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authorKen Kellner <ken@kenkellner.com>2016-10-21 17:20:49 (GMT)
committerKen Kellner <ken@kenkellner.com>2016-10-21 17:20:49 (GMT)
commit5bdbacd78ac498850d425310b9313157f3956b72 (patch)
tree1d0f89174112410a23323c39bc6c5a1bb5d9f1f2
parentd726353e207e31b6bf5e630e5d1e44ed010d399b (diff)
Finalize TWS 2016 talk.
-rw-r--r--figures/figure_resp_summary.R21
-rw-r--r--figures/figure_richness.R2
-rw-r--r--presentations/compress_pdf.bat2
-rw-r--r--presentations/figures_tws2016.R38
-rw-r--r--presentations/talk_tws2016.tex240
5 files changed, 173 insertions, 130 deletions
diff --git a/figures/figure_resp_summary.R b/figures/figure_resp_summary.R
index 0f747e8..1719d1b 100644
--- a/figures/figure_resp_summary.R
+++ b/figures/figure_resp_summary.R
@@ -6,7 +6,13 @@
# scale: 'mu' for management-unit level, 'hl' for harvest level
# figmin & figmax: y-limits for figure
-resp.summary.figure <- function(scale,ylims,cols,text.cex=1){
+resp.summary.figure <- function(scale,ylims,cols,text.cex=1,highlight.shrubland=FALSE){
+
+ #Define shrubland species
+ shrubland <- c('INBU','EATO','CARW','HOWA','BAWW','WEVI',
+ 'NOBO','GRCA','BRTH','PRAW','YBCH',
+ 'BHCO','MODO','KEWA','COYE','BWWA')
+ threat <- c('WEWA','HOWA','CERW','BAWW')
#Set up scale-dependent figure variables
if(scale=='mu'){
@@ -67,9 +73,18 @@ resp.summary.figure <- function(scale,ylims,cols,text.cex=1){
upplim <- val-(sign(val)*0.5)
lowlim <- sign(val)-(sign(val)*0.5)
+ sel.lab <- namerank[1:abs(val),index]
+
+ bolded <- rep(1,abs(val))
+ if(highlight.shrubland){
+ bolded[which(sel.lab%in%shrubland)] <- 4
+ sel.lab[which(sel.lab%in%threat)] <-
+ paste(sel.lab[which(sel.lab%in%threat)],'*',sep="")
+ }
+
text(x[j,i],seq(upplim,lowlim,length.out=abs(val)),
- labels=namerank[1:abs(val),index],cex=text.cex)
+ labels=sel.lab,cex=text.cex,font=bolded)
index <- index+1
if(val==0){
@@ -83,7 +98,7 @@ resp.summary.figure <- function(scale,ylims,cols,text.cex=1){
arrows(mean(x),0,mean(x),ylims[2]-2)
arrows(mean(x),0,mean(x),ylims[1]+2)
- text(mean(x),ylims[2]-1,labels='Positive Response')
+ text(mean(x),ylims[2]-1,labels='Positive Response (relative to Control)')
text(mean(x),ylims[1]+1,labels='Negative Response')
} \ No newline at end of file
diff --git a/figures/figure_richness.R b/figures/figure_richness.R
index a025b20..15ffb65 100644
--- a/figures/figure_richness.R
+++ b/figures/figure_richness.R
@@ -37,7 +37,7 @@ richness.figure <- function(scale,figmin,figmax,cols,pchs,ltys,xlab="Year"){
plot(1:10,rich.means[1,],ylim=c(figmin,figmax),
main="",type='o',cex=2,lty=ltys[1],col=cols[1],
- lwd=2,pch=pchs[1],xaxt='n',xlab=xlab,ylab='Richness',
+ lwd=2,pch=pchs[1],xaxt='n',xlab=xlab,ylab='Richness Index',
xlim=c(0.5,10.5))
axis(side=1,at=c(1,3,5,7,9), labels=c('2006', '2008', '2010','2012','2014'),tck=0)
diff --git a/presentations/compress_pdf.bat b/presentations/compress_pdf.bat
index f380dc1..7007132 100644
--- a/presentations/compress_pdf.bat
+++ b/presentations/compress_pdf.bat
@@ -1 +1 @@
-"C:\Program Files\gs\gs9.19\bin\gswin64c.exe" -sDEVICE=pdfwrite -dMaxSubsetPct=100 -dPDFSETTINGS=/prepress -dAutoFilterColorImages=false -dColorImageFilter=/FlateEncode -sOutputFile="talk_tws2016_small.pdf" -dNOPAUSE -dBATCH "talk_tws2016.pdf" \ No newline at end of file
+"C:\Program Files\gs\gs9.19\bin\gswin64c.exe" -sDEVICE=pdfwrite -dMaxSubsetPct=100 -dPDFSETTINGS=/prepress -dEmbedAllFonts=true -dAutoFilterColorImages=false -dColorImageFilter=/FlateEncode -sOutputFile="../../../documents/research/hee_bird_abundance/presentations/talk_tws2016.pdf" -dNOPAUSE -dBATCH "talk_tws2016.pdf" \ No newline at end of file
diff --git a/presentations/figures_tws2016.R b/presentations/figures_tws2016.R
index 222e091..2b461f3 100644
--- a/presentations/figures_tws2016.R
+++ b/presentations/figures_tws2016.R
@@ -53,7 +53,7 @@ dev.off()
png(filename="presentations/images/mu_resp.png",width=6,height=3.8,units="in",res=400, pointsize=10,
type='cairo')
-resp.summary.figure('mu',c(-5,11),cols.mu[2:3])
+resp.summary.figure('mu',c(-5,11),cols.mu[2:3],highlight.shrubland=TRUE)
dev.off()
@@ -78,7 +78,7 @@ bird.figure('CERW','mu',color=cols.mu,title=
par(fig=c(0.46,1,0,0.55),new=TRUE)
bird.figure('WEWA','mu',color=cols.mu,title=
'Worm-eating Warbler',legendpos='none',legcex=1,
- extralabels=F,xlab="",ylab="")
+ extralabels=F,xlab="",ylab="",cred=T)
dev.off()
####################################################
@@ -98,7 +98,8 @@ dev.off()
png(filename="presentations/images/hl_resp.png",width=6,height=3.8,units="in",res=400, pointsize=10,
type='cairo')
-resp.summary.figure('hl',c(-8.5,20.5),cols.hl[c(2,2,3,3)],text.cex=0.65)
+resp.summary.figure('hl',c(-8.5,20.5),cols.hl[c(2,2,3,3)],text.cex=0.65,
+ highlight.shrubland=TRUE)
dev.off()
@@ -122,17 +123,40 @@ png(filename="presentations/images/focal_hl.png",width=6,height=3.8,units="in",r
par(fig=c(0,0.54,0.45,1),new=FALSE)
bird.figure('BAWW','hl',color=cols.hl,title=
'Black-and-white Warbler',legendpos='none',legcex=1,
- extralabels=F,xlab=NULL)
+ extralabels=F,xlab=NULL,se=T)
par(fig=c(0.46,1,0.45,1),new=TRUE)
bird.figure('HOWA','hl',color=cols.hl,title=
'Hooded Warbler',legendpos='none',legcex=1,
- extralabels=F,xlab=NULL,ylab="")
+ extralabels=F,xlab=NULL,ylab="",se=T)
par(fig=c(0,0.54,0,0.55),new=TRUE)
bird.figure('CERW','hl',color=cols.hl,title=
'Cerulean Warbler',legendpos='topright',legcex=0.8,
- legend.lwd=1, extralabels=F,xlab="")
+ legend.lwd=1, extralabels=F,xlab="",se=T)
par(fig=c(0.46,1,0,0.55),new=TRUE)
bird.figure('WEWA','hl',color=cols.hl,title=
'Worm-eating Warbler',legendpos='none',legcex=1,
- extralabels=F,xlab="",ylab="")
+ extralabels=F,xlab="",ylab="",se=T)
+dev.off()
+
+#####################################################
+#Ruhl Bird Mist Net Captures in Clearcuts Figure
+
+#Read in data
+mist <- read.csv('data/hee_mistnets_2015.csv',header=T)
+counts <- sort(summary(mist$Species),decreasing=T)
+
+codes <- c('WEWA','REVI','HOWA','WEVI','YBCH','GRCA','SCTA','KEWA','OVEN')
+
+colors.sub <- c(rep(cols.mu[1],2),rep(cols.mu[2],4),cols.mu[1])
+
+png(filename="presentations/images/mistnet_counts.png",width=6,height=3.8,units="in",res=400, pointsize=10,
+ type='cairo')
+
+#Set up plot
+par(mgp=c(3,1,0),mar = c(4.5,4.5,1,1) + 0.1,oma=c(0,0,0,0))
+x <- barplot(counts[1:7],ylim=c(0,300),ylab='Number of Captures (2015)',col=colors.sub,
+ names=codes[1:7],xlab='Species')
+legend('topright',legend=c('Mature Forest','Early Successional'),
+ fill=cols.mu[1:2])
+
dev.off()
diff --git a/presentations/talk_tws2016.tex b/presentations/talk_tws2016.tex
index 1aceaa1..6b7f17a 100644
--- a/presentations/talk_tws2016.tex
+++ b/presentations/talk_tws2016.tex
@@ -15,22 +15,19 @@
%\section{Introduction}
- \begin{frame}{Conservation of Migratory Birds}
+ \begin{frame}{Bird Conservation in Midwestern U.S.}
- \textbf{Population Declines}\textsuperscript{1}
-
- \bigskip
-
- \textbf{Habitat Loss}
+ \textbf{Habitat Loss} $\rightarrow$ \textbf{Population Declines}%\textsuperscript{1}
+
\begin{itemize}
- \item Conversion of forest to agriculture/development\textsuperscript{1}
+ \item Development%\textsuperscript{1}
\item Fragmentation
- \item Maturation of existing forest\textsuperscript{2}
+ \item \textbf{Maturation of existing forest}%\textsuperscript{2}
\end{itemize}
- \bigskip
- \textsuperscript{1}\scriptsize{Robbins et al. 1989};
- \textsuperscript{2}\scriptsize{Trani et al. 2001}
+ %\bigskip
+ %\textsuperscript{1}\scriptsize{Robbins et al. 1989};
+ %\textsuperscript{2}\scriptsize{Trani et al. 2001}
\end{frame}
@@ -40,74 +37,105 @@
\end{center}
\begin{itemize}
- \item \textbf{74\%} of shrubland species are declining\textsuperscript{1}
- \item \textbf{51\%} of species use young forest habitat\textsuperscript{2}
+ \item \textbf{75\%} of shrubland species declining%\textsuperscript{1}
+ \item \textbf{50\%} of species use young forest habitat%\textsuperscript{2}
\end{itemize}
- \textsuperscript{1}\scriptsize{Sauer et al. 2013};
- \textsuperscript{2}\scriptsize{Probst \& Thompson 1996}
+ %\textsuperscript{1}\scriptsize{Sauer et al. 2013};
+ %\textsuperscript{2}\scriptsize{Probst \& Thompson 1996}
\end{frame}
- \begin{frame}{Forest Management}
- %\begin{columns}
- %\begin{column}{0.48\textwidth}
+ \begin{frame}{Forest Management}
\begin{center}
\includegraphics[width=0.8\paperwidth]{images/clearcut_long.png}
- \textbf{Even-aged:} Clearcuts, Shelterwoods
+ \textbf{Even-aged:} Large canopy openings
\bigskip
\includegraphics[width=0.8\paperwidth]{images/singletree_long.png}
- \textbf{Uneven-aged:} Single-tree \& group selection, patch cuts
+ \textbf{Uneven-aged:} Smaller, more numerous canopy openings
\end{center}
- %\end{column}
- %\begin{column}{0.48\textwidth}
- % \begin{center}
- % \textbf{Harvest Type}
-
- % \end{center}
- %\end{column}
- %\end{columns}
- \end{frame}
+ \end{frame}
\begin{frame}{Research Questions}
- How does forest management impact:
+ How do different forest management approaches impact:
\begin{itemize}
- \item \textbf{Abundance} of individual species over time?
+ \item \textbf{Density} of shrubland and mature forest species?
\item \textbf{Richness} of the breeding bird community?
+ \item Species of \textbf{conservation concern} in Indiana?
\end{itemize}
+
\bigskip
+
+ \begin{columns}
+
+ \begin{column}{0.24\textwidth}
+
+ \centering
+ \includegraphics[width=0.15\paperwidth]{images/blackandwhite_warbler.png}
+
+ \footnotesize Black-and-white Warbler
+
+ \end{column}
+
+ \begin{column}{0.24\textwidth}
+
+ \centering
+ \includegraphics[width=0.15\paperwidth]{images/hooded_warbler.png}
+
+ \footnotesize Hooded Warbler
+
+ \end{column}
+
+ \begin{column}{0.24\textwidth}
+
+ \centering
+
+ \includegraphics[width=0.15\paperwidth]{images/cerulean_warbler.png}
+
+ \footnotesize Cerulean Warbler
+
+ \end{column}
+
+ \begin{column}{0.24\textwidth}
+
+ \centering
+
+ \includegraphics[width=0.15\paperwidth]{images/worm_eating_warbler.png}
+
+ \footnotesize Worm-eating Warbler
+
+ \end{column}
- Are there consistent patterns:
- \begin{itemize}
- \item Based on \textbf{scale} and \textbf{intensity} of management?
- \item For \textbf{shrubland} vs. \textbf{mature forest} birds?
- \end{itemize}
+
+
+ \end{columns}
\end{frame}
%\section{Methods}
- \begin{frame}{Hardwood Ecosystem Experiment}
+ \begin{frame}{Methods}
\begin{columns}
\begin{column}{0.48\textwidth}
- \textbf{Scale}
+ \textbf{Location \& Scale}
\begin{itemize}
+ \item Southern Indiana, USA
\item 3,603 ha study area
- \item 100 years (in year 10)
+ \item 10 years
\end{itemize}
\textbf{Design}
\begin{itemize}
- \item Three management treatments $\times$ 3 replicates
- \item Pre-treatment data collected
+ \item Three management treatments
+ \item Pre- and post-treatment periods
\end{itemize}
\end{column}
@@ -119,18 +147,18 @@
\end{columns}
\end{frame}
- \begin{frame}{Hardwood Ecosystem Experiment}
+ \begin{frame}{Methods}
\begin{columns}
\begin{column}{0.42\textwidth}
- \textbf{Harvests}
+ \textbf{Management Treatments}
\begin{itemize}
\item \textbf{Even-Aged}: Clearcuts \& Shelterwoods
\item \textbf{Uneven-Aged}: Patch Cuts \& Single-tree Selection
\end{itemize}
- \textbf{HEE Bird Study}
+ \textbf{Bird Surveys}
\begin{itemize}
\item 240 survey points
@@ -148,7 +176,11 @@
\begin{frame}{Analysis: Before-After Control-Impact}
\begin{center}
- \includegraphics[width=0.85\paperwidth]{images/baci.png}
+ $y = \alpha + \beta_{treat} + \beta_{period} + \boldsymbol{\beta_{treat} \times \beta_{period}}$
+
+ \bigskip
+
+ \includegraphics[width=0.7\paperwidth]{images/baci.png}
\end{center}
\end{frame}
@@ -156,6 +188,10 @@
\begin{frame}{Analysis: Scales}
\begin{center}
\includegraphics[width=0.85\paperwidth]{images/hee_scales.png}
+
+ \bigskip
+
+ Separate multispecies $N$-mixture models fit for each scale
\end{center}
\end{frame}
@@ -202,51 +238,7 @@
\includegraphics[width=0.85\paperwidth]{images/mu_resp.png}
\end{center}
\end{frame}
-
- \begin{frame}{Focal Species}
- \begin{columns}
-
- \begin{column}{0.48\textwidth}
-
- \centering
- \includegraphics[width=0.2\paperwidth]{images/blackandwhite_warbler.png}
-
- Black-and-white Warbler
-
- \bigskip
-
- \includegraphics[width=0.2\paperwidth]{images/cerulean_warbler.png}
-
- Cerulean Warbler
-
- \end{column}
-
- \begin{column}{0.48\textwidth}
-
- \centering
- \includegraphics[width=0.2\paperwidth]{images/hooded_warbler.png}
-
- Hooded Warbler
-
- \bigskip
-
- \includegraphics[width=0.2\paperwidth]{images/worm_eating_warbler.png}
-
- Worm-eating Warbler
-
- \end{column}
-
- \end{columns}
- \end{frame}
-
-
- \begin{frame}{Focal Species - Management Unit Scale}
- \begin{center}
- \includegraphics[width=0.85\paperwidth]{images/focal_mu.png}
- \end{center}
- \end{frame}
-
\begin{frame}{Richness - Management Unit Scale}
\begin{center}
\includegraphics[width=0.85\paperwidth]{images/mu_rich.png}
@@ -260,52 +252,52 @@
\end{center}
\end{frame}
-
- \begin{frame}{Focal Species - Harvest Scale}
- \begin{center}
- \includegraphics[width=0.85\paperwidth]{images/focal_hl.png}
- \end{center}
- \end{frame}
-
-
\begin{frame}{Richness - Harvest Scale}
\begin{center}
\includegraphics[width=0.85\paperwidth]{images/hl_rich.png}
\end{center}
\end{frame}
+
+\begin{frame}{Focal Species - Harvest Scale}
+ \begin{center}
+ \includegraphics[width=0.85\paperwidth]{images/focal_hl.png}
+ \end{center}
+\end{frame}
+
%\section{Conclusions}
-
+
\begin{frame}{Conclusions}
- \begin{itemize}
- \item Changes in abundance were related to \textbf{scale} and \textbf{harvest intensity}
- \begin{itemize}
- \item More species affected (and impact greater) at harvest scale
- \item Harvest size (and intensity) positively related to changes in abundance
- \end{itemize}
- \bigskip
- \item Diversity of forest habitat and bird species richness are \textbf{positively related}:
- \begin{itemize}
- \item Richness increased \textbf{16\%} following even-aged management
- \item Richness increased \textbf{19\%} following uneven-aged management
- \end{itemize}
- \end{itemize}
+ \begin{itemize}
+ \item \textbf{Habitat diversity} impacted bird community responses
+ \begin{itemize}
+ \item Richness higher in both management treatments (16-19\%), highest in uneven-aged sites
+ \item Effects buffered at management unit scale
+ \end{itemize}
+ \bigskip
+ \item Complex effects of \textbf{opening size}
+ \begin{itemize}
+ \item Greatest number of species impacted by 0.4-2 ha openings
+ \item Richness maximized in clearcut openings (4 ha)
+ \item Minimal impact of single-tree selection
+ \end{itemize}
+ \end{itemize}
\end{frame}
\begin{frame}{Conclusions}
\begin{itemize}
- \item \textbf{Early-successional} birds had a consistent response to harvest
+ \item \textbf{Shrubland/edge birds}: consistent responses
\begin{itemize}
- \item Large, immediate increases
- \item Increases positively related to harvest 'intensity' (and sometimes size)
+ \item Large, immediate increases following harvest
\item Slow decline as density of harvested plots increases
\end{itemize}
\bigskip
- \item \textbf{Mature-forest} birds did not show a consistent response to harvest
+ \item \textbf{Mature-forest birds}: inconsistent response
\begin{itemize}
- \item Some (e.g. Ovenbird) declined
- \item Others (e.g. Cerulean Warbler) increased
+ \item Declines (e.g. Worm-eating Warbler) and increases (e.g. Cerulean Warbler)
+ \item Post-harvest, mature forest birds remained abundant
+ \item Importance of multiple sampling approaches
\end{itemize}
\end{itemize}
\end{frame}
@@ -344,8 +336,20 @@
\bigskip
- Kellner, K. F.; Ruhl, P. J.; Dunning Jr., J. B.; Riegel, J. K. and Swihart, R. K. \textit{In press.} Multi-scale responses of breeding birds to experimental forest management in Indiana, USA. Forest Ecology and Management 382: 64-75.
+ Kellner, K. F.; Ruhl, P. J.; Dunning Jr., J. B.; Riegel, J. K. and Swihart, R. K. 2016. Multi-scale responses of breeding birds to experimental forest management in Indiana, USA. Forest Ecology and Management 382: 64-75.
\end{frame}
+ \begin{frame}{Focal Species - Management Unit Scale}
+ \begin{center}
+ \includegraphics[width=0.85\paperwidth]{images/focal_mu.png}
+ \end{center}
+ \end{frame}
+
+ \begin{frame}{Current Research: Mist-Netting in Clearcuts}
+ \begin{center}
+ \includegraphics[width=0.85\paperwidth]{images/mistnet_counts.png}
+ \end{center}
+ \end{frame}
+
\end{document} \ No newline at end of file