Merge pull request #103 from sfcheung/devel

Update to 0.1.5.6

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: semfindr
 Title: Influential Cases in Structural Equation Modeling
-Version: 0.1.5.5
+Version: 0.1.5.6
 Authors@R: c(
     person(given = "Shu Fai",
            family = "Cheung",

NEWS.md

@@ -1,4 +1,4 @@
-# semfindr 0.1.5.5
+# semfindr 0.1.5.6
 
 - Fixed typos in the article on
   multiple-group models. (0.1.5.1)
@@ -19,6 +19,8 @@
 - Add `index_plot()` for generating
   an index plot for an arbitrary
   statistic. (0.1.5.5)
+- Make plot functions to work with NAs.
+  (0.1.5.6)
 
 
 # semfindr 0.1.5

R/est_change_plot.R

@@ -256,6 +256,10 @@ est_change_plot <- function(change,
       }
     x0$gcd <- NULL
     x0$row_id <- as.integer(seq_len(nrow(change)))
+    x0 <- stats::na.omit(x0)
+    if (nrow(x0) == 0) {
+        stop("No cases have valid values.")
+      }
     p <- ggplot2::ggplot(data = x0, ggplot2::aes(x = .data[["row_id"]],
                                                  y = .data[["change"]]))
     p <- p + do.call(ggplot2::geom_point, point_aes)
@@ -379,6 +383,10 @@ est_change_gcd_plot <- function(change,
     if (!missing(parameters)) {
         x0 <- x0[x0$param %in% parameters, ]
       }
+    x0 <- stats::na.omit(x0)
+    if (nrow(x0) == 0) {
+        stop("No cases have valid values.")
+      }
     p <- ggplot2::ggplot(data = x0,
                 ggplot2::aes(x = .data[[gcd_name]],
                              y = .data[["change"]]))

R/generic_index_plot.R

@@ -188,6 +188,11 @@ index_plot <- function(object,
       object <- object[, column, drop = TRUE]
     }
 
+  object <- object[!is.na(object)]
+  if (length(object) == 0) {
+      stop("No cases have valid values.")
+    }
+
   if (absolute) {
       object <- abs(object)
     }

R/influence_plot.R

@@ -261,6 +261,10 @@ gcd_plot <- function(influence_out,
     } else {
       gcd_label <- "Generalized Cook's Distance"
     }
+  dat <- dat[!is.na(dat$gcd), ]
+  if (nrow(dat) == 0) {
+      stop("All cases have gCD missing.")
+    }
   p <- ggplot2::ggplot(dat, ggplot2::aes(.data$row_id, .data$gcd))
   p <- p + do.call(ggplot2::geom_point, point_aes)
   p <- p + ggplot2::labs(title = gcd_label)
@@ -432,6 +436,11 @@ gcd_gof_plot <- function(influence_out,
       gcd_label <- "Generalized Cook's Distance"
       change_label <- "Change in Fit Measure"
     }
+  dat <- dat[!is.na(dat$gcd) &
+             !is.na(dat$fm), ]
+  if (nrow(dat) == 0) {
+      stop("No cases have non-missing values.")
+    }
 
   point_aes <- utils::modifyList(list(),
                                  point_aes)
@@ -564,6 +573,12 @@ gcd_gof_md_plot <- function(influence_out,
       gcd_label_short <- "gCD"
       change_label <- "Change in Fit Measure"
     }
+  dat <- dat[!is.na(dat$gcd) &
+             !is.na(dat$fm) &
+             !is.na(dat$md), ]
+  if (nrow(dat) == 0) {
+      stop("No cases have valid values.")
+    }
 
   point_aes <- utils::modifyList(list(shape = 21,
                                       alpha = .50,

README.md

@@ -9,7 +9,7 @@
 [![R-CMD-check](https://github.com/sfcheung/semfindr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sfcheung/semfindr/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
-(Version 0.1.5.5, updated on 2023-10-05, [release history](https://sfcheung.github.io/semfindr/news/index.html))
+(Version 0.1.5.6, updated on 2023-10-05, [release history](https://sfcheung.github.io/semfindr/news/index.html))
 
 # semfindr: Finding influential cases in SEM <img src="man/figures/logo.png" align="right" height="150" />
 

tests/testthat/test-nonconvergence_plot.R

@@ -0,0 +1,64 @@
+skip_on_cran()
+# Slow tests
+
+library(testthat)
+library(lavaan)
+
+mod <-
+'
+f1 =~ x1 + x2 + x3
+f2 =~ x4 + x5 + x6
+'
+set.seed(154151)
+dat <- HolzingerSwineford1939[sample.int(301, 60), ]
+
+fit <- suppressWarnings(lavaan::cfa(mod, dat))
+
+fit_rerun <- lavaan_rerun(fit, to_rerun = 1:20, allow_inadmissible = TRUE, parallel = FALSE)
+
+fit_rerun
+out <- influence_stat(fit_rerun)
+
+p <- gcd_plot(out)
+test_that("NA in rerun", {
+    expect_equal(nrow(p$data), 19)
+    # expect_no_warning(print(p))
+  })
+
+p <- md_plot(out)
+test_that("NA in rerun", {
+    expect_equal(nrow(p$data), 20)
+    # expect_no_warning(print(p))
+  })
+
+p <- gcd_gof_plot(out, "chisq")
+test_that("NA in rerun", {
+    expect_equal(nrow(p$data), 19)
+    # expect_no_warning(print(p))
+  })
+
+p <- gcd_gof_md_plot(out, "chisq", circle_size = 35)
+test_that("NA in rerun", {
+    expect_equal(nrow(p$data), 19)
+    # expect_no_warning(print(p))
+  })
+
+out <- est_change(fit_rerun)
+
+p <- est_change_plot(out)
+test_that("NA in rerun", {
+    expect_equal(nrow(p$data), 247)
+    # expect_no_warning(print(p))
+  })
+
+p <- est_change_gcd_plot(out)
+test_that("NA in rerun", {
+    expect_equal(nrow(p$data), 247)
+    # expect_no_warning(print(p))
+  })
+
+p <- index_plot(out, "f1=~x3")
+test_that("NA in rerun", {
+    expect_equal(nrow(p$data), 19)
+    # expect_no_warning(print(p))
+  })