README.md
In SCCWRP/PHABMetrics: Tools For Calculating PHAB Metrics
Marcus W. Beck, marcusb@sccwrp.org, Robert Butler, r7butler@yahoo.com, Raphael D. Mazor, raphaelm@sccwrp.org, Mark Engeln
PHABMetrics
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)
## id StationCode SampleDate SampleAgencyCode
## 1 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## 2 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## 3 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## 4 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## 5 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## 6 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## LocationCode Replicate MethodName AnalyteName FractionName UnitName
## 1 X 1 FieldMeasure pH None none
## 2 X 1 FieldMeasure Temperature None Deg C
## 3 X 4 Velocity Area Velocity None ft/s
## 4 X 6 Velocity Area Velocity None ft/s
## 5 X 8 Velocity Area Velocity None ft/s
## 6 X 12 Velocity Area Velocity None ft/s
## Result ResQualCode QACode VariableResult
## 1 NA NR FEU Not Recorded
## 2 15.20 = None NA
## 3 0.72 = None NA
## 4 1.12 = None NA
## 5 1.01 = None NA
## 6 0.00 = None NA
The core function is phabmetrics(). Calulcate PHAB metrics with sample
data:
alldat <- phabmetrics(sampdat)
## [1] "XWIDTHdata"
## [1] id result
## <0 rows> (or 0-length row.names)
## [1] "XWIDTH.sd"
## 105PS0231_2013-08-29_DFW-ABL 205PS0202_2013-07-17_MPSL-DFW
## 4.03 0.64
## 308PS0204_2013-05-21_DFW-ABL 520PS0455_2013-07-22_MPSL-DFW
## 3.00 7.49
## [1] "results"
## PCT_CF.result PCT_CF.count PCT_CF.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0.0
## 205PS0202_2013-07-17_MPSL-DFW 0 10 0.0
## 308PS0204_2013-05-21_DFW-ABL 0 10 0.0
## 520PS0455_2013-07-22_MPSL-DFW 1 10 3.2
## PCT_DR.result PCT_DR.count PCT_DR.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0
## 205PS0202_2013-07-17_MPSL-DFW 0 10 0
## 308PS0204_2013-05-21_DFW-ABL 0 10 0
## 520PS0455_2013-07-22_MPSL-DFW 0 10 0
## PCT_GL.result PCT_GL.count PCT_GL.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0.0
## 205PS0202_2013-07-17_MPSL-DFW 71 10 19.8
## 308PS0204_2013-05-21_DFW-ABL 3 10 4.8
## 520PS0455_2013-07-22_MPSL-DFW 48 10 25.2
## PCT_POOL.result PCT_POOL.count PCT_POOL.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0.0
## 205PS0202_2013-07-17_MPSL-DFW 0 10 0.0
## 308PS0204_2013-05-21_DFW-ABL 1 10 3.2
## 520PS0455_2013-07-22_MPSL-DFW 14 10 23.1
## PCT_RA.result PCT_RA.count PCT_RA.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0
## 205PS0202_2013-07-17_MPSL-DFW 0 10 0
## 308PS0204_2013-05-21_DFW-ABL 0 10 0
## 520PS0455_2013-07-22_MPSL-DFW 0 10 0
## PCT_RI.result PCT_RI.count PCT_RI.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0.0
## 205PS0202_2013-07-17_MPSL-DFW 29 10 19.8
## 308PS0204_2013-05-21_DFW-ABL 94 10 8.4
## 520PS0455_2013-07-22_MPSL-DFW 22 10 31.6
## PCT_RN.result PCT_RN.count PCT_RN.sd
## 105PS0231_2013-08-29_DFW-ABL 100 10 0.0
## 205PS0202_2013-07-17_MPSL-DFW 0 10 0.0
## 308PS0204_2013-05-21_DFW-ABL 2 10 4.2
## 520PS0455_2013-07-22_MPSL-DFW 14 10 19.6
## PCT_FAST.result PCT_SLOW.result
## 105PS0231_2013-08-29_DFW-ABL 100 0
## 205PS0202_2013-07-17_MPSL-DFW 29 71
## 308PS0204_2013-05-21_DFW-ABL 96 4
## 520PS0455_2013-07-22_MPSL-DFW 37 62
## PCT_CF_WT.result PCT_CF_WT.count
## 105PS0231_2013-08-29_DFW-ABL 0 10
## 205PS0202_2013-07-17_MPSL-DFW 0 10
## 308PS0204_2013-05-21_DFW-ABL 0 10
## 520PS0455_2013-07-22_MPSL-DFW 1 10
## PCT_GL_WT.result PCT_GL_WT.count
## 105PS0231_2013-08-29_DFW-ABL 0 10
## 205PS0202_2013-07-17_MPSL-DFW 71 10
## 308PS0204_2013-05-21_DFW-ABL 3 10
## 520PS0455_2013-07-22_MPSL-DFW 48 10
## PCT_POOL_WT.result PCT_POOL_WT.count
## 105PS0231_2013-08-29_DFW-ABL 0 10
## 205PS0202_2013-07-17_MPSL-DFW 0 10
## 308PS0204_2013-05-21_DFW-ABL 1 10
## 520PS0455_2013-07-22_MPSL-DFW 14 10
## PCT_RA_WT.result PCT_RA_WT.count
## 105PS0231_2013-08-29_DFW-ABL 0 10
## 205PS0202_2013-07-17_MPSL-DFW 0 10
## 308PS0204_2013-05-21_DFW-ABL 0 10
## 520PS0455_2013-07-22_MPSL-DFW 0 10
## PCT_RI_WT.result PCT_RI_WT.count
## 105PS0231_2013-08-29_DFW-ABL 0 10
## 205PS0202_2013-07-17_MPSL-DFW 29 10
## 308PS0204_2013-05-21_DFW-ABL 94 10
## 520PS0455_2013-07-22_MPSL-DFW 22 10
## PCT_RN_WT.result PCT_RN_WT.count
## 105PS0231_2013-08-29_DFW-ABL 100 10
## 205PS0202_2013-07-17_MPSL-DFW 0 10
## 308PS0204_2013-05-21_DFW-ABL 2 10
## 520PS0455_2013-07-22_MPSL-DFW 14 10
## PCT_FAST_WT.result PCT_SLOW_WT.result
## 105PS0231_2013-08-29_DFW-ABL 100 0
## 205PS0202_2013-07-17_MPSL-DFW 29 71
## 308PS0204_2013-05-21_DFW-ABL 96 4
## 520PS0455_2013-07-22_MPSL-DFW 37 62
## PCT_FAST.count PCT_SLOW.count
## 105PS0231_2013-08-29_DFW-ABL 4 2
## 205PS0202_2013-07-17_MPSL-DFW 4 2
## 308PS0204_2013-05-21_DFW-ABL 4 2
## 520PS0455_2013-07-22_MPSL-DFW 4 2
## PCT_FAST_WT.count PCT_SLOW_WT.count
## 105PS0231_2013-08-29_DFW-ABL 4 2
## 205PS0202_2013-07-17_MPSL-DFW 4 2
## 308PS0204_2013-05-21_DFW-ABL 4 2
## 520PS0455_2013-07-22_MPSL-DFW 4 2
## H_FlowHab.result H_FlowHab.count
## 105PS0231_2013-08-29_DFW-ABL 0.00 1
## 205PS0202_2013-07-17_MPSL-DFW 0.60 2
## 308PS0204_2013-05-21_DFW-ABL 0.29 4
## 520PS0455_2013-07-22_MPSL-DFW 1.29 5
## Ev_FlowHab.result Ev_FlowHab.count
## 105PS0231_2013-08-29_DFW-ABL 0.00 1
## 205PS0202_2013-07-17_MPSL-DFW 0.87 2
## 308PS0204_2013-05-21_DFW-ABL 0.21 4
## 520PS0455_2013-07-22_MPSL-DFW 0.80 5
## [1] "results$PCT_CF.sd"
## [1] 0.0 0.0 0.0 3.2
## [1] "results$PCT_DR.sd"
## [1] 0 0 0 0
## [1] "results$PCT_GL.sd"
## [1] 0.0 19.8 4.8 25.2
## [1] "W1H_BRDG"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_D~ Riparian Bridges/Abut~ 0 22 0 W1H_BR~
## 2 205PS0202_2013-07-17_M~ Riparian Bridges/Abut~ 0 22 0 W1H_BR~
## 3 520PS0455_2013-07-22_M~ Riparian Bridges/Abut~ 0 22 0 W1H_BR~
## 4 105PS0231_2013-08-29_D~ Riparian Bridges/Abut~ 0 22 0 W1H_BR~
## [1] "W1H_BLDG"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-A~ Riparian Buildings 0 22 0 W1H_BL~
## 2 205PS0202_2013-07-17_MPSL-~ Riparian Buildings 0.728 22 0.131 W1H_BL~
## 3 520PS0455_2013-07-22_MPSL-~ Riparian Buildings 0.182 22 0.304 W1H_BL~
## 4 105PS0231_2013-08-29_DFW-A~ Riparian Buildings 0 22 0 W1H_BL~
## [1] "W1H_LDFL"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DF~ Riparian Landfill/Tr~ 0.25 22 0.551 W1H_LD~
## 2 205PS0202_2013-07-17_MP~ Riparian Landfill/Tr~ 0.477 22 0.715 W1H_LD~
## 3 520PS0455_2013-07-22_MP~ Riparian Landfill/Tr~ 0.136 22 0.441 W1H_LD~
## 4 105PS0231_2013-08-29_DF~ Riparian Landfill/Tr~ 0 22 0 W1H_LD~
## [1] "W1H_LOG"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-ABL Riparian Logging 0 22 0 W1H_LOG
## 2 205PS0202_2013-07-17_MPSL-DFW Riparian Logging 0 22 0 W1H_LOG
## 3 520PS0455_2013-07-22_MPSL-DFW Riparian Logging 0 22 0 W1H_LOG
## 4 105PS0231_2013-08-29_DFW-ABL Riparian Logging 0 22 0 W1H_LOG
## [1] "W1H_MINE"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-ABL Riparian Mining 0 22 0 W1H_MINE
## 2 205PS0202_2013-07-17_MPSL-DFW Riparian Mining 0 22 0 W1H_MINE
## 3 520PS0455_2013-07-22_MPSL-DFW Riparian Mining 0 22 0 W1H_MINE
## 4 105PS0231_2013-08-29_DFW-ABL Riparian Mining 0 22 0 W1H_MINE
## [1] "W1H_ORVY"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_D~ Riparian Orchards/Vin~ 0 22 0 W1H_OR~
## 2 205PS0202_2013-07-17_M~ Riparian Orchards/Vin~ 0 22 0 W1H_OR~
## 3 520PS0455_2013-07-22_M~ Riparian Orchards/Vin~ 0 22 0 W1H_OR~
## 4 105PS0231_2013-08-29_D~ Riparian Orchards/Vin~ 0 22 0 W1H_OR~
## [1] "W1H_PARK"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-A~ Riparian Park/Lawn 0 22 0 W1H_PA~
## 2 205PS0202_2013-07-17_MPSL-~ Riparian Park/Lawn 0.114 22 0.376 W1H_PA~
## 3 520PS0455_2013-07-22_MPSL-~ Riparian Park/Lawn 0 22 0 W1H_PA~
## 4 105PS0231_2013-08-29_DFW-A~ Riparian Park/Lawn 0 22 0 W1H_PA~
## [1] "W1H_PSTR"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW~ Riparian Pasture/Ra~ 0 22 0 W1H_PS~
## 2 205PS0202_2013-07-17_MPS~ Riparian Pasture/Ra~ 0 22 0 W1H_PS~
## 3 520PS0455_2013-07-22_MPS~ Riparian Pasture/Ra~ 0 22 0 W1H_PS~
## 4 105PS0231_2013-08-29_DFW~ Riparian Pasture/Ra~ 0 22 0 W1H_PS~
## [1] "W1H_PVMT"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-ABL Riparian Pavement 0.0303 22 0.142 W1H_PV~
## 2 205PS0202_2013-07-17_MPSL-D~ Riparian Pavement 0 22 0 W1H_PV~
## 3 520PS0455_2013-07-22_MPSL-D~ Riparian Pavement 0.273 22 0.336 W1H_PV~
## 4 105PS0231_2013-08-29_DFW-ABL Riparian Pavement 0 22 0 W1H_PV~
## [1] "W1H_PIPE"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-ABL Riparian Pipes 0 22 0 W1H_PIPE
## 2 205PS0202_2013-07-17_MPSL-DFW Riparian Pipes 0 22 0 W1H_PIPE
## 3 520PS0455_2013-07-22_MPSL-DFW Riparian Pipes 0 22 0 W1H_PIPE
## 4 105PS0231_2013-08-29_DFW-ABL Riparian Pipes 0 22 0 W1H_PIPE
## [1] "W1H_ROAD"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-ABL Riparian Road 0.243 22 0.328 W1H_ROAD
## 2 205PS0202_2013-07-17_MPSL-DFW Riparian Road 0 22 0 W1H_ROAD
## 3 520PS0455_2013-07-22_MPSL-DFW Riparian Road 0.0455 22 0.213 W1H_ROAD
## 4 105PS0231_2013-08-29_DFW-ABL Riparian Road 0 22 0 W1H_ROAD
## [1] "W1H_CROP"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-A~ Riparian Row Crops 0 22 0 W1H_CR~
## 2 205PS0202_2013-07-17_MPSL-~ Riparian Row Crops 0 22 0 W1H_CR~
## 3 520PS0455_2013-07-22_MPSL-~ Riparian Row Crops 0 22 0 W1H_CR~
## 4 105PS0231_2013-08-29_DFW-A~ Riparian Row Crops 0 22 0 W1H_CR~
## [1] "W1H_VEGM"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21~ Riparian Vegetation Man~ 0 22 0 W1H_VE~
## 2 205PS0202_2013-07-17~ Riparian Vegetation Man~ 0 22 0 W1H_VE~
## 3 520PS0455_2013-07-22~ Riparian Vegetation Man~ 0 22 0 W1H_VE~
## 4 105PS0231_2013-08-29~ Riparian Vegetation Man~ 0 22 0 W1H_VE~
## [1] "W1H_WALL"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-A~ Riparian Wall/Dike 0.136 22 0.441 W1H_WA~
## 2 205PS0202_2013-07-17_MPSL-~ Riparian Wall/Dike 0.545 22 0.575 W1H_WA~
## 3 520PS0455_2013-07-22_MPSL-~ Riparian Wall/Dike 0.636 22 0.727 W1H_WA~
## 4 105PS0231_2013-08-29_DFW-A~ Riparian Wall/Dike 0 22 0 W1H_WA~
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning in max(df$Result, na.rm = T): no non-missing arguments to max;
## returning -Inf
## # A tibble: 22 x 8
## SampleAgencyCode LocationCode MethodName `Riparian Groun~
## <chr> <chr> <chr> <chr>
## 1 DFW-ABL BlockA, Left FieldObse~ 2
## 2 DFW-ABL BlockA, Rig~ FieldObse~ 3
## 3 DFW-ABL BlockB, Left FieldObse~ 2
## 4 DFW-ABL BlockB, Rig~ FieldObse~ 4
## 5 DFW-ABL BlockC, Left FieldObse~ 2
## 6 DFW-ABL BlockC, Rig~ FieldObse~ 4
## 7 DFW-ABL BlockD, Left FieldObse~ 4
## 8 DFW-ABL BlockD, Rig~ FieldObse~ 4
## 9 DFW-ABL BlockE, Left FieldObse~ 2
## 10 DFW-ABL BlockE, Rig~ FieldObse~ 4
## # ... with 12 more rows, and 4 more variables: `Riparian GroundCover Woody
## # Shrubs` <chr>, `Riparian Lower Canopy All Vegetation` <chr>, `Riparian
## # Upper Canopy All Trees` <chr>, GroundCoverPresence <lgl>
## [1] 22
## [1] 22
## # A tibble: 22 x 8
## SampleAgencyCode LocationCode MethodName `Riparian Groun~
## <chr> <chr> <chr> <chr>
## 1 MPSL-DFW BlockA, Left FieldObse~ 3
## 2 MPSL-DFW BlockA, Rig~ FieldObse~ 0
## 3 MPSL-DFW BlockB, Left FieldObse~ 3
## 4 MPSL-DFW BlockB, Rig~ FieldObse~ 1
## 5 MPSL-DFW BlockC, Left FieldObse~ 1
## 6 MPSL-DFW BlockC, Rig~ FieldObse~ 1
## 7 MPSL-DFW BlockD, Left FieldObse~ 1
## 8 MPSL-DFW BlockD, Rig~ FieldObse~ 0
## 9 MPSL-DFW BlockE, Left FieldObse~ 0
## 10 MPSL-DFW BlockE, Rig~ FieldObse~ 1
## # ... with 12 more rows, and 4 more variables: `Riparian GroundCover Woody
## # Shrubs` <chr>, `Riparian Lower Canopy All Vegetation` <chr>, `Riparian
## # Upper Canopy All Trees` <chr>, GroundCoverPresence <lgl>
## [1] 22
## [1] 20
## # A tibble: 22 x 8
## SampleAgencyCode LocationCode MethodName `Riparian Groun~
## <chr> <chr> <chr> <chr>
## 1 DFW-ABL BlockA, Left FieldObse~ 1
## 2 DFW-ABL BlockA, Rig~ FieldObse~ 1
## 3 DFW-ABL BlockB, Left FieldObse~ 1
## 4 DFW-ABL BlockB, Rig~ FieldObse~ 2
## 5 DFW-ABL BlockC, Left FieldObse~ 0
## 6 DFW-ABL BlockC, Rig~ FieldObse~ 1
## 7 DFW-ABL BlockD, Left FieldObse~ 1
## 8 DFW-ABL BlockD, Rig~ FieldObse~ 1
## 9 DFW-ABL BlockE, Left FieldObse~ 2
## 10 DFW-ABL BlockE, Rig~ FieldObse~ 1
## # ... with 12 more rows, and 4 more variables: `Riparian GroundCover Woody
## # Shrubs` <chr>, `Riparian Lower Canopy All Vegetation` <chr>, `Riparian
## # Upper Canopy All Trees` <chr>, GroundCoverPresence <lgl>
## [1] 22
## [1] 17
## # A tibble: 22 x 8
## SampleAgencyCode LocationCode MethodName `Riparian Groun~
## <chr> <chr> <chr> <chr>
## 1 MPSL-DFW BlockA, Left FieldObse~ 2
## 2 MPSL-DFW BlockA, Rig~ FieldObse~ 3
## 3 MPSL-DFW BlockB, Left FieldObse~ 3
## 4 MPSL-DFW BlockB, Rig~ FieldObse~ 2
## 5 MPSL-DFW BlockC, Left FieldObse~ 3
## 6 MPSL-DFW BlockC, Rig~ FieldObse~ 1
## 7 MPSL-DFW BlockD, Left FieldObse~ 1
## 8 MPSL-DFW BlockD, Rig~ FieldObse~ 2
## 9 MPSL-DFW BlockE, Left FieldObse~ 2
## 10 MPSL-DFW BlockE, Rig~ FieldObse~ 1
## # ... with 12 more rows, and 4 more variables: `Riparian GroundCover Woody
## # Shrubs` <chr>, `Riparian Lower Canopy All Vegetation` <chr>, `Riparian
## # Upper Canopy All Trees` <chr>, GroundCoverPresence <lgl>
## [1] 22
## [1] 21
## [1] "PCT_MAP.count"
## 105PS0231_2013-08-29_DFW-ABL 205PS0202_2013-07-17_MPSL-DFW
## 105 103
## 308PS0204_2013-05-21_DFW-ABL 520PS0455_2013-07-22_MPSL-DFW
## 103 90
## [1] "out$PCT_DR.sd"
## [1] 0 0 0 0
## [1] "out$PCT_CF.sd"
## [1] 0.0 0.0 0.0 3.2
## [1] "out$PCT_GL.sd"
## [1] 0.0 19.8 4.8 25.2
The following 159 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_N_F" "FL_N_M"
## [17] "FL_Q_F" "FL_Q_M" "H_AqHab" "H_FlowHab"
## [21] "H_SubNat" "MWVM_F" "MWVM_M" "NFC_DLU"
## [25] "NFC_EFR" "NFC_ERN" "PBM_E" "PBM_S"
## [29] "PBM_V" "PCT_BDRK" "PCT_BIGR" "PCT_CB"
## [33] "PCT_CF" "PCT_CF_WT" "PCT_CPOM" "PCT_DR"
## [37] "PCT_FAST" "PCT_FAST_WT" "PCT_FN" "PCT_GC"
## [41] "PCT_GF" "PCT_GL" "PCT_GL_WT" "PCT_HP"
## [45] "PCT_MAA" "PCT_MAP" "PCT_MAU" "PCT_MCP"
## [49] "PCT_MIAT1" "PCT_MIAT1P" "PCT_MIATP" "PCT_NSA"
## [53] "PCT_OT" "PCT_POOL" "PCT_POOL_WT" "PCT_RA"
## [57] "PCT_RA_WT" "PCT_RC" "PCT_RI" "PCT_RI_WT"
## [61] "PCT_RN" "PCT_RN_WT" "PCT_RR" "PCT_RS"
## [65] "PCT_SA" "PCT_SAFN" "PCT_SB" "PCT_SFGF"
## [69] "PCT_SLOW" "PCT_SLOW_WT" "PCT_WD" "PCT_XB"
## [73] "PWVZ" "RBP_CHN" "RBP_EPI" "RBP_SED"
## [77] "SB_PP_D10" "SB_PP_D25" "SB_PP_D50" "SB_PP_D75"
## [81] "SB_PP_D90" "SB_PT_D10" "SB_PT_D25" "SB_PT_D50"
## [85] "SB_PT_D75" "SB_PT_D90" "SINU" "SLOPE_0"
## [89] "SLOPE_0_5" "SLOPE_1" "SLOPE_2" "W1_HALL_EMAP"
## [93] "W1_HALL_SWAMP" "W1H_BLDG" "W1H_BRDG" "W1H_CROP"
## [97] "W1H_LDFL" "W1H_LOG" "W1H_MINE" "W1H_ORVY"
## [101] "W1H_PARK" "W1H_PIPE" "W1H_PSTR" "W1H_PVMT"
## [105] "W1H_ROAD" "W1H_VEGM" "W1H_WALL" "XBEARING"
## [109] "XBKF_H" "XBKF_W" "XC" "XCDENBK"
## [113] "XCDENMID" "XCM" "XCMG" "XEMBED"
## [117] "XFC_ALG" "XFC_AQM" "XFC_BIG" "XFC_BRS"
## [121] "XFC_HUM" "XFC_LTR" "XFC_LWD" "XFC_NAT_EMAP"
## [125] "XFC_NAT_SWAMP" "XFC_OHV" "XFC_RCK" "XFC_UCB"
## [129] "XG" "XGB" "XGH" "XGW"
## [133] "XM" "XMIAT" "XMIATP" "XPCAN"
## [137] "XPCM" "XPCMG" "XPGVEG" "XPMGVEG"
## [141] "XPMID" "XSDGM" "XSLOPE" "XSPGM"
## [145] "XWAK" "XWDA" "XWDEPTH" "XWDM"
## [149] "XWDO" "XWDR" "XWIDTH" "XWPH"
## [153] "XWSC" "XWSL" "XWTB" "XWTC"
## [157] "XWTF" "XWV_F" "XWV_M"
alldat
## StationCode CFC_ALG.count CFC_ALG.result
## 1 105PS0231_2013-08-29_DFW-ABL 11 2
## 2 205PS0202_2013-07-17_MPSL-DFW 11 3
## 3 308PS0204_2013-05-21_DFW-ABL 11 4
## 4 520PS0455_2013-07-22_MPSL-DFW 11 11
## CFC_ALL_EMAP.count CFC_ALL_EMAP.result CFC_ALL_SWAMP.count
## 1 8 5 9
## 2 8 7 9
## 3 8 7 9
## 4 8 8 9
## CFC_ALL_SWAMP.result CFC_AQM.count CFC_AQM.result CFC_BRS.count
## 1 6 11 11 11
## 2 8 11 10 11
## 3 8 11 2 11
## 4 9 11 10 11
## CFC_BRS.result CFC_HUM.count CFC_HUM.result CFC_LTR.count CFC_LTR.result
## 1 4 11 0 11 9
## 2 10 11 5 11 11
## 3 10 11 0 11 6
## 4 11 11 11 11 9
## CFC_LWD.count CFC_LWD.result CFC_OHV.count CFC_OHV.result CFC_RCK.count
## 1 11 0 11 11 11
## 2 11 0 11 10 11
## 3 11 3 11 7 11
## 4 11 10 11 11 11
## CFC_RCK.result CFC_UCB.count CFC_UCB.result Ev_AqHab.count
## 1 0 11 4 6
## 2 11 11 11 7
## 3 11 11 3 8
## 4 11 11 10 8
## Ev_AqHab.result Ev_FlowHab.count Ev_FlowHab.result Ev_SubNat.count
## 1 0.50 1 0.00 8
## 2 0.89 2 0.87 6
## 3 0.78 4 0.21 7
## 4 0.77 5 0.80 8
## Ev_SubNat.result FL_N_F.result FL_N_M.result FL_Q_F.count FL_Q_F.result
## 1 0.65 NA NA 0 NA
## 2 0.79 NA NA 11 1.202
## 3 0.87 NA NA 12 17.163
## 4 0.71 NA NA 14 70.402
## FL_Q_M.count FL_Q_M.result H_AqHab.count H_AqHab.result H_FlowHab.count
## 1 0 NA 6 0.89 1
## 2 11 0.034 7 1.73 2
## 3 12 0.486 8 1.63 4
## 4 14 1.993 8 1.60 5
## H_FlowHab.result H_SubNat.count H_SubNat.result MWVM_F.count
## 1 0.00 8 1.36 0
## 2 0.60 6 1.41 11
## 3 0.29 7 1.70 12
## 4 1.29 8 1.47 14
## MWVM_F.result MWVM_M.count MWVM_M.result NFC_DLU.result NFC_EFR.result
## 1 -Inf 0 -Inf Range NO
## 2 0.4 11 0.1 Suburban, Town NO
## 3 1.1 12 0.3 Forest NO
## 4 2.7 14 0.8 Urban/Industrial NO
## NFC_ERN.result PBM_E.count PBM_E.result PBM_S.count PBM_S.result
## 1 NO 22 23 22 0
## 2 NO 22 86 22 5
## 3 NO 22 5 22 82
## 4 NO 22 9 22 0
## PBM_V.count PBM_V.result PCT_BDRK.count PCT_BDRK.result PCT_BIGR.count
## 1 22 77 2 0 6
## 2 22 9 2 0 6
## 3 22 14 2 0 6
## 4 22 91 2 0 6
## PCT_BIGR.result PCT_CB.count PCT_CB.result PCT_CF.count PCT_CF.result
## 1 30 105 5 10 0
## 2 71 105 23 10 0
## 3 59 105 28 10 0
## 4 71 105 45 10 1
## PCT_CF.sd PCT_CF_WT.count PCT_CF_WT.result PCT_CPOM.count
## 1 0.0 10 0 105
## 2 0.0 10 0 105
## 3 0.0 10 0 104
## 4 3.2 10 1 95
## PCT_CPOM.result PCT_DR.count PCT_DR.result PCT_DR.sd PCT_FAST.count
## 1 19 10 0 0 4
## 2 84 10 0 0 4
## 3 12 10 0 0 4
## 4 82 10 0 0 4
## PCT_FAST.result PCT_FAST_WT.count PCT_FAST_WT.result PCT_FN.count
## 1 100 4 100 105
## 2 29 4 29 105
## 3 96 4 96 105
## 4 37 4 37 105
## PCT_FN.result PCT_GC.count PCT_GC.result PCT_GF.count PCT_GF.result
## 1 1 105 23 105 19
## 2 3 105 49 105 10
## 3 4 105 18 105 9
## 4 0 105 17 105 1
## PCT_GL.count PCT_GL.result PCT_GL.sd PCT_GL_WT.count PCT_GL_WT.result
## 1 10 0 0.0 10 0
## 2 10 71 19.8 10 71
## 3 10 3 4.8 10 3
## 4 10 48 25.2 10 48
## PCT_HP.count PCT_HP.result PCT_MAA.count PCT_MAA.result PCT_MAP.count
## 1 105 1 105 2 105
## 2 105 0 105 16 103
## 3 105 0 104 9 103
## 4 105 1 95 56 90
## PCT_MAP.result PCT_MAU.count PCT_MAU.result PCT_MCP.count PCT_MCP.result
## 1 2 105 0 105 82
## 2 18 105 0 105 0
## 3 9 104 0 104 0
## 4 57 95 0 95 2
## PCT_MIAT1.count PCT_MIAT1.result PCT_MIAT1P.count PCT_MIAT1P.result
## 1 101 0 26 0
## 2 105 0 41 0
## 3 71 0 59 0
## 4 95 0 3 0
## PCT_MIATP.count PCT_MIATP.result PCT_NSA.count PCT_NSA.result
## 1 101 26 105 2
## 2 105 39 102 19
## 3 71 83 101 9
## 4 95 3 80 64
## PCT_OT.count PCT_OT.result PCT_POOL.count PCT_POOL.result PCT_POOL.sd
## 1 105 0 10 0 0.0
## 2 105 0 10 0 0.0
## 3 105 0 10 1 3.2
## 4 105 0 10 14 23.1
## PCT_POOL_WT.count PCT_POOL_WT.result PCT_RA.count PCT_RA.result
## 1 10 0 10 0
## 2 10 0 10 0
## 3 10 1 10 0
## 4 10 14 10 0
## PCT_RA.sd PCT_RA_WT.count PCT_RA_WT.result PCT_RC.count PCT_RC.result
## 1 0 10 0 105 0
## 2 0 10 0 105 0
## 3 0 10 0 105 0
## 4 0 10 0 105 10
## PCT_RI.count PCT_RI.result PCT_RI.sd PCT_RI_WT.count PCT_RI_WT.result
## 1 10 0 0.0 10 0
## 2 10 29 19.8 10 29
## 3 10 94 8.4 10 94
## 4 10 22 31.6 10 22
## PCT_RN.count PCT_RN.result PCT_RN.sd PCT_RN_WT.count PCT_RN_WT.result
## 1 10 100 0.0 10 100
## 2 10 0 0.0 10 0
## 3 10 2 4.2 10 2
## 4 10 14 19.6 10 14
## PCT_RR.count PCT_RR.result PCT_RS.count PCT_RS.result PCT_SA.count
## 1 105 0 105 0 105
## 2 105 0 105 0 105
## 3 105 0 105 0 105
## 4 105 0 105 0 105
## PCT_SA.result PCT_SAFN.count PCT_SAFN.result PCT_SB.count PCT_SB.result
## 1 49 2 50 105 2
## 2 10 2 13 105 0
## 3 27 2 30 105 13
## 4 12 2 12 105 7
## PCT_SFGF.count PCT_SFGF.result PCT_SLOW.count PCT_SLOW.result
## 1 3 69 2 0
## 2 3 24 2 71
## 3 3 39 2 4
## 4 3 13 2 62
## PCT_SLOW_WT.count PCT_SLOW_WT.result PCT_WD.count PCT_WD.result
## 1 2 0 105 1
## 2 2 71 105 5
## 3 2 4 105 2
## 4 2 62 105 4
## PCT_XB.count PCT_XB.result PWVZ.count PWVZ.result RBP_CHN.result
## 1 105 0 0 NA NA
## 2 105 0 11 18.2 13
## 3 105 0 12 25.0 19
## 4 105 3 14 14.3 16
## RBP_EPI.result RBP_SED.result SB_PP_D10.count SB_PP_D10.result
## 1 NA NA 103 1.03
## 2 12 13 100 1.03
## 3 20 20 103 1.03
## 4 18 13 89 1.03
## SB_PP_D25.count SB_PP_D25.result SB_PP_D50.count SB_PP_D50.result
## 1 103 1.03 103 1.03
## 2 100 15.00 100 36.00
## 3 103 1.03 103 33.00
## 4 89 37.00 89 93.00
## SB_PP_D75.count SB_PP_D75.result SB_PP_D90.count SB_PP_D90.result
## 1 103 19 103 42
## 2 100 60 100 75
## 3 103 160 103 625
## 4 89 172 89 290
## SB_PT_D10.count SB_PT_D10.result SB_PT_D25.count SB_PT_D25.result
## 1 104 1.03 104 1.03
## 2 100 1.03 100 15.00
## 3 103 1.03 103 1.03
## 4 101 1.03 101 43.00
## SB_PT_D50.count SB_PT_D50.result SB_PT_D75.count SB_PT_D75.result
## 1 104 3.515 104 20
## 2 100 36.500 100 60
## 3 103 33.000 103 160
## 4 101 111.000 101 210
## SB_PT_D90.count SB_PT_D90.result SINU.NOT_WORKING SLOPE_0.count
## 1 104 44 28.64934 10
## 2 100 75 28.64934 10
## 3 103 625 28.64934 10
## 4 101 5660 28.64934 10
## SLOPE_0.result SLOPE_0_5.count SLOPE_0_5.result SLOPE_1.count
## 1 10000 10 0 10
## 2 0 10 10000 10
## 3 0 10 10000 10
## 4 10000 10 0 10
## SLOPE_1.result SLOPE_2.count SLOPE_2.result W1_HALL_EMAP.count
## 1 0 10 0 11
## 2 10000 10 10000 11
## 3 10000 10 10000 11
## 4 0 10 0 11
## W1_HALL_EMAP.result W1_HALL_SWAMP.count W1_HALL_SWAMP.result
## 1 0.00 14 0.00
## 2 1.87 14 1.87
## 3 0.66 14 0.66
## 4 1.28 14 1.28
## W1H_BLDG.count W1H_BLDG.result W1H_BLDG.sd W1H_BRDG.count
## 1 22 0.00 0.000 22
## 2 22 0.73 0.131 22
## 3 22 0.00 0.000 22
## 4 22 0.18 0.304 22
## W1H_BRDG.result W1H_BRDG.sd W1H_CROP.count W1H_CROP.result W1H_CROP.sd
## 1 0 0 22 0 0
## 2 0 0 22 0 0
## 3 0 0 22 0 0
## 4 0 0 22 0 0
## W1H_LDFL.count W1H_LDFL.result W1H_LDFL.sd W1H_LOG.count W1H_LOG.result
## 1 22 0.00 0.000 22 0
## 2 22 0.48 0.715 22 0
## 3 22 0.25 0.551 22 0
## 4 22 0.14 0.441 22 0
## W1H_LOG.sd W1H_MINE.count W1H_MINE.result W1H_MINE.sd W1H_ORVY.count
## 1 0 22 0 0 22
## 2 0 22 0 0 22
## 3 0 22 0 0 22
## 4 0 22 0 0 22
## W1H_ORVY.result W1H_ORVY.sd W1H_PARK.count W1H_PARK.result W1H_PARK.sd
## 1 0 0 22 0.00 0.000
## 2 0 0 22 0.11 0.376
## 3 0 0 22 0.00 0.000
## 4 0 0 22 0.00 0.000
## W1H_PIPE.count W1H_PIPE.result W1H_PIPE.sd W1H_PSTR.count
## 1 22 0 0 22
## 2 22 0 0 22
## 3 22 0 0 22
## 4 22 0 0 22
## W1H_PSTR.result W1H_PSTR.sd W1H_PVMT.count W1H_PVMT.result W1H_PVMT.sd
## 1 0 0 22 0.00 0.000
## 2 0 0 22 0.00 0.000
## 3 0 0 22 0.03 0.142
## 4 0 0 22 0.27 0.336
## W1H_ROAD.count W1H_ROAD.result W1H_ROAD.sd W1H_VEGM.count
## 1 22 0.00 0.000 22
## 2 22 0.00 0.000 22
## 3 22 0.24 0.328 22
## 4 22 0.05 0.213 22
## W1H_VEGM.result W1H_VEGM.sd W1H_WALL.count W1H_WALL.result W1H_WALL.sd
## 1 0 0 22 0.00 0.000
## 2 0 0 22 0.55 0.575
## 3 0 0 22 0.14 0.441
## 4 0 0 22 0.64 0.727
## XBEARING.count XBEARING.result XBEARING.sd XBKF_H.count XBKF_H.result
## 1 10 0.01 0 11 0.78
## 2 10 0.01 0 11 0.24
## 3 10 0.01 0 11 1.24
## 4 10 0.01 0 11 0.30
## XBKF_H.sd XBKF_W.count XBKF_W.result XBKF_W.sd XC.count XC.result XC.sd
## 1 0.10 11 21.0 7.40 22 8 11.0
## 2 0.06 11 3.4 0.55 22 57 13.6
## 3 0.44 11 22.2 7.31 22 57 21.6
## 4 0.00 11 30.2 7.43 22 34 22.0
## XCDENBK.count XCDENBK.result XCDENBK.sd XCDENMID.count XCDENMID.result
## 1 22 67 33.2 44 6
## 2 0 NA NA 44 98
## 3 22 97 8.8 44 81
## 4 22 90 24.5 44 15
## XCDENMID.sd XCM.count XCM.result XCMG.count XCMG.result XEMBED.count
## 1 18.8 2 44 4 132 26
## 2 5.3 2 91 4 142 25
## 3 17.1 2 92 4 128 27
## 4 30.0 2 73 4 123 47
## XEMBED.result XEMBED.sd XFC_ALG.count XFC_ALG.result XFC_ALG.sd
## 1 36 19.8 11 0.9 2.0
## 2 24 26.8 11 1.4 2.3
## 3 36 33.9 11 1.8 2.5
## 4 7 14.0 11 27.3 16.9
## XFC_AQM.count XFC_AQM.result XFC_AQM.sd XFC_BIG.count XFC_BIG.result
## 1 11 51.6 13.1 4 1.8
## 2 11 4.5 1.5 4 35.9
## 3 11 0.9 2.0 4 18.7
## 4 11 4.5 1.5 4 59.7
## XFC_BRS.count XFC_BRS.result XFC_BRS.sd XFC_HUM.count XFC_HUM.result
## 1 11 1.8 2.5 11 0.0
## 2 11 4.5 1.5 11 5.9
## 3 11 4.5 1.5 11 0.0
## 4 11 8.6 8.1 11 5.0
## XFC_HUM.sd XFC_LTR.count XFC_LTR.result XFC_LTR.sd XFC_LWD.count
## 1 0.0 11 4.1 2.0 11
## 2 9.7 11 6.8 6.0 11
## 3 0.0 11 2.7 2.6 11
## 4 0.0 11 4.1 2.0 11
## XFC_LWD.result XFC_LWD.sd XFC_NAT_EMAP.count XFC_NAT_EMAP.result
## 1 0.0 0.0 5 12.2
## 2 0.0 0.0 5 40.9
## 3 1.4 2.3 5 28.2
## 4 4.5 1.5 5 68.3
## XFC_NAT_SWAMP.count XFC_NAT_SWAMP.result XFC_OHV.count XFC_OHV.result
## 1 7 67.9 11 8.6
## 2 7 52.2 11 6.4
## 3 7 31.8 11 5.0
## 4 7 76.9 11 5.0
## XFC_OHV.sd XFC_RCK.count XFC_RCK.result XFC_RCK.sd XFC_UCB.count
## 1 8.1 11 0.0 0.0 11
## 2 6.4 11 12.3 10.1 11
## 3 7.1 11 15.9 10.4 11
## 4 0.0 11 45.7 16.4 11
## XFC_UCB.result XFC_UCB.sd XG.count XG.result XGB.count XGB.result XGB.sd
## 1 1.8 2.5 2 88 22 8 14.5
## 2 17.7 10.1 2 51 22 38 26.3
## 3 1.4 2.3 2 36 22 60 24.0
## 4 4.5 1.5 2 50 22 36 27.7
## XGH.count XGH.result XGH.sd XGW.count XGW.result XGW.sd XM.count
## 1 22 71 26.7 22 17 18.6 22
## 2 22 8 16.0 22 43 30.3 22
## 3 22 10 9.5 22 26 19.5 22
## 4 22 19 18.1 22 31 15.1 22
## XM.result XM.sd XMIAT.count XMIAT.result XMIAT.sd XMIATP.count
## 1 36 23.3 101 0.1 0.16 26
## 2 34 16.7 105 0.2 0.21 41
## 3 35 18.3 71 0.2 0.15 59
## 4 39 19.3 95 0.0 0.04 3
## XMIATP.result XMIATP.sd XPCAN.count XPCAN.result XPCM.count XPCM.result
## 1 0.3 0.12 22 0.45 22 0.45
## 2 0.4 0.12 22 1.00 22 1.00
## 3 0.3 0.10 22 1.00 22 1.00
## 4 0.2 0.00 22 0.95 22 0.95
## XPCMG.count XPCMG.result XPGVEG.count XPGVEG.result XPMGVEG.count
## 1 22 0.45 22 1 22
## 2 22 1.00 22 1 22
## 3 22 1.00 22 1 22
## 4 22 0.95 22 1 22
## XPMGVEG.result XPMID.count XPMID.result XSDGM.count XSDGM.result
## 1 1.00 22 0.95 104 5.1
## 2 0.91 22 1.00 100 20.6
## 3 0.77 22 1.00 103 19.3
## 4 0.95 22 1.00 101 97.6
## XSLOPE.count XSLOPE.result XSLOPE.sd XSPGM.result XWAK.count XWAK.result
## 1 10 0.00 0 4.776569 1 195
## 2 10 0.01 0 20.563869 1 230
## 3 10 0.01 0 19.282021 1 140
## 4 10 0.00 0 56.476045 1 80
## XWAK.sd XWDA.count XWDA.result XWDEPTH.count XWDEPTH.result XWDEPTH.sd
## 1 NA 105 0.2696774 105 41.8 36.16
## 2 NA 105 0.2833333 105 6.8 8.01
## 3 NA 105 0.1738318 105 18.6 18.65
## 4 NA 105 0.1107807 105 29.8 43.73
## XWDM.count XWDM.result XWDM.sd XWDO.count XWDO.result XWDO.sd XWDR.count
## 1 21 79.8 15.3 1 9.0 NA 21
## 2 21 14.7 9.0 1 9.0 NA 21
## 3 21 40.1 14.9 1 15.2 NA 21
## 4 21 77.0 53.2 1 8.8 NA 21
## XWDR.result XWIDTH.count XWIDTH.result XWIDTH.sd XWPH.count XWPH.result
## 1 37.08134 21 15.5 4.03 1 7.99
## 2 35.29412 21 2.4 0.64 1 8.02
## 3 57.52688 21 10.7 3.00 0 NA
## 4 90.26846 21 26.9 7.49 1 7.83
## XWPH.sd XWSC.count XWSC.result XWSC.sd XWSL.count XWSL.result XWSL.sd
## 1 NA 1 423.5 NA 1 0.2 NA
## 2 NA 1 1129.0 NA 1 0.6 NA
## 3 NA 1 317.3 NA 1 0.2 NA
## 4 NA 1 117.0 NA 1 0.0 NA
## XWTB.count XWTB.result XWTB.sd XWTC.count XWTC.result XWTC.sd XWTF.count
## 1 0 NA NA 1 14.7 NA 1
## 2 1 3.0 NA 1 15.5 NA 1
## 3 1 0.8 NA 1 15.2 NA 1
## 4 1 4.7 NA 1 22.4 NA 1
## XWTF.result XWTF.sd XWV_F.count XWV_F.result XWV_F.sd XWV_M.count
## 1 58.5 NA 0 NA NA 0
## 2 59.9 NA 11 0.24 0.1828164 11
## 3 59.4 NA 12 0.50 0.4605530 12
## 4 72.3 NA 14 1.43 0.8051704 14
## XWV_M.result XWV_M.sd
## 1 NA NA
## 2 0.07 0.05573669
## 3 0.15 0.14041251
## 4 0.44 0.24547880
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
Metadata
Resources: SOP, Technical memo
Contact: Raphael Mazor, Robert Butler
SCCWRP/PHABMetrics documentation built on Oct. 28, 2021, 10:23 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Marcus W. Beck, marcusb@sccwrp.org, Robert Butler, r7butler@yahoo.com, Raphael D. Mazor, raphaelm@sccwrp.org, Mark Engeln
PHABMetrics
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)
## id StationCode SampleDate SampleAgencyCode
## 1 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## 2 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## 3 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## 4 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## 5 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## 6 308PS0204_2013-05-21_DFW-ABL 308PS0204 2013-05-21 DFW-ABL
## LocationCode Replicate MethodName AnalyteName FractionName UnitName
## 1 X 1 FieldMeasure pH None none
## 2 X 1 FieldMeasure Temperature None Deg C
## 3 X 4 Velocity Area Velocity None ft/s
## 4 X 6 Velocity Area Velocity None ft/s
## 5 X 8 Velocity Area Velocity None ft/s
## 6 X 12 Velocity Area Velocity None ft/s
## Result ResQualCode QACode VariableResult
## 1 NA NR FEU Not Recorded
## 2 15.20 = None NA
## 3 0.72 = None NA
## 4 1.12 = None NA
## 5 1.01 = None NA
## 6 0.00 = None NA
The core function is phabmetrics(). Calulcate PHAB metrics with sample
data:
alldat <- phabmetrics(sampdat)
## [1] "XWIDTHdata"
## [1] id result
## <0 rows> (or 0-length row.names)
## [1] "XWIDTH.sd"
## 105PS0231_2013-08-29_DFW-ABL 205PS0202_2013-07-17_MPSL-DFW
## 4.03 0.64
## 308PS0204_2013-05-21_DFW-ABL 520PS0455_2013-07-22_MPSL-DFW
## 3.00 7.49
## [1] "results"
## PCT_CF.result PCT_CF.count PCT_CF.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0.0
## 205PS0202_2013-07-17_MPSL-DFW 0 10 0.0
## 308PS0204_2013-05-21_DFW-ABL 0 10 0.0
## 520PS0455_2013-07-22_MPSL-DFW 1 10 3.2
## PCT_DR.result PCT_DR.count PCT_DR.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0
## 205PS0202_2013-07-17_MPSL-DFW 0 10 0
## 308PS0204_2013-05-21_DFW-ABL 0 10 0
## 520PS0455_2013-07-22_MPSL-DFW 0 10 0
## PCT_GL.result PCT_GL.count PCT_GL.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0.0
## 205PS0202_2013-07-17_MPSL-DFW 71 10 19.8
## 308PS0204_2013-05-21_DFW-ABL 3 10 4.8
## 520PS0455_2013-07-22_MPSL-DFW 48 10 25.2
## PCT_POOL.result PCT_POOL.count PCT_POOL.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0.0
## 205PS0202_2013-07-17_MPSL-DFW 0 10 0.0
## 308PS0204_2013-05-21_DFW-ABL 1 10 3.2
## 520PS0455_2013-07-22_MPSL-DFW 14 10 23.1
## PCT_RA.result PCT_RA.count PCT_RA.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0
## 205PS0202_2013-07-17_MPSL-DFW 0 10 0
## 308PS0204_2013-05-21_DFW-ABL 0 10 0
## 520PS0455_2013-07-22_MPSL-DFW 0 10 0
## PCT_RI.result PCT_RI.count PCT_RI.sd
## 105PS0231_2013-08-29_DFW-ABL 0 10 0.0
## 205PS0202_2013-07-17_MPSL-DFW 29 10 19.8
## 308PS0204_2013-05-21_DFW-ABL 94 10 8.4
## 520PS0455_2013-07-22_MPSL-DFW 22 10 31.6
## PCT_RN.result PCT_RN.count PCT_RN.sd
## 105PS0231_2013-08-29_DFW-ABL 100 10 0.0
## 205PS0202_2013-07-17_MPSL-DFW 0 10 0.0
## 308PS0204_2013-05-21_DFW-ABL 2 10 4.2
## 520PS0455_2013-07-22_MPSL-DFW 14 10 19.6
## PCT_FAST.result PCT_SLOW.result
## 105PS0231_2013-08-29_DFW-ABL 100 0
## 205PS0202_2013-07-17_MPSL-DFW 29 71
## 308PS0204_2013-05-21_DFW-ABL 96 4
## 520PS0455_2013-07-22_MPSL-DFW 37 62
## PCT_CF_WT.result PCT_CF_WT.count
## 105PS0231_2013-08-29_DFW-ABL 0 10
## 205PS0202_2013-07-17_MPSL-DFW 0 10
## 308PS0204_2013-05-21_DFW-ABL 0 10
## 520PS0455_2013-07-22_MPSL-DFW 1 10
## PCT_GL_WT.result PCT_GL_WT.count
## 105PS0231_2013-08-29_DFW-ABL 0 10
## 205PS0202_2013-07-17_MPSL-DFW 71 10
## 308PS0204_2013-05-21_DFW-ABL 3 10
## 520PS0455_2013-07-22_MPSL-DFW 48 10
## PCT_POOL_WT.result PCT_POOL_WT.count
## 105PS0231_2013-08-29_DFW-ABL 0 10
## 205PS0202_2013-07-17_MPSL-DFW 0 10
## 308PS0204_2013-05-21_DFW-ABL 1 10
## 520PS0455_2013-07-22_MPSL-DFW 14 10
## PCT_RA_WT.result PCT_RA_WT.count
## 105PS0231_2013-08-29_DFW-ABL 0 10
## 205PS0202_2013-07-17_MPSL-DFW 0 10
## 308PS0204_2013-05-21_DFW-ABL 0 10
## 520PS0455_2013-07-22_MPSL-DFW 0 10
## PCT_RI_WT.result PCT_RI_WT.count
## 105PS0231_2013-08-29_DFW-ABL 0 10
## 205PS0202_2013-07-17_MPSL-DFW 29 10
## 308PS0204_2013-05-21_DFW-ABL 94 10
## 520PS0455_2013-07-22_MPSL-DFW 22 10
## PCT_RN_WT.result PCT_RN_WT.count
## 105PS0231_2013-08-29_DFW-ABL 100 10
## 205PS0202_2013-07-17_MPSL-DFW 0 10
## 308PS0204_2013-05-21_DFW-ABL 2 10
## 520PS0455_2013-07-22_MPSL-DFW 14 10
## PCT_FAST_WT.result PCT_SLOW_WT.result
## 105PS0231_2013-08-29_DFW-ABL 100 0
## 205PS0202_2013-07-17_MPSL-DFW 29 71
## 308PS0204_2013-05-21_DFW-ABL 96 4
## 520PS0455_2013-07-22_MPSL-DFW 37 62
## PCT_FAST.count PCT_SLOW.count
## 105PS0231_2013-08-29_DFW-ABL 4 2
## 205PS0202_2013-07-17_MPSL-DFW 4 2
## 308PS0204_2013-05-21_DFW-ABL 4 2
## 520PS0455_2013-07-22_MPSL-DFW 4 2
## PCT_FAST_WT.count PCT_SLOW_WT.count
## 105PS0231_2013-08-29_DFW-ABL 4 2
## 205PS0202_2013-07-17_MPSL-DFW 4 2
## 308PS0204_2013-05-21_DFW-ABL 4 2
## 520PS0455_2013-07-22_MPSL-DFW 4 2
## H_FlowHab.result H_FlowHab.count
## 105PS0231_2013-08-29_DFW-ABL 0.00 1
## 205PS0202_2013-07-17_MPSL-DFW 0.60 2
## 308PS0204_2013-05-21_DFW-ABL 0.29 4
## 520PS0455_2013-07-22_MPSL-DFW 1.29 5
## Ev_FlowHab.result Ev_FlowHab.count
## 105PS0231_2013-08-29_DFW-ABL 0.00 1
## 205PS0202_2013-07-17_MPSL-DFW 0.87 2
## 308PS0204_2013-05-21_DFW-ABL 0.21 4
## 520PS0455_2013-07-22_MPSL-DFW 0.80 5
## [1] "results$PCT_CF.sd"
## [1] 0.0 0.0 0.0 3.2
## [1] "results$PCT_DR.sd"
## [1] 0 0 0 0
## [1] "results$PCT_GL.sd"
## [1] 0.0 19.8 4.8 25.2
## [1] "W1H_BRDG"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_D~ Riparian Bridges/Abut~ 0 22 0 W1H_BR~
## 2 205PS0202_2013-07-17_M~ Riparian Bridges/Abut~ 0 22 0 W1H_BR~
## 3 520PS0455_2013-07-22_M~ Riparian Bridges/Abut~ 0 22 0 W1H_BR~
## 4 105PS0231_2013-08-29_D~ Riparian Bridges/Abut~ 0 22 0 W1H_BR~
## [1] "W1H_BLDG"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-A~ Riparian Buildings 0 22 0 W1H_BL~
## 2 205PS0202_2013-07-17_MPSL-~ Riparian Buildings 0.728 22 0.131 W1H_BL~
## 3 520PS0455_2013-07-22_MPSL-~ Riparian Buildings 0.182 22 0.304 W1H_BL~
## 4 105PS0231_2013-08-29_DFW-A~ Riparian Buildings 0 22 0 W1H_BL~
## [1] "W1H_LDFL"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DF~ Riparian Landfill/Tr~ 0.25 22 0.551 W1H_LD~
## 2 205PS0202_2013-07-17_MP~ Riparian Landfill/Tr~ 0.477 22 0.715 W1H_LD~
## 3 520PS0455_2013-07-22_MP~ Riparian Landfill/Tr~ 0.136 22 0.441 W1H_LD~
## 4 105PS0231_2013-08-29_DF~ Riparian Landfill/Tr~ 0 22 0 W1H_LD~
## [1] "W1H_LOG"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-ABL Riparian Logging 0 22 0 W1H_LOG
## 2 205PS0202_2013-07-17_MPSL-DFW Riparian Logging 0 22 0 W1H_LOG
## 3 520PS0455_2013-07-22_MPSL-DFW Riparian Logging 0 22 0 W1H_LOG
## 4 105PS0231_2013-08-29_DFW-ABL Riparian Logging 0 22 0 W1H_LOG
## [1] "W1H_MINE"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-ABL Riparian Mining 0 22 0 W1H_MINE
## 2 205PS0202_2013-07-17_MPSL-DFW Riparian Mining 0 22 0 W1H_MINE
## 3 520PS0455_2013-07-22_MPSL-DFW Riparian Mining 0 22 0 W1H_MINE
## 4 105PS0231_2013-08-29_DFW-ABL Riparian Mining 0 22 0 W1H_MINE
## [1] "W1H_ORVY"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_D~ Riparian Orchards/Vin~ 0 22 0 W1H_OR~
## 2 205PS0202_2013-07-17_M~ Riparian Orchards/Vin~ 0 22 0 W1H_OR~
## 3 520PS0455_2013-07-22_M~ Riparian Orchards/Vin~ 0 22 0 W1H_OR~
## 4 105PS0231_2013-08-29_D~ Riparian Orchards/Vin~ 0 22 0 W1H_OR~
## [1] "W1H_PARK"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-A~ Riparian Park/Lawn 0 22 0 W1H_PA~
## 2 205PS0202_2013-07-17_MPSL-~ Riparian Park/Lawn 0.114 22 0.376 W1H_PA~
## 3 520PS0455_2013-07-22_MPSL-~ Riparian Park/Lawn 0 22 0 W1H_PA~
## 4 105PS0231_2013-08-29_DFW-A~ Riparian Park/Lawn 0 22 0 W1H_PA~
## [1] "W1H_PSTR"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW~ Riparian Pasture/Ra~ 0 22 0 W1H_PS~
## 2 205PS0202_2013-07-17_MPS~ Riparian Pasture/Ra~ 0 22 0 W1H_PS~
## 3 520PS0455_2013-07-22_MPS~ Riparian Pasture/Ra~ 0 22 0 W1H_PS~
## 4 105PS0231_2013-08-29_DFW~ Riparian Pasture/Ra~ 0 22 0 W1H_PS~
## [1] "W1H_PVMT"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-ABL Riparian Pavement 0.0303 22 0.142 W1H_PV~
## 2 205PS0202_2013-07-17_MPSL-D~ Riparian Pavement 0 22 0 W1H_PV~
## 3 520PS0455_2013-07-22_MPSL-D~ Riparian Pavement 0.273 22 0.336 W1H_PV~
## 4 105PS0231_2013-08-29_DFW-ABL Riparian Pavement 0 22 0 W1H_PV~
## [1] "W1H_PIPE"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-ABL Riparian Pipes 0 22 0 W1H_PIPE
## 2 205PS0202_2013-07-17_MPSL-DFW Riparian Pipes 0 22 0 W1H_PIPE
## 3 520PS0455_2013-07-22_MPSL-DFW Riparian Pipes 0 22 0 W1H_PIPE
## 4 105PS0231_2013-08-29_DFW-ABL Riparian Pipes 0 22 0 W1H_PIPE
## [1] "W1H_ROAD"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-ABL Riparian Road 0.243 22 0.328 W1H_ROAD
## 2 205PS0202_2013-07-17_MPSL-DFW Riparian Road 0 22 0 W1H_ROAD
## 3 520PS0455_2013-07-22_MPSL-DFW Riparian Road 0.0455 22 0.213 W1H_ROAD
## 4 105PS0231_2013-08-29_DFW-ABL Riparian Road 0 22 0 W1H_ROAD
## [1] "W1H_CROP"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-A~ Riparian Row Crops 0 22 0 W1H_CR~
## 2 205PS0202_2013-07-17_MPSL-~ Riparian Row Crops 0 22 0 W1H_CR~
## 3 520PS0455_2013-07-22_MPSL-~ Riparian Row Crops 0 22 0 W1H_CR~
## 4 105PS0231_2013-08-29_DFW-A~ Riparian Row Crops 0 22 0 W1H_CR~
## [1] "W1H_VEGM"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21~ Riparian Vegetation Man~ 0 22 0 W1H_VE~
## 2 205PS0202_2013-07-17~ Riparian Vegetation Man~ 0 22 0 W1H_VE~
## 3 520PS0455_2013-07-22~ Riparian Vegetation Man~ 0 22 0 W1H_VE~
## 4 105PS0231_2013-08-29~ Riparian Vegetation Man~ 0 22 0 W1H_VE~
## [1] "W1H_WALL"
## # A tibble: 4 x 6
## id AnalyteName Result Count sd Metric
## <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 308PS0204_2013-05-21_DFW-A~ Riparian Wall/Dike 0.136 22 0.441 W1H_WA~
## 2 205PS0202_2013-07-17_MPSL-~ Riparian Wall/Dike 0.545 22 0.575 W1H_WA~
## 3 520PS0455_2013-07-22_MPSL-~ Riparian Wall/Dike 0.636 22 0.727 W1H_WA~
## 4 105PS0231_2013-08-29_DFW-A~ Riparian Wall/Dike 0 22 0 W1H_WA~
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning in max(df$Result, na.rm = T): no non-missing arguments to max;
## returning -Inf
## # A tibble: 22 x 8
## SampleAgencyCode LocationCode MethodName `Riparian Groun~
## <chr> <chr> <chr> <chr>
## 1 DFW-ABL BlockA, Left FieldObse~ 2
## 2 DFW-ABL BlockA, Rig~ FieldObse~ 3
## 3 DFW-ABL BlockB, Left FieldObse~ 2
## 4 DFW-ABL BlockB, Rig~ FieldObse~ 4
## 5 DFW-ABL BlockC, Left FieldObse~ 2
## 6 DFW-ABL BlockC, Rig~ FieldObse~ 4
## 7 DFW-ABL BlockD, Left FieldObse~ 4
## 8 DFW-ABL BlockD, Rig~ FieldObse~ 4
## 9 DFW-ABL BlockE, Left FieldObse~ 2
## 10 DFW-ABL BlockE, Rig~ FieldObse~ 4
## # ... with 12 more rows, and 4 more variables: `Riparian GroundCover Woody
## # Shrubs` <chr>, `Riparian Lower Canopy All Vegetation` <chr>, `Riparian
## # Upper Canopy All Trees` <chr>, GroundCoverPresence <lgl>
## [1] 22
## [1] 22
## # A tibble: 22 x 8
## SampleAgencyCode LocationCode MethodName `Riparian Groun~
## <chr> <chr> <chr> <chr>
## 1 MPSL-DFW BlockA, Left FieldObse~ 3
## 2 MPSL-DFW BlockA, Rig~ FieldObse~ 0
## 3 MPSL-DFW BlockB, Left FieldObse~ 3
## 4 MPSL-DFW BlockB, Rig~ FieldObse~ 1
## 5 MPSL-DFW BlockC, Left FieldObse~ 1
## 6 MPSL-DFW BlockC, Rig~ FieldObse~ 1
## 7 MPSL-DFW BlockD, Left FieldObse~ 1
## 8 MPSL-DFW BlockD, Rig~ FieldObse~ 0
## 9 MPSL-DFW BlockE, Left FieldObse~ 0
## 10 MPSL-DFW BlockE, Rig~ FieldObse~ 1
## # ... with 12 more rows, and 4 more variables: `Riparian GroundCover Woody
## # Shrubs` <chr>, `Riparian Lower Canopy All Vegetation` <chr>, `Riparian
## # Upper Canopy All Trees` <chr>, GroundCoverPresence <lgl>
## [1] 22
## [1] 20
## # A tibble: 22 x 8
## SampleAgencyCode LocationCode MethodName `Riparian Groun~
## <chr> <chr> <chr> <chr>
## 1 DFW-ABL BlockA, Left FieldObse~ 1
## 2 DFW-ABL BlockA, Rig~ FieldObse~ 1
## 3 DFW-ABL BlockB, Left FieldObse~ 1
## 4 DFW-ABL BlockB, Rig~ FieldObse~ 2
## 5 DFW-ABL BlockC, Left FieldObse~ 0
## 6 DFW-ABL BlockC, Rig~ FieldObse~ 1
## 7 DFW-ABL BlockD, Left FieldObse~ 1
## 8 DFW-ABL BlockD, Rig~ FieldObse~ 1
## 9 DFW-ABL BlockE, Left FieldObse~ 2
## 10 DFW-ABL BlockE, Rig~ FieldObse~ 1
## # ... with 12 more rows, and 4 more variables: `Riparian GroundCover Woody
## # Shrubs` <chr>, `Riparian Lower Canopy All Vegetation` <chr>, `Riparian
## # Upper Canopy All Trees` <chr>, GroundCoverPresence <lgl>
## [1] 22
## [1] 17
## # A tibble: 22 x 8
## SampleAgencyCode LocationCode MethodName `Riparian Groun~
## <chr> <chr> <chr> <chr>
## 1 MPSL-DFW BlockA, Left FieldObse~ 2
## 2 MPSL-DFW BlockA, Rig~ FieldObse~ 3
## 3 MPSL-DFW BlockB, Left FieldObse~ 3
## 4 MPSL-DFW BlockB, Rig~ FieldObse~ 2
## 5 MPSL-DFW BlockC, Left FieldObse~ 3
## 6 MPSL-DFW BlockC, Rig~ FieldObse~ 1
## 7 MPSL-DFW BlockD, Left FieldObse~ 1
## 8 MPSL-DFW BlockD, Rig~ FieldObse~ 2
## 9 MPSL-DFW BlockE, Left FieldObse~ 2
## 10 MPSL-DFW BlockE, Rig~ FieldObse~ 1
## # ... with 12 more rows, and 4 more variables: `Riparian GroundCover Woody
## # Shrubs` <chr>, `Riparian Lower Canopy All Vegetation` <chr>, `Riparian
## # Upper Canopy All Trees` <chr>, GroundCoverPresence <lgl>
## [1] 22
## [1] 21
## [1] "PCT_MAP.count"
## 105PS0231_2013-08-29_DFW-ABL 205PS0202_2013-07-17_MPSL-DFW
## 105 103
## 308PS0204_2013-05-21_DFW-ABL 520PS0455_2013-07-22_MPSL-DFW
## 103 90
## [1] "out$PCT_DR.sd"
## [1] 0 0 0 0
## [1] "out$PCT_CF.sd"
## [1] 0.0 0.0 0.0 3.2
## [1] "out$PCT_GL.sd"
## [1] 0.0 19.8 4.8 25.2
The following 159 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_N_F" "FL_N_M"
## [17] "FL_Q_F" "FL_Q_M" "H_AqHab" "H_FlowHab"
## [21] "H_SubNat" "MWVM_F" "MWVM_M" "NFC_DLU"
## [25] "NFC_EFR" "NFC_ERN" "PBM_E" "PBM_S"
## [29] "PBM_V" "PCT_BDRK" "PCT_BIGR" "PCT_CB"
## [33] "PCT_CF" "PCT_CF_WT" "PCT_CPOM" "PCT_DR"
## [37] "PCT_FAST" "PCT_FAST_WT" "PCT_FN" "PCT_GC"
## [41] "PCT_GF" "PCT_GL" "PCT_GL_WT" "PCT_HP"
## [45] "PCT_MAA" "PCT_MAP" "PCT_MAU" "PCT_MCP"
## [49] "PCT_MIAT1" "PCT_MIAT1P" "PCT_MIATP" "PCT_NSA"
## [53] "PCT_OT" "PCT_POOL" "PCT_POOL_WT" "PCT_RA"
## [57] "PCT_RA_WT" "PCT_RC" "PCT_RI" "PCT_RI_WT"
## [61] "PCT_RN" "PCT_RN_WT" "PCT_RR" "PCT_RS"
## [65] "PCT_SA" "PCT_SAFN" "PCT_SB" "PCT_SFGF"
## [69] "PCT_SLOW" "PCT_SLOW_WT" "PCT_WD" "PCT_XB"
## [73] "PWVZ" "RBP_CHN" "RBP_EPI" "RBP_SED"
## [77] "SB_PP_D10" "SB_PP_D25" "SB_PP_D50" "SB_PP_D75"
## [81] "SB_PP_D90" "SB_PT_D10" "SB_PT_D25" "SB_PT_D50"
## [85] "SB_PT_D75" "SB_PT_D90" "SINU" "SLOPE_0"
## [89] "SLOPE_0_5" "SLOPE_1" "SLOPE_2" "W1_HALL_EMAP"
## [93] "W1_HALL_SWAMP" "W1H_BLDG" "W1H_BRDG" "W1H_CROP"
## [97] "W1H_LDFL" "W1H_LOG" "W1H_MINE" "W1H_ORVY"
## [101] "W1H_PARK" "W1H_PIPE" "W1H_PSTR" "W1H_PVMT"
## [105] "W1H_ROAD" "W1H_VEGM" "W1H_WALL" "XBEARING"
## [109] "XBKF_H" "XBKF_W" "XC" "XCDENBK"
## [113] "XCDENMID" "XCM" "XCMG" "XEMBED"
## [117] "XFC_ALG" "XFC_AQM" "XFC_BIG" "XFC_BRS"
## [121] "XFC_HUM" "XFC_LTR" "XFC_LWD" "XFC_NAT_EMAP"
## [125] "XFC_NAT_SWAMP" "XFC_OHV" "XFC_RCK" "XFC_UCB"
## [129] "XG" "XGB" "XGH" "XGW"
## [133] "XM" "XMIAT" "XMIATP" "XPCAN"
## [137] "XPCM" "XPCMG" "XPGVEG" "XPMGVEG"
## [141] "XPMID" "XSDGM" "XSLOPE" "XSPGM"
## [145] "XWAK" "XWDA" "XWDEPTH" "XWDM"
## [149] "XWDO" "XWDR" "XWIDTH" "XWPH"
## [153] "XWSC" "XWSL" "XWTB" "XWTC"
## [157] "XWTF" "XWV_F" "XWV_M"
alldat
## StationCode CFC_ALG.count CFC_ALG.result
## 1 105PS0231_2013-08-29_DFW-ABL 11 2
## 2 205PS0202_2013-07-17_MPSL-DFW 11 3
## 3 308PS0204_2013-05-21_DFW-ABL 11 4
## 4 520PS0455_2013-07-22_MPSL-DFW 11 11
## CFC_ALL_EMAP.count CFC_ALL_EMAP.result CFC_ALL_SWAMP.count
## 1 8 5 9
## 2 8 7 9
## 3 8 7 9
## 4 8 8 9
## CFC_ALL_SWAMP.result CFC_AQM.count CFC_AQM.result CFC_BRS.count
## 1 6 11 11 11
## 2 8 11 10 11
## 3 8 11 2 11
## 4 9 11 10 11
## CFC_BRS.result CFC_HUM.count CFC_HUM.result CFC_LTR.count CFC_LTR.result
## 1 4 11 0 11 9
## 2 10 11 5 11 11
## 3 10 11 0 11 6
## 4 11 11 11 11 9
## CFC_LWD.count CFC_LWD.result CFC_OHV.count CFC_OHV.result CFC_RCK.count
## 1 11 0 11 11 11
## 2 11 0 11 10 11
## 3 11 3 11 7 11
## 4 11 10 11 11 11
## CFC_RCK.result CFC_UCB.count CFC_UCB.result Ev_AqHab.count
## 1 0 11 4 6
## 2 11 11 11 7
## 3 11 11 3 8
## 4 11 11 10 8
## Ev_AqHab.result Ev_FlowHab.count Ev_FlowHab.result Ev_SubNat.count
## 1 0.50 1 0.00 8
## 2 0.89 2 0.87 6
## 3 0.78 4 0.21 7
## 4 0.77 5 0.80 8
## Ev_SubNat.result FL_N_F.result FL_N_M.result FL_Q_F.count FL_Q_F.result
## 1 0.65 NA NA 0 NA
## 2 0.79 NA NA 11 1.202
## 3 0.87 NA NA 12 17.163
## 4 0.71 NA NA 14 70.402
## FL_Q_M.count FL_Q_M.result H_AqHab.count H_AqHab.result H_FlowHab.count
## 1 0 NA 6 0.89 1
## 2 11 0.034 7 1.73 2
## 3 12 0.486 8 1.63 4
## 4 14 1.993 8 1.60 5
## H_FlowHab.result H_SubNat.count H_SubNat.result MWVM_F.count
## 1 0.00 8 1.36 0
## 2 0.60 6 1.41 11
## 3 0.29 7 1.70 12
## 4 1.29 8 1.47 14
## MWVM_F.result MWVM_M.count MWVM_M.result NFC_DLU.result NFC_EFR.result
## 1 -Inf 0 -Inf Range NO
## 2 0.4 11 0.1 Suburban, Town NO
## 3 1.1 12 0.3 Forest NO
## 4 2.7 14 0.8 Urban/Industrial NO
## NFC_ERN.result PBM_E.count PBM_E.result PBM_S.count PBM_S.result
## 1 NO 22 23 22 0
## 2 NO 22 86 22 5
## 3 NO 22 5 22 82
## 4 NO 22 9 22 0
## PBM_V.count PBM_V.result PCT_BDRK.count PCT_BDRK.result PCT_BIGR.count
## 1 22 77 2 0 6
## 2 22 9 2 0 6
## 3 22 14 2 0 6
## 4 22 91 2 0 6
## PCT_BIGR.result PCT_CB.count PCT_CB.result PCT_CF.count PCT_CF.result
## 1 30 105 5 10 0
## 2 71 105 23 10 0
## 3 59 105 28 10 0
## 4 71 105 45 10 1
## PCT_CF.sd PCT_CF_WT.count PCT_CF_WT.result PCT_CPOM.count
## 1 0.0 10 0 105
## 2 0.0 10 0 105
## 3 0.0 10 0 104
## 4 3.2 10 1 95
## PCT_CPOM.result PCT_DR.count PCT_DR.result PCT_DR.sd PCT_FAST.count
## 1 19 10 0 0 4
## 2 84 10 0 0 4
## 3 12 10 0 0 4
## 4 82 10 0 0 4
## PCT_FAST.result PCT_FAST_WT.count PCT_FAST_WT.result PCT_FN.count
## 1 100 4 100 105
## 2 29 4 29 105
## 3 96 4 96 105
## 4 37 4 37 105
## PCT_FN.result PCT_GC.count PCT_GC.result PCT_GF.count PCT_GF.result
## 1 1 105 23 105 19
## 2 3 105 49 105 10
## 3 4 105 18 105 9
## 4 0 105 17 105 1
## PCT_GL.count PCT_GL.result PCT_GL.sd PCT_GL_WT.count PCT_GL_WT.result
## 1 10 0 0.0 10 0
## 2 10 71 19.8 10 71
## 3 10 3 4.8 10 3
## 4 10 48 25.2 10 48
## PCT_HP.count PCT_HP.result PCT_MAA.count PCT_MAA.result PCT_MAP.count
## 1 105 1 105 2 105
## 2 105 0 105 16 103
## 3 105 0 104 9 103
## 4 105 1 95 56 90
## PCT_MAP.result PCT_MAU.count PCT_MAU.result PCT_MCP.count PCT_MCP.result
## 1 2 105 0 105 82
## 2 18 105 0 105 0
## 3 9 104 0 104 0
## 4 57 95 0 95 2
## PCT_MIAT1.count PCT_MIAT1.result PCT_MIAT1P.count PCT_MIAT1P.result
## 1 101 0 26 0
## 2 105 0 41 0
## 3 71 0 59 0
## 4 95 0 3 0
## PCT_MIATP.count PCT_MIATP.result PCT_NSA.count PCT_NSA.result
## 1 101 26 105 2
## 2 105 39 102 19
## 3 71 83 101 9
## 4 95 3 80 64
## PCT_OT.count PCT_OT.result PCT_POOL.count PCT_POOL.result PCT_POOL.sd
## 1 105 0 10 0 0.0
## 2 105 0 10 0 0.0
## 3 105 0 10 1 3.2
## 4 105 0 10 14 23.1
## PCT_POOL_WT.count PCT_POOL_WT.result PCT_RA.count PCT_RA.result
## 1 10 0 10 0
## 2 10 0 10 0
## 3 10 1 10 0
## 4 10 14 10 0
## PCT_RA.sd PCT_RA_WT.count PCT_RA_WT.result PCT_RC.count PCT_RC.result
## 1 0 10 0 105 0
## 2 0 10 0 105 0
## 3 0 10 0 105 0
## 4 0 10 0 105 10
## PCT_RI.count PCT_RI.result PCT_RI.sd PCT_RI_WT.count PCT_RI_WT.result
## 1 10 0 0.0 10 0
## 2 10 29 19.8 10 29
## 3 10 94 8.4 10 94
## 4 10 22 31.6 10 22
## PCT_RN.count PCT_RN.result PCT_RN.sd PCT_RN_WT.count PCT_RN_WT.result
## 1 10 100 0.0 10 100
## 2 10 0 0.0 10 0
## 3 10 2 4.2 10 2
## 4 10 14 19.6 10 14
## PCT_RR.count PCT_RR.result PCT_RS.count PCT_RS.result PCT_SA.count
## 1 105 0 105 0 105
## 2 105 0 105 0 105
## 3 105 0 105 0 105
## 4 105 0 105 0 105
## PCT_SA.result PCT_SAFN.count PCT_SAFN.result PCT_SB.count PCT_SB.result
## 1 49 2 50 105 2
## 2 10 2 13 105 0
## 3 27 2 30 105 13
## 4 12 2 12 105 7
## PCT_SFGF.count PCT_SFGF.result PCT_SLOW.count PCT_SLOW.result
## 1 3 69 2 0
## 2 3 24 2 71
## 3 3 39 2 4
## 4 3 13 2 62
## PCT_SLOW_WT.count PCT_SLOW_WT.result PCT_WD.count PCT_WD.result
## 1 2 0 105 1
## 2 2 71 105 5
## 3 2 4 105 2
## 4 2 62 105 4
## PCT_XB.count PCT_XB.result PWVZ.count PWVZ.result RBP_CHN.result
## 1 105 0 0 NA NA
## 2 105 0 11 18.2 13
## 3 105 0 12 25.0 19
## 4 105 3 14 14.3 16
## RBP_EPI.result RBP_SED.result SB_PP_D10.count SB_PP_D10.result
## 1 NA NA 103 1.03
## 2 12 13 100 1.03
## 3 20 20 103 1.03
## 4 18 13 89 1.03
## SB_PP_D25.count SB_PP_D25.result SB_PP_D50.count SB_PP_D50.result
## 1 103 1.03 103 1.03
## 2 100 15.00 100 36.00
## 3 103 1.03 103 33.00
## 4 89 37.00 89 93.00
## SB_PP_D75.count SB_PP_D75.result SB_PP_D90.count SB_PP_D90.result
## 1 103 19 103 42
## 2 100 60 100 75
## 3 103 160 103 625
## 4 89 172 89 290
## SB_PT_D10.count SB_PT_D10.result SB_PT_D25.count SB_PT_D25.result
## 1 104 1.03 104 1.03
## 2 100 1.03 100 15.00
## 3 103 1.03 103 1.03
## 4 101 1.03 101 43.00
## SB_PT_D50.count SB_PT_D50.result SB_PT_D75.count SB_PT_D75.result
## 1 104 3.515 104 20
## 2 100 36.500 100 60
## 3 103 33.000 103 160
## 4 101 111.000 101 210
## SB_PT_D90.count SB_PT_D90.result SINU.NOT_WORKING SLOPE_0.count
## 1 104 44 28.64934 10
## 2 100 75 28.64934 10
## 3 103 625 28.64934 10
## 4 101 5660 28.64934 10
## SLOPE_0.result SLOPE_0_5.count SLOPE_0_5.result SLOPE_1.count
## 1 10000 10 0 10
## 2 0 10 10000 10
## 3 0 10 10000 10
## 4 10000 10 0 10
## SLOPE_1.result SLOPE_2.count SLOPE_2.result W1_HALL_EMAP.count
## 1 0 10 0 11
## 2 10000 10 10000 11
## 3 10000 10 10000 11
## 4 0 10 0 11
## W1_HALL_EMAP.result W1_HALL_SWAMP.count W1_HALL_SWAMP.result
## 1 0.00 14 0.00
## 2 1.87 14 1.87
## 3 0.66 14 0.66
## 4 1.28 14 1.28
## W1H_BLDG.count W1H_BLDG.result W1H_BLDG.sd W1H_BRDG.count
## 1 22 0.00 0.000 22
## 2 22 0.73 0.131 22
## 3 22 0.00 0.000 22
## 4 22 0.18 0.304 22
## W1H_BRDG.result W1H_BRDG.sd W1H_CROP.count W1H_CROP.result W1H_CROP.sd
## 1 0 0 22 0 0
## 2 0 0 22 0 0
## 3 0 0 22 0 0
## 4 0 0 22 0 0
## W1H_LDFL.count W1H_LDFL.result W1H_LDFL.sd W1H_LOG.count W1H_LOG.result
## 1 22 0.00 0.000 22 0
## 2 22 0.48 0.715 22 0
## 3 22 0.25 0.551 22 0
## 4 22 0.14 0.441 22 0
## W1H_LOG.sd W1H_MINE.count W1H_MINE.result W1H_MINE.sd W1H_ORVY.count
## 1 0 22 0 0 22
## 2 0 22 0 0 22
## 3 0 22 0 0 22
## 4 0 22 0 0 22
## W1H_ORVY.result W1H_ORVY.sd W1H_PARK.count W1H_PARK.result W1H_PARK.sd
## 1 0 0 22 0.00 0.000
## 2 0 0 22 0.11 0.376
## 3 0 0 22 0.00 0.000
## 4 0 0 22 0.00 0.000
## W1H_PIPE.count W1H_PIPE.result W1H_PIPE.sd W1H_PSTR.count
## 1 22 0 0 22
## 2 22 0 0 22
## 3 22 0 0 22
## 4 22 0 0 22
## W1H_PSTR.result W1H_PSTR.sd W1H_PVMT.count W1H_PVMT.result W1H_PVMT.sd
## 1 0 0 22 0.00 0.000
## 2 0 0 22 0.00 0.000
## 3 0 0 22 0.03 0.142
## 4 0 0 22 0.27 0.336
## W1H_ROAD.count W1H_ROAD.result W1H_ROAD.sd W1H_VEGM.count
## 1 22 0.00 0.000 22
## 2 22 0.00 0.000 22
## 3 22 0.24 0.328 22
## 4 22 0.05 0.213 22
## W1H_VEGM.result W1H_VEGM.sd W1H_WALL.count W1H_WALL.result W1H_WALL.sd
## 1 0 0 22 0.00 0.000
## 2 0 0 22 0.55 0.575
## 3 0 0 22 0.14 0.441
## 4 0 0 22 0.64 0.727
## XBEARING.count XBEARING.result XBEARING.sd XBKF_H.count XBKF_H.result
## 1 10 0.01 0 11 0.78
## 2 10 0.01 0 11 0.24
## 3 10 0.01 0 11 1.24
## 4 10 0.01 0 11 0.30
## XBKF_H.sd XBKF_W.count XBKF_W.result XBKF_W.sd XC.count XC.result XC.sd
## 1 0.10 11 21.0 7.40 22 8 11.0
## 2 0.06 11 3.4 0.55 22 57 13.6
## 3 0.44 11 22.2 7.31 22 57 21.6
## 4 0.00 11 30.2 7.43 22 34 22.0
## XCDENBK.count XCDENBK.result XCDENBK.sd XCDENMID.count XCDENMID.result
## 1 22 67 33.2 44 6
## 2 0 NA NA 44 98
## 3 22 97 8.8 44 81
## 4 22 90 24.5 44 15
## XCDENMID.sd XCM.count XCM.result XCMG.count XCMG.result XEMBED.count
## 1 18.8 2 44 4 132 26
## 2 5.3 2 91 4 142 25
## 3 17.1 2 92 4 128 27
## 4 30.0 2 73 4 123 47
## XEMBED.result XEMBED.sd XFC_ALG.count XFC_ALG.result XFC_ALG.sd
## 1 36 19.8 11 0.9 2.0
## 2 24 26.8 11 1.4 2.3
## 3 36 33.9 11 1.8 2.5
## 4 7 14.0 11 27.3 16.9
## XFC_AQM.count XFC_AQM.result XFC_AQM.sd XFC_BIG.count XFC_BIG.result
## 1 11 51.6 13.1 4 1.8
## 2 11 4.5 1.5 4 35.9
## 3 11 0.9 2.0 4 18.7
## 4 11 4.5 1.5 4 59.7
## XFC_BRS.count XFC_BRS.result XFC_BRS.sd XFC_HUM.count XFC_HUM.result
## 1 11 1.8 2.5 11 0.0
## 2 11 4.5 1.5 11 5.9
## 3 11 4.5 1.5 11 0.0
## 4 11 8.6 8.1 11 5.0
## XFC_HUM.sd XFC_LTR.count XFC_LTR.result XFC_LTR.sd XFC_LWD.count
## 1 0.0 11 4.1 2.0 11
## 2 9.7 11 6.8 6.0 11
## 3 0.0 11 2.7 2.6 11
## 4 0.0 11 4.1 2.0 11
## XFC_LWD.result XFC_LWD.sd XFC_NAT_EMAP.count XFC_NAT_EMAP.result
## 1 0.0 0.0 5 12.2
## 2 0.0 0.0 5 40.9
## 3 1.4 2.3 5 28.2
## 4 4.5 1.5 5 68.3
## XFC_NAT_SWAMP.count XFC_NAT_SWAMP.result XFC_OHV.count XFC_OHV.result
## 1 7 67.9 11 8.6
## 2 7 52.2 11 6.4
## 3 7 31.8 11 5.0
## 4 7 76.9 11 5.0
## XFC_OHV.sd XFC_RCK.count XFC_RCK.result XFC_RCK.sd XFC_UCB.count
## 1 8.1 11 0.0 0.0 11
## 2 6.4 11 12.3 10.1 11
## 3 7.1 11 15.9 10.4 11
## 4 0.0 11 45.7 16.4 11
## XFC_UCB.result XFC_UCB.sd XG.count XG.result XGB.count XGB.result XGB.sd
## 1 1.8 2.5 2 88 22 8 14.5
## 2 17.7 10.1 2 51 22 38 26.3
## 3 1.4 2.3 2 36 22 60 24.0
## 4 4.5 1.5 2 50 22 36 27.7
## XGH.count XGH.result XGH.sd XGW.count XGW.result XGW.sd XM.count
## 1 22 71 26.7 22 17 18.6 22
## 2 22 8 16.0 22 43 30.3 22
## 3 22 10 9.5 22 26 19.5 22
## 4 22 19 18.1 22 31 15.1 22
## XM.result XM.sd XMIAT.count XMIAT.result XMIAT.sd XMIATP.count
## 1 36 23.3 101 0.1 0.16 26
## 2 34 16.7 105 0.2 0.21 41
## 3 35 18.3 71 0.2 0.15 59
## 4 39 19.3 95 0.0 0.04 3
## XMIATP.result XMIATP.sd XPCAN.count XPCAN.result XPCM.count XPCM.result
## 1 0.3 0.12 22 0.45 22 0.45
## 2 0.4 0.12 22 1.00 22 1.00
## 3 0.3 0.10 22 1.00 22 1.00
## 4 0.2 0.00 22 0.95 22 0.95
## XPCMG.count XPCMG.result XPGVEG.count XPGVEG.result XPMGVEG.count
## 1 22 0.45 22 1 22
## 2 22 1.00 22 1 22
## 3 22 1.00 22 1 22
## 4 22 0.95 22 1 22
## XPMGVEG.result XPMID.count XPMID.result XSDGM.count XSDGM.result
## 1 1.00 22 0.95 104 5.1
## 2 0.91 22 1.00 100 20.6
## 3 0.77 22 1.00 103 19.3
## 4 0.95 22 1.00 101 97.6
## XSLOPE.count XSLOPE.result XSLOPE.sd XSPGM.result XWAK.count XWAK.result
## 1 10 0.00 0 4.776569 1 195
## 2 10 0.01 0 20.563869 1 230
## 3 10 0.01 0 19.282021 1 140
## 4 10 0.00 0 56.476045 1 80
## XWAK.sd XWDA.count XWDA.result XWDEPTH.count XWDEPTH.result XWDEPTH.sd
## 1 NA 105 0.2696774 105 41.8 36.16
## 2 NA 105 0.2833333 105 6.8 8.01
## 3 NA 105 0.1738318 105 18.6 18.65
## 4 NA 105 0.1107807 105 29.8 43.73
## XWDM.count XWDM.result XWDM.sd XWDO.count XWDO.result XWDO.sd XWDR.count
## 1 21 79.8 15.3 1 9.0 NA 21
## 2 21 14.7 9.0 1 9.0 NA 21
## 3 21 40.1 14.9 1 15.2 NA 21
## 4 21 77.0 53.2 1 8.8 NA 21
## XWDR.result XWIDTH.count XWIDTH.result XWIDTH.sd XWPH.count XWPH.result
## 1 37.08134 21 15.5 4.03 1 7.99
## 2 35.29412 21 2.4 0.64 1 8.02
## 3 57.52688 21 10.7 3.00 0 NA
## 4 90.26846 21 26.9 7.49 1 7.83
## XWPH.sd XWSC.count XWSC.result XWSC.sd XWSL.count XWSL.result XWSL.sd
## 1 NA 1 423.5 NA 1 0.2 NA
## 2 NA 1 1129.0 NA 1 0.6 NA
## 3 NA 1 317.3 NA 1 0.2 NA
## 4 NA 1 117.0 NA 1 0.0 NA
## XWTB.count XWTB.result XWTB.sd XWTC.count XWTC.result XWTC.sd XWTF.count
## 1 0 NA NA 1 14.7 NA 1
## 2 1 3.0 NA 1 15.5 NA 1
## 3 1 0.8 NA 1 15.2 NA 1
## 4 1 4.7 NA 1 22.4 NA 1
## XWTF.result XWTF.sd XWV_F.count XWV_F.result XWV_F.sd XWV_M.count
## 1 58.5 NA 0 NA NA 0
## 2 59.9 NA 11 0.24 0.1828164 11
## 3 59.4 NA 12 0.50 0.4605530 12
## 4 72.3 NA 14 1.43 0.8051704 14
## XWV_M.result XWV_M.sd
## 1 NA NA
## 2 0.07 0.05573669
## 3 0.15 0.14041251
## 4 0.44 0.24547880
Required data checks
-
For every function, make sure there are no duplicate or conflicting values for every unique combination of
id,LocationCode,AnalyteName, andVariableResult(orResult). This should be specific to the metric classes just to be safe. For example, every combination should have only one entry inVariableResultforAnalyteName %in% c('Microalgae Thickness', 'Macrophyte Cover', 'Macroalgae Cover, Attached', 'Macroalgae Cover, Unattached')for the algae metrics. Thealgae.Rfunction 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 thatchkinp()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')foralgae()c('Bankfull Height', 'Bankfull Width', 'StationWaterDepth', 'Wetted Width')forbankmorph()c('Cascade/Falls', 'Dry', 'Glide', 'Pool', 'Rapid', 'Riffle', 'Run'))forchannelmorph()c(Slope', 'Length, Segment', 'Elevation Difference', 'Bearing', 'Proportion', 'Length, Reach')forchannelsinuosity()c('Canopy Cover')fordensiometer()c('Distance from Bank', 'StationWaterDepth', 'Velocity', 'Distance, Float', 'Float Time', 'Wetted Width')forflow()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')forhabitat()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')fordisturbance()c('Riffle/Run Channel Alteration', 'Riffle/Run Epifaunal Substrate', 'Riffle/Run Sediment Deposition', 'Dominant Land Use', 'Evidence of Fire', 'Evidence of Recent Rainfall')formisc()c('Bank Stability')forbankstability()c("Alkalinity as CaCO3", "Oxygen, Dissolved", "pH", "Salinity", "SpecificConductivity", "Temperature", "Turbidity")forquality()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')forripveg()c('Substrate Size Class', 'Embeddedness', 'CPOM')forsubstrate()
-
Check for required values in
LocationCode(note thatchkinp()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 withtidyr::complete()but may be unnecessary since this will increase data volume
Metadata
Resources: SOP, Technical memo Contact: Raphael Mazor, Robert Butler
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