The following is a set of arguments for use in rraf, pgen, and psex to correct rare allele frequencies that were lost in estimating round-robin allele frequencies.

## Arguments

e

a numeric epsilon value to use for all missing allele frequencies.

d

the unit by which to take the reciprocal. div = "sample" will be 1/(n samples), d = "mlg" will be 1/(n mlg), and d = "rrmlg" will be 1/(n mlg at that locus). This is overridden by e.

mul

a multiplier for div. Default is mul = 1. This parameter is overridden by e

sum_to_one

when TRUE, the original frequencies will be reduced so that all allele frequencies will sum to one. Default: FALSE

## Details

By default (d = "sample", e = NULL, sum_to_one = FALSE, mul = 1), this will add 1/(n samples) to all zero-value alleles. The basic formula is 1/(d * m) unless e is specified. If sum_to_one = TRUE, then the frequencies will be scaled as x/sum(x) AFTER correction, indicating that the allele frequencies will be reduced. See the examples for details. The general pattern of correction is that the value of the MAF will be rrmlg > mlg > sample

## Motivation

When calculating allele frequencies from a round-robin approach, rare alleles are often lost resulting in zero-valued allele frequencies (Arnaud-Haond et al. 2007, Parks and Werth 1993). This can be problematic when calculating values for pgen and psex because frequencies of zero will result in undefined values for samples that contain those rare alleles. The solution to this problem is to give an estimate for the frequency of those rare alleles, but the question of HOW to do that arises. These arguments provide a way to define how rare alleles are to be estimated/corrected.

## Using these arguments

These arguments are for use in the functions rraf, pgen, and psex. They will replace the dots (...) that appear at the end of the function call. For example, if you want to set the minor allele frequencies to a specific value (let's say 0.001), regardless of locus, you can insert e = 0.001 along with any other arguments (note, position is not specific):


pgen(my_data, e = 0.001, log = FALSE)
psex(my_data, method = "multiple", e = 0.001)

## References

Arnaud-Haond, S., Duarte, C. M., Alberto, F., & Serrão, E. A. 2007. Standardizing methods to address clonality in population studies. Molecular Ecology, 16(24), 5115-5139.

Parks, J. C., & Werth, C. R. 1993. A study of spatial features of clones in a population of bracken fern, Pteridium aquilinum (Dennstaedtiaceae). American Journal of Botany, 537-544.

rraf, pgen, psex, rrmlg

Zhian N. Kamvar

## Examples

# \dontrun{

data(Pram)
#-------------------------------------

# If you set correction = FALSE, you'll notice the zero-valued alleles

rraf(Pram, correction = FALSE)
#> $PrMS6A1 #> PrMS6A1.165 PrMS6A1.168 #> 0.5360825 0.4639175 #> #>$Pr9C3A1
#> Pr9C3A1.216 Pr9C3A1.226
#>   0.5357143   0.4642857
#>
#> $PrMS39A1 #> PrMS39A1.130 PrMS39A1.213 PrMS39A1.214 PrMS39A1.242 PrMS39A1.246 PrMS39A1.250 #> 0.500000000 0.000000000 0.007575758 0.000000000 0.121212121 0.363636364 #> PrMS39A1.254 #> 0.007575758 #> #>$PrMS45A1
#> PrMS45A1.154 PrMS45A1.166 PrMS45A1.186
#>    0.0000000    0.5057471    0.4942529
#>
#> $PrMS43A1 #> PrMS43A1.213 PrMS43A1.281 PrMS43A1.285 PrMS43A1.345 PrMS43A1.349 PrMS43A1.357 #> 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 #> PrMS43A1.360 PrMS43A1.364 PrMS43A1.368 PrMS43A1.372 PrMS43A1.376 PrMS43A1.380 #> 0.00000000 0.00000000 0.07692308 0.11538462 0.15384615 0.03846154 #> PrMS43A1.384 PrMS43A1.388 PrMS43A1.465 PrMS43A1.469 PrMS43A1.473 PrMS43A1.477 #> 0.11538462 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 #> PrMS43A1.481 PrMS43A1.485 PrMS43A1.489 PrMS43A1.493 PrMS43A1.497 PrMS43A1.505 #> 0.07692308 0.38461538 0.03846154 0.00000000 0.00000000 0.00000000 #> # By default, however, the data will be corrected by 1/n rraf(Pram) #>$PrMS6A1
#> PrMS6A1.165 PrMS6A1.168
#>   0.5360825   0.4639175
#>
#> $Pr9C3A1 #> Pr9C3A1.216 Pr9C3A1.226 #> 0.5357143 0.4642857 #> #>$PrMS39A1
#> PrMS39A1.130 PrMS39A1.213 PrMS39A1.214 PrMS39A1.242 PrMS39A1.246 PrMS39A1.250
#>  0.500000000  0.001371742  0.007575758  0.001371742  0.121212121  0.363636364
#> PrMS39A1.254
#>  0.007575758
#>
#> $PrMS45A1 #> PrMS45A1.154 PrMS45A1.166 PrMS45A1.186 #> 0.001371742 0.505747126 0.494252874 #> #>$PrMS43A1
#> PrMS43A1.213 PrMS43A1.281 PrMS43A1.285 PrMS43A1.345 PrMS43A1.349 PrMS43A1.357
#>  0.001371742  0.001371742  0.001371742  0.001371742  0.001371742  0.001371742
#> PrMS43A1.360 PrMS43A1.364 PrMS43A1.368 PrMS43A1.372 PrMS43A1.376 PrMS43A1.380
#>  0.001371742  0.001371742  0.076923077  0.115384615  0.153846154  0.038461538
#> PrMS43A1.384 PrMS43A1.388 PrMS43A1.465 PrMS43A1.469 PrMS43A1.473 PrMS43A1.477
#>  0.115384615  0.001371742  0.001371742  0.001371742  0.001371742  0.001371742
#> PrMS43A1.481 PrMS43A1.485 PrMS43A1.489 PrMS43A1.493 PrMS43A1.497 PrMS43A1.505
#>  0.076923077  0.384615385  0.038461538  0.001371742  0.001371742  0.001371742
#>

# Of course, this is a diploid organism, we might want to set 1/2n

rraf(Pram, mul = 1/2)
#> $PrMS6A1 #> PrMS6A1.165 PrMS6A1.168 #> 0.5360825 0.4639175 #> #>$Pr9C3A1
#> Pr9C3A1.216 Pr9C3A1.226
#>   0.5357143   0.4642857
#>
#> $PrMS39A1 #> PrMS39A1.130 PrMS39A1.213 PrMS39A1.214 PrMS39A1.242 PrMS39A1.246 PrMS39A1.250 #> 0.5000000000 0.0006858711 0.0075757576 0.0006858711 0.1212121212 0.3636363636 #> PrMS39A1.254 #> 0.0075757576 #> #>$PrMS45A1
#> PrMS45A1.154 PrMS45A1.166 PrMS45A1.186
#> 0.0006858711 0.5057471264 0.4942528736
#>
#> $PrMS43A1 #> PrMS43A1.213 PrMS43A1.281 PrMS43A1.285 PrMS43A1.345 PrMS43A1.349 PrMS43A1.357 #> 0.0006858711 0.0006858711 0.0006858711 0.0006858711 0.0006858711 0.0006858711 #> PrMS43A1.360 PrMS43A1.364 PrMS43A1.368 PrMS43A1.372 PrMS43A1.376 PrMS43A1.380 #> 0.0006858711 0.0006858711 0.0769230769 0.1153846154 0.1538461538 0.0384615385 #> PrMS43A1.384 PrMS43A1.388 PrMS43A1.465 PrMS43A1.469 PrMS43A1.473 PrMS43A1.477 #> 0.1153846154 0.0006858711 0.0006858711 0.0006858711 0.0006858711 0.0006858711 #> PrMS43A1.481 PrMS43A1.485 PrMS43A1.489 PrMS43A1.493 PrMS43A1.497 PrMS43A1.505 #> 0.0769230769 0.3846153846 0.0384615385 0.0006858711 0.0006858711 0.0006858711 #> # To set MAF = 1/2mlg rraf(Pram, d = "mlg", mul = 1/2) #>$PrMS6A1
#> PrMS6A1.165 PrMS6A1.168
#>   0.5360825   0.4639175
#>
#> $Pr9C3A1 #> Pr9C3A1.216 Pr9C3A1.226 #> 0.5357143 0.4642857 #> #>$PrMS39A1
#> PrMS39A1.130 PrMS39A1.213 PrMS39A1.214 PrMS39A1.242 PrMS39A1.246 PrMS39A1.250
#>  0.500000000  0.005102041  0.007575758  0.005102041  0.121212121  0.363636364
#> PrMS39A1.254
#>  0.007575758
#>
#> $PrMS45A1 #> PrMS45A1.154 PrMS45A1.166 PrMS45A1.186 #> 0.005102041 0.505747126 0.494252874 #> #>$PrMS43A1
#> PrMS43A1.213 PrMS43A1.281 PrMS43A1.285 PrMS43A1.345 PrMS43A1.349 PrMS43A1.357
#>  0.005102041  0.005102041  0.005102041  0.005102041  0.005102041  0.005102041
#> PrMS43A1.360 PrMS43A1.364 PrMS43A1.368 PrMS43A1.372 PrMS43A1.376 PrMS43A1.380
#>  0.005102041  0.005102041  0.076923077  0.115384615  0.153846154  0.038461538
#> PrMS43A1.384 PrMS43A1.388 PrMS43A1.465 PrMS43A1.469 PrMS43A1.473 PrMS43A1.477
#>  0.115384615  0.005102041  0.005102041  0.005102041  0.005102041  0.005102041
#> PrMS43A1.481 PrMS43A1.485 PrMS43A1.489 PrMS43A1.493 PrMS43A1.497 PrMS43A1.505
#>  0.076923077  0.384615385  0.038461538  0.005102041  0.005102041  0.005102041
#>

# derived at each locus with different sample sizes, it's only appropriate to
# correct based on those sample sizes.

rraf(Pram, d = "rrmlg", mul = 1/2)
#> $PrMS6A1 #> PrMS6A1.165 PrMS6A1.168 #> 0.5360825 0.4639175 #> #>$Pr9C3A1
#> Pr9C3A1.216 Pr9C3A1.226
#>   0.5357143   0.4642857
#>
#> $PrMS39A1 #> PrMS39A1.130 PrMS39A1.213 PrMS39A1.214 PrMS39A1.242 PrMS39A1.246 PrMS39A1.250 #> 0.500000000 0.007575758 0.007575758 0.007575758 0.121212121 0.363636364 #> PrMS39A1.254 #> 0.007575758 #> #>$PrMS45A1
#> PrMS45A1.154 PrMS45A1.166 PrMS45A1.186
#>  0.005747126  0.505747126  0.494252874
#>
#> $PrMS43A1 #> PrMS43A1.213 PrMS43A1.281 PrMS43A1.285 PrMS43A1.345 PrMS43A1.349 PrMS43A1.357 #> 0.03846154 0.03846154 0.03846154 0.03846154 0.03846154 0.03846154 #> PrMS43A1.360 PrMS43A1.364 PrMS43A1.368 PrMS43A1.372 PrMS43A1.376 PrMS43A1.380 #> 0.03846154 0.03846154 0.07692308 0.11538462 0.15384615 0.03846154 #> PrMS43A1.384 PrMS43A1.388 PrMS43A1.465 PrMS43A1.469 PrMS43A1.473 PrMS43A1.477 #> 0.11538462 0.03846154 0.03846154 0.03846154 0.03846154 0.03846154 #> PrMS43A1.481 PrMS43A1.485 PrMS43A1.489 PrMS43A1.493 PrMS43A1.497 PrMS43A1.505 #> 0.07692308 0.38461538 0.03846154 0.03846154 0.03846154 0.03846154 #> # If we were going to use these frequencies for simulations, we might want to # ensure that they all sum to one. rraf(Pram, d = "mlg", mul = 1/2, sum_to_one = TRUE) #>$PrMS6A1
#> PrMS6A1.165 PrMS6A1.168
#>   0.5360825   0.4639175
#>
#> $Pr9C3A1 #> Pr9C3A1.216 Pr9C3A1.226 #> 0.5357143 0.4642857 #> #>$PrMS39A1
#> PrMS39A1.130 PrMS39A1.213 PrMS39A1.214 PrMS39A1.242 PrMS39A1.246 PrMS39A1.250
#>  0.494949495  0.005050505  0.007499235  0.005050505  0.119987756  0.359963269
#> PrMS39A1.254
#>  0.007499235
#>
#> $PrMS45A1 #> PrMS45A1.154 PrMS45A1.166 PrMS45A1.186 #> 0.005076142 0.503179882 0.491743976 #> #>$PrMS43A1
#> PrMS43A1.213 PrMS43A1.281 PrMS43A1.285 PrMS43A1.345 PrMS43A1.349 PrMS43A1.357
#>  0.004716981  0.004716981  0.004716981  0.004716981  0.004716981  0.004716981
#> PrMS43A1.360 PrMS43A1.364 PrMS43A1.368 PrMS43A1.372 PrMS43A1.376 PrMS43A1.380
#>  0.004716981  0.004716981  0.071117562  0.106676343  0.142235123  0.035558781
#> PrMS43A1.384 PrMS43A1.388 PrMS43A1.465 PrMS43A1.469 PrMS43A1.473 PrMS43A1.477
#>  0.106676343  0.004716981  0.004716981  0.004716981  0.004716981  0.004716981
#> PrMS43A1.481 PrMS43A1.485 PrMS43A1.489 PrMS43A1.493 PrMS43A1.497 PrMS43A1.505
#>  0.071117562  0.355587808  0.035558781  0.004716981  0.004716981  0.004716981
#>

#-------------------------------------
# When we calculate these frequencies based on population, they are heavily
# influenced by the number of observed mlgs.

rraf(Pram, by_pop = TRUE, d = "rrmlg", mul = 1/2)
#>               PrMS6A1.165 PrMS6A1.168 Pr9C3A1.216 Pr9C3A1.226 PrMS39A1.130
#> Nursery_CA      0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> Nursery_OR      0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> JHallCr_OR      0.6166667   0.3833333   0.6166667   0.3833333          0.5
#> NFChetHigh_OR   0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> Coast_OR        0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> HunterCr_OR     0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> Winchuck_OR     0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> ChetcoMain_OR   0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> PistolRSF_OR    0.5000000   0.5000000   0.5000000   0.5000000          0.5
#>               PrMS39A1.213 PrMS39A1.214 PrMS39A1.242 PrMS39A1.246 PrMS39A1.250
#> Nursery_CA      0.02500000   0.02500000   0.02500000   0.35000000   0.15000000
#> Nursery_OR      0.03571429   0.03571429   0.03571429   0.07142857   0.35714286
#> JHallCr_OR      0.01923077   0.01923077   0.01923077   0.01923077   0.48076923
#> NFChetHigh_OR   0.02000000   0.02000000   0.02000000   0.04000000   0.42000000
#> Coast_OR        0.04545455   0.04545455   0.04545455   0.40909091   0.09090909
#> HunterCr_OR     0.16666667   0.16666667   0.16666667   0.33333333   0.16666667
#> Winchuck_OR     0.06250000   0.06250000   0.06250000   0.06250000   0.50000000
#> ChetcoMain_OR   0.10000000   0.10000000   0.10000000   0.20000000   0.20000000
#> PistolRSF_OR    0.25000000   0.25000000   0.25000000   0.25000000   0.50000000
#>               PrMS39A1.254 PrMS45A1.154 PrMS45A1.166 PrMS45A1.186 PrMS43A1.213
#> Nursery_CA      0.02500000   0.01666667     0.500000     0.500000   0.16666667
#> Nursery_OR      0.03571429   0.02631579     0.500000     0.500000   0.12500000
#> JHallCr_OR      0.01923077   0.01851852     0.537037     0.462963   0.07142857
#> NFChetHigh_OR   0.02000000   0.01612903     0.500000     0.500000   0.05555556
#> Coast_OR        0.04545455   0.04166667     0.500000     0.500000   0.25000000
#> HunterCr_OR     0.16666667   0.12500000     0.500000     0.500000   0.25000000
#> Winchuck_OR     0.06250000   0.06250000     0.500000     0.500000   0.16666667
#> ChetcoMain_OR   0.10000000   0.07142857     0.500000     0.500000   0.16666667
#> PistolRSF_OR    0.25000000   0.25000000     0.500000     0.500000   0.50000000
#>               PrMS43A1.281 PrMS43A1.285 PrMS43A1.345 PrMS43A1.349 PrMS43A1.357
#> Nursery_CA      0.16666667   0.16666667   0.16666667   0.16666667   0.16666667
#> Nursery_OR      0.12500000   0.12500000   0.12500000   0.12500000   0.12500000
#> JHallCr_OR      0.07142857   0.07142857   0.07142857   0.07142857   0.07142857
#> NFChetHigh_OR   0.05555556   0.05555556   0.05555556   0.05555556   0.05555556
#> Coast_OR        0.25000000   0.25000000   0.25000000   0.25000000   0.25000000
#> HunterCr_OR     0.25000000   0.25000000   0.25000000   0.25000000   0.25000000
#> Winchuck_OR     0.16666667   0.16666667   0.16666667   0.16666667   0.16666667
#> ChetcoMain_OR   0.16666667   0.16666667   0.16666667   0.16666667   0.16666667
#> PistolRSF_OR    0.50000000   0.50000000   0.50000000   0.50000000   0.50000000
#>               PrMS43A1.360 PrMS43A1.364 PrMS43A1.368 PrMS43A1.372 PrMS43A1.376
#> Nursery_CA      0.16666667   0.16666667   0.16666667   0.33333333   0.16666667
#> Nursery_OR      0.12500000   0.12500000   0.12500000   0.25000000   0.12500000
#> JHallCr_OR      0.07142857   0.07142857   0.07142857   0.07142857   0.42857143
#> NFChetHigh_OR   0.05555556   0.05555556   0.11111111   0.05555556   0.05555556
#> Coast_OR        0.25000000   0.25000000   0.25000000   0.25000000   0.25000000
#> HunterCr_OR     0.25000000   0.25000000   0.50000000   0.25000000   0.25000000
#> Winchuck_OR     0.16666667   0.16666667   0.16666667   0.16666667   0.33333333
#> ChetcoMain_OR   0.16666667   0.16666667   0.16666667   0.16666667   0.50000000
#> PistolRSF_OR    0.50000000   0.50000000   0.50000000   0.50000000   0.50000000
#>               PrMS43A1.380 PrMS43A1.384 PrMS43A1.388 PrMS43A1.465 PrMS43A1.469
#> Nursery_CA      0.16666667   0.16666667   0.16666667   0.16666667   0.16666667
#> Nursery_OR      0.12500000   0.12500000   0.12500000   0.12500000   0.12500000
#> JHallCr_OR      0.07142857   0.07142857   0.07142857   0.07142857   0.07142857
#> NFChetHigh_OR   0.11111111   0.16666667   0.05555556   0.05555556   0.05555556
#> Coast_OR        0.25000000   0.25000000   0.25000000   0.25000000   0.25000000
#> HunterCr_OR     0.25000000   0.25000000   0.25000000   0.25000000   0.25000000
#> Winchuck_OR     0.16666667   0.16666667   0.16666667   0.16666667   0.16666667
#> ChetcoMain_OR   0.16666667   0.16666667   0.16666667   0.16666667   0.16666667
#> PistolRSF_OR    0.50000000   0.50000000   0.50000000   0.50000000   0.50000000
#>               PrMS43A1.473 PrMS43A1.477 PrMS43A1.481 PrMS43A1.485 PrMS43A1.489
#> Nursery_CA      0.16666667   0.16666667   0.16666667    0.3333333   0.16666667
#> Nursery_OR      0.12500000   0.12500000   0.12500000    0.3750000   0.12500000
#> JHallCr_OR      0.07142857   0.07142857   0.07142857    0.4285714   0.07142857
#> NFChetHigh_OR   0.05555556   0.05555556   0.16666667    0.2777778   0.05555556
#> Coast_OR        0.25000000   0.25000000   0.25000000    0.2500000   0.25000000
#> HunterCr_OR     0.25000000   0.25000000   0.25000000    0.2500000   0.25000000
#> Winchuck_OR     0.16666667   0.16666667   0.50000000    0.1666667   0.16666667
#> ChetcoMain_OR   0.16666667   0.16666667   0.16666667    0.1666667   0.16666667
#> PistolRSF_OR    0.50000000   0.50000000   0.50000000    0.5000000   0.50000000
#>               PrMS43A1.493 PrMS43A1.497 PrMS43A1.505
#> Nursery_CA      0.16666667   0.16666667   0.16666667
#> Nursery_OR      0.12500000   0.12500000   0.12500000
#> JHallCr_OR      0.07142857   0.07142857   0.07142857
#> NFChetHigh_OR   0.05555556   0.05555556   0.05555556
#> Coast_OR        0.25000000   0.25000000   0.25000000
#> HunterCr_OR     0.50000000   0.25000000   0.25000000
#> Winchuck_OR     0.16666667   0.16666667   0.16666667
#> ChetcoMain_OR   0.16666667   0.16666667   0.16666667
#> PistolRSF_OR    0.50000000   0.50000000   0.50000000

# This can be fixed by specifying a specific value

rraf(Pram, by_pop = TRUE, e = 0.01)
#>               PrMS6A1.165 PrMS6A1.168 Pr9C3A1.216 Pr9C3A1.226 PrMS39A1.130
#> Nursery_CA      0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> Nursery_OR      0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> JHallCr_OR      0.6166667   0.3833333   0.6166667   0.3833333          0.5
#> NFChetHigh_OR   0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> Coast_OR        0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> HunterCr_OR     0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> Winchuck_OR     0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> ChetcoMain_OR   0.5000000   0.5000000   0.5000000   0.5000000          0.5
#> PistolRSF_OR    0.5000000   0.5000000   0.5000000   0.5000000          0.5
#>               PrMS39A1.213 PrMS39A1.214 PrMS39A1.242 PrMS39A1.246 PrMS39A1.250
#> Nursery_CA            0.01         0.01   0.01000000   0.35000000   0.15000000
#> Nursery_OR            0.01         0.01   0.03571429   0.07142857   0.35714286
#> JHallCr_OR            0.01         0.01   0.01000000   0.01923077   0.48076923
#> NFChetHigh_OR         0.01         0.02   0.01000000   0.04000000   0.42000000
#> Coast_OR              0.01         0.01   0.01000000   0.40909091   0.09090909
#> HunterCr_OR           0.01         0.01   0.01000000   0.33333333   0.16666667
#> Winchuck_OR           0.01         0.01   0.01000000   0.01000000   0.50000000
#> ChetcoMain_OR         0.01         0.01   0.01000000   0.20000000   0.20000000
#> PistolRSF_OR          0.01         0.01   0.01000000   0.01000000   0.50000000
#>               PrMS39A1.254 PrMS45A1.154 PrMS45A1.166 PrMS45A1.186 PrMS43A1.213
#> Nursery_CA      0.01000000         0.01     0.500000     0.500000         0.01
#> Nursery_OR      0.03571429         0.01     0.500000     0.500000         0.01
#> JHallCr_OR      0.01000000         0.01     0.537037     0.462963         0.01
#> NFChetHigh_OR   0.02000000         0.01     0.500000     0.500000         0.01
#> Coast_OR        0.01000000         0.01     0.500000     0.500000         0.01
#> HunterCr_OR     0.01000000         0.01     0.500000     0.500000         0.01
#> Winchuck_OR     0.01000000         0.01     0.500000     0.500000         0.01
#> ChetcoMain_OR   0.10000000         0.01     0.500000     0.500000         0.01
#> PistolRSF_OR    0.01000000         0.01     0.500000     0.500000         0.01
#>               PrMS43A1.281 PrMS43A1.285 PrMS43A1.345 PrMS43A1.349 PrMS43A1.357
#> Nursery_CA            0.01         0.01         0.01         0.01         0.01
#> Nursery_OR            0.01         0.01         0.01         0.01         0.01
#> JHallCr_OR            0.01         0.01         0.01         0.01         0.01
#> NFChetHigh_OR         0.01         0.01         0.01         0.01         0.01
#> Coast_OR              0.01         0.01         0.01         0.01         0.01
#> HunterCr_OR           0.01         0.01         0.01         0.01         0.01
#> Winchuck_OR           0.01         0.01         0.01         0.01         0.01
#> ChetcoMain_OR         0.01         0.01         0.01         0.01         0.01
#> PistolRSF_OR          0.01         0.01         0.01         0.01         0.01
#>               PrMS43A1.360 PrMS43A1.364 PrMS43A1.368 PrMS43A1.372 PrMS43A1.376
#> Nursery_CA            0.01        0.010    0.1666667   0.33333333   0.01000000
#> Nursery_OR            0.01        0.125    0.1250000   0.25000000   0.01000000
#> JHallCr_OR            0.01        0.010    0.0100000   0.01000000   0.42857143
#> NFChetHigh_OR         0.01        0.010    0.1111111   0.05555556   0.05555556
#> Coast_OR              0.01        0.010    0.2500000   0.01000000   0.01000000
#> HunterCr_OR           0.01        0.010    0.5000000   0.01000000   0.01000000
#> Winchuck_OR           0.01        0.010    0.0100000   0.01000000   0.33333333
#> ChetcoMain_OR         0.01        0.010    0.0100000   0.01000000   0.50000000
#> PistolRSF_OR          0.01        0.010    0.0100000   0.01000000   0.50000000
#>               PrMS43A1.380 PrMS43A1.384 PrMS43A1.388 PrMS43A1.465 PrMS43A1.469
#> Nursery_CA       0.0100000   0.01000000         0.01         0.01         0.01
#> Nursery_OR       0.0100000   0.01000000         0.01         0.01         0.01
#> JHallCr_OR       0.0100000   0.07142857         0.01         0.01         0.01
#> NFChetHigh_OR    0.1111111   0.16666667         0.01         0.01         0.01
#> Coast_OR         0.0100000   0.25000000         0.01         0.01         0.01
#> HunterCr_OR      0.0100000   0.01000000         0.01         0.01         0.01
#> Winchuck_OR      0.1666667   0.01000000         0.01         0.01         0.01
#> ChetcoMain_OR    0.0100000   0.01000000         0.01         0.01         0.01
#> PistolRSF_OR     0.0100000   0.01000000         0.01         0.01         0.01
#>               PrMS43A1.473 PrMS43A1.477 PrMS43A1.481 PrMS43A1.485 PrMS43A1.489
#> Nursery_CA            0.01    0.0100000    0.0100000    0.3333333   0.16666667
#> Nursery_OR            0.01    0.0100000    0.0100000    0.3750000   0.12500000
#> JHallCr_OR            0.01    0.0100000    0.0100000    0.4285714   0.07142857
#> NFChetHigh_OR         0.01    0.0100000    0.1666667    0.2777778   0.05555556
#> Coast_OR              0.01    0.0100000    0.0100000    0.2500000   0.25000000
#> HunterCr_OR           0.01    0.0100000    0.0100000    0.0100000   0.01000000
#> Winchuck_OR           0.01    0.0100000    0.5000000    0.0100000   0.01000000
#> ChetcoMain_OR         0.01    0.1666667    0.1666667    0.1666667   0.01000000
#> PistolRSF_OR          0.01    0.0100000    0.0100000    0.5000000   0.01000000
#>               PrMS43A1.493 PrMS43A1.497 PrMS43A1.505
#> Nursery_CA            0.01         0.01         0.01
#> Nursery_OR            0.01         0.01         0.01
#> JHallCr_OR            0.01         0.01         0.01
#> NFChetHigh_OR         0.01         0.01         0.01
#> Coast_OR              0.01         0.01         0.01
#> HunterCr_OR           0.50         0.01         0.01
#> Winchuck_OR           0.01         0.01         0.01
#> ChetcoMain_OR         0.01         0.01         0.01
#> PistolRSF_OR          0.01         0.01         0.01

# }