The pace of life for forest trees
Creators: name: Bialic-Murphy, Lalasia
name: McElderry, Robert
Publisher: name: Zenodo
Year: 2024

description: The input data needed to replicate the analyses for the paper titled: 'The pace of life for forest trees'. 

Readme file for the paper titled: The pace of life for forest trees.

Bialic-Murphy, et al 2024

 

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Data:

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Initial inputs

TreeMort_TreeData.Rdata --Cannot share original data due to third-party data restrictions. The included subset are the data from networks that are fully open access. The other datasets can be accessed by submitting a data request to the networks. See DMA statement for more details

hex_250k.csv --Contains climate data at grid cell level. Data coordinates are not provided due to sensitive species.

 

Outputs from Script 1 and grid-level input data needed to replicate models and analysis, i.e., Script 2 - 6

TreeMort_Growth_1yr_woGrid.Rdata --Growth function parameters

TreeMort_sigmag_1yr_woGrid.Rdata --Variance estimates for growth function

TreeMort_Survival_1yr_woGrid.Rdata --Survival function parameters

Min_Max_Size.Rdata --Species size characteristics

Forest network data that included sensitive species and indigenous data sovereignty were not included in this paper, but these data are available for research purposes by submitting a data request to the following networks: Alberta Forestry Division forestry.alberta.ca, Saskatchewan Minister of Environment https://geohub.saskatchewan.ca, British Columbia https://www2.gov.bc.ca/gov, Placette-échantillon permanente Données Québec donneesquebec.ca,  ForestGeo https://forestgeo.si.edu, and ForestPlots.

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R code associated needed to replicate the results of this study are available at https://github/Lalasia/pace_of_life.com

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1_Fit_Vital_R  --Load data and fit vital rate functions.

2_IPM_4_HPC.R  --Load vital rate parameter estimates, set up IPMs, calculate LHTs 

2_IPM_4_HPC.sh  --Sets up 2_IPM_4_HPC.R to run on an HPC.

3_IPM_postProc.R  --Compiles all runs generated from 2_IPM_4_HPC.R. Creates data files for subsequent scripts

4_Clusters_analysis.R  --Runs cluster analysis and generates figures

5_Bayesian_model.R  --Runs analysis of environmental effects on LHTs

6_Hull_volume.R --Calculates the convex hull of LHTs and analyses patterns

Error_Checks --Contains modified versions of 2_IPM_4_HPC.sh and 2_IPM_4_HPC.R (See Note 2 below).

 

--Run these scripts to recreate our analyses and results.

 

--NOTE 1 | The raw data from networks with sensitive species and data restrictions are not included here but can be accessed by submitting a data request to the associated networks. See our DMA statement for more details.

Here, we provide the raw tree-by-tree data from the fully open-access networks. This affects the first R script only. The grid-level output data, generated in script 1 and shared in the data folder, can be used to replicate the results of this study.

 

--NOTE 2 | The bash script [2_IPM_4_HPC.sh] sets up an array to run the IPM script [2_IPM_4_HPC.R] in batches of 100 species on a high-performance computing cluster.

 

We ran into an issue for two species [index=30 & 962] that had an immortal survival-growth matrix. To find this error, we duplicated the IPM R and bash scripts and modified the indexing. These files are in the folder named "Error Check".

 

3_IPM_postProc.R is then used to recompile the IPM outputs.

 

--Data inputs required for these scripts and the intermediate output data that are both produced and later required by these scripts are stored in the folder named "data".

 

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