BCG.Metric.Membership: BCG Metric Membership

In leppott/BCGcalc: Biological Condition Gradient, calculator

BCG Metric Membership

Description

Biological Condition Gradient fuzzy membership for metrics.

Usage

BCG.Metric.Membership(
  df.metrics,
  df.rules,
  input.shape = "wide",
  col_SAMPLEID = "SAMPLEID",
  col_INDEX_NAME = "INDEX_NAME",
  col_INDEX_CLASS = "INDEX_CLASS",
  col_LEVEL = "LEVEL",
  col_METRIC_NAME = "METRIC_NAME",
  col_RULE_TYPE = "RULE_TYPE",
  col_LOWER = "LOWER",
  col_UPPER = "UPPER",
  col_METRIC_VALUE = "METRIC_VALUE",
  col_INCREASE = "INCREASE",
  ...
)

Arguments

df.metrics	Wide data frame with metric values to be evaluated.
df.rules	Data frame of metric thresholds to check.
input.shape	Shape of df.metrics; wide or long. Default is wide.
col_SAMPLEID	Column name for sample id. Default = "SAMPLEID"
col_INDEX_NAME	Column name for index name. Default = "INDEX_NAME"
col_INDEX_CLASS	Column name for index class Default = "INDEX_CLASS"
col_LEVEL	Column name for level. Default = "LEVEL"
col_METRIC_NAME	Column name for metric name. Default = "METRIC_NAME"
col_RULE_TYPE	Column name for rule type (e.g., Rule0). Default = "RULE_TYPE"
col_LOWER	Column name for lower limit. Default = "LOWER"
col_UPPER	Column name for upper limit. Default = "UPPER"
col_METRIC_VALUE	Column name for metric value. Default = "METRIC_VALUE"
col_INCREASE	Column name for if the metric value increases. Default = "INCREASE"
...	Arguments passed to 'BCG.MetricMembership' used internally

Details

Converts metric values into BCG membership values. Uses a rules table to define the metrics, scoring range, and direction for each named index.

Deprecated col_SITE_TYPE for col_INDEX_CLASS in v2.0.0.9001.

Value

Returns a data frame of results in the long format.

Examples

# library(readxl)
# library(BioMonTools)

# Calculate Metrics
df_samps_bugs <- readxl::read_excel(
                           system.file("extdata/Data_BCG_PugLowWilVal.xlsx"
                                             , package = "BCGcalc")
                           , guess_max = 10^6)
myDF <- df_samps_bugs
myCols <- c("Area_mi2", "SurfaceArea", "Density_m2", "Density_ft2")
# populate missing columns prior to metric calculation
col_missing <- c("INFRAORDER", "HABITAT", "ELEVATION_ATTR", "GRADIENT_ATTR"
                 , "WSAREA_ATTR", "HABSTRUCT", "UFC")
myDF[, col_missing] <- NA
df_met_val_bugs <- BioMonTools::metric.values(myDF
                                              , "bugs"
                                              , fun.cols2keep = myCols)

# Import Rules
df_rules <- readxl::read_excel(system.file("extdata/Rules.xlsx"
                                           , package = "BCGcalc")
                      , sheet="Rules") 

# Run function
df_met_memb <- BCG.Metric.Membership(df_met_val_bugs, df_rules)

# Show Results
#View(df_met_memb)

# Save Results
write.table(df_met_memb
            , file.path(tempdir(), "Metric_Membership.tsv")
            , row.names = FALSE
            , col.names = TRUE
            , sep = "\t")

leppott/BCGcalc documentation built on April 12, 2024, 8:35 a.m.