knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" )
AnAgeScrapeR lets you extract data for one or more species from the AnAge database: http://genomics.senescence.info/species/. The official citation is for the data is:
Tacutu, R., Thornton, D., Johnson, E., Budovsky, A., Barardo, D., Craig, T., Diana, E., Lehmann, G., Toren, D., Wang, J., Fraifeld, V. E., de Magalhaes, J. P. (2018) "Human Ageing Genomic Resources: new and updated databases." Nucleic Acids Research 46(D1):D1083-D1090.
You can install AnAgeScrapeR from GitHub. Dependencies are all from the tidyverse.
# install.packages("remotes") remotes::install_github("mastoffel/AnAgeScrapeR", dependencies = TRUE)
So far, only the latin species names can be used (case insensitive). By default, there should be a space between Genus and Species name, but other delimiters can be used with the name_sep argument. The database is downloaded into your working directory (as it's a zip file which is difficult to directly read into R) when you extract data for the first time. Afterwards you can set download_data to FALSE, except for you want to download it again to be sure you have the newest version.
library(AnAgeScrapeR) species <- c("felis catus", "Sterna paradisaea") dat <- scrape_AnAge(latin_name = species, vars = c("maximum_longevity_yrs","female_maturity_days")) dat
There are quite a few more life history traits to extract, which can be found in AnAge_variables. The unit in which a variable is measured is simply the last bit of the variable name.
data(AnAge_variables)
AnAge_variables
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