From noreply at r-forge.r-project.org  Fri Mar  1 15:55:07 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  1 Mar 2019 15:55:07 +0100 (CET)
Subject: [CHNOSZ-commits] r415 - in pkg/CHNOSZ: . R inst
Message-ID: <20190301145507.D309E18CE30@r-forge.r-project.org>

Author: jedick
Date: 2019-03-01 15:55:07 +0100 (Fri, 01 Mar 2019)
New Revision: 415

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/examples.R
   pkg/CHNOSZ/inst/NEWS
Log:
submit version 1.3.0 to CRAN


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-02-25 13:16:27 UTC (rev 414)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-01 14:55:07 UTC (rev 415)
@@ -1,6 +1,6 @@
-Date: 2019-02-25
+Date: 2019-02-26
 Package: CHNOSZ
-Version: 1.2.0-22
+Version: 1.3.0
 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/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R	2019-02-25 13:16:27 UTC (rev 414)
+++ pkg/CHNOSZ/R/examples.R	2019-03-01 14:55:07 UTC (rev 415)
@@ -8,7 +8,7 @@
   topics <- c("thermo", "examples",
     "util.array", "util.blast", "util.data", "util.expression",
     "util.fasta", "util.formula", "util.matrix", "util.misc", "util.seq", "util.units",
-    "util.water", "taxonomy", "info", "protein.info", "hkf", "water", "IAPWS95", "subcrt", "berman",
+    "util.water", "taxonomy", "info", "retrieve", "protein.info", "hkf", "water", "IAPWS95", "subcrt", "berman",
     "makeup", "basis", "swap.basis", "species", "affinity", "solubility", "equilibrate", 
     "diagram", "buffer", "nonideal", "NaCl", "add.protein", "protein", "ionize.aa", "yeast.aa",
     "objective", "revisit", "EOSregress", "wjd")

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-02-25 13:16:27 UTC (rev 414)
+++ pkg/CHNOSZ/inst/NEWS	2019-03-01 14:55:07 UTC (rev 415)
@@ -1,5 +1,5 @@
-CHANGES IN CHNOSZ 1.2.0-19 (2019-02-25)
----------------------------------------
+CHANGES IN CHNOSZ 1.3.0 (2019-02-26)
+------------------------------------
 
 CRAN COMPLIANCE
 


From noreply at r-forge.r-project.org  Sat Mar  2 11:54:27 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat,  2 Mar 2019 11:54:27 +0100 (CET)
Subject: [CHNOSZ-commits] r416 - in pkg/CHNOSZ: . R inst
Message-ID: <20190302105427.7571B18CBF0@r-forge.r-project.org>

Author: jedick
Date: 2019-03-02 11:54:27 +0100 (Sat, 02 Mar 2019)
New Revision: 416

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/util.data.R
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/NEWS
Log:
obigt2eos(): fix error using info() for AkDi species


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-01 14:55:07 UTC (rev 415)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-02 10:54:27 UTC (rev 416)
@@ -1,6 +1,6 @@
-Date: 2019-02-26
+Date: 2019-03-02
 Package: CHNOSZ
-Version: 1.3.0
+Version: 1.3.0-1
 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/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R	2019-03-01 14:55:07 UTC (rev 415)
+++ pkg/CHNOSZ/R/util.data.R	2019-03-02 10:54:27 UTC (rev 416)
@@ -401,9 +401,11 @@
     # species in the Akinfiev-Diamond model (AkDi) have NA for Z 20190219
     isAkDi <- is.na(obigt$z.T)
     # remove scaling factors for the HKF species, but not for the AkDi species
-    obigt[!isAkDi, 13:20] <- t(t(obigt[!isAkDi, 13:20]) * 10^c(-1,2,0,4,0,4,5,0))
+    # protect this by an if statement to workaround error in subassignment to empty subset of data frame in R < 3.6.0
+    # (https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17483) 20190302
+    if(any(!isAkDi)) obigt[!isAkDi, 13:20] <- t(t(obigt[!isAkDi, 13:20]) * 10^c(-1,2,0,4,0,4,5,0))
     # for AkDi species, set NA values in remaining columns (for display only)
-    obigt[isAkDi, 16:19] <- NA
+    if(any(isAkDi)) obigt[isAkDi, 16:19] <- NA
     # if all of the species are AkDi, change the variable names
     if(all(isAkDi)) colnames(obigt)[13:20] <- c('a','b','xi','XX1','XX2','XX3','XX4','Z') 
     else colnames(obigt)[13:20] <- c('a1','a2','a3','a4','c1','c2','omega','Z') 

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2019-03-01 14:55:07 UTC (rev 415)
+++ pkg/CHNOSZ/inst/CHECKLIST	2019-03-02 10:54:27 UTC (rev 416)
@@ -2,8 +2,6 @@
 release checklist for CHNOSZ
 ****************************
 
-- compile vignettes with release version number and date
-
 - run examples() and demos() to check their output
 
 - check output of demo("sources") to make sure all data sources are cited
@@ -34,6 +32,9 @@
 - reduce size of vignettes: after upgrading rmarkdown, replace files in
   rmarkdown/rmd/h/bootstrap/fonts/ with empty files
 
+- backwards compatibility: build and check the package with the
+  *minimum* R version (from the DESCRIPTION file)
+
 OTHER THINGS TO CHECK:
 
 - remove all "<<-" from sources (leftover from debugging)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-03-01 14:55:07 UTC (rev 415)
+++ pkg/CHNOSZ/inst/NEWS	2019-03-02 10:54:27 UTC (rev 416)
@@ -1,3 +1,12 @@
+CHANGES IN CHNOSZ 1.3.0-1 (2019-03-02)
+--------------------------------------
+
+- Fix unexported function obigt2eos(), which was affected by "Assignment
+  to empty subset of data.frame fails check of length of value"
+  (https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17483). The bug
+  caused errors in R-release (3.5.2) but not R-devel, when using info()
+  for species with the AkDi model.
+
 CHANGES IN CHNOSZ 1.3.0 (2019-02-26)
 ------------------------------------
 


From noreply at r-forge.r-project.org  Sat Mar  2 12:01:02 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat,  2 Mar 2019 12:01:02 +0100 (CET)
Subject: [CHNOSZ-commits] r417 - in pkg/CHNOSZ: . R man
Message-ID: <20190302110102.973C318C3DE@r-forge.r-project.org>

Author: jedick
Date: 2019-03-02 12:01:02 +0100 (Sat, 02 Mar 2019)
New Revision: 417

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/examples.R
   pkg/CHNOSZ/man/examples.Rd
Log:
demos(): add AkDi to list of demos that are run


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-02 10:54:27 UTC (rev 416)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-02 11:01:02 UTC (rev 417)
@@ -1,6 +1,6 @@
 Date: 2019-03-02
 Package: CHNOSZ
-Version: 1.3.0-1
+Version: 1.3.0-2
 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/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R	2019-03-02 10:54:27 UTC (rev 416)
+++ pkg/CHNOSZ/R/examples.R	2019-03-02 11:01:02 UTC (rev 417)
@@ -29,7 +29,7 @@
 demos <- function(which=c("sources", "protein.equil", "affinity", "NaCl", "density", 
   "ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp", "glycinate",
   "mosaic", "copper", "solubility", "gold", "wjd", "bugstab", "Shh", "saturation",
-  "adenine", "DEW", "lambda", "TCA", "go-IU", "bison"), save.png=FALSE) {
+  "adenine", "DEW", "lambda", "TCA", "go-IU", "bison", "AkDi"), save.png=FALSE) {
   # run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
   for(i in 1:length(which)) {
     # say something so the user sees where we are

Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd	2019-03-02 10:54:27 UTC (rev 416)
+++ pkg/CHNOSZ/man/examples.Rd	2019-03-02 11:01:02 UTC (rev 417)
@@ -17,7 +17,7 @@
     "density", "ORP", "revisit", "findit", "ionize", "buffer",
     "protbuff", "yeastgfp", "glycinate", "mosaic", "copper",
     "solubility", "gold", "wjd", "bugstab", "Shh", "saturation",
-    "adenine", "DEW", "lambda", "TCA", "go-IU", "bison"),
+    "adenine", "DEW", "lambda", "TCA", "go-IU", "bison", "AkDi"),
     save.png=FALSE)
 }
 


From noreply at r-forge.r-project.org  Sat Mar  2 15:16:57 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat,  2 Mar 2019 15:16:57 +0100 (CET)
Subject: [CHNOSZ-commits] r418 - in pkg/CHNOSZ: . R inst
Message-ID: <20190302141657.A3A6C18C4AF@r-forge.r-project.org>

Author: jedick
Date: 2019-03-02 15:16:57 +0100 (Sat, 02 Mar 2019)
New Revision: 418

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/add.obigt.R
   pkg/CHNOSZ/R/diagram.R
   pkg/CHNOSZ/R/thermo.R
   pkg/CHNOSZ/R/util.data.R
   pkg/CHNOSZ/inst/NEWS
Log:
various fixes to maintain compatibility with R version 3.1.0


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-02 14:16:57 UTC (rev 418)
@@ -1,6 +1,6 @@
 Date: 2019-03-02
 Package: CHNOSZ
-Version: 1.3.0-2
+Version: 1.3.0-3
 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	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/R/add.obigt.R	2019-03-02 14:16:57 UTC (rev 418)
@@ -128,7 +128,8 @@
     if(length(isys)==1) file <- system.file(paste0("extdata/OBIGT/", sysfiles[isys]), package="CHNOSZ")
   }
   # read data from the file
-  to2 <- read.csv(file, as.is=TRUE)
+  # we need explicit colClasses here to avoid automatic detection as character for long numeric values in R 3.1.0  20190302
+  to2 <- read.csv(file, as.is=TRUE, colClasses=c(rep("character", 7), rep("numeric", 13)))
   # load only selected species if requested
   if(!is.null(species)) {
     idat <- match(species, to2$name)

Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/R/diagram.R	2019-03-02 14:16:57 UTC (rev 418)
@@ -515,7 +515,8 @@
 	  }
 	}
         # https://stackoverflow.com/questions/34570860/adding-na-to-make-all-list-elements-equal-length 20181029
-        lapply(linesout, `length<-`, max(lengths(linesout)))
+        # for compatibility with R 3.1.0, don't use lengths() here 20190302
+        lapply(linesout, `length<-`, max(sapply(linesout, length)))
       }
       ## label plot function
       plot.names <- function(out, xs, ys, xlim, ylim, names) {

Modified: pkg/CHNOSZ/R/thermo.R
===================================================================
--- pkg/CHNOSZ/R/thermo.R	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/R/thermo.R	2019-03-02 14:16:57 UTC (rev 418)
@@ -44,7 +44,8 @@
   # need explicit "/" for Windows
   sourcefiles <- paste0(OBIGTdir, "/", c(sources_aq, sources_cr, sources_liq, sources_gas), ".csv")
   sourcefiles[!sources=="Berman_cr"] <- paste0(sourcefiles[!sources=="Berman_cr"], ".xz")
-  datalist <- lapply(sourcefiles, read.csv, as.is=TRUE)
+  # we need explicit colClasses here to avoid automatic detection as character for long numeric values in R 3.1.0  20190302
+  datalist <- lapply(sourcefiles, read.csv, as.is=TRUE, colClasses=c(rep("character", 7), rep("numeric", 13)))
   obigt <- do.call(rbind, datalist)
   # also read references file
   refs <- read.csv(file.path(OBIGTdir, "refs.csv"), as.is=TRUE)

Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/R/util.data.R	2019-03-02 14:16:57 UTC (rev 418)
@@ -399,7 +399,7 @@
   # and apply column names depending on the EOS
   if(identical(state, "aq")) {
     # species in the Akinfiev-Diamond model (AkDi) have NA for Z 20190219
-    isAkDi <- is.na(obigt$z.T)
+    isAkDi <- is.na(obigt[, 20])
     # remove scaling factors for the HKF species, but not for the AkDi species
     # protect this by an if statement to workaround error in subassignment to empty subset of data frame in R < 3.6.0
     # (https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17483) 20190302

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/inst/NEWS	2019-03-02 14:16:57 UTC (rev 418)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.0-1 (2019-03-02)
+CHANGES IN CHNOSZ 1.3.0-3 (2019-03-02)
 --------------------------------------
 
 - Fix unexported function obigt2eos(), which was affected by "Assignment
@@ -7,6 +7,10 @@
   caused errors in R-release (3.5.2) but not R-devel, when using info()
   for species with the AkDi model.
 
+- Various fixes to maintain compatibility with R version 3.1.0 (don't
+  use lengths(), and provide explicit colClasses to read.csv() to avoid
+  automatic detection of character for long numeric values).
+
 CHANGES IN CHNOSZ 1.3.0 (2019-02-26)
 ------------------------------------
 


From noreply at r-forge.r-project.org  Sat Mar  2 16:12:02 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat,  2 Mar 2019 16:12:02 +0100 (CET)
Subject: [CHNOSZ-commits] r419 - in pkg/CHNOSZ: . inst
Message-ID: <20190302151202.E3A9718C5B3@r-forge.r-project.org>

Author: jedick
Date: 2019-03-02 16:12:02 +0100 (Sat, 02 Mar 2019)
New Revision: 419

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
Log:
submit version 1.3.1 to CRAN


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-02 14:16:57 UTC (rev 418)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-02 15:12:02 UTC (rev 419)
@@ -1,6 +1,6 @@
 Date: 2019-03-02
 Package: CHNOSZ
-Version: 1.3.0-3
+Version: 1.3.1
 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	2019-03-02 14:16:57 UTC (rev 418)
+++ pkg/CHNOSZ/inst/NEWS	2019-03-02 15:12:02 UTC (rev 419)
@@ -1,5 +1,5 @@
-CHANGES IN CHNOSZ 1.3.0-3 (2019-03-02)
---------------------------------------
+CHANGES IN CHNOSZ 1.3.1 (2019-03-02)
+------------------------------------
 
 - Fix unexported function obigt2eos(), which was affected by "Assignment
   to empty subset of data.frame fails check of length of value"
@@ -7,9 +7,9 @@
   caused errors in R-release (3.5.2) but not R-devel, when using info()
   for species with the AkDi model.
 
-- Various fixes to maintain compatibility with R version 3.1.0 (don't
-  use lengths(), and provide explicit colClasses to read.csv() to avoid
-  automatic detection of character for long numeric values).
+- Fixes to maintain compatibility with R version 3.1.0: don't use
+  lengths(), and provide explicit colClasses to read.csv() to avoid
+  automatic assignment of character for long numeric values.
 
 CHANGES IN CHNOSZ 1.3.0 (2019-02-26)
 ------------------------------------


From noreply at r-forge.r-project.org  Sun Mar  3 07:54:51 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun,  3 Mar 2019 07:54:51 +0100 (CET)
Subject: [CHNOSZ-commits] r420 - in pkg/CHNOSZ: . R inst inst/extdata/thermo
	man tests/testthat
Message-ID: <20190303065451.AE5D418C5C8@r-forge.r-project.org>

Author: jedick
Date: 2019-03-03 07:54:49 +0100 (Sun, 03 Mar 2019)
New Revision: 420

Added:
   pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/thermo.R
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/retrieve.Rd
   pkg/CHNOSZ/man/thermo.Rd
   pkg/CHNOSZ/tests/testthat/test-retrieve.R
Log:
add precalculated stoichiometric matrix to speed up retrieve()


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-02 15:12:02 UTC (rev 419)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-03 06:54:49 UTC (rev 420)
@@ -1,6 +1,6 @@
-Date: 2019-03-02
+Date: 2019-03-03
 Package: CHNOSZ
-Version: 1.3.1
+Version: 1.3.1-1
 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/thermo.R
===================================================================
--- pkg/CHNOSZ/R/thermo.R	2019-03-02 15:12:02 UTC (rev 419)
+++ pkg/CHNOSZ/R/thermo.R	2019-03-03 06:54:49 UTC (rev 420)
@@ -17,10 +17,15 @@
     buffers = read.csv(file.path(thermodir, "buffer.csv"), as.is=1:3),
     protein = read.csv(file.path(thermodir, "protein.csv"), as.is=1:4),
     groups = read.csv(file.path(thermodir, "groups.csv"), row.names=1, check.names=FALSE),
+    stoich = read.csv(file.path(thermodir, "stoich.csv.xz"), as.is=TRUE),
     basis = NULL,
     species = NULL,
     opar = NULL
   )
+  # store stoich as matrix (with non-unique row names), not data frame
+  formula <- thermo$stoich[, 1]
+  thermo$stoich <- as.matrix(thermo$stoich[, 2:ncol(thermo$stoich)])
+  rownames(thermo$stoich) <- formula
   # give a summary of what we are doing
   if(!"thermo" %in% ls(CHNOSZ)) message("reset: creating \"thermo\" object")
   else message("reset: resetting \"thermo\" object")

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2019-03-02 15:12:02 UTC (rev 419)
+++ pkg/CHNOSZ/inst/CHECKLIST	2019-03-03 06:54:49 UTC (rev 420)
@@ -10,6 +10,9 @@
   co <- check.obigt()
   write.csv(co, "obigt_check.csv", row.names=FALSE, na="")
 
+- recreate extdata/thermo/stoich.csv.xz after all data updates
+  (see testthat/test-retrieve.R for instructions)
+
 - check that uniprot.aa() works with current UniProt web pages
 
 - run R_PAPERSIZE=letter R CMD Rd2pdf chnosz/
@@ -18,31 +21,26 @@
 - run R CMD check using R compiled without long doubles (emulating Solaris checks on CRAN)
   (CFLAGS=-ffloat-store ./configure --disable-long-double)
 
-- build the package on the source directory;
-  try both qpdf and ghostscript to compact vignettes:
+- size reduction of vignettes: after installing/upgrading rmarkdown, replace files in
+  rmarkdown/rmd/h/bootstrap/fonts/ with empty files
+
+- build the package using both qpdf and ghostscript to compact vignettes:
   R CMD build --compact-vignettes=both chnosz/
 
-- check reverse dependencies on CRAN: LipidMS, canprot, ecipex, iemisc as of 2019-02-09
-
 - vignettes/obigt.bib: check correct year for CHNOSZ reference
 
 - documentation links: after installation, run doc/mklinks.sh
   and insert the modified anintro.html in the package
 
-- reduce size of vignettes: after upgrading rmarkdown, replace files in
-  rmarkdown/rmd/h/bootstrap/fonts/ with empty files
-
 - backwards compatibility: build and check the package with the
   *minimum* R version (from the DESCRIPTION file)
 
-OTHER THINGS TO CHECK:
+- check reverse dependencies on CRAN: LipidMS, canprot, ecipex, iemisc as of 2019-02-09
 
-- remove all "<<-" from sources (leftover from debugging)
+OTHER THINGS TO WORK ON:
 
 - update list of documentation topics in examples() with any new ones
 
-- check for stale URLs in Rd files
-
 - clean up all TODO, XXX, etc. in Rd files (and hopefully R files too)
 
 - update .Rinstignore with any new/deleted files

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-03-02 15:12:02 UTC (rev 419)
+++ pkg/CHNOSZ/inst/NEWS	2019-03-03 06:54:49 UTC (rev 420)
@@ -1,3 +1,10 @@
+CHANGES IN CHNOSZ 1.3.1-1 (2019-03-03)
+--------------------------------------
+
+- Add thermo/stoich.csv.xz (stored as thermo()$stoich), containing a
+  precalculated stochiometric matrix for the default database, to speed
+  up retrieve().
+
 CHANGES IN CHNOSZ 1.3.1 (2019-03-02)
 ------------------------------------
 

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


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

Modified: pkg/CHNOSZ/man/retrieve.Rd
===================================================================
--- pkg/CHNOSZ/man/retrieve.Rd	2019-03-02 15:12:02 UTC (rev 419)
+++ pkg/CHNOSZ/man/retrieve.Rd	2019-03-03 06:54:49 UTC (rev 420)
@@ -36,8 +36,8 @@
 If the argument list is empty, then the function returns an empty (length 0) numeric value.
 A special argument value \samp{all} can be used to retrieve all species in the thermodynamic database, including filtering on state and hiding of the groups.
 
-The first time the function is run, it uses \code{\link{i2A}} to build the stoichiometric matrix for the current database.
-Following runs use the previously calculated stoichiometric matrix, unless a change to the database is detected, which triggers a recalculation.
+To speed up operation, the function uses a precalculated stoichiometric matrix for the default database, which is loaded with the package (see \code{\link{thermo}}).
+If the function detects a change to any chemical formulas in database, it triggers a recalculation using \code{\link{i2A}}.
 }
 
 \seealso{

Modified: pkg/CHNOSZ/man/thermo.Rd
===================================================================
--- pkg/CHNOSZ/man/thermo.Rd	2019-03-02 15:12:02 UTC (rev 419)
+++ pkg/CHNOSZ/man/thermo.Rd	2019-03-03 06:54:49 UTC (rev 420)
@@ -226,6 +226,14 @@
        \code{name} \tab character \tab Name of species\cr
     }
 
+    \item \code{thermo$stoich}
+    A precalculated stoichiometric matrix for the default database. This is a matrix, not a data frame, and as such can accept duplicated row names, corresponding to chemical formulas of the species. See \code{\link{retrieve}}, and the first test in \code{testthat/test-retrieve.R} for how to update this.
+    \tabular{lll}{
+       \code{rownames} \tab character \tab Chemical formulas from \code{thermo$obigt}\cr
+       \code{...} \tab numeric \tab Stoichiometry, one column for each element present in any species
+    }
+
+
   }  % end of itemize with long descriptions
 
 } % end of format

Modified: pkg/CHNOSZ/tests/testthat/test-retrieve.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-retrieve.R	2019-03-02 15:12:02 UTC (rev 419)
+++ pkg/CHNOSZ/tests/testthat/test-retrieve.R	2019-03-03 06:54:49 UTC (rev 420)
@@ -1,5 +1,16 @@
 context("retrieve")
 
+test_that("packaged stoichiometric matrix matches the default database", {
+  expect_identical(rownames(thermo()$stoich), thermo()$obigt$formula)
+  # test added 20190303
+  # if this test fails, update extdata/thermo/stoich.csv.xz and rebuild the package:
+  # reset()
+  # formula <- thermo()$obigt$formula
+  # stoich <- i2A(formula)
+  # write.csv(stoich, "stoich.csv")
+  # system("xz stoich.csv")
+})
+
 test_that("errors and recalculations produce expected messages", {
   # this should give an error about one non-element
   expect_error(retrieve(c("A", "B", "C")), '"A" is not an element')


From noreply at r-forge.r-project.org  Mon Mar  4 09:13:34 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  4 Mar 2019 09:13:34 +0100 (CET)
Subject: [CHNOSZ-commits] r421 - in pkg/CHNOSZ: . R inst man tests/testthat
Message-ID: <20190304081334.328DC18C1CC@r-forge.r-project.org>

Author: jedick
Date: 2019-03-04 09:13:33 +0100 (Mon, 04 Mar 2019)
New Revision: 421

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/examples.R
   pkg/CHNOSZ/R/retrieve.R
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/retrieve.Rd
   pkg/CHNOSZ/tests/testthat/test-retrieve.R
Log:
retrieve(): update stoichiometric matrix if database changes


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-03 06:54:49 UTC (rev 420)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-04 08:13:33 UTC (rev 421)
@@ -1,6 +1,6 @@
-Date: 2019-03-03
+Date: 2019-03-04
 Package: CHNOSZ
-Version: 1.3.1-1
+Version: 1.3.1-2
 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/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R	2019-03-03 06:54:49 UTC (rev 420)
+++ pkg/CHNOSZ/R/examples.R	2019-03-04 08:13:33 UTC (rev 421)
@@ -8,7 +8,8 @@
   topics <- c("thermo", "examples",
     "util.array", "util.blast", "util.data", "util.expression",
     "util.fasta", "util.formula", "util.matrix", "util.misc", "util.seq", "util.units",
-    "util.water", "taxonomy", "info", "retrieve", "protein.info", "hkf", "water", "IAPWS95", "subcrt", "berman",
+    "util.water", "taxonomy", "info", "retrieve", "add.obigt", "protein.info",
+    "hkf", "water", "IAPWS95", "subcrt", "berman",
     "makeup", "basis", "swap.basis", "species", "affinity", "solubility", "equilibrate", 
     "diagram", "buffer", "nonideal", "NaCl", "add.protein", "protein", "ionize.aa", "yeast.aa",
     "objective", "revisit", "EOSregress", "wjd")

Modified: pkg/CHNOSZ/R/retrieve.R
===================================================================
--- pkg/CHNOSZ/R/retrieve.R	2019-03-03 06:54:49 UTC (rev 420)
+++ pkg/CHNOSZ/R/retrieve.R	2019-03-04 08:13:33 UTC (rev 421)
@@ -2,23 +2,38 @@
 # retrieve species with given elements
 # 20190214 initial version
 # 20190224 use ... for multiple arguments (define a chemical system)
+# 20190304 update the stoichiometric matrix instead of doing a full recalculation when the database changes
 
 retrieve <- function(..., state = NULL, add.charge = TRUE, hide.groups = TRUE, req1 = FALSE) {
   ## stoichiometric matrix
   # what are the formulas of species in the current database?
   formula <- thermo()$obigt$formula
-  # get a previously calculated stoichiometric matrix, if it matches the current database
+  # get a previously calculated stoichiometric matrix
   stoich <- thermo()$stoich
-  if(!is.null(stoich)) {
-    # if it doesn't match the current database, don't use it
-    if(!identical(rownames(stoich), formula)) stoich <- NULL
-  }
-  if(is.null(stoich)) {
-    # Create the stoichiometric matrix for the current database
-    # and suppress warning messages about missing elements
-    message("retrieve: creating stoichiometric matrix")
-    # NOTE: row names are the formulas, so we can detect if the database changes
-    stoich <- suppressWarnings(i2A(formula))
+  # if it doesn't match the current database, update it
+  if(!identical(rownames(stoich), formula)) {
+    message("retrieve: updating stoichiometric matrix")
+    # first put rows in the right order for the current database
+    istoich <- match(formula, rownames(stoich))
+    stoich <- stoich[na.omit(istoich), ]
+    # deal with any missing formulas
+    if(any(is.na(istoich))) {
+      # convert the stoichiometric matrix to data frame with a 'formula' column
+      oldstoich <- cbind(formula = rownames(stoich), as.data.frame(stoich))
+      # get the stoichiometry of the additional formulas
+      # and suppress warning messages about missing elements
+      addstoich <- suppressWarnings(i2A(formula[is.na(istoich)]))
+      addstoich <- cbind(formula = rownames(addstoich), as.data.frame(addstoich))
+      # merge the old and added stoichiometries, and assign 0 for missing elements in either one
+      newstoich <- merge(oldstoich, addstoich, all = TRUE)
+      newstoich[is.na(newstoich)] <- 0
+      # convert the data frame to matrix with rownames corresponding to formulas
+      stoich <- as.matrix(newstoich[, 2:ncol(newstoich)])
+      rownames(stoich) <- newstoich$formula
+      # put rows in the right order for the current database
+      istoich <- match(formula, rownames(stoich))
+      stoich <- stoich[istoich, ]
+    }
     # store the stoichiometric matrix for later calculations
     thermo("stoich" = stoich)
   }

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2019-03-03 06:54:49 UTC (rev 420)
+++ pkg/CHNOSZ/inst/CHECKLIST	2019-03-04 08:13:33 UTC (rev 421)
@@ -2,7 +2,7 @@
 release checklist for CHNOSZ
 ****************************
 
-- run examples() and demos() to check their output
+- run examples() and demos() and inspect their output (especially plots)
 
 - check output of demo("sources") to make sure all data sources are cited
 
@@ -37,7 +37,7 @@
 
 - check reverse dependencies on CRAN: LipidMS, canprot, ecipex, iemisc as of 2019-02-09
 
-OTHER THINGS TO WORK ON:
+OTHER THINGS TO DO (depending on changes made in development):
 
 - update list of documentation topics in examples() with any new ones
 

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-03-03 06:54:49 UTC (rev 420)
+++ pkg/CHNOSZ/inst/NEWS	2019-03-04 08:13:33 UTC (rev 421)
@@ -1,10 +1,13 @@
-CHANGES IN CHNOSZ 1.3.1-1 (2019-03-03)
+CHANGES IN CHNOSZ 1.3.1-2 (2019-03-04)
 --------------------------------------
 
-- Add thermo/stoich.csv.xz (stored as thermo()$stoich), containing a
+- Add thermo/stoich.csv.xz (loaded as thermo()$stoich), containing a
   precalculated stochiometric matrix for the default database, to speed
   up retrieve().
 
+- retrieve() now updates the stoichiometric matrix when the database
+  changes, instead of performing a full recalculation.
+
 CHANGES IN CHNOSZ 1.3.1 (2019-03-02)
 ------------------------------------
 

Modified: pkg/CHNOSZ/man/retrieve.Rd
===================================================================
--- pkg/CHNOSZ/man/retrieve.Rd	2019-03-03 06:54:49 UTC (rev 420)
+++ pkg/CHNOSZ/man/retrieve.Rd	2019-03-04 08:13:33 UTC (rev 421)
@@ -37,7 +37,7 @@
 A special argument value \samp{all} can be used to retrieve all species in the thermodynamic database, including filtering on state and hiding of the groups.
 
 To speed up operation, the function uses a precalculated stoichiometric matrix for the default database, which is loaded with the package (see \code{\link{thermo}}).
-If the function detects a change to any chemical formulas in database, it triggers a recalculation using \code{\link{i2A}}.
+If the function detects a change to any chemical formulas in database, it updates the stoichiometric matrix using \code{\link{i2A}}.
 }
 
 \seealso{

Modified: pkg/CHNOSZ/tests/testthat/test-retrieve.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-retrieve.R	2019-03-03 06:54:49 UTC (rev 420)
+++ pkg/CHNOSZ/tests/testthat/test-retrieve.R	2019-03-04 08:13:33 UTC (rev 421)
@@ -18,6 +18,6 @@
   expect_error(retrieve(c("A", "B", "C", "D")), '"A", "D" are not elements')
   # this should recalculate the stoichiometric matrix
   add.obigt("SUPCRT92")
-  expect_message(retrieve("Ti"), "creating stoichiometric matrix")
+  expect_message(retrieve("Ti"), "updating stoichiometric matrix")
   reset()
 })


From noreply at r-forge.r-project.org  Tue Mar  5 02:48:00 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  5 Mar 2019 02:48:00 +0100 (CET)
Subject: [CHNOSZ-commits] r422 - in pkg/CHNOSZ: . R inst man tests/testthat
Message-ID: <20190305014800.5EE2918C75B@r-forge.r-project.org>

Author: jedick
Date: 2019-03-05 02:47:59 +0100 (Tue, 05 Mar 2019)
New Revision: 422

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/retrieve.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/retrieve.Rd
   pkg/CHNOSZ/tests/testthat/test-retrieve.R
Log:
retrieve(): improve argument structure


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-04 08:13:33 UTC (rev 421)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-05 01:47:59 UTC (rev 422)
@@ -1,6 +1,6 @@
-Date: 2019-03-04
+Date: 2019-03-05
 Package: CHNOSZ
-Version: 1.3.1-2
+Version: 1.3.1-3
 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/retrieve.R
===================================================================
--- pkg/CHNOSZ/R/retrieve.R	2019-03-04 08:13:33 UTC (rev 421)
+++ pkg/CHNOSZ/R/retrieve.R	2019-03-05 01:47:59 UTC (rev 422)
@@ -1,10 +1,15 @@
 # CHNOSZ/retrieve.R
 # retrieve species with given elements
 # 20190214 initial version
-# 20190224 use ... for multiple arguments (define a chemical system)
+# 20190224 define a chemical system using multiple arguments [defunct; use list() for chemical system]
 # 20190304 update the stoichiometric matrix instead of doing a full recalculation when the database changes
+# 20190305 use c() for combination of elements, list() for chemical system,
+#          and add 'ligands' argument to retrieve element-bearing species
 
-retrieve <- function(..., state = NULL, add.charge = TRUE, hide.groups = TRUE, req1 = FALSE) {
+retrieve <- function(elements = NULL, ligands = NULL, state = NULL, add.charge = TRUE, hide.groups = TRUE) {
+  ## empty argument handling
+  if(is.null(elements)) return(integer())
+
   ## stoichiometric matrix
   # what are the formulas of species in the current database?
   formula <- thermo()$obigt$formula
@@ -38,65 +43,73 @@
     thermo("stoich" = stoich)
   }
 
-  ## species identification
-  args <- list(...)
-  ispecies <- numeric()
-  # automatically add charge to a system 20190225
-  if(add.charge & length(args) > 1) {
-    if(!"Z" %in% unlist(args)) args <- c(args, "Z")
-  }
-  # for a numeric first argument, limit the result to only those species 20190225
-  for(elements in args) {
-    if(identical(elements, "all")) {
-      ispecies <- 1:nrow(thermo()$obigt)
-      names(ispecies) <- thermo()$obigt$formula
+  ## handle 'ligands' argument
+  if(!is.null(ligands)) {
+
+    # if 'ligands' is cr, liq, gas, or aq, use that as the state
+    if(any(ligands %in% c("cr", "liq", "gas", "aq")) & length(ligands)==1) {
+      state <- ligands
+      ispecies <- retrieve(elements, add.charge = add.charge)
     } else {
-      not.present <- ! elements %in% colnames(stoich)
-      if(any(not.present)) {
-        if(sum(not.present)==1) stop('"', elements[not.present], '" is not an element that is present in any species')
-        else stop('"', paste(elements[not.present], collapse='", "'), '" are not elements that are present in any species')
+      # include the element in the system defined by the ligands list
+      ligands <- c(elements, as.list(ligands))
+      # call retrieve() for each argument and take the intersection
+      r1 <- retrieve(elements, add.charge = add.charge)
+      r2 <- retrieve(ligands, add.charge = add.charge)
+      ispecies <- intersect(r1, r2)
+    }
+
+  } else {
+
+    ## species identification
+    ispecies <- list()
+    # automatically add charge to a system 20190225
+    if(add.charge & is.list(elements) & !"Z" %in% elements) elements <- c(elements, "Z")
+    # proceed element-by-element
+    for(i in seq_along(elements)) {
+      element <- unlist(elements[i])
+      if(identical(element, "all")) {
+        ispecies[[i]] <- 1:nrow(thermo()$obigt)
+      } else {
+        if(! element %in% colnames(stoich)) stop('"', element, '" is not an element that is present in any species')
+        # identify the species that have the element
+        has.element <- rowSums(stoich[, element, drop = FALSE] != 0) == 1
+        ispecies[[i]] <- which(has.element)
       }
-      # identify the species that have the elements
-      has.elements <- rowSums(stoich[, elements, drop = FALSE] != 0) == length(elements)
-      # which species are these (i.e. the species index)
-      # for req1, remember the species containing the first element 20190225
-      if(length(ispecies)==0) ispecies1 <- which(has.elements)
-      ispecies <- c(ispecies, which(has.elements))
-      ispecies <- ispecies[!duplicated(ispecies)]
     }
+
+    # now we have an list of ispecies (one vector for each element)
+    # what we do next depends on whether the argument is a list() or c()
+    if(is.list(elements)) {
+      # for a chemical system, all species are included that do not contain any other elements
+      ispecies <- unique(unlist(ispecies))
+      ielements <- colnames(thermo()$stoich) %in% elements
+      otherstoich <- thermo()$stoich[, !ielements]
+      iother <- rowSums(otherstoich[ispecies, ] != 0) > 0
+      ispecies <- ispecies[!iother]
+    } else {
+      # get species that have all the elements; the species must be present in each vector
+      # Reduce() hint from https://stackoverflow.com/questions/27520310/union-of-intersecting-vectors-in-a-list-in-r
+      ispecies <- Reduce(intersect, ispecies)
+    }
+
   }
-  # for a chemical system, defined by multiple arguments, the species can not contain any _other_ elements
-  if(length(args) > 1) {
-    syselements <- unlist(args)
-    isyselements <- colnames(thermo()$stoich) %in% syselements
-    notsysstoich <- thermo()$stoich[, !isyselements]
-    iother <- rowSums(notsysstoich[ispecies, ] != 0) > 0
-    ispecies <- ispecies[!iother]
-  }
-  # keep only species that contain the first element
-  if(req1) {
-    ispecies <- intersect(ispecies1, ispecies)
-    names(ispecies) <- thermo()$obigt$name[ispecies]
-  }
+
   # exclude groups
   if(hide.groups) {
     igroup <- grepl("^\\[.*\\]$", thermo()$obigt$name[ispecies])
     ispecies <- ispecies[!igroup]
   }
-  #if(hide.electron) {
-  #  ielectron <- names(ispecies) == "(Z-1)"
-  #  ispecies <- ispecies[!ielectron]
-  #}
-  #if(hide.proton) {
-  #  iproton <- names(ispecies) == "H+"
-  #  ispecies <- ispecies[!iproton]
-  #}
-  # filter states
+  # filter on state
   if(!is.null(state)) {
     istate <- thermo()$obigt$state[ispecies] %in% state
     ispecies <- ispecies[istate]
   }
-  # for names, use e- instead of (Z-1)
+
+  # assign names; use e- instead of (Z-1)
+  names(ispecies) <- thermo()$obigt$formula[ispecies]
   names(ispecies)[names(ispecies)=="(Z-1)"] <- "e-"
+  # if there's nothing, don't give it a name
+  if(length(ispecies)==0) ispecies <- integer()
   ispecies
 }

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-03-04 08:13:33 UTC (rev 421)
+++ pkg/CHNOSZ/inst/NEWS	2019-03-05 01:47:59 UTC (rev 422)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.1-2 (2019-03-04)
+CHANGES IN CHNOSZ 1.3.1-3 (2019-03-05)
 --------------------------------------
 
 - Add thermo/stoich.csv.xz (loaded as thermo()$stoich), containing a
@@ -8,6 +8,9 @@
 - retrieve() now updates the stoichiometric matrix when the database
   changes, instead of performing a full recalculation.
 
+- Add 'ligands' argument to retrieve(), for getting metal-bearing
+  species with a range of possible elements in the ligands.
+
 CHANGES IN CHNOSZ 1.3.1 (2019-03-02)
 ------------------------------------
 

Modified: pkg/CHNOSZ/man/retrieve.Rd
===================================================================
--- pkg/CHNOSZ/man/retrieve.Rd	2019-03-04 08:13:33 UTC (rev 421)
+++ pkg/CHNOSZ/man/retrieve.Rd	2019-03-05 01:47:59 UTC (rev 422)
@@ -7,37 +7,35 @@
 }
 
 \usage{
-  retrieve(..., state = NULL, add.charge = TRUE, hide.groups = TRUE,
-    req1 = FALSE)
+  retrieve(elements = NULL, ligands = NULL, state = NULL,
+    add.charge = TRUE, hide.groups = TRUE)
 }
 
 \arguments{
-  \item{...}{list, one or more arguments, each of which is a character vector with the names of one or more chemical elements}
+  \item{elements}{character, combination of elements, or list, elements in a chemical system}
+  \item{ligands}{character, elements present in any ligands}
   \item{state}{character, filter the result on these state(s).}
   \item{add.charge}{logical, add charge to the system?}
   \item{hide.groups}{logical, exclude groups from the result?}
-  \item{req1}{logical, include only species that contain the first element in the system?}
 }
 
 \details{
-This function retrieves the species in the thermodynamic database (see \code{\link{thermo}}) that have all of the elements specified in the arguments.
-A single argument is interpreted as a combination of one or more elements that must be present in each species.
+This function retrieves the species in the thermodynamic database (see \code{\link{thermo}}) that have the indicated \code{elements}.
+A character value of \code{elements} is interpreted as a combination of one or more elements that must be present in each species.
+A list value of \code{elements} is used to specify a chemical system -- the species must contain one or more of the indicated elements, but no other elements.
+\code{ligands}, if present, gives the elements that may be present in any ligands; this can be used to retrieve all species in a system bearing the \code{elements} (usually a single metal).
+
+The result includes charged species if \code{add.charge} is TRUE (the default) or the user supplies the \dQuote{element} of charge (\samp{Z}).
 Results can be filtered on physical state by setting the \code{state} argument.
-
-If more than one argument is present, all of the species identified by each argument are combined, and all species containing any other elements are excluded.
-This can be used to retrieve all of the species in the database within a given chemical system.
-A chemical system includes charged species if \code{add.charge} is TRUE (the default) or the user supplies the \dQuote{element} of charge (\samp{Z}).
-If \code{req1} is TRUE, the result corresponds to the intersection of all of the species in the system with those identified by the first argument (i.e. those bearing the first element).
-
 Groups used in group-additivity calculations, which have names with square brackets (e.g. [-CH2-]), are excluded unless \code{hide.groups} is FALSE.
-
-The return value is a named numeric vector giving the species index (i.e. rownumber(s) of \code{thermo()$obigt}) with names corresponding to the chemical formulas of the species.
-However, if the electron is in the result, its name (\samp{e-}) is used instead of its chemical formula (\samp{(Z-1)}).
-If the argument list is empty, then the function returns an empty (length 0) numeric value.
 A special argument value \samp{all} can be used to retrieve all species in the thermodynamic database, including filtering on state and hiding of the groups.
 
+The return value is a named integer vector giving the species index (i.e. rownumber(s) of \code{thermo()$obigt}) with names corresponding to the chemical formulas of the species.
+If the electron is in the result, its name (\samp{e-}) is used instead of its chemical formula (\samp{(Z-1)}).
+An empty (length 0) integer value is returned if no \code{elements} are specified or no species are retrieved.
+
 To speed up operation, the function uses a precalculated stoichiometric matrix for the default database, which is loaded with the package (see \code{\link{thermo}}).
-If the function detects a change to any chemical formulas in database, it updates the stoichiometric matrix using \code{\link{i2A}}.
+If the function detects a change to any chemical formulas in the database, it updates the stoichiometric matrix using \code{\link{i2A}}.
 }
 
 \seealso{
@@ -54,19 +52,22 @@
 retrieve("Au")
 # all species that have both Au and Cl
 retrieve(c("Au", "Cl"))
-# all species that have Au and/or Cl, including charged species, but no other elements
+# Au-Cl system: species that have Au and/or Cl,
+# including charged species, but no other elements
+retrieve(list("Au", "Cl"))
+# all Au-bearing species in the Au-Cl system
 retrieve("Au", "Cl")
-# all uncharged species that have Au and/or Cl
+# all uncharged Au-bearing species in the Au-Cl system
 retrieve("Au", "Cl", add.charge = FALSE)
 
 # minerals in the system SiO2-MgO-CaO-CO2
-retrieve("Si", "Mg", "Ca", "C", "O", state="cr")
+retrieve(list("Si", "Mg", "Ca", "C", "O"), state="cr")
 
-# make an Eh-pH diagram for aqueous S-bearing species
-basis("CHNOSe")
-ispecies <- retrieve("S", "O", "H", req1 = TRUE, state = "aq")
-species(ispecies)
-a <- affinity(pH = c(0, 14), Eh = c(-1, 1))
+# an Eh-pH diagram for Mn-bearing aqueous species
+basis(c("Mn+2", "H2O", "H+", "e-"))
+iMn <- retrieve("Mn", c("O", "H"), "aq")
+species(iMn)
+a <- affinity(pH = c(6, 14), Eh = c(-1, 1))
 diagram(a, fill = "terrain")
 }
 

Modified: pkg/CHNOSZ/tests/testthat/test-retrieve.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-retrieve.R	2019-03-04 08:13:33 UTC (rev 421)
+++ pkg/CHNOSZ/tests/testthat/test-retrieve.R	2019-03-05 01:47:59 UTC (rev 422)
@@ -12,11 +12,7 @@
 })
 
 test_that("errors and recalculations produce expected messages", {
-  # this should give an error about one non-element
   expect_error(retrieve(c("A", "B", "C")), '"A" is not an element')
-  # this should give an error about two non-elements
-  expect_error(retrieve(c("A", "B", "C", "D")), '"A", "D" are not elements')
-  # this should recalculate the stoichiometric matrix
   add.obigt("SUPCRT92")
   expect_message(retrieve("Ti"), "updating stoichiometric matrix")
   reset()


From noreply at r-forge.r-project.org  Tue Mar  5 10:00:55 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  5 Mar 2019 10:00:55 +0100 (CET)
Subject: [CHNOSZ-commits] r423 - in pkg/CHNOSZ: . inst/extdata/OBIGT
	inst/extdata/thermo tests/testthat vignettes
Message-ID: <20190305090055.7D1E818C90F@r-forge.r-project.org>

Author: jedick
Date: 2019-03-05 10:00:54 +0100 (Tue, 05 Mar 2019)
New Revision: 423

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz
   pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv.xz
   pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
   pkg/CHNOSZ/tests/testthat/test-retrieve.R
   pkg/CHNOSZ/vignettes/mklinks.sh
Log:
OBIGT: change +1 and -1 charges in some formulas to + and -


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-05 01:47:59 UTC (rev 422)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-05 09:00:54 UTC (rev 423)
@@ -1,6 +1,6 @@
 Date: 2019-03-05
 Package: CHNOSZ
-Version: 1.3.1-3
+Version: 1.3.1-4
 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/extdata/OBIGT/biotic_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz	2019-03-05 01:47:59 UTC (rev 422)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz	2019-03-05 09:00:54 UTC (rev 423)
@@ -1,4 +1,4 @@
-?7zXZ???F!
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??5i?*U9??X??0w??tG???????A???Yo|??XQ$?{??16?\O?]x??t%	??~?A2K???2?
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Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz	2019-03-05 01:47:59 UTC (rev 422)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv.xz	2019-03-05 09:00:54 UTC (rev 423)
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-???0N/J~??$?U?[????BW?W????&?=????	?)?O??	?/?a????OW?}f`l1????&B?q??:?f:R?
-s?C|\??G?I?????(uh??W?rT??/???`????;?-??2=QR?c????L????9????P??=??WH???C??;v?SAd???7?q??????vlRO(???u?a?E??sTF??(?G??xz8?7?h?G+!?U??%?N???;?)?D??/????sh>?<????	v?J4?;.?La?=???.v?+???O?@Dd4c?a?K`??p??1@-???????
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-?p?)???VzL?Z1?-???w??Q?#??0?m?m4???y?_?W?A??>?J?	6C~?9???J??kr??2??????(??dh?????dQh??JXG?L=??=????????&?<?eir??1?V#{????t?i>??N?[)?=????*???:???????!D/????????r?!?!???/?!???NJ?.W??F?/Fpg?(?9????_?O?9?LU?5?#P0??
-8?]????????U5??I?oR'+v??U(v}?3NSbY?q???;??N?5!M}I?q
-+p9?O???7??n???	?}m?K?#?????[6?U??jj?X
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-?????G?:?;?`?!?????sp?VZ??S}ys?=?
????/w??^??.???/?? ???????Y??C?6??5?????y:s??\???)?~KBI??v?????\5?%]?YC??'w?)!:Ehk*Y??"82:Jz???????B?+p\?-2????}Y?	??(Lj?????t????2;X???{o?D????G
-????~^?????cX??????r?d??Tm??F-Hv????z[C????????9w
?CY??&q????A????xA?B????u??
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 423

From noreply at r-forge.r-project.org  Wed Mar  6 04:15:10 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  6 Mar 2019 04:15:10 +0100 (CET)
Subject: [CHNOSZ-commits] r424 - in pkg/CHNOSZ: . R tests/testthat
Message-ID: <20190306031510.3E07418C338@r-forge.r-project.org>

Author: jedick
Date: 2019-03-06 04:15:08 +0100 (Wed, 06 Mar 2019)
New Revision: 424

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/retrieve.R
   pkg/CHNOSZ/tests/testthat/test-retrieve.R
Log:
retrieve(): error message lists all unrecognized elements in arguments


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-05 09:00:54 UTC (rev 423)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-06 03:15:08 UTC (rev 424)
@@ -1,6 +1,6 @@
-Date: 2019-03-05
+Date: 2019-03-06
 Package: CHNOSZ
-Version: 1.3.1-4
+Version: 1.3.1-5
 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/retrieve.R
===================================================================
--- pkg/CHNOSZ/R/retrieve.R	2019-03-05 09:00:54 UTC (rev 423)
+++ pkg/CHNOSZ/R/retrieve.R	2019-03-06 03:15:08 UTC (rev 424)
@@ -43,6 +43,14 @@
     thermo("stoich" = stoich)
   }
 
+  ## generate error for missing element(s)
+  allelements <- c(unlist(elements), unlist(ligands))
+  not.present <- ! allelements %in% c(colnames(stoich), "all")
+  if(any(not.present)) {
+    if(sum(not.present)==1) stop('"', allelements[not.present], '" is not an element that is present in any species in the database')
+    else stop('"', paste(allelements[not.present], collapse='", "'), '" are not elements that are present in any species in the database')
+  }
+
   ## handle 'ligands' argument
   if(!is.null(ligands)) {
 
@@ -71,7 +79,6 @@
       if(identical(element, "all")) {
         ispecies[[i]] <- 1:nrow(thermo()$obigt)
       } else {
-        if(! element %in% colnames(stoich)) stop('"', element, '" is not an element that is present in any species')
         # identify the species that have the element
         has.element <- rowSums(stoich[, element, drop = FALSE] != 0) == 1
         ispecies[[i]] <- which(has.element)

Modified: pkg/CHNOSZ/tests/testthat/test-retrieve.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-retrieve.R	2019-03-05 09:00:54 UTC (rev 423)
+++ pkg/CHNOSZ/tests/testthat/test-retrieve.R	2019-03-06 03:15:08 UTC (rev 424)
@@ -13,7 +13,14 @@
 
 test_that("errors and recalculations produce expected messages", {
   expect_error(retrieve(c("A", "B", "C")), '"A" is not an element')
+  expect_error(retrieve(c("A", "B", "C", "D")), '"A", "D" are not elements')
   add.obigt("SUPCRT92")
   expect_message(retrieve("Ti"), "updating stoichiometric matrix")
   reset()
 })
+
+test_that("retrieve('all') works", {
+  all1 <- sort(retrieve("all"))
+  all2 <- sort(retrieve(as.list(colnames(thermo()$stoich))))
+  expect_identical(all1, all2)
+})


From noreply at r-forge.r-project.org  Wed Mar  6 06:25:05 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  6 Mar 2019 06:25:05 +0100 (CET)
Subject: [CHNOSZ-commits] r425 - in pkg/CHNOSZ: . R inst inst/extdata/Berman
	man
Message-ID: <20190306052505.6950518C62F@r-forge.r-project.org>

Author: jedick
Date: 2019-03-06 06:25:03 +0100 (Wed, 06 Mar 2019)
New Revision: 425

Added:
   pkg/CHNOSZ/inst/extdata/Berman/BDat_2017.csv
   pkg/CHNOSZ/inst/extdata/Berman/Berman_1988.csv
   pkg/CHNOSZ/inst/extdata/Berman/Berman_1990.csv
   pkg/CHNOSZ/inst/extdata/Berman/DS_2010.csv
   pkg/CHNOSZ/inst/extdata/Berman/FDMCS_2014.csv
   pkg/CHNOSZ/inst/extdata/Berman/JUN_1992.csv
   pkg/CHNOSZ/inst/extdata/Berman/SHD_1991.csv
   pkg/CHNOSZ/inst/extdata/Berman/ZS_1992.csv
Removed:
   pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv
   pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv
   pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv
   pkg/CHNOSZ/inst/extdata/Berman/DS10.csv
   pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv
   pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv
   pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv
   pkg/CHNOSZ/inst/extdata/Berman/ZS92.csv
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/berman.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/extdata.Rd
Log:
berman(): use years in filenames of extdata/Berman/*.csv to determine chronological order


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-06 03:15:08 UTC (rev 424)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-06 05:25:03 UTC (rev 425)
@@ -1,6 +1,6 @@
 Date: 2019-03-06
 Package: CHNOSZ
-Version: 1.3.1-5
+Version: 1.3.1-6
 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/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R	2019-03-06 03:15:08 UTC (rev 424)
+++ pkg/CHNOSZ/R/berman.R	2019-03-06 05:25:03 UTC (rev 425)
@@ -12,26 +12,25 @@
   ncond <- max(length(T), length(P))
   T <- rep(T, length.out=ncond)
   P <- rep(P, length.out=ncond)
-  # get thermodynamic parameters
-  dir <- system.file("extdata/Berman/", package="CHNOSZ")
-  Ber88 <- read.csv(paste0(dir, "/Ber88.csv"), as.is=TRUE)
-  Ber90 <- read.csv(paste0(dir, "/Ber90.csv"), as.is=TRUE)
-  SHD91 <- read.csv(paste0(dir, "/SHD91.csv"), as.is=TRUE)
-  ZS92 <- read.csv(paste0(dir, "/ZS92.csv"), as.is=TRUE)
-  JUN92 <- read.csv(paste0(dir, "/JUN92.csv"), as.is=TRUE)
-  DS10 <- read.csv(paste0(dir, "/DS10.csv"), as.is=TRUE)
-  FDM14 <- read.csv(paste0(dir, "/FDM+14.csv"), as.is=TRUE)
-  BDat17 <- read.csv(paste0(dir, "/BDat17.csv"), as.is=TRUE)
+  # get thermodynamic parameters from data files
+  path <- system.file("extdata/Berman/", package="CHNOSZ")
+  files <- dir(path, "\\.csv$")
+  # put files in reverse chronological order (youngest first)
+  files <- rev(files[order(sapply(strsplit(files, "_"), "[", 2))])
+  # read the parameters from each file
+  dat <- list()
+  for(i in 1:length(files)) dat[[i]] <- read.csv(file.path(path, files[i]), as.is = TRUE)
+  # assemble the parameters in a single data frame
+  dat <- do.call(rbind, dat)
+  # is there a user-supplied data file?
   userfile <- get("thermo", CHNOSZ)$opt$Berman
   userfileexists <- FALSE
-  dat <- rbind(BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
   if(!is.na(userfile)) {
     if(userfile!="") {
       if(file.exists(userfile)) {
         userfileexists <- TRUE
         BDat_user <- read.csv(userfile, as.is=TRUE)
-        # assemble the files in reverse chronological order
-        dat <- rbind(BDat_user, BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
+        dat <- rbind(BDat_user, dat)
       } else stop("the file named in thermo$opt$Berman (", userfile, ") does not exist")
     } 
   }

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-03-06 03:15:08 UTC (rev 424)
+++ pkg/CHNOSZ/inst/NEWS	2019-03-06 05:25:03 UTC (rev 425)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.1-3 (2019-03-05)
+CHANGES IN CHNOSZ 1.3.1-6 (2019-03-06)
 --------------------------------------
 
 - Add thermo/stoich.csv.xz (loaded as thermo()$stoich), containing a
@@ -11,6 +11,11 @@
 - Add 'ligands' argument to retrieve(), for getting metal-bearing
   species with a range of possible elements in the ligands.
 
+- In extdata/Berman, rename .csv files to include whole year. berman()
+  now uses the years in the filenames to assemble the data in reverse
+  chronological order, and keeps only the most recent data for any
+  duplicated minerals.
+
 CHANGES IN CHNOSZ 1.3.1 (2019-03-02)
 ------------------------------------
 

Deleted: pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv	2019-03-06 03:15:08 UTC (rev 424)
+++ pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -1,2 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,0,0,0,2.72,0.0008,-0.1485,0.0004,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/BDat_2017.csv (from rev 424, pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/BDat_2017.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/BDat_2017.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -0,0 +1,2 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,0,0,0,2.72,0.0008,-0.1485,0.0004,,,,,,,,,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv	2019-03-06 03:15:08 UTC (rev 424)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -1,68 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-akermanite,-3663786,-3860441,212,9.252,387.06,-2938.8,0,-40790000,0,0,0,2.5011,0.00067224,-0.0785,0,358,298,0,0,0,452,,,,,,,,
-albite,-3703293,-3921618,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
-"albite,high",-3703293,-3921618,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
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Deleted: pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv	2019-03-06 03:15:08 UTC (rev 424)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -1,5 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
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-annite,-4793115,-5142800,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
-ilmenite,-1155794,-1232448,108.628,3.17,150,-441.6,-3323700,348150000,0,0,0,2.7248,0.00029968,-0.0584,0.000123,,,,,,,,,,,,,,
-phlogopite,-5830350,-6210391,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/Berman_1988.csv (from rev 424, pkg/CHNOSZ/inst/extdata/Berman/Ber88.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Berman_1988.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/Berman_1988.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -0,0 +1,68 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
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+lawsonite,-4509709,-4865666,229.176,10.144,728.67,-8248.1,0,850560000,0,0,0,2.6283,0,-0.0769,0.0001922,,,,,,,,,,,,,,
+lime,-603350,-635090,37.75,1.676,58.79,-133.9,-1147100,102980000,0,0,0,3.461,0.00067406,-0.1022,0.0002565,,,,,,,,,,,,,,
+magnesite,-1029875,-1113636,65.21,2.803,162.3,-1109.3,-4882600,874660000,0,0,0,1.8436,0.00415968,-0.089,0.0002212,,,,,,,,,,,,,,
+magnetite,-1014235,-1117403,146.114,4.452,207.93,0,-7243300,664360000,0,0,0,3.0291,0.0013847,-0.0582,0.0001751,848,298,0,-0.19502,0.00061037,1565,,,,,,,,
+margarite,-5852244,-6236603,265.084,12.958,699.8,-5587.1,-6807700,734320000,0,0,0,2.1019,0.00124556,-0.1155,0.0002886,,,,,,,,,,,,,,
+meionite,-13105915,-13849723,730,34.036,1511.35,-13243.3,0,-751610000,0,0,0,0.934,0,-0.111,0,,,,,,,,,,,,,,
+merwinite,-4309707,-4537497,251.777,9.847,453.62,-3250,0,-344230000,0,0,0,2.9376,0.00087235,-0.0551,0.0001381,,,,,,,,,,,,,,
+monticellite,-2132222,-2250027,108.3,5.148,226.34,-1542.7,-1179700,-23290000,0,0,0,2.7863,0.00076339,-0.0904,0.0002,,,,,,,,,,,,,,
+muscovite,-5596723,-5976740,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,3.3527,0,-0.1717,0.0004295,,,,,,,,,,,,,,
+paragonite,-5563572,-5944208,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,3.9424,0.00059701,-0.1973,0.0004933,,,,,,,,,,,,,,
+periclase,-569209,-601500,26.951,1.125,61.11,-296.2,-621200,5840000,0,0,0,3.7477,3.556E-05,-0.0622,0.0001511,,,,,,,,,,,,,,
+phlogopite,-5827224,-6207342,334.158,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
+K-feldspar,-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3738804,-3959704,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+"K-feldspar,low",-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+prehnite,-5820154,-6198606,288.634,14.016,716.05,-6404.6,-2182500,268500000,0,0,0,0.1468,0.01128353,-0.1427,0,,,,,,,,,,,,,,
+pyrope,-5936009,-6286548,266.359,11.316,640.72,-4542.1,-4701900,0,0,0,0,2.2519,0.00037044,-0.0576,4.42E-05,,,,,,,,,,,,,,
+pyrophyllite,-5266865,-5640781,239.4,12.76,665.93,-5897.4,-4979900,661810000,0,0,0,1.2637,0.00381661,-0.1354,0,,,,,,,,,,,,,,
+quartz,-856288,-910700,41.46,2.269,80.01,-240.3,-3546700,491570000,0,0,0,2.3895,0,-0.2434,0.0010137,848,373,0.0237,-0.09187,0.00024607,0,,,,,,,,
+"quartz,beta",-855033,-908627,44.207,2.37,80.01,-240.3,-3546700,491570000,0,0,0,0,0,-0.1238,0.0007087,,,,,,,,,,,,,,
+rutile,-889497,-944750,50.46,1.882,77.84,0,-3367800,402940000,0,0,0,2.5716,0.00015409,-0.0454,5.84E-05,,,,,,,,,,,,,,
+sillimanite,-2439265,-2586091,95.93,4.983,256.73,-1887.2,-2977400,250960000,0,0,0,1.3431,0,-0.0753,0,,,,,,,,,,,,,,
+sphene,-2455134,-2596652,129.29,5.565,234.62,-1040.3,-5118300,591460000,0,0,0,2.52,0,-0.059,0,,,,,,,,,,,,,,
+spinel,-2176537,-2300313,84.535,3.977,235.9,-1766.6,-1710400,40620000,0,0,0,2.1691,0.00050528,-0.0489,0,,,,,,,,,,,,,,
+talc,-5517657,-5897387,261.24,13.61,664.11,-5187.2,-2147200,-327370000,0,0,0,2.9447,0,-0.1699,0.0005665,,,,,,,,,,,,,,
+tremolite,-11578548,-12305578,551.15,27.268,1229.36,-6401.9,-32089900,4208810000,0,0,0,2.4374,0.00098338,-0.1392,0.0003481,,,,,,,,,,,,,,
+"tridymite,low",-854026,-907750,43.77,2.675,75.37,0,-5958100,958250000,0,0,0,1.9339,0,-0.2508,0,383,298,0,0.4267,-0.00144575,130,,,,,,,,
+"tridymite,high",-853844,-907045,45.524,2.737,75.37,0,-5958100,958250000,0,0,0,0.4829,0,-0.074,0.0003735,,,,,,,,,,,,,,
+wollastonite,-1546123,-1631500,81.81,3.983,149.07,-690.3,-3659300,484350000,0,0,0,2.818,0,-0.1245,0.0003113,,,,,,,,,,,,,,
+pseudowollastonite,-1543085,-1627427,85.279,4.016,141.16,-417.2,-5857600,940740000,0,0,0,2.818,0,-0.1245,0.0003113,,,,,,,,,,,,,,
+zoisite,-6494148,-6889488,297.576,13.588,749.17,-6509.3,-2380500,124860000,0,0,0,3.467,0,-0.0515,0.0001288,,,,,,,,,,,,,,
+clinozoisite,-6496497,-6894968,287.076,13.673,749.17,-6509.3,-2380500,124860000,0,0,0,3.467,0,-0.0515,0.0001288,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/Berman_1990.csv (from rev 424, pkg/CHNOSZ/inst/extdata/Berman/Ber90.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Berman_1990.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/Berman_1990.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -0,0 +1,5 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+almandine,-4943492,-5267216,340.007,11.511,573.96,-1483.1,-29292000,5022080000,0,0,0,1.8613,0.00074539,-0.0558,3.21E-05,,,,,,,,,,,,,,
+annite,-4793115,-5142800,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
+ilmenite,-1155794,-1232448,108.628,3.17,150,-441.6,-3323700,348150000,0,0,0,2.7248,0.00029968,-0.0584,0.000123,,,,,,,,,,,,,,
+phlogopite,-5830350,-6210391,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/DS10.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/DS10.csv	2019-03-06 03:15:08 UTC (rev 424)
+++ pkg/CHNOSZ/inst/extdata/Berman/DS10.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -1,6 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-3106.646,2047911.742,-563018581,0,0,0,2.796487,0,-0.17457,0.00151,,,,,,,,,,,,,,
-andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-1441.44,-22441040.802,3146543781,0,0,0,2.072525,0.000561,-0.06539136,0.0001635,,,,,,,,,,,,,,
-ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-8966.454,-21705844.286,3236159154,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
-grunerite,-8964807,-9623000,725,27.8,1347.83,-9356.91,-20228480,3039190000,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
-ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-8787.112,30183568.71,-5666432624,0,0,0,1.801543,0.001152,-0.06838,2.4E-05,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/DS_2010.csv (from rev 424, pkg/CHNOSZ/inst/extdata/Berman/DS10.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/DS_2010.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/DS_2010.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -0,0 +1,6 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-3106.646,2047911.742,-563018581,0,0,0,2.796487,0,-0.17457,0.00151,,,,,,,,,,,,,,
+andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-1441.44,-22441040.802,3146543781,0,0,0,2.072525,0.000561,-0.06539136,0.0001635,,,,,,,,,,,,,,
+ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-8966.454,-21705844.286,3236159154,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
+grunerite,-8964807,-9623000,725,27.8,1347.83,-9356.91,-20228480,3039190000,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
+ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-8787.112,30183568.71,-5666432624,0,0,0,1.801543,0.001152,-0.06838,2.4E-05,,,,,,,,,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv	2019-03-06 03:15:08 UTC (rev 424)
+++ pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -1,2 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-2100,-10000,220000000,0,0,0,4.18,0,-0.1345,0.00017,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/FDMCS_2014.csv (from rev 424, pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/FDMCS_2014.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/FDMCS_2014.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -0,0 +1,2 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-2100,-10000,220000000,0,0,0,4.18,0,-0.1345,0.00017,,,,,,,,,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv	2019-03-06 03:15:08 UTC (rev 424)
+++ pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -1,3 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-glaucophane,-11225858,-11960500,535,26.05,1717.5,-19272,7050000,0,0,0,0,2.2,0.00088,-0.116,0.00029,,,,,,,,,,,,,,
-pumpellyite,-13448936,-14402300,584,29.55,1576,-10603.8,-28304200,3838351000,0,0,0,3.467,0,-0.051516,0.0001288,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/JUN_1992.csv (from rev 424, pkg/CHNOSZ/inst/extdata/Berman/JUN92.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/JUN_1992.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/JUN_1992.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -0,0 +1,3 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+glaucophane,-11225858,-11960500,535,26.05,1717.5,-19272,7050000,0,0,0,0,2.2,0.00088,-0.116,0.00029,,,,,,,,,,,,,,
+pumpellyite,-13448936,-14402300,584,29.55,1576,-10603.8,-28304200,3838351000,0,0,0,3.467,0,-0.051516,0.0001288,,,,,,,,,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv	2019-03-06 03:15:08 UTC (rev 424)
+++ pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -1,12 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-muscovite,-5603417,-5983434,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,3.3527,0,-0.1717,0.0004295,,,,,,,,,,,,,,
-phlogopite,-5837044,-6217085,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
-K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
-"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
-"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
-paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,3.9424,0.00059701,-0.1973,0.0004933,,,,,,,,,,,,,,
-albite,-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
-"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
-"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
-jadeite,-2853285,-3031921,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,2.3118,0.00025785,-0.086,0.0002149,,,,,,,,,,,,,,
-annite,-4799809,-5149494,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/SHD_1991.csv (from rev 424, pkg/CHNOSZ/inst/extdata/Berman/SHD91.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/SHD_1991.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/SHD_1991.csv	2019-03-06 05:25:03 UTC (rev 425)
@@ -0,0 +1,12 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+muscovite,-5603417,-5983434,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,3.3527,0,-0.1717,0.0004295,,,,,,,,,,,,,,
+phlogopite,-5837044,-6217085,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
+K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,3.9424,0.00059701,-0.1973,0.0004933,,,,,,,,,,,,,,
+albite,-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 425

From noreply at r-forge.r-project.org  Wed Mar  6 07:38:40 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  6 Mar 2019 07:38:40 +0100 (CET)
Subject: [CHNOSZ-commits] r426 - in pkg/CHNOSZ: . inst/extdata/Berman man
Message-ID: <20190306063840.4B4FF18C176@r-forge.r-project.org>

Author: jedick
Date: 2019-03-06 07:38:39 +0100 (Wed, 06 Mar 2019)
New Revision: 426

Added:
   pkg/CHNOSZ/inst/extdata/Berman/BDat17_2017.csv
   pkg/CHNOSZ/inst/extdata/Berman/Ber88_1988.csv
   pkg/CHNOSZ/inst/extdata/Berman/Ber90_1990.csv
   pkg/CHNOSZ/inst/extdata/Berman/DS10_2010.csv
   pkg/CHNOSZ/inst/extdata/Berman/FDM+14_2014.csv
   pkg/CHNOSZ/inst/extdata/Berman/JUN92_1992.csv
   pkg/CHNOSZ/inst/extdata/Berman/SHD91_1991.csv
   pkg/CHNOSZ/inst/extdata/Berman/ZS92_1992.csv
Removed:
   pkg/CHNOSZ/inst/extdata/Berman/BDat_2017.csv
   pkg/CHNOSZ/inst/extdata/Berman/Berman_1988.csv
   pkg/CHNOSZ/inst/extdata/Berman/Berman_1990.csv
   pkg/CHNOSZ/inst/extdata/Berman/DS_2010.csv
   pkg/CHNOSZ/inst/extdata/Berman/FDMCS_2014.csv
   pkg/CHNOSZ/inst/extdata/Berman/JUN_1992.csv
   pkg/CHNOSZ/inst/extdata/Berman/SHD_1991.csv
   pkg/CHNOSZ/inst/extdata/Berman/ZS_1992.csv
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/man/extdata.Rd
Log:
extdata/Berman: rename files to include reference string


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-06 05:25:03 UTC (rev 425)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-06 06:38:39 UTC (rev 426)
@@ -1,6 +1,6 @@
 Date: 2019-03-06
 Package: CHNOSZ
-Version: 1.3.1-6
+Version: 1.3.1-7
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Copied: pkg/CHNOSZ/inst/extdata/Berman/BDat17_2017.csv (from rev 425, pkg/CHNOSZ/inst/extdata/Berman/BDat_2017.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/BDat17_2017.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/BDat17_2017.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -0,0 +1,2 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
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Deleted: pkg/CHNOSZ/inst/extdata/Berman/BDat_2017.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/BDat_2017.csv	2019-03-06 05:25:03 UTC (rev 425)
+++ pkg/CHNOSZ/inst/extdata/Berman/BDat_2017.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -1,2 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-548363000,87284120000,0,0,0,2.72,0.0008,-0.1485,0.0004,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/Ber88_1988.csv (from rev 425, pkg/CHNOSZ/inst/extdata/Berman/Berman_1988.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber88_1988.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber88_1988.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -0,0 +1,68 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
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Copied: pkg/CHNOSZ/inst/extdata/Berman/Ber90_1990.csv (from rev 425, pkg/CHNOSZ/inst/extdata/Berman/Berman_1990.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber90_1990.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber90_1990.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -0,0 +1,5 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
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Deleted: pkg/CHNOSZ/inst/extdata/Berman/Berman_1988.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Berman_1988.csv	2019-03-06 05:25:03 UTC (rev 425)
+++ pkg/CHNOSZ/inst/extdata/Berman/Berman_1988.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -1,68 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
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-enstatite,-1458181,-1545552,66.17,3.133,166.58,-1200.6,-2270600,279150000,0,0,0,2.4656,0.0007467,-0.0749,4.47E-05,,,,,,,,,,,,,,
-"enstatite,proto",-1456965,-1543959,67.438,3.242,166.58,-1200.6,-2270600,279150000,0,0,0,1.6832,0.0011665,-0.075,4.48E-05,,,,,,,,,,,,,,
-fayalite,-1380154,-1479360,150.93,4.63,248.93,-1923.9,0,-139100000,0,0,0,2.6546,0.00079482,-0.073,0,,,,,,,,,,,,,,
-ferrosilite,-1117472,-1194375,95.882,3.296,169.06,-1193,-2097100,292530000,0,0,0,3.1808,0.0007585,-0.099,0,,,,,,,,,,,,,,
-forsterite,-2055023,-2174420,94.01,4.366,238.64,-2001.3,0,-116240000,0,0,0,2.9464,0.00088633,-0.0791,0.0001351,,,,,,,,,,,,,,
-gehlenite,-3785954,-3988158,198.6,9.033,373.09,-2276.8,-4778500,477910000,0,0,0,2.4926,5.664E-05,-0.0996,0.0002488,,,,,,,1600,698,-221.74,0,17291000,0.3695,-0.0001469,0
-grossular,-6270974,-6632859,255.15,12.538,573.43,-2039.4,-18887200,2319310000,0,0,0,1.8994,0.00079756,-0.0654,0.0001635,,,,,,,,,,,,,,
-hematite,-743681,-825627,87.437,3.027,146.86,0,-5576800,525630000,0,0,0,3.831,1.65E-05,-0.0479,3.04E-05,955,298,0,-0.07403,0.00027921,1287,,,,,,,,
-ilmenite,-1155320,-1231947,108.628,3.17,150,-441.6,-3323700,348150000,0,0,0,2.7248,0.00029968,-0.0584,0.000123,,,,,,,,,,,,,,
-jadeite,-2846482,-3025118,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,2.3118,0.00025785,-0.086,0.0002149,,,,,,,,,,,,,,
-kaolinite,-3799770,-4120327,203.7,9.952,523.23,-4426.7,-2244300,92310000,0,0,0,3.2,0,-0.12,0,,,,,,,,,,,,,,
-kyanite,-2443370,-2594220,82.43,4.412,262.68,-2001.4,-1999700,-63180000,0,0,0,2.3973,0,-0.0646,0,,,,,,,,,,,,,,
-lawsonite,-4509709,-4865666,229.176,10.144,728.67,-8248.1,0,850560000,0,0,0,2.6283,0,-0.0769,0.0001922,,,,,,,,,,,,,,
-lime,-603350,-635090,37.75,1.676,58.79,-133.9,-1147100,102980000,0,0,0,3.461,0.00067406,-0.1022,0.0002565,,,,,,,,,,,,,,
-magnesite,-1029875,-1113636,65.21,2.803,162.3,-1109.3,-4882600,874660000,0,0,0,1.8436,0.00415968,-0.089,0.0002212,,,,,,,,,,,,,,
-magnetite,-1014235,-1117403,146.114,4.452,207.93,0,-7243300,664360000,0,0,0,3.0291,0.0013847,-0.0582,0.0001751,848,298,0,-0.19502,0.00061037,1565,,,,,,,,
-margarite,-5852244,-6236603,265.084,12.958,699.8,-5587.1,-6807700,734320000,0,0,0,2.1019,0.00124556,-0.1155,0.0002886,,,,,,,,,,,,,,
-meionite,-13105915,-13849723,730,34.036,1511.35,-13243.3,0,-751610000,0,0,0,0.934,0,-0.111,0,,,,,,,,,,,,,,
-merwinite,-4309707,-4537497,251.777,9.847,453.62,-3250,0,-344230000,0,0,0,2.9376,0.00087235,-0.0551,0.0001381,,,,,,,,,,,,,,
-monticellite,-2132222,-2250027,108.3,5.148,226.34,-1542.7,-1179700,-23290000,0,0,0,2.7863,0.00076339,-0.0904,0.0002,,,,,,,,,,,,,,
-muscovite,-5596723,-5976740,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,3.3527,0,-0.1717,0.0004295,,,,,,,,,,,,,,
-paragonite,-5563572,-5944208,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,3.9424,0.00059701,-0.1973,0.0004933,,,,,,,,,,,,,,
-periclase,-569209,-601500,26.951,1.125,61.11,-296.2,-621200,5840000,0,0,0,3.7477,3.556E-05,-0.0622,0.0001511,,,,,,,,,,,,,,
-phlogopite,-5827224,-6207342,334.158,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
-K-feldspar,-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
-"K-feldspar,high",-3738804,-3959704,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
-"K-feldspar,low",-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
-prehnite,-5820154,-6198606,288.634,14.016,716.05,-6404.6,-2182500,268500000,0,0,0,0.1468,0.01128353,-0.1427,0,,,,,,,,,,,,,,
-pyrope,-5936009,-6286548,266.359,11.316,640.72,-4542.1,-4701900,0,0,0,0,2.2519,0.00037044,-0.0576,4.42E-05,,,,,,,,,,,,,,
-pyrophyllite,-5266865,-5640781,239.4,12.76,665.93,-5897.4,-4979900,661810000,0,0,0,1.2637,0.00381661,-0.1354,0,,,,,,,,,,,,,,
-quartz,-856288,-910700,41.46,2.269,80.01,-240.3,-3546700,491570000,0,0,0,2.3895,0,-0.2434,0.0010137,848,373,0.0237,-0.09187,0.00024607,0,,,,,,,,
-"quartz,beta",-855033,-908627,44.207,2.37,80.01,-240.3,-3546700,491570000,0,0,0,0,0,-0.1238,0.0007087,,,,,,,,,,,,,,
-rutile,-889497,-944750,50.46,1.882,77.84,0,-3367800,402940000,0,0,0,2.5716,0.00015409,-0.0454,5.84E-05,,,,,,,,,,,,,,
-sillimanite,-2439265,-2586091,95.93,4.983,256.73,-1887.2,-2977400,250960000,0,0,0,1.3431,0,-0.0753,0,,,,,,,,,,,,,,
-sphene,-2455134,-2596652,129.29,5.565,234.62,-1040.3,-5118300,591460000,0,0,0,2.52,0,-0.059,0,,,,,,,,,,,,,,
-spinel,-2176537,-2300313,84.535,3.977,235.9,-1766.6,-1710400,40620000,0,0,0,2.1691,0.00050528,-0.0489,0,,,,,,,,,,,,,,
-talc,-5517657,-5897387,261.24,13.61,664.11,-5187.2,-2147200,-327370000,0,0,0,2.9447,0,-0.1699,0.0005665,,,,,,,,,,,,,,
-tremolite,-11578548,-12305578,551.15,27.268,1229.36,-6401.9,-32089900,4208810000,0,0,0,2.4374,0.00098338,-0.1392,0.0003481,,,,,,,,,,,,,,
-"tridymite,low",-854026,-907750,43.77,2.675,75.37,0,-5958100,958250000,0,0,0,1.9339,0,-0.2508,0,383,298,0,0.4267,-0.00144575,130,,,,,,,,
-"tridymite,high",-853844,-907045,45.524,2.737,75.37,0,-5958100,958250000,0,0,0,0.4829,0,-0.074,0.0003735,,,,,,,,,,,,,,
-wollastonite,-1546123,-1631500,81.81,3.983,149.07,-690.3,-3659300,484350000,0,0,0,2.818,0,-0.1245,0.0003113,,,,,,,,,,,,,,
-pseudowollastonite,-1543085,-1627427,85.279,4.016,141.16,-417.2,-5857600,940740000,0,0,0,2.818,0,-0.1245,0.0003113,,,,,,,,,,,,,,
-zoisite,-6494148,-6889488,297.576,13.588,749.17,-6509.3,-2380500,124860000,0,0,0,3.467,0,-0.0515,0.0001288,,,,,,,,,,,,,,
-clinozoisite,-6496497,-6894968,287.076,13.673,749.17,-6509.3,-2380500,124860000,0,0,0,3.467,0,-0.0515,0.0001288,,,,,,,,,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/Berman_1990.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Berman_1990.csv	2019-03-06 05:25:03 UTC (rev 425)
+++ pkg/CHNOSZ/inst/extdata/Berman/Berman_1990.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -1,5 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-almandine,-4943492,-5267216,340.007,11.511,573.96,-1483.1,-29292000,5022080000,0,0,0,1.8613,0.00074539,-0.0558,3.21E-05,,,,,,,,,,,,,,
-annite,-4793115,-5142800,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
-ilmenite,-1155794,-1232448,108.628,3.17,150,-441.6,-3323700,348150000,0,0,0,2.7248,0.00029968,-0.0584,0.000123,,,,,,,,,,,,,,
-phlogopite,-5830350,-6210391,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/DS10_2010.csv (from rev 425, pkg/CHNOSZ/inst/extdata/Berman/DS_2010.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/DS10_2010.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/DS10_2010.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -0,0 +1,6 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-3106.646,2047911.742,-563018581,0,0,0,2.796487,0,-0.17457,0.00151,,,,,,,,,,,,,,
+andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-1441.44,-22441040.802,3146543781,0,0,0,2.072525,0.000561,-0.06539136,0.0001635,,,,,,,,,,,,,,
+ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-8966.454,-21705844.286,3236159154,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
+grunerite,-8964807,-9623000,725,27.8,1347.83,-9356.91,-20228480,3039190000,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
+ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-8787.112,30183568.71,-5666432624,0,0,0,1.801543,0.001152,-0.06838,2.4E-05,,,,,,,,,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/DS_2010.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/DS_2010.csv	2019-03-06 05:25:03 UTC (rev 425)
+++ pkg/CHNOSZ/inst/extdata/Berman/DS_2010.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -1,6 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-3106.646,2047911.742,-563018581,0,0,0,2.796487,0,-0.17457,0.00151,,,,,,,,,,,,,,
-andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-1441.44,-22441040.802,3146543781,0,0,0,2.072525,0.000561,-0.06539136,0.0001635,,,,,,,,,,,,,,
-ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-8966.454,-21705844.286,3236159154,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
-grunerite,-8964807,-9623000,725,27.8,1347.83,-9356.91,-20228480,3039190000,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
-ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-8787.112,30183568.71,-5666432624,0,0,0,1.801543,0.001152,-0.06838,2.4E-05,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/FDM+14_2014.csv (from rev 425, pkg/CHNOSZ/inst/extdata/Berman/FDMCS_2014.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/FDM+14_2014.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/FDM+14_2014.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -0,0 +1,2 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-2100,-10000,220000000,0,0,0,4.18,0,-0.1345,0.00017,,,,,,,,,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/FDMCS_2014.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/FDMCS_2014.csv	2019-03-06 05:25:03 UTC (rev 425)
+++ pkg/CHNOSZ/inst/extdata/Berman/FDMCS_2014.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -1,2 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-2100,-10000,220000000,0,0,0,4.18,0,-0.1345,0.00017,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/JUN92_1992.csv (from rev 425, pkg/CHNOSZ/inst/extdata/Berman/JUN_1992.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/JUN92_1992.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/JUN92_1992.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -0,0 +1,3 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+glaucophane,-11225858,-11960500,535,26.05,1717.5,-19272,7050000,0,0,0,0,2.2,0.00088,-0.116,0.00029,,,,,,,,,,,,,,
+pumpellyite,-13448936,-14402300,584,29.55,1576,-10603.8,-28304200,3838351000,0,0,0,3.467,0,-0.051516,0.0001288,,,,,,,,,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/JUN_1992.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/JUN_1992.csv	2019-03-06 05:25:03 UTC (rev 425)
+++ pkg/CHNOSZ/inst/extdata/Berman/JUN_1992.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -1,3 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-glaucophane,-11225858,-11960500,535,26.05,1717.5,-19272,7050000,0,0,0,0,2.2,0.00088,-0.116,0.00029,,,,,,,,,,,,,,
-pumpellyite,-13448936,-14402300,584,29.55,1576,-10603.8,-28304200,3838351000,0,0,0,3.467,0,-0.051516,0.0001288,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/SHD91_1991.csv (from rev 425, pkg/CHNOSZ/inst/extdata/Berman/SHD_1991.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/SHD91_1991.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/SHD91_1991.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -0,0 +1,12 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+muscovite,-5603417,-5983434,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,3.3527,0,-0.1717,0.0004295,,,,,,,,,,,,,,
+phlogopite,-5837044,-6217085,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
+K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,3.9424,0.00059701,-0.1973,0.0004933,,,,,,,,,,,,,,
+albite,-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+jadeite,-2853285,-3031921,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,2.3118,0.00025785,-0.086,0.0002149,,,,,,,,,,,,,,
+annite,-4799809,-5149494,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/SHD_1991.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/SHD_1991.csv	2019-03-06 05:25:03 UTC (rev 425)
+++ pkg/CHNOSZ/inst/extdata/Berman/SHD_1991.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -1,12 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-muscovite,-5603417,-5983434,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,3.3527,0,-0.1717,0.0004295,,,,,,,,,,,,,,
-phlogopite,-5837044,-6217085,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
-K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
-"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
-"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
-paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,3.9424,0.00059701,-0.1973,0.0004933,,,,,,,,,,,,,,
-albite,-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
-"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
-"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
-jadeite,-2853285,-3031921,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,2.3118,0.00025785,-0.086,0.0002149,,,,,,,,,,,,,,
-annite,-4799809,-5149494,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,

Copied: pkg/CHNOSZ/inst/extdata/Berman/ZS92_1992.csv (from rev 425, pkg/CHNOSZ/inst/extdata/Berman/ZS_1992.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/ZS92_1992.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/ZS92_1992.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -0,0 +1,11 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+fluormuscovite,-5772803,-6111401,299.03,14.087,680.36024,-6515.743,0,110583120,0,0,0,3.35273302,0,-0.17169021,0.00042947,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluorphlogopite,-6063382,-6403168,336.394,14.637,653.70816,-5175.19,0,-324594720,0,0,0,3.44473262,0,-0.16969784,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluorannite,-4983910,-5293254,422.291,15.075,742.82736,-6817.41,0,418441840,0,0,0,3.44473262,0,-0.16969784,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluortremolite,-11782144,-12457969,570.279,27.045,1272.64728,-9493.496,0,-10517739.2,0,0,0,2.43738877,0.00098338,-0.13917727,0.00034809,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluorapatite,-6443050,-6823447,387.857,15.753,668.77056,-4534.201,0,-746341920,0,0,0,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+hydroxyapatite,-6297702,-6694689,398.735,15.822,758.81024,-6480.598,0,-447939040,0,0,0,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+chlorapatite,-6217424,-6597260,399.907,16.403,663.87528,-4435.877,0,-690234480,0,0,0,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluortalc,-5717018,-6056244,264.052,13.33,602.74704,-4766.831,0,-292588712,0,0,0,2.94468112,0,-0.16988979,0.0005665,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+chlorphlogopite,-5600840,-5939422,360.703,16.59,573.45904,-2063.549,-16465713.6,2105765360,0,0,0,3.44473262,0,-0.16969784,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+chlorannite,-4582036,-4890196,449.529,17.247,690.44368,-4760.137,-8725313.6,1376828880,0,0,0,3.44473262,0,-0.16969784,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,

Deleted: pkg/CHNOSZ/inst/extdata/Berman/ZS_1992.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/ZS_1992.csv	2019-03-06 05:25:03 UTC (rev 425)
+++ pkg/CHNOSZ/inst/extdata/Berman/ZS_1992.csv	2019-03-06 06:38:39 UTC (rev 426)
@@ -1,11 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
-fluormuscovite,-5772803,-6111401,299.03,14.087,680.36024,-6515.743,0,110583120,0,0,0,3.35273302,0,-0.17169021,0.00042947,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/chnosz -r 426

From noreply at r-forge.r-project.org  Wed Mar  6 09:17:43 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  6 Mar 2019 09:17:43 +0100 (CET)
Subject: [CHNOSZ-commits] r427 - in pkg/CHNOSZ: . inst inst/extdata/Berman
	inst/extdata/OBIGT inst/extdata/thermo vignettes
Message-ID: <20190306081743.661B818BDB4@r-forge.r-project.org>

Author: jedick
Date: 2019-03-06 09:17:42 +0100 (Wed, 06 Mar 2019)
New Revision: 427

Added:
   pkg/CHNOSZ/inst/extdata/Berman/VGT92_1992.csv
   pkg/CHNOSZ/inst/extdata/Berman/VPT01_2001.csv
   pkg/CHNOSZ/inst/extdata/Berman/VPV05_2005.csv
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
   pkg/CHNOSZ/vignettes/mklinks.sh
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
extdata/Berman: add data from Vidal et al. (1992, 2001, 2005)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-06 06:38:39 UTC (rev 426)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-06 08:17:42 UTC (rev 427)
@@ -1,6 +1,6 @@
 Date: 2019-03-06
 Package: CHNOSZ
-Version: 1.3.1-7
+Version: 1.3.1-8
 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	2019-03-06 06:38:39 UTC (rev 426)
+++ pkg/CHNOSZ/inst/NEWS	2019-03-06 08:17:42 UTC (rev 427)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.1-6 (2019-03-06)
+CHANGES IN CHNOSZ 1.3.1-8 (2019-03-06)
 --------------------------------------
 
 - Add thermo/stoich.csv.xz (loaded as thermo()$stoich), containing a
@@ -16,6 +16,9 @@
   chronological order, and keeps only the most recent data for any
   duplicated minerals.
 
+- Add data for sudoite, daphnite, Mg-amesite, and Fe-amesite to
+  extdata/Berman (Vidal et al., 1992, 2001, 2005).
+
 CHANGES IN CHNOSZ 1.3.1 (2019-03-02)
 ------------------------------------
 

Added: pkg/CHNOSZ/inst/extdata/Berman/VGT92_1992.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/VGT92_1992.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/VGT92_1992.csv	2019-03-06 08:17:42 UTC (rev 427)
@@ -0,0 +1,2 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+sudoite,NA,-8655273,390.5,20.51,1115.84,-8507.5,-19777440,2959147000,0,0,0,2.6451,0,-0.182,0,,,,,,,,,,,,,,

Added: pkg/CHNOSZ/inst/extdata/Berman/VPT01_2001.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/VPT01_2001.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/VPT01_2001.csv	2019-03-06 08:17:42 UTC (rev 427)
@@ -0,0 +1,3 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+daphnite,NA,-7120845,559.4,21.588,1229.23,-10256.5,-12276900,2121510000,0,0,0,2.6451,0,-0.182,0,,,,,,,,,,,,,,
+Mg-amesite,NA,-9035900,403.2,20.52,1144.45,-8327.2,-20058040,2820786000,0,0,0,2.6451,0,-0.182,0,,,,,,,,,,,,,,

Added: pkg/CHNOSZ/inst/extdata/Berman/VPV05_2005.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/VPV05_2005.csv	                        (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/VPV05_2005.csv	2019-03-06 08:17:42 UTC (rev 427)
@@ -0,0 +1,2 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+Fe-amesite,NA,-7607460,514.8,20.9,1219.81,-10021.5,-14439720,2392326000,0,0,0,2.6451,0,-0.182,0,,,,,,,,,,,,,,

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv	2019-03-06 06:38:39 UTC (rev 426)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv	2019-03-06 08:17:42 UTC (rev 427)
@@ -85,3 +85,7 @@
 ferro-actinolite,Fac,Ca2Fe5Si8O22(OH)2,cr,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 grunerite,Gru,Fe7Si8O22(OH)2,cr,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 ilvaite,Ilv,CaFe2FeSi2O7O(OH),cr,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+sudoite,Sud,Mg2Al4Si3O10(OH)8,cr,VGT92,NA,06.Mar.19,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+daphnite,Daph,Fe5Al2Si3O10(OH)8,cr,VPT01,NA,06.Mar.19,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Mg-amesite,Mg-Am,Mg4Al4Si2O10(OH)8,cr,VPT01,NA,06.Mar.19,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Fe-amesite,Fe-Am,Fe4Al4Si2O10(OH)8,cr,VPV05,NA,06.Mar.19,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2019-03-06 06:38:39 UTC (rev 426)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2019-03-06 08:17:42 UTC (rev 427)
@@ -27,8 +27,8 @@
 Ber88,"R. G. Berman",1988,"J. Petrol. 29, 445-522",minerals,https://doi.org/10.1093/petrology/29.2.445
 SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",https://doi.org/10.1016/0016-7037(88)90181-0
 SH88.1,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","values of GHS",https://doi.org/10.1016/0016-7037(88)90181-0
-SH88.2,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","H<sub>2</sub>AsO<sub>3</sub><sup>-</sup>",https://doi.org/10.1016/0016-7037(88)90181-0
-SH88.3,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","Ag<sup>+</sup>",https://doi.org/10.1016/0016-7037(88)90181-0
+SH88.2,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",H<sub>2</sub>AsO<sub>3</sub><sup>-</sup>,https://doi.org/10.1016/0016-7037(88)90181-0
+SH88.3,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",Ag<sup>+</sup>,https://doi.org/10.1016/0016-7037(88)90181-0
 SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",https://doi.org/10.1016/0016-7037(89)90341-4
 SHS89.1,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","aqueous SiO<sub>2</sub>",https://doi.org/10.1016/0016-7037(89)90341-4
 Ber90,"R. G. Berman",1990,"Am. Mineral. 75, 328-344",annite,http://ammin.geoscienceworld.org/content/75/3-4/328
@@ -46,6 +46,7 @@
 SPRONS92.2,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","Ca-bearing minerals; &quot;Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 &quot;",
 Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine; not present in slop files after slop98.dat",https://doi.org/10.1016/0016-7037(92)90392-V
 Sho92.1,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diketopiperazine GHS",https://doi.org/10.1016/0016-7037(92)90392-V
+VGT92,"O. Vidal, B. Goff? and T. Theye",1992,"J. Metamorphic Geol. 10, 603-614",sudoite,https://doi.org/10.1111/j.1525-1314.1992.tb00109.x
 ZS92,"C. Zhu and D. A. Sverjensky",1982,"Geochim. Cosmochim. Acta 56, 3435-3467","F,Cl,OH biotite and apatite endmembers. GHS and V were taken from Table 6 of @ZS92; heat capacity and volume parameters from `berman.dat`.",https://doi.org/10.1016/0016-7037(92)90390-5
 Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",https://doi.org/10.1016/0016-7037(93)90542-5
 Sho93.1,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","carbon monoxide and ethylene",https://doi.org/10.1016/0016-7037(93)90542-5
@@ -80,7 +81,7 @@
 SSWS97.5,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","Zn<sup>+2</sup> and Zn-hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0
 SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","metal complexes",https://doi.org/10.1016/S0016-7037(97)00009-4
 SSH97.1,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Au(HS)<sub>2</sub><sup>-</sup> and Ag(HS)<sub>2</sub><sup>-</sup>",https://doi.org/10.1016/S0016-7037(97)00009-4
-SSH97.2,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","HSiO<sub>3</sub><sup>-</sup>",https://doi.org/10.1016/S0016-7037(97)00009-4
+SSH97.2,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412",HSiO<sub>3</sub><sup>-</sup>,https://doi.org/10.1016/S0016-7037(97)00009-4
 SSH97.3,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Au-, Ag-, Cu- and Zn-chloride complexes",https://doi.org/10.1016/S0016-7037(97)00009-4
 SSH97.4,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Zn-acetate complexes",https://doi.org/10.1016/S0016-7037(97)00009-4
 SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266","uranium species",https://doi.org/10.1016/S0016-7037(97)00240-8
@@ -98,7 +99,7 @@
 SS98a,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group ions and complexes",https://doi.org/10.1016/S0016-7037(98)00049-0
 SS98a.1,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group solids",https://doi.org/10.1016/S0016-7037(98)00049-0
 SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",Rh<sup>+3</sup>,https://doi.org/10.1016/S0016-7037(98)00049-0
-SS98a.3,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",Pd<sup>+2</sup> and Pt<sup>+2</sup> and their complexes,https://doi.org/10.1016/S0016-7037(98)00049-0
+SS98a.3,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","Pd<sup>+2</sup> and Pt<sup>+2</sup> and their complexes",https://doi.org/10.1016/S0016-7037(98)00049-0
 HS99,"J. R. Haas and E. L. Shock",1998,"Geochim. Cosmochim. Acta 63, 3429-3441","chloroethylene species",https://doi.org/10.1016/S0016-7037(99)00276-8
 MS99,"W. M. Murphy and E. L. Shock",1999,"Rev. Mineral. Geochem. 38, 221-253",actinides,http://rimg.geoscienceworld.org/content/38/1/221
 PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",https://doi.org/10.1016/S0016-7037(99)00146-5
@@ -116,6 +117,7 @@
 Ste01,"A. Stefansson",2001,"Chem. Geol. 172, 225-250","aqueous H<sub>4</sub>SiO<sub>4</sub>",https://doi.org/10.1016/S0009-2541(00)00263-1
 SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH<sub>3</sub>, CF<sub>4</sub>, CH<sub>3</sub>F, Cl<sub>2</sub>, ClO<sub>2</sub>, N<sub>2</sub>O, NF<sub>3</sub>, NO, PH<sub>3</sub>, and SF<sub>6</sub>",https://doi.org/10.1016/S0016-7037(01)00717-7
 TS01,"B. Tagirov and J. Schott",2001,"Geochim. Cosmochim. Acta 65, 3965-3992","aqueous Al<sup>+3</sup> and complexes",https://doi.org/10.1016/S0016-7037(01)00705-0
+VPT01,"O. Vidal, T. Parra and F. Trotet",2001,"Am. J. Sci. 301, 557-592","daphnite and Mg-amesite",https://doi.org/10.2475/ajs.301.6.557
 GKL02,"R. N. Goldberg et al.",2002,"J. Phys. Chem. Ref. Data 31, 231-370","glycine, diglycine, and triglycine (+1 and -1 ions) GHS",https://doi.org/10.1063/1.1416902
 AD03.1,"N. N. Akinfiev and L. W. Diamond",2003,"Geochim. Cosmochim. Acta 67, 613-629","dissolved gas species; parameters estimated from the experimental Henry's constant",https://doi.org/10.1016/S0016-7037(02)01141-9
 AD03.2,"N. N. Akinfiev and L. W. Diamond",2003,"Geochim. Cosmochim. Acta 67, 613-629","dissolved gas species; parameters estimated from standard-state properties at 25 &deg; C",https://doi.org/10.1016/S0016-7037(02)01141-9
@@ -126,8 +128,9 @@
 AS04,"J. Apps and N. Spycher",2004,"Data qualification for thermodynamic data used to support THC calculations. Bechtel SAIC Company, LLC. ANL-NBS-HS-000043 REV 00 (DOC.20041118.0004)","aqueous SiO<sub>2</sub>",
 MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531","hydronium jarosite",https://doi.org/10.1007/s00269-004-0405-z
 SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",https://doi.org/10.1016/j.gca.2003.06.001
+VPV05,"O. Vidal, T. Parra and P. Viellard",2005,"Am. Mineral. 90, 347-358",Fe-amesite,https://doi.org/10.2138/am.2005.1554
 ZZX+05,"Y. Zhu et al.",2005,"J. Hazard. Mater. A120, 37-44","barium arsenate and barium hydrogen arsenate: G",https://doi.org/10.1016/j.jhazmat.2004.12.025
-AVZP06,"N. N. Akinfiev et al.",2006,"Geochem. Int. 44, 867-878","AgCl<sub>3</sub><sup>-2</sup>",https://doi.org/10.1134/S0016702906090035
+AVZP06,"N. N. Akinfiev et al.",2006,"Geochem. Int. 44, 867-878",AgCl<sub>3</sub><sup>-2</sup>,https://doi.org/10.1134/S0016702906090035
 HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",https://doi.org/10.1016/j.jct.2005.10.013
 LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic-acid bases, nucleosides, and nucleotides",https://doi.org/10.1016/j.gca.2006.04.010
 LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","citric acid and citrate",https://doi.org/10.1016/j.gca.2006.04.010

Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)

Modified: pkg/CHNOSZ/vignettes/mklinks.sh
===================================================================
--- pkg/CHNOSZ/vignettes/mklinks.sh	2019-03-06 06:38:39 UTC (rev 426)
+++ pkg/CHNOSZ/vignettes/mklinks.sh	2019-03-06 08:17:42 UTC (rev 427)
@@ -37,7 +37,7 @@
 sed -i '120,$s/<code>diagram()<\/code>/<code><a href="..\/html\/diagram.html" style="background-image:none;">diagram()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>basis()<\/code>/<code><a href="..\/html\/basis.html" style="background-image:none;">basis()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>species()<\/code>/<code><a href="..\/html\/species.html" style="background-image:none;">species()<\/a><\/code>/g' anintro.html
-sed -i '120,$s/<code>reset()<\/code>/<code><a href="..\/html\/thermo.html" style="background-image:none;">reset()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>reset()<\/code>/<code><a href="..\/html\/reset.html" style="background-image:none;">reset()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>describe.reaction()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">describe.reaction()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>swap.basis()<\/code>/<code><a href="..\/html\/swap.basis.html" style="background-image:none;">swap.basis()<\/a><\/code>/g' anintro.html
 sed -i '120,$s/<code>water.lines()<\/code>/<code><a href="..\/html\/util.plot.html" style="background-image:none;">water.lines()<\/a><\/code>/g' anintro.html

Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib	2019-03-06 06:38:39 UTC (rev 426)
+++ pkg/CHNOSZ/vignettes/obigt.bib	2019-03-06 08:17:42 UTC (rev 427)
@@ -1256,15 +1256,15 @@
 }
 
 @Article{BPAH07,
-  author        = {Pascale B\'en\'ezeth and Donald A. Palmer and Lawrence M. Anovitz and Juske Horita},
-  journal       = {Geochimica et Cosmochimica Acta},
-  title         = {{D}awsonite synthesis and reevaluation of its thermodynamic properties from solubility measurements: {I}mplications for mineral trapping of {CO}$_2$},
-  year          = {2007},
-  volume        = {71},
-  number        = {18},
-  pages         = {4438--4455},
-  doi           = {10.1016/j.gca.2007.07.003},
-  issn          = {0016-7037},
+  author    = {Pascale B\'en\'ezeth and Donald A. Palmer and Lawrence M. Anovitz and Juske Horita},
+  journal   = {Geochimica et Cosmochimica Acta},
+  title     = {{D}awsonite synthesis and reevaluation of its thermodynamic properties from solubility measurements: {I}mplications for mineral trapping of {CO}$_2$},
+  year      = {2007},
+  volume    = {71},
+  number    = {18},
+  pages     = {4438--4455},
+  doi       = {10.1016/j.gca.2007.07.003},
+  issn      = {0016-7037},
 }
 
 @Book{FSR76,
@@ -1422,3 +1422,39 @@
   zs        = {0},
 }
 
+ at Article{VPT01,
+  author    = {Vidal, Olivier and Parra, Teddy and Trotet, Fabien},
+  journal   = {American Journal of Science},
+  title     = {{A} thermodynamic model for fe-mg aluminous chlorite using data from phase equilibrium experiments and natural pelitic assemblages in the 100? to 600?{C}, 1 to 25 kb range},
+  year      = {2001},
+  volume    = {301},
+  number    = {6},
+  pages     = {557--592},
+  doi       = {10.2475/ajs.301.6.557},
+}
+
+ at Article{VPV05,
+  author    = {Vidal, Olivier and Parra, Teddy and Viellard, Philippe},
+  journal   = {American Mineralogist},
+  title     = {{T}hermodynamic properties of the {T}schermak solid solution in {F}e-chlorite: {A}pplication to natural examples and possible role of oxidation},
+  year      = {2005},
+  volume    = {90},
+  number    = {2-3},
+  pages     = {347--358},
+  doi       = {10.2138/am.2005.1554},
+  issn      = {0003-004X},
+  publisher = {Mineralogical Society of America},
+  source    = {Crossref},
+}
+
+ at Article{VGT92,
+  author        = {Vidal, O. and Goff?, B. and Theye, T.},
+  journal       = {Journal of Metamorphic Geology},
+  title         = {{E}xperimental study of the stability of sudoite and magnesiocarpholite and calculation of a new petrogenetic grid for the system {F}e{O}--{M}g{O}--{A}l$_2${O}$_3$--{S}i{O}$_2$--{H}$_2${O}},
+  year          = {1992},
+  volume        = {10},
+  number        = {5},
+  pages         = {603--614},
+  doi           = {10.1111/j.1525-1314.1992.tb00109.x},
+}
+


From noreply at r-forge.r-project.org  Sat Mar  9 01:43:48 2019
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat,  9 Mar 2019 01:43:48 +0100 (CET)
Subject: [CHNOSZ-commits] r428 - in pkg/CHNOSZ: . R vignettes
Message-ID: <20190309004348.70A9D18C659@r-forge.r-project.org>

Author: jedick
Date: 2019-03-09 01:43:47 +0100 (Sat, 09 Mar 2019)
New Revision: 428

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/solubility.R
   pkg/CHNOSZ/vignettes/obigt.bib
Log:
solubility(): use info() to get formulas for checking species charges


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-06 08:17:42 UTC (rev 427)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-09 00:43:47 UTC (rev 428)
@@ -1,6 +1,6 @@
-Date: 2019-03-06
+Date: 2019-03-09
 Package: CHNOSZ
-Version: 1.3.1-8
+Version: 1.3.1-9
 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/solubility.R
===================================================================
--- pkg/CHNOSZ/R/solubility.R	2019-03-06 08:17:42 UTC (rev 427)
+++ pkg/CHNOSZ/R/solubility.R	2019-03-09 00:43:47 UTC (rev 428)
@@ -100,8 +100,10 @@
       }
     }
     # add ions present in the species of interest
+    # instead of using aout$species$name, use info() to get formulas 20190309
+    species.formulas <- info(aout$species$ispecies)$formula
     for(i in 1:length(loga.equil)) {
-      species.ion <- aout$species$name[i]
+      species.ion <- species.formulas[i]
       Z.species.ion <- makeup(species.ion)["Z"]
       if(!is.na(Z.species.ion)) {
         sum.mZ2 <- sum.mZ2 + 10^loga.equil[[i]] * Z.species.ion^2

Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib	2019-03-06 08:17:42 UTC (rev 427)
+++ pkg/CHNOSZ/vignettes/obigt.bib	2019-03-09 00:43:47 UTC (rev 428)
@@ -1221,7 +1221,7 @@
 
 @Article{ZZX+05,
   author    = {Zhu, Yinian and Zhang, Xuehong and Xie, Qinglin and Chen, Yudao and Wang, Dunqiu and Liang, Yanpeng and Lu, Jie},
-  journal   = {Journal of Hazardous materials},
+  journal   = {Journal of Hazardous Materials},
   title     = {{S}olubility and stability of barium arsenate and barium hydrogen arsenate at 25 ?{C}},
   year      = {2005},
   volume    = {120},