re node and tips names in tree_glottolog_newick.txt

[HedvigS]

On the website under the tab download there's a newick file with all glottolog trees. I needed to just check something quickly, so I grabbed it and extracted one of the trees and was about to try something out. However, I ran into some trouble in R with the way ape.:read.tree() deals with the node and tip labels.

> trees <- ape::read.tree(file = "tree_glottolog_newick.txt")
> mayan <- trees[204][[1]]
> 
> mayan$tip.label
 [1] "Aguacateco-l-"              "Ixil-l-"                    "Mam-l-"                     "Tektiteko-l-"               "Kaqchikel-l-"              
 [6] "Tzutujil-l-"                "Achi-l-"                    "Kiche-l-"                   "Sacapulteco-l-"             "Sipacapense-l-"            
[11] "Kekchí-l-"                  "Poqomam-l-"                 "Poqomchi-l-"                "Uspanteco-l-"               "Chol-l-"                   
[16] "BuenaVistaChontal"          "MiramarChontal"             "TamultédelasSábanasChontal" "Cholti-l-"                  "Chortí-l-"                 
[21] "EpigraphicMayan-l-"         "ChanalCancuc"               "Tenango"                    "Tzotzil-l-"                 "Chuj-l-"                   
[26] "Tojolabal-l-"               "Akateko-l-"                 "Popti-l-"                   "Qanjobal-l-"                "Motozintleco"              
[31] "Tuzanteco"                  "Itzá-l-"                    "MopánMaya-l-"               "Lacanjá"                    "Najá"                      
[36] "YucatecMaya-l-"             "Chicomuceltec-l-"           "Huastec-l-"                
> 

For full clarity, the way this part of the newick file looks is:

((((('Aguacateco [agua1252][agu]-l-':1,'Ixil [ixil1251][ixl]-l-':1)'Ixilan [ixil1250]':1,('Mam [mamm1241][mam]-l-':1,'Tektiteko [tekt1235][ttc]-l-':1)'Mamean [mame1240]':1)'Greater Mamean [grea1277]':1,((('Kaqchikel [kaqc1270][cak]-l-':1,'Tz''utujil [tzut1248][tzj]-l-':1)'Cakchiquel-Tzutujil [cakc1244]':1,('Achi [achi1256][acr]-l-':1,'K''iche'' [kich1262][quc]-l-':1)'Quiche-Achi [quic1275]':1,'Sacapulteco [saca1238][quv]-l-':1,'Sipacapense [sipa1247][qum]-l-':1)'Core Quichean [core1251]':1,'Kekchí [kekc1242][kek]-l-':1,('Poqomam [poqo1253][poc]-l-':1,'Poqomchi'' [poqo1254][poh]-l-':1)'Poqom [poco1241]':1,'Uspanteco [uspa1245][usp]-l-':1)'Greater Quichean [grea1276]':1)'Quichean-Mamean [quic1274]':1,(((('Chol [chol1282][ctu]-l-':1,('Buena Vista Chontal [buen1245]':1,'Miramar Chontal [mira1253]':1,'Tamulté de las Sábanas Chontal [tamu1247]':1)'Tabasco Chontal [taba1266][chf]-l-':1)'Chol-Chontal [chol1281]':1,('Cholti [chol1283]-l-':1,'Chortí [chor1273][caa]-l-':1)'Chorti-Cholti [chor1272]':1,'Epigraphic Mayan [epig1241][emy]-l-':1)'Cholan [chol1287]':1,(('Chanal Cancuc [chan1320]':1,'Tenango [tena1239]':1)'Tzeltal [tzel1254][tzh]-l-':1,'Tzotzil [tzot1259][tzo]-l-':1)'Tzeltalan [tzel1253]':1)'Cholan-Tzeltalan [chol1286]':1,(('Chuj [chuj1250][cac]-l-':1,'Tojolabal [tojo1241][toj]-l-':1)'Chujean [chuj1249]':1,(('Akateko [west2635][knj]-l-':1,'Popti'' [popt1235][jac]-l-':1,'Q''anjob''al [qanj1241][kjb]-l-':1)'Kanjobal-Jacaltec [kanj1263]':1,('Motozintleco [moto1243]':1,'Tuzanteco [tuza1238]':1)'Mocho [moch1257][mhc]-l-':1)'Kanjobalan [kanj1262]':1)'Kanjobalan-Chujean [kanj1261]':1)'Western Mayan [west2865]':1,(('Itzá [itza1241][itz]-l-':1,'Mopán Maya [mopa1243][mop]-l-':1)'Mopan-Itza [mopa1242]':1,(('Lacanjá [laca1244]':1,'Najá [naja1242]':1)'Lacandon [laca1243][lac]-l-':1,'Yucatec Maya [yuca1254][yua]-l-':1)'Yucatec-Lacandon [yuca1253]':1)'Yucatecan [yuca1252]':1)'Core Mayan [core1254]':1,('Chicomuceltec [chic1271][cob]-l-':1,'Huastec [huas1242][hus]-l-':1)'Huastecan Mayan [huas1241]':1)'Mayan [maya1287]':1;

So, something is going awry here with spaces and I'm digging into it. This isn't really your problem, but I was wondering if there is any chance that in future this file could just contain the plain glottocode and nothing else for nodes and tips (no spaces, brackets etc)?

phytools::read.newick() is doing better, so I'll probably be able to solve this issue right now. However, I was thinking that mayeb this'll make others stumble so to make it easier maybe just have the bare glottocodes?

[xrotwang]

I don't think this file will change in the future. If anything, it will disappear, because the newick trees are available from https://github.com/glottolog/glottolog-cldf as well (with Newick containing only the Glottocode as languoid label). So the file here is only kept for backwards compatibility and changing it in any way would defeat the purpose.

[HedvigS]

Ok, fair enough.

Do you mean the content in "subclassification" in the values table? Sure, I can go looking there instead. I get it with the backwards compatibility.

Are the parameters by the way getting a Description in the parameters table?

[xrotwang]

Well, there is one, AFAICT, see link above https://github.com/glottolog/glottolog-cldf/blob/master/cldf/parameters.csv#L5

[SimonGreenhill]

(it's not the spaces that are the issue, it's that [.*?] are seen as comments by APEs parser)

[HedvigS]

Well, there is one, AFAICT, see link above https://github.com/glottolog/glottolog-cldf/blob/master/cldf/parameters.csv#L5

Huh, funny.. in my clone that I just pulled that table looks like this:

ID	Name	Description	type
level	Level		categorical
category	Category		categorical
classification	Classification
subclassification	Subclassification
aes	Agglomerated Endangerment Status		sequential
med	Most Extensive Description		sequential

I'll go do some git investigations.

[HedvigS]

(it's not the spaces that are the issue, it's that [.*?] are seen as comments by APEs parser)

Oh good to know!!

[HedvigS]

I figured it out, i was using a clone of a fork of glottolog-cldf. I do that sometimes in case there's changes I want to try out. The files at glottolog/glottolog-cldf are, of course, as Robert said above.

Okay, all good!