Add tidySEM to lesson 1

01 path analysis/Appendix - advanced plotting.R

@@ -0,0 +1,129 @@
+library(lavaan)
+library(tidySEM)
+library(dplyr)
+
+income_psych <- read.csv("income_psych.csv")
+
+mediation_model <- '
+  mood_neg ~ anxiety
+    income ~ anxiety + mood_neg
+'
+fit <- sem(mediation_model, data = income_psych)
+
+## See below for how "plot1.png" and "plot2.png" were made.
+
+
+
+# Changing Nodes (Vars) ---------------------------------------------------
+
+(nods <- get_nodes(fit))
+
+nods <- nods %>% 
+  mutate(label = c("Negative\nMood", "Income", "Anxiety")) # \n is a break line
+
+graph_sem(fit,
+          nodes = nods)
+
+
+# Changing Layout ---------------------------------------------------------
+
+lay <- get_layout(
+  NA,        "mood_neg", NA,
+  "anxiety", NA,         "income",
+  rows = 2
+)
+
+graph_sem(fit,
+          nodes = nods, 
+          layout = lay, angle = 90)
+
+
+
+# Changing Edges (Paths) --------------------------------------------------
+
+
+(edgs <- get_edges(fit,
+                   columns = c("est_std", "confint_std", "pval_std"),
+                   digits = 3))
+
+edgs <- edgs %>% 
+  mutate(
+    label = paste0(est_std, "\n", confint_std),
+    color = "black",
+    color = replace(color, as.numeric(est_std) > 0 & to!=from, "green"),
+    color = replace(color, as.numeric(est_std) < 0, "red"),
+    linetype = "solid",
+    linetype = replace(linetype, as.numeric(pval_std) > 0.05, "dashed")
+  )
+
+graph_sem(fit,
+          nodes = nods, 
+          layout = lay, angle = 90,
+          edges = edgs)
+
+
+# Making "plot1" ----------------------------------------------------------
+
+mediation_model <- '
+  mood_neg ~ anxiety
+    income ~ anxiety + mood_neg
+'
+
+fit <- sem(mediation_model, data = income_psych)
+
+
+
+
+nods <- get_nodes(fit) %>% 
+  mutate(label = c("Negative\nMood", "Income", "Anxiety")) # \n is a break line
+
+lay <- get_layout(
+  NA,         "mood_neg", NA,
+  "anxiety", NA,        "income",
+  rows = 2
+)
+
+edgs <- get_edges(fit) %>% 
+  filter(to != from) %>% 
+  mutate(label = "")
+
+graph_sem(fit,
+          nodes = nods, edges = edgs,
+          layout = lay, angle = 90)
+
+ggplot2::ggsave("plot1.png", height = 3, width = 6)
+
+
+
+
+
+# Making "plot2" ----------------------------------------------------------
+
+
+mediation_model <- '
+  mood_neg ~ a * anxiety
+   anxiety ~ b * shyness
+    income ~ c * anxiety + d * mood_neg + e * shyness
+'
+
+fit <- sem(mediation_model, data = income_psych)
+
+nods <- get_nodes(fit) %>% 
+  mutate(label = c("Negative\nMood", "Anxiety", "Income", "Shyness")) # \n is a break line
+
+lay <- get_layout(
+  NA,        NA,         "mood_neg", NA,
+  NA,        "anxiety", NA,          "income",
+  "shyness", NA,        NA,          NA,
+  rows = 3
+)
+
+edgs <- get_edges(fit) %>% 
+  filter(to != from) %>% 
+  mutate(label = "")
+
+graph_sem(fit,
+          nodes = nods, edges = edgs,
+          layout = lay, angle = 90)
+
+ggplot2::ggsave("plot2.png", height = 3, width = 6)