[CHNOSZ-commits] r723 - in pkg/CHNOSZ: . R inst inst/tinytest man

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

Author: jedick
Date: 2022-04-16 11:02:02 +0200 (Sat, 16 Apr 2022)
New Revision: 723

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/affinity.R
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/tinytest/test-affinity.R
   pkg/CHNOSZ/man/affinity.Rd
Log:
Change default for affinity() to loga.protein = 0


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2022-04-16 08:19:03 UTC (rev 722)
+++ pkg/CHNOSZ/DESCRIPTION	2022-04-16 09:02:02 UTC (rev 723)
@@ -1,6 +1,6 @@
 Date: 2022-04-16
 Package: CHNOSZ
-Version: 1.9.9-15
+Version: 1.9.9-16
 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/affinity.R
===================================================================
--- pkg/CHNOSZ/R/affinity.R	2022-04-16 08:19:03 UTC (rev 722)
+++ pkg/CHNOSZ/R/affinity.R	2022-04-16 09:02:02 UTC (rev 723)
@@ -13,7 +13,7 @@
 #source("species.R")
 
 affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rhomin=FALSE,
-  return.buffer=FALSE, return.sout=FALSE, balance="PBB", iprotein=NULL, loga.protein=-3, transect = NULL) {
+  return.buffer=FALSE, return.sout=FALSE, balance="PBB", iprotein=NULL, loga.protein=0, transect = NULL) {
   # ...: variables over which to calculate
   # property: what type of energy
   #   (G.basis,G.species,logact.basis,logK,logQ,A)

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2022-04-16 08:19:03 UTC (rev 722)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2022-04-16 09:02:02 UTC (rev 723)
@@ -10,7 +10,7 @@
 \newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
 \newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
 
-\section{Changes in CHNOSZ version 1.9.9-14 (2022-04-11)}{
+\section{Changes in CHNOSZ version 1.9.9-16 (2022-04-16)}{
 
   \subsection{MAJOR CHANGE}{
     \itemize{
@@ -51,9 +51,6 @@
       (\samp{G}, \samp{S}, and \samp{Cp} at 25 \degC) to formation constants of
       aqueous species as a function of temperature.
 
-      \item Add a \strong{zap} argument to \code{mod.OBIGT()} to clear
-      parameters of preexisting species.
-
       \item Add vignette \strong{customizing.Rmd} with description of database
       format, data-entry conventions, and examples of customizing the
       thermodynamic database using \code{add.OBIGT()}, \code{mod.OBIGT()}, and
@@ -76,6 +73,18 @@
     }
   }
 
+  \subsection{OTHER CHANGES}{
+    \itemize{
+
+      \item Add a \strong{zap} argument to \code{mod.OBIGT()} to clear
+      parameters of preexisting species (used by \code{logB_to_OBIGT()}).
+
+      \item Change default for \code{affinity()} to \code{loga.protein = 0}
+      (was -3).
+
+    }
+  }
+
   \subsection{REMOVED FEATURES}{
     \itemize{
 

Modified: pkg/CHNOSZ/inst/tinytest/test-affinity.R
===================================================================
--- pkg/CHNOSZ/inst/tinytest/test-affinity.R	2022-04-16 08:19:03 UTC (rev 722)
+++ pkg/CHNOSZ/inst/tinytest/test-affinity.R	2022-04-16 09:02:02 UTC (rev 723)
@@ -122,6 +122,7 @@
 # TODO: add comparison with results from loading proteins via species()
 
 info <- "affinity() for proteins (with/without 'iprotein') returns same value as in previous package versions"
+# These values were calculated using versions 0.6, 0.8 and 0.9-7 (25 degrees C, 1 bar, basis species "CHNOS" or "CHNOS+")
 A.2303RT.nonionized <- -3795.297
 A.2303RT.ionized <- -3075.222
 # first for nonionized protein
@@ -128,13 +129,13 @@
 basis("CHNOS")
 # try it with iprotein
 ip <- pinfo("CSG_HALJP")
-expect_equal(affinity(iprotein = ip)$values[[1]][1], A.2303RT.nonionized, tolerance = 1e-5, info = info)
+expect_equal(affinity(iprotein = ip, loga.protein = -3)$values[[1]][1], A.2303RT.nonionized, tolerance = 1e-5, info = info)
 # then with the protein loaded as a species
 species("CSG_HALJP")
 expect_equal(affinity()$values[[1]][1], A.2303RT.nonionized, tolerance = 1e-5, info = info)
 # now for ionized protein
 basis("CHNOS+")
-expect_equal(affinity(iprotein = ip)$values[[1]][1], A.2303RT.ionized, tolerance = 1e-5, info = info)
+expect_equal(affinity(iprotein = ip, loga.protein = -3)$values[[1]][1], A.2303RT.ionized, tolerance = 1e-5, info = info)
 species("CSG_HALJP")
 expect_equal(affinity()$values[[1]][1], A.2303RT.ionized, tolerance = 1e-5, info = info)
 

Modified: pkg/CHNOSZ/man/affinity.Rd
===================================================================
--- pkg/CHNOSZ/man/affinity.Rd	2022-04-16 08:19:03 UTC (rev 722)
+++ pkg/CHNOSZ/man/affinity.Rd	2022-04-16 09:02:02 UTC (rev 723)
@@ -9,7 +9,7 @@
 \usage{
   affinity(..., property = NULL, sout = NULL, exceed.Ttr = FALSE,
     exceed.rhomin = FALSE, return.buffer = FALSE, return.sout = FALSE,
-    balance = "PBB", iprotein = NULL, loga.protein = -3, transect = NULL)
+    balance = "PBB", iprotein = NULL, loga.protein = 0, transect = NULL)
 }
 
 \arguments{