Creating country checklists using GBIF and rgbif

I wrote this function in order to create simple summaries of GBIF data per country (i.e. checklists based on the available GBIF information) to supply to other people without R expertise. I suspect there is a lot that could be improved (and perhaps I have even missed something obvious within the rgbif package that would have made it easier). Anyhow, this is where it is at. I have been using the function 'lapply-ed' across a vector of country ISO 2 character codes. Occasionally it fails (particularly with countries where there is a lot of data), hence the try...catch approach for when applying over such lists.

Of course, I realise that GBIF is not comprehensive in its coverage, and that there are often issues that need addressing with occurrence data and taxonomic precision; this code was written for a quick first assessment useful for comparing the presence/absence of potentially invasive species in countries in the context of horizon scanning. Use this code at your own risk!

Feedback/improvements welcome!

An update on Sheffield's urban trees

Just a small post to say that I've updated some of the trees on my map of the Urban Trees of Sheffield. Despite no longer living in Sheffield, I'm still a member of the most excellent Sorby Natural History Society, and in August of this year the annual tree walk took place, resulting in some extra identifications which I've tried to include on the map. Thanks to Joan Egan for writing her 'Report of the trees in the city centre meeting. Sunday 10 August' in the November 2014 Sorby Newsletter.

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

See here for the original post: http://sacrevert.blogspot.co.uk/2013/06/urban-trees-of-sheffield-interactive.html

England's new Red List of Vascular Plants

It seems to be an incredibly productive season for botanical publishing. A new bryophyte atlas on the way; fliers for a reprint of the BSBI handbook Docks & Knotweeds with BSBI News, and for books on Yorkshire's Hawkweeds and Bedfordshire's Orchids; but one of the most exciting publications has been that of the new Vascular Plant Red List for England

New #EnglandRedList shows that ~5th of wildflower species now threatened @BSBIbotany pic.twitter.com/e93DxbLbXS
— BRC (@___BRC___) September 17, 2014

The launch of the Red List was also a celebration of the contribution of David Pearman to British botany. His name might ring the loudest bell to many as co-editor of the 2002 New Atlas (now rather expensive, apparently because Defra pulped all of the left over copies -- the less said about that the better). However, David has also contributed a huge amount to many other areas of botany, including several interesting pieces encouraging a more critical perspective on the impacts of alien plants. For example, see this article for a stimulating read! His views on the native statuses of British plants have also been very influencial: see this paper for a host of fascinating examples.

David Roy of BRC and David Pearman at his eponymous celebration and Red List launch

The Pearman celebration segued into the launch of the England Vascular Plant Red List launch very nicely. This exciting publication has used new interesting methods, and of course plant distribution data collected over more than 80 years by BSBI members and others, to reveal a rather worrying picture of England's native floral diversity. The new analysis has found that around a fifth of our wildflowers are now under threat. Many plants were found to have undergone worse declines in England than in Great Britain as a whole, highlighting the importance of this new England-level analysis.

Of course, we have known for a long time that particular habitats have been under a lot of pressure in England, but it is fantastic to have the broad, volunteer-led distribution data revealing the same thing as smaller, habitat-focused studies. It all helps to form a compelling picture of ecological change that should convince politicians and funding bodies that plant conservation is both necessary and really worthwhile.

Oh, and whilst you can purchase the Red List (a fascinating read with lots of nice photos) at Summerfield Books, you can also take home a nice shiny pdf immediately! I have to admit to not having read mine probably yet, but this is far more than just a list, there are around 60 pages of text, analysis and photos, with the list (covering all native plants in England as far as I can tell) covering another ~110 pages. GB Red List designations are also included. I'm looking forward to settling down with it and learning a lot more about the British flora!

Atlas 2020 recording with the Oxfordshire Flora Group

It's been a while since I've blogged, but, a lot has been happening (no excuse really when I look at Louise's efforts at http://bsbipublicity.blogspot.co.uk !) Anyway, last week I went out with the Oxfordshire Flora Group, a group affiliated with the BSBI and the Ashmolean Natural History Society; seeing as this was only the second, in what will hopefully be a long-running series of Atlas 2020 recording meetings, I felt that it was a good time to do some blogging and promote the OFG meetings. In conjunction with this rebirth, vice-county 23 (or the old-fashioned county of Oxfordshire for those who don't habitually think in terms of Victorian vice-counties) also has a recently appointed new vice-county recorder, Sue Helm, and a new page on the BSBI website to boot. The page explains the myriad opportunities to get involved in plant monitoring and recording in Oxfordshire, and also assists with understanding the rather complex web of botanical societies and mailing lists extant in Oxon.!

But, back to the recording: Seven of us met up just south of Sibford Ferris in north Oxfordshire to accumulate records for a 2 x 2 km square (tetrad) in a region with precious few modern botanical records -- so just recording the car park would have a been a good achievement! Luckily we did get a bit further than that, and did a good circumnavigation of the tetrad, even gaining access to some private land, allowing us to add some extra stream-dwelling species to our list (just over 200 in the end since you ask).

The OFG inspect a verge. I think this was the Schedonorus pratensis v. arundinacea debate!

Needless to say, we all learnt a lot from each other, and an excellent day was had by all. We also had a good few conundrums to keep us on our toes. 

The mystery willowherb.

 This willowherb was a case in point. The general conclusion seemed to be that it was a hybrid -- but between which species? The jizz didn't seem quite right for E. parviflorum, but perhaps we shouldn't be doing willowherbs on jizz anyway. Although Crawley says that E. parviflorum is more-or-less unmistakable on jizz... anyway, one for the bag in the end. At home under the microscope I convinced myself that it might be E. hirsutum x parviflorum, but really it needs sending off to the referee. Another one for the to-do list! No doubt it will come back as parviflorum and I'll feel a fool!


But it wasn't all hybrid willowherbs, much of the trip was far more palatable. We found a ungrazed corner of pasture that must have been on the Cotswolds oolitic limestone. Here was Burnet Saxifrage, Chalk Knapweed, Rough Hawkbit and other denizens of high pH soils; a wondeful respite from the typical intensely managed pasture we are used to seeing in the countryside today. We then passed by an arable field, picking up a number of typical plants of such situations, including the Black Bindweed below.

Fallopia convolvulus

Not a rare plant at all, but one which I find strangely charming. The slightly manufactured perfection of the Polygonaceae in handy pocket size; the fearsome knotweed becalmed: who could fail to be charmed? By now it was raining, and a bit of a drudge was needed to circle around the bottom of the tetrad and re-enter it from the south. By good luck, the final habitat was a really special one: an abandoned quarry. The ground of the quarry was quite disturbed, presumably from rabbit grazing rather than recent use. Clearly an interesting habitat in which to look for new species. We were quickly rewarded with Basil Thyme (Clinopodium acinos), a plant which is relatively rare in Oxfordshire, with only around 20 sites or so. I had only seen it before around the entrances to rabbit burrows at Watlington Hill; here it was in abundance on every bit of bare ground, and even on some of the bare rock faces of the quarry. A wonderful end to a enjoyable day. Thanks OFG! And see you all next time (all welcome, regardless of ability!)

Clinopodium acinos

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.


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.