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added a draft for the state-dependent OU tutorial #74

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106 changes: 106 additions & 0 deletions tutorials/cont_traits/data/diprotodontia_continuous.nex
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#NEXUS
[Data written by write.nexus.data.R, Tue Jun 10 15:02:17 2025]
BEGIN DATA;
DIMENSIONS NTAX=97 NCHAR=1;
FORMAT DATATYPE=CONTINUOUS MISSING=? GAP=- INTERLEAVE=NO;
MATRIX [ln (body mass (kg))]
acrobates_pygmaeus -4.3428059215206
aepyprymnus_rufescens 1.03673688495002
ailurops_ursinus 1.94591014905531
bettongia_gaimardi 0.325700139639302
bettongia_lesueur 0.36967902319398
bettongia_penicillata 0.0963777915222527
bettongia_tropica 0.169194100886454
burramys_parvus -3.11677060193105
cercartetus_caudatus -3.77008950953948
cercartetus_concinnus -3.2188758248682
cercartetus_lepidus -4.60367130986435
cercartetus_nanus -2.81341071676004
dactylopsila_trivirgata -0.899667172070274
dendrolagus_dorianus 2.25978197066874
dendrolagus_goodfellowi 2.00148000021012
dendrolagus_lumholtzi 1.89461234337939
dendrolagus_matschiei 1.95727390770563
distoechurus_pennatus -2.95420652672549
dorcopsis_hageni 1.70474627405495
dorcopsulus_vanheurni 0.636767287123741
gymnobelideus_leadbeateri -2.01245601689921
hemibelideus_lemuroides 0.0392207131532813
hypsiprymnodon_moschatus -0.62689138478288
lagorchestes_conspicillatus 1.00814220998695
lagorchestes_hirsutus 0.306432675976722
lagostrophus_fasciatus 0.659321488075848
lasiorhinus_krefftii 3.35454592881834
lasiorhinus_latifrons 3.26437677597863
macropus_agilis 2.63245522647221
macropus_antilopinus 3.38939129662852
macropus_dorsalis 2.42036457308855
macropus_eugenii 1.61685831303758
macropus_fuliginosus 3.29239948348687
macropus_giganteus 3.72460717482746
macropus_irma 2.07944154167984
macropus_parma 1.43587231014343
macropus_parryi 2.53606147625598
macropus_robustus 3.38939129662852
macropus_rufogriseus 2.80487438573775
macropus_rufus 3.57596814169475
onychogalea_fraenata 1.65365095086042
onychogalea_unguifera 1.75785791755237
petauroides_volans 0.131905070879939
petaurus_abidi -1.2801341652915
petaurus_breviceps -2.05924683439432
petaurus_norfolcensis -1.30011666487884
petrogale_assimilis 1.53015225146172
petrogale_brachyotis 1.38629436111989
petrogale_burbidgei 0.229523158278249
petrogale_concinna 0.280732983363574
petrogale_herberti 1.86652674780105
petrogale_inornata 1.51633968445958
petrogale_lateralis 1.66467203156154
petrogale_mareeba 1.42310833424261
petrogale_penicillata 1.86652674780105
petrogale_persephone 1.72019722830809
petrogale_purpureicollis 1.66467203156154
petrogale_rothschildi 1.51431591492238
petrogale_xanthopus 1.98100077921117
petropseudes_dahli 0.629690740428164
phalanger_carmelitae 0.607284234779769
phalanger_gymnotis 0.8754687373539
phalanger_lullulae 0.65167393235337
phalanger_orientalis 0.830188032820743
phalanger_sericeus 0.694646056683681
phalanger_vestitus 0.615185639090233
phascolarctos_cinereus 1.73110140935257
potorous_gilbertii 0.0837297483314996
potorous_longipes 0.555338080147092
potorous_tridactylus 0.0532279217885611
pseudocheirus_peregrinus -0.15163717466296
pseudochirops_albertisii -0.242262662260921
pseudochirops_archeri 0.112399682488911
pseudochirops_corinnae 0.116003675756306
pseudochirops_cupreus 0.567629308030175
pseudochirulus_canescens -0.356674943938732
pseudochirulus_caroli -0.785218610780435
pseudochirulus_forbesi -0.447600464710949
pseudochirulus_herbertensis 0.093799949070671
pseudochirulus_mayeri -1.87650069768315
setonix_brachyurus 1.03714460324006
spilocuscus_maculatus 1.42436778176936
spilocuscus_rufoniger 1.79175946922805
strigocuscus_celebensis 0
strigocuscus_pelengensis 0
tarsipes_rostratus -4.60517018598809
thylogale_billardierii 1.69247858326036
thylogale_browni 1.70074007084089
thylogale_brunii 1.56778223716527
thylogale_calabyi 1.46467337793464
thylogale_stigmatica 1.45994785501401
thylogale_thetis 1.52605086869767
trichosurus_caninus 1.13624841369115
trichosurus_vulpecula 0.693730510390013
vombatus_ursinus 3.24843462710975
wallabia_bicolor 2.69546973113021
wyulda_squamicaudata 0.587347679673312
;
END;

113 changes: 113 additions & 0 deletions tutorials/cont_traits/data/diprotodontia_discrete_diet.nex
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#NEXUS
[Data written by write.nexus.data.R, Tue Jun 10 15:02:15 2025]
BEGIN DATA;
DIMENSIONS NTAX=97 NCHAR=1;
FORMAT DATATYPE=STANDARD MISSING=? GAP=- INTERLEAVE=NO symbols="01";
MATRIX [herbivory]
acrobates_pygmaeus 0
aepyprymnus_rufescens 1
ailurops_ursinus 1
bettongia_gaimardi 1
bettongia_lesueur 1
bettongia_penicillata 1
bettongia_tropica 1
burramys_parvus 0
cercartetus_caudatus 0
cercartetus_concinnus 0
cercartetus_lepidus 0
cercartetus_nanus 0
dactylopsila_trivirgata 0
dendrolagus_dorianus 1
dendrolagus_goodfellowi 1
dendrolagus_lumholtzi 1
dendrolagus_matschiei 1
distoechurus_pennatus 0
dorcopsis_hageni 1
dorcopsulus_vanheurni 1
gymnobelideus_leadbeateri 0
hemibelideus_lemuroides 1
hypsiprymnodon_moschatus 0
lagorchestes_conspicillatus 1
lagorchestes_hirsutus 1
lagostrophus_fasciatus 1
lasiorhinus_krefftii 1
lasiorhinus_latifrons 1
macropus_agilis 1
macropus_antilopinus 1
macropus_dorsalis 1
macropus_eugenii 1
macropus_fuliginosus 1
macropus_giganteus 1
macropus_irma 1
macropus_parma 1
macropus_parryi 1
macropus_robustus 1
macropus_rufogriseus 1
macropus_rufus 1
onychogalea_fraenata 1
onychogalea_unguifera 1
petauroides_volans 1
petaurus_abidi 0
petaurus_breviceps 0
petaurus_norfolcensis 0
petrogale_assimilis 1
petrogale_brachyotis 1
petrogale_burbidgei 1
petrogale_concinna 1
petrogale_herberti 1
petrogale_inornata 1
petrogale_lateralis 1
petrogale_mareeba 0
petrogale_penicillata 1
petrogale_persephone 1
petrogale_purpureicollis 1
petrogale_rothschildi 1
petrogale_xanthopus 1
petropseudes_dahli 1
phalanger_carmelitae 0
phalanger_gymnotis 1
phalanger_lullulae 0
phalanger_orientalis 0
phalanger_sericeus 0
phalanger_vestitus 0
phascolarctos_cinereus 1
potorous_gilbertii 0
potorous_longipes 0
potorous_tridactylus 0
pseudocheirus_peregrinus 1
pseudochirops_albertisii 1
pseudochirops_archeri 1
pseudochirops_corinnae 1
pseudochirops_cupreus 1
pseudochirulus_canescens 1
pseudochirulus_caroli 1
pseudochirulus_forbesi 1
pseudochirulus_herbertensis 1
pseudochirulus_mayeri 1
setonix_brachyurus 1
spilocuscus_maculatus 1
spilocuscus_rufoniger 1
strigocuscus_celebensis 1
strigocuscus_pelengensis 0
tarsipes_rostratus 1
thylogale_billardierii 1
thylogale_browni 1
thylogale_brunii 1
thylogale_calabyi 1
thylogale_stigmatica 1
thylogale_thetis 1
trichosurus_caninus 1
trichosurus_vulpecula 1
vombatus_ursinus 1
wallabia_bicolor 1
wyulda_squamicaudata 0
;
END;



[
herbivory
0: non-herbivory; plant consumption <90%
1: herbivory; plant consumption >=90%
]
114 changes: 114 additions & 0 deletions tutorials/cont_traits/data/diprotodontia_discrete_island.nex
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#NEXUS
[Data written by write.nexus.data.R, Tue Jun 10 15:02:15 2025]
BEGIN DATA;
DIMENSIONS NTAX=97 NCHAR=1;
FORMAT DATATYPE=STANDARD MISSING=? GAP=- INTERLEAVE=NO symbols="012";
MATRIX [island_endemicity]
acrobates_pygmaeus 0
aepyprymnus_rufescens 0
ailurops_ursinus 2
bettongia_gaimardi 0
bettongia_lesueur 0
bettongia_penicillata 0
bettongia_tropica 0
burramys_parvus 0
cercartetus_caudatus 0
cercartetus_concinnus 0
cercartetus_lepidus 0
cercartetus_nanus 0
dactylopsila_trivirgata 0
dendrolagus_dorianus 1
dendrolagus_goodfellowi 1
dendrolagus_lumholtzi 0
dendrolagus_matschiei 1
distoechurus_pennatus 1
dorcopsis_hageni 1
dorcopsulus_vanheurni 1
gymnobelideus_leadbeateri 0
hemibelideus_lemuroides 0
hypsiprymnodon_moschatus 0
lagorchestes_conspicillatus 0
lagorchestes_hirsutus 0
lagostrophus_fasciatus 0
lasiorhinus_krefftii 0
lasiorhinus_latifrons 0
macropus_agilis 0
macropus_antilopinus 0
macropus_dorsalis 0
macropus_eugenii 0
macropus_fuliginosus 0
macropus_giganteus 0
macropus_irma 0
macropus_parma 0
macropus_parryi 0
macropus_robustus 0
macropus_rufogriseus 0
macropus_rufus 0
onychogalea_fraenata 0
onychogalea_unguifera 0
petauroides_volans 0
petaurus_abidi 1
petaurus_breviceps 0
petaurus_norfolcensis 0
petrogale_assimilis 0
petrogale_brachyotis 0
petrogale_burbidgei 0
petrogale_concinna 0
petrogale_herberti 0
petrogale_inornata 0
petrogale_lateralis 0
petrogale_mareeba 0
petrogale_penicillata 0
petrogale_persephone 0
petrogale_purpureicollis 0
petrogale_rothschildi 0
petrogale_xanthopus 0
petropseudes_dahli 0
phalanger_carmelitae 1
phalanger_gymnotis 1
phalanger_lullulae 2
phalanger_orientalis 1
phalanger_sericeus 1
phalanger_vestitus 1
phascolarctos_cinereus 0
potorous_gilbertii 0
potorous_longipes 0
potorous_tridactylus 0
pseudocheirus_peregrinus 0
pseudochirops_albertisii 1
pseudochirops_archeri 0
pseudochirops_corinnae 1
pseudochirops_cupreus 1
pseudochirulus_canescens 1
pseudochirulus_caroli 1
pseudochirulus_forbesi 1
pseudochirulus_herbertensis 0
pseudochirulus_mayeri 1
setonix_brachyurus 0
spilocuscus_maculatus 0
spilocuscus_rufoniger 1
strigocuscus_celebensis 2
strigocuscus_pelengensis 2
tarsipes_rostratus 0
thylogale_billardierii 0
thylogale_browni 1
thylogale_brunii 1
thylogale_calabyi 1
thylogale_stigmatica 0
thylogale_thetis 0
trichosurus_caninus 0
trichosurus_vulpecula 0
vombatus_ursinus 0
wallabia_bicolor 0
wyulda_squamicaudata 0
;
END;



[
island_endemicity
0: Occurs on mainland
1: Occurs on large land bridge islands
2: Occurs only on isolated islands
]
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