Merge pull request #6 from c2-d2/fix-azm

Correct azithromycin MICs

published/01.correct-azm.R

@@ -0,0 +1,13 @@
+#!/usr/bin/env Rscript
+
+df <- read.delim("table_s1.tsv",
+ header = TRUE,
+ stringsAsFactors = F)
+df[df$Year < 2005,]$AZI.MIC = 2*df[df$Year < 2005,]$AZI.MIC
+write.table(
+ df,
+ "table_s1.corrected_azm.tsv",
+ sep = "\t",
+ quote = F,
+ row.names = F
+)

published/merge_and_clean.R → published/02.merge_and_clean.R

@@ -1,6 +1,6 @@
 #!/usr/bin/env Rscript
 
-df.sup <- read.delim("table_s1.tsv",
+df.sup <- read.delim("table_s1.corrected_azm.tsv",
  header = TRUE,
  stringsAsFactors = F)
 df.mlst <- read.delim("mlst.tsv",

published/Makefile

@@ -9,8 +9,10 @@ include ../*.mk
 all: isolates.tsv
 
 isolates.tsv: mlst.tsv table_s1.tsv
- ./merge_and_clean.R
+ ./01.correct-azm.R
+ ./02.merge_and_clean.R
 
 clean:
- rm -f .*.complete isolates.tsv
+ rm -f .*.complete isolates.tsv table_s1.corrected_azm.tsv
+