Adding test files to lab report book

Lab report/OA.qmd

@@ -0,0 +1,41 @@
+## Ocean acificiation indicator
+
+### Sent by F. Gomez on 02/19/2023
+
+Notes from Fabian:
+
+derived surface omega series from the MOM-Topaz hindcast 0.10deg resolution model \*txt files have this structure: column1: year, column2=month, and column3=carbon system variable The mean magnitude of the simulated omega trends, around 9e-3 year-1, is consistent with observed trends in the Subtropical North Atlantic
+
+Question: What is causing the acceleration after 2008?\
+Answer: made a Taylor decomposition to figure out what was driving that acceleration in the simulated ??Ar anomaly. Interannual ??Ar changes were mostly driven by the balance between dic and alkalinity. There was a positive trend from the 1980s until mid 2000s, which contributed to moderate the ??Ar decline. But that trend vanished in the last 15 years or so, which probably has to do with this accelerated decline in ??Ar in the last decade. 
+
+```{r}
+rm(list = ls())
+
+dat <- read.table("../../indicator_data/surface_omega_series.txt", skip = 0, header = F)
+head(dat)
+tail(dat)
+dat$dates <- paste0(month.abb[dat$V2], dat$V1)
+```
+
+Format indicator object
+
+```{r}
+datdata <- dat$dates 
+inddata <- data.frame(dat$V3) 
+labs <- c("Ocean acidification", "Surface aragonite saturation", "") 
+indnames <- data.frame(matrix(labs, nrow = 3, byrow = F)) 
+s <- list(labels = indnames, indicators = inddata, datelist = datdata)
+class(s) <-"indicatordata"
+```
+
+Save and plot 
+
+```{r}
+plotIndicatorTimeSeries(s)
+inddata <- s 
+save(inddata, file = "../../indicator_objects/OA.RData")
+```
+
+
+

Lab report/_quarto.yml

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+project:
+  type: book
+
+book:
+  title: "Caribbean ESR Lab Report"
+  author: "Carissa Gervasi"
+  date: "2/6/2024"
+
+
+  chapters:
+    - index.qmd
+    - part: "Part 1: Indicators"
+      chapters:
+      - OA.qmd
+    - part: "Second Part"
+      chapters:
+      - Products/Products.qmd
+    - references.qmd
+
+bibliography: references.bib
+
+format:
+  html:
+    theme: flatly
+  pdf:
+    documentclass: scrreprt
+
+editor: visual

Lab report/index.qmd

@@ -4,23 +4,10 @@ format: html
 editor: visual
 ---
 
-## Quarto
+## ESR Lab Reports
 
-Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
+ESR lab reports are quarto books that compile the R scripts for each indicator as well as any other descriptions of how the ESR will be put together. 
 
-## Running Code
+## Caribbean ESR
 
-When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
-
-```{r}
-1 + 1
-```
-
-You can add options to executable code like this
-
-```{r}
-#| echo: false
-2 * 2
-```
-
-The `echo: false` option disables the printing of code (only output is displayed).
+This lab report is for the Caribbean ESR that was compiled from 2023-2024. This is the first ESR for the Caribbean region. Here we can add more text about why this ESR is being compiled.