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Exporting tables for Juice

Source: R/write_juice.R
write_juice.Rd

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 class '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

Miguel Alvarez kamapu78@gmail.com

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"))
#> Processing header data...
#> Processing vegetation table...
#> DONE!
#> 
#> Data set name: Plot Observations
#> Number of observations: 20
#> Recorded species: 104
## Installed 'Juice' version of 'Wetlands_veg'
Veg <- file.path(path.package("vegtable"), "juice", "Wetlands_juice.txt")
Veg <- read_juice(Veg)

summary(Veg)
#>             Length Class      Mode
#> cross_table 88     data.frame list
#> header      24     data.frame list