~chhei/geotimecpts

d8dff006312141faa578723668d8a96a77aafaf1 — christian 1 year, 4 months ago 880cc8d + 753b539
Merged origin/master into master to close old git branch in fossil

FossilOrigin-Name: b3d12c185404deb0dbe5e01e8114a0ca4b5b8d70e73ea9581db71d8b2668ea9f
D .gitignore => .gitignore +0 -1
@@ 1,1 0,0 @@
*.history

M CGMW_RGB.txt => CGMW_RGB.txt +1 -1
@@ 2,7 2,7 @@
# Geological Map of the World (CGMW)
#
# Translated from PDF version by 
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
# May 2013
#
# LICENSE:

M CGWM_RGB.txt => CGWM_RGB.txt +1 -1
@@ 2,7 2,7 @@
# Geological Map of the World (CGMW)
#
# Translated from PDF version by 
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
# May 2013
#
# LICENSE:

M Exxon88/Exxon88.cpt => Exxon88/Exxon88.cpt +1 -1
@@ 2,7 2,7 @@
#
# TIMESCALE: Exxon 1988 (Haq et al., 1987) 
# 
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
# 
# LICENSE: 
# This work is licensed under a 

M GTS2004/GTS2004_ages.cpt => GTS2004/GTS2004_ages.cpt +1 -1
@@ 2,7 2,7 @@
# 
# TIMESCALE: GTS2004 (Gradstein et al.,2004)
#
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
# 
# LICENSE: 
# This work is licensed under a 

M GTS2004/GTS2004_epochs.cpt => GTS2004/GTS2004_epochs.cpt +1 -1
@@ 2,7 2,7 @@
# 
# TIMESCALE: GTS2004 (Gradstein et al.,2004)
#
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, chhei@paleoearthlabs.org
# 
# LICENSE: 
# This work is licensed under a 

M GTS2012/GTS2012_ages.cpt => GTS2012/GTS2012_ages.cpt +1 -1
@@ 2,7 2,7 @@
#
# TIMESCALE:  GTS2012 (Gradstein et al. ,2012) 
# 
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
# 
# LICENSE: 
# This work is licensed under a 

M GTS2012/GTS2012_eons.cpt => GTS2012/GTS2012_eons.cpt +1 -1
@@ 2,7 2,7 @@
#
# TIMESCALE:  GTS2012 (Gradstein et al., 2012) 
# 
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
# 
# LICENSE: 
# This work is licensed under a 

M GTS2012/GTS2012_epochs.cpt => GTS2012/GTS2012_epochs.cpt +1 -1
@@ 2,7 2,7 @@
#
# TIMESCALE:  GTS2004 (Gradstein et al., 2012) 
# 
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
#
# LICENSE: 
# This work is licensed under a 

M GTS2012/GTS2012_eras.cpt => GTS2012/GTS2012_eras.cpt +1 -1
@@ 2,7 2,7 @@
#
# TIMESCALE:  GTS2012 (Gradstein et al., 2012) 
# 
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
# 
# LICENSE: 
# This work is licensed under a 

M GTS2012/GTS2012_periods.cpt => GTS2012/GTS2012_periods.cpt +1 -1
@@ 2,7 2,7 @@
#
# TIMESCALE:  GTS2012 (Gradstein et al., 2012) 
# 
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
# 
# LICENSE: 
# This work is licensed under a 

M GTS2012/GTS2012_stages.cpt => GTS2012/GTS2012_stages.cpt +1 -1
@@ 4,7 4,7 @@
# 
# GIVEN ARE TOPS of STAGES in Milliions of years before present
#
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
# 
# LICENSE: 
# This work is licensed under a 

M MagAnomaly/CandeKent96_Channell95.cpt => MagAnomaly/CandeKent96_Channell95.cpt +1 -1
@@ 2,7 2,7 @@
#
# TIMESCALE: Magnetic anomalies - Cande & Kent (1996) and Channel (1996)
# 
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
#
# LICENSE: 
# This work is licensed under a 

M MagAnomaly/GeeK07.cpt => MagAnomaly/GeeK07.cpt +1 -1
@@ 11,7 11,7 @@
# cryptochrons that have been elevated to the status of new normal polarity 
# subchrons.
#
# Christian Heine, mailto:chhei@mensa.uberspace.de
# Christian Heine, mailto:chhei@paleoearthlabs.org
#
# Normal polarity: white
# Reverse polarity: black

M README.md => README.md +50 -31
@@ 1,48 1,67 @@
# Geological time color palettes

This repository contains color palettes for geological time for use with the 
[Generic Mapping Tools](http://gmt.soest.hawaii.edu). The color palettes are
in RGB format and follow the specifications published by the International Commission
for Stratigraphy (ICS) as published on [their website](http://www.stratigraphy.org).
This repository contains color palettes of geological time scales (GTS) for use with the 
[Generic Mapping Tools (GMT)](http://generic-mapping-tools.org) and [GPlates](https://gplates.org). 

Currently, the following incarnations of the geological time scale are covered (some only partly, feel free to contribute):
The color palettes use RGB colours, follow the GMT formattting and are based on the specifications published by the [International Commission for Stratigraphy (ICS) ](http://www.stratigraphy.org). They are available for geomagnetic and legacy geological time scales, with the formatting allowing easy conversion and comparison of stratigraphic and absolute ages.

1. GTS2012 Strat chart available from [ICS website - PDF](http://stratigraphy.org/ICSchart/ChronostratChart2012.pdf)  
2. GTS2004: PDF not available online.
3. Exxon88: The old Exxon/Haq timescale from 1988.   
Currently, the following incarnations of the geological time scale are covered (some only partly):

The cpts are also accessible through [cpt-city](http://soliton.vm.bytemark.co.uk/pub/cpt-city/) with the direct link to the cpts being the ["Heine collection" here](http://soliton.vm.bytemark.co.uk/pub/cpt-city/heine/).
1. ICS [GTS2012 time scale](http://stratigraphy.org/ICSchart/ChronostratChart2012.pdf) (link to PDF)
2. ICS GTS2004 ([Gradstein, 2004](https://onlinelibrary.wiley.com/doi/abs/10.1080/00241160410006483))
3. Exxon88: The old Exxon/Haq timescale from 1988. ([Haq et al., 1988](https://pubs.geoscienceworld.org/books/book/1039/chapter/10526493/Mesozoic-and-Cenozoic-Chronostratigraphy-and)) 

Also, check my website [TectonicWaters](https://wiki.paleoearthlabs.org/) for examples of how these color scales can be used with [GPlates](http://www.gplates.org).
## Using the GeoTime CPTs

## Geological time scale colors
Clone or download the repository (see "Usage" below). In GMT or GPlates you can then simply load the GeoTimeCPTs as color palettes. 

Some link collections here:
* https://ngmdb.usgs.gov/Info/standards/#TimeScale - This is the USGS North American Map standard.
* http://www.bgs.ac.uk/data/maps/maps.cfc?method=listResults&mapName=&series=INDC&scale=&pageSize=100  Index to colours used on geological maps
* https://www.swisstopo.admin.ch/de/wissen-fakten/geologie/geologische-daten/geologische-karten.html - Geologische Karten - SwissTopo
* https://www.strati.ch
* http://stratigraphy.org/upload/bak/bio.htm
* OSDN - http://www.odsn.de/odsn/services/conv_ts/conv_ts.html convert mesozoic and cenozoic time scales
* https://engineering.purdue.edu/Stratigraphy/charts/rgb.html
* https://engineering.purdue.edu/Stratigraphy/resources/geowhen/region_all.html
Check my [TectonicWaters blog](https://wiki.paleoearthlabs.org/) for examples of how these color scales can be used with [GPlates](http://www.gplates.org) and [GMT](https://generic-mapping-tools.org):

* [GPlates: Colouring features by absolute age](https://wiki.paleoearthlabs.org/tectonicwaters/gplates_coloring_features_by_absolute_age)
* [GeoTimeCPTs updated](https://wiki.paleoearthlabs.org/tectonicwaters/updated_geological_time_scale_colour_palettes)
* [The initial post demonstrating the use](https://wiki.paleoearthlabs.org/tectonicwaters/2013/1025_geological_colours)

## Ideas
The cpts are also accessible through [cpt-city](http://soliton.vm.bytemark.co.uk/pub/cpt-city/) with the direct link to the cpts being the ["Heine collection" here](http://soliton.vm.bytemark.co.uk/pub/cpt-city/heine/). 

abbreviations for intervals -- https://gist.github.com/jczaplew/7546689
do not set all boundaries as this is hard to maintain?
magnetic time scale as well - intervals
regional 
colors - these are independent of the timescale but globally applicable? Use surveys.
why not a simple list ?
Contributions to extend the coverage of timescales and to the repository are welcome.

## This repository

The GeoTimeCPTs repository, wiki and forum are hosted using the [Fossil source code management software](https://fossil-scm.org).

Please consider contributing to the repository by helping to convert the missing sections or timescales to the repository. 
A GIT Mirror exists on my [Sourcehut](https://sourcehut.org) account here: [https://git.sr.ht/~chhei/geotimecpts](https://git.sr.ht/~chhei/geotimecpts). **If you are accessing this repository on Sourcehut under the following URL: https://git.sr.ht/~chhei/geotimecpts note that this is a downstream mirror of the [original Fossil repository](https://code.paleoearthlabs.org/geotimecpts)**. Please use the original repository for documentation, issues, and a forum. I have deleted my git clones on GitHub and BitBucket in favour of hosting privately and on [Sourcehut](https://sourcehut.org).

This work is licensed under a [Creative Commons Attribution-ShareAlike 3.0 Unported License](http://creativecommons.org/licenses/by-sa/3.0/deed.en_US).
### Usage

This repository is hosted using the self-contained [Fossil](https://fossil-scm.org) distributed version control software which has some minor differences to the popular GIT repositories: 

Christian Heine,
mailto:chhei\at/paleoearthlabs.org
\ No newline at end of file
  * A zip file of the repository content can be downloaded on the [Downloads page](https://code.paleoearthlabs.org/geotimecpts/download)
  * A [Forum](https://code.paleoearthlabs.org/geotimecpts/forum) to discuss the scripts
  * An [issue tracker](https://code.paleoearthlabs.org/geotimecpts/rptview?rn=1s) to log tickets
  * A [timeline](https://code.paleoearthlabs.org/geotimecpts/timeline)

Tickets and forum can be used anonymously, however, users can also [create an account](https://code.paleoearthlabs.org/geotimecpts/register).

To clone the repository, you have to install [Fossil](https://fossil-scm.org) first. The workflow is similar to `git`, yet you will also have access to the wiki, documentation, and tickets in one go:

 - `fossil clone https://code.paleoearthlabs.org/geotimecpts/ geotimecpts`
 - `cd`/`mkdir` to the directory which you want to be the root of your directory tree for this repository, then
 - `fossil open <path>/<to>/<gptools clone>/geotimecpts.fossil`

For detailed instructions, please see the [Fossil Quick Start guide](https://fossil-scm.org/home/doc/trunk/www/quickstart.wiki).

## Licenses

The GeoTimeCPTs (cpt files, scripts, images) are licensed under a GNU Public License v3. Documentation is licensed under a
	
[Creative Commons Attribution-ShareAlike 3.0 Unported License](http://creativecommons.org/licenses/by-sa/3.0/deed.en_US).

The following files are covered by separate licenses/copyright and are explicitly excluded from the above license:

* [ChronostratChart2012.pdf](file?name=GTS2012/ChronostratChart2012.pdf&ci=tip) - available on the International Commission of Stratigraphy website at [www.stratigraphy.org](https://stratigraphy.org/chart). An Excel version is available [here](https://stratigraphy.org/ICSchart/CGMW_ICS_colour_codes.xlsx). Copyright resides with the [International Commission of Stratigraphy](http://stratigraphy.org).
* [CGMW\_RGB.pdf](file?name=CGMW_RGB.pdf&ci=tip) and [CGMW\_CMYK.pdf](file?name=CGMW_CMYK.pdf&ci=tip) - Original file is availale via the CGMW website here [http://ccgm.org/img/cms/Stratigraphic%20Chart_Codes%20CMYK_RGB.pdf](http://ccgm.org/img/cms/Stratigraphic%20Chart_Codes%20CMYK_RGB.pdf). The files served there are those from the ICS and hence copyright rests with the [International Commission of Stratigraphy](http://stratigraphy.org) ?and with the Commission of the Geological Map of the World (CGMW).  


----

(c) [Christian Heine](mailto:code@paleoearthlabs.org), 2012-2021

M citations.bib => citations.bib +5 -8
@@ 9,7 9,7 @@



@incollection{Haq.SEPM-SP.88,
@incollection{Haq.SEPM-SP.1988,
	Author = {Haq, Bilal U. and Hardenbol, Jan and Vail, Peter R.},
	Booktitle = {{Sea-level research: An integrated approach}},
	Date-Added = {2013-10-31 09:21:48 +0000},


@@ 31,7 31,7 @@ Four cycle charts summarizing the chronostratigraphy, coastal-onlap patterns, an
},
	Bdsk-Url-1 = {http://dx.doi.org/10.2110/pec.88.01.0071}}

@book{Gradstein.04,
@book{Gradstein.2004,
	Author = {Gradstein, F.M. and Ogg, J.G. and Smith, A.G. and Agterberg, F.P. and Bleeker, W. and Cooper, R.A. and Davydov, V. and Gibbard, P. and Hinnov, L.A. and House, M.R. and Lourens, L. and Luterbacher, H.P. and McArthur, J. and Melchin, M.J. and Robb, L.J. and Shergold, J. and Villeneuve, M. and Wardlaw, B.R. and Ali, J. and Brinkhuis, H. and Hilgen, F.J. and Hooker, J. and Howarth, R.J. and Knoll, A.H. and Laskar, J. and Monechi, S. and Plumb, K.A. and Powell, J. and Raffi, I. and R{\"o}hl, U. and Sadler, P. and Sanfilippo, A. and Schmitz, B. and Shackleton, N.J. and Shields, G.A. and Strauss, H. and Van Dam, J. and van Kolfschoten, T. and Veizer, J. and Wilson, D.},
	Booktitle = {{A Geologic Time Scale}},
	Date-Added = {2013-10-31 09:15:26 +0000},


@@ 44,7 44,7 @@ Four cycle charts summarizing the chronostratigraphy, coastal-onlap patterns, an
	Year = {2004},
	Bdsk-Url-1 = {http://www.stratigraphy.org}}

@incollection{Gee.ToG.07,
@incollection{Gee.ToG.2007,
	Address = {Amsterdam},
	Author = {Gee, J. S. and Kent, D. V.},
	Booktitle = {{Treatise on Geophysics}},


@@ 53,7 53,6 @@ Four cycle charts summarizing the chronostratigraphy, coastal-onlap patterns, an
	Date-Modified = {2013-10-31 09:14:26 +0000},
	Doi = {10.1016/B978-044452748-6.00097-3},
	Editor = {Kono, M.},
	Filetitle = {GeomagPolarityTimeScaleGeeK},
	Isbn = {978-0-444-52748-6},
	Keywords = {Anomaly amplitude envelope; Anomaly skewness; CAMH; Central Anomaly; Cretaceous quiet zone; Cryptochrons; C-sequence; Excursions; Gabbros; Geomagnetic polarity time scale; Jurassic quiet zone; Low-temperature oxidation; Maghemitization; Magnetite; Marine magnetic anomalies; Mid-ocean ridge basalts; M-sequence; NRM; Paleointensity fluctuations; Peridotites; Serpentinization; Sheeted dikes; Telechemistry; Source layers; Titanomagnetite; TRM},
	Pages = {455--507},


@@ 62,11 61,9 @@ Four cycle charts summarizing the chronostratigraphy, coastal-onlap patterns, an
	Volume = {5},
	Year = {2007},
	Abstract = {Marine magnetic anomalies provide the framework for the geomagnetic polarity timescale for the Late Jurassic to Recent (since 160 Ma). Magnetostratigraphic records confirm that the polarity reversal sequence interpreted from magnetic anomalies is complete to a resolution of better than 30 ky. In addition to this record of polarity reversals, magnetic anomalies also appear to preserve information on geomagnetic intensity fluctuations. The correspondence of coherent near-bottom anomaly variations with independent estimates of field intensity provides strong evidence that geomagnetic intensity modulates the magnetization of the ocean crust. Indeed, many short wavelength anomaly variations in sea-surface magnetic profiles over fast-spreading ridges are likely attributable to geomagnetic intensity variations. Although longer-term geomagnetic field behavior may also be reflected in anomaly amplitudes, documenting such a signal requires a better understanding of time-dependent changes in the magnetic source (e.g., from low-temperature alteration) that may also affect magnetic anomalies.  The extrusive layer, with an average remanence of xxxm-1, is the largest contributor to magnetic anomalies. However, enhanced sampling of oceanic gabbros (average remanence m-1) and, to a lesser extent, dikes (average remanence xxxm-1) reveals that these deeper (and thicker) layers likely generate anomalies comparable to those from the lavas. Lava accumulation at intermediate- and fast-spreading ridges typically occurs over a narrow (1--3km) region and dike emplacement is even more narrowly confined, resulting in a relatively high fidelity record of geomagnetic field behavior. The slow cooling of the gabbroic layer, however, results in gently dipping polarity boundaries that significantly affect the skewness of the resulting anomalies, which is also a sensitive measure of net rotations of the source layer(s). The magnetizations of the dikes and gabbros are characterized by high stability and are not expected to significantly change with time, although there are insufficient data to confirm this. The lavas, however, typically show evidence of low-temperature alteration, which has been long regarded as a process that progressively reduces the magnetization (and degrades the geomagnetic signal) in the extrusive layer and reduces the amplitude of magnetic anomalies. Sufficient data have become available to examine this conventional wisdom. There is a substantial (4x) reduction in magnetization from on-axis samples to immediately off-axis drillsites (0.5My), but little further change in half-dozen or so deep crustal sites to 60Ma. High paleointensity that characterizes the last few thousand years may contribute significantly to the high on-axis magnetization. The task of evaluating changes in remanence of the extrusive layer is made more difficult by substantial cooling-rate-dependent changes in magnetic properties and the systematic variation in remanence with iron content (magnetic telechemistry). The commonly cited magnetic anomaly amplitude envelope is in fact not systematically observed -- the Central Anomaly is elevated at slow-spreading ridges but is not as prominent at faster spreading rates. Nonetheless, magnetic anomaly amplitudes are consistent with magnetization change is poorly constrained. Direct determinations of the degree of low-temperature oxidation reveal the presence of highly oxidized titanomagnetite in samples less than 1My old, suggesting a short (105 years) time constant though the effects of low-temperature oxidation are quite heterogeneous. While low-temperature oxidation does have some affect on lava magnetization and anomaly amplitudes, there is increasing evidence that marine magnetic anomalies are capable of recording a broad spectrum of geomagnetic field behavior, ranging from millennial-scale paleointensity variations to polarity reversals to apparent polar wander to, more speculatively, long-term changes in average field strength. Several emerging tools and approaches -- autonomous vehicles, oriented samples, absolute paleointensity of near-ridge lavas, and measurements of the vector anomalous field -- are therefore likely to significantly advance our understanding of the geomagnetic signal recorded in the oceanic crust, as well as our ability to utilize this information in addressing outstanding problems in crustal accretion processes.},
	Annote = {http://www.sciencedirect.com/science/article/pii/B9780444527486000973},
	Bdsk-File-1 = {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},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/B9780444527486000973}}
	Annote = {http://www.sciencedirect.com/science/article/pii/B9780444527486000973}}

@book{Gradstein.12,
@book{Gradstein.2012,
	Author = {Gradstein, Felix M. and Ogg, James G. and Schmitz, Mark and Ogg, Gabi},
	Booktitle = {{A Geologic Time Scale}},
	Date-Added = {2013-10-31 09:14:10 +0000},