clean up code

USDAForestService · Apr 7, 2022 · 04dcacd · 04dcacd
1 parent 44d7b1b
commit 04dcacd
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Showing 3 changed files with 40 additions and 18 deletions.
diff --git a/R/check.auxiliary.R b/R/check.auxiliary.R
@@ -178,6 +178,20 @@ check.auxiliary <- function(pltx, puniqueid, module="GB", strata=FALSE,
     auxnmlst <- names(auxlut)
     missvars <- {}
 
+    if (is.null(auxlut)) {
+      auxlut <- unique(pltx[, c(unitvar2, unitvar), with=FALSE])
+    } else {
+      if (any(grepl("ONEUNIT", unitvars))) {
+        unittest <- unitvars[any(grepl("ONEUNIT", unitvars))]
+        if (length(unittest) > 1) {
+            stop("more than one ONEUNIT variable")
+        }
+        if (!unittest %in% names(auxlut)) {
+            auxlut[, (unittest) := 1]
+        }
+      }
+    }
+
     ## Check predictors
     ############################################################################
     if (length(c(strvar, predfac)) > 0) {

diff --git a/R/modMApop.R b/R/modMApop.R
@@ -537,6 +537,7 @@ modMApop <- function(popType="VOL",
   ## Remove nonsampled plots and conditions (if nonsamp.filter != "NONE")
   ## Applies plot and condition filters
   ###################################################################################
+
   popcheck <- check.popdata(gui=gui, module="MA", popType=popType, 
                     tabs=popTabs, tabIDs=popTabIDs, pltassgn=pltassgn, dsn=dsn, 
                     pltassgnid=pltassgnid, pjoinid=pjoinid, condid="CONDID", 
@@ -596,7 +597,7 @@ modMApop <- function(popType="VOL",
       auxlut <- unitzonal
       makedummy <- TRUE
   }
-
+ 
   auxdat <- check.auxiliary(pltx=pltassgnx, puniqueid=pltassgnid, 
                   module="MA", strata=strata, unitvar=unitvar, unitvar2=unitvar2, 
                   unitarea=unitarea, areavar=areavar, minplotnum.unit=minplotnum.unit, 

diff --git a/R/spGetPlots.R b/R/spGetPlots.R
@@ -1126,6 +1126,7 @@ spGetPlots <- function(bnd = NULL,
         seed_layer <- seedchk
       }
     }
+
     if (isveg) {
       vsubpsppchk <- chkdbtab(tablst, vsubpspp_layer)
       if (is.null(vsubpsppchk) && vsubpspp_layer == "vsubpspp") {
@@ -1182,21 +1183,6 @@ spGetPlots <- function(bnd = NULL,
     ## Get fields in plot table
     pltfields <- DBI::dbListFields(dbconn, "plot")
 
-    ## Check pjoinid
-    pjoinid <- pcheck.varchar(var2check=pjoinid, varnm="pjoinid", 
-		checklst=pltfields, gui=gui, caption="Joinid in plot?")
-
-    if (is.null(pjoinid)) {
-      if (xyjoinid %in% pltfields) {
-        pjoinid  <- xyjoinid
-      } else {
-        if (xyjoinid == "PLT_CN" && "CN" %in% pltfields) {
-          pjoinid <- "CN"
-        } else {
-          stop(xyjoinid, " not in plt")
-        }
-      }
-    }
 
     for (i in 1:length(stcds)) { 
       stcd <- stcds[i]
@@ -1274,6 +1260,23 @@ spGetPlots <- function(bnd = NULL,
           		formatC(plt$PLOT, width=5, digits=5, flag=0))] 
         }
       }
+
+      ## Check pjoinid
+      pjoinid <- pcheck.varchar(var2check=pjoinid, varnm="pjoinid", 
+		checklst=c(pltfields, "PLOT_ID"), gui=gui, caption="Joinid in plot?")
+
+      if (is.null(pjoinid)) {
+        if (xyjoinid %in% c(pltfields, "PLOT_ID")) {
+          pjoinid  <- xyjoinid
+        } else {
+          if (xyjoinid == "PLT_CN" && "CN" %in% pltfields) {
+            pjoinid <- "CN"
+          } else {
+            stop(xyjoinid, " not in plt")
+          }
+        }
+      }
+
       ## If duplicate plots, sort descending based on INVYR or CN and select 1st row
       if (nrow(plt) > length(unique(plt[[pjoinid]]))) {
         if ("INVYR" %in% names(plt)) {
@@ -1283,7 +1286,7 @@ spGetPlots <- function(bnd = NULL,
         }
         plt <- plt[, head(.SD, 1), by=pjoinid]
       }
-
+ 
       ## Get most current plots in database for measEndyr.filter & !measEndyr.filter
       #######################################################################
       p2fromqry <- pfromqry
@@ -1591,6 +1594,9 @@ spGetPlots <- function(bnd = NULL,
 
         if (nrow(pltids) > 0) {
           plt <- plt[plt[[pjoinid]] %in% pltids[[xyjoinid]], ]
+          if (nrow(pltids) > nrow(plt)) {
+            message("number of plots in database is less than XY plots: ", nrow(pltids) - nrow(plt))
+          }
           xyids <- plt[[puniqueid]]
 
 #          cond.qry <- paste0("select distinct cond.* from ", p2fromqry, 
@@ -1626,9 +1632,10 @@ spGetPlots <- function(bnd = NULL,
             tree <- tree[tree[[tuniqueid]] %in% xyids, ]
             DBI::dbClearResult(rs)
           }
+
           if (isseed) {
             seed.qry <- paste0("select distinct seed.* from ", p2fromqry, 
-                               " join ", seed_layer, 
+                               " join ", seed_layer, " seed",  
                                " on(seed.PLT_CN = p.CN) where ", stfilter, 
                                " and p.", puniqueid, 
                                " in(", addcommas(xyids, quotes=TRUE), ")")