Data Package Metadata   View Summary

Habitat selection/Caracolus caracolla and other snails (2016 Ongoing)

General Information
Data Package:
Local Identifier:knb-lter-luq.194.45
Title:Habitat selection/Caracolus caracolla and other snails (2016 Ongoing)
Alternate Identifier:DOI PLACE HOLDER
Abstract:

Various habitat characteristics are presented, as well as the apparency of common plant taxa at 7 heights (every 0.5 m from ground level to 3 m). The files are divided because variables measured varied by year. This is Version 2016 of these data.

Publication Date:2017-03-20
Language:English

Time Period
Begin:
1996-03-01
End:
2016-07-01

People and Organizations
Contact:Willig, Michael R. (University of Connecticut) [  email ]
Contact:Presley, Steven J. (University of Connecticut) [  email ]
Creator:Willig, Michael R. (University of Connecticut)
Associate:Bloch, Christopher P. (Bridgewater State College, associated researcher)
Associate:Cox, Stephen 
Associate:Melendez-Colom, Eda (University of Puerto Rico, Rio Piedras Campus, data manager)

Data Entities
Data Table Name:
Plant Apparency 1996-2016
Description:
Various habitat characteristics and apparency of common plant taxa at 7 heights (every 0.5 m from ground level to 3 m) observed from 1996 to 2016 in the LFDP.
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-luq/194/45/ab2a091ceea1ed19d226e924c4f5eff0
Name:Plant Apparency 1996-2016
Description:Various habitat characteristics and apparency of common plant taxa at 7 heights (every 0.5 m from ground level to 3 m) observed from 1996 to 2016 in the LFDP.
Number of Records:206180
Number of Columns:26

Time Period
Begin:
1996-07-01
End:
2016-07-01
Methods and protocols used in the collection of this data package
Description:

The original data file was converted to a Long data matrix data file using R with the following function: mydataTransposed <- melt(mydata, id.vars = c("YEAR", "Season", "Point", "RC", "LC", "VC", "DWC", "NAIL1", "NAIL2", "NAIL3", "NAIL4", "NAIL", "DENS_INN_1", "DENS_INN_2", "DENS_INN_3", "DENS_INN_4", "DENS_INN_AVG", "DENS_OUT_1", "DENS_OUT_2", "DENS_OUT_3", "DENS_OUT_4", "DENS_OUT_AVG", "AVG"), variable.name = "SpeciesCode", value.name = "SpeciesCount") .


Table Structure
Object Name:PlantApparency1996-2016-Transposed-withIntersectHeight.csv
Size:15599757
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,

Table Column Descriptions
 YEARSeasonPointRCLCVCDWCNAIL1NAIL2NAIL3NAIL4NAILDENS-INN-1DENS-INN-2DENS-INN-3DENS-INN-4DENS-INN-AVGDENS-OUT-1DENS-OUT-2DENS-OUT-3DENS-OUT-4DENS-OUT-AVGAVGSpeciesCodeInterceptHeightSpeciesCount
Column Name:Year of observation or monitoring  
Time of the year with respect to raining conditions  
Point of measurement  
Rock Cover  
Litter Cover  
Vine Cover  
Dead Wood Cover  
Nail test 1  
Nail test 2  
Nail test 3  
Nail test 4  
Average of the 4 replicates of the nail test.  
Densio-meter first reading #1  
Densio-meter first reading #2  
Densio-meter first reading #3  
Densio-meter first reading #4  
Densio-meter first 4 and last 4 readings average  
Densio-meter last #1 reading  
Densio-meter last #2 reading  
Densio-meter last #3 reading  
Densio-meter last #4 reading  
Densio-meter last 4 readings average  
Densio-meter first 4 and last 4 readings average  
Species Code  
Height of Intercept  
Apparency of the species at a specific height  
Definition:Year (in yyyy) format when the observation or monitoring was made at the field.Time of the year with respect to the amount of rain that usually falls on the Luquillo Mountains; wet or dryPoint in the grid where the observation was performed. There is no record of the grid point if no observation was performed.Ranked variable representing percent rock cover. A blank cell means measurement was not taken.Ranked variable representing percent cover of leaf litter. A blank cell means measurement was not taken.Ranked variable representing percent cover of vinesRanked variable representing percent cover of dead wood. A blank cell means measurement was not taken.Number of leaves pulled up by a nail driven into the ground near the point in position 1. A blank cell means measurement was not taken.Number of leaves pulled up by a nail driven into the ground near the point in position 2. A blank cell means measurement was not taken.Number of leaves pulled up by a nail driven into the ground near the point in position 3. A blank cell means measurement was not taken.Number of leaves pulled up by a nail driven into the ground near the point in position 4. A blank cell means measurement was not taken.Average of 4 replicates of the nail test. A blank cell means measurement was not taken.First #1 reading from a spherical densiometer. A blank cell means measurement was not takenFirst #2 reading from a spherical densiometer. A blank cell means measurement was not taken.First #3 reading from a spherical densiometer. A blank cell means measurement was not taken.First #4 reading from a spherical densiometer. A blank cell means measurement was not taken.Average of the first 4 and last 4 readings from a spherical densiomete. A blank cell means measurement was not taken.Last #1 reading from a spherical densiometer. A blank cell means measurement was not taken.Last #2 reading from a spherical densiometer. A blank cell means measurement was not taken.Last #3 reading from a spherical densiometer. A blank cell means measurement was not taken.Last #4 reading from a spherical densiometer. A blank cell means measurement was not taken.Average of the last 4 readings from a spherical densiometer. A blank cell means measurement was not taken.Average of the first 4 and last 4 readings from a spherical densiomete. A blank cell means measurement was not taken.Species code extracted from the original file columns and converted into a value in the transformation of the data file from a Wide to a Long data matrix. R was used to do this transformation.Height in meters at which the Apparency (number of intercepts) of the corresponding species was observed.Apparency of the species at the height specified by the last 3 characters in the corresponding species code. Apparency was defined as the number of intercepts of each species (or rocks or dead plant matter) on the plant apparency deviceThis value was extracted from the original file columns in the transformation of the data file from a Wide to a Long data matrix. R was used to do this transformation.
Storage Type:date  
string  
string  
                  string  
string  
string  
string  
string  
string  
string  
string  
string  
string  
string  
string  
   
Measurement Type:dateTimenominalnominalratioratioratioratioratioratioratioratiorationominalnominalnominalnominalnominalnominalnominalnominalnominalnominalnominalnominalratioratio
Measurement Values Domain:
FormatYYYY
Precision
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codewet
Definitionseason when rainfall is greater than in other months of the year
Source
Code Definition
Codedry
Definitionseason when rainfall is less than in other months of the year
Source
DefinitionPoint in the grid where the observation was performed. There is no record of the grid point if no observation was performed.
Unitpercent
Typereal
Unitpercent
Typereal
Unitpercent
Typereal
Unitpercent
Typereal
Unitnumber
Typereal
Unitnumber
Typereal
Unitnumber
Typereal
Unitnumber
Typereal
Unitnumber
Typereal
DefinitionFirst #1 reading from a spherical densiometer. A blank cell means measurement was not taken
DefinitionFirst #2 reading from a spherical densiometer. A blank cell means measurement was not taken.
DefinitionFirst #3 reading from a spherical densiometer. A blank cell means measurement was not taken.
DefinitionFirst #4 reading from a spherical densiometer. A blank cell means measurement was not taken.
DefinitionAverage of the first 4 and last 4 readings from a spherical densiomete. A blank cell means measurement was not taken.
DefinitionLast #1 reading from a spherical densiometer. A blank cell means measurement was not taken.
DefinitionLast #2 reading from a spherical densiometer. A blank cell means measurement was not taken.
DefinitionLast #3 reading from a spherical densiometer. A blank cell means measurement was not taken.
DefinitionLast #4 reading from a spherical densiometer. A blank cell means measurement was not taken.
DefinitionAverage of the last 4 readings from a spherical densiometer. A blank cell means measurement was not taken.
DefinitionAverage of the first 4 and last 4 readings from a spherical densiomete. A blank cell means measurement was not taken.
DefinitionSpecies code extracted from the original file columns and converted into a value in the transformation of the data file from a Wide to a Long data matrix. R was used to do this transformation.
Unitmeter
Typereal
Unitnumber
Typereal
Missing Value Code:                
Code-999
ExplMeasurement not taken
Code-999
ExplMeasurement not taken
Code-999
ExplMeasurement not taken
                             
Accuracy Report:                                                    
Accuracy Assessment:                                                    
Coverage:                                                    
Methods:                                                    

Data Package Usage Rights

Data Policies

LTER Network Data Access Policy, Data Access Requirements, and General Data Use Agreement
approved by the LTER Coordinating Committee April 6, 2005

Long Term Ecological Research Network Data Access Policy

The LTER data policy includes three specific sections designed to express shared network policies regarding the release of LTER data products, user registration for accessing data, and the licensing agreements specifying the conditions for data use.

LTER Network Data Release Policy

Data and information derived from publicly funded research in the U.S. LTER Network, totally or partially from LTER funds from NSF, Institutional Cost-Share, or Partner Agency or Institution where a formal memorandum of understanding with LTER has been established, are made available online with as few restrictions as possible, on a nondiscriminatory basis. LTER Network scientists should make every effort to release data in a timely fashion and with attention to accurate and complete metadata.

Data[current-user:created]

There are two data types:

Type I – data are to be released to the general public according to the terms of the general data use agreement (see Section 3 below) within 2 years from collection and no later than the publication of the main findings from the dataset and,

Type II - data are to be released to restricted audiences according to terms specified by the owners of the data. Type II data are considered to be exceptional and should be rare in occurrence. The justification for exceptions must be well documented and approved by the lead PI and Site Data Manager. Some examples of Type II data restrictions may include: locations of rare or endangered species, data that are covered under prior licensing or copyright (e.g., SPOT satellite data), or covered by the Human Subjects Act. Researchers that make use of Type II Data may be subject to additional restrictions to protect any applicable commercial or confidentiality interests.

While the spirit of this document is to promote maximum availability for ecological data in either Type I or II status, there are criteria by which priority for data release may be determined. Primary observations collected for core research activities directly supported by LTER research must receive the highest priority for data release. Data collected by other sources to which LTER supported research has added value is also a high priority Other types of data including non-LTER data that was acquired for LTER research, student thesis data, schoolyard LTER data, or legacy data that already suffer from inadequate documentation or format obsolescence may be ranked a lower priority by a site with justifications provided in their data management policy. Finally, some data may be determined of lowest priority for archiving on the grounds that they are interim data that led to final products that carry the scientific value. These might include data files created during stages within an analytic workflow, raw or replicate data values that were subsequently aggregated or processed for release, or individual outputs from stochastic models.

Metadata

Metadata documenting archived/online data sets of all types listed above will be made available when, or before, the dataset itself is released according to the terms above.
All metadata will be publicly available regardless of any restrictions on access to the data.
All metadata will follow LTER recommended standards and will minimally contain adequate information on proper citation, access, contact information, and discovery. Complete information including methods, structure, semantics, and quality control/assurance is expected for most datasets and is strongly encouraged.
LTER Network Data Access Requirements

The access to all LTER data is subject to requirements set forth by this policy document to enable data providers to track usage, evaluate its impact in the community, and confirm users' acceptance of the terms of acceptable use. These requirements are standardized across the LTER Network to provide contractual exchange of data between Site Data Providers, Network Data Providers, and Data Users that can be encoded into electronic form and exchanged between computers. This will allow direct access to data via a common portal once these requirements have been fulfilled. The following information may be required directly or by proxy prior to the transference of any data object:

Registration

1. Name

2. Affiliation

3. Email Address

4. Full Contact Information

Acceptance of the General Public Use Agreement or Restricted Data Use Agreement, as applicable.
A Statement of Intended Use that is compliant with the above agreements. Such statements may be made submitted explicitly or made implicitly via the data access portal interface.

General Data Use Agreement

LUQ  data and metadata is released under public domain:  CC BY – Attribution.

Conditions of Use

The consumer of these data (“Data User” herein) has an ethical obligation to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or coauthorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available “as is.” The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.
Disclaimer

While substantial efforts are made to ensure the accuracy of data and documentation contained in this Data Set, complete accuracy of data and metadata cannot be guaranteed. All data and metadata are made available "as is". The Data User holds all parties involved in the production or distribution of the Data Set harmless for damages resulting from its use or interpretation.[current-user:name]

Keywords

By Thesaurus:
Core Areasdisturbance, populations
LTER Controlled Vocabularyorganisms, plants, processes, biological processes, life history, habitat selection, disturbance, substrates, canopies

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Ranked variables (Rock Cover, Litter Cover, Dead Wood Cover, Vine Cover) assume one of five states depending on the relative amount of cover (1 = 0-20%, 2 = 21-40%, 3 = 41-60%, 4 = 61-80%, 5 = 81-100%). Canopy openness was evaluated using a spherical densiometer positioned 0.5 m away from the point in each of the cardinal directions. The average of these four readings can be considered a description of canopy openness. A nail was driven into the forest floor 1 m from the point in each of the cardinal directions, the number of leaves obtained thus is used as an estimate of litter cover. Plant apparency (Cook and Stubbendieck 1986) for common species was also recorded. The number of foliar intercepts, defined as a species-specific count of vegetation touching a wooden dowel, was counted at each of 7 heights (0, 0.5, 1.0, 1.5, 2.0, 2.5, and 3.0 m) using a plant apparency device (Cary 1992, Secrest 1995). Four 0.5-m dowels were positioned at 90-degree angles at each height. The device was positioned 1.5 m from the central point in each cardinal direction, and the number of intercepts recorded. Blank cells in the data files indicate missing values or variables that were not measured during a sampling period.

These methods, instrumentation, and/or protocols apply to the data table Plant Apparency 1996-2016:

Methods and protocols used in the collection of this data package
Description:

The original data file was converted to a Long data matrix data file using R with the following function: mydataTransposed <- melt(mydata, id.vars = c("YEAR", "Season", "Point", "RC", "LC", "VC", "DWC", "NAIL1", "NAIL2", "NAIL3", "NAIL4", "NAIL", "DENS_INN_1", "DENS_INN_2", "DENS_INN_3", "DENS_INN_4", "DENS_INN_AVG", "DENS_OUT_1", "DENS_OUT_2", "DENS_OUT_3", "DENS_OUT_4", "DENS_OUT_AVG", "AVG"), variable.name = "SpeciesCode", value.name = "SpeciesCount") .

People and Organizations

Creators:
Individual: Michael R. Willig
Organization:University of Connecticut
Address:
Center for Environmental Sciences and Engineering University of Connecticut 270 Middle Turnpike, Unit 5210,
Storrs, CT 6269 US
Phone:
(860) 486-1455 (voice)
Phone:
(860) 486-1753 (facsimile)
Email Address:
michael.willig@uconn.edu
Web Address:
http://hydrodictyon.eeb.uconn.edu/people/willig/
Contacts:
Individual: Michael R. Willig
Organization:University of Connecticut
Address:
Center for Environmental Sciences and Engineering University of Connecticut 270 Middle Turnpike, Unit 5210,
Storrs, CT 6269 US
Phone:
(860) 486-1455 (voice)
Phone:
(860) 486-1753 (facsimile)
Email Address:
michael.willig@uconn.edu
Web Address:
http://hydrodictyon.eeb.uconn.edu/people/willig/
Individual: Steven J. Presley
Organization:University of Connecticut
Address:
3107 Horsebarn Hill Road,
Storrs, CT 6269 US
Phone:
(860) 486-1772 (voice)
Phone:
(860) 486-5488 (facsimile)
Email Address:
steven.presley@uconn.edu
Web Address:
http://hydrodictyon.eeb.uconn.edu/people/willig/student_pages/Steve%20Presley.htm
Associated Parties:
Individual: Christopher P. Bloch
Organization:Bridgewater State College
Address:
Bridgewater State College Department of Biological Sciences,
Bridgewater, MA 2325 US
Phone:
(508) 531-2087 (voice)
Phone:
(508) 531-1785 (facsimile)
Email Address:
cbloch@bridgew.edu
Role:associated researcher
Individual: Stephen Cox
Address:
The Institute of Environmental and Human Health Texas Tech University,
Lubbock, TX 79409 US
Phone:
(806) 885-0249 (voice)
Email Address:
scox@lternet.edu
Web Address:
www.tiehh.ttu.edu/scox
Role:associated researcher
Individual: Eda Melendez-Colom
Organization:University of Puerto Rico, Rio Piedras Campus
Address:
University of Puerto Rico at Rio Piedras, Ponce de Leon Ave.,
San Juan, PR 00931 US
Phone:
(787) 764-0000 (voice)
Email Address:
edacorreo@yahoo.com
Role:data manager

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
1996-03-01
End:
2016-07-01
Sampling Site: 
Description:The Luquillo Forest Dynamics Plot (LFDP), previously known as the Hurricane Recovery Plot (Zimmerman et. al. 1994) and the Luquillo long-term ecological research grid (Soil Survey 1995), is a 16-ha forest plot (SW corner 18° 20' N, 65° 49' W) located near El Verde Field Station. The plot is 500 m N-S and 320 m E-W and is divided into 400 20 x 20 m quadrats, with each quadrat sub divided into 16 5 x 5 m sub-quadrats. The field station and LFDP are in the Luquillo Mountains of northeastern Puerto Rico, approximately 35 km southeast of San Juan.
Site Coordinates:
Longitude (degree): -65.8167Latitude (degree): 18.3333
Altitude (meter):333

Temporal, Geographic and/or Taxonomic information that applies to Data Table: Plant Apparency 1996-2016


Time Period
Begin:
1996-07-01
End:
2016-07-01

Project

Additional Info

Additional Information:
 

A previous version of this data set containing old data exists but it has been deprecated. The data files structures are being changed from a >140 data columns to a <25 columns data file. MYSQL Scripts are programed to performed this partial transposition of data columns to rows. See Set of files to convert a data file with n columns to a k + 2 columns table

Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList' in ns 'http://www.xml-cml.org/schema/stmml-1.1' ('stmml:unitList')
        |     |     |  \___attribute 'schemaLocation' in ns 'http://www.w3.org/2001/XMLSchema-instance' ('xsi:schemaLocation') = 'http://www.xml-cml.org/schema/stmml-1.1 http://nis.lternet.edu/schemas/EML/eml-2.1.0/stmml.xsd'
        |     |     |___text '\n        '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.1' ('stmml:unit')
        |     |     |     |  \___attribute 'abbreviation' = '%'
        |     |     |     |  \___attribute 'constantToSI' = '0'
        |     |     |     |  \___attribute 'id' = 'percent'
        |     |     |     |  \___attribute 'multiplierToSI' = '100'
        |     |     |     |  \___attribute 'name' = 'percent'
        |     |     |     |  \___attribute 'parentSI' = 'numberPerNumber'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.1' ('stmml:description')
        |     |     |     |     |___text 'ratio of two quantities as percent composition (1:100)'
        |     |     |     |___text '\n        '
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

UNM logo UW-M logo