This document provides orientation to the data, code, and outputs provided within the repository.

###---------DATA----------###
The data folder is organized into multiple subfolders, described as follows.
In DataAllASCII, you will find the ASCII files for each pass within a given site on a given day. The files are named SiteCode_YYYY-MM-DD_0_PassNumber.
In DataBlockAreas, you will find the ArcGIS excel output for each unit mapped within a habitat type. This includes the geometric area, latitude, and longitude of each unit. Each file is for a given habitat type.
In DataFlowDiversions, you will find diversion data for the four canals within the management reach (15-min data within 2019-21 sample period and daily data for 1978-2021 study period). You will also find reach gain data, natural flow data, and data on draft dates at Island Park Reservoir as calculated by Rob Van Kirk in code not provided.
In DataFlowMMT, you will find data taken from WinRiverII ADCP measurement summaries estimating streamflow for a given pass on a given date. Each file is for a given single-channel measurement site.
In DataFlowSuitModsBySite, you will find the summary of model type required for a given life stage and site within a given species (file), as well as the relationship between width + flow. These were hand-input from 0_SuitFlowRelationships.RMD and 0_WidthPropFlowRelationships.RMD.
In DataMMTSummary, you will find the WinRiverII ADCP measurement summaries for channel width for a given pass on a given date.
In DataShapeFiles, you will find subfolders for the shapefiles created for the habitat units (Figure 1) and center-line comparison (Figure 4).


We acknowledge that references to site names/habitat types change throughout the data + code as our project evolved + we received reviewer feedback. We did not have an easy way to go back and update all files names and code calls. So please reference the following:
BB1 = SmallPool (within braided reaches, sampled within braids downstream of the Trestle bridge in the lower subreach). Habitat type = BP3 in manuscript (Table 2).
BB2 = MedPool (within braided reaches, sampled within braids downstream of the Trestle bridge in the lower subreach). Habitat type = BP2 in manuscript (Table 2).
BB3 = BigPool (within braided reaches, sampled within braids downstream of the Trestle bridge in the lower subreach). Habitat type= BP1 in manuscript (Table 2).
RR1 and RL1 = BigFlat (within braided reaches, sampled within braids in the upper subreach). Habitat type = BWR in manuscript (Table 2).
RR2 and RL3 = SmallFlat (within braided reaches, sampled within braids in the upper subreach). Habitat type = BNR in manuscript (Table 2).
RR3 and RL2 = BigU (within braided reaches, sampled within braids in the upper subreach). Habitat type = BWB in manuscript (Table 2).
RR4 and RL4 = SmallU (within braided reaches, sampled within braids in the upper subreach). Habitat type = BNB in manuscript (Table 2).
TP0 (within single channel, sampled just upstream of the Trestle bridge at the downstream-most extent of the upper subreach). Habitat type = SP in manuscript (Table 2). 
TP1 (within single channel, sampled in lower subreach). Habitat type = SR in manuscript (Table 2).
TP2 (within single channel, sampled in lower subreach). Habitat type = SB in manuscript (Table 2).


###---------CODE----------###
Code is ordered by number prefix from 0_ to 3_. With one exception, the code should generally be operated in that order if starting from the beginning. However, if downloading the repository in full, then each code piece should run on its own without the need for consecutive runs of individual pieces.

The code 0_ReachGains.R analyzes streamflow in the management reach, both measured in the field and recorded broadly, to quantify reach gains + losses (related to river-aquifer dynamics).
The code 0_SuitFlowRelationships.RMD explores statistical relationships between suitability and streamflow for a given species + life stage at each site. The suitabilites were calculated within 1_SPECIES.R. The information gleaned from this RMD is input back into 1_SPECIES.R.
The RMD output SuitFlowRelationships.html accompainies code 0_SuitFlowRelationships.RMD.
The code 0_WidthPropFlowRelationships.RMD explores statistical relationships between wetted width and streamflow for a given site.
The code 1_SPECIES.R, where species is BrownTrout, RainbowTrout, or MountainWhitefish creates the suitability curves from relevant literature, reads in ADCP data + calculates habitat suitability for each site + streamflow, and calculates continuous WUA.
The code 2_InputsForViz.R takes in the WUA vectors created in 1_SPECIES and creates additional output for 3_VizforPublication.R.
The code 2_VizBySpecies.R takes in WUA vectors created in 1_SPECIES and creates annual output for each species.
The code 3_SensitivityAnalysis.R tests the sensitivity of our WUA output to our habitat type assignments.
The code 3_VizforPublication.R takes in output from 1_SPECIES and 2_InputsForViz to create figures + statistics shown in manuscript.

The code files aictable.R and logit.transform.R are utility files with functions needed to conduct analysis in other code files.

###---------OUTPUT----------###
Organized by subfolders: BrownTrout, MountainWhitefish, RainbowTrout, and Publication. The species folders hold data and graphic output from 1_SPECIES.R, 2_InputsForViz, and 2_VizBySpecies. The Publication folder contains all the figures published in the manuscript and its supplement.