Plot dbh class by species (and maybe table it?)

[maurolepore]

David Kenfak proposed to add a funciton to easily plot dbh classes by species.

library(tidyverse)
#> Warning: package 'purrr' was built under R version 3.5.3
library(skimr)
#> Warning: package 'skimr' was built under R version 3.5.3
#> 
#> Attaching package: 'skimr'
#> The following object is masked from 'package:stats':
#> 
#>     filter

census <- fgeo.data::luquillo_tree5_random %>% 
  filter(!is.na(dbh)) %>% 
  filter(sp %in% unique(sp)[1:3])

# Plot
census %>% 
  group_by(sp) %>% 
  ggplot(aes(dbh)) +
  geom_histogram() +
  facet_wrap("sp", ncol = 1)
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

Created on 2019-03-18 by the reprex package (v0.2.1)

--

A quick histogram may also be useful in the form of a table with the skimr package

library(tidyverse)
# Table
census %>%
  select(sp, matches("dbh")) %>% 
  group_by(sp) %>% 
  skim(dbh)

[maurolepore]

# Setup --------------------------------------------------------------------
suppressPackageStartupMessages(library(ggplot2))

plot_dbh_by_species <- function(data, 
                                binwidth = NULL, 
                                labels = NULL, 
                                theme = theme_classic()) {
  lapply(
    split(data, data$sp), 
    plot_dbh, 
    binwidth = binwidth, 
    labels = labels, 
    theme = theme
  )
}

plot_dbh <- function(data, binwidth, labels, theme) {
  ggplot(data, aes(dbh)) +
    geom_histogram(binwidth = binwidth) +
    labels + 
    facet_wrap("sp", ncol = 1) +
    theme
}

# Parameters to tweak ------------------------------------------------------
# Replace with your data
census <- fgeo.x::tree6_3species
# Change the width of each bar or leave it as is for automatic width
binwidth <- NULL
# Change axes labels
labels <- labs(x = "Diameter", y = "Count")
# Change theme https://ggplot2.tidyverse.org/reference/index.html#section-themes
theme <- theme_classic()
# Change size of each plot in each page
height <- 5
width <- 8

# Print each plot to a page in a .pdf file ----------------------------------
pdf("plots.pdf", paper = "letter", height = height, width = width)
plot_dbh_by_species(census, binwidth, labels, theme)
dev.off()

^{Created on 2019-05-08 by the reprex package (v0.2.1)}

Result

Each page of the .pdf file should now have a plot simlar to this one:

[maurolepore]

Suggestions by David:

• Remove top box (keep name)
• Try to separate bars a bit
• Ensure the xlimits are fixed for all species at the max(data$dbh)
• Also, look at the possibility of using percentages in the Y axis