viral_hepatitis

load data from google drive

location_levels=c("Jordan", "Global", "Low SDI", "Low-middle SDI", "Middle SDI", "High-middle SDI", "High SDI")
hepatitis <- c("Acute hepatitis A", "Acute hepatitis B", "Acute hepatitis C", "Acute hepatitis E", "Chronic hepatitis B including cirrhosis", "Chronic hepatitis C including cirrhosis", "Liver cancer due to hepatitis B"  , "Liver cancer due to hepatitis C"  )

ds<- read.csv("IHME-GBD_2021_DATA-fc56ed34-1.csv") %>% 
  mutate(location=factor(location, levels=location_levels)) %>% 
  filter(cause %nin% c("Liver cancer due to hepatitis B"  , "Liver cancer due to hepatitis C", "Liver cancer"))

show types of columns

sapply(ds, class)

##     measure    location         sex         age       cause      metric 
## "character"    "factor" "character" "character" "character" "character" 
##        year         val       upper       lower 
##   "integer"   "numeric"   "numeric"   "numeric"

show all unique column values of the dataframem excluding the last 3 columns

lapply(ds[, -c(8, 9, 10)], unique)

## $measure
## [1] "Deaths"                                
## [2] "DALYs (Disability-Adjusted Life Years)"
## [3] "YLDs (Years Lived with Disability)"    
## [4] "YLLs (Years of Life Lost)"             
## [5] "Prevalence"                            
## [6] "Incidence"                             
## 
## $location
## [1] Global          High-middle SDI High SDI        Low-middle SDI 
## [5] Low SDI         Middle SDI      Jordan         
## 7 Levels: Jordan Global Low SDI Low-middle SDI Middle SDI ... High SDI
## 
## $sex
## [1] "Male"   "Female" "Both"  
## 
## $age
## [1] "All ages"         "15-49 years"      "50-69 years"      "70+ years"       
## [5] "Age-standardized" "0-14 years"      
## 
## $cause
##  [1] "Chronic hepatitis B including cirrhosis"   
##  [2] "Chronic hepatitis C including cirrhosis"   
##  [3] "Cirrhosis and other chronic liver diseases"
##  [4] "Acute hepatitis"                           
##  [5] "Acute hepatitis A"                         
##  [6] "Acute hepatitis B"                         
##  [7] "Acute hepatitis C"                         
##  [8] "Acute hepatitis E"                         
##  [9] "Total burden related to hepatitis B"       
## [10] "Total burden related to hepatitis C"       
## 
## $metric
## [1] "Number" "Rate"  
## 
## $year
## [1] 1980 1990 2000 2010 2021 2020

Jordan

Incidence in numbers over years

ds %>%  
  filter(measure=="Incidence", sex=="Both", age=="All ages", cause %in% hepatitis, metric == "Number", location=="Jordan") %>%
  mutate(val=paste(round(val, 2), "(UI:", round(lower, 2), "-", round(upper, 2), ")")) %>% 
  select(year, cause, val) %>% 
  spread(year, val) %>% 
  gt()

cause	1990	2000	2010	2020	2021
Acute hepatitis A	134192.03 (UI: 124114.94 - 143547.12 )	157090.65 (UI: 146985.23 - 167387.86 )	218153.73 (UI: 205047.09 - 232481.54 )	289270.6 (UI: 273334.31 - 304922.38 )	292506.72 (UI: 277253.62 - 308697.01 )
Acute hepatitis B	40009.25 (UI: 31210.39 - 51535.58 )	42211.37 (UI: 31271.76 - 55145.79 )	48807.66 (UI: 35619.69 - 65423.97 )	59483.29 (UI: 42092.74 - 79174.97 )	56523.57 (UI: 41176.27 - 74961.88 )
Acute hepatitis C	3568.48 (UI: 3034.88 - 4144.85 )	4298.21 (UI: 3721.26 - 4958.44 )	5194.11 (UI: 4508.6 - 5906.1 )	10151.56 (UI: 8658.45 - 11760.89 )	10633.15 (UI: 9063.45 - 12317.2 )
Acute hepatitis E	5420.8 (UI: 4408.33 - 6724.17 )	6664.95 (UI: 5359.5 - 8230.7 )	10090.34 (UI: 8199.51 - 12326.16 )	14533 (UI: 11917.53 - 17586.14 )	14990.63 (UI: 12352.25 - 18133.09 )
Chronic hepatitis B including cirrhosis	5364.09 (UI: 4102.41 - 6781.3 )	3636.65 (UI: 2791 - 4693.31 )	3307.05 (UI: 2603.76 - 4109.66 )	4324.01 (UI: 3466.11 - 5325.09 )	4044.07 (UI: 3287.35 - 4786.43 )
Chronic hepatitis C including cirrhosis	2357.45 (UI: 1903.84 - 2846.94 )	2839.53 (UI: 2339.27 - 3414.89 )	3430.96 (UI: 2849.03 - 4041.79 )	6706.04 (UI: 5523.99 - 8047.41 )	7024.78 (UI: 5695.18 - 8376.44 )

Prevalence in numbers over years

ds %>%  
  filter(measure=="Prevalence", sex=="Both", age=="All ages", cause %in% hepatitis, metric == "Number", location=="Jordan") %>%
  mutate(val=paste(round(val, 2), "(UI:", round(lower, 2), "-", round(upper, 2), ")")) %>% 
  select(year, cause, val) %>% 
  spread(year, val) %>% 
  gt()

cause	1990	2000	2010	2020	2021
Acute hepatitis A	10225.62 (UI: 9478.57 - 10921.54 )	12035.1 (UI: 11271.55 - 12812.43 )	16769.84 (UI: 15764.45 - 17870.3 )	22245.19 (UI: 21021.66 - 23448.54 )	22494.18 (UI: 21322.41 - 23738.59 )
Acute hepatitis B	4560.43 (UI: 3535.37 - 5893.07 )	4864.29 (UI: 3600.16 - 6357.39 )	5626.24 (UI: 4104.55 - 7544.46 )	6841.79 (UI: 4830.1 - 9111.88 )	6506.43 (UI: 4732.96 - 8634.06 )
Acute hepatitis C	411.75 (UI: 350.18 - 478.25 )	495.95 (UI: 429.38 - 572.13 )	599.32 (UI: 520.22 - 681.47 )	1171.33 (UI: 999.05 - 1357.03 )	1226.9 (UI: 1045.78 - 1421.22 )
Acute hepatitis E	415.39 (UI: 337.72 - 515.22 )	510.91 (UI: 410.96 - 631.12 )	773.83 (UI: 629.27 - 945.47 )	1115.46 (UI: 913.78 - 1349.77 )	1150.68 (UI: 947.78 - 1392.1 )
Chronic hepatitis B including cirrhosis	183822.6 (UI: 156351.73 - 212020.88 )	190961.86 (UI: 166778.79 - 219051.69 )	200835.45 (UI: 176427.98 - 228019.12 )	241598.22 (UI: 213926.34 - 272319.18 )	239580.4 (UI: 215767.58 - 266969.71 )
Chronic hepatitis C including cirrhosis	52095.71 (UI: 41275.84 - 63378.07 )	65727.61 (UI: 52718.97 - 80046.23 )	80861.5 (UI: 66089.58 - 96325.2 )	183258.87 (UI: 148184.66 - 220257.44 )	195093.32 (UI: 156976.99 - 236667.89 )

Prevalence in numbers according to sex in 2021

ds %>%  
  filter(measure=="Prevalence",  age=="All ages", cause %in% hepatitis, metric == "Number", location=="Jordan", year==2021) %>%
  mutate(val=paste(round(val, 2), "(UI:", round(lower, 2), "-", round(upper, 2), ")")) %>% 
  select(sex, cause, val) %>% 
  spread(sex, val) %>% 
  gt()

cause	Both	Female	Male
Acute hepatitis A	22494.18 (UI: 21322.41 - 23738.59 )	10715.41 (UI: 10127.77 - 11323.34 )	11778.78 (UI: 11087.08 - 12499.56 )
Acute hepatitis B	6506.43 (UI: 4732.96 - 8634.06 )	2789.1 (UI: 1901.67 - 4021.62 )	3717.33 (UI: 2513.84 - 5338.24 )
Acute hepatitis C	1226.9 (UI: 1045.78 - 1421.22 )	723.92 (UI: 616.15 - 848.71 )	502.98 (UI: 425.74 - 583.48 )
Acute hepatitis E	1150.68 (UI: 947.78 - 1392.1 )	525.69 (UI: 423.96 - 643.47 )	625 (UI: 510.94 - 757.58 )
Chronic hepatitis B including cirrhosis	239580.4 (UI: 215767.58 - 266969.71 )	102275.88 (UI: 90390.18 - 114074.68 )	137304.52 (UI: 118763.39 - 158360.89 )
Chronic hepatitis C including cirrhosis	195093.32 (UI: 156976.99 - 236667.89 )	120705.18 (UI: 96221.75 - 147436.27 )	74388.14 (UI: 60438.97 - 90602.19 )

Prevalence in numbers according to age in 2021

ds %>%  
  filter(measure=="Prevalence",  sex=="Both", cause %in% hepatitis, metric == "Number", location=="Jordan", year==2021) %>%
  mutate(val=paste(round(val, 2), "(UI:", round(lower, 2), "-", round(upper, 2), ")")) %>% 
  select(age, cause, val) %>% 
  spread(age, val) %>% 
  gt()

cause	0-14 years	15-49 years	50-69 years	70+ years	All ages
Acute hepatitis A	16797.43 (UI: 15538.11 - 17998.38 )	5572.3 (UI: 4690.56 - 6219.94 )	123.95 (UI: 69.39 - 187.65 )	0.5 (UI: 0.1 - 1.38 )	22494.18 (UI: 21322.41 - 23738.59 )
Acute hepatitis B	419.65 (UI: 297.37 - 557.81 )	4538.84 (UI: 3131.39 - 6366.02 )	1340.16 (UI: 827.92 - 1952.73 )	207.79 (UI: 110.79 - 329.23 )	6506.43 (UI: 4732.96 - 8634.06 )
Acute hepatitis C	370.21 (UI: 295.36 - 463.55 )	545.89 (UI: 401.93 - 723.2 )	230.42 (UI: 152.23 - 320.8 )	80.38 (UI: 56.92 - 113.84 )	1226.9 (UI: 1045.78 - 1421.22 )
Acute hepatitis E	539.51 (UI: 373.7 - 711.48 )	508.6 (UI: 346.44 - 700.1 )	77.94 (UI: 48.1 - 117.04 )	24.62 (UI: 15.4 - 36.82 )	1150.68 (UI: 947.78 - 1392.1 )
Chronic hepatitis B including cirrhosis	17993.11 (UI: 14462.56 - 21577.23 )	151881.41 (UI: 135083.81 - 171178.23 )	58888.99 (UI: 52538.05 - 65643.7 )	10816.89 (UI: 9322.67 - 12537.61 )	239580.4 (UI: 215767.58 - 266969.71 )
Chronic hepatitis C including cirrhosis	25772.14 (UI: 19441.89 - 33598.82 )	102194.35 (UI: 80179.1 - 126837.77 )	50976.62 (UI: 39856.61 - 62865.97 )	16150.2 (UI: 12734.32 - 19677.33 )	195093.32 (UI: 156976.99 - 236667.89 )

DALYs in numbers according to age in 2021 (Jordan vs Global)

ds %>%  
  filter(measure=="DALYs (Disability-Adjusted Life Years)",  sex=="Both", cause %in% hepatitis, metric == "Number", location %in% c("Jordan", "Global"), year==2021, age!="All ages") %>%
  select(age, cause, val, location) %>% 
  ggplot(aes(x=age, y=val, fill=cause))+
  geom_col(position="fill")+
  theme_classic()+
  scale_y_continuous(labels = scales::percent_format(scale = 100)) +
  labs(y="")+
  theme(axis.text.x.bottom = element_text(angle=45, hjust=1, vjust=1))+
  facet_wrap(.~location)+
  theme(strip.background = element_blank())

Table 1: Incidence and Prevalence of Acute Hepatitis (A, B, C, D) in Jordan vs. Global Data

Comparison of Age-Standardized Incidence Rates of Hepatitis by Type in 2021: Jordan vs. Global and Other SDI Regions

ds %>%  
  filter(measure=="Incidence", sex=="Both", age=="Age-standardized",  cause %in% hepatitis, metric == "Rate", year==2021) %>%
  mutate(val=paste(round(val, 2), "(UI:", round(lower, 2), "-", round(upper, 2), ")")) %>% 
  select(location, cause, val) %>% 
  spread(cause, val) %>% 
  gt()

location	Acute hepatitis A	Acute hepatitis B	Acute hepatitis C	Acute hepatitis E	Chronic hepatitis B including cirrhosis	Chronic hepatitis C including cirrhosis
Jordan	2362.97 (UI: 2230.62 - 2510.15 )	484.65 (UI: 352.01 - 635.32 )	99.03 (UI: 85.21 - 112.02 )	120.7 (UI: 101.19 - 144.91 )	34.83 (UI: 28.23 - 41.28 )	65.43 (UI: 53.96 - 77.55 )
Global	2273.72 (UI: 2150.13 - 2403.76 )	784.73 (UI: 627.37 - 968.45 )	92.64 (UI: 82.13 - 104.65 )	260.41 (UI: 215.39 - 312.21 )	61.51 (UI: 52.44 - 69.81 )	59.37 (UI: 48.9 - 70.74 )
Low SDI	2667.7 (UI: 2447.86 - 2897.46 )	1393.98 (UI: 1116.02 - 1717.64 )	142.6 (UI: 125.82 - 160.48 )	282.79 (UI: 233.55 - 338.04 )	116.33 (UI: 97.56 - 134.49 )	93.28 (UI: 77.38 - 110.68 )
Low-middle SDI	2485.43 (UI: 2305.27 - 2681.18 )	774.8 (UI: 626.58 - 939.41 )	116.9 (UI: 104.31 - 130.47 )	297.18 (UI: 246.75 - 356.25 )	58.62 (UI: 50.63 - 66.17 )	71.77 (UI: 58.78 - 86.29 )
Middle SDI	2131.51 (UI: 2009.05 - 2253.01 )	797.98 (UI: 624.29 - 1005.99 )	79.45 (UI: 69.97 - 90.42 )	266.05 (UI: 220.4 - 320.71 )	56.69 (UI: 48.04 - 65.21 )	52.01 (UI: 42.69 - 61.99 )
High-middle SDI	1938.13 (UI: 1800 - 2067.84 )	605.8 (UI: 448.08 - 796.69 )	66.64 (UI: 58.54 - 75.34 )	237.66 (UI: 197.76 - 286.64 )	38.76 (UI: 30.83 - 47.33 )	43.4 (UI: 35.61 - 51.7 )
High SDI	1277.66 (UI: 1173.77 - 1375.22 )	287.32 (UI: 237.52 - 348.01 )	56.84 (UI: 49.84 - 63.9 )	128.48 (UI: 109.06 - 150.84 )	19.55 (UI: 16.99 - 21.99 )	35.83 (UI: 29.29 - 42.94 )

Comparison of Age-Standardized Prevalence Rates of Hepatitis by Type in 2021: Jordan vs. Global and Other SDI Regions

ds %>%  
  filter(measure=="Prevalence", sex=="Both", age=="Age-standardized",  cause %in% hepatitis, metric == "Rate", year==2021) %>%
  mutate(val=paste(round(val, 2), "(UI:", round(lower, 2), "-", round(upper, 2), ")")) %>% 
  select(location, cause, val) %>% 
  spread(cause, val) %>% 
  gt()

location	Acute hepatitis A	Acute hepatitis B	Acute hepatitis C	Acute hepatitis E	Chronic hepatitis B including cirrhosis	Chronic hepatitis C including cirrhosis
Jordan	181.7 (UI: 171.5 - 193.03 )	55.77 (UI: 40.47 - 73.17 )	11.43 (UI: 9.83 - 12.93 )	9.26 (UI: 7.77 - 11.12 )	2122.48 (UI: 1918.29 - 2360.22 )	1818.29 (UI: 1476.06 - 2206.82 )
Global	169.78 (UI: 161.32 - 178.68 )	90.12 (UI: 71.93 - 111.29 )	10.69 (UI: 9.48 - 12.08 )	19.99 (UI: 16.53 - 23.97 )	3490.14 (UI: 3197.57 - 3789.02 )	1704.79 (UI: 1373.46 - 2061.7 )
Low SDI	188.46 (UI: 177.43 - 200.61 )	159.85 (UI: 127.72 - 197.22 )	16.45 (UI: 14.52 - 18.52 )	21.71 (UI: 17.92 - 25.96 )	6589.66 (UI: 6037.89 - 7162.34 )	2683.12 (UI: 2168.26 - 3222.34 )
Low-middle SDI	176.56 (UI: 165.84 - 187.62 )	89.07 (UI: 71.91 - 108.06 )	13.49 (UI: 12.04 - 15.05 )	22.82 (UI: 18.94 - 27.36 )	3236.52 (UI: 2970.95 - 3512.34 )	2049.35 (UI: 1640.24 - 2497.14 )
Middle SDI	162.83 (UI: 153.54 - 172.01 )	91.9 (UI: 71.85 - 115.9 )	9.17 (UI: 8.07 - 10.43 )	20.42 (UI: 16.92 - 24.63 )	3476.98 (UI: 3167.27 - 3792.47 )	1642.8 (UI: 1328.41 - 1986.5 )
High-middle SDI	148.94 (UI: 138.29 - 158.9 )	69.84 (UI: 51.64 - 91.86 )	7.69 (UI: 6.75 - 8.69 )	18.24 (UI: 15.18 - 22.01 )	2902.15 (UI: 2615.53 - 3194.68 )	1423.33 (UI: 1151.43 - 1729.23 )
High SDI	98.28 (UI: 90.28 - 105.78 )	33.14 (UI: 27.39 - 40.14 )	6.56 (UI: 5.75 - 7.37 )	9.86 (UI: 8.36 - 11.58 )	1013.73 (UI: 938.31 - 1093.2 )	949.64 (UI: 768.19 - 1152.89 )

Table 2: Burden of Hepatitis-Related Cancer and Cirrhosis in Jordan vs. Low/Middle/High SDI Regions

chronic_hepatitis_cirrhosis<- c("Chronic hepatitis B including cirrhosis", "Chronic hepatitis C including cirrhosis", "Liver cancer due to hepatitis B", "Liver cancer due to hepatitis C")

ds %>%  
  filter(measure=="DALYs (Disability-Adjusted Life Years)", sex=="Both", age=="Age-standardized",  cause %in% chronic_hepatitis_cirrhosis, metric == "Rate", year==2021) %>%
  mutate(val=paste(round(val, 2), "(UI:", round(lower, 2), "-", round(upper, 2), ")")) %>% 
  select(location, cause, val) %>% 
  spread(cause, val) %>% 
  gt()

location	Chronic hepatitis B including cirrhosis	Chronic hepatitis C including cirrhosis
Jordan	51.87 (UI: 35.38 - 72.87 )	72.94 (UI: 52.9 - 96.49 )
Global	161.92 (UI: 137.25 - 186.25 )	137.99 (UI: 117.99 - 159.91 )
Low SDI	322.71 (UI: 264.21 - 386.61 )	249.3 (UI: 203.4 - 302.86 )
Low-middle SDI	253.06 (UI: 200.9 - 302.18 )	242.65 (UI: 200.78 - 285.44 )
Middle SDI	172.14 (UI: 147.37 - 198.01 )	121.26 (UI: 106.04 - 141.19 )
High-middle SDI	108.23 (UI: 89.42 - 127.14 )	67.79 (UI: 55.41 - 83.95 )
High SDI	42.7 (UI: 35.19 - 50.33 )	92.46 (UI: 80.7 - 107.79 )

Table 3: DALYs and Mortality Rates for Hepatitis in Jordan and Comparative Regions

Age-Standardized DALYs (Disability-Adjusted Life Years) Rates for Hepatitis and Related Conditions in 2021: Jordan vs. Global and Other SDI Regions

total_hepatitis=c("Chronic hepatitis B including cirrhosis", "Chronic hepatitis C including cirrhosis" , "Acute hepatitis" , "Acute hepatitis A","Acute hepatitis B", "Acute hepatitis C", "Acute hepatitis E", "Liver cancer due to hepatitis B", "Liver cancer due to hepatitis C" ,  "Total burden related to hepatitis B", "Total burden related to hepatitis C")

ds %>%  
  filter(measure=="DALYs (Disability-Adjusted Life Years)", sex=="Both", age=="Age-standardized",  cause %in% total_hepatitis, metric == "Rate", year==2021) %>%
  mutate(val=paste(round(val, 2), "(UI:", round(lower, 2), "-", round(upper, 2), ")")) %>% 
  select(location, cause, val) %>% 
  spread(cause, val) %>% 
  gt()

location	Acute hepatitis	Acute hepatitis A	Acute hepatitis B	Acute hepatitis C	Acute hepatitis E	Chronic hepatitis B including cirrhosis	Chronic hepatitis C including cirrhosis	Total burden related to hepatitis B	Total burden related to hepatitis C
Jordan	11.21 (UI: 8.49 - 14.32 )	4.7 (UI: 3.31 - 6.64 )	5.06 (UI: 3.5 - 7.15 )	0.8 (UI: 0.52 - 1.24 )	0.66 (UI: 0.39 - 1.01 )	51.87 (UI: 35.38 - 72.87 )	72.94 (UI: 52.9 - 96.49 )	69.9 (UI: 50.36 - 93.06 )	85.81 (UI: 64.34 - 110.68 )
Global	56.74 (UI: 44.11 - 75.55 )	24.95 (UI: 17.32 - 39.12 )	25.19 (UI: 18.32 - 31.15 )	3.41 (UI: 1.48 - 5.88 )	3.18 (UI: 1.73 - 5.23 )	161.92 (UI: 137.25 - 186.25 )	137.99 (UI: 117.99 - 159.91 )	252.48 (UI: 219.37 - 285.18 )	177.24 (UI: 155.21 - 201.04 )
Low SDI	119.4 (UI: 93.11 - 159.57 )	43.21 (UI: 28.39 - 71.24 )	62.52 (UI: 43.45 - 82.08 )	8.99 (UI: 1.89 - 19.45 )	4.69 (UI: 2.25 - 8.4 )	322.71 (UI: 264.21 - 386.61 )	249.3 (UI: 203.4 - 302.86 )	445.65 (UI: 370.13 - 522.65 )	293.97 (UI: 242.56 - 352.15 )
Low-middle SDI	102.72 (UI: 77.97 - 141.34 )	50.44 (UI: 33.21 - 86.19 )	39.75 (UI: 25.65 - 54.94 )	7.17 (UI: 2.77 - 12.32 )	5.36 (UI: 2.62 - 9.96 )	253.06 (UI: 200.9 - 302.18 )	242.65 (UI: 200.78 - 285.44 )	329.77 (UI: 270.43 - 382.35 )	287.18 (UI: 243.29 - 328.84 )
Middle SDI	35.26 (UI: 28.47 - 42.46 )	11.21 (UI: 7.52 - 19.62 )	19.46 (UI: 13.14 - 26.5 )	1.76 (UI: 1.14 - 2.6 )	2.83 (UI: 1.56 - 4.63 )	172.14 (UI: 147.37 - 198.01 )	121.26 (UI: 106.04 - 141.19 )	282.27 (UI: 244.78 - 323.1 )	153.04 (UI: 135.53 - 174.81 )
High-middle SDI	11.58 (UI: 9.58 - 14.03 )	4.5 (UI: 3.24 - 6.42 )	5.76 (UI: 4.52 - 7.18 )	0.43 (UI: 0.29 - 0.63 )	0.9 (UI: 0.61 - 1.34 )	108.23 (UI: 89.42 - 127.14 )	67.79 (UI: 55.41 - 83.95 )	194.77 (UI: 163.63 - 232.42 )	99.31 (UI: 85.37 - 116.88 )
High SDI	4.81 (UI: 3.63 - 6.36 )	2.91 (UI: 1.99 - 4.01 )	1.4 (UI: 1.12 - 1.75 )	0.17 (UI: 0.11 - 0.26 )	0.33 (UI: 0.25 - 0.44 )	42.7 (UI: 35.19 - 50.33 )	92.46 (UI: 80.7 - 107.79 )	77.61 (UI: 67.69 - 87.44 )	136.82 (UI: 122.59 - 152.8 )

Age-Standardized Mortality Rates for Hepatitis and Related Conditions in 2021: Jordan vs. Global and Other SDI Regions

total_hepatitis=c("Chronic hepatitis B including cirrhosis", "Chronic hepatitis C including cirrhosis" , "Acute hepatitis" , "Acute hepatitis A","Acute hepatitis B", "Acute hepatitis C", "Acute hepatitis E", "Liver cancer due to hepatitis B", "Liver cancer due to hepatitis C" ,  "Total burden related to hepatitis B", "Total burden related to hepatitis C")

ds %>%  
  filter(measure=="Deaths", sex=="Both", age=="Age-standardized",  cause %in% total_hepatitis, metric == "Rate", year==2021) %>%
  mutate(val=paste(round(val, 2), "(UI:", round(lower, 2), "-", round(upper, 2), ")")) %>% 
  select(location, cause, val) %>% 
  spread(cause, val) %>% 
  gt()

location	Acute hepatitis	Acute hepatitis A	Acute hepatitis B	Acute hepatitis C	Acute hepatitis E	Chronic hepatitis B including cirrhosis	Chronic hepatitis C including cirrhosis	Total burden related to hepatitis B	Total burden related to hepatitis C
Jordan	0.21 (UI: 0.15 - 0.3 )	0.05 (UI: 0.03 - 0.08 )	0.13 (UI: 0.08 - 0.2 )	0.02 (UI: 0.01 - 0.04 )	0.01 (UI: 0.01 - 0.02 )	2.25 (UI: 1.55 - 3.17 )	3.2 (UI: 2.23 - 4.24 )	2.84 (UI: 2.01 - 3.81 )	3.81 (UI: 2.82 - 4.9 )
Global	0.92 (UI: 0.73 - 1.2 )	0.35 (UI: 0.24 - 0.57 )	0.45 (UI: 0.33 - 0.57 )	0.07 (UI: 0.03 - 0.11 )	0.05 (UI: 0.02 - 0.08 )	5.03 (UI: 4.26 - 5.85 )	4.29 (UI: 3.67 - 4.98 )	7.57 (UI: 6.57 - 8.58 )	6.1 (UI: 5.38 - 6.82 )
Low SDI	2.62 (UI: 2.08 - 3.4 )	0.84 (UI: 0.52 - 1.56 )	1.46 (UI: 1.01 - 1.93 )	0.23 (UI: 0.04 - 0.49 )	0.1 (UI: 0.04 - 0.19 )	10.75 (UI: 8.8 - 12.78 )	8.29 (UI: 6.82 - 10.13 )	14.17 (UI: 11.86 - 16.52 )	10.14 (UI: 8.46 - 11.99 )
Low-middle SDI	1.95 (UI: 1.53 - 2.56 )	0.86 (UI: 0.58 - 1.43 )	0.83 (UI: 0.51 - 1.16 )	0.17 (UI: 0.06 - 0.28 )	0.09 (UI: 0.04 - 0.16 )	8.33 (UI: 6.63 - 10.07 )	8.19 (UI: 6.71 - 9.71 )	10.34 (UI: 8.4 - 12.15 )	9.93 (UI: 8.43 - 11.45 )
Middle SDI	0.58 (UI: 0.49 - 0.68 )	0.15 (UI: 0.09 - 0.28 )	0.35 (UI: 0.25 - 0.46 )	0.03 (UI: 0.02 - 0.05 )	0.04 (UI: 0.02 - 0.08 )	5.7 (UI: 4.85 - 6.63 )	3.9 (UI: 3.36 - 4.49 )	8.97 (UI: 7.72 - 10.38 )	5.37 (UI: 4.72 - 6.06 )
High-middle SDI	0.15 (UI: 0.13 - 0.17 )	0.03 (UI: 0.02 - 0.04 )	0.1 (UI: 0.08 - 0.12 )	0.01 (UI: 0 - 0.01 )	0.01 (UI: 0.01 - 0.02 )	3.52 (UI: 2.9 - 4.13 )	2.12 (UI: 1.77 - 2.56 )	6.13 (UI: 5.18 - 7.28 )	3.61 (UI: 3.15 - 4.1 )
High SDI	0.03 (UI: 0.03 - 0.04 )	0.01 (UI: 0.01 - 0.01 )	0.02 (UI: 0.02 - 0.02 )	0 (UI: 0 - 0 )	0 (UI: 0 - 0 )	1.35 (UI: 1.13 - 1.57 )	2.95 (UI: 2.59 - 3.41 )	2.54 (UI: 2.21 - 2.89 )	5.21 (UI: 4.64 - 5.76 )

Table 4: Socio-Demographic Index (SDI) Classification and Regional Comparisons Table 5: Summary of Statistical Analyses and Significant Findings

Figures ## Figure 1: Trends in Incidence of Acute Hepatitis in Jordan and Globally

ds %>%  
  filter(measure=="Incidence", sex=="Both", age=="Age-standardized",  cause =="Acute hepatitis", metric == "Rate") %>%
  select(location, year, val) %>% 
  ggplot(aes(x=year, y=val, color=fct_reorder(location, val, tail,n=1, .desc=T)))+
  geom_point()+
  geom_line()+
  theme_classic()+
  labs(color="Location", y="Age-standardized Incidence per 100,000", x="Year")+
  scale_y_continuous(limits=c(1000,7000), breaks=seq(1000,7000,1000), labels=paste0(1:7, ",000"))

Figure 2: Prevalence of Hepatitis-Related Cancer and Cirrhosis by Region and SDI Level

ds %>%  
  filter(measure=="Prevalence", sex=="Both", age=="Age-standardized",  cause %in% c("Chronic hepatitis B including cirrhosis", "Chronic hepatitis C including cirrhosis", "Liver cancer"), metric == "Rate") %>%
  select(location, year, val, cause) %>% 
  ggplot(aes(x=year, y=val, color=location))+
  geom_point()+
  geom_line()+
  theme_classic()+
  labs(color="Location", y="Age-standardized Prevalence per 100,000", x="Year")+
  facet_wrap(.~cause, scales="free")+
  theme(strip.background = element_blank())

  # scale_y_continuous(limits=c(1000,7000), breaks=seq(1000,7000,1000), labels=paste0(1:7, ",000"))

Figure 3: DALYs Attributed to Hepatitis in Jordan vs. Low/Middle/High SDI Regions

# Filter the data
filtered_data <- ds %>%
  filter(measure == "DALYs (Disability-Adjusted Life Years)", 
         sex == "Both", 
         age == "Age-standardized",  
         cause %in% c("Acute hepatitis A", "Acute hepatitis B", "Acute hepatitis C", "Acute hepatitis E", "Chronic hepatitis B including cirrhosis", "Chronic hepatitis C including cirrhosis"), 
         metric == "Rate", 
         year == 2021) %>%
  select(location, cause, val) %>% 
  mutate(cause=factor(cause, levels=c("Acute hepatitis A", "Acute hepatitis B", "Acute hepatitis C", "Acute hepatitis E", "Chronic hepatitis B including cirrhosis", "Chronic hepatitis C including cirrhosis"), labels = c("Acute hepatitis A", "Acute hepatitis B", "Acute hepatitis C", "Acute hepatitis E", "Chronic hepatitis B", "Chronic hepatitis C")))


# Create a column plot using ggplot2
# Create a column plot using ggplot2
ggplot(filtered_data, aes(x = cause, y = val, fill = location)) +
  geom_col(position = "dodge") +
  labs(x = "Cause",
       y = "Age-standardized DALYs Rate per 100,000",
       fill = "Location") +
  theme_classic() +
  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))

Figure 4: Mortality Rates for Hepatitis in Jordan Compared to Global Figures

# Filter the data
filtered_data <- ds %>%
  filter(measure == "Deaths", 
         sex == "Both", 
         age == "Age-standardized",  
         cause %in% c("Acute hepatitis A", "Acute hepatitis B", "Acute hepatitis C", "Acute hepatitis E", "Chronic hepatitis B including cirrhosis", "Chronic hepatitis C including cirrhosis"), 
         metric == "Rate", 
         year == 2021) %>%
  select(location, cause, val) %>% 
  mutate(cause=factor(cause, levels=c("Acute hepatitis A", "Acute hepatitis B", "Acute hepatitis C", "Acute hepatitis E", "Chronic hepatitis B including cirrhosis", "Chronic hepatitis C including cirrhosis"), labels = c("Acute hepatitis A", "Acute hepatitis B", "Acute hepatitis C", "Acute hepatitis E", "Chronic hepatitis B", "Chronic hepatitis C")))


# Create a column plot using ggplot2
# Create a column plot using ggplot2
ggplot(filtered_data, aes(x = cause, y = val, fill = location)) +
  geom_col(position = "dodge") +
  labs(x = "Cause",
       y = "Age-standardized Death Rate per 100,000",
       fill = "Location") +
  theme_classic() +
  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))

viral_hepatitis_jordan

2024-05-23