Dataset for: Bedding scale correlation on Mars in western Arabia Terra

A.M. Annex et al.

Data Product Overview

This repository contains all source data for the publication. Below is a description of each general data product type, software that can load the data, and a list of the file names along with the short description of the data product.

HiRISE Digital Elevation Models (DEMs).

HiRISE DEMs produced using the Ames Stereo Pipeline are in geotiff format ending with ‘*X_0_DEM-adj.tif’, the “X” prefix denotes the spatial resolution of the data product in meters. Geotiff files are able to be read by free GIS software like QGIS.

HiRISE map-projected imagery (DRGs).

Map-projected HiRISE images produced using the Ames Stereo Pipeline are in geotiff format ending with ‘*0_Y_DRG-cog.tif’, the “Y” prefix denotes the spatial resolution of the data product in centimeters. Geotiff files are able to be read by free GIS software like QGIS. The DRG files are formatted as COG-geotiffs for enhanced compression and ease of use.

3D Topography files (.ply).

Traingular Mesh versions of the HiRISE/CTX topography data used for 3D figures in “.ply” format. Meshes are greatly geometrically simplified from source files. Topography files can be loaded in a variety of open source tools like ParaView and Meshlab. Textures can be applied using embedded texture coordinates.

3D Geological Model outputs (.vtk)

VTK 3D file format files of model output over the spatial domain of each study site. VTK files can be loaded by ParaView open source software. The “block” files contain the model evaluation over a regular grid over the model extent. The “surfaces” files contain just the bedding surfaces as interpolated from the “block” files using the marching cubes algorithm.

Geological Model geologic maps (geologic_map.tif).

Geologic maps from geological models are standard geotiffs readable by conventional GIS software. The maximum value for each geologic map is the “no-data” value for the map. Geologic maps are calculated at a lower resolution than the topography data for storage efficiency.

Beds Geopackage File (.gpkg).

Geopackage vector data file containing all mapped layers and associated metadata including dip corrected bed thickness as well as WKB encoded 3D linestrings representing the sampled topography data to which the bedding orientations were fit. Geopackage files can be read using GIS software like QGIS and ArcGIS as well as the OGR/GDAL suite. A full description of each column in the file is provided below.

Column	Type	Description
uuid	String	unique identifier
stratum_order	Real	0-indexed bed order
section	Real	section number
layer_id	Real	bed number/index
layer_id_bk	Real	unused backup bed number/index
source_raster	String	dem file path used
raster	String	dem file name
gsd	Real	ground sampling distant for dem
wkn	String	well known name for dem
rtype	String	raster type
minx	Real	minimum x position of trace in dem crs
miny	Real	minimum y position of trace in dem crs
maxx	Real	maximum x position of trace in dem crs
maxy	Real	maximum y position of trace in dem crs
method	String	internal interpolation method
sl	Real	slope in degrees
az	Real	azimuth in degrees
error	Real	maximum error ellipse angle
stdr	Real	standard deviation of the residuals
semr	Real	standard error of the residuals
X	Real	mean x position in CRS
Y	Real	mean y position in CRS
Z	Real	mean z position in CRS
b1	Real	plane coefficient 1
b2	Real	plane coefficient 2
b3	Real	plane coefficient 3
b1_se	Real	standard error plane coefficient 1
b2_se	Real	standard error plane coefficient 2
b3_se	Real	standard error plane coefficient 3
b1_ci_low	Real	plane coefficient 1 95% confidence interval low
b1_ci_high	Real	plane coefficient 1 95% confidence interval high
b2_ci_low	Real	plane coefficient 2 95% confidence interval low
b2_ci_high	Real	plane coefficient 2 95% confidence interval high
b3_ci_low	Real	plane coefficient 3 95% confidence interval low
b3_ci_high	Real	plane coefficient 3 95% confidence interval high
pca_ev_1	Real	pca explained variance ratio pc 1
pca_ev_2	Real	pca explained variance ratio pc 2
pca_ev_3	Real	pca explained variance ratio pc 3
condition_number	Real	condition number for regression
n	Integer64	number of data points used in regression
rls	Integer(Boolean)	unused flag
demeaned_regressions	Integer(Boolean)	centering indicator
meansl	Real	mean section slope
meanaz	Real	mean section azimuth
angular_error	Real	angular error for section
mB_1	Real	mean plane coefficient 1 for section
mB_2	Real	mean plane coefficient 2 for section
mB_3	Real	mean plane coefficient 3 for section
R	Real	mean plane normal orientation vector magnitude
num_valid	Integer64	number of valid planes in section
meanc	Real	mean stratigraphic position
medianc	Real	median stratigraphic position
stdc	Real	standard deviation of stratigraphic index
stec	Real	standard error of stratigraphic index
was_monotonic_increasing_layer_id	Integer(Boolean)	monotonic layer_id after projection to stratigraphic index
was_monotonic_increasing_meanc	Integer(Boolean)	monotonic meanc after projection to stratigraphic index
was_monotonic_increasing_z	Integer(Boolean)	monotonic z increasing after projection to stratigraphic index
meanc_l3sigma_std	Real	lower 3-sigma meanc standard deviation
meanc_u3sigma_std	Real	upper 3-sigma meanc standard deviation
meanc_l2sigma_sem	Real	lower 3-sigma meanc standard error
meanc_u2sigma_sem	Real	upper 3-sigma meanc standard error
thickness	Real	difference in meanc
thickness_fromz	Real	difference in Z value
dip_cor	Real	dip correction
dc_thick	Real	thickness after dip correction
dc_thick_fromz	Real	z thickness after dip correction
dc_thick_dev	Integer(Boolean)	dc_thick <= total mean dc_thick
dc_thick_fromz_dev	Integer(Boolean)	dc_thick <= total mean dc_thick_fromz
thickness_fromz_dev	Integer(Boolean)	dc_thick <= total mean thickness_fromz
dc_thick_dev_bg	Integer(Boolean)	dc_thick <= section mean dc_thick
dc_thick_fromz_dev_bg	Integer(Boolean)	dc_thick <= section mean

A spot height identifies the elevation (z value) above sea level of natural and man-made geographic features. It includes: * spot heights * vertical control points * water level/lake elevations Instructions for downloading this dataset: * select the link below and scroll down the metadata record page until you find Transfer Options in the Distribution Information section * select the link beside the Data for download label * you must provide your name, organization and email address in order to access the dataset This product requires the use of GIS software. *[GIS]: geographic information system

A spot height identifies the elevation (z value) above sea level of natural and man-made geographic features. It includes: * spot heights * vertical control points * water level/lake elevations This product requires the use of GIS software. *[GIS]: geographic information system

This data set represents a series of 502 mixed-species bird flock compositions, and derived taxonomic, functional, and phylogenetic diversity indices, that were gathered along a gradient of forest fragment sizes (range = 10-173 ha) in the Colombian Western Andes. We sampled mixed-species flocks using transect surveys along 14 transects in 8 fragments and a continuous forest reference site in the same landscape and at the same elevation (~1900-2200 m.a.s.l.). We also used buffer analysis to quantify the proportion of forest cover and forest edge within 1 km of each transect, and calculated local vegetation density and complexity, as well as distance from edge, for each 100-meter transect segment (n = 70 segments). Flock composition data observed on a transect were used to calculate overall species richness and flock size as well as two indices of functional and phylogenetic diversity; we calculated the stadardized effect size (SES) of each measure to account for the correlation between these measures and species richness. We also provide the raw counts of each species for each flock composition. These data were used for the analyses in Jones and Robinson (2020).

Methods Study System and Sites

We conducted all fieldwork in subtropical humid forests located within the municipality of El Cairo, Valle del Cauca department in Colombia. The study region is part of the Serrania de los Paraguas in the Western Andes mountain range, a center of avian threatened species diversity and endemism within Colombia. The study landscape in this municipality consists of a patchwork of forest fragments embedded in a matrix of cattle pasture, regenerating scrub, and coffee farms. Within this landscape, we selected eight fragments representing a gradient in patch sizes (range 10 to 170 ha). Sites are in the same altitudinal belt (1900-2200 m.a.s.l.) and matrix type (cattle pasture) to control for effects of altitude and matrix type on flock size and composition. Within-patch disturbance is common in fragmented Andean forests in Colombia, particularly illegal selective logging, which in our landscape typically occurred as removal of select old-growth trees for lumber by landowners; logging histories varied considerably from historical to ongoing, and extensive to limited, both within and between patches. We established 500-meter transects through forest interior (n = 14 total transects) which were opportunistically placed on existing trails, at variable distances from the edge of the fragments. We further divided each transect into 100-meter segments to account for heterogeneity in vegetation structure within transects. We accounted for edge effects by measuring the distance to forest edge of each transect segment.

We stratified forest fragments into large (≥ 100 ha), medium (~30-50 ha), and small (≤ 20 ha) size categories and selected a minimum of two replicates of each; these represent the range of fragment sizes available in our study landscape. We also included a non-fragmented reference site (Reserva Natural Comunitária Cerro El Inglés, ~750 ha) connected to over 10,000 ha of continuous forest to the north and west along the spine of the Serranía de los Paraguas. We only selected fragments with primary or late-successional secondary forest; vegetation structure and canopy height varied substantially between patches based on intensities of selective logging and land-use histories (see above). Fragments were all separated by ≥ 100 meters to minimize among-patch movement of birds, and all transects in different fragments were at least 250 meters apart.

Transect Surveys for Mixed-species Flocks

We performed transect surveys for mixed-species flocks, adapted from Goodale et al. (2014), in forest fragments from June-August 2017 (boreal migrants absent) and January-March 2018 (boreal migrants present). Both sampling periods corresponded to a dry season in the Western Andes, which has a bimodal two-dry, two-wet seasonality pattern. For each transect, we spent two and a half sequential field days performing continuous transect surveys; we conducted surveys in small fragments, large fragments, and continuous forest sites in random order to avoid a temporal bias in sampling. Surveys were distributed across the morning (7:30-11:30) and evening (15:00-17:30) hours. Transects were walked slowly and continuously by 2-3 observers, including local birdwatchers familiar with all species (Harrison Jones present for all surveys); flocking birds were identified by both sight and sound. When we encountered a flock, we noted the time of day and transect segment in which it was observed and spent up to a maximum of 45 minutes characterizing it with 10x binoculars. At least 5 minutes were spent with each flock, following it if possible. Because detection of species in flocks was imperfect, we only included a flock observation in the analysis if we felt that at least 80% of the individuals were observed (e.g. after spending several minutes of continuous observation at the end of the survey period without observing a new species or individual); incomplete flock observations were not included in analyses. We feel that our survey methodology accurately described flock composition because birds moved and called frequently in flocks, leading to high detectability. We noted the start and end time of each survey, and the presence of incomplete flocks to calculate flock encounter rate. We also supplemented the transect surveys with data from flocks opportunistically observed on a transect while performing other fieldwork. Some flocks in the data set represent flock compositions recorded near but not on a transect; these compositions have no associated transect segment.

Calculation of Landscape-level Variables

    We obtained landscape-level variables for analyses using geographic information software (GIS) analysis in ArcGIS (ArcMap 10.3.1; Esri; Redlands, CA). To quantify landscape composition and configuration, we buffered each transect (n = 14) by 1 km; buffers extended from the entire length of the transect. We then calculated measures of landscape composition and configuration using a recent land-cover/use categorization made by the Corporación Autónoma Regional del Valle del Cauca, converted to a 25-m cell-size raster. To quantify landscape composition, we calculated percentages of the forest-cover type within each buffer using the ‘isectpolyrst’ tool in Geospatial Modelling Environment (version 0.7.4.0). We measured landscape configuration for each transect as edge density, or length of all forest edges (in meters) divided by total buffer area (in hectares). The distance to edge was calculated in meters for each 100-meter transect segment (n = 70) as the shortest straight-line distance between the center point of the segment and the nearest edge of the fragment. 

Vegetation Measurements and Principal Component Analysis

    We measured vegetation structure in each 100-m transect segment used for flock sampling. Vegetation measurements were made from June-August 2017; based on our observations of vegetation, we assumed variation between the two sampling periods was minimal. We used the sampling methodology of James and Shugart (1970), following the modifications made by Stratford and Stouffer (2013), and further modified to be used with belt transects. Broadly, the methodology comprises two components for every 100-meter transect segment: (1) the quantification of canopy cover, ground cover, canopy height, and foliage height diversity of vegetation using point sampling every 10 meters and (2) the quantification of shrub, vine, fern, palm, and tree fern and tree density using 3 meter-wide belt sampling.

For the point sampling, we measured eight variables at ten-meter intervals, for 10 points per 100-meter segment. As a measure of foliage height diversity along the transect, we noted the presence or absence of live vegetation at five heights: <0.5 m, >0.5–3 m, >3–10 m, >10–20 m, and >20 m. Above 3 meters, we used a rangefinder to determine heights while sighting through a tube with crosshairs. Canopy and ground cover were calculated to the nearest 1/8th of the field of view by sighting through a vertical canopy densiometer (GRS Densiometer, Geographic Resource Solutions, Arcata, CA). For each segment, we averaged values for canopy cover, and ground cover, and calculated the proportion of points at which vegetation was present for each height category. For the belt transect sampling, we surveyed vegetation along the same transects and calculated densities for each 100-m transect interval. We counted all shrubs, vines, ferns, tree ferns, and palms encountered on 1.5 meters to either side. Secondly, we counted all trees (woody vegetation > 2 m in height) within 1.5 meters of the transect and measured their diameter at breast height (DBH). Trees were later categorized into six DBH size classes for analysis: 1-7 cm, 8-15 cm, 16-23 cm, 24-30 cm, 31-50 cm, and > 50 cm. We additionally recorded the largest tree’s DBH.

    To quantify foliage height diversity, we calculated the Shannon Diversity Index of the proportion of points with vegetation present in each of the five height bands for each segment (n = 70 segments). To reduce redundancy and minimize correlation between variables, we (separately) ordinated our tree DBH and understory plant density data using principal component analysis (PCA: McGarigal et al. 2000) for each 100-meter transect segment. We column (Z score) standardized data prior to ordination to account for differences in the units of measurement and used the covariance matrix to run the PCA. The principal components were interpreted using the significance of the principal component loadings. The PCA was run in R (version 3.5.1) using the princomp function in the stats package. The Shannon Index was calculated using the diversity function of the vegan package

This data shows areas where survey leg report and bathymetry, backscatter and sub-bottom profile data exists and allows you to download the data. The data was collected between 1996 and 2021.Bathymetry is the measurement of how deep is the sea. Bathymetry is the study of the shape and features of the seabed. The name comes from Greek words meaning "deep" and “measure". Bathymetry is collected on board boats working at sea and airplanes over land and coastline. The boats use special equipment called a multibeam echosounder. A multibeam echosounder is a type of sonar that is used to map the seabed. Sound waves are emitted in a fan shape beneath the boat. The amount of time it takes for the sound waves to bounce off the bottom of the sea and return to a receiver is used to determine water depth. The strength of the sound wave is used to determine how hard the bottom of the sea is. In other words, backscatter is the measure of sound that is reflected by the seafloor and received by the sonar. A strong sound wave indicates a hard surface (rocks, gravel), and a weak return signal indicates a soft surface (silt, mud). Another piece of equipment is used called a sub-bottom profiler.Sub-bottom profile data shows the rock features and the sediment layers that are below the seabed. LiDAR is another way to map the seabed, using airplanes. Two laser light beams are emitted from a sensor on-board an airplane. The red beam reaches the water surface and bounces back; while the green beam penetrates the water hits the seabed and bounces back. The difference in time between the two beams returning allows the water depth to be calculated. LiDAR is only suitable for shallow waters (up to 30m depth).This data shows areas which have data available for download in Irish waters. It is a vector dataset. Vector data portray the world using points, lines, and polygons (areas).This data is shown as polygons. Each polygon holds information on the survey leg details (name, vessel, year,date etc). It also provides links where available to download bathymetry (GEOTIFF, ESRI GRID, xyz), backscatter (GEOTIFF), survey report (pdf) and sub-bottom profile (SEGY) data in various formats.The data available for download are raster datasets. Raster data is another name for gridded data. Raster data stores information in pixels (grid cells). Each raster grid makes up a matrix of cells (or pixels) organised into rows and columns.This data was collected using a boat or plane. Data is output in xyz format. X and Y are the location and Z is the depth or backscatter value. A software package converts it into gridded data. The grid cell size varies. If the resolution is 10m - Each grid cell size is 10 meter by 10 meter. This means that each cell (pixel) represents an area of 10 meter squared.ESRI GRID datasets contain the depth value. This means you can click on a location and get its depth.GEOTIFFS are images of the data and only record colour values. We use software to create a 3D effect of what the seabed looks like. By using vertical exaggeration, artificial sun-shading (mostly as if there is a light source in the northwest) and colouring the depths using colour maps, it is possible to highlight the subtle relief of the seabed. The darker shading represents a deeper depths and lighter shading represents shallower depths.The gridded XYZ data is also available.This data shows areas that have been surveyed. There are plans to fill in the missing areas between 2020 and 2026. The deeper offshore waters were mapped as part of the Irish National Seabed Survey (INSS) between 1999 and 2005. INtegrated Mapping FOr the Sustainable Development of Ireland's MArine Resource (INFOMAR) is mapping the inshore areas. (2006 - 2026).