Merge pull request #21 from nlmixr2/infusiontime

Add infusiontime/dur
nlmixr2 · Nov 6, 2024 · 1e877df · 1e877df
2 parents 01ef650 + 18ab522
commit 1e877df
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Showing 8 changed files with 2,263 additions and 2,092 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: monolix2rx
 Title: Converts 'Monolix' Models to 'rxode2'
-Version: 0.0.3
+Version: 0.0.3.9000
 Authors@R:
    c(person("Matthew","Fidler", role = c("aut", "cre"), email = "matthew.fidler@gmail.com", comment=c(ORCID="0000-0001-8538-6691")),
      person("Justin", "Wilkins", role = "ctb", email = "justin.wilkins@occams.com", comment=c(ORCID="0000-0002-7099-9396")))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,5 @@
+# monolix2rx (development version)
+
 # monolix2rx 0.0.3
 
 * For initial conditions starting with `rxCov_` don't add to ini

diff --git a/R/content.R b/R/content.R
@@ -22,7 +22,8 @@
         occasion=NA_character_,
         rate=NA_character_,
         additionaldose=NA_character_,
-        missingdependentvariable=NA_character_)
+        missingdependentvariable=NA_character_,
+        infusiontime=NA_character_)
     .monolix2rx$contLst <- character(0)
     .monolix2rx$ssNbdoses <- 7L
     .monolix2rx$yname <- character(0)

diff --git a/R/dataImport.R b/R/dataImport.R
@@ -124,7 +124,8 @@
                                           occasion="occ",
                                           rate="rate",
                                           additionaldose="addl",
-                                          missingdependentvariable="mdv"))
+                                          missingdependentvariable="mdv",
+                                          infusiontime="dur"))
                           }
                           n
                         }, character(1), USE.NAMES = FALSE)

diff --git a/inst/mlxtranContent.g b/inst/mlxtranContent.g
@@ -14,6 +14,7 @@ ytypeLine: identifier '=' '{' 'use' '=' ('observationtype' | 'observationType')
 admLine: identifier '=' '{' 'use' '=' 'administration' '}';
 occLine: identifier '=' '{' 'use' '=' 'occasion' '}';
 rateLine: identifier '=' '{' 'use' '=' 'rate' '}';
+durLine: identifier '=' '{' 'use' '=' 'infusiontime' '}';
 mdvLine: identifier '=' '{' 'use' '=' ('missingdependentvariable' | 'missingDependentVariable' ) '}';
 nbd: decimalint;
 ssLine: identifier '=' '{' 'use' '=' ('steadystate' | 'steadyState' ) (',' 'nbdoses' '=' nbd)? '}';
@@ -65,6 +66,7 @@ statement: idLine singleLineComment?
     | admLine singleLineComment?
     | occLine singleLineComment?
     | rateLine singleLineComment?
+    | durLine singleLineComment?
     | mdvLine singleLineComment?
     | ssLine singleLineComment?
     | regressorLine singleLineComment?

diff --git a/src/mlxtranContent.c b/src/mlxtranContent.c
@@ -184,6 +184,16 @@ int content_process_rate(const char *name, D_ParseNode *pn) {
   return 0;
 }
 
+int content_process_dur(const char *name, D_ParseNode *pn) {
+  if (!strcmp(name, "durLine")) {
+    D_ParseNode *xpn = d_get_child(pn, 0);
+    char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
+    monolix2rxContentSetUse1("infusiontime", v);
+    return 1;
+  }
+  return 0;
+}
+
 int content_process_adm(const char *name, D_ParseNode *pn) {
   if (!strcmp(name, "admLine")) {
     D_ParseNode *xpn = d_get_child(pn, 0);
@@ -325,6 +335,7 @@ void wprint_parsetree_content(D_ParserTables pt, D_ParseNode *pn, int depth, pri
       content_process_cat(name, pn) ||
       content_process_occ(name, pn) ||
       content_process_rate(name, pn) ||
+      content_process_dur(name, pn) ||
       content_process_ytypeObs(name, pn) ||
       content_process_addl(name, pn) ||
       content_process_mdv(name, pn)

diff --git a/src/mlxtranContent.g.d_parser.h b/src/mlxtranContent.g.d_parser.h
diff --git a/tests/testthat/test-content.R b/tests/testthat/test-content.R
@@ -34,7 +34,7 @@ Sex = {type=categorical, categories={M, F}}")
   tmp2 <- list(use1 = c(identifier = "ID", time = "TIME", eventidentifier = "EVID",
                         amount = "AMT", interdoseinterval = NA, censored = NA, limit = NA,
                         observationtype = "YTYPE", administration = "ADM", steadystate = NA,
-                        observation = "DV", occasion=NA, rate=NA, additionaldose=NA, missingdependentvariable=NA),
+                        observation = "DV", occasion=NA, rate=NA, additionaldose=NA, missingdependentvariable=NA, infusiontime=NA),
                cont = c("WT", "CRCL"),
                cat = list(Race = list(cat = c("Caucasian", "Black", "Latin"),
                                       quote = c(FALSE, FALSE, FALSE)),
@@ -73,7 +73,7 @@ limit = {use=limit}")
   tmp2 <- list(use1 = c(identifier = "ID", time = "TIME", eventidentifier = "EVID",
                         amount = "AMT", interdoseinterval = "II", censored = "cens", limit = "limit",
                         observationtype = "YTYPE", administration = "ADM", steadystate = "SS", observation = "DV",
-                        occasion=NA, rate=NA, additionaldose=NA, missingdependentvariable=NA),
+                        occasion=NA, rate=NA, additionaldose=NA, missingdependentvariable=NA, infusiontime=NA),
                cont = c("WT", "CRCL"),
                cat = list(Race = list(cat = c("Caucasian", "Black", "Latin"),
                                      quote = c(FALSE, FALSE, FALSE)),
@@ -158,3 +158,8 @@ test_that("mdv", {
   expect_equal(as.character(.content("mdv = {use=missingdependentvariable}")),
                 "mdv = {use=missingdependentvariable}")
 })
+
+test_that("dur", {
+  expect_equal(as.character(.content("dur = {use=infusiontime}")),
+               "dur = {use=infusiontime}")
+})