about charJSON

and how to create it

..... used by phyloJIVE

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About charJSON

charJSON is a JSON data structure for representing qualitative and quantitative traits/characters. It can be parsed by most programming languages. Here is a formal description of charJSON in Extended Backus-Naur Form (EBNF).

charJSON is designed to be portable. It lacks the rigour of delta and LUCID matrices which it is NOT designed to replace. It requires no implicit code or assumptions. It is not designed to create keys nor to help code them. Rather, just as a light weight means to transport trait information.

Here we provide scripts which can transform csv tables of trait information (produced by lucid, delta, excel, or mesquite) into charJSON.

Instructions and test cases

Here are scripts for windows and unix/linux/mac that will convert a csv file to charJSON.

The original File must

have column names in the first row for EVERY value including the first column
have species or taxon names in the first column

It can have

numeric, strings, or boolean values
multiple character states, each separated by || i.e. two pipe characters

awk or gnuawk can be used.
* for windows you will need to install something like gawk
* no software is required for macs (OS X) or linux

to use the script open a command window or terminal
get to the folder/directory in which you wish to work
type a command as follows

awk -F "," -f csv2json.awk YOUR_INPUTFILE >> YOURDESIRED_outputfile.json
e.g.
awk -F "," -f csv2json.awk hornwort.csv >> hornwarts.json

Example 1

awk -F "," -f csv2json.awk acacia.txt >> acacia.json

takes ....

"scientificName","seed mass","Inflorescence colour","plant height","Phyllode length median","Inflorescence arrangement","Stipule length median","Inflorescence shape"," leaflet pairs 2nd leaf","range size","genome size","Phyllode arrangement","Pulvinus length median","first leaf pinnae pairs","section taxonomy"
"Acacia diphylla","5.4","unknown","","","unknown","","unknown","1.9","","","unknown","","2.0","unknown"
Acacia courtii,"","white to cream||pale yellow","20","115","simple","0.25","cylindrical","","2","","scattered","","","juliflorae"

makes ....

{
"Acacia diphylla" : {
   "seed mass" : [ 5.4] ,
   "Inflorescence colour" : [ "unknown"] ,
   "plant height" : [ ] ,
   "Phyllode length median" : [ ] ,
   "Inflorescence arrangement" : [ "unknown"] ,
   "Stipule length median" : [ ] ,
   "Inflorescence shape" : [ "unknown"] ,
   " leaflet pairs 2nd leaf" : [ 1.9] ,
   "range size" : [ ] ,
   "genome size" : [ ] ,
   "Phyllode arrangement" : [ "unknown"] ,
   "Pulvinus length median" : [ ] ,
   "first leaf pinnae pairs" : [ 2.0] ,
   "section taxonomy" : [ "unknown"] }
,
"Acacia courtii" : {
   "seed mass" : [ ] ,
   "Inflorescence colour" : [ "white to cream", "pale yellow"] ,
   "plant height" : [ 20] ,
   "Phyllode length median" : [ 115] ,
   "Inflorescence arrangement" : [ "simple"] ,
   "Stipule length median" : [ 0.25] ,
   "Inflorescence shape" : [ "cylindrical"] ,
   " leaflet pairs 2nd leaf" : [ ] ,
   "range size" : [ 2] ,
   "genome size" : [ ] ,
   "Phyllode arrangement" : [ "scattered"] ,
   "Pulvinus length median" : [ ] ,
   "first leaf pinnae pairs" : [ ] ,
   "section taxonomy" : [ "juliflorae"] }
}

Example 2

awk -F "," -f csv2json.awk hornwort.csv >> hornwarts.json

takes...

taxon,raw max temp warmest period,modelled max temp warmest period,raw precipitation driest quarter,modelled precipitation driest quarter,raw mean temp driest quater,modelled_mean_temp_driest_quater,raw thpk 1 1000 g thickness,modelled thpk 1 1000 g thickness
Dendroceros subgenus apoceros,28,28.64999962,252.3333333,247,19,19.40000057,150,150
Dendroceros_subgenus_dendroceros,27.44444444,28.05257573,169.1666667,167.2409091,15.88888889,16.75318181,272.0555556,301.3257576
Megaceros_flagellaris,27.42857143,28.58099998,171.4285714,170.66,16,17.44700016,253.4285714,226.16
Megaceros_gracilis,23.28333333,23.58369219,212.0583333,212.48,11.83333333,12.2307692,279.0416667,278.2092308
Megaceros_pellucidus,18.09090909,18.35666676,264.1818182,267.1666667,11.90909091,12.20333341,308.6363636,322.6333333
Anthoceros fragilis,30,30.19999981,55,61,18.75,18.89999962,285.25,295.5
Anthoceros laminiferus,27,27.79999924,211,211,16,16.10000038,599,599
Anthoceros_punctatus,30,28.08274507,61,143.051634,18.5,15.41660129,295.5,292.8313725
Folioceros fuciformis,28.5,29.2249999,157.75,157.75,18.75,19.04999971,195.25,195.25
Notothylas javanicus,38,38.5,0,0,22.5,23.25,150,150
Phaeoceros engelii,25.16666667,,84.16666667,,18.16666667,,597.3333333,
Phaeoceros evanidus,28,28.25,135.6,144.5,14.2,13.875,227.8,219
Phaeoceros tuberosus,31.66666667,33.15000057,33.16666667,28.75,21.16666667,21.64999962,315.8333333,277.75
Phaeoceros_carolinianus ,25.828125,27.29704755,157.328125,158.4253968,13.1875,14.16438104,267.40625,276.8314286
Phaeoceros_inflatus,23.51428571,25.36589483||23,149.8,158.1031579,14.34285714,15.77442107,256.2285714,270.7410526

makes.....

{
"Dendroceros subgenus apoceros" : {
   "raw max temp warmest period" : [ 28] ,
   "modelled max temp warmest period" : [ 28.64999962] ,
   "raw precipitation driest quarter" : [ 252.3333333] ,
   "modelled precipitation driest quarter" : [ 247] ,
   "raw mean temp driest quater" : [ 19] ,
   "modelled_mean_temp_driest_quater" : [ 19.40000057] ,
   "raw thpk 1 1000 g thickness" : [ 150] ,
   "modelled thpk 1 1000 g thickness" : [ 150] }
,
"Dendroceros_subgenus_dendroceros" : {
   "raw max temp warmest period" : [ 27.44444444] ,
   "modelled max temp warmest period" : [ 28.05257573] ,
   "raw precipitation driest quarter" : [ 169.1666667] ,
   "modelled precipitation driest quarter" : [ 167.2409091] ,
   "raw mean temp driest quater" : [ 15.88888889] ,
   "modelled_mean_temp_driest_quater" : [ 16.75318181] ,
   "raw thpk 1 1000 g thickness" : [ 272.0555556] ,
   "modelled thpk 1 1000 g thickness" : [ 301.3257576] }
,
"Megaceros_flagellaris" : {
   "raw max temp warmest period" : [ 27.42857143] ,
   "modelled max temp warmest period" : [ 28.58099998] ,
   "raw precipitation driest quarter" : [ 171.4285714] ,
   "modelled precipitation driest quarter" : [ 170.66] ,
   "raw mean temp driest quater" : [ 16] ,
   "modelled_mean_temp_driest_quater" : [ 17.44700016] ,
   "raw thpk 1 1000 g thickness" : [ 253.4285714] ,
   "modelled thpk 1 1000 g thickness" : [ 226.16] }
,
"Megaceros_gracilis" : {
   "raw max temp warmest period" : [ 23.28333333] ,
   "modelled max temp warmest period" : [ 23.58369219] ,
   "raw precipitation driest quarter" : [ 212.0583333] ,
   "modelled precipitation driest quarter" : [ 212.48] ,
   "raw mean temp driest quater" : [ 11.83333333] ,
   "modelled_mean_temp_driest_quater" : [ 12.2307692] ,
   "raw thpk 1 1000 g thickness" : [ 279.0416667] ,
   "modelled thpk 1 1000 g thickness" : [ 278.2092308] }
,
"Megaceros_pellucidus" : {
   "raw max temp warmest period" : [ 18.09090909] ,
   "modelled max temp warmest period" : [ 18.35666676] ,
   "raw precipitation driest quarter" : [ 264.1818182] ,
   "modelled precipitation driest quarter" : [ 267.1666667] ,
   "raw mean temp driest quater" : [ 11.90909091] ,
   "modelled_mean_temp_driest_quater" : [ 12.20333341] ,
   "raw thpk 1 1000 g thickness" : [ 308.6363636] ,
   "modelled thpk 1 1000 g thickness" : [ 322.6333333] }
,
"Anthoceros fragilis" : {
   "raw max temp warmest period" : [ 30] ,
   "modelled max temp warmest period" : [ 30.19999981] ,
   "raw precipitation driest quarter" : [ 55] ,
   "modelled precipitation driest quarter" : [ 61] ,
   "raw mean temp driest quater" : [ 18.75] ,
   "modelled_mean_temp_driest_quater" : [ 18.89999962] ,
   "raw thpk 1 1000 g thickness" : [ 285.25] ,
   "modelled thpk 1 1000 g thickness" : [ 295.5] }
,
"Anthoceros laminiferus" : {
   "raw max temp warmest period" : [ 27] ,
   "modelled max temp warmest period" : [ 27.79999924] ,
   "raw precipitation driest quarter" : [ 211] ,
   "modelled precipitation driest quarter" : [ 211] ,
   "raw mean temp driest quater" : [ 16] ,
   "modelled_mean_temp_driest_quater" : [ 16.10000038] ,
   "raw thpk 1 1000 g thickness" : [ 599] ,
   "modelled thpk 1 1000 g thickness" : [ 599] }
,
"Anthoceros_punctatus" : {
   "raw max temp warmest period" : [ 30] ,
   "modelled max temp warmest period" : [ 28.08274507] ,
   "raw precipitation driest quarter" : [ 61] ,
   "modelled precipitation driest quarter" : [ 143.051634] ,
   "raw mean temp driest quater" : [ 18.5] ,
   "modelled_mean_temp_driest_quater" : [ 15.41660129] ,
   "raw thpk 1 1000 g thickness" : [ 295.5] ,
   "modelled thpk 1 1000 g thickness" : [ 292.8313725] }
,
"Folioceros fuciformis" : {
   "raw max temp warmest period" : [ 28.5] ,
   "modelled max temp warmest period" : [ 29.2249999] ,
   "raw precipitation driest quarter" : [ 157.75] ,
   "modelled precipitation driest quarter" : [ 157.75] ,
   "raw mean temp driest quater" : [ 18.75] ,
   "modelled_mean_temp_driest_quater" : [ 19.04999971] ,
   "raw thpk 1 1000 g thickness" : [ 195.25] ,
   "modelled thpk 1 1000 g thickness" : [ 195.25] }
,
"Notothylas javanicus" : {
   "raw max temp warmest period" : [ 38] ,
   "modelled max temp warmest period" : [ 38.5] ,
   "raw precipitation driest quarter" : [ 0] ,
   "modelled precipitation driest quarter" : [ 0] ,
   "raw mean temp driest quater" : [ 22.5] ,
   "modelled_mean_temp_driest_quater" : [ 23.25] ,
   "raw thpk 1 1000 g thickness" : [ 150] ,
   "modelled thpk 1 1000 g thickness" : [ 150] }
,
"Phaeoceros engelii" : {
   "raw max temp warmest period" : [ 25.16666667] ,
   "modelled max temp warmest period" : [ ] ,
   "raw precipitation driest quarter" : [ 84.16666667] ,
   "modelled precipitation driest quarter" : [ ] ,
   "raw mean temp driest quater" : [ 18.16666667] ,
   "modelled_mean_temp_driest_quater" : [ ] ,
   "raw thpk 1 1000 g thickness" : [ 597.3333333] ,
   "modelled thpk 1 1000 g thickness" : [ ] }
,
"Phaeoceros evanidus" : {
   "raw max temp warmest period" : [ 28] ,
   "modelled max temp warmest period" : [ 28.25] ,
   "raw precipitation driest quarter" : [ 135.6] ,
   "modelled precipitation driest quarter" : [ 144.5] ,
   "raw mean temp driest quater" : [ 14.2] ,
   "modelled_mean_temp_driest_quater" : [ 13.875] ,
   "raw thpk 1 1000 g thickness" : [ 227.8] ,
   "modelled thpk 1 1000 g thickness" : [ 219] }
,
"Phaeoceros tuberosus" : {
   "raw max temp warmest period" : [ 31.66666667] ,
   "modelled max temp warmest period" : [ 33.15000057] ,
   "raw precipitation driest quarter" : [ 33.16666667] ,
   "modelled precipitation driest quarter" : [ 28.75] ,
   "raw mean temp driest quater" : [ 21.16666667] ,
   "modelled_mean_temp_driest_quater" : [ 21.64999962] ,
   "raw thpk 1 1000 g thickness" : [ 315.8333333] ,
   "modelled thpk 1 1000 g thickness" : [ 277.75] }
,
"Phaeoceros_carolinianus " : {
   "raw max temp warmest period" : [ 25.828125] ,
   "modelled max temp warmest period" : [ 27.29704755] ,
   "raw precipitation driest quarter" : [ 157.328125] ,
   "modelled precipitation driest quarter" : [ 158.4253968] ,
   "raw mean temp driest quater" : [ 13.1875] ,
   "modelled_mean_temp_driest_quater" : [ 14.16438104] ,
   "raw thpk 1 1000 g thickness" : [ 267.40625] ,
   "modelled thpk 1 1000 g thickness" : [ 276.8314286] }
,
"Phaeoceros_inflatus" : {
   "raw max temp warmest period" : [ 23.51428571] ,
   "modelled max temp warmest period" : [ 25.36589483, 23] ,
   "raw precipitation driest quarter" : [ 149.8] ,
   "modelled precipitation driest quarter" : [ 158.1031579] ,
   "raw mean temp driest quater" : [ 14.34285714] ,
   "modelled_mean_temp_driest_quater" : [ 15.77442107] ,
   "raw thpk 1 1000 g thickness" : [ 256.2285714] ,
   "modelled thpk 1 1000 g thickness" : [ 270.7410526] }
}