Set dpi in vignettes to reduce package size

git-svn-id: svn://scm.r-forge.r-project.org/svnroot/chnosz/pkg/CHNOSZ@815 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

DESCRIPTION

@@ -1,6 +1,6 @@
-Date: 2023-11-28
+Date: 2023-11-29
 Package: CHNOSZ
-Version: 2.0.0-34
+Version: 2.0.0-35
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

inst/NEWS.Rd

@@ -15,7 +15,7 @@
 \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{<I>C<sub>P</sub></I>}}{Cp}}}
 \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{&Delta;<I>G</I>&deg;}}{ΔG°}}}
 
-\section{Changes in CHNOSZ version 2.0.0-32 (2023-11-15)}{
+\section{Changes in CHNOSZ version 2.0.0-34 (2023-11-28)}{
 
     \itemize{
 
@@ -30,6 +30,7 @@
         \item How can minerals with polymorphic transitions be added to the database?
         \item How can I make a diagram with the trisulfur radical ion (S\s{3}\S{-})?
         \item In OBIGT, what is the meaning of \code{T} for solids, liquids, and gases?
+        \item How do I plot mineral buffers for pH?
 
       }
 

vignettes/FAQ.Rmd

@@ -135,6 +135,8 @@ knitr::knit_hooks$set(
            '</div>', sep = '\n')
    }
 )
+# Set dpi 20231129
+dpi <- 72
 ```
 
 ```{r echo = F, cache = F}
@@ -207,7 +209,7 @@ This vignette was compiled on `r Sys.Date()` with CHNOSZ version `r sessionInfo(
 As one syllable that starts with an *sh* sound and [rhymes with *Oz*](https://en.wiktionary.org/wiki/Rhymes:English/%C9%92z).
 CHNOSZ and [schnoz](https://en.wiktionary.org/wiki/schnozz) are homophones.
 
-*Answered on 2023-05-22.*
+*Added on 2023-05-22.*
 
 ## How should CHNOSZ be cited?
 
@@ -235,7 +237,7 @@ reset()
 
 * Additional minerals from @HDNB78, that were available in SUPCRT92 but may conflict with the @Ber88 compilation, can be loaded from an optional database with `add.OBIGT("SUPCRT92")`. When using these data, it is appropriate to cite @HDNB78 rather than SUPCRT92.
 
-*Answered on 2023-05-27; PPM example added on 2023-11-15.*
+*Added on 2023-05-27; PPM example added on 2023-11-15.*
 
 ## What thermodynamic models are used in CHNOSZ?
 
@@ -246,7 +248,7 @@ reset()
 * Activity coefficients are implemented via adjusted standard Gibbs energies at specified ionic strength [@Alb96], which converts all activity variables in the workflow to molalities.
 * A related adjustment is available to convert standard Gibbs energies for gases from the 1 bar standard state used in SUPCRT92 to a variable-pressure standard state [@AC93,Ch.12].
 
-*Answered on 2018-11-13; moved to FAQ from <https://chnosz.net/> website on 2023-05-27; added references for **revised** HKF on 2023-11-17.*
+*Added to <https://chnosz.net/> website on 2018-11-13; moved to FAQ on 2023-05-27; added references for **revised** HKF on 2023-11-17.*
 
 ## When and why do equal-activity boundaries depend on total activity?
 
@@ -331,10 +333,10 @@ reset()
 ```
 </div>
 
-```{r DEW_Ctot, echo = FALSE, message = FALSE, results = "hide", fig.width = 8, fig.height = 4, out.width = "100%", fig.align = "center", pngquant = pngquant, cache = TRUE}
+```{r DEW_Ctot, echo = FALSE, message = FALSE, results = "hide", fig.width = 8, fig.height = 4, out.width = "100%", fig.align = "center", pngquant = pngquant, cache = TRUE, dpi = dpi}
 ```
 
-*Answered on 2023-05-17.*
+*Added on 2023-05-17.*
 
 ## How can minerals with polymorphic transitions be added to the database?
 
@@ -493,12 +495,12 @@ for(property in c("G", "H", "S", "Cp")) {
 reset()
 ```
 </div>
-```{r pyrrhotite_T, echo = FALSE, message = FALSE, results = "hide", fig.width = 8, fig.height = 2.5, out.width = "100%", fig.align = "center", pngquant = pngquant}
+```{r pyrrhotite_T, echo = FALSE, message = FALSE, results = "hide", fig.width = 8, fig.height = 2.5, out.width = "100%", fig.align = "center", pngquant = pngquant, dpi = dpi}
 ```
 
 For additional polymorphs, we could repeat the above procedure using polymorph 2 as the starting point to calculate `G`, `H`, and `S` of polymorph 3, and so on.
 
-*Answered on 2023-06-23.*
+*Added on 2023-06-23.*
 
 ## How can I make a diagram with the trisulfur radical ion (`r S3minus`)?
 
@@ -671,10 +673,10 @@ OBIGT()
 
 Here are the three plots that we made:
 
-```{r trisulfur, echo = FALSE, message = FALSE, results = "hide", fig.width = 10, fig.height = 3.33, out.width = "100%", out.extra='class="full-width"', pngquant = pngquant, cache = TRUE}
+```{r trisulfur, echo = FALSE, message = FALSE, results = "hide", fig.width = 10, fig.height = 3.33, out.width = "100%", out.extra='class="full-width"', pngquant = pngquant, cache = TRUE, dpi = dpi}
 ```
 
-*Answered on 2023-09-08.*
+*Added on 2023-09-08.*
 
 ## In OBIGT, what is the meaning of `T` for solids, liquids, and gases?
 
@@ -747,7 +749,7 @@ In previous versions of CHNOSZ, values of Δ*G*° above the *C~p~* equation limi
 
 **4. Finally, if `T` is NA or 0, then no upper temerature limit is imposed by `subcrt()`.**
 
-*Answered on 2023-11-15.*
+*Added on 2023-11-15.*
 
 ## How do I plot mineral buffers for pH?
 
@@ -799,7 +801,7 @@ title("Mineral data from Helgeson et al. (1978)\n(as used in SUPCRT92)",
   font.main = 1, cex.main = 0.9)
 OBIGT()
 ```
-```{r KMQ_diagram, message = FALSE, fig.width = 8, fig.height = 4, results = "hide", echo = FALSE}
+```{r KMQ_diagram, message = FALSE, fig.width = 8, fig.height = 4, out.width = "100%", results = "hide", echo = FALSE, dpi = dpi}
 ```
 
 In this diagram, the gray area is below the reducing stability limit of water (i.e., where the equilibrium fugacity of `r H2` exceeds unity).
@@ -820,6 +822,6 @@ If we use the thermodynamic parameters for minerals from @HDNB78, we get the lin
 ```{r KMQ_diagram, eval = FALSE, echo = 10:14}
 ```
 
-*Answered on 2023-11-28.*
+*Added on 2023-11-28.*
 
 ## References

vignettes/custom_data.Rmd

@@ -22,6 +22,9 @@ library(knitr)
 knit_hooks$set(pngquant = hook_pngquant)
 pngquant <- "--speed=1 --quality=0-25"
 if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL
+
+## Set dpi 20231129
+dpi <- 72
 ```
 
 ```{r HTML, include = FALSE}
@@ -510,7 +513,7 @@ A constant molality of `r F_` is based on the assumption of complete dissociatio
 An ionic strength of 0.9 mol/kg is estimated for a solution with 1.8 m NaCl (use `NaCl(1.8, T = 300)`).
 `r NOTE`: because the ionic strength is non-zero, the calculations here refer to molality instead of activity of species (see [An Introduction to CHNOSZ](anintro.html#from-activity-to-molality)).
 
-```{r diagram1, message = FALSE, results = "hide", fig.width = 6, fig.height = 5, out.width = "75%", fig.align = "center", pngquant = pngquant}
+```{r diagram1, message = FALSE, results = "hide", fig.width = 6, fig.height = 5, out.width = "75%", fig.align = "center", pngquant = pngquant, dpi = dpi}
 basis(c("H+", "WO4-2", "F-", "H2O", "O2"))
 basis("F-", log10(0.1))
 iaq <- retrieve("W", c("O", "H", "F"), "aq")
@@ -539,7 +542,7 @@ a_F <- F_tot / (1 + 10^(logK_HF - pH))
 ```
 
 Now that we have the molality of `r F_` as a function of pH, we can provide it in the call to `r affinity_`.
-```{r diagram2, message = FALSE, results = "hide", results = "hide", fig.width = 6, fig.height = 5, out.width = "75%", fig.align = "center", pngquant = pngquant}
+```{r diagram2, message = FALSE, results = "hide", results = "hide", fig.width = 6, fig.height = 5, out.width = "75%", fig.align = "center", pngquant = pngquant, dpi = dpi}
 basis(c("H+", "WO4-2", "F-", "H2O", "O2"))
 iaq <- retrieve("W", c("O", "H", "F"), "aq")
 species(iaq)

vignettes/equilibrium.Rmd

@@ -35,7 +35,7 @@ link-citations: true
     padding:10px;
   }
 }
-/* zero margin around pre blocks (looks more like R console output) */
+/* Zero margin around pre blocks (looks more like R console output) */
 pre {
   margin-top: 0;
   margin-bottom: 0;
@@ -58,11 +58,14 @@ function ToggleDiv(ID) {
 </script>
 
 ```{r setup, include=FALSE}
-## use pngquant to optimize PNG images
+## Use pngquant to optimize PNG images
 library(knitr)
 knit_hooks$set(pngquant = hook_pngquant)
 pngquant <- "--speed=1 --quality=0-25"
 if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL
+
+## Set dpi 20231129
+dpi <- 72
 ```
 
 ```{r CHNOSZ_reset, include=FALSE}
@@ -196,7 +199,7 @@ Press the button to show all of the code for making the figure.
 <div id="D-AAplot" style="display: none">
 ```{r AAplot, eval = FALSE}
 showtime <- function(st) {
-  # plot time in lower-right of figure region
+  # Plot time in lower-right of figure region
   f <- usrfig()
   par(xpd=TRUE)
   if(st[3] > 2) col <- "red" else col <- "black"
@@ -206,7 +209,7 @@ showtime <- function(st) {
 
 layout(t(matrix(c(1:7, 11, 8:10, 12), nrow=4)), widths=c(1, 4, 4, 4), heights=c(0.7, 4, 4))
 
-## row 0 (column titles)
+## Row 0 (column titles)
 opar <- par(mar=c(0, 0, 0, 0))
 plot.new()
 plot.new()
@@ -217,57 +220,57 @@ plot.new()
 text(0.58, 0.5, "equilibration", cex=1.4)
 par(opar)
 
-## row 1 (balance = 1)
+## Row 1 (balance = 1)
 opar <- par(mar=c(0, 0, 0, 0))
 plot.new()
 text(0.5, 0.5, "balance = 1", srt=90, cex=1.4)
 par(opar)
-# figure A
+# Figure A
 st <- system.time(dA <- aaA())
 showtime(st)
 title(main="loga(species) = -3", cex.main=1)
 label.figure("A", yfrac=0.92, xfrac=0.1, font = 2)
-# figure B
+# Figure B
 st <- system.time(dB <- aaB())
 showtime(st)
 title(main=paste("loga(total species) =", round(dB$loga.balance[1], 2)), cex.main=1)
 label.figure("C", yfrac=0.92, xfrac=0.1, font = 2)
 
-## row 2 (balance = nCO2)
+## Row 2 (balance = nCO2)
 opar <- par(mar=c(0, 0, 0, 0))
 plot.new()
 text(0.5, 0.5, 'balance = "CO2"', srt=90, cex=1.4)
 par(opar)
-# figure C
+# Figure C
 st <- system.time(dC <- aaC())
 showtime(st)
 title(main="loga(species) = -3", cex.main=1)
 label.figure("B", yfrac=0.92, xfrac=0.1, font = 2)
-# figure D
+# Figure D
 st <- system.time(dD <- aaD())
 showtime(st)
 title(main=paste("loga(total CO2) =", round(dD$loga.balance[1], 2)), cex.main=1)
 label.figure("D", yfrac=0.92, xfrac=0.1, font = 2)
 
-## right (speciation at different total activity of CO2)
+## Right column (speciation at different total activity of CO2)
 par(xpd=NA)
 lines(c(-66, -64.5), c(4, 9), lty=2)
 lines(c(-66, -64.5), c(-8, -8.5), lty=2)
 par(xpd=FALSE)
-# figure E
+# Figure E
 st <- system.time(dE <- aaE())
 showtime(st)
 title(main=paste("loga(total CO2) =", round(dE$loga.balance[1], 2)), cex.main=1)
 label.figure("E", yfrac=0.92, xfrac=0.1, font = 2)
-# figure F
+# Figure F
 st <- system.time(dF <- aaF())
 showtime(st)
 title(main=paste("loga(total CO2) =", round(dF$loga.balance[1], 2)), cex.main=1)
 label.figure("F", yfrac=0.92, xfrac=0.1, font = 2)
 ```
 </div>
 
-```{r AAplot, echo = FALSE, results = "hide", message = FALSE, fig.width = 13/2, fig.height = 8.7/2, out.width = "100%", pngquant = pngquant}
+```{r AAplot, echo = FALSE, results = "hide", message = FALSE, fig.width = 13/2, fig.height = 8.7/2, out.width = "100%", pngquant = pngquant, dpi = dpi}
 ```
 
 Diagrams **A** and **B** use the *maximum affinity method*, where the reference
@@ -367,10 +370,10 @@ prF <- function() {
 ```
 </div>
 
-```{r PRplot, echo = FALSE, results = "hide", message = FALSE, fig.width = 13/2, fig.height = 8.7/2, out.width = "100%", pngquant = pngquant}
+```{r PRplot, echo = FALSE, results = "hide", message = FALSE, fig.width = 13/2, fig.height = 8.7/2, out.width = "100%", pngquant = pngquant, dpi = dpi}
 layout(t(matrix(1:12, nrow=4)), widths=c(1, 4, 4, 4), heights=c(0.7, 4, 4))
 
-## row 0 (column titles)
+## Row 0 (column titles)
 opar <- par(mar=c(0, 0, 0, 0))
 plot.new()
 plot.new()
@@ -381,38 +384,38 @@ plot.new()
 text(0.58, 0.5, "as.residue = TRUE\n(balance = 1)", cex=1.4)
 par(opar)
 
-## row 1 (maximum affinity 2D)
+## Row 1 (maximum affinity 2D)
 opar <- par(mar=c(0, 0, 0, 0))
 plot.new()
 text(0.5, 0.5, "maximum affinity", srt=90, cex=1.4)
 par(opar)
-# figure A (balance = "length")
+# Figure A (balance = "length")
 st <- system.time(dA <- prA())
 showtime(st)
 label.figure("A", yfrac=0.9, xfrac=0.1, font = 2)
-# figure C (normalize = TRUE)
+# Figure C (normalize = TRUE)
 st <- system.time(dC <- prC())
 showtime(st)
 label.figure("C", yfrac=0.9, xfrac=0.1, font = 2)
-# figure E (as.residue = TRUE)
+# Figure E (as.residue = TRUE)
 st <- system.time(dE <- prE())
 showtime(st)
 label.figure("E", yfrac=0.9, xfrac=0.1, font = 2)
 
-## row 2 (equilibrate 1D)
+## Row 2 (equilibrate 1D)
 opar <- par(mar=c(0, 0, 0, 0))
 plot.new()
 text(0.5, 0.5, "equilibration", srt=90, cex=1.4)
 par(opar)
-# figure B (balance = "length")
+# Figure B (balance = "length")
 st <- system.time(prB())
 showtime(st)
 label.figure("B", yfrac=0.9, xfrac=0.1, font = 2)
-# figure D (normalize = TRUE)
+# Figure D (normalize = TRUE)
 st <- system.time(prD())
 showtime(st)
 label.figure("D", yfrac=0.9, xfrac=0.1, font = 2)
-# figure F (as.residue = TRUE)
+# Figure F (as.residue = TRUE)
 st <- system.time(prF())
 showtime(st)
 label.figure("F", yfrac=0.9, xfrac=0.1, font = 2)
@@ -446,11 +449,11 @@ Here is another figure showing the effects of normalization.
 This is like Figure 5 of @Dic08, extended to more extreme conditions.
 If you wish to reproduce the diagram from the 2008 paper more closely, uncomment the `add.OBIGT()` command.
 
-```{r ProteinSpeciation, results = "hide", message = FALSE, fig.width = 8, fig.height = 5.5, out.width = "100%", pngquant = pngquant}
+```{r ProteinSpeciation, results = "hide", message = FALSE, fig.width = 8, fig.height = 5.5, out.width = "100%", pngquant = pngquant, dpi = dpi}
 organisms <- c("METSC", "METJA", "METFE",  "METVO", "METBU",
                "HALJP", "ACEKI", "GEOSE", "BACLI", "AERSA")
 proteins <- c(rep("CSG", 6), rep("SLAP", 4))
-# use red for Methano* genera
+# Use red for Methano* genera
 col <- c(rep(2, 5), rep(1, 5))
 basis("CHNOS+")
 species(proteins, organisms)