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phabmetrics's Introduction

Marcus W. Beck, [email protected], Raphael D. Mazor, [email protected], Mark Engeln

PHABMetrics

Travis-CI Build Status AppVeyor Build Status

This package provides functions to calculate PHAB metrics using field data.

Installing the package

The development version of this package can be installed from Github:

install.packages('devtools')
library(devtools)
install_github('SCCWRP/PHABMetrics')
library(PHABMetrics)

Usage

Input data format:

head(sampdat)
## # A tibble: 6 x 12
##   StationCode SampleDate Replicate LocationCode AnalyteName UnitName
##   <chr>       <chr>          <int> <chr>        <chr>       <chr>   
## 1 402M00002   8/13/2015          1 X            Salinity    ppt     
## 2 402M00002   8/13/2015          7 X            Velocity    ft/s    
## 3 402M00002   8/13/2015          6 X            Velocity    ft/s    
## 4 402M00002   8/13/2015         11 X            Velocity    ft/s    
## 5 402M00002   8/13/2015         10 X            Velocity    ft/s    
## 6 402M00002   8/13/2015          8 X            Velocity    ft/s    
## # ... with 6 more variables: VariableResult <chr>, FractionName <chr>,
## #   Result <dbl>, ResQualCode <chr>, QACode <chr>, id <chr>

The core function is phabmetrics(). Calulcate PHAB metrics with sample data:

alldat <- phabmetrics(sampdat)

The following 161 metrics are calculated:

##   [1] "CFC_ALG"       "CFC_ALL_EMAP"  "CFC_ALL_SWAMP" "CFC_AQM"      
##   [5] "CFC_BRS"       "CFC_HUM"       "CFC_LTR"       "CFC_LWD"      
##   [9] "CFC_OHV"       "CFC_RCK"       "CFC_UCB"       "Ev_AqHab"     
##  [13] "Ev_FlowHab"    "Ev_SubNat"     "FL_F"          "FL_M"         
##  [17] "FL_N_F"        "FL_N_M"        "FL_Q_F"        "FL_Q_M"       
##  [21] "H_AqHab"       "H_FlowHab"     "H_SubNat"      "MWVM_F"       
##  [25] "MWVM_M"        "NFC_DLU"       "NFC_EFR"       "NFC_ERN"      
##  [29] "PBM_E"         "PBM_S"         "PBM_V"         "PCT_BDRK"     
##  [33] "PCT_BIGR"      "PCT_CB"        "PCT_CF"        "PCT_CF_WT"    
##  [37] "PCT_CPOM"      "PCT_DR"        "PCT_FAST"      "PCT_FAST_WT"  
##  [41] "PCT_FN"        "PCT_GC"        "PCT_GF"        "PCT_GL"       
##  [45] "PCT_GL_WT"     "PCT_HP"        "PCT_MAA"       "PCT_MAP"      
##  [49] "PCT_MAU"       "PCT_MCP"       "PCT_MIAT1"     "PCT_MIAT1P"   
##  [53] "PCT_MIATP"     "PCT_NSA"       "PCT_OT"        "PCT_POOL"     
##  [57] "PCT_POOL_WT"   "PCT_RA"        "PCT_RA_WT"     "PCT_RC"       
##  [61] "PCT_RI"        "PCT_RI_WT"     "PCT_RN"        "PCT_RN_WT"    
##  [65] "PCT_RR"        "PCT_RS"        "PCT_SA"        "PCT_SAFN"     
##  [69] "PCT_SB"        "PCT_SFGF"      "PCT_SLOW"      "PCT_SLOW_WT"  
##  [73] "PCT_WD"        "PCT_XB"        "PWVZ"          "RBP_CHN"      
##  [77] "RBP_EPI"       "RBP_SED"       "SB_PP_D10"     "SB_PP_D25"    
##  [81] "SB_PP_D50"     "SB_PP_D75"     "SB_PP_D90"     "SB_PT_D10"    
##  [85] "SB_PT_D25"     "SB_PT_D50"     "SB_PT_D75"     "SB_PT_D90"    
##  [89] "SINU"          "SLOPE_0"       "SLOPE_0_5"     "SLOPE_1"      
##  [93] "SLOPE_2"       "W1_HALL_EMAP"  "W1_HALL_SWAMP" "W1H_BLDG"     
##  [97] "W1H_BRDG"      "W1H_CROP"      "W1H_LDFL"      "W1H_LOG"      
## [101] "W1H_MINE"      "W1H_ORVY"      "W1H_PARK"      "W1H_PIPE"     
## [105] "W1H_PSTR"      "W1H_PVMT"      "W1H_ROAD"      "W1H_VEGM"     
## [109] "W1H_WALL"      "XBEARING"      "XBKF_H"        "XBKF_W"       
## [113] "XC"            "XCDENBK"       "XCDENMID"      "XCM"          
## [117] "XCMG"          "XEMBED"        "XFC_ALG"       "XFC_AQM"      
## [121] "XFC_BIG"       "XFC_BRS"       "XFC_HUM"       "XFC_LTR"      
## [125] "XFC_LWD"       "XFC_NAT_EMAP"  "XFC_NAT_SWAMP" "XFC_OHV"      
## [129] "XFC_RCK"       "XFC_UCB"       "XG"            "XGB"          
## [133] "XGH"           "XGW"           "XM"            "XMIAT"        
## [137] "XMIATP"        "XPCAN"         "XPCM"          "XPCMG"        
## [141] "XPGVEG"        "XPMGVEG"       "XPMID"         "XSDGM"        
## [145] "XSLOPE"        "XSPGM"         "XWAK"          "XWDA"         
## [149] "XWDEPTH"       "XWDM"          "XWDO"          "XWDR"         
## [153] "XWIDTH"        "XWPH"          "XWSC"          "XWSL"         
## [157] "XWTB"          "XWTC"          "XWTF"          "XWV_F"        
## [161] "XWV_M"

alldat
##           StationCode CFC_ALG.result CFC_ALL_EMAP.result
## 1 402M00002_8/13/2015             11                   6
## 2  SMC00710_5/20/2009             22                   5
## 3  SMC00957_6/21/2010             77                   7
## 4   SMC04383_6/9/2010              2                   7
##   CFC_ALL_SWAMP.result CFC_AQM.result CFC_BRS.result CFC_HUM.result
## 1                    7             11             11              0
## 2                    6             20             22              0
## 3                    8             56             77             14
## 4                    8             16              6              4
##   CFC_LTR.result CFC_LWD.result CFC_OHV.result CFC_RCK.result
## 1             11              0             11             11
## 2             20              0             22             22
## 3             77              7             77              0
## 4              2              8             16              0
##   CFC_UCB.result Ev_AqHab.count Ev_AqHab.result Ev_FlowHab.count
## 1             11              7       0.9195058                3
## 2              0              8       0.7011374                3
## 3             70              8       0.6239169                5
## 4              2              6       0.7003733                4
##   Ev_FlowHab.result Ev_SubNat.count Ev_SubNat.result  FL_F.result
## 1         0.7394590              10                0  2.855641769
## 2         0.8901335               7                0  0.000000000
## 3         0.5132618               3                0  0.002344635
## 4         0.6979406               8                0 14.754146820
##   FL_M.result FL_N_F.result FL_N_M.result FL_Q_F.result FL_Q_M.result
## 1  0.08086277            NA            NA      2.855642    0.08086277
## 2  0.00000000            NA            NA      0.000000    0.00000000
## 3  0.08280000   0.002344635        0.0828            NA            NA
## 4  0.41779091            NA            NA     14.754147    0.41779091
##   H_AqHab.count H_AqHab.result H_FlowHab.count H_FlowHab.result
## 1             7       1.789276               3        0.8123787
## 2             8       1.457974               3        0.9779116
## 3             8       1.297399               5        0.8260630
## 4             6       1.254901               4        0.9675511
##   H_SubNat.count H_SubNat.result MWVM_F.result MWVM_M.result
## 1             10               0          2.29      0.697992
## 2              7               0          0.58      0.176784
## 3              3               0          1.00      0.304800
## 4              8               0          0.88      0.268224
##   NFC_DLU.result NFC_EFR.result NFC_ERN.result PBM_E.result PBM_S.result
## 1          Other             NO             NO     13.63636     4.545455
## 2 Suburban, Town             NO             NO     40.66667     0.000000
## 3 Suburban, Town             NO             NO     36.36364    45.454545
## 4         Forest             NO             NO      0.00000   100.000000
##   PBM_V.result PCT_BDRK.result PCT_BIGR.result PCT_CB.result PCT_CF.count
## 1     81.81818               0        27.83505      11.34021           10
## 2     59.33333               0        72.44094      32.28346           70
## 3     18.18182               0         0.00000       0.00000           20
## 4      0.00000               0        56.19048      16.19048           20
##   PCT_CF.result PCT_CF.sd PCT_CF_WT.count PCT_CF_WT.result PCT_CPOM.result
## 1           0.0 0.0000000              10                0        20.61856
## 2           0.0 0.0000000              70                0        56.69291
## 3           0.0 0.0000000              20                0        48.57143
## 4           1.5 0.3077935              20                3        26.66667
##   PCT_DR.count PCT_DR.result PCT_DR.sd PCT_FAST.result PCT_FAST_WT.result
## 1           10             0         0             4.0                4.0
## 2           70             0         0            31.5              220.5
## 3           20             0         0            15.5               31.0
## 4           20             0         0            76.5              153.0
##   PCT_FN.result PCT_GC.result PCT_GF.result PCT_GL.count PCT_GL.result
## 1     35.051546      9.278351      4.123711           10            38
## 2      0.000000     39.370079     10.236220           70            64
## 3      0.000000      0.000000     21.904762           20            55
## 4      1.904762     13.333333     28.571429           20            19
##   PCT_GL.sd PCT_GL_WT.count PCT_GL_WT.result PCT_HP.result PCT_MAA.result
## 1  4.817791              10               38             0        2.12766
## 2  3.947481              70              448             0       69.60000
## 3  6.190825              20              110             0       10.47619
## 4  3.079645              20               38             0       36.36364
##   PCT_MAP.result PCT_MAU.result PCT_MCP.result PCT_MIAT1.result
## 1        2.12766       0.000000      13.829787         3.260870
## 2       69.60000       0.000000       3.937008         0.000000
## 3       11.42857       0.952381      39.047619         0.952381
## 4       39.39394       4.040404       0.000000         0.000000
##   PCT_MIAT1P.result PCT_MIATP.result PCT_NSA.result PCT_OT.result
## 1         75.000000         4.347826       5.319149     19.587629
## 2          0.000000        86.842105      69.600000      2.362205
## 3          2.222222        42.857143      12.380952      0.000000
## 4          0.000000        38.775510      39.795918      0.000000
##   PCT_POOL.count PCT_POOL.result PCT_POOL.sd PCT_POOL_WT.count
## 1             10            58.0    3.653005                10
## 2             70             4.5    1.410108                70
## 3             20            29.5    4.459172                20
## 4             20             4.5    1.436370                20
##   PCT_POOL_WT.result PCT_RA.count PCT_RA.result PCT_RA.sd PCT_RA_WT.count
## 1               58.0           10             0         0              10
## 2               31.5           70             0         0              70
## 3               59.0           20             0         0              20
## 4                9.0           20             0         0              20
##   PCT_RA_WT.result PCT_RC.result PCT_RI.count PCT_RI.result PCT_RI.sd
## 1                0             0           10           4.0 0.9660918
## 2                0             0           70          23.5 2.2273010
## 3                0             0           20           0.0 0.0000000
## 4                0             0           20          73.0 2.5567249
##   PCT_RI_WT.count PCT_RI_WT.result PCT_RN.count PCT_RN.result PCT_RN.sd
## 1              10              4.0           10           0.0  0.000000
## 2              70            164.5           70           8.0  2.526096
## 3              20              0.0           20          15.5  1.450953
## 4              20            146.0           20           2.0  2.430075
##   PCT_RN_WT.count PCT_RN_WT.result PCT_RR.result PCT_RS.result
## 1              10                0             0             0
## 2              70               56             0             0
## 3              20               31             0             0
## 4              20                4             0             0
##   PCT_SA.result PCT_SAFN.result PCT_SB.result PCT_SFGF.result
## 1      9.278351        44.32990     7.2164948        48.45361
## 2     14.960630        14.96063     0.7874016        25.19685
## 3     78.095238        78.09524     0.0000000       100.00000
## 4     13.333333        15.23810    20.0000000        43.80952
##   PCT_SLOW.result PCT_SLOW_WT.result PCT_WD.result PCT_XB.result
## 1            96.0               96.0      4.123711      0.000000
## 2            68.5              479.5      0.000000      0.000000
## 3            84.5              169.0      0.000000      0.000000
## 4            23.5               47.0      0.000000      6.666667
##   PWVZ.result RBP_CHN.result RBP_EPI.result RBP_SED.result
## 1    45.45455             NA             NA             NA
## 2    15.78947             19             14             17
## 3     0.00000             NA             NA             NA
## 4     0.00000             17             17             18
##   SB_PP_D10.result SB_PP_D25.result SB_PP_D50.result SB_PP_D75.result
## 1             0.03             0.03             1.03            40.00
## 2             1.03             9.00            40.00           157.00
## 3             1.03             1.03             1.03             1.03
## 4             1.03             9.00            40.00           625.00
##   SB_PP_D90.result SB_PT_D10.result SB_PT_D25.result SB_PT_D50.result
## 1              157             0.03             0.03             1.03
## 2              157             1.03             9.00            40.00
## 3                9             1.03             1.03             1.03
## 4              625             1.03             9.00            40.00
##   SB_PT_D75.result SB_PT_D90.result SINU.NOT_WORKING SLOPE_0.count
## 1            40.00              157         28.64934            10
## 2           157.00              157         31.83260            10
## 3             1.03                9         28.64934            10
## 4           625.00              625         28.64934            10
##   SLOPE_0.result SLOPE_0_5.count SLOPE_0_5.result SLOPE_1.count
## 1         0.0000              10         666.6667            10
## 2       666.6667              10           0.0000            10
## 3       666.6667              10           0.0000            10
## 4       666.6667              10           0.0000            10
##   SLOPE_1.result SLOPE_2.count SLOPE_2.result W1_HALL_EMAP.result
## 1       666.6667            10       666.6667                   4
## 2         0.0000            10         0.0000                   8
## 3         0.0000            10         0.0000                  28
## 4         0.0000            10         0.0000                   8
##   W1_HALL_SWAMP.result W1H_BLDG.count W1H_BLDG.result W1H_BLDG.sd
## 1                    4             11               1           0
## 2                    8             11               2           0
## 3                   28             11               7           0
## 4                    8             11               2           0
##   W1H_BRDG.count W1H_BRDG.result W1H_BRDG.sd W1H_CROP.count
## 1             11               1           0             11
## 2             11               2           0             11
## 3             11               7           0             11
## 4             11               2           0             11
##   W1H_CROP.result W1H_CROP.sd W1H_LDFL.count W1H_LDFL.result W1H_LDFL.sd
## 1               1           0             11               1           0
## 2               2           0             11               2           0
## 3               7           0             11               7           0
## 4               2           0             11               2           0
##   W1H_LOG.count W1H_LOG.result W1H_LOG.sd W1H_MINE.count W1H_MINE.result
## 1            11              1          0             11               1
## 2            11              2          0             11               2
## 3            11              7          0             11               7
## 4            11              2          0             11               2
##   W1H_MINE.sd W1H_ORVY.count W1H_ORVY.result W1H_ORVY.sd W1H_PARK.count
## 1           0             11               1           0             11
## 2           0             11               2           0             11
## 3           0             11               7           0             11
## 4           0             11               2           0             11
##   W1H_PARK.result W1H_PARK.sd W1H_PIPE.count W1H_PIPE.result W1H_PIPE.sd
## 1               1           0             11               1           0
## 2               2           0             11               2           0
## 3               7           0             11               7           0
## 4               2           0             11               2           0
##   W1H_PSTR.count W1H_PSTR.result W1H_PSTR.sd W1H_PVMT.count
## 1             11               1           0             11
## 2             11               2           0             11
## 3             11               7           0             11
## 4             11               2           0             11
##   W1H_PVMT.result W1H_PVMT.sd W1H_ROAD.count W1H_ROAD.result W1H_ROAD.sd
## 1               1           0             11               1           0
## 2               2           0             11               2           0
## 3               7           0             11               7           0
## 4               2           0             11               2           0
##   W1H_VEGM.count W1H_VEGM.result W1H_VEGM.sd W1H_WALL.count
## 1             11               1           0             11
## 2             11               2           0             11
## 3             11               7           0             11
## 4             11               2           0             11
##   W1H_WALL.result W1H_WALL.sd XBEARING.count XBEARING.result XBEARING.sd
## 1               1           0             11     0.009090909 0.003015113
## 2               2           0             12     0.007500000 0.004522670
## 3               7           0             11     0.009090909 0.003015113
## 4               2           0             11     0.009090909 0.003015113
##   XBKF_H.count XBKF_H.result XBKF_H.sd XBKF_W.count XBKF_W.result
## 1           11     0.6590909 0.0202260           11     15.545455
## 2           77     0.4918182 0.7186184           77      6.130909
## 3           22     0.3581818 0.1206189           22      3.029091
## 4           22     0.8645455 0.1197111           22     18.681818
##   XBKF_W.sd XC.count XC.result    XC.sd XCDENBK.count XCDENBK.result
## 1 2.8762349       22  15.11364 14.06781             0             NA
## 2 1.7371500       22  58.75000 25.11580             0             NA
## 3 0.8329232       22  20.68182 24.53353             0             NA
## 4 5.4864019       22  28.97727 21.65282             0             NA
##   XCDENBK.sd XCDENMID.count XCDENMID.result XCDENMID.sd XCM.result
## 1         NA             44        77.00535    35.08415   56.36364
## 2         NA             88        84.75936    18.59386  117.38636
## 3         NA             44        53.87701    34.32184   43.86364
## 4         NA             44        50.00000    35.09978   51.13636
##   XCMG.result XEMBED.count XEMBED.result XEMBED.sd XFC_ALG.count
## 1    80.90909           12      45.41667  30.70818            11
## 2   155.45455           41      13.29268  11.04591            22
## 3    69.09091            0            NA        NA            77
## 4    95.34091           14      44.28571  28.00118            22
##   XFC_ALG.result XFC_ALG.sd XFC_AQM.count XFC_AQM.result XFC_AQM.sd
## 1     12.2727273  10.090500            11      22.954545  23.500484
## 2     22.5000000  14.433757            22       4.545455   1.471225
## 3     84.7727273   8.680948            77       3.636364   2.241411
## 4      0.4545455   1.471225            22      32.954545  35.670753
##   XFC_BIG.result XFC_BRS.count XFC_BRS.result XFC_BRS.sd XFC_HUM.count
## 1      32.500000            11      14.090909   10.44466            11
## 2      62.500000            22       5.000000    0.00000            22
## 3      22.727273            77       5.000000    0.00000            77
## 4       6.818182            22       3.181818    7.32664            22
##   XFC_HUM.result XFC_HUM.sd XFC_LTR.count XFC_LTR.result XFC_LTR.sd
## 1      0.0000000   0.000000            11      10.454545   9.341987
## 2      0.0000000   0.000000            22       4.545455   1.471225
## 3      5.6818182  16.556504            77      20.681818  15.025397
## 4      0.9090909   1.973855            22       2.272727   7.356124
##   XFC_LWD.count XFC_LWD.result XFC_LWD.sd XFC_NAT_EMAP.result
## 1            11      0.0000000   0.000000            83.40909
## 2            22      0.0000000   0.000000            76.13636
## 3            77      0.4545455   1.446825            50.45455
## 4            22      5.4545455   9.625004            32.50000
##   XFC_NAT_SWAMP.result XFC_OHV.count XFC_OHV.result XFC_OHV.sd
## 1            116.81818            11      36.818182   16.39706
## 2             85.22727            22       8.636364    7.89542
## 3             74.77273            77      28.409091   19.76386
## 4             67.72727            22      23.409091   23.53500
##   XFC_RCK.count XFC_RCK.result XFC_RCK.sd XFC_UCB.count XFC_UCB.result
## 1            11           27.5   28.19574            11      5.0000000
## 2            22           62.5   22.75647            22      0.0000000
## 3            77            0.0    0.00000            77     16.5909091
## 4            22            0.0    0.00000            22      0.4545455
##   XFC_UCB.sd XG.result XGB.count XGB.result   XGB.sd XGH.count XGH.result
## 1   0.000000  24.54545        22   82.04545 11.84313        22   19.54545
## 2   0.000000  38.06818        22   14.88636 14.27780        22   12.27273
## 3  16.352959  25.22727        22   20.34091 34.86620        22   20.90909
## 4   1.471225  44.20455        22   33.86364 14.81487        22   21.02273
##      XGH.sd XGW.count XGW.result    XGW.sd XM.count XM.result    XM.sd
## 1  9.116846        22   5.000000  0.000000       22  41.25000 16.63241
## 2  9.847319        22  25.795455 15.047274       22  58.63636 26.91175
## 3 26.865466        22   4.318182  8.632091       22  23.18182 23.74445
## 4 12.165992        22  23.181818  5.884899       22  22.15909 17.17029
##   XMIAT.count XMIAT.result  XMIAT.sd XMIATP.count XMIATP.result XMIATP.sd
## 1          92    0.1032609 0.5372807            4     2.3750000 1.2500000
## 2         114    0.3245614 0.1725967           99     0.3737374 0.1256297
## 3         105    0.1666667 0.3319281           45     0.3888889 0.4147684
## 4          98    0.1173469 0.1613573           38     0.3026316 0.1032887
##   XPCAN.result XPCM.result XPCMG.result XPGVEG.result XPMGVEG.result
## 1    0.9090909           1            1             1              0
## 2    1.0000000           1            1             1              0
## 3    0.6818182           1            1             1              0
## 4    1.0000000           1            1             1              0
##   XPMID.result XSDGM.result XSLOPE.count XSLOPE.result   XSLOPE.sd
## 1     1.000000     1.377776           11   0.009090909 0.003015113
## 2     1.000000    31.377005           12   0.000000000 0.000000000
## 3     1.466667     1.655960           11   0.000000000 0.000000000
## 4     1.000000    39.827686           11   0.000000000 0.000000000
##   XSPGM.result XWAK.result XWDA.count XWDA.result XWDEPTH.count
## 1     1.377776         341         97   0.3629066            97
## 2    31.377005         198        735   0.2432594           735
## 3     1.655960         200        240   0.3511581           240
## 4    39.827686         310        210   0.1377978           210
##   XWDEPTH.result XWDEPTH.sd XWDM.count XWDM.result XWDO.result XWDR.count
## 1      33.845361   24.49036         17    60.17647        3.90         21
## 2       7.733333   20.43468         42    14.21429        8.86        147
## 3       5.116667   22.07518         21     9.47619        7.19         48
## 4      14.600000   18.81383         21    31.09524        9.70         42
##   XWDR.result XWIDTH.count XWIDTH.result XWIDTH.sd XWPH.result XWSC.result
## 1    27.55530           21      9.326190 16.252179        7.62    1806.000
## 2    41.10837          147      3.179048 17.316949        7.91     764.000
## 3    28.47720           48      1.457083  8.350054        7.57    1985.474
## 4    72.57012           42     10.595238 16.582599        8.51    1188.000
##   XWSL.result XWTB.result XWTC.result XWTF.result XWV_F.result
## 1        0.92          NA       20.50      68.900    0.5009091
## 2        0.45        10.8       16.22      61.196    0.1973684
## 3        1.20          NA       18.68      65.624    1.0000000
## 4        0.60          NA       20.90      69.620    0.2287500
##   XWV_M.result
## 1   0.15267709
## 2   0.06015789
## 3   0.30480000
## 4   0.06972300

Required data checks

  • For every function, make sure there are no duplicate or conflicting values for every unique combination of id, LocationCode, AnalyteName, and VariableResult (or Result). This should be specific to the metric classes just to be safe. For example, every combination should have only one entry in VariableResult for AnalyteName %in% c('Microalgae Thickness', 'Macrophyte Cover', 'Macroalgae Cover, Attached', 'Macroalgae Cover, Unattached') for the algae metrics. The algae.R function will remove duplicate entries but a checker should be built that verifies a unique value can be determined.

  • Required column names, see those in sampdat.

  • Check for required values in AnalyteName (note that chkinp() can check of the columns exist but we’ll need a checker on data input to check for these and only these):

    • c('Microalgae Thickness', 'Macrophyte Cover', 'Macroalgae Cover, Attached', 'Macroalgae Cover, Unattached') for algae()
    • c('Bankfull Height', 'Bankfull Width', 'StationWaterDepth', 'Wetted Width') for bankmorph()
    • c('Cascade/Falls', 'Dry', 'Glide', 'Pool', 'Rapid', 'Riffle', 'Run')) for channelmorph()
    • c(Slope', 'Length, Segment', 'Elevation Difference', 'Bearing', 'Proportion', 'Length, Reach') for channelsinuosity()
    • c('Canopy Cover') for densiometer()
    • c('Distance from Bank', 'StationWaterDepth', 'Velocity', 'Distance, Float', 'Float Time', 'Wetted Width') for flow()
    • c('Fish Cover Macrophytes', 'Fish Cover Artificial Structures', 'Fish Cover Boulders', 'Fish Cover Filamentous Algae', 'Fish Cover Woody Debris >0.3 m', 'Fish Cover Live Trees/Roots', 'Fish Cover Overhang.Veg', 'Fish Cover Woody Debris <0.3 m', 'Fish Cover Undercut Banks') for habitat()
    • c('Riparian Bridges/Abutments', 'Riparian Buildings', 'Riparian Landfill/Trash', 'Riparian Logging', 'Riparian Mining', 'Riparian Orchards/Vineyards', 'Riparian Park/Lawn', 'Riparian Pasture/Range', 'Riparian Pavement', 'Riparian Pipes', 'Riparian Road', 'Riparian Row Crops', 'Riparian Vegetation Management', 'Riparian Wall/Dike') for disturbance()
    • c('Riffle/Run Channel Alteration', 'Riffle/Run Epifaunal Substrate', 'Riffle/Run Sediment Deposition', 'Dominant Land Use', 'Evidence of Fire', 'Evidence of Recent Rainfall') for misc()
    • c('Bank Stability') for bankstability()
    • c("Alkalinity as CaCO3", "Oxygen, Dissolved", "pH", "Salinity", "SpecificConductivity", "Temperature", "Turbidity") for quality()
    • c('Riparian GroundCover Barren', 'Riparian GroundCover NonWoody Plants', 'Riparian GroundCover Woody Shrubs', 'Riparian Lower Canopy All Vegetation', 'Riparian Upper Canopy All Trees', 'Riparian Lower Canopy All Vegetation', 'Riparian Upper Canopy All Trees', 'Riparian GroundCover Woody Shrubs', 'Riparian GroundCover NonWoody Plants') for ripveg()
    • c('Substrate Size Class', 'Embeddedness', 'CPOM') for substrate()

  • Check for required values in LocationCode (note that chkinp() can check if the columns exist but we’ll need a checker on data input to check for these and only these)

  • Maybe we need to add a checker to make sure all values in each field are present but with appropriate NA values for Result, VariableResult, this can be done with tidyr::complete() but may be unnecessary since this will increase data volume

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Contributors

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