Using secsse with complete phylogenies (with extinction)
Pedro Santos Neves
2025-10-13
Source:vignettes/complete_tree.Rmd
complete_tree.RmdIntroduction
Most current studies of evolutionary dynamics make use of molecular phylogenies, which, for most groups, contain only information on extant species. However, when data on extinct species is available, usually through the presence of fossil data, we can use complete trees. Thus, we can leverage the data from extinct lineages for maximum-likelihood estimation with secsse.
Note that here “complete tree” should not be taken as a complete sampling fraction, that is, all known species being present in the phylogeny and there being no missing data, but rather the assumption that all currently extinct species are included. This follows the nomenclature of Nee et al. (1994), who also coined the term “reconstructed tree” for phylogenies for which there is no information on extinct lineages.
Set-up
Like all ML analyses with secsse, we first need a few things to start
with, starting with a dated phylogeny. For the purpose of this vignette,
we are going to simulate phylogenies with secsse_sim(). We
will simulate a reconstructed and a complete version of the same tree
under the CR model.
In order to simulate the trees, we need to specify the model and set
starting parameters. Here we simulate a similar constant rate (CR)
example to that of the Simulating with secsse vignette. For
more details on this model and full details of the functionality of
secsse_sim(), see
vignette("sim_with_secsse", package = "secsse").
library(secsse)
spec_matrix <- c()
spec_matrix <- rbind(spec_matrix, c(0, 0, 0, 1))
spec_matrix <- rbind(spec_matrix, c(1, 1, 1, 1))
lambda_list <- secsse::create_lambda_list(state_names = c(0, 1),
num_concealed_states = 2,
transition_matrix = spec_matrix,
model = "CR")
mu_vector <- secsse::create_mu_vector(state_names = c(0, 1),
num_concealed_states = 2,
model = "CR",
lambda_list = lambda_list)
shift_matrix <- c()
shift_matrix <- rbind(shift_matrix, c(0, 1, 3))
shift_matrix <- rbind(shift_matrix, c(1, 0, 4))
q_matrix <- secsse::create_q_matrix(state_names = c(0, 1),
num_concealed_states = 2,
shift_matrix = shift_matrix,
diff.conceal = FALSE)
# Set-up starting parameters
speciation_rate <- 0.8
extinction_rate <- 0.2
q_01 <- 0.1
q_10 <- 0.1
used_params <- c(speciation_rate, extinction_rate, q_01, q_10)
sim_lambda_list <- secsse::fill_in(lambda_list, used_params)
sim_mu_vector <- secsse::fill_in(mu_vector, used_params)
sim_q_matrix <- secsse::fill_in(q_matrix, used_params)
# Simulate and plot the tree
sim_tree_complete <- secsse::secsse_sim(lambdas = sim_lambda_list,
mus = sim_mu_vector,
qs = sim_q_matrix,
crown_age = 5,
num_concealed_states = 2,
seed = 40,
drop_extinct = FALSE)
if (requireNamespace("diversitree")) {
traits_for_plot_complete <- data.frame(
trait = as.numeric(sim_tree_complete$obs_traits),
row.names = sim_tree_complete$phy$tip.label
)
diversitree::trait.plot(tree = sim_tree_complete$phy,
dat = traits_for_plot_complete,
cols = list("trait" = c("blue", "red")),
type = "p")
} else {
plot(sim_tree_complete$phy)
}
#> Loading required namespace: diversitree
Fitting the model
Finally, we run secsse_ml() on our complete tree, much
in the same way as we would for one with extant species. However, this
time we make sure to set the is_complete_tree argument to
TRUE (defaults to FALSE if omitted). This
enables secsse to use the information present in extinct lineages.
idparsopt <- 1:4 # our maximum rate parameter was 4 -> We are keeping
# concealed and examined traits the same for the MLE.
idparsfix <- c(0) # we want to keep all zeros at zero
initparsopt <- rep(0.1, 4)
initparsfix <- c(0.0) # all zeros remain at zero.
sampling_fraction <- c(1, 1)
idparslist <- list()
idparslist[[1]] <- lambda_list
idparslist[[2]] <- mu_vector
idparslist[[3]] <- q_matrix
complete_tree_ml_CR <- secsse_ml(phy = sim_tree_complete$phy,
traits = sim_tree_complete$obs_traits,
num_concealed_states = 2,
idparslist = idparslist,
idparsopt = idparsopt,
initparsopt = initparsopt,
idparsfix = idparsfix,
parsfix = initparsfix,
sampling_fraction = sampling_fraction,
verbose = FALSE)
#> Note: you set some transitions as impossible to happen.
#> 1 0.1 0.1 0.1 0.1 -226.053144072171 initial
#> 2 0.105 0.1 0.1 0.1 -222.624992789665 reflect
#> 3 0.105 0.1 0.1 0.1 -222.624992789665 reflect
#> 4 0.10846394984326 0.0944288126055149 0.10846394984326 0.0990675332014694 -219.965808429334 expand
#> 5 0.114897886062343 0.0902873160476524 0.101011959521619 0.0983692199082245 -215.726427815449 expand
#> 6 0.114897886062343 0.0902873160476524 0.101011959521619 0.0983692199082245 -215.726427815449 reflect
#> 7 0.124172002998582 0.0905356861233287 0.102660370839572 0.101313961616394 -210.395261485277 expand
#> 8 0.136331330154724 0.0787355101510194 0.112245294610444 0.0948548055460873 -203.330536909212 expand
#> 9 0.136331330154724 0.0787355101510194 0.112245294610444 0.0948548055460873 -203.330536909212 reflect
#> 10 0.157463962842126 0.0655976490744996 0.104834174336294 0.103698336063287 -193.028018234305 expand
#> 11 0.188580384493981 0.0584948324319094 0.11398400869047 0.0996649403718381 -181.130224277722 expand
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#> 17 0.290567786992314 0.0104768915751455 0.13578248786944 0.109885889970718 -154.238752592333 contract inside
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#> 37 0.361306082996556 0.00210566130103047 0.142307910206395 0.105020910393752 -143.428094610213 expand
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#> 141 1.18015620480503 0.593313837489484 0.134707172315066 0.302603849165442 -119.030691710359 expand
#> 142 1.18015620480503 0.593313837489484 0.134707172315066 0.302603849165442 -119.030691710359 contract outside
#> 143 1.13905110617649 0.537990190207286 0.127643237142019 0.276731132560106 -119.030496273459 reflect
#> 144 1.13905110617649 0.537990190207286 0.127643237142019 0.276731132560106 -119.030496273459 reflect
#> 145 1.1839026845525 0.591688997847642 0.131113994881961 0.296632063312233 -119.018733303153 reflect
#> 146 1.1839026845525 0.591688997847642 0.131113994881961 0.296632063312233 -119.018733303153 contract outside
#> 147 1.1839026845525 0.591688997847642 0.131113994881961 0.296632063312233 -119.018733303153 contract inside
#> 148 1.16299382930346 0.568071141889172 0.12655415510746 0.283687719619061 -119.014244591286 reflect
#> 149 1.16299382930346 0.568071141889172 0.12655415510746 0.283687719619061 -119.014244591286 contract outside
#> 150 1.16299382930346 0.568071141889172 0.12655415510746 0.283687719619061 -119.014244591286 reflect
#> 151 1.18183859412282 0.583371565670755 0.127467293219699 0.288699430560235 -119.012486905491 reflect
#> 152 1.18183859412282 0.583371565670755 0.127467293219699 0.288699430560235 -119.012486905491 reflect
#> 153 1.18183859412282 0.583371565670755 0.127467293219699 0.288699430560235 -119.012486905491 contract outside
#> 154 1.18183859412282 0.583371565670755 0.127467293219699 0.288699430560235 -119.012486905491 reflect
#> 155 1.18183859412282 0.583371565670755 0.127467293219699 0.288699430560235 -119.012486905491 reflect
#> 156 1.18663933756348 0.590599257348817 0.126274129101747 0.289064228335955 -119.010566853208 reflect
#> 157 1.18663933756348 0.590599257348817 0.126274129101747 0.289064228335955 -119.010566853208 contract inside
#> 158 1.18663933756348 0.590599257348817 0.126274129101747 0.289064228335955 -119.010566853208 reflect
#> 159 1.18663933756348 0.590599257348817 0.126274129101747 0.289064228335955 -119.010566853208 reflect
#> 160 1.18229285458931 0.593270608850708 0.124963414420486 0.288754494082214 -119.00914687766 reflect
#> 161 1.18229285458931 0.593270608850708 0.124963414420486 0.288754494082214 -119.00914687766 contract inside
#> 162 1.18229285458931 0.593270608850708 0.124963414420486 0.288754494082214 -119.00914687766 contract outside
#> 163 1.18229285458931 0.593270608850708 0.124963414420486 0.288754494082214 -119.00914687766 contract inside
#> 164 1.18229285458931 0.593270608850708 0.124963414420486 0.288754494082214 -119.00914687766 contract inside
#> 165 1.18229285458931 0.593270608850708 0.124963414420486 0.288754494082214 -119.00914687766 reflect
#> 166 1.18229285458931 0.593270608850708 0.124963414420486 0.288754494082214 -119.00914687766 reflect
#> 167 1.18389979992006 0.591665295314289 0.124521329443114 0.287354525305092 -119.008855015692 reflect
#> 168 1.18389979992006 0.591665295314289 0.124521329443114 0.287354525305092 -119.008855015692 reflect
#> 169 1.18389979992006 0.591665295314289 0.124521329443114 0.287354525305092 -119.008855015692 contract outside
#> 170 1.18389979992006 0.591665295314289 0.124521329443114 0.287354525305092 -119.008855015692 reflect
#> 171 1.18389979992006 0.591665295314289 0.124521329443114 0.287354525305092 -119.008855015692 reflect
#> 172 1.18534298990503 0.595492141648686 0.124161978444791 0.288098930328376 -119.00883310488 contract outside
#> 173 1.18102461960129 0.588257957962216 0.124227791828297 0.285903469394202 -119.008733808586 reflect
#> 174 1.18102461960129 0.588257957962216 0.124227791828297 0.285903469394202 -119.008733808586 contract outside
#> 175 1.18102461960129 0.588257957962216 0.124227791828297 0.285903469394202 -119.008733808586 contract inside
#> 176 1.18102461960129 0.588257957962216 0.124227791828297 0.285903469394202 -119.008733808586 reflect
#> 177 1.18102461960129 0.588257957962216 0.124227791828297 0.285903469394202 -119.008733808586 contract inside
#> 178 1.18102461960129 0.588257957962216 0.124227791828297 0.285903469394202 -119.008733808586 reflect
#> 179 1.18163137432161 0.591020147519972 0.124281246893238 0.286833875875913 -119.008674763936 expand
#> 180 1.18163137432161 0.591020147519972 0.124281246893238 0.286833875875913 -119.008674763936 reflect
#> 181 1.18163137432161 0.591020147519972 0.124281246893238 0.286833875875913 -119.008674763936 contract inside
#> 182 1.18040731012604 0.587831584993564 0.124262122156054 0.285744656767106 -119.008659331507 reflect
#> 183 1.1838089688506 0.593958049914604 0.123916352644397 0.287120039134702 -119.008595141927 expand
#> 184 1.1838089688506 0.593958049914604 0.123916352644397 0.287120039134702 -119.008595141927 reflect
#> 185 1.1838089688506 0.593958049914604 0.123916352644397 0.287120039134702 -119.008595141927 reflect
#> 186 1.18108301110908 0.590566402626596 0.123853488108084 0.285886526969845 -119.008449690196 expand
#> 187 1.18108301110908 0.590566402626596 0.123853488108084 0.285886526969845 -119.008449690196 reflect
#> 188 1.18108301110908 0.590566402626596 0.123853488108084 0.285886526969845 -119.008449690196 reflect
#> 189 1.18108301110908 0.590566402626596 0.123853488108084 0.285886526969845 -119.008449690196 reflect
#> 190 1.18126624403249 0.590765346314271 0.123929021107902 0.285682759100823 -119.00812363323 expand
#> 191 1.18126624403249 0.590765346314271 0.123929021107902 0.285682759100823 -119.00812363323 reflect
#> 192 1.18126624403249 0.590765346314271 0.123929021107902 0.285682759100823 -119.00812363323 reflect
#> 193 1.18126624403249 0.590765346314271 0.123929021107902 0.285682759100823 -119.00812363323 reflect
#> 194 1.17701554760984 0.58204569973376 0.124198056368901 0.28288868268641 -119.008090002144 expand
#> 195 1.18166207624503 0.588990667655862 0.123042058121046 0.283367746936406 -119.007792998399 expand
#> 196 1.17677097193283 0.585269353601853 0.123472332752349 0.282300854666181 -119.007357588763 expand
#> 197 1.18078459194942 0.58737696171985 0.123527213521649 0.282472529887513 -119.006803468722 expand
#> 198 1.18078459194942 0.58737696171985 0.123527213521649 0.282472529887513 -119.006803468722 reflect
#> 199 1.18302415562449 0.592992742486755 0.121532265508384 0.280212088167685 -119.006485895014 expand
#> 200 1.17475328390074 0.582056187857021 0.122706083878624 0.276905945396904 -119.00464709958 expand
#> 201 1.17475328390074 0.582056187857021 0.122706083878624 0.276905945396904 -119.00464709958 reflect
#> 202 1.18592992584814 0.599588013906333 0.120948474570743 0.278057590333724 -119.00425545771 expand
#> 203 1.18151856510018 0.593128597011786 0.120073656237595 0.273851968978201 -119.003845019521 reflect
#> 204 1.17629226721776 0.584886379264436 0.121233309203965 0.269308717676867 -118.999316847186 expand
#> 205 1.17629226721776 0.584886379264436 0.121233309203965 0.269308717676867 -118.999316847186 reflect
#> 206 1.17629226721776 0.584886379264436 0.121233309203965 0.269308717676867 -118.999316847186 reflect
#> 207 1.16999677277372 0.582009936622804 0.118439863923735 0.257346409295215 -118.996936299859 expand
#> 208 1.17011322951688 0.586429146191164 0.11895972325627 0.253308365943551 -118.992012616234 expand
#> 209 1.17011322951688 0.586429146191164 0.11895972325627 0.253308365943551 -118.992012616234 reflect
#> 210 1.15177509073242 0.556455455552318 0.118689691051483 0.234532405855552 -118.989392668871 expand
#> 211 1.15177509073242 0.556455455552318 0.118689691051483 0.234532405855552 -118.989392668871 reflect
#> 212 1.15177509073242 0.556455455552318 0.118689691051483 0.234532405855552 -118.989392668871 reflect
#> 213 1.14187782225646 0.555546451777078 0.114025624780965 0.201712896753061 -118.984840194681 expand
#> 214 1.14187782225646 0.555546451777078 0.114025624780965 0.201712896753061 -118.984840194681 contract inside
#> 215 1.1487062718407 0.554526577972081 0.118213583314406 0.215248227546343 -118.978848733701 expand
#> 216 1.1487062718407 0.554526577972081 0.118213583314406 0.215248227546343 -118.978848733701 reflect
#> 217 1.14881130412639 0.57103062698951 0.111753102848159 0.184311472829843 -118.975215617431 expand
#> 218 1.14881130412639 0.57103062698951 0.111753102848159 0.184311472829843 -118.975215617431 reflect
#> 219 1.15813534461802 0.568295162148681 0.114265366733577 0.184077234809279 -118.956837516369 expand
#> 220 1.15813534461802 0.568295162148681 0.114265366733577 0.184077234809279 -118.956837516369 reflect
#> 221 1.15813534461802 0.568295162148681 0.114265366733577 0.184077234809279 -118.956837516369 reflect
#> 222 1.17085560142166 0.601051345833555 0.111418832676128 0.160698917181692 -118.947082693364 expand
#> 223 1.16505282059051 0.580834539179159 0.110452438680749 0.118343255800559 -118.935001230262 expand
#> 224 1.16505282059051 0.580834539179159 0.110452438680749 0.118343255800559 -118.935001230262 reflect
#> 225 1.1913336128603 0.609244272050412 0.114124816237998 0.154140915879873 -118.928919477033 reflect
#> 226 1.19240373572685 0.620203416099888 0.112504131117956 0.120744003849573 -118.925318819902 reflect
#> 227 1.19240373572685 0.620203416099888 0.112504131117956 0.120744003849573 -118.925318819902 reflect
#> 228 1.19240373572685 0.620203416099888 0.112504131117956 0.120744003849573 -118.925318819902 reflect
#> 229 1.19240373572685 0.620203416099888 0.112504131117956 0.120744003849573 -118.925318819902 reflect
#> 230 1.19240373572685 0.620203416099888 0.112504131117956 0.120744003849573 -118.925318819902 reflect
#> 231 1.20896679188731 0.633302273221952 0.113277748285212 0.121106461036005 -118.92399049454 contract inside
#> 232 1.19655872644949 0.61977643213112 0.11259265492475 0.132412827558764 -118.923970025073 contract inside
#> 233 1.19655872644949 0.61977643213112 0.11259265492475 0.132412827558764 -118.923970025073 contract inside
#> 234 1.19655872644949 0.61977643213112 0.11259265492475 0.132412827558764 -118.923970025073 contract inside
#> 235 1.21165212958324 0.636048950148585 0.111073061029989 0.116320549216109 -118.923050038551 reflect
#> 236 1.20401647097165 0.632171292978038 0.111283921037522 0.117533397631762 -118.923049371942 contract inside
#> 237 1.201772144216 0.626660994984657 0.111329828647672 0.113005246433372 -118.922969665202 contract inside
#> 238 1.201772144216 0.626660994984657 0.111329828647672 0.113005246433372 -118.922969665202 reflect
#> 239 1.20020195968437 0.624727319700692 0.111739686267592 0.124308582607437 -118.92296723633 contract inside
#> 240 1.20121302685229 0.62694312146498 0.110611073513362 0.118105349710212 -118.922916671486 contract inside
#> 241 1.20671507528656 0.631824098219607 0.111157014137018 0.117271306428198 -118.922655757392 contract inside
#> 242 1.20093107158042 0.622924337438533 0.111134594878587 0.118783439525082 -118.922649125603 reflect
#> 243 1.20093107158042 0.622924337438533 0.111134594878587 0.118783439525082 -118.922649125603 contract inside
#> 244 1.20093107158042 0.622924337438533 0.111134594878587 0.118783439525082 -118.922649125603 reflect
#> 245 1.20093107158042 0.622924337438533 0.111134594878587 0.118783439525082 -118.922649125603 contract outside
#> 246 1.20286979757809 0.626321968665357 0.111589099448687 0.119663642092529 -118.92264247094 contract outside
#> 247 1.20286979757809 0.626321968665357 0.111589099448687 0.119663642092529 -118.92264247094 reflect
#> 248 1.20451913218164 0.627656998959478 0.111216739742733 0.116672090611331 -118.922601422571 contract inside
#> 249 1.20511180995663 0.629010017299946 0.11122957948499 0.117887876113529 -118.922590043623 contract inside
#> 250 1.20274255313491 0.625323079324118 0.111230242256564 0.118532269772716 -118.922589738891 contract inside
#> 251 1.20274255313491 0.625323079324118 0.111230242256564 0.118532269772716 -118.922589738891 contract inside
#> 252 1.20274255313491 0.625323079324118 0.111230242256564 0.118532269772716 -118.922589738891 contract outside
#> 253 1.20428884628395 0.627207674297252 0.111193763882451 0.119330856285375 -118.922581839277 reflect
#> 254 1.2037984678448 0.627214293046893 0.111068900754876 0.117844759642631 -118.922572559729 reflect
#> 255 1.2037984678448 0.627214293046893 0.111068900754876 0.117844759642631 -118.922572559729 contract inside
#> 256 1.2037984678448 0.627214293046893 0.111068900754876 0.117844759642631 -118.922572559729 contract inside
#> 257 1.2037984678448 0.627214293046893 0.111068900754876 0.117844759642631 -118.922572559729 contract inside
#> 258 1.2037984678448 0.627214293046893 0.111068900754876 0.117844759642631 -118.922572559729 contract inside
#> 259 1.2037984678448 0.627214293046893 0.111068900754876 0.117844759642631 -118.922572559729 contract inside
#> 260 1.2037984678448 0.627214293046893 0.111068900754876 0.117844759642631 -118.922572559729 contract inside
#> 261 1.2037984678448 0.627214293046893 0.111068900754876 0.117844759642631 -118.922572559729 reflect
#> 262 1.20369684850428 0.626861397978246 0.111085305503206 0.117803653033344 -118.922572027484 contract outside
#> 263 1.20372347682502 0.626770377399411 0.111096776871494 0.118123033445439 -118.922571831734 contract inside
#> 264 1.20372347682502 0.626770377399411 0.111096776871494 0.118123033445439 -118.922571831734 reflect
#> 265 1.20400786640976 0.627187967993156 0.111104911107502 0.117915512749141 -118.922571213737 contract inside
#> 266 1.20400786640976 0.627187967993156 0.111104911107502 0.117915512749141 -118.922571213737 contract outside
#> 267 1.20403776479867 0.62716232908723 0.11107299461899 0.117952993788391 -118.922571059043 reflect
#> 268 1.20403776479867 0.62716232908723 0.11107299461899 0.117952993788391 -118.922571059043 contract inside
#> 269 1.20403776479867 0.62716232908723 0.11107299461899 0.117952993788391 -118.922571059043 contract outside
#> 270 1.20415557436473 0.627449354927478 0.111070721314223 0.117836547025389 -118.922571045077 reflect
#> 271 1.20402274204359 0.627213271505334 0.111087000922256 0.117874560712197 -118.922571004917 contract inside
#> 272 1.20399769423173 0.62721706669071 0.111072834247118 0.117964674625156 -118.922570846308 reflect
#> 273 1.20399769423173 0.62721706669071 0.111072834247118 0.117964674625156 -118.922570846308 contract inside
#> 274 1.20399769423173 0.62721706669071 0.111072834247118 0.117964674625156 -118.922570846308 contract inside
#> 275 1.20399769423173 0.62721706669071 0.111072834247118 0.117964674625156 -118.922570846308 contract inside
#> 276 1.20399769423173 0.62721706669071 0.111072834247118 0.117964674625156 -118.922570846308 reflect
#> 277 1.20399769423173 0.62721706669071 0.111072834247118 0.117964674625156 -118.922570846308 reflect
#> 278 1.20399769423173 0.62721706669071 0.111072834247118 0.117964674625156 -118.922570846308 contract outside
#> 279 1.20399769423173 0.62721706669071 0.111072834247118 0.117964674625156 -118.922570846308 reflect
#> 280 1.20399769423173 0.62721706669071 0.111072834247118 0.117964674625156 -118.922570846308 reflect
#> 281 1.20399940063899 0.627234596962633 0.11108145361411 0.117976262857979 -118.922570841295 reflect
#> 282 1.20403852997753 0.627269414276962 0.111076577349176 0.118012159433761 -118.922570834691 contract inside
#> 283 1.20404878369069 0.627275103468104 0.111078328777441 0.117960327819312 -118.922570830493 contract inside
#> 284 1.20404878369069 0.627275103468104 0.111078328777441 0.117960327819312 -118.922570830493 contract inside
#> 285 1.20404878369069 0.627275103468104 0.111078328777441 0.117960327819312 -118.922570830493 reflect
#> 286 1.20402612374377 0.627264230292705 0.111079984454828 0.117980655510596 -118.922570826327 contract inside
#> 287 1.20402612374377 0.627264230292705 0.111079984454828 0.117980655510596 -118.922570826327 contract inside
#> 288 1.20404223961105 0.627278071795187 0.111077622759176 0.117993764652386 -118.92257082578 contract inside
#> 289 1.20404223961105 0.627278071795187 0.111077622759176 0.117993764652386 -118.92257082578 reflect
#> 290 1.20403545193751 0.627274310823728 0.111080997619586 0.118002035745941 -118.922570824978 contract outside
#> 291 1.20403735650304 0.627266843866782 0.1110810555686 0.117990427024256 -118.9225708243 contract inside
#> 292 1.20404595373283 0.627286407961984 0.111080200802237 0.117990107553166 -118.922570824297 contract inside
#> 293 1.20403318706845 0.627270319414269 0.111079976820236 0.117987369576601 -118.922570824136 contract inside
#> 294 1.20404011345341 0.627276271137206 0.11107909022888 0.117993124799092 -118.922570823949 contract inside
#> 295 1.20404100305542 0.627275285430181 0.111079622472597 0.117984368071943 -118.922570823674 contract outside
#> 296 1.20403871040975 0.627271957399785 0.111080389074315 0.117989584756888 -118.922570823615 contract inside
#> 297 1.20403871040975 0.627271957399785 0.111080389074315 0.117989584756888 -118.922570823615 reflect
#> 298 1.20403871040975 0.627271957399785 0.111080389074315 0.117989584756888 -118.922570823615 contract inside
#> 299 1.20403467889115 0.627267026501592 0.111079531150185 0.117987937589761 -118.922570823601 contract inside
#> 300 1.20403877965098 0.627273752048068 0.111079462131892 0.117990293566972 -118.922570823551 contract inside
#> 301 1.20403894652601 0.627273067523487 0.111079708211271 0.117986655893919 -118.922570823525 contract inside
#> 302 1.20403897277586 0.62727184501782 0.111079762240733 0.117988947429823 -118.922570823524 contract outside
#> 303 1.20403827743453 0.627271690084097 0.111080002503776 0.117989021687423 -118.922570823512 contract inside
#> 304 1.20403671149211 0.627269807580001 0.111079632461026 0.117988333616238 -118.922570823511 contract inside
#> 305 1.20403850335383 0.627272677298582 0.111079619243016 0.117989266610562 -118.92257082349 contract inside
#> 306 1.20403850335383 0.627272677298582 0.111079619243016 0.117989266610562 -118.92257082349 contract inside
#> 307 1.20403850335383 0.627272677298582 0.111079619243016 0.117989266610562 -118.92257082349 reflect
#> 308 1.20403850335383 0.627272677298582 0.111079619243016 0.117989266610562 -118.92257082349 contract inside
#> 309 1.20403850335383 0.627272677298582 0.111079619243016 0.117989266610562 -118.92257082349 reflect
#> 310 1.20403781209111 0.627272036858426 0.111079742595911 0.11798842825427 -118.92257082349 contract inside
#> 311 1.20403876364202 0.627273164038462 0.111079780762577 0.117988607375506 -118.922570823489 contract inside
#> 312 1.20403876364202 0.627273164038462 0.111079780762577 0.117988607375506 -118.922570823489 reflect
#> 313 1.20403812852436 0.627272099609996 0.111079783076327 0.117988861507853 -118.922570823484 contract inside
#> 314 1.20403812852436 0.627272099609996 0.111079783076327 0.117988861507853 -118.922570823484 contract inside
#> 315 1.20403812852436 0.627272099609996 0.111079783076327 0.117988861507853 -118.922570823484 reflect
#> 316 1.20403812852436 0.627272099609996 0.111079783076327 0.117988861507853 -118.922570823484 contract inside
#> 317 1.20403812852436 0.627272099609996 0.111079783076327 0.117988861507853 -118.922570823484 contract outside
#> 318 1.20403851677264 0.627272746798799 0.111079754078884 0.117989476650369 -118.922570823484 contract inside
#> 319 1.20403825077114 0.627272401375816 0.111079740836903 0.117989401447484 -118.922570823483 contract inside
#> 320 1.20403825077114 0.627272401375816 0.111079740836903 0.117989401447484 -118.922570823483 reflect
#> 321 1.20403825077114 0.627272401375816 0.111079740836903 0.117989401447484 -118.922570823483 reflect
#> 322 1.20403824170692 0.62727225909659 0.111079770554468 0.117989078148193 -118.922570823483 contract inside
#> 323 1.20403840144785 0.627272521728211 0.111079758115194 0.117989335906706 -118.922570823483 contract inside
#> 324 1.20403840144785 0.627272521728211 0.111079758115194 0.117989335906706 -118.922570823483 reflect
#> 325 1.2040382850872 0.627272306335908 0.111079790087981 0.11798931379497 -118.922570823483 contract inside
#> 326 1.2040382850872 0.627272306335908 0.111079790087981 0.11798931379497 -118.922570823483 contract inside
#> 327 1.2040382850872 0.627272306335908 0.111079790087981 0.11798931379497 -118.922570823483 contract inside
#> 328 1.2040382734677 0.627272328860406 0.111079772920001 0.117989215909017 -118.922570823483 contract inside
#> 329 1.2040382734677 0.627272328860406 0.111079772920001 0.117989215909017 -118.922570823483 contract inside
#> 330 1.2040382734677 0.627272328860406 0.111079772920001 0.117989215909017 -118.922570823483 reflect
#> 331 1.20403828684318 0.627272370247745 0.111079766776953 0.11798931247142 -118.922570823483 contract inside
#> Optimization has terminated successfully.Now we can see what our results look like.
CR_par_complete <- secsse::extract_par_vals(idparslist, complete_tree_ml_CR$MLpars)
complete_tree_ml_CR
#> $MLpars
#> $MLpars[[1]]
#> $MLpars[[1]][[1]]
#> 0A 1A 0B 1B
#> 0A 1.204038 0 0 0
#> 1A 0.000000 0 0 0
#> 0B 0.000000 0 0 0
#> 1B 0.000000 0 0 0
#>
#> $MLpars[[1]][[2]]
#> 0A 1A 0B 1B
#> 0A 0 0.000000 0 0
#> 1A 0 1.204038 0 0
#> 0B 0 0.000000 0 0
#> 1B 0 0.000000 0 0
#>
#> $MLpars[[1]][[3]]
#> 0A 1A 0B 1B
#> 0A 0 0 0.000000 0
#> 1A 0 0 0.000000 0
#> 0B 0 0 1.204038 0
#> 1B 0 0 0.000000 0
#>
#> $MLpars[[1]][[4]]
#> 0A 1A 0B 1B
#> 0A 0 0 0 0.000000
#> 1A 0 0 0 0.000000
#> 0B 0 0 0 0.000000
#> 1B 0 0 0 1.204038
#>
#>
#> $MLpars[[2]]
#> 0A 1A 0B 1B
#> 0.6272724 0.6272724 0.6272724 0.6272724
#>
#> $MLpars[[3]]
#> 0A 1A 0B 1B
#> 0A NA 0.1110798 0.1110798 0.0000000
#> 1A 0.1179893 NA 0.0000000 0.1110798
#> 0B 0.1179893 0.0000000 NA 0.1110798
#> 1B 0.0000000 0.1179893 0.1179893 NA
#>
#>
#> $ML
#> [1] -118.9226
#>
#> $conv
#> [1] 0
CR_par_complete
#> [1] 1.2040383 0.6272724 0.1110798 0.1179893
spec_rates_complete <- CR_par_complete[1]
ext_rates_complete <- CR_par_complete[2]
Q_01_complete <- CR_par_complete[3]
Q_10_complete <- CR_par_complete[4]
spec_rates_complete
#> [1] 1.204038
ext_rates_complete
#> [1] 0.6272724
Q_01_complete
#> [1] 0.1110798
Q_10_complete
#> [1] 0.1179893Comparing with reconstructed trees
It would be interesting to see how they compare with the same tree without any extant species. Let’s follow the standard procedure using a similar phylogeny - the same tree we used before - but where all the extinct lineages have been removed. We’ll keep all other model specification the same.
sim_tree_reconstructed <- secsse::secsse_sim(lambdas = sim_lambda_list,
mus = sim_mu_vector,
qs = sim_q_matrix,
crown_age = 5,
num_concealed_states = 2,
seed = 40,
drop_extinct = TRUE)
if (requireNamespace("diversitree")) {
traits_for_plot_reconstructed <- data.frame(
trait = as.numeric(sim_tree_reconstructed$obs_traits),
row.names = sim_tree_reconstructed$phy$tip.label
)
diversitree::trait.plot(tree = sim_tree_reconstructed$phy,
dat = traits_for_plot_reconstructed,
cols = list("trait" = c("blue", "red")),
type = "p")
} else {
plot(sim_tree_reconstructed$phy)
}
reconstructed_tree_ml <- secsse_ml(phy = sim_tree_reconstructed$phy,
traits = sim_tree_reconstructed$obs_traits,
num_concealed_states = 2,
idparslist = idparslist,
idparsopt = idparsopt,
initparsopt = initparsopt,
idparsfix = idparsfix,
parsfix = initparsfix,
sampling_fraction = sampling_fraction,
verbose = FALSE,
is_complete_tree = FALSE)
#> Note: you set some transitions as impossible to happen.
#> 1 0.1 0.1 0.1 0.1 -172.875078258569 initial
#> 2 0.105 0.1 0.1 0.1 -170.344718232659 reflect
#> 3 0.105 0.1 0.1 0.1 -170.344718232659 reflect
#> 4 0.10846394984326 0.0944288126055149 0.0990675332014694 0.0947368421052632 -168.339915109481 expand
#> 5 0.114897886062343 0.0902873160476524 0.0983692199082245 0.100700389105058 -165.153351507163 expand
#> 6 0.114897886062343 0.0902873160476524 0.0983692199082245 0.100700389105058 -165.153351507163 reflect
#> 7 0.124172002998582 0.0905356861233287 0.101313961616394 0.0870592756268613 -161.269920784813 expand
#> 8 0.136331330154724 0.0787355101510194 0.0948548055460873 0.0847641977057073 -155.947949383467 expand
#> 9 0.136331330154724 0.0787355101510194 0.0948548055460873 0.0847641977057073 -155.947949383467 reflect
#> 10 0.157463962842126 0.0655976490744996 0.103698336063287 0.0778361067955936 -148.3943476587 expand
#> 11 0.188580384493981 0.0584948324319094 0.0996649403718381 0.0546113442033615 -139.747573354153 expand
#> 12 0.188580384493981 0.0584948324319094 0.0996649403718381 0.0546113442033615 -139.747573354153 reflect
#> 13 0.232811307810817 0.0269459250512547 0.104513689147747 0.0343053348823108 -129.521925125698 expand
#> 14 0.250333207168013 0.0242967293163897 0.106866374342769 0.0326053585274697 -126.598809244646 reflect
#> 15 0.275886868150326 0.0164978330464061 0.0995375741889073 0.0174820235083253 -122.600447833159 reflect
#> 16 0.290567786992314 0.0104768915751455 0.109885889970718 0.00460841097754229 -120.734216084971 reflect
#> 17 0.290567786992314 0.0104768915751455 0.109885889970718 0.00460841097754229 -120.734216084971 contract inside
#> 18 0.302225873216359 0.00107913758124338 0.107970254509982 0.00659359407478444 -119.056703161083 reflect
#> 19 0.302225873216359 0.00107913758124338 0.107970254509982 0.00659359407478444 -119.056703161083 contract inside
#> 20 0.302225873216359 0.00107913758124338 0.107970254509982 0.00659359407478444 -119.056703161083 contract inside
#> 21 0.312285510183205 0.00318560730171753 0.106518346468716 0.00125892545339878 -118.020154437063 reflect
#> 22 0.312285510183205 0.00318560730171753 0.106518346468716 0.00125892545339878 -118.020154437063 contract inside
#> 23 0.312285510183205 0.00318560730171753 0.106518346468716 0.00125892545339878 -118.020154437063 contract inside
#> 24 0.312285510183205 0.00318560730171753 0.106518346468716 0.00125892545339878 -118.020154437063 contract inside
#> 25 0.312285510183205 0.00318560730171753 0.106518346468716 0.00125892545339878 -118.020154437063 contract inside
#> 26 0.312285510183205 0.00318560730171753 0.106518346468716 0.00125892545339878 -118.020154437063 reflect
#> 27 0.312285510183205 0.00318560730171753 0.106518346468716 0.00125892545339878 -118.020154437063 contract inside
#> 28 0.312285510183205 0.00318560730171753 0.106518346468716 0.00125892545339878 -118.020154437063 contract inside
#> 29 0.312285510183205 0.00318560730171753 0.106518346468716 0.00125892545339878 -118.020154437063 contract inside
#> 30 0.312285510183205 0.00318560730171753 0.106518346468716 0.00125892545339878 -118.020154437063 contract inside
#> 31 0.311975886483372 0.000307571893640992 0.107124377998727 0.00227973406558924 -117.975927510944 reflect
#> 32 0.311975886483372 0.000307571893640992 0.107124377998727 0.00227973406558924 -117.975927510944 contract inside
#> 33 0.311975886483372 0.000307571893640992 0.107124377998727 0.00227973406558924 -117.975927510944 contract inside
#> 34 0.314300060266505 0.000524698894255259 0.107506157963815 0.000410888583939416 -117.75064463182 reflect
#> 35 0.314300060266505 0.000524698894255259 0.107506157963815 0.000410888583939416 -117.75064463182 contract inside
#> 36 0.314300060266505 0.000524698894255259 0.107506157963815 0.000410888583939416 -117.75064463182 contract inside
#> 37 0.317194250945904 1.87956244945526e-05 0.104553010277531 0.00404064250960386 -117.384010204045 expand
#> 38 0.317194250945904 1.87956244945526e-05 0.104553010277531 0.00404064250960386 -117.384010204045 reflect
#> 39 0.317194250945904 1.87956244945526e-05 0.104553010277531 0.00404064250960386 -117.384010204045 contract inside
#> 40 0.322997554822907 0.00146097635164075 0.103583162817777 0.00171460507012047 -116.833961894515 expand
#> 41 0.322997554822907 0.00146097635164075 0.103583162817777 0.00171460507012047 -116.833961894515 contract inside
#> 42 0.322997554822907 0.00146097635164075 0.103583162817777 0.00171460507012047 -116.833961894515 reflect
#> 43 0.324111649019096 0.000309011684285863 0.102051455049226 0.00431316544669658 -116.66562673292 reflect
#> 44 0.330487626127272 0.0011842616228226 0.0985226946238639 0.00659330348699666 -116.029524273779 expand
#> 45 0.340845770670618 0.00296533454250933 0.0956704973163768 0.00476529797233103 -115.099836695707 expand
#> 46 0.340845770670618 0.00296533454250933 0.0956704973163768 0.00476529797233103 -115.099836695707 reflect
#> 47 0.353600508799687 0.00185601131787818 0.0884512807407444 0.0115112868650257 -113.919369745543 expand
#> 48 0.374187627138457 0.0053385214923914 0.0814070381558836 0.0116630322366045 -112.3850620513 expand
#> 49 0.374187627138457 0.0053385214923914 0.0814070381558836 0.0116630322366045 -112.3850620513 reflect
#> 50 0.409326999036413 0.00744509145414511 0.0665341598453629 0.0198363348876671 -110.228416947083 expand
#> 51 0.455950892768664 0.00870113443738378 0.049465047583087 0.0301816367134543 -108.375444875144 expand
#> 52 0.510708991218392 0.0161715524778564 0.0348143075590543 0.0303542884215312 -107.432902730282 expand
#> 53 0.510708991218392 0.0161715524778564 0.0348143075590543 0.0303542884215312 -107.432902730282 reflect
#> 54 0.510708991218392 0.0161715524778564 0.0348143075590543 0.0303542884215312 -107.432902730282 contract outside
#> 55 0.510708991218392 0.0161715524778564 0.0348143075590543 0.0303542884215312 -107.432902730282 contract inside
#> 56 0.510708991218392 0.0161715524778564 0.0348143075590543 0.0303542884215312 -107.432902730282 reflect
#> 57 0.510708991218392 0.0161715524778564 0.0348143075590543 0.0303542884215312 -107.432902730282 contract inside
#> 58 0.510708991218392 0.0161715524778564 0.0348143075590543 0.0303542884215312 -107.432902730282 contract outside
#> 59 0.510708991218392 0.0161715524778564 0.0348143075590543 0.0303542884215312 -107.432902730282 contract inside
#> 60 0.510708991218392 0.0161715524778564 0.0348143075590543 0.0303542884215312 -107.432902730282 reflect
#> 61 0.508824741525864 0.0173008321030006 0.0374273583639574 0.0249366119432526 -107.240502132596 expand
#> 62 0.508824741525864 0.0173008321030006 0.0374273583639574 0.0249366119432526 -107.240502132596 reflect
#> 63 0.53809692841299 0.0235872326130078 0.0325625080717702 0.0187432174487847 -106.907801392802 expand
#> 64 0.53439003032128 0.0235865780197069 0.0371056639683004 0.0113027891110001 -106.525532373352 expand
#> 65 0.53439003032128 0.0235865780197069 0.0371056639683004 0.0113027891110001 -106.525532373352 reflect
#> 66 0.5340004992546 0.0266857992724508 0.0402285253811706 0.00341378806617909 -106.287169885813 reflect
#> 67 0.5340004992546 0.0266857992724508 0.0402285253811706 0.00341378806617909 -106.287169885813 contract inside
#> 68 0.5340004992546 0.0266857992724508 0.0402285253811706 0.00341378806617909 -106.287169885813 reflect
#> 69 0.5340004992546 0.0266857992724508 0.0402285253811706 0.00341378806617909 -106.287169885813 contract inside
#> 70 0.562941237119947 0.0295590257852529 0.0330667321601993 0.00434441777073942 -106.247880300005 reflect
#> 71 0.562941237119947 0.0295590257852529 0.0330667321601993 0.00434441777073942 -106.247880300005 contract inside
#> 72 0.562941237119947 0.0295590257852529 0.0330667321601993 0.00434441777073942 -106.247880300005 contract inside
#> 73 0.549205620905223 0.0289137834878741 0.0378094498323469 0.000859484302334466 -106.096460945127 reflect
#> 74 0.549205620905223 0.0289137834878741 0.0378094498323469 0.000859484302334466 -106.096460945127 contract inside
#> 75 0.549205620905223 0.0289137834878741 0.0378094498323469 0.000859484302334466 -106.096460945127 reflect
#> 76 0.559302132372207 0.0302655348062248 0.0357215956580168 5.86281638104725e-05 -106.052723006437 reflect
#> 77 0.559302132372207 0.0302655348062248 0.0357215956580168 5.86281638104725e-05 -106.052723006437 contract inside
#> 78 0.559302132372207 0.0302655348062248 0.0357215956580168 5.86281638104725e-05 -106.052723006437 contract inside
#> 79 0.559302132372207 0.0302655348062248 0.0357215956580168 5.86281638104725e-05 -106.052723006437 contract inside
#> 80 0.559302132372207 0.0302655348062248 0.0357215956580168 5.86281638104725e-05 -106.052723006437 contract inside
#> 81 0.559302132372207 0.0302655348062248 0.0357215956580168 5.86281638104725e-05 -106.052723006437 contract inside
#> 82 0.559302132372207 0.0302655348062248 0.0357215956580168 5.86281638104725e-05 -106.052723006437 contract inside
#> 83 0.559302132372207 0.0302655348062248 0.0357215956580168 5.86281638104725e-05 -106.052723006437 reflect
#> 84 0.559302132372207 0.0302655348062248 0.0357215956580168 5.86281638104725e-05 -106.052723006437 contract inside
#> 85 0.558431929933234 0.0298749441049505 0.035969651713017 0.000178842474549609 -106.046162982012 reflect
#> 86 0.558431929933234 0.0298749441049505 0.035969651713017 0.000178842474549609 -106.046162982012 contract inside
#> 87 0.558431929933234 0.0298749441049505 0.035969651713017 0.000178842474549609 -106.046162982012 contract inside
#> 88 0.558431929933234 0.0298749441049505 0.035969651713017 0.000178842474549609 -106.046162982012 contract inside
#> 89 0.558431929933234 0.0298749441049505 0.035969651713017 0.000178842474549609 -106.046162982012 contract inside
#> 90 0.558431929933234 0.0298749441049505 0.035969651713017 0.000178842474549609 -106.046162982012 contract inside
#> 91 0.558431929933234 0.0298749441049505 0.035969651713017 0.000178842474549609 -106.046162982012 contract inside
#> 92 0.558431929933234 0.0298749441049505 0.035969651713017 0.000178842474549609 -106.046162982012 reflect
#> 93 0.561368371661694 0.0302383870769221 0.0353007055702253 7.52366358815801e-05 -106.045538587714 reflect
#> 94 0.561368371661694 0.0302383870769221 0.0353007055702253 7.52366358815801e-05 -106.045538587714 contract inside
#> 95 0.561599053484838 0.0302329786535637 0.0352574096122994 6.91283987402058e-05 -106.044433427991 reflect
#> 96 0.562741724987115 0.0297760217114063 0.0350499337984652 0.000308681412717629 -106.035474210551 expand
#> 97 0.561675258994926 0.0299980590623853 0.0353256404473228 7.12649796727395e-05 -106.033895568355 reflect
#> 98 0.561675258994926 0.0299980590623853 0.0353256404473228 7.12649796727395e-05 -106.033895568355 reflect
#> 99 0.565735356417873 0.0297144209224687 0.0344970986528868 0.000248794565533596 -106.023444762285 expand
#> 100 0.568386402250843 0.029336642934724 0.0340139711140017 0.000395810793629017 -106.012660392414 expand
#> 101 0.568386402250843 0.029336642934724 0.0340139711140017 0.000395810793629017 -106.012660392414 reflect
#> 102 0.569361042404728 0.0291087219915301 0.0339862270023498 0.000241240922108158 -105.992286045712 expand
#> 103 0.569361042404728 0.0291087219915301 0.0339862270023498 0.000241240922108158 -105.992286045712 reflect
#> 104 0.573907603116341 0.0277802814642848 0.0332622207994529 0.000741785810779991 -105.96497181479 expand
#> 105 0.573907603116341 0.0277802814642848 0.0332622207994529 0.000741785810779991 -105.96497181479 reflect
#> 106 0.583275778120026 0.0267060703445391 0.0317493058039813 0.000800483777463293 -105.944342760159 expand
#> 107 0.584200072772402 0.0265763974696496 0.0317451648401504 0.000580040676680345 -105.926040090526 expand
#> 108 0.584200072772402 0.0265763974696496 0.0317451648401504 0.000580040676680345 -105.926040090526 reflect
#> 109 0.592998887532079 0.0234266153899655 0.0307340945236298 0.00130778716408751 -105.873011610949 expand
#> 110 0.592998887532079 0.0234266153899655 0.0307340945236298 0.00130778716408751 -105.873011610949 reflect
#> 111 0.592998887532079 0.0234266153899655 0.0307340945236298 0.00130778716408751 -105.873011610949 reflect
#> 112 0.610883850362527 0.019986138465943 0.0285552896670703 0.00129474742790528 -105.866509911554 expand
#> 113 0.580514383158544 0.0240954000569692 0.0332967567962473 0.000701996197915317 -105.80253497995 expand
#> 114 0.612989061634799 0.0158920320500579 0.0292691847988027 0.00193613954569016 -105.723162594669 expand
#> 115 0.612989061634799 0.0158920320500579 0.0292691847988027 0.00193613954569016 -105.723162594669 reflect
#> 116 0.623296168743568 0.0111276698628249 0.0292319156348527 0.00168197783286598 -105.582434475065 expand
#> 117 0.596399217370897 0.0112807630917696 0.0341169163210849 0.00199871238015702 -105.362262467446 expand
#> 118 0.596399217370897 0.0112807630917696 0.0341169163210849 0.00199871238015702 -105.362262467446 reflect
#> 119 0.628622629084903 0.00389238951255326 0.0304401076042553 0.0025141808960981 -105.346693286929 reflect
#> 120 0.628622629084903 0.00389238951255326 0.0304401076042553 0.0025141808960981 -105.346693286929 contract inside
#> 121 0.615464204384667 0.000817959331078692 0.0332821584292261 0.00386816223227333 -105.148256674696 expand
#> 122 0.615464204384667 0.000817959331078692 0.0332821584292261 0.00386816223227333 -105.148256674696 reflect
#> 123 0.596967101133538 0.00129712930730114 0.0370595077876801 0.00319219345572805 -105.016615189705 reflect
#> 124 0.596967101133538 0.00129712930730114 0.0370595077876801 0.00319219345572805 -105.016615189705 contract inside
#> 125 0.596967101133538 0.00129712930730114 0.0370595077876801 0.00319219345572805 -105.016615189705 reflect
#> 126 0.596967101133538 0.00129712930730114 0.0370595077876801 0.00319219345572805 -105.016615189705 contract inside
#> 127 0.596967101133538 0.00129712930730114 0.0370595077876801 0.00319219345572805 -105.016615189705 contract inside
#> 128 0.596967101133538 0.00129712930730114 0.0370595077876801 0.00319219345572805 -105.016615189705 contract inside
#> 129 0.596967101133538 0.00129712930730114 0.0370595077876801 0.00319219345572805 -105.016615189705 contract inside
#> 130 0.598750751197438 0.000266139457095902 0.0367372260899352 0.00381688165767498 -105.016462035099 reflect
#> 131 0.598750751197438 0.000266139457095902 0.0367372260899352 0.00381688165767498 -105.016462035099 contract inside
#> 132 0.598750751197438 0.000266139457095902 0.0367372260899352 0.00381688165767498 -105.016462035099 reflect
#> 133 0.598750751197438 0.000266139457095902 0.0367372260899352 0.00381688165767498 -105.016462035099 contract inside
#> 134 0.58316619219529 0.00102283422876455 0.0398093405743552 0.00333748461564549 -105.000865269074 reflect
#> 135 0.58316619219529 0.00102283422876455 0.0398093405743552 0.00333748461564549 -105.000865269074 contract inside
#> 136 0.58316619219529 0.00102283422876455 0.0398093405743552 0.00333748461564549 -105.000865269074 contract inside
#> 137 0.58316619219529 0.00102283422876455 0.0398093405743552 0.00333748461564549 -105.000865269074 contract inside
#> 138 0.58316619219529 0.00102283422876455 0.0398093405743552 0.00333748461564549 -105.000865269074 contract inside
#> 139 0.596992383635164 0.000185783373798333 0.0372604137126838 0.00356349880801285 -104.99334408057 reflect
#> 140 0.596992383635164 0.000185783373798333 0.0372604137126838 0.00356349880801285 -104.99334408057 contract inside
#> 141 0.588668984738499 5.23739788803082e-05 0.0387645403055278 0.00388072486388901 -104.990603913637 reflect
#> 142 0.588668984738499 5.23739788803082e-05 0.0387645403055278 0.00388072486388901 -104.990603913637 reflect
#> 143 0.588668984738499 5.23739788803082e-05 0.0387645403055278 0.00388072486388901 -104.990603913637 contract inside
#> 144 0.585303953281615 0.000227089202178369 0.0395547556434143 0.00356219078727876 -104.981015161808 reflect
#> 145 0.585303953281615 0.000227089202178369 0.0395547556434143 0.00356219078727876 -104.981015161808 contract inside
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#> 149 0.585303953281615 0.000227089202178369 0.0395547556434143 0.00356219078727876 -104.981015161808 reflect
#> 150 0.591126637818643 7.70334965094786e-05 0.0384993319958436 0.00348909961148044 -104.973277969986 expand
#> 151 0.592019802377596 3.46710150647972e-05 0.0384601754157396 0.00328389467219037 -104.962023991872 expand
#> 152 0.592019802377596 3.46710150647972e-05 0.0384601754157396 0.00328389467219037 -104.962023991872 reflect
#> 153 0.592019802377596 3.46710150647972e-05 0.0384601754157396 0.00328389467219037 -104.962023991872 contract inside
#> 154 0.596363572180309 0.000171995369872475 0.0378360028958919 0.00280395710788419 -104.949763762036 expand
#> 155 0.596363572180309 0.000171995369872475 0.0378360028958919 0.00280395710788419 -104.949763762036 contract inside
#> 156 0.590096778958335 0.000421670475819113 0.0392127292842967 0.0024024943123182 -104.929597506305 expand
#> 157 0.590096778958335 0.000421670475819113 0.0392127292842967 0.0024024943123182 -104.929597506305 reflect
#> 158 0.590096778958335 0.000421670475819113 0.0392127292842967 0.0024024943123182 -104.929597506305 reflect
#> 159 0.600486632033871 0.000579791258099639 0.0379017512786822 0.00106317080014912 -104.882662561769 expand
#> 160 0.600486632033871 0.000579791258099639 0.0379017512786822 0.00106317080014912 -104.882662561769 reflect
#> 161 0.600486632033871 0.000579791258099639 0.0379017512786822 0.00106317080014912 -104.882662561769 reflect
#> 162 0.594792842840427 0.000927400675141778 0.0392028807611588 0.00052672786258804 -104.856567178236 reflect
#> 163 0.594792842840427 0.000927400675141778 0.0392028807611588 0.00052672786258804 -104.856567178236 contract inside
#> 164 0.597403110521081 0.000783968941045366 0.0387954260727845 0.000441220832853511 -104.850512633526 reflect
#> 165 0.597403110521081 0.000783968941045366 0.0387954260727845 0.000441220832853511 -104.850512633526 reflect
#> 166 0.597403110521081 0.000783968941045366 0.0387954260727845 0.000441220832853511 -104.850512633526 contract inside
#> 167 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 reflect
#> 168 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 contract inside
#> 169 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 reflect
#> 170 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 reflect
#> 171 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 reflect
#> 172 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 contract inside
#> 173 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 contract inside
#> 174 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 contract inside
#> 175 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 contract inside
#> 176 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 contract inside
#> 177 0.596699648188313 0.000927125385080896 0.0390843628945253 9.49561510659955e-05 -104.836930689522 contract inside
#> 178 0.594463250304314 0.001029269916865 0.039519224255961 3.80545901887168e-05 -104.835405298645 reflect
#> 179 0.594463250304314 0.001029269916865 0.039519224255961 3.80545901887168e-05 -104.835405298645 contract inside
#> 180 0.594463250304314 0.001029269916865 0.039519224255961 3.80545901887168e-05 -104.835405298645 contract inside
#> 181 0.594463250304314 0.001029269916865 0.039519224255961 3.80545901887168e-05 -104.835405298645 reflect
#> 182 0.592742464643719 0.00104830075831574 0.0398617274354039 2.12371400224227e-05 -104.834433901875 reflect
#> 183 0.5944018015454 0.00100075520973611 0.039558502950893 1.07913151959921e-05 -104.832973166393 reflect
#> 184 0.5944018015454 0.00100075520973611 0.039558502950893 1.07913151959921e-05 -104.832973166393 reflect
#> 185 0.5944018015454 0.00100075520973611 0.039558502950893 1.07913151959921e-05 -104.832973166393 contract inside
#> 186 0.595530380373157 0.000955246400181525 0.0393552472655653 7.9876873171262e-06 -104.83215055869 reflect
#> 187 0.595530380373157 0.000955246400181525 0.0393552472655653 7.9876873171262e-06 -104.83215055869 contract inside
#> 188 0.595530380373157 0.000955246400181525 0.0393552472655653 7.9876873171262e-06 -104.83215055869 contract outside
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#> 190 0.595530380373157 0.000955246400181525 0.0393552472655653 7.9876873171262e-06 -104.83215055869 reflect
#> 191 0.594890159018849 0.000963740087587354 0.0394802014855443 4.44492648601407e-06 -104.831692022391 reflect
#> 192 0.594890159018849 0.000963740087587354 0.0394802014855443 4.44492648601407e-06 -104.831692022391 reflect
#> 193 0.593985835069285 0.00093153355228052 0.0396657921434717 1.30335461571842e-05 -104.830334784449 expand
#> 194 0.593985835069285 0.00093153355228052 0.0396657921434717 1.30335461571842e-05 -104.830334784449 reflect
#> 195 0.593985835069285 0.00093153355228052 0.0396657921434717 1.30335461571842e-05 -104.830334784449 contract inside
#> 196 0.593985835069285 0.00093153355228052 0.0396657921434717 1.30335461571842e-05 -104.830334784449 reflect
#> 197 0.595816316817263 0.0008716422066363 0.0393348963481716 1.49404001025461e-06 -104.829091255945 expand
#> 198 0.595816316817263 0.0008716422066363 0.0393348963481716 1.49404001025461e-06 -104.829091255945 reflect
#> 199 0.59323812965355 0.000823781999804844 0.0398527558472499 1.64990192715567e-05 -104.826319946788 expand
#> 200 0.59323812965355 0.000823781999804844 0.0398527558472499 1.64990192715567e-05 -104.826319946788 reflect
#> 201 0.59360536284108 0.000821349429552826 0.0397906940223004 4.50681816810245e-07 -104.825578250153 reflect
#> 202 0.596209632673036 0.000647167453315021 0.0393406520346873 6.49926490550474e-06 -104.821644931466 expand
#> 203 0.596209632673036 0.000647167453315021 0.0393406520346873 6.49926490550474e-06 -104.821644931466 reflect
#> 204 0.59501795843555 0.000518682776191705 0.0396171756247461 1.89857147898207e-05 -104.816493714328 expand
#> 205 0.595349042384443 0.000523474593929441 0.0395598790531295 2.54924039955726e-06 -104.81611897711 reflect
#> 206 0.596980510235431 0.000155024279559113 0.0393645069708197 2.9245377694187e-05 -104.805911796664 expand
#> 207 0.596980510235431 0.000155024279559113 0.0393645069708197 2.9245377694187e-05 -104.805911796664 reflect
#> 208 0.597185448091403 5.90173657387282e-05 0.039362382619277 2.71303003845315e-05 -104.802599493054 reflect
#> 209 0.597185448091403 5.90173657387282e-05 0.039362382619277 2.71303003845315e-05 -104.802599493054 contract inside
#> 210 0.597185448091403 5.90173657387282e-05 0.039362382619277 2.71303003845315e-05 -104.802599493054 contract inside
#> 211 0.597185448091403 5.90173657387282e-05 0.039362382619277 2.71303003845315e-05 -104.802599493054 reflect
#> 212 0.597185448091403 5.90173657387282e-05 0.039362382619277 2.71303003845315e-05 -104.802599493054 contract inside
#> 213 0.595703101464146 1.93642359987306e-05 0.0396657709849345 3.28826782432019e-05 -104.799843687186 reflect
#> 214 0.595703101464146 1.93642359987306e-05 0.0396657709849345 3.28826782432019e-05 -104.799843687186 contract inside
#> 215 0.595703101464146 1.93642359987306e-05 0.0396657709849345 3.28826782432019e-05 -104.799843687186 contract inside
#> 216 0.595703101464146 1.93642359987306e-05 0.0396657709849345 3.28826782432019e-05 -104.799843687186 contract inside
#> 217 0.595703101464146 1.93642359987306e-05 0.0396657709849345 3.28826782432019e-05 -104.799843687186 contract inside
#> 218 0.595703101464146 1.93642359987306e-05 0.0396657709849345 3.28826782432019e-05 -104.799843687186 contract inside
#> 219 0.595703101464146 1.93642359987306e-05 0.0396657709849345 3.28826782432019e-05 -104.799843687186 reflect
#> 220 0.595703101464146 1.93642359987306e-05 0.0396657709849345 3.28826782432019e-05 -104.799843687186 reflect
#> 221 0.592750614639318 2.13013620828562e-05 0.0402432070141546 4.07444119703475e-05 -104.798973311991 expand
#> 222 0.592750614639318 2.13013620828562e-05 0.0402432070141546 4.07444119703475e-05 -104.798973311991 reflect
#> 223 0.592750614639318 2.13013620828562e-05 0.0402432070141546 4.07444119703475e-05 -104.798973311991 contract inside
#> 224 0.592750614639318 2.13013620828562e-05 0.0402432070141546 4.07444119703475e-05 -104.798973311991 contract inside
#> 225 0.592072349584627 1.46466090721466e-05 0.0403782309701643 4.38162465243028e-05 -104.798938045318 reflect
#> 226 0.592072349584627 1.46466090721466e-05 0.0403782309701643 4.38162465243028e-05 -104.798938045318 contract inside
#> 227 0.592072349584627 1.46466090721466e-05 0.0403782309701643 4.38162465243028e-05 -104.798938045318 contract inside
#> 228 0.594251687725819 1.39212612275051e-05 0.0399514040582965 3.7317609950124e-05 -104.798904578252 reflect
#> 229 0.59296996644012 2.01382596203192e-06 0.0402068467599245 4.13858627902265e-05 -104.798336914196 reflect
#> 230 0.59296996644012 2.01382596203192e-06 0.0402068467599245 4.13858627902265e-05 -104.798336914196 reflect
#> 231 0.59296996644012 2.01382596203192e-06 0.0402068467599245 4.13858627902265e-05 -104.798336914196 contract inside
#> 232 0.59296996644012 2.01382596203192e-06 0.0402068467599245 4.13858627902265e-05 -104.798336914196 reflect
#> 233 0.59296996644012 2.01382596203192e-06 0.0402068467599245 4.13858627902265e-05 -104.798336914196 contract inside
#> 234 0.59296996644012 2.01382596203192e-06 0.0402068467599245 4.13858627902265e-05 -104.798336914196 contract inside
#> 235 0.59296996644012 2.01382596203192e-06 0.0402068467599245 4.13858627902265e-05 -104.798336914196 contract inside
#> 236 0.59296996644012 2.01382596203192e-06 0.0402068467599245 4.13858627902265e-05 -104.798336914196 contract inside
#> 237 0.59296996644012 2.01382596203192e-06 0.0402068467599245 4.13858627902265e-05 -104.798336914196 contract inside
#> 238 0.592909881931518 7.94583537638934e-07 0.040219202022874 4.13892060075962e-05 -104.798289526555 reflect
#> 239 0.592909881931518 7.94583537638934e-07 0.040219202022874 4.13892060075962e-05 -104.798289526555 contract inside
#> 240 0.592909881931518 7.94583537638934e-07 0.040219202022874 4.13892060075962e-05 -104.798289526555 reflect
#> 241 0.592909881931518 7.94583537638934e-07 0.040219202022874 4.13892060075962e-05 -104.798289526555 contract inside
#> 242 0.592909881931518 7.94583537638934e-07 0.040219202022874 4.13892060075962e-05 -104.798289526555 reflect
#> 243 0.592909881931518 7.94583537638934e-07 0.040219202022874 4.13892060075962e-05 -104.798289526555 contract inside
#> 244 0.592909881931518 7.94583537638934e-07 0.040219202022874 4.13892060075962e-05 -104.798289526555 contract inside
#> 245 0.592909881931518 7.94583537638934e-07 0.040219202022874 4.13892060075962e-05 -104.798289526555 contract inside
#> 246 0.592909881931518 7.94583537638934e-07 0.040219202022874 4.13892060075962e-05 -104.798289526555 contract inside
#> 247 0.593408033892853 7.05467647948307e-07 0.0401215785662535 3.99506301229262e-05 -104.798285112687 contract inside
#> 248 0.593152892418261 4.22317051803925e-07 0.0401717124563449 4.065927509319e-05 -104.798265524173 reflect
#> 249 0.593152892418261 4.22317051803925e-07 0.0401717124563449 4.065927509319e-05 -104.798265524173 contract inside
#> 250 0.593152892418261 4.22317051803925e-07 0.0401717124563449 4.065927509319e-05 -104.798265524173 reflect
#> 251 0.593298572650608 2.25519675106366e-07 0.0401432817681312 4.01565929167679e-05 -104.798256938532 reflect
#> 252 0.593298572650608 2.25519675106366e-07 0.0401432817681312 4.01565929167679e-05 -104.798256938532 contract inside
#> 253 0.592892214953541 3.71624294220153e-08 0.0402230984262205 4.12084685906179e-05 -104.798252843472 expand
#> 254 0.592892214953541 3.71624294220153e-08 0.0402230984262205 4.12084685906179e-05 -104.798252843472 reflect
#> 255 0.592892214953541 3.71624294220153e-08 0.0402230984262205 4.12084685906179e-05 -104.798252843472 contract inside
#> 256 0.592892214953541 3.71624294220153e-08 0.0402230984262205 4.12084685906179e-05 -104.798252843472 contract inside
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#> 258 0.593229946105692 9.78410014581887e-08 0.0401568517406657 4.0239474676964e-05 -104.798244885372 reflect
#> 259 0.593229946105692 9.78410014581887e-08 0.0401568517406657 4.0239474676964e-05 -104.798244885372 contract inside
#> 260 0.593235565339754 3.69778821737087e-08 0.04015581538732 4.01542916150522e-05 -104.798239448279 reflect
#> 261 0.593235565339754 3.69778821737087e-08 0.04015581538732 4.01542916150522e-05 -104.798239448279 reflect
#> 262 0.593235565339754 3.69778821737087e-08 0.04015581538732 4.01542916150522e-05 -104.798239448279 contract inside
#> 263 0.593235565339754 3.69778821737087e-08 0.04015581538732 4.01542916150522e-05 -104.798239448279 contract outside
#> 264 0.593235565339754 3.69778821737087e-08 0.04015581538732 4.01542916150522e-05 -104.798239448279 contract inside
#> 265 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 expand
#> 266 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 contract inside
#> 267 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 contract inside
#> 268 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 contract inside
#> 269 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 contract inside
#> 270 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 reflect
#> 271 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 reflect
#> 272 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 contract inside
#> 273 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 contract outside
#> 274 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 reflect
#> 275 0.593059442396243 1.45763949640278e-08 0.0401904431088218 4.0511773348996e-05 -104.798232318525 reflect
#> 276 0.593116551710247 1.81096071428922e-08 0.0401792834992918 4.02826876442992e-05 -104.798227965102 expand
#> 277 0.593074783160659 3.9481272376566e-09 0.0401874934644805 4.03779112681605e-05 -104.798227097859 reflect
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#> 280 0.593069080972636 2.23588678813097e-08 0.0401886988476613 4.0238034571227e-05 -104.798220231347 expand
#> 281 0.593069080972636 2.23588678813097e-08 0.0401886988476613 4.0238034571227e-05 -104.798220231347 reflect
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#> 283 0.593069080972636 2.23588678813097e-08 0.0401886988476613 4.0238034571227e-05 -104.798220231347 contract inside
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#> 285 0.593140368680481 1.24805746518993e-08 0.0401749028158103 3.97397878467856e-05 -104.798204197208 expand
#> 286 0.593140368680481 1.24805746518993e-08 0.0401749028158103 3.97397878467856e-05 -104.798204197208 reflect
#> 287 0.593172462962902 6.0711246788354e-08 0.0401687721367195 3.93496728460509e-05 -104.798191160947 expand
#> 288 0.593261069669615 4.493051828379e-08 0.0401516489837142 3.86972147916797e-05 -104.798172277927 expand
#> 289 0.593261069669615 4.493051828379e-08 0.0401516489837142 3.86972147916797e-05 -104.798172277927 reflect
#> 290 0.593430513974343 7.78822221825903e-08 0.0401187592496502 3.76605491809752e-05 -104.798154964665 expand
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#> 292 0.593482964447526 1.48260369809051e-07 0.0401090001933282 3.6606179251394e-05 -104.798117246193 reflect
#> 293 0.593482964447526 1.48260369809051e-07 0.0401090001933282 3.6606179251394e-05 -104.798117246193 reflect
#> 294 0.594041483833058 2.56682191719074e-07 0.0400010111034654 3.26146668675636e-05 -104.798097519773 expand
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#> 296 0.594024434823792 3.46532852700065e-07 0.0400052530050683 3.11092224440893e-05 -104.798019564587 expand
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#> 301 0.59452662597686 7.39395104434146e-07 0.0399103247777277 2.38748751331932e-05 -104.797903635684 expand
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#> 303 0.594244601906405 7.34708613339301e-07 0.039965931295267 2.39818219690222e-05 -104.797771634071 reflect
#> 304 0.594162488199002 1.05144363226718e-06 0.0399842524692607 2.02899913268733e-05 -104.797564324613 expand
#> 305 0.594162488199002 1.05144363226718e-06 0.0399842524692607 2.02899913268733e-05 -104.797564324613 reflect
#> 306 0.594284604964182 1.46907918766403e-06 0.0399648767204812 1.2182588469562e-05 -104.797230509794 expand
#> 307 0.594284604964182 1.46907918766403e-06 0.0399648767204812 1.2182588469562e-05 -104.797230509794 reflect
#> 308 0.59428016643277 2.32243690360297e-06 0.0399725895949721 3.1906450289375e-07 -104.796670554253 expand
#> 309 0.59428016643277 2.32243690360297e-06 0.0399725895949721 3.1906450289375e-07 -104.796670554253 reflect
#> 310 0.59428016643277 2.32243690360297e-06 0.0399725895949721 3.1906450289375e-07 -104.796670554253 contract inside
#> 311 0.59428016643277 2.32243690360297e-06 0.0399725895949721 3.1906450289375e-07 -104.796670554253 reflect
#> 312 0.59428016643277 2.32243690360297e-06 0.0399725895949721 3.1906450289375e-07 -104.796670554253 contract inside
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#> 326 0.593642149513953 2.43646686786617e-06 0.0400981563262859 1.01348479663483e-06 -104.796483293357 expand
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#> 329 0.593371567338061 2.52145520817316e-06 0.0401517313754856 8.16711049829751e-07 -104.7964163871 contract inside
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#> 331 0.593075766139623 2.61942008673617e-06 0.0402103899820395 4.93939696321455e-07 -104.796362373299 reflect
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#> 333 0.593075766139623 2.61942008673617e-06 0.0402103899820395 4.93939696321455e-07 -104.796362373299 reflect
#> 334 0.593075766139623 2.61942008673617e-06 0.0402103899820395 4.93939696321455e-07 -104.796362373299 contract inside
#> 335 0.593075766139623 2.61942008673617e-06 0.0402103899820395 4.93939696321455e-07 -104.796362373299 reflect
#> 336 0.592532300841031 2.7599129099649e-06 0.040317880749801 5.12766874430901e-07 -104.796357626957 reflect
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#> 338 0.593016209361449 2.65473915530714e-06 0.0402223905684642 1.09847339028656e-07 -104.7963394707 reflect
#> 339 0.593016209361449 2.65473915530714e-06 0.0402223905684642 1.09847339028656e-07 -104.7963394707 contract inside
#> 340 0.593016209361449 2.65473915530714e-06 0.0402223905684642 1.09847339028656e-07 -104.7963394707 reflect
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#> 354 0.592797482152763 2.71889403862903e-06 0.0402656979503052 2.47349483601526e-08 -104.796326842703 contract inside
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#> 357 0.59280163284836 2.71789720402914e-06 0.0402648916351897 2.97697187048389e-10 -104.796325687184 reflect
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#> 372 0.592744732446822 2.73221453101232e-06 0.0402761477548346 2.92819756134901e-10 -104.796325598706 reflect
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#> 375 0.592744732446822 2.73221453101232e-06 0.0402761477548346 2.92819756134901e-10 -104.796325598706 contract inside
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#> 383 0.592774626150647 2.72458042892001e-06 0.0402702341759646 8.92973225185641e-11 -104.796325514722 reflect
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#> 400 0.592771929204522 2.72520599605978e-06 0.0402707677566648 1.1795481024019e-11 -104.796325504818 contract inside
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#> 403 0.592768679904685 2.7259287286691e-06 0.0402714105470635 6.14330377726279e-11 -104.796325501583 expand
#> 404 0.592770577708426 2.72548302041405e-06 0.0402710351422291 2.31258446350963e-12 -104.796325500803 reflect
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#> 417 0.592767079736384 2.72624322579707e-06 0.0402717271673856 1.37274681940534e-12 -104.796325495527 expand
#> 418 0.592767079736384 2.72624322579707e-06 0.0402717271673856 1.37274681940534e-12 -104.796325495527 contract inside
#> 419 0.592767079736384 2.72624322579707e-06 0.0402717271673856 1.37274681940534e-12 -104.796325495527 reflect
#> 420 0.592767079736384 2.72624322579707e-06 0.0402717271673856 1.37274681940534e-12 -104.796325495527 reflect
#> 421 0.592767079736384 2.72624322579707e-06 0.0402717271673856 1.37274681940534e-12 -104.796325495527 contract inside
#> 422 0.592765343618046 2.72657733448056e-06 0.040272070644916 1.31137790993911e-11 -104.796325493302 expand
#> 423 0.592765343618046 2.72657733448056e-06 0.040272070644916 1.31137790993911e-11 -104.796325493302 contract inside
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#> 465 0.592599859785057 2.54710967931339e-06 0.0403048908612483 9.2664481851657e-09 -104.796322276965 expand
#> 466 0.592590013417677 2.53474654862999e-06 0.0403068446267875 9.7812462592006e-09 -104.796322274343 reflect
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#> 469 0.592544190027589 2.4386436170922e-06 0.0403159512676834 1.39240803542527e-08 -104.796321367126 contract inside
#> 470 0.592531484607212 2.40925859724794e-06 0.0403184774047291 1.51142349744077e-08 -104.796321129407 expand
#> 471 0.592507281146046 2.33986890519213e-06 0.0403232944822428 1.80843803813838e-08 -104.796320371119 expand
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#> 480 0.592488214307086 1.92378886751542e-06 0.0403272209734431 3.18118982371669e-08 -104.796307811838 expand
#> 481 0.592488214307086 1.92378886751542e-06 0.0403272209734431 3.18118982371669e-08 -104.796307811838 reflect
#> 482 0.59257508651536 1.92067666201906e-06 0.0403100227170399 3.03010861046675e-08 -104.796302461395 expand
#> 483 0.592689972462615 1.8432413986057e-06 0.0402873094123563 2.98905811627514e-08 -104.796296240633 expand
#> 484 0.592588567315535 1.42052429273355e-06 0.040307535703047 4.63686895303009e-08 -104.796285141286 expand
#> 485 0.592520629788114 8.2510169478697e-07 0.0403212021804139 6.70867092071859e-08 -104.796268927743 expand
#> 486 0.592520629788114 8.2510169478697e-07 0.0403212021804139 6.70867092071859e-08 -104.796268927743 reflect
#> 487 0.592723395262199 3.60364963644088e-08 0.0402813508662542 8.81660403269145e-08 -104.79623551486 expand
#> 488 0.592723395262199 3.60364963644088e-08 0.0402813508662542 8.81660403269145e-08 -104.79623551486 contract inside
#> 489 0.592723395262199 3.60364963644088e-08 0.0402813508662542 8.81660403269145e-08 -104.79623551486 reflect
#> 490 0.592723395262199 3.60364963644088e-08 0.0402813508662542 8.81660403269145e-08 -104.79623551486 contract inside
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#> 492 0.592723395262199 3.60364963644088e-08 0.0402813508662542 8.81660403269145e-08 -104.79623551486 reflect
#> 493 0.592723395262199 3.60364963644088e-08 0.0402813508662542 8.81660403269145e-08 -104.79623551486 contract inside
#> 494 0.592723395262199 3.60364963644088e-08 0.0402813508662542 8.81660403269145e-08 -104.79623551486 contract inside
#> 495 0.592723395262199 3.60364963644088e-08 0.0402813508662542 8.81660403269145e-08 -104.79623551486 contract inside
#> 496 0.592723395262199 3.60364963644088e-08 0.0402813508662542 8.81660403269145e-08 -104.79623551486 contract inside
#> 497 0.592723395262199 3.60364963644088e-08 0.0402813508662542 8.81660403269145e-08 -104.79623551486 contract inside
#> 498 0.592788268050317 5.62370421967324e-10 0.0402685248098465 8.78004288715985e-08 -104.796234569045 reflect
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#> 500 0.592788268050317 5.62370421967324e-10 0.0402685248098465 8.78004288715985e-08 -104.796234569045 reflect
#> 501 0.592788268050317 5.62370421967324e-10 0.0402685248098465 8.78004288715985e-08 -104.796234569045 contract inside
#> 502 0.592788268050317 5.62370421967324e-10 0.0402685248098465 8.78004288715985e-08 -104.796234569045 contract inside
#> 503 0.592788268050317 5.62370421967324e-10 0.0402685248098465 8.78004288715985e-08 -104.796234569045 contract inside
#> 504 0.592788268050317 5.62370421967324e-10 0.0402685248098465 8.78004288715985e-08 -104.796234569045 contract inside
#> 505 0.592788268050317 5.62370421967324e-10 0.0402685248098465 8.78004288715985e-08 -104.796234569045 reflect
#> 506 0.592788268050317 5.62370421967324e-10 0.0402685248098465 8.78004288715985e-08 -104.796234569045 contract inside
#> 507 0.592788268050317 5.62370421967324e-10 0.0402685248098465 8.78004288715985e-08 -104.796234569045 contract outside
#> 508 0.592788268050317 5.62370421967324e-10 0.0402685248098465 8.78004288715985e-08 -104.796234569045 contract inside
#> 509 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 reflect
#> 510 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 511 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 512 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
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#> 515 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 516 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 517 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 518 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 519 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 520 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 521 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 522 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 523 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 524 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 525 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 526 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 527 0.592721808297973 1.77176863508512e-09 0.0402816774375807 8.92763261428463e-08 -104.796234377008 contract inside
#> 528 0.592744360887675 1.43626284489824e-09 0.0402772140099135 8.87734504075266e-08 -104.796234301822 reflect
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#> 531 0.592742163785228 2.32674731808088e-10 0.0402776492852501 8.88620637943048e-08 -104.796234261342 reflect
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#> 547 0.592744999250055 2.03628985068553e-11 0.0402770881843463 8.88042403564864e-08 -104.796234254784 reflect
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#> 550 0.592744999250055 2.03628985068553e-11 0.0402770881843463 8.88042403564864e-08 -104.796234254784 contract inside
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#> 562 0.592741949450258 2.97858790237471e-12 0.0402776917888265 8.88742553910142e-08 -104.79623425371 expand
#> 563 0.592741949450258 2.97858790237471e-12 0.0402776917888265 8.88742553910142e-08 -104.79623425371 contract inside
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#> 571 0.592742104997511 1.55467034660677e-12 0.0402776610042835 8.88707667662385e-08 -104.796234253623 reflect
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#> 575 0.592742118184131 1.1626245913796e-12 0.0402776583946017 8.88704815848994e-08 -104.796234253607 reflect
#> 576 0.592742392572598 6.30794511230374e-13 0.0402776040893666 8.88642396499008e-08 -104.796234253536 reflect
#> 577 0.592742475022466 2.31789218771462e-13 0.0402775877714932 8.88623832267087e-08 -104.796234253512 reflect
#> 578 0.592742475022466 2.31789218771462e-13 0.0402775877714932 8.88623832267087e-08 -104.796234253512 reflect
#> 579 0.592742475022466 2.31789218771462e-13 0.0402775877714932 8.88623832267087e-08 -104.796234253512 contract inside
#> 580 0.592742475022466 2.31789218771462e-13 0.0402775877714932 8.88623832267087e-08 -104.796234253512 reflect
#> 581 0.592742475022466 2.31789218771462e-13 0.0402775877714932 8.88623832267087e-08 -104.796234253512 contract inside
#> 582 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 reflect
#> 583 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 reflect
#> 584 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 contract inside
#> 585 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 contract inside
#> 586 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 contract inside
#> 587 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 contract inside
#> 588 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 contract inside
#> 589 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 reflect
#> 590 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 contract inside
#> 591 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 contract inside
#> 592 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 reflect
#> 593 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 contract inside
#> 594 0.592742715856525 1.35940512642239e-13 0.0402775401070252 8.88568951519178e-08 -104.796234253486 contract inside
#> 595 0.592742704537037 3.26026462146869e-14 0.0402775423473499 8.88571580516224e-08 -104.796234253484 reflect
#> 596 0.592742704537037 3.26026462146869e-14 0.0402775423473499 8.88571580516224e-08 -104.796234253484 reflect
#> 597 0.592742704537037 3.26026462146869e-14 0.0402775423473499 8.88571580516224e-08 -104.796234253484 contract inside
#> 598 0.592742774729383 6.53190591533354e-14 0.0402775284552732 8.88555558212313e-08 -104.796234253481 reflect
#> 599 0.592742774729383 6.53190591533354e-14 0.0402775284552732 8.88555558212313e-08 -104.796234253481 contract inside
#> 600 0.592742774729383 6.53190591533354e-14 0.0402775284552732 8.88555558212313e-08 -104.796234253481 reflect
#> 601 0.592742774729383 6.53190591533354e-14 0.0402775284552732 8.88555558212313e-08 -104.796234253481 contract inside
#> 602 0.592742793143943 2.69014335221175e-14 0.040277524810783 8.88551380428738e-08 -104.796234253479 reflect
#> 603 0.592742793143943 2.69014335221175e-14 0.040277524810783 8.88551380428738e-08 -104.796234253479 contract inside
#> 604 0.592742793143943 2.69014335221175e-14 0.040277524810783 8.88551380428738e-08 -104.796234253479 reflect
#> 605 0.592742891865312 3.59411306949475e-14 0.0402775052724171 8.8852887566364e-08 -104.796234253477 expand
#> 606 0.592742891865312 3.59411306949475e-14 0.0402775052724171 8.8852887566364e-08 -104.796234253477 contract inside
#> 607 0.592742891865312 3.59411306949475e-14 0.0402775052724171 8.8852887566364e-08 -104.796234253477 contract inside
#> 608 0.592742891865312 3.59411306949475e-14 0.0402775052724171 8.8852887566364e-08 -104.796234253477 reflect
#> 609 0.592742890225155 1.11867402868128e-14 0.0402775055970365 8.8852925564544e-08 -104.796234253476 reflect
#> 610 0.592742890225155 1.11867402868128e-14 0.0402775055970365 8.8852925564544e-08 -104.796234253476 contract inside
#> 611 0.592742890225155 1.11867402868128e-14 0.0402775055970365 8.8852925564544e-08 -104.796234253476 contract inside
#> 612 0.592742904569493 7.84918602213347e-15 0.0402775027580893 8.88525992919065e-08 -104.796234253476 reflect
#> 613 0.592742904569493 7.84918602213347e-15 0.0402775027580893 8.88525992919065e-08 -104.796234253476 contract inside
#> 614 0.592742904569493 7.84918602213347e-15 0.0402775027580893 8.88525992919065e-08 -104.796234253476 reflect
#> 615 0.592742904569493 7.84918602213347e-15 0.0402775027580893 8.88525992919065e-08 -104.796234253476 contract inside
#> 616 0.592742904569493 7.84918602213347e-15 0.0402775027580893 8.88525992919065e-08 -104.796234253476 contract inside
#> 617 0.592742904569493 7.84918602213347e-15 0.0402775027580893 8.88525992919065e-08 -104.796234253476 contract inside
#> 618 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 reflect
#> 619 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 contract inside
#> 620 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 reflect
#> 621 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 contract inside
#> 622 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 contract inside
#> 623 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 reflect
#> 624 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 contract inside
#> 625 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 reflect
#> 626 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 reflect
#> 627 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 contract inside
#> 628 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 reflect
#> 629 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 contract inside
#> 630 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 contract inside
#> 631 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 shrink
#> 632 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 reflect
#> 633 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 reflect
#> 634 0.592742925614366 2.65396244248284e-15 0.0402774985930121 8.88521196576265e-08 -104.796234253476 reflect
#> 635 0.592742918531967 6.8255030852451e-16 0.0402774999947203 8.88522809080758e-08 -104.796234253476 expand
#> 636 0.592742918531967 6.8255030852451e-16 0.0402774999947203 8.88522809080758e-08 -104.796234253476 reflect
#> 637 0.592742918531967 6.8255030852451e-16 0.0402774999947203 8.88522809080758e-08 -104.796234253476 reflect
#> 638 0.592742918531967 6.8255030852451e-16 0.0402774999947203 8.88522809080758e-08 -104.796234253476 reflect
#> 639 0.592742918531967 6.8255030852451e-16 0.0402774999947203 8.88522809080758e-08 -104.796234253476 reflect
#> 640 0.592742915543818 4.03922872093927e-16 0.0402775005861176 8.88523489073465e-08 -104.796234253476 shrink
#> 641 0.592742915543818 4.03922872093927e-16 0.0402775005861176 8.88523489073465e-08 -104.796234253476 reflect
#> 642 0.592742915543818 4.03922872093927e-16 0.0402775005861176 8.88523489073465e-08 -104.796234253476 shrink
#> 643 0.592742915543818 4.03922872093927e-16 0.0402775005861176 8.88523489073465e-08 -104.796234253476 reflect
#> 644 0.592742914640615 8.64249315726846e-17 0.0402775007648743 8.88523695079275e-08 -104.796234253476 reflect
#> 645 0.592742914640615 8.64249315726846e-17 0.0402775007648743 8.88523695079275e-08 -104.796234253476 contract inside
#> 646 0.592742915092216 2.45173901833306e-16 0.040277500675496 8.8852359207637e-08 -104.796234253476 shrink
#> 647 0.592742915092216 2.45173901833306e-16 0.040277500675496 8.8852359207637e-08 -104.796234253476 reflect
#> 648 0.592742915092216 2.45173901833306e-16 0.040277500675496 8.8852359207637e-08 -104.796234253476 reflect
#> 649 0.592742915092216 2.45173901833306e-16 0.040277500675496 8.8852359207637e-08 -104.796234253476 shrink
#> 650 0.592742915092216 2.45173901833306e-16 0.040277500675496 8.8852359207637e-08 -104.796234253476 shrink
#> 651 0.592742915092216 2.45173901833306e-16 0.040277500675496 8.8852359207637e-08 -104.796234253476 contract outside
#> 652 0.592742915092216 2.45173901833306e-16 0.040277500675496 8.8852359207637e-08 -104.796234253476 contract outside
#> 653 0.592742915092216 2.45173901833306e-16 0.040277500675496 8.8852359207637e-08 -104.796234253476 contract inside
#> 654 0.592742915092216 2.45173901833306e-16 0.040277500675496 8.8852359207637e-08 -104.796234253476 shrink
#> 655 0.592742915092216 2.45173901833306e-16 0.040277500675496 8.8852359207637e-08 -104.796234253476 contract outside
#> 656 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 657 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 658 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 shrink
#> 659 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 660 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 661 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 shrink
#> 662 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 contract outside
#> 663 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 664 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 665 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 contract inside
#> 666 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 shrink
#> 667 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 668 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 contract inside
#> 669 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 shrink
#> 670 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 671 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 contract inside
#> 672 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 contract inside
#> 673 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 contract inside
#> 674 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 shrink
#> 675 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 676 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 677 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 678 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 shrink
#> 679 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 680 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 contract inside
#> 681 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 shrink
#> 682 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 contract inside
#> 683 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 684 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 685 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 shrink
#> 686 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 reflect
#> 687 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 contract outside
#> 688 0.592742915111106 2.51771048780016e-16 0.0402775006717573 8.88523587771388e-08 -104.796234253476 shrink
#> Optimization has terminated successfully.
reconstructed_tree_ml_CR <- reconstructed_tree_ml$ML
CR_par_reconstructed <- secsse::extract_par_vals(
idparslist,
reconstructed_tree_ml$MLpars
)
reconstructed_tree_ml
#> $MLpars
#> $MLpars[[1]]
#> $MLpars[[1]][[1]]
#> 0A 1A 0B 1B
#> 0A 0.5927429 0 0 0
#> 1A 0.0000000 0 0 0
#> 0B 0.0000000 0 0 0
#> 1B 0.0000000 0 0 0
#>
#> $MLpars[[1]][[2]]
#> 0A 1A 0B 1B
#> 0A 0 0.0000000 0 0
#> 1A 0 0.5927429 0 0
#> 0B 0 0.0000000 0 0
#> 1B 0 0.0000000 0 0
#>
#> $MLpars[[1]][[3]]
#> 0A 1A 0B 1B
#> 0A 0 0 0.0000000 0
#> 1A 0 0 0.0000000 0
#> 0B 0 0 0.5927429 0
#> 1B 0 0 0.0000000 0
#>
#> $MLpars[[1]][[4]]
#> 0A 1A 0B 1B
#> 0A 0 0 0 0.0000000
#> 1A 0 0 0 0.0000000
#> 0B 0 0 0 0.0000000
#> 1B 0 0 0 0.5927429
#>
#>
#> $MLpars[[2]]
#> 0A 1A 0B 1B
#> 2.51771e-16 2.51771e-16 2.51771e-16 2.51771e-16
#>
#> $MLpars[[3]]
#> 0A 1A 0B 1B
#> 0A NA 4.027750e-02 4.027750e-02 0.0000000
#> 1A 8.885236e-08 NA 0.000000e+00 0.0402775
#> 0B 8.885236e-08 0.000000e+00 NA 0.0402775
#> 1B 0.000000e+00 8.885236e-08 8.885236e-08 NA
#>
#>
#> $ML
#> [1] -104.7962
#>
#> $conv
#> [1] 0
CR_par_reconstructed
#> [1] 5.927429e-01 2.517710e-16 4.027750e-02 8.885236e-08
spec_rates_reconstructed <- CR_par_reconstructed[1]
ext_rates_reconstructed <- CR_par_reconstructed[2]
Q_01_reconstructed <- CR_par_reconstructed[3]
Q_10_reconstructed <- CR_par_reconstructed[4]
knitr::kable(
data.frame(
Reconstructed_tree = c(
spec_rates_reconstructed,
ext_rates_reconstructed,
Q_01_reconstructed,
Q_10_reconstructed
),
Complete_tree = c(
spec_rates_complete,
ext_rates_complete,
Q_01_complete,
Q_10_complete
),
Generating_parameters = c(
speciation_rate,
extinction_rate,
q_01,
q_10
),
row.names = c(
"Speciation rate",
"Extinction rate",
"Transition rate 01",
"Transition rate 10"
)
)
)| Reconstructed_tree | Complete_tree | Generating_parameters | |
|---|---|---|---|
| Speciation rate | 0.5927429 | 1.2040383 | 0.8 |
| Extinction rate | 0.0000000 | 0.6272724 | 0.2 |
| Transition rate 01 | 0.0402775 | 0.1110798 | 0.1 |
| Transition rate 10 | 0.0000001 | 0.1179893 | 0.1 |
We see that including extinct species results in a better esimation particularly of the extinction rate. This effect is especially noticeable if there are many extinct species present in the tree. Additionally, we see that the estimation of the transition rate from state 1 to 0 also improved.
As a final note, do note that this is just a simple simulation example and care should be exercised with model selection and specification when fitting secsse to empirical datasets to make predictions about evolutionary patterns.
References
Nee S, May RM, Harvey PH. The reconstructed evolutionary process. Philos Trans R Soc Lond B Biol Sci. 1994 May 28;344(1309):305-11. https://doi.org/10.1098/rstb.1994.0068.