fixed error in removeOutlier function

Author: Konrad1991

Dockerfile

@@ -43,7 +43,9 @@ RUN install2.r --error --skipinstalled \
     ggpmisc \
     jose \
     R6 \
-    patchwork
+    patchwork \
+    cowplot \
+    quarto
 
 USER shiny
 COPY ./app/ ./myapp

MTT/DESCRIPTION

@@ -8,5 +8,5 @@ Maintainer: <[email protected]>
 Description: Import xml files from platereader. Calculation of LD50. Creating boxplots of raw data and the curves used for calculation of LD50.
 License: GPL-2
 Imports: tidyr, ggplot2, drc, R6, quarto, openxlsx, cowplot, gridExtra
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8

MTT/NAMESPACE

@@ -3,6 +3,7 @@
 export(XML2DF)
 export(ic50)
 export(import)
+export(removeOutlier)
 export(report_pdf)
 export(save)
 import(drc)

MTT/R/import.R

@@ -137,16 +137,19 @@ import <- function(path, names = names_default(), conc = conc_default()) {
 #' @param l a list containing column indices which defines the different groups
 #' @param dep the column index which defines the dependent variable
 removeOutlier <- function(df, l, dep) {
-  int <- sapply(seq_along(1:length(df)), function(x) {
-    paste0(df[, l], collapse = "_")
-  })
+  ps <- function(a, b) {
+    paste0(a, "_", b)
+  }
+  int <- Reduce(ps, as.list(df[, l]))
   intUnique <- unique(int)
+  
   dfor <- lapply(intUnique, function(x) {
    temp <- df[int == x, ]
    bs <- boxplot.stats(temp$abs)
    if (length(bs$out) == 0) return(temp)
    temp[temp$abs %in% bs$out, "abs"] <- NA
    return(temp)
   })
-  do.call(rbind, dfor)
+  df <- do.call(rbind, dfor)
+  df[!is.na(df$abs), ]
 }

MTT/man/removeOutlier.Rd

@@ -0,0 +1,2 @@
+install.packages("/home/konrad/Documents/GitHub/RProjects/shinychem/MTT",
+                 type = "source", repos = NULL)

build_and_run.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
 
-docker build -t my-shiny-app .
-docker push konradkraemer/biostats:latest
+docker build -t konradkraemer/biostats:latest .
+docker push konradkraemer/biostats:latest
+

installMTT.R

@@ -3,5 +3,6 @@
 #/usr/bin/shiny-server
 sudo -u shiny /usr/bin/shiny-server
 
-# rstudio switch to terminal alt, shift, m
-# rstudio run command from script in terminal: strg, alt, enter
+#cd /srv/shiny-server
+
+#Rscript -e 'shiny::runApp(".", port = 3838)'