qc_taxa: Quality Control Check on User Data Against Master Taxa List

In leppott/MBSStools: MBSS tool suite for calculations and data manipulation

Quality Control Check on User Data Against Master Taxa List

Description

This function compares the user's data frame to a data frame with the official (or user supplied) master taxa list (fish or benthic macroinvertebrates).

Usage

qc_taxa(
  DF_User,
  DF_Official = NULL,
  fun.Community = NULL,
  useMBSSTaxaInfo = "only_MBSS"
)

Arguments

DF_User	User taxa data.
DF_Official	Official MBSS master taxa list. Can be a local file or from a URL. Default is NULL. A NULL value will use the official online files.
fun.Community	Community name for which to compare the master taxa list (bugs or fish).
useMBSSTaxaInfo	Select how to handle new/different taxa. See 'Details' for more information. Valid values are "only_MBSS", "only_user", "add_new". Default = "only_MBSS".

Details

Output is a data frame with matches.

Messages are output to the console with the number of matches and which user taxa did not match the official list.

The official list is stored online but the user can input their own saved copy.

Any columns in the user input file that match the official master taxa list will be renamed with the "_NonMBBS" suffix.

New/different taxa in the user data are handled by the 'useMBSSTaxaInfo' parameter. For taxa that did not match the master taxa list the user has options on how to handle the differences for the phylogeny (e.g., columns for phylum, class, family, etc.) and autecology (e.g., columns for FFG, habit, tolerance value, etc.). The options are below.

* only_MBSS = use only MBSS master taxa information. Any non-matching taxa will not have any master taxa information.

* only_user = only use the information provided by the user. Information from the 'MBSS' will not be used. This should only be used for non-official calculations of the MBSS IBIs.

* add_new = hybrid approach that uses MBSS master taxa information, when present, but includes user information for non-matching taxa if the column names match.

Default master taxa lists are saved as CSV files online at:

https://github.com/leppott/MBSStools_SupportFiles

The files can be downloaded with the following code.

**Benthic Macroinvertebrate** url_mt_bugs <- "https://github.com/leppott/MBSStools_SupportFiles/raw/master/Data/CHAR_Bugs.csv" df_mt_bugs <- read.csv(url_mt_bugs)

**Fish** url_mt_fish <- "https://github.com/leppott/MBSStools_SupportFiles/raw/master/Data/CHAR_Fish.csv" df_mt_fish<- read.csv(url_mt_fish)

These files are maintained by MBSS staff. Update dates will be logged on the GitHub repository.

Expected fields include:

**Benthic Macroinvertebrates**

+ TAXON, Phylum, Class, Order, Family, Genus, Other_Taxa, Tribe, FFG, FAM_TV, Habit, FinalTolVal07, Comment

**Fish**

+ SPECIES, TYPE, PTOLR, NATIVE, TROPHIC, SILT, PIRHALLA, DATA.ADDED, REASON, SOURCE, FAM, GENUS, SP_SCI, IN_KEY, APPROX_ID

Value

input data frame with master taxa information added to it.

Examples

## Not run: 
# Example 1, Master Taxa List, Bugs
url_mt_bugs <- "https://github.com/leppott/MBSStools_SupportFiles/raw/master/Data/CHAR_Bugs.csv"
df_mt_bugs <- read.csv(url_mt_bugs)

# User data
DF_User<- taxa_bugs_genus
DF_Official = NULL   # NULL df_mt_bugs
fun.Community = "bugs"
useMBSSTaxaInfo = "only_MBSS"

df_qc_taxa_bugs <- qc_taxa(DF_User
                          , DF_Official
                          , fun.Community
                          , useMBSSTaxaInfo)

# QC input/output
dim(DF_User)
dim(df_qc_taxa_bugs)
names(DF_User)
names(df_qc_taxa_bugs)

~~~~~~~~~~~~~~~~~~~~~~~~

# Example 2, Master Taxa List, Fish
url_mt_fish <- "https://github.com/leppott/MBSStools_SupportFiles/raw/master/Data/CHAR_Fish.csv"
df_mt_fish<- read.csv(url_mt_fish)

DF_User<- taxa_fish
DF_Official = NULL  # NULL df_mt_fish
fun.Community = "fish"
useMBSSTaxaInfo = "add_new"

df_qc_taxa_fish <- qc_taxa(DF_User
                           , DF_Official
                           , fun.Community
                           , useMBSSTaxaInfo)

# QC input/output
dim(DF_User)
dim(df_qc_taxa_fish)
names(DF_User)
names(df_qc_taxa_fish)

## End(Not run)

leppott/MBSStools documentation built on April 8, 2024, 9:57 p.m.