updating file paths and BUC shapefile with updated map

created new map with BUC shapefile for 21/22 CCG trust map

02-geomapping-ICS.R

@@ -70,7 +70,7 @@ regions_spdf = SpatialPolygonsDataFrame(region_s, data.frame(region_full))
 
 ## 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 <- readOGR("/Users/muhammad-faaiz.shanawas/Documents/Live Projects/Cyber Map/Shapefiles/Sustainability_and_Transformation_Partnerships_(April_2020)_Boundaries_EN_BUC/Sustainability_and_Transformation_Partnerships_(April_2020)_Boundaries_EN_BUC.shp")
+stp_spdf <- readOGR("./Inputs/shapefiles/20_21/Sustainability_and_Transformation_Partnerships_(April_2020)_Boundaries_EN_BUC/Sustainability_and_Transformation_Partnerships_(April_2020)_Boundaries_EN_BUC.shp")
 
 proj4string(stp_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
 
@@ -85,7 +85,7 @@ stp_spdf <- stp_spdf %>% sp::spTransform(CRS("+init=epsg:4326")) # reproject to
 
 ## Load CCG 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
-ccg_spdf <- readOGR("./Inputs/shapefile/Clinical_Commissioning_Groups_(April_2020)_EN_BFC_V2.shp")
+ccg_spdf <- readOGR("./Inputs/shapefiles/20_21/Clinical_Commissioning_Groups_(April_2020)_EN_BFC_V2.shp")
 
 proj4string(ccg_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
 

02-geomapping-ICS_21_22.R

@@ -36,7 +36,7 @@ library(leaflet)
 
 
 ## Load 'curated' DSPT file
-data <- read.csv("/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/data/DSPT_CCG_21_22_snapshot09_09_22.csv")
+data <- read.csv("./data/DSPT Snapshots/21_22/DSPT_CCG_21_22_snapshot09_09_22.csv")
 data <- data[-107,]
 
 dsptlevels=c("21/22 Standards Exceeded","21/22 Standards Met","21/22 Approaching Standards","21/22 Standards Not Met","21/22 Not Published")
@@ -50,7 +50,7 @@ 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 <- readOGR("/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/Inputs/shapefile/STP_APR_2021_EN_BUC_V2.shp")
+stp_spdf <- readOGR("./Inputs/shapefiles/21_22/STP_APR_2021_EN_BUC_V2.shp")
 
 proj4string(stp_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
 
@@ -65,7 +65,7 @@ stp_data = stp_spdf@data
 
 ## Load CCG shapefile
 
-ccg_spdf <- readOGR("/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/Inputs/shapefile/CCG_APR_2021_EN_BFC.shp")
+ccg_spdf <- readOGR("./Inputs/shapefiles/21_22/CCG_APR_2021_EN_BUC.shp")
 
 proj4string(ccg_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
 
@@ -76,7 +76,7 @@ ccg_spdf <- ccg_spdf %>% sp::spTransform(CRS("+init=epsg:4326")) # reproject to
 # Write to shapefile
 #writeOGR(ccg_spdf, layer = 'myshp_simplified', 'C:/temp', driver="ESRI Shapefile")
 
-region_spdf = readOGR('/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/Inputs/shapefile/NHS_England_Regions_(April_2020)_Boundaries_EN_BUC.shp')
+region_spdf = readOGR('./Inputs/shapefiles/20_21/NHS_England_Regions_(April_2020)_Boundaries_EN_BUC.shp')
 proj4string(region_spdf) <- CRS("+init=epsg:27700")  # BNG projection system
 
 region_spdf@proj4string # check system
@@ -85,11 +85,11 @@ region_spdf <- region_spdf %>% sp::spTransform(CRS("+init=epsg:4326")) # reproje
 
 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_s, data.frame(region_full))
-
+###regions_spdf = SpatialPolygonsDataFrame(region_s, data.frame(region_full))
+regions_spdf = region_spdf
 
 
 ##Load correspondence from ODS to ONS codes
@@ -102,7 +102,7 @@ regions_spdf = SpatialPolygonsDataFrame(region_s, data.frame(region_full))
 # Create a points shapefile for Trusts
 ##########+
 ##########+###################################
-trusts_data = read.csv("/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/data/DSPT_trusts_21_22_snapshot09_09_22.csv")
+trusts_data = read.csv("./data/DSPT Snapshots/21_22/DSPT_trusts_21_22_snapshot09_09_22.csv")
 trusts_data <- subset(trusts_data, !(ODS.Code %in% c('RBZ', 'RW6', 'RTV')))
 
 
@@ -119,20 +119,19 @@ trust_spdf_points <- sp::SpatialPointsDataFrame(
 #Further prep
 #############################################
 # Join DSPT data and ONS code
-lookupdata = read.csv('/Users/muhammad-faaiz.shanawas/Documents/Github/open-cyber/data/Clinical_Commissioning_Group_to_STPs_(April_2021)_Lookup_in_England.csv')
+lookupdata = read.csv('./data/auxiliary/21_22/Clinical_Commissioning_Group_to_STPs_(April_2021)_Lookup_in_England.csv')
 data_merged = left_join(data, lookupdata, by = c("ODS.Code" = "CCG21CDH"))
 data_merged = data_merged[-107,]
 
 
 #load in ccg-stp-region lookup data
-regions_lookup = read.csv('/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/data/Clinical_Commissioning_Group_to_STP_and_NHS_England_(Region)_(April_2021)_Lookup_in_England.csv')
+regions_lookup = read.csv('./data/auxiliary/21_22/Clinical_Commissioning_Group_to_STP_and_NHS_England_(Region)_(April_2021)_Lookup_in_England.csv')
 data_regions = unique(select(regions_lookup, 'STP21CD', 'STP21NM', 'NHSER21NM'))
 
 # Join the reduced DSPT info with the CCG shapefile
 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@data
 stp_spdfdata = merge(stp_spdfdata, select(data_regions, 'STP21CD', 'NHSER21NM'), by = "STP21CD", all = TRUE)
@@ -293,7 +292,7 @@ m03
 
 # save the widget in a html file if needed.
 #library(htmlwidgets)
-saveWidget(m04, "ICS_composite_map1_21_22.html")
+saveWidget(m03, "outputs/ICS_composite_map1_21_22_vrun20231129.html")
 
 
 
@@ -302,12 +301,12 @@ saveWidget(m04, "ICS_composite_map1_21_22.html")
 # Summary metric
 #############################################
 #get the stp codes for trusts from etr
-etr = read.csv('/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/data/etr.csv', header = FALSE)
+etr = read.csv('./data/auxiliary/21_22/etr.csv', header = FALSE)
 etr = etr[,c('V1', 'V4')]
 etr = select(etr, 'ODS.Code' = 'V1', 'STP21CDH' = 'V4')
 
 #get the final 4 stp codes of the 4 care trusts from ect (modified to change column names and select relevant columns)
-ect = read.csv('/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/data/ect_modified_21_22.csv')
+ect = read.csv('./data/auxiliary/21_22/ect_modified_21_22.csv')
 ect = select(ect, 'ODS.Code', 'STP21CDH')
 
 etr_ect = rbind(etr, ect)
@@ -328,7 +327,7 @@ trusts_data_merged = left_join(trusts_data_merged, stp_codes)
 
 
 #load in ccg-stp-region lookup data
-regions_lookup = read.csv('/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/data/Clinical_Commissioning_Group_to_STP_and_NHS_England_(Region)_(April_2021)_Lookup_in_England.csv')
+regions_lookup = read.csv('./data/auxiliary/21_22/Clinical_Commissioning_Group_to_STP_and_NHS_England_(Region)_(April_2021)_Lookup_in_England.csv')
 data_regions = unique(select(regions_lookup, 'STP21CD', 'STP21NM', 'NHSER21NM'))
 
 trusts_data_merged = left_join(trusts_data_merged, data_regions)
@@ -621,7 +620,7 @@ m07
 #load in the snapshot data to create summary tables and charts
 ###############################################################
 #load in the snapshot data and filter for the 5 relevant CSUs
-data_snapshot = read.csv('/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/data/DSPT search results 09_09_2022 12_44_07.csv')
+data_snapshot = read.csv('./data/DSPT Snapshots/21_22/DSPT search results 09_09_2022 12_44_07.csv')
 data_summary = data_snapshot %>% select('Organisation.Name', 'Status', 'Primary.Sector')
 data_summary = data_summary %>% filter(Primary.Sector == "Commissioning Support Unit (CSU)")
 data_csu = data_summary %>% filter(str_detect(Organisation.Name, 'CSU'))
@@ -655,4 +654,4 @@ ct_final = ctable(data_s$Primary.Sector, data_s$Status,
                   prop = "r", chisq = FALSE, headings = FALSE
 )
 ct_final %>% print(method="browser")
-ct_final %>% print(file=paste0("/Users/muhammad-faaiz.shanawas/Documents/GitHub/open-cyber/cross_table_summary_21_22",Sys.Date(),".html"))
+ct_final %>% print(file=paste0("./outputs/cross_table_summary_21_22",Sys.Date(),".html"))

02-geomapping-ICS_22_23.R

@@ -98,7 +98,7 @@ trust_spdf_points <- sp::SpatialPointsDataFrame(
 #Further prep
 #############################################
 # Join DSPT data and ONS code
-lookupdata = read.csv('./data/aux/22_23/Sub_ICB_Locations_to_Integrated_Care_Boards_to_NHS_England_(Region)_(April_2023)_Lookup_in_England (1).csv')
+lookupdata = read.csv('./data/auxiliary/22_23/Sub_ICB_Locations_to_Integrated_Care_Boards_to_NHS_England_(Region)_(April_2023)_Lookup_in_England (1).csv')
 lookup_icb = lookupdata[!duplicated(lookupdata$ICB23CD), ]
 
 
@@ -363,4 +363,4 @@ m04
 
 # save the widget in a html file if needed.
 #library(htmlwidgets)
-saveWidget(m04, "./outputs/icb_composite_map_16_11_23.html")
+saveWidget(m04, "./outputs/icb_composite_map_16_11_23.html")

21_22.md

@@ -63,7 +63,7 @@ Summary statistics from the DSPT 2021/22 toolkit are shown.
 The compliance of individual CCGs and Trusts are mapped below, with ICS boundaries. Toggle the boxes on the top right-hand side to add layers.
 
 
-<iframe src="./outputs/ccg_trusts_map_03_10_22.html" height="600px" width="100%" style="border:none;"></iframe>
+<iframe src="./outputs/ccg_trusts_map_03_10_22_BUC.html" height="600px" width="100%" style="border:none;"></iframe>
 
 <hr class="nhsuk-u-margin-top-0 nhsuk-u-margin-bottom-6">