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(v0.7.1.9033) 5000 new fungi

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-09 23:22:10 +02:00
parent 6a349bf757
commit 6598c5615d
31 changed files with 136 additions and 109 deletions
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26
data-raw/reproduction_of_microorganisms.R
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@ -11,10 +11,10 @@ library(dplyr)
library(AMR)
# unzip and extract taxon.tab (around 1.5 GB) from the CoL archive, then:
data_col <- data.table::fread("Downloads/taxon.tab")
data_col <- data.table::fread("data-raw/taxon.tab")
# read the xlsx file from DSMZ (only around 2.5 MB):
data_dsmz <- readxl::read_xlsx("Downloads/DSMZ_bactnames.xlsx")
data_dsmz <- readxl::read_xlsx("data-raw/DSMZ_bactnames.xlsx")
# the CoL data is over 3.7M rows:
data_col %>% freq(kingdom)
@ -99,23 +99,25 @@ MOs <- data_total %>%
# and not all fungi: Aspergillus, Candida, Trichphyton and Pneumocystis are the most important,
# so only keep these orders from the fungi:
& !(kingdom == "Fungi"
& !order %in% c("Eurotiales", "Mucorales", "Saccharomycetales", "Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"))
& !order %in% c("Eurotiales", "Microascales", "Mucorales", "Saccharomycetales", "Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"))
)
# or the genus has to be one of the genera we found in our hospitals last decades (Northern Netherlands, 2002-2018)
| genus %in% c("Absidia", "Acremonium", "Actinotignum", "Alternaria", "Anaerosalibacter", "Ancylostoma", "Anisakis", "Apophysomyces",
"Arachnia", "Ascaris", "Aureobacterium", "Aureobasidium", "Balantidum", "Bilophilia", "Branhamella", "Brochontrix",
"Brugia", "Calymmatobacterium", "Catabacter", "Cdc", "Chilomastix", "Chryseomonas", "Cladophialophora", "Cladosporium",
"Clonorchis", "Cordylobia", "Curvularia", "Demodex", "Dermatobia", "Diphyllobothrium", "Dracunculus", "Echinococcus",
"Enterobius", "Euascomycetes", "Exophiala", "Fasciola", "Fusarium", "Hendersonula", "Hymenolepis", "Kloeckera",
"Enterobius", "Euascomycetes", "Exophiala", "Fasciola", "Fusarium", "Hendersonula", "Hymenolepis", "Hypomyces", "Kloeckera",
"Koserella", "Larva", "Leishmania", "Lelliottia", "Loa", "Lumbricus", "Malassezia", "Metagonimus", "Molonomonas",
"Mucor", "Nattrassia", "Necator", "Novospingobium", "Onchocerca", "Opistorchis", "Paragonimus", "Paramyxovirus",
"Mucor", "Nattrassia", "Necator", "Nectria", "Novospingobium", "Onchocerca", "Opistorchis", "Paragonimus", "Paramyxovirus",
"Pediculus", "Phoma", "Phthirus", "Pityrosporum", "Pseudallescheria", "Pulex", "Rhizomucor", "Rhizopus", "Rhodotorula",
"Salinococcus", "Sanguibacteroides", "Schistosoma", "Scopulariopsis", "Scytalidium", "Sporobolomyces", "Stomatococcus",
"Strongyloides", "Syncephalastraceae", "Taenia", "Torulopsis", "Trichinella", "Trichobilharzia", "Trichomonas",
"Strongyloides", "Syncephalastraceae", "Taenia", "Torulopsis", "Trichinella", "Trichobilharzia", "Trichoderma", "Trichomonas",
"Trichosporon", "Trichuris", "Trypanosoma", "Wuchereria")
# or the taxonomic entry is old - the species was renamed
| !is.na(col_id_new)
)
) %>%
# really no Plantae (e.g. Dracunculus exist both as worm and as plant)
filter(kingdom != "Plantae")
# filter old taxonomic names so only the ones with an existing reference will be kept
MOs <- MOs %>%
@ -222,7 +224,7 @@ MOs <- MOs %>%
distinct(fullname, .keep_all = TRUE)
# what characters are in the fullnames?
paste(unique(sort(unlist(strsplit(x = paste(MOs$fullname, collapse = ""), split = "")))), collapse = "")
table(sort(unlist(strsplit(x = paste(MOs$fullname, collapse = ""), split = ""))))
# Add abbreviations so we can easily know which ones are which ones.
# These will become valid and unique microbial IDs for the AMR package.
@ -522,12 +524,20 @@ MOs <- MOs %>%
# everything distinct?
sum(duplicated(MOs$mo))
sum(duplicated(MOs$fullname))
colnames(MOs)
# here we welcome the new ones:
MOs %>% filter(!fullname %in% AMR::microorganisms$fullname) %>% View()
# and the ones we lost:
AMR::microorganisms %>% filter(!fullname %in% MOs$fullname) %>% View()
# and these IDs have changed:
MOs %>%
filter(fullname %in% AMR::microorganisms$fullname) %>%
left_join(AMR::microorganisms %>% select(mo, fullname), by = "fullname", suffix = c("_new", "_old")) %>%
filter(mo_new != mo_old) %>%
select(mo_old, mo_new, everything()) %>%
View()
# set prevalence per species
MOs <- MOs %>%