In this practice we will play around with the ‘turdus’ data set that we used in Assigment 1. The goal of this exercise is exploring more options and become more familiar when creating functions and loops.
As you should know by now, this data set contains metadata from recordings for the entire genus Turdus. Turdus is a cosmopolitan and very vocal group. A .csv file with the Turdus metadata can be download as follows:
# set working directory
setwd("PUT THE FOLDER LOCATION WHERE YOU WANT TO SAVE THE FILE HERE")
download.file("https://marceloarayasalas.weebly.com/uploads/2/5/5/2/25524573/metadata_turdus_recordings_feb-2018.csv", destfile = "metadata_turdus_recordings_feb-2018.csv")
You can also download the file manually from here.
Let’s take a look at the entire data set to have an idea of the type of data available:
View(turdus)| Recording_ID | Genus | Specific_epithet | Subspecies | English_name | Recordist | Country | Locality | Latitude | Longitude | Vocalization_type | Audio_file | License | Url | Quality | Time | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 199449 | Turdus | litsitsirupa | litsitsirupa | Groundscraper Thrush | Niall Perrins | South Africa | Mabusa, Nkangala, Mpumalanga | -25.3617 | 29.088 | call | //www.xeno-canto.org/199449/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/199449 | no score | 08:00 | 2014-10-19 |
| 347146 | Turdus | litsitsirupa | Groundscraper Thrush | Peter Boesman | Namibia | Omaruru area west | -21.4475 | 15.888 | song and call | //www.xeno-canto.org/347146/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/347146 | A | 8:30 | 2016-11-11 | |
| 300630 | Turdus | litsitsirupa | simensis | Groundscraper Thrush | Peter Boesman | Ethiopia | Debre Birhan area | 9.6707 | 39.534 | song | //www.xeno-canto.org/300630/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/300630 | A | 15:00 | 2015-12-02 |
| 300628 | Turdus | litsitsirupa | simensis | Groundscraper Thrush | Peter Boesman | Ethiopia | Debre Libanos area | 9.7117 | 38.858 | song | //www.xeno-canto.org/300628/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/300628 | A | 10:00 | 2015-12-01 |
| 298557 | Turdus | litsitsirupa | litsitsirupa ? | Groundscraper Thrush | Frank Lambert | Malawi | Dzalanyama Forest Reserve, southern access road, Central Region | -14.2649 | 33.546 | alarm?, call | //www.xeno-canto.org/298557/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/298557 | A | 11:09 | 2015-11-26 |
| 292929 | Turdus | litsitsirupa | Groundscraper Thrush | Faansie Peacock | South Africa | Eweni, Champagne Castle, Drakensberg, KwaZulu-Natal | -29.0476 | 29.423 | song | //www.xeno-canto.org/292929/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/292929 | A | 05:30 | 2015-11-21 | |
| 153875 | Turdus | litsitsirupa | Groundscraper Thrush | Rolf A. de By | Namibia | Monte Christo, Joe’s place | -22.3420 | 16.973 | song | //www.xeno-canto.org/153875/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/153875 | A | 06:11 | 2013-11-02 | |
| 347148 | Turdus | litsitsirupa | Groundscraper Thrush | Peter Boesman | Namibia | Omaruru area west | -21.4475 | 15.888 | song | //www.xeno-canto.org/347148/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/347148 | B | 8:30 | 2016-11-11 | |
| 347147 | Turdus | litsitsirupa | Groundscraper Thrush | Peter Boesman | Namibia | Omaruru area west | -21.4475 | 15.888 | song | //www.xeno-canto.org/347147/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/347147 | B | 8:30 | 2016-11-11 | |
| 347145 | Turdus | litsitsirupa | Groundscraper Thrush | Peter Boesman | Namibia | Omaruru area west | -21.4475 | 15.888 | call and song | //www.xeno-canto.org/347145/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/347145 | B | 8:30 | 2016-11-11 | |
| 300629 | Turdus | litsitsirupa | simensis | Groundscraper Thrush | Peter Boesman | Ethiopia | Debre Libanos area | 9.7117 | 38.858 | song and call | //www.xeno-canto.org/300629/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/300629 | B | 10:00 | 2015-12-01 |
| 300625 | Turdus | litsitsirupa | simensis | Groundscraper Thrush | Peter Boesman | Ethiopia | Gefersa reservoir, Addis Ababa | 9.0670 | 38.626 | flight call | //www.xeno-canto.org/300625/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/300625 | B | 16:00 | 2015-11-29 |
| 298558 | Turdus | litsitsirupa | litsitsirupa ? | Groundscraper Thrush | Frank Lambert | Malawi | Dzalanyama Forest Reserve, southern access road, Central Region | -14.2649 | 33.546 | alarm?, call | //www.xeno-canto.org/298558/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/298558 | B | 11:07 | 2015-11-26 |
| 395191 | Turdus | litsitsirupa | Groundscraper Thrush | Robert Davis | Congo (Democratic Republic) | Kolwezi, Katanga | -10.7644 | 25.680 | song | //www.xeno-canto.org/395191/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/395191 | C | 08:30 | 2017-10-14 | |
| 300627 | Turdus | litsitsirupa | simensis | Groundscraper Thrush | Peter Boesman | Ethiopia | Debre Libanos area | 9.7117 | 38.858 | flight call | //www.xeno-canto.org/300627/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/300627 | C | 10:00 | 2015-12-01 |
| 300626 | Turdus | litsitsirupa | simensis | Groundscraper Thrush | Peter Boesman | Ethiopia | Sululta plain | 9.2339 | 38.755 | flight call | //www.xeno-canto.org/300626/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/300626 | C | 11:00 | 2015-11-30 |
| 104594 | Turdus | litsitsirupa | litsitsirupa | Groundscraper Thrush | Rory Nefdt | Zambia | Lazy J Ranch, Lusaka | -15.4920 | 28.450 | Song | //www.xeno-canto.org/104594/download | //creativecommons.org/licenses/by-nc-nd/2.5/ | https://www.xeno-canto.org/104594 | C | 15:50 hrs | 2012-06-23 |
| 51299 | Turdus | litsitsirupa | Groundscraper Thrush | Bram Piot | Ethiopia | Gefersa Reservoir | 9.0700 | 38.623 | Song (? or calls) | //www.xeno-canto.org/51299/download | //creativecommons.org/licenses/by-nc-nd/2.5/ | https://www.xeno-canto.org/51299 | D | 08:00 | 2010-05-08 | |
| 389455 | Turdus | flavipes | Yellow-legged Thrush | Lari Boesing | Brazil | Piracaia, São Paulo | -23.0652 | -46.244 | song | //www.xeno-canto.org/389455/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/389455 | no score | 05:30 | 2014-10-14 | |
| 389226 | Turdus | flavipes | Yellow-legged Thrush | Lari Boesing | Brazil | Nazaré Paulista, São Paulo | -23.2452 | -46.332 | song | //www.xeno-canto.org/389226/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/389226 | no score | 19:00 | 2014-09-14 | |
| 364453 | Turdus | flavipes | Yellow-legged Thrush | Miguel Angel Torres | Venezuela | La Puente, Bruzual, Yaracuy | 10.2466 | -68.931 | male, song | //www.xeno-canto.org/364453/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/364453 | no score | 10:00 | 2017-04-12 | |
| 353642 | Turdus | flavipes | Yellow-legged Thrush | Andres Angulo | Colombia | San Lorenzo ridge , Sierra Nevada de Santa Marta, Santa Marta, Magdalena | 11.1034 | -74.080 | song | //www.xeno-canto.org/353642/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/353642 | no score | 06:00 | 2017-01-09 | |
| 344433 | Turdus | flavipes | Yellow-legged Thrush | Gustavo Luz | Brazil | Praia Grande | NA | NA | song | //www.xeno-canto.org/344433/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/344433 | no score | 08:30 | 2016-11-27 | |
| 340961 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Ricardo José Mitidieri | Brazil | PETP Jacarandá, Teresópolis, State of Rio de Janeiro | -22.4350 | -42.933 | song | //www.xeno-canto.org/340961/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/340961 | no score | 11:30 | 2016-10-30 |
| 335352 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Ricardo José Mitidieri | Brazil | Rio Bonito de Cima - Nova Friburgo - RJ | -22.3917 | -42.375 | song | //www.xeno-canto.org/335352/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/335352 | no score | 16:30 | 2016-09-16 |
| 333210 | Turdus | flavipes | Yellow-legged Thrush | Jerome Fischer | Brazil | Fazenda Angelim, Ubatuba SP | -23.3930 | -45.065 | call, male | //www.xeno-canto.org/333210/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/333210 | no score | 06:15 | 2016-09-03 | |
| 269499 | Turdus | flavipes | Yellow-legged Thrush | Jerome Fischer | Brazil | Green Trail, Reserva Ecológica de Guapiaçu, RJ | -22.4179 | -42.738 | song | //www.xeno-canto.org/269499/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/269499 | no score | 07:00 | 2015-08-20 | |
| 256917 | Turdus | flavipes | Yellow-legged Thrush | Leandro Castillo | Argentina | Iguazú, Misiónes | -25.9777 | -54.114 | song | //www.xeno-canto.org/256917/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/256917 | no score | 13:00 | 2014-11-22 | |
| 212455 | Turdus | flavipes | Yellow-legged Thrush | Fernando Igor de Godoy | Brazil | APA Capivari Monos, São Paulo, SP | -23.9557 | -46.650 | song | //www.xeno-canto.org/212455/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/212455 | no score | 05:30 | 2010-09-20 | |
| 212454 | Turdus | flavipes | Yellow-legged Thrush | Fernando Igor de Godoy | Brazil | APA Capivari Monos, São Paulo, SP | -23.9557 | -46.650 | song | //www.xeno-canto.org/212454/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/212454 | no score | 05:30 | 2010-09-20 | |
| 212452 | Turdus | flavipes | Yellow-legged Thrush | Fernando Igor de Godoy | Brazil | APA Capivari Monos, São Paulo, SP | -23.9557 | -46.650 | song | //www.xeno-canto.org/212452/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/212452 | no score | 05:30 | 2010-09-20 | |
| 211299 | Turdus | flavipes | Yellow-legged Thrush | Douglas Eduardo Rocha | Brazil | Santa Bárbara do Leste, Santa Bárbara do Leste, Minas Gerais | -19.9755 | -42.102 | song | //www.xeno-canto.org/211299/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/211299 | no score | 12:00 | 2015-01-25 | |
| 211298 | Turdus | flavipes | Yellow-legged Thrush | Douglas Eduardo Rocha | Brazil | Santa Bárbara do Leste, Santa Bárbara do Leste, Minas Gerais | -19.9702 | -42.107 | song | //www.xeno-canto.org/211298/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/211298 | no score | 11:30 | 2015-01-25 | |
| 211279 | Turdus | flavipes | Yellow-legged Thrush | Douglas Eduardo Rocha | Brazil | Santa Bárbara do Leste, Santa Bárbara do Leste, Minas Gerais | -19.9785 | -42.108 | song | //www.xeno-canto.org/211279/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/211279 | no score | 12:00 | 2015-01-25 | |
| 211278 | Turdus | flavipes | Yellow-legged Thrush | Douglas Eduardo Rocha | Brazil | Santa Bárbara do Leste, Santa Bárbara do Leste, Minas Gerais | -19.9785 | -42.108 | song | //www.xeno-canto.org/211278/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/211278 | no score | 12:30 | 2015-01-25 | |
| 390827 | Turdus | flavipes | Yellow-legged Thrush | Guilherme Willrich | Brazil | Joinville, Santa Catarina | -26.3234 | -48.969 | male, song | //www.xeno-canto.org/390827/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/390827 | A | 08:00 | 2017-10-06 | |
| 386877 | Turdus | flavipes | Yellow-legged Thrush | Odirlei Vieira da Fonseca | Brazil | Rebio Tinguá, Nova Iguaçu, RJ | -22.5939 | -43.435 | song | //www.xeno-canto.org/386877/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/386877 | A | 17:00 | 2017-09-07 | |
| 361276 | Turdus | flavipes | Yellow-legged Thrush | Odirlei Vieira da Fonseca | Brazil | Agulhas Negras (Puesto de Avanzada), Planalto, PN Itatiaia, Rio de Janeiro | -22.3731 | -44.703 | male, song | //www.xeno-canto.org/361276/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/361276 | A | 16:30 | 2017-02-08 | |
| 356993 | Turdus | flavipes | Yellow-legged Thrush | Henry Miller Carneiro Alexandre | Brazil | Horto Florestal , Ubatuba, São Paulo | -23.4151 | -45.112 | song | //www.xeno-canto.org/356993/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/356993 | A | 07:15 | 2016-12-30 | |
| 352267 | Turdus | flavipes | Yellow-legged Thrush | Odirlei Vieira da Fonseca | Brazil | Parna Caparaó, Alto Caparaó, Minas Gerais | -20.4556 | -41.809 | male, song | //www.xeno-canto.org/352267/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/352267 | A | 13:30 | 2016-10-31 | |
| 348571 | Turdus | flavipes | Yellow-legged Thrush | Rodrigo Dela Rosa | Brazil | Capim-azul- São José dos Campos-São Paulo | -22.8745 | -45.865 | male, song | //www.xeno-canto.org/348571/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/348571 | A | 18:30 | 2011-10-12 | |
| 345038 | Turdus | flavipes | Yellow-legged Thrush | Rodrigo Dela Rosa | Brazil | Fazenda montes claros, Sao Jose dos Campos, state of Sao Paulo | -23.0401 | -46.033 | male, song | //www.xeno-canto.org/345038/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/345038 | A | 08:30 | 2012-08-05 | |
| 342561 | Turdus | flavipes | Yellow-legged Thrush | Nick Komar | Brazil | Parque Ecologico do Tiete, Guarulhos, São Paulo | -23.4935 | -46.519 | song | //www.xeno-canto.org/342561/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/342561 | A | 12:30 | 2016-11-10 | |
| 342021 | Turdus | flavipes | Yellow-legged Thrush | Rodrigo Dela Rosa | Brazil | Salesópolis, São Paulo | -23.5723 | -45.735 | male, song | //www.xeno-canto.org/342021/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/342021 | A | 08:00 | 2016-11-07 | |
| 335288 | Turdus | flavipes | Yellow-legged Thrush | Robson Silva e Silva | Brazil | Rio Preto, Itanhaém, São Paulo | -24.2056 | -46.916 | male, song | //www.xeno-canto.org/335288/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/335288 | A | 07:00 | 2016-09-09 | |
| 312940 | Turdus | flavipes | Yellow-legged Thrush | GABRIEL LEITE | Colombia | near La Minca below RNA El Dorado, Sierra de Santa Marta, Magdalena | 11.1334 | -74.100 | song | //www.xeno-canto.org/312940/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/312940 | A | 09:00 | 2016-04-03 | |
| 295830 | Turdus | flavipes | Yellow-legged Thrush | Jerome Fischer | Brazil | Itatiaia National Park - Agulhas Negras road | -22.3667 | -44.733 | song | //www.xeno-canto.org/295830/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/295830 | A | 13:10 | 2015-12-17 | |
| 288357 | Turdus | flavipes | Yellow-legged Thrush | Marcelo Villegas | Brazil | São José dos Pinhais, São José dos Pinhais, Paraná | -25.5749 | -49.078 | song | //www.xeno-canto.org/288357/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/288357 | A | 07:00 | 2014-12-11 | |
| 286752 | Turdus | flavipes | flavipes (ssp assumed from location) | Yellow-legged Thrush | Jeremy Minns | Brazil | Serra do Mar State Park. Santa Virgínia | -23.3248 | -45.133 | call | //www.xeno-canto.org/286752/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/286752 | A | 09:55 | 1998-01-30 |
| 285542 | Turdus | flavipes | Yellow-legged Thrush | GABRIEL LEITE | Brazil | Caraguatatuba, Paraibuna, São Paulo | -23.5813 | -45.492 | song | //www.xeno-canto.org/285542/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/285542 | A | 08:00 | 2015-10-19 | |
| 278386 | Turdus | flavipes | Yellow-legged Thrush | Fábio Barata | Brazil | Peruíbe, Peruíbe, São Paulo | -24.3639 | -47.021 | song | //www.xeno-canto.org/278386/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/278386 | A | 09:00 | 2015-09-08 | |
| 278384 | Turdus | flavipes | Yellow-legged Thrush | Fábio Barata | Brazil | Peruíbe, Peruíbe, São Paulo | -24.3639 | -47.021 | song | //www.xeno-canto.org/278384/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/278384 | A | 10:00 | 2015-09-08 | |
| 273596 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Peter Boesman | Colombia | RNA Reinita Cielo Azul, San Vicente de Chucurí, Santander, Colombia, 1800m, N | 5.8460 | -73.375 | song | //www.xeno-canto.org/273596/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/273596 | A | 09:00 | 2011-02-01 |
| 273595 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Peter Boesman | Colombia | RNA Reinita Cielo Azul, San Vicente de Chucurí, Santander, Colombia, 1800m, N | 5.8460 | -73.375 | song and subsong | //www.xeno-canto.org/273595/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/273595 | A | 09:00 | 2011-02-01 |
| 263396 | Turdus | flavipes | Yellow-legged Thrush | Jacob R. Saucier | Guyana | Mount Ayanganna, Cuyuni-Mazaruni | 5.3779 | -59.984 | song | //www.xeno-canto.org/263396/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/263396 | A | 10:30 | 2014-03-30 | |
| 245155 | Turdus | flavipes | Yellow-legged Thrush | Oscar Humberto Marín Gómez | Colombia | Bosque La Meseta, Vereda San José de Suaita, Suaita, Santander | 6.1800 | -73.420 | song | //www.xeno-canto.org/245155/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/245155 | A | 17:15 | 2014-07-03 | |
| 245154 | Turdus | flavipes | Yellow-legged Thrush | Oscar Humberto Marín Gómez | Colombia | Bosque La Meseta, Vereda San José de Suaita, Suaita, Santander | 6.1800 | -73.420 | song | //www.xeno-canto.org/245154/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/245154 | A | 17:10 | 2014-07-03 | |
| 245153 | Turdus | flavipes | Yellow-legged Thrush | Oscar Humberto Marín Gómez | Colombia | Bosque La Meseta, Vereda San José de Suaita, Suaita, Santander | 6.1800 | -73.420 | song | //www.xeno-canto.org/245153/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/245153 | A | 16:45 | 2014-07-03 | |
| 245151 | Turdus | flavipes | Yellow-legged Thrush | Oscar Humberto Marín Gómez | Colombia | Bosque La Meseta, Vereda San José de Suaita, Suaita, Santander | 6.1800 | -73.420 | song | //www.xeno-canto.org/245151/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/245151 | A | 13:50 | 2014-07-03 | |
| 245150 | Turdus | flavipes | Yellow-legged Thrush | Oscar Humberto Marín Gómez | Colombia | Bosque La Meseta, Vereda San José de Suaita, Suaita, Santander | 6.1800 | -73.420 | song | //www.xeno-canto.org/245150/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/245150 | A | 13:20 | 2014-07-03 | |
| 245137 | Turdus | flavipes | Yellow-legged Thrush | Oscar Humberto Marín Gómez | Colombia | Bosque La Meseta, Vereda San José de Suaita, Suaita, Santander | 6.1800 | -73.420 | song | //www.xeno-canto.org/245137/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/245137 | A | 07:00 | 2014-07-03 | |
| 245118 | Turdus | flavipes | Yellow-legged Thrush | Oscar Humberto Marín Gómez | Colombia | Bosque La Meseta, Vereda San José de Suaita, Suaita, Santander | 6.1800 | -73.420 | song, inmature? | //www.xeno-canto.org/245118/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/245118 | A | 10:50 | 2014-07-02 | |
| 245117 | Turdus | flavipes | Yellow-legged Thrush | Oscar Humberto Marín Gómez | Colombia | Bosque La Meseta, Vereda San José de Suaita, Suaita, Santander | 6.1800 | -73.420 | song, inmature? | //www.xeno-canto.org/245117/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/245117 | A | 10:50 | 2014-07-02 | |
| 244225 | Turdus | flavipes | Yellow-legged Thrush | Joe Klaiber | Venezuela | Altamira Edo Barinas | 8.8211 | -70.501 | song | //www.xeno-canto.org/244225/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/244225 | A | 00:00 | 2009-03-15 | |
| 243701 | Turdus | flavipes | Yellow-legged Thrush | Eric DeFonso | Brazil | South Entrance, Serra dos Órgâos NP, RJ | -22.4942 | -43.002 | song | //www.xeno-canto.org/243701/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/243701 | A | 08:25 | 2014-09-12 | |
| 236242 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Niels Krabbe | Colombia | Magdalena: San Lorenzo ridge, Sierra Nevada de Santa Marta | 11.1009 | -74.072 | song | //www.xeno-canto.org/236242/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/236242 | A | 06:05 | 2007-02-24 |
| 236239 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Niels Krabbe | Colombia | Magdalena: San Lorenzo ridge, Sierra Nevada de Santa Marta | 11.1009 | -74.072 | raspy call | //www.xeno-canto.org/236239/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/236239 | A | 17:20 | 2007-02-11 |
| 236237 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Niels Krabbe | Colombia | Magdalena: San Lorenzo ridge, Sierra Nevada de Santa Marta | 11.1009 | -74.072 | song | //www.xeno-canto.org/236237/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/236237 | A | 17:00 | 2007-02-11 |
| 236236 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Niels Krabbe | Colombia | Magdalena: San Lorenzo ridge, Sierra Nevada de Santa Marta | 11.1009 | -74.072 | male song | //www.xeno-canto.org/236236/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/236236 | A | 09:25 | 2007-02-08 |
| 236234 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Niels Krabbe | Colombia | Magdalena: San Lorenzo ridge, Sierra Nevada de Santa Marta | 11.1009 | -74.072 | call | //www.xeno-canto.org/236234/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/236234 | A | 16:45 | 2007-02-06 |
| 236233 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Niels Krabbe | Colombia | Magdalena: San Lorenzo ridge, Sierra Nevada de Santa Marta | 11.1009 | -74.072 | call, song | //www.xeno-canto.org/236233/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/236233 | A | 18:15 | 2007-02-06 |
| 236232 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Niels Krabbe | Colombia | Magdalena: San Lorenzo ridge, Sierra Nevada de Santa Marta | 11.1009 | -74.072 | call of a male | //www.xeno-canto.org/236232/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/236232 | A | 17:45 | 2007-02-04 |
| 236231 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Niels Krabbe | Colombia | Magdalena: San Lorenzo ridge, Sierra Nevada de Santa Marta | 11.1009 | -74.072 | call, song | //www.xeno-canto.org/236231/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/236231 | A | 17:35 | 2007-02-04 |
| 236230 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Niels Krabbe | Colombia | Magdalena: San Lorenzo ridge, Sierra Nevada de Santa Marta | 11.1009 | -74.072 | song | //www.xeno-canto.org/236230/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/236230 | A | 16:28 | 2007-02-04 |
| 228371 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Peter Boesman | Venezuela | Yacambu NP, Lara | 9.7167 | -69.583 | song | //www.xeno-canto.org/228371/download | //creativecommons.org/licenses/by-nc-nd/4.0/ | https://www.xeno-canto.org/228371 | A | 09:30 | 1997-03-09 |
| 219932 | Turdus | flavipes | Yellow-legged Thrush | Joe Klaiber | Venezuela | Altamira, Barinas | 8.2990 | -70.085 | song | //www.xeno-canto.org/219932/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/219932 | A | 00:00 | 2010-04-22 | |
| 212059 | Turdus | flavipes | flavipes (ssp assumed from location) | Yellow-legged Thrush | Jeremy Minns | Brazil | Intervales State Park. Bocanha and Lageado | -24.2667 | -48.450 | song | //www.xeno-canto.org/212059/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/212059 | A | 16:26 | 2003-10-08 |
| 212056 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Ubatuba, SP. Praia Vermelha do Sul | -23.5111 | -45.174 | song | //www.xeno-canto.org/212056/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/212056 | A | 08:12 | 1994-10-08 |
| 212044 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Intervales State Park. Bocanha and Lageado | -24.2667 | -48.450 | song | //www.xeno-canto.org/212044/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/212044 | A | 16:26 | 2003-10-08 |
| 212041 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Serra do Mar National Park - Santa Virginia - Sao Paulo State | -23.3933 | -45.150 | song | //www.xeno-canto.org/212041/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/212041 | A | 09:16 | 2001-10-26 |
| 189494 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Luiz Gabriel Mazzoni | Brazil | Santa Bárbara, Minas Gerais, Minas Gerais | -20.0973 | -43.632 | song | //www.xeno-canto.org/189494/download | //creativecommons.org/licenses/by-nc-sa/4.0/ | https://www.xeno-canto.org/189494 | A | 16:55 | 2011-10-30 |
| 168493 | Turdus | flavipes | Yellow-legged Thrush | Rodrigo Dela Rosa | Brazil | São José dos Campos, São Paulo | -23.0726 | -45.939 | male, song | //www.xeno-canto.org/168493/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/168493 | A | 07:00 | 2013-10-13 | |
| 149021 | Turdus | flavipes | Yellow-legged Thrush | Noé Eiterer | Brazil | Araponga, Minas Gerais | -20.6665 | -42.522 | song | //www.xeno-canto.org/149021/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/149021 | A | 16:00 | 2013-09-21 | |
| 147554 | Turdus | flavipes | Yellow-legged Thrush | Fernand DEROUSSEN | Venezuela | Barinitas, Bolivar, Barinas | 8.8863 | -70.488 | male, song | //www.xeno-canto.org/147554/download | //creativecommons.org/licenses/by-nc-nd/3.0/ | https://www.xeno-canto.org/147554 | A | 18:30 | 2009-02-17 | |
| 143141 | Turdus | flavipes | Yellow-legged Thrush | Fernand DEROUSSEN | Venezuela | Henri Pittier National Park, Mario Briceno Iragorry, Aragua | 10.3557 | -67.720 | song | //www.xeno-canto.org/143141/download | //creativecommons.org/licenses/by-nc-nd/3.0/ | https://www.xeno-canto.org/143141 | A | 10:00 | 2009-02-13 | |
| 121135 | Turdus | flavipes | Yellow-legged Thrush | Vitor de Q. Piacentini | Brazil | Boa Nova, Wet Forest, Bahia | NA | NA | song | //www.xeno-canto.org/121135/download | //creativecommons.org/licenses/by-nc-nd/3.0/ | https://www.xeno-canto.org/121135 | A | ? | 2007-02-28 | |
| 110601 | Turdus | flavipes | Yellow-legged Thrush | Antonio Silveira | Brazil | Serra de Itapetinga,Atibaia, São Paulo State | -23.2280 | -46.534 | song | //www.xeno-canto.org/110601/download | //creativecommons.org/licenses/by-nc-nd/2.5/ | https://www.xeno-canto.org/110601 | A | 11.30am | 2008-12-06 | |
| 110248 | Turdus | flavipes | Yellow-legged Thrush | Robson Silva e Silva | Brazil | Alto Ribeira State Park (PETAR),Iporanga, São Paulo State | -24.5410 | -48.713 | male, song | //www.xeno-canto.org/110248/download | //creativecommons.org/licenses/by-nc-nd/2.5/ | https://www.xeno-canto.org/110248 | A | 07:40 | 2012-09-20 | |
| 101690 | Turdus | flavipes | venezuelensis | Yellow-legged Thrush | Jeremy Minns | Colombia | Sierra Nevada de Santa Marta. Tienda Las Moras | 11.0973 | -74.078 | Song | //www.xeno-canto.org/101690/download | //creativecommons.org/licenses/by-nc-nd/2.5/ | https://www.xeno-canto.org/101690 | A | 11:54 | 2012-04-17 |
| 91385 | Turdus | flavipes | Yellow-legged Thrush | Glauco Kohler | Brazil | RPPN Chácara Edith, Brusque, Santa Catarina | -27.1017 | -48.889 | song | //www.xeno-canto.org/91385/download | //creativecommons.org/licenses/by-nc-nd/2.5/ | https://www.xeno-canto.org/91385 | A | 7:15 | 2011-12-11 | |
| 82355 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Ubatuba, SP. Praia Vermelha do Sul | -23.5111 | -45.174 | Song or calls? | //www.xeno-canto.org/82355/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/82355 | A | 07:18 | 2003-08-09 |
| 82354 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Serra da Bocaina State Park. Parati-Cunha road | -23.2001 | -44.817 | Song | //www.xeno-canto.org/82354/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/82354 | A | 05:27 | 2003-01-02 |
| 82353 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Santa Catarina; near Urubici | -27.8300 | -49.580 | Song | //www.xeno-canto.org/82353/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/82353 | A | 18:47 | 2002-11-28 |
| 82352 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Santa Catarina; near Urubici | -27.8300 | -49.580 | Song | //www.xeno-canto.org/82352/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/82352 | A | 17:50 | 2002-11-28 |
| 82351 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Serra dos Orgaos National Park. Teresopolis | -22.4667 | -43.010 | Song | //www.xeno-canto.org/82351/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/82351 | A | 07:28 | 2002-09-12 |
| 82350 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Boa Nova, BA - wet forest | -14.3834 | -40.100 | Song | //www.xeno-canto.org/82350/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/82350 | A | 07:08 | 2001-11-08 |
| 82349 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Boa Nova, BA - wet forest | -14.3834 | -40.100 | Song | //www.xeno-canto.org/82349/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/82349 | A | 06:57 | 2001-11-07 |
| 82348 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Serra do Mar State Park. Santa Virgínia | -23.3248 | -45.133 | Song | //www.xeno-canto.org/82348/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/82348 | A | 07:15 | 2001-10-26 |
| 82347 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Itanhaem. Chacaras Bopiranga | -24.1834 | -46.900 | Song | //www.xeno-canto.org/82347/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/82347 | A | 06:03 | 2001-10-03 |
| 82346 | Turdus | flavipes | flavipes | Yellow-legged Thrush | Jeremy Minns | Brazil | Boraceia Biological Station, SP state | -23.6334 | -45.867 | Call | //www.xeno-canto.org/82346/download | //creativecommons.org/licenses/by-nc-sa/3.0/ | https://www.xeno-canto.org/82346 | A | 16:25 | 2000-05-31 |
Let’s also extract 2 data subsets that we can use for function/loop building, testing and troubleshooting. The following code creates 2 data frames. The first one containsthe data for the American Robin and the second one with the data of the 20 species with the highest number of observations:
# American robin
amrb <- turdus[turdus$English_name == "American Robin",]
# n by species
n <- tapply(turdus$English_name, turdus$English_name, length)
# order by n
n <- n[order(n, decreasing = TRUE)]
# get first 20
n <- n[1:20]
# subset the highest 20
turdus2 <- turdus[turdus$English_name %in% names(n), ]Exercise 1
When creating functions: keep in mind that there are many ways in which data can be input into a function. A good input data format would be the one less prone to errors (e.g. better column names than indices) and that is intuitive for future users (including yourself).
1.1 Create a data frame containing the mean latitude and mean Julian day for the American Robin data
1.2 Create a function that produces the data frame as in 1.1
1.3 Create a for loop to obtain the same data as in 1.1 for all species
1.4 Plot latitude vs Julian day from the output data frame from 1.3
1.5 Convert the for loop from 1.3 into a Xapply
1.6 Convert the Xapply loop into a function itself
1.7 Create a loop to make a multipannel plot witht lat-dat graphs for each species in “turdus2”. Note that in this case all the data has to be used, not just the mean for each especies. Use par(mfrow = c(5, 4)) before starting the loop to split the graphic device
1.8 Convert the loop into a function. The function should set the number of columns and rows of the multipannel plot based on the number of plots (e.g. species)
1.9 Add an additional logical argument that allow users to decide whether to include the correlation coefficient of latitude vs mean Julian day to the plot
1.10 Create the same plot as in 1.6 but this time using the latitudinal range instead of the mean latitude
Session information
## R version 3.4.4 (2018-03-15)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.4 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] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] kableExtra_0.7.0 knitr_1.20
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.17 xml2_1.2.0 magrittr_1.5
## [4] hms_0.4.0 rvest_0.3.2 munsell_0.4.3
## [7] viridisLite_0.2.0 colorspace_1.3-2 R6_2.2.2
## [10] rlang_0.2.0 plyr_1.8.4 stringr_1.2.0
## [13] httr_1.3.1 tools_3.4.4 htmltools_0.3.6
## [16] yaml_2.1.16 rprojroot_1.3-2 digest_0.6.13
## [19] tibble_1.4.2 readr_1.1.1 evaluate_0.10.1
## [22] rmarkdown_1.8 stringi_1.1.6 compiler_3.4.4
## [25] pillar_1.2.3 scales_0.5.0 backports_1.1.2
## [28] pkgconfig_2.0.1