Plot taxon occurrence frequences as the number of 'event_id' by 'location_id' combinations in which a taxon is observed.

plot_taxa_occur_freq(
data,
id = NA_character_,
min_occurrence = 0,
facet_var = NA_character_,
color_var = NA_character_,
facet_scales = "free",
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 and taxon tables, or a flat table containing columns of the observation and taxon tables. (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. (numeric) Minimum number of occurrences allowed for taxa included in the plot. (character) Name of column to use for faceting. Must be a column of the observation or taxon table. (character) Name of column to use for plot colors. (character) Should scales be free ("free", default value), fixed ("fixed"), or free in one dimension ("free_x", "free_y")? (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 13 columns of the combined observation and taxon tables.

## Examples

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

# Plot the dataset
plot_taxa_occur_freq(dataset)

# Facet by location and color by taxon_rank
plot_taxa_occur_freq(
data = dataset,
facet_var = "location_id",
color_var = "taxon_rank")

# Color by location and only include taxa with >= 5 occurrences
plot_taxa_occur_freq(
data = dataset,
color_var = "location_id",
min_occurrence = 5)

# Flatten, filter using a time cutoff, then plot
dataset %>%
flatten_data() %>%
dplyr::filter(lubridate::as_date(datetime) > "2003-07-01") %>%
plot_taxa_occur_freq()
}
# Plot the example dataset
plot_taxa_occur_freq(ants_L1)