To set the work directory.
To import the data.
Toluca3regionsLC <- read.genalex("Toluca3regionsLC_farthest_Migrate.csv", ploidy = 3, geo = FALSE, region = FALSE)
First, let’s analyze the full lineage-corrected data set of Toluca population in Mexico.
To check the basic information about the whole Toluca population.
Toluca3regionsLC
##
## This is a genclone object
## -------------------------
## Genotype information:
##
## 25 original multilocus genotypes
## 25 triploid individuals
## 12 codominant loci
##
## Population information:
##
## 1 stratum - Pop
## 3 populations defined - Potato_Rural Potato_Valley S. demissum_Wild
setPop(Toluca3regionsLC)<- ~ Pop
popNames(Toluca3regionsLC)
## [1] "Potato_Valley" "Potato_Rural" "S. demissum_Wild"
poppr(Toluca3regionsLC)
## | Potato_Valley
## | Potato_Rural
## | S. demissum_Wild
## | Total
## Pop N MLG eMLG SE H G lambda E.5 Hexp Ia rbarD
## 1 Potato_Valley 11 11 10 0 2.40 11 0.909 1 0.497 -0.111 -0.0105
## 2 Potato_Rural 9 9 9 0 2.20 9 0.889 1 0.561 1.055 0.1028
## 3 S. demissum_Wild 5 5 5 0 1.61 5 0.800 1 0.458 -0.623 -0.0714
## 4 Total 25 25 10 0 3.22 25 0.960 1 0.521 0.295 0.0279
## File
## 1 Toluca3regionsLC
## 2 Toluca3regionsLC
## 3 Toluca3regionsLC
## 4 Toluca3regionsLC
To analyze the index of association (Ia) and standardized index of association (rbarD) and to report P-values based on 10001 permutations of data.
RBARDToluca3regionsLCALL <- ia(Toluca3regionsLC, hist = FALSE, sample = 10001)
RBARDToluca3regionsLCALL
## Ia p.Ia rbarD p.rD
## 0.29502375 0.02119576 0.02787128 0.02029594
To report the test results for Hardy-Weinberg equilibrium.
# Because no Monte Carlo test available for polyploids, the number of replicates for the Monte Carlo procedure (B) is zero. Thus, exact test based on Monte Carlo permutations of alleles is not performed.
Toluca3regionsLCALLHW <- hw.test(Toluca3regionsLC, B = 0)
Toluca3regionsLCALLHW
## chi^2 df Pr(chi^2 >)
## D13 673.08106 952 1.000000e+00
## G11 318.45239 442 9.999979e-01
## Pi04 126.56250 16 0.000000e+00
## Pi4B 72.97442 50 1.867382e-02
## Pi63 40.66125 16 6.228985e-04
## Pi70 45.40609 7 1.140494e-07
## SSR11 42.99100 16 2.803236e-04
## SSR2 59.18006 16 7.189302e-07
## SSR3 42.10484 77 9.995924e-01
## SSR4 161.79412 77 5.619148e-08
## SSR6 33.96044 112 1.000000e+00
## SSR8 35.24058 30 2.339918e-01
To list a table showing the results for Hardy-Weinberg equilibrium.
kable(Toluca3regionsLCALLHW, digits = 4)
chi^2 | df | Pr(chi^2 >) | |
---|---|---|---|
D13 | 673.0811 | 952 | 1.0000 |
G11 | 318.4524 | 442 | 1.0000 |
Pi04 | 126.5625 | 16 | 0.0000 |
Pi4B | 72.9744 | 50 | 0.0187 |
Pi63 | 40.6613 | 16 | 0.0006 |
Pi70 | 45.4061 | 7 | 0.0000 |
SSR11 | 42.9910 | 16 | 0.0003 |
SSR2 | 59.1801 | 16 | 0.0000 |
SSR3 | 42.1048 | 77 | 0.9996 |
SSR4 | 161.7941 | 77 | 0.0000 |
SSR6 | 33.9604 | 112 | 1.0000 |
SSR8 | 35.2406 | 30 | 0.2340 |
Next, to split the full data set according to “Host”.
splitStrata(Toluca3regionsLC) <- ~Host/Region
Toluca3regionsLC
##
## This is a genclone object
## -------------------------
## Genotype information:
##
## 25 original multilocus genotypes
## 25 triploid individuals
## 12 codominant loci
##
## Population information:
##
## 2 strata - Host Region
## 3 populations defined - Potato_Valley Potato_Rural S. demissum_Wild
setPop(Toluca3regionsLC) <- ~Host
To check the basic information.
Toluca3regionsLC
##
## This is a genclone object
## -------------------------
## Genotype information:
##
## 25 original multilocus genotypes
## 25 triploid individuals
## 12 codominant loci
##
## Population information:
##
## 2 strata - Host Region
## 2 populations defined - Potato S. demissum
To produce a basic summary table.
poppr(Toluca3regionsLC)
## | Potato
## | S. demissum
## | Total
## Pop N MLG eMLG SE H G lambda E.5 Hexp Ia rbarD
## 1 Potato 20 20 10 0 3.00 20 0.95 1 0.530 0.454 0.0428
## 2 S. demissum 5 5 5 0 1.61 5 0.80 1 0.458 -0.623 -0.0714
## 3 Total 25 25 10 0 3.22 25 0.96 1 0.521 0.295 0.0279
## File
## 1 Toluca3regionsLC
## 2 Toluca3regionsLC
## 3 Toluca3regionsLC
To analyze the index of association (Ia) and standardized index of association (rbarD) and to report P-values based on 10001 permutations of data.
RBARDToluca3regionsLCALLbyHostsep <- (lapply(seppop(Toluca3regionsLC), ia, index="rbarD", hist = FALSE, sample = 10001))
RBARDToluca3regionsLCALLbyHostsep
## $Potato
## Ia p.Ia rbarD p.rD
## 0.45411139 0.00529894 0.04276048 0.00519896
##
## $`S. demissum`
## Ia p.Ia rbarD p.rD
## -0.62321792 0.93621276 -0.07143753 0.97520496
To list a table showing the RBARD results.
kable(RBARDToluca3regionsLCALLbyHostsep, digits = 4)
|
|
To report the test results of Hardy-Weinberg equilibrium of lineage-corrected populations split by host.
PinfToluca3regionsLCALLbyHostHW <-(lapply(seppop(Toluca3regionsLC), hw.test, B = 0))
PinfToluca3regionsLCALLbyHostHW
## $Potato
## chi^2 df Pr(chi^2 >)
## D13 486.25074 665 1.000000e+00
## G11 287.95068 352 9.946547e-01
## Pi04 106.02493 16 2.553513e-15
## Pi4B 60.86983 50 1.395136e-01
## Pi63 31.61420 16 1.122080e-02
## Pi70 29.44490 7 1.200037e-04
## SSR11 38.47954 16 1.292289e-03
## SSR2 62.11141 16 2.298335e-07
## SSR3 32.61834 30 3.393420e-01
## SSR4 138.01302 77 2.444370e-05
## SSR6 26.40138 77 1.000000e+00
## SSR8 29.85664 30 4.730137e-01
##
## $`S. demissum`
## chi^2 df Pr(chi^2 >)
## D13 47.000000 77 0.99723767
## G11 21.550000 50 0.99985359
## Pi04 21.550000 16 0.15832473
## Pi4B 6.388889 7 0.49514361
## Pi63 6.250000 2 0.04393693
## Pi70 17.500000 7 0.01444155
## SSR11 8.316327 7 0.30552862
## SSR2 6.388889 7 0.49514361
## SSR3 21.550000 30 0.86990587
## SSR4 6.388889 7 0.49514361
## SSR6 8.316327 30 0.99996917
## SSR8 6.562500 7 0.47580578
To list a table showing the results of Hardy-Weinberg equilibrium.
kable(PinfToluca3regionsLCALLbyHostHW, digits = 4)
|
|
Finally, to split the full data set according to “Host” and “Region”.
setPop(Toluca3regionsLC) <- ~Host/Region
To check the basic information.
Toluca3regionsLC
##
## This is a genclone object
## -------------------------
## Genotype information:
##
## 25 original multilocus genotypes
## 25 triploid individuals
## 12 codominant loci
##
## Population information:
##
## 2 strata - Host Region
## 3 populations defined - Potato_Valley Potato_Rural S. demissum_Wild
To produce a basic summary table.
poppr(Toluca3regionsLC)
## | Potato_Valley
## | Potato_Rural
## | S. demissum_Wild
## | Total
## Pop N MLG eMLG SE H G lambda E.5 Hexp Ia rbarD
## 1 Potato_Valley 11 11 10 0 2.40 11 0.909 1 0.497 -0.111 -0.0105
## 2 Potato_Rural 9 9 9 0 2.20 9 0.889 1 0.561 1.055 0.1028
## 3 S. demissum_Wild 5 5 5 0 1.61 5 0.800 1 0.458 -0.623 -0.0714
## 4 Total 25 25 10 0 3.22 25 0.960 1 0.521 0.295 0.0279
## File
## 1 Toluca3regionsLC
## 2 Toluca3regionsLC
## 3 Toluca3regionsLC
## 4 Toluca3regionsLC
To analyze the index of association (Ia) and standardized index of association (rbarD) and to report P-values based on 10001 permutations of data.
RBARDToluca3regionsLCALLbyRegionsep <- (lapply(seppop(Toluca3regionsLC), ia, index="rbarD", hist = FALSE, sample = 10001))
RBARDToluca3regionsLCALLbyRegionsep
## $Potato_Valley
## Ia p.Ia rbarD p.rD
## -0.11055339 0.65346931 -0.01048736 0.65666867
##
## $Potato_Rural
## Ia p.Ia rbarD p.rD
## 1.05458290 0.00119976 0.10275762 0.00099980
##
## $`S. demissum_Wild`
## Ia p.Ia rbarD p.rD
## -0.62321792 0.94051190 -0.07143753 0.97710458
To list a table showing the RBARD results.
kable(RBARDToluca3regionsLCALLbyRegionsep, digits = 4)
|
|
|
To report the test results of Hardy-Weinberg equilibrium of lineage-corrected populations split by “Host” and “Region”.
setPop(Toluca3regionsLC) <- ~Host/Region
PinfToluca3regionsLCALLbyRegionHW <-(lapply(seppop(Toluca3regionsLC), hw.test, B = 0))
PinfToluca3regionsLCALLbyRegionHW
## $Potato_Valley
## chi^2 df Pr(chi^2 >)
## D13 130.00000 156 9.363000e-01
## G11 83.83291 156 9.999996e-01
## Pi04 30.93750 7 6.384591e-05
## Pi4B 25.63000 30 6.938750e-01
## Pi63 17.49306 7 1.447909e-02
## Pi70 23.08172 7 1.649636e-03
## SSR11 21.83163 7 2.715837e-03
## SSR2 38.50000 7 2.434056e-06
## SSR3 15.26531 16 5.052996e-01
## SSR4 24.64000 30 7.423313e-01
## SSR6 14.36704 30 9.928561e-01
## SSR8 22.47980 16 1.283640e-01
##
## $Potato_Rural
## chi^2 df Pr(chi^2 >)
## D13 214.23500 275 9.972989e-01
## G11 62.86388 112 9.999512e-01
## Pi04 51.75000 16 1.201958e-05
## Pi4B 59.04000 50 1.786791e-01
## Pi63 14.27552 16 5.781966e-01
## Pi70 11.56641 7 1.157500e-01
## SSR11 18.00000 16 3.238970e-01
## SSR2 32.62111 16 8.292627e-03
## SSR3 18.90000 16 2.738830e-01
## SSR4 99.84375 77 4.115019e-02
## SSR6 12.06000 16 7.398392e-01
## SSR8 25.66406 30 6.921620e-01
##
## $`S. demissum_Wild`
## chi^2 df Pr(chi^2 >)
## D13 47.000000 77 0.99723767
## G11 21.550000 50 0.99985359
## Pi04 21.550000 16 0.15832473
## Pi4B 6.388889 7 0.49514361
## Pi63 6.250000 2 0.04393693
## Pi70 17.500000 7 0.01444155
## SSR11 8.316327 7 0.30552862
## SSR2 6.388889 7 0.49514361
## SSR3 21.550000 30 0.86990587
## SSR4 6.388889 7 0.49514361
## SSR6 8.316327 30 0.99996917
## SSR8 6.562500 7 0.47580578
To list a table showing the results of Hardy-Weinberg Equilibrium.
kable(PinfToluca3regionsLCALLbyRegionHW, digits = 4)
|
|
|
Please note that the values based on permutations could be different slightly among repeated runs.
Session information
sessionInfo()
## R version 3.3.1 (2016-06-21)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.11.6 (El Capitan)
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] knitr_1.14 pegas_0.9 ape_3.5 igraph_1.0.1
## [5] poppr_2.2.1 adegenet_2.0.1 ade4_1.7-4
##
## loaded via a namespace (and not attached):
## [1] phangorn_2.0.4 gtools_3.5.0 reshape2_1.4.2 splines_3.3.1
## [5] lattice_0.20-34 colorspace_1.2-7 htmltools_0.3.5 yaml_2.1.13
## [9] mgcv_1.8-15 DBI_0.5-1 sp_1.2-3 plyr_1.8.4
## [13] stringr_1.1.0 munsell_0.4.3 gtable_0.2.0 codetools_0.2-15
## [17] coda_0.18-1 evaluate_0.10 permute_0.9-4 httpuv_1.3.3
## [21] parallel_3.3.1 spdep_0.6-8 highr_0.6 Rcpp_0.12.7
## [25] xtable_1.8-2 scales_0.4.0 backports_1.0.4 formatR_1.4
## [29] gdata_2.17.0 vegan_2.4-1 mime_0.5 deldir_0.1-12
## [33] fastmatch_1.0-4 ggplot2_2.1.0 digest_0.6.10 stringi_1.1.2
## [37] gmodels_2.16.2 dplyr_0.5.0 shiny_0.14.2 grid_3.3.1
## [41] rprojroot_1.1 quadprog_1.5-5 tools_3.3.1 LearnBayes_2.15
## [45] magrittr_1.5 tibble_1.2 cluster_2.0.5 seqinr_3.3-3
## [49] MASS_7.3-45 Matrix_1.2-7.1 nnls_1.4 assertthat_0.1
## [53] rmarkdown_1.2 R6_2.2.0 boot_1.3-18 nlme_3.1-128