GIS team blog
Welcome to Kew's GIS team blog. Here you will find information about the Geographic Information Science (GIS) Unit and its staff. We'll be posting updates on new developments in the field and our projects, also our thoughts and musings!
Here in the Geographic Information Science (GIS) unit we handle the majority of the mapping needs for staff in the Herbarium and other departments at Kew. One of the most common requests from botanists is for a simple distribution map as part of the publication of a new species or a revision of a group. The maps are usually simple dot distribution maps showing where the species has been found.
Take a look at this example from a recent edition of Kew Bulletin (Timothy M. A. Utteridge. Four new species of Maesa Forssk. (Primulaceae) from Malesia. Kew Bulletin. September 2012, Volume 67, Issue 3, pp 367-378.)
Distribution of Maesa fraseriana [▲] and M. malayana [●] (Map reproduced with kind permission from Kew Bulletin and the Board of Trustees of the Royal Botanic Gardens, Kew)
Often all that is needed is a simple map with country boundaries, points (or other symbols) to illustrate the location of specimens or observations of the species, and a few mandatory cartographic elements such as a north arrow and a scale bar.
Until recently, the botanists at Kew would have to rely on the GIS unit to complete this task. A few brave souls have had a crack at doing their own maps, but the feedback we often get is that GIS software is overly complex and comes with a steep learning curve. It simply takes too long to produce the maps - “we just want a simple dot map!”. Well, the botanists' prayers may just have been answered with the development of a new web mapping tool called SimpleMappr.
Web mapping technology has improved significantly over the last few years and it seems that now you can create these simple maps quickly and easily without the need for a complex GIS. In this post we will give a quick overview of SimpleMappr and will present the pros and cons.
First, go to the SimpleMappr home page here: http://www.simplemappr.net. From the home page you can see the map viewer with a toolbar on the left, the settings on the right and some tabs at the top (Help is on the far right).
SimpleMappr home page
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You can click the zoom button to get to your area of interest and then try some of the settings on the right to add different layers and labels. For example, try turning on the ‘State/Provinces’ layer and labels by checking the boxes. You may also want to add a graticule grid to show the lines of latitude and longitude. For cartographic correctness you should also project your map and there are a few options with SimpleMappr. Choose the most appropriate one according to the location of your species. You can also crop your map using the crop button - note that you need to have the crop highlighted before you save, otherwise it will default to the full size map. Click the download button to save your map. You can download in multiple formats e.g. svg, png, tif, pptx, docx, or kml, and you can adjust the dimensions as well as add a border, legend and scale bar.
Quick map of Madagascar showing provinces with labels
Adding points and layers
Click on the 'point data' tab and either manually add latitude and longitude co-ordinate pairs, or cut and paste from another format, for example from an Excel table. You can then customise your points by shape, size and colour. Note that with each layer you can add a different species.
Cutting and pasting decimal latitude and longitude co-ordinate pairs from Excel (on the right) into the point layer window of SimpleMappr (on the left)
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Another neat option is the ability to highlight regions e.g. countries or provinces. You can add this by typing the name of a country or by using ISO codes. You can then set the colour that the regions will be highlighted with. In the example below I used MDG[AV], MDG[TL] MDG[FI] to highlight the major regions in Madagascar where my species occurs. Before you know it you can produce a reasonable looking map to a standard that would be acceptable in many journals. You can see a couple of examples below that were generated in a few minutes.
The left-hand map shows points for the species, and provinces highlighted in grey. The right-hand map shows points with a relief map background
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Another nice feature is the ability to link existing accounts such as Google, Twitter, LinkedIn, Flickr, Facebook and Yahoo to SimpleMappr. This means you can save your maps either to edit and finalise later or to use as a template so that you don't have to start from scratch again.
Range of login options to SimpleMappr
A recent article from Kew botanist Paul Wilkin utilised SimpleMapr to produce a dot distribution map for a species of Dracaena in northeastern and central Thailand - no GIS needed! Although a scale bar might have been nice...
Distribution of Dracaena jayniana in northeastern and central Thailand based on both specimen data (●) and observations (■). Map Created with SimpleMappr, http://www.simplemappr.net. (Map reproduced with kind permission of Kew Bulletin and the Board of Trustees of the Royal Botanic Gardens, Kew)
- The interface is clean and easy to use and quickly gives pleasing maps
- There are many customisation options that cover most of the requirements for standard maps used in publications
- The developer is very responsive and deals with bugs and new feature requests quickly - see the Feedback tab on the website
- There is a mailing list so you can stay informed of recent activity (scroll to the bottom of the Feedback section to find the link)
- For the developers there is an API (application programming interface)
- The addition of projections was a great improvement, but more could be added. Also the lack of projection around 180 degrees is problematic for distributions across the pacific
- Positioning of labels cannot be controlled. It would be good to have some automatic avoidance for text against point data (i.e. you do not want text obscuring the points - although we are being very fussy now!)
- Map elements such as scale bar and legend cannot be adjusted (but in some cases you can adjust them afterwards in an image editing program)
- The Help section is a little on the light side - some screencasts or tutorials would be useful
The final verdict
There are a few minor shortcomings, but we believe this is one of the best web mapping tools available at present for producing publication-ready maps. It has lots of potential when linked with the API. So, will the GIS unit now be out of a job? Unlikely... we have plenty of exciting analyses of plant data to be getting on with, as you’ll see in upcoming posts.
- Steve and the GIS team -
1 comment on 'Mapping tools for botanists, part one: SimpleMappr'
The Harapan Rainforest in the Indonesian province of Jambi, Sumatra is one of the few effectively protected areas in the lowlands of Sumatra. It is a former logging concession which has been leased for 99 years by the The Royal Society for the Protection of Birds (RSPB) in collaboration with their Indonesian partner, Burung Indonesia. As part of the lease agreement, the area needs to be managed and re-vegetated by the RSPB. In the past Kew has helped to provide some of the botanical background for this project. The project’s primary purpose is to map the remaining vegetation of the project area and provide input and recommendations for restoration and carbon capture at the site.
Memories of the forest
Over 14 days the Harapan Rainforest field teams clocked up:
95 km covered by foot
Eight days boat access to remote sites
One birthday party
187 old secondary forest plots
94 young secondary forest plots
11 very young secondary forest (thicket) plots
28 scrub plots
Five cleared plots
As well as getting a lot of field data recorded we also enjoyed our surroundings, the hospitality of the Harapan Rainforest team, and life in the forest.
Fond memories of fungi from Jenny
In the field I particularly loved the broad range of fungi found throughout Harapan Rainforest. From super tiny (the thickness of a hair) to large carpets. They came in all shapes and sizes...
Fungi in the Harapan Rainforest
Interesting botany bits from Marie
For me it was excellent to visit enough sites to be able to see a pattern evolving between the presence of different species and their associated category of vegetation.
For example swamp forests that included Pandanus species, Barringtonia species, and members of the Anacardiaceae (cashew or sumac) family with their poisonous sap, which is clear at first, and then turns jet black on exposure to air, including Gluta renghas, which reacts with skin and blisters the skin badly. I was really excited to see it as it was a massive tree and hadn’t been cut, presumably because the wood and sap is so poisonous. Despite the poisonous aspect of some of the species of the Anacardiaceae family, I have a real soft spot for them.
Gluta renghas L. - Left: cut, Right: bleeding
I also enjoyed the different types of Macaranga associated with sites of regenerating vegetation. Macaranga gigantea for example, was very clearly a secondary vegetation plant. Many of these species are now committed to memory as we spent so much time looking at them as we traveled backwards and forwards up and down the river each day visiting different sites.
We also encountered an interesting member of the Rubiaceae (coffee) family - at first I thought it was a strangler fig because of its latticed trunk – in the older specimens you could see right through the stem to the other side. It was a massive tree and too high for us to collect from.
We looked through binoculars and managed to find some of the inflorescences (flowers) and leaves on the forest floor. We thought it might be Rubiaceae but no one had come across one like this before. Back in the Herbarium at Kew I was able to identify it as a Pertusadina eurhyncha (Miq.) Ridsdale. There were some very large tree specimens of this species found at different sites so it was very satisfying to be able to put a name on it and, as Pak Deden said when I told him about it: 'It's very good if you identified the tree, because it’s rather common in this area. The tree is very important, because it has a big trunk and a good canopy.'
Pertusadina eurhyncha (Miq.) Ridsdale
The final collection of the trip for our team was a specimen from the Sapindaceae family – a wild lychee or rambutan type plant with the MOST delicious fruits, which were a combination of lovely juicy lychees and blackcurrant sweets. Specimens were made for the Herbarium but we got to eat the left-over fruits – yum yum!
Life in the Harapan Rainforest
The Harapan Rainforest team made us feel really welcome, they worked hard and were a lot of fun in the field. We couldn’t have collected as much data as we did without everyone’s expertise and enthusiasm.
Our Indonesian counterparts were very good company and watchful for our safety. There were so many slippery fallen trunks to cross and small streams to jump in the forest, that there were constant calls of 'hati hati' ('be careful' in Indonesian). Repetition really is the way to learn a different language because if you hear it enough you will learn it.
It was also very kind of the team down at Bato to turn the field office into a room for us ladies too – they provided us with mattresses and it was a comfortable place to lay our heads after a hard day’s work in the field and was quite, ahem, ‘homely’ (messy) after we got our mosquito nets set up and emptied the contents of our bags out.
All in all we came away with many happy memories and friends, as well as very useful data!
Field Team at Bato Camp Harapan Rainforest
The Kew team celebrate the end of the fieldwork with avocado shakes
- Jenny and Marie -
Here are two videos about Harapan Rainforest.
Protecting Sumatra's Ancient Forests
Conservation drone at Harapan Rainforest
Find out more about the project
- Have a look at Kew's Harapan project pages
- Read the article in Kew magazine about the expedition
- RSBP's Harapan Rainforest pages
- Expedition and Collection map
- Vegetation maps online
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We have done a lot of work collecting data in the Harapan Rainforest, in lowland Sumatra. In this blog we present an overview of how all that data is used to produce a vegetation map.
Our focus was to summarize the condition of the Harapan Rainforest. Satellite imagery (taken by the French satellite SPOT in 2009) was used to generate a very basic classified image. These pictures were three years old, but were the most recent high resolution images that we could find of the entire Harapan Rainforest boundary, with low cloud cover (it is very wet and cloudy there).
In general, we view forests in shades of red, as a false colour composite (FCC). This is where the image colours are shifted to allow us to use near infra-red. Healthy vegetation reflects the near infra red (making it look red in the resultant image). The naked eye can discriminate more shades of red than any other colour.
Image: Colours in the image represent - Red shades: Vegetation - Cyan shades: Low vegetation/clearings - White/black: No data due to cloud/cloud shadows
In this map, the darker the red the more developed the forest (or at least this is the theory we wanted to test).
A quick classification of the SPOT imagery gave us an indication of vegetation differences that we might be able to identify on the ground within the forest. We were not entirely sure what those differences were and that was why we needed to verify them with ground-based observations.
Image: Colours were associated with ‘best guess’ vegetation classes (without any ground-truth data). Good forest in red tones, younger forest in blues, and disturbed areas in the greens
In the forest
In the forest we used pre-prepared image analysis maps (such as the classification map above) to guide our daily route of ‘plots’ through the forest. We were looking at the different blocks of colour as an indication of different forest cover levels. We also looked at changes between 2009 and 2011, which would indicate re-growth or forest loss. We loaded these images onto android smart phones (we used the Samsung Galaxy S2 and Samsung Galaxy Note devices, in the field) to view, interact and set interest points using Locus Pro.
Image: All the information we gathered in the field was entered into digital forms (ODK collect) on the smart phones.
At each plot we collected the following data:
- location coordinates
- environment e.g. hill slope, swamp, etc.
- percentage forest cover
- size of trees
- dominant tree species
- dominant understory vegetation
Image: Roki Afriandi and Purnomo record tree size and species for large trees in the plot
Periodically, we sent data up to the server whenever we had a WiFi connection back at base camp. Back at Kew the data was collated and published on the GIS Unit Expedition Maps webpage. Geotagged tweets as well as our ODK datasheets were mapped in near-real-time.
It was a very successful field campaign and we surveyed over 300 plots assessing detailed canopy measurements and environmental variables with associated geo-locations, photographs and videos.
Back at Kew
Back in the office at Kew we cleaned up the data, filled-in blanks and attached photos taken with our own cameras. The field data was broken into thirds. One third was used to train the satellite imagery into defined forest categories and the last two-thirds to test the classification.
The forest categories we used were: Old Secondary Forest/Disturbed, Young Secondary Forest/Disturbed, Very Young Secondary Forest (Thicket/Disturbed), Scrub, and Cleared. After a few iterations a base map was produced for the area. Our results show that all forest levels showed good potential for regeneration by species identified in the field. There was a lot more intact forest than we had suspected from our initial work with the satellite imagery. See some of the results shown on the map here.
Image: Final vegetation map
We are finishing up this phase of the project, but are still updating our online expedition maps with geo-located photographs and our next blog will show you some of the highlights.
- Jenny -
Find out more about the project
1 comment on 'Mapping the Harapan Rainforest - how we did it'
On our latest project in Harapan (Sumatra) we took the opportunity to experiment with feeding back live data from the field. We also wanted to continue the trend of tweeting from the field. We tried this on other trips (see Kew in Madagascar also here and Kew in Ethiopia). To take it a step further, we decided to map the tweets. You can see the map here.
Sample map from our Harapan Twitter feed
This post is a quick response to those of you who were asking how we did it. We’ll outline the process and point you in the right direction for the code, so you can have a go yourself.
To start with you need to make sure your tweets are geotagged. Geotagging is the process of adding a latitude and longitude co-ordinate to something, in this case, your tweet. To enable geotagging go to the Twitter settings page and click “Enable Geotagging”. You also need to make sure geotagging is enabled on your mobile device. Now, when you send a tweet you should see a little marker symbol, which means your tweets can be mapped. For more info see this blog post: (http://blog.twitter.com/2009/11/think-globally-tweet-locally.html)
To get the tweets to a website we need to access the twitter feed. For this we use a JSON query:
This can work for a Twitter user name e.g. KewGIS, as above, or a search term such as a hash tag like #KewHarapan:
This returns formatted text of the last 100 tweets. We then filter out all tweets without geotags (using jquery to handle the data and tweet.geo is not null) and build the Google Maps markers. Finally, the tweets are formatted to html (with images and links etc.) and added to the popup window. Another view of the tweets is given below the map.
We should point out, this is experimental for us, we are not coders, but are geeky enough to hack a bit of code that works. Thanks to all those who make their code available to others. Most of the mapping code is borrowed from: Mike Williams at Google Maps API Tutorial and updated to Google maps 3 API. Links from twitter feeds came from Jack Barber.
You can find a copy of the code used for the twitter map here.
Also, you can have a play on our experimental pages.
Experimental twitter map
- Justin and Steve -
1 comment on 'Mapping live data and tweets from the field'
Fly-camping: life on the river - a photo essay
Half the Kew GIS team staff took the two small wooden motorboats and our local team members out for three days on the river to explore the harder to reach sections of the Harapan Rainforest. Whilst there they stayed in fly-camps - temporary advanced camps usually some distance from base camp which get their name from the idea of flying in and out out (i.e. quickly!).
If the rain had been on our side, the river would be twice as full as it currently is, and we could have taken a speedboat.
This however, was the relaxing way to travel, if you don’t mind crashing into a few hidden, submerged trees and pushing the boat up a few rapids!
There is plenty of wildlife along the river. We saw a lot more than we were able to photograph and often had a few stowaways!
Frequent sightings were: 1) enormous monitor lizards - usually much larger than the little one in the photo. The biggest we saw was close to 6ft long;
2) troops of Macaques;
3) and many birds, especially Kingfishers (this one was still for a second, but obviously far away!).
We found a fly-camp base by the side of the river where we could set up our tents. Some machete action was needed to clear the tangle of roots and plants. We also set up our water purification system. I was warned over and again that it would need clean-water as a source, but we only had river water so thought we would give it a try. I don’t think that clay sediment which doesn’t fall out of the water when still was the ideal test candidate - and after a few litres of water, the system stopped working altogether. I think some sort of pre-filter is required. Our system seemed a great idea at first but was not really practical in this instance.
It is a hot day everyday and the bees at our campsite seemed particularly happy to crawl along my arm drinking in the sweat - lovely!
We couldn’t find a cook to accompany us on our journey, but all the local staff as well as Pak Deden, the botanist from Bogor, were ready and willing to cook up delicious food every meal time.
In a thunderstorm, there is no better place to be than out in the jungle under a relatively dry tarpaulin with some lovely Indonesian food - as long as the leeches stay away (I only got one bite that evening!)
- Jenny -
Find out more
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About the GIS team
Kew was one of the first botanic gardens to have a dedicated Geographic Information Science (GIS) Unit. This was officially established in 1998 with the mission to ‘provide an interface for Kew's plant diversity research, presenting data and producing tools to underpin surveys and inventories, conservation and environmental monitoring’.
More than ever, GIS is part of our lives from GPS devices in smart phones to the latest satellite images in Google Earth. We use GIS techniques to support Kew’s science and conservation and most importantly, we like maps too! We are going to use this blog to tell you about the projects we are involved in and the new technology and techniques we are investigating. Make sure you subscribe to the GIS unit blog feed to keep up-to-date with all things GIS.
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