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1.
Rescaling species optima estimated by weighted averaging   总被引：1，自引：0，他引：1  
The common practice of linear deshrinking in weighted averaging is known to be equivalent to a linear rescaling of the estimated species optima. In published lists of species optima, the use of rescaling is recommended, as it allows values derived from different data sets to be compared and used for new inferences, assuming that taxonomic consistency is assured. Rescaling optima is also shown to influence WA estimates of species tolerances. Non-linear rescaling is also discussed, in the form of cubical rescaling and weighted averaging-partial least squares (WA-PLS). The use of a different deshrinking equation in a small data set did lead to similar prediction errors, probably because of the small size of the data set used.  相似文献   

2.
Different calibration methods and data manipulations are being employed for quantitative paleoenvironmental reconstructions, but are rarely compared using the same data. Here, we compare several diatom-based models [weighted averaging (WA), weighted averaging with tolerance-downweighting (WAT), weighted averaging partial least squares, artificial neural networks (ANN) and Gaussian logit regression (GLR)] in different situations of data manipulation. We tested whether log-transformation of environmental gradients and square-root transformation of species data improved the predictive abilities and the reconstruction capabilities of the different calibration methods and discussed them in regard to species response models along environmental gradients. Using a calibration data set from New England, we showed that all methods adequately modelled the variables pH, alkalinity and total phosphorus (TP), as indicated by similar root mean square errors of prediction. However, WAT had lower performance statistics than simple WA and showed some unusual values in reconstruction, but setting a minimum tolerance for the modern species, such as available in the new computer program C2 version 1.4, resolved these problems. Validation with the instrumental record from Walden Pond (Massachusetts, USA) showed that WA and WAT reconstructed most closely pH and that GLR reconstructions showed the best agreement with measured alkalinity, whereas ANN and GLR models were superior in reconstructing the secondary gradient variable TP. Log-transformation of environmental gradients improved model performance for alkalinity, but not much for TP. While square-root transformation of species data improved the performance of the ANN models, they did not affect the WA models. Untransformed species data resulted in better accordance of the TP inferences with the instrumental record using WA, indicating that, in some cases, ecological information encoded in the modern and fossil species data might be lost by square-root transformation. Thus it may be useful to consider different species data transformations for different environmental reconstructions. This study showed that the tested methods are equally suitable for the reconstruction of parameters that mainly control the diatom assemblages, but that ANN and GLR may be superior in modelling a secondary gradient variable. For example, ANN and GLR may be advantageous for modelling lake nutrient levels in North America, where TP gradients are relatively short.  相似文献   

3.
The relationship between surface-sediment cladoceran and chironomid communities to lake depth was analysed in 53 lakes distributed across timberline in northern Fennoscandia using multivariate statistical approaches. The study sites are small and bathymerically simple, with water depth ranging from 0.85-27.0 m (mean 6.36 m). Maximum lake depth was the most important factor in explaining the cladoceran distributions and the second most important factor in explaining the chironomid distributions in these subarctic lakes, as assessed on the basis of a series of constrained RDAs, Monte Carlo permutation tests, and variance partitioning. Quantitative inference models for maximum lake depth were created for both groups of animals. Well-performing calibration functions for predicting lake depth were obtained in each case using linear partial least squares (PLS) regression and calibration, weighted averaging (WA) with an 'inverse' deshrinking regression, and weighted averaging partial least squares (WA-PLS). Quantitative reconstructions of lake level fluctuations should be possible from cladoceran and chironomid core data with a root mean squared error of prediction (RMSEP), as estimated by jack-knifing, of about 1.6-3.0 m.  相似文献   

4.
Paleolimnological information is often extracted from diatom records using weighted averaging calibration and regression techniques. Larger calibration sample sets yield better inferences because they better characterize the environmental characteristics and species assemblages of the sample region. To optimize inferred information from fossil assemblages, however, it is worth knowing if fewer calibration samples can be used. Furthermore, confidence in environmental reconstructions is greater if we consider the relative importance of (A) similarity between fossil and calibration assemblages and (B) how well fossil taxa respond to the environmental variable of interest. We examine these issues using ~200-year sediment profiles from four Minnesota lakes and a 145-lake surface sediment training set calibrated for total phosphorus (TP). Training set sample sizes ranging from 10 to 145 were created through random sample selection, and models based on these training sets were used to calculate diatom-inferred (DI) TP data from fossil samples. Relationships between DI-TP variability and sample size were used to determine the minimum sample size needed to optimize the model for paleo-reconstruction. Similarly, similarities between fossil and modern assemblages were calculated for each size training set. Finally, fossil and modern assemblages were compared to determine whether older fossil samples had poorer similarity with modern analogs. More than 50–80 samples, depending on lake, were needed to stabilize variability in DI-TP results, and >110 training set samples were needed to minimize modern-fossil assemblage dissimilarities. Dissimilarities appeared to increase with sample age, but only one of the four studied cores displayed a significant trend. We have two recommendations for future studies: (1) be cautious when dealing with smaller training sets, especially if they are used to interpret older fossil assemblages and (2) understand how well fossil taxa are attuned to the variable of interest, as it is critical to evaluating the quality of the diatom-inferred data.  相似文献   

5.
The 167 sample lake-water pH-diatom calibration data-set created as part of the Palaeolimnology Programme within the Surface Water Acidification Project (SWAP) is re-analysed numerically using nine different numerical methods, six based on simple two-way weighted-averaging (WA), and the other three involving Gaussian logit regression (GLR) and maximum-likelihood (ML) calibration, the modern analogue technique, or weighted-averaging partial least-squares regression and calibration. Root mean squared error of prediction and maximum bias were estimated for all nine methods based on 10,000 internal and 10,000 external cross-validations involving a training-set, an optimisation-set, and a test-set. The results show that WA with a monotonic deshrinking spline equals or slightly outperforms WA with linear inverse deshrinking, especially in external cross-validation. Methods that employ tolerance downweighting generally have an inferior performance except when combined with monotonic deshrinking. It appears that simple two-way WA extensively used in SWAP cannot be significantly bettered. Thanks to increased computing power, better software, and more rigorous cross-validations, GLR shows good performance, especially in external cross-validation.  相似文献   

6.
Using an expanded surface sample data set, representing lakes distributed across a transect from southernmost Canada to the Canadian High Arctic, a revised midge-palaeotemperature inference model was developed for eastern Canada. Modelling trials with weighted averaging (with classical and inverse deshrinking; with and without tolerance downweighting) and weighted averaging partial least squares (WA-PLS) regression, with and without square-root transformation of the species data, were used to identify the best model. Comparison of measured and predicted temperatures revealed that a 2 component WA-PLS model for square-root transformed percentage species data provided the model with the highest explained variance (r =0.88) and the lowest error estimate (RMSEP jack =2.26 °C). Comparison of temperature inferences based on the new and old models indicates that the original model may have seriously under-estimated the magnitude of late-glacial temperature oscillations in Atlantic Canada. The new inferences suggest that summer surface water temperatures in Splan Pond, New Brunswick were approximately 10 to 12 °C immediately following deglaciation and during the Younger Dryas. During the Allerod and early Holocene, surface water temperatures of 20 to 24 °C were attained. The new model thus provides the basis for more accurate palaeotemperature reconstructions throughout easternmost Canada.  相似文献   

7.
The diatom composition in surface sediments from 119 northern Swedish lakes was studied to examine the relationship with lake-water pH, alkalinity, and colour. Diatom-based predictive models, using weighted-averaging (WA) regression and calibration, partial least squares (PLS) regression and calibration, and weighted-averaging partial least squares (WA-PLS) regression and calibration, were developed for inferences of water chemistry conditions. The non-linear response between the diatom assemblages and pH and alkalinity was best modelled by weighted-averaging methods. The lowest prediction error for pH was obtained using weighted averaging, with or without tolerance downweighting. For alkalinity there was still some information in the residual structure after extracting the first weighted-averaging component, which resulted in a slight improvement of predictions when using a two component WA-PLS model. The best colour predictions were obtained using a two component PLS model. Principal component analysis (PCA) of the prediction errors, with some characteristics of the training set included as passive variables, was performed to compare the results for the different alkalinity predictive models. The results indicate that calibration techniques utilizing more than one component (PLS and WA-PLS) can improve the predictions for lakes with diatom taxa that have broad tolerances. Furthermore, we show that WA-PLS performs best compared with the other techniques for those lakes that have a high relative abundance of the most dominant taxa and a corresponding low sample heterogeneity.  相似文献   

8.
The contemporary distribution of benthic diatoms and their use as ecological indicators were examined in a coastal wetland, the Ebro Delta, as a representative of environmental conditions in Mediterranean coastal wetlands. A total of 424 diatom taxa were identified across 24 sites encompassing a wide range of wetland habitat types (coastal lagoons, salt and brackish marshes, shallow bays, microbial mats and nearshore marine waters) and conductivities. Canonical correspondence analysis showed that water conductivity and water depth were the main factors structuring the diatom assemblages. Cluster analysis identified five habitat types according to the similarity in diatom species composition: salt marshes, brackish marshes, brackish coastal lagoons and bays, coastal lagoons with fresher conditions, and nearshore open sea. For each wetland habitat, diatom indicator species were identified. Partial canonical correspondence analysis showed that water conductivity, a proxy for salinity, was the most statistically significant and independent variable for explaining the distribution of benthic diatoms in the study area. A transfer function, using a weighted average regression model, was developed for conductivity and displayed reasonable performance (r 2 = 0.64; RMSEP = 0.302 log10 mS/cm). Our study in the Ebro Delta provides a basis for using diatom assemblages to make quantitative conductivity inferences, and for using diatom indicator species to identify wetland habitats. These approaches are complementary and may be valuable for paleoenvironmental studies of (1) effects of large-scale, natural changes in the Delta (e.g. sea-level fluctuations), and (2) impacts of short-term anthropogenic changes, such as the introduction and development of rice agriculture.  相似文献   

9.
Diatoms were identified and enumerated from a surface sediment calibration set of 50 lakes in northwestern Québec. The relationship between species composition and environmental variables was examined using canonical correspondence analysis (CCA). Forward selection and Monte Carlo permutation tests in CCA indicated that diatom species distributions in the data set are most strongly correlated to lakewater pH. A strong (r 2 boot = 0.83) weighted averaging calibration model, that includes bootstrapped error estimates, was developed for inferring past lakewater pH. Using this model, temporal changes in pH were reconstructed for two kettle lakes, Lac de la Pépinière and Lac Perron. Based on limnological data, both the study lakes were expected to have recently acidified due to increased acidic precipitation and increases in anthropogenic metal loading. However, our long-term pH inference data indicate that these lakes were naturally acidic during pre-industrial times. Nonetheless, the rate of acidification, particularly in Lac de la Pépinière, has accelerated in the last ∼75 years. These long-term pH records developed for the dilute lakes in northwestern Québec suggest that the region has received increased atmospheric pollutants from the nearby Horne smelter in Rouyn-Noranda. The pH inference profiles are markedly different from many other paleolimnological studies in acid-sensitive regions of Canada that have become acidic primarily as a result of industrial activities. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users.  相似文献   

10.
Most calibration data sets used to infer past environmental conditions from biological proxies are derived from many sites. An alternative strategy is to derive the calibration data set from within a single site. Transfer functions derived from such intra-site calibration data sets are usually applied to fossil assemblages from the focal lake, but a recent development has been to apply these transfer functions to other sites. Transfer functions derived from intra-site calibration data sets can have impressive cross-validation performance, but that gives little indication of their performance when applied to other sites. Here, we develop transfer functions for lake depth from intra-lake chironomid calibration data sets in Norway and Alaska and test the resulting models by cross-validation and against known depth in external lakes. Lake depth is a statistically significant predictor of chironomid assemblages at all these lakes, and most intra-lake transfer functions perform reasonably well under cross-validation, but their performance against external data is erratic. Downcore reconstructions from transfer functions developed on different lakes are dissimilar. Ignoring the poorly performing transfer functions, only 3 of 14 downcore reconstructions are statistically significant. Few assemblages downcore had good modern analogues in the calibration data set, even when the core was from the same lake as the calibration data set. We conclude that intra-site calibration data sets can find site-specific rather than general relationships between species and the environment and thus should be applied with care and to external sites only after careful and critical validation.  相似文献   

11.
Indirect and direct gradient ordination techniques were used to study the relationship between present-day benthic and periphytic diatom assemblages and environmental factors along an altitudinal gradient in Papua New Guinea. Both within the screened initial data-set and a narrowly-defined subset of soft-water lakes, shifts in diatom assemblages are clearly related to altitudinal differences. This relation is used to construct transfer functions for inferring altitude (and hence average water temperature) from the diatom records. Calibration by canonical correspondence analysis (CCA) and simple weighted averaging calibration proved to be superior to models using WA with tolerance downweighting and to a simple WA model based on a selection of 52 indicator taxa. From the calibration models and the linear relationship between altitude and epilimnetic water temperature, the average lake water temperature can be predicted with an accuracy of 3.2°C. After further refinement, a transfer function for palaeotemperature based on diatoms would be of potential value for climatic reconstructions in tropical regions.  相似文献   

12.
?ngstr?m-Prescott equation (AP) is the algorithm recommended by the Food and Agriculture Organization (FAO) of the United Nations for calculating the surface solar radiation (R_s) to support the estimation of crop evapotranspiration.Thus,the a_s and b_s coefficients in the AP are vital.This study aims to obtain coefficients a_s and b_s in the AP,which are optimized for China’s comprehensive agricultural divisions.The average monthly solar radiation and relative sunshine duration data at 121 stations from 1957–2016 were collected.Using data from 1957 to 2010,we calculated the monthly a_s and b_s coefficients for each subregion by least-squares regression.Then,taking the observation values of R_s from 2011 to 2016 as the true values,we estimated and compared the relative accuracy of R_s calculated using the regression values of coefficients a_s and b_s and that calculated with the FAO recommended coefficients.The monthly coefficients,a_s and b_s,of each subregion are significantly different,both temporally and spatially,from the FAO recommended coefficients.The relative error range (0–54%) of R_s calculated via the regression values of the a_s and b_s coefficients is better than the relative error range (0–77%) of R_s calculated using the FAO suggested coefficients.The station-mean relative error was reduced by 1%to 6%.However,the regression values of the a_s and b_s coefficients performed worse in certain months and agricultural subregions during verification.Therefore,we selected the a_s and b_s coefficients with the minimum R_(s )estimation error as the final coefficients and constructed a coefficient recommendation table for 36 agricultural production and management subregions in China.These coefficient recommendations enrich the case study of coefficient calibration for the AP in China and can improve the accuracy of calculating R_s and crop evapotranspiration based on existing data.  相似文献   

13.
We identified, enumerated, and interpreted the diatom assemblages preserved in the surface sediments of 59 lakes located between Whitehorse in the Yukon and Tuktoyaktuk in the Northwest Territories (Canada). The lakes are distributed along a latitudinal gradient that includes several ecoclimatic zones. It also spans large gradients in limnological variables. Thus, the study lakes are ideal for environmental calibration of modern diatom assemblages. Canonical correspondence analysis, with forward selection and Monte Carlo permutation tests, showed that maximum lake depth and summer surface-water temperature were the two environmental variables that accounted for most of the variance in the diatom data. The concentrations of sodium and calcium were also important explanatory variables. Using weighted-averaging regression and calibration techniques, we developed a predictive statistical model to infer lake surface-water temperature, and we evaluated the feasibility of using diatoms as paleoclimate proxies. This model may be used to derive paleotemperature inferences from fossil diatom assemblages at appropriate sites in the western Canadian Arctic.  相似文献   

14.
Quantitative inference models for water-chemistry variables are derived from epiphytic diatom assemblages in 186 lentic and mostly shallow freshwaters in lower Belgium (Flanders). When the complete pH range is considered (pH 3.4–9.3), robust transfer functions are obtained for median pH (jack-knifed r 2 = 0.88, RMSEP = 0.38 pH units or 6.4% of the observed range) and dissolved inorganic carbon concentration (jack-knifed r 2 = 0.86, RMSEP = 0.194 log10 mg DIC l−1 or 10.2% of the observed range) by means of weighted-averaging partial least squares regression (WA-PLS). For these variables, the calibration models are as reliable as those based on sedimentary diatom assemblages. Inferences of pH may be improved by combining estimates from epiphytic and sediment assemblages. In circumneutral and alkaline conditions, WA-PLS calibration of maximum or median total phosphorus is possible (log-transformed; jack-knifed r 2 = 0.64 or 0.66 and RMSEP = 14% or 12.3% of the observed range, respectively). It makes little difference if taxa showing no response to TP are taken into consideration or not. These models considerably expand the prospects of using historical herbarium materials to hindcast environmental conditions and also allow more accurate interpretation of current compositional changes in epiphytic communities. Compared to littoral sediment assemblages, fewer water-column variables can be inferred reliably from epiphyton. This probably results from differences between the effective gradients in both habitats, together with lower in situ species diversity and less effective spatial integration (i.e. lower recruitment of phytoplankton) in the epiphyton. A comparison of the HOF response-model types and WA-optima of diatom taxa for epiphytic and sediment assemblages shows that the relationship to individual variables, and in particular to those related to trophic status, may differ with habitat. Thus, the combination of samples from both habitat types in the same calibration model is not recommended. Electronic Supplementary Material Supplementary material is available and is accessible for authorised users in the online version of this article at  相似文献   

15.
RECENT DEVELOPMENTS IN MULTIVARIATE CALIBRATION   总被引：1，自引：0，他引：1  
With the goal of understanding global chemical processes,environmental chemists have some of the mostcomplex sample analysis problems.Multivariate calibration is a tool that can be applied successfully inmany situations where traditional univariate analyses cannot.The purpose of this paper is to reviewmultivariate calibration,with an emphasis being placed on the developments in recent years.The inverseand classical models are discussed briefly,with the main emphasis on the biased calibration methods.Principal component regression(PCR)and partial least squares(PLS)are discussed,along with methodsfor quantitative and qualitative validation of the calibration models.Non-linear PCR,non-linear PLSand locally weighted regression are presented as calibration methods for non-linear data.Finally,calibration techniques using a matrix of data per sample(second-order calibration)are discussed briefly.  相似文献   

16.
This study investigated the distribution of subfossil diatom assemblages in surficial sediments of 100 lakes along steep ecological and climatic gradients in northernmost Sweden (Abisko region, 67.07° N to 68.48° N latitude, 17.67° E to 23.52° E longitude) to develop and cross-validate transfer functions for paleoenvironmental reconstruction. Of 19 environmental variables determined for each site, 15 were included in the statistical analysis. Lake-water pH (8.0%), sedimentary loss-on-ignition (LOI, 5.9% and estimated mean July air temperature (July T, 4.8%) explained the greatest amounts of variation in the distribution of diatom taxa among the 100 lakes. Temperature and pH optima and tolerances were calculated for abundant taxa. Transfer functions, based on WA-PLS (weighted averaging partial least squares), were developed for pH (r2 = 0.77, root-mean-square-error of prediction (RMSEP) = 0.19 pH units, maximum bias = 0.31, as assessed by leave-one-out cross-validation) based on 99 lakes and for July T (r2 = 0.75, RMSEP = 0.96 °C, max. bias = 1.37 °C) based on the full 100 lake set. We subsequently assessed the ability of the diatom transfer functions to estimate lake-water pH and July T using a form of independent cross-validation. To do this, the 100-lake set was divided in two subsets. An 85-lake training-set (based on single limnological measurements) was used to develop transfer functions with similar performance as those based on the full 100 lakes, and a 15-lake test-set (with 2 years of monthly limnological measurements throughout the ice-free seasons) was used to test the transfer functions developed from the 85-lake training-set. Results from the intra-set cross-validation exercise demonstrated that lake-specific prediction errors (RMSEP) for the 15-lake test-set corresponded closely with the median measured values (pH) and the estimations based on spatial interpolations of data from weather stations (July T). The prediction errors associated with diatom inferences were usually within the range of seasonal and interannual variability. Overall, our results confirm that diatoms can provide reliable and robust estimates of lake-water pH and July T, that WA-PLS is a robust calibration method and that long-term environmental data are needed for further improvement of paleolimnological transfer functions.  相似文献   

17.
A computer program for reconstructing environmental variables (e.g. lake-water pH) from fossil assemblages (e.g. diatoms) by weighted averaging regression and calibration is described. The estimation of sample-specific errors of prediction by bootstrapping is outlined. The program runs on IBM-compatible personal computers.  相似文献   

18.
Semi-parametric geographically weighted generalized linear models (S-GWGLMs) are a useful tool in modeling a regression relationship where the impact of certain explanatory variables on a non-Gaussian distributed response variable is global while that of others is spatially varying. In this article, we propose for S-GWGLMs a new estimation method, called two-stage geographically weighted maximum likelihood estimation, and further develop a likelihood ratio statistic-based bootstrap test to determine constant coefficients in the models. The performance of the estimation and test methods is then evaluated by simulations. The results show that the proposed estimation method performs as well as the existing method in estimating both constant and spatially varying coefficients but it is more efficient in terms of computation time; the bootstrap test is of accurate size under the null hypothesis and satisfactory power in identifying spatially varying coefficients. A real-world data set is finally analyzed to demonstrate the application of the proposed estimation and test methods.  相似文献   

19.
Diatom analyses were undertaken of sediment cores covering a range of water depths in a small eutrophic lake (Lough Augher, Co. Tyrone, N. Ireland). The significance of between-core variability in diatom relative frequency stratigraphy was assessed by Canonical Correspondence Analysis (CCA) where the ordination axes were constrained to external environmental variables (sediment depth, core location coordinates, water depth, effective fetch, distance-from-shore and distance-from-inflow). After the removal of the effect of sediment age by partialling it out, the resultant first two axes from the partial-CCA were significantly correlated with water depth and distance-from-shore, indicating non-uniform diatom stratigraphies across the lake. Despite this variability, all cores show the same succession of species and, therefore, record the eutrophication of the lake. Diatom-inferred total phosphorus (DI-TP) was inferred for six cores using weighted averaging regression and calibration. Apart from considerable differences of DI-TP in surficial sediment samples, there was good between-core repeatability of DI-TP profiles. These data support the use of DI-TP for establishing background nutrient concentrations for lakes, and associated implications for lake restoration schemes using single cores. Comparisons of DI-TP profiles and total diatom accumulation rate data for the individual cores indicate that diatom production peaked prior to the maximum TP concentrations in the lake.  相似文献   

20.
An analysis of modern phytolith assemblages is presented.Phytolith assemblages were studied in modern surface soils and sediments of 28sites from east Otago, New Zealand, within a range of vegetation types andmicroclimates. No simple distinction could be made between vegetation types onthe basis of phytolith assemblage composition. A Principal Components Analysis(PCA) of the phytolith data set revealed that festucoid, chloridoid andspherical phytolith morphotypes formed strong associations with sites fromwetland, grassland, and forest vegetation types, respectively. Moreimportantly, a comparison of sample replicates from each field site using Squared ChordDistance (SCD) assemblage analysis showed that wetland and grassland sitestended to produce more internally consistent phytolith assemblages than forestsites. Environmental variables including pH, conductivity, altitude,precipitation and temperature were also gathered for each site. The ability ofeach environmental variable to reflect variance in the entire phytolithdata set was estimated by a series of Redundancy Analyses (RDA) with MonteCarlo permutation tests of statistical significance. After a forward selectionprocess, transfer functions were generated using Partial Least Squares (PLS)regression and calibration with jack-knife validation. The final transferfunctions have root mean squared errors of prediction for pH (0.47), logconductivity (0.38 S cm), average annual precipitation (63mm), and average annual (0.28 °C), spring (0.38 °C) andautumn temperature (0.41 °C); the smallest group of environmental variablesexplaining the most variance in the modern phytolith data set. The most usefultransfer functions for application to fossil phytolith data andpaleoenvironmental interpretation are pH, log conductivity and annualprecipitation. The relationship between changes in pH and annual precipitationand phytolith assemblage composition found in this study presents aprima facie relationship with the potential to providedirect proxies for soil weathering and indirectly for paleoenvironmentalreconstruction.  相似文献   

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