Using self organizing maps on compositional data

Self-organizing maps (Kohonen 1997) is a type of artificial neural network developed to explore patterns in high-dimensional multivariate data. The conventional version of the algorithm involves the use of Euclidean metric in the process of adaptation of the model vectors, thus rendering in theory a whole methodology incompatible with non-Euclidean geometries. In this contribution we explore the two main aspects of the problem: 1. Whether the conventional approach using Euclidean metric can shed valid results with compositional data. 2. If a modification of the conventional approach replacing vectorial sum and scalar multiplication by the canonical operators in the simplex (i.e. perturbation and powering) can converge to an adequate solution. Preliminary tests showed that both methodologies can be used on compositional data. However, the modified version of the algorithm performs poorer than the conventional version, in particular, when the data is pathological. Moreover, the conventional ap- proach converges faster to a solution, when data is \well-behaved". Key words: Self Organizing Map; Artificial Neural networks; Compositional data

Incorporating Legacy Soil pH Databases into Digital Soil Maps

Soil data and reliable soil maps are imperative for environmental management. conservation and policy. Data from historical point surveys, e.g. experiment site data and farmers fields can serve this purpose. However, legacy soil information is not necessarily collected for spatial analysis and mapping such that the data may not have immediately useful geo-references. Methods are required to utilise these historical soil databases so that we can produce quantitative maps of soil propel-ties to assess spatial and temporal trends but also to assess where future sampling is required. This paper discusses two such databases: the Representative Soil Sampling Scheme which has monitored the agricultural soil in England and Wales from 1969 to 2003 (between 400 and 900 bulked soil samples were taken annually from different agricultural fields); and the former State Chemistry Laboratory, Victoria, Australia where between 1973 and 1994 approximately 80,000 soil samples were submitted for analysis by farmers. Previous statistical analyses have been performed using administrative regions (with sharp boundaries) for both databases, which are largely unrelated to natural features. For a more detailed spatial analysis that call be linked to climate and terrain attributes, gradual variation of these soil properties should be described. Geostatistical techniques such as ordinary kriging are suited to this. This paper describes the format of the databases and initial approaches as to how they can be used for digital soil mapping. For this paper we have selected soil pH to illustrate the analyses for both databases.

PhotoLin: a program to identify and analyze linear structures in aerial photographs, satellite images and maps

A computer program, PhotoLin, written for an IBM-PC-compatible microcomputer is described which detects linear features in aerial photographs, satellite images and topographic maps. The program accepts images saved to PCX files as input and applies noise correction and smoothing filters and thinning routines. The output consists of a skeleton containing the median lines of linear features which can be represented on a map. The branches of the skeleton can be broken into sections of constant length for which the mean orientations are obtained for the preparation of rose diagrams. (C) 2001 Elsevier B.V. Ltd. All rights reserved.

Facies associations and controls on the evolution from a coastal bay to a lagoon system, Santa Catarina Coast, Brazil

The diverse Holocene morphological features along the south coast of the state of Santa Catarina include lagoons and residual lakes, a barrier, a delta (constructed by the Tubarao River), and pre-existing incised valleys that have flooded and filled. This scenario contains the sedimentary record of the transition from a bay to a lagoon system, which occurred during the rise and subsequent semi-stabilisation of the relative sea-level during the Holocene. The geomorphological evolution of this area was investigated using a combination of morphology, stratigraphic analysis of rotary push cores, vibracores and trenches with radiocarbon dating, taxonomic determination and taphonomic characterisation of Holocene fossil molluscs. Palaeogeographic maps were constructed to illustrate how the bay evolved over the last 8000 years. The relative sea-level rise and local sedimentary processes were the prime forcing factors determining the depositional history and palaeogeographic changes. The Holocene sedimentary succession began between 8000 and 5700 cal BP with the deposits of transgressive sandsheets. These deposits correspond to the initial marine flooding surface that was formed while the relative sea-level rose at a higher rate than the input of sediments, prior to the formation of the coastal barrier. The change from a bay to a lagoon system occurred around 5700 and 2500 cal BP during the mid-Holocene highstand with the formation of the barrier and with the achievement of a balance between sea-level rise and sedimentary supply. Until 2500 cal BP, the presence of this barrier, the following gentle decline in sea level and the initial emergence of back-barrier features restricted the hydro-dynamic circulation inside the bay and favoured an increase in the Tubarao River delta progradation rate. The final stage, during the last 2500 years, was marked by the increasing back-barrier width, with the establishment of salt marshes, the arrival of the delta in the back-barrier, and the advance of aeolian dunes along the outer lagoon margins. This study shed light on the mechanisms of coastal bay evolution in a setting existed prior to the beginning of barrier lagoon sedimentation. (C) 2012 Elsevier B.V. All rights reserved.

Isopach Maps and Discussion of the Ordovician and Devonian of Montana and Adjacent Areas

The intensive postwar search for new petroleum horizons has resulted in widespread prospecting in the northern Great Plains. No commercial production has as yet been derived from Ordovician or Devonian rocks in Montana, but the relat­ively few tests that have penetrated to critical depths have disclosed encouraging conditions which merit further consider­ation, especially in Devonian strata.

A 950 yr temperature reconstruction from Duckhole Lake, southern Tasmania, Australia

A lack of quantitative high resolution paleoclimate data from the Southern Hemisphere limits the ability to examine current trends within the context of long-term natural climate variability. This study presents a temperature reconstruction for southern Tasmania based on analyses of a sediment core from Duckhole Lake (43.365°S, 146.875°E). The relationship between non-destructive whole core scanning reflectance spectroscopy measurements in the visible spectrum (380–730 nm) and the instrumental temperature record (ad 1911–2000) was used to develop a calibration-in-time reflectance spectroscopy-based temperature model. Results showed that a trough in reflectance from 650 to 700 nm, which represents chlorophyll and its derivatives, was significantly correlated to annual mean temperature. A calibration model was developed (R = 0.56, p auto < 0.05, root mean squared error of prediction (RMSEP) = 0.21°C, five-year filtered data, calibration period 1911–2000) and applied down-core to reconstruct annual mean temperatures in southern Tasmania over the last c. 950 years. This indicated that temperatures were initially cool c. ad 1050, but steadily increased until the late ad 1100s. After a brief cool period in the ad 1200s, temperatures again increased. Temperatures steadily decreased during the ad 1600s and remained relatively stable until the start of the 20th century when they rapidly decreased, before increasing from ad 1960s onwards. Comparisons with high resolution temperature records from western Tasmania, New Zealand and South America revealed some similarities, but also highlighted differences in temperature variability across the mid-latitudes of the Southern Hemisphere. These are likely due to a combination of factors including the spatial variability in climate between and within regions, and differences between records that document seasonal (i.e. warm season/late summer) versus annual temperature variability. This highlights the need for further records from the mid-latitudes of the Southern Hemisphere in order to constrain past natural spatial and seasonal/annual temperature variability in the region, and to accurately identify and attribute changes to natural variability and/or anthropogenic activities.

Recent environmental change and trace metal pollution in World Heritage Bathurst Harbour, southwest Tasmania, Australia

Bathurst Harbour in World Heritage southwest Tasmania, Australia, is one of the world’s most pristine estuarine systems. At present there is a lack of data on pollution impacts or long-term natural variability in the harbor. A ca. 350-year-old 210Pb-dated sediment core was analysed for trace metals to track pollution impacts from local and long-range sources. Lead and antimony increased from AD 1870 onwards, which likely reflects remote (i.e. mainland Australian and global) atmospheric pollution sources. Variability in the concentrations of copper and zinc closely followed the history of mining activities in western Tasmania, which began in the AD 1880s. Tin was generally low throughout the core, except for a large peak in AD 1989 ± 0.5 years, which may be a consequence of input from a local small-scale alluvial tin mine. Changes in diatom assemblages were also investigated. The diatom flora was composed mostly of planktonic freshwater and benthic brackish-marine species, consistent with stratified estuarine conditions. Since mining began, however, an overall decrease in the proportion of planktonic to benthic taxa occurred, with the exception of two distinct peaks in the twentieth century that coincided with periods of high rainfall. Despite the region’s remoteness, trace metal analyses revealed evidence of atmospheric pollution from Tasmanian and possibly longer-range mining activities. This, together with recent low rainfall, appears to have contributed to altering the diatom assemblages in one of the most pristine temperate estuaries in the world.

Light noble gases in 12 meteorites from the Omani desert, Australia, Mauritania, Canada, and Sweden

We measured the concentrations and isotopic compositions of He, Ne, and Ar in 14 fragments from 12 different meteorites: three carbonaceous chondrites, six L chondrites (three most likely paired), one H chondrite, one R chondrite, and one ungrouped chondrite. The data obtained for the CV3 chondrites Ramlat as Sahmah (RaS) 221 and RaS 251 support the hypothesis of exposure age peaks for CV chondrites at approximately 9 Ma and 27 Ma. The exposure age for Shişr 033 (CR chondrite) of 7.3 Ma is also indicative of a possible CR chondrite exposure age peak. The three L chondrites Jiddat al Harasis (JaH) 091, JaH 230, and JaH 296, which are most likely paired, fall together with Hallingeberg into the L chondrite exposure age peak of approximately 15 Ma. The two L chondrites Shelburne and Lake Torrens fall into the peaks at approximately 40 Ma and 5 Ma, respectively. The ages for Bassikounou (H chondrite) and RaS 201 (R chondrite) are approximately 3.5 Ma and 5.8 Ma, respectively. Six of the studied meteorites show clear evidence for 3He diffusive losses, the deficits range from approximately 17% for one Lake Torrens aliquot to approximately 45% for RaS 211. The three carbonaceous chondrites RaS 221, RaS 251, and Shişr 033 all have excess 4He, either of planetary or solar origin. However, very high 4He/20Ne ratios occur at relatively low 20Ne/22Ne ratios, which is unexpected and needs further study. The measured 40Ar ages fit well into established systematics. They are between 2.5 and 4.5 Ga for the carbonaceous chondrites, older than 3.6 Ga for the L and H chondrites, and about 2.4 Ga for the R chondrite as well as for the ungrouped chondrite. Interestingly, none of our studied L chondrites has been degassed in the 470 Ma break-up event. Using the amount of trapped 36Ar as a proxy for noble gas contamination due to terrestrial weathering we are able to demonstrate that the samples studied here are not or only very slightly affected by terrestrial weathering (at least in terms of their noble gas budget).

Registration And Visualisation Of Deformation Maps From Terrestrial Radar Interferometry Using Photogrammetry And Structure From Motion

This paper describes a general workflow for the registration of terrestrial radar interferometric data with 3D point clouds derived from terrestrial photogrammetry and structure from motion. After the determination of intrinsic and extrinsic orientation parameters, data obtained by terrestrial radar interferometry were projected on point clouds and then on the initial photographs. Visualisation of slope deformation measurements on photographs provides an easily understandable and distributable information product, especially of inaccessible target areas such as steep rock walls or in rockfall run-out zones. The suitability and error propagation of the referencing steps and final visualisation of four approaches are compared: (a) the classic approach using a metric camera and stereo-image photogrammetry; (b) images acquired with a metric camera, automatically processed using structure from motion; (c) images acquired with a digital compact camera, processed with structure from motion; and (d) a markerless approach, using images acquired with a digital compact camera using structure from motion without artificial ground control points. The usability of the completely markerless approach for the visualisation of high-resolution radar interferometry assists the production of visualisation products for interpretation.

Hazard index maps for woody material recruitment and transport in alpine catchments

A robust and reliable risk assessment procedure for hydrologic hazards deserves particular attention to the role of transported woody material during flash floods or debris flows. At present, woody material transport phenomena are not systematically considered within the procedures for the elaboration of hazard maps. The consequence is a risk of losing prediction accuracy and of underestimating hazard impacts. Transported woody material frequently interferes with the sediment regulation capacity of open check dams and moreover, when obstruction phenomena at critical crosssections of the stream occur, inundations can be triggered. The paper presents a procedure for the determination of the relative propensity of mountain streams to the entrainment and delivery of recruited woody material on the basis of empirical indicators. The procedure provided the basis for the elaboration of a hazard index map for all torrent catchments of the Autonomous Province of Bolzano/Bozen. The plausibility of the results has been thoroughly checked by a backward oriented analysis on natural hazard events, documented since 1998 at the Department of Hydraulic Engineering of the aforementioned Alpine Province. The procedure provides hints for the consideration of the effects, induced by woody material transport, during the elaboration of hazard zone maps.

Seagrass time-series analysis products, in Moreton Bay, Australia, with links to GeoTIFFs

The spatial and temporal dynamics of seagrasses have been well studied at the leaf to patch scales, however, the link to large spatial extent landscape and population dynamics is still unresolved in seagrass ecology. Traditional remote sensing approaches have lacked the temporal resolution and consistency to appropriately address this issue. This study uses two high temporal resolution time-series of thematic seagrass cover maps to examine the spatial and temporal dynamics of seagrass at both an inter- and intra-annual time scales, one of the first globally to do so at this scale. Previous work by the authors developed an object-based approach to map seagrass cover level distribution from a long term archive of Landsat TM and ETM+ images on the Eastern Banks (~200 km**2), Moreton Bay, Australia. In this work a range of trend and time-series analysis methods are demonstrated for a time-series of 23 annual maps from 1988 to 2010 and a time-series of 16 monthly maps during 2008-2010. Significant new insight was presented regarding the inter- and intra-annual dynamics of seagrass persistence over time, seagrass cover level variability, seagrass cover level trajectory, and change in area of seagrass and cover levels over time. Overall we found that there was no significant decline in total seagrass area on the Eastern Banks, but there was a significant decline in seagrass cover level condition. A case study of two smaller communities within the Eastern Banks that experienced a decline in both overall seagrass area and condition are examined in detail, highlighting possible differences in environmental and process drivers. We demonstrate how trend and time-series analysis enabled seagrass distribution to be appropriately assessed in context of its spatial and temporal history and provides the ability to not only quantify change, but also describe the type of change. We also demonstrate the potential use of time-series analysis products to investigate seagrass growth and decline as well as the processes that drive it. This study demonstrates clear benefits over traditional seagrass mapping and monitoring approaches, and provides a proof of concept for the use of trend and time-series analysis of remotely sensed seagrass products to benefit current endeavours in seagrass ecology.

Raster maps for 29 environmental variables in three geographical regions

Aim: Greater understanding of the processes underlying biological invasions is required to determine and predict invasion risk. Two subspecies of olive (Olea europaea subsp. europaea and Olea europaea subsp. cuspidata) have been introduced into Australia from the Mediterranean Basin and southern Africa during the 19th century. Our aim was to determine to what extent the native environmental niches of these two olive subspecies explain the current spatial segregation of the subspecies in their non-native range. We also assessed whether niche shifts had occurred in the non-native range, and examined whether invasion was associated with increased or decreased occupancy of niche space in the non-native range relative to the native range. Location: South-eastern Australia, Mediterranean Basin and southern Africa. Methods: Ecological niche models (ENMs) were used to quantify the similarity of native and non-native realized niches. Niche shifts were characterized by the relative contribution of niche expansion, stability and contraction based on the relative occupancy of environmental space by the native and non-native populations. Results: Native ENMs indicated that the spatial segregation of the two subspecies in their non-native range was partly determined by differences in their native niches. However, we found that environmentally suitable niches were less occupied in the non-native range relative to the native range, indicating that niche shifts had occurred through a contraction of the native niches after invasion, for both subspecies. Main conclusions: The mapping of environmental factors associated with niche expansion, stability or contraction allowed us to identify areas of greater invasion risk. This study provides an example of successful invasions that are associated with niche shifts, illustrating that introduced plant species are sometimes readily able to establish in novel environments. In these situations the assumption of niche stasis during invasion, which is implicitly assumed by ENMs, may be unreasonable.