accum {algaeClassify}

Split a dataframe column with binomial name into genus and species columns. Plots change in species richness over time, generates species accumulation curve, and compares SAC against simulated idealized curve assuming all unique taxa have equal probability of being sampled at any point in the time series. (author Dietmar Straile)

Description

Split a dataframe column with binomial name into genus and species columns. Plots change in species richness over time, generates species accumulation curve, and compares SAC against simulated idealized curve assuming all unique taxa have equal probability of being sampled at any point in the time series. (author Dietmar Straile)

Usage

accum(
  b_data,
  phyto_name = "phyto_name",
  column = NA,
  n = 100,
  save.pdf = FALSE,
  lakename = "",
  datename = "date_dd_mm_yy",
  dateformat = "%d-%m-%y"
)

Arguments

b_data

Name of data.frame object

phyto_name

Character string: field containing phytoplankton id (species, genus, etc.)

column

column name or number for field containing abundance (biomass,biovol, etc.). Can be NA if the dataset only contains a species list for each sampling date.

n

number of simulations for randomized ideal species accumulation curve

save.pdf

TRUE/FALSE- should plots be displayed or saved to a pdf?

lakename

optional character string for adding lake name to pdf output

datename

character string name of b_data field containing date

dateformat

character string: posix format for datename column

Value

a two panel plot with trends in richness on top, and cumulative richness vs. simulated accumulation curve on bottom

Examples

data(lakegeneva)
#example dataset with 50 rows
head(lakegeneva)

accum(b_data=lakegeneva,column='biovol_um3_ml',n=10,save.pdf=FALSE)