CSC-sky-island-forest

USGS Climate Science Center funded project

Project Title: Predicting sky island forest vulnerability to climate change: fine scale climate variability, drought tolerance, and fire response.

Data

Each data file referred to has an associated machine readable metadata file. IF the file is named file.csv, the metadata file is file-metadata.csv. The metadata files describe each variable (column) in the data files.

Tagged trees

We plan to tag 10 individuals per species per mountain range. We will stratify across elevation, aspect and relative slope position by selecting trees from Poulos's plots when possible as described in the proposal methods.

The tree tag numbers, latitude and longitude, etc are stored in data/tagged_trees.csv

Leaf data

From each tagged tree we collected ~10 sun leaves. Five of these were designated "CN leaves" for C:N analysis. The total area and dry mass of these leaves are both stored in data/leaves/CN-leaves.csv with one row per tagged tree. From these data we will calculate LMA. Note that areas are missing for all pines in this file. For pines, we did not use porjected area but instead measured fascicle diameter and needle length. These data are in CN-leaves-pines-dimensions.csv with one row per fascicle. We will summarize these dimensions per tagged tree to calculate equivalent area.

The elemental composition data require 2 files: data/leaves/elemental-analysis-raw.csv which gives isotope and percentage N and C by tray and well and CN-leaves-trays-wells.csv which is a lookup table from tray and well to tree tag number.

See scripts/leaf-data-clean.R for code for cleaning and merging the data for all summer 2014 leaves. The result, CNleaves (a dataframe) contains the locations, species codes, mass and area for LMA, and elemental analysis data on every tree. scripts/leaf-stats.R produces figures and conducts statistical analyses.

Conductance data

Stem conductance data are stored in two files:

• csc-trees-curves.csv : contains one row per conductance measurement
• csc-trees-stems.csv : contains one row per stem measured

The code to calculate conductivities and to create xylem vulnerability curves from these data are in the scripts directory:

1. hydro.R: contains functions for making curve calculations.

2. cond-read-data.R: run our source this file to read in your current data. It hard-codes the paths to your stem and curves files. It also defines a function called "simpleCurve()" which takes on argument which is a tag id (string, not numeric). So, after sourcing our running this file, you can type:

simpleCurve("1012")

To produce a curve for that stem. So this is what you will want to do while running curves. first, start an R session in the scripts directory, then type:

source("cond-read-data.R")
simpleCurve("tag")

If you change the data, resource by rerunning simpleCurve("1012")

3. The final script is cond-make-figs.R produces cleaner figs for curves by species. It sources cond-read-data.R which in turn sources hydro.R.

Reports

Quarterly SC-CSC reports are in SC-CSC-reports folder, named by year and quarter.