forestSummaries/source_script_NETN.R at main · KateMMiller/forestSummaries · GitHub

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#--------------------------------
# Source Script for forestNETN Data Summaries
# Written by Kate Miller 6/30/2022
#--------------------------------

# Imports/Libraries
library(forestNETN)
library(forestTrends)
library(tidyverse)
library(sf)

importData()

# Downgrade Fraxinus to subcanopy species
VIEWS_NETN$Taxa_NETN$IsCanopyExclusion[VIEWS_NETN$Taxa_NETN$Genus == "Fraxinus"] <- TRUE
#VIEWS_NETN$Taxa_NETN$IsCanopyExclusion[VIEWS_NETN$Taxa_NETN$Genus == "Fagus"] <- FALSE

# Set parameters
park = 'MORR'#'ACAD'
from = 2006
from_4yr = 2022 #2021
to = 2024
report_year = 2024 # used for file path and output naming, in case differs from last year sampled
QAQC = FALSE
locType = 'all'
cycle_latest = 5
park_crs = ifelse(park %in% c("ACAD", "MIMA"), 26919, 26918)
num_plots = case_when(park == "ACAD" ~ 176,
                      park == "MABI" ~ 24,
                      park == "MIMA" ~ 20,
                      park == "MORR" ~ 28,
                      park == "ROVA" ~ 40,
                      park == "SAGA" ~ 21,
                      park == "SARA" ~ 32,
                      park == "WEFA" ~ 10)
plot_size = ifelse(park == "ACAD", 225, 400)
from_prev = 2016
to_prev = 2019

args_all = list(park = park, from = from, to = to, QAQC = QAQC, locType = locType)
args_4yr = list(park = park, from = from_4yr, to = to, QAQC = QAQC, locType = locType)
args_vs = list(park = park, from = from, to = to, QAQC = QAQC, locType = "VS")

# Set up file structure
# report_year = 2024 # only here for testing. Defined in MIDN_figures_and_tables.RMD params.
if(!exists("path")){path = paste0('./output/', report_year, "/NETN/")} #general path that should work for everyone

invisible(lapply(park, function(x) {
  if(!dir.exists(paste0(path, x))){dir.create(paste0(path, x))}
})
)
# Set up file structure
#parks <- c("ACAD", "MABI", "MIMA", "MORR", "ROVA", "SAGA", "SARA", "WEFA")
#parks <- c("ACAD", "MABI", "MIMA", "SAGA", "SARA")
parks <- c("ACAD", "MORR", "ROVA", "WEFA")

if(!dir.exists(paste0("./output/", report_year))){dir.create(paste0("./output/", report_year, "/"))}
if(!dir.exists(paste0("./output/", report_year, "/NETN/"))){dir.create(paste0("./output/", report_year, "/NETN/"))}

invisible(lapply(parks, function(x) {
  if(!dir.exists(paste0(path, x))){dir.create(paste0(path, x))}
})
)

new_path = paste0(path, park, "/")

if(!dir.exists(new_path)){dir.create(new_path)}

folders <- c("ArcPro_projects", "figures", "map_exports", "shapefiles", "tables")

invisible(lapply(folders, function(x) {
  if(!dir.exists(paste0(new_path, x))){dir.create(paste0(new_path, x))}
})
)

trspp_grps <- read.csv("NPS_tree_species_groups.csv")

# Source files
# source('./scripts/forest_summary_code_NETN.R')
# source('./scripts/regen_debt_metrics_NETN.R')
# source('./scripts/tree_regen_stem_changes_by_species_loess_NETN.R')

#
# source("./scripts/forest_summary_code_ACAD.R")