Add $EVENT block #1230

kylebaron · 2024-09-08T03:55:56Z

This PR adds a new block ($EVENT) which functions exactly like ($TABLE), but it gets called before $TABLE gets called. The only reason for this is so that dynamic dosing events can happen prior to output calculations in $TABLE.

Example with `$EVENT`

library(mrgsolve)
#> 
#> Attaching package: 'mrgsolve'
#> The following object is masked from 'package:stats':
#> 
#>     filter
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

code <- '
$PLUGIN evtools

$CMT B

$MAIN 
double a = 1; 

$ODE
dxdt_B = -0.1*B;

$EVENT
if(TIME==0) {
  evt::ev dose = evt::infuse(100, 1, 10);
  evt::ii(dose, 24); 
  evt::addl(dose, 4);
  evt::ss(dose, 1);
  self.push(dose);
}
a = 2;

$ERROR
capture cp = B/12; 

$CAPTURE a
'

mod <- mcode("test", code, soloc = "build")
#> Creating build directory: build
#> Building test ... done.

out <- mrgsim(mod, end = 196)
plot(out)

out
#> Model:  test 
#> Dim:    197 x 5 
#> Time:   0 to 196 
#> ID:     1 
#>     ID time     B a    cp
#> 1:   1    0 17.14 2 1.429
#> 2:   1    1 25.03 2 2.086
#> 3:   1    2 32.16 2 2.680
#> 4:   1    3 38.62 2 3.218
#> 5:   1    4 44.46 2 3.705
#> 6:   1    5 49.74 2 4.145
#> 7:   1    6 54.53 2 4.544
#> 8:   1    7 58.85 2 4.905

as.list(mod)$cpp_variables
#>      type var context
#> 1  double   a    main
#> 2 capture  cp   table
p <- deparse(mod@shlib$pointers)

Example with `$ERROR`

code2 <- '
$PLUGIN evtools

$CMT B

$ODE
dxdt_B = -0.1*B;

$ERROR
if(TIME==0) {
  evt::ev dose = evt::infuse(100, 1, 10);
  evt::ii(dose, 24); 
  evt::addl(dose, 4);
  evt::ss(dose, 1);
  self.push(dose);
}

capture cp = B/12; 
'

mod2 <- mcode("test2", code2, soloc = "build")
#> Building test2 ... done.
out2 <- mrgsim(mod2, end = 196)
plot(out2)

out2
#> Model:  test2 
#> Dim:    197 x 4 
#> Time:   0 to 196 
#> ID:     1 
#>     ID time     B    cp
#> 1:   1    0 17.14 0.000
#> 2:   1    1 25.03 2.086
#> 3:   1    2 32.16 2.680
#> 4:   1    3 38.62 3.218
#> 5:   1    4 44.46 3.705
#> 6:   1    5 49.74 4.145
#> 7:   1    6 54.53 4.544
#> 8:   1    7 58.85 4.905

Identical outputs

head(out)
#>   ID time        B a       cp
#> 1  1    0 17.14309 2 1.428591
#> 2  1    1 25.02797 2 2.085664
#> 3  1    2 32.16250 2 2.680208
#> 4  1    3 38.61809 2 3.218174
#> 5  1    4 44.45935 2 3.704946
#> 6  1    5 49.74474 2 4.145395
head(out2)
#>   ID time        B       cp
#> 1  1    0 17.14309 0.000000
#> 2  1    1 25.02797 2.085664
#> 3  1    2 32.16250 2.680208
#> 4  1    3 38.61809 3.218174
#> 5  1    4 44.45935 3.704946
#> 6  1    5 49.74474 4.145395

identical(out$B, out2$B)
#> [1] TRUE

^{Created on 2024-09-10 with reprex v2.1.1}

kylebaron · 2024-09-10T01:16:48Z

src/devtran.cpp

+      if(call_event && !this_rec->is_lagged()) {
+        prob.table_call();
+      }
+
      if(this_rec->output()) {


Second bit of "workaround" code to maintain event creation in both $EVENT and $TABLE.

kylebaron · 2024-09-10T01:20:48Z

R/mread.R

@@ -461,6 +462,7 @@ mread <- function(model, project = getOption("mrgsolve.project", getwd()),
  x@shlib[["nm_import"]] <- mread.env[["nm_import"]]
  x@shlib[["source"]] <- file.path(build[["soloc"]],build[["compfile"]])
  x@shlib[["md5"]] <- build[["md5"]]
+  x@shlib[["call_event"]] <- "EVENT" %in% names(spec)


We will pass this into the C+ simulation code to tell if we are using $EVENT to create modeled doses.

kylebaron · 2024-09-10T12:05:11Z

src/devtran.cpp

+          prob.event_call();
+        } else {
+          prob.table_call();
+        }
      }


This is the first work around to maintain event code in $EVENT and $TABLE. Basically, if the user has $EVENT block, then call that one here; otherwise call $TABLE. Down below, we'll call $TABLE if $EVENT was called and do nothing if it wasn't.

kylebaron · 2024-09-10T12:06:04Z

src/housemodel-mread-source.cpp

+// MODELED EVENTS:
+__BEGIN_event__
+__END_event__
+
 // TABLE CODE BLOCK:


This was programmatically generaged; every model will have this in the source going fowward.

kylebaron · 2024-09-10T12:07:41Z

inst/base/mrgsolv.h

+//! signature for <code>$EVENT</code>
+#define MRGSOLVE_EVENT_SIGNATURE const dvec& _A_, const dvec& _A_0_,  dvec& _THETA_,  const dvec& _F_, const dvec& _R_,  databox& self, const dvec& _pred_, dvec& _capture_, mrgsolve::resim& simeps
+#define MRGSOLVE_EVENT_SIGNATURE_N 9
+


This is important; I'm having $EVENT function identical to $TABLE. Anything you could do in one, you could do in the other.

I could re-use that signature macro to emphasize this (e.g. use MRGSOLVE_TABLE_SIGNATURE for the event; what do you think? maybe it would be confusing or look like a mistake or it could ensure they act the same.

it could ensure they act the same.

I like the idea of sharing for this reason, and I think the confusion could be made less likely by the combination of 1) putting in a code comment and 2) moving the macros next to each other.

Another idea: what about renaming MRGSOLVE_TABLE_SIGNATURE/MRGSOLVE_TABLE_SIGNATURE_N to indicate both TABLE and EVENT and then using it for both? I suppose MRGSOLVE_TABLE_OR_EVENT_SIGNATURE is getting a bit long, but I think it'd resolve both points above.

Thanks. I moved the macros next to each other and noted they are the same. I ended up copying the TABLE macro into the EVENT macro. So they will have different names in the code, but guaranteed to be in sync.

I'm going to send this off to winbuilder just to make sure the macros are behaving as I think they will on gcc. If that comes back ok, will merge.

kyleam · 2024-09-11T19:25:23Z

This really isn't bad.

I agree. I think this all looks straightforward and manageable.

kylebaron · 2024-09-24T12:52:09Z

R/class_mrgmod.R

@@ -794,7 +794,8 @@ parin <- function(x) {
    ss_n = 500, 
    ss_fixed = FALSE, 
    interrupt = -1, 
-    etasrc = "omega"
+    etasrc = "omega", 
+    call_event = x@shlib$call_event


We've saved a logical value indicating of $EVENT is in the model; if so, tell whether or not to call.

kylebaron · 2024-09-24T12:54:17Z

R/compile.R

+                           model = "",
+                           omats,
+                           smats,
+                           set = list(), 


just light touchup; this code is really old and probably don't need to pass all the functions separately.

kylebaron · 2024-09-24T12:58:59Z

R/modspec.R

@@ -368,7 +368,7 @@ param_re_find <- "\\bparam\\s+\\w+\\s*="
 # please-deprecate
 move_global <- function(x,env) {

-  what <- intersect(c("PREAMBLE","MAIN", "ODE", "TABLE", "PRED"),names(x))
+  what <- intersect(c("PREAMBLE","MAIN", "ODE", "TABLE", "EVENT", "PRED"),names(x))


I updated this, but it's not in use any more (see comment). I'd rather get rid of it at this point, but it may or may not be in scope of this PR.

Taking a quick look at move_global, I think a dedicated/separate PR would be better.

kylebaron · 2024-09-24T12:59:34Z

R/modspec.R

  to_ns <- bind_rows(
    pream$vars,
    pred$vars,
    main$vars,
    ode$vars,
-    table$vars
+    table$vars, 
+    event$vars
  )


All of this is happening in the new version (move_global2()).

kylebaron · 2024-09-24T13:00:24Z

R/mread.R

+    init_fun = main_func(x),
+    table_fun = table_func(x),
+    event_fun = event_func(x),
+    config_fun = config_func(x),
    model = model(x),


I added argument names for safety ... was getting called by position before.

kylebaron · 2024-09-24T13:02:25Z

inst/base/mrgsolv.h

+//! signature for <code>$EVENT</code>
+#define MRGSOLVE_EVENT_SIGNATURE const dvec& _A_, const dvec& _A_0_,  dvec& _THETA_,  const dvec& _F_, const dvec& _R_,  databox& self, const dvec& _pred_, dvec& _capture_, mrgsolve::resim& simeps
+#define MRGSOLVE_EVENT_SIGNATURE_N 9
+


I could re-use that signature macro to emphasize this (e.g. use MRGSOLVE_TABLE_SIGNATURE for the event; what do you think? maybe it would be confusing or look like a mistake or it could ensure they act the same.

kyleam

LGTM

kyleam · 2024-09-25T03:47:07Z

inst/base/mrgsolv.h

+//! signature for <code>$EVENT</code>
+#define MRGSOLVE_EVENT_SIGNATURE const dvec& _A_, const dvec& _A_0_,  dvec& _THETA_,  const dvec& _F_, const dvec& _R_,  databox& self, const dvec& _pred_, dvec& _capture_, mrgsolve::resim& simeps
+#define MRGSOLVE_EVENT_SIGNATURE_N 9
+


it could ensure they act the same.

I like the idea of sharing for this reason, and I think the confusion could be made less likely by the combination of 1) putting in a code comment and 2) moving the macros next to each other.

Another idea: what about renaming MRGSOLVE_TABLE_SIGNATURE/MRGSOLVE_TABLE_SIGNATURE_N to indicate both TABLE and EVENT and then using it for both? I suppose MRGSOLVE_TABLE_OR_EVENT_SIGNATURE is getting a bit long, but I think it'd resolve both points above.

kyleam · 2024-09-25T03:47:22Z

inst/maintenance/unit-cpp/test-event-block.R

+  # Known that cp isn't calculated when $TABLE is used
+  expect_equal(outer$cp[1], 0)


kyleam · 2024-09-25T03:48:07Z

R/modspec.R

@@ -368,7 +368,7 @@ param_re_find <- "\\bparam\\s+\\w+\\s*="
 # please-deprecate
 move_global <- function(x,env) {

-  what <- intersect(c("PREAMBLE","MAIN", "ODE", "TABLE", "PRED"),names(x))
+  what <- intersect(c("PREAMBLE","MAIN", "ODE", "TABLE", "EVENT", "PRED"),names(x))


Taking a quick look at move_global, I think a dedicated/separate PR would be better.

kylebaron · 2024-09-25T12:17:00Z

inst/base/mrgsolv.h

+//! signature for <code>$EVENT</code> same as what we use for <code>$TABLE</code>
+#define MRGSOLVE_EVENT_SIGNATURE MRGSOLVE_TABLE_SIGNATURE
+#define MRGSOLVE_EVENT_SIGNATURE_N MRGSOLVE_TABLE_SIGNATURE_N
+


Re ordered so that EVENT is by TABLE and re-using the definition so that it's in sync.

* using log directory 'd:/RCompile/CRANguest/R-release/mrgsolve.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'mrgsolve/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'mrgsolve' version '1.5.1.9002' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [11s] NOTE Maintainer: 'Kyle T Baron <kyleb@metrumrg.com>' Version contains large components (1.5.1.9002) * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'mrgsolve' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [21s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [16s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [21s] OK Running 'testthat.R' [21s] * checking PDF version of manual ... [18s] OK * checking HTML version of manual ... [20s] OK * DONE Status: 1 NOTE

kylebaron added 6 commits September 7, 2024 22:54

model pointers are now stored in the model object

30ed899

add pointers getter

e6968f4

add

50eabb3

tweak implementation

8e83538

move call to after events are processed

ba67c9e

different calling sequence when EVENT is in the mix

665def8

kylebaron commented Sep 10, 2024

View reviewed changes

kylebaron added 11 commits September 9, 2024 20:31

tweak logic

6ea4d71

add handler for EVENT blocks

ce6bc9c

more changes for EVENT block

017b67a

drop pointer cache; will re-do later

b8de0f2

revert changes in funset

7a29e1a

revert more funset

59935fb

revert more

f900793

revert

aae568a

spaces

efbbf4e

revert

e78c79c

don't save x back

da42b01

kylebaron commented Sep 10, 2024

View reviewed changes

kylebaron marked this pull request as draft September 10, 2024 14:06

kylebaron requested a review from kyleam September 10, 2024 14:06

kylebaron added 5 commits September 12, 2024 07:12

tests for event blocjk

99160c9

more tests on event block

78da749

fix comment

e49ddd7

tests for event-block

3614e1e

fix tests

4dc7cad

kylebaron added 3 commits September 14, 2024 08:52

don't pass by position; make defaults consistent

9eeed73

bump version for testing

9f4637d

move EVENT

5dc2327

kylebaron commented Sep 24, 2024

View reviewed changes

kylebaron added 2 commits September 24, 2024 07:55

revert compiled check

1d02ff2

update file header

78341f5

kylebaron commented Sep 24, 2024

View reviewed changes

kylebaron marked this pull request as ready for review September 24, 2024 13:03

kyleam approved these changes Sep 25, 2024

View reviewed changes

event and table have the same signature

3f41e40

kylebaron commented Sep 25, 2024

View reviewed changes

kylebaron merged commit 683bf7b into main Sep 25, 2024
7 checks passed

kylebaron mentioned this pull request Sep 25, 2024

Check spec for duplicate blocks and allow multiple $PLUGIN #1238

Merged

kylebaron deleted the event-block branch September 25, 2024 12:31

kylebaron mentioned this pull request Oct 17, 2024

Release/1.5.2 #1249

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Add $EVENT block #1230

Add $EVENT block #1230

kylebaron commented Sep 8, 2024 •

edited

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		# Known that cp isn't calculated when $TABLE is used
		expect_equal(outer$cp[1], 0)

Add $EVENT block #1230

Add $EVENT block #1230

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kylebaron commented Sep 8, 2024 • edited Loading

Example with $EVENT

Example with $ERROR

Identical outputs

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kyleam commented Sep 11, 2024

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kylebaron commented Sep 8, 2024 •

edited

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Example with `$EVENT`

Example with `$ERROR`