Add source_repositories csv

data-raw/source_repositories.R

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+library(ctv)
+library(purrr)
+library(dplyr)
+
+source_from_desc <- read.ctv("Epidemiology.md") |>
+  pluck("packagelist", "name") |>
+  pkgsearch::cran_packages() |>
+  transmute(
+    package = Package,
+    github_repo = dplyr::coalesce(
+      stringr::str_match(URL, "https://github.com/([^/]+/[^/,]+)")[, 2],
+      stringr::str_match(BugReports, "https://github.com/([^/]+/[^/,]+)/issues")[, 2]
+    )
+  )
+
+source_from_manual <- tribble(
+  ~ package, ~ github_repo,
+  "coarseDataTools", "nickreich/coarseDataTools",
+  "covid19france", "Covid19R/covid19france",
+  "covid19us", "aedobbyn/covid19us",
+  "epiR", "mstevenson888/epiR",
+  "EpiReport", "EU-ECDC/EpiReport",
+  "episensr", "dhaine/episensr",
+  "etm", "mclements/etm",
+  "mediation", "kosukeimai/mediation",
+  "outbreaker2", "reconhub/outbreaker2",
+  "riskCommunicator", "jgrembi/riskCommunicator",
+  "TransPhylo", "xavierdidelot/TransPhylo",
+  "tsiR", "adbecker/tsiR"
+)
+
+anti_join(source_from_desc, source_from_manual, by = "package") |>
+  full_join(source_from_manual) |>
+  dplyr::arrange(package) |>
+  write.csv("data/source_repositories.csv", row.names = FALSE)

data/source_repositories.csv

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+"package","github_repo"
+"AMR","msberends/AMR"
+"Bernadette","bernadette-eu/Bernadette"
+"COVID19","covid19datahub/COVID19"
+"CovidMutations","MSQ-123/CovidMutations"
+"DSAIDE","ahgroup/DSAIDE"
+"EnvStats","alexkowa/EnvStats"
+"Epi",NA
+"EpiContactTrace","stewid/EpiContactTrace"
+"EpiCurve","IamKDO/EpiCurve"
+"EpiEstim","mrc-ide/EpiEstim"
+"EpiILM","waleedalmutiry/EpiILM"
+"EpiILMCT","waleedalmutiry/EpiILMCT"
+"EpiModel","EpiModel/EpiModel"
+"EpiNow2","epiforecasts/EpiNow2"
+"EpiReport","EU-ECDC/EpiReport"
+"EpiSignalDetection","EU-ECDC/EpiSignalDetection"
+"HIMA","YinanZheng/HIMA"
+"NADA",NA
+"R0","tobadia/R0"
+"RSurveillance","roStats/RSurveillance"
+"SimInf","stewid/SimInf"
+"SpatialEpi","rudeboybert/SpatialEpi"
+"TransPhylo","xavierdidelot/TransPhylo"
+"adegenet","thibautjombart/adegenet"
+"apisensr","dhaine/apisensr"
+"argo",NA
+"bets.covid19","qingyuanzhao/bets.covid19"
+"bkmr","jenfb/bkmr"
+"cfr","epiverse-trace/cfr"
+"cholera","lindbrook/cholera"
+"cmprsk",NA
+"coarseDataTools","nickreich/coarseDataTools"
+"contactdata","bisaloo/contactdata"
+"corona",NA
+"coronavirus","RamiKrispin/coronavirus"
+"covid19.analytics","mponce0/covid19.analytics"
+"covid19br","fndemarqui/covid19br"
+"covid19dbcand","MohammedFCIS/covid19dbcand"
+"covid19france","Covid19R/covid19france"
+"covid19italy","RamiKrispin/covid19italy"
+"covid19sf","RamiKrispin/covid19sf"
+"covid19swiss","Covid19R/covid19swiss"
+"covid19us","aedobbyn/covid19us"
+"dbparser","ropensci/dbparser"
+"dde","mrc-ide/dde"
+"deSolve",NA
+"earlyR","reconhub/earlyR"
+"endtoend",NA
+"epiDisplay",NA
+"epiR","mstevenson888/epiR"
+"epibasix",NA
+"epicontacts","reconhub/epicontacts"
+"epiflows","reconhub/epiflows"
+"epimdr","objornstad/epimdr"
+"epinet",NA
+"episensr","dhaine/episensr"
+"epitools",NA
+"epitrix","reconhub/epitrix"
+"epitweetr","EU-ECDC/epitweetr"
+"etm","mclements/etm"
+"finalsize","epiverse-trace/finalsize"
+"i2extras","reconverse/i2extras"
+"incidence","reconhub/incidence"
+"incidence2","reconverse/incidence2"
+"linelist","epiverse-trace/linelist"
+"malariaAtlas","malaria-atlas-project/malariaAtlas"
+"mediation","kosukeimai/mediation"
+"mem","lozalojo/mem"
+"memapp","lozalojo/memapp"
+"mma",NA
+"modelSSE",NA
+"mstate","hputter/mstate"
+"nbTransmission","sarahleavitt/nbTransmission"
+"nhanesA","cjendres1/nhanes"
+"nosoi","slequime/nosoi"
+"o2geosocial","alxsrobert/o2geosocial"
+"odin","mrc-ide/odin"
+"outbreaker2","reconhub/outbreaker2"
+"outbreaks","reconhub/outbreaks"
+"pomp","kingaa/pomp"
+"popEpi","FinnishCancerRegistry/popEpi"
+"powerSurvEpi",NA
+"riskCommunicator","jgrembi/riskCommunicator"
+"socialmixr","epiforecasts/socialmixr"
+"surveillance",NA
+"trendeval","reconverse/trendeval"
+"trending","reconverse/trending"
+"tsiR","adbecker/tsiR"