{ "_id": "6a1fcb4ab401979e734327cd", "Package": "SRS", "Type": "Package", "Title": "Scaling with Ranked Subsampling", "Version": "0.2.3", "Authors@R": "c(person(\"Lukas\", \"Beule\", role = c(\"aut\", \"cre\"),\nemail = \"lukas.beule@julius-kuehn.de\"),\nperson(\"Vitor\", \"Heidrich\", role = \"aut\"),\nperson(\"Petr\", \"Karlovsky\", role = \"aut\") )", "Description": "Analysis of species count data in ecology often requires\nnormalization to an identical sample size. Rarefying (random\nsubsampling without replacement), which is a popular method for\nnormalization, has been widely criticized for its poor\nreproducibility and potential distortion of the community\nstructure. In the context of microbiome count data, researchers\nexplicitly advised against the use of rarefying. An alternative\nto rarefying is scaling with ranked subsampling (SRS). SRS\nconsists of two steps. In the first step, the total counts for\nall OTUs (operational taxonomic units) or species in each\nsample are divided by a scaling factor chosen in such a way\nthat the sum of the scaled counts Cscaled equals Cmin. In the\nsecond step, the non-integer Cscaled values are converted into\nintegers by an algorithm that we dub ranked subsampling. The\nCscaled value for each OTU or species is split into the integer\npart Cint (Cint = floor(Cscaled)) and the fractional part Cfrac\n(Cfrac = Cscaled - Cints). Since the sum of Cint is smaller or\nequal to Cmin, additional delta C = Cmin - the sum of Cint\ncounts have to be added to the library to reach the total count\nof Cmin. This is achieved as follows. OTUs are ranked in the\ndescending order of their Cfrac values. Beginning with the OTU\nof the highest rank, single count per OTU is added to the\nnormalized library until the total number of added counts\nreaches delta C and the sum of all counts in the normalized\nlibrary equals Cmin. When the lowest Cfrag involved in picking\ndelta C counts is shared by several OTUs, the OTUs used for\nadding a single count to the library are selected in the order\nof their Cint values. This selection minimizes the effect of\nnormalization on the relative frequencies of OTUs. OTUs with\nidentical Cfrag as well as Cint are sampled randomly without\nreplacement. See Beule & Karlovsky (2020)\n for details.", "License": "CC BY-SA 4.0", "Encoding": "UTF-8", "Author": "Lukas Beule [aut, cre], Vitor Heidrich [aut], Petr Karlovsky\n[aut]", "Maintainer": "Lukas Beule ", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 06:32:17 UTC", "User": "root" }, "Config/pak/sysreqs": "cmake make libuv1-dev zlib1g-dev", "Repository": "https://lukasbeule.r-universe.dev", "Date/Publication": "2022-03-27 13:30:09 UTC", "RemoteUrl": "https://github.com/cran/SRS", "RemoteRef": "HEAD", "RemoteSha": "5020814288a7404b31ea8668fb2d23f0c0dada3d", "MD5sum": "e526360ea4b444929b840bdd8cc50081", "_user": "lukasbeule", "_type": "src", "_file": "SRS_0.2.3.tar.gz", "_fileid": "a52ff1227f3827f856a6c010b23c3c06492ae8a227271d219be2f9f018efa9ef", "_filesize": 138906, "_sha256": "a52ff1227f3827f856a6c010b23c3c06492ae8a227271d219be2f9f018efa9ef", "_created": "2026-06-03T06:32:17.000Z", "_published": "2026-06-03T06:35:54.960Z", "_distro": "noble", "_jobs": [ { "job": 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