ds.cox.zphSLMA: Tests the proportional hazards assumption for a Cox...

In neelsoumya/dsSurvivalClient: dsSurvival: Privacy preserving survival models for federated individual patient meta-analysis in DataSHIELD

Tests the proportional hazards assumption for a Cox proportional hazards model

Description

This function tests the proportional hazards assumption for a Cox proportional hazards model.

Usage

ds.cox.zphSLMA(
  fit = NULL,
  transform = "km",
  terms = TRUE,
  singledf = FALSE,
  global = TRUE,
  datasources = NULL
)

Arguments

fit	character string (potentially including * symbol without spaces) specifying the name of the fitted server-side Cox proportioanl hazards model that has been created using ds.coxphSLMAassign()
transform	character string specifying how the survival times should be transformed before the test is performed. Possible values are "km", "rank", "identity" or a function of one argument.
terms	logical if TRUE, do a test for each term in the model rather than for each separate covariate. For a factor variable with k levels, for instance, this would lead to a k-1 degree of freedom test. The plot for such variables will be a single curve evaluating the linear predictor over time.
singledf	logical use a single degree of freedom test for terms that have multiple coefficients, i.e., the test that corresponds most closely to the plot. If terms=FALSE this argument has no effect.
global	logical should a global chi-square test be done, in addition to the per-variable or per-term tests tests.
datasources	a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default. For more information see Details.

Details

This is a function that performs diagnostics on a fitted Cox proportional hazards model.

Server function called: cox.zphSLMADS.

Value

cox.zphSLMADS returns to the client-side the diagnostics of the Cox proportional hazards model

Author(s)

Soumya Banerjee and Tom Bishop, 2021

Examples

## Not run: 

  ## Version 1.0.0
  
  # connecting to the Opal servers

  require('DSI')
  require('DSOpal')
  require('dsBaseClient')

  builder <- DSI::newDSLoginBuilder()
  builder$append(server = "study1", 
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver")
  builder$append(server = "study2", 
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver")
  builder$append(server = "study3",
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver")
  logindata <- builder$build()
  
  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
  
  # make sure that the outcome is numeric 
  ds.asNumeric(x.name = "D$cens",
            newobj = "EVENT",
            datasources = connections)

  ds.asNumeric(x.name = "D$survtime",
            newobj = "SURVTIME",
            datasources = connections)

  dsSurvivalClient::ds.Surv(time='SURVTIME', event='EVENT', objectname='surv_object')

  dsSurvivalClient::ds.coxph.SLMA(formula = 'surv_object ~  D$female', 
            dataName = 'D', datasources = connections)
  
  # clear the Datashield R sessions and logout
  datashield.logout(connections)

## End(Not run)

neelsoumya/dsSurvivalClient documentation built on July 1, 2023, 10:32 p.m.