Rename some files in OBIGT/testing

git-svn-id: svn://scm.r-forge.r-project.org/svnroot/chnosz/pkg/CHNOSZ@858 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

DESCRIPTION

@@ -1,6 +1,6 @@
-Date: 2024-12-24
+Date: 2024-12-25
 Package: CHNOSZ
-Version: 2.1.0-30
+Version: 2.1.0-31
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

R/add.OBIGT.R

@@ -120,8 +120,8 @@ add.OBIGT <- function(file, species = NULL, force = TRUE) {
   if(!file.exists(file)) {
 
     # List all files in OBIGT and OBIGT/testing
-    OBIGT_files <- dir(system.file("extdata/OBIGT/", package = "CHNOSZ"), full.names = TRUE)
-    testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), full.names = TRUE)
+    OBIGT_files <- dir(system.file("extdata/OBIGT", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE)
+    testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE)
     all_files <- c(OBIGT_files, testing_files)
     # Match argument to file names without path or .csv suffix
     all_names <- gsub(".csv", "", basename(all_files))

R/examples.R

@@ -30,7 +30,7 @@ examples <- function(save.png = FALSE) {
   cat("Time elapsed: ", proc.time() - .ptime, "\n")
 }
 
-demos <- function(which = c("sources", "protein.equil", "affinity", "NaCl", "density", 
+demos <- function(which = c("references", "protein.equil", "affinity", "NaCl", "density", 
   "ORP", "ionize", "buffer", "protbuff", "glycinate",
   "mosaic", "copper", "arsenic", "solubility", "gold", "contour", "sphalerite", "minsol",
   "Shh", "saturation", "adenine", "DEW", "lambda", "potassium", "TCA", "aluminum",

R/thermo.R

@@ -78,7 +78,7 @@ OBIGT <- function(no.organics = FALSE) {
   # Create OBIGT data frame
   OBIGT <- do.call(rbind, datalist)
   # Also read references file
-  refs <- read.csv(file.path(OBIGTdir, "refs.csv"), as.is = TRUE)
+  refs <- read.csv(file.path(OBIGTdir, "../refs.csv"), as.is = TRUE)
   # Get thermo from CHNOSZ environment
   thermo <- get("thermo", CHNOSZ)
   # Set OBIGT and refs

demo/00Index

@@ -1,4 +1,4 @@
-sources         Cross-check the reference list with the thermodynamic database
+references      Cross-check the references in refs.csv with the thermodynamic database
 protein.equil   Chemical activities of two proteins in metastable equilibrium
 affinity        Affinities of metabolic reactions and amino acid synthesis
 NaCl            Equilibrium constant for aqueous NaCl dissociation

demo/aluminum.R

@@ -25,7 +25,7 @@ basis(delete = TRUE)
 # boehmite from Hemingway et al., 1991
 r1 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE) 
 ## Second calculation: get SiO2(aq) from Apps and Spycher, 2004
-add.OBIGT("AS04")
+add.OBIGT("SiO2")
 r2 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE) 
 reset()
 ## Third calculation: get Si(OH)4 from Akinfiev and Plyasunov, 2014
@@ -48,7 +48,7 @@ points(seq(125, 350, 25), -c(3.489, 3.217, 2.967, 2.734, 2.517, 2.314, 2.124, 1.
 title(main = describe.reaction(r4$reaction), cex.main = 1.1)
 legend("bottomright", lty = c(0, 0, 1, 2, 3, 0), pch = c(1, 4, NA, NA, NA, NA), lwd = c(1, 1, 1.5, 1, 1, 0),
        col = c("black", "red", "black", "red", "purple", NA), bty = "n", cex = 0.9,
-       legend = c("Hemley et al., 1980", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("AS04")', 'add.OBIGT("AD")', ""))
+       legend = c("Hemley et al., 1980", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("SiO2")', 'add.OBIGT("AD")', ""))
 legend("bottomright", lty = 4, pch = NA, lwd = 1, col = "blue", legend = 'add.OBIGT("SUPCRT92")', bty = "n", cex = 0.9)
 legend("topleft", c("Boehmite - Kaolinite", "After Zhu and Lu, 2009 Fig. A1"), bty = "n")
 # Helgeson et al., 1978 (HDNB78): http://www.worldcat.org/oclc/13594862
@@ -105,7 +105,7 @@ sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "SiO2"), c(-1, -2, -1, 2
 pK <- -sres$out$logK
 lines(invTK, pK, lwd = 1.5)
 # Plot line: SiO2 from Apps and Spycher, 2004
-add.OBIGT("AS04")
+add.OBIGT("SiO2")
 sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "SiO2"), c(-1, -2, -1, 2, 2), T = T)
 pK <- -sres$out$logK
 lines(invTK, pK, col = "red", lty = 2)
@@ -133,7 +133,7 @@ par(xpd = FALSE)
 legend("topright", c("Kaolinite solubility", "After Tutolo et al., 2014 Fig. 2"), bty = "n")
 legend("bottomleft", lty = c(0, 0, 0, 1, 2, 3, 4), pch = c(1, NA, 4, NA, NA, NA, NA),
        lwd = c(1, 1, 1, 1.5, 1, 1, 1), col = c("black", "black", "red", "black", "red", "purple", "blue"),
-       legend = c("Various sources \u2013", "  see Tutolo et al., 2014", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("AS04")', 'add.OBIGT("AD")', 'add.OBIGT("SUPCRT92")'),
+       legend = c("Various sources \u2013", "  see Tutolo et al., 2014", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("SiO2")', 'add.OBIGT("AD")', 'add.OBIGT("SUPCRT92")'),
        bty = "n", cex = 0.9)
 
 ###########

demo/references.R

@@ -0,0 +1,36 @@
+# CHNOSZ/demo/reference.R
+## Cross-checking references
+library(CHNOSZ)
+
+# The available reference keys
+available_refs <- thermo()$refs$key
+
+# The used reference keys
+# List all files in OBIGT and OBIGT/testing
+OBIGT_files <- dir(system.file("extdata/OBIGT", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE)
+testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE)
+all_files <- c(OBIGT_files, testing_files)
+all_data <- lapply(all_files, read.csv)
+all_data <- do.call(rbind, all_data)
+used_refs <- na.omit(c(all_data$ref1, all_data$ref2))
+
+# Print messages for unavailable and unused refs
+unavailable_refs <- used_refs[!used_refs %in% available_refs]
+unused_refs <- available_refs[!available_refs %in% used_refs]
+if(length(unavailable_refs) > 0 | length(unused_refs) > 0) {
+
+  if(length(unavailable_refs) > 0) {
+    print("References used in database but not available in refs.csv:")
+    print(unique(unavailable_refs))
+  }
+
+  if(length(unused_refs) > 0) {
+    print("References available in refs.csv but not used in database:")
+    print(unique(unused_refs))
+  }
+
+} else {
+
+  print("All references accounted for!")
+
+}

inst/CHECKLIST

@@ -1,6 +1,6 @@
 ****************************
 Release checklist for CHNOSZ
-   (updated 2024-02-11)
+   (updated 2024-12-25)
 ****************************
 
 - Run examples() and demos() and inspect their output (especially plots)
@@ -19,11 +19,11 @@ Updating data in OBIGT
 - Add BibTeX references to vignettes/OBIGT.bib
   (used in the OBIGT.Rmd vignette).
 
-- Add references and notes to extdata/OBIGT/refs.csv
+- Add references and notes to extdata/refs.csv
   (also used in the OBIGT.Rmd vignette and thermo.refs()).
 
-- Check output of demo/sources.R to make sure all references
-  are cited (printed results should be character(0)).
+- Check output of demo/references.R to cross-check references in refs.csv with
+  OBIGT files.
 
 - Rebuild extdata/thermo/stoich.csv.xz after all data updates
   (used in retrieve() to search the databse by element):

inst/NEWS.Rd

@@ -52,13 +52,13 @@
       have been moved to \file{SLOP98.csv}.
 
       \item Make new directory \file{OBIGT/testing} to hold optional data files
-      for testing (currently \file{AS04.csv}, \file{GEMSFIT.csv},
-      \file{IGEM24.csv}, and \file{KBJ24.csv}).
+      for testing (currently \file{SiO2.csv}, \file{GEMSFIT.csv},
+      \file{IGEM.csv}, and \file{Sandia.csv}).
 
-      \item Add \file{IGEM24.csv}: updated data for Au and Cu complexes and
+      \item Add \file{IGEM.csv}: updated data for Au and Cu complexes and
       SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS.
 
-      \item Add \file{KBJ24.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
+      \item Add \file{Sandia.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
       \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al.
         (2024)}.
 

inst/extdata/OBIGT/refs.csv → inst/extdata/refs.csv

@@ -300,4 +300,3 @@ RSS+24,"K. Robinson et al.",2024,"Geochim. Cosmochim. Acta 372, 62-80","alkylami
 RSS+24.1,"K. Robinson et al.",2024,"Geochim. Cosmochim. Acta 372, 62-80","corrected V for tripropylaminium",https://doi.org/10.1016/j.gca.2024.03.013
 TAT+24,"B. R. Tagirov, N. N. Akinfiev et al.",2024,"Geochim. Cosmochim. Acta","Au-(hydro)sulfide species and SO<sub>4</sub><sup>-2</sup>-bearing species",https://doi.org/10.1016/j.gca.2024.08.022
 TAZ24,"B. R. Tagirov, N. N. Akinfiev and A. V. Zotov",2024,"Geol. Ore Deposits 66, 581--597","Au hydroxide and chloride complexes",https://doi.org/10.1134/S1075701524600403
-

man/add.OBIGT.Rd

@@ -2,7 +2,7 @@
 \name{add.OBIGT}
 \alias{add.OBIGT}
 \alias{mod.OBIGT}
-\title{Functions to work with the thermodynamic database}
+\title{Functions to Work with the Thermodynamic Database}
 \description{
 Add or modify species in the thermodynamic database.
 }
@@ -135,11 +135,11 @@ OBIGT()
 # Another use of add.OBIGT(): calculate Delta G of
 # H4SiO4 = SiO2 + 2H2O using various sources of data for SiO2.
 # First, get H4SiO4 from Stefansson, 2001
-add.OBIGT("AS04", "H4SiO4")
+add.OBIGT("SiO2", "H4SiO4")
 T <- seq(0, 350, 10)
 s1 <- subcrt(c("H4SiO4", "SiO2", "H2O"), c(-1, 1, 2), T = T)
 # Now, get SiO2 from Apps and Spycher, 2004
-add.OBIGT("AS04", "SiO2")
+add.OBIGT("SiO2", "SiO2")
 s2 <- subcrt(c("H4SiO4", "SiO2", "H2O"), c(-1, 1, 2), T = T)
 # Plot logK from the first and second calculations
 plot(T, s1$out$G, type = "l", xlab = axis.label("T"),

man/examples.Rd

@@ -13,7 +13,7 @@
 
 \usage{
   examples(save.png = FALSE)
-  demos(which = c("sources", "protein.equil", "affinity", "NaCl",
+  demos(which = c("references", "protein.equil", "affinity", "NaCl",
     "density", "ORP", "ionize", "buffer", "protbuff",
     "glycinate", "mosaic", "copper", "arsenic", "solubility", "gold",
     "contour", "sphalerite", "minsol", "Shh", "saturation",
@@ -32,7 +32,7 @@
 The demo(s) to run is/are specified by \code{which}; the default is to run them in the order of the list below.
 
   \describe{
-    \item{sources}{Cross-check the reference list with the thermodynamic database}
+    \item{references}{Cross-check the references in refs.csv with the thermodynamic database}
     \item{protein.equil}{Chemical activities of two proteins in metastable equilibrium (Dick and Shock, 2011)}
     \item{affinity}{Affinities of metabolic reactions and amino acid synthesis (Amend and Shock, 1998, 2001)}
     \item{NaCl}{Equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992)}

vignettes/OBIGT.Rmd

@@ -217,7 +217,7 @@ Except for Optional Data, all data are present in the default database, which is
 Each section below corresponds to one of the CSV data files in the `extdata/OBIGT` package directory.
 Clicking on a button opens that section, which contains a list of primary references (from column `ref1` in the file) in chronological order.
 Any secondary references (`ref2`) are listed with bullet points under the primary reference.
-Each citation is followed by the number of species, and a note taken from the file `extdata/OBIGT/refs.csv`.
+Each citation is followed by the number of species, and a note taken from the file `extdata/refs.csv`.
 Additional comments (from this vignette) are present for some sections.
 
 Abbreviations: T (temperature), P (pressure), GHS (standard Gibbs energy, enthalpy, entropy), Cp (heat capacity), V (volume), HKF (<abbr title="Tanger and Helgeson, 1988">revised</abbr> <abbr title="Helgeson et al., 1981">Helgeson-Kirkham-Flowers</abbr> equations).
@@ -397,8 +397,9 @@ Most of the comments below were transcribed from the DEW spreadsheet. (Comments
 ## <a id="optional-Testing" class="anchor"></a> `r setfile("testing")`
 
 These are optional data files used for testing purposes.
+Load the data with e.g. `add.OBIGT("GEMSFIT")`.
 
-<h3>AS04</h3>
+<h3>SiO2</h3>
 
 Aqueous SiO<sub>2</sub> from @AS04 and HSiO<sub>3</sub><sup>-</sup> modified to be consistent with it.
 This file also has H<sub>4</sub>SiO<sub>4</sub> from an earlier publication [@Ste01] that is roughly consistent with the SiO<sub>2</sub> here.
@@ -408,11 +409,11 @@ See `demo(aluminum)` and the vignette [<span style="color:blue">*Regressing ther
 
 Internally consistent dataset for aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl obtained with the [GEMSFIT](https://doi.org/10.1016/j.apgeochem.2014.10.013) package [@MWKH16;@MWKL17].
 
-<h3>IGEM24</h3>
+<h3>IGEM</h3>
 
 Updates for Au and Cu complexes and SO<sub>4</sub><sup>-2</sup>-bearing species from researchers at the Institute of Geology of Ore Deposits, Petrography, Mineralogy, and Geochemistry, Russian Academy of Sciences (IGEM RAS) [@AZ23;@TTA+23;@TAT+24;@TAZ24].
 
-<h3>KBJ24</h3>
+<h3>Sandia</h3>
 
 Model for the Mg(OH)<sub>2</sub>-MgCl<sub>2</sub>-H<sub>2</sub>O system at 25 to 150 &deg;C from researchers at Sandia National Laboratories [@KBJ24].
 

vignettes/anintro.Rmd

@@ -1513,7 +1513,7 @@ Examples are in [<span style="color:blue">`demo(DEW)`</span>](../demo).
 
 <span style="color:red">`add.OBIGT("GEMSFIT")`</span> -- Thermodynamic data for aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl obtained from global optimization of Gibbs energies with the GEMSFIT package [@MWKL17].
 
-<span style="color:red">`add.OBIGT("AS04")`</span> -- This file has data for aqueous `r sio2` from @AS04 and modified HSiO<sub>3</sub><sup>-</sup>.
+<span style="color:red">`add.OBIGT("SiO2")`</span> -- This file has data for aqueous `r sio2` from @AS04 and modified HSiO<sub>3</sub><sup>-</sup>.
 These data reflect a revised (higher) solubility of quartz compared to previous compilations, but are not included in the default database in order to maintain compatibility with existing data for minerals that are linked to the older aqueous `r sio2` data.
 See [<span style="color:blue">`demo(aluminum)`</span>](../demo) for an example.
 

vignettes/custom_data.Rmd

@@ -204,7 +204,7 @@ OPTIONAL but useful:
 
 - `r abbrv` *may be* an abbreviation (e.g. Qtz for quartz). It is used by `r info_` (together with `r name` and `r formula`) to look up species in the database.
 - `r date` is a timestamp for the data entry (YYYY-MM-DD format in the default OBIGT database).
-- `r ref1` and `r ref2` are bibliographic reference keys. They have matching entries in `extdata/OBIGT/refs.csv`, which is used by `r thermo.refs_` to display references, and in `vignettes/OBIGT.bib`, which is used in the [<span style="color:blue">*OBIGT thermodynamic database*</span>](OBIGT.html) vignette to produce a reference list. 
+- `r ref1` and `r ref2` are bibliographic reference keys. They have matching entries in `extdata/refs.csv`, which is used by `r thermo.refs_` to display references, and in `vignettes/OBIGT.bib`, which is used in the [<span style="color:blue">*OBIGT thermodynamic database*</span>](OBIGT.html) vignette to produce a reference list. 
 
 `r NOTE`: Other functions in CHNOSZ do not depend on `r date`, `r ref1`, and `r ref2`, so you can put anything there that is convenient for you.
 

vignettes/eos-regress.Rmd

@@ -357,8 +357,8 @@ EOSplot(NaVdat, coefficients = coefficients, Z = 1, add = TRUE, lty = 2,
 Some mineral stability diagrams use the activity of `r h4sio4` as a variable.
 However, the primary species for dissolved silica in CHNOSZ is `r sio2`(aq).
 As recommended by @WJ17, let us use data for `r sio2`(aq) from @AS04, which gives a higher solubility of quartz compared to values from @SHS89 that are loaded by default in the package:
-```{r AS04, message=FALSE}
-add.OBIGT("AS04")
+```{r add_SiO2, message=FALSE}
+add.OBIGT("SiO2")
 ```
 
 The pseudo-reaction with zero properties, `r h4sio4` = `r sio2`  + 2 `r h2o`, defines the properties of the pseudospecies `r h4sio4`.