Sustainable computational science: the ReScience initiative

Computer science o ers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel con dent their research is reproducible. But this is not exactly true. Jonathan Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. e actual scholarship is the full so ware environment, code, and data that produced the result. is implies new work ows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically di erent from other traditional scienti c journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and so ware tests

Freshwater inflows in the Nueces Delta, TX : impacts on porewater salinity and estimation of needs

textEstuarine wetlands and salt marshes are fundamentally driven by variations in freshwater inflow. In semi-arid salt marshes, such as the Nueces River Delta, TX, the stochastic nature of freshwater inflow events exposes resident organisms to a wide range of environmental conditions. In this study, we investigate (1) the relative importance of environmental variables on porewater salinity and (2) determination of freshwater inflow needs based on the response of emergent plants to salinity variations. Porewater salinity variations were tracked on a continuous basis with deployed conductivity sensors and on a synoptic basis with soil water extracts. We found that spatial patterns of porewater salinity were characterized by a high degree of variability in creekbank areas (23.8 ± 7.68) relative to interior marsh areas (44.2 ± 3.4). Our observations were used to test a simple model capable of predicting porewater salinities based on environmental variables. Both empirical measurements and model simulations indicated that semiannual tides play a critical role in controlling porewater flushing from precipitation and freshwater inflow events. Estimation of freshwater inflow needs for the Nueces Delta proceeded in two steps. First, we examined the response of three common emergent plants species (Borrichia frutescens, Spartina alterniflora, and Salicornia virginica) to variations in salinity. The abundance of one species in particular (S. alterniflora) was tightly coupled to salinity variations whereby salinities exceeding 25 ± 5 resulted in dramatic declines in coverage. Next, the relationship between freshwater inflow and porewater salinity was examined with respect to the salinity “tolerance” of S. alterniflora. Estimated inflow needs based on maintenance of substantial (> 20%) S. alterniflora coverage was comparable to both previous inflow needs estimates and mean annual inflows observed over the course of the study. The results of this study suggest that S. alterniflora abundance provides a reliable indicator of overall estuarine hydrological condition in the Nueces Delta.Marine Scienc

jsta/nsws: v0.1

National Surface Water Survey Packag

jsta/peatcollapse_methods: 0.1

In-situ simulation of sea-level rise impacts on coastal wetlands using a flow-through mesocosm approac

Wikiproject Lakes Workshop

People are increasingly looking towards the internet for information about specific natural areas such as lakes. However, basic information about these areas is often only available to non-professional scientists via scattered state-based web portals. One of the few general public-facing sources of this information that includes lake locations, types, and other characteristics is [Wikipedia](https://wikipedia.org). However, because only a small fraction of lakes in the world have a dedicated page on Wikipedia, people are not able to easily find basic information about their local lake or lakes they might like to visit. During this workshop, Participants will learn about the underlying structure of Wikipedia pages, recommended practices, and reasonable workflows for editing existing lake pages as well as creating new ones. Workshop materials will be archived at [https://doi.org/10.6084/m9.figshare.6157226](https://doi.org/10.6084/m9.figshare.6157226)

[Re] Least-cost modelling on irregular landscape graphs

A reference implementation of "Least-cost modelling on irregular landscape graphs", T. Etherington, Landscape Ecology, 2012

Porewater salinity dynamics in irregularly flooded marshes

Porewater salinity is a critical factor that determines the<br>distribution and abundance of emergent marsh plants. In<br>regularly flooded salt marshes, strong diurnal and semidiurnal<br>tides consistently inundate the sediments and flush<br>accumulated salts. Porewater salinity dynamics are well<br>defined in these marshes due to predictable tidal inundation.<br>However, the relative impact of environmental variables such<br>as tidal period, precipitation, and freshwater inflow is not well<br>understood in irregularly flooded salt marshes. Given, the<br>microtidal nature of our study area (the Nueces Delta) we<br>initially predicted that meteorological activity rather than tidal<br>fluctuations would drive porewater salinity dynamics.<br><br

lakemorpho: Calculating lake morphometry metrics in R [version 1; referees: 2 approved]

Metrics describing the shape and size of lakes, known as lake morphometry metrics, are important for any limnological study. In cases where a lake has long been the subject of study these data are often already collected and are openly available. Many other lakes have these data collected, but access is challenging as it is often stored on individual computers (or worse, in filing cabinets) and is available only to the primary investigators. The vast majority of lakes fall into a third category in which the data are not available. This makes broad scale modelling of lake ecology a challenge as some of the key information about in-lake processes are unavailable. While this valuable in situ information may be difficult to obtain, several national datasets exist that may be used to model and estimate lake morphometry. In particular, digital elevation models and hydrography have been shown to be predictive of several lake morphometry metrics. The R package lakemorpho has been developed to utilize these data and estimate the following morphometry metrics: surface area, shoreline length, major axis length, minor axis length, major and minor axis length ratio, shoreline development, maximum depth, mean depth, volume, maximum lake length, mean lake width, maximum lake width, and fetch. In this software tool article we describe the motivation behind developing lakemorpho, discuss the implementation in R, and describe the use of lakemorpho with an example of a typical use case

DOES LAKE AND STREAM CONNECTIVITY CONTROL PHOSPHORUS RETENTION IN LAKES?

Lake water residence time and depth are known to be strong predictors of phosphorus (P) retention. However, there is substantial variation in P retention among lakes with the same depth and residence time. One potential explanatory factor for this remaining variation is that connectivity among lakes as well as connectivity between lakes and nearby streams influences either lake P trapping or the quality of stream delivered P. Therefore, we examined the extent to which connectivity among lakes versus connectivity between lakes and streams contributes to differences in P retention among lakes. Specifically, we evaluated the effect of lake-based and stream-based connectivity metrics on P retention using a hierarchical parameterization of the Vollenweider equation. We compared Vollenweider’s k in lakes with high and low stream versus lake connectivity. We found that variation in k is more strongly associated with lake connectivity metrics compared to stream connectivity metrics. This result suggests that lake-associated processes, which likely control P trapping, play a larger role in determining P retention than stream-associated processes which may affect variation in the type of delivered P