tr <- read.tree("/Users/carrietribble/Desktop/arbor_hackathon_docs/heliconia/Heliconia_all_dated_mod.phy")
trait <- read.csv('/Users/carrietribble/Desktop/arbor_hackathon_docs/heliconia/Heliconia_phylogeny_matrix.csv')
td <- treeplyr::make.treedata(tr, trait)
ace_arbor <- aRbor::aceArbor( select_(td, "InflorL"), charType='continuous', aceType = 'marginal')The mean value of InflorL extant values is 0.5427895, the reconstructed nodes have a mean value of 0.5434116. The original range of your data values is 0.07 to 3. The estimated node values range from 0.1064772 to 1.8471608. When we include the 95% confidence invervals for those estimates, the estimates range from -0.1053476 to 2.0914694. A portion of those estimates are displayed below.
| lowerCI95 | estimate | upperCI95 | |
|---|---|---|---|
| 191 | -0.0173080 | 0.4252032 | 0.8677145 |
| 192 | 0.0171425 | 0.4334778 | 0.8498131 |
| 193 | -0.0074521 | 0.4154564 | 0.8383650 |
| 194 | -0.0036365 | 0.2988343 | 0.6013051 |
| 195 | 0.1962479 | 0.5166668 | 0.8370857 |
| 196 | 0.3681162 | 0.5873769 | 0.8066376 |
| 197 | 0.2558298 | 0.5136536 | 0.7714774 |
| 198 | 0.2868183 | 0.5410689 | 0.7953194 |
| 199 | 0.3355337 | 0.5740100 | 0.8124862 |
| 200 | 0.2198461 | 0.4510244 | 0.6822026 |
| 201 | 0.2291984 | 0.4478164 | 0.6664345 |
| 202 | 0.3004194 | 0.4679435 | 0.6354675 |
| 203 | 0.1551561 | 0.4201140 | 0.6850720 |
| 204 | 0.1247209 | 0.3957570 | 0.6667931 |
| 205 | 0.0336143 | 0.3927010 | 0.7517878 |
| 206 | 0.0931921 | 0.4171581 | 0.7411240 |
| 207 | 0.1557509 | 0.4093899 | 0.6630290 |
| 208 | 0.0113636 | 0.3617488 | 0.7121341 |
| 209 | 0.1469907 | 0.3518700 | 0.5567494 |
| 210 | 0.1014583 | 0.3767233 | 0.6519884 |
The plot below shows the relationship between the width of your 95% confidence intervals and time as indicated by node ages.
Be aware that the function dropped some tips of your phylogeny:
| x |
|---|
| Musella_lasiocarpa |
| Ensete_ventricosum |
| Ensete_superbum |
| Musa_coccinea |
| Musa_sp12 |
| Musa_ornata |
| Musa_basjoo |
| Monocostus_uniflorus |
| Globba_winitii |
| Canna_jaegeriana |
| Thaumatococcus_daniellii |
| Halopegia_azurea |
| Orchidantha_maxillarioides |
| Ravenala_madagascariensis |
| Strelitzia_reginae |
| Strelitzia_caudata |
| H_willisiana_Collins_EC9957 |
| H_mooreana_Ortega_49_AF |
| H_sp_Specht_0608 |
| H_sp_Kress_943698 |
| H_x_rauliniana_Abalo_sn_AF_A |
| H_berryi_Wasshousen_2106_AF |
| H_gloriosa_Collins_96203 |
| H_plowmania_Kress_943677 |
| H_waoraniana_Kress_965694_AF |
| H_x_rauliniana_Abalo_sn_AF_B |
| H_penduloides_Kress_sn |
| H_atratensis_Kress_903142 |
| H_sp_Specht_0805 |
It might has dropped information from your trait data as well: No data was dropped.