transfer from old repo

courses/covariates.Rmd

@@ -0,0 +1,135 @@
+---
+title: "Which covariates to adjust for? (DAGs)"
+author: "AGDamsbo"
+date: "`r Sys.Date()`"
+output:
+  pdf_document: default
+  html_document: default
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+# Labels
+
+```{r}
+
+```
+
+```{r}
+library(ggdag)
+library(ggplot2)
+theme_set(theme_dag())
+```
+
+
+```{r}
+ex_ca_dag <- dagify(ever_smoker ~ ami + socio_eco,
+  pad ~ ever_smoker,
+  edu ~ socio_eco,
+  ever_smoker ~ socio_eco,
+  pase_0 ~ ever_smoker + edu + pad,
+  labels = c(
+    "pase_0" = "Physical\n activity",
+    "ami" = "AMI",
+    "ever_smoker" = "Smoking",
+    "pad" = "PAD",
+    "socio_eco" = "Socio\n status",
+    "edu" = "Education"
+  ),
+  # latent = "unhealthy",
+  exposure = "edu",
+  outcome = "pase_0"
+)
+
+ggdag(ex_ca_dag, text = FALSE, use_labels = "label")
+```
+
+```{r}
+ggdag_paths(ex_ca_dag, text = FALSE, use_labels = "label", shadow = TRUE)
+```
+
+```{r}
+ggdag_adjustment_set(ex_ca_dag, text = FALSE, use_labels = "label", shadow = TRUE)
+```
+
+# Excercise
+
+```{r}
+dag <- dagify(death ~ chd + HF + age + sex + wght,
+                    HF~chd,
+                    age~chd,
+                    chd~sex,
+                    HF~sex,
+                    wght~sex,
+                    
+  # latent = "unhealthy",
+  exposure = "chd",
+  outcome = "death"
+)
+
+dag |> ggdag(text = TRUE)
+
+dag |> ggdag_adjustment_set(text = TRUE, shadow = TRUE)
+```
+
+
+```{r}
+dag <- dagify(ami~fat+age+sex+obm1+obp1+SESm1,
+              fat~sCm1+sex+sCp1+obm1+SESm1,
+              sCp1~sCm1+obm1,
+              sCm1~age,
+              obp1~obm1+SESm1,
+              obm1~SESm1,
+              SESm1~age,
+  # latent = "unhealthy",
+  exposure = "fat",
+  outcome = "ami"
+)
+
+dag |> ggdag(text = TRUE)
+
+dag |> ggdag_adjustment_set(text = TRUE, shadow = TRUE)
+```
+
+
+```{r}
+dag <- dagify(wgt~DM1+GA+smoke+par+BS,
+              GA~DM1+smoke+par+BS+SES,
+              smoke~DM1+par+SES,
+              par~DM1+SES,
+              BS~DM1+SES,
+              DM1~SES,
+  # latent = "unhealthy",
+  exposure = "DM1",
+  outcome = "wgt"
+)
+
+dag |> ggdag(text = TRUE,stylized = TRUE)
+
+dag |> ggdag_adjustment_set(text = TRUE, shadow = TRUE,stylized = TRUE)
+```
+
+```{r}
+testImplications <- function( covariance.matrix, sample.size ){
+	library(ggm)
+	tst <- function(i){ pcor.test( pcor(i,covariance.matrix), length(i)-2, sample.size )$pvalue }
+tos <- function(i){ paste(i,collapse=" ") }
+implications <- list(c("A","B"),
+		c("A","D","E"),
+		c("B","E"),
+		c("D","Z","A","B"),
+		c("D","Z","B","E"),
+		c("E","Z","A"))
+	data.frame( implication=unlist(lapply(implications,tos)),
+		pvalue=unlist( lapply( implications, tst ) ) )
+
+}
+
+library(dagitty)
+
+testImplications()
+```
+
+