From 41137cb2f556b8c645c338470f49c4e45dd404d3 Mon Sep 17 00:00:00 2001
From: emmaSkarstein <36135547+emmaSkarstein@users.noreply.github.com>
Date: Wed, 11 Mar 2020 11:58:57 +0100
Subject: [PATCH 1/2] Changed all cases of df[,column-name] to
 df[[column-name]] in order to avoid problems when subsetting tibbles (without
 changing behavior for regular data frames).

---
 R/MakeBinomStack.R | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/MakeBinomStack.R b/R/MakeBinomStack.R
index 6e56c51..b2f2336 100644
--- a/R/MakeBinomStack.R
+++ b/R/MakeBinomStack.R
@@ -26,7 +26,7 @@ MakeBinomStack=function(data, observs, tag="points", intercept=TRUE, mesh, presn
   if(length(presname)>1) stop("more than one name given for presences column")
   if(length(trialname)>1) stop("more than one name given for number of trials column")
   if(!presname%in%names(observs@data)) stop(paste(presname," not in names of presences data frame", sep=""))
-  if(!is.logical(observs@data[,presname]) & !trialname%in%names(observs@data))
+  if(!is.logical(observs@data[[presname]]) & !trialname%in%names(observs@data))
     stop(paste(trialname," not in names of presences data frame", sep=""))
 
   if(is.null(coordnames)) coordnames <- colnames(data@coords)
@@ -36,21 +36,21 @@ MakeBinomStack=function(data, observs, tag="points", intercept=TRUE, mesh, presn
   }
 
   NearestCovs <- GetNearestCovariate(points=observs, covs=data)
-  if(InclCoords) {    data@data[,coordnames] <- data@coords  }
-  if(intercept) NearestCovs@data[,paste("int",tag,sep=".")] <- 1 # add intercept
+  if(InclCoords) {    data@data[[coordnames]] <- data@coords  }
+  if(intercept) NearestCovs@data[[paste("int",tag,sep=".")]] <- 1 # add intercept
   if(!is.null(polynoms)) {
     NearestCovs <- AddDistToRangeToSpatialPoints(data = NearestCovs, polynoms = polynoms, scale=scale)
   }
 
 # If presences are Boolean, reformat
-  if(is.logical(observs@data[,presname])) {
-    observs@data[,presname] <- as.integer(observs@data[,presname])
-    observs@data[,trialname] <- rep(1, nrow(observs@data))
+  if(is.logical(observs@data[[presname]])) {
+    observs@data[[presname]] <- as.integer(observs@data[[presname]])
+    observs@data[[trialname]] <- rep(1, nrow(observs@data))
   }
   # Projector matrix from mesh to data.
   projmat <- inla.spde.make.A(mesh, as.matrix(NearestCovs@coords)) # from mesh to point observations
 
-  stk.binom <- inla.stack(data=list(resp=cbind(NA,observs@data[,presname] ), Ntrials=observs@data[,trialname]), A=list(1,projmat), tag=tag,
+  stk.binom <- inla.stack(data=list(resp=cbind(NA,observs@data[[presname]] ), Ntrials=observs@data[[trialname]]), A=list(1,projmat), tag=tag,
                           effects=list(NearestCovs@data, list(i=1:mesh$n)))
 
   stk.binom

From 4f4f8f0e62d5040a6ca2f90d9c462624bc92a749 Mon Sep 17 00:00:00 2001
From: emmaSkarstein <36135547+emmaSkarstein@users.noreply.github.com>
Date: Wed, 18 Mar 2020 18:41:26 +0100
Subject: [PATCH 2/2] Changed back to original subsetting some places.

Changed back subsetting all places except where we check class of observs@data[[presname]], as previous changes seemed to cause one error when running the tests. Now I think we will avoid the problems with tibbles, but this also means that the dataframe subsetting is inconsistent throughout the code.
---
 R/MakeBinomStack.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/MakeBinomStack.R b/R/MakeBinomStack.R
index b2f2336..a8b336e 100644
--- a/R/MakeBinomStack.R
+++ b/R/MakeBinomStack.R
@@ -36,21 +36,21 @@ MakeBinomStack=function(data, observs, tag="points", intercept=TRUE, mesh, presn
   }
 
   NearestCovs <- GetNearestCovariate(points=observs, covs=data)
-  if(InclCoords) {    data@data[[coordnames]] <- data@coords  }
-  if(intercept) NearestCovs@data[[paste("int",tag,sep=".")]] <- 1 # add intercept
+  if(InclCoords) {    data@data[,coordnames] <- data@coords  }
+  if(intercept) NearestCovs@data[,paste("int",tag,sep=".")] <- 1 # add intercept
   if(!is.null(polynoms)) {
     NearestCovs <- AddDistToRangeToSpatialPoints(data = NearestCovs, polynoms = polynoms, scale=scale)
   }
 
 # If presences are Boolean, reformat
   if(is.logical(observs@data[[presname]])) {
-    observs@data[[presname]] <- as.integer(observs@data[[presname]])
-    observs@data[[trialname]] <- rep(1, nrow(observs@data))
+    observs@data[,presname] <- as.integer(observs@data[,presname])
+    observs@data[,trialname] <- rep(1, nrow(observs@data))
   }
   # Projector matrix from mesh to data.
   projmat <- inla.spde.make.A(mesh, as.matrix(NearestCovs@coords)) # from mesh to point observations
 
-  stk.binom <- inla.stack(data=list(resp=cbind(NA,observs@data[[presname]] ), Ntrials=observs@data[[trialname]]), A=list(1,projmat), tag=tag,
+  stk.binom <- inla.stack(data=list(resp=cbind(NA,observs@data[,presname] ), Ntrials=observs@data[,trialname]), A=list(1,projmat), tag=tag,
                           effects=list(NearestCovs@data, list(i=1:mesh$n)))
 
   stk.binom