P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 07:51:57 +02:00
Code Releases Activity

(v0.7.0.9001) new pathovars, small fixes

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-06-07 22:47:37 +02:00
parent 04c75e8e36
commit f02679fb63
83 changed files with 686 additions and 583 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
data-raw/eucast_rules.tsv
View File

@ -165,7 +165,7 @@ family is Enterobacteriaceae TIC, PIP R, S PIP R Table 09: Interpretive rules fo
genus is .* ERY S AZM, CLR S Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
genus is .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
genus is .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
genus is Staphylococcus TOB R KAN, amik R Table 12: Interpretive rules for aminoglycosides Expert Rules
genus is Staphylococcus TOB R KAN, AMK R Table 12: Interpretive rules for aminoglycosides Expert Rules
genus is Staphylococcus GEN R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules
family is Enterobacteriaceae GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules
family is Enterobacteriaceae GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules

1 if_mo_property like_is_one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group
165 genus is .* ERY S AZM, CLR S Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
166 genus is .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
167 genus is .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
168 genus is Staphylococcus TOB R KAN, amik KAN, AMK R Table 12: Interpretive rules for aminoglycosides Expert Rules
169 genus is Staphylococcus GEN R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules
170 family is Enterobacteriaceae GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules
171 family is Enterobacteriaceae GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules

6
data-raw/internals.R
View File

@ -18,7 +18,7 @@ eucast_rules_file <- dplyr::arrange(
reference.rule)
# Translations -----
translations_file <- utils::read.table(file = "data-raw/translations.tsv",
translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
sep = "\t",
stringsAsFactors = FALSE,
header = TRUE,
@ -27,7 +27,9 @@ translations_file <- utils::read.table(file = "data-raw/translations.tsv",
strip.white = TRUE,
encoding = "UTF-8",
fileEncoding = "UTF-8",
na.strings = c(NA, "", NULL))
na.strings = c(NA, "", NULL),
allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
quote = "")
# Export to package as internal data ----
usethis::use_data(eucast_rules_file, translations_file,