Fix variable encoding for direct paths

R/classicProcess.R

@@ -319,7 +319,7 @@ procModelGraphSingleModel <- function(modelOptions, globalDependent, options) {
 .procEncodePath <- function(path) {
   # Encode all variables in a path
   return(lapply(path, function(v) {
-    if (v %in% c("mediators", "moderators", "confounders", "directs"))
+    if (v %in% c("mediators", "moderators", "confounders", "directs", ""))
       return(v)
     if (grepl("M", v))
       return(gsub("M", .procVarEncoding()[["M"]], v))

tests/testthat/test-classic-process-unit.R

@@ -0,0 +1,161 @@
+
+context('Unit tests for classic process analysis')
+
+test_that("Test that .procModelIsComplete works", {
+  mockModelComplete <- list(
+    inputType = "inputVariables",
+    processRelationships = list(list(processDependent = "contNormal",
+                                     processIndependent = "contGamma", processType = "mediators",
+                                     processVariable = "contcor1"))
+  )
+  mockModelNotComplete <- mockModelComplete
+  mockModelNotComplete[["processRelationships"]][[1]][["processVariable"]] <- ""
+
+  mockModelEmpty <- mockModelComplete
+  mockModelEmpty[["processRelationships"]] <- list()
+
+  mockModelCompleteDirect <- list(
+    inputType = "inputVariables",
+    processRelationships = list(list(processDependent = "contNormal",
+                                     processIndependent = "contGamma", processType = "directs",
+                                     processVariable = ""))
+  )
+
+  expect_true(jaspProcess:::.procModelIsComplete(mockModelComplete))
+  expect_true(jaspProcess:::.procModelIsComplete(mockModelCompleteDirect))
+  expect_false(jaspProcess:::.procModelIsComplete(mockModelNotComplete))
+  expect_false(jaspProcess:::.procModelIsComplete(mockModelEmpty))
+})
+
+test_that("Test that .procIsReady works", {
+  optsEmptyDependent <- list(
+    dependent = ""
+  )
+
+  optsEmptyCovariatesFactors <- list(
+    dependent = "contNormal",
+    covariates = list(),
+    factors = list()
+  )
+
+  optsEmptyModels <- list(
+    dependent = "contNormal",
+    covariates = list("contGamma"),
+    factors = list(),
+    processModels = list()
+  )
+
+  optsReady <- list(
+    dependent = "contNormal",
+    covariates = list("contGamma"),
+    factors = list(),
+    processModels = list(list(
+      inputType = "inputVariables",
+      processRelationships = list(list(processDependent = "contNormal",
+                                       processIndependent = "contGamma", processType = "mediators",
+                                       processVariable = "contcor1"))
+    ))
+  )
+
+  expect_false(jaspProcess:::.procIsReady(optsEmptyDependent))
+  expect_false(jaspProcess:::.procIsReady(optsEmptyCovariatesFactors))
+  expect_false(jaspProcess:::.procIsReady(optsEmptyModels))
+  expect_true(jaspProcess:::.procIsReady(optsReady))
+})
+
+test_that("Test that .procProcessRelationshipsToGraph works - mediation", {
+  processRelationships <- list(list(processDependent = "contNormal",
+                                    processIndependent = "contGamma", processType = "mediators",
+                                    processVariable = "contcor1"))
+
+  graph <- jaspProcess:::.procProcessRelationshipsToGraph(processRelationships)
+
+  expect_true(igraph::is_igraph(graph))
+  expect_true(igraph::is_dag(graph))
+  expect_equal(igraph::V(graph)$name, c("contGamma", "contNormal", "contcor1"))
+  expect_equal(igraph::E(graph)$source, c("contGamma", "contGamma", "contcor1"))
+  expect_equal(igraph::E(graph)$target, c("contNormal", "contcor1", "contNormal"))
+})
+
+test_that("Test that .procProcessRelationshipsToGraph works - moderation", {
+  processRelationships <- list(list(processDependent = "contNormal",
+                                    processIndependent = "contGamma", processType = "moderators",
+                                    processVariable = "contcor1"))
+
+  graph <- jaspProcess:::.procProcessRelationshipsToGraph(processRelationships)
+
+  expect_true(igraph::is_igraph(graph))
+  expect_true(igraph::is_dag(graph))
+  expect_equal(igraph::V(graph)$name, c("contGamma", "contNormal", "contcor1", "contGamma:contcor1"))
+  expect_equal(igraph::E(graph)$source, c("contGamma", "contcor1", "contGamma:contcor1"))
+  expect_equal(igraph::E(graph)$target, c("contNormal", "contNormal", "contNormal"))
+})
+
+test_that("Test that .procProcessRelationshipsToGraph works - moderated moderation", {
+  processRelationships <- list(list(processDependent = "contNormal",
+                                    processIndependent = "contGamma", processType = "moderators",
+                                    processVariable = "contcor1"),
+                               list(processDependent = "contNormal",
+                                    processIndependent = "contcor1", processType = "moderators",
+                                    processVariable = "contcor2"))
+
+  graph <- jaspProcess:::.procProcessRelationshipsToGraph(processRelationships)
+
+  expect_true(igraph::is_igraph(graph))
+  expect_true(igraph::is_dag(graph))
+  expect_equal(igraph::V(graph)$name, c("contGamma", "contNormal", "contcor1", "contGamma:contcor1", "contcor2", "contGamma:contcor2", "contGamma__contcor1__contcor2", "contcor1:contcor2"))
+  expect_equal(igraph::E(graph)$source, c("contGamma", "contcor1", "contGamma:contcor1", "contcor2", "contGamma:contcor2", "contGamma__contcor1__contcor2", "contcor1:contcor2"))
+  expect_equal(igraph::E(graph)$target, c("contNormal", "contNormal", "contNormal", "contNormal", "contNormal", "contNormal", "contNormal"))
+})
+
+test_that("Test that .procProcessRelationshipsToGraph works - direct", {
+  processRelationships <- list(list(processDependent = "contNormal",
+                                    processIndependent = "contGamma", processType = "directs",
+                                    processVariable = ""))
+
+  graph <- jaspProcess:::.procProcessRelationshipsToGraph(processRelationships)
+
+  expect_true(igraph::is_igraph(graph))
+  expect_true(igraph::is_dag(graph))
+  expect_equal(igraph::V(graph)$name, c("contGamma", "contNormal"))
+  expect_equal(igraph::E(graph)$source, c("contGamma"))
+  expect_equal(igraph::E(graph)$target, c("contNormal"))
+})
+
+test_that("Test that .procProcessRelationshipsToGraph works - confounder", {
+  processRelationships <- list(list(processDependent = "contNormal",
+                                    processIndependent = "contGamma", processType = "confounders",
+                                    processVariable = "contcor1"))
+
+  graph <- jaspProcess:::.procProcessRelationshipsToGraph(processRelationships)
+
+  expect_true(igraph::is_igraph(graph))
+  expect_true(igraph::is_dag(graph))
+  expect_equal(igraph::V(graph)$name, c("contGamma", "contNormal", "contcor1"))
+  expect_equal(igraph::E(graph)$source, c("contGamma", "contcor1", "contcor1"))
+  expect_equal(igraph::E(graph)$target, c("contNormal", "contGamma", "contNormal"))
+})
+
+test_that("Test that .procGraphAddAttributes works", {
+  edgeList <- matrix(c("contGamma", "contNormal",
+                       "contGamma", "contcor1",
+                       "contcor1", "contNormal",
+                       "contcor2", "contNormal",
+                       "contGamma:contcor2", "contNormal"
+                       ), ncol = 2, byrow = TRUE)
+  graph <- igraph::graph_from_edgelist(edgeList)
+  igraph::E(graph)$source <- edgeList[,1]
+  igraph::E(graph)$target <- edgeList[,2]
+  graph <- jaspProcess:::.procGraphAddAttributes(graph)
+
+  expect_equal(igraph::V(graph)$isInt, c(FALSE, FALSE, FALSE, FALSE, TRUE))
+  expect_equal(igraph::V(graph)$intVars, strsplit(unique(as.vector(t(edgeList))), ":|__"))
+  expect_equal(igraph::V(graph)$intLength, c(1, 1, 1, 1, 2))
+  expect_equal(igraph::V(graph)$isDep, c(FALSE, TRUE, FALSE, FALSE, FALSE))
+  expect_equal(igraph::V(graph)$isExo, c(TRUE, FALSE, FALSE, TRUE, TRUE))
+  expect_equal(igraph::V(graph)$isMed, c(FALSE, FALSE, TRUE, FALSE, FALSE))
+  expect_equal(igraph::V(graph)$isPartOfInt, c(FALSE, FALSE, FALSE, TRUE, FALSE))
+  expect_equal(igraph::V(graph)$isTreat, c(TRUE, FALSE, FALSE, FALSE, FALSE))
+  expect_equal(igraph::E(graph)$isMod, c(TRUE, FALSE, FALSE, TRUE, FALSE))
+  expect_equal(igraph::E(graph)$modVars, list("contcor2", NULL, NULL, "contGamma", NULL))
+})