Macroinvertebrate Metrics

Welcome

This document has been created following the generic assessment guidance.

Description

Basic details about the assessment.

question	response
name_short	Macroinvertebrate Metrics
name_long	Freshwater Macroinvertebrate Metrics
parameter	River Invertebrates
status	testing
type	metric

Input

A list of questions required to run this assessment.

sample_id	question	response	label	parameter
12345	Taxon abundance	12	Baetidae	River Family Inverts
12346	Live abundance	12	Baetidae	BANKSIDE_INVERTS

Assessment

Function code used to run this assessment.

Code

assessment_function <- function(data, ...) {
  # Calculated invert metrics...
  # Note, any non-standard base R library must be call using require().
  require(dplyr)
  require(whpt)
  require(macroinvertebrateMetrics)
  input <- data
  input$label <- trimws(input$label)
  input <- dplyr::filter(
    input,
    parameter %in% c(
      "River Family Inverts",
      "BANKSIDE_INVERTS",
      "F_BMWP_TST",
      "MTL_TL4",
      "MTL_TL5"
    )
  )
  input <- dplyr::filter(input, question %in% c(
    "Taxon abundance",
    "Live abundance"
  ))
   if(nrow(input) < 1) {
     return(NULL)
   }
  input <- ungroup(input)
  input <- dplyr::select(
    input, "sample_id", "question", "response", "label", "parameter"
  )
  output <- macroinvertebrateMetrics::calc_metric(input)
  sample_details <- select(input, sample_id, parameter)
  sample_details <- distinct(sample_details)
  output <- dplyr::select(
    output, sample_id, question, response
  )
  output <- inner_join(output, sample_details, by = join_by(sample_id))

  return(output)
}

Outcome

The outcome of your assessment.

#> Loading required package: whpt
#> 
#> Attaching package: 'whpt'
#> The following object is masked from 'package:hera':
#> 
#>     demo_data
#> Loading required package: macroinvertebrateMetrics
#> 
#> Attaching package: 'macroinvertebrateMetrics'
#> The following object is masked from 'package:whpt':
#> 
#>     demo_data
#> The following object is masked from 'package:hera':
#> 
#>     demo_data

question	response
EPSI Score TL2	100
EPSI Condition TL2	Minimally sedimented/unsedimented
PSI Score TL3	100
PSI Condition TL3	Minimally sedimented/unsedimented
Riverfly Score	2
Riverfly NTAXA	1
Riverfly ASPT	2
SPEAR ratio TL2	100
SPEAR toxic ratio TL2	-12.7607142857143
SPEAR class TL2	High
WHPT_SCORE	5.9
WHPT_ASPT	5.9
WHPT_NTAXA	1
WHPT_P_SCORE	5.5
WHPT_P_ASPT	5.5
WHPT_P_NTAXA	1

Check

Run checks on the assessment.

#> Test passed 🥇
#> Test passed 🎊

check	value
standard_names	TRUE
standard_required	TRUE
standard_required_values	TRUE

Update

Update the catalogue of assessments to make them available.

#> ✔ Setting active project to "/home/runner/work/hera/hera".
#> ✔ Saving "catalogue" to "data/catalogue.rda".
#> ☐ Document your data (see <https://r-pkgs.org/data.html>).

After updating the catalogue, rebuild the package, click on Build > Install and Restart menu or ‘Install and Restart’ button in the Build pane.

Test

This section tests if this assessment is usable using assessment function.

Launch app

Below is an interactive application displaying the results of your assessment.