mirror of https://github.com/msberends/AMR.git
(v1.4.0.9002) bugfix
This commit is contained in:
parent
4e9ccb4435
commit
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.4.0.9001
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Version: 1.4.0.9002
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Date: 2020-10-19
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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@ -1,4 +1,4 @@
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# AMR 1.4.0.9001
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# AMR 1.4.0.9002
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## <small>Last updated: 19 October 2020</small>
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### New
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2
R/ab.R
2
R/ab.R
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@ -82,7 +82,7 @@
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#' ab_name("J01FA01") # "Erythromycin"
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#' ab_name("eryt") # "Erythromycin"
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as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
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meet_criteria(x, allow_class = c("character", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_class = c("character", "numeric", "integer", "factor"), allow_NA = TRUE)
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meet_criteria(flag_multiple_results, allow_class = "logical", has_length = 1)
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meet_criteria(info, allow_class = "logical", has_length = 1)
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4
R/mo.R
4
R/mo.R
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@ -158,7 +158,7 @@ as.mo <- function(x,
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ignore_pattern = getOption("AMR_ignore_pattern"),
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language = get_locale(),
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...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
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meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
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meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)
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@ -275,7 +275,7 @@ exec_as.mo <- function(x,
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actual_uncertainty = 1,
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actual_input = NULL,
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language = get_locale()) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
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meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
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meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)
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@ -146,7 +146,7 @@
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#' mo_info("E. coli")
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#' }
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mo_name <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...), language = language, only_unknown = FALSE)
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@ -159,7 +159,7 @@ mo_fullname <- mo_name
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#' @rdname mo_property
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#' @export
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mo_shortname <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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@ -192,7 +192,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_subspecies <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
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@ -201,7 +201,7 @@ mo_subspecies <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_species <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
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@ -210,7 +210,7 @@ mo_species <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_genus <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
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@ -219,7 +219,7 @@ mo_genus <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_family <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
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@ -228,7 +228,7 @@ mo_family <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_order <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
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@ -237,7 +237,7 @@ mo_order <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_class <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
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@ -246,7 +246,7 @@ mo_class <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_phylum <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
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@ -255,7 +255,7 @@ mo_phylum <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_kingdom <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
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@ -268,7 +268,7 @@ mo_domain <- mo_kingdom
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#' @rdname mo_property
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#' @export
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mo_type <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = FALSE)
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@ -277,7 +277,7 @@ mo_type <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_gramstain <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x.mo <- as.mo(x, language = language, ...)
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@ -311,7 +311,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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is_gram_negative <- function(x, ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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grams <- mo_gramstain(x, language = NULL, ...)
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"Gram-negative" == grams & !is.na(grams)
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}
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@ -319,7 +319,7 @@ is_gram_negative <- function(x, ...) {
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#' @rdname mo_property
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#' @export
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is_gram_positive <- function(x, ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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grams <- mo_gramstain(x, language = NULL, ...)
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"Gram-positive" == grams & !is.na(grams)
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}
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@ -327,7 +327,7 @@ is_gram_positive <- function(x, ...) {
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#' @rdname mo_property
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#' @export
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mo_snomed <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo_validate(x = x, property = "snomed", language = language, ...)
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@ -336,7 +336,7 @@ mo_snomed <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_ref <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo_validate(x = x, property = "ref", language = language, ...)
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@ -345,7 +345,7 @@ mo_ref <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_authors <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- mo_validate(x = x, property = "ref", language = language, ...)
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@ -357,7 +357,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_year <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- mo_validate(x = x, property = "ref", language = language, ...)
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@ -369,7 +369,7 @@ mo_year <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_rank <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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mo_validate(x = x, property = "rank", language = language, ...)
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@ -378,7 +378,7 @@ mo_rank <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_taxonomy <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- as.mo(x, language = language, ...)
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@ -400,7 +400,7 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_synonyms <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- as.mo(x, language = language, ...)
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@ -429,7 +429,7 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_info <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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x <- as.mo(x, language = language, ...)
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@ -455,7 +455,7 @@ mo_info <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(open, allow_class = "logical", has_length = 1)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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@ -488,7 +488,7 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
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meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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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.github.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">1.4.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9001</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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-1409001" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0.9001">
|
||||
<a href="#amr-1409001" class="anchor"></a>AMR 1.4.0.9001<small> Unreleased </small>
|
||||
<div id="amr-1409002" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0.9002">
|
||||
<a href="#amr-1409002" class="anchor"></a>AMR 1.4.0.9002<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-19-october-2020" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
|
|
|
@ -12,7 +12,7 @@ articles:
|
|||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2020-10-19T15:08Z
|
||||
last_built: 2020-10-19T18:44Z
|
||||
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">1.4.0.9001</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
Loading…
Reference in New Issue