cover unit tests as.alienData() - issue #18

TheoreticalEcosystemEcology · Feb 17, 2017 · 0d46869 · 0d46869
1 parent a9f3ca5
commit 0d46869
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Showing 2 changed files with 44 additions and 23 deletions.
diff --git a/R/as.alienData.R b/R/as.alienData.R
@@ -67,8 +67,7 @@ as.alienData <- function(idObs = NULL, interactPair = NULL, coOcc = NULL, coAbun
 
     # Check for duplicates rows
     if (nrow(idObs[duplicated(idObs), ]) != 0) {
-        stop(cat("some idObs entries are duplicated: \n", idObs[duplicated(idObs), 
-            ]))
+        stop("some idObs entries are duplicated")
     }
 
     # Cast all columns has factors
@@ -117,6 +116,8 @@ as.alienData <- function(idObs = NULL, interactPair = NULL, coOcc = NULL, coAbun
         ## Check if idFrom and idTo are in levels(idSp) or levels(idInd) and not both
         ## interactPair are observations at species level OR at individual level but not
         ## both
+
+
         if (any(levels(interactPair$idFrom) %in% levels(idObs$idSp)) & any(levels(interactPair$idFrom) %in% 
             levels(idObs$idInd))) {
             stop("'idFrom' values belongs to 'idSp' and 'idInd' in 'idObs'. Interaction can't be at the species AND individual levels")
@@ -131,13 +132,11 @@ as.alienData <- function(idObs = NULL, interactPair = NULL, coOcc = NULL, coAbun
         if (any(c(levels(interactPair$idFrom), levels(interactPair$idTo)) %in% levels(idObs$idSp))) {
 
             if (!all(levels(interactPair$idFrom) %in% levels(idObs$idSp))) {
-                stop(cat("Some species ids in 'idFrom' are not in 'idObs': \n", levels(interactPair$idFrom)[which(!levels(interactPair$idFrom) %in% 
-                  levels(idObs$idSp))]))
+                stop("Some species ids in 'idFrom' are not in 'idObs'")
             }
 
             if (!all(levels(interactPair$idTo) %in% levels(idObs$idSp))) {
-                stop(cat("Some species ids in 'idTo' are not in 'idObs': \n", levels(interactPair$idFrom)[which(!levels(interactPair$idFrom) %in% 
-                  levels(idObs$idSp))]))
+                stop("Some species ids in 'idTo' are not in 'idObs'")
             }
 
         }
@@ -146,23 +145,19 @@ as.alienData <- function(idObs = NULL, interactPair = NULL, coOcc = NULL, coAbun
         if (any(c(levels(interactPair$idFrom), levels(interactPair$idTo)) %in% levels(idObs$idInd))) {
 
             if (!all(levels(interactPair$idFrom) %in% levels(idObs$idInd))) {
-                stop(cat("Some individus ids in 'idFrom' are not in 'idObs': \n", 
-                  levels(interactPair$idFrom)[which(!levels(interactPair$idFrom) %in% 
-                    levels(idObs$idInd))]))
+                stop("Some individus ids in 'idFrom' are not in 'idObs'")
             }
 
             if (!all(levels(interactPair$idTo) %in% levels(idObs$idInd))) {
-                stop(cat("Some individus ids in 'idTo' are not in 'idObs': \n", levels(interactPair$idFrom)[which(!levels(interactPair$idFrom) %in% 
-                  levels(idObs$idInd))]))
+                stop("Some individus ids in 'idTo' are not in 'idObs'")
             }
 
         }
 
         # Check if rows are not duplicated
         if (nrow(interactPair[duplicated(interactPair[, c("idFrom", "idTo")]), ]) != 
             0) {
-            stop(cat("Some 'idFrom' and 'idTo' are duplicated:\n", interactPair[duplicated(interactPair[, 
-                c("idFrom", "idTo")]), ]))
+            stop("Some 'idFrom' and 'idTo' are duplicated")
         }
 
     }

diff --git a/tests/testthat/test-alienData.R b/tests/testthat/test-alienData.R
@@ -1,16 +1,42 @@
 context("alienData function")
 
-load('./argsAlienData.RData')
-out <- as.alienData(idObs=idObs,interactPair=interactPair,traitSp=traitSp,traitInd=traitInd,verbose=FALSE)
-
-test_that("check data structure", {
-  expect_is(out, "alienData")
-  # Even if items from the list are NULL, all items have to be returned
-  expect_equal(names(out),c("idObs","interactSp","interactInd","coOcc","coAbund","siteEnv","traitSp","traitInd","phylo"))
-})
+# load('./argsAlienData.RData')
+# out <- as.alienData(idObs=idObs,interactPair=interactPair,traitSp=traitSp,traitInd=traitInd,verbose=FALSE)
+#
+# test_that("check data structure", {
+#   expect_is(out, "alienData")
+#   # Even if items from the list are NULL, all items have to be returned
+#   expect_equal(names(out),c("idObs","interactSp","interactInd","coOcc","coAbund","siteEnv","traitSp","traitInd","phylo"))
+# })
 
 test_that("check data integrity", {
-  # create fake data
-  idObs <- data.frame(idSite=rep(3,c("")), idTime=NULL)
+
+  # Generate fake data for idObs
+  len <- 3
+  sites <- sample(paste("site",letters[1:3],sep="_"),len,replace=TRUE) # 3 sites
+  sp <- paste0("sp",sample(1:len,len,replace=TRUE)) # 3 species
+  ind <- 1:len # 3 individus
+  idObs <- data.frame(idSite=sites,idTime=rep(NA,len),idSp=sp, idInd=ind,stringsAsFactors=FALSE)
+
+  interactPair <-  data.frame(idTo=c("1","sp1"),idFrom=c("1","2"),strength=c(NA,NA),verbose=FALSE,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"'idTo' values belongs to 'idSp' and 'idInd' in 'idObs'. Interaction can't be at the species AND individual levels")
+
+  interactPair <-  data.frame(idTo=c("1","2"),idFrom=c("sp1","2"),strength=c(NA,NA),verbose=FALSE,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"'idFrom' values belongs to 'idSp' and 'idInd' in 'idObs'. Interaction can't be at the species AND individual levels")
+
+  interactPair <- data.frame(idTo="sp4",idFrom="sp1",strength=NA,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"Some species ids in 'idTo' are not in 'idObs'")
+
+  interactPair <-  data.frame(idTo="4",idFrom="1",strength=NA,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"Some individus ids in 'idTo' are not in 'idObs'")
+
+  interactPair <- data.frame(idTo="sp1",idFrom="sp4",strength=NA,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"Some species ids in 'idFrom' are not in 'idObs'")
+
+  interactPair <-  data.frame(idTo="1",idFrom="4",strength=NA,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"Some individus ids in 'idFrom' are not in 'idObs'")
+
+  interactPair <-  data.frame(idTo=c("2","2","3"),idFrom=c("2","2","2"),strength=c(NA,NA,NA),verbose=FALSE,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"Some 'idFrom' and 'idTo' are duplicated")
 
 })