It is a R package for creating herbarium labels, based on Darwin Core Template. Including the following functionalities:
Parsing scientific names, and filling the relevant fields, including: FAMILY, GENUS, SPECIES etc.
Checking the spelling based on The Plant List Database, Florae Reipublicae Popularis Sinicae (FRPS), Flora of China.
herblabel is available on R-forge, and you can use the following command to install:
install.packages("herblabel", repos="http://R-Forge.R-project.org")
This packages depends on "openxlsx"
install.packages("openxlsx")
Usually the package "Rcpp" which "openxlsx" depends on should be installed automatically. If not, please type to following command to install Rcpp:
install.packages("Rcpp")
The Rtools tool chain should also be installed and well configured. "https://cran.r-project.org/bin/windows/Rtools/"
For more information, please refer to (in Chinese): http://blog.sciencenet.cn/blog-255662-849868.html
Generating herbarium labels
R
library(openxlsx)
library(herblabel)
path <- system.file("extdata", "DARWIN_CORE_HERBARIUM_RECORDS.xlsx",
package = "herblabel")
dat <- read.xlsx(path)
herbarium_label(dat, theme = "KFBG", outfile = "herbarium_labels_KFBG.rtf") ### KFBG Style
herbarium_label(dat, theme = "PE", outfile = "herbarium_labels_PE.rtf") ### PE Style
herbarium_label(dat, theme = "KUN", outfile = "herbarium_labels_KUN.rtf") ### KUN Style
herbarium_label(dat, theme = "HU", outfile = "herbarium_labels_HU.rtf") ### Harvard University
herbarium_label(dat, spellcheck = FALSE, outfile = "herbarium_labels_no_checking.rtf")
2. Annotation Labels
R
library(herblabel)
library(openxlsx)
path <- system.file("extdata", "ANNOTATION_TEMPLATE.xlsx",
package = "herblabel")
dat <- read.xlsx(path)
annotation_label(dat)
The R script "run_herblabel" helps you to generate herbarium labels by a simple click. See https://github.com/helixcn/run_herblabel
Jinlong Zhang, Huiling Zhu, Jingang Liu, Gunter A. Fischer. (2016). Principles behind designing herbarium specimen labels and the R package 'herblabel'. Biodiversity Science, 24(12): 1345-1352 (DOI: 10.17520/biods.2016230)
Please feel free to send an email to Jinlong Zhang jinlongzhang01@gmail.com if you have any questions.
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