Merge pull request #458 from StuartWheater/v6.3.5-dev

Update to glmSLMADS.assign and tidyups

Author: StuartWheater

DESCRIPTION

@@ -5,7 +5,7 @@ Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a
     been designed to only share non disclosive summary statistics, with built in automated output
     checking based on statistical disclosure control. With data sites setting the threshold values for
     the automated output checks. For more details, see 'citation("dsBase")'.
-Version: 6.3.5.9000
+Version: 6.3.5
 Authors@R: c(person(given = "Paul",
                     family = "Burton",
                     role = c("aut"),

R/glmSLMADS.assign.R

@@ -18,40 +18,25 @@
 #' @export
 glmSLMADS.assign <- function(formula, family, offsetName, weightsName, dataName){
 
-#############################################################
-#MODULE 1: CAPTURE THE nfilter SETTINGS                     #
-thr <- dsBase::listDisclosureSettingsDS()                   #
-nfilter.tab <- as.numeric(thr$nfilter.tab)                  #
-nfilter.glm <- as.numeric(thr$nfilter.glm)                  #
-#nfilter.subset<-as.numeric(thr$nfilter.subset)             #
-#nfilter.string<-as.numeric(thr$nfilter.string)             #
-#############################################################
+  # Convert transmitable text for special link variance combinations back to full representation
+  if(family=="quasigamma.link_log")
+  {family<-"quasi(link=log,variance=mu^2)"}
 
-########################################
-############
-#Convert transmitable text for special link variance combinations back to full representation
-if(family=="quasigamma.link_log")
-{family<-"quasi(link=log,variance=mu^2)"}
+  if(family=="Gamma.link_log")
+  {family<-"Gamma(link=log)"}
 
-if(family=="Gamma.link_log")
-{family<-"Gamma(link=log)"}
-#############
+  # Correctly name offset, weights and data objects in function call
+  # (to allow glmPredict to work correctly later)
+  calltext <- paste0("mg<-glm(formula,family=",family,",offset=",
+             offsetName,",weights=",weightsName,",data=", dataName,",x=TRUE)")
 
-#Activate family object (this may not be necessary as character string may already be OK
-#but just checking
-final.family.object<-eval(parse(text=family))
+  eval(parse(text=calltext))
 
+  # update the call object to include the actual formula
+  mg$call$formula <- formula
 
-#Correctly name offset, weights and data objects in function call
-#(to allow glmPredict to work correctly later)
-calltext<-paste0("mg<-glm(formula,family=",family,",offset=",
-           offsetName,",weights=",weightsName,",data=", dataName,",x=TRUE)")
-
-eval(parse(text=calltext))
-
-return(mg)		
+  return(mg)
 
 }
-
 # ASSIGN FUNCTION
 # glmSLMADS.assign

azure-pipelines.yml

@@ -253,7 +253,6 @@ jobs:
       echo 'branch:'$(branchName) >> $(datetime).txt
       echo 'os:'$(lsb_release -ds) >> $(datetime).txt
       echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
-      echo 'opal:'$(opal system --opal localhost:8080 --user administrator --password "datashield_test&" --version) >> $(datetime).txt
 
     workingDirectory: $(Pipeline.Workspace)/logs
     displayName: 'Write versions to file'

docs/404.html

@@ -2,4 +2,4 @@ pandoc: 3.1.3
 pkgdown: 2.2.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2025-11-30T16:44Z
+last_built: 2026-02-20T10:54Z