Why "P value" > 1 when anlaysing survey data using the TableSubgroupMultiCox? #81
Description
Hi Prof. Jinseob Kim,
Thank you for your excellent work. However, when I use this function , 'TableSubgroupMultiCox,' to perform a subgroup analysis on survey data, the P value appears to be greater than 1. What's going on? Below is my data structure, relevant code, and results.
code
str(data_test)
'data.frame': 3616 obs. of 12 variables:
$ Age : int 51 57 62 65 77 61 65 77 52 72 ...
$ Gender : Factor w/ 2 levels "Female","Male": 2 2 1 1 1 2 2 2 2 1 ...
$ Smoking_status : Factor w/ 3 levels "Never smoker",..: 3 2 1 1 1 1 2 2 3 2 ...
$ Drinking_status: Factor w/ 3 levels "nondrinker","low-to-moderate drinker",..: NA 2 NA 1 1 2 1 3 3 NA ...
$ Hypertension : Factor w/ 2 levels "No","Yes": 2 1 1 2 2 2 2 2 1 1 ...
$ All_cause : num 0 0 0 0 1 0 0 0 0 0 ...
$ permth_int : int 86 85 89 95 79 98 88 91 92 90 ...
$ LiverR : num 4.93 9.02 7.92 6.83 7.34 ...
$ LiverR_cat : Factor w/ 3 levels "<6","6 to 10",..: 1 2 2 2 2 1 1 2 2 1 ...
$ SDMVPSU : int 2 2 2 1 2 1 1 1 2 1 ...
$ SDMVSTRA : int 92 92 96 98 98 93 93 99 95 94 ...
$ wt : num 4396 70730 9856 76457 8572 ...
data_svy <- svydesign(data=data_test,
id=~SDMVPSU,
strata=~SDMVSTRA,
weights=~wt,
nest=TRUE)
res <- TableSubgroupMultiCox(
formula = Surv(permth_int, All_cause) ~ LiverR_cat,
var_subgroups = c("Gender",
"Smoking_status",
"Drinking_status",
"Hypertension"),
var_cov = c("Age", "Smoking_status", "Drinking_status"),
data = data_svy
)
results
<style> </style>| Variable | Count | Percent | Levels | Point Estimate | Lower | Upper | KM | P value | P for interaction | |
|---|---|---|---|---|---|---|---|---|---|---|
| LiverR_cat | Overall | 3076 | 100 | LiverR_cat=<6 | Reference | 8.1 | NA | |||
| 1 | LiverR_cat=6 to 10 | 2 | 1.29 | 3.1 | 17.9 | 0.002 | NA | |||
| 2 | LiverR_cat=>=10 | 5.18 | 2.27 | 11.84 | 38.4 | <0.001 | NA | |||
| 3 | Gender | NA | NA | NA | NA | NA | NA | NA | NA | 0.904 |
| 4 | Female | 1602 | 52.1 | LiverR_cat=<6 | Reference | 6.5 | NA | |||
| 5 | LiverR_cat=6 to 10 | 2.88 | 1.49 | 5.56 | 17.3 | 3.142 | NA | |||
| 6 | LiverR_cat=>=10 | 4.57 | 1.16 | 17.97 | 15.9 | 2.173 | NA | |||
| 7 | Male | 1474 | 47.9 | LiverR_cat=<6 | Reference | 10.7 | NA | |||
| 8 | LiverR_cat=6 to 10 | 1.46 | 0.77 | 2.78 | 18.3 | 1.167 | NA | |||
| 9 | LiverR_cat=>=10 | 4.94 | 1.9 | 12.84 | 51.8 | 3.278 | NA | |||
| 10 | Smoking_status | NA | NA | NA | NA | NA | NA | NA | NA | 0.545 |
| 11 | Never smoker | 1616 | 52.5 | LiverR_cat=<6 | Reference | 4.2 | NA | |||
| 12 | LiverR_cat=6 to 10 | 2.13 | 1.21 | 3.76 | 10.9 | 2.622 | NA | |||
| 13 | LiverR_cat=>=10 | 3.03 | 0.45 | 20.23 | 10.2 | 1.146 | NA | |||
| 14 | Former smoker | 931 | 30.3 | LiverR_cat=<6 | Reference | 9.2 | NA | |||
| 15 | LiverR_cat=6 to 10 | 2.13 | 1 | 4.54 | 22.5 | 1.97 | NA | |||
| 16 | LiverR_cat=>=10 | 6.29 | 2.6 | 15.22 | 93 | 4.078 | NA | |||
| 17 | Current smoker | 529 | 17.2 | LiverR_cat=<6 | Reference | 18.3 | NA | |||
| 18 | LiverR_cat=6 to 10 | 1.55 | 0.6 | 4.03 | 25.1 | 0.907 | NA | |||
| 19 | LiverR_cat=>=10 | 5.14 | 1.47 | 18.04 | 62.8 | 2.557 | NA | |||
| 20 | Drinking_status | NA | NA | NA | NA | NA | NA | NA | NA | 0.686 |
| 21 | nondrinker | 1124 | 36.5 | LiverR_cat=<6 | Reference | 7.7 | NA | |||
| 22 | LiverR_cat=6 to 10 | 2.47 | 1.48 | 4.12 | 19.6 | 3.476 | NA | |||
| 23 | LiverR_cat=>=10 | 10.19 | 2.59 | 40.12 | 15.4 | 3.322 | NA | |||
| 24 | low-to-moderate drinker | 1668 | 54.2 | LiverR_cat=<6 | Reference | 7.4 | NA | |||
| 25 | LiverR_cat=6 to 10 | 1.51 | 0.84 | 2.71 | 16.1 | 1.375 | NA | |||
| 26 | LiverR_cat=>=10 | 4.32 | 1.44 | 12.93 | 33.1 | 2.613 | NA | |||
| 27 | heavydrinker | 284 | 9.2 | LiverR_cat=<6 | Reference | 4.6 | NA | |||
| 28 | LiverR_cat=6 to 10 | 3.98 | 1.42 | 11.17 | 15.9 | 2.628 | NA | |||
| 29 | LiverR_cat=>=10 | 7.85 | 2.38 | 25.85 | 43.6 | 3.388 | NA | |||
| 30 | Hypertension | NA | NA | NA | NA | NA | NA | NA | NA | 0.209 |
| 31 | No | 832 | 27 | LiverR_cat=<6 | Reference | 6.5 | NA | |||
| 32 | LiverR_cat=6 to 10 | 1.46 | 0.7 | 3.04 | 9.9 | 1.001 | NA | |||
| 33 | LiverR_cat=>=10 | 1.41 | 0.17 | 11.64 | 8.5 | 0.317 | NA | |||
| 34 | Yes | 2244 | 73 | LiverR_cat=<6 | Reference | 9.2 | NA | |||
| 35 | LiverR_cat=6 to 10 | 2.14 | 1.29 | 3.53 | 19.9 | 2.966 | NA | |||
| 36 | LiverR_cat=>=10 | 5.79 | 2.59 | 12.94 | 47.7 | 4.284 | NA |