Make sure the UI is uncompressed before checking for meta information #661

mattfidler · 2024-03-07T20:32:20Z

Note I got the following:

library(nlmixr2)
#> Loading required package: nlmixr2data
library(xpose)
#> Error in library(xpose): there is no package called 'xpose'
library(xpose.nlmixr2)
#> Error in library(xpose.nlmixr2): there is no package called 'xpose.nlmixr2'
library(ggplot2)

nimo <- function() {
ini({
    ## Note that the UI can take expressions
    ## Also note that these initial estimates should be provided on the log-scale
    tcl <- log(0.001)
    tv1 <- log(1.45)
    tQ <- log(0.004)
    tv2 <- log(44)
    tkss <- log(12)
    tkint <- log(0.3)
    tksyn <- log(1)
    tkdeg <- log(7)
    ## Initial estimates should be high for SAEM ETAs
    eta.cl  ~ 2
    eta.v1  ~ 2
    eta.kss ~ 2
    ##  Also true for additive error (also ignored in SAEM)
    add.err <- 10
    })
model({
      cl <- exp(tcl + eta.cl)
      v1 <- exp(tv1 + eta.v1)
      Q  <- exp(tQ)
      v2 <- exp(tv2)
      kss <- exp(tkss + eta.kss)
      kint <- exp(tkint)
      ksyn <- exp(tksyn)
      kdeg <- exp(tkdeg)
      
      k <- cl/v1
      k12 <- Q/v1
      k21 <- Q/v2
      
      eff(0) <- ksyn/kdeg ##initializing compartment
      
      ## Concentration is calculated
      conc = 0.5*(central/v1-eff-kss)+0.5*sqrt((central/v1-eff-kss)**2+4*kss*central/v1)
      
      d/dt(central)  = -(k+k12)*conc*v1+k21*peripheral-kint*eff*conc*v1/(kss+conc)
      d/dt(peripheral) = k12*conc*v1-k21*peripheral  ##Free Drug second compartment amount
      d/dt(eff) = ksyn - kdeg*eff - (kint-kdeg)*conc*eff/(kss+conc)
      
      IPRED=log(conc)
      
      IPRED ~ add(add.err)
      })
}

fit <- nlmixr(nimo, nimoData, est="saem", control=saemControl(print=0))
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of saem model...
#> ✔ done
#> → finding duplicate expressions in saem model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → optimizing duplicate expressions in saem model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> ✔ done
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> rxode2 2.1.2 using 8 threads (see ?getRxThreads)
#>   no cache: create with `rxCreateCache()`
#> Calculating covariance matrix
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of saem model...
#> ✔ done
#> → finding duplicate expressions in saem predOnly model 0...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → finding duplicate expressions in saem predOnly model 1...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → optimizing duplicate expressions in saem predOnly model 1...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → finding duplicate expressions in saem predOnly model 2...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → optimizing duplicate expressions in saem predOnly model 2...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> ✔ done
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> → Calculating residuals/tables
#> ✔ done
#> → compress origData in nlmixr2 object, save 26920
#> → compress phiM in nlmixr2 object, save 207080
#> → compress parHistData in nlmixr2 object, save 19928
#> → compress saem0 in nlmixr2 object, save 14176
nimo_sim <- rxSolve(fit, nimoData)
#> Error in exists("meta", envir = ui): invalid 'envir' argument

^{Created on 2024-03-07 with reprex v2.1.0}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.3 (2024-02-29)
#>  os       Pop!_OS 22.04 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/Chicago
#>  date     2024-03-07
#>  pandoc   2.9.2.1 @ /usr/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package       * version  date (UTC) lib source
#>  backports       1.4.1    2021-12-13 [3] RSPM (R 4.2.0)
#>  cachem          1.0.8    2023-05-01 [3] RSPM (R 4.2.0)
#>  checkmate       2.3.1    2023-12-04 [3] RSPM (R 4.3.0)
#>  cli             3.6.2    2023-12-11 [3] RSPM (R 4.3.0)
#>  colorspace      2.1-0    2023-01-23 [3] RSPM (R 4.2.0)
#>  crayon          1.5.2    2022-09-29 [3] RSPM (R 4.2.0)
#>  data.table      1.15.2   2024-02-29 [3] RSPM (R 4.3.0)
#>  digest          0.6.34   2024-01-11 [3] RSPM (R 4.3.0)
#>  dparser         1.3.1-11 2023-12-08 [3] RSPM (R 4.3.0)
#>  dplyr           1.1.4    2023-11-17 [3] RSPM (R 4.3.0)
#>  evaluate        0.23     2023-11-01 [3] RSPM (R 4.3.0)
#>  fansi           1.0.6    2023-12-08 [3] RSPM (R 4.3.0)
#>  fastmap         1.1.1    2023-02-24 [3] RSPM (R 4.2.0)
#>  fs              1.6.3    2023-07-20 [3] RSPM (R 4.2.0)
#>  generics        0.1.3    2022-07-05 [3] RSPM (R 4.2.0)
#>  ggplot2       * 3.5.0    2024-02-23 [3] RSPM (R 4.3.0)
#>  glue            1.7.0    2024-01-09 [3] RSPM (R 4.3.0)
#>  gtable          0.3.4    2023-08-21 [3] RSPM (R 4.2.0)
#>  htmltools       0.5.7    2023-11-03 [3] RSPM (R 4.3.0)
#>  knitr           1.45     2023-10-30 [3] RSPM (R 4.3.0)
#>  lattice         0.22-5   2023-10-24 [3] RSPM (R 4.3.0)
#>  lazyeval        0.2.2    2019-03-15 [3] RSPM (R 4.2.0)
#>  lbfgsb3c        2020-3.3 2023-11-28 [3] RSPM (R 4.3.0)
#>  lifecycle       1.0.4    2023-11-07 [3] RSPM (R 4.3.0)
#>  lotri           0.4.3    2023-03-20 [3] RSPM (R 4.2.0)
#>  magrittr        2.0.3    2022-03-30 [3] RSPM (R 4.2.0)
#>  Matrix          1.6-5    2024-01-11 [3] RSPM (R 4.3.0)
#>  memoise         2.0.1    2021-11-26 [3] RSPM (R 4.2.0)
#>  munsell         0.5.0    2018-06-12 [3] RSPM (R 4.2.0)
#>  n1qn1           6.0.1-11 2022-10-18 [3] RSPM (R 4.2.0)
#>  nlme            3.1-164  2023-11-27 [3] RSPM (R 4.3.0)
#>  nlmixr2       * 2.1.1    2024-02-01 [3] RSPM (R 4.3.0)
#>  nlmixr2data   * 2.0.9    2024-01-31 [3] RSPM (R 4.3.0)
#>  nlmixr2est      2.2.1    2024-01-31 [3] RSPM (R 4.3.0)
#>  nlmixr2plot     2.0.8    2024-01-31 [3] RSPM (R 4.3.0)
#>  pillar          1.9.0    2023-03-22 [3] RSPM (R 4.2.0)
#>  pkgconfig       2.0.3    2019-09-22 [3] RSPM (R 4.2.0)
#>  PreciseSums     0.6      2023-04-22 [3] RSPM (R 4.2.0)
#>  purrr           1.0.2    2023-08-10 [3] RSPM (R 4.2.0)
#>  qs              0.25.7   2023-12-06 [3] RSPM (R 4.3.0)
#>  R.cache         0.16.0   2022-07-21 [3] RSPM (R 4.2.0)
#>  R.methodsS3     1.8.2    2022-06-13 [3] RSPM (R 4.2.0)
#>  R.oo            1.26.0   2024-01-24 [3] RSPM (R 4.3.0)
#>  R.utils         2.12.3   2023-11-18 [3] RSPM (R 4.3.0)
#>  R6              2.5.1    2021-08-19 [3] RSPM (R 4.2.0)
#>  RApiSerialize   0.1.2    2022-08-25 [3] RSPM (R 4.2.0)
#>  Rcpp            1.0.12   2024-01-09 [3] RSPM (R 4.3.0)
#>  RcppParallel    5.1.7    2023-02-27 [3] RSPM (R 4.2.0)
#>  reprex          2.1.0    2024-01-11 [3] RSPM (R 4.3.0)
#>  rex             1.2.1    2021-11-26 [3] RSPM (R 4.2.0)
#>  rlang           1.1.3    2024-01-10 [3] RSPM (R 4.3.0)
#>  rmarkdown       2.26     2024-03-05 [3] RSPM (R 4.3.0)
#>  rxode2        * 2.1.2    2024-01-30 [3] RSPM (R 4.3.0)
#>  rxode2et        2.0.12   2024-01-30 [3] RSPM (R 4.3.0)
#>  rxode2ll        2.0.11   2023-03-17 [3] RSPM (R 4.2.0)
#>  rxode2parse     2.0.18   2024-01-30 [3] RSPM (R 4.3.0)
#>  rxode2random    2.0.13   2024-01-30 [3] RSPM (R 4.3.0)
#>  scales          1.3.0    2023-11-28 [3] RSPM (R 4.3.0)
#>  sessioninfo     1.2.2    2021-12-06 [3] RSPM (R 4.2.0)
#>  stringfish      0.16.0   2023-11-28 [3] RSPM (R 4.3.0)
#>  styler          1.10.2   2023-08-29 [3] RSPM (R 4.2.0)
#>  symengine       0.2.6    2024-02-25 [3] RSPM (R 4.3.0)
#>  sys             3.4.2    2023-05-23 [3] RSPM (R 4.2.0)
#>  tibble          3.2.1    2023-03-20 [3] RSPM (R 4.3.0)
#>  tidyselect      1.2.0    2022-10-10 [3] RSPM (R 4.2.0)
#>  units           0.8-5    2023-11-28 [3] RSPM (R 4.3.0)
#>  utf8            1.2.4    2023-10-22 [3] RSPM (R 4.3.0)
#>  vctrs           0.6.5    2023-12-01 [3] RSPM (R 4.3.0)
#>  withr           3.0.0    2024-01-16 [3] RSPM (R 4.3.2)
#>  xfun            0.42     2024-02-08 [3] RSPM (R 4.3.0)
#>  yaml            2.3.8    2023-12-11 [3] RSPM (R 4.3.0)
#> 
#>  [1] /home/matt/R/x86_64-pc-linux-gnu-library/4.3
#>  [2] /usr/local/lib/R/site-library
#>  [3] /usr/lib/R/site-library
#>  [4] /usr/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Originally posted by @mattfidler in nlmixr2/nlmixr2#208 (reply in thread)

mattfidler · 2024-03-07T20:42:32Z

It seems that this is some sort of edge case because this works:

library(rxode2)
#> rxode2 2.1.2 using 8 threads (see ?getRxThreads)
#>   no cache: create with `rxCreateCache()`

nimo <- function() {
  ini({
    tcl <- -6.20447388279654
    tv1 <- 0.191575008970249
    tQ <- -5.87988849322313
    tv2 <- 1.20088373795058
    tkss <- 2.05936091989241
    tkint <- -1.57948966650851
    tksyn <- 0.830859686356613
    tkdeg <- 2.38731427957655
    add.err <- c(0, 0.686603620607056)
    eta.cl ~ 0.91005447260584
    eta.v1 ~ 0.173555359121338
    eta.kss ~ 0.0114928866324284
  })
  model({
    cl <- exp(tcl + eta.cl)
    v1 <- exp(tv1 + eta.v1)
    Q <- exp(tQ)
    v2 <- exp(tv2)
    kss <- exp(tkss + eta.kss)
    kint <- exp(tkint)
    ksyn <- exp(tksyn)
    kdeg <- exp(tkdeg)
    k <- cl/v1
    k12 <- Q/v1
    k21 <- Q/v2
    eff(0) <- ksyn/kdeg
    conc = 0.5 * (central/v1 - eff - kss) + 0.5 * sqrt((central/v1 - 
                                                          eff - kss)^2 + 4 * kss * central/v1)
    d/dt(central) = -(k + k12) * conc * v1 + k21 * peripheral - 
      kint * eff * conc * v1/(kss + conc)
    d/dt(peripheral) = k12 * conc * v1 - k21 * peripheral
    d/dt(eff) = ksyn - kdeg * eff - (kint - kdeg) * conc * 
      eff/(kss + conc)
    IPRED = log(conc)
    IPRED ~ add(add.err)
  })
}

nimo <- nimo()

# should have raw in it because it is compressed not really an environment
print(class(nimo))
#> [1] "rxUi" "raw"

nimo_sim <- rxSolve(nimo, nlmixr2data::nimoData)

print(nimo_sim)
#> ── Solved rxode2 object ──
#> ── Parameters ($params): ──
#> # A tibble: 12 × 13
#>    id      tcl   tv1    tQ   tv2  tkss tkint tksyn tkdeg add.err   eta.cl eta.v1
#>    <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>   <dbl>    <dbl>  <dbl>
#>  1 1     -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687 -0.975    0.166
#>  2 2     -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687 -1.32     0.318
#>  3 3     -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687  0.955   -0.448
#>  4 5     -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687  0.0768  -0.127
#>  5 6     -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687  0.00911  0.223
#>  6 7     -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687  0.799   -0.135
#>  7 8     -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687 -1.00    -0.168
#>  8 9     -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687  0.256   -0.453
#>  9 10    -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687 -0.160   -0.375
#> 10 11    -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687 -0.300   -0.396
#> 11 12    -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687 -0.364   -0.511
#> 12 13    -6.20 0.192 -5.88  1.20  2.06 -1.58 0.831  2.39   0.687  0.339    0.352
#> # ℹ 1 more variable: eta.kss <dbl>
#> ── Initial Conditions ($inits): ──
#>    central peripheral        eff 
#>          0          0          0 
#> ── First part of data (object): ──
#> # A tibble: 321 × 20
#>      id   time       cl    v1       Q    v2   kss  kint  ksyn  kdeg        k
#>   <int>  <dbl>    <dbl> <dbl>   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>    <dbl>
#> 1     1   1.28 0.000762  1.43 0.00280  3.32  9.50 0.206  2.30  10.9 0.000533
#> 2     1  23.2  0.000762  1.43 0.00280  3.32  9.50 0.206  2.30  10.9 0.000533
#> 3     1  46.9  0.000762  1.43 0.00280  3.32  9.50 0.206  2.30  10.9 0.000533
#> 4     1  95.2  0.000762  1.43 0.00280  3.32  9.50 0.206  2.30  10.9 0.000533
#> 5     1 144.   0.000762  1.43 0.00280  3.32  9.50 0.206  2.30  10.9 0.000533
#> 6     1 167.   0.000762  1.43 0.00280  3.32  9.50 0.206  2.30  10.9 0.000533
#> # ℹ 315 more rows
#> # ℹ 9 more variables: k12 <dbl>, k21 <dbl>, conc <dbl>, IPRED <dbl>,
#> #   ipredSim <dbl>, sim <dbl>, central <dbl>, peripheral <dbl>, eff <dbl>

^{Created on 2024-03-07 with reprex v2.1.0}

mattfidler mentioned this issue Mar 7, 2024

Test for compressed ui not really working nlmixr2/nlmixr2est#422

Open

mattfidler added a commit that referenced this issue Mar 7, 2024

Add fix for #661 (tested in nlmixr2est)

394c45f

mattfidler linked a pull request Mar 7, 2024 that will close this issue

661 make sure the UI is uncompressed before checking for meta information #662

Merged

mattfidler closed this as completed in #662 Mar 13, 2024

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Make sure the UI is uncompressed before checking for meta information #661

Make sure the UI is uncompressed before checking for meta information #661

mattfidler commented Mar 7, 2024

mattfidler commented Mar 7, 2024

Make sure the UI is uncompressed before checking for meta information #661

Make sure the UI is uncompressed before checking for meta information #661

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mattfidler commented Mar 7, 2024

mattfidler commented Mar 7, 2024