aligning with common.cols arg

NMautoverse · Aug 19, 2024 · 73bc765 · 73bc765
1 parent e94a538
commit 73bc765
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/R/NMcheckData.R b/R/NMcheckData.R
@@ -440,7 +440,7 @@ NMcheckData <- function(data,file,covs,covs.occ,cols.num,col.id="ID",
         if(!is.null(col.id)&&nrow(findings.row)>0){
             if(col.id%in%colnames(findings.row)) findings.row[,(col.id):=NULL]
 
-            findings.row <- mergeCheck(findings.row,data[,c(c.row,col.id.orig),with=F],by.x="row",by.y=c.row,all.x=T,fun.commoncols=stop,quiet=TRUE)
+            findings.row <- mergeCheck(findings.row,data[,c(c.row,col.id.orig),with=F],by.x="row",by.y=c.row,all.x=T,common.cols=stop,quiet=TRUE)
             setnames(findings.row,col.id.orig,col.id)        
             findings <- rbind(findings[level!="row"],findings.row,fill=T)
 
@@ -457,7 +457,7 @@ NMcheckData <- function(data,file,covs,covs.occ,cols.num,col.id="ID",
                 findings <- mergeCheck(findings,
                                        data[,c(c.row,col.row.orig),with=F],
                                        by.x="row",by.y=c.row,all.x=T,
-                                       fun.commoncols=stop,quiet=TRUE)
+                                       common.cols=stop,quiet=TRUE)
                 setnames(findings,col.row.orig,col.row)
             }
             if(!col.id%in%colnames(findings)) findings[,(col.id):=NA_real_]

diff --git a/R/flagsAssign.R b/R/flagsAssign.R
@@ -324,14 +324,14 @@ flagsAssign <- function(data, tab.flags, subset.data, col.flagn, col.flagc,
 
 
     dim0 <- dim(data.flags)
-    data.flags <- mergeCheck(data.flags,unique(tab.flags[,c("FLAG","flag")]),all.x=TRUE,by="FLAG",ncols.expect=1,fun.commoncols=base::stop,quiet=TRUE)
+    data.flags <- mergeCheck(data.flags,unique(tab.flags[,c("FLAG","flag")]),all.x=TRUE,by="FLAG",ncols.expect=1,common.cols=base::stop,quiet=TRUE)
     ##    stopifnot(all(dim(data.flags)==(dim0+c(0,1))))
 
 ### rename FLAG and flag, and add back backed up columns if relevant
     setnames(data.flags,c("FLAG","flag"),c(col.flagn,col.flagc))
     ## setnames(tab.flags,c("FLAG","flag"),c(col.flagn,col.flagc))
     if(backed.up.old.flags){
-        data.flags <- mergeCheck(data.flags,flags.orig.data,by=col.row,fun.commoncols=base::stop,quiet=TRUE)
+        data.flags <- mergeCheck(data.flags,flags.orig.data,by=col.row,common.cols=base::stop,quiet=TRUE)
     }
 
     ## add the data where flags have not been assigned

diff --git a/R/mergeCheck.R b/R/mergeCheck.R
@@ -24,8 +24,8 @@
 ##'     is a mistake, and the default is to throw a warning if this
 ##'     happens. If using mergeCheck in programming, you may want to
 ##'     make sure this is not happening and use
-##'     fun.commoncols=stop. If you want nothing to happen, you can do
-##'     fun.commoncols=NULL. You can also use `common.cols="drop.x"`
+##'     common.cols=stop. If you want nothing to happen, you can do
+##'     common.cols=NULL. You can also use `common.cols="drop.x"`
 ##'     to drop "non-by" columns in `x` with identical column names in
 ##'     `y`. Use "drop.y" to drop them in `y` and avoid the
 ##'     conflicts. The last option is to use `common.cols="merge.by"`