# The code below shows how to contruct a taxmap object from scratch.
# Typically, taxmap objects would be the output of a parsing function,
# not created from scratch, but this is for demostration purposes.
notoryctidae <- taxon(
name = taxon_name("Notoryctidae"),
rank = taxon_rank("family"),
id = taxon_id(4479)
)
notoryctes <- taxon(
name = taxon_name("Notoryctes"),
rank = taxon_rank("genus"),
id = taxon_id(4544)
)
typhlops <- taxon(
name = taxon_name("typhlops"),
rank = taxon_rank("species"),
id = taxon_id(93036)
)
mammalia <- taxon(
name = taxon_name("Mammalia"),
rank = taxon_rank("class"),
id = taxon_id(9681)
)
felidae <- taxon(
name = taxon_name("Felidae"),
rank = taxon_rank("family"),
id = taxon_id(9681)
)
felis <- taxon(
name = taxon_name("Felis"),
rank = taxon_rank("genus"),
id = taxon_id(9682)
)
catus <- taxon(
name = taxon_name("catus"),
rank = taxon_rank("species"),
id = taxon_id(9685)
)
panthera <- taxon(
name = taxon_name("Panthera"),
rank = taxon_rank("genus"),
id = taxon_id(146712)
)
tigris <- taxon(
name = taxon_name("tigris"),
rank = taxon_rank("species"),
id = taxon_id(9696)
)
plantae <- taxon(
name = taxon_name("Plantae"),
rank = taxon_rank("kingdom"),
id = taxon_id(33090)
)
solanaceae <- taxon(
name = taxon_name("Solanaceae"),
rank = taxon_rank("family"),
id = taxon_id(4070)
)
solanum <- taxon(
name = taxon_name("Solanum"),
rank = taxon_rank("genus"),
id = taxon_id(4107)
)
lycopersicum <- taxon(
name = taxon_name("lycopersicum"),
rank = taxon_rank("species"),
id = taxon_id(49274)
)
tuberosum <- taxon(
name = taxon_name("tuberosum"),
rank = taxon_rank("species"),
id = taxon_id(4113)
)
homo <- taxon(
name = taxon_name("homo"),
rank = taxon_rank("genus"),
id = taxon_id(9605)
)
sapiens <- taxon(
name = taxon_name("sapiens"),
rank = taxon_rank("species"),
id = taxon_id(9606)
)
hominidae <- taxon(
name = taxon_name("Hominidae"),
rank = taxon_rank("family"),
id = taxon_id(9604)
)
unidentified <- taxon(
name = taxon_name("unidentified")
)
tiger <- hierarchy(mammalia, felidae, panthera, tigris)
cat <- hierarchy(mammalia, felidae, felis, catus)
human <- hierarchy(mammalia, hominidae, homo, sapiens)
mole <- hierarchy(mammalia, notoryctidae, notoryctes, typhlops)
tomato <- hierarchy(plantae, solanaceae, solanum, lycopersicum)
potato <- hierarchy(plantae, solanaceae, solanum, tuberosum)
potato_partial <- hierarchy(solanaceae, solanum, tuberosum)
unidentified_animal <- hierarchy(mammalia, unidentified)
unidentified_plant <- hierarchy(plantae, unidentified)
info <- data.frame(stringsAsFactors = FALSE,
name = c("tiger", "cat", "mole", "human", "tomato", "potato"),
n_legs = c(4, 4, 4, 2, 0, 0),
dangerous = c(TRUE, FALSE, FALSE, TRUE, FALSE, FALSE))
abund <- data.frame(code = rep(c("T", "C", "M", "H"), 2),
sample_id = rep(c("A", "B"), each = 2),
count = c(1,2,5,2,6,2,4,0),
taxon_index = rep(1:4, 2))
phylopic_ids <- c("e148eabb-f138-43c6-b1e4-5cda2180485a",
"12899ba0-9923-4feb-a7f9-758c3c7d5e13",
"11b783d5-af1c-4f4e-8ab5-a51470652b47",
"9fae30cd-fb59-4a81-a39c-e1826a35f612",
"b6400f39-345a-4711-ab4f-92fd4e22cb1a",
"63604565-0406-460b-8cb8-1abe954b3f3a")
foods <- list(c("mammals", "birds"),
c("cat food", "mice"),
c("insects"),
c("Most things, but especially anything rare or expensive"),
c("light", "dirt"),
c("light", "dirt"))
reaction <- function(x) {
ifelse(x$data$info$dangerous,
paste0("Watch out! That ", x$data$info$name, " might attack!"),
paste0("No worries; its just a ", x$data$info$name, "."))
}
ex_taxmap <- taxmap(tiger, cat, mole, human, tomato, potato,
data = list(info = info,
phylopic_ids = phylopic_ids,
foods = foods,
abund = abund),
funcs = list(reaction = reaction))
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