added check for bmd and ac50 in bmd.high flagging (#41)

* added check for bmd and ac50 in bmd.high flagging

* added check for modl = 'none' and return warning if all results are modl = 'none'

R/mc6.R

@@ -49,20 +49,29 @@ mc6 <- function(ae, wr = FALSE) {
 
   ## Load level 5 and, if needed, level 3 data 
   ft <- tcplLoadData(lvl = 5L, type = "mc", fld = "aeid", val = ae, add.fld = TRUE)
-  setkey(ft, m4id)
-  if (any(ms$nddr)) {
-    dr <- .load6DR(ae)
-    setkey(dr, m4id, aeid, spid)
-    setkey(ft, m4id, aeid, spid)
-    dr <- dr[ft]
-  } 
 
   ## Check if any level 5 data was loaded
   if (nrow(ft) == 0) {
     warning("No level 5 data for AEID", ae, ". Level 6 processing incomplete;",
             " no updates\n  made to the mc6 table for AEID", ae, ".")
     if(wr) return(FALSE) else return(list(FALSE, NULL))
   }
+
+  ## Remove modl == none and check if any data remains
+  ft <- ft[modl != "none",]
+  if (nrow(ft) == 0) {
+    warning("All level 5 data for AEID", ae, " have winning model of 'none'. Level 6 processing incomplete;",
+            " no updates\n  made to the mc6 table for AEID", ae, ".")
+    if(wr) return(FALSE) else return(list(FALSE, NULL))
+  }
+
+  setkey(ft, m4id)
+  if (any(ms$nddr)) {
+    dr <- .load6DR(ae)
+    setkey(dr, m4id, aeid, spid)
+    setkey(ft, m4id, aeid, spid)
+    dr <- dr[ft]
+  }
 
   ## Load assay information to check for cell viability. Fill with 0 if unavailable.
   tbl <- "assay_component_endpoint"
@@ -90,7 +99,7 @@ mc6 <- function(ae, wr = FALSE) {
 
   ## Initialize f, the list of data.tables containing the flag information
   f <- vector(mode = "list", length = max(ms$mthd_id))
-  
+
   ## Generate and evaluate flag expressions
   mthd_funcs <- mc6_mthds()
   exprs <- lapply(ms$mthd_id, function(x) mthd_funcs[[ms[J(x), mthd]]](x)) # XXX this breaks if functions appear more than once in mc6_mthds() 

R/mc6_mthds.R

@@ -173,7 +173,7 @@ mc6_mthds <- function() {
                 "flag", "fval", "fval_unit")
       init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
       e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
-      e2 <- bquote(ft[ , test := bmd > ac50])
+      e2 <- bquote(ifelse(all(c("ac50","bmd") %in% names(ft)),ft[ , test := bmd > ac50],ft))
       e3 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
       cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
       e4 <- bquote(ft[ , .(cr) := NULL])