In focei, text covariates are converted to doubles (but it appears that the model still estimates)

[billdenney]

When looking at that code, any covariates would also be converted to doubles, and that seems like a problem, too. It would break Boolean checks like (STUDYID == "Study 1"). So, should covariates (.covNames in the code here) not be converted to doubles, either?

Originally posted by @billdenney in #272 (comment)

[billdenney]

The reprex is below. Note that the model estimates the value of cllow, but it also reports that all of the covariates are NA. I assume that the best would be to turn off covariate conversions, but I don't want to unintentionally break things there.

# run with the fix-272 branch
devtools::load_all("c:/git/nlmixr2/nlmixr2est/")
#> ℹ Loading nlmixr2est
#> Loading required package: nlmixr2data

one_compartment_textcov <- function() {
  ini({
    tka <- 0.45
    tcl <- 1
    tv <- 3.45
    cllow <- 0.001
    eta.ka ~ 0.6
    eta.cl ~ 0.3
    eta.v ~ 0.1
    add.sd <- 0.7
  })
  # and a model block with the error sppecification and model specification
  model({
    ka <- exp(tka + eta.ka)
    cl <- exp(tcl + eta.cl + cllow*(LowID == "Yes"))
    v <- exp(tv + eta.v)
    d/dt(depot) = -ka * depot
    d/dt(center) = ka * depot - cl / v * center
    cp = center / v
    cp ~ add(add.sd)
  })
}

fitdata <- theo_sd
fitdata$ID <- paste("theo", fitdata$ID)
fitdata$LowID <- ifelse(as.numeric(theo_sd$ID) < 7, "Yes", "No")
fit <- nlmixr2(one_compartment_textcov, fitdata,  est="focei", control = foceiControl(print = 0))
#> rxode2 2.0.10.9000 using 8 threads (see ?getRxThreads)
#>   no cache: create with `rxCreateCache()`
#> calculating covariance matrix
#> done
#> → Calculating residuals/tables
#> ✔ done
#> → compress origData in nlmixr2 object, save 8512
#> → compress parHist in nlmixr2 object, save 2560
fit
#> ── nlmixr² FOCEi (outer: nlminb) ──
#> 
#>          OBJF      AIC      BIC Log-likelihood Condition Number
#> FOCEi 116.807 375.4068 398.4692      -179.7034         261.6035
#> 
#> ── Time (sec fit$time): ──
#> 
#>         setup optimize covariance table other
#> elapsed 0.016    0.938      0.938  0.06 0.998
#> 
#> ── Population Parameters (fit$parFixed or fit$parFixedDf): ──
#> 
#>            Est.     SE    %RSE    Back-transformed(95%CI) BSV(CV%) Shrink(SD)%
#> tka       0.463  0.282    60.9         1.59 (0.914, 2.76)     69.8      1.20% 
#> tcl        1.01  0.545      54         2.74 (0.943, 7.99)     26.8      4.08% 
#> tv         3.46 0.0943    2.73          31.8 (26.4, 38.2)     14.0      10.5% 
#> cllow  0.000994 0.0418 4.2e+03 0.000994 (-0.0809, 0.0829)                     
#> add.sd    0.694                                     0.694                     
#>  
#>   Covariance Type (fit$covMethod): |r|
#>   No correlations in between subject variability (BSV) matrix
#>   Full BSV covariance (fit$omega) or correlation (fit$omegaR; diagonals=SDs) 
#>   Distribution stats (mean/skewness/kurtosis/p-value) available in fit$shrink 
#>   Information about run found (fit$runInfo):
#>    • column 'LowID' has only 'NA' values for id '12' 
#>    • column 'LowID' has only 'NA' values for id '11' 
#>    • column 'LowID' has only 'NA' values for id '10' 
#>    • column 'LowID' has only 'NA' values for id '9' 
#>    • column 'LowID' has only 'NA' values for id '8' 
#>    • column 'LowID' has only 'NA' values for id '7' 
#>    • column 'LowID' has only 'NA' values for id '6' 
#>    • column 'LowID' has only 'NA' values for id '5' 
#>    • column 'LowID' has only 'NA' values for id '4' 
#>    • column 'LowID' has only 'NA' values for id '3' 
#>    • column 'LowID' has only 'NA' values for id '2' 
#>    • column 'LowID' has only 'NA' values for id '1' 
#>    • zero gradient replaced with small number (0.000000) 
#>    • gradient problems with initial estimate and covariance; see $scaleInfo 
#>    • using R matrix to calculate covariance, can check sandwich or S matrix with $covRS and $covS 
#>    • R matrix non-positive definite but corrected by R = sqrtm(R%*%R) 
#>    • S matrix non-positive definite 
#>    • last objective function was not at minimum, possible problems in optimization 
#>    • ETAs were reset to zero during optimization; (Can control by foceiControl(resetEtaP=.)) 
#>    • initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=)) 
#>    • column 'LowID' has only 'NA' values for id 'theo 1' 
#>    • column 'LowID' has only 'NA' values for id 'theo 2' 
#>    • column 'LowID' has only 'NA' values for id 'theo 3' 
#>    • column 'LowID' has only 'NA' values for id 'theo 4' 
#>    • column 'LowID' has only 'NA' values for id 'theo 5' 
#>    • column 'LowID' has only 'NA' values for id 'theo 6' 
#>    • column 'LowID' has only 'NA' values for id 'theo 7' 
#>    • column 'LowID' has only 'NA' values for id 'theo 8' 
#>    • column 'LowID' has only 'NA' values for id 'theo 9' 
#>    • column 'LowID' has only 'NA' values for id 'theo 10' 
#>    • column 'LowID' has only 'NA' values for id 'theo 11' 
#>    • column 'LowID' has only 'NA' values for id 'theo 12' 
#>    • NAs introduced by coercion 
#>   Censoring (fit$censInformation): No censoring
#>   Minimization message (fit$message):  
#>     false convergence (8) 
#>   In an ODE system, false convergence may mean "useless" evaluations were performed.
#>   See https://tinyurl.com/yyrrwkce
#>   It could also mean the convergence is poor, check results before accepting fit
#>   You may also try a good derivative free optimization:
#>     nlmixr2(...,control=list(outerOpt="bobyqa"))
#> 
#> ── Fit Data (object fit is a modified tibble): ──
#> # A tibble: 132 × 23
#>   ID      TIME    DV  PRED    RES   WRES IPRED   IRES  IWRES CPRED   CRES  CWRES
#>   <fct>  <dbl> <dbl> <dbl>  <dbl>  <dbl> <dbl>  <dbl>  <dbl> <dbl>  <dbl>  <dbl>
#> 1 theo 1  0     0.74  0     0.74   1.07   0     0.74   1.07   0     0.74   1.07 
#> 2 theo 1  0.25  2.84  3.26 -0.424 -0.227  3.85 -1.01  -1.45   3.22 -0.380 -0.179
#> 3 theo 1  0.57  6.57  5.83  0.736  0.297  6.78 -0.215 -0.310  5.78  0.791  0.288
#> # … with 129 more rows, and 11 more variables: eta.ka <dbl>, eta.cl <dbl>,
#> #   eta.v <dbl>, depot <dbl>, center <dbl>, ka <dbl>, cl <dbl>, v <dbl>,
#> #   tad <dbl>, dosenum <dbl>, LowID <dbl>

^{Created on 2022-10-27 with reprex v2.0.2}

[mattfidler]

Yes turn off the conversions.

I think this was accidentally turned on by me in nlmixr2 rewrite.