Add plot method for osmasem2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: metaSEM
 Type: Package
 Title: Meta-Analysis using Structural Equation Modeling
-Version: 1.4.4
+Version: 1.4.5
 Date: 2024-07-27
 Depends: R (>= 3.4.0), OpenMx
 Imports: Matrix, MASS, ellipse, graphics, stats, utils, mvtnorm, numDeriv, lavaan

NAMESPACE

@@ -14,6 +14,7 @@ S3method(plot, meta)
 S3method(plot, character)
 S3method(plot, wls)
 S3method(plot, osmasem)
+S3method(plot, osmasem2)
 S3method(plot, mxRAMmodel)
 # S3method(plot, osmasem3L)
 

R/meta2semPlot.R

@@ -119,25 +119,41 @@ plot.osmasem <- function(x, manNames=NULL, latNames=NULL, labels=c("labels", "RA
  if (!requireNamespace("semPlot", quietly=TRUE)) 
  stop("\"semPlot\" package is required for this function.")
 
- if (!is.element(class(x), c("osmasem", "osmasem3L")))
- stop("\"x\" must be an object of either class \"osmasem\" or \"osmasem3L\".")
+ if (!is.element(class(x), c("osmasem", "osmasem2", "osmasem3L")))
+ stop("\"x\" must be an object of either class \"osmasem\", \"osmasem2\", or \"osmasem3L\".")
 
- A <- x$mx.fit$Amatrix$result
- S <- x$mx.fit$Smatrix$result
- ## S can be calculated when diag.constraints=FALSE
- if (is.null(S)) {
+ if (is.element(class(x), "osmasem2")) {
+ A <- x$mx.fit$Amatrix$values
+ S <- x$mx.fit$Smatrix$values
+ } else {
+ ## osmasem and osmasem3L: different from osmasem2 coz they replace error
+ ## variances with other parameters 
+ A <- x$mx.fit$Amatrix$result
+ S <- x$mx.fit$Smatrix$result
+ ## S can be calculated when diag.constraints=FALSE
+ if (is.null(S)) {
  S <- x$mx.fit$algebras$Smatrix$result
+ }
  }
 
  F <- x$mx.fit$Fmatrix$values
  Id <- diag(nrow(S))
 
  ## Approximate sample covariance matrix
  ## The means in osmasem are correlation matrix
- ObsCovs <- vec2symMat(apply(x$data$data[, x$labels$ylabels], 2, mean, na.rm=TRUE), diag=FALSE) 
- ImpCovs <- x$mx.fit$impliedR$result
-
- if (is.null(manNames)) manNames <- x$labels$obslabels
+ if (is.element(class(x), "osmasem2")) { 
+ ObsCovs <- vec2symMat(apply(x$data$data[, x$data$ylabels], 2, mean, na.rm=TRUE),
+ diag=!x$cor.analysis) 
+ ImpCovs <- x$mx.fit$expSigma$result
+ if (is.null(manNames)) manNames <- x$data$obslabels
+ } else {
+ ## A labels slot is required because osmasem allows subset.
+ ## labels can be shorter than those in data$labels
+ ObsCovs <- vec2symMat(apply(x$data$data[, x$labels$ylabels], 2, mean,
+ na.rm=TRUE), diag=FALSE) 
+ ImpCovs <- x$mx.fit$impliedR$result
+ if (is.null(manNames)) manNames <- x$labels$obslabels
+ }
  ## If manNames is still NULL
  if (is.null(manNames)) manNames <- paste("X", seq(1, nrow(F), 1), sep="")
 
@@ -156,11 +172,28 @@ plot.osmasem <- function(x, manNames=NULL, latNames=NULL, labels=c("labels", "RA
  } 
  }
 
- out <- semPlot::ramModel(A=A, S=S, F=F, manNames=manNames, latNames=latNames, ObsCovs=ObsCovs, 
- ImpCovs=ImpCovs)
-
- labels <- match.arg(labels)
- if (labels=="labels") {
+ if (is.element(class(x), "osmasem2")) {
+ if (x$mean.analysis) {
+ ## osmasem2 with mean structure
+ M <- x$mx.fit$Mmatrix$values
+ colnames(M) <- colnames(F)
+ out <- semPlot::ramModel(A=A, S=S, F=F, M=M, manNames=manNames,
+ latNames=latNames, ObsCovs=ObsCovs, 
+ ImpCovs=ImpCovs)
+ } else {
+ ## osmasem2 without mean structure
+ out <- semPlot::ramModel(A=A, S=S, F=F, manNames=manNames, latNames=latNames,
+ ObsCovs=ObsCovs, ImpCovs=ImpCovs)
+ }
+ } else {
+ ## osmasem and osmasem3L
+ out <- semPlot::ramModel(A=A, S=S, F=F, manNames=manNames, latNames=latNames,
+ ObsCovs=ObsCovs, ImpCovs=ImpCovs)
+ }
+
+ if (is.element(class(x), c("osmasem", "osmasem3L"))) {
+ labels <- match.arg(labels)
+ if (labels=="labels") {
  A.labels <- x$mx.fit$A0$labels
  S.labels <- x$mx.fit$S0$labels
  labels <- c(c(A.labels), c(S.labels))
@@ -170,7 +203,8 @@ plot.osmasem <- function(x, manNames=NULL, latNames=NULL, labels=c("labels", "RA
  na.index <- is.na(out@Pars$label)
  ##out@Pars$label[na.index] <- sprintf("%.2f", out@Pars$est[na.index])
  out@Pars$label[na.index] <- ""
- } 
+ }
+ }
 
  invisible( semPlot::semPaths(out, what=what, nCharNodes=nCharNodes,
  nCharEdges=nCharEdges, layout=match.arg(layout),
@@ -179,6 +213,17 @@ plot.osmasem <- function(x, manNames=NULL, latNames=NULL, labels=c("labels", "RA
  weighted=weighted, ...) )
 }
 
+plot.osmasem2 <- function(x, manNames=NULL, latNames=NULL, labels=c("labels", "RAM"),
+ what="est", nCharNodes=0, nCharEdges=0,
+ layout=c("tree", "circle", "spring", "tree2", "circle2"),
+ sizeMan=8, sizeLat=8, edge.label.cex=1.3, color="white",
+ weighted=FALSE, ...) {
+ plot.osmasem(x, manNames=manNames, latNames=latNames, labels=labels,
+ what=what, nCharNodes=nCharNodes, nCharEdges=nCharEdges,
+ layout=layout, sizeMan=sizeMan, sizeLat=sizeLat,
+ edge.label.cex=edge.label.cex, color=color, weighted=weighted, ...)
+}
+
 ## plot.osmasem3L <- function(x, manNames=NULL, latNames=NULL, labels=c("labels", "RAM"),
 ## what="est", nCharNodes=0, nCharEdges=0,
 ## layout=c("tree", "circle", "spring", "tree2", "circle2"),

R/osmasem2.R

@@ -401,10 +401,10 @@ osmasem2 <- function(model.name="osmasem2", RAM, data, cor.analysis=TRUE,
  } else {
  mx.fit <- mx.model
  }
-
+ 
  out <- list(mx.fit=mx.fit, mx.ind=mx.ind, mx.sat=mx.sat,
  cor.analysis=cor.analysis, mean.analysis=mean.analysis,
- n=sum(data$n), intervals.type=intervals.type)
+ n=sum(data$n), intervals.type=intervals.type, data=data)
  class(out) <- "osmasem2"
  out
 } 

man/metaSEM-package.Rd

@@ -14,7 +14,7 @@
 \tabular{ll}{
 Package: \tab metaSEM\cr
 Type: \tab Package\cr
-Version: \tab 1.4.4\cr
+Version: \tab 1.4.5\cr
 Date: \tab 2024-07-27\cr
 License: \tab GPL (>=2)\cr
 LazyLoad: \tab yes\cr

man/osmasem.Rd

@@ -87,7 +87,7 @@ modeling with moderating effects on SEM parameters. \emph{Psychological
  Methods}, \bold{25} (4), 430-455. https://doi.org/10.1037/met0000245
 } 
 \seealso{ \code{\link[metaSEM]{Cor2DataFrame}}, \code{\link[metaSEM]{create.vechsR}},
- \code{\link[metaSEM]{create.Tau2}}, \code{\link[metaSEM]{create.V}}, \code{\link[metaSEM]{osmasem}}, \code{\link[metaSEM]{Nohe15}}
+ \code{\link[metaSEM]{create.Tau2}}, \code{\link[metaSEM]{create.V}}, \code{\link[metaSEM]{osmasem}}, \code{\link[metaSEM]{Nohe15}}, \code{\link[metaSEM]{issp05}}
 }
 
 % Add one or more standard keywords, see file 'KEYWORDS' in the

man/plot.Rd

@@ -3,6 +3,7 @@
 \alias{plot.character}
 \alias{plot.wls}
 \alias{plot.osmasem}
+\alias{plot.osmasem2}
 \alias{plot.mxRAMmodel}
 
 \title{Plot methods for various objects
@@ -42,6 +43,11 @@
  layout=c("tree", "circle", "spring", "tree2", "circle2"),
  sizeMan=8, sizeLat=8, edge.label.cex=1.3, color="white",
  weighted=FALSE, \dots)
+\method{plot}{osmasem2}(x, manNames=NULL, latNames=NULL, labels=c("labels", "RAM"),
+ what="est", nCharNodes=0, nCharEdges=0,
+ layout=c("tree", "circle", "spring", "tree2", "circle2"),
+ sizeMan=8, sizeLat=8, edge.label.cex=1.3, color="white",
+ weighted=FALSE, \dots)
 \method{plot}{mxRAMmodel}(x, manNames=NULL, latNames=NULL, labels=c("labels", "RAM"),
  what="est", nCharNodes=0, nCharEdges=0,
  layout=c("tree", "circle", "spring", "tree2", "circle2"),