Tree ring analyses after cofecha crossdating & bayesian models of tree ring growth, Water Use Efficiency, and δ13C as presented in our manuscript in Oecologia http://link.springer.com/article/10.1007/s00442-021-04892-0.
Heilman KA, Trouet VM, Belmecheri S, et al (2021) Increased water use efficiency leads to decreased precipitation sensitivity of tree growth, but is offset by high temperatures. Oecologia. https://doi.org/10.1007/s00442-021-04892-0
This repository holds the code used to quantify the effects of climate, tree size, stand strucutre, and CO2 on tree ring growth across the savanna-forest boundary region in the Uppermidwest US. Specifically, we develop bayesian heiarchical models to understand the joint effects of multiple envirmental factors on tree growth across 9 sites in the upper midwest.
It also houses a variety of general scripts used to process tree ring widths, growth sensitivities to climate, and site level differences in climate sensitivity.
Contains R code to run jags bayesian models of tree ring growth and bayesian models of water use efficiency and δ13C . Analysis covers 9 sites across the upper midwest US, spanning the savanna-forest boundary.
- Aggregation of tree ring rwls into a single dataframe, with associated climate data, and back-calculated tree diameter are is conducted in RW_trends.R (calls code from tree_age_agg.R)
- Separation of ring width and iWUE data into testing and training datasets conducted in clean_separate_data.R (Requires outputs from RW_trends.R & calc_WUE.R)
- All bayesian models (including the selected model) explored in this analysis are detailed in RWI_models.Rmd
- Selected tree ring growth model is run in RWI_bayes_model.R (run with globally scaled covarate data)
- Selected tree ring growth model after doing cohort/structure covariate scaling is in RWI_bayes_model_scaled_struct_cohort.R
- Chosen WUE and δ13C bayesian heiarichical models are in WUE_bayes_model
- Paper figures for the manuscript are generated in Paper_figures.R (global scaling) & Paper_figures_cohort_struct_scaled.R
- Summary tables are generated in Summary_tables.Rmd
- WUE tables are generated in WUE_d13C_model_tables.Rmd
- R code used to read in all the δ13C values, correct for the suess effect and do some preliminary plotting and cleaning of the data in read_plot_deltaC.R
- R code used to calucluate intrinsic water use efficiency from the stable isotope values output from read_plot_deltaC.R is calc_WUE.R
Contains R code for detrending tree ring widths, and conducting preliminary correlations with climate for each site.
Contains rcode used to train and demonstrate basic climate correlations and stand mapping for tree ring analyses
- Basic detrending options in dplr are in dplR_detrend.R
- Some code to generate stand maps from plot coordinates is in UNDERC_plot_maps.R
- A basic guide to generating tree ring growth - climate correlations/responses is in Climate_response_UNDERC.R
Contains the code used to read in IRMS data and do standard corrections.
- R code used to read in IRMS raw data and correct for standards IRMS_Data_Process_Raw.R
- R code used to identify potential years with similar climate to do sampling on is in Picking_isotope_years.R
-Stable Isotope & iWUE data: Heilman, K. 2020. Quercus spp Tree Ring Isotopes, Midwest US ver 0. Environmental Data Initiative. https://doi.org/10.6073/pasta/5fb5ebba1cef5c236aba80f32aa771a7 (Accessed 2021-02-18).
-Tree Ring data are archived in site-level zip files: Heilman, K. 2020. Tree Rings, Avon Hills Scientific and Natural Area, Minnesota ver 0. Environmental Data Initiative. https://doi.org/10.6073/pasta/eba1457b8ea2b2da9d7413bca501cd2a (Accessed 2021-02-18).
Heilman, K. 2020. Tree Rings, Bonanza Prairie Scientific and Natural Area ver 0. Environmental Data Initiative. https://doi.org/10.6073/pasta/fc86ca8a52ea170b36ff9456f83b5682 (Accessed 2021-02-18).
Heilman, K. 2020. Tree Rings, Englund Ecotone Scientific and Natural Area, Minnesota ver 0. Environmental Data Initiative. https://doi.org/10.6073/pasta/010be23542658a4cd0e93fd1be6277d8 (Accessed 2021-02-18).
Heilman, K. 2020. Tree Rings, Glacial Park, McHenry County Conservation District, Illinois ver 0. Environmental Data Initiative. https://doi.org/10.6073/pasta/13a05a445fb73b319401fdcfef011935 (Accessed 2021-02-18).
Heilman, K. 2020. Tree Rings, Glacial Lakes State Park Site 1, Minnesota ver 0. Environmental Data Initiative. https://doi.org/10.6073/pasta/70449da6c90055d7b614e8dc2998ba42 (Accessed 2021-02-18).
Heilman, K. 2020. Tree Rings, Glacial Lakes State Park Site 2, Minnesota ver 0. Environmental Data Initiative. https://doi.org/10.6073/pasta/5427c7526f48424fcd8a50474ca20380 (Accessed 2021-02-18).
Heilman, K. 2020. Tree Rings, Glacial Lakes State Park Site 3, Minnesota ver 0. Environmental Data Initiative. https://doi.org/10.6073/pasta/a20a2311145bba28181cea354d9cb505 (Accessed 2021-02-18).
Heilman, K. 2020. Tree Rings, Mound Prairie Scientific and Natural Area, Minnesota ver 0. Environmental Data Initiative. https://doi.org/10.6073/pasta/157f332c116923026be7d781c4f06956 (Accessed 2021-02-18).
Heilman, K. 2020. Tree Rings, Uncas Dunes Scientific and Natural Area, Minnesota ver 0. Environmental Data Initiative. https://doi.org/10.6073/pasta/6229c214814dc38a7bf11cfd57e01eaf (Accessed 2021-02-18).
Please cite the manuscript if using these data, and/or the code: [I'll update manuscript citation details here, once accepted]