jennytay/futurebioimpacts_flow_temp

Analysis of the impacts to habitat and biology from projected stream flow and temperature changes due to climate change

FutureBioImpacts_Flow_Temp

This repository has data files and R Markdown files that we used to analyze the impacts to biology from projected streamflow and temperature changes due to climate change.

Biology model folder

mod_chub_rf: random forest model that predicts probability of occurence of arroyo chub using streamflow metrics at all timeframes
mod_chub_rf_3: random forest model that predicts probability of occurence of arroyo chub using streamflow metrics at 3-year timeframes
mod_chub_rf_all: random forest model that predicts probability of occurence of arroyo chub using streamflow metrics at all-year timeframes
mod_sucker_rf: random forest model that predicts probability of occurence of Santa Ana sucker using streamflow metrics at all timeframes
mod_sucker_rf_3: random forest model that predicts probability of occurence of Santa Ana sucker using streamflow metrics at 3-year timeframes
mod_sucker_rf_all: random forest model that predicts probability of occurence of Santa Ana sucker using streamflow metrics at all-year timeframes
mod_toad_rf: random forest model that predicts probability of occurence of arroyo toad using streamflow metrics at all timeframes
mod_toad_rf_3: random forest model that predicts probability of occurence of arroyo toad using streamflow metrics at 3-year timeframes
mod_toad_rf_all: random forest model that predicts probability of occurence of arroyo toad using streamflow metrics at all-year timeframes
mod_trout_rf: random forest model that predicts probability of occurence of rainbow trout using streamflow metrics at all timeframes
mod_trout_rf_3: random forest model that predicts probability of occurence of rainbow trout using streamflow metrics at 3-year timeframes
mod_trout_rf_all: random forest model that predicts probability of occurence of rainbow trout using streamflow metrics at all-year timeframes
mod_turtle_rf: random forest model that predicts probability of occurence of western pond turtle using streamflow metrics at all timeframes
mod_vireo_rf: random forest model that predicts probability of occurence of Least Bell's vireo using streamflow metrics at all timeframes
mod_vireo_rf_3: random forest model that predicts probability of occurence of Least Bell's vireo using streamflow metrics at 3-year timeframes
mod_vireo_rf_all: random forest model that predicts probability of occurence of Least Bell's vireo using streamflow metrics at all-year timeframes

Flow Metrics

bsflowmetest.RData: Flow metric predictions for the baseline wet, dry, and moderate year for all the NHD stream reaches in the study region
flowmetdt2.RData: Flow metric predictions for the end-of-century wet, dry and moderate year for all the NHD stream reaches in the study region
flowmet_all.RData: Flow metric predictions for the five flow metrics reported in manuscript one for the baseline and end-of-century wet, dry, and moderate years, for the NHD stream reaches in the study region, after removing the stream reaches that are altered

Stream Temperature Models

max_temp_model.rda: Linear regression model used to predict the maximum 7-day maximum stream temperature
mean_temp_model.rda: Linear regression model used to predict the maximum 7-day mean stream temperature
min_temp_model.rda: Linear regression model used to predict the minimum 7-day minimum stream temperature

Stream temperature

baseline_stream_temp.RData: Baseline annual stream temperature metric data for NHD stream reaches in the study region
baseline_stream_temp_wtrshd: Same as above, with watershed name and stream reach elevation
fut_strm_tmp.RData: Future annual predicted stream temperature metric data for NHD stream reaches in the study region
fut_strm_tmp_wtrshd.RData: Same as above, with watershed name and stream reach elevation
spp_tmp_dat.RData: Species presence and absence data associated with NHD stream reach COMIDs and dates and the modeled baseline temperature metrics
tmp_metrics_change.RData: A shapefile with the difference in the end-of-century and the baseline temperature metrics for all the NHD stream reaches in the study region

geographic data

wtrshd_bundry.RData: Shapefile with the names and geometries of the six watersheds in the study region
elv_comid.RData: Stream elevations from StreamCat for each of the NHD stream reach COMIDs in the study region, along with the 'high' or 'low' designation that we used
NHD_strm_rvr_map.RData: Shapefile of the NHD stream reaches in the study region with COMID, filtered for only streams and rivers
clusters.RData: Shapefile with the selection of NHD stream reaches with no dams in the watershed and in the cluster with low land modifaction that we used in our analysis

Species Data

SppOcc.RData: Dataframe with the species name, COMID and month and year of observation, occurrence outcome, and source of observation.

Scripts

flow.Rmd: Analysis of changes to streamflow
Temp.Rmd: Analysis of changes to stream temperature
bio_predictions.Rmd: Analysis for changes to habitat suitability
Timeframe_Comparrison.Rmd: Comparrison of results from models using short term (3 years) of streamflow data and the entire timeseries
StudyRegionMap.Rmd: script used to prepare the map of the study region for the manuscript