common_params: Define parameters that are common to all functions

Description

Define parameters that are common to all functions

Usage

common_params(
  type,
  response,
  vd_i,
  td_i,
  d_data,
  vb_i,
  tb_i,
  b_data,
  b,
  b_tf,
  na_rm,
  metric_tf,
  comm_d,
  comm_b,
  comm_t,
  method,
  binary
)

Arguments

type: a string defining the type of stability ("functional" or "compositional") to be calculated.
response: a string stating whether the stability metric should be calculated using the log-response ratio between the values in the disturbed system and the baseline (response = "lrr") or using the state variable values in the disturbed system alone (response == "v").
vd_i: a numeric vector containing the state variable in the disturbed system or a string specifying the name of the column containing said variable in the dataframe provided in d_data.
td_i: a numeric vector containing the time or a string specifying the name of the column containing the time in the dataframe provided in d_data.
d_data: an optional data frame containing the time series of the state variable values in a disturbed system.
vb_i: an optional numeric vector containing the state variable in the baseline, or a string for the name of the column in b_data containing said variable in the dataframe with baseline values.
tb_i: an optional numeric vector containing the time period over which the baseline was measured, or a string for the name of the column in b_data containing said the time variable in the dataframe with baseline values.
b_data: an optional data frame containing the time series of the state variable values in the baseline.
b: a string stating whether the baseline is defined by a separate baseline that is specified by the user (b = "input") or by a period of the disturbed system (b = "d") prior to the disturbance. This period is specified by b_tf.
b_tf: a numerical vector, specifying the beginning and end of the pre-disturbance time period for the disturbed time-series that defines the baseline. Obligatory if (b = "d"), see 'Details'.
na_rm: a logical determining whether NAs should be taken out prior to the estimation of the stability metric. Defaults to TRUE.
metric_tf: a numerical vector, specifying the beginning and end of the time period over which the stability metric should be measured.
comm_d: a data frame containing long format community data (species as columns over time as rows) to calculate compositional metrics.
comm_b: a data frame containing long format community data (species names as columns over time as rows) to calculate compositional metrics.
comm_t: the name of the time variable in comm_b and comm_d.
method: a string identifying the dissimilarity index to be used to calculate dissimilarity. For more options, see ?vegdist. Defaults to "bray".
binary: a boolean stating whether presence/absence standardization should be performed before calculating the dissimilarity. For more options, see ?vegdist. Defaults to "bray".