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rerun for BUC geomap #3

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rerun for BUC geomap #3

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23 changes: 11 additions & 12 deletions 02-geomapping-ICS_21_22.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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")
Expand All @@ -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

Expand All @@ -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

Expand All @@ -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
Expand All @@ -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
Expand All @@ -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')))


Expand All @@ -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)
Expand Down Expand Up @@ -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")



Expand Down
Binary file added data/DSPT Snapshots/20_21/DSPT Progress as of 17_06_2019 15_25_54 publish.xlsx
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