data_preparation: ForestGEO-like data preparation.

In ervanSTRI/AGBflux_pack: Set of functions to format, correct and compute AGB fluxes from CTFS-formated data.

Description

Main routine to format, detect major obvious errors, and gap-fill those errors in ForestGEO-like data.

Usage

data_preparation(path, stem, site, dbh_units = "mm", WD = NULL,
  taper_correction = TRUE, fill_missing = TRUE,
  use_palm_allometry = TRUE, flag_stranglers = TRUE,
  dbh_stranglers = 500, maxrel = 0.2, write_errors_to = NULL,
  graph_problems_to = NULL, exclude_interval = NULL)

Arguments

path	String giving a path to a parent directory containing species and census datasets.
stem	TRUE(default) or FALSE reflect that your censuses are ForestGEO stem or tree (aka full) tables, respectively.
site	String giving the name of your site – one of one of site.info$site (e.g., 'barro colorado island'.
dbh_units	set the unit ("mm" or "cm") of DBH values, by default dbh_units=="mm".
WD	Optional, provide an external data.frame of wood densities by species.
taper_correction	TRUE or FALSE, apply Cushman et al (2014) taper correction.
fill_missing	TRUE or FALSE, interpolate missing DBH values.
use_palm_allometry	TRUE or FALSE, if TRUE, compute biomass of palm trees using a palm-specific allometric model from Goodman et al. (2013).
flag_stranglers	TRUE or FALSE, individuals of known strangler fig species greater than 'dbh_stranglers' are flagged
dbh_stranglers	(optional) Minimal diameter (in mm) of strangler figs, default = 500.
maxrel	A numeric value: the threshold for flagging major errors in productivity, applied as absval(individual-tree-productivity) > maxrel * (average-productivity-per-hectare).
write_errors_to	A string giving a directory with the format "path/to/file" (without extension) to output all records for trees with major errors in productivity to a csv file. Defaults to not write such a file.
graph_problems_to	A string giving a directory with the format "path/to/file" (without extension) to output graphs showing problematic trees. The output may be multiple files, for example: path/to/file_1.pdf,path/to/file_2.pdf, path/to/file_3.pdf, and so on. Defaults to not write such files.
exclude_interval	NULL by default. If needed a vector (e.g. c(1,2)) indicating which census interval(s) must be discarded from computation due, for instance, to a change in measurement protocol.

Value

A data.table (data.frame) with all relevant variables.

Examples

data_preparation(
  path = agb_example("data"),
  site = "barro colorado island",
  stem = TRUE
)

ervanSTRI/AGBflux_pack documentation built on Oct. 15, 2021, 6:44 p.m.