Example of Species Accumulation Curve

Species Estimate (2 Level) Graphs

damn pak

Tuesday, March 24, 2015

data <- read.csv("http://www.personal.psu.edu/dkp5177/PR.2.CHAO2.csv",
                 header=TRUE, na.strings = NA)
require(ggplot2)

## Loading required package: ggplot2

require(gridExtra)

## Loading required package: gridExtra

## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
## logical.return = TRUE, : there is no package called 'gridExtra'

require(knitR)

## Loading required package: knitR

## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
## logical.return = TRUE, : there is no package called 'knitR'

require(qplots)

## Loading required package: qplots

## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
## logical.return = TRUE, : there is no package called 'qplots'

PUERTO RICO

Species Estimation vs. Samples (Low-shade farm (blue) and High-shade farm (red) with 95% Confidence Interval)

ggplot(data, aes(x = lspr.s)) + 
  geom_line(data = data,aes(y = lspr.sest), colour="blue") + 
  geom_ribbon(aes(ymin=sest.ls.lb, ymax=sest.ls.ub), alpha=0.2, fill = "blue") +
  geom_line(data = data, aes( y = hspr.sest), colour = "red")+ 
  geom_ribbon(aes(ymin=sest.hs.lb,ymax=sest.hs.ub),alpha = 0.2,fill = "red")+
  ylab(label="Species Estimated") + 
  xlab(label = "Samples") + 
  ggtitle("Species Estimation vs. Samples (Puerto Rico Shade")+
  theme(
    panel.background = element_blank(),
  panel.grid.major = element_blank(),
    panel.grid.minor = element_blank())

## Warning: Removed 6 rows containing missing values (geom_path).

Species Estimation vs. Individuals (Low-shade farm(blue) and High-shade farm (red) with 95% Confidence Interval)

ggplot() + 
geom_line(data = data, aes(x=individuals.ls,y = lspr.sest),colour ="blue")+
geom_ribbon(data = data, aes(x=individuals.ls, ymin =sest.ls.lb , ymax = sest.ls.ub), 
     alpha = 0.2, fill ="blue") +
geom_line(data = data,aes(x=individuals.hs,y=hspr.sest), colour = "red") + 
geom_ribbon(data = data, aes(x=individuals.hs, ymin =sest.hs.lb , ymax = sest.hs.ub), 
     alpha = 0.2, fill ="red") +
  ylab(label="Species Estimated") + 
  xlab(label = "Number of Individuals") +
  ggtitle("Species Estimation vs. Individuals (Puerto Rico Shade")+
  theme(panel.background = element_blank(),
  panel.grid.major = element_blank(),
    panel.grid.minor = element_blank())

## Warning: Removed 6 rows containing missing values (geom_path).