Problem
Hi there,
I want to run a post-hoc test on a cox proportional hazards model. I ran an anova on my Surv() model but when trying to post-hoc TukeyHSD() on the anova, I got the error message "no applicable method for 'TukeyHSD' applied to an object of class "c('anova', 'data.frame')"" so, I think I was running the wrong test. I turned to survdiff() but am having trouble with that as well.
I get a lot of errors about parentheses and commas when I run my code attached below. However, when I copy and paste the same code into the coxme() function -rather than the survdiff() function- the code runs perfectly. I may not be using the correct function, but I did a little research and thought this would work for me.
Please and thank you!
Code
survdiff (Surv( (days_surv,censor) ~ inv + soil + inv*soil + drought_trt + drought_trt*soil + drought_trt*inv + drought_trt*soil*inv + (1|df_type) + (1|block) + (1|siteID), data = survdrt, p.adjust.method = "bonferroni", rho = 1 ) )
Data
structure(list(siteID = c(2L, 2L, 1L, 1L, 2L, 3L, 3L, 3L, 1L,
1L, 2L, 2L, 2L, 3L, 2L, 1L, 2L, 3L, 1L, 2L, 1L, 1L, 2L, 1L, 3L,
3L, 3L, 3L, 1L, 3L, 2L, 2L, 1L, 1L, 2L, 3L, 3L, 2L, 1L, 2L, 2L,
1L, 1L, 2L, 3L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 3L, 3L,
2L, 2L, 1L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 2L, 2L, 3L, 1L, 1L,
3L, 2L, 3L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 3L, 3L,
3L, 2L, 3L, 2L, 1L, 2L, 2L, 1L, 1L, 3L, 1L, 1L), soil = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L), .Label = c("L", "S"), class = "factor"), df_type = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L), .Label = c("primadonna", "street_fighter_1",
"street_fighter_2"), class = "factor"), inv = structure(c(2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L), .Label = c("Br", "Un"), class = "factor"), drought_trt = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L), .Label = c("drought", "wet"), class = "factor"),
block = c(7L, 3L, 4L, 1L, 6L, 4L, 5L, 10L, 2L, 9L, 1L, 8L,
9L, 3L, 5L, 8L, 5L, 4L, 2L, 7L, 6L, 10L, 4L, 9L, 6L, 1L,
5L, 9L, 3L, 7L, 1L, 2L, 7L, 5L, 3L, 2L, 3L, 9L, 1L, 10L,
6L, 8L, 4L, 8L, 8L, 10L, 8L, 9L, 3L, 6L, 10L, 1L, 8L, 5L,
5L, 10L, 8L, 7L, 9L, 7L, 6L, 3L, 1L, 7L, 9L, 4L, 2L, 2L,
2L, 4L, 6L, 4L, 1L, 5L, 3L, 1L, 1L, 4L, 7L, 10L, 8L, 9L,
2L, 3L, 9L, 7L, 10L, 6L, 8L, 9L, 8L, 4L, 2L, 4L, 5L, 6L,
6L, 5L, 5L, 2L, 3L), days_surv = c(80L, 80L, 80L, 80L, 80L,
80L, 80L, 80L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L,
83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 69L,
73L, 79L, 80L, 80L, 80L, 80L, 80L, 80L, 80L, 80L, 80L, 83L,
83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L,
83L, 83L, 83L, 83L, 73L, 73L, 80L, 80L, 80L, 80L, 80L, 83L,
83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 83L, 17L, 17L,
20L, 20L, 27L, 27L, 27L, 29L, 34L, 41L, 69L, 69L, 73L, 73L,
73L, 73L, 73L, 73L, 73L, 73L, 77L, 77L, 77L, 80L, 80L, 80L
), censor = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L
), death_date = structure(c(14L, 14L, 14L, 14L, 14L, 14L,
14L, 14L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L,
15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 10L, 11L,
13L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 15L, 15L,
15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L,
15L, 15L, 15L, 11L, 11L, 14L, 14L, 14L, 14L, 14L, 15L, 15L,
15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 19L, 19L, 20L,
20L, 1L, 1L, 1L, 7L, 9L, 3L, 10L, 10L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 12L, 12L, 12L, 14L, 14L, 14L), .Label = c("2018_10_1",
"2018_10_12", "2018_10_15", "2018_10_19", "2018_10_22", "2018_10_24",
"2018_10_3", "2018_10_5", "2018_10_8", "2018_11_13", "2018_11_16",
"2018_11_20", "2018_11_22", "2018_11_23", "2018_11_26", "2018_9_17",
"2018_9_18", "2018_9_19", "2018_9_21", "2018_9_24", "2018_9_28"
), class = "factor"), death_date_NA = structure(c(14L, 14L,
14L, 14L, 14L, 14L, 14L, 14L, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 10L,
11L, 13L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, 11L, 11L, 14L, 14L, 14L, 14L, 14L, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, 19L, 19L, 20L, 20L, 1L, 1L, 1L, 7L,
9L, 3L, 10L, 10L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
12L, 12L, 12L, 14L, 14L, 14L), .Label = c("2018_10_1", "2018_10_12",
"2018_10_15", "2018_10_19", "2018_10_22", "2018_10_24", "2018_10_3",
"2018_10_5", "2018_10_8", "2018_11_13", "2018_11_16", "2018_11_20",
"2018_11_22", "2018_11_23", "2018_11_26", "2018_9_17", "2018_9_18",
"2018_9_19", "2018_9_21", "2018_9_24", "2018_9_28"), class = "factor")), row.names = 100:200, class = "data.frame")