Playing with Shiny

Last year I made a shiny app that will allow me to quickly assess what type of specimen is needed for the collections given the species. Over the past few months, I’ve come up with ways to make it more informative and interactive and you can now find the link here. This is still very much a work in progress as I add more features to make our collections data more easily accessible and understandable.

Example of application when you enter/select “Tyto alba” in the Species field.

Species summary tab

Provides an overview on how specimens are available by specimen type/nature based on species. Once you start typing in the blank field it should list options that you can select from. If you cannot find a species, it is likely that there are no specimens of that kind or you are searching with an updated scientific name that is different from the database.

1. Specimen count by specimen type Lists all the different specimen types for the input species. Description is written out in depth based on the specimen nature codes and their descriptions in EMu.

2. Specimen count by year The count of specimens for each year based only on study skins and skeletons; rest are ignored for visualization purposes.

3. Specimen count by month The count of specimens by the month they were collected.

4. Specimen count by state A map showing the number of specimens collected in each state. Given the nature of the locality data, the map is only limited to the United States. Higher values are in yellow while lower values are in dark purple. States where we have no specimens are grayed out. Note, this map is generated with only georeferenced data.

5. Specimen count by county A map showing the number of specimens collected in each county of California. Given the nature of the locality data, the map is only limited to California. Higher values are in yellow while lower values are in dark purple. Counties where we have no specimens are grayed out. Note, this map is generated with only georeferenced data.

6. Global specimen distribution An interactive map (Feaflet) showing the global distribution of specimen localities. Adjust the zoom using the +/- sign on the top left corner of the map. Note, this map is generated with only georeferenced data.

7. Weights by sex Simple box plots of each specimen’s weight based on sex (male, female, unknown). Raw data points are scattered over the box plots.

8. Detailed counts by year Last is a long table including the counts of specimens by year and counts by year and type.

Example of application when you enter the catalog number “12345” in the LACM field.

LACM lookup

For looking up specimens based on LACM number. It will provide information on species, collection date, collector, and locality. There are a few instances where you will enter a number but have no results; this is likely that there is missing information on the specimen. This is a feature that will be fixed in the next update.