Merge pull request #24 from acornamr/dev

2.6.2
acornamr · Aug 8, 2023 · 1f208b7 · 1f208b7
2 parents b00d033 + d08a06a
commit 1f208b7
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Showing 4 changed files with 6 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: acorn
 Type: Package
 Title: A Dashboard for ACORN AMR Data
-Version: 2.6.1
+Version: 2.6.2
 Authors@R: c(person(given = "Olivier", family = "Celhay", 
                 email = "olivier.celhay@gmail.com", 
                 role = c("aut", "cre"), 

diff --git a/inst/acorn/app.R b/inst/acorn/app.R
@@ -1,4 +1,4 @@
-app_version <- "2.6.1"  # Make sure that the app version is identical in DESCRIPTION
+app_version <- "2.6.2"  # Make sure that the app version is identical in DESCRIPTION
 session_start_time <- format(Sys.time(), "%Y-%m-%d_%HH%M")
 
 # Increase limit upload to 50 Mb.

diff --git a/inst/acorn/www/R/data/06_make_ast_group.R b/inst/acorn/www/R/data/06_make_ast_group.R
@@ -61,7 +61,9 @@ for(i in amr.var$varname.ast) { # Select the variables containing raw AST data
   amr[,i] <- gsub("<=", "", amr[,i]) # Replaces <= with blank
   amr[,i] <- gsub(">=", "", amr[,i]) # Replaces >= with blank
   amr[,i] <- gsub("\u2264", "", amr[,i]) # Replaces unicode-2264 (unicode <= with blank) [UPDATED ACORN2]
-  amr[,i] <- gsub("\u2265", "", amr[,i]) # Replaces unicode-2264 (unicode >= with blank) [UPDATED ACORN2]
+  amr[,i] <- gsub("\u2265", "", amr[,i]) # Replaces unicode-2265 (unicode >= with blank) [UPDATED ACORN2]
+  amr[,i] <- gsub("\u00b5g/ml", "", amr[,i]) # Replaces unicode-00b5 g/ml (unicode ug/ml with blank) [UPDATED ACORN2]
+  amr[,i] <- gsub("\u03bcg/ml", "", amr[,i]) # Replaces unicode-03bc g/ml (unicode ug/ml with blank) [UPDATED ACORN2]
   amr[,i] <- gsub("/.*", "", amr[,i]) # Anything with a slash MIC (e.g. co-amoxiclav 8/4), remove the "/" and the second MIC which should be the b-lac inhibitor or sulfa, for co-trimoxazole [UPDATED ACORN2]
   amr[,i] <- gsub("<[0-9]{1,3}", "0", amr[,i]) # Anything with < followed by a number (upto 3 digits) is replaced by "0" (i.e. low MIC = S)
   amr[,i] <- gsub(">[0-9]{1,3}", "512", amr[,i]) # Anything with > followed by a number (upto 3 digits) is replaced by "512" (i.e. high MIC = R)

diff --git a/inst/acorn/www/R/data/07_ast_interpretation.R b/inst/acorn/www/R/data/07_ast_interpretation.R
@@ -153,7 +153,7 @@ tmp.amr2 <- cbind(tmp.amr, tmp.amr1) # Combine both data.frames
 
 amr <- bind_rows(tmp.amr2 %>% mutate_all(as.character), 
                  amr %>% mutate_all(as.character)) %>%
-  mutate(specdate = parse_date_time(specdate, c("dmY", "Ymd", "dbY", "Ymd HMS")),
+  mutate(specdate = parse_date_time(specdate, c("dmY", "Ymd", "dbY", "Ymd HMS", "dmY HM")),
          spectype.whonet = as.numeric(spectype.whonet),
          specid.acorn = as.numeric(specid.acorn ),
          orgnum.acorn = as.numeric(orgnum.acorn))