In condwanaland/nebula:

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(nebula)

We present

While other software Some includes Image Pro Premier with the OtolithM app, or ImageJ.

While Image Pro Premier and OtolithM present a full featured software suite for otolith analysis, its closed source nature and associated license cost fundamentally limit who can access it. While an academic institution may have a license, it will often still be restricted to a set of computers in a specified location.

In addition, the output format of Image Pro is not conducive to immediate analysis. Most otolith analyses will require data to be in Tidy format with columns for otolith id, increment number, increment distance, and increment position. While other metadata may be necessary, this format covers allows the simplest entry into comparative age and growth plots, and modelling.

example_data <- data.frame(
                stringsAsFactors = FALSE,
                      otolith_id = c("X1","X1","X1","X1",
                                     "X1","X2","X2","X2","X2","X2"),
                increment_number = c(0L, 1L, 2L, 3L, 4L, 0L, 1L, 2L, 3L, 4L),
              increment_distance = c(7.163,1.076,2.189,2.67,
                                     2.564,3.544,2.74,2.602,2.107,2.985),
              increment_position = c(7.163,8.239,10.428,
                                     13.098,15.662,3.544,6.284,8.886,10.993,13.977)
            )

example_data

Here otolith_id is, increment_number counts subsequent rings (and therefore is representative of 'age'), increment_distance measures the distance from the current ring to the previous ring, and increment_position measures the distance from the current ring to the otolith annulus (centre)

Note that each otolith starts with an increment_number of 0 - this is because the first marker should be placed at the otolith annulus.