[CHNOSZ-commits] r462 - in pkg/CHNOSZ: . inst tests/testthat

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

Author: jedick
Date: 2019-05-06 07:13:15 +0200 (Mon, 06 May 2019)
New Revision: 462

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/tests/testthat/test-mosaic.R
Log:
edit NEWS


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-05-05 09:41:57 UTC (rev 461)
+++ pkg/CHNOSZ/DESCRIPTION	2019-05-06 05:13:15 UTC (rev 462)
@@ -1,6 +1,6 @@
-Date: 2019-05-05
+Date: 2019-05-06
 Package: CHNOSZ
-Version: 1.3.2-9
+Version: 1.3.2-10
 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/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-05-05 09:41:57 UTC (rev 461)
+++ pkg/CHNOSZ/inst/NEWS	2019-05-06 05:13:15 UTC (rev 462)
@@ -1,15 +1,14 @@
-CHANGES IN CHNOSZ 1.3.2-9 (2019-05-05)
---------------------------------------
+CHANGES IN CHNOSZ 1.3.2-10 (2019-05-06)
+---------------------------------------
 
 BUG FIXES
 
-- In mosaic(), affinities of formation of species were not calculated
-  using activities of basis species that are adjusted (i.e. lowered)
-  according to their mole fractions. Previously, constant activities
-  were used for each changing basis species, leading to an artificial
-  inflation of the affinities of species, especially near the
-  transitions where the changing basis species are nearly equal in
-  abundance.
+- In mosaic(), constant activities were used for each changing basis
+  species, leading to an artificial inflation of the affinities of
+  species around the transitions where the basis species become equally
+  abundant. Now, affinities of formation of species are calculated using
+  activities of basis species that are adjusted (i.e. lowered) according
+  to their relative abundances.
 
 - The 'mixing' argument of mosaic() has been removed; it is no longer
   needed with the improved handling of activities of basis species.
@@ -22,11 +21,10 @@
   species are zero everywhere, in particular near the transitions of
   basis species.
 
-- In mosaic(), groups of changing basis species are equilibrated using
-  a total activity given by the activity of the starting basis species
-  in the incoming basis() definition. This is not directly related to
-  the bug above, but instead provides a means to constrain the amount of
-  an element in the basis species.
+- In mosaic(), groups of changing basis species are equilibrated for a
+  total activity given by the activity of the starting basis species in
+  the incoming basis() definition. This provides a means to specify the
+  the amount of a conserved element in the basis species.
 
 - In mosaic(), include the result of equilibrate() for each group of
   basis species in the output ('E.bases').
@@ -39,7 +37,7 @@
   plotted with diagram(). This can be useful for conserving two elements
   in a system: one in the basis species, the other in the formed
   species. Thanks to Kirt Robinson for the feature request and test
-  system.
+  system for acetamide, which has been added to ?equilibrate.
 
 - Add function moles(), to calculate the total number of moles of
   elements in the output from equilibrate().

Modified: pkg/CHNOSZ/tests/testthat/test-mosaic.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-mosaic.R	2019-05-05 09:41:57 UTC (rev 461)
+++ pkg/CHNOSZ/tests/testthat/test-mosaic.R	2019-05-06 05:13:15 UTC (rev 462)
@@ -51,7 +51,7 @@
 })
 
 test_that("mosaic() - equilibrate() produces equilibrium activities", {
-  # test added 20190505, based on an calculation sent by Kirt Robinson
+  # test added 20190505, based on a calculation sent by Kirt Robinson
   basis(c("CO2", "NH3", "O2", "H2O", "H+"))
   species(c("acetamide", "acetic acid", "acetate"))
   m <- mosaic(c("NH3", "NH4+"), pH = c(0, 14))