correct_all: Full correction of a Forest Inventories Dataset
In EcoFoG/ForestData: Post-inventory processing of Forest Census datasets

Description Usage Arguments Value Examples

correct_all performs corrections for tree life status, overgrown recruits cases, size measurement errors and POM changes, by calling correct_alive, correct_size and correct_recruits in this order.

correct_all(
  data,
  id_col = getOption("id_col"),
  time_col = getOption("time_col"),
  status_col = getOption("status_col"),
  plot_col = getOption("plot_col"),
  byplot = TRUE,
  dead_confirmation_censuses = 2,
  use_size = FALSE,
  invariant_columns = c("Genus", "Species", "binomial_name", "Forest", "Family"),
  size_col = getOption("size_col"),
  species_col = "binomial_name",
  POM_col = getOption("POM_col"),
  measure_type = getOption("measure_type"),
  positive_growth_threshold = 5,
  negative_growth_threshold = -2,
  default_POM = 1.3,
  pioneers = c("Cecropia", "Pourouma"),
  pioneers_treshold = 7.5,
  dbh_min = 10
)

`data`	data.frame, containing forest inventories in the form of a long-format time series - one line corresponds to a measurement for one individual at a given census time.
`id_col`	character, name of the column containing trees unique IDs.
`time_col`	character, name of the column containing census years.
`status_col`	character, name of the column corresponding to tree status: 0/FALSE for dead, 1/TRUE for alive.
`plot_col`	character, name of the column containing plot indices or names.
`byplot`	logical, indicating whether the function has to process the data by plot (TRUE)or for the whole dataset (FALSE).
`dead_confirmation_censuses`	integer, defaults to 2: number of consecutive censuses for which a tree is unseen that are needed to consider the tree as dead. NB: for the trees unseen during the dead_confirmation_censuses -1 last inventories, the status cannot be corrected, thus mortality rates should not be calculated for these censuses.
`use_size`	character, defaults to FALSE. Optional argument specifying whether to use measurement column (circumference or diameter) to create a vital status field in case it does not already exist. See Details.
`invariant_columns`	character vector, containing the name of the columns for which value remain constant for a given tree (for example species name or coordinates). When a row is added by the function correct_alive, values for invariant columns are taken from the value for other censuses. Defaults to null
`size_col`	character, name of the column corresponding to tree size (circumference or diameter) measurements .
`species_col`	character, name of th column containing full species names (or other taxonomic identification)
`POM_col`	character, name of the column corresponding the Point Of Measurement (POM).
`measure_type`	character, partially matching “Circumference” or “Diameter”, indicating what is the type of the measurements.
`positive_growth_threshold`	positive numeric or integer, threshold over which an annual DIAMETER growth is considered abnormal (in cm). Defaults to 5 cm.
`negative_growth_threshold`	negative numeric or integer, threshold under which an absolute DIAMETER difference is considered abnormal. To be given in centimeters. Defaults to -2 cm. Note that this threshold is applied between two consecutive censuses, regardless of the time between them, as it assumes that a tree diameter cannot decrease more than this value, even over a long period.
`default_POM`	scalar numeric, default POM used in the dataset, in the same unit as the POM. When the value in POM_col is different from default_POM, the corrected size is given at default_POM . It defaults to 1.3 meters-according to current practice of measurement of diameter at breast height (DBH).
`pioneers`	character vector containing full species name (or other taxonomic identification)for which a specific positive growth threshold (used for instance for fast growing species for which the threshold to detect an abnormal growth is high).
`pioneers_treshold`	Positive DIAMETER growth limit to apply to pioneer species (specified in 'pioneers'), similar to . Expressed in centimeters. Defaults to 7.5 cm
`dbh_min`	scalar integer or numeric, indicating the minimum DIAMETER (in centimeters) at the default measurement height from which trees are recorded. Defaults to 10 cm.

A data.frame with additional columns: status_corr and size_corr for corrected tree vital status and size, code_corr for correction tag and types.

data(example_census)

# Short version: parameters specified using prepare_forestdata and default values

prepare_forestdata(example_census,
plot_col="Plot",
id_col="idTree",
time_col="CensusYear",
 status_col = "CodeAlive",
 size_col="Circ",
 measure_type = "C",
 POM_col = "POM")

all_cors <- suppressWarnings(correct_all(example_census,
invariant_columns = c("Genus",
                      "Species",
                      "binomial_name",
                      "Forest",
                      "Family"),
species_col = "binomial_name",#tag pioneer
measure_type = getOption("measure_type"),
pioneers = c("Cecropia","Pourouma"),#tag pioneer
pioneers_treshold = 7.5))

# Full call:

all_cors <- suppressWarnings(correct_all(example_census,
id_col = "idTree",
time_col = "CensusYear",
status_col = "CodeAlive",
plot_col = "Plot",
byplot = TRUE,
dead_confirmation_censuses = 2,
use_size = FALSE,
invariant_columns = c("Genus",
                      "Species",
                      "binomial_name",
                      "Forest",
                      "Family"),
size_col = "Circ",
species_col = "binomial_name",#tag pioneer
POM_col = "POM",
measure_type = "C",
positive_growth_threshold = 5,
negative_growth_threshold = -2,
default_POM = 1.3,
pioneers = c("Cecropia","Pourouma"),#tag pioneer
pioneers_treshold = 7.5,
dbh_min = 10))

str(all_cors)