{
  "_id": "6a10279eacfb0bcc41c90355",
  "Package": "lirrr",
  "Type": "Package",
  "Title": "Functions collected/wrote by Daijiang Li",
  "Version": "0.0.3",
  "Date": "2025-10-02",
  "Authors@R": "c(person(\"Daijiang\", \"Li\", , \"daijianglee@gmail.com\", role = c(\"aut\", \"cre\")))",
  "Description": "To keep all my functions in one place, and to use them\nmore easily.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "yes",
  "RoxygenNote": "7.3.3",
  "Additional_repositories": "https://ropensci.r-universe.dev",
  "Remotes": [
    "cran/PhyloMeasures"
  ],
  "Config/pak/sysreqs": "libabsl-dev libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libgdal-dev gdal-bin libgeos-dev make\nlibicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nlibproj-dev libsqlite3-dev libudunits2-dev",
  "Repository": "https://daijiang.r-universe.dev",
  "Date/Publication": "2025-10-15 23:04:59 UTC",
  "RemoteUrl": "https://github.com/daijiang/lirrr",
  "RemoteRef": "HEAD",
  "RemoteSha": "e25b8526cd5c405017d99e96d34c0ed71c45497c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-13 08:37:20 UTC",
    "User": "root"
  },
  "Author": "Daijiang Li [aut, cre]",
  "Maintainer": "Daijiang Li <daijianglee@gmail.com>",
  "MD5sum": "664839ce83717746cbac68bdc742bf03",
  "_user": "daijiang",
  "_type": "src",
  "_file": "lirrr_0.0.3.tar.gz",
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  "_created": "2026-05-13T08:37:20.000Z",
  "_published": "2026-05-22T09:53:34.566Z",
  "_distro": "noble",
  "_jobs": [
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      "job": 77356337480,
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  "_buildurl": "https://github.com/r-universe/daijiang/actions/runs/25787838918",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/daijiang/lirrr",
  "_commit": {
    "id": "e25b8526cd5c405017d99e96d34c0ed71c45497c",
    "author": "Daijiang Li <daijianglee@gmail.com>",
    "committer": "Daijiang Li <daijianglee@gmail.com>",
    "message": "update grid cells func\n",
    "time": 1760569499
  },
  "_maintainer": {
    "name": "Daijiang Li",
    "email": "daijianglee@gmail.com",
    "login": "daijiang",
    "uuid": 1696911
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  "_dependencies": [
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      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
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      "package": "plyr",
      "role": "Imports"
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    {
      "package": "dplyr",
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    {
      "package": "purrr",
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    {
      "package": "stringr",
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      "role": "Imports"
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    {
      "package": "tidyr",
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    },
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      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "rotl",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "picante",
      "role": "Imports"
    },
    {
      "package": "phylocomr",
      "role": "Imports"
    },
    {
      "package": "PhyloMeasures",
      "role": "Imports"
    },
    {
      "package": "tidytree",
      "role": "Imports"
    },
    {
      "package": "ggtree",
      "role": "Imports"
    },
    {
      "package": "sf",
      "role": "Imports"
    },
    {
      "package": "raster",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "betapart",
      "role": "Suggests"
    }
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  "_owner": "daijiang",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-20",
      "n": 1
    },
    {
      "week": "2025-42",
      "n": 3
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  ],
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  "_stars": 1,
  "_contributors": [
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      "uuid": 1696911
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    "type": "user",
    "name": "Daijiang Li"
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/lirrr"
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/lirrr.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "cap_first_letter",
    "dist_to_df",
    "get_n_polytomy",
    "get_pd_alpha",
    "logit_tran",
    "make_world_grids",
    "mvpd",
    "panel.cor",
    "panel.hist",
    "pd2",
    "phylo_betapart",
    "rand_test",
    "rm_site_noobs",
    "rm_sp_noobs",
    "tnrs_match_names_2",
    "unifrac2",
    "var_to_rownames"
  ],
  "_datasets": [
    {
      "name": "comm_a",
      "title": "Example community data",
      "object": "comm_a",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Acer_rubrum",
        "Achillea_millefolium",
        "Amelanchier_spp",
        "Andropogon_gerardii",
        "Anemone_quinquefolia",
        "Apocynum_androsaemifolium",
        "Aquilegia_canadensis",
        "Aralia_nudicaulis",
        "Betula_papyrifera",
        "Chimaphila_umbellata",
        "Clintonia_borealis",
        "Comandra_umbellata",
        "Comptonia_peregrina",
        "Cornus_canadensis",
        "Corylus_americana"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "comm_b",
      "title": "#' Example community data",
      "object": "comm_b",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Acer_rubrum",
        "Amelanchier_spp",
        "Anemone_quinquefolia",
        "Apocynum_androsaemifolium",
        "Aralia_nudicaulis",
        "Aronia_melanocarpa",
        "Betula_papyrifera",
        "Brachyelytrum_erectum",
        "Carex_spp"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "tree",
      "title": "#' Example phylogeny",
      "object": "tree",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "world_moll",
      "title": "#' Example phylogeny",
      "object": "world_moll",
      "class": [
        "sf",
        "data.frame"
      ],
      "fields": [
        "featurecla",
        "scalerank",
        "labelrank",
        "sovereignt",
        "sov_a3",
        "adm0_dif",
        "level",
        "type",
        "tlc",
        "admin",
        "adm0_a3",
        "geou_dif",
        "geounit",
        "gu_a3",
        "su_dif",
        "subunit",
        "su_a3",
        "brk_diff",
        "name",
        "name_long",
        "brk_a3",
        "brk_name",
        "brk_group",
        "abbrev",
        "postal",
        "formal_en",
        "formal_fr",
        "name_ciawf",
        "note_adm0",
        "note_brk",
        "name_sort",
        "name_alt",
        "mapcolor7",
        "mapcolor8",
        "mapcolor9",
        "mapcolor13",
        "pop_est",
        "pop_rank",
        "pop_year",
        "gdp_md",
        "gdp_year",
        "economy",
        "income_grp",
        "fips_10",
        "iso_a2",
        "iso_a2_eh",
        "iso_a3",
        "iso_a3_eh",
        "iso_n3",
        "iso_n3_eh",
        "un_a3",
        "wb_a2",
        "wb_a3",
        "woe_id",
        "woe_id_eh",
        "woe_note",
        "adm0_iso",
        "adm0_diff",
        "adm0_tlc",
        "adm0_a3_us",
        "adm0_a3_fr",
        "adm0_a3_ru",
        "adm0_a3_es",
        "adm0_a3_cn",
        "adm0_a3_tw",
        "adm0_a3_in",
        "adm0_a3_np",
        "adm0_a3_pk",
        "adm0_a3_de",
        "adm0_a3_gb",
        "adm0_a3_br",
        "adm0_a3_il",
        "adm0_a3_ps",
        "adm0_a3_sa",
        "adm0_a3_eg",
        "adm0_a3_ma",
        "adm0_a3_pt",
        "adm0_a3_ar",
        "adm0_a3_jp",
        "adm0_a3_ko",
        "adm0_a3_vn",
        "adm0_a3_tr",
        "adm0_a3_id",
        "adm0_a3_pl",
        "adm0_a3_gr",
        "adm0_a3_it",
        "adm0_a3_nl",
        "adm0_a3_se",
        "adm0_a3_bd",
        "adm0_a3_ua",
        "adm0_a3_un",
        "adm0_a3_wb",
        "continent",
        "region_un",
        "subregion",
        "region_wb",
        "name_len",
        "long_len",
        "abbrev_len",
        "tiny",
        "homepart",
        "min_zoom",
        "min_label",
        "max_label",
        "label_x",
        "label_y",
        "ne_id",
        "wikidataid",
        "name_ar",
        "name_bn",
        "name_de",
        "name_en",
        "name_es",
        "name_fa",
        "name_fr",
        "name_el",
        "name_he",
        "name_hi",
        "name_hu",
        "name_id",
        "name_it",
        "name_ja",
        "name_ko",
        "name_nl",
        "name_pl",
        "name_pt",
        "name_ru",
        "name_sv",
        "name_tr",
        "name_uk",
        "name_ur",
        "name_vi",
        "name_zh",
        "name_zht",
        "fclass_iso",
        "tlc_diff",
        "fclass_tlc",
        "fclass_us",
        "fclass_fr",
        "fclass_ru",
        "fclass_es",
        "fclass_cn",
        "fclass_tw",
        "fclass_in",
        "fclass_np",
        "fclass_pk",
        "fclass_de",
        "fclass_gb",
        "fclass_br",
        "fclass_il",
        "fclass_ps",
        "fclass_sa",
        "fclass_eg",
        "fclass_ma",
        "fclass_pt",
        "fclass_ar",
        "fclass_jp",
        "fclass_ko",
        "fclass_vn",
        "fclass_tr",
        "fclass_id",
        "fclass_pl",
        "fclass_gr",
        "fclass_it",
        "fclass_nl",
        "fclass_se",
        "fclass_bd",
        "fclass_ua",
        "geometry"
      ],
      "rows": 242,
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "cap_first_letter",
      "title": "Make the first letter upper case",
      "topics": [
        "cap_first_letter"
      ]
    },
    {
      "page": "comm_a",
      "title": "Example community data",
      "topics": [
        "comm_a"
      ]
    },
    {
      "page": "comm_b",
      "title": "#' Example community data",
      "topics": [
        "comm_b"
      ]
    },
    {
      "page": "dist_to_df",
      "title": "Change a distance matrix or a matrix to a data frame",
      "topics": [
        "dist_to_df"
      ]
    },
    {
      "page": "get_n_polytomy",
      "title": "Calculate number of polytomies",
      "topics": [
        "get_n_polytomy"
      ]
    },
    {
      "page": "get_pd_alpha",
      "title": "Calculate alpha phylogenetic diversity",
      "topics": [
        "get_pd_alpha"
      ]
    },
    {
      "page": "highlight_subset_sp_in_phylogeny",
      "title": "Highlight all branches linking a subset of species in a phylogeny",
      "topics": [
        "highlight_subset_sp_in_phylogeny"
      ]
    },
    {
      "page": "logit_tran",
      "title": "Logit transformation",
      "topics": [
        "logit_tran"
      ]
    },
    {
      "page": "make_world_grids",
      "title": "Make grid cells across the lands of world",
      "topics": [
        "make_world_grids"
      ]
    },
    {
      "page": "mvpd",
      "title": "MPD and VPD (mean and variance of pairwise distance)",
      "topics": [
        "mvpd"
      ]
    },
    {
      "page": "panel.cor",
      "title": "'panel.cor' to plot absolute value of correlations",
      "topics": [
        "panel.cor"
      ]
    },
    {
      "page": "panel.hist",
      "title": "'panel.hist' to plot absolute value of correlations",
      "topics": [
        "panel.hist"
      ]
    },
    {
      "page": "pd2",
      "title": "Faith's PD",
      "topics": [
        "pd2"
      ]
    },
    {
      "page": "phylo_betapart",
      "title": "Phylogenetic beta diversity partition",
      "topics": [
        "phylo_betapart"
      ]
    },
    {
      "page": "rand_test",
      "title": "Randomization tests",
      "topics": [
        "rand_test"
      ]
    },
    {
      "page": "rm_site_noobs",
      "title": "Remove site that has no observations (site by sp matrix)",
      "topics": [
        "rm_site_noobs"
      ]
    },
    {
      "page": "rm_sp_noobs",
      "title": "Remove sp that not observed at any site (site by sp matrix)",
      "topics": [
        "rm_sp_noobs"
      ]
    },
    {
      "page": "tnrs_match_names_2",
      "title": "Match taxa names with the Open Tree of Life",
      "topics": [
        "tnrs_match_names_2"
      ]
    },
    {
      "page": "tree",
      "title": "#' Example phylogeny",
      "topics": [
        "tree",
        "world_moll"
      ]
    },
    {
      "page": "unifrac2",
      "title": "unifrac",
      "topics": [
        "unifrac2"
      ]
    },
    {
      "page": "var_to_rownames",
      "title": "Function to add a column as row names, and remove it from columns",
      "topics": [
        "var_to_rownames"
      ]
    }
  ],
  "_readme": "https://github.com/daijiang/lirrr/raw/HEAD/README.md",
  "_rundeps": [
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    "aplot",
    "askpass",
    "base64enc",
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    "class",
    "classInt",
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    "fastmap",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
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    "gdtools",
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    "proxy",
    "purrr",
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    "vegan",
    "viridisLite",
    "withr",
    "wk",
    "xfun",
    "XML",
    "yaml",
    "yulab.utils"
  ],
  "_score": 2,
  "_indexed": true,
  "_nocasepkg": "lirrr",
  "_universes": [
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  ],
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