crosstable: Generating cross tables from database lists

In kamapu/vegtables: Handling Vegetation Data Sets

Generating cross tables from database lists

Description

cross table is the most common format required by statistical packages used to analyse vegetation data (e.g. vegan).

You may use for convenience a formula as 'abundance ~ plot + species + ...'. Additional variables used for rows (...) can be for instance the layers. For objects of class vegtable, the formula can also include variables from the species list (for example AcceptedName, AuthorName) or even taxon traits.

If required, tables already formatted as cross tables can be converted into column-oriented tables by using the function cross2db().

Usage

crosstable(formula, data, ...)

## S4 method for signature 'formula,data.frame'
crosstable(
  formula,
  data,
  FUN,
  na_to_zero = FALSE,
  use_nas = TRUE,
  as_matrix = FALSE,
  ...
)

## S4 method for signature 'formula,vegtable'
crosstable(
  formula,
  data,
  FUN,
  level,
  include_lower = FALSE,
  na_to_zero = FALSE,
  use_nas = TRUE,
  ...
)

cross2db(object, ...)

## S3 method for class 'data.frame'
cross2db(object, layers = FALSE, na_strings, ...)

## S3 method for class 'matrix'
cross2db(object, ...)

Arguments

formula	A formula indicating the variables used in the cross table. This formula can be represented as 'abundance ~ cols + rows', where 'abundance' is the numeric variable quantified for a row in a column, for instance the abundance of a species in a plot. Further variables can be set as additional rows indices in a cross table.
data	Either a data frame or an object of class vegtable.
...	Further arguments passed to the function stats::aggregate().
FUN	Function used to aggregate values in the case of a multiple occurrence of a species in a plot, for instance.
na_to_zero	A logical value indicating whether zeros should be inserted into empty cells or not.
use_nas	Logical value indicating whether NAs should be considered as levels for categorical variables or not.
as_matrix	A logical value, whether output should be done as matrix or data frame.
level	A character vector with taxonomic ranks (levels) requested in the cross table.
include_lower	A logical value indicating wether lower value to the requested levels should be merged or not. It works only if 'level' is not missing. Note that if you like to include higher ranks or rankless taxa in the cross table, you will rahter need to run merge_taxa() on slot species.
object	A data frame or a matrix including a cross table. Note that cross2db() assumes observations as columns and species (and layers) as rows in the data.frame-method but species as columns and observations as rows in the matrix-method.
layers	Logical value, whether the cross table includes a layer column or not.
na_strings	Character vector indicating no records in the cross table.

Value

An object of class data.frame.

Author(s)

Miguel Alvarez [e-mail]

Examples

# Produce a subset
veg <- subset(Kenya_veg, REFERENCE == 2331, slot = "header")

## transform cover to percentage
veg <- cover_trans(veg, to = "cover_perc", rule = "middle")

## cross table of the first 5 plots
Cross <- crosstable(cover_perc ~ ReleveID + AcceptedName + AuthorName,
  data = veg[1:5, ], FUN = mean, na_to_zero = TRUE)
head(Cross)

## cross table of recorded genera
Cross <- crosstable(cover_perc ~ ReleveID + AcceptedName + AuthorName,
    data = veg, FUN = mean, level = "genus")
head(Cross[ , 1:7])

## cross table of data merged to genus
Cross <- crosstable(cover_perc ~ ReleveID + AcceptedName + AuthorName,
    data = veg, FUN = sum, level = "genus", include_lower = TRUE)
head(Cross[ , 1:7])

## the same for families
Cross <- crosstable(cover_perc ~ ReleveID + AcceptedName + AuthorName,
    data = veg, FUN = sum, level = "family", include_lower = TRUE)
head(Cross[ , 1:7])

kamapu/vegtables documentation built on Feb. 17, 2024, 8:29 a.m.