Created
December 10, 2012 02:07
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setwd('~/Documents/zooplankton') | |
data = read.csv("Env_x_Zoop use this data set _.csv") | |
chla = data[,3] | |
conduct = data[,4] | |
logTotal = data[,6] | |
richness = data[,7] | |
sumZoo = data[,8] | |
for(i in 9:34){sumZoo = sumZoo + data[,i]} | |
comm_conduct = data[1:13,4] | |
res_conduct = data[14:28,4] | |
############################# | |
#1a | |
plot(conduct, chla, xlab="Salinity (as measured by conductivity) (µS)", | |
ylab="Chlorophyll a", main="Salinity and the response of Chlorophyll a") | |
dev.copy(png,'1a.chla_vs_conductivity.png', width = 514, height = 398, units = "px") | |
dev.off() | |
#1b | |
plot(conduct, sumZoo, xlab="Salinity (as measured by conductivity) (µS)", | |
ylab="Total Zooplankton Abundance", main="Salinity and the response of Zooplankton abundance") | |
dev.copy(png,'1b.total_zoo_vs_conductivity.png', width = 514, height = 398, units = "px") | |
dev.off() | |
#1c | |
plot(conduct, richness, xlab="Salinity (as measured by conductivity) (µS)", | |
ylab="Richness", main="Conductivity vs Richness") | |
dev.copy(png,'1c.richness_vs_conductivity.png', width = 514, height = 398, units = "px") | |
dev.off() | |
############################# | |
#2a | |
plot(conduct, chla, xlab="Salinity (as measured by conductivity) (µS)", | |
ylab="Chlorophyll a", main="Salinity and the response of Chlorophyll a") | |
lm_chla = lm(chla~conduct) #compute linear model (regression) | |
abline(lm_chla) #plot regression | |
lm_coef <- round(coef(lm_chla), 3) # extract coefficients | |
mtext(bquote(y == .(lm_coef[2])*x + .(lm_coef[1])), adj=1, padj=0) # display equation | |
dev.copy(png,'2a.lm_chla_vs_conductivity.png', width = 514, height = 398, units = "px") | |
dev.off() | |
#2b | |
plot(conduct, logTotal, xlab="Salinity (as measured by conductivity) (µS)", | |
ylab="logTotal", main="Salinity and the response of logTotal") | |
lm_logTotal = lm(logTotal~conduct) | |
abline(lm_logTotal) | |
lm_coef <- round(coef(lm_chla), 3) | |
mtext(bquote(y == .(lm_coef[2])*x + .(lm_coef[1])), adj=1, padj=0) | |
dev.copy(png,'2b.lm_logTotal_vs_conductivity.png', width = 514, height = 398, units = "px") | |
dev.off() | |
#2c | |
plot(conduct, richness, xlab="Salinity (as measured by conductivity) (µS)", | |
ylab="Richness", main="Salinity and the response of Richness") | |
lm_richness = lm(richness~conduct) | |
abline(lm_richness) | |
lm_coef <- round(coef(lm_chla), 3) | |
mtext(bquote(y == .(lm_coef[2])*x + .(lm_coef[1])), adj=1, padj=0) | |
dev.copy(png,'2c.lm_richness_vs_conductivity.png', width = 514, height = 398, units = "px") | |
dev.off() | |
############################# | |
#3a | |
g_range <- range(0, comm_conduct, res_conduct) #calculate y-range | |
plot(res_conduct, type="o", col="blue", ylim=g_range, axes=FALSE, ann=FALSE) | |
axis(1, at=1:16) | |
axis(2, las=1, at=200*0:g_range[2]) | |
box() | |
lines(comm_conduct, type="o", pch=22, lty=2, col="red") | |
title(main="Salinity of Commercial and Residental Ponds") | |
title(xlab="Pond Number") | |
title(ylab="Salinity (as measured by conductivity) (µS)") | |
legend(1, g_range[2], c("Residential","Commercial"), cex=0.8, col=c("blue","red"), | |
pch=21:22, lty=1:2); | |
dev.copy(png,'3a.commercial_and_residential_conductivity.png', width = 514, height = 398, units = "px") | |
dev.off() | |
############################# | |
#4a | |
i=0; | |
shannon = 1:29; | |
for(i in 1:29){ | |
shannon[i]=0; | |
for(j in 8:34){ | |
if(data[i,j]>0) shannon[i] = shannon[i] - (data[i,j]/sumZoo[i])*log(data[i,j]/sumZoo[i]) | |
} | |
} | |
plot(1:29, shannon, xlab = "Pond Number", ylab = "Shannon Index", main = "Pond Diversity") | |
dev.copy(png,'4a.shannon_index.png', width = 514, height = 398, units = "px") | |
dev.off() |
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