Estimating the spatial scales of regionalized variables by nested sampling, hierarchical analysis of variance and residual maximum likelihood

The variogram is essential for local estimation and mapping of any variable by kriging. The variogram itself must usually be estimated from sample data. The sampling density is a compromise between precision and cost, but it must be sufficiently dense to encompass the principal spatial sources of variance. A nested, multi-stage, sampling with separating distances increasing in geometric progression from stage to stage will do that. The data may then be analyzed by a hierarchical analysis of variance to estimate the components of variance for every stage, and hence lag. By accumulating the components starting from the shortest lag one obtains a rough variogram for modest effort. For balanced designs the analysis of variance is optimal; for unbalanced ones, however, these estimators are not necessarily the best, and the analysis by residual maximum likelihood (REML) will usually be preferable. The paper summarizes the underlying theory and illustrates its application with data from three surveys, one in which the design had four stages and was balanced and two implemented with unbalanced designs to economize when there were more stages. A Fortran program is available for the analysis of variance, and code for the REML analysis is listed in the paper. (c) 2005 Elsevier Ltd. All rights reserved.

Assessment of the effect of time and temperature on the availability of residual phosphate in a glasshouse study of four soils using the Olsen method

The Olsen method is an indicator of plant-available phosphorus (P). The effect of time and temperature on residual phosphate in soils was measured using the Olsen method in a pot experiment. Four soils were investigated: two from Pakistan and one each from England (calcareous) and Colombia (acidic). Two levels of residual phosphate were developed in each soil after addition of phosphate by incubation at either 10degreesC or 45degreesC. The amount of phosphate added was based on the P maximum of each soil, calculated using the Langmuir equation. Rvegrass was used as the test crop. The pooled data for the four soils incubated at 10degreesC showed good correlation between Olsen P and dry matter yield or P uptake (r(2) = 0.85 and 0.77, respectively), whereas at 45 degreesC, each soil had its own relationship and pooled data did not show correlation of Olsen P with dry matter yield or P uptake. When the data at both temperatures were pooled, Olsen P was a good indicator of yield and uptake for the English soil. For the Pakistani soils, Olsen P after 45 degreesC treatment was an underestimate relative to the 10 degreesC data and for the Colombian soil it was an overestimate. The reasons for these differences need to be explored further before high temperature incubation can be used to simulate long-term changes in the field.

Comparing sampling needs for variograms of soil properties computed by the method of moments and residual maximum likelihood

It has been generally accepted that the method of moments (MoM) variogram, which has been widely applied in soil science, requires about 100 sites at an appropriate interval apart to describe the variation adequately. This sample size is often larger than can be afforded for soil surveys of agricultural fields or contaminated sites. Furthermore, it might be a much larger sample size than is needed where the scale of variation is large. A possible alternative in such situations is the residual maximum likelihood (REML) variogram because fewer data appear to be required. The REML method is parametric and is considered reliable where there is trend in the data because it is based on generalized increments that filter trend out and only the covariance parameters are estimated. Previous research has suggested that fewer data are needed to compute a reliable variogram using a maximum likelihood approach such as REML, however, the results can vary according to the nature of the spatial variation. There remain issues to examine: how many fewer data can be used, how should the sampling sites be distributed over the site of interest, and how do different degrees of spatial variation affect the data requirements? The soil of four field sites of different size, physiography, parent material and soil type was sampled intensively, and MoM and REML variograms were calculated for clay content. The data were then sub-sampled to give different sample sizes and distributions of sites and the variograms were computed again. The model parameters for the sets of variograms for each site were used for cross-validation. Predictions based on REML variograms were generally more accurate than those from MoM variograms with fewer than 100 sampling sites. A sample size of around 50 sites at an appropriate distance apart, possibly determined from variograms of ancillary data, appears adequate to compute REML variograms for kriging soil properties for precision agriculture and contaminated sites. (C) 2007 Elsevier B.V. All rights reserved.

Estimating the spatial scale of herbicide and soil interactions by nested sampling, hierarchical analysis of variance and residual maximum likelihood

An unbalanced nested sampling design was used to investigate the spatial scale of soil and herbicide interactions at the field scale. A hierarchical analysis of variance based on residual maximum likelihood (REML) was used to analyse the data and provide a first estimate of the variogram. Soil samples were taken at 108 locations at a range of separating distances in a 9 ha field to explore small and medium scale spatial variation. Soil organic matter content, pH, particle size distribution, microbial biomass and the degradation and sorption of the herbicide, isoproturon, were determined for each soil sample. A large proportion of the spatial variation in isoproturon degradation and sorption occurred at sampling intervals less than 60 m, however, the sampling design did not resolve the variation present at scales greater than this. A sampling interval of 20-25 m should ensure that the main spatial structures are identified for isoproturon degradation rate and sorption without too great a loss of information in this field.

Estimating the spatial scales of regionalized variables by nested sampling, hierarchical analysis of variance and residual maximum likelihood

The variogram is essential for local estimation and mapping of any variable by kriging. The variogram itself must usually be estimated from sample data. The sampling density is a compromise between precision and cost, but it must be sufficiently dense to encompass the principal spatial sources of variance. A nested, multi-stage, sampling with separating distances increasing in geometric progression from stage to stage will do that. The data may then be analyzed by a hierarchical analysis of variance to estimate the components of variance for every stage, and hence lag. By accumulating the components starting from the shortest lag one obtains a rough variogram for modest effort. For balanced designs the analysis of variance is optimal; for unbalanced ones, however, these estimators are not necessarily the best, and the analysis by residual maximum likelihood (REML) will usually be preferable. The paper summarizes the underlying theory and illustrates its application with data from three surveys, one in which the design had four stages and was balanced and two implemented with unbalanced designs to economize when there were more stages. A Fortran program is available for the analysis of variance, and code for the REML analysis is listed in the paper. (c) 2005 Elsevier Ltd. All rights reserved.

Clinical and subclinical mastitis in smallholder dairy farms in Tanzania: Risk, intervention and knowledge transfer

In a cross-sectional study of 400 randomly selected smallholder dairy farms in the Tanga and Iringa regions of Tanzania, 14.2% (95% confidence interval (CI) = 11.6-17.3) of cows had developed clinical mastitis during the previous year. The point prevalence of subclinical mastitis, defined as a quarter positive by the California Mastitis Test (CMT) or by bacteriological culture, was 46.2% (95% Cl = 43.6-48.8) and 24.3% (95% Cl = 22.2-26.6), respectively. In a longitudinal disease study in Iringa, the incidence of clinical mastitis was 31.7 cases per 100 cow-years. A randomised intervention trial indicated that intramammary antibiotics significantly reduced the proportion of bacteriologically positive quarters in the short-term (14 days post-infusion) but teat dipping had no detectable effect on bacteriological infection and CMT positive quarters. Other risk and protective factors were identified from both the cross-sectional and longitudinal included animals with Boran breeding (odds ratio (OR) = 3,40, 95% CI = 1.00-11.57, P < 0.05 for clinical mastitis, and OR = 3.51, 95% CI = 1.299.55, P < 0.01 for a CMT positive quarter), while the practice of residual calf suckling was protective for a bacteriologically positive quarter (OR = 0.63, 95% Cl = 0.48-0.81, P <= 0.001) and for a CMT positive quarter (OR = 0.69, 95% Cl = 0.63-0.75, P < 0.001). A mastitis training course for farmers and extension officers was held, and the knowledge gained and use of different methods of dissemination were assessed over time. In a subsequent randomised controlled trial, there were strong associations between knowledge gained and both the individual question asked and the combination of dissemination methods (village meeting, video and handout) used. This study demonstrated that both clinical and subclinical mastitis is common in smallholder dairying in Tanzania, and that some of the risk and protective factors for mastitis can be addressed by practical management of dairy cows following effective knowledge transfer. (c) 2006 Elsevier B.V. All rights reserved.

Clinical and subclinical mastitis in smallholder dairy farms in Tanzania: Risk, intervention and knowledge transfer

In a cross-sectional study of 400 randomly selected smallholder dairy farms in the Tanga and Iringa regions of Tanzania, 14.2% (95% confidence interval (CI) = 11.6-17.3) of cows had developed clinical mastitis during the previous year. The point prevalence of subclinical mastitis, defined as a quarter positive by the California Mastitis Test (CMT) or by bacteriological culture, was 46.2% (95% Cl = 43.6-48.8) and 24.3% (95% Cl = 22.2-26.6), respectively. In a longitudinal disease study in Iringa, the incidence of clinical mastitis was 31.7 cases per 100 cow-years. A randomised intervention trial indicated that intramammary antibiotics significantly reduced the proportion of bacteriologically positive quarters in the short-term (14 days post-infusion) but teat dipping had no detectable effect on bacteriological infection and CMT positive quarters. Other risk and protective factors were identified from both the cross-sectional and longitudinal included animals with Boran breeding (odds ratio (OR) = 3,40, 95% CI = 1.00-11.57, P < 0.05 for clinical mastitis, and OR = 3.51, 95% CI = 1.299.55, P < 0.01 for a CMT positive quarter), while the practice of residual calf suckling was protective for a bacteriologically positive quarter (OR = 0.63, 95% Cl = 0.48-0.81, P <= 0.001) and for a CMT positive quarter (OR = 0.69, 95% Cl = 0.63-0.75, P < 0.001). A mastitis training course for farmers and extension officers was held, and the knowledge gained and use of different methods of dissemination were assessed over time. In a subsequent randomised controlled trial, there were strong associations between knowledge gained and both the individual question asked and the combination of dissemination methods (village meeting, video and handout) used. This study demonstrated that both clinical and subclinical mastitis is common in smallholder dairying in Tanzania, and that some of the risk and protective factors for mastitis can be addressed by practical management of dairy cows following effective knowledge transfer. (c) 2006 Elsevier B.V. All rights reserved.

Near infrared reflectance spectroscopy (NIRS) to predict biological parameters of maize silage: effects of particle comminution, oven drying temperature and the presence of residual moisture

Maize silage nutritive quality is routinely determined by near infrared reflectance spectroscopy (NIRS). However, little is known about the impact of sample preparation on the accuracy of the calibration to predict biological traits. A sample population of 48 maize silages representing a wide range of physiological maturities was used in a study to determine the impact of different sample preparation procedures (i.e., drying regimes; the presence or absence of residual moisture; the degree of particle comminution) on resultant NIR prediction statistics. All silages were scanned using a total of 12 combinations of sample pre-treatments. Each sample preparation combination was subjected to three multivariate regression techniques to give a total of 36 predictions per biological trait. Increased sample preparations procedure, relative to scanning the unprocessed whole plant (WP) material, always resulted in a numerical minimisation of model statistics. However, the ability of each of the treatments to significantly minimise the model statistics differed. Particle comminution was the most important factor, oven-drying regime was intermediate, and residual moisture presence was the least important. Models to predict various biological parameters of maize silage will be improved if material is subjected to a high degree of particle comminution (i.e., having been passed through a 1 mm screen) and developed on plant material previously dried at 60 degrees C. The extra effort in terms of time and cost required to remove sample residual moisture cannot be justified. (c) 2005 Elsevier B.V. All rights reserved.

Risk factors for tick attachment to smallholder dairy cattle in Tanzania

A cross-sectional study was conducted in Tanga and Iringa regions of Tanzania, and a longitudinal study in Tanga, to investigate tick-control methods and other factors influencing tick attachment to the cattle of smallholder dairy farms. Most farmers reported applying acaricides at intervals of 1-2 weeks, most used acaricides that require on-farm dilution and most farmers incorrectly diluted the acaricides. Rhipicephalus appendiculatus and Boophilus spp. ticks were those most-frequently encountered on the cattle, but few cattle carried ticks of any species (only 13 and 4.6% of tick counts of the cattle yielded adult R. appendiculatus and Boophilus spp., respectively). Animals were more likely to carry one or more adult Boophilus spp. ticks if they also carried one or more R. appendiculatus adults (OR = 14.4, CI = 9.2, 22.5). The use of pour-on acaricides was associated with lower odds that animals carried a R. appendiculatus tick (OR = 0.29, CI = 0. 18, 0.49) but higher odds that they carried a Boophilus spp. tick (OR = 2.48, CI = 1.55, 3.97). Animals > 4 months old and those with a recent history of grazing had higher odds of carrying either a R. appendiculatus (ORs = 3.41 and 2.58, CIs = 2.34, 4.98 and 1.80, 3.71), or a Boophilus spp. tick (ORs = 5.70 and 2.18, CIs = 2.34, 4.98 and 1.49. 3.25), but zero-grazing management did not prevent ticks attaching to cattle even when combined with high-frequency acaricide treatments. The odds that animals carried ticks varied amongst the agro-ecological zones (AEZs) and administrative districts where the farms were situated-but there was still considerable residual variation in tick infestation at the farm level. (c) 2004 Elsevier B.V. All rights reserved.

A longitudinal study of sero-conversion to tick-borne pathogens in smallholder dairy youngstock in Tanzania

A longitudinal study of sero-conversion of youngstock to the tick-borne pathogens Theileria parva, T mutans, Anaplasma marginale, Babesia bigemina and B. bovis was conducted over two years on smallholder dairy farms in Tanga region, Tanzania. There was evidence of maternal antibodies to all tick-borne pathogens in animals less than 18 weeks of age. Seroprevalence increased as expected with age in animals older than this but seroprevalence profiles underestimated the force of infection due to waning antibody levels between samplings. By the end of the 2-year study, less than 50% of study animals had seroconverted to each of the tick-borne pathogens investigated, consistent with the low levels of tick attachment observed on the study animals. Some associations between seroconversion to tick-borne pathogens, and counts of their known tick vectors on the animals, were identified as expected. However, some were not, suggesting that counts of some tick species may act as an index of rates of attachment of other vector species. Variation in acaricide treatment frequencies was not associated with variations in tick-borne pathogen seroprevalence suggesting that acaricides may be used more frequently than necessary on many farms. Most animals were zero-grazed, a management system associated with a significantly lower likelihood that animals seroconverted to any tick-borne pathogen exceptA. marginale. Seroprevalence varied locally with farm location (particularly for Babesia spp.) but was not well predicted by indices of ecological conditions. Our findings suggest that attempts to achieve a state of 'endemic stability' for tick-bome pathogens may be unreasonable on the smallholder dairy farms studied but reductions in the frequency of use of acaricides may be possible following prospective studies of effects on mortality and morbidity due to tick-bome pathogens. (c) 2005 Elsevier B.V. All rights reserved.

A case study of sample design for longitudinal research: young lives

This paper presents a case study to illustrate the range of decisions involved in designing a sampling strategy for a complex, longitudinal research study. It is based on experience from the Young Lives project and identifies the approaches used to sample children for longitudinal follow-up in four less developed countries (LDCs). The rationale for decisions made and the resulting benefits, and limitations, of the approaches adopted are discussed. Of particular importance is the choice of sampling approach to yield useful analysis; specific examples are presented of how this informed the design of the Young Lives sampling strategy.