[CHNOSZ-commits] r551 - in pkg/CHNOSZ: . R inst tests/testthat

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

Author: jedick
Date: 2020-07-07 04:09:27 +0200 (Tue, 07 Jul 2020)
New Revision: 551

Added:
   pkg/CHNOSZ/tests/testthat/test-mod.OBIGT.R
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/add.OBIGT.R
   pkg/CHNOSZ/R/info.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/tests/testthat/test-thermo.R
Log:
Revise NEWS and add warning for aqueous methane (now CH4)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2020-07-06 15:49:37 UTC (rev 550)
+++ pkg/CHNOSZ/DESCRIPTION	2020-07-07 02:09:27 UTC (rev 551)
@@ -1,6 +1,6 @@
-Date: 2020-07-06
+Date: 2020-07-07
 Package: CHNOSZ
-Version: 1.3.6-24
+Version: 1.3.6-25
 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/add.OBIGT.R
===================================================================
--- pkg/CHNOSZ/R/add.OBIGT.R	2020-07-06 15:49:37 UTC (rev 550)
+++ pkg/CHNOSZ/R/add.OBIGT.R	2020-07-07 02:09:27 UTC (rev 551)
@@ -31,6 +31,7 @@
   # if the first argument is numeric, it's the species index
   if(is.numeric(args[[1]][1])) {
     ispecies <- args[[1]]
+    args <- args[-1]
   } else {
     # if the name of the first argument is missing, assume it's the species name
     if(names(args)[1]=="") names(args)[1] <- "name"

Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R	2020-07-06 15:49:37 UTC (rev 550)
+++ pkg/CHNOSZ/R/info.R	2020-07-07 02:09:27 UTC (rev 551)
@@ -80,6 +80,7 @@
   # returns the rownumbers of thermo()$OBIGT having an exact match of 'species' to
   # thermo()$OBIGT$[species|abbrv|formula] or NA otherwise
   # a match to thermo()$OBIGT$state is also required if 'state' is not NULL
+
   # (first occurence of a match to species is returned otherwise)
   thermo <- get("thermo", CHNOSZ)
   # find matches for species name, abbreviation or formula
@@ -123,6 +124,10 @@
       a.s.text <- paste("'", available.states, "'", sep="", collapse=" ")
       message("info.character: requested state '", state, "' for ", species, 
         " but only ", a.s.text, " ", a.s.verb, " available")
+      # warn about looking for aqueous methane (changed to CH4) 20200707
+      if(identical(species, "methane") & identical(state, "aq")) {
+        warning("'methane' is not an aqueous species; use 'CH4' instead\nTo revert to the old behavior, run mod.OBIGT(info('CH4'), name = 'methane')")
+      }
       return(NA)
     }
     matches.species <- matches.state

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2020-07-06 15:49:37 UTC (rev 550)
+++ pkg/CHNOSZ/inst/NEWS	2020-07-07 02:09:27 UTC (rev 551)
@@ -1,22 +1,27 @@
-CHANGES IN CHNOSZ 1.3.6-23 (2020-07-06)
+CHANGES IN CHNOSZ 1.3.6-24 (2020-07-07)
 ---------------------------------------
 
 MAJOR CHANGES
 
-- File, function, and object names consistently use the uppercase
-  abbreviation OBIGT. In particular, the active database now resides at
-  thermo()$OBIGT, and functions add.OBIGT() and mod.OBIGT() replace the
-  previous add.obigt() and mod.obigt().
+- The naming convention for methane has changed. The name "methane"
+  now applies exclusively to the gas; "CH4", as before, represents the
+  aqueous species. This behavior is consistent with inorganic gases
+  but differs from most organic substances, where the English names
+  refer to the aqueous species. This change was made because in the past
+  there was no way to use info() or subcrt() with a single character
+  argument to identify gaseous methane, which is common in geochemistry.
+  (Note that info("CH4", "gas") can still be used.) A hack to revert to
+  the old behavior is mod.OBIGT(info("CH4"), name = "methane").
 
+- The all-uppercase abbreviation OBIGT is now used for all file,
+  function, and object names. In particular, the active database now
+  sits at thermo()$OBIGT, and functions add.OBIGT() and mod.OBIGT()
+  replace the previous add.obigt() and mod.obigt().
+
 CHANGES TO OBIGT DATABASE
 
 - Update species parameters for the 2019 Deep Earth Water (DEW) model.
 
-- organic_aq.csv, AkDi.csv, DEW.csv: Remove "methane" as the name of
-  CH4(aq). This means that info("methane") now refers to the gas rather
-  than the aqueous species. This is consistent with the behavior for the
-  names of inorganic species, e.g. carbon dioxide and oxygen.
-
 - OBIGT/SUPCRT92.csv: Change lowercase to uppercase "A" (Angstrom) in
   names of minerals with suffixes indicating interlayer spacing
   (amesite, clinochlore, cronstedtite, daphnite).
@@ -87,6 +92,10 @@
 - TODO: demo/saturation.R: put Al+3 first in basis definition (it's
   confusing to have H2O first when the reacitons are balanced on Al)
 
+- TODO: diagram(): make error or warning for NA values of affinity
+
+- TODO: use markup in NEWS
+
 CHANGES IN CHNOSZ 1.3.6 (2020-03-16)
 ------------------------------------
 

Added: pkg/CHNOSZ/tests/testthat/test-mod.OBIGT.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-mod.OBIGT.R	                        (rev 0)
+++ pkg/CHNOSZ/tests/testthat/test-mod.OBIGT.R	2020-07-07 02:09:27 UTC (rev 551)
@@ -0,0 +1,34 @@
+context("mod.OBIGT")
+
+# clear out any previous basis definition or database alterations
+suppressMessages(reset())
+
+test_that("minimal usage of mod.OBIGT() creates usable data entries", {
+  # we need at least a name and some property
+  expect_error(mod.OBIGT("test"), "species name and a property")
+  # a valid formula is needed
+  expect_warning(expect_error(mod.OBIGT("test", date=today()), "is not a simple chemical formula"),
+               "please supply a valid chemical formula")
+  # the default state is aq
+  expect_message(itest <- mod.OBIGT("test", formula="Z0", date=today()), "added test\\(aq\\)")
+  # set the charge so following test use hkf() rather than AkDi()
+  mod.OBIGT("test", z = 0)
+  # we should get NA values of G for a species with NA properties 
+  expect_true(all(is.na(subcrt(itest)$out[[1]]$G)))
+  # a single value of G comes through to subcrt
+  mod.OBIGT("test", G=100)
+  expect_equal(subcrt("test", T=25, P=1)$out[[1]]$G, 100)
+  # values for Cp and c1 integrate to the same values of G
+  G.Cp <- subcrt(mod.OBIGT(list(name="test", S=0, Cp=100)))$out[[1]]$G
+  G.c1 <- subcrt(mod.OBIGT(list(name="test", S=0, c1=100)))$out[[1]]$G
+  expect_equal(G.Cp, G.c1)
+})
+
+test_that("mod.OBIGT() works with numeric argument (species index)", {
+  # test added 20200707
+  i1 <- info("CH4")
+  # previously this failed with an error
+  i2 <- mod.OBIGT(i1, name = "methane")
+  expect_identical(i1, i2)
+  expect_identical(info(i2)$name, "methane")
+})

Modified: pkg/CHNOSZ/tests/testthat/test-thermo.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-thermo.R	2020-07-06 15:49:37 UTC (rev 550)
+++ pkg/CHNOSZ/tests/testthat/test-thermo.R	2020-07-07 02:09:27 UTC (rev 551)
@@ -21,24 +21,3 @@
   # be nice and restore the database
   suppressMessages(reset())
 })
-
-test_that("minimal usage of mod.OBIGT() creates usable data entries", {
-  # we need at least a name and some property
-  expect_error(mod.OBIGT("test"), "species name and a property")
-  # a valid formula is needed
-  expect_warning(expect_error(mod.OBIGT("test", date=today()), "is not a simple chemical formula"),
-               "please supply a valid chemical formula")
-  # the default state is aq
-  expect_message(itest <- mod.OBIGT("test", formula="Z0", date=today()), "added test\\(aq\\)")
-  # set the charge so following test use hkf() rather than AkDi()
-  mod.OBIGT("test", z = 0)
-  # we should get NA values of G for a species with NA properties 
-  expect_true(all(is.na(subcrt(itest)$out[[1]]$G)))
-  # a single value of G comes through to subcrt
-  mod.OBIGT("test", G=100)
-  expect_equal(subcrt("test", T=25, P=1)$out[[1]]$G, 100)
-  # values for Cp and c1 integrate to the same values of G
-  G.Cp <- subcrt(mod.OBIGT(list(name="test", S=0, Cp=100)))$out[[1]]$G
-  G.c1 <- subcrt(mod.OBIGT(list(name="test", S=0, c1=100)))$out[[1]]$G
-  expect_equal(G.Cp, G.c1)
-})