[CHNOSZ-commits] r891 - in pkg/CHNOSZ: . vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri May 9 03:01:47 CEST 2025
Author: jedick
Date: 2025-05-09 03:01:47 +0200 (Fri, 09 May 2025)
New Revision: 891
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/vig.bib
Log:
Remove unused entries from vig.bib
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2025-05-08 12:34:30 UTC (rev 890)
+++ pkg/CHNOSZ/DESCRIPTION 2025-05-09 01:01:47 UTC (rev 891)
@@ -1,6 +1,6 @@
-Date: 2025-05-08
+Date: 2025-05-09
Package: CHNOSZ
-Version: 2.1.0-62
+Version: 2.1.0-63
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/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2025-05-08 12:34:30 UTC (rev 890)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2025-05-09 01:01:47 UTC (rev 891)
@@ -925,7 +925,10 @@
NOTE: If `diagram()` was passed the output of `equilibrate()` or `solubility()`, then its output contains logarithms of activities instead of dimensionless affinities.
-### 17. Count elements with <span style="color:green;font-family:monospace;">makeup()</span> and sum and write chemical formulas
+### 17. Writing chemical formulas and counting and summing elements with <span style="color:green;font-family:monospace;">makeup()</span>
+
+`makeup()` is used internally by some functions in CHNOSZ but is also available for the user.
+
### 18. A brief introduction to proteins and groupwise relative stabilities
### 19: Accessing and changing settings with <span style="color:red;font-family:monospace;">thermo()</span>
@@ -1288,7 +1291,7 @@
- 2010-09-30 First version, titled "Getting started with CHNOSZ".
- 2017-02-15 Rewritten and switched from Sweave to [knitr](https://yihui.org/knitr/).
-- 2025-04-07 Revised with AI assistance (mostly in [Basic Functionality](#basic-functionality) and [Buffers](#buffers)).
+- 2025-04-07 Reworked entire vignette; used AI assistance for [Basic Functionality](#basic-functionality) and [Buffers](#buffers).
<p>
```{r the_end}
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2025-05-08 12:34:30 UTC (rev 890)
+++ pkg/CHNOSZ/vignettes/vig.bib 2025-05-09 01:01:47 UTC (rev 891)
@@ -17,17 +17,6 @@
url = {https://search.worldcat.org/title/51242181},
}
- at Article{AH00,
- author = {Amend, Jan P. and Helgeson, Harold C.},
- journal = {Biophysical Chemistry},
- title = {{C}alculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. {II}. {U}nfolded proteins},
- year = {2000},
- volume = {84},
- number = {2},
- pages = {105--136},
- doi = {10.1016/S0301-4622(00)00116-2},
-}
-
@Book{AC93,
author = {Anderson, Greg M. and Crerar, David A.},
publisher = {Oxford University Press},
@@ -48,16 +37,6 @@
doi = {10.1134/S1075701510020054},
}
- at Book{BJH84,
- author = {Bowers, Teresa S. and Jackson, Kenneth J. and Helgeson, Harold C.},
- publisher = {Springer-Verlag},
- title = {{E}quilibrium {A}ctivity {D}iagrams for {C}oexisting {M}inerals and {A}queous {S}olutions at {P}ressures and {T}emperatures to 5 kb and 600°{C}},
- year = {1984},
- address = {Heidelberg},
- doi = {10.1007/978-3-642-46511-6},
- pages = {397},
-}
-
@Article{CBLM00,
author = {Cooke, David R. and Bull, Stuart W. and Large, Ross R. and McGoldrick, Peter J.},
journal = {Economic Geology},
@@ -80,26 +59,6 @@
doi = {10.1186/1467-4866-9-10},
}
- at Article{Dic09,
- author = {Dick, Jeffrey M.},
- journal = {BMC Systems Biology},
- title = {Calculation of the relative metastabilities of proteins in subcellular compartments of \emph{{S}accharomyces cerevisiae}},
- year = {2009},
- pages = {75},
- volume = {3},
- doi = {10.1186/1752-0509-3-75},
-}
-
- at Article{Dic14,
- author = {Dick, Jeffrey M.},
- journal = {Journal of the Royal Society, Interface},
- title = {Average oxidation state of carbon in proteins},
- year = {2014},
- pages = {20131095},
- volume = {11},
- doi = {10.1098/rsif.2013.1095},
-}
-
@Article{DLH06,
author = {Dick, Jeffrey M. and LaRowe, Douglas E. and Helgeson, Harold C.},
journal = {Biogeosciences},
@@ -120,17 +79,6 @@
url = {https://search.worldcat.org/title/517586},
}
- at Article{GHB_03,
- author = {Ghaemmaghami, Sina and Huh, Won-Ki and Bower, Kiowa and Howson, Russell W. and Belle, Archana and Dephoure, Noah and O'Shea, Erin K. and Weissman, Jonathan S.},
- journal = {Nature},
- title = {Global analysis of protein expression in yeast},
- year = {2003},
- number = {6959},
- pages = {737--741},
- volume = {425},
- doi = {10.1038/nature02046},
-}
-
@Book{Hel64,
author = {Helgeson, Harold C.},
publisher = {Pergamon Press},
@@ -226,49 +174,6 @@
url = {https://www.worldcat.org/oclc/693388901},
}
- at Article{Kit14,
- author = {Kitadai, Norio},
- journal = {Journal of Molecular Evolution},
- title = {{T}hermodynamic prediction of glycine polymerization as a function of temperature and p{H} consistent with experimentally obtained results},
- year = {2014},
- number = {3-4},
- pages = {171--187},
- volume = {78},
- doi = {10.1007/s00239-014-9616-1},
-}
-
- at Article{LD12,
- author = {LaRowe, Douglas E. and Dick, Jeffrey M.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {Calculation of the standard molal thermodynamic properties of crystalline peptides},
- year = {2012},
- pages = {70--91},
- volume = {80},
- doi = {10.1016/j.gca.2011.11.041},
-}
-
- at Article{LH06a,
- author = {LaRowe, Douglas E. and Helgeson, Harold C.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {Biomolecules in hydrothermal systems: Calculation of the standard molal thermodynamic properties of nucleic-acid bases, nucleosides, and nucleotides at elevated temperatures and pressures},
- year = {2006},
- number = {18},
- pages = {4680--4724},
- volume = {70},
- doi = {10.1016/j.gca.2006.04.010},
-}
-
- at Article{LH06b,
- author = {LaRowe, Douglas E. and Helgeson, Harold C.},
- journal = {Thermochimica Acta},
- title = {{T}he energetics of metabolism in hydrothermal systems: {C}alculation of the standard molal thermodynamic properties of magnesium-complexed adenosine nucleotides and {NAD} and {NADP} at elevated temperatures and pressures},
- year = {2006},
- volume = {448},
- number = {2},
- pages = {82--106},
- doi = {10.1016/j.tca.2006.06.008},
-}
-
@Article{LBT_11,
author = {Liu, Weihua and Borg, Stacey J. and Testemale, Denis and Etschmann, Barbara and Hazemann, Jean-Louis and Brugger, Joel},
journal = {Geochimica et Cosmochimica Acta},
@@ -345,28 +250,6 @@
doi = {10.1126/science.1199911},
}
- at Article{PM90,
- author = {Privalov, P. L. and Makhatadze, G. I.},
- journal = {Journal of Molecular Biology},
- title = {Heat capacity of proteins. {II}. {P}artial molar heat capacity of the unfolded polypeptide chain of proteins: {P}rotein unfolding effects},
- year = {1990},
- number = {2},
- pages = {385--391},
- volume = {213},
- doi = {10.1016/S0022-2836(05)80198-6},
-}
-
- at Article{RH98,
- author = {Richard, Laurent and Helgeson, Harold C.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{C}alculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest},
- year = {1998},
- volume = {62},
- number = {23-24},
- pages = {3591--3636},
- doi = {10.1016/S0016-7037(97)00345-1},
-}
-
@Book{RH95,
author = {Robie, Richard A. and Hemingway, Bruce S.},
publisher = {U.S. Geological Survey},
@@ -530,26 +413,6 @@
doi = {10.1063/1.1461829},
}
- at Article{ZZL_16,
- author = {Kurt Zimmer and Yilun Zhang and Peng Lu and Yanyan Chen and Guanru Zhang and Mehmet Dalkilic and Chen Zhu},
- journal = {Computers \& Geosciences},
- title = {{SUPCRTBL}: {A} revised and extended thermodynamic dataset and software package of {SUPCRT}92},
- year = {2016},
- pages = {97--111},
- volume = {90},
- doi = {10.1016/j.cageo.2016.02.013},
-}
-
- at Book{CWM89,
- editor = {Cox, J. D. and Wagman, D. D. and Medvedev, V. A.},
- publisher = {Hemisphere Publishing Corporation},
- title = {{CODATA} {K}ey {V}alues for {T}hermodynamics},
- year = {1989},
- address = {New York},
- pages = {271},
- url = {https://www.worldcat.org/oclc/18559968},
-}
-
@Article{HW97,
author = {Hn\v{e}dkovsk\'y, Lubom\'ir and Wood, Robert H.},
journal = {Journal of Chemical Thermodynamics},
@@ -583,16 +446,6 @@
doi = {10.1016/S0016-7037(02)01141-9},
}
- at Article{CPCC17,
- author = {Caporuscio, F. A. and Palaich, S. E. M. and Cheshire, M. C. and Jov\'e Col\'on, C. F.},
- journal = {Journal of Nuclear Materials},
- title = {{C}orrosion of copper and authigenic sulfide mineral growth in hydrothermal bentonite experiments},
- year = {2017},
- pages = {137--146},
- volume = {485},
- doi = {10.1016/j.jnucmat.2016.12.036},
-}
-
@Article{MDS_13,
author = {Mayumi, Daisuke and Dolfing, Jan and Sakata, Susumu and Maeda, Haruo and Miyagawa, Yoshihiro and Ikarashi, Masayuki and Tamaki, Hideyuki and Takeuchi, Mio and Nakatsu, Cindy H. and Kamagata, Yoichi},
journal = {Nature Communications},
@@ -603,17 +456,6 @@
doi = {10.1038/ncomms2998},
}
- at Article{Man13,
- author = {Manning, Craig E.},
- journal = {Reviews in Mineralogy and Geochemistry},
- title = {{T}hermodynamic modeling of fluid-rock interaction at mid-crustal to upper-mantle conditions},
- year = {2013},
- number = {1},
- pages = {135--164},
- volume = {76},
- doi = {10.2138/rmg.2013.76.5},
-}
-
@Article{Ber88,
author = {Berman, R. G.},
journal = {Journal of Petrology},
@@ -625,17 +467,6 @@
doi = {10.1093/petrology/29.2.445},
}
- at Article{SVI12,
- author = {Sabatini, Antonio and Vacca, Alberto and Iotti, Stefano},
- journal = {PLOS One},
- title = {{B}alanced biochemical reactions: {A} new approach to unify chemical and biochemical thermodynamics},
- year = {2012},
- number = {1},
- pages = {e29529},
- volume = {7},
- doi = {10.1371/journal.pone.0029529},
-}
-
@Article{BB85,
author = {Berman, Robert G. and Brown, Thomas H.},
journal = {Contributions to Mineralogy and Petrology},
@@ -711,17 +542,6 @@
doi = {10.2113/gselements.5.5.281},
}
- at Article{PAB_14,
- author = {Pokrovski, Gleb S. and Akinfiev, Nikolay N. and Borisova, Anastassia Y. and Zotov, Alexandre V. and Kouzmanov, Kalin},
- journal = {Geological Society, London, Special Publications},
- title = {{G}old speciation and transport in geological fluids: insights from experiments and physical-chemical modelling},
- year = {2014},
- number = {1},
- pages = {9--70},
- volume = {402},
- doi = {10.1144/SP402.4},
-}
-
@Article{SZS_17,
author = {Singh, Arunima K. and Zhou, Lan and Shinde, Aniketa and Suram, Santosh K. and Montoya, Joseph H. and Winston, Donald and Gregoire, John M. and Persson, Kristin A.},
journal = {Chemistry of Materials},
@@ -774,17 +594,6 @@
doi = {10.1103/PhysRevB.85.235438},
}
- at Article{DYT20,
- author = {Dick, Jeffrey M. and Yu, Miao and Tan, Jingqiang},
- journal = {Biogeosciences},
- title = {Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences},
- year = {2020},
- number = {23},
- pages = {6145--6162},
- volume = {17},
- doi = {10.5194/bg-17-6145-2020},
-}
-
@Article{And75,
author = {Anderson, G. M.},
journal = {Economic Geology},
@@ -901,17 +710,6 @@
doi = {10.1016/j.acags.2021.100059},
}
- at Article{MWKL17,
- author = {Miron, George D. and Wagner, Thomas and Kulik, Dmitrii A. and Lothenbach, Barbara},
- journal = {American Journal of Science},
- title = {An internally consistent thermodynamic dataset for aqueous species in the system {Ca-Mg-Na-K-Al-Si-O-H-C-Cl} to 800 °{C} and 5 kbar},
- year = {2017},
- number = {7},
- pages = {755--806},
- volume = {317},
- doi = {10.2475/07.2017.01},
-}
-
@Article{WWH_21,
author = {Xin-Song Wang and A. E. Williams-Jones and Rui-Zhong Hu and Lin-Bo Shang and Xian-Wu Bi},
journal = {Geochimica et Cosmochimica Acta},
More information about the CHNOSZ-commits
mailing list