From 96e1acabe870d70b3cfba6edaa42ea8ef879f213 Mon Sep 17 00:00:00 2001 From: Bram Gadeyne Date: Mon, 13 May 2019 13:18:33 +0200 Subject: [PATCH 1/5] Add .gitignore file --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b86a353 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +/.Rproj.user/ +*.Rproj \ No newline at end of file From 1c8d37307a34d19ac34892b4c4bcbeb4ee91dbc9 Mon Sep 17 00:00:00 2001 From: Bram Gadeyne Date: Mon, 13 May 2019 13:19:02 +0200 Subject: [PATCH 2/5] splitup dependencies so that they can be run seperately in docker --- dependencies.R | 34 ++++++++++++++++++++++++++++++++++ global.R | 36 ++---------------------------------- 2 files changed, 36 insertions(+), 34 deletions(-) create mode 100644 dependencies.R diff --git a/dependencies.R b/dependencies.R new file mode 100644 index 0000000..1b77cd6 --- /dev/null +++ b/dependencies.R @@ -0,0 +1,34 @@ +# 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) +} + +# load all packages +lapply(required_packages, require, character.only = TRUE) \ No newline at end of file diff --git a/global.R b/global.R index 8d6d564..cb7cce9 100644 --- a/global.R +++ b/global.R @@ -4,41 +4,9 @@ #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) -} - -# load all packages -lapply(required_packages, require, character.only = TRUE) +# INSTALL DEPENDENCIES ---------------------------------------------------- +source('dependencies.R') # DATA TRANSFORMATION AND NEW VARIABLES ----------------------------------- From 6bfccafecf72e5ab1fbac4bbe1d87634406654c2 Mon Sep 17 00:00:00 2001 From: Bram Gadeyne Date: Mon, 13 May 2019 13:23:04 +0200 Subject: [PATCH 3/5] Move data files to data folder. Remove date suffix --- admissions_sample_181019.csv => data/admissions.csv | 0 antimicrobials_sample_181019.csv => data/antimicrobials.csv | 0 microbiology_sample_181019.csv => data/microbiology.csv | 0 global.R | 6 +++--- 4 files changed, 3 insertions(+), 3 deletions(-) rename admissions_sample_181019.csv => data/admissions.csv (100%) rename antimicrobials_sample_181019.csv => data/antimicrobials.csv (100%) rename microbiology_sample_181019.csv => data/microbiology.csv (100%) diff --git a/admissions_sample_181019.csv b/data/admissions.csv similarity index 100% rename from admissions_sample_181019.csv rename to data/admissions.csv diff --git a/antimicrobials_sample_181019.csv b/data/antimicrobials.csv similarity index 100% rename from antimicrobials_sample_181019.csv rename to data/antimicrobials.csv diff --git a/microbiology_sample_181019.csv b/data/microbiology.csv similarity index 100% rename from microbiology_sample_181019.csv rename to data/microbiology.csv diff --git a/global.R b/global.R index cb7cce9..d596b8c 100644 --- a/global.R +++ b/global.R @@ -10,9 +10,9 @@ source('dependencies.R') # 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("admissions.csv") +antimicrobials <- read_csv("antimicrobials.csv") +microbiology <- read_csv("microbiology.csv") admissions <- admissions %>% mutate(year = year(adm_start_date), From 9dcfe3894540844f1d41e21a50c505fec4f7a93a Mon Sep 17 00:00:00 2001 From: Bram Gadeyne Date: Mon, 13 May 2019 14:26:27 +0200 Subject: [PATCH 4/5] add .Rhistory to gitignore --- .gitignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index b86a353..dfb998c 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ /.Rproj.user/ -*.Rproj \ No newline at end of file +*.Rproj +.Rhistory \ No newline at end of file From 4e5bfa304b9e61da1785d485a16f231a715c2f71 Mon Sep 17 00:00:00 2001 From: Bram Gadeyne Date: Mon, 13 May 2019 14:27:48 +0200 Subject: [PATCH 5/5] load dependencies only in shiny app (not after install) --- dependencies.R | 5 +---- global.R | 8 +++++--- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/dependencies.R b/dependencies.R index 1b77cd6..726382e 100644 --- a/dependencies.R +++ b/dependencies.R @@ -28,7 +28,4 @@ new.packages <- required_packages[!(required_packages %in% installed.packages()[ if (length(new.packages)) { install.packages(new.packages) -} - -# load all packages -lapply(required_packages, require, character.only = TRUE) \ No newline at end of file +} \ No newline at end of file diff --git a/global.R b/global.R index d596b8c..be91f04 100644 --- a/global.R +++ b/global.R @@ -7,12 +7,14 @@ # INSTALL DEPENDENCIES ---------------------------------------------------- source('dependencies.R') +# load all packages +lapply(required_packages, require, character.only = TRUE) # DATA TRANSFORMATION AND NEW VARIABLES ----------------------------------- -admissions <- read_csv("admissions.csv") -antimicrobials <- read_csv("antimicrobials.csv") -microbiology <- read_csv("microbiology.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),