calculate_habitat_change: Calculate habitat change
In kdybala/bioenergmod: Bioenergetics Modeling

Description Usage Arguments Details Value Author(s) Examples

View source: R/calculate_habitat_change.R

Calculates habitat added or lost between time steps.

1 2	calculate_habitat_change(tothabitat, flood, time, value, accessible = NULL, alt = 1, wetsplit = TRUE)

`tothabitat`	Data frame with two columns: "habitat" giving the names of each land cover type of interest and "area" giving the total area potentially available
`flood`	Long-format data frame with proportion flooded values for each time step and land cover type of interest; land cover names should be in a column named "habitat"
`time`	Name of column in `flood` containing timesteps
`value`	Name of column in `flood` containing the percent flooded values for each time step
`accessible`	Optional; data frame with same structure as `flood` containing proportion of flooded area that is accessible for each time step and land cover of interest (e.g. suitable depth)
`alt`	Optional; value to be used for land cover types with missing accessibility data, e.g. assume 1 or 0
`wetsplit`	Optional; if `TRUE`, split total area of open water labeled "wetlands" into seasonal vs. permanent; see Details

This function calculates the total area of open water (and optionally accessible open water) for each land cover type of interest during each time step from the total area of each land cover type and estimates for each time step of the proportion open water (and optionally the proportion of the open water area that is accessible). The function then calculates the daily change in the total area of open water as area added since the last time step and area lost before the start of the next time step. Area added and lost is only calculated for total open water area, not accessible open water area.

The wetsplit option is useful if proportion accessible varies by wetland type (seasonal vs. permanent) but proportion flooded is only available for all wetlands. If wetsplit=TRUE, the flood data frame requires a column labeled "prop.perm" that reflects the proportion of open water wetlands estimated to be permanent wetlands during each time step, and the accessible data frame requires land cover types (in the "habitat" column) called "seas" and "perm".

Returns a list with 3-5 elements, formatted for input into the bioenergetics modeling function and for plotting, including:

(1) openwater: total area of open water for each time step (rows) and land cover type (columns)

(2) added: total area of open water added since the previous time step

(3) returned: total area of open water lost before the start of the next time step

(4) (optionally) accessible: total area of accessible open water for each time step and land cover type

(5) (optionally) prop.accessible: proportion accessible for each time step and land cover type, including alt values filled in where previously missing

Kristen Dybala, kdybala@pointblue.org

tot = data.frame(habitat=c('A','B','C'), area=c(100,200,300))
flood = data.frame(habitat=c(rep('A',3),rep('B',3),rep('C',3)), yday=rep(c(1:3),3),
   value=c(0.9,0.8,0.7, 0.1,0.15,0.2, 0.5,0.5,0.5))
depth = data.frame(habitat=c(rep('A',3),rep('B',3),rep('C',3)), yday=rep(c(1:3),3),
   value=rep(0.9,9))
calculate_habitat_change(tothabitat=tot, flood=flood, time='yday',
   value='value', accessible=NULL, alt=0, wetsplit=FALSE)
calculate_habitat_change(tothabitat=tot, flood=flood, time='yday',
   value='value', accessible=depth, wetsplit=FALSE)