sfcheung · sfcheung · Aug 17, 2025 · Aug 15, 2025 · Aug 15, 2025 · Aug 17, 2025
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: semptools
 Title: Customizing Structural Equation Modelling Plots
-Version: 0.3.2.1
+Version: 0.3.2.2
 Authors@R: c(
     person(given = "Shu Fai",
            family = "Cheung",

diff --git a/NAMESPACE b/NAMESPACE
@@ -11,6 +11,7 @@ export(is_dv_residvar)
 export(keep_nodes)
 export(lavaan_indicator_order)
 export(layout_matrix)
+export(mark_ci)
 export(mark_se)
 export(mark_sig)
 export(move_node)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,9 @@
-# semptools 0.3.2.1
+# semptools 0.3.2.2
+
+## New Features
+
+- Added `mark_ci()` for adding confidence
+  intervals to a plot. (0.3.2.2)
 
 ## Improvement
 

diff --git a/R/mark_se.R b/R/mark_se.R
@@ -1,116 +1,157 @@
-#'@title Add Standard Error Estimates to Parameter Estimates (Edge
-#' Labels)
+#' @title Add Standard Error/Confidence Interval Estimates to Parameter 
+#'   Estimates (Edge Labels)
 #'
-#'@description Add standard error estimates, in parentheses, to
-#'   parameter estimates (edge labels) in a [qgraph::qgraph] object.
+#' @description Add standard error or confidence interval estimates, 
+#'   in parentheses, to parameter estimates (edge labels) in a 
+#'   [qgraph::qgraph] object.
 #'
-#'@details Modify a [qgraph::qgraph] object generated by
+#' @details Modify a [qgraph::qgraph] object generated by
 #'   \code{\link[semPlot]{semPaths}} (currently in parentheses) to the
 #'   labels. Require either the original object used in the semPaths call,
-#'   or a data frame with the standard error for each parameter. The latter
-#'   option is for standard errors not computed by lavaan but by
-#'   other functions.
+#'   or a data frame with the standard error (or confidence interval) for 
+#'   each parameter. The latter option is for standard errors/confidence
+#'   interval not computed by lavaan but by other functions.
 #'
-#'Currently supports only plots based on \code{\link[lavaan]{lavaan}}
-#'output.
+#' Currently supports only plots based on \code{\link[lavaan]{lavaan}}
+#'   output.
 #'
-#'This function is a variant of, and can be combined with,  the
-#'  \code{\link{mark_sig}} function.
+#' This function is a variant of, and can be combined with, the
+#'   \code{\link{mark_sig}} function.
 #'
-#'@return If the input is a [qgraph::qgraph] object, the function
-#'  returns a qgraph based on the original one, with standard error
-#'  estimates appended. If the input is a list of qgraph objects, the
-#'  function returns a list of the same length.
+#' @return If the input is a [qgraph::qgraph] object, the function
+#'   returns a qgraph based on the original one, with standard error
+#'   or confidence interval estimates appended. If the input is a list 
+#'   of qgraph objects, the function returns a list of the same length.
 #'
-#'@param semPaths_plot A qgraph object generated by
+#' @param semPaths_plot A qgraph object generated by
 #'   \code{\link[semPlot]{semPaths}}, or a similar qgraph object
 #'   modified by other [semptools] functions.
 #'
-#'@param object The object used by semPaths to generate the plot. Use
+#' @param object The object used by semPaths to generate the plot. Use
 #'   the same argument name used in \code{\link[semPlot]{semPaths}} to
 #'   make the meaning of this argument obvious. Currently only object
 #'   of class `lavaan` is supported.
 #'
-#'@param sep A character string to separate the coefficient and the
+#' @param sep A character string to separate the coefficient and the
 #'   standard error (in parentheses). Default to " " (one space). Use
 #'   \code{"\n"} to enforce a line break.
 #'
-#'@param digits Integer indicating number of decimal places for the
+#' @param digits Integer indicating number of decimal places for the
 #'   appended standard errors. Default is 2L.
 #'
-#'@param ests A data.frame from the
+#' @param ests A data.frame from the
 #'   \code{\link[lavaan]{parameterEstimates}} function, or
-#'   from other function with these columns:? `lhs`, `op`,
-#'   `rhs`, and `se`. Only used when
-#'   \code{object} is not specified.
+#'   from other function with these columns: `lhs`, `op`,
+#'   `rhs`, `se` (for SE), and `ci.lower` and
+#'   `ci.upper` (for CI). Only used when \code{object} is 
+#'   not specified.
 #'
-#'@param std_type If standardized solution is used in the plot,
+#' @param std_type If standardized solution is used in the plot,
 #'   set this either to the type of standardization (e.g., `"std.all"`)
 #'   or to `TRUE`. It will be passed to [lavaan::standardizedSolution()]
 #'   to compute the standard errors for the standardized solution.
 #'   Used only if standard errors are not supplied directly
 #'   through `ests`.
 #'
-#'@examples
-#'mod_pa <-
-#'   'x1 ~~ x2
-#'    x3 ~  x1 + x2
-#'    x4 ~  x1 + x3
+#' @examples
+#' mod_pa <-
+#'    'x1 ~~ x2
+#'     x3 ~  x1 + x2
+#'     x4 ~  x1 + x3
+#'    '
+#' fit_pa <- lavaan::sem(mod_pa, pa_example)
+#' lavaan::parameterEstimates(fit_pa)[ , c("lhs", "op", "rhs",
+#'                                         "est", "pvalue", "se")]
+#' m <- matrix(c("x1",   NA,   NA,
+#'                 NA, "x3", "x4",
+#'               "x2",   NA,   NA), byrow = TRUE, 3, 3)
+#' p_pa <- semPlot::semPaths(fit_pa, whatLabels = "est",
+#'                           style = "ram",
+#'                           nCharNodes = 0, nCharEdges = 0,
+#'                           layout = m)
+#' p_pa2 <- mark_se(p_pa, fit_pa)
+#' plot(p_pa2)
+#' 
+#' mod_cfa <-
+#'   'f1 =~ x01 + x02 + x03
+#'    f2 =~ x04 + x05 + x06 + x07
+#'    f3 =~ x08 + x09 + x10
+#'    f4 =~ x11 + x12 + x13 + x14
 #'   '
-#'fit_pa <- lavaan::sem(mod_pa, pa_example)
-#'lavaan::parameterEstimates(fit_pa)[ , c("lhs", "op", "rhs",
-#'                                        "est", "pvalue", "se")]
-#'m <- matrix(c("x1",   NA,   NA,
-#'                NA, "x3", "x4",
-#'              "x2",   NA,   NA), byrow = TRUE, 3, 3)
-#'p_pa <- semPlot::semPaths(fit_pa, whatLabels = "est",
-#'                          style = "ram",
-#'                          nCharNodes = 0, nCharEdges = 0,
-#'                          layout = m)
-#'p_pa2 <- mark_se(p_pa, fit_pa)
-#'plot(p_pa2)
-#'
-#'mod_cfa <-
+#' fit_cfa <- lavaan::sem(mod_cfa, cfa_example)
+#' lavaan::parameterEstimates(fit_cfa)[ , c("lhs", "op", "rhs",
+#'                                          "est", "pvalue", "se")]
+#' p_cfa <- semPlot::semPaths(fit_cfa, whatLabels = "est",
+#'                            style = "ram",
+#'                            nCharNodes = 0, nCharEdges = 0)
+#' # Place standard errors on a new line
+#' p_cfa2 <- mark_se(p_cfa, fit_cfa, sep = "\n")
+#' plot(p_cfa2)
+#' 
+#' mod_sem <-
 #'  'f1 =~ x01 + x02 + x03
 #'   f2 =~ x04 + x05 + x06 + x07
 #'   f3 =~ x08 + x09 + x10
 #'   f4 =~ x11 + x12 + x13 + x14
+#'   f3 ~  f1 + f2
+#'   f4 ~  f1 + f3
 #'  '
-#'fit_cfa <- lavaan::sem(mod_cfa, cfa_example)
-#'lavaan::parameterEstimates(fit_cfa)[ , c("lhs", "op", "rhs",
-#'                                         "est", "pvalue", "se")]
-#'p_cfa <- semPlot::semPaths(fit_cfa, whatLabels = "est",
-#'                           style = "ram",
-#'                           nCharNodes = 0, nCharEdges = 0)
-#'# Place standard errors on a new line
-#'p_cfa2 <- mark_se(p_cfa, fit_cfa, sep = "\n")
-#'plot(p_cfa2)
-#'
-#'mod_sem <-
-#' 'f1 =~ x01 + x02 + x03
-#'  f2 =~ x04 + x05 + x06 + x07
-#'  f3 =~ x08 + x09 + x10
-#'  f4 =~ x11 + x12 + x13 + x14
-#'  f3 ~  f1 + f2
-#'  f4 ~  f1 + f3
-#' '
-#'fit_sem <- lavaan::sem(mod_sem, sem_example)
-#'lavaan::parameterEstimates(fit_sem)[ , c("lhs", "op", "rhs",
-#'                                         "est", "pvalue", "se")]
-#'p_sem <- semPlot::semPaths(fit_sem, whatLabels = "est",
-#'                           style = "ram",
-#'                           nCharNodes = 0, nCharEdges = 0)
-#'# Mark significance, and then add standard errors
-#'p_sem2 <- mark_sig(p_sem, fit_sem)
-#'p_sem3 <- mark_se(p_sem2, fit_sem, sep = "\n")
-#'plot(p_sem3)
-#'
-#'@importFrom rlang .data
-#'@export
+#' fit_sem <- lavaan::sem(mod_sem, sem_example)
+#' lavaan::parameterEstimates(fit_sem)[ , c("lhs", "op", "rhs",
+#'                                          "est", "pvalue", "se")]
+#' p_sem <- semPlot::semPaths(fit_sem, whatLabels = "est",
+#'                            style = "ram",
+#'                            nCharNodes = 0, nCharEdges = 0)
+#' # Mark significance, and then add standard errors
+#' p_sem2 <- mark_sig(p_sem, fit_sem)
+#' p_sem3 <- mark_se(p_sem2, fit_sem, sep = "\n")
+#' plot(p_sem3)
+#' 
+#' # Add confidence intervals
+#' p_sem4 <- mark_ci(p_sem, fit_sem, sep = "\n")
+#' plot(p_sem4)
+#' 
+#' @importFrom rlang .data
+#' @export
+
+mark_se <- function(semPaths_plot, object = NULL, sep = " ", digits = 2L,
+                    ests = NULL,
+                    std_type = FALSE) {
+  .mark_se_ci(
+    semPaths_plot = semPaths_plot,
+    object = object,
+    what = "se",
+    sep = sep,
+    digits = digits,
+    ests = ests,
+    std_type = std_type
+  )
+}
 
-mark_se <- function(semPaths_plot, object, sep = " ", digits = 2L,
+#' @rdname mark_se
+#' @export
+
+mark_ci <- function(semPaths_plot, object = NULL, sep = " ", digits = 2L,
                     ests = NULL,
                     std_type = FALSE) {
+  .mark_se_ci(
+    semPaths_plot = semPaths_plot,
+    object = object,
+    what = "ci",
+    sep = sep,
+    digits = digits,
+    ests = ests,
+    std_type = std_type
+  )
+}
+
+.mark_se_ci <- function(semPaths_plot, object = NULL,
+                       what = c("se", "ci"),
+                       sep = " ", digits = 2L,
+                       ests = NULL,
+                       std_type = FALSE) {
+  argg <- c(as.list(environment()))
+  what <- match.arg(what)
   if ("triangle" %in% semPaths_plot$graphAttributes$Nodes$shape) {
     rlang::inform(paste("The semPaths plot seems to have one or",
                         "more intercepts. Support for models with",
@@ -120,12 +161,12 @@ mark_se <- function(semPaths_plot, object, sep = " ", digits = 2L,
   }
   if (is.null(ests)) {
     if (isFALSE(std_type)) {
-      ests <- lavaan::parameterEstimates(object, se = TRUE, ci = FALSE,
+      ests <- lavaan::parameterEstimates(object, se = TRUE, ci = what == "ci",
                                          zstat = FALSE, pvalue = FALSE)
     } else {
       if (isTRUE(std_type)) std_type <- "std.all"
       ests <- lavaan::standardizedSolution(object, type = std_type,
-                                           se = TRUE, ci = FALSE,
+                                           se = TRUE, ci = what == "ci",
                                            zstat = FALSE, pvalue = FALSE)
     }
   }
@@ -134,10 +175,13 @@ mark_se <- function(semPaths_plot, object, sep = " ", digits = 2L,
       rlang::abort(paste("length of qgraph list does not match",
                          "number of groups in model fit object."))
     }
-    ests_list <- split(ests, ests$group)
-    mapply(mark_se, semPaths_plot, ests = ests_list, SIMPLIFY = FALSE)
+    argg$ests <- split(ests, ests$group)
+    .mapply(.mark_se_ci, dots = argg[c("semPaths_plot", "ests")],
+            MoreArgs = argg[
+              setdiff(names(argg), c("semPaths_plot", "object", "ests"))
+            ])
   } else {
-    if (!missing(object) && lavaan::lavInspect(object, "ngroups") > 1) {
+    if (!is.null(object) && lavaan::lavInspect(object, "ngroups") > 1) {
       rlang::abort(paste("length of qgraph list does not match",
                          "number of groups in model fit object."))
     }
@@ -167,11 +211,25 @@ mark_se <- function(semPaths_plot, object, sep = " ", digits = 2L,
     # Remove ~*~. Not used.
     to_keep <- to_keep & (ests$op != "~*~")
 
-    ests_ses <- ests[to_keep, c("lhs", "rhs", "se")]
+    if (what == "se") {
+      ests_cols <- c("lhs", "rhs", "se")
+      cols_rev <- c("se", "se_rev")
+    } else if (what == "ci") {
+      ests_cols <- c("lhs", "rhs", "ci.lower", "ci.upper")
+      cols_rev <- c("ci.lower", "ci.upper", "ci.lower_rev", "ci.upper_rev")
+    }
+    ests_ses <- ests[to_keep, ests_cols]
     ests_ses_rev <- ests_ses
     colnames(ests_ses_rev) <- gsub("\\<se\\>",
                                    "se_rev",
                                    colnames(ests_ses_rev))
+    colnames(ests_ses_rev) <- gsub("\\<ci\\.lower\\>",
+                                   "ci.lower_rev",
+                                   colnames(ests_ses_rev))
+
+    colnames(ests_ses_rev) <- gsub("\\<ci\\.upper\\>",
+                                   "ci.upper_rev",
+                                   colnames(ests_ses_rev))
     ests_ses_tmp <- ests_ses
     colnames(ests_ses_tmp) <- gsub("\\<rhs\\>",
                                    "from_names",
@@ -200,19 +258,40 @@ mark_se <- function(semPaths_plot, object, sep = " ", digits = 2L,
                       all.x = TRUE,
                       all.y = FALSE,
                       sort = FALSE)
-    all_na <- apply(edge_ses[, c("se", "se_rev")],
+    all_na <- apply(edge_ses[, cols_rev],
                     MARGIN = 1,
                     FUN = function(x) all(is.na(x)))
-    edge_ses$se <- suppressWarnings(
+    if (what == "se") {
+      edge_ses$se <- suppressWarnings(
                       apply(edge_ses[, c("se", "se_rev")],
                             MARGIN = 1,
                             FUN = max,
                             na.rm = TRUE))
-    edge_ses$se[all_na] <- NA
+      edge_ses$se[all_na] <- NA
+    } else if (what == "ci") {
+      edge_ses$ci.lower <- suppressWarnings(
+                      apply(edge_ses[, c("ci.lower", "ci.lower_rev")],
+                            MARGIN = 1,
+                            FUN = min,
+                            na.rm = TRUE))
+      edge_ses$ci.upper <- suppressWarnings(
+                      apply(edge_ses[, c("ci.upper", "ci.upper_rev")],
+                            MARGIN = 1,
+                            FUN = max,
+                            na.rm = TRUE))
+      edge_ses[all_na, c("ci.lower", "ci.upper")] <- NA
+    }
     edge_ses <- edge_ses[order(edge_ses$id), ]
     labels_old <- semPaths_plot$graphAttributes$Edges$labels
+    if (what == "se") {
+      to_add <- formatC(edge_ses$se, digits, format = "f")
+    } else if (what == "ci") {
+      to_add <- paste(formatC(edge_ses$ci.lower, digits, format = "f"),
+                      formatC(edge_ses$ci.upper, digits, format = "f"),
+                      sep = ", ")
+    }
     labels_new <- paste0(labels_old, sep,
-                         "(", formatC(edge_ses$se, digits, format = "f"), ")")
+                         "(", to_add, ")")
     semPaths_plot$graphAttributes$Edges$labels <- labels_new
     semPaths_plot
   }

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 [![R-CMD-check](https://github.com/sfcheung/semptools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sfcheung/semptools/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
-(Version 0.3.2.1, updated on 2025-07-20, [release history](https://sfcheung.github.io/semptools/news/index.html))
+(Version 0.3.2.2, updated on 2025-08-17, [release history](https://sfcheung.github.io/semptools/news/index.html))
 
 # semptools <img src="man/figures/logo.png" align="right" height="150" />