growthTrendR (version 0.2.1)

CFS_scale: Quality assessment: ring-width measurement at plot level

Description

Apply a k-nearest neighbors (k-NN) method based on geographic location for the same species. It compares the median tree-ring measurements of a specific site to those of nearby sites

Usage

CFS_scale(
  target_site,
  ref_sites,
  scale.label_data_ref = "",
  scale.max_dist_km = 20,
  scale.N_nbs = 10
)

Value

A data table containing the median ring-width measurements of the involved sites, along with the distances from the specific site

Arguments

target_site

data.table with columns uid_site, site_id, species, longitude and latitude

ref_sites

reference sites including species, uid_site, latitude, longitude, uid_radius, year, rw_mm in long format

scale.label_data_ref

description of ref_sites

scale.max_dist_km

maximum distance to search the neighbors in km

scale.N_nbs

number of nearest-neighbors (maximum)

Examples

# loading formatted
dt.samples_trt <- readRDS(system.file("extdata", "dt.samples_trt.rds", package = "growthTrendR"))
all.sites <- dt.samples_trt$tr_all_wide[,.N, by = c("species", "uid_site", "site_id")][, N:=NULL]
dupes <- all.sites[, .N, by = .(species, site_id)][N > 1]
# e.g. taking the target sites
target_site <- all.sites[c(1,2), -"uid_site"]
ref.sites <- merge(
dt.samples_trt$tr_all_wide[,c("species", "uid_site", "site_id",
 "latitude","longitude", "uid_radius")],
dt.samples_trt$tr_all_long$tr_7_ring_widths, by = c("uid_radius"))
dt.scale <- CFS_scale( target_site = target_site, ref_sites = ref.sites,
scale.label_data_ref = "demo-samples", scale.max_dist_km = 200, scale.N_nbs = 2)