We are using a common dataset across the R and Python coding examples.

The code below reads in the csv file final_with_deceased.csv. It also calls the libraries we are going to use.

library(ggplot2)
library(dplyr)
library(tidyr)

mydata <- as.data.frame(read.csv("final_with_deceased.csv"))

The first step when working with a data file is an exploratory data analysis.


head(mydata, 5) # prints first five rows
tail(mydata, 5) # prints last five rows
sample_n(mydata, 5) # prints five randomly selected rows

print(dim(mydata)) # print number of columns and rows
[1] 156030     27
summary(mydata) # overview of each variable in the dataset
   person_id      birth_datetime     race_source_value  ethnicity_source_value gender_source_value visit_occurrence_id
 Min.   :     1   Length:156030      Length:156030      Length:156030          Length:156030       Min.   :      1    
 1st Qu.: 30962   Class :character   Class :character   Class :character       Class :character    1st Qu.: 782279    
 Median : 62112   Mode  :character   Mode  :character   Mode  :character       Mode  :character    Median :1566715    
 Mean   : 62078                                                                                    Mean   :1566862    
 3rd Qu.: 93254                                                                                    3rd Qu.:2358876    
 Max.   :124150                                                                                    Max.   :3139398    
                                                                                                                      
 visit_start_date   visit_end_date      visit_type         condition         observation_source age_at_visit_years
 Length:156030      Length:156030      Length:156030      Length:156030      Length:156030      Min.   :  0.01    
 Class :character   Class :character   Class :character   Class :character   Class :character   1st Qu.: 16.16    
 Mode  :character   Mode  :character   Mode  :character   Mode  :character   Mode  :character   Median : 36.07    
                                                                                                Mean   : 37.86    
                                                                                                3rd Qu.: 57.17    
                                                                                                Max.   :110.73    
                                                                                                                  
 measurement_Date   body_height_cm        bmi         body_temperature_c body_weight_kg      systolic       diastolic     
 Length:156030      Min.   : 50.6    Min.   :12.70    Min.   :36.1       Min.   :  1.80   Min.   : 97.0   Min.   : 67.00  
 Class :character   1st Qu.:159.7    1st Qu.:27.20    1st Qu.:38.5       1st Qu.: 66.80   1st Qu.:113.0   1st Qu.: 76.00  
 Mode  :character   Median :167.7    Median :28.00    Median :39.7       Median : 78.00   Median :120.0   Median : 80.00  
                    Mean   :163.1    Mean   :27.24    Mean   :39.7       Mean   : 73.22   Mean   :121.3   Mean   : 80.42  
                    3rd Qu.:176.1    3rd Qu.:29.80    3rd Qu.:40.9       3rd Qu.: 87.40   3rd Qu.:128.0   3rd Qu.: 84.00  
                    Max.   :198.7    Max.   :53.30    Max.   :42.2       Max.   :181.20   Max.   :201.0   Max.   :121.00  
                    NA's   :152974   NA's   :153062   NA's   :70085      NA's   :76295    NA's   :76285   NA's   :76285   
 heart_rate_bpm  oxygen_saturation_percent respiratory_rate_per_minute flu_last_administered tdap_last_administered
 Min.   : 50.0   Min.   :66.10             Min.   :12.00               Length:156030         Length:156030         
 1st Qu.: 85.1   1st Qu.:78.50             1st Qu.:18.20               Class :character      Class :character      
 Median :122.0   Median :82.00             Median :25.50               Mode  :character      Mode  :character      
 Mean   :123.4   Mean   :82.01             Mean   :25.56                                                           
 3rd Qu.:161.5   3rd Qu.:85.50             3rd Qu.:32.70                                                           
 Max.   :200.0   Max.   :89.00             Max.   :40.00                                                           
 NA's   :76295   NA's   :79221             NA's   :76295                                                           
 mmr_last_administered polio_last_administered   deceased        
 Length:156030         Length:156030           Length:156030     
 Class :character      Class :character        Class :character  
 Mode  :character      Mode  :character        Mode  :character  
                                                                 
                                                                 
                                                                 
                                                                 

All of our dates are character variables, so let’s convert those to dates.


mydata <- mydata %>%
            mutate(visit_start_date = as.Date(visit_start_date)) %>%
            mutate(visit_end_date = as.Date(visit_end_date) ) %>%
            mutate(birth_datetime = as.Date(birth_datetime)) %>%
            mutate(flu_last_administered = as.Date(flu_last_administered) ) %>%
            mutate(tdap_last_administered = as.Date(tdap_last_administered) ) %>%
            mutate(mmr_last_administered = as.Date(mmr_last_administered)) %>%
            mutate(polio_last_administered = as.Date(polio_last_administered))

summary(mydata)
   person_id      birth_datetime       race_source_value  ethnicity_source_value gender_source_value visit_occurrence_id
 Min.   :     1   Min.   :1909-06-24   Length:156030      Length:156030          Length:156030       Min.   :      1    
 1st Qu.: 30962   1st Qu.:1953-03-09   Class :character   Class :character       Class :character    1st Qu.: 782279    
 Median : 62112   Median :1971-06-14   Mode  :character   Mode  :character       Mode  :character    Median :1566715    
 Mean   : 62078   Mean   :1971-12-17                                                                 Mean   :1566862    
 3rd Qu.: 93254   3rd Qu.:1994-04-29                                                                 3rd Qu.:2358876    
 Max.   :124150   Max.   :2020-04-21                                                                 Max.   :3139398    
                                                                                                                        
 visit_start_date     visit_end_date        visit_type         condition         observation_source age_at_visit_years
 Min.   :1909-09-17   Min.   :1909-09-17   Length:156030      Length:156030      Length:156030      Min.   :  0.01    
 1st Qu.:2007-05-16   1st Qu.:2007-10-26   Class :character   Class :character   Class :character   1st Qu.: 16.16    
 Median :2020-02-22   Median :2020-02-24   Mode  :character   Mode  :character   Mode  :character   Median : 36.07    
 Mean   :2009-10-28   Mean   :2009-12-29                                                            Mean   : 37.86    
 3rd Qu.:2020-03-07   3rd Qu.:2020-03-09                                                            3rd Qu.: 57.17    
 Max.   :2020-05-26   Max.   :2020-05-27                                                            Max.   :110.73    
                                                                                                                      
 measurement_Date   body_height_cm        bmi         body_temperature_c body_weight_kg      systolic       diastolic     
 Length:156030      Min.   : 50.6    Min.   :12.70    Min.   :36.1       Min.   :  1.80   Min.   : 97.0   Min.   : 67.00  
 Class :character   1st Qu.:159.7    1st Qu.:27.20    1st Qu.:38.5       1st Qu.: 66.80   1st Qu.:113.0   1st Qu.: 76.00  
 Mode  :character   Median :167.7    Median :28.00    Median :39.7       Median : 78.00   Median :120.0   Median : 80.00  
                    Mean   :163.1    Mean   :27.24    Mean   :39.7       Mean   : 73.22   Mean   :121.3   Mean   : 80.42  
                    3rd Qu.:176.1    3rd Qu.:29.80    3rd Qu.:40.9       3rd Qu.: 87.40   3rd Qu.:128.0   3rd Qu.: 84.00  
                    Max.   :198.7    Max.   :53.30    Max.   :42.2       Max.   :181.20   Max.   :201.0   Max.   :121.00  
                    NA's   :152974   NA's   :153062   NA's   :70085      NA's   :76295    NA's   :76285   NA's   :76285   
 heart_rate_bpm  oxygen_saturation_percent respiratory_rate_per_minute flu_last_administered tdap_last_administered
 Min.   : 50.0   Min.   :66.10             Min.   :12.00               Min.   :1908-10-06    Min.   :1921-06-24    
 1st Qu.: 85.1   1st Qu.:78.50             1st Qu.:18.20               1st Qu.:2006-10-14    1st Qu.:2009-09-19    
 Median :122.0   Median :82.00             Median :25.50               Median :2019-09-13    Median :2013-06-11    
 Mean   :123.4   Mean   :82.01             Mean   :25.56               Mean   :2009-04-26    Mean   :2007-07-04    
 3rd Qu.:161.5   3rd Qu.:85.50             3rd Qu.:32.70               3rd Qu.:2019-11-07    3rd Qu.:2016-11-04    
 Max.   :200.0   Max.   :89.00             Max.   :40.00               Max.   :2019-12-31    Max.   :2020-05-25    
 NA's   :76295   NA's   :79221             NA's   :76295                                     NA's   :31146         
 mmr_last_administered polio_last_administered   deceased        
 Min.   :1910-07-21    Min.   :1909-09-11      Length:156030     
 1st Qu.:1956-12-04    1st Qu.:1957-01-03      Class :character  
 Median :1975-01-21    Median :1975-04-08      Mode  :character  
 Mean   :1975-06-06    Mean   :1975-08-21                        
 3rd Qu.:1997-09-01    3rd Qu.:1998-01-02                        
 Max.   :2020-05-19    Max.   :2020-05-25                        
 NA's   :1807          NA's   :228                               

Next, lets look into any missing data.


n <- nrow(mydata) # n is number of rows (observations)

missing_count <- colSums(is.na(mydata)) # calculate number missing
missing_pct <- missing_count/n * 100 # calculate percent missing
non_missing_count <- n - missing_count # calculate number non-missing

print(cbind(missing_count, missing_pct, non_missing_count))
                            missing_count missing_pct non_missing_count
person_id                               0   0.0000000            156030
birth_datetime                          0   0.0000000            156030
race_source_value                       0   0.0000000            156030
ethnicity_source_value                  0   0.0000000            156030
gender_source_value                     0   0.0000000            156030
visit_occurrence_id                     0   0.0000000            156030
visit_start_date                        0   0.0000000            156030
visit_end_date                          0   0.0000000            156030
visit_type                              0   0.0000000            156030
condition                               0   0.0000000            156030
observation_source                      0   0.0000000            156030
age_at_visit_years                      0   0.0000000            156030
measurement_Date                        0   0.0000000            156030
body_height_cm                     152974  98.0414023              3056
bmi                                153062  98.0978017              2968
body_temperature_c                  70085  44.9176440             85945
body_weight_kg                      76295  48.8976479             79735
systolic                            76285  48.8912389             79745
diastolic                           76285  48.8912389             79745
heart_rate_bpm                      76295  48.8976479             79735
oxygen_saturation_percent           79221  50.7729283             76809
respiratory_rate_per_minute         76295  48.8976479             79735
flu_last_administered                   0   0.0000000            156030
tdap_last_administered              31146  19.9615459            124884
mmr_last_administered                1807   1.1581106            154223
polio_last_administered               228   0.1461257            155802
deceased                                0   0.0000000            156030

Now we need to prepare our data for analysis.


# create a variable for length of stay
mydata$los = as.numeric(mydata$visit_end_date - mydata$visit_start_date)
summary(mydata$los)
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
    0.00     0.00     0.00    61.74     0.00 38325.00 
# modify labels for the deceased column
mydata$deceased_flag = mydata$deceased
mydata = mydata %>%
  mutate(deceased_flag = recode(deceased_flag, 'Y' = 'Deceased', 'N' = 'Alive'))

# make a column for visit month and year
mydata$visit_year = as.numeric(format(mydata$visit_start_date, "%Y"))
mydata$visit_month = as.numeric(format(mydata$visit_start_date, "%m"))

# make gender, race, and ethnicity factors

mydata$race_source_value = as.factor(mydata$race_source_value)
mydata$ethnicity_source_value = as.factor(mydata$ethnicity_source_value)
mydata$gender_source_value = as.factor(mydata$gender_source_value)

# make other categorical variables into factors


mydata$visit_type = as.factor(mydata$visit_type)
mydata$deceased = as.factor(mydata$deceased)
mydata$deceased_flag = as.factor(mydata$deceased_flag)

After we do this work, we can summarize the data again!


summary(mydata)
   person_id      birth_datetime       race_source_value ethnicity_source_value gender_source_value visit_occurrence_id
 Min.   :     1   Min.   :1909-06-24   asian : 10813     hispanic   : 17192     F:77339             Min.   :      1    
 1st Qu.: 30962   1st Qu.:1953-03-09   black : 13118     nonhispanic:138838     M:78691             1st Qu.: 782279    
 Median : 62112   Median :1971-06-14   native:   805                                                Median :1566715    
 Mean   : 62078   Mean   :1971-12-17   other :   158                                                Mean   :1566862    
 3rd Qu.: 93254   3rd Qu.:1994-04-29   white :131136                                                3rd Qu.:2358876    
 Max.   :124150   Max.   :2020-04-21                                                                Max.   :3139398    
                                                                                                                       
 visit_start_date     visit_end_date                      visit_type      condition         observation_source
 Min.   :1909-09-17   Min.   :1909-09-17   Emergency Room Visit:    20   Length:156030      Length:156030     
 1st Qu.:2007-05-16   1st Qu.:2007-10-26   Inpatient Visit     : 21056   Class :character   Class :character  
 Median :2020-02-22   Median :2020-02-24   Outpatient Visit    :134954   Mode  :character   Mode  :character  
 Mean   :2009-10-28   Mean   :2009-12-29                                                                      
 3rd Qu.:2020-03-07   3rd Qu.:2020-03-09                                                                      
 Max.   :2020-05-26   Max.   :2020-05-27                                                                      
                                                                                                              
 age_at_visit_years measurement_Date   body_height_cm        bmi         body_temperature_c body_weight_kg  
 Min.   :  0.01     Length:156030      Min.   : 50.6    Min.   :12.70    Min.   :36.1       Min.   :  1.80  
 1st Qu.: 16.16     Class :character   1st Qu.:159.7    1st Qu.:27.20    1st Qu.:38.5       1st Qu.: 66.80  
 Median : 36.07     Mode  :character   Median :167.7    Median :28.00    Median :39.7       Median : 78.00  
 Mean   : 37.86                        Mean   :163.1    Mean   :27.24    Mean   :39.7       Mean   : 73.22  
 3rd Qu.: 57.17                        3rd Qu.:176.1    3rd Qu.:29.80    3rd Qu.:40.9       3rd Qu.: 87.40  
 Max.   :110.73                        Max.   :198.7    Max.   :53.30    Max.   :42.2       Max.   :181.20  
                                       NA's   :152974   NA's   :153062   NA's   :70085      NA's   :76295   
    systolic       diastolic      heart_rate_bpm  oxygen_saturation_percent respiratory_rate_per_minute
 Min.   : 97.0   Min.   : 67.00   Min.   : 50.0   Min.   :66.10             Min.   :12.00              
 1st Qu.:113.0   1st Qu.: 76.00   1st Qu.: 85.1   1st Qu.:78.50             1st Qu.:18.20              
 Median :120.0   Median : 80.00   Median :122.0   Median :82.00             Median :25.50              
 Mean   :121.3   Mean   : 80.42   Mean   :123.4   Mean   :82.01             Mean   :25.56              
 3rd Qu.:128.0   3rd Qu.: 84.00   3rd Qu.:161.5   3rd Qu.:85.50             3rd Qu.:32.70              
 Max.   :201.0   Max.   :121.00   Max.   :200.0   Max.   :89.00             Max.   :40.00              
 NA's   :76285   NA's   :76285    NA's   :76295   NA's   :79221             NA's   :76295              
 flu_last_administered tdap_last_administered mmr_last_administered polio_last_administered deceased        los          
 Min.   :1908-10-06    Min.   :1921-06-24     Min.   :1910-07-21    Min.   :1909-09-11      N:139602   Min.   :    0.00  
 1st Qu.:2006-10-14    1st Qu.:2009-09-19     1st Qu.:1956-12-04    1st Qu.:1957-01-03      Y: 16428   1st Qu.:    0.00  
 Median :2019-09-13    Median :2013-06-11     Median :1975-01-21    Median :1975-04-08                 Median :    0.00  
 Mean   :2009-04-26    Mean   :2007-07-04     Mean   :1975-06-06    Mean   :1975-08-21                 Mean   :   61.74  
 3rd Qu.:2019-11-07    3rd Qu.:2016-11-04     3rd Qu.:1997-09-01    3rd Qu.:1998-01-02                 3rd Qu.:    0.00  
 Max.   :2019-12-31    Max.   :2020-05-25     Max.   :2020-05-19    Max.   :2020-05-25                 Max.   :38325.00  
                       NA's   :31146          NA's   :1807          NA's   :228                                          
  deceased_flag      visit_year    visit_month    
 Alive   :139602   Min.   :1909   Min.   : 1.000  
 Deceased: 16428   1st Qu.:2007   1st Qu.: 3.000  
                   Median :2020   Median : 3.000  
                   Mean   :2009   Mean   : 4.689  
                   3rd Qu.:2020   3rd Qu.: 7.000  
                   Max.   :2020   Max.   :12.000  
                                                  

The last step in data cleaning is separating out the conditions! Right now, they are all in one string together, separated by a colon (:).


head(mydata$condition, 10)
 [1] "Dyspnea:Pneumonia:Respiratory distress:Wheezing"          "Viral sinusitis"                                         
 [3] "Sore throat symptom:Dyspnea:Wheezing"                     "Perennial allergic rhinitis"                             
 [5] "Cough"                                                    "Chronic sinusitis"                                       
 [7] "Dyspnea:Wheezing:Cough"                                   "Chronic sinusitis"                                       
 [9] "Cough"                                                    "Respiratory distress:Sore throat symptom:Cough:Pneumonia"
# we're going to separate each condition into a row
longdata <- mydata %>% mutate(condition = strsplit(condition, ':')) %>%
  unnest(condition) %>%
  group_by(person_id) %>%
  mutate(row=row_number()) 

longdata$condition <- as.factor(longdata$condition)
summary(longdata$condition)
                                 Acute bacterial sinusitis                                           Acute bronchitis 
                                                       939                                                       7097 
                       Acute respiratory distress syndrome                                  Acute respiratory failure 
                                                      2454                                                       9139 
                                   Acute viral pharyngitis                                                     Asthma 
                                                      8347                                                        202 
                                          Childhood asthma                                          Chronic sinusitis 
                                                      1715                                                      26783 
                                                     Cough                                            Cystic fibrosis 
                                                     63448                                                         39 
                                                   Dyspnea                                   Emphysematous bronchitis 
                                                     18533                                                       1875 
                                                Hemoptysis                                           Nasal congestion 
                                                       904                                                       4324 
             Non-small cell carcinoma of lung, TNM stage 1                                 Non-small cell lung cancer 
                                                      1424                                                       1429 
                               Perennial allergic rhinitis        Perennial allergic rhinitis with seasonal variation 
                                                      2935                                                       2964 
                                                 Pneumonia Primary small cell malignant neoplasm of lung, TNM stage 1 
                                                     20464                                                        275 
                                       Pulmonary emphysema                                       Respiratory distress 
                                                      2130                                                      19139 
                                Seasonal allergic rhinitis                                                  Sinusitis 
                                                      1506                                                        943 
                              Small cell carcinoma of lung                                        Sore throat symptom 
                                                       274                                                      13166 
                                 Streptococcal sore throat                                            Viral sinusitis 
                                                      1840                                                      16232 
                                                  Wheezing 
                                                     18533 
# look at conditions by visit types

longdata %>% group_by(visit_type, condition) %>% summarize(n = n())
NA
NA
NA

Distribution Plots of single variables

Distributions can be shown several ways.

One way is a column histogram. Let’s look at age at visit (in years).


# this histogram has 30 bins
mydata %>%
  ggplot(aes(x=age_at_visit_years)) +
  geom_histogram(bins=30, color="#e9ecef", alpha=0.4) +
    labs(title = "Distribution of Age at Visit (years)") +
      xlab("Age (years)")


# this histogram only has 25 bins
mydata %>%
  ggplot(aes(x=age_at_visit_years)) +
  geom_histogram(bins=25, color="#e9ecef", alpha=0.4) +
    labs(title = "Distribution of Age at Visit (years)") +
      xlab("Age (years)")

NA
NA

Boxplots are another way to show distributions.

  
# boxplot of BMI
ggplot(data=subset(mydata, !is.na(bmi)), aes(y=bmi)) +
    geom_boxplot() +
    ggtitle("BMI Distribution") +
    ylab("BMI")

Let’s also look at the distribution of the length of stay.


mydata %>%
  ggplot(aes(x=los)) +
  geom_histogram(bins=30, color="#e9ecef", alpha=0.4) +
    labs(title = "Distribution of Length of Stay (Days)") +
      xlab("Days")

NA
NA

Running this code shows there is clearly a value that makes no sense!

We can look in the data for which observations may be causing this issue. We’ll look at visits that are not outpatient visits that do have more than 100 days in the hospital.


mydata %>%
  filter(los > 100, visit_type != 'Outpatient Visit')
NA

Let’s just look at values that are less than 100 days and that are not outpatient visits


mydata %>%
  filter(los < 100, visit_type != 'Outpatient Visit') %>%
  ggplot(aes(x=los)) +
    geom_histogram(fill="#69b3a2", color="#e9ecef", alpha=0.8, bins=30) + 
      labs(title ="Distribution of Length of Stay (Non-Outpatient Visits)") + 
      xlab("Length of Stay (Days)")



mydata %>%
  filter(los < 100, visit_type != 'Outpatient Visit') %>%
  ggplot(aes(x=los)) +
    geom_density(fill="#69b3a2", color="#e9ecef", alpha=0.8) + 
      labs(title ="Distribution of Length of Stay (Non-Outpatient Visits)") + 
      xlab("Length of Stay (Days)")

Histogram and Density across groups

We can make histograms and density plots of any continuous variable grouped by a second variable.

Here are some of blood pressure by gender.


# create a new dataset that is long-- with a row for systolic and a row for diastolic blood pressure per visit and person

bplong <- mydata %>%
  pivot_longer(cols = systolic:diastolic, names_to = 'Blood_Pressure_Type', values_to = 'Blood_Pressure_Value' )

bplong %>%
  filter(!is.na(Blood_Pressure_Value)) %>%
  ggplot(aes(x=gender_source_value, y=Blood_Pressure_Value , fill=Blood_Pressure_Type)) +
  geom_boxplot() +
    scale_fill_manual(values=c("darkgreen", "orange")) +
    labs(title = "Blood Pressure by Gender") + 
      xlab("Gender")

We can also use a bar chart to plot the mean and a standard error bar for each of the above categories.


bplong %>%
  filter(!is.na(Blood_Pressure_Value)) %>%
  ggplot(aes(x = interaction(Blood_Pressure_Type, gender_source_value), y = Blood_Pressure_Value)) +
  geom_bar(stat = 'summary', fun = 'mean') +
  labs(title = "Mean Blood Pressure by Gender") +
  xlab("Blood Pressure and Gender") +
  ylab("Blood Pressure (mmHg)")

You can also overlay the distributions of blood pressure by gender and have panels in your plot for systolic and diastolic.

bp <- ggplot(bplong %>% filter(!is.na(Blood_Pressure_Value)), aes(x = Blood_Pressure_Value, fill=gender_source_value)) +
  geom_density(alpha = 0.4) +
  scale_color_manual(values = c("pink", "lightblue")) +
  facet_wrap(~Blood_Pressure_Type)

bp

Now let’s look at a comparison of length of stay for inpatient visits by gender.


# Histogram
mydata %>%
  filter(los < 100, visit_type != 'Outpatient Visit') %>%
  ggplot(aes(x=los,fill=gender_source_value)) +
    geom_histogram(alpha=0.8, bins=30) + 
    scale_fill_manual(values=c("pink", "lightblue")) +
      labs(title ="Distribution of Length of Stay (Non-Outpatient Visits)") + 
      xlab("Length of Stay (Days)")


# Density plots
mydata %>%
  filter(los < 100, visit_type != 'Outpatient Visit') %>%
  ggplot(aes(x=los, fill=gender_source_value)) +
    geom_density( alpha=0.4) +
    scale_fill_manual(values=c("pink", "lightblue"))+
      labs(title ="Distribution of Length of Stay (Non-Outpatient Visits)") + 
      xlab("Length of Stay (Days)")


# Boxplots

mydata %>%
  filter(los < 100, visit_type == 'Inpatient Visit') %>%
  ggplot(aes(y=los, x=gender_source_value, fill=gender_source_value)) +
  geom_boxplot() +
  scale_fill_manual(values=c("pink", "lightblue")) +
    labs(title = "Length of Stay for Inpatient Visits by Gender") + 
      xlab("Gender") +
      ylab("Length of Stay (days)")


# Violin Plots


mydata %>%
  filter(los < 100, visit_type == 'Inpatient Visit') %>%
  ggplot(aes(y=los, x=gender_source_value, fill=gender_source_value)) +
  geom_violin() +
  scale_fill_manual(values=c("pink", "lightblue")) +
    labs(title = "Length of Stay for Inpatient Visits by Gender") + 
      xlab("Gender") +
      ylab("Length of Stay (days)")

There are a lot of ways to explore relationships between continuous data, as well.


mydata %>%
  filter(!is.na(respiratory_rate_per_minute)) %>%
  filter(!is.na(oxygen_saturation_percent)) %>%
  ggplot(aes(x = respiratory_rate_per_minute, y = oxygen_saturation_percent)) +
  geom_point(color='steelblue', alpha = .1) +
  labs(title ="Oxygen Saturation vs. Respiratory Rate") +
  xlab("Respiratory Rate (breaths per minute") +
  ylab("Oxygen Saturation (%)")

We can also look at age versus oxygen saturation by outcome.



mydata %>%
  filter(!is.na(oxygen_saturation_percent)) %>%
  filter(!is.na(age_at_visit_years)) %>%
  ggplot(aes(x = age_at_visit_years, y = oxygen_saturation_percent, color=deceased_flag)) +
  geom_point(alpha = .1) +
  labs(title ="Age vs. Oxygen Saturation by Outcome", color = "Outcome") +
  xlab("Age (years)") +
  ylab("Oxygen Saturation (%)")

NA

Here’s another comparison with age.

mydata %>%
  filter(los < 100, visit_type != 'Outpatient Visit', !is.na(age_at_visit_years), !is.na(gender_source_value)) %>%
  ggplot(aes(x = age_at_visit_years, y = los, color=gender_source_value)) +
  geom_point(alpha = .1) +
  labs(title ="Age vs. Length of Stay by Gender for Non-Outpatient Visits", color = "Gender") +
  xlab("Age (years)") +
  ylab("Length of Stay (Days)")

NA
NA

We can also look at visit counts over time! These data come from a simluated dataset based on COVID data.


data2020 = mydata %>% filter(visit_year == 2020)
visitcounts = count(data2020, visit_start_date)


visitcounts %>%
  ggplot(aes(x=visit_start_date, y=n)) +
  geom_line() +
  xlab("Date") +
  ylab("Visit count") +
  labs(title = "Daily Visit Counts (2020)")

NA
NA

Let’s categorize visits as COVID-related or non-COVID-related and plot both series.


data2020$COVID = grepl('COVID',data2020$observation_source, fixed = TRUE)

COVIDvisitcounts = count(data2020, visit_start_date, COVID)

COVIDvisitcounts$COVID_formatted = ifelse(COVIDvisitcounts$COVID == TRUE, "COVID-related", "Non-COVID")


COVIDvisitcounts %>%
  ggplot(aes(x=visit_start_date, y=n, color=COVID_formatted)) +
  geom_line() +
  xlab("Date") +
  ylab("Visit count") +
  labs(title = "Daily Visit Counts (2020)", color="Category")

NA
NA
NA
NA
---
title: "R Notebook for Data Viz for Clinical Data"
output: html_notebook
---

We are using a common dataset across the R and Python coding examples.

The code below reads in the csv file final_with_deceased.csv. It also calls the libraries we are going to use.

```{r}
library(ggplot2)
library(dplyr)
library(tidyr)

mydata <- as.data.frame(read.csv("final_with_deceased.csv"))

```

The first step when working with a data file is an exploratory data analysis.

```{r}

head(mydata, 5) # prints first five rows
tail(mydata, 5) # prints last five rows
sample_n(mydata, 5) # prints five randomly selected rows

print(dim(mydata)) # print number of columns and rows
summary(mydata) # overview of each variable in the dataset

```

All of our dates are character variables, so let's convert those to dates.

```{r}

mydata <- mydata %>%
            mutate(visit_start_date = as.Date(visit_start_date)) %>%
            mutate(visit_end_date = as.Date(visit_end_date) ) %>%
            mutate(birth_datetime = as.Date(birth_datetime)) %>%
            mutate(flu_last_administered = as.Date(flu_last_administered) ) %>%
            mutate(tdap_last_administered = as.Date(tdap_last_administered) ) %>%
            mutate(mmr_last_administered = as.Date(mmr_last_administered)) %>%
            mutate(polio_last_administered = as.Date(polio_last_administered))

summary(mydata)

```

Next, lets look into any missing data.

```{r}

n <- nrow(mydata) # n is number of rows (observations)

missing_count <- colSums(is.na(mydata)) # calculate number missing
missing_pct <- missing_count/n * 100 # calculate percent missing
non_missing_count <- n - missing_count # calculate number non-missing

print(cbind(missing_count, missing_pct, non_missing_count))
```

Now we need to prepare our data for analysis.

```{r}

# create a variable for length of stay
mydata$los = as.numeric(mydata$visit_end_date - mydata$visit_start_date)
summary(mydata$los)

# modify labels for the deceased column
mydata$deceased_flag = mydata$deceased
mydata = mydata %>%
  mutate(deceased_flag = recode(deceased_flag, 'Y' = 'Deceased', 'N' = 'Alive'))

# make a column for visit month and year
mydata$visit_year = as.numeric(format(mydata$visit_start_date, "%Y"))
mydata$visit_month = as.numeric(format(mydata$visit_start_date, "%m"))

# make gender, race, and ethnicity factors

mydata$race_source_value = as.factor(mydata$race_source_value)
mydata$ethnicity_source_value = as.factor(mydata$ethnicity_source_value)
mydata$gender_source_value = as.factor(mydata$gender_source_value)

# make other categorical variables into factors


mydata$visit_type = as.factor(mydata$visit_type)
mydata$deceased = as.factor(mydata$deceased)
mydata$deceased_flag = as.factor(mydata$deceased_flag)
```

After we do this work, we can summarize the data again!

```{r}

summary(mydata)

```

The last step in data cleaning is separating out the conditions! Right now, they are all in one string together, separated by a colon (:).

```{r}

head(mydata$condition, 10)

# we're going to separate each condition into a row
longdata <- mydata %>% mutate(condition = strsplit(condition, ':')) %>%
  unnest(condition) %>%
  group_by(person_id) %>%
  mutate(row=row_number()) 

longdata$condition <- as.factor(longdata$condition)
summary(longdata$condition)

# look at conditions by visit types

longdata %>% group_by(visit_type, condition) %>% summarize(n = n())



```

### Distribution Plots of single variables

Distributions can be shown several ways.

One way is a column histogram. Let's look at age at visit (in years).

```{r}

# this histogram has 30 bins
mydata %>%
  ggplot(aes(x=age_at_visit_years)) +
  geom_histogram(bins=30, color="#e9ecef", alpha=0.4) +
    labs(title = "Distribution of Age at Visit (years)") +
      xlab("Age (years)")

# this histogram only has 25 bins
mydata %>%
  ggplot(aes(x=age_at_visit_years)) +
  geom_histogram(bins=25, color="#e9ecef", alpha=0.4) +
    labs(title = "Distribution of Age at Visit (years)") +
      xlab("Age (years)")


```

Boxplots are another way to show distributions.

```{r}
  
# boxplot of BMI
ggplot(data=subset(mydata, !is.na(bmi)), aes(y=bmi)) +
    geom_boxplot() +
    ggtitle("BMI Distribution") +
    ylab("BMI")

```

Let's also look at the distribution of the length of stay.

```{r}

mydata %>%
  ggplot(aes(x=los)) +
  geom_histogram(bins=30, color="#e9ecef", alpha=0.4) +
    labs(title = "Distribution of Length of Stay (Days)") +
      xlab("Days")


```

Running this code shows there is clearly a value that makes no sense!

We can look in the data for which observations may be causing this issue. We'll look at visits that are not outpatient visits that do have more than 100 days in the hospital.

```{r}

mydata %>%
  filter(los > 100, visit_type != 'Outpatient Visit')

```

Let's just look at values that are less than 100 days and that are not outpatient visits

```{r}

mydata %>%
  filter(los < 100, visit_type != 'Outpatient Visit') %>%
  ggplot(aes(x=los)) +
    geom_histogram(fill="#69b3a2", color="#e9ecef", alpha=0.8, bins=30) + 
      labs(title ="Distribution of Length of Stay (Non-Outpatient Visits)") + 
      xlab("Length of Stay (Days)")


mydata %>%
  filter(los < 100, visit_type != 'Outpatient Visit') %>%
  ggplot(aes(x=los)) +
    geom_density(fill="#69b3a2", color="#e9ecef", alpha=0.8) + 
      labs(title ="Distribution of Length of Stay (Non-Outpatient Visits)") + 
      xlab("Length of Stay (Days)")

```

### Histogram and Density across groups

We can make histograms and density plots of any continuous variable grouped by a second variable.

Here are some of blood pressure by gender.

```{r}

# create a new dataset that is long-- with a row for systolic and a row for diastolic blood pressure per visit and person

bplong <- mydata %>%
  pivot_longer(cols = systolic:diastolic, names_to = 'Blood_Pressure_Type', values_to = 'Blood_Pressure_Value' )

bplong %>%
  filter(!is.na(Blood_Pressure_Value)) %>%
  ggplot(aes(x=gender_source_value, y=Blood_Pressure_Value , fill=Blood_Pressure_Type)) +
  geom_boxplot() +
    scale_fill_manual(values=c("darkgreen", "orange")) +
    labs(title = "Blood Pressure by Gender") + 
      xlab("Gender")

```

We can also use a bar chart to plot the mean and a standard error bar for each of the above categories.

```{r}

bplong %>%
  filter(!is.na(Blood_Pressure_Value)) %>%
  ggplot(aes(x = interaction(Blood_Pressure_Type, gender_source_value), y = Blood_Pressure_Value)) +
  geom_bar(stat = 'summary', fun = 'mean') +
  labs(title = "Mean Blood Pressure by Gender") +
  xlab("Blood Pressure and Gender") +
  ylab("Blood Pressure (mmHg)")

```

You can also overlay the distributions of blood pressure by gender and have panels in your plot for systolic and diastolic.

```{r}
bp <- ggplot(bplong %>% filter(!is.na(Blood_Pressure_Value)), aes(x = Blood_Pressure_Value, fill=gender_source_value)) +
  geom_density(alpha = 0.4) +
  scale_color_manual(values = c("pink", "lightblue")) +
  facet_wrap(~Blood_Pressure_Type)

bp
```

Now let's look at a comparison of length of stay for inpatient visits by gender.

```{r}

# Histogram
mydata %>%
  filter(los < 100, visit_type != 'Outpatient Visit') %>%
  ggplot(aes(x=los,fill=gender_source_value)) +
    geom_histogram(alpha=0.8, bins=30) + 
    scale_fill_manual(values=c("pink", "lightblue")) +
      labs(title ="Distribution of Length of Stay (Non-Outpatient Visits)") + 
      xlab("Length of Stay (Days)")

# Density plots
mydata %>%
  filter(los < 100, visit_type != 'Outpatient Visit') %>%
  ggplot(aes(x=los, fill=gender_source_value)) +
    geom_density( alpha=0.4) +
    scale_fill_manual(values=c("pink", "lightblue"))+
      labs(title ="Distribution of Length of Stay (Non-Outpatient Visits)") + 
      xlab("Length of Stay (Days)")

# Boxplots

mydata %>%
  filter(los < 100, visit_type == 'Inpatient Visit') %>%
  ggplot(aes(y=los, x=gender_source_value, fill=gender_source_value)) +
  geom_boxplot() +
  scale_fill_manual(values=c("pink", "lightblue")) +
    labs(title = "Length of Stay for Inpatient Visits by Gender") + 
      xlab("Gender") +
      ylab("Length of Stay (days)")

# Violin Plots


mydata %>%
  filter(los < 100, visit_type == 'Inpatient Visit') %>%
  ggplot(aes(y=los, x=gender_source_value, fill=gender_source_value)) +
  geom_violin() +
  scale_fill_manual(values=c("pink", "lightblue")) +
    labs(title = "Length of Stay for Inpatient Visits by Gender") + 
      xlab("Gender") +
      ylab("Length of Stay (days)")

```

There are a lot of ways to explore relationships between continuous data, as well.

```{r}

mydata %>%
  filter(!is.na(respiratory_rate_per_minute)) %>%
  filter(!is.na(oxygen_saturation_percent)) %>%
  ggplot(aes(x = respiratory_rate_per_minute, y = oxygen_saturation_percent)) +
  geom_point(color='steelblue', alpha = .1) +
  labs(title ="Oxygen Saturation vs. Respiratory Rate") +
  xlab("Respiratory Rate (breaths per minute") +
  ylab("Oxygen Saturation (%)")

```
We can also look at age versus oxygen saturation by outcome.

```{r}


mydata %>%
  filter(!is.na(oxygen_saturation_percent)) %>%
  filter(!is.na(age_at_visit_years)) %>%
  ggplot(aes(x = age_at_visit_years, y = oxygen_saturation_percent, color=deceased_flag)) +
  geom_point(alpha = .1) +
  labs(title ="Age vs. Oxygen Saturation by Outcome", color = "Outcome") +
  xlab("Age (years)") +
  ylab("Oxygen Saturation (%)")
  
```

Here's another comparison with age.

```{r}
mydata %>%
  filter(los < 100, visit_type != 'Outpatient Visit', !is.na(age_at_visit_years), !is.na(gender_source_value)) %>%
  ggplot(aes(x = age_at_visit_years, y = los, color=gender_source_value)) +
  geom_point(alpha = .1) +
  labs(title ="Age vs. Length of Stay by Gender for Non-Outpatient Visits", color = "Gender") +
  xlab("Age (years)") +
  ylab("Length of Stay (Days)")


```

We can also look at visit counts over time! These data come from a simluated dataset based on COVID data.


```{r}

data2020 = mydata %>% filter(visit_year == 2020)
visitcounts = count(data2020, visit_start_date)


visitcounts %>%
  ggplot(aes(x=visit_start_date, y=n)) +
  geom_line() +
  xlab("Date") +
  ylab("Visit count") +
  labs(title = "Daily Visit Counts (2020)")


```

Let's categorize visits as COVID-related or non-COVID-related and plot both series.

```{r}

data2020$COVID = grepl('COVID',data2020$observation_source, fixed = TRUE)

COVIDvisitcounts = count(data2020, visit_start_date, COVID)

COVIDvisitcounts$COVID_formatted = ifelse(COVIDvisitcounts$COVID == TRUE, "COVID-related", "Non-COVID")


COVIDvisitcounts %>%
  ggplot(aes(x=visit_start_date, y=n, color=COVID_formatted)) +
  geom_line() +
  xlab("Date") +
  ylab("Visit count") +
  labs(title = "Daily Visit Counts (2020)", color="Category")




```

