1 Biomark, Inc. 705 South 8th St., Boise, Idaho, 83702, USA

Correspondence: Kevin E. See <>

Choosing Habitat Covariates

One of the crucial steps in building this carrying capacity model was choosing which habitat covariates to include. Random forest models naturally incorporate interactions between correlated covariates, which is essential since nearly all habitat variables are considered correlated to one degree or another, however, we aimed to avoid overly redundant variables (i.e., variables that measure similar aspects of the habitat). Further, including too many covariates can result in overfitting of the model (e.g., including as many covariates as data points). Our goal was to select a group of covariates that captured as many different aspects of the stream habitat (e.g., substrate, flow, riparian condition, channel unit configuration, etc.) as possible, while still holding information about fish densities.

To prevent overfitting, we pared down the more than 100 metrics generated by the CHaMP protocol describing the quantity and quality of fish habitat for each survey site. Habitat metrics were first grouped into broad categories that included channel unit configuration, complexity, fish cover, riparian areas, side channels, stream size, substrate, temperature, water quality, and woody debris. Habitat metrics measuring any large wood volume were scaled by the site length (in 100 m units). To assist in determining the habitat metrics to include in the QRF model, we used the Maximal Information-Based Nonparametric Exploration (MINE) class of statistics (Reshef et al. 2011) to determine those habitat characteristics (covariates) most highly associated with the log of observed parr densities. We calculated the maximal information coefficient (MIC), using the R package minerva (Filosi et al. 2019), to measure the strength of the linear or non-linear association between the natural log of fish density and each habitat metric (Reshef et al. 2011). MIC is a measure of correlation that incorporates potential non-linear associations; for example, if there is a quadratic association the MIC value could be high, even when the standard correlation coefficient is low. We excluded categorical variables such as channel type (e.g., meandering, pool-riffle, plane-bed, etc.) because we assumed that other quantitative metrics would capture the differences between those qualitative categorical metrics.

Within each category, metrics were ranked according to their MIC value (Table 1 and Figures 1 and 2). The MIC value of each measured habitat characteristic and parr density was used to inform decisions on which habitat covariates to include in the QRF parr capacity model. We selected one or two variables amongst those with the highest MIC scores within each category, attempting to avoid covariates that were too highly correlated (Table 2), while focusing on covariates we thought could influence fish behavior. For example, cumulative drainage area, mean annual flow and observed discharge are all highly correlated, but fish really only experience the observed discharge, so we chose to include that metric in our QRF model. We also tried to include covariates that can be directly influenced by rehabilitation actions or have been shown to impact salmonid juvenile density. Finally, we attempted to avoid metrics with too many missing values, or too many zero values, in the data set, as well as metrics that may have too much observer error (Rosgen et al. 2018).

Results

We chose 12 metrics, highlighted in bold in Table 1. Their correlations with each other are displayed in Figure 3. Those with a high correlation coefficient (\(\geq\) 0.5 or \(\leq\) -0.5) are plotted against each other in Figure 4 to show the variety in values even for pairs of metrics with relatively high correlations.

Literature Cited

Filosi, M., R. Visintainer, and D. Albanese. 2019. Minerva: Maximal information-based nonparametric exploration for variable analysis.

Reshef, D. N., Y. A. Reshef, H. K. Finucane, S. R. Grossman, G. McVean, P. J. Turnbaugh, E. S. Lander, M. Mitzenmacher, and P. C. Sabeti. 2011. Detecting novel associations in large data sets. Science 334:1518–1524.

Rosgen, D., A. Taillacq, B. Rosgen, and D. Geenen. 2018. A technical review of the Columbia Habitat Monitoring Program’s protocol, data quality.

Tables

Table S1: MIC statistic for top metrics within each habitat category, sorted by category and MIC value. The percent of records for which each habitat metric measurement was missing or zero is also shown. Metrics selected for the QRF model are in bold.
Category Name Abbrv MIC Percent Missing Percent 0-value
ChannelUnit Channel Unit Frequency CU_Freq 0.241 0.021 0.021
ChannelUnit Fast Turbulent Frequency FstTurb_Freq 0.230 0.021 0.082
ChannelUnit Fast NonTurbulent Frequency FstNT_Freq 0.209 0.021 0.308
ChannelUnit Slow Water Frequency SlowWater_Freq 0.208 0.021 0.073
ChannelUnit Fast Turbulent Percent FstTurb_Pct 0.195 0.021 0.082
ChannelUnit Channel Unit Count CU_Ct 0.189 0.021 0.021
ChannelUnit Fast Turbulent Count FstTurb_Ct 0.178 0.021 0.082
ChannelUnit Slow Water Percent SlowWater_Pct 0.177 0.021 0.073
ChannelUnit Fast NonTurbulent Percent FstNT_Pct 0.169 0.021 0.308
ChannelUnit Fast NonTurbulent Count FstNT_Ct 0.166 0.021 0.308
Complexity Wetted Width To Depth Ratio Avg WetWDRat_Avg 0.247 0.003 0.003
Complexity Bankfull Width To Depth Ratio Avg BfWDRat_Avg 0.245 0.003 0.003
Complexity Wetted Depth SD DpthWet_SD 0.232 0.003 0.003
Complexity Wetted Channel Braidedness WetBraid 0.212 0.003 0.003
Complexity Bankfull Channel Braidedness BfBraid 0.211 0.003 0.003
Complexity Wetted Channel Qualifying Island Count Wet_QIsland_Ct 0.209 0.003 0.835
Complexity Bankfull Width CV BfWdth_CV 0.209 0.003 0.003
Complexity Bankfull Width To Depth Ratio CV BfWDRat_CV 0.202 0.003 0.003
Complexity Detrended Elevation SD DetrendElev_SD 0.196 0.003 0.003
Complexity Bankfull Channel Qualifying Island Count Bf_QIsland_Ct 0.193 0.003 0.780
Cover Fish Cover: Total FishCovTotal 0.225 0.021 0.030
Cover Fish Cover: None FishCovNone 0.224 0.021 0.021
Cover Fish Cover: LW FishCovLW 0.213 0.021 0.155
Cover Fish Cover: Terrestrial Vegetation FishCovTVeg 0.204 0.021 0.052
Cover Percent Undercut by Length UcutLgth_Pct 0.185 0.000 0.476
Cover Percent Undercut by Area UcutArea_Pct 0.184 0.000 0.476
Cover Fish Cover: Aquatic Vegetation FishCovAqVeg 0.166 0.296 0.631
Cover Fish Cover: Artificial FishCovArt 0.136 0.021 0.851
Riparian Riparian Cover: Understory RipCovUstory 0.206 0.000 0.000
Riparian RipCovUstoryNone RipCovUstoryNone 0.206 0.000 0.000
Riparian Riparian Cover: No Canopy RipCovCanNone 0.194 0.000 0.000
Riparian Riparian Cover: Some Canopy RipCovCanSome 0.194 0.000 0.095
Riparian Riparian Cover: Big Tree RipCovBigTree 0.184 0.000 0.183
Riparian Riparian Cover: Ground RipCovGrnd 0.182 0.000 0.000
Riparian RipCovGrndNone RipCovGrndNone 0.170 0.000 0.003
Riparian Riparian Cover: Woody RipCovWood 0.168 0.000 0.000
Riparian Riparian Cover: Non-Woody RipCovNonWood 0.166 0.000 0.000
Riparian Riparian Cover: Coniferous RipCovConif 0.164 0.009 0.192
SideChannel Bankfull Side Channel Width BfSCWdth 0.223 0.796 0.796
SideChannel Wetted Side Channel Width WetSCWdth 0.213 0.832 0.832
SideChannel Wetted Side Channel Percent By Area WetSC_Pct 0.209 0.021 0.820
SideChannel SCSm_Freq SCSm_Freq 0.153 0.021 0.921
SideChannel SCSm_Ct SCSm_Ct 0.153 0.021 0.921
SideChannel SC_Area_Pct SC_Area_Pct 0.153 0.021 0.921
Size Mean Annual Flow MeanU 0.346 0.476 0.476
Size Wetted Width Integrated WetWdth_Int 0.332 0.003 0.003
Size Bankfull Width Integrated BfWdthInt 0.324 0.003 0.003
Size Wetted Width Avg WetWdth_Avg 0.324 0.003 0.003
Size Drainage Area (Flowline) CUMDRAINAG 0.302 0.341 0.341
Size Bankfull Width Avg BfWdth_Avg 0.298 0.003 0.003
Size DpthThlwg_Avg DpthThlwg_Avg 0.280 0.003 0.003
Size Discharge Q 0.259 0.037 0.037
Size Bankfull Depth Avg DpthBf_Avg 0.245 0.018 0.018
Size Bankfull Depth Max DpthBf_Max 0.240 0.018 0.018
Substrate Substrate < 6mm SubLT6 0.237 0.049 0.055
Substrate Substrate < 2mm SubLT2 0.227 0.049 0.082
Substrate Substrate: D16 SubD16 0.219 0.012 0.012
Substrate Substrate: Embeddedness Avg SubEmbed_Avg 0.204 0.293 0.317
Substrate Substrate: D50 SubD50 0.197 0.012 0.012
Substrate Substrate Est: Sand and Fines SubEstSandFines 0.190 0.021 0.030
Substrate Substrate Est: Cobbles SubEstCbl 0.185 0.021 0.027
Substrate Substrate: D84 SubD84 0.185 0.012 0.012
Substrate Substrate Est: Boulders SubEstBldr 0.183 0.021 0.149
Substrate Substrate: Embeddedness SD SubEmbed_SD 0.181 0.302 0.320
Temperature Avg. August Temperature avg_aug_temp 0.272 0.000 0.000
Temperature Elev_M Elev_M 0.262 0.363 0.363
Temperature August Temperature aug_temp 0.188 0.155 0.155
Temperature Solar Access: Summer Avg SolarSummr_Avg 0.186 0.070 0.070
WaterQuality Conductivity Cond 0.254 0.024 0.027
WaterQuality Alkalinity Alk 0.225 0.009 0.027
WaterQuality Drift Biomass DriftBioMass 0.000 0.277 0.384
Wood Large Wood Volume: Bankfull Slow Water LWVol_BfSlow 0.213 0.003 0.232
Wood Large Wood Volume: Wetted Slow Water LWVol_WetSlow 0.207 0.003 0.290
Wood Large Wood Frequency: Wetted LWFreq_Wet 0.199 0.003 0.125
Wood Large Wood Volume: Bankfull LWVol_Bf 0.189 0.003 0.085
Wood Large Wood Volume: Wetted Fast Turbulent LWVol_WetFstTurb 0.187 0.003 0.274
Wood Large Wood Frequency: Bankfull LWFreq_Bf 0.178 0.003 0.085
Wood Large Wood Volume: Bankfull Fast NonTurbulent LWVol_BfFstNT 0.175 0.003 0.521
Wood Large Wood Volume: Wetted LWVol_Wet 0.166 0.003 0.125
Wood Large Wood Volume: Wetted Fast NonTurbulent LWVol_WetFstNT 0.159 0.003 0.595
Table S2: Pearson correlation coefficient between each variable within a habitat category.
Category Metric 1 Metric 2 r
Channel Unit Slow Water Frequency Channel Unit Frequency 0.88
Slow Water Count Channel Unit Count 0.87
Fast Turbulent Frequency Channel Unit Frequency 0.84
Fast NonTurbulent Count Fast NonTurbulent Frequency 0.84
Fast Turbulent Count Fast Turbulent Frequency 0.80
Slow Water Count Slow Water Frequency 0.77
Slow Water Percent Fast Turbulent Percent -0.74
Channel Unit Count Channel Unit Frequency 0.73
Fast Turbulent Count Channel Unit Count 0.73
Slow Water Frequency Channel Unit Count 0.69
Fast NonTurbulent Count Fast NonTurbulent Percent 0.65
Fast NonTurbulent Frequency Channel Unit Frequency 0.63
Fast Turbulent Count Channel Unit Frequency 0.60
Slow Water Count Channel Unit Frequency 0.59
Slow Water Frequency Fast Turbulent Frequency 0.59
Fast Turbulent Frequency Channel Unit Count 0.56
Fast NonTurbulent Count Channel Unit Count 0.56
Fast Turbulent Percent Fast NonTurbulent Percent -0.55
Slow Water Count Slow Water Percent 0.54
Fast NonTurbulent Percent Fast NonTurbulent Frequency 0.52
Fast NonTurbulent Frequency Channel Unit Count 0.46
Slow Water Percent Slow Water Frequency 0.46
Fast Turbulent Percent Fast NonTurbulent Count -0.45
Slow Water Count Fast Turbulent Count 0.41
Slow Water Count Fast Turbulent Percent -0.40
Fast NonTurbulent Count Channel Unit Frequency 0.39
Fast Turbulent Count Slow Water Frequency 0.39
Slow Water Frequency Fast NonTurbulent Frequency 0.38
Fast Turbulent Percent Fast NonTurbulent Frequency -0.37
Fast Turbulent Frequency Fast NonTurbulent Frequency 0.36
Fast Turbulent Percent Slow Water Frequency -0.31
Slow Water Count Fast Turbulent Frequency 0.30
Slow Water Count Fast NonTurbulent Count 0.29
Fast Turbulent Percent Channel Unit Count -0.26
Fast Turbulent Count Fast Turbulent Percent 0.26
Slow Water Percent Channel Unit Count 0.26
Slow Water Percent Channel Unit Frequency 0.21
Slow Water Count Fast NonTurbulent Frequency 0.21
Fast NonTurbulent Count Slow Water Frequency 0.20
Fast Turbulent Count Fast NonTurbulent Frequency 0.19
Fast Turbulent Count Fast NonTurbulent Count 0.19
Fast Turbulent Percent Channel Unit Frequency -0.19
Fast Turbulent Count Fast NonTurbulent Percent -0.19
Fast Turbulent Percent Fast Turbulent Frequency 0.18
Slow Water Percent Fast Turbulent Count -0.17
Fast NonTurbulent Percent Fast Turbulent Frequency -0.16
Slow Water Percent Fast NonTurbulent Percent -0.14
Fast NonTurbulent Count Fast Turbulent Frequency 0.13
Fast NonTurbulent Percent Slow Water Frequency -0.11
Slow Water Count Fast NonTurbulent Percent -0.09
Slow Water Percent Fast Turbulent Frequency -0.09
Fast NonTurbulent Percent Channel Unit Count 0.06
Slow Water Percent Fast NonTurbulent Frequency 0.03
Fast NonTurbulent Percent Channel Unit Frequency 0.02
Slow Water Percent Fast NonTurbulent Count 0.01
Complexity Bankfull Width CV Bankfull Width To Depth Ratio CV 0.84
Wetted Channel Braidedness Bankfull Channel Braidedness 0.83
Bankfull Width To Depth Ratio Avg Wetted Width To Depth Ratio Avg 0.78
Wetted Channel Braidedness Wetted Channel Qualifying Island Count 0.78
Bankfull Channel Braidedness Bankfull Channel Qualifying Island Count 0.78
Bankfull Width CV Wetted Width CV 0.76
Wetted Channel Qualifying Island Count Bankfull Channel Qualifying Island Count 0.76
Wetted Channel Braidedness Bankfull Channel Qualifying Island Count 0.66
Bankfull Channel Braidedness Wetted Channel Qualifying Island Count 0.61
Bankfull Width To Depth Ratio CV Wetted Width CV 0.57
Wetted Width CV Wetted Width To Depth Ratio CV 0.57
Thalweg Depth CV Wetted Width To Depth Ratio CV 0.51
Bankfull Width To Depth Ratio CV Wetted Width To Depth Ratio CV 0.50
Bankfull Width CV Wetted Width To Depth Ratio CV 0.46
Thalweg Depth CV Wetted Width CV 0.44
Wetted Depth SD Bankfull Width To Depth Ratio Avg 0.35
Thalweg Depth CV Bankfull Width To Depth Ratio CV 0.30
Thalweg Depth CV Bankfull Width CV 0.29
Wetted Channel Qualifying Island Count Bankfull Width CV 0.25
Bankfull Channel Qualifying Island Count Bankfull Width CV 0.25
Sinuosity Wetted Depth SD 0.24
Detrended Elevation SD Wetted Depth SD 0.23
Bankfull Width CV Wetted Width To Depth Ratio Avg -0.23
Bankfull Channel Qualifying Island Count Bankfull Width To Depth Ratio CV 0.23
Wetted Channel Qualifying Island Count Bankfull Width To Depth Ratio CV 0.22
Wetted Channel Braidedness Bankfull Width CV 0.21
Bankfull Channel Braidedness Bankfull Width CV 0.21
Wetted Depth SD Wetted Width To Depth Ratio Avg 0.21
Sinuosity Wetted Width To Depth Ratio CV 0.20
Bankfull Width To Depth Ratio CV Wetted Width To Depth Ratio Avg -0.20
Bankfull Channel Qualifying Island Count Wetted Width CV 0.20
Sinuosity Bankfull Width To Depth Ratio CV 0.20
Bankfull Channel Braidedness Bankfull Width To Depth Ratio CV 0.19
Wetted Channel Qualifying Island Count Wetted Width CV 0.19
Detrended Elevation SD Bankfull Width To Depth Ratio CV -0.19
Sinuosity Thalweg Depth CV 0.19
Wetted Channel Braidedness Bankfull Width To Depth Ratio CV 0.18
Bankfull Channel Braidedness Wetted Width CV 0.17
Wetted Channel Braidedness Bankfull Width To Depth Ratio Avg 0.17
Bankfull Channel Braidedness Bankfull Width To Depth Ratio Avg 0.16
Detrended Elevation SD Bankfull Width CV -0.16
Wetted Channel Braidedness Wetted Width CV 0.16
Sinuosity Wetted Width CV 0.14
Sinuosity Bankfull Width CV 0.14
Detrended Elevation SD Wetted Width CV -0.13
Detrended Elevation SD Wetted Width To Depth Ratio CV -0.13
Sinuosity Wetted Width To Depth Ratio Avg -0.12
Wetted Channel Qualifying Island Count Bankfull Width To Depth Ratio Avg 0.12
Bankfull Channel Qualifying Island Count Wetted Width To Depth Ratio CV 0.11
Bankfull Channel Qualifying Island Count Bankfull Width To Depth Ratio Avg 0.11
Detrended Elevation SD Thalweg Depth CV -0.11
Bankfull Channel Braidedness Wetted Width To Depth Ratio CV 0.10
Sinuosity Detrended Elevation SD -0.10
Bankfull Width To Depth Ratio Avg Wetted Width CV 0.10
Detrended Elevation SD Bankfull Channel Qualifying Island Count -0.09
Detrended Elevation SD Wetted Channel Qualifying Island Count -0.09
Wetted Channel Qualifying Island Count Wetted Width To Depth Ratio CV 0.08
Wetted Width CV Wetted Width To Depth Ratio Avg -0.08
Bankfull Channel Braidedness Wetted Depth SD 0.08
Wetted Depth SD Wetted Width To Depth Ratio CV 0.08
Detrended Elevation SD Wetted Width To Depth Ratio Avg 0.08
Detrended Elevation SD Wetted Channel Braidedness -0.07
Thalweg Depth CV Bankfull Channel Qualifying Island Count 0.07
Detrended Elevation SD Bankfull Channel Braidedness -0.07
Wetted Depth SD Bankfull Width To Depth Ratio CV 0.07
Bankfull Width To Depth Ratio CV Bankfull Width To Depth Ratio Avg 0.07
Bankfull Channel Braidedness Wetted Width To Depth Ratio Avg 0.07
Wetted Channel Braidedness Wetted Depth SD 0.06
Thalweg Depth CV Wetted Depth SD 0.06
Thalweg Depth CV Bankfull Channel Braidedness 0.06
Sinuosity Bankfull Channel Qualifying Island Count 0.06
Wetted Channel Braidedness Wetted Width To Depth Ratio CV 0.06
Sinuosity Wetted Channel Qualifying Island Count 0.06
Wetted Depth SD Wetted Width CV 0.05
Wetted Channel Braidedness Wetted Width To Depth Ratio Avg 0.04
Bankfull Width To Depth Ratio Avg Wetted Width To Depth Ratio CV 0.04
Thalweg Depth CV Wetted Width To Depth Ratio Avg -0.04
Sinuosity Bankfull Channel Braidedness 0.03
Thalweg Depth CV Bankfull Width To Depth Ratio Avg -0.03
Bankfull Channel Qualifying Island Count Wetted Depth SD 0.03
Wetted Width To Depth Ratio CV Wetted Width To Depth Ratio Avg 0.03
Thalweg Depth CV Wetted Channel Qualifying Island Count 0.02
Wetted Channel Qualifying Island Count Wetted Width To Depth Ratio Avg -0.02
Sinuosity Bankfull Width To Depth Ratio Avg 0.02
Wetted Depth SD Bankfull Width CV 0.02
Sinuosity Wetted Channel Braidedness 0.02
Bankfull Width CV Bankfull Width To Depth Ratio Avg 0.01
Detrended Elevation SD Bankfull Width To Depth Ratio Avg -0.01
Wetted Channel Qualifying Island Count Wetted Depth SD 0.01
Thalweg Depth CV Wetted Channel Braidedness 0.01
Bankfull Channel Qualifying Island Count Wetted Width To Depth Ratio Avg -0.01
Cover Fish Cover: None Fish Cover: Total -0.94
Percent Undercut by Length Percent Undercut by Area 0.80
Fish Cover: Aquatic Vegetation Fish Cover: Total 0.70
Fish Cover: Terrestrial Vegetation Fish Cover: Total 0.68
Fish Cover: None Fish Cover: Aquatic Vegetation -0.67
Fish Cover: Terrestrial Vegetation Fish Cover: None -0.65
Fish Cover: LW Fish Cover: Total 0.54
Fish Cover: LW Fish Cover: None -0.50
Fish Cover: LW Fish Cover: Terrestrial Vegetation 0.35
Fish Cover: Total Percent Undercut by Area 0.29
Fish Cover: Aquatic Vegetation Percent Undercut by Length 0.28
Fish Cover: None Percent Undercut by Area -0.27
Fish Cover: Total Percent Undercut by Length 0.25
Fish Cover: None Percent Undercut by Length -0.22
Fish Cover: LW Percent Undercut by Area 0.20
Fish Cover: Terrestrial Vegetation Percent Undercut by Area 0.20
Fish Cover: Aquatic Vegetation Percent Undercut by Area 0.18
Fish Cover: Artificial Fish Cover: None -0.12
Fish Cover: Artificial Fish Cover: Total 0.11
Fish Cover: LW Percent Undercut by Length 0.11
Fish Cover: Artificial Fish Cover: Aquatic Vegetation 0.07
Fish Cover: Terrestrial Vegetation Percent Undercut by Length 0.06
Fish Cover: Artificial Percent Undercut by Length -0.05
Fish Cover: Artificial Percent Undercut by Area -0.03
Fish Cover: LW Fish Cover: Aquatic Vegetation -0.02
Fish Cover: Terrestrial Vegetation Fish Cover: Aquatic Vegetation 0.02
Fish Cover: LW Fish Cover: Artificial 0.02
Fish Cover: Terrestrial Vegetation Fish Cover: Artificial -0.01
Riparian Riparian Cover: Understory RipCovUstoryNone -1.00
Riparian Cover: No Canopy Riparian Cover: Some Canopy -1.00
Riparian Cover: Ground RipCovGrndNone -0.99
Riparian Cover: Understory Riparian Cover: Woody 0.85
Riparian Cover: Woody RipCovUstoryNone -0.85
Riparian Cover: Ground Riparian Cover: Non-Woody 0.83
Riparian Cover: Big Tree Riparian Cover: No Canopy -0.83
Riparian Cover: Big Tree Riparian Cover: Some Canopy 0.83
Riparian Cover: Non-Woody RipCovGrndNone -0.83
Riparian Cover: Woody Riparian Cover: No Canopy -0.73
Riparian Cover: Woody Riparian Cover: Some Canopy 0.73
Riparian Cover: Big Tree Riparian Cover: Coniferous 0.59
Riparian Cover: Big Tree Riparian Cover: Woody 0.59
Riparian Cover: Coniferous Riparian Cover: No Canopy -0.52
Riparian Cover: Coniferous Riparian Cover: Some Canopy 0.52
Riparian Cover: Understory Riparian Cover: No Canopy -0.49
Riparian Cover: Understory Riparian Cover: Some Canopy 0.49
Riparian Cover: No Canopy RipCovUstoryNone 0.49
RipCovUstoryNone Riparian Cover: Some Canopy -0.49
Riparian Cover: Coniferous Riparian Cover: Woody 0.43
Riparian Cover: Big Tree Riparian Cover: Understory 0.35
Riparian Cover: Big Tree RipCovUstoryNone -0.35
Riparian Cover: Coniferous Riparian Cover: Understory 0.24
Riparian Cover: Coniferous RipCovUstoryNone -0.24
Riparian Cover: Non-Woody Riparian Cover: Woody -0.21
Riparian Cover: Big Tree Riparian Cover: Non-Woody -0.20
Riparian Cover: Non-Woody Riparian Cover: No Canopy 0.17
Riparian Cover: Non-Woody Riparian Cover: Some Canopy -0.17
RipCovUstoryNone RipCovGrndNone 0.17
Riparian Cover: Understory RipCovGrndNone -0.17
Riparian Cover: Ground Riparian Cover: Understory 0.16
Riparian Cover: Ground RipCovUstoryNone -0.16
Riparian Cover: Woody RipCovGrndNone -0.16
Riparian Cover: Ground Riparian Cover: Woody 0.15
Riparian Cover: Coniferous Riparian Cover: Non-Woody -0.13
Riparian Cover: Big Tree Riparian Cover: Ground -0.12
Riparian Cover: Big Tree RipCovGrndNone 0.11
Riparian Cover: Ground Riparian Cover: No Canopy 0.09
Riparian Cover: Ground Riparian Cover: Some Canopy -0.09
Riparian Cover: No Canopy RipCovGrndNone -0.08
RipCovGrndNone Riparian Cover: Some Canopy 0.08
Riparian Cover: Coniferous RipCovGrndNone -0.01
Riparian Cover: Non-Woody Riparian Cover: Understory -0.01
Riparian Cover: Non-Woody RipCovUstoryNone 0.01
Riparian Cover: Coniferous Riparian Cover: Ground 0.00
Side Channel SCSm_Freq SCSm_Ct 0.90
SCSm_Freq SC_Area_Pct 0.49
SCSm_Ct SC_Area_Pct 0.49
Wetted Side Channel Percent By Area SCSm_Ct 0.44
Wetted Side Channel Percent By Area SCSm_Freq 0.40
Wetted Side Channel Percent By Area SC_Area_Pct 0.30
Size Wetted Width Integrated Wetted Width Avg 0.98
Bankfull Width Integrated Bankfull Width Avg 0.97
Bankfull Width Avg Wetted Width Avg 0.95
Wetted Width Integrated Bankfull Width Avg 0.95
Wetted Width Integrated Bankfull Width Integrated 0.92
Bankfull Width Integrated Wetted Width Avg 0.91
Bankfull Depth Avg DpthThlwg_Avg 0.85
Bankfull Depth Max DpthThlwg_Avg 0.84
Bankfull Width Avg Bankfull Depth Avg 0.83
Wetted Width Avg Bankfull Depth Avg 0.82
Wetted Width Avg Discharge 0.82
Bankfull Depth Max Bankfull Depth Avg 0.82
Bankfull Depth Max Residual Pool Depth 0.81
Wetted Width Integrated Discharge 0.79
Bankfull Width Integrated Bankfull Depth Avg 0.79
Wetted Width Integrated Bankfull Depth Avg 0.79
Wetted Width Avg DpthThlwg_Avg 0.79
Wetted Width Integrated DpthThlwg_Avg 0.78
Bankfull Width Avg DpthThlwg_Avg 0.77
Bankfull Width Avg Discharge 0.77
DpthThlwg_Avg Residual Pool Depth 0.76
Bankfull Width Integrated DpthThlwg_Avg 0.75
Bankfull Width Integrated Discharge 0.74
Bankfull Width Avg Bankfull Depth Max 0.74
DpthThlwg_Avg Discharge 0.74
Drainage Area (Flowline) Wetted Width Avg 0.73
Bankfull Width Integrated Bankfull Depth Max 0.73
Drainage Area (Flowline) Wetted Width Integrated 0.72
Drainage Area (Flowline) Bankfull Width Avg 0.72
Drainage Area (Flowline) Discharge 0.70
Wetted Width Avg Bankfull Depth Max 0.70
Bankfull Width Avg Residual Pool Depth 0.69
Wetted Width Integrated Bankfull Depth Max 0.69
Drainage Area (Flowline) Bankfull Width Integrated 0.68
Bankfull Depth Avg Residual Pool Depth 0.68
Bankfull Depth Avg Discharge 0.68
Wetted Width Avg Residual Pool Depth 0.67
Wetted Width Integrated Residual Pool Depth 0.67
Bankfull Width Integrated Residual Pool Depth 0.67
Residual Pool Depth Discharge 0.60
Bankfull Depth Max Discharge 0.59
Drainage Area (Flowline) Bankfull Depth Avg 0.56
Drainage Area (Flowline) Residual Pool Depth 0.54
Drainage Area (Flowline) DpthThlwg_Avg 0.52
Drainage Area (Flowline) Bankfull Depth Max 0.46
Gradient Bankfull Width Avg -0.44
Gradient Bankfull Width Integrated -0.43
Gradient Wetted Width Avg -0.42
Gradient Wetted Width Integrated -0.42
Gradient DpthThlwg_Avg -0.39
Gradient Residual Pool Depth -0.33
Gradient Bankfull Depth Avg -0.33
Drainage Area (Flowline) Gradient -0.31
Gradient Bankfull Depth Max -0.31
Gradient Discharge -0.30
Precipitation Drainage Area (Flowline) -0.15
Precipitation Bankfull Depth Avg 0.11
Precipitation Bankfull Depth Max 0.10
Precipitation DpthThlwg_Avg 0.09
Precipitation Discharge -0.05
Precipitation Gradient 0.03
Precipitation Wetted Width Integrated -0.02
Precipitation Bankfull Width Integrated -0.02
Precipitation Wetted Width Avg -0.02
Precipitation Bankfull Width Avg -0.01
Precipitation Residual Pool Depth -0.01
Substrate Substrate < 2mm Substrate < 6mm 0.95
Substrate: D50 Substrate: D84 0.87
Substrate: Embeddedness Avg Substrate: Embeddedness SD 0.86
Substrate: D84 Substrate Est: Boulders 0.80
Substrate: D50 Substrate Est: Boulders 0.71
Substrate < 2mm Substrate Est: Sand and Fines 0.68
Substrate < 6mm Substrate Est: Sand and Fines 0.67
Substrate Est: Sand and Fines Substrate Est: Cobbles -0.67
Substrate: D16 Substrate: D50 0.61
Substrate Est: Coarse and Fine Gravel Substrate Est: Boulders -0.59
Substrate: D84 Substrate Est: Coarse and Fine Gravel -0.52
Substrate < 6mm Substrate Est: Cobbles -0.46
Substrate: D50 Substrate Est: Sand and Fines -0.45
Substrate: D16 Substrate Est: Sand and Fines -0.43
Substrate < 2mm Substrate Est: Cobbles -0.43
Substrate: D50 Substrate Est: Coarse and Fine Gravel -0.43
Substrate: D16 Substrate Est: Cobbles 0.42
Substrate: Embeddedness Avg Substrate < 2mm 0.42
Substrate: D16 Substrate < 6mm -0.42
Substrate: Embeddedness Avg Substrate Est: Sand and Fines 0.40
Substrate: D50 Substrate Est: Cobbles 0.40
Substrate: D84 Substrate Est: Sand and Fines -0.39
Substrate: D16 Substrate < 2mm -0.39
Substrate: D50 Substrate < 6mm -0.38
Substrate: Embeddedness Avg Substrate < 6mm 0.38
Substrate: D16 Substrate: D84 0.38
Substrate Est: Sand and Fines Substrate Est: Boulders -0.36
Substrate: D50 Substrate < 2mm -0.35
Substrate: Embeddedness SD Substrate < 2mm 0.34
Substrate: D84 Substrate Est: Cobbles 0.33
Substrate: Embeddedness SD Substrate Est: Sand and Fines 0.31
Substrate: Embeddedness SD Substrate < 6mm 0.31
Substrate: Embeddedness Avg Substrate: D16 -0.30
Substrate Est: Coarse and Fine Gravel Substrate Est: Cobbles -0.30
Substrate: D16 Substrate Est: Boulders 0.29
Substrate: D84 Substrate < 6mm -0.28
Substrate: Embeddedness SD Substrate: D16 -0.27
Substrate: Embeddedness Avg Substrate Est: Cobbles -0.25
Substrate: D84 Substrate < 2mm -0.25
Substrate Est: Coarse and Fine Gravel Substrate Est: Sand and Fines -0.23
Substrate < 2mm Substrate Est: Coarse and Fine Gravel -0.22
Substrate Est: Boulders Substrate Est: Cobbles 0.22
Substrate < 6mm Substrate Est: Boulders -0.19
Substrate: Embeddedness SD Substrate Est: Cobbles -0.19
Substrate < 2mm Substrate Est: Boulders -0.19
Substrate: Embeddedness Avg Substrate Est: Coarse and Fine Gravel -0.18
Substrate < 6mm Substrate Est: Coarse and Fine Gravel -0.18
Substrate: Embeddedness Avg Substrate: D50 -0.17
Substrate: Embeddedness SD Substrate Est: Coarse and Fine Gravel -0.15
Substrate: Embeddedness SD Substrate: D50 -0.13
Substrate: D16 Substrate Est: Coarse and Fine Gravel -0.12
Substrate: Embeddedness Avg Substrate: D84 -0.08
Substrate: Embeddedness SD Substrate: D84 -0.05
Substrate: Embeddedness Avg Substrate Est: Boulders -0.03
Substrate: Embeddedness SD Substrate Est: Boulders -0.02
Temperature Avg. August Temperature August Temperature 0.98
Elev_M Avg. August Temperature -0.61
Elev_M August Temperature -0.61
Solar Access: Summer Avg August Temperature 0.19
Solar Access: Summer Avg Avg. August Temperature 0.13
Elev_M Solar Access: Summer Avg 0.12
Water Quality Conductivity Alkalinity 0.78
Alkalinity Drift Biomass 0.16
Conductivity Drift Biomass 0.16
Wood Large Wood Volume: Wetted Slow Water Large Wood Volume: Bankfull Slow Water 0.91
Large Wood Frequency: Wetted Large Wood Frequency: Bankfull 0.91
Large Wood Volume: Wetted Large Wood Volume: Bankfull 0.90
Large Wood Volume: Wetted Large Wood Volume: Wetted Slow Water 0.88
Large Wood Volume: Bankfull Large Wood Volume: Bankfull Slow Water 0.84
Large Wood Volume: Wetted Large Wood Volume: Bankfull Slow Water 0.81
Large Wood Volume: Wetted Fast NonTurbulent Large Wood Volume: Bankfull Fast NonTurbulent 0.79
Large Wood Volume: Bankfull Large Wood Volume: Wetted Slow Water 0.78
Large Wood Volume: Wetted Large Wood Volume: Wetted Fast NonTurbulent 0.60
Large Wood Volume: Bankfull Large Wood Volume: Bankfull Fast NonTurbulent 0.56
Large Wood Volume: Bankfull Large Wood Frequency: Bankfull 0.56
Large Wood Volume: Wetted Large Wood Volume: Wetted Fast Turbulent 0.53
Large Wood Volume: Wetted Large Wood Volume: Bankfull Fast NonTurbulent 0.52
Large Wood Volume: Wetted Large Wood Frequency: Wetted 0.51
Large Wood Volume: Wetted Large Wood Frequency: Bankfull 0.51
Large Wood Volume: Bankfull Large Wood Volume: Wetted Fast NonTurbulent 0.50
Large Wood Volume: Bankfull Large Wood Volume: Wetted Fast Turbulent 0.50
Large Wood Volume: Bankfull Large Wood Frequency: Wetted 0.45
Large Wood Volume: Wetted Slow Water Large Wood Volume: Wetted Fast NonTurbulent 0.45
Large Wood Volume: Bankfull Slow Water Large Wood Frequency: Bankfull 0.43
Large Wood Volume: Wetted Slow Water Large Wood Frequency: Wetted 0.42
Large Wood Volume: Wetted Slow Water Large Wood Volume: Bankfull Fast NonTurbulent 0.40
Large Wood Volume: Wetted Slow Water Large Wood Frequency: Bankfull 0.40
Large Wood Volume: Bankfull Slow Water Large Wood Volume: Wetted Fast NonTurbulent 0.39
Large Wood Volume: Bankfull Slow Water Large Wood Frequency: Wetted 0.39
Large Wood Volume: Bankfull Slow Water Large Wood Volume: Bankfull Fast NonTurbulent 0.38
Large Wood Volume: Wetted Fast Turbulent Large Wood Frequency: Bankfull 0.37
Large Wood Volume: Wetted Fast Turbulent Large Wood Frequency: Wetted 0.35
Large Wood Frequency: Bankfull Large Wood Volume: Bankfull Fast NonTurbulent 0.27
Large Wood Volume: Wetted Fast NonTurbulent Large Wood Frequency: Wetted 0.24
Large Wood Frequency: Wetted Large Wood Volume: Bankfull Fast NonTurbulent 0.22
Large Wood Volume: Wetted Fast NonTurbulent Large Wood Frequency: Bankfull 0.22
Large Wood Volume: Wetted Slow Water Large Wood Volume: Wetted Fast Turbulent 0.15
Large Wood Volume: Bankfull Slow Water Large Wood Volume: Wetted Fast Turbulent 0.14
Large Wood Volume: Wetted Fast Turbulent Large Wood Volume: Wetted Fast NonTurbulent 0.12
Large Wood Volume: Wetted Fast Turbulent Large Wood Volume: Bankfull Fast NonTurbulent 0.12

Figures

Barplots of MIC statistics, faceted by habitat category.

Figure S1: Barplots of MIC statistics, faceted by habitat category.

Barplot of MIC statistics, colored by habitat category.

Figure S2: Barplot of MIC statistics, colored by habitat category.

Correlation plot of habitat metrics used in the QRF model.

Figure S3: Correlation plot of habitat metrics used in the QRF model.

Pairs plot of habitat metrics used in QRF model with a correlation coefficient greater than 0.5 or less than -0.5.

Figure S4: Pairs plot of habitat metrics used in QRF model with a correlation coefficient greater than 0.5 or less than -0.5.