From a77d0bc2365cf25023fad33a968504cdf2baaa1c Mon Sep 17 00:00:00 2001
From: Pannier <spannier@fu-berlin.de>
Date: Wed, 10 Oct 2018 17:41:53 +0200
Subject: [PATCH] fixed bug due to changes in MuMIn package

---
 .Rprofile          |  3 ---
 DESCRIPTION        |  2 +-
 R/ebp.R            |  5 ++++-
 R/summary.emdi.R   | 12 ++++++------
 man/direct.Rd      |  4 ++--
 man/map_plot.Rd    |  5 +++--
 man/write.excel.Rd |  4 ++--
 7 files changed, 18 insertions(+), 17 deletions(-)
 delete mode 100644 .Rprofile

diff --git a/.Rprofile b/.Rprofile
deleted file mode 100644
index 916dba48..00000000
--- a/.Rprofile
+++ /dev/null
@@ -1,3 +0,0 @@
-#### -- Packrat Autoloader (version 0.4.9-1) -- ####
-source("packrat/init.R")
-#### -- End Packrat Autoloader -- ####
diff --git a/DESCRIPTION b/DESCRIPTION
index cba99834..c614dc7e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -22,7 +22,7 @@ License: GPL-2
 URL: https://github.com/SoerenPannier/emdi
 LazyData: true
 Copyright: inst/COPYRIGHTS
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
 Imports:
     nlme,
     moments,
diff --git a/R/ebp.R b/R/ebp.R
index 25bd1ed2..cbe8ee93 100644
--- a/R/ebp.R
+++ b/R/ebp.R
@@ -172,7 +172,10 @@ ebp <- function(fixed,
   # Save function call ---------------------------------------------------------
 
   call <- match.call()
-  
+  if(inherits(call$fixed, "name"))
+  {
+    call$fixed <- fixed
+  }
   # Data manipulation and notational framework ---------------------------------
   if(!is.null(seed)) {
     if (cpus > 1 && parallel_mode != "socket") {
diff --git a/R/summary.emdi.R b/R/summary.emdi.R
index 2529d19c..d179daf6 100644
--- a/R/summary.emdi.R
+++ b/R/summary.emdi.R
@@ -143,19 +143,19 @@ summary.emdi <- function(object, ...) {
                        Shapiro_p = c(shapiro_p_res, shapiro_p_ran),
                        row.names = c("Error", "Random_effect")
     )
-    
-    r_squared <- r.squaredGLMM(object$model)
+    tempMod <- object$model
+    tempMod$call$fixed <- object$fixed
+    r_squared <- r.squaredGLMM(tempMod)
     if (is.matrix(r_squared)) {
-      r_marginal <- r_squared["delta", 1]
-      r_conditional <- r_squared["delta", 2]
+      r_marginal <- r_squared[1, 1]
+      r_conditional <- r_squared[1, 2]
     } else {
       r_marginal <- r_squared[1]
       r_conditional <- r_squared[2]
     }
     icc_mixed <- icc(object$model)
     
-    coeff_det <- data.frame(#R2             = r_squared,
-      #ICC            = icc_mixed,
+    coeff_det <- data.frame(
       Marginal_R2    = r_marginal,
       Conditional_R2 = r_conditional,
       row.names      = ""
diff --git a/man/direct.Rd b/man/direct.Rd
index 3dec792d..a8b6f75f 100644
--- a/man/direct.Rd
+++ b/man/direct.Rd
@@ -6,8 +6,8 @@
 \usage{
 direct(y, smp_data, smp_domains, weights = NULL, design = NULL,
   threshold = NULL, var = FALSE, boot_type = "naive", B = 50,
-  seed = 123, X_calib = NULL, totals = NULL, custom_indicator = NULL,
-  na.rm = FALSE)
+  seed = 123, X_calib = NULL, totals = NULL,
+  custom_indicator = NULL, na.rm = FALSE)
 }
 \arguments{
 \item{y}{a character string indicating the variable that is used for 
diff --git a/man/map_plot.Rd b/man/map_plot.Rd
index a6a3115e..5fdd1e43 100644
--- a/man/map_plot.Rd
+++ b/man/map_plot.Rd
@@ -5,8 +5,9 @@
 \title{Visualizes regional disaggregrated estimates on a map}
 \usage{
 map_plot(object, indicator = "all", MSE = FALSE, CV = FALSE,
-  map_obj = NULL, map_dom_id = NULL, map_tab = NULL, color = c("white",
-  "red4"), scale_points = NULL, guide = "colourbar", return_data = FALSE)
+  map_obj = NULL, map_dom_id = NULL, map_tab = NULL,
+  color = c("white", "red4"), scale_points = NULL,
+  guide = "colourbar", return_data = FALSE)
 }
 \arguments{
 \item{object}{an object of type emdi, containing the estimates to be 
diff --git a/man/write.excel.Rd b/man/write.excel.Rd
index 4bf387f2..b0a5bc91 100644
--- a/man/write.excel.Rd
+++ b/man/write.excel.Rd
@@ -8,8 +8,8 @@
 write.excel(object, file = "excel_output.xlsx", indicator = "all",
   MSE = FALSE, CV = FALSE, split = FALSE)
 
-write.ods(object, file = "ods_output.ods", indicator = "all", MSE = FALSE,
-  CV = FALSE, split = FALSE)
+write.ods(object, file = "ods_output.ods", indicator = "all",
+  MSE = FALSE, CV = FALSE, split = FALSE)
 }
 \arguments{
 \item{object}{an object of type "emdi", representing point and