[CHNOSZ-commits] r815 - in pkg/CHNOSZ: . inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 29 02:16:06 CET 2023
Author: jedick
Date: 2023-11-29 02:16:06 +0100 (Wed, 29 Nov 2023)
New Revision: 815
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/vignettes/FAQ.Rmd
pkg/CHNOSZ/vignettes/custom_data.Rmd
pkg/CHNOSZ/vignettes/equilibrium.Rmd
pkg/CHNOSZ/vignettes/multi-metal.Rmd
Log:
Set dpi in vignettes to reduce package size
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2023-11-28 12:25:23 UTC (rev 814)
+++ pkg/CHNOSZ/DESCRIPTION 2023-11-29 01:16:06 UTC (rev 815)
@@ -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 at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2023-11-28 12:25:23 UTC (rev 814)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2023-11-29 01:16:06 UTC (rev 815)
@@ -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{Δ<I>G</I>°}}{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?
}
Modified: pkg/CHNOSZ/vignettes/FAQ.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/FAQ.Rmd 2023-11-28 12:25:23 UTC (rev 814)
+++ pkg/CHNOSZ/vignettes/FAQ.Rmd 2023-11-29 01:16:06 UTC (rev 815)
@@ -135,6 +135,8 @@
'</div>', sep = '\n')
}
)
+# Set dpi 20231129
+dpi <- 72
```
```{r echo = F, cache = F}
@@ -207,7 +209,7 @@
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 @@
* 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 @@
* 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 @@
```
</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 @@
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 @@
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 @@
**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 @@
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 @@
```{r KMQ_diagram, eval = FALSE, echo = 10:14}
```
-*Answered on 2023-11-28.*
+*Added on 2023-11-28.*
## References
Modified: pkg/CHNOSZ/vignettes/custom_data.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/custom_data.Rmd 2023-11-28 12:25:23 UTC (rev 814)
+++ pkg/CHNOSZ/vignettes/custom_data.Rmd 2023-11-29 01:16:06 UTC (rev 815)
@@ -22,6 +22,9 @@
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 @@
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 @@
```
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)
Modified: pkg/CHNOSZ/vignettes/equilibrium.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.Rmd 2023-11-28 12:25:23 UTC (rev 814)
+++ pkg/CHNOSZ/vignettes/equilibrium.Rmd 2023-11-29 01:16:06 UTC (rev 815)
@@ -35,7 +35,7 @@
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 @@
</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 @@
<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 @@
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()
@@ -217,49 +220,49 @@
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)
@@ -267,7 +270,7 @@
```
</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 @@
```
</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 @@
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 @@
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)
Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd 2023-11-28 12:25:23 UTC (rev 814)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd 2023-11-29 01:16:06 UTC (rev 815)
@@ -64,8 +64,6 @@
knit_hooks$set(pngquant = hook_pngquant)
pngquant <- "--speed=1 --quality=0-25"
if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL
-## logK with a thin space 20200627
-logK <- "log <i>K</i>"
## Resolution settings
# Change this to TRUE to make high-resolution plots
@@ -77,6 +75,12 @@
res2.lo <- 200
res2.hi <- 400
res2 <- ifelse(hires, res2.hi, res2.lo)
+
+## Set dpi 20231129
+dpi <- 72
+
+## logK with a thin space 20200627
+logK <- "log <i>K</i>"
```
```{r CHNOSZ_reset, include=FALSE}
@@ -138,7 +142,7 @@
The second diagram is just like the first, except the function `mash()` is used to label the fields with names of species from both systems, and a legend is added to indicate the temperature and pressure.
-```{r mash, echo = 9:14, results = "hide", message = FALSE, fig.width = 10, fig.height = 5, out.width = "100%"}
+```{r mash, echo = 9:14, results = "hide", message = FALSE, fig.width = 10, fig.height = 5, out.width = "100%", dpi = dpi}
```
Note that these are predominance diagrams, so they show only the species with highest activity; there is in fact a distribution of activities of aqueous species that is not visible here.
@@ -313,7 +317,7 @@
Finally, the `diagram()`s are plotted; the `min.area` argument is used to remove labels for very small fields.
Regarding the legend, it should be noted that although the DFT calculations for solids are made for zero temperature and zero pressure [@SZS_17], the standard Gibbs energies of aqueous species [e.g. @WEP_82] are modified by a correction term so that they can be combined with DFT energies to reproduce the experimental energy for dissolution of a representative material for each metal at 25 °C and 1 bar [@PWLC12].
-```{r mixing1, echo = 16:47, message = FALSE, results = "hide", fig.width = 9, fig.height = 3, out.width = "100%", out.extra='class="full-width"', pngquant = pngquant}
+```{r mixing1, echo = 16:47, message = FALSE, results = "hide", fig.width = 9, fig.height = 3, out.width = "100%", out.extra='class="full-width"', pngquant = pngquant, dpi = dpi}
```
In these diagrams, changing the Fe:V ratio affects the fully reduced metallic species.
@@ -401,7 +405,7 @@
This is plotted as a color map in the second diagram.
(See the source of this vignette for the code used to make the scale bar.)
-```{r FeVO4, echo = 31:44, message = FALSE, results = "hide", fig.width = 11, fig.height = 5, out.width = "100%", pngquant = FALSE}
+```{r FeVO4, echo = 31:44, message = FALSE, results = "hide", fig.width = 11, fig.height = 5, out.width = "100%", pngquant = pngquant, dpi = dpi}
```
Now we locate the pH and Eh that maximize the affinity (that is, minimize Δ*G*~pbx~) of FeVO~4~ compared to the stable species.
@@ -512,7 +516,7 @@
After that we add the legend and title.
-```{r stack1_2, echo=5:17, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "75%", fig.align = "center", pngquant = pngquant}
+```{r stack1_2, echo=5:17, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "75%", fig.align = "center", pngquant = pngquant, dpi = dpi}
```
This diagram has a distinctive chalcopyrite "hook" surrounded by a thin bornite field.
@@ -638,7 +642,7 @@
```
</div>
-```{r stack2, echo = FALSE, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "75%", fig.align = "center", pngquant = pngquant}
+```{r stack2, echo = FALSE, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "75%", fig.align = "center", pngquant = pngquant, dpi = dpi}
```
After running the code to make this diagram, we can list the reference keys for the minerals and aqueous species.
@@ -729,7 +733,7 @@
```
</div>
-```{r mixing2, echo = FALSE, results = "hide", message = FALSE, fig.width = 8, fig.height = 6.5, out.width = "100%", pngquant = pngquant}
+```{r mixing2, echo = FALSE, results = "hide", message = FALSE, fig.width = 8, fig.height = 6.5, out.width = "100%", pngquant = pngquant, dpi = dpi}
```
These diagrams show that changing the amounts of the metals affects the stability of minerals involved in reactions with chalcopyrite.
@@ -793,7 +797,7 @@
```
</div>
-```{r stack3, echo = FALSE, results = "hide", message = FALSE, fig.width = 6, fig.height = 4, out.width = "100%", pngquant = pngquant}
+```{r stack3, echo = FALSE, results = "hide", message = FALSE, fig.width = 6, fig.height = 4, out.width = "100%", pngquant = pngquant, dpi = dpi}
```
The resulting diagram is similar to Figure 2 of @Sve87; that diagram also shows calculations of the solubility of Cu and concentration of SO~4~^-2^ in model Cu ore-forming fluids.
@@ -876,7 +880,7 @@
```
</div>
-```{r solubility, echo = FALSE, results = "hide", message = FALSE, fig.width = 7, fig.height = 3, out.width = "100%", fig.align = "center", pngquant = pngquant}
+```{r solubility, echo = FALSE, results = "hide", message = FALSE, fig.width = 7, fig.height = 3, out.width = "100%", fig.align = "center", pngquant = pngquant, dpi = dpi}
```
After running the code above, we can inspect the value of `calc` to show the estimated ionic strength and activity of Cl^-^; the latter is very close to unity.
@@ -1007,7 +1011,7 @@
```{r rebalance, eval = FALSE, echo = 36:49}
```
-```{r rebalance, echo = FALSE, results = "hide", message = FALSE, fig.width = 6.5, fig.height = 5, out.width = "100%", fig.align = "center", pngquant = pngquant}
+```{r rebalance, echo = FALSE, results = "hide", message = FALSE, fig.width = 6.5, fig.height = 5, out.width = "100%", fig.align = "center", pngquant = pngquant, dpi = dpi}
```
The final diagram is like one shown in Figure 5 of @Bri80 and Figure 5 of @MH85.
@@ -1027,7 +1031,7 @@
The reactions are balanced on O~2~, which means that no O~2~ appears in the reaction between any two minerals, but Fe^+2^ and/or Cu^+^ can be present, depending on the chemical composition.
Saturation limits are shown for species that have no O~2~ in their formation reactions.
-```{r non-metal, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "80%", fig.align = "center", pngquant = pngquant}
+```{r non-metal, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "80%", fig.align = "center", pngquant = pngquant, dpi = dpi}
basis(c("Fe+2", "Cu+", "hydrogen sulfide", "oxygen", "H2O", "H+"))
basis("H2S", 2)
species(c("pyrite", "magnetite", "hematite", "covellite", "tenorite",
@@ -1142,7 +1146,7 @@
```
</div>
-```{r mosaic-combo, echo = FALSE, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "80%", fig.align = "center", pngquant = pngquant}
+```{r mosaic-combo, echo = FALSE, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "80%", fig.align = "center", pngquant = pngquant, dpi = dpi}
```
The diagram shows the ionization of acetic acid and NH~3~ at different pHs.
More information about the CHNOSZ-commits
mailing list