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authorKen Kellner <ken.kellner@gmail.com>2016-05-16 18:57:12 (GMT)
committerKen Kellner <ken.kellner@gmail.com>2016-05-16 18:57:12 (GMT)
commita74437e4d16b25e9dbefa0b120d0b6903d019a06 (patch)
tree7fd94f68aea70c352433079d61ee3e55dd4b9ea1
parent6602aecfb008638fa72831b2986436e959018b0f (diff)
Updated figures and supplements for Plant Ecology.
-rw-r--r--figures/figure_height.R11
-rw-r--r--figures/figure_pellets.R6
-rw-r--r--figures/figure_transect.R6
-rw-r--r--supplements/supplement_s1.Rmd9
-rw-r--r--supplements/supplement_s2.Rmd10
5 files changed, 28 insertions, 14 deletions
diff --git a/figures/figure_height.R b/figures/figure_height.R
index 58c24b9..fafa51c 100644
--- a/figures/figure_height.R
+++ b/figures/figure_height.R
@@ -25,11 +25,14 @@ hts2.Z.rab <- as.numeric(scale(sample.hts2.rab))
#Separate figures
+tiff(filename="figures/Fig3.tiff",width=84,height=84,units="mm",res=1200, pointsize=8,
+ compression = "lzw",type='cairo')
+
require(extrafont)
#myfont <- "CM Roman"
myfont <- 'Times'
-pdf(file="paper/figure_height.pdf",width=3.9,height=3.9,family=myfont,pointsize=12)
+#pdf(file="paper/figure_height.pdf",width=3.9,height=3.9,family=myfont,pointsize=12)
par(mfrow=c(3,1),
oma = c(4,4,0,0) + 0.1,
@@ -109,13 +112,13 @@ embed_fonts("paper/figure_height.pdf")
######################################
#Combined figure
-#tiff(filename="Fig2_BrHt.tiff",width=3.9,height=3.9,units="in",res=400, pointsize=8,
-# compression = "lzw",type='cairo')
+tiff(filename="figures/Fig3.tiff",width=84,height=84,units="mm",res=1200, pointsize=8,
+ compression = "lzw",type='cairo')
require(extrafont)
#font_install('fontcm')
#loadfonts()
myfont <- "CM Roman"
-pdf(file="../dissertation/figures/fig3-2.pdf",width=3.9,height=3.9,family=myfont,pointsize=12)
+#pdf(file="../dissertation/figures/fig3-2.pdf",width=3.9,height=3.9,family=myfont,pointsize=12)
par(mgp=c(3,1,0),mar = c(5,4.5,2,2) + 0.1)
plot(sample.hts,pdeer/max(pdeer),type='l',lwd=2,xlab="Seedling Height (cm)"
diff --git a/figures/figure_pellets.R b/figures/figure_pellets.R
index 84d2eb3..486f6ae 100644
--- a/figures/figure_pellets.R
+++ b/figures/figure_pellets.R
@@ -59,15 +59,15 @@ rabbit.se <- c(sd(pellet$Rabbit[pellet$Treat=="Matrix"])/sqrt(length(pellet$Rabb
plot.data <- cbind(rabbit.means,deer.means)
-#tiff(filename="Fig3_Pellets.tiff",width=5,height=3.9,units="in",res=400, pointsize=8,
-# compression = "lzw",type='cairo')
+tiff(filename="figures/Fig2.tiff",width=84,height=84,units="mm",res=1200, pointsize=8,
+ compression = "lzw",type='cairo')
require(extrafont)
#font_install('fontcm')
#loadfonts()
#myfont <- 'CM Roman'
myfont <- 'Times'
-pdf(file="paper/figure_pellets.pdf",width=5,height=3.9,family=myfont,pointsize=12)
+#pdf(file="paper/figure_pellets.pdf",width=5,height=3.9,family=myfont,pointsize=12)
par(mgp=c(2.5,1,0),mar = c(2.5,3.7,1.3,0.5) + 0.1)
diff --git a/figures/figure_transect.R b/figures/figure_transect.R
index f300fcf..22459ac 100644
--- a/figures/figure_transect.R
+++ b/figures/figure_transect.R
@@ -96,15 +96,15 @@ for(i in 1:length(ever.browsed.deer)){
de = c(mean(ever.browsed.deer[deer.control==1]),mean(ever.browsed.deer[deer.edge==1]),
mean(ever.browsed.deer[deer.harvest==1]))
-#tiff(filename="Fig1_BrProb.tiff",width=3.9,height=3.9,units="in",res=400, pointsize=8,
-# compression = "lzw",type='cairo')
+tiff(filename="figures/Fig1.tiff",width=84,height=84,units="mm",res=1200, pointsize=8,
+ compression = "lzw",type='cairo')
require(extrafont)
#font_install('fontcm')
#loadfonts()
#myfont <- "CM Roman"
myfont <- "Times"
-pdf(file="paper/figure_transect.pdf",width=5,height=3.9,family=myfont,pointsize=12)
+#pdf(file="paper/figure_transect.pdf",width=5,height=3.9,family=myfont,pointsize=12)
par(mgp=c(2.5,1,0),mar = c(2.5,3.5,1.3,0.5) + 0.1)
diff --git a/supplements/supplement_s1.Rmd b/supplements/supplement_s1.Rmd
index dc3a302..adbe13b 100644
--- a/supplements/supplement_s1.Rmd
+++ b/supplements/supplement_s1.Rmd
@@ -1,10 +1,15 @@
---
title: "Supplement S1: Generation of Competition Index"
-author: "Kenneth F. Kellner"
-date: "April 20, 2016"
output: pdf_document
---
+Supplementary Information for:
+
+Oak seedling herbivory by mammals and insects across an edge created by timber harvest in the Central Hardwoods. Plant Ecology.
+Kenneth F. Kellner and Robert K. Swihart
+Department of Forestry and Natural Resources, Purdue University
+email: kkellner@purdue.edu
+
For each visit to each subplot during the study, we measured five interspecific competition-related variables:
1. Percent cover of herbaceous vegetation (ordinal scale 0-6)
diff --git a/supplements/supplement_s2.Rmd b/supplements/supplement_s2.Rmd
index 1e01381..d7acbb9 100644
--- a/supplements/supplement_s2.Rmd
+++ b/supplements/supplement_s2.Rmd
@@ -1,10 +1,16 @@
---
title: "Supplement S2: BUGS Model Code"
-author: "Kenneth F. Kellner"
-date: "April 20, 2016"
output: pdf_document
---
+Supplementary Information for:
+
+Oak seedling herbivory by mammals and insects across an edge created by timber harvest in the Central Hardwoods. Plant Ecology.
+Kenneth F. Kellner and Robert K. Swihart
+Department of Forestry and Natural Resources, Purdue University
+email: kkellner@purdue.edu
+
+
```{r, eval=FALSE}
model {
model {