Browse Source

(v1.3.0.9007) tibble printing

new-mo-algorithm
parent
commit
5e45fdcf2a
  1. 4
      DESCRIPTION
  2. 8
      NAMESPACE
  3. 8
      NEWS.md
  4. 16
      R/disk.R
  5. 36
      R/eucast_rules.R
  6. 16
      R/mic.R
  7. 49
      R/mo.R
  8. 7
      R/mo_property.R
  9. 18
      R/rsi.R
  10. 55
      R/zzz.R
  11. BIN
      data-raw/antibiotics.dta
  12. BIN
      data-raw/antibiotics.sas
  13. BIN
      data-raw/antibiotics.sav
  14. BIN
      data-raw/antibiotics.xlsx
  15. BIN
      data-raw/antivirals.dta
  16. BIN
      data-raw/antivirals.sas
  17. BIN
      data-raw/antivirals.sav
  18. BIN
      data-raw/antivirals.xlsx
  19. BIN
      data-raw/intrinsic_resistant.dta
  20. BIN
      data-raw/intrinsic_resistant.sas
  21. BIN
      data-raw/intrinsic_resistant.sav
  22. BIN
      data-raw/intrinsic_resistant.xlsx
  23. BIN
      data-raw/microorganisms.dta
  24. BIN
      data-raw/microorganisms.old.dta
  25. BIN
      data-raw/microorganisms.old.sas
  26. BIN
      data-raw/microorganisms.old.sav
  27. BIN
      data-raw/microorganisms.old.xlsx
  28. BIN
      data-raw/microorganisms.sas
  29. BIN
      data-raw/microorganisms.sav
  30. BIN
      data-raw/microorganisms.xlsx
  31. BIN
      data-raw/rsi_translation.dta
  32. BIN
      data-raw/rsi_translation.sas
  33. BIN
      data-raw/rsi_translation.sav
  34. BIN
      data-raw/rsi_translation.xlsx
  35. BIN
      data/microorganisms.codes.rda
  36. 2
      docs/404.html
  37. 2
      docs/LICENSE-text.html
  38. 2
      docs/articles/datasets.html
  39. 2
      docs/articles/index.html
  40. 2
      docs/authors.html
  41. 2
      docs/index.html
  42. 54
      docs/news/index.html
  43. 2
      docs/pkgdown.yml
  44. 2
      docs/reference/AMR.html
  45. 2
      docs/reference/WHONET.html
  46. 2
      docs/reference/ab_property.html
  47. 2
      docs/reference/antibiotic_class_selectors.html
  48. 2
      docs/reference/antibiotics.html
  49. 2
      docs/reference/as.ab.html
  50. 5
      docs/reference/as.mo.html
  51. 2
      docs/reference/as.rsi.html
  52. 2
      docs/reference/eucast_rules.html
  53. 2
      docs/reference/example_isolates.html
  54. 2
      docs/reference/example_isolates_unclean.html
  55. 4
      docs/reference/index.html
  56. 2
      docs/reference/intrinsic_resistant.html
  57. 10
      docs/reference/microorganisms.codes.html
  58. 2
      docs/reference/microorganisms.html
  59. 2
      docs/reference/microorganisms.old.html
  60. 2
      docs/reference/mo_property.html
  61. 2
      docs/reference/rsi_translation.html
  62. 2
      docs/survey.html
  63. 3
      man/as.mo.Rd
  64. 4
      man/microorganisms.codes.Rd

4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 1.3.0.9006
Date: 2020-08-21
Version: 1.3.0.9007
Date: 2020-08-26
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

8
NAMESPACE

@ -40,6 +40,10 @@ S3method(format,bug_drug_combinations) @@ -40,6 +40,10 @@ S3method(format,bug_drug_combinations)
S3method(kurtosis,data.frame)
S3method(kurtosis,default)
S3method(kurtosis,matrix)
S3method(pillar_shaft,disk)
S3method(pillar_shaft,mic)
S3method(pillar_shaft,mo)
S3method(pillar_shaft,rsi)
S3method(plot,mic)
S3method(plot,resistance_predict)
S3method(plot,rsi)
@ -58,6 +62,10 @@ S3method(skewness,matrix) @@ -58,6 +62,10 @@ S3method(skewness,matrix)
S3method(summary,mic)
S3method(summary,mo)
S3method(summary,rsi)
S3method(type_sum,disk)
S3method(type_sum,mic)
S3method(type_sum,mo)
S3method(type_sum,rsi)
export("%like%")
export("%like_case%")
export(ab_atc)

8
NEWS.md

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
# AMR 1.3.0.9006
## <small>Last updated: 21 August 2020</small>
# AMR 1.3.0.9007
## <small>Last updated: 26 August 2020</small>
### New
* Data set `intrinsic_resistant`. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns: `microorganism` and `antibiotic`.
@ -34,7 +34,11 @@ @@ -34,7 +34,11 @@
#> Class <disk>
#> [1] 24 24
```
* Speed improvement for `eucast_rules()`
* Overall speed improvement by tweaking joining functions
* Function `mo_shortname()` now return the genus for input where the species is unknown
* BORSA is now recognised as an abbreviation for a *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus"
* Support for coloured `tibble` printing of classes `mo`, `rsi`, `mic` and `disk`
# AMR 1.3.0

16
R/disk.R

@ -114,6 +114,22 @@ is.disk <- function(x) { @@ -114,6 +114,22 @@ is.disk <- function(x) {
inherits(x, "disk")
}
#' @method pillar_shaft disk
#' @export
pillar_shaft.disk <- function(x, ...) {
style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE)
new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
out <- trimws(format(x))
out[is.na(x)] <- style_na(NA)
new_pillar_shaft_simple(out, align = "right", min_width = 3)
}
#' @method type_sum disk
#' @export
type_sum.disk <- function(x, ...) {
"disk"
}
#' @method print disk
#' @export
#' @noRd

36
R/eucast_rules.R

@ -350,6 +350,9 @@ eucast_rules <- function(x, @@ -350,6 +350,9 @@ eucast_rules <- function(x,
verbose = verbose,
...)
# data preparation ----
message(font_blue("NOTE: Preparing data..."), appendLF = FALSE)
AMC <- cols_ab["AMC"]
AMK <- cols_ab["AMK"]
AMP <- cols_ab["AMP"]
@ -429,7 +432,7 @@ eucast_rules <- function(x, @@ -429,7 +432,7 @@ eucast_rules <- function(x,
rule_name = character(0),
stringsAsFactors = FALSE)
# helper function for editing the table
# helper function for editing the table ----
edit_rsi <- function(to, rule, rows, cols) {
cols <- unique(cols[!is.na(cols) & !is.null(cols)])
if (length(rows) > 0 & length(cols) > 0) {
@ -508,10 +511,21 @@ eucast_rules <- function(x, @@ -508,10 +511,21 @@ eucast_rules <- function(x,
changed = 0))
}
# save original table
old_cols <- colnames(x)
old_attributes <- attributes(x)
x <- as.data.frame(x, stringsAsFactors = FALSE) # no tibbles, data.tables, etc.
# create unique row IDs - combination of the MO and all ABx columns (so they will only run once per unique combination)
x$`.rowid` <- sapply(as.list(as.data.frame(t(x[, c(col_mo, cols_ab), drop = FALSE]))), function(x) {
x[is.na(x)] <- "."
paste0(x, collapse = "")
})
# save original table, with the new .rowid column
x_original.bak <- x
# keep only unique rows for MO and ABx
x <- x %>% distinct(`.rowid`, .keep_all = TRUE)
x_original <- x
x_original_attr <- attributes(x)
x_original <- as.data.frame(x_original, stringsAsFactors = FALSE) # no tibbles, data.tables, etc.
# join to microorganisms data set
x <- as.data.frame(x, stringsAsFactors = FALSE)
@ -520,6 +534,7 @@ eucast_rules <- function(x, @@ -520,6 +534,7 @@ eucast_rules <- function(x,
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", ""))
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL)
x$genus_species <- paste(x$genus, x$species)
message(font_blue("OK."))
if (ab_missing(AMP) & !ab_missing(AMX)) {
# ampicillin column is missing, but amoxicillin is available
@ -528,7 +543,7 @@ eucast_rules <- function(x, @@ -528,7 +543,7 @@ eucast_rules <- function(x,
}
# nolint start
# antibiotic classes
# antibiotic classes ----
aminoglycosides <- c(TOB, GEN, KAN, NEO, NET, SIS)
tetracyclines <- c(DOX, MNO, TCY) # since EUCAST v3.1 tigecycline (TGC) is set apart
polymyxins <- c(PLB, COL)
@ -544,7 +559,7 @@ eucast_rules <- function(x, @@ -544,7 +559,7 @@ eucast_rules <- function(x,
fluoroquinolones <- c(OFX, CIP, NOR, LVX, MFX)
# nolint end
# Help function to get available antibiotic column names ------------------
# help function to get available antibiotic column names ------------------
get_antibiotic_columns <- function(x, df) {
x <- trimws(unlist(strsplit(x, ",", fixed = TRUE)))
y <- character(0)
@ -923,7 +938,12 @@ eucast_rules <- function(x, @@ -923,7 +938,12 @@ eucast_rules <- function(x,
verbose_info
} else {
# reset original attributes
attributes(x_original) <- x_original_attr
x_original
x_original <- x_original[, c(col_mo, cols_ab, ".rowid"), drop = FALSE]
x_original.bak <- x_original.bak[, setdiff(colnames(x_original.bak), c(col_mo, cols_ab)), drop = FALSE]
x_original.bak <- x_original.bak %>%
left_join(x_original, by = ".rowid")
x_original.bak <- x_original.bak[, old_cols, drop = FALSE]
attributes(x_original.bak) <- old_attributes
x_original.bak
}
}

16
R/mic.R

@ -171,6 +171,22 @@ droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...) @@ -171,6 +171,22 @@ droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...)
x
}
#' @method pillar_shaft mic
#' @export
pillar_shaft.mic <- function(x, ...) {
style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE)
new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
out <- trimws(format(x))
out[is.na(x)] <- style_na(NA)
new_pillar_shaft_simple(out, align = "right", min_width = 4)
}
#' @method type_sum mic
#' @export
type_sum.mic <- function(x, ...) {
"mic"
}
#' @method print mic
#' @export
#' @noRd

49
R/mo.R

@ -159,7 +159,8 @@ @@ -159,7 +159,8 @@
#' select(microorganism_name) %>%
#' as.mo()
#'
#' # and can even contain 2 columns, which is convenient for genus/species combinations:
#' # and can even contain 2 columns, which is convenient
#' # for genus/species combinations:
#' df$mo <- df %>%
#' select(genus, species) %>%
#' as.mo()
@ -459,13 +460,15 @@ exec_as.mo <- function(x, @@ -459,13 +460,15 @@ exec_as.mo <- function(x,
x <- gsub("(th|ht|t)+", "(th|ht|t)+", x)
x <- gsub("a+", "a+", x)
x <- gsub("u+", "u+", x)
# allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica and -a (needs perl for the negative backward lookup):
# allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica, -ia and -a (needs perl for the negative backward lookup):
x <- gsub("(u\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+)(?![a-z])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
x <- gsub("(\\[iy\\]\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+a\\+)(?![a-z])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
x <- gsub("(\\[iy\\]\\+u\\+m)(?![a-z])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
x <- gsub("(\\[iy\\]\\+a\\+)(?![a-z])",
"([iy]*a+|[iy]+a*)", x, perl = TRUE)
x <- gsub("e+", "e+", x)
x <- gsub("o+", "o+", x)
x <- gsub("(.)\\1+", "\\1+", x)
@ -636,7 +639,7 @@ exec_as.mo <- function(x, @@ -636,7 +639,7 @@ exec_as.mo <- function(x,
}
# translate known trivial abbreviations to genus + species ----
if (toupper(x_backup_without_spp[i]) %in% c("MRSA", "MSSA", "VISA", "VRSA")
if (toupper(x_backup_without_spp[i]) %in% c("MRSA", "MSSA", "VISA", "VRSA", "BORSA")
| x_backup_without_spp[i] %like_case% " (mrsa|mssa|visa|vrsa) ") {
x[i] <- lookup(fullname == "Staphylococcus aureus")
next
@ -1523,12 +1526,50 @@ format_uncertainty_as_df <- function(uncertainty_level, @@ -1523,12 +1526,50 @@ format_uncertainty_as_df <- function(uncertainty_level,
df
}
#' @method pillar_shaft mo
#' @export
pillar_shaft.mo <- function(x, ...) {
# import from the pillar package, without being dependent on it!
style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE)
style_subtle <- import_fn("style_subtle", "pillar", error_on_fail = FALSE)
new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
if (is.null(style_na) | is.null(style_subtle) | is.null(new_pillar_shaft_simple)) {
return(x)
}
out <- format(x)
# grey out the kingdom (part until first "_")
out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(style_subtle("\\1"), "\\2"), out[!is.na(x)])
# and grey out every _
out[!is.na(x)] <- gsub("_", style_subtle("_"), out[!is.na(x)])
# markup NA and UNKNOWN
out[is.na(x)] <- style_na(" NA")
out[x == "UNKNOWN"] <- style_na(" UNKNOWN")
# make it always fit exactly
new_pillar_shaft_simple(out,
align = "left",
width = max(nchar(x)) + ifelse(length(x[x %in% c(NA, "UNKNOWN")]) > 0,
2,
0))
}
#' @method type_sum mo
#' @export
type_sum.mo <- function(x, ...) {
"mo"
}
#' @method print mo
#' @export
#' @noRd
print.mo <- function(x, ...) {
print.mo <- function(x, print.shortnames = FALSE, ...) {
cat("Class <mo>\n")
x_names <- names(x)
if (is.null(x_names) & print.shortnames == TRUE) {
x_names <- tryCatch(mo_shortname(x, ...), error = function(e) NULL)
}
x <- as.character(x)
names(x) <- x_names
print.default(x, quote = FALSE)

7
R/mo_property.R

@ -161,13 +161,18 @@ mo_shortname <- function(x, language = get_locale(), ...) { @@ -161,13 +161,18 @@ mo_shortname <- function(x, language = get_locale(), ...) {
}
# get first char of genus and complete species in English
shortnames <- paste0(substr(mo_genus(x.mo, language = NULL), 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL)))
genera <- mo_genus(x.mo, language = NULL)
shortnames <- paste0(substr(genera, 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL)))
# exceptions for where no species is known
shortnames[shortnames %like% ".[.] spp[.]"] <- genera[shortnames %like% ".[.] spp[.]"]
# exceptions for Staphylococci
shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
# exceptions for Streptococci: Streptococcus Group A -> GAS
shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S")
# unknown species etc.
shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"])), ")")
load_mo_failures_uncertainties_renamed(metadata)
translate_AMR(shortnames, language = language, only_unknown = FALSE)

18
R/rsi.R

@ -670,6 +670,24 @@ exec_as.rsi <- function(method, @@ -670,6 +670,24 @@ exec_as.rsi <- function(method,
class = c("rsi", "ordered", "factor"))
}
#' @method pillar_shaft rsi
#' @export
pillar_shaft.rsi <- function(x, ...) {
out <- trimws(format(x))
out[is.na(x)] <- font_grey(" NA")
out[x == "S"] <- font_green_bg(font_white(" S "))
out[x == "I"] <- font_yellow_bg(font_black(" I "))
out[x == "R"] <- font_red_bg(font_white(" R "))
new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
new_pillar_shaft_simple(out, align = "left", width = 3)
}
#' @method type_sum rsi
#' @export
type_sum.rsi <- function(x, ...) {
"rsi"
}
#' @method print rsi
#' @export
#' @noRd

55
R/zzz.R

@ -27,7 +27,19 @@ @@ -27,7 +27,19 @@
assign(x = "MO.old_lookup",
value = create_MO.old_lookup(),
envir = asNamespace("AMR"))
# support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
s3_register("pillar::pillar_shaft", "mo")
s3_register("tibble::type_sum", "mo")
s3_register("pillar::pillar_shaft", "rsi")
s3_register("tibble::type_sum", "rsi")
s3_register("pillar::pillar_shaft", "mic")
s3_register("tibble::type_sum", "mic")
s3_register("pillar::pillar_shaft", "disk")
s3_register("tibble::type_sum", "disk")
}
pillar_shaft <- import_fn("pillar_shaft", "pillar", error_on_fail = FALSE)
type_sum <- import_fn("type_sum", "tibble", error_on_fail = FALSE)
.onAttach <- function(...) {
if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(Sys.getenv("AMR_silentstart", FALSE)))) {
@ -73,3 +85,46 @@ create_MO.old_lookup <- function() { @@ -73,3 +85,46 @@ create_MO.old_lookup <- function() {
# so arrange data on prevalence first, then full name
MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
}
# copied from vctrs::s3_register
s3_register <- function (generic, class, method = NULL) {
stopifnot(is.character(generic), length(generic) == 1)
stopifnot(is.character(class), length(class) == 1)
pieces <- strsplit(generic, "::")[[1]]
stopifnot(length(pieces) == 2)
package <- pieces[[1]]
generic <- pieces[[2]]
caller <- parent.frame()
get_method_env <- function() {
top <- topenv(caller)
if (isNamespace(top)) {
asNamespace(environmentName(top))
}
else {
caller
}
}
get_method <- function(method, env) {
if (is.null(method)) {
get(paste0(generic, ".", class), envir = get_method_env())
}
else {
method
}
}
method_fn <- get_method(method)
stopifnot(is.function(method_fn))
setHook(packageEvent(package, "onLoad"), function(...) {
ns <- asNamespace(package)
method_fn <- get_method(method)
registerS3method(generic, class, method_fn, envir = ns)
})
if (!isNamespaceLoaded(package)) {
return(invisible())
}
envir <- asNamespace(package)
if (exists(generic, envir)) {
registerS3method(generic, class, method_fn, envir = envir)
}
invisible()
}

BIN
data-raw/antibiotics.dta

Binary file not shown.

BIN
data-raw/antibiotics.sas

Binary file not shown.

BIN
data-raw/antibiotics.sav

Binary file not shown.

BIN
data-raw/antibiotics.xlsx

Binary file not shown.

BIN
data-raw/antivirals.dta

Binary file not shown.

BIN
data-raw/antivirals.sas

Binary file not shown.

BIN
data-raw/antivirals.sav

Binary file not shown.

BIN
data-raw/antivirals.xlsx

Binary file not shown.

BIN
data-raw/intrinsic_resistant.dta

Binary file not shown.

BIN
data-raw/intrinsic_resistant.sas

Binary file not shown.

BIN
data-raw/intrinsic_resistant.sav

Binary file not shown.

BIN
data-raw/intrinsic_resistant.xlsx

Binary file not shown.

BIN
data-raw/microorganisms.dta

Binary file not shown.

BIN
data-raw/microorganisms.old.dta

Binary file not shown.

BIN
data-raw/microorganisms.old.sas

Binary file not shown.

BIN
data-raw/microorganisms.old.sav

Binary file not shown.

BIN
data-raw/microorganisms.old.xlsx

Binary file not shown.

BIN
data-raw/microorganisms.sas

Binary file not shown.

BIN
data-raw/microorganisms.sav

Binary file not shown.

BIN
data-raw/microorganisms.xlsx

Binary file not shown.

BIN
data-raw/rsi_translation.dta

Binary file not shown.

BIN
data-raw/rsi_translation.sas

Binary file not shown.

BIN
data-raw/rsi_translation.sav

Binary file not shown.

BIN
data-raw/rsi_translation.xlsx

Binary file not shown.

BIN
data/microorganisms.codes.rda

Binary file not shown.

2
docs/404.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/LICENSE-text.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/articles/datasets.html

@ -39,7 +39,7 @@ @@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/articles/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/authors.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/index.html

@ -43,7 +43,7 @@ @@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

54
docs/news/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>
@ -236,13 +236,13 @@ @@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309006" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9006">
<a href="#amr-1309006" class="anchor"></a>AMR 1.3.0.9006<small> Unreleased </small>
<div id="amr-1309007" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9007">
<a href="#amr-1309007" class="anchor"></a>AMR 1.3.0.9007<small> Unreleased </small>
</h1>
<div id="last-updated-21-august-2020" class="section level2">
<div id="last-updated-26-august-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-21-august-2020" class="anchor"></a><small>Last updated: 21 August 2020</small>
<a href="#last-updated-26-august-2020" class="anchor"></a><small>Last updated: 26 August 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -293,7 +293,11 @@ @@ -293,7 +293,11 @@
<span class="co">#&gt; [1] 24 24</span>
</pre></div>
</li>
<li><p>Speed improvement for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></p></li>
<li><p>Overall speed improvement by tweaking joining functions</p></li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_shortname()</a></code> now return the genus for input where the species is unknown</p></li>
<li><p>BORSA is now recognised as an abbreviation for a <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("BORSA")</a></code> will return “Staphylococcus”</p></li>
<li><p>Support for coloured <code>tibble</code> printing of classes <code>mo</code>, <code>rsi</code>, <code>mic</code> and <code>disk</code></p></li>
</ul>
</div>
</div>
@ -394,7 +398,7 @@ @@ -394,7 +398,7 @@
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
<p>Negative effects of this change are:</p>
<ul>
<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
<li>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</li>
<li>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</li>
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@ -731,7 +735,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ @@ -731,7 +735,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</pre></div>
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
</li>
<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
@ -1000,7 +1004,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ @@ -1000,7 +1004,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</li>
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
</li>
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
<li>Frequency tables (<code>freq()</code>):
<ul>
<li><p>speed improvement for microbial IDs</p></li>
<li><p>fixed factor level names for R Markdown</p></li>
@ -1009,12 +1013,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ @@ -1009,12 +1013,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<p>support for boxplots:</p>
<div class="sourceCode" id="cb20"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
<span class="fu">freq</span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
<span class="co"># grouped boxplots:</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
<span class="fu">freq</span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
</pre></div>
</li>
@ -1025,7 +1029,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ @@ -1025,7 +1029,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li>
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
</li>
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@ -1266,7 +1270,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ @@ -1266,7 +1270,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</li>
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
<li>Frequency tables (<code>freq()</code> function):
<ul>
<li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@ -1275,15 +1279,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ @@ -1275,15 +1279,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co"># OLD WAY</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(genus = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">genus</span>)
<span class="fu">freq</span>(<span class="kw">genus</span>)
<span class="co"># NEW WAY</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
<span class="fu">freq</span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
<span class="co"># Even supports grouping variables:</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">gender</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
<span class="fu">freq</span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
</pre></div>
</li>
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
@ -1367,21 +1371,21 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ @@ -1367,21 +1371,21 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code></p></li>
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
<li>
<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
<p>Frequency tables - <code>freq()</code>:</p>
<ul>
<li>
<p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb32"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
<span class="fu">freq</span>(<span class="kw">gender</span>)
</pre></div>
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb33"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span>
<span class="fu">freq</span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw">count</span>, <span class="op">-</span><span class="kw">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span>
</pre></div>
</li>
@ -1400,7 +1404,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ @@ -1400,7 +1404,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> parameter</p></li>
<li>
<p>AI improvements for <code>as.mo</code>:</p>
@ -1567,13 +1571,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ @@ -1567,13 +1571,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb40"><pre class="downlit">
<span class="kw">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="kw">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">age</span>, <span class="kw">gender</span>), ncol = <span class="fl">2</span>))
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">my_matrix</span>)
<span class="fu">freq</span>(<span class="kw">my_matrix</span>)
</pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb41"><pre class="downlit">
<span class="kw">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(age = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">age</span>, gender = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">gender</span>)
<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>)
<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span>(<span class="kw">age</span>)
<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span>(<span class="kw">gender</span>)
</pre></div>
</li>
</ul>
@ -1648,13 +1652,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ @@ -1648,13 +1652,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
</li>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
</li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
</li>
<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
</li>
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>

2
docs/pkgdown.yml

@ -2,7 +2,7 @@ pandoc: 2.7.3 @@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-08-21T09:34Z
last_built: 2020-08-26T09:09Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
docs/reference/AMR.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/WHONET.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/ab_property.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/antibiotic_class_selectors.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/antibiotics.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/as.ab.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

5
docs/reference/as.mo.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>
@ -443,7 +443,8 @@ This package contains the complete taxonomic tree of almost all microorganisms ( @@ -443,7 +443,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>microorganism_name</span>) <span class='op'>%&gt;%</span>
<span class='fu'>as.mo</span>()
<span class='co'># and can even contain 2 columns, which is convenient for genus/species combinations:</span>
<span class='co'># and can even contain 2 columns, which is convenient</span>
<span class='co'># for genus/species combinations:</span>
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>mo</span> <span class='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>genus</span>, <span class='kw'>species</span>) <span class='op'>%&gt;%</span>
<span class='fu'>as.mo</span>()

2
docs/reference/as.rsi.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/eucast_rules.html

@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied @@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/example_isolates.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/example_isolates_unclean.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

4
docs/reference/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>
@ -527,7 +527,7 @@ @@ -527,7 +527,7 @@
<td>
<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
</td>
<td><p>Translation table with 5,582 common microorganism codes</p></td>
<td><p>Translation table with 5,583 common microorganism codes</p></td>
</tr><tr>
<td>

2
docs/reference/intrinsic_resistant.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

10
docs/reference/microorganisms.codes.html

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Translation table with 5,582 common microorganism codes — microorganisms.codes • AMR (for R)</title>
<title>Translation table with 5,583 common microorganism codes — microorganisms.codes • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,7 +48,7 @@ @@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Translation table with 5,582 common microorganism codes — microorganisms.codes" />
<meta property="og:title" content="Translation table with 5,583 common microorganism codes — microorganisms.codes" />
<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>
@ -233,7 +233,7 @@ @@ -233,7 +233,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Translation table with 5,582 common microorganism codes</h1>
<h1>Translation table with 5,583 common microorganism codes</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
</div>
@ -247,7 +247,7 @@ @@ -247,7 +247,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,582 observations and 2 variables:</p><ul>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,583 observations and 2 variables:</p><ul>
<li><p><code>code</code><br /> Commonly used code of a microorganism</p></li>
<li><p><code>mo</code><br /> ID of the microorganism in the <a href='microorganisms.html'>microorganisms</a> data set</p></li>
</ul>

2
docs/reference/microorganisms.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/microorganisms.old.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/mo_property.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/reference/rsi_translation.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

2
docs/survey.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
</span>
</div>

3
man/as.mo.Rd

@ -203,7 +203,8 @@ df$mo <- df \%>\% @@ -203,7 +203,8 @@ df$mo <- df \%>\%
select(microorganism_name) \%>\%