DOI: 10.5061/dryad.tqjq2bw63
title: Estimating the global population size and highlighting conservation priority areas for the endangered Titicaca grebe

description: The Titicaca grebe (Rollandia microptera) is a poorly studied endangered
 species, only found in the Lake Titicaca watershed of Peru and Bolivia.
 Population surveys undertaken in the early twenty-first century suggested
 that the species had declined in number by &gt;70%. We conducted a
 population survey of the grebe between March and August 2022 in Peru and
 Bolivia, using both maximum entropy and Bayesian occupancy models to
 estimate factors affecting habitat suitability for the grebe. We conducted
 surveys between March and August 2022 in Peru and Bolivia. Contrary to the
 International Union for Conservation of Nature (IUCN) population estimates
 of &lt;1,000 individuals, there are likely tens of thousands of
 individual grebes. The population estimation was sensitive to the type of
 model used. Distance from shore and fishing intensity were the most
 significant factors influencing grebe populations. The Reserva Nacional
 del Titicaca, the only protected area in the lake, covers some of the most
 suitable Titicaca grebe habitat across its entire range.  The
 population of the Titicaca grebe is significantly higher than previous
 estimates, but we do not recommend a change to its conservation status
 because of the lack of conservation efforts for this species, and the
 long-term risks associated with global warming and fisheries bycatch.
description: # Estimating the Global Population Size and Highlighting Conservation
 Priority Areas for the Endangered Titicaca Grebe
 [https://doi.org/10.5061/dryad.tqjq2bw63](https://doi.org/10.5061/dryad.tqjq2bw63) ## Description of the data and file structure This is supplemental material of the article "Estimating the Global Population Size and Highlighting Conservation Priority Areas for the Endangered Titicaca Grebe" This includes the R code used in this analysis, the population data, and the rasters which were produced as part of the output. It also includes a word document with a link to the function used to convert continous rasters to binary rasters which is referenced in the text, but not in the bibliography as it was published as part of a blog rather than as part of a published R package. ## File Explanations `Rollandia_microptera_points_rounded.csv` - rounded data points of the locations of Titicaca Grebes observed in this study. The locations have been rounded due to the species' endangered status ### Data Inputs #### On Dryad `R._microptera_Occupancy_Model_All_Input_Data.xlsx` - Data inputs used for the Occupancy Model.  * Column A - names of locations * Species - Scientific name of the Titicaca Grebe * V1, V2, V3 - whether the Titicaca Grebe was observed in this survey  * Vegetation - % of pixel covered by totora * Distance_tiol_Park - Distance to the Reserva Nacional del Titicaca, in metres * Distance_Shore - distance to the lakeshore,  in metres * Distance_Village - Distance to the nearest habitable place,  in metres * Distance_Cages - Distance from pisciculture,  in metres * Nets - No. of fishing nets observed  * Fish_Cages - No. of fish cages observed  * Cages_Present_Biry - Binary as to whether fish cages are in the pixel  * Fishing_Intensity - Pixel value in the probability of fisheries rasters  * Water_Depth - Depth in metres of the lake  * det.covs.Time_Start. - 3 columns, number of minutes since midnight when survey started* * det.covs.Duration - 3 columns, duration in minutes of the survey * * det.covs.Survey_Party - 3 columns, survey party involved* * det.covs.day - 3 columns, number of days since the start of the year of survey * * det.covs.Transect_Length - 3 columns, length of transect in km * * Lat_Start - Latitude of the start of the survey  * Lat_End - Latitude of the end of the survey  * Long_Start - Longitude of the start of the survey * Long_End - Longitude of the end of the survey  * coords.x & coords.y - midpoint of the survey  *Note that all  det.covs, or detection covariates, are in three columns to represent the (up to) three repeated surveys of each site  null indicates no survey occurred `Grebe_Surveys_not_Used_in_Analysis.xlsx` - surveys not included in the analysis outside of Lake Titicaca #### On Zenodo (found in Supplementary Information link) `Rollandia_microptera_Totora_1km_only.png & Totora_1km.asc`- Totora raster `Rollandia_microptera_Distance_Shore_1km_only.png`  & `Distance_Shore_1km.asc`- distance from shore raster `Rollandia_microptera_Distance_Cages_1km_only.png` & `Cages_Present_1km.asc` - distance from cages raster `Rollandia_microptera_Distance_Settlement_1km_only.png` & `Distance_Settlement_1km.asc` - distance from settlements raster `Rollandia_microptera_Bathymetry_1km_only.png` & `Bathymetry_1km.asc` - water depth raster `Rollandia_microptera_Fishing_Intensity_only.png` & `Fishing_Intensity.asc`- probability of fisheries raster `Distance_Protected_Area_1km.asc` - Distance to protected area raster ### Code and Calculations (found in Supplementary Information and Software links) `PopDensityCalcs.xlsx` - Population density calculations `Morrow_Function_Link.docx` - link to blogpost where function I used in my own code originated from  `code-jwd.R`, `Grebe_Thresholding.R`, `Example_spOccupancy.R`- code used in the analysis, with explanatory notes in the code ### Data Outputs (found in Supplementary Information link) `GrebeOccupancyRaster.tif` and `Occupany_Map.png`- raster of the occupancy model results  `Fifty_Percent_Occupany_Minimum_threshold_Map.tif` - Binary Occupancy Map with 50% cutoff  `Fifty_Percent_MaxEnt_Minimum_threshold_Map.tif` - Binary MaxEnt Map with 50% cutoff `BinaryOccupany_Minimum_threshold_Map.tif` - Binary Occupancy Map with minimum presence cutoff `BinaryMaxEnt_Minimum_threshold_Map.tif` - Binary MaxEnt Map with minimum presence cutoff `SD_Occurance_Map.png` - Standard Deviation of Occupancy Map predictions `AbundanceMaps.png & NMixMap.tiff` - N-mixture map results