Merge pull request #88 from sfcheung/devel

Update to 0.1.9.6

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: manymome
 Title: Mediation, Moderation and Moderated-Mediation After Model Fitting
-Version: 0.1.9.5
+Version: 0.1.9.6
 Authors@R:
     c(person(given = "Shu Fai",
            family = "Cheung",

NEWS.md

@@ -1,9 +1,12 @@
-# manymome 0.1.9.5
+# manymome 0.1.9.6
 
 - Updated badges in README.md. (0.1.9.1)
 - Updated pkgdown site. (0.1.9.2)
 - Added support for Monte Carlo confidence intervals. (0.1.9.3 to 0.1.9.4)
 - Updated some vignettes for Monte Carlo confidence intervals. (0.1.9.5)
+- Used a more reliable test for Monte Carlo CIs. (0.1.9.6)
+- Fixed an error in pkgdown site. (0.1.9.6)
+- Updated the logo for readability. (0.1.9.6)
 
 # manymome 0.1.9
 

README.md

@@ -9,7 +9,7 @@
 [![R-CMD-check](https://github.com/sfcheung/manymome/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sfcheung/manymome/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
-(Version 0.1.9.5, updated on 2023-04-12, [release history](https://sfcheung.github.io/manymome/news/index.html))
+(Version 0.1.9.6, updated on 2023-04-12, [release history](https://sfcheung.github.io/manymome/news/index.html))
 
 # manymome  <img src="man/figures/logo.png" align="right" height="150" />
 

_pkgdown.yml

@@ -64,6 +64,8 @@ reference:
   - lm2boot_out
   - fit2boot_out
   - fit2boot_out_do_boot
+  - do_mc
+  - fit2mc_out
 - title: For 'lavaan'
 - contents:
   - factor2var

inst/CITATION

@@ -10,6 +10,6 @@ bibentry(
   textVersion =
   paste("Cheung, S. F., & Cheung, S.-H. (2023).",
         "manymome: An R package for computing the indirect effects, conditional effects, and conditional indirect effects.",
-        "R package version 0.1.9.5",
+        "R package version 0.1.9.6",
         "https://github.com/sfcheung/manymome/")
 )

tests/testthat/test_index_mome.R

@@ -84,6 +84,16 @@ ind_momome_mc <- index_of_momome(x = "x", y = "y", m = "m1", w = "w1", z = "w4",
 # confint(ind_momome)
 # print(parameterEstimates(fitmomo_boot)[32, c("est", "ci.lower", "ci.upper")], nd = 8)
 
+user_perc <- function(x, level = .95) {
+    boot_out <- list(t0 = mean(x, na.rm = TRUE),
+                     t = matrix(x, ncol = 1),
+                     R = length(x))
+    out0 <- boot::boot.ci(boot_out,
+                          type = "perc",
+                          conf = level)$percent[4:5]
+    out0
+  }
+
 test_that("index_of_mome and index_of_momome", {
     expect_equal(
         coef(ind_mome1),
@@ -138,20 +148,20 @@ test_that("index_of_mome and index_of_momome, Monte Carlo", {
       )
     expect_equal(
         unlist(confint(ind_mome1_mc)),
-        quantile(ind_mome1_mc$mc_diff, probs = c(.025, .975)),
-        tolerance = 1e-2,
+        user_perc(ind_mome1_mc$mc_diff),
+        tolerance = 1e-4,
         ignore_attr = TRUE
       )
     expect_equal(
         unlist(confint(ind_mome2_mc)),
-        quantile(ind_mome2_mc$mc_diff, probs = c(.025, .975)),
-        tolerance = 1e-1,
+        user_perc(ind_mome2_mc$mc_diff),
+        tolerance = 1e-4,
         ignore_attr = TRUE
       )
     expect_equal(
         unlist(confint(ind_momome_mc)),
-        quantile(ind_momome_mc$mc_diff, probs = c(.025, .975)),
-        tolerance = 1e-1,
+        user_perc(ind_momome_mc$mc_diff),
+        tolerance = 1e-4,
         ignore_attr = TRUE
       )
   })