Hospital Staying | healthyR

Introduction

In this post, I present a time series visualization of hospital stays using the R package healthyR, based on the SyntheaMass dataset.

Load data

suppressPackageStartupMessages(
  {
    library(healthyR)
    library(timetk)
    library(dplyr)
    library(purrr)
  }
)

# Get Length of Stay Data
data_tbl <- read.csv("/Users/nnthieu/SyntheaData/SyntheaCovid19/encounters.csv")
names(data_tbl)

##  [1] "Id"                  "START"               "STOP"               
##  [4] "PATIENT"             "ORGANIZATION"        "PROVIDER"           
##  [7] "PAYER"               "ENCOUNTERCLASS"      "CODE"               
## [10] "DESCRIPTION"         "BASE_ENCOUNTER_COST" "TOTAL_CLAIM_COST"   
## [13] "PAYER_COVERAGE"      "REASONCODE"          "REASONDESCRIPTION"

Prepare time series data

# create column named 'length_of_stay' by 'STOP' minus by 'START' 
df_tbl <- data_tbl |> filter(ENCOUNTERCLASS=="inpatient") |>
  mutate(
    length_of_stay = as.numeric(difftime(STOP, START, units = "days"))
  ) |> mutate(STOP = as.Date(STOP)) |>
  select(STOP, length_of_stay)

head(df_tbl)

##         STOP length_of_stay
## 1 2020-03-05             15
## 2 2019-10-27              1
## 3 2020-05-14              1
## 4 2010-12-18              1
## 5 2010-12-24              1
## 6 2019-07-07              1

df_tbl <- df_tbl |>
  summarise_by_time(
    .date_var = STOP,
    .by = "day",
    visits = mean(length_of_stay, na.rm = TRUE)
  ) |>
  filter_by_time(
    .date_var = STOP,
    .start_date = "2012",
    .end_date = "2019"
  ) |>
  set_names("Date", "Values")

head(df_tbl)

## # A tibble: 6 × 2
##   Date       Values
##   <date>      <dbl>
## 1 2012-01-01   1   
## 2 2012-01-02   1   
## 3 2012-01-03   1.33
## 4 2012-01-04   1   
## 5 2012-01-05   1   
## 6 2012-01-06   1.11

Time series plot

ts_alos_plt(
  .data = df_tbl
  , .date_col = Date
  , .value_col = Values
  , .by = "month"
  , .interactive = TRUE
)

Conclusion

As demonstrated above, the R package healthyR can be used to visualize hospital stays through time series plots.

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