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phyto_code/phyto-data-processing-FASTR.Rmd

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+---
+title: "Phytoplankton Data Processing for FASTR"
+author: "Ted Flynn"
+date: "2024-03-18"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+
+suppressWarnings(suppressMessages(library(tidyverse)))
+suppressWarnings(suppressMessages(library(lubridate)))
+suppressWarnings(suppressMessages(library(RColorBrewer)))
+suppressWarnings(suppressMessages(library(vegan)))
+suppressWarnings(suppressMessages(library(janitor)))
+suppressWarnings(suppressMessages(library(here)))
+
+# Set plot output directory 
+plots <- here("phyto-final","plots")
+
+# Set visual theme in ggplot
+theme_set(theme_bw())
+
+# Clean workspace
+rm(list=ls()) 
+
+```
+
+## R Markdown
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r cars}
+summary(cars)
+```
+
+## Including Plots
+
+You can also embed plots, for example:
+
+```{r pressure, echo=FALSE}
+plot(pressure)
+```
+
+Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.