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covarSearchAuto doesn't work with the example #27

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mattfidler opened this issue Oct 22, 2022 · 1 comment
Open

covarSearchAuto doesn't work with the example #27

mattfidler opened this issue Oct 22, 2022 · 1 comment

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@mattfidler
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At least from nlmixr2

> rxode2::.rxWithWd(tempdir(), {# with temporary directory
+ > 
+ > auto1 <- covarSearchAuto(fit, varsVec = c("ka", "cl"),
+ >     covarsVec = c("WT"))
+ > 
+ > })

── starting forward search... ─────────────────────────────────────────────────────────────────────────────────────────────────────────
Key: U: Unscaled Parameters; X: Back-transformed parameters; G: Gill difference gradient approximation
F: Forward difference gradient approximation
C: Central difference gradient approximation
M: Mixed forward and central difference gradient approximation
Unscaled parameters for Omegas=chol(solve(omega));
Diagonals are transformed, as specified by foceiControl(diagXform=)
|-----+---------------+-----------+-----------+-----------+-----------|
|    #| Objective Fun |       tka |       tcl |        tv |    add.sd |
|.....................| cov_WT_ka |        o1 |        o2 |        o3 |
|    1|     116.80360 |   -0.7319 |   -0.4146 |     1.000 |   -0.5984 |
|.....................|    -1.000 |   -0.2735 |    0.1279 |    0.5549 |
|    U|      116.8036 |    0.4638 |     1.013 |     3.459 |    0.6946 |
|.....................|     0.000 |     1.257 |     1.951 |     2.689 |
|    X|      116.8036 |     1.590 |     2.753 |     31.79 |    0.6946 |
|.....................|     0.000 |     1.257 |     1.951 |     2.689 |
|    G|    Gill Diff. |   0.02023 |    0.1352 |   -0.3409 |   0.06867 |
|.....................| -0.001704 |    0.1258 |    0.1391 |  -0.01370 |
|    2|     179.09946 |   -0.7521 |   -0.5497 |     1.341 |   -0.6671 |
|.....................|   -0.9983 |   -0.3994 |  -0.01121 |    0.5686 |


...


── forward search complete ──

Error in inherits(fit, "nlmixr2FitCore") : object 'fit' not foundLoading nlmixr2
> traceback()
12: backwardSearch(varsVec, covarsVec, catvarsVec, fitorig = fit, 
        fitupdated = resFwd[[1]], pVal = pVal$bck, reFitCovars = FALSE, 
        outputDir = outputDir, restart = restart)
11: nlmixr2extra::covarSearchAuto(fit = fit, varsVec = varsVec, covarsVec = covarsVec, 
        pVal = pVal, catvarsVec = catvarsVec, searchType = searchType, 
        restart = restart) at hardReexports.R#274
10: covarSearchAuto(fit, varsVec = c("ka", "cl"), covarsVec = c("WT")) at file39e0e80c04c.R#34
9: force(code)
8: rxode2::.rxWithWd(tempdir(), {
       auto1 <- covarSearchAuto(fit, varsVec = c("ka", "cl"), covarsVec = c("WT"))
   }) at file39e0e80c04c.R#32
7: eval(ei, envir)
6: eval(ei, envir)
5: withVisible(eval(ei, envir))
4: source(tmp, echo = !quiet, local = env, max.deparse.length = Inf)
3: FUN(X[[i]], ...)
2: lapply(files, pkgload::run_example, run_donttest = run_donttest, 
       run_dontrun = run_dontrun)
@vsarsani
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Hmm. I can't reproduce this in my environment. Should I pull all the recent changes?

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