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(v1.8.1.9013) add Toxoplasma

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dr. M.S. (Matthijs) Berends
2022-06-10 13:15:23 +02:00
parent b84d647cac
commit 7f981e7778
29 changed files with 432 additions and 124 deletions
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data-raw/toxoplasma.R Normal file
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microorganisms <- microorganisms |> bind_rows(
# Toxoplasma
data.frame(mo = "P_TXPL_GOND", # species
fullname = "Toxoplasma gondii",
kingdom = "(unknown kingdom)",
phylum = "Apicomplexa",
class = "Conoidasida",
order = "Eucoccidiorida",
family = "Sarcocystidae",
genus = "Toxoplasma",
species = "gondii",
subspecies = "",
rank = "species",
ref = "Nicolle et al., 1908",
species_id = NA_real_,
source = "manually added",
prevalence = 2,
stringsAsFactors = FALSE),
data.frame(mo = "P_TXPL", # genus
fullname = "Toxoplasma",
kingdom = "(unknown kingdom)",
phylum = "Apicomplexa",
class = "Conoidasida",
order = "Eucoccidiorida",
family = "Sarcocystidae",
genus = "Toxoplasma",
species = "",
subspecies = "",
rank = "genus",
ref = "Nicolle et al., 1909",
species_id = NA_real_,
source = "manually added",
prevalence = 2,
stringsAsFactors = FALSE),
data.frame(mo = "[FAM]_SRCCYSTD", # family
fullname = "Sarcocystidae",
kingdom = "(unknown kingdom)",
phylum = "Apicomplexa",
class = "Conoidasida",
order = "Eucoccidiorida",
family = "Sarcocystidae",
genus = "",
species = "",
subspecies = "",
rank = "family",
ref = "Poche, 1913",
species_id = NA_real_,
source = "manually added",
prevalence = 2,
stringsAsFactors = FALSE),
data.frame(mo = "[ORD]_EUCCCDRD", # order
fullname = "Eucoccidiorida",
kingdom = "(unknown kingdom)",
phylum = "Apicomplexa",
class = "Conoidasida",
order = "Eucoccidiorida",
family = "",
genus = "",
species = "",
subspecies = "",
rank = "order",
ref = "Leger et al., 1910",
species_id = NA_real_,
source = "manually added",
prevalence = 2,
stringsAsFactors = FALSE),
) |>
arrange(fullname)