mirror of https://github.com/msberends/AMR.git
69 lines
2.3 KiB
R
69 lines
2.3 KiB
R
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)
|