write_juice: Exporting tables for Juice

In vegtable: Handling Vegetation Data Sets

Exporting tables for Juice

Description

This function produce txt files as inport formats for Juice (https://www.sci.muni.cz/botany/juice/).

This function produces two output files to be imported into a Juice file: A vegetation table produced by crosstable() and a header table. Both tables share the file name plus a suffix (table for the vegetation table and header for the header).

For the import in Juice, you go to the menu ⁠File -> Import -> Table -> from Spreadsheet File (e.g. EXCEL Table)⁠ and then follow the wizard. Do not forget to select the proper settings in the wizard: 1) 'Character delimiting columns: Comma' (for default argument values). 2) 'Use the second column as layer information: Unchecked'. 3) 'Cover values: Percentage Values'.

To further import the header table you need to go to the menu ⁠File -> Import -> Header Data -> From Comma Delimited File⁠.

In the header (see Value), the first column (⁠Table number⁠) corresponds to the plot number assigned by Juice at import, while the column (⁠Releve number⁠) is the number originally assigned to the plot (e.g. Turboveg ID).

Usage

write_juice(data, file, formula, ...)

## S4 method for signature 'vegtable,character,formula'
write_juice(
  data,
  file,
  formula,
  FUN,
  db_name = "Plot Observations",
  header,
  coords,
  sep = ",",
  ...
)

read_juice(file, encoding = "LATIN-1", sep = ";", na = "", ...)

Arguments

data	An object of class vegtable.
file	Character value indicating the name of output files (without file extension).
formula	A formula passed to crosstable().
...	Further arguments. While write_juice() passes them to the function crosstable(), read_juice() passes those arguments to readLines().
FUN	Funtion passed to crosstable().
db_name	Name for data set displayed in inport wizard.
header	Variables of header to be exported.
coords	Names of coordinate variables in header of data.
sep	Separator used to split rows into columns.
encoding	Argument passed to readLines.
na	Character used as not available values.

Value

For read_juice(), a list with two elements: A data frame of species by plot (cross_table), and a data frame with header data (header).

Author(s)

Miguel Alvarez [e-mail]

Examples

## Subset and transform cover values to percentage
vegetation <- Kenya_veg[1:20, ]
vegetation <- cover_trans(x = vegetation, to = "cover_percent", rule = "middle")

## Write in tempdir
write_juice(data = vegetation, file = file.path(tempdir(), "SWEA"),
    formula = cover_percent ~ ReleveID + AcceptedName, FUN = mean,
    header = c("ReleveID", "COMM_TYPE"))
## Installed 'Juice' version of 'Wetlands_veg'
Veg <- file.path(path.package("vegtable"), "juice", "Wetlands_juice.txt")
Veg <- read_juice(Veg)

summary(Veg)

vegtable documentation built on March 31, 2023, 10:33 p.m.