update

.Rhistory

@@ -0,0 +1,31 @@
+ps
+## Load libraries
+library(devtools)
+library(rmarkdown)
+library(dada2)
+library(ShortRead)
+library(ggplot2)
+library("ggforce")
+library(phyloseq)
+library(vegan)
+library(knitr)
+library(ALDEx2)
+library(CoDaSeq)
+library(zCompositions)
+library(igraph)
+library(car)
+library(grDevices)
+library(propr)
+library(cowplot)
+library(randomcoloR)
+library(dplyr)
+library(reshape2)
+library(tibble)
+library(exactRankTests)
+library(nlme)
+library(data.table)
+library(Rmisc)
+##set wd
+setwd("~/Desktop/PANAMA_HYPOXIA")
+## Save version information
+writeLines(capture.output(sessionInfo()), "sessionInfo.txt")

Panama_Tents_2019.Rmd

@@ -174,7 +174,7 @@ ps
 # remove chloroplasts and mitochondria and Eukaryota
 get_taxa_unique(ps, "Family") #679
 get_taxa_unique(ps, "Order") #411
-get_taxa_unique(ps, "Kingdom") #2
+get_taxa_unique(ps, "Kingdom") #3
 ps <- subset_taxa(ps, Family !="Mitochondria")
 ps <- subset_taxa(ps, Order !="Chloroplast")
 ps <- subset_taxa(ps, Kingdom !="Eukaryota")
@@ -202,10 +202,10 @@ ps
 plot_richness(ps,x="Treatment",color="Species",measures=c("Observed"))
 # look at data and chose filtering method for very low abundance ASVs
 ntaxa(ps) #22823
-ps5<-filter_taxa(ps5, function(x) mean(x) >5, TRUE)
+ps5<-filter_taxa(ps, function(x) mean(x) >5, TRUE)
 ntaxa(ps5) #879
-get_taxa_unique(ps, "Genus") 
-get_taxa_unique(ps5, "Genus") 
+get_taxa_unique(ps, "Genus") #1000
+get_taxa_unique(ps5, "Genus") #298
 # filtered ASVs with very low abundance with phyloseq, now export otu and taxa tables from phyloseq for codaseq, SAVE these following tables for replication
 otu = as(otu_table(ps5), "matrix")
 taxon = as(tax_table(ps5), "matrix")

Panama_ps5_silva_metadata.txt

@@ -0,0 +1,57 @@
+""	"Site"	"Logger.MiniDOT"	"Treatment"	"Origin"	"Species"
+"AA-1"	"Tierra Oscura"	"7"	"Resident"	"resident"	"Siderastrea siderea"
+"AA-10"	"Punta Caracol"	"8"	"Control plots"	"transplant"	"Agaricia lamarcki"
+"AA-11"	"Punta Caracol"	"8"	"Control plots"	"transplant"	"Agaricia lamarcki"
+"AA-12"	"Punta Caracol"	"8"	"Control plots"	"transplant"	"Agaricia lamarcki"
+"AA-13"	"Punta Caracol"	"8"	"Control plots"	"transplant"	"Siderastrea siderea"
+"AA-15"	"Punta Caracol"	"8"	"Control plots"	"transplant"	"Siderastrea siderea"
+"AA-16"	"Punta Caracol"	"8"	"Control plots"	"resident"	"Siderastrea siderea"
+"AA-17"	"Punta Caracol"	"4"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-18"	"Punta Caracol"	"4"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-19"	"Punta Caracol"	"4"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-2"	"Tierra Oscura"	"7"	"Resident"	"resident"	"Siderastrea siderea"
+"AA-20"	"Punta Caracol"	"4"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-21"	"Punta Caracol"	"4"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-22"	"Punta Caracol"	"4"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-23"	"Punta Caracol"	"4"	"Hypoxia plots"	"resident"	"Siderastrea siderea"
+"AA-24"	"Punta Caracol"	"2"	"Control plots"	"transplant"	"Agaricia lamarcki"
+"AA-25"	"Punta Caracol"	"2"	"Control plots"	"transplant"	"Agaricia lamarcki"
+"AA-26"	"Punta Caracol"	"2"	"Control plots"	"transplant"	"Agaricia lamarcki"
+"AA-27"	"Punta Caracol"	"2"	"Control plots"	"transplant"	"Siderastrea siderea"
+"AA-28"	"Punta Caracol"	"2"	"Control plots"	"transplant"	"Siderastrea siderea"
+"AA-29"	"Punta Caracol"	"2"	"Control plots"	"transplant"	"Siderastrea siderea"
+"AA-3"	"Tierra Oscura"	"7"	"Resident"	"resident"	"Siderastrea siderea"
+"AA-30"	"Punta Caracol"	"2"	"Control plots"	"resident"	"Siderastrea siderea"
+"AA-31"	"Punta Caracol"	"1"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-32"	"Punta Caracol"	"1"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-33"	"Punta Caracol"	"1"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-34"	"Punta Caracol"	"1"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-35"	"Punta Caracol"	"1"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-36"	"Punta Caracol"	"1"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-37"	"Punta Caracol"	"1"	"Hypoxia plots"	"resident"	"Siderastrea siderea"
+"AA-38"	"Punta Caracol"	"5"	"Control plots"	"transplant"	"Agaricia lamarcki"
+"AA-39"	"Punta Caracol"	"5"	"Control plots"	"transplant"	"Agaricia lamarcki"
+"AA-4"	"Finca"	"6"	"Resident"	"resident"	"Siderastrea siderea"
+"AA-40"	"Punta Caracol"	"5"	"Control plots"	"transplant"	"Agaricia lamarcki"
+"AA-41"	"Punta Caracol"	"5"	"Control plots"	"transplant"	"Siderastrea siderea"
+"AA-42"	"Punta Caracol"	"5"	"Control plots"	"transplant"	"Siderastrea siderea"
+"AA-43"	"Punta Caracol"	"5"	"Control plots"	"transplant"	"Siderastrea siderea"
+"AA-45"	"Punta Caracol"	"9"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-46"	"Punta Caracol"	"9"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-47"	"Punta Caracol"	"9"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-48"	"Punta Caracol"	"9"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-49"	"Punta Caracol"	"9"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-5"	"Finca"	"6"	"Resident"	"resident"	"Agaricia lamarcki"
+"AA-50"	"Punta Caracol"	"9"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-51"	"Punta Caracol"	"9"	"Hypoxia plots"	"resident"	"Agaricia lamarcki"
+"AA-52"	"Punta Caracol"	"3"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-53"	"Punta Caracol"	"3"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-54"	"Punta Caracol"	"3"	"Hypoxia plots"	"transplant"	"Agaricia lamarcki"
+"AA-55"	"Punta Caracol"	"3"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-56"	"Punta Caracol"	"3"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-57"	"Punta Caracol"	"3"	"Hypoxia plots"	"transplant"	"Siderastrea siderea"
+"AA-58"	"Punta Caracol"	"3"	"Hypoxia plots"	"resident"	"Siderastrea siderea"
+"AA-6"	"Finca"	"6"	"Resident"	"resident"	"Siderastrea siderea"
+"AA-7"	"Finca"	"6"	"Resident"	"resident"	"Agaricia lamarcki"
+"AA-8"	"Finca"	"6"	"Resident"	"resident"	"Agaricia lamarcki"
+"AA-9"	"Finca"	"6"	"Resident"	"resident"	"Siderastrea siderea"