ncrn / birdviz

Code for NCRN bird visualizer

BirdViz

Code for NCRN bird visualizer

birdviz's Issues

Consistent BCI color ramp

Make the colors the same for the map and the graph

Replace detection plot

Replace plot in visualizer with detectsPlot() from NCRNbirds

Replace plot of BCI

Replace the plot of BCI with BCIplot() from NCRNbirds

Ebirds API

Update to new version of Ebirds API.

Update the "About the Maps" text

This text is no longer up to date, it should be fixed.

Export data from tables

Re-examine the situation with DT and data export.

Reverse BCI legend

Reverse order of items in BCI legend to match the graph.

adjust date slider to highlight one year

Adjust slider highlighter so that only highlights one year at a time.

Add Max to data table

For the Data Tables add a Maximum Observed line or option where possible

Birds of Conservation Concern Filter

Consider creating a filter that would highlight any bird considered a species of conservation concern by Partners in Flight. This would include the 2 categories: "watchlist species" and "stewardship species"

Other filters to consider creating would be native vs. non-native.
Migratory vs. resident
or any of the bird guild designations that come from the Bird Community Index score (ground nester, insectivore, etc.)

Names are not preserved across species

When you change from the Latin Name to AOU of Common name the species is not preserved. Fix this.

Change color pallettes

Change the colors to one of the viridis palettes for accessibility and consistency.

Add network switches to global.r

Add switches to change networks in global.r

We need

• NCRN

• NETN

• ERMN

• MIDN

• GULN

Handling NAs in ggvis graphs

Missing values, either y or x values caused by no survey or species not observed in a survey, are causing problems with ggvis plotting correctly. Missing y-values cause ggvis to plot NA above max value and missing x-values (usually year) removes the year from the axis.

Transition to ggplot may solve these issues.

Match color ramp for BCI on map with that of the graph

map and graph use different color ramps - fix.

add SE to detectsPlot?

If desired, provide radio button or force detectsPlot to show SE

Add save map button

Make sue of htmlwidgets.

Maximum Observed in individual species Graphs

For individual species graphs, add an option to just see max observed rather than each visit.

Make a BCI table that breaks things down by guild

This will require an update to NCRNbirds.

Improve NPSpecies about

Make clear the limitations of this data.

Remove hard coding of years

Should just figure that out from the data

Fix axis labels on graphs

On graphs the years and number of plots now run together due to there being a lot of years. Fix this by putting number of plots underneath.

Put more items per page on datatable

Have a bigger number of items per page so that it will show all entries on the species list and on the other tables in a single screen.

Inconsistent bird lists on map

When you chose "Number of Species" on the map, the point color and the hover text respect your choice in the "Distance from Observer" drop down. However the species list generated when you click a point does not. The band parameter is not being passed by getChecklist to getBirds.

Tables: Error in BCI: length of 'dimnames' [2] not equal to array extent

When viewing MIDN data in the Tables tab the BCI by park section gives following error:

Error: length of 'dimnames' [2] not equal to array extent

add network's project metadata (html files)

Remove Latin Names

For the visualizer it is probably best to remove Latin Names as an option, but print them next to the common name when there is space.

Add Save Plot buttons

Add this for all plots

get bands from getDesign

Now that getDesign() exists bands should come from there rather than be hard coded.

fix the linkage between table and maps

The idea is that when you click a row on the table, the data can been seen on the map. Once all the controls have been altered, this will need to be reconnected to transfer all the filtering selections from the table tab to the map tab.

Change upper table for parks on tables tab

When you do a table for a single park it would be nice to have the upper table be just that park with each column a different year. Need to check that the table does not get too wide.

Map Legend Disappears

The map legend will disappear when you select "Any Distance Band" from the dropdown in the map controls.

BCI - toggle between visits

Let users see BCI graph based on all visits or just some visits

Update control order

On the map side bar - change control order to:

Species
Common Names
Year
Distance
Visit

Turn some controls into modules

Currently the map, table, plots and to some extent species lists all share some similar controls. It might be better if these were turned into "shiny modules" so the code only needs to be maintained in one place.

Possible controls are

• Parks
• Species
• Bands
• Visits
• Years

Add sampling cycles

Once NCNR/NCRNbirds#111 is done and there is cycle data available, then the year drop-down should be determined by the cycles, which in the case of ERMN is every 2 years rather than every year.

X-axis labels in graphs (## points) needs to be flexible to years sampled per park

When you graph data, parks that don't have data for a species in each year (2006:2017) causes the app to crash in the indiv species graph (DetectsPlotData) .

In the species richness graphs, when there were no obs in a park, RichnessPlotData and then ggviss plots a 0 value instead of NA on the graph

in plots code, server.R:

labels=paste(paste(c(2006:2017), paste0("(",sapply(X=2006:2017,Y=PlotParkUse(),FUN=function(X,Y){nrow(getPoints(Y,years=X))}),")"))))

JP suggests to pull the actual years from getVisits()

update map controls to handle multiple networks

when you open viz, map should zoom to bounds of selected network.

Data tables and graphs should toggle forest or grassland

Once NCRN/NCRNbirds#74 is done, tables and graphs and maybe maps should be able to toggle to forest only, grassland only or all.

Distance bands in Map

Distance from Observer. I see how this is dynamic now pulling from bands.csv but didn’t it used to have “any distance” as an option in the past? “Any distance” or “unlimited radius” seems more appropriate than the somewhat arbitrary 200 MaxDistance in the csv.

Upper table does not work for ERMN

Upper table has “Error: length of ‘dimnames’ [2] not equal to array extent”. Fix.

Species number tables should also point out birds of conservation concern

Once we can filter the birds by this - we should add it to the tables.

Make the zoom conform to each networks bands

On the map the zoom options should match each network's bands.

add max detections in the table

remove validate(need())

There are still some internal reactive dependencies being checked via the old validate (need() ) interface. This should be updated to req().

Replace richness plot

Replace the plot of species richness with richnessPlot() from NCRNbids

detects plot does not respect visits for ERMN

ERMN: detectsPlot is plotting visits 1 and 2 as the same and 3 and 4 as the same, probably because they are surveyed on the same day.

Check all plots.

Do we want to add in grassland data?

• add filters to query by grassland
• update index calculations
• etc

Default to species richness as first choice

The maps, and tables and graphs should have species richness as the default choice, as that always has data, whereas the species richness will always have good data and be the more general choice. Change the controls to make richness be the default choice.

get Visits from getDesign()

Now that getDesign() exists, the Visits should come from there rather than being hard-coded.