Merge pull request #127 from goldingn/master

fixing what the last PR broke

R/zoonHelpers.R

@@ -160,7 +160,7 @@ RunModels <- function(df, modelFunction, paras, workEnv){
                                             paras),
                            envir = workEnv)
 
-      pred <- ZoonPredict(.model$model,
+      pred <- ZoonPredict(modelFold,
                           newdata = df[df$fold == i, 6:NCOL(df), drop = FALSE])
 
       dfOut$predictions[df$fold == i] <- pred 
@@ -175,7 +175,7 @@ RunModels <- function(df, modelFunction, paras, workEnv){
   # If external validation dataset exists, predict that;.
   if(0 %in% df$fold){
 
-    pred <- ZoonPredict(.model$model,
+    pred <- ZoonPredict(modelFold,
                         newdata = df[df$fold == 0, 6:NCOL(df), drop = FALSE])
 
     dfOut$predictions[df$fold == 0] <- pred 
@@ -353,7 +353,7 @@ ExtractAndCombData <- function(occurrence, ras){
 
 Chain <- function(...){
   ans <- list(...)
-  attr(ans, 'isChain') <- TRUE
+  attr(ans, 'chain') <- TRUE
   return (ans)
 }
 

tests/testthat/test-ChangeWorkflow.R

@@ -91,6 +91,6 @@ test_that('RerunWorkflow works', {
 
   expect_true(all.equal(w1, w2))
 
-
 })
 
+

tests/testthat/test-wholeWorkflows.R

@@ -21,7 +21,8 @@ test_that('simple, package data workflow works.', {
   expect_equal(names(work1$process.output[[1]]$df), 
     c('value', 'type', 'fold', 'longitude',   'latitude',   'layer'))
   expect_equal(dim(work1$process.output[[1]][[1]]),  c(269, 6))
-  expect_is((work1$model.output[[1]])$model, c('glm', 'lm'))
+  expect_is((work1$model.output[[1]])$model, c('zoonModel'))
+  expect_is((work1$model.output[[1]])$model$model, c('glm', 'lm'))
   expect_is((work1$model.output[[1]])$data, c('data.frame'))
   expect_is(work1$report[[1]], 'RasterLayer')
 
@@ -44,7 +45,8 @@ test_that('Check basic quoted workflow.', {
   expect_equal(names(work1$process.output[[1]]$df), 
     c('value', 'type', 'fold', 'longitude',   'latitude',   'layer'))
   expect_equal(dim(work1$process.output[[1]][[1]]),  c(269, 6))
-  expect_is((work1$model.output[[1]])$model, c('glm', 'lm'))
+  expect_is((work1$model.output[[1]])$model, c('zoonModel'))
+  expect_is((work1$model.output[[1]])$model$model, c('glm', 'lm'))
   expect_is((work1$model.output[[1]])$data, c('data.frame'))
   expect_is(work1$report[[1]], 'RasterLayer')
 
@@ -72,7 +74,8 @@ test_that('modules downloading data work', {
   expect_true(all(work2$occurrence.output[[1]][,'latitude'] > 45))
   expect_true(all(work2$occurrence.output[[1]][,'type']=='presence'))
   expect_is(work2$covariate.output[[1]], 'RasterLayer')
-  expect_is((work2$model.output[[1]])$model, 'randomForest')
+  expect_is((work2$model.output[[1]])$model, 'zoonModel')
+  expect_is((work2$model.output[[1]])$model$model, 'randomForest')
   expect_is(work2$report[[1]], 'RasterLayer')
 })
 
@@ -195,7 +198,8 @@ test_that('simple, crossvalidation workflow works.', {
   expect_equal(names(workCross$process.output[[1]]$df), 
     c('value', 'type', 'fold', 'longitude', 'latitude', 'layer'))
   expect_equal(dim(workCross$process.output[[1]]$df),  c(269, 6))
-  expect_is((workCross$model.output[[1]])$model, c('glm', 'lm'))
+  expect_is((workCross$model.output[[1]])$model, c('zoonModel'))
+  expect_is((workCross$model.output[[1]])$model$model, c('glm', 'lm'))
   expect_is(workCross$report[[1]], 'RasterLayer')  
 
 })
@@ -230,7 +234,8 @@ test_that('chains work.', {
   expect_equal(names(chain1$process.output[[1]]$df), 
     c('value', 'type', 'fold', 'longitude', 'latitude', 'layer'))
   expect_equal(dim(chain1$process.output[[1]]$df),  c(457, 6))
-  expect_is((chain1$model.output[[1]])$model, c('glm', 'lm'))
+  expect_is((chain1$model.output[[1]])$model, c('zoonModel'))
+  expect_is((chain1$model.output[[1]])$model$model, c('glm', 'lm'))
   expect_is(chain1$report[[1]], 'RasterLayer')  
 
   expect_true(exists('chain2'))
@@ -240,7 +245,8 @@ test_that('chains work.', {
   expect_equal(names(chain2$process.output[[1]]$df), 
     c('value', 'type', 'fold', 'longitude', 'latitude', 'layer.1', 'layer.2'))
   expect_equal(dim(chain2$process.output[[1]]$df),  c(269, 7))
-  expect_is((chain2$model.output[[1]])$model, c('glm', 'lm'))
+  expect_is((chain2$model.output[[1]])$model, c('zoonModel'))
+  expect_is((chain2$model.output[[1]])$model$model, c('glm', 'lm'))
   expect_is(chain2$report[[1]], 'RasterLayer')  
 
   expect_true(exists('chain4'))
@@ -250,7 +256,8 @@ test_that('chains work.', {
   expect_equal(names(chain4$process.output[[1]]$df), 
     c('value', 'type', 'fold', 'longitude', 'latitude', 'layer'))
   expect_equal(dim(chain4$process.output[[1]]$df),  c(269, 6))
-  expect_is((chain4$model.output[[1]])$model, c('glm', 'lm'))
+  expect_is((chain4$model.output[[1]])$model, c('zoonModel'))
+  expect_is((chain4$model.output[[1]])$model$model, c('glm', 'lm'))
   expect_is(chain4$report[[1]], 'list')  
 
 
@@ -273,10 +280,9 @@ test_that('workflow with mix of syntax works.', {
   expect_equal(names(workSyn$process.output[[1]]$df), 
     c('value', 'type', 'fold', 'longitude',   'latitude',   'layer'))
   expect_equal(dim(workSyn$process.output[[1]][[1]]),  c(269, 6))
-  expect_is((workSyn$model.output[[1]])$model, c('glm', 'lm'))
+  expect_is((workSyn$model.output[[1]])$model, c('zoonModel'))
+  expect_is((workSyn$model.output[[1]])$model$model, c('glm', 'lm'))
   expect_is((workSyn$model.output[[1]])$data, c('data.frame'))
   expect_is(workSyn$report[[1]], 'list')
 
 })
-
-