Species Occupancy Plot Viewer

This Shiny app has been designed to present the modelled outputs associated with the Data Paper entitled “Annual estimates of occupancy for bryophytes, lichens and invertebrates in the UK, 1970 – 2015” published in Scientific Data (full citation below). The dropdown selection boxes at the side of the page can be used to select the taxonomic group and a species of interest from the complete set of 5,293 species analysed by the authors. The aim here was to generate annual estimates of species occupancy from data collected by UK recording schemes and to assess trends and patterns of change over time. This data is freely available from the NERC EIDC repository.

Plots of estimates of annual occupancy and detection probabilities

The right-hand plot presents the model generated estimates of the probability of occurrence (ψ_it in equation 2 of the data paper) for the selected UK species. The coloured points represent the average occupancy for each year. Points are coloured blue if the model estimate is considered to have converged (i.e. an rhat value of less than 1.1) and are coloured red if the estimate is not considered to have converged (an rhat value greater than 1.1). The grey shaded area represents the uncertainty around the estimate in the form of the 95% credible interval. Grey points along the top of the plot represent those years with data contributing to the estimate in that year, years without data are estimated as a combination of a prior and data in the adjacent years. nrecs is the number of records of this species within the analysed dataset.

The left-hand plot presents the model generated estimates of the probability of detection (p_itv in equation 6 of the data paper) for each category of list length (1 record, 2-3 records or 4+ records). The solid lines present the average values with the shaded area representing the associated 95% credible intervals.

Please see the methods section of the data paper for more information on how these estimates were generated.

Species trend and associated data

The following table presents information associated with the selected species. This includes the group and species name, the number of years of data meeting the modelling criteria, the first and last year of data, the total number of records of this species used in the model run, the mean growth rate (calculated as the annual percentage growth rate) including the upper and lower credible intervals of this estimate and the associated precision. This data is also provided, for all species, within the dataset repository.

Additional information and guidance

Please note that these species level estimates were generated for use within aggregated multispecies indicators and not for interpretation at the single species level. Levels of confidence across estimates can vary so please use this information with care.

Outhwaite, C.L., Powney, G.D., August, T.A., Chandler, R.E., Rorke, S., Pescott, O., Harvey, M., Roy, H.E., Fox, R., Walker, K., Roy, D.B., Alexander, K., Ball, S., Bantock, T., Barber, T., Beckmann, B.C., Cook, T., Flanagan, J., Fowles, A., Hammond, P., Harvey, P., Hepper, D., Hubble, D., Kramer, J., Lee, P., MacAdam, C., Morris, R., Norris, A., Palmer, S., Plant, C., Simkin, J., Stubbs, A., Sutton, P., Telfer, M., Wallace, I. & Isaac, N.J.B. (2019) Annual estimates of occupancy for bryophytes, lichens and invertebrates in the UK (1970-2015). Scientific Data, 6, 1–12.

The dataset itself can be cited as follows: Outhwaite, C.L.; Powney, G.D.; August, T.A.; Chandler, R.E.; Rorke, S.; Pescott, O.; Harvey, M.; Roy, H.E.; Fox, R.; Walker, K.; Roy, D.B.; Alexander, K.; Ball, S.; Bantock, T.; Barber, T.; Beckmann, B.C.; Cook, T.; Flanagan, J.; Fowles, A.; Hammond, P.; Harvey, P.; Hepper, D.; Hubble, D.; Kramer, J.; Lee, P.; MacAdam, C.; Morris, R.; Norris, A.; Palmer, S.; Plant, C.; Simkin, J.; Stubbs, A.; Sutton, P.; Telfer, M.; Wallace, I.; Isaac, N.J.B. (2019). Annual estimates of occupancy for bryophytes, lichens and invertebrates in the UK (1970-2015). NERC Environmental Information Data Centre. https://doi.org/10.5285/0ec7e549-57d4-4e2d-b2d3-2199e1578d84