Merge pull request #16 from tombisho/vcov2

Revert "undoing push to neelsoumya repo"

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: 2.0.0
+Version: 2.1.0
 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

NAMESPACE

@@ -9,3 +9,4 @@ export(listDisclosureSettingsDS)
 export(plotsurvfitDS)
 export(summarySurvDS)
 export(survfitDS)
+export(vcovDS.coxph)

R/vcovDS.coxph.R

@@ -0,0 +1,36 @@
+#' 
+#' @title Returns variance-covariance matrix of Cox Proportional Hazard model.
+#' @description returns a variance-covariance matrix of Cox Proportional Hazard model from the server side environment.
+#' @details Serverside aggregate function {vcovDS.coxph} called by clientside function 
+#' {ds.vcov.coxph}.
+#' returns a list which contains a variance-covariance matrix for a Cox model.
+#' This request is not disclosive, because the disclosure checks should be performed in the main function for building
+#' the Cox model (e.g. checking for over saturation).
+#' For further details see help for the native {vcov} function.
+#' @param object name of server-side coxph object.
+#' @return a variance-covariance matrix.
+#' @author Soumya Banerjee and Tom Bishop (2022).
+#' @export
+vcovDS.coxph<-function(object=NULL)
+{
+
+  if (is.null(object))
+  {
+    stop("Please provide the name of a survival::coxph object", call.=FALSE)
+  }
+
+  surv_obj<-eval(parse(text=object), envir = parent.frame())
+
+  if (class(surv_obj)!="coxph")
+  {
+    stop("Object is not of class survival::coxph, please check the name", call.=FALSE)
+  }
+
+  vcov_res <- stats::vcov(surv_obj)
+
+  return(vcov_res)
+
+
+}
+#AGGREGATE FUNCTION
+# vcovDS.coxph

inst/DATASHIELD

@@ -3,18 +3,9 @@ AggregateMethods:
     coxphSummaryDS,
     cox.zphSLMADS,
     summarySurvDS,
-    plotsurvfitDS
+    plotsurvfitDS,
+    vcovDS.coxph
 AssignMethods:
     coxphSLMAassignDS,
     SurvDS,
     survfitDS
-Options:
-    datashield.privacyLevel=5,
-    default.nfilter.glm=0.33,
-    default.nfilter.kNN=3,
-    default.nfilter.string=80,
-    default.nfilter.subset=3,
-    default.nfilter.stringShort=20,
-    default.nfilter.tab=3,
-    default.nfilter.noise=0.25,
-    default.nfilter.levels=0.33