title: Random model trees: an effective and scalable regression method

authors: Pfahringer, Bernhard

subjects: computer science

abstract: We present and investigate ensembles of randomized model trees as a novel regression method. Such ensembles combine the scalability of tree-based methods with predictive performance rivaling the state of the art in numeric prediction. An extensive empirical investigation shows that Random Model Trees produce predictive performance which is competitive with state-of-the-art methods like Gaussian Processes Regression or Additive Groves of Regression Trees. The training
and optimization of Random Model Trees scales better than Gaussian Processes Regression to larger datasets, and enjoys a constant advantage over Additive Groves of the order of one to two orders of magnitude.

text: Random model trees: an effective and scalable regression method We present and investigate ensembles of randomized model trees as a novel regression method. Such ensembles combine the scalability of tree-based methods with predictive performance rivaling the state of the art in numeric prediction. An extensive empirical investigation shows that Random Model Trees produce predictive performance which is competitive with state-of-the-art methods like Gaussian Processes Regression or Additive Groves of Regression Trees. The training
and optimization of Random Model Trees scales better than Gaussian Processes Regression to larger datasets, and enjoys a constant advantage over Additive Groves of the order of one to two orders of magnitude.

year: 2010-06

title: Temporal variability in the water quality of a deep temperate oligotrophic lake

authors: Kpodonu, Alfred Theodore Nutefe Kwasi

subjects: Temporal variability

abstract: Lakes change over time in response to climate and catchment disturbance, even in the absence of anthropogenic stressors. This temporal change may impact the setting of reference conditions for lakes. Many sources of information including monitoring data, historical information, modelling and paleolimnology can be used to understand temporal dynamics of lakes. In this thesis, the contribution of catchment disturbance by volcanic eruptions, introduction and proliferation of invasive mammals, and climate variability, to temporal variability in lake reference conditions was studied in a deep lake (Lake Okataina) in the Central North Island in New Zealand that is close to reference state. The lake and its catchment have been subject to anthropogenic and natural biotic and abiotic disturbances during the last millennium. Polynesian settlements were thought to have been established in and around the lake catchment in the early 14th century following the Kaharoa eruption of AD 1314 ± 12. Mt Tarawera erupted 10 June 1886 and damaged large tracts of vegetation in the Okataina catchment. Following European settlements around the catchment in the early 20th century, mammals which were hitherto not present, were liberated into the forest and rainbow trout (Oncorhynchus mykiss) were released into the lake. Large populations of the dama wallaby (Macropus eugenii), wild boar (Sus scrofa), red deer (Cervus elaphus) and the Australian brushtail possum (Trichosurus vulpecula) exist in the catchment. These mammals have become the “new normal” in many New Zealand catchments.
To understand the role of volcanic eruptions and invasive mammals in shifting baseline conditions of lakes, two 49 cm cores were retrieved from a central deep location at Lake Okataina.  The core was sliced at 1 cm intervals and slices dated using 210Pb, with the tephra from the Kaharoa and Tarawera eruptions used to validate the dates and benchmark events. Dating indicated the length of the core encompassed the period between the Kaharoa eruption of AD 1314 ± 12 and 2009.  Various inorganic and organic geochemical proxies in the sediment core slices were analysed to determine: changes in catchment erosion, phosphorus speciation, phytoplankton community assemblage, primary productivity, sources of organic matter loading, redox potential, and internal phosphorus loading to the lake. 
A suite of statistical techniques, including structural equation modelling (SEM), general linear modelling (GLM), nonmetric multidimensional scaling (NMDS) and correlation analysis was used to interpret vertical changes in the composition of the core slices and relationships amongst analytes. SEM was used to compare the relative importance of climate and catchment disturbance in changing the primary productivity of Lake Okataina after the Tarawera eruption (1886) and European settlement (1900). Changes in historical primary productivity inferred from total organic carbon in sediment core slices were modelled as a function of geochemical proxies for erosion (Al and Ti) and records of climate variability (Southern Oscillation Index and Temperature Anomaly). The results of this study showed that erosion is the main driver of changes in primary productivity although climate contributes substantially to the variations, and also contributes to changes in erosion itself.
The relationship between phosphorus speciation and algal community dynamics in the lake over the past ~ 700 years was established by applying NMDS and GLM to sequentially extracted phosphorus species and algal pigments from the sediment core. Pigments representing diatoms, cyanobacteria, chlorophytes and chryptophytes were measured vertically through the core at 1 cm intervals, as well as phosphorus associated with apatite and CaCO₃, Fe and Mn (oxy) hydroxides, Al (oxy) hydroxides and labile phosphorus. Highly significant correlations were established amongst the algal groups and the phosphorus fractions. The NMDS showed diatoms were strongly correlated with phosphorus fractions associated with permanent burial (apatite and CaCO3 and Al (oxy) hydroxides), while cyanobacteria and chlorophytes were correlated with potentially bioavailable phosphorus (Fe and Mn (oxy) hydroxides and labile phosphorus). Chlorophytes, cyanobacteria and chryptophytes co-dominated when diatom populations were reduced, and vice versa. Using GLM, phosphorus fractions could be used to hindcast historical variations in the composition of algal communities (as inferred from pigments), with the exception of alloxanthin (representative of chryptophytes).
Long-term changes in the water quality of Lake Okataina were inferred from sediments deposited from 1836 to 2009, during which time the forested catchment was disturbed by both a pyroclastic volcanic eruption (Tarawera 1886) and invasive mammals (commencing c. 1900). Multiple sediment geochemical proxies were analysed stratigraphically to ascertain trends in organic matter loading (TOC, TN, δ ¹³C and δ ¹⁵N and TOC/TN ratio), primary productivity (Ni, Cu), redox potential (U, V and Mo) and phosphorus retention capacity (Al/Fe and Al/P ratios) of the lake. The chronosequence of the proxies showed that the main source of organic matter loading to the lake is algae although terrestrial loading was increased immediately after the eruption of 1886. Erosion of inorganic materials was relatively high after the eruption but decreased after about twenty years, possibly linked to vegetation regrowth. After 1920 there was a sustained increase in the terrestrial flux of inorganic material. The redox potential of the lake also changed substantially from about 1930, suggesting a reduced degree of bottom water oxygenation. Primary productivity increased considerably after about 1960, while the phosphorus retention capacity of the lake has substantially decreased over the last 50 years. 
Using eleven years (2003 to 2013) of contemporary monthly monitoring data, I tested for patterns of temporal coherence in three deep oligotrophic lakes of the Rotorua region, which have similar catchment geology, trophic state and morphometry. Variables measured in the upper 1 m and bottom 2 m of the lakes, or variables calculated from depth profiles, as well as water level, were included in the coherence analysis.  The directly measured variables included temperature, dissolved oxygen, nutrients and chlorophyll a, and the calculated variables were depths of the thermocline, deep chlorophyll maximum and euphotic zone, as well as Schmidt stability. Temporal coherence was calculated for each of variable using Pearson correlation coefficient values after LOESS decomposition. The average temporal coherence for the lake pairs was high (r=0.65) indicating that the variability in most lake water quality properties is not lake-specific, but instead responds strongly to regional climate. Surface variables were more coherent than those at depth. Physical variables were more coherent than chemical variables, and the variables derived from the depth profiles were less coherent than directly measured variables. Our results indicate the strong influence of regional climate on physical variables in particular, which propagates into progressively reducing influence on chemical and biological variables. The effects of climate are progressively filtered from physical to chemical and biological variables. Coherence analysis is a useful tool to tease apart the relative influence of climate change on these variables and provides a contemporary context for lake behaviour in response to climate forcing, rather than using specific lakes which are benchmarked to a pre-anthropogenic era. 
The results of this thesis show that while the effect of eruptions is catastrophic, it is also relatively transient compared with the recent impacts of invasive mammals and climate warming, which are more continuous perturbations to the lake and landscape dynamics. Climate variability and invasive mammals tended to act synergistically to increase catchment loads of sediment and nutrients to the lake, effectively creating a shifting reference condition for a lake that would otherwise be considered relatively stable. With current climate change scenarios for New Zealand showing increasing temperatures, and without significant control of exotic mammals, recent trends in phytoplankton assemblages observed in this study, towards domination by cyanobacteria and chlorophytes, may be expected to be reinforced, and bottom-water oxygen levels may decline further. In setting targets for lake restoration goals, management of populations of invasive mammals should be included where there are substantial areas of native forest, because of the potential for these species to reduce vegetative cover, increase loads of sediment and nutrients to lakes, and negatively impact water quality.

text: Temporal variability in the water quality of a deep temperate oligotrophic lake Lakes change over time in response to climate and catchment disturbance, even in the absence of anthropogenic stressors. This temporal change may impact the setting of reference conditions for lakes. Many sources of information including monitoring data, historical information, modelling and paleolimnology can be used to understand temporal dynamics of lakes. In this thesis, the contribution of catchment disturbance by volcanic eruptions, introduction and proliferation of invasive mammals, and climate variability, to temporal variability in lake reference conditions was studied in a deep lake (Lake Okataina) in the Central North Island in New Zealand that is close to reference state. The lake and its catchment have been subject to anthropogenic and natural biotic and abiotic disturbances during the last millennium. Polynesian settlements were thought to have been established in and around the lake catchment in the early 14th century following the Kaharoa eruption of AD 1314 ± 12. Mt Tarawera erupted 10 June 1886 and damaged large tracts of vegetation in the Okataina catchment. Following European settlements around the catchment in the early 20th century, mammals which were hitherto not present, were liberated into the forest and rainbow trout (Oncorhynchus mykiss) were released into the lake. Large populations of the dama wallaby (Macropus eugenii), wild boar (Sus scrofa), red deer (Cervus elaphus) and the Australian brushtail possum (Trichosurus vulpecula) exist in the catchment. These mammals have become the “new normal” in many New Zealand catchments.
To understand the role of volcanic eruptions and invasive mammals in shifting baseline conditions of lakes, two 49 cm cores were retrieved from a central deep location at Lake Okataina.  The core was sliced at 1 cm intervals and slices dated using 210Pb, with the tephra from the Kaharoa and Tarawera eruptions used to validate the dates and benchmark events. Dating indicated the length of the core encompassed the period between the Kaharoa eruption of AD 1314 ± 12 and 2009.  Various inorganic and organic geochemical proxies in the sediment core slices were analysed to determine: changes in catchment erosion, phosphorus speciation, phytoplankton community assemblage, primary productivity, sources of organic matter loading, redox potential, and internal phosphorus loading to the lake. 
A suite of statistical techniques, including structural equation modelling (SEM), general linear modelling (GLM), nonmetric multidimensional scaling (NMDS) and correlation analysis was used to interpret vertical changes in the composition of the core slices and relationships amongst analytes. SEM was used to compare the relative importance of climate and catchment disturbance in changing the primary productivity of Lake Okataina after the Tarawera eruption (1886) and European settlement (1900). Changes in historical primary productivity inferred from total organic carbon in sediment core slices were modelled as a function of geochemical proxies for erosion (Al and Ti) and records of climate variability (Southern Oscillation Index and Temperature Anomaly). The results of this study showed that erosion is the main driver of changes in primary productivity although climate contributes substantially to the variations, and also contributes to changes in erosion itself.
The relationship between phosphorus speciation and algal community dynamics in the lake over the past ~ 700 years was established by applying NMDS and GLM to sequentially extracted phosphorus species and algal pigments from the sediment core. Pigments representing diatoms, cyanobacteria, chlorophytes and chryptophytes were measured vertically through the core at 1 cm intervals, as well as phosphorus associated with apatite and CaCO₃, Fe and Mn (oxy) hydroxides, Al (oxy) hydroxides and labile phosphorus. Highly significant correlations were established amongst the algal groups and the phosphorus fractions. The NMDS showed diatoms were strongly correlated with phosphorus fractions associated with permanent burial (apatite and CaCO3 and Al (oxy) hydroxides), while cyanobacteria and chlorophytes were correlated with potentially bioavailable phosphorus (Fe and Mn (oxy) hydroxides and labile phosphorus). Chlorophytes, cyanobacteria and chryptophytes co-dominated when diatom populations were reduced, and vice versa. Using GLM, phosphorus fractions could be used to hindcast historical variations in the composition of algal communities (as inferred from pigments), with the exception of alloxanthin (representative of chryptophytes).
Long-term changes in the water quality of Lake Okataina were inferred from sediments deposited from 1836 to 2009, during which time the forested catchment was disturbed by both a pyroclastic volcanic eruption (Tarawera 1886) and invasive mammals (commencing c. 1900). Multiple sediment geochemical proxies were analysed stratigraphically to ascertain trends in organic matter loading (TOC, TN, δ ¹³C and δ ¹⁵N and TOC/TN ratio), primary productivity (Ni, Cu), redox potential (U, V and Mo) and phosphorus retention capacity (Al/Fe and Al/P ratios) of the lake. The chronosequence of the proxies showed that the main source of organic matter loading to the lake is algae although terrestrial loading was increased immediately after the eruption of 1886. Erosion of inorganic materials was relatively high after the eruption but decreased after about twenty years, possibly linked to vegetation regrowth. After 1920 there was a sustained increase in the terrestrial flux of inorganic material. The redox potential of the lake also changed substantially from about 1930, suggesting a reduced degree of bottom water oxygenation. Primary productivity increased considerably after about 1960, while the phosphorus retention capacity of the lake has substantially decreased over the last 50 years. 
Using eleven years (2003 to 2013) of contemporary monthly monitoring data, I tested for patterns of temporal coherence in three deep oligotrophic lakes of the Rotorua region, which have similar catchment geology, trophic state and morphometry. Variables measured in the upper 1 m and bottom 2 m of the lakes, or variables calculated from depth profiles, as well as water level, were included in the coherence analysis.  The directly measured variables included temperature, dissolved oxygen, nutrients and chlorophyll a, and the calculated variables were depths of the thermocline, deep chlorophyll maximum and euphotic zone, as well as Schmidt stability. Temporal coherence was calculated for each of variable using Pearson correlation coefficient values after LOESS decomposition. The average temporal coherence for the lake pairs was high (r=0.65) indicating that the variability in most lake water quality properties is not lake-specific, but instead responds strongly to regional climate. Surface variables were more coherent than those at depth. Physical variables were more coherent than chemical variables, and the variables derived from the depth profiles were less coherent than directly measured variables. Our results indicate the strong influence of regional climate on physical variables in particular, which propagates into progressively reducing influence on chemical and biological variables. The effects of climate are progressively filtered from physical to chemical and biological variables. Coherence analysis is a useful tool to tease apart the relative influence of climate change on these variables and provides a contemporary context for lake behaviour in response to climate forcing, rather than using specific lakes which are benchmarked to a pre-anthropogenic era. 
The results of this thesis show that while the effect of eruptions is catastrophic, it is also relatively transient compared with the recent impacts of invasive mammals and climate warming, which are more continuous perturbations to the lake and landscape dynamics. Climate variability and invasive mammals tended to act synergistically to increase catchment loads of sediment and nutrients to the lake, effectively creating a shifting reference condition for a lake that would otherwise be considered relatively stable. With current climate change scenarios for New Zealand showing increasing temperatures, and without significant control of exotic mammals, recent trends in phytoplankton assemblages observed in this study, towards domination by cyanobacteria and chlorophytes, may be expected to be reinforced, and bottom-water oxygen levels may decline further. In setting targets for lake restoration goals, management of populations of invasive mammals should be included where there are substantial areas of native forest, because of the potential for these species to reduce vegetative cover, increase loads of sediment and nutrients to lakes, and negatively impact water quality.

year: 2016

title: The spatial equity and sustainability of general practitioner services: A mixed methods analysis of the Waikato DHB region

authors: Whitehead, Jesse

subjects: spatial equity

abstract: The New Zealand Primary Health Care Strategy states that quality primary health care is the first level of contact with the health system and should be universally accessible. Effective primary health care is an essential component of health systems, and is associated with more equitable distributions of health outcomes. However, not all New Zealanders have ready access to primary health care. For instance, adult residents of the Waikato region, and in particular Māori, have higher levels of unmet need for primay care than others. Improving the spatial equity of health services is a key step in achieving health equity. Health systems should contribute to achieving health equity and maintaining sustainable and equitable services into the future. 

This thesis research examines the spatial equity and sustainability of general practitioner (GP) services in the Waikato DHB region, using a mixed-methods approach to identify not only where inequities exist, but why they occur. A conceptual framework establishes a foundation for examining spatial equity and sustainability in New Zealand. Next, a systematic literature review identifies common definitions and measures of spatial equity. Primary Health Organisation (PHO) enrolment data is used to examine patterns of patient enrolment at GP services, and a range of health needs indicators were assessed for their suitability in the New Zealand primary care context. These findings inform the development of a Geographic Information Systems (GIS) model of spatial accessibility that is tailored to the Waikato District Health Board (DHB) context. The GIS model is then used, in combination with in-depth qualitative interviews, to examine the spatial equity and sustainability of GP services in the Waikato DHB region. 

Key findings include that spatial equity is commonly defined as a ‘need-based distribution of resources’, which can be quantified using a range of statistical and geospatial measures and techniques. PHO enrolment analysis revealed that most patients do not enrol with their closest service, and that the size of the ‘catchment area’ served by GP clinics varies with rurality. Analysis of indicators of health need suggest that ‘Ambulatory Sensitive Hospitalisations’ are a robust indicator; however, area-level socioeconomic deprivation is also strongly associated with other indicators of need and data is more widely available to researchers. Mixed-methods analysis suggests that GP services are not distributed equitably within the Waikato DHB region and that key barriers to access include the affordability, appropriateness, and availability of services. New Zealand’s history of colonisation and discrimination are identified as fundamental drivers of health inequity. Furthermore, population growth and ageing suggest that current levels of access to GP services are unlikely to be maintained in the future, while participants identify key economic, professional, organisation, and social dimensions that influence service sustainability in New Zealand.

text: The spatial equity and sustainability of general practitioner services: A mixed methods analysis of the Waikato DHB region The New Zealand Primary Health Care Strategy states that quality primary health care is the first level of contact with the health system and should be universally accessible. Effective primary health care is an essential component of health systems, and is associated with more equitable distributions of health outcomes. However, not all New Zealanders have ready access to primary health care. For instance, adult residents of the Waikato region, and in particular Māori, have higher levels of unmet need for primay care than others. Improving the spatial equity of health services is a key step in achieving health equity. Health systems should contribute to achieving health equity and maintaining sustainable and equitable services into the future. 

This thesis research examines the spatial equity and sustainability of general practitioner (GP) services in the Waikato DHB region, using a mixed-methods approach to identify not only where inequities exist, but why they occur. A conceptual framework establishes a foundation for examining spatial equity and sustainability in New Zealand. Next, a systematic literature review identifies common definitions and measures of spatial equity. Primary Health Organisation (PHO) enrolment data is used to examine patterns of patient enrolment at GP services, and a range of health needs indicators were assessed for their suitability in the New Zealand primary care context. These findings inform the development of a Geographic Information Systems (GIS) model of spatial accessibility that is tailored to the Waikato District Health Board (DHB) context. The GIS model is then used, in combination with in-depth qualitative interviews, to examine the spatial equity and sustainability of GP services in the Waikato DHB region. 

Key findings include that spatial equity is commonly defined as a ‘need-based distribution of resources’, which can be quantified using a range of statistical and geospatial measures and techniques. PHO enrolment analysis revealed that most patients do not enrol with their closest service, and that the size of the ‘catchment area’ served by GP clinics varies with rurality. Analysis of indicators of health need suggest that ‘Ambulatory Sensitive Hospitalisations’ are a robust indicator; however, area-level socioeconomic deprivation is also strongly associated with other indicators of need and data is more widely available to researchers. Mixed-methods analysis suggests that GP services are not distributed equitably within the Waikato DHB region and that key barriers to access include the affordability, appropriateness, and availability of services. New Zealand’s history of colonisation and discrimination are identified as fundamental drivers of health inequity. Furthermore, population growth and ageing suggest that current levels of access to GP services are unlikely to be maintained in the future, while participants identify key economic, professional, organisation, and social dimensions that influence service sustainability in New Zealand.

year: 2020