OFR 97-492: NURE Data Frequently Asked Questions

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National Geochemical Database—Reformatted Data from the National Uranium Resource Evaluation (NURE) Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) Program

By Steven M. Smith
Version 1.40 (2006)

Frequently Asked Questions Concerning the National Uranium Resource Evaluation (NURE) Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) Data and Reformatting Process

 



  Why are there negative concentration values in the data? What do they mean?

A negative concentration value indicates that the sample was analyzed but that the concentration was below the determination limits of the analytical method. All instrumental methods for analyzing the concentrations of various elements in sediments, waters, rocks, or plants have lower determination limits. Concentrations below this lower determination limit are too small to be detected by the method. For example, one of the Oak Ridge Multielement Emission Spectrochemical Analysis methods could not detect concentrations of silver (Ag) that were less than 2 parts-per-million (ppm). When the analytical method determined that a sample contained less than 2 ppm Ag, a value of "-2" was recorded in the Ag_ppm field. Unfortunately, we don't know if that means that the sample contains 1.8 ppm Ag or 0.0001 ppm Ag. The best that can be said is that the concentration is <2 ppm Ag.

Some analytical methods record different negative numbers for an element in successive samples. For example, undetected concentrations of zinc (Zn) range from -10 to -137 ppm within sediment samples from the Leadville quadrangle. This happens with some of the multielement methods like neutron activation analysis (NAA). When trying to analyze several elements simultaneously, some elements will "interfere" with the detection of others. The NAA instrumentation will report the best value that it could determine and then indicate that the concentration was less than that value. Since every sample has different suites of elements and interferences, the method can report a wide range of negative values; including some large ones like -137 ppm Zn (<137 ppm Zn)


  How do I use the negative concentrations or "less than" values in calculations?

There are very good methods for interpreting data with "less than" values. Unfortunately, they are rarely used in the geosciences.

Some users simply throw out or ignore all "less than" values. This is the least desirable method you could use. Calculations based upon the remaining concentrations will result in artificially high mean values. Regression or other analyses will also be biased high. For example, if you throw out all -2 values for silver and then calculate the average of the remaining concentrations, the mean value will be much greater than estimated crustal abundances of about 0.1 ppm Ag in rocks. Of course, throwing away the low values is OK if all you want is a simple map of sampled locations containing concentrations of a desired element greater than a high cutoff value, higher than the largest "less than" in the data set. For example, if the highest limit is 10, (recorded in the data base as -10), a map of all values >=50 will not be affected by ignoring the "less than" values.

The most commonly-used method is to replace all "less than" values with a replacement value. This is the next worst method, after deleting "less thans". The problem is that the value used to replace "less thans" may produce an artificial signal that is not in the original data. Or it may obscure a pattern that is present. Replacement methods have no theoretical basis, and are dangerous. People argue over whether to use 1/2 the reported limit, or 0.7 times the limit, or some other multiplier. In reality they are all equally invalid.

When all "less than" values for an element are the same, users can still report percentiles such as the median. Thus for a limit of -5 ppm Cu (copper) the median may still be determined as 8, or perhaps even <5. This works well for many elements with lower determination limits that are well below estimated crustal abundance ranges. When comparing groups of data, nonparametric statistic methods based on ranks can be used without hesitation. A <5 is ranked as below a value of 8, for example, while all <5's are considered equal and tied in value. Nonparametric tests use this type of information easily.

Elements with multiple "less than" values require more complex methods than are traditionally used in the geosciences. Guidance for this situation is found in the textbook "Nondetects And Data Analysis: Statistics for censored environmental data", by Dennis Helsel, published by Wiley (2005). Methods are available for calculating simple statistics such as the mean, for testing between groups, and for computing regression equations.

For elements with a large population of "less than" values, the precision is insufficient to answer some questions that might be asked of the data. To illustrate, the Leadville 1:250,000-scale quadrangle contains numerous silver-producing mines but 97% of the sediment data for this quadrangle were reported as -5 ppm Ag (<5 ppm Ag). These data are therefore insufficient to answer questions about average levels or background levels of Ag in sediments within the area, other than that background levels are <5 ppm. However, these data could be compared to and found generally lower in concentration than those of another area that contains silver concentrations greater than 5 ppm in say 10-20% of its samples, as compared to the 3% found in this quadrangle.


  What about blank fields or values of zero for element concentrations?

Blank fields indicate that the element in question was not determined in that sample. Occasionally, a field is blank when an analytical method was unable to give a reliable indication of the concentration of an element. Zero values were often used in the original data files as space filler values. Most zero values were removed during the reformatting process but a few are occasionally noted. These will be removed as they are found. Meanwhile, all zero values within element concentration fields should be treated as blank or "null" values.

Be aware that during the file conversion process from .dbf to other formats, some spreadsheet or database programs will place zero values into all blank numeric fields. Many of these programs will give the user an option of whether or not to fill blank numeric fields with zeros or some other "null" value.

Another problem occurs when certain programs choose to display all numeric values to two decimal places as a default. Thus a value of 0.002 ppm U (uranium) may be displayed as 0.00 ppm U. Usually the remainder of the decimal places are present though not displayed.


  Why do some of the latitude-longitude coordinates contain values of zero? Why not throw out those records without coordinates?

Many samples are missing coordinates. Apparently during the NURE HSSR sample collection phase, some sample locations were not recorded either on the maps, on the field notes, or in the digital data. Some of these coordinates have been found and added to the reformatted data. Others may eventually be obtained by inspecting field notes or maps. Most will probably not be found. In addition, the coordinates were sometimes changed to zero during the reformatting process when the values were obviously wrong. The original value (and sometimes a possible correct value) were recorded in the accompanying COORDPRB field.

Although sample records with missing coordinates are not useful for precisely-located, geographically-based data needs, the data are still useful for regional needs. For example, data that can only be identified to the nearest county, quadrangle, or state can still be used to calculate average elemental concentrations for those areas.


  The latitude-longitude coordinates are expressed in decimal degrees but what datum was used?

The current use of Global Positioning Systems and Geographic Information System software has increased awareness of the importance of recording datums and ellipsoids. However, this information was not commonly recorded in the past and it wasn't recorded for the NURE HSSR program. We do know that during the time these samples were collected (late 1970's and very early 1980's), there were very few choices of datums or ellipsoids in use within the United States. Most of the NURE HSSR sample sites were plotted on and then digitized from U.S. Geological Survey topographic maps or locally available county maps. Almost all, if not all, USGS maps available during this time were based on the North American Datum of 1927 (NAD27) that used the Clarke 1866 ellipsoid. Many of the available county maps were projected using the State Plane Coordinate System and also marked with latitude and longitude tick marks. It is probably safe to assume that the NAD27 datum and Clarke 1866 ellipsoid were also used for these individual county maps.


  I need to locate samples along a certain stream or at a certain place. Are the sample locations identified by site names or descriptions? How can I find the data records for just the samples I need?

The NURE HSSR database does not contain site names associated with sample locations. The only site identifiers were sequential ID numbers assigned by the laboratory. There was no specific place on any of the standardized sample collection note forms to record a geographic name associated with a specific sample. Just about the only way to determine the location of a sample is by using the latitude and longitude coordinates from the database. Most users who only want sample data from a particular stream or well site usually end up plotting the latitude - longitude sample locations on a map to make their final determination.

For a few quadrangles, the NURE GJBX-series publications contain a computer-plotted sample location map that can be overlaid on a base map to determine sites. The Oak Ridge Gaseous Diffusion Plant (ORGDP) was the only laboratory to consistently include a computer-generated site location map overlay (1:250,000 scale) for their area of responsibility (i.e. the central U.S. plains States). The ORGDP also was the only laboratory to include field comments from the original sample collection note forms in the database. Therefore, if the person responsible for collecting a sample for ORGDP happened to include a stream name or well name in their comments, it is possible that this information was preserved in the COMMENTS or COMMENT2 free form comment fields.


  I can't find the NURE HSSR data I want for a certain quadrangle. Where can I get it? Is there any more geochemical data coming?

There are at least four circumstances that have prompted forms of this question.

  1. I can't find the link for downloading NURE HSSR data.   From these web pages, all data can be downloaded by quadrangle. To download data, first go to the quadrangle page for the area in which you are interested (Note: Quadrangle pages are listed under state pages). About half way down each of the quadrangle pages is section entitled "Download the Data." Follow the instructions to download the desired quadrangle NURE HSSR data file. Also see the answer about querying a database.

  2. I clicked on a quadrangle but all I got was a page entitled "Quadrangles Without NURE HSSR Data." When will NURE HSSR data for these quadrangles be available?   To the best of my knowledge, no NURE HSSR samples were ever collected for these quadrangles. The NURE program ended in the mid-1980's and therefore no new NURE samples are scheduled to be collected or analyzed for these quadrangles. It is possible that other programs may collect and analyze geochemical samples for these quadrangles but since those data will not be NURE HSSR data, they will not be available through this web site.

  3. I checked the available data for a quadrangle but the specific element or sample type that I want wasn't there. Will more data be added later?   When a quadrangle has been reformatted and released on these pages, it is considered finished. All known files and sources of NURE HSSR data have been checked and either added or referenced in the "Other NURE Geochemical Data for the _____ Quadrangle" section. There is the slight possibility that more data will be found as the reformatting effort continues. If this happens, the data will be added and the quadrangle page will be updated. This is expected to be a rare occurrence.

  4. I have examined the NURE HSSR data and found that it is not adequate for my needs. Do you know of any other sources of geochemical data?   The U.S. Geological Survey has been developing a National Geochemical Database. These NURE HSSR data are one part of that effort. In addition, there are two in-house U.S. Geological Survey Databases (RASS and PLUTO) that are being reformatted and released by the National Geochemical Database project. These data will be released on the Mineral Resources Downloadable Data Sets Page. The Alaska RASS data is also currently available on the Web. These databases contain geochemical analyses for samples of stream sediments, rocks, soils, heavy-mineral concentrates, waters, and plants that were collected in support of USGS studies. Inquiries concerning USGS National Geochemical Databases (including RASS and PLUTO data) can be directed to Steven M. Smith (smsmith@usgs.gov).


  The link to the quadrangle I want isn't active. When will the data for this quadrangle be available?

Data for all of the NURE HSSR quadrangles have now been reformatted. All links should be active. If you click on a link to a quadrangle that is not, please contact Steven M. Smith (smsmith@usgs.gov) and we will see that the link is fixed.


  I want to retrieve the reformatted NURE HSSR data from parts of several quadrangles or partial data from a large area. Is there a way to query a database and get just the data I need?

In past versions of this web site, the NURE HSSR data were only available as individual compressed data files that were downloaded by quadrangle. However, the NURE HSSR data are now available online in two databases that provide many more options: The NURE HSSR sediment database (also includes data for soils and some rocks) at http://tin.er.usgs.gov/nure/sediment/ and the water NURE HSSR database at http://tin.er.usgs.gov/nure/water/. From these two web sites, NURE HSSR data can be selected, examined, summarized, and downloaded by political boundaries (State and County), by quadrangle (1:250,000-scale, 1:100,000-scale, and 1:63,360-scale for Alaska or 1:24,000-scale for the Lower 48 States), and by hydrologic unit (drainage region, subregion, river basin, or sub-basin). When the desired data have been selected, option buttons on the "Check Out" page allow you to restrict your data to only the fields you want. Selected data can then be downloaded as a dBase file, a Shapefile, an HTML table, or ASCII text (tab- or comma-delimited). These web sites do not have the capability to query and select data by a user-defined area.

The USGS-Reformatted NURE HSSR databases are not yet available on CD-ROM.


  I already have the NURE HSSR data on CD-ROM (USGS DDS-1, USGS DDS-18-A, or USGS DDS-18-B or other various sources derived from these CD-ROMs). Can I still use data from these sources? Why would I want to use these newly-reformatted data?

The data from these earlier sources can still be used. However, the user must be knowledgable about the differences between laboratories in the original program and very careful to avoid some of the systematic errors that were introduced into the data during that initial database compilation process. This release of NURE HSSR data has attempted to standardize coding, combine multiple records for individual samples, and provide consistent data without systematic errors so that the user is not required to become an expert on the NURE program.

For more details on the differences between the earlier releases of NURE HSSR data and this reformatting effort see Why a new NURE HSSR data format? For a brief summary of the NURE program see History of NURE HSSR Program.


  I want to use these data in a report or to create a map. How should I reference this source?

This report is a standard U.S. Geological Survey Open-File Report and should be referenced as such. However, this report is only found on the Web and so it does not have page numbers. You may wish to use the following bibliographic reference adjusted for the required style of your intended publication.

Smith, S.M., 1997, National Geochemical Database: Reformatted data from the National Uranium Resource Evaluation (NURE) Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) Program, Version 1.40 (2006): U.S. Geological Survey Open-File Report 97-492, WWW release only, URL: https://pubs.usgs.gov/of/1997/ofr-97-0492/, last accessed Feb. 1, 2006.

(Replace the date with that of your "last access".)


  Where can I find copies of the NURE GJBX-series, PGJ/F-series, or GJQ-series publications listed in the bibliography?

The NURE program released several hundred reports in paper form or on microfiche. As government documents, all of these reports should be archived for public inspection in Regional Government Document Depository Libraries. Copies of individual reports were also sent to several Local Government Document Depository Libraries, State Geological Survey Libraries, University Libraries, and U.S. Geological Survey Libraries. Additionally, NURE reports were commonly purchased by individuals, businesses, public and university libraries, and research institutions. Some of these resources will have a limited number of NURE reports while others may have very large collections.

Probably the best way to access these collections of NURE reports is to work with your local public or university library. Most libraries can locate copies of NURE reports through the OCLC Database and obtain them via Interlibrary Loan.

In the late 1970's and early 1980's, NURE press releases often identified the locations where reports would be available for viewing. The following is a partial list compiled from half a dozen press releases that illustrates the various places where NURE reports can be found. This list is not complete, and at least 20 years out of date. It is very possible that the NURE collections at these locations are incomplete and may have since been moved elsewhere.

A few NURE reports may still be available for purchase from the Department of Energy's Office of Scientific & Technical Information (OSTI) in Oak Ridge, Tennessee. You must contact them before ordering to determine if they still have the desired publication and the cost of the publication. They may be contacted for orders by:

E-mail:   reports@adonis.osti.gov
Phone:   865-576-8401
Fax:   865-576-5728
Address:   P.O. Box 62, Oak Ridge. TN  37831
Web:   http://www.osti.gov/contact.html

Some of the NURE reports can be downloaded as Portable Document Format files from this web site on the Selected Publications from the NURE HSSR Program page


13.   I don't see my problem listed here and I still need help. Is there someone I can contact?

Questions and comments concerning the information and data found within this U.S. Geological Survey Open-File Report 97-492 should be sent to Steven M. Smith (smsmith@usgs.gov).

 

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