Quantitative Estimates of Small Ectotherm Temperature Regulation Effectiveness

Easy and rapid quantitative estimation of small terrestrial ectotherm temperature regulation effectiveness in R. ectotemp is built on classical formulas that evaluate temperature regulation by means of various indices, inaugurated by Hertz et al. (1993) . Options for bootstrapping and permutation testing are included to test hypotheses about divergence between organisms, species or populations.


ectotemp

Easy and rapid quantitative estimation of small terrestrial ectotherm temperature regulation effectiveness in R.

ectotemp consists of a modest function library that can be used to evaluate temperature regulation effectivenes in small terrestrial ectotherms, once data describing field-active body temperatures (Tb), environmental (operative) temperatures (Te) and preferred temperatures (the set-point range, Tset) have been collected. To this aim, ectotemp builds on classical work by Hertz et al. (1993, and references therein), Christian and Weavers (1996), and Blouin-Demers and Weatherhead (2001). Options for bootstrapping and permutation testing are included to test hypotheses about divergence between organisms, species or populations. Users of this package do not need to be particularly experienced in R, but are expected to be familiar with the background, appropriate choice, and caveats of the available functions (Hertz et al. 1993, Christian and Weavers 1996, Wills and Beaupre 2000, Blouin-Demers and Nadeau 2005).

Ectotemp provides functions for the following types of analyses:

  • The thermal quality of the habitat (de) and associated descriptive statistics, which estimate the degree to which environmental temperature matches the set-point range;

  • The accuracy of temperature regulation (db) and associated descriptive statistics, which estimate the degree to which ectotherms experience body temperature outside of their set-point range;

  • Choice between several approaches to calculate effectiveness of temperature regulation (E), including bootstrap resampling of the original distributions of Tb and Te to determine confidence interval for the mean, and permutation tests for between-population or species comparisons;

  • Exploitation of the thermal environment (Ex); the amount of time when field body temperatures (Tb) are within the set-point range, relative to the total amount of time during which this could have been possible as indicated by operative temperatures (Te).

Installation

The released version of ectotemp can be installed from CRAN with:

install.packages("ectotemp")

Or the latest, development version from GitHub with:

library(devtools)
install_github("wouterbeukema/ectotemp")

Examples

Analyse
Output summary of bootstrap_E, which combines operative and body temperature data (Te, Tb) and the bounds of the set-point range (predetermined values, 19.35°C and 26.44°C in the example below) with the desired method to estimate thermoregulation effectiveness (E; either ‘hertz’ or ‘blouin’), and the number of bootstrap samples drawn with replacement (10.000 in the example below). The output consists of the mean, its 95% confidence interval, and the full list of obtained E values.

>head(E_bootstrapped$'Confidence Interval')
$`mean`
[1] 2.930867
$lower
[1] 2.918643
$upper
[1] 2.943091

Compare
Permutation testing to compare the effectiveness of thermoregulation (E) between populations or species. The function compare_E relies on similar input information as in the above example. First, an empirical value that describes the actual difference in E between two entities is calculated, which is subsequently compared to a null distribution obtained through sampling without replacement from the pooled Te and Tb values of both entities. The output includes permutation test results and a graphical overview of the empirical difference in E along with the permuted null distribution.

 
>E_diff <- compare_E(datasp1, datasp2,
                  19.35, 26.44, 
                  14.44, 18.33,
                  'blouin',
                  10000)
>E_diff
$`Empirical difference in E`
[1] 3.256671
 
$`p value`
[1] 0.001

References

Blouin-Demers, G., & Weatherhead, P. J. (2001). Thermal ecology of black rat snakes (Elaphe obsoleta) in a thermally challenging environment. Ecology, 82(11), 3025-3043.
Blouin-Demers, G., & Nadeau, P. (2005). The cost-benefit model of thermoregulation does not predict lizard thermoregulatory behavior. Ecology, 86(3), 560-566.
Christian, K. A., & Weavers, B. W. (1996). Thermoregulation of monitor lizards in Australia: an evaluation of methods in thermal biology. Ecological monographs, 66(2), 139-157.
Hertz, P. E., Huey, R. B., & Stevenson, R. D. (1993). Evaluating temperature regulation by field-active ectotherms: the fallacy of the inappropriate question. The American Naturalist, 142(5), 796-818.
Wills, C. A., & Beaupre, S. J. (2000). An application of randomization for detecting evidence of thermoregulation in timber rattlesnakes (Crotalus horridus) from northwest Arkansas. Physiological and Biochemical Zoology, 73(3), 325-334.

News

ectotemp 0.1.2

  • Added examples (incl. figure) and badges to README.md; formatted all formula abbreviations correctly.

  • Fixed an error that hindered the compare_E function when the species to be compared were characterised by inequal amounts of Te values.

ectotemp 0.1.1

  • Fixed typos in DESCRIPTION, added additional information to this file and changed the title field to title case.

  • Released by CRAN.

ectotemp 0.1.0

  • Initial release of the ectotemp package

Reference manual

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install.packages("ectotemp")

0.1.2 by Wouter Beukema, 4 months ago


https://CRAN.R-project.org/package=ectotemp


Report a bug at https://github.com/wouterbeukema/ectotemp/issues


Browse source code at https://github.com/cran/ectotemp


Authors: Wouter Beukema [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports dplyr, psych, stats, graphics


See at CRAN