Convert abundance to presence data

Converts abundance data to presence data with imperfect detection. Considering imperfect detection per individual: if any of them are detected it is considered as presence unit; if none of them are detected it is considered as absence unit.

abundance2pres(abun, ipd)

Arguments

abun

A data.frame with the first column with the sample id and the second with abundance values

ipd

A numeric value that determines the individual probability of detection followin a binomial distribution.

Details

Value

Returns a data frame with the abundance of each unit and the presence/absence data.

References

Author

Note

See also

Examples

set.seed(1111)

#Create random values for the required variables: 
#data frame with abundance values and the imperfect detection value
sample_id <- sample(1:40, size = 10, replace = FALSE)
abundance <- sample(0:6, size = 10, replace = TRUE)

abun_df <- data.frame(id = sample_id, abun = abundance)
head(abun_df, n = 10)
#>    id abun
#> 1  26    6
#> 2  36    4
#> 3   6    0
#> 4  40    4
#> 5  31    6
#> 6   1    3
#> 7  13    4
#> 8  24    3
#> 9   2    1
#> 10 18    5

ipd <- 0.5

#Create a new data frame with a new column indicating if the species have been detected or not
pres_df <- abundance2pres(abun = abun_df, ipd = ipd)
head(pres_df, n = 10)
#>    sampleID abundance occurrences
#> 1        26         6           1
#> 2        36         4           1
#> 3         6         0           0
#> 4        40         4           1
#> 5        31         6           1
#> 6         1         3           1
#> 7        13         4           0
#> 8        24         3           1
#> 9         2         1           0
#> 10       18         5           1