qc.checks: QC checks on metric values

In leppott/BioMonTools: Tools for Biomonitoring and Bioassessment

QC checks on metric values

Description

Apply "QC checks" on calculated metrics and station/sample attributes to "flag" samples for the user. Examples include watershed size or total number of individuals. Can have checks for both high and low values. Checks are stored in separate file. For structure see df.checks in example.

Usage

qc.checks(df.metrics, df.checks, input.shape = "wide")

Arguments

df.metrics	Wide data frame with metric values to be evaluated.
df.checks	Data frame of metric thresholds to check.
input.shape	Shape of df.metrics; wide or long. Default is wide.

Details

used reshape2 package

Value

Returns a data frame of SampleID checks and results; Pass and Fail.

Examples

library(readxl)

# Calculate Metrics
df.samps.bugs <- read_excel(system.file("./extdata/Data_Benthos.xlsx"
                                       , package="BioMonTools")
                           , guess_max = 10^6)

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

# Run Function
myDF <- df.samps.bugs
df.metric.values.bugs <- metric.values(myDF, "bugs", fun.cols2keep=myCols)

# Import Checks
df.checks <- read_excel(system.file("./extdata/MetricFlags.xlsx"
                                          , package="BioMonTools")
                                          , sheet="Flags")
## Not run: 
# View Checks
View(df.checks)

## End(Not run)

# Run Function
df.flags <- qc.checks(df.metric.values.bugs, df.checks)

# Summarize Results
table(df.flags[,"CHECKNAME"], df.flags[,"FLAG"], useNA="ifany")

leppott/BioMonTools documentation built on March 1, 2025, 7:18 a.m.