R/composition_metrics.R
In zsmith27/Benthos: Benthos
#==============================================================================
# Composition Metrics
#==============================================================================
#'Percentage of a Specified Taxon
#'@description Calculate the percentage of each sample represented by the
#'specified taxon or taxa.
#'@param wide.df Taxonomic counts aggregated at the appropriate taxonomic
#' rank in a wide data format. Use the wide function to prepare the data.
#'@param taxon The taxon or taxa of interest. To specify more than one taxa
#'use: c("TAXA1", "TAXA2", "TAXA3").
#'@return A numeric vector containing the percentage of each sample
#'represented by the specified taxon or taxa.
#'@details
# #'@seealso \code{\link{wide}} for converting a long data format to a wide
#'data format.
#'@export
pct_taxon <- function(wide.df, taxon) {
taxon.vec <- blank_col(taxon, wide.df)
all.vec <- rowSums(wide.df[, 8:ncol(wide.df)])
final.vec <- taxon.vec / all.vec * 100
return(final.vec)
}
#==============================================================================
#'Proportion of Gastropoda, Oligochaeta, and Dipteran Individuals
#'
#'@param class.wide Taxonomic counts aggregated at the class level
#'classification in a wide data format. Use the wide function to
#'prepare the data.
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return One minus the proportional number of gastropods (Class: Gastropoda),
#' oligochaetes (Class: Oligochaeta), and dipteran (Order: Diptera) individuals.
#' This metric typically decreases with degradation.
#'@export
gold <- function(class.wide, order.wide) {
god <- blank_col("GASTROPODA", class.wide) +
blank_col("OLIGOCHAETA", class.wide) +
blank_col("DIPTERA", order.wide)
final.vec <- (1 - (god / rowSums(order.wide[, 8:ncol(order.wide)]))) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of Ephemeropteran Individuals Minus Baetid
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as Ephemeropterans
#' (Order: Ephemeroptera) minus the percentage of baetid (Family: Baetidae)
#' in the sample. This metric typically decreases with degradation.
#'@export
pct_epmeroptera_no_baetid <- function(order.wide, family.wide) {
baetid <- (blank_col("BAETIDAE", family.wide))
ephem <- (blank_col("EPHEMEROPTERA", order.wide))
final.vec <- ((ephem - baetid) /
rowSums(order.wide[, 8:ncol(order.wide)])) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of EPT Individuals
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as ephemeropterans
#' (Order: Ephemeroptera), plecopterans (Order: Plecoptera),
#' and trichopterans (Order: Trichoptera) (EPT). This metric will typically
#' decrease with degradation.
#'@export
pct_ept <- function(order.wide) {
EPT <- blank_col("EPHEMEROPTERA", order.wide) +
blank_col("PLECOPTERA", order.wide) +
blank_col("TRICHOPTERA", order.wide)
final.vec <- EPT / rowSums(order.wide[, 8:ncol(order.wide)]) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of EPT Individuals Minus Hydropsychid and Baetid Individuals
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as ephemeropterans
#' (Order: Ephemeroptera), plecopterans (Order: Plecoptera),
#' and trichopterans (Order: Trichoptera) (EPT) minus the percentage of
#' hydropsychids (Family: Hydropsychidae) and baetids (Family: Baetidae).
#' These two families are typically tolerant and can be hyperdominant,
#' resulting in elevated percentages of EPT that may not accurately
#' describe the degradation gradient of interest. This metric will
#' typically decrease with degradation.
#'@export
pct_ept_hydro_baetid <- function(order.wide, family.wide) {
hydropsychidae <- blank_col("HYDROPSYCHIDAE", family.wide)
baetidae <- blank_col("BAETIDAE", family.wide)
ept <- (blank_col("EPHEMEROPTERA", order.wide) +
blank_col("PLECOPTERA", order.wide) +
blank_col("TRICHOPTERA", order.wide))
final.vec <- ifelse(ept == 0, 0, (1 - ((hydropsychidae + baetidae) / ept)) * 100)
return(final.vec)
}
#==============================================================================
#'Percentage of EPT Individuals Minus Hydropsychid Individuals
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as ephemeropterans
#' (Order: Ephemeroptera), plecopterans (Order: Plecoptera),
#' and trichopterans (Order: Trichoptera) (EPT) minus the percentage of
#' hydropsychids (Family: Hydropsychidae).
#' This family is typically tolerant and can be hyperdominant,
#' resulting in elevated percentages of EPT that may not accurately
#' describe the degradation gradient of interest. This metric will
#' typically decrease with degradation.
#'@export
pct_ept_no_hydro <- function(order.wide, family.wide) {
hydropsychidae <- blank_col("HYDROPSYCHIDAE", family.wide)
ept <- (blank_col("EPHEMEROPTERA", order.wide) +
blank_col("PLECOPTERA", order.wide) +
blank_col("TRICHOPTERA", order.wide))
final.vec <- ifelse(ept == 0, 0, (1 - (hydropsychidae / ept)) * 100)
return(final.vec)
}
#==============================================================================
#'Percentage EPT Individuals Identified as Hydropsychids
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of EPT (Orders: Ephemeroptera, Plecoptera,
#' and Trichoptera) individuals identified as hydropsychids
#' (Family: Hydropsychidae). This metric typically increases with degradation.
#'@export
pct_hydro_ept <- function(order.wide, family.wide) {
hydro <- (blank_col("HYDROPSYCHIDAE", family.wide))
ept <- (blank_col("EPHEMEROPTERA", order.wide) +
blank_col("PLECOPTERA", order.wide) +
blank_col("TRICHOPTERA", order.wide))
final.vec <- ifelse(ept == 0, 0, (hydro / ept) * 100)
return(final.vec)
}
#==============================================================================
#'Percentage of Trichopterans Represented by Hydropsychids
#'
#'@param order.wide Taxonomic counts aggregated at the class level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of trichopteran (Order:Trichoptera) individuals
#'that are hydropsychids (Family: Hydropsychidae). This metric typically
#'increases with degradation.
#'@export
pct_hydro_trichoptera <- function(order.wide, family.wide) {
final.vec <- ifelse(order.wide[, "TRICHOPTERA"] == 0, 0,
(blank_col("HYDROPSYCHIDAE", family.wide) /
blank_col("TRICHOPTERA", order.wide)) * 100)
return(final.vec)
}
#==============================================================================
#'Percentage of Trichopterans Minus Hydropsychids
#'
#'@param order.wide Taxonomic counts aggregated at the class level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of trichopteran (Order:Trichoptera) individuals
#'minus the percentage of hydropsychids (Family: Hydropsychidae).
#'This metric typically decreases with degradation.
#'@export
pct_trichoptera_no_hydro <- function(order.wide, family.wide) {
trichop.vec <- pct_taxon(order.wide, "TRICHOPTERA")
hydro.vec <- pct_taxon(family.wide, "HYDROPSYCHIDAE")
final.vec <- trichop.vec - hydro.vec
return(final.vec)
}
#==============================================================================
#'Percentage of COTE Individuals
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as coleopterans
#' (Order: Coleoptera), odonates (Order: Odonata), trichopterans
#' (Order: Trichoptera), and ephemeropterans (Order: Ephemeroptera) (COTE).
#' These organisms were used by Kamman (2007) as a lentic benthic
#' macroinverterbate metric.
#'
#' Citation:
#' KAMMAN, N. 2007. Development of Biocriteria for Vermont and
#' New Hampshire Lakes Criteria Development for Macroinvertebrates
#' for Three Lake Classes and Implementation Procedure for Biological
#' Assessment of Vermont Lakes. Pages 1–21. Vermont Department
#' of Environemental Conservation, Waterbury, VT.
#'@export
pct_cote <- function(order.wide) {
COTE <- blank_col("COLEOPTERA", order.wide) +
blank_col("ODONATA", order.wide) +
blank_col("TRICHOPTERA", order.wide) +
blank_col("EPHEMEROPTERA", order.wide)
final.vec <- COTE / rowSums(order.wide[, 8:ncol(order.wide)]) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of POTEC Individuals
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as plecopterans
#' (Order: Plecoptera), odonates (Order: Odonata), trichopterans
#' (Order: Trichoptera), ephemeropterans (Order: Ephemeroptera),
#' and coleopterans (Order: Coleoptera) (POTEC). This is an
#' exploratory metric combining EPT taxa with COTE taxa.
#' Coleopterans (Order: Coleoptera), odonates (Order: Odonata),
#' trichopterans (Order: Trichoptera), and ephemeropterans
#' (Order: Ephemeroptera) (COTE) were used by Kamman (2007) as
#' a lentic benthic macroinverterbate metric.
#'
#' Citation:
#' KAMMAN, N. 2007. Development of Biocriteria for Vermont and
#' New Hampshire Lakes Criteria Development for Macroinvertebrates
#' for Three Lake Classes and Implementation Procedure for Biological
#' Assessment of Vermont Lakes. Pages 1–21. Vermont Department
#' of Environemental Conservation, Waterbury, VT.
#'@export
pct_potec <- function(order.wide) {
POTEC <- blank_col("PLECOPTERA", order.wide) +
blank_col("ODONATA", order.wide) +
blank_col("TRICHOPTERA", order.wide) +
blank_col("EPHEMEROPTERA", order.wide) +
blank_col("COLEOPTERA", order.wide)
final.vec <- POTEC / rowSums(order.wide[, 8:ncol(order.wide)]) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of Limestone Individuals
#'
#'@param order.wide order.wide = Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as isopods (Order: Isopoda),
#'amphipods (Order: Amphipoda), and ephemerellids (Family: Ephemerellidae).
#'@export
pct_limestone <- function(order.wide, family.wide) {
IAE <- blank_col("ISOPODA", order.wide) +
blank_col("AMPHIPODA", order.wide) +
blank_col("EPHEMERELLIDAE", family.wide)
final.vec <- IAE / rowSums(order.wide[, 8:ncol(order.wide)]) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of Oligochaet and Chironomid Individuals
#'
#'@param class.wide Taxonomic counts aggregated at the class level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as oligochaets
#' (Class: Oligochaeta) and chironomids (Family: Chironomidae).
#'@export
pct_oligo_chiro <- function(class.wide, family.wide){
chiro <- blank_col("CHIRONOMIDAE", family.wide)
oligo <- blank_col("OLIGOCHAETA", class.wide)
final.vec <- ((chiro + oligo) / rowSums(family.wide[, 8:ncol(family.wide)])) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of Annelid and Chironomid Individuals
#'
#'@param phylum.wide Taxonomic counts aggregated at the phylum level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as annelids (Phylum: Annelida)
#'and chironomids (Family: Chironomidae). This metric typically increases with
#'degradation.
#'@export
pct_annelid_chiro <- function(phylum.wide, family.wide){
chiro <- blank_col("CHIRONOMIDAE", family.wide)
annelid <- blank_col("ANNELIDA", phylum.wide)
final.vec <- ((chiro + annelid) /
rowSums(family.wide[, 8:ncol(family.wide)])) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of Unidentified Individuals
#'
#'@param taxa.wide Taxonomic counts aggregated at the specific taxonomic
#' classification (e.g., Order, Family, or Genus) in a wide data format.
#' Use the wide function to prepare the data.
#'@return The percentage of individuals that were not identified at the
#'specified taxonomic level.
#'@export
pct_unidentified <- function(taxa.wide) {
final.vec <- blank_col("UNIDENTIFIED", taxa.wide) /
rowSums(taxa.wide[, 8:ncol(taxa.wide)]) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of EPT Taxa Excluding Tolerant Taxa
#'
#'@param long Taxonomic counts arrange in a long data format (i.e., each
#'row represents a unique sample and taxon).
#'@param rank The taxonomic rank used to perform the analysis. You must
#'sepecify either 'FAMILY' or "GENUS.'
#'@param master A master taxa list including taxonomic ranks Phylum through
#'the specified taxonomic rank (Family or Genus) and the an
#'associated list of tolerance values. The default is set to the master taxa
#'list included in the BIBI package. The master taxa list can be viewed with
#'the following script: data(master)
#'@param tolerance_value The name of the column in the master taxon list
#'(specified using the master variable) that contains tolerance values on
#'a scale of 0-10. Tolerant organisms are classified as organisms with a
#'tolerance value >= 7. The defualt is set to the the BIBI tolerance values,
#'which are tolerance values summarized from multiple sources.
#'@return Percent of the assembalge represented by Trichoptera individuals,
#' excluding tolerant Trichoptera taxa.
#'@export
pct_trichoptera_no_tolerant <- function (long, rank, master, tolerance_value = "BIBI_TV") {
wide.df <- wide(long, rank)
Order <- split(long[, rank], long$ORDER)
trichop <- unique(Order$TRICHOPTERA)
taxa.list <- trichop
new.df <- wide.df[, names(wide.df) %in% taxa.list]
new.df <- new.df[, !(names(new.df) %in% "UNIDENTIFIED")]
# Find all of the tolerant taxa
master$TOLERANCE <- ifelse(master[, tolerance_value] >= 7, "TOLERANT", NA)
tol <- split(master[, rank], master$TOLERANCE)
name.list <- as.character(unlist(unique(tol$TOLERANT)))
# Remove any tolerant taxa from the trichop data frame
no.tol.trichop <- data.frame(new.df[, !(names(new.df) %in% name.list)])
# Caculate richness values using vegan
sum.no.tol.trichop <- apply(no.tol.trichop[, 8:ncol(no.tol.trichop)], 1, sum)
total.sum <- apply(new.df[, 8:ncol(new.df)], 1, sum)
#sum.no.tol.trichop <- rowsum(no.tol.trichop[, 8:ncol(no.tol.trichop)])
#total.sum <- rowsum(new.df[, 8:ncol(new.df)])
final.vec <- ifelse(sum.no.tol.trichop == 0, 0, (sum.no.tol.trichop / total.sum) * 100)
return(final.vec)
}
zsmith27/Benthos documentation built on May 5, 2019, 2:38 a.m.
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#==============================================================================
# Composition Metrics
#==============================================================================
#'Percentage of a Specified Taxon
#'@description Calculate the percentage of each sample represented by the
#'specified taxon or taxa.
#'@param wide.df Taxonomic counts aggregated at the appropriate taxonomic
#' rank in a wide data format. Use the wide function to prepare the data.
#'@param taxon The taxon or taxa of interest. To specify more than one taxa
#'use: c("TAXA1", "TAXA2", "TAXA3").
#'@return A numeric vector containing the percentage of each sample
#'represented by the specified taxon or taxa.
#'@details
# #'@seealso \code{\link{wide}} for converting a long data format to a wide
#'data format.
#'@export
pct_taxon <- function(wide.df, taxon) {
taxon.vec <- blank_col(taxon, wide.df)
all.vec <- rowSums(wide.df[, 8:ncol(wide.df)])
final.vec <- taxon.vec / all.vec * 100
return(final.vec)
}
#==============================================================================
#'Proportion of Gastropoda, Oligochaeta, and Dipteran Individuals
#'
#'@param class.wide Taxonomic counts aggregated at the class level
#'classification in a wide data format. Use the wide function to
#'prepare the data.
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return One minus the proportional number of gastropods (Class: Gastropoda),
#' oligochaetes (Class: Oligochaeta), and dipteran (Order: Diptera) individuals.
#' This metric typically decreases with degradation.
#'@export
gold <- function(class.wide, order.wide) {
god <- blank_col("GASTROPODA", class.wide) +
blank_col("OLIGOCHAETA", class.wide) +
blank_col("DIPTERA", order.wide)
final.vec <- (1 - (god / rowSums(order.wide[, 8:ncol(order.wide)]))) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of Ephemeropteran Individuals Minus Baetid
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as Ephemeropterans
#' (Order: Ephemeroptera) minus the percentage of baetid (Family: Baetidae)
#' in the sample. This metric typically decreases with degradation.
#'@export
pct_epmeroptera_no_baetid <- function(order.wide, family.wide) {
baetid <- (blank_col("BAETIDAE", family.wide))
ephem <- (blank_col("EPHEMEROPTERA", order.wide))
final.vec <- ((ephem - baetid) /
rowSums(order.wide[, 8:ncol(order.wide)])) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of EPT Individuals
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as ephemeropterans
#' (Order: Ephemeroptera), plecopterans (Order: Plecoptera),
#' and trichopterans (Order: Trichoptera) (EPT). This metric will typically
#' decrease with degradation.
#'@export
pct_ept <- function(order.wide) {
EPT <- blank_col("EPHEMEROPTERA", order.wide) +
blank_col("PLECOPTERA", order.wide) +
blank_col("TRICHOPTERA", order.wide)
final.vec <- EPT / rowSums(order.wide[, 8:ncol(order.wide)]) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of EPT Individuals Minus Hydropsychid and Baetid Individuals
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as ephemeropterans
#' (Order: Ephemeroptera), plecopterans (Order: Plecoptera),
#' and trichopterans (Order: Trichoptera) (EPT) minus the percentage of
#' hydropsychids (Family: Hydropsychidae) and baetids (Family: Baetidae).
#' These two families are typically tolerant and can be hyperdominant,
#' resulting in elevated percentages of EPT that may not accurately
#' describe the degradation gradient of interest. This metric will
#' typically decrease with degradation.
#'@export
pct_ept_hydro_baetid <- function(order.wide, family.wide) {
hydropsychidae <- blank_col("HYDROPSYCHIDAE", family.wide)
baetidae <- blank_col("BAETIDAE", family.wide)
ept <- (blank_col("EPHEMEROPTERA", order.wide) +
blank_col("PLECOPTERA", order.wide) +
blank_col("TRICHOPTERA", order.wide))
final.vec <- ifelse(ept == 0, 0, (1 - ((hydropsychidae + baetidae) / ept)) * 100)
return(final.vec)
}
#==============================================================================
#'Percentage of EPT Individuals Minus Hydropsychid Individuals
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as ephemeropterans
#' (Order: Ephemeroptera), plecopterans (Order: Plecoptera),
#' and trichopterans (Order: Trichoptera) (EPT) minus the percentage of
#' hydropsychids (Family: Hydropsychidae).
#' This family is typically tolerant and can be hyperdominant,
#' resulting in elevated percentages of EPT that may not accurately
#' describe the degradation gradient of interest. This metric will
#' typically decrease with degradation.
#'@export
pct_ept_no_hydro <- function(order.wide, family.wide) {
hydropsychidae <- blank_col("HYDROPSYCHIDAE", family.wide)
ept <- (blank_col("EPHEMEROPTERA", order.wide) +
blank_col("PLECOPTERA", order.wide) +
blank_col("TRICHOPTERA", order.wide))
final.vec <- ifelse(ept == 0, 0, (1 - (hydropsychidae / ept)) * 100)
return(final.vec)
}
#==============================================================================
#'Percentage EPT Individuals Identified as Hydropsychids
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of EPT (Orders: Ephemeroptera, Plecoptera,
#' and Trichoptera) individuals identified as hydropsychids
#' (Family: Hydropsychidae). This metric typically increases with degradation.
#'@export
pct_hydro_ept <- function(order.wide, family.wide) {
hydro <- (blank_col("HYDROPSYCHIDAE", family.wide))
ept <- (blank_col("EPHEMEROPTERA", order.wide) +
blank_col("PLECOPTERA", order.wide) +
blank_col("TRICHOPTERA", order.wide))
final.vec <- ifelse(ept == 0, 0, (hydro / ept) * 100)
return(final.vec)
}
#==============================================================================
#'Percentage of Trichopterans Represented by Hydropsychids
#'
#'@param order.wide Taxonomic counts aggregated at the class level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of trichopteran (Order:Trichoptera) individuals
#'that are hydropsychids (Family: Hydropsychidae). This metric typically
#'increases with degradation.
#'@export
pct_hydro_trichoptera <- function(order.wide, family.wide) {
final.vec <- ifelse(order.wide[, "TRICHOPTERA"] == 0, 0,
(blank_col("HYDROPSYCHIDAE", family.wide) /
blank_col("TRICHOPTERA", order.wide)) * 100)
return(final.vec)
}
#==============================================================================
#'Percentage of Trichopterans Minus Hydropsychids
#'
#'@param order.wide Taxonomic counts aggregated at the class level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of trichopteran (Order:Trichoptera) individuals
#'minus the percentage of hydropsychids (Family: Hydropsychidae).
#'This metric typically decreases with degradation.
#'@export
pct_trichoptera_no_hydro <- function(order.wide, family.wide) {
trichop.vec <- pct_taxon(order.wide, "TRICHOPTERA")
hydro.vec <- pct_taxon(family.wide, "HYDROPSYCHIDAE")
final.vec <- trichop.vec - hydro.vec
return(final.vec)
}
#==============================================================================
#'Percentage of COTE Individuals
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as coleopterans
#' (Order: Coleoptera), odonates (Order: Odonata), trichopterans
#' (Order: Trichoptera), and ephemeropterans (Order: Ephemeroptera) (COTE).
#' These organisms were used by Kamman (2007) as a lentic benthic
#' macroinverterbate metric.
#'
#' Citation:
#' KAMMAN, N. 2007. Development of Biocriteria for Vermont and
#' New Hampshire Lakes Criteria Development for Macroinvertebrates
#' for Three Lake Classes and Implementation Procedure for Biological
#' Assessment of Vermont Lakes. Pages 1–21. Vermont Department
#' of Environemental Conservation, Waterbury, VT.
#'@export
pct_cote <- function(order.wide) {
COTE <- blank_col("COLEOPTERA", order.wide) +
blank_col("ODONATA", order.wide) +
blank_col("TRICHOPTERA", order.wide) +
blank_col("EPHEMEROPTERA", order.wide)
final.vec <- COTE / rowSums(order.wide[, 8:ncol(order.wide)]) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of POTEC Individuals
#'
#'@param order.wide Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as plecopterans
#' (Order: Plecoptera), odonates (Order: Odonata), trichopterans
#' (Order: Trichoptera), ephemeropterans (Order: Ephemeroptera),
#' and coleopterans (Order: Coleoptera) (POTEC). This is an
#' exploratory metric combining EPT taxa with COTE taxa.
#' Coleopterans (Order: Coleoptera), odonates (Order: Odonata),
#' trichopterans (Order: Trichoptera), and ephemeropterans
#' (Order: Ephemeroptera) (COTE) were used by Kamman (2007) as
#' a lentic benthic macroinverterbate metric.
#'
#' Citation:
#' KAMMAN, N. 2007. Development of Biocriteria for Vermont and
#' New Hampshire Lakes Criteria Development for Macroinvertebrates
#' for Three Lake Classes and Implementation Procedure for Biological
#' Assessment of Vermont Lakes. Pages 1–21. Vermont Department
#' of Environemental Conservation, Waterbury, VT.
#'@export
pct_potec <- function(order.wide) {
POTEC <- blank_col("PLECOPTERA", order.wide) +
blank_col("ODONATA", order.wide) +
blank_col("TRICHOPTERA", order.wide) +
blank_col("EPHEMEROPTERA", order.wide) +
blank_col("COLEOPTERA", order.wide)
final.vec <- POTEC / rowSums(order.wide[, 8:ncol(order.wide)]) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of Limestone Individuals
#'
#'@param order.wide order.wide = Taxonomic counts aggregated at the order level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as isopods (Order: Isopoda),
#'amphipods (Order: Amphipoda), and ephemerellids (Family: Ephemerellidae).
#'@export
pct_limestone <- function(order.wide, family.wide) {
IAE <- blank_col("ISOPODA", order.wide) +
blank_col("AMPHIPODA", order.wide) +
blank_col("EPHEMERELLIDAE", family.wide)
final.vec <- IAE / rowSums(order.wide[, 8:ncol(order.wide)]) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of Oligochaet and Chironomid Individuals
#'
#'@param class.wide Taxonomic counts aggregated at the class level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as oligochaets
#' (Class: Oligochaeta) and chironomids (Family: Chironomidae).
#'@export
pct_oligo_chiro <- function(class.wide, family.wide){
chiro <- blank_col("CHIRONOMIDAE", family.wide)
oligo <- blank_col("OLIGOCHAETA", class.wide)
final.vec <- ((chiro + oligo) / rowSums(family.wide[, 8:ncol(family.wide)])) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of Annelid and Chironomid Individuals
#'
#'@param phylum.wide Taxonomic counts aggregated at the phylum level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@param family.wide Taxonomic counts aggregated at the family level
#' classification in a wide data format. Use the wide function to
#' prepare the data.
#'@return The percentage of individuals identified as annelids (Phylum: Annelida)
#'and chironomids (Family: Chironomidae). This metric typically increases with
#'degradation.
#'@export
pct_annelid_chiro <- function(phylum.wide, family.wide){
chiro <- blank_col("CHIRONOMIDAE", family.wide)
annelid <- blank_col("ANNELIDA", phylum.wide)
final.vec <- ((chiro + annelid) /
rowSums(family.wide[, 8:ncol(family.wide)])) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of Unidentified Individuals
#'
#'@param taxa.wide Taxonomic counts aggregated at the specific taxonomic
#' classification (e.g., Order, Family, or Genus) in a wide data format.
#' Use the wide function to prepare the data.
#'@return The percentage of individuals that were not identified at the
#'specified taxonomic level.
#'@export
pct_unidentified <- function(taxa.wide) {
final.vec <- blank_col("UNIDENTIFIED", taxa.wide) /
rowSums(taxa.wide[, 8:ncol(taxa.wide)]) * 100
return(final.vec)
}
#==============================================================================
#'Percentage of EPT Taxa Excluding Tolerant Taxa
#'
#'@param long Taxonomic counts arrange in a long data format (i.e., each
#'row represents a unique sample and taxon).
#'@param rank The taxonomic rank used to perform the analysis. You must
#'sepecify either 'FAMILY' or "GENUS.'
#'@param master A master taxa list including taxonomic ranks Phylum through
#'the specified taxonomic rank (Family or Genus) and the an
#'associated list of tolerance values. The default is set to the master taxa
#'list included in the BIBI package. The master taxa list can be viewed with
#'the following script: data(master)
#'@param tolerance_value The name of the column in the master taxon list
#'(specified using the master variable) that contains tolerance values on
#'a scale of 0-10. Tolerant organisms are classified as organisms with a
#'tolerance value >= 7. The defualt is set to the the BIBI tolerance values,
#'which are tolerance values summarized from multiple sources.
#'@return Percent of the assembalge represented by Trichoptera individuals,
#' excluding tolerant Trichoptera taxa.
#'@export
pct_trichoptera_no_tolerant <- function (long, rank, master, tolerance_value = "BIBI_TV") {
wide.df <- wide(long, rank)
Order <- split(long[, rank], long$ORDER)
trichop <- unique(Order$TRICHOPTERA)
taxa.list <- trichop
new.df <- wide.df[, names(wide.df) %in% taxa.list]
new.df <- new.df[, !(names(new.df) %in% "UNIDENTIFIED")]
# Find all of the tolerant taxa
master$TOLERANCE <- ifelse(master[, tolerance_value] >= 7, "TOLERANT", NA)
tol <- split(master[, rank], master$TOLERANCE)
name.list <- as.character(unlist(unique(tol$TOLERANT)))
# Remove any tolerant taxa from the trichop data frame
no.tol.trichop <- data.frame(new.df[, !(names(new.df) %in% name.list)])
# Caculate richness values using vegan
sum.no.tol.trichop <- apply(no.tol.trichop[, 8:ncol(no.tol.trichop)], 1, sum)
total.sum <- apply(new.df[, 8:ncol(new.df)], 1, sum)
#sum.no.tol.trichop <- rowsum(no.tol.trichop[, 8:ncol(no.tol.trichop)])
#total.sum <- rowsum(new.df[, 8:ncol(new.df)])
final.vec <- ifelse(sum.no.tol.trichop == 0, 0, (sum.no.tol.trichop / total.sum) * 100)
return(final.vec)
}
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