Ecological theories often encompass multiple levels of biological organization, such as genes, individuals, populations, and communities. Despite substantial progress toward ecological theory spanning multiple levels, ecological data rarely are connected in this way. This is unfortunate because different types of ecological data often emerge from the same underlying processes and, therefore, are naturally connected among levels. Here, we describe an approach to integrate data collected at multiple levels (e.g., individuals, populations) in a single statistical analysis. The resulting integrated models make full use of existing data and might strengthen links between statistical ecology and ecological models and theories that span multiple levels of organization. Integrated models are increasingly feasible due to recent advances in computational statistics, which allow fast calculations of multiple likelihoods that depend on complex mechanistic models. We discuss recently developed integrated models and outline a simple application using data on freshwater fishes in south-eastern Australia. Available data on freshwater fishes include population survey data, mark-recapture data, and individual growth trajectories. We use these data to estimate age-specific survival and reproduction from size-structured data, accounting for imperfect detection of individuals. Given that such parameter estimates would be infeasible without an integrated model, we argue that integrated models will strengthen ecological theory by connecting theoretical and mathematical models directly to empirical data. Although integrated models remain conceptually and computationally challenging, integrating ecological data among levels is likely to be an important step toward unifying ecology among levels.

Statistical decision theory (SDT) is a sub-field of decision theory that formally incorporates statistical investigation into a decision-theoretic framework to account for uncertainties in a decision problem. SDT provides a unifying analysis of three types of information: statistical results from a data set, knowledge of the consequences of potential choices (i.e., loss), and prior beliefs about a system. SDT links the theoretical development of a large body of statistical methods including point estimation, hypothesis testing, and confidence interval estimation. The theory and application of SDT have mainly been developed and published in the fields of mathematics, statistics, operations research, and other decision sciences, but have had limited exposure in ecology. Thus, we provide an introduction to SDT for ecologists and describe its utility for linking the conventionally separate tasks of statistical investigation and decision making in a single framework. We describe the basic framework of both Bayesian and frequentist SDT, its traditional use in statistics, and discuss its application to decision problems that occur in ecology. We demonstrate SDT with two types of decisions: Bayesian point estimation, and an applied management problem of selecting a prescribed fire rotation for managing a grassland bird species. Central to SDT, and decision theory in general, are loss functions. Thus, we also provide basic guidance and references for constructing loss functions for an SDT problem.

Ecological flow (EFlow) statistics have been designated to characterize the magnitude, frequency, and duration of extreme high- and low-flows, the timing of seasonal flows, and the consistency of the historic regime. This Child Item contains a table of 178 EFlows for the time periods 1940-1969, 1970-1999, and 2000-2018, with absolute and percent change between periods, where applicable. Statistics were computed by Water Year (WY) for all 178 metrics and absolute and percent change were calculated by comparing metrics between combinations of two of the three time periods (1940-1969 and 1970-1999; 1940-1969 and 2000-2018; 1970-1999 and 2000-2018). Streamgages from the original dataset (n = 409) were excluded from one or more time periods of analysis because of extensive data gaps that would yield incomplete EFlows; therefore, stations were indexed into the earliest possible time period relative to their installation date (for example, a streamgage with an operating start year of 1958 would be included in the analysis for the time periods 1970-1999 and 2000-2018), which resulted in different sample sizes for each period: 1940-1969 (n = 90), 1970-1999 (n = 167), and 2000-2018 (n = 243). Similarly, multiple stations were wholly excluded because of frequent discontinuities in the daily mean streamflow through all three time periods. Finally, a streamgage must have fallen within at least two time periods to have a change value. As such, not all stations are represented in the change analysis (change between 1940-1969 and 1970-1999 [n = 90]; change between 1940-1969 and 2000-2018 [n = 90]; change between 1970-1999 and 2000-2018 [n = 167]).

All statistics were done in R Studio

In 1991, the U.S. Geological Survey (USGS) began a study of more than 50 major river basins across the Nation as part of the National Water-Quality Assessment (NAWQA) project of the National Water-Quality Program. One of the major goals of the NAWQA project is to determine how water-quality and ecological conditions change over time. To support that goal, long-term consistent and comparable ecological monitoring has been conducted on streams and rivers throughout the Nation. Fish, invertebrate, and diatom data collected as part of the NAWQA program were retrieved from the USGS Aquatic Bioassessment database for use in trend analysis. Ultimately, these data will provide insight into how natural features and human activities have contributed to changes in ecological condition over time in the Nation’s streams and rivers. This USGS data release contains all of the input and output files necessary to reproduce the results of the ecological trend analysis described in the associated U.S. Geological Survey Scientific Investigations Report. Data preparation for input to the model is also fully described in the above mentioned report.

Environmental Radiation Data (ERD) is an electronic and print journal compiled and distributed quarterly by the Office of Radiation and Indoor Air's National Air and Radiation Environmental Laboratory (NAREL) in Montgomery, Alabama. It contains data from RadNet (previously known as ERAMS.)

An analysis of the tweets from ESA2016 meeting.Used r-package 'tm'All code on Github here: https://cjlortie.github.io/esa2016.tweets/

In the last decade, a plethora of algorithms have been developed for spatial ecology studies. In our case, we use some of these codes for underwater research work in applied ecology analysis of threatened endemic fishes and their natural habitat. For this, we developed codes in Rstudio® script environment to run spatial and statistical analyses for ecological response and spatial distribution models (e.g., Hijmans & Elith, 2017; Den Burg et al., 2020). The employed R packages are as follows: caret (Kuhn et al., 2020), corrplot (Wei & Simko, 2017), devtools (Wickham, 2015), dismo (Hijmans & Elith, 2017), gbm (Freund & Schapire, 1997; Friedman, 2002), ggplot2 (Wickham et al., 2019), lattice (Sarkar, 2008), lattice (Musa & Mansor, 2021), maptools (Hijmans & Elith, 2017), modelmetrics (Hvitfeldt & Silge, 2021), pander (Wickham, 2015), plyr (Wickham & Wickham, 2015), pROC (Robin et al., 2011), raster (Hijmans & Elith, 2017), RColorBrewer (Neuwirth, 2014), Rcpp (Eddelbeuttel & Balamura, 2018), rgdal (Verzani, 2011), sdm (Naimi & Araujo, 2016), sf (e.g., Zainuddin, 2023), sp (Pebesma, 2020) and usethis (Gladstone, 2022).

It is important to follow all the codes in order to obtain results from the ecological response and spatial distribution models. In particular, for the ecological scenario, we selected the Generalized Linear Model (GLM) and for the geographic scenario we selected DOMAIN, also known as Gower's metric (Carpenter et al., 1993). We selected this regression method and this distance similarity metric because of its adequacy and robustness for studies with endemic or threatened species (e.g., Naoki et al., 2006). Next, we explain the statistical parameterization for the codes immersed in the GLM and DOMAIN running:

In the first instance, we generated the background points and extracted the values of the variables (Code2_Extract_values_DWp_SC.R). Barbet-Massin et al. (2012) recommend the use of 10,000 background points when using regression methods (e.g., Generalized Linear Model) or distance-based models (e.g., DOMAIN). However, we considered important some factors such as the extent of the area and the type of study species for the correct selection of the number of points (Pers. Obs.). Then, we extracted the values of predictor variables (e.g., bioclimatic, topographic, demographic, habitat) in function of presence and background points (e.g., Hijmans and Elith, 2017).

Subsequently, we subdivide both the presence and background point groups into 75% training data and 25% test data, each group, following the method of Soberón & Nakamura (2009) and Hijmans & Elith (2017). For a training control, the 10-fold (cross-validation) method is selected, where the response variable presence is assigned as a factor. In case that some other variable would be important for the study species, it should also be assigned as a factor (Kim, 2009).

After that, we ran the code for the GBM method (Gradient Boost Machine; Code3_GBM_Relative_contribution.R and Code4_Relative_contribution.R), where we obtained the relative contribution of the variables used in the model. We parameterized the code with a Gaussian distribution and cross iteration of 5,000 repetitions (e.g., Friedman, 2002; kim, 2009; Hijmans and Elith, 2017). In addition, we considered selecting a validation interval of 4 random training points (Personal test). The obtained plots were the partial dependence blocks, in function of each predictor variable.

Subsequently, the correlation of the variables is run by Pearson's method (Code5_Pearson_Correlation.R) to evaluate multicollinearity between variables (Guisan & Hofer, 2003). It is recommended to consider a bivariate correlation ± 0.70 to discard highly correlated variables (e.g., Awan et al., 2021).

Once the above codes were run, we uploaded the same subgroups (i.e., presence and background groups with 75% training and 25% testing) (Code6_Presence&backgrounds.R) for the GLM method code (Code7_GLM_model.R). Here, we first ran the GLM models per variable to obtain the p-significance value of each variable (alpha ≤ 0.05); we selected the value one (i.e., presence) as the likelihood factor. The generated models are of polynomial degree to obtain linear and quadratic response (e.g., Fielding and Bell, 1997; Allouche et al., 2006). From these results, we ran ecological response curve models, where the resulting plots included the probability of occurrence and values for continuous variables or categories for discrete variables. The points of the presence and background training group are also included.

On the other hand, a global GLM was also run, from which the generalized model is evaluated by means of a 2 x 2 contingency matrix, including both observed and predicted records. A representation of this is shown in Table 1 (adapted from Allouche et al., 2006). In this process we select an arbitrary boundary of 0.5 to obtain better modeling performance and avoid high percentage of bias in type I (omission) or II (commission) errors (e.g., Carpenter et al., 1993; Fielding and Bell, 1997; Allouche et al., 2006; Kim, 2009; Hijmans and Elith, 2017).

Table 1. Example of 2 x 2 contingency matrix for calculating performance metrics for GLM models. A represents true presence records (true positives), B represents false presence records (false positives - error of commission), C represents true background points (true negatives) and D represents false backgrounds (false negatives - errors of omission).

Validation set

Model

True

False

Presence

A

B

Background

C

D

We then calculated the Overall and True Skill Statistics (TSS) metrics. The first is used to assess the proportion of correctly predicted cases, while the second metric assesses the prevalence of correctly predicted cases (Olden and Jackson, 2002). This metric also gives equal importance to the prevalence of presence prediction as to the random performance correction (Fielding and Bell, 1997; Allouche et al., 2006).

The last code (i.e., Code8_DOMAIN_SuitHab_model.R) is for species distribution modelling using the DOMAIN algorithm (Carpenter et al., 1993). Here, we loaded the variable stack and the presence and background group subdivided into 75% training and 25% test, each. We only included the presence training subset and the predictor variables stack in the calculation of the DOMAIN metric, as well as in the evaluation and validation of the model.

Regarding the model evaluation and estimation, we selected the following estimators:

1) partial ROC, which evaluates the approach between the curves of positive (i.e., correctly predicted presence) and negative (i.e., correctly predicted absence) cases. As farther apart these curves are, the model has a better prediction performance for the correct spatial distribution of the species (Manzanilla-Quiñones, 2020).

2) ROC/AUC curve for model validation, where an optimal performance threshold is estimated to have an expected confidence of 75% to 99% probability (De Long et al., 1988).

These data include the abundance, emergence, and persistence of puncturevine (Tribulus terrestris), a harmful invasive species in Western North America. We mapped the demography and distribution of this plant in Boise, ID, United States in summer 2020. These data include both the mapped plots and puncturevine points as well as .csv files with spatial covariates related to puncturevine outbreaks.

Multidimensional scaling (MDS) is a dimensionality reduction technique for microbial ecology data analysis that represents the multivariate structure while preserving pairwise distances between samples. While its improvements have enhanced the ability to reveal data patterns by sample groups, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. In this study, we introduce a new MDS-based ordination, “F-informed MDS,†which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using simulated compositional datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and ..., , # Multidimensional scaling informed by F-statistic: Visualizing grouped microbiome data with inference

• Dataset DOI: 10.5061/dryad.vmcvdnd3x
• Software: https://github.com/soob-kim/FinfoMDS
  (also in prep for Bioconductor submission)
• File or folder names are italicized. Package or variable names are monospaced.Â

File: Data.zip

Description:Â Raw data used in this study. Includes 3 folders and 1 file (see below).

1. Folder Simulated contains pairwise distances and ordination results from three simulated datasets. Includes 7 subfolders and 6 files.
   • Six files are the original dataset and its associated labels set. The names are formatted as "sim_<*x*>-<*type*>.*csv*" where <*x*> is the replicate number and <*type*> indicates whether the file is the design matrix ("data") or response vector ("Y").
   • Seven subfolders are grouped by the ordination method. Likewise, the file ...,

The evolution of traits involved in ecological interactions such as predator-prey, host-parasite, and plant-pollinator interactions, are likely to be shaped by the phylogenetic history of both parties. We develop generalized linear mixed-effects models (GLMM) that estimate the effect of both parties' phylogenetic history on trait evolution, both in isolation but also in terms of how the two histories interact. Using data on the incidence and abundance of 206 flea species on 121 mammal species, we illustrate our method and compare it to previously used methods for detecting host-parasite coevolution. At large spatial scales we find that the phylogenetic interaction effect was substantial, indicating that related parasite species were more likely to be found on related host species. At smaller spatial scales, and when sampling effort was not controlled for, phylogenetic effects on the number and types of parasite species harbored by hosts were found to dominate. We go on to show that in situations where these additional phylogenetic effects exist, then previous methods have very high Type I error rates when testing for the phylogenetic interaction. Our GLMM method represents a robust and reliable approach to quantify the phylogenetic effects of traits determined by, or defined by, ecological interactions and has the advantage that it can easily be extended and interpreted in a broader context than existing permutation tests.

An Environmental Quality Index (EQI) for all counties in the United States for the time period 2000-2005 was developed which incorporated data from five environmental domains: air, water, land, built, and socio-demographic. The EQI was developed in four parts: domain identification; data source identification and review; variable construction; and data reduction using principal components analysis (PCA). The methods applied provide a reproducible approach that capitalizes almost exclusively on publically-available data sources. The primary goal in creating the EQI is to use it as a composite environmental indicator for research on human health. A series of peer reviewed manuscripts utilized the EQI in examining health outcomes. This dataset is not publicly accessible because: This series of papers are considered Human health research - not to be loaded onto ScienceHub. It can be accessed through the following means: The EQI data can be accessed at: https://edg.epa.gov/data/Public/ORD/NHEERL/EQI. Format: EQI data, metadata, formats, and data dictionary all available at website. This dataset is associated with the following publications: Gray, C., L. Messer, K. Rappazzo, J. Jagai, S. Grabich, and D. Lobdell. The association between physical inactivity and obesity is modified by five domains of environmental quality in U.S. adults: A cross-sectional study. PLoS ONE. Public Library of Science, San Francisco, CA, USA, 13(8): e0203301, (2018). Patel, A., J. Jagai, L. Messer, C. Gray, K. Rappazzo, S. DeflorioBarker, and D. Lobdell. Associations between environmental quality and infant mortality in the United States, 2000-2005. Archives of Public Health. BioMed Central Ltd, London, UK, 76(60): 1, (2018). Gray, C., D. Lobdell, K. Rappazzo, Y. Jian, J. Jagai, L. Messer, A. Patel, S. Deflorio-Barker, C. Lyttle, J. Solway, and A. Rzhetsky. Associations between environmental quality and adult asthma prevalence in medical claims data. ENVIRONMENTAL RESEARCH. Elsevier B.V., Amsterdam, NETHERLANDS, 166: 529-536, (2018).

RobinsonEtAl2012_ButterfliesRobinsonEtAl2012_TransectLocations

A vector GIS dataset of candidate areas for terrestrial ecological restoration based on landscape context. The dataset was created using NLCD 2011 (www.mrlc.gov) and morphological spatial pattern analysis (MSPA) (http://forest.jrc.ec.europa.eu/download/software/guidos/mspa/). There are 13 attributes for the polygons in the dataset, including presence and length of roads, candidate area size, size of surround contiguous natural areas, soil productivity, presence and length of road, areas suitable for wetland restoration, and others.

This dataset is associated with the following publication: Wickham, J., K. Riiters, P. Vogt, J. Costanza, and A. Neale. An inventory of continental U.S. terrestrial candidate ecological restoration areas based on landscape context. RESTORATION ECOLOGY. Blackwell Publishing, Malden, MA, USA, 25(6): 894-902, (2017).

Data from underwater video cameras and underwater visual census to obtain real fish densities considering the habitat characteristics in the individual detectability. In addition, simulation for demonstrating (1) how to calibrate the cameras for accounting for the effects of an "external" continuous variable on detectability and (2) how to apply such a cameras calibration for estimate fish density at new sites.

Characteristics of the two data sets analysed, including the number of turbines investigated, the total number of turbine-nights, the number of bat call recordings, the total number of carcasses found, and the average wind speed with standard deviation.

This dataset contains adult mosquito surveys and sampling data by species and date, as well as anonymized neighborhood and environmental sensor data for research conducted in neighborhoods in Baltimore, Maryland USA (2012-2017).

This dataset includes the following files:
Metadata_Updated_for_Public_Archive.xlsx. Descriptive metadata for all sheets including redacted (confidential) data files. Mastercontainer_Public_Archive.xlsx. These are data from container surveys conducted between 2012-2016. Masterkapsurvey_Public_Archive_v20220928.xlsx. Anonymized surveys of residents in sample neighborhood blocks in years 2012, 2013, 2014, and 2016. MASTERadult.xlsx. Counts and identification of (primarily) female adult mosquitoes that were actively trapped over years and block clusters. MASTER_Bloodfed.xlsx. Includes identification of blood meal source of 2015 and 2016 subsamples of adult female mosquitoes. Master_iButton.xlsx. Raw relative humidity and temperature data recorded by iButton during 2015-2017 as well as year-long summaries by sensor for 2016 and 2017. The Cary Institute of Ecosystem Studies furnishes data under the following conditions: The data have received quality assurance scrutiny, and, although we are confident of the accuracy of these data, Cary Institute will not be held liable for errors in these data. Data are subject to change resulting from updates in data screening or models used. To cite these data, click on the Cite button on this page. Metadata associated with the confidential data from this study may be found here. Questions about these data should be directed to Dr. Shannon LaDeau, ladeaus@caryinstitute.org or Cary Data Management, datamanagement@caryinstitute.org.

The Geoecology database is a compilation of environmental data for the period 1941 to 1981. The Geoecology database contains selected data on terrain and soils, water resources, forestry, vegetation, agriculture, land use, wildlife, air quality, climate, natural areas, and endangered species. Data on selected human population characteristics are also included to complement the environmental files. Data represent the conterminous United States at the county level. These historical data are provided as a source of 1970s baseline environmental conditions for the United States.

This dataset was created for the following publication: Cheruvelil, K.S., S. Yuan, K.E. Webster, P.-N. Tan, J.-F. Lapierre, S.M. Collins, C.E. Fergus, C.E. Scott, E.N. Henry, P.A. Soranno, C.T. Filstrup, T. Wagner. Under review. Creating multi-themed ecological regions for macrosystems ecology: Testing a flexible, repeatable, and accessible clustering method. Submitted to Ecology and Evolution July 2016. This dataset includes lake total phosphorus (TP) and Secchi data from summer, epilimnetic water samples, as well as 52 geographic variables at the HU-12 scale; it is a subset of the larger LAGOS-NE database (Lake multi-scaled geospatial and temporal database, described in Soranno et al. 2015). LAGOS-NE compiles multiple, individual lake water chemistry datasets into an integrated database. We accessed LAGOSLIMNO version 1.054.1 for lake water chemistry data and LAGOSGEO version 1.03 for geographic data. In the LAGOSLIMNO database, lake water chemistry data were collected from individual state agency sampling and volunteer programs designed to monitor lake water quality. Water chemistry analyses follow standard lab methods. In the LAGOSGEO database geographic data were collected from national scale geographic information systems (GIS) data layers. The dataset is a subset of the following integrated databases: LAGOSLIMNO v.1.054.1 and LAGOSGEO v.1.03. For full documentation of these databases, please see the publication below: Soranno, P.A., E.G. Bissell, K.S. Cheruvelil, S.T. Christel, S.M. Collins, C.E. Fergus, C.T. Filstrup, J.F. Lapierre, N.R. Lottig, S.K. Oliver, C.E. Scott, N.J. Smith, S. Stopyak, S. Yuan, M.T. Bremigan, J.A. Downing, C. Gries, E.N. Henry, N.K. Skaff, E.H. Stanley, C.A. Stow, P.-N. Tan, T. Wagner, K.E. Webster. 2015. Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science and data reuse. GigaScience 4:28 doi:10.1186/s13742-015-0067-4 .