undoing push to neelsoumya repo

Revert "updating from neelsoumya repo" This reverts commit 52aaf6b, reversing changes made to 8e3ca92.
neelsoumya · Jul 19, 2022 · 3edbb30 · 3edbb30
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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: 2.0.0
 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

diff --git a/LICENSE.md b/LICENSE.md
diff --git a/NAMESPACE b/NAMESPACE
@@ -9,4 +9,3 @@ export(listDisclosureSettingsDS)
 export(plotsurvfitDS)
 export(summarySurvDS)
 export(survfitDS)
-export(vcovDS.coxph)
diff --git a/R/vcovDS.coxph.R b/R/vcovDS.coxph.R
diff --git a/build_man_test.R b/build_man_test.R
@@ -0,0 +1,45 @@
+###########################################
+# Script to build manuals and test code
+#
+# Usage:
+#   R --no-save < build_man_test.R
+#
+###########################################
+
+###################
+# load libraries
+###################
+library(devtools)
+library(testthat)
+library(dsBase)
+library(dsBaseClient)
+require('DSI')
+require('DSOpal')
+library(dsSurvival)
+library(dsSurvivalClient)
+
+##################
+# build manuals
+##################
+devtools::build_manual()
+
+########################
+# update documentation
+########################
+devtools::check_man()
+
+##################
+# build vignettes
+##################
+devtools::build_vignettes()
+
+##################
+# Testing
+##################
+devtools::test()
+
+##################
+# clean up
+##################
+gc()
+
diff --git a/inst/DATASHIELD b/inst/DATASHIELD
@@ -3,9 +3,18 @@ AggregateMethods:
     coxphSummaryDS,
     cox.zphSLMADS,
     summarySurvDS,
-    plotsurvfitDS,
-    vcovDS.coxph
+    plotsurvfitDS
 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
diff --git a/man/vcovDS.coxph.Rd b/man/vcovDS.coxph.Rd
diff --git a/screenshot_survival_models.png b/screenshot_survival_models.png
diff --git a/vignettes/development_plan.pdf b/vignettes/development_plan.pdf