R/importERMN.R
In NCRN/NPSForVeg: Data anaylsis and graphing for NPS forest vegetation monitoring.
Defines functions
importERMN
Documented in
importERMN
#' @include NPSForVeg_Class_def.R
#'
#' @title importERMN
#'
#' @description This function imports data from the standard ERMN .csv files and saves it as \code{NPSForVeg} objects.
#' The required .csv files are: Plots, Events, Cycles_ERMN, Trees, Saplings, Seedlings, Herbs, CWD and CommonNames.
#'
#' @param Dir The directory where the data is found. Path should not have a trailing slash.
#'
#' @return Returns a list containing 8 \code{NPSForVeg} objects, one for each park, named using the standard 4 letter park code (e.g. ALPO, BLUE etc.) as part of a list.
#'
#' @export
#'
importERMN<-function(Dir){
InPlots<-read.csv(paste(Dir,"Plots.csv",sep="/"),as.is=T, header=T)
InPlots$Event_Earliest<-as.Date(as.character(InPlots$Event_Earliest), format="%Y%m%d")
InPlots$Event_Latest<-as.Date(as.character(InPlots$Event_Latest),format="%Y%m%d")
InEvents<-read.csv(paste(Dir,"Events.csv",sep="/"),as.is=T, header=T)
InEvents$Event_Date<-as.Date(as.character(InEvents$Event_Date_Txt), format="%Y%m%d")
InCycles<-read.csv(paste(Dir,"Cycles.csv",sep="/"), as.is=T, header=T)
InTrees<-read.csv(paste(Dir,"Trees.csv",sep="/"),as.is=T, header=T)
InTrees$Equiv_Dead_DBH_cm[InTrees$Equiv_Dead_DBH_cm==999999]<-NA
InTrees$Equiv_Live_DBH_cm[InTrees$Equiv_Live_DBH_cm==999999]<-NA
InTrees$SumDeadBasalArea_cm2[InTrees$SumDeadBasalArea_cm2==785398000000]<-NA
InTrees$SumLiveBasalArea_cm2[InTrees$SumLiveBasalArea_cm2==785398000000]<-NA
InSaps<-read.csv(paste(Dir,"Saplings.csv",sep="/"),as.is=T, header=T)
InSeeds<-read.csv(paste(Dir,"Seedlings.csv",sep="/"),as.is=T, header=T)
InHerbs<-read.csv(paste(Dir,"Herbs.csv",sep="/"),as.is=T, header=T)
InCommons<-read.csv(paste(Dir,"CommonNames.csv",sep="/"), as.is=T, header=T)
InCommons$Common[InCommons$NCRN_Common!=""]<-InCommons$NCRN_Common[InCommons$NCRN_Common!=""]
InCommons$TSN<-as.character(InCommons$TSN)
InCWD1<-read.csv(paste(Dir,"CWD.csv",sep="/"), as.is=T, header=T)
InCWD<-InCWD1 %>% filter(Latin_Name!='Not sampled') %>% droplevels()
ALPO<-new("NPSForVeg",
ParkCode="ALPO",
ShortName="Allegheny Portage",
LongName="Allegheny Portage Railroad National Historic Site",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="ALPO",],
Events=InEvents[InEvents$Unit_Code=="ALPO",],
Trees=InTrees[InTrees$Unit_Code=="ALPO",],
Saplings=InSaps[InSaps$Unit_Code=="ALPO",],
Seedlings=InSeeds[InSeeds$Unit_Code=="ALPO",],
Herbs=InHerbs[InHerbs$Unit_Code=="ALPO",],
CWD=InCWD[InCWD$Unit_Code=="ALPO",],
Commons=InCommons)
BLUE<-new("NPSForVeg",
ParkCode="BLUE",
ShortName="Bluestone",
LongName="Bluestone National Scenic River",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="BLUE",],
Events=InEvents[InEvents$Unit_Code=="BLUE",],
Trees=InTrees[InTrees$Unit_Code=="BLUE",],
Saplings=InSaps[InSaps$Unit_Code=="BLUE",],
Seedlings=InSeeds[InSeeds$Unit_Code=="BLUE",],
Herbs=InHerbs[InHerbs$Unit_Code=="BLUE",],
CWD=InCWD[InCWD$Unit_Code=="BLUE",],
Commons=InCommons)
DEWA<-new("NPSForVeg",
ParkCode="DEWA",
ShortName="Delaware Water Gap",
LongName="Delaware Water Gap National Recreation Area",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="DEWA",],
Events=InEvents[InEvents$Unit_Code=="DEWA",],
Trees=InTrees[InTrees$Unit_Code=="DEWA",],
Saplings=InSaps[InSaps$Unit_Code=="DEWA",],
Seedlings=InSeeds[InSeeds$Unit_Code=="DEWA",],
Herbs=InHerbs[InHerbs$Unit_Code=="DEWA",],
CWD=InCWD[InCWD$Unit_Code=="DEWA",],
Commons=InCommons)
FONE<-new("NPSForVeg",
ParkCode="FONE",
ShortName="Fort Necessity",
LongName="Fort Necessity National Battlefield",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="FONE",],
Events=InEvents[InEvents$Unit_Code=="FONE",],
Trees=InTrees[InTrees$Unit_Code=="FONE",],
Saplings=InSaps[InSaps$Unit_Code=="FONE",],
Seedlings=InSeeds[InSeeds$Unit_Code=="FONE",],
Herbs=InHerbs[InHerbs$Unit_Code=="FONE",],
CWD=InCWD[InCWD$Unit_Code=="FONE",],
Commons=InCommons)
FRHI<-new("NPSForVeg",
ParkCode="FRHI",
ShortName="Friendship Hill",
LongName="Friendship Hill National Historic Site",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="FRHI",],
Events=InEvents[InEvents$Unit_Code=="FRHI",],
Trees=InTrees[InTrees$Unit_Code=="FRHI",],
Saplings=InSaps[InSaps$Unit_Code=="FRHI",],
Seedlings=InSeeds[InSeeds$Unit_Code=="FRHI",],
Herbs=InHerbs[InHerbs$Unit_Code=="FRHI",],
CWD=InCWD[InCWD$Unit_Code=="FRHI",],
Commons=InCommons)
GARI<-new("NPSForVeg",
ParkCode="GARI",
ShortName="Gauley",
LongName="Gauley River National Recreation Area",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="GARI",],
Events=InEvents[InEvents$Unit_Code=="GARI",],
Trees=InTrees[InTrees$Unit_Code=="GARI",],
Saplings=InSaps[InSaps$Unit_Code=="GARI",],
Seedlings=InSeeds[InSeeds$Unit_Code=="GARI",],
Herbs=InHerbs[InHerbs$Unit_Code=="GARI",],
CWD=InCWD[InCWD$Unit_Code=="GARI",],
Commons=InCommons)
JOFL<-new("NPSForVeg",
ParkCode="JOFL",
ShortName="Johnstown Flood",
LongName="Johnstown Flood National Memorial",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="JOFL",],
Events=InEvents[InEvents$Unit_Code=="JOFL",],
Trees=InTrees[InTrees$Unit_Code=="JOFL",],
Saplings=InSaps[InSaps$Unit_Code=="JOFL",],
Seedlings=InSeeds[InSeeds$Unit_Code=="JOFL",],
Herbs=InHerbs[InHerbs$Unit_Code=="JOFL",],
CWD=InCWD[InCWD$Unit_Code=="JOFL",],
Commons=InCommons)
NERI<-new("NPSForVeg",
ParkCode="NERI",
ShortName="New River",
LongName="New River Gorge National River",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="NERI",],
Events=InEvents[InEvents$Unit_Code=="NERI",],
Trees=InTrees[InTrees$Unit_Code=="NERI",],
Saplings=InSaps[InSaps$Unit_Code=="NERI",],
Seedlings=InSeeds[InSeeds$Unit_Code=="NERI",],
Herbs=InHerbs[InHerbs$Unit_Code=="NERI",],
CWD=InCWD[InCWD$Unit_Code=="NERI",],
Commons=InCommons)
return(c(ALPO,BLUE,DEWA,FONE,FRHI,GARI,JOFL,NERI))
}
NCRN/NPSForVeg documentation built on March 26, 2024, 7:13 a.m.
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Defines functions importERMN
Documented in importERMN
#' @include NPSForVeg_Class_def.R
#'
#' @title importERMN
#'
#' @description This function imports data from the standard ERMN .csv files and saves it as \code{NPSForVeg} objects.
#' The required .csv files are: Plots, Events, Cycles_ERMN, Trees, Saplings, Seedlings, Herbs, CWD and CommonNames.
#'
#' @param Dir The directory where the data is found. Path should not have a trailing slash.
#'
#' @return Returns a list containing 8 \code{NPSForVeg} objects, one for each park, named using the standard 4 letter park code (e.g. ALPO, BLUE etc.) as part of a list.
#'
#' @export
#'
importERMN<-function(Dir){
InPlots<-read.csv(paste(Dir,"Plots.csv",sep="/"),as.is=T, header=T)
InPlots$Event_Earliest<-as.Date(as.character(InPlots$Event_Earliest), format="%Y%m%d")
InPlots$Event_Latest<-as.Date(as.character(InPlots$Event_Latest),format="%Y%m%d")
InEvents<-read.csv(paste(Dir,"Events.csv",sep="/"),as.is=T, header=T)
InEvents$Event_Date<-as.Date(as.character(InEvents$Event_Date_Txt), format="%Y%m%d")
InCycles<-read.csv(paste(Dir,"Cycles.csv",sep="/"), as.is=T, header=T)
InTrees<-read.csv(paste(Dir,"Trees.csv",sep="/"),as.is=T, header=T)
InTrees$Equiv_Dead_DBH_cm[InTrees$Equiv_Dead_DBH_cm==999999]<-NA
InTrees$Equiv_Live_DBH_cm[InTrees$Equiv_Live_DBH_cm==999999]<-NA
InTrees$SumDeadBasalArea_cm2[InTrees$SumDeadBasalArea_cm2==785398000000]<-NA
InTrees$SumLiveBasalArea_cm2[InTrees$SumLiveBasalArea_cm2==785398000000]<-NA
InSaps<-read.csv(paste(Dir,"Saplings.csv",sep="/"),as.is=T, header=T)
InSeeds<-read.csv(paste(Dir,"Seedlings.csv",sep="/"),as.is=T, header=T)
InHerbs<-read.csv(paste(Dir,"Herbs.csv",sep="/"),as.is=T, header=T)
InCommons<-read.csv(paste(Dir,"CommonNames.csv",sep="/"), as.is=T, header=T)
InCommons$Common[InCommons$NCRN_Common!=""]<-InCommons$NCRN_Common[InCommons$NCRN_Common!=""]
InCommons$TSN<-as.character(InCommons$TSN)
InCWD1<-read.csv(paste(Dir,"CWD.csv",sep="/"), as.is=T, header=T)
InCWD<-InCWD1 %>% filter(Latin_Name!='Not sampled') %>% droplevels()
ALPO<-new("NPSForVeg",
ParkCode="ALPO",
ShortName="Allegheny Portage",
LongName="Allegheny Portage Railroad National Historic Site",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="ALPO",],
Events=InEvents[InEvents$Unit_Code=="ALPO",],
Trees=InTrees[InTrees$Unit_Code=="ALPO",],
Saplings=InSaps[InSaps$Unit_Code=="ALPO",],
Seedlings=InSeeds[InSeeds$Unit_Code=="ALPO",],
Herbs=InHerbs[InHerbs$Unit_Code=="ALPO",],
CWD=InCWD[InCWD$Unit_Code=="ALPO",],
Commons=InCommons)
BLUE<-new("NPSForVeg",
ParkCode="BLUE",
ShortName="Bluestone",
LongName="Bluestone National Scenic River",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="BLUE",],
Events=InEvents[InEvents$Unit_Code=="BLUE",],
Trees=InTrees[InTrees$Unit_Code=="BLUE",],
Saplings=InSaps[InSaps$Unit_Code=="BLUE",],
Seedlings=InSeeds[InSeeds$Unit_Code=="BLUE",],
Herbs=InHerbs[InHerbs$Unit_Code=="BLUE",],
CWD=InCWD[InCWD$Unit_Code=="BLUE",],
Commons=InCommons)
DEWA<-new("NPSForVeg",
ParkCode="DEWA",
ShortName="Delaware Water Gap",
LongName="Delaware Water Gap National Recreation Area",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="DEWA",],
Events=InEvents[InEvents$Unit_Code=="DEWA",],
Trees=InTrees[InTrees$Unit_Code=="DEWA",],
Saplings=InSaps[InSaps$Unit_Code=="DEWA",],
Seedlings=InSeeds[InSeeds$Unit_Code=="DEWA",],
Herbs=InHerbs[InHerbs$Unit_Code=="DEWA",],
CWD=InCWD[InCWD$Unit_Code=="DEWA",],
Commons=InCommons)
FONE<-new("NPSForVeg",
ParkCode="FONE",
ShortName="Fort Necessity",
LongName="Fort Necessity National Battlefield",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="FONE",],
Events=InEvents[InEvents$Unit_Code=="FONE",],
Trees=InTrees[InTrees$Unit_Code=="FONE",],
Saplings=InSaps[InSaps$Unit_Code=="FONE",],
Seedlings=InSeeds[InSeeds$Unit_Code=="FONE",],
Herbs=InHerbs[InHerbs$Unit_Code=="FONE",],
CWD=InCWD[InCWD$Unit_Code=="FONE",],
Commons=InCommons)
FRHI<-new("NPSForVeg",
ParkCode="FRHI",
ShortName="Friendship Hill",
LongName="Friendship Hill National Historic Site",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="FRHI",],
Events=InEvents[InEvents$Unit_Code=="FRHI",],
Trees=InTrees[InTrees$Unit_Code=="FRHI",],
Saplings=InSaps[InSaps$Unit_Code=="FRHI",],
Seedlings=InSeeds[InSeeds$Unit_Code=="FRHI",],
Herbs=InHerbs[InHerbs$Unit_Code=="FRHI",],
CWD=InCWD[InCWD$Unit_Code=="FRHI",],
Commons=InCommons)
GARI<-new("NPSForVeg",
ParkCode="GARI",
ShortName="Gauley",
LongName="Gauley River National Recreation Area",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="GARI",],
Events=InEvents[InEvents$Unit_Code=="GARI",],
Trees=InTrees[InTrees$Unit_Code=="GARI",],
Saplings=InSaps[InSaps$Unit_Code=="GARI",],
Seedlings=InSeeds[InSeeds$Unit_Code=="GARI",],
Herbs=InHerbs[InHerbs$Unit_Code=="GARI",],
CWD=InCWD[InCWD$Unit_Code=="GARI",],
Commons=InCommons)
JOFL<-new("NPSForVeg",
ParkCode="JOFL",
ShortName="Johnstown Flood",
LongName="Johnstown Flood National Memorial",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="JOFL",],
Events=InEvents[InEvents$Unit_Code=="JOFL",],
Trees=InTrees[InTrees$Unit_Code=="JOFL",],
Saplings=InSaps[InSaps$Unit_Code=="JOFL",],
Seedlings=InSeeds[InSeeds$Unit_Code=="JOFL",],
Herbs=InHerbs[InHerbs$Unit_Code=="JOFL",],
CWD=InCWD[InCWD$Unit_Code=="JOFL",],
Commons=InCommons)
NERI<-new("NPSForVeg",
ParkCode="NERI",
ShortName="New River",
LongName="New River Gorge National River",
Network="ERMN",
TPlotSize=c(1,pi*15*15),
SapPlotSize=c(4, pi*2*2),
SeedPlotSize=c(4, pi*2*2),
HPlotSize=c(12,1),
Cycles=InCycles,
Plots=InPlots[InPlots$Unit_Code=="NERI",],
Events=InEvents[InEvents$Unit_Code=="NERI",],
Trees=InTrees[InTrees$Unit_Code=="NERI",],
Saplings=InSaps[InSaps$Unit_Code=="NERI",],
Seedlings=InSeeds[InSeeds$Unit_Code=="NERI",],
Herbs=InHerbs[InHerbs$Unit_Code=="NERI",],
CWD=InCWD[InCWD$Unit_Code=="NERI",],
Commons=InCommons)
return(c(ALPO,BLUE,DEWA,FONE,FRHI,GARI,JOFL,NERI))
}
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