Local distribution maps for biological records in R

I thought it worth sharing this map that I created for a poster that Ambroise Baker and myself have prepared for the upcoming BSBI Annual Exhibition Meeting. It shows the occurrences of the non-native grass Polypogon viridis in Sheffield, based on records made by Ambroise and myself this year (2013). The map took a fair bit of fiddling around; working out how to correctly specify the manual scaling of the points seemed to cause me particular trouble!

Of course, R could also be used to create more traditional atlas dot maps; coastal outlines of Britain are freely available in more than one R package, and occurrence data relating to the UK grid could be manipulated in R to centre on monads, tetrads or hectads. External tools could also be used to do this before loading the data into R, e.g. see here.

	library (sp)
	library (rgdal)
	library (OpenStreetMap)
	library (ggplot2)
	setwd("C:/.../water_bent")
	water_bent<-read.csv("water_bent.csv") #columns: x; y; Size
	water_bent4map<-water_bent
	coordinates(water_bent4map) = ~x+y # turns dataframe into a SpatialPointsDataFrame
	proj4string(water_bent4map) = CRS("+init=epsg:27700") # tells it to be UK OSGrid
	# retrieve basemap
	map <- openmap(c(53.40,-1.550),
	c(53.36,-1.475),type="osm-bw") # corners of retrieved map, see ?openmap
	osm.Shef <- openproj (map, proj4string(water_bent4map)) # reproject map to OSGB
	water_bent4map$Size <- as.factor(water_bent4map$Size)
	autoplot(osm.Shef) +
	geom_point(data=as.data.frame(water_bent4map),aes(x=x, y=y, size=Size),
	col="red", alpha=0.6) +
	theme(axis.title.x=element_blank(), # suppress axis label
	axis.title.y=element_blank(), # suppress axis label
	axis.text.x=element_text(colour="black",size="19"),
	axis.text.y=element_text(colour="black",size="19"),
	legend.position=c(0.112,0.877),
	legend.text=element_text(size=18),
	legend.title=element_text(size=20)) +
	annotate("text", label = "(SK)", x = 430350, y = 385100, size=14) +
	scale_size_manual(values = c(8,12,18), name = "Population size", labels = c("1-2","20-50",">100")) #scale points by size #manually

view raw simple_occurrence_map.R hosted with ❤ by GitHub

The result is below. I'd be grateful to hear from anyone who can suggest any refinements to my code, or the general way in which I've gone about this.

Polypogon viridis in Sheffield, UK, 2013

Water Bent new to Sheffield and South Yorkshire

Several studies of urban areas have found that the composition of the flora can change considerably between survey periods. For example, a survey of the street flora of Aberystwyth between the 1970s and 1998-9 found a large turnover of species (Chater et al. 2000), with species associated with drier, warmer conditions becoming more prevalent. In this way it can be of interest to monitor the urban flora, because the rapid changes in the plants that make their homes there may provide an insight into how our urban environment is changing. In this spirit, Ambroise Baker and myself were excited to independently discover the alien grass Water Bent (Polypogon viridis) new to the streets of Sheffield and South Yorkshire. Whilst some records of this plant do exist for vice-county 63 (e.g., from wool shoddy, Halifax, 1960, F. Houseman), this appears to be the first find of Water Bent for the modern county of South Yorkshire (GTD Wilmore, pers. comm., 2013).

Surprisingly, Ambroise and myself have not just discovered one new colony, but 6, in 5 different 1 km squares (monads) in Sheffield, with some populations of considerable size, suggesting that this species has been amongst us for at least a few years. This is a species that appears to be spreading throughout the British Isles; its principal habitat is pavement edges and waste ground, although some records from canals have also been made. It is not clear that this species negatively affects any of our native flora, although, with a warming climate, it will be interesting to monitor for any habitat changes that might occur in the future. So far, our records of this alien grass are:

Eastwood Rd, Sharrow, SK335858, 11.06.2013, a few plants (AB)

Robertson Rd, Walkley, SK324884, 16.06.2013, one large plant (OP)

Stewart Rd, Sharrow, SK333857, 19.06.2013, thousands of plants (AB)

Truswell Rd, Crookes, SK324874, 12.07.2013, over 20 plants (OP)

Armthrop Rd, Nether Green, SK315855, July 2013, one large plant (AB)

Clumber Rd, SK313864, July 2013, over 20 plants (AB).

It seems likely that Water Bent is lurking in other parts of Sheffield’s suburbia, and, given that it has also just been recorded for the first time in Derbyshire (Willmot & Moyes, 2012/13, Derbyshire Flora Group Newsletter No. 22), this is a great opportunity to get some good baseline data to monitor the spread of an alien plant in an urban area. The above photo demonstrates how it is most likely to look at this time of year. Water Bent is, unsurprisingly, most similar to a bent grass (Agrostis spp.); indeed, it was previously classified in that genus; however, one key difference is that the glumes (very small leaves at the base of the flower spikes) fall with the flowers. In our other common bents, and in meadow grasses (Poa spp.), parts of the flower remain on the stalks as the plant dies. The fact that the glumes fall with the seeds in Water Bent gradually creates a skeletal flower-head. This is demonstrated as a progression from the flower-head on the right to the one on the left in the photo.

Urban Trees of Sheffield -- An interactive tour

"But let it be remembered, that the principles of a science are to be taught as truly with

 reference to the commonest forms as to the rarest.  And have we not the fields and the rivers?

But besides this, is not the whole suburb of this metropolis one magnificient botanic garden?"

 John Lindley, in his Inaugural Address as Professor of Botany in London University, 1827

(Quoted in Walters, 1993, Wild & Garden Plants)

View The Trees of Sheffield -- An Interactive Map in a larger map

This is something that I have had at the back of my mind for a few years, and have been, very slowly, mentally collecting notes on. I've finally decided to get on with it and put it out there. The idea was basically to provide a guide to the more interesting or unusual of Sheffield's urban trees, perhaps for a walking tour, or for those who would like to see a certain species.

Google Maps also allows collaborations on these types of maps, so, if you would like to get involved, and edit the map in some way, please let me know. I know there are lots of relatively common, interesting trees, in Sheffield's streets and gardens that are not on here. So, if you know of one that is easily viewable, and is not too far from the city centre, please let me know. I particularly need to add the trees of Weston Park; outside of the botanic garden, this probably has the best collection of trees in a location near to the city centre. 

The other place close to the city centre with a great collection of trees would be Tapton Experimental Gardens; unfortunately this is still closed as the University of Sheffield decides its fate. If I am not mistaken, Weston Park has, amongst others, Hungarian Oak, two varieties of Tulip Tree, the Tree-of-heaven, and Cappadocian Maple. The only tree I can remember seeing in Tapton is Bronvaux Medlar (+Craetaegomespilus dardarii), one of the very few trees that is a chimera of two species, rather than a hybrid; however, I am sure there are many more interesting species in there!

Another nice thing about Google Maps is that it allows data layers such as the one above to be exported as KML files. This should allow one to generate the corresponding biological records of the trees by opening the file in a GIS software like QGIS, reprojecting the layer to the OS National Grid, and exporting the points. Another exciting software for analysing the environmental importance of trees is the USDA Forest Service's application iTree. If one has enough information on the locations and sizes of trees in an area, this free piece of software will calculate all sorts of interesting metrics: the trees' cooling effects; their contribution to the reduction of urban pollution; and carbon storage to name a few! These 'urban ecosystem services' are discussed in many places, but I have found the relatively short, but very readable book, by William G. Wilson called 'Constructed Climates' to be a great introduction to this fascinating topic.

Coppiced Hornbeam in Hedges

I was out surveying around Watton in Norfolk recently, and found these wonderful coppice Hornbeams in a field hedge.

According to Edward Milner's Trees of Britain and Ireland (2011), the prime use of Hornbeam was as firewood, and he cites the 17th century arborist and gardener John Evelyn as reporting that it burns "like a candle". I don't know if the poles resulting from cutting these specimens would have been used in such a way. The coppice effect may just be the outcome of the hedge having been laid many times in its past, and then being neglected at some point; presumably if the main function of a hedge is to be stockproof, the poles would have been laid rather than harvested. Alternatively, some hedges were managed by coppicing, especially if their primary function was not for containing animals; so perhaps this hedge was essentially only a boundary marker, and so has been managed by coppicing for a long time.

It seems from Oliver Rackham's Ancient Woodland (2003, 2nd Ed.) that Hornbeam is relatively rare in hedges. He states in Chapter 14 that "in a few places hornbeam grows in ancient hedges, particularly in the Harleston [Norfolk] hornbeam area". Interestingly, in the recent Flora of Suffolk (Sanford & Fisk, 2010), the authors suggest that in that county, hedges with Hornbeam are often the remaining "ghostly" edges of long grubbed out woods. Suggestively, this hedge was accompanied by a ditch, a common boundary marker of ancient woodlands.

Hornbeam was only occasional to rare in the hedges of this site near Watton, but the glorious, fresh, colours of the leaves, coupled with the twisted, degrading bases, was a real treat.

Creating masked vice-county rasters in Quantum GIS

I was inspired by Teresa Frost to have a go at making a good base-map for South Yorkshire (well, the Watsonian vice-county 63 to be precise) in Quantum GIS (v. 1.8.0). I thought it would be relatively straight-forward, but, I soon came up against an irritating problem, that of successfully trimming a raster of elevations using a vector of vc63. I overview the process below, because by the look of the many mentions of this topic on many forums and mailing lists, there is a need for more examples! There are no doubt easier ways of achieving what follows, but this is what worked for me.

Firstly, I retrieved the Land-Form PANORAMA^® data from the Ordnance Survey's new(ish) OpenData website, and the Watsonian vice-county boundaries from the NBN. The Land-Form download contains, amongst other things, Digital Terrain Models (DTM) in ASCII format, by 10 km grid squares.

In order to merge all of the necessary 10km DTM square into one raster, it was first necessary to get a list of all the 10 km squares overlapping vc63: this Biological Records Centre website was handy for that.

1) In Quantum GIS, the Raster --> Miscellaneous --> Merge option allows the import of multiple rasters and merges them to one raster layer in your project. I chose OSGB 1936 (EPSG:4277) (the Ordnance Survey National Grid) as the Spatial Ref. System for this work.

2) Visualising the DTM data is also a minor challenge, and can be overcome by right-clicking the raster layer, and choosing 'Properties'. Under 'Style', change the color band option to 'pseudocolor' and you should now see the DTM data, albeit in fairly lurid colours.

3) Import the vc63 shapefile via the normal route (Layer --> Import Vector Layer). (If you get it from NBN, it should already be georeferenced to the OS National Grid, but you can check that the bottom right box in the QGIS window says EPSG:4277).

4) As far as I know, it is necessary to polygonise the vice-county boundary in order to use it to "mask" (i.e. clip) the raster image. Luckily, there is a handy plugin for this (Plugins --> Fetch Python Plugins... --> search and install 'Polygonize'). Whilst you are there, it is also worth installing the plugins "Value Table", and, by adding a new repository, the "1-Band Raster Colour Table" (see this stackexchange question for advice on this).

5) Polygonize your shapefile using the new plugin. (Vector --> Polygonizer --> Polygonizer). As it says, try the "old" method if the new one doesn't seem to work.

6) The mask step was the most complex, and, despite trying numerous routes, it was this method that worked in the end: Raster Masks in QGIS/FOSSGIS. The result is below (don't let the change in colour put you off!):

7) Actually, this didn't quite work, because the clipped raster was still showing the "null data" outside the clipping boundary as coloured. Luckily I could get around this by reprojecting the clipped raster to a new file (using the same Spatial Ref. System) using a Raster --> Warp (Reproject).

8) Then I applied a b/w DTM colour scheme using the 1-Band Raster Colour Table plugin (under Raster menu) mentioned earlier. This generates a text file style, that can subsequently be imported and applied via right-clicking on the raster layer, and choosing 'Properties', then the 'Style' tab, also mentioned earlier.

Now I just need to add rivers and urban areas! Think I'll save that for another day : ) All in all, this did take a fair bit of messing around to accomplish, and occasional quirks of QGIS did slow me down (for example, layers sometimes need to be exported (right click and "Save as..." for vectors; Raster --> Warp (Reproject) for rasters) and re-imported, before they can be selected as layers for masking or other transformations). Additionally, very few of the methods suggested out on the web seemed to work, until I found the method used above. But, once you know the pitfalls, work-arounds seem to be possible. Also, more background knowledge on my part wouldn't go amiss...