Merge pull request #23 from nlmixr2/22-ignore-line

Add ignoreline to content parser
nlmixr2 · Nov 28, 2024 · b5d1723 · b5d1723
2 parents 1349c50 + f2a33f4
commit b5d1723
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Showing 9 changed files with 2,604 additions and 2,203 deletions.
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.0.2
-Date: 2024-09-20 17:23:09 UTC
-SHA: 50a6d133e91e263750f7208c21c5cfc094ff5d07
+Version: 0.0.3
+Date: 2024-10-24 03:47:22 UTC
+SHA: 01ef6508874c5a3dd198fba94580c8014fc3ea4c
diff --git a/R/content.R b/R/content.R
@@ -48,6 +48,7 @@
                cont=.monolix2rx$contLst,
                cat=.monolix2rx$catLst2,
                reg=.monolix2rx$regLst,
+               ignore=.monolix2rx$ignoreLst,
                nbdoses=.monolix2rx$ssNbdoses,
                yname=.monolix2rx$yname,
                ynameQuote=.monolix2rx$ynameQuote,
@@ -186,6 +187,7 @@ as.character.monolix2rxContent <- function(x, ...) {
   }, character(1), USE.NAMES = FALSE)
   c(.cur[!is.na(.cur)],
     .asCharacterReg(x),
+    .asCharacterIgnore(x),
     vapply(x$cont, function(n) {
       paste0(n, " = {use=covariate, type=continuous}")
     }, character(1), USE.NAMES = FALSE),

diff --git a/R/ind.R b/R/ind.R
@@ -12,6 +12,7 @@
     .fileinfoIni()
     .monolix2rx$inpLst <- character(0)
     .monolix2rx$regLst <- character(0)
+    .monolix2rx$ignoreLst <- character(0)
     .monolix2rx$catLst2 <- NULL
     .monolix2rx$ind <- NULL
   }
@@ -90,6 +91,7 @@
   .ind <- list(input=.monolix2rx$inpLst,
                cat=.monolix2rx$catLst2,
                reg=.monolix2rx$regLst,
+               ignore=.monolix2rx$ignoreLst,
                file=.monolix2rx$file)
   class(.ind) <- "monolix2rxInd"
   .indIni(full=TRUE)
@@ -110,6 +112,15 @@
   # What does that mean?
   .monolix2rx$regLst <- c(.monolix2rx$regLst, reg)
 }
+#' Flag a column as ignored
+#'
+#' @param ignore column to ignore
+#' @return nothing, called for side effect
+#' @noRd
+#' @author Matthew L. Fidler
+.indIgnore <- function(ignore) {
+  .monolix2rx$ignoreLst <- c(.monolix2rx$ignoreLst, ignore)
+}
 
 #' As.character for regressor items
 #'
@@ -124,6 +135,19 @@
            paste0(n, " = {use = regressor}")
          }, character(1), USE.NAMES = FALSE)
 }
+#' Change expression to ignored line
+#'
+#' @param x line to ignore
+#' @return character vector representing ignored variables
+#' @author Matthew L. Fidler
+#' @noRd
+.asCharacterIgnore <- function(x) {
+  if (length(x$ignore) == 0L) return(character(0))
+  vapply(x$ignore,
+         function(n) {
+           paste0(n, " = {use = ignoredline}")
+         }, character(1), USE.NAMES = FALSE)
+}
 
 #' as.character for the categorical variables in `$cat`
 #'
@@ -173,6 +197,7 @@ as.character.monolix2rxInd <- function(x, ...) {
   }
   .ret <- c(.ret, .asCharacterReg(x))
   .ret <- c(.ret, .asCharacterCat(x))
+  .ret <- c(.ret, .asCharacterIgnore(x))
   c(.ret, .asCharacterFile(x))
 }
 

diff --git a/inst/mlxtranContent.g b/inst/mlxtranContent.g
@@ -21,7 +21,7 @@ ssLine: identifier '=' '{' 'use' '=' ('steadystate' | 'steadyState' ) (',' 'nbdo
 regressorLine: identifier '=' '{' 'use' '=' 'regressor' '}';
 contLine: identifier '=' '{' 'use' '=' 'covariate' ',' 'type' '=' 'continuous' '}';
 catLine: identifier '=' '{' 'use' '=' 'covariate' ',' 'type' '=' 'categorical' '}';
-
+ignoreLine: identifier '=' '{' 'use' '=' ('ignore' | 'ignoreLine' | 'ignoreline' | 'ignored' | 'ignoredLine' | 'ignoredline') '}';
 ytypeType: char_t1 | char_t2 | identifier | number;
 ytypeOp1: 'ytype' '='  ytypeType;
 ytypeOp2: 'ytype' '=' '{' ytypeType (',' ytypeType)* '}';
@@ -69,6 +69,7 @@ statement: idLine singleLineComment?
     | durLine singleLineComment?
     | mdvLine singleLineComment?
     | ssLine singleLineComment?
+    | ignoreLine singleLineComment?
     | regressorLine singleLineComment?
     | contLine singleLineComment?
     | catLine singleLineComment?

diff --git a/src/mlxtranContent.c b/src/mlxtranContent.c
@@ -73,6 +73,7 @@ extern sbuf curLine;
 int individual_process_catCov(const char *name, D_ParseNode *pn, int i);
 int individual_process_catId(const char *name, D_ParseNode *pn);
 int individual_process_regressor(const char *name, D_ParseNode *pn);
+int individual_process_ignore(const char *name, D_ParseNode *pn);
 
 int content_process_identifier(const char *name, D_ParseNode *pn) {
   if (!strcmp(name, "idLine")) {
@@ -318,6 +319,7 @@ void wprint_parsetree_content(D_ParserTables pt, D_ParseNode *pn, int depth, pri
   int nch = d_get_number_of_children(pn);
   if (individual_process_catId(name, pn) ||
       individual_process_regressor(name, pn) ||
+      individual_process_ignore(name, pn) ||
       content_process_identifier(name, pn) ||
       content_process_time(name, pn) ||
       content_process_evid(name, pn) ||

diff --git a/src/mlxtranContent.g.d_parser.h b/src/mlxtranContent.g.d_parser.h
diff --git a/src/mlxtranInd.c b/src/mlxtranInd.c
@@ -112,6 +112,17 @@ int individual_process_regressor(const char *name, D_ParseNode *pn) {
   return 0;
 }
 
+int individual_process_ignore(const char *name, D_ParseNode *pn) {
+  if (!strcmp("ignoreLine", name)) {
+    D_ParseNode *xpn = d_get_child(pn, 0);
+    char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
+    monolix2rxSingle(v, ".indIgnore");
+    return 1;
+  }
+  return 0;
+}
+
+
 void wprint_parsetree_individual(D_ParserTables pt, D_ParseNode *pn, int depth, print_node_fn_t fn, void *client_data) {
   char *name = (char*)pt.symbols[pn->symbol].name;
   int nch = d_get_number_of_children(pn);
@@ -130,7 +141,8 @@ void wprint_parsetree_individual(D_ParserTables pt, D_ParseNode *pn, int depth,
     return;
   } else if (individual_process_catId(name, pn) ||
              individual_process_inpId(name, pn) ||
-             individual_process_regressor(name, pn)) {
+             individual_process_regressor(name, pn) ||
+             individual_process_ignore(name, pn)) {
     // return early; no need to process more
     return;
   }

diff --git a/tests/testthat/test-content.R b/tests/testthat/test-content.R
@@ -41,6 +41,7 @@ Sex = {type=categorical, categories={M, F}}")
                           Sex = list(cat = c("M", "F"),
                                      quote = c(FALSE, FALSE))),
                reg = c("E0", "Emax"),
+               ignore = character(0),
                nbdoses = 7L,
                yname = c("1", "2"),
                ynameQuote=c(TRUE, TRUE),
@@ -80,6 +81,7 @@ limit = {use=limit}")
                           Sex = list(cat = c("M", "F"),
                                      quote = c(FALSE, FALSE))),
                reg = c("E0", "Emax"),
+               ignore=character(0),
                nbdoses = 10L,
                yname = c("1", "2"),
                ynameQuote=c(TRUE, TRUE),
@@ -163,3 +165,47 @@ test_that("dur", {
   expect_equal(as.character(.content("dur = {use=infusiontime}")),
                "dur = {use=infusiontime}")
 })
+
+test_that("content ignore", {
+
+    tmp <- .content("ID = {use=identifier}
+TIME = {use=time}
+EVID = {use=eventidentifier}
+AMT = {use=amount}
+DV = {use=observation, name={y1, y2}, yname={'1', '2'}, type={continuous, event}}
+ADM = {use=administration}
+YTYPE = {use=observationtype}
+WT={use=covariate, type=continuous}
+CRCL={use=covariate, type=continuous}
+E0 = {use = regressor}
+Emax = {use = regressor}
+Race = {type=categorical, categories={Caucasian, Black, Latin}}
+Sex = {type=categorical, categories={M, F}}
+FLAG = {use=ignoredline}")
+
+
+    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,
+                          infusiontime = NA),
+                 cont = c("WT", "CRCL"),
+                 cat = list(Race = list(cat = c("Caucasian", "Black", "Latin"),
+                                        quote = c(FALSE, FALSE, FALSE)),
+                            Sex = list(cat = c("M", "F"),
+                                       quote = c(FALSE, FALSE))),
+                 reg = c("E0", "Emax"),
+                 ignore = "FLAG",
+                 nbdoses = 7L,
+                 yname = c("1", "2"),
+                 ynameQuote = c(TRUE, TRUE),
+                 ytype = character(0),
+                 ytypeQuote = logical(0),
+                 name = c("y1", "y2"),
+                 type = c("continuous", "event"))
+
+    class(tmp2) <- "monolix2rxContent"
+
+    expect_equal(tmp, tmp2)
+})
diff --git a/tests/testthat/test-ind.R b/tests/testthat/test-ind.R
@@ -18,6 +18,7 @@ Sex = {type=categorical, categories={M, F}}")
                            Sex = list(cat = c("M", "F"),
                                       quote = c(FALSE, FALSE))),
                 reg = "E0",
+                ignore = character(0),
                 file=character(0))
   class(.tmp2) <- "monolix2rxInd"
 
@@ -34,6 +35,7 @@ SEX = {type=categorical, categories={Female, Male}}")
                            SEX = list(cat = c("Female", "Male"),
                                       quote = c(FALSE, FALSE))),
                 reg = character(0),
+                ignore = character(0),
                 file=character(0))
   class(.tmp2) <- "monolix2rxInd"
   expect_equal(.tmp, .tmp2)