Transform Frequency of occurrence (FO) to Species relative abundance (SRA) or Species percentage cover(%SC)
Source:R/vegetation_abundance.R
vegetation_abundance.RdFrom a database with Frequency of occurrences of species identified along a linear transect and occasional species (i.e. species found within vegetation plots but not along the linear transects), Species relative abundance (SRA) and percentage species cover(%SC) are computed, either considering or not considering occasional species.
Terminology:
Frequency of occurrence (FO) : number of species occurrences out of 'N' points of vegetation measurements along a transect line
Species relative abundance (SRA) : ratio between frequency of occurrence and the sum of frequency of occurrences values for all species in the transect, then multiplied by 100
Species percentage cover (%SC): conversion of frequency of occurrence to 100 measurements (e.g. if a species had a FO= 20 measurements out of 50 total measurements along the transect line, the FO will be multiplied by 2). To all occasional species (i.e. species found within vegetation plots but not along the linear transects) a %SC value = 0.3% is attributed.
see MarcoPittarello/iPastoralist for a full graphical explanation
Arguments
- database
database with FO and occasional species as 999. Rows are species and columns are surveys. The first column of the database reports the species names. Database class must be data.frame
- method
"SRA_fo": SRA calculated from FO without occasional species.see MarcoPittarello/iPastoralist for a full graphical explanation
"SC_fo": %SC calculated by multiplying FO for a coefficient so that the number of total measurements along the transect line refer to 100 (occasional species are excluded). see MarcoPittarello/iPastoralist for a full graphical explanation
"SC_fo_occ": like SC_fo but with in addition the occasional species, considered as 0.3%. The total %SC per each surveys will be > 100 %. see MarcoPittarello/iPastoralist for a full graphical explanation
"SRA_SC.fo.occ": SRA calculated from SC_fo_occ, i.e. rescale SC_fo_occ so that the total sum per each survey sum up to 100 %. see MarcoPittarello/iPastoralist for a full graphical explanation
- species.cover.coefficient
Coeffient that multiplies FO so that the number of total touches refer to 100. Only required when method = "SC_fo_occ","SC_fo", "SRA_SC.fo.occ"