Error trap lists provided without names to obsCovs and attempts to use variables in formulas that are not in covariates. Fixes #246

4 files changed, 60 insertions, 2 deletions

diff --git a/R/getDesign.R b/R/getDesign.R
index 79f20e6..8597b2d 100644
--- a/R/getDesign.R
+++ b/R/getDesign.R
@@ -23,6 +23,11 @@ setMethod("getDesign", "unmarkedFrame",
     } else {
         siteCovs <- siteCovs(umf)
     }
+    miss_vars <-all.vars(stateformula)[!all.vars(stateformula) %in% names(siteCovs)]
+    if(length(miss_vars) > 0){
+      stop(paste("Variable(s)", paste(miss_vars, collapse=", "), 
+                 "not found in siteCovs"), call.=FALSE)
+    }
     X.mf <- model.frame(stateformula, siteCovs, na.action = NULL)
     X <- model.matrix(stateformula, X.mf)
     X.offset <- as.vector(model.offset(X.mf))
@@ -49,6 +54,11 @@ setMethod("getDesign", "unmarkedFrame",
         obsCovs <- cbind(obsCovs, obsNum = as.factor(rep(1:R, M)))
     }
 
+    miss_vars <-all.vars(detformula)[!all.vars(detformula) %in% names(obsCovs)]
+    if(length(miss_vars) > 0){
+      stop(paste("Variable(s)", paste(miss_vars, collapse=", "), 
+                 "not found in obsCovs"), call.=FALSE)
+    }
     V.mf <- model.frame(detformula, obsCovs, na.action = NULL)
     V <- model.matrix(detformula, V.mf)
     V.offset <- as.vector(model.offset(V.mf))
diff --git a/R/unmarkedFrame.R b/R/unmarkedFrame.R
index b6a9273..3b8895f 100644
--- a/R/unmarkedFrame.R
+++ b/R/unmarkedFrame.R
@@ -161,7 +161,10 @@ setClass("unmarkedFrameDSO",
 #Convert covs provided as list of matrices/dfs to data frame
 covsToDF <- function(covs, name, obsNum, numSites){
   if(!inherits(covs, "list")) return(covs)
-
+  
+  if(is.null(names(covs)) | any(is.na(names(covs))) | any(names(covs)=="")){
+    stop("All elements of list provided to ", name, " argument must be named", call.=FALSE)
+  }
   lapply(covs, function(x){
     if(!inherits(x, c("matrix", "data.frame")))
       stop(paste("At least one element of", name, "is not a matrix or data frame."))
diff --git a/tests/testthat/test_occu.R b/tests/testthat/test_occu.R
index 7ea3afe..fdcede8 100644
--- a/tests/testthat/test_occu.R
+++ b/tests/testthat/test_occu.R
@@ -126,7 +126,11 @@ test_that("occu can fit models with covariates",{
   stMat <- fm@estimates@estimates$state@covMat
   expect_equivalent(detMat, matrix(rep(NA,9),nrow=3))
   expect_equivalent(stMat, matrix(rep(NA,4),nrow=2))
-
+  
+  # Trap attempts to use a variable in formula that isn't in covariates
+  fake <- rnorm(3)
+  expect_error(fm <- occu(~ o1 + o2 ~ fake, data = umf))
+  expect_error(fm <- occu(~ o1 + fake ~ o1, data = umf))
 })
 
 test_that("occu handles NAs",{
diff --git a/tests/testthat/test_unmarkedFrame.R b/tests/testthat/test_unmarkedFrame.R
index b5c6044..c3194fe 100644
--- a/tests/testthat/test_unmarkedFrame.R
+++ b/tests/testthat/test_unmarkedFrame.R
@@ -214,4 +214,45 @@ test_that("yearlySiteCovs processing works",{
   expect_equivalent(dim(as_df2),c(50,25))
 })
 
+test_that("lists provided to obsCovs or yearlySiteCovs must be named", {
+    y <- matrix(1:27, 3)
+    sc <- data.frame(x1 = 1:3)
+    ysc <- list(x2 = matrix(1:9, 3))
+    oc <- list(x3 = matrix(1:27, 3))
+
+    umf1 <- unmarkedMultFrame(
+        y = y,
+        siteCovs = sc,
+        yearlySiteCovs = ysc,
+        obsCovs = oc,
+        numPrimary = 3)
+    expect_is(umf1, "unmarkedMultFrame")
 
+
+    oc <- list(matrix(1:27, 3))
+    umf1 <- expect_error(unmarkedMultFrame(
+        y = y,
+        siteCovs = sc,
+        yearlySiteCovs = ysc,
+        obsCovs = oc,
+        numPrimary = 3))
+
+    oc <- list(x3 = matrix(1:27, 3))
+    ysc <- list(matrix(1:9, 3))
+    umf1 <- expect_error(unmarkedMultFrame(
+        y = y,
+        siteCovs = sc,
+        yearlySiteCovs = ysc,
+        obsCovs = oc,
+        numPrimary = 3))
+
+    ysc <- list(x2 = matrix(1:9, 3))
+    oc <- list(x3 = matrix(1:27, 3), matrix(1:27, 3))
+
+    umf1 <- expect_error(unmarkedMultFrame(
+        y = y,
+        siteCovs = sc,
+        yearlySiteCovs = ysc,
+        obsCovs = oc,
+        numPrimary = 3))
+})