INFCvpeSUM: Estimate tree bole volume or phytomass for stems groups, with...

In npuletti/ForIT: Functions to estimate tree volume and phytomass in the Italian forest inventory 2005

Description

Cumulative estimation of the volume or phytomass of groups of trees is just the summation of the values computed with INFCvpe(), but the computation of accuracy estimates is improved using these summation functions.
Two approaches are available.

• Via INFCvpe_summarise() that processes and returns a data frame

• or by following aggregation functions within a standard summarise():

  • INFCvpe_sum()

  • INFCvpe_ConfInt()

  • INFCvpe_OutOfDomain()

Usage

INFCvpe_summarise(
  in.data,
  EPPOcode_C,
  dbh_C,
  h_tot_C,
  quantity = "vol",
  p = 0.95
)

INFCvpe_sum(EPPOcode, dbh, h_tot, quantity = "vol")

INFCvpe_ConfInt(EPPOcode, dbh, h_tot, quantity = "vol", p = 0.95)

INFCvpe_OutOfDomain(EPPOcode, dbh, h_tot)

Arguments

in.data	A dataframe (or tibble) containing tally data to be matched with "EPPOcode_C", "dbh_C" and "htot_C" arguments
EPPOcode_C	A string, the name of the column in in.data with the species EPPO codes
dbh_C	A string, the name of the column in in.data with the brest height diameter values
h_tot_C	A string, the name of the column in in.data with the tree total height values
quantity	(default = "vol") A character vector specifying required quantity/ies: c("vol", "dw1" : "dw4"). Use qantities() to decode definitions. for INFCvpe_summarise(), if length(unique(quantity)) > 1, rows in in.data will be replicated for each value. for INFCvpe_SUM functions, length(quantity) must be 1
p	(default p = 95%) probability used to compute cihw (with length = 1 or length = length(dbh)) OPZIONE 2 INFCvpe_SUM functions:
EPPOcode	A character vector with the species EPPO codes (with length = 1 or length = length(dbh))
dbh	A numeric vector with the brest height diameter values
h_tot	A numeric vector with the tree total height values (with length = 1 or length = length(dbh))

Details

Functions developed following Tabacchi et al. (2011). Relevant excerpt are collected in the INFCvpeSUM_theoryAndExamples.pdf file. NOTA: vedi https://trello.com/c/PCaZZFe4)

Value

• INFCvpe_summarise() returns a dataframe (tibble) with the grouping columns defined with group_by(), and the following columns:

  • quantity: as additional grouping column,

  • n : number of trees in the group,

  • n_out : the number of (dbh, htot) pairs that are 'out of the domain',

  • est : the estimated value,

  • cihw : confidence interval half width

  • p: probability used computing cihw

• INFCvpe_SUM - the functions of this family return a numeric vector, aggregating rows within the same group,

  • INFCvpe_sum() returns the sum of the estimated quantities,

  • INFCvpe_ConfInt() returns 'confidence interval half width',

  • INFCvpe_OutOfDomain() returns the number of 'out of domain' (dhb, h_tot) pairs included in the summation

See Also

INFCvpe() to compute individual estimates, with detailed accuracy evaluation

Examples

tst <- dplyr::tribble(
  ~UC, ~specie, ~d130, ~h_dendro,
  # Example data in Tabacchi et al. (2011) pag. 25
  "U1","ACROP",10,7,
  "U1","ACROP",15,9,
  "U1","ACROP",20,12,
  "U1","ACROP",30,20,
  "U1","ACROP",32,21,
  "U1","ACROP",24,18,
  "U1","ACROP",36,21,
  "U1","ACROP",40,22,
  "U1","ACROP",8,8,
  "U1","ACROP",18,12,

  # Example continuation, pag. 27
  "U2","ABIAL",38,21,
  "U2","ABIAL",52,28,
  "U2","FAUSY",25,16,
  "U2","FAUSY",30,18,
  "U2","FAUSY",12,10,

  # Extra line, to test 'out of domain'
  "U2","ABIAL",5,32)

tst %>%
  dplyr::filter(!(d130 == 5 & h_dendro == 32)) %>%
  dplyr::group_by(specie) %>%
  INFCvpe_summarise("specie", "d130", "h_dendro") %>%
  dplyr::ungroup() %>%
  dplyr::mutate(specie = factor(specie,
                         levels = c("ACROP", "ABIAL", "FAUSY"),
                         labels = c("aceri", "abete bianco", "faggio"),
                         ordered = TRUE),
                dplyr::across(c("est", "cihw"), ~round(.x, 1))
         ) %>%
  dplyr::select(specie, est, cihw) %>%
  dplyr::arrange(specie) %>%
  t()
# ForIT (ver 2) output
# specie "aceri"  "abete bianco" "faggio"
# est    "4623.0" "4044.2"       "1079.4"
# cihw   "567.5"  "661.2"        "275.4"

# In (Tabacchi et al., 2011, 'Tabella 2')
# specie "aceri"  "abete bianco" "faggio"
# est    "4623.0" "4044.2"       "1079.4"
# cihw   "567.4"  "662.4"        "279.2"

# Using 'INFCvpe_summarise()'
tst %>%
  INFCvpe_summarise("specie", "d130", "h_dendro", quantity = c("vol", "dw4"))

tst %>%
  dplyr::mutate(cld = ceiling(d130/5)*5) %>%
  dplyr::group_by(UC, specie, cld) %>%
  INFCvpe_summarise("specie", "d130", "h_dendro")

tst %>%
  dplyr::group_by(UC) %>%
  INFCvpe_summarise("specie", "d130", "h_dendro", quantity = "dw4")

# Using 'INFCvpeSUM' aggregation functions
tst %>%
  dplyr::group_by(UC) %>%
  dplyr::summarise(
    n_stems = dplyr::n(),
    OoD = INFCvpe_OutOfDomain(specie, d130, h_dendro),
    dw4 = INFCvpe_sum(specie, d130, h_dendro, quantity = "dw4"),
    dw4_ConfInt = INFCvpe_ConfInt(specie, d130, h_dendro, quantity = "dw4")
  )

tst %>%
  dplyr::group_by(UC) %>%
  dplyr::summarise(
    n_stems = dplyr::n(),
    OoD = INFCvpe_OutOfDomain(specie, d130, h_dendro),
    vol = INFCvpe_sum(specie, d130, h_dendro),
    vol_ConfInt = INFCvpe_ConfInt(specie, d130, h_dendro)
  )
rm(tst)

npuletti/ForIT documentation built on Dec. 29, 2021, 7:50 a.m.