radar2 init

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+*.Rproj
+.DS_Store

global.R

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+# WELCOME TO RadaR
+
+#RadaR is licensed under the GNU General Public License (GPL) v2.0 (https://github.com/ceefluz/radar/blob/master/LICENSE)
+
+# LIST OF REQUIRED PACKAGES -----------------------------------------------
+library(shiny)
+library(shinydashboard)
+library(shinydashboardPlus)
+library(dashboardthemes)
+library(shinyWidgets)
+library(shinycssloaders)
+library(shinyjs)
+library(DT)
+library(tidyverse)
+library(ggtext)
+library(AMR)
+library(cleaner)
+library(scales)
+library(ggiraph)
+
+specialties <- read_csv("specialties.csv")
+
+specialties <- specialties %>% 
+  mutate(specialty_shiny = if_else(specialty != "Outpatients", paste0(specialty, " (", str_replace_all(specialism, ";", ", "), ")"), "Outpatients"),
+         department = if_else(is.na(department), "NO DEPARTMENT GIVEN", department))
+  
+specialties <- separate_rows(specialties, specialism, sep = ";")
+
+specialties <- separate_rows(specialties, department, sep = ";")
+
+pathogens <- read_csv("grouping microorganisms.csv")
+
+radar_data <- readRDS("bk_2019.rds")
+
+radar_data <- radar_data %>% 
+  left_join(specialties) %>% 
+  mutate(specialty = if_else(is.na(specialty), "NO SPECIALTY GIVEN", specialty),
+         specialty_shiny = if_else(is.na(specialty_shiny), "NO SPECIALTY GIVEN", specialty_shiny),
+         name = mo_name(mo),
+         FLC = OXAC) %>% 
+  left_join(pathogens) 
+
+lab_ab <- c("CFCC", "CFCL", "CFOC", "CFSC", "CFTC", "COCL", "GEHI", "QUDA")
+
+radar_data <- radar_data %>%
+  select_at(vars(!contains(lab_ab))) %>% 
+  rename_if(is.rsi, function(x) ifelse(is.na(suppressWarnings(as.ab(x))),
+                                       x,
+                                       suppressWarnings(as.ab(x)))) %>% 
+  mutate(group_all = 1) # dummy variable to disable grouping
+
+radar_data <- radar_data %>% 
+  mutate(CRO = if_else(is.na(CRO) & !is.na(CTX), CTX, CRO))
+         
+
+radar_data_first <- radar_data %>% 
+  filter_first_isolate(col_patient_id = "patientid", episode_days = 365) %>% 
+  mutate(mo = as.mo(mo, Becker = TRUE))
+
+intrinsic_info <- intrinsic_resistant %>% 
+  mutate(mo = as.mo(microorganism), 
+         intrinsic_r = TRUE)
+
+
+download_box <- function(exportname, plot) {
+  downloadHandler(
+    filename = function() {
+      paste(exportname, Sys.Date(), ".png", sep = "")
+    },
+    content = function(file) {
+      ggsave(file, plot = plot, device = "png", width = 8)
+    }
+  )
+}

grouping microorganisms.csv

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+name,pathogen_group
+Coagulase-negative Staphylococcus (CoNS),2
+Escherichia coli,1
+Staphylococcus aureus,1
+Enterococcus faecium,1
+Klebsiella pneumoniae,1
+Enterococcus faecalis,1
+Pseudomonas aeruginosa,1
+Streptococcus pneumoniae,1
+Streptococcus mitis,1
+Enterobacter cloacae,1
+Micrococcus luteus,2
+Milleri Group Streptococcus (MGS),1
+Klebsiella oxytoca,1
+Bacteroides fragilis,1
+Serratia marcescens,1
+Klebsiella variicola,1
+Streptococcus agalactiae,1
+Streptococcus dysgalactiae,1
+Proteus mirabilis,1
+Candida glabrata,1
+Cutibacterium acnes,2
+Candida albicans,1
+Streptococcus salivarius,2
+Bacillus,3
+Haemophilus influenzae,1
+Streptococcus parasanguinis,1
+Aerococcus urinae,1
+Enterococcus casseliflavus,1
+Streptococcus pyogenes,1
+Citrobacter freundii,1
+Listeria monocytogenes,1
+Parvimonas micra,1
+Rothia mucilaginosa,2
+Bacillus cereus,3
+Bacteroides thetaiotaomicron,1
+Corynebacterium jeikeium,3
+Citrobacter koseri,1
+Gemella morbillorum,1
+(unknown Gram-positives),3
+Salmonella,1
+Salmonella enterica,1
+Veillonella,1
+Fusobacterium nucleatum,1
+Hafnia alvei,1
+Rothia dentocariosa,2
+Schaalia odontolytica,2
+Stenotrophomonas maltophilia,1
+Streptococcus lutetiensis,1
+Acinetobacter,1
+Acinetobacter lwoffii,1
+Aeromonas,1
+Alistipes onderdonkii,1
+Actinomyces oris,1
+Anaerococcus octavius,1
+Bacillus licheniformis,3
+Bacteroides ovatus,1
+Bacteroides vulgatus,1
+Brevibacterium,3
+Corynebacterium,3
+Eggerthella lenta,1
+Enterococcus avium,1
+Granulicatella adiacens,1
+Klebsiella aerogenes,1
+Lactobacillus gasseri,1
+Lactobacillus rhamnosus,1
+Morganella morganii,1
+Abiotrophia defectiva,1
+Achromatium,3
+Actinobaculum,2
+Aeromonas hydrophila,1
+Alloscardovia omnicolens,2
+Aliivibrio finisterrensis,2
+Actinomyces dentalis,2
+Anaerococcus,1
+Anaerococcus vaginalis,1
+Bacillus pumilus,3
+Bacteroides uniformis,1
+Bifidobacterium longum,2
+Butyrivibrio,2
+Cellulosimicrobium cellulans,2
+Campylobacter ureolyticus,1
+Capnocytophaga sputigena,1
+Corynebacterium afermentans,3
+Corynebacterium amycolatum,3
+Corynebacterium aurimucosum,3
+Corynebacterium mucifaciens,3
+Corynebacterium minutissimum,3
+Corynebacterium tuberculostearicum,3
+Corynebacterium urealyticum,3
+Cutibacterium avidum,2
+Eubacterium limosum,3
+Eikenella corrodens,1
+Enterobacillus,2
+(unknown Gram-negatives),2
+Helcococcus kunzii,1
+Kocuria,1
+Kocuria rhizophila,1
+Lachnoanaerobaculum orale,3
+Lactobacillus fermentum,2
+Lactobacillus plantarum,2
+Lactobacillus paracasei,2
+Lancefieldella parvula,2
+Micrococcus,2
+Moraxella atlantae,1
+Moraxella catarrhalis,1
+Moraxella osloensis,1
+Neisseria,2
+Neisseria subflava,2
+Odoribacter splanchnicus,1
+Pantoea agglomerans,2
+Pediococcus pentosaceus,1
+Paenibacillus,1
+Paenibacillus illinoisensis,1
+Parabacteroides distasonis,1
+Providencia rettgeri,1
+Prevotella melaninogenica,1
+Pseudomonas putida,1
+Rhodococcus hoagii,1
+Schaalia meyeri,1
+Schaalia turicensis,1
+Solobacterium moorei,2
+Staphylococcus,2
+Streptococcus equinus,1
+Streptococcus gallolyticus,1
+Streptococcus salivarius thermophilus,2
+Veillonella atypica,1
+Weissella,1
+Candida dubliniensis,1
+Candida nivariensis,1
+Candida parapsilosis,1
+Issatchenkia orientalis,1
+Kluyveromyces marxianus,2
+Meyerozyma guilliermondii,1

specialties.csv

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+specialty ,specialism,department 
+Abdominal surgery ,CHAB,A3VA;K4VA
+Cardiology,CARD,B1VA;B2VA;C1CC
+Cardiothoracic surgery ,CTCH,C2VA
+Children cardiology,KCAR,M2VA
+Children surgery ,CHKC,M1VA
+Children gastroenterology,KMDL,M1VA
+Children general/immunology/nephrology,KALG;KIRI;KMET;KNEF,M4VA;L1KV
+Children special,KALG;KIRI;KMET;KNEF,L1SC
+Children ICU,KICK,KICK
+Children onco/hematology,KOHE,M2VA
+Children Lung,KLOA,M4VA 
+Children neurology ,NEKI,M4VA
+Dermatology,D4VA,DERM
+Dialyses,,DIAL
+Ear-nose-throat ,KNOH,A1VA
+Opthalmology ,OOGH,A1VA
+Gastroenterology and hepatology general,MDLZ,C3VA
+Gastroenterology and hepatology transplantation,MDLT,C3VA
+Gynaecology,OGGY;OGGO,L4VA
+Hematology,IHEM;IHTR,E2VA;B4VA;D1VA
+Hepatobiliary surgery,CHHP,C4VA
+Infectious diseases  ,IINF,E1VA
+Intensive care,ICVO,ICV2;ICV3;ICV4
+Internal medicine general,IALG;IEND,E3VA;E4VA
+Internal medicine oncology,IONC,D2VA
+Lung diseases,LONG,D2VA;E4VA
+Neonatology,KICN,KICN
+Nephrology general,INEF,D4VA
+Nephrology transplant,INTR,D4VA
+Neurology,NEAL,K2VA
+Neurosurgery,NCHI,K1VA;NEUC
+Obstetrics,OGVK,K3VA;L3VA
+Oncologic surgery,CHON,A3VA;K4VA
+Orthopedic surgery,ORTH,A2VA
+Plastic surgery,PLCH,A2VA
+Psychiatry,PSYC,
+Rheumatology,REUM,D3VA
+Trauma surgery,CHTR,J2VA
+Urology,UROL,L4VA
+Vascular surgery,CHVA,C4VA
+Other ,CRLR;CRRE;IACZ;MKKA,
+Outpatients,BUCK;CAR;CCC;CCCB;CHVA;CTSC;DBL1;DER;DIAB;DIAL;ECHO;ENDO;EPBA;HCK;IEND;IHEM;INEF;INT;IONC;KALG;KCAR;KDWE;KIND;KMDL;KMET;KNO;KOHE;LON;MDL;MKA;MRI;NEU;NEUC;ODOK;OGVK;ONC1;ORTH;PET;PRIK;PSS2;REKI;RTH;RTPR;THOR;TRPL;UCO;URO;VAAT;ZAAR,

ui.R

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+
+
+ui <- dashboardPagePlus(
+  title = "RadaR",
+  skin = "black", collapse_sidebar = TRUE, sidebar_background = "light", 
+  # HEADER ------------------------------------------------------------------
+  
+  dashboardHeader(
+    title = span(img(src = "radar.png", height = 30), strong("RadaR 2.0")),
+    titleWidth = 500,
+    
+    tags$li(
+      a(
+        strong("About RadaR"),
+        height = 40,
+        href = "https://www.jmir.org/2019/6/e12843/",
+        title = "",
+        target = "_blank"
+      ),
+      class = "dropdown",
+    )
+  ),
+  
+  # SIDEBAR -----------------------------------------------------------------
+  
+  dashboardSidebar(disable = TRUE,
+                   sidebarMenu(id = "sidebar_id",
+                               menuItem(icon = icon("check-square"),
+                                        materialSwitch(
+                                          inputId = "allInput",
+                                          label = "All specialties selected", 
+                                          value = TRUE, 
+                                          status = "danger")),
+                     menuItem(icon = icon("user-nurse"), 
+                              checkboxGroupInput(inputId = "specialtyInput", 
+                                                 label = "Select specialties", 
+                                                 choices = sort(unique(radar_data$specialty_shiny)))),
+                     menuItem(icon = icon("hospital"),
+                              checkboxGroupInput(inputId = "departmentInput", 
+                                                 label = "Select departments" ,
+                                                 choices = sort(unique(radar_data$department))))
+                     )
+                   ),
+  
+  
+  # BODY --------------------------------------------------------------------
+  
+  dashboardBody(
+    
+    # fluidRow(
+    #   column = 12,
+    # infoBoxOutput(outputId = "no_tests", width = 4),
+    # infoBoxOutput(outputId = "no_pos", width = 4),
+    # infoBoxOutput(outputId = "top_mo", width = 4)
+    # ),
+    # br(),
+    fluidRow(
+      tags$style(
+      ".nav-tabs {background-color: white;}
+      .nav-tabs-custom .nav-tabs li.active:hover a, .nav-tabs-custom .nav-tabs li.active a {background-color: transparent; border-color: transparent;}
+      .nav-tabs-custom .nav-tabs li.active {border-top-color: black;}"),
+      div(
+        id = "resistance", 
+        column(
+          width = 6,
+          uiOutput("box2")
+
+        ),
+        column(
+          width = 6,
+          uiOutput("box1")
+        ),
+        column(
+          width = 6,
+          uiOutput("box3")
+        ),
+        column(
+          width = 6,
+          uiOutput("box4")
+        )
+      )
+    )
+  )
+)

www/radar.svg

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+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 25.0.0, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 viewBox="0 0 24 24" style="enable-background:new 0 0 24 24;" xml:space="preserve">
+<style type="text/css">
+	.st0{fill:none;}
+	.st1{fill:#231F20;}
+</style>
+<path class="st0" d="M0,0h24v24H0V0z"/>
+<path class="st1" d="M19.1,4.9l-1.4,1.4C19.1,7.8,20,9.8,20,12c0,4.4-3.6,8-8,8s-8-3.6-8-8c0-4.1,3.1-7.4,7-7.9v2C8.2,6.6,6,9,6,12
+	c0,3.3,2.7,6,6,6s6-2.7,6-6c0-1.7-0.7-3.2-1.8-4.2l-1.4,1.4C15.6,9.9,16,10.9,16,12c0,2.2-1.8,4-4,4s-4-1.8-4-4c0-1.9,1.3-3.4,3-3.9
+	v2.1c-0.6,0.4-1,1-1,1.7c0,1.1,0.9,2,2,2s2-0.9,2-2c0-0.7-0.4-1.4-1-1.7V2h-1C6.5,2,2,6.5,2,12s4.5,10,10,10s10-4.5,10-10
+	C22,9.2,20.9,6.7,19.1,4.9z"/>
+</svg>

www/radar_style.css

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+.btn-success {
+    font-size: 18px;
+    font-family: inherit;
+    padding: 5px 12px;
+    height: 55px;
+    min-width: 21.85%;
+    margin: 0px 10px 14px 20px;
+    text-align: left;
+    color: white;
+    background: #727477;
+    text-indent: 4px;
+    vertical-align: middle;
+    border-radius: 0px;
+    border-color: transparent;
+    box-shadow: 0 2px 5px 0 rgba(0,0,0,0.18), 0 1px 5px 0 rgba(0,0,0,0.15);
+    text-transform: uppercase;
+    -webkit-transition: all 0.25s cubic-bezier(0.02, 0.01, 0.47, 1);
+    transition: all 0.25s cubic-bezier(0.02, 0.01, 0.47, 1);
+    -webkit-transform: translate3d(0, 0, 0);
+    transform: translate3d(0, 0, 0);
+}
+.btn-success:hover {
+    background-color:#d1351b;
+    font-size: 18px;
+    font-family: inherit;
+    padding: 5px 12px;
+    height: 55px;
+    min-width: 21.85%;
+    margin: 0px 10px 14px 20px;
+    text-align: left;
+    color: white;
+    text-indent: 4px;
+    vertical-align: middle;
+    border-radius: 0px;
+    border-color: transparent;
+    box-shadow: 0 5px 11px 0 rgba(0,0,0,0.18), 0 4px 15px 0 rgba(0,0,0,0.15);
+    -webkit-transition: box-shadow 0.4s ease-out;
+    transition: box-shadow 0.4s ease-out;
+}
+.btn-warning, .btn-warning:hover {
+    font-size: 18px;
+    font-family: inherit;
+    padding: 5px 12px;
+    height: 55px;
+    min-width: 21.85%;
+    margin: 0px 10px 14px 20px;
+    text-align: left;
+    color: white;
+    background: #d1351b;
+    text-indent: 4px;
+    vertical-align: middle;
+    border-radius: 0px;
+    border-color: transparent;
+    box-shadow: 0 2px 5px 0 rgba(0,0,0,0.18), 0 1px 5px 0 rgba(0,0,0,0.15);
+    text-transform: uppercase;
+    -webkit-transition: all 0.25s cubic-bezier(0.02, 0.01, 0.47, 1);
+    transition: all 0.25s cubic-bezier(0.02, 0.01, 0.47, 1);
+    -webkit-transform: translate3d(0, 0, 0);
+    transform: translate3d(0, 0, 0);
+}
+.fa {
+    margin-right: 10px;
+}
+.fa.fa-gear.opt {
+    margin-right: 0px;
+}
+.fa.fa-search-plus.opt {
+    margin-right: 0px
+}
+#intro {
+    margin-bottom: 0;
+    align-items: center;
+    display: block;
+    margin: 0 auto;
+    background: #d1351b;
+    color: white;
+    min-width: 25%;
+    border-color: white
+}
+#sidebar_button {
+    height: 55px;
+}
+section.sidebar .shiny-bound-input.action-button, section.sidebar .shiny-bound-input.action-link {
+    margin: auto;
+    display: block;
+}
+.btn-danger {
+    background-color: #d1351b;
+    border-color: #d1351b;
+    height: 55px;
+    width: 300px;
+    border-radius: 0;
+    position: relative;
+    font-size: 18px;
+}
+.btn-primary {
+    background-color: darkgrey;
+    border-color: darkgrey;
+    color: white;
+    height: 55px;
+    width: 300px;
+    border-radius: 0;
+    position: relative;
+    font-size: 18px;
+}
+.btn-primary:hover {
+    background-color: #d1351b;
+    border-color: #d1351b;
+    color: white;
+    border-color: #d1351b;
+
+}
+.fa.fa-user, .fa.fa-thumbs-o-up, .fa.fa-flask.flask-box, .fa.fa-spinner.spinner-box {
+    color: white;
+    font-size: 20;
+    margin-right: 10px;
+    font-size: 30px;
+    vertical-align: middle;
+}
+
+.skin-black .treeview-menu > li > a {
+    color: white;
+    white-space: pre-line;
+}
+.skin-black .treeview-menu > li:hover > a {
+    color: white;
+    white-space: pre-line;
+    background-color:#606164;;
+}
+
+
+ .info-box {
+     min-height:55px;
+     float:center;
+     box-shadow:5px 5px 5px lightgrey;
+     border-bottom: 0px;
+ }
+}
+ .info-box-icon.bg-black {
+     height:55px; 
+}
+.bg-black {
+    background-color: #727477 !important;
+    height: 55px;
+    line-height:55px;
+
+}
+.text-success {
+    color: #d1351b;
+    font-size: large;
+
+}
+ .skin-black .main-header .navbar {
+     background-color:#d1351b 
+}
+ .skin-black .main-header .navbar .nav > li > a {
+     color:#fff 
+}
+ .skin-black .main-header .navbar .nav > li > a:hover {
+     background:#ffffff;
+     color:#d1351b 
+}
+ .skin-black .main-header .navbar .sidebar-toggle {
+     color:#ffffff 
+}
+ .skin-black .main-header .navbar .sidebar-toggle:hover {
+     color:#d1351b;
+     background:#fff 
+}
+ .skin-black .main-header .navbar .navbar-custom-menu .navbar-nav > li > a, .skin-black .main-header .navbar .navbar-right > li > a {
+     border-left:1px solid #d1351b;
+     border-right-width:0 
+}
+ .main-header .logo {
+     font-family:"Helvetica Neue", sans-serif ;
+     font-weight:bold;
+     letter-spacing:-1px; 
+     font-size:30px; 
+     color:#ffffff;
+}
+ .modal-dialog{
+     max-width:1000px;
+     border-radius: 5px;
+     border: 2px solid white; 
+}
+ .modal-body{
+     max-height:700px;
+     align-content:center;
+     border: 2px solid white;
+     border-radius: 5px;
+}
+ .modal-sm {
+     max-width:1200px; 
+     align-content:center;
+     border-radius: 5px;
+     border: 2px solid white;
+}
+ .sidebar {
+     height:90vh;
+     overflow-y:auto 
+}
+ .skin-black .main-header > .logo {
+     background-color:#d1351b;
+     color:#ffffff;
+     border-bottom:0 solid transparent;
+     border-right:1px solid #d1351b;
+}
+ .skin-black .main-header > .logo:hover {
+     background-color:#d1351b 
+}
+ .nav-tabs-custom > .nav-tabs > li.active {
+     border-top-color:#616365 
+}
+ .nav-tabs-custom {
+     box-shadow:5px 5px 5px lightgrey 
+}
+ .skin-black .left-side, .skin-black .main-sidebar, .skin-black .wrapper {
+     background-color:#727477;
+}
+ .skin-black .sidebar-menu > li.active > a, .skin-black .sidebar-menu > li:hover > a {
+     color:#fff;
+     background:#606164;
+     border-left-color:#d1351b;
+}
+ .skin-black .sidebar-menu > li > .treeview-menu {
+     margin:0 1px; 
+     background:#8a8c8f;
+     box-shadow:inset 0px 0px 7px #000000;
+     padding-bottom:2px 
+}
+ .skin-black .sidebar a {
+     color:#ffffff 
+}
+.navbar-nav > .messages-menu > .dropdown-menu, .navbar-nav > .notifications-menu > .dropdown-menu, .navbar-nav > .tasks-menu > .dropdown-menu {
+    width: 400px;
+    padding: 0;
+    margin: 10px;
+    top: 100%;
+    background-color: #fefefee6;
+    box-shadow: 10px 10px 10px darkgrey;
+}
+.navbar-nav > .messages-menu > .dropdown-menu > li.header, .navbar-nav > .notifications-menu > .dropdown-menu > li.header, .navbar-nav > .tasks-menu > .dropdown-menu > li.header {
+    border-top-left-radius: 0px;
+    border-top-right-radius: 0px;
+    border-bottom-right-radius: 0;
+    border-bottom-left-radius: 0;
+    background-color: #d1351b;
+    padding: 7px 10px;
+    border-bottom: 1px solid #d1351be6;
+    color: #ffffff;
+    font-size: 14px;
+}
+.navbar-nav > .messages-menu > .dropdown-menu > li .menu, .navbar-nav > .notifications-menu > .dropdown-menu > li .menu, .navbar-nav > .tasks-menu > .dropdown-menu > li .menu {
+    max-height: 1200px;
+    margin: 0;
+    padding: 0;
+    list-style: none;
+    overflow-x: hidden;
+}
+.navbar-nav > .notifications-menu > .dropdown-menu > li .menu > li > a {
+    color: #000000;
+    overflow: hidden;
+    white-space: normal;
+}
+ #coxreg {
+     overflow-y: auto;
+     max-height: 200px;
+     background-color: lightgrey;
+     box-shadow: inset 0px -5px 5px darkgrey 
+}
+ #coxreg_aic {
+     background-color: lightgrey 
+}
+ #logreg {
+     overflow-y: auto;
+     max-height: 200px;
+     background-color: lightgrey;
+     box-shadow: inset 0px -5px 5px darkgrey 
+}
+ #logreg_aic {
+     background-color: lightgrey 
+}
+.shiny-output-error { 
+    visibility: hidden; 
+}
+.shiny-output-error:before { 
+    visibility: hidden; 
+}
+