make_vector_data: Make VOCC vector data from sdmTMB output predict funciton

Description Usage Arguments

View source: R/make-vector-data.R

Description

Make VOCC vector data from sdmTMB output predict funciton

Usage

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make_vector_data(
  data,
  ssid = NULL,
  start_time = NULL,
  end_time = NULL,
  skip_time = NULL,
  input_cell_size = 2,
  scale_fac = 1,
  min_dist = input_cell_size * scale_fac/2,
  time_var = "year",
  delta_t_total = 10,
  delta_t_step = 2,
  indices = c(1, 2),
  variable_names = "est",
  round_fact = NULL,
  min_thresholds = NULL,
  max_thresholds = NULL,
  plus_minus = c(0.5),
  match_logic = NULL
)

Arguments

data

List of dataframes each containing output from predict.

ssid

Vector of ssid to be included.

start_time

Starting time for VOCC calculation. Default is NULL and all data is used.

end_time

End time for VOCC calculation. Default is NULL and all data is used.

skip_time

Time steps to be excluded. Default is NULL and all data is used.

input_cell_size

Cell size of predict grid.

scale_fac

Factor by which cells are aggregated for VOCC.

time_var

Name of column containing time data.

delta_t_total

Mean time between start and end values.

delta_t_step

Time between each time step in same units as above.

indices

Vector of length equal to number of time steps retained for analysis, where 1 = starting time step(s), 2 = end time step(s).

variable_names

Name(s) of column containing parameter(s).

round_fact

Speed up searches by rounding (1 = integers; 10 = 10ths; 100 = 100ths). If NULL, will use 10x precision of the plus_minus threshold when 'match_logic' = NULL.

min_thresholds

Optional vector of negative thresholds. Apply 'Inf' for no min threshold. Include if sensitivity to the direction of climate change is not symmetrical and 'match_logic' = NULL.

max_thresholds

Optional vector of positive thresholds. Apply 'Inf' for no max threshold. Include if sensitivity to the direction of climate change is not symmetrical and 'match_logic' = NULL.

plus_minus

Vector of plus/minus threshold(s) to define a symmetical (default = 1 unit) climate match.

match_logic

An optional vector of logical functions applied using 'rounding' of allnclimate values. If max_thresholds are not provided, the default of 'NULL' applies symmetrical plus/minus thresholds.


pbs-assess/gfranges documentation built on Dec. 13, 2021, 4:50 p.m.