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After I generate the index file (and convert it to index.new with the provided script), the lines representing the migration path are "fixed". What I mean is that they are present from time 0 to the end of the considered time period.
additionally, the "lines layer" is not present in the toggle layer visibility menu.
Thank you for any help you could provide me
@terrycojones
index.zip

I ran Spread3 with log file from BSSVS analysis. I have 183 collumns of rates and 183 collumns of indicators, yet nothing happened, the option "setup location attributes coordinates" did not show.
When I use 100 collumns of rates and 100 collumns of indicators, the option "setup location attributes coordinates" appeared.
Is that means there are too much nodes？

Thanks a lot!

If there is no _%HPD_modality attribute on the tree, then the SpreaD3 gui raises an error:

setSelectedIndex: 0 out of bounds

STDOUT shows the real error:

locationsgeo_%HPD_modality attribute could not be found on the internal node. Resulting visualisation may be incomplete!

... and yes, the visualisation is incomplete (no HPD ranges).

The Spherical Diffusion phylogeography package for BEAST2 doesn't seem to log this attribute, and the HPD info is in locationsgeo{1,2}_95%_HPD={..}.

Perhaps the GUI should display a more helpful error message (like the one in STDOUT).

Does the BEAST2 package need to log the modality for SpreaD3 to work?

When for example 10.000 trees are being loaded, the JSlider only allows for an approximate number of burn-in to be set. Suggest to add a textfield to specify the exact number to be used.

Upon 'render-to-d3' Spread should create a tiny HTTP server on localhost and serve the content (.json .html .js bundle) statically, pointing the browser to it.

When loading a log file for the summarising a BSSVS analysis, the wind says 'Loading tree file...'

The tooltips could carry more information, i.e. we could use them to display attribute values used for mapping aesthetics (color, area, width, etc).

Please update the release and tag.

see https://rega.kuleuven.be/cev/ecv/software/SpreaD3 has newer version

When I click 'render' for render to d3, I get an error saying 'spreaD3_v0.96.jar (No such file or directory)'

A few months ago when I used spreaD3 it did work, so not sure what the issue is now. It does seem that the program now isn't 'seeing' within some of my files on my MacBook (OS Catalina) , as at the file upload step, it can only see inside the dropbox folder, and not documents on my computer.

Any advice extremely welcome.

The rendered files are stored 3(!) empty folders away from the base directory that is created. Much more user friendly is to move the files to the base dir.

perhaps offer option to pass names if possible - location1, location2 etc is not very informative

We need a box that allows entering value rather than a slider here: the 500 limit is just arbitrary and may not suffice. If you really want a slider here than we should accommodate a percentage as burn-in

https://github.com/phylogeography/SpreaD3/blob/f49e4a09fa70eff5cc32c9623c9bc97167fc3296/src/parsers/DiscreteLocationsParser.java#L44C4-L44C43

I cannot setup location coordinates from an example csv of BEAST_CLASSIC "H5N1locations.dat", in spite of it was intact and valid csv. I have looked at the code and suppose that the problem in the used regular expression "\\s" as it matches a newline and we get 4 columns instead of 3.

Hi all

I'm helping someone use spread3. He just showed me a loaded index.html page with a map in it. There's a menu on the left labelled "Export" and it has a single option, "SVG", in it. But when he clicks on SVG, he's just taken to the map again. View Source shows the same minimal HTML that loads the spread3 main.js JavaScript but there's no sign of SVG anywhere. He gets the same bahaviour in Firefox & Safari.

Does the SVG option actually work?

Terry

Dear Spread3 experts,

I load the log file and it says in the text at the bottom of the window that it has been opened, but no box to specify location attributes appears?

(this box does appear when I upload Tree file for the same runs but i want to compute the bayes factors, so need the log option)

Previousy I did this with the rates.log files- I think this is correct, not just the .log files?
I am using the output of combined log files from Log combiner

extremely grateful for any assistance
thanks
Camilla

Error occurred during a continuous phylogeography spreaD3 analysis. When 'Render to D3' is performed and a name containing an underscore is entered, the following error message appears:

c:\Users\MK\Downloads>java -jar spreaD3_v0.9.6.jar
MRSD is in yyyy/MM/dd format : 2016/7/22
Parsed time line
Parsed the tree
Parsed tree attributes
Parsed map attributes
Created JSON file
Unexpected problem on thread SwingWorker-pool-2-thread-4: C:\Users\MK\Documents\SISMID\continuousPhylogeography\WNT_output4\renderers\d3\d3renderer\index.html (The system cannot find the path specified)
Stack trace:
java.io.FileNotFoundException: C:\Users\MK\Documents\SISMID\continuousPhylogeography\WNT_output4\renderers\d3\d3renderer\index.html (The system cannot find the path specified)
at java.io.FileOutputStream.open0(Native Method)
at java.io.FileOutputStream.open(Unknown Source)
at java.io.FileOutputStream.(Unknown Source)
at java.io.FileOutputStream.(Unknown Source)
at renderers.d3.D3Renderer.render(Unknown Source)
at gui.panels.D3RenderPanel$1.doInBackground(Unknown Source)
at gui.panels.D3RenderPanel$1.doInBackground(Unknown Source)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

Hi,
I used SpreaD3 to reproduce the image of Ebola virus dataset in example 1, the html file was generated but empty, could you please help me to check where the problem is?
(BTW: my operation systerm is Win10, and I have also set the Chrome's permission.)
I packed all the files and uploaded as attachment, please check it at your convenience, I would be very grateful for your time.
Subsection 4.1.zip

Sincere thanks,

Ouyang Peng.

Asking users to open a browser with settings configured to access local files reduces usability. There are several tools for compressing all JS/CSS/HTML into a single HTML file, such as https://github.com/dfsq/compressJS.sh and Webpack: https://webpack.github.io/

When performing a continuous phylogeography rendering using spreaD3, some Windows machines generate the following error upon clicking 'Render to D3' and entering a file name: File Not Found Exception: spreaD3_v0.9.6.jar. This problem only occurs when starting spreaD3 by double-clicking on the jar file. When running from the command line using 'java -jar spreaD3_v0.9.6.jar' on those same machines, the problem does not occur.

MCC tree with continuous traits can possibly be annotated with multiple HPD values. Current auto-magic code will just select the first one it finds. We need an option to choose from. After parsing all of these one can then merge into one JSON file and create joint visualisation, coloring HPD contours by their HPD confidence levels.

On OSX 10.10.5, almost none of the toggle buttons at the left seem to work in Safari (tested on 2 different systems with the same OSX version). I can't reproduce this (my OSX: 10.11.3), so perhaps later Safari versions don't suffer from this issue.

We have formed json file and renderers also index.html files, but when I open the html files, it showed Nothing, I feel nervous for I have plot this example file for two days, but get the empty plot. Thankyou!

for discrete traits: there is a polygon' as well ascircular polygon’ option to play with. I suggest that ‘empty’ stuff is simply not shown -> avoids confusion in the sense that people will think that there perhaps should be something, and they will send lots of spam …

Hello,

I'm using Java v 1.8 and Mac OS 12.3.1. When I attempt to load my tree file, under the "LOAD" button, and there are no files shown. I have attached a screenshot of what this looks like. (In the bottom left corner of the SpreaD3 software it says "Could Not Open!"

Any insight into this issue would be greatly appreciated!

JRE on Macs calls the app the name of the class containing the main method. Simplest solution would be to refactor.

The most recent sampling date selection (in MCC tree with continuous traits) does not update when choosing decimal format until another operation is done in that panel

Upon selecting decimal format for entering most recent sampling date (when loading a continuous analysis; in the Data panel), the text field next to it disappears but reappears after moving the mouse (over it).

when saving, there is a light grey cross on the figure. If possible, it seems best to remove this

Controls are vertically aligned down the side with many controls off the page, so to change a setting: (i) scroll down and visualization disappears; (ii) change setting; and (iii) scroll back up to see change in visualization. It would be better to always align the visualization to the top of the browser window.

point area attribute: when selecting country, the point area disappears.

Data file created using the SPREAD software can not be opened in any firefox, chrome, and internet browser in window 10 system.
The opening file is blank.
Same file is fine when opened in safari (mac browser).

Hi there,

From my analysis, I'm wondering whether the analysis is limited by the borders of the lat/lon spectrum. I've noticed that my results suggest that the routes taken by my pathogen are often the 'long way round' ie. from South Asia to west coast of South America, but instead of crossing the Pacific, it goes west.

This issue might rectify itself when I start using my full dataset, but the results on my test dataset seem to suggest that perhaps the location analysis doesn't accommodate transport anticlockwise ie across the dateline. Could you confirm if I need to adjust any settings to accommodate for this or if this feature isn't yet available?

Thanks!

Amy

Hello,

I'm trying to visualize the virus phylogeography and transmissions among South-East Asia and pacific ocean islands (fiji, french polynesia, etc...). I used /data/geoJSON_maps/world.geojson to plot our MCC tree from BEAST. The problem on the result (attached) is that the pacific ocean region is splitted by the international date line and put at both edge of the map, so that there is a lot of lines jumping from the left to right (right to left) on the map. The problem remains if I use the subregion maps, e.g. /data/geoJSON_maps/region_wb_East_Asia_and_Pacific_subunits.geojson.

I want to make a map centered on the pacific ocean. It seems that I need to modify the javascript code generated by SpreaD3, main.js to change the coordinate of the map-center but I'm not clear which points should be modified. I very appreciate if you could give me some comments on this issue.

Best,

1. Go to Rendering panel
2. Load .json file
3. Nothing seems to be happening, options do not appear
4. Resize window
5. Options now become visible

It would be more consistent with the other analysis, and probably avoid user problems, if the posterior tree distribution needs to be loaded first (with its location attribute selection), and only then the MCC true for the slicing.

Add sufficient information, for different platforms this time, on how to start Google Chrome with a command-line option so that JSON files can be loaded from within Google Chrome.

as per your own suggestion: perhaps include a line opacity attribute. Or a line width attribute :-)

the size/color/opacity of the point names cannot be changed. If not much work...

It is hard to know/see what HPD level is selected with the slider. The log in the bottom left corner can help, but either only shows HPD levels rounded to one decimal or it indicates only such values can be select (despite the fact that you often want something like 0.95). I think that a box to specify the exact value would be more useful...

I was certain I implemented this. Needs testing

command is ant jar

0.9.5 Error log

Buildfile: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/build.xml

compile:
    [mkdir] Created dir: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/classes
    [mkdir] Created dir: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/classes/icons
    [mkdir] Created dir: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/classes/colorpicker/swing/resources
    [mkdir] Created dir: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/classes/renderers/d3/d3renderer
    [javac] Compiling 226 source files to /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 6
    [javac] warning: [options] source value 6 is obsolete and will be removed in a future release
    [javac] warning: [options] target value 1.6 is obsolete and will be removed in a future release
    [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
    [javac] /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/src/gui/MergePanel.java:23: warning: SynchronizedSymbolTable is internal proprietary API and may be removed in a future release
    [javac] import com.sun.org.apache.xerces.internal.util.SynchronizedSymbolTable;
    [javac]                                               ^
    [javac] /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/src/parsers/ContinuousTreeParser.java:12: error: package com.sun.corba.se.impl.javax.rmi.CORBA does not exist
    [javac] import com.sun.corba.se.impl.javax.rmi.CORBA.Util;
    [javac]                                             ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/src/colorpicker/swing/ColorPickerDemo.java uses unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 error
    [javac] 5 warnings

BUILD FAILED
/home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/build.xml:68: Compile failed; see the compiler error output for details.

Total time: 2 seconds

git error log

Buildfile: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/build.xml

compile:
    [mkdir] Created dir: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/classes
    [mkdir] Created dir: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/classes/icons
    [mkdir] Created dir: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/classes/colorpicker/swing/resources
    [mkdir] Created dir: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/classes/renderers/d3/d3renderer
    [javac] Compiling 226 source files to /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 6
    [javac] warning: [options] source value 6 is obsolete and will be removed in a future release
    [javac] warning: [options] target value 1.6 is obsolete and will be removed in a future release
    [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
    [javac] /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/src/gui/MergePanel.java:23: warning: SynchronizedSymbolTable is internal proprietary API and may be removed in a future release
    [javac] import com.sun.org.apache.xerces.internal.util.SynchronizedSymbolTable;
    [javac]                                               ^
    [javac] /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/src/parsers/ContinuousTreeParser.java:12: error: package com.sun.corba.se.impl.javax.rmi.CORBA does not exist
    [javac] import com.sun.corba.se.impl.javax.rmi.CORBA.Util;
    [javac]                                             ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: /home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/src/colorpicker/swing/ColorPickerDemo.java uses unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 1 error
    [javac] 5 warnings

BUILD FAILED
/home/guoyi/Downloads/SpreaD3-0.9.5/SpreaD3/build.xml:68: Compile failed; see the compiler error output for details.

Total time: 2 seconds