exsic (version 1.1.1)

exsic-package: Provides botanists with convenience functions to create exsiccatae indices

Description

The tool allows creating simple specimen indices as found in taxonomic treatments based on a table of specimen records. An example file of tabulated speciment data is provided. In addition, four different exsiccatae styles are provided. The naming of the columns in the specimen table follows largely the conventions used in the BRAHMS software package. Each specimen record must at least have content in the following nine fields: id, genus, species, collcite, number, colldate, country, majorarea, minorarea. If not present, the fields are added and filled with dummy values like 's.d.' for no date or 'Unknown country/area'. Highly recommended fields include: collector, addcoll. Optional fields include: locnotes, phenology, elevation, latitude, longitude, and dups The produced indices will sort countries and species alphabetically. Within a country records will be sorted alphabetically by 'majorarea' (if present) and by collector and collecting nunber. A web page in standard html format is created based on a template. The template may be changed and specified in most word processing software. The package provides one main function 'exsic'. See the example in this section on how to access it.

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)