Nothing
inst/doc/FIESTA_tutorial_dat.R
In FIESTA: Forest Inventory Estimation and Analysis
## ----setup, include = F-------------------------------------------------------
library(knitr)
knitr::opts_chunk$set(message = F, warning = F)
## ----include=FALSE------------------------------------------------------------
# Sets up output folding
hooks = knitr::knit_hooks$get()
hook_foldable = function(type) {
force(type)
function(x, options) {
res = hooks[[type]](x, options)
if (isFALSE(options[[paste0("fold.", type)]])) return(res)
paste0(
"<details><summary>", type, "</summary>\n\n",
res,
"\n\n</details>"
)
}
}
knitr::knit_hooks$set(
output = hook_foldable("output"),
plot = hook_foldable("plot")
)
## ----echo=-1------------------------------------------------------------------
data.table::setDTthreads(2)
## ----message = F, warning = F-------------------------------------------------
# Load library
library(FIESTA)
## -----------------------------------------------------------------------------
WYconddat.nfs <- datFilter(
x = WYcond,
xfilter = "ADFORCD > 0"
)
names(WYconddat.nfs)
WYcond.nfs <- WYconddat.nfs$xf
dim(WYcond)
dim(WYcond.nfs)
## -----------------------------------------------------------------------------
WYtreedat.dead <- datFilter(
x = WYtree,
xfilter = "STATUSCD == 2 & STANDING_DEAD_CD == 1 & SPCD == 746"
)
names(WYtreedat.dead)
WYtree.deadasp <- WYtreedat.dead$xf
dim(WYtree.deadasp)
dim(WYtree)
## -----------------------------------------------------------------------------
WYtreedat.dead2 <- datFilter(
x = WYtree,
xfilter = "STATUSCD == 2 & STANDING_DEAD_CD == 1 & SPCD == 746",
othertabnms = c("WYplt", "WYcond")
)
names(WYtreedat.dead2)
WYtree.deadasp2 <- WYtreedat.dead2$xf
head(WYtree.deadasp2)
dim(WYtree.deadasp2)
WYtree.deadasptabs <- WYtreedat.dead2$cliptabs
names(WYtree.deadasptabs)
WYplt.deadasp <- WYtree.deadasptabs$clip_WYplt
WYcond.deadasp <- WYtree.deadasptabs$clip_WYcond
dim(WYplt.deadasp)
dim(WYcond.deadasp)
## -----------------------------------------------------------------------------
## Get number of plots by county
datFreq(
x = WYplt,
xvar="COUNTYCD"
)
## Get number of plots by county and plot status
datFreq(
x = WYplt,
xvar=c("COUNTYCD", "PLOT_STATUS_CD")
)
## Get number of plots by county and plot status with subtotals
datFreq(
x = WYplt,
xvar = c("COUNTYCD", "PLOT_STATUS_CD"),
subtotal = TRUE
)
## Get number of plots by county and plot status with subtotals
datFreq(
x = WYplt,
xvar = c("COUNTYCD", "PLOT_STATUS_CD"),
subtotal = TRUE,
subtotalcol = "COUNTYCD"
)
## -----------------------------------------------------------------------------
## Get summed condition proportions by forest type class and stand size class
datPivot(
x = WYcond,
pvar = "CONDPROP_UNADJ",
xvar = "FORTYPCD",
yvar = "STDSZCD"
)
## Get average height by species group code and status code
datPivot(
x = WYtree,
pvar = "HT",
xvar = "SPGRPCD",
yvar = "TREECLCD",
pfun = mean
)
## -----------------------------------------------------------------------------
FIESTAutils::ref_diacl2in
WYtreelut <- datLUTclass(
x = WYtree,
xvar = "DIA",
LUT = FIESTAutils::ref_diacl2in,
LUTclassnm = "DIACL2IN"
)
names(WYtreelut)
WYtree2 <- WYtreelut$xLUT
head(WYtree2)
dim(WYtree)
dim(WYtree2)
## -----------------------------------------------------------------------------
diacl25 <- data.frame(
MIN = c(5,25),
MAX = c(25, 100),
DIACL25 = c("5.0-24.9", "25.0+" )
)
diacl25
WYtreelut2 <- datLUTclass(
x = WYtree,
xvar = "DIA",
LUT = diacl25,
LUTclassnm = "DIACL25"
)
names(WYtreelut2)
WYtree2 <- WYtreelut2$xLUT
head(WYtree2)
dim(WYtree)
dim(WYtree2)
## -----------------------------------------------------------------------------
cutbreaks <- c(0,25,50,100)
WYcondlut <- datLUTclass(
x = WYcond,
xvar = "LIVE_CANOPY_CVR_PCT",
cutbreaks = cutbreaks
)
names(WYcondlut)
head(WYcondlut$xLUT)
WYcondlut$LUT
## -----------------------------------------------------------------------------
head(FIESTAutils::ref_codes)
unique(FIESTAutils::ref_codes$VARIABLE)
## -----------------------------------------------------------------------------
ref_dstrbcd <- FIESTAutils::ref_codes[FIESTAutils::ref_codes$VARIABLE == "DSTRBCD",]
head(ref_dstrbcd)
## -----------------------------------------------------------------------------
WYcondlut <- datLUTnm(
x = WYcond,
xvar = "DSTRBCD1",
LUT = ref_dstrbcd,
LUTvar = "VALUE",
LUTnewvar = "MEANING",
LUTnewvarnm = "DSTRB1NM"
)
names(WYcondlut)
WYcond2 <- WYcondlut$xLUT
head(WYcond2[WYcond2$DSTRBCD1 > 0, ])
## -----------------------------------------------------------------------------
WYcondlut2 <- datLUTnm(
x = WYcond,
xvar = "DSTRBCD1",
FIAname = TRUE
)
names(WYcondlut2)
WYcond3 <- WYcondlut2$xLUT
head(WYcond3[WYcond3$DSTRBCD1 > 0, ])
## -----------------------------------------------------------------------------
condsumdat <- datSumCond(
cond = WYcond,
csumvar = "LIVE_CANOPY_CVR_PCT"
)
names(condsumdat)
condsum <- condsumdat$condsum
head(condsum)
## -----------------------------------------------------------------------------
condsum[condsum$PLT_CN == 40405596010690,]
WYcond[WYcond$PLT_CN == 40405596010690,]
## -----------------------------------------------------------------------------
condsum <- datSumCond(
cond = WYcond,
plt = WYplt,
csumvar = "LIVE_CANOPY_CVR_PCT"
)$condsum
head(condsum)
## -----------------------------------------------------------------------------
condsum <- datSumCond(
cond = WYcond,
plt = WYplt,
csumvar = "LIVE_CANOPY_CVR_PCT",
cfilter = "STDSZCD == 1"
)$condsum
head(condsum)
## Check results
condsum[condsum$CN == 40405596010690,]
WYcond[WYcond$PLT_CN == 40405596010690,]
## -----------------------------------------------------------------------------
condnf <- datSumCond(
cond = WYcond,
plt = WYplt,
csumvar = "CONDPROP_UNADJ",
csumvarnm = "cond_nf",
cfilter = "COND_STATUS_CD %in% c(2,3)"
)$condsum
condnf[condnf$CN == 40404737010690,]
WYcond[WYcond$PLT_CN == 40404737010690,]
## -----------------------------------------------------------------------------
condres <- datSumCond(
cond = WYcond,
plt = WYplt,
csumvar = "CONDPROP_UNADJ",
csumvarnm = "cond_reserved",
cfilter = "RESERVCD == 1"
)$condsum
WYcond[WYcond$PLT_CN == 46792188020004,]
## -----------------------------------------------------------------------------
treesumdat1 <- datSumTree(
tree = WYtree,
plt = WYplt,
tsumvarlst = c("BA", "VOLCFNET"),
TPA = FALSE,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2
)
names(treesumdat1)
treesum1 <- treesumdat1$treedat
head(treesum1)
treesumdat1$sumvars
## -----------------------------------------------------------------------------
treesumdat2 <- datSumTree(
tree = WYtree,
plt = WYplt,
tsumvarlst = c("BA", "VOLCFNET"),
TPA = TRUE,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2
)
names(treesumdat2)
treesum2 <- treesumdat2$treedat
head(treesum2)
## -----------------------------------------------------------------------------
checkvars <- c("PLT_CN", "CONDID", "SUBP", "TREE", "STATUSCD", "SPCD", "DIA", "HT",
"BA", "VOLCFNET", "TPA_UNADJ")
testplt <- WYtree[WYtree$PLT_CN == 40404758010690, checkvars]
testplt
sum(testplt[testplt$STATUSCD == 1, "BA"], na.rm=TRUE)
sum(testplt[testplt$STATUSCD == 1, "BA"] * testplt[testplt$STATUSCD == 1, "TPA_UNADJ"], na.rm=TRUE)
treesum1[treesum1$CN == 40404758010690,]
treesum2[treesum2$CN == 40404758010690,]
## -----------------------------------------------------------------------------
treesumdat3 <- datSumTree(
tree = WYtree,
plt = WYplt,
tsumvarlst = c("DIA", "HT"),
TPA = FALSE,
tfun = mean,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2
)
names(treesumdat3)
treesum3 <- treesumdat3$treedat
head(treesum3)
## Test DIA and HT results for 1 plot
testplt
mean(testplt[testplt$STATUSCD == 1, "DIA"], na.rm=TRUE)
mean(testplt[testplt$STATUSCD == 1, "HT"], na.rm=TRUE)
treesum3[treesum3$CN == 40404758010690,]
## -----------------------------------------------------------------------------
treesumdat4a <- datSumTree(
tree = WYtree,
plt = WYplt,
tsumvarlst = "TPA_UNADJ",
TPA = TRUE,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2
)
names(treesumdat4a)
treesum4a <- treesumdat4a$treedat
head(treesum4a)
## -----------------------------------------------------------------------------
treesumdat4b <- datSumTree(
tree = WYtree,
plt = WYplt,
cond = WYcond,
tsumvarlst = "VOLCFNET",
tfilter = "STATUSCD == 1",
bycond = FALSE,
getadjplot = TRUE
)
names(treesumdat4b)
treesum4b <- treesumdat4b$treedat
head(treesum4b)
## -----------------------------------------------------------------------------
treesumdat4c <- datSumTree(
tree = WYtree,
plt = WYplt,
cond = WYcond,
tsumvarlst = "VOLCFNET",
tfilter = "STATUSCD == 1",
bycond = FALSE,
getadjplot = FALSE
)
treesum4c <- treesumdat4c$treedat
cn <- 40407815010690
WYcond[WYcond$PLT_CN == cn, ]
treesum4b[treesum4b$CN == cn, ]
treesum4c[treesum4c$CN == cn, ]
## -----------------------------------------------------------------------------
treesumdat5a <- datSumTree(
tree = WYtree,
plt = WYplt,
seed = WYseed,
tsumvarlst = "TPA_UNADJ",
TPA = TRUE,
addseed = TRUE,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2
)
names(treesumdat5a)
treesum5a <- treesumdat5a$treedat
head(treesum5a)
treesum5a[treesum5a$CN %in% cn,]
WYseed[WYseed$PLT_CN == cn,]
## -----------------------------------------------------------------------------
treesumdat5b <- datSumTree(
tree = WYtree,
plt = WYplt,
cond = WYcond,
seed = WYseed,
tsumvarlst = "TPA_UNADJ",
TPA = TRUE,
addseed = TRUE,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2,
getadjplot =TRUE
)
names(treesumdat5b)
treesum5b <- treesumdat5b$treedat
head(treesum5b)
treesum5a[treesum5a$CN %in% cn,]
treesum5b[treesum5b$CN %in% cn,]
WYcond[WYcond$PLT_CN %in% cn,]
## -----------------------------------------------------------------------------
treedomBA <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "BA",
TPA = TRUE,
tdomtot = TRUE,
tdomtotnm = "BA_LIVE",
tdomprefix = "BA_LIVE",
tround = 2,
tfilter = "STATUSCD==1"
)
names(treedomBA)
tdomdat <- treedomBA$tdomdat
tdomvarlut <- treedomBA$tdomvarlut
tdomlst <- treedomBA$tdomlst
tdomtotnm <- treedomBA$tdomtotnm
head(tdomdat)
tdomvarlut
tdomlst
tdomtotnm
dim(WYplt)
dim(tdomdat)
## -----------------------------------------------------------------------------
treedomCNT <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 0,
tfilter = "STATUSCD==1"
)
names(treedomCNT)
tdomdat.tree <- treedomCNT$tdomdat
tdomvarlut <- treedomCNT$tdomvarlut
tdomlst <- treedomCNT$tdomlst
tdomtotnm <- treedomCNT$tdomtotnm
head(tdomdat.tree)
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(
cond = WYcond,
plt = WYplt,
seed = WYseed,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 0
)
names(treedomCNTs)
tdomdat.seed <- treedomCNTs$tdomdat
tdomvarlut <- treedomCNTs$tdomvarlut
tdomlst <- treedomCNTs$tdomlst
tdomtotnm <- treedomCNTs$tdomtotnm
head(tdomdat.seed)
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
seed = WYseed,
puniqueid = "CN",
bycond =FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 0,
tfilter = "STATUSCD==1",
addseed = TRUE
)
names(treedomCNTs)
tdomdat.treeseed <- treedomCNTs$tdomdat
tdomvarlut <- treedomCNTs$tdomvarlut
tdomlst <- treedomCNTs$tdomlst
tdomtotnm <- treedomCNTs$tdomtotnm
head(tdomdat.treeseed)
cn <- 40404730010690
tdomdat.tree[tdomdat.tree$CN == cn,]
tdomdat.seed[tdomdat.seed$CN == cn,]
tdomdat.treeseed[tdomdat.treeseed$CN == cn,]
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
seed = WYseed,
puniqueid ="CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
savedata = FALSE,
tfilter = "STATUSCD==1",
addseed = TRUE,
presence = TRUE
)
names(treedomCNTs)
tdomdat.pres <- treedomCNTs$tdomdat.pres
head(tdomdat.pres)
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(tree=WYtree, cond=WYcond, plt=WYplt, seed=WYseed,
puniqueid="CN", bycond=FALSE, tsumvar="PLT_CN", TPA=TRUE, tdomtot=TRUE,
tdomprefix="CNT", savedata=FALSE, tround=0, tfilter="STATUSCD==1",
addseed=TRUE, presence=TRUE, proportion=TRUE)
names(treedomCNTs)
tdomdat.pres <- treedomCNTs$tdomdat.pres
tdomdat.prop <- treedomCNTs$tdomdat.prop
head(tdomdat.pres)
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
seed = WYseed,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 0,
tfilter = "STATUSCD==1",
addseed = TRUE,
presence = TRUE,
proportion = TRUE,
cover = TRUE,
tdombarplot = TRUE
)
names(treedomCNTs)
tdomdat.pres <- treedomCNTs$tdomdat.pres
tdomdat.prop <- treedomCNTs$tdomdat.prop
tdomdat.cov <- treedomCNTs$tdomdat.cov
cn=40404742010690
tdomdat.tree[tdomdat.tree$CN == cn,]
tdomdat.seed[tdomdat.seed$CN == cn,]
tdomdat.treeseed[tdomdat.treeseed$CN == cn,]
tdomdat.pres[tdomdat.pres$CN == cn,]
tdomdat.prop[tdomdat.prop$CN == cn,]
tdomdat.cov[tdomdat.cov$CN == cn,]
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
seed = WYseed,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 0,
tfilter = "STATUSCD==1",
addseed = TRUE,
presence = TRUE,
proportion = TRUE,
tdombarplot = TRUE
)
names(treedomCNTs)
tdomdat.pres <- treedomCNTs$tdomdat.pres
tdomdat.prop <- treedomCNTs$tdomdat.prop
head(tdomdat.pres)
## -----------------------------------------------------------------------------
treedomBA <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "BA",
TPA = TRUE,
tdomprefix = "BA",
tdomvarlst = 113,
tround = 2,
tfilter = "STATUSCD==1"
)
names(treedomBA)
ba.limber <- treedomBA$tdomdat
head(ba.limber)
## -----------------------------------------------------------------------------
## Total basal area per acre by species and diameter class
DIALUT <- FIESTAutils::ref_diacl2in[FIESTAutils::ref_diacl2in$MIN <= 37, ]
names(DIALUT)[names(DIALUT) == "MEANING"] <- "DIACL2IN"
## Append diameter classes to tree table
datlut <- datLUTclass(
x = WYtree,
xvar = "DIA",
LUT = DIALUT,
LUTclassnm = "DIACL2IN"
)
WYtree2 <- datlut$xLUT
## Species and diameter class
treedomDIACNTs <- datSumTreeDom(
tree = WYtree2,
cond = WYcond,
plt = WYplt,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 2,
tfilter = "STATUSCD==1 & DIA > 30",
presence = TRUE,
proportion = TRUE,
tdomvar2 = "DIACL2IN",
tdombarplot = TRUE
)
names(treedomDIACNTs)
tdomdat.pres <- treedomDIACNTs$tdomdat.pres
tdomdat.prop <- treedomDIACNTs$tdomdat.prop
head(tdomdat.pres)
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## ----setup, include = F-------------------------------------------------------
library(knitr)
knitr::opts_chunk$set(message = F, warning = F)
## ----include=FALSE------------------------------------------------------------
# Sets up output folding
hooks = knitr::knit_hooks$get()
hook_foldable = function(type) {
force(type)
function(x, options) {
res = hooks[[type]](x, options)
if (isFALSE(options[[paste0("fold.", type)]])) return(res)
paste0(
"<details><summary>", type, "</summary>\n\n",
res,
"\n\n</details>"
)
}
}
knitr::knit_hooks$set(
output = hook_foldable("output"),
plot = hook_foldable("plot")
)
## ----echo=-1------------------------------------------------------------------
data.table::setDTthreads(2)
## ----message = F, warning = F-------------------------------------------------
# Load library
library(FIESTA)
## -----------------------------------------------------------------------------
WYconddat.nfs <- datFilter(
x = WYcond,
xfilter = "ADFORCD > 0"
)
names(WYconddat.nfs)
WYcond.nfs <- WYconddat.nfs$xf
dim(WYcond)
dim(WYcond.nfs)
## -----------------------------------------------------------------------------
WYtreedat.dead <- datFilter(
x = WYtree,
xfilter = "STATUSCD == 2 & STANDING_DEAD_CD == 1 & SPCD == 746"
)
names(WYtreedat.dead)
WYtree.deadasp <- WYtreedat.dead$xf
dim(WYtree.deadasp)
dim(WYtree)
## -----------------------------------------------------------------------------
WYtreedat.dead2 <- datFilter(
x = WYtree,
xfilter = "STATUSCD == 2 & STANDING_DEAD_CD == 1 & SPCD == 746",
othertabnms = c("WYplt", "WYcond")
)
names(WYtreedat.dead2)
WYtree.deadasp2 <- WYtreedat.dead2$xf
head(WYtree.deadasp2)
dim(WYtree.deadasp2)
WYtree.deadasptabs <- WYtreedat.dead2$cliptabs
names(WYtree.deadasptabs)
WYplt.deadasp <- WYtree.deadasptabs$clip_WYplt
WYcond.deadasp <- WYtree.deadasptabs$clip_WYcond
dim(WYplt.deadasp)
dim(WYcond.deadasp)
## -----------------------------------------------------------------------------
## Get number of plots by county
datFreq(
x = WYplt,
xvar="COUNTYCD"
)
## Get number of plots by county and plot status
datFreq(
x = WYplt,
xvar=c("COUNTYCD", "PLOT_STATUS_CD")
)
## Get number of plots by county and plot status with subtotals
datFreq(
x = WYplt,
xvar = c("COUNTYCD", "PLOT_STATUS_CD"),
subtotal = TRUE
)
## Get number of plots by county and plot status with subtotals
datFreq(
x = WYplt,
xvar = c("COUNTYCD", "PLOT_STATUS_CD"),
subtotal = TRUE,
subtotalcol = "COUNTYCD"
)
## -----------------------------------------------------------------------------
## Get summed condition proportions by forest type class and stand size class
datPivot(
x = WYcond,
pvar = "CONDPROP_UNADJ",
xvar = "FORTYPCD",
yvar = "STDSZCD"
)
## Get average height by species group code and status code
datPivot(
x = WYtree,
pvar = "HT",
xvar = "SPGRPCD",
yvar = "TREECLCD",
pfun = mean
)
## -----------------------------------------------------------------------------
FIESTAutils::ref_diacl2in
WYtreelut <- datLUTclass(
x = WYtree,
xvar = "DIA",
LUT = FIESTAutils::ref_diacl2in,
LUTclassnm = "DIACL2IN"
)
names(WYtreelut)
WYtree2 <- WYtreelut$xLUT
head(WYtree2)
dim(WYtree)
dim(WYtree2)
## -----------------------------------------------------------------------------
diacl25 <- data.frame(
MIN = c(5,25),
MAX = c(25, 100),
DIACL25 = c("5.0-24.9", "25.0+" )
)
diacl25
WYtreelut2 <- datLUTclass(
x = WYtree,
xvar = "DIA",
LUT = diacl25,
LUTclassnm = "DIACL25"
)
names(WYtreelut2)
WYtree2 <- WYtreelut2$xLUT
head(WYtree2)
dim(WYtree)
dim(WYtree2)
## -----------------------------------------------------------------------------
cutbreaks <- c(0,25,50,100)
WYcondlut <- datLUTclass(
x = WYcond,
xvar = "LIVE_CANOPY_CVR_PCT",
cutbreaks = cutbreaks
)
names(WYcondlut)
head(WYcondlut$xLUT)
WYcondlut$LUT
## -----------------------------------------------------------------------------
head(FIESTAutils::ref_codes)
unique(FIESTAutils::ref_codes$VARIABLE)
## -----------------------------------------------------------------------------
ref_dstrbcd <- FIESTAutils::ref_codes[FIESTAutils::ref_codes$VARIABLE == "DSTRBCD",]
head(ref_dstrbcd)
## -----------------------------------------------------------------------------
WYcondlut <- datLUTnm(
x = WYcond,
xvar = "DSTRBCD1",
LUT = ref_dstrbcd,
LUTvar = "VALUE",
LUTnewvar = "MEANING",
LUTnewvarnm = "DSTRB1NM"
)
names(WYcondlut)
WYcond2 <- WYcondlut$xLUT
head(WYcond2[WYcond2$DSTRBCD1 > 0, ])
## -----------------------------------------------------------------------------
WYcondlut2 <- datLUTnm(
x = WYcond,
xvar = "DSTRBCD1",
FIAname = TRUE
)
names(WYcondlut2)
WYcond3 <- WYcondlut2$xLUT
head(WYcond3[WYcond3$DSTRBCD1 > 0, ])
## -----------------------------------------------------------------------------
condsumdat <- datSumCond(
cond = WYcond,
csumvar = "LIVE_CANOPY_CVR_PCT"
)
names(condsumdat)
condsum <- condsumdat$condsum
head(condsum)
## -----------------------------------------------------------------------------
condsum[condsum$PLT_CN == 40405596010690,]
WYcond[WYcond$PLT_CN == 40405596010690,]
## -----------------------------------------------------------------------------
condsum <- datSumCond(
cond = WYcond,
plt = WYplt,
csumvar = "LIVE_CANOPY_CVR_PCT"
)$condsum
head(condsum)
## -----------------------------------------------------------------------------
condsum <- datSumCond(
cond = WYcond,
plt = WYplt,
csumvar = "LIVE_CANOPY_CVR_PCT",
cfilter = "STDSZCD == 1"
)$condsum
head(condsum)
## Check results
condsum[condsum$CN == 40405596010690,]
WYcond[WYcond$PLT_CN == 40405596010690,]
## -----------------------------------------------------------------------------
condnf <- datSumCond(
cond = WYcond,
plt = WYplt,
csumvar = "CONDPROP_UNADJ",
csumvarnm = "cond_nf",
cfilter = "COND_STATUS_CD %in% c(2,3)"
)$condsum
condnf[condnf$CN == 40404737010690,]
WYcond[WYcond$PLT_CN == 40404737010690,]
## -----------------------------------------------------------------------------
condres <- datSumCond(
cond = WYcond,
plt = WYplt,
csumvar = "CONDPROP_UNADJ",
csumvarnm = "cond_reserved",
cfilter = "RESERVCD == 1"
)$condsum
WYcond[WYcond$PLT_CN == 46792188020004,]
## -----------------------------------------------------------------------------
treesumdat1 <- datSumTree(
tree = WYtree,
plt = WYplt,
tsumvarlst = c("BA", "VOLCFNET"),
TPA = FALSE,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2
)
names(treesumdat1)
treesum1 <- treesumdat1$treedat
head(treesum1)
treesumdat1$sumvars
## -----------------------------------------------------------------------------
treesumdat2 <- datSumTree(
tree = WYtree,
plt = WYplt,
tsumvarlst = c("BA", "VOLCFNET"),
TPA = TRUE,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2
)
names(treesumdat2)
treesum2 <- treesumdat2$treedat
head(treesum2)
## -----------------------------------------------------------------------------
checkvars <- c("PLT_CN", "CONDID", "SUBP", "TREE", "STATUSCD", "SPCD", "DIA", "HT",
"BA", "VOLCFNET", "TPA_UNADJ")
testplt <- WYtree[WYtree$PLT_CN == 40404758010690, checkvars]
testplt
sum(testplt[testplt$STATUSCD == 1, "BA"], na.rm=TRUE)
sum(testplt[testplt$STATUSCD == 1, "BA"] * testplt[testplt$STATUSCD == 1, "TPA_UNADJ"], na.rm=TRUE)
treesum1[treesum1$CN == 40404758010690,]
treesum2[treesum2$CN == 40404758010690,]
## -----------------------------------------------------------------------------
treesumdat3 <- datSumTree(
tree = WYtree,
plt = WYplt,
tsumvarlst = c("DIA", "HT"),
TPA = FALSE,
tfun = mean,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2
)
names(treesumdat3)
treesum3 <- treesumdat3$treedat
head(treesum3)
## Test DIA and HT results for 1 plot
testplt
mean(testplt[testplt$STATUSCD == 1, "DIA"], na.rm=TRUE)
mean(testplt[testplt$STATUSCD == 1, "HT"], na.rm=TRUE)
treesum3[treesum3$CN == 40404758010690,]
## -----------------------------------------------------------------------------
treesumdat4a <- datSumTree(
tree = WYtree,
plt = WYplt,
tsumvarlst = "TPA_UNADJ",
TPA = TRUE,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2
)
names(treesumdat4a)
treesum4a <- treesumdat4a$treedat
head(treesum4a)
## -----------------------------------------------------------------------------
treesumdat4b <- datSumTree(
tree = WYtree,
plt = WYplt,
cond = WYcond,
tsumvarlst = "VOLCFNET",
tfilter = "STATUSCD == 1",
bycond = FALSE,
getadjplot = TRUE
)
names(treesumdat4b)
treesum4b <- treesumdat4b$treedat
head(treesum4b)
## -----------------------------------------------------------------------------
treesumdat4c <- datSumTree(
tree = WYtree,
plt = WYplt,
cond = WYcond,
tsumvarlst = "VOLCFNET",
tfilter = "STATUSCD == 1",
bycond = FALSE,
getadjplot = FALSE
)
treesum4c <- treesumdat4c$treedat
cn <- 40407815010690
WYcond[WYcond$PLT_CN == cn, ]
treesum4b[treesum4b$CN == cn, ]
treesum4c[treesum4c$CN == cn, ]
## -----------------------------------------------------------------------------
treesumdat5a <- datSumTree(
tree = WYtree,
plt = WYplt,
seed = WYseed,
tsumvarlst = "TPA_UNADJ",
TPA = TRUE,
addseed = TRUE,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2
)
names(treesumdat5a)
treesum5a <- treesumdat5a$treedat
head(treesum5a)
treesum5a[treesum5a$CN %in% cn,]
WYseed[WYseed$PLT_CN == cn,]
## -----------------------------------------------------------------------------
treesumdat5b <- datSumTree(
tree = WYtree,
plt = WYplt,
cond = WYcond,
seed = WYseed,
tsumvarlst = "TPA_UNADJ",
TPA = TRUE,
addseed = TRUE,
tfilter = "STATUSCD == 1",
bycond = FALSE,
tround = 2,
getadjplot =TRUE
)
names(treesumdat5b)
treesum5b <- treesumdat5b$treedat
head(treesum5b)
treesum5a[treesum5a$CN %in% cn,]
treesum5b[treesum5b$CN %in% cn,]
WYcond[WYcond$PLT_CN %in% cn,]
## -----------------------------------------------------------------------------
treedomBA <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "BA",
TPA = TRUE,
tdomtot = TRUE,
tdomtotnm = "BA_LIVE",
tdomprefix = "BA_LIVE",
tround = 2,
tfilter = "STATUSCD==1"
)
names(treedomBA)
tdomdat <- treedomBA$tdomdat
tdomvarlut <- treedomBA$tdomvarlut
tdomlst <- treedomBA$tdomlst
tdomtotnm <- treedomBA$tdomtotnm
head(tdomdat)
tdomvarlut
tdomlst
tdomtotnm
dim(WYplt)
dim(tdomdat)
## -----------------------------------------------------------------------------
treedomCNT <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 0,
tfilter = "STATUSCD==1"
)
names(treedomCNT)
tdomdat.tree <- treedomCNT$tdomdat
tdomvarlut <- treedomCNT$tdomvarlut
tdomlst <- treedomCNT$tdomlst
tdomtotnm <- treedomCNT$tdomtotnm
head(tdomdat.tree)
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(
cond = WYcond,
plt = WYplt,
seed = WYseed,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 0
)
names(treedomCNTs)
tdomdat.seed <- treedomCNTs$tdomdat
tdomvarlut <- treedomCNTs$tdomvarlut
tdomlst <- treedomCNTs$tdomlst
tdomtotnm <- treedomCNTs$tdomtotnm
head(tdomdat.seed)
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
seed = WYseed,
puniqueid = "CN",
bycond =FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 0,
tfilter = "STATUSCD==1",
addseed = TRUE
)
names(treedomCNTs)
tdomdat.treeseed <- treedomCNTs$tdomdat
tdomvarlut <- treedomCNTs$tdomvarlut
tdomlst <- treedomCNTs$tdomlst
tdomtotnm <- treedomCNTs$tdomtotnm
head(tdomdat.treeseed)
cn <- 40404730010690
tdomdat.tree[tdomdat.tree$CN == cn,]
tdomdat.seed[tdomdat.seed$CN == cn,]
tdomdat.treeseed[tdomdat.treeseed$CN == cn,]
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
seed = WYseed,
puniqueid ="CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
savedata = FALSE,
tfilter = "STATUSCD==1",
addseed = TRUE,
presence = TRUE
)
names(treedomCNTs)
tdomdat.pres <- treedomCNTs$tdomdat.pres
head(tdomdat.pres)
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(tree=WYtree, cond=WYcond, plt=WYplt, seed=WYseed,
puniqueid="CN", bycond=FALSE, tsumvar="PLT_CN", TPA=TRUE, tdomtot=TRUE,
tdomprefix="CNT", savedata=FALSE, tround=0, tfilter="STATUSCD==1",
addseed=TRUE, presence=TRUE, proportion=TRUE)
names(treedomCNTs)
tdomdat.pres <- treedomCNTs$tdomdat.pres
tdomdat.prop <- treedomCNTs$tdomdat.prop
head(tdomdat.pres)
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
seed = WYseed,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 0,
tfilter = "STATUSCD==1",
addseed = TRUE,
presence = TRUE,
proportion = TRUE,
cover = TRUE,
tdombarplot = TRUE
)
names(treedomCNTs)
tdomdat.pres <- treedomCNTs$tdomdat.pres
tdomdat.prop <- treedomCNTs$tdomdat.prop
tdomdat.cov <- treedomCNTs$tdomdat.cov
cn=40404742010690
tdomdat.tree[tdomdat.tree$CN == cn,]
tdomdat.seed[tdomdat.seed$CN == cn,]
tdomdat.treeseed[tdomdat.treeseed$CN == cn,]
tdomdat.pres[tdomdat.pres$CN == cn,]
tdomdat.prop[tdomdat.prop$CN == cn,]
tdomdat.cov[tdomdat.cov$CN == cn,]
## -----------------------------------------------------------------------------
treedomCNTs <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
seed = WYseed,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 0,
tfilter = "STATUSCD==1",
addseed = TRUE,
presence = TRUE,
proportion = TRUE,
tdombarplot = TRUE
)
names(treedomCNTs)
tdomdat.pres <- treedomCNTs$tdomdat.pres
tdomdat.prop <- treedomCNTs$tdomdat.prop
head(tdomdat.pres)
## -----------------------------------------------------------------------------
treedomBA <- datSumTreeDom(
tree = WYtree,
cond = WYcond,
plt = WYplt,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "BA",
TPA = TRUE,
tdomprefix = "BA",
tdomvarlst = 113,
tround = 2,
tfilter = "STATUSCD==1"
)
names(treedomBA)
ba.limber <- treedomBA$tdomdat
head(ba.limber)
## -----------------------------------------------------------------------------
## Total basal area per acre by species and diameter class
DIALUT <- FIESTAutils::ref_diacl2in[FIESTAutils::ref_diacl2in$MIN <= 37, ]
names(DIALUT)[names(DIALUT) == "MEANING"] <- "DIACL2IN"
## Append diameter classes to tree table
datlut <- datLUTclass(
x = WYtree,
xvar = "DIA",
LUT = DIALUT,
LUTclassnm = "DIACL2IN"
)
WYtree2 <- datlut$xLUT
## Species and diameter class
treedomDIACNTs <- datSumTreeDom(
tree = WYtree2,
cond = WYcond,
plt = WYplt,
puniqueid = "CN",
bycond = FALSE,
tsumvar = "PLT_CN",
TPA = TRUE,
tdomtot = TRUE,
tdomprefix = "CNT",
tround = 2,
tfilter = "STATUSCD==1 & DIA > 30",
presence = TRUE,
proportion = TRUE,
tdomvar2 = "DIACL2IN",
tdombarplot = TRUE
)
names(treedomDIACNTs)
tdomdat.pres <- treedomDIACNTs$tdomdat.pres
tdomdat.prop <- treedomDIACNTs$tdomdat.prop
head(tdomdat.pres)
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