Some bugs and other small things.

.Rbuildignore

@@ -6,6 +6,8 @@
 ^\.github$
 ^\.git$
 ^checkEffects.R$
+^checkTheEffects.R$
+^checkEffects*.out$
 ^ONEWS$
 ^ONEWS_gh$
 ^README.md$

.gitignore

@@ -15,6 +15,8 @@ inst/doc
 autom4te.cache
 config.log
 config.status
+checkTheEffects.R
+checkEffects*.out
 docs/*
 !docs/manual/
 docs/manual/Older/

DESCRIPTION

@@ -2,8 +2,8 @@ Encoding: UTF-8
 Package: RSiena
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.6.8
-Date: 2026-06-06
+Version: 1.6.9
+Date: 2026-06-10
 Authors@R: c(person("Tom A.B.", "Snijders", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-3157-4157")),
               person("Ruth M.", "Ripley", role = "aut"),
               person("Krists", "Boitmanis", role = c( "aut","ctb")),

NEWS.md

@@ -1,3 +1,19 @@
+2026-06-10
+
+# RSiena 1.6.9
+
+## Changes in RSiena:
+### Functionality
+  * `print.sienaGroup` now also specifies the node sets for covariates
+    and restricts printed line lengths to 64.
+  * Use of `r` in `estimate_onestep` effectuated.
+  * `checkEffects.R` corrected so that it will run without errors
+    and can be used for batch checking (will take a long time).
+### Bug correction
+  * `make_specification` corrected for a continuous dependent behavior variable
+    and for two dependent networks and varying actor covariates (`effects.r`).
+  * Use of `prevAns` with one-step estimator corrected (`initializeFRAN.r`). 
+
 2026-06-06
 
 # RSiena 1.6.8
@@ -7,7 +23,7 @@
   * Selection of effects for combinations of two dependent networks
     and an actor covariate improved, which leads to including
     more effects for combinations where one of the dependent networks
-    is bipartite.
+    is bipartite (`effects.r`, `effectsDocumentation.r`).
 ### Functionality
   * New function `estimate_onestep`.
   * Option `onestep` for `update_theta.sienaEffects` changed.

R/effects.r

@@ -421,8 +421,7 @@ getEffects <- function(x, nintn = 10, behNintn=4, getDocumentation=FALSE, onePer
 				}
 				for (k in seq(along=xx$depvars))
 				{
-					if ((types[k] %in% c('behavior', 'continuous')) &&
-						(attr(xx$depvars[[k]], 'nodeSet') == nodeSet))
+					if (types[k] %in% c('behavior', 'continuous'))
 					{
 						objEffects <-
 							rbind(objEffects,
@@ -1214,7 +1213,7 @@ getEffects <- function(x, nintn = 10, behNintn=4, getDocumentation=FALSE, onePer
 							covarname=names(xx$vCovars)[k],
 							nodeSets, # this is attr(depvar, 'nodeSet')
 							attr(xx$depvars[[j]], 'nodeSet'),
-							attr(xx$cCovars[[k]], 'nodeSet'),
+							attr(xx$vCovars[[k]], 'nodeSet'),
 							name=varname))
 				}
 				for (k in seq(along = xx$dycCovars))
@@ -1247,15 +1246,16 @@ getEffects <- function(x, nintn = 10, behNintn=4, getDocumentation=FALSE, onePer
 				}
 				for (k in seq(along=xx$depvars))
 				{
-					if (types[k] %in% c('behavior', 'continuous') &&
-						attr(xx$depvars[[k]], 'nodeSet') == nodeSets[1])
+					if (types[k] %in% c('behavior', 'continuous'))
 					{
 						objEffects <-
 							rbind(objEffects,
-								createEffects("covarABipNetObjective", otherName,
-									names(xx$depvars)[k], name=varname,
-									groupName=groupName, group=group,
-									netType=netType))
+								covarNetNetEff(otherName,
+									covarname=names(xx$depvars)[k],
+									nodeSets, # this is attr(depvar, 'nodeSet')
+									attr(xx$depvars[[j]], 'nodeSet'),
+									attr(xx$depvars[[k]], 'nodeSet'),
+									name=varname))
 					}
 				}
 			}

R/initializeFRAN.r

@@ -278,7 +278,7 @@ initializeFRAN <- function(z, x, data, effects, prevAns=NULL, initC,
 				if (x$useOneStep)
 				{
 					keepStill <- which(prevAns$fixed)
-					if (length(keepStill == 0))
+					if (length(keepStill) == 0)
 					{
 						keepStill <- 0
 					}				
@@ -2153,7 +2153,7 @@ update_theta.sienaEffects <- function(x, prevAns, varName=NULL,
 	eff <- updateTheta(x, prevAns=prevAns, varName=varName)
 	if (onestep)
 	{
-		est_onestep <- estimate_onestep(prevAns, fixed=keepUnchanged)
+		est_onestep <- estimate_onestep(prevAns, fixed=keepUnchanged, r=r)
 		effsF <- prevAns$requestedEffects 
 		requested <- which(names(prevAns$requestedEffects)=="requested")
 		effsF$initialValue <- est_onestep

R/sienaprint.r

@@ -13,6 +13,39 @@
 ## * even if these main effects were not requested.
 ## *
 ## ****************************************************************************/
+
+##@printWithLineMax for print.siena; prints character strings
+printWithLineMax <- function(heading, contents, contentkinds){
+# function to print contents with categories contentkinds
+# with a heading; line length maximum 4 + 60
+# heading is a character string,
+# contents and contentkinds are characters strings of the same length
+	if (length(contents) != length(contentkinds))
+	{
+		stop("Error in printWithLineMax: contents and contentkinds have different length")
+	}
+	vsets <- unique(contentkinds)
+	for (vk in vsets)
+	{
+		cat(heading, "<", vk, "> : \n")
+		contentk <- contents[contentkinds==vk]
+		cumlength <- 0
+		cat("   ")
+		for (k in seq_along(contentk))
+		{
+			cumlength <- cumlength + nchar(contentk[k])
+			if (cumlength > 60)
+			{
+				cat("\n   ")
+				cumlength <- 0
+			}
+			cat(contentk[k])
+			if (k < length(contentk)){cat(", ")}				
+		}
+		cat("\n")
+	}
+	cat("\n")
+}	
 ##@print.sienadata Methods
 print.sienadata <- function(x, ...)
 {
@@ -51,38 +84,6 @@ print.sienadata <- function(x, ...)
 			}
 		}
 	}
-    ##@printWithLineMax internal print.siena; prints character strings
-	printWithLineMax <- function(heading, contents, contentkinds){
-	# function to print contents with categories contentkinds
-	# with a heading; line length maximum 4 + 60
-	# heading is a character string, 
-	# contents and contentkinds are characters strings of the same length
-		if (length(contents) != length(contentkinds))
-		{
-			stop("Error in printWithLineMax: contents and contentkinds have different length")
-		}
-		vsets <- unique(contentkinds)
-		for (vk in vsets)
-		{
-			cat(heading, "<", vk, "> : \n")
-			contentk <- contents[contentkinds==vk]
-			cumlength <- 0
-			cat("   ")
-			for (k in seq_along(contentk))
-			{
-				cumlength <- cumlength + nchar(contentk[k])
-				if (cumlength > 60)
-				{
-					cat("\n   ")
-					cumlength <- 0
-				}
-				cat(contentk[k])
-				if (k < length(contentk)){cat(", ")}				
-			}
-			cat("\n")
-		}
-		cat("\n")
-	}	
 # begin main method siena.print proper
 	if ((!inherits(x, "sienadata")) & (!inherits(x, "siena")))
 	{
@@ -243,16 +244,20 @@ print.sienaGroup <- function(x, ...)
 	cat('Dependent variables: \n')
 	cat(paste(att$netnames, ":", att$types,'\n'))
 	cat('Total number of groups:', length(x),'\n')
-	cat('Total number of periods:', att$observations,'\n')
+	cat('Total number of periods:', att$observations,'\n')	
 	if (length(x[[1]]$vCovars) > 0)
 	{
-		cat('Changing covariates: ',
-			paste(names(x[[1]]$vCovars), collapse = ", "), "\n")
-	}
+		vnodesets <- sapply(x[[1]]$vCovars, function(v){attr(v,"nodeSet")})
+		printWithLineMax("Changing covariates for node set", names(x[[1]]$vCovars), vnodesets)
+	}		
 	if (length(x[[1]]$dyvCovars) > 0)
 	{
-		cat('Changing dyadic covariates: ',
-			paste(names(x[[1]]$dyvCovars), collapse=", "), "\n")
+		kindNodeSets <- rep("", length(x[[1]]$dyvCovars))
+		for (k in seq_along(x[[1]]$dyvCovars))
+		{
+			kindNodeSets[k] <- paste(attr(x[[1]]$dyvCovars[[k]],"nodeSet"), collapse=", ")
+		}
+		printWithLineMax("Changing dyadic covariates for node sets", names(x[[1]]$dyvCovars), kindNodeSets)
 	}
 	cat("\n")
 	invisible(x)