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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
Live testing regular expressions …
Published:
As some point in your career you’ll find yourself needing to parse large amounts of alpha numeric data and selecting sections which match certain string patterns. For example, maybe you are parsing the contents of a webpage looking for hyperlinks, or summarizing the contents of a log file, or searching for values of parameters in a file heavy with text.
Use DockerHub to store and retrieve your containers
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So you have just built your first docker image (or podman image, but more about that in a minute). And it runs! And you are excited! So you start to tell people how cool you are, that you can run “stuff” inside a container. But then are quickly brought back down to earth when you realize that you don’t know how move this image to other platforms, like the cloud. It resides “somewhere” on your local machine, in a location that isn’t obvious.
Run your model in a container
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Containers aren’t new, but to the scientific community (as of writing), they kinda are! So what are containers? Well, simply put, they are a running instance of an image! Oh Right … totally get it!
Stop using the library() function
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Yes, i know, you love using the library() function in R! But it can be a real problem for several reasons:
Use markdown on GitHub
Published:
Markdown for GitHub is the language of choice when creating issues, pull requests, using discussions, or editing your README file on GitHub.
Include DESCRIPTION file in all R projects
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The DESCRIPTION file is a necessary staple for all R packages. Among other things (which we won’t get into, since this isn’t a post about creating R packages) it is the location for you to list all dependencies of your package. So when your package is installed the user also gets all the dependent packages installed too! Nice and tidy!
Use reproducible examples (in R) when asking for help
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Regardless of the language you are coding in, at some point, there will come a time when you just need to ask for help. When you do, you should always include a reproducible example to help explain your problem. Failing to do so will just irritate readers and limit the number of helpful responses.
Delete your last commit from GitHub
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We’ve all done it, you’ll be happily commiting and pushing to GitHub from either the command line or, more than likely, your favorite IDE when you panic and realize that you just mistakenly pushed something to GitHub. You start sweating, and frenetically start googling how to reverse this. Well it turns out it is pretty simple.
portfolio
stocksmart
R package serving stock assessment data for all federally managed species
NEUS-Atlantis
End-to-end Ecosystem model for the northeast USA
NEFSCSpatial
R package serving spatial data (vectors) in simple features sf format
buoydata
R package serving National Data Buoy Center (NDBC) data from all buoys around the world
comlandr
R package to pull and process commercial fishing data from the Northeast USA shelf
survdat
R package serving data from the NEFSC Bottom Trawl Survey
mscatch
R package to expand total catch by species and area to length and age comps
oisst
R package to easily download Optimum Interpolation Sea Surface Temperature from NOAA data
lemans
R package to run the LeMANS (Length-based Multispecies Analysis by Numerical Simulation) Model
publications
On lumping species in food webs
Published in Ecology, 1998
Species in community food webs are commonly aggregated or lumped on the basis of overlap in predators and prey. This note reports an unexpected result of lumping species in observed food webs and …
Recommended citation: Solow, A. R., & Beet, A. R. (1998). Ecology "79(6), p2013-2018.".
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Physical Factors affecting Copepod Migration
Published in American Naturalist, 1998
“Study of the mesoscale spatial variability of zooplankton populations was a major element in FLEX, a survey of a l00km square box in the North Sea over …
Recommended citation: Steele, John; Beet, Andrew (1998). ASC 1998 - R. Conference contribution .
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Testing for Shifts in the Vertical Distribution of Plankton Using a Robust Kolmogorov-Smirnov Like Statistic
Published in Journal of Agricultural, Biological, and Environmental Statistics, 1998
Ecological communities often occur along important physical gradients such as altitude, moisture, and light. The two sample Kolmogorov-Smirnov statistic can be used to test for equality of …
Recommended citation: Smith, W., Beet, A. R. and Solow, A. R. (1998). Journal of Agricultural, Biological, and Environmental Statistics "3(4), p421-429.".
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On an early result on stability and complexity
Published in American Naturalist, 1999
In a recent paper, Solow and Beet (1998) showed that the links in observed community food webs are not randomly distributed. Instead, these webs appear to be lumpy in the sense of being composed of relatively tightly connected compartments …
Recommended citation: Solow, A. R., Costello, C., & Beet, A. (1999). American Naturalist "154(5), 587-588.".
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Comparing two vertical plankton distributions
Published in Limnology and Oceanography, 2000
Traditional statistical methods for testing for differences in vertical plankton distributions are invalid when the distributions are patchy. This note describes a …
Recommended citation: Solow, A. R., Bollens, S. M., & Beet, A. (2000). Limnology and Oceanography "45(2), 506-509.".
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Optimal seasonal sampling for estimating an interannual trend
Published in Israel Journal of Zoology, 2000
Many biological populations exhibit both seasonal variability and interannual trend in abundance. When interest centers on the latter, economy can be gained by …
Recommended citation: Solow, A. R., Beet, A., & Cowan, D. (2000). Israel Journal of Zoology "46(4), 351-354.".
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Patterns in abundance and growth of juvenile lobster, Homarus americanus
Published in Marine and Freshwater Research, 2002
The combined effort of assessing abundance and measuring the time between settlement and recruitment is fundamental to forecasting future recruitment to the lobster fishery. This study represents the first monthly year-round sampling for …
Recommended citation: Cowan, D. F., Solow, A. R., & Beet, A. (2002). Marine and Freshwater Research "52(8), 1095-1102.".
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Comparing vertical plankton profiles with replication
Published in Marine Ecology Progress series, 2003
Traditional statistical methods for testing for differences between vertical plankton distributions are invalid if the distributions are patchy. This Note describes a statistical test for …
Recommended citation: Beet, A., Solow, A. R., & Bollens, S. M. (2003). Marine Ecology Progress Series "262:285-287.".
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Marine protected areas in non-linear ecosystems
Published in Proceedings of the Royal Society. London. Ser. B., 2003
The very large changes observed within marine communities, owing to excessive harvesting, have been attributed to switches between alternative stable states. Correspondingly large reductions in overall fishing effort are usually …
Recommended citation: Steele, J. H., and Beet, A. R. (2003). Proceedings of the Royal Society. London. Ser. B. "270 (Suppl.) S230-S233.".
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A note on the statistics of the largest geomagnetic storms per solar cycle
Published in Journal of Atmospheric and Solar-Terrestrial Physics, 2004
This note points out a problem with the way in which extreme value distributions have been fit to the intensities of the largest geomagnetic storms …
Recommended citation: Solow, A. R., & Beet, A. R. (2004). Journal of Atmospheric and Solar-Terrestrial Physics "66(18), 1731-1732.".
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A test for a regime shift
Published in Fisheries Oceanography, 2005
This note describes a formal statistical approach to testing for a regime shift based on population time series for a system of interacting species or groups. Under this approach …
Recommended citation: Solow, A. R., & Beet, A. R. (2005). Fisheries Oceanography "14(3), 236-240.".
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Is the effect of the NAO on North-east Arctic cod, Gadus morhua, recruitment stock-dependent?
Published in Fisheries Oceanography, 2007
There is considerable interest in understanding the effect of the North Atlantic Oscillation (NAO) on recruitment to North Atlantic cod stocks. An earlier analysis of data for the North‐east Arctic cod stock showed that, while there is …
Recommended citation: Solow, A. R., & Beet, A. R. (2007). Fisheries Oceanography "16(5), 479-481.".
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Balancing end-to-end budgets of the Georges Bank ecosystem
Published in Progress in Oceanography, 2007
Oceanographic regimes on the continental shelf display a great range in the time scales of physical exchange, biochemical processes and trophic transfers. The close surface-to-seabed physical coupling at intermediate scales of weeks to months means that the open ocean …
Recommended citation: J.H. Steele, J.S. Collie, J.J. Bisagni, D.J. Gifford, M.J. Fogarty, J.S. Link, B.K. Sullivan, M.E. Sieracki, A.R. Beet, D.G. Mountain, E.G. Durbin, D. Palka, W.T. Stockhausen. (2007). Progress in Oceanography "Volume 74, Issue 4, Pages 423-448, ISSN 0079-661.".
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The untamed shrew: on the termination of an eradication programme for an introduced species
Published in Journal of Applied Ecology, 2008
One option in managing introductions of non-native pest species is to eradicate the introduced species by trapping or otherwise removing individuals. A central issue in …
Recommended citation: Solow, A., Seymour, A., Beet, A., & Harris, S. (2008). Journal of Applied Ecology "45(2), 424-427.".
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On the incompleteness of the historical record of North Atlantic tropical cyclones
Published in Geophysical Research Letters, 2008
There is some question as to whether the historical record of observed North Atlantic tropical cyclones prior to the advent of satellite coverage is complete. This question is central to understanding the historical trend in tropical cyclone activity and …
Recommended citation: Solow, A. R., & Beet, A. R. (2008). Geophysical Research Letters " 35(11).".
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A nonparametric test for change in variability using a proxy record with an application to ENSO
Published in Geophysical Research Letters, 2008
A common problem in climate science is determining whether the pattern of variability in a particular process or variable has changed over time. When the modern observational record is short, this problem can be addressed by …
Recommended citation: Solow, A. R., & Beet, A. R. (2008). Geophysical Research Letters " 35(19).".
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Re-analysis of a salp population time-series
Published in Marine Ecology Progress Series, 2010
Weekly abundances of 2 salp populations (Salpa fusiformis and Thalia democratica) were determined for the period from 1967 to 1990 at a coastal station in the Western Mediterranean using a …
Recommended citation: Sutherland, K. R., Beet, A. R., & Solow, A. R. (2010). Marine Ecology Progress Series " 418:147-150.".
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An estimate of the cost of acute health effects from food- and water-borne marine pathogens and toxins in the USA
Published in Journal of Water Health, 2011
Large and growing segments of the United States population consume seafood or engage in marine recreation. These activities provide significant benefits but also bring risk of exposure to marine-borne illness. To manage these risks, it is important to understand the incidence and cost of marine-borne disease. We review …
Recommended citation: Ralston, E. P., Kite-Powell, H., & Beet, A. (2011). Journal of Water Health "9 (4): 680–694.".
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A Bayesian approach to finding groups in a food web
Published in Israel Journal of Ecology & Evolution, 2013
A food web describes the feeding links between species in a community. The species in many food webs are organized into groups of highly linked species that are weakly linked to species in other groups. A Bayesian approach …
Recommended citation: Solow, A. R., & Beet, A. R. (2013). Israel Journal of Ecology & Evolution "59(1), 37–41".
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A test for a shift in the boundary of the geographical range of a species
Published in Biology Letters, 2014
One predicted impact of climate change is a poleward shift in the boundaries of species ranges. Existing methods for identifying such a boundary shift based on changes in the observed pattern …
Recommended citation: Solow, A., Beet, A., Roll, U., & Stone, L. (2014). Biology Letters "1020130808.".
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Testing for simple structure in a spatial time series with an application to the distribution of Alexandrium resting cysts in the Gulf of Maine
Published in Marine Ecology Progress Series, 2014
We describe a test of the goodness of fit of a simple model for the mean of a spatial time series. Under this model, the mean consists of …
Recommended citation: Solow, A. R., Beet, A. R., Keafer, B. A., & Anderson, D. M. (2014). Marine Ecology Progress Series "501:291-296.".
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On Uncertain Sightings and Inference about Extinction
Published in Marine Ecology Progress Series, 2014
The extinction of many species can only be inferred from the record of sightings of individuals. Solow et al. (2012, Uncertain sightings and the extinction of the Ivory‐billed Woodpecker …
Recommended citation: Solow, A. R., & Beet, A. R. (2014). Conservation Biology "28(4), 1119-1123.".
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The human health effects of Florida Red Tide (FRT) blooms: An expanded analysis
Published in Environment International, 2014
Human respiratory and digestive illnesses can be caused by exposures to brevetoxins from blooms of the marine alga Karenia brevis, also known as Florida red tide (FRT). K. brevis requires …
Recommended citation: Porter Hoagland, Di Jin, Andrew Beet, Barbara Kirkpatrick, Andrew Reich, Steve Ullmann, Lora E. Fleming, Gary Kirkpatrick. (2014). Environment International "Volume 68, Pages 144-153, ISSN 0160-4120".
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Natural and unnatural oil slicks in the Gulf of Mexico
Published in Journal of Geophysical Research: Oceans, 2015
When wind speeds are 2–10 m s−1, reflective contrasts in the ocean surface make oil slicks visible to synthetic aperture radar (SAR) under all sky conditions. Neural network analysis of satellite SAR images quantified the magnitude and distribution of surface oil in the Gulf of Mexico from persistent, natural seeps and from the Deepwater Horizon (DWH) discharge …
Recommended citation: MacDonald, I. R., Garcia-Pineda, O., Beet, A., Asl, S. D., Feng, L., Graettinger, G., French-McCay, D., Holmes, J., Hu, C., Huffer, F., Leifer, I., Muller-Karger, F., Solow, A., Silva, M., & Swayze, G. (2015). Journal of Geophysical Research: Oceans "Volume 120, Issue 12, 8364-8380.".
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The Most Recent Cascadia Earthquake and Native American Narratives
Published in Mathematical Geosciences, 2019
The Cascadia subduction zone fault lies just off the Pacific coast of the USA and Canada. Although this fault has been seismically inactive over the written history of the Cascadia region, it has the potential to …
Recommended citation: Solow, A., Beet, A. & McManus, S. (2019). Math Geosci "51, 683–690.".
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Neurological illnesses associated with Florida red tide (Karenia brevis) blooms
Published in Harmful Algae, 2019
Human respiratory and gastrointestinal illnesses can result from exposures to brevetoxins originating from coastal Florida red tide blooms, comprising the marine alga Karenia brevis (K. brevis). Only limited research on the extent of human health risks …
Recommended citation: Roberto Efrain -Diaz, Melissa A.Friedman, Di Jin, Andrew Beet, Barbara Kirkpatrick, Andrew Reich, Gary Kirkpatrick, Steven G.Ullmann, Lora E.Fleming, Porter Hoagland. (2019). Harmful Algae "Volume 82, 2019, Pages 73-81, ISSN 1568-9883.".
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A simulation study of trend detection methods for integrated ecosystem assessment
Published in ICES Journal of Marine Science, 2019
The identification of trends in ecosystem indicators has become a core component of ecosystem approaches to resource management, although oftentimes assumptions of statistical models are not properly accounted for in the reporting process. To explore …
Recommended citation: Sean Hardison, Charles T Perretti, Geret S DePiper, Andrew Beet. (2019). ICES Journal of Marine Science "Volume 76, Issue 7, Pages 2060–2069.".
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Lessening the Hazards of Florida Red Tides: A Common Sense Approach
Published in Frontiers in Marine Science, 2020
In the Gulf of Mexico, especially along the southwest Florida coast, blooms of the dinoflagellate Karenia brevis are a coastal natural hazard. The organism produces a potent class of toxins, known as brevetoxins, which are …
Recommended citation: Hoagland, P., Kirkpatrick, B., Jin, D., Kirkpatrick, G., Fleming, L.E., Ullmann, S.G., Beet, A., Hitchcock, G., Harrison, K.K., Li, Z.C., Garrison, B. Diaz, R.E., Lovko, V. (2020). Frontiers in Marine Science "7 (538).".
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Salinity Intrusion in a Modified River-Estuary System: An Integrated Modeling Framework for Source-to-Sea Management
Published in Frontiers in Marine Science, 2020
Along the US Atlantic and Gulf coasts, port authorities and governments have been competing for access to federal funds to deepen the channels and berths in each of the major estuary-based harbors, thereby facilitating access by …
Recommended citation: Hoagland, P., Beet, A., Ralston, D., Parsons, G., Shirazi, Y., Carr, E. (2020). Frontiers in Marine Science "7 (425).".
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A northeast United States Atlantis marine ecosystem model with ocean reanalysis and ocean color forcing
Published in Ecological Modelling, 2022
The northeast United States Atlantis model (NEUSv2) is an end-to-end ecosystem model that can simulate biogeochemical, ecological, fishery, management, and socio-economic processes within marine ecosystems. As a major update …
Recommended citation: Joseph C. Caracappa, Andrew Beet, Sarah Gaichas, Robert J. Gamble, Kimberly J.W. Hyde, Scott I. Large, Ryan E. Morse, Charles A. Stock, Vincent S. Saba. (2022). Ecological Modelling "Volume 471, 2022, 110038.".
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talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown file that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.