Comments (4)
seth127
commented on September 23, 2024
I also wanted to put inherit_param_estimates() and initial_estimates() on this list. I think this should be as simple as adding an S3 dispatch that just dispatches through to bbi_nonmem_model, but I haven't looked into too deeply.
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seth127
commented on September 23, 2024
Whenever we come back to this, I also wanted to throw out the idea of just keeping bbi_nonmem_model as a parent class to bbi_nmboot_model. To be clear, currently we have this:
class(boot_run)
[1] "bbi_nmboot_model" "bbi_base_model" "bbi_model" "list" I'm proposing this:
class(boot_run)
[1] "bbi_nmboot_model" "bbi_nonmem_model" "bbi_base_model" "bbi_model" "list" We would need to think through the repercussions of this more, but naively I think it might be an easy and elegant solution for some number of the functions mentioned in this issue. For example, open the fold below to see my quick testing from hacking the class manually.
manually adding bbi_nonmem_model class
Currently fails (as of 1.10.0.8003)
> class(boot_run)
[1] "bbi_nmboot_model" "bbi_base_model" "bbi_model" "list"
> model_diff(boot_run)
Error in UseMethod("model_diff") :
no applicable method for 'model_diff' applied to an object of class "c('bbi_nmboot_model', 'bbi_base_model', 'bbi_model', 'list')"
> inherit_param_estimates(boot_run)
Error in check_model_object(.mod, "bbi_nonmem_model") :
Must pass a model object with one of the following classes: `bbi_nonmem_model`
Got object of class: `bbi_nmboot_model, bbi_base_model, bbi_model, list`Works if I manually add the class
> class(boot_run)
[1] "bbi_nmboot_model" "bbi_base_model" "bbi_model" "list"
> class(boot_run) <- c("bbi_nonmem_model", class(boot_run))
> class(boot_run)
[1] "bbi_nonmem_model" "bbi_nmboot_model" "bbi_base_model" "bbi_model" "list"
> model_diff(boot_run)
< 106-boot > 106
@@ 1,3 @@ @@ 1,3 @@
< $PROBLEM Bootstrap run of model 106 > $PROBLEM From bbr: see 106.yaml for details
$INPUT C NUM ID TIME SEQ CMT EVID AMT DV AGE WT HT EGFR ALB BMI SEX A $INPUT C NUM ID TIME SEQ CMT EVID AMT DV AGE WT HT EGFR ALB BMI SEX A
AG AG
@@ 52,2 @@ @@ 52,5 @@
$EST MAXEVAL=9999 METHOD=1 INTER SIGL=6 NSIG=3 PRINT=1 MSFO=./106.msf $EST MAXEVAL=9999 METHOD=1 INTER SIGL=6 NSIG=3 PRINT=1 MSFO=./106.msf
~ > $COV PRINT=E
~ > $TABLE NUM CL V2 Q V3 KA ETAS(1:LAST) IPRED NPDE CWRES NOPRINT ONEHEA
~ : DER FILE=106.tab
~ > $TABLE NUM CL V2 Q V3 KA ETAS(1:LAST) NOAPPEND NOPRINT ONEHEADER FILE
~ : =106par.tab
> boot_run <- inherit_param_estimates(boot_run)
> model_diff(boot_run)
< 106-boot > 106
@@ 1,3 @@ @@ 1,3 @@
< $PROBLEM Bootstrap run of model 106 > $PROBLEM From bbr: see 106.yaml for details
$INPUT C NUM ID TIME SEQ CMT EVID AMT DV AGE WT HT EGFR ALB BMI SEX A $INPUT C NUM ID TIME SEQ CMT EVID AMT DV AGE WT HT EGFR ALB BMI SEX A
AG AG
@@ 34,20 @@ @@ 34,23 @@
$THETA ; log values $THETA ; log values
< (0.443) ; 1 KA (1/hr) - 1.5 > (0.5) ; 1 KA (1/hr) - 1.5
< (4.12) ; 2 V2 (L) - 60 > (3.5) ; 2 V2 (L) - 60
< (1.17) ; 3 CL (L/hr) - 3.5 > (1) ; 3 CL (L/hr) - 3.5
< (4.21) ; 4 V3 (L) - 70 > (4) ; 4 V3 (L) - 70
< (1.28) ; 5 Q (L/hr) - 4 > (2) ; 5 Q (L/hr) - 4
< (0.485) ; 6 CLEGFR~CL () > (1) ; 6 CLEGFR~CL ()
< (-0.0378) ; 7 AGE~CL () > (1) ; 7 AGE~CL ()
< (0.419) ; 8 ALB~CL () > (0.5) ; 8 ALB~CL ()
$OMEGA BLOCK(3) $OMEGA BLOCK(3)
< 0.219 ;ETA(KA) > 0.2 ;ETA(KA)
< 0.0668 0.0824 ;ETA(V2) > 0.01 0.2 ;ETA(V2)
< 0.121 0.0704 0.114 ;ETA(CL) > 0.01 0.01 0.2 ;ETA(CL)
$SIGMA $SIGMA
< 0.0399 ; 1 pro error > 0.05 ; 1 pro error
$EST MAXEVAL=9999 METHOD=1 INTER SIGL=6 NSIG=3 PRINT=1 MSFO=./106.msf $EST MAXEVAL=9999 METHOD=1 INTER SIGL=6 NSIG=3 PRINT=1 MSFO=./106.msf
~ > $COV PRINT=E
~ > $TABLE NUM CL V2 Q V3 KA ETAS(1:LAST) IPRED NPDE CWRES NOPRINT ONEHEA
~ : DER FILE=106.tab
~ > $TABLE NUM CL V2 Q V3 KA ETAS(1:LAST) NOAPPEND NOPRINT ONEHEADER FILE
~ : =106par.tab from bbr.
barrettk
commented on September 23, 2024
We would need to think through the repercussions of this more, but naively I think it might be an easy and elegant solution for some number of the functions mentioned in this issue.
I think this would work very well for the new nmsim model type, but yeah there are definitely a number of cases we'd need to have additional handling for nmboot model objects, such as pulling in gradients, tables, build_path_from_model, etc. that wont work either because the directory is different, or because the actual model file itself (.ctl) doesnt actually get submitted/generate submission files.
Thought: could it make sense to do this for the nmsim model type, but not nmboot model objects?
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barrettk
commented on September 23, 2024
check_up_to_date for bootstrap runs was implemented in 8e6134a - @seth127 @kylebaron you guys may specifically want to take a look at this handling to make sure its implemented the way we want it to be.
- Something Seth noted though: we have to return a final object of
length 2with namesmodelanddata. So if we want to include additional checks, they either have to be grouped intodataormodel, or be isolated from the returned vector
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Related Issues (20)
- Address deprecated warning in function `check_grd`
- Bootstrap runs should inherit attached bbi_args HOT 1
- inherit_param_estimates: revisit rounding and use matrix-handling PR HOT 1
- check_nonmem_finished and get_model_status refactor: improve wait times & change functionality HOT 9
- WK files created by bbr - delete by default? HOT 7
- Consider fail-safe for checking on terminated models HOT 4
- bbi package installation failed HOT 8
- Option to start bootstrap runs at final estimates from parent run HOT 3
- No error or warning when trying to overwrite run when `.wait = FALSE` HOT 15
- Re-name msf file in bootstrap run control stream HOT 1
- Submitting bootstrap run in batches can leave lots of unused compute HOT 2
- Bootstrap batch submission sometimes chokes when called before setup is done HOT 2
- Revisit `check_up_to_date` for `nmboot` models HOT 1
- push back minimum snapshot? HOT 5
- Feature: update $TABLE with a certain format HOT 1
- `bbi_init`: parse `nmfe_options` separately from other `.bbi_args`
- .exclude argument in run_log()
- Can't execute bbr commands via the clusters HOT 8
- Check if model can be passed to `nm_join()`
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