From 27dafda8e1a48f07cd3ef98c0f1bd414c3a61bb6 Mon Sep 17 00:00:00 2001 From: Colin Smith Date: Wed, 19 Jun 2019 12:08:46 -0500 Subject: [PATCH] Update documentation and website --- R/make_eml.R | 6 - docs/CODE_OF_CONDUCT.html | 2 +- docs/CONTRIBUTING.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/automate_data_publication.html | 6 +- docs/articles/create_eml.html | 468 +++++------------- docs/articles/create_metadata_templates.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 5 +- docs/pkgdown.yml | 4 +- docs/reference/define_catvars.html | 2 +- docs/reference/extract_geocoverage.html | 2 +- docs/reference/import_templates.html | 2 +- docs/reference/index.html | 2 +- docs/reference/make_eml.html | 14 +- docs/reference/template_arguments.html | 2 +- .../template_categorical_variables.html | 2 +- docs/reference/template_core_metadata.html | 2 +- docs/reference/template_directories.html | 2 +- .../template_geographic_coverage.html | 2 +- docs/reference/template_table_attributes.html | 2 +- .../template_taxonomic_coverage.html | 2 +- docs/reference/validate_arguments.html | 2 +- docs/reference/validate_personnel.html | 2 +- docs/reference/validate_templates.html | 2 +- docs/reference/validate_x.html | 2 +- docs/reference/view_unit_dictionary.html | 2 +- man/make_eml.Rd | 6 - tests/testthat/test_make_eml.R | 16 +- vignettes/create_eml.Rmd | 9 +- 31 files changed, 162 insertions(+), 416 deletions(-) diff --git a/R/make_eml.R b/R/make_eml.R index 47ad92b4..47f2ccb6 100644 --- a/R/make_eml.R +++ b/R/make_eml.R @@ -140,8 +140,6 @@ #' eml.path = './eml', #' dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions', #' temporal.coverage = c('2014-05-01', '2015-10-31'), -#' geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada', -#' geographic.coordinates = c('55.895', '112.094','55.895', '112.094'), #' maintenance.description = 'completed', #' data.table = c('decomp.csv', 'nitrogen.csv'), #' data.table.description = c('Decomposition data', 'Nitrogen data'), @@ -161,8 +159,6 @@ #' eml.path = './eml', #' dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions', #' temporal.coverage = c('2014-05-01', '2015-10-31'), -#' geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada', -#' geographic.coordinates = c('55.895', '112.094','55.895', '112.094'), #' maintenance.description = 'completed', #' other.entity = c('ancillary_data.zip', 'processing_and_analysis.R'), #' other.entity.description = c('Ancillary data', 'Data processing and analysis script'), @@ -182,8 +178,6 @@ #' eml.path = './eml', #' dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions', #' temporal.coverage = c('2014-05-01', '2015-10-31'), -#' geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada', -#' geographic.coordinates = c('55.895', '112.094','55.895', '112.094'), #' maintenance.description = 'completed', #' data.table = c('decomp.csv', 'nitrogen.csv'), #' data.table.description = c('Decomposition data', 'Nitrogen data'), diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html index 28b12295..9a65a3fa 100644 --- a/docs/CODE_OF_CONDUCT.html +++ b/docs/CODE_OF_CONDUCT.html @@ -191,7 +191,7 @@

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index f26fbc24..0a77215d 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -182,7 +182,7 @@

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index bc6d2ad9..07b8fee3 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -163,7 +163,7 @@

License

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/articles/automate_data_publication.html b/docs/articles/automate_data_publication.html index dfff0e98..e1ce2139 100644 --- a/docs/articles/automate_data_publication.html +++ b/docs/articles/automate_data_publication.html @@ -132,7 +132,7 @@

Publish The new data and EML are then published via the data repository API.
-Processes of automated publication for a dataset with ongoing collection

Processes of automated publication for a dataset with ongoing collection

+Processes of automated publication for a dataset with ongoing collection

Processes of automated publication for a dataset with ongoing collection

@@ -163,7 +163,7 @@

Use information The public uses this information.
-An example implementation

An example implementation

+An example implementation

An example implementation

Automated data publication coupled with repository event notifications enable highly efficient, reproducible, and valuable science workflows.

@@ -189,7 +189,7 @@

-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

diff --git a/docs/articles/create_eml.html b/docs/articles/create_eml.html index bdd82ca6..e38b12e7 100644 --- a/docs/articles/create_eml.html +++ b/docs/articles/create_eml.html @@ -174,6 +174,8 @@

  • temporal.coverage Beginning and ending dates of the data using the format YYYY-MM-DD
  • +geographic.description (required if not using the geographic_coverage.txt template) Description of the data packages geographic area.
    • +
  • geographic.coordinates (required if not using the geographic_coverage.txt template) A vector of decimal degree coordinates in the order: north, east, south, west, where latitudes south of the equator and longitudes west of the prime meridian are negative.
  • maintenance.description Indicator of whether data collection is ‘ongoing’ or ‘completed’
    • @@ -201,8 +203,6 @@

    eml.path = './pkg_301/eml', dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions', temporal.coverage = c('2014-05-01', '2015-10-31'), - geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada', - geographic.coordinates = c('55.895', '112.094','55.895', '112.094'), maintenance.description = 'completed', data.table = c('decomp.csv', 'nitrogen.csv'), data.table.description = c('Decomposition data', 'Nitrogen data'), @@ -217,8 +217,8 @@ 

    ## [1] "edi.301.1.xml"
    # View EML
    $eml
-<eml:eml packageId="edi.301.1" schemaLocation="eml://ecoinformatics.org/eml-2.1.1  http://nis.lternet.edu/schemas/EML/eml-2.1.1/eml.xsd" system="edi" xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.1">
- <access authSystem="https://pasta.edirepository.org/authentication" order="allowFirst" scope="document">
+<eml:eml packageId="edi.301.1" system="edi" schemaLocation="eml://ecoinformatics.org/eml-2.1.1  http://nis.lternet.edu/schemas/EML/eml-2.1.1/eml.xsd" xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <access scope="document" order="allowFirst" authSystem="https://pasta.edirepository.org/authentication">
   <allow>
    <principal>uid=csmith,o=EDI,dc=edirepository,dc=org</principal>
    <permission>all</permission>
@@ -357,11 +357,11 @@ 
    
    <userId directory="https://orcid.org">https://orcid.org/0000-0001-5856-8473</userId>
    <role>Equipment Lead</role>
   </associatedParty>
-  <pubDate>2019-06-03</pubDate>
+  <pubDate>2019-06-19</pubDate>
   <abstract>
    <para>Development of the oil sands has led to increasing atmospheric N
   deposition, with values as high as 17 kg N ha^-1 yr^-1; regional
-  background levels &amp;lt;2 kg N ha^-1 yr^-1. Bogs, being ombrotrophic,
+  background levels &lt;2 kg N ha^-1 yr^-1. Bogs, being ombrotrophic,
   may be especially susceptible to increasing N deposition. To examine
   responses to N deposition, over five years, we experimentally applied
   N (as NH4NO3) to a bog near Mariana Lakes, Alberta, at rates of 0, 5,
@@ -374,7 +374,7 @@ 
    
   vascular plant litter was affected by N inputs, on average losing 8
   and 38 % of initial mass, respectively, over 5 months of
   decomposition. Water addition alone had no significant effect on
-  decomposition of cellulose, Sphagnum, or vascular plant litter (p &amp;gt;
+  decomposition of cellulose, Sphagnum, or vascular plant litter (p &gt;
   0.15).</para>
   </abstract>
   <keywordSet>
@@ -392,32 +392,23 @@ 
    
    <para>Articles derived from this dataset: Article 1, Article 2, Article 3</para>
   </additionalInfo>
   <intellectualRights>
-   <para>This data package is released to the “public domain” under Creative
-  Commons CC0 1.0 “No Rights Reserved” (see:
+   <para>This data package is released to the “public domain” under Creative
+  Commons CC0 1.0 “No Rights Reserved” (see:
   https://creativecommons.org/publicdomain/zero/1.0/). It is considered
   professional etiquette to provide attribution of the original work if
   this data package is shared in whole or by individual components. A
   generic citation is provided for this data package on the website
-  https://portal.edirepository.org (herein “website”) in the summary
+  https://portal.edirepository.org (herein “website”) in the summary
   metadata page. Communication (and collaboration) with the creators of
   this data package is recommended to prevent duplicate research or
   publication. This data package (and its components) is made available
-  “as is” and with no warranty of accuracy or fitness for use. The
+  “as is” and with no warranty of accuracy or fitness for use. The
   creators of this data package and the website shall not be liable for
   any damages resulting from misinterpretation or misuse of the data
   package or its components. Periodic updates of this data package may
   be available from the website. Thank you.</para>
   </intellectualRights>
   <coverage>
-   <geographicCoverage>
-    <geographicDescription>Alberta, Canada, 100 km south of Fort McMurray, Canada</geographicDescription>
-    <boundingCoordinates>
-     <westBoundingCoordinate>112.094</westBoundingCoordinate>
-     <eastBoundingCoordinate>112.094</eastBoundingCoordinate>
-     <northBoundingCoordinate>55.895</northBoundingCoordinate>
-     <southBoundingCoordinate>55.895</southBoundingCoordinate>
-    </boundingCoordinates>
-   </geographicCoverage>
    <geographicCoverage>
     <geographicDescription>site_1</geographicDescription>
     <boundingCoordinates>
@@ -546,47 +537,37 @@ 
    
   <methods>
    <methodStep>
     <description>
-     <para>In 2014 and 2015, we quantified decomposition of plant litter material
-  collected from each plot. In late May, we collected vascular plant
-  litter from the surface of each plot, along with</para>
      <para>
+      In 2014 and 2015, we quantified decomposition of plant litter material
+  collected from each plot. In late May, we collected vascular plant
+  litter from the surface of each plot, along with
       <emphasis>Sphagnum</emphasis>
-     </para>
-     <para>peat (</para>
-     <para>
+      peat (
       <emphasis>S.
   fuscum</emphasis>
-     </para>
-     <para>-derived), from roughly 5-15 cm below the capitula.
+      -derived), from roughly 5-15 cm below the capitula.
   We placed nylon mesh litter bags with mixed vascular plant litter
-  (approx. 1.7 g dry mass; roughly equal masses of</para>
-     <para>
+  (approx. 1.7 g dry mass; roughly equal masses of
       <emphasis>Rhododendron groenlandicum</emphasis>
-     </para>
-     <para>,</para>
-     <para>
+      ,
       <emphasis>Andromeda
   polifolia</emphasis>
-     </para>
-     <para>
+      ,
       <emphasis>Chamaedaphne calyculata</emphasis>
-     </para>
-     <para>,</para>
-     <para>
+      ,
       <emphasis>Smilacina trifolia</emphasis>
-     </para>
-     <para>, and</para>
-     <para>
+      , and
       <emphasis>Rubus
   chamaemorus</emphasis>
-     </para>
-     <para>) or peat approximately 10 cm below the peat
+      ) or peat approximately 10 cm below the peat
   surface in early June (in 2014, 3 bags per plot of vascular litter and
-  3 bags of</para>
-     <para>peat; in 2015, 4 bags of each
+  3 bags of
+      <emphasis>Sphagnum</emphasis>
+      peat; in 2015, 4 bags of each
   material). Upon retrieval in October of each year, we manually removed
   debris from each retrieved bag before drying at 55 C for a minimum of
-  5 days, and weighing.</para>
+  5 days, and weighing.
+     </para>
     </description>
    </methodStep>
   </methods>
@@ -595,10 +576,8 @@ 
    
    <personnel>
     <individualName>
      <givenName>Kelman</givenName>
-     <givenName>R</givenName>
      <surName>Wieder</surName>
     </individualName>
-    <organizationName>Villanova University</organizationName>
     <electronicMailAddress>kelman.wieder@villanova.edu</electronicMailAddress>
     <userId directory="https://orcid.org">https://orcid.org/0000-0001-5856-8473</userId>
     <role>Principal Investigator</role>
@@ -609,10 +588,8 @@ 
    
     <personnel>
      <individualName>
       <givenName>Melanie</givenName>
-      <givenName>A</givenName>
       <surName>Vile</surName>
      </individualName>
-     <organizationName>Villanova University</organizationName>
      <electronicMailAddress>mvile@villanova.edu</electronicMailAddress>
      <role>Principal Investigator</role>
     </personnel>
@@ -625,7 +602,6 @@ 
    
       <givenName>Joe</givenName>
       <surName>Smith</surName>
      </individualName>
-     <organizationName>Villanova University</organizationName>
      <role>Principal Investigator</role>
     </personnel>
     <funding>NSF: 101</funding>
@@ -637,7 +613,6 @@ 
    
       <givenName>Joe</givenName>
       <surName>Smith</surName>
      </individualName>
-     <organizationName>Villanova University</organizationName>
      <role>Principal Investigator</role>
     </personnel>
     <funding>111001</funding>
@@ -649,7 +624,6 @@ 
    
       <givenName>Chase</givenName>
       <surName>Gacho</surName>
      </individualName>
-     <organizationName>University of New Mexico</organizationName>
      <electronicMailAddress>gachase@unm.edu</electronicMailAddress>
      <role>Principal Investigator</role>
     </personnel>
@@ -661,7 +635,7 @@ 
    
    <entityDescription>Decomposition data</entityDescription>
    <physical>
     <objectName>decomp.csv</objectName>
-    <size unit="bytes">15547</size>
+    <size unit="byte">15547</size>
     <authentication method="MD5">2d7897ddbfccc840fddffc4c7d468ba5</authentication>
     <dataFormat>
      <textFormat>
@@ -684,12 +658,8 @@ 
    
        <nonNumericDomain>
         <enumeratedDomain>
          <codeDefinition>
-          <code>Sphagnum</code>
-          <definition>Sphagnum</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>Vascular</code>
-          <definition>Vascular</definition>
+          <code>NA</code>
+          <definition>NA</definition>
          </codeDefinition>
         </enumeratedDomain>
        </nonNumericDomain>
@@ -706,10 +676,7 @@ 
    
      <storageType>date</storageType>
      <measurementScale>
       <dateTime>
-       <formatString>YYYY-MM-DD</formatString>
    -
    Warning in structure(x$children, class = "XMLNodeList"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
-  Consider 'structure(list(), *)' instead.
    -
           <dateTimeDomain/>
+       <formatString>YYYY-MM-DD</formatString>
       </dateTime>
      </measurementScale>
      <missingValueCode>
@@ -726,16 +693,8 @@ 
    
        <nonNumericDomain>
         <enumeratedDomain>
          <codeDefinition>
-          <code>1</code>
-          <definition>Arm 1</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>2</code>
-          <definition>Arm 2</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>3</code>
-          <definition>Arm 3</definition>
+          <code>NA</code>
+          <definition>NA</definition>
          </codeDefinition>
         </enumeratedDomain>
        </nonNumericDomain>
@@ -755,32 +714,8 @@ 
    
        <nonNumericDomain>
         <enumeratedDomain>
          <codeDefinition>
-          <code>C</code>
-          <definition>Control, no water, no N added</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>0</code>
-          <definition>0 kg N/ha/yr added</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>5</code>
-          <definition>5 kg N/ha/yr added</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>10</code>
-          <definition>10 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>15</code>
-          <definition>15 kg N/ha/yr added</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>20</code>
-          <definition>20 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>25</code>
-          <definition>25 kg N/ha/yr added</definition>
+          <code>NA</code>
+          <definition>NA</definition>
          </codeDefinition>
         </enumeratedDomain>
        </nonNumericDomain>
@@ -797,10 +732,7 @@ 
    
      <storageType>date</storageType>
      <measurementScale>
       <dateTime>
-       <formatString>YYYY</formatString>
    -
    Warning in structure(x$children, class = "XMLNodeList"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
-  Consider 'structure(list(), *)' instead.
    -
           <dateTimeDomain/>
+       <formatString>YYYY</formatString>
       </dateTime>
      </measurementScale>
      <missingValueCode>
@@ -857,7 +789,7 @@ 
    
    <entityDescription>Nitrogen data</entityDescription>
    <physical>
     <objectName>nitrogen.csv</objectName>
-    <size unit="bytes">6733</size>
+    <size unit="byte">6733</size>
     <authentication method="MD5">2b10baaea5692bf96cafab9ae636f831</authentication>
     <dataFormat>
      <textFormat>
@@ -877,10 +809,7 @@ 
    
      <storageType>date</storageType>
      <measurementScale>
       <dateTime>
-       <formatString>YYYY</formatString>
    -
    Warning in structure(x$children, class = "XMLNodeList"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
-  Consider 'structure(list(), *)' instead.
    -
           <dateTimeDomain/>
+       <formatString>YYYY</formatString>
       </dateTime>
      </measurementScale>
      <missingValueCode>
@@ -897,32 +826,8 @@ 
    
        <nonNumericDomain>
         <enumeratedDomain>
          <codeDefinition>
-          <code>C</code>
-          <definition>Control, no water, no N added</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>0</code>
-          <definition>0 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>5</code>
-          <definition>5 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>10</code>
-          <definition>10 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>15</code>
-          <definition>15 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>20</code>
-          <definition>20 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>25</code>
-          <definition>25 kg N/ha/yr added as NH4NO3</definition>
+          <code>NA</code>
+          <definition>NA</definition>
          </codeDefinition>
         </enumeratedDomain>
        </nonNumericDomain>
@@ -942,16 +847,8 @@ 
    
        <nonNumericDomain>
         <enumeratedDomain>
          <codeDefinition>
-          <code>1</code>
-          <definition>Arm 1</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>2</code>
-          <definition>Arm 2</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>3</code>
-          <definition>Arm3</definition>
+          <code>NA</code>
+          <definition>NA</definition>
          </codeDefinition>
         </enumeratedDomain>
        </nonNumericDomain>
@@ -1147,11 +1044,11 @@ 
    
  </dataset>
  <additionalMetadata>
   <metadata>
-   <unitList>
-    <unit id="gramsPerSquaredMeterPerCentimeter" multiplierToSI="0.1" name="gramsPerSquaredMeterPerCentimeter" parentSI="kilogramsPerSquaredMeterPerMeter" unitType="areal mass density per length">
+   <unitList xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <unit id="gramsPerSquaredMeterPerCentimeter" name="gramsPerSquaredMeterPerCentimeter" parentSI="kilogramsPerSquaredMeterPerMeter" unitType="areal mass density per length" multiplierToSI="0.1">
      <description>grams per meter squared per centimeter</description>
     </unit>
-    <unit id="milligramsPerGram" multiplierToSI="1000" name="milligramsPerGram" parentSI="kilogramsPerSquaredMeterPerMeter" unitType="mass">
+    <unit id="milligramsPerGram" name="milligramsPerGram" parentSI="kilogramsPerSquaredMeterPerMeter" unitType="mass" multiplierToSI="1000">
      <description>milligrams per gram</description>
     </unit>
    </unitList>
@@ -1175,6 +1072,8 @@ 
    
 
  • 
 temporal.coverage Beginning and ending dates of the data using the format YYYY-MM-DD
    • 
 
  • 
+geographic.description (required if not using the geographic_coverage.txt template) Description of the data packages geographic area.
    • 
+
  • 
 geographic.coordinates (required if not using the geographic_coverage.txt template) A vector of decimal degree coordinates in the order: north, east, south, west, where latitudes south of the equator and longitudes west of the prime meridian are negative.
    • 
 
  • 
 maintenance.description Indicator of whether data collection is ‘ongoing’ or ‘completed’
    • 
@@ -1200,8 +1099,6 @@ 
    
   eml.path = './pkg_301/eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
-  geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada',
-  geographic.coordinates = c('55.895', '112.094','55.895', '112.094'),
   maintenance.description = 'completed',
   other.entity = c('ancillary_data.zip', 'processing_and_analysis.R'),
   other.entity.description = c('Ancillary data', 'Data processing and analysis script'),
@@ -1216,8 +1113,8 @@ 
    
 
    ## [1] "edi.301.1.xml" "edi.301.2.xml"
    
 
    # View EML
    
 
    $eml
-<eml:eml packageId="edi.301.2" schemaLocation="eml://ecoinformatics.org/eml-2.1.1  http://nis.lternet.edu/schemas/EML/eml-2.1.1/eml.xsd" system="edi" xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.1">
- <access authSystem="https://pasta.edirepository.org/authentication" order="allowFirst" scope="document">
+<eml:eml packageId="edi.301.2" system="edi" schemaLocation="eml://ecoinformatics.org/eml-2.1.1  http://nis.lternet.edu/schemas/EML/eml-2.1.1/eml.xsd" xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <access scope="document" order="allowFirst" authSystem="https://pasta.edirepository.org/authentication">
   <allow>
    <principal>uid=csmith,o=EDI,dc=edirepository,dc=org</principal>
    <permission>all</permission>
@@ -1356,11 +1253,11 @@ 
    
    <userId directory="https://orcid.org">https://orcid.org/0000-0001-5856-8473</userId>
    <role>Equipment Lead</role>
   </associatedParty>
-  <pubDate>2019-06-03</pubDate>
+  <pubDate>2019-06-19</pubDate>
   <abstract>
    <para>Development of the oil sands has led to increasing atmospheric N
   deposition, with values as high as 17 kg N ha^-1 yr^-1; regional
-  background levels &amp;lt;2 kg N ha^-1 yr^-1. Bogs, being ombrotrophic,
+  background levels &lt;2 kg N ha^-1 yr^-1. Bogs, being ombrotrophic,
   may be especially susceptible to increasing N deposition. To examine
   responses to N deposition, over five years, we experimentally applied
   N (as NH4NO3) to a bog near Mariana Lakes, Alberta, at rates of 0, 5,
@@ -1373,7 +1270,7 @@ 
    
   vascular plant litter was affected by N inputs, on average losing 8
   and 38 % of initial mass, respectively, over 5 months of
   decomposition. Water addition alone had no significant effect on
-  decomposition of cellulose, Sphagnum, or vascular plant litter (p &amp;gt;
+  decomposition of cellulose, Sphagnum, or vascular plant litter (p &gt;
   0.15).</para>
   </abstract>
   <keywordSet>
@@ -1391,32 +1288,23 @@ 
    
    <para>Articles derived from this dataset: Article 1, Article 2, Article 3</para>
   </additionalInfo>
   <intellectualRights>
-   <para>This data package is released to the “public domain” under Creative
-  Commons CC0 1.0 “No Rights Reserved” (see:
+   <para>This data package is released to the “public domain” under Creative
+  Commons CC0 1.0 “No Rights Reserved” (see:
   https://creativecommons.org/publicdomain/zero/1.0/). It is considered
   professional etiquette to provide attribution of the original work if
   this data package is shared in whole or by individual components. A
   generic citation is provided for this data package on the website
-  https://portal.edirepository.org (herein “website”) in the summary
+  https://portal.edirepository.org (herein “website”) in the summary
   metadata page. Communication (and collaboration) with the creators of
   this data package is recommended to prevent duplicate research or
   publication. This data package (and its components) is made available
-  “as is” and with no warranty of accuracy or fitness for use. The
+  “as is” and with no warranty of accuracy or fitness for use. The
   creators of this data package and the website shall not be liable for
   any damages resulting from misinterpretation or misuse of the data
   package or its components. Periodic updates of this data package may
   be available from the website. Thank you.</para>
   </intellectualRights>
   <coverage>
-   <geographicCoverage>
-    <geographicDescription>Alberta, Canada, 100 km south of Fort McMurray, Canada</geographicDescription>
-    <boundingCoordinates>
-     <westBoundingCoordinate>112.094</westBoundingCoordinate>
-     <eastBoundingCoordinate>112.094</eastBoundingCoordinate>
-     <northBoundingCoordinate>55.895</northBoundingCoordinate>
-     <southBoundingCoordinate>55.895</southBoundingCoordinate>
-    </boundingCoordinates>
-   </geographicCoverage>
    <geographicCoverage>
     <geographicDescription>site_1</geographicDescription>
     <boundingCoordinates>
@@ -1545,47 +1433,37 @@ 
    
   <methods>
    <methodStep>
     <description>
-     <para>In 2014 and 2015, we quantified decomposition of plant litter material
-  collected from each plot. In late May, we collected vascular plant
-  litter from the surface of each plot, along with</para>
      <para>
+      In 2014 and 2015, we quantified decomposition of plant litter material
+  collected from each plot. In late May, we collected vascular plant
+  litter from the surface of each plot, along with
       <emphasis>Sphagnum</emphasis>
-     </para>
-     <para>peat (</para>
-     <para>
+      peat (
       <emphasis>S.
   fuscum</emphasis>
-     </para>
-     <para>-derived), from roughly 5-15 cm below the capitula.
+      -derived), from roughly 5-15 cm below the capitula.
   We placed nylon mesh litter bags with mixed vascular plant litter
-  (approx. 1.7 g dry mass; roughly equal masses of</para>
-     <para>
+  (approx. 1.7 g dry mass; roughly equal masses of
       <emphasis>Rhododendron groenlandicum</emphasis>
-     </para>
-     <para>,</para>
-     <para>
+      ,
       <emphasis>Andromeda
   polifolia</emphasis>
-     </para>
-     <para>
+      ,
       <emphasis>Chamaedaphne calyculata</emphasis>
-     </para>
-     <para>,</para>
-     <para>
+      ,
       <emphasis>Smilacina trifolia</emphasis>
-     </para>
-     <para>, and</para>
-     <para>
+      , and
       <emphasis>Rubus
   chamaemorus</emphasis>
-     </para>
-     <para>) or peat approximately 10 cm below the peat
+      ) or peat approximately 10 cm below the peat
   surface in early June (in 2014, 3 bags per plot of vascular litter and
-  3 bags of</para>
-     <para>peat; in 2015, 4 bags of each
+  3 bags of
+      <emphasis>Sphagnum</emphasis>
+      peat; in 2015, 4 bags of each
   material). Upon retrieval in October of each year, we manually removed
   debris from each retrieved bag before drying at 55 C for a minimum of
-  5 days, and weighing.</para>
+  5 days, and weighing.
+     </para>
     </description>
    </methodStep>
   </methods>
@@ -1594,10 +1472,8 @@ 
    
    <personnel>
     <individualName>
      <givenName>Kelman</givenName>
-     <givenName>R</givenName>
      <surName>Wieder</surName>
     </individualName>
-    <organizationName>Villanova University</organizationName>
     <electronicMailAddress>kelman.wieder@villanova.edu</electronicMailAddress>
     <userId directory="https://orcid.org">https://orcid.org/0000-0001-5856-8473</userId>
     <role>Principal Investigator</role>
@@ -1608,10 +1484,8 @@ 
    
     <personnel>
      <individualName>
       <givenName>Melanie</givenName>
-      <givenName>A</givenName>
       <surName>Vile</surName>
      </individualName>
-     <organizationName>Villanova University</organizationName>
      <electronicMailAddress>mvile@villanova.edu</electronicMailAddress>
      <role>Principal Investigator</role>
     </personnel>
@@ -1624,7 +1498,6 @@ 
    
       <givenName>Joe</givenName>
       <surName>Smith</surName>
      </individualName>
-     <organizationName>Villanova University</organizationName>
      <role>Principal Investigator</role>
     </personnel>
     <funding>NSF: 101</funding>
@@ -1636,7 +1509,6 @@ 
    
       <givenName>Joe</givenName>
       <surName>Smith</surName>
      </individualName>
-     <organizationName>Villanova University</organizationName>
      <role>Principal Investigator</role>
     </personnel>
     <funding>111001</funding>
@@ -1648,7 +1520,6 @@ 
    
       <givenName>Chase</givenName>
       <surName>Gacho</surName>
      </individualName>
-     <organizationName>University of New Mexico</organizationName>
      <electronicMailAddress>gachase@unm.edu</electronicMailAddress>
      <role>Principal Investigator</role>
     </personnel>
@@ -1704,6 +1575,8 @@ 
    
 
  • 
 temporal.coverage Beginning and ending dates of the data using the format YYYY-MM-DD
    • 
 
  • 
+geographic.description (required if not using the geographic_coverage.txt template) Description of the data packages geographic area.
    • 
+
  • 
 geographic.coordinates (required if not using the geographic_coverage.txt template) A vector of decimal degree coordinates in the order: north, east, south, west, where latitudes south of the equator and longitudes west of the prime meridian are negative.
    • 
 
  • 
 maintenance.description Indicator of whether data collection is ‘ongoing’ or ‘completed’
    • 
@@ -1736,8 +1609,6 @@ 
    
   eml.path = './pkg_301/eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
-  geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada',
-  geographic.coordinates = c('55.895', '112.094','55.895', '112.094'),
   maintenance.description = 'completed',
   data.table = c('decomp.csv', 'nitrogen.csv'),
   data.table.description = c('Decomposition data', 'Nitrogen data'),
@@ -1754,8 +1625,8 @@ 
    
 
    ## [1] "edi.301.1.xml" "edi.301.2.xml" "edi.301.3.xml"
    
 
    # View EML
    
 
    $eml
-<eml:eml packageId="edi.301.3" schemaLocation="eml://ecoinformatics.org/eml-2.1.1  http://nis.lternet.edu/schemas/EML/eml-2.1.1/eml.xsd" system="edi" xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.1">
- <access authSystem="https://pasta.edirepository.org/authentication" order="allowFirst" scope="document">
+<eml:eml packageId="edi.301.3" system="edi" schemaLocation="eml://ecoinformatics.org/eml-2.1.1  http://nis.lternet.edu/schemas/EML/eml-2.1.1/eml.xsd" xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <access scope="document" order="allowFirst" authSystem="https://pasta.edirepository.org/authentication">
   <allow>
    <principal>uid=csmith,o=EDI,dc=edirepository,dc=org</principal>
    <permission>all</permission>
@@ -1894,11 +1765,11 @@ 
    
    <userId directory="https://orcid.org">https://orcid.org/0000-0001-5856-8473</userId>
    <role>Equipment Lead</role>
   </associatedParty>
-  <pubDate>2019-06-03</pubDate>
+  <pubDate>2019-06-19</pubDate>
   <abstract>
    <para>Development of the oil sands has led to increasing atmospheric N
   deposition, with values as high as 17 kg N ha^-1 yr^-1; regional
-  background levels &amp;lt;2 kg N ha^-1 yr^-1. Bogs, being ombrotrophic,
+  background levels &lt;2 kg N ha^-1 yr^-1. Bogs, being ombrotrophic,
   may be especially susceptible to increasing N deposition. To examine
   responses to N deposition, over five years, we experimentally applied
   N (as NH4NO3) to a bog near Mariana Lakes, Alberta, at rates of 0, 5,
@@ -1911,7 +1782,7 @@ 
    
   vascular plant litter was affected by N inputs, on average losing 8
   and 38 % of initial mass, respectively, over 5 months of
   decomposition. Water addition alone had no significant effect on
-  decomposition of cellulose, Sphagnum, or vascular plant litter (p &amp;gt;
+  decomposition of cellulose, Sphagnum, or vascular plant litter (p &gt;
   0.15).</para>
   </abstract>
   <keywordSet>
@@ -1929,32 +1800,23 @@ 
    
    <para>Articles derived from this dataset: Article 1, Article 2, Article 3</para>
   </additionalInfo>
   <intellectualRights>
-   <para>This data package is released to the “public domain” under Creative
-  Commons CC0 1.0 “No Rights Reserved” (see:
+   <para>This data package is released to the “public domain” under Creative
+  Commons CC0 1.0 “No Rights Reserved” (see:
   https://creativecommons.org/publicdomain/zero/1.0/). It is considered
   professional etiquette to provide attribution of the original work if
   this data package is shared in whole or by individual components. A
   generic citation is provided for this data package on the website
-  https://portal.edirepository.org (herein “website”) in the summary
+  https://portal.edirepository.org (herein “website”) in the summary
   metadata page. Communication (and collaboration) with the creators of
   this data package is recommended to prevent duplicate research or
   publication. This data package (and its components) is made available
-  “as is” and with no warranty of accuracy or fitness for use. The
+  “as is” and with no warranty of accuracy or fitness for use. The
   creators of this data package and the website shall not be liable for
   any damages resulting from misinterpretation or misuse of the data
   package or its components. Periodic updates of this data package may
   be available from the website. Thank you.</para>
   </intellectualRights>
   <coverage>
-   <geographicCoverage>
-    <geographicDescription>Alberta, Canada, 100 km south of Fort McMurray, Canada</geographicDescription>
-    <boundingCoordinates>
-     <westBoundingCoordinate>112.094</westBoundingCoordinate>
-     <eastBoundingCoordinate>112.094</eastBoundingCoordinate>
-     <northBoundingCoordinate>55.895</northBoundingCoordinate>
-     <southBoundingCoordinate>55.895</southBoundingCoordinate>
-    </boundingCoordinates>
-   </geographicCoverage>
    <geographicCoverage>
     <geographicDescription>site_1</geographicDescription>
     <boundingCoordinates>
@@ -2083,47 +1945,37 @@ 
    
   <methods>
    <methodStep>
     <description>
-     <para>In 2014 and 2015, we quantified decomposition of plant litter material
-  collected from each plot. In late May, we collected vascular plant
-  litter from the surface of each plot, along with</para>
      <para>
+      In 2014 and 2015, we quantified decomposition of plant litter material
+  collected from each plot. In late May, we collected vascular plant
+  litter from the surface of each plot, along with
       <emphasis>Sphagnum</emphasis>
-     </para>
-     <para>peat (</para>
-     <para>
+      peat (
       <emphasis>S.
   fuscum</emphasis>
-     </para>
-     <para>-derived), from roughly 5-15 cm below the capitula.
+      -derived), from roughly 5-15 cm below the capitula.
   We placed nylon mesh litter bags with mixed vascular plant litter
-  (approx. 1.7 g dry mass; roughly equal masses of</para>
-     <para>
+  (approx. 1.7 g dry mass; roughly equal masses of
       <emphasis>Rhododendron groenlandicum</emphasis>
-     </para>
-     <para>,</para>
-     <para>
+      ,
       <emphasis>Andromeda
   polifolia</emphasis>
-     </para>
-     <para>
+      ,
       <emphasis>Chamaedaphne calyculata</emphasis>
-     </para>
-     <para>,</para>
-     <para>
+      ,
       <emphasis>Smilacina trifolia</emphasis>
-     </para>
-     <para>, and</para>
-     <para>
+      , and
       <emphasis>Rubus
   chamaemorus</emphasis>
-     </para>
-     <para>) or peat approximately 10 cm below the peat
+      ) or peat approximately 10 cm below the peat
   surface in early June (in 2014, 3 bags per plot of vascular litter and
-  3 bags of</para>
-     <para>peat; in 2015, 4 bags of each
+  3 bags of
+      <emphasis>Sphagnum</emphasis>
+      peat; in 2015, 4 bags of each
   material). Upon retrieval in October of each year, we manually removed
   debris from each retrieved bag before drying at 55 C for a minimum of
-  5 days, and weighing.</para>
+  5 days, and weighing.
+     </para>
     </description>
    </methodStep>
   </methods>
@@ -2132,10 +1984,8 @@ 
    
    <personnel>
     <individualName>
      <givenName>Kelman</givenName>
-     <givenName>R</givenName>
      <surName>Wieder</surName>
     </individualName>
-    <organizationName>Villanova University</organizationName>
     <electronicMailAddress>kelman.wieder@villanova.edu</electronicMailAddress>
     <userId directory="https://orcid.org">https://orcid.org/0000-0001-5856-8473</userId>
     <role>Principal Investigator</role>
@@ -2146,10 +1996,8 @@ 
    
     <personnel>
      <individualName>
       <givenName>Melanie</givenName>
-      <givenName>A</givenName>
       <surName>Vile</surName>
      </individualName>
-     <organizationName>Villanova University</organizationName>
      <electronicMailAddress>mvile@villanova.edu</electronicMailAddress>
      <role>Principal Investigator</role>
     </personnel>
@@ -2162,7 +2010,6 @@ 
    
       <givenName>Joe</givenName>
       <surName>Smith</surName>
      </individualName>
-     <organizationName>Villanova University</organizationName>
      <role>Principal Investigator</role>
     </personnel>
     <funding>NSF: 101</funding>
@@ -2174,7 +2021,6 @@ 
    
       <givenName>Joe</givenName>
       <surName>Smith</surName>
      </individualName>
-     <organizationName>Villanova University</organizationName>
      <role>Principal Investigator</role>
     </personnel>
     <funding>111001</funding>
@@ -2186,7 +2032,6 @@ 
    
       <givenName>Chase</givenName>
       <surName>Gacho</surName>
      </individualName>
-     <organizationName>University of New Mexico</organizationName>
      <electronicMailAddress>gachase@unm.edu</electronicMailAddress>
      <role>Principal Investigator</role>
     </personnel>
@@ -2198,7 +2043,7 @@ 
    
    <entityDescription>Decomposition data</entityDescription>
    <physical>
     <objectName>decomp.csv</objectName>
-    <size unit="bytes">15547</size>
+    <size unit="byte">15547</size>
     <authentication method="MD5">2d7897ddbfccc840fddffc4c7d468ba5</authentication>
     <dataFormat>
      <textFormat>
@@ -2221,12 +2066,8 @@ 
    
        <nonNumericDomain>
         <enumeratedDomain>
          <codeDefinition>
-          <code>Sphagnum</code>
-          <definition>Sphagnum</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>Vascular</code>
-          <definition>Vascular</definition>
+          <code>NA</code>
+          <definition>NA</definition>
          </codeDefinition>
         </enumeratedDomain>
        </nonNumericDomain>
@@ -2243,10 +2084,7 @@ 
    
      <storageType>date</storageType>
      <measurementScale>
       <dateTime>
-       <formatString>YYYY-MM-DD</formatString>
    
-
    Warning in structure(x$children, class = "XMLNodeList"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
-  Consider 'structure(list(), *)' instead.
    
-
           <dateTimeDomain/>
+       <formatString>YYYY-MM-DD</formatString>
       </dateTime>
      </measurementScale>
      <missingValueCode>
@@ -2263,16 +2101,8 @@ 
    
        <nonNumericDomain>
         <enumeratedDomain>
          <codeDefinition>
-          <code>1</code>
-          <definition>Arm 1</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>2</code>
-          <definition>Arm 2</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>3</code>
-          <definition>Arm 3</definition>
+          <code>NA</code>
+          <definition>NA</definition>
          </codeDefinition>
         </enumeratedDomain>
        </nonNumericDomain>
@@ -2292,32 +2122,8 @@ 
    
        <nonNumericDomain>
         <enumeratedDomain>
          <codeDefinition>
-          <code>C</code>
-          <definition>Control, no water, no N added</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>0</code>
-          <definition>0 kg N/ha/yr added</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>5</code>
-          <definition>5 kg N/ha/yr added</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>10</code>
-          <definition>10 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>15</code>
-          <definition>15 kg N/ha/yr added</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>20</code>
-          <definition>20 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>25</code>
-          <definition>25 kg N/ha/yr added</definition>
+          <code>NA</code>
+          <definition>NA</definition>
          </codeDefinition>
         </enumeratedDomain>
        </nonNumericDomain>
@@ -2334,10 +2140,7 @@ 
    
      <storageType>date</storageType>
      <measurementScale>
       <dateTime>
-       <formatString>YYYY</formatString>
    
-
    Warning in structure(x$children, class = "XMLNodeList"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
-  Consider 'structure(list(), *)' instead.
    
-
           <dateTimeDomain/>
+       <formatString>YYYY</formatString>
       </dateTime>
      </measurementScale>
      <missingValueCode>
@@ -2394,7 +2197,7 @@ 
    
    <entityDescription>Nitrogen data</entityDescription>
    <physical>
     <objectName>nitrogen.csv</objectName>
-    <size unit="bytes">6733</size>
+    <size unit="byte">6733</size>
     <authentication method="MD5">2b10baaea5692bf96cafab9ae636f831</authentication>
     <dataFormat>
      <textFormat>
@@ -2414,10 +2217,7 @@ 
    
      <storageType>date</storageType>
      <measurementScale>
       <dateTime>
-       <formatString>YYYY</formatString>
    
-
    Warning in structure(x$children, class = "XMLNodeList"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
-  Consider 'structure(list(), *)' instead.
    
-
           <dateTimeDomain/>
+       <formatString>YYYY</formatString>
       </dateTime>
      </measurementScale>
      <missingValueCode>
@@ -2434,32 +2234,8 @@ 
    
        <nonNumericDomain>
         <enumeratedDomain>
          <codeDefinition>
-          <code>C</code>
-          <definition>Control, no water, no N added</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>0</code>
-          <definition>0 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>5</code>
-          <definition>5 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>10</code>
-          <definition>10 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>15</code>
-          <definition>15 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>20</code>
-          <definition>20 kg N/ha/yr added as NH4NO3</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>25</code>
-          <definition>25 kg N/ha/yr added as NH4NO3</definition>
+          <code>NA</code>
+          <definition>NA</definition>
          </codeDefinition>
         </enumeratedDomain>
        </nonNumericDomain>
@@ -2479,16 +2255,8 @@ 
    
        <nonNumericDomain>
         <enumeratedDomain>
          <codeDefinition>
-          <code>1</code>
-          <definition>Arm 1</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>2</code>
-          <definition>Arm 2</definition>
-         </codeDefinition>
-         <codeDefinition>
-          <code>3</code>
-          <definition>Arm3</definition>
+          <code>NA</code>
+          <definition>NA</definition>
          </codeDefinition>
         </enumeratedDomain>
        </nonNumericDomain>
@@ -2714,11 +2482,11 @@ 
    
  </dataset>
  <additionalMetadata>
   <metadata>
-   <unitList>
-    <unit id="gramsPerSquaredMeterPerCentimeter" multiplierToSI="0.1" name="gramsPerSquaredMeterPerCentimeter" parentSI="kilogramsPerSquaredMeterPerMeter" unitType="areal mass density per length">
+   <unitList xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <unit id="gramsPerSquaredMeterPerCentimeter" name="gramsPerSquaredMeterPerCentimeter" parentSI="kilogramsPerSquaredMeterPerMeter" unitType="areal mass density per length" multiplierToSI="0.1">
      <description>grams per meter squared per centimeter</description>
     </unit>
-    <unit id="milligramsPerGram" multiplierToSI="1000" name="milligramsPerGram" parentSI="kilogramsPerSquaredMeterPerMeter" unitType="mass">
+    <unit id="milligramsPerGram" name="milligramsPerGram" parentSI="kilogramsPerSquaredMeterPerMeter" unitType="mass" multiplierToSI="1000">
      <description>milligrams per gram</description>
     </unit>
    </unitList>
@@ -2749,7 +2517,7 @@ 
    
 
 
 
    
-  
    Site built with pkgdown 1.3.0.9000.
    
+  
    Site built with pkgdown 1.3.0.
    
 
    
       
 
diff --git a/docs/articles/create_metadata_templates.html b/docs/articles/create_metadata_templates.html
index c6b058e9..c0aed92b 100644
--- a/docs/articles/create_metadata_templates.html
+++ b/docs/articles/create_metadata_templates.html
@@ -1796,7 +1796,7 @@ 
    
 
 
 
    
-  
    Site built with pkgdown 1.3.0.9000.
    
+  
    Site built with pkgdown 1.3.0.
    
 
    
       
 
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 36df948a..96fde167 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -153,7 +153,7 @@ 
    All vignettes
    
 
 
 
    
-  
    Site built with pkgdown 1.3.0.9000.
    
+  
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diff --git a/docs/authors.html b/docs/authors.html
index 1ac62d06..4e06b9ce 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -165,7 +165,7 @@ 
    
 
 
 
    
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+  
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diff --git a/docs/index.html b/docs/index.html
index 1da5f49b..911703f2 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -187,8 +187,7 @@ 
    License
    
 
    
 
    Developers
    
 
      
-
    • Colin Smith 
       Author, maintainer   
      (https://orcid.org/0000-0003-2261-9931)
-
      • 
+
    • Colin Smith 
       Author, maintainer  ORCID 
      • 
 
    
 
    
 
@@ -208,7 +207,7 @@ 
    Dev status
    
 
 
 
    
-  
    Site built with pkgdown 1.3.0.9000.
    
+  
    Site built with pkgdown 1.3.0.
    
 
    
       
 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 37a5dc34..4eea6d63 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
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 pandoc: 1.19.2.1
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-pkgdown_sha: 7e788c41d20ab28d4bf97556e18382391d359c9f
+pkgdown: 1.3.0
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diff --git a/docs/reference/define_catvars.html b/docs/reference/define_catvars.html
index 526c5b33..a35d2f88 100644
--- a/docs/reference/define_catvars.html
+++ b/docs/reference/define_catvars.html
@@ -263,7 +263,7 @@ 
    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.3.0.9000.
    
+  
    Site built with pkgdown 1.3.0.
    
 
    
       
    
diff --git a/docs/reference/extract_geocoverage.html b/docs/reference/extract_geocoverage.html
index 09154ca7..c1fc3083 100644
--- a/docs/reference/extract_geocoverage.html
+++ b/docs/reference/extract_geocoverage.html
@@ -287,7 +287,7 @@ 
    Contents
    
 
 
 
    
-  
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+  
    Site built with pkgdown 1.3.0.
    
 
    
       
    
diff --git a/docs/reference/import_templates.html b/docs/reference/import_templates.html
index 99dc32d3..33b48683 100644
--- a/docs/reference/import_templates.html
+++ b/docs/reference/import_templates.html
@@ -302,7 +302,7 @@ 
    Contents
    
 
 
 
    
-  
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+  
    Site built with pkgdown 1.3.0.
    
 
    
       
    
diff --git a/docs/reference/index.html b/docs/reference/index.html
index c133d939..6bd59003 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -235,7 +235,7 @@ 
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+  
    Site built with pkgdown 1.3.0.
    
 
    
       
    
diff --git a/docs/reference/make_eml.html b/docs/reference/make_eml.html
index dcab1cb9..4ff53676 100644
--- a/docs/reference/make_eml.html
+++ b/docs/reference/make_eml.html
@@ -327,15 +327,13 @@ 
    Examp
   eml.path = './eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
-  geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada',
-  geographic.coordinates = c('55.895', '112.094','55.895', '112.094'),
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   data.table.description = c('Decomposition data', 'Nitrogen data'),
   user.id = 'csmith',
   user.domain = 'EDI',
   package.id = 'edi.260.1'
-)
    #> Making EML ...
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    #> </eml>
    #> Writing EML (edi.260.1.xml)
    #> Validating EML
    #> EML passed validation!
    #> Done.
    
+)
    #> Making EML ...
    #> Creating nodes ...
    #> <eml>
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 # View EML directory contents (NOTE: edi.260.1 exists)
 dir('./eml')
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 # Make EML (for data package with other entities)
@@ -346,15 +344,13 @@ 
    Examp
   eml.path = './eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
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-)
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 # View EML directory contents (NOTE: edi.260.2 exists)
 dir('./eml')
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 # Make EML (for data package with data tables and other entities)
@@ -365,8 +361,6 @@ 
    Examp
   eml.path = './eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
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@@ -375,7 +369,7 @@ 
    Examp
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-)
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+)
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 # View EML directory contents (NOTE: edi.260.3 exists)
 dir('./eml')
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 # Clean up
@@ -402,7 +396,7 @@ 
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-  
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+  
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diff --git a/docs/reference/template_arguments.html b/docs/reference/template_arguments.html
index ce2d0ea0..5987c9e7 100644
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@@ -384,7 +384,7 @@ 
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-  
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+  
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index 803dd9c7..09659e0d 100644
--- a/docs/reference/template_categorical_variables.html
+++ b/docs/reference/template_categorical_variables.html
@@ -248,7 +248,7 @@ 
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-  
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+  
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diff --git a/docs/reference/template_core_metadata.html b/docs/reference/template_core_metadata.html
index 3564c97d..9f10485f 100644
--- a/docs/reference/template_core_metadata.html
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@@ -289,7 +289,7 @@ 
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-  
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+  
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index 722ed9fa..bbcef299 100644
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@@ -220,7 +220,7 @@ 
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-  
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+  
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diff --git a/docs/reference/template_geographic_coverage.html b/docs/reference/template_geographic_coverage.html
index c900952e..3b29580d 100644
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@@ -285,7 +285,7 @@ 
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-  
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+  
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diff --git a/docs/reference/template_table_attributes.html b/docs/reference/template_table_attributes.html
index 0829e437..89687481 100644
--- a/docs/reference/template_table_attributes.html
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@@ -260,7 +260,7 @@ 
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-  
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+  
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index 20b51a9b..de7d29d3 100644
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diff --git a/docs/reference/validate_arguments.html b/docs/reference/validate_arguments.html
index 96cdf446..dede8571 100644
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@@ -183,7 +183,7 @@ 
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-  
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+  
    Site built with pkgdown 1.3.0.
    
 
    
       
    
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index f282c993..2f6335cc 100644
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@@ -179,7 +179,7 @@ 
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-  
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    Site built with pkgdown 1.3.0.
    
 
    
       
    
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index 09b9bfd5..c116dc70 100644
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@@ -183,7 +183,7 @@ 
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-  
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+  
    Site built with pkgdown 1.3.0.
    
 
    
       
    
diff --git a/man/make_eml.Rd b/man/make_eml.Rd
index 490f3949..a5671948 100644
--- a/man/make_eml.Rd
+++ b/man/make_eml.Rd
@@ -143,8 +143,6 @@ make_eml(
   eml.path = './eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
-  geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada',
-  geographic.coordinates = c('55.895', '112.094','55.895', '112.094'),
   maintenance.description = 'completed',
   data.table = c('decomp.csv', 'nitrogen.csv'),
   data.table.description = c('Decomposition data', 'Nitrogen data'),
@@ -164,8 +162,6 @@ make_eml(
   eml.path = './eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
-  geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada',
-  geographic.coordinates = c('55.895', '112.094','55.895', '112.094'),
   maintenance.description = 'completed',
   other.entity = c('ancillary_data.zip', 'processing_and_analysis.R'),
   other.entity.description = c('Ancillary data', 'Data processing and analysis script'),
@@ -185,8 +181,6 @@ make_eml(
   eml.path = './eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
-  geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada',
-  geographic.coordinates = c('55.895', '112.094','55.895', '112.094'),
   maintenance.description = 'completed',
   data.table = c('decomp.csv', 'nitrogen.csv'),
   data.table.description = c('Decomposition data', 'Nitrogen data'),
diff --git a/tests/testthat/test_make_eml.R b/tests/testthat/test_make_eml.R
index 3ff205ba..71a756e2 100644
--- a/tests/testthat/test_make_eml.R
+++ b/tests/testthat/test_make_eml.R
@@ -384,7 +384,7 @@ testthat::test_that('Error out when required arguments are missing', {
   expect_warning(
     suppressMessages(
       make_eml(
-        path = '/Users/csmith/Documents/EDI/r/EMLassemblyline/inst/examples/templates_new_geocoverage',
+        path = system.file('/examples/templates_new_geocoverage', package = 'EMLassemblyline'),
         dataset.title = dataset.title,
         temporal.coverage = temporal.coverage,
         maintenance.description = maintenance.description,
@@ -420,7 +420,7 @@ testthat::test_that('Error out when required arguments are missing', {
   expect_warning(
     suppressMessages(
       make_eml(
-        path = '/Users/csmith/Documents/EDI/r/EMLassemblyline/inst/examples/templates_new_geocoverage',
+        path = system.file('/examples/templates_new_geocoverage', package = 'EMLassemblyline'),
         data.path = data.path,
         eml.path = eml.path,
         dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions: 2014-2015',
@@ -528,7 +528,7 @@ testthat::test_that('Error out when required arguments are missing', {
   expect_warning(
     suppressMessages(
       make_eml(
-        path = '/Users/csmith/Documents/EDI/r/EMLassemblyline/inst/examples/templates_new_geocoverage',
+        path = system.file('/examples/templates_new_geocoverage', package = 'EMLassemblyline'),
         data.path = data.path,
         eml.path = eml.path,
         dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions: 2014-2015',
@@ -866,7 +866,7 @@ testthat::test_that('Expect equal', {
   expect_warning(
     suppressMessages(
       make_eml(
-        path = '/Users/csmith/Documents/EDI/r/EMLassemblyline/inst/examples/templates_bb',
+        path = system.file('/examples/templates_bb', package = 'EMLassemblyline'),
         data.path = data.path,
         eml.path = eml.path,
         dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions: 2014-2015',
@@ -933,7 +933,7 @@ testthat::test_that('Expect equal', {
   
   expect_message(
     make_eml(
-      path = '/Users/csmith/Documents/EDI/r/EMLassemblyline/inst/examples/templates_new_geocoverage',
+      path = system.file('/examples/templates_new_geocoverage', package = 'EMLassemblyline'),
       data.path = data.path,
       eml.path = eml.path,
       dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions: 2014-2015',
@@ -952,7 +952,7 @@ testthat::test_that('Expect equal', {
   # other.entity
   
   output <- make_eml(
-    path = '/Users/csmith/Documents/EDI/r/EMLassemblyline/inst/examples/templates_new_geocoverage',
+    path = system.file('/examples/templates_new_geocoverage', package = 'EMLassemblyline'),
     data.path = data.path,
     eml.path = eml.path,
     dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions: 2014-2015',
@@ -983,7 +983,7 @@ testthat::test_that('Expect equal', {
   # Using data.url
   
   output <- make_eml(
-    path = '/Users/csmith/Documents/EDI/r/EMLassemblyline/inst/examples/templates_new_geocoverage',
+    path = system.file('/examples/templates_new_geocoverage', package = 'EMLassemblyline'),
     data.path = data.path,
     eml.path = eml.path,
     dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions: 2014-2015',
@@ -1552,7 +1552,7 @@ testthat::test_that('Test usage with x (all templates, 2 data tables, and 1 othe
   
   expect_warning(
     make_eml(
-      path = '/Users/csmith/Documents/EDI/r/EMLassemblyline/inst/examples/templates_new_geocoverage',
+      path = system.file('/examples/templates_new_geocoverage', package = 'EMLassemblyline'),
       data.path = data.path,
       eml.path = eml.path,
       dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions: 2014-2015',
diff --git a/vignettes/create_eml.Rmd b/vignettes/create_eml.Rmd
index d93ae03d..3d1ad964 100644
--- a/vignettes/create_eml.Rmd
+++ b/vignettes/create_eml.Rmd
@@ -109,6 +109,7 @@ The most common data package only contains tables. To make EML for this package
 *  **eml.path** Path to where the EML file will be written
 *  **dataset.title** Title of the data package
 *  **temporal.coverage** Beginning and ending dates of the data using the format YYYY-MM-DD
+*  **geographic.description** (required if not using the _geographic_coverage.txt_ template) Description of the data packages geographic area.
 *  **geographic.coordinates** (required if not using the _geographic_coverage.txt_ template) A vector of decimal degree coordinates in the order: north, east, south, west, where latitudes south of the equator and longitudes west of the prime meridian are negative.
 *  **maintenance.description** Indicator of whether data collection is ‘ongoing’ or ‘completed’
 *  **data.table** Data table file names.
@@ -129,8 +130,6 @@ make_eml(
   eml.path = './pkg_301/eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
-  geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada',
-  geographic.coordinates = c('55.895', '112.094','55.895', '112.094'),
   maintenance.description = 'completed',
   data.table = c('decomp.csv', 'nitrogen.csv'),
   data.table.description = c('Decomposition data', 'Nitrogen data'),
@@ -167,6 +166,7 @@ Some data packages only contain non-tabular data (e.g. geospatial vector, NetCDF
 *  **eml.path** Path to where the EML file will be written
 *  **dataset.title** Title of the data package
 *  **temporal.coverage** Beginning and ending dates of the data using the format YYYY-MM-DD
+*  **geographic.description** (required if not using the _geographic_coverage.txt_ template) Description of the data packages geographic area.
 *  **geographic.coordinates** (required if not using the _geographic_coverage.txt_ template) A vector of decimal degree coordinates in the order: north, east, south, west, where latitudes south of the equator and longitudes west of the prime meridian are negative.
 *  **maintenance.description** Indicator of whether data collection is ‘ongoing’ or ‘completed’
 *  **other.entity** File names of non-tabular data and/or other digital objects
@@ -186,8 +186,6 @@ make_eml(
   eml.path = './pkg_301/eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
-  geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada',
-  geographic.coordinates = c('55.895', '112.094','55.895', '112.094'),
   maintenance.description = 'completed',
   other.entity = c('ancillary_data.zip', 'processing_and_analysis.R'),
   other.entity.description = c('Ancillary data', 'Data processing and analysis script'),
@@ -223,6 +221,7 @@ A third type of data package contains both data tables and other entities. To ma
 *  **eml.path** Path to where the EML file will be written
 *  **dataset.title** Title of the data package
 *  **temporal.coverage** Beginning and ending dates of the data using the format YYYY-MM-DD
+*  **geographic.description** (required if not using the _geographic_coverage.txt_ template) Description of the data packages geographic area.
 *  **geographic.coordinates** (required if not using the _geographic_coverage.txt_ template) A vector of decimal degree coordinates in the order: north, east, south, west, where latitudes south of the equator and longitudes west of the prime meridian are negative.
 *  **maintenance.description** Indicator of whether data collection is ‘ongoing’ or ‘completed’
 *  **data.table** Data table file names.
@@ -245,8 +244,6 @@ make_eml(
   eml.path = './pkg_301/eml',
   dataset.title = 'Sphagnum and Vascular Plant Decomposition under Increasing Nitrogen Additions',
   temporal.coverage = c('2014-05-01', '2015-10-31'),
-  geographic.description = 'Alberta, Canada, 100 km south of Fort McMurray, Canada',
-  geographic.coordinates = c('55.895', '112.094','55.895', '112.094'),
   maintenance.description = 'completed',
   data.table = c('decomp.csv', 'nitrogen.csv'),
   data.table.description = c('Decomposition data', 'Nitrogen data'),