List dbh bubble-plots by quadrat (good for .pdf output).

plot_dbh_bubbles_by_quadrat(vft,
  title_quad = "Site Name, YYYY, Quadrat:",
  header = header_dbh_bubbles(), theme = theme_dbh_bubbles(),
  lim_min = 0, lim_max = 20, subquadrat_side = 5, tag_size = 2,
  move_edge = 0, status_d = "dead")

Arguments

vft

A ForestGEO ViewFullTable (dataframe).

title_quad

A string to use as a title.

header

A string to use as a header (see headers).

theme

An object of class "theme".

lim_min, lim_max

Minimum and maximum limits of the plot area.

subquadrat_side

Length in meters of the side of a subquadrat.

tag_size

A number giving tag size. Passed to ggrepel::geom_text_repel.

move_edge

A number to adjust the extension of the grid lines beyond the plot limits.

status_d

A character string indicating the value of the variable status that corresponds to dead stems.

Value

A list which each element is a plot of class ggplot.

See also

Other plot functions: autoplot.fgeo_habitat, autoplot.sp_elev, autoplot_by_species.sp_elev, elev, plot_tag_status_by_subquadrat, sp_elev, sp

Other functions to list plots from ForestGEO ViewFullTable: plot_tag_status_by_subquadrat

Other functions to plot dbh bubbles: header_dbh_bubbles, theme_dbh_bubbles

Examples

assert_is_installed("fgeo.x") # Create a small VieFullTable first_n <- function(x, n) x %in% sort(unique(x))[1:n] small_vft <- fgeo.x::vft_4quad %>% dplyr::filter(first_n(CensusID, 1) & first_n(QuadratID, 2)) %>% dplyr::sample_n(50) plot_dbh_bubbles_by_quadrat(small_vft)
#> * Appending tags of dead trees with the suffix '.d'
#> * Standarizing `dbh` by the count of `dbh` measurements
#> $`621`
#> Warning: Use of `.df$tagged_tag` is discouraged. Use `tagged_tag` instead.
#> Warning: Use of `.df$dbh_standarized` is discouraged. Use `dbh_standarized` instead.
#> Warning: Removed 12 rows containing missing values (geom_point).
#> #> $`721`
#> Warning: Use of `.df$tagged_tag` is discouraged. Use `tagged_tag` instead.
#> Warning: Use of `.df$dbh_standarized` is discouraged. Use `dbh_standarized` instead.
#> Warning: Removed 15 rows containing missing values (geom_point).
#>
# To print all plots into a .pdf file see `?pdf()` plot_dbh_bubbles_by_quadrat(small_vft)
#> * Appending tags of dead trees with the suffix '.d'
#> * Standarizing `dbh` by the count of `dbh` measurements
#> $`621`
#> Warning: Use of `.df$tagged_tag` is discouraged. Use `tagged_tag` instead.
#> Warning: Use of `.df$dbh_standarized` is discouraged. Use `dbh_standarized` instead.
#> Warning: Removed 12 rows containing missing values (geom_point).
#> #> $`721`
#> Warning: Use of `.df$tagged_tag` is discouraged. Use `tagged_tag` instead.
#> Warning: Use of `.df$dbh_standarized` is discouraged. Use `dbh_standarized` instead.
#> Warning: Removed 15 rows containing missing values (geom_point).
#>
# Be careful if subsetting by DBH: You may unintentionally remove dead trees. # You should explicietly inlcude missing `DBH` values with `is.na(DBH)` include_missing_dbh <- subset(small_vft, DBH > 20 | is.na(DBH)) plot_dbh_bubbles_by_quadrat(include_missing_dbh)
#> * Appending tags of dead trees with the suffix '.d'
#> * Standarizing `dbh` by the count of `dbh` measurements
#> $`621`
#> Warning: Use of `.df$tagged_tag` is discouraged. Use `tagged_tag` instead.
#> Warning: Use of `.df$dbh_standarized` is discouraged. Use `dbh_standarized` instead.
#> Warning: Removed 12 rows containing missing values (geom_point).
#> #> $`721`
#> Warning: Use of `.df$tagged_tag` is discouraged. Use `tagged_tag` instead.
#> Warning: Use of `.df$dbh_standarized` is discouraged. Use `dbh_standarized` instead.
#> Warning: Removed 15 rows containing missing values (geom_point).
#>
# Customizing the maps ---------------------------------------------------- # A custom title and header myheader <- paste( " ", "Head column 1 Head column 2 ", " ", " ........................................................................", " ........................................................................", sep = "\n" ) plot_dbh_bubbles_by_quadrat( small_vft, title_quad = "My Site, 2018. Quad:", header = myheader )
#> * Appending tags of dead trees with the suffix '.d'
#> * Standarizing `dbh` by the count of `dbh` measurements
#> $`621`
#> Warning: Use of `.df$tagged_tag` is discouraged. Use `tagged_tag` instead.
#> Warning: Use of `.df$dbh_standarized` is discouraged. Use `dbh_standarized` instead.
#> Warning: Removed 12 rows containing missing values (geom_point).
#> #> $`721`
#> Warning: Use of `.df$tagged_tag` is discouraged. Use `tagged_tag` instead.
#> Warning: Use of `.df$dbh_standarized` is discouraged. Use `dbh_standarized` instead.
#> Warning: Removed 15 rows containing missing values (geom_point).
#>
# Skip R CMD check for speed # \donttest{ # Tweak the theme with ggplot library(ggplot2) plot_dbh_bubbles_by_quadrat( small_vft, title_quad = "My Site, 2018. Quad:", header = header_dbh_bubbles("spanish"), tag_size = 3, theme = theme_dbh_bubbles( axis.text = NULL, # NULL shows axis.text; element_blank() doesn't. plot.title = element_text(size = 15), plot.subtitle = element_text(size = 5), panel.background = element_rect(fill = "grey") ) )
#> * Appending tags of dead trees with the suffix '.d'
#> * Standarizing `dbh` by the count of `dbh` measurements
#> $`621`
#> Warning: Use of `.df$tagged_tag` is discouraged. Use `tagged_tag` instead.
#> Warning: Use of `.df$dbh_standarized` is discouraged. Use `dbh_standarized` instead.
#> Warning: Removed 12 rows containing missing values (geom_point).
#> #> $`721`
#> Warning: Use of `.df$tagged_tag` is discouraged. Use `tagged_tag` instead.
#> Warning: Use of `.df$dbh_standarized` is discouraged. Use `dbh_standarized` instead.
#> Warning: Removed 15 rows containing missing values (geom_point).
#>
# }