RInSp-package: R Individual Specialization

In RInSp: R Individual Specialization

R Individual Specialization

Description

“R Individual Specialization” (RInSp) is an R package for analysing resource use data to calculate ecological measures of within-population niche variation based on data on individuals' resource use (e.g., stomach contents, repeated observations of prey choice or habitat use). The package implements several ecological niche metrics to measure individual and population niche width in order to measure individual specialization. This version of RInSp is able to compute Araujo's E, measures of clustering and pairwise similarity among individuals, IS, Petraitis' W, and Roughgarden's WIC/TNW, and an example of a measure of nestedness (NODF). For some of these indices Monte Carlo re-sampling procedures for testing significance are provided.

To cite package check the command CITATION or use:

Zaccarelli, N., Mancinelli, G. and Bolnick, D.I. (2013) RInSp: an R package for the analysis of individual specialisation in resource use. Methods in Ecology and Evolution, 4(11): 1018-1023, doi: 10.1111/2041-210X.12079

This package can be used on Mac, Windows and UNIX platforms, and on both i386 and x64 architectures. It is based on IndSpec1.0 developed by Prof. D. Bolnick (Bolnick et al. 2002), and on Dieta1 developed by Dr. M.A. Araujo (Araujo et al. 2008).

The original source code of IndSpec1.0 is available from the “Ecological Archives” of the Ecological Society of America (http://esapubs.org/archive/): identifier E083-056-S1; http://esapubs.org/archive/ecol/E083/056/. The original source code Dieta1 is available from the “Ecological Archives” of the Ecological Society of America (http://esapubs.org/archive/): identifier E089-115-A1; http://esapubs.org/archive/ecol/E089/115/.

Version 1.1 of the package fixes three issues:

1. in Eindex the case of highly specialised individuals is now handled correctly;

2. in like.Wi the probability for each value of Petraitis' W is properly handled;

3. in Emc the C code taken from Dieta1.c has been fixed for an error in the calculation of the weight matrix when highly specilised individuals are present.

Version 1.2.3 of the package has been changed to address the following things:

1. we introduce a filter to remove from the PS matrix all values which are lower than a set threshold (i.e., the parameter "precision"). In this way some interactions are removed due to their negligible weight in the PS matrix. The affected functions are: Eindex, Emc, PSicalc and the C code used for the resampling;

2. in Eindex users are now warned for cases of isolated individuals by means of a text message and by the value of the variable Isolation;

3. all progressbars are removed from all functions, so in case your problem is big have a little bit of patience;

4. now Eindex and Emc will work corectly with the Barrat index in case of isolated individuals;

5. Undefined global functions or variables are now properly registered in the NAMESPACE file;

6. native routines have been registered and symbol search has een disabled;

7. unprotected variables have been taken care of.

Version 1.2.4 of the package has been changed to address the following things:

1. import.RInSp has been fixed for an error affecting the subsetting;

2. in import.RInSp we have add some flexibility in defining the separator and the decimal character in input files;

3. all procedures have been revised to fix issues with the use of class(.).

Version 1.2.5 of the package has been changed to address some warnings during the CRAN check procedure.

The Authors thank for their help in imprving the package Miss Georgia Karoline Kosmala ([e-mail]), Miss Ambika Kamath ([e-mail]), Miss Isabel Fisk Baruque ([e-mail]), Mr Diogo B. Provete, and Dr. Marcio S. Araujo ([e-mail]).

Details

Package:	RInSp
Type:	Package
Version:	1.2.5
Date:	2022-05-18
License:	GPL (>= 2)

Author(s)

Dr. Nicola ZACCARELLI [e-mail],
Dr. Giorgio MANCINELLI [e-mail],
and Prof. Dan BOLNICK [e-mail]

References

Almeida-Neto M., Guimaraes P., Guimaraes P.R., Loyola R.D., and Ulrich W. 2008. A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos 117: 1227-1239.

Araujo M.S., Guimaraes Jr., P.R., Svanback, R., Pinheiro, A., Guimaraes P., dos Reis, S.F., and Bolnick, D.I. 2008. Network analysis reveals contrasting effects of intraspecific competition on individual vs. population diets. Ecology 89: 1981-1993.

Araujo M.A., Layman C., and Bolnick D.I. 2011. The ecological causes of individual specialization. Ecology Letters 14: 948-958.

Aversen. J.N. 1969. Jackknifing U-statistics. Annals of Mathematical Statistics 40: 2076-2100.

Barrat A., Barthelemy M., Pastor-Satorras R., and Vespignani A. 2004. The architecture of complex weighted networks. Proceedings of the National Academy of Sciences 101: 3747-3752

Bolnick, D.I., L.H. Yang, J.A. Fordyce, J.M. Davis, and Svanback, R. 2002. Measuring individual-level resource specialization. Ecology 83: 2936-2941.

Bolnick, D.I., and Paull, J.S. 2009. Morphological and dietary differences between individuals are weakly but positively correlated within a population of threespine Stickleback. Evolutionary Ecology Research 11: 1217-1233.

Onnela J.P., Saramaki J., Kertesz J., and Kaski K. 2005. Intensity and coherence of motifs in weighted complex networks. Physics Review E 71: 065103.

Roughgarden, J. 1974. Niche width: biogeographic patterns among Anolis lizard populations. American Naturalist 108: 429-411.

Saramaki J., Kivela M., Onnela J.P., Kaski K., and Kertesz J. 2007. Generalizations of the clustering coefficient to weighted complex networks. Physics Review E 75: 027105.

Schoener, T.W. 1968. The Anolis lizards of Bimini: resources partitioning in a complex fauna. Ecology 49: 704-726.

Zaccarelli, N., Bolnick, D.I., and Mancinelli, G. 2013. RInSp: an R package for the analysis of individual specialization in resource use. Methods in Ecology and Evolution 4: 1018-1023.

RInSp documentation built on May 20, 2022, 9:06 a.m.