mapequation / bioregions

Infomap Bioregions: Interactive mapping of biogeographical regions from species distributions

New Project

✨ Bootstrapped with Create Snowpack App (CSA).

Available Scripts

npm start

Runs the app in the development mode. Open http://localhost:8080 to view it in the browser.

The page will reload if you make edits. You will also see any lint errors in the console.

npm run build

Builds a static copy of your site to the build/ folder. Your app is ready to be deployed!

For the best production performance: Add a build bundler plugin like "@snowpack/plugin-webpack" to your snowpack.config.js config file.

npm test

Launches the application test runner. Run with the --watch flag (npm test -- --watch) to run in interactive watch mode.

bioregions's Issues

new File not supported in Safari/IE

"FileConstructor is not a constructor", https://stackoverflow.com/questions/30727052/file-constructor-in-ie-and-safari.

Used to create file from example data downloaded as a blob.

Workaround: Use the blob directly and add name as a dynamic property instead.

Advanced settings in version 2.0

Hello and thanks for such a cool tool.

Is there a source for understanding all the advanced parameters? What does the variable markov time do? I have a lot of noise in my results and I am playing with several parameters, but for some of them I don't know what I am doing. I would like to understand better:

• Variable markov time (and damping)
• state network
• patch sparse cells
• render data while zooming
• Markov time (why are there two places to change it, one with a range and one without a range?

Thanks a lot!

Best,

Cesc

Export settings to be able to reproduce result

Export settings that affect the clustering (min/max cell size/capacity etc)

can't export data neather as shapefile or as table (is not available)

Hi, I'd like to work with the data, but I can't download it. Can you help me? Or does anyone know someone who could send me the data? Cheers Kira

Can't load big shapefile

Dear Mr Edler,

I'm trying to construct a Bioregion Map from species distribution in shapefile format. The file is quite big (1.16 GB) since it contains 348 species with large global distributions. I've been using Firefox, Safari and Chrome but couldn't load the information. Can u help me? Is there anyway I can dwonload the tool and use it offline?

By the way, contratulations for the great tool u have developed

Thanks for your help!
Best regards

Species cells not clipped to land in exported png in Firefox

Highlight cluster in world map when clicked from table

SVG bin strokes shows up in Inkscape

If the code is hot-reloaded, the SVG saved after that will not have that issue!

Cell size in seconds below one degree?

Problem loading big file in Firefox and Chrome, works in Safari

Loading a ~300Mb text file gives "allocation size overflow" in Firefox, and zero sized result on Chrome.

Loading without response if no worker available

Happens when served from subdirectory. Workaround: Put static folder in root directory. Should check that it gets a response from the main worker (with up-to-date version tag), and show warning otherwise.

Don't weight links on abundance

The generated network has for some time included a link per record, which means a link between a species and a grid cell can appear multiple times and become aggregated within Infomap.

Save by data url doesn't work for big svg file

Create a Blob and Use URL.createObjectURL instead

Can not change the defalut setting about the for parameters(Max cell size, Min cell size,Max cell capacity,Min cell capacity) and Can i change the default grid resolution into 0.5 degree?

Infomap for marine data

Hi,

Is there a way for me to use the Infomap Bioregions webapp to do clustering with marine species data? I'm very interested in exploring this method but when I loaded my marine species distribution list, the clusters were set to the nearest land polygons.

Visualization of overlapping clusters.

Hi,

I got an analysis with i.e. 13 clusters, some of which are overlapping. I can't seem to find a way to isolate some of those clusters, to save them as image (svg or png). The shp file puts these clusters outside of the region of analysis, so I am unable to locate them in its place. Any help would be appreciated.

Thanks.

Possibility to tune number of clusters

Custom tesselation of space

A user should be able to upload a custom shape layer defining the smallest subdivision of space instead of the default square grid cells.

Also support by default option to choose voronoi, triangular and hexagonal tesselation.

Semantic-ui styled dropdowns

The element doesn't trigger onChange with className="ui dropdown", but a workaround is to use ordinary divs and listen for onClick on menu items.

Show mini map with highlighted cluster next to each cluster table

Shapefile exportation

Two issues regarding perhaps the same problem:

• I can't open the exported shapefile in a GIS (e.g.: ArcGIS). Error explication of ArcGis: "Number of shapes does not match the number of table records". This problem was not there last year.

• When open shapefile in R software, it opens as a multipolygon with bioregions info not matching with Infomap website output. Last year the exported shapefile used to open in R as specific polygons for each grid cell.

Any suggestion or help ?

Highlight the different steps from loading to parsing and analysing etc

Use semantic-ui top attached steps

Map unresponsive when loading second network

Happens when the map is unmounted and re-mounted, which was introduced since replacing empty map with image, and loading a second species dataset deletes the old.

Uncaught RangeError: Maximum call stack size exceeded

Seems to be an intermittent recursion bug in patching partially filled quadtree nodes.

Constraining the "quadtree" mapping algorithm with a shapefile?

I wonder whether the "adaptive resolution" algorithm could be improved to take into account a shapefile that imposes limits between "cells". For example, a shapefile of elevation belts with the contrain that any cell must be embedded in a single elevation belt. This could help create cells that are more homogeous in terms of environmental conditions, instead of squares or combinations of connected squares that could still include a lot of environmental heterogeneity.

Clustering only works in Firefox

Problem is that the Infomap worker is spawned from within another worker, which is only supported in Firefox. Workaround: Send network to main thread and start Infomap worker from there and send the result back.

Shape file download

I have been unable to download results as a shapefile using Safari.

Shapefile species count incorrect

Hi,

I am having an issue with the web tool where I am uploading one large shapefile of the range polygons of 1033 species, but Infomap Bioregions is only able to show 1029. Do you know what might be causing this issue and what the solution might be?

Many thanks!

Min bin size can be violated in one level if not a power of 2

If e.g. min bin size is 3, it will create bins at size 2.

Option to choose exact minimum resolution

Now the option is limited 2^x but should be generalised to y*2^x, so that we could have for example exactly 10" resolution minimum. Now constrained to:

deg, min, sec
1, 60, 3600
1/2, 30, 1800
1/4, 15, 900
1/8, 7.5, 450
1/16, 3.75, 225
1/32, 1.875, 112.5
1/64, 0.9375, 56.25
1/128, 0.46875, 28.125,
1/256, 0.234375, 14.0625,
1/512 0.1171875, 7.03125

Data UI not visible if not the data tab is open

Let the Dimmer component be rendered outside control panel tabs

Can't upload my species distribution .csv file

Hello,
I have not been successful in uploading species distribution .csv files in the last few days. The same file which I was successful before. Is there a bug going on? I am using chrome. Anyone else went through this?

uploading spatially aggregated file

I have a file of 65,000 species as rows against 2,048 columns; each cell is 0 (not recorded, note this is not true absence) or 1 (present). Each column is a 5 degree latitude- longitude c-square. The original file of species * latitude longitude points was tens of GB in size so we already did the aggregation step to 5-degree cells to reduce file size. Can I upload this to infomap bioregions somehow?

Identify bioregions in exported data

Add name of most common species to more easily identify them

Save SVG only works in Chrome

Safari doesn't even download a file, type/encoding doesn't work in Firefox

Issue loading range maps

Hi,

I'm trying to load several range maps (one shapefile for each species) to Infomap, however I'm only able to load one shapefile at time. When try to load more than one shapefile the program only include the first one. How I can procced to have loaded several range maps for run the program?

Thank you,

Export clusters as single MultiPolygon features

Now it creates a polygon for each grid cell

Cancel file loading doesn't cancel the process, just hides it

When the fetching is done, the file loading re-appears with the next step. The cancel event must stop the file request promise so that it doesn't trigger next steps when resolved.

Map/data coordinate mismatch when resizing window

Old bug

Error: dn.format is not a function

I can't export tables or shp files, I get this error. Analysis is done ok, however. Any help would be appreciated.

Firefox crashes when reading files > 70Mb

Bug in Firefox's FileReaderSync that is used to load the file from within the main worker, as FileReader is not supported in workers in Firefox.

Workaround:
Check filesize, and if big enough, read it from main thread asynchronously with FileReader and send result to main worker? Or hint about using another browser?