Geology topics

Ralph Mac Nally

Publications and source records attributed to Ralph Mac Nally.

3 recordsLinked to original sources

USGS2012

Perils of correlating CUSUM-transformed variables to infer ecological relationships (Breton et al. 2006; Glibert 2010)

We comment on a nonstandard statistical treatment of time-series data first published by Breton et al. (2006) in Limnology and Oceanography and, more recently, used by Glibert (2010) in Reviews in Fisheries Science. In both papers, the authors make strong inferences about the underlying causes of population variability based on correlations between cumulative sum (CUSUM) transformations of organism abundances and environmental variables. Breton et al. (2006) reported correlations between CUSUM-transformed values of diatom biomass in Belgian coastal waters and the North Atlantic Oscillation, and between meteorological and hydrological variables. Each correlation of CUSUM-transformed variables was judged to be statistically significant. On the basis of these correlations, Breton et al. (2006) developed "the first evidence of synergy between climate and human-induced river-based nitrate inputs with respect to their effects on the magnitude of spring Phaeocystis colony blooms and their dominance over diatoms."

Limnology and Oceanography↗

USGS2010

Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary

We examined trends in abundance of four pelagic fish species (delta smelt, longfin smelt, striped bass, and threadfin shad) in the upper San Francisco Estuary, California, USA, over 40 years using Bayesian change point models. Change point models identify times of abrupt or unusual changes in absolute abundance (step changes) or in rates of change in abundance (trend changes). We coupled Bayesian model selection with linear regression splines to identify biotic or abiotic covariates with the strongest associations with abundances of each species. We then refitted change point models conditional on the selected covariates to explore whether those covariates could explain statistical trends or change points in species abundances. We also fitted a multispecies change point model that identified change points common to all species. All models included hierarchical structures to model data uncertainties, including observation errors and missing covariate values. There were step declines in abundances of all four species in the early 2000s, with a likely common decline in 2002. Abiotic variables, including water clarity, position of the 2 isohaline (X2), and the volume of freshwater exported from the estuary, explained some variation in species' abundances over the time series, but no selected covariates could explain statistically the post-2000 change points for any species.

California↗

USGS2010

Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR)

Four species of pelagic fish of particular management concern in the upper San Francisco Estuary, California, USA, have declined precipitously since ca. 2002: delta smelt ( Hypomesus transpacificus ), longfin smelt ( Spirinchus thaleichthys ), striped bass ( Morone saxatilis ), and threadfin shad ( Dorosoma petenense ). The estuary has been monitored since the late 1960s with extensive collection of data on the fishes, their pelagic prey, phytoplankton biomass, invasive species, and physical factors. We used multivariate autoregressive (MAR) modeling to discern the main factors responsible for the declines. An expert-elicited model was built to describe the system. Fifty-four relationships were built into the model, only one of which was of uncertain direction a priori. Twenty-eight of the proposed relationships were strongly supported by or consistent with the data, while 26 were close to zero (not supported by the data but not contrary to expectations). The position of the 2 isohaline (a measure of the physical response of the estuary to freshwater flow) and increased water clarity over the period of analyses were two factors affecting multiple declining taxa (including fishes and the fishes' main zooplankton prey). Our results were relatively robust with respect to the form of stock–recruitment model used and to inclusion of subsidiary covariates but may be enhanced by using detailed state–space models that describe more fully the life-history dynamics of the declining species.

California↗