model testing woodhouse’s western US, northern mex, Tex systematics
Devon DeRaad
12/16/2021
library(delimitR)
#force R to find compatible python installation
Sys.setenv(PATH = paste("/panfs/pfs.local/work/bi/bin/conda/bin/", Sys.getenv("PATH"), sep=":"))
#setwd
setwd("/home/d669d153/work/aph.rad/delimitr/all.wood.sec.contact")Set priors here:
#location of our observed sfs (cannot be full path, must be in wd, drop .obs file extension)
observedSFS <- 'all_MSFS'
#location of our traits file (2 column file which maps alleles to species, must be in wd)
traitsfile <- 'all.wood.traits.file.txt'
#guide tree
observedtree <- c('((0,1),2);','((0,2),1);','((1,2),0);')
#migration matrix (must be symmetrical)
migmatrix <- matrix(c(FALSE, TRUE, TRUE,
TRUE, FALSE, TRUE,
TRUE, TRUE, FALSE),
nrow = 3, ncol = 3, byrow = TRUE)
#test divergence with gene flow?
divwgeneflow <- FALSE
#test secondary contact?
seccontact <- TRUE
#what is the maximum number of migration events to consider on your guide tree?
maxedges <- 2
#how many species are in your guide tree?
obsspecies<- 3
#the number of "alleles" retained after downsampling SFS
obssamplesize <- c(28,10,24)
#The user must specify the number of linkage blocks to simulate
#For unlinked SNPs, this is equal to the number of SNPs used to build your observed SFS
obssnps <- 1278
#The user must also provide a prefix
#This will be used to name the fsc2 input files, as well as other output files
#This should be unique for all guide tree + prior combinations in a folder, or files will be overwritten
obsprefix <- 'all.wood.guidetree'
#The user must specify priors on population sizes
#The first vector is for population 0, the second for population 1, and the third for population 2
#Note that these are in terms of the number of haploid individuals (as specified in the fsc2 documentation)
obspopsizeprior <- list(c(10000,1000000),c(10000,1000000),c(10000,1000000))
#priors for divergence times given in terms of the number of generations and must be supplied as a list of vectors
#Divergence time priors should be provided in order of coalescent interval
obsdivtimeprior <- list(c(10000,100000),c(100000,500000))
#prior on migration rates, program only allows one prior for all migration rates in the default model sets
obsmigrateprior <- list(c(0.000005,0.0005))Set up fastsimcoal models and sim 10K reps of each model:
#set up your prior models for fastsimcoal2
setup_fsc2(tree=observedtree,
nspec=obsspecies,
samplesizes=obssamplesize,
nsnps=obssnps,
prefix=obsprefix,
migmatrix=migmatrix,
popsizeprior=obspopsizeprior,
divtimeprior=obsdivtimeprior,
migrateprior=obsmigrateprior,
secondarycontact= seccontact,
divwgeneflow= divwgeneflow,
maxmigrations = maxedges)
# fastsimcoalsims() requires the prefix used to generate the model files, the path to fastsimcoal2, and # of reps
#Generally, a minimum of 10,000 replicates under each model should be simulated.
fastsimcoalsims(prefix=obsprefix,
pathtofsc='/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26',
nreps=10000)## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_1.tpl -e all.wood.guidetree_1.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_2.tpl -e all.wood.guidetree_2.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_3.tpl -e all.wood.guidetree_3.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_4.tpl -e all.wood.guidetree_4.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_5.tpl -e all.wood.guidetree_5.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_6.tpl -e all.wood.guidetree_6.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_7.tpl -e all.wood.guidetree_7.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_8.tpl -e all.wood.guidetree_8.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_9.tpl -e all.wood.guidetree_9.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_10.tpl -e all.wood.guidetree_10.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_11.tpl -e all.wood.guidetree_11.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_12.tpl -e all.wood.guidetree_12.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_13.tpl -e all.wood.guidetree_13.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_14.tpl -e all.wood.guidetree_14.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_15.tpl -e all.wood.guidetree_15.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_16.tpl -e all.wood.guidetree_16.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_17.tpl -e all.wood.guidetree_17.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_18.tpl -e all.wood.guidetree_18.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_19.tpl -e all.wood.guidetree_19.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_20.tpl -e all.wood.guidetree_20.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_21.tpl -e all.wood.guidetree_21.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_22.tpl -e all.wood.guidetree_22.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_23.tpl -e all.wood.guidetree_23.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_24.tpl -e all.wood.guidetree_24.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_25.tpl -e all.wood.guidetree_25.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_26.tpl -e all.wood.guidetree_26.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_27.tpl -e all.wood.guidetree_27.est -n 1 --msfs -q --multiSFS -x -E10000"
## [1] "/panfs/pfs.local/work/bi/bin/fsc26_linux64/fsc26 -t all.wood.guidetree_28.tpl -e all.wood.guidetree_28.est -n 1 --msfs -q --multiSFS -x -E10000"Build prior and reduced prior:
#need to turn our mSFS into a binned (bSFS) specify bin number here
#number should not be greater than the sample size of the population with the fewest samples, as this results in sparse sampling of the SFS
#Large values lead to a more complete summary of the data, but also lead to a more sparsely sampled SFS and increased computation times
nclasses <- 6
#to make prior, provide:
#prefix used to name the model files, the number of species, the number of classes to be included in the SFS,
#a path to the working directory, the name of the traits file, the threshold,
#the name of the folder to store the prior in, and the number of cores to use.
FullPrior <- makeprior(prefix=obsprefix,
nspec=obsspecies,
nclasses=nclasses,
getwd(),
traitsfile = traitsfile,
threshold=100,
thefolder = 'Prior',
ncores = 10)
#remove extraneous files
#clean_working(prefix=obsprefix)
#remove invariant data
ReducedPrior <- Prior_reduced(FullPrior)build random forest classifier:
#build random forest
myRF <- RF_build_abcrf(ReducedPrior,FullPrior,5000)## Warning in lda.default(x, grouping, ...): variables are collinear## Growing trees.. Progress: 0%. Estimated remaining time: 6 hours, 8 minutes, 31 seconds.
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## Growing trees.. Progress: 91%. Estimated remaining time: 10 minutes, 5 seconds.
## Growing trees.. Progress: 92%. Estimated remaining time: 9 minutes, 37 seconds.
## Growing trees.. Progress: 92%. Estimated remaining time: 9 minutes, 2 seconds.
## Growing trees.. Progress: 93%. Estimated remaining time: 8 minutes, 31 seconds.
## Growing trees.. Progress: 93%. Estimated remaining time: 7 minutes, 57 seconds.
## Growing trees.. Progress: 94%. Estimated remaining time: 7 minutes, 24 seconds.
## Growing trees.. Progress: 94%. Estimated remaining time: 6 minutes, 49 seconds.
## Growing trees.. Progress: 95%. Estimated remaining time: 6 minutes, 24 seconds.
## Growing trees.. Progress: 95%. Estimated remaining time: 5 minutes, 44 seconds.
## Growing trees.. Progress: 96%. Estimated remaining time: 5 minutes, 11 seconds.
## Growing trees.. Progress: 96%. Estimated remaining time: 4 minutes, 37 seconds.
## Growing trees.. Progress: 97%. Estimated remaining time: 4 minutes, 5 seconds.
## Growing trees.. Progress: 97%. Estimated remaining time: 3 minutes, 26 seconds.
## Growing trees.. Progress: 98%. Estimated remaining time: 2 minutes, 55 seconds.
## Growing trees.. Progress: 98%. Estimated remaining time: 2 minutes, 25 seconds.
## Growing trees.. Progress: 98%. Estimated remaining time: 1 minute, 48 seconds.
## Growing trees.. Progress: 99%. Estimated remaining time: 1 minute, 17 seconds.
## Growing trees.. Progress: 99%. Estimated remaining time: 42 seconds.
## Growing trees.. Progress: 100%. Estimated remaining time: 16 seconds.
## Growing trees.. Progress: 100%. Estimated remaining time: 5 seconds.
## Growing trees.. Progress: 100%. Estimated remaining time: 0 seconds.
## Computing prediction error.. Progress: 14%. Estimated remaining time: 3 minutes, 10 seconds.
## Computing prediction error.. Progress: 28%. Estimated remaining time: 2 minutes, 37 seconds.
## Computing prediction error.. Progress: 42%. Estimated remaining time: 2 minutes, 5 seconds.
## Computing prediction error.. Progress: 57%. Estimated remaining time: 1 minute, 35 seconds.
## Computing prediction error.. Progress: 71%. Estimated remaining time: 1 minute, 3 seconds.
## Computing prediction error.. Progress: 85%. Estimated remaining time: 33 seconds.
## Computing prediction error.. Progress: 99%. Estimated remaining time: 2 seconds.#view RF
myRF##
## Call:
## abcrf(formula = Models ~ ., data = Trainingdata, ntree = ntrees, paral = TRUE)
## includes the axes of a preliminary LDA
##
## Number of simulations: 280000
## Out-of-bag prior error rate: 36.4325%
##
## Confusion matrix:
## all.wood.guidetree_1_MSFS all.wood.guidetree_2_MSFS
## all.wood.guidetree_1_MSFS 9970 0
## all.wood.guidetree_2_MSFS 0 8912
## all.wood.guidetree_3_MSFS 464 16
## all.wood.guidetree_4_MSFS 0 3
## all.wood.guidetree_5_MSFS 0 2005
## all.wood.guidetree_6_MSFS 0 0
## all.wood.guidetree_7_MSFS 0 0
## all.wood.guidetree_8_MSFS 23 31
## all.wood.guidetree_9_MSFS 7 19
## all.wood.guidetree_10_MSFS 18 0
## all.wood.guidetree_11_MSFS 0 0
## all.wood.guidetree_12_MSFS 543 0
## all.wood.guidetree_13_MSFS 0 0
## all.wood.guidetree_14_MSFS 0 57
## all.wood.guidetree_15_MSFS 0 0
## all.wood.guidetree_16_MSFS 0 0
## all.wood.guidetree_17_MSFS 27 0
## all.wood.guidetree_18_MSFS 8 0
## all.wood.guidetree_19_MSFS 16 0
## all.wood.guidetree_20_MSFS 0 0
## all.wood.guidetree_21_MSFS 466 0
## all.wood.guidetree_22_MSFS 0 0
## all.wood.guidetree_23_MSFS 0 92
## all.wood.guidetree_24_MSFS 0 0
## all.wood.guidetree_25_MSFS 0 0
## all.wood.guidetree_26_MSFS 17 0
## all.wood.guidetree_27_MSFS 25 0
## all.wood.guidetree_28_MSFS 16 0
## all.wood.guidetree_3_MSFS all.wood.guidetree_4_MSFS
## all.wood.guidetree_1_MSFS 5 0
## all.wood.guidetree_2_MSFS 0 0
## all.wood.guidetree_3_MSFS 6130 0
## all.wood.guidetree_4_MSFS 0 9607
## all.wood.guidetree_5_MSFS 0 395
## all.wood.guidetree_6_MSFS 0 61
## all.wood.guidetree_7_MSFS 0 50
## all.wood.guidetree_8_MSFS 934 12
## all.wood.guidetree_9_MSFS 680 1
## all.wood.guidetree_10_MSFS 242 0
## all.wood.guidetree_11_MSFS 0 0
## all.wood.guidetree_12_MSFS 692 0
## all.wood.guidetree_13_MSFS 0 19
## all.wood.guidetree_14_MSFS 38 79
## all.wood.guidetree_15_MSFS 0 0
## all.wood.guidetree_16_MSFS 0 0
## all.wood.guidetree_17_MSFS 1089 2
## all.wood.guidetree_18_MSFS 842 3
## all.wood.guidetree_19_MSFS 288 1
## all.wood.guidetree_20_MSFS 0 0
## all.wood.guidetree_21_MSFS 792 0
## all.wood.guidetree_22_MSFS 0 11
## all.wood.guidetree_23_MSFS 18 106
## all.wood.guidetree_24_MSFS 0 0
## all.wood.guidetree_25_MSFS 0 0
## all.wood.guidetree_26_MSFS 1081 0
## all.wood.guidetree_27_MSFS 904 2
## all.wood.guidetree_28_MSFS 283 0
## all.wood.guidetree_5_MSFS all.wood.guidetree_6_MSFS
## all.wood.guidetree_1_MSFS 0 0
## all.wood.guidetree_2_MSFS 1026 0
## all.wood.guidetree_3_MSFS 12 0
## all.wood.guidetree_4_MSFS 322 0
## all.wood.guidetree_5_MSFS 7446 0
## all.wood.guidetree_6_MSFS 13 7502
## all.wood.guidetree_7_MSFS 16 0
## all.wood.guidetree_8_MSFS 103 269
## all.wood.guidetree_9_MSFS 91 0
## all.wood.guidetree_10_MSFS 2 129
## all.wood.guidetree_11_MSFS 0 45
## all.wood.guidetree_12_MSFS 0 52
## all.wood.guidetree_13_MSFS 0 20
## all.wood.guidetree_14_MSFS 194 18
## all.wood.guidetree_15_MSFS 0 111
## all.wood.guidetree_16_MSFS 0 0
## all.wood.guidetree_17_MSFS 0 104
## all.wood.guidetree_18_MSFS 5 3
## all.wood.guidetree_19_MSFS 0 36
## all.wood.guidetree_20_MSFS 0 0
## all.wood.guidetree_21_MSFS 0 0
## all.wood.guidetree_22_MSFS 0 0
## all.wood.guidetree_23_MSFS 171 4
## all.wood.guidetree_24_MSFS 0 1283
## all.wood.guidetree_25_MSFS 0 0
## all.wood.guidetree_26_MSFS 0 155
## all.wood.guidetree_27_MSFS 2 1
## all.wood.guidetree_28_MSFS 0 52
## all.wood.guidetree_7_MSFS all.wood.guidetree_8_MSFS
## all.wood.guidetree_1_MSFS 0 0
## all.wood.guidetree_2_MSFS 0 0
## all.wood.guidetree_3_MSFS 0 362
## all.wood.guidetree_4_MSFS 0 0
## all.wood.guidetree_5_MSFS 3 0
## all.wood.guidetree_6_MSFS 0 22
## all.wood.guidetree_7_MSFS 6464 0
## all.wood.guidetree_8_MSFS 0 3688
## all.wood.guidetree_9_MSFS 297 446
## all.wood.guidetree_10_MSFS 93 502
## all.wood.guidetree_11_MSFS 0 0
## all.wood.guidetree_12_MSFS 0 121
## all.wood.guidetree_13_MSFS 1 0
## all.wood.guidetree_14_MSFS 2 20
## all.wood.guidetree_15_MSFS 0 0
## all.wood.guidetree_16_MSFS 2939 0
## all.wood.guidetree_17_MSFS 0 851
## all.wood.guidetree_18_MSFS 127 320
## all.wood.guidetree_19_MSFS 40 177
## all.wood.guidetree_20_MSFS 26 0
## all.wood.guidetree_21_MSFS 40 47
## all.wood.guidetree_22_MSFS 11 0
## all.wood.guidetree_23_MSFS 25 3
## all.wood.guidetree_24_MSFS 0 0
## all.wood.guidetree_25_MSFS 50 0
## all.wood.guidetree_26_MSFS 1 1126
## all.wood.guidetree_27_MSFS 115 210
## all.wood.guidetree_28_MSFS 8 244
## all.wood.guidetree_9_MSFS all.wood.guidetree_10_MSFS
## all.wood.guidetree_1_MSFS 0 0
## all.wood.guidetree_2_MSFS 0 0
## all.wood.guidetree_3_MSFS 226 64
## all.wood.guidetree_4_MSFS 0 0
## all.wood.guidetree_5_MSFS 0 0
## all.wood.guidetree_6_MSFS 0 3
## all.wood.guidetree_7_MSFS 33 1
## all.wood.guidetree_8_MSFS 320 459
## all.wood.guidetree_9_MSFS 3565 469
## all.wood.guidetree_10_MSFS 535 2700
## all.wood.guidetree_11_MSFS 0 0
## all.wood.guidetree_12_MSFS 3 244
## all.wood.guidetree_13_MSFS 0 0
## all.wood.guidetree_14_MSFS 2 0
## all.wood.guidetree_15_MSFS 0 0
## all.wood.guidetree_16_MSFS 2 2
## all.wood.guidetree_17_MSFS 102 316
## all.wood.guidetree_18_MSFS 1194 490
## all.wood.guidetree_19_MSFS 238 1464
## all.wood.guidetree_20_MSFS 0 0
## all.wood.guidetree_21_MSFS 92 249
## all.wood.guidetree_22_MSFS 0 0
## all.wood.guidetree_23_MSFS 11 0
## all.wood.guidetree_24_MSFS 0 5
## all.wood.guidetree_25_MSFS 0 0
## all.wood.guidetree_26_MSFS 195 514
## all.wood.guidetree_27_MSFS 626 316
## all.wood.guidetree_28_MSFS 108 1259
## all.wood.guidetree_11_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 37
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 0
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 0
## all.wood.guidetree_11_MSFS 8871
## all.wood.guidetree_12_MSFS 25
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 1513
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 16
## all.wood.guidetree_18_MSFS 0
## all.wood.guidetree_19_MSFS 8
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 20
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 0
## all.wood.guidetree_27_MSFS 0
## all.wood.guidetree_28_MSFS 0
## all.wood.guidetree_12_MSFS
## all.wood.guidetree_1_MSFS 21
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 1174
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 8
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 989
## all.wood.guidetree_9_MSFS 208
## all.wood.guidetree_10_MSFS 868
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 6844
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 908
## all.wood.guidetree_18_MSFS 133
## all.wood.guidetree_19_MSFS 791
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 1160
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 5
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 1069
## all.wood.guidetree_27_MSFS 344
## all.wood.guidetree_28_MSFS 1019
## all.wood.guidetree_13_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 14
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 92
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 2
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 3
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 9691
## all.wood.guidetree_14_MSFS 72
## all.wood.guidetree_15_MSFS 383
## all.wood.guidetree_16_MSFS 44
## all.wood.guidetree_17_MSFS 13
## all.wood.guidetree_18_MSFS 2
## all.wood.guidetree_19_MSFS 5
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 29
## all.wood.guidetree_23_MSFS 3
## all.wood.guidetree_24_MSFS 41
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 8
## all.wood.guidetree_27_MSFS 0
## all.wood.guidetree_28_MSFS 1
## all.wood.guidetree_14_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 31
## all.wood.guidetree_3_MSFS 82
## all.wood.guidetree_4_MSFS 21
## all.wood.guidetree_5_MSFS 81
## all.wood.guidetree_6_MSFS 16
## all.wood.guidetree_7_MSFS 1
## all.wood.guidetree_8_MSFS 136
## all.wood.guidetree_9_MSFS 30
## all.wood.guidetree_10_MSFS 5
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 6755
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 272
## all.wood.guidetree_18_MSFS 116
## all.wood.guidetree_19_MSFS 1
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 3146
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 185
## all.wood.guidetree_27_MSFS 76
## all.wood.guidetree_28_MSFS 0
## all.wood.guidetree_15_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 143
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 2
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 1
## all.wood.guidetree_11_MSFS 1038
## all.wood.guidetree_12_MSFS 14
## all.wood.guidetree_13_MSFS 229
## all.wood.guidetree_14_MSFS 6
## all.wood.guidetree_15_MSFS 7854
## all.wood.guidetree_16_MSFS 13
## all.wood.guidetree_17_MSFS 120
## all.wood.guidetree_18_MSFS 0
## all.wood.guidetree_19_MSFS 120
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 166
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 1
## all.wood.guidetree_27_MSFS 0
## all.wood.guidetree_28_MSFS 0
## all.wood.guidetree_16_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 1
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 5
## all.wood.guidetree_7_MSFS 3190
## all.wood.guidetree_8_MSFS 0
## all.wood.guidetree_9_MSFS 72
## all.wood.guidetree_10_MSFS 163
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 4
## all.wood.guidetree_16_MSFS 6709
## all.wood.guidetree_17_MSFS 1
## all.wood.guidetree_18_MSFS 135
## all.wood.guidetree_19_MSFS 307
## all.wood.guidetree_20_MSFS 38
## all.wood.guidetree_21_MSFS 108
## all.wood.guidetree_22_MSFS 10
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 21
## all.wood.guidetree_25_MSFS 94
## all.wood.guidetree_26_MSFS 2
## all.wood.guidetree_27_MSFS 26
## all.wood.guidetree_28_MSFS 143
## all.wood.guidetree_17_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 94
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 14
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 703
## all.wood.guidetree_9_MSFS 112
## all.wood.guidetree_10_MSFS 235
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 225
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 21
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 3293
## all.wood.guidetree_18_MSFS 453
## all.wood.guidetree_19_MSFS 331
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 18
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 2
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 996
## all.wood.guidetree_27_MSFS 169
## all.wood.guidetree_28_MSFS 145
## all.wood.guidetree_18_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 188
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 1
## all.wood.guidetree_8_MSFS 331
## all.wood.guidetree_9_MSFS 1591
## all.wood.guidetree_10_MSFS 473
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 31
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 1
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 439
## all.wood.guidetree_18_MSFS 2642
## all.wood.guidetree_19_MSFS 496
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 223
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 509
## all.wood.guidetree_27_MSFS 1520
## all.wood.guidetree_28_MSFS 328
## all.wood.guidetree_19_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 51
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 4
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 150
## all.wood.guidetree_9_MSFS 195
## all.wood.guidetree_10_MSFS 991
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 206
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 34
## all.wood.guidetree_17_MSFS 288
## all.wood.guidetree_18_MSFS 393
## all.wood.guidetree_19_MSFS 3248
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 110
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 13
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 285
## all.wood.guidetree_27_MSFS 131
## all.wood.guidetree_28_MSFS 676
## all.wood.guidetree_20_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 61
## all.wood.guidetree_8_MSFS 0
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 1
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 44
## all.wood.guidetree_17_MSFS 0
## all.wood.guidetree_18_MSFS 1
## all.wood.guidetree_19_MSFS 0
## all.wood.guidetree_20_MSFS 8706
## all.wood.guidetree_21_MSFS 22
## all.wood.guidetree_22_MSFS 4
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 2108
## all.wood.guidetree_26_MSFS 0
## all.wood.guidetree_27_MSFS 19
## all.wood.guidetree_28_MSFS 26
## all.wood.guidetree_21_MSFS
## all.wood.guidetree_1_MSFS 4
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 672
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 22
## all.wood.guidetree_8_MSFS 415
## all.wood.guidetree_9_MSFS 937
## all.wood.guidetree_10_MSFS 1203
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 639
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 29
## all.wood.guidetree_17_MSFS 401
## all.wood.guidetree_18_MSFS 988
## all.wood.guidetree_19_MSFS 1062
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 5949
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 182
## all.wood.guidetree_27_MSFS 761
## all.wood.guidetree_28_MSFS 848
## all.wood.guidetree_22_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 10
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 35
## all.wood.guidetree_8_MSFS 0
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 3
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 27
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 30
## all.wood.guidetree_17_MSFS 2
## all.wood.guidetree_18_MSFS 2
## all.wood.guidetree_19_MSFS 0
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 9596
## all.wood.guidetree_23_MSFS 49
## all.wood.guidetree_24_MSFS 45
## all.wood.guidetree_25_MSFS 375
## all.wood.guidetree_26_MSFS 1
## all.wood.guidetree_27_MSFS 7
## all.wood.guidetree_28_MSFS 0
## all.wood.guidetree_23_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 31
## all.wood.guidetree_3_MSFS 59
## all.wood.guidetree_4_MSFS 22
## all.wood.guidetree_5_MSFS 70
## all.wood.guidetree_6_MSFS 5
## all.wood.guidetree_7_MSFS 16
## all.wood.guidetree_8_MSFS 37
## all.wood.guidetree_9_MSFS 90
## all.wood.guidetree_10_MSFS 0
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 2728
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 2
## all.wood.guidetree_17_MSFS 39
## all.wood.guidetree_18_MSFS 122
## all.wood.guidetree_19_MSFS 0
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 6348
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 97
## all.wood.guidetree_27_MSFS 239
## all.wood.guidetree_28_MSFS 1
## all.wood.guidetree_24_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 2055
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 13
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 58
## all.wood.guidetree_11_MSFS 46
## all.wood.guidetree_12_MSFS 30
## all.wood.guidetree_13_MSFS 13
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 135
## all.wood.guidetree_16_MSFS 6
## all.wood.guidetree_17_MSFS 18
## all.wood.guidetree_18_MSFS 1
## all.wood.guidetree_19_MSFS 63
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 8344
## all.wood.guidetree_25_MSFS 2
## all.wood.guidetree_26_MSFS 95
## all.wood.guidetree_27_MSFS 1
## all.wood.guidetree_28_MSFS 246
## all.wood.guidetree_25_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 96
## all.wood.guidetree_8_MSFS 0
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 1
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 124
## all.wood.guidetree_17_MSFS 0
## all.wood.guidetree_18_MSFS 2
## all.wood.guidetree_19_MSFS 1
## all.wood.guidetree_20_MSFS 1230
## all.wood.guidetree_21_MSFS 23
## all.wood.guidetree_22_MSFS 339
## all.wood.guidetree_23_MSFS 5
## all.wood.guidetree_24_MSFS 19
## all.wood.guidetree_25_MSFS 7370
## all.wood.guidetree_26_MSFS 1
## all.wood.guidetree_27_MSFS 81
## all.wood.guidetree_28_MSFS 120
## all.wood.guidetree_26_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 270
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 15
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 1113
## all.wood.guidetree_9_MSFS 308
## all.wood.guidetree_10_MSFS 466
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 206
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 6
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 1402
## all.wood.guidetree_18_MSFS 521
## all.wood.guidetree_19_MSFS 354
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 90
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 1
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 2574
## all.wood.guidetree_27_MSFS 450
## all.wood.guidetree_28_MSFS 420
## all.wood.guidetree_27_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 89
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 13
## all.wood.guidetree_8_MSFS 100
## all.wood.guidetree_9_MSFS 666
## all.wood.guidetree_10_MSFS 199
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 9
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 1
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 4
## all.wood.guidetree_17_MSFS 181
## all.wood.guidetree_18_MSFS 1194
## all.wood.guidetree_19_MSFS 107
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 205
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 19
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 495
## all.wood.guidetree_27_MSFS 3516
## all.wood.guidetree_28_MSFS 362
## all.wood.guidetree_28_MSFS class.error
## all.wood.guidetree_1_MSFS 0 0.0030
## all.wood.guidetree_2_MSFS 0 0.1088
## all.wood.guidetree_3_MSFS 47 0.3870
## all.wood.guidetree_4_MSFS 0 0.0393
## all.wood.guidetree_5_MSFS 0 0.2554
## all.wood.guidetree_6_MSFS 5 0.2498
## all.wood.guidetree_7_MSFS 1 0.3536
## all.wood.guidetree_8_MSFS 170 0.6312
## all.wood.guidetree_9_MSFS 216 0.6435
## all.wood.guidetree_10_MSFS 1109 0.7300
## all.wood.guidetree_11_MSFS 0 0.1129
## all.wood.guidetree_12_MSFS 116 0.3156
## all.wood.guidetree_13_MSFS 0 0.0309
## all.wood.guidetree_14_MSFS 0 0.3245
## all.wood.guidetree_15_MSFS 0 0.2146
## all.wood.guidetree_16_MSFS 18 0.3291
## all.wood.guidetree_17_MSFS 116 0.6707
## all.wood.guidetree_18_MSFS 303 0.7358
## all.wood.guidetree_19_MSFS 846 0.6752
## all.wood.guidetree_20_MSFS 0 0.1294
## all.wood.guidetree_21_MSFS 406 0.4051
## all.wood.guidetree_22_MSFS 0 0.0404
## all.wood.guidetree_23_MSFS 0 0.3652
## all.wood.guidetree_24_MSFS 35 0.1656
## all.wood.guidetree_25_MSFS 1 0.2630
## all.wood.guidetree_26_MSFS 411 0.7426
## all.wood.guidetree_27_MSFS 459 0.6484
## all.wood.guidetree_28_MSFS 3695 0.6305#view misclassification rate for simulated data under our four models
classification.error<-myRF[["model.rf"]]$confusion.matrix
classification.error## all.wood.guidetree_1_MSFS all.wood.guidetree_2_MSFS
## all.wood.guidetree_1_MSFS 9970 0
## all.wood.guidetree_2_MSFS 0 8912
## all.wood.guidetree_3_MSFS 464 16
## all.wood.guidetree_4_MSFS 0 3
## all.wood.guidetree_5_MSFS 0 2005
## all.wood.guidetree_6_MSFS 0 0
## all.wood.guidetree_7_MSFS 0 0
## all.wood.guidetree_8_MSFS 23 31
## all.wood.guidetree_9_MSFS 7 19
## all.wood.guidetree_10_MSFS 18 0
## all.wood.guidetree_11_MSFS 0 0
## all.wood.guidetree_12_MSFS 543 0
## all.wood.guidetree_13_MSFS 0 0
## all.wood.guidetree_14_MSFS 0 57
## all.wood.guidetree_15_MSFS 0 0
## all.wood.guidetree_16_MSFS 0 0
## all.wood.guidetree_17_MSFS 27 0
## all.wood.guidetree_18_MSFS 8 0
## all.wood.guidetree_19_MSFS 16 0
## all.wood.guidetree_20_MSFS 0 0
## all.wood.guidetree_21_MSFS 466 0
## all.wood.guidetree_22_MSFS 0 0
## all.wood.guidetree_23_MSFS 0 92
## all.wood.guidetree_24_MSFS 0 0
## all.wood.guidetree_25_MSFS 0 0
## all.wood.guidetree_26_MSFS 17 0
## all.wood.guidetree_27_MSFS 25 0
## all.wood.guidetree_28_MSFS 16 0
## all.wood.guidetree_3_MSFS all.wood.guidetree_4_MSFS
## all.wood.guidetree_1_MSFS 5 0
## all.wood.guidetree_2_MSFS 0 0
## all.wood.guidetree_3_MSFS 6130 0
## all.wood.guidetree_4_MSFS 0 9607
## all.wood.guidetree_5_MSFS 0 395
## all.wood.guidetree_6_MSFS 0 61
## all.wood.guidetree_7_MSFS 0 50
## all.wood.guidetree_8_MSFS 934 12
## all.wood.guidetree_9_MSFS 680 1
## all.wood.guidetree_10_MSFS 242 0
## all.wood.guidetree_11_MSFS 0 0
## all.wood.guidetree_12_MSFS 692 0
## all.wood.guidetree_13_MSFS 0 19
## all.wood.guidetree_14_MSFS 38 79
## all.wood.guidetree_15_MSFS 0 0
## all.wood.guidetree_16_MSFS 0 0
## all.wood.guidetree_17_MSFS 1089 2
## all.wood.guidetree_18_MSFS 842 3
## all.wood.guidetree_19_MSFS 288 1
## all.wood.guidetree_20_MSFS 0 0
## all.wood.guidetree_21_MSFS 792 0
## all.wood.guidetree_22_MSFS 0 11
## all.wood.guidetree_23_MSFS 18 106
## all.wood.guidetree_24_MSFS 0 0
## all.wood.guidetree_25_MSFS 0 0
## all.wood.guidetree_26_MSFS 1081 0
## all.wood.guidetree_27_MSFS 904 2
## all.wood.guidetree_28_MSFS 283 0
## all.wood.guidetree_5_MSFS all.wood.guidetree_6_MSFS
## all.wood.guidetree_1_MSFS 0 0
## all.wood.guidetree_2_MSFS 1026 0
## all.wood.guidetree_3_MSFS 12 0
## all.wood.guidetree_4_MSFS 322 0
## all.wood.guidetree_5_MSFS 7446 0
## all.wood.guidetree_6_MSFS 13 7502
## all.wood.guidetree_7_MSFS 16 0
## all.wood.guidetree_8_MSFS 103 269
## all.wood.guidetree_9_MSFS 91 0
## all.wood.guidetree_10_MSFS 2 129
## all.wood.guidetree_11_MSFS 0 45
## all.wood.guidetree_12_MSFS 0 52
## all.wood.guidetree_13_MSFS 0 20
## all.wood.guidetree_14_MSFS 194 18
## all.wood.guidetree_15_MSFS 0 111
## all.wood.guidetree_16_MSFS 0 0
## all.wood.guidetree_17_MSFS 0 104
## all.wood.guidetree_18_MSFS 5 3
## all.wood.guidetree_19_MSFS 0 36
## all.wood.guidetree_20_MSFS 0 0
## all.wood.guidetree_21_MSFS 0 0
## all.wood.guidetree_22_MSFS 0 0
## all.wood.guidetree_23_MSFS 171 4
## all.wood.guidetree_24_MSFS 0 1283
## all.wood.guidetree_25_MSFS 0 0
## all.wood.guidetree_26_MSFS 0 155
## all.wood.guidetree_27_MSFS 2 1
## all.wood.guidetree_28_MSFS 0 52
## all.wood.guidetree_7_MSFS all.wood.guidetree_8_MSFS
## all.wood.guidetree_1_MSFS 0 0
## all.wood.guidetree_2_MSFS 0 0
## all.wood.guidetree_3_MSFS 0 362
## all.wood.guidetree_4_MSFS 0 0
## all.wood.guidetree_5_MSFS 3 0
## all.wood.guidetree_6_MSFS 0 22
## all.wood.guidetree_7_MSFS 6464 0
## all.wood.guidetree_8_MSFS 0 3688
## all.wood.guidetree_9_MSFS 297 446
## all.wood.guidetree_10_MSFS 93 502
## all.wood.guidetree_11_MSFS 0 0
## all.wood.guidetree_12_MSFS 0 121
## all.wood.guidetree_13_MSFS 1 0
## all.wood.guidetree_14_MSFS 2 20
## all.wood.guidetree_15_MSFS 0 0
## all.wood.guidetree_16_MSFS 2939 0
## all.wood.guidetree_17_MSFS 0 851
## all.wood.guidetree_18_MSFS 127 320
## all.wood.guidetree_19_MSFS 40 177
## all.wood.guidetree_20_MSFS 26 0
## all.wood.guidetree_21_MSFS 40 47
## all.wood.guidetree_22_MSFS 11 0
## all.wood.guidetree_23_MSFS 25 3
## all.wood.guidetree_24_MSFS 0 0
## all.wood.guidetree_25_MSFS 50 0
## all.wood.guidetree_26_MSFS 1 1126
## all.wood.guidetree_27_MSFS 115 210
## all.wood.guidetree_28_MSFS 8 244
## all.wood.guidetree_9_MSFS all.wood.guidetree_10_MSFS
## all.wood.guidetree_1_MSFS 0 0
## all.wood.guidetree_2_MSFS 0 0
## all.wood.guidetree_3_MSFS 226 64
## all.wood.guidetree_4_MSFS 0 0
## all.wood.guidetree_5_MSFS 0 0
## all.wood.guidetree_6_MSFS 0 3
## all.wood.guidetree_7_MSFS 33 1
## all.wood.guidetree_8_MSFS 320 459
## all.wood.guidetree_9_MSFS 3565 469
## all.wood.guidetree_10_MSFS 535 2700
## all.wood.guidetree_11_MSFS 0 0
## all.wood.guidetree_12_MSFS 3 244
## all.wood.guidetree_13_MSFS 0 0
## all.wood.guidetree_14_MSFS 2 0
## all.wood.guidetree_15_MSFS 0 0
## all.wood.guidetree_16_MSFS 2 2
## all.wood.guidetree_17_MSFS 102 316
## all.wood.guidetree_18_MSFS 1194 490
## all.wood.guidetree_19_MSFS 238 1464
## all.wood.guidetree_20_MSFS 0 0
## all.wood.guidetree_21_MSFS 92 249
## all.wood.guidetree_22_MSFS 0 0
## all.wood.guidetree_23_MSFS 11 0
## all.wood.guidetree_24_MSFS 0 5
## all.wood.guidetree_25_MSFS 0 0
## all.wood.guidetree_26_MSFS 195 514
## all.wood.guidetree_27_MSFS 626 316
## all.wood.guidetree_28_MSFS 108 1259
## all.wood.guidetree_11_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 37
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 0
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 0
## all.wood.guidetree_11_MSFS 8871
## all.wood.guidetree_12_MSFS 25
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 1513
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 16
## all.wood.guidetree_18_MSFS 0
## all.wood.guidetree_19_MSFS 8
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 20
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 0
## all.wood.guidetree_27_MSFS 0
## all.wood.guidetree_28_MSFS 0
## all.wood.guidetree_12_MSFS
## all.wood.guidetree_1_MSFS 21
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 1174
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 8
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 989
## all.wood.guidetree_9_MSFS 208
## all.wood.guidetree_10_MSFS 868
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 6844
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 908
## all.wood.guidetree_18_MSFS 133
## all.wood.guidetree_19_MSFS 791
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 1160
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 5
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 1069
## all.wood.guidetree_27_MSFS 344
## all.wood.guidetree_28_MSFS 1019
## all.wood.guidetree_13_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 14
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 92
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 2
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 3
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 9691
## all.wood.guidetree_14_MSFS 72
## all.wood.guidetree_15_MSFS 383
## all.wood.guidetree_16_MSFS 44
## all.wood.guidetree_17_MSFS 13
## all.wood.guidetree_18_MSFS 2
## all.wood.guidetree_19_MSFS 5
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 29
## all.wood.guidetree_23_MSFS 3
## all.wood.guidetree_24_MSFS 41
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 8
## all.wood.guidetree_27_MSFS 0
## all.wood.guidetree_28_MSFS 1
## all.wood.guidetree_14_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 31
## all.wood.guidetree_3_MSFS 82
## all.wood.guidetree_4_MSFS 21
## all.wood.guidetree_5_MSFS 81
## all.wood.guidetree_6_MSFS 16
## all.wood.guidetree_7_MSFS 1
## all.wood.guidetree_8_MSFS 136
## all.wood.guidetree_9_MSFS 30
## all.wood.guidetree_10_MSFS 5
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 6755
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 272
## all.wood.guidetree_18_MSFS 116
## all.wood.guidetree_19_MSFS 1
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 3146
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 185
## all.wood.guidetree_27_MSFS 76
## all.wood.guidetree_28_MSFS 0
## all.wood.guidetree_15_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 143
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 2
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 1
## all.wood.guidetree_11_MSFS 1038
## all.wood.guidetree_12_MSFS 14
## all.wood.guidetree_13_MSFS 229
## all.wood.guidetree_14_MSFS 6
## all.wood.guidetree_15_MSFS 7854
## all.wood.guidetree_16_MSFS 13
## all.wood.guidetree_17_MSFS 120
## all.wood.guidetree_18_MSFS 0
## all.wood.guidetree_19_MSFS 120
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 166
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 1
## all.wood.guidetree_27_MSFS 0
## all.wood.guidetree_28_MSFS 0
## all.wood.guidetree_16_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 1
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 5
## all.wood.guidetree_7_MSFS 3190
## all.wood.guidetree_8_MSFS 0
## all.wood.guidetree_9_MSFS 72
## all.wood.guidetree_10_MSFS 163
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 4
## all.wood.guidetree_16_MSFS 6709
## all.wood.guidetree_17_MSFS 1
## all.wood.guidetree_18_MSFS 135
## all.wood.guidetree_19_MSFS 307
## all.wood.guidetree_20_MSFS 38
## all.wood.guidetree_21_MSFS 108
## all.wood.guidetree_22_MSFS 10
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 21
## all.wood.guidetree_25_MSFS 94
## all.wood.guidetree_26_MSFS 2
## all.wood.guidetree_27_MSFS 26
## all.wood.guidetree_28_MSFS 143
## all.wood.guidetree_17_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 94
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 14
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 703
## all.wood.guidetree_9_MSFS 112
## all.wood.guidetree_10_MSFS 235
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 225
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 21
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 3293
## all.wood.guidetree_18_MSFS 453
## all.wood.guidetree_19_MSFS 331
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 18
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 2
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 996
## all.wood.guidetree_27_MSFS 169
## all.wood.guidetree_28_MSFS 145
## all.wood.guidetree_18_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 188
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 1
## all.wood.guidetree_8_MSFS 331
## all.wood.guidetree_9_MSFS 1591
## all.wood.guidetree_10_MSFS 473
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 31
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 1
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 439
## all.wood.guidetree_18_MSFS 2642
## all.wood.guidetree_19_MSFS 496
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 223
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 509
## all.wood.guidetree_27_MSFS 1520
## all.wood.guidetree_28_MSFS 328
## all.wood.guidetree_19_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 51
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 4
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 150
## all.wood.guidetree_9_MSFS 195
## all.wood.guidetree_10_MSFS 991
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 206
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 34
## all.wood.guidetree_17_MSFS 288
## all.wood.guidetree_18_MSFS 393
## all.wood.guidetree_19_MSFS 3248
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 110
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 13
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 285
## all.wood.guidetree_27_MSFS 131
## all.wood.guidetree_28_MSFS 676
## all.wood.guidetree_20_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 61
## all.wood.guidetree_8_MSFS 0
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 1
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 44
## all.wood.guidetree_17_MSFS 0
## all.wood.guidetree_18_MSFS 1
## all.wood.guidetree_19_MSFS 0
## all.wood.guidetree_20_MSFS 8706
## all.wood.guidetree_21_MSFS 22
## all.wood.guidetree_22_MSFS 4
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 2108
## all.wood.guidetree_26_MSFS 0
## all.wood.guidetree_27_MSFS 19
## all.wood.guidetree_28_MSFS 26
## all.wood.guidetree_21_MSFS
## all.wood.guidetree_1_MSFS 4
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 672
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 22
## all.wood.guidetree_8_MSFS 415
## all.wood.guidetree_9_MSFS 937
## all.wood.guidetree_10_MSFS 1203
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 639
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 29
## all.wood.guidetree_17_MSFS 401
## all.wood.guidetree_18_MSFS 988
## all.wood.guidetree_19_MSFS 1062
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 5949
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 182
## all.wood.guidetree_27_MSFS 761
## all.wood.guidetree_28_MSFS 848
## all.wood.guidetree_22_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 10
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 35
## all.wood.guidetree_8_MSFS 0
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 3
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 27
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 30
## all.wood.guidetree_17_MSFS 2
## all.wood.guidetree_18_MSFS 2
## all.wood.guidetree_19_MSFS 0
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 9596
## all.wood.guidetree_23_MSFS 49
## all.wood.guidetree_24_MSFS 45
## all.wood.guidetree_25_MSFS 375
## all.wood.guidetree_26_MSFS 1
## all.wood.guidetree_27_MSFS 7
## all.wood.guidetree_28_MSFS 0
## all.wood.guidetree_23_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 31
## all.wood.guidetree_3_MSFS 59
## all.wood.guidetree_4_MSFS 22
## all.wood.guidetree_5_MSFS 70
## all.wood.guidetree_6_MSFS 5
## all.wood.guidetree_7_MSFS 16
## all.wood.guidetree_8_MSFS 37
## all.wood.guidetree_9_MSFS 90
## all.wood.guidetree_10_MSFS 0
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 2728
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 2
## all.wood.guidetree_17_MSFS 39
## all.wood.guidetree_18_MSFS 122
## all.wood.guidetree_19_MSFS 0
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 6348
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 97
## all.wood.guidetree_27_MSFS 239
## all.wood.guidetree_28_MSFS 1
## all.wood.guidetree_24_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 2055
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 13
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 58
## all.wood.guidetree_11_MSFS 46
## all.wood.guidetree_12_MSFS 30
## all.wood.guidetree_13_MSFS 13
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 135
## all.wood.guidetree_16_MSFS 6
## all.wood.guidetree_17_MSFS 18
## all.wood.guidetree_18_MSFS 1
## all.wood.guidetree_19_MSFS 63
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 0
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 8344
## all.wood.guidetree_25_MSFS 2
## all.wood.guidetree_26_MSFS 95
## all.wood.guidetree_27_MSFS 1
## all.wood.guidetree_28_MSFS 246
## all.wood.guidetree_25_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 0
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 96
## all.wood.guidetree_8_MSFS 0
## all.wood.guidetree_9_MSFS 0
## all.wood.guidetree_10_MSFS 1
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 0
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 0
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 124
## all.wood.guidetree_17_MSFS 0
## all.wood.guidetree_18_MSFS 2
## all.wood.guidetree_19_MSFS 1
## all.wood.guidetree_20_MSFS 1230
## all.wood.guidetree_21_MSFS 23
## all.wood.guidetree_22_MSFS 339
## all.wood.guidetree_23_MSFS 5
## all.wood.guidetree_24_MSFS 19
## all.wood.guidetree_25_MSFS 7370
## all.wood.guidetree_26_MSFS 1
## all.wood.guidetree_27_MSFS 81
## all.wood.guidetree_28_MSFS 120
## all.wood.guidetree_26_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 270
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 15
## all.wood.guidetree_7_MSFS 0
## all.wood.guidetree_8_MSFS 1113
## all.wood.guidetree_9_MSFS 308
## all.wood.guidetree_10_MSFS 466
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 206
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 6
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 0
## all.wood.guidetree_17_MSFS 1402
## all.wood.guidetree_18_MSFS 521
## all.wood.guidetree_19_MSFS 354
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 90
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 0
## all.wood.guidetree_24_MSFS 1
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 2574
## all.wood.guidetree_27_MSFS 450
## all.wood.guidetree_28_MSFS 420
## all.wood.guidetree_27_MSFS
## all.wood.guidetree_1_MSFS 0
## all.wood.guidetree_2_MSFS 0
## all.wood.guidetree_3_MSFS 89
## all.wood.guidetree_4_MSFS 0
## all.wood.guidetree_5_MSFS 0
## all.wood.guidetree_6_MSFS 0
## all.wood.guidetree_7_MSFS 13
## all.wood.guidetree_8_MSFS 100
## all.wood.guidetree_9_MSFS 666
## all.wood.guidetree_10_MSFS 199
## all.wood.guidetree_11_MSFS 0
## all.wood.guidetree_12_MSFS 9
## all.wood.guidetree_13_MSFS 0
## all.wood.guidetree_14_MSFS 1
## all.wood.guidetree_15_MSFS 0
## all.wood.guidetree_16_MSFS 4
## all.wood.guidetree_17_MSFS 181
## all.wood.guidetree_18_MSFS 1194
## all.wood.guidetree_19_MSFS 107
## all.wood.guidetree_20_MSFS 0
## all.wood.guidetree_21_MSFS 205
## all.wood.guidetree_22_MSFS 0
## all.wood.guidetree_23_MSFS 19
## all.wood.guidetree_24_MSFS 0
## all.wood.guidetree_25_MSFS 0
## all.wood.guidetree_26_MSFS 495
## all.wood.guidetree_27_MSFS 3516
## all.wood.guidetree_28_MSFS 362
## all.wood.guidetree_28_MSFS class.error
## all.wood.guidetree_1_MSFS 0 0.0030
## all.wood.guidetree_2_MSFS 0 0.1088
## all.wood.guidetree_3_MSFS 47 0.3870
## all.wood.guidetree_4_MSFS 0 0.0393
## all.wood.guidetree_5_MSFS 0 0.2554
## all.wood.guidetree_6_MSFS 5 0.2498
## all.wood.guidetree_7_MSFS 1 0.3536
## all.wood.guidetree_8_MSFS 170 0.6312
## all.wood.guidetree_9_MSFS 216 0.6435
## all.wood.guidetree_10_MSFS 1109 0.7300
## all.wood.guidetree_11_MSFS 0 0.1129
## all.wood.guidetree_12_MSFS 116 0.3156
## all.wood.guidetree_13_MSFS 0 0.0309
## all.wood.guidetree_14_MSFS 0 0.3245
## all.wood.guidetree_15_MSFS 0 0.2146
## all.wood.guidetree_16_MSFS 18 0.3291
## all.wood.guidetree_17_MSFS 116 0.6707
## all.wood.guidetree_18_MSFS 303 0.7358
## all.wood.guidetree_19_MSFS 846 0.6752
## all.wood.guidetree_20_MSFS 0 0.1294
## all.wood.guidetree_21_MSFS 406 0.4051
## all.wood.guidetree_22_MSFS 0 0.0404
## all.wood.guidetree_23_MSFS 0 0.3652
## all.wood.guidetree_24_MSFS 35 0.1656
## all.wood.guidetree_25_MSFS 1 0.2630
## all.wood.guidetree_26_MSFS 411 0.7426
## all.wood.guidetree_27_MSFS 459 0.6484
## all.wood.guidetree_28_MSFS 3695 0.6305#write error rates to file
write.csv(classification.error, file = "classification.error.csv")
plot(myRF, training = ReducedPrior)
## Press <ENTER> to Continue
#prep data
myobserved <- prepobserved(
observedSFS,
FullPrior,
ReducedPrior,
nclasses,
obsspecies,
traitsfile=traitsfile,
threshold = 100)apply RF classifier to our observed data
#Now, we're ready to apply the RF classifier to the observed data.
#we use the function RF_predict_abcrf(), which requires the RF object, the observed dataset,
#the Reduced Prior, the Full Prior, and the number of trees, which should match that used to construct the classifier
prediction <- RF_predict_abcrf(myRF, myobserved, ReducedPrior, FullPrior, 5000)## Growing trees.. Progress: 1%. Estimated remaining time: 1 hour, 7 minutes, 27 seconds.
## Growing trees.. Progress: 2%. Estimated remaining time: 51 minutes, 9 seconds.
## Growing trees.. Progress: 3%. Estimated remaining time: 47 minutes, 30 seconds.
## Growing trees.. Progress: 4%. Estimated remaining time: 45 minutes, 20 seconds.
## Growing trees.. Progress: 6%. Estimated remaining time: 43 minutes, 59 seconds.
## Growing trees.. Progress: 7%. Estimated remaining time: 42 minutes, 51 seconds.
## Growing trees.. Progress: 8%. Estimated remaining time: 42 minutes, 12 seconds.
## Growing trees.. Progress: 9%. Estimated remaining time: 41 minutes, 1 seconds.
## Growing trees.. Progress: 10%. Estimated remaining time: 40 minutes, 10 seconds.
## Growing trees.. Progress: 12%. Estimated remaining time: 39 minutes, 26 seconds.
## Growing trees.. Progress: 13%. Estimated remaining time: 38 minutes, 46 seconds.
## Growing trees.. Progress: 14%. Estimated remaining time: 38 minutes, 24 seconds.
## Growing trees.. Progress: 15%. Estimated remaining time: 37 minutes, 45 seconds.
## Growing trees.. Progress: 16%. Estimated remaining time: 37 minutes, 9 seconds.
## Growing trees.. Progress: 18%. Estimated remaining time: 36 minutes, 42 seconds.
## Growing trees.. Progress: 19%. Estimated remaining time: 36 minutes, 12 seconds.
## Growing trees.. Progress: 20%. Estimated remaining time: 35 minutes, 40 seconds.
## Growing trees.. Progress: 21%. Estimated remaining time: 35 minutes, 1 seconds.
## Growing trees.. Progress: 22%. Estimated remaining time: 34 minutes, 31 seconds.
## Growing trees.. Progress: 24%. Estimated remaining time: 33 minutes, 54 seconds.
## Growing trees.. Progress: 25%. Estimated remaining time: 33 minutes, 24 seconds.
## Growing trees.. Progress: 26%. Estimated remaining time: 32 minutes, 53 seconds.
## Growing trees.. Progress: 27%. Estimated remaining time: 32 minutes, 21 seconds.
## Growing trees.. Progress: 28%. Estimated remaining time: 31 minutes, 52 seconds.
## Growing trees.. Progress: 30%. Estimated remaining time: 31 minutes, 14 seconds.
## Growing trees.. Progress: 31%. Estimated remaining time: 30 minutes, 44 seconds.
## Growing trees.. Progress: 32%. Estimated remaining time: 30 minutes, 12 seconds.
## Growing trees.. Progress: 33%. Estimated remaining time: 29 minutes, 40 seconds.
## Growing trees.. Progress: 34%. Estimated remaining time: 29 minutes, 8 seconds.
## Growing trees.. Progress: 36%. Estimated remaining time: 28 minutes, 37 seconds.
## Growing trees.. Progress: 37%. Estimated remaining time: 28 minutes, 8 seconds.
## Growing trees.. Progress: 38%. Estimated remaining time: 27 minutes, 39 seconds.
## Growing trees.. Progress: 39%. Estimated remaining time: 27 minutes, 8 seconds.
## Growing trees.. Progress: 40%. Estimated remaining time: 26 minutes, 36 seconds.
## Growing trees.. Progress: 41%. Estimated remaining time: 26 minutes, 2 seconds.
## Growing trees.. Progress: 43%. Estimated remaining time: 25 minutes, 30 seconds.
## Growing trees.. Progress: 44%. Estimated remaining time: 24 minutes, 56 seconds.
## Growing trees.. Progress: 45%. Estimated remaining time: 24 minutes, 23 seconds.
## Growing trees.. Progress: 46%. Estimated remaining time: 23 minutes, 54 seconds.
## Growing trees.. Progress: 47%. Estimated remaining time: 23 minutes, 26 seconds.
## Growing trees.. Progress: 48%. Estimated remaining time: 22 minutes, 55 seconds.
## Growing trees.. Progress: 50%. Estimated remaining time: 22 minutes, 22 seconds.
## Growing trees.. Progress: 51%. Estimated remaining time: 21 minutes, 50 seconds.
## Growing trees.. Progress: 52%. Estimated remaining time: 21 minutes, 18 seconds.
## Growing trees.. Progress: 53%. Estimated remaining time: 20 minutes, 48 seconds.
## Growing trees.. Progress: 54%. Estimated remaining time: 20 minutes, 16 seconds.
## Growing trees.. Progress: 56%. Estimated remaining time: 19 minutes, 44 seconds.
## Growing trees.. Progress: 57%. Estimated remaining time: 19 minutes, 11 seconds.
## Growing trees.. Progress: 58%. Estimated remaining time: 18 minutes, 39 seconds.
## Growing trees.. Progress: 59%. Estimated remaining time: 18 minutes, 9 seconds.
## Growing trees.. Progress: 60%. Estimated remaining time: 17 minutes, 39 seconds.
## Growing trees.. Progress: 61%. Estimated remaining time: 17 minutes, 7 seconds.
## Growing trees.. Progress: 63%. Estimated remaining time: 16 minutes, 36 seconds.
## Growing trees.. Progress: 64%. Estimated remaining time: 16 minutes, 5 seconds.
## Growing trees.. Progress: 65%. Estimated remaining time: 15 minutes, 32 seconds.
## Growing trees.. Progress: 66%. Estimated remaining time: 15 minutes, 0 seconds.
## Growing trees.. Progress: 67%. Estimated remaining time: 14 minutes, 29 seconds.
## Growing trees.. Progress: 69%. Estimated remaining time: 13 minutes, 56 seconds.
## Growing trees.. Progress: 70%. Estimated remaining time: 13 minutes, 24 seconds.
## Growing trees.. Progress: 71%. Estimated remaining time: 12 minutes, 52 seconds.
## Growing trees.. Progress: 72%. Estimated remaining time: 12 minutes, 20 seconds.
## Growing trees.. Progress: 73%. Estimated remaining time: 11 minutes, 48 seconds.
## Growing trees.. Progress: 75%. Estimated remaining time: 11 minutes, 18 seconds.
## Growing trees.. Progress: 76%. Estimated remaining time: 10 minutes, 46 seconds.
## Growing trees.. Progress: 77%. Estimated remaining time: 10 minutes, 15 seconds.
## Growing trees.. Progress: 78%. Estimated remaining time: 9 minutes, 44 seconds.
## Growing trees.. Progress: 79%. Estimated remaining time: 9 minutes, 13 seconds.
## Growing trees.. Progress: 80%. Estimated remaining time: 8 minutes, 41 seconds.
## Growing trees.. Progress: 82%. Estimated remaining time: 8 minutes, 10 seconds.
## Growing trees.. Progress: 83%. Estimated remaining time: 7 minutes, 40 seconds.
## Growing trees.. Progress: 84%. Estimated remaining time: 7 minutes, 8 seconds.
## Growing trees.. Progress: 85%. Estimated remaining time: 6 minutes, 36 seconds.
## Growing trees.. Progress: 86%. Estimated remaining time: 6 minutes, 4 seconds.
## Growing trees.. Progress: 88%. Estimated remaining time: 5 minutes, 32 seconds.
## Growing trees.. Progress: 89%. Estimated remaining time: 5 minutes, 0 seconds.
## Growing trees.. Progress: 90%. Estimated remaining time: 4 minutes, 29 seconds.
## Growing trees.. Progress: 91%. Estimated remaining time: 3 minutes, 57 seconds.
## Growing trees.. Progress: 92%. Estimated remaining time: 3 minutes, 24 seconds.
## Growing trees.. Progress: 94%. Estimated remaining time: 2 minutes, 52 seconds.
## Growing trees.. Progress: 95%. Estimated remaining time: 2 minutes, 21 seconds.
## Growing trees.. Progress: 96%. Estimated remaining time: 1 minute, 48 seconds.
## Growing trees.. Progress: 97%. Estimated remaining time: 1 minute, 18 seconds.
## Growing trees.. Progress: 98%. Estimated remaining time: 44 seconds.
## Growing trees.. Progress: 100%. Estimated remaining time: 12 seconds.
## Computing prediction error.. Progress: 13%. Estimated remaining time: 3 minutes, 22 seconds.
## Computing prediction error.. Progress: 27%. Estimated remaining time: 2 minutes, 50 seconds.
## Computing prediction error.. Progress: 40%. Estimated remaining time: 2 minutes, 19 seconds.
## Computing prediction error.. Progress: 53%. Estimated remaining time: 1 minute, 48 seconds.
## Computing prediction error.. Progress: 67%. Estimated remaining time: 1 minute, 17 seconds.
## Computing prediction error.. Progress: 80%. Estimated remaining time: 46 seconds.
## Computing prediction error.. Progress: 93%. Estimated remaining time: 15 seconds.#show results
prediction## selected model votes model1 votes model2 votes model3
## 1 all.wood.guidetree_11_MSFS 15 444 33
## 2 all.wood.guidetree_11_MSFS 15 444 33
## 3 all.wood.guidetree_11_MSFS 15 444 33
## votes model4 votes model5 votes model6 votes model7 votes model8 votes model9
## 1 293 409 107 33 126 66
## 2 293 409 107 33 126 66
## 3 293 409 107 33 126 66
## votes model10 votes model11 votes model12 votes model13 votes model14
## 1 158 451 110 326 45
## 2 158 451 110 326 45
## 3 158 451 110 326 45
## votes model15 votes model16 votes model17 votes model18 votes model19
## 1 412 40 199 146 205
## 2 412 40 199 146 205
## 3 412 40 199 146 205
## votes model20 votes model21 votes model22 votes model23 votes model24
## 1 351 36 274 22 51
## 2 351 36 274 22 51
## 3 351 36 274 22 51
## votes model25 votes model26 votes model27 votes model28 post.proba
## 1 283 150 76 139 0.7639233
## 2 283 150 76 139 0.7639233
## 3 283 150 76 139 0.7639233#write results to file
write.csv(as.matrix(prediction), file="prediction.csv")
#write out model info to screen
files <- list.files(pattern = "*.tpl")
for (i in files){
cat(i,readLines(i),"\n","\n")
}## all.wood.guidetree_1.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 2 historical event 0 0 1 1 1 0 keep 0 1 2 1 1 0 keep //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_10.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 MIG1$ 0 0 MIG2$ MIG1$ MIG2$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 1 1 1 0 keep Tdiv2$ 1 2 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_11.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 2 historical event 0 0 2 1 1 0 keep Tdiv2$ 2 1 1 1 0 keep //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_12.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 0 0 0 MIG1$ 0 MIG1$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event 0 0 2 1 1 0 keep Tdiv2$ 2 1 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_13.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 2 historical event Tdiv1$ 0 2 1 1 0 keep Tdiv2$ 2 1 1 1 0 keep //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_14.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 MIG1$ 0 MIG1$ 0 0 0 0 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 2 1 1 0 keep Tdiv2$ 2 1 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_15.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 MIG1$ 0 0 0 MIG1$ 0 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 2 1 1 0 keep Tdiv2$ 2 1 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_16.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 0 0 0 MIG1$ 0 MIG1$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 2 1 1 0 keep Tdiv2$ 2 1 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_17.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 MIG1$ MIG2$ MIG1$ 0 0 MIG2$ 0 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 2 1 1 0 keep Tdiv2$ 2 1 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_18.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 MIG1$ 0 MIG1$ 0 MIG2$ 0 MIG2$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 2 1 1 0 keep Tdiv2$ 2 1 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_19.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 MIG1$ 0 0 MIG2$ MIG1$ MIG2$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 2 1 1 0 keep Tdiv2$ 2 1 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_2.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 2 historical event 0 0 1 1 1 0 keep Tdiv2$ 1 2 1 1 0 keep //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_20.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 2 historical event 0 1 2 1 1 0 keep Tdiv2$ 2 0 1 1 0 keep //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_21.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 MIG1$ 0 0 0 MIG1$ 0 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event 0 1 2 1 1 0 keep Tdiv2$ 2 0 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_22.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 2 historical event Tdiv1$ 1 2 1 1 0 keep Tdiv2$ 2 0 1 1 0 keep //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_23.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 MIG1$ 0 MIG1$ 0 0 0 0 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 1 2 1 1 0 keep Tdiv2$ 2 0 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_24.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 MIG1$ 0 0 0 MIG1$ 0 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 1 2 1 1 0 keep Tdiv2$ 2 0 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_25.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 0 0 0 MIG1$ 0 MIG1$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 1 2 1 1 0 keep Tdiv2$ 2 0 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_26.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 MIG1$ MIG2$ MIG1$ 0 0 MIG2$ 0 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 1 2 1 1 0 keep Tdiv2$ 2 0 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_27.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 MIG1$ 0 MIG1$ 0 MIG2$ 0 MIG2$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 1 2 1 1 0 keep Tdiv2$ 2 0 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_28.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 MIG1$ 0 0 MIG2$ MIG1$ MIG2$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 1 2 1 1 0 keep Tdiv2$ 2 0 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_3.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 0 0 0 MIG1$ 0 MIG1$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event 0 0 1 1 1 0 keep Tdiv2$ 1 2 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_4.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 2 historical event Tdiv1$ 0 1 1 1 0 keep Tdiv2$ 1 2 1 1 0 keep //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_5.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 MIG1$ 0 MIG1$ 0 0 0 0 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 1 1 1 0 keep Tdiv2$ 1 2 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_6.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 MIG1$ 0 0 0 MIG1$ 0 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 1 1 1 0 keep Tdiv2$ 1 2 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_7.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 0 0 0 0 MIG1$ 0 MIG1$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 1 1 1 0 keep Tdiv2$ 1 2 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_8.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 MIG1$ MIG2$ MIG1$ 0 0 MIG2$ 0 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 1 1 1 0 keep Tdiv2$ 1 2 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##
## all.wood.guidetree_9.tpl //Number of population samples (demes) 3 //Population effective sizes (number of genes) N0$ N1$ N2$ //Sample sizes 28 10 24 //Growth rates: negative growth implies population expansion 0 0 0 //Number of migration matrices : 0 implies no migration between demes 2 //migrationmatrix 0 0 0 0 0 0 0 0 0 //migrationmatrix 0 MIG1$ 0 MIG1$ 0 MIG2$ 0 MIG2$ 0 //historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event Tdiv1$ 0 1 1 1 0 keep Tdiv2$ 1 2 1 1 0 keep 0 0 0 0 1 0 1 Tmig1end$ 0 0 0 1 0 0 //Number of independent loci [chromosome] 1278 //Per chromosome: Number of linkage blocks 1 //per Block: data type, num loc. rec. rate and mut rate + optional paramters SNP 1 0 0 0.01
##