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vhaqualsafety.Rmd
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vhaqualsafety.Rmd
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---
title: "VHA Population Quality & Safety Report"
output:
flexdashboard::flex_dashboard:
orientation: rows
vertical_layout: scroll
---
```{r setup, include=FALSE}
library(flexdashboard)
# load vha data
vha <- read.csv("./Desktop/VHA_Facility_Quality_and_Safety_Report_Population_Quality_of_Care.csv", header = T, stringsAsFactors = F)
# load lat-long data of us cities
latlong <- read.csv("./Definitive Logic/flexdashboards/uscitiesv1.csv", header = T, stringsAsFactors = F)
```
Row
---
### VA Healthcare Centers with MH Inpatient Services
```{r}
library(dplyr)
mhipservices <- vha %>%
select(In.House.Services.Acute.Mental.Health) %>%
mutate(yesnum = ifelse(grepl("Yes", vha$In.House.Services.Acute.Mental.Health), 1, 0)) %>%
summarise(sumyes = sum(yesnum))
valueBox(mhipservices$sumyes, icon = "fa-bed", color = "goldenrod")
```
### VA Healthcare Centers without MH Inpatient Services
```{r}
library(dplyr)
mhipservices <- vha %>%
select(In.House.Services.Acute.Mental.Health) %>%
mutate(nonum = ifelse(grepl("No", vha$In.House.Services.Acute.Mental.Health), 1, 0)) %>%
summarise(sumno = sum(nonum))
valueBox(mhipservices$sumno, icon = "fa-ambulance", color = "olivedrab")
```
Row
---
### Map of VA Facilities
```{r}
library(dplyr)
ll <- latlong %>%
select(city, state_id, lat, lng) %>%
mutate(City = city, ST = state_id, cityST = paste0(city, state_id)) %>%
select(City, ST, cityST, lat, lng)
vamap <- vha %>%
select(City, ST, VISN.Name, Facility.Name, Station, Complexity,
In.House.Services.Acute.Mental.Health, In.House.Services.Acute.Med.Surg,
In.House.Services.Emergency.Dept, In.House.Services.Intensive.Care.Unit,
In.House.Services.Nursing.Home.Unit) %>%
mutate(cityST = paste0(City, ST)) %>%
filter(In.House.Services.Acute.Mental.Health == "Yes")
valatlng1 <- inner_join(vamap, ll, by="cityST") %>%
mutate(color = ifelse(Complexity == "1a", "orange",
ifelse(Complexity == "1b", "green",
ifelse(Complexity == "1c", "blue",
ifelse(Complexity == "2", "maroon", "black")))))
# Create a palette that maps factor levels to colors
library(leaflet)
leaflet() %>%
addTiles() %>%
addCircleMarkers(lat = valatlng1$lat,
lng = valatlng1$lng,
popup = paste("<b>Station:</b>", valatlng1$Station, "<br>",
"<b>VISN Name:</b>", valatlng1$VISN.Name, "<br>",
"<b>Facility Name:</b>", valatlng1$Facility.Name, "<br>",
"<b>City, State:</b>", valatlng1$City.x, valatlng1$ST.x, "<br>",
"<b>Complexity:</b>", valatlng1$Complexity, "<br>",
"<b>Inpatient MH Services:</b>", valatlng1$In.House.Services.Acute.Mental.Health, "<br>",
"<b>Inpatient Med/Surgical Services:</b>", valatlng1$In.House.Services.Acute.Med.Surg, "<br>",
"<b>Emergency Medicine Services:</b>", valatlng1$In.House.Services.Emergency.Dept, "<br>",
"<b>Intensive Care Unit Services:</b>", valatlng1$In.House.Services.Intensive.Care.Unit, "<br>",
"<b>Nursing Home Services:</b>", valatlng1$In.House.Services.Nursing.Home.Unit, "<br>"),
radius = ifelse(grepl("1a|1b|1c", valatlng1$Complexity), 10, 6),
color = valatlng1$color,
stroke = FALSE, fillOpacity = 0.5) %>%
addLegend(position = "bottomleft",
title = "Complexity",
labels = c("1a: High: Highest Complexity",
"1b: High: Second Highest Complexity",
"1c: High: Third Highest Complexity",
"2: Medium Complexity",
"3: Low Complexity"),
colors = c("orange", "green", "blue", "maroon", "black"))
```
### Map of VA Facilities
```{r}
ll <- latlong %>%
select(city, state_id, lat, lng) %>%
mutate(City = city, ST = state_id, cityST = paste0(city, state_id)) %>%
select(City, ST, cityST, lat, lng)
vamap <- vha %>%
select(City, ST, VISN.Name, Facility.Name, Station, Complexity,
In.House.Services.Acute.Mental.Health, In.House.Services.Acute.Med.Surg,
In.House.Services.Emergency.Dept, In.House.Services.Intensive.Care.Unit,
In.House.Services.Nursing.Home.Unit) %>%
mutate(cityST = paste0(City, ST)) %>%
filter(In.House.Services.Acute.Mental.Health == "No")
valatlng2 <- inner_join(vamap, ll, by="cityST") %>%
mutate(color = ifelse(Complexity == "1a", "orange",
ifelse(Complexity == "1b", "green",
ifelse(Complexity == "1c", "blue",
ifelse(Complexity == "2", "maroon", "black")))))
# Create a palette that maps factor levels to colors
library(leaflet)
leaflet() %>%
addTiles() %>%
addCircleMarkers(lat = valatlng2$lat,
lng = valatlng2$lng,
popup = paste("<b>Station:</b>", valatlng2$Station, "<br>",
"<b>VISN Name:</b>", valatlng2$VISN.Name, "<br>",
"<b>Facility Name:</b>", valatlng2$Facility.Name, "<br>",
"<b>City, State:</b>", valatlng2$City.x, valatlng2$ST.x, "<br>",
"<b>Complexity:</b>", valatlng2$Complexity, "<br>",
"<b>Inpatient MH Services:</b>", valatlng2$In.House.Services.Acute.Mental.Health, "<br>",
"<b>Inpatient Med/Surgical Services:</b>", valatlng2$In.House.Services.Acute.Med.Surg, "<br>",
"<b>Emergency Medicine Services:</b>", valatlng2$In.House.Services.Emergency.Dept, "<br>",
"<b>Intensive Care Unit Services:</b>", valatlng2$In.House.Services.Intensive.Care.Unit, "<br>",
"<b>Nursing Home Services:</b>", valatlng2$In.House.Services.Nursing.Home.Unit, "<br>"),
radius = ifelse(grepl("1a|1b|1c", valatlng2$Complexity), 10, 6),
color = valatlng2$color,
stroke = FALSE, fillOpacity = 0.5) %>%
addLegend(position = "bottomleft",
title = "Complexity",
labels = c("1a: High Complexity",
"1b: High Complexity",
"1c: High Complexity",
"2: Medium Complexity",
"3: Low Complexity"),
colors = c("orange", "green", "blue", "maroon", "black"))
```
Row
---
### Graphical Representation of Relationships
```{r}
library(igraph)
library(visNetwork)
library(dplyr)
n <- length(unique(valatlng1$VISN.Name))
g <- make_tree(n, children = 10) %>%
set_vertex_attr("group", value = valatlng1$VISN.Name, n)
visIgraph(g, idToLabel = TRUE)
V(g)$label <- valatlng1$Facility.Name
```
### Graphical Representation of Relationships
```{r}
library(igraph)
library(visNetwork)
library(dplyr)
n <- length(unique(valatlng2$VISN.Name))
g <- make_tree(n, children = 10) %>%
set_vertex_attr("group", value = valatlng2$VISN.Name, n)
visIgraph(g, idToLabel = TRUE)
V(g)$label <- valatlng2$Facility.Name
```