> On Oct 7, 2017, at 9:01 AM, Ted Beginner (RStudio) via R-help
> <r-help@r-project.org> wrote:
>
>
> For adjusted survival curves I took the sample code from here:
> https://rpubs.com/daspringate/survival
> and adapted for my date, but ... have a QUESTION.
>
> library(survival)
> library(survminer)
> df<-read.csv("base.csv", header = TRUE, sep = ";")
> head(df)
> ID start stop censor sex age stage treatment
> 1 1 0 66 0 2 1 3 1
> 2 2 0 18 0 1 2 4 2
> 3 3 0 43 1 2 3 3 1
> 4 4 0 47 1 2 3 NA 2
> 5 5 0 26 0 1 4 3 NA
>
> # THANKS, DAVID WINSEMIUS for remark!!! ("R regression functions allow you to
> use column names.")
> model <- coxph( Surv(time = start,
> time2 = stop,
> event = censor) ~ treatment + age + sex + stage, data = df)
>
> plot(survfit(model),
> las=1,
> xscale = 1.00,
> xlab = "Months after diagnosis",
> ylab = "Proportion survived",
> main = "Baseline Hazard Curve")
>
> #HOW TO EXPLAIN TO R, THAT treatment, age, sex and stage ARE FACTORS, AND NOT
> CONTINUOUS VAR?
> treat <- with (df,
> data.frame (
> treatment = levels(treatment),
> age = rep(levels(age)[1], 2),
> sex = rep(levels(sex)[1], 2),
> stage = rep(levels(stage)[1], 2)))
Perhaps:
treat2 <- treat
treat2[,c('treatment', 'age', 'sex', 'stage')] <- lapply(
treat2[,c('treatment', 'age', 'sex', 'stage')], factor)
> treat2
ID start stop censor sex age stage treatment
1 1 0 66 0 2 1 3 1
2 2 0 18 0 1 2 4 2
3 3 0 43 1 2 3 3 1
4 4 0 47 1 2 3 <NA> 2
5 5 0 26 0 1 4 3 <NA>
> str(treat2)
'data.frame': 5 obs. of 8 variables:
$ ID : int 1 2 3 4 5
$ start : int 0 0 0 0 0
$ stop : int 66 18 43 47 26
$ censor : int 0 0 1 1 0
$ sex : Factor w/ 2 levels "1","2": 2 1 2 2 1
$ age : Factor w/ 4 levels "1","2","3","4": 1 2 3 3 4
$ stage : Factor w/ 2 levels "3","4": 1 2 1 NA 1
I saw Peter Dalgaard's reply and I'm guessing that your 'age' was grouped into
some categorical variable, perhaps decades?
>
> str(treat)
> [[alternative HTML version deleted]]
You should learn to post in plain text and use dput to present your data
structures. At your console do this
dput(treat)
# and this will appear. Copy it to your plain-text message:
structure(list(ID = 1:5, start = c(0L, 0L, 0L, 0L, 0L), stop = c(66L,
18L, 43L, 47L, 26L), censor = c(0L, 0L, 1L, 1L, 0L), sex = c(2L,
1L, 2L, 2L, 1L), age = c(1L, 2L, 3L, 3L, 4L), stage = c(3L, 4L,
3L, NA, 3L), treatment = c(1L, 2L, 1L, 2L, NA)), .Names = c("ID",
"start", "stop", "censor", "sex", "age", "stage", "treatment"
), class = "data.frame", row.names = c("1", "2", "3", "4", "5"
)):
Then we can just do this:
treat <- structure(list(ID = 1:5, start = c(0L, 0L, 0L, 0L, 0L), stop = c(66L,
18L, 43L, 47L, 26L), censor = c(0L, 0L, 1L, 1L, 0L), sex = c(2L,
1L, 2L, 2L, 1L), age = c(1L, 2L, 3L, 3L, 4L), stage = c(3L, 4L,
3L, NA, 3L), treatment = c(1L, 2L, 1L, 2L, NA)), .Names = c("ID",
"start", "stop", "censor", "sex", "age", "stage", "treatment"
), class = "data.frame", row.names = c("1", "2", "3", "4", "5"
))
--
David Winsemius
Alameda, CA, USA
'Any technology distinguishable from magic is insufficiently advanced.'
-Gehm's Corollary to Clarke's Third Law
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