This repository holds the data and code for the manuscript "Native perennial and non-native annual grasses shape pathogen community composition and disease severity in a California grassland" by Amy E. Kendig, Erin R. Spear, S. Caroline Daws, S. Luke Flory, and Erin A. Mordecai published in Journal of Ecology.
- code: descriptions below
- original-data: descriptions below
- intermediate-data: datasets produced by processing original data
- output: outputs of R scripts that are used as inputs to other R scripts or as figures or tables in manuscript
- metadata: metadata for each data file in original-data, see manuscript for details on data collection
- invasion-pathogen-communities.Rproj: RStudio project for running R scripts
| code | desription |
|---|---|
| fungal_data_processing.R | R script to format foliar fungal pathogen isolate data from JRBP compilation |
| damage_data_processing.R | R script to format disease severity data from JRBP compilation |
| background_plant_data_procssing.R | R script to format grass density data from the observational study and manipulated experiment |
| fungal_community_differences.R | R script to assess differences between foliar fungal pathogen communities associated with native perennial and non-native annual grasses (Question 1a) |
| damage_differences.R | R script to assess differences in disease severity between native perennial and non-native annual grasses (Question 1b) |
| fungal_community_host_density.R | R script to assess the effects of native perennial and non-native annual grass densities on foliar fungal pathogen communities (Question 2a) |
| damage_host_density.R | R script to assess the effects of native perennial and non-native annual grass densities on disease severity (Question 2b) |
| density_figures.R | R script to create figures for Questions 2a and 2b |
| manipulated_experiment_map.R | R script to create Fig. S2 |
| data | description |
|---|---|
| 2016ExperimentPlotList_26Apr16_PlotAssignments.csv | treatments applied to plots in the manipulated experiment at JRBP |
| BgPlantSizeStatus_JepsonCalFloraJRBP_021120.csv | species-level data for grasses at JRBP |
| competition_plot_seeds_composition_damage | plant density data collected from the manipulated experiment at JRBP in 2016 |
| Data File 3 - Full Dataset.csv | foliar fungal isolates, sequences, OTUs, and estimated species identities collected from grasses at Jasper Ridge Biological Preserve (JRBP) in 2015-2017 |
| JRBP_PathogenDamage_21July2016_Full.csv | disease severity data collected from grasses in the manipulated experiment and observational study at JRBP in 2016 |
| JRBP_plant_count_combined_2015-04-10.csv | plant density data collected from the observational study at JRBP in 2015 |
| JRBPmidAprPathPrcntDamCulturesData_25Apr2015ERS.csv | disease severity data collected from grasses in the observational study at JRBP in April 2015 |
| JRBPmidMarPathPrcntDamData_5Apr2015ERS.csv | disease severity data collected from grasses in the observational study at JRBP in March 2015 |
| JRBPtransects11to14PathPrcntDam28Apr_7May2015ERS.csv | disease severity data collected from grasses in transects at JRBP in April 2015 |
| transect_seeds_composition_damage.csv | plant density data collected from the observational study at JRBP in 2016 |
Please contact me with any questions about raw data if you are interested in using it for your own project.
Kendig, A. E., E. R. Spear, S. C. Daws, S. L. Flory, and E. A. Mordecai. (2020). Data from: Native perennial and non-native annual grasses shape pathogen community composition and disease severity in a California grassland. (Version v1.0). Zenodo. http://doi.org/10.5281/zenodo.4062434