Interesting Paper: Current and future nature-based tourism in the Eastern Arc Mountains

Greetings from Moshi, Tanzania, where I am still busy with the fieldwork. Just want to point the dear readers to a new paper, that is currently in Press in “Ecosystem Services”. Titled “The current and future value of nature-based tourism in the Eastern Arc Mountains of Tanzania” the study analyses and gives estimates for the current and future economic value of nature-based tourism in Tanzania. The analysis is based on a dataset including the spatial location of lodgings and visitor estimates and provides predictive outlooks for two different land-use scenarios (no-change, hopeful-future). They conclude that eco-tourism in the Tanzanian EAM (Eastern Arc Mountains) can provide, among other values for ecosystem service, substantial revenue in the future if the management effectiveness of protected areas can be improved.

Bayliss, J., et al., The current and future value of nature-based tourism in the Eastern Arc Mountains
of Tanzania. Ecosystem Services (2014),

Sadly they only included the EAM from Tanzania in their study and thus left out the Taita Hills. During my stay in Taita I observed multiple disturbances such as fuelwood extractions and larger loggings in the last forest patches of Taita. Having multiple endemic bird (Taita Thrush, Taita Apalis, …) and plant species (eg. Saintpaulia teitensis) the forests of the Taita hills surely can be considered a part of the renown EAM Biodiversity hotspot. But due to the high population density at Taita there should be more economic opportunities and initiatives, such as the Taita-Taveta Wildlife Forum has been promoting, to increase the support of both local people and government to protect these last forest patches and ensure future connectivity.


Fuelwood collection. Photographed near Ngangao Forest

Fuelwood collection. Photographed near Ngangao Forest

Recent loggings within parts of Vuria Forest.

Recent loggings within parts of Vuria Forest.

Anyway, lets hope that this study can back up some arguments in the science-policy dialog with decision makers in Tanzania and abroad.

BIOFRAG – Biodiversity responses to Forest Fragmentation

Another interesting project closely related to PREDICTS is the BIOFRAG Project, which tries to construct a global database of research papers dealing with Forest Fragmentation and its impacts on Biodiversity taxa. One final goal of the BIOFRAG project is the development of a new fragmentation index using watersheds delineation algorithm and fragment descriptors in order to characterize Fragment traits. I am very interested in seeing the final outcome of this approach and maybe I even find the time to implement their algorithm in LecoS for QGIS as soon as it is released. Their database paper, lead authored by Marion Pfeifer, was just released to the public as open-access paper. You can read it in full here.

Pfeifer et al. (2014) BIOFRAG – a new database for analyzing BIOdiversity responses to forest FRAGmentation. Ecology and Evolution. doi: 10.1002/ece3.1036

If you consider of contributing data then more information can be found on the BIOFRAG blog and all researchers involved with forest fragmentation research should consider contributing to them and also to PREDICTS   (see here) if you haven’t already done so. And as usual: If you were studying in Africa, then please get in touch with me! I will contact you as soon as I return from my Fieldwork in Kenya and Tanzania at the end of May.

Out in the field – Working in the agricultural Mosaic of the Taita Hills

And here are some news from my current field work that is part of my Thesis. After spending some quiet, but exiting days in Nairobi (maybe later more about that) I finally arrived in Wundanyi, Taita Hills, where a substantial part of my work will be conducted along the CHIESA transect. Suited in the coastel area in proximity to Mombasa the Taita Hills are renown for their extraordinary bird diversity and endemic species and as such are considered to be part of the Eastern Arc Mountains Diversity hotspot. The Taita hills encompass a variety of different land-use forms, but the majority of them surely are tropical homegardens as most of the “Taita” people are subsistence farmers growing crops in the highly fertile soil of the mountain slopes. Besides homegardens there are riverine forests in the valleys, shrubland vegetation in the lower altitudes, exotic tree plantations and of course the remaining indigenous forests remaining on the Taita hills mountain tops. Every last forest part is known well and was traditionally protected by the locals as part of their culture. However in the later centuries the remaining forest area became more and more scarcer and even during my visits in some of the forest fragments with the highest biodiversity value (Chawia, Ngangao) I saw frequent signs of fuelwood and timber extraction. Clearly a lack of funding for biodiversity protection seems to be the problem, but also an economic perspective and opportunities such as ecotourism might enhance locals perception if and how these last forest parts should be protected.

Past Funding

Past Funding

Cloud Forest Vuria

Cloud Forest Vuria



My work in the Taita hills is all about birds. Specifically I am conducting avian diversity and abundance assessments along an altitudinal transect encompassing a variety of different land-use systems. Although avian assessments have been conducted in Taita many times before, they were often restricted to the forest fragments and for instance didn’t look at the bird diversity in homegardens in different altitudes. The resulting data will just be used for my thesis as validation dataset, but I am hoping that it has maybe some value on its own as well. Initial results show that especially the homegarden in Taita support quite a high diversity of birds, which is even similar to levels in the remaining forest fragments (although the community is somewhat different and biotic homogenization is likely on-going).


It can be quite challenging to conduct avian research in tropical human-dominated landscapes. Not only do you have to arrange for transport to the specific transect areas and lodging (in my case provided by the University of Helsinki Research station in Wundanyi), but also account for the frequent interruption by children and farmers asking what you are doing. Furthermore it is not an easy task to count birds in for instance a maize or sugarcane plantation due to the limited accessibility and my intention not to damage the farmers crops. Most of the farmers however happily provide access to their land and are very interested in what kind of research this “Mzungu” is doing on their farm. From my own experience here I can tell that the Taita people are very kind and it is a pleasure to work with them on their land. They are very respectful and even walking around late at night or very early in the morning seems to be no problem here (in contrast to for instance Nairobi or Mombasa).

Speckled Mousebird

Speckled Mousebird

Female Chamaleon

Female Chameleon

In the end my sampling goes on quite well and much better than I expected. Although it is technically raining season and long heavy rains can be expected every day, the mornings were exceptionally dry and weather was mostly favourable for ornithological research. Generally this time of the year in East Africa is especially interesting for bird assessments as many local bird species are in their breeding plumage and nesting, but also because European migrants are often still around or on their way back to Europe (for instance I saw and heard an European Willow Warbler some days ago). Lets see what else the next weeks will have for be in terms of avian diversity.

The PREDICTS project – We need your data!

As part of my Thesis project I have recently joined up with the researchers and interns of the PREDICTS project. PREDICTS stands for Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (yeah, fancy and down-to-the-point acronym) and is aiming to investigate the impact of various human pressures on biological diversity on a global scale. PREDICTS gets its data from contributing authors and is constantly looking for new data contributors. All contributors will become coauthors of a paper describing the database and  at the end of the project the whole database will be released to the public!

We want your data! For instance Wildcat (Felis sylvestris) encounters over land-use gradients!

We want your data! For instance Wildcat (Felis sylvestris) encounters in different habitat types!

If you have diversity or community composition data collected from more than one terrestrial site which are somehow influenced by humanity and are raised using a standardized methodology, then it is more than likely that we could use it. What we need is the

  • Locations of sampling points, as precisely as possible
    (with the coordinate system used, if possible)
  • An indication of the type of land cover that each sampling point represents
    (e.g. primary forest, secondary forest, intensively-farmed crop, hedgerow)
  • An indication of how intensively the site is used by people
  • Data on the presence / absence, or ideally a measure of abundance, of each species at each site
  • The date(s) that each measurement was taken

We need more openness in terms of data sharing in conservation and ecology research! It is unbelievable that some important research data even today can go lost if for instance the original author died or his lab burned to the ground. Some might argue that it should be mandatory to share data if your research is 100% funded by public sources. Some understandable reasons that speak against data sharing after publication are for instance that you are a young emerging scientist and want to keep your hardly earned golden eggs to yourself. However this can be debated as well as data sharing not only gives you more citations, but maybe even into contact with other researchers in your field. In other cases researchers sometimes don’t want to share raw sampling data because of conservation concerns, but even here there are options to coarsen coordinates before public release.

Recent initiatives on openness in terms of ecological data sharing like and already provide a splendid place where you as an Author can dump raw data from papers you wrote years ago. You can even place the raw data from your most current projects and put an embargo on the download so that the item will be released to the public for instance one year after the associated article has been published.


For my thesis I am especially looking for all kinds of African community data that has been published. We already have a lot of studies in the database, but for my project i need more data especially of less sampled taxa (insects, amphibians,…), different temporal resolutions and a greater diversity of land-use types.  So especially if you have data on African species communities in any form (diversity metrics, abundance metrics, I even take occurence matrices) which were sampled in somehow anthropogenic disturbed habitats: Please contact me or wait for me to contact you :)

Martin Jung

Statistical inferences using p-values

And another quick post for today. Here is a nice infographic I just found on the Nature News page. Nice demonstration how p-values can fail us in making hypothesis inferences. Just another article bashing p-values you could say. Or “Just switch already to Bayesian stats or report real effect strengths instead of p-values”. Although the matter is clear for many ecologists out there, the majority still happily uses p-values inferring that they proved their working hypothesis wrong or true. At my former and also at my current university p-values are still being taught and used in all courses related to data analysis. Students are being asked and expected to always (!) report the p-value and trained to look specifically for something they claim is statistical significance of an effect. And then people are wondering why the hell everyone still uses century old techniques. Often while not even knowing what it exactly means. I certainly believe (and I say that while being still educated :) ) that especially in the education of future ecologists and conservationists statistics courses should become mandatory for all (under)graduates. In times of big data analysis basic statistical knowledge has to be a must for everyone.

Courtesy of Nature, Nuzzo 2014

The related Nature News article can be found here. More nice infos and facts about my research in Africa and fieldwork trip will appear around May.

EDIT: And as a funny addition check out this awesome R-function which gives you an appropriate significance description for every p-value :D

Global Forest Change data now available for Download

The previously reported Global Forest data from Hansen et al. (2013) is now finally up for download.

Access the data here, but beware of the size of the individual granules as they easily be some gigabytes. The time for some awesome analysis and probably a bunch of papers has come…


Google Maps routing for QGIS

Just a little post with something not totally related with Ecology, but nevertheless quite useful for the daily work with GIS. Some time ago i got hand on a nice Garmin GPS device (Etrex 30) and i am constantly playing around with the options and opportunities for it. Especially in the interaction framework of fieldwork and desktop-based GIS processing. Now i was at the lucky situation to have some time available to go birding in the area of Vestamager southwest of Copenhagen, Denmark. My intention was to bicycle there and use the GPS for orientation (although i perfectly know the route :) ).

Thus i wrote this simple little R processing script (see a general introduction how to create R-scripts for processing here), which uses the route(…) function of the ggmap package to generate line layers from a point x to point y. Note, that by using this function you are agreeing to the Google Maps API Terms of Service and you are only allowed to send 2500 queries per day.

Generate the route from x to y and specify bicycle as output.

Generate the route from x to y and specify bicycle as output.

The generated output line is automatically loaded into QGIS after processing and has the total length and duration of the trip in its attribute-table.

Queried route for Copenhagen with googlemaps displayed on an OSM background in QGIS

Queried route for Copenhagen with googlemaps displayed on an OSM background in QGIS

To use the script, create a new one in the processing toolbox and copy the contents below into it. Then copy it into your “~/.qgis2/processing/rscripts” folder. I will also post the script in the QGIS scripts section here on this blog.

# GGmap routing script by Martin Jung
# Homepage:
##Vector processing=group
##x = string Copenhagen, Denmark
##y = string Berlin, Germany
##type= string driving
##output = output vector
if (!require(ggmap)){print("ggmap not installed. Will install it now");install.packages(ggmap, dependencies = TRUE)}

r <- route(from=x,to=y,mode=type,structure="route",output="simple",alternatives=F,messaging=F) # get the route
cs <- CRS("+proj=longlat +datum=WGS84 +no_defs") # WGS84 projection

l <- Lines(list(Line(r[c("lon","lat")])),ID=paste0(type,"_track"))
sl <- SpatialLines(list(l),cs)

data <- data.frame(from=x,to=y,type=type,length_km=sum(r$km,na.rm=T),duration_h=sum(r$hours,na.rm=T))
output <- SpatialLinesDataFrame(sl,data=data,match.ID=F)

To use existing shapefiles from within QGIS, users are advised to take a look at the pgrouting extension for Postgis. See a nice tutorial for installation and configuration on windows machines here.

The Rostrum

Ecology, Entomology, Statistics and Science Policy


Environmental Change - Understand, Predict, Adapt

Dynamic Ecology

Multa novit vulpes

The Molecular Ecologist

A blog about Conservation and Ecology and everything between


METeorological Visualisation Utilities using R for Science and Teaching

A Birder´s Blog

"Everybody loves what they know"


A new metric to quantify biodiversity response to fragmentation

Trust Me, I'm a Geographer

Using Technology to Explore Our World

Duncan Golicher's weblog

Research, scripts and life in Chiapas

Daniel J. Hocking

Ecology, conservation biology, & statistical modeling for a changing world

Climate Change Ecology

The Science, Economics, and Politics of Climate Change

Jeff Ollerton

Blogging about biodiversity

Darren's Side Projects

Warning: self-taught coding ahead! Mostly Javascript (Google Maps API, Google Chart Tools, jQuery, etc.), some HTML5, maybe some Python and R here and there. I make no guarantees that the work on this page is complete, efficiently coded, relevant, unplagerized, or follows any resemblance of a set of best-practices. Also, most examples shown here work best in Google Chrome - again, no guarantees.

Marginally significant

Posts with more discussion and less p-values

Jean-Pierre Rossi - Blog

A blog about forest insects, R, GRASS, LaTeX and the likes

Assembling my Network

The ecology is theoretical but the fun is real.

Journal of Ecology blog

The official blog of the Journal of Ecology - a journal of the British Ecological Society

Ecology for a Crowded Planet

Like captain planet, but with more statistics.


Get every new post delivered to your Inbox.

Join 58 other followers