create a vignette for Kaplan Meier #41

Lpierott · 2024-11-29T14:08:11Z

guidelines how to construct a KM at GR

Use of the vignette

adding extras codes to the KM ggsurvfit

updated the example of creation of variable

DanChaltiel · 2025-01-31T09:10:33Z

vignettes/Adverse Event (AE grade) .Rmd

Ideally, this file should be added to another branch, linked to another issue and another PR.
Otherwise, we won't be able to merge this PR about the KM vignette before completing the AE vignette.

I am not quite sure why the AE vignette is within the KM vignette.

It is not "within" it is "beside.
On GH Desktop you are on the KM branch, 6-vignette-kaplan-meier.
If you want to work on another vignette, you should switch your branch to another one, preferably one created from #40 (there is a "create branch" link somewhere).
Then in GH Desktop you can change the branch you are working on easily.
This is a bit of gymnastics, but it helps keeping things clean

DanChaltiel

Thank you so much Livia, this is really coming together 😁😁

DanChaltiel · 2025-01-31T09:11:32Z

vignettes/kaplan_meier.Rmd

-    death_eos = status,
-    date_progression = date_enrol + time*runif(n(), 0.6, 0.8),
-    date_progression = if_else(runif(n())>0.2, NA, date_progression), 
+    date_first_visit = t0_v2 + abs(rnorm(n(), 500, 20)), 


are you sure about the variable renaming? Survival is usually calculated from enrollment or randomization, even if there is a visit (for screening, clinical checking, etc.) that happened before and would be the "first visit".
I agree with you on date_of_last_visit though, much better.
However, it would be better to stick to one naming convention: either date_of_xxx or date_xxx, as you wish.

As I understood is not always the same name for every project/data. So that first date and last date might be more understandable. However, when Ill present it to our team members in our next meeting i'll ask them.

Wouldn't follow_up_start and follow_up_end be more correct then? (or something similar)

vignettes/kaplan_meier.Rmd

DanChaltiel · 2025-01-31T09:37:39Z

vignettes/kaplan_meier.Rmd

 print(km.model_PFS)
+# il y a beaucoup de NA, c pas genial


Que veux-tu dire ?
Si tu parles de la médiane qui est NA, c'est normal : quand la médiane n'est pas atteinte (il y a moins d'événements que la moitié des patients), on ne peut calculer que la borne inf de l'intervalle de confiance.

on peut voir ca ensemble?

DanChaltiel · 2025-01-31T09:39:48Z

vignettes/kaplan_meier.Rmd

 print(km.model_PFS)
+# il y a beaucoup de NA, c pas genial
 summary(km.model_PFS)


In summary(), the output is unreadable without the times argument as it describes every time in the database.
Also, I prefer using tidy_survfit() from ggsurvfit, it has the broom::tidy() vibe, although you have to use select() on the output to reduce the clutter.
What do you think about it?

I removed it

Don't you think it is nice to explain the times argument? Clinicians often want to see the "x-Year survival" and this is how I calculate it. Do you do it in a different way?

tidy_survfit(km.model_PFS, times=c(0.05, 0.10, 0.20)) %>% select(strata, time, n.risk, n.event, estimate, conf.high, conf.low)

DanChaltiel · 2025-01-31T09:45:39Z

vignettes/kaplan_meier.Rmd

    status == 0  ~ pmax(date_of_last_visit,na.rm = T)
  )) %>% 
  mutate(time_days=status_date-date_first_visit ) %>%  
-  mutate(time_years=time_days/365.25 )  
+  mutate(time_months=time_days/30.5 )  


Our times are very low, aren't they?
In ggsurvfit::df_colon, times range from 0.02 to 9 years, which is a rather natural scale.
I'm not sure where this comes from, but maybe we can cheat by rescaling when creating data_surv?

Also, don't you think creating both time_os and time_pfs (and both KM curves) would be educationally valuable? I think juniors can struggle with that.

good point! Alexi should work on this!

Oh, so Alexis should work on this vignette before we publish it?

DanChaltiel · 2025-01-31T09:52:29Z

vignettes/kaplan_meier.Rmd

@@ -106,7 +126,7 @@ Kaplan-Meier by Daniel D. Sjoberg, Mark Baillie, Charlotta Fruechtenicht, Steven

 ```{r}

-km = survfit2(Surv(time, status) ~ surg, data = df_colon) %>%
+km = survfit2(Surv(time_days, status) ~ surg, data = data_surv_v2) %>%
  ggsurvfit(linetype_aes = TRUE) +
  add_confidence_interval() +
  add_risktable(


There was an error in the ggsurvfit vignette, we should use this theme:
theme(legend.position="inside", legend.position.inside = c(0.85, 0.85))

I changed it for your code. It works but when looking at the html output, the plots do not look great.

DanChaltiel · 2025-01-31T09:53:53Z

vignettes/kaplan_meier.Rmd

@@ -106,7 +126,7 @@ Kaplan-Meier by Daniel D. Sjoberg, Mark Baillie, Charlotta Fruechtenicht, Steven

 ```{r}


As this is a vignette an not a standard HTML document, figures are tiny by default 😕
Try {r fig.width = 10} instead

that answers to my presvious comment. Fabulous!

init

64cf999

Use of the vignette

Lpierott linked an issue Nov 29, 2024 that may be closed by this pull request

Vignette: Kaplan Meier #6

Open

Lpierott and others added 6 commits November 29, 2024 15:43

wip add variable creation

4a0b3ee

wip KM plots

80ac1fe

adding extra coding to the KM

f4404c3

adding extras codes to the KM ggsurvfit

Update the example creation of variable

1fa1add

updated the example of creation of variable

dummy dataset

5cc6bfe

try: remove VignetteIndexEntry

1b67348

DanChaltiel assigned Lpierott Jan 15, 2025

Lpierott added 5 commits January 30, 2025 13:27

change Dan simulation

07d560a

create vignette AE

3403397

AE grade create vignette

86c9eb7

updates title

db53961

start

bb38a1d

DanChaltiel reviewed Jan 31, 2025

View reviewed changes

Lpierott added 3 commits February 7, 2025 12:57

Update kaplan_meier.Rmd

f504044

Update kaplan_meier.Rmd

326bbd8

Update kaplan_meier.Rmd

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create a vignette for Kaplan Meier #41

create a vignette for Kaplan Meier #41

Lpierott commented Nov 29, 2024

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		@@ -106,7 +126,7 @@ Kaplan-Meier by Daniel D. Sjoberg, Mark Baillie, Charlotta Fruechtenicht, Steven

		```{r}

create a vignette for Kaplan Meier #41

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create a vignette for Kaplan Meier #41

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