Merge branch 'staging' of https://github.com/USDAForestService/ForestVegetationSimulator-Interface into open_main

Author: wagnerds

.gitattributes

@@ -0,0 +1 @@
+*.tif filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -1,20 +1,22 @@
-
-.RData
-.Rhistory
-.Rproj.user/*
-BuildfvsOL.R
-ForestVegetationSimulator-Interface.Rproj
-fvsOL/.Rhistory
-fvsOL/LaunchFVS.R
-build_fvsOL.R
-fvsOL/data/fvsOnlineHelpRender.RData
-fvsOL/data/prms.RData
-fvsOL/launch.R
-fvsOL/NAMESPACE
-rFVS/NAMESPACE
-rFVS/rFVSmadeTag
-fvsOL/fvsOLmadeTag
-fvsOL/man/*
-rFVS/man/*
-*.gz
-.Rproj.user
+
+fvsOL/inst/extdata/.Rhistory
+.RData
+.Rhistory
+.Rproj.user/*
+BuildfvsOL.R
+ForestVegetationSimulator-Interface.Rproj
+fvsOL/.Rhistory
+fvsOL/LaunchFVS.R
+build_fvsOL.R
+fvsOL/data/fvsOnlineHelpRender.RData
+fvsOL/data/prms.RData
+fvsOL/launch.R
+fvsOL/NAMESPACE
+rFVS/NAMESPACE
+rFVS/rFVSmadeTag
+fvsOL/fvsOLmadeTag
+fvsOL/man/*
+rFVS/man/*
+*.gz
+.Rproj.user
+

fvsOL/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fvsOL
 Title: Forest Vegetation Simulator
-Version: 2025.07.01
+Version: 2025.09.30
 Authors@R: c(person("Nicholas", "Crookston", email = "ncrookston.fs@gmail.com",
                   role = c("aut")),
              person("FVS", "Staff", email = "sm.fs.fvs-support@usda.gov",
@@ -12,7 +12,7 @@ Depends:
   ggplot2 (>= 3.3.3), parallel (>= 4.0.0), RSQLite (>= 2.2.4), plyr (>= 1.8.6), dplyr (>= 1.0.4), 
   colourpicker (>= 1.1.0), rgl (>= 0.105.0), leaflet (>= 2.0.4.1), zip (>= 2.1.1), openxlsx (>= 4.2.3), 
   shinyFiles (>= 0.9.3)
-Suggests: rgdal (>= 1.5-23), nlme (>= 3.1-140)
+Suggests: nlme (>= 3.1-140)
 License: MIT
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

fvsOL/R/componentWins.R

@@ -100,7 +100,7 @@ keyword.dbs.SQLIn.Win <- function(title, prms, globals, input, output)
       tags$style(type="text/css", 
         "#freeEditCols{font-family:monospace;font-size:90%;width:95%;}"), 
       tags$p(id="freeEditCols", 
-             HTML(paste0("&nbsp;",paste0("....+....",1:8,collapse="")))),
+             HTML(paste0("&nbsp;",paste0("....+....",1:12,collapse="")))),
       tags$style(type="text/css", 
         "#freeEdit{font-family:monospace;font-size:90%;width:95%;}"), 
       tags$textarea(id="freeEdit", rows=10, globals$currentCmdDefs["freeEdit"]),
@@ -138,7 +138,7 @@ keyword.dbs.SQLOut.Win <- function(title, prms, globals, input, output)
       tags$style(type="text/css", 
         "#freeEditCols{font-family:monospace;font-size:90%;width:95%;}"), 
       tags$p(id="freeEditCols", 
-             HTML(paste0("&nbsp;",paste0("....+....",1:8,collapse="")))),
+             HTML(paste0("&nbsp;",paste0("....+....",1:12,collapse="")))),
       tags$style(type="text/css", 
         "#freeEdit{font-family:monospace;font-size:90%;width:95%;}"), 
       tags$textarea(id="freeEdit", rows=10, globals$currentCmdDefs["freeEdit"]),

fvsOL/R/externalCallable.R

@@ -413,7 +413,7 @@ extnAddComponentKwds <- function(prjDir=getwd(),runUUID,cmps,groups=NULL,stands=
 #' @param autoOut a vector of character strings corresponding to the automatic
 #'   output selections to be set (not the svs ones), where these values "turn on"
 #'   the corresponding selections and existing selections are not changed (if NULL
-#'   no changes are made): "Treelists", "Carbon", "Fire", "Dead", "CanProfile", 
+#'   no changes are made): "Treelists", "autoFIAVBC", "Carbon", "Fire", "Dead", "CanProfile", 
 #'   "SnagDet",  "StrClass", "CalibStats", "Climate", "Econ", "DM_Sz_Sum", 
 #'   "RD_Sum",  "RD_Det", "RD_Beetle", "InvStats", "Regen", "KeepTextTables"
 #' @param svsOut a vector of two character strings where the first is the
@@ -449,7 +449,7 @@ extnSetRunOptions <- function(prjDir=getwd(),runUUID,autoOut=NULL,svsOut=NULL,
   if (attr(class(fvsRun),"package") != "fvsOL") stop("Don't recognize the loaded object")
   if (!is.null(autoOut))
   {
-    autoSets = c(autoTreelists = "Treelists", autoCarbon = "Carbon",               
+    autoSets = c(autoTreelists = "Treelists", autoFIAVBC = "FIAVBC Outputs", autoCarbon = "Carbon",               
       autoFire = "Fire",  autoDead = "Dead", autoCanProfile = "CanProfile", 
       autoSnagDet = "SnagDet",  autoStrClass = "StrClass", 
       autoCalibStats = "CalibStats", autoClimate = "Climate",  

fvsOL/R/fvsOutUtilities.R

@@ -118,8 +118,12 @@ filterRows <- function (dat, title, groups, stdid, mgtid, year, species, dbhclas
 
 setupSummary <- function(asum,composite=FALSE)
 {
-  std=if (length(grep("SCuFt$",colnames(asum)))) 
-    c("Tpa","MCuFt","SCuFt","SBdFt") else c("Tpa","TCuFt","MCuFt","BdFt")
+  std=if (length(grep("SCuFt$",colnames(asum))) &&
+          length(grep("TCuFt$",colnames(asum))))
+        c("Tpa","TCuFt","MCuFt","SCuFt","BdFt")
+      else if (length(grep("SCuFt$",colnames(asum))))
+        c("Tpa","MCuFt","SCuFt","SBdFt")
+      else c("Tpa","TCuFt","MCuFt","BdFt")
   rstd=paste("R",std,sep="")
   stdden = c("BA","SDI","CCF","TopHt","QMD")
   stddenAT = paste0("AT",stdden)

fvsOL/R/fvsRunUtilities.R

@@ -781,7 +781,8 @@ mkModMCats <- function(globals)
   catsel=list(
     "Volume Modifiers" = c(
       "Adjust merchantability limits" = "merch_vol",
-      "Add Volume Defect" = "keyword.base.Defect"),
+      "Add Volume Defect" = "keyword.base.Defect",
+      "Use FIA Cubic Volume Equations (FIAVBC)" = "fia_method"),
     "Mortality Modifiers" = c(
       "Adjust mortality rates" = "keyword.base.FixMort",
       "Adjust maximum SDI" = "keyword.base.SDIMax",

fvsOL/R/mkInputElements.R

@@ -110,6 +110,7 @@ mkCheckBox <- function (pkey, pmt, choices, fpvs)
 mkSelectInput <- function (inputId, label, choices, fpvs, 
                            type="list", valpair=FALSE)
 {
+  llast <- FALSE
   choices = trim(scan(text=choices,what=" ",sep="\n",quiet=TRUE))
   sel = grep ("^>",choices)
   if (length(sel)) choices[sel] = trim(substring(choices[sel],2))
@@ -127,10 +128,17 @@ cat ("in mkSelectInput type=",type," fpvs=",fpvs," sel=",sel,"\n")
   names(mklist) = choices
 
   if (length(sel) && edt==0) 
-    {
-      if (sel==length(choices)) sel <- sel-1
+    { 
+      if (sel==length(choices)){
+        sel <- sel - 1 
+        llast <- TRUE
+      } 
       if (!valpair) sel = match(as.character(sel),mklist) 
-      if (is.na(sel)) sel <- "0" else as.character(if (valpair) sel <- sel else sel <- sel-2)
+      if (is.na(sel)) sel <- "0" else as.character(if (valpair) sel <- sel else {
+        if (llast) sel <- sel - 1
+        else sel <- sel - 2
+      })
+      #if (is.na(sel)) sel <- "0" else as.character(if (valpair) sel <- sel else if(sel == length(choices)) sel <- sel-1 else sel <- sel-2)
   } 
   if(!length(sel) && edt==0) sel="0"
   if(!length(sel) && edt==1 && !valpair) sel=mklist[1]
@@ -464,25 +472,34 @@ mkVarList <- function (globals)
      "Age: Age at beginning of an FVS cycle"="Age", 
      "AgeCmp: Estimated average age for the dominant size class"="AgeCmp",
      "Aspect: Aspect in degrees"="Aspect", 
+     "BAbvBio: Before thin above ground biomass" = "BAbvBio",
+     "BAbvCrb: Before thin above ground carbon" = "BAbvCrb",
      "BaDBH: Before thin quadractic mean DBH"="BaDBH", 
      "BBA: Before thin basal area"="BBA", 
-     "BBdFt: Before thin board foot (western variants) sawtimber (eastern variants) volume"="BBdFt", 
+     "BBdFt: Before thin board foot volume"="BBdFt", 
      "BCanCov: Before thin percent canopy cover (StrClass keyword required)"="BCanCov", 
      "BCCF: Before thin CCF"="BCCF", 
      "BDBHwtBA: Before thin average DBH weighted by stand basal area"="BDBHwtBA", 
-     "BHTWTBA: Before thin average height weighted by stand basal area"="BHTWTBA",
+     "BHTWTBA: Before thin average height weighted by stand basal area (Lorey's Height)"="BHTWTBA",
+     "BFolBio: Before thin foliage biomass" = "BFolBio",
+     "BFolCrb: Before thin foliage carbon" = "BfolCrb",
      "BMaxHS: Before thin height of tallest tree in uppermost stratum (StrClass keyword required)"="BMaxHS", 
-     "BMCuFt: Before thin merchantable (western variants) sawtimber (eastern variants) cubic foot volume"="BMCuFt", 
+     "BMCuFt: Before thin merchantable cubic foot volume"="BMCuFt", 
+     "BMerBio: Before thin merchantable biomass" = "BMerBio",
+     "BMerCrb: Before thin merchantable carbon" = "BMerCrb",
      "BMinHS: Before thin height of shortest tree in uppermost stratum (StrClass keyword required)"="BMinHS", 
      "BNumSS: Before thin number of valid strata (StrClass keyword required)"="BNumSS", 
      "BRDen: Before thin relative density (Curtis 1982)"="BRDen", 
      "BRDen2: Before thin relative density, SILVAH (Marquis and Ernst 1992)"="BRDen2", 
      "BSClass: Before thin stand structural classification (StrClass keyword required)"="BSClass", 
+     "BSawBio: Before thin sawlog biomass" = "BSawBio",
+     "BSawCrb: Before thin sawlog carbon" = "BSawCrb",
+     "BSCuFt: Before thin sawlog cubic foot volume"="BSCuFt",
      "BSDI: Before thin stand density index"="BSDI", 
      "BSDI2: Before thin stand density index (based on Zeide 1983)"="BSDI2", 
      "BSDIMax: Before thin maximum stand density index"="BSDIMax", 
      "BStrDbh: Before thin dbh of the stand uppermost stratum (StrClass keyword required)"="BStrDbh", 
-     "BTCuFt: Before thin total (western variants) or merchantable (pulpwood + sawtimber, eastern variants) cubic foot volume"="BTCuFt", 
+     "BTCuFt: Before thin total cubic foot volume"="BTCuFt", 
      "BTopHt: Before thin top height"="BTopHt", 
      "BTPA: Before thin trees/acre"="BTPA", 
      "CEndYear: Year at end of cycle"="CEndYear", 
@@ -512,28 +529,46 @@ mkVarList <- function (globals)
      "Yes: The constant 1"="Yes", 
      "AADBH: After thin average DBH"="AADBH", 
      "ABA: After thin basal area"="ABA", 
-     "ABdFt: After thin board foot (western variants) sawtimber (eastern variants) volume"="ABdFt", 
+     "ABdFt: After thin board foot volume"="ABdFt", 
+     "AAbvBio: After thin above ground biomass" = "AAbvBio",
+     "AAbvCrb: After thin above ground carbon" = "AAbvCrb",
      "ACanCov: After thin percent canopy cover (StrClass keyword required)"="ACanCov", 
      "ACCF: After thin CCF"="ACCF", 
      "ADBHwtBA: After thin average DBH weighted by stand basal area"="ADBHwtBA",
-     "AHTWTBA: After thin average height weighted by stand basal area"="AHTWTBA",
+     "AFolBio: After thin foliar biomass" = "AFolBio",
+     "AFolCrb: After thin foliar carbon" = "AFolCrb",
+     "AHTWTBA: After thin average height weighted by stand basal area (Lorey's Height)"="AHTWTBA",
      "AMaxHS: After thin height of tallest tree in uppermost stratum (StrClass keyword required)"="AMaxHS", 
-     "AMCuFt: After thin merchantable (western variants) sawtimber (eastern variants) cubic foot volume"="AMCuFt", 
+     "AMerBio: After thin merchantable biomass" = "AMerBio",
+     "AMerCrb: After thin merchantable carbon" = "AMerCrb",
+     "AMCuFt: After thin merchantable cubic foot volume"="AMCuFt", 
      "AMinHS: After thin height of shortest tree in uppermost stratum (StrClass keyword required)"="AMinHS", 
      "ANumSS: After thin number of valid strata (StrClass keyword required)"="ANumSS", 
      "ARDEN: After thin relative density (Curtis 1982)"="ARDEN", 
      "ARDen2: After thin relative density, SILVAH (Marquis and Ernst 1992)"="ARDen2", 
      "ASClass: After thin stand structural classification (StrClass keyword required)"="ASClass", 
+     "ASawBio: After thin sawlog biomass" = "ASawBio",
+     "ASawCrb: After thin sawlog carbon" = "ASawCrb",
+     "ASCuFt: After thin sawlog cubic foot volume" = "ASCuFt",
      "ASDI: After thin stand density index"="ASDI", 
      "ASDI2: After thin stand density index (based on Zeide 1983)"="ASDI2", 
      "ASDIMax: After thin maximum stand density index"="ASDIMax", 
      "AStrDbh: After thin dbh of the stand uppermost stratum (StrClass keyword required)"="AStrDbh", 
-     "ATCuFt: After thin total (western variants) or merchantable (pulpwood + sawtimber, eastern variants) cubic foot volume"="ATCuFt", 
+     "ATCuFt: After thin total cubic foot volume"="ATCuFt", 
      "ATopHt: After thin top height"="ATopHt", 
      "ATPA: After thin trees/acre"="ATPA", 
      "Cut: Cutting flag: 0 if no cutting, 1 otherwise"="Cut", 
+     "RAbvBio: Removed above ground biomass" = "RAbvBio",
+     "RAbvCrb: Removed above ground carbon" = "RAbvCrb",
      "RBdFt: Removed board feet volume"="RBdFt", 
-     "RMCuFt: Removed merch cubic feet volume"="RMCuFt", 
+     "RFolBio: Removed Foliar biomass" = "RFolBio",
+     "RFolCrb: Removed Foliar carbon" = "RFolCrb",
+     "RMCuFt: Removed merchantible cubic feet volume"="RMCuFt", 
+     "RMerBio: Removed merchantable biomass" = "RMerBio",
+     "RMerCrb: Removed merchantable carbon" = "RMerCrb",
+     "RSawBio: Removed sawlog biomass" = "RSawBio",
+     "RSawCrb: Removed sawlog carbon" = "RSawCrb",
+     "RSCuFt: Removed sawlog cubic foot volume" = "RSCuFt",
      "RTCuFt: Removed total cubic feet volume"="RTCuFt", 
      "RTPA: Removed trees/acre"="RTPA", 
      "ACC: Accreation form last cycle"="ACC", 
@@ -681,7 +716,7 @@ mkFreeformEltList <- function (globals,input,prms,title,kwds)
       tags$style(type="text/css", 
         "#freeEditCols{font-family:monospace;font-size:90%;width:95%;}"), 
       tags$p(id="freeEditCols", 
-             HTML(paste0("&nbsp;",paste0("....+....",1:8,collapse="")))),
+             HTML(paste0("&nbsp;",paste0("....+....",1:12,collapse="")))),
       tags$style(type="text/css", 
         "#freeEdit{font-family:monospace;font-size:90%;width:100%;cursor:auto;}"), 
       tags$script(paste0('$(document).ready(function(){ $("textarea").on("focus",',