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.

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 17 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 17 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 17 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 17 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 17 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 17 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 17 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 17 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 17 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 17 rows containing missing values (geom_point).

#> 
# }

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

Arguments

Value

See also

Examples