{ "_id": "6a2130a5cd65a98ecbd24e57", "Package": "pooledpeaks", "Title": "Genetic Analysis of Pooled Samples", "Version": "1.2.2", "Authors@R": "c( \nperson(\"Kathleen\", \"Kuesters\", email = \"kathleen.kuesters@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-0238-7889\")),\nperson(\"Jeffrey\", \"Long\", role = c(\"aut\")),\nperson(\"Jessica\", \"Blanton\", role = c(\"aut\")),\nperson(\"Walter\", \"Blank\", role = c(\"ctb\")),\nperson(\"Jeffrey\", \"Kovach\", role = c(\"ctb\")),\nperson(\"Ronald\", \"Blanton\", role = c(\"ctb\")))", "Description": "Analyzing genetic data obtained from pooled samples. This\npackage can read in Fragment Analysis output files, process the\ndata, and score peaks, as well as facilitate various analyses,\nincluding cluster analysis, calculation of genetic distances\nand diversity indices, as well as bootstrap resampling for\nstatistical inference. Specifically tailored to handle genetic\ndata efficiently, researchers can explore population structure,\ngenetic differentiation, and genetic relatedness among samples.\nWe updated some functions from Covarrubias-Pazaran et al.\n(2016) to allow for the use of\nnew file formats and referenced the following to write our\ngenetic analysis functions: Long et al. (2022)\n, Jost (2008)\n, Nei (1973)\n, Foulley et al. (2006)\n, Chao et al. (2008)\n.", "URL": "https://github.com/kmkuesters/pooledpeaks", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "BugReports": "https://github.com/kmkuesters/pooledpeaks/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev libjpeg-dev libssl-dev\nlibpoppler-cpp-dev poppler-data", "Repository": "https://kmkuesters.r-universe.dev", "Date/Publication": "2025-05-09 00:12:14 UTC", "RemoteUrl": "https://github.com/kmkuesters/pooledpeaks", "RemoteRef": "HEAD", "RemoteSha": "1bcc8b6fd48c2b1b7fafc587d2af8523a814da2b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 07:56:17 UTC", "User": "root" }, "Author": "Kathleen Kuesters [aut, cre, cph] (ORCID:\n),\nJeffrey Long [aut],\nJessica Blanton [aut],\nWalter Blank [ctb],\nJeffrey Kovach [ctb],\nRonald Blanton [ctb]", "Maintainer": "Kathleen Kuesters ", "MD5sum": "fffb6e1c612256425ead75cc86a8340c", "_user": "kmkuesters", "_type": "src", "_file": "pooledpeaks_1.2.2.tar.gz", "_fileid": "0fec06677d32dd807b84b983c49bee9808301afb1bbc7a7505cdd8f9b2f0ea8f", "_filesize": 2532218, "_sha256": "0fec06677d32dd807b84b983c49bee9808301afb1bbc7a7505cdd8f9b2f0ea8f", "_created": "2026-06-04T07:56:17.000Z", "_published": "2026-06-04T08:00:37.877Z", "_distro": "noble", "_jobs": [ { "job": 79474725730, "time": 171, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7406079242" }, { "job": 79474725823, "time": 161, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7406075844" }, { "job": 79474725702, "time": 187, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7406073954" }, { "job": 79474725723, "time": 189, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7406074932" }, { "job": 79474175805, "time": 208, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7406022120" }, { "job": 79474725699, "time": 114, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7406060395" }, { "job": 79474725746, "time": 142, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7406069390" }, { "job": 79474725761, "time": 148, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7406071504" }, { "job": 79474725764, "time": 138, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7406068649" } ], "_buildurl": "https://github.com/r-universe/kmkuesters/actions/runs/26938571465", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/kmkuesters/pooledpeaks", "_commit": { "id": "1bcc8b6fd48c2b1b7fafc587d2af8523a814da2b", "author": "Kathleen Kuesters <75321402+kmkuesters@users.noreply.github.com>", "committer": "Kathleen Kuesters <75321402+kmkuesters@users.noreply.github.com>", "message": "CRAN Submission\n", "time": 1746749534 }, "_maintainer": { "name": "Kathleen Kuesters", "email": "kathleen.kuesters@gmail.com", "orcid": "0000-0003-0238-7889" }, "_registered": true, "_dependencies": [ { "package": "ape", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "Fragman", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "pdftools", "role": "Imports" }, { "package": "qpdf", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "plyr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "kmkuesters", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "kmkuesters", "count": 76, "uuid": 75321402 }, { "user": "ns-rse", 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Clustering", "topics": [ "cluster" ] }, { "page": "ClusterFromSamples", "title": "Cluster From Samples", "topics": [ "ClusterFromSamples" ] }, { "page": "data_manipulation", "title": "Data Manipulation for Marker Data", "topics": [ "data_manipulation" ] }, { "page": "DistCor", "title": "Distance Correlation", "topics": [ "DistCor" ] }, { "page": "EmpiricalSE", "title": "Calculate Empirical Standard Error", "topics": [ "EmpiricalSE" ] }, { "page": "fsa_batch_imp", "title": "Batch Import of .fsa files", "topics": [ "fsa_batch_imp" ] }, { "page": "fsa_metadata", "title": "Retrieve Metadata", "topics": [ "fsa_metadata" ] }, { "page": "GeneIdentityMatrix", "title": "Gene Identity Matrix", "topics": [ "GeneIdentityMatrix" ] }, { "page": "GeneticDistanceMatrix", "title": "Genetic Distance Matrix", "topics": [ "GeneticDistanceMatrix" ] }, { "page": "GST", "title": "Nei's GST", "topics": [ "GST" ] }, { "page": "JostD", "title": "Calculate Jost's D", "topics": [ "JostD" ] }, { "page": "JostD_KK", "title": "Pairwise Jost D between replicates", "topics": [ "JostD_KK" ] }, { "page": "lf_to_tdf", "title": "Transform LF to TDF", "topics": [ "lf_to_tdf" ] }, { "page": "LoadData", "title": "Load Genetic Data", "topics": [ "LoadData" ] }, { "page": "MDSplot", "title": "Multi Dimensional Scaling (MDS) Plot", "topics": [ "MDSplot" ] }, { "page": "PCDM", "title": "Post-consolidation Data Manipulation", "topics": [ "PCDM" ] }, { "page": "preGST", "title": "Pre GST Calculation", "topics": [ "preGST" ] }, { "page": "preJostD", "title": "Calculate Pre-Jost's D", "topics": [ "preJostD" ] }, { "page": "Rep_check", "title": "Replicate Check for Duplicate Samples", "topics": [ "Rep_check" ] }, { "page": "RWCDistanceMatrix", "title": "Random Walk Covariance Distance Matrix", "topics": [ "RWCDistanceMatrix" ] }, { "page": "SampleOfLoci", "title": "Sample Of Loci", "topics": [ "SampleOfLoci" ] }, { "page": "score_markers_rev3", "title": "Score Markers Wrapper", "topics": [ 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