[CHNOSZ-commits] r233 - in pkg/CHNOSZ: . R data demo inst inst/extdata/OBIGT man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Oct 1 10:40:38 CEST 2017


Author: jedick
Date: 2017-10-01 10:40:37 +0200 (Sun, 01 Oct 2017)
New Revision: 233

Added:
   pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/info.R
   pkg/CHNOSZ/R/subcrt.R
   pkg/CHNOSZ/data/thermo.R
   pkg/CHNOSZ/demo/activity_ratios.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
   pkg/CHNOSZ/man/subcrt.Rd
Log:
add Berman_cr.csv


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/DESCRIPTION	2017-10-01 08:40:37 UTC (rev 233)
@@ -1,6 +1,6 @@
-Date: 2017-09-30
+Date: 2017-10-01
 Package: CHNOSZ
-Version: 1.1.0-31
+Version: 1.1.0-32
 Title: Thermodynamic Calculations for Geobiochemistry
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R	2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/R/info.R	2017-10-01 08:40:37 UTC (rev 233)
@@ -73,7 +73,7 @@
   return(out)
 }
 
-info.character <- function(species, state=NULL, check.protein=TRUE) {
+info.character <- function(species, state=NULL, check.protein=TRUE, grep.state=FALSE) {
   # 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$state is also required if 'state' is not NULL
@@ -113,7 +113,8 @@
     # special treatment for H2O: aq retrieves the liq
     if(species %in% c("H2O", "water") & state=="aq") state <- "liq"
     # the matches for both species and state
-    matches.state <- matches.species & grepl(state, get("thermo")$obigt$state)
+    if(grep.state) matches.state <- matches.species & grepl(state, thermo$obigt$state)
+    else matches.state <- matches.species & state == thermo$obigt$state
     if(!any(matches.state)) {
       # the requested state is not available for this species
       available.states <- thermo$obigt$state[matches.species]
@@ -160,19 +161,19 @@
   # use new obigt2eos function here
   this <- obigt2eos(this, this$state)
   # identify any missing GHS values
-  naGHS <- which(is.na(this[8:10]))
+  naGHS <- is.na(this[8:10])
   # a missing one of G, H or S can cause problems for subcrt calculations at high T
-  if(length(naGHS)==1) {
+  if(sum(naGHS)==1) {
     # calculate a single missing one of G, H, or S from the others
     GHS <- as.numeric(GHS(as.character(this$formula), G=this[,8], H=this[,9], S=this[,10]))
     message("info.numeric: ", colnames(this)[8:10][naGHS], " of ",
       this$name, "(", this$state, ") is NA; set to ", round(GHS[naGHS],2))
-    this[, naGHS+7] <- GHS[naGHS]
+    this[, which(naGHS)+7] <- GHS[naGHS]
   } 
   # now perform consistency checks for GHS and EOS parameters if check.it=TRUE
   if(check.it) {
     # check GHS if they were all present
-    if(length(naGHS)==0) calcG <- checkGHS(this)
+    if(sum(naGHS)==0) calcG <- checkGHS(this)
     # check tabulated heat capacities against EOS parameters
     calcCp <- checkEOS(this, this$state, "Cp")
     # fill in NA heat capacity

Modified: pkg/CHNOSZ/R/subcrt.R
===================================================================
--- pkg/CHNOSZ/R/subcrt.R	2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/R/subcrt.R	2017-10-01 08:40:37 UTC (rev 233)
@@ -122,7 +122,7 @@
     for(i in 1:length(species)) {
       mysearch <- species[i]
       if(can.be.numeric(mysearch)) mysearch <- thermo$obigt$name[as.numeric(mysearch)]
-      si <- info.character(mysearch, state[i])
+      si <- info.character(mysearch, state[i], grep.state=TRUE)
       # that could have the side-effect of adding a protein; re-read thermo
       thermo <- get("thermo", "CHNOSZ")
       if(is.na(si[1])) stop('no info found for ',species[i],' ',state[i])

Modified: pkg/CHNOSZ/data/thermo.R
===================================================================
--- pkg/CHNOSZ/data/thermo.R	2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/data/thermo.R	2017-10-01 08:40:37 UTC (rev 233)
@@ -10,7 +10,7 @@
 local({
   # create obigt data frame
   sources_aq <- paste0(c("H2O", "inorganic", "organic", "biotic"), "_aq")
-  sources_cr <- paste0(c("inorganic", "organic"), "_cr")
+  sources_cr <- paste0(c("inorganic", "organic", "Berman"), "_cr")
   sources_liq <- paste0(c("organic"), "_liq")
   sources_gas <- paste0(c("inorganic", "organic"), "_gas")
   OBIGTdir <- system.file("extdata/OBIGT/", package="CHNOSZ")

Modified: pkg/CHNOSZ/demo/activity_ratios.R
===================================================================
--- pkg/CHNOSZ/demo/activity_ratios.R	2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/demo/activity_ratios.R	2017-10-01 08:40:37 UTC (rev 233)
@@ -13,7 +13,7 @@
 # make the pseudospecies H4SiO4 available for use as a basis species
 add.obigt("CHNOSZ_aq", "pseudo-H4SiO4")
 basis(c("Al+3", "pseudo-H4SiO4", "K+", "H2O", "H+", "O2"))
-species(c("gibbsite", "muscovite", "kaolinite", "pyrophyllite", "k-feldspar"))
+species(c("gibbsite", "muscovite", "kaolinite", "pyrophyllite", "K-feldspar"))
 a <- affinity(H4SiO4 = c(-6, -2, res), `K+` = c(-3, 6, res))
 diagram(a, ylab = ratlab("K+"), fill = fill, yline = 1.7)
 title(main = syslab(c("K2O", "Al2O3", "SiO2", "H2O")))

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/inst/NEWS	2017-10-01 08:40:37 UTC (rev 233)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-30 (2017-09-30)
+CHANGES IN CHNOSZ 1.1.0-32 (2017-10-01)
 ---------------------------------------
 
 MAJOR CHANGES:
@@ -26,6 +26,12 @@
   species) to their defaults. data(thermo) is still used to reset
   *everything* (the database and all computational and system settings).
 
+- In add.obigt(), using 'file' without a file suffix now can be used to
+  locate corresponding files (such as CHNOSZ_aq.csv or DEW_aq.csv) in
+  the extdata/OBIGT package directory.
+
+- add.obigt() gets new argument 'species' for selecting species to add.
+
 DATABASE UPDATES:
 
 - Add DEW_aq.csv with aqueous species data from the DEW spreadsheet
@@ -33,12 +39,11 @@
   database in CHNOSZ are not included. For the time being, only
   selected species are fully referenced.
 
-- In add.obigt(), using 'file' without a file suffix now can be used to
-  locate corresponding files (such as CHNOSZ_aq.csv or DEW_aq.csv) in
-  the extdata/OBIGT package directory.
+- Add Berman_cr.csv with names and formulas for minerals whose
+  thermodynamic properties are calculated using the Berman (1988)
+  formulation. The state "cr_Berman" is used to distinguish these
+  minerals from the Helgeson data.
 
-- add.obigt() gets new argument 'species' for selecting species to add.
-
 - Data file CHNOSZ_aq.csv is no longer added to the database by default.
   It is now intended to hold provisional updates. Updated heat capacity
   and volume HKF parameters for adenine (Lowe et al., 2017) have been

Added: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
===================================================================
(Binary files differ)


Property changes on: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
___________________________________________________________________
Added: svn:mime-type
   + application/x-xz

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz	2017-10-01 08:40:37 UTC (rev 233)
@@ -1,66 +1,58 @@
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\ No newline at end of file

Modified: pkg/CHNOSZ/man/subcrt.Rd
===================================================================
--- pkg/CHNOSZ/man/subcrt.Rd	2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/man/subcrt.Rd	2017-10-01 08:40:37 UTC (rev 233)
@@ -132,7 +132,7 @@
 subcrt(c("glucose", "ethanol", "CO2"))
 
 ## properties of reactions
-subcrt(c("H2O", "H+", "k-feldspar", "kaolinite", "K+", "SiO2"),
+subcrt(c("H2O", "H+", "K-feldspar", "kaolinite", "K+", "SiO2"),
   c(-1, -2, -2, 1, 2, 4))
 subcrt(c("glucose", "ethanol", "CO2"), c(-1, 2, 2))
 # to specify the states



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