Identify (guess) relevé scale

This function identifies the phytosociological scale(s) possibly in use in a given relevé (or makes an educated guess about it).

Usage

releve_scale(
  x,
  absence.values = c("0", "."),
  parentheses.values = c("(+)", "(x)"),
  output = "all",
  scales.order = c("PA_x", "PA_1", "OBBsim", "OBBsoc", "EBBsim", "EBBsoc", "OBBsiX",
    "OBBsoX", "EBBsiX", "EBBsoX")
)

Arguments

x

vector A numericor character vector with the relevé values (e.g. extracted from a relevé table).

absence.values

character A vector, with values representing absences. Defaults to c(".","0").

parentheses.values

vector A numericor character vector with the admissible values inside parentheses. Defaults to "(+)" and "(x)". Traditionally "(+)" or "(x)" indicate the presence of a taxon that was out of the relevé area but that was observed in its close surroundings.

output

character "all" returns all possible scales in use in the given relevé; "most probable" returns the most probable scale (an educated guess informed by scales.order).

scales.order

character A vector with any of the following components: "PA_x", "PA_1", "OBBsim", "OBBsoc", "EBBsim", "EBBsoc", "OBBsiX", "OBBsoX", "EBBsiX" and "EBBsoX". See Details.

Value

A character vector with the all possible scales that are in use in the relevé (output = "all"), or the most probable scale (output = "most probable").

Details

The vector scales.order not only indicates which scales should be tested but also indicates the order that such scales should be presented when ambiguity is present (i.e. given the relevé values, it is not possible to determine unambiguously which scale is in use). In regional contexts where some scales are pervasive, such scales should definitely come first, so that output = "most probable" has better chances of success. By default, scales.order = c("PA_x", "PA_1", "OBBsim", "OBBsoc", "EBBsim", "EBBsoc", "OBBsiX", "OBBsoX", "EBBsiX", "EBBsoX"), which is thought for the Iberian Peninsula tradition, where OBBsim and OBBsoc are widely used. "PC_int", "PC_dec", "OTV_5" and "OTV_9" should never be included in scales.order as are always evaluated in a second moment of the function and only if "(", "r", "+", "2m", "2a", "2b" and "x" are not present at the beginning of any of the relevé values.

This function considers the following scales:

PA_x

Presence-absence scale with presences denoted as "x".

PA_1

Presence-absence scale with presences denoted as 1 or "1". In this scale parentheses.values are not expected to occur.

OBBsim

The original (simple, i.e. without sociability) Braun-Blanquet scale (including "r"): "r", "+", "1", "2", "3", "4" and "5".

OBBsoc

The original Braun-Blanquet scale (including "r") with sociability values: "r", "+", "+.1", "+.2", "+.3", "1.1", "1.2", "1.3", "2.1", "2.2", "2.3", "2.4", "3.1", "3.2", "3.3", "3.4", "3.5", "4.1", "4.2", "4.3", "4.4", "4.5", "5.1", "5.2", "5.3", "5.4" and "5.5".

EBBsim

The extended Braun-Blanquet scale: "r", "+", "1", "2m", "2a", "2b", "3", "4" and "5".

EBBsoc

The extended Braun-Blanquet scale with sociability values: "r", "+", "+.1", "+.2", "+.3", "1.1", "1.2", "1.3", "2m.1", "2m.2", "2m.3", "2m.4", "2m.5", "2a.1", "2a.2", "2a.3", "2a.4", "2a.5", "2b.1", "2b.2", "2b.3", "2b.4", "2b.5", "3.1", "3.2", "3.3", "3.4", "3.5", "4.1", "4.2", "4.3", "4.4", "4.5", "5.1", "5.2", "5.3", "5.4" and "5.5".

OBBsiX

The same scale as OBB_sim but containing also "x" as a simple presence of a taxon.

OBBsoX

The same scale as OBB_sim but containing also "x" as a simple presence of a taxon.

EBBsiX

The same scale as OBB_sim but containing also "x" as a simple presence of a taxon.

EBBsoX.

The same scale as OBB_sim but containing also "x" as a simple presence of a taxon.

PC_int

Percentage cover scale, using integer numbers. In this scale parentheses.values are not expected to occur.

PC_dec

Percentage cover scale, using decimal numbers. In this scale parentheses.values are not expected to occur.

OTV_5

Ordinal transform values scale, with five levels. In this scale parentheses.values are not expected to occur.

OTV_9

Ordinal transform values scale, with nine levels. In this scale parentheses.values are not expected to occur.

In some cases, authors use a cover-abundance scale in the relevé but some taxa are registered only as present (without the respective cover-abundance value, e.g. with "x"). The function can also detect such cases for OBB_sim, OBB_soc, EBBsim and EBBsoc (adding "x" as a possible value). The respective names of such scales are: OBBsiX, OBBsoX, EBBsiX and EBBsoX. By default, all scales (except PA_1, PC_int, PC_dec, OTV_5 and OTV_9) also contain "(+)" and "(x)" as possible values within parentheses, but this can be changed in the parentheses.values argument. Using several different absence.values simultaneously can produce inconsistencies and should be done carefully. Some databases (like SIVIM) store "+.1" simply as "+", therefore, in the scales with sociability values, both values are admitted as valid. Not all combinations of abundance-cover/sociability are implemented, as some seem not to be used at all. Yet some other values might be added in future.

In relevés using the percentage cover scales (PC_int and PC_dec), the ordinal transform values scales (OTV_5 and OTV_9) and the presence-absence scale with presences denoted as 1 or "1" (PA_1), parentheses.values are not expected to occur (if any value of the relevé has parentheses, the function will simply ignore the evaluation of these scales).

Using 1 or "1" as presence is strongly discouraged as database storage value, as relevés can become indistinguishable from any other scale that uses 1 or "1" as a value!

Author

Tiago Monteiro-Henriques. E-mail: tmh.dev@icloud.com.