Data description (updated on 09-08-2018)
Number of species
| Total number | Analyzed so far | Species with at least 1 song | Proportion analyzed | Proportion with at least 1 song |
|---|---|---|---|---|
| 358 | 315 | 246 | 0.88 | 0.687 |
Species with 0 songs
## [1] "69 species"| Boissonneaua jardini | Archilochus alexandri |
| Boissonneaua matthewsii | Archilochus colubris |
| Avocettula recurvirostris | Calliphlox amethystina |
| Chalcostigma olivaceum | Calliphlox bryantae |
| Discosura conversii | Calliphlox evelynae |
| Discosura langsdorffi | Calliphlox mitchellii |
| Discosura popelairii | Calothorax lucifer |
| Doryfera johannae | Campylopterus duidae |
| Ensifera ensifera | Chaetocercus bombus |
| Eriocnemis aline | Chaetocercus mulsant |
| Eriocnemis glaucopoides | Chlorostilbon canivetii |
| Eriocnemis mosquera | Chlorostilbon lucidus |
| Eriocnemis nigrivestis | Chlorostilbon poortmani |
| Eulampis holosericeus | Chlorostilbon ricordii |
| Goldmania violiceps | Cyanophaia bicolor |
| Heliodoxa branickii | Cynanthus latirostris |
| Heliodoxa xanthogonys | Cynanthus sordidus |
| Oreotrochilus chimborazo | Doricha eliza |
| Phaethornis koepckeae | Hylocharis leucotis |
| Polyonymus caroli | Hylocharis xantusii |
| Thalurania ridgwayi | Lampornis calolaemus |
| Heliangelus strophianus | Lampornis castaneoventris |
| Coeligena helianthea | Lamprolaima rhami |
| Coeligena orina | Microstilbon burmeisteri |
| Heliangelus micraster | Myrmia micrura |
| Lophornis chalybeus | Orthorhyncus cristatus |
| Taphrospilus hypostictus | Rhodopis vesper |
| Lophornis adorabilis | Selasphorus calliope |
| Lophornis gouldii | Selasphorus platycercus |
| Lophornis magnificus | Selasphorus rufus |
| Lophornis stictolophus | Selasphorus scintilla |
| Oreotrochilus leucopleurus | Amazilia viridifrons |
| Phaethornis stuarti | Aglaeactis aliciae |
| Aerodramus fuciphagus | Tilmatura dupontii |
| Phlogophilus harterti | Boissonneaua jardini |
Recordings per library
| Library | Number of recordings | |
|---|---|---|
| 10 | Xeno-Canto | 6183 |
| 6 | Macaulay Library | 974 |
| 1 | Borror | 767 |
| 4 | FLMNH | 308 |
| 9 | Theresa Feo & Chris Clark | 201 |
| 2 | British Library | 183 |
| 5 | LBUCR | 56 |
| 8 | Museo de Zoologia, UNAM | 31 |
| 3 | Chris Clark | 14 |
| 7 | Marcelo Araya-Salas | 5 |
| 11 | TOTAL | 8722 |
Mean/range # of recordings per species (elements)
| mean | range | |
|---|---|---|
| Number of “individual element” recordings | 2.51 | 0 - 16 |
| Number of “full song” recordings | 1.18 | 0 - 13 |
Last selection file addition per observer
| By | Last day |
|---|---|
| Mrcl Ary | 2018-08-09 |
| Jln Rdrg | 2018-08-08 |
| Xmn Obr | 2018-08-08 |
| Prscll R | 2018-08-08 |
| Dvd Sgz | 2018-08-08 |
| Jdth Smt | 2018-08-08 |
| Kthrn Kj | 2018-08-08 |
| Clr O’Kn | 2018-02-25 |
Mean recordings per observer
| Species | Mean # recs/elements | Mean # recs/full songs | |
|---|---|---|---|
| Clr O’Kn | 8 | 1.38 | 0.000 |
| Dvd Sgüe | 116 | 2.56 | 1.138 |
| Jdth Smt | 34 | 2.53 | 0.941 |
| Jln Rdrg | 37 | 2.73 | 0.405 |
| Kthrn Kj | 8 | 3.38 | 1.375 |
| Mrcl Ary | 1 | 6.00 | 0.000 |
| Prscll R | 68 | 1.25 | 0.074 |
| Xmn Obr | 42 | 4.24 | 4.214 |
Total recordings and selection tables per observer
The objective of this table is to highlight mismatches between the number of recordings analyzed and the selection tables available. In theory, each analyzed recording should have a corresponding selection table. Please figure out where the mismatches come from (if any). Note that there is another table down below showing the same type of data split be species.
Key:
- Reddish cells highlight species with mistached numbers of analyzed recordings and available selection tables:
| Number of recs/elements | Number of selection tables/elements | Number of recs/full songs | Number of selection tables/full songs | Total number of selection files | |
|---|---|---|---|---|---|
| Dvd Sgüe | 297 | 287 | 132 | 136 | 423 |
| Xmn Obr | 178 | 177 | 177 | 178 | 355 |
| Jln Rdrg | 101 | 101 | 15 | 15 | 116 |
| Jdth Smt | 86 | 88 | 32 | 32 | 120 |
| Prscll R | 85 | 81 | 5 | 2 | 83 |
| Kthrn Kj | 27 | 30 | 11 | 0 | 30 |
| Clr O’Kn | 11 | 11 | 0 | 0 | 11 |
| Mrcl Ary | 6 | 6 | 0 | 0 | 6 |
Selections that couldn’t be assigned to any observer
## character(0)Total recordings and selection tables per species
This table is highlights mismatches between the number of recordings analyzed and the selection tables available per species.
Key:
- Reddish cells highlight species with mistached numbers of analyzed recordings and available selection tables:
Recordings per species and vocalization type by observer
Key:
- Orange rows highlight species with way too few “element selected” recordings based on the number of “song recordings” available for that species (Note: we are aiming for selections from 5 different recordings per species)
- Reddish cells highlight species with way too few “full song selected” recordings based on the number of “song recordings” available for that species (Note: we are aiming for 5 recordings with full songs selected and a maximum of 10 recordings or those that are available). It also includes Phaethornis species that I know are very vocal and should have more songs
Phylogenetic tree
## [1] "273 species"
Next steps
Analyze recordings from “Caprimulgiformes” outgroups (Aegothelidae, Hemiprocnidae, Nyctibiidae, Apodidae, Podargidae, Steatornithidae, Caprimulgidae)Check bee hummingbird species that have lost song according to Clark et al 2018- Check my own hummingbird phylogeny
Fix sound file names- Print spectrograms highlighting selected songs (removing long gaps in between)
Copy Feo&Clark recordings to main folderAdd Mellisuga minima and Phaeochroa cuvierii own data (P. cuvierii not available)
Session information
## R version 3.4.4 (2018-03-15)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/openblas-base/libblas.so.3
## LAPACK: /usr/lib/libopenblasp-r0.2.18.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] pbmcapply_1.2.4 future_1.6.2 pbapply_1.3-4
## [4] googledrive_0.1.1 phytools_0.6-44 ape_5.0
## [7] taxize_0.9.0 Rraven_1.0.3 warbleR_1.1.15
## [10] NatureSounds_1.0.0 seewave_2.1.0 tuneR_1.3.3
## [13] maps_3.3.0 dplyr_0.7.5 stringdist_0.9.4.6
## [16] knitr_1.20 kableExtra_0.9.0 googlesheets_0.2.2
## [19] RColorBrewer_1.1-2 ggplot2_2.2.1
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-137 bitops_1.0-6
## [3] bold_0.5.0 httr_1.3.1
## [5] rprojroot_1.3-2 numDeriv_2016.8-1
## [7] Deriv_3.8.4 tools_3.4.4
## [9] backports_1.1.2 R6_2.2.2
## [11] lazyeval_0.2.1 colorspace_1.3-2
## [13] tidyselect_0.2.4 mnormt_1.5-5
## [15] phangorn_2.3.1 curl_3.1
## [17] compiler_3.4.4 soundgen_1.2.1
## [19] rvest_0.3.2 animation_2.5
## [21] expm_0.999-2 xml2_1.2.0
## [23] scales_0.5.0 mvtnorm_1.0-8
## [25] quadprog_1.5-5 readr_1.1.1
## [27] proxy_0.4-22 dtw_1.20-1
## [29] stringr_1.3.1 digest_0.6.15
## [31] Sim.DiffProc_4.0 rmarkdown_1.9
## [33] jpeg_0.1-8 pkgconfig_2.0.1
## [35] htmltools_0.3.6 plotrix_3.7
## [37] highr_0.6 rlang_0.2.1
## [39] rstudioapi_0.7 bindr_0.1.1
## [41] combinat_0.0-8 jsonlite_1.5
## [43] RCurl_1.95-4.11 magrittr_1.5
## [45] Matrix_1.2-14 Rcpp_0.12.18
## [47] munsell_0.4.3 scatterplot3d_0.3-40
## [49] stringi_1.2.2 yaml_2.1.19
## [51] clusterGeneration_1.3.4 MASS_7.3-50
## [53] plyr_1.8.4 grid_3.4.4
## [55] listenv_0.6.0 lattice_0.20-35
## [57] splines_3.4.4 hms_0.4.0
## [59] pillar_1.2.3 igraph_1.1.2
## [61] rjson_0.2.20 fftw_1.0-4
## [63] reshape2_1.4.3 codetools_0.2-15
## [65] fastmatch_1.1-0 crul_0.5.0
## [67] glue_1.2.0 evaluate_0.10.1
## [69] msm_1.6.6 data.table_1.10.4-3
## [71] foreach_1.4.4 cellranger_1.1.0
## [73] gtable_0.2.0 purrr_0.2.4
## [75] reshape_0.8.7 assertthat_0.2.0
## [77] pracma_2.1.4 coda_0.19-1
## [79] survival_2.42-6 viridisLite_0.3.0
## [81] signal_0.7-6 tibble_1.4.2
## [83] iterators_1.0.10 bindrcpp_0.2.2
## [85] globals_0.10.3 rgl_0.95.1441