Merge pull request #17 from sfcheung/devel

0.3.2: Update for SE-based CI and p-value

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: manymome.table
 Title: Publication-Ready Tables for 'manymome' Results
-Version: 0.3.0
+Version: 0.3.2
 Authors@R:
     c(person(given = "Shu Fai",
            family = "Cheung",
@@ -20,7 +20,7 @@ BugReports: https://github.com/sfcheung/manymome.table/issues
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests:
     knitr,
     rmarkdown,

NEWS.md

@@ -1,3 +1,17 @@
+# manymome.table 0.3.2
+
+- The optional arguments (`...`) of
+  `as_flextable.cond_indirect_effects()`
+  and `as_flextable.indirect_list()`
+  are now passed to `flextable::autofit()`
+  when preparing the final output.
+  (0.3.1)
+
+- Updated to print SE-based confidence
+  intervals and *p*-values when a path
+  has no mediator and effect not
+  standardized. (0.3.2)
+
 # manymome.table 0.3.0
 
 - Minor changes to the `README.md`

R/as_flextable.cond_indirect_effects.R

@@ -103,9 +103,20 @@
 #' `<[pcut]`, `"[pcut]"` replaced by
 #' the value of `pcut`. Default is .001.
 #'
+#' @param level The level of confidence
+#' for the confidence intervals computed
+#' from the original standard errors
+#' (e.g., the standard errors in
+#' [stats::lm()] or `lavaan`).
+#' Used only for paths without mediators
+#' and both x- and y-variables are not
+#' standardized. Default is .95.
 #'
 #' @param ... Additional arguments.
-#' Ignored.
+#' To be passed to [flextable::autofit()]
+#' in preparing the final table. For
+#' example, if some lines are too lone
+#' and wrapped, try adding `add_w = .2`.
 #'
 #' @examples
 #'
@@ -172,6 +183,7 @@ as_flextable.cond_indirect_effects <- function(x,
                                        show_indicators = FALSE,
                                        show_path = TRUE,
                                        pcut = .001,
+                                       level = .95,
                                        ...) {
     # TODO: Remove after an update to manymome
     indirect_raw_ci <- FALSE
@@ -182,15 +194,44 @@ as_flextable.cond_indirect_effects <- function(x,
     x_i <- full_output[[1]]
     std_x <- isTRUE(x_i$standardized_x)
     std_y <- isTRUE(x_i$standardized_y)
-
-    x_list <- list2indirect_list(full_output)
-    coef0 <- manymome::indirect_effects_from_list(x_list,
-                                                  add_sig = FALSE,
-                                                  pvalue = pvalue,
-                                                  se = se)
+    # x_list <- list2indirect_list(full_output)
+    # coef0 <- manymome::indirect_effects_from_list(x_list,
+    #                                               add_sig = FALSE,
+    #                                               pvalue = pvalue,
+    #                                               se = se)
+    coef0 <- as.data.frame(x,
+                           digits = TRUE,
+                           add_sig = FALSE,
+                           pvalue = pvalue,
+                           pvalue_digits = pval_digits,
+                           se = se,
+                           level = level,
+                           to_string = FALSE)
     # Fix the column names
     if (std_x || std_y) {
-        colnames(coef0)[colnames(coef0) %in% "ind"] <- "std"
+        coef0 <- coef0[, -which(colnames(coef0) == "ind")]
+        colnames(coef0)[colnames(coef0) %in% "std"] <- "std"
+      }
+    # Remove component path estimates
+    j <- max(match(c("ind", "std", "CI.lo", "CI.hi", "SE", "pvalue"),
+                   colnames(coef0)), na.rm = TRUE)
+    if (j < ncol(coef0)) {
+        coef0 <- coef0[, seq_len(j), drop = FALSE]
+      }
+
+    # Remove the `Stat` column, for consistency.
+    # TODO:
+    # - May keep this column in the future.
+    j <- match("Stat", colnames(coef0))
+    if (!is.na(j)) {
+        coef0 <- coef0[, -j, drop = FALSE]
+      }
+
+    # Remove the columns with moderator values.
+    # Add them using this function, for compatibility.
+    j <- min(match(c("ind", "std"), colnames(coef0)), na.rm = TRUE)
+    if (j > 1) {
+        coef0 <- coef0[, -seq_len(j - 1), drop = FALSE]
       }
 
     x0 <- x_i$x
@@ -215,9 +256,10 @@ as_flextable.cond_indirect_effects <- function(x,
     has_pvalue <- "pvalue" %in% colnames(coef0)
     has_ci <- "CI.lo" %in% colnames(coef0)
     has_se <- "SE" %in% colnames(coef0)
-
     if (has_ci) {
-        level <- x_i$level
+        if (!is.null(x_i$level)) {
+            level <- x_i$level
+          }
         level_str <- paste0(format(level * 100),
                             "% CI")
       } else {
@@ -289,7 +331,6 @@ as_flextable.cond_indirect_effects <- function(x,
         w_df <- w_df[, !tmp, drop = FALSE]
       }
     coef0 <- cbind(w_df, coef0)
-
     ft <- flextable::flextable(coef0)
 
     # Format Cells
@@ -500,6 +541,6 @@ as_flextable.cond_indirect_effects <- function(x,
                                         colwidths = flextable::ncol_keys(ft))
       }
 
-    ft <- flextable::autofit(ft)
+    ft <- flextable::autofit(ft, ...)
     ft
   }

R/as_flextable.indirect_list.R

@@ -110,7 +110,10 @@
 #' the value of `pcut`. Default is .001.
 #'
 #' @param ... Additional arguments.
-#' Ignored.
+#' To be passed to [flextable::autofit()]
+#' in preparing the final table. For
+#' example, if some lines are too lone
+#' and wrapped, try adding `add_w = .2`.
 #'
 #' @examples
 #'
@@ -452,6 +455,6 @@ as_flextable.indirect_list <- function(x,
                 part = "footer")
       }
 
-    ft <- flextable::autofit(ft)
+    ft <- flextable::autofit(ft, ...)
     ft
   }

README.md

@@ -8,7 +8,7 @@
 [![R-CMD-check](https://github.com/sfcheung/manymome.table/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sfcheung/manymome.table/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
-(Version 0.3.0, updated on 2024-03-04, [release history](https://sfcheung.github.io/manymome.table/news/index.html))
+(Version 0.3.2, updated on 2024-12-09, [release history](https://sfcheung.github.io/manymome.table/news/index.html))
 
 # manymome.table
 

inst/tinytest/test_cond_effect.R

@@ -0,0 +1,55 @@
+if (requireNamespace("officer", quietly = TRUE) &&
+    length(unclass(packageVersion("manymome.table"))[[1]]) == 4) {
+
+library(tinytest)
+library(manymome)
+library(officer)
+library(flextable)
+
+dat <- data_med_mod_a
+lm_m <- lm(m ~ x*w + c1 + c2, dat)
+lm_y <- lm(y ~ m + x + c1 + c2, dat)
+fit_lm <- lm2list(lm_m, lm_y)
+
+out_xm_on_w <- cond_effects(wlevels = "w",
+                            x = "x",
+                            y = "m",
+                            fit = fit_lm)
+
+std_xm_on_w <- cond_effects(wlevels = "w",
+                            x = "x",
+                            y = "m",
+                            standardized_x = TRUE,
+                            fit = fit_lm)
+
+tmp1 <- as_flextable(out_xm_on_w,
+                     var_labels = c(w = "Moderator"),
+                     se = TRUE,
+                     pvalue = TRUE,
+                     digits = 3,
+                     level = .90)
+
+smp1 <- as_flextable(std_xm_on_w,
+                     var_labels = c(w = "Moderator"),
+                     se = TRUE,
+                     pvalue = TRUE,
+                     digits = 4)
+
+tmp <- to_html(tmp1)
+expect_equal(ncol_keys(tmp1), 7)
+expect_match(tmp, "[Moderator]")
+expect_match(tmp, "(Moderator)")
+expect_match(tmp, "90% CI")
+expect_match(tmp, "SE")
+expect_match(tmp, formatC(coef(out_xm_on_w)[1], digits = 3, format = "f"))
+expect_match(tmp, formatC(confint(out_xm_on_w, level = .90)[2, 2], digits = 3, format = "f"))
+
+smp <- to_html(smp1)
+expect_equal(ncol_keys(smp1), 4)
+expect_match(smp, "[Moderator]")
+expect_match(smp, "(Moderator)")
+expect_false(grepl("90% CI", smp, fixed = TRUE))
+expect_false(grepl("SE", smp, fixed = TRUE))
+expect_match(smp, formatC(coef(std_xm_on_w)[1], digits = 3, format = "f"))
+
+}

inst/tinytest/test_cond_ind.R

@@ -188,10 +188,11 @@ tmp4 <- formatC(tmp3$pvalue[3], digits = 5, format = "f")
 tmp4 <- gsub("^0.", ".", tmp4)
 expect_match(tmp, tmp4)
 
-
+# In the latest version of manymome,
+# SE-based CI will be included for moderation-only unstandardized paths.
 tmp1 <- as_flextable(outmo_1, digits = 4)
 tmp <- to_html(tmp1)
-expect_equal(ncol_keys(tmp1), 2)
+expect_equal(ncol_keys(tmp1), 5)
 expect_match(tmp, "[gp]")
 expect_false(grepl("gpgp2", tmp, fixed = TRUE))
 expect_match(tmp, formatC(coef(outmo_1)[1], digits = 4, format = "f"))