PosterPDF Available

ANIMOVE: A FREE AND OPEN SOURCE FRAMEWORK FOR THE ANALYSIS OF ANIMAL MOVEMENTS WITH QGIS

Authors:
Matteo Ghetta at Sant'Anna School of Advanced Studies
Matteo Ghetta
Giuseppe Puddu at Lago di Vico Natural Regional Reserve;
Giuseppe Puddu
  • Lago di Vico Natural Regional Reserve;
P. Cavallini at Faunalia
P. Cavallini
  • Faunalia
Download file PDF
Read file
Download citation

Abstract

In 2022 the QGIS software will be 20 years old. This program has the characteristics of being free and open-source and this allows to have access to the code and be able to improve it, but above all it allows to implement plugins that, exploiting the core-software, perform specific algorithms. Here, we presented the AniMove plugin, adapted to version 3.xx of the QGIS program. This plugin allows to perform the main calculation operations about the Home Range evaluation (MCP, Random HR, Random HR path), and some tools to estimation of the Kernel Density. For all the algorithms used, there is the possibility of varying different calculation parameters. The plugin, already fully functional, maintains, however, a framework logic, that is to be expandable and integrable with new routines and calculation algorithms that can be interesting in the world of applied zoology analysis and radio tagging. The tool is fully integrated with the hundreds of features and algorithms in QGIS
Content uploaded by Giuseppe Puddu
Author content
All content in this area was uploaded by Giuseppe Puddu on Jun 11, 2022
Content may be subject to copyright.
Abstract - In 2022, the QGIS software will be 20 years old. This program has the characteristics of being free and open-source and this allows to have access to the code and be able to improve it, but above all it allows to implement
plugins that, exploiting the core-software, perform specific algorithms. Here, we presented the AniMove plugin, adapted to version 3.xx of the QGIS program. This plugin allows to perform the main calculation operations about the
HomeRange evaluation (MCP, Random HR, Random HR path), and some tools to estimation of the Kernel Densitys. For all the algorithms used, there is the possibility of varying different calculation parameters. The plugin, already fully
functional, maintains, however, a framework logic, that is to be expandable and integrable with new routines and calculation algorithms that can be interesting in the world of applied zoology analysis and radio tagging. The tool is
already fully integrated with the hundreds of features in QGIS, and it is easy to create models that extend its capabilities, e.g., land use, social indices, etc. Further development will automate some of these features to create an animal
movement analysis suite.
ANIMOVE: A FREE AND OPEN SOURCE FRAMEWORK FOR THE ANALYSIS OF
ANIMAL MOVEMENTS WITH QGIS
Ghetta M.1, Puddu G.2, Cavallini P. 1
1) Piazza Giuseppe Garibaldi 5 –Pontedera (PI). Faunalia S.r.l. ino@faunalia.eu
2) S.R. Cassia Cimina km 12.00 –Caprarola (VT). Regione Lazio –Ente Monti Cimini gpuddu@regione.lazio.it
The origins of GIS software are closely related to forest management or urban planning, yet in
recent decades many other disciplines have incorporated GIS software as a tool. The interest of
scientists in using QGIS in new fields of study seems related to the development of new
functions and plugins. QGIS is the most widely used free and open-source geospatial software in
the world. Among the main strengths of this geographic information system are: incorporation
of tools via plugins and a growing community of users and developers.
Rosas-Chavoya et al. (2022) conducted a bibliometric analysis of papers published on Scopus from 2005 to 2020 (931
manuscripts). The annual rate of increase in publications was 40.3%. Seventy-two percent (fig. 1) of the publications
were in six fields of study, of which Earth and Planetary Sciences (15.4 %) and Environmental Science (14.2 %) were the
most representative. Italy was the country with the highest scientific output, while the United States was the most
influential country (being the first, in terms of number of citations). In terms of countries, the largest number of articles
found were from Portugal, Italy, Brazil and France. There is a growing trend of acceptance of QGIS worldwide and
widespread development of collaborative networks.
Figure 1. Distribution of publications according to field of study and discipline.
References
Faunalia (2018) https://www.faunalia.eu/en/dev/animove
Rosas-Chavoya, M., Gallardo-Salazar, J.L., López-Serrano, P.M., Alcántara-Concepción, P.C., León-Miranda, A.K. 2022. QGIS a constatly growing free and open-source geospatial
software contributing to scientific development. Cuadernos de Investigación Geográfica 48. http://doi.org/10.18172/cig.5143
DOWNLOAD AniMove plugin
https://gitlab.com/faunalia/animove/-/blob/master/README.md
AniMove algorithms for QGIS
QGIS provides a processing environment that can be used to call native and third party algorithms, making your
spatial analysis tasks more productive and easy to accomplish.
AniMove plugin implements, as a processing submodule, kernel analyses with the following algorithms:
•href: the reference bandwidth is used in the estimation.
•LSCV (The Least Square Cross Validation): the LSCV bandwidth is used in the estimation.
•Scott's Rule of Thumb: the Scott's rule of thumb is used for bandwidth estimation.
•Silverman's Rule of Thumb: the Silverman's rule of thumb is used for bandwidth estimation.
•kernel with adjusted h
Utilization distribution and contour lines are produced, and area of the contour polygons are calculated.
Additionally, restricted Minimum Convex Polygons (MCP) are implemented, as:
•MCP calculation of the smallest convex polygon enclosing all the relocations of the animal, excluding an user-
selected percentage of locations furthest from a centre.
Some of the bandwidth methods are only available with statsmodels (LSCV, maximum-likelihood cross-validation).
•A new tool called "Random path" that allows to randomize paths (lines) with many options: keep angles,
randomize angles (range as user choice), randomize starting points, keep starting points, use a point layer for
starting points, check if the random path crosses features of a specified line/polygon layer.
MCP
Kernel
The porting of the plugin AniMove to QGIS 3 has been financially
supported by Ente Monti Cimini -Riserva Naturale Lago di Vico
within the project "LIFE18 NAT/IT/000720“ –Lanner*.
QGIS + AniMove provide, in a free and open-source environment, a powerful and advanced tool for processing zoological data from telemetry surveys,
covering a scientific aspect that has been missing until now.
We believe the problem could be solved by the use of several free and open source programs, available both for
GNU/Linux, Mac OSX and MS Windows operating systems. We aim at producing the most advanced software. All
resulting software is and will be freely available (under GPL or similar licences).
Our approach is to use simply QGIS to run many useful analyses (e.g. basic statistics, Minimum Convex Polygon).
For more advanced analyses, we have developed AniMove plugin (Faunalia, 2018). Developing python plugins for
QGIS is easy, cheap, and fast. Our aim is to have a toolbox in which anybody can add her/his own preferred
analyses.
... The IDW interpolation tool is available in QGIS software, which is based on GIS [30,31]. Furthermore, QGIS has the advantage of providing us with a plugin that implements specific algorithms using the main program [32]. A plugin called Smart Map has been developed, which is integrated into QGIS version 3.10 or higher, to draw digital maps using interpolation techniques such as OK and machine learning (ML). ...
Reliability of smart noise pollution map
Article
Full-text available
  • Jul 2023
The problem of noise pollution in Baghdad, the capital city of Iraq, is getting worse every day as a result of the increased volume of traffic. This presents a considerable risk, particularly on the main roads that connect densely populated neighborhoods such as the Al-Sadr City district with the central neighborhoods of the capital. In order to inform decision-makers in urban development and environmental policy about the high values of noise pollution that require remediation and regulation, noise maps are produced. However, two fundamental problems are generally faced in creating a more reliable noise map in the shortest possible time: the excessive time requirements for measuring noise and determining the method of map creation. Therefore, the role of geographic information system (GIS) software in producing noise maps is evident due to the difficulty of increasing the spatial density of measurements and integrating them with spatial information. Hence, an appropriate interpolation method is required. In this article, Moran’s I index was calculated to assess the spatial autocorrelation of measured traffic noise points. A comparison was made between the Smart Map Plugin ordinary kriging (OK) and the inverse distance weighting (IDW) deterministic interpolation method to determine the best method for producing noise maps for the main entrance and exit roads of Al-Sadr City. The noise values were modeled using the best-performing method. Furthermore, the predictive raster data are displayed in the spatial context as a starting point and reference for identifying and understanding the levels of traffic noise in the selected study area. The locations of selected points for measuring traffic noise values were determined in an organized and homogeneous manner, where noise points for the main entrance and exit roads were opposite each other, and the distance between consecutive noise points on each road was 100 m. Traffic noise measurements were carried out at each selected point using the SVAN977 sound and vibration analyzer. At each measurement point, three noise values (LAeq, Max, Min) were obtained during the three peak times, 7–9 AM, 12–2 PM, and 4–6 PM. QGIS software was used to compare the two interpolation methods, with its strength lying in the use of plugins that facilitate spatial analysis, processing tools, and algorithms. The Smart Map Plugin provided facilities to choose the appropriate semi-variogram in the OK interpolation method. The root mean square error was used to compare the two interpolation methods in order to determine the most suitable method for producing traffic noise maps in the study area. The results indicated that the Smart Map Plugin using OK outperformed the IDW method, as spatial distribution pattern and homogeneity affect the accuracy of interpolation. Moreover, based on the analysis of the three noise attributes (LAeq, Max, Min), the performance of the Smart Map Plugin (OK) was found to be better than IDW when the Moran’s I value was high.
View
Infrastructures and Next Generation EU: mitigation and preservation areas for European mammals
Conference Paper
Full-text available
  • Jun 2022
As a response to the economic crisis due to the COVID-19 pandemic, on July 2020 the European Council agreed on a massive recovery plan for the European Union denominated Next Generation EU. The first medium- and long-term purpose of such plan is guaranteeing a better future for next generations of European citizens. In this framework, there are several objectives focusing on promoting energetic transition and territorial cohesion through the development of different infrastructures. This plan implies unprecedented challenges in terms of building and upgrading roads, railways, powerlines, windfarms and solar plants, all of them infrastructures that entail well-known negative impacts on mammals. In order to limit such impacts, a careful planning of this forthcoming infrastructure development would be of paramount importance. In this study, we provided an example of preliminary evaluation of present and potential impacts of the planned infrastructure development on European mammals. More concretely, based on the principle that any infrastructurerelated impact depends on the interaction between species exposure and vulnerability, we overlapped the spatial distribution of current infrastructures and the distribution areas of the mammals that the IUCN listed as threatened by Roads and railroads, Utility and service lines, and Renewable energy. As a first result, we highlighted areas with high concentration of current infrastructures and mammal species threatened by them. We denominated such regions as Priority Mitigation Areas, where the current infrastructures and their upgrades, but also new infrastructures, should be urgently mitigated in order to limit their impact on local communities of vulnerable mammals. As a second result, we also highlighted areas with low concentration of current infrastructures but high concentration of mammal species threatened by them. We denominated such regions as Priority Preservation Areas, where future development should be avoided or at least carefully planned. This kind of approach, based on large-scale information but also on easily accessible data, entails clear limitations, but it also represents an interesting first evaluation of the potential negative impacts of infrastructure building and upgrading by providing an identification of priority areas where we should focus our next steps for planning conservation strategies for European mammals.
View
The bats of the Aosta/Pré-Saint-Didier railway line: a case of conservation concern
Conference Paper
Full-text available
  • Jun 2022
The Aosta/Pré-Saint-Didier is a single-track railway line. It is 31.3 km long, including about 9 km of tunnels. It was inaugurated in 1929 and powered by electricity until 1968, when diesel trains were introduced. On 24 December 2015, the circulation of trains was suspended due to the low use of the line and the need for extraordinary maintenance work. Since that date, the rail tunnels have remained almost undisturbed: no works have been carried out and the human presence has been limited to occasional visitors. It is known that bats may roost in abandoned rail tunnels. Therefore, as part of the surveys funded by Regione Autonoma Valle d’Aosta (Dipartimento Ambiente – Struttura biodiversità e aree naturali protette) for the implementation of the Habitats Directive, we performed some bat surveys in the tunnels of this railway line. In view of a possible reactivation of the railway line, the results of these surveys should be properly considered. We inspected the tunnels in August 2017, February 2020 and January 2021, searching for bats, droppings and prey remains. Additional surveys, limited to one tunnel only, were conducted yearly, from 2018 to 2021, in the month of June, and in September 2020. Since we did not use endoscopes, the presence of individuals deeply hidden in crevices may have been overlooked. Bats were identified based on their morphology, without handling them, excepted for two dead individuals, which were identified from skull and dental measurements. Colony counts were performed from photographs. Bat droppings were dissected and hair, if present, identified under optical microscope. In August 2017, we found a maternity colony of mouse-eared bats in one of the tunnels. The photographs and the finding of a dead individual proved the occurrence of Myotis myotis, while that of Myotis blythii was neither ascertained nor excluded (all the individuals of the photos lacked the pale forehead spot between the ears which is a distinctive, but not always present, trait of M. blythii). The colony has continued to use the tunnel, showing an increase in numbers: bats aged one year (i.e. with the exclusion of those born in the year) in 2018, 2019, 2020 and 2021 were respectively 68, 77, 96 and 105. During summer we also observed some isolated mouse-eared bats, presumably males, roosting in the tunnel of the colony and in the four nearest tunnels: they hanged from the ceiling, occupying small cavities clearly marked (brown colored). In September, groups of 2–4 individuals were observed at the same sites, presumably gathered there to mate. In other three tunnels we collected prey remains and droppings proving that, at least occasionally, they are used by individuals belonging to the genus Plecotus. In winter we did not observe any bats in the tunnels used by mouse-eared during summer, but in other five tunnels we found a dead Myotis crypticus and some hibernating bats belonging to Rhinolophus ferrumequinum (3 individuals in 2020 and 1 in 2021), Barbastella barbastellus (2 individuals in 2020 and 1 in 2021) and Pipistrellus spp. (6 individuals in 2021) The results confirm the importance of rail tunnels for bat conservation, even after only a few years from the closure of the railway lines. In the Aosta/Pré-Saint-Didier line we recorded the occurrence of at least 6 species, using the tunnels for different biological roles (day resting, maternity, mating, prey consumption, hibernating). The component of main interest is represented by the maternity colony of mouse-eared bats. Previously, a similar colony had used the Aymavilles Castle. All the individuals of the castle that were directly examined (N=17) belonged to M. myotis, but the occurrence of M. blythii could not be excluded. In 1994, at least 170 bats aged one year were counted at that site, but according to local witnesses the colony had been formerly much larger and had faced eradication attempts in the ’70s and ’80s. During the ’90s the presence of the bats was discontinuous and after 2002 the colony did not return to the castle. In spite of intensive search, the colony that once used the castle was not found elsewhere until 2017, when the roost of the Aosta/Pré- Saint-Didier railway line was discovered: the small distance between the two sites (1.5 km) suggests that the colony of the rail tunnel is the same as that of the castle. Currently, only six reproductive colonies of M. myotis are known in the whole territory of the Aosta Valley, Piedmont and Liguria and that of the railway tunnel is the only one known in the Aosta Valley. Moreover, no breeding colonies of M. blythii are known in the Aosta Valley, although the species occurs in the region If the Aosta/Pré-Saint-Didier railway line is reactivated, as planned by the Regional Administration and Rete Ferroviaria Italiana, M. myotis could risk extinction in the Aosta Valley. Negative consequences on M. blythii cannot be excluded as well.
View
First telemetry data on golden jackal (Canis aureus) in Italy: insights on the species’ spatial ecology
Conference Paper
Full-text available
  • Jun 2022
Understanding the spatial ecology and habitat requirements of a colonizing species is the main step to gain information on the species’ behaviour which is useful to delineate adequate management and conservation strategies. The golden jackal (Canis aureus) has been showing a notable expansion in Europe over the last five decades and, in Italy, the highest population densities are reported in Friuli Venezia Giulia (hereafter, FVG) Region. Here, reproductive packs exert a pivotal ecological role as a source population for the colonization of the other Italian administrative Regions. Among the many factors which have been described as important for its expansion, the ecological plasticity (i.e., the capability to take advantage of different habitats) has been considered as crucial. However, few studies of habitat selection have been conducted using bio-logging technology (e.g., GPS collars). In the last 20 years, this technology has been frequently used and improved, enabling researchers to deeply investigate the ecology and behaviour of cryptic species, including carnivores. Using the first telemetry data obtained from collared individuals in Italy, the goal of our study was to investigate the spatial ecology of the golden jackal, with special focus dedicated on home-range estimation and habitat selection. Our results should provide better understanding on the ecology of a colonizing species in the light of its expansion within a highly anthropized environment, such as the Italian lowland. Our study was conducted mainly in FVG, the north-eastern most administrative Italian Region, covering an area of 7,921 km2 with 1.2 million inhabitants. We fitted eight individuals (three females, five males) with radio- (VHF) (n = 1) or satellite (GPS) collars (n = 7) in 2019-2021. Two individuals were defined as dispersers, since they moved from their pre-reproductive territories (> 20 km far away) toward new areas. Four jackals were live captured with Belisle snares or box traps, and the latest four were recovered and released after vehicle collisions. We acquired a minimum of two locations per day from the VHF monitoring, meanwhile the GPS fix schedule was set to acquire 3-4 locations per day. We performed the 50% and 95% home-range estimation through a minimum convex polygon (MCP) for the VHF collared jackal; and 50% and 95% utilization distributions (UD) home-range using a kernel density estimator with plug-in bandwidth selection for the GPS collared jackals. We used the Corine Land Cover 2018 reclassified into 11 land cover categories, to investigate the degree of habitat selection through selection ratios at the third-order of selection (Design III) within 50% and 95% UD on the seven GPS collared jackals. All computations were performed through the Software R (v. 3.5) and using ‘ks’ and ‘adehabitatHS’ packages. The monitoring periods for each individual were highly variable, from a minimum of 36 days to a maximum of 342 days. Overall, we obtained 3,827 locations, of which 67 were VHF locations. 50% and 95% MCP home-ranges for the VHF collared individual were 0.18 km2 and 1.01 km2, respectively. A high variability was shown in both the 50% and 95% kernel UDs, with a mean home-range of 3.24 km2 (min = 0.15 km2, max = 14.84 km2) for 50% and 31.22 km2 (min = 2.22 km2, max = 135.92 km2) for 95% UD. The pattern of global habitat selection by golden jackals significantly deviated from random both within 50% UD (2 = 143.96, df = 22, p < 0.001) and 95% UD (2 = 649.77, df = 22, p < 0.001). Within 50% UD, jackals selected coniferous forests and avoided areas without vegetation. Within 95% UD, jackals selected cultivations with natural elements, while they avoided complex cultivation patterns. However, contrary to the 95% UD, at 50% UD habitat selection at individual level was not statistically significant for all individuals. Home-range estimation through the 50% and 95% UDs with kernel methods showed high variability most likely due to the different monitoring periods and individual variations (resident vs dispersal). However, 50% and 95% home-ranges were in line with other published studies with the exception of a young female who showed an extremely large home-range (135.92 km2) due to dispersal patterns. Interestingly, the VHF collared individual displayed its 50% and 95% MCP home-ranges within those of its putative father (GPS collared). The habitat selection analyses provided interesting results: 50% UDs were inspected through field surveys and were mainly related to resting sites; as expected jackals selected for natural vegetated areas and avoided areas without vegetation, as they cannot provide shelter. At 95% UDs, habitat selection highlighted how jackals can exploit human resources since they selected for agricultural areas (all agricultural areas covered 35.10% of the overall land cover types, whereas vegetated natural areas covered 54.79%). Indeed, as reported by different studies in Europe, agricultural areas can provide abundant food resources. At the individual level, those jackals who showed non-random selection had different patterns due to the different ecological conditions. It is noteworthy that one individual showed selection at both 50% and 95% UDs for anthropic land cover types (i.e., urban areas, crops and complex cultivations), as it was feeding very close to human settlements and roads. At the same time, all the other individuals avoided urban areas at the 95% UD individual level. In conclusion, we point out the ecological plasticity of golden jackal which enables the species to exploit different habitats, even near human settlements, which might be one of the main factors which has been promoting the expansion in Europe in the last decades. Moreover, GPS collars provide high quality data collected over time useful to deeply investigate different topics (e.g., habitat suitability), compared to other limited techniques (i.e., camera-trapping and jackal-howling).
View
ResearchGate has not been able to resolve any references for this publication.