This function is a generic interface into creating summaries of the Portal plant species data. It contains a number of arguments to specify both the kind of data to summarize, at what level of aggregation, various choices for dealing with data quality, and output format.
plant_abundance generates a table of plant abundance
Usage
summarize_plant_data(
path = get_default_data_path(),
level = "Site",
type = "All",
length = "all",
plots = length,
unknowns = FALSE,
correct_sp = TRUE,
shape = "flat",
output = "abundance",
na_drop = switch(tolower(level), quadrat = FALSE, plot = FALSE, treatment = TRUE, site
= TRUE, TRUE),
zero_drop = switch(tolower(level), quadrat = TRUE, plot = FALSE, treatment = TRUE, site
= TRUE, TRUE),
min_quads = 1,
effort = TRUE,
download_if_missing = TRUE,
quiet = FALSE
)
plant_abundance(..., shape = "flat")
summarise_plant_data(
path = get_default_data_path(),
level = "Site",
type = "All",
length = "all",
plots = length,
unknowns = FALSE,
correct_sp = TRUE,
shape = "flat",
output = "abundance",
na_drop = switch(tolower(level), quadrat = FALSE, plot = FALSE, treatment = TRUE, site
= TRUE, TRUE),
zero_drop = switch(tolower(level), quadrat = TRUE, plot = FALSE, treatment = TRUE, site
= TRUE, TRUE),
min_quads = 1,
effort = TRUE,
download_if_missing = TRUE,
quiet = FALSE
)Arguments
- path
either the file path that contains the PortalData folder or "repo", which then pulls data from the PortalData GitHub repository
- level
summarize by "Plot", "Treatment", "Site", or "Quadrat"
- type
specify subset of species; If type=Annuals, removes all non-annual species. If type=Summer Annuals, returns all annual species that can be found in the summer If type=Winter Annuals, returns all annual species that can be found in the winter If type=Non-woody, removes shrub and subshrub species If type=Perennials, returns all perennial species (includes shrubs and subshrubs) If type=Shrubs, returns only shrubs and subshrubs
- length
specify subset of plots; use "All" plots or only "Longterm" plots (to be deprecated)
- plots
specify subset of plots; can be a vector of plots, or specific sets: "all" plots or "Longterm" plots (plots that have had the same treatment for the entire time series)
- unknowns
either removes all individuals not identified to species (unknowns = FALSE) or sums them in an additional column (unknowns = TRUE)
- correct_sp
correct species names suspected to be incorrect in early data (T/F)
- shape
return data as a "crosstab" or "flat" list
- output
specify whether to return "abundance", or "cover" [cover data starts in summer 2015]
- na_drop
logical, drop NA values (representing insufficient sampling) filling missing combinations of year-month-treatment/plot-species with NA could represent one of a few slightly different meanings: 1) that combo doesn't exist 2) that combo was skipped that month, or 3) that combo was trapped, but is unusable (a negative period code))
- zero_drop
logical, drop 0s (representing sufficient sampling, but no detection)
- min_quads
numeric [1:16], minimum number of quadrats (out of 16) for a plot to be included
- effort
logical as to whether or not the effort columns should be included in the output
- download_if_missing
if the specified file path doesn't have the PortalData folder, then download it
- quiet
logical, whether to run without version messages
- ...
arguments passed to
summarize_plant_data