join {analogue}R Documentation

Merge species data sets on common columns (species)

Description

Merges any number of species matrices on their common columns to create a new data set with number of columns equal to the number of unqiue columns across all data frames. Needed for analysis of fossil data sets with respect to training set samples.

Usage

join(..., verbose = FALSE, na.replace = TRUE, split = TRUE)

## S3 method for class 'join':
head(x, ...)

## S3 method for class 'join':
tail(x, ...)

Arguments

... for join, data frames containing the data sets to be merged. For the head and tail methods, additional arguments to head and tail, in particular "n" to control the number of rows of each joined data set to display.
verbose logical; if TRUE, the function prints out the dimensions of the data frames in "...", as well as those of the returned, merged data frame.
na.replace logical; samples where a column in one data frame that have no matching column in the other will contain missing values (NA). If na.replace is TRUE, these missing values are replaced with zeros. This is standard practice in ecology and palaeoecology. If you want to replace with another value, then set na.replace to FALSE and do the replacement later.
split logical; should the merged data sets samples be split back into individual data frames, but now with common columns (i.e. species)?
x an object of class "join", usually the result of a call to join.

Value

If split = TRUE, an object of class "join", a list of data frames, with as many components as the number of data frames originally merged.
Otherwise, an object of class c("join", "data.frame"), a data frame containing the merged data sets.
head.join and tail.join return a list, each component of which is the result of a call to head or tail on each data set compont of the joined object.

Author(s)

Gavin L. Simpson

See Also

merge

Examples

## load the example data
data(swapdiat)
data(swappH)
data(rlgh)

## merge training and test set on columns
dat <- join(swapdiat, rlgh, verbose = TRUE)

## extract the merged data sets and convert to proportions
swapdiat <- dat[[1]] / 100
rlgh <- dat[[2]] / 100

## load the example data
data(ImbrieKipp)
data(SumSST)
data(V12.122)

## merge training and test set on columns
dat <- join(ImbrieKipp, V12.122, verbose = TRUE)

## extract the merged data sets and convert to proportions
ImbrieKipp <- dat[[1]] / 100
V12.122 <- dat[[2]] / 100

## show just the first few lines of each data set
head(dat, n = 4)

## show just the last few lines of each data set
tail(dat, n = 4)

[Package analogue version 0.6-6 Index]