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(v1.7.1.9074) as.mo() improvement, ASCII replacements for unit tests

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dr. M.S. (Matthijs) Berends
2021-12-14 22:39:23 +01:00
parent bd4bb1d72f
commit 76dee66852
33 changed files with 6809 additions and 6787 deletions
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11
R/mo.R
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@ -103,10 +103,10 @@
#' @inheritSection catalogue_of_life Catalogue of Life
# (source as a section here, so it can be inherited by other man pages:)
#' @section Source:
#' 1. Becker K *et al.* **Coagulase-Negative Staphylococci**. 2014. Clin Microbiol Rev. 27(4): 870–926; \doi{10.1128/CMR.00109-13}
#' 1. Becker K *et al.* **Coagulase-Negative Staphylococci**. 2014. Clin Microbiol Rev. 27(4): 870-926; \doi{10.1128/CMR.00109-13}
#' 2. Becker K *et al.* **Implications of identifying the recently defined members of the *S. aureus* complex, *S. argenteus* and *S. schweitzeri*: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).** 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028}
#' 3. Becker K *et al.* **Emergence of coagulase-negative staphylococci** 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
#' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571}
#' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571-95; \doi{10.1084/jem.57.4.571}
#' 5. `r gsub("{year}", CATALOGUE_OF_LIFE$year, CATALOGUE_OF_LIFE$version, fixed = TRUE)`, <http://www.catalogueoflife.org>
#' 6. List of Prokaryotic names with Standing in Nomenclature (`r CATALOGUE_OF_LIFE$yearmonth_LPSN`), \doi{10.1099/ijsem.0.004332}
#' 7. `r SNOMED_VERSION$current_source`, retrieved from the `r SNOMED_VERSION$title`, OID `r SNOMED_VERSION$current_oid`, version `r SNOMED_VERSION$current_version`; url: <`r SNOMED_VERSION$url`>
@ -486,8 +486,7 @@ exec_as.mo <- function(x,
}
# remove spp and species
x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x, ignore.case = TRUE, perl = TRUE)
x <- gsub("( spp?.?| ss |subsp.?|subspecies|biovar|serovar|species)", "", x, ignore.case = TRUE, perl = TRUE)
x <- gsub("(^| )[ .]*(spp|ssp|ss|sp|subsp|subspecies|biovar|biotype|serovar|species)[ .]*( |$)", "", x, ignore.case = TRUE, perl = TRUE)
x <- strip_whitespace(x, dyslexia_mode)
x_backup <- x
@ -614,6 +613,8 @@ exec_as.mo <- function(x,
on.exit(close(progress))
}
xx <<- x_backup[!already_known]
for (i in which(!already_known)) {
if (initial_search == TRUE) {
@ -754,7 +755,7 @@ exec_as.mo <- function(x,
# - EIEC (Entero-Invasive E. coli)
# - EPEC (Entero-Pathogenic E. coli)
# - ETEC (Entero-Toxigenic E. coli)
# - NMEC (Neonatal Meningitis‐causing E. coli)
# - NMEC (Neonatal Meningitis-causing E. coli)
# - STEC (Shiga-toxin producing E. coli)
# - UPEC (Uropathogenic E. coli)
if (toupper(x_backup_without_spp[i]) %in% c("AIEC", "ATEC", "DAEC", "EAEC", "EHEC", "EIEC", "EPEC", "ETEC", "NMEC", "STEC", "UPEC")