[CHNOSZ-commits] r718 - in pkg/CHNOSZ: . inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 6 16:12:40 CEST 2022
Author: jedick
Date: 2022-04-06 16:12:40 +0200 (Wed, 06 Apr 2022)
New Revision: 718
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/vignettes/OBIGT.Rmd
pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
Revise CH4 disclaimer in OBIGT.Rmd
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2022-04-06 06:25:32 UTC (rev 717)
+++ pkg/CHNOSZ/DESCRIPTION 2022-04-06 14:12:40 UTC (rev 718)
@@ -1,6 +1,6 @@
Date: 2022-04-06
Package: CHNOSZ
-Version: 1.9.9-10
+Version: 1.9.9-11
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 2022-04-06 06:25:32 UTC (rev 717)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2022-04-06 14:12:40 UTC (rev 718)
@@ -32,24 +32,19 @@
\itemize{
\item Add the following \emph{Disclaimer} to the Aqueous Inorganic
- section of \strong{OBIGT.Rmd}: The maintenance of separate data files for
- inorganic and organic species is done only for convenience, and is not
- meant to imply a preference for any substrate, mechanism, or process. In
- particular, CH\s{4} (methane) is an organic compound that can also be
- formed abiotically (\href{https://doi.org/10.1002/rog.20011}{Etiope and
- Sherwood Lollar, 2013}). The words \emph{organic} and \emph{inorganic}
- (for substrates), \emph{biological} and \emph{thermochemical} (for
- mechanisms), and \emph{methanogenesis}, \emph{pyrolysis}, and
- \emph{synthesis} (for processes) can be used to describe different
- methane-generating pathways in nature
- (\href{https://doi.org/10.1007/978-3-319-39312-4_166}{Strąpoć, 2018}).
- The details of this classification system are out of scope for the OBIGT
- database. For practical reasons, CH\s{4} is placed in the
- \dQuote{inorganic} data files in OBIGT simply so that the database can be
- pruned of organic compounds \emph{except} CH\s{4} by running
- \code{OBIGT(no.organics = TRUE)}. The ability to remove hundreds of
- less-common organic species while keeping CH\s{4} is useful for some
- models of inorganic reactions in hydrothermal systems.
+ section of \strong{OBIGT.Rmd}: A choice has been made to put inorganic
+ and organic species into separate data files. There is a well-known
+ ambiguity owing to the slightly different usage of these \emph{-ic} words
+ in different fields. That is, while CH\s{4} (methane) is classified in
+ chemistry as an organic compound, in nature it can be derived from living
+ organisms or formed abiotically
+ (\href{https://doi.org/10.1002/rog.20011}{Etiope and Sherwood Lollar,
+ 2013}) – that is, through inorganic processes. For practical reasons,
+ CH\s{4} is placed in the \dQuote{inorganic} data files in OBIGT simply so
+ that the database can be pruned of organic compounds \emph{except}
+ CH\s{4} by running \code{OBIGT(no.organics = TRUE)}. The ability to
+ remove hundreds of more complex organic compounds while keeping CH\s{4}
+ is useful for some models of inorganic reactions in hydrothermal systems.
}
}
Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2022-04-06 06:25:32 UTC (rev 717)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2022-04-06 14:12:40 UTC (rev 718)
@@ -246,12 +246,11 @@
<div id="D-aqueous-inorganic" style="display: none">
## <a id="aqueous-inorganic" class="anchor"></a> `r setfile("inorganic_aq.csv")`
-*Disclaimer*: The maintenance of separate data files for inorganic and organic species is done only for convenience, and is not meant to imply a preference for any substrate, mechanism, or process.
-In particular, CH<sub>4</sub> (methane) is an organic compound that can also be formed abiotically [@ES13].
-The words *organic* and *inorganic* (for substrates), *biological* and *thermochemical* (for mechanisms), and *biogenic*, *abiogenic*, and *pyrolytic* (for processes) can be used to describe different methane-generating pathways in nature [@Str18].
-The details of this classification system are out of scope for the OBIGT database.
+*Disclaimer*: A choice has been made to put inorganic and organic species into separate data files.
+There is a well-known ambiguity owing to the slightly different usage of these *-ic* words in different fields.
+That is, while CH<sub>4</sub> (methane) is classified in chemistry as an organic compound, in nature it can be derived from living organisms or formed abiotically [@ES13] -- that is, through inorganic processes.
For practical reasons, CH<sub>4</sub> is placed in the "inorganic" data files in OBIGT simply so that the database can be pruned of organic compounds *except* CH<sub>4</sub> by running `OBIGT(no.organics = TRUE)`.
-The ability to remove hundreds of less-common organic species while keeping CH<sub>4</sub> is useful for some models of inorganic reactions in hydrothermal systems.
+The ability to remove hundreds of more complex organic compounds while keeping CH<sub>4</sub> is useful for some models of inorganic reactions in hydrothermal systems.
```{r reflist, results="asis", echo=FALSE}
```
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2022-04-06 06:25:32 UTC (rev 717)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2022-04-06 14:12:40 UTC (rev 718)
@@ -1777,15 +1777,3 @@
volume = {51},
doi = {10.1002/rog.20011},
}
-
- at InBook{Str18,
- author = {Str{\k{a}}po{\'{c}}, Dariusz},
- editor = {White, William M.},
- pages = {100--107},
- publisher = {Springer International Publishing},
- title = {Biogenic Methane},
- year = {2018},
- address = {Cham},
- booktitle = {Encyclopedia of Geochemistry},
- doi = {10.1007/978-3-319-39312-4_166},
-}
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