Sigma: Period to lose unit probit viability

Description Usage Arguments Details Value References Examples

View source: R/Sigma.R

Description

Sigma calculates the period to lose one probit viability (\mjseqn\sigma) under storage at a given moisture content and temperature. \loadmathjax

Usage

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Sigma(vcindex, vcdirect, mc, temp, years = FALSE)

Arguments

vcindex

An integer value indicating the index of seed viability. constants to be used from the viabilityconstants dataset in the package.

vcdirect

A numeric vector of length 4 with the four viability constants viz.: \mjseqnK_E, \mjseqnC_W, \mjseqnC_H and \mjseqnC_Q.

mc

Moisture content.

temp

Temperature in °C.

years

If TRUE, returns the output period in years instead of days.

Details

This function computes the period to lose one probit viability (\mjseqn\sigma) according to the improved seed viability equation of \insertCiteellis_improved_1980;textualviabilitymetrics as follows.

\mjsdeqn

v=K_i-\fracp\sigma

or

\mjsdeqn

v=K_i-\left ( \frac1\sigma \right )\cdot p

Where, \mjseqnv is the probit percentage viability at storage time \mjseqnp (final viability), \mjseqnK_i is the probit percentage viability of the seedlot at the beginning of storage (seedlot constant) and \mjseqn\frac1\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\frac1\sigma.

The slope is determined as follows.

\mjsdeqn\sigma

= 10^K_E-C_W\logm-C_Ht-C_Qt^2

Where, \mjseqnv is the probit percentage viability at storage time \mjseqnp (final viability), \mjseqnK_i is the probit percentage viability of the seedlot at the beginning of storage (seedlot constant), \mjseqnm is the moisture content (fresh weight basis), \mjseqnt is the temperature and \mjseqnK_E, \mjseqnC_W, \mjseqnC_H and \mjseqnC_Q are the species-specific seed viability constants.

The value of the species-specific seed viability constants can be specified either directly in the argument vcdirect or as the index value of the required seed viability constants from the viabilityconstants dataset through the argument 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.

Value

The period to lose one probit in days or years (according to argument years).

References

\insertAllCited

Examples

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#----------------------------------------------------------------------------
# Days/Years to lose unit probit viability for rice seeds stored at
# 5 degree celsius and 10% moisture content.
#----------------------------------------------------------------------------
# Fetch the index from viabilityconstants dataset
viabilityconstants[grepl("oryza", x = viabilityconstants$Species,
                         ignore.case = TRUE),]
# Use index 87
Sigma(vcindex = 87, mc = 10, temp = 5)
Sigma(vcindex = 87, mc = 10, temp = 5, years = TRUE)

# Input the viability constants directly
Sigma(vcdirect = c(8.242, 4.345, 0.0307, 0.000501), mc = 10, temp = 5)
Sigma(vcdirect = c(8.242, 4.345, 0.0307, 0.000501), mc = 10, temp = 5,
      years = TRUE)

# Warning if moisture content is beyond limits (0-100 %)
Sigma(vcindex = 87, mc = 110, temp = 5)

# Warning if temperature is beyond limits (-20 to 90 degree C)
Sigma(vcindex = 87, mc = 10, temp = 95)

#----------------------------------------------------------------------------
# Days/Years to lose unit probit viability for soybean seeds stored at
# -18 degree celsius and 8% moisture content.
#----------------------------------------------------------------------------
# Fetch the index from viabilityconstants dataset
viabilityconstants[grepl("glycine", x = viabilityconstants$Species,
                         ignore.case = TRUE),]
# Use index  59
Sigma(vcindex = 59, mc = 8, temp = -18)
Sigma(vcindex = 59, mc = 8, temp = -18, years = TRUE)

# Input the viability constants directly
Sigma(vcdirect = c(7.292, 3.996, 0.0295, 0.000491), mc = 8, temp = -18)
Sigma(vcdirect = c(7.292, 3.996, 0.0295, 0.000491), mc = 8, temp = -18,
      years = TRUE)

# Warning if moisture content is beyond limits (0-100 %)
Sigma(vcindex = 59, mc = 110, temp = 5)

# Warning if temperature is beyond limits (-20 to 90 degree C)
Sigma(vcindex = 59, mc = 10, temp = 95)

aravind-j/viabilitymetrics documentation built on May 15, 2021, 9:10 a.m.