Census counts of the non-indigenous benthic foraminifera Trochammina hadai Uchio obtained in 1983-2010 in San Francisco Bay, California

Frequently anticipated questions:

• What does this data set describe?
  1. How might this data set be cited?
  2. What geographic area does the data set cover?
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
  5. What is the general form of this data set?
  6. How does the data set represent geographic features?
  7. How does the data set describe geographic features?
• Who produced the data set?
  1. Who are the originators of the data set?
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
• Why was the data set created?
• How was the data set created?
  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
  3. What similar or related data should the user be aware of?
• How reliable are the data; what problems remain in the data set?
  1. How well have the observations been checked?
  2. How accurate are the geographic locations?
  3. How accurate are the heights or depths?
  4. Where are the gaps in the data? What is missing?
  5. How consistent are the relationships among the data, including topology?
• How can someone get a copy of the data set?
  1. Are there legal restrictions on access or use of the data?
  2. Who distributes the data?
  3. What's the catalog number I need to order this data set?
  4. What legal disclaimers am I supposed to read?
  5. How can I download or order the data?
• Who wrote the metadata?

What does this data set describe?

1. How might this data set be cited?
   McGann, Mary, 20240722, Census counts of the non-indigenous benthic foraminifera Trochammina hadai Uchio obtained in 1983-2010 in San Francisco Bay, California: data release DOI: 10.5066/P13UOJDV, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

   Online Links:

   • https://doi.org/10.5066/P13UOJDV
   • https://www.sciencebase.gov/catalog/item/661415dad34e633466530203

   Other_Citation_Details:

   Suggested Citation: McGann, M., 2024, Census counts of the non-indigenous benthic foraminifera Trochammina hadai Uchio obtained in 1983-2010 in San Francisco Bay, California: U.S. Geological Survey data release, https://doi.org/10.5066/P13UOJDV.

2. What geographic area does the data set cover?

   West_Bounding_Coordinate: -123.0245
   East_Bounding_Coordinate: -121.8075
   North_Bounding_Coordinate: 38.1269
   South_Bounding_Coordinate: 37.4258
   

3. What does it look like?
4. Does the data set describe conditions during a particular time period?

   Beginning_Date: 19-Apr-1983

   Ending_Date: 20-Mar-2010

   Currentness_Reference:

   Ground condition at time data were collected.

5. What is the general form of this data set?

   Geospatial_Data_Presentation_Form: comma-delimited text
   

6. How does the data set represent geographic features?
   1. How are geographic features stored in the data set?
      This is a Point data set. It contains the following vector data types (SDTS terminology):
      • Point (381)
   2. What coordinate system is used to represent geographic features?
      Horizontal positions are specified in geographic coordinates, that is, latitude and longitude. Latitudes are given to the nearest 0.0001. Longitudes are given to the nearest 0.0001. Latitude and longitude values are specified in Decimal degrees. The horizontal datum used is North American Datum of 1927.
      The ellipsoid used is Clarke 1866.
      The semi-major axis of the ellipsoid used is 6378206.4.
      The flattening of the ellipsoid used is 1/294.978698214.
      
7. How does the data set describe geographic features?

   A comma-separated values file with the first line being a header line.

   Results of census counts of the non-indigenous benthic foraminiferal species Trochammina hadai (Source: Producer defined.)

   Sampling_institution

   Institution which collected the sediment sample. (Source: Producer defined)

   Value	Definition
   USGS_Water_Mission_Area	Sampling institution
   USGS_Pacific_Coastal_and_Marine_Science_Center	Sampling institution
   San_Francisco_Estuary_Institute	Sampling institution

   USGS_field_activity_number

   Unique alphanumeric identifier given to the USGS field activity. (Source: Producer defined.) USGS field activity number

   USGS_sample_identification_number

   Unique alphanumeric identifier given to the sediment sample collected by the U.S. Geological Survey. BRP refers to the San Francisco Bar Province; CP refers to the Central Bay Province; GGP refers to the Golden Gate Province; OSP refers to the Offshore Province; SBP refers to the South Bay Province; SPP refers to the San Pablo Bay Province; and SSP refers to the Susuin Bay Province. These seven provinces are presented in McGann and others, 2013. NAN indicates the parameter was not determined. (Source: Producer defined.) USGS sample identification number

   SFEI_sample_identification_number

   Unique alphanumeric identifier given to the sediment sample collected by the San Francisco Estuary Institute (SFEI). NAN indicates the parameter was not determined. (Source: SFEI) SFEI sample identification number

   Site_description

   Geographic description of the sample site in San Francisco Bay. The seven provinces are presented in McGann and others, 2013. (Source: Producer defined.) Site description

   Date_Collected

   Date (Source: Producer defined.)

   Range of values
   Minimum:	4/19/1983
   Maximum:	3/20/2010
   Units:	M/D/YYYY

   Latitude

   Latitude of the site at which the surface sediment sample was collected. (Source: Producer defined.)

   Range of values
   Minimum:	37.4258
   Maximum:	38.1269
   Units:	decimal degrees
   Resolution:	0.0001

   Longitude

   Longitude of the site at which the surface sediment sample was collected. (Source: Producer defined.)

   Range of values
   Minimum:	-123.0245
   Maximum:	-121.8075
   Units:	decimal degrees
   Resolution:	0.0001

   Water_Depth_m

   Water depth of surface sample collected. 9999 indicates the parameter was not determined. (Source: Producer defined.)

   Range of values
   Minimum:	0.0
   Maximum:	70.0
   Units:	meters
   Resolution:	0.1

   Total_Trochammina_hadai_counted

   Total number of Trochammina hadai specimens recovered in each sample. Trochammina hadai represents Trochammina hadai Uchio, 1962. (Source: Producer defined)

   Range of values
   Minimum:	0
   Maximum:	1342
   Units:	each
   Resolution:	1

   Trochammina_hadai_percent_abundance

   Abundance percent of Trochammina hadai in each sample. Trochammina hadai represents Trochammina hadai Uchio, 1962. The percent of Trochammina hadai was calculated by dividing the number of Trochammina hadai specimens in each sample by the total number of foraminiferal specimens collected in each sample, multiplied by 100. (Source: Producer defined)

   Range of values
   Minimum:	0.0
   Maximum:	100.0
   Units:	percentage
   Resolution:	0.1

   Total_foraminifera_counted

   Total number of benthic foraminiferal specimens recovered in each sample. (Source: Producer defined)

   Range of values
   Minimum:	0
   Maximum:	1550
   Units:	each
   Resolution:	1

   Entity_and_Attribute_Overview:

   The first line of the comma-separated values file is a header line.

   Entity_and_Attribute_Detail_Citation: U.S. Geological Survey
   

Who produced the data set?

1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
   • Mary McGann
2. Who also contributed to the data set?
3. To whom should users address questions about the data?
   U.S. Geological Survey, Pacific Coastal and Marine Science Center

   Attn: PCMSC Science Data Coordinator

   2885 Mission Street

   Santa Cruz, CA
   

   650-329-4979 (voice)

   pcmsc_data@usgs.gov

Why was the data set created?

How was the data set created?

1. From what previous works were the data drawn?
2. How were the data generated, processed, and modified?

   Date: 2013 (process 1 of 1)

   Surface sediment samples were analyzed for benthic foraminifera. These sediment samples were wet-sieved through stacked 0.063 mm, 0.150 mm, and 1.0 mm screens to remove the silt and clay-sized fractions (less than 0.063 mm). Sediment remaining on each screen was transferred to filter paper, air-dried, and then recombined with the other size fractions. Foraminifera were extracted from the greater than 0.063 mm to 1.0 mm fractions. Each sample was split with the aid of a microsplitter into an aliquot containing at least 300 benthic foraminifers. While viewing under a microscope, specimens were removed from the matrix with a small, moistened picking brush, and placed on pre-glued microfaunal slides. All specimens were picked, including the non-indigenous species Trochammina hadai, identified using the nomenclature registered in the World Foraminiferal Database, and tabulated. If the sample contained less than 300 foraminifera, all that were present were picked. The percent of Trochammina hadai was calculated by dividing the number of Trochammina hadai specimens in each sample by the total number of foraminiferal specimens collected in each sample, multiplied by 100. The foraminiferal slides and residues of this study are on file at the U.S. Geological Survey, Santa Cruz, California.

3. What similar or related data should the user be aware of?
   McGann, M., Erikson, L., Wan, E., C. Powell, II, and Maddocks, R.F., 2013, Distribution of biologic, anthropogenic, and volcanic constituents as a proxy for sediment transport in the San Francisco Bay Coastal System.

   Online Links:

   • http://doi.org/10.1016/j.margeo.2013.05.006

   Other_Citation_Details:

   McGann, M., Erikson, L., Wan, E., Powell, C., II, and Maddocks, R.F., 1977, Distribution of biologic, anthropogenic, and volcanic constituents as a proxy for sediment transport in the San Francisco Bay Coastal System: Marine Geology, v. 345, p. 113�142.

How reliable are the data; what problems remain in the data set?

1. How well have the observations been checked?
   Microscopes are operationally checked every year to assure optics are aligned and visual acuity can be maximized during sorting and identifications. Specimen identifications were compared to reference material (actual specimens and published monographs) to ensure identifications were accurate. Specimen enumeration (counts) were checked with original laboratory bench sorting sheets to assure numbers were correct, and the sorting and data entry into spreadsheets was rechecked at least once.
2. How accurate are the geographic locations?
   A formal accuracyassessment of the horizontal positional information in the data set has not been conducted. The horizontal accuracy was determined with a Leica GPS for R/V Polaris cruises 1983-611-DD, 1986-602-DD, and P-1-87-SF, a Garmin ProNav GPS 100 for R/V David Johnston cruises 1993-602-DD and J-1-98-SF, and a Garmin 4212 GPS for R/V Parke Snavely cruises S-7-10-SF and S-8-10-SF.
3. How accurate are the heights or depths?
   A formal accuracy assessment of the vertical positional information in the data set has not been conducted. Depth was determined using a Garmin GPSMAP with depth sounder for for R/V Polaris cruises 1983-611-DD, 1986-602-DD, and P-1-87-SF, and a Furuno FCV585 depth sounder for R/V David Johnston and R/V Parke Snavely cruises 1993-602-DD, J-1-98-SF, S-7-10-SF, and S-8-10-SF.
4. Where are the gaps in the data? What is missing?
   Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the metadata for each part of this data release carefully for additional details.
5. How consistent are the relationships among the observations, including topology?
   Data were checked for logical consistency by the laboratory staff before release to confirm that numerical values were not outside a reasonable range for a particular field. Cumulative counts of percentage data for the total foraminiferal assemblage had to equal approximately 100 percent to ensure numbers were reported correctly.

How can someone get a copy of the data set?

1. Who distributes the data set? (Distributor 1 of 1)
   
   U.S. Geological Survey - ScienceBase

   Denver Federal Center, Building 810, Mail Stop 302

   Denver, CO
   

   1-888-275-8747 (voice)

   sciencebase@usgs.gov
2. What's the catalog number I need to order this data set? These data are available in a comma-delimited text file�(SF_Bay_T_hadai_1983-2010_counts.csv) which contains census counts of the non-indigenous benthic foraminifera Trochammina hadai obtained in 1987-2010 in San Francisco Bay, California.
3. What legal disclaimers am I supposed to read?
   Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty.
4. How can I download or order the data?
   • Availability in digital form:

     Data format:	.csv file in format comma-delimited text (version Microsoft Excel 16.83 for Mac) Size: 0.04695
     Network links:	https://www.sciencebase.gov/catalog/file/get/661415dad34e633466530203 https://doi.org/10.5066/P13UOJDV

   • Cost to order the data: None.

5. What hardware or software do I need in order to use the data set?
   These data can be viewed with any text editor software.

Who wrote the metadata?

Dates:

Last modified: 22-Jul-2024

Metadata author:

U.S. Geological Survey, Pacific Coastal and Marine Science Center

Attn: PCMSC Science Data Coordinator

2885 Mission Street

Santa Cruz, CA

831-427-4747 (voice)

pcmsc_data@usgs.gov

Metadata standard:

Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)