Plot diversity (taxa richness) through time

plot_taxa_diversity(
  data,
  id = NA_character_,
  time_window_size = "day",
  observation = NULL,
  alpha = 1
)

Arguments

data: (list or tbl_df, tbl, data.frame) The dataset object returned by read_data(), a named list of tables containing the observation table, or a flat table containing columns of the observation table.
id: (character) Identifier of dataset to be used in plot subtitles. Is automatically assigned when data is a dataset object containing the id field, or is a table containing the package_id column.
time_window_size: (character) Define the time window over which to aggregate observations for calculating richness. Can be: "day" or "year"
observation: (tbl_df, tbl, data.frame) DEPRECATED: Use data instead.
alpha: (numeric) Alpha-transparency scale of data points. Useful when many data points overlap. Allowed values are between 0 and 1, where 1 is 100% opaque. Default is 1.

Value

(gg, ggplot) A gg, ggplot object if assigned to a variable, otherwise a plot to your active graphics device

Details

The data parameter accepts a range of input types but ultimately requires the 9 columns of the observation table.

Examples

if (FALSE) {
# Read a dataset of interest
dataset <- read_data("edi.193.5")

# Plot the dataset
plot_taxa_diversity(dataset)

# Plot the dataset with observations aggregated by year
plot_taxa_diversity(dataset, time_window_size = "year")

# Flatten the dataset, manipulate, then plot
dataset %>% 
  flatten_data() %>% 
  dplyr::filter(
    lubridate::as_date(datetime) > "2007-01-01") %>%
  plot_taxa_diversity()
  
# Plot from the observation table directly
plot_taxa_diversity(dataset$tables$observation)
}

# Plot the example dataset
plot_taxa_diversity(ants_L1)