0.07620864    -0.01962499
#>   eye.Cl(eye==1) eye.Cl(eye==2) eye.Ka(eye==1) eye.Ka(eye==2) iov.Cl(occ==1)
#> 1    -0.25102634      0.1354374   -0.135230741    -0.01605664    0.081212198
#> 2    -0.24832622      0.2233348   -0.380770273    -0.37101991    0.207985292
#> 3     0.24081384     -0.3826770    0.133361609    -0.32496203   -0.099983807
#> 4    -0.11021791      0.3655308    0.009423897     0.08736599   -0.002580804
#> 5     0.21155058      0.3626918    0.194977611    -0.19452347    0.058392202
#> 6     0.03663028     -0.1003754    0.068047203     0.32368023    0.167658084
#>   iov.Cl(occ==2) iov.Ka(occ==1) iov.Ka(occ==2)       V2       V3      TCl
#> 1    -0.06556217   -0.032678168   -0.061277262 40.21091 296.6424 18.86433
#> 2    -0.05016896    0.130258486   -0.103721118 40.21091 296.6424 18.86433
#> 3     0.06144127   -0.262726137   -0.104186144 40.21091 296.6424 18.86433
#> 4     0.03954265   -0.037289852   -0.021344468 40.21091 296.6424 18.86433
#> 5     0.12713682   -0.007530921    0.081238197 40.21091 296.6424 18.86433
#> 6    -0.02811353    0.026801132   -0.002702762 40.21091 296.6424 18.86433
#>        eta.Cl       TKA      eta.Ka        Q       Kin     Kout   EC50
#> 1  0.19368101 0.5686675  0.26184170 10.54673 0.5434136 1.323825 200.09
#> 2 -0.16262369 0.5686675  0.12969487 10.54673 0.5434136 1.323825 200.09
#> 3  0.22164455 0.5686675  0.24501105 10.54673 0.5434136 1.323825 200.09
#> 4  0.05997662 0.5686675  0.03059399 10.54673 0.5434136 1.323825 200.09
#> 5  0.45691421 0.5686675 -0.20098716 10.54673 0.5434136 1.323825 200.09
#> 6 -0.19943300 0.5686675 -0.36846082 10.54673 0.5434136 1.323825 200.09

For between eye variability and between occasion variability each individual simulates a number of variables that become the between eye and between occasion variability; In the case of the eye:

eye.Cl = (eye == 1) * `eye.Cl(eye==1)` + (eye == 2) * `eye.Cl(eye==2)`

So when you look the simulation each of these variables (ie eye.Cl(eye==1), eye.Cl(eye==2), etc) they change for each individual and when combined make the between eye variability or the between occasion variability that can be seen in some pharamcometric models.

2024-06-25