# Vignette, BCGcalc

#### Erik.Leppo@tetratech.com

#### 2026-07-31

# Purpose

The `BCGcalc` package was created to enable users to generate Biological Condition Gradient (BCG) model outputs for macroinvertebrate data from freshwater wadeable streams in the Puget Lowlands and Willamette Valley ecoregions (Stamp and Gerritsen 2018). With modification, this R code can be used to generate outputs for other BCG models as well.

This vignette covers the basics going from raw data to model results. Any of the code in this Vignette can be copied and pasted to an R session and it will produce the same results as shown here. Each section of code (gray box) is independent such that no other code needs to be run except what is in that section. Thus, there is some repetition of steps between sections.

No files are exported in the examples in the vignette. All “write” statements have been commented out. If you wish to save the output remove the “#” from before each line of code. Several different “write” functions were used in the examples. This was intentional such that intermediate files are output as TSV (tab-separated values) files and final results are output as CSV (comma-separated values) files. Both formats will open in Excel.

# Background

When applying the BCG, users should keep in mind that they can run any data through the model and get a result. However, if samples for the Puget Lowlands and Willamette Valley macroinvertebrate BCG model do not meet the criteria below, results should be interpreted with caution because they are outside the experience of this particular BCG model.

## Criteria

- Size: wadeable streams with drainage areas ranging from 1 to 100 mi2

- Geographic area: Puget Lowlands (eco code 2) and Willamette Valley (eco code 3) EPA level3 ecoregions

- Stream type: freshwater, perennial; no unique habitats (such as springs and seeps)

- Target number of organisms: 500-count (subsampled to 600 total individuals where needed)

- Sampling area: ≥8 ft2

- Level of taxonomic resolution: lowest practical level except for mites, which should be collapsed to the Order-level (Trombidiformes)

- Collection gear: D-Frame kick-nets with 500-micrometer net mesh

- Collection method: a targeted “riffle only” sampling scheme (like those used by King County and ODEQ) or WA ECY’s multi-habitat, ‘reach-wide’ sampling scheme

- Collection period: July through October

Results should be interpreted with caution if they are flagged for any of the criteria listed in the ‘Flags’ section at the end of the vignette (e.g., brackish influence, extreme dominance by one or two taxa).

## Disclaimer

Version 1 of the Puget Lowlands and Willamette Valley macroinvertebrate BCG model has known limitations and will need further testing in coming years. The model should be regarded as a beta version, with potential for refinement over time as the model is used with new data.

## Literature cited

Stamp, J. and J. Gerritsen. 2018. Calibration of the Biological Condition Gradient (BCG) for Macroinvertebrate Assemblages in Puget Lowland/Willamette Valley Freshwater Wadeable Streams. Prepared by Tetra Tech for the US EPA Office of Water, Office of Science and Technology and US EPA Region 10.

# Installation

The package is hosted on GitHub (https://github.com/leppott/BCGcalc) and can be installed using the following lines of code. It is necessary to install the `devtools` package.

    # Installing the BCGcalc library (with the vignette) from GitHub
    library(devtools)
    install_github("leppott/BCGcalc", force=TRUE, build_vignettes=TRUE)

# Help

After the BCGcalc package has been installed running the following line of code will open the help file with links to all functions.

    help(package="BCGcalc")

# ‘extdata’ files

When you install the BCGcalc R package, the following files are contained in the ‘extdata’ folder in the BCGcalc library folder:

- TaxaMaster_Bug_BCG_PugLowWilVal – this Excel file contains the master taxa list from the Puget Lowlands and Willamette Valley BCG project, and associated attribute information (NonTarget, BCG attribute, Thermal_Indicator, FFG, Habit, LifeCycle, TolVal). This file is not referenced by the R code; rather its purpose is to help users create their own input data files.

- Rules - Excel file that contains worksheets with the BCG rules that the R code references; the worksheet titled ‘BCG_PugLowWilVal_500ct’ is used for the 500-count model. The worksheet titled ‘BCG_PugLowWilVal_300ct’ is used for the (preliminary) 300-count model.

- Data_BCG_PugLowWilVal – Excel file that can be used as a template for your input file. It contains data for the 678 samples that were in the Puget Lowlands and Willamette Valley BCG calibration dataset. Column headings for required fields are highlighted in green.

- MetricNames – Excel file that contains a list of all the potential metrics that can be calculated with the BCGcalc R tool. This file is not referenced by the R code.

- MetricFlags - if any of these criteria are not met, the sample is flagged to alerts users that the sample is unusual (e.g., brackish water, too few organisms, reduced sampling effort). Results for flagged samples should be interpreted with caution.

- PL_WV_ThermalIndicator_20180326 – detailed information on how the thermal indicator designations were made for the Puget Lowlands and Willamette Valley, using temperature tolerance analyses and expert elicitation.

- ExampleMunge_Slope – see Example, New Data section below

- ExampleMunge_UnformatedData - see Example, New Data section below

# Data Preparation

There are a number of required fields for the input file. If any fields are missing the user will be prompted as to which are missing and the user can decide whether to continue or quit. If the user continues, the missing fields will be added but will be filled with zero or NA (as appropriate). Any metrics based on the missing fields will not be valid.

Required Fields:

- SAMPLEID

  - Unique sample identifier

  - Valid entries: character or number, must be unique

- TAXAID

  - Unique taxa identifier

  - Valid entries: character or number, must be unique

- N_TAXA

  - Number of individuals

  - Valid entries: number

- EXCLUDE

  - Non-unique/non-distinct taxa are excluded from richness metric calculations but are counted in the other metrics. Appendix B of the ‘BCGcalc_README_20180919’ Word document describes the Exclude Taxa Decision Criteria that was used during BCG model calibration.

  - Valid entries: TRUE or FALSE

  - Non-unique/non-distinct taxa should be entered as “TRUE”

- NONTARGET

  - Non-target taxa are not part of the intended capture list; e.g., fish, herps, water column taxa. They are excluded from all metric calculations.

  - Valid entries: TRUE or FALSE.

  - NonTarget taxa should be entered as “TRUE”

- INDEX_NAME

  - Name of the BCG rules worksheet in the ‘Rules’ file (in the ‘extdata’ folder) that the R code is referencing.

  - Valid entries for the Puget Lowlands/Willamette Valley model: BCG_PugLowWilVal_500ct or BCG_PugLowWilVal_300ct.

- SITE_TYPE

  - Select which BCG model to apply: Low (lo) gradient (<1% NHD+ v2 flowline slope) or high (hi) gradient (≥ 1% NHD+ v2 flowline slope).

  - Valid entries: “hi” or “lo”.

- PHYLUM, SUBPHYLUM, CLASS, ORDER, FAMILY, SUBFAMILY, TRIBE, GENUS

  - Phylogeny (see source file ‘TaxaMaster_Bug_BCG_PugLowWilVal’; note: this may not cover all of the taxa in your input file).

  - Other phylogenetic rankings (e.g., SubOrder or SuperFamily) can be included but are not used in the current metric calculations.

  - Valid entries: text

- BCG_Attr

  - BCG attribute assignments for the Puget Lowlands and Willamette Valley (Stamp and Gerritsen 2018).

  - Valid entries: 1i, 1m, 2, 3, 4, 5, 6; if not available, leave blank or enter ‘NA’.

- FFG, HABIT, LIFE_CYCLE, TOLVAL, THERMAL_INDICATOR

  - FFG

    - Valid values for FFG: CG, CF, PR, SC, SH

    - Function feeding group entries in the ‘TaxaMaster_Bug_BCG_PugLowWilVal’ file were compiled from ODEQ, WA ECY and the EPA National Aquatic Resource Surveys (NARS) but the BCG workgroup did not try to reach consensus.

  - HABIT

    - Valid values for HABIT: BU, CB, CN, SP, SW

    - Habit designations need to come from the user (the BCG workgroup did not attempt to reach regional consensus/reconcile differences across entities).

  - LIFE_CYLCE

    - Valid values for LIFE_CYCLE: UNI, SEMI, MULTI

    - Life cycle designations need to come from the user (the BCG workgroup did not attempt to reach regional consensus/reconcile differences across entities).

  - THERMAL_INDICATOR

    - Valid values for THERMAL_INDICATOR: COLD, COLD_COOL, COOL_WARM, WARM 
    - Specific to the Puget Lowlands and Willamette Valley. Detailed information on how the designations were made can be found in the PL_WV_ThermalIndicator_20180326 file in the ‘extdata’ folder.

Fields that are optional but encouraged: Area_mi2, SurfaceArea, Density_m2, Density_ft2. These fields are used for flagging unusual samples (see Flag section below). The R code can be adapted to include these fields in the output (see examples below).

Important!

- BCG_Attr: For the BCG model results to be accurate and valid, users should make sure the BCG attributes in their input file match with those that are in the Excel file titled ‘TaxaMaster_Bug_BCG_PugLowWilVal.’ Several of the BCG rules are based on BCG attribute metrics.The BCG workgroup went through a lengthy process to reach consensus on the BCG attribute assignments (BCG_Attr) for the Puget Lowlands and Willamette Valley (for more details, see Stamp and Gerritsen 2018).

- Site type: the designations in the BCG calibration dataset were based on the NHD+ v2 flowline slope but users can also base their gradient designations on other sources (such as reach-scale measurements). The 1% threshold should be regarded as a fuzzy versus distinct line, as it represents a transitional zone where streams likely share characteristics of both low and high gradient stream types. Because of this, we recommend that users run sites with 0.5% to 1.5% slope through both BCG models and report both sets of results.

- Operational taxonomic units (OTUs): All benthic macroinvertebrate taxa should be identified to the appropriate operational taxonomic unit (OTU). For the Puget Lowlands/Willamette Valley BCG model, this is the lowest practical level except for mites, which should be collapsed to the Order-level (Trombidiformes).

- Subsampling: The Puget Lowlands/Willamette Valley BCG model was calibrated for 500-count samples (+/- 20%). If any of your samples have more than 600 organisms, run your dataset through the Rarify (subsampling) routine (600 is +20% of the 500-count target), which is described below. The subsampling is done to make richness metrics comparable across the 500-count samples. Samples with less an 400 organisms will be flagged for small sample size and should be investigated further before accepting the model output.

The master taxa list is a data object in the package. It can be viewed or saved with the code below.

    library(BCGcalc)

    View(TaxaMaster_Ben_BCG_PugLowWilVal)

    # Save to working directory
    #write.csv(TaxaMaster_Ben_BCG_PugLowWilVal
    #          , "TaxaMaster_Ben_BCG_PugLowWilVal_20180927.csv")

The first few lines are also displayed below.

PugLowWilVal BCG Master Taxa
TaxaID | Phylum | SubPhylum | Class | SubClass | Order | SuperFamily | Family | Tribe | Genus | SubGenus | Species | BCG_Attr | NonTarget | Thermal_Indicator | Long_Lived | FFG | Habit | Life_Cycle | TolVal
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
Oligochaeta | Annelida | Clitellata | Oligochaeta | Oligochaeta | NA | NA | NA | NA | NA | NA | NA | 4 | FALSE | NA | no | GC | CN | Uni | 7
Trombidiformes | Arthropoda | Chelicerata | Arachnida | Acari | Trombidiformes | NA | NA | NA | NA | NA | NA | 4 | FALSE | NA | no | NA | CN | Uni | 7
Elmidae | Arthropoda | Hexapoda | Insecta | Pterygota | Coleoptera | NA | Elmidae | NA | NA | NA | NA | 4 | FALSE | NA | yes | GC | CN | Uni | 7
Lara | Arthropoda | Hexapoda | Insecta | Pterygota | Coleoptera | NA | Elmidae | NA | Lara | NA | NA | 4 | FALSE | cold_cool | yes | SH | CN | Uni | 7
Optioservus | Arthropoda | Hexapoda | Insecta | Pterygota | Coleoptera | NA | Elmidae | NA | Optioservus | NA | NA | 4 | FALSE | cool_warm | yes | SC | CN | Uni | 7
Heterlimnius corpulentus | Arthropoda | Hexapoda | Insecta | Pterygota | Coleoptera | NA | Elmidae | Elmini | Heterlimnius | NA | corpulentus | 3 | FALSE | cold_cool | yes | GC | CN | Uni | 7

# Package Functions

The suite of functions in the `BCGcalc` package are presented in two sections.
The first section will cover the core functions from metric calculation to model results. The example will cover all steps in a single example. Additional functions will be covered individually and each function will have its own self contained example.

1. BCG Core Functions

   A. Metric Calculation (BioMonTools package)

   B. Metric Membership (Scoring)

   C. Level Membership

   D. Level Assignment

   E. Add Flags

2. Additional (Optional) Functions

   A. Subsample (BioMonTools package)

   B. Metric Calculation, Save Specific Metrics

   C. Flags (BioMonTools package)

## Core Functions

Once your input file is formatted and ready to go, the next step is to run it through the R code. The R code generates BCG level assignments for each sample. Along the way it calculates the following: metric values, metric membership values, BCG level membership and BCG level assignments. It also adds flags to the BCG level assignment file.

Below are two examples of R code that can be used to generate BCG model outputs. This code is written for 500-count samples (which is what the PugLowWilVal BCG model is calibrated for).

The first example below is for test data that is automatically downloaded onto your computer when you install the BCGcalc R package. If it’s your first time running this code, and you are a novice R user, we recommend trying this code first (you can follow it verbatim, no edits needed, and it should generate the desired output).

The second example is for a ‘new’ data file (to simulate you running the R code on your own data).

### Example, Test Data

The code below uses the test data that is contained in the package and is already of the proper format.

If you decide to run the example below, the following four files will appear in your working directory.

- metrics.values.Test.tsv

- Metric.Membership.Test.tsv

- Level.Membership.Test.tsv

- Levels.Flags.Test.csv

    # Packages
    library(BCGcalc)
    library(readxl)
    library(reshape2)
    library(BioMonTools)

    # Import
    df.samps.bugs <- read_excel(
      system.file("./extdata/Data_BCG_PugLowWilVal.xlsx",
                  package="BCGcalc"),
      guess_max = 10^6)

    # QC for TRUE/FALSE (both ok)
    # Exclude to TRUE/FALSE
    table(df.samps.bugs$Exclude)
    # NonTarget to TRUE/FALSE
    table(df.samps.bugs$NonTarget)

    # Add missing columns
    col_add_char <- c("INFRAORDER",
                      "HABITAT",
                      "ELEVATION_ATTR",
                      "GRADIENT_ATTR",
                      "WSAREA_ATTR",
                      "HABSTRUCT")
    col_add_num <- "UFC"
    df.samps.bugs[, col_add_char] <- NA_character_
    df.samps.bugs[, col_add_num] <- NA_integer_

    # 1.A. Calculate Metrics
    # Extra columns to keep in results
    keep.cols <- c("Area_mi2",
                   "SurfaceArea",
                   "Density_m2",
                   "Density_ft2")
    # Run Function
    df.metrics <- metric.values(df.samps.bugs,
                                "bugs",
                                fun.cols2keep = keep.cols)
    # QC
    dim(df.metrics)
    # View(df.metrics)
    # Save
    # write.table(df.metrics,
    #             "Metric.Values.Test.tsv",
    #             col.names = TRUE,
    #             row.names = FALSE,
    #             sep = "\t")

    # 1.B. Metric Membership
    # Import Rules
    df.rules <- read_excel(
      system.file("./extdata/Rules.xlsx",
                  package = "BCGcalc"),
      sheet = "Rules")
    # Run function
    df.Metric.Membership <- BCG.Metric.Membership(df.metrics,
                                                  df.rules)
    # Show Results
    # View(df.Metric.Membership)
    # Save Results
    # write.table(df.Metric.Membership,
    #             "Metric.Membership.Test.tsv",
    #             row.names = FALSE,
    #             col.names = TRUE,
    #             sep = "\t")

    # 1.C. Level Assignment
    # Run Function
    df.Level.Membership <- BCG.Level.Membership(df.Metric.Membership,
                                                df.rules)
    # Show results
    # View(df.Level.Membership)
    # Save Results
    # write.table(df.Level.Membership,
    #             "Level.Membership.Test.tsv",
    #             row.names = FALSE,
    #             col.names = TRUE,
    #             sep = "\t")

    # 1.D. Level Membership
    # Run Function
    df.Levels <- BCG.Level.Assignment(df.Level.Membership)

    # 1.E. Flags
    # Import QC Checks
    df.checks <- read_excel(system.file("./extdata/MetricFlags.xlsx",
                                        package = "BCGcalc"),
                            sheet = "Flags")
    # Run Function
    df.flags <- qc.checks(df.metrics, df.checks)
    # Change terminology; PASS/FAIL to NA/flag
    df.flags[, "FLAG"][df.flags[, "FLAG"] == "FAIL"] <- "flag"
    df.flags[, "FLAG"][df.flags[, "FLAG"] == "PASS"] <- NA
    # long to wide format
    df.flags.wide <- dcast(df.flags,
                           SAMPLEID ~ CHECKNAME,
                           value.var = "FLAG")
    # Calc number of "flag"s by row.
    df.flags.wide$NumFlags <- rowSums(df.flags.wide == "flag", na.rm = TRUE)
    # Rearrange columns
    NumCols <- ncol(df.flags.wide)
    df.flags.wide <- df.flags.wide[, c(1, NumCols, 2:(NumCols-1))]
    # Merge Levels and Flags
    df.Levels.Flags <- merge(df.Levels,
                             df.flags.wide,
                             by.x = "SampleID",
                             by.y = "SAMPLEID",
                             all.x = TRUE)
    # Show Results
    # View(df.Levels.Flags)
    # Summarize Results
    table(df.flags[, "CHECKNAME"], df.flags[, "FLAG"], useNA = "ifany")
    # Save Results
    # write.csv(df.Levels.Flags, "Levels.Flags.Test.csv")

### Example, New Data

The flexibility of R allows the user to get data from a multitude of sources and then manipulate (munge) it to fit the format needed for the functions in `BCGcalc`. The example below shows how to import a file, add slope from a 2nd file, and to make a few changes to the data in order to use it with the package. When the data source is fixed this routine can be modified and then used on all future datasets to prepare them for use with `BCGcalc`.

Before running this on your own data, you will need to update the directories, the name of the input file and potentially a few other fields. In this example, the input file is called ‘ExampleMunge_UnformatedData.xlsx’. Remember - when you type in your working directory that you either need two backslashes “\” or one forward slash “/”. If you copy and paste the directory from Windows File Explorer , it comes in as one backslash so you will need to manually correct this for the code to work.

    # Setup
    library(readxl)
    library(dplyr)
    library(BCGcalc)
    library(BioMonTools)
    library(reshape2)

    # Read File
    ## FileName
    fn.data <- system.file("./extdata/ExampleMunge_UnformatedData.xlsx"
                           , package="BCGcalc")
    # wd <- "F:\\myDocs"
    # fn.data <- file.path(wd, "ExampleMunge_UnformatedData.xlsx")

    ## Worksheet
    sh.data <- "SamplesWithBioticAttributesAndR"
    ## Import
    ### set "guess" to a large number to avoid type being wrong
    df.data <- read_excel(fn.data,
                          sheet = sh.data,
                          guess_max = 12000)
    dim(df.data)

    # Munge
    ## Col Names
    ### convert to upper case
    names(df.data) <- toupper(names(df.data))
    ### Rename Columns (base R) [dplyr::rename not working]
    names(df.data)[names(df.data) == "SAMPLE ID"] <- "SAMPLEID"
    names(df.data)[names(df.data) == "TAXON"] <- "TAXAID"
    names(df.data)[names(df.data) == "SAMPLE ID"] <- "SAMPLEID"
    names(df.data)[names(df.data) == "QUANTITY SUBSAMPLING"] <- "N_TAXA"
    #names(df.data)[names(df.data) == "HILSENHOFF BIOTIC TOLERANCE INDEX"] <- "TOLVAL"
    # df.data <- df.data %>% rename("SAMPLEID"="SAMPLE ID"
    #                              , "TAXAID"="TAXON"
    #                              , "N_TAXA"="QUANTITY SUBSAMPLING"
    #                              , "TOLVAL"="HILSENHOFF BIOTIC TOLERANCE INDEX"
    #                              )
    ### Create columns
    df.data$EXCLUDE    <- !df.data$UNIQUE
    df.data$NONTARGET  <- df.data$`OUTSIDE PROTOCOL`
    # df.data$FFG        <- NA
    # df.data$FFG[df.data$PREDATOR==TRUE]  <- "PR"
    # df.data$HABIT      <- NA
    # df.data$HABIT[df.data$CLINGER==TRUE] <- "CN"
    # df.data$LIFE_CYCLE <- NA
    df.data$SITE_TYPE  <- NA
    # df.data$BCG_ATTR   <- NA
    # df.data$THERMAL_INDICATOR <- NA
    df.data$INDEX_NAME <- "BCG_PugLowWilVal_500ct"
    df.data$SURFACEAREA <- df.data$`SURFACE AREA`
    df.data$AREA_MI2 <- NA
    df.data$DENSITY_M2 <- NA
    df.data$DENSITY_FT2 <- NA

    # Add slope (and then gradient for SiteType) from NHD+ v2
    fn.slope <- system.file("./extdata/ExampleMunge_Slope.xlsx",
                            package="BCGcalc")
    # fn.slope <- file.path(wd, "ExampleMunge_Slope.xlsx")
    df.slope <- read_excel(fn.slope)
    names(df.slope) <- toupper(names(df.slope))
    # merge files
    df.comb.slope <- merge(df.data,
                           df.slope,
                           by.x = "SITE CODE",
                           by.y = "SITE_CODE",
                           all.x = TRUE)
    # QC (rows)
    dim(df.data)
    dim(df.comb.slope)
    nrow(df.data) == nrow(df.comb.slope)
    df.comb.slope$SITE_TYPE <- df.comb.slope$`SLOPE CATEGORY`

    # Update Taxa Attributes from Master Taxa List in Package
    df.taxamaster <- TaxaMaster_Ben_BCG_PugLowWilVal
    names(df.taxamaster) <- toupper(names(df.taxamaster))
    ## Assume phylogenetic information is correct.
    col.auteco <- c("TAXAID",
                    "BCG_ATTR",
                    "THERMAL_INDICATOR",
                    "LONG_LIVED",
                    "FFG",
                    "HABIT",
                    "LIFE_CYCLE",
                    "TOLVAL")
    df.comb.slope.auteco <- merge(df.comb.slope,
                                  df.taxamaster[, col.auteco],
                                  by.x = "TAXAID",
                                  by.y = "TAXAID",
                                  all.x = TRUE)
    nrow(df.comb.slope) == nrow(df.comb.slope.auteco)

    # SiteClass to Index_Class
    df.comb.slope.auteco$INDEX_CLASS <- df.comb.slope.auteco$SITE_TYPE

    # Create Anlaysis File
    col2keep <- c("SAMPLEID",
                  "INDEX_NAME",
                  "INDEX_CLASS",
                  "AREA_MI2",
                  "SURFACEAREA",
                  "DENSITY_M2",
                  "DENSITY_FT2",
                  "TAXAID",
                  "N_TAXA",
                  "EXCLUDE",
                  "NONTARGET",
                  "PHYLUM",
                  "SUBPHYLUM",
                  "CLASS",
                  "ORDER",
                  "FAMILY",
                  "SUBFAMILY",
                  "TRIBE",
                  "GENUS",
                  "FFG",
                  "HABIT",
                  "LIFE_CYCLE",
                  "TOLVAL",
                  "BCG_ATTR",
                  "THERMAL_INDICATOR")
    df.samps.bugs <- as.data.frame(df.comb.slope.auteco[, col2keep ])

    #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    # Repeat code from previous example
    # (with minor edits)
    #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    # QC for TRUE/FALSE (both ok)
    # Exclude to TRUE/FALSE
    table(df.samps.bugs$EXCLUDE)
    # NonTarget to TRUE/FALSE
    table(df.samps.bugs$NONTARGET)

    # 1.A. Calculate Metrics
    # Extra columns to keep in results
    keep.cols <- toupper(c("Area_mi2",
                           "SurfaceArea",
                           "Density_m2",
                           "Density_ft2"))
    # Run Function
    df.metrics <- metric.values(df.samps.bugs,
                                "bugs",
                                fun.cols2keep = keep.cols,
                                boo.Shiny = TRUE)
    # QC
    dim(df.metrics)
    # View(df.metrics)
    # Save
    # write.table(df.metrics
    #             , "Metric.Values.New.tsv"
    #             , col.names = TRUE
    #             , row.names = FALSE
    #             , sep = "\t")

    # 1.B. Metric Membership
    # Import Rules
    df.rules <- read_excel(system.file("./extdata/Rules.xlsx"
                                 , package="BCGcalc")
                           , sheet="Rules")
    names(df.rules)[names(df.rules) %in% "Index_Name"] <- "INDEX_NAME"
    # Run function
    df.Metric.Membership <- BCG.Metric.Membership(df.metrics, df.rules)
    # Show Results
    # View(df.Metric.Membership)
    # Save Results
    # write.table(df.Metric.Membership,
    #             "Metric.Membership.New.tsv",
    #             row.names = FALSE,
    #             col.names = TRUE,
    #             sep = "\t")

    # 1.C. Level Assignment
    # Run Function
    df.Level.Membership <- BCG.Level.Membership(
      df.Metric.Membership,
      df.rules)
    # # Show results
    # View(df.Level.Membership)
    # Save Results
    # write.table(df.Level.Membership,
    #             "Level.Membership.New.tsv",
    #             row.names = FALSE,
    #             col.names = TRUE,
    #             sep = "\t")

    # 1.D. Level Membership
    # Run Function
    df.Levels <- BCG.Level.Assignment(df.Level.Membership)

    # 1.E. Flags
    # Import QC Checks
    df.checks <- read_excel(
      system.file("./extdata/MetricFlags.xlsx",
                  package = "BCGcalc"),
      sheet = "Flags")
    # Run Function
    df.flags <- qc.checks(df.metrics, df.checks)
    # Change terminology; PASS/FAIL to NA/flag
    df.flags[, "FLAG"][df.flags[, "FLAG"] == "FAIL"] <- "flag"
    df.flags[, "FLAG"][df.flags[, "FLAG"] == "PASS"] <- NA
    # long to wide format
    df.flags.wide <- dcast(df.flags,
                           SAMPLEID ~ CHECKNAME,
                           value.var="FLAG")
    # Calc number of "flag"s by row.
    df.flags.wide$NumFlags <- rowSums(df.flags.wide == "flag", na.rm = TRUE)
    # Rearrange columns
    NumCols <- ncol(df.flags.wide)
    df.flags.wide <- df.flags.wide[, c(1, NumCols, 2:(NumCols - 1))]
    # Merge Levels and Flags
    df.Levels.Flags <- merge(df.Levels,
                             df.flags.wide,
                             by.x = "SampleID",
                             by.y = "SAMPLEID",
                             all.x = TRUE)
    # Show Results
    # View(df.Levels.Flags)
    # Summarize Results
    table(df.flags[, "CHECKNAME"], df.flags[, "FLAG"], useNA = "ifany")
    # Save Results
    # write.csv(df.Levels.Flags, "Levels.Flags.New.csv")

## Additional (Optional) Functions

There are some ancillary tasks that are included in the `BCGcalc` package for convenience.

### Subsample (Rarify)

The `rarify` function subsamples count data to a fixed count per sample. It takes as an input a 3 column data frame (SampleID, TaxonID, Count) and returns a similar dataframe with revised Counts. The names of the columns does not matter as they are specified in the code. Any non-count taxa (e.g., fish in a bug sample) should be removed prior to using the `rarify` function. The function code is from USEPA Corvallis John Van Sickle’s R code for RIVPACS (v1.0, 2005-06-10) and was tweaked for the addition of a user provided seed so repeatable results can be obtained. It is included in the package BioMonTools (https://github.com/leppott/BioMonTools).

The other function inputs are subsample size (target number of organisms in each sample) and seed. The seed is given so the results can be reproduced from the same input file. If no seed is given a random seed is used. An example seed is the date of admission to the Union for each state where the data is collected (e.g., Washington is 18891111). These values can be found on Wikipedia on the right sidebar for each State.

If you are running the 500-count BCG model and any of your samples have more than 600 organisms (the upper limit for the model), you should randomly subsample your data to 600 (600 is +20% of the 500-count target). This is done to make richness metrics comparable across the 500-count samples. You can do this with the Rarify routine.

Before you run the code below on your own data, you’ll need to update the directories, the name of the input file and potentially a few other fields. In this example, the input file is called ‘ExampleMunge_UnformatedData.xlsx’.

After you are done with the subsampling, bring the updated N_Taxa field into your input file (see example file titled ‘ExampleDataFile’; we retained the original data in an optional field called N_Taxa_orig). Then run your data file through the BCGcalc example code described previously in this document.

    library(BCGcalc)
    library(knitr)
    library(BioMonTools)

    # Subsample to 600 organisms (from over 600 organisms) for 12 samples.

    ## FileName
    ### Package example
    df_data <- BioMonTools::data_bio2rarify
    ### Excel
    # wd <- "F:\\myDocs"
    # fn_data <- file.path(wd, "ExampleMunge_UnformatedData.xlsx")
    # readxl::read_excel(fn.data)
    ### CSV
    # fn_data <-
    # df_data <- read.csv(fn_data)
    #
    df_biodata <- df_data
    #dim(df_biodata)
    #View(df_biodata)

    # subsample
    mySize  <- 600
    Seed_OR <- 18590214
    Seed_WA <- 18891111
    Seed_US <- 17760704
    bugs_mysize <- BioMonTools::rarify(inbug = df_biodata,
                                       sample.ID = "SampleID",
                                       abund = "N_Taxa",
                                       subsiz = mySize,
                                       mySeed = Seed_US)
    #dim(bugs.mysize)
    #View(bugs.mysize)

    # Compare pre- and post- subsample counts
    df_compare <- merge(df_biodata,
                        bugs_mysize,
                        by=c("SampleID", "TaxaID"),
                        suffixes = c("_Orig","_600"))
    df_compare <- df_compare[, c("SampleID",
                                 "TaxaID",
                                 "N_Taxa_Orig",
                                 "N_Taxa_600")]
    #View(df.compare)

    # compare totals
    tbl_compare <- head(df_compare)
    tbl_compare_caption <- "First few rows of original and rarified data."
    kable(tbl_compare, caption=tbl_compare_caption)

First few rows of original and rarified data.
SampleID | TaxaID | N_Taxa_Orig | N_Taxa_600
--- | --- | --- | ---
01103CSR_Bug_2001-08-27_0 | Ceratopogoninae | 237 | 179
01103CSR_Bug_2001-08-27_0 | Cheumatopsyche | 2 | 0
01103CSR_Bug_2001-08-27_0 | Chironomini | 8 | 4
01103CSR_Bug_2001-08-27_0 | Cladocera | 2 | 2
01103CSR_Bug_2001-08-27_0 | Coenagrionidae | 2 | 1
01103CSR_Bug_2001-08-27_0 | Corbicula | 2 | 1

    tbl_totals <- aggregate(
      cbind(N_Taxa_Orig, N_Taxa_600) ~ SampleID,
      df_compare, sum)
    tbl_totals_caption <- "Comparison of total individuals per sample."
    kable(tbl_totals, caption=tbl_totals_caption)

Comparison of total individuals per sample.
SampleID | N_Taxa_Orig | N_Taxa_600
--- | --- | ---
01103CSR_Bug_2001-08-27_0 | 816 | 600
02087REF_Bug_2002-08-22_0 | 542 | 542
03013CSR_Bug_2003-07-01_0 | 508 | 508
03053CSR_Bug_2003-08-14_0 | 573 | 573
03054CSR_Bug_2003-08-18_0 | 558 | 558
06012CSR_Bug_2006-09-05_0 | 545 | 545
06019CSRw_Bug_2006-09-14_0 | 711 | 600
06021CSR_Bug_2006-08-01_0 | 706 | 600
06022CSR_Bug_2006-08-17_0 | 555 | 555
06024CSR_Bug_2006-07-27_0 | 569 | 569
06025CSR_Bug_2006-08-03_0 | 543 | 543
06027CSR_Bug_2006-07-17_0 | 569 | 569

    # save the data
    #write.table(bugs.mysize,paste("bugs",mySize,"txt",sep="."),sep="\t")

### Metric Calculation, Save Specific Metrics

You can adapt the code so that the metric calculation output only includes a subset of the metrics.

For example, you may only want to view the following metrics;

- Metrics that go into the BCG model calculation (there are 12). See example #1 below.

- Thermal indicator metrics (ti), c=cold, cc = cold/cool, cw = cool/warm, w= warm.
  See example #2 below.

You can select specific metrics one of two ways:

1. If you know the names of the metrics, write them into the `metric.values`
   function R code as shown in Example #1 below; or

2. Run the ‘normal’ `metrics.values` R code for to generate an output that includes the full set of metrics, then examine the results and run additional code as shown in Example # 2 to limit the output to the desired metrics.

#### Example 1

Knowing the names of the metrics, use them as input in the metric.values function.

    # Packages
    library(BCGcalc)
    library(readxl)
    library(knitr)
    library(BioMonTools)

    # Load Data
    df.data <- read_excel(system.file("./extdata/Data_BCG_PugLowWilVal.xlsx"
                                           , package="BCGcalc")
                          , guess_max = 10^6)
    # Columns to keep
    myCols <- c("Area_mi2",
                "SurfaceArea",
                "Density_m2",
                "Density_ft2")
    # Metrics of Interest (BCG)
    col.met2keep <- c("ni_total",
                      "nt_total",
                      "nt_BCG_att1i2",
                      "pt_BCG_att1i23",
                      "pi_BCG_att1i23",
                      "pt_BCG_att56",
                      "pi_BCG_att56",
                      "nt_EPT_BCG_att1i23",
                      "pi_NonInsJugaRiss_BCG_att456",
                      "pt_NonIns_BCG_att456",
                      "nt_EPT",
                      "pi_NonIns_BCG_att456")
    # Run Function
    df.metval <- metric.values(df.data,
                               "bugs",
                               fun.cols2keep = myCols,
                               fun.MetricNames = col.met2keep,
                               boo.Shiny = TRUE)

    # Select columns
    col.ID <- c("SAMPLEID",
                toupper(myCols),
                "INDEX_NAME")
    # Ouput
    df.metval.bcg12 <- df.metval[, c(col.ID, col.met2keep)]
    # RMD table
    kable(head(df.metval.bcg12), caption = "Select Metrics, Example 1")

#### Example 2

Examine the results file and select certain metrics to keep.

    # Packages
    library(BCGcalc)
    library(readxl)
    library(knitr)
    library(BioMonTools)

    # Load Data
    df.data <- read_excel(system.file("./extdata/Data_BCG_PugLowWilVal.xlsx"
                                           , package="BCGcalc")
                          , guess_max = 10^6)

    # Add missing columns
    col_add_char <- c("INFRAORDER",
                      "HABITAT",
                      "ELEVATION_ATTR",
                      "GRADIENT_ATTR",
                      "WSAREA_ATTR",
                      "HABSTRUCT")
    col_add_num <- c("UFC",
                     "SAMP_AREA_M2")
    df.data[, col_add_char] <- NA_character_
    df.data[, col_add_num] <- NA_integer_

    # Columns to keep
    myCols <- c("Area_mi2",
                "SurfaceArea",
                # "Density_m2",
                "Density_ft2")

    # Run Function
    df.metval <- metric.values(df.data,
                               "bugs",
                               fun.cols2keep=myCols)
    #> Joining with `by = join_by(SAMPLEID, INDEX_NAME, INDEX_CLASS)`
    # Metrics of Interest
    ## thermal indicator (_ti_)
    #names(df.metval)[grepl("_ti_", names(df.metval))]
    col.met2keep <- c("ni_total",
                      "nt_total",
                      paste0("nt_ti_",
                             c("stenocold",
                               "cold",
                               "cool",
                               "warm",
                               "stenowarm")),
                      paste0("pi_ti_",
                             c("stenocold",
                               "cold",
                               "cool",
                               "warm",
                               "stenowarm")),
                      paste0("pt_ti_",
                             c("stenocold",
                               "cold",
                               "cool",
                               "warm",
                               "stenowarm"))
              )
    col.ID <- c("SAMPLEID",
                toupper(myCols),
                "INDEX_NAME")
    # Ouput
    df.metval.ci <- df.metval[, c(col.ID, col.met2keep)]
    # RMD table
    kable(head(df.metval.ci), caption = "Select Metrics, Example 2")

Select Metrics, Example 2
SAMPLEID | AREA_MI2 | SURFACEAREA | DENSITY_FT2 | INDEX_NAME | ni_total | nt_total | nt_ti_stenocold | nt_ti_cold | nt_ti_cool | nt_ti_warm | nt_ti_stenowarm | pi_ti_stenocold | pi_ti_cold | pi_ti_cool | pi_ti_warm | pi_ti_stenowarm | pt_ti_stenocold | pt_ti_cold | pt_ti_cool | pt_ti_warm | pt_ti_stenowarm
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
02087REF_Bug_2002-08-22_0 | 1.791475 | NA | NA | BCG_PugLowWilVal_500ct | 6 | 4 | 0 | 2 | 2 | 1 | 0 | 0 | 66.66667 | 33.33333 | 16.66667 | 0 | 0 | 50.00000 | 50.00000 | 25.00000 | 0
03054CSR_Bug_2003-08-18_0 | 71.249741 | 8 | NA | BCG_PugLowWilVal_500ct | 3 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 100.00000 | 0.00000 | 0.00000 | 0 | 0 | 100.00000 | 0.00000 | 0.00000 | 0
06012CSR_Bug_2006-09-05_0 | 82.338353 | 8 | NA | BCG_PugLowWilVal_500ct | 25 | 4 | 0 | 3 | 3 | 1 | 0 | 0 | 80.00000 | 76.00000 | 20.00000 | 0 | 0 | 75.00000 | 75.00000 | 25.00000 | 0
06019CSRw_Bug_2006-09-14_0 | 85.519766 | 8 | NA | BCG_PugLowWilVal_500ct | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0.00000 | 0.00000 | 0.00000 | 0 | 0 | 0.00000 | 0.00000 | 0.00000 | 0
06021CSR_Bug_2006-08-01_0 | 1.478739 | 8 | NA | BCG_PugLowWilVal_500ct | 6 | 3 | 0 | 1 | 1 | 1 | 0 | 0 | 16.66667 | 33.33333 | 33.33333 | 0 | 0 | 33.33333 | 33.33333 | 33.33333 | 0
06027CSR_Bug_2006-07-17_0 | 33.632627 | 8 | NA | BCG_PugLowWilVal_500ct | 1 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 0.00000 | 100.00000 | 100.00000 | 0 | 0 | 0.00000 | 100.00000 | 100.00000 | 0

### Flags

Results should be interpreted with caution if they are flagged for any of the criteria listed below. If you run the BCGcalc code on the Test data above, columns with flags will be added into the file with the Level Assignments.

The checks for hi and lo gradient are the same so only one set of checks is shown below.

    #>
    #> There are 1 missing fields in the data:
    #> SAMP_AREA_M2
    #>
    #> If you continue the metrics associated with these fields will be invalid.
    #> For example, if the HABIT field is missing all habit related metrics will not be correct.
    #> Do you wish to continue (YES or NO)?
    #> boo.Shiny == TRUE and interactive == FALSE
    #>                so prompt skipped and value set to '1'.
    #> Warning in metric.values.bugs(myDF = fun.DF, MetricNames = fun.MetricNames, : Metrics related to the following fields are invalid:
    #>    SAMP_AREA_M2
    #> Joining with `by = join_by(SAMPLEID, INDEX_NAME, INDEX_CLASS)`

Flags, Hi Gradient
Index_Name | INDEX_CLASS | Metric_Name | Symbol | Value | CheckName | BioMonTools_MetNam | Comment | SITE_TYPE | INDEX_REGION
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BCG_PugLowWilVal_500ct | Hi | ni_total | > | 600.0 | individuals, Large | TRUE | NA | Hi | Hi
BCG_PugLowWilVal_500ct | Hi | ni_total | < | 450.0 | individuals, small | TRUE | NA | Hi | Hi
BCG_PugLowWilVal_500ct | Hi | Density_m2 | < | 500.0 | Low density (m2) | FALSE | NA | Hi | Hi
BCG_PugLowWilVal_500ct | Hi | Density_ft2 | < | 47.0 | Low density (ft2) | FALSE | NA | Hi | Hi
BCG_PugLowWilVal_500ct | Hi | Area_mi2 | < | 2.0 | catchment, small | FALSE | NA | Hi | Hi
BCG_PugLowWilVal_500ct | Hi | Area_mi2 | > | 100.0 | catchment, Large | FALSE | NA | Hi | Hi
BCG_PugLowWilVal_500ct | Hi | SurfaceArea | < | 8.0 | surface area, small | FALSE | NA | Hi | Hi
BCG_PugLowWilVal_500ct | Hi | ni_brackish | > | 0.0 | brackish organisms present | TRUE | NA | Hi | Hi
BCG_PugLowWilVal_500ct | Hi | ni_Ramello | >= | 10.0 | Ramellogammarus | TRUE | NA | Hi | Hi
BCG_PugLowWilVal_500ct | Hi | pi_dom02 | >= | 50.0 | individuals, dominant 02, Large | TRUE | NA | Hi | Hi
BCG_PugLowWilVal_300ct | Hi | ni_total | > | 360.0 | individuals, Large | TRUE | NA | Hi | Hi
BCG_PugLowWilVal_300ct | Hi | ni_total | < | 240.0 | individuals, small | TRUE | NA | Hi | Hi
BCG_PugLowWilVal_300ct | Hi | Density_m2 | < | 300.0 | Low density (m2) | FALSE | NA | Hi | Hi
BCG_PugLowWilVal_300ct | Hi | Density_ft2 | < | 28.2 | Low density (ft2) | FALSE | NA | Hi | Hi
BCG_PugLowWilVal_300ct | Hi | Area_mi2 | < | 2.0 | catchment, small | FALSE | NA | Hi | Hi
BCG_PugLowWilVal_300ct | Hi | Area_mi2 | > | 100.0 | catchment, Large | FALSE | NA | Hi | Hi
BCG_PugLowWilVal_300ct | Hi | SurfaceArea | < | 8.0 | surface area, small | FALSE | NA | Hi | Hi
BCG_PugLowWilVal_300ct | Hi | ni_brackish | > | 0.0 | brackish organisms present | TRUE | NA | Hi | Hi
BCG_PugLowWilVal_300ct | Hi | ni_Ramello | >= | 10.0 | Ramellogammarus | TRUE | NA | Hi | Hi
BCG_PugLowWilVal_300ct | Hi | pi_dom02 | >= | 50.0 | individuals, dominant 02, Large | TRUE | NA | Hi | Hi

Levels and Flags.
SampleID | INDEX_NAME | INDEX_CLASS | L1 | L2 | L3 | L4 | L5 | L6 | Membership_Total | Membership_Total_QC | Primary_BCG_Level | Primary_Membership | Secondary_BCG_Level | Secondary_Membership | Membership_Diff | Membership_Close | Continuous_BCG_Level | BCG_Status | BCG_Status2 | NumFlags | Low density (ft2) | Ramellogammarus | brackish organisms present | catchment, Large | catchment, small | individuals, Large | individuals, dominant 02, Large | individuals, small | surface area, small
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
02087REF_Bug_2002-08-22_0 | BCG_PugLowWilVal_500ct | Hi | 0 | 0 | 0 | 0 | 0 | 1 | 1 | PASS | 6 | 1 | NA | 0 | 1 | NA | 6 | 6 | 6 | 3 | NA | NA | NA | NA | flag | NA | flag | flag | NA
03054CSR_Bug_2003-08-18_0 | BCG_PugLowWilVal_500ct | Lo | 0 | 0 | 0 | 0 | 0 | 1 | 1 | PASS | 6 | 1 | NA | 0 | 1 | NA | 6 | 6 | 6 | 2 | NA | NA | NA | NA | NA | NA | flag | flag | NA
06012CSR_Bug_2006-09-05_0 | BCG_PugLowWilVal_500ct | Hi | 0 | 0 | 0 | 0 | 0 | 1 | 1 | PASS | 6 | 1 | NA | 0 | 1 | NA | 6 | 6 | 6 | 2 | NA | NA | NA | NA | NA | NA | flag | flag | NA
06019CSRw_Bug_2006-09-14_0 | BCG_PugLowWilVal_500ct | Lo | 0 | 0 | 0 | 0 | 0 | 1 | 1 | PASS | 6 | 1 | NA | 0 | 1 | NA | 6 | 6 | 6 | 2 | NA | NA | NA | NA | NA | NA | flag | flag | NA
06021CSR_Bug_2006-08-01_0 | BCG_PugLowWilVal_500ct | Hi | 0 | 0 | 0 | 0 | 0 | 1 | 1 | PASS | 6 | 1 | NA | 0 | 1 | NA | 6 | 6 | 6 | 3 | NA | NA | NA | NA | flag | NA | flag | flag | NA
06027CSR_Bug_2006-07-17_0 | BCG_PugLowWilVal_500ct | Lo | 0 | 0 | 0 | 0 | 0 | 1 | 1 | PASS | 6 | 1 | NA | 0 | 1 | NA | 6 | 6 | 6 | 2 | NA | NA | NA | NA | NA | NA | flag | flag | NA

Flag Summary.
| flag | NA
--- | --- | ---
Low density (ft2) | 0 | 294
Ramellogammarus | 0 | 294
brackish organisms present | 0 | 294
catchment, Large | 0 | 294
catchment, small | 63 | 231
individuals, Large | 0 | 294
individuals, dominant 02, Large | 290 | 4
individuals, small | 294 | 0
surface area, small | 27 | 267