b1_indicator_instructions_output.Rmd
The results folder created from running the analysis scripts on the B1 abundance data contains the following six folders
These two folders contains both the species folders with the relative abundance species trends plots for each OSPAR region and birds subdivision and the traffic light plots for the OSPAR regions and OSPAR I and II bird subdivisions, for both the breeding and non-breeding species.
The traffic light plot displays the latest species’ six year means compared to the upper and species’ thresholds using three colours
Dark green - latest six year mean above upper threshold of 1.3.
Light green - latest six year mean between upper threshold and species threshold of either 0.7 (species laying more than one egg) or 0.8 (species laying one egg).
Red - latest six year mean below species threshold of either 0.7 or 0.8.
Comparision of the latest threshold status to the status in 2014 is shown using arrows thickness and direction in the traffic light plots
vertical thick arrow pointing down for latest change from above upper threshold to below species threshold.
vertical thin arrow pointing down for either latest change from above upper threshold to between threshold or between thresholds to below species threshold.
vertical thin arrow pointing up for either latest change from below species threshold to between thresholds or between thresholds to above upper threshold.
vertical thick arrow pointing up for latest change below threshold to above upper threshold.
These two folder contain the “Residuals Vs Fitted” and “Normal Q-Q” plots generated by the log-linear model used to calculate the baseline value. The plots are contained in separate species folders as well as collated in a html table. A summary of the log-linear regression model, including p-values, baseline_count and first relative abundance value is provided in a setting baseline csv file.
This folder contains the trend plots of the proportion of species with six year relative abundance means above the species thresholds, for each OSPAR regions, breeding and non-breeding (wintering) species
The data underlying the plots are contained with the folders in the EMECO_checks folder.
OSPARxx_unsm_all csv files containing the species yearly relative abundance values for each OSPAR region and birds subdivision. (used in the species trend plots)
OSPAR_xx_unsum_all_mean csv files containing the species relative abundance six year geometric mean values for each OSPAR region and birds subdivision. (used in the species trend plots)
Breeding Seabirds Indicator Latest Six Year Mean csv file containing latest relative abundance six year means for each species in each OSPAR region and birds subdivision, along with their number of eggs laid and functional group. (used in traffic light plots)
Breeding Seabirds Indicator 2014 Six Year Mean csv file containing 2014 relative abundance six year means for each species in each OSPAR region and birds subdivision, along with their number of eggs laid and functional group. (used in traffic light plots)
OSPAR_xx Six Year Mean Abundance Values csv files for each OSPAR region containing yearly relative abundance six year mean values for each species (used in trend plots of the proportion of species with six year relative abundance means above the species thresholds)
WinteringWaterbird_RegionalIndices csv file containing the species yearly relative abundance values for each OSPAR region and birds subdivision. (used in the species trend plots).
WinteringWaterbird_RegionalIndices_mean csv file containing the species relative abundance six year geometric mean values for each OSPAR region and birds subdivision. (used in the species trend plots).
Wintering Seabirds Indicator Latest Six Year Mean csv file containing latest relative abundance six year means for each species in each OSPAR region and birds subdivision, along with their number of eggs laid and functional group. (used in traffic light plots).
Wintering Seabirds Indicator 2014 Six Year Mean csv file containing 2014 relative abundance six year means for each species in each OSPAR region and birds subdivision, along with their number of eggs laid and functional group. (used in traffic light plots).
OSPARxx Wintering Waterbirds Six Year Mean Abundance Values csv files for each OSPAR region containing yearly relative abundance six year mean values for each species (used in trend plots of the proportion of species with six year relative abundance means above the species thresholds)
Proportion All Species Achieving GES csv file containing the proportion of species with latest relative abundance six year mean above species thresholds (used in Trends_All plot).
Proportion Breeding Species Achieving GES csv file containing the proportion of species with latest relative abundance six year mean above species thresholds (used in Trends_Breeding plot).
Proportion Wintering Species Achieving GES csv file containing the proportion of species with latest relative abundance six year mean above species thresholds (used in Trends_Wintering plot).
Proportion OSPARxx Species Achieving GES csv files containing the proportion of species with latest relative abundance six year mean above species thresholds, for each OSPAR region (used in Trends_OSPARxx plots).
Functional Group Assessment Table csv file percentage of species with latest relative abundance six year mean above species thresholds, for both breeding and non-breeding species, for each functional groups and OSPAR regions and bird subdivisions (values for functional group assessment table).
The EMECO checks folder also contains the results from applying the weighting values containing the source weighting year, weighting value and imputated counts for that source year provided by the countries for each species in the each OSPAR regions and birds subdivision.
RegionalWeightingsForBreedingCounts csv file calculated weighting proportions for breeding species.
RegionalWeightingsForWinteringCounts csv file calculated weighting proportions for non-breeding species.