title: Selected data exploration methods in hydroclimatology

authors: Vetrova, Varvara

subjects: hydrclimatology

abstract: The volumes of climatological data are rapidly growing due to development of new acquisition platforms and advances in data storage technologies. Such advances provide new challenging problems for data analysis methods. As a result, there is an increasing interest in application and development of new machine learning and data mining methods in climatological data analysis.

This dissertation contributes to the field of data analysis by evaluation of selected methods and developing new techniques with application to hydro-climatological datasets. 

It is shown that data pre-processing with the decimated wavelet discrete transform can cause false predictive accuracy in regression machine learning algorithms. A general result is obtained that a decimated wavelet discrete transform based on a pyramidal algorithm requires utilizing some future values of the time series concerned. When the discrete wavelet transform is utilized as a pre-processing step for forecasting the time series, the necessary independence of calibration and validation data is compromised. This in turn translates into over-optimistic forecasting accuracy or even giving the illusion of forecasting skill when there in none. The obtained result is general and has wide implications in any discipline where the discrete wavelet transform is utilised in forecasting frameworks.

In addition, a general framework for creating simple predictive models is presented, based on LASSO regularised regression. The method is illustrated for time series modelling with external event forcing but the approach has general applicability. 

As a contribution to association discovery, two tests of bivariate association are developed. The first method is designed for detecting threshold-like associations in a scatter plot with particular reference to testing the significance of the extent of a data-sparse region within a scatter plot. The second method is a more general test of non-random associations. Both methods utilise significance testing based on randomizations.

Finally, LASSO regularized regression is investigated as a tool for discovering informative large scale climatogical predictors of local hydrological processes. A cross-validation scheme is proposed, which is related to practical forecasts of the next time interval to come, while at the same time maximising use of available information. The proposed methodology was applied to a case study predicting next-season river discharges in the Upper Waitaki River in New Zealand. The proposed forecasting methodology and cross-validation frameworks are applicable for similar hydroclimatological forecasting situations. The physical aspect of this part of the study included discovering the influence of the Interdecadal Pacific Oscillation on winter discharges in the upper Waitaki catchment.

text: Selected data exploration methods in hydroclimatology The volumes of climatological data are rapidly growing due to development of new acquisition platforms and advances in data storage technologies. Such advances provide new challenging problems for data analysis methods. As a result, there is an increasing interest in application and development of new machine learning and data mining methods in climatological data analysis.

This dissertation contributes to the field of data analysis by evaluation of selected methods and developing new techniques with application to hydro-climatological datasets. 

It is shown that data pre-processing with the decimated wavelet discrete transform can cause false predictive accuracy in regression machine learning algorithms. A general result is obtained that a decimated wavelet discrete transform based on a pyramidal algorithm requires utilizing some future values of the time series concerned. When the discrete wavelet transform is utilized as a pre-processing step for forecasting the time series, the necessary independence of calibration and validation data is compromised. This in turn translates into over-optimistic forecasting accuracy or even giving the illusion of forecasting skill when there in none. The obtained result is general and has wide implications in any discipline where the discrete wavelet transform is utilised in forecasting frameworks.

In addition, a general framework for creating simple predictive models is presented, based on LASSO regularised regression. The method is illustrated for time series modelling with external event forcing but the approach has general applicability. 

As a contribution to association discovery, two tests of bivariate association are developed. The first method is designed for detecting threshold-like associations in a scatter plot with particular reference to testing the significance of the extent of a data-sparse region within a scatter plot. The second method is a more general test of non-random associations. Both methods utilise significance testing based on randomizations.

Finally, LASSO regularized regression is investigated as a tool for discovering informative large scale climatogical predictors of local hydrological processes. A cross-validation scheme is proposed, which is related to practical forecasts of the next time interval to come, while at the same time maximising use of available information. The proposed methodology was applied to a case study predicting next-season river discharges in the Upper Waitaki River in New Zealand. The proposed forecasting methodology and cross-validation frameworks are applicable for similar hydroclimatological forecasting situations. The physical aspect of this part of the study included discovering the influence of the Interdecadal Pacific Oscillation on winter discharges in the upper Waitaki catchment.

year: 2016

title: Black and White: investigations on the ecology, biology and biological control of sapstain fungi in New Zealand

authors: Thwaites, Joanne M.

abstract: This study examined ecology, colonisation, biological control and detection of sapstain fungi in New Zealand.
A nationwide survey of New Zealand sapstain fungi was undertaken between 1996 and1998. In total, 1035 sites were sampled in the North and South Islands. From these collections, 1755 potential sapstain fungi were isolated and seventeen individual species were identified. The predominant sapstain fungi identified were Sphaeropsis sapinea,
Ophiostoma ips, O. floccosum, O. piliferum, O. querci and Leptographium procerum. This data was subsequently evaluated according to ecological criteria, including geographical and temporal distribution of sapstain fungi. A greater diversity of sapstain fungi was found in areas of New Zealand that were primarily plantation forestry. S. sapinea was isolated during more generalised forest sampling, and from both native and plantation forests. Ophiostoma species were isolated more frequently from Pinus radiata plantations, processing plants including mills and ports and were mainly isolated from harvested forest material such as logs, wood chips, and other wood products. S. sapinea was isolated more frequently in spring and summer while Ophiostoma species predominated during autumn and winter periods, probably linked with insect vectoring. This was the first attempt to link the sapstain organisms identified in New Zealand with their overall distribution within sectors of the forest industry, in different wood species, and in different types of wood samples.
New Zealand is one of the world's largest exporters of softwood logs. Exports of forest products provide 4% of New Zealand’s gross domestic product (GDP) with Japan, Korea, United States and the Philippines as major export markets for P. radiata logs. Conditions found within the holds of ships were thought likely to be ideal for the rapid colonisation of the sapstain fungi that results in dark penetrating stains. Log export research was designed to determine the extent of sapstain colonisation at specific points in the processing of logs from harvesting to the export destination. Two trials were established, in New Zealand summer and in winter, where mature P. radiata logs were harvested in New Zealand and shipped to export ports in Japan. Microclimatic conditions (temperature and relative humidity) on board the ships were recorded using data loggers both above deck and below deck. Nine species of sapstain fungi were isolated from logs during the summer trial. The most common species isolated were O. floccosum, O. querci and O. setosum. In contrast, a different combination of nine species was detected during the winter trial. S. sapinea, O. querci, O. floccosum, O. setosum and Ophiostoma piceae were most commonly isolated. The results of this study showed that the New Zealand sapstain fungi were being exported on logs. However, many of these fungi were previously recorded in Japan. In addition, no serious pathogens were detected. 

It was recognised during the sapstain fungal survey and export trials that a more thorough fundamental understanding of sapstain colonisation was required to properly determine the impacts of sapstain fungi to the New Zealand forest industry. In vitro and field studies were established to measure the relative colonisation of different species of sapstain fungi using synthetic media and P. radiata wood. These studies were undertaken to determine which sapstain species colonised, and how species interacted with each other following inoculation. In addition, the impacts of environmental conditions on the establishment and development of fungi and the resulting associated stains were determined. Temperature was found to affect the growth of various species of sapstain fungi on synthetic media and on P. radiata wood and logs. In the field studies O. floccosum was found to be the most successful coloniser of P. radiata logs in both winter and summer. Environmental factors such as temperature and moisture content were found to affect stain development. All fungal treatments developed sapstain discolouration from 15 days following inoculation in the summer field trial. In contrast, no stain was evident on any treatment in the winter field trial 60 days following inoculation. The colonisation of P. radiata by sapstain fungi was determined using microscopic techniques. Sapstain fungal hyphae were abundantly present in the ray parenchyma cells, tracheid lumen and resin canals of P. radiata wood. No differences in hyphal penetration were observed between the different sapstain fungal species at the cellular level. From these results a better understanding of the biology of sapstain species emerged. This new knowledge of the mechanisms and environmental triggers of fungal colonisation and stain development will aid in the more advanced technologies and management strategies to successfully control sapstain.

The many negative environmental impacts associated with traditional anti-sapstain chemical treatments led to increased interest in the more benign treatments of logs and wood using biological control technologies. The potential biological treatment of sapstain fungi using albino strains of O. floccosum, O. piceae and O. pluriannulatum was evaluated. These albino fungi demonstrated varied growth characteristics at different temperatures on both synthetic media and on P. radiata wood specimens. Comparable growth was found when evaluating wild type and albino sapstain strains in synthetic media and P. radiata wood in laboratory and field studies. Four field trials showed considerable variation in the biological control potential of the albino strains against wild type sapstain fungi. The mode of action of the albino strains was found to be competitive, through the use of primary resource capture of wood nutrients. However, albino O. floccosum strains were shown to produce zonal barriers when challenged with S. sapinea.

Proteomic analysis of cell wall proteins was undertaken to differentiate sapstain fungi from other wood inhabiting fungi and in an attempt to develop a method of determining the presence of sapstain fungi in wood prior to the development of stain. Proteins were extracted from the cell walls of various sapstain fungi (L. procerum, O. ips, O. Querci and S. sapinea) and wood inhabiting fungi (Alternaria alternata, Epicoccum nigrum, Trichoderma koningi) grown in liquid culture. Two dimensional (2D) protein profiles were made and compared. A total of 93 proteins were analysed using mass spectroscopy and the profiles compared to protein databases. This is the first investigation using proteomics of the cell wall proteins of Ophiostoma species and S. sapinea.

This study addressed the importance of sapstain fungi in New Zealand on P. radiata and increased our understanding of ecological requirements of the different sapstain species. Differences between these species with respect to colonisation and the development of associated stains were identified and investigated, enabling a critical evaluation of those species that were found to be most significant to the New Zealand forest industry. The future of sapstain management depends on a thorough ecological understanding of key sapstain fungal species involved in the cosmetic degradation of wood and an ability to manage the impacts of these species on the New Zealand forest industry using a combination of forest management practises and biological and chemical control techniques.

text: Black and White: investigations on the ecology, biology and biological control of sapstain fungi in New Zealand This study examined ecology, colonisation, biological control and detection of sapstain fungi in New Zealand.
A nationwide survey of New Zealand sapstain fungi was undertaken between 1996 and1998. In total, 1035 sites were sampled in the North and South Islands. From these collections, 1755 potential sapstain fungi were isolated and seventeen individual species were identified. The predominant sapstain fungi identified were Sphaeropsis sapinea,
Ophiostoma ips, O. floccosum, O. piliferum, O. querci and Leptographium procerum. This data was subsequently evaluated according to ecological criteria, including geographical and temporal distribution of sapstain fungi. A greater diversity of sapstain fungi was found in areas of New Zealand that were primarily plantation forestry. S. sapinea was isolated during more generalised forest sampling, and from both native and plantation forests. Ophiostoma species were isolated more frequently from Pinus radiata plantations, processing plants including mills and ports and were mainly isolated from harvested forest material such as logs, wood chips, and other wood products. S. sapinea was isolated more frequently in spring and summer while Ophiostoma species predominated during autumn and winter periods, probably linked with insect vectoring. This was the first attempt to link the sapstain organisms identified in New Zealand with their overall distribution within sectors of the forest industry, in different wood species, and in different types of wood samples.
New Zealand is one of the world's largest exporters of softwood logs. Exports of forest products provide 4% of New Zealand’s gross domestic product (GDP) with Japan, Korea, United States and the Philippines as major export markets for P. radiata logs. Conditions found within the holds of ships were thought likely to be ideal for the rapid colonisation of the sapstain fungi that results in dark penetrating stains. Log export research was designed to determine the extent of sapstain colonisation at specific points in the processing of logs from harvesting to the export destination. Two trials were established, in New Zealand summer and in winter, where mature P. radiata logs were harvested in New Zealand and shipped to export ports in Japan. Microclimatic conditions (temperature and relative humidity) on board the ships were recorded using data loggers both above deck and below deck. Nine species of sapstain fungi were isolated from logs during the summer trial. The most common species isolated were O. floccosum, O. querci and O. setosum. In contrast, a different combination of nine species was detected during the winter trial. S. sapinea, O. querci, O. floccosum, O. setosum and Ophiostoma piceae were most commonly isolated. The results of this study showed that the New Zealand sapstain fungi were being exported on logs. However, many of these fungi were previously recorded in Japan. In addition, no serious pathogens were detected. 

It was recognised during the sapstain fungal survey and export trials that a more thorough fundamental understanding of sapstain colonisation was required to properly determine the impacts of sapstain fungi to the New Zealand forest industry. In vitro and field studies were established to measure the relative colonisation of different species of sapstain fungi using synthetic media and P. radiata wood. These studies were undertaken to determine which sapstain species colonised, and how species interacted with each other following inoculation. In addition, the impacts of environmental conditions on the establishment and development of fungi and the resulting associated stains were determined. Temperature was found to affect the growth of various species of sapstain fungi on synthetic media and on P. radiata wood and logs. In the field studies O. floccosum was found to be the most successful coloniser of P. radiata logs in both winter and summer. Environmental factors such as temperature and moisture content were found to affect stain development. All fungal treatments developed sapstain discolouration from 15 days following inoculation in the summer field trial. In contrast, no stain was evident on any treatment in the winter field trial 60 days following inoculation. The colonisation of P. radiata by sapstain fungi was determined using microscopic techniques. Sapstain fungal hyphae were abundantly present in the ray parenchyma cells, tracheid lumen and resin canals of P. radiata wood. No differences in hyphal penetration were observed between the different sapstain fungal species at the cellular level. From these results a better understanding of the biology of sapstain species emerged. This new knowledge of the mechanisms and environmental triggers of fungal colonisation and stain development will aid in the more advanced technologies and management strategies to successfully control sapstain.

The many negative environmental impacts associated with traditional anti-sapstain chemical treatments led to increased interest in the more benign treatments of logs and wood using biological control technologies. The potential biological treatment of sapstain fungi using albino strains of O. floccosum, O. piceae and O. pluriannulatum was evaluated. These albino fungi demonstrated varied growth characteristics at different temperatures on both synthetic media and on P. radiata wood specimens. Comparable growth was found when evaluating wild type and albino sapstain strains in synthetic media and P. radiata wood in laboratory and field studies. Four field trials showed considerable variation in the biological control potential of the albino strains against wild type sapstain fungi. The mode of action of the albino strains was found to be competitive, through the use of primary resource capture of wood nutrients. However, albino O. floccosum strains were shown to produce zonal barriers when challenged with S. sapinea.

Proteomic analysis of cell wall proteins was undertaken to differentiate sapstain fungi from other wood inhabiting fungi and in an attempt to develop a method of determining the presence of sapstain fungi in wood prior to the development of stain. Proteins were extracted from the cell walls of various sapstain fungi (L. procerum, O. ips, O. Querci and S. sapinea) and wood inhabiting fungi (Alternaria alternata, Epicoccum nigrum, Trichoderma koningi) grown in liquid culture. Two dimensional (2D) protein profiles were made and compared. A total of 93 proteins were analysed using mass spectroscopy and the profiles compared to protein databases. This is the first investigation using proteomics of the cell wall proteins of Ophiostoma species and S. sapinea.

This study addressed the importance of sapstain fungi in New Zealand on P. radiata and increased our understanding of ecological requirements of the different sapstain species. Differences between these species with respect to colonisation and the development of associated stains were identified and investigated, enabling a critical evaluation of those species that were found to be most significant to the New Zealand forest industry. The future of sapstain management depends on a thorough ecological understanding of key sapstain fungal species involved in the cosmetic degradation of wood and an ability to manage the impacts of these species on the New Zealand forest industry using a combination of forest management practises and biological and chemical control techniques.

year: 2003

title: Military Settlement in the Middle Waikato Basin

authors: Allen, Peter D.H.

abstract: Military settlement formed a brief but distinctive phase in the European occupation of the Middle Waikato Basin. Prior to the 1863 - 1864 Waikato War, few Europeans, other than a small number of missionaries and traders, were settled in the region. The setting of the Middle Waikato Basin was largely unmodified by Man, except along the major rivers where a dense Maori population was settled. 
During the 1850's, the encroachment of European settlers upon Maori tribal lands in many North Island regions, including the Waikato, led to an increase in tension between the two populations and open conflict. This conflict slowed down the progress of colonization in the North Island. To enable colonization to continue in those regions disturbed by Maori unrest, a scheme of military settlement was devised. The aim of this scheme was the formation of compact, self-sufficient defensive settlements to act as a deterrent to Maori unrest. These settlements would also provide an assurance to settlers of security for their life and property.
 Military settlement in the Middle Waikato Basin consisted of two phases. In the first phase, the nodal points of the military settlements, the townships, were established and occupied by the military settlers. In the second phase, farm districts were surveyed around the nodal points and the military settlers moved out from the townships to occupy and develop the land they were allocated. A number of factors, relating to deficiencies in the scheme of military settlement and to the particular problems of settlement in the region, contributed to the failure of the military settlers to successfully establish farms on the land they were allocated. 
The scheme of military settlement largely failed as a method of colonization in the Middle Waikato Basin. However, the pattern of human occupation, established in the initial phase of military settlement, remained when the need for defensive settlements had gone, and forms the basis of the present pattern of settlement.

text: Military Settlement in the Middle Waikato Basin Military settlement formed a brief but distinctive phase in the European occupation of the Middle Waikato Basin. Prior to the 1863 - 1864 Waikato War, few Europeans, other than a small number of missionaries and traders, were settled in the region. The setting of the Middle Waikato Basin was largely unmodified by Man, except along the major rivers where a dense Maori population was settled. 
During the 1850's, the encroachment of European settlers upon Maori tribal lands in many North Island regions, including the Waikato, led to an increase in tension between the two populations and open conflict. This conflict slowed down the progress of colonization in the North Island. To enable colonization to continue in those regions disturbed by Maori unrest, a scheme of military settlement was devised. The aim of this scheme was the formation of compact, self-sufficient defensive settlements to act as a deterrent to Maori unrest. These settlements would also provide an assurance to settlers of security for their life and property.
 Military settlement in the Middle Waikato Basin consisted of two phases. In the first phase, the nodal points of the military settlements, the townships, were established and occupied by the military settlers. In the second phase, farm districts were surveyed around the nodal points and the military settlers moved out from the townships to occupy and develop the land they were allocated. A number of factors, relating to deficiencies in the scheme of military settlement and to the particular problems of settlement in the region, contributed to the failure of the military settlers to successfully establish farms on the land they were allocated. 
The scheme of military settlement largely failed as a method of colonization in the Middle Waikato Basin. However, the pattern of human occupation, established in the initial phase of military settlement, remained when the need for defensive settlements had gone, and forms the basis of the present pattern of settlement.

year: 1969