-
Notifications
You must be signed in to change notification settings - Fork 24
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* added FAQ page * added a page for how to map species occurrence, but it's not in bookdown yet * fixed some header formatting to make ToC cleaner * fixed internal link
- Loading branch information
1 parent
b7cd917
commit 8a5b622
Showing
8 changed files
with
106 additions
and
8 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,74 @@ | ||
## Frequency Asked Questions | ||
|
||
#### General | ||
|
||
* [I have data and want to publish to OBIS - what do I do?](contribute.html) | ||
* [Why is it important to share and format data?](contribute.html#why-publish-data-to-obis) | ||
* [How do I handle sensitive data?](contribute.html#how-to-handle-sensitive-data) | ||
* [I am having trouble understanding how Core and Extension tables relate to each other](relational_db.html) | ||
* [How does the OBIS format avoid redundancy in data](relational_db.html#how-to-avoid-redundancy) | ||
* [Where can I learn about "Darwin Core"?](darwin_core.html) | ||
* [How are extension tables (e.g. eMOF, occurrence) linked with the core table?](formatting.html#extensions-in-obis) | ||
* [What is the difference between Occurence Core and Event Core?](formatting.html#dataset-structure) | ||
* [What are the responsibilities of node managers?](nodes.html) | ||
|
||
#### Formatting Data | ||
|
||
* [Is there a checklist of all required Darwin Core fields for OBIS?](checklist.html) | ||
* [How does data flow in OBIS?](data_standards.html) | ||
* [What should I do if I do not have the data for required fields by OBIS?](common_formatissues.html#missing-required-fields) | ||
* [How do I construct an eventID?](identifiers.html#eventid) | ||
* [How do I construct occurrenceID?](identifiers.html#occurrenceid) | ||
* [What data goes into Occurrence core (or extension) and how do I set up this file?](format_occurrence.html) | ||
* [How do I set up an Event core table?](format_event.html) | ||
* [What data goes into extendedMeasurementOrFact and how do I set it up?](format_emof.html) | ||
* [How do I map Measurement or Fact terms in OBIS with preferred BODC vocabulary?](vocabulary.html#measurementorfact-vocabularies) | ||
* [I can't find a suitable vocabulary, how do I request a new vocabulary term?](vocabulary.html#requesting-new-vocabulary-terms) | ||
* [How should I match raw data fields with Darwin Core terminology?](vocabulary.html#map-your-data-with-dwc-vocabulary) | ||
* [How do I format dates?](common_formatissues.html#temporal-dates-and-times) | ||
* [How do I handle historical data?](common_formatissues.html#historical-data) | ||
* [How do I convert coordinates to decimal degrees?](common_formatissues.html#converting-coordinates) | ||
* [How do I convert different geographical formats to WGS84?](common_formatissues.html#geographical-format-conversion) | ||
* [How do I compile acoustic, imaging, or other multimedia data for OBIS?](other_data_types.html#multimedia-data-acoustic-imaging) | ||
* [How do I compile habitat data for OBIS?](other_data_types.html#habitat-data) | ||
* [How do I compile tracking data for OBIS?](other_data_types.html#tracking-data) | ||
* [How do I compile DNA and genetic data for OBIS?](dna_data.html) | ||
|
||
#### Tools | ||
|
||
* [How do I use the WoRMS taxon match tool?](name_matching.html) | ||
* [Can I fetch a full classification for a list of species from WoRMS?](name_matching.html#how-to-fetch-a-full-classification-for-a-list-of-species-from-worms) | ||
* [What do I do if my scientificName does not return a match from WoRMS?](name_matching.html#what-to-do-with-non-matching-names) | ||
|
||
#### Quality Control | ||
|
||
* [How do I do data quality control?](data_qc.html#how-to-conduct-quality-control) | ||
* [What are the OBIS quality control flags?]() | ||
* [Why are certain records dropped in OBIS?](data_qc.html#why-are-records-dropped) | ||
* What do I do when I am uncertain about the: | ||
* [Temporal range of a dataset OR eventDate](common_qc.html#uncertain-temporal-range) | ||
* [Geospatial location](common_qc.html#uncertain-geolocation) | ||
* [Taxonomic identification](common_qc.html#uncertain-taxonomic-information) | ||
* [Individual count](common_qc.html#individualcount) | ||
* [What do I do with freshwater species that are part of my marine dataset?](common_qc.html#non-marine-species) | ||
|
||
#### Publishing | ||
|
||
* [How do I add my data to the OBIS database?](data_publication.html) | ||
* [What metadata do I have to provide? Where? How?](eml.html#metadata-sections) | ||
* [How do you know which license to choose?](data_publication.html#licenses) | ||
* [How do I access the IPT?](ipt.html#how-to-access-the-ipt) | ||
* [How do I use the IPT?](ipt.html#create-your-resource-on-the-ipt) | ||
* [Are there instructions for IPT administrators?](ipt_admin.html) | ||
* [How do I add DOI to my dataset?](data_sharing.html#adding-a-doi-to-datasets) | ||
* [How do I publish to both GBIF and OBIS?](data_sharing.html#simultaneous-publishing-to-gbif) | ||
* [How do I update my already published dataset?](data_sharing.html#update-your-data-in-obis) | ||
|
||
#### Accessing data | ||
|
||
* [How do I download data from OBIS?](access.html#obis-homepage-and-dataset-pages) | ||
* [How can I use R to access OBIS data?](access.html#r-package) | ||
* [How do I use the OBIS API to fetch and filter data?](access.html#api) | ||
* [How do I contact the data provider?](access.html#api) | ||
* [How can I cite OBIS datasets and downloads?](citing.html) | ||
* [What are the definitions of the field names in the downloads generated by OBIS?](access.html#interpreting-downloaded-files-from-obis) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,23 @@ | ||
## Making maps of species in OBIS | ||
|
||
### Mapping with the robis R package | ||
|
||
If you’d like to visualize occurrence data using R, you can do this using the `robis` package. | ||
|
||
After loading the installed package, let’s first fetch some occurrence data using the `occurrence` function. We will look at data for seahorses in the Genus Hippocampus. | ||
|
||
```R | ||
library(robis) | ||
hippoc <- occurrence("Hippocampus") | ||
``` | ||
|
||
We have two options for mapping: | ||
|
||
```R | ||
map_ggplot(hippoc) | ||
map_leaflet(hippoc) | ||
``` | ||
|
||
`map_ggplot` will produce a static map: | ||
|
||
Whereas `map_leaflet` will produce an interactive leaflet map. For documentation on how to add to or change these maps (e.g.,change base map, add polygons or points, etc.), see the [Leaflet for R](https://rstudio.github.io/leaflet/). |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters