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

vegandevs/vegan: CRAN 2.4 release

This is a minor release that fixes the following issues orditkplot passes CRAN tests. anova(<cca-object>, by = "axis") ignored partial terms. Function uses now forward testing which is less dangerously biased than the previous marginal tests. summary and inertcomp for RDA, CCA and frieds failed if constraints had zero rank. meandist labels are no longer cropped in plots. Canberra distance in vegdist can now handle negative entries in input

weecology/retriever: v2.1.0

v2.1.0 Major changes Add Python interface Add Retriever to conda Auto complete of Retriever commands on Unix systems Minor changes Add license to datasets Change the structure of raw data from string to list Add testing on any modified dataset Improve memory usage in cross-tab processing Add capabilitiy for datasets to use custom Encoding Use new Python interface for regression testing Use Frictionless Data specification terminology for internals New datasets Add ant dataset and weather data to the portal dataset NYC TreesCount PREDICTS aquatic_animal_excretion biodiversity_response bird_migration_data chytr_disease_distr croche_vegetation_data dicerandra_frutescens flensburg_food_web great_basin_mammal_abundance macroalgal_communities macrocystis_variation marine_recruitment_data mediter_basin_plant_traits nematode_traits ngreatplains-flowering-dates portal-dev portal predator_prey_body_ratio predicts socean_diet_data species_exctinction_rates streamflow_conditions tree_canopy_geometries turtle_offspring_nesting Add vertnet individual datasets vertnet_amphibians vertnet_birds vertnet_fishes vertnet_mammals vertnet_reptile