title: The need for open source software in machine learning

authors: Sonnenburg, Soren

subjects: machine learning

abstract: Open source tools have recently reached a level of maturity which makes them suitable for building large-scale real-world systems. At the same time, the field of machine learning has developed a large body of powerful learning algorithms for diverse applications. However, the true potential of these methods is not used, since existing implementations are not openly shared, resulting in software with low usability, and weak interoperability. We argue that this situation can be significantly improved by increasing incentives for researchers to publish their software under an open source model. Additionally, we outline the problems authors are faced with when trying to publish algorithmic implementations of machine learning methods. We believe that a resource of peer reviewed software accompanied by short articles would be highly valuable to both the machine learning and the general scientific community.

text: The need for open source software in machine learning Open source tools have recently reached a level of maturity which makes them suitable for building large-scale real-world systems. At the same time, the field of machine learning has developed a large body of powerful learning algorithms for diverse applications. However, the true potential of these methods is not used, since existing implementations are not openly shared, resulting in software with low usability, and weak interoperability. We argue that this situation can be significantly improved by increasing incentives for researchers to publish their software under an open source model. Additionally, we outline the problems authors are faced with when trying to publish algorithmic implementations of machine learning methods. We believe that a resource of peer reviewed software accompanied by short articles would be highly valuable to both the machine learning and the general scientific community.

year: 2007

title: Surface elevation changes and sediment characteristics of intertidal surfaces undergoing mangrove expansion and mangrove removal, Waikaraka Estuary, Tauranga Harbour, New Zealand

authors: Stokes, Debra J.

subjects: New Zealand

abstract: Since the 1940s mangroves have expanded their areal coverage in many estuaries in the northern half of the North Island of New Zealand. The extent of mangrove colonization in Waikaraka Estuary, Tauranga Harbour, has been documented using photogrammetric analysis, and the impacts of subsequent mangrove removal are analysed. Surface elevation changes in response to mangrove removal are measured using RSETs (Rod Surface Elevation Table) and erosion pins, and sediment accumulation rates were calculated from sediment trap results. Temporal changes to surface sediment texture are analysed. Mangrove physiognomy is described from analysis of mean plant height, plant density and pneumatophore density. Plant heights reflect the shrubby growth form of mangroves growing toward their southern climatic limit, with mean plant heights under 1.5 m. Mangrove coverage has increased from approximately 16,000 m2 in 1943 to 115,000 m2 in 2003. Since May 2005, 9,600 m2 of mangrove vegetation has been removed from the estuary. For the monitoring period of March 2006 to March 2007, rates of surface elevation change in cleared areas ranged from - 9 mm to - 38 mm yr (mean -14 mm yr). Conversely, surface elevation under mangrove forest varied between sites, ranging from -5 mm to 14 mm yr (mean 3 mm yr). Results from RSETs and erosion pins and a coarsening of surface sediment texture at the cleared sites, is consistent with sediment release after mangrove removal.

text: Surface elevation changes and sediment characteristics of intertidal surfaces undergoing mangrove expansion and mangrove removal, Waikaraka Estuary, Tauranga Harbour, New Zealand Since the 1940s mangroves have expanded their areal coverage in many estuaries in the northern half of the North Island of New Zealand. The extent of mangrove colonization in Waikaraka Estuary, Tauranga Harbour, has been documented using photogrammetric analysis, and the impacts of subsequent mangrove removal are analysed. Surface elevation changes in response to mangrove removal are measured using RSETs (Rod Surface Elevation Table) and erosion pins, and sediment accumulation rates were calculated from sediment trap results. Temporal changes to surface sediment texture are analysed. Mangrove physiognomy is described from analysis of mean plant height, plant density and pneumatophore density. Plant heights reflect the shrubby growth form of mangroves growing toward their southern climatic limit, with mean plant heights under 1.5 m. Mangrove coverage has increased from approximately 16,000 m2 in 1943 to 115,000 m2 in 2003. Since May 2005, 9,600 m2 of mangrove vegetation has been removed from the estuary. For the monitoring period of March 2006 to March 2007, rates of surface elevation change in cleared areas ranged from - 9 mm to - 38 mm yr (mean -14 mm yr). Conversely, surface elevation under mangrove forest varied between sites, ranging from -5 mm to 14 mm yr (mean 3 mm yr). Results from RSETs and erosion pins and a coarsening of surface sediment texture at the cleared sites, is consistent with sediment release after mangrove removal.

year: 2009

title: Kōura (Paranephrops planifrons) populations in the Te Arawa lakes: An ecological assessment using the traditional Māori tau kōura harvesting method and recommendations for sustainable management

authors: Kusabs, Ian Andrew

subjects: Kōura

abstract: Freshwater crayfish are amongst the most influential of biota in many aquatic systems. They have various ecological functions, acting as shredders, detritivores and predators which in turn influence other macroinvertebrate fauna. Furthermore, freshwater crayfish are increasingly used as indicator species because of the important role they play in aquatic ecosystems and their iconic and heritage values. Kōura or freshwater crayfish (Paranephrops planifrons White) are endemic to New Zealand where they are an important component of freshwater ecosystems and a source of food for freshwater fish and humans. This study was undertaken to gain a better understanding of kōura populations in the Te Arawa lakes by quantifying relative kōura abundance and distribution and assessing the effects of environmental factors on kōura populations. In addition, basic biological information on sex ratios, breeding and moulting was collected as a basis for setting regulations and management policies for the sustainable management of kōura in the Te Arawa lakes.
Historically, kōura were an important food for the indigenous Māori people, particularly in the central North Island (CNI) lakes where large numbers were harvested for consumption and trading. Today, kōura are considered a ‘taonga’ species and support important customary fisheries in some CNI lakes (Rotomā, Rotoiti, Tarawera, and Taupō) where large populations of kōura still exist. Nevertheless, there is considerable anecdotal evidence of declines in populations of kōura in the Te Arawa lakes district since European settlement. A number of environmental factors have been implicated in this decline, including introductions of exotic fish and plant species as well as reduced concentrations of dissolved oxygen in the bottom waters of lakes due to eutrophication.
Although the ecology of stream-dwelling P. planifrons is well studied in New Zealand, there is limited published biological information on kōura in lakes. The lack of quantitative information on kōura abundance and ecology makes it difficult for iwi (Māori tribes) and government agencies to manage lake dwelling kōura populations. Until recently the main reason for the lack of quantitative information on lake kōura was the absence of suitable representative sampling methods. In a preliminary study of kōura sampling methods in the Te Arawa lakes, it was found that conventional sampling methods, baited traps, SCUBA and underwater video camera surveys had a number of disadvantages. Trapping was found to be highly biased towards large individuals and complicated by reductions in bait quality with time and changes in natural food abundance. SCUBA and underwater video camera surveys are also biased towards large individuals and are strongly dependent on underwater visibility. Given the disadvantages of these conventional kōura assessment methods, a traditional Māori harvesting method, the tau kōura, was adapted for the monitoring of lake kōura populations. The tau kōura captured large numbers and a wide size range (6 – 50 mm Orbit Carapace Length, OCL) of kōura in both shallow (5 m mean depth) and moderately deep water (10 – 17 m depth) in Ōkere Arm and Te Ākau, Lake Rotoiti, respectively. This method also distinguished differences in size structure and biomass between sites and provided information on sex ratios, egg-bearing and moulting. The development of the tau kōura thus enabled research and monitoring of lake kōura populations that may have not previously been representatively sampled and have generally been little studied in New Zealand despite their ecological and cultural significance.
The tau kōura was used to examine population dynamics of kōura, along a eutrophication gradient in seven Te Arawa lakes, in April, July and November 2009. Mean catch per unit effort (CPUE) and depth distribution of kōura were influenced by the combined effects of lake bed sediments, lake morphology, and hypolimnetic conditions related to trophic state. Although limited by the number of lakes that I was able to characterise, my data indicates that lake bed substrate (median sediment particle size) had a stronger influence on population characteristics than the level of enrichment/primary production as indexed by chlorophyll a (Chl-a). Nevertheless, the negative correlations between kōura abundance, with sediment carbon to nitrogen ratio (C/N), and the positive correlation between abundance and Chl-a, suggest that lake productivity does influence kōura. This component of the study indicates that eutrophication has reduced available kōura habitat in the Te Arawa lakes, particularly those that are sheltered, steep-sided and have fine lake bed sediments (with the Rotomahana mud tephra being particularly important). Lake bed substrate composition represented by sediment particle size is therefore a key factor to consider when selecting tau kōura sites for research, monitoring, restoration and harvesting, and when estimating kōura stocks in lakes. I concluded that measures to improve water quality in the Te Arawa lakes should benefit kōura populations by increasing the amount of oxygenated habitat available in the summer and autumn. 
Kōura support important customary fisheries for iwi in some Te Arawa lakes, particularly Rotoiti, Rotomā and Tarawera. However, until recently, there was limited published biological information to provide a basis for fisheries regulations. This knowledge gap has resulted in the adoption of conservative fisheries regulations and management policies by the fishery managers, the Te Arawa Lakes Trust (TALT) and Ministry of Primary Industries (MPI). A further objective of the research was therefore to examine the biological traits of lake kōura and to consider implications of these traits on the current fishing regulations and sustainable management of kōura populations in the Te Arawa lakes. 
From a review of past literature and the research findings from this study, it can be concluded that kōura populations in the Te Arawa lakes are currently not over-exploited due mostly to a low number participating in harvesting (almost exclusively Te Arawa) and because commercial harvesting is prohibited. However, the TALT wishes to encourage the revitalisation of traditional fishing practices (e.g., tau kōura) while adhering to the principles of kaitiakitanga ‒ the sustainable protection of resources. The establishment of sustainable management policies and regulations adheres to the principles of kaitiakitanga.
A number of management changes arising from the information collected in this study are suggested to protect and enhance the kōura fishery in the future. These are (1) set a slot limit with minimum size limit of 28 mm OCL and a maximum size limit of 39 mm OCL, (2) prohibit the taking of egg-bearing females, (3) limit deep-water harvest methods to the use of the tau kōura, and (4) implementing a tau kōura harvest season beginning on 1 December and ending on 31 March. These measures will protect breeding females if they are captured and the closed season will allow the majority of females to breed and release their young prior to fishing activity. Improving water quality (and thus increasing available kōura habitat) and preventing the introduction of predatory fish species such as eels (Anguilla spp.), catfish (Ameiurus nebulosus), and perch (Perca fluviatilis), that are efficient predators of kōura, are of the utmost importance in ensuring the sustainability of kōura populations in the Te Arawa lakes.

text: Kōura (Paranephrops planifrons) populations in the Te Arawa lakes: An ecological assessment using the traditional Māori tau kōura harvesting method and recommendations for sustainable management Freshwater crayfish are amongst the most influential of biota in many aquatic systems. They have various ecological functions, acting as shredders, detritivores and predators which in turn influence other macroinvertebrate fauna. Furthermore, freshwater crayfish are increasingly used as indicator species because of the important role they play in aquatic ecosystems and their iconic and heritage values. Kōura or freshwater crayfish (Paranephrops planifrons White) are endemic to New Zealand where they are an important component of freshwater ecosystems and a source of food for freshwater fish and humans. This study was undertaken to gain a better understanding of kōura populations in the Te Arawa lakes by quantifying relative kōura abundance and distribution and assessing the effects of environmental factors on kōura populations. In addition, basic biological information on sex ratios, breeding and moulting was collected as a basis for setting regulations and management policies for the sustainable management of kōura in the Te Arawa lakes.
Historically, kōura were an important food for the indigenous Māori people, particularly in the central North Island (CNI) lakes where large numbers were harvested for consumption and trading. Today, kōura are considered a ‘taonga’ species and support important customary fisheries in some CNI lakes (Rotomā, Rotoiti, Tarawera, and Taupō) where large populations of kōura still exist. Nevertheless, there is considerable anecdotal evidence of declines in populations of kōura in the Te Arawa lakes district since European settlement. A number of environmental factors have been implicated in this decline, including introductions of exotic fish and plant species as well as reduced concentrations of dissolved oxygen in the bottom waters of lakes due to eutrophication.
Although the ecology of stream-dwelling P. planifrons is well studied in New Zealand, there is limited published biological information on kōura in lakes. The lack of quantitative information on kōura abundance and ecology makes it difficult for iwi (Māori tribes) and government agencies to manage lake dwelling kōura populations. Until recently the main reason for the lack of quantitative information on lake kōura was the absence of suitable representative sampling methods. In a preliminary study of kōura sampling methods in the Te Arawa lakes, it was found that conventional sampling methods, baited traps, SCUBA and underwater video camera surveys had a number of disadvantages. Trapping was found to be highly biased towards large individuals and complicated by reductions in bait quality with time and changes in natural food abundance. SCUBA and underwater video camera surveys are also biased towards large individuals and are strongly dependent on underwater visibility. Given the disadvantages of these conventional kōura assessment methods, a traditional Māori harvesting method, the tau kōura, was adapted for the monitoring of lake kōura populations. The tau kōura captured large numbers and a wide size range (6 – 50 mm Orbit Carapace Length, OCL) of kōura in both shallow (5 m mean depth) and moderately deep water (10 – 17 m depth) in Ōkere Arm and Te Ākau, Lake Rotoiti, respectively. This method also distinguished differences in size structure and biomass between sites and provided information on sex ratios, egg-bearing and moulting. The development of the tau kōura thus enabled research and monitoring of lake kōura populations that may have not previously been representatively sampled and have generally been little studied in New Zealand despite their ecological and cultural significance.
The tau kōura was used to examine population dynamics of kōura, along a eutrophication gradient in seven Te Arawa lakes, in April, July and November 2009. Mean catch per unit effort (CPUE) and depth distribution of kōura were influenced by the combined effects of lake bed sediments, lake morphology, and hypolimnetic conditions related to trophic state. Although limited by the number of lakes that I was able to characterise, my data indicates that lake bed substrate (median sediment particle size) had a stronger influence on population characteristics than the level of enrichment/primary production as indexed by chlorophyll a (Chl-a). Nevertheless, the negative correlations between kōura abundance, with sediment carbon to nitrogen ratio (C/N), and the positive correlation between abundance and Chl-a, suggest that lake productivity does influence kōura. This component of the study indicates that eutrophication has reduced available kōura habitat in the Te Arawa lakes, particularly those that are sheltered, steep-sided and have fine lake bed sediments (with the Rotomahana mud tephra being particularly important). Lake bed substrate composition represented by sediment particle size is therefore a key factor to consider when selecting tau kōura sites for research, monitoring, restoration and harvesting, and when estimating kōura stocks in lakes. I concluded that measures to improve water quality in the Te Arawa lakes should benefit kōura populations by increasing the amount of oxygenated habitat available in the summer and autumn. 
Kōura support important customary fisheries for iwi in some Te Arawa lakes, particularly Rotoiti, Rotomā and Tarawera. However, until recently, there was limited published biological information to provide a basis for fisheries regulations. This knowledge gap has resulted in the adoption of conservative fisheries regulations and management policies by the fishery managers, the Te Arawa Lakes Trust (TALT) and Ministry of Primary Industries (MPI). A further objective of the research was therefore to examine the biological traits of lake kōura and to consider implications of these traits on the current fishing regulations and sustainable management of kōura populations in the Te Arawa lakes. 
From a review of past literature and the research findings from this study, it can be concluded that kōura populations in the Te Arawa lakes are currently not over-exploited due mostly to a low number participating in harvesting (almost exclusively Te Arawa) and because commercial harvesting is prohibited. However, the TALT wishes to encourage the revitalisation of traditional fishing practices (e.g., tau kōura) while adhering to the principles of kaitiakitanga ‒ the sustainable protection of resources. The establishment of sustainable management policies and regulations adheres to the principles of kaitiakitanga.
A number of management changes arising from the information collected in this study are suggested to protect and enhance the kōura fishery in the future. These are (1) set a slot limit with minimum size limit of 28 mm OCL and a maximum size limit of 39 mm OCL, (2) prohibit the taking of egg-bearing females, (3) limit deep-water harvest methods to the use of the tau kōura, and (4) implementing a tau kōura harvest season beginning on 1 December and ending on 31 March. These measures will protect breeding females if they are captured and the closed season will allow the majority of females to breed and release their young prior to fishing activity. Improving water quality (and thus increasing available kōura habitat) and preventing the introduction of predatory fish species such as eels (Anguilla spp.), catfish (Ameiurus nebulosus), and perch (Perca fluviatilis), that are efficient predators of kōura, are of the utmost importance in ensuring the sustainability of kōura populations in the Te Arawa lakes.

year: 2015