This function is a generic interface into creating summaries of the Portal rodent species data. It contains a number of arguments to specify the kind of data to summarize (at what level of aggregation) and various choices for dealing with data quality, and output format.
abundance generates a table of rodent abundance
* biomass() generates a table of rodent biomass
* energy() generates a table of rodent energy
(computed as 5.69 * (biomass ^ 0.75) after White et al 2004)
* rates() generates a table of rodent growth rates
(computed as r=log(N[t+1]/N[t])
Usage
summarize_rodent_data(
path = get_default_data_path(),
clean = TRUE,
level = "Site",
type = "Rodents",
length = "all",
plots = length,
unknowns = FALSE,
shape = "crosstab",
time = "period",
output = "abundance",
fillweight = (output != "abundance"),
na_drop = TRUE,
zero_drop = switch(tolower(level), plot = FALSE, treatment = TRUE, site = TRUE),
min_traps = 1,
min_plots = 24,
effort = FALSE,
download_if_missing = TRUE,
quiet = FALSE,
include_unsampled = FALSE
)
abundance(...)
biomass(...)
energy(...)
rates(...)
summarise_rodent_data(
path = get_default_data_path(),
clean = TRUE,
level = "Site",
type = "Rodents",
length = "all",
plots = length,
unknowns = FALSE,
shape = "crosstab",
time = "period",
output = "abundance",
fillweight = (output != "abundance"),
na_drop = TRUE,
zero_drop = switch(tolower(level), plot = FALSE, treatment = TRUE, site = TRUE),
min_traps = 1,
min_plots = 24,
effort = FALSE,
download_if_missing = TRUE,
quiet = FALSE,
include_unsampled = FALSE
)Arguments
- path
either the file path that contains the PortalData folder or "repo", which then pulls data from the PortalData GitHub repository
- clean
logical, load only QA/QC rodent data (TRUE) or all data (FALSE)
- level
summarize by "Plot", "Treatment", or "Site"
- type
specify subset of species; either all "Rodents" or only "Granivores"
- 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)
- shape
return data as a "crosstab" or "flat" list
- time
specify the format of the time index in the output, either "period" (sequential Portal surveys), "newmoon" (lunar cycle numbering), "date" (calendar date), or "all" (for all time indices)
- output
specify whether to return "abundance", or "biomass", or "energy", or "rates"
- fillweight
specify whether to fill in unknown weights with other records from that individual or species, where possible
- 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_traps
minimum number of traps for a plot to be included
- min_plots
minimum number of plots within a period for an observation 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 producing messages
- include_unsampled
logical, overrides settings for `na_drop` and `zero_drop`, setting both to FALSE
- ...
arguments passed to
summarize_rodent_data