Merge pull request #20 from StuartWheater/main

Removal of 'listDisclosureSettingsDS' and minor updates
neelsoumya · Dec 8, 2022 · 34245dd · 34245dd
2 parents b2959fd + 4c9c15a
commit 34245dd
Show file tree

Hide file tree

Showing 15 changed files with 15 additions and 143 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,2 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^.github$
+^dssurvival lay summary.pdf$
+^DAGStat_sofack \(1\).pdf$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: dsSurvival
 Title: dsSurvival: Privacy preserving survival models for federated individual patient meta-analysis in DataSHIELD
 Description: DataSHIELD server side base functions for building survival models.
-Version: 2.1.0
+Version: 2.1.1
 Author: Soumya Banerjee, Demetris Avraam, Xavier Escriba Montagut, Juan Gonzalez, Paul Burton and Tom R P Bishop <[email protected]>
 Maintainer: Soumya Banerjee, Demetris Avraam, Xavier Escriba Montagut, Juan Gonzalez, Paul Burton and Tom R P Bishop <[email protected]>
 License: GPL-3
@@ -16,4 +16,4 @@ Imports:
     reshape2,
     dsBase,
     fANCOVA
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.2
diff --git a/NAMESPACE b/NAMESPACE
@@ -5,7 +5,6 @@ export(cox.zphSLMADS)
 export(coxphSLMADS)
 export(coxphSLMAassignDS)
 export(coxphSummaryDS)
-export(listDisclosureSettingsDS)
 export(plotsurvfitDS)
 export(summarySurvDS)
 export(survfitDS)

diff --git a/R/SurvDS.R b/R/SurvDS.R
@@ -29,7 +29,7 @@ SurvDS<-function(time = NULL,
 {
       #########################################################################
       # DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS                       #
-      thr <- listDisclosureSettingsDS()                                       #
+      thr <- dsBase::listDisclosureSettingsDS()                               #
       #nfilter.tab<-as.numeric(thr$nfilter.tab)                               #
       #nfilter.glm<-as.numeric(thr$nfilter.glm)                               #
       #nfilter.subset<-as.numeric(thr$nfilter.subset)                         #

diff --git a/R/cox.zphSLMADS.R b/R/cox.zphSLMADS.R
@@ -39,7 +39,7 @@ cox.zphSLMADS<-function(fit = NULL,
 
       #########################################################################
       # DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS                       #
-      thr <- listDisclosureSettingsDS()                                       #
+      thr <- dsBase::listDisclosureSettingsDS()                               #
       #nfilter.tab<-as.numeric(thr$nfilter.tab)                               #
       #nfilter.glm<-as.numeric(thr$nfilter.glm)                               #
       #nfilter.subset<-as.numeric(thr$nfilter.subset)                         #

diff --git a/R/coxphSLMADS.R b/R/coxphSLMADS.R
@@ -43,7 +43,7 @@ coxphSLMADS<-function(formula = NULL,
 
       #########################################################################
       # DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS                       #
-      thr <- listDisclosureSettingsDS()                                       #
+      thr <- dsBase::listDisclosureSettingsDS()                               #
       #nfilter.tab<-as.numeric(thr$nfilter.tab)                               #
       #nfilter.glm<-as.numeric(thr$nfilter.glm)                               #
       #nfilter.subset<-as.numeric(thr$nfilter.subset)                         #

diff --git a/R/coxphSLMAassignDS.R b/R/coxphSLMAassignDS.R
@@ -43,7 +43,7 @@ coxphSLMAassignDS<-function(formula = NULL,
 
       #########################################################################
       # DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS                       #
-      thr <- listDisclosureSettingsDS()                                       #
+      thr <- dsBase::listDisclosureSettingsDS()                               #
       #nfilter.tab<-as.numeric(thr$nfilter.tab)                               #
       #nfilter.glm<-as.numeric(thr$nfilter.glm)                               #
       #nfilter.subset<-as.numeric(thr$nfilter.subset)                         #

diff --git a/R/coxphSummaryDS.R b/R/coxphSummaryDS.R
@@ -23,7 +23,7 @@ coxphSummaryDS<-function(x = NULL
 
       #########################################################################
       # DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS                       #
-      thr <- listDisclosureSettingsDS()                                       #
+      thr <- dsBase::listDisclosureSettingsDS()                               #
       #nfilter.tab<-as.numeric(thr$nfilter.tab)                               #
       #nfilter.glm<-as.numeric(thr$nfilter.glm)                               #
       #nfilter.subset<-as.numeric(thr$nfilter.subset)                         #
@@ -39,7 +39,7 @@ coxphSummaryDS<-function(x = NULL
       if (is.null(x))
       {
          stop("The name of the server-side fit Cox proportional hazards model must be set", call.=FALSE)
-      } 	
+      }
 
 
       # evaluate the model fit parameter in parent environment

diff --git a/R/listDisclosureSettingsDS.R b/R/listDisclosureSettingsDS.R
diff --git a/R/plotsurvfitDS.R b/R/plotsurvfitDS.R
@@ -24,7 +24,7 @@ plotsurvfitDS<-function(formula = NULL,
 
   #########################################################################
   # DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS                       #
-  # thr <- listDisclosureSettingsDS()                                     #
+  # thr <- dsBase::listDisclosureSettingsDS()                             #
   #nfilter.tab<-as.numeric(thr$nfilter.tab)                               #
   #nfilter.glm<-as.numeric(thr$nfilter.glm)                               #
   #nfilter.subset<-as.numeric(thr$nfilter.subset)                         #

diff --git a/R/summarySurvDS.R b/R/summarySurvDS.R
@@ -18,7 +18,7 @@ summarySurvDS<-function(object=NULL)
 
       #########################################################################
       # DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS                       #
-      thr <- listDisclosureSettingsDS()                                       #
+      thr <- dsBase::listDisclosureSettingsDS()                               #
       #nfilter.tab<-as.numeric(thr$nfilter.tab)                               #
       #nfilter.glm<-as.numeric(thr$nfilter.glm)                               #
       #nfilter.subset<-as.numeric(thr$nfilter.subset)                         #

diff --git a/R/survfitDS.R b/R/survfitDS.R
@@ -18,7 +18,7 @@ survfitDS<-function(formula=NULL)
 {
       #########################################################################
       # DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS                       #
-      thr <- listDisclosureSettingsDS()                                       #
+      thr <- dsBase::listDisclosureSettingsDS()                               #
       #nfilter.tab<-as.numeric(thr$nfilter.tab)                               #
       #nfilter.glm<-as.numeric(thr$nfilter.glm)                               #
       #nfilter.subset<-as.numeric(thr$nfilter.subset)                         #

diff --git a/R/vcovDS.coxph.R b/R/vcovDS.coxph.R
@@ -21,7 +21,7 @@ vcovDS.coxph<-function(object=NULL)
 
   surv_obj<-eval(parse(text=object), envir = parent.frame())
 
-  if (class(surv_obj)!="coxph")
+  if (! any(c("coxph") %in% class(surv_obj)))
   {
     stop("Object is not of class survival::coxph, please check the name", call.=FALSE)
   }

diff --git a/man/listDisclosureSettingsDS.Rd b/man/listDisclosureSettingsDS.Rd
diff --git a/tests/testthat/test-smk-listDisclosureSettingsDS.R b/tests/testthat/test-smk-listDisclosureSettingsDS.R