Tag-loss estimation

In 2005, we publish a new method to estimate tag-loss rate in double-tagging experiments.

This method is based on Capture-Mark-Recapture using time-at-liberty.

It was first published in:

Rivalan, P., Godfrey, M. H., Prévot-Julliard, A.-C. & Girondot, M. 2005. Maximum likelihood estimates of tag loss in leatherback sea turtles. Journal of Wildlife Management, 69, 540-548.

And the most recent update is published in:

Pfaller, J.B., Williams, K.L., Frick, M.G., Shamblin, B.M., Nairn, C.J., Girondot, M., 2019. Genetic determination of tag loss dynamics in nesting loggerhead turtles: A new chapter in “the tag loss problem”. Marine Biology 166, 97.

The original software is no more available because the method is now scripted in R as a set of functions within the package phenology available in CRAN.



From a global tests of many different methods, Venerus et al. (2013) conclude that:

«The RIVfull method was unbiased and performed best in all scenarios A–D, (median relative biases were less than 2%).»

This work has been cited by:

Briane J-P, Rivalan P, Girondot M (2007) The inverse problem applied to the Observed Clutch Frequency of Leatherbacks from Yalimapo beach, French Guiana. Chelonian Conserv Biol 6:63-69

Cheng IJ, Huang CT, Hung PY, Ke BZ and others (2009) Ten years of monitoring the nesting ecology of the green turtle, Chelonia mydas, on Lanyu (Orchid Island), Taiwan. Zool Stud 48:83-94

Ellison LE, O'Shea TJ, Neubaum DJ, Neubaum MA and others (2007) A comparison of conventional capture versus PIT reader techniques for estimating survival and capture probabilities of big brown bats (Eptesicus fuscus). Acta Chiropt 9:149-160

Fossette S, Kelle L, Girondot M, Goverse E and others (2008) The world's largest leatherback rookeries: A review of conservation-oriented research in French Guiana/Suriname and Gabon. J Exp Mar Biol Ecol 356:69-82

Georges JY, Fossette S (2006) Estimating body mass in the leatherback turtle Dermochelys coriacea. Marine Ecology Progress Series 318:255-262

Girondot M, Godfrey MH, Ponge L, Rivalan P (2007) Modeling approaches to quantify leatherback nesting trends in French Guiana and Suriname. Chelonian Conserv Biol 6:37-46

Heard GW, Scroggie MP, Malone B (2008) Visible implant alphanumeric tags as an alternative to toe-clipping for marking amphibians - a case study. Wildl Res 35:747-759

James MC, Sherrill-Mix SA, Myers RA (2007) Population characteristics and seasonal migrations of leatherback sea turtles at high latitudes. Marine Ecology Progress Series 337:245-254

Kendall WL, Converse SJ, Doherty PF, Naughton MB and others (2009) Sampling design considerations for demographic studies: a case of colonial seabirds. Ecol Appl 19:55-68

McMahon CR, White GC (2009) Tag loss probabilities are not independent: Assessing and quantifying the assumption of independent tag transition probabilities from direct observations. J Exp Mar Biol Ecol 372 36-42

Oosthuizen WC, Bester MN, de Bruyn PJN, Hofmeyr GJG (2009) Intra-archipelago moult dispersion of southern elephant seals at the Prince Edward Islands, southern Indian Ocean. Afr J Mar Sci 31:457-462

Ordonez C, Troeng S, Meylan A, Meylan P and others (2007) Chiriqui Beach, Panama, the most important leatherback nesting beach in Central America. Chelonian Conserv Biol 6:122-126

Pfaller, J.B., Williams, K.L., Frick, M.G., Shamblin, B.M., Nairn, C.J., Girondot, M., 2019. Genetic determination of tag loss dynamics in nesting loggerhead turtles: A new chapter in “the tag loss problem”. Marine Biology 166, 97.

Rivalan P, Pradel R, Choquet R, Girondot M and others (2006) Estimating clutch frequency in the sea turtle Dermochelys coriacea using stopover duration. Mar Ecol-Prog Ser 317:285-295

Rivalan P, Prévot-Julliard A-C, Choquet R, Pradel R and others (2005) Trade-off between current reproduction investment and delay until next reproduction in the leatherback sea turtle. Oecologia 145:564-574

Schwarz, L.K., Hindell, M.A., McMahon, C.R., Costa, D.P., 2012. The implications of assuming independent tag loss in southern elephant seals. Ecosphere 3, art81.

Tucker AD (2010) Nest site fidelity and clutch frequency of loggerhead turtles are better elucidated by satellite telemetry than by nocturnal tagging efforts: Implications for stock estimation. J Exp Mar Biol Ecol 383:48-55

Van Houtan K.S. & Halley J.M. (2011) Long-term climate forcing in loggerhead sea turtle nesting. PLoS One, 6: e19043.

Venerus, L.A., Irigoyen, A.J. & Parma, A.M. (2013) Assessment of biases in the estimation of tag shedding rates through a mark-resight experiment. Fisheries Research, 140, 133-148.

To be able to use the method in R, use:


install.packages("phenology")

install.packages("http://www.ese.u-psud.fr/epc/conservation/CRAN/HelpersMG.tar.gz", repos=NULL, type="source")

install.packages("http://www.ese.u-psud.fr/epc/conservation/CRAN/phenology.tar.gz", repos=NULL, type="source")


The functions to be used are:

Tagloss_LengthObs, Tagloss_L, Tagloss_daymax, Tagloss_fit, Tagloss_format, Tagloss_mcmc, Tagloss_model, Tagloss_simulate, logLik.Tagloss, plot.TaglossData, plot.Tagloss