As many of you know, a new version of the Neotoma R package, 2.0, was released in February of this year. V2.0 is a major update, that points to the new PostgreSQL version of the backend database and includes a major redesign of the R data objects so that they now hold the full suite of all data and metadata associated with a dataset at a site.
We had hoped to keep supporting the 1.0 R package for at least the next several months, but unfortunately this package was housed on an older Penn State server that effectively has been shut down. This shutdown was unexpected to the Neotoma team. There is some chance that we will be able to restore the services supporting the 1.0 R package, but so far this seems unlikely. In any case, the 1.0 R package was pointing to pointing to an static version of the database that is already at least a year out of date.
We apologize that the full sunsetting of the 1.0 R package has been more abrupt than intended and are sorry for any disruptions that this may have caused to anyone’s analytical workflows. Fortunately, Simon and Soccoro have been hard at work adding new features to the 2.0 R package and preparing example vignettes to show users how to use the 2.0 features. Simon just posted the following information to Neotoma’s Slack workspace, in #it_r.
In preparation for the #db_epd workshop in Prague and the AMQUA workshop, @Socorro and I have been working on getting a bunch more changes to the
neotoma2 R package finished up, and some more vignette/workflows written up. You can see the drafts here:
· https://open.neotomadb.org/EPD_binder/simple_workflow.html (searching, plots across time, space & climate)
· https://open.neotomadb.org/EPD_binder/complex_workflow.html (building chronologies)
We'd very much appreciate your feedback, either directly or through DMs. The Rmd documents from which these were generated can be found here: https://github.com/neotomadb/EPD_binder If you feel comfortable working with GitHub we welcome your contributions here as well.
Posted by Jack Williams on 05/27
We are excited to announce, at long last, the beta release of the Neotoma R package, neotoma2. Many, many thanks to Simon Goring and Socorro Dominguez for this huge effort, and all of the folks who have contributed suggestions, code, vignette examples, etc. along the way.
The new R package works with the latest Neotoma web services, and is designed to work more closely with the R tidyverse, making data access and analysis more streamlined.
Nested sites, datasets and samples to more closely mirror the data model of the database.
Filter functions to allow you remove sites and datasets easily
New set_*() functions, allowing you to add new records directly into your analysis seamlessly
The neotoma2 package is currently hosted on GitHub (https://github.com/NeotomaDB/neotoma2) while we iron out the kinks and see how people use the package.
If you’d like to use the package we’ve provided some RMarkdown vignettes to get you started. Installation is as easy as:
We’ll be running a live coding day on Wednesday Feb 16 from 9:00am - 12:00pm (Pacific) on Zoom (https://uwmadison.zoom.us/j/97083802266?pwd=OEd3a2hyUlJwLzJyc3Q1dUFtMlVjUT09). Folks are invited to join and talk with us about their needs, and see the package in action as we work to improve our online resources.
Bug reports can be made to Simon Goring (email@example.com), online at https://github.com/NeotomaDB/neotoma2/issues or in the #it_r channel of our Slack workspace (https://join.slack.com/t/neotomadb/shared_invite/zt-cvsv53ep-wjGeCTkq7IhP6eUNA9NxYQ).
Folks are more than welcome to contribute to the project. Please let us know if you’d like to help out with documentation, examples, code, or helping us craft useful case studies for using the R package!
Posted by Jessica Blois on 02/11
For PIs writing proposals to NSF, standard text about Neotoma resources is available here: https://www.neotomadb.org/documents
Posted by Jack Williams on 09/20
On April 28, 2020, Neotoma leaders organized and convened an all-day (17hour) online zoom webinar in remembrance of Eric’s life and work, across four sessions organized by continent and timezone: Asia and IndoPacific, Europe, Africa, and the Americas. All talks were recorded and posted to YouTube.
Website for Eric24H event: https://sites.google.com/view/ericgrimm/home
YouTube Channel: https://www.youtube.com/channel/UCRED5fsSanfbhGBs4gt6iBA
The event includes a nice series of short (15 min) introductory overviews about Neotoma, that are excellent starting points for students or other newcomers to Neotoma. They include talks about the history of Neotoma (Russ Graham), its current directions (Jack Williams), what makes Neotoma unique as a long-lasting data resource (Andrea Thomer), and lessons learned by the next generation of Neotoma stewards and leaders (Jessica Blois and Simon Goring).
Posted by Jack Williams on 05/14
The original version only supported pollen data, whereas this new version supports pollen, diatom, ostracodes, testate amoebae, and vertebrates. This new version can be extended to other variables as well, with some case-by-case decisions needed about how to handle expected range values, missing values, units, etc.
Posted by Jack Williams on 02/02
I'm pleased to report several additional milestones in the porting of Neotoma services over from Windows/SQLServer to Linux/Postgres:
1) An updated version of Tilia (v3.0.1) was released today to Data Stewards, and is ready and enabled for Stewards to resume uploading data to Neotoma. Eric had been working on this new version for several months, with roughly 70 new datasets uploaded, to ensure it was fully connected with the new postgres version of Neotoma. This version of Tilia can download sites, upload new sites, and add new datasets to existing sites. There are a few minor known issues that we are working on fixing.
2) Neotoma Explorer has now been fully repointed to the new version of Neotoma, so as new sites are added, you will be able to find them in Explorer. Jonathan Nelson at Penn State soon will start to work on next-stage improvements to Explorer, in response to Neotoma user and steward requests. [11/25/20 Update: Several bugs have been reported, in some search windows and in Stratigraphic Diagrammer and its display of chronologies. We're working on them now and discussing in Slack: https://neotomadb.slack.com.]
3) Landing pages for individual Neotoma datasets are now re-enabled. For example, https://data.neotomadb.org/14194 Simon Goring is also about to turn on the minting of DOIs for all Neotoma records. This capability has been available for a while, but has been put on hold while bugs were ironed out of the uploading process; we wanted to avoid minting DOIs for datasets that might need to be removed if errors were found.
See the updated summary table for details about individual components, their current status, and their locations.
Posted by Jack Williams on 11/20
It is with great sorrow that we pass along the news that Eric Grimm, one of the co-founders of the Neotoma Paleoecology Database, passed away unexpectedly over the weekend. Eric was a giant in the fields of palynology and paleoecology, whose work was marked both by great breadth of vision and deep meticulousness. Eric’s vision and hard work was instrumental in creating a culture of open data and transparent science so that as individuals, we could all contribute to a greater good of answering globally relevant questions about the influence of climate on Earth’s vegetation and the interactions among species. His contributions to the fields of paleoecology and open biological and geological databases cannot be overemphasized. He will be sorely missed by all of us, as a leader, and as our friend.
Eric’s vision of an open and shared data architecture for paleoecology, first realized as the continental pollen databases, and now as the multi-proxy Neotoma Paleoecology Database, lives on. We have known that for an institution to be sustainable, it cannot be solely dependent on any single person. Hence, several years ago, we embarked on a process of expanding and solidifying the governance and day-to-day work of maintaining the Neotoma database and its software ecosystem, following Eric’s example of open, collaborative work. So the Neotoma Executive Team and Leadership Council is in the process of planning our next steps forward. We have many ideas here, but they will take some days to solidify into plans and can also can wait until we process the news and our grief.
In the meantime, if you have any questions about this news, or anything related to Tilia or Neotoma, you can contact the Neotoma Executive Team (firstname.lastname@example.org), or Jack Williams (Exec Chair, email@example.com) or Jessica Blois (Assoc Exec Chair, firstname.lastname@example.org) directly, and we can figure out how best to address them.
Jack and Jessica, on behalf of the Neotoma Executive Committee
Posted by Jack Williams on 11/16
There is a new version of the R package available on GitHub. This update has been submitted to but not accepted yet by CRAN.
Posted by Jack Williams on 10/16