List plots of species distribution and topography (good for pdf output).

These functions extend autoplot.sp() and autoplot.elev() and return not a single plot but a list of plots. They are particularly useful if you want to print a .pdf file with one plot per page. They automatically plot the variables sp and elev of a ForestGEO-like dataset of class 'sp' or 'sp_elev'.

Create a 'sp' object with:

    object <- sp(DATA-WITH-VARIABLE-sp)

Create a 'sp_elev' object with:

    object <- sp_elev(DATA-WITH-VARIABLE-sp, DATA-WITH-VARIABLE-elev)

See sections Usage and Examples.

# S3 method for sp_elev
autoplot_by_species(
  object,
  species = "all",
  fill = "black",
  shape = 21,
  point_size = 3,
  contour_size = 0.5,
  low = "blue",
  high = "red",
  hide_color_legend = FALSE,
  bins = NULL,
  add_elevation_labels = TRUE,
  label_size = 3,
  label_color = "grey",
  xyjust = 1,
  fontface = "italic",
  xlim = NULL,
  ylim = NULL,
  custom_theme = NULL,
  ...
)

# S3 method for sp
autoplot_by_species(
  object,
  species = "all",
  fill = "black",
  shape = 21,
  point_size = 3,
  hide_color_legend = FALSE,
  xlim = NULL,
  ylim = NULL,
  custom_theme = NULL,
  ...
)

Arguments

object	An object created with `sp()` or `sp_elev()`.
species	A character vector giving values in the column `sp`. The output will be a list with as many plots as elements in this vector. The string "all" (default) plots all unique values of `sp`.
fill	Character; either a color or "sp", which maps each species to a different color.
shape	A number giving point shape (as in `graphics::points()`). Passed to `ggplot2::geom_point()`.
point_size	A number giving point size. Passed to `ggplot2::geom_point()`.
contour_size	A number giving the size of the contour of elevation lines. Passed to `ggplot2::stat_contour()` (see `ggplot2::geom_contour()`).
low, high	A string giving a color of the elevation lines representing low and high elevation.
hide_color_legend	Logical; `TRUE` hides the color legend.
bins	A number giving the number of elevation lines to plot.
add_elevation_labels	Logical; `FALSE` hides elevation labels.
label_size, label_color, fontface	A number (`label_size`) or character string (`label_color` and `fontface`) giving the size, colour and fontface of the text labels for the elevation lines.
xyjust	A number to adjust the position of the text labels of the elevation lines.
xlim, ylim	A vector of length 2, for example `c(0, 500)`, giving the minimum and maximum limits of the vertical and horizontal coordinates.
custom_theme	A valid `ggplot2::theme()`. `NULL` uses the default theme `theme_default()`.
...	Not used (included for compatibility across methods).

Value

A list of objects of class "ggplot".

Details

autoplot_by_species(sp_elev(DATA-WITH-VARIABLE-sp) (without elevation data) is equivalent to autoplot_by_species(sp(DATA-WITH-VARIABLE-sp)).

fgeo.plot wraps some functions from the ggplot2 package. For more control you can use ggplot2 directly.

Examples

assert_is_installed("fgeo.x")

# Species ---------------------------------------------------------------
# Small dataset with a few species for quick examples
census <- fgeo.x::tree6_3species

# Showing only two species for speed
autoplot_by_species(sp(census))[1:2]
#> $CASARB
#> 
#> $PREMON
#> 

# To print all plots in a .pdf see `?pdf()`
autoplot_by_species(sp(census))
#> $CASARB
#> 
#> $PREMON
#> 
#> $SLOBER
#> 

# Species and elevation (optional) ---------------------------------------

# Species and elevation
elevation <- fgeo.x::elevation
autoplot_by_species(sp_elev(census, elevation))
#> $CASARB
#> 
#> $PREMON
#> 
#> $SLOBER
#>

List plots of species distribution and topography (good for pdf output).

Arguments

Value

Details

See also

Examples