Description Usage Arguments Value Examples
View source: R/compute_recruitment.R
This function computes recruitment in forest inventories according to plot
1 2 3 4 5 6 7 8 9 10 11 | compute_recruitment(
data,
status_col = "status_corr",
time_col = ifelse(is.null(getOption("time_col")), "CensusYear",
getOption("time_col")),
id_col = ifelse(is.null(getOption("id_col")), "idTree", getOption("id_col")),
dead_confirmation_censuses = 2,
byplot = TRUE,
plot_col = ifelse(is.null(getOption("plot_col")), "Plot", getOption("plot_col")),
corrected = TRUE
)
|
data |
A data.frame containing a time-series tree-wise forest inventory -i.e. every line is a single tree measurement for a single year. |
status_col |
Character. The name of the column containing tree vital status - 0=dead; 1=alive. |
time_col |
Character. The name of the column containing census year |
id_col |
Character. The name of the column containing trees unique ids |
dead_confirmation_censuses |
Integer, defaults to 2. This is the number of censuses needed to state that a tree is considered dead, if unseen. In Paracou, we use the rule-of-thumb that if a tree is unseen twice, its probability to be actually dead is close to 1. The choice of this value involves that trees unseen during the X-1 last inventories can not be corrected for death, and thus mortality rates should not be calculated for these censuses. |
byplot |
Logical. If there are several plots in your dataset, the correction is performed by plot, in case these would not be censuses the same years or with the same frequencies one another. |
plot_col |
Character. The name of the column containing the plots indices. |
corrected |
Logical. Indicates whether the dataset has been corrected for errors in tree life status; if not it will be corrected beforehand using correct_alive function |
A data.frame with absolute and annual recruitment rates by plot and census interval.
1 2 3 4 5 6 7 8 9 10 11 12 | ## Not run:
data("example_census")
suppressWarnings(compute_recruitment(example_census,
status_col="status_corr",
time_col="CensusYear",
id_col="idTree",
dead_confirmation_censuses=2,
byplot = TRUE,
plot_col = "Plot",
corrected = TRUE))
## End(Not run)
|
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