Nothing
R/TEF.R
In tRophicPosition: Bayesian Trophic Position Estimation with Stable Isotopes
#' Trophic enrichment factors from bibliography
#'
#' This function returns trophic enrichment factors (TEF), given an author,
#' element and a type. For convenience 'type' includes a number of categories
#' depending on the author. At the moment it includes TEF data from Post (2002)
#' and from McCutchan et al (2003). This function is maintained for
#' compatibility backwards of version 0.6.8.
#'
#' @param author could be either "Post" or "McCutchan" at the moment.
#' @param element can be "both", "N" or "C"
#' @param type this argument only works for "McCutchan" author (their Table 3).
#' "all" returns all TEF data; "whole" and "muscle" returns TEF separated per
#' type analysis; "acidified" and "unacidified" returns TEF separated per
#' acidification; and "Rainbow Trout" and "Brook Trout" returns TEF separated
#' per fish species (according to their Table 1).
#' @param seed integer to have replicated results
#'
#' @return a list (if element = "both") or a vector (if element ="N" or element
#' = "C") containing TDF values
#' @export
#'
#' @examples
#' # TEF() is deprecated, use TDF() instead:
#' TDF(author = "McCutchan", element = "N")
#'
TEF <- function (author = "Post", element = "both", type = "all", seed = 3) {
.Deprecated("TDF")
meanSD <- function(x, mean, sd) {
set.seed(seed = seed)
x <- stats::rnorm(x, mean, sd)
X <- x
MEAN <- mean
SD <- sd
Z <- (((X - mean(X, na.rm = TRUE))/sd(X, na.rm = TRUE))) * SD
MEAN + Z
}
meanSE <- function(x, mean, se) {
sd <- se * sqrt(x)
meanSD(x, mean, sd)
}
if (author == "Post") {
set.seed(seed = seed)
deltaN <- meanSD(56, 3.4, 0.98)
set.seed(seed = seed)
deltaC <- meanSD(107, 0.39, 1.3)
if (element == "N") {
message("You selected Post's (2002)
d15N: 56 values with 3.4 mean +- 0.98 sd")
return(deltaN)
} else if (element == "C") {
message("You selected Post's (2002)
d13C: 107 values with 0.39 mean +- 1.3 sd")
return(deltaC)
} else if (element == "both") {
message("You selected Post's (2002)
d15N: 56 values with 3.4 mean +- 0.98 sd")
message("d13C: 107 values with 0.39 mean +- 1.3 sd")
return(list(deltaN = deltaN, deltaC = deltaC))
} } else if (author == "McCutchan") {
set.seed(seed = seed)
allN <- meanSE(73, 2.3, 0.18)
set.seed(seed = seed)
wholeN <- meanSE(58, 2.1, 0.21)
set.seed(seed = seed)
muscleN <- meanSE(15, 2.9, 0.32)
set.seed(seed = seed)
unacidifiedN <- meanSE(15, 1.1, 0.29)
set.seed(seed = seed)
acidifiedN <- meanSE(36, 2.4, 0.24)
#raisedInvN <- meanSE(25, 1.4, 0.21)
#highProtN <- meanSE(25, 3.3, 0.26)
#plantAlgaeN <- meanSE(25, 2.2, 0.3)
set.seed(seed = seed)
rainbowTroutN <- meanSE(4, 3.2, 0.2)
set.seed(seed = seed)
brookTroutN <- meanSE(8, 3.8, 0.17)
set.seed(seed = seed)
allC <- meanSE(102, 0.5, 0.13)
set.seed(seed = seed)
wholeC <- meanSE(84, 0.3, 0.14)
set.seed(seed = seed)
muscleC <- meanSE(18, 1.3, 0.3)
set.seed(seed = seed)
unacidifiedC <- meanSE(62, 0.5, 0.17)
set.seed(seed = seed)
acidifiedC <- meanSE(22, -0.2, 0.21)
set.seed(seed = seed)
rainbowTroutC <- meanSE(4, 1.9, 0.51)
set.seed(seed = seed)
brookTroutC <- meanSE(8, 3.3, 0.29)
if (type == "all") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
All d15N: 73 values with 2.3 mean +- 0.18 se")
return(allN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
All d13C: 102 values with 0.5 mean +- 0.13 se")
return(allC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
All d15N: 73 values with 2.3 mean +- 0.18 se")
message("All d13C: 102 values with 0.5 mean +- 0.13 se")
return(list(deltaN = allN, deltaC = allC))
}
} else if (type == "whole") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Whole tissue d15N: 58 values with 2.1 mean +- 0.21 se")
return(wholeN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Whole tissue d13C: 84 values with 0.3 mean +- 0.14 se")
return(wholeC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Whole tissue d15N: 58 values with 2.1 mean +- 0.21 se")
message("Whole tissue d13C: 84 values with 0.3 mean +- 0.14 se")
return(list(deltaN = wholeN, deltaC = wholeC))
}
} else if (type == "muscle") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Muscle tissue d15N: 15 values with 2.9 mean +- 0.32 se")
return(muscleN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Muscle tissue d13C: 18 values with 1.3 mean +- 0.3 se")
return(muscleC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Muscle tissue d15N: 15 values with 2.9 mean +- 0.32 se")
message("Muscle tissue d13C: 18 values with 1.3 mean +- 0.3 se")
return(list(deltaN = muscleN, deltaC = muscleC))
}
} else if (type == "unacidified") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Unacidified tissue d15N: 15 values with 1.1 mean +- 0.29 se")
return(unacidifiedN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Unacidified tissue d13C: 62 values with 0.5 mean +- 0.17 se")
return(unacidifiedC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Unacidified tissue d15N: 15 values with 1.1 mean +- 0.29 se")
message("Unacidified tissue d13C: 62 values with 0.5 mean +- 0.17 se")
return(list(deltaN = unacidifiedN, deltaC = unacidifiedC))
}
} else if (type == "acidified") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Acidified tissue d13C: 22 values with -0.2 mean +- 0.21 se")
return(acidifiedN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Acidified tissue d15N: 36 values with 2.4 mean +- 0.24 se")
return(acidifiedC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Acidified tissue d15N: 36 values with 2.4 mean +- 0.24 se")
message("Acidified tissue d13C: 22 values with -0.2 mean +- 0.21 se")
return(list(deltaN = acidifiedN, deltaC = acidifiedC))
}
} else if (type == "rainbowTrout") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Rainbow Trout tissue d15N: 4 values with 3.2 mean +- 0.2 se")
return(rainbowTroutN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Muscle tissue d13C: 4 values with 1.9 mean +- 0.51 se")
return(rainbowTroutC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Rainbow Trout tissue d15N: 4 values with 3.2 mean +- 0.2 se")
message("Rainbow Trout muscle tissue d13C: 4 values with 1.9 mean +-
0.51 se")
return(list(deltaN = rainbowTroutN, deltaC = rainbowTroutC))
}
} else if (type == "brookTrout") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Brook Trout tissue d13C: 8 values with 3.3 mean +- 0.29 se")
return(brookTroutN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Brook Trout tissue d15N: 8 values with 3.8 mean +- 0.17 se")
return(brookTroutC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Brook Trout tissue d15N: 8 values with 3.8 mean +- 0.17 se")
message("Brook Trout tissue d13C: 8 values with 3.3 mean +- 0.29 se")
return(list(deltaN = brookTroutN, deltaC = brookTroutC))
}
}
}
}
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tRophicPosition documentation built on Dec. 28, 2022, 2:27 a.m.
R Package Documentation
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#' Trophic enrichment factors from bibliography
#'
#' This function returns trophic enrichment factors (TEF), given an author,
#' element and a type. For convenience 'type' includes a number of categories
#' depending on the author. At the moment it includes TEF data from Post (2002)
#' and from McCutchan et al (2003). This function is maintained for
#' compatibility backwards of version 0.6.8.
#'
#' @param author could be either "Post" or "McCutchan" at the moment.
#' @param element can be "both", "N" or "C"
#' @param type this argument only works for "McCutchan" author (their Table 3).
#' "all" returns all TEF data; "whole" and "muscle" returns TEF separated per
#' type analysis; "acidified" and "unacidified" returns TEF separated per
#' acidification; and "Rainbow Trout" and "Brook Trout" returns TEF separated
#' per fish species (according to their Table 1).
#' @param seed integer to have replicated results
#'
#' @return a list (if element = "both") or a vector (if element ="N" or element
#' = "C") containing TDF values
#' @export
#'
#' @examples
#' # TEF() is deprecated, use TDF() instead:
#' TDF(author = "McCutchan", element = "N")
#'
TEF <- function (author = "Post", element = "both", type = "all", seed = 3) {
.Deprecated("TDF")
meanSD <- function(x, mean, sd) {
set.seed(seed = seed)
x <- stats::rnorm(x, mean, sd)
X <- x
MEAN <- mean
SD <- sd
Z <- (((X - mean(X, na.rm = TRUE))/sd(X, na.rm = TRUE))) * SD
MEAN + Z
}
meanSE <- function(x, mean, se) {
sd <- se * sqrt(x)
meanSD(x, mean, sd)
}
if (author == "Post") {
set.seed(seed = seed)
deltaN <- meanSD(56, 3.4, 0.98)
set.seed(seed = seed)
deltaC <- meanSD(107, 0.39, 1.3)
if (element == "N") {
message("You selected Post's (2002)
d15N: 56 values with 3.4 mean +- 0.98 sd")
return(deltaN)
} else if (element == "C") {
message("You selected Post's (2002)
d13C: 107 values with 0.39 mean +- 1.3 sd")
return(deltaC)
} else if (element == "both") {
message("You selected Post's (2002)
d15N: 56 values with 3.4 mean +- 0.98 sd")
message("d13C: 107 values with 0.39 mean +- 1.3 sd")
return(list(deltaN = deltaN, deltaC = deltaC))
} } else if (author == "McCutchan") {
set.seed(seed = seed)
allN <- meanSE(73, 2.3, 0.18)
set.seed(seed = seed)
wholeN <- meanSE(58, 2.1, 0.21)
set.seed(seed = seed)
muscleN <- meanSE(15, 2.9, 0.32)
set.seed(seed = seed)
unacidifiedN <- meanSE(15, 1.1, 0.29)
set.seed(seed = seed)
acidifiedN <- meanSE(36, 2.4, 0.24)
#raisedInvN <- meanSE(25, 1.4, 0.21)
#highProtN <- meanSE(25, 3.3, 0.26)
#plantAlgaeN <- meanSE(25, 2.2, 0.3)
set.seed(seed = seed)
rainbowTroutN <- meanSE(4, 3.2, 0.2)
set.seed(seed = seed)
brookTroutN <- meanSE(8, 3.8, 0.17)
set.seed(seed = seed)
allC <- meanSE(102, 0.5, 0.13)
set.seed(seed = seed)
wholeC <- meanSE(84, 0.3, 0.14)
set.seed(seed = seed)
muscleC <- meanSE(18, 1.3, 0.3)
set.seed(seed = seed)
unacidifiedC <- meanSE(62, 0.5, 0.17)
set.seed(seed = seed)
acidifiedC <- meanSE(22, -0.2, 0.21)
set.seed(seed = seed)
rainbowTroutC <- meanSE(4, 1.9, 0.51)
set.seed(seed = seed)
brookTroutC <- meanSE(8, 3.3, 0.29)
if (type == "all") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
All d15N: 73 values with 2.3 mean +- 0.18 se")
return(allN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
All d13C: 102 values with 0.5 mean +- 0.13 se")
return(allC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
All d15N: 73 values with 2.3 mean +- 0.18 se")
message("All d13C: 102 values with 0.5 mean +- 0.13 se")
return(list(deltaN = allN, deltaC = allC))
}
} else if (type == "whole") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Whole tissue d15N: 58 values with 2.1 mean +- 0.21 se")
return(wholeN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Whole tissue d13C: 84 values with 0.3 mean +- 0.14 se")
return(wholeC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Whole tissue d15N: 58 values with 2.1 mean +- 0.21 se")
message("Whole tissue d13C: 84 values with 0.3 mean +- 0.14 se")
return(list(deltaN = wholeN, deltaC = wholeC))
}
} else if (type == "muscle") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Muscle tissue d15N: 15 values with 2.9 mean +- 0.32 se")
return(muscleN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Muscle tissue d13C: 18 values with 1.3 mean +- 0.3 se")
return(muscleC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Muscle tissue d15N: 15 values with 2.9 mean +- 0.32 se")
message("Muscle tissue d13C: 18 values with 1.3 mean +- 0.3 se")
return(list(deltaN = muscleN, deltaC = muscleC))
}
} else if (type == "unacidified") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Unacidified tissue d15N: 15 values with 1.1 mean +- 0.29 se")
return(unacidifiedN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Unacidified tissue d13C: 62 values with 0.5 mean +- 0.17 se")
return(unacidifiedC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Unacidified tissue d15N: 15 values with 1.1 mean +- 0.29 se")
message("Unacidified tissue d13C: 62 values with 0.5 mean +- 0.17 se")
return(list(deltaN = unacidifiedN, deltaC = unacidifiedC))
}
} else if (type == "acidified") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Acidified tissue d13C: 22 values with -0.2 mean +- 0.21 se")
return(acidifiedN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Acidified tissue d15N: 36 values with 2.4 mean +- 0.24 se")
return(acidifiedC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Acidified tissue d15N: 36 values with 2.4 mean +- 0.24 se")
message("Acidified tissue d13C: 22 values with -0.2 mean +- 0.21 se")
return(list(deltaN = acidifiedN, deltaC = acidifiedC))
}
} else if (type == "rainbowTrout") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Rainbow Trout tissue d15N: 4 values with 3.2 mean +- 0.2 se")
return(rainbowTroutN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Muscle tissue d13C: 4 values with 1.9 mean +- 0.51 se")
return(rainbowTroutC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Rainbow Trout tissue d15N: 4 values with 3.2 mean +- 0.2 se")
message("Rainbow Trout muscle tissue d13C: 4 values with 1.9 mean +-
0.51 se")
return(list(deltaN = rainbowTroutN, deltaC = rainbowTroutC))
}
} else if (type == "brookTrout") {
if (element == "N") {
message("You selected McCutchan's et al (2003)
Brook Trout tissue d13C: 8 values with 3.3 mean +- 0.29 se")
return(brookTroutN)
} else if (element == "C") {
message("You selected McCutchan's et al (2003)
Brook Trout tissue d15N: 8 values with 3.8 mean +- 0.17 se")
return(brookTroutC)
} else if (element == "both") {
message("You selected McCutchan's et al (2003)
Brook Trout tissue d15N: 8 values with 3.8 mean +- 0.17 se")
message("Brook Trout tissue d13C: 8 values with 3.3 mean +- 0.29 se")
return(list(deltaN = brookTroutN, deltaC = brookTroutC))
}
}
}
}
Try the tRophicPosition package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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