exsic (version 1.1.1)

exsic: Creates three botanical indices (exsiccatae or index of specimens; numerical list of species; index to numbered collections).

Description

It uses a data.frame expecting a minimum set of columns; if those are not found they will be added and filled with 'unknown' or similar values as will be other columns with missing data but used for sorting the final indices.

Usage

exsic(data, file = NULL, html = "exsic.html", sortfilter = NULL, format = format.SBMG, headers = c("Citations of Specimens", "Numerical List of Species", "Index to Numbered Collections", "*Numbers refer to species in the Numerical List.*\n\r"))

Arguments

data

a table in exsic format

file

Path to the .csv file containing the database

html

Path to the resulting .html file

sortfilter

a table containing filters for country and species

format

a table containing format options for elements in the exsiccatae index

headers

A list of text lines for labeling the indices

Value

boolean TRUE if all steps executed successfully

See Also

Other main: index.citations; index.collections; index.countries; index.species.short; index.species; prepare.table; read.exsic; section.exsic; write.exsic

Examples

# Example
load(system.file("data/config.rda", package="exsic"))
###########################################################
# This runs the example file


# Read input file
df = system.file("samples/exsic.csv", package="exsic")
# read only first 10 records
data = read.exsic(df)[1:10,]

# Prepare output file
td = tempdir()
of = file.path(td,"out.html")


# Example 1: mostly default parameters
# Prepare exsiccatae indices
exsic(data, html = of) 


# Example 2: using another format
of = file.path(td,"out_PK.html")
exsic(data, html = of, format = format.PK)