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Report felling dates of individual tree-ring series

Source: R/fd_report.R
fd_report.Rd

This function reports the felling date estimate of individual tree-ring series, based on the presence/absence of sapwood and/or waney edge. There are three possible modes of reporting:

  • a terminus post quem or earliest possible felling date: when only heartwood rings have been observed and measured

  • a felling date range or interval: when sapwood rings have been recorded, but no bark or waney edge is present.

  • an exact felling date: when bark or waney edge is present on the measured sample.

Usage

fd_report(
  x,
  series = "series",
  last = "last",
  n_sapwood = "n_sapwood",
  waneyedge = "waneyedge",
  sw_data = "Hollstein_1980",
  cred_mass = 0.954,
  densfun = "lognormal"
)

Arguments

x

Name of a data.frame with at least four columms, providing information on

  • the id's of the tree-ring series ("series")

  • the number of sapwood rings observed ("n_sapwood)

  • the presence of waney edge ("waneyedge")

  • the year assigned to the last measured ring ("last").

Optionally, a column specifying the sapwood data set (sw_data) can also be included.

series

Name of the column in x where id's of the tree-ring series are listed as character values.

last

Name of the column in x which lists the calendar year assigned to the last measured ring (should be a numeric vector).

n_sapwood

Name of the column in x where the number of observed sapwood rings are listed (should be numeric vector).

waneyedge

Name of the column in x indicating the presence (TRUE)/absence (FALSE) of waney edge (should be a logical vector).

sw_data

There are two options:

  • A character string providing the name of the sapwood data set to use for modelling. It should be one of the data sets listed in sw_data_overview(),

  • or the name of a data.frame with sapwood data in columns n_sapwood and count, or

  • or character string naming a column in x that lists for each series the sapwood model to use, e.g. sw_data = "sapwood_model_column".

cred_mass

A numeric scalar [0, 1] specifying the mass within the credible interval (default = .954).

densfun

Name of the density function to fit to the sapwood distribution. Should be one of:

  • lognormal (the default value),

  • normal,

  • weibull,

  • gamma.

Value

A data.frame with felling date estimates per tree-ring series. Columns include:

  • series: series identifier

  • last: last measured ring

  • n_sapwood: number of sapwood rings

  • waneyedge: TRUE/FALSE for waney edge

  • lower, upper: numeric bounds for the estimated felling date

  • felling_date: a character summary (e.g., "between 1500 and 1510")

  • sapwood_model: the sapwood data/model used

See also

sw_interval(), sw_data_overview(), sw_interval_plot()

Examples

df <- data.frame(
     id = c("trs1", "trs2", "trs3", "trs4"),
     swr = c(7, 1, 10, 12),
     waneyedge = c(FALSE, FALSE, FALSE, TRUE),
     end = c(1482, 1475, 1490, 1498)
)
fd_report(df,
     series = "id",
     n_sapwood = "swr",
     last = "end",
     sw_data = "Wazny_1990"
)
#>   series last n_sapwood waneyedge lower upper          felling_date
#> 1   trs1 1482         7     FALSE  1483  1501 between 1483 and 1501
#> 2   trs2 1475         1     FALSE  1482  1500 between 1482 and 1500
#> 3   trs3 1490        10     FALSE  1490  1506 between 1490 and 1506
#> 4   trs4 1498        12      TRUE    NA  1498               in 1498
#>   sapwood_model
#> 1    Wazny_1990
#> 2    Wazny_1990
#> 3    Wazny_1990
#> 4    Wazny_1990

# Example with different sw_model for individual series
# You can add a user-defined sapwood dataset as well.

sapwood_model_column <- c(
     "Sohar_2012_ELL_c",
     "Wazny_1990",
     "Hollstein_1980",
     "vanDaalen_Norway"
)

df2 <- cbind(df, sw_data = sapwood_model_column)

fd_report(df2,
     series = "id",
     n_sapwood = "swr",
     last = "end",
     sw_data = "sw_data"
)
#>   series last n_sapwood waneyedge lower upper          felling_date
#> 1   trs1 1482         7     FALSE  1482  1493 between 1482 and 1493
#> 2   trs2 1475         1     FALSE  1482  1500 between 1482 and 1500
#> 3   trs3 1490        10     FALSE  1490  1514 between 1490 and 1514
#> 4   trs4 1498        12      TRUE    NA  1498               in 1498
#>      sapwood_model
#> 1 Sohar_2012_ELL_c
#> 2       Wazny_1990
#> 3   Hollstein_1980
#> 4 vanDaalen_Norway
#' @importFrom rlang .data