diff --git a/DESCRIPTION b/DESCRIPTION
index 034fab43..bb38c078 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: AMR
-Version: 1.2.0.9015
-Date: 2020-06-25
+Version: 1.2.0.9016
+Date: 2020-06-26
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 778e1a17..3094fc49 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,5 @@
-# AMR 1.2.0.9015
-## Last updated: 25-Jun-2020
+# AMR 1.2.0.9016
+## Last updated: 26-Jun-2020
### New
* Function `ab_from_text()` to retrieve antimicrobial drugs from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally:
@@ -31,7 +31,7 @@
* Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set
### Changed
-* Fixed a bug for using `susceptibility` or `resistance()` outside `summarise()`
+* Using unexisting columns in all `count_*()`, `proportion_*()`, `susceptibility()` and `resistance()` functions wil now return an error instead of dropping them silently
* Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
* All `*_join_microorganisms()` functions and `bug_drug_combinations()` now return the original data class (e.g. `tibble`s and `data.table`s)
* Fixed a bug where `as.ab()` would return an error on invalid input values
diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index 94d81b5a..6516566e 100755
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -202,33 +202,33 @@ import_fn <- function(name, pkg) {
}
stop_if <- function(expr, ..., call = TRUE) {
- msg <- paste0(c(...), collapse = "")
- if (!isFALSE(call)) {
- if (isTRUE(call)) {
- call <- as.character(sys.call(-1)[1])
- } else {
- # so you can go back more than 1 call, as used in rsi_calc(), that now throws a reference to e.g. n_rsi()
- call <- as.character(sys.call(call)[1])
- }
- msg <- paste0("in ", call, "(): ", msg)
- }
if (isTRUE(expr)) {
+ msg <- paste0(c(...), collapse = "")
+ if (!isFALSE(call)) {
+ if (isTRUE(call)) {
+ call <- as.character(sys.call(-1)[1])
+ } else {
+ # so you can go back more than 1 call, as used in rsi_calc(), that now throws a reference to e.g. n_rsi()
+ call <- as.character(sys.call(call)[1])
+ }
+ msg <- paste0("in ", call, "(): ", msg)
+ }
stop(msg, call. = FALSE)
}
}
stop_ifnot <- function(expr, ..., call = TRUE) {
- msg <- paste0(c(...), collapse = "")
- if (!isFALSE(call)) {
- if (isTRUE(call)) {
- call <- as.character(sys.call(-1)[1])
- } else {
- # so you can go back more than 1 call, as used in rsi_calc(), that now throws a reference to e.g. n_rsi()
- call <- as.character(sys.call(call)[1])
- }
- msg <- paste0("in ", call, "(): ", msg)
- }
if (!isTRUE(expr)) {
+ msg <- paste0(c(...), collapse = "")
+ if (!isFALSE(call)) {
+ if (isTRUE(call)) {
+ call <- as.character(sys.call(-1)[1])
+ } else {
+ # so you can go back more than 1 call, as used in rsi_calc(), that now throws a reference to e.g. n_rsi()
+ call <- as.character(sys.call(call)[1])
+ }
+ msg <- paste0("in ", call, "(): ", msg)
+ }
stop(msg, call. = FALSE)
}
}
diff --git a/R/ab.R b/R/ab.R
index 31da9d82..c1efbcc0 100755
--- a/R/ab.R
+++ b/R/ab.R
@@ -209,7 +209,7 @@ as.ab <- function(x, ...) {
# correct for digital reading text (OCR)
x_spelling <- gsub("[NRD]", "[NRD]", x_spelling)
}
-
+
# try if name starts with it
found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab
if (length(found) > 0) {
diff --git a/R/ab_from_text.R b/R/ab_from_text.R
index c5e39598..5d6d7275 100644
--- a/R/ab_from_text.R
+++ b/R/ab_from_text.R
@@ -58,12 +58,17 @@ ab_from_text <- function(text, collapse = NULL, translate_ab = "name", ...) {
}
text_split <- unlist(strsplit(text, "[ ;.,:/\\|-]"))
- result <- as.ab(unique(c(text_split[grep(to_regex(abbr), text_split)],
- text_split[grep(to_regex(names), text_split)],
- # regular expression must not be too long, so split synonyms in two:
- text_split[grep(to_regex(synonyms[c(1:0.5 * length(synonyms))]), text_split)],
- text_split[grep(to_regex(synonyms[c(0.5 * length(synonyms):length(synonyms))]), text_split)])),
- ...)
+ result <- suppressWarnings(
+ as.ab(unique(c(text_split[grep(to_regex(abbr), text_split)],
+ text_split[grep(to_regex(names), text_split)],
+ # regular expression must not be too long, so split synonyms in two:
+ text_split[grep(to_regex(synonyms[c(1:0.5 * length(synonyms))]), text_split)],
+ text_split[grep(to_regex(synonyms[c(0.5 * length(synonyms):length(synonyms))]), text_split)])),
+ ...))
+ result <- result[!is.na(result)]
+ if (length(result) == 0) {
+ result <- as.ab(NA)
+ }
translate_ab <- get_translate_ab(translate_ab)
if (!isFALSE(translate_ab)) {
result <- ab_property(result, property = translate_ab)
diff --git a/R/mic.R b/R/mic.R
index 1715b87d..14d95c63 100755
--- a/R/mic.R
+++ b/R/mic.R
@@ -130,7 +130,8 @@ as.mic <- function(x, na.rm = FALSE) {
}
all_valid_mics <- function(x) {
- x_mic <- suppressWarnings(as.mic(x[!is.na(x)]))
+ x_mic <- tryCatch(suppressWarnings(as.mic(x[!is.na(x)])),
+ error = function(e) NA)
!any(is.na(x_mic)) & !all(is.na(x))
}
diff --git a/R/rsi.R b/R/rsi.R
index 16050fc5..6ff21c6c 100755
--- a/R/rsi.R
+++ b/R/rsi.R
@@ -166,10 +166,10 @@ as.rsi.default <- function(x, ...) {
}
}
- x <- x %>% unlist()
+ x <- as.character(unlist(x))
x.bak <- x
- na_before <- x[is.na(x) | x == ""] %>% length()
+ na_before <- length(x[is.na(x) | x == ""])
# remove all spaces
x <- gsub(" +", "", x)
# remove all MIC-like values: numbers, operators and periods
@@ -188,7 +188,7 @@ as.rsi.default <- function(x, ...) {
x <- gsub("^I+$", "I", x)
x <- gsub("^R+$", "R", x)
x[!x %in% c("S", "I", "R")] <- NA
- na_after <- x[is.na(x) | x == ""] %>% length()
+ na_after <- length(x[is.na(x) | x == ""])
if (!isFALSE(list(...)$warn)) { # so as.rsi(..., warn = FALSE) will never throw a warning
if (na_before != na_after) {
diff --git a/R/rsi_calc.R b/R/rsi_calc.R
index ee1ada71..9de3fdcc 100755
--- a/R/rsi_calc.R
+++ b/R/rsi_calc.R
@@ -48,18 +48,23 @@ rsi_calc <- function(...,
"Please read Details in the help page (`?proportion`) as this may have a considerable impact on your analysis.", call = -2)
ndots <- length(dots)
- if ("data.frame" %in% class(dots_df)) {
+ if (is.data.frame(dots_df)) {
# data.frame passed with other columns, like: example_isolates %>% proportion_S(AMC, GEN)
dots <- as.character(dots)
- dots <- dots[dots != "."]
+ # remove first element, it's the data.frame
+ if (length(dots) == 1) {
+ dots <- character(0)
+ } else {
+ dots <- dots[2:length(dots)]
+ }
if (length(dots) == 0 | all(dots == "df")) {
# for complete data.frames, like example_isolates %>% select(AMC, GEN) %>% proportion_S()
# and the old rsi function, which has "df" as name of the first parameter
x <- dots_df
- } else if (length(dots) == 1 | all(!dots %in% colnames(dots_df))) {
- x <- dots_df
} else {
- x <- dots_df[, dots[dots %in% colnames(dots_df)], drop = FALSE]
+ dots_not_exist <- dots[!dots %in% colnames(dots_df)]
+ stop_if(length(dots_not_exist) > 0, "column(s) not found: ", paste0("'", dots_not_exist, "'", collapse = ", "), call = -2)
+ x <- dots_df[, dots, drop = FALSE]
}
} else if (ndots == 1) {
# only 1 variable passed (can also be data.frame), like: proportion_S(example_isolates$AMC) and example_isolates$AMC %>% proportion_S()
diff --git a/docs/404.html b/docs/404.html
index 20e4bb6f..eca69945 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.2.0.9015
+ 1.2.0.9016
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 7f22924c..ad80d18f 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.2.0.9015
+ 1.2.0.9016
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 9872d93b..346ec7c4 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.2.0.9015
+ 1.2.0.9016
diff --git a/docs/authors.html b/docs/authors.html
index d050bcd0..b59291f2 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.2.0.9015
+ 1.2.0.9016
diff --git a/docs/index.html b/docs/index.html
index 81b9a28b..87b69ddb 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -43,7 +43,7 @@
AMR (for R)
- 1.2.0.9015
+ 1.2.0.9016
diff --git a/docs/news/index.html b/docs/news/index.html
index b214d5a4..452737c1 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.2.0.9015
+ 1.2.0.9016
@@ -229,13 +229,13 @@
Source: NEWS.md
-
-
diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html
index 79f5d734..06312d91 100644
--- a/docs/reference/proportion.html
+++ b/docs/reference/proportion.html
@@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
AMR (for R)
- 1.2.0.9014
+ 1.2.0.9016