Abundance

```{r}

#estimating abundance of either D. glynnii or C. latusorum in P. grandis in La Paz using circular plot sampling conducted in 2009, biodiversity sampling in 2004, and 6 transects in 2006.

library(drc)
library(ggplot2)
library(magrittr)
require(tidyverse)
require(drc)
require(modelr)
require(broom)
library(data.table)
library(dplyr)
library(udpipe)
library(purrr)
library(reshape2)
library(stringr)
library(cowplot)
library(ggpubr)
library(Rmisc)
library(devtools)
library(cutoff)

#POLAR/CIRCULAR PLOT SAMPLING 2009
polar<-read.csv("polar_plot_2009_transposed.csv")

sum_polar<-summarySE(polar, measurevar="number_of_colonies", groupvars = c("sym.spp"))


p<-ggbarplot(
  polar, x = "sym.spp", y = "number_of_colonies",  legend = "none", xlab=FALSE, ylab = "No. of colonies",
  add = c("mean_sd", "jitter"),
  fill = "sym.spp", palette =c("D.glynnii"="#fbb040", "C.latusorum"="#8b5e3c", "C.latusorum/D.glynnii mixture"="white"))+
  theme_classic2()

p + theme_pubr()
p + labs_pubr()
p + theme_classic2()




#BIODIVERSITY SAMPLING 2004

survey<-read.csv("survey_data_2004.csv")

sum_survey<-summarySE(survey, measurevar="No_of_colonies", groupvars = c("sym.spp"))


sp<-ggbarplot(
  survey, x = "sym.spp", y = "No_of_colonies",  width = 0.5, lab.size =20, legend = "none", xlab=FALSE, ylab = "No. of colonies",
  add = c("mean_sd", "jitter"),
  fill = "sym.spp", 
  palette =c("D.glynnii"="#fbb040", "C.latusorum"="#8b5e3c", "C.latusorum/D.glynnii mixture"="white"))+ theme_classic2()


#TRANSECT ESTABLISHMENT AND SAMPLING 2006

transect<-read.csv("transects_2008.csv")

sum_transect<-summarySE(transect, measurevar="No_of_colonies", groupvars = c("sym.spp"))


tp<-ggbarplot(
  transect, x = "sym.spp", y = "No_of_colonies",  width = 0.5, lab.size = 4, legend = "none", xlab=FALSE, ylab = "No. of colonies",
  add = c("mean_sd", "jitter"),
  fill = "sym.spp", palette =c("D.glynnii"="#fbb040", "C.latusorum"="#8b5e3c", "C.latusorum/D.glynnii mixture"="white"))+ theme_classic2()

```