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adding newick files of cross validated chronograms to dryad folder
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@LunaSare
LunaSare committed Jul 18, 2022
1 parent e19deff commit beef5c0
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21 changes: 20 additions & 1 deletion dryad/README.Rmd
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Expand Up @@ -110,7 +110,7 @@ file.copy(from = "../figures/fringillidae-topologies/fringillidae_paraphyletic_t
files_in_path <- list.files(path = "../figures/figure-fringillidae/source_chronograms")
# get only newick file names
# get source chronograms newick file names
newick_files <- files_in_path[grep("[.]tre", files_in_path)]
# order files numerically
Expand All @@ -122,7 +122,26 @@ for (file_name in newick_files) {
file.copy(from = paste0("../figures/figure-fringillidae/source_chronograms/", file_name),
to = paste0("../dryad/Sanchez-Reyes_etal_2022_supplementary_figure_S", index, "_source.tre"),
overwrite = TRUE)
write(paste0("https://raw.githubusercontent.com/LunaSare/datelifeMS1/main/dryad/Sanchez-Reyes_etal_2022_supplementary_figure_S", index, "_source.tre"), file = "../dryad/urls.txt", append=TRUE)
}
# get cross validated chronograms newick file names
files_in_path <- list.files(path = "../figures/fringillidae-cross-validation")
newick_files <- files_in_path[grep("[.]tre", files_in_path)]
# order files numerically
newick_files <- stringr::str_sort(newick_files, numeric = TRUE)
index <- 1
for (file_name in newick_files) {
index <- index + 1
file.copy(from = paste0("../figures/fringillidae-cross-validation/", file_name),
to = paste0("../dryad/Sanchez-Reyes_etal_2022_supplementary_figure_S", index, "_cross_validated.tre"),
overwrite = TRUE)
write(paste0("https://raw.githubusercontent.com/LunaSare/datelifeMS1/main/dryad/Sanchez-Reyes_etal_2022_supplementary_figure_S", index, "_cross_validated.tre"), file = "../dryad/urls.txt", append=TRUE)
}
```

# Description of data files
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34 changes: 34 additions & 0 deletions dryad/README.md
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Expand Up @@ -103,6 +103,40 @@ file.copy(from = "../figures/fringillidae-topologies/fringillidae_monophyletic_t
file.copy(from = "../figures/fringillidae-topologies/fringillidae_paraphyletic_topology.tre",
to = "../dryad/Sanchez-Reyes_etal_2022_figure_4B_topology_finches_ncbi.tre",
overwrite = TRUE)

files_in_path <- list.files(path = "../figures/figure-fringillidae/source_chronograms")

# get source chronograms newick file names
newick_files <- files_in_path[grep("[.]tre", files_in_path)]

# order files numerically
newick_files <- stringr::str_sort(newick_files, numeric = TRUE)

index <- 1
for (file_name in newick_files) {
index <- index + 1
file.copy(from = paste0("../figures/figure-fringillidae/source_chronograms/", file_name),
to = paste0("../dryad/Sanchez-Reyes_etal_2022_supplementary_figure_S", index, "_source.tre"),
overwrite = TRUE)
write(paste0("https://raw.githubusercontent.com/LunaSare/datelifeMS1/main/dryad/Sanchez-Reyes_etal_2022_supplementary_figure_S", index, "_source.tre"), file = "../dryad/urls.txt", append=TRUE)
}

# get cross validated chronograms newick file names
files_in_path <- list.files(path = "../figures/fringillidae-cross-validation")

newick_files <- files_in_path[grep("[.]tre", files_in_path)]

# order files numerically
newick_files <- stringr::str_sort(newick_files, numeric = TRUE)

index <- 1
for (file_name in newick_files) {
index <- index + 1
file.copy(from = paste0("../figures/fringillidae-cross-validation/", file_name),
to = paste0("../dryad/Sanchez-Reyes_etal_2022_supplementary_figure_S", index, "_cross_validated.tre"),
overwrite = TRUE)
write(paste0("https://raw.githubusercontent.com/LunaSare/datelifeMS1/main/dryad/Sanchez-Reyes_etal_2022_supplementary_figure_S", index, "_cross_validated.tre"), file = "../dryad/urls.txt", append=TRUE)
}
```

# Description of data files
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Binary file modified dryad/README.pdf
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1 change: 1 addition & 0 deletions dryad/Sanchez-Reyes_etal_2022_supplementary_figure_S10_cross_validated.tre
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(Peucedramus_taeniatus:31.208523,(((((Cardinalis_sinuatus:5.769341,Cardinalis_cardinalis:5.769341)n60:9.323996,(Cyanocompsa_brissonii:9.346845,(Pheucticus_melanocephalus:3.600352,Pheucticus_aureoventris:3.600352)n66:5.746492)n61:5.746492)n56:0.822095,(Platyspiza_crassirostris:7.957716,Porphyrospiza_caerulescens:7.957716)n57:7.957716)n51:0.822095,(Peucaea_botterii:12.079346,((Emberiza_flaviventris:10.815645,(((Emberiza_fucata:3.258647,Schoeniclus_rusticus:3.258647)n81:3.258647,((Emberiza_pusilla:4.324078,Emberiza_rutila:4.324078)n85:1.291141,(Emberiza_chrysophrys:4.40093,(Schoeniclus_spodocephala:3.380498,Schoeniclus_aureolus:3.380498)n87:1.020432)n86:1.214289)n82:0.902074)n73:3.666502,(Schoeniclus_elegans:7.107542,Emberiza_schoeniclus:7.107542)n74:3.076253)n70:0.63185)n62:0.63185,((Melophus_lathami:5.594949,(Emberiza_melanocephala:3.639034,Emberiza_bruniceps:3.639034)n80:1.955915)n67:4.391189,(Emberiza_cioides:7.152651,(Emberiza_hortulana:3.720028,(Emberiza_leucocephalos:0.287405,Emberiza_citrinella:0.287405)n79:3.432623)n76:3.432623)n68:2.833487)n63:1.461357)n55:0.63185)n52:4.658182)n47:6.320467,((Fringilla_montifringilla:6.556329,Fringilla_coelebs:6.556329)n49:16.064861,((Coccothraustes_coccothraustes:14.600655,(Eophona_personata:4.082886,Eophona_migratoria:4.082886)n72:10.517769)n53:7.583733,((Haemorhous_mexicanus:17.161327,(Chloris_sinica:13.828263,((Acanthis_flammea:5.452725,Loxia_curvirostra:5.452725)n77:5.042474,((Spinus_spinus:4.858731,Spinus_psaltria:4.858731)n83:0.931748,(Serinus_canaria:2.895239,Carduelis_carduelis:2.895239)n84:2.895239)n78:4.70472)n75:3.333064)n69:3.333064)n58:3.333064,((Carpodacus_erythrinus:6.109472,Carpodacus_roseus:6.109472)n64:6.109472,(Pyrrhula_pyrrhula:9.090047,(Bucanetes_githagineus:5.96115,Eremopsaltria_mongolica:5.96115)n71:3.128897)n65:3.128897)n59:8.275449)n54:1.689995)n50:0.436804)n48:0.436804)n46:8.150528)n45:1;
1 change: 1 addition & 0 deletions dryad/Sanchez-Reyes_etal_2022_supplementary_figure_S11_cross_validated.tre
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(Urocynchramus_pylzowi:33.70956,(Peucedramus_taeniatus:31.665546,((((Calcarius_pictus:3.389229,Calcarius_ornatus:3.389229)n215:10.040231,(Calcarius_mccownii:9.115624,(Calcarius_lapponicus:4.80179,(Plectrophenax_nivalis:0.487955,Plectrophenax_hyperboreus:0.487955)n260:4.313835)n226:4.313835)n216:4.313835)n207:6.821996,(((((Tersina_viridis:10.502528,(Cyanerpes_cyaneus:9.394583,(Cyanerpes_caeruleus:4.419789,(Cyanerpes_lucidus:2.209895,Cyanerpes_nitidus:2.209895)n368:2.209895)n334:4.974793)n295:1.107945)n266:1.107945,((Hemispingus_rufosuperciliaris:9.178141,((Hemispingus_verticalis:3.724305,Hemispingus_xanthophthalmus:3.724305)n311:3.747143,(((Hemispingus_atropileus:0.295224,Hemispingus_auricularis:0.295224)n370:5.925763,(Hemispingus_parodii:0.634606,Hemispingus_calophrys:0.634606)n371:5.586381)n314:0.62523,((Hemispingus_superciliaris:4.837117,(Hemispingus_piurae:3.832567,(Hemispingus_frontalis:3.610789,Hemispingus_melanotis:3.610789)n377:0.221779)n341:1.00455)n326:1.00455,(Hemispingus_trifasciatus:2.920834,Donacospiza_albifrons:2.920834)n327:2.920834)n315:1.00455)n312:0.62523)n302:1.706693)n272:1.706692,(Embernagra_platensis:10.260294,Porphyrospiza_caerulescens:10.260294)n273:0.624538)n267:0.725641)n235:3.757193,((Parkerthraustes_humeralis:12.036538,(Melopyrrha_nigra:10.057943,Platyspiza_crassirostris:10.057943)n250:1.978595)n239:1.09444,(Rowettia_goughensis:12.48515,(Chlorophonia_occipitalis:1.996208,Chlorophonia_flavirostris:1.996208)n243:10.488942)n240:0.645827)n236:2.236689)n218:2.236689,(((Cardinalis_sinuatus:5.856377,(Cardinalis_phoeniceus:3.741279,Cardinalis_cardinalis:3.741279)n344:2.115098)n253:5.158342,((Caryothraustes_poliogaster:3.406948,Caryothraustes_canadensis:3.406948)n274:5.679647,(Rhodothraupis_celaeno:6.856331,Periporphyrus_erythromelas:6.856331)n275:2.230265)n254:1.928123)n224:6.129498,((Pheucticus_aureoventris:3.737746,(Pheucticus_melanocephalus:3.463831,Pheucticus_ludovicianus:3.463831)n376:0.273915)n233:10.827909,(Spiza_americana:10.271646,((Passerina_cyanea:6.861583,((Passerina_amoena:3.511853,Passerina_caerulea:3.511853)n328:2.741753,(Passerina_rositae:5.645629,(Passerina_leclancherii:4.842418,(Passerina_versicolor:2.014452,Passerina_ciris:2.014452)n357:2.827965)n339:0.803211)n329:0.607977)n313:0.607977)n277:1.443,(Cyanocompsa_parellina:7.389253,(Cyanoloxia_cyanoides:6.906321,(Cyanocompsa_brissonii:2.832261,Cyanoloxia_glaucocaerulea:2.832261)n337:4.07406)n283:0.482932)n278:0.915331)n268:1.967063)n234:4.294008)n225:2.578562)n219:0.460138)n211:0.460138,(Phaeothlypis_fulvicauda:16.096836,((Buarremon_torquatus:10.574594,(Peucaea_botterii:4.801976,Peucaea_aestivalis:4.801976)n259:5.772618)n244:2.384065,(((Emberiza_capensis:5.066284,(Fringillaria_impetuani:4.342871,Fringillaria_tahapisi:4.342871)n338:0.723413)n284:2.580944,(Emberiza_flaviventris:5.578383,Emberiza_cabanisi:5.578383)n285:2.068845)n257:3.707192,(((Schoeniclus_siemsseni:5.872614,Schoeniclus_elegans:5.872614)n281:2.859558,((Schoeniclus_yessoensis:6.290558,(Emberiza_pallasi:4.98604,Emberiza_schoeniclus:4.98604)n319:1.304518)n293:1.325287,(Emberiza_fucata:6.499518,(Schoeniclus_rusticus:5.141484,((Emberiza_chrysophrys:3.060601,(Emberiza_variabilis:2.177645,Emberiza_tristrami:2.177645)n378:0.882957)n352:1.794614,(Emberiza_pusilla:4.400944,(Emberiza_sulphurata:3.946674,(Emberiza_rutila:3.750428,(Schoeniclus_spodocephala:3.682629,Schoeniclus_aureolus:3.682629)n369:0.067799)n363:0.196246)n360:0.454271)n353:0.454271)n333:0.286269)n316:1.358034)n294:1.116327)n282:1.116327)n261:2.341682,((Melophus_lathami:5.81236,(Emberiza_melanocephala:3.854457,Emberiza_bruniceps:3.854457)n332:1.957903)n269:4.98093,((Emberiza_jankowskii:4.054394,(Emberiza_cia:2.168973,(Emberiza_godlewskii:1.319128,Emberiza_cioides:1.319128)n388:0.849845)n361:1.885421)n296:5.150399,((Emberiza_buchanani:4.715831,(Emberiza_caesia:2.343794,Emberiza_hortulana:2.343794)n351:2.372037)n317:1.647563,(Emberiza_cirlus:4.872134,(Emberiza_stewarti:3.380874,(Emberiza_leucocephalos:0.622141,Emberiza_citrinella:0.622141)n380:2.758733)n348:1.49126)n318:1.49126)n297:2.841399)n270:1.588497)n262:0.280564)n258:0.280565)n245:1.604239)n217:3.138177)n212:1.967657)n208:2.186962)n203:2.186962,((Fringilla_montifringilla:6.641963,(Fringilla_coelebs:3.84426,Fringilla_teydea:3.84426)n303:2.797703)n205:15.23606,(((Euphonia_cyanocephala:3.66462,Euphonia_musica:3.66462)n246:9.275967,((Euphonia_pectoralis:8.534584,(Euphonia_affinis:6.657107,(Euphonia_finschi:4.402194,Euphonia_chlorotica:4.402194)n322:2.254913)n290:1.877477)n264:2.482144,((Euphonia_fulvicrissa:2.485204,Euphonia_gouldi:2.485204)n279:6.713212,(Euphonia_laniirostris:5.235318,Euphonia_hirundinacea:5.235318)n280:3.963098)n265:1.818313)n247:1.923858)n209:8.377043,(((Hesperiphona_vespertina:10.012903,Coccothraustes_coccothraustes:10.012903)n229:3.735672,((Eophona_migratoria:3.964756,Eophona_personata:3.964756)n248:9.408495,(Mycerobas_affinis:10.642931,Mycerobas_carnipes:10.642931)n249:2.73032)n230:0.375324)n213:7.008659,(((Rhodospiza_obsoleta:10.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