Transform visually estimated species cover to cover-abundance values

Convert visually estimated percentage cover using the simplified cover classes in the table below.

Usage

PhytoCover(database, method)

Arguments

database

A data frame with species in rows and surveys in columns. The first column contains non-missing, non-empty, unique species names; spaces in species names are allowed. Remaining columns contain percentages from 0 to 100, numeric strings, or "+" for trace cover. Factors are accepted through their labels. NA and blank strings are interpreted as absence (0).

method

One of "BrBl", "Maarel", or "TassTapp".

Value

A data frame with species names as row names and the original survey names as column names. The species-name column is omitted. "BrBl" returns character columns; the other methods return numeric columns.

Details

Conversion table

Visually estimated cover (%)	BrBl	Maarel	TassTapp
0	0	0	0
0 < cover < 1, or +	+	2	0.3
1 <= cover <= 5	1	3	2.8
5 < cover <= 15	2a	5	10
15 < cover <= 25	2b	5	20.5
25 < cover <= 50	3	7	38
50 < cover <= 75	4	8	63
75 < cover <= 100	5	9	88

These are the package's simplified, cover-based conversions, rather than a reconstruction of abundance from percentage cover. The full extended Braun-Blanquet scale includes abundance categories not inferred here. In particular, "Maarel" preserves the package convention of assigning 5 to both 2a and 2b; the full ordinal transformation distinguishes these as 5 and 6. The "TassTapp" values are fixed representatives of cover classes, not percentages normalized to sum to 100 within a survey.

Missing values are treated as absence for compatibility. Use this convention only when missing cells actually represent species absence, not unknown cover.

References

Braun-Blanquet, J. (1964). Pflanzensoziologie. Springer, Vienna.

van der Maarel, E. (1979). Transformation of cover-abundance values in phytosociology and its effects on community similarity. Vegetatio, 39, 97-114.

Tasser, E. and Tappeiner, U. (2005). New model to predict rooting in diverse plant community compositions. Ecological Modelling, 185, 195-211.

Examples

# Rows are species; columns after the first are surveys.
cover <- data.frame(
  Species = c("Festuca rubra", "Poa pratensis", "Trifolium repens"),
  survey1 = c("12.3", "+", NA),
  survey2 = c("5", "0", "27")
)
PhytoCover(cover, "BrBl")
#>                  survey1 survey2
#> Festuca rubra         2a       1
#> Poa pratensis          +       0
#> Trifolium repens       0       3
PhytoCover(cover, "Maarel")
#>                  survey1 survey2
#> Festuca rubra          5       3
#> Poa pratensis          2       0
#> Trifolium repens       0       7
PhytoCover(cover, "TassTapp")
#>                  survey1 survey2
#> Festuca rubra       10.0     2.8
#> Poa pratensis        0.3     0.0
#> Trifolium repens     0.0    38.0