Unit Testing functions in meta-analysis sub-workflow

modules/meta.analysis/tests/testthat/test.jagify.R

@@ -0,0 +1,33 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+
+test_that("jagify correctly assigns treatment index of 1 to all control treatments, regardless of alphabetical order", {
+  ## generate test data; controls assigned to early alphabet and late alphabet trt names
+  testresult <- data.frame(citation_id = 1,
+                           site_id = rep(1:2, each = 5),
+                           name = rep(letters[1:5],2),
+                           trt_id = as.character(rep(letters[1:5],2)),
+                           control = c(1, rep(0,8), 1), 
+                           greenhouse = c(rep(0,5), rep(1,5)),
+                           date = 1,
+                           time = NA,
+                           cultivar_id = 1,
+                           specie_id = 1,
+                           n = 2,
+                           mean = sqrt(1:10),
+                           stat = 1,
+                           statname = "SE",
+                           treatment_id = 1:10
+  )
+  i <- sapply(testresult, is.factor)
+  testresult[i] <- lapply(testresult[i], as.character)
+
+  jagged.data <- jagify(testresult)
+  expect_equal(jagged.data$trt_num[jagged.data$trt == "control"], c(1, 1)) 
+})

modules/meta.analysis/tests/testthat/test.meta.analysis.R

@@ -0,0 +1,3 @@
+test_that("`pecan.ma`", {
+
+})

modules/meta.analysis/tests/testthat/test.run.meta.analysis.R

@@ -1,42 +1,11 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2012 University of Illinois, NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the 
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
+test_that("`runModule.run.meta.analysis`", {
 
-context("run.meta.analysis")
+})
 
+test_that("`run.meta.analysis`", {
 
-test_that("singleMA gives expected result for example inputs",{
-  ## need to calculate x
-  ## x <- singleMA(....)
-  #expect_equal(round(summary(x)$statistics["beta.o", "Mean"]), 5)
 })
 
-test_that("jagify correctly assigns treatment index of 1 to all control treatments, regardless of alphabetical order", {
-  ## generate test data; controls assigned to early alphabet and late alphabet trt names
-  testresult <- data.frame(citation_id = 1,
-                           site_id = rep(1:2, each = 5),
-                           name = rep(letters[1:5],2),
-                           trt_id = as.character(rep(letters[1:5],2)),
-                           control = c(1, rep(0,8), 1), 
-                           greenhouse = c(rep(0,5), rep(1,5)),
-                           date = 1,
-                           time = NA,
-                           cultivar_id = 1,
-                           specie_id = 1,
-                           n = 2,
-                           mean = sqrt(1:10),
-                           stat = 1,
-                           statname = "SE",
-                           treatment_id = 1:10
-  )
-  i <- sapply(testresult, is.factor)
-  testresult[i] <- lapply(testresult[i], as.character)
+test_that("`run.meta.analysis.pft`", {
 
-  jagged.data <- jagify(testresult)
-  expect_equal(jagged.data$trt_num[jagged.data$trt == "control"], c(1, 1)) 
-})
+})

modules/meta.analysis/tests/testthat/test.single.MA.R

@@ -0,0 +1,5 @@
+test_that("`single.MA` gives expected result for example inputs", {
+  ## need to calculate x
+  ## x <- singleMA(....)
+  #expect_equal(round(summary(x)$statistics["beta.o", "Mean"]), 5)
+})