FinalViability: Predict variables from the seed viability equation
In aravind-j/viabilitymetrics: Seed Viability Calculations and Curve Fitting
Description
Usage
Arguments
Details
Value
Note
References
See Also
Examples
View source: R/FinalViability.R
Description
Predict the variables, final viability, storage period, storage temperature
and storage period from the improved seed viability equation
\insertCiteellis_improved_1980viabilitymetrics.
FinalViabilityCompute the final viability after a period of
storage at a set of storage conditions (seed moisture content and
temperature).
StoragePeriodCompute the storage period from
the final viability and the storage conditions (seed moisture content and
temperature).
StorageMCCompute the storage moisture content
to give final viability at a particular storage temperature.
StorageTempCompute the storage temperature to give final
viability at a particular storage temperature.
\loadmathjax
Usage
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FinalViability(initial, period, vcindex, vcdirect, mc, temp, years = FALSE)
StorageMC(initial, final, period, vcindex, vcdirect, temp, years = FALSE)
StorageTemp(
initial,
final,
period,
vcindex,
vcdirect,
mc,
years = FALSE,
unit = c("celsius", "fahrenheit")
)
StoragePeriod(initial, final, vcindex, vcdirect, mc, temp, years = FALSE)
Arguments
initial
The initial viability (%).
period
The time period of storage in days or years according to the
argument years).
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.
final
The final viability (%).
unit
The unit of temperature.
Details
The improved seed viability equation of
\insertCiteellis_improved_1980viabilitymetrics describes the relationship
between final viability, storage period and storage environment conditions as
follows.
\mjsdeqnv=K_i-\fracp\sigma
or
\mjsdeqnv=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\dfrac1\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\dfrac1\sigma.
The slope is determined as follows.
\mjsdeqn\sigma = 10^K_E-C_W\logm-C_Ht-C_Qt^2
Where, \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.
On the basis of the the improved seed viability equation, \mjseqnv,
\mjseqnp, \mjseqnm and \mjseqnt can be estimated as follows.
\mjsdeqnv=K_i-\fracp\sigma
\mjsdeqnp = \sigma(K_i-v)
\mjsdeqnm = 10^\left[ \left( K_E - C_Ht - C_Qt^2 -\log \left(
\fracpK_i-v \right) \right) \bigg/ C_W \right]
\mjsdeqnt = \frac-C_H \pm \sqrtC_H^2-4C_Q\left (
C_W\logm-K_E+ \log\left ( \fracpK_i-v \right ) \right
)2C_Q
The value of the species-specific seed viability constants can be specified
either directly in the arguement 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
For FinalViability, the final viability (%).
For StorageMC, the storage moisture content (%).
For StorageTemp, the storage temperature (°C).
For StoragePeriod, the duration of storage (according to argument
years).
Note
For initial and/or final viability percentage values of 0% and 100%,
adjust it according to sample size using the
PercentAdjust function to
avoid infinity or extreme values in output.
References
\insertAllCited
See Also
Examples
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# 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)
## Not run:
# Error if initial viability is beyond limits (0-100 %)
FinalViability(initial = 110, period = 365, vcindex = 87, mc = 10, temp = 5)
## End(Not run)
# 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)
## Not run:
# 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)
## End(Not run)
# 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)
## Not run:
# 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)
## End(Not run)
# 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)
## Not run:
# 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)
## End(Not run)
# 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)
aravind-j/viabilitymetrics documentation built on May 15, 2021, 9:10 a.m.
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Description Usage Arguments Details Value Note References See Also Examples
View source: R/FinalViability.R
Description
Predict the variables, final viability, storage period, storage temperature and storage period from the improved seed viability equation \insertCiteellis_improved_1980viabilitymetrics.
FinalViabilityCompute the final viability after a period of storage at a set of storage conditions (seed moisture content and temperature).
StoragePeriodCompute the storage period from the final viability and the storage conditions (seed moisture content and temperature).
StorageMCCompute the storage moisture content to give final viability at a particular storage temperature.
StorageTempCompute the storage temperature to give final viability at a particular storage temperature.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | FinalViability(initial, period, vcindex, vcdirect, mc, temp, years = FALSE)
StorageMC(initial, final, period, vcindex, vcdirect, temp, years = FALSE)
StorageTemp(
initial,
final,
period,
vcindex,
vcdirect,
mc,
years = FALSE,
unit = c("celsius", "fahrenheit")
)
StoragePeriod(initial, final, vcindex, vcdirect, mc, temp, years = FALSE)
|
Arguments
initial |
The initial viability (%). |
period |
The time period of storage in days or years according to the
argument |
vcindex |
An integer value indicating the index of seed viability.
constants to be used from the |
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 |
final |
The final viability (%). |
unit |
The unit of temperature. |
Details
The improved seed viability equation of \insertCiteellis_improved_1980viabilitymetrics describes the relationship between final viability, storage period and storage environment conditions as follows.
\mjsdeqnv=K_i-\fracp\sigma
or
\mjsdeqnv=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\dfrac1\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\dfrac1\sigma.
The slope is determined as follows.
\mjsdeqn\sigma= 10^K_E-C_W\logm-C_Ht-C_Qt^2
Where, \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.
On the basis of the the improved seed viability equation, \mjseqnv, \mjseqnp, \mjseqnm and \mjseqnt can be estimated as follows.
\mjsdeqnv=K_i-\fracp\sigma
\mjsdeqnp = \sigma(K_i-v)
\mjsdeqnm = 10^\left[ \left( K_E - C_Ht - C_Qt^2 -\log \left( \fracpK_i-v \right) \right) \bigg/ C_W \right]
\mjsdeqnt = \frac-C_H \pm \sqrtC_H^2-4C_Q\left ( C_W\logm-K_E+ \log\left ( \fracpK_i-v \right ) \right )2C_Q
The value of the species-specific seed viability constants can be specified
either directly in the arguement 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
For FinalViability, the final viability (%).
For StorageMC, the storage moisture content (%).
For StorageTemp, the storage temperature (°C).
For StoragePeriod, the duration of storage (according to argument
years).
Note
For initial and/or final viability percentage values of 0% and 100%,
adjust it according to sample size using the
PercentAdjust function to
avoid infinity or extreme values in output.
References
\insertAllCitedSee Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 | # 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)
## Not run:
# Error if initial viability is beyond limits (0-100 %)
FinalViability(initial = 110, period = 365, vcindex = 87, mc = 10, temp = 5)
## End(Not run)
# 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)
## Not run:
# 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)
## End(Not run)
# 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)
## Not run:
# 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)
## End(Not run)
# 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)
## Not run:
# 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)
## End(Not run)
# 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)
|
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