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https://github.com/gavinsimpson/bennion-frontiers-2015

Code for analyses in Bennion et al paper submitted to Frontiers for a special issue
https://github.com/gavinsimpson/bennion-frontiers-2015

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Code for analyses in Bennion et al paper submitted to Frontiers for a special issue

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# Frontiers in Ecology & Evolution Special Issue



The R codes and scripts here implement the analyses and figures

reported in Bennion, Simpson, and Goldsmith (in review) *Frontiers in

Ecology and Evolution*, submitted to the special issue *Using

paleolimnology for management and restoration of lakes*. The paper will

be available via Open Access as per Frontiers model following acceptance

of the manuscript.



The files are licenced under the MIT licence; see the `LICENCE` file

details, but basically as long as the source of the files and the

specified information in `LICENCE` is included in any subsequent

re-distribution of the code, you can do what you want with it.



## Manuscript abstract



Efforts to restore enriched lakes have increased yet there remains 

uncertainty about whether restoration targets can be achieved and over 

what timescale. Paleoecological techniques, principally diatom 

analyses, were used to examine the degree of impact and recovery in 12 

European lakes subject to eutrophication and subsequent reduction in 

nutrient loading. Dissimilarity scores showed that all sites 

experienced progressive deviation from the reference sample (core 

bottom) prior to nutrient reduction, and principal curves indicated 

gradual compositional change with enrichment. When additive models were 

applied to the latter, the changes were statistically significant in 9 

of the 12 sites.



Shifts in diatom composition following reduction in nutrient loading 

were more equivocal, with a reversal towards the reference flora seen 

only in four of the deep lakes and one of the shallow lakes. Of these, 

only two were significant (Lake Bled and Mjøsa). Alternative nutrient 

sources seem to explain the lack of apparent recovery in the other deep 

lakes. In three shallow lakes diatom assemblages were replaced by a 

community associated with lower productivity but not the one seen prior 

to enrichment. Internal loading and top down control may influence 

recovery in shallow lakes and climate change may have confounded 

recovery in several of the study sites. Hence, ecosystem recovery is 

not simply a reversal of the degradation pathway and may take several 

decades to complete or, for some lakes, may not take place at all. By 

assessing ecological change over a decadal to centennial timescale, the 

study highlights the important role that paleolimnology can play in 

establishing a benchmark against which managers can evaluate the degree 

to which their restoration efforts are successful.



## Description of the `.R` files



There are five `.R` files included here which do the following:



 1. `functions.R` contains a `ttplot()` function that acts as a wrapper

 to the `plot()` method for `timetrack()` in the **analogue** package.

 This is used to provide a consistent base-graphics plot for the timetrack

 plots included in the paper.

 2. `core-data-processing.R` contains code to read and process the sediment

 core data presented in the paper.

 3. `wiser-analysis.R` contains the code to do the passive overlay of the

 core samples on to deep and shallow-lake training sets, aka timetracks.

 This work was done as part of the EU Seventh Framework Programme project

 [WISER](http://www.wiser.eu), hence the file name.

 4. `principal-curves.R` fits principal curves to each of the sediment

 core records.

 5. `additive-modelling-prcurve-data-script.R` contains the time series

 via additive modelling code and code to produced the time series figures

 showing the fitted trend in principal curve scores and the derivatives

 of the fitted trend which we used to identify periods of change in the

 diatom community composition.