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2024-03-29T11:11:11Z
User contributions
MediaWiki 1.26.3
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11917
Category:Trees Working Group
2016-10-18T23:35:51Z
<p>Petebrew: /* Recommendations of legacy datasets */</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>Jansma, E., Brewer, P. W. & Zandhuis, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. [http://dx.doi.org/10.1016/j.dendro.2009.06.009 DOI]</ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
<br />
<poll><br />
What should the scope of this working group be?<br />
Solely the needs of the paleoclimate community <br />
Concentrate on the needs of the paleoclimate community initially while keeping in mind wider needs<br />
Handle the needs of as many communities as possible <br />
</poll><br />
<br />
<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
<br />
=== Detrending ===<br />
<br />
Maintaining references back to raw ring-width measurements is important to maintain data transparency. When detrending has been performed a detailed record of what has been done should be stored along with the software/library used. Implementations of different detrending techniques in different software can produce different results. To ensure results can be replicated the following fields will be necessary in addition to the detrended data:<br />
<br />
* Software used<br />
* Version used<br />
* Detrend method name:<br />
** Polynomial<br />
** Exponential<br />
** Moving average / Floating <br />
** High pass filter<br />
** Cubic spline<br />
* In the case of some methods (e.g. polynomial, moving average) then a parameter may be required. I can only think of methods that require one parameter, but for future proofing it would make sense to be able to pass multiple parameters.<br />
<br />
=== Stable isotopes ===<br />
<br />
Some recommendations were made for an 'International Tree Ring Isotope Databank' ITRIDB by Csank<ref>Csank, A.Z. (2009) An International Tree-Ring Isotope Data Bank– A Proposed Repository for Tree-Ring Isotopic Data. Tree-Ring Research 65(2):163-164. [http://dx.doi.org/10.3959/1536-1098-65.2.163 DOI]</ref><br />
<br />
== Location information ==<br />
<br />
Prior to the wide availability and affordability of GPS handsets, location information in dendrochronology tended to be low accuracy coordinates for a particular study site. This is what is stored in the ITRDB. However, for many years now the many (majority? all?) researchers have collected GPS coordinates for each individual tree. A clear distinction is needed in the ontology to record what the location information is recording. <br />
<br />
Chronologies are by definition an amalgamation of data from multiple trees. Location information for these can therefore be represented either as multiple coordinates (one for each tree) and/or a polygon denoting the extent of the area covered by the chronology. Should such a polygon be the smallest area encompassing all tree coordinates or should it be the freehand area covering the area the researcher feels the chronology represents? <br />
<br />
Further complications arise when handling tree-ring data collected from non-living trees. Sample from snags can be reasonably expected to be at least close to where the tree grew, but archaeological and other cultural samples can be found miles from their initial growth location. Very long range transport/trade of wood has taken place for millenia. Some studies have successfully determined the provenance of transported/traded samples through dendrochronological analyses and/or isotopic work. In these cases it would be good to also be able to store this sort of information. Regardless though, the type of location must be clearly stored with all locality data.<br />
<br />
<br />
== Taxonomic information ==<br />
<br />
Taxonomic information is clearly essential for tree ring (and other biological proxies). The current most comprehensive database of authoritative taxonomic information is the [http://catalogueoflife.org Catalogue of Life]. As of 2016 it contains over 1.6m species from 158 contributing databases covering plants, animals, fungi and microorganisms. This is an estimated 84% of all known species. From the perspective of LinkedEarth, unfortunately this data is not currently available as linked data, although the organization does have plans to provide linked data as part of future funding applications (P. Schalk pers. comm. Nov 2015).<br />
<br />
<br />
== Recommendations for new datasets ==<br />
<br />
Recommendations for collecting dendroarchaeological data have been made by Brewer and Jansma<ref>Brewer, P.W. and Jansma, E. (2016) Dendrochronological Data in Archaeology: A Guide to Good Practice, Archaeology Data Service / Digital Antiquity v1.1. [http://guides.archaeologydataservice.ac.uk/g2gp/Dendro_Toc Link]</ref>. These are specific to the collection of samples for cultural dendrochronology, but still relevant in part to wider tree-ring research. <br />
<br />
<br />
<br />
== Recommendations for legacy datasets ==<br />
The task of standardizing and upgrading legacy datasets cannot be underestimated. Recommendations for how to handle datasets will likely vary depending on the context. For instance, if a dataset owner wants to upgrade their own legacy data they should have access to the vast majority of data/metadata. Given the time/money they should be able to upgrade to a similar quality as new datasets. In contrast, upgrading the existing NOAA/ITRDB holdings of others will be far more challenging as the majority of datasets are missing key information or key information is stored ambiguously. For orphaned datasets it's very likely that a substantial amount of information is already lost with no hope of recovery.<br />
<br />
In general, legacy datasets should be upgraded to meet a minimum set of criteria:<br />
# Type of data: raw measurements or derived chronologies<br />
# Measurement variable stored<br />
# Measurement units stored<br />
# Missing rings handled clearly and consistently<br />
# Taxon<br />
# Location <br />
# Location type<br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11870
Category:Trees Working Group
2016-10-18T17:37:49Z
<p>Petebrew: Taxonomic information</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>Jansma, E., Brewer, P. W. & Zandhuis, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. [http://dx.doi.org/10.1016/j.dendro.2009.06.009 DOI]</ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
<br />
<poll><br />
What should the scope of this working group be?<br />
Solely the needs of the paleoclimate community <br />
Concentrate on the needs of the paleoclimate community initially while keeping in mind wider needs<br />
Handle the needs of as many communities as possible <br />
</poll><br />
<br />
<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
<br />
=== Detrending ===<br />
<br />
Maintaining references back to raw ring-width measurements is important to maintain data transparency. When detrending has been performed a detailed record of what has been done should be stored along with the software/library used. Implementations of different detrending techniques in different software can produce different results. To ensure results can be replicated the following fields will be necessary in addition to the detrended data:<br />
<br />
* Software used<br />
* Version used<br />
* Detrend method name:<br />
** Polynomial<br />
** Exponential<br />
** Moving average / Floating <br />
** High pass filter<br />
** Cubic spline<br />
* In the case of some methods (e.g. polynomial, moving average) then a parameter may be required. I can only think of methods that require one parameter, but for future proofing it would make sense to be able to pass multiple parameters.<br />
<br />
=== Stable isotopes ===<br />
<br />
Some recommendations were made for an 'International Tree Ring Isotope Databank' ITRIDB by Csank<ref>Csank, A.Z. (2009) An International Tree-Ring Isotope Data Bank– A Proposed Repository for Tree-Ring Isotopic Data. Tree-Ring Research 65(2):163-164. [http://dx.doi.org/10.3959/1536-1098-65.2.163 DOI]</ref><br />
<br />
== Location information ==<br />
<br />
Prior to the wide availability and affordability of GPS handsets, location information in dendrochronology tended to be low accuracy coordinates for a particular study site. This is what is stored in the ITRDB. However, for many years now the many (majority? all?) researchers have collected GPS coordinates for each individual tree. A clear distinction is needed in the ontology to record what the location information is recording. <br />
<br />
Chronologies are by definition an amalgamation of data from multiple trees. Location information for these can therefore be represented either as multiple coordinates (one for each tree) and/or a polygon denoting the extent of the area covered by the chronology. Should such a polygon be the smallest area encompassing all tree coordinates or should it be the freehand area covering the area the researcher feels the chronology represents? <br />
<br />
Further complications arise when handling tree-ring data collected from non-living trees. Sample from snags can be reasonably expected to be at least close to where the tree grew, but archaeological and other cultural samples can be found miles from their initial growth location. Very long range transport/trade of wood has taken place for millenia. Some studies have successfully determined the provenance of transported/traded samples through dendrochronological analyses and/or isotopic work. In these cases it would be good to also be able to store this sort of information. Regardless though, the type of location must be clearly stored with all locality data.<br />
<br />
<br />
== Taxonomic information ==<br />
<br />
Taxonomic information is clearly essential for tree ring (and other biological proxies). The current most comprehensive database of authoritative taxonomic information is the [http://catalogueoflife.org Catalogue of Life]. As of 2016 it contains over 1.6m species from 158 contributing databases covering plants, animals, fungi and microorganisms. This is an estimated 84% of all known species. From the perspective of LinkedEarth, unfortunately this data is not currently available as linked data, although the organization does have plans to provide linked data as part of future funding applications (P. Schalk pers. comm. Nov 2015).<br />
<br />
<br />
== Recommendations for new datasets ==<br />
<br />
Recommendations for collecting dendroarchaeological data have been made by Brewer and Jansma<ref>Brewer, P.W. and Jansma, E. (2016) Dendrochronological Data in Archaeology: A Guide to Good Practice, Archaeology Data Service / Digital Antiquity v1.1. [http://guides.archaeologydataservice.ac.uk/g2gp/Dendro_Toc Link]</ref>. These are specific to the collection of samples for cultural dendrochronology, but still relevant in part to wider tree-ring research. <br />
<br />
<br />
<br />
== Recommendations of legacy datasets ==<br />
The task of standardizing and upgrading legacy datasets cannot be underestimated. Recommendations for how to handle datasets will likely vary depending on the context. For instance, if a dataset owner wants to upgrade their own legacy data they should have access to the vast majority of data/metadata. Given the time/money they should be able to upgrade to a similar quality as new datasets. In contrast, upgrading the existing NOAA/ITRDB holdings of others will be far more challenging as the majority of datasets are missing key information or key information is stored ambiguously. For orphaned datasets it's very likely that a substantial amount of information is already lost with no hope of recovery.<br />
<br />
In general, legacy datasets should be upgraded to meet a minimum set of criteria:<br />
# Type of data: raw measurements or derived chronologies<br />
# Measurement variable stored<br />
# Measurement units stored<br />
# Missing rings handled clearly and consistently<br />
# Taxon<br />
# Location <br />
# Location type<br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category_talk:Trees_Working_Group&diff=11869
Category talk:Trees Working Group
2016-10-18T17:22:17Z
<p>Petebrew: /* initiated discussion on detrending -- JEG (talk) 17:35, 17 October 2016 (PDT) */</p>
<hr />
<div>== initiated discussion on detrending -- [[User:Jeg|JEG]] ([[User talk:Jeg|talk]]) 17:35, 17 October 2016 (PDT) ==<br />
<br />
First off, this page looks great - thanks to anyone who has contributed.<br />
<br />
Re: detrending, this reminds me that in the rest of LinkedEarth, we encourage users to distinguished between native observations and any processed form thereof. Because detrending may result in a loss of information, I would encourage the group to describe:<br />
# Guidelines to store raw data, for each measurement type<br />
<br />
# Guidelines to store metadata about detrending method (e.g. method name, software implementation, parameter values, etc). <br />
<br />
Cheers,<br />
[[User:Jeg|JEG]]<br />
<br />
===Re: initiated discussion on detrending -- [[User:Petebrew|Petebrew]] ([[User talk:Petebrew|talk]]) 10:22, 18 October 2016 (PDT)===<br />
<br />
I've put in some basics for what I think is needed, but isn't this a problem shared by all proxies? These are fairly standard mathematical techniques that I'd assume are used in other proxies too?</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Chronologies_Working_Group&diff=11868
Category:Chronologies Working Group
2016-10-18T16:47:48Z
<p>Petebrew: /* Growth rings */</p>
<hr />
<div>[[Category:Working Group]]<br />
[[File:Chronology_pic.png|thumb|right|alt=An imaginary chronology based on U/Th dates, generated via Bchron|Credit: Julien Emile-Geay (Own work)]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''chronologies''', and aims to formulate a set of recommendations for such a standard.<br />
<br />
This WG needs to work closely with other WGs, as constraints will vary by archive. Nevertheless, some aspects are common enough that it is worth pursuing some general recommendations, and devise ''ad hoc'' adjustments for individual archives if need be. It is recommended that every WG coordinator join this WG to keep track of discussions.<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the age models themselves<br />
** the chronological measurements (ChronData tables, in LiDP/LinkedEarth parlance)<br />
** their uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal chronology table''', so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
While it is recognized that most real-word chronologies are of mixed types (e.g. a Holocene lake sediment chronology may blend radiocarbon dates, {{SimpleNuclide2|Lead|210}} dates, and volcanic ash markers), it is critical to first define guidelines for how to report ''pure'' chronologies. Once the foundations are sound, they will be easier to compose together.<br />
<br />
== Tie-point chronologies ==<br />
<br />
=== Radiocarbon ===<br />
The following came from P. Reimer by way of T. Guilderson. <br />
<br />
Key references: Stuiver & Polach [1977] <ref name="SP77">Minze Stuiver and H. A. Polach, 1977. Discussion: Reporting of 14C Data. Radiocarbon 19, 3, 355-363. </ref> and Reimer et al., [2004] <ref>Paula J. Reimer, T. A. Brown, and R. W. Reimer, 2004. Discussion: Reporting and calibration of post-bomb 14C Data. Radiocarbon, 46, 3, 1299-1304.</ref><br />
<br />
==== metadata ====<br />
* Sample ID<br />
* type/matrix<br />
* location (lat, lon, masl/mbsl altitude/depth, depth/height in section/core and referenced)<br />
<br />
==== Radiocarbon Measurements ====<br />
<br />
* Chemical pretreatment/preparation (oxidation, chemical leach (%), a/b/a, soxhlet, ultrafiltration, none, etc)<br />
<br />
* Method: GPC, LSC, AMS, etc<br />
<br />
* Laboratory ID# (eg. OS####; CAMS####; QUB####)<br />
<br />
* δ{{SimpleNuclide2|Carbon|13}} ratio actual/estimated (PDB/V-PDB) <ref>Note, the AMS measured {{SimpleNuclide2|Carbon|13}} has low precision (a few per mil, compared to IRMS). Most AMS labs do NOT report the machine measured {{SimpleNuclide2|Carbon|13}} value because it is frequently misused. This should be estimated as per SP77 or an IRMS-based value/estimate. </ref><br />
<br />
* Conventional radiocarbon age as years BP and one-sigma standard deviation <ref> Note, that by definition, conventional radiocarbon age is the Libby based age. Most AMS laboratories report 1-sigma sd of the analysis or the 1-sigma sd reproducibility for similar aged/sized material. </ref><br />
<br />
* F14C ({{SimpleNuclide2|Carbon|13}} and background correction applied)<ref> This is slightly different than Stuiver and Polach who have "D14C" as the optional parameter. </ref>:<br />
<br />
We suggest the inclusion of the background and d13C corrected Fraction modern (F14C) as it is the primary reported value. In the past there has been some inconsistencies in the literature/laboratories with regards to fraction modern. By using/requesting F14C you will be explicitly requesting {{SimpleNuclide2|Carbon|13}} and background corrected Fraction Modern (aka F14C, as per Reimer et al.[2004]) as intended by SP77).<br />
* Correction applied to radiocarbon date prior to, or during conversion to calibrated age:<br />
** marine reservoir effect: <br />
*** Marine reservoir age, ± one-sigma sd (or square root of the variance) uncertainty, reference/source<br />
*** DELTA_R value, ± one-sigma sd (or square root of the variance) uncertainty, reference/source<br />
* hard/soft water effect: value, ± one-sigma sd (or square root of var) uncertainty, reference/source<br />
* other corrections: value ({{SimpleNuclide2|Carbon|14}} years), ± one-sigma sd (or square root of var), reference/source<br />
<br />
* Calibration or conversion to calibrated ages:<br />
As of present, the international radiocarbon community recommends the use of the INTCAL13 (aka Marine 13<ref>P. J. Reimer et al., 2013. INTCAL13 and MARINE13 Radiocarbon age calibration curves, 0-50,000 years CAL BP. Radiocarbon, 55, 1869-1887.</ref>) and SHCAL13 <ref>A. G. Hogg, et al., 2013. SHCal13 Southern Hemisphere calibration, 0-50,000 years cal BP. Radiocarbon 55, 1889-1903.</ref> data products. <br />
* Calibration of post-bomb (post 1954/1957) samples should also include the calibration data-set utilized, description/reference of any corrections applied, and the software/algorithm utilized to convert the F14C data to years AD.<br />
<br />
=== Lead ===<br />
<br />
no known existing standard/template<br />
=== U-series ===<br />
<br />
== Layer-counted chronologies ==<br />
<br />
Comboul et al<ref>Comboul, M., J. Emile-Geay, M. N. Evans, N. Mirnateghi, K. M. Cobb, and D. M. Thompson (2014), A probabilistic model of chronological errors in layer-counted climate proxies: applications to annually banded coral archives, Climate of the Past, 10(2), 825–841, doi:10.5194/cp-10-825-2014</ref> argue that it is critical to report uncertainties in layer-counted chronologies, and that these can be expressed in terms of an undercounting and overcounting rate. However, there needs to be agreement about how to measure and report this rate for various archives. <br />
<br />
=== Varves ===<br />
<br />
=== Growth rings ===<br />
Trees, corals, speleothems<br />
<br />
Tree-rings typically provide an absolute chronology but there needs to be the facility to also work with 'floating' chronologies anchored typically by radiocarbon. A hybrid dendro-radiocarbon chronological framework should be supported. <br />
<br />
Tree-rings data can also be stored at subannual level e.g. with early and latewood parameters. These are typically stored as two different data series as they are normally used to reconstruct different climatic parameters. In chronological terms these datasets represent portions of the year but precisely which portions depends on the species and location. In the southern hemisphere the earlywood will typically grow in the final months of the year and the latewood the first months of the following year. For paleoclimate reconstructions it's therefore essential to include metadata regarding the months each data point covers.<br />
<br />
A convention that continues to cause confusion when representing dendrochronological data is the use of the astronomical calendar. The astronomical calendar includes the year 0 so matches the AD calendar, but is one year different in the BC period. Astronomical dates are easier to handle in statistical analyses but have been erroneously quoted as BC years in even some very prestigious articles. Whatever method is used, it should be clear and consistent.<br />
<br />
=== Ice layers ===<br />
Role of flow models. <br />
<br />
<br />
== Age-modeling software ==<br />
<br />
<br />
Nick/Liz: please provide guidelines on how age modeling software should be reported. <br />
Content:<br />
* method (e.g. Bacon, OxCal, BChron, BAM)<br />
* version<br />
* parameters<br />
<br />
Form: what does this look like in JSON? <br />
<br />
== Polls ==<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
For '''NEW DATASETS''': (this is a dummy poll; please update)<br />
<poll><br />
What is your favorite chronology poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
For '''LEGACY DATASETS''':<br />
<poll><br />
What should we do with legacy chronologies?<br />
Contact original authors to obtain their uncalibrated dates<br />
Curse authors who were too short-sighted to archive uncalibrated dates<br />
Ignore them altogether<br />
</poll><br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11867
Category:Trees Working Group
2016-10-18T16:23:12Z
<p>Petebrew: /* Detrending */</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>Jansma, E., Brewer, P. W. & Zandhuis, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. [http://dx.doi.org/10.1016/j.dendro.2009.06.009 DOI]</ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
<br />
<poll><br />
What should the scope of this working group be?<br />
Solely the needs of the paleoclimate community <br />
Concentrate on the needs of the paleoclimate community initially while keeping in mind wider needs<br />
Handle the needs of as many communities as possible <br />
</poll><br />
<br />
<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
<br />
=== Detrending ===<br />
<br />
Maintaining references back to raw ring-width measurements is important to maintain data transparency. When detrending has been performed a detailed record of what has been done should be stored along with the software/library used. Implementations of different detrending techniques in different software can produce different results. To ensure results can be replicated the following fields will be necessary in addition to the detrended data:<br />
<br />
* Software used<br />
* Version used<br />
* Detrend method name:<br />
** Polynomial<br />
** Exponential<br />
** Moving average / Floating <br />
** High pass filter<br />
** Cubic spline<br />
* In the case of some methods (e.g. polynomial, moving average) then a parameter may be required. I can only think of methods that require one parameter, but for future proofing it would make sense to be able to pass multiple parameters.<br />
<br />
=== Stable isotopes ===<br />
<br />
Some recommendations were made for an 'International Tree Ring Isotope Databank' ITRIDB by Csank<ref>Csank, A.Z. (2009) An International Tree-Ring Isotope Data Bank– A Proposed Repository for Tree-Ring Isotopic Data. Tree-Ring Research 65(2):163-164. [http://dx.doi.org/10.3959/1536-1098-65.2.163 DOI]</ref><br />
<br />
== Location information ==<br />
<br />
Prior to the wide availability and affordability of GPS handsets, location information in dendrochronology tended to be low accuracy coordinates for a particular study site. This is what is stored in the ITRDB. However, for many years now the many (majority? all?) researchers have collected GPS coordinates for each individual tree. A clear distinction is needed in the ontology to record what the location information is recording. <br />
<br />
Chronologies are by definition an amalgamation of data from multiple trees. Location information for these can therefore be represented either as multiple coordinates (one for each tree) and/or a polygon denoting the extent of the area covered by the chronology. Should such a polygon be the smallest area encompassing all tree coordinates or should it be the freehand area covering the area the researcher feels the chronology represents? <br />
<br />
Further complications arise when handling tree-ring data collected from non-living trees. Sample from snags can be reasonably expected to be at least close to where the tree grew, but archaeological and other cultural samples can be found miles from their initial growth location. Very long range transport/trade of wood has taken place for millenia. Some studies have successfully determined the provenance of transported/traded samples through dendrochronological analyses and/or isotopic work. In these cases it would be good to also be able to store this sort of information. Regardless though, the type of location must be clearly stored with all locality data.<br />
<br />
== Recommendations for new datasets ==<br />
<br />
Recommendations for collecting dendroarchaeological data have been made by Brewer and Jansma<ref>Brewer, P.W. and Jansma, E. (2016) Dendrochronological Data in Archaeology: A Guide to Good Practice, Archaeology Data Service / Digital Antiquity v1.1. [http://guides.archaeologydataservice.ac.uk/g2gp/Dendro_Toc Link]</ref>. These are specific to the collection of samples for cultural dendrochronology, but still relevant in part to wider tree-ring research. <br />
<br />
<br />
<br />
== Recommendations of legacy datasets ==<br />
The task of standardizing and upgrading legacy datasets cannot be underestimated. Recommendations for how to handle datasets will likely vary depending on the context. For instance, if a dataset owner wants to upgrade their own legacy data they should have access to the vast majority of data/metadata. Given the time/money they should be able to upgrade to a similar quality as new datasets. In contrast, upgrading the existing NOAA/ITRDB holdings of others will be far more challenging as the majority of datasets are missing key information or key information is stored ambiguously. For orphaned datasets it's very likely that a substantial amount of information is already lost with no hope of recovery.<br />
<br />
In general, legacy datasets should be upgraded to meet a minimum set of criteria:<br />
# Type of data: raw measurements or derived chronologies<br />
# Measurement variable stored<br />
# Measurement units stored<br />
# Missing rings handled clearly and consistently<br />
# Taxon<br />
# Location <br />
# Location type<br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11866
Category:Trees Working Group
2016-10-18T16:22:01Z
<p>Petebrew: /* Detrending */</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>Jansma, E., Brewer, P. W. & Zandhuis, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. [http://dx.doi.org/10.1016/j.dendro.2009.06.009 DOI]</ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
<br />
<poll><br />
What should the scope of this working group be?<br />
Solely the needs of the paleoclimate community <br />
Concentrate on the needs of the paleoclimate community initially while keeping in mind wider needs<br />
Handle the needs of as many communities as possible <br />
</poll><br />
<br />
<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
<br />
=== Detrending ===<br />
<br />
Maintaining references back to raw ring-width measurements is important to maintain data transparency. When detrending has been performed a detailed record of what has been done should be stored along with the software/library used. Implementations of different detrending techniques in different software can produce different results. To ensure results can be replicated the following fields will be necessary in addition to the detrended data:<br />
<br />
* Software used<br />
* Version used<br />
* Detrend method name:<br />
* Polynomial<br />
* Exponential<br />
* Moving average / Floating <br />
* High pass filter<br />
* Cubic spline<br />
* In the case of some methods (e.g. polynomial, moving average) then a parameter may be required. I can only think of methods that require one parameter, but for future proofing it would make sense to be able to pass multiple parameters.<br />
<br />
=== Stable isotopes ===<br />
<br />
Some recommendations were made for an 'International Tree Ring Isotope Databank' ITRIDB by Csank<ref>Csank, A.Z. (2009) An International Tree-Ring Isotope Data Bank– A Proposed Repository for Tree-Ring Isotopic Data. Tree-Ring Research 65(2):163-164. [http://dx.doi.org/10.3959/1536-1098-65.2.163 DOI]</ref><br />
<br />
== Location information ==<br />
<br />
Prior to the wide availability and affordability of GPS handsets, location information in dendrochronology tended to be low accuracy coordinates for a particular study site. This is what is stored in the ITRDB. However, for many years now the many (majority? all?) researchers have collected GPS coordinates for each individual tree. A clear distinction is needed in the ontology to record what the location information is recording. <br />
<br />
Chronologies are by definition an amalgamation of data from multiple trees. Location information for these can therefore be represented either as multiple coordinates (one for each tree) and/or a polygon denoting the extent of the area covered by the chronology. Should such a polygon be the smallest area encompassing all tree coordinates or should it be the freehand area covering the area the researcher feels the chronology represents? <br />
<br />
Further complications arise when handling tree-ring data collected from non-living trees. Sample from snags can be reasonably expected to be at least close to where the tree grew, but archaeological and other cultural samples can be found miles from their initial growth location. Very long range transport/trade of wood has taken place for millenia. Some studies have successfully determined the provenance of transported/traded samples through dendrochronological analyses and/or isotopic work. In these cases it would be good to also be able to store this sort of information. Regardless though, the type of location must be clearly stored with all locality data.<br />
<br />
== Recommendations for new datasets ==<br />
<br />
Recommendations for collecting dendroarchaeological data have been made by Brewer and Jansma<ref>Brewer, P.W. and Jansma, E. (2016) Dendrochronological Data in Archaeology: A Guide to Good Practice, Archaeology Data Service / Digital Antiquity v1.1. [http://guides.archaeologydataservice.ac.uk/g2gp/Dendro_Toc Link]</ref>. These are specific to the collection of samples for cultural dendrochronology, but still relevant in part to wider tree-ring research. <br />
<br />
<br />
<br />
== Recommendations of legacy datasets ==<br />
The task of standardizing and upgrading legacy datasets cannot be underestimated. Recommendations for how to handle datasets will likely vary depending on the context. For instance, if a dataset owner wants to upgrade their own legacy data they should have access to the vast majority of data/metadata. Given the time/money they should be able to upgrade to a similar quality as new datasets. In contrast, upgrading the existing NOAA/ITRDB holdings of others will be far more challenging as the majority of datasets are missing key information or key information is stored ambiguously. For orphaned datasets it's very likely that a substantial amount of information is already lost with no hope of recovery.<br />
<br />
In general, legacy datasets should be upgraded to meet a minimum set of criteria:<br />
# Type of data: raw measurements or derived chronologies<br />
# Measurement variable stored<br />
# Measurement units stored<br />
# Missing rings handled clearly and consistently<br />
# Taxon<br />
# Location <br />
# Location type<br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11798
Peter Brewer
2016-10-13T18:39:00Z
<p>Petebrew: Added PropertyValue: Current Position = Research Associate</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Current Affiliation=Laboratory of Tree Ring Research|<br />
Current Position=Research Associate|<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Expertise=Data_standards|<br />
Expertise=Software_development|<br />
Expertise=Dendrochronology|<br />
Github ID=petebrew|<br />
Google Scholar ID=i0sfmZ4AAAAJ|<br />
Has User ID=Petebrew|<br />
Highest Degree=PhD|<br />
Name ©=Peter Brewer|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group|<br />
University=University of Arizona}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Software_development&diff=11797
Software development
2016-10-13T18:38:41Z
<p>Petebrew: Created blank page</p>
<hr />
<div></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Data_standards&diff=11796
Data standards
2016-10-13T18:38:04Z
<p>Petebrew: Created page with "Agreed upon standards for describing data and metadata"</p>
<hr />
<div>Agreed upon standards for describing data and metadata</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Chronologies_Working_Group&diff=11774
Category:Chronologies Working Group
2016-10-10T20:20:54Z
<p>Petebrew: /* Growth rings */</p>
<hr />
<div>[[Category:Working Group]]<br />
[[File:Chronology_pic.png|thumb|right|alt=An imaginary chronology based on U/Th dates, generated via Bchron|Credit: Julien Emile-Geay (Own work)]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''chronologies''', and aims to formulate a set of recommendations for such a standard.<br />
<br />
This WG needs to work closely with other WGs, as constraints will vary by archive. Nevertheless, some aspects are common enough that it is worth pursuing some general recommendations, and devise ''ad hoc'' adjustments for individual archives if need be. It is recommended that every WG coordinator join this WG to keep track of discussions.<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the age models themselves<br />
** the chronological measurements (ChronData tables, in LiDP/LinkedEarth parlance)<br />
** their uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal chronology table''', so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
While it is recognized that most real-word chronologies are of mixed types (e.g. a Holocene lake sediment chronology may blend radiocarbon dates, {{SimpleNuclide2|Lead|210}} dates, and volcanic ash markers), it is critical to first define guidelines for how to report ''pure'' chronologies. Once the foundations are sound, they will be easier to compose together.<br />
<br />
== Tie-point chronologies ==<br />
<br />
=== Radiocarbon ===<br />
The following came from P. Reimer by way of T. Guilderson. <br />
<br />
Key references: Stuiver & Polach [1977] <ref name="SP77">Minze Stuiver and H. A. Polach, 1977. Discussion: Reporting of 14C Data. Radiocarbon 19, 3, 355-363. </ref> and Reimer et al., [2004] <ref>Paula J. Reimer, T. A. Brown, and R. W. Reimer, 2004. Discussion: Reporting and calibration of post-bomb 14C Data. Radiocarbon, 46, 3, 1299-1304.</ref><br />
<br />
==== metadata ====<br />
* Sample ID<br />
* type/matrix<br />
* location (lat, lon, masl/mbsl altitude/depth, depth/height in section/core and referenced)<br />
<br />
==== Radiocarbon Measurements ====<br />
<br />
* Chemical pretreatment/preparation (oxidation, chemical leach (%), a/b/a, soxhlet, ultrafiltration, none, etc)<br />
<br />
* Method: GPC, LSC, AMS, etc<br />
<br />
* Laboratory ID# (eg. OS####; CAMS####; QUB####)<br />
<br />
* δ{{SimpleNuclide2|Carbon|13}} ratio actual/estimated (PDB/V-PDB) <ref>Note, the AMS measured {{SimpleNuclide2|Carbon|13}} has low precision (a few per mil, compared to IRMS). Most AMS labs do NOT report the machine measured {{SimpleNuclide2|Carbon|13}} value because it is frequently misused. This should be estimated as per SP77 or an IRMS-based value/estimate. </ref><br />
<br />
* Conventional radiocarbon age as years BP and one-sigma standard deviation <ref> Note, that by definition, conventional radiocarbon age is the Libby based age. Most AMS laboratories report 1-sigma sd of the analysis or the 1-sigma sd reproducibility for similar aged/sized material. </ref><br />
<br />
* F14C ({{SimpleNuclide2|Carbon|13}} and background correction applied)<ref> This is slightly different than Stuiver and Polach who have "D14C" as the optional parameter. </ref>:<br />
<br />
We suggest the inclusion of the background and d13C corrected Fraction modern (F14C) as it is the primary reported value. In the past there has been some inconsistencies in the literature/laboratories with regards to fraction modern. By using/requesting F14C you will be explicitly requesting {{SimpleNuclide2|Carbon|13}} and background corrected Fraction Modern (aka F14C, as per Reimer et al.[2004]) as intended by SP77).<br />
* Correction applied to radiocarbon date prior to, or during conversion to calibrated age:<br />
** marine reservoir effect: <br />
*** Marine reservoir age, ± one-sigma sd (or square root of the variance) uncertainty, reference/source<br />
*** DELTA_R value, ± one-sigma sd (or square root of the variance) uncertainty, reference/source<br />
* hard/soft water effect: value, ± one-sigma sd (or square root of var) uncertainty, reference/source<br />
* other corrections: value ({{SimpleNuclide2|Carbon|14}} years), ± one-sigma sd (or square root of var), reference/source<br />
<br />
* Calibration or conversion to calibrated ages:<br />
As of present, the international radiocarbon community recommends the use of the INTCAL13 (aka Marine 13<ref>P. J. Reimer et al., 2013. INTCAL13 and MARINE13 Radiocarbon age calibration curves, 0-50,000 years CAL BP. Radiocarbon, 55, 1869-1887.</ref>) and SHCAL13 <ref>A. G. Hogg, et al., 2013. SHCal13 Southern Hemisphere calibration, 0-50,000 years cal BP. Radiocarbon 55, 1889-1903.</ref> data products. <br />
* Calibration of post-bomb (post 1954/1957) samples should also include the calibration data-set utilized, description/reference of any corrections applied, and the software/algorithm utilized to convert the F14C data to years AD.<br />
<br />
=== Lead ===<br />
<br />
no known existing standard/template<br />
=== U-series ===<br />
<br />
== Layer-counted chronologies ==<br />
<br />
Comboul et al<ref>Comboul, M., J. Emile-Geay, M. N. Evans, N. Mirnateghi, K. M. Cobb, and D. M. Thompson (2014), A probabilistic model of chronological errors in layer-counted climate proxies: applications to annually banded coral archives, Climate of the Past, 10(2), 825–841, doi:10.5194/cp-10-825-2014</ref> argue that it is critical to report uncertainties in layer-counted chronologies, and that these can be expressed in terms of an undercounting and overcounting rate. However, there needs to be agreement about how to measure and report this rate for various archives. <br />
<br />
=== Varves ===<br />
<br />
=== Growth rings ===<br />
Trees, corals, speleothems<br />
<br />
Tree-rings typically provide an absolute chronology but there needs to be the facility to also work with 'floating' chronologies anchored typically by radiocarbon. A hybrid dendro-radiocarbon chronological framework should be supported. <br />
<br />
Tree-rings data can also be stored at subannual level e.g. with early and latewood parameters.<br />
<br />
A convention that continues to cause confusion when representing dendrochronological data is the use of the astronomical calendar. The astronomical calendar includes the year 0 so matches the AD calendar, but is one year different in the BC period. Astronomical dates are easier to handle in statistical analyses but have been erroneously quoted as BC years in even some very prestigious articles. Whatever method is used, it should be clear and consistent.<br />
<br />
=== Ice layers ===<br />
Role of flow models. <br />
<br />
<br />
== Age-modeling software ==<br />
<br />
<br />
Nick/Liz: please provide guidelines on how age modeling software should be reported. <br />
Content:<br />
* method (e.g. Bacon, OxCal, BChron, BAM)<br />
* version<br />
* parameters<br />
<br />
Form: what does this look like in JSON? <br />
<br />
== Polls ==<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
For '''NEW DATASETS''': (this is a dummy poll; please update)<br />
<poll><br />
What is your favorite chronology poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
For '''LEGACY DATASETS''':<br />
<poll><br />
What should we do with legacy chronologies?<br />
Contact original authors to obtain their uncalibrated dates<br />
Curse authors who were too short-sighted to archive uncalibrated dates<br />
Ignore them altogether<br />
</poll><br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11773
Peter Brewer
2016-10-10T18:06:55Z
<p>Petebrew: </p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Current Affiliation=Laboratory of Tree Ring Research|<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Expertise=Dendrochronology |<br />
Expertise=Data_standards |<br />
Expertise=Software_development |<br />
Github ID=petebrew|<br />
Google Scholar ID=i0sfmZ4AAAAJ|<br />
Has User ID=Petebrew|<br />
Highest Degree=PhD|<br />
Name ©=Peter Brewer|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group|<br />
University=University of Arizona}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11772
Peter Brewer
2016-10-10T18:06:35Z
<p>Petebrew: </p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Current Affiliation=Laboratory of Tree Ring Research|<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Expertise=Paleoclimatology |<br />
Expertise=Data_standards |<br />
Expertise=Software_development |<br />
Github ID=petebrew|<br />
Google Scholar ID=i0sfmZ4AAAAJ|<br />
Has User ID=Petebrew|<br />
Highest Degree=PhD|<br />
Name ©=Peter Brewer|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group|<br />
University=University of Arizona}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11771
Category:Trees Working Group
2016-10-10T17:48:44Z
<p>Petebrew: /* Location information */</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>Jansma, E., Brewer, P. W. & Zandhuis, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. [http://dx.doi.org/10.1016/j.dendro.2009.06.009 DOI]</ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
<br />
<poll><br />
What should the scope of this working group be?<br />
Solely the needs of the paleoclimate community <br />
Concentrate on the needs of the paleoclimate community initially while keeping in mind wider needs<br />
Handle the needs of as many communities as possible <br />
</poll><br />
<br />
<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
<br />
=== Detrending ===<br />
<br />
Maintaining references back to raw ring-width measurements is important to maintain data transparency. When detrending has been performed a detailed record of what has been done should be stored along with the software/library used. Implementations of different detrending techniques in different software can produce different results. <br />
<br />
<br />
=== Stable isotopes ===<br />
<br />
Some recommendations were made for an 'International Tree Ring Isotope Databank' ITRIDB by Csank<ref>Csank, A.Z. (2009) An International Tree-Ring Isotope Data Bank– A Proposed Repository for Tree-Ring Isotopic Data. Tree-Ring Research 65(2):163-164. [http://dx.doi.org/10.3959/1536-1098-65.2.163 DOI]</ref><br />
<br />
== Location information ==<br />
<br />
Prior to the wide availability and affordability of GPS handsets, location information in dendrochronology tended to be low accuracy coordinates for a particular study site. This is what is stored in the ITRDB. However, for many years now the many (majority? all?) researchers have collected GPS coordinates for each individual tree. A clear distinction is needed in the ontology to record what the location information is recording. <br />
<br />
Chronologies are by definition an amalgamation of data from multiple trees. Location information for these can therefore be represented either as multiple coordinates (one for each tree) and/or a polygon denoting the extent of the area covered by the chronology. Should such a polygon be the smallest area encompassing all tree coordinates or should it be the freehand area covering the area the researcher feels the chronology represents? <br />
<br />
Further complications arise when handling tree-ring data collected from non-living trees. Sample from snags can be reasonably expected to be at least close to where the tree grew, but archaeological and other cultural samples can be found miles from their initial growth location. Very long range transport/trade of wood has taken place for millenia. Some studies have successfully determined the provenance of transported/traded samples through dendrochronological analyses and/or isotopic work. In these cases it would be good to also be able to store this sort of information. Regardless though, the type of location must be clearly stored with all locality data.<br />
<br />
== Recommendations for new datasets ==<br />
<br />
Recommendations for collecting dendroarchaeological data have been made by Brewer and Jansma<ref>Brewer, P.W. and Jansma, E. (2016) Dendrochronological Data in Archaeology: A Guide to Good Practice, Archaeology Data Service / Digital Antiquity v1.1. [http://guides.archaeologydataservice.ac.uk/g2gp/Dendro_Toc Link]</ref>. These are specific to the collection of samples for cultural dendrochronology, but still relevant in part to wider tree-ring research. <br />
<br />
<br />
<br />
== Recommendations of legacy datasets ==<br />
The task of standardizing and upgrading legacy datasets cannot be underestimated. Recommendations for how to handle datasets will likely vary depending on the context. For instance, if a dataset owner wants to upgrade their own legacy data they should have access to the vast majority of data/metadata. Given the time/money they should be able to upgrade to a similar quality as new datasets. In contrast, upgrading the existing NOAA/ITRDB holdings of others will be far more challenging as the majority of datasets are missing key information or key information is stored ambiguously. For orphaned datasets it's very likely that a substantial amount of information is already lost with no hope of recovery.<br />
<br />
In general, legacy datasets should be upgraded to meet a minimum set of criteria:<br />
# Type of data: raw measurements or derived chronologies<br />
# Measurement variable stored<br />
# Measurement units stored<br />
# Missing rings handled clearly and consistently<br />
# Taxon<br />
# Location <br />
# Location type<br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11770
Category:Trees Working Group
2016-10-10T17:45:14Z
<p>Petebrew: /* Recommendations of legacy datasets */</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>Jansma, E., Brewer, P. W. & Zandhuis, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. [http://dx.doi.org/10.1016/j.dendro.2009.06.009 DOI]</ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
<br />
<poll><br />
What should the scope of this working group be?<br />
Solely the needs of the paleoclimate community <br />
Concentrate on the needs of the paleoclimate community initially while keeping in mind wider needs<br />
Handle the needs of as many communities as possible <br />
</poll><br />
<br />
<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
<br />
=== Detrending ===<br />
<br />
Maintaining references back to raw ring-width measurements is important to maintain data transparency. When detrending has been performed a detailed record of what has been done should be stored along with the software/library used. Implementations of different detrending techniques in different software can produce different results. <br />
<br />
<br />
=== Stable isotopes ===<br />
<br />
Some recommendations were made for an 'International Tree Ring Isotope Databank' ITRIDB by Csank<ref>Csank, A.Z. (2009) An International Tree-Ring Isotope Data Bank– A Proposed Repository for Tree-Ring Isotopic Data. Tree-Ring Research 65(2):163-164. [http://dx.doi.org/10.3959/1536-1098-65.2.163 DOI]</ref><br />
<br />
== Location information ==<br />
<br />
Prior to the wide availability and affordability of GPS handsets, location information in dendrochronology tended to be low accuracy coordinates for a particular study site. This is what is stored in the ITRDB. However, for many years now the many (majority? all?) researchers have collected GPS coordinates for each individual tree. A clear distinction is needed in the ontology to record what the location information is recording. <br />
<br />
Chronologies are by definition an amalgamation of data from multiple trees. Location information for these can therefore be represented either as multiple coordinates (one for each tree) and/or a polygon denoting the extent of the area covered by the chronology. Should such a polygon be the smallest area encompassing all tree coordinates or should it be the freehand area covering the area the researcher feels the chronology represents? <br />
<br />
Further complications arise when handling tree-ring data collected from non-living trees. Sample from snags can be reasonably expected to be at least close to where the tree grew, but archaeological and other cultural samples can be found miles from their initial growth location. Very long range transport/trade of wood has taken place for millenia. The type of location must be clearly stored with all locality data.<br />
<br />
<br />
== Recommendations for new datasets ==<br />
<br />
Recommendations for collecting dendroarchaeological data have been made by Brewer and Jansma<ref>Brewer, P.W. and Jansma, E. (2016) Dendrochronological Data in Archaeology: A Guide to Good Practice, Archaeology Data Service / Digital Antiquity v1.1. [http://guides.archaeologydataservice.ac.uk/g2gp/Dendro_Toc Link]</ref>. These are specific to the collection of samples for cultural dendrochronology, but still relevant in part to wider tree-ring research. <br />
<br />
<br />
<br />
== Recommendations of legacy datasets ==<br />
The task of standardizing and upgrading legacy datasets cannot be underestimated. Recommendations for how to handle datasets will likely vary depending on the context. For instance, if a dataset owner wants to upgrade their own legacy data they should have access to the vast majority of data/metadata. Given the time/money they should be able to upgrade to a similar quality as new datasets. In contrast, upgrading the existing NOAA/ITRDB holdings of others will be far more challenging as the majority of datasets are missing key information or key information is stored ambiguously. For orphaned datasets it's very likely that a substantial amount of information is already lost with no hope of recovery.<br />
<br />
In general, legacy datasets should be upgraded to meet a minimum set of criteria:<br />
# Type of data: raw measurements or derived chronologies<br />
# Measurement variable stored<br />
# Measurement units stored<br />
# Missing rings handled clearly and consistently<br />
# Taxon<br />
# Location <br />
# Location type<br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11769
Category:Trees Working Group
2016-10-10T17:41:33Z
<p>Petebrew: Location information and recommendations for new/legacy datasets</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>Jansma, E., Brewer, P. W. & Zandhuis, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. [http://dx.doi.org/10.1016/j.dendro.2009.06.009 DOI]</ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
<br />
<poll><br />
What should the scope of this working group be?<br />
Solely the needs of the paleoclimate community <br />
Concentrate on the needs of the paleoclimate community initially while keeping in mind wider needs<br />
Handle the needs of as many communities as possible <br />
</poll><br />
<br />
<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
<br />
=== Detrending ===<br />
<br />
Maintaining references back to raw ring-width measurements is important to maintain data transparency. When detrending has been performed a detailed record of what has been done should be stored along with the software/library used. Implementations of different detrending techniques in different software can produce different results. <br />
<br />
<br />
=== Stable isotopes ===<br />
<br />
Some recommendations were made for an 'International Tree Ring Isotope Databank' ITRIDB by Csank<ref>Csank, A.Z. (2009) An International Tree-Ring Isotope Data Bank– A Proposed Repository for Tree-Ring Isotopic Data. Tree-Ring Research 65(2):163-164. [http://dx.doi.org/10.3959/1536-1098-65.2.163 DOI]</ref><br />
<br />
== Location information ==<br />
<br />
Prior to the wide availability and affordability of GPS handsets, location information in dendrochronology tended to be low accuracy coordinates for a particular study site. This is what is stored in the ITRDB. However, for many years now the many (majority? all?) researchers have collected GPS coordinates for each individual tree. A clear distinction is needed in the ontology to record what the location information is recording. <br />
<br />
Chronologies are by definition an amalgamation of data from multiple trees. Location information for these can therefore be represented either as multiple coordinates (one for each tree) and/or a polygon denoting the extent of the area covered by the chronology. Should such a polygon be the smallest area encompassing all tree coordinates or should it be the freehand area covering the area the researcher feels the chronology represents? <br />
<br />
Further complications arise when handling tree-ring data collected from non-living trees. Sample from snags can be reasonably expected to be at least close to where the tree grew, but archaeological and other cultural samples can be found miles from their initial growth location. Very long range transport/trade of wood has taken place for millenia. The type of location must be clearly stored with all locality data.<br />
<br />
<br />
== Recommendations for new datasets ==<br />
<br />
Recommendations for collecting dendroarchaeological data have been made by Brewer and Jansma<ref>Brewer, P.W. and Jansma, E. (2016) Dendrochronological Data in Archaeology: A Guide to Good Practice, Archaeology Data Service / Digital Antiquity v1.1. [http://guides.archaeologydataservice.ac.uk/g2gp/Dendro_Toc Link]</ref>. These are specific to the collection of samples for cultural dendrochronology, but still relevant in part to wider tree-ring research. <br />
<br />
<br />
<br />
== Recommendations of legacy datasets ==<br />
The task of standardizing and upgrading legacy datasets cannot be underestimated. Recommendations for how to handle datasets will likely vary depending on the context. For instance, if a dataset owner wants to upgrade their own legacy data they should have access to the vast majority of data/metadata. Given the time/money they should be able to upgrade to a similar quality as new datasets. In contrast, upgrading the existing NOAA/ITRDB holdings of others will be far more challenging as the majority of datasets are missing key information or key information is stored ambiguously. For orphaned datasets it's very likely that a substantial amount of information is already lost with no hope of recovery.<br />
<br />
In general, legacy datasets should be upgraded to meet a minimum set of criteria:<br />
# Measurement variable stored<br />
# Measurement units stored<br />
# Missing rings handled clearly and consistently<br />
<br />
<br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11768
Category:Trees Working Group
2016-10-10T16:35:16Z
<p>Petebrew: Scope poll</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>JANSMA, E., BREWER, P. W. & ZANDHUIS, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. - [http://www.sciencedirect.com/science/article/pii/S1125786509000563 Science Direct]</ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
<br />
<poll><br />
What should the scope of this working group be?<br />
Solely the needs of the paleoclimate community <br />
Concentrate on the needs of the paleoclimate community initially while keeping in mind wider needs<br />
Handle the needs of as many communities as possible <br />
</poll><br />
<br />
<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
=== Detrending ===<br />
<br />
Maintaining references back to raw ring-width measurements is important to maintain data transparency. When detrending has been performed a detailed record of what has been done should be stored along with the software/library used. Implementations of different detrending techniques in different software can produce different results. <br />
<br />
How to document the type of detrending applied to enable reproducibility.<br />
<br />
=== Stable water isotopes ===<br />
<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
<br />
<poll><br />
What is your favorite poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11744
Category:Trees Working Group
2016-10-07T17:16:29Z
<p>Petebrew: </p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>JANSMA, E., BREWER, P. W. & ZANDHUIS, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. - [http://www.sciencedirect.com/science/article/pii/S1125786509000563 Science Direct]</ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
=== Detrending ===<br />
<br />
Maintaining references back to raw ring-width measurements is important to maintain data transparency. When detrending has been performed a detailed record of what has been done should be stored along with the software/library used. Implementations of different detrending techniques in different software can produce different results. <br />
<br />
How to document the type of detrending applied to enable reproducibility.<br />
<br />
=== Stable water isotopes ===<br />
<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
<br />
<poll><br />
What is your favorite poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11743
Category:Trees Working Group
2016-10-07T17:06:18Z
<p>Petebrew: </p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>JANSMA, E., BREWER, P. W. & ZANDHUIS, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. - [http://www.sciencedirect.com/science/article/pii/S1125786509000563 Science Direct]</ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
=== Detrending ===<br />
<br />
How to document the type of detrending applied to enable reproducibility.<br />
<br />
=== Stable water isotopes ===<br />
<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
<br />
<poll><br />
What is your favorite poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11742
Category:Trees Working Group
2016-10-07T17:04:44Z
<p>Petebrew: TRiDaS</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
The discussion within this group can build upon the work done by the Tree Ring Data Standard (TRiDaS) consortium <ref>JANSMA, E., BREWER, P. W. & ZANDHUIS, I. (2010) TRiDaS 1.1: The tree ring data standard. Dendrochronologia 28, 99-130. </ref>. While the contributors were weighted towards dendroarchaeologists, the standard was intended to be universal for all uses of tree-ring data. The requirements laid out be the TRiDaS contributors are therefore going to largely be relevant to discussions here.<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
=== Detrending ===<br />
<br />
How to document the type of detrending applied to enable reproducibility.<br />
<br />
=== Stable water isotopes ===<br />
<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
<br />
<poll><br />
What is your favorite poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11741
Category:Trees Working Group
2016-10-07T16:54:01Z
<p>Petebrew: Event data</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
=== Event information === <br />
<br />
Tree-rings provide the potential to store information about specific events. The most common of these is a forest fire (stored as a fire scar or other anatomical damage), but may include the effects of defoliating insects, volcanic eruptions etc. This sort of event data is represented as binary yes/no occurrences in particular rings and is quite distinct from the continuous measurement variables (e.g. ring-widths, isotope concentrations etc) that are typical with most proxies.<br />
<br />
<br />
=== Tree rings ===<br />
<br />
=== Detrending ===<br />
<br />
How to document the type of detrending applied to enable reproducibility.<br />
<br />
=== Stable water isotopes ===<br />
<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
<br />
<poll><br />
What is your favorite poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11740
Category:Trees Working Group
2016-10-07T16:47:42Z
<p>Petebrew: Measurement variables</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
<br />
=== Measurement variables ===<br />
<br />
The traditional variable measured in dendrochronology is of course the whole ring-width. It is common now to collect a wealth of other variables from tree-rings including:<br />
<br />
* Whole ring width<br />
* Early wood width<br />
* Late wood width<br />
* Whole ring density<br />
* Early wood density<br />
* Late wood density<br />
* Maximum density<br />
* Latewood percentage<br />
* Vessel size<br />
* Blue intensity (density proxy)<br />
<br />
<br />
<br />
=== Tree rings ===<br />
<br />
=== Detrending ===<br />
<br />
How to document the type of detrending applied to enable reproducibility.<br />
<br />
=== Stable water isotopes ===<br />
<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
<br />
<poll><br />
What is your favorite poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11739
Category:Trees Working Group
2016-10-07T16:40:22Z
<p>Petebrew: Questioning the scope of the discussion</p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
Tree rings are used by many different researchers, for many different reasons. The LinkedEarth community is well rooted in the paleoclimate community and while the ontology and data standard has great potential for use outside this community, we need to decide how to address the overlap in our discussions. Should be concentrate on the needs of the paleoclimate community exclusively to begin with, and intend to go back and revise at a later date? Or should we attempt to accommodate all potential users of tree-ring data from day 1?<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
=== Tree rings ===<br />
<br />
=== Detrending ===<br />
<br />
How to document the type of detrending applied to enable reproducibility.<br />
<br />
=== Stable water isotopes ===<br />
<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
<br />
<poll><br />
What is your favorite poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Trees_Working_Group&diff=11738
Category:Trees Working Group
2016-10-07T16:34:03Z
<p>Petebrew: </p>
<hr />
<div>[[Category:Working Group]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''trees''' (see [[:Category:Wood | this page]] for a definition of the wood archive), and aims to formulate a set of recommendations for such a standard. Note that chronological aspects should be discussed within the [[:Category:Chronologies_Working_Group|Chronologies WG]].<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the measurements themselves<br />
** any inference made from the measurements (e.g. calibration to temperature)<br />
** the underlying uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal data table''' for each type of observation, so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
== Scope ==<br />
<br />
== Sensors ==<br />
An initial recommendation is to focus on different sensors:<br />
<br />
=== Tree rings ===<br />
<br />
=== Detrending ===<br />
<br />
How to document the type of detrending applied to enable reproducibility.<br />
<br />
=== Stable water isotopes ===<br />
<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
<br />
<poll><br />
What is your favorite poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Category:Chronologies_Working_Group&diff=11737
Category:Chronologies Working Group
2016-10-07T16:31:03Z
<p>Petebrew: Consideration of tree-ring chronologies</p>
<hr />
<div>[[Category:Working Group]]<br />
[[File:Chronology_pic.png|thumb|right|alt=An imaginary chronology based on U/Th dates, generated via Bchron|Credit: Julien Emile-Geay (Own work)]]<br />
<br />
== Overview ==<br />
In the Linked Earth context, a [[:Category:Working_Group|working group]] (WG) is a self-organized coalition of knowledgeable experts, whose activities are governed [[:Category:Working_Group|herewith]]. This page is dedicated to the discussion of data and metadata standards for '''chronologies''', and aims to formulate a set of recommendations for such a standard.<br />
<br />
This WG needs to work closely with other WGs, as constraints will vary by archive. Nevertheless, some aspects are common enough that it is worth pursuing some general recommendations, and devise ''ad hoc'' adjustments for individual archives if need be. It is recommended that every WG coordinator join this WG to keep track of discussions.<br />
<br />
__MEMBERS__<br />
<br />
== Specific tasks ==<br />
<br />
We recommend that discussions focus on the following techniques, and explore potential commonalities.<br />
<br />
For each chronology type, we recommend:<br />
* structuring discussions around what scientific questions one would want to ask of the data<br />
* listing essential, recommended, and optional information for:<br />
** the age models themselves<br />
** the chronological measurements (ChronData tables, in LiDP/LinkedEarth parlance)<br />
** their uncertainties, and what those numbers correspond to (e.g. 1-sigma or 2-sigma?)<br />
* provide an '''ideal chronology table''', so the community knows what to report and how to report it.<br />
* provide separate recommendations for new and legacy datasets<br />
<br />
While it is recognized that most real-word chronologies are of mixed types (e.g. a Holocene lake sediment chronology may blend radiocarbon dates, {{SimpleNuclide2|Lead|210}} dates, and volcanic ash markers), it is critical to first define guidelines for how to report ''pure'' chronologies. Once the foundations are sound, they will be easier to compose together.<br />
<br />
== Tie-point chronologies ==<br />
<br />
=== Radiocarbon ===<br />
The following came from P. Reimer by way of T. Guilderson. <br />
<br />
Key references: Stuiver & Polach [1977] <ref name="SP77">Minze Stuiver and H. A. Polach, 1977. Discussion: Reporting of 14C Data. Radiocarbon 19, 3, 355-363. </ref> and Reimer et al., [2004] <ref>Paula J. Reimer, T. A. Brown, and R. W. Reimer, 2004. Discussion: Reporting and calibration of post-bomb 14C Data. Radiocarbon, 46, 3, 1299-1304.</ref><br />
<br />
==== metadata ====<br />
* Sample ID<br />
* type/matrix<br />
* location (lat, lon, masl/mbsl altitude/depth, depth/height in section/core and referenced)<br />
<br />
==== Radiocarbon Measurements ====<br />
<br />
* Chemical pretreatment/preparation (oxidation, chemical leach (%), a/b/a, soxhlet, ultrafiltration, none, etc)<br />
<br />
* Method: GPC, LSC, AMS, etc<br />
<br />
* Laboratory ID# (eg. OS####; CAMS####; QUB####)<br />
<br />
* δ{{SimpleNuclide2|Carbon|13}} ratio actual/estimated (PDB/V-PDB) <ref>Note, the AMS measured {{SimpleNuclide2|Carbon|13}} has low precision (a few per mil, compared to IRMS). Most AMS labs do NOT report the machine measured {{SimpleNuclide2|Carbon|13}} value because it is frequently misused. This should be estimated as per SP77 or an IRMS-based value/estimate. </ref><br />
<br />
* Conventional radiocarbon age as years BP and one-sigma standard deviation <ref> Note, that by definition, conventional radiocarbon age is the Libby based age. Most AMS laboratories report 1-sigma sd of the analysis or the 1-sigma sd reproducibility for similar aged/sized material. </ref><br />
<br />
* F14C ({{SimpleNuclide2|Carbon|13}} and background correction applied)<ref> This is slightly different than Stuiver and Polach who have "D14C" as the optional parameter. </ref>:<br />
<br />
We suggest the inclusion of the background and d13C corrected Fraction modern (F14C) as it is the primary reported value. In the past there has been some inconsistencies in the literature/laboratories with regards to fraction modern. By using/requesting F14C you will be explicitly requesting {{SimpleNuclide2|Carbon|13}} and background corrected Fraction Modern (aka F14C, as per Reimer et al.[2004]) as intended by SP77).<br />
* Correction applied to radiocarbon date prior to, or during conversion to calibrated age:<br />
** marine reservoir effect: <br />
*** Marine reservoir age, ± one-sigma sd (or square root of the variance) uncertainty, reference/source<br />
*** DELTA_R value, ± one-sigma sd (or square root of the variance) uncertainty, reference/source<br />
* hard/soft water effect: value, ± one-sigma sd (or square root of var) uncertainty, reference/source<br />
* other corrections: value ({{SimpleNuclide2|Carbon|14}} years), ± one-sigma sd (or square root of var), reference/source<br />
<br />
* Calibration or conversion to calibrated ages:<br />
As of present, the international radiocarbon community recommends the use of the INTCAL13 (aka Marine 13<ref>P. J. Reimer et al., 2013. INTCAL13 and MARINE13 Radiocarbon age calibration curves, 0-50,000 years CAL BP. Radiocarbon, 55, 1869-1887.</ref>) and SHCAL13 <ref>A. G. Hogg, et al., 2013. SHCal13 Southern Hemisphere calibration, 0-50,000 years cal BP. Radiocarbon 55, 1889-1903.</ref> data products. <br />
* Calibration of post-bomb (post 1954/1957) samples should also include the calibration data-set utilized, description/reference of any corrections applied, and the software/algorithm utilized to convert the F14C data to years AD.<br />
<br />
=== Lead ===<br />
<br />
no known existing standard/template<br />
=== U-series ===<br />
<br />
== Layer-counted chronologies ==<br />
<br />
Comboul et al<ref>Comboul, M., J. Emile-Geay, M. N. Evans, N. Mirnateghi, K. M. Cobb, and D. M. Thompson (2014), A probabilistic model of chronological errors in layer-counted climate proxies: applications to annually banded coral archives, Climate of the Past, 10(2), 825–841, doi:10.5194/cp-10-825-2014</ref> argue that it is critical to report uncertainties in layer-counted chronologies, and that these can be expressed in terms of an undercounting and overcounting rate. However, there needs to be agreement about how to measure and report this rate for various archives. <br />
<br />
=== Varves ===<br />
<br />
=== Growth rings ===<br />
Trees, corals, speleothems<br />
<br />
Tree-rings typically provide an absolute chronology but there needs to be the facility to also work with 'floating' chronologies anchored typically by radiocarbon. A hybrid dendro-radiocarbon chronological framework should be supported. <br />
<br />
Tree-rings data can also be stored at subannual level e.g. with early and latewood parameters.<br />
<br />
=== Ice layers ===<br />
Role of flow models. <br />
<br />
<br />
== Age-modeling software ==<br />
<br />
<br />
Nick/Liz: please provide guidelines on how age modeling software should be reported. <br />
Content:<br />
* method (e.g. Bacon, OxCal, BChron, BAM)<br />
* version<br />
* parameters<br />
<br />
Form: what does this look like in JSON? <br />
<br />
== Polls ==<br />
<br />
Here are polls that the group might want to consider:<br />
<br />
For '''NEW DATASETS''': (this is a dummy poll; please update)<br />
<poll><br />
What is your favorite chronology poll?<br />
A poll that is droll<br />
A poll with a role<br />
A poll with a roll<br />
</poll><br />
<br />
For '''LEGACY DATASETS''':<br />
<poll><br />
What should we do with legacy chronologies?<br />
Contact original authors to obtain their uncalibrated dates<br />
Curse authors who were too short-sighted to archive uncalibrated dates<br />
Ignore them altogether<br />
</poll><br />
<br />
==References==<br />
<references \></div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11384
Peter Brewer
2016-09-27T21:22:58Z
<p>Petebrew: Added PropertyValue: Expertise = Dendrochronology, data standards, software development</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Current Affiliation=Laboratory of Tree Ring Research|<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Expertise=Dendrochronology,_data_standards,_software_development|<br />
Github ID=petebrew|<br />
Google Scholar ID=i0sfmZ4AAAAJ|<br />
Has User ID=Petebrew|<br />
Highest Degree=PhD|<br />
Name ©=Peter Brewer|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group|<br />
University=University of Arizona}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11382
Peter Brewer
2016-09-27T21:22:40Z
<p>Petebrew: Added PropertyValue: Current Affiliation = Laboratory of Tree Ring Research</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Current Affiliation=Laboratory of Tree Ring Research|<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Github ID=petebrew|<br />
Google Scholar ID=i0sfmZ4AAAAJ|<br />
Has User ID=Petebrew|<br />
Highest Degree=PhD|<br />
Name ©=Peter Brewer|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group|<br />
University=University of Arizona}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11381
Peter Brewer
2016-09-27T21:22:31Z
<p>Petebrew: Added PropertyValue: University = University of Arizona</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Github ID=petebrew|<br />
Google Scholar ID=i0sfmZ4AAAAJ|<br />
Has User ID=Petebrew|<br />
Highest Degree=PhD|<br />
Name ©=Peter Brewer|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group|<br />
University=University of Arizona}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11380
Peter Brewer
2016-09-27T21:22:23Z
<p>Petebrew: Added PropertyValue: Github ID = petebrew</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Github ID=petebrew|<br />
Google Scholar ID=i0sfmZ4AAAAJ|<br />
Has User ID=Petebrew|<br />
Highest Degree=PhD|<br />
Name ©=Peter Brewer|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11379
Peter Brewer
2016-09-27T21:22:16Z
<p>Petebrew: Added PropertyValue: Google Scholar ID = i0sfmZ4AAAAJ</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Google Scholar ID=i0sfmZ4AAAAJ|<br />
Has User ID=Petebrew|<br />
Highest Degree=PhD|<br />
Name ©=Peter Brewer|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11378
Peter Brewer
2016-09-27T21:21:55Z
<p>Petebrew: Added PropertyValue: Highest Degree = PhD</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Has User ID=Petebrew|<br />
Highest Degree=PhD|<br />
Name ©=Peter Brewer|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11377
Peter Brewer
2016-09-27T21:21:46Z
<p>Petebrew: Added PropertyValue: Name © = Peter Brewer</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Has User ID=Petebrew|<br />
Name ©=Peter Brewer|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11376
Peter Brewer
2016-09-27T21:21:42Z
<p>Petebrew: Added PropertyValue: OrcidNumber © = 0000-0001-8972-3210</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Has User ID=Petebrew|<br />
OrcidNumber ©=0000-0001-8972-3210|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11375
Peter Brewer
2016-09-27T21:21:22Z
<p>Petebrew: Added PropertyValue: Email © = p.brewer@ltrr.arizona.edu</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Email ©=p.brewer@ltrr.arizona.edu|<br />
Has User ID=Petebrew|<br />
Subscribes To=Category:Trees_Working_Group|<br />
Subscribes To=Category:Chronologies_Working_Group}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11374
Peter Brewer
2016-09-27T21:21:02Z
<p>Petebrew: Added PropertyValue: Subscribes To = Category:Chronologies_Working_Group</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Has User ID=Petebrew|<br />
Subscribes To=Category:Chronologies_Working_Group|<br />
Subscribes To=Category:Trees_Working_Group}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11373
Peter Brewer
2016-09-27T21:20:54Z
<p>Petebrew: Added PropertyValue: Subscribes To = Category:Trees_Working_Group</p>
<hr />
<div>[[Category:Person_©]]{{#set:<br />
Has User ID=Petebrew|<br />
Subscribes To=Category:Trees_Working_Group}}</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11371
Peter Brewer
2016-09-27T21:20:41Z
<p>Petebrew: Setting categories as Person_©</p>
<hr />
<div>[[Category:Person_©]]</div>
Petebrew
https://wiki.linked.earth/wiki/index.php?title=Peter_Brewer&diff=11372
Peter Brewer
2016-09-27T21:20:41Z
<p>Petebrew: Added PropertyValue: Has_User_ID = Petebrew</p>
<hr />
<div>[[Category:Person_©]]{{#set:|<br />
Has User ID=Petebrew}}</div>
Petebrew