1.

prerenal

library(gmodels) 
## Registered S3 method overwritten by 'gdata':
##   method         from     
##   reorder.factor DescTools
prerenal <- master %>% filter(final_type_of_aki==1) %>% select(response_group,alcoholic_hepatitis_admission)
gmodels::CrossTable(prerenal$response_group,prerenal$alcoholic_hepatitis_admission, prop.chisq=F,chisq = T,prop.r=F, prop.c=F,
           prop.t=F)
## 
##  
##    Cell Contents
## |-------------------------|
## |                       N |
## |-------------------------|
## 
##  
## Total Observations in Table:  902 
## 
##  
##                         | prerenal$alcoholic_hepatitis_admission 
## prerenal$response_group |         0 |         1 | Row Total | 
## ------------------------|-----------|-----------|-----------|
##             no response |       185 |        21 |       206 | 
## ------------------------|-----------|-----------|-----------|
##        overall response |       607 |        89 |       696 | 
## ------------------------|-----------|-----------|-----------|
##            Column Total |       792 |       110 |       902 | 
## ------------------------|-----------|-----------|-----------|
## 
##  
## Statistics for All Table Factors
## 
## 
## Pearson's Chi-squared test 
## ------------------------------------------------------------
## Chi^2 =  0.9982308     d.f. =  1     p =  0.317739 
## 
## Pearson's Chi-squared test with Yates' continuity correction 
## ------------------------------------------------------------
## Chi^2 =  0.7707446     d.f. =  1     p =  0.3799868 
## 
##

HRS_AKI

HRS_AKI <- master %>% filter(final_type_of_aki==2) %>% select(response_group,alcoholic_hepatitis_admission)
gmodels::CrossTable(HRS_AKI$response_group,HRS_AKI$alcoholic_hepatitis_admission, prop.chisq=F,chisq = T,prop.r=F, prop.c=F,
           prop.t=F)
## 
##  
##    Cell Contents
## |-------------------------|
## |                       N |
## |-------------------------|
## 
##  
## Total Observations in Table:  247 
## 
##  
##                        | HRS_AKI$alcoholic_hepatitis_admission 
## HRS_AKI$response_group |         0 |         1 | Row Total | 
## -----------------------|-----------|-----------|-----------|
##            no response |       126 |        30 |       156 | 
## -----------------------|-----------|-----------|-----------|
##       overall response |        79 |        12 |        91 | 
## -----------------------|-----------|-----------|-----------|
##           Column Total |       205 |        42 |       247 | 
## -----------------------|-----------|-----------|-----------|
## 
##  
## Statistics for All Table Factors
## 
## 
## Pearson's Chi-squared test 
## ------------------------------------------------------------
## Chi^2 =  1.487656     d.f. =  1     p =  0.2225806 
## 
## Pearson's Chi-squared test with Yates' continuity correction 
## ------------------------------------------------------------
## Chi^2 =  1.090213     d.f. =  1     p =  0.296424 
## 
##

ATN

ATN <- master %>% filter(final_type_of_aki==3) %>% select(response_group,alcoholic_hepatitis_admission)
gmodels::CrossTable(ATN$response_group,ATN$alcoholic_hepatitis_admission, prop.chisq=F,chisq = T,prop.r=F, prop.c=F,
           prop.t=F)
## 
##  
##    Cell Contents
## |-------------------------|
## |                       N |
## |-------------------------|
## 
##  
## Total Observations in Table:  625 
## 
##  
##                    | ATN$alcoholic_hepatitis_admission 
## ATN$response_group |         0 |         1 | Row Total | 
## -------------------|-----------|-----------|-----------|
##        no response |       303 |        72 |       375 | 
## -------------------|-----------|-----------|-----------|
##   overall response |       203 |        47 |       250 | 
## -------------------|-----------|-----------|-----------|
##       Column Total |       506 |       119 |       625 | 
## -------------------|-----------|-----------|-----------|
## 
##  
## Statistics for All Table Factors
## 
## 
## Pearson's Chi-squared test 
## ------------------------------------------------------------
## Chi^2 =  0.01556947     d.f. =  1     p =  0.9006996 
## 
## Pearson's Chi-squared test with Yates' continuity correction 
## ------------------------------------------------------------
## Chi^2 =  0.0004324852     d.f. =  1     p =  0.9834082 
## 
##

2.

master_no_ah 90 days

master_no_ah <- master %>% filter(alcoholic_hepatitis_admission==0,final_type_of_aki %in% c(1,2,3))
master_no_ah$final_type_of_aki <- factor(master_no_ah$final_type_of_aki)
levels(master_no_ah$final_type_of_aki) <- c("Prerenal","HRS","ATN")
master_no_ah$status_90days <- factor(master_no_ah$status_90days)
master_no_ah <- master_no_ah %>% rename(Group=final_type_of_aki)



tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ Group , data = master_no_ah) %>%
  ggcuminc() +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 90, by = 30), limits = c(0, 90))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ Group , data = master_no_ah) %>% 
  tbl_cuminc(
    times = 90, 
    label_header = "**90-days **") %>% 
  add_p()
Characteristic **90-days ** p-value1
Group <0.001
    Prerenal 23% (20%, 26%)
    HRS 51% (44%, 58%)
    ATN 56% (52%, 61%)
1 Gray’s Test

master_no_ah 60 days

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ Group , data = master_no_ah) %>%
  ggcuminc() +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 60, by = 20), limits = c(0, 60))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".
## Warning: Removed 58 rows containing missing values (`geom_step()`).

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ Group , data = master_no_ah) %>% 
  tbl_cuminc(
    times = 60, 
    label_header = "**60-days **") %>% 
  add_p()
Characteristic **60-days ** p-value1
Group <0.001
    Prerenal 20% (17%, 23%)
    HRS 47% (40%, 55%)
    ATN 51% (47%, 56%)
1 Gray’s Test

master_no_ah 30 days

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ Group , data = master_no_ah) %>%
  ggcuminc() +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 30, by = 10), limits = c(0, 30))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".
## Warning: Removed 128 rows containing missing values (`geom_step()`).

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ Group , data = master_no_ah) %>% 
  tbl_cuminc(
    times = 30, 
    label_header = "**30-days **") %>% 
  add_p()
Characteristic **30-days ** p-value1
Group <0.001
    Prerenal 12% (9.5%, 14%)
    HRS 37% (30%, 44%)
    ATN 43% (39%, 47%)
1 Gray’s Test

3.

rrt 90 days

master_rrt <- master %>% filter(rrt==1) 


master_rrt$alcoholic_hepatitis_admission <- factor(master_rrt$alcoholic_hepatitis_admission)
master_rrt$status_90days <- factor(master_rrt$status_90days)

levels(master_rrt$alcoholic_hepatitis_admission) <- c("No AH","AH")


tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = master_rrt) %>%
  ggcuminc(linetype_aes = T) +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 90, by = 30), limits = c(0, 90))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = master_rrt) %>% 
  tbl_cuminc(
    times = 90, 
    label_header = "**90-days **") %>% 
  add_p()
Characteristic **90-days ** p-value1
alcoholic_hepatitis_admission 0.6
    No AH 61% (55%, 66%)
    AH 69% (56%, 78%)
1 Gray’s Test

rrt 60 days

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = master_rrt) %>%
  ggcuminc(linetype_aes = T) +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 60, by = 20), limits = c(0, 60))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".
## Warning: Removed 13 rows containing missing values (`geom_step()`).

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = master_rrt) %>% 
  tbl_cuminc(
    times = 60, 
    label_header = "**60-days **") %>% 
  add_p()
Characteristic **60-days ** p-value1
alcoholic_hepatitis_admission 0.6
    No AH 58% (51%, 63%)
    AH 64% (51%, 74%)
1 Gray’s Test

rrt 30 days

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = master_rrt) %>%
  ggcuminc(linetype_aes = T) +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 30, by = 10), limits = c(0, 30))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".
## Warning: Removed 43 rows containing missing values (`geom_step()`).

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = master_rrt) %>% 
  tbl_cuminc(
    times = 30, 
    label_header = "**30-days **") %>% 
  add_p()
Characteristic **30-days ** p-value1
alcoholic_hepatitis_admission 0.6
    No AH 49% (43%, 55%)
    AH 46% (34%, 57%)
1 Gray’s Test

Table 1 rrt

3.De novo CKD

denovo_cohort <- master %>% filter(death_in_90days_status==0,liver_transplant ==0,ckd==0) %>% mutate(denovo_ckd=ifelse(eGFR<60,"De-novo CKD","No CKD"))

table(denovo_cohort$alcoholic_hepatitis_admission,denovo_cohort$denovo_ckd,useNA = "always")
##       
##        De-novo CKD No CKD <NA>
##   0             50     83   25
##   1              8     16    0
##   <NA>           0      0    0
chisq.test(table(denovo_cohort$alcoholic_hepatitis_admission,denovo_cohort$denovo_ckd)) 
## 
##  Pearson's Chi-squared test with Yates' continuity correction
## 
## data:  table(denovo_cohort$alcoholic_hepatitis_admission, denovo_cohort$denovo_ckd)
## X-squared = 0.028321, df = 1, p-value = 0.8664

4.Table sensitivity

sensitivity_group <- master %>% mutate(s_group=case_when(alcoholic_hepatitis_admission==1 ~ "AH",
                                                         alcoholic_hepatitis_admission==0 & etiology_cirrhosis==1 ~"Alcohol-no AH")) %>% filter(!is.na(s_group))

T1_sensitivity <- CreateTableOne(vars = all_var,strata ="s_group" ,includeNA = F,addOverall = TRUE,data = sensitivity_group, factorVars = cat_var)
## Warning in ModuleReturnVarsExist(vars, data): The data frame does not have:
## days_icu days_discharge_to_transplant Dropped
#print table one 
T1_sensitivity_print <-  print(T1_sensitivity,exact=c("kidney_transplant","Alcoholic_hepatitis","HCC" ),nonnormal=num_var,showAllLevels = F,missing = T,quote = FALSE, noSpaces = TRUE, printToggle = FALSE)
#save 
write.csv(T1_sensitivity_print, file = "C:\\Users\\to909\\Desktop\\Projects\\alcoholic_hepatitis_admission\\T1_sensitivity.csv")

5.

missing <- master
missing$liver_transplant <- as.numeric(as.character(missing$liver_transplant))
missing <- missing %>% mutate(liver_transplant_new=ifelse(is.na(liver_transplant),0,liver_transplant))
gmodels::CrossTable(missing$liver_transplant_new,missing$alcoholic_hepatitis_admission, prop.chisq=F,chisq = T,prop.r=F, prop.c=T,
           prop.t=F)
## 
##  
##    Cell Contents
## |-------------------------|
## |                       N |
## |           N / Col Total |
## |-------------------------|
## 
##  
## Total Observations in Table:  2062 
## 
##  
##                              | missing$alcoholic_hepatitis_admission 
## missing$liver_transplant_new |         0 |         1 | Row Total | 
## -----------------------------|-----------|-----------|-----------|
##                            0 |      1605 |       290 |      1895 | 
##                              |     0.912 |     0.957 |           | 
## -----------------------------|-----------|-----------|-----------|
##                            1 |       154 |        13 |       167 | 
##                              |     0.088 |     0.043 |           | 
## -----------------------------|-----------|-----------|-----------|
##                 Column Total |      1759 |       303 |      2062 | 
##                              |     0.853 |     0.147 |           | 
## -----------------------------|-----------|-----------|-----------|
## 
##  
## Statistics for All Table Factors
## 
## 
## Pearson's Chi-squared test 
## ------------------------------------------------------------
## Chi^2 =  6.92191     d.f. =  1     p =  0.0085146 
## 
## Pearson's Chi-squared test with Yates' continuity correction 
## ------------------------------------------------------------
## Chi^2 =  6.335074     d.f. =  1     p =  0.01183732 
## 
##

Fine and Gray event: death competing risk: liver transplant

tidycmprsk::crr(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission+MELD_Na_baseline+age_admission+sex,failcode=1,cencode=0, data = master_rrt) %>% tbl_regression(exp = TRUE)
## 3 cases omitted due to missing values
Characteristic HR1 95% CI1 p-value
alcoholic_hepatitis_admission
    No AH — —
    AH 0.97 0.67, 1.38 0.9
MELD_Na_baseline 1.02 1.01, 1.04 0.004
age_admission 1.00 0.99, 1.02 0.5
sex
    1 — —
    2 0.92 0.70, 1.20 0.5
1 HR = Hazard Ratio, CI = Confidence Interval

Table LT in AH vs no LT: liver_transplant_90days

master_rrt <- master_rrt %>% mutate(liver_transplant_90days=ifelse(status_90days==2,1,0))

gmodels::CrossTable(master_rrt$liver_transplant_90days,master_rrt$alcoholic_hepatitis_admission, prop.chisq=F,chisq = T,prop.r=F, prop.c=T,
           prop.t=F)
## 
##  
##    Cell Contents
## |-------------------------|
## |                       N |
## |           N / Col Total |
## |-------------------------|
## 
##  
## Total Observations in Table:  373 
## 
##  
##                                    | master_rrt$alcoholic_hepatitis_admission 
## master_rrt$liver_transplant_90days |     No AH |        AH | Row Total | 
## -----------------------------------|-----------|-----------|-----------|
##                                  0 |       250 |        62 |       312 | 
##                                    |     0.833 |     0.849 |           | 
## -----------------------------------|-----------|-----------|-----------|
##                                  1 |        50 |        11 |        61 | 
##                                    |     0.167 |     0.151 |           | 
## -----------------------------------|-----------|-----------|-----------|
##                       Column Total |       300 |        73 |       373 | 
##                                    |     0.804 |     0.196 |           | 
## -----------------------------------|-----------|-----------|-----------|
## 
##  
## Statistics for All Table Factors
## 
## 
## Pearson's Chi-squared test 
## ------------------------------------------------------------
## Chi^2 =  0.1096267     d.f. =  1     p =  0.7405695 
## 
## Pearson's Chi-squared test with Yates' continuity correction 
## ------------------------------------------------------------
## Chi^2 =  0.02392301     d.f. =  1     p =  0.877081 
## 
##

Table LT in AH vs no LT: liver_transplant

gmodels::CrossTable(master_rrt$liver_transplant,master_rrt$alcoholic_hepatitis_admission, prop.chisq=F,chisq = T,prop.r=F, prop.c=T,
           prop.t=F)
## 
##  
##    Cell Contents
## |-------------------------|
## |                       N |
## |           N / Col Total |
## |-------------------------|
## 
##  
## Total Observations in Table:  173 
## 
##  
##                             | master_rrt$alcoholic_hepatitis_admission 
## master_rrt$liver_transplant |     No AH |        AH | Row Total | 
## ----------------------------|-----------|-----------|-----------|
##                           0 |        89 |        20 |       109 | 
##                             |     0.627 |     0.645 |           | 
## ----------------------------|-----------|-----------|-----------|
##                           1 |        53 |        11 |        64 | 
##                             |     0.373 |     0.355 |           | 
## ----------------------------|-----------|-----------|-----------|
##                Column Total |       142 |        31 |       173 | 
##                             |     0.821 |     0.179 |           | 
## ----------------------------|-----------|-----------|-----------|
## 
##  
## Statistics for All Table Factors
## 
## 
## Pearson's Chi-squared test 
## ------------------------------------------------------------
## Chi^2 =  0.03696235     d.f. =  1     p =  0.8475417 
## 
## Pearson's Chi-squared test with Yates' continuity correction 
## ------------------------------------------------------------
## Chi^2 =  1.485666e-30     d.f. =  1     p =  1 
## 
##

sensitivity_group

sensitivity_group <- master %>% mutate(s_group=case_when(alcoholic_hepatitis_admission==1 ~ "AH",
                                                         alcoholic_hepatitis_admission==0 & etiology_cirrhosis==1 ~"Alcohol-no AH")) %>% filter(!is.na(s_group))

sensitivity_group 90 days

sensitivity_group$s_group <- factor(sensitivity_group$s_group)
sensitivity_group$status_90days <- factor(sensitivity_group$status_90days)

levels(sensitivity_group$s_group) <- c("AH","Alcohol-no AH")


tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ s_group , data = sensitivity_group) %>%
  ggcuminc() +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 90, by = 30), limits = c(0, 90))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ s_group , data = sensitivity_group) %>% 
  tbl_cuminc(
    times = 90, 
    label_header = "**90-days **") %>% 
  add_p()
Characteristic **90-days ** p-value1
s_group 0.054
    AH 45% (39%, 51%)
    Alcohol-no AH 38% (34%, 42%)
1 Gray’s Test

sensitivity_group 60 days

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ s_group , data = sensitivity_group) %>%
  ggcuminc() +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 60, by = 20), limits = c(0, 60))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".
## Warning: Removed 30 rows containing missing values (`geom_step()`).

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ s_group , data = sensitivity_group) %>% 
  tbl_cuminc(
    times = 60, 
    label_header = "**60-days **") %>% 
  add_p()
Characteristic **60-days ** p-value1
s_group 0.054
    AH 41% (35%, 47%)
    Alcohol-no AH 34% (30%, 38%)
1 Gray’s Test

sensitivity_group 30 days

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ s_group , data = sensitivity_group) %>%
  ggcuminc() +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 30, by = 10), limits = c(0, 30))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".
## Warning: Removed 78 rows containing missing values (`geom_step()`).

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ s_group , data = sensitivity_group) %>% 
  tbl_cuminc(
    times = 30, 
    label_header = "**30-days **") %>% 
  add_p()
Characteristic **30-days ** p-value1
s_group 0.054
    AH 31% (25%, 36%)
    Alcohol-no AH 26% (22%, 29%)
1 Gray’s Test

Table AH vs ALD without AH: liver_transplant_90days

sensitivity_group<- sensitivity_group %>% mutate(liver_transplant_90days=ifelse(status_90days==2,1,0))

gmodels::CrossTable(sensitivity_group$liver_transplant_90days,sensitivity_group$alcoholic_hepatitis_admission, prop.chisq=F,chisq = T,prop.r=F, prop.c=T,
           prop.t=F)
## 
##  
##    Cell Contents
## |-------------------------|
## |                       N |
## |           N / Col Total |
## |-------------------------|
## 
##  
## Total Observations in Table:  842 
## 
##  
##                                           | sensitivity_group$alcoholic_hepatitis_admission 
## sensitivity_group$liver_transplant_90days |         0 |         1 | Row Total | 
## ------------------------------------------|-----------|-----------|-----------|
##                                         0 |       515 |       292 |       807 | 
##                                           |     0.955 |     0.964 |           | 
## ------------------------------------------|-----------|-----------|-----------|
##                                         1 |        24 |        11 |        35 | 
##                                           |     0.045 |     0.036 |           | 
## ------------------------------------------|-----------|-----------|-----------|
##                              Column Total |       539 |       303 |       842 | 
##                                           |     0.640 |     0.360 |           | 
## ------------------------------------------|-----------|-----------|-----------|
## 
##  
## Statistics for All Table Factors
## 
## 
## Pearson's Chi-squared test 
## ------------------------------------------------------------
## Chi^2 =  0.3292237     d.f. =  1     p =  0.5661165 
## 
## Pearson's Chi-squared test with Yates' continuity correction 
## ------------------------------------------------------------
## Chi^2 =  0.1551676     d.f. =  1     p =  0.6936452 
## 
##

Table AH vs ALD without AH: variable liver_transplant

gmodels::CrossTable(sensitivity_group$liver_transplant,sensitivity_group$s_group, prop.chisq=F,chisq = T,prop.r=F, prop.c=T,
           prop.t=F)
## 
##  
##    Cell Contents
## |-------------------------|
## |                       N |
## |           N / Col Total |
## |-------------------------|
## 
##  
## Total Observations in Table:  249 
## 
##  
##                                    | sensitivity_group$s_group 
## sensitivity_group$liver_transplant |            AH | Alcohol-no AH |     Row Total | 
## -----------------------------------|---------------|---------------|---------------|
##                                  0 |            51 |           144 |           195 | 
##                                    |         0.797 |         0.778 |               | 
## -----------------------------------|---------------|---------------|---------------|
##                                  1 |            13 |            41 |            54 | 
##                                    |         0.203 |         0.222 |               | 
## -----------------------------------|---------------|---------------|---------------|
##                       Column Total |            64 |           185 |           249 | 
##                                    |         0.257 |         0.743 |               | 
## -----------------------------------|---------------|---------------|---------------|
## 
##  
## Statistics for All Table Factors
## 
## 
## Pearson's Chi-squared test 
## ------------------------------------------------------------
## Chi^2 =  0.09578721     d.f. =  1     p =  0.756945 
## 
## Pearson's Chi-squared test with Yates' continuity correction 
## ------------------------------------------------------------
## Chi^2 =  0.0178354     d.f. =  1     p =  0.893759 
## 
##

REQEUST 4.

HRS 90 days

HRS_AKI_master <- master %>% filter(final_type_of_aki==2)

HRS_AKI_master$alcoholic_hepatitis_admission <- factor(HRS_AKI_master$alcoholic_hepatitis_admission)
HRS_AKI_master$status_90days <- factor(HRS_AKI_master$status_90days)

levels(HRS_AKI_master$alcoholic_hepatitis_admission) <- c("No AH","AH")


tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = HRS_AKI_master) %>%
  ggcuminc(linetype_aes = T) +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 90, by = 30), limits = c(0, 90))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = HRS_AKI_master) %>% 
  tbl_cuminc(
    times = 90, 
    label_header = "**90-days **") %>% 
  add_p()
Characteristic **90-days ** p-value1
alcoholic_hepatitis_admission 0.008
    No AH 51% (44%, 58%)
    AH 78% (58%, 89%)
1 Gray’s Test

HRS 60 days

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = HRS_AKI_master) %>%
  ggcuminc(linetype_aes = T) +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 60, by = 20), limits = c(0, 60))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".
## Warning: Removed 11 rows containing missing values (`geom_step()`).

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = HRS_AKI_master) %>% 
  tbl_cuminc(
    times = 60, 
    label_header = "**60-days **") %>% 
  add_p()
Characteristic **60-days ** p-value1
alcoholic_hepatitis_admission 0.008
    No AH 47% (40%, 55%)
    AH 75% (54%, 87%)
1 Gray’s Test

HRS 30 days

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = HRS_AKI_master) %>%
  ggcuminc(linetype_aes = T) +
  add_confidence_interval() +
  add_risktable()+
  scale_x_continuous(breaks = seq(0, 30, by = 10), limits = c(0, 30))+
  theme(panel.background = element_rect(fill = "white", color = NA),
        plot.background = element_rect(fill = "white", color = NA),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
## Plotting outcome "1".
## Warning: Removed 37 rows containing missing values (`geom_step()`).

tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission , data = HRS_AKI_master) %>% 
  tbl_cuminc(
    times = 30, 
    label_header = "**30-days **") %>% 
  add_p()
Characteristic **30-days ** p-value1
alcoholic_hepatitis_admission 0.008
    No AH 37% (30%, 44%)
    AH 47% (29%, 62%)
1 Gray’s Test

#alcoholic_hepatitis_admission hrs

tidycmprsk::crr(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission,failcode=1,cencode=0, data = HRS_AKI_master) %>% tbl_regression(exp = TRUE)
Characteristic HR1 95% CI1 p-value
alcoholic_hepatitis_admission
    No AH — —
    AH 1.78 1.19, 2.65 0.005
1 HR = Hazard Ratio, CI = Confidence Interval

#alcoholic_hepatitis_admission hrs adjusted

tidycmprsk::crr(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission+MELD_Na_baseline+age_admission+sex,failcode=1,cencode=0, data = HRS_AKI_master) %>% tbl_regression(exp = TRUE)
## 6 cases omitted due to missing values
Characteristic HR1 95% CI1 p-value
alcoholic_hepatitis_admission
    No AH — —
    AH 1.82 1.16, 2.86 0.009
MELD_Na_baseline 1.03 1.00, 1.06 0.047
age_admission 1.02 1.00, 1.04 0.017
sex
    1 — —
    2 0.83 0.58, 1.19 0.3
1 HR = Hazard Ratio, CI = Confidence Interval

#updated

ah <- sensitivity_group %>% filter(s_group=="AH") %>% mutate(meld_score_cat=ifelse(MELD_baseline<21,"<21",">=21"))

gmodels::CrossTable(ah$meld_score_cat,ah$final_type_of_aki, prop.chisq=F,chisq = T,prop.r=F, prop.c=T,
           prop.t=F)
## Warning in chisq.test(t, correct = FALSE, ...): Chi-squared approximation may
## be incorrect
## 
##  
##    Cell Contents
## |-------------------------|
## |                       N |
## |           N / Col Total |
## |-------------------------|
## 
##  
## Total Observations in Table:  299 
## 
##  
##                   | ah$final_type_of_aki 
## ah$meld_score_cat |         1 |         2 |         3 |         4 |         5 | Row Total | 
## ------------------|-----------|-----------|-----------|-----------|-----------|-----------|
##               <21 |        42 |         5 |        18 |         3 |         4 |        72 | 
##                   |     0.385 |     0.122 |     0.151 |     0.273 |     0.211 |           | 
## ------------------|-----------|-----------|-----------|-----------|-----------|-----------|
##              >=21 |        67 |        36 |       101 |         8 |        15 |       227 | 
##                   |     0.615 |     0.878 |     0.849 |     0.727 |     0.789 |           | 
## ------------------|-----------|-----------|-----------|-----------|-----------|-----------|
##      Column Total |       109 |        41 |       119 |        11 |        19 |       299 | 
##                   |     0.365 |     0.137 |     0.398 |     0.037 |     0.064 |           | 
## ------------------|-----------|-----------|-----------|-----------|-----------|-----------|
## 
##  
## Statistics for All Table Factors
## 
## 
## Pearson's Chi-squared test 
## ------------------------------------------------------------
## Chi^2 =  20.99603     d.f. =  4     p =  0.0003172437 
## 
## 
##

cohort 373

#updated 2 alcoholic_hepatitis_admission*tb_admit

# Fine and Gray  event: death competing risk: liver transplant 

tidycmprsk::crr(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission*tb_admit,failcode=1,cencode=0, data = master_rrt) %>% tbl_regression(exp = TRUE) %>% add_n()
## 1 cases omitted due to missing values
Characteristic N HR1 95% CI1 p-value
alcoholic_hepatitis_admission 372
    No AH — —
    AH 1.52 0.93, 2.47 0.10
tb_admit 372 1.02 1.00, 1.03 0.011
alcoholic_hepatitis_admission * tb_admit 372
    AH * tb_admit 0.98 0.95, 1.00 0.042
1 HR = Hazard Ratio, CI = Confidence Interval

#updated 2 alcoholic_hepatitis_admission*age_admission

# Fine and Gray  event: death competing risk: liver transplant 
tidycmprsk::crr(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission*age_admission,failcode=1,cencode=0, data = master_rrt) %>% tbl_regression(exp = TRUE) %>% add_n()
Characteristic N HR1 95% CI1 p-value
alcoholic_hepatitis_admission 373
    No AH — —
    AH 0.43 0.11, 1.63 0.2
age_admission 373 1.00 0.99, 1.01 0.8
alcoholic_hepatitis_admission * age_admission 373
    AH * age_admission 1.02 0.99, 1.05 0.13
1 HR = Hazard Ratio, CI = Confidence Interval

#updated 2 alcoholic_hepatitis_admission*age_admission

# Fine and Gray  event: death competing risk: liver transplant 
tidycmprsk::crr(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission*eGFR_CRE,failcode=1,cencode=0, data = master_rrt) %>% tbl_regression(exp = TRUE) %>% add_n()
## 109 cases omitted due to missing values
Characteristic N HR1 95% CI1 p-value
alcoholic_hepatitis_admission 264
    No AH — —
    AH 3.40 0.95, 12.2 0.061
eGFR_CRE 264 1.01 1.01, 1.02 <0.001
alcoholic_hepatitis_admission * eGFR_CRE 264
    AH * eGFR_CRE 0.98 0.97, 1.00 0.019
1 HR = Hazard Ratio, CI = Confidence Interval

cohort 2062

#updated 2 alcoholic_hepatitis_admission*tb_admit

# Fine and Gray  event: death competing risk: liver transplant 

tidycmprsk::crr(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission*tb_admit,failcode=1,cencode=0, data = master) %>% tbl_regression(exp = TRUE) %>% add_n()
## 30 cases omitted due to missing values
Characteristic N HR1 95% CI1 p-value
alcoholic_hepatitis_admission 2,032 0.98 0.74, 1.32 >0.9
tb_admit 2,032 1.04 1.03, 1.05 <0.001
alcoholic_hepatitis_admission * tb_admit 2,032 0.99 0.98, 1.00 0.2
1 HR = Hazard Ratio, CI = Confidence Interval

#updated 2 alcoholic_hepatitis_admission*age_admission

# Fine and Gray  event: death competing risk: liver transplant 
tidycmprsk::crr(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission*age_admission,failcode=1,cencode=0, data = master) %>% tbl_regression(exp = TRUE) %>% add_n()
Characteristic N HR1 95% CI1 p-value
alcoholic_hepatitis_admission 2,062 0.90 0.39, 2.10 0.8
age_admission 2,062 1.00 1.00, 1.01 0.7
alcoholic_hepatitis_admission * age_admission 2,062 1.01 0.99, 1.02 0.4
1 HR = Hazard Ratio, CI = Confidence Interval

#updated 2 alcoholic_hepatitis_admission*age_admission

# Fine and Gray  event: death competing risk: liver transplant 
tidycmprsk::crr(Surv(time_90days,status_90days) ~ alcoholic_hepatitis_admission*eGFR_CRE,failcode=1,cencode=0, data = master) %>% tbl_regression(exp = TRUE) %>% add_n()
## 365 cases omitted due to missing values
Characteristic N HR1 95% CI1 p-value
alcoholic_hepatitis_admission 1,697 1.49 0.69, 3.21 0.3
eGFR_CRE 1,697 1.01 1.00, 1.01 <0.001
alcoholic_hepatitis_admission * eGFR_CRE 1,697 1.00 0.99, 1.00 0.4
1 HR = Hazard Ratio, CI = Confidence Interval

#01/25/2024 alcoholic_hepatitis_admission==0

master_no_ah_2 <- master %>% filter(alcoholic_hepatitis_admission==0,final_type_of_aki %in% c(2,3))
master_no_ah_2$final_type_of_aki <- factor(master_no_ah_2$final_type_of_aki)
levels(master_no_ah_2$final_type_of_aki) <- c("HRS","ATN")
master_no_ah_2$status_90days <- factor(master_no_ah_2$status_90days)
master_no_ah_2 <- master_no_ah_2 %>% rename(Group=final_type_of_aki)




tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ Group , data = master_no_ah_2) %>% 
  tbl_cuminc(
    times = 90, 
    label_header = "**No_ah 90-days **") %>% 
  add_p()
Characteristic **No_ah 90-days ** p-value1
Group 0.11
    HRS 51% (44%, 58%)
    ATN 56% (52%, 61%)
1 Gray’s Test

alcoholic_hepatitis_admission==1

master_ah_2 <- master %>% filter(alcoholic_hepatitis_admission==1,final_type_of_aki %in% c(2,3))
master_ah_2$final_type_of_aki <- factor(master_ah_2$final_type_of_aki)
levels(master_ah_2$final_type_of_aki) <- c("HRS","ATN")
master_ah_2$status_90days <- factor(master_ah_2$status_90days)
master_ah_2 <- master_ah_2 %>% rename(Group=final_type_of_aki)




tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ Group , data = master_ah_2) %>% 
  tbl_cuminc(
    times = 90, 
    label_header = "**Ah 90-days **") %>% 
  add_p()
Characteristic **Ah 90-days ** p-value1
Group 0.033
    HRS 78% (58%, 89%)
    ATN 53% (43%, 62%)
1 Gray’s Test

01/25/2024 alcoholic_hepatitis_admission==0

master_no_ah_2 <- master %>% filter(alcoholic_hepatitis_admission==0,final_type_of_aki %in% c(2,3))
master_no_ah_2$final_type_of_aki <- factor(master_no_ah_2$final_type_of_aki)
levels(master_no_ah_2$final_type_of_aki) <- c("HRS","ATN")
master_no_ah_2$status_90days <- factor(master_no_ah_2$status_90days)
master_no_ah_2 <- master_no_ah_2 %>% rename(Group=final_type_of_aki)




tidycmprsk::cuminc(Surv(time_90days,status_90days) ~ Group , data = master_no_ah_2) %>% 
  tbl_cuminc(
    times = 90, 
    label_header = "**No_ah 90-days **") %>% 
  add_p()
Characteristic **No_ah 90-days ** p-value1
Group 0.11
    HRS 51% (44%, 58%)
    ATN 56% (52%, 61%)
1 Gray’s Test