Difference between revisions of "Arne Pommerening's Forest Biometrics & Quantitative Ecology Lab"

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== Sample input files ==
 
== Sample input files ==
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The following data are from my management demonstration (MDF) plot 6 in Clocaenog Forest (North Wales) surveyed in 2004. This is an interesting site where a formerly mono-species Japanese larch plantation has gradually been colonised by Sitka spruce and other species (see the plot map at the top of this page).
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The following data are from my management demonstration plot (MDP) 6 in Clocaenog Forest (North Wales) surveyed in 2004. This is an interesting site where a formerly mono-species Japanese larch plantation has gradually been colonised by Sitka spruce and other species (see the plot map at the top of this page).
  
 
* Configuration file [[media:Clg6.cfg‎|Clg6.cfg]]
 
* Configuration file [[media:Clg6.cfg‎|Clg6.cfg]]
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== Sample output files ==
 
== Sample output files ==
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These data also refer to  MDF plot 6 in Clocaenog Forest (North Wales) surveyed in 2004.
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These data also refer to  MDP 6 in Clocaenog Forest (North Wales) surveyed in 2004.
  
 
* Protocol file logging all processes and presenting basic results [[media:Clg6_protocol.zip‎|Clg6_protocol.zip]] (please unzip)
 
* Protocol file logging all processes and presenting basic results [[media:Clg6_protocol.zip‎|Clg6_protocol.zip]] (please unzip)

Revision as of 15:55, 7 January 2013

Tree location map of Clocaenog plot 6. Orange: Japanese larch (Larix kaempferi (Lamb.) Carr.), Olive: Sitka spruce (Picea sitchensis (Bong.) Carr.), Maroon: Rowan (Sorbus aucuparia L.), White: other species (including Scots pine, lodgepole pine, Norway spruce, sessile oak, ash, birch, willow and holly). The size of the circles are scaled by stem diameter at 1.3 m above ground level. The map was prepared with the R script TreeDiversityIndices.R‎ in conjunction with the spatstat package.

CRANCOD - A Program for the Analysis and Reconstruction of Spatial Forest Structure

It is widely acknowledged that forest structure is a driving factor for growth, competition and birth & death processes which, in return, influence the structural composition of woodlands. Also any impact on forests - whether natual or human-induced - is primarily a change of forest structure.

In the last few decades an impressive number of structural indices (also referred to as nearest neigbour summary statistics [NNSS]) have been developed to quantify spatial forest structure. Of particular interest in this regard is the development of a family of individual tree neighbourhood-based indices, which are measures of small-scale variations in tree locations, species and dimensions, developed by Gadow and colleagues at Göttingen University (Germany). Especially when expressed as frequency distributions these indices offer valuable information on spatial woodland structure. Forest structure is closely correlated to and an expression of biodiversity at forest stand level (α diversity). Therefore the structural quantities used in CRANCOD play an important role as surrogate measures of biodiversity (Pommerening, 2002).

The CRANCOD program is a scientific laboratory for analysing and experimenting with nearest neighbour summary statistics and second-order characteristics. CRANCOD has been designed for use with large research plots including full enumerations of trees and in addition offers the opportunity to analyse forest inventory data consisting of multiple sample plots of circular or rectangular shape and varying plot size based on a systematic grid. The program has inbuilt flexibility with the user able to select the number of neighbour trees and to choose between six different methods of edge correction. CRANCOD can, of course, also be used to analyse research and sample plots without spatial information (stand analysis).

The integrated sampling simulator ISIS allows the simulation of sampling with systematic selection of sample plots of varying plot geometry.

Saving individual-tree results in addition to the summary files provides the opportunity to carry out individual tree based follow-up research. A special visualisation tool allows the user to visually explore nearest neighbour summary statistics. Tree species codings and colours can be flexibly edited externally. A number of language options allow optimal adaptation of the program in different countries.

The philosophy and objectives of the program are described in greater detail in the user manual and in the papers given below. The publications also describe experiments and investigations that can be carried out with CRANCOD.

File:Mdi.png
Mean directional index in Clocaenog plot 6. The arithmetic mean, the bar plots and the density distributions indicate slight regularity of tree locations. The mean directional index was calculated with the R script TreeDiversityIndices.R‎.

Author, copyrights and contact: Prof. Dr. Arne Pommerening, Bern University of Applied Sciences, School of Agricultural, Forest and Food Sciences. Email: arne.pommerening@bfh.ch

Software version: 1.4

Copyright and licenses: The core version of CRANCOD is a public domain software. However, the program is protected by intellectual property rights and users are expected to acknowledge CRANCOD and its developer when publishing results.

Publications relating to CRANCOD and to forest structure

Pommerening, A., 2002. Approaches to quantifying forest structures. Forestry 75, 305-324. [PdF file]
Pommerening, A., 2006. Evaluating structural indices by reversing forest structural analysis. For. Ecol. Manage. 224, 266–277. [PdF file]
Pommerening, A. and Stoyan, D., 2006. Edge-correction needs in estimating indices of spatial forest structure. Can. J. For. Res. 36, 1723–1739. [PdF file]
Mason, W. L., Connolly, T., Pommerening, A. and Edwards, C., 2007. Spatial structure of semi-natural and plantation stands of Scots pine (Pinus sylvestris L.) in northern Scotland. Forestry 80, 567-586. [PdF file]
Pommerening, A. and Stoyan, D., 2008. Reconstructing spatial tree point patterns from nearest neighbour summary statistics measured in small subwindows. Can. J. For. Res. 38, 1110–1122. [PdF file]
Pommerening, A., 2008. Analysing & modelling spatial woodland structure. Habilitation thesis BOKU University Vienna. Bangor, 145p. [PdF file]
Davies, O. and Pommerening, A., 2008. The contribution of structural indices to the modelling of Sitka spruce (Picea sitchensis) and birch (Betula spp.) crowns. For. Ecol. Manage. 256, 68–77. [PdF file]
Crecente-Campo, F., Pommerening, A. and Rodríguez-Soalleiro, R., 2009. Impacts of thinning on structure, growth and risk of crown fire in a Pinus sylvestris L. plantation in northern Spain. For. Ecol. Manage. 257, 1945-1954. [PdF file]
Motz, K., Sterba, H. and Pommerening, A., 2010. Sampling measures of tree diversity. For. Ecol. Manage. 260, 1985–1996. [PdF file]
Pommerening, A., LeMay, V. and Stoyan, D., 2011. Model-based analysis of the influence of ecological processes on forest point pattern formation - A case study. Ecol. Model.. 222, 666-678. [PdF file]
Pommerening, A., Gonçalves, A. C. and Rodríguez-Soalleiro, R., 2011. Species mingling and diameter differentiation as second-order characteristics. Allg. Forst- u. J.-Ztg. 182, 115-129. [PdF file]
Gonçalves, A. C. and Pommerening, A., 2011. Spatial dynamics of cone production in Mediterranean climates: A case study of Pinus pinea L. in Portugal. For. Ecol. Manage. 266, 83–93. [PdF file]
Gadow, K. v., Zhang, C. Y., Wehenkel, C., Pommerening, A., Corral-Rivas, J., Korol, M., Myklush, S., Hui, G. Y., Kiviste, A. and Zhao, X. H., 2012. Forest structure and diversity, 29 - 83. In: Pukkala, T. and Gadow, K. v. (Eds.), 2012: Continuous cover forestry. 2nd edition. Managing Forest Ecosystems 23. Springer. Dordrecht, 296p. [PdF file]

Mingling distribution of beech (Fagus sylvatica L., red) and ash (Fraxinus excelsior L., green) in the mixed species woodland Södderich 55B (near Göttingen, Germany). A common situation in woodlands managed for valuable hardwoods: Whilst dominant ash trees mostly have neighbours of different species, the dominated beech trees are arranged in conspecific clusters. The mingling index was calculated with the R script TreeDiversityIndices.R‎.

System requirements

As with any Java application CRANCOD can be used on Windows, Linux and Macintosh computers:

  • Windows XP, Vista, 7
  • Mac OS X
  • Equivalent Linux version
  • Java Runtime Environment (JRE)

Installation

  1. Download the file Crancod.zip onto your computer and unzip it.
  2. Save the file Crancod.jar on your computer's desktop or in a dedicated target folder.
  3. If not previously installed download and install the Java Runtime Environment (JRE).
  4. Launch the CRANCOD program by double clicking on the file Crancod.jar.

Documentation

  • Download the user manual here.
  • Check out the (slightly) updated poster presentation of CRANCOD at the annual conference of the British Ecological Society in 2006.

Sample input files

The following data are from my management demonstration plot (MDP) 6 in Clocaenog Forest (North Wales) surveyed in 2004. This is an interesting site where a formerly mono-species Japanese larch plantation has gradually been colonised by Sitka spruce and other species (see the plot map at the top of this page).

Sample output files

These data also refer to MDP 6 in Clocaenog Forest (North Wales) surveyed in 2004.

Clg6_protocol.html is an HTML file and can be opened and viewed with any internet browser. All files with the extension *.out are ASCII files and can be opened and viewed in MS Excel.

A structural group of four trees in Clocaenog plot 6 with a Japanese larch in the centre and two Japanese larch and two Sitka pruce neighbours. Such groups form the basis of NNSS. The visualisation was computed in CRANCOD.
The characteristics of the Japanese larch tree in the centre of the structural group of four trees (see left-hand Figure) in Clocaenog plot 6. From CRANCOD.

R scripts

Some of the functionality of CRANCOD and other methods have also been implemented in the R language. When using R scripts from the list below for research purposes please acknowledge the author.


Additional text resources

Visitors of this website who are unfamiliar with the topic of forest structure analysis and forestry summary characteristics may want to read the following documents:

Feedback and cooperation

The developer of the CRANCOD software and the R scripts is particularly interested in feedback concerning any aspect of the program to improve its functionality and usefulness in future versions. Please report your feedback to arne.pommerening@bfh.ch. The author is very open to any kind of cooperation, particularly in terms of joint publications, and it would also be possible to manage CRANCOD as an open-source software with an international project team in the future.

Recent workshops and (summer) schools involving CRANCOD

  • Lectures on forest growth and yield at Göttingen University (Germany), 23 - 27 July 2012
  • "Analysing & Modelling Spatial Forest Structure – an Introduction" at Tartu University, Estonia, 8 - 12 October 2012

Disclaimer

The CRANCOD software, all its libraries and algorithms and the R scripts have been prepared with great care. However, neither the developer nor Bern University of Applied Sciences can be made liable in the unlikely case of damage caused to your computer while using CRANCOD or of incorrect outputs.

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