mrds: add_df_covar_line – R documentation

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add_df_covar_line

Add covariate levels detection function plots

Description

Add a line or lines to a plot of the detection function which correspond to a a given covariate combination. These can be particularly useful when there is a small number of factor levels or if quantiles of a continuous covariate are specified.

Usage

add_df_covar_line(ddf, data, ndist = 250, pdf = FALSE, breaks = "Sturges", ...)

Arguments

`ddf`	a fitted detection function object.
`data`	a `data.frame` with the covariate combination you want to plot.
`ndist`	number of distances at which to evaluate the detection function.
`pdf`	should the line be drawn on the probability density scale; ignored for line transects.
`breaks`	required to ensure that PDF lines are the right size, should match what is supplied to original `plot` command. Defaults to "Sturges" breaks, as in `hist`. Only used if `pdf=TRUE`.
`...`	extra arguments to give to `line` (`lty`, `lwd`, `col`).

Details

All covariates must be specified in data. Plots can become quite busy when this approach is used. It may be useful to fix some covariates at their median level and plot set values of a covariate of interest. For example setting weather (e.g., Beaufort) to its median and plotting levels of observer, then creating a second plot for a fixed observer with levels of weather.

Arguments to lines are supplied in ... and aesthetics like line type (lty), line width (lwd) and colour (col) are recycled. By default lty is used to distinguish between the lines. It may be useful to add a legend to the plot (lines are plotted in the order of data).

Value

invisibly, the values of detectability over the truncation range.

Author(s)

David L Miller

Examples

## Not run: 
# fit an example model
data(book.tee.data)
egdata <- book.tee.data$book.tee.dataframe
result <- ddf(dsmodel = ~mcds(key = "hn", formula = ~sex),
              data = egdata[egdata$observer==1, ], method = "ds",
              meta.data = list(width = 4))

# make a base plot, showpoints=FALSE makes the plot less busy
plot(result, showpoints=FALSE)

# add lines for sex one at a time
add_df_covar_line(result, data.frame(sex=0), lty=2)
add_df_covar_line(result, data.frame(sex=1), lty=3)

# add a legend
legend(3, 1, c("Average", "sex==0", "sex==1"), lty=1:3)

# alternatively we can add both at once
# fixing line type and varying colour
plot(result, showpoints=FALSE)
add_df_covar_line(result, data.frame(sex=c(0,1)), lty=1,
                  col=c("red", "green"))
# add a legend
legend(3, 1, c("Average", "sex==0", "sex==1"), lty=1,
       col=c("black", "red", "green"))

## End(Not run)

mrds

Mark-Recapture Distance Sampling

v2.2.4

GPL (>= 2)

Authors

Jeff Laake <jeff.laake@noaa.gov>, David Borchers <dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David Miller <dave@ninepointeightone.net> and Jon Bishop

Initial release