mirror of https://github.com/msberends/AMR.git
(v1.2.0.9004) rsi_df() fix for groups
This commit is contained in:
parent
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Package: AMR
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Version: 1.2.0.9003
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Date: 2020-06-05
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Version: 1.2.0.9004
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Date: 2020-06-09
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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6
NEWS.md
6
NEWS.md
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@ -1,12 +1,14 @@
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# AMR 1.2.0.9003
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## <small>Last updated: 05-Jun-2020</small>
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# AMR 1.2.0.9004
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## <small>Last updated: 09-Jun-2020</small>
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### Changed
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* Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
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* All `*_join_microorganisms()` functions now return the original data class (e.g. tibbles and data.tables)
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* Fixed a bug where `as.ab()` would return an error on invalid input values
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* Fixed a bug for using grouped versions of `rsi_df()`, `proportion_df()` and `count_df()`
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* Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*)
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* Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()`
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* Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set
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# AMR 1.2.0
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@ -114,9 +114,16 @@ get_column_abx <- function(x,
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verbose = FALSE,
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...) {
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message(font_blue("NOTE: Auto-guessing columns suitable for analysis..."), appendLF = FALSE)
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message(font_blue("NOTE: Auto-guessing columns suitable for analysis"), appendLF = FALSE)
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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if (NROW(x) > 10000) {
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# only test maximum of 10,000 values per column
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message(font_blue(paste0(" (using only ", font_bold("the first 10,000 rows"), ")...")), appendLF = FALSE)
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x <- x[1:10000, , drop = FALSE]
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} else {
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message(font_blue("..."), appendLF = FALSE)
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}
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x_bak <- x
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# only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
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# or already have the rsi class (as.rsi)
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20
R/rsi_calc.R
20
R/rsi_calc.R
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@ -220,10 +220,18 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
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.data <- .data[, which(!colnames(.data) %in% groups), drop = FALSE]
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}
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for (i in seq_len(ncol(.data))) {
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col_results <- as.data.frame(as.matrix(table(.data[, i, drop = TRUE])))
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values <- .data[, i, drop = TRUE]
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if (isTRUE(combine_SI)) {
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values <- factor(values, levels = c("SI", "R"), ordered = TRUE)
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} else if (isTRUE(combine_IR)) {
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values <- factor(values, levels = c("S", "IR"), ordered = TRUE)
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} else {
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values <- factor(values, levels = c("S", "I", "R"), ordered = TRUE)
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}
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col_results <- as.data.frame(as.matrix(table(values)))
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col_results$interpretation <- rownames(col_results)
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col_results$isolates <- col_results[, 1, drop = TRUE]
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if (nrow(col_results) > 0) {
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if (NROW(col_results) > 0 && sum(col_results$isolates, na.rm = TRUE) > 0) {
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if (sum(col_results$isolates, na.rm = TRUE) >= minimum) {
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col_results$value <- col_results$isolates / sum(col_results$isolates, na.rm = TRUE)
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} else {
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@ -237,6 +245,12 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
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isolates = col_results$isolates,
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stringsAsFactors = FALSE)
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if (data_has_groups) {
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if (nrow(group_values) < nrow(out_new)) {
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# repeat group_values for the number of rows in out_new
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repeated <- rep(seq_len(nrow(group_values)),
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each = nrow(out_new) / nrow(group_values))
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group_values <- group_values[repeated, , drop = FALSE]
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}
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out_new <- cbind(group_values, out_new)
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}
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out <- rbind(out, out_new)
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@ -273,7 +287,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
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if (data_has_groups) {
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# ordering by the groups and two more: "antibiotic" and "interpretation"
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out <- out[do.call("order", out[, seq_len(length(groups) + 2)]), ]
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out <- ungroup(out[do.call("order", out[, seq_len(length(groups) + 2)]), ])
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} else {
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out <- out[order(out$antibiotic, out$interpretation), ]
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}
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@ -89,7 +89,8 @@
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"CTF" "J01DC07" 43708 "Cefotiam" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "c(\"cefotiam\", \"cefotiam?\", \"cefotiamum\", \"ceradolan\", \"ceradon\", \"haloapor\")" 1.2 "g" 4 "g"
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"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "" "c(\"cefotiam cilexetil\", \"pansporin t\")"
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"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "" ""
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"FOX" "J01DC01" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfox\", \"cfsc\", \"cfx\", \"cfxt\", \"cx\", \"fox\", \"fx\")" "c(\"cefoxitin\", \"cefoxitina\", \"cefoxitine\", \"cefoxitinum\", \"cefoxotin\", \"cephoxitin\", \"mefoxin\", \"mefoxitin\", \"rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")"
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"FOX" "J01DC01" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfox\", \"cfx\", \"cfxt\", \"cx\", \"fox\", \"fx\")" "c(\"cefoxitin\", \"cefoxitina\", \"cefoxitine\", \"cefoxitinum\", \"cefoxotin\", \"cephoxitin\", \"mefoxin\", \"mefoxitin\", \"rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")"
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"FOX1" "Cefoxitin screening" "Cephalosporins (2nd gen.)" "cfsc" "" "NA"
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"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "" "cefozopran"
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"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "" "c(\"cefpimizol\", \"cefpimizole\", \"cefpimizole sodium\", \"cefpimizolum\")"
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"CPM" "J01DD11" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "c(\"cefpiramide\", \"cefpiramide acid\", \"cefpiramido\", \"cefpiramidum\")" 2 "g"
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@ -322,7 +322,16 @@ antibiotics[which(antibiotics$ab == as.ab("cefuroxim")), "abbreviations"][[1]] <
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antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]], "cftx"))
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antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]], "cftz"))
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antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]], "cfpi"))
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antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]], "cfxt", "cfsc"))
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antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]], "cfxt"))
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# Add cefoxitin screening
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class(antibiotics$ab) <- "character"
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antibiotics <- rbind(antibiotics,data.frame(ab = "FOX1", atc = NA, cid = NA,
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name = "Cefoxitin screening",
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group = "Cephalosporins (2nd gen.)", atc_group1 = NA, atc_group2 = NA,
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abbreviations = "cfsc", synonyms = NA,
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oral_ddd = NA, oral_units = NA, iv_ddd = NA, iv_units = NA,
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loinc = NA,
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stringsAsFactors = FALSE))
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# More GLIMS codes
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antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "cftz"))
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antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]], "cftr"))
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@ -579,7 +588,7 @@ antibiotics <- antibiotics %>%
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# set as data.frame again
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antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
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class(antibiotics$ab) <- c("ab", "character")
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antibiotics <- antibiotics %>% arrange(name)
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antibiotics <- antibiotics %>% dplyr::arrange(name)
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# make all abbreviations and synonyms lower case, unique and alphabetically sorted ----
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for (i in 1:nrow(antibiotics)) {
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Binary file not shown.
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
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</span>
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</div>
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@ -229,13 +229,13 @@
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<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1209003" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9003">
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<a href="#amr-1209003" class="anchor"></a>AMR 1.2.0.9003<small> Unreleased </small>
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<div id="amr-1209004" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9004">
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<a href="#amr-1209004" class="anchor"></a>AMR 1.2.0.9004<small> Unreleased </small>
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</h1>
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<div id="last-updated-05-jun-2020" class="section level2">
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<div id="last-updated-09-jun-2020" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-05-jun-2020" class="anchor"></a><small>Last updated: 05-Jun-2020</small>
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<a href="#last-updated-09-jun-2020" class="anchor"></a><small>Last updated: 09-Jun-2020</small>
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</h2>
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<div id="changed" class="section level3">
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<h3 class="hasAnchor">
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@ -244,9 +244,12 @@
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<li>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</li>
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<li>All <code>*_join_microorganisms()</code> functions now return the original data class (e.g. tibbles and data.tables)</li>
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<li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li>
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<li>Fixed a bug for using grouped versions of <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>
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</li>
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<li>Added function <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</li>
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<li>Added official antimicrobial names to all <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> functions, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code>
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</li>
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<li>Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the <code>antibiotics</code> data set</li>
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</ul>
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</div>
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</div>
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-06-05T11:55Z
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last_built: 2020-06-09T14:15Z
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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article: https://msberends.gitlab.io/AMR/articles
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@ -6,7 +6,7 @@
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>Data sets with 557 antimicrobials — antibiotics • AMR (for R)</title>
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<title>Data sets with 558 antimicrobials — antibiotics • AMR (for R)</title>
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<!-- favicons -->
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<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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@ -48,7 +48,7 @@
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<link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script>
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<meta property="og:title" content="Data sets with 557 antimicrobials — antibiotics" />
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<meta property="og:title" content="Data sets with 558 antimicrobials — antibiotics" />
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<meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_property() functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes." />
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<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
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@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
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</span>
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</div>
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@ -226,7 +226,7 @@
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<div class="row">
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<div class="col-md-9 contents">
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<div class="page-header">
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<h1>Data sets with 557 antimicrobials</h1>
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<h1>Data sets with 558 antimicrobials</h1>
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<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
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<div class="hidden name"><code>antibiotics.Rd</code></div>
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</div>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
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<h3>For the antibiotics data set: a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 455 observations and 14 variables:</h3>
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<h3>For the antibiotics data set: a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 456 observations and 14 variables:</h3>
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<ul>
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<li><p><code>ab</code><br /> Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<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">1.2.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9004</span>
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</span>
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</div>
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<td>
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<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
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</td>
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<td><p>Data sets with 557 antimicrobials</p></td>
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<td><p>Data sets with 558 antimicrobials</p></td>
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||||
</tr><tr>
|
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<td>
|
||||
|
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@ -4,9 +4,9 @@
|
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\name{antibiotics}
|
||||
\alias{antibiotics}
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\alias{antivirals}
|
||||
\title{Data sets with 557 antimicrobials}
|
||||
\title{Data sets with 558 antimicrobials}
|
||||
\format{
|
||||
\subsection{For the \link{antibiotics} data set: a \code{\link{data.frame}} with 455 observations and 14 variables:}{
|
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\subsection{For the \link{antibiotics} data set: a \code{\link{data.frame}} with 456 observations and 14 variables:}{
|
||||
\itemize{
|
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\item \code{ab}\cr Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
|
||||
\item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}
|
||||
|
|
|
|||
Loading…
Reference in New Issue