Merge pull request #2 from gadeynebram/docker_changes

Changes in function of docker deployment
ceefluz · May 14, 2019 · 60197ed · 60197ed
2 parents 2057355 + 4e5bfa3
commit 60197ed
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Showing 6 changed files with 39 additions and 35 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,3 @@
+/.Rproj.user/
+*.Rproj
+.Rhistory
diff --git a/admissions_sample_181019.csv → data/admissions.csv b/admissions_sample_181019.csv → data/admissions.csv
diff --git a/antimicrobials_sample_181019.csv → data/antimicrobials.csv b/antimicrobials_sample_181019.csv → data/antimicrobials.csv
diff --git a/microbiology_sample_181019.csv → data/microbiology.csv b/microbiology_sample_181019.csv → data/microbiology.csv
diff --git a/dependencies.R b/dependencies.R
@@ -0,0 +1,31 @@
+# LIST OF REQUIRED PACKAGES -----------------------------------------------
+
+required_packages <- c(
+  "AMR",
+  "data.table",
+  "DT",
+  "ggridges",
+  "lubridate",
+  "plotly",
+  "qicharts2",
+  "rintrojs",
+  "shiny",
+  "shinyBS",
+  "shinycssloaders",
+  "shinydashboard",
+  "shinyjs",
+  "shinyWidgets",
+  "survival",
+  "survminer",
+  "tidyverse",
+  "viridis",
+  "zoo"
+)
+
+# install missing packages
+
+new.packages <- required_packages[!(required_packages %in% installed.packages()[,"Package"])]
+
+if (length(new.packages)) {
+  install.packages(new.packages)
+}
diff --git a/global.R b/global.R
@@ -4,47 +4,17 @@
 
 #RadaR is licensed under the GNU General Public License (GPL) v2.0 (https://github.com/ceefluz/radar/blob/master/LICENSE)
 
-# LIST OF REQUIRED PACKAGES -----------------------------------------------
-
-required_packages <- c(
-  "AMR",
-  "data.table",
-  "DT",
-  "ggridges",
-  "lubridate",
-  "plotly",
-  "qicharts2",
-  "rintrojs",
-  "shiny",
-  "shinyBS",
-  "shinycssloaders",
-  "shinydashboard",
-  "shinyjs",
-  "shinyWidgets",
-  "survival",
-  "survminer",
-  "tidyverse",
-  "viridis",
-  "zoo"
-)
-
-# install missing packages
-
-new.packages <- required_packages[!(required_packages %in% installed.packages()[,"Package"])]
-
-if (length(new.packages)) {
-  install.packages(new.packages)
-}
+# INSTALL DEPENDENCIES ----------------------------------------------------
 
+source('dependencies.R')
 # load all packages
 lapply(required_packages, require, character.only = TRUE)
 
-
 # DATA TRANSFORMATION AND NEW VARIABLES -----------------------------------
 
-admissions <- read_csv("admissions_sample_181019.csv")
-antimicrobials <- read_csv("antimicrobials_sample_181019.csv")
-microbiology <- read_csv("microbiology_sample_181019.csv")
+admissions <- read_csv("data/admissions.csv")
+antimicrobials <- read_csv("data/antimicrobials.csv")
+microbiology <- read_csv("data/microbiology.csv")
 
 admissions <- admissions %>%
   mutate(year = year(adm_start_date),