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Topsoil is a desktop application and Java library that creates data visualizations for geochronologists and other earth scientists. The project is led and maintained by CIRDLES, an undergraduate research lab at the College of Charleston in Charleston, South Carolina.
"Topsoil" is an anagram of "Isoplot", the name of an enormously successful Microsoft Excel Add-In with similar capabilities that now works only in older versions of Excel.
If you are interested in learning more about Topsoil, please contact Jim Bowring.
To cite Topsoil, please provide a footnote or acknowledgement as follows:
J.F. Bowring, PI CIRDLES.org Open Source Development Team. Topsoil - A community driven replacement for ISOPLOT. Apache License, Version 2.0. https://github.com/CIRDLES/topsoil.
We have an article in production that will become the official citable reference, stay tuned.
Kenneth R. Ludwig was born in 1944 in Berkeley, California. He received his B.S. (Chemistry, 1965), M.S. (Geology, 1967) and Ph.D. (Geochemistry, 1973) degrees all from the California Institute of Technology. He worked for the U.S. Geological Survey from 1973 to 1995, when he was recruited by the BGC to found a uranium-decay dating program. Ludwig served as Director and President of BGC from 2000 to 2003. Ludwig is notable among geochronologists as being expert in both the uranium-lead and uranium-series methods. Ken Ludwig has long served as the leader in statistical analysis of isotopic data in general and for U-Pb data in particular, from optimal data acquisition to final data reduction and statistically rigorous interpretations. Ken has patiently developed algorithms and plotting routines that have allowed thousands of isotope geochemists to better understand the power and limitations of their data. Much of this has been accomplished through his popular software package, Isoplot. Isoplot is a toolkit for data analysis and graphical presentation of isotope data, from isochrons to U-Pb and U-series Concordia plots, to calculation of weighted means. This program is in use in more than one hundred isotope laboratories for both research and teaching. His SQUID software for ion-microprobe data analysis is also widely used by the international community. Ludwig’s efforts at software distribution and improvement are legendary, largely unfunded, and have played an important role in the evolution of our science. Modern mass spectrometers can produce data with unprecedented precision, and new applications for geochronology are proliferating; now more than ever, cutting edge science relies on statistical analysis of dates and their uncertainties.
The isotope geochemistry community depends on the Isoplot and SQUID software packages, and there is great demand for their upkeep, modification, and adaption to new operating systems. In this light, and with Ken’s blessing, we have begun to develop a new system, Topsoil, to support the next generation of geochronologists.
Topsoil will run on Windows (x86 and x64), Linux (x86 and x64), and Mac (x64 only). Topsoil requires the latest version of Java (1.8 or higher), the installer for which can be found here.
To install Topsoil, download the latest JAR file from the releases page.
To run Topsoil, simply double click on the JAR file.
The easiest way to import data into Topsoil is to copy and paste it into the data table. First, select and copy the data in Excel that you want to import. The selected data must contiguous (although omissions are allowed) and have no more than one row of headers.
The data may then be pasted into Topsoil either by using the paste shortcut (Ctrl-p or ⌘-p on Mac) or by pressing the paste button in the center of the empty table.
To get started using Topsoil, let's walk through a simple use case that demonstrates the application's basic functionality.
Before starting, please install Topsoil.
After opening Topsoil, we first need to import some data. Copy the table below by first highlighting the text. Then, click on the Topsoil data table and paste it in by using the paste shortcut (control-v on Windows or command-v on Mac).
| 207Pb*/235U | ±2σ (%) | 206Pb*/238U | ±2σ (%) | corr coef |
|---|---|---|---|---|
| 29.165688743 | 1.519417676 | 0.712165893 | 1.395116767 | 0.918191745 |
| 29.031535970 | 1.799945600 | 0.714916493 | 1.647075269 | 0.915069472 |
| 29.002008069 | 1.441943510 | 0.709482828 | 1.324922704 | 0.918845083 |
| 29.203969765 | 1.320690194 | 0.707078490 | 1.216231698 | 0.920906132 |
| 29.194452092 | 1.359029744 | 0.709615006 | 1.248057588 | 0.918344571 |
| 29.293320455 | 1.424328137 | 0.710934267 | 1.309135282 | 0.919124777 |
| 28.497489852 | 1.353243890 | 0.686951820 | 1.245648095 | 0.920490463 |
| 29.218573677 | 1.383868032 | 0.715702180 | 1.271276031 | 0.918639641 |
| 28.884872020 | 1.264304654 | 0.702153693 | 1.164978444 | 0.921438073 |
| 28.863259209 | 1.455550200 | 0.700081472 | 1.335582301 | 0.917579003 |
| 29.014325453 | 1.614480021 | 0.701464404 | 1.478394505 | 0.915709384 |
| 29.917885787 | 1.564622589 | 0.725185047 | 1.434906094 | 0.917094067 |
| 30.159907714 | 1.488528691 | 0.724886106 | 1.366282212 | 0.917874287 |
| 28.963153308 | 1.480754780 | 0.698240706 | 1.359750830 | 0.918282249 |
| 29.350104553 | 1.513999270 | 0.711983592 | 1.384417989 | 0.914411266 |
| 29.979576581 | 1.595745814 | 0.724426340 | 1.458894294 | 0.914239775 |
| 29.344673618 | 1.551935035 | 0.714166474 | 1.420060290 | 0.915025602 |
Now that we have data, let's make it into a new chart. To do this, first click the "Error Ellipse Chart" button on the toolbar. A dialog should now appear asking you to choose the columns that correspond to each of the variables. For this example, Topsoil's default selection is correct, so ensure that the x- and y-errors are identified as 1σ and percentages (or else choose the correct options from the drop down menus) and press "Create chart".
Congratulations! You have successfully created your first chart with Topsoil!