R/zchunk_L2231.land_input_3_irr.R
In bpbond/gcamdata: Build the GCAM Input Datasets
Defines functions
module_aglu_L2231.land_input_3_irr
Documented in
module_aglu_L2231.land_input_3_irr
# Copyright 2019 Battelle Memorial Institute; see the LICENSE file.
#' module_aglu_L2231.land_input_3_irr
#'
#' Produce L2231.LN3_Logit, L2231.LN3_HistUnmgdAllocation, L2231.LN3_UnmgdAllocation,
#' L2231.LN3_HistMgdAllocation_noncrop, L2231.LN3_MgdAllocation_noncrop, L2231.LN3_UnmgdCarbon,
#' L2231.LN3_MgdCarbon_noncrop, L2231.LN3_NoEmissCarbon, L2231.LN3_NodeCarbon, and
#' protected lands related outputs: L2231.LN3_HistUnmgdAllocation_noprot, L2231.LN3_UnmgdAllocation_noprot,
#' L2231.LN1_HistUnmgdAllocation_prot, L2231.LN1_UnmgdAllocation_prot, L2231.LN1_UnmgdCarbon_prot,
#' L2231.LN1_Logit_prot.
#'
#'
#' @param command API command to execute
#' @param ... other optional parameters, depending on command
#' @return Depends on \code{command}: either a vector of required inputs,
#' a vector of output names, or (if \code{command} is "MAKE") all
#' the generated outputs: \code{L2231.LN3_Logit}, \code{L2231.LN3_HistUnmgdAllocation}, \code{L2231.LN3_UnmgdAllocation}, \code{L2231.LN3_NoEmissCarbon}, \code{L2231.LN3_NodeCarbon}, \code{L2231.LN3_HistMgdAllocation_noncrop}, \code{L2231.LN3_MgdAllocation_noncrop}, \code{L2231.LN3_UnmgdCarbon}, \code{L2231.LN3_MgdCarbon_noncrop}. The corresponding file in the
#' original data system was \code{L2231.land_input_3_irr.R} (aglu level2).
#' @details
#' \itemize{
#' \item{"L2231.LN3_Logit: Logit exponent of the third land nest by region.
#' AgLU regions are given externally defined constant logit information."}
#' \item{"L2231.LN3_HistUnmgdAllocation: Historical land cover for unmanaged land (LT_GLU) in the third nest by region.
#' Historical land cover for unmanaged land in the third nest, from L125 land cover data."}
#' \item{"L2231.LN3_UnmgdAllocation: Land cover in the model base periods for unmanaged land (LT_GLU) in the third nest by region.
#' Land cover in the model base periods for unmanaged land in the third nest, from L125 land cover data."}
#' \item{"L2231.LN3_HistMgdAllocation_noncrop: Historical land cover for non-crop managed land (LT_GLU) in the third nest by region.
#' Historical land cover for non-crop managed land in the third nest, from L125 land cover data."}
#' \item{"L2231.LN3_MgdAllocation_noncrop,: Land cover in the model base periods for non-crop managed land (LT_GLU) in the third nest by region.
#' Land cover in the model base periods for non-crop managed land in the third nest, from L125 land cover data."}
#' \item{"L2231.LN3_UnmgdCarbon: Carbon content for unmanaged land (LT_GLU) in third nest by region.
#' Carbon content info for unmanaged land in the third nest including soil and vegetative carbon,
#' from L125 land cover data, L121 carbon content data, and GCAMLandLeaf_CdensityLT assumptions."}
#' \item{"L2231.LN3_MgdCarbon_noncrop: Carbon content for non-crop managed land (LT_GLU) in third nest by region.
#' Carbon content info for non-crop managed land in the third nest including soil and vegetative carbon,
#' from L125 land cover data, L121 carbon content data, and GCAMLandLeaf_CdensityLT assumptions."}
#' \item{"L2231.LN3_NoEmissCarbon: Sets the no-emiss-carbon-calc as the type of carbon to use in forest leaves by region."}
#' \item{"L2231.LN3_NodeCarbon: Sets the node-carbon-calc to drive the carbon calc between forest leaves, by region, and
#' places the node carbon calc in the node just above the leaves."}
#' \item{"L2231.LN3_HistUnmgdAllocation_noprot: Historical unmanaged land data from L223.LN3_HistUnmgdAllocation is multiplied
#' by specified fraction to give unprotected land allocation in the third nest. OtherArableLands omitted."}
#' \item{"L2231.LN3_UnmgdAllocation_noprot: Unmanaged land data from L223.LN3_UnmgdAllocation is multiplied by specified
#' fraction to give "unprotected land allocation in the third nest. OtherArableLands omitted."}
#' \item{"L2231.LN1_HistUnmgdAllocation_prot: Historical unmanaged land data from L223.LN3_HistUnmgdAllocation is multiplied by
#' specified fraction to give protected land allocation in the first nest. OtherArableLands omitted."}
#' \item{"L2231.LN1_UnmgdAllocation_prot: Unmanaged land data from L223.LN3_UnmgdAllocation is multiplied by specified fraction
#' to give protected land allocation in the first nest. OtherArableLands omitted."}
#' \item{" L2231.LN1_UnmgdCarbon_prot: Carbon content info for protected unmanaged land (LT_GLU) in the first nest including
#' soil and vegetative carbon."}
#' \item{"L2231.LN1_Logit_prot: Logit info for protected lands in the first land nest by region"}
#' }
#' @importFrom assertthat assert_that
#' @importFrom dplyr bind_rows distinct filter if_else left_join mutate select
#' @author ACS September 2017
module_aglu_L2231.land_input_3_irr <- function(command, ...) {
if(command == driver.DECLARE_INPUTS) {
return(c(FILE = "common/GCAM_region_names",
FILE = "water/basin_to_country_mapping",
FILE = "aglu/GCAMLandLeaf_CdensityLT",
FILE = "aglu/A_LT_Mapping",
FILE = "aglu/A_LandNode_logit",
FILE = "aglu/A_LandLeaf_Unmgd3",
FILE = "aglu/A_LandLeaf3",
"L121.CarbonContent_kgm2_R_LT_GLU",
"L125.LC_bm2_R_LT_Yh_GLU",
"L120.LC_prot_land_frac_GLU",
"L120.LC_soil_veg_carbon_GLU"))
} else if(command == driver.DECLARE_OUTPUTS) {
return(c("L2231.LN3_Logit",
"L2231.LN3_HistUnmgdAllocation",
"L2231.LN3_UnmgdAllocation",
"L2231.LN3_NoEmissCarbon",
"L2231.LN3_NodeCarbon",
"L2231.LN3_HistMgdAllocation_noncrop",
"L2231.LN3_MgdAllocation_noncrop",
"L2231.LN3_UnmgdCarbon",
"L2231.LN3_MgdCarbon_noncrop",
# Protected land related outputs:
"L2231.LN3_HistUnmgdAllocation_noprot",
"L2231.LN3_UnmgdAllocation_noprot",
"L2231.LN1_HistUnmgdAllocation_prot",
"L2231.LN1_UnmgdAllocation_prot",
"L2231.LN1_UnmgdCarbon_prot",
"L2231.LN1_Logit_prot"))
} else if(command == driver.MAKE) {
all_data <- list(...)[[1]]
# Load required inputs
GCAM_region_names <- get_data(all_data, "common/GCAM_region_names")
basin_to_country_mapping <- get_data(all_data, "water/basin_to_country_mapping")
GCAMLandLeaf_CdensityLT <- get_data(all_data, "aglu/GCAMLandLeaf_CdensityLT")
A_LT_Mapping <- get_data(all_data, "aglu/A_LT_Mapping")
A_LandNode_logit <- get_data(all_data, "aglu/A_LandNode_logit")
A_LandLeaf_Unmgd3 <- get_data(all_data, "aglu/A_LandLeaf_Unmgd3")
A_LandLeaf3 <- get_data(all_data, "aglu/A_LandLeaf3")
L121.CarbonContent_kgm2_R_LT_GLU <- get_data(all_data, "L121.CarbonContent_kgm2_R_LT_GLU")
L125.LC_bm2_R_LT_Yh_GLU <- get_data(all_data, "L125.LC_bm2_R_LT_Yh_GLU", strip_attributes = TRUE)
#This chunk just deals with the unmanaged forest nodes. Therefore we filter the protected area fractions just for unmanaged forests.
L120.LC_prot_land_frac_GLU <- get_data(all_data, "L120.LC_prot_land_frac_GLU", strip_attributes = TRUE) %>%
mutate(Land_Type =if_else(Land_Type == aglu.FOREST_NODE_NAMES, "UnmanagedForest" ,Land_Type)) %>%
filter(Land_Type %in% c(A_LandLeaf_Unmgd3$UnmanagedLandLeaf)) %>%
left_join_error_no_match(basin_to_country_mapping %>%rename(GLU=GLU_code) %>% select(GLU,GLU_name),by=c("GLU")) %>%
mutate(UnmanagedLandLeaf = paste0(Land_Type,"_",GLU_name)) %>%
filter(year==MODEL_FINAL_BASE_YEAR) %>%
select(-year)
if(aglu.CARBON_DATA_SOURCE=="moirai"){
L121.CarbonContent_kgm2_R_LT_GLU <- get_data(all_data, "L120.LC_soil_veg_carbon_GLU")
}else{
L121.CarbonContent_kgm2_R_LT_GLU <- get_data(all_data, "L121.CarbonContent_kgm2_R_LT_GLU")
}
# silence package check notes
GCAM_region_ID <- region <- value <- year <- GLU <- GLU_name <- GLU_code <-
LandLeaf <- Land_Type <- LandNode <- LandNode1 <- LandNode2 <- LandNode3 <- UnmanagedLandLeaf <-
logit.year.fillout <- logit.exponent <- logit.type <- soilTimeScale <- `mature age` <- mature.age <-
soil_c <- veg_c <- LC_bm2 <- LV_milUSD75 <- LV_USD75_bm2 <- LV_USD75_m2 <- HarvCropLand_bm2 <-
unManagedLandValue <- LandAllocatorRoot <- hist.veg.carbon.density <- hist.soil.carbon.density <-
veg.carbon.density <- soil.carbon.density <- allocation <- Land_Type.y <- mature.age.year.fillout <-
min.veg.carbon.density <- min.soil.carbon.density <- no.emiss.carbon.calc <- . <- min_allocation <-
base_allocation <- prot_frac <- NULL
# Process inputs
# Replace GLU names and Add region names as needed
L121.CarbonContent_kgm2_R_LT_GLU %>%
left_join_error_no_match(GCAM_region_names, by = "GCAM_region_ID") %>%
replace_GLU(map = basin_to_country_mapping) %>%
rename(mature.age = `mature age`) ->
L121.CarbonContent_kgm2_R_LT_GLU
L125.LC_bm2_R_LT_Yh_GLU %>%
left_join_error_no_match(GCAM_region_names, by = "GCAM_region_ID") %>%
replace_GLU(map = basin_to_country_mapping) ->
L125.LC_bm2_R_LT_Yh_GLU
# Build tables
# L223.LN3_Logit: Logit exponent of the third nest.
# First, Determine the node combinations applicable at this level.
# Then, match in logit exponents based on the land node 2.
# Finally, append GLU names and keep only relevant columns
L125.LC_bm2_R_LT_Yh_GLU %>%
select(region, GLU, Land_Type) %>%
# not all land types have node matches, so use left_join
left_join(select(A_LT_Mapping, Land_Type, LandNode1, LandNode2, LandNode3),
by = "Land_Type") %>%
select(-Land_Type) %>%
distinct() %>%
na.omit() %>%
mutate(LandAllocatorRoot = "root",
logit.year.fillout = min(MODEL_BASE_YEARS)) %>%
# logit.type is NA by default, so left_join
left_join(select(A_LandNode_logit, logit.exponent, logit.type, LandNode), by = c("LandNode3" = "LandNode")) %>%
append_GLU(var1 = "LandNode1", var2 = "LandNode2", var3 = "LandNode3") %>%
select(LEVEL2_DATA_NAMES[["LN3_Logit"]], LOGIT_TYPE_COLNAME) ->
L223.LN3_Logit
# Land Use History
# Unmanaged land tables
#
# These tables are formed from a master table, made by filtering and adding
# node_leaf_names in L125.LC.
L125.LC_bm2_R_LT_Yh_GLU %>%
filter(Land_Type %in% A_LandLeaf_Unmgd3$UnmanagedLandLeaf,
year %in% c(aglu.LAND_HISTORY_YEARS, MODEL_BASE_YEARS)) %>%
mutate(allocation = round(value, aglu.DIGITS_LAND_USE)) %>%
add_node_leaf_names(nesting_table = A_LandLeaf_Unmgd3, leaf_name = "UnmanagedLandLeaf",
LN1 = "LandNode1", LN2 = "LandNode2", LN3 = "LandNode3") ->
L223.LC_bm2_R_Unmgd3_Yh_GLU
# L223.LN3_HistUnmgdAllocation: Historical land cover, unmanaged land in the third nest
# L223.LN3_UnmgdAllocation: Model base period land cover, unmanaged land in the third nest
# Formed from filtering the master table by different years.
L223.LC_bm2_R_Unmgd3_Yh_GLU %>%
filter(year %in% aglu.LAND_HISTORY_YEARS) %>%
select(LEVEL2_DATA_NAMES[["LN3_HistUnmgdAllocation"]],GCAM_region_ID,GLU) %>%
left_join_error_no_match(basin_to_country_mapping %>%rename(GLU=GLU_name) %>% select(GLU_code,GLU),by=c("GLU"))->
L223.LN3_HistUnmgdAllocation
L223.LC_bm2_R_Unmgd3_Yh_GLU %>%
filter(year %in% MODEL_BASE_YEARS) %>%
select(LEVEL2_DATA_NAMES[["LN3_UnmgdAllocation"]],GCAM_region_ID,GLU) %>%
left_join_error_no_match(basin_to_country_mapping %>%rename(GLU=GLU_name) %>% select(GLU_code,GLU),by=c("GLU"))->
L223.LN3_UnmgdAllocation
# Managed land - non-crop (forest)
# This code will cover any land types we wish to make a `LandLeaf` at level 3 in the future.
#
# These tables are formed from a master table, made by filtering and adding
# node_leaf_names in L125.LC.
L125.LC_bm2_R_LT_Yh_GLU %>%
filter(Land_Type %in% A_LandLeaf3$LandLeaf,
year %in% c(aglu.LAND_HISTORY_YEARS, MODEL_BASE_YEARS)) %>%
mutate(allocation = round(value, aglu.DIGITS_LAND_USE)) %>%
add_node_leaf_names(nesting_table = A_LandLeaf3, leaf_name = "LandLeaf",
LN1 = "LandNode1", LN2 = "LandNode2", LN3 = "LandNode3") ->
L223.LC_bm2_R_Mgd3_Yh_GLU
# L223.LN3_HistMgdAllocation_noncrop: Historical land cover, managed land in the third nest (noncrop)
# L223.LN3_MgdAllocation_noncrop: Model base period land cover, managed land in the third nest (noncrop)
# Formed from filtering the master table by different years.
L223.LC_bm2_R_Mgd3_Yh_GLU %>%
filter(year %in% aglu.LAND_HISTORY_YEARS) %>%
select(LEVEL2_DATA_NAMES[["LN3_HistMgdAllocation"]],GCAM_region_ID,GLU) %>%
left_join_error_no_match(basin_to_country_mapping %>%rename(GLU=GLU_name) %>% select(GLU_code,GLU),by=c("GLU"))->
L223.LN3_HistMgdAllocation_noncrop
L223.LC_bm2_R_Mgd3_Yh_GLU %>%
filter(year %in% MODEL_BASE_YEARS) %>%
select(LEVEL2_DATA_NAMES[["LN3_MgdAllocation"]],GCAM_region_ID,GLU) %>%
left_join_error_no_match(basin_to_country_mapping %>%rename(GLU=GLU_name) %>% select(GLU_code,GLU),by=c("GLU"))->
L223.LN3_MgdAllocation_noncrop
# L223.LN3_UnmgdCarbon: Carbon content info, unmanaged land in the third nest
L223.LC_bm2_R_Unmgd3_Yh_GLU %>%
filter(year == max(MODEL_BASE_YEARS)) %>%
left_join_error_no_match(select(GCAMLandLeaf_CdensityLT, Land_Type, LandLeaf), by = c("Land_Type" = "LandLeaf")) %>%
rename(Cdensity_LT = Land_Type.y) %>%
add_carbon_info(carbon_info_table = L121.CarbonContent_kgm2_R_LT_GLU) %>%
select(LEVEL2_DATA_NAMES[["LN3_UnmgdCarbon"]]) ->
L223.LN3_UnmgdCarbon
# If any regions are zero in all periods, they will return missing values here. The specific value doesn't matter because
# these land use types will be zero in all periods, but there is an assert in the code prohibiting mature age from being zero.
L223.LN3_UnmgdCarbon[is.na(L223.LN3_UnmgdCarbon)] <- 1
# L223.LN3_MgdCarbon_noncrop: Carbon content info, managed land in the third nest, non-crop (forest)
L223.LC_bm2_R_Mgd3_Yh_GLU %>%
filter(year == max(MODEL_BASE_YEARS)) %>%
left_join_error_no_match(select(GCAMLandLeaf_CdensityLT, Land_Type, LandLeaf), by = c("Land_Type" = "LandLeaf")) %>%
rename(Cdensity_LT = Land_Type.y) %>%
add_carbon_info(carbon_info_table = L121.CarbonContent_kgm2_R_LT_GLU) %>%
reduce_mgd_carbon() %>%
select(LEVEL2_DATA_NAMES[["LN3_MgdCarbon"]]) ->
L223.LN3_MgdCarbon_noncrop
# L223.LN3_NoEmissCarbon: Set the no-emiss-carbon-calc as the type of carbon to use in forest leaves.
# Set Forests to use node-carbon-calc at the node level and no-emiss-carbon-calc at the leaf
# to allow them to switch between each other without lots of emissions+uptake.
L223.LN3_UnmgdCarbon %>%
filter(grepl("Forest", UnmanagedLandLeaf)) %>%
select(region, LandAllocatorRoot, LandNode1, LandNode2, LandNode3, UnmanagedLandLeaf) %>%
rename(LandLeaf = UnmanagedLandLeaf) ->
L223.LN3_NoEmissCarbon
L223.LN3_MgdCarbon_noncrop %>%
select(region, LandAllocatorRoot, LandNode1, LandNode2, LandNode3, LandLeaf) %>%
bind_rows(L223.LN3_NoEmissCarbon, .) %>%
# Need to create an empty tag, to do so we have to have a whitespace column and an
# extra column with extraneous data
mutate(no.emiss.carbon.calc = " ",
extra = "junk") ->
L223.LN3_NoEmissCarbon
# L223.LN3_NodeCarbon: Set the node-carbon-calc to drive the carbon calc between forest leaves
L223.LN3_NoEmissCarbon %>%
select(-LandLeaf) %>%
distinct() %>%
rename(node.carbon.calc = no.emiss.carbon.calc) ->
L223.LN3_NodeCarbon
# UNPROTECTED LANDS in the third nest
# Note that OtherArableLand is specifically NOT adjusted.
# function to process unprotected lands
# remove OtherArableLand types from UnmanageLandLeaf and adjust allocation
# grepl is used in filtering out OtherArableLand from UnmanagedLandLeaf
# because entries in UnmanagedLandLeaf are formatted as landtype_basin.
# Note: because of the NodeCarbonCalc, the use of protected lands for forests
# alters land use change emissions. To minimize the consequences,
# we'd like to keep protected lands constant in the historical period and
# equal to the aglu.PROTECT_LAND_FRACT * base_allocation (i.e., value in the final historical year).
# However, in some cases that results in negative land allocation. In those cases,
# we revert to calculating protected area as aglu.PROTECT_LAND_FRACT * allocation in the current year
create_noprot_unmgd <- function(data, base_data, min_data) {
data %>%
filter(!grepl("OtherArable", UnmanagedLandLeaf)) %>%
left_join(base_data %>% select(-GLU_code,-GCAM_region_ID) , by=c("region", "LandAllocatorRoot", "LandNode1", "LandNode2", "LandNode3", "UnmanagedLandLeaf")) %>%
left_join(min_data, by=c("region", "LandAllocatorRoot", "LandNode1", "LandNode2", "LandNode3", "UnmanagedLandLeaf")) %>%
left_join(L120.LC_prot_land_frac_GLU %>% rename(GLU_code =GLU ), by= c("GCAM_region_ID","GLU_code","UnmanagedLandLeaf")) %>%
mutate(prot_frac = if_else(is.na(prot_frac),aglu.PROTECT_DEFAULT,prot_frac),
allocation = if_else(min_allocation < prot_frac * base_allocation,
(1 - prot_frac) * allocation,
allocation - prot_frac * base_allocation))# %>%
#select(-base_allocation, -min_allocation)
} # end create_noprot
# Find unmanaged land allocation in the base year. This is used
# to set the amount of protected land (if possible)
L223.LN3_UnmgdAllocation %>%
filter(!grepl("OtherArable", UnmanagedLandLeaf),
year == max(MODEL_BASE_YEARS)) %>%
rename(base_allocation = allocation) %>%
select(-year) ->
BYUnmgdAllocation
# Find the minimum amount of land in the entire historical period
# by land type and region. This is used to determine how protected
# lands in the historical period are calculated (either as fraction of
# current year or as a fraction of final historical year)
bind_rows(L223.LN3_HistUnmgdAllocation, L223.LN3_UnmgdAllocation) %>%
filter(!grepl("OtherArable", UnmanagedLandLeaf)) %>%
group_by(region, LandAllocatorRoot, LandNode1, LandNode2, LandNode3, UnmanagedLandLeaf) %>%
summarize(min_allocation = min(allocation)) %>%
ungroup() ->
MINUnmgdAllocation
# L223.LN3_HistUnmgdAllocation_noprot: historical unmanaged land cover, no protect
L223.LN3_HistUnmgdAllocation_noprot <- create_noprot_unmgd(L223.LN3_HistUnmgdAllocation, BYUnmgdAllocation, MINUnmgdAllocation)
# L223.LN3_UnmgdAllocation_noprot: unmanaged land cover, no protect
L223.LN3_UnmgdAllocation_noprot <- create_noprot_unmgd(L223.LN3_UnmgdAllocation, BYUnmgdAllocation, MINUnmgdAllocation)
# PROTECTED LANDS in the first nest
# modified land allocations, different names, different nesting structure
# function to process protected lands
# Note: because of the NodeCarbonCalc, the use of protected lands for forests
# alters land use change emissions. To minimize the consequences,
# we'd like to keep protected lands constant in the historical period and
# equal to the aglu.PROTECT_LAND_FRACT * base_allocation (i.e., value in the final historical year).
# However, in some cases that results in negative land allocation. In those cases,
# we revert to calculating protected area as aglu.PROTECT_LAND_FRACT * allocation in the current year
create_prot_unmgd <- function(data, base_data, min_data) {
data %>%
filter(!grepl("OtherArable", UnmanagedLandLeaf)) %>%
left_join(base_data %>% select(-GLU_code,-GCAM_region_ID), by=c("region", "LandAllocatorRoot", "LandNode1", "LandNode2", "LandNode3", "UnmanagedLandLeaf")) %>%
left_join(min_data, by=c("region", "LandAllocatorRoot", "LandNode1", "LandNode2", "LandNode3", "UnmanagedLandLeaf")) %>%
left_join(L120.LC_prot_land_frac_GLU %>% rename(GLU_code =GLU ), by= c("GCAM_region_ID","GLU_code","UnmanagedLandLeaf")) %>%
mutate(prot_frac = if_else(is.na(prot_frac),aglu.PROTECT_DEFAULT,prot_frac),
UnmanagedLandLeaf = paste0("Protected", UnmanagedLandLeaf),
LandNode1 = UnmanagedLandLeaf,
LandNode2 = NULL,
LandNode3 = NULL,
allocation = if_else(min_allocation < prot_frac * base_allocation,
prot_frac * allocation,
prot_frac * base_allocation)) %>%
select(-base_allocation, -min_allocation)
}
# L223.LN1_HistUnmgdAllocation_prot: historical unmanaged land cover, protected
L223.LN1_HistUnmgdAllocation_prot <- create_prot_unmgd(L223.LN3_HistUnmgdAllocation, BYUnmgdAllocation, MINUnmgdAllocation)
# L223.LN1_UnmgdAllocation_prot: unmanaged land cover, protected
L223.LN1_UnmgdAllocation_prot <- create_prot_unmgd(L223.LN3_UnmgdAllocation, BYUnmgdAllocation, MINUnmgdAllocation)
# L223.LN1_UnmgdCarbon_prot: unmanaged carbon info, protected
L223.LN3_UnmgdCarbon %>%
filter(!grepl("OtherArable", UnmanagedLandLeaf)) %>%
mutate(UnmanagedLandLeaf = paste0("Protected", UnmanagedLandLeaf),
LandNode1 = UnmanagedLandLeaf,
LandNode2 = NULL,
LandNode3 = NULL) ->
L223.LN1_UnmgdCarbon_prot
# L223.LN1_Logit_prot: Logit for protected land in the first nest.
L223.LN1_UnmgdAllocation_prot %>%
mutate(unManagedLandValue = aglu.UNMANAGED_LAND_VALUE,
logit.year.fillout = min(MODEL_BASE_YEARS),
logit.exponent = aglu.LN1_PROTUNMGD_LOGIT_EXP,
logit.type = aglu.LN1_PROTUNMGD_LOGIT_TYPE) %>%
select(LEVEL2_DATA_NAMES[["LN1_ValueLogit"]], LOGIT_TYPE_COLNAME) ->
L223.LN1_Logit_prot
# Produce outputs
L223.LN3_Logit %>%
add_title("Logit exponent of the third land nest by region") %>%
add_units("NA") %>%
add_comments("Logit exponent of the third land nest by region. AgLU regions") %>%
add_comments("are given externally defined constant logit information.") %>%
add_legacy_name("L2231.LN3_Logit") %>%
add_precursors("common/GCAM_region_names",
"water/basin_to_country_mapping",
"aglu/A_LandNode_logit",
"aglu/A_LT_Mapping",
"L125.LC_bm2_R_LT_Yh_GLU") ->
L2231.LN3_Logit
L223.LN3_HistUnmgdAllocation %>%
select(LEVEL2_DATA_NAMES[["LN3_HistUnmgdAllocation"]]) %>%
add_title("Historical land cover for unmanaged land (LT_GLU) in the third nest by region.") %>%
add_units("billion square meters (bm2)") %>%
add_comments("Historical land cover for unmanaged land (LT_GLU) in the third nest, from L125 land cover data.") %>%
add_legacy_name("L2231.LN3_HistUnmgdAllocation") %>%
add_precursors("common/GCAM_region_names",
"water/basin_to_country_mapping",
"aglu/A_LandLeaf_Unmgd3",
"L125.LC_bm2_R_LT_Yh_GLU",
"L120.LC_prot_land_frac_GLU") ->
L2231.LN3_HistUnmgdAllocation
L223.LN3_UnmgdAllocation %>%
select(LEVEL2_DATA_NAMES[["LN3_UnmgdAllocation"]]) %>%
add_title("Land cover in the model base periods for unmanaged land (LT_GLU) in the third nest by region") %>%
add_units("billion square meters (bm2) ") %>%
add_comments("Land cover in the model base periods for unmanaged land (LT_GLU) in the third nest, from L125 land cover data.") %>%
add_legacy_name("L2231.LN3_UnmgdAllocation") %>%
same_precursors_as("L2231.LN3_HistUnmgdAllocation") ->
L2231.LN3_UnmgdAllocation
L223.LN3_NoEmissCarbon %>%
add_title("Sets the no-emiss-carbon-calc as the type of carbon to use in forest leaves") %>%
add_units("NA") %>%
add_comments("Sets the no-emiss-carbon-calc as the type of carbon to use in forest leaves, by region.") %>%
add_legacy_name("L2231.LN3_NoEmissCarbon") %>%
same_precursors_as("L2231.LN3_UnmgdCarbon") ->
L2231.LN3_NoEmissCarbon
L223.LN3_NodeCarbon %>%
add_title("Sets the node-carbon-calc to drive the carbon calc between forest leaves") %>%
add_units("NA") %>%
add_comments("Sets the node-carbon-calc to drive the carbon calc between forest leaves, by region, ") %>%
add_comments("and places the node carbon calc in the node just above the leaves.") %>%
add_legacy_name("L2231.LN3_NodeCarbon") %>%
same_precursors_as("L2231.LN3_NoEmissCarbon")->
L2231.LN3_NodeCarbon
L223.LN3_HistMgdAllocation_noncrop %>%
select(LEVEL2_DATA_NAMES[["LN3_HistMgdAllocation"]]) %>%
add_title("Historical land cover for non-crop (forest) managed land (LT_GLU) in the third nest by region.") %>%
add_units("billion square meters (bm2)") %>%
add_comments("Historical land cover for non-crop (forest) managed land (LT_GLU) in the third nest, from L125 land cover data.") %>%
add_legacy_name("L2231.LN3_HistMgdAllocation_noncrop") %>%
add_precursors("common/GCAM_region_names",
"water/basin_to_country_mapping",
"aglu/A_LandLeaf3",
"L125.LC_bm2_R_LT_Yh_GLU") ->
L2231.LN3_HistMgdAllocation_noncrop
L223.LN3_MgdAllocation_noncrop %>%
select(LEVEL2_DATA_NAMES[["LN3_MgdAllocation"]]) %>%
add_title("Land cover in the model base periods for non-crop (forest) managed land (LT_GLU) in the third nest by region") %>%
add_units("billion square meters (bm2) ") %>%
add_comments("Land cover in the model base periods for non-crop (forest) managed land (LT_GLU) in the third nest, from L125 land cover data.") %>%
add_legacy_name("L2231.LN3_MgdAllocation_noncrop") %>%
same_precursors_as("L2231.LN3_HistMgdAllocation_noncrop") ->
L2231.LN3_MgdAllocation_noncrop
L223.LN3_UnmgdCarbon %>%
add_title("Carbon content for unmanaged land (LT_GLU) in third nest by region.") %>%
add_units("Varies") %>%
add_comments("Carbon content info for unmanaged land (LT_GLU) in the third nest including soil and vegetative carbon, ") %>%
add_comments("from L125 land cover data, L121 carbon content data, and GCAMLandLeaf_CdensityLT assumptions") %>%
add_legacy_name("L2231.LN3_UnmgdCarbon") %>%
add_precursors("common/GCAM_region_names",
"water/basin_to_country_mapping",
"aglu/GCAMLandLeaf_CdensityLT",
"aglu/A_LandLeaf_Unmgd3",
"L121.CarbonContent_kgm2_R_LT_GLU",
"L120.LC_soil_veg_carbon_GLU",
"L125.LC_bm2_R_LT_Yh_GLU") ->
L2231.LN3_UnmgdCarbon
L223.LN3_MgdCarbon_noncrop %>%
add_title("Carbon content for non-crop (forest) managed land (LT_GLU) in third nest by region.") %>%
add_units("Varies") %>%
add_comments("Carbon content info for non-crop (forest) managed land (LT_GLU) in the third nest including soil and vegetative carbon, ") %>%
add_comments("from L125 land cover data, L121 carbon content data, and GCAMLandLeaf_CdensityLT assumptions.") %>%
add_legacy_name("L2231.LN3_MgdCarbon_noncrop") %>%
add_precursors("common/GCAM_region_names",
"water/basin_to_country_mapping",
"aglu/GCAMLandLeaf_CdensityLT",
"aglu/A_LandLeaf3",
"L121.CarbonContent_kgm2_R_LT_GLU",
"L120.LC_soil_veg_carbon_GLU",
"L125.LC_bm2_R_LT_Yh_GLU") ->
L2231.LN3_MgdCarbon_noncrop
# Protected lands related outputs:
L223.LN3_HistUnmgdAllocation_noprot %>%
select(LEVEL2_DATA_NAMES[["LN3_HistUnmgdAllocation"]]) %>%
add_title("Unprotected historical unmanged lands in the third nest by basin.") %>%
add_units("thou km2") %>%
add_comments("Historical unmanaged land data from L223.LN3_HistUnmgdAllocation is multiplied by ") %>%
add_comments("specified fraction to give unprotected land allocation in the third nest. OtherArableLands omitted.") %>%
add_legacy_name("L223.LN3_HistUnmgdAllocation_noprot") %>%
same_precursors_as(L223.LN3_HistUnmgdAllocation) ->
L2231.LN3_HistUnmgdAllocation_noprot
L223.LN3_UnmgdAllocation_noprot %>%
select(LEVEL2_DATA_NAMES[["LN3_UnmgdAllocation"]]) %>%
add_title("Unprotected unmanged lands in the third nest by basin.") %>%
add_units("thou km2") %>%
add_comments("Unmanaged land data from L223.LN3_UnmgdAllocation is multiplied by specified fraction to give ") %>%
add_comments("unprotected land allocation in the third nest. OtherArableLands omitted.") %>%
add_legacy_name("L223.LN3_UnmgdAllocation_noprot") %>%
same_precursors_as(L223.LN3_UnmgdAllocation) ->
L2231.LN3_UnmgdAllocation_noprot
L223.LN1_HistUnmgdAllocation_prot %>%
select(LEVEL2_DATA_NAMES[["LN1_HistUnmgdAllocation"]]) %>%
add_title("Protected historical unmanged lands in the first nest by basin.") %>%
add_units("thou km2") %>%
add_comments("Historical unmanaged land data from L223.LN3_HistUnmgdAllocation is multiplied by ") %>%
add_comments("specified fraction to give protected land allocation in the first nest. OtherArableLands omitted.") %>%
add_legacy_name("L223.LN1_HistUnmgdAllocation_prot") %>%
same_precursors_as(L223.LN3_HistUnmgdAllocation) ->
L2231.LN1_HistUnmgdAllocation_prot
L223.LN1_UnmgdAllocation_prot %>%
select(LEVEL2_DATA_NAMES[["LN1_UnmgdAllocation"]]) %>%
add_title("Protected unmanged lands in the first nest by basin.") %>%
add_units("thou km2") %>%
add_comments("Unmanaged land data from L223.LN3_UnmgdAllocation is multiplied by specified fraction to give ") %>%
add_comments("protected land allocation in the first nest. OtherArableLands omitted.") %>%
add_legacy_name("L223.LN1_UnmgdAllocation_prot") %>%
same_precursors_as(L223.LN3_UnmgdAllocation) ->
L2231.LN1_UnmgdAllocation_prot
L223.LN1_UnmgdCarbon_prot %>%
add_title("Carbon content for protected unmanaged land (LT_GLU) in first nest by region.") %>%
add_units("Varies") %>%
add_comments("Carbon content info for protected unmanaged land (LT_GLU) in the first nest including soil and vegetative carbon.") %>%
add_legacy_name("L223.LN1_UnmgdCarbon_prot") %>%
same_precursors_as(L223.LN3_UnmgdCarbon) ->
L2231.LN1_UnmgdCarbon_prot
L223.LN1_Logit_prot %>%
add_title("Logit info for protected lands in the first land nest by region") %>%
add_units("NA") %>%
add_comments("Logit exponent of the first land nest by region. AgLU regions") %>%
add_comments("are given externally defined constant logit information.") %>%
add_legacy_name("L223.LN1_Logit_prot") %>%
same_precursors_as(L2231.LN1_UnmgdAllocation_prot) ->
L2231.LN1_Logit_prot
return_data(L2231.LN3_Logit, L2231.LN3_HistUnmgdAllocation, L2231.LN3_UnmgdAllocation, L2231.LN3_NoEmissCarbon, L2231.LN3_NodeCarbon, L2231.LN3_HistMgdAllocation_noncrop, L2231.LN3_MgdAllocation_noncrop, L2231.LN3_UnmgdCarbon, L2231.LN3_MgdCarbon_noncrop,
# protected land outputs:
L2231.LN3_HistUnmgdAllocation_noprot, L2231.LN3_UnmgdAllocation_noprot, L2231.LN1_HistUnmgdAllocation_prot, L2231.LN1_UnmgdAllocation_prot, L2231.LN1_UnmgdCarbon_prot, L2231.LN1_Logit_prot)
} else {
stop("Unknown command")
}
}
bpbond/gcamdata documentation built on March 22, 2023, 4:52 a.m.
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Defines functions module_aglu_L2231.land_input_3_irr
Documented in module_aglu_L2231.land_input_3_irr
# Copyright 2019 Battelle Memorial Institute; see the LICENSE file.
#' module_aglu_L2231.land_input_3_irr
#'
#' Produce L2231.LN3_Logit, L2231.LN3_HistUnmgdAllocation, L2231.LN3_UnmgdAllocation,
#' L2231.LN3_HistMgdAllocation_noncrop, L2231.LN3_MgdAllocation_noncrop, L2231.LN3_UnmgdCarbon,
#' L2231.LN3_MgdCarbon_noncrop, L2231.LN3_NoEmissCarbon, L2231.LN3_NodeCarbon, and
#' protected lands related outputs: L2231.LN3_HistUnmgdAllocation_noprot, L2231.LN3_UnmgdAllocation_noprot,
#' L2231.LN1_HistUnmgdAllocation_prot, L2231.LN1_UnmgdAllocation_prot, L2231.LN1_UnmgdCarbon_prot,
#' L2231.LN1_Logit_prot.
#'
#'
#' @param command API command to execute
#' @param ... other optional parameters, depending on command
#' @return Depends on \code{command}: either a vector of required inputs,
#' a vector of output names, or (if \code{command} is "MAKE") all
#' the generated outputs: \code{L2231.LN3_Logit}, \code{L2231.LN3_HistUnmgdAllocation}, \code{L2231.LN3_UnmgdAllocation}, \code{L2231.LN3_NoEmissCarbon}, \code{L2231.LN3_NodeCarbon}, \code{L2231.LN3_HistMgdAllocation_noncrop}, \code{L2231.LN3_MgdAllocation_noncrop}, \code{L2231.LN3_UnmgdCarbon}, \code{L2231.LN3_MgdCarbon_noncrop}. The corresponding file in the
#' original data system was \code{L2231.land_input_3_irr.R} (aglu level2).
#' @details
#' \itemize{
#' \item{"L2231.LN3_Logit: Logit exponent of the third land nest by region.
#' AgLU regions are given externally defined constant logit information."}
#' \item{"L2231.LN3_HistUnmgdAllocation: Historical land cover for unmanaged land (LT_GLU) in the third nest by region.
#' Historical land cover for unmanaged land in the third nest, from L125 land cover data."}
#' \item{"L2231.LN3_UnmgdAllocation: Land cover in the model base periods for unmanaged land (LT_GLU) in the third nest by region.
#' Land cover in the model base periods for unmanaged land in the third nest, from L125 land cover data."}
#' \item{"L2231.LN3_HistMgdAllocation_noncrop: Historical land cover for non-crop managed land (LT_GLU) in the third nest by region.
#' Historical land cover for non-crop managed land in the third nest, from L125 land cover data."}
#' \item{"L2231.LN3_MgdAllocation_noncrop,: Land cover in the model base periods for non-crop managed land (LT_GLU) in the third nest by region.
#' Land cover in the model base periods for non-crop managed land in the third nest, from L125 land cover data."}
#' \item{"L2231.LN3_UnmgdCarbon: Carbon content for unmanaged land (LT_GLU) in third nest by region.
#' Carbon content info for unmanaged land in the third nest including soil and vegetative carbon,
#' from L125 land cover data, L121 carbon content data, and GCAMLandLeaf_CdensityLT assumptions."}
#' \item{"L2231.LN3_MgdCarbon_noncrop: Carbon content for non-crop managed land (LT_GLU) in third nest by region.
#' Carbon content info for non-crop managed land in the third nest including soil and vegetative carbon,
#' from L125 land cover data, L121 carbon content data, and GCAMLandLeaf_CdensityLT assumptions."}
#' \item{"L2231.LN3_NoEmissCarbon: Sets the no-emiss-carbon-calc as the type of carbon to use in forest leaves by region."}
#' \item{"L2231.LN3_NodeCarbon: Sets the node-carbon-calc to drive the carbon calc between forest leaves, by region, and
#' places the node carbon calc in the node just above the leaves."}
#' \item{"L2231.LN3_HistUnmgdAllocation_noprot: Historical unmanaged land data from L223.LN3_HistUnmgdAllocation is multiplied
#' by specified fraction to give unprotected land allocation in the third nest. OtherArableLands omitted."}
#' \item{"L2231.LN3_UnmgdAllocation_noprot: Unmanaged land data from L223.LN3_UnmgdAllocation is multiplied by specified
#' fraction to give "unprotected land allocation in the third nest. OtherArableLands omitted."}
#' \item{"L2231.LN1_HistUnmgdAllocation_prot: Historical unmanaged land data from L223.LN3_HistUnmgdAllocation is multiplied by
#' specified fraction to give protected land allocation in the first nest. OtherArableLands omitted."}
#' \item{"L2231.LN1_UnmgdAllocation_prot: Unmanaged land data from L223.LN3_UnmgdAllocation is multiplied by specified fraction
#' to give protected land allocation in the first nest. OtherArableLands omitted."}
#' \item{" L2231.LN1_UnmgdCarbon_prot: Carbon content info for protected unmanaged land (LT_GLU) in the first nest including
#' soil and vegetative carbon."}
#' \item{"L2231.LN1_Logit_prot: Logit info for protected lands in the first land nest by region"}
#' }
#' @importFrom assertthat assert_that
#' @importFrom dplyr bind_rows distinct filter if_else left_join mutate select
#' @author ACS September 2017
module_aglu_L2231.land_input_3_irr <- function(command, ...) {
if(command == driver.DECLARE_INPUTS) {
return(c(FILE = "common/GCAM_region_names",
FILE = "water/basin_to_country_mapping",
FILE = "aglu/GCAMLandLeaf_CdensityLT",
FILE = "aglu/A_LT_Mapping",
FILE = "aglu/A_LandNode_logit",
FILE = "aglu/A_LandLeaf_Unmgd3",
FILE = "aglu/A_LandLeaf3",
"L121.CarbonContent_kgm2_R_LT_GLU",
"L125.LC_bm2_R_LT_Yh_GLU",
"L120.LC_prot_land_frac_GLU",
"L120.LC_soil_veg_carbon_GLU"))
} else if(command == driver.DECLARE_OUTPUTS) {
return(c("L2231.LN3_Logit",
"L2231.LN3_HistUnmgdAllocation",
"L2231.LN3_UnmgdAllocation",
"L2231.LN3_NoEmissCarbon",
"L2231.LN3_NodeCarbon",
"L2231.LN3_HistMgdAllocation_noncrop",
"L2231.LN3_MgdAllocation_noncrop",
"L2231.LN3_UnmgdCarbon",
"L2231.LN3_MgdCarbon_noncrop",
# Protected land related outputs:
"L2231.LN3_HistUnmgdAllocation_noprot",
"L2231.LN3_UnmgdAllocation_noprot",
"L2231.LN1_HistUnmgdAllocation_prot",
"L2231.LN1_UnmgdAllocation_prot",
"L2231.LN1_UnmgdCarbon_prot",
"L2231.LN1_Logit_prot"))
} else if(command == driver.MAKE) {
all_data <- list(...)[[1]]
# Load required inputs
GCAM_region_names <- get_data(all_data, "common/GCAM_region_names")
basin_to_country_mapping <- get_data(all_data, "water/basin_to_country_mapping")
GCAMLandLeaf_CdensityLT <- get_data(all_data, "aglu/GCAMLandLeaf_CdensityLT")
A_LT_Mapping <- get_data(all_data, "aglu/A_LT_Mapping")
A_LandNode_logit <- get_data(all_data, "aglu/A_LandNode_logit")
A_LandLeaf_Unmgd3 <- get_data(all_data, "aglu/A_LandLeaf_Unmgd3")
A_LandLeaf3 <- get_data(all_data, "aglu/A_LandLeaf3")
L121.CarbonContent_kgm2_R_LT_GLU <- get_data(all_data, "L121.CarbonContent_kgm2_R_LT_GLU")
L125.LC_bm2_R_LT_Yh_GLU <- get_data(all_data, "L125.LC_bm2_R_LT_Yh_GLU", strip_attributes = TRUE)
#This chunk just deals with the unmanaged forest nodes. Therefore we filter the protected area fractions just for unmanaged forests.
L120.LC_prot_land_frac_GLU <- get_data(all_data, "L120.LC_prot_land_frac_GLU", strip_attributes = TRUE) %>%
mutate(Land_Type =if_else(Land_Type == aglu.FOREST_NODE_NAMES, "UnmanagedForest" ,Land_Type)) %>%
filter(Land_Type %in% c(A_LandLeaf_Unmgd3$UnmanagedLandLeaf)) %>%
left_join_error_no_match(basin_to_country_mapping %>%rename(GLU=GLU_code) %>% select(GLU,GLU_name),by=c("GLU")) %>%
mutate(UnmanagedLandLeaf = paste0(Land_Type,"_",GLU_name)) %>%
filter(year==MODEL_FINAL_BASE_YEAR) %>%
select(-year)
if(aglu.CARBON_DATA_SOURCE=="moirai"){
L121.CarbonContent_kgm2_R_LT_GLU <- get_data(all_data, "L120.LC_soil_veg_carbon_GLU")
}else{
L121.CarbonContent_kgm2_R_LT_GLU <- get_data(all_data, "L121.CarbonContent_kgm2_R_LT_GLU")
}
# silence package check notes
GCAM_region_ID <- region <- value <- year <- GLU <- GLU_name <- GLU_code <-
LandLeaf <- Land_Type <- LandNode <- LandNode1 <- LandNode2 <- LandNode3 <- UnmanagedLandLeaf <-
logit.year.fillout <- logit.exponent <- logit.type <- soilTimeScale <- `mature age` <- mature.age <-
soil_c <- veg_c <- LC_bm2 <- LV_milUSD75 <- LV_USD75_bm2 <- LV_USD75_m2 <- HarvCropLand_bm2 <-
unManagedLandValue <- LandAllocatorRoot <- hist.veg.carbon.density <- hist.soil.carbon.density <-
veg.carbon.density <- soil.carbon.density <- allocation <- Land_Type.y <- mature.age.year.fillout <-
min.veg.carbon.density <- min.soil.carbon.density <- no.emiss.carbon.calc <- . <- min_allocation <-
base_allocation <- prot_frac <- NULL
# Process inputs
# Replace GLU names and Add region names as needed
L121.CarbonContent_kgm2_R_LT_GLU %>%
left_join_error_no_match(GCAM_region_names, by = "GCAM_region_ID") %>%
replace_GLU(map = basin_to_country_mapping) %>%
rename(mature.age = `mature age`) ->
L121.CarbonContent_kgm2_R_LT_GLU
L125.LC_bm2_R_LT_Yh_GLU %>%
left_join_error_no_match(GCAM_region_names, by = "GCAM_region_ID") %>%
replace_GLU(map = basin_to_country_mapping) ->
L125.LC_bm2_R_LT_Yh_GLU
# Build tables
# L223.LN3_Logit: Logit exponent of the third nest.
# First, Determine the node combinations applicable at this level.
# Then, match in logit exponents based on the land node 2.
# Finally, append GLU names and keep only relevant columns
L125.LC_bm2_R_LT_Yh_GLU %>%
select(region, GLU, Land_Type) %>%
# not all land types have node matches, so use left_join
left_join(select(A_LT_Mapping, Land_Type, LandNode1, LandNode2, LandNode3),
by = "Land_Type") %>%
select(-Land_Type) %>%
distinct() %>%
na.omit() %>%
mutate(LandAllocatorRoot = "root",
logit.year.fillout = min(MODEL_BASE_YEARS)) %>%
# logit.type is NA by default, so left_join
left_join(select(A_LandNode_logit, logit.exponent, logit.type, LandNode), by = c("LandNode3" = "LandNode")) %>%
append_GLU(var1 = "LandNode1", var2 = "LandNode2", var3 = "LandNode3") %>%
select(LEVEL2_DATA_NAMES[["LN3_Logit"]], LOGIT_TYPE_COLNAME) ->
L223.LN3_Logit
# Land Use History
# Unmanaged land tables
#
# These tables are formed from a master table, made by filtering and adding
# node_leaf_names in L125.LC.
L125.LC_bm2_R_LT_Yh_GLU %>%
filter(Land_Type %in% A_LandLeaf_Unmgd3$UnmanagedLandLeaf,
year %in% c(aglu.LAND_HISTORY_YEARS, MODEL_BASE_YEARS)) %>%
mutate(allocation = round(value, aglu.DIGITS_LAND_USE)) %>%
add_node_leaf_names(nesting_table = A_LandLeaf_Unmgd3, leaf_name = "UnmanagedLandLeaf",
LN1 = "LandNode1", LN2 = "LandNode2", LN3 = "LandNode3") ->
L223.LC_bm2_R_Unmgd3_Yh_GLU
# L223.LN3_HistUnmgdAllocation: Historical land cover, unmanaged land in the third nest
# L223.LN3_UnmgdAllocation: Model base period land cover, unmanaged land in the third nest
# Formed from filtering the master table by different years.
L223.LC_bm2_R_Unmgd3_Yh_GLU %>%
filter(year %in% aglu.LAND_HISTORY_YEARS) %>%
select(LEVEL2_DATA_NAMES[["LN3_HistUnmgdAllocation"]],GCAM_region_ID,GLU) %>%
left_join_error_no_match(basin_to_country_mapping %>%rename(GLU=GLU_name) %>% select(GLU_code,GLU),by=c("GLU"))->
L223.LN3_HistUnmgdAllocation
L223.LC_bm2_R_Unmgd3_Yh_GLU %>%
filter(year %in% MODEL_BASE_YEARS) %>%
select(LEVEL2_DATA_NAMES[["LN3_UnmgdAllocation"]],GCAM_region_ID,GLU) %>%
left_join_error_no_match(basin_to_country_mapping %>%rename(GLU=GLU_name) %>% select(GLU_code,GLU),by=c("GLU"))->
L223.LN3_UnmgdAllocation
# Managed land - non-crop (forest)
# This code will cover any land types we wish to make a `LandLeaf` at level 3 in the future.
#
# These tables are formed from a master table, made by filtering and adding
# node_leaf_names in L125.LC.
L125.LC_bm2_R_LT_Yh_GLU %>%
filter(Land_Type %in% A_LandLeaf3$LandLeaf,
year %in% c(aglu.LAND_HISTORY_YEARS, MODEL_BASE_YEARS)) %>%
mutate(allocation = round(value, aglu.DIGITS_LAND_USE)) %>%
add_node_leaf_names(nesting_table = A_LandLeaf3, leaf_name = "LandLeaf",
LN1 = "LandNode1", LN2 = "LandNode2", LN3 = "LandNode3") ->
L223.LC_bm2_R_Mgd3_Yh_GLU
# L223.LN3_HistMgdAllocation_noncrop: Historical land cover, managed land in the third nest (noncrop)
# L223.LN3_MgdAllocation_noncrop: Model base period land cover, managed land in the third nest (noncrop)
# Formed from filtering the master table by different years.
L223.LC_bm2_R_Mgd3_Yh_GLU %>%
filter(year %in% aglu.LAND_HISTORY_YEARS) %>%
select(LEVEL2_DATA_NAMES[["LN3_HistMgdAllocation"]],GCAM_region_ID,GLU) %>%
left_join_error_no_match(basin_to_country_mapping %>%rename(GLU=GLU_name) %>% select(GLU_code,GLU),by=c("GLU"))->
L223.LN3_HistMgdAllocation_noncrop
L223.LC_bm2_R_Mgd3_Yh_GLU %>%
filter(year %in% MODEL_BASE_YEARS) %>%
select(LEVEL2_DATA_NAMES[["LN3_MgdAllocation"]],GCAM_region_ID,GLU) %>%
left_join_error_no_match(basin_to_country_mapping %>%rename(GLU=GLU_name) %>% select(GLU_code,GLU),by=c("GLU"))->
L223.LN3_MgdAllocation_noncrop
# L223.LN3_UnmgdCarbon: Carbon content info, unmanaged land in the third nest
L223.LC_bm2_R_Unmgd3_Yh_GLU %>%
filter(year == max(MODEL_BASE_YEARS)) %>%
left_join_error_no_match(select(GCAMLandLeaf_CdensityLT, Land_Type, LandLeaf), by = c("Land_Type" = "LandLeaf")) %>%
rename(Cdensity_LT = Land_Type.y) %>%
add_carbon_info(carbon_info_table = L121.CarbonContent_kgm2_R_LT_GLU) %>%
select(LEVEL2_DATA_NAMES[["LN3_UnmgdCarbon"]]) ->
L223.LN3_UnmgdCarbon
# If any regions are zero in all periods, they will return missing values here. The specific value doesn't matter because
# these land use types will be zero in all periods, but there is an assert in the code prohibiting mature age from being zero.
L223.LN3_UnmgdCarbon[is.na(L223.LN3_UnmgdCarbon)] <- 1
# L223.LN3_MgdCarbon_noncrop: Carbon content info, managed land in the third nest, non-crop (forest)
L223.LC_bm2_R_Mgd3_Yh_GLU %>%
filter(year == max(MODEL_BASE_YEARS)) %>%
left_join_error_no_match(select(GCAMLandLeaf_CdensityLT, Land_Type, LandLeaf), by = c("Land_Type" = "LandLeaf")) %>%
rename(Cdensity_LT = Land_Type.y) %>%
add_carbon_info(carbon_info_table = L121.CarbonContent_kgm2_R_LT_GLU) %>%
reduce_mgd_carbon() %>%
select(LEVEL2_DATA_NAMES[["LN3_MgdCarbon"]]) ->
L223.LN3_MgdCarbon_noncrop
# L223.LN3_NoEmissCarbon: Set the no-emiss-carbon-calc as the type of carbon to use in forest leaves.
# Set Forests to use node-carbon-calc at the node level and no-emiss-carbon-calc at the leaf
# to allow them to switch between each other without lots of emissions+uptake.
L223.LN3_UnmgdCarbon %>%
filter(grepl("Forest", UnmanagedLandLeaf)) %>%
select(region, LandAllocatorRoot, LandNode1, LandNode2, LandNode3, UnmanagedLandLeaf) %>%
rename(LandLeaf = UnmanagedLandLeaf) ->
L223.LN3_NoEmissCarbon
L223.LN3_MgdCarbon_noncrop %>%
select(region, LandAllocatorRoot, LandNode1, LandNode2, LandNode3, LandLeaf) %>%
bind_rows(L223.LN3_NoEmissCarbon, .) %>%
# Need to create an empty tag, to do so we have to have a whitespace column and an
# extra column with extraneous data
mutate(no.emiss.carbon.calc = " ",
extra = "junk") ->
L223.LN3_NoEmissCarbon
# L223.LN3_NodeCarbon: Set the node-carbon-calc to drive the carbon calc between forest leaves
L223.LN3_NoEmissCarbon %>%
select(-LandLeaf) %>%
distinct() %>%
rename(node.carbon.calc = no.emiss.carbon.calc) ->
L223.LN3_NodeCarbon
# UNPROTECTED LANDS in the third nest
# Note that OtherArableLand is specifically NOT adjusted.
# function to process unprotected lands
# remove OtherArableLand types from UnmanageLandLeaf and adjust allocation
# grepl is used in filtering out OtherArableLand from UnmanagedLandLeaf
# because entries in UnmanagedLandLeaf are formatted as landtype_basin.
# Note: because of the NodeCarbonCalc, the use of protected lands for forests
# alters land use change emissions. To minimize the consequences,
# we'd like to keep protected lands constant in the historical period and
# equal to the aglu.PROTECT_LAND_FRACT * base_allocation (i.e., value in the final historical year).
# However, in some cases that results in negative land allocation. In those cases,
# we revert to calculating protected area as aglu.PROTECT_LAND_FRACT * allocation in the current year
create_noprot_unmgd <- function(data, base_data, min_data) {
data %>%
filter(!grepl("OtherArable", UnmanagedLandLeaf)) %>%
left_join(base_data %>% select(-GLU_code,-GCAM_region_ID) , by=c("region", "LandAllocatorRoot", "LandNode1", "LandNode2", "LandNode3", "UnmanagedLandLeaf")) %>%
left_join(min_data, by=c("region", "LandAllocatorRoot", "LandNode1", "LandNode2", "LandNode3", "UnmanagedLandLeaf")) %>%
left_join(L120.LC_prot_land_frac_GLU %>% rename(GLU_code =GLU ), by= c("GCAM_region_ID","GLU_code","UnmanagedLandLeaf")) %>%
mutate(prot_frac = if_else(is.na(prot_frac),aglu.PROTECT_DEFAULT,prot_frac),
allocation = if_else(min_allocation < prot_frac * base_allocation,
(1 - prot_frac) * allocation,
allocation - prot_frac * base_allocation))# %>%
#select(-base_allocation, -min_allocation)
} # end create_noprot
# Find unmanaged land allocation in the base year. This is used
# to set the amount of protected land (if possible)
L223.LN3_UnmgdAllocation %>%
filter(!grepl("OtherArable", UnmanagedLandLeaf),
year == max(MODEL_BASE_YEARS)) %>%
rename(base_allocation = allocation) %>%
select(-year) ->
BYUnmgdAllocation
# Find the minimum amount of land in the entire historical period
# by land type and region. This is used to determine how protected
# lands in the historical period are calculated (either as fraction of
# current year or as a fraction of final historical year)
bind_rows(L223.LN3_HistUnmgdAllocation, L223.LN3_UnmgdAllocation) %>%
filter(!grepl("OtherArable", UnmanagedLandLeaf)) %>%
group_by(region, LandAllocatorRoot, LandNode1, LandNode2, LandNode3, UnmanagedLandLeaf) %>%
summarize(min_allocation = min(allocation)) %>%
ungroup() ->
MINUnmgdAllocation
# L223.LN3_HistUnmgdAllocation_noprot: historical unmanaged land cover, no protect
L223.LN3_HistUnmgdAllocation_noprot <- create_noprot_unmgd(L223.LN3_HistUnmgdAllocation, BYUnmgdAllocation, MINUnmgdAllocation)
# L223.LN3_UnmgdAllocation_noprot: unmanaged land cover, no protect
L223.LN3_UnmgdAllocation_noprot <- create_noprot_unmgd(L223.LN3_UnmgdAllocation, BYUnmgdAllocation, MINUnmgdAllocation)
# PROTECTED LANDS in the first nest
# modified land allocations, different names, different nesting structure
# function to process protected lands
# Note: because of the NodeCarbonCalc, the use of protected lands for forests
# alters land use change emissions. To minimize the consequences,
# we'd like to keep protected lands constant in the historical period and
# equal to the aglu.PROTECT_LAND_FRACT * base_allocation (i.e., value in the final historical year).
# However, in some cases that results in negative land allocation. In those cases,
# we revert to calculating protected area as aglu.PROTECT_LAND_FRACT * allocation in the current year
create_prot_unmgd <- function(data, base_data, min_data) {
data %>%
filter(!grepl("OtherArable", UnmanagedLandLeaf)) %>%
left_join(base_data %>% select(-GLU_code,-GCAM_region_ID), by=c("region", "LandAllocatorRoot", "LandNode1", "LandNode2", "LandNode3", "UnmanagedLandLeaf")) %>%
left_join(min_data, by=c("region", "LandAllocatorRoot", "LandNode1", "LandNode2", "LandNode3", "UnmanagedLandLeaf")) %>%
left_join(L120.LC_prot_land_frac_GLU %>% rename(GLU_code =GLU ), by= c("GCAM_region_ID","GLU_code","UnmanagedLandLeaf")) %>%
mutate(prot_frac = if_else(is.na(prot_frac),aglu.PROTECT_DEFAULT,prot_frac),
UnmanagedLandLeaf = paste0("Protected", UnmanagedLandLeaf),
LandNode1 = UnmanagedLandLeaf,
LandNode2 = NULL,
LandNode3 = NULL,
allocation = if_else(min_allocation < prot_frac * base_allocation,
prot_frac * allocation,
prot_frac * base_allocation)) %>%
select(-base_allocation, -min_allocation)
}
# L223.LN1_HistUnmgdAllocation_prot: historical unmanaged land cover, protected
L223.LN1_HistUnmgdAllocation_prot <- create_prot_unmgd(L223.LN3_HistUnmgdAllocation, BYUnmgdAllocation, MINUnmgdAllocation)
# L223.LN1_UnmgdAllocation_prot: unmanaged land cover, protected
L223.LN1_UnmgdAllocation_prot <- create_prot_unmgd(L223.LN3_UnmgdAllocation, BYUnmgdAllocation, MINUnmgdAllocation)
# L223.LN1_UnmgdCarbon_prot: unmanaged carbon info, protected
L223.LN3_UnmgdCarbon %>%
filter(!grepl("OtherArable", UnmanagedLandLeaf)) %>%
mutate(UnmanagedLandLeaf = paste0("Protected", UnmanagedLandLeaf),
LandNode1 = UnmanagedLandLeaf,
LandNode2 = NULL,
LandNode3 = NULL) ->
L223.LN1_UnmgdCarbon_prot
# L223.LN1_Logit_prot: Logit for protected land in the first nest.
L223.LN1_UnmgdAllocation_prot %>%
mutate(unManagedLandValue = aglu.UNMANAGED_LAND_VALUE,
logit.year.fillout = min(MODEL_BASE_YEARS),
logit.exponent = aglu.LN1_PROTUNMGD_LOGIT_EXP,
logit.type = aglu.LN1_PROTUNMGD_LOGIT_TYPE) %>%
select(LEVEL2_DATA_NAMES[["LN1_ValueLogit"]], LOGIT_TYPE_COLNAME) ->
L223.LN1_Logit_prot
# Produce outputs
L223.LN3_Logit %>%
add_title("Logit exponent of the third land nest by region") %>%
add_units("NA") %>%
add_comments("Logit exponent of the third land nest by region. AgLU regions") %>%
add_comments("are given externally defined constant logit information.") %>%
add_legacy_name("L2231.LN3_Logit") %>%
add_precursors("common/GCAM_region_names",
"water/basin_to_country_mapping",
"aglu/A_LandNode_logit",
"aglu/A_LT_Mapping",
"L125.LC_bm2_R_LT_Yh_GLU") ->
L2231.LN3_Logit
L223.LN3_HistUnmgdAllocation %>%
select(LEVEL2_DATA_NAMES[["LN3_HistUnmgdAllocation"]]) %>%
add_title("Historical land cover for unmanaged land (LT_GLU) in the third nest by region.") %>%
add_units("billion square meters (bm2)") %>%
add_comments("Historical land cover for unmanaged land (LT_GLU) in the third nest, from L125 land cover data.") %>%
add_legacy_name("L2231.LN3_HistUnmgdAllocation") %>%
add_precursors("common/GCAM_region_names",
"water/basin_to_country_mapping",
"aglu/A_LandLeaf_Unmgd3",
"L125.LC_bm2_R_LT_Yh_GLU",
"L120.LC_prot_land_frac_GLU") ->
L2231.LN3_HistUnmgdAllocation
L223.LN3_UnmgdAllocation %>%
select(LEVEL2_DATA_NAMES[["LN3_UnmgdAllocation"]]) %>%
add_title("Land cover in the model base periods for unmanaged land (LT_GLU) in the third nest by region") %>%
add_units("billion square meters (bm2) ") %>%
add_comments("Land cover in the model base periods for unmanaged land (LT_GLU) in the third nest, from L125 land cover data.") %>%
add_legacy_name("L2231.LN3_UnmgdAllocation") %>%
same_precursors_as("L2231.LN3_HistUnmgdAllocation") ->
L2231.LN3_UnmgdAllocation
L223.LN3_NoEmissCarbon %>%
add_title("Sets the no-emiss-carbon-calc as the type of carbon to use in forest leaves") %>%
add_units("NA") %>%
add_comments("Sets the no-emiss-carbon-calc as the type of carbon to use in forest leaves, by region.") %>%
add_legacy_name("L2231.LN3_NoEmissCarbon") %>%
same_precursors_as("L2231.LN3_UnmgdCarbon") ->
L2231.LN3_NoEmissCarbon
L223.LN3_NodeCarbon %>%
add_title("Sets the node-carbon-calc to drive the carbon calc between forest leaves") %>%
add_units("NA") %>%
add_comments("Sets the node-carbon-calc to drive the carbon calc between forest leaves, by region, ") %>%
add_comments("and places the node carbon calc in the node just above the leaves.") %>%
add_legacy_name("L2231.LN3_NodeCarbon") %>%
same_precursors_as("L2231.LN3_NoEmissCarbon")->
L2231.LN3_NodeCarbon
L223.LN3_HistMgdAllocation_noncrop %>%
select(LEVEL2_DATA_NAMES[["LN3_HistMgdAllocation"]]) %>%
add_title("Historical land cover for non-crop (forest) managed land (LT_GLU) in the third nest by region.") %>%
add_units("billion square meters (bm2)") %>%
add_comments("Historical land cover for non-crop (forest) managed land (LT_GLU) in the third nest, from L125 land cover data.") %>%
add_legacy_name("L2231.LN3_HistMgdAllocation_noncrop") %>%
add_precursors("common/GCAM_region_names",
"water/basin_to_country_mapping",
"aglu/A_LandLeaf3",
"L125.LC_bm2_R_LT_Yh_GLU") ->
L2231.LN3_HistMgdAllocation_noncrop
L223.LN3_MgdAllocation_noncrop %>%
select(LEVEL2_DATA_NAMES[["LN3_MgdAllocation"]]) %>%
add_title("Land cover in the model base periods for non-crop (forest) managed land (LT_GLU) in the third nest by region") %>%
add_units("billion square meters (bm2) ") %>%
add_comments("Land cover in the model base periods for non-crop (forest) managed land (LT_GLU) in the third nest, from L125 land cover data.") %>%
add_legacy_name("L2231.LN3_MgdAllocation_noncrop") %>%
same_precursors_as("L2231.LN3_HistMgdAllocation_noncrop") ->
L2231.LN3_MgdAllocation_noncrop
L223.LN3_UnmgdCarbon %>%
add_title("Carbon content for unmanaged land (LT_GLU) in third nest by region.") %>%
add_units("Varies") %>%
add_comments("Carbon content info for unmanaged land (LT_GLU) in the third nest including soil and vegetative carbon, ") %>%
add_comments("from L125 land cover data, L121 carbon content data, and GCAMLandLeaf_CdensityLT assumptions") %>%
add_legacy_name("L2231.LN3_UnmgdCarbon") %>%
add_precursors("common/GCAM_region_names",
"water/basin_to_country_mapping",
"aglu/GCAMLandLeaf_CdensityLT",
"aglu/A_LandLeaf_Unmgd3",
"L121.CarbonContent_kgm2_R_LT_GLU",
"L120.LC_soil_veg_carbon_GLU",
"L125.LC_bm2_R_LT_Yh_GLU") ->
L2231.LN3_UnmgdCarbon
L223.LN3_MgdCarbon_noncrop %>%
add_title("Carbon content for non-crop (forest) managed land (LT_GLU) in third nest by region.") %>%
add_units("Varies") %>%
add_comments("Carbon content info for non-crop (forest) managed land (LT_GLU) in the third nest including soil and vegetative carbon, ") %>%
add_comments("from L125 land cover data, L121 carbon content data, and GCAMLandLeaf_CdensityLT assumptions.") %>%
add_legacy_name("L2231.LN3_MgdCarbon_noncrop") %>%
add_precursors("common/GCAM_region_names",
"water/basin_to_country_mapping",
"aglu/GCAMLandLeaf_CdensityLT",
"aglu/A_LandLeaf3",
"L121.CarbonContent_kgm2_R_LT_GLU",
"L120.LC_soil_veg_carbon_GLU",
"L125.LC_bm2_R_LT_Yh_GLU") ->
L2231.LN3_MgdCarbon_noncrop
# Protected lands related outputs:
L223.LN3_HistUnmgdAllocation_noprot %>%
select(LEVEL2_DATA_NAMES[["LN3_HistUnmgdAllocation"]]) %>%
add_title("Unprotected historical unmanged lands in the third nest by basin.") %>%
add_units("thou km2") %>%
add_comments("Historical unmanaged land data from L223.LN3_HistUnmgdAllocation is multiplied by ") %>%
add_comments("specified fraction to give unprotected land allocation in the third nest. OtherArableLands omitted.") %>%
add_legacy_name("L223.LN3_HistUnmgdAllocation_noprot") %>%
same_precursors_as(L223.LN3_HistUnmgdAllocation) ->
L2231.LN3_HistUnmgdAllocation_noprot
L223.LN3_UnmgdAllocation_noprot %>%
select(LEVEL2_DATA_NAMES[["LN3_UnmgdAllocation"]]) %>%
add_title("Unprotected unmanged lands in the third nest by basin.") %>%
add_units("thou km2") %>%
add_comments("Unmanaged land data from L223.LN3_UnmgdAllocation is multiplied by specified fraction to give ") %>%
add_comments("unprotected land allocation in the third nest. OtherArableLands omitted.") %>%
add_legacy_name("L223.LN3_UnmgdAllocation_noprot") %>%
same_precursors_as(L223.LN3_UnmgdAllocation) ->
L2231.LN3_UnmgdAllocation_noprot
L223.LN1_HistUnmgdAllocation_prot %>%
select(LEVEL2_DATA_NAMES[["LN1_HistUnmgdAllocation"]]) %>%
add_title("Protected historical unmanged lands in the first nest by basin.") %>%
add_units("thou km2") %>%
add_comments("Historical unmanaged land data from L223.LN3_HistUnmgdAllocation is multiplied by ") %>%
add_comments("specified fraction to give protected land allocation in the first nest. OtherArableLands omitted.") %>%
add_legacy_name("L223.LN1_HistUnmgdAllocation_prot") %>%
same_precursors_as(L223.LN3_HistUnmgdAllocation) ->
L2231.LN1_HistUnmgdAllocation_prot
L223.LN1_UnmgdAllocation_prot %>%
select(LEVEL2_DATA_NAMES[["LN1_UnmgdAllocation"]]) %>%
add_title("Protected unmanged lands in the first nest by basin.") %>%
add_units("thou km2") %>%
add_comments("Unmanaged land data from L223.LN3_UnmgdAllocation is multiplied by specified fraction to give ") %>%
add_comments("protected land allocation in the first nest. OtherArableLands omitted.") %>%
add_legacy_name("L223.LN1_UnmgdAllocation_prot") %>%
same_precursors_as(L223.LN3_UnmgdAllocation) ->
L2231.LN1_UnmgdAllocation_prot
L223.LN1_UnmgdCarbon_prot %>%
add_title("Carbon content for protected unmanaged land (LT_GLU) in first nest by region.") %>%
add_units("Varies") %>%
add_comments("Carbon content info for protected unmanaged land (LT_GLU) in the first nest including soil and vegetative carbon.") %>%
add_legacy_name("L223.LN1_UnmgdCarbon_prot") %>%
same_precursors_as(L223.LN3_UnmgdCarbon) ->
L2231.LN1_UnmgdCarbon_prot
L223.LN1_Logit_prot %>%
add_title("Logit info for protected lands in the first land nest by region") %>%
add_units("NA") %>%
add_comments("Logit exponent of the first land nest by region. AgLU regions") %>%
add_comments("are given externally defined constant logit information.") %>%
add_legacy_name("L223.LN1_Logit_prot") %>%
same_precursors_as(L2231.LN1_UnmgdAllocation_prot) ->
L2231.LN1_Logit_prot
return_data(L2231.LN3_Logit, L2231.LN3_HistUnmgdAllocation, L2231.LN3_UnmgdAllocation, L2231.LN3_NoEmissCarbon, L2231.LN3_NodeCarbon, L2231.LN3_HistMgdAllocation_noncrop, L2231.LN3_MgdAllocation_noncrop, L2231.LN3_UnmgdCarbon, L2231.LN3_MgdCarbon_noncrop,
# protected land outputs:
L2231.LN3_HistUnmgdAllocation_noprot, L2231.LN3_UnmgdAllocation_noprot, L2231.LN1_HistUnmgdAllocation_prot, L2231.LN1_UnmgdAllocation_prot, L2231.LN1_UnmgdCarbon_prot, L2231.LN1_Logit_prot)
} else {
stop("Unknown command")
}
}
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