This is the main function of the secpRod package. It will calculate secondary production for all groups based on the methods described in the taxa information object. Depending on input values varying summaries are returned.
Usage
calc_production(
taxaSampleListMass = NULL,
taxaInfo = NULL,
bootNum = 100,
taxaSummary = TRUE,
lengthValue = NULL,
massValue = "mass",
abunValue = "density",
dateCol = "dateID",
repCol = "repID",
envData = NULL,
...
)Arguments
- taxaSampleListMass
data.frame of sample length-masses and abundances
- taxaInfo
dataframe (or coercible); The taxonomic information for calculating secondary production. This must include a taxonomic ID column with the same name as that of
taxaSampleListMass- bootNum
integer. The number of bootstrapped samples to create
- taxaSummary
logical. If TRUE (default) the taxaSummary will be with annual summary information will be returned.
- lengthValue
string of the column name containing length class measurements. If NULL (default)
- massValue
string of the column name containing the mass measurement
- abunValue
string of the column name containing the abundance or density measurement
- dateCol
string of the column name containing the date information. This can be either a recognized date object (e.g., Date, POSIX)
- repCol
string of the column name containing the replicate information
- envData
data.frame of additional environmental data for each sampling event. If present, this is combined with the dateDf information and passed to the IGR function for growth rate estimations.The environmental variables passed should align with the start of each sampling interval.
- ...
additional arguments passed to function
- infoCols
integer vector; Any columns in the sizeInfo object that are not the taxonomic ID, sampling metadata, or size class columns. ** This is soft-deprecated and is not currently used. It may go away soon **