Rearrange chapters to have all modules in one chapter.

Also, fix the links to the overall schema interactive docs, and
suppress warnings on the builds. Images and schemas are now fully
complete.

docs/_bookdown.yml

@@ -7,11 +7,11 @@ rmd_files: ["index.Rmd",
     "eml-features.md",
     "eml-contributors.md",
     "eml-220info.md",
+    "eml-schema.md",
     "eml-modules-resources.md",
     "eml-modules-data-structure.md",
     "eml-modules-discovery-interpret.md",
     "eml-modules-utility.md",
-    "eml-schema.md",
     "eml-validation-refs.md",
     "eml-semantic-annotation-primer.md",
     "eml-internationalization.md",

docs/build_book.R

@@ -4,8 +4,8 @@
 # of the repo as the index page for the entire book, rather than duplicating
 # the content or writing new content.
 
-bookdown::render_book("index.Rmd", "bookdown::gitbook")
+suppressWarnings(bookdown::render_book("index.Rmd", "bookdown::gitbook"))
 
 # Copy the HTML Bookdown produces from the ../README.md file to index.html
 file.copy("../dist/eml-ecological-metadata-language.html", "../dist/index.html", overwrite = TRUE)
-file.copy(dir("../img", full.names = TRUE), "../dist/images", recursive = TRUE)
+file.copy(dir("../img", full.names = TRUE), "../dist/images", recursive = TRUE)

docs/eml-modules-data-structure.md

@@ -1,4 +1,4 @@
-# Data Structure Modules
+## Data Structure Modules
 
 The following three modules are used to document the logical layout of a
 dataset. Many datasets are comprised of multiple entities (e.g. a series
@@ -16,7 +16,7 @@ eml-entity module is extended for each of these types (dataTable,
 spatialRaster, spatialVector, etc\...) which are described in the next
 section.
 
-## The eml-entity module - Entity level information within datasets
+### The eml-entity module - Entity level information within datasets
 
 Links:
 
@@ -46,7 +46,7 @@ The eml-entity module, like other modules, may be "referenced" via the
 and then used as a reference in other locations within the EML document
 via its ID.
 
-## The eml-attribute module - Attribute level information within dataset entities
+### The eml-attribute module - Attribute level information within dataset entities
 
 Links:
 
@@ -66,7 +66,7 @@ the \<references\> tag. This allows an attribute document to be
 described once, and then used as a reference in other locations within
 the EML document via its ID.
 
-### Philosophy of Attribute Units
+#### Philosophy of Attribute Units
 
 The concept of \"unit\" represents one of the most fundamental
 categories of metadata. The classic example of data entropy is the case
@@ -149,7 +149,7 @@ explicitly label attributes that contain Gregorian date and time values,
 and allows them to provide the information needed to parse these values
 into their appropriate components (e.g., days, months, years)./
 
-## The eml-constraint module - Relationships among and within dataset entities
+### The eml-constraint module - Relationships among and within dataset entities
 
 Links:
 
@@ -162,7 +162,7 @@ management system. These constraints include primary key constraints,
 foreign key constraints, unique key constraints, check constraints, and
 not null constraints, among potential others.
 
-## The eml-dataTable module - Logical information about data table entities
+### The eml-dataTable module - Logical information about data table entities
 
 Links:
 
@@ -183,7 +183,7 @@ physical distribution of the data table, its overall coverage, the
 methodology used in creating the data, and other logical structure
 information such as its orientation, case sensitivity, etc.
 
-## The eml-spatialRaster module - Logical information about regularly gridded geospatial image data
+### The eml-spatialRaster module - Logical information about regularly gridded geospatial image data
 
 Links:
 
@@ -198,7 +198,7 @@ organization of the raster cells, the cell data values, and if derived
 via imaging sensors, characteristics about the image and its individual
 bands.
 
-## The eml-spatialVector module - Logical information about non-gridded geospatial image data
+### The eml-spatialVector module - Logical information about non-gridded geospatial image data
 
 Links:
 
@@ -212,7 +212,7 @@ relationships among them. Specific attributes of a spatial vector can be
 documented here including the vector\'s geometry type, count and
 topology level.
 
-## Schema for validating spatial referencing descriptions
+### Schema for validating spatial referencing descriptions
 
 This module defines both projected and unprojected coordinate systems
 for referencing the spatial coordinates of a dataset to the earth. The
@@ -222,7 +222,7 @@ coordinate systems that may be referred to by name in the
 horizCoordSysName element. A custom projection may be defined using this
 schema for any projection that does not appear in this dictionary.
 
-## The eml-storedProcedure module - Data tables resulting from procedures stored in a database
+### The eml-storedProcedure module - Data tables resulting from procedures stored in a database
 
 Links:
 
@@ -236,7 +236,7 @@ then invoke them directly from front-end applications. It allows the
 optional description of any parameters that are expected to be passed to
 the procedure when it is called.
 
-## The eml-view module - Data tables resulting from a database query
+### The eml-view module - Data tables resulting from a database query
 
 Links:
 

docs/eml-modules-discovery-interpret.md

@@ -1,4 +1,4 @@
-# Discovery and Interpretation Modules
+## Discovery and Interpretation Modules
 
 The following six modules are used to qualify the resources being
 described in more detail. They are used to describe access control
@@ -11,7 +11,7 @@ in many locations in order to limit the scope of the description. For
 instance, the eml-coverage module may be used for a particular column of
 a dataset, rather than the entire dataset as a whole.
 
-## The eml-access module - Access control rules for resources
+### The eml-access module - Access control rules for resources
 
 Links:
 
@@ -160,7 +160,7 @@ rules can be overridden for particular data entities by adding
 additional \<access\> elements in the physical/distribution trees of
 those entities.
 
-## The eml-physical module - Physical file format
+### The eml-physical module - Physical file format
 
 Links:
 
@@ -188,7 +188,7 @@ the \<references\> tag. This allows a physical document to be described
 once, and then used as a reference in other locations within the EML
 document via its ID.
 
-## The eml-party module - People and organization information
+### The eml-party module - People and organization information
 
 Links:
 
@@ -207,7 +207,7 @@ The eml-party module, like other modules, may be \"referenced\" via the
 used as a reference in other locations within the EML document via its
 ID.
 
-## The eml-coverage module - Geographic, temporal, and taxonomic extents of resources
+### The eml-coverage module - Geographic, temporal, and taxonomic extents of resources
 
 Links:
 
@@ -261,7 +261,7 @@ the \<references\> tag. This allows the coverage extent to be described
 once, and then used as a reference in other locations within the EML
 document via its ID.
 
-## The eml-project module - Research context information for resources
+### The eml-project module - Research context information for resources
 
 Links:
 
@@ -281,7 +281,7 @@ the \<references\> tag. This allows a research project to be described
 once, and then used as a reference in other locations within the EML
 document via its ID.
 
-## The eml-methods module - Methodological information for resources
+### The eml-methods module - Methodological information for resources
 
 Links:
 

docs/eml-modules-resources.md

@@ -1,6 +1,6 @@
-# The EML Module and Resources
+## The EML Module and Resources
 
-## The eml module - A metadata container
+### The eml module - A metadata container
 
 Links:
 
@@ -32,7 +32,7 @@ reserved for the inclusion of metadata that may be highly discipline
 specific and not covered in this version of EML, or it may be used to
 internally extend fields within the EML standard.
 
-## The eml-resource module - Base information for all resources
+### The eml-resource module - Base information for all resources
 
 Links:
 
@@ -62,7 +62,7 @@ document in a library of protocols. Likewise, citations are used
 throughout the top-level resource modules by importing the literature
 module.
 
-## The eml-dataset module - Dataset specific information
+### The eml-dataset module - Dataset specific information
 
 Links:
 
@@ -89,7 +89,7 @@ the \<references\> tag. This allows a dataset to be described once, and
 then used as a reference in other locations within the EML document via
 its ID.
 
-## The eml-literature module - Citation-specific information
+### The eml-literature module - Citation-specific information
 
 Links:
 
@@ -105,7 +105,7 @@ Similar to other eml modules, each of the CitationType elements may be reference
 As of EML 2.2.0, each CitationType element can use the \<bibtex\> element as an alternative to encoding citations in the EML XML structures. BibTeX entries generally play well inside of XML structures, but XML escaping is still needed for special characters so consider embedding BibTeX entries in CDATA blocks if XML escaping is cumbersome.
 
 
-### eml-literature module - literature cited
+#### eml-literature module - literature cited
 
 Citations to articles or other resources that are referenced in the data set or its associated metadata should be included in a \<literatureCited\> element. \<literatureCited\> is a CitationListType cataloging one or more citations that represent a bibliography of works related to the data set for reference, comparison, or other purposes. These citations can be a series of \<citation\> elements, a \<bibtex\> element featuring one or more BibTeX-style citations, or a mix of the two types. 
 
@@ -180,7 +180,7 @@ Citations to articles or other resources that are referenced in the data set or
 </dataset>
 ```
 
-### eml-literature module - usage citation
+#### eml-literature module - usage citation
 
 A citation to an article or other resource in which the data set is used or referenced should be included in a \<usageCitation\> element, a CitationType detailing a literature resource that has used or references this data set. It is not expected that one or more usage citations will necessarily be an exhaustive list of resources that employ the data set, but rather will serve as a example(s) and pointer(s) to scholarly works in which this data set has been used. The \<usageCitation\> element can be a \<citation\> or \<bibtex\> element.
 
@@ -227,7 +227,7 @@ A citation to an article or other resource in which the data set is used or refe
 </dataset>
 ```
 
-### eml-literature module - reference publication 
+#### eml-literature module - reference publication 
 
 A citation to an article or other resource that serves as an important reference for a data set should be documented in a \<referencePublication\> element. Anyone using the data set should generally cite the data set itself (using the creator, pubDate, title, publisher, and packageId fields), and consider providing an additional citation to the reference publication. The \<referencePublication\> element will typically be used when the data set and a companion or associated paper are published near concurrently. Common cases where a reference publication may be useful include when a data paper is published that describes the dataset, or when a paper is intended to be the canonical or exemplar reference to the dataset – these are features that distinguish the \<referencePublication\> CitationType from the \<usageCitation\> CitationType.
 
@@ -257,7 +257,7 @@ A citation to an article or other resource that serves as an important reference
 ```
 
 
-## The eml-software module - Software specific information
+### The eml-software module - Software specific information
 
 Links:
 
@@ -276,7 +276,7 @@ the \<references\> tag. This allows a software resource to be described
 once, and then used as a reference in other locations within the EML
 document via its ID.
 
-## The eml-protocol module - Research protocol specific information
+### The eml-protocol module - Research protocol specific information
 
 Links:
 

docs/eml-modules-utility.md

@@ -1,12 +1,12 @@
-# Utility Modules
+## Utility Modules
 
 The following modules are used to highlight the information being
 documented in each of the above modules where prose may be needed to
 convey the critical metadata. The eml-text module provides a number of
 text-based constructs to enhance a document (including sections,
 paragraphs, lists, subscript, superscript, emphasis, etc.)
 
-## The eml-text module - Text field formatting
+### The eml-text module - Text field formatting
 
 Links:
 
@@ -29,7 +29,7 @@ text blocks. Combinations of plain text, docbook sections, and markdown
 sections can be interleaved in any order, but most people will likely
 find the markdown syntax the easiest to use.
 
-## The eml-semantics module - Semantic annotations for formalized statements about EML components
+### The eml-semantics module - Semantic annotations for formalized statements about EML components
 
 Links:
 

docs/eml-schema.md

@@ -5,6 +5,4 @@ of a valid EML document.  In this chapter, all of the elements and types
 defined within those EML schemas are displayed using diagrams illustrating 
 the relationships among these components.
 
-```{r echo=FALSE}
-knitr::include_url("./schema/index.html", height="1200px")
-```
+<a href="./schema/index.html" target="_blank">Browse EML Schema Documentation</a>