From 5f77530f8fd2f3f9db2215c61baab65c479bce5b Mon Sep 17 00:00:00 2001
From: "Jason K. Moore" <moorepants@gmail.com>
Date: Mon, 10 Aug 2015 14:34:02 -0700
Subject: [PATCH 1/2] Started a mixed effects example for one variable RCBD.

---
 examples/rcbd_one_var_year.R            | 41 +++++++++++++++++++++++++
 examples/wheat_yield_data_with_year.csv | 33 ++++++++++++++++++++
 2 files changed, 74 insertions(+)
 create mode 100644 examples/rcbd_one_var_year.R
 create mode 100644 examples/wheat_yield_data_with_year.csv

diff --git a/examples/rcbd_one_var_year.R b/examples/rcbd_one_var_year.R
new file mode 100644
index 0000000..8f6da6a
--- /dev/null
+++ b/examples/rcbd_one_var_year.R
@@ -0,0 +1,41 @@
+# This is an example of a single variate RCBD that has an addition random
+# effect.
+#
+# To run the script type:
+# source('rcbd_one_var_year.R', print.eval = TRUE)
+#
+# The code that will be displayed to the user is bounded by this separator:
+#-----------------------------------------------------------------------------#
+
+# Load the necessary libraries.
+#-----------------------------------------------------------------------------#
+library('nlme')  # for lme()
+#-----------------------------------------------------------------------------#
+
+sep <- function(n){
+  # This function simply prints a line of "=" to the screen as a separator and
+  # will not show up in the app. It is only here for nice printing.
+  line <- paste0(paste(replicate(n, "="), collapse = ""), '\n')
+  cat(line)
+}
+
+# Load the data.
+#-----------------------------------------------------------------------------#
+my.data <- read.csv("wheat_yield_data_with_year.csv")
+#-----------------------------------------------------------------------------#
+
+# Set Block, Treatment, and Year as factors.
+#-----------------------------------------------------------------------------#
+my.data$Block <- as.factor(my.data$Block)
+my.data$Treatment <- as.factor(my.data$Treatment)
+my.data$Year <- as.factor(my.data$Year)
+#-----------------------------------------------------------------------------#
+
+# Construct a mized effects model and print the summary results.
+cat('Linear mixed effect model results\n')
+sep(79)
+#-----------------------------------------------------------------------------#
+model <- lme(fixed = Yield ~ Treatment, random = ~1|Block/Year, data = my.data)
+summary(model)
+#-----------------------------------------------------------------------------#
+sep(79)
diff --git a/examples/wheat_yield_data_with_year.csv b/examples/wheat_yield_data_with_year.csv
new file mode 100644
index 0000000..cc23036
--- /dev/null
+++ b/examples/wheat_yield_data_with_year.csv
@@ -0,0 +1,33 @@
+Year,Block,Treatment,Yield
+1999,1,Variety A,4.776113643
+1999,2,Variety A,4.167309262
+1999,3,Variety A,7.449164952
+1999,4,Variety A,7.757967337
+1999,1,Variety B,8.6989031
+1999,2,Variety B,6.332884039
+1999,3,Variety B,9.673666482
+1999,4,Variety B,10.81933243
+1999,1,Variety C,9.663780964
+1999,2,Variety C,7.861877074
+1999,3,Variety C,12.72423637
+1999,4,Variety C,8.837111214
+1999,1,Variety D,5.968923961
+1999,2,Variety D,7.078335949
+1999,3,Variety D,9.021241207
+1999,4,Variety D,8.428939255
+2000,1,Variety A,3.91823493
+2000,2,Variety A,4.58761123
+2000,3,Variety A,7.64636576
+2000,4,Variety A,7.91800989
+2000,1,Variety B,9.06640113
+2000,2,Variety B,6.31342374
+2000,3,Variety B,7.57774909
+2000,4,Variety B,10.95260769
+2000,1,Variety C,9.41454649
+2000,2,Variety C,8.40584383
+2000,3,Variety C,13.03441029
+2000,4,Variety C,7.72061644
+2000,1,Variety D,6.65400835
+2000,2,Variety D,6.56413817
+2000,3,Variety D,8.33194168
+2000,4,Variety D,8.85568545

From d895b82dcda11b658d8d682aad2df50468bbf7ef Mon Sep 17 00:00:00 2001
From: msimmond <mbsimmonds@ucdavis.edu>
Date: Tue, 11 Aug 2015 10:51:58 -0700
Subject: [PATCH 2/2] block is nested within year (Year/Block)

---
 examples/rcbd_one_var_year.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/rcbd_one_var_year.R b/examples/rcbd_one_var_year.R
index 8f6da6a..3f2dfa0 100644
--- a/examples/rcbd_one_var_year.R
+++ b/examples/rcbd_one_var_year.R
@@ -35,7 +35,7 @@ my.data$Year <- as.factor(my.data$Year)
 cat('Linear mixed effect model results\n')
 sep(79)
 #-----------------------------------------------------------------------------#
-model <- lme(fixed = Yield ~ Treatment, random = ~1|Block/Year, data = my.data)
+model <- lme(fixed = Yield ~ Treatment, random = ~1|Year/Block, data = my.data)
 summary(model)
 #-----------------------------------------------------------------------------#
 sep(79)