In jedick/JMDplots: Plots from Papers by Jeffrey M. Dick

library(knitr)
## use pngquant to reduce size of PNG images
knit_hooks$set(pngquant = hook_pngquant)
pngquant <- "--speed=1 --quality=0-25"
# in case pngquant isn't available
if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL 

This vignette runs the code to make most of the supplementary figures from the following paper:

Dick JM. 2019. CHNOSZ: Thermodynamic calculations and diagrams for geochemistry. Frontiers in Earth Science 7: 180. doi: 10.3389/feart.2019.00180

This vignette was compiled on r Sys.Date() with JMDplots r packageDescription("JMDplots")$Version and CHNOSZ r packageDescription("CHNOSZ")$Version.

library(JMDplots)

Comparison of logK and maximum affinity methods (Figure S1)

chnosz10S1()

Eh-pH diagram like Fig. 5A of Caporuscio et al. (2017) (Figure S2)

chnosz10S2()

Gibbs energy of transformation for an assemblage of n-alkanes (Figure S3)

chnosz10S3()

findit() calculations for sulfur species (Figure S4)

This feature and figure were removed in CHNOSZ 2.0.0 and JMDplots 1.2.17, respectively. Please refer to earlier versions of the packages.

Debye-Hückel extended term parameter extrapolated from plots of Manning et al. (2013) (Figure S5)

chnosz10S5()

Figure 6 modified to exclude DEW data for acetate (Figure S6A)

chnosz10S6A()

Figure S6A modified to use default bgamma equation (Figure S6B)

chnosz10S6B()

logK of NaCl dissociation (Figure S7)

chnosz10S7()

Calcite solubility: comparison with Manning et al. (2013) (Figure S8)

chnosz10S8()

Compare gold solubility in HCh and CHNOSZ: hematite-magnetite buffer (Figure S9)

chnosz10S9()

Compare gold solubility in HCh and CHNOSZ: pyrite-pyrrhotite-magnetite buffer (Figure S10)

chnosz10S10()

jedick/JMDplots documentation built on April 12, 2025, 1:35 p.m.