Weighted rank regression for clustered data analysis

We consider ranked-based regression models for clustered data analysis. A weighted Wilcoxon rank method is proposed to take account of within-cluster correlations and varying cluster sizes. The asymptotic normality of the resulting estimators is established. A method to estimate covariance of the estimators is also given, which can bypass estimation of the density function. Simulation studies are carried out to compare different estimators for a number of scenarios on the correlation structure, presence/absence of outliers and different correlation values. The proposed methods appear to perform well, in particular, the one incorporating the correlation in the weighting achieves the highest efficiency and robustness against misspecification of correlation structure and outliers. A real example is provided for illustration.

Rank-based regression for analysis of repeated measures

We consider rank-based regression models for repeated measures. To account for possible withinsubject correlations, we decompose the total ranks into between- and within-subject ranks and obtain two different estimators based on between- and within-subject ranks. A simple perturbation method is then introduced to generate bootstrap replicates of the estimating functions and the parameter estimates. This provides a convenient way for combining the corresponding two types of estimating function for more efficient estimation.

Induced smoothing for rank regression with censored survival times

Adaptions of weighted rank regression to the accelerated failure time model for censored survival data have been successful in yielding asymptotically normal estimates and flexible weighting schemes to increase statistical efficiencies. However, for only one simple weighting scheme, Gehan or Wilcoxon weights, are estimating equations guaranteed to be monotone in parameter components, and even in this case are step functions, requiring the equivalent of linear programming for computation. The lack of smoothness makes standard error or covariance matrix estimation even more difficult. An induced smoothing technique overcame these difficulties in various problems involving monotone but pure jump estimating equations, including conventional rank regression. The present paper applies induced smoothing to the Gehan-Wilcoxon weighted rank regression for the accelerated failure time model, for the more difficult case of survival time data subject to censoring, where the inapplicability of permutation arguments necessitates a new method of estimating null variance of estimating functions. Smooth monotone parameter estimation and rapid, reliable standard error or covariance matrix estimation is obtained.

Efficient regression analysis with ranked-set sampling

This article is motivated by a lung cancer study where a regression model is involved and the response variable is too expensive to measure but the predictor variable can be measured easily with relatively negligible cost. This situation occurs quite often in medical studies, quantitative genetics, and ecological and environmental studies. In this article, by using the idea of ranked-set sampling (RSS), we develop sampling strategies that can reduce cost and increase efficiency of the regression analysis for the above-mentioned situation. The developed method is applied retrospectively to a lung cancer study. In the lung cancer study, the interest is to investigate the association between smoking status and three biomarkers: polyphenol DNA adducts, micronuclei, and sister chromatic exchanges. Optimal sampling schemes with different optimality criteria such as A-, D-, and integrated mean square error (IMSE)-optimality are considered in the application. With set size 10 in RSS, the improvement of the optimal schemes over simple random sampling (SRS) is great. For instance, by using the optimal scheme with IMSE-optimality, the IMSEs of the estimated regression functions for the three biomarkers are reduced to about half of those incurred by using SRS.

Tissue culture of forest trees: Clonal multiplication of Eucalyptus grandis L

Axillary shoot proliferation was obtained using explants of Eucalyptus grandis L. juvenile and mature stages on a defined medium. Murashige and Skoog medium (MS) supplemented with benzyladenine (BA), naphthalene acetic acid (NAA) and additional thiamine. Excised shoots were induced to root on a sequence of three media: (1) White's medium containing indoleacetic acid (IAA), NAA and indole butyric acid; (IBA), (2) half-strength MS medium with charcoal and (3) half-strength MS liquid medium. The two types of explants differed in rooting response, with juvenile-derived shoots giving 60% rooting and adult-derived ones only 35%. Thus, the factors limiting cloning of selected trees in vitro are determined to be those controlling rooting of shoots in E. grandis.

Timing of fungicide applications for control of husk spot caused by Pseudocercospora macadamiae in macadamia

Pseudocercospora macadamiae is an important pathogen of macadamia in Australia, causing a disease known as husk spot. Growers strive to control the disease with a number of carbendazim and copper treatments. The aim of this study was to consider the macadamia fruit developmental stage at which fungicide application is most effective against husk spot, and whether application of copper-only applications at full-size fruit developmental stage toward the end of the season contributed to effective disease control. Fungicides were applied to macadamia trees at four developmental stages in three orchards in two subsequent production seasons. The effects of the treatments on disease incidence and severity were quantified using area under disease progress curve (AUDPC) and logistic regression models. Although disease incidence varied between cultivars, incidence and severity on cv. A16 showed consistent differences between the treatments. Most significant reduction in husk spot incidence occurred when spraying commenced at match-head sized-fruit developmental stage. All treatments significantly reduced husk spot incidence and severity compared with the untreated controls, and a significant positive linear relationship (R2 = 73%) between AUDPC and severity showed that timing of the first fungicide application is important for effective disease control. Application of fungicide at full-size fruit stage reduced disease incidence but had no impact on premature fruit drop.

Contagious dispersal of seeds of synchronously fruiting species beneath invasive and native fleshy-fruited trees

In subtropical Australia, many native and invasive plant species rely on a shared suite of frugivores, largely birds, for seed dispersal. Many native plants fruit during summer in this region, whereas most invasive plants fruit during winter, thus providing the opportunity for contagious dispersal of seeds beneath synchronously fruiting species. We sampled invasive and native seed rain beneath the canopy of a native summer-fruiting tree Guioa semiglauca and an invasive winter-fruiting tree Cinnamomum camphora, in three study sites over the course of a year. In July, during peak fruiting season for C. camphora and other invasive species, seed rain of invasive species was higher beneath C. camphora than G. semiglauca. This was partly due to the invasive tree Ligustrum lucidum, whose seed rain was three times higher beneath C. camphora than beneath the native tree. In February, seed rain of native species was more abundant beneath the canopy of G. semiglauca than beneath C. camphora, despite the fact that C. camphora was also fruiting at this time. This was probably due to the larger fruit crop produced by G. semiglauca at this time of year. Our study provides evidence that the presence of invasive bird-dispersed plants may facilitate contagious seed dispersal of other invaders, and likewise native species may facilitate seed spread of other native plants.

Wood properties and processing outcomes for plantation grown African mahogany (Khaya senegalensis) trees from Clare, Queensland (18 and 20 year-old trees) and Katherine, Northern Territory (14 year-old trees).

Khaya senegalensis, African mahogany, a high-value hardwood, was introduced in the Northern Territory (NT) in the 1950s; included in various trials there and at Weipa, Q in the 1960s-1970s; planted on ex mine sites at Weipa (160 ha) until 1985; revived in farm plantings in Queensland and in trials in the NT in the 1990s; adopted for large-scale, annual planting in the Douglas-Daly region, NT from 2006 and is to have the planted area in the NT extended to at least 20,000 ha. The recent serious interest from plantation growers, including Forest Enterprises Australia Ltd (FEA), has seen the establishment of some large scale commercial plantations. FEA initiated the current study to process relatively young plantation stands from both Northern Territory and Queensland plantations to investigate the sawn wood and veneer recovery and quality from trees ranging from 14 years (NT – 36 trees) to 18-20 years (North Queensland – 31 trees). Field measures of tree size and straightness were complemented with log end splitting assessment and cross-sectional disc sample collection for laboratory wood properties measurements including colour and shrinkage. End-splitting scores assessed on sawn logs were relatively low compared to fast grown plantation eucalypts and did not impact processing negatively. Heartwood proportion in individual trees ranged from 50% up to 92 % of butt cross-sectional disc area for the visually-assessed dark coloured central heartwood and lighter coloured transition wood combined. Dark central heartwood proportion was positively related to tree size (R2 = 0.57). Chemical tests failed to assist in determining heartwood – sapwood boundary. Mean basic density of whole disc samples was 658 kg/m3 and ranged among trees from 603 to 712 kg/m3. When freshly sawn, the heartwood of African mahogany was orange-red to red. Transition wood appeared to be pinkish and the sapwood was a pale yellow colour. Once air dried the heartwood colour generally darkens to pinkish-brown or orange-brown and the effect of prolonged time and sun exposure is to darken and change the heartwood to a red-brown colour. A portable colour measurement spectrophotometer was used to objectively assess colour variation in CIE L*, a* and b* values over time with drying and exposure to sunlight. Capacity to predict standard colour values accurately after varying periods of direct sunlight exposure using results obtained on initial air-dried surfaces decreased with increasing time to sun exposure. The predictions are more accurate for L* values which represent brightness than for variation in the a* values (red spectrum). Selection of superior breeding trees for colour is likely to be based on dried samples exposed to sunlight to reliably highlight wood colour differences. A generally low ratio between tangential and radial shrinkages was found, which was reflected in a low incidence of board distortion (particularly cupping) during drying. A preliminary experiment was carried out to investigate the quality of NIR models to predict shrinkage and density. NIR spectra correlated reasonably well with radial shrinkage and air dried density. When calibration models were applied to their validation sets, radial shrinkage was predicted to an accuracy of 76% with Standard Error of Prediction of 0.21%. There was also a strong predictive power for wood density. These are encouraging results suggesting that NIR spectroscopy has good potential to be used as a non-destructive method to predict shrinkage and wood density using 12mm diameter increment core samples. Average green off saw recovery was 49.5% (range 40 to 69%) for Burdekin Agricultural College (BAC) logs and 41.9% (range 20 to 61%) for Katherine (NT) logs. These figures are about 10% higher than compared to 30-year-old Khaya study by Armstrong et al. (2007) however they are inflated as the green boards were not docked to remove wane prior to being tallied. Of the recovered sawn, dried and dressed volume from the BAC logs, based on the cambial face of boards, 27% could potentially be used for select grade, 40% for medium feature grade and 26% for high feature grades. The heart faces had a slightly higher recovery of select (30%) and medium feature (43%) grade boards with a reduction in the volume of high feature (22%) and reject (6%) grade boards. Distribution of board grades for the NT site aged 14 years followed very similar trends to those of the BAC site boards with an average (between facial and cambial face) 27% could potentially be used for select grade, 42% for medium feature grade, 26% for high feature grade and 5% reject. Relatively to some other subtropical eucalypts, there was a low incidence of borer attack. The major grade limiting defects for both medium and high feature grade boards recovered from the BAC site were knots and wane. The presence of large knots may reflect both management practices and the nature of the genetic material at the site. This stand was not managed for timber production with a very late pruning implemented at about age 12 years. The large amount of wane affected boards is indicative of logs with a large taper and the presence of significant sweep. Wane, knots and skip were the major grade limiting defects for the NT site reflecting considerable amounts of sweep with large taper as might be expected in younger trees. The green veneer recovered from billets of seven Khaya trees rotary peeled on a spindleless lathe produced a recovery of 83% of green billet volume. Dried veneer recovery ranged from 40 to 74 % per billet with an average of 64%. All of the recovered grades were suitable for use in structural ply in accordance to AS/NZ 2269: 2008. The majority of veneer sheets recovered from all billets was C grade (27%) with 20% making D grade and 13% B grade. Total dry sliced veneer recovery from the logs of the two largest logs from each location was estimated to be 41.1%. Very positive results have been recorded in this small scale study. The amount of colour development observed and the very reasonable recoveries of both sawn and veneer products, with a good representation of higher grades in the product distribution, is encouraging. The prospects for significant improvement in these results from well managed and productive stands grown for high quality timber should be high. Additionally, the study has shown the utility of non-destructive evaluation techniques for use in tree improvement programs to improve the quality of future plantations. A few trees combined several of the traits desired of individuals for a first breeding population. Fortunately, the two most promising trees (32, 19) had already been selected for breeding on external traits, and grafts of them are established in the seed orchard.

Forest health guide: symptoms of insect and fungal damage on trees

The Forest health guide: symptoms of insect and fungal damage on trees is intended to help forestry and quarantine staff undertake tree health assessments, in both forest and urban environments. The guide is designed to be used as a quick reference to common symptoms of damage, not as an identification guide to particular insect pests and pathogens.

What was behind the bark? : An assessment of decay among urban Tilia, Betula and Acer trees felled as hazardous in the Helsinki City area

Old trees growing in urban environments are often felled due to symptoms of mechanical defects that could be hazardous to people and property. The decisions concerning these removals are justified by risk assessments carried out by tree care professionals. The major motivation for this study was to determine the most common profiles of potential hazard characteristics for the three most common urban tree genera in Helsinki City: Tilia, Betula and Acer, and in this way improve management practices and protection of old amenity trees. For this research, material from approximately 250 urban trees was collected in cooperation with the City of Helsinki Public Works Department during 2001 - 2004. From the total number of trees sampled, approximately 70% were defined as hazardous. The tree species had characteristic features as potential hazard profiles. For Tilia trees, hollowed heartwood with low fungal activity and advanced decay caused by Ganoderma lipsiense were the two most common profiles. In Betula spp., the primary reason for tree removal was usually lowered amenity value in terms of decline of the crown. Internal cracks, most often due to weak fork formation, were common causes of potential failure in Acer spp. Decay caused by Rigidoporus populinus often increased the risk of stem breakage in these Acer trees. Of the decay fungi observed, G. lipsiense was most often the reason for the increased risk of stem collapse. Other fungi that also caused extensive decay were R. populinus, Inonotus obliquus, Kretzschmaria deusta and Phellinus igniarius. The most common decay fungi in terms of incidence were Pholiota spp., but decay caused by these species did not have a high potential for causing stem breakage, because it rarely extended to the cambium. The various evaluations used in the study suggested contradictions in felling decisions based on trees displaying different stages of decay. For protection of old urban trees, it is crucial to develop monitoring methods so that tree care professionals could better analyse the rate of decay progression towards the sapwood and separate those trees with decreasing amounts of sound wood from those with decay that is restricted to the heartwood area.

Digitoitujen väri-infrailmakuvien numeerinen monikuvatulkinta metsäninventoinnissa

The use of remote sensing imagery as auxiliary data in forest inventory is based on the correlation between features extracted from the images and the ground truth. The bidirectional reflectance and radial displacement cause variation in image features located in different segments of the image but forest characteristics remaining the same. The variation has so far been diminished by different radiometric corrections. In this study the use of sun azimuth based converted image co-ordinates was examined to supplement auxiliary data extracted from digitised aerial photographs. The method was considered as an alternative for radiometric corrections. Additionally, the usefulness of multi-image interpretation of digitised aerial photographs in regression estimation of forest characteristics was studied. The state owned study area located in Leivonmäki, Central Finland and the study material consisted of five digitised and ortho-rectified colour-infrared (CIR) aerial photographs and field measurements of 388 plots, out of which 194 were relascope (Bitterlich) plots and 194 were concentric circular plots. Both the image data and the field measurements were from the year 1999. When examining the effect of the location of the image point on pixel values and texture features of Finnish forest plots in digitised CIR photographs the clearest differences were found between front-and back-lighted image halves. Inside the image half the differences between different blocks were clearly bigger on the front-lighted half than on the back-lighted half. The strength of the phenomenon varied by forest category. The differences between pixel values extracted from different image blocks were greatest in developed and mature stands and smallest in young stands. The differences between texture features were greatest in developing stands and smallest in young and mature stands. The logarithm of timber volume per hectare and the angular transformation of the proportion of broadleaved trees of the total volume were used as dependent variables in regression models. Five different converted image co-ordinates based trend surfaces were used in models in order to diminish the effect of the bidirectional reflectance. The reference model of total volume, in which the location of the image point had been ignored, resulted in RMSE of 1,268 calculated from test material. The best of the trend surfaces was the complete third order surface, which resulted in RMSE of 1,107. The reference model of the proportion of broadleaved trees resulted in RMSE of 0,4292 and the second order trend surface was the best, resulting in RMSE of 0,4270. The trend surface method is applicable, but it has to be applied by forest category and by variable. The usefulness of multi-image interpretation of digitised aerial photographs was studied by building comparable regression models using either the front-lighted image features, back-lighted image features or both. The two-image model turned out to be slightly better than the one-image models in total volume estimation. The best one-image model resulted in RMSE of 1,098 and the two-image model resulted in RMSE of 1,090. The homologous features did not improve the models of the proportion of broadleaved trees. The overall result gives motivation for further research of multi-image interpretation. The focus may be improving regression estimation and feature selection or examination of stratification used in two-phase sampling inventory techniques. Keywords: forest inventory, digitised aerial photograph, bidirectional reflectance, converted image co­ordinates, regression estimation, multi-image interpretation, pixel value, texture, trend surface

Interactions between transgenic trees and mycorrhizal and pathogenic fungi

The development of biotechnology techniques in plant breeding and the new commercial applications have raised public and scientific concerns about the safety of genetically modified (GM) crops and trees. To find out the feasibility of these new technologies in the breeding of commercially important Finnish hardwood species and to estimate the ecological risks of the produced transgenic plants, the experiments of this study have been conducted as a part of a larger project focusing on the risk assessment of GM-trees. Transgenic Betula pendula and Populus trees were produced via Agrobacterium mediated transformation. Stilbene synthase (STS) gene from pine (Pinus sylvestris) and chitinase gene from sugar beet (Beta vulgaris) were transferred to (hybrid) aspen and birch, respectively, to improve disease resistance against fungal pathogens. To modify lignin biosynthesis, a 4-coumarate:coenzyme A ligase (4CL) gene fragment in antisense orientation was introduced into two birch clones. In in vitro test, one transgenic aspen line expressing pine STS gene showed increased resistance to decay fungus Phellinus tremulae. In the field, chitinase transgenic birch lines were more susceptible to leaf spot (Pyrenopeziza betulicola) than the non-transgenic control clone while the resistance against birch rust (Melampsoridium betulinum) was improved. No changes in the content or composition of lignin were detected in the 4CL antisense birch lines. In order to evaluate the ecological effects of the produced GM trees on non-target organisms, an in vitro mycorrhiza experiment with Paxillus involutus and a decomposition experiment in the field were performed. The expression of a transgenic chitinase did not disturb the establishment of mycorrhizal symbiosis between birch and P. involutus in vitro. 4CL antisense transformed birch lines showed retarded root growth but were able to form normal ectomycorrhizal associations with the mycorrhizal fungus in vitro. 4CL lines also showed normal litter decomposition. Unexpected growth reductions resulting from the gene transformation were observed in chitinase transgenic and 4CL antisense birch lines. These results indicate that genetic engineering can provide a tool in increasing disease resistance in Finnish tree species. More extensive data with several ectomycorrhizal species is needed to evaluate the consequences of transgene expression on beneficial plant-fungus symbioses. The potential pleiotropic effects of the transgene should also be taken into account when considering the safety of transgenic trees.

Species-site matching in mixed species plantations of native trees in tropical Australia

Mixed species plantations using native trees are increasingly being considered for sustainable timber production. Successful application of mixed species forestry systems requires knowledge of the potential spatial interaction between species in order to minimise the chance of dominance and suppression and to maximise wood production. Here, we examined species performances across 52 experimental plots of tree mixtures established on cleared rainforest land to analyse relationships between the growth of component species and climate and soil conditions. We derived site index (SI) equations for ten priority species to evaluate performance and site preferences. Variation in SI of focus species demonstrated that there are strong species-specific responses to climate and soil variables. The best predictor of tree growth for rainforest species Elaeocarpus grandis and Flindersia brayleyana was soil type, as trees grew significantly better on well-draining than on poorly drained soil profiles. Both E. grandis and Eucalyptus pellita showed strong growth response to variation in mean rain days per month. Our study generates understanding of the relative performance of species in mixed species plantations in the Wet Tropics of Australia and improves our ability to predict species growth compatibilities at potential planting sites within the region. Given appropriate species selections and plantation design, mixed plantations of high-value native timber species are capable of sustaining relatively high productivity at a range of sites up to age 10 years, and may offer a feasible approach for large-scale reforestation.