This function will allow you to reset multilocus lineages for your data set.
mll.reset(x, value)
x | |
---|---|
value | a character vector that specifies which levels you wish to be reset. |
an object of the same type as x
This method has no assignment method. If "original" is not contained in "value", it is assumed that the "original" definition will be used to reset the MLGs.
# This data set was a subset of a larger data set, so the multilocus # genotypes are not all sequential data(Pinf) mll(Pinf) <- "original" mll(Pinf)#> [1] 17 24 17 17 54 22 14 19 1 84 83 69 79 74 75 75 13 38 4 #> [20] 5 53 37 30 51 56 39 45 59 62 80 42 61 41 33 110 58 50 46 #> [39] 98 57 95 77 52 93 99 94 21 96 97 97 97 97 34 34 34 6 104 #> [58] 109 115 105 40 55 116 117 8 47 7 15 25 11 10 47 23 12 36 36 #> [77] 35 36 72 71 63 68 63 63 12 106# If we use mll.reset, then it will become sequential Pinf.new <- mll.reset(Pinf, TRUE) # reset all mll(Pinf.new)#> [1] 13 18 13 13 38 16 11 14 1 57 56 48 54 51 52 52 10 26 2 3 37 25 20 35 40 #> [26] 27 31 43 45 55 30 44 29 21 69 42 34 32 63 41 60 53 36 58 64 59 15 61 62 62 #> [51] 62 62 22 22 22 4 65 68 70 66 28 39 71 72 6 33 5 12 19 8 7 33 17 9 24 #> [76] 24 23 24 50 49 46 47 46 46 9 67# \dontrun{ # It is possible to reset only specific mll definitions. For example, let's # say that we wanted to filter our multilocus genotypes by nei's distance mlg.filter(Pinf, dist = nei.dist, missing = "mean") <- 0.02 # And we wanted to set those as custom genotypes, mll.custom(Pinf) <- mll(Pinf, "contracted") mll.levels(Pinf) <- .genlab("MLG", nmll(Pinf, "custom")) # We could reset just the original and the filtered if we wanted to and keep # the custom as it were. Pinf.new <- mll.reset(Pinf, c("original", "contracted")) mll(Pinf.new, "original")#> [1] 13 18 13 13 38 16 11 14 1 57 56 48 54 51 52 52 10 26 2 3 37 25 20 35 40 #> [26] 27 31 43 45 55 30 44 29 21 69 42 34 32 63 41 60 53 36 58 64 59 15 61 62 62 #> [51] 62 62 22 22 22 4 65 68 70 66 28 39 71 72 6 33 5 12 19 8 7 33 17 9 24 #> [76] 24 23 24 50 49 46 47 46 46 9 67#> [1] 13 18 13 13 38 16 11 14 1 57 56 48 54 51 52 52 10 26 2 3 37 25 20 35 40 #> [26] 27 31 43 45 55 30 44 29 21 69 42 34 32 63 41 60 53 36 58 64 59 15 61 62 62 #> [51] 62 62 22 22 22 4 65 68 70 66 28 39 71 72 6 33 5 12 19 8 7 33 17 9 24 #> [76] 24 23 24 50 49 46 47 46 46 9 67#> [1] MLG11 MLG10 MLG11 MLG11 MLG33 MLG13 MLG10 MLG11 MLG01 MLG52 MLG51 MLG43 #> [13] MLG49 MLG46 MLG47 MLG47 MLG09 MLG21 MLG02 MLG03 MLG32 MLG20 MLG15 MLG30 #> [25] MLG35 MLG22 MLG26 MLG38 MLG40 MLG50 MLG25 MLG39 MLG24 MLG16 MLG63 MLG37 #> [37] MLG29 MLG27 MLG57 MLG36 MLG55 MLG48 MLG31 MLG53 MLG58 MLG54 MLG12 MLG56 #> [49] MLG56 MLG56 MLG56 MLG56 MLG17 MLG17 MLG17 MLG04 MLG59 MLG62 MLG64 MLG60 #> [61] MLG23 MLG34 MLG65 MLG66 MLG19 MLG28 MLG05 MLG10 MLG14 MLG07 MLG06 MLG28 #> [73] MLG13 MLG08 MLG19 MLG19 MLG18 MLG19 MLG45 MLG44 MLG41 MLG42 MLG41 MLG41 #> [85] MLG08 MLG61 #> 66 Levels: MLG01 MLG02 MLG03 MLG04 MLG05 MLG06 MLG07 MLG08 MLG09 ... MLG66# If "original" is not one of the values, then that is used as a baseline. Pinf.orig <- mll.reset(Pinf, "contracted") mll(Pinf.orig, "contracted")#> [1] 17 24 17 17 54 22 14 19 1 84 83 69 79 74 75 75 13 38 4 #> [20] 5 53 37 30 51 56 39 45 59 62 80 42 61 41 33 110 58 50 46 #> [39] 98 57 95 77 52 93 99 94 21 96 97 97 97 97 34 34 34 6 104 #> [58] 109 115 105 40 55 116 117 8 47 7 15 25 11 10 47 23 12 36 36 #> [77] 35 36 72 71 63 68 63 63 12 106#> [1] 13 18 13 13 38 16 11 14 1 57 56 48 54 51 52 52 10 26 2 3 37 25 20 35 40 #> [26] 27 31 43 45 55 30 44 29 21 69 42 34 32 63 41 60 53 36 58 64 59 15 61 62 62 #> [51] 62 62 22 22 22 4 65 68 70 66 28 39 71 72 6 33 5 12 19 8 7 33 17 9 24 #> [76] 24 23 24 50 49 46 47 46 46 9 67# }