P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-09-06 08:09:42 +02:00
Code Releases Activity

(v1.1.0.9021) 1st isolates update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-05-28 10:51:56 +02:00
parent 86d44054f0
commit d9a4b0bcaf
51 changed files with 483 additions and 1106 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
data-raw/reproduction_of_microorganisms.R
View File

@@ -920,6 +920,22 @@ testthat::test_file("tests/testthat/test-data.R")
testthat::test_file("tests/testthat/test-mo.R")
testthat::test_file("tests/testthat/test-mo_property.R")
# edit 2020-05-28
# Not sure why it now says M. tuberculosis was renamed to M. africanum (B_MYCBC_AFRC), but that's not true
microorganisms <- microorganisms %>%
bind_rows(microorganisms %>%
filter(mo == "B_MYCBC_AFRC") %>%
mutate(mo = "B_MYCBC_TBRC", snomed = list(c("113861009", "113858008")),
ref = "Lehmann et al., 2018",species_id = "778540",
source = "DSMZ", species = "tuberculosis",
fullname = "Mycobacterium tuberculosis")) %>%
arrange(fullname)
class(microorganisms$mo) <- c("mo", "character")
microorganisms.old <- microorganisms.old %>% filter(fullname != "Mycobacterium tuberculosis")
usethis::use_data(microorganisms, overwrite = TRUE, version = 2)
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
# OLD CODE ----------------------------------------------------------------