cinid.table: Compute the larvae instar in an individual and a population...

Description Usage Arguments Details Value Author(s) References Examples

View source: R/cinid.table.R


This function assigns any larva with a known headcapsule width to the most probable instar among four possible ones in the focused Curculionid species. Estimating the larval instar is achieved by means of two distinct methods so-called "deterministic" and "stochastic", respectively.

Furthermore, from the population of larvae to be assigned to the most probable instar, both mean and standard deviation of the headcapsule width are estimated for each of the four larval instars, together with the relative frequency of the four instars in the original population.


cinid.table(HCW, mu4, sd4, threshold = 0.95, file = NULL, w = c(1, 1, 1, 1))



vector of individual HeadCapsule Width (HCW). The measures must be in micrometers. The 'NA' values are dismissed by the function.


estimated mean of the fourth instar. This parameter must be in micrometers. See 'Details'.


estimated standard deviation of the fourth instar. This parameter must be in micrometers. See 'Details'.


determination criterion. The value has to be set between 0.25 and 1. The default criterion is set as 0.95. See 'Details'.


a character string giving the name of the file where outputs are recorded. Two files are then created, a first one named file_indiv.txt and a second one named file_pop.txt. The NULL value set by default means that the outputs are not recorded


vector of instars' weight. By default, the hypothesis is that each instar has the same weight. If any knowledge about relative abundance of each instar is available, instar's weights can be adapted.


The quality of the estimated mu4 and sd4 passed to the function is not controlled. Therefore, these two values must be estimated from a quite large sample, and on larvae that ideally do not belong to the dataset.

The larval instar is considered to be correctly assigned to an individual whenever the greatest value of the four relative probabilities computed is higher than the threshold. A threshold equal to 0.25 corresponds to a randomly assigned instar. A threshold equal to 0.95 means that the relative probability of the assigned instar must be higher or equal than 0.95.


The returned value is a list of two elements :


data.frame with eleven values (in column) for each Curculionid individual larva (in row). The columns are the observed headcapsule width (HCW), the larval instar estimated with the deterministic method (instar_determ) and with the stochastic one (instar_stoch), the probability (p) and relative density (rd) to belong to the first, second, third and fourth larval instar.


matrix with six parameters (in row) for the first, second, third, fourth and indetermined larval instar (in column). The rows are the estimated mean (mu) and standard deviation (sd) of the headcapsule width distribution, the number of individuals and frequency estimated with both the deterministic method (N_determin and F_determ) and the stochastic one (N_stoch and F_stoch).


Aurelie Siberchicot, Adrien Merville, Marie-Claude Bel-Venner and Samuel Venner


Merville A., Vallier A., Venner S., Siberchicot A., Fouchet D., Heddi A. and Bel-Venner M.-C. (2014). Determining the instar of a weevil larva (Coleoptera:Curculionidae) using a parsimonious method. European Journal of Entomology. 111(4): 567-573. doi: 10.14411/eje.2014.056


soryzae <- s.oryzae$data
mu4.soryzae <- s.oryzae$mu4
sd4.soryzae <- s.oryzae$sd4

HCW.soryzae <- cinid.table(soryzae, mu4 = mu4.soryzae, sd4 = sd4.soryzae)

Example output

  HCW instar_determ instar_stoch     p1    p2 p3 p4    rd1    rd2 rd3 rd4
1 228             1            1 0.7546 0e+00  0  0 0.9999 0.0001   0   0
2 241             1            1 0.3103 4e-04  0  0 0.9968 0.0032   0   0
3 226             1            1 0.8379 0e+00  0  0 0.9999 0.0001   0   0
4 175             1            1 0.0108 0e+00  0  0 1.0000 0.0000   0   0
5 201             1            1 0.2520 0e+00  0  0 1.0000 0.0000   0   0
6 201             1            1 0.2520 0e+00  0  0 1.0000 0.0000   0   0
          Instar1   Instar2   Instar3  Instar4 InstarIndet
mu       222.2120 304.97200 440.51700 589.0000          NA
sd        18.5160  18.08503  20.97657  24.4300          NA
N_determ  17.0000  20.00000  20.00000  40.0000           0
F_determ   0.1753   0.20620   0.20620   0.4124           0
N_stoch   17.0000  20.00000  20.00000  40.0000           0
F_stoch    0.1753   0.20620   0.20620   0.4124           0

CINID documentation built on July 8, 2020, 5:16 p.m.