## This script prepares the everglades dataset on macroinvertebrate species composition
# along a surface-water total phosphorus gradient
# used in Baker & King 2010 (https://www.doi.org/10.1111/j.2041-210X.2009.00007.x)
# Variable Metadata -------------------------------------------------------
## column desriptions and units
# TP.ugL: surface-water total phosphorus in micrograms/liter
# site: name of sampling station
# variable: macroinvertebrate taxa names
# value: macroinvertebrate densities in number/meter-squared
# Provide citation --------------------------------------------------------
# df.citation <- "CITATION GOES HERE"
# Import the original data ---------------------------------------------------------
everglades.env <- read.table("data-raw/everglades_env.txt")
everglades.taxa <- read.table("data-raw/everglades_taxa.txt")
# Load attributes ---------------------------------------------------------
attributes <- read.csv("data-raw/metadata/attributes-everglades-baker.csv")
# Pre-munging the observations dataset -------------------------------------------------------
## add row names as column
everglades.env$site <- rownames(everglades.env)
everglades.taxa$site <- rownames(everglades.taxa)
## combine data and convert to long format
data <- everglades.env %>%
# join taxa with environemntal variables
dplyr::left_join(everglades.taxa, by="site") %>%
# remove punctuation and spaces from site names
dplyr::mutate(site = gsub("[ [:punct:]]", "",site)) %>%
# force site to factor
dplyr::mutate(site=as.factor(site)) %>%
tidyr::pivot_longer(c(-TP.ugL, -site), names_to="taxa", values_to="values")
# Create package standard dataset -----------------------------------------
everglades <- munge_dataset(data, attributes)
# Save the data as .rda ---------------------------------------------------
usethis::use_data(everglades, overwrite = TRUE) # uncomment this line and run it.
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