{ "_id": "6aabd3ff3d719c1f8406f885", "Package": "sit", "Type": "Package", "Title": "Analyse Mark-Release-Recapture Data from Sterile Insect\nTechnique (SIT) Field Experiments", "Version": "1.1.2.9015", "Authors@R": "c(person(\"Françoise\", \"Chirara\", email =\n\"francoise.chirara@cirad.fr\", role = c(\"ctb\"), comment = \"Logo\ndesigner\"), person(\"Facundo\", \"Muñoz\", email =\n\"facundo.munoz@cirad.fr\", role = c(\"aut\", \"cre\"), comment =\nc(\"Package developer\", ORCID = \"0000-0002-5061-4241\")),\nperson(\"Joint FAO/IAEA Centre of Nuclear Techniques in Food and\nAgriculture\", role = c(\"fnd\", \"cph\")))", "Description": "Import field data about the study design such as the\nlocation and types of adult and egg traps, the release events,\nthe trap surveys and the egg hatches. Provide functions to\ncompute and plot various parameters of interest concerning\ncompetitiveness of sterile males, dispersal behaviour, survival\nrates and density of the wild male population.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "URL": "https://umr-astre.pages.mia.inra.fr/sit,\nhttps://forgemia.inra.fr/umr-astre/sit", "BugReports": "https://forgemia.inra.fr/umr-astre/sit/issues", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.0", "Config/testthat/edition": "3", "Language": "en-GB", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibicu-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev", "Repository": "https://cirad-astre.r-universe.dev", "Date/Publication": "2023-11-09 13:27:45 UTC", "RemoteUrl": "https://forge.inrae.fr/umr-astre/sit", "RemoteRef": "HEAD", "RemoteSha": "5565f8063e4f5a93d20279822f9538b4cd371e70", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-17 10:55:50 UTC", "User": "root" }, "Author": "Françoise Chirara [ctb] (Logo designer),\nFacundo Muñoz [aut, cre] (Package developer, ORCID:\n),\nJoint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture\n[fnd, cph]", "Maintainer": "Facundo Muñoz ", "_user": "cirad-astre", "_type": "src", "_file": "sit_1.1.2.9015.tar.gz", "_fileid": "https://r2.ropensci.org/fdf846ab2d0fc8cd643d09cd54f0ef57f980b99849f220997cbdc30734da264e", "_filesize": 788384, "_sha256": "fdf846ab2d0fc8cd643d09cd54f0ef57f980b99849f220997cbdc30734da264e", "_expires": "2026-12-26T11:50:22.000Z", "_created": "2026-09-17T10:55:50.000Z", "_published": "2026-09-17T11:50:23.769Z", "_jobs": [ { "job": 105174961605, "time": 318, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "10494261891" }, { "job": 105174961587, "time": 310, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "10492992429" }, { "job": 105174961764, "time": 214, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "10495373067" }, { "job": 105174961811, "time": 234, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "10495079785" }, { "job": 105173800296, "time": 248, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "10494186107" }, { "job": 105174961674, "time": 177, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10494541395" }, { "job": 105174961710, "time": 225, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "10493806907" }, { "job": 105174961665, "time": 250, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "10493986908" }, { "job": 105174961749, "time": 199, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "10493911706" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cirad-astre/actions/runs/35212684558", "_status": "failure", "_upstream": "https://forge.inrae.fr/umr-astre/sit", "_commit": { "id": "5565f8063e4f5a93d20279822f9538b4cd371e70", "author": "Facundo Muñoz ", "committer": "Facundo Muñoz ", "message": "Readme. Update status badge.\n", "time": 1699536465 }, "_maintainer": { "name": "Facundo Muñoz", "email": "facundo.munoz@cirad.fr", "login": "famuvie", "description": "Bayesian methods and Spatial(-temporal) statistics applied to the interplay between life sciences and the environment", "uuid": 5693966, "orcid": "0000-0002-5061-4241" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "dm", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "sf", "role": "Imports" }, { "package": "units", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "spelling", "role": "Suggests" }, { "package": "tmap", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "DiagrammeR", "role": "Suggests" }, { "package": "DiagrammeRsvg", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "kableExtra", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "forge-umr-astre", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_userbio": { "uuid": 39591813, "type": "organization", "name": "Cirad - UMR ASTRE. Also at https://gitlab.cirad.fr/astre/ and https://forge.inrae.fr/umr-astre/", "followers": 1, "description": "Animals, Health, Territories, Risks and Ecosystems" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/sit" }, "_pkgdown": "https://umr-astre.pages.mia.inra.fr/sit", "_searchresults": 134, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/sit.html" ], "_cranurl": false, "_exports": [ "dispersal", "fertility_rate", "flight_range", "fried_index", "inverse_radial_density", "lincoln_index", "print_variable_table", "sit", "sit_adult_surveys", "sit_competitiveness", "sit_diffusion", "sit_egg_surveys", "sit_flight_range", "sit_mdt", "sit_revents", "sit_survival", "sit_trap_types", "sit_traps", "sit_wild_size", "sterile_wild_male_ratio", "survey_ages", "survey_distances_from_release", "validate_sit" ], "_datasets": [ { "name": "fake_adults", "title": "Fake SIT data for testing and examples", "object": "fake_adults", "class": [ "data.frame" ], "fields": [ "trap", "survey", "duration", "population", "species", "sex", "n" ], "rows": 5, "table": true, "tojson": true }, { "name": "fake_eggs", "title": "Fake SIT data for testing and examples", "object": "fake_eggs", "class": [ "data.frame" ], "fields": [ "trap", "survey", "duration", "fertile", "n" ], "rows": 4, "table": true, "tojson": true }, { "name": "fake_rareal", "title": "Fake SIT data for testing and examples", "object": "fake_rareal", "class": [ "data.frame" ], "fields": [ "date", "colour", "n" ], "rows": 2, "table": true, "tojson": true }, { "name": "fake_rpoints", "title": "Fake SIT data for testing and examples", "object": "fake_rpoints", "class": [ "sf", "data.frame" ], "fields": [ "date", "colour", "n", "geometry" ], "rows": 3, "table": true, "tojson": true }, { "name": "fake_trap_types", "title": "Fake SIT data for testing and examples", "object": "fake_trap_types", "class": [ "data.frame" ], "fields": [ "name", "label", "stage" ], "rows": 1, "table": true, "tojson": true }, { "name": "fake_traps", "title": "Fake SIT data for testing and examples", "object": "fake_traps", "class": [ "sf", "data.frame" ], "fields": [ "id", "type", "area", "geometry" ], "rows": 5, "table": true, "tojson": true }, { "name": "sit_prototype", "title": "A prototypical 'sit' object with fake data", "object": "sit_prototype", "class": [ "sit", "dm" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "dispersal", "title": "Dispersal data", "topics": [ "dispersal" ] }, { "page": "fake_sit", "title": "Fake SIT data for testing and examples", "topics": [ "fake_adults", "fake_eggs", "fake_rareal", "fake_rpoints", "fake_sit", "fake_traps", "fake_trap_types" ] }, { "page": "fertility_rate", "title": "Fertility rate", "topics": [ "fertility_rate" ] }, { "page": "fried_index", "title": "Fried index", "topics": [ "fried_index" ] }, { "page": "inverse_radial_density", "title": "Inverse radial density weights", "topics": [ "inverse_radial_density" ] }, { "page": "lincoln_index", "title": "Lincoln index", "topics": [ "lincoln_index" ] }, { "page": "sit", "title": "Build a 'sit' object", "topics": [ "sit" ] }, { "page": "sit_adult_surveys", "title": "Import or retrieve adult surveys", "concept": [ "importing" ], "topics": [ "sit_adult_surveys", "sit_adult_surveys.data.frame", "sit_adult_surveys.sit" ] }, { "page": "sit_competitiveness", "title": "Estimate competitiveness of sterile males", "concept": [ "estimates\n\n\n\nComputes the Fried Index, which estimates the competitiveness based on\n\nobserved fertility rates and the sterile-wild male ratio.\n\n\n\nIt is strongly recommended to estimate competitiveness based on surveys from\n\nareal releases. The calculation requires the estimation of the sterile-wild\n\nmale ratio from surveys pooled across traps and days, which requires a\n\nroughly homogeneous distribution of sterile males." ], "topics": [ "sit_competitiveness" ] }, { "page": "sit_diffusion", "title": "Diffusion", "concept": [ "estimates\n\n\n\nEstimate the diffusion coefficient.\n\n\n\nAssuming that mosquitoes fly randomly (Brownian motion), their dispersion\n\nfollow \nlist(list(\"https://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion#Fick's_first_law\"), list(\"Fick's first law\"))\n\n\nof diffusion, which postulates that flux goes from regions of high\n\nconcentration to regions of low concentration, with a magnitude that is\n\nproportional to the concentration gradient (spatial derivative). The\n\nproportionality constant is the diffusivity $D$ and depend of the species'\n\nbehaviour for that location, season and weather conditions.\n\n\n\nUnder this model, \nlist(list(\"https://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion#Example_solution_2:_Brownian_particle_and_Mean_squared_displacement\"), list(\"the \", list(\"Mean Squared Displacement\"), \" (MSD) of mosquitoes from their release point at time $t$ is\"))\n\n\nlist(list(\"\\\\text{MSD}(t) = 4Dt.\"))\n\n\n\n\nFrom which we can solve for the Diffusion coefficient by using the distances\n\nfrom the release point at which sterile males were captured to estimated the\n\nMSD at a given age.\n\n\n\nThis function computes the MSD of the individuals (possibly, by population)\n\nat the different observed ages, and derives $D$ as the regression slope.\n\nThe resulting object can be plotted to see the underlying regression model." ], "topics": [ "sit_diffusion" ] }, { "page": "sit_egg_surveys", "title": "Import or retrieve egg surveys", "concept": [ "importing" ], "topics": [ "sit_egg_surveys", "sit_egg_surveys.data.frame", "sit_egg_surveys.sit" ] }, { "page": "sit_flight_range", "title": "Flight Range", "concept": [ "estimates\n\n\n\nFlight range of sterile individuals at specified levels." ], "topics": [ "sit_flight_range" ] }, { "page": "sit_mdt", "title": "Mean Distance Travelled and Mean Dispersal Distance", "concept": [ "estimates\n\n\n\nCompute the Mean Distance Travelled (MDT) realised in a SIT experiment.\n\nThe Mean Dispersal Distance (MDD) is the MDT without accounting for\n\ninhomogeneous arrangements of traps. See Details.\n\n\n\nThe mean distance travelled (MDT) is the average distance travelled by all\n\nlist(\"captured\")\n individuals, weighted by the relative density of traps.\n\n\n\nIn practice, it is computed as the average distance between the traps\n\nand the release point, weighted by the number of individuals from the\n\nreleased population and by the relative density of traps.\n\n\n\nMDT estimates result in \nlist(\"NaN\")\n, when there are no observations of captures in\n\nthe corresponding group. This is more likely when estimates are requested by\n\npopulation and age.\n\n\n\nlist(list(\"\\n\", \" \\\\text{MDT}_{jk} = \\\\sum_{i = 1}^{n_t} w_i \\\\, n_{ijk} \\\\, d_i \\\\bigg/\\n\", \" \\\\sum_{i = 1}^{n_t} w_i \\\\, n_{ijk}\\n\"))" ], "topics": [ "sit_mdt" ] }, { "page": "sit_prototype", "title": "A prototypical 'sit' object with fake data", "topics": [ "sit_prototype" ] }, { "page": "sit_revents", "title": "Import or extract release events", "concept": [ "importing" ], "topics": [ "c.sit_revents", "sit_revents", "sit_revents.data.frame", "sit_revents.sf", "sit_revents.sit" ] }, { "page": "sit_survival", "title": "Survival statistics", "topics": [ "sit_survival" ] }, { "page": "sit_trap_types", "title": "Import or extract trap types", "topics": [ "sit_trap_types", "sit_trap_types.data.frame", "sit_trap_types.sit" ] }, { "page": "sit_traps", "title": "Import or extract trap information", "concept": [ "importing" ], "topics": [ "c.sit_traps", "sit_traps", "sit_traps.character", "sit_traps.numeric", "sit_traps.sf", "sit_traps.sit" ] }, { "page": "sit_wild_size", "title": "Size of the Wild Population", "topics": [ "sit_wild_size" ] }, { "page": "sterile_wild_male_ratio", "title": "Sterile-Wild male ratio", "topics": [ "sterile_wild_male_ratio" ] }, { "page": "survey_ages", "title": "Age of captured sterile males", "topics": [ "survey_ages" ] } ], "_pkglogo": "https://forge.inrae.fr/umr-astre/sit/raw/HEAD/man/figures/logo.png", "_readme": "https://forge.inrae.fr/umr-astre/sit/raw/HEAD/README.md", "_rundeps": [ "backports", "cachem", "class", "classInt", "cli", "cpp11", "DBI", "dm", "dplyr", "e1071", "evaluate", "fastmap", "generics", "glue", "highr", "KernSmooth", "knitr", "lifecycle", "magrittr", "memoise", "pillar", "pkgconfig", "proxy", "purrr", "R6", "Rcpp", "rlang", "s2", "sf", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "units", "utf8", "vctrs", "withr", "wk", "xfun", "yaml" ], "_score": 2.8260748027008264, "_indexed": false, "_nocasepkg": 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