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authorKen Kellner <ken.kellner@gmail.com>2016-09-30 20:57:48 (GMT)
committerKen Kellner <ken.kellner@gmail.com>2016-09-30 20:57:48 (GMT)
commit71e4e8fbd92da8bc9bfefe08b23faef0b0b4514b (patch)
treef03fe90a6fa436698fd11387aa7998f5d1792deb
parenta94146321d0322e9ed718f4b779ffeb7ec3571af (diff)
Start TWS 2016 talk. Update some figures.
-rw-r--r--figures/figure_birddens.R21
-rw-r--r--figures/figure_multidens.R2
-rw-r--r--figures/figure_resp_summary.R84
-rw-r--r--figures/figure_richness.R4
-rw-r--r--presentations/compress_pdf.bat2
-rw-r--r--presentations/figures_fscc2016.R16
-rw-r--r--presentations/figures_heevideo.R57
-rw-r--r--presentations/figures_resp.R72
-rw-r--r--presentations/figures_tws2016.R138
-rw-r--r--presentations/figures_video.R97
-rw-r--r--presentations/talk_tws2016.tex335
-rw-r--r--presentations/video_hee_research.md15
12 files changed, 654 insertions, 189 deletions
diff --git a/figures/figure_birddens.R b/figures/figure_birddens.R
index 6c2ca6c..42f78eb 100644
--- a/figures/figure_birddens.R
+++ b/figures/figure_birddens.R
@@ -2,13 +2,13 @@
bird.figure <- function(sp,scale,
cred=FALSE,se=FALSE,
legendpos='topleft',defaultpar=TRUE,legcex=1,
- ylab=expression(paste("Density (males ha"^{-1},")")),
- title=NULL,color=NULL,extralabels=FALSE,legend.lwd=2){
+ ylab=expression(paste("Density Index (males ha"^{-1},")")),
+ xlab="Year",title=NULL,color=NULL,extralabels=FALSE,legend.lwd=2){
#Set up options based on arguments
ind <- which(sp==species)
if(is.null(title)){title=sp}
- if(defaultpar){par(mgp=c(3,1,0),mar = c(4.5,4.5,2,2) + 0.1,oma=c(0,0,0,0))}
+ if(defaultpar){par(mgp=c(3,1,0),mar = c(3.5,4.5,2,2) + 0.1,oma=c(0,0,0,0))}
if(cred){
qu <- function(x){as.numeric(quantile(x,0.975,na.rm=T))}
@@ -24,12 +24,15 @@ bird.figure <- function(sp,scale,
if(!is.null(color)){
#colors = c('black','red','blue')
colors <- color
- }else{colors = (gray(seq(0.4,0.1,length=3)))}
- lty <- c(1:3)
+ lty <- rep(1,3)
+ }else{
+ colors = (gray(seq(0.4,0.1,length=3)))
+ lty <- c(1:3)
+ }
pch <- c(17:19)
ntreat <- 3
N <- Ntreat
- legendtx <- c('NH','EA','UA')
+ legendtx <- c('No Harvest','Even-Aged','Uneven-Aged')
}
if(scale=='hl'){
if(!is.null(color)){
@@ -69,10 +72,10 @@ bird.figure <- function(sp,scale,
#Set up plot
plot(1:10,abun.matrix[1,],main=title,type='o',cex=2,lty=1,col=colors[1],
- lwd=2,pch=17,xaxt='n',xlab="Year",ylab=ylab,
+ lwd=2,pch=17,xaxt='n',xlab="",ylab=ylab,
xlim=c(0.5,10.5),ylim=c(figmin,figmax))
- axis(side=1,at=c(1,3,5,7,9),
- labels=c('2006', '2008', '2010','2012','2014'),tck=0)
+ if(!is.null(xlab)){axis(side=1,at=c(1,3,5,7,9),
+ labels=c('2006', '2008', '2010','2012','2014'),tck=0)}
#Draw error bars, if applicable
if(cred|se){
diff --git a/figures/figure_multidens.R b/figures/figure_multidens.R
index 375022b..340b90d 100644
--- a/figures/figure_multidens.R
+++ b/figures/figure_multidens.R
@@ -63,7 +63,7 @@ multidens.figure <- function(sp.include,sp.name=NULL,scale,
}
if(scale=='hl'){
ntreat <- 5
- legend.labs <- c('No Harvest','Clearcut','Patch','Shelter','Single-tree')
+ legend.labs <- c('No Harvest','Clearcut','Patch Cut','Shelterwood','Single-tree')
Ntreat <- Ntreat.harvest
}
diff --git a/figures/figure_resp_summary.R b/figures/figure_resp_summary.R
new file mode 100644
index 0000000..145960d
--- /dev/null
+++ b/figures/figure_resp_summary.R
@@ -0,0 +1,84 @@
+
+
+resp.summary.figure <- function(scale,ylims,cols,text.cex=1){
+
+ #Set up scale-dependent figure variables
+ if(scale=='mu'){
+ treat.ind <- c(13,13,14,14)
+ ntreat <- length(treat.ind)
+ out <- out.mu
+ legendtext <- c('Even-Aged','Uneven-Aged')
+ }
+
+ if(scale=='hl'){
+ treat.ind <- c(20,20,21,21,22,22,23,23)
+ ntreat <- length(treat.ind)
+ out <- out.hl
+ legendtext <- c('Clearcut','Shelterwood','Patch Cut','Single-tree')
+ }
+
+ #Get counts of species responding in each direction
+ #Get ranks of species effect sizes
+ namerank <- matrix(NA,nrow=20,ncol=ntreat)
+ sum.counts <- vector(length=ntreat)
+ for (i in 1:ntreat){
+
+ if(i%%2==1){
+ ind <- out$mean[[treat.ind[i]]]>0&!out$overlap0[[treat.ind[i]]]
+ vals <- out$mean[[treat.ind[i]]][ind]
+ sp <- species[ind]
+ if(length(sp)>0){
+ namerank[1:length(sp),i] <- sp[order(vals,decreasing=T)]
+ sum.counts[i] <- length(sp)
+ } else{sum.counts[i] <- 0}
+ } else {
+ ind <- out$mean[[treat.ind[i]]]<0&!out$overlap0[[treat.ind[i]]]
+ vals <- out$mean[[treat.ind[i]]][ind]
+ sp <- species[ind]
+ if(length(sp)>0){
+ namerank[1:length(sp),i] <- sp[order(-vals,decreasing=T)]
+ sum.counts[i] <- -1*length(sp)
+ } else{sum.counts[i] <- 0}
+ }
+ }
+
+ barplot.vals <- matrix(sum.counts,ncol=ntreat/2,byrow=F)
+
+ #Set up plot
+ par(mar = c(3,3.5,0.5,1) + 0.1, oma=c(0,0,0,0),mgp=c(2.5,1,0))
+ x <- barplot(barplot.vals,beside=T,ylim=ylims,col=rep(cols,each=2),
+ names=legendtext,
+ ylab='Number of Species')
+ abline(h=0,lwd=2)
+ box()
+
+ #Add alpha codes
+ index <- 1
+ for (i in 1:ncol(barplot.vals)){
+ for (j in 1:nrow(barplot.vals)){
+
+ val <- barplot.vals[j,i]
+ upplim <- val-(sign(val)*0.5)
+ lowlim <- sign(val)-(sign(val)*0.5)
+
+
+ text(x[j,i],seq(upplim,lowlim,length.out=abs(val)),
+ labels=namerank[1:abs(val),index],cex=text.cex)
+ index <- index+1
+
+ if(val==0){
+ if(index%%2==1){dir=-1}else{dir=1}
+ text(x[j,i],dir,'N/A')
+ }
+ }
+ }
+
+ #Add arrows/descriptions
+ 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[1]+1,labels='Negative Response')
+
+}
+
diff --git a/figures/figure_richness.R b/figures/figure_richness.R
index d8d5171..101e0df 100644
--- a/figures/figure_richness.R
+++ b/figures/figure_richness.R
@@ -1,5 +1,5 @@
-richness.figure <- function(scale,figmin,figmax,cols,pchs,ltys){
+richness.figure <- function(scale,figmin,figmax,cols,pchs,ltys,xlab="Year"){
if(scale=='mu'){
ntreat <- 3
@@ -28,7 +28,7 @@ richness.figure <- function(scale,figmin,figmax,cols,pchs,ltys){
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="Year",ylab='Richness',
+ lwd=2,pch=pchs[1],xaxt='n',xlab=xlab,ylab='Richness',
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 4cd2261..f380dc1 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_fscc2016_small.pdf" -dNOPAUSE -dBATCH "talk_fscc2016.pdf" \ No newline at end of file
+"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
diff --git a/presentations/figures_fscc2016.R b/presentations/figures_fscc2016.R
index e542e13..ce285d0 100644
--- a/presentations/figures_fscc2016.R
+++ b/presentations/figures_fscc2016.R
@@ -8,6 +8,7 @@ load('output/hl_bird_abun.Rdata')
source('figures/figure_multidens.R')
source('figures/figure_richness.R')
source('figures/figure_birddens.R')
+source('figures/figure_resp_summary.R')
#Load color palette
cols.mu <- c(rgb(128,194,0,max=255),
@@ -56,16 +57,22 @@ dev.off()
#################################################################
#Species Response Summary Figure - Management Scale
+png(filename="presentations/images/mu_resp.png",width=5,height=4,units="in",res=400, pointsize=10,
+ type='cairo')
+resp.summary.figure('mu',c(-5,11),cols.mu[2:3])
-
+dev.off()
#################################################################
#Species Response Summary Figure - Harvest Scale
+png(filename="presentations/images/hl_resp.png",width=5,height=4,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)
-
+dev.off()
##################################################################
#Abundance figures
@@ -225,7 +232,4 @@ tan <- readPNG('presentations/images/scta.png')
rasterImage(rub, scta.sum$Date[1],5,scta.sum$Date[1]+30,10)
rasterImage(tan,scta.sum$Date[22]-5,10,scta.sum$Date[22]+15,13)
-dev.off()
-
-
-
+dev.off() \ No newline at end of file
diff --git a/presentations/figures_heevideo.R b/presentations/figures_heevideo.R
new file mode 100644
index 0000000..15c723f
--- /dev/null
+++ b/presentations/figures_heevideo.R
@@ -0,0 +1,57 @@
+###########################
+## Figures for HEE Video ##
+###########################
+
+#Read in output
+load('output/mu_bird_abun.Rdata')
+load('output/hl_bird_abun.Rdata')
+source('figures/figure_birddens.R')
+source('figures/figure_richness.R')
+
+#Color palette
+colors.mu = c('black','firebrick1','dodgerblue')
+colors.hl <- c('black','firebrick1','orange','dodgerblue','forestgreen')
+
+#########################################################################
+#Cerulean Warbler
+png(filename="presentations/images/fig_cerw.png",width=16/3,height=9/3,
+ units="in",res=1000, pointsize=10,
+ type='cairo')
+
+bird.figure('CERW','hl',color=colors.hl,title='Cerulean Warbler',legendpos='topright',legcex=0.7,
+ extralabels=T)
+
+dev.off()
+
+#########################################################################
+#Black-and-white Warbler
+
+png(filename="presentations/images/fig_baww.png",width=16/3,height=9/3,units="in",res=1000, pointsize=10,
+ type='cairo')
+
+bird.figure('BAWW','hl',se=F,color=colors.hl,title='Black-and-white Warbler',legendpos='topleft',legcex=0.7,
+ extralabels=T)
+
+dev.off()
+
+#########################################################################
+#Hooded Warbler
+
+png(filename="presentations/images/fig_howa.png",width=16/3,height=9/3,units="in",res=1000, pointsize=10,
+ type='cairo')
+
+bird.figure('HOWA','hl',se=F,color=colors.hl,title='Hooded Warbler',legendpos='topleft',legcex=0.7,
+ extralabels=T)
+
+dev.off()
+
+#########################################################################
+#Management-scale Richness
+
+png(filename="presentations/images/fig_rich.png",width=16/3,height=9/3,
+ units="in",res=1000, pointsize=10,
+ type='cairo')
+
+richness.figure('mu',16,30,cols=colors.mu,pch=17:19,ltys=rep(1,3))
+
+dev.off() \ No newline at end of file
diff --git a/presentations/figures_resp.R b/presentations/figures_resp.R
deleted file mode 100644
index 5eb2d6a..0000000
--- a/presentations/figures_resp.R
+++ /dev/null
@@ -1,72 +0,0 @@
-
-png(filename="presentations/images/mu_resp.png",width=5,height=4,units="in",res=400, pointsize=10,
- type='cairo')
-
-par(mar = c(3,3.5,0.5,1) + 0.1, oma=c(0,0,0,0),mgp=c(2.5,1,0))
-dat <- matrix(c(6,0,10,-1),ncol=2,byrow=F)
-
-colors <- c(rgb(128,194,0,max=255),
- rgb(244,124,66,max=255),
- rgb(241,194,50,max=255))[c(2,2,3,3)]
-
-x <- barplot(dat,beside=T,ylim=c(-3,12),col=colors,names=c('Even-Aged','Uneven-Aged'),
- ylab='Number of Species')
-abline(h=0,lwd=2)
-box()
-
-text(1.5,seq(5.5,1.5,length.out=6),labels=c('RHWO','CHSP','WEVI','NOPA','INBU','CERW'))
-text(4.5,seq(9.5,1.5,length.out=10),labels=c('CHSP','EATO','KEWA','WEVI','BWWA','INBU',
- 'MODO','BAWW','CARW','CERW'))
-text(5.5,-0.5,labels='OVEN')
-text(2.5,-0.5,labels='N/A')
-text(mean(x),11,labels='Positive Response')
-text(mean(x),-2,labels='Negative Response')
-arrows(mean(x),0,mean(x),10)
-arrows(mean(x),0,mean(x),-1.5)
-
-dev.off()
-
-############################
-
-png(filename="presentations/images/hl_resp.png",width=5,height=4,units="in",res=400, pointsize=10,
- type='cairo')
-
-par(mar = c(3,3.5,0.5,1) + 0.1, oma=c(0,0,0,0),mgp=c(2.5,1,0))
-dat <- matrix(c(16,-4,0,0,16,-5,3,-1),ncol=4,byrow=F)
-
-colors <- c(rgb(244,124,66,max=255),
- rgb(244,124,66,max=255),
- rgb(248, 172, 135,max=255),
- rgb(248, 172, 135,max=255),
- rgb(241,194,50,max=255),
- rgb(241,194,50,max=255),
- rgb(255, 212, 128,max=255),
- rgb(255, 212, 128,max=255)
- )
-
-x <- barplot(dat,beside=T,ylim=c(-8,19),col=colors,
- names=c('Clearcut','Shelterwood','Patch Cut','Single-tree'),
- ylab='Number of Species')
-abline(h=0,lwd=2)
-box()
-
-text(1.5,seq(15.5,1.5,length.out=16),cex=0.65,
- labels=c('YBCH','PRAW','WEVI','AMGO','GRCA','BWWA','INBU','COYE','RHWO','EATO',
- 'MODO','CHSP','CARW','CACH','BAWW','KEWA'))
-text(2.5,seq(-3.5,-0.5,length.out=4),cex=0.65,
- labels=c('WEWA','REVI','OVEN','ACFL'))
-text(4.5,1,'N/A')
-text(5.5,-1,'N/A')
-text(7.5,seq(15.5,1.5,length.out=16),cex=0.65,
- labels=c('WEVI','YBCH','INBU','GRCA','BWWA','EATO','AMGO','CHSP','PRAW','COYE',
- 'BAWW','KEWA','NOCA','MODO','CARW','BHCO'))
-text(8.5,seq(-4.5,-0.5,length.out=5),cex=0.65,labels=c('WEWA','REVI','WOTH','ACFL','OVEN'))
-text(10.5,seq(0.5,2.5,length.out=3),cex=0.65,labels=c('YTWA','KEWA','NOCA'))
-text(11.5,-0.5,cex=0.65,labels=c('OVEN'))
-
-text(mean(x),18,labels='Positive Response')
-text(mean(x),-6.5,labels='Negative Response')
-arrows(mean(x),0,mean(x),17)
-arrows(mean(x),0,mean(x),-5.5)
-
-dev.off() \ No newline at end of file
diff --git a/presentations/figures_tws2016.R b/presentations/figures_tws2016.R
new file mode 100644
index 0000000..222e091
--- /dev/null
+++ b/presentations/figures_tws2016.R
@@ -0,0 +1,138 @@
+################################
+## Figures from TWS 2016 Talk ##
+################################
+
+#Read in output
+load('output/mu_bird_abun.Rdata')
+load('output/hl_bird_abun.Rdata')
+source('figures/figure_multidens.R')
+source('figures/figure_richness.R')
+source('figures/figure_birddens.R')
+source('figures/figure_resp_summary.R')
+
+#Color palette
+cols.mu = c('black','firebrick1','dodgerblue')
+cols.hl <- c('black','firebrick1','orange','dodgerblue','forestgreen')
+
+#################################################################
+#BACI Figure
+
+#Simulate data
+set.seed(2016)
+control <- rnorm(10,0.3,0.05)
+treatment <- c(rnorm(3,0.3,0.05),rnorm(7,1,0.1))
+
+png(filename="presentations/images/baci.png",width=6,height=3.8,units="in",res=400, pointsize=10,
+ type='cairo')
+
+par(mgp=c(3,1,0),mar = c(4.5,4.5,1,1) + 0.1,oma=c(0,0,0,0))
+structure <- c(1:10)
+plot(structure,treatment,type='l',col=cols.mu[2],lwd=2,ylim=c(0,1.5),
+ xlab='Year',ylab='Density')
+
+lines(structure,control,col=cols.mu[1],lwd=2)
+abline(v=3.5,lty=2)
+
+text(3,1,'Treatment Applied',srt=90)
+text(mean(c(0.5,3.5)),0.1,'Before',font=2)
+text(mean(c(3.5,10.5)),0.1,'After',font=2)
+
+arrows(7,0.7,7,control[7]+0.05,length=0.1,lwd=2)
+arrows(7,0.7,7,treatment[7]-0.05,length=0.1,lwd=2)
+
+arrows(2,0.33,2,control[2]+0.01,length=0.05,lwd=2)
+arrows(2,0.33,2,treatment[2]-0.01,length=0.05,lwd=2)
+
+legend('topright',col=cols.mu[1:2],lwd=2,legend=c('Control','Treatment'))
+
+dev.off()
+
+#################################################################
+#Species Response Summary Figure - Management Scale
+
+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])
+
+dev.off()
+
+##################################################
+#Individual Species, Management Unit Scale
+
+png(filename="presentations/images/focal_mu.png",width=6,height=3.8,units="in",res=400, pointsize=7,
+ type='cairo')
+
+par(fig=c(0,0.54,0.45,1),new=FALSE)
+bird.figure('BAWW','mu',color=cols.mu,title=
+ 'Black-and-white Warbler',legendpos='none',legcex=1,
+ extralabels=F,xlab=NULL)
+par(fig=c(0.46,1,0.45,1),new=TRUE)
+bird.figure('HOWA','mu',color=cols.mu,title=
+ 'Hooded Warbler',legendpos='none',legcex=1,
+ extralabels=F,xlab=NULL,ylab="")
+par(fig=c(0,0.54,0,0.55),new=TRUE)
+bird.figure('CERW','mu',color=cols.mu,title=
+ 'Cerulean Warbler',legendpos='topright',legcex=0.9,
+ legend.lwd=1, extralabels=F,xlab="")
+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="")
+dev.off()
+
+####################################################
+#Richness, Management Scale
+
+png(filename="presentations/images/mu_rich.png",width=6,height=3.8,units="in",res=400, pointsize=10,
+ type='cairo')
+
+richness.figure(scale='mu',figmin=16.5,figmax=29,cols=cols.mu,
+ pchs=17:19,ltys=rep(1,3),xlab="")
+
+dev.off()
+
+#################################################################
+#Species Response Summary Figure - Harvest Scale
+
+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)
+
+dev.off()
+
+#####################################################
+#Richness, Harvest Scale
+
+png(filename="presentations/images/hl_rich.png",width=6,height=3.8,units="in",res=400, pointsize=10,
+ type='cairo')
+
+richness.figure(scale='hl',figmin=16.5,figmax=32,cols=cols.hl,
+ pchs=c(17,15,16,18,21),ltys=rep(1,5),xlab="")
+
+dev.off()
+
+##################################################
+#Individual Species, Harvest Scale
+
+png(filename="presentations/images/focal_hl.png",width=6,height=3.8,units="in",res=400, pointsize=7,
+ type='cairo')
+
+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)
+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="")
+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="")
+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="")
+dev.off()
diff --git a/presentations/figures_video.R b/presentations/figures_video.R
deleted file mode 100644
index fad841f..0000000
--- a/presentations/figures_video.R
+++ /dev/null
@@ -1,97 +0,0 @@
-###########################
-## Figures for HEE Video ##
-###########################
-
-#Read in output
-load('output/hl_bird_abun.Rdata')
-source('figures/figure_birddens.R')
-
-png(filename="presentations/images/fig_cerw.png",width=16/3,height=9/3,
- units="in",res=1000, pointsize=10,
- type='cairo')
-bird.figure('CERW','hl',color=T,title='Cerulean Warbler',legendpos='topright',legcex=0.7,
- extralabels=T)
-
-dev.off()
-
-
-png(filename="presentations/images/fig_baww.png",width=16/3,height=9/3,units="in",res=1000, pointsize=10,
- type='cairo')
-bird.figure('BAWW','hl',se=F,color=T,title='Black-and-white Warbler',legendpos='topleft',legcex=0.7,
- extralabels=T)
-
-dev.off()
-
-png(filename="presentations/images/fig_howa.png",width=16/3,height=9/3,units="in",res=1000, pointsize=10,
- type='cairo')
-bird.figure('HOWA','hl',se=F,color=T,title='Hooded Warbler',legendpos='topleft',legcex=0.7,
- extralabels=T)
-
-dev.off()
-
-###########
-#Richness figure
-
-load('output/mu_bird_abun.Rdata')
-
-#Set plotting options
-colors <- c('black','firebrick1','dodgerblue')
-figmax <- 30
-figmin <- 16
-pch <- c(17:19)
-lty <- rep(1,3)
-
-#Functions to calculate 95% CI
-qu <- function(x){as.numeric(quantile(x,0.975,na.rm=T))}
-ql <- function(x){as.numeric(quantile(x,0.025,na.rm=T))}
-
-#Calculate treatment x year means
-rich.means <- rich.upper <- rich.lower <- matrix(NA,nrow=3,ncol=10)
-
-for (i in 1:3){
- rich.means[i,] <- colMeans(Rtreat[,,i])
- rich.lower[i,] <- apply(Rtreat[,,i],2,ql)
- rich.upper[i,] <- apply(Rtreat[,,i],2,qu)
-}
-
-#Set up plot
-png(filename="presentations/images/fig_rich.png",width=16/3,height=9/3,
- units="in",res=1000, pointsize=10,
- type='cairo')
-
-par(mar = c(4,3.5,0.5,1) + 0.1, oma=c(0,0,0,0),mgp=c(2.5,1,0))
-plot(1:10,rich.means[1,],ylim=c(figmin,figmax),
- main="",type='o',cex=2,lty=lty[1],col=colors[1],
- lwd=2,pch=pch[1],xaxt='n',xlab="Year",ylab='Species Richness',
- 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)
-
-#Error bars
-wd=0.1
-for (i in 1:10){
- for (j in 1:3){
- segments(i,rich.lower[j,i],i,rich.upper[j,i])
- segments(i-wd,rich.lower[j,i],i+wd,rich.lower[j,i])
- segments(i-wd,rich.upper[j,i],i+wd,rich.upper[j,i])
- }
-}
-
-#Draw lines
-for (j in 1:3){
- lines(1:10,rich.means[j,],type='o',cex=2,lty=lty[j],col=colors[j],
- lwd=2,pch=pch[j])
- lines(c(7,9),rich.means[j,c(7,9)],lty=lty[j],col=colors[j],lwd=2)
-}
-
-#Draw vertical line at time of harvest
-abline(v=3.5,lty=2)
-
-#Add extra text
-text(2,16,'Before Harvest')
-text(7.5,16,'After Harvest')
-
-#Add legend
-legend('topleft',c('No Harvest','Even-Aged','Uneven-Aged'),cex=1,
- pch=pch,lwd=2,col=colors,bg="white",lty=lty)
-
-dev.off() \ No newline at end of file
diff --git a/presentations/talk_tws2016.tex b/presentations/talk_tws2016.tex
new file mode 100644
index 0000000..d752dee
--- /dev/null
+++ b/presentations/talk_tws2016.tex
@@ -0,0 +1,335 @@
+\documentclass{beamer}
+\usetheme{metropolis} % Use metropolis theme
+\title{Multi-scale Migratory Bird Responses \\ to Experimental Forest Management}
+\date{October 19, 2016}
+\author{\textbf{Kenneth F. Kellner}, Patrick J. Ruhl, John B. Dunning Jr., \\ Jeffery K. Riegel, Robert K. Swihart}
+\institute{Department of Forestry and Natural Resources, Purdue University}
+\setbeamertemplate{frame footer}{Kellner - Birds \& Management}
+
+%\definecolor{firebrick}{HTML}{FF3030}
+%\setbeamercolor{progress bar}{fg=firebrick}
+
+\begin{document}
+
+\maketitle
+
+ %\section{Introduction}
+
+ \begin{frame}{Forest Maturation}
+ \end{frame}
+
+ \begin{frame}{Importance of Early-Successional Habitat}
+ \begin{itemize}
+ \item \textbf{74\%} of shrubland species are declining (Sauer et al. 2013)
+ \item \textbf{51\%} of species use young forest habitat (Probst and Thompson 1996)
+ \item Provides \textbf{food} and \textbf{cover}
+ \end{itemize}
+ \begin{center}
+ \includegraphics[width=0.8\paperwidth]{images/clearcut.png}
+ \end{center}
+ \end{frame}
+
+ \begin{frame}{Forest Management}
+ \begin{columns}
+ \begin{column}{0.48\textwidth}
+ \begin{center}
+ \textbf{Silviculture}
+ \bigskip
+
+ \includegraphics[width=0.4\paperwidth]{images/clearcut.png}
+
+ Even-aged
+
+ \bigskip
+
+ \includegraphics[width=0.4\paperwidth]{images/singletree.png}
+
+ Uneven-aged
+ \end{center}
+ \end{column}
+ \begin{column}{0.48\textwidth}
+ \begin{center}
+
+ \end{center}
+ \end{column}
+ \end{columns}
+
+ \end{frame}
+
+
+ \begin{frame}{Research Questions}
+
+ How does forest management impact:
+ \begin{itemize}
+ \item \textbf{Abundance} of individual species over time?
+ \item \textbf{Richness} of the breeding bird community?
+ \end{itemize}
+ \bigskip
+
+ Are there consistent patterns:
+ \begin{itemize}
+ \item Based on \textbf{scale} and \textbf{intensity} of management?
+ \item For "\textbf{early successional}" vs. "\textbf{mature forest}" birds?
+ \end{itemize}
+
+ \end{frame}
+
+%\section{Methods}
+
+ \begin{frame}{Hardwood Ecosystem Experiment}
+ \begin{columns}
+ \begin{column}{0.48\textwidth}
+
+ \textbf{Scale}
+
+ \begin{itemize}
+ \item Spans 30 linear km
+ \item 100 years (in year 10)
+ \end{itemize}
+
+ \textbf{Design}
+
+ \begin{itemize}
+ \item Three management treatments $\times$ 3 replicates
+ \item Pre-treatment data collected
+ \end{itemize}
+
+ \end{column}
+ \begin{column}{0.48\textwidth}
+
+ \fbox{\includegraphics[width=0.35\paperwidth]{images/hee_area.png}}
+
+ \end{column}
+ \end{columns}
+ \end{frame}
+
+ \begin{frame}{Hardwood Ecosystem Experiment}
+ \begin{columns}
+ \begin{column}{0.42\textwidth}
+
+ \textbf{Harvests}
+
+ \begin{itemize}
+ \item \textbf{Even-Aged}: Clearcuts \& Shelterwoods
+ \item \textbf{Uneven-Aged}: Patch Cuts \& Single-tree Selection
+ \end{itemize}
+
+ \textbf{HEE Bird Study}
+
+ \begin{itemize}
+ \item 240 survey points
+ \item 10 min counts 2x/year
+ \end{itemize}
+
+ \end{column}
+ \begin{column}{0.56\textwidth}
+
+ \fbox{\includegraphics[width=0.45\paperwidth]{images/hee_cores.png}}
+
+ \end{column}
+ \end{columns}
+ \end{frame}
+
+ \begin{frame}{Analysis: Before-After Control-Impact}
+ \begin{center}
+ \includegraphics[width=0.85\paperwidth]{images/baci.png}
+ \end{center}
+ \end{frame}
+
+
+ \begin{frame}{Analysis: Scales}
+ \begin{center}
+ \includegraphics[width=0.85\paperwidth]{images/hee_scales.png}
+ \end{center}
+ \end{frame}
+
+%\section{Results}
+
+ \begin{frame}{Summary}
+ \begin{itemize}
+ \item \textbf{4,272} surveys conducted by \textbf{45} technicians over \textbf{10} years
+ \item \textbf{45,799} birds of \textbf{65} species detected
+ \item Most commonly detected species:
+ \end{itemize}
+
+ \bigskip
+
+ \begin{columns}
+ \begin{column}{0.3\textwidth}
+ \begin{center}
+ \includegraphics[width=0.2\paperwidth]{images/red_eyed_vireo.png}
+
+ Red-eyed Vireo (\textit{n}=6963)
+ \end{center}
+ \end{column}
+ \begin{column}{0.3\textwidth}
+ \begin{center}
+ \includegraphics[width=0.2\paperwidth]{images/acadian_flycatcher.png}
+
+ Acadian Flycatcher (\textit{n}=4115)
+ \end{center}
+ \end{column}
+ \begin{column}{0.3\textwidth}
+ \begin{center}
+ \includegraphics[width=0.2\paperwidth]{images/worm_eating_warbler.png}
+
+ Worm-eating Warbler (\textit{n}=3484)
+ \end{center}
+ \end{column}
+ \end{columns}
+
+ \end{frame}
+
+
+ \begin{frame}{Species Responses - Management Unit Scale}
+ \begin{center}
+ \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/hooded_warbler.png}
+
+ Hooded Warbler
+
+ \end{column}
+
+ \begin{column}{0.48\textwidth}
+
+ \centering
+ \includegraphics[width=0.2\paperwidth]{images/cerulean_warbler.png}
+
+ Cerulean 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}
+ \end{center}
+ \end{frame}
+
+
+ \begin{frame}{Species Responses - Harvest Scale}
+ \begin{center}
+ \includegraphics[width=0.85\paperwidth]{images/hl_resp.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}
+
+
+ \begin{frame}{Richness - Harvest Scale}
+ \begin{center}
+ \includegraphics[width=0.85\paperwidth]{images/hl_rich.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{18\%} following even-aged management
+ \item Richness increased \textbf{22\%} following uneven-aged management
+ \end{itemize}
+ \end{itemize}
+ \end{frame}
+
+ \begin{frame}{Conclusions}
+ \begin{itemize}
+ \item \textbf{Early-successional} birds had a consistent response to harvest
+ \begin{itemize}
+ \item Large, immediate increases
+ \item Increases positively related to harvest 'intensity' (and sometimes size)
+ \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
+ \begin{itemize}
+ \item Some (e.g. Ovenbird) declined
+ \item Others (e.g. Cerulean Warbler) increased
+ \end{itemize}
+ \end{itemize}
+ \end{frame}
+
+
+ \begin{frame}{Acknowledgments}
+ \begin{columns}
+ \begin{column}{0.48\textwidth}
+ \begin{itemize}
+ \item 40+ technicians
+ \item Rebecca Kalb, Andy Meier, Charlotte Owings
+ \item HEE Executive Committee
+ \item Purdue FNR
+ \item Indiana DNR
+ \item HEE partners
+ \end{itemize}
+ \end{column}
+
+ \begin{column}{0.48\textwidth}
+ \begin{center}
+ \includegraphics[width=0.3\paperwidth]{images/hee_logo.png}
+
+ \includegraphics[width=0.2\paperwidth]{images/fnrlogo.png}
+ \includegraphics[width=0.2\paperwidth]{images/dnrlogo.png}
+ \end{center}
+ \end{column}
+
+ \end{columns}
+
+ \end{frame}
+
+
+ \begin{frame}{More Information}
+
+ kkellner@purdue.edu
+
+ \bigskip
+
+ Kellner, K. F.; Ruhl, P. J.; Dunning Jr., J. B.; Riegel, J. K. and Swihart, R. K. \textit{In revision.} Multi-scale responses of breeding birds to experimental forest management in Indiana, USA. \textit{Forest Ecology and Management}.
+
+ \end{frame}
+
+\end{document} \ No newline at end of file
diff --git a/presentations/video_hee_research.md b/presentations/video_hee_research.md
index a8fddcb..fa0e2e9 100644
--- a/presentations/video_hee_research.md
+++ b/presentations/video_hee_research.md
@@ -1,3 +1,8 @@
+---
+output:
+ pdf_document:
+ fig_caption: no
+---
HEE Video - Wildlife Responses
==============================
@@ -24,4 +29,12 @@ Overall, species richness was highest in the clearcuts, where it was 29% higher
**5. What does it mean?**
-Creating early successional habitat via timber harvest increases the diversity of habitat types available to birds at the landscape scale, particularly since young forest is more scarce in Indiana than it once was. Maintaining this habitat diversity will help to maintain a corresponding diverse group of songbird species. This requires balancing creation of new early successional habitat with preservation of mature forest habitat. \ No newline at end of file
+Creating early successional habitat via timber harvest increases the diversity of habitat types available to birds at the landscape scale, particularly since young forest is more scarce in Indiana than it once was. Maintaining this habitat diversity will help to maintain a corresponding diverse group of songbird species. This requires balancing creation of new early successional habitat with preservation of mature forest habitat.
+
+![](images/fig_cerw.png)
+
+![](images/fig_baww.png)
+
+![](images/fig_howa.png)
+
+![](images/fig_rich.png) \ No newline at end of file