R/FinalViability.R
In aravind-j/viabilitymetrics: Seed Viability Calculations and Curve Fitting
Defines functions
StoragePeriod
StorageTemp
StorageMC
FinalViability
Documented in
FinalViability
StorageMC
StoragePeriod
StorageTemp
#' Predict variables from the seed viability equation
#'
#' Predict the variables, final viability, storage period, storage temperature
#' and storage period from the improved seed viability equation
#' \insertCite{ellis_improved_1980}{viabilitymetrics}. \describe{
#' \item{\code{FinalViability}}{Compute the final viability after a period of
#' storage at a set of storage conditions (seed moisture content and
#' temperature).} \item{\code{StoragePeriod}}{Compute the storage period from
#' the final viability and the storage conditions (seed moisture content and
#' temperature).} \item{\code{StorageMC}}{Compute the storage moisture content
#' to give final viability at a particular storage temperature.}
#' \item{\code{StorageTemp}}{Compute the storage temperature to give final
#' viability at a particular storage temperature.} } \loadmathjax
#'
#' The improved seed viability equation of
#' \insertCite{ellis_improved_1980}{viabilitymetrics} describes the relationship
#' between final viability, storage period and storage environment conditions as
#' follows.
#'
#' \mjsdeqn{v=K_{i}-\frac{p}{\sigma}}
#'
#' or
#'
#' \mjsdeqn{v=K_{i}-\left ( \frac{1}{\sigma} \right )\cdot p}
#'
#' Where, \mjseqn{v} is the probit percentage viability at storage time
#' \mjseqn{p} (final viability), \mjseqn{K_{i}} is the probit percentage
#' viability of the seedlot at the beginning of storage (seedlot constant) and
#' \mjseqn{\dfrac{1}{\sigma}} is the slope.
#'
#' Germination percentages plotted against storage times yield a sigmoid seed
#' survival curve which is converted to a linear relationship by the probit
#' transformation with slope \mjseqn{\dfrac{1}{\sigma}}.
#'
#' The slope is determined as follows.
#'
#' \mjsdeqn{\sigma = 10^{K_{E}-C_{W}\log{m}-C_{H}t-C_{Q}t^2}}
#'
#' Where, \mjseqn{m} is the moisture content (fresh weight basis), \mjseqn{t} is
#' the temperature and \mjseqn{K_{E}}, \mjseqn{C_{W}}, \mjseqn{C_{H}} and
#' \mjseqn{C_{Q}} are the species-specific seed viability constants.
#'
#' On the basis of the the improved seed viability equation, \mjseqn{v},
#' \mjseqn{p}, \mjseqn{m} and \mjseqn{t} can be estimated as follows.
#'
#' \mjsdeqn{v=K_{i}-\frac{p}{\sigma}}
#'
#' \mjsdeqn{p = \sigma(K_{i}-v)}
#'
#' \mjsdeqn{m = 10^{\left[ {\left( K_{E} - C_{H}t - C_{Q}t^{2} -\log \left(
#' \frac{p}{K_{i}-v} \right) \right) } \bigg/ {C_{W}} \right]}}
#'
#' \mjsdeqn{t = \frac{-C_{H} \pm \sqrt{C_{H}^{2}-4C_{Q}\left (
#' C_{W}\log{m}-K_{E}+ \log\left ( \frac{p}{K_{i}-v} \right ) \right
#' )}}{2C_{Q}}}
#'
#' The value of the species-specific seed viability constants can be specified
#' either directly in the arguement \code{vcdirect} or as the index value of
#' the required seed viability constants from the
#' \code{\link{viabilityconstants}} dataset through the argument \code{vcindex}.
#'
#' The value of this prediction is appropriate for temperature between -20 to 90
#' °C and seed moisture content between 5 to 25\%. For values beyond this range,
#' a warning will be displayed.
#'
#' @param initial The initial viability (\%).
#' @param final The final viability (\%).
#' @param period The time period of storage in days or years according to the
#' argument \code{years}).
#' @inheritParams Sigma
#' @param unit The unit of temperature.
#'
#' @encoding UTF-8
#' @import Rdpack
#' @import mathjaxr
#'
#' @references
#'
#' \insertAllCited
#'
#' @name FinalViability
#'
#' @note For initial and/or final viability percentage values of 0\% and 100\%,
#' adjust it according to sample size using the
#' \code{\link[viabilitymetrics:Percent2Probit]{PercentAdjust}} function to
#' avoid infinity or extreme values in output.
#'
#' @return For \code{FinalViability}, the final viability (\%).
#'
#' For \code{StorageMC}, the storage moisture content (\%).
#'
#' For \code{StorageTemp}, the storage temperature (°C).
#'
#' For \code{StoragePeriod}, the duration of storage (according to argument
#' \code{years}).
#'
#' @examples
#' # Fetch the index from viabilityconstants dataset
#' viabilityconstants[grepl("oryza", x = viabilityconstants$Species,
#' ignore.case = TRUE),]
#'
#' #----------------------------------------------------------------------------
#' # Final viability
#' #----------------------------------------------------------------------------
#' # Use index 87
#' FinalViability(initial = 98, period = 365, vcindex = 87, mc = 10, temp = 5,
#' years = FALSE)
#' FinalViability(initial = 98, period = 1, vcindex = 87, mc = 10, temp = 5,
#' years = TRUE)
#'
#' # Input the viability constants directly
#' FinalViability(initial = 98, period = 365,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 10, temp = 5, years = FALSE)
#' FinalViability(initial = 98, period = 1,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 10, temp = 5, years = TRUE)
#'
#' \dontrun{
#' # Error if initial viability is beyond limits (0-100 %)
#' FinalViability(initial = 110, period = 365, vcindex = 87, mc = 10, temp = 5)
#' }
#'
#' # Warning if moisture content is beyond limits (0-100 %)
#' FinalViability(initial = 98, period = 365, vcindex = 87, mc = 110, temp = 5)
#'
#' # Warning if temperature is beyond limits (-20 to 90 degree C)
#' FinalViability(initial = 98, period = 365, vcindex = 87, mc = 10, temp = 95)
#'
#' # With initial viability 100
#' FinalViability(initial = 100, period = 365, vcindex = 87, mc = 10, temp = 5,
#' years = FALSE)
#' FinalViability(initial = 100, period = 1, vcindex = 87, mc = 10, temp = 5,
#' years = TRUE)
#'
#' # With intial viability of 100%, use of PercentAdjust() to avoid extremes
#' FinalViability(initial = PercentAdjust(100, n = 50), period = 365,
#' vcindex = 87, mc = 10, temp = 5, years = FALSE)
#' FinalViability(initial = PercentAdjust(100, n = 50), period = 1,
#' vcindex = 87, mc = 10, temp = 5, years = TRUE)
#'
#' #----------------------------------------------------------------------------
#' # Storage moisture content
#' #----------------------------------------------------------------------------
#' # Use index 87
#' StorageMC(initial = 98, final = 95, period = 3650, vcindex = 87, temp = 5,
#' years = FALSE)
#' StorageMC(initial = 98, final = 95, period = 10, vcindex = 87, temp = 5,
#' years = TRUE)
#'
#' # Input the viability constants directly
#' StorageMC(initial = 98, final = 95, period = 3650,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' temp = 5, years = FALSE)
#' StorageMC(initial = 98, final = 95, period = 10,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' temp = 5, years = TRUE)
#'
#' \dontrun{
#' # Error if initial viability is beyond limits (0-100 %)
#' StorageMC(initial = 110, final = 95, period = 3650, vcindex = 87, temp = 5)
#'
#' # Error if final viability is beyond limits (0-100 %)
#' StorageMC(initial = 98, final = -10, period = 3650, vcindex = 87, temp = 5)
#' }
#'
#' # Warning if temperature is beyond limits (-20 to 90 degree C)
#' StorageMC(initial = 98, final = 95, period = 3650, vcindex = 87, temp = 95)
#'
#' #----------------------------------------------------------------------------
#' # Storage temperature
#' #----------------------------------------------------------------------------
#' # Use index 87
#'
#' # In Celsius
#' StorageTemp(initial = 98, final = 95, period = 3650, vcindex = 87, mc = 8,
#' years = FALSE)
#' StorageTemp(initial = 98, final = 95, period = 10, vcindex = 87, mc = 8,
#' years = TRUE)
#'
#' # In Fahrenheit
#' StorageTemp(initial = 98, final = 95, period = 3650, vcindex = 87, mc = 8,
#' years = FALSE, unit = "fahrenheit")
#' StorageTemp(initial = 98, final = 95, period = 10, vcindex = 87, mc = 8,
#' years = TRUE, unit = "fahrenheit")
#'
#' # Input the viability constants directly
#' StorageTemp(initial = 98, final = 95, period = 3650,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 8, years = FALSE)
#' StorageTemp(initial = 98, final = 95, period = 10,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 8, years = TRUE)
#'
#' \dontrun{
#' # Error if initial viability is beyond limits (0-100 %)
#' StorageTemp(initial = 110, final = 95, period = 3650, vcindex = 87, mc = 8)
#'
#' # Error if final viability is beyond limits (0-100 %)
#' StorageTemp(initial = 98, final = -10, period = 3650, vcindex = 87, mc = 8)
#' }
#'
#' # Warning if moisture content is beyond limits (0-100 %)
#' StorageTemp(initial = 98, final = 95, period = 3650, vcindex = 87, mc = 110)
#'
#'
#' #----------------------------------------------------------------------------
#' # Storage period
#' #----------------------------------------------------------------------------
#' # Use index 87
#' StoragePeriod(initial = 98, final = 95, vcindex = 87, mc = 10, temp = 5,
#' years = FALSE)
#' StoragePeriod(initial = 98, final = 95, vcindex = 87, mc = 10, temp = 5,
#' years = TRUE)
#'
#' # Input the viability constants directly
#' StoragePeriod(initial = 98, final = 95,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 10, temp = 5, years = FALSE)
#' StoragePeriod(initial = 98, final = 95,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 10, temp = 5, years = TRUE)
#'
#' \dontrun{
#' # Error if initial viability is beyond limits (0-100 %)
#' StoragePeriod(initial = 110, final = 95, vcindex = 87, mc = 10, temp = 5)
#'
#' # Error if final viability is beyond limits (0-100 %)
#' StoragePeriod(initial = 98, final = -5, vcindex = 87, mc = 10, temp = 5)
#' }
#'
#'
#' # Warning if moisture content is beyond limits (0-100 %)
#' StoragePeriod(initial = 98, final = 95, vcindex = 87, mc = 110, temp = 5)
#'
#' # Warning if temperature is beyond limits (-20 to 90 degree C)
#' StoragePeriod(initial = 98, final = 95, vcindex = 87, mc = 10, temp = 95)
#'
#' # With initial viability 100
#' StoragePeriod(initial = 100, final = 95, vcindex = 87, mc = 10, temp = 5,
#' years = FALSE)
#' StoragePeriod(initial = 100, final = 95, vcindex = 87, mc = 10, temp = 5,
#' years = TRUE)
#'
#' # With intial viability of 100%, use of PercentAdjust() to avoid extremes
#' StoragePeriod(initial = PercentAdjust(100, n = 50), final = 95,
#' vcindex = 87, mc = 10, temp = 5, years = FALSE)
#' StoragePeriod(initial = PercentAdjust(100, n = 50), final = 95,
#' vcindex = 87, mc = 10, temp = 5, years = TRUE)
#'
#' @seealso \code{\link[viabilitymetrics]{Sigma}},
#' \code{\link[viabilitymetrics:Percent2Probit]{PercentAdjust}}
#'
#' @rdname FinalViability
#' @export
FinalViability <- function(initial, period, vcindex, vcdirect, mc, temp,
years = FALSE) {
# Check if initial is of type numeric with unit length
if (!is.numeric(initial) || length(initial) != 1){
stop("'initial' should be a numeric vector of length 1.")
}
# Check limits of initial viability
if (FALSE %in% (findInterval(initial, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"initial" is beyond limits (0 < "initial" < 100).')
}
# Check if period is of type numeric with unit length
if (!is.numeric(period) || length(period) != 1){
stop("'period' should be a numeric vector of length 1.")
}
if (years == TRUE) {
period <- period * 365
} else {
period <- period
}
Ki <- Percent2NED(initial)
sig <- Sigma(vcindex = vcindex, vcdirect = vcdirect, mc = mc, temp = temp,
years = FALSE)
finalv <- Ki - (period / sig)
finalv <- NED2Percent(finalv)
return(finalv)
}
#' @rdname FinalViability
#' @export
StorageMC <- function(initial, final, period, vcindex, vcdirect, temp,
years = FALSE) {
# check if both vcindex and vcdirect are given as input
chk <- c(missing(vcindex), missing(vcdirect))
if (identical(chk, c(FALSE, FALSE))) {
stop('Provide only either one of the two arguments\n',
'"vcindex" or "vcdirect" and not both.')
}
# Check if initial is of type numeric with unit length
if (!is.numeric(initial) || length(initial) != 1){
stop("'initial' should be a numeric vector of length 1.")
}
# Check limits of initial viability
if (FALSE %in% (findInterval(initial, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"initial" is beyond limits (0 < "initial" < 100).')
}
# Check if final is of type numeric with unit length
if (!is.numeric(final) || length(final) != 1){
stop("'final' should be a numeric vector of length 1.")
}
# Check limits of final viability
if (FALSE %in% (findInterval(final, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"final" is beyond limits (0 < "final" < 100).')
}
# Check if period is of type numeric with unit length
if (!is.numeric(period) || length(period) != 1){
stop("'period' should be a numeric vector of length 1.")
}
# Check if temp is of type numeric with unit length
if (!is.numeric(temp) || length(temp) != 1){
stop("'temp' should be a numeric vector of length 1.")
}
# Check limits of temperature
if (FALSE %in% (findInterval(temp, c(-20, 90),
rightmost.closed = TRUE) == 1)) {
warning('"temp" is beyond limits (-20 < "temp" < 90).')
}
if (years == TRUE) {
period <- period * 365
} else {
period <- period
}
Ki <- Percent2NED(initial)
v <- Percent2NED(final)
# Check if argument years is of type logical with unit length
if (!missing(years)){
if (!is.logical(years) || length(years) != 1){
stop("'years' should be a numeric vector of length 1.")
}
}
#If input is vcindex
if (!missing(vcindex)) {
# Extract constants from vcindex
# check if vcindex is an integer
if (vcindex %% 1 != 0 && length(n) != 1) {
stop('"vcindex" is not an integer vector of unit length.')
}
# check if vcindex is present in viabilityconstants
if (!(vcindex %in% viabilityconstants$Index)) {
stop( paste("specified 'vcindex' is not present in the",
" 'viabilityconstants' dataset.\n",
"Input a value in the range 1-",
max(viabilityconstants$Index), sep = ""))
}
vcdirect <- NULL
vc <- viabilityconstants[vcindex, ]
Ke <- as.numeric(vc[, 3])
Cw <- as.numeric(vc[, 4])
Ch <- as.numeric(vc[, 5])
Cq <- as.numeric(vc[, 6])
rm(vc)
} else {#If input is vcdirect
# Extract constants from vcdirect
# check if vcdirect is a numeric vector of length 4 with Ke, Cw, Ch, Cq
if (length(vcdirect) != 4) {
stop(paste0(c('"vcdirect" is not of length 4;', '\n',
'All four seed viability constants are not specified.')))
} else {
# check if vcdirect is numeric vector
if (!is.numeric(vcdirect)) {
stop('"vcdirect" is not a numeric vector.')
}
}
vcindex <- NULL
names(vcdirect) <- c("Ke", "Cw", "Ch", "Cq")
Ke <- as.numeric(vcdirect[1])
Cw <- as.numeric(vcdirect[2])
Ch <- as.numeric(vcdirect[3])
Cq <- as.numeric(vcdirect[4])
}
logmc <- (Ke - Ch*temp - Cq*(temp^2) - log10(period/(Ki - v)))/Cw
mc <- 10^logmc
#mc <- exp(logmc*log(10))
return(mc)
}
#' @rdname FinalViability
#' @export
StorageTemp <- function(initial, final, period, vcindex, vcdirect, mc,
years = FALSE, unit = c("celsius", "fahrenheit")) {
# check if both vcindex and vcdirect are given as input
chk <- c(missing(vcindex), missing(vcdirect))
if (identical(chk, c(FALSE, FALSE))) {
stop('Provide only either one of the two arguments\n',
'"vcindex" or "vcdirect" and not both.')
}
# Check if initial is of type numeric with unit length
if (!is.numeric(initial) || length(initial) != 1){
stop("'initial' should be a numeric vector of length 1.")
}
# Check limits of initial viability
if (FALSE %in% (findInterval(initial, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"initial" is beyond limits (0 < "initial" < 100).')
}
# Check if final is of type numeric with unit length
if (!is.numeric(final) || length(final) != 1){
stop("'final' should be a numeric vector of length 1.")
}
# Check limits of final viability
if (FALSE %in% (findInterval(final, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"final" is beyond limits (0 < "final" < 100).')
}
# Check if period is of type numeric with unit length
if (!is.numeric(period) || length(period) != 1){
stop("'period' should be a numeric vector of length 1.")
}
# Check if mc is of type numeric with unit length
if (!is.numeric(mc) || length(mc) != 1){
stop("'mc' should be a numeric vector of length 1.")
}
#Check limits of moisture content
if (FALSE %in% (findInterval(mc, c(0, 100), rightmost.closed = TRUE) == 1)) {
warning('"mc" is beyond limits (0 < "mc" < 100).')
}
# Check if argument years is of type logical with unit length
if(!missing(years)){
if(!is.logical(years) || length(years) != 1){
stop("'years' should be a numeric vector of length 1.")
}
}
unit <- match.arg(unit)
Ki <- Percent2NED(initial)
v <- Percent2NED(final)
# Check if argument years is of type logical with unit length
if(!missing(years)){
if(!is.logical(years) || length(years) != 1){
stop("'years' should be a numeric vector of length 1.")
}
}
if (years == TRUE) {
period <- period * 365
} else {
period <- period
}
#If input is vcindex
if (!missing(vcindex)) {
# Extract constants from vcindex
# check if vcindex is an integer
if (vcindex %% 1 != 0) {
stop('"vcindex" is not an integer.')
}
# check if vcindex is present in viabilityconstants
if (!(vcindex %in% viabilityconstants$Index)) {
stop( paste("specified 'vcindex' is not present in the",
" 'viabilityconstants' dataset.\n",
"Input a value in the range 1-",
max(viabilityconstants$Index), sep = ""))
}
vcdirect <- NULL
vc <- viabilityconstants[vcindex, ]
Ke <- as.numeric(vc[, 3])
Cw <- as.numeric(vc[, 4])
Ch <- as.numeric(vc[, 5])
Cq <- as.numeric(vc[, 6])
rm(vc)
} else {#If input is vcdirect
# Extract constants from vcdirect
# check if vcdirect is a numeric vector of length 4 with Ke, Cw, Ch, Cq
if (length(vcdirect) != 4) {
stop(paste0(c('"vcdirect" is not of length 4;', '\n',
'All four seed viability constants are not specified.')))
} else {
# check if vcdirect is numeric vector
if (!is.numeric(vcdirect)) {
stop('"vcdirect" is not a numeric vector.')
}
}
vcindex <- NULL
names(vcdirect) <- c("Ke", "Cw", "Ch", "Cq")
Ke <- as.numeric(vcdirect[1])
Cw <- as.numeric(vcdirect[2])
Ch <- as.numeric(vcdirect[3])
Cq <- as.numeric(vcdirect[4])
}
# Solve quadratic for temp
A <- Cq
B <- Ch
C <- (Cw*log10(mc)) - Ke + log10(period/(Ki - v))
temp <- ((-B) + sqrt(B^2 - (4*A*C)))/(2*A)
if (unit == "fahrenheit") {
temp <- (temp * (9/5)) + 32
}
return(temp)
}
#' @rdname FinalViability
#' @export
StoragePeriod <- function(initial, final, vcindex, vcdirect, mc, temp,
years = FALSE) {
# Check if initial is of type numeric with unit length
if (!is.numeric(initial) || length(initial) != 1){
stop("'initial' should be a numeric vector of length 1.")
}
# Check limits of initial viability
if (FALSE %in% (findInterval(initial, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"initial" is beyond limits (0 < "initial" < 100).')
}
# Check if final is of type numeric with unit length
if (!is.numeric(final) || length(final) != 1){
stop("'final' should be a numeric vector of length 1.")
}
# Check limits of final viability
if (FALSE %in% (findInterval(final, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"final" is beyond limits (0 < "final" < 100).')
}
Ki <- Percent2NED(initial)
sig <- Sigma(vcindex = vcindex, vcdirect = vcdirect, mc = mc, temp = temp,
years = FALSE)
v <- Percent2NED(final)
period <- sig*(Ki - v)
if (years == TRUE) {
period <- period / 365
} else {
period <- period
}
if (period < 1) {
warning("Negative storage period computed.")
}
return(period)
}
aravind-j/viabilitymetrics documentation built on May 15, 2021, 9:10 a.m.
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.
Defines functions StoragePeriod StorageTemp StorageMC FinalViability
Documented in FinalViability StorageMC StoragePeriod StorageTemp
#' Predict variables from the seed viability equation
#'
#' Predict the variables, final viability, storage period, storage temperature
#' and storage period from the improved seed viability equation
#' \insertCite{ellis_improved_1980}{viabilitymetrics}. \describe{
#' \item{\code{FinalViability}}{Compute the final viability after a period of
#' storage at a set of storage conditions (seed moisture content and
#' temperature).} \item{\code{StoragePeriod}}{Compute the storage period from
#' the final viability and the storage conditions (seed moisture content and
#' temperature).} \item{\code{StorageMC}}{Compute the storage moisture content
#' to give final viability at a particular storage temperature.}
#' \item{\code{StorageTemp}}{Compute the storage temperature to give final
#' viability at a particular storage temperature.} } \loadmathjax
#'
#' The improved seed viability equation of
#' \insertCite{ellis_improved_1980}{viabilitymetrics} describes the relationship
#' between final viability, storage period and storage environment conditions as
#' follows.
#'
#' \mjsdeqn{v=K_{i}-\frac{p}{\sigma}}
#'
#' or
#'
#' \mjsdeqn{v=K_{i}-\left ( \frac{1}{\sigma} \right )\cdot p}
#'
#' Where, \mjseqn{v} is the probit percentage viability at storage time
#' \mjseqn{p} (final viability), \mjseqn{K_{i}} is the probit percentage
#' viability of the seedlot at the beginning of storage (seedlot constant) and
#' \mjseqn{\dfrac{1}{\sigma}} is the slope.
#'
#' Germination percentages plotted against storage times yield a sigmoid seed
#' survival curve which is converted to a linear relationship by the probit
#' transformation with slope \mjseqn{\dfrac{1}{\sigma}}.
#'
#' The slope is determined as follows.
#'
#' \mjsdeqn{\sigma = 10^{K_{E}-C_{W}\log{m}-C_{H}t-C_{Q}t^2}}
#'
#' Where, \mjseqn{m} is the moisture content (fresh weight basis), \mjseqn{t} is
#' the temperature and \mjseqn{K_{E}}, \mjseqn{C_{W}}, \mjseqn{C_{H}} and
#' \mjseqn{C_{Q}} are the species-specific seed viability constants.
#'
#' On the basis of the the improved seed viability equation, \mjseqn{v},
#' \mjseqn{p}, \mjseqn{m} and \mjseqn{t} can be estimated as follows.
#'
#' \mjsdeqn{v=K_{i}-\frac{p}{\sigma}}
#'
#' \mjsdeqn{p = \sigma(K_{i}-v)}
#'
#' \mjsdeqn{m = 10^{\left[ {\left( K_{E} - C_{H}t - C_{Q}t^{2} -\log \left(
#' \frac{p}{K_{i}-v} \right) \right) } \bigg/ {C_{W}} \right]}}
#'
#' \mjsdeqn{t = \frac{-C_{H} \pm \sqrt{C_{H}^{2}-4C_{Q}\left (
#' C_{W}\log{m}-K_{E}+ \log\left ( \frac{p}{K_{i}-v} \right ) \right
#' )}}{2C_{Q}}}
#'
#' The value of the species-specific seed viability constants can be specified
#' either directly in the arguement \code{vcdirect} or as the index value of
#' the required seed viability constants from the
#' \code{\link{viabilityconstants}} dataset through the argument \code{vcindex}.
#'
#' The value of this prediction is appropriate for temperature between -20 to 90
#' °C and seed moisture content between 5 to 25\%. For values beyond this range,
#' a warning will be displayed.
#'
#' @param initial The initial viability (\%).
#' @param final The final viability (\%).
#' @param period The time period of storage in days or years according to the
#' argument \code{years}).
#' @inheritParams Sigma
#' @param unit The unit of temperature.
#'
#' @encoding UTF-8
#' @import Rdpack
#' @import mathjaxr
#'
#' @references
#'
#' \insertAllCited
#'
#' @name FinalViability
#'
#' @note For initial and/or final viability percentage values of 0\% and 100\%,
#' adjust it according to sample size using the
#' \code{\link[viabilitymetrics:Percent2Probit]{PercentAdjust}} function to
#' avoid infinity or extreme values in output.
#'
#' @return For \code{FinalViability}, the final viability (\%).
#'
#' For \code{StorageMC}, the storage moisture content (\%).
#'
#' For \code{StorageTemp}, the storage temperature (°C).
#'
#' For \code{StoragePeriod}, the duration of storage (according to argument
#' \code{years}).
#'
#' @examples
#' # Fetch the index from viabilityconstants dataset
#' viabilityconstants[grepl("oryza", x = viabilityconstants$Species,
#' ignore.case = TRUE),]
#'
#' #----------------------------------------------------------------------------
#' # Final viability
#' #----------------------------------------------------------------------------
#' # Use index 87
#' FinalViability(initial = 98, period = 365, vcindex = 87, mc = 10, temp = 5,
#' years = FALSE)
#' FinalViability(initial = 98, period = 1, vcindex = 87, mc = 10, temp = 5,
#' years = TRUE)
#'
#' # Input the viability constants directly
#' FinalViability(initial = 98, period = 365,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 10, temp = 5, years = FALSE)
#' FinalViability(initial = 98, period = 1,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 10, temp = 5, years = TRUE)
#'
#' \dontrun{
#' # Error if initial viability is beyond limits (0-100 %)
#' FinalViability(initial = 110, period = 365, vcindex = 87, mc = 10, temp = 5)
#' }
#'
#' # Warning if moisture content is beyond limits (0-100 %)
#' FinalViability(initial = 98, period = 365, vcindex = 87, mc = 110, temp = 5)
#'
#' # Warning if temperature is beyond limits (-20 to 90 degree C)
#' FinalViability(initial = 98, period = 365, vcindex = 87, mc = 10, temp = 95)
#'
#' # With initial viability 100
#' FinalViability(initial = 100, period = 365, vcindex = 87, mc = 10, temp = 5,
#' years = FALSE)
#' FinalViability(initial = 100, period = 1, vcindex = 87, mc = 10, temp = 5,
#' years = TRUE)
#'
#' # With intial viability of 100%, use of PercentAdjust() to avoid extremes
#' FinalViability(initial = PercentAdjust(100, n = 50), period = 365,
#' vcindex = 87, mc = 10, temp = 5, years = FALSE)
#' FinalViability(initial = PercentAdjust(100, n = 50), period = 1,
#' vcindex = 87, mc = 10, temp = 5, years = TRUE)
#'
#' #----------------------------------------------------------------------------
#' # Storage moisture content
#' #----------------------------------------------------------------------------
#' # Use index 87
#' StorageMC(initial = 98, final = 95, period = 3650, vcindex = 87, temp = 5,
#' years = FALSE)
#' StorageMC(initial = 98, final = 95, period = 10, vcindex = 87, temp = 5,
#' years = TRUE)
#'
#' # Input the viability constants directly
#' StorageMC(initial = 98, final = 95, period = 3650,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' temp = 5, years = FALSE)
#' StorageMC(initial = 98, final = 95, period = 10,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' temp = 5, years = TRUE)
#'
#' \dontrun{
#' # Error if initial viability is beyond limits (0-100 %)
#' StorageMC(initial = 110, final = 95, period = 3650, vcindex = 87, temp = 5)
#'
#' # Error if final viability is beyond limits (0-100 %)
#' StorageMC(initial = 98, final = -10, period = 3650, vcindex = 87, temp = 5)
#' }
#'
#' # Warning if temperature is beyond limits (-20 to 90 degree C)
#' StorageMC(initial = 98, final = 95, period = 3650, vcindex = 87, temp = 95)
#'
#' #----------------------------------------------------------------------------
#' # Storage temperature
#' #----------------------------------------------------------------------------
#' # Use index 87
#'
#' # In Celsius
#' StorageTemp(initial = 98, final = 95, period = 3650, vcindex = 87, mc = 8,
#' years = FALSE)
#' StorageTemp(initial = 98, final = 95, period = 10, vcindex = 87, mc = 8,
#' years = TRUE)
#'
#' # In Fahrenheit
#' StorageTemp(initial = 98, final = 95, period = 3650, vcindex = 87, mc = 8,
#' years = FALSE, unit = "fahrenheit")
#' StorageTemp(initial = 98, final = 95, period = 10, vcindex = 87, mc = 8,
#' years = TRUE, unit = "fahrenheit")
#'
#' # Input the viability constants directly
#' StorageTemp(initial = 98, final = 95, period = 3650,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 8, years = FALSE)
#' StorageTemp(initial = 98, final = 95, period = 10,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 8, years = TRUE)
#'
#' \dontrun{
#' # Error if initial viability is beyond limits (0-100 %)
#' StorageTemp(initial = 110, final = 95, period = 3650, vcindex = 87, mc = 8)
#'
#' # Error if final viability is beyond limits (0-100 %)
#' StorageTemp(initial = 98, final = -10, period = 3650, vcindex = 87, mc = 8)
#' }
#'
#' # Warning if moisture content is beyond limits (0-100 %)
#' StorageTemp(initial = 98, final = 95, period = 3650, vcindex = 87, mc = 110)
#'
#'
#' #----------------------------------------------------------------------------
#' # Storage period
#' #----------------------------------------------------------------------------
#' # Use index 87
#' StoragePeriod(initial = 98, final = 95, vcindex = 87, mc = 10, temp = 5,
#' years = FALSE)
#' StoragePeriod(initial = 98, final = 95, vcindex = 87, mc = 10, temp = 5,
#' years = TRUE)
#'
#' # Input the viability constants directly
#' StoragePeriod(initial = 98, final = 95,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 10, temp = 5, years = FALSE)
#' StoragePeriod(initial = 98, final = 95,
#' vcdirect = c(8.242, 4.345, 0.0307, 0.000501),
#' mc = 10, temp = 5, years = TRUE)
#'
#' \dontrun{
#' # Error if initial viability is beyond limits (0-100 %)
#' StoragePeriod(initial = 110, final = 95, vcindex = 87, mc = 10, temp = 5)
#'
#' # Error if final viability is beyond limits (0-100 %)
#' StoragePeriod(initial = 98, final = -5, vcindex = 87, mc = 10, temp = 5)
#' }
#'
#'
#' # Warning if moisture content is beyond limits (0-100 %)
#' StoragePeriod(initial = 98, final = 95, vcindex = 87, mc = 110, temp = 5)
#'
#' # Warning if temperature is beyond limits (-20 to 90 degree C)
#' StoragePeriod(initial = 98, final = 95, vcindex = 87, mc = 10, temp = 95)
#'
#' # With initial viability 100
#' StoragePeriod(initial = 100, final = 95, vcindex = 87, mc = 10, temp = 5,
#' years = FALSE)
#' StoragePeriod(initial = 100, final = 95, vcindex = 87, mc = 10, temp = 5,
#' years = TRUE)
#'
#' # With intial viability of 100%, use of PercentAdjust() to avoid extremes
#' StoragePeriod(initial = PercentAdjust(100, n = 50), final = 95,
#' vcindex = 87, mc = 10, temp = 5, years = FALSE)
#' StoragePeriod(initial = PercentAdjust(100, n = 50), final = 95,
#' vcindex = 87, mc = 10, temp = 5, years = TRUE)
#'
#' @seealso \code{\link[viabilitymetrics]{Sigma}},
#' \code{\link[viabilitymetrics:Percent2Probit]{PercentAdjust}}
#'
#' @rdname FinalViability
#' @export
FinalViability <- function(initial, period, vcindex, vcdirect, mc, temp,
years = FALSE) {
# Check if initial is of type numeric with unit length
if (!is.numeric(initial) || length(initial) != 1){
stop("'initial' should be a numeric vector of length 1.")
}
# Check limits of initial viability
if (FALSE %in% (findInterval(initial, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"initial" is beyond limits (0 < "initial" < 100).')
}
# Check if period is of type numeric with unit length
if (!is.numeric(period) || length(period) != 1){
stop("'period' should be a numeric vector of length 1.")
}
if (years == TRUE) {
period <- period * 365
} else {
period <- period
}
Ki <- Percent2NED(initial)
sig <- Sigma(vcindex = vcindex, vcdirect = vcdirect, mc = mc, temp = temp,
years = FALSE)
finalv <- Ki - (period / sig)
finalv <- NED2Percent(finalv)
return(finalv)
}
#' @rdname FinalViability
#' @export
StorageMC <- function(initial, final, period, vcindex, vcdirect, temp,
years = FALSE) {
# check if both vcindex and vcdirect are given as input
chk <- c(missing(vcindex), missing(vcdirect))
if (identical(chk, c(FALSE, FALSE))) {
stop('Provide only either one of the two arguments\n',
'"vcindex" or "vcdirect" and not both.')
}
# Check if initial is of type numeric with unit length
if (!is.numeric(initial) || length(initial) != 1){
stop("'initial' should be a numeric vector of length 1.")
}
# Check limits of initial viability
if (FALSE %in% (findInterval(initial, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"initial" is beyond limits (0 < "initial" < 100).')
}
# Check if final is of type numeric with unit length
if (!is.numeric(final) || length(final) != 1){
stop("'final' should be a numeric vector of length 1.")
}
# Check limits of final viability
if (FALSE %in% (findInterval(final, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"final" is beyond limits (0 < "final" < 100).')
}
# Check if period is of type numeric with unit length
if (!is.numeric(period) || length(period) != 1){
stop("'period' should be a numeric vector of length 1.")
}
# Check if temp is of type numeric with unit length
if (!is.numeric(temp) || length(temp) != 1){
stop("'temp' should be a numeric vector of length 1.")
}
# Check limits of temperature
if (FALSE %in% (findInterval(temp, c(-20, 90),
rightmost.closed = TRUE) == 1)) {
warning('"temp" is beyond limits (-20 < "temp" < 90).')
}
if (years == TRUE) {
period <- period * 365
} else {
period <- period
}
Ki <- Percent2NED(initial)
v <- Percent2NED(final)
# Check if argument years is of type logical with unit length
if (!missing(years)){
if (!is.logical(years) || length(years) != 1){
stop("'years' should be a numeric vector of length 1.")
}
}
#If input is vcindex
if (!missing(vcindex)) {
# Extract constants from vcindex
# check if vcindex is an integer
if (vcindex %% 1 != 0 && length(n) != 1) {
stop('"vcindex" is not an integer vector of unit length.')
}
# check if vcindex is present in viabilityconstants
if (!(vcindex %in% viabilityconstants$Index)) {
stop( paste("specified 'vcindex' is not present in the",
" 'viabilityconstants' dataset.\n",
"Input a value in the range 1-",
max(viabilityconstants$Index), sep = ""))
}
vcdirect <- NULL
vc <- viabilityconstants[vcindex, ]
Ke <- as.numeric(vc[, 3])
Cw <- as.numeric(vc[, 4])
Ch <- as.numeric(vc[, 5])
Cq <- as.numeric(vc[, 6])
rm(vc)
} else {#If input is vcdirect
# Extract constants from vcdirect
# check if vcdirect is a numeric vector of length 4 with Ke, Cw, Ch, Cq
if (length(vcdirect) != 4) {
stop(paste0(c('"vcdirect" is not of length 4;', '\n',
'All four seed viability constants are not specified.')))
} else {
# check if vcdirect is numeric vector
if (!is.numeric(vcdirect)) {
stop('"vcdirect" is not a numeric vector.')
}
}
vcindex <- NULL
names(vcdirect) <- c("Ke", "Cw", "Ch", "Cq")
Ke <- as.numeric(vcdirect[1])
Cw <- as.numeric(vcdirect[2])
Ch <- as.numeric(vcdirect[3])
Cq <- as.numeric(vcdirect[4])
}
logmc <- (Ke - Ch*temp - Cq*(temp^2) - log10(period/(Ki - v)))/Cw
mc <- 10^logmc
#mc <- exp(logmc*log(10))
return(mc)
}
#' @rdname FinalViability
#' @export
StorageTemp <- function(initial, final, period, vcindex, vcdirect, mc,
years = FALSE, unit = c("celsius", "fahrenheit")) {
# check if both vcindex and vcdirect are given as input
chk <- c(missing(vcindex), missing(vcdirect))
if (identical(chk, c(FALSE, FALSE))) {
stop('Provide only either one of the two arguments\n',
'"vcindex" or "vcdirect" and not both.')
}
# Check if initial is of type numeric with unit length
if (!is.numeric(initial) || length(initial) != 1){
stop("'initial' should be a numeric vector of length 1.")
}
# Check limits of initial viability
if (FALSE %in% (findInterval(initial, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"initial" is beyond limits (0 < "initial" < 100).')
}
# Check if final is of type numeric with unit length
if (!is.numeric(final) || length(final) != 1){
stop("'final' should be a numeric vector of length 1.")
}
# Check limits of final viability
if (FALSE %in% (findInterval(final, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"final" is beyond limits (0 < "final" < 100).')
}
# Check if period is of type numeric with unit length
if (!is.numeric(period) || length(period) != 1){
stop("'period' should be a numeric vector of length 1.")
}
# Check if mc is of type numeric with unit length
if (!is.numeric(mc) || length(mc) != 1){
stop("'mc' should be a numeric vector of length 1.")
}
#Check limits of moisture content
if (FALSE %in% (findInterval(mc, c(0, 100), rightmost.closed = TRUE) == 1)) {
warning('"mc" is beyond limits (0 < "mc" < 100).')
}
# Check if argument years is of type logical with unit length
if(!missing(years)){
if(!is.logical(years) || length(years) != 1){
stop("'years' should be a numeric vector of length 1.")
}
}
unit <- match.arg(unit)
Ki <- Percent2NED(initial)
v <- Percent2NED(final)
# Check if argument years is of type logical with unit length
if(!missing(years)){
if(!is.logical(years) || length(years) != 1){
stop("'years' should be a numeric vector of length 1.")
}
}
if (years == TRUE) {
period <- period * 365
} else {
period <- period
}
#If input is vcindex
if (!missing(vcindex)) {
# Extract constants from vcindex
# check if vcindex is an integer
if (vcindex %% 1 != 0) {
stop('"vcindex" is not an integer.')
}
# check if vcindex is present in viabilityconstants
if (!(vcindex %in% viabilityconstants$Index)) {
stop( paste("specified 'vcindex' is not present in the",
" 'viabilityconstants' dataset.\n",
"Input a value in the range 1-",
max(viabilityconstants$Index), sep = ""))
}
vcdirect <- NULL
vc <- viabilityconstants[vcindex, ]
Ke <- as.numeric(vc[, 3])
Cw <- as.numeric(vc[, 4])
Ch <- as.numeric(vc[, 5])
Cq <- as.numeric(vc[, 6])
rm(vc)
} else {#If input is vcdirect
# Extract constants from vcdirect
# check if vcdirect is a numeric vector of length 4 with Ke, Cw, Ch, Cq
if (length(vcdirect) != 4) {
stop(paste0(c('"vcdirect" is not of length 4;', '\n',
'All four seed viability constants are not specified.')))
} else {
# check if vcdirect is numeric vector
if (!is.numeric(vcdirect)) {
stop('"vcdirect" is not a numeric vector.')
}
}
vcindex <- NULL
names(vcdirect) <- c("Ke", "Cw", "Ch", "Cq")
Ke <- as.numeric(vcdirect[1])
Cw <- as.numeric(vcdirect[2])
Ch <- as.numeric(vcdirect[3])
Cq <- as.numeric(vcdirect[4])
}
# Solve quadratic for temp
A <- Cq
B <- Ch
C <- (Cw*log10(mc)) - Ke + log10(period/(Ki - v))
temp <- ((-B) + sqrt(B^2 - (4*A*C)))/(2*A)
if (unit == "fahrenheit") {
temp <- (temp * (9/5)) + 32
}
return(temp)
}
#' @rdname FinalViability
#' @export
StoragePeriod <- function(initial, final, vcindex, vcdirect, mc, temp,
years = FALSE) {
# Check if initial is of type numeric with unit length
if (!is.numeric(initial) || length(initial) != 1){
stop("'initial' should be a numeric vector of length 1.")
}
# Check limits of initial viability
if (FALSE %in% (findInterval(initial, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"initial" is beyond limits (0 < "initial" < 100).')
}
# Check if final is of type numeric with unit length
if (!is.numeric(final) || length(final) != 1){
stop("'final' should be a numeric vector of length 1.")
}
# Check limits of final viability
if (FALSE %in% (findInterval(final, c(0, 100),
rightmost.closed = TRUE) == 1)) {
stop('"final" is beyond limits (0 < "final" < 100).')
}
Ki <- Percent2NED(initial)
sig <- Sigma(vcindex = vcindex, vcdirect = vcdirect, mc = mc, temp = temp,
years = FALSE)
v <- Percent2NED(final)
period <- sig*(Ki - v)
if (years == TRUE) {
period <- period / 365
} else {
period <- period
}
if (period < 1) {
warning("Negative storage period computed.")
}
return(period)
}
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.