pushing changes from fork to branch

Author: faaiz-25

.DS_Store

@@ -4,6 +4,7 @@
 # Dependencies: main_jan21.R output
 #########################################################################################
 
+library(rgdal)
 library(dplyr)
 library(ggplot2)
 library(tidyverse)
@@ -28,9 +29,6 @@ library(plotly)
 library(htmlwidgets)
 library(leaflet.minicharts)
 library(leaflet)
-library(sf)
-library(sp)
-library(st)
 
 #############################################
 # DSPT curated file
@@ -52,45 +50,45 @@ data$Short.Status = factor(data$Status,dsptlevels)
 
 ## Load STP shapefile
 # Source: https://geoportal.statistics.gov.uk/datasets/clinical-commissioning-groups-april-2020-full-clipped-boundaries-en/explore?location=52.950000%2C-2.000000%2C7.02
-stp_spdf <- read_sf("/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/Inputs/shapefile/STP_APR_2021_EN_BUC_V2.shp")
+stp_spdf <- readOGR("/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/Inputs/shapefile/STP_APR_2021_EN_BUC_V2.shp")
 
-#proj4string(stp_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
+proj4string(stp_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
 
-#stp_spdf@proj4string # check system
+stp_spdf@proj4string # check system
 
-stp_spdf <- stp_spdf %>% st_transform(CRS("+init=epsg:4326")) # reproject to latlong system
+stp_spdf <- stp_spdf %>% sp::spTransform(CRS("+init=epsg:4326")) # reproject to latlong system
 
-stp_data = stp_spdf
+stp_data = stp_spdf@data
 #############################################
 # CCG shapefile
 #############################################
 
 ## Load CCG shapefile
 
-ccg_spdf <- read_sf("/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/Inputs/shapefile/CCG_APR_2021_EN_BFC.shp")
+ccg_spdf <- readOGR("/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/Inputs/shapefile/CCG_APR_2021_EN_BFC.shp")
 
-#proj4string(ccg_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
+proj4string(ccg_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
 
-#ccg_spdf@proj4string # check system
+ccg_spdf@proj4string # check system
 
-ccg_spdf <- ccg_spdf %>% st_transform(CRS("+init=epsg:4326")) # reproject to latlong system
+ccg_spdf <- ccg_spdf %>% sp::spTransform(CRS("+init=epsg:4326")) # reproject to latlong system
 
 # Write to shapefile
 #writeOGR(ccg_spdf, layer = 'myshp_simplified', 'C:/temp', driver="ESRI Shapefile")
 
-region_spdf = read_sf('/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/Inputs/shapefile/NHS_England_Regions_(April_2020)_Boundaries_EN_BUC.shp')
-#proj4string(region_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
+region_spdf = readOGR('/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/Inputs/shapefile/NHS_England_Regions_(April_2020)_Boundaries_EN_BUC.shp')
+proj4string(region_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
 
-#region_spdf@proj4string # check system
+region_spdf@proj4string # check system
 
-region_spdf <- region_spdf %>% st_transform(CRS("+init=epsg:4326")) # reproject to latlong system
+region_spdf <- region_spdf %>% sp::spTransform(CRS("+init=epsg:4326")) # reproject to latlong system
 
 region_full <- region_spdf
 
-#region_s <- rgeos::gSimplify(region_full,tol=0.01, topologyPreserve=FALSE)
+region_s <- rgeos::gSimplify(region_full,tol=0.01, topologyPreserve=FALSE)
 
 # Create a spatial polygon data frame (includes shp attributes)
-#regions_spdf = SpatialPolygonsDataFrame(region_full, data.frame(region_full))
+regions_spdf = SpatialPolygonsDataFrame(region_s, data.frame(region_full))
 
 
 
@@ -131,15 +129,15 @@ regions_lookup = read.csv('/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-
 data_regions = unique(select(regions_lookup, 'STP21CD', 'STP21NM', 'NHSER21NM'))
 
 # Join the reduced DSPT info with the CCG shapefile
-ccg_spdf <- left_join(ccg_spdf,data_merged,by=c("CCG21CD"="CCG21CD"))
-data_ccg_spdf <- ccg_spdf
+ccg_spdf@data <- left_join(ccg_spdf@data,data_merged,by=c("CCG21CD"="CCG21CD"))
+data_ccg_spdf <- ccg_spdf@data
 
 
 #merge and assign to stp_spdf data
-stp_spdfdata = stp_spdf
+stp_spdfdata = stp_spdf@data
 stp_spdfdata = merge(stp_spdfdata, select(data_regions, 'STP21CD', 'NHSER21NM'), by = "STP21CD", all = TRUE)
 #stp_spdfdata = na.omit(stp_spdfdata)
-stp_spdf = stp_spdfdata
+stp_spdf@data = stp_spdfdata
 
 
 
@@ -157,18 +155,18 @@ catpal <- colorFactor(my_palette, dsptlevels,reverse=F,ordered=T)
 ## Plotting
 # Prepare the text for tooltips:
 mytext <- paste(
-  "<b>SUB-ICB 2022 code (ODS): </b>", ccg_spdf$ICB22CD, "<br/>",
-  "<b>SUB-ICB 2022 name: </b>", ccg_spdf$LOC22NM,"<br/>",
-  "<b>2021 STP name: </b>", ccg_spdf$STP21NM,"<br/>",
-  "<b>Region name: </b>", ccg_spdf$NHSER22NM,"<br/>",
-  "<b>DSPT Status: </b>", ccg_spdf$Short.Status, "<br/>",
+  "<b>SUB-ICB 2022 code (ODS): </b>", ccg_spdf@data$ICB22CD,"<br/>",
+  "<b>SUB-ICB 2022 name: </b>", ccg_spdf@data$LOC22NM,"<br/>",
+  "<b>2021 STP name: </b>", ccg_spdf@data$STP21NM,"<br/>",
+  "<b>Region name: </b>", ccg_spdf@data$NHSER22NM,"<br/>",
+  "<b>DSPT Status: </b>", ccg_spdf@data$Short.Status, "<br/>",
   sep="") %>%
   lapply(htmltools::HTML)
 
 mytext_ics <- paste(
-  "<b>ICS/STP 2021 code: </b>", stp_spdf$STP21CD,"<br/>",
-  "<b>ICS/STP 2021 name: </b>", stp_spdf$STP21NM,"<br/>",
-  "<b>Region name: </b>", stp_spdf$NHSER21NM,"<br/>",
+  "<b>ICS/STP 2021 code: </b>", stp_spdf@data$STP21CD,"<br/>",
+  "<b>ICS/STP 2021 name: </b>", stp_spdf@data$STP21NM,"<br/>",
+  "<b>Region name: </b>", stp_spdf@data$NHSER21NM,"<br/>",
   sep="") %>%
   lapply(htmltools::HTML)
 
@@ -196,7 +194,7 @@ m<-leaflet(ccg_spdf) %>%
   ) %>%
   addLegend( pal=catpal, values=~Status, opacity=0.9, title = "21/22 DSPT Status (CCG)", position = "bottomleft" )
 
-m
+#m
 
 #############################################
 # Mapping - CCGS + ICS layer
@@ -250,11 +248,11 @@ m02_l <- m02 %>% addLegend( data=ccg_spdf,pal=catpal, values=~Short.Status, opac
 get_popup_content <- function(my_spdf) {
   paste0(
     "<b>Provider </b>",
-    "<br><b>- Provider code</b>:", my_spdf$ODS.Code,
-    "<br><b>- Provider name:</b> ", my_spdf$ODS.Org.Name,
-    #"<br><b>- STP/ICS (HQ postcode-based):</b> ", my_spdf$STP20NM,
-    #"<br><b>- Region:</b> ", my_spdf$`NHSER20NM`,
-    "<br><b>- DSPT status:</b> ", my_spdf$Status,
+    "<br><b>- Provider code</b>:", my_spdf@data$ODS.Code,
+    "<br><b>- Provider name:</b> ", my_spdf@data$ODS.Org.Name,
+    #"<br><b>- STP/ICS (HQ postcode-based):</b> ", my_spdf@data$STP20NM,
+    #"<br><b>- Region:</b> ", my_spdf@data$`NHSER20NM`,
+    "<br><b>- DSPT status:</b> ", my_spdf@data$Status,
     sep="" 
   )
 }
@@ -379,8 +377,8 @@ data_metric_ICS <- data_metric_ICS %>% mutate(metric_CCG_simple = Simple.Score_C
 
 
 
-stp_spdf <- stp_spdf %>% left_join(data_metric_ICS,by=c("STP21CD"="STP21CD"))
-stp_data = stp_spdf
+stp_spdf@data <- stp_spdf@data %>% left_join(data_metric_ICS,by=c("STP21CD"="STP21CD"))
+stp_data = stp_spdf@data
 
 
 # Create a continuous palette function
@@ -393,20 +391,20 @@ pal_metric <- colorNumeric(
 
 #create the label text for the first composite map
 mytext_ics_score <- paste(
-  "<b>STP code (ODS): </b>", stp_spdf$STP21CD,"<br/>",
-  "<b>STP name (ODS): </b>", stp_spdf$STP21NM,"<br/>",
-  "<b>ICS score (CCG+Trust simple), range [-3,3]: </b>",round(stp_spdf$metric_CCGp_Trusts.x,2),"<br/>",
+  "<b>STP code (ODS): </b>", stp_spdf@data$STP21CD,"<br/>",
+  "<b>STP name (ODS): </b>", stp_spdf@data$STP21NM,"<br/>",
+  "<b>ICS score (CCG+Trust simple), range [-3,3]: </b>",round(stp_spdf@data$metric_CCGp_Trusts,2),"<br/>",
   sep="") %>%
   lapply(htmltools::HTML)
 
 
 
 #create the label text to display the stp info for each polygon
 mytext_new <- paste(
-  "<b>STP code (ODS): </b>", stp_spdf$STP21CD,"<br/>",
-  "<b>STP name (ODS): </b>", stp_spdf$STP21NM,"<br/>",
-  "<b>Region: </b>", stp_spdf$NHSER21NM,"<br/>",
-  "<b>ICS score (CCG population + Trust simple), range [-3,3]: </b>",round(stp_spdf$metric_CCGp_Trusts,2),"<br/>",
+  "<b>STP code (ODS): </b>", stp_spdf@data$STP21CD,"<br/>",
+  "<b>STP name (ODS): </b>", stp_spdf@data$STP21NM,"<br/>",
+  "<b>Region: </b>", stp_spdf@data$NHSER21NM,"<br/>",
+  "<b>ICS score (CCG population + Trust simple), range [-3,3]: </b>",round(stp_spdf@data$metric_CCGp_Trusts,2),"<br/>",
   sep="") %>%
   lapply(htmltools::HTML)
 
@@ -419,7 +417,7 @@ m04 = leaflet() %>%
   addMapPane(name = "ICS polygons", zIndex = 400) %>%
   addMapPane(name = "ICS Labels", zIndex = 450) %>%
   addPolygons(
-    data=region_spdf,
+    data=regions_spdf,
     group="Region boundary",
     fillOpacity=0,
     color='blue',
@@ -453,52 +451,51 @@ m04
 # Mapping the composite ICS for CCG(population weighted) and Trusts (Weighted for EPRR risk)
 ##############################################################################################
 
-# #create new map labels to contain the dspt metric and stp region info
-# mytext_new <- paste(
-#   "<b>STP code (ODS): </b>", stp_spdf$stp20cd,"<br/>",
-#   "<b>STP name (ODS): </b>", stp_spdf$stp20nm,"<br/>",
-#   "<b>Region: </b>", stp_spdf$NHSER20NM.y,"<br/>",
-#   "<b>ICS score (CCG+Trust simple), range [-3,3]: </b>",round(stp_spdf$metric_CCGp_Trusts_EPRR.x,2),"<br/>",
-#   sep="") %>%
-#   lapply(htmltools::HTML)
-# 
-# 
-# 
-# m05 = leaflet() %>%
-#   addMapPane(name = "regionBorder", zIndex = 425) %>%
-#   addMapPane(name = "ICS polygons", zIndex = 400) %>%
-#   addMapPane(name = "ICS Labels", zIndex = 450) %>%
-#   addMapPane(name = "Minicharts", zIndex = 435) %>%
-#   addPolygons(
-#     data=region_spdf,
-#     group="Region boundary",
-#     fillOpacity=0,
-#     color='blue',
-#     weight=5,
-#     options = leafletOptions(pane = "regionBorder")
-#   ) %>%
-#   addTiles()  %>% 
-#   setView( lat=53, lng=-2 , zoom=6) %>%
-#   addPolygons(
-#     data=stp_spdf,
-#     group="ICS",
-#     fillOpacity=1,
-#     fillColor=~pal_metric(metric_CCGp_Trusts_EPRR),
-#     color="black",
-#     weight=1,
-#     options = leafletOptions(pane = "ICS polygons")) %>%
-#   addPolygons(
-#     data=stp_spdf,
-#     group="ICS",
-#     fillOpacity=0,
-#     fillColor=~pal_metric(metric_CCGp_Trusts_EPRR),
-#     color="black",
-#     weight= 0,
-#     options = leafletOptions(pane = "ICS Labels"),
-#     label = mytext_new ) %>%
-#   addLegend("bottomright",pal=pal_metric,values=-3:3,title="ICS score - CCG Population/Trust EPRR")
-# 
-# m05
+#create new map labels to contain the dspt metric and stp region info
+mytext_new <- paste(
+  "<b>STP code (ODS): </b>", stp_spdf@data$stp20cd,"<br/>",
+  "<b>STP name (ODS): </b>", stp_spdf@data$stp20nm,"<br/>",
+  "<b>Region: </b>", stp_spdf@data$NHSER20NM.y,"<br/>",
+  "<b>ICS score (CCG+Trust simple), range [-3,3]: </b>",round(stp_spdf@data$metric_CCGp_Trusts_EPRR,2),"<br/>",
+  sep="") %>%
+  lapply(htmltools::HTML)
+
+
+m05 = leaflet() %>%
+  addMapPane(name = "regionBorder", zIndex = 425) %>%
+  addMapPane(name = "ICS polygons", zIndex = 400) %>%
+  addMapPane(name = "ICS Labels", zIndex = 450) %>%
+  addMapPane(name = "Minicharts", zIndex = 435) %>%
+  addPolygons(
+    data=regions_spdf,
+    group="Region boundary",
+    fillOpacity=0,
+    color='blue',
+    weight=5,
+    options = leafletOptions(pane = "regionBorder")
+  ) %>%
+  addTiles()  %>% 
+  setView( lat=53, lng=-2 , zoom=6) %>%
+  addPolygons(
+    data=stp_spdf,
+    group="ICS",
+    fillOpacity=1,
+    fillColor=~pal_metric(metric_CCGp_Trusts_EPRR),
+    color="black",
+    weight=1,
+    options = leafletOptions(pane = "ICS polygons")) %>%
+  addPolygons(
+    data=stp_spdf,
+    group="ICS",
+    fillOpacity=0,
+    fillColor=~pal_metric(metric_CCGp_Trusts_EPRR),
+    color="black",
+    weight= 0,
+    options = leafletOptions(pane = "ICS Labels"),
+    label = mytext_new ) %>%
+  addLegend("bottomright",pal=pal_metric,values=-3:3,title="ICS score - CCG Population/Trust EPRR")
+
+m05
 
 
 
@@ -537,14 +534,13 @@ stp_filter_numpatients <- gppopdata %>% filter(SEX=="ALL",AGE=="ALL",ORG_TYPE=="
 #stp_filter_numpatients <- stp_filter_numpatients[c("STP21CD", "NUMBER_OF_PATIENTS")]
 #stp_filter_numpatients <- unique(stp_filter_numpatients)
 #merge together the separated dspt data with the gp population data and stp spatial data frame for mapping
-data_trust_spdf_pie = left_join(x = stp_spdf, y = data_trusts_aggregate, by = "STP21CD")
+data_trust_spdf_pie = left_join(x = stp_spdf@data, y = data_trusts_aggregate, by = "STP21CD")
 #data_trust_spdf_pie = merge(x = data_trust_spdf_pie, y = stp_filter_numpatients, by = "STP21CD")
 data_trust_spdf_pie[41, 7] = 51.0
 data_trust_spdf_pie[41, 6] = 0.0
 
 #create the map with the ICS boundaries displayed in black
 
-class(data_trust_spdf_pie) = 'data.frame'
 m06 <- leaflet() %>%
   addTiles %>%
   addPolygons(
@@ -577,7 +573,7 @@ m06
 gppopdata_blue <- gppopdata %>% filter(SEX=="ALL",AGE=="ALL",ORG_TYPE=="ICB") %>% select(c("ONS_CODE","NUMBER_OF_PATIENTS"))
 gppopdata_blue <- gppopdata_blue %>% rename("STP21CD" = 1)
 
-stp_spdfdata <- stp_spdf
+stp_spdfdata <- stp_spdf@data
 
 stp_spdfdata1 = merge(stp_spdfdata, gppopdata_blue, by = "STP21CD")