R/dwmHelper.R
In hunter-stanke/rFIA_TX: Duplicate rFIA for TX
Defines functions
dwmHelper
dwmHelper2
dwmHelper1
dwmHelper1 <- function(x, plts, db, grpBy, byPlot){
## Selecting the plots for one county
db$PLOT <- plts[[x]]
## Carrying out filter across all tables
#db <- clipFIA(db, mostRecent = FALSE)
## Which grpByNames are in which table? Helps us subset below
grpP <- names(db$PLOT)[names(db$PLOT) %in% grpBy]
grpC <- names(db$COND)[names(db$COND) %in% grpBy & names(db$COND) %in% grpP == FALSE]
### Only joining tables necessary to produce plot level estimates, adjusted for non-response
data <- db$PLOT %>%
left_join(db$COND, by = c('PLT_CN')) %>%
left_join(db$COND_DWM_CALC, by = c('PLT_CN', 'CONDID')) #%>%
#filter(DIA >= 5)
## Comprehensive indicator function
data$aDI <- data$landD * data$aD_p * data$aD_c * data$sp
if (byPlot){
grpBy <- c('YEAR', grpBy, 'PLOT_STATUS_CD')
t <- data %>%
mutate(YEAR = INVYR) %>%
distinct(PLT_CN, CONDID, .keep_all = TRUE) %>%
group_by(.dots = grpBy, PLT_CN) %>%
summarize(VOL_1HR = sum(FWD_SM_VOLCF_ADJ * aDI, na.rm = TRUE),
VOL_10HR = sum(FWD_MD_VOLCF_ADJ * aDI, na.rm = TRUE),
VOL_100HR = sum(FWD_LG_VOLCF_ADJ * aDI, na.rm = TRUE),
VOL_1000HR = sum(CWD_VOLCF_ADJ * aDI, na.rm = TRUE),
VOL_PILE = sum(PILE_VOLCF_ADJ * aDI, na.rm = TRUE),
VOL = sum(VOL_1HR, VOL_10HR, VOL_100HR, VOL_1000HR, VOL_PILE, na.rm = TRUE),
BIO_DUFF = sum(DUFF_BIOMASS* aDI / 2000, na.rm = TRUE),
BIO_LITTER = sum(LITTER_BIOMASS * aDI / 2000, na.rm = TRUE),
BIO_1HR = sum(FWD_SM_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
BIO_10HR = sum(FWD_MD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
BIO_100HR = sum(FWD_LG_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
BIO_1000HR = sum(CWD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
BIO_PILE = sum(PILE_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
BIO = sum(BIO_LITTER, BIO_DUFF, BIO_1HR, BIO_10HR, BIO_100HR, BIO_1000HR, BIO_PILE, na.rm = TRUE),
CARB_DUFF = sum(DUFF_CARBON* aDI / 2000, na.rm = TRUE),
CARB_LITTER = sum(LITTER_CARBON * aDI / 2000, na.rm = TRUE),
CARB_1HR = sum(FWD_SM_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
CARB_10HR = sum(FWD_MD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
CARB_100HR = sum(FWD_LG_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
CARB_1000HR = sum(CWD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
CARB_PILE = sum(PILE_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
CARB = sum(CARB_LITTER, CARB_DUFF, CARB_1HR, CARB_10HR, CARB_100HR, CARB_1000HR, CARB_PILE, na.rm = TRUE))
} else {
# Compute estimates
t <- data %>%
distinct(STRATUM_CN, PLT_CN, CONDID, COND_STATUS_CD, .keep_all = TRUE) %>%
group_by(STRATUM_CN, PROP_BASIS, PLT_CN, .dots = grpBy) %>%
summarize(vsmPlot = sum(FWD_SM_VOLCF_ADJ * aDI, na.rm = TRUE),
vmdPlot = sum(FWD_MD_VOLCF_ADJ * aDI, na.rm = TRUE),
vlgPlot = sum(FWD_LG_VOLCF_ADJ * aDI, na.rm = TRUE),
vcPlot = sum(CWD_VOLCF_ADJ * aDI, na.rm = TRUE),
vpPlot = sum(PILE_VOLCF_ADJ * aDI, na.rm = TRUE),
vPlot = sum(vsmPlot, vmdPlot, vlgPlot, vcPlot, vpPlot, na.rm = TRUE),
bdPlot = sum(DUFF_BIOMASS* aDI / 2000, na.rm = TRUE),
blPlot = sum(LITTER_BIOMASS * aDI / 2000, na.rm = TRUE),
bsmPlot = sum(FWD_SM_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bmdPlot = sum(FWD_MD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
blgPlot = sum(FWD_LG_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bcPlot = sum(CWD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bpPlot = sum(PILE_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bPlot = sum(bdPlot, blPlot, bsmPlot, bmdPlot, blgPlot, bcPlot, bpPlot, na.rm = TRUE),
cdPlot = sum(DUFF_CARBON* aDI / 2000, na.rm = TRUE),
clPlot = sum(LITTER_CARBON * aDI / 2000, na.rm = TRUE),
csmPlot = sum(FWD_SM_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cmdPlot = sum(FWD_MD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
clgPlot = sum(FWD_LG_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
ccPlot = sum(CWD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cpPlot = sum(PILE_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cPlot = sum(cdPlot, clPlot, csmPlot, cmdPlot, clgPlot, ccPlot, cpPlot, na.rm = TRUE),
fa = sum(CONDPROP_UNADJ * aDI, na.rm = TRUE),
plotIn = ifelse(sum(aDI > 0, na.rm = TRUE), 1,0))
}
pltOut <- list(t = t)
return(pltOut)
}
dwmHelper2 <- function(x, popState, t, grpBy, method){
## DOES NOT MODIFY OUTSIDE ENVIRONMENT
if (str_to_upper(method) %in% c("SMA", 'EMA', 'LMA', 'ANNUAL')) {
grpBy <- c(grpBy, 'INVYR')
#aGrpBy <- c(aGrpBy, 'INVYR')
popState[[x]]$P2POINTCNT <- popState[[x]]$P2POINTCNT_INVYR
popState[[x]]$p2eu <- popState[[x]]$p2eu_INVYR
}
## Strata level estimates
tEst <- t %>%
## Rejoin with population tables
right_join(select(popState[[x]], -c(STATECD)), by = c('STRATUM_CN', 'PLT_CN')) %>%
mutate(
## AREA
aAdj = case_when(
## When NA, stay NA
is.na(PROP_BASIS) ~ NA_real_,
## If the proportion was measured for a macroplot,
## use the macroplot value
PROP_BASIS == 'MACR' ~ as.numeric(ADJ_FACTOR_MACR),
## Otherwise, use the subpplot value
PROP_BASIS == 'SUBP' ~ ADJ_FACTOR_SUBP),
fa = fa * aAdj) %>%
group_by(ESTN_UNIT_CN, ESTN_METHOD, STRATUM_CN, .dots = grpBy) %>%
summarize(a_t = length(unique(PLT_CN)) / first(P2POINTCNT),
aStrat = mean(fa * a_t, na.rm = TRUE),
vsmStrat = mean(vsmPlot * a_t, na.rm = TRUE),
vmdStrat = mean(vmdPlot * a_t, na.rm = TRUE),
vlgStrat = mean(vlgPlot * a_t, na.rm = TRUE),
vcStrat = mean(vcPlot * a_t, na.rm = TRUE),
vpStrat = mean(vpPlot * a_t, na.rm = TRUE),
vStrat = mean(vPlot * a_t, na.rm = TRUE),
bdStrat = mean(bdPlot * a_t, na.rm = TRUE),
blStrat = mean(blPlot * a_t, na.rm = TRUE),
bsmStrat = mean(bsmPlot * a_t, na.rm = TRUE),
bmdStrat = mean(bmdPlot * a_t, na.rm = TRUE),
blgStrat = mean(blgPlot * a_t, na.rm = TRUE),
bcStrat = mean(bcPlot * a_t, na.rm = TRUE),
bpStrat = mean(bpPlot * a_t, na.rm = TRUE),
bStrat = mean(bPlot * a_t, na.rm = TRUE),
cdStrat = mean(cdPlot * a_t, na.rm = TRUE),
clStrat = mean(clPlot * a_t, na.rm = TRUE),
csmStrat = mean(csmPlot * a_t, na.rm = TRUE),
cmdStrat = mean(cmdPlot * a_t, na.rm = TRUE),
clgStrat = mean(clgPlot * a_t, na.rm = TRUE),
ccStrat = mean(ccPlot * a_t, na.rm = TRUE),
cpStrat = mean(cpPlot * a_t, na.rm = TRUE),
cStrat = mean(cPlot * a_t, na.rm = TRUE),
plotIn = sum(plotIn, na.rm = TRUE),
n = n(),
## We don't want a vector of these values, since they are repeated
nh = first(P2POINTCNT),
a = first(AREA_USED),
w = first(P1POINTCNT) / first(P1PNTCNT_EU),
p2eu = first(p2eu),
ndif = nh - n,
# ## Strata level variances
av = stratVar(ESTN_METHOD, fa, aStrat, ndif, a, nh),
vsmVar = stratVar(ESTN_METHOD, vsmPlot, vsmStrat, ndif, a, nh),
vmdVar = stratVar(ESTN_METHOD, vmdPlot, vmdStrat, ndif, a, nh),
vlgVar = stratVar(ESTN_METHOD, vlgPlot, vlgStrat, ndif, a, nh),
vcVar = stratVar(ESTN_METHOD, vcPlot, vcStrat, ndif, a, nh),
vpVar = stratVar(ESTN_METHOD, vpPlot, vpStrat, ndif, a, nh),
vVar = stratVar(ESTN_METHOD, vPlot, vStrat, ndif, a, nh),
bdVar = stratVar(ESTN_METHOD, bdPlot, bdStrat, ndif, a, nh),
blVar = stratVar(ESTN_METHOD, blPlot, blStrat, ndif, a, nh),
bsmVar = stratVar(ESTN_METHOD, bsmPlot, bsmStrat, ndif, a, nh),
bmdVar = stratVar(ESTN_METHOD, bmdPlot, bmdStrat, ndif, a, nh),
blgVar = stratVar(ESTN_METHOD, blgPlot, blgStrat, ndif, a, nh),
bcVar = stratVar(ESTN_METHOD, bcPlot, bcStrat, ndif, a, nh),
bpVar = stratVar(ESTN_METHOD, bpPlot, bpStrat, ndif, a, nh),
bVar = stratVar(ESTN_METHOD, bPlot, bStrat, ndif, a, nh),
cdVar = stratVar(ESTN_METHOD, cdPlot, cdStrat, ndif, a, nh),
clVar = stratVar(ESTN_METHOD, clPlot, clStrat, ndif, a, nh),
csmVar = stratVar(ESTN_METHOD, csmPlot, csmStrat, ndif, a, nh),
cmdVar = stratVar(ESTN_METHOD, cmdPlot, cmdStrat, ndif, a, nh),
clgVar = stratVar(ESTN_METHOD, clgPlot, clgStrat, ndif, a, nh),
ccVar = stratVar(ESTN_METHOD, ccPlot, ccStrat, ndif, a, nh),
cpVar = stratVar(ESTN_METHOD, cpPlot, cpStrat, ndif, a, nh),
cVar = stratVar(ESTN_METHOD, cPlot, cStrat, ndif, a, nh),
# ## Strata level co-variances
cvEst_vsm = stratVar(ESTN_METHOD, vsmPlot, vsmStrat, ndif, a, nh, fa, aStrat),
cvEst_vmd = stratVar(ESTN_METHOD, vmdPlot, vmdStrat, ndif, a, nh, fa, aStrat),
cvEst_vlg = stratVar(ESTN_METHOD, vlgPlot, vlgStrat, ndif, a, nh, fa, aStrat),
cvEst_vc = stratVar(ESTN_METHOD, vcPlot, vcStrat, ndif, a, nh, fa, aStrat),
cvEst_vp = stratVar(ESTN_METHOD, vpPlot, vpStrat, ndif, a, nh, fa, aStrat),
cvEst_v = stratVar(ESTN_METHOD, vPlot, vStrat, ndif, a, nh, fa, aStrat),
cvEst_bd = stratVar(ESTN_METHOD, bdPlot, bdStrat, ndif, a, nh, fa, aStrat),
cvEst_bl = stratVar(ESTN_METHOD, blPlot, blStrat, ndif, a, nh, fa, aStrat),
cvEst_bsm = stratVar(ESTN_METHOD, bsmPlot, bsmStrat, ndif, a, nh, fa, aStrat),
cvEst_bmd = stratVar(ESTN_METHOD, bmdPlot, bmdStrat, ndif, a, nh, fa, aStrat),
cvEst_blg = stratVar(ESTN_METHOD, blgPlot, blgStrat, ndif, a, nh, fa, aStrat),
cvEst_bc = stratVar(ESTN_METHOD, bcPlot, bcStrat, ndif, a, nh, fa, aStrat),
cvEst_bp = stratVar(ESTN_METHOD, bpPlot, bpStrat, ndif, a, nh, fa, aStrat),
cvEst_b = stratVar(ESTN_METHOD, bPlot, bStrat, ndif, a, nh, fa, aStrat),
cvEst_cd = stratVar(ESTN_METHOD, cdPlot, cdStrat, ndif, a, nh, fa, aStrat),
cvEst_cl = stratVar(ESTN_METHOD, clPlot, clStrat, ndif, a, nh, fa, aStrat),
cvEst_csm = stratVar(ESTN_METHOD, csmPlot, csmStrat, ndif, a, nh, fa, aStrat),
cvEst_cmd = stratVar(ESTN_METHOD, cmdPlot, cmdStrat, ndif, a, nh, fa, aStrat),
cvEst_clg = stratVar(ESTN_METHOD, clgPlot, clgStrat, ndif, a, nh, fa, aStrat),
cvEst_cc = stratVar(ESTN_METHOD, ccPlot, ccStrat, ndif, a, nh, fa, aStrat),
cvEst_cp = stratVar(ESTN_METHOD, cpPlot, cpStrat, ndif, a, nh, fa, aStrat),
cvEst_c = stratVar(ESTN_METHOD, cPlot, cStrat, ndif, a, nh, fa, aStrat)) %>%
## Estimation unit
group_by(ESTN_UNIT_CN, .dots = grpBy) %>%
summarize(aEst = unitMean(ESTN_METHOD, a, nh, w, aStrat),
vsmEst = unitMean(ESTN_METHOD, a, nh, w, vsmStrat),
vmdEst = unitMean(ESTN_METHOD, a, nh, w, vmdStrat),
vlgEst = unitMean(ESTN_METHOD, a, nh, w, vlgStrat),
vcEst = unitMean(ESTN_METHOD, a, nh, w, vcStrat),
vpEst = unitMean(ESTN_METHOD, a, nh, w, vpStrat),
vEst = unitMean(ESTN_METHOD, a, nh, w, vStrat),
bdEst = unitMean(ESTN_METHOD, a, nh, w, bdStrat),
blEst = unitMean(ESTN_METHOD, a, nh, w, blStrat),
bsmEst = unitMean(ESTN_METHOD, a, nh, w, bsmStrat),
bmdEst = unitMean(ESTN_METHOD, a, nh, w, bmdStrat),
blgEst = unitMean(ESTN_METHOD, a, nh, w, blgStrat),
bcEst = unitMean(ESTN_METHOD, a, nh, w, bcStrat),
bpEst = unitMean(ESTN_METHOD, a, nh, w, bpStrat),
bEst = unitMean(ESTN_METHOD, a, nh, w, bStrat),
cdEst = unitMean(ESTN_METHOD, a, nh, w, cdStrat),
clEst = unitMean(ESTN_METHOD, a, nh, w, clStrat),
csmEst = unitMean(ESTN_METHOD, a, nh, w, csmStrat),
cmdEst = unitMean(ESTN_METHOD, a, nh, w, cmdStrat),
clgEst = unitMean(ESTN_METHOD, a, nh, w, clgStrat),
ccEst = unitMean(ESTN_METHOD, a, nh, w, ccStrat),
cpEst = unitMean(ESTN_METHOD, a, nh, w, cpStrat),
cEst = unitMean(ESTN_METHOD, a, nh, w, cStrat),
plotIn = sum(plotIn, na.rm = TRUE),
N = first(p2eu),
# Estimation of unit variance
aVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, av, aStrat, aEst),
vsmVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vsmVar, vsmStrat, vsmEst),
vmdVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vmdVar, vmdStrat, vmdEst),
vlgVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vlgVar, vlgStrat, vlgEst),
vcVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vcVar, vcStrat, vcEst),
vpVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vpVar, vpStrat, vpEst),
vVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vVar, vStrat, vEst),
bdVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bdVar, bdStrat, bdEst),
blVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, blVar, blStrat, blEst),
bsmVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bsmVar, bsmStrat, bsmEst),
bmdVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bmdVar, bmdStrat, bmdEst),
blgVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, blgVar, blgStrat, blgEst),
bcVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bcVar, bcStrat, bcEst),
bpVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bpVar, bpStrat, bpEst),
bVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bVar, bStrat, cbEst),
cdVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, cdVar, cdStrat, cdEst),
clVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, clVar, clStrat, clEst),
csmVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, csmVar, csmStrat, csmEst),
cmdVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, cmdVar, cmdStrat, cmdEst),
clgVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, clgVar, clgStrat, clgEst),
ccVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, ccVar, ccStrat, ccEst),
cpVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, cpVar, cpStrat, cpEst),
cVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, cVar, cStrat, cEst),
# Estimation of unit covariance
cvEst_vsm = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_vsm, vsmStrat, vsmEst, aStrat, aEst),
cvEst_vmd = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_vmd, vmdStrat, vmdEst, aStrat, aEst),
cvEst_vlg = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_vlg, vlgStrat, vlgEst, aStrat, aEst),
cvEst_vc = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_vc, vcStrat, vcEst, aStrat, aEst),
cvEst_vp = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_vp, vpStrat, vpEst, aStrat, aEst),
cvEst_v = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_v, vStrat, vEst, aStrat, aEst),
cvEst_bd = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bd, bdStrat, bdEst, aStrat, aEst),
cvEst_bl = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bl, blStrat, blEst, aStrat, aEst),
cvEst_bsm = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bsm, bsmStrat, bsmEst, aStrat, aEst),
cvEst_bmd = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bmd, bmdStrat, bmdEst, aStrat, aEst),
cvEst_blg = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_blg, blgStrat, blgEst, aStrat, aEst),
cvEst_bc = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bc, bcStrat, bcEst, aStrat, aEst),
cvEst_bp = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bp, bpStrat, bpEst, aStrat, aEst),
cvEst_b = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_b, bStrat, cbEst, aStrat, aEst),
cvEst_cd = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_cd, cdStrat, cdEst, aStrat, aEst),
cvEst_cl = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_cl, clStrat, clEst, aStrat, aEst),
cvEst_csm = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_csm, csmStrat, csmEst, aStrat, aEst),
cvEst_cmd = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_cmd, cmdStrat, cmdEst, aStrat, aEst),
cvEst_clg = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_clg, clgStrat, clgEst, aStrat, aEst),
cvEst_cc = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_cc, ccStrat, ccEst, aStrat, aEst),
cvEst_cp = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_cp, cpStrat, cpEst, aStrat, aEst),
cvEst_c = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_c, cStrat, cEst, aStrat, aEst))
out <- list(tEst = tEst)
return(out)
}
dwmHelper <- function(x, combos, data, grpBy, totals, SE){
# Update domain indicator for each each column speficed in grpBy
ad = 1
for (n in 1:ncol(combos[[x]])){
# Area domain indicator for each column in
aObs <- as.character(combos[[x]][[grpBy[n]]]) == as.character(data[[grpBy[n]]])
if (length(which(is.na(aObs))) == length(aObs)) aObs <- 1
ad <- data$aDI * aObs * ad
}
if(SE){
data$aDI <- ad
data$aDI[is.na(data$aDI)] <- 0
cwd <- data %>%
distinct(PLT_CN, CONDID, EVALID, COND_STATUS_CD, .keep_all = TRUE) %>%
group_by(ESTN_UNIT_CN, ESTN_METHOD, STRATUM_CN, PLT_CN) %>%
summarize(vsmPlot = sum(FWD_SM_VOLCF_ADJ * aDI, na.rm = TRUE),
vmdPlot = sum(FWD_MD_VOLCF_ADJ * aDI, na.rm = TRUE),
vlgPlot = sum(FWD_LG_VOLCF_ADJ * aDI, na.rm = TRUE),
vcPlot = sum(CWD_VOLCF_ADJ * aDI, na.rm = TRUE),
vpPlot = sum(PILE_VOLCF_ADJ * aDI, na.rm = TRUE),
vPlot = sum(vsmPlot, vmdPlot, vlgPlot, vcPlot, vpPlot, na.rm = TRUE),
bdPlot = sum(DUFF_BIOMASS* aDI / 2000, na.rm = TRUE),
blPlot = sum(LITTER_BIOMASS * aDI / 2000, na.rm = TRUE),
bsmPlot = sum(FWD_SM_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bmdPlot = sum(FWD_MD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
blgPlot = sum(FWD_LG_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bcPlot = sum(CWD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bpPlot = sum(PILE_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bPlot = sum(bdPlot, blPlot, bsmPlot, bmdPlot, blgPlot, bcPlot, bpPlot, na.rm = TRUE),
cdPlot = sum(DUFF_CARBON* aDI / 2000, na.rm = TRUE),
clPlot = sum(LITTER_CARBON * aDI / 2000, na.rm = TRUE),
csmPlot = sum(FWD_SM_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cmdPlot = sum(FWD_MD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
clgPlot = sum(FWD_LG_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
ccPlot = sum(CWD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cpPlot = sum(PILE_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cPlot = sum(cdPlot, clPlot, csmPlot, cmdPlot, clgPlot, ccPlot, cpPlot, na.rm = TRUE),
fa = sum(CONDPROP_UNADJ * aDI * aAdj, na.rm = TRUE),
plotIn = ifelse(sum(aDI > 0, na.rm = TRUE), 1,0),
a = first(AREA_USED),
p1EU = first(P1PNTCNT_EU),
p1 = first(P1POINTCNT),
p2 = first(P2POINTCNT)) %>%
# Stratum level
group_by(ESTN_UNIT_CN, ESTN_METHOD, STRATUM_CN) %>%
summarize(aStrat = mean(fa, na.rm = TRUE),
vsmStrat = mean(vsmPlot, na.rm = TRUE),
vmdStrat = mean(vmdPlot, na.rm = TRUE),
vlgStrat = mean(vlgPlot, na.rm = TRUE),
vcStrat = mean(vcPlot, na.rm = TRUE),
vpStrat = mean(vpPlot, na.rm = TRUE),
vStrat = mean(vPlot, na.rm = TRUE),
bdStrat = mean(bdPlot, na.rm = TRUE),
blStrat = mean(blPlot, na.rm = TRUE),
bsmStrat = mean(bsmPlot, na.rm = TRUE),
bmdStrat = mean(bmdPlot, na.rm = TRUE),
blgStrat = mean(blgPlot, na.rm = TRUE),
bcStrat = mean(bcPlot, na.rm = TRUE),
bpStrat = mean(bpPlot, na.rm = TRUE),
bStrat = mean(bPlot, na.rm = TRUE),
cdStrat = mean(cdPlot, na.rm = TRUE),
clStrat = mean(clPlot, na.rm = TRUE),
csmStrat = mean(csmPlot, na.rm = TRUE),
cmdStrat = mean(cmdPlot, na.rm = TRUE),
clgStrat = mean(clgPlot, na.rm = TRUE),
ccStrat = mean(ccPlot, na.rm = TRUE),
cpStrat = mean(cpPlot, na.rm = TRUE),
cStrat = mean(cPlot, na.rm = TRUE),
plotIn = sum(plotIn, na.rm = TRUE),
a = first(a),
w = first(p1) / first(p1EU), # Stratum weight
nh = first(p2), # Number plots in stratum
# Strata level variances
av = ifelse(first(ESTN_METHOD == 'simple'),
var(fa * first(a) / nh),
(sum(fa^2) - sum(nh * aStrat^2)) / (nh * (nh-1))),
vsmV = ifelse(first(ESTN_METHOD == 'simple'),
var(vsmPlot * first(a) / nh),
(sum(vsmPlot^2) - sum(nh * vsmStrat^2)) / (nh * (nh-1))), # Stratified and double cases
vmdV = ifelse(first(ESTN_METHOD == 'simple'),
var(vmdPlot * first(a) / nh),
(sum(vmdPlot^2) - sum(nh * vmdStrat^2)) / (nh * (nh-1))), # Stratified and double cases
vlgV = ifelse(first(ESTN_METHOD == 'simple'),
var(vlgPlot * first(a) / nh),
(sum(vlgPlot^2) - sum(nh * vlgStrat^2)) / (nh * (nh-1))), # Stratified and double cases
vcV = ifelse(first(ESTN_METHOD == 'simple'),
var(vcPlot * first(a) / nh),
(sum(vcPlot^2) - sum(nh * vcStrat^2)) / (nh * (nh-1))), # Stratified and double cases
vpV = ifelse(first(ESTN_METHOD == 'simple'),
var(vpPlot * first(a) / nh),
(sum(vpPlot^2) - sum(nh * vpStrat^2)) / (nh * (nh-1))), # Stratified and double cases
vV = ifelse(first(ESTN_METHOD == 'simple'),
var(vPlot * first(a) / nh),
(sum(vPlot^2) - sum(nh * vStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bdV = ifelse(first(ESTN_METHOD == 'simple'),
var(bdPlot * first(a) / nh),
(sum(bdPlot^2) - sum(nh * bdStrat^2)) / (nh * (nh-1))), # Stratified and double cases
blV = ifelse(first(ESTN_METHOD == 'simple'),
var(blPlot * first(a) / nh),
(sum(blPlot^2) - sum(nh * blStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bsmV = ifelse(first(ESTN_METHOD == 'simple'),
var(bsmPlot * first(a) / nh),
(sum(bsmPlot^2) - sum(nh * bsmStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bmdV = ifelse(first(ESTN_METHOD == 'simple'),
var(bmdPlot * first(a) / nh),
(sum(bmdPlot^2) - sum(nh * bmdStrat^2)) / (nh * (nh-1))), # Stratified and double cases
blgV = ifelse(first(ESTN_METHOD == 'simple'),
var(blgPlot * first(a) / nh),
(sum(blgPlot^2) - sum(nh * blgStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bcV = ifelse(first(ESTN_METHOD == 'simple'),
var(bcPlot * first(a) / nh),
(sum(bcPlot^2) - sum(nh * bcStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bpV = ifelse(first(ESTN_METHOD == 'simple'),
var(bpPlot * first(a) / nh),
(sum(bpPlot^2) - sum(nh * bpStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bV = ifelse(first(ESTN_METHOD == 'simple'),
var(bPlot * first(a) / nh),
(sum(bPlot^2) - sum(nh * bStrat^2)) / (nh * (nh-1))), # Stratified and double cases
cdV = ifelse(first(ESTN_METHOD == 'simple'),
var(cdPlot * first(a) / nh),
(sum(cdPlot^2) - sum(nh * cdStrat^2)) / (nh * (nh-1))), # Stratified and double cases
clV = ifelse(first(ESTN_METHOD == 'simple'),
var(clPlot * first(a) / nh),
(sum(clPlot^2) - sum(nh * clStrat^2)) / (nh * (nh-1))), # Stratified and double cases
csmV = ifelse(first(ESTN_METHOD == 'simple'),
var(csmPlot * first(a) / nh),
(sum(csmPlot^2) - sum(nh * csmStrat^2)) / (nh * (nh-1))), # Stratified and double cases
cmdV = ifelse(first(ESTN_METHOD == 'simple'),
var(cmdPlot * first(a) / nh),
(sum(cmdPlot^2) - sum(nh * cmdStrat^2)) / (nh * (nh-1))), # Stratified and double cases
clgV = ifelse(first(ESTN_METHOD == 'simple'),
var(clgPlot * first(a) / nh),
(sum(clgPlot^2) - sum(nh * clgStrat^2)) / (nh * (nh-1))), # Stratified and double cases
ccV = ifelse(first(ESTN_METHOD == 'simple'),
var(ccPlot * first(a) / nh),
(sum(ccPlot^2) - sum(nh * ccStrat^2)) / (nh * (nh-1))), # Stratified and double cases
cpV = ifelse(first(ESTN_METHOD == 'simple'),
var(cpPlot * first(a) / nh),
(sum(cpPlot^2) - sum(nh * cpStrat^2)) / (nh * (nh-1))), # Stratified and double cases
cV = ifelse(first(ESTN_METHOD == 'simple'),
var(cPlot * first(a) / nh),
(sum(cPlot^2) - sum(nh * cStrat^2)) / (nh * (nh-1))), # Stratified and double cases
# Strata level covariances
vsmCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vsmPlot),
(sum(fa*vsmPlot) - sum(nh * aStrat *vsmStrat)) / (nh * (nh-1))), # Stratified and double cases
vmdCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vmdPlot),
(sum(fa*vmdPlot) - sum(nh * aStrat *vmdStrat)) / (nh * (nh-1))), # Stratified and double cases
vlgCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vlgPlot),
(sum(fa*vlgPlot) - sum(nh * aStrat *vlgStrat)) / (nh * (nh-1))), # Stratified and double cases
vcCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vcPlot),
(sum(fa*vcPlot) - sum(nh * aStrat *vcStrat)) / (nh * (nh-1))), # Stratified and double cases
vpCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vpPlot),
(sum(fa*vpPlot) - sum(nh * aStrat *vpStrat)) / (nh * (nh-1))), # Stratified and double cases
vCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vPlot),
(sum(fa*vPlot) - sum(nh * aStrat *vStrat)) / (nh * (nh-1))), # Stratified and double cases
bdCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bdPlot),
(sum(fa*bdPlot) - sum(nh * aStrat *bdStrat)) / (nh * (nh-1))), # Stratified and double cases
blCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,blPlot),
(sum(fa*blPlot) - sum(nh * aStrat *blStrat)) / (nh * (nh-1))), # Stratified and double cases
bsmCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bsmPlot),
(sum(fa*bsmPlot) - sum(nh * aStrat *bsmStrat)) / (nh * (nh-1))), # Stratified and double cases
bmdCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bmdPlot),
(sum(fa*bmdPlot) - sum(nh * aStrat *bmdStrat)) / (nh * (nh-1))), # Stratified and double cases
blgCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,blgPlot),
(sum(fa*blgPlot) - sum(nh * aStrat *blgStrat)) / (nh * (nh-1))), # Stratified and double cases
bcCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bcPlot),
(sum(fa*bcPlot) - sum(nh * aStrat *bcStrat)) / (nh * (nh-1))), # Stratified and double cases
bpCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bpPlot),
(sum(fa*bpPlot) - sum(nh * aStrat *bpStrat)) / (nh * (nh-1))), # Stratified and double cases
bCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bPlot),
(sum(fa*bPlot) - sum(nh * aStrat *bStrat)) / (nh * (nh-1))), # Stratified and double cases
cdCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,cdPlot),
(sum(fa*cdPlot) - sum(nh * aStrat *cdStrat)) / (nh * (nh-1))), # Stratified and double cases
clCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,blPlot),
(sum(fa*clPlot) - sum(nh * aStrat *clStrat)) / (nh * (nh-1))), # Stratified and double cases
csmCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,csmPlot),
(sum(fa*csmPlot) - sum(nh * aStrat *csmStrat)) / (nh * (nh-1))), # Stratified and double cases
cmdCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,cmdPlot),
(sum(fa*cmdPlot) - sum(nh * aStrat *cmdStrat)) / (nh * (nh-1))), # Stratified and double cases
clgCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,clgPlot),
(sum(fa*clgPlot) - sum(nh * aStrat *clgStrat)) / (nh * (nh-1))), # Stratified and double cases
ccCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,ccPlot),
(sum(fa*ccPlot) - sum(nh * aStrat *ccStrat)) / (nh * (nh-1))), # Stratified and double cases
cpCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,cpPlot),
(sum(fa*cpPlot) - sum(nh * aStrat *cpStrat)) / (nh * (nh-1))), # Stratified and double cases
cCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,cPlot),
(sum(fa*cPlot) - sum(nh * aStrat *cStrat)) / (nh * (nh-1)))) %>% # Stratified and double cases
## Estimation unit level
group_by(ESTN_UNIT_CN) %>%
summarize(aEst = unitMean(ESTN_METHOD, a, nh, w, aStrat),
vsmEst = unitMean(ESTN_METHOD, a, nh, w, vsmStrat),
vmdEst = unitMean(ESTN_METHOD, a, nh, w, vmdStrat),
vlgEst = unitMean(ESTN_METHOD, a, nh, w, vlgStrat),
vcEst = unitMean(ESTN_METHOD, a, nh, w, vcStrat),
vpEst = unitMean(ESTN_METHOD, a, nh, w, vpStrat),
vEst = unitMean(ESTN_METHOD, a, nh, w, vStrat),
bdEst = unitMean(ESTN_METHOD, a, nh, w, bdStrat),
blEst = unitMean(ESTN_METHOD, a, nh, w, blStrat),
bsmEst = unitMean(ESTN_METHOD, a, nh, w, bsmStrat),
bmdEst = unitMean(ESTN_METHOD, a, nh, w, bmdStrat),
blgEst = unitMean(ESTN_METHOD, a, nh, w, blgStrat),
bcEst = unitMean(ESTN_METHOD, a, nh, w, bcStrat),
bpEst = unitMean(ESTN_METHOD, a, nh, w, bpStrat),
bEst = unitMean(ESTN_METHOD, a, nh, w, bStrat),
cdEst = unitMean(ESTN_METHOD, a, nh, w, cdStrat),
clEst = unitMean(ESTN_METHOD, a, nh, w, clStrat),
csmEst = unitMean(ESTN_METHOD, a, nh, w, csmStrat),
cmdEst = unitMean(ESTN_METHOD, a, nh, w, cmdStrat),
clgEst = unitMean(ESTN_METHOD, a, nh, w, clgStrat),
ccEst = unitMean(ESTN_METHOD, a, nh, w, ccStrat),
cpEst = unitMean(ESTN_METHOD, a, nh, w, cpStrat),
cEst = unitMean(ESTN_METHOD, a, nh, w, cStrat),
plotIn = sum(plotIn, na.rm = TRUE),
# Estimation of unit variance
aVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, av, aStrat, aEst),
vsmVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vsmV, vsmStrat, vsmEst),
vmdVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vmdV, vmdStrat, vmdEst),
vlgVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vlgV, vlgStrat, vlgEst),
vcVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vcV, vcStrat, vcEst),
vpVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vpV, vpStrat, vpEst),
vVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vV, vStrat, vEst),
bdVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bdV, bdStrat, bdEst),
blVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, blV, blStrat, blEst),
bsmVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bsmV, bsmStrat, bsmEst),
bmdVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bmdV, bmdStrat, bmdEst),
blgVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, blgV, blgStrat, blgEst),
bcVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bcV, bcStrat, bcEst),
bpVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bpV, bpStrat, bpEst),
bVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bV, bStrat, cbEst),
cdVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, cdV, cdStrat, cdEst),
clVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, clV, clStrat, clEst),
csmVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, csmV, csmStrat, csmEst),
cmdVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, cmdV, cmdStrat, cmdEst),
clgVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, clgV, clgStrat, clgEst),
ccVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, ccV, ccStrat, ccEst),
cpVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, cpV, cpStrat, cpEst),
cVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, cV, cStrat, cEst),
# Estimation of unit covariance
vsmCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vsmCV, vsmStrat, vsmEst, aStrat, aEst),
vmdCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vmdCV, vmdStrat, vmdEst, aStrat, aEst),
vlgCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vlgCV, vlgStrat, vlgEst, aStrat, aEst),
vcCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vcCV, vcStrat, vcEst, aStrat, aEst),
vpCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vpCV, vpStrat, vpEst, aStrat, aEst),
vCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vCV, vStrat, vEst, aStrat, aEst),
bdCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bdCV, bdStrat, bdEst, aStrat, aEst),
blCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, blCV, blStrat, blEst, aStrat, aEst),
bsmCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bsmCV, bsmStrat, bsmEst, aStrat, aEst),
bmdCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bmdCV, bmdStrat, bmdEst, aStrat, aEst),
blgCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, blgCV, blgStrat, blgEst, aStrat, aEst),
bcCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bcCV, bcStrat, bcEst, aStrat, aEst),
bpCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bpCV, bpStrat, bpEst, aStrat, aEst),
bCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bCV, bStrat, cbEst, aStrat, aEst),
cdCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, cdCV, cdStrat, cdEst, aStrat, aEst),
clCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, clCV, clStrat, clEst, aStrat, aEst),
csmCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, csmCV, csmStrat, csmEst, aStrat, aEst),
cmdCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, cmdCV, cmdStrat, cmdEst, aStrat, aEst),
clgCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, clgCV, clgStrat, clgEst, aStrat, aEst),
ccCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, ccCV, ccStrat, ccEst, aStrat, aEst),
cpCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, cpCV, cpStrat, cpEst, aStrat, aEst),
cCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, cCV, cStrat, cEst, aStrat, aEst)) %>%
# Compute totals
summarize(AREA_TOTAL = sum(aEst, na.rm = TRUE),
VOL_DUFF = NA,
VOL_LITTER = NA,
VOL_1HR = sum(vsmEst, na.rm = TRUE),
VOL_10HR = sum(vmdEst, na.rm = TRUE),
VOL_100HR = sum(vlgEst, na.rm = TRUE),
VOL_1000HR = sum(vcEst, na.rm = TRUE),
VOL_PILE = sum(vpEst, na.rm = TRUE),
VOL = sum(vEst, na.rm = TRUE),
BIO_DUFF = sum(bdEst, na.rm = TRUE),
BIO_LITTER = sum(blEst, na.rm = TRUE),
BIO_1HR = sum(bsmEst, na.rm = TRUE),
BIO_10HR = sum(bmdEst, na.rm = TRUE),
BIO_100HR = sum(blgEst, na.rm = TRUE),
BIO_1000HR = sum(bcEst, na.rm = TRUE),
BIO_PILE = sum(bpEst, na.rm = TRUE),
BIO = sum(bEst, na.rm = TRUE),
CARB_DUFF = sum(cdEst, na.rm = TRUE),
CARB_LITTER = sum(clEst, na.rm = TRUE),
CARB_1HR = sum(csmEst, na.rm = TRUE),
CARB_10HR = sum(cmdEst, na.rm = TRUE),
CARB_100HR = sum(clgEst, na.rm = TRUE),
CARB_1000HR = sum(ccEst, na.rm = TRUE),
CARB_PILE = sum(cpEst, na.rm = TRUE),
CARB = sum(cEst, na.rm = TRUE),
nPlots = sum(plotIn, na.rm = TRUE),
# Per Acre
VOL_DUFF_ACRE = NA,
VOL_LITTER_ACRE = NA,
VOL_1HR_ACRE = VOL_1HR / AREA_TOTAL,
VOL_10HR_ACRE = VOL_10HR / AREA_TOTAL,
VOL_100HR_ACRE = VOL_100HR / AREA_TOTAL,
VOL_1000HR_ACRE = VOL_1000HR / AREA_TOTAL,
VOL_PILE_ACRE = VOL_PILE / AREA_TOTAL,
VOL_ACRE = VOL / AREA_TOTAL,
BIO_DUFF_ACRE = BIO_DUFF / AREA_TOTAL,
BIO_LITTER_ACRE = BIO_LITTER / AREA_TOTAL,
BIO_1HR_ACRE = BIO_1HR / AREA_TOTAL,
BIO_10HR_ACRE = BIO_10HR / AREA_TOTAL,
BIO_100HR_ACRE = BIO_100HR / AREA_TOTAL,
BIO_1000HR_ACRE = BIO_1000HR / AREA_TOTAL,
BIO_PILE_ACRE = BIO_PILE / AREA_TOTAL,
BIO_ACRE = BIO / AREA_TOTAL,
CARB_DUFF_ACRE = CARB_DUFF / AREA_TOTAL,
CARB_LITTER_ACRE = CARB_LITTER / AREA_TOTAL,
CARB_1HR_ACRE = CARB_1HR / AREA_TOTAL,
CARB_10HR_ACRE = CARB_10HR / AREA_TOTAL,
CARB_100HR_ACRE = CARB_100HR / AREA_TOTAL,
CARB_1000HR_ACRE = CARB_1000HR / AREA_TOTAL,
CARB_PILE_ACRE = CARB_PILE / AREA_TOTAL,
CARB_ACRE = CARB / AREA_TOTAL,
# Sampling Errors totals
AREA_TOTAL_SE = sqrt(sum(aVar, na.rm = TRUE)) / AREA_TOTAL * 100,
VOL_DUFF_SE = NA,
VOL_LITTER_SE = NA,
VOL_1HR_SE = sqrt(sum(vsmVar, na.rm = TRUE)) / VOL_1HR * 100,
VOL_10HR_SE = sqrt(sum(vmdVar, na.rm = TRUE)) / VOL_10HR * 100,
VOL_100HR_SE = sqrt(sum(vlgVar, na.rm = TRUE)) / VOL_100HR * 100,
VOL_1000HR_SE = sqrt(sum(vcVar, na.rm = TRUE)) / VOL_1000HR * 100,
VOL_PILE_SE = sqrt(sum(vpVar, na.rm = TRUE)) / VOL_PILE * 100,
VOL_SE = sqrt(sum(vVar, na.rm = TRUE)) / VOL * 100,
BIO_DUFF_SE = sqrt(sum(bdVar, na.rm = TRUE)) / BIO_DUFF * 100,
BIO_LITTER_SE = sqrt(sum(blVar, na.rm = TRUE)) / BIO_LITTER * 100,
BIO_1HR_SE = sqrt(sum(bsmVar, na.rm = TRUE)) / BIO_1HR * 100,
BIO_10HR_SE = sqrt(sum(bmdVar, na.rm = TRUE)) / BIO_10HR * 100,
BIO_100HR_SE = sqrt(sum(blgVar, na.rm = TRUE)) / BIO_100HR * 100,
BIO_1000HR_SE = sqrt(sum(bcVar, na.rm = TRUE)) / BIO_1000HR * 100,
BIO_PILE_SE = sqrt(sum(bpVar, na.rm = TRUE)) / BIO_PILE * 100,
BIO_SE = sqrt(sum(bVar, na.rm = TRUE)) / BIO * 100,
CARB_DUFF_SE = sqrt(sum(cdVar, na.rm = TRUE)) / CARB_DUFF * 100,
CARB_LITTER_SE = sqrt(sum(clVar, na.rm = TRUE)) / CARB_LITTER * 100,
CARB_1HR_SE = sqrt(sum(csmVar, na.rm = TRUE)) / CARB_1HR * 100,
CARB_10HR_SE = sqrt(sum(cmdVar, na.rm = TRUE)) / CARB_10HR * 100,
CARB_100HR_SE = sqrt(sum(clgVar, na.rm = TRUE)) / CARB_100HR * 100,
CARB_1000HR_SE = sqrt(sum(ccVar, na.rm = TRUE)) / CARB_1000HR * 100,
CARB_PILE_SE = sqrt(sum(cpVar, na.rm = TRUE)) / CARB_PILE * 100,
CARB_SE = sqrt(sum(cVar, na.rm = TRUE)) / CARB * 100,
# Per Acre variances
vsmVar = (1/AREA_TOTAL^2) * (sum(vsmVar, na.rm = TRUE) + (VOL_1HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_1HR_ACRE * sum(vsmCV, na.rm = TRUE))),
vmdVar = (1/AREA_TOTAL^2) * (sum(vmdVar, na.rm = TRUE) + (VOL_10HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_10HR_ACRE * sum(vmdCV, na.rm = TRUE))),
vlgVar = (1/AREA_TOTAL^2) * (sum(vlgVar, na.rm = TRUE) + (VOL_100HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_100HR_ACRE * sum(vlgCV, na.rm = TRUE))),
vcVar = (1/AREA_TOTAL^2) * (sum(vcVar, na.rm = TRUE) + (VOL_1000HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_1000HR_ACRE *sum(vcCV, na.rm = TRUE))),
vpVar = (1/AREA_TOTAL^2) * (sum(vpVar, na.rm = TRUE) + (VOL_PILE_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_PILE_ACRE * sum(vpCV, na.rm = TRUE))),
vVar = (1/AREA_TOTAL^2) * (sum(vVar, na.rm = TRUE) + (VOL_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_ACRE * sum(vCV, na.rm = TRUE))),
bdVar = (1/AREA_TOTAL^2) * (sum(bdVar, na.rm = TRUE) + (BIO_DUFF_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_DUFF_ACRE * sum(bdCV, na.rm = TRUE))),
blVar = (1/AREA_TOTAL^2) * (sum(blVar, na.rm = TRUE) + (BIO_LITTER_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_LITTER_ACRE * sum(blCV, na.rm = TRUE))),
bsmVar = (1/AREA_TOTAL^2) * (sum(bsmVar, na.rm = TRUE) + (BIO_1HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_1HR_ACRE * sum(bsmCV, na.rm = TRUE))),
bmdVar = (1/AREA_TOTAL^2) * (sum(bmdVar, na.rm = TRUE) + (BIO_10HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_10HR_ACRE * sum(bmdCV, na.rm = TRUE))),
blgVar = (1/AREA_TOTAL^2) * (sum(blgVar, na.rm = TRUE) + (BIO_100HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_100HR_ACRE * sum(blgCV, na.rm = TRUE))),
bcVar = (1/AREA_TOTAL^2) * (sum(bcVar, na.rm = TRUE) + (BIO_1000HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_1000HR_ACRE * sum(bcCV, na.rm = TRUE))),
bpVar = (1/AREA_TOTAL^2) * (sum(bpVar, na.rm = TRUE) + (BIO_PILE_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_PILE_ACRE * sum(bpCV, na.rm = TRUE))),
bVar = (1/AREA_TOTAL^2) * (sum(bVar, na.rm = TRUE) + (BIO_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_ACRE * sum(bCV, na.rm = TRUE))),
cdVar = (1/AREA_TOTAL^2) * (sum(cdVar, na.rm = TRUE) + (CARB_DUFF_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_DUFF_ACRE * sum(cdCV, na.rm = TRUE))),
clVar = (1/AREA_TOTAL^2) * (sum(clVar, na.rm = TRUE) + (CARB_LITTER_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_LITTER_ACRE * sum(clCV, na.rm = TRUE))),
csmVar = (1/AREA_TOTAL^2) * (sum(csmVar, na.rm = TRUE) + (CARB_1HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_1HR_ACRE * sum(csmCV, na.rm = TRUE))),
cmdVar = (1/AREA_TOTAL^2) * (sum(cmdVar, na.rm = TRUE) + (CARB_10HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_10HR_ACRE * sum(cmdCV, na.rm = TRUE))),
clgVar = (1/AREA_TOTAL^2) * (sum(clgVar, na.rm = TRUE) + (CARB_100HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_100HR_ACRE * sum(clgCV, na.rm = TRUE))),
ccVar = (1/AREA_TOTAL^2) * (sum(ccVar, na.rm = TRUE) + (CARB_1000HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_1000HR_ACRE * sum(ccCV, na.rm = TRUE))),
cpVar = (1/AREA_TOTAL^2) * (sum(cpVar, na.rm = TRUE) + (CARB_PILE_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_PILE_ACRE * sum(cpCV, na.rm = TRUE))),
cVar = (1/AREA_TOTAL^2) * (sum(cVar, na.rm = TRUE) + (CARB_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_ACRE * sum(cCV, na.rm = TRUE))),
# Per acre sampling errors
VOL_DUFF_ACRE_SE = NA,
VOL_LITTER_ACRE_SE = NA,
VOL_1HR_ACRE_SE = sqrt(sum(vsmVar, na.rm = TRUE)) / VOL_1HR_ACRE * 100,
VOL_10HR_ACRE_SE = sqrt(sum(vmdVar, na.rm = TRUE)) / VOL_10HR_ACRE * 100,
VOL_100HR_ACRE_SE = sqrt(sum(vlgVar, na.rm = TRUE)) / VOL_100HR_ACRE * 100,
VOL_1000HR_ACRE_SE = sqrt(sum(vcVar, na.rm = TRUE)) / VOL_1000HR_ACRE * 100,
VOL_PILE_ACRE_SE = sqrt(sum(vpVar, na.rm = TRUE)) / VOL_PILE_ACRE * 100,
VOL_ACRE_SE = sqrt(sum(vVar, na.rm = TRUE)) / VOL_ACRE * 100,
BIO_DUFF_ACRE_SE = sqrt(sum(bdVar, na.rm = TRUE)) / BIO_DUFF_ACRE * 100,
BIO_LITTER_ACRE_SE = sqrt(sum(blVar, na.rm = TRUE)) / BIO_LITTER_ACRE * 100,
BIO_1HR_ACRE_SE = sqrt(sum(bsmVar, na.rm = TRUE)) / BIO_1HR_ACRE * 100,
BIO_10HR_ACRE_SE = sqrt(sum(bmdVar, na.rm = TRUE)) / BIO_10HR_ACRE * 100,
BIO_100HR_ACRE_SE = sqrt(sum(blgVar, na.rm = TRUE)) / BIO_100HR_ACRE * 100,
BIO_1000HR_ACRE_SE = sqrt(sum(bcVar, na.rm = TRUE)) / BIO_1000HR_ACRE * 100,
BIO_PILE_ACRE_SE = sqrt(sum(bpVar, na.rm = TRUE)) / BIO_PILE_ACRE * 100,
BIO_ACRE_SE = sqrt(sum(bVar, na.rm = TRUE)) / BIO_ACRE * 100,
CARB_DUFF_ACRE_SE = sqrt(sum(cdVar, na.rm = TRUE)) / CARB_DUFF_ACRE * 100,
CARB_LITTER_ACRE_SE = sqrt(sum(clVar, na.rm = TRUE)) / CARB_LITTER_ACRE * 100,
CARB_1HR_ACRE_SE = sqrt(sum(csmVar, na.rm = TRUE)) / CARB_1HR_ACRE * 100,
CARB_10HR_ACRE_SE = sqrt(sum(cmdVar, na.rm = TRUE)) / CARB_10HR_ACRE * 100,
CARB_100HR_ACRE_SE = sqrt(sum(clgVar, na.rm = TRUE)) / CARB_100HR_ACRE * 100,
CARB_1000HR_ACRE_SE = sqrt(sum(ccVar, na.rm = TRUE)) / CARB_1000HR_ACRE * 100,
CARB_PILE_ACRE_SE = sqrt(sum(cpVar, na.rm = TRUE)) / CARB_PILE_ACRE * 100,
CARB_ACRE_SE = sqrt(sum(cVar, na.rm = TRUE)) / CARB_ACRE * 100)
if (totals) {
cwd <- cwd %>%
select(names(cwd)[str_detect(names(cwd), 'Var', negate = TRUE)], nPlots)
} else {
cwd <- cwd %>%
select(names(cwd)[str_detect(names(cwd), 'Var', negate = TRUE) & str_detect(names(cwd), 'ACRE')], nPlots)
}
# Rejoin w/ groupby names
cwd <- data.frame(combos[[x]], cwd)
} else {
### BELOW DOES NOT PRODUCE SAMPLING ERRORS, use EXPNS instead (much quicker)
cwd <- data %>%
filter(EVAL_TYP == 'EXPDWM') %>%
distinct(ESTN_UNIT_CN, STRATUM_CN, PLT_CN, CND_CN, .keep_all = TRUE) %>%
group_by(.dots = grpBy, PLT_CN) %>%
summarize(VOL_1HR = sum(FWD_SM_VOLCF_ADJ * aDI * EXPNS, na.rm = TRUE),
VOL_10HR = sum(FWD_MD_VOLCF_ADJ * aDI * EXPNS, na.rm = TRUE),
VOL_100HR = sum(FWD_LG_VOLCF_ADJ * aDI * EXPNS, na.rm = TRUE),
VOL_1000HR = sum(CWD_VOLCF_ADJ * aDI * EXPNS, na.rm = TRUE),
VOL_PILE = sum(PILE_VOLCF_ADJ * aDI * EXPNS, na.rm = TRUE),
VOL = sum(VOL_1HR, VOL_10HR, VOL_100HR, VOL_1000HR, VOL_PILE, na.rm = TRUE),
BIO_DUFF = sum(DUFF_BIOMASS* aDI * EXPNS / 2000, na.rm = TRUE),
BIO_LITTER = sum(LITTER_BIOMASS * aDI * EXPNS / 2000, na.rm = TRUE),
BIO_1HR = sum(FWD_SM_DRYBIO_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
BIO_10HR = sum(FWD_MD_DRYBIO_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
BIO_100HR = sum(FWD_LG_DRYBIO_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
BIO_1000HR = sum(CWD_DRYBIO_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
BIO_PILE = sum(PILE_DRYBIO_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
BIO = sum(BIO_DUFF, BIO_LITTER, BIO_1HR, BIO_10HR, BIO_100HR, BIO_1000HR, BIO_PILE, na.rm = TRUE),
CARB_DUFF = sum(DUFF_CARBON* aDI * EXPNS / 2000, na.rm = TRUE),
CARB_LITTER = sum(LITTER_CARBON * aDI * EXPNS / 2000, na.rm = TRUE),
CARB_1HR = sum(FWD_SM_CARBON_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
CARB_10HR = sum(FWD_MD_CARBON_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
CARB_100HR = sum(FWD_LG_CARBON_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
CARB_1000HR = sum(CWD_CARBON_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
CARB_PILE = sum(PILE_CARBON_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
CARB = sum(CARB_DUFF, CARB_LITTER, CARB_1HR, CARB_10HR, CARB_100HR, CARB_1000HR, CARB_PILE, na.rm = TRUE),
fa = sum(CONDPROP_UNADJ * aDI * aAdj * EXPNS, na.rm = TRUE),
plotIn = ifelse(sum(aDI > 0, na.rm = TRUE), 1,0)) %>%
group_by(.dots = grpBy) %>%
summarize(AREA_TOTAL = sum(fa, na.rm = TRUE),
VOL_DUFF = NA,
VOL_LITTER = NA,
VOL_1HR = sum(VOL_1HR, na.rm = TRUE),
VOL_10HR = sum(VOL_10HR, na.rm = TRUE),
VOL_100HR = sum(VOL_100HR, na.rm = TRUE),
VOL_1000HR = sum(VOL_1000HR, na.rm = TRUE),
VOL_PILE = sum(VOL_PILE, na.rm = TRUE),
VOL = sum(VOL, na.rm = TRUE),
BIO_DUFF = sum(BIO_DUFF, na.rm = TRUE),
BIO_LITTER = sum(BIO_LITTER, na.rm = TRUE),
BIO_1HR = sum(BIO_1HR, na.rm = TRUE),
BIO_10HR = sum(BIO_10HR, na.rm = TRUE),
BIO_100HR = sum(BIO_100HR, na.rm = TRUE),
BIO_1000HR = sum(BIO_1000HR, na.rm = TRUE),
BIO_PILE = sum(BIO_PILE, na.rm = TRUE),
BIO = sum(BIO, na.rm = TRUE),
CARB_DUFF = sum(CARB_DUFF, na.rm = TRUE),
CARB_LITTER = sum(CARB_LITTER, na.rm = TRUE),
CARB_1HR = sum(CARB_1HR, na.rm = TRUE),
CARB_10HR = sum(CARB_10HR, na.rm = TRUE),
CARB_100HR = sum(CARB_100HR, na.rm = TRUE),
CARB_1000HR = sum(CARB_1000HR, na.rm = TRUE),
CARB_PILE = sum(CARB_PILE, na.rm = TRUE),
CARB = sum(CARB, na.rm = TRUE),
VOL_DUFF_ACRE = NA,
VOL_LITTER_ACRE = NA,
VOL_1HR_ACRE = VOL_1HR / AREA_TOTAL,
VOL_10HR_ACRE = VOL_10HR / AREA_TOTAL,
VOL_100HR_ACRE = VOL_100HR / AREA_TOTAL,
VOL_1000HR_ACRE = VOL_1000HR / AREA_TOTAL,
VOL_PILE_ACRE = VOL_PILE / AREA_TOTAL,
VOL_ACRE = VOL / AREA_TOTAL,
BIO_DUFF_ACRE = BIO_DUFF / AREA_TOTAL,
BIO_LITTER_ACRE = BIO_LITTER / AREA_TOTAL,
BIO_1HR_ACRE = BIO_1HR / AREA_TOTAL,
BIO_10HR_ACRE = BIO_10HR / AREA_TOTAL,
BIO_100HR_ACRE = BIO_100HR / AREA_TOTAL,
BIO_1000HR_ACRE = BIO_1000HR / AREA_TOTAL,
BIO_PILE_ACRE = BIO_PILE / AREA_TOTAL,
BIO_ACRE = BIO / AREA_TOTAL,
CARB_DUFF_ACRE = CARB_DUFF / AREA_TOTAL,
CARB_LITTER_ACRE = CARB_LITTER / AREA_TOTAL,
CARB_1HR_ACRE = CARB_1HR / AREA_TOTAL,
CARB_10HR_ACRE = CARB_10HR / AREA_TOTAL,
CARB_100HR_ACRE = CARB_100HR / AREA_TOTAL,
CARB_1000HR_ACRE = CARB_1000HR / AREA_TOTAL,
CARB_PILE_ACRE = CARB_PILE / AREA_TOTAL,
CARB_ACRE = CARB / AREA_TOTAL,
nPlots = sum(plotIn, na.rm = TRUE))
# Remove the total values if told to do so
if (totals) {
cwd <- cwd %>%
select(grpBy, names(cwd)[str_detect(names(cwd), 'Var', negate = TRUE)], nPlots)
} else {
cwd <- cwd %>%
select(grpBy, names(cwd)[str_detect(names(cwd), 'Var', negate = TRUE) & str_detect(names(cwd), 'ACRE')], nPlots)
}
} # End SE Conditional
# Do some cleanup
#gc()
#Return a dataframe
cwd
}
hunter-stanke/rFIA_TX documentation built on Jan. 1, 2021, 3:22 a.m.
R Package Documentation
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Defines functions dwmHelper dwmHelper2 dwmHelper1
dwmHelper1 <- function(x, plts, db, grpBy, byPlot){
## Selecting the plots for one county
db$PLOT <- plts[[x]]
## Carrying out filter across all tables
#db <- clipFIA(db, mostRecent = FALSE)
## Which grpByNames are in which table? Helps us subset below
grpP <- names(db$PLOT)[names(db$PLOT) %in% grpBy]
grpC <- names(db$COND)[names(db$COND) %in% grpBy & names(db$COND) %in% grpP == FALSE]
### Only joining tables necessary to produce plot level estimates, adjusted for non-response
data <- db$PLOT %>%
left_join(db$COND, by = c('PLT_CN')) %>%
left_join(db$COND_DWM_CALC, by = c('PLT_CN', 'CONDID')) #%>%
#filter(DIA >= 5)
## Comprehensive indicator function
data$aDI <- data$landD * data$aD_p * data$aD_c * data$sp
if (byPlot){
grpBy <- c('YEAR', grpBy, 'PLOT_STATUS_CD')
t <- data %>%
mutate(YEAR = INVYR) %>%
distinct(PLT_CN, CONDID, .keep_all = TRUE) %>%
group_by(.dots = grpBy, PLT_CN) %>%
summarize(VOL_1HR = sum(FWD_SM_VOLCF_ADJ * aDI, na.rm = TRUE),
VOL_10HR = sum(FWD_MD_VOLCF_ADJ * aDI, na.rm = TRUE),
VOL_100HR = sum(FWD_LG_VOLCF_ADJ * aDI, na.rm = TRUE),
VOL_1000HR = sum(CWD_VOLCF_ADJ * aDI, na.rm = TRUE),
VOL_PILE = sum(PILE_VOLCF_ADJ * aDI, na.rm = TRUE),
VOL = sum(VOL_1HR, VOL_10HR, VOL_100HR, VOL_1000HR, VOL_PILE, na.rm = TRUE),
BIO_DUFF = sum(DUFF_BIOMASS* aDI / 2000, na.rm = TRUE),
BIO_LITTER = sum(LITTER_BIOMASS * aDI / 2000, na.rm = TRUE),
BIO_1HR = sum(FWD_SM_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
BIO_10HR = sum(FWD_MD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
BIO_100HR = sum(FWD_LG_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
BIO_1000HR = sum(CWD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
BIO_PILE = sum(PILE_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
BIO = sum(BIO_LITTER, BIO_DUFF, BIO_1HR, BIO_10HR, BIO_100HR, BIO_1000HR, BIO_PILE, na.rm = TRUE),
CARB_DUFF = sum(DUFF_CARBON* aDI / 2000, na.rm = TRUE),
CARB_LITTER = sum(LITTER_CARBON * aDI / 2000, na.rm = TRUE),
CARB_1HR = sum(FWD_SM_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
CARB_10HR = sum(FWD_MD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
CARB_100HR = sum(FWD_LG_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
CARB_1000HR = sum(CWD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
CARB_PILE = sum(PILE_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
CARB = sum(CARB_LITTER, CARB_DUFF, CARB_1HR, CARB_10HR, CARB_100HR, CARB_1000HR, CARB_PILE, na.rm = TRUE))
} else {
# Compute estimates
t <- data %>%
distinct(STRATUM_CN, PLT_CN, CONDID, COND_STATUS_CD, .keep_all = TRUE) %>%
group_by(STRATUM_CN, PROP_BASIS, PLT_CN, .dots = grpBy) %>%
summarize(vsmPlot = sum(FWD_SM_VOLCF_ADJ * aDI, na.rm = TRUE),
vmdPlot = sum(FWD_MD_VOLCF_ADJ * aDI, na.rm = TRUE),
vlgPlot = sum(FWD_LG_VOLCF_ADJ * aDI, na.rm = TRUE),
vcPlot = sum(CWD_VOLCF_ADJ * aDI, na.rm = TRUE),
vpPlot = sum(PILE_VOLCF_ADJ * aDI, na.rm = TRUE),
vPlot = sum(vsmPlot, vmdPlot, vlgPlot, vcPlot, vpPlot, na.rm = TRUE),
bdPlot = sum(DUFF_BIOMASS* aDI / 2000, na.rm = TRUE),
blPlot = sum(LITTER_BIOMASS * aDI / 2000, na.rm = TRUE),
bsmPlot = sum(FWD_SM_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bmdPlot = sum(FWD_MD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
blgPlot = sum(FWD_LG_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bcPlot = sum(CWD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bpPlot = sum(PILE_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bPlot = sum(bdPlot, blPlot, bsmPlot, bmdPlot, blgPlot, bcPlot, bpPlot, na.rm = TRUE),
cdPlot = sum(DUFF_CARBON* aDI / 2000, na.rm = TRUE),
clPlot = sum(LITTER_CARBON * aDI / 2000, na.rm = TRUE),
csmPlot = sum(FWD_SM_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cmdPlot = sum(FWD_MD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
clgPlot = sum(FWD_LG_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
ccPlot = sum(CWD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cpPlot = sum(PILE_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cPlot = sum(cdPlot, clPlot, csmPlot, cmdPlot, clgPlot, ccPlot, cpPlot, na.rm = TRUE),
fa = sum(CONDPROP_UNADJ * aDI, na.rm = TRUE),
plotIn = ifelse(sum(aDI > 0, na.rm = TRUE), 1,0))
}
pltOut <- list(t = t)
return(pltOut)
}
dwmHelper2 <- function(x, popState, t, grpBy, method){
## DOES NOT MODIFY OUTSIDE ENVIRONMENT
if (str_to_upper(method) %in% c("SMA", 'EMA', 'LMA', 'ANNUAL')) {
grpBy <- c(grpBy, 'INVYR')
#aGrpBy <- c(aGrpBy, 'INVYR')
popState[[x]]$P2POINTCNT <- popState[[x]]$P2POINTCNT_INVYR
popState[[x]]$p2eu <- popState[[x]]$p2eu_INVYR
}
## Strata level estimates
tEst <- t %>%
## Rejoin with population tables
right_join(select(popState[[x]], -c(STATECD)), by = c('STRATUM_CN', 'PLT_CN')) %>%
mutate(
## AREA
aAdj = case_when(
## When NA, stay NA
is.na(PROP_BASIS) ~ NA_real_,
## If the proportion was measured for a macroplot,
## use the macroplot value
PROP_BASIS == 'MACR' ~ as.numeric(ADJ_FACTOR_MACR),
## Otherwise, use the subpplot value
PROP_BASIS == 'SUBP' ~ ADJ_FACTOR_SUBP),
fa = fa * aAdj) %>%
group_by(ESTN_UNIT_CN, ESTN_METHOD, STRATUM_CN, .dots = grpBy) %>%
summarize(a_t = length(unique(PLT_CN)) / first(P2POINTCNT),
aStrat = mean(fa * a_t, na.rm = TRUE),
vsmStrat = mean(vsmPlot * a_t, na.rm = TRUE),
vmdStrat = mean(vmdPlot * a_t, na.rm = TRUE),
vlgStrat = mean(vlgPlot * a_t, na.rm = TRUE),
vcStrat = mean(vcPlot * a_t, na.rm = TRUE),
vpStrat = mean(vpPlot * a_t, na.rm = TRUE),
vStrat = mean(vPlot * a_t, na.rm = TRUE),
bdStrat = mean(bdPlot * a_t, na.rm = TRUE),
blStrat = mean(blPlot * a_t, na.rm = TRUE),
bsmStrat = mean(bsmPlot * a_t, na.rm = TRUE),
bmdStrat = mean(bmdPlot * a_t, na.rm = TRUE),
blgStrat = mean(blgPlot * a_t, na.rm = TRUE),
bcStrat = mean(bcPlot * a_t, na.rm = TRUE),
bpStrat = mean(bpPlot * a_t, na.rm = TRUE),
bStrat = mean(bPlot * a_t, na.rm = TRUE),
cdStrat = mean(cdPlot * a_t, na.rm = TRUE),
clStrat = mean(clPlot * a_t, na.rm = TRUE),
csmStrat = mean(csmPlot * a_t, na.rm = TRUE),
cmdStrat = mean(cmdPlot * a_t, na.rm = TRUE),
clgStrat = mean(clgPlot * a_t, na.rm = TRUE),
ccStrat = mean(ccPlot * a_t, na.rm = TRUE),
cpStrat = mean(cpPlot * a_t, na.rm = TRUE),
cStrat = mean(cPlot * a_t, na.rm = TRUE),
plotIn = sum(plotIn, na.rm = TRUE),
n = n(),
## We don't want a vector of these values, since they are repeated
nh = first(P2POINTCNT),
a = first(AREA_USED),
w = first(P1POINTCNT) / first(P1PNTCNT_EU),
p2eu = first(p2eu),
ndif = nh - n,
# ## Strata level variances
av = stratVar(ESTN_METHOD, fa, aStrat, ndif, a, nh),
vsmVar = stratVar(ESTN_METHOD, vsmPlot, vsmStrat, ndif, a, nh),
vmdVar = stratVar(ESTN_METHOD, vmdPlot, vmdStrat, ndif, a, nh),
vlgVar = stratVar(ESTN_METHOD, vlgPlot, vlgStrat, ndif, a, nh),
vcVar = stratVar(ESTN_METHOD, vcPlot, vcStrat, ndif, a, nh),
vpVar = stratVar(ESTN_METHOD, vpPlot, vpStrat, ndif, a, nh),
vVar = stratVar(ESTN_METHOD, vPlot, vStrat, ndif, a, nh),
bdVar = stratVar(ESTN_METHOD, bdPlot, bdStrat, ndif, a, nh),
blVar = stratVar(ESTN_METHOD, blPlot, blStrat, ndif, a, nh),
bsmVar = stratVar(ESTN_METHOD, bsmPlot, bsmStrat, ndif, a, nh),
bmdVar = stratVar(ESTN_METHOD, bmdPlot, bmdStrat, ndif, a, nh),
blgVar = stratVar(ESTN_METHOD, blgPlot, blgStrat, ndif, a, nh),
bcVar = stratVar(ESTN_METHOD, bcPlot, bcStrat, ndif, a, nh),
bpVar = stratVar(ESTN_METHOD, bpPlot, bpStrat, ndif, a, nh),
bVar = stratVar(ESTN_METHOD, bPlot, bStrat, ndif, a, nh),
cdVar = stratVar(ESTN_METHOD, cdPlot, cdStrat, ndif, a, nh),
clVar = stratVar(ESTN_METHOD, clPlot, clStrat, ndif, a, nh),
csmVar = stratVar(ESTN_METHOD, csmPlot, csmStrat, ndif, a, nh),
cmdVar = stratVar(ESTN_METHOD, cmdPlot, cmdStrat, ndif, a, nh),
clgVar = stratVar(ESTN_METHOD, clgPlot, clgStrat, ndif, a, nh),
ccVar = stratVar(ESTN_METHOD, ccPlot, ccStrat, ndif, a, nh),
cpVar = stratVar(ESTN_METHOD, cpPlot, cpStrat, ndif, a, nh),
cVar = stratVar(ESTN_METHOD, cPlot, cStrat, ndif, a, nh),
# ## Strata level co-variances
cvEst_vsm = stratVar(ESTN_METHOD, vsmPlot, vsmStrat, ndif, a, nh, fa, aStrat),
cvEst_vmd = stratVar(ESTN_METHOD, vmdPlot, vmdStrat, ndif, a, nh, fa, aStrat),
cvEst_vlg = stratVar(ESTN_METHOD, vlgPlot, vlgStrat, ndif, a, nh, fa, aStrat),
cvEst_vc = stratVar(ESTN_METHOD, vcPlot, vcStrat, ndif, a, nh, fa, aStrat),
cvEst_vp = stratVar(ESTN_METHOD, vpPlot, vpStrat, ndif, a, nh, fa, aStrat),
cvEst_v = stratVar(ESTN_METHOD, vPlot, vStrat, ndif, a, nh, fa, aStrat),
cvEst_bd = stratVar(ESTN_METHOD, bdPlot, bdStrat, ndif, a, nh, fa, aStrat),
cvEst_bl = stratVar(ESTN_METHOD, blPlot, blStrat, ndif, a, nh, fa, aStrat),
cvEst_bsm = stratVar(ESTN_METHOD, bsmPlot, bsmStrat, ndif, a, nh, fa, aStrat),
cvEst_bmd = stratVar(ESTN_METHOD, bmdPlot, bmdStrat, ndif, a, nh, fa, aStrat),
cvEst_blg = stratVar(ESTN_METHOD, blgPlot, blgStrat, ndif, a, nh, fa, aStrat),
cvEst_bc = stratVar(ESTN_METHOD, bcPlot, bcStrat, ndif, a, nh, fa, aStrat),
cvEst_bp = stratVar(ESTN_METHOD, bpPlot, bpStrat, ndif, a, nh, fa, aStrat),
cvEst_b = stratVar(ESTN_METHOD, bPlot, bStrat, ndif, a, nh, fa, aStrat),
cvEst_cd = stratVar(ESTN_METHOD, cdPlot, cdStrat, ndif, a, nh, fa, aStrat),
cvEst_cl = stratVar(ESTN_METHOD, clPlot, clStrat, ndif, a, nh, fa, aStrat),
cvEst_csm = stratVar(ESTN_METHOD, csmPlot, csmStrat, ndif, a, nh, fa, aStrat),
cvEst_cmd = stratVar(ESTN_METHOD, cmdPlot, cmdStrat, ndif, a, nh, fa, aStrat),
cvEst_clg = stratVar(ESTN_METHOD, clgPlot, clgStrat, ndif, a, nh, fa, aStrat),
cvEst_cc = stratVar(ESTN_METHOD, ccPlot, ccStrat, ndif, a, nh, fa, aStrat),
cvEst_cp = stratVar(ESTN_METHOD, cpPlot, cpStrat, ndif, a, nh, fa, aStrat),
cvEst_c = stratVar(ESTN_METHOD, cPlot, cStrat, ndif, a, nh, fa, aStrat)) %>%
## Estimation unit
group_by(ESTN_UNIT_CN, .dots = grpBy) %>%
summarize(aEst = unitMean(ESTN_METHOD, a, nh, w, aStrat),
vsmEst = unitMean(ESTN_METHOD, a, nh, w, vsmStrat),
vmdEst = unitMean(ESTN_METHOD, a, nh, w, vmdStrat),
vlgEst = unitMean(ESTN_METHOD, a, nh, w, vlgStrat),
vcEst = unitMean(ESTN_METHOD, a, nh, w, vcStrat),
vpEst = unitMean(ESTN_METHOD, a, nh, w, vpStrat),
vEst = unitMean(ESTN_METHOD, a, nh, w, vStrat),
bdEst = unitMean(ESTN_METHOD, a, nh, w, bdStrat),
blEst = unitMean(ESTN_METHOD, a, nh, w, blStrat),
bsmEst = unitMean(ESTN_METHOD, a, nh, w, bsmStrat),
bmdEst = unitMean(ESTN_METHOD, a, nh, w, bmdStrat),
blgEst = unitMean(ESTN_METHOD, a, nh, w, blgStrat),
bcEst = unitMean(ESTN_METHOD, a, nh, w, bcStrat),
bpEst = unitMean(ESTN_METHOD, a, nh, w, bpStrat),
bEst = unitMean(ESTN_METHOD, a, nh, w, bStrat),
cdEst = unitMean(ESTN_METHOD, a, nh, w, cdStrat),
clEst = unitMean(ESTN_METHOD, a, nh, w, clStrat),
csmEst = unitMean(ESTN_METHOD, a, nh, w, csmStrat),
cmdEst = unitMean(ESTN_METHOD, a, nh, w, cmdStrat),
clgEst = unitMean(ESTN_METHOD, a, nh, w, clgStrat),
ccEst = unitMean(ESTN_METHOD, a, nh, w, ccStrat),
cpEst = unitMean(ESTN_METHOD, a, nh, w, cpStrat),
cEst = unitMean(ESTN_METHOD, a, nh, w, cStrat),
plotIn = sum(plotIn, na.rm = TRUE),
N = first(p2eu),
# Estimation of unit variance
aVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, av, aStrat, aEst),
vsmVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vsmVar, vsmStrat, vsmEst),
vmdVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vmdVar, vmdStrat, vmdEst),
vlgVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vlgVar, vlgStrat, vlgEst),
vcVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vcVar, vcStrat, vcEst),
vpVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vpVar, vpStrat, vpEst),
vVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, vVar, vStrat, vEst),
bdVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bdVar, bdStrat, bdEst),
blVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, blVar, blStrat, blEst),
bsmVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bsmVar, bsmStrat, bsmEst),
bmdVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bmdVar, bmdStrat, bmdEst),
blgVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, blgVar, blgStrat, blgEst),
bcVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bcVar, bcStrat, bcEst),
bpVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bpVar, bpStrat, bpEst),
bVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, bVar, bStrat, cbEst),
cdVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, cdVar, cdStrat, cdEst),
clVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, clVar, clStrat, clEst),
csmVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, csmVar, csmStrat, csmEst),
cmdVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, cmdVar, cmdStrat, cmdEst),
clgVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, clgVar, clgStrat, clgEst),
ccVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, ccVar, ccStrat, ccEst),
cpVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, cpVar, cpStrat, cpEst),
cVar = unitVarNew(method = 'var', ESTN_METHOD, a, nh, first(p2eu), w, cVar, cStrat, cEst),
# Estimation of unit covariance
cvEst_vsm = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_vsm, vsmStrat, vsmEst, aStrat, aEst),
cvEst_vmd = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_vmd, vmdStrat, vmdEst, aStrat, aEst),
cvEst_vlg = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_vlg, vlgStrat, vlgEst, aStrat, aEst),
cvEst_vc = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_vc, vcStrat, vcEst, aStrat, aEst),
cvEst_vp = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_vp, vpStrat, vpEst, aStrat, aEst),
cvEst_v = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_v, vStrat, vEst, aStrat, aEst),
cvEst_bd = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bd, bdStrat, bdEst, aStrat, aEst),
cvEst_bl = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bl, blStrat, blEst, aStrat, aEst),
cvEst_bsm = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bsm, bsmStrat, bsmEst, aStrat, aEst),
cvEst_bmd = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bmd, bmdStrat, bmdEst, aStrat, aEst),
cvEst_blg = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_blg, blgStrat, blgEst, aStrat, aEst),
cvEst_bc = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bc, bcStrat, bcEst, aStrat, aEst),
cvEst_bp = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_bp, bpStrat, bpEst, aStrat, aEst),
cvEst_b = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_b, bStrat, cbEst, aStrat, aEst),
cvEst_cd = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_cd, cdStrat, cdEst, aStrat, aEst),
cvEst_cl = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_cl, clStrat, clEst, aStrat, aEst),
cvEst_csm = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_csm, csmStrat, csmEst, aStrat, aEst),
cvEst_cmd = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_cmd, cmdStrat, cmdEst, aStrat, aEst),
cvEst_clg = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_clg, clgStrat, clgEst, aStrat, aEst),
cvEst_cc = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_cc, ccStrat, ccEst, aStrat, aEst),
cvEst_cp = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_cp, cpStrat, cpEst, aStrat, aEst),
cvEst_c = unitVarNew(method = 'cov', ESTN_METHOD, a, nh, first(p2eu), w, cvEst_c, cStrat, cEst, aStrat, aEst))
out <- list(tEst = tEst)
return(out)
}
dwmHelper <- function(x, combos, data, grpBy, totals, SE){
# Update domain indicator for each each column speficed in grpBy
ad = 1
for (n in 1:ncol(combos[[x]])){
# Area domain indicator for each column in
aObs <- as.character(combos[[x]][[grpBy[n]]]) == as.character(data[[grpBy[n]]])
if (length(which(is.na(aObs))) == length(aObs)) aObs <- 1
ad <- data$aDI * aObs * ad
}
if(SE){
data$aDI <- ad
data$aDI[is.na(data$aDI)] <- 0
cwd <- data %>%
distinct(PLT_CN, CONDID, EVALID, COND_STATUS_CD, .keep_all = TRUE) %>%
group_by(ESTN_UNIT_CN, ESTN_METHOD, STRATUM_CN, PLT_CN) %>%
summarize(vsmPlot = sum(FWD_SM_VOLCF_ADJ * aDI, na.rm = TRUE),
vmdPlot = sum(FWD_MD_VOLCF_ADJ * aDI, na.rm = TRUE),
vlgPlot = sum(FWD_LG_VOLCF_ADJ * aDI, na.rm = TRUE),
vcPlot = sum(CWD_VOLCF_ADJ * aDI, na.rm = TRUE),
vpPlot = sum(PILE_VOLCF_ADJ * aDI, na.rm = TRUE),
vPlot = sum(vsmPlot, vmdPlot, vlgPlot, vcPlot, vpPlot, na.rm = TRUE),
bdPlot = sum(DUFF_BIOMASS* aDI / 2000, na.rm = TRUE),
blPlot = sum(LITTER_BIOMASS * aDI / 2000, na.rm = TRUE),
bsmPlot = sum(FWD_SM_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bmdPlot = sum(FWD_MD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
blgPlot = sum(FWD_LG_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bcPlot = sum(CWD_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bpPlot = sum(PILE_DRYBIO_ADJ * aDI / 2000, na.rm = TRUE),
bPlot = sum(bdPlot, blPlot, bsmPlot, bmdPlot, blgPlot, bcPlot, bpPlot, na.rm = TRUE),
cdPlot = sum(DUFF_CARBON* aDI / 2000, na.rm = TRUE),
clPlot = sum(LITTER_CARBON * aDI / 2000, na.rm = TRUE),
csmPlot = sum(FWD_SM_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cmdPlot = sum(FWD_MD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
clgPlot = sum(FWD_LG_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
ccPlot = sum(CWD_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cpPlot = sum(PILE_CARBON_ADJ * aDI / 2000, na.rm = TRUE),
cPlot = sum(cdPlot, clPlot, csmPlot, cmdPlot, clgPlot, ccPlot, cpPlot, na.rm = TRUE),
fa = sum(CONDPROP_UNADJ * aDI * aAdj, na.rm = TRUE),
plotIn = ifelse(sum(aDI > 0, na.rm = TRUE), 1,0),
a = first(AREA_USED),
p1EU = first(P1PNTCNT_EU),
p1 = first(P1POINTCNT),
p2 = first(P2POINTCNT)) %>%
# Stratum level
group_by(ESTN_UNIT_CN, ESTN_METHOD, STRATUM_CN) %>%
summarize(aStrat = mean(fa, na.rm = TRUE),
vsmStrat = mean(vsmPlot, na.rm = TRUE),
vmdStrat = mean(vmdPlot, na.rm = TRUE),
vlgStrat = mean(vlgPlot, na.rm = TRUE),
vcStrat = mean(vcPlot, na.rm = TRUE),
vpStrat = mean(vpPlot, na.rm = TRUE),
vStrat = mean(vPlot, na.rm = TRUE),
bdStrat = mean(bdPlot, na.rm = TRUE),
blStrat = mean(blPlot, na.rm = TRUE),
bsmStrat = mean(bsmPlot, na.rm = TRUE),
bmdStrat = mean(bmdPlot, na.rm = TRUE),
blgStrat = mean(blgPlot, na.rm = TRUE),
bcStrat = mean(bcPlot, na.rm = TRUE),
bpStrat = mean(bpPlot, na.rm = TRUE),
bStrat = mean(bPlot, na.rm = TRUE),
cdStrat = mean(cdPlot, na.rm = TRUE),
clStrat = mean(clPlot, na.rm = TRUE),
csmStrat = mean(csmPlot, na.rm = TRUE),
cmdStrat = mean(cmdPlot, na.rm = TRUE),
clgStrat = mean(clgPlot, na.rm = TRUE),
ccStrat = mean(ccPlot, na.rm = TRUE),
cpStrat = mean(cpPlot, na.rm = TRUE),
cStrat = mean(cPlot, na.rm = TRUE),
plotIn = sum(plotIn, na.rm = TRUE),
a = first(a),
w = first(p1) / first(p1EU), # Stratum weight
nh = first(p2), # Number plots in stratum
# Strata level variances
av = ifelse(first(ESTN_METHOD == 'simple'),
var(fa * first(a) / nh),
(sum(fa^2) - sum(nh * aStrat^2)) / (nh * (nh-1))),
vsmV = ifelse(first(ESTN_METHOD == 'simple'),
var(vsmPlot * first(a) / nh),
(sum(vsmPlot^2) - sum(nh * vsmStrat^2)) / (nh * (nh-1))), # Stratified and double cases
vmdV = ifelse(first(ESTN_METHOD == 'simple'),
var(vmdPlot * first(a) / nh),
(sum(vmdPlot^2) - sum(nh * vmdStrat^2)) / (nh * (nh-1))), # Stratified and double cases
vlgV = ifelse(first(ESTN_METHOD == 'simple'),
var(vlgPlot * first(a) / nh),
(sum(vlgPlot^2) - sum(nh * vlgStrat^2)) / (nh * (nh-1))), # Stratified and double cases
vcV = ifelse(first(ESTN_METHOD == 'simple'),
var(vcPlot * first(a) / nh),
(sum(vcPlot^2) - sum(nh * vcStrat^2)) / (nh * (nh-1))), # Stratified and double cases
vpV = ifelse(first(ESTN_METHOD == 'simple'),
var(vpPlot * first(a) / nh),
(sum(vpPlot^2) - sum(nh * vpStrat^2)) / (nh * (nh-1))), # Stratified and double cases
vV = ifelse(first(ESTN_METHOD == 'simple'),
var(vPlot * first(a) / nh),
(sum(vPlot^2) - sum(nh * vStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bdV = ifelse(first(ESTN_METHOD == 'simple'),
var(bdPlot * first(a) / nh),
(sum(bdPlot^2) - sum(nh * bdStrat^2)) / (nh * (nh-1))), # Stratified and double cases
blV = ifelse(first(ESTN_METHOD == 'simple'),
var(blPlot * first(a) / nh),
(sum(blPlot^2) - sum(nh * blStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bsmV = ifelse(first(ESTN_METHOD == 'simple'),
var(bsmPlot * first(a) / nh),
(sum(bsmPlot^2) - sum(nh * bsmStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bmdV = ifelse(first(ESTN_METHOD == 'simple'),
var(bmdPlot * first(a) / nh),
(sum(bmdPlot^2) - sum(nh * bmdStrat^2)) / (nh * (nh-1))), # Stratified and double cases
blgV = ifelse(first(ESTN_METHOD == 'simple'),
var(blgPlot * first(a) / nh),
(sum(blgPlot^2) - sum(nh * blgStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bcV = ifelse(first(ESTN_METHOD == 'simple'),
var(bcPlot * first(a) / nh),
(sum(bcPlot^2) - sum(nh * bcStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bpV = ifelse(first(ESTN_METHOD == 'simple'),
var(bpPlot * first(a) / nh),
(sum(bpPlot^2) - sum(nh * bpStrat^2)) / (nh * (nh-1))), # Stratified and double cases
bV = ifelse(first(ESTN_METHOD == 'simple'),
var(bPlot * first(a) / nh),
(sum(bPlot^2) - sum(nh * bStrat^2)) / (nh * (nh-1))), # Stratified and double cases
cdV = ifelse(first(ESTN_METHOD == 'simple'),
var(cdPlot * first(a) / nh),
(sum(cdPlot^2) - sum(nh * cdStrat^2)) / (nh * (nh-1))), # Stratified and double cases
clV = ifelse(first(ESTN_METHOD == 'simple'),
var(clPlot * first(a) / nh),
(sum(clPlot^2) - sum(nh * clStrat^2)) / (nh * (nh-1))), # Stratified and double cases
csmV = ifelse(first(ESTN_METHOD == 'simple'),
var(csmPlot * first(a) / nh),
(sum(csmPlot^2) - sum(nh * csmStrat^2)) / (nh * (nh-1))), # Stratified and double cases
cmdV = ifelse(first(ESTN_METHOD == 'simple'),
var(cmdPlot * first(a) / nh),
(sum(cmdPlot^2) - sum(nh * cmdStrat^2)) / (nh * (nh-1))), # Stratified and double cases
clgV = ifelse(first(ESTN_METHOD == 'simple'),
var(clgPlot * first(a) / nh),
(sum(clgPlot^2) - sum(nh * clgStrat^2)) / (nh * (nh-1))), # Stratified and double cases
ccV = ifelse(first(ESTN_METHOD == 'simple'),
var(ccPlot * first(a) / nh),
(sum(ccPlot^2) - sum(nh * ccStrat^2)) / (nh * (nh-1))), # Stratified and double cases
cpV = ifelse(first(ESTN_METHOD == 'simple'),
var(cpPlot * first(a) / nh),
(sum(cpPlot^2) - sum(nh * cpStrat^2)) / (nh * (nh-1))), # Stratified and double cases
cV = ifelse(first(ESTN_METHOD == 'simple'),
var(cPlot * first(a) / nh),
(sum(cPlot^2) - sum(nh * cStrat^2)) / (nh * (nh-1))), # Stratified and double cases
# Strata level covariances
vsmCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vsmPlot),
(sum(fa*vsmPlot) - sum(nh * aStrat *vsmStrat)) / (nh * (nh-1))), # Stratified and double cases
vmdCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vmdPlot),
(sum(fa*vmdPlot) - sum(nh * aStrat *vmdStrat)) / (nh * (nh-1))), # Stratified and double cases
vlgCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vlgPlot),
(sum(fa*vlgPlot) - sum(nh * aStrat *vlgStrat)) / (nh * (nh-1))), # Stratified and double cases
vcCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vcPlot),
(sum(fa*vcPlot) - sum(nh * aStrat *vcStrat)) / (nh * (nh-1))), # Stratified and double cases
vpCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vpPlot),
(sum(fa*vpPlot) - sum(nh * aStrat *vpStrat)) / (nh * (nh-1))), # Stratified and double cases
vCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,vPlot),
(sum(fa*vPlot) - sum(nh * aStrat *vStrat)) / (nh * (nh-1))), # Stratified and double cases
bdCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bdPlot),
(sum(fa*bdPlot) - sum(nh * aStrat *bdStrat)) / (nh * (nh-1))), # Stratified and double cases
blCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,blPlot),
(sum(fa*blPlot) - sum(nh * aStrat *blStrat)) / (nh * (nh-1))), # Stratified and double cases
bsmCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bsmPlot),
(sum(fa*bsmPlot) - sum(nh * aStrat *bsmStrat)) / (nh * (nh-1))), # Stratified and double cases
bmdCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bmdPlot),
(sum(fa*bmdPlot) - sum(nh * aStrat *bmdStrat)) / (nh * (nh-1))), # Stratified and double cases
blgCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,blgPlot),
(sum(fa*blgPlot) - sum(nh * aStrat *blgStrat)) / (nh * (nh-1))), # Stratified and double cases
bcCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bcPlot),
(sum(fa*bcPlot) - sum(nh * aStrat *bcStrat)) / (nh * (nh-1))), # Stratified and double cases
bpCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bpPlot),
(sum(fa*bpPlot) - sum(nh * aStrat *bpStrat)) / (nh * (nh-1))), # Stratified and double cases
bCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,bPlot),
(sum(fa*bPlot) - sum(nh * aStrat *bStrat)) / (nh * (nh-1))), # Stratified and double cases
cdCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,cdPlot),
(sum(fa*cdPlot) - sum(nh * aStrat *cdStrat)) / (nh * (nh-1))), # Stratified and double cases
clCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,blPlot),
(sum(fa*clPlot) - sum(nh * aStrat *clStrat)) / (nh * (nh-1))), # Stratified and double cases
csmCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,csmPlot),
(sum(fa*csmPlot) - sum(nh * aStrat *csmStrat)) / (nh * (nh-1))), # Stratified and double cases
cmdCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,cmdPlot),
(sum(fa*cmdPlot) - sum(nh * aStrat *cmdStrat)) / (nh * (nh-1))), # Stratified and double cases
clgCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,clgPlot),
(sum(fa*clgPlot) - sum(nh * aStrat *clgStrat)) / (nh * (nh-1))), # Stratified and double cases
ccCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,ccPlot),
(sum(fa*ccPlot) - sum(nh * aStrat *ccStrat)) / (nh * (nh-1))), # Stratified and double cases
cpCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,cpPlot),
(sum(fa*cpPlot) - sum(nh * aStrat *cpStrat)) / (nh * (nh-1))), # Stratified and double cases
cCV = ifelse(first(ESTN_METHOD == 'simple'),
cov(fa,cPlot),
(sum(fa*cPlot) - sum(nh * aStrat *cStrat)) / (nh * (nh-1)))) %>% # Stratified and double cases
## Estimation unit level
group_by(ESTN_UNIT_CN) %>%
summarize(aEst = unitMean(ESTN_METHOD, a, nh, w, aStrat),
vsmEst = unitMean(ESTN_METHOD, a, nh, w, vsmStrat),
vmdEst = unitMean(ESTN_METHOD, a, nh, w, vmdStrat),
vlgEst = unitMean(ESTN_METHOD, a, nh, w, vlgStrat),
vcEst = unitMean(ESTN_METHOD, a, nh, w, vcStrat),
vpEst = unitMean(ESTN_METHOD, a, nh, w, vpStrat),
vEst = unitMean(ESTN_METHOD, a, nh, w, vStrat),
bdEst = unitMean(ESTN_METHOD, a, nh, w, bdStrat),
blEst = unitMean(ESTN_METHOD, a, nh, w, blStrat),
bsmEst = unitMean(ESTN_METHOD, a, nh, w, bsmStrat),
bmdEst = unitMean(ESTN_METHOD, a, nh, w, bmdStrat),
blgEst = unitMean(ESTN_METHOD, a, nh, w, blgStrat),
bcEst = unitMean(ESTN_METHOD, a, nh, w, bcStrat),
bpEst = unitMean(ESTN_METHOD, a, nh, w, bpStrat),
bEst = unitMean(ESTN_METHOD, a, nh, w, bStrat),
cdEst = unitMean(ESTN_METHOD, a, nh, w, cdStrat),
clEst = unitMean(ESTN_METHOD, a, nh, w, clStrat),
csmEst = unitMean(ESTN_METHOD, a, nh, w, csmStrat),
cmdEst = unitMean(ESTN_METHOD, a, nh, w, cmdStrat),
clgEst = unitMean(ESTN_METHOD, a, nh, w, clgStrat),
ccEst = unitMean(ESTN_METHOD, a, nh, w, ccStrat),
cpEst = unitMean(ESTN_METHOD, a, nh, w, cpStrat),
cEst = unitMean(ESTN_METHOD, a, nh, w, cStrat),
plotIn = sum(plotIn, na.rm = TRUE),
# Estimation of unit variance
aVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, av, aStrat, aEst),
vsmVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vsmV, vsmStrat, vsmEst),
vmdVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vmdV, vmdStrat, vmdEst),
vlgVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vlgV, vlgStrat, vlgEst),
vcVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vcV, vcStrat, vcEst),
vpVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vpV, vpStrat, vpEst),
vVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, vV, vStrat, vEst),
bdVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bdV, bdStrat, bdEst),
blVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, blV, blStrat, blEst),
bsmVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bsmV, bsmStrat, bsmEst),
bmdVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bmdV, bmdStrat, bmdEst),
blgVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, blgV, blgStrat, blgEst),
bcVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bcV, bcStrat, bcEst),
bpVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bpV, bpStrat, bpEst),
bVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, bV, bStrat, cbEst),
cdVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, cdV, cdStrat, cdEst),
clVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, clV, clStrat, clEst),
csmVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, csmV, csmStrat, csmEst),
cmdVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, cmdV, cmdStrat, cmdEst),
clgVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, clgV, clgStrat, clgEst),
ccVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, ccV, ccStrat, ccEst),
cpVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, cpV, cpStrat, cpEst),
cVar = unitVar(method = 'var', ESTN_METHOD, a, nh, w, cV, cStrat, cEst),
# Estimation of unit covariance
vsmCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vsmCV, vsmStrat, vsmEst, aStrat, aEst),
vmdCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vmdCV, vmdStrat, vmdEst, aStrat, aEst),
vlgCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vlgCV, vlgStrat, vlgEst, aStrat, aEst),
vcCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vcCV, vcStrat, vcEst, aStrat, aEst),
vpCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vpCV, vpStrat, vpEst, aStrat, aEst),
vCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, vCV, vStrat, vEst, aStrat, aEst),
bdCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bdCV, bdStrat, bdEst, aStrat, aEst),
blCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, blCV, blStrat, blEst, aStrat, aEst),
bsmCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bsmCV, bsmStrat, bsmEst, aStrat, aEst),
bmdCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bmdCV, bmdStrat, bmdEst, aStrat, aEst),
blgCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, blgCV, blgStrat, blgEst, aStrat, aEst),
bcCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bcCV, bcStrat, bcEst, aStrat, aEst),
bpCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bpCV, bpStrat, bpEst, aStrat, aEst),
bCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, bCV, bStrat, cbEst, aStrat, aEst),
cdCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, cdCV, cdStrat, cdEst, aStrat, aEst),
clCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, clCV, clStrat, clEst, aStrat, aEst),
csmCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, csmCV, csmStrat, csmEst, aStrat, aEst),
cmdCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, cmdCV, cmdStrat, cmdEst, aStrat, aEst),
clgCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, clgCV, clgStrat, clgEst, aStrat, aEst),
ccCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, ccCV, ccStrat, ccEst, aStrat, aEst),
cpCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, cpCV, cpStrat, cpEst, aStrat, aEst),
cCV = unitVar(method = 'cov', ESTN_METHOD, a, nh, w, cCV, cStrat, cEst, aStrat, aEst)) %>%
# Compute totals
summarize(AREA_TOTAL = sum(aEst, na.rm = TRUE),
VOL_DUFF = NA,
VOL_LITTER = NA,
VOL_1HR = sum(vsmEst, na.rm = TRUE),
VOL_10HR = sum(vmdEst, na.rm = TRUE),
VOL_100HR = sum(vlgEst, na.rm = TRUE),
VOL_1000HR = sum(vcEst, na.rm = TRUE),
VOL_PILE = sum(vpEst, na.rm = TRUE),
VOL = sum(vEst, na.rm = TRUE),
BIO_DUFF = sum(bdEst, na.rm = TRUE),
BIO_LITTER = sum(blEst, na.rm = TRUE),
BIO_1HR = sum(bsmEst, na.rm = TRUE),
BIO_10HR = sum(bmdEst, na.rm = TRUE),
BIO_100HR = sum(blgEst, na.rm = TRUE),
BIO_1000HR = sum(bcEst, na.rm = TRUE),
BIO_PILE = sum(bpEst, na.rm = TRUE),
BIO = sum(bEst, na.rm = TRUE),
CARB_DUFF = sum(cdEst, na.rm = TRUE),
CARB_LITTER = sum(clEst, na.rm = TRUE),
CARB_1HR = sum(csmEst, na.rm = TRUE),
CARB_10HR = sum(cmdEst, na.rm = TRUE),
CARB_100HR = sum(clgEst, na.rm = TRUE),
CARB_1000HR = sum(ccEst, na.rm = TRUE),
CARB_PILE = sum(cpEst, na.rm = TRUE),
CARB = sum(cEst, na.rm = TRUE),
nPlots = sum(plotIn, na.rm = TRUE),
# Per Acre
VOL_DUFF_ACRE = NA,
VOL_LITTER_ACRE = NA,
VOL_1HR_ACRE = VOL_1HR / AREA_TOTAL,
VOL_10HR_ACRE = VOL_10HR / AREA_TOTAL,
VOL_100HR_ACRE = VOL_100HR / AREA_TOTAL,
VOL_1000HR_ACRE = VOL_1000HR / AREA_TOTAL,
VOL_PILE_ACRE = VOL_PILE / AREA_TOTAL,
VOL_ACRE = VOL / AREA_TOTAL,
BIO_DUFF_ACRE = BIO_DUFF / AREA_TOTAL,
BIO_LITTER_ACRE = BIO_LITTER / AREA_TOTAL,
BIO_1HR_ACRE = BIO_1HR / AREA_TOTAL,
BIO_10HR_ACRE = BIO_10HR / AREA_TOTAL,
BIO_100HR_ACRE = BIO_100HR / AREA_TOTAL,
BIO_1000HR_ACRE = BIO_1000HR / AREA_TOTAL,
BIO_PILE_ACRE = BIO_PILE / AREA_TOTAL,
BIO_ACRE = BIO / AREA_TOTAL,
CARB_DUFF_ACRE = CARB_DUFF / AREA_TOTAL,
CARB_LITTER_ACRE = CARB_LITTER / AREA_TOTAL,
CARB_1HR_ACRE = CARB_1HR / AREA_TOTAL,
CARB_10HR_ACRE = CARB_10HR / AREA_TOTAL,
CARB_100HR_ACRE = CARB_100HR / AREA_TOTAL,
CARB_1000HR_ACRE = CARB_1000HR / AREA_TOTAL,
CARB_PILE_ACRE = CARB_PILE / AREA_TOTAL,
CARB_ACRE = CARB / AREA_TOTAL,
# Sampling Errors totals
AREA_TOTAL_SE = sqrt(sum(aVar, na.rm = TRUE)) / AREA_TOTAL * 100,
VOL_DUFF_SE = NA,
VOL_LITTER_SE = NA,
VOL_1HR_SE = sqrt(sum(vsmVar, na.rm = TRUE)) / VOL_1HR * 100,
VOL_10HR_SE = sqrt(sum(vmdVar, na.rm = TRUE)) / VOL_10HR * 100,
VOL_100HR_SE = sqrt(sum(vlgVar, na.rm = TRUE)) / VOL_100HR * 100,
VOL_1000HR_SE = sqrt(sum(vcVar, na.rm = TRUE)) / VOL_1000HR * 100,
VOL_PILE_SE = sqrt(sum(vpVar, na.rm = TRUE)) / VOL_PILE * 100,
VOL_SE = sqrt(sum(vVar, na.rm = TRUE)) / VOL * 100,
BIO_DUFF_SE = sqrt(sum(bdVar, na.rm = TRUE)) / BIO_DUFF * 100,
BIO_LITTER_SE = sqrt(sum(blVar, na.rm = TRUE)) / BIO_LITTER * 100,
BIO_1HR_SE = sqrt(sum(bsmVar, na.rm = TRUE)) / BIO_1HR * 100,
BIO_10HR_SE = sqrt(sum(bmdVar, na.rm = TRUE)) / BIO_10HR * 100,
BIO_100HR_SE = sqrt(sum(blgVar, na.rm = TRUE)) / BIO_100HR * 100,
BIO_1000HR_SE = sqrt(sum(bcVar, na.rm = TRUE)) / BIO_1000HR * 100,
BIO_PILE_SE = sqrt(sum(bpVar, na.rm = TRUE)) / BIO_PILE * 100,
BIO_SE = sqrt(sum(bVar, na.rm = TRUE)) / BIO * 100,
CARB_DUFF_SE = sqrt(sum(cdVar, na.rm = TRUE)) / CARB_DUFF * 100,
CARB_LITTER_SE = sqrt(sum(clVar, na.rm = TRUE)) / CARB_LITTER * 100,
CARB_1HR_SE = sqrt(sum(csmVar, na.rm = TRUE)) / CARB_1HR * 100,
CARB_10HR_SE = sqrt(sum(cmdVar, na.rm = TRUE)) / CARB_10HR * 100,
CARB_100HR_SE = sqrt(sum(clgVar, na.rm = TRUE)) / CARB_100HR * 100,
CARB_1000HR_SE = sqrt(sum(ccVar, na.rm = TRUE)) / CARB_1000HR * 100,
CARB_PILE_SE = sqrt(sum(cpVar, na.rm = TRUE)) / CARB_PILE * 100,
CARB_SE = sqrt(sum(cVar, na.rm = TRUE)) / CARB * 100,
# Per Acre variances
vsmVar = (1/AREA_TOTAL^2) * (sum(vsmVar, na.rm = TRUE) + (VOL_1HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_1HR_ACRE * sum(vsmCV, na.rm = TRUE))),
vmdVar = (1/AREA_TOTAL^2) * (sum(vmdVar, na.rm = TRUE) + (VOL_10HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_10HR_ACRE * sum(vmdCV, na.rm = TRUE))),
vlgVar = (1/AREA_TOTAL^2) * (sum(vlgVar, na.rm = TRUE) + (VOL_100HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_100HR_ACRE * sum(vlgCV, na.rm = TRUE))),
vcVar = (1/AREA_TOTAL^2) * (sum(vcVar, na.rm = TRUE) + (VOL_1000HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_1000HR_ACRE *sum(vcCV, na.rm = TRUE))),
vpVar = (1/AREA_TOTAL^2) * (sum(vpVar, na.rm = TRUE) + (VOL_PILE_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_PILE_ACRE * sum(vpCV, na.rm = TRUE))),
vVar = (1/AREA_TOTAL^2) * (sum(vVar, na.rm = TRUE) + (VOL_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * VOL_ACRE * sum(vCV, na.rm = TRUE))),
bdVar = (1/AREA_TOTAL^2) * (sum(bdVar, na.rm = TRUE) + (BIO_DUFF_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_DUFF_ACRE * sum(bdCV, na.rm = TRUE))),
blVar = (1/AREA_TOTAL^2) * (sum(blVar, na.rm = TRUE) + (BIO_LITTER_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_LITTER_ACRE * sum(blCV, na.rm = TRUE))),
bsmVar = (1/AREA_TOTAL^2) * (sum(bsmVar, na.rm = TRUE) + (BIO_1HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_1HR_ACRE * sum(bsmCV, na.rm = TRUE))),
bmdVar = (1/AREA_TOTAL^2) * (sum(bmdVar, na.rm = TRUE) + (BIO_10HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_10HR_ACRE * sum(bmdCV, na.rm = TRUE))),
blgVar = (1/AREA_TOTAL^2) * (sum(blgVar, na.rm = TRUE) + (BIO_100HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_100HR_ACRE * sum(blgCV, na.rm = TRUE))),
bcVar = (1/AREA_TOTAL^2) * (sum(bcVar, na.rm = TRUE) + (BIO_1000HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_1000HR_ACRE * sum(bcCV, na.rm = TRUE))),
bpVar = (1/AREA_TOTAL^2) * (sum(bpVar, na.rm = TRUE) + (BIO_PILE_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_PILE_ACRE * sum(bpCV, na.rm = TRUE))),
bVar = (1/AREA_TOTAL^2) * (sum(bVar, na.rm = TRUE) + (BIO_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * BIO_ACRE * sum(bCV, na.rm = TRUE))),
cdVar = (1/AREA_TOTAL^2) * (sum(cdVar, na.rm = TRUE) + (CARB_DUFF_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_DUFF_ACRE * sum(cdCV, na.rm = TRUE))),
clVar = (1/AREA_TOTAL^2) * (sum(clVar, na.rm = TRUE) + (CARB_LITTER_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_LITTER_ACRE * sum(clCV, na.rm = TRUE))),
csmVar = (1/AREA_TOTAL^2) * (sum(csmVar, na.rm = TRUE) + (CARB_1HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_1HR_ACRE * sum(csmCV, na.rm = TRUE))),
cmdVar = (1/AREA_TOTAL^2) * (sum(cmdVar, na.rm = TRUE) + (CARB_10HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_10HR_ACRE * sum(cmdCV, na.rm = TRUE))),
clgVar = (1/AREA_TOTAL^2) * (sum(clgVar, na.rm = TRUE) + (CARB_100HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_100HR_ACRE * sum(clgCV, na.rm = TRUE))),
ccVar = (1/AREA_TOTAL^2) * (sum(ccVar, na.rm = TRUE) + (CARB_1000HR_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_1000HR_ACRE * sum(ccCV, na.rm = TRUE))),
cpVar = (1/AREA_TOTAL^2) * (sum(cpVar, na.rm = TRUE) + (CARB_PILE_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_PILE_ACRE * sum(cpCV, na.rm = TRUE))),
cVar = (1/AREA_TOTAL^2) * (sum(cVar, na.rm = TRUE) + (CARB_ACRE^2 * sum(aVar, na.rm = TRUE) - 2 * CARB_ACRE * sum(cCV, na.rm = TRUE))),
# Per acre sampling errors
VOL_DUFF_ACRE_SE = NA,
VOL_LITTER_ACRE_SE = NA,
VOL_1HR_ACRE_SE = sqrt(sum(vsmVar, na.rm = TRUE)) / VOL_1HR_ACRE * 100,
VOL_10HR_ACRE_SE = sqrt(sum(vmdVar, na.rm = TRUE)) / VOL_10HR_ACRE * 100,
VOL_100HR_ACRE_SE = sqrt(sum(vlgVar, na.rm = TRUE)) / VOL_100HR_ACRE * 100,
VOL_1000HR_ACRE_SE = sqrt(sum(vcVar, na.rm = TRUE)) / VOL_1000HR_ACRE * 100,
VOL_PILE_ACRE_SE = sqrt(sum(vpVar, na.rm = TRUE)) / VOL_PILE_ACRE * 100,
VOL_ACRE_SE = sqrt(sum(vVar, na.rm = TRUE)) / VOL_ACRE * 100,
BIO_DUFF_ACRE_SE = sqrt(sum(bdVar, na.rm = TRUE)) / BIO_DUFF_ACRE * 100,
BIO_LITTER_ACRE_SE = sqrt(sum(blVar, na.rm = TRUE)) / BIO_LITTER_ACRE * 100,
BIO_1HR_ACRE_SE = sqrt(sum(bsmVar, na.rm = TRUE)) / BIO_1HR_ACRE * 100,
BIO_10HR_ACRE_SE = sqrt(sum(bmdVar, na.rm = TRUE)) / BIO_10HR_ACRE * 100,
BIO_100HR_ACRE_SE = sqrt(sum(blgVar, na.rm = TRUE)) / BIO_100HR_ACRE * 100,
BIO_1000HR_ACRE_SE = sqrt(sum(bcVar, na.rm = TRUE)) / BIO_1000HR_ACRE * 100,
BIO_PILE_ACRE_SE = sqrt(sum(bpVar, na.rm = TRUE)) / BIO_PILE_ACRE * 100,
BIO_ACRE_SE = sqrt(sum(bVar, na.rm = TRUE)) / BIO_ACRE * 100,
CARB_DUFF_ACRE_SE = sqrt(sum(cdVar, na.rm = TRUE)) / CARB_DUFF_ACRE * 100,
CARB_LITTER_ACRE_SE = sqrt(sum(clVar, na.rm = TRUE)) / CARB_LITTER_ACRE * 100,
CARB_1HR_ACRE_SE = sqrt(sum(csmVar, na.rm = TRUE)) / CARB_1HR_ACRE * 100,
CARB_10HR_ACRE_SE = sqrt(sum(cmdVar, na.rm = TRUE)) / CARB_10HR_ACRE * 100,
CARB_100HR_ACRE_SE = sqrt(sum(clgVar, na.rm = TRUE)) / CARB_100HR_ACRE * 100,
CARB_1000HR_ACRE_SE = sqrt(sum(ccVar, na.rm = TRUE)) / CARB_1000HR_ACRE * 100,
CARB_PILE_ACRE_SE = sqrt(sum(cpVar, na.rm = TRUE)) / CARB_PILE_ACRE * 100,
CARB_ACRE_SE = sqrt(sum(cVar, na.rm = TRUE)) / CARB_ACRE * 100)
if (totals) {
cwd <- cwd %>%
select(names(cwd)[str_detect(names(cwd), 'Var', negate = TRUE)], nPlots)
} else {
cwd <- cwd %>%
select(names(cwd)[str_detect(names(cwd), 'Var', negate = TRUE) & str_detect(names(cwd), 'ACRE')], nPlots)
}
# Rejoin w/ groupby names
cwd <- data.frame(combos[[x]], cwd)
} else {
### BELOW DOES NOT PRODUCE SAMPLING ERRORS, use EXPNS instead (much quicker)
cwd <- data %>%
filter(EVAL_TYP == 'EXPDWM') %>%
distinct(ESTN_UNIT_CN, STRATUM_CN, PLT_CN, CND_CN, .keep_all = TRUE) %>%
group_by(.dots = grpBy, PLT_CN) %>%
summarize(VOL_1HR = sum(FWD_SM_VOLCF_ADJ * aDI * EXPNS, na.rm = TRUE),
VOL_10HR = sum(FWD_MD_VOLCF_ADJ * aDI * EXPNS, na.rm = TRUE),
VOL_100HR = sum(FWD_LG_VOLCF_ADJ * aDI * EXPNS, na.rm = TRUE),
VOL_1000HR = sum(CWD_VOLCF_ADJ * aDI * EXPNS, na.rm = TRUE),
VOL_PILE = sum(PILE_VOLCF_ADJ * aDI * EXPNS, na.rm = TRUE),
VOL = sum(VOL_1HR, VOL_10HR, VOL_100HR, VOL_1000HR, VOL_PILE, na.rm = TRUE),
BIO_DUFF = sum(DUFF_BIOMASS* aDI * EXPNS / 2000, na.rm = TRUE),
BIO_LITTER = sum(LITTER_BIOMASS * aDI * EXPNS / 2000, na.rm = TRUE),
BIO_1HR = sum(FWD_SM_DRYBIO_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
BIO_10HR = sum(FWD_MD_DRYBIO_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
BIO_100HR = sum(FWD_LG_DRYBIO_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
BIO_1000HR = sum(CWD_DRYBIO_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
BIO_PILE = sum(PILE_DRYBIO_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
BIO = sum(BIO_DUFF, BIO_LITTER, BIO_1HR, BIO_10HR, BIO_100HR, BIO_1000HR, BIO_PILE, na.rm = TRUE),
CARB_DUFF = sum(DUFF_CARBON* aDI * EXPNS / 2000, na.rm = TRUE),
CARB_LITTER = sum(LITTER_CARBON * aDI * EXPNS / 2000, na.rm = TRUE),
CARB_1HR = sum(FWD_SM_CARBON_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
CARB_10HR = sum(FWD_MD_CARBON_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
CARB_100HR = sum(FWD_LG_CARBON_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
CARB_1000HR = sum(CWD_CARBON_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
CARB_PILE = sum(PILE_CARBON_ADJ * aDI * EXPNS / 2000, na.rm = TRUE),
CARB = sum(CARB_DUFF, CARB_LITTER, CARB_1HR, CARB_10HR, CARB_100HR, CARB_1000HR, CARB_PILE, na.rm = TRUE),
fa = sum(CONDPROP_UNADJ * aDI * aAdj * EXPNS, na.rm = TRUE),
plotIn = ifelse(sum(aDI > 0, na.rm = TRUE), 1,0)) %>%
group_by(.dots = grpBy) %>%
summarize(AREA_TOTAL = sum(fa, na.rm = TRUE),
VOL_DUFF = NA,
VOL_LITTER = NA,
VOL_1HR = sum(VOL_1HR, na.rm = TRUE),
VOL_10HR = sum(VOL_10HR, na.rm = TRUE),
VOL_100HR = sum(VOL_100HR, na.rm = TRUE),
VOL_1000HR = sum(VOL_1000HR, na.rm = TRUE),
VOL_PILE = sum(VOL_PILE, na.rm = TRUE),
VOL = sum(VOL, na.rm = TRUE),
BIO_DUFF = sum(BIO_DUFF, na.rm = TRUE),
BIO_LITTER = sum(BIO_LITTER, na.rm = TRUE),
BIO_1HR = sum(BIO_1HR, na.rm = TRUE),
BIO_10HR = sum(BIO_10HR, na.rm = TRUE),
BIO_100HR = sum(BIO_100HR, na.rm = TRUE),
BIO_1000HR = sum(BIO_1000HR, na.rm = TRUE),
BIO_PILE = sum(BIO_PILE, na.rm = TRUE),
BIO = sum(BIO, na.rm = TRUE),
CARB_DUFF = sum(CARB_DUFF, na.rm = TRUE),
CARB_LITTER = sum(CARB_LITTER, na.rm = TRUE),
CARB_1HR = sum(CARB_1HR, na.rm = TRUE),
CARB_10HR = sum(CARB_10HR, na.rm = TRUE),
CARB_100HR = sum(CARB_100HR, na.rm = TRUE),
CARB_1000HR = sum(CARB_1000HR, na.rm = TRUE),
CARB_PILE = sum(CARB_PILE, na.rm = TRUE),
CARB = sum(CARB, na.rm = TRUE),
VOL_DUFF_ACRE = NA,
VOL_LITTER_ACRE = NA,
VOL_1HR_ACRE = VOL_1HR / AREA_TOTAL,
VOL_10HR_ACRE = VOL_10HR / AREA_TOTAL,
VOL_100HR_ACRE = VOL_100HR / AREA_TOTAL,
VOL_1000HR_ACRE = VOL_1000HR / AREA_TOTAL,
VOL_PILE_ACRE = VOL_PILE / AREA_TOTAL,
VOL_ACRE = VOL / AREA_TOTAL,
BIO_DUFF_ACRE = BIO_DUFF / AREA_TOTAL,
BIO_LITTER_ACRE = BIO_LITTER / AREA_TOTAL,
BIO_1HR_ACRE = BIO_1HR / AREA_TOTAL,
BIO_10HR_ACRE = BIO_10HR / AREA_TOTAL,
BIO_100HR_ACRE = BIO_100HR / AREA_TOTAL,
BIO_1000HR_ACRE = BIO_1000HR / AREA_TOTAL,
BIO_PILE_ACRE = BIO_PILE / AREA_TOTAL,
BIO_ACRE = BIO / AREA_TOTAL,
CARB_DUFF_ACRE = CARB_DUFF / AREA_TOTAL,
CARB_LITTER_ACRE = CARB_LITTER / AREA_TOTAL,
CARB_1HR_ACRE = CARB_1HR / AREA_TOTAL,
CARB_10HR_ACRE = CARB_10HR / AREA_TOTAL,
CARB_100HR_ACRE = CARB_100HR / AREA_TOTAL,
CARB_1000HR_ACRE = CARB_1000HR / AREA_TOTAL,
CARB_PILE_ACRE = CARB_PILE / AREA_TOTAL,
CARB_ACRE = CARB / AREA_TOTAL,
nPlots = sum(plotIn, na.rm = TRUE))
# Remove the total values if told to do so
if (totals) {
cwd <- cwd %>%
select(grpBy, names(cwd)[str_detect(names(cwd), 'Var', negate = TRUE)], nPlots)
} else {
cwd <- cwd %>%
select(grpBy, names(cwd)[str_detect(names(cwd), 'Var', negate = TRUE) & str_detect(names(cwd), 'ACRE')], nPlots)
}
} # End SE Conditional
# Do some cleanup
#gc()
#Return a dataframe
cwd
}
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