Issue with plotsurvfitDS after using ds.Surv and ds.survfit #12

naudinlo · 2022-11-10T15:10:32Z

naudinlo
Nov 10, 2022

Describe the bug
Hello, when using dsSurvivalClient::ds.Surv and dsSurvivalClient::ds.survfit I have an issue. I cannot plot the output with plotsurvfitDS as it is an object and not a vector, making the ds.plotsurvfit.R code failing at line 119.

To Reproduce
Steps to reproduce the behavior:

ds.Surv(time="D_patients$dob_day", time2="D_patients$dod_day", "D_patients$expire_flag", type="counting", objectname='surv_object')
ds.survfit(formula='surv_object~1', objectname='survfit_object')
ds.plotsurvfit(formula='surv_object')

Generates the error:

[1] "Command 'plotsurvfitDS(formula = \"surv_object\", NULL)' failed on 'abc': Error while evaluating 'dsSurvival::plotsurvfitDS(formula = \"surv_object\", NULL)' -> Error : $ operator is invalid for atomic vectors\n"

Answered by neelsoumya

Nov 24, 2022

@naudinlo @tombisho I tried all this code on my laptop on R and R Studio. I did not use the docker image. Can you please try using this setup and let me know if it works for you?

i.e. do the following

Install R and R Studio on your laptop
Install all the required packages using these commands in R or R Studio:

install.packages('devtools')
library(devtools)
devtools::install_github('neelsoumya/dsSurvivalClient')
devtools::install_github('datashield/dsBaseClient@6.1.1')
install.packages('metafor')
install.packages('DSOpal')
install.packages('DSI')
install.packages('opalr')
install.packages('meta')
install.packages('fANCOVA')
install.packages('survival')

Run the following script

###…

View full answer

neelsoumya · 2022-11-12T08:22:45Z

neelsoumya
Nov 12, 2022
Maintainer

can you please give some more details like what VM are you using, what data are you using and what versions of Opal and R you have? Also can you reproduce this error using synthetic data? Then I can try to reproduce this error message.

0 replies

naudinlo · 2022-11-21T13:55:01Z

naudinlo
Nov 21, 2022
Author

Thanks for your answer.

On the client side, we use the rocker/rstudio:4.1.2 docker image which has Ubuntu 20.04.5 LTS and R version 4.1.2.
For opal, we use the obiba/opal:4.5 image where we installed dsSurvival version 2.1.0 (we also tried to use the demo server at https://opal-demo.obiba.org/ with the same result).
We tried to use the data that can be found in the SURVIVAL project on https://opal-demo.obiba.org/.

builder <- DSI::newDSLoginBuilder(.silent = TRUE)
builder$append(
 server = "chu",
 url = "https://opal-demo.obiba.org/",
 user = "administrator", password = "password",
 driver = "OpalDriver",
 options='list(ssl_verifyhost=0, ssl_verifypeer=0)',
 profile="survival"
)
logindata <- builder$build()
connections <- DSI::datashield.login(logins = logindata)
datashield.assign.table(connections, symbol = "D", table = "SURVIVAL.EXPAND_WITH_MISSING1")
ds.asNumeric(x.name = "D$cens", newobj = "EVENT", datasources = connections)
ds.asNumeric(x.name = "D$starttime", newobj = "STARTTIME", datasources = connections)
ds.asNumeric(x.name = "D$endtime", newobj = "ENDTIME", datasources = connections)
ds.Surv(time="STARTTIME", time2="ENDTIME", event="EVENT", type="counting", objectname='surv_object')
ds.survfit(formula='surv_object~1', objectname='survfit_object')
ds.plotsurvfit(formula = 'survfit_object')

The last line fails with the following error:

Error in xy.coords(x, y, xlabel, ylabel, log) :
 'x' is a list, but does not have components 'x' and ‘y’

Thanks,

0 replies

neelsoumya · 2022-11-23T08:06:16Z

neelsoumya
Nov 23, 2022
Maintainer

Thanks @naudinlo

Could you please try this using just R and R Studio and just client-side package installations?
This uses the demo server at

https://opal-sandbox.mrc-epid.cam.ac.uk

The following steps work for me and I can generate the survival curves.

Could you please follow this simple script:

https://github.com/neelsoumya/dsSurvival/blob/main/vignettes/simple_script.R

This works with just client side installations i.e. R and R Studio

I installed all the required packages using this script:

https://raw.githubusercontent.com/neelsoumya/dsSurvival/main/installer_R_Rstudio.R

My output from sessionInfo() shows the following:

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] dsBaseClient_6.1.1 DSOpal_1.4.0 opalr_3.2.0 httr_1.4.3
[5] dsSurvivalClient_2.1.0 DSI_1.5.0 R6_2.5.1 progress_1.2.2
[9] ggplot2_3.3.6 metafor_3.4-0 metadat_1.2-0 Matrix_1.4-1
[13] survival_3.4-0 tinytex_0.41 rmarkdown_2.15 knitr_1.39

0 replies

neelsoumya · 2022-11-23T17:07:29Z

neelsoumya
Nov 23, 2022
Maintainer

@naudinlo @tombisho

I also tried your code and ran it on my laptop (Mac OS X) and R and R Studio (no docker image). This works fine. Here is the code below (I modified the code slightly by loading the libraries):

###################
# load libraries
###################
library(survival)
library(metafor)
library(dsSurvivalClient)
require('DSI')
require('DSOpal')
require('dsBaseClient')


builder <- DSI::newDSLoginBuilder(.silent = TRUE)
builder$append(
  server = "chu",
  url = "https://opal-demo.obiba.org/",
  user = "administrator", password = "password",
  driver = "OpalDriver",
  options='list(ssl_verifyhost=0, ssl_verifypeer=0)',
  profile="survival"
)
logindata <- builder$build()
connections <- DSI::datashield.login(logins = logindata)
datashield.assign.table(connections, symbol = "D", table = "SURVIVAL.EXPAND_WITH_MISSING1")
ds.asNumeric(x.name = "D$cens", newobj = "EVENT", datasources = connections)
ds.asNumeric(x.name = "D$starttime", newobj = "STARTTIME", datasources = connections)
ds.asNumeric(x.name = "D$endtime", newobj = "ENDTIME", datasources = connections)
ds.Surv(time="STARTTIME", time2="ENDTIME", event="EVENT", type="counting", objectname='surv_object')
ds.survfit(formula='surv_object~1', objectname='survfit_object')
ds.plotsurvfit(formula = 'survfit_object')


sessionInfo()

sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] dsBaseClient_6.1.1 DSOpal_1.4.0 opalr_3.2.0 httr_1.4.3
[5] dsSurvivalClient_2.1.0 DSI_1.5.0 R6_2.5.1 progress_1.2.2
[9] metafor_3.4-0 metadat_1.2-0 Matrix_1.4-1 survival_3.4-0

0 replies

neelsoumya · 2022-11-24T08:43:45Z

neelsoumya
Nov 24, 2022
Maintainer

@naudinlo @tombisho I tried all this code on my laptop on R and R Studio. I did not use the docker image. Can you please try using this setup and let me know if it works for you?

i.e. do the following

Install R and R Studio on your laptop
Install all the required packages using these commands in R or R Studio:

install.packages('devtools')
library(devtools)
devtools::install_github('neelsoumya/dsSurvivalClient')
devtools::install_github('datashield/dsBaseClient@6.1.1')
install.packages('metafor')
install.packages('DSOpal')
install.packages('DSI')
install.packages('opalr')
install.packages('meta')
install.packages('fANCOVA')
install.packages('survival')

Run the following script

###################
# load libraries
###################
library(survival)
library(metafor)
library(dsSurvivalClient)
require('DSI')
require('DSOpal')
require('dsBaseClient')

builder <- DSI::newDSLoginBuilder(.silent = TRUE)
builder$append(
  server = "chu",
  url = "https://opal-demo.obiba.org/",
  user = "administrator", password = "password",
  driver = "OpalDriver",
  options='list(ssl_verifyhost=0, ssl_verifypeer=0)',
  profile="survival"
)

logindata <- builder$build()
connections <- DSI::datashield.login(logins = logindata)

datashield.assign.table(connections, symbol = "D", table = "SURVIVAL.EXPAND_WITH_MISSING1")

ds.asNumeric(x.name = "D$cens", newobj = "EVENT", datasources = connections)
ds.asNumeric(x.name = "D$starttime", newobj = "STARTTIME", datasources = connections)
ds.asNumeric(x.name = "D$endtime", newobj = "ENDTIME", datasources = connections)
ds.Surv(time="STARTTIME", time2="ENDTIME", event="EVENT", type="counting", objectname='surv_object')
ds.survfit(formula='surv_object~1', objectname='survfit_object')
ds.plotsurvfit(formula = 'survfit_object')


sessionInfo()

0 replies

neelsoumya · 2023-02-09T18:59:28Z

neelsoumya
Feb 9, 2023
Maintainer

@naudinlo did this code work for you?

1 reply

neelsoumya May 18, 2023
Maintainer

@naudinlo did this help fix your problem?

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Issue with plotsurvfitDS after using ds.Surv and ds.survfit #12

naudinlo Nov 10, 2022

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