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0fdabff1ba
| Author | SHA1 | Date | |
|---|---|---|---|
| 0fdabff1ba | |||
| 062c49fca1 |
7
.github/workflows/check.yaml
vendored
7
.github/workflows/check.yaml
vendored
@ -53,9 +53,11 @@ jobs:
|
||||
- {os: macOS-latest, r: 'devel', allowfail: false}
|
||||
- {os: macOS-latest, r: 'release', allowfail: false}
|
||||
- {os: macOS-latest, r: 'oldrel', allowfail: false}
|
||||
|
||||
- {os: windows-latest, r: 'devel', allowfail: false}
|
||||
- {os: windows-latest, r: 'release', allowfail: false}
|
||||
- {os: windows-latest, r: 'oldrel', allowfail: false}
|
||||
|
||||
- {os: ubuntu-20.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
@ -66,7 +68,8 @@ jobs:
|
||||
- {os: ubuntu-20.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
# - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
- {os: ubuntu-20.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
|
||||
- {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
@ -77,7 +80,7 @@ jobs:
|
||||
- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
# - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
# - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
- {os: ubuntu-16.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
|
||||
|
||||
env:
|
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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|
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@ -1,5 +1,5 @@
|
||||
Package: AMR
|
||||
Version: 1.5.0.9021
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Version: 1.5.0.9023
|
||||
Date: 2021-02-21
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Authors@R: c(
|
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|
||||
5
NEWS.md
5
NEWS.md
@ -1,4 +1,4 @@
|
||||
# AMR 1.5.0.9021
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||||
# AMR 1.5.0.9023
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||||
## <small>Last updated: 21 February 2021</small>
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|
||||
### New
|
||||
@ -58,7 +58,8 @@
|
||||
* Functions `print()` and `summary()` on a Principal Components Analysis object (`pca()`) now print additional group info if the original data was grouped using `dplyr::group_by()`
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||||
* Improved speed and reliability of `guess_ab_col()`. As this also internally improves the reliability of `first_isolate()` and `mdro()`, this might have a slight impact on the results of those functions.
|
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* Fix for `mo_name()` when used in other languages than English
|
||||
* The `like()` function (and its fast alias `%like%`) now always use Perl compatibility, improving speed for many functions in this package
|
||||
* The `like()` function (and its fast alias `%like%`) now always use Perl compatibility, improving speed for many functions in this package (e.g., `as.mo()` is now up to 4 times faster)
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||||
* *Staphylococcus cornubiensis* is now correctly categorised as coagulase-positive
|
||||
|
||||
### Other
|
||||
* Big documentation updates
|
||||
|
||||
@ -112,7 +112,7 @@ check_dataset_integrity <- function() {
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||||
require("AMR")
|
||||
})
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||||
stop_if(!valid_microorganisms | !valid_antibiotics,
|
||||
"the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object names was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
|
||||
"the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object name(s) was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
|
||||
invisible(TRUE)
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||||
}
|
||||
|
||||
@ -538,7 +538,7 @@ meet_criteria <- function(object,
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if (!is.null(pkg_env$meet_criteria_error_txt)) {
|
||||
error_txt <- pkg_env$meet_criteria_error_txt
|
||||
pkg_env$meet_criteria_error_txt <- NULL
|
||||
stop(error_txt, call. = FALSE)
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||||
stop(error_txt, call. = FALSE) # don't use stop_() here, pkg may not be loaded yet
|
||||
}
|
||||
pkg_env$meet_criteria_error_txt <- NULL
|
||||
|
||||
@ -867,7 +867,13 @@ font_grey <- function(..., collapse = " ") {
|
||||
try_colour(..., before = "\033[38;5;249m", after = "\033[39m", collapse = collapse)
|
||||
}
|
||||
font_grey_bg <- function(..., collapse = " ") {
|
||||
try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = collapse)
|
||||
if (tryCatch(rstudioapi::getThemeInfo()$dark == TRUE, error = function(e) FALSE)) {
|
||||
# similar to HTML #444444
|
||||
try_colour(..., before = "\033[48;5;238m", after = "\033[49m", collapse = collapse)
|
||||
} else {
|
||||
# similar to HTML #eeeeee
|
||||
try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = collapse)
|
||||
}
|
||||
}
|
||||
font_green_bg <- function(..., collapse = " ") {
|
||||
try_colour(..., before = "\033[42m", after = "\033[49m", collapse = collapse)
|
||||
|
||||
@ -26,6 +26,7 @@
|
||||
globalVariables(c(".rowid",
|
||||
"ab",
|
||||
"ab_txt",
|
||||
"affect_mo_name",
|
||||
"angle",
|
||||
"antibiotic",
|
||||
"antibiotics",
|
||||
|
||||
40
R/mo.R
40
R/mo.R
@ -178,13 +178,6 @@ as.mo <- function(x,
|
||||
return(set_clean_class(x, new_class = c("mo", "character")))
|
||||
}
|
||||
|
||||
if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
|
||||
& isFALSE(Becker)
|
||||
& isFALSE(Lancefield), error = function(e) FALSE)) {
|
||||
# to improve speed, special case for taxonomically correct full names (case-insensitive)
|
||||
return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
|
||||
}
|
||||
|
||||
# start off with replaced language-specific non-ASCII characters with ASCII characters
|
||||
x <- parse_and_convert(x)
|
||||
# replace mo codes used in older package versions
|
||||
@ -198,6 +191,13 @@ as.mo <- function(x,
|
||||
x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
|
||||
x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
|
||||
uncertainty_level <- translate_allow_uncertain(allow_uncertain)
|
||||
|
||||
if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
|
||||
& isFALSE(Becker)
|
||||
& isFALSE(Lancefield), error = function(e) FALSE)) {
|
||||
# to improve speed, special case for taxonomically correct full names (case-insensitive)
|
||||
return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
|
||||
}
|
||||
|
||||
if (!is.null(reference_df)
|
||||
&& check_validity_mo_source(reference_df)
|
||||
@ -481,11 +481,11 @@ exec_as.mo <- function(x,
|
||||
|
||||
# Fill in fullnames and MO codes at once
|
||||
known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
|
||||
x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname), property, drop = TRUE]
|
||||
x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
|
||||
known_codes <- toupper(x_backup) %in% MO_lookup$mo
|
||||
x[known_codes] <- MO_lookup[match(toupper(x_backup)[known_codes], MO_lookup$mo), property, drop = TRUE]
|
||||
already_known <- known_names | known_codes
|
||||
|
||||
|
||||
# now only continue where the right taxonomic output is not already known
|
||||
if (any(!already_known)) {
|
||||
x_known <- x[already_known]
|
||||
@ -766,21 +766,24 @@ exec_as.mo <- function(x,
|
||||
# Streptococci, like GBS = Group B Streptococci (B_STRPT_GRPB)
|
||||
x[i] <- lookup(mo == toupper(gsub("g([abcdfghk])s",
|
||||
"B_STRPT_GRP\\1",
|
||||
x_backup_without_spp[i])), uncertainty = -1)
|
||||
x_backup_without_spp[i],
|
||||
perl = TRUE)), uncertainty = -1)
|
||||
next
|
||||
}
|
||||
if (x_backup_without_spp[i] %like_case% "(streptococ|streptokok).* [abcdfghk]$") {
|
||||
# Streptococci in different languages, like "estreptococos grupo B"
|
||||
x[i] <- lookup(mo == toupper(gsub(".*(streptococ|streptokok|estreptococ).* ([abcdfghk])$",
|
||||
"B_STRPT_GRP\\2",
|
||||
x_backup_without_spp[i])), uncertainty = -1)
|
||||
x_backup_without_spp[i],
|
||||
perl = TRUE)), uncertainty = -1)
|
||||
next
|
||||
}
|
||||
if (x_backup_without_spp[i] %like_case% "group [abcdfghk] (streptococ|streptokok|estreptococ)") {
|
||||
# Streptococci in different languages, like "Group A Streptococci"
|
||||
x[i] <- lookup(mo == toupper(gsub(".*group ([abcdfghk]) (streptococ|streptokok|estreptococ).*",
|
||||
"B_STRPT_GRP\\1",
|
||||
x_backup_without_spp[i])), uncertainty = -1)
|
||||
x_backup_without_spp[i],
|
||||
perl = TRUE)), uncertainty = -1)
|
||||
next
|
||||
}
|
||||
if (x_backup_without_spp[i] %like_case% "haemoly.*strep") {
|
||||
@ -843,7 +846,7 @@ exec_as.mo <- function(x,
|
||||
# Salmonella Group A to Z, just return S. species for now
|
||||
x[i] <- lookup(genus == "Salmonella", uncertainty = -1)
|
||||
next
|
||||
} else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup[i], ignore.case = FALSE) &
|
||||
} else if (x_backup[i] %like_case% "[sS]almonella [A-Z][a-z]+ ?.*" &
|
||||
!x_backup[i] %like% "t[iy](ph|f)[iy]") {
|
||||
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
|
||||
# except for S. typhi, S. paratyphi, S. typhimurium
|
||||
@ -984,7 +987,6 @@ exec_as.mo <- function(x,
|
||||
g.x_backup_without_spp %pm>% substr(1, x_length / 2),
|
||||
".* ",
|
||||
g.x_backup_without_spp %pm>% substr((x_length / 2) + 1, x_length))
|
||||
print(x_split)
|
||||
found <- lookup(fullname_lower %like_case% x_split,
|
||||
haystack = data_to_check)
|
||||
if (!is.na(found)) {
|
||||
@ -1109,7 +1111,7 @@ exec_as.mo <- function(x,
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (3) look for genus only, part of name\n"))
|
||||
}
|
||||
if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like_case% " ") {
|
||||
if (!grepl("^[A-Z][a-z]+", b.x_trimmed, ignore.case = FALSE)) {
|
||||
if (!b.x_trimmed %like_case% "^[A-Z][a-z]+") {
|
||||
if (isTRUE(debug)) {
|
||||
message("Running '", paste(b.x_trimmed, "species"), "'")
|
||||
}
|
||||
@ -1853,7 +1855,7 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
width = 0.98 * getOption("width")),
|
||||
collapse = "")
|
||||
# after strwrap, make taxonomic names italic
|
||||
candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates)
|
||||
candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates, perl = TRUE)
|
||||
candidates <- gsub(paste(font_italic(c("Also", "matched"), collapse = NULL), collapse = " "),
|
||||
"Also matched",
|
||||
candidates, fixed = TRUE)
|
||||
@ -1977,13 +1979,13 @@ parse_and_convert <- function(x) {
|
||||
if (NCOL(x) > 2) {
|
||||
stop("a maximum of two columns is allowed", call. = FALSE)
|
||||
} else if (NCOL(x) == 2) {
|
||||
# support Tidyverse selection like: df %pm>% select(colA, colB)
|
||||
# support Tidyverse selection like: df %>% select(colA, colB)
|
||||
# paste these columns together
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
colnames(x) <- c("A", "B")
|
||||
x <- paste(x$A, x$B)
|
||||
} else {
|
||||
# support Tidyverse selection like: df %pm>% select(colA)
|
||||
# support Tidyverse selection like: df %>% select(colA)
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
|
||||
}
|
||||
}
|
||||
@ -1991,6 +1993,8 @@ parse_and_convert <- function(x) {
|
||||
parsed <- iconv(x, to = "UTF-8")
|
||||
parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
|
||||
parsed <- gsub('"', "", parsed, fixed = TRUE)
|
||||
parsed <- gsub(" +", " ", parsed, perl = TRUE)
|
||||
parsed <- trimws(parsed)
|
||||
}, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
|
||||
parsed
|
||||
}
|
||||
|
||||
@ -694,22 +694,22 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
|
||||
|
||||
mo_validate <- function(x, property, language, ...) {
|
||||
check_dataset_integrity()
|
||||
|
||||
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & length(list(...)) == 0, error = function(e) FALSE)) {
|
||||
# special case for mo_* functions where class is already <mo>
|
||||
return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
|
||||
}
|
||||
|
||||
dots <- list(...)
|
||||
Becker <- dots$Becker
|
||||
if (is.null(Becker)) {
|
||||
if (is.null(Becker) | property %in% c("kingdom", "phylum", "class", "order", "family", "genus")) {
|
||||
Becker <- FALSE
|
||||
}
|
||||
Lancefield <- dots$Lancefield
|
||||
if (is.null(Lancefield)) {
|
||||
if (is.null(Lancefield) | property %in% c("kingdom", "phylum", "class", "order", "family", "genus")) {
|
||||
Lancefield <- FALSE
|
||||
}
|
||||
has_Becker_or_Lancefield <- Becker %in% c(TRUE, "all") | Lancefield %in% c(TRUE, "all")
|
||||
|
||||
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & !has_Becker_or_Lancefield, error = function(e) FALSE)) {
|
||||
# special case for mo_* functions where class is already <mo>
|
||||
return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
|
||||
}
|
||||
|
||||
# try to catch an error when inputting an invalid argument
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
|
||||
@ -722,8 +722,7 @@ mo_validate <- function(x, property, language, ...) {
|
||||
# because it's already a valid MO
|
||||
x <- exec_as.mo(x, property = property, initial_search = FALSE, language = language, ...)
|
||||
} else if (!all(x %in% MO_lookup[, property, drop = TRUE])
|
||||
| Becker %in% c(TRUE, "all")
|
||||
| Lancefield %in% c(TRUE, "all")) {
|
||||
| has_Becker_or_Lancefield) {
|
||||
x <- exec_as.mo(x, property = property, language = language, ...)
|
||||
}
|
||||
|
||||
|
||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
Binary file not shown.
@ -51,18 +51,19 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
"lentus", "lugdunensis", "massiliensis", "microti",
|
||||
"muscae", "nepalensis", "pasteuri", "petrasii",
|
||||
"pettenkoferi", "piscifermentans", "pseudoxylosus",
|
||||
"rostri", "saccharolyticus", "saprophyticus",
|
||||
"pulvereri", "rostri", "saccharolyticus", "saprophyticus",
|
||||
"sciuri", "simulans", "stepanovicii", "succinus",
|
||||
"vitulinus", "warneri", "xylosus")
|
||||
"vitulinus", "vitulus", "warneri", "xylosus")
|
||||
| (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
|
||||
"mo", drop = TRUE]
|
||||
} else if (type == "CoPS") {
|
||||
MO_staph[which(MO_staph$species %in% c("coagulase-positive",
|
||||
"simiae", "agnetis",
|
||||
"agnetis", "argenteus",
|
||||
"cornubiensis",
|
||||
"delphini", "lutrae",
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schweitzeri", "argenteus")
|
||||
"schweitzeri", "simiae")
|
||||
| (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
|
||||
"mo", drop = TRUE]
|
||||
}
|
||||
|
||||
@ -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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -192,7 +192,6 @@
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Benchmarks</h1>
|
||||
|
||||
<h4 class="date">21 February 2021</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>benchmarks.Rmd</code></div>
|
||||
@ -226,42 +225,22 @@
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span>, <span class="co"># Vancomycin Resistant S. aureus</span>
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="co"># [1] "^st.* au"</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># as.mo("sau") 12.0 12.0 13.0 14.0 14.0 16 10</span>
|
||||
<span class="co"># as.mo("stau") 55.0 67.0 88.0 95.0 98.0 120 10</span>
|
||||
<span class="co"># as.mo("STAU") 57.0 66.0 110.0 100.0 130.0 250 10</span>
|
||||
<span class="co"># as.mo("staaur") 12.0 12.0 17.0 13.0 14.0 54 10</span>
|
||||
<span class="co"># as.mo("STAAUR") 11.0 12.0 17.0 13.0 14.0 61 10</span>
|
||||
<span class="co"># as.mo("S. aureus") 30.0 32.0 62.0 69.0 93.0 95 10</span>
|
||||
<span class="co"># as.mo("S aureus") 29.0 33.0 43.0 37.0 53.0 71 10</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 2.2 2.4 2.6 2.6 2.8 3 10</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 270.0 290.0 330.0 310.0 380.0 430 10</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 190.0 210.0 240.0 250.0 270.0 290 10</span>
|
||||
<span class="co"># as.mo("MRSA") 12.0 12.0 14.0 13.0 15.0 16 10</span>
|
||||
<span class="co"># as.mo("VISA") 21.0 22.0 29.0 24.0 25.0 79 10</span>
|
||||
<span class="co"># as.mo("VRSA") 21.0 24.0 35.0 28.0 56.0 58 10</span></code></pre></div>
|
||||
<span class="co"># as.mo("sau") 11.0 12.0 27.0 13.0 49.0 51 10</span>
|
||||
<span class="co"># as.mo("stau") 53.0 57.0 76.0 74.0 93.0 100 10</span>
|
||||
<span class="co"># as.mo("STAU") 53.0 54.0 69.0 56.0 58.0 190 10</span>
|
||||
<span class="co"># as.mo("staaur") 11.0 12.0 21.0 13.0 42.0 44 10</span>
|
||||
<span class="co"># as.mo("STAAUR") 11.0 12.0 16.0 13.0 14.0 48 10</span>
|
||||
<span class="co"># as.mo("S. aureus") 27.0 27.0 38.0 32.0 35.0 75 10</span>
|
||||
<span class="co"># as.mo("S aureus") 27.0 29.0 38.0 30.0 36.0 73 10</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 3.1 3.2 6.9 3.5 3.7 38 10</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 270.0 260.0 280.0 290 10</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 160.0 200.0 200.0 200.0 210.0 230 10</span>
|
||||
<span class="co"># as.mo("MRSA") 10.0 11.0 12.0 11.0 13.0 14 10</span>
|
||||
<span class="co"># as.mo("VISA") 19.0 20.0 26.0 22.0 24.0 61 10</span>
|
||||
<span class="co"># as.mo("VRSA") 19.0 20.0 24.0 21.0 22.0 56 10</span></code></pre></div>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations can take up to 500-1000 times as much time.</p>
|
||||
<p>To improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
||||
@ -291,8 +270,8 @@
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># mo_name(x) 125 144 182 171 186 298 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.171 seconds. You only lose time on your unique input values.</p>
|
||||
<span class="co"># mo_name(x) 137 146 178 172 193 282 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.172 seconds. You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div id="precalculated-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@ -305,11 +284,11 @@
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 7.08 7.37 15.90 7.94 9.02 48.9 10</span>
|
||||
<span class="co"># B 23.50 24.00 25.20 24.10 26.20 30.1 10</span>
|
||||
<span class="co"># C 1.54 1.62 1.76 1.71 1.81 2.3 10</span></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0017 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 7.12 7.56 7.89 7.7 8.39 8.69 10</span>
|
||||
<span class="co"># B 23.90 24.50 35.10 24.8 27.40 77.50 10</span>
|
||||
<span class="co"># C 1.73 1.84 1.95 1.9 2.09 2.36 10</span></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0019 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
|
||||
@ -322,15 +301,15 @@
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 1.63 1.92 1.99 2.01 2.11 2.29 10</span>
|
||||
<span class="co"># B 1.67 1.89 2.01 1.96 2.12 2.62 10</span>
|
||||
<span class="co"># C 1.86 1.87 1.96 1.97 2.04 2.13 10</span>
|
||||
<span class="co"># D 1.63 1.82 1.90 1.94 2.00 2.06 10</span>
|
||||
<span class="co"># E 1.60 1.94 3.05 1.97 2.24 12.60 10</span>
|
||||
<span class="co"># F 1.66 1.90 2.18 1.95 2.01 4.33 10</span>
|
||||
<span class="co"># G 1.84 1.89 1.99 1.98 2.02 2.24 10</span>
|
||||
<span class="co"># H 1.79 1.95 2.08 2.06 2.25 2.36 10</span></code></pre></div>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 1.54 1.57 1.73 1.69 1.88 2.00 10</span>
|
||||
<span class="co"># B 1.51 1.52 1.75 1.70 1.86 2.41 10</span>
|
||||
<span class="co"># C 1.55 1.60 1.70 1.70 1.81 1.86 10</span>
|
||||
<span class="co"># D 1.55 1.59 1.71 1.66 1.83 1.94 10</span>
|
||||
<span class="co"># E 1.50 1.55 1.68 1.61 1.78 2.10 10</span>
|
||||
<span class="co"># F 1.51 1.62 1.75 1.79 1.82 2.02 10</span>
|
||||
<span class="co"># G 1.52 1.53 1.68 1.60 1.80 2.02 10</span>
|
||||
<span class="co"># H 1.53 1.54 1.63 1.60 1.67 1.84 10</span></code></pre></div>
|
||||
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div id="results-in-other-languages" class="section level3">
|
||||
@ -358,13 +337,13 @@
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># en 17.21 17.88 21.68 18.14 19.20 71.64 100</span>
|
||||
<span class="co"># de 20.08 20.74 26.58 21.26 22.41 159.80 100</span>
|
||||
<span class="co"># nl 24.88 25.81 31.01 26.32 27.03 74.57 100</span>
|
||||
<span class="co"># es 19.91 20.80 26.33 21.28 22.60 80.34 100</span>
|
||||
<span class="co"># it 19.96 20.63 25.21 21.20 22.25 76.35 100</span>
|
||||
<span class="co"># fr 19.61 20.38 26.62 21.15 22.59 80.90 100</span>
|
||||
<span class="co"># pt 19.87 20.58 27.65 20.92 23.22 80.73 100</span></code></pre></div>
|
||||
<span class="co"># en 17.38 17.71 25.63 18.11 19.75 81.61 100</span>
|
||||
<span class="co"># de 20.14 20.61 24.87 20.91 21.57 85.23 100</span>
|
||||
<span class="co"># nl 25.02 25.46 28.40 25.83 26.58 78.47 100</span>
|
||||
<span class="co"># es 19.90 20.41 24.86 20.77 21.78 81.38 100</span>
|
||||
<span class="co"># it 20.01 20.44 24.40 20.80 21.57 76.08 100</span>
|
||||
<span class="co"># fr 19.85 20.23 29.97 20.89 23.56 192.40 100</span>
|
||||
<span class="co"># pt 19.90 20.26 26.53 20.75 22.56 85.69 100</span></code></pre></div>
|
||||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 68 KiB After Width: | Height: | Size: 68 KiB |
@ -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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -236,9 +236,9 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1509021" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.5.0.9021">
|
||||
<a href="#amr-1509021" class="anchor"></a>AMR 1.5.0.9021<small> Unreleased </small>
|
||||
<div id="amr-1509023" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.5.0.9023">
|
||||
<a href="#amr-1509023" class="anchor"></a>AMR 1.5.0.9023<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-21-february-2021" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
@ -326,7 +326,9 @@
|
||||
</li>
|
||||
<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
|
||||
<li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
|
||||
<li>The <code><a href="../reference/like.html">like()</a></code> function (and its fast alias <code><a href="../reference/like.html">%like%</a></code>) now always use Perl compatibility, improving speed for many functions in this package</li>
|
||||
<li>The <code><a href="../reference/like.html">like()</a></code> function (and its fast alias <code><a href="../reference/like.html">%like%</a></code>) now always use Perl compatibility, improving speed for many functions in this package (e.g., <code><a href="../reference/as.mo.html">as.mo()</a></code> is now up to 4 times faster)</li>
|
||||
<li>
|
||||
<em>Staphylococcus cornubiensis</em> is now correctly categorised as coagulase-positive</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other" class="section level3">
|
||||
|
||||
@ -12,7 +12,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2021-02-21T19:14Z
|
||||
last_built: 2021-02-21T22:18Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR//reference
|
||||
article: https://msberends.github.io/AMR//articles
|
||||
|
||||
@ -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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -86,3 +86,13 @@ test_that("CoL version info works", {
|
||||
|
||||
expect_output(print(catalogue_of_life_version()))
|
||||
})
|
||||
|
||||
test_that("CoNS/CoPS are up to date", {
|
||||
uncategorised <- subset(microorganisms,
|
||||
genus == "Staphylococcus" &
|
||||
!species %in% c("", "aureus") &
|
||||
!mo %in% c(MO_CONS, MO_COPS))
|
||||
expect(NROW(uncategorised) == 0,
|
||||
failure_message = paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
|
||||
uncategorised$species, " (", uncategorised$mo, ")"))
|
||||
})
|
||||
|
||||
@ -1,6 +1,5 @@
|
||||
---
|
||||
title: "Benchmarks"
|
||||
date: '`r format(Sys.Date(), "%d %B %Y")`'
|
||||
output:
|
||||
rmarkdown::html_vignette:
|
||||
toc: true
|
||||
@ -20,7 +19,7 @@ knitr::opts_chunk$set(
|
||||
fig.width = 7.5,
|
||||
fig.height = 4.5,
|
||||
dpi = 75
|
||||
)
|
||||
)
|
||||
```
|
||||
|
||||
One of the most important features of this package is the complete microbial taxonomic database, supplied by the [Catalogue of Life](http://catalogueoflife.org). We created a function `as.mo()` that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.
|
||||
|
||||
Loading…
Reference in New Issue
Block a user