Use environment variable to control vignette size

git-svn-id: svn://scm.r-forge.r-project.org/svnroot/chnosz/pkg/CHNOSZ@818 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

DESCRIPTION

@@ -1,6 +1,6 @@
 Date: 2023-11-29
 Package: CHNOSZ
-Version: 2.0.0-37
+Version: 2.0.0-38
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

inst/CHECKLIST

@@ -1,6 +1,6 @@
 ****************************
 Release checklist for CHNOSZ
-    (updated 2023-03-10)
+    (updated 2023-11-29)
 ****************************
 
 - Run examples() and demos() and inspect their output (especially plots)
@@ -73,11 +73,9 @@ exit_file("Skipping tests so development builds on R-Forge work")
 Making vignettes for website (https://chnosz.net)
 *************************************************
 
-- Use dpi <- 72 in anintro.Rmd
+- Build package after setting CHNOSZ_BUILD_LARGE_VIGNETTES environment variable.
 
-- Use hires <- TRUE in multi-metal.Rmd
-
-- After making vignettes, run doc/mklinks.sh in installed directory
+- Install the package and run doc/mklinks.sh within the installation directory.
   (this adds links to the HTML renditions of Rd files)
 
 ***************

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 2.0.0-36 (2023-11-29)}{
+\section{Changes in CHNOSZ version 2.0.0-38 (2023-11-29)}{
 
     \itemize{
 
@@ -74,6 +74,11 @@
       vaporization, or decomposition). The temperature limit for \Cp equations
       is stored as the opposite (negative) value in OBIGT. See \viglink{FAQ}
       for details.
+
+      \item The environment variable CHNOSZ_BUILD_LARGE_VIGNETTES is used to
+      control `dpi` in knitr chunk options. Setting this variable results in
+      larger vignettes (used for the CHNOSZ website); if this variable is unset
+      (as on CRAN), a smaller package is built.
 
     }
 

vignettes/FAQ.Rmd

@@ -135,8 +135,11 @@ knitr::knit_hooks$set(
            '</div>', sep = '\n')
    }
 )
+
 # Set dpi 20231129
-dpi <- 72
+knitr::opts_chunk$set(
+  dpi = if(nzchar(Sys.getenv("CHNOSZ_BUILD_LARGE_VIGNETTES"))) 100 else 72
+)
 ```
 
 ```{r echo = F, cache = F}
@@ -333,7 +336,7 @@ 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, dpi = dpi}
+```{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}
 ```
 
 *Added on 2023-05-17.*
@@ -495,7 +498,7 @@ 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, dpi = dpi}
+```{r pyrrhotite_T, echo = FALSE, message = FALSE, results = "hide", fig.width = 8, fig.height = 2.5, out.width = "100%", fig.align = "center", pngquant = pngquant}
 ```
 
 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.
@@ -673,7 +676,7 @@ 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, dpi = dpi}
+```{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}
 ```
 
 *Added on 2023-09-08.*
@@ -802,7 +805,7 @@ 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, out.width = "100%", results = "hide", echo = FALSE, dpi = dpi}
+```{r KMQ_diagram, message = FALSE, fig.width = 8, fig.height = 4, out.width = "100%", results = "hide", echo = FALSE}
 ```
 
 The gray area, which is automatically drawn by `diagram()`, is below the reducing stability limit of water; that is, this area is where the equilibrium fugacity of `r H2` exceeds unity.

vignettes/custom_data.Rmd

@@ -23,8 +23,10 @@ knit_hooks$set(pngquant = hook_pngquant)
 pngquant <- "--speed=1 --quality=0-25"
 if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL
 
-## Set dpi 20231129
-dpi <- 72
+# Set dpi 20231129
+knitr::opts_chunk$set(
+  dpi = if(nzchar(Sys.getenv("CHNOSZ_BUILD_LARGE_VIGNETTES"))) 100 else 72
+)
 ```
 
 ```{r HTML, include = FALSE}
@@ -513,7 +515,7 @@ 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, dpi = dpi}
+```{r diagram1, message = FALSE, results = "hide", fig.width = 6, fig.height = 5, out.width = "75%", fig.align = "center", pngquant = pngquant}
 basis(c("H+", "WO4-2", "F-", "H2O", "O2"))
 basis("F-", log10(0.1))
 iaq <- retrieve("W", c("O", "H", "F"), "aq")
@@ -542,7 +544,7 @@ 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, dpi = dpi}
+```{r diagram2, message = FALSE, results = "hide", results = "hide", fig.width = 6, fig.height = 5, out.width = "75%", fig.align = "center", pngquant = pngquant}
 basis(c("H+", "WO4-2", "F-", "H2O", "O2"))
 iaq <- retrieve("W", c("O", "H", "F"), "aq")
 species(iaq)

vignettes/eos-regress.Rmd

@@ -79,11 +79,8 @@ knit_hooks$set(pngquant = hook_pngquant)
 # pngquant isn't available on R-Forge ...
 if (!nzchar(Sys.which("pngquant"))) {
   pngquant <- NULL 
-  # Save space by using a lower resolution
-  dpi <- 50
 } else {
   pngquant <- "--speed=1 --quality=0-50"
-  dpi <- 72
 }
 
 ## Colorize messages 20171031
@@ -92,6 +89,11 @@ color_block = function(color) {
   function(x, options) sprintf('<pre style="color:%s">%s</pre>', color, x)
 }
 knit_hooks$set(warning = color_block('magenta'), error = color_block('red'), message = color_block('blue'))
+
+# Set dpi 20231129
+knitr::opts_chunk$set(
+  dpi = if(nzchar(Sys.getenv("CHNOSZ_BUILD_LARGE_VIGNETTES"))) 72 else 50
+)
 ```
 
 
@@ -159,7 +161,7 @@ Cplm_low <- EOSregress(Cpdat, var, T.max = 600)
 Cplm_low$coefficients
 ```
 
-```{r EOSplot, fig.margin = TRUE, fig.cap = "Heat capacity of aqueous methane.", fig.width=3.5, fig.height=3.5, cache=TRUE, results="hide", message=FALSE, echo=FALSE, dpi=dpi, out.width=672, out.height=336, pngquant=pngquant}
+```{r EOSplot, fig.margin = TRUE, fig.cap = "Heat capacity of aqueous methane.", fig.width=3.5, fig.height=3.5, cache=TRUE, results="hide", message=FALSE, echo=FALSE, out.width=672, out.height=336, pngquant=pngquant}
 EOSplot(Cpdat, coefficients = round(Cplm_low$coefficients, 1))
 EOSplot(Cpdat, coeficients = Cplm_high, add = TRUE, lty = 3)
 PS01_data <- convert(EOScoeffs("CH4", "Cp"), "J")
@@ -239,7 +241,7 @@ Vcoeffs <- round(c(Vnonlm$coefficients, QBorn = Vomega), 1)
 Vcoeffs_database <- convert(EOScoeffs("CH4", "V"), "J")
 ```
 
-```{r Vplot, fig.margin=TRUE, results="hide", message=FALSE, echo=FALSE, fig.width=3.5, fig.height=7, fig.cap="Volume of aqueous methane.", dpi=dpi, out.width=672, out.height=672, pngquant=pngquant}
+```{r Vplot, fig.margin=TRUE, results="hide", message=FALSE, echo=FALSE, fig.width=3.5, fig.height=7, fig.cap="Volume of aqueous methane.", out.width=672, out.height=672, pngquant=pngquant}
 par(mfrow = c(2, 1))
 # plot 1
 EOSplot(Vdat, coefficients = Vcoeffs)
@@ -278,7 +280,7 @@ Nadat <- prop.PT[, c("T", "P", "Cp")]
 As noted above, &omega; for electrolytes is not a constant.
 What happens if we apply the constant-&omega; model anyway, knowing it's not applicable (especially at high temperature)?
 
-```{r Nalm, fig.margin=TRUE, fig.width=3.5, fig.height=3.5, fig.cap="Heat capacity of Na<sup>+</sup> (inapplicable: constant &omega;).", dpi=dpi, out.width=672, out.height=336, pngquant=pngquant}
+```{r Nalm, fig.margin=TRUE, fig.width=3.5, fig.height=3.5, fig.cap="Heat capacity of Na<sup>+</sup> (inapplicable: constant &omega;).", out.width=672, out.height=336, pngquant=pngquant}
 var <- c("invTTheta2", "TXBorn")
 Nalm <- EOSregress(Nadat, var, T.max = 600)
 EOSplot(Nadat, coefficients = Nalm$coefficients, fun.legend = NULL)
@@ -302,7 +304,7 @@ omega.guess <- coef(Nalm)[3]
 Then, we can use an iterative procedure that refines successive guesses of `r wPrTr`.
 The convergence criterion is measured by the difference in sequential regressed values of &omega;.
 
-```{r Nawhile, fig.margin=TRUE, fig.width=3.5, fig.height=3.5, fig.cap="Heat capacity of Na<sup>+</sup> (variable &omega;).", dpi=dpi, out.width=672, out.height=336, pngquant=pngquant}
+```{r Nawhile, fig.margin=TRUE, fig.width=3.5, fig.height=3.5, fig.cap="Heat capacity of Na<sup>+</sup> (variable &omega;).", out.width=672, out.height=336, pngquant=pngquant}
 diff.omega <- 999
 while(abs(diff.omega) > 1) {
   Nalm1 <- EOSregress(Nadat, var1, omega.PrTr = tail(omega.guess, 1), Z = 1)
@@ -324,7 +326,7 @@ Note that the regressed value of &omega; has volumetric units (cm<sup>3</sup> ba
 Compared to `r Cp0`, the regression of `r V0` is very finicky.
 Given a starting guess of `r wPrTr` of 1400000 cm<sup>3</sup> bar/mol, the iteration converges on 1394890 instead of the "true" database value of 1383230 (represented by dashed line in the plot).
 
-```{r NaVolume, fig.margin=TRUE, fig.width=3.5, fig.height=3.5, fig.cap="Volume of Na<sup>+</sup> (variable &omega;).", results="hide", message=FALSE, echo=FALSE, dpi=dpi, out.width=672, out.height=336, pngquant=pngquant}
+```{r NaVolume, fig.margin=TRUE, fig.width=3.5, fig.height=3.5, fig.cap="Volume of Na<sup>+</sup> (variable &omega;).", results="hide", message=FALSE, echo=FALSE, out.width=672, out.height=336, pngquant=pngquant}
 T <- convert(seq(0, 600, 25), "K")
 P <- 1000
 prop.PT <- subcrt("Na+", T = T, P = P, grid = "T", convert = FALSE)$out[[1]]
@@ -429,7 +431,7 @@ info(info(c("calc-H4SiO4", "H4SiO4")))
 ```{r width80, include=FALSE}
 ```
 
-```{r subcrt_H4SiO4, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, echo=FALSE, results="hide", message=FALSE, dpi=dpi, out.width="100%", cache=TRUE, fig.cap="Comparison of H<sub>4</sub>SiO<sub>4</sub> pseudospecies.", pngquant=pngquant}
+```{r subcrt_H4SiO4, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, echo=FALSE, results="hide", message=FALSE, out.width="100%", cache=TRUE, fig.cap="Comparison of H<sub>4</sub>SiO<sub>4</sub> pseudospecies.", pngquant=pngquant}
 s1 <- subcrt(c("calc-H4SiO4", "SiO2", "H2O"), c(-1, 1, 2))
 plot(s1$out$T, s1$out$G, type = "l", ylim = c(-500, 2000),
   xlab = axis.label("T"), ylab = axis.label("DG0"))
@@ -453,7 +455,7 @@ For example, the almost 800 J/mol offset in &Delta;<i>G</i>&deg; at 350 &deg;C c
 The following example uses the `H4SiO4` from Stef&aacute;nsson (2001) to make an activity diagram for the K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O system.
 This is similar to the diagram on p. 361 of [Garrels and Christ, 1965](https://www.worldcat.org/oclc/517586), but is quantitatively a closer match to the diagram in the [User's Guide to PHREEQC](https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/html/final-75.html).
 
-```{r activity_diagram, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, echo=TRUE, results="hide", message=FALSE, dpi=dpi, out.width="100%", cache=TRUE, fig.cap="Activity diagram for K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O.", pngquant=pngquant}
+```{r activity_diagram, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, echo=TRUE, results="hide", message=FALSE, out.width="100%", cache=TRUE, fig.cap="Activity diagram for K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O.", pngquant=pngquant}
 basis(c("Al+3", "H4SiO4", "K+", "H2O", "H+", "O2"))
 species(c("gibbsite", "muscovite", "kaolinite", "pyrophyllite", "K-feldspar"))
 a <- affinity(H4SiO4 = c(-8, 0, 300), `K+` = c(-1, 8, 300))

vignettes/equilibrium.Rmd

@@ -64,8 +64,10 @@ knit_hooks$set(pngquant = hook_pngquant)
 pngquant <- "--speed=1 --quality=0-25"
 if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL
 
-## Set dpi 20231129
-dpi <- 72
+# Set dpi 20231129
+knitr::opts_chunk$set(
+  dpi = if(nzchar(Sys.getenv("CHNOSZ_BUILD_LARGE_VIGNETTES"))) 100 else 72
+)
 ```
 
 ```{r CHNOSZ_reset, include=FALSE}
@@ -270,7 +272,7 @@ 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, dpi = dpi}
+```{r AAplot, echo = FALSE, results = "hide", message = FALSE, fig.width = 13/2, fig.height = 8.7/2, out.width = "100%", pngquant = pngquant}
 ```
 
 Diagrams **A** and **B** use the *maximum affinity method*, where the reference
@@ -370,7 +372,7 @@ 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, dpi = dpi}
+```{r PRplot, echo = FALSE, results = "hide", message = FALSE, fig.width = 13/2, fig.height = 8.7/2, out.width = "100%", pngquant = pngquant}
 layout(t(matrix(1:12, nrow=4)), widths=c(1, 4, 4, 4), heights=c(0.7, 4, 4))
 
 ## Row 0 (column titles)
@@ -449,7 +451,7 @@ 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, dpi = dpi}
+```{r ProteinSpeciation, results = "hide", message = FALSE, fig.width = 8, fig.height = 5.5, out.width = "100%", pngquant = pngquant}
 organisms <- c("METSC", "METJA", "METFE",  "METVO", "METBU",
                "HALJP", "ACEKI", "GEOSE", "BACLI", "AERSA")
 proteins <- c(rep("CSG", 6), rep("SLAP", 4))