EcoGenetics (version 1.2.1-4)

eco.formula: Formula construction for ecogen objects

Description

When a data frame is present in a slot of an object, any individual column can be accessed using the notation: my_object@my_data_frame[, column_to_be_accessed]. The later constitutes an explicit name for the variable present in the object. The present function generalizes this concept, allowing to construct a formula for the variables present in an ecogen object (columns of the data frames in slots). The function creates an explicit formula that can be used to parse ecogen objects into other functions (see examples below). For this purpose, each name in the formula is substituted with explicit names of columns if:

- The name corresponds to the name of an individual column in the data frames of the ecogen object, or

- The name is surrounded by U() and corresponds to the name of a slot. Complete data frames (as P, E, etc.) or subsets (as U[, 1:5]) can be passed with this method and all the columns will be explicitly included in the formula.

In other situations, names are not replaced.

Usage

eco.formula(eco, formula, out.mode = c("formula", "expression"),
  expand.tables = "+")

Arguments

eco

Object of class "ecogen".

formula

formula with names of colums from the slots XY, P, G, A, E, or C

out.mode

Output results explicit formula (default) or expression.

expand.tables

method for tables coertion. Default is "+"

Examples

# NOT RUN {
require(vegan)
data(eco.test)

# Note that in this example "Condition" is not replaced; 
# the function Condition has a special meaning in rda,
# indicating conditioning variables; in eco.formula it is only text.

form <- eco.formula(eco, P1 + P2 + P3 + U(A) ~ E1 + E2 + Condition(X+Y))
rda(form)

form2 <- eco.formula(eco, P1 + P2 + P3 + U(A) ~ E1 + E2 + X + Y)
lm(form2)


# parsing with magrittr
eco.formula(eco, P1 + P2 + P3 + U(A) ~ U(E) + Condition(X+Y)) %>% rda
# }
# NOT RUN {
# }