[CHNOSZ-commits] r389 - in pkg/CHNOSZ: . R inst/extdata/OBIGT inst/extdata/thermo tests/testthat

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2019-02-09 06:15:07 +0100 (Sat, 09 Feb 2019)
New Revision: 389

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/info.R
   pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv
   pkg/CHNOSZ/inst/extdata/thermo/SK95.csv
   pkg/CHNOSZ/tests/testthat/test-recalculate.R
Log:
info(): add OldAA.csv to list of optional data files for searching


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-02-09 04:54:47 UTC (rev 388)
+++ pkg/CHNOSZ/DESCRIPTION	2019-02-09 05:15:07 UTC (rev 389)
@@ -1,6 +1,6 @@
 Date: 2019-02-09
 Package: CHNOSZ
-Version: 1.1.3-96
+Version: 1.1.3-98
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R	2019-02-09 04:54:47 UTC (rev 388)
+++ pkg/CHNOSZ/R/info.R	2019-02-09 05:15:07 UTC (rev 389)
@@ -248,7 +248,7 @@
   }
   # if we got here there were no approximate matches
   # 20190127 look for the species in optional data files 
-  for(opt in c("SLOP98", "SUPCRT92")) {
+  for(opt in c("SLOP98", "SUPCRT92", "OldAA")) {
     optdat <- read.csv(system.file(paste0("extdata/OBIGT/", opt, ".csv"), package="CHNOSZ"), as.is=TRUE)
     if(species %in% optdat$name) {
       message('info.approx: ', species, ' is in an optional database; use add.obigt("', opt, '", "', species, '") to load it')

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv	2019-02-09 04:54:47 UTC (rev 388)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv	2019-02-09 05:15:07 UTC (rev 389)
@@ -37,29 +37,29 @@
 Cd(Gly)2,NA,Cd(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-185236,-250387,68.18,148.7,92.1,14.355,27.2722,-4.9746,-3.9063,93.0282,27.2523,-0.03,0
 Eu(Gly)+,NA,Eu(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-208959,-236026,49.509,89.8,50.3,8.5841,13.176,0.5767,-3.3236,57.1645,15.2476,-0.1738,1
 Eu(Gly)2,NA,Eu(C2H4NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-288477,-346709,97.734,190.4,108.7,16.6314,32.8272,-7.1514,-4.136,117.4699,35.7476,-0.03,0
-Ca(Alan)+,NA,Ca(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-209172,-247643,35.015,104.6,50.7,8.7124,13.4888,0.454,-3.3365,67.7227,18.2713,0.0279,1
-Ca(Alan)2,NA,Ca(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-285446,-365834,79.755,239.1,127.3,19.1765,39.0448,-9.6021,-4.393,146.0369,45.6768,-0.03,0
-Mg(Alan)+,NA,Mg(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-186539,-232305,8.428,109.5,46.8,8.3169,12.5282,0.821,-3.2968,74.3351,19.275,0.4322,1
-Mg(Alan)2,NA,Mg(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-263631,-353761,44.962,248.8,123,18.5836,37.5967,-9.0318,-4.3331,151.6713,47.6352,-0.03,0
-Sr(Alan)+,NA,Sr(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-211130,-248184,43.155,98.9,51.4,8.77,13.6312,0.3947,-3.3424,63.2691,17.1163,-0.0948,1
-Sr(Alan)2,NA,Sr(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-286831,-365053,90.407,228.1,128.1,19.2869,39.3109,-9.699,-4.404,139.5534,43.4233,-0.03,0
-Ba(Alan)+,NA,Ba(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-210713,-244263,56.557,93.7,56.8,9.4348,15.2528,-0.2391,-3.4095,58.4325,16.085,-0.2977,1
-Ba(Alan)2,NA,Ba(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-286687,-360171,107.946,218.2,134.1,20.104,41.3073,-10.4865,-4.4865,133.7647,41.4112,-0.03,0
-Mn(Alan)+,NA,Mn(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-134280,-173740,29.425,112.3,51.8,8.8873,13.9167,0.2842,-3.3542,73.0237,19.8433,0.1124,1
-Mn(Alan)2,NA,Mn(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-213474,-295365,72.44,254.2,128.5,19.3395,39.4414,-9.7539,-4.4094,154.8617,48.744,-0.03,0
-Fe(Alan)+,NA,Fe(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-103952,-146326,18.518,103.3,46.1,8.1661,12.1558,0.976,-3.2814,69.2856,18.01,0.2792,1
-Fe(Alan)2,NA,Fe(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-184387,-269655,58.166,236.6,122.2,18.4732,37.3244,-8.9189,-4.3219,144.5703,45.1671,-0.03,0
-Ni(Alan)+,NA,Ni(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-94227,-137691,15.46,95.2,38.5,7.1451,9.664,1.9536,-3.1784,64.9703,16.36,0.326,1
-Ni(Alan)2,NA,Ni(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-175945,-264092,50.92,220.8,113.8,17.318,34.504,-7.8105,-4.2053,135.3083,41.9478,-0.03,0
-Cu(Alan)+,NA,Cu(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,06.Feb.19,-71295,-110530,25.46,108.7,43.4,7.7387,11.1165,1.3762,-3.2385,70.7759,19.11,0.0974,1
-Cu(Alan)2,NA,Cu(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,06.Feb.19,-156054,-238480,65.92,247.2,119.2,18.0655,36.3271,-8.523,-4.2807,150.7452,47.3132,-0.03,0
-Zn(Alan)+,NA,Zn(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-117313,-161024,17.46,107.4,43.8,7.8514,11.3891,1.2746,-3.2497,71.8106,18.835,0.2956,1
-Zn(Alan)2,NA,Zn(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-198512,-284509,60.92,244.5,119.6,18.1164,36.4558,-8.5823,-4.286,149.2015,46.7767,-0.03,0
-Pb(Alan)+,NA,Pb(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-87891,-120835,59.148,93,53.4,8.964,14.1088,0.1992,-3.3622,57.5413,15.9017,-0.3372,1
-Pb(Alan)2,NA,Pb(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-167671,-240311,111.336,216.4,130.4,19.5944,40.0653,-10.0034,-4.4352,132.7356,41.0535,-0.03,0
-Co(Alan)+,NA,Co(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-94799,-136805,20.46,104,43.6,7.8202,11.3148,1.299,-3.2467,69.3955,18.1475,0.2482,1
-Co(Alan)2,NA,Co(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-175193,-260392,60.92,238,119.4,18.0995,36.4127,-8.5626,-4.2842,145.3423,45.4353,-0.03,0
-Cd(Alan)+,NA,Cd(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-100782,-141576,29.698,113.7,53.4,9.1151,14.4742,0.063,-3.3773,73.7914,20.1183,0.1098,1
-Cd(Alan)2,NA,Cd(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-181340,-264540,72.797,256.8,130.4,19.5944,40.0653,-10.0034,-4.4352,156.4053,49.2806,-0.03,0
-Eu(Alan)+,NA,Eu(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-206029,-242617,50.149,135,68.4,11.0532,19.2058,-1.7947,-3.5729,83.4588,24.4724,-0.2006,1
-Eu(Alan)2,NA,Eu(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-282521,-359634,99.56,298.5,147,21.8707,45.6205,-12.1799,-4.6649,180.847,57.7759,-0.03,0
+Ca(Ala)+,NA,Ca(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-209172,-247643,35.015,104.6,50.7,8.7124,13.4888,0.454,-3.3365,67.7227,18.2713,0.0279,1
+Ca(Ala)2,NA,Ca(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-285446,-365834,79.755,239.1,127.3,19.1765,39.0448,-9.6021,-4.393,146.0369,45.6768,-0.03,0
+Mg(Ala)+,NA,Mg(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-186539,-232305,8.428,109.5,46.8,8.3169,12.5282,0.821,-3.2968,74.3351,19.275,0.4322,1
+Mg(Ala)2,NA,Mg(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-263631,-353761,44.962,248.8,123,18.5836,37.5967,-9.0318,-4.3331,151.6713,47.6352,-0.03,0
+Sr(Ala)+,NA,Sr(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-211130,-248184,43.155,98.9,51.4,8.77,13.6312,0.3947,-3.3424,63.2691,17.1163,-0.0948,1
+Sr(Ala)2,NA,Sr(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-286831,-365053,90.407,228.1,128.1,19.2869,39.3109,-9.699,-4.404,139.5534,43.4233,-0.03,0
+Ba(Ala)+,NA,Ba(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-210713,-244263,56.557,93.7,56.8,9.4348,15.2528,-0.2391,-3.4095,58.4325,16.085,-0.2977,1
+Ba(Ala)2,NA,Ba(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-286687,-360171,107.946,218.2,134.1,20.104,41.3073,-10.4865,-4.4865,133.7647,41.4112,-0.03,0
+Mn(Ala)+,NA,Mn(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-134280,-173740,29.425,112.3,51.8,8.8873,13.9167,0.2842,-3.3542,73.0237,19.8433,0.1124,1
+Mn(Ala)2,NA,Mn(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-213474,-295365,72.44,254.2,128.5,19.3395,39.4414,-9.7539,-4.4094,154.8617,48.744,-0.03,0
+Fe(Ala)+,NA,Fe(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-103952,-146326,18.518,103.3,46.1,8.1661,12.1558,0.976,-3.2814,69.2856,18.01,0.2792,1
+Fe(Ala)2,NA,Fe(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-184387,-269655,58.166,236.6,122.2,18.4732,37.3244,-8.9189,-4.3219,144.5703,45.1671,-0.03,0
+Ni(Ala)+,NA,Ni(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-94227,-137691,15.46,95.2,38.5,7.1451,9.664,1.9536,-3.1784,64.9703,16.36,0.326,1
+Ni(Ala)2,NA,Ni(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-175945,-264092,50.92,220.8,113.8,17.318,34.504,-7.8105,-4.2053,135.3083,41.9478,-0.03,0
+Cu(Ala)+,NA,Cu(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,06.Feb.19,-71295,-110530,25.46,108.7,43.4,7.7387,11.1165,1.3762,-3.2385,70.7759,19.11,0.0974,1
+Cu(Ala)2,NA,Cu(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,06.Feb.19,-156054,-238480,65.92,247.2,119.2,18.0655,36.3271,-8.523,-4.2807,150.7452,47.3132,-0.03,0
+Zn(Ala)+,NA,Zn(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-117313,-161024,17.46,107.4,43.8,7.8514,11.3891,1.2746,-3.2497,71.8106,18.835,0.2956,1
+Zn(Ala)2,NA,Zn(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-198512,-284509,60.92,244.5,119.6,18.1164,36.4558,-8.5823,-4.286,149.2015,46.7767,-0.03,0
+Pb(Ala)+,NA,Pb(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-87891,-120835,59.148,93,53.4,8.964,14.1088,0.1992,-3.3622,57.5413,15.9017,-0.3372,1
+Pb(Ala)2,NA,Pb(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-167671,-240311,111.336,216.4,130.4,19.5944,40.0653,-10.0034,-4.4352,132.7356,41.0535,-0.03,0
+Co(Ala)+,NA,Co(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-94799,-136805,20.46,104,43.6,7.8202,11.3148,1.299,-3.2467,69.3955,18.1475,0.2482,1
+Co(Ala)2,NA,Co(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-175193,-260392,60.92,238,119.4,18.0995,36.4127,-8.5626,-4.2842,145.3423,45.4353,-0.03,0
+Cd(Ala)+,NA,Cd(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-100782,-141576,29.698,113.7,53.4,9.1151,14.4742,0.063,-3.3773,73.7914,20.1183,0.1098,1
+Cd(Ala)2,NA,Cd(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-181340,-264540,72.797,256.8,130.4,19.5944,40.0653,-10.0034,-4.4352,156.4053,49.2806,-0.03,0
+Eu(Ala)+,NA,Eu(C3H6NO2)+,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-206029,-242617,50.149,135,68.4,11.0532,19.2058,-1.7947,-3.5729,83.4588,24.4724,-0.2006,1
+Eu(Ala)2,NA,Eu(C3H6NO2)2,aq,"SK95.1 [S98]",CHNOSZ.2,3.Sep.06,-282521,-359634,99.56,298.5,147,21.8707,45.6205,-12.1799,-4.6649,180.847,57.7759,-0.03,0

Modified: pkg/CHNOSZ/inst/extdata/thermo/SK95.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/SK95.csv	2019-02-09 04:54:47 UTC (rev 388)
+++ pkg/CHNOSZ/inst/extdata/thermo/SK95.csv	2019-02-09 05:15:07 UTC (rev 389)
@@ -27,29 +27,29 @@
 Cd(Gly)2,NA,Cd(C2H4NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-180576,-246607,65,148.7,92.1,14.355,27.2722,-4.9746,-3.9063,93.0282,27.2523,-0.03,0
 Eu(Gly)+,NA,Eu(C2H4NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-206629,-234136,47.919,89.8,50.3,8.5841,13.176,0.5767,-3.3236,57.1645,15.2476,-0.1738,1
 Eu(Gly)2,NA,Eu(C2H4NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-283817,-342929,94.554,190.4,108.7,16.6314,32.8272,-7.1514,-4.136,117.4699,35.7476,-0.03,0
-Ca(Alan)+,NA,Ca(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-208472,-247083,34.555,104.6,50.7,8.7124,13.4888,0.454,-3.3365,67.7227,18.2713,0.0279,1
-Ca(Alan)2,NA,Ca(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-284046,-364714,78.835,239.1,127.3,19.1765,39.0448,-9.6021,-4.393,146.0369,45.6768,-0.03,0
-Mg(Alan)+,NA,Mg(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-185839,-231745,7.968,109.5,46.8,8.3169,12.5282,0.821,-3.2968,74.3351,19.275,0.4322,1
-Mg(Alan)2,NA,Mg(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-262231,-352641,44.042,248.8,123,18.5836,37.5967,-9.0318,-4.3331,151.6713,47.6352,-0.03,0
-Sr(Alan)+,NA,Sr(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-210430,-247624,42.695,98.9,51.4,8.77,13.6312,0.3947,-3.3424,63.2691,17.1163,-0.0948,1
-Sr(Alan)2,NA,Sr(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-285431,-363933,89.487,228.1,128.1,19.2869,39.3109,-9.699,-4.404,139.5534,43.4233,-0.03,0
-Ba(Alan)+,NA,Ba(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-210013,-243703,56.097,93.7,56.8,9.4348,15.2528,-0.2391,-3.4095,58.4325,16.085,-0.2977,1
-Ba(Alan)2,NA,Ba(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-285287,-359051,107.026,218.2,134.1,20.104,41.3073,-10.4865,-4.4865,133.7647,41.4112,-0.03,0
-Mn(Alan)+,NA,Mn(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-133580,-173180,28.965,112.3,51.8,8.8873,13.9167,0.2842,-3.3542,73.0237,19.8433,0.1124,1
-Mn(Alan)2,NA,Mn(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-212074,-294245,71.52,254.2,128.5,19.3395,39.4414,-9.7539,-4.4094,154.8617,48.744,-0.03,0
-Fe(Alan)+,NA,Fe(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-103252,-145766,18.058,103.3,46.1,8.1661,12.1558,0.976,-3.2814,69.2856,18.01,0.2792,1
-Fe(Alan)2,NA,Fe(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-182987,-268535,57.246,236.6,122.2,18.4732,37.3244,-8.9189,-4.3219,144.5703,45.1671,-0.03,0
-Ni(Alan)+,NA,Ni(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-93527,-137131,15,95.2,38.5,7.1451,9.664,1.9536,-3.1784,64.9703,16.36,0.326,1
-Ni(Alan)2,NA,Ni(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-174545,-262972,50,220.8,113.8,17.318,34.504,-7.8105,-4.2053,135.3083,41.9478,-0.03,0
-Cu(Alan)+,NA,Cu(C3H6NO2)+,aq,SK95,CHNOSZ,12.Oct.07,-70595,-109970,25,108.7,43.4,7.7387,11.1165,1.3762,-3.2385,70.7759,19.11,0.0974,1
-Cu(Alan)2,NA,Cu(C3H6NO2)2,aq,SK95,CHNOSZ,12.Oct.07,-154654,-237360,65,247.2,119.2,18.0655,36.3271,-8.523,-4.2807,150.7452,47.3132,-0.03,0
-Zn(Alan)+,NA,Zn(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-116613,-160464,17,107.4,43.8,7.8514,11.3891,1.2746,-3.2497,71.8106,18.835,0.2956,1
-Zn(Alan)2,NA,Zn(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-197112,-283389,60,244.5,119.6,18.1164,36.4558,-8.5823,-4.286,149.2015,46.7767,-0.03,0
-Pb(Alan)+,NA,Pb(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-87191,-120275,58.688,93,53.4,8.964,14.1088,0.1992,-3.3622,57.5413,15.9017,-0.3372,1
-Pb(Alan)2,NA,Pb(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-166271,-239191,110.416,216.4,130.4,19.5944,40.0653,-10.0034,-4.4352,132.7356,41.0535,-0.03,0
-Co(Alan)+,NA,Co(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-94099,-136245,20,104,43.6,7.8202,11.3148,1.299,-3.2467,69.3955,18.1475,0.2482,1
-Co(Alan)2,NA,Co(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-173793,-259272,60,238,119.4,18.0995,36.4127,-8.5626,-4.2842,145.3423,45.4353,-0.03,0
-Cd(Alan)+,NA,Cd(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-100082,-141016,29.238,113.7,53.4,9.1151,14.4742,0.063,-3.3773,73.7914,20.1183,0.1098,1
-Cd(Alan)2,NA,Cd(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-179940,-263420,71.877,256.8,130.4,19.5944,40.0653,-10.0034,-4.4352,156.4053,49.2806,-0.03,0
-Eu(Alan)+,NA,Eu(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-205329,-242057,49.689,135,68.4,11.0532,19.2058,-1.7947,-3.5729,83.4588,24.4724,-0.2006,1
-Eu(Alan)2,NA,Eu(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-281121,-358514,98.64,298.5,147,21.8707,45.6205,-12.1799,-4.6649,180.847,57.7759,-0.03,0
+Ca(Ala)+,NA,Ca(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-208472,-247083,34.555,104.6,50.7,8.7124,13.4888,0.454,-3.3365,67.7227,18.2713,0.0279,1
+Ca(Ala)2,NA,Ca(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-284046,-364714,78.835,239.1,127.3,19.1765,39.0448,-9.6021,-4.393,146.0369,45.6768,-0.03,0
+Mg(Ala)+,NA,Mg(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-185839,-231745,7.968,109.5,46.8,8.3169,12.5282,0.821,-3.2968,74.3351,19.275,0.4322,1
+Mg(Ala)2,NA,Mg(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-262231,-352641,44.042,248.8,123,18.5836,37.5967,-9.0318,-4.3331,151.6713,47.6352,-0.03,0
+Sr(Ala)+,NA,Sr(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-210430,-247624,42.695,98.9,51.4,8.77,13.6312,0.3947,-3.3424,63.2691,17.1163,-0.0948,1
+Sr(Ala)2,NA,Sr(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-285431,-363933,89.487,228.1,128.1,19.2869,39.3109,-9.699,-4.404,139.5534,43.4233,-0.03,0
+Ba(Ala)+,NA,Ba(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-210013,-243703,56.097,93.7,56.8,9.4348,15.2528,-0.2391,-3.4095,58.4325,16.085,-0.2977,1
+Ba(Ala)2,NA,Ba(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-285287,-359051,107.026,218.2,134.1,20.104,41.3073,-10.4865,-4.4865,133.7647,41.4112,-0.03,0
+Mn(Ala)+,NA,Mn(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-133580,-173180,28.965,112.3,51.8,8.8873,13.9167,0.2842,-3.3542,73.0237,19.8433,0.1124,1
+Mn(Ala)2,NA,Mn(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-212074,-294245,71.52,254.2,128.5,19.3395,39.4414,-9.7539,-4.4094,154.8617,48.744,-0.03,0
+Fe(Ala)+,NA,Fe(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-103252,-145766,18.058,103.3,46.1,8.1661,12.1558,0.976,-3.2814,69.2856,18.01,0.2792,1
+Fe(Ala)2,NA,Fe(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-182987,-268535,57.246,236.6,122.2,18.4732,37.3244,-8.9189,-4.3219,144.5703,45.1671,-0.03,0
+Ni(Ala)+,NA,Ni(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-93527,-137131,15,95.2,38.5,7.1451,9.664,1.9536,-3.1784,64.9703,16.36,0.326,1
+Ni(Ala)2,NA,Ni(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-174545,-262972,50,220.8,113.8,17.318,34.504,-7.8105,-4.2053,135.3083,41.9478,-0.03,0
+Cu(Ala)+,NA,Cu(C3H6NO2)+,aq,SK95,CHNOSZ,12.Oct.07,-70595,-109970,25,108.7,43.4,7.7387,11.1165,1.3762,-3.2385,70.7759,19.11,0.0974,1
+Cu(Ala)2,NA,Cu(C3H6NO2)2,aq,SK95,CHNOSZ,12.Oct.07,-154654,-237360,65,247.2,119.2,18.0655,36.3271,-8.523,-4.2807,150.7452,47.3132,-0.03,0
+Zn(Ala)+,NA,Zn(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-116613,-160464,17,107.4,43.8,7.8514,11.3891,1.2746,-3.2497,71.8106,18.835,0.2956,1
+Zn(Ala)2,NA,Zn(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-197112,-283389,60,244.5,119.6,18.1164,36.4558,-8.5823,-4.286,149.2015,46.7767,-0.03,0
+Pb(Ala)+,NA,Pb(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-87191,-120275,58.688,93,53.4,8.964,14.1088,0.1992,-3.3622,57.5413,15.9017,-0.3372,1
+Pb(Ala)2,NA,Pb(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-166271,-239191,110.416,216.4,130.4,19.5944,40.0653,-10.0034,-4.4352,132.7356,41.0535,-0.03,0
+Co(Ala)+,NA,Co(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-94099,-136245,20,104,43.6,7.8202,11.3148,1.299,-3.2467,69.3955,18.1475,0.2482,1
+Co(Ala)2,NA,Co(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-173793,-259272,60,238,119.4,18.0995,36.4127,-8.5626,-4.2842,145.3423,45.4353,-0.03,0
+Cd(Ala)+,NA,Cd(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-100082,-141016,29.238,113.7,53.4,9.1151,14.4742,0.063,-3.3773,73.7914,20.1183,0.1098,1
+Cd(Ala)2,NA,Cd(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-179940,-263420,71.877,256.8,130.4,19.5944,40.0653,-10.0034,-4.4352,156.4053,49.2806,-0.03,0
+Eu(Ala)+,NA,Eu(C3H6NO2)+,aq,SK95,CHNOSZ,3.Sep.06,-205329,-242057,49.689,135,68.4,11.0532,19.2058,-1.7947,-3.5729,83.4588,24.4724,-0.2006,1
+Eu(Ala)2,NA,Eu(C3H6NO2)2,aq,SK95,CHNOSZ,3.Sep.06,-281121,-358514,98.64,298.5,147,21.8707,45.6205,-12.1799,-4.6649,180.847,57.7759,-0.03,0

Modified: pkg/CHNOSZ/tests/testthat/test-recalculate.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-recalculate.R	2019-02-09 04:54:47 UTC (rev 388)
+++ pkg/CHNOSZ/tests/testthat/test-recalculate.R	2019-02-09 05:15:07 UTC (rev 389)
@@ -2,7 +2,7 @@
 
 # SK95: Shock and Korestky, 1995
 # doi:10.1016/0016-7037(95)00058-8
-test_that("recalculated values from SK95 are correctly enetered in OBIGT", {
+test_that("recalculated values from SK95 are correctly entered in OBIGT", {
   # test added 20190206
   # thermodynamic data entries for amino acid glycinate and alanate complexes
   # (no longer in default database)
@@ -11,31 +11,31 @@
   iaa <- info(c("alanate", "glycinate"))
   iGly <- grep("\\(Gly\\)\\+$", thermo$obigt$name)
   iGly2 <- grep("\\(Gly\\)2$", thermo$obigt$name)
-  iAlan <- grep("\\(Alan\\)\\+$", thermo$obigt$name)
-  iAlan2 <- grep("\\(Alan\\)2$", thermo$obigt$name)
+  iAla <- grep("\\(Ala\\)\\+$", thermo$obigt$name)
+  iAla2 <- grep("\\(Ala\\)2$", thermo$obigt$name)
   # get values used in OBIGT
   aa_GHS_OBIGT <- thermo$obigt[iaa, c("G", "H", "S")]
   Gly_GHS_OBIGT <- thermo$obigt[iGly, c("G", "H", "S")]
   Gly2_GHS_OBIGT <- thermo$obigt[iGly2, c("G", "H", "S")]
-  Alan_GHS_OBIGT <- thermo$obigt[iAlan, c("G", "H", "S")]
-  Alan2_GHS_OBIGT <- thermo$obigt[iAlan2, c("G", "H", "S")]
+  Ala_GHS_OBIGT <- thermo$obigt[iAla, c("G", "H", "S")]
+  Ala2_GHS_OBIGT <- thermo$obigt[iAla2, c("G", "H", "S")]
   # get values from SK95
   SK95 <- system.file("extdata/thermo/SK95.csv", package="CHNOSZ")
   add.obigt(SK95)
   aa_GHS_SK95 <- thermo$obigt[iaa, c("G", "H", "S")]
   Gly_GHS_SK95 <- thermo$obigt[iGly, c("G", "H", "S")]
   Gly2_GHS_SK95 <- thermo$obigt[iGly2, c("G", "H", "S")]
-  Alan_GHS_SK95 <- thermo$obigt[iAlan, c("G", "H", "S")]
-  Alan2_GHS_SK95 <- thermo$obigt[iAlan2, c("G", "H", "S")]
+  Ala_GHS_SK95 <- thermo$obigt[iAla, c("G", "H", "S")]
+  Ala2_GHS_SK95 <- thermo$obigt[iAla2, c("G", "H", "S")]
   # calculate differences for alanate and glycinate
   # nb. round values to avoid floating-point difficulties with unique() etc.
-  Alan_GHS_Delta <- round(aa_GHS_SK95[1, ] - aa_GHS_OBIGT[1, ], 2)
+  Ala_GHS_Delta <- round(aa_GHS_SK95[1, ] - aa_GHS_OBIGT[1, ], 2)
   Gly_GHS_Delta <- round(aa_GHS_SK95[2, ] - aa_GHS_OBIGT[2, ], 2)
   # test that the differences are the same in the corresponding complexes
   expect_equivalent(Gly_GHS_Delta, unique(round(Gly_GHS_SK95 - Gly_GHS_OBIGT, 2)))
   expect_equivalent(Gly_GHS_Delta, unique(round((Gly2_GHS_SK95 - Gly2_GHS_OBIGT)/2, 2)))
-  expect_equivalent(Alan_GHS_Delta, unique(round(Alan_GHS_SK95 - Alan_GHS_OBIGT, 2)))
-  expect_equivalent(Alan_GHS_Delta, unique(round((Alan2_GHS_SK95 - Alan2_GHS_OBIGT)/2, 2)))
+  expect_equivalent(Ala_GHS_Delta, unique(round(Ala_GHS_SK95 - Ala_GHS_OBIGT, 2)))
+  expect_equivalent(Ala_GHS_Delta, unique(round((Ala2_GHS_SK95 - Ala2_GHS_OBIGT)/2, 2)))
   # clean up
   data(thermo)
 })