---
title: "setup"
author: "Stijn Schreven"
date: "30 mei 2018"
output: html_document
---

# Load packages  

```{r}
library(phyloseq) # also the basis of data object. Data analysis and visualisation
library(microbiome) # data analysis and visualisation
library(microbiomeutilities) # some utility tools 
library(RColorBrewer) # nice color options
library(ggpubr) # publication quality figures, based on ggplot2
library(DT) # interactive tables in html and markdown
library(data.table) # alternative to data.frame
library(plyr)
library(dplyr) # data handling
library(ape)
library(DESeq2) # abundance testing
library(reshape2)
library(scales)
library(knitr)
library(seqtime)
library(ggrepel)
library(nlme)
library(lme4)
library(sciplot)
library(pscl)
library(apeglm)
library(ashr)
library(vsn)
library(hexbin)
library(pheatmap)
library(decontam)
library(Hmisc)
library(picante)
library(emmeans)
library(multcomp)
library(multcompView)

# for appropriate compositional data analysis
library(ALDEx2)
library(compositions)
library(zCompositions)
library(CoDaSeq)
library(propr)
```

# Directory structure (do only once)  

```{r}
# Create Folders as following
#Tables  
dir.create("tables")

# Figures 
dir.create("figures")  

# Phyloseq objects  
dir.create("phyobjects")  

# Custom codes/notes  
dir.create("codes_notes")
```

