Cholecystitis

Cholecystitis is an inflammation in a person’s gallbladder, which is a small, digestive organ beneath the liver. This inflammation can occur for a multitude of reasons, from a tumor growing in the gallbladder to an infection like AIDS. However, the number one reason that Cholecystitis occurs is because of gallstones build-up up in the gallbladder, which block the tube leading out of the gallbladder. Since gallstones are the most common way that Cholecystitis occurs in the human body, the method of screen testing for Cholecystitis is testing for gallstones presence in the gallbladder. This project will be running and analyzing the effectiveness of the Cholecystitis screen test pertaining to gallstones using the four following methods for testing effectiveness of an epidemiological test: sensitivity, specificity, positive predictive value (PPV), and negative predictive value(NPV)

Importing Packages

The following four packages will be loaded for the purposes of loading the data, organizing the data, and analyzing the accuracy of the Cholecystitis test from the data: the tidyverse, the knitr , the kableExtra,and the epiR packages:

library(tidyverse)
## -- Attaching packages ------------------------------------------ tidyverse 1.3.0 --
## v ggplot2 3.3.2     v purrr   0.3.4
## v tibble  3.0.1     v dplyr   1.0.0
## v tidyr   1.1.0     v stringr 1.4.0
## v readr   1.3.1     v forcats 0.5.0
## -- Conflicts --------------------------------------------- tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag()    masks stats::lag()
library(knitr)
library(kableExtra)
## 
## Attaching package: 'kableExtra'
## The following object is masked from 'package:dplyr':
## 
##     group_rows
library(epiR)
## Loading required package: survival
## Package epiR 1.0-15 is loaded
## Type help(epi.about) for summary information
## Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
## 

Importing The Data

The function read.csv() will be used to import the Cholecystitis screen test data:

test_data <- read.csv("~/R projects/GB data - dummy coding.csv")

Structure and View of the Data

Before viewing the data, the structure of the data has to be understood. To have an idea of the structure of the data, the dim() function will be utilized to find how many rows and columns are present in the test data:

dim(test_data)
## [1] 456  21

dim() showcases that there are 456 observations (rows) accompanied by 21 variables (columns). The names of the 21 variables will be required to know which specific variables to run for epidemiological testing, and to do that, the names() function will be utilized to give the name of each variable present in the test data:

names(test_data)
##  [1] "Accession"                                                  
##  [2] "New.GB.length"                                              
##  [3] "New.GB.width"                                               
##  [4] "GB_length"                                                  
##  [5] "GB_width"                                                   
##  [6] "gallstones"                                                 
##  [7] "wall_thickening"                                            
##  [8] "pericholecystic.fluid"                                      
##  [9] "Murphys"                                                    
## [10] "temperature"                                                
## [11] "WBC"                                                        
## [12] "alk_phos"                                                   
## [13] "bilirubin"                                                  
## [14] "AST"                                                        
## [15] "ALT"                                                        
## [16] "cholecystectom_date"                                        
## [17] "pathology_dx"                                               
## [18] "cholecystostomy_date"                                       
## [19] "if.no.surgery..last.available.follow.up.without.acute.chole"
## [20] "FU_duration"                                                
## [21] "Final_Dx"

Finally, to get a good idea of what the data set looks like, it will be loaded in a table using the kableExtra package alongside the customization that comes with it:

test_data %>%
  kbl() %>%
   kable_classic("striped", full_width = F, html_font = "Cambria")%>%
  scroll_box(width = "100%", height = "200px")
Accession New.GB.length New.GB.width GB_length GB_width gallstones wall_thickening pericholecystic.fluid Murphys temperature WBC alk_phos bilirubin AST ALT cholecystectom_date pathology_dx cholecystostomy_date if.no.surgery..last.available.follow.up.without.acute.chole FU_duration Final_Dx
6902660 2.9 0.7 2.90 0.80 1 0 0 0 36.4 8.80 53.0 0.9 22 17 9/27/2019 #REF! 0
6902558 3.0 2.2 2.30 0.90 1 0 0 0 37.1 4.27 69.0 0.1 24 9 #REF! NA
6645194 3.3 1.6 2.20 0.80 1 0 0 1 37.0 7.48 75.0 0.4 27 39 #REF! NA
6770001 3.7 1.3 3.50 1.20 1 0 0 0 NA 7.40 NA NA NA NA 1/21/2020 #REF! 0
6857976 3.8 3.5 3.80 1.70 1 1 0 2 36.6 6.70 68.0 0.3 18 12 12/19/2019 #REF! 0
6658810 3.8 2.4 3.00 1.60 1 1 0 2 36.8 17.75 203.0 1.8 742 727 7/3/2019 cholecystectomy chronic cholecystitis with cholelithiasis #REF! 2
6652986 4.1 2.4 3.90 2.00 1 0 0 0 36.5 6.30 82.0 0.6 25 18 1/24/2020 #REF! 0
6778742 4.3 2.3 4.30 0.90 1 0 0 0 36.8 3.69 63.0 0.2 16 10 1/30/2020 #REF! 0
6757283 4.4 2.0 5.20 1.90 1 0 0 0 36.4 18.20 731.0 0.1 208 77 #REF! NA
6803775 4.4 2.7 3.20 1.70 1 0 0 0 NA 9.50 6.6 0.3 20 23 1/7/2020 #REF! 0
6855281 4.4 3.0 4.60 1.90 1 1 0 0 36.3 9.40 270.0 13.3 182 26 1/22/2020 #REF! 0
6757495 4.6 1.6 4.60 1.60 1 1 0 1 36.9 9.40 113.0 0.2 85 42 4/5/2019 #REF! 0
6865830 4.6 3.4 4.40 1.40 1 1 NA 2 36.2 9.50 60.0 0.3 22 17 #REF! NA
6717866 4.6 2.3 5.10 1.90 1 1 0 0 36.4 3.57 119.0 0.9 18 6 #REF! NA
6700684 4.7 3.1 4.70 2.30 1 1 0 0 37.0 9.39 83.0 0.2 19 22 1/21/2019 chronic and subacute cholecystitis with cholelithiasis #REF! 2
6736540 4.8 3.8 4.70 1.80 1 1 0 0 37.0 7.30 70.0 0.1 21 14 2/2/2019 chronic cholecystiis with cholelithiasis #REF! 2
6725654 4.8 2.5 4.40 2.50 1 0 0 0 37.1 11.50 83.0 0.1 18 17 6/6/2019 #REF! 0
6688283 5.1 4.6 5.10 2.40 1 0 0 0 36.6 6.85 101.0 0.4 18 12 1/16/2019 chronic cholecystitis, cholelithiasis #REF! 2
6720026 5.3 3.7 5.30 3.80 1 0 0 0 37.1 8.33 57.0 0.2 16 13 10/10/2019 #REF! 0
6888799 5.3 1.6 5.30 1.60 1 0 0 0 36.7 5.80 70.0 0.2 18 11 3/31/2019 chronic cholecystitis with cholelithiasis #REF! 2
6768368 5.3 1.5 5.30 1.20 1 0 0 0 36.2 6.22 105.0 0.3 21 17 #REF! NA
6688282 5.3 3.4 5.30 2.40 1 1 1 0 36.9 43.24 687.0 4.7 183 50 3/3/2019 #REF! 0
6819038 5.3 2.4 5.00 1.90 1 0 0 0 NA NA NA NA NA NA 3/26/2019 #REF! NA
6758716 5.4 4.6 5.40 4.60 0 0 0 0 37.0 12.10 80.0 0.1 16 22 1/16/2020 acute and chronic cholecystitis, a/w extensive fat necrosis, suggestive of perforation #REF! 1
6758320 5.4 1.8 5.40 1.40 1 0 0 0 37.2 8.90 131.0 2.4 72 52 2/28/2019 focal mild chronic inflammation #REF! 2
6685974 5.4 3.5 5.40 2.30 1 0 0 0 NA NA NA NA NA NA 9/16/2019 #REF! 0
6735155 5.5 3.7 5.50 3.30 1 0 0 0 36.5 11.15 62.0 0.6 16 16 #REF! NA
6814093 5.5 3.8 5.20 2.70 1 0 0 0 36.9 4.70 NA NA NA NA 3/4/2019 cholelithiasis with mild chronic cholecystitis #REF! 2
6873906 5.6 2.5 5.30 1.30 1 0 0 0 36.7 4.40 43.0 0.2 31 7 1/28/2020 #REF! 0
6880342 5.6 2.9 5.30 2.40 1 1 0 0 36.7 6.70 113.0 0.5 25 14 3/29/2019 chronic cholecystitis and cholelithiasis #REF! 2
6780909 5.6 3.1 5.60 2.50 1 0 0 0 36.3 5.50 121.0 0.8 307 201 2/21/2019 cholelithiasis #REF! 0
6709290 5.7 2.8 5.20 2.20 1 1 0 2 37.2 15.10 81.0 0.5 23 26 1/25/2019 acute cholecystits with cholelithiasis #REF! 1
6905771 5.7 1.9 4.90 1.80 0 1 0 0 36.3 5.50 88.0 0.8 24 22 4/8/2019 gallbladder with autolysis and features of chronic cholesytitis #REF! 2
6835798 5.7 2.2 5.50 1.60 0 0 0 0 36.6 6.70 282.0 9.5 95 288 3/11/2019 acute and chronic cholecystits and cholelithiais #REF! 1
6754421 5.7 2.9 5.70 1.80 1 0 0 0 NA NA NA NA NA NA 2/28/2019 #REF! NA
6823029 5.8 2.0 5.60 1.50 1 0 0 0 NA NA NA NA NA NA 10/3/2019 #REF! 0
6737247 5.9 2.3 2.60 0.60 1 1 0 1 36.8 7.70 116.0 0.1 28 87 2/4/2019 Acute cholecystitis with cholelithiasis #REF! 1
6876073 5.9 1.8 5.90 1.80 1 1 0 0 37.0 10.90 48.0 0.4 33 30 12/30/2019 #REF! 0
6785032 5.9 2.7 5.90 2.70 1 0 0 0 NA NA NA NA NA NA 12/10/2019 #REF! 0
6758760 6.0 3.6 5.80 2.50 1 0 0 0 36.5 11.80 73.0 0.1 21 12 12/8/2019 #REF! 0
6906316 6.0 4.4 4.10 2.90 0 0 0 0 36.4 11.20 211.0 0.3 15 9 5/17/2019 cholelithiasis and chronic cholecystitis #REF! 2
6715379 6.0 3.9 4.60 1.30 1 0 0 0 36.7 7.74 117.0 0.7 24 16 5/25/2019 cholecystectomy mild chronic cholecystitis and cholelithiasis #REF! 2
6897754 6.1 2.6 6.10 2.60 1 0 0 0 38.0 7.30 247.0 0.4 28 28 5/9/2019 #REF! 0
6795063 6.1 4.2 6.10 3.10 1 0 0 0 36.2 6.90 87.0 1.0 168 204 #REF! NA
6688352 6.1 2.4 5.60 2.00 1 0 0 0 36.9 NA NA NA NA NA 3/26/2019 #REF! 0
6897084 6.2 4.4 6.20 2.70 1 0 0 0 37.5 10.22 132.0 0.2 13 8 3/31/2019 chronic cholecystitis with cholelithiasis #REF! 2
6872496 6.2 2.3 4.90 1.50 1 0 0 0 36.9 8.10 60.0 0.5 26 36 6/28/2019 chronic cholecystitis and cholelithiasis #REF! 2
6678658 6.2 1.9 5.60 1.40 0 0 0 0 36.7 8.60 66.0 1.2 11 7 4/5/2019 chronic cholecystitis with cholelithiasis #REF! 2
6648224 6.2 2.7 6.00 2.70 1 0 0 0 NA NA NA NA NA NA 11/10/2019 #REF! 0
6895488 6.2 3.8 6.20 3.50 1 0 0 0 NA NA NA NA NA NA 2/18/2020 #REF! 0
6778567 6.3 3.4 6.30 2.50 1 0 0 0 36.3 6.30 65.0 0.6 20 10 #REF! NA
6736531 6.4 1.9 6.40 1.50 1 1 0 2 37.0 7.23 118.0 0.1 168 101 8/18/2019 chronic cholecystitis with cholelithiasis #REF! 2
6747309 6.4 2.1 6.40 2.10 1 1 1 2 36.6 9.70 78.0 0.4 24 25 2/7/2019 chronic cholecystitis with cholelithiasis #REF! 2
6758120 6.4 3.8 6.40 3.00 0 0 0 0 36.5 8.70 116.0 0.4 44 17 10/30/2019 Autolyzed gallbladder with focal chronic inflammation and cholesterolosis. #REF! 2
6897815 6.4 2.4 6.40 2.40 1 0 0 0 36.8 12.25 249.0 1.6 287 749 4/2/2019 chronic cholecystitis and holelithiasis #REF! 2
6670697 6.4 4.2 6.40 1.50 1 0 0 0 37.7 21.80 270.0 3.3 284 138 1/14/2019 acute and chronic cholecystitis and cholelithiasis #REF! 1
6876647 6.5 2.8 6.50 2.50 1 0 0 0 36.3 15.70 125.0 41.5 73 21 4/5/2019 #REF! NA
6658462 6.6 5.0 6.60 3.80 1 0 0 0 37.1 15.40 146.0 0.5 26 31 1/7/2019 aucte suprative and chronic acalcuous cholecystitis #REF! 1
6833397 6.6 3.0 6.60 3.00 1 0 0 0 NA NA NA NA NA NA 12/2/2019 #REF! 0
6862786 6.7 3.5 6.70 2.50 1 1 0 2 36.8 10.70 88.0 0.4 24 22 3/20/2019 acute and chronic cholecystitis and cholelithiasis #REF! 1
6693356 6.7 2.8 6.60 2.30 1 0 0 0 36.6 8.55 96.0 0.4 31 38 1/7/2020 #REF! 0
6791288 6.7 3.0 6.70 3.20 1 0 0 0 36.6 3.80 80.0 1.4 22 12 1/26/2020 #REF! 0
6659171 6.8 3.2 7.00 3.00 1 0 0 0 36.5 4.50 144.0 0.3 342 613 5/23/2019 chronic cholecystitis, cholelithiasis #REF! 2
6869558 6.8 4.6 6.80 2.70 1 0 0 0 36.5 6.60 97.0 0.4 22 23 3/22/2019 chronic cholecystitis snd cholelithiasis and cholrsterolosis #REF! 2
6678662 6.9 4.3 8.30 2.80 1 1 0 0 36.5 9.01 64.0 0.4 20 24 1/19/2019 chronic and subacute cholecystitis with cholelithiasis #REF! 2
6802274 7.0 4.2 6.60 3.20 1 1 0 0 36.7 12.50 101.0 0.5 19 32 2/28/2019 acute and chronic cholecystitis, cholelithiasis #REF! 1
6688223 7.0 4.9 7.00 4.10 1 1 1 0 37.3 19.16 107.0 0.6 21 17 1/21/2019 acute and chronic cholecystitis with necrosis and cholelithiasis #REF! 1
6715057 7.1 3.7 7.10 3.10 1 0 0 0 37.1 9.97 85.0 0.2 26 39 1/26/2019 chronic cholecysticis wutg cholelithiasis #REF! 2
6858288 7.1 3.5 7.90 3.20 1 0 0 0 36.4 7.70 90.0 0.2 23 33 3/20/2019 chronic cholecystitis with cholelithiasis and cholesteroosis #REF! 2
6849620 7.1 3.4 6.60 2.30 1 0 0 0 36.6 11.50 59.0 0.3 26 16 3/22/2019 cholelithiasis and cholesterolosis #REF! 0
6654795 7.1 3.0 5.00 1.70 1 0 0 0 NA 7.80 76.0 0.6 35 25 #REF! NA
6817460 7.1 3.6 6.20 3.70 1 0 0 0 36.4 13.88 121.0 0.9 39 24 #REF! NA
6650123 7.1 3.6 4.10 3.40 1 1 0 0 36.6 11.10 123.0 1.1 25 19 1/4/2019 acute and chronic cholecystitis with cholelithiasis #REF! 1
6804759 7.2 1.9 7.20 1.70 1 1 0 1 36.3 12.70 38.0 1.0 34 12 2/27/2019 chronic cholecystitis snd cholelithiasis #REF! 2
6684880 7.2 4.0 7.20 4.20 1 1 0 0 36.2 4.80 132.0 1.1 31 16 12/20/2019 #REF! 0
6858283 7.2 4.4 7.00 3.20 1 0 0 0 36.7 9.00 65.0 1.8 405 310 1/22/2020 #REF! 0
6683904 7.2 5.8 6.60 3.20 1 1 0 2 36.4 9.35 104.0 1.9 98 25 1/17/2019 #REF! NA
6718769 7.2 2.9 6.70 3.60 1 0 0 0 NA NA NA NA NA NA #REF! NA
6746235 7.3 5.0 6.80 2.40 1 0 0 0 36.6 5.60 72.0 0.1 67 16 3/3/2019 #REF! NA
6757513 7.3 2.8 4.30 2.70 0 0 0 0 36.6 9.70 93.0 0.2 84 200 2/10/2019 chronic cholecystitis with cholelithiasis #REF! 2
6815970 7.4 3.9 7.40 2.30 1 0 0 0 37.0 9.20 72.0 0.3 19 20 #REF! NA
6646089 7.4 3.9 7.40 3.50 1 0 0 0 36.7 12.12 97.0 0.4 26 29 9/15/2019 #REF! 0
6697557 7.4 3.0 7.00 2.10 1 0 0 0 36.7 9.11 69.0 0.8 69 79 #REF! NA
6830247 7.5 5.1 7.50 3.40 1 1 1 0 36.4 22.70 122.0 0.8 33 31 3/8/2019 Gangreous cholecystitis and cholelithiasis #REF! 1
6780641 7.5 2.6 7.50 2.60 1 0 0 0 36.7 6.55 414.0 7.9 281 468 2/20/2019 chronic cholecystitis, cholelithiasis #REF! 2
6675217 7.6 2.7 6.70 2.00 1 0 0 0 36.8 12.43 95.0 0.1 21 21 11/15/2019 #REF! 0
6835549 7.6 2.4 7.60 2.40 1 0 0 0 37.0 5.70 56.0 0.2 25 14 7/12/2019 #REF! 0
6751139 7.6 3.2 6.20 2.90 1 1 0 0 36.6 7.30 224.0 0.2 22 122 2/8/2019 chronic with acute cholecytitis with ectensive mucosal mecrosis. Cholelithiasis #REF! 2
6688579 7.6 3.9 7.60 3.20 1 0 0 0 37.1 4.78 203.0 1.0 265 484 1/17/2019 chronic cholecystitis, cholelithiasis #REF! 2
6845550 7.6 5.3 7.30 3.30 0 0 0 0 36.7 6.00 105.0 1.3 54 22 10/30/2019 cholecystecomy autolyzed gladder wirh focal chronic inflammation and cholesterolosis #REF! 2
6667871 7.6 4.6 7.10 3.70 1 0 0 0 36.6 10.97 0.1 46.0 14 8 1/9/2019 chronic cholecystic with cholelithiasis #REF! 2
6819887 7.7 7.1 7.70 4.80 1 0 0 2 36.7 12.70 112.0 1.2 467 413 3/5/2019 acute and chronic cholecystitis and cholelithiaisis #REF! 1
6712341 7.8 4.1 7.80 3.40 1 0 0 0 37.0 4.30 98.0 0.3 16 14 1/25/2019 chronic cholecystitis and cholelithiasis #REF! 2
6698766 7.8 2.7 7.80 2.70 1 1 0 1 36.5 7.34 61.0 0.4 20 19 1/19/2019 chronic and subacute cholecystitis with cholelithiasis #REF! 2
6704468 7.8 4.7 7.80 2.90 1 0 0 0 NA 11.90 234.0 0.4 109 234 2/21/2019 cholelithiasis without inflammation #REF! 0
6766576 7.8 4.2 7.80 4.20 0 0 0 0 36.8 4.30 147.0 1.1 537 668 2/13/2019 chronic cholecystitis and cholelithiasis and minute fragment of liver tissue #REF! 2
6769913 7.9 5.6 7.50 2.90 1 0 1 0 36.5 16.00 116.0 0.2 21 19 2/15/2019 acute cholecystitis with cholelithiasis #REF! 1
6762433 7.9 5.1 7.90 4.20 1 0 0 0 37.4 13.90 141.0 0.3 19 7 #REF! NA
6885755 7.9 3.5 7.30 3.30 0 0 0 0 36.8 7.15 104.0 0.8 37 17 10/30/2019 Pt developed another bouts of abdominal pain and the GB was resected revealing Autolyzed gallbladder with chronic inflammation #REF! 2
6865894 7.9 3.5 7.90 3.10 1 1 0 1 36.4 13.60 80.0 0.9 89 61 3/20/2019 chronic cholecystis with cholelithiasis and cholesterolosis #REF! 2
6800655 7.9 4.1 7.90 4.00 1 0 0 0 36.3 NA 73.0 1.7 91 91 3/6/2019 #REF! NA
6862622 7.9 5.6 7.90 4.20 1 0 0 0 NA NA NA NA NA NA 7/30/2019 #REF! 0
6758361 8.0 3.2 8.00 3.20 1 1 1 2 37.1 7.80 128.0 0.1 35 45 2/10/2019 acute and chroni cholecystitis #REF! 1
6835338 8.0 2.5 8.00 3.20 1 1 0 1 37.1 13.88 65.0 0.5 39 28 4/18/2019 chronic cholecystits with cholelithiasis #REF! 2
6889846 8.0 4.3 8.00 3.60 1 0 0 0 36.7 8.20 70.0 0.5 30 49 #REF! NA
6828401 8.0 2.1 7.80 2.60 1 1 1 0 36.8 4.97 143.0 2.3 893 1091 3/7/2019 chronic cholecystitis and cholelithiasis #REF! 2
6732504 8.0 4.1 7.80 2.90 1 0 0 0 NA NA NA NA NA NA 7/31/2019 #REF! 0
6778992 8.1 2.8 8.10 2.80 1 0 0 0 36.7 9.10 81.0 0.4 17 16 8/1/2019 #REF! 0
6804140 8.1 3.9 8.10 2.40 1 1 1 1 36.3 6.90 128.0 0.5 397 264 10/18/2019 #REF! 0
6906463 8.1 2.5 7.50 2.30 1 1 1 2 37.0 13.20 209.0 1.7 639 481 4/3/2019 chronic cholecystitis, cholelithaisis #REF! 2
6688368 8.2 2.9 8.20 2.90 1 0 0 0 36.8 6.01 175.0 0.8 199 355 1/17/2019 chronic cholecystitis, cholelithiasis, choledocholithiasis #REF! 2
6784194 8.2 4.0 4.60 1.30 1 1 0 0 36.6 18.20 176.0 0.9 46 104 2/20/2019 chronic cholecystitis, cholelithiasis #REF! 2
6878621 8.3 2.6 8.30 2.40 1 1 1 2 36.4 8.22 52.0 0.1 21 12 3/25/2019 chronic cholecystitis and cholelithiasis #REF! 2
6816477 8.3 5.8 8.40 5.00 0 0 0 0 36.8 4.80 389.0 3.7 109 72 5/10/2019 chronic cholecystitis and cholelithiais #REF! 2
6684878 8.4 3.3 8.40 2.30 1 0 0 0 36.7 6.68 60.0 0.2 24 12 10/18/2019 #REF! 0
6709521 8.4 4.6 8.80 3.30 1 1 0 1 37.1 13.49 80.0 0.2 20 29 1/24/2019 chronic cholecystitis with cholelithiasis #REF! 2
6822537 8.4 3.6 8.40 3.00 1 1 0 1 37.3 18.00 95.0 0.5 14 19 3/7/2019 acute cholecystitis and cholelithiasis #REF! 1
6808654 8.4 4.0 8.40 4.00 1 1 1 0 36.4 4.20 81.0 1.0 18 23 3/5/2019 acute cholecustitis with cholelithiasis #REF! 1
6778180 8.4 4.3 8.40 4.30 0 1 1 0 36.8 25.95 237.0 1.1 54 114 2/18/2019 #REF! NA
6887796 8.4 3.5 6.70 3.20 0 0 0 2 36.5 NA 202.0 1.6 140 207 3/29/2019 chronic cholecystitis and cholelithiasis #REF! 2
6823866 8.4 3.1 8.40 2.60 1 0 0 0 37.8 5.25 NA NA NA NA 3/18/2019 #REF! NA
6801063 8.5 1.9 7.90 1.60 1 0 0 0 36.3 11.40 101.0 0.3 56 33 #REF! NA
6799057 8.5 3.2 8.50 3.00 1 0 0 0 NA 4.10 117.0 1.1 61 21 1/3/2020 #REF! 0
6693819 8.6 3.7 8.40 2.20 1 0 0 0 36.6 9.20 98.0 0.4 18 11 7/23/2019 cholecystectomy chronic cholecystitis #REF! 2
6811783 8.6 2.9 7.00 2.70 1 0 0 0 36.8 6.80 69.0 0.6 51 44 3/1/2019 acute and chronic cholecystitis with cholelithiasis #REF! 1
6766743 8.6 4.4 8.60 2.80 0 0 0 0 37.1 15.50 204.0 0.6 15 31 9/12/2019 cholecystectomy chronic cholecystitis with focally thickened fibrotic wall; cholelithiasis #REF! 2
6817313 8.6 4.3 8.90 3.20 1 0 0 2 37.4 29.20 69.0 1.3 33 24 4/26/2019 acute and chronic cholecystitis and cholelithiasis #REF! 1
6815373 8.7 3.5 8.70 3.10 1 0 0 2 36.6 13.10 90.0 0.4 142 100 #REF! NA
6886089 8.7 2.9 8.70 2.50 0 0 0 0 36.8 8.20 248.0 0.4 39 50 3/28/2019 chronic cholecystitis and cholelithiasis #REF! 2
6680509 8.7 3.8 8.70 2.60 1 0 0 0 36.7 3.87 50.0 0.5 16 11 12/20/2019 #REF! 0
6875890 8.7 5.5 8.70 4.70 1 0 0 0 37.8 23.50 115.0 0.5 20 14 3/26/2019 #REF! NA
6898024 8.7 2.9 8.00 2.70 0 1 0 0 37.1 10.20 291.0 0.8 20 24 4/15/2019 chronic cholecystitis and cholelithiasis #REF! 2
6654436 8.8 4.1 8.80 3.00 1 0 0 0 36.9 12.10 101.0 0.2 17 16 #REF! NA
6840608 9.0 2.4 9.00 2.30 1 0 0 0 NA 8.10 70.0 0.7 22 33 #REF! NA
6902969 9.0 2.9 9.00 2.90 1 0 0 0 36.4 13.20 83.0 1.5 151 121 4/3/2019 chronic cholecystitis, cholelithaisis and cholesterosis #REF! 2
6794560 9.1 3.7 9.00 2.90 1 0 0 0 36.9 6.20 105.0 0.4 23 22 2/25/2019 chronic cholecystitis with cholelithiasis focal moderate dysplasia #REF! 2
6790320 9.2 4.0 9.40 2.90 1 0 0 0 36.8 7.80 12.0 0.4 177 138 3/2/2019 acute cholecystitis cholelithiasis and cholefocholothiasis, mucosal autolysis #REF! 1
6769713 9.3 5.4 9.20 4.80 1 0 0 2 36.5 9.40 190.0 0.2 52 53 2/14/2019 acute and chronic cholecystitis with necrosis and cholelithiasis #REF! 1
6812005 9.3 3.5 6.60 1.90 0 0 0 0 36.3 4.50 82.0 0.5 60 197 3/5/2019 chronic cholecystitis with cholelithiasis #REF! 2
6770316 9.3 3.8 9.30 3.40 1 1 1 2 36.7 9.20 88.0 0.6 63 47 2/14/2019 chronic cholecystitis with cholelithiasis and cholesterolosis #REF! 2
6878434 9.4 5.2 9.40 3.50 1 1 1 2 36.6 8.40 101.0 0.4 15 11 3/25/2019 chronic cholecystitis with focal acute inflammation #REF! 2
6878423 9.4 3.6 9.40 2.30 1 0 0 0 36.8 7.50 105.0 0.4 33 20 7/30/2019 #REF! 0
6780985 9.4 3.9 9.40 3.90 1 0 0 0 36.4 14.88 107.0 0.4 28 9 9/26/2019 #REF! 0
6845633 9.4 3.8 9.40 2.90 0 0 0 0 36.8 8.25 557.0 2.7 358 220 3/14/2019 chronic cholecystitis and cholelithiasis #REF! 2
6725203 9.4 2.6 9.40 2.30 1 0 0 0 NA NA NA NA NA NA 9/24/2019 #REF! 0
6906764 9.5 3.7 9.50 3.60 1 1 0 0 36.5 9.20 97.0 0.2 14 15 4/16/2019 acute cholecystitis and cholelithiasis #REF! 1
6845451 9.8 4.1 8.50 3.30 1 0 0 0 36.2 4.30 102.0 0.4 24 19 2/14/2020 #REF! 0
6758337 10.1 4.5 9.50 3.70 0 1 1 2 36.8 17.90 190.0 0.5 59 190 2/11/2020 acute gangrenous cholecystitis #REF! 1
6787839 10.1 2.9 10.10 2.50 1 0 0 0 NA 36.60 9.2 69.0 86 85 8/9/2019 #REF! 0
6845529 10.1 2.5 10.50 3.60 1 0 0 0 36.8 6.80 13.6 90.0 176 99 1/30/2020 #REF! 0
6658707 10.2 6.3 7.30 2.90 1 1 1 0 36.7 13.85 139.0 0.2 18 39 1/7/2019 cholelithiasis with acute necrituzing cholecystitis with fibrinopurulent excudate and granulation tissue #REF! 1
6820686 10.3 3.6 8.60 2.50 1 0 0 2 36.2 6.40 65.0 0.8 49 135 3/11/2019 acute and chronic cholecystits and cholelithiais with focal reactive epithelial atypia #REF! 1
6739749 10.4 3.7 9.70 3.30 1 0 0 0 36.4 6.36 116.0 0.4 39 39 3/8/2019 cholecystitis with cholelithiasis #REF! 1
6898045 10.4 3.8 10.40 3.80 1 0 0 0 36.3 9.90 129.0 3.0 448 772 4/2/2020 chronic cholecystitis amd cholelithiasis #REF! 2
6906877 10.5 6.4 10.50 4.30 1 0 0 0 36.2 7.30 97.0 0.2 23 20 11/17/2019 #REF! 0
6866070 10.5 3.5 9.30 2.70 1 0 0 0 36.4 8.00 109.0 0.3 37 46 3/23/2019 chronic cholecytitis and cholelithiasus and choledocholithiasis #REF! 2
6738935 10.5 5.3 10.50 3.30 1 1 0 1 36.8 11.20 54.0 0.4 28 18 2/4/2019 acute and chronic cholecystitis with cholelithiasis #REF! 1
6769206 10.5 7.1 7.30 3.70 1 1 1 0 36.7 18.00 87.0 0.4 18 12 3/23/2019 cholecystectomy acute and chronic cholecystitis 2/15/2019 cholecystosyomy #REF! 1
6770748 10.6 3.2 10.30 3.00 1 1 0 2 36.7 8.80 124.0 0.4 18 21 1/24/2020 #REF! 0
6668079 10.6 4.7 10.60 3.50 1 0 0 0 36.6 8.37 145.0 2.3 406 290 1/10/2019 chronic cholecystitis with cholelithiasis #REF! 2
6858673 10.7 4.6 10.70 4.60 1 1 1 2 36.8 10.60 76.0 0.3 17 10 3/18/2019 acute cholecystitis and cholelithiasis #REF! 1
6758138 10.9 3.9 10.90 4.10 1 1 1 2 36.6 11.47 391.0 0.4 177 99 #REF! NA
6711076 10.9 4.7 10.90 4.70 1 0 0 0 36.5 12.90 136.0 1.6 800 672 1/24/2019 chronic cholecysitis with cholelithiasis #REF! 2
6758694 11.0 4.7 11.00 4.00 1 1 1 0 36.3 11.50 NA NA NA NA 2/12/2019 8/23/2019 #REF! NA
6766786 11.1 3.9 10.50 2.80 1 1 0 2 37.2 17.10 66.0 0.9 25 15 2/13/2019 acute and chronic cholycistitis with cholelithiasis #REF! 1
6678713 11.3 4.0 10.30 4.50 1 1 0 1 37.0 13.56 78.0 0.8 14 16 1/13/2019 acute gangrenous cholecystitis and cholelithiaisis #REF! 1
6784389 11.5 3.4 11.50 2.90 1 1 0 0 36.7 13.00 106.0 0.2 21 24 2/20/2019 chronic cholecystitis, cholelithiasis #REF! 2
6757024 11.6 4.6 11.60 3.80 1 1 0 0 36.7 12.10 78.0 0.3 17 14 2/9/2019 acute and chronic cholecystitis with cholelithiasis #REF! 1
6790698 11.7 5.2 11.70 3.80 1 1 1 1 36.7 9.55 104.0 0.5 28 34 2/24/2019 acute and chroni cholecystitis and cholelithiasis #REF! 1
6657766 12.2 4.4 12.20 4.00 1 1 0 0 36.7 9.45 93.0 0.3 16 18 1/6/2019 cholelithiasis with chronic cholecystitis #REF! 2
6811593 12.2 3.4 11.40 2.90 1 0 0 1 36.8 9.60 72.0 0.9 23 23 3/3/2019 acute cholecystitis with cholelithiasis #REF! 1
6660264 12.6 7.9 12.60 4.70 1 0 0 0 37.1 4.30 124.0 0.4 23 21 1/7/2019 acute and chronic cholecystitis with cholelithiasis #REF! 1
6756383 13.2 5.9 8.80 4.90 1 0 0 0 36.3 7.10 1037.0 2.0 130 101 5/16/2019 #REF! 0
6659190 14.1 3.5 11.00 3.50 1 1 1 0 37.0 15.02 53.0 0.1 15 10 1/7/2019 acute, subacute, chronic cholecystits, cholelithiasis #REF! 1
6845905 NA NA 8.90 1.60 1 1 0 1 37.8 13.90 218.0 0.1 18 13 9/18/2019 #REF! 0
6670856 NA NA 7.00 1.90 0 0 0 0 NA 9.50 73.0 0.0 19 16 #REF! NA
6860139 NA NA 6.60 1.80 0 0 0 0 37.1 7.10 5.0 0.1 13 9 12/19/2019 #REF! 0
6722722 NA NA 7.10 1.70 0 0 0 0 NA 5.40 50.0 0.1 17 13 #REF! NA
6758240 NA NA 5.30 1.80 0 0 0 0 36.9 5.00 57.0 0.1 25 14 12/29/2019 #REF! 0
6658798 NA NA 3.90 1.40 0 0 0 0 36.6 13.75 63.0 0.1 17 14 2/23/2019 #REF! 0
6736322 NA NA 7.00 1.60 0 0 0 0 36.8 NA 63.0 0.1 17 10 #REF! NA
6788125 NA NA 3.70 0.40 0 0 0 2 36.7 7.00 64.0 0.1 16 9 5/12/2019 #REF! 0
6763593 NA NA 3.70 1.50 0 0 0 0 36.7 14.60 65.0 0.1 23 35 #REF! NA
6750325 NA NA 6.10 2.90 0 0 0 0 37.0 6.10 66.0 0.1 22 14 #REF! NA
6748873 NA NA 7.40 1.20 0 0 0 0 NA 5.50 67.0 0.1 29 37 4/24/2019 #REF! 0
6688454 NA NA 3.00 0.40 0 0 0 0 36.7 9.60 68.0 0.1 25 21 5/11/2019 #REF! 0
6722709 NA NA 7.10 2.00 0 0 0 0 37.0 9.10 69.0 0.1 15 10 1/26/2020 #REF! 0
6678994 NA NA 6.50 0.70 0 0 0 0 36.7 4.45 70.0 0.1 23 14 9/7/2019 #REF! 0
6750114 NA NA 5.40 2.00 0 0 0 0 36.9 7.12 73.0 0.1 31 42 #REF! NA
6671582 NA NA 1.90 0.50 0 0 0 0 37.0 6.01 74.0 0.1 24 17 #REF! NA
6736310 NA NA 4.60 1.10 0 0 0 0 36.8 7.23 76.0 0.1 19 29 7/7/2019 #REF! 0
6718472 NA NA 5.30 2.60 0 0 0 0 36.5 14.67 77.0 0.1 17 19 11/12/2019 #REF! 0
6718579 NA NA 5.00 2.20 0 0 0 0 37.1 7.70 78.0 0.1 12 11 11/1/2019 #REF! 0
6721015 NA NA 8.40 3.30 0 0 0 0 36.7 7.70 81.0 0.1 22 27 10/19/2019 #REF! 0
6748261 NA NA 8.70 3.70 0 0 0 0 36.3 12.40 81.0 0.1 25 29 #REF! NA
6779252 NA NA 5.50 2.50 0 0 0 0 36.8 6.50 82.0 0.1 15 5 3/22/2020 #REF! 0
6659765 NA NA 4.30 0.80 0 0 0 0 36.7 10.25 82.0 0.1 21 8 2/21/2019 #REF! 0
6736136 NA NA 7.20 1.70 0 0 0 0 36.3 7.95 83.0 0.1 22 22 9/19/2019 #REF! 0
6871783 NA NA 5.70 2.80 0 0 0 0 36.6 8.80 90.0 0.1 21 26 #REF! NA
6736592 NA NA 5.80 1.30 0 0 0 0 37.0 11.70 95.0 0.1 16 8 #REF! NA
6756911 NA NA 5.40 1.70 0 0 0 0 36.7 5.50 107.0 0.1 27 15 #REF! NA
6648838 NA NA 4.80 2.40 0 0 0 0 36.5 9.95 121.0 0.1 8 8 1/23/2020 #REF! 0
6758290 NA NA 7.40 2.00 0 0 0 0 36.6 12.26 125.0 0.1 22 17 12/4/2019 #REF! 0
6768088 NA NA 4.90 2.10 0 0 0 0 36.7 8.20 132.0 0.1 30 12 9/13/2019 #REF! 0
6780613 NA NA 7.70 2.10 0 0 0 0 36.2 6.60 141.0 0.1 18 16 11/1/2019 #REF! 0
6809465 NA NA 5.80 2.40 0 0 0 0 36.3 12.60 147.0 0.1 60 128 3/16/2019 #REF! NA
6736929 NA NA 5.30 1.80 0 0 0 0 36.8 11.40 50.0 0.2 19 10 #REF! NA
6836807 NA NA 5.60 1.80 0 0 0 0 36.7 7.00 55.0 0.2 14 8 12/31/2019 #REF! 0
6832945 NA NA 5.60 2.30 0 0 0 0 36.9 5.10 57.0 0.2 23 26 #REF! NA
6659511 NA NA 11.32 4.14 0 0 0 0 37.3 7.20 58.0 0.2 49 28 7/8/2019 #REF! 0
6730441 NA NA 8.60 2.30 0 0 0 0 36.9 6.30 59.0 0.2 15 6 12/27/2019 #REF! 0
6717954 NA NA 4.50 2.10 0 0 0 0 36.7 10.20 61.0 0.2 18 18 2/8/2019 #REF! NA
6910306 NA NA 2.20 0.60 0 0 0 2 36.8 5.60 65.0 0.2 17 8 #REF! NA
6802615 NA NA 4.80 1.30 0 0 0 0 36.6 7.70 70.0 0.2 17 9 12/20/2019 #REF! 0
6853284 NA NA 6.50 2.10 0 0 0 0 36.8 9.50 70.0 0.2 20 10 1/8/2020 #REF! 0
6906476 NA NA 5.10 2.00 0 0 0 0 36.9 7.70 72.0 0.2 25 18 1/24/2020 #REF! 0
6680016 NA NA 9.40 3.40 0 0 0 0 36.2 8.51 73.0 0.2 13 11 10/28/2019 #REF! 0
6686270 NA NA 6.70 1.70 0 0 0 0 37.0 8.64 73.0 0.2 16 9 9/11/2019 #REF! 0
6703670 NA NA 7.00 1.90 0 0 0 0 NA 6.24 75.0 0.2 17 16 12/4/2019 #REF! 0
6799294 NA NA 5.10 1.20 0 0 0 0 36.9 11.60 81.0 0.2 11 12 #REF! NA
6701838 NA NA 3.40 1.20 0 0 0 0 36.6 5.32 85.0 0.2 18 13 12/28/2019 #REF! 0
6836422 NA NA 8.00 3.80 0 0 0 0 36.8 9.40 85.0 0.2 13 12 #REF! NA
6889674 NA NA 4.80 2.00 0 0 0 0 37.2 3.54 90.0 0.2 30 26 #REF! NA
6811846 NA NA 3.50 2.50 0 0 0 0 36.6 12.50 91.0 0.2 20 15 8/14/2019 #REF! 0
6722735 NA NA 4.00 1.90 0 0 0 0 36.9 4.40 97.0 0.2 85 17 9/8/2019 #REF! 0
6811174 NA NA 4.40 1.60 0 0 0 0 36.7 12.40 97.0 0.2 19 13 1/21/2020 #REF! 0
6796901 NA NA 6.40 3.00 0 0 0 0 37.3 4.17 102.0 0.2 36 15 1/28/2020 #REF! 0
6763192 NA NA 6.40 2.00 0 0 0 0 NA 11.80 111.0 0.2 15 6 5/15/2019 #REF! 0
6876370 NA NA 5.80 1.70 0 0 0 0 36.6 8.40 114.0 0.2 16 12 #REF! NA
6901666 NA NA 4.20 2.00 0 0 0 0 36.6 4.80 123.0 0.2 12 11 11/28/2019 #REF! 0
6744478 NA NA 6.80 2.70 0 0 0 0 36.3 9.60 129.0 0.2 22 35 2/17/2019 #REF! NA
6896714 NA NA 7.30 3.50 0 0 0 0 37.0 14.40 142.0 0.2 16 12 #REF! NA
6876807 NA NA 5.60 1.80 0 0 0 0 36.8 7.07 159.0 0.2 17 12 3/29/2020 #REF! 0
6896243 NA NA 7.00 1.90 0 0 0 0 36.2 9.30 674.0 0.2 55 10 7/31/2019 #REF! 0
6734271 NA NA 5.90 1.70 0 0 0 0 36.6 5.10 43.0 0.3 17 15 #REF! NA
6735171 NA NA 4.50 1.70 0 0 0 0 36.8 4.01 49.0 0.3 22 14 2/4/2019 #REF! NA
6722321 NA NA 5.00 2.60 0 0 0 0 36.8 5.50 51.0 0.3 41 16 9/30/2019 #REF! 0
6808189 NA NA 5.70 1.70 0 0 0 0 37.0 6.10 54.0 0.3 42 22 3/27/2019 #REF! NA
6699034 NA NA 6.00 1.80 0 0 0 0 36.2 7.10 55.0 0.3 27 39 #REF! NA
6823378 NA NA 6.60 3.20 0 0 0 0 36.8 7.90 56.0 0.3 13 11 1/3/2020 #REF! 0
6824800 NA NA 4.40 1.40 0 0 0 0 36.5 14.40 56.0 0.3 33 22 5/13/2019 #REF! 0
6838130 NA NA 6.30 1.80 0 0 0 0 36.3 5.50 57.0 0.3 17 11 12/16/2019 #REF! 0
6895473 NA NA 6.90 3.30 0 0 0 0 36.8 9.90 61.0 0.3 14 6 5/22/2019 #REF! 0
6754874 NA NA 5.40 2.20 0 0 0 0 36.7 7.80 63.0 0.3 37 53 1/23/2020 #REF! 0
6858035 NA NA 6.60 2.50 0 0 0 2 36.5 10.90 66.0 0.3 26 13 #REF! NA
6769675 NA NA 8.40 3.30 0 0 0 0 36.6 4.40 68.0 0.3 18 9 #REF! NA
6881914 NA NA 4.10 1.40 0 0 0 0 37.1 6.00 68.0 0.3 19 22 6/4/2019 #REF! 0
6652150 NA NA 6.10 2.30 0 0 0 0 37.6 6.80 72.0 0.3 28 47 #REF! NA
6908339 NA NA 6.00 2.40 0 0 0 0 36.9 9.50 73.0 0.3 22 25 12/14/2019 #REF! 0
6676877 NA NA 6.00 2.10 0 0 0 0 36.5 11.10 73.0 0.3 26 17 12/5/2019 #REF! 0
6829596 NA NA 6.10 3.20 0 0 0 0 37.1 13.50 73.0 0.3 30 18 #REF! NA
6816350 NA NA 7.60 2.10 0 0 0 0 37.2 9.90 77.0 0.3 27 18 #REF! NA
6778748 NA NA 9.60 3.70 0 0 0 0 37.3 12.90 77.0 0.3 16 14 1/9/2020 #REF! 0
6828404 NA NA 7.50 2.40 0 1 0 0 36.6 10.10 78.0 0.3 18 9 10/15/2019 #REF! 0
6709805 NA NA 7.70 3.80 0 0 0 0 36.0 12.00 81.0 0.3 21 25 #REF! NA
6695190 NA NA 7.00 1.90 0 0 0 0 36.9 7.77 83.0 0.3 18 13 #REF! NA
6777597 NA NA 9.30 2.70 0 0 0 0 36.5 5.20 84.0 0.3 15 12 5/5/2019 #REF! 0
6816055 NA NA 3.90 1.30 0 0 0 0 37.1 7.65 86.0 0.3 28 29 1/2/2020 #REF! 0
6793400 NA NA 8.20 2.20 0 0 0 0 NA 6.40 89.0 0.3 38 45 3/14/2019 #REF! NA
6674939 NA NA 6.50 2.60 0 0 0 0 36.5 3.69 90.0 0.3 114 201 11/25/2019 #REF! 0
6888201 NA NA 4.80 2.70 0 0 0 0 36.2 6.45 101.0 0.3 20 12 11/13/2019 #REF! 0
6650208 NA NA 5.90 2.00 0 0 0 0 37.2 7.13 111.0 0.3 24 15 9/6/2019 #REF! 0
6785260 NA NA 4.60 1.10 0 0 0 0 36.7 7.90 144.0 0.3 23 17 #REF! NA
6778178 NA NA 11.70 3.30 0 0 0 0 37.0 13.80 152.0 0.3 23 25 10/4/2019 #REF! 0
6782584 NA NA 5.20 3.00 0 0 0 0 36.4 9.20 166.0 0.3 20 18 1/29/2020 #REF! 0
6762469 NA NA 5.70 2.80 0 0 0 0 36.6 7.40 170.0 0.3 19 10 7/15/2019 #REF! 0
6765237 NA NA 8.60 2.60 0 0 0 0 36.5 20.70 185.0 0.3 17 8 #REF! NA
6796409 NA NA 6.80 3.10 0 0 0 0 36.3 11.00 33.0 0.4 152 61 3/13/2019 #REF! NA
6663241 NA NA 7.50 2.80 0 0 0 0 NA NA 34.0 0.4 13 10 6/12/2019 #REF! 0
6766292 NA NA 6.50 2.30 0 0 0 0 36.6 11.02 52.0 0.4 18 15 #REF! NA
6776812 NA NA 5.10 1.80 0 0 0 0 NA 6.70 53.0 0.4 24 36 #REF! NA
6699426 NA NA 7.00 2.00 0 0 0 0 37.0 10.40 54.0 0.4 27 14 #REF! NA
6738859 NA NA 6.60 2.70 0 0 0 0 36.9 5.60 57.0 0.4 27 18 #REF! NA
6687275 NA NA 5.50 2.10 0 0 0 0 NA 6.58 60.0 0.4 22 11 #REF! NA
6720361 NA NA 5.50 2.80 0 0 0 0 36.4 8.90 61.0 0.4 17 11 1/10/2020 #REF! 0
6796165 NA NA 6.70 1.20 0 0 0 0 37.1 11.63 62.0 0.4 30 16 #REF! NA
6776929 NA NA 6.40 2.60 0 0 0 0 36.7 4.40 67.0 0.4 19 19 11/22/2019 #REF! 0
6758473 NA NA 6.40 2.80 0 0 0 0 36.3 9.10 68.0 0.4 67 88 #REF! NA
6758673 NA NA 4.30 1.20 0 0 0 0 36.9 9.70 68.0 0.4 102 62 5/14/2019 #REF! 0
6872552 NA NA 5.50 1.50 0 0 0 2 36.8 9.23 69.0 0.4 17 18 1/27/2020 #REF! 0
6670696 NA NA 6.00 2.40 0 0 0 0 36.5 5.51 70.0 0.4 22 30 2/11/2019 #REF! 0
6667803 NA NA 6.20 2.30 0 0 0 0 37.1 6.43 73.0 0.4 15 9 12/2/2019 #REF! 0
6822412 NA NA 6.60 2.50 0 0 0 0 36.6 7.40 74.0 0.4 19 19 9/19/2019 #REF! 0
6724627 NA NA 7.40 2.60 0 0 0 2 36.8 20.10 75.0 0.4 16 12 11/13/2019 #REF! 0
6771420 NA NA 6.90 2.60 0 0 0 0 36.2 5.70 79.0 0.4 27 15 #REF! NA
6826866 NA NA 5.60 2.00 0 0 0 0 37.0 8.50 81.0 0.4 17 19 5/10/2019 #REF! 0
6811868 NA NA 4.80 1.30 0 0 0 0 36.8 6.80 83.0 0.4 32 31 #REF! NA
6735209 NA NA 5.30 2.20 0 0 0 0 36.3 6.80 85.0 0.4 54 137 2/10/2019 #REF! NA
6827948 NA NA 7.70 3.40 0 0 0 0 36.6 8.80 85.0 0.4 52 77 #REF! NA
6774831 NA NA 5.90 2.40 0 0 0 0 36.6 9.50 89.0 0.4 23 13 9/8/2019 #REF! 0
6684634 NA NA 5.60 2.30 0 0 0 0 36.5 10.93 92.0 0.4 20 18 3/14/2019 #REF! 0
6808444 NA NA 5.50 1.50 0 0 0 0 36.5 12.50 95.0 0.4 20 41 1/31/2020 #REF! 0
6657923 NA NA 6.60 3.00 0 0 0 0 NA 5.90 96.0 0.4 22 16 8/29/2019 #REF! 0
6770191 NA NA 7.50 2.80 0 0 0 0 36.9 11.30 98.0 0.4 30 22 12/13/2019 #REF! 0
6865278 NA NA 6.50 3.20 0 0 0 0 36.9 13.10 101.0 0.4 51 24 6/4/2019 #REF! 0
6779962 NA NA 7.60 1.60 0 0 0 0 36.6 4.90 114.0 0.4 21 16 4/29/2019 #REF! 0
6716655 NA NA 5.40 2.70 0 0 0 0 36.6 4.03 123.0 0.4 30 18 #REF! NA
6896670 NA NA 5.80 2.80 0 0 0 0 36.6 12.50 146.0 0.4 13 16 #REF! NA
6678751 NA NA 5.10 1.60 0 0 0 0 36.9 10.66 149.0 0.4 14 11 8/27/2019 #REF! 0
6882768 NA NA 8.00 1.70 0 0 0 0 36.8 34.79 150.0 0.4 16 35 12/12/2019 #REF! 0
6681794 NA NA 7.80 2.20 0 0 0 0 36.3 10.70 163.0 0.4 71 77 8/14/2019 #REF! 0
6857348 NA NA 7.60 2.10 0 1 1 0 36.4 17.40 200.0 0.4 152 829 7/15/2019 #REF! 0
6848596 NA NA 5.50 2.00 0 0 0 0 NA 4.20 33.0 0.5 21 16 5/30/2019 #REF! 0
6829459 NA NA 7.00 2.70 0 0 0 0 36.9 4.60 41.0 0.5 30 38 12/6/2019 #REF! 0
6702253 NA NA 8.30 2.10 0 0 0 1 36.7 9.30 49.0 0.5 33 33 #REF! NA
6868583 NA NA 9.80 2.80 0 0 0 0 37.0 14.70 49.0 0.5 15 13 #REF! NA
6906327 NA NA 5.90 2.70 0 0 0 0 36.7 7.00 63.0 0.5 18 17 1/15/2020 #REF! 0
6705568 NA NA 7.30 2.30 0 0 0 0 36.8 17.60 63.0 0.5 30 17 #REF! NA
6711333 NA NA 7.50 1.70 0 0 0 0 36.8 17.60 63.0 0.5 30 17 #REF! NA
6849036 NA NA 7.60 2.40 0 0 0 0 36.2 8.40 65.0 0.5 35 32 3/27/2019 #REF! NA
6909899 NA NA 4.20 1.30 0 0 0 0 NA 10.90 65.0 0.5 16 10 12/10/2019 #REF! 0
6678085 NA NA 6.60 1.50 0 0 0 0 36.5 5.00 66.0 0.5 31 17 7/31/2019 #REF! 0
6724817 NA NA 6.30 3.00 0 0 0 0 36.7 18.50 66.0 0.5 58 86 10/14/2019 #REF! 0
6700370 NA NA 4.80 1.60 0 0 0 0 37.0 9.40 69.0 0.5 28 36 #REF! NA
6696107 NA NA 6.00 1.80 0 0 0 0 37.0 7.20 71.0 0.5 31 31 11/21/2019 #REF! 0
6812015 NA NA 8.90 3.70 0 0 0 0 36.4 7.90 72.0 0.5 17 11 #REF! NA
6765290 NA NA 3.80 1.10 0 0 0 0 NA NA 74.0 0.5 57 98 10/8/2019 #REF! 0
6902609 NA NA 6.40 2.10 0 0 0 0 36.3 7.30 84.0 0.5 20 10 #REF! NA
6690261 NA NA 5.60 3.40 0 0 0 0 36.9 4.35 90.0 0.5 72 76 #REF! NA
6679841 NA NA 5.20 2.20 0 0 0 0 36.7 4.20 92.0 0.5 32 30 1/9/2020 #REF! 0
6821735 NA NA 6.40 2.50 0 0 0 0 36.7 9.10 94.0 0.5 18 15 10/7/2019 #REF! 0
6800491 NA NA 3.40 1.30 0 0 0 0 36.6 4.40 95.0 0.5 17 20 #REF! NA
6691612 NA NA 4.90 1.90 0 0 0 0 37.9 10.48 95.0 0.5 45 13 #REF! NA
6646452 NA NA 5.90 2.30 0 0 0 0 36.7 10.07 99.0 0.5 50 110 1/17/2020 #REF! 0
6878097 NA NA 6.10 3.00 0 0 0 0 36.8 7.00 106.0 0.5 30 19 10/10/2019 #REF! 0
6814328 NA NA 6.10 2.60 0 0 0 0 36.6 11.20 130.0 0.5 36 52 3/19/2019 #REF! NA
6835575 NA NA 5.70 2.90 0 0 0 0 36.5 10.80 133.0 0.5 24 20 1/2/2020 #REF! 0
6775822 NA NA 13.80 5.10 0 0 0 0 36.9 6.20 170.0 0.5 22 19 #REF! NA
6716652 NA NA 6.70 2.40 0 0 0 0 36.8 17.70 192.0 0.5 19 26 #REF! NA
6715370 NA NA 8.80 1.40 0 0 0 0 36.6 15.67 303.0 0.5 25 25 3/18/2019 #REF! 0
6763086 NA NA 5.60 1.80 0 0 0 0 36.8 7.30 34.0 0.6 18 15 #REF! NA
6885377 NA NA 7.70 2.10 0 0 0 0 37.0 7.50 45.0 0.6 33 31 #REF! NA
6816880 NA NA 7.20 3.70 0 0 0 0 36.8 9.30 45.0 0.6 24 20 1/23/2020 #REF! 0
6682675 NA NA 5.40 0.70 0 1 0 0 36.6 4.04 47.0 0.6 6 5 1/10/2020 #REF! 0
6712931 NA NA 5.80 2.00 0 0 0 0 36.9 6.99 71.0 0.6 16 17 11/7/2019 #REF! 0
6815735 NA NA 6.30 2.00 0 0 0 0 36.6 12.20 72.0 0.6 15 5 #REF! NA
6674885 NA NA 5.60 1.40 0 0 0 0 37.2 10.80 75.0 0.6 25 28 #REF! NA
6824544 NA NA 9.00 2.70 0 0 0 0 37.1 7.77 77.0 0.6 27 14 4/29/2019 #REF! 0
6872627 NA NA 3.80 0.70 0 0 0 0 37.0 6.80 80.0 0.6 36 36 10/1/2019 #REF! 0
6882390 NA NA 4.10 2.50 0 0 0 0 36.2 23.20 81.0 0.6 15 13 #REF! NA
6712683 NA NA 6.30 1.60 0 0 0 0 37.6 17.27 82.0 0.6 18 14 5/17/2019 #REF! 0
6889823 NA NA 4.60 3.30 0 0 0 0 36.9 5.20 87.0 0.6 27 13 12/19/2019 #REF! 0
6684662 NA NA 5.30 1.10 0 0 0 0 36.3 8.10 88.0 0.6 30 20 9/15/2019 #REF! 0
6700722 NA NA 5.20 2.10 0 0 0 0 36.5 14.48 88.0 0.6 125 68 1/13/2020 #REF! 0
6852587 NA NA 9.10 3.50 0 0 0 0 36.4 9.50 99.0 0.6 34 35 11/29/2019 #REF! 0
6795729 NA NA 5.80 2.30 0 0 0 0 37.3 9.12 105.0 0.6 115 179 3/21/2019 #REF! NA
6906728 NA NA 4.10 1.50 0 0 0 0 36.3 13.00 106.0 0.6 19 25 11/21/2019 #REF! 0
6820468 NA NA 8.00 3.40 0 0 0 0 37.0 11.80 115.0 0.6 25 35 4/17/2019 #REF! 0
6825843 NA NA 8.60 2.00 0 0 0 0 36.9 8.80 135.0 0.6 15 9 11/21/2019 #REF! 0
6681644 NA NA 6.60 2.40 0 0 0 0 36.7 10.00 35.0 0.7 29 35 #REF! NA
6652536 NA NA 9.60 1.70 0 0 0 0 37.2 10.30 47.0 0.7 20 10 11/22/2019 #REF! 0
6766775 NA NA 3.20 2.20 0 0 0 0 37.0 8.60 66.0 0.7 21 20 12/24/2019 #REF! 0
6717930 NA NA 6.90 2.80 0 0 0 0 36.8 5.70 68.0 0.7 25 20 9/14/2019 #REF! 0
6802557 NA NA 7.70 2.60 0 0 0 0 NA 7.80 75.0 0.7 22 21 1/13/2020 #REF! 0
6804400 NA NA 6.80 3.30 0 0 1 0 37.3 8.90 81.0 0.7 108 108 10/8/2019 #REF! 0
6883532 NA NA 5.20 2.80 0 0 0 0 36.9 8.30 96.0 0.7 19 13 7/6/2019 #REF! 0
6837684 NA NA 7.00 3.90 0 0 0 0 36.4 16.40 110.0 0.7 33 32 #REF! NA
6777704 NA NA 4.90 1.60 0 0 0 2 36.8 7.10 499.0 0.7 60 74 12/16/2019 #REF! 0
6876351 NA NA 11.00 3.50 0 0 0 0 36.4 5.40 46.0 0.8 796 984 9/26/2019 #REF! 0
6877667 NA NA 6.40 2.40 0 0 0 0 36.7 5.00 79.0 0.8 22 42 #REF! NA
6880969 NA NA 5.60 2.00 0 0 0 0 37.1 9.70 92.0 0.8 14 8 1/29/2020 #REF! 0
6905000 NA NA 5.80 1.90 0 0 0 0 36.3 7.50 106.0 0.8 23 21 3/11/2020 #REF! 0
6876282 NA NA 7.30 2.60 0 0 0 0 36.6 7.77 116.0 0.8 36 51 1/24/2020 #REF! 0
6725962 NA NA 7.10 1.70 0 0 0 0 36.8 5.70 137.0 0.8 31 28 2/7/2019 #REF! NA
6837145 NA NA 7.80 2.40 0 0 0 0 37.2 10.40 63.0 0.9 18 14 10/25/2019 #REF! 0
6862899 NA NA 6.00 2.20 0 1 0 0 37.2 4.50 237.0 0.9 48 99 1/21/2020 #REF! 0
6660224 NA NA 5.60 2.40 0 0 0 0 36.3 4.36 313.0 0.9 524 313 #REF! NA
6716949 NA NA 7.40 2.10 0 0 0 0 36.2 6.50 46.0 1.0 26 16 1/27/2020 #REF! 0
6700289 NA NA 6.30 3.50 0 0 0 0 38.0 16.72 61.0 1.0 50 42 1/28/2020 #REF! 0
6737750 NA NA 5.90 2.70 0 0 0 0 36.2 5.70 89.0 1.0 21 11 10/30/2019 #REF! 0
6702867 NA NA 7.90 2.80 0 0 0 0 36.5 9.51 47.0 1.1 23 16 3/14/2019 #REF! 0
6701265 NA NA 5.80 1.50 0 0 0 0 36.6 12.50 76.0 1.1 23 32 #REF! NA
6667630 NA NA 5.20 1.70 0 0 0 0 36.7 7.20 85.0 1.1 24 18 #REF! NA
6898162 NA NA 7.30 4.10 0 0 0 0 36.8 3.20 110.0 1.1 181 111 9/17/2019 #REF! 0
6856856 NA NA 8.50 2.30 0 1 1 0 36.4 7.10 216.0 1.2 1002 1912 7/15/2019 #REF! 0
6835375 NA NA 7.30 2.40 0 0 0 0 36.5 10.44 51.0 1.3 50 40 #REF! NA
6817734 NA NA 4.30 2.10 0 0 0 0 36.6 7.30 64.0 1.4 42 17 1/29/2020 #REF! 0
6717266 NA NA 5.20 1.70 0 1 0 0 36.8 6.40 186.0 1.4 38 18 5/29/2019 #REF! 0
6776985 NA NA 5.80 1.90 0 0 0 0 36.6 7.70 52.0 1.5 21 17 8/9/2019 #REF! 0
6869578 NA NA 7.40 2.40 0 0 0 0 36.8 10.70 138.0 1.5 173 97 #REF! NA
6680993 NA NA 6.20 2.60 0 0 0 0 36.6 2.42 65.0 1.6 33 20 #REF! NA
6806196 NA NA 5.70 1.70 0 0 0 0 36.2 7.70 57.0 1.8 55 22 #REF! NA
6813931 NA NA 7.60 3.10 0 0 0 0 36.4 10.60 94.0 1.8 20 8 #REF! NA
6877598 NA NA 5.60 2.30 0 0 0 0 36.8 3.90 46.0 2.0 66 57 10/30/2019 #REF! 0
6841761 NA NA 7.20 1.90 0 0 0 0 36.7 3.40 331.0 2.0 267 57 8/5/2019 #REF! 0
6845384 NA NA 9.20 3.40 0 0 0 0 36.9 3.60 219.0 2.3 134 95 12/10/2019 #REF! 0
6698395 NA NA 5.70 1.40 0 0 0 0 37.3 9.69 104.0 3.1 71 30 11/27/2019 #REF! 0
6643378 NA NA 8.20 2.40 0 0 0 0 37.1 9.44 69.0 6.5 136 106 1/18/2020 #REF! 0
6686511 NA NA 12.20 3.40 0 1 0 2 36.7 19.87 112.0 NA 28 14 2/19/2019 #REF! 0
6906660 NA NA 6.70 1.90 0 0 0 0 36.3 2.80 NA NA NA NA 4/11/2019 #REF! NA
6833558 NA NA 4.60 0.60 0 0 0 0 36.7 5.40 NA NA NA NA 11/1/2019 #REF! 0
6675024 NA NA 7.30 3.10 0 0 0 0 36.7 15.60 NA NA NA NA #REF! NA
6802811 NA NA 7.70 3.10 0 0 0 0 36.4 NA NA NA NA NA 12/6/2019 #REF! 0
6821213 NA NA 4.20 1.80 0 NA 0 0 36.5 NA NA NA NA NA 2/14/2020 #REF! 0
6796333 NA NA 5.50 2.40 0 0 0 0 36.7 NA NA NA NA NA #REF! NA
6759785 NA NA 5.70 2.60 0 0 0 0 36.8 NA NA NA NA NA #REF! NA
6762069 NA NA 6.70 2.50 0 0 0 0 36.8 NA NA NA NA NA #REF! NA
6677185 NA NA 5.00 2.20 0 0 0 0 36.9 NA NA NA NA NA #REF! NA
6835036 NA NA 6.60 2.30 0 0 0 0 37.1 NA NA NA NA NA #REF! NA
6778890 NA NA 2.60 0.70 0 0 0 0 NA NA NA NA NA NA #REF! NA
6735708 NA NA 3.30 0.90 0 0 0 0 NA NA NA NA NA NA 6/7/2019 #REF! 0
6886175 NA NA 3.50 1.50 0 0 0 0 NA NA NA NA NA NA #REF! NA
6801685 NA NA 3.70 1.80 0 0 0 0 NA NA NA NA NA NA 4/23/2019 #REF! 0
6889205 NA NA 4.40 1.80 0 0 0 0 NA NA NA NA NA NA #REF! NA
6683872 NA NA 4.80 2.30 0 1 0 0 NA NA NA NA NA NA #REF! NA
6712273 NA NA 4.90 1.40 0 0 0 0 NA NA NA NA NA NA 3/6/2019 #REF! 0
6651753 NA NA 5.10 2.20 0 0 0 0 NA NA NA NA NA NA #REF! NA
6576934 NA NA 5.20 2.20 0 0 0 0 NA NA NA NA NA NA #REF! NA
6735577 NA NA 5.30 2.20 0 0 0 0 NA NA NA NA NA NA 10/15/2019 #REF! 0
6706231 NA NA 5.40 1.00 0 0 0 0 NA NA NA NA NA NA #REF! NA
6762962 NA NA 5.40 1.90 0 1 0 0 NA NA NA NA NA NA 4/12/2019 #REF! 0
6553234 NA NA 5.50 0.80 0 0 0 0 NA NA NA NA NA NA #REF! NA
6883110 NA NA 5.50 2.40 0 0 0 0 NA NA NA NA NA NA 6/11/2019 #REF! 0
6805939 NA NA 5.50 2.70 0 0 0 0 NA NA NA NA NA NA #REF! NA
6811497 NA NA 5.60 1.70 0 0 0 0 NA NA NA NA NA NA 1/16/2020 #REF! 0
6790803 NA NA 5.60 2.00 0 0 0 0 NA NA NA NA NA NA 12/14/2019 #REF! 0
6807226 NA NA 5.60 2.20 0 0 0 0 NA NA NA NA NA NA 7/24/2019 #REF! 0
6760618 NA NA 5.70 2.10 0 0 0 0 NA NA NA NA NA NA #REF! NA
6741565 NA NA 5.80 2.30 0 0 0 0 NA NA NA NA NA NA #REF! NA
6674469 NA NA 5.80 2.70 0 0 0 0 NA NA NA NA NA NA #REF! NA
6774328 NA NA 5.90 2.10 0 0 0 0 NA NA NA NA NA NA 10/23/2019 #REF! 0
6870329 NA NA 5.90 2.20 0 0 0 0 NA NA NA NA NA NA 1/9/2020 #REF! 0
6767522 NA NA 6.00 1.80 0 0 0 0 NA NA NA NA NA NA #REF! NA
6840187 NA NA 6.00 2.10 0 0 0 0 NA NA NA NA NA NA 12/3/2019 #REF! 0
6833511 NA NA 6.20 1.90 0 0 0 0 NA NA NA NA NA NA 12/27/2019 #REF! 0
6768834 NA NA 6.30 3.10 0 0 0 0 NA NA NA NA NA NA 8/19/2019 #REF! 0
6784694 NA NA 6.40 2.00 0 0 0 0 NA NA NA NA NA NA 2/19/2020 #REF! 0
6685317 NA NA 6.40 2.30 0 0 0 0 NA NA NA NA NA NA #REF! NA
6870774 NA NA 6.40 2.70 0 0 0 0 NA NA NA NA NA NA 3/4/2020 #REF! 0
6656560 NA NA 6.50 2.00 0 0 0 0 NA NA NA NA NA NA 5/31/2019 #REF! 0
6764127 NA NA 6.50 2.40 0 0 0 0 NA NA NA NA NA NA 10/24/2019 #REF! 0
6864305 NA NA 6.60 1.00 0 0 0 0 NA NA NA NA NA NA 7/16/2019 #REF! 0
6676153 NA NA 6.70 2.10 0 0 0 0 NA NA NA NA NA NA 6/5/2019 #REF! 0
6818823 NA NA 6.70 2.40 0 0 0 0 NA NA NA NA NA NA 7/27/2019 #REF! 0
6720148 NA NA 6.70 3.60 0 0 0 0 NA NA NA NA NA NA 11/26/2019 #REF! 0
6783006 NA NA 6.80 1.90 0 0 0 0 NA NA NA NA NA NA 9/23/2019 #REF! 0
6708843 NA NA 7.00 1.80 0 0 0 0 NA NA NA NA NA NA #REF! NA
6809725 NA NA 7.00 2.10 0 0 0 0 NA NA NA NA NA NA 4/22/2019 #REF! 0
6425029 NA NA 7.00 2.10 0 0 0 0 NA NA NA NA NA NA #REF! NA
6818149 NA NA 7.00 2.90 0 0 0 0 NA NA NA NA NA NA 1/13/2020 #REF! 0
6783468 NA NA 7.00 3.40 0 0 0 0 NA NA NA NA NA NA 1/17/2020 #REF! 0
6790658 NA NA 7.10 2.40 0 0 0 0 NA NA NA NA NA NA #REF! NA
6670837 NA NA 7.20 2.50 0 0 0 0 NA NA NA NA NA NA 11/15/2019 #REF! 0
6792860 NA NA 7.30 1.70 0 0 0 0 NA NA NA NA NA NA 1/28/2020 #REF! 0
6826384 NA NA 7.40 2.30 0 0 0 0 NA NA NA NA NA NA 3/12/2020 #REF! 0
6747131 NA NA 7.50 2.30 0 0 0 0 NA NA NA NA NA NA 1/31/2020 #REF! 0
6806009 NA NA 7.50 2.90 0 0 0 0 NA NA NA NA NA NA 7/19/2019 #REF! 0
6822060 NA NA 7.50 3.30 0 0 0 0 NA NA NA NA NA NA 3/19/2020 #REF! 0
6822908 NA NA 7.60 2.00 0 0 0 0 NA NA NA NA NA NA 7/23/2019 #REF! 0
6828591 NA NA 7.70 2.00 0 0 0 0 NA NA NA NA NA NA 4/29/2019 #REF! 0
6855861 NA NA 7.70 2.60 0 0 0 0 NA NA NA NA NA NA 1/16/2020 #REF! 0
6868746 NA NA 7.70 2.70 0 0 0 0 NA NA NA NA NA NA 1/29/2020 #REF! 0
6825780 NA NA 7.90 2.40 0 0 0 0 NA NA NA NA NA NA 5/2/2019 #REF! 0
6709819 NA NA 8.00 3.30 0 0 0 0 NA NA NA NA NA NA 5/6/2019 #REF! 0
6899524 NA NA 8.10 2.10 0 0 0 0 NA NA NA NA NA NA 11/20/2020 #REF! 0
6603728 NA NA 9.40 2.60 0 0 0 0 NA NA NA NA NA NA 6/19/2019 #REF! 0

Filtering Down to Necessary Data for Testing

As the data is present, there are 456 observations alongside 21 variables. 21 variables gives unnecessary extra information to analyze. For the epidemiological testing and analysis that is required for this project, only two categorical variables are required: gallstones, which are the presence or absence of gallstones in the gallbladder, and Final_Dx, which is the presence or absence of the inflammation that results in Cholecystitis in the gallbladder. To only examine these two variables, the select() function would be utilized, separating the gallstones and Final_Dx from the rest of the unecessary data:

gall_and_infl_test <- select(test_data, gallstones, Final_Dx)

Now that the two categorical variables required for testing are selected, the next step is to find the necessary observations to do epidemiological testing. To do that, the table() function (while including any potential empty observations), will be utilized to figure out how many categorical observations there are using

table(gall_and_infl_test$gallstones, useNA = "always")
## 
##    0    1 <NA> 
##  300  156    0

For the variable gallstones, there are two categorical observations: 0 for no gallstones present and 1 for gallstones present.

table(gall_and_infl_test$Final_Dx, useNA = "always")
## 
##    0    1    2 <NA> 
##  224   35   60  137

For the variable Final_Dx, which is the inflammation detected by the test, there are four categorical observations: 0 which represents no inflammation present, 1 which represents inflammation present, 2 which represents in between, and NA which represents not available.

For testing the effectiveness of the Cholecystitis screening test, both observations for gallstones and two observations for Final_Dx: 0 for no inflammation present and 1 for inflammation present, will be selected and utilized. Here’s what the data set looks like now after filtering for the required observations for testing:

true_gall_and_infl_test <- filter(gall_and_infl_test, Final_Dx == 1 | Final_Dx == 0)
true_gall_and_infl_test %>%
  kbl() %>%
   kable_classic("striped", html_font = "Cambria", position = "center")%>%
  scroll_box(width = "100%", height = "200px")
gallstones Final_Dx
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
0 1
1 0
1 0
1 0
1 1
0 1
1 0
1 1
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 1
1 1
1 0
1 1
1 0
1 0
1 1
1 1
1 0
1 1
1 0
1 0
1 0
1 1
1 0
1 0
1 1
1 0
1 1
1 0
1 1
1 0
1 0
1 0
1 0
1 1
1 1
1 0
1 1
1 1
1 0
1 1
1 1
1 0
1 0
1 0
1 1
1 0
0 1
1 0
1 0
1 1
1 1
1 1
1 0
1 1
1 1
1 0
1 1
1 1
1 1
1 1
1 1
1 1
1 1
1 0
1 1
1 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0
0 0

Now that the necessary observations for running epidemiological testing in the two categorical variables have been acquired, the next step is to isolate the four possible outcomes of the data for testing the effectiveness of the Cholecystitis screen test.

Formatting The Testing Table

To be able to perform the four epidemiological tests: sensitivity, specificity, PPV, and NPV, a certain format of the conditions is required so that when the function epi.tests() is used, an accurate result will be acquired. To visualize the format for the epidemiological tests, a picture from the Penn State Elbery College of Science: Epidemiological Research Methods will be provided:

There are four possible outcomes all inserted into a table:
A for True Positive; in the data: 1 gallstone present and 1 Final_Dx (inflammation) present
B for False Positive; in the data: 1 gallstone present and 0 Final_Dx (inflammation) present
C for False Negative; in the data: 0 gallstone present and 1 Final_Dx (inflammation) present
D for True Negative; in the data: 0 gallstone present and 0 Final_Dx (inflammation) present

To set our table up in the format of the test, it is required to extract the four possible outcomes (results) of the Cholecystitis screen test data and put them in a table. To do that, the table() function will be used:

Cholecystitis_results <- table(true_gall_and_infl_test$gallstones, true_gall_and_infl_test$Final_Dx)
Cholecystitis_results %>%
  kbl() %>%
   kable_classic(full_width = F, html_font = "Cambria", position = "left", font_size = 22)
0 1
0 175 3
1 49 32

Comparing this table to the formatting provided by the Penn State Elbery College of Science, there’s a clear and glaring problem: True negatives (0-0) and true positives (1-1) alongside false positives(1-0) and false negatives(0-1) have swapped places. This will cause inaccuracies in running the epidemiological tests for determining the accuracy of the Cholecystitis test.

To fix this error, a simple table formatting fix would be required, where normally a table in R is indented from [1:N], it would be indented instead to [N:1], or in this case, from [1:2] to [2:1]:

Cholecystitis_results <- table(true_gall_and_infl_test$gallstones, true_gall_and_infl_test$Final_Dx)[2:1,2:1]
Cholecystitis_results %>%
  kbl() %>%
   kable_classic(full_width = F, html_font = "Cambria", position = "left", font_size = 22)
1 0
1 32 49
0 3 175

Now that the Cholecystitis screen test outcomes are formatted correctly, the epidemiological testing and analysis can begin.

Running The Test: Results

The function epi.tests() from the epi.R package to produce the sensitivity, specificity, PPV, and NPV of the Cholecystitis test:

epi.tests(Cholecystitis_results)
##           Outcome +    Outcome -      Total
## Test +           32           49         81
## Test -            3          175        178
## Total            35          224        259
## 
## Point estimates and 95 % CIs:
## ---------------------------------------------------------
## Apparent prevalence                    0.31 (0.26, 0.37)
## True prevalence                        0.14 (0.10, 0.18)
## Sensitivity                            0.91 (0.77, 0.98)
## Specificity                            0.78 (0.72, 0.83)
## Positive predictive value              0.40 (0.29, 0.51)
## Negative predictive value              0.98 (0.95, 1.00)
## Positive likelihood ratio              4.18 (3.20, 5.46)
## Negative likelihood ratio              0.11 (0.04, 0.32)
## ---------------------------------------------------------

Analyzing The Results

Sensitivity

Sensitivity of a medical screen test is the measurement of how often a test correctly generates a positive result for patients who have the condition they’re being tested for. In the context of Cholecystitis, the sensitivity of the Cholecystitis screen test measures how often the test will correctly generate a true positive result for patients who have Cholecystitis. The equation to find the sensitivity is as follows:

(True Positives / (True Positives + False negatives)) * 100

In the testing, the sensitivity of the Cholecystitis screen test was 91%, meaning that of the patients who did have Cholecystitis, 91% got a true positive result while 9% got a false negative result, which is negative result (no gallstones) while still having Cholecystitis. 91% sensitivity means that the test is good at determining whether a patient who has Cholecystitis is told they they have Cholecystitis by finding the presence of gallstones in the gallbladder. If the test wasn’t good at determining Cholecystitis by presence of gallstones, then another medical screen test would be required to replace this particular Cholecystitis screen test, as gallstone presence wouldn’t be a good indicator to telling a patient whether they have Cholecystitis.

Specificity

Specificity of a medical screen test is the measurement of the test’s ability to correctly generate a negative result for patients who don’t have the condition that they’re being tested for. In the context of Cholecystitis, the specificity of the Cholecystitis screen test measures how often the test will correctly generate a true negative result for patients who don’t have Cholecystitis. The equation to find the specificity is as follows:

(True Negatives / (True Negatives + False Positives)) * 100

As a general rule, sensitivity and specificity exist on a balance; when sensitivity is high, it generally means that specificity is low, and it is no different for the specificity of the Cholecystitis screen test, which is 78%. 78% specificity means that 78% of patients who didn’t have Chilecystitis were told that they didn’t have Cholecystitis, while 22% percent of patients who didn’t have Cholecystitis were told that they did have Cholecystitis. This is due to the fact 22% of patients in the data set tested positive for gallstones but didn’t actually have Cholecystitis. 78% specificty means that the test is okay at determining whether a patient who doesn’t have Cholecystitis is actually told that they don’t have Cholecystitis.

Positive Predictive Value (PPV)

The Positive Predictive Value (PPV) is the percent chance that a patient actually has the disease that they’ve tested positive for in a screen test in a given population. In the context of Cholecystitis, It is the percent chance that a patient who tests positive for the screen test of gallstones actually has Cholecystitis. PPV is calculated by the following equation:

(True Positive / (True Positive + False Positive)) * 100

In the epidemiological testing, the PPV came out to 40%. While it seems low, this is generally an ok PPV compared to other PPV for different tests like prostate cancer and breast cancer, who respectively, have 30% and 4.3%-52.4%. The number is generally low due to the fact that when epidemiological screening tests are being designed, they’re designed with a high-risk population in mind, meaning that when the population being tested is at low-risk of Cholecystitis, even if they have gallstones, they’re less likely to have Cholecystitis.

Negative Predictive Value (NPV)

The Negative Predictive Value (NPV) is the percent chance that a patinet actually doesn’t has the disease that they’ve tested negative for in a screen test in a given population. In the context of Cholecystitis, It is the percent chance that a patient who tests negative for the screen test of gallstones doesn’t have Cholecystitis. PPV is calculated by the following equation:

(True Negative / (True Negative + False Negative)) * 100

In the epidemiological testing, the NPV came out to 98%. This is incredibly high and basically means that if a patient tests negative for gallstones, they usually don’t have Cholecystitis.

Is the Cholecystitis Screening Test Effective?

A screening test’s true purpose is to be able to eliminate the possibility of a certain condition being present. The test should also come positive for patients with the actual condition that they’re being screen tested for, because giving false negatives for patients who have a certain medical condition is catastrophic. With that said, the Cholecystitis screening test that screens gallstones presence is a good test at determining whether a medical patient has cholecystitis or not. If the patient tests negative for gallstones, there’s a 98% chance that they don’t have Cholecystitis. If the patient tests positive for gallstones, there’s a 40% chance that they have Cholecystitis mainly due to the fact that there’s a 22% a patient has received false positive, where they have gallstones but not Cholecystitis. This is where additional testing is required to determine whether the patient has Cholecystitis. Finally, when a patient actually has Cholecystitis, the condition they’re being screen tested for, there’s a 91% chance that they’ll be accurately told that they have Cholecystitis due to the presence of gallstones, which means that this test is effective at finding people who have Cholecystitis.

Putting everything together, the Cholecystitis screen test is great at eliminating the possibility of Cholecystitis being present if patients don’t have gallstones, and this test is great at telling patients who have Cholecystitis that they actually have Cholecystitis due to the presence of gallstones in the gallbladder.