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Fix biomass missing cols #1

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merged 4 commits into from
Jul 21, 2024
Merged

Fix biomass missing cols #1

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636c5d2
Fixes errors due to missing columns in current FIA databases.
Jul 18, 2024
b4dbaaa
restores so Jenkins method will work
Jul 18, 2024
7c8aafd
removes STANDING_DEAD and modelSnag functionality
Jul 18, 2024
ac23433
Fixes pre-existing bug in Jenkins calculations for foliage, removing …
Jul 18, 2024
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29 changes: 14 additions & 15 deletions R/biomass_new.R
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Original file line number Diff line number Diff line change
Expand Up @@ -63,8 +63,8 @@ bioStarter <- function(x,
warning(paste('Method', method,
'unknown. Defaulting to Temporally Indifferent (TI).'))
}
if (any(stringr::str_to_upper(component) %in% c('AG', 'ROOTS', 'BOLE', "TOP", "FOLIAGE", "STUMP", "SAPLING", "WDLD_SPP", "TOTAL")) == FALSE) {
stop('Unknown component. Must be a combination of: "AG", "ROOTS", "BOLE", "TOP", "FOLIAGE", "STUMP", "SAPLING", and "WDLD_SPP". Alternatively, use "TOTAL" for a sum of all components, and set "byComponent=TRUE" to estimate all components simultaneously.')
if (any(stringr::str_to_upper(component) %in% c('AG', 'ROOTS', 'STEM', "BRANCH", "FOLIAGE", "STUMP", "TOTAL")) == FALSE) {
stop('Unknown component. Must be a combination of: "AG", "ROOTS", "STEM", "BRANCH", "FOLIAGE", "STUMP". Alternatively, use "TOTAL" for a sum of all components, and set "byComponent=TRUE" to estimate all components simultaneously.')
}

## Biomass method warnings
Expand All @@ -91,8 +91,8 @@ bioStarter <- function(x,

## When component = AG or total, replace with component names
component = stringr::str_to_upper(unique(component))
if ('TOTAL' %in% component | byComponent) {component <- c('ROOTS', 'BOLE', "TOP", "FOLIAGE", "STUMP", "SAPLING", "WDLD_SPP")}
if ('AG' %in% component & byComponent == FALSE) {component <- unique(c(component[component != 'AG'], 'BOLE', "TOP", "STUMP", "SAPLING", "WDLD_SPP"))}
if ('TOTAL' %in% component | byComponent) {component <- c("ROOTS", "STEM", "BRANCH", "FOLIAGE", "STUMP")}
if ('AG' %in% component & byComponent == FALSE) {component <- unique(c(component[component != "AG"], "STEM", "BRANCH", "FOLIAGE", "STUMP"))}



Expand Down Expand Up @@ -196,10 +196,9 @@ bioStarter <- function(x,
jBoleBio = (jTotal * stemRatio) + (jTotal * barkRatio),
jLeafBio = jTotal * leafRatio,
adj = dplyr::case_when(is.na(DIA) ~ NA_real_,
!is.na(DRYBIO_WDLD_SPP) ~ DRYBIO_WDLD_SPP / (jTotal - jLeafBio),
DIA >= 5 ~ DRYBIO_BOLE / jBoleBio,
DIA >= 5 ~ DRYBIO_STEM / jBoleBio,
TRUE ~ JENKINS_SAPLING_ADJUSTMENT),
DRYBIO_FOLIAGE = dplyr::case_when(STATUSCD == 1 ~ jLeafBio * adj,
DRYBIO_FOLIAGE = dplyr::case_when(STATUSCD == 1 ~ jLeafBio,
STATUSCD == 2 ~ 0,
TRUE ~ NA_real_)) %>%
as.data.frame()
Expand All @@ -209,15 +208,15 @@ bioStarter <- function(x,
if (bioMethod == 'JENKINS') {
db$TREE <- db$TREE %>%
## Replacing component ratio biomass estimates w/ Jenkins
dplyr::mutate(DRYBIO_BOLE = jBoleBio,
dplyr::mutate(DRYBIO_STEM = jBoleBio,
## adj defined above - ratio of volume-based biomass estimates and
## diameter-based estimates for bole volume
DRYBIO_TOP = DRYBIO_TOP / adj,
DRYBIO_BRANCH = DRYBIO_BRANCH / adj,
DRYBIO_STUMP = DRYBIO_STUMP / adj,
DRYBIO_BG = DRYBIO_BG / adj,
DRYBIO_SAPLING = DRYBIO_SAPLING / adj,
DRYBIO_WDLD_SPP = DRYBIO_WDLD_SPP / adj,
DRYBIO_FOLIAGE = DRYBIO_WDLD_SPP / adj)
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This looks like a bug in rFIA originally

# DRYBIO_SAPLING = DRYBIO_SAPLING / adj,
# DRYBIO_WDLD_SPP = DRYBIO_WDLD_SPP / adj,
DRYBIO_FOLIAGE = DRYBIO_FOLIAGE / adj)
}


Expand Down Expand Up @@ -263,8 +262,8 @@ bioStarter <- function(x,
db$TREE <- db$TREE %>%
dplyr::select(c(PLT_CN, CONDID, DIA, SPCD, TPA_UNADJ,
SUBP, TREE, dplyr::all_of(grpT), tD, typeD,
DRYBIO_TOP, DRYBIO_BOLE, DRYBIO_STUMP, DRYBIO_ROOTS = DRYBIO_BG,
DRYBIO_SAPLING, DRYBIO_WDLD_SPP, DRYBIO_FOLIAGE)) %>%
DRYBIO_BRANCH, DRYBIO_STEM, DRYBIO_STUMP, DRYBIO_ROOTS = DRYBIO_BG,
DRYBIO_FOLIAGE)) %>%
## Drop plots outside our domain of interest
dplyr::filter(!is.na(DIA) & TPA_UNADJ > 0 & tD == 1 & typeD == 1) %>%
## Drop visits not used in our eval of interest
Expand All @@ -291,7 +290,7 @@ bioStarter <- function(x,

## Convert to long format, where biomass component is the observation (multiple per tree)
data <- data %>%
tidyr::pivot_longer(cols = DRYBIO_TOP:DRYBIO_FOLIAGE,
tidyr::pivot_longer(cols = DRYBIO_BRANCH:DRYBIO_FOLIAGE,
names_to = c(".value", 'COMPONENT'),
names_sep = 7) %>%
dplyr::rename(DRYBIO = DRYBIO_) %>%
Expand Down
62 changes: 31 additions & 31 deletions R/carbon_new.R
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Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@ carbonStarter <- function(x,
COND_STATUS_CD, CONDID,
dplyr::all_of(grpC), aD, landD,
CARBON_DOWN_DEAD, CARBON_LITTER,
CARBON_SOIL_ORG, CARBON_STANDING_DEAD,
CARBON_SOIL_ORG, #CARBON_STANDING_DEAD,
CARBON_UNDERSTORY_AG, CARBON_UNDERSTORY_BG)) %>%
## Drop non-forested plots, and those otherwise outside our domain of interest
dplyr::filter(aD == 1 & landD == 1) %>%
Expand Down Expand Up @@ -202,7 +202,7 @@ carbonStarter <- function(x,
dplyr::summarize(AG_UNDER_LIVE = sum(CONDPROP_UNADJ * CARBON_UNDERSTORY_AG * aDI, na.rm = TRUE),
BG_UNDER_LIVE = sum(CONDPROP_UNADJ * CARBON_UNDERSTORY_BG * aDI, na.rm = TRUE),
DOWN_DEAD = sum(CONDPROP_UNADJ * CARBON_DOWN_DEAD * aDI, na.rm = TRUE),
STAND_DEAD_MOD = sum(CONDPROP_UNADJ * CARBON_STANDING_DEAD * aDI, na.rm = TRUE),
# STAND_DEAD_MOD = sum(CONDPROP_UNADJ * CARBON_STANDING_DEAD * aDI, na.rm = TRUE),
LITTER = sum(CONDPROP_UNADJ * CARBON_LITTER * aDI, na.rm = TRUE),
SOIL_ORG = sum(CONDPROP_UNADJ * CARBON_SOIL_ORG * aDI, na.rm = TRUE),
PROP_FOREST = sum(CONDPROP_UNADJ * aDI, na.rm = TRUE)) %>%
Expand All @@ -224,16 +224,16 @@ carbonStarter <- function(x,
dplyr::left_join(t, by = c('PLT_CN', grpBy))

## Decide which estimate to use for snags
if (modelSnag){
t <- t %>%
dplyr::mutate(STAND_DEAD = STAND_DEAD_MOD) %>%
dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))
# if (modelSnag){
# t <- t %>%
# dplyr::mutate(STAND_DEAD = STAND_DEAD_MOD) %>%
# dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))

} else {
t <- t %>%
dplyr::mutate(STAND_DEAD = AG_OVER_DEAD + BG_OVER_DEAD) %>%
dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))
}
# } else {
# t <- t %>%
# dplyr::mutate(STAND_DEAD = AG_OVER_DEAD + BG_OVER_DEAD) %>%
# dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))
# }


## Convert to long format, where rows are ecosystem components
Expand Down Expand Up @@ -301,7 +301,7 @@ carbonStarter <- function(x,
dplyr::mutate(AG_UNDER_LIVE = CONDPROP_UNADJ * CARBON_UNDERSTORY_AG * aDI,
BG_UNDER_LIVE = CONDPROP_UNADJ * CARBON_UNDERSTORY_BG * aDI,
DOWN_DEAD = CONDPROP_UNADJ * CARBON_DOWN_DEAD * aDI,
STAND_DEAD_MOD = CONDPROP_UNADJ * CARBON_STANDING_DEAD * aDI,
# STAND_DEAD_MOD = CONDPROP_UNADJ * CARBON_STANDING_DEAD * aDI,
LITTER = CONDPROP_UNADJ * CARBON_LITTER * aDI,
SOIL_ORG = CONDPROP_UNADJ * CARBON_SOIL_ORG * aDI,
PROP_FOREST = CONDPROP_UNADJ * aDI) %>%
Expand Down Expand Up @@ -351,16 +351,16 @@ carbonStarter <- function(x,


## Decide which estimate to use for snags
if (modelSnag){
t <- t %>%
dplyr::mutate(STAND_DEAD = STAND_DEAD_MOD) %>%
dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))
# if (modelSnag){
# t <- t %>%
# dplyr::mutate(STAND_DEAD = STAND_DEAD_MOD) %>%
# dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))

} else {
t <- t %>%
dplyr::mutate(STAND_DEAD = AG_OVER_DEAD + BG_OVER_DEAD) %>%
dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))
}
# } else {
# t <- t %>%
# dplyr::mutate(STAND_DEAD = AG_OVER_DEAD + BG_OVER_DEAD) %>%
# dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))
# }

## Convert to long format, where rows are ecosystem components
t <- t %>%
Expand Down Expand Up @@ -415,16 +415,16 @@ carbonStarter <- function(x,


## Decide which estimate to use for snags
if (modelSnag){
tPlt <- tPlt %>%
dplyr::mutate(STAND_DEAD = STAND_DEAD_MOD) %>%
dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))

} else {
tPlt <- tPlt %>%
dplyr::mutate(STAND_DEAD = AG_OVER_DEAD + BG_OVER_DEAD) %>%
dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))
}
# if (modelSnag){
# tPlt <- tPlt %>%
# dplyr::mutate(STAND_DEAD = STAND_DEAD_MOD) %>%
# dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))

# } else {
# tPlt <- tPlt %>%
# dplyr::mutate(STAND_DEAD = AG_OVER_DEAD + BG_OVER_DEAD) %>%
# dplyr::select(-c(AG_OVER_DEAD, BG_OVER_DEAD, STAND_DEAD_MOD))
# }

## Convert to long format, where rows are ecosystem components
tPlt <- tPlt %>%
Expand Down