diff --git a/.gitignore b/.gitignore index 3750db3..58d241a 100644 --- a/.gitignore +++ b/.gitignore @@ -11,4 +11,5 @@ Data/ *_files */02_range_maps_files/figure-html/* -*cache/ \ No newline at end of file +*cache/ +*.motus \ No newline at end of file diff --git a/00_workflow.qmd b/00_workflow.qmd index f2def03..7b9a4c7 100644 --- a/00_workflow.qmd +++ b/00_workflow.qmd @@ -1,5 +1,5 @@ --- -title: Workflow +title: Plans --- ## Order of operations diff --git a/01_select_projects.qmd b/01_select_projects.qmd new file mode 100644 index 0000000..0b2a3b6 --- /dev/null +++ b/01_select_projects.qmd @@ -0,0 +1,108 @@ +--- +title: Selecting Projects +--- + +Here we explore a list of open or semi open Motus projects to select more +project ids which we can use in our pilot study. + +## Setup + +```{r} +#| message: false +source("XX_setup.R") +library(readxl) +``` + + +## Cleaning and Filtering + +**Cleaning** + +The species names (English and scientific) listed here aren't always consistent, +so we'll omit them and use only the species IDs to match them with the +NatureCounts metadata from [`XX_setup`](XX_setup.html). + +Then we consolidate the deployments in those projects as some listed some +deployments under one species name and others under another (even if the species +was the same) + +**Filtering** + +- keep only `access == 1` which are fully public projects +- omit species ID 129470 which are listed as attached to a Human...(?) +- omit projects with non-Canadian species + +```{r} +p_sp <- read_excel("Data/Raw/TagsSpeciesProject.xlsx") |> + rename_with(.cols = contains("No column"), \(x) "access") |> + filter(access == 1, # Only completely open projects + speciesID != 129470) |> # Don't worry about Human tags :D + select(-speciesName, -motusEnglishName, -access) |> # Species Names are not consistent + summarize(across(everything(), sum), .by = c("tagProjectID", "speciesID")) |> + left_join(select(species, species_id, scientific_name, english_name), + by = c("speciesID" = "species_id")) |> + mutate(good = !is.na(scientific_name), + other = str_detect(english_name, "Eurasian|European|Elaenia")) |> + group_by(tagProjectID) |> + filter(all(!other | is.na(other))) |> # Omit projects with non-Canadian species + mutate(good_tags = sum(num_deployments[good]), + prop_good_tags = good_tags / sum(num_deployments)) |> + ungroup() |> + select(-other) |> + arrange(desc(prop_good_tags)) + +gt(p_sp) |> + fmt_number("prop_good_tags", decimals = 2) +``` + +## Summarize + +Now we can summarize these projects by how many species, deployments (tags) and +the average number of deployments per species. + +We'll aim to include projects with a bread of species but also reasonable coverage, +so we exclude projects with less than 100% passerines and fewer than three species. +```{r} +p <- p_sp |> + filter(prop_good_tags == 1) |> + group_by(tagProjectID) |> + summarize(total_tags = sum(num_deployments), + n_species = n_distinct(speciesID), + mean_tags_per_species = mean(num_deployments), + species = list(unique(english_name))) |> + filter(n_species > 3) |> + arrange(desc(mean_tags_per_species), desc(n_species), desc(total_tags)) + +gt(p) |> + fmt_number(columns = "mean_tags_per_species", decimals = 1) +``` + + +## Data sizes + +Now, we can check the amount of data per project (see what we're in for!) + +For reference, 7,006,847,799 bytes is ~ 7 GB + +```{r} +#| cache: true +dir.create("Data/Temp") +status <- map( + set_names(p$tagProjectID), + \(x) tellme(x, dir = "Data/Temp", new = TRUE)) |> + list_rbind(names_to = "proj_id") +unlink("Data/Temp", recursive = TRUE) +``` + +So this, isn't too bad, data-wise, I think we could use all projects. + +```{r} +status |> + mutate(Megabytes = numBytes / 1000000) |> + arrange(desc(numBytes)) |> + gt() |> + fmt_number(decimals = 0) +``` + + + diff --git a/01_download.qmd b/02_download.qmd similarity index 100% rename from 01_download.qmd rename to 02_download.qmd diff --git a/02_range_maps.qmd b/03_range_maps.qmd similarity index 100% rename from 02_range_maps.qmd rename to 03_range_maps.qmd diff --git a/03_basic_filters.qmd b/04_basic_filters.qmd similarity index 100% rename from 03_basic_filters.qmd rename to 04_basic_filters.qmd diff --git a/XX_setup.R b/XX_setup.R index 3c5aac0..c1a5572 100644 --- a/XX_setup.R +++ b/XX_setup.R @@ -35,7 +35,7 @@ projects <- setNames(projects, projects) # naturecounts::nc_metadata() # Update naturecounts taxonomy lists species <- naturecounts::meta_species_taxonomy() |> - filter(order_taxon == "Passeriformes") + filter(order_taxon %in% c("Passeriformes", "Piciformes")) # ---- functions ---- source("XX_functions.R") \ No newline at end of file diff --git a/_freeze/02_download/execute-results/html.json b/_freeze/02_download/execute-results/html.json new file mode 100644 index 0000000..e715e44 --- /dev/null +++ b/_freeze/02_download/execute-results/html.json @@ -0,0 +1,15 @@ +{ + "hash": "3318bb26aa41ac5a5e76f5b9fbb8f896", + "result": { + "engine": "knitr", + "markdown": "---\ntitle: Download/Update Data\nfreeze: auto\n---\n\n\nIn this step we download, or update, our Motus SQLite databases.\n\n## Setup\n\n\n::: {.cell}\n\n```{.r .cell-code}\nsource(\"XX_setup.R\")\n```\n:::\n\n\nThis step can take a lot of time and it may not be necessary to be constantly updating the data bases. Set `update <- TRUE` to update, `update <- FALSE` to just check the number of new observations.\n\n\n::: {.cell}\n\n```{.r .cell-code}\nupdate <- FALSE\n```\n:::\n\n\n## Status\n\nGet the status of each project (i.e. how much data left to download?)\n\n- This will create new `project-XXX.motus` SQLite data bases for us if it doesn't already exist (but will not download the data)\n\n\n::: {.cell}\n\n```{.r .cell-code}\nstatus <- map(\n projects, \n \\(x) tellme(x, dir = \"Data/Raw\", new = file.exists(paste0(\"project-\", x, \".motus\")))) |>\n list_rbind(names_to = \"proj_id\")\n```\n\n::: {.cell-output .cell-output-stderr}\n\n```\nWarning: Database Data/Raw/project-551.motus already exists, so I'm ignoring\nthe 'new = TRUE' option\n```\n\n\n:::\n\n```{.r .cell-code}\ngt(status)\n```\n\n::: {.cell-output-display}\n\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n\n \n\n\n\n\n\n \n\n\n\n\n\n \n\n\n\n\n\n \n \n \n
proj_idnumHitsnumBytesnumRunsnumBatchesnumGPS
484281689284296911311859
55163532145960939487716722318937
3731785549827244397658
1681819330457896132297
\n
\n```\n\n:::\n:::\n\n\n## Download data\n\n**If this is the first time running, it will take time!**\n\n- `tagme()` without arguments will update all databases in the folder\n- we can run this intermittently to update the databases as new data arrives\n\n\n::: {.cell}\n\n```{.r .cell-code}\nif(update) tagme(dir = \"Data/Raw\")\n```\n:::\n\n\n## Remove deprecated batches\n\nDeprecated batches are removed from the Motus server, but are still present in data that was previously downloaded. This step cleans up the database.\n\n\n::: {.cell}\n\n```{.r .cell-code}\nif(update) {\n walk(projects, \\(x) {\n message(\"\\nProject \", x)\n t <- tagme(x, dir = \"Data/Raw\", update = FALSE)\n deprecateBatches(t, ask = FALSE)\n DBI::dbDisconnect(t)\n })\n}\n```\n:::\n\n## Reproducibility\n\n:::{.callout-note collapse=true}\n### Session Info\n::: {.cell}\n\n```{.r .cell-code}\ndevtools::session_info()\n```\n\n::: {.cell-output .cell-output-stdout}\n\n```\n─ Session info ───────────────────────────────────────────────────────────────\n setting value\n version R version 4.3.2 (2023-10-31)\n os Ubuntu 22.04.3 LTS\n system x86_64, linux-gnu\n ui X11\n language en_CA:en\n collate en_CA.UTF-8\n ctype en_CA.UTF-8\n tz America/Toronto\n date 2024-01-24\n pandoc 3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)\n\n─ Packages ───────────────────────────────────────────────────────────────────\n package * version date (UTC) lib source\n assertr * 3.0.0 2022-11-05 [1] 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CRAN (R 4.3.1)\n xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.2)\n xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)\n yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.2)\n\n [1] /home/steffi/R/x86_64-pc-linux-gnu-library/4.3\n [2] /usr/local/lib/R/site-library\n [3] /usr/lib/R/site-library\n [4] /usr/lib/R/library\n\n──────────────────────────────────────────────────────────────────────────────\n```\n\n\n:::\n:::\n:::\n\n", + "supporting": [], + "filters": [ + "rmarkdown/pagebreak.lua" + ], + "includes": {}, + "engineDependencies": {}, + "preserve": {}, + "postProcess": true + } +} \ No newline at end of file diff --git a/docs/00_workflow.html b/docs/00_workflow.html index 8172292..77b0617 100644 --- a/docs/00_workflow.html +++ b/docs/00_workflow.html @@ -7,9 +7,9 @@ - + -Motus tracking of urban migration stopovers - Workflow +Motus tracking of urban migration stopovers - Plans + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ +
+ +
+ + +
+ + + +
+ +
+
+

Selecting Projects

+
+ + + +
+ +
+
Author
+
+

Steffi LaZerte

+
+
+ +
+
Published
+
+

January 24, 2024

+
+
+ + +
+ + + +
+ + +

Here we explore a list of open or semi open Motus projects to select more project ids which we can use in our pilot study.

+
+

Setup

+
+
source("XX_setup.R")
+library(readxl)
+
+
+
+

Cleaning and Filtering

+

Cleaning

+

The species names (English and scientific) listed here aren’t always consistent, so we’ll omit them and use only the species IDs to match them with the NatureCounts metadata from XX_setup.

+

Then we consolidate the deployments in those projects as some listed some deployments under one species name and others under another (even if the species was the same)

+

Filtering

+
    +
  • keep only access == 1 which are fully public projects
    • +
  • omit species ID 129470 which are listed as attached to a Human…(?)
    • +
  • omit projects with non-Canadian species
    • +
+
+
p_sp <- read_excel("Data/Raw/TagsSpeciesProject.xlsx") |>
+  rename_with(.cols = contains("No column"), \(x) "access") |>
+  filter(access == 1,             # Only completely open projects
+         speciesID != 129470) |>  # Don't worry about Human tags :D
+  select(-speciesName, -motusEnglishName, -access) |> # Species Names are not consistent
+  summarize(across(everything(), sum), .by = c("tagProjectID", "speciesID")) |>
+  left_join(select(species, species_id, scientific_name, english_name),
+            by = c("speciesID" = "species_id")) |>
+  mutate(good = !is.na(scientific_name),
+         other = str_detect(english_name, "Eurasian|European|Elaenia")) |>
+  group_by(tagProjectID) |>
+  filter(all(!other | is.na(other))) |> # Omit projects with non-Canadian species
+  mutate(good_tags = sum(num_deployments[good]),
+         prop_good_tags =  good_tags / sum(num_deployments)) |>
+  ungroup() |>
+  select(-other) |>
+  arrange(desc(prop_good_tags))
+
+gt(p_sp) |>
+  fmt_number("prop_good_tags", decimals = 2)
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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tagProjectIDspeciesIDnum_deploymentsscientific_nameenglish_namegoodgood_tagsprop_good_tags
8519250112Plectrophenax nivalisSnow BuntingTRUE1121.00
221155802Catharus ustulatusSwainson's ThrushTRUE21.00
2404221839Junco hyemalisDark-eyed JuncoTRUE391.00
2491661053Setophaga coronataYellow-rumped WarblerTRUE531.00
2581560010Hylocichla mustelinaWood ThrushTRUE201.00
2581695010Parkesia motacillaLouisiana WaterthrushTRUE201.00
259189408Ammospiza nelsoniNelson's SparrowTRUE1031.00
2591895039Ammospiza caudacutaSaltmarsh SparrowTRUE1031.00
2591896056Ammospiza maritimaSeaside SparrowTRUE1031.00
3061577069Turdus migratoriusAmerican RobinTRUE711.00
306158302Ixoreus naeviusVaried ThrushTRUE711.00
3081577030Turdus migratoriusAmerican RobinTRUE301.00
31014050176Progne subisPurple MartinTRUE1761.00
3521558075Catharus ustulatusSwainson's ThrushTRUE2571.00
3521590030Dumetella carolinensisGray CatbirdTRUE2571.00
352185502Pipilo maculatusSpotted TowheeTRUE2571.00
3521883010Pooecetes gramineusVesper SparrowTRUE2571.00
3521890021Ammodramus savannarumGrasshopper SparrowTRUE2571.00
3521945023Passerina amoenaLazuli BuntingTRUE2571.00
3521961031Sturnella neglectaWestern MeadowlarkTRUE2571.00
3521976025Molothrus aterBrown-headed CowbirdTRUE2571.00
3522042040Spinus pinusPine SiskinTRUE2571.00
3601425054Hirundo rusticaBarn SwallowTRUE541.00
3611692011Limnothlypis swainsoniiSwainson's WarblerTRUE111.00
3631682035Setophaga striataBlackpoll WarblerTRUE351.00
364168201Setophaga striataBlackpoll WarblerTRUE551.00
364203102Pinicola enucleatorPine GrosbeakTRUE551.00
3642033038Haemorhous purpureusPurple FinchTRUE551.00
3642042014Spinus pinusPine SiskinTRUE551.00
370155906Catharus guttatusHermit ThrushTRUE61.00
3713626115Locustella naeviaCommon Grasshopper WarblerTRUE571.00
3713627122Acrocephalus schoenobaenusSedge WarblerTRUE571.00
3713647520Curruca communisGreater WhitethroatTRUE571.00
377160601Toxostoma leconteiLeConte's ThrasherTRUE81.00
377163707Phainopepla nitensPhainopeplaTRUE81.00
3801425044Hirundo rusticaBarn SwallowTRUE841.00
3803540740Riparia ripariaBank SwallowTRUE841.00
387408181Melozone cabanisiCabanis's Ground-SparrowTRUE11.00
3881565191Turdus philomelosSong ThrushTRUE911.00
3911690031Protonotaria citreaProthonotary WarblerTRUE311.00
3931404024Eremophila alpestrisHorned LarkTRUE1301.00
3931630031Anthus spragueiiSprague's PipitTRUE1301.00
3931891014Centronyx bairdiiBaird's SparrowTRUE1301.00
393191305Rhynchophanes mccowniiThick-billed LongspurTRUE1301.00
3931916056Calcarius ornatusChestnut-collared LongspurTRUE1301.00
4081894083Ammospiza nelsoniNelson's SparrowTRUE831.00
41419500137Passerina cirisPainted BuntingTRUE1371.00
4171693081Seiurus aurocapillaOvenbirdTRUE2261.00
4171899058Melospiza melodiaSong SparrowTRUE2261.00
4171903063Zonotrichia albicollisWhite-throated SparrowTRUE2261.00
4174138424Vireo olivaceusRed-eyed VireoTRUE2261.00
4241405063Progne subisPurple MartinTRUE631.00
4261883036Pooecetes gramineusVesper SparrowTRUE371.00
426189501Ammospiza caudacutaSaltmarsh SparrowTRUE371.00
430155902Catharus guttatusHermit ThrushTRUE61.00
430173104Icteria virensYellow-breasted ChatTRUE61.00
4383627129Acrocephalus schoenobaenusSedge WarblerTRUE911.00
4383646730Sylvia borinGarden WarblerTRUE911.00
4383647532Curruca communisGreater WhitethroatTRUE911.00
464155501Catharus fuscescensVeeryTRUE591.00
4641558028Catharus ustulatusSwainson's ThrushTRUE591.00
464159004Dumetella carolinensisGray CatbirdTRUE591.00
464164601Leiothlypis peregrinaTennessee WarblerTRUE591.00
464165406Setophaga americanaNorthern ParulaTRUE591.00
464166001Setophaga caerulescensBlack-throated Blue WarblerTRUE591.00
464166601Setophaga virensBlack-throated Green WarblerTRUE591.00
464168005Setophaga palmarumPalm WarblerTRUE591.00
464168802Mniotilta variaBlack-and-white WarblerTRUE591.00
464168902Setophaga ruticillaAmerican RedstartTRUE591.00
464169305Seiurus aurocapillaOvenbirdTRUE591.00
464170003Geothlypis trichasCommon YellowthroatTRUE591.00
4661425091Hirundo rusticaBarn SwallowTRUE1131.00
4663540721Riparia ripariaBank SwallowTRUE1131.00
466406671Hirundo rustica erythrogasterBarn Swallow (American)TRUE1131.00
46935407909Riparia ripariaBank SwallowTRUE9091.00
4751892066Centronyx henslowiiHenslow's SparrowTRUE661.00
48218880135Passerculus sandwichensisSavannah SparrowTRUE1351.00
484158302Ixoreus naeviusVaried ThrushTRUE1221.00
4841855061Pipilo maculatusSpotted TowheeTRUE1221.00
484190504Zonotrichia leucophrysWhite-crowned SparrowTRUE1221.00
4841906055Zonotrichia atricapillaGolden-crowned SparrowTRUE1221.00
4891952033Dolichonyx oryzivorusBobolinkTRUE331.00
4961555015Catharus fuscescensVeeryTRUE541.00
496155801Catharus ustulatusSwainson's ThrushTRUE541.00
4961559038Catharus guttatusHermit ThrushTRUE541.00
4971903068Zonotrichia albicollisWhite-throated SparrowTRUE681.00
499189904Melospiza melodiaSong SparrowTRUE41.00
515155901Catharus guttatusHermit ThrushTRUE421.00
515157707Turdus migratoriusAmerican RobinTRUE421.00
515159006Dumetella carolinensisGray CatbirdTRUE421.00
515159703Toxostoma rufumBrown ThrasherTRUE421.00
5151903025Zonotrichia albicollisWhite-throated SparrowTRUE421.00
524157701Turdus migratoriusAmerican RobinTRUE11.00
5294206774Oenanthe oenanthe/seebohmiNorthern/Atlas WheatearTRUE741.00
531141202Tachycineta bicolorTree SwallowTRUE51.00
531185502Pipilo maculatusSpotted TowheeTRUE51.00
531408241Pipilo maculatus x erythrophthalmusSpotted x Eastern Towhee (hybrid)TRUE51.00
5361558020Catharus ustulatusSwainson's ThrushTRUE201.00
537155504Catharus fuscescensVeeryTRUE61.00
537171502Cardellina canadensisCanada WarblerTRUE61.00
545159702Toxostoma rufumBrown ThrasherTRUE31.00
545166201Setophaga coronata coronataYellow-rumped Warbler (Myrtle)TRUE31.00
551134209Vireo solitariusBlue-headed VireoTRUE2031.00
5511559045Catharus guttatusHermit ThrushTRUE2031.00
5511658024Setophaga magnoliaMagnolia WarblerTRUE2031.00
5511662042Setophaga coronata coronataYellow-rumped Warbler (Myrtle)TRUE2031.00
5511899017Melospiza melodiaSong SparrowTRUE2031.00
5511936066Cardinalis cardinalisNorthern CardinalTRUE2031.00
570155802Catharus ustulatusSwainson's ThrushTRUE21.00
604209102Passer domesticusHouse SparrowTRUE21.00
607159002Dumetella carolinensisGray CatbirdTRUE101.00
607169301Seiurus aurocapillaOvenbirdTRUE101.00
607169403Parkesia noveboracensisNorthern WaterthrushTRUE101.00
607170001Geothlypis trichasCommon YellowthroatTRUE101.00
607171302Setophaga citrinaHooded WarblerTRUE101.00
607173101Icteria virensYellow-breasted ChatTRUE101.00
609121727Empidonax traillii extimusWillow Flycatcher (Southwestern)TRUE71.00
61235407100Riparia ripariaBank SwallowTRUE1001.00
6171683018Setophaga ceruleaCerulean WarblerTRUE181.00
6191558020Catharus ustulatusSwainson's ThrushTRUE411.00
619166005Setophaga caerulescensBlack-throated Blue WarblerTRUE411.00
6191689016Setophaga ruticillaAmerican RedstartTRUE411.00
621165608Setophaga petechiaYellow WarblerTRUE81.00
623176901Piranga ludovicianaWestern TanagerTRUE31.00
623194101Pheucticus melanocephalusBlack-headed GrosbeakTRUE31.00
623407891Icteria virens auricollisYellow-breasted Chat (auricollis)TRUE31.00
6271642040Vermivora chrysopteraGolden-winged WarblerTRUE401.00
6341904010Zonotrichia querulaHarris's SparrowTRUE101.00
645156003Hylocichla mustelinaWood ThrushTRUE31.00
657155807Catharus ustulatusSwainson's ThrushTRUE101.00
657190503Zonotrichia leucophrysWhite-crowned SparrowTRUE101.00
6601412010Tachycineta bicolorTree SwallowTRUE101.00
6613540724Riparia ripariaBank SwallowTRUE241.00
6781560015Hylocichla mustelinaWood ThrushTRUE151.00
691204801Spinus psaltriaLesser GoldfinchTRUE11.00
55680402NANAFALSE130.87
556142302Petrochelidon pyrrhonotaCliff SwallowTRUE130.87
556142801Poecile atricapillusBlack-capped ChickadeeTRUE130.87
556155601Catharus minimusGray-cheeked ThrushTRUE130.87
556163303Bombycilla cedrorumCedar WaxwingTRUE130.87
556203301Haemorhous purpureusPurple FinchTRUE130.87
556413843Vireo olivaceusRed-eyed VireoTRUE130.87
556451682Junco hyemalis hyemalis/carolinensisDark-eyed Junco (Slate-colored)TRUE130.87
406357023NANAFALSE1430.86
4061558014Catharus ustulatusSwainson's ThrushTRUE1430.86
4061876024Spizelloides arboreaAmerican Tree SparrowTRUE1430.86
4061892057Centronyx henslowiiHenslow's SparrowTRUE1430.86
406190301Zonotrichia albicollisWhite-throated SparrowTRUE1430.86
4064221813Junco hyemalisDark-eyed JuncoTRUE1430.86
4064516834Junco hyemalis hyemalis/carolinensisDark-eyed Junco (Slate-colored)TRUE1430.86
115166101Setophaga coronataYellow-rumped WarblerTRUE50.83
115169201Limnothlypis swainsoniiSwainson's WarblerTRUE50.83
115169601Geothlypis formosaKentucky WarblerTRUE50.83
115187601Spizelloides arboreaAmerican Tree SparrowTRUE50.83
115195001Passerina cirisPainted BuntingTRUE50.83
115318561NANAFALSE50.83
520445010NANAFALSE180.62
52047501NANAFALSE180.62
5201694018Parkesia noveboracensisNorthern WaterthrushTRUE180.62
282357022NANAFALSE330.60
2821952011Dolichonyx oryzivorusBobolinkTRUE330.60
2821960022Sturnella magna/lilianaeEastern/Chihuahuan MeadowlarkTRUE330.60
5824516859Junco hyemalis hyemalis/carolinensisDark-eyed Junco (Slate-colored)TRUE590.60
5824728240NANAFALSE590.60
614498028NANAFALSE410.48
614787117NANAFALSE410.48
6141857041Pipilo erythrophthalmusEastern TowheeTRUE410.48
437612NANAFALSE640.30
437703NANAFALSE640.30
4383042NANAFALSE640.30
4463030NANAFALSE640.30
4467074NANAFALSE640.30
41950064Passerina cirisPainted BuntingTRUE640.30
193768036NANAFALSE130.25
19378713NANAFALSE130.25
1931560011Hylocichla mustelinaWood ThrushTRUE130.25
193169602Geothlypis formosaKentucky WarblerTRUE130.25
9469052NANAFALSE50.06
9189401Ammospiza nelsoniNelson's SparrowTRUE50.06
9189504Ammospiza caudacutaSaltmarsh SparrowTRUE50.06
91001904NANAFALSE50.06
91002509NANAFALSE50.06
91004203NANAFALSE50.06
91004501NANAFALSE50.06
91244221NANAFALSE50.06
91244303NANAFALSE50.06
27407024NANAFALSE00.00
2741006NANAFALSE00.00
27418014NANAFALSE00.00
27463014NANAFALSE00.00
27469032NANAFALSE00.00
27476058NANAFALSE00.00
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68407032NANAFALSE00.00
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586499015NANAFALSE00.00
60877202NANAFALSE00.00
608787146NANAFALSE00.00
6112571841NANAFALSE00.00
6112572011NANAFALSE00.00
6112572165NANAFALSE00.00
632787120NANAFALSE00.00
6351001901NANAFALSE00.00
6351002302NANAFALSE00.00
6351004301NANAFALSE00.00
6441003001NANAFALSE00.00
6441214011NANAFALSE00.00
64610043010NANAFALSE00.00
64612447010NANAFALSE00.00
6481242402NANAFALSE00.00
64812548014NANAFALSE00.00
64923030NANAFALSE00.00
65110068040NANAFALSE00.00
664768051NANAFALSE00.00
66749905NANAFALSE00.00
672787145NANAFALSE00.00
67420075NANAFALSE00.00
6881002403NANAFALSE00.00
6881002705NANAFALSE00.00
6881004308NANAFALSE00.00
6881005302NANAFALSE00.00
69010043010NANAFALSE00.00
6901004607NANAFALSE00.00
+ +
+
+
+
+
+

Summarize

+

Now we can summarize these projects by how many species, deployments (tags) and the average number of deployments per species.

+

We’ll aim to include projects with a bread of species but also reasonable coverage, so we exclude projects with less than 100% passerines and fewer than three species.

+
+
p <- p_sp |>
+  filter(prop_good_tags == 1) |>
+  group_by(tagProjectID) |>
+  summarize(total_tags = sum(num_deployments),
+            n_species = n_distinct(speciesID),
+            mean_tags_per_species = mean(num_deployments),
+            species = list(unique(english_name))) |>
+  filter(n_species > 3) |>
+  arrange(desc(mean_tags_per_species), desc(n_species), desc(total_tags))
+
+gt(p) |>
+  fmt_number(columns = "mean_tags_per_species", decimals = 1)
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
tagProjectIDtotal_tagsn_speciesmean_tags_per_speciesspecies
417226456.5Ovenbird, Song Sparrow, White-throated Sparrow, Red-eyed Vireo
551203633.8Blue-headed Vireo, Hermit Thrush, Magnolia Warbler, Yellow-rumped Warbler (Myrtle), Song Sparrow, Northern Cardinal
484122430.5Varied Thrush, Spotted Towhee, White-crowned Sparrow, Golden-crowned Sparrow
352257928.6Swainson's Thrush, Gray Catbird, Spotted Towhee, Vesper Sparrow, Grasshopper Sparrow, Lazuli Bunting, Western Meadowlark, Brown-headed Cowbird, Pine Siskin
393130526.0Horned Lark, Sprague's Pipit, Baird's Sparrow, Thick-billed Longspur, Chestnut-collared Longspur
36455413.8Blackpoll Warbler, Pine Grosbeak, Purple Finch, Pine Siskin
5154258.4Hermit Thrush, American Robin, Gray Catbird, Brown Thrasher, White-throated Sparrow
46459124.9Veery, Swainson's Thrush, Gray Catbird, Tennessee Warbler, Northern Parula, Black-throated Blue Warbler, Black-throated Green Warbler, Palm Warbler, Black-and-white Warbler, American Redstart, Ovenbird, Common Yellowthroat
6071061.7Gray Catbird, Ovenbird, Northern Waterthrush, Common Yellowthroat, Hooded Warbler, Yellow-breasted Chat
+ +
+
+
+
+
+

Data sizes

+

Now, we can check the amount of data per project (see what we’re in for!)

+

For reference, 7,006,847,799 bytes is ~ 7 GB

+
+
dir.create("Data/Temp")
+status <- map(
+  set_names(p$tagProjectID), 
+  \(x) tellme(x, dir = "Data/Temp",  new = TRUE)) |>
+  list_rbind(names_to = "proj_id")
+unlink("Data/Temp", recursive = TRUE)
+
+

So this, isn’t too bad, data-wise, I think we could use all projects.

+
+
status |> 
+  mutate(Megabytes = numBytes / 1000000) |>
+  arrange(desc(numBytes)) |>
+  gt() |>
+  fmt_number(decimals = 0)
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
proj_idnumHitsnumBytesnumRunsnumBatchesnumGPSMegabytes
55174,368,2137,006,847,7991,283,2863,059386,2107,007
35270,567,6126,655,989,4121,053,00839,044659,5036,656
41747,585,9404,500,299,2341,007,0442,647379,9514,500
48425,653,6242,470,082,1181,076,3913,515495,5252,470
5152,198,407256,103,381425,9804,517572,886256
3931,444,599160,645,21780,0534,799447,871161
36494,46725,729,83117,0001,888330,57926
46480,67321,734,41534,7521,873253,37722
6079391,544,99745614729,6342
+ +
+
+
+ + +
+ + Back to top
+ + +
+ + + + + \ No newline at end of file diff --git a/docs/01_download.html b/docs/02_download.html similarity index 87% rename from docs/01_download.html rename to docs/02_download.html index 2b2508b..453c7c9 100644 --- a/docs/01_download.html +++ b/docs/02_download.html @@ -7,7 +7,7 @@ - + Motus tracking of urban migration stopovers - Download/Update Data @@ -734,35 +744,35 @@

Status

484 -0 -0 -0 -0 -0 +2816 +892842 +969 +113 +11859 551 -1317609 -123845723 -14857 -119 -9755 +6353214 +596093948 +77167 +223 +18937 373 -0 -0 -0 -0 -0 +1785 +549827 +244 +39 +7658 168 -0 -0 -0 -0 -0 +1819 +330457 +896 +13 +2297 @@ -779,21 +789,21 @@

Download data

  • we can run this intermittently to update the databases as new data arrives
    • -
    if(update) tagme(dir = "Data/Raw")
    +
    if(update) tagme(dir = "Data/Raw")

    Remove deprecated batches

    Deprecated batches are removed from the Motus server, but are still present in data that was previously downloaded. This step cleans up the database.

    -
    if(update) {
-  walk(projects, \(x) {
-    message("\nProject ", x)
-    t <- tagme(x, dir = "Data/Raw", update = FALSE)
-    deprecateBatches(t, ask = FALSE)
-    DBI::dbDisconnect(t)
-  })
-}
    +
    if(update) {
+  walk(projects, \(x) {
+    message("\nProject ", x)
+    t <- tagme(x, dir = "Data/Raw", update = FALSE)
+    deprecateBatches(t, ask = FALSE)
+    DBI::dbDisconnect(t)
+  })
+}
    @@ -811,7 +821,7 @@

    Reproducibility

    -
    devtools::session_info()
    +
    devtools::session_info()
    ─ Session info ───────────────────────────────────────────────────────────────
  setting  value
@@ -823,7 +833,7 @@ 
    Reproducibility
    
  collate  en_CA.UTF-8
  ctype    en_CA.UTF-8
  tz       America/Toronto
- date     2024-01-17
+ date     2024-01-24
  pandoc   3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
 
 ─ Packages ───────────────────────────────────────────────────────────────────
@@ -836,43 +846,44 @@ 
    Reproducibility
    
  callr           3.7.3      2022-11-02 [1] CRAN (R 4.3.0)
  class           7.3-22     2023-05-03 [4] CRAN (R 4.3.1)
  classInt        0.4-10     2023-09-05 [1] CRAN (R 4.3.1)
- cli             3.6.1      2023-03-23 [1] CRAN (R 4.3.0)
+ cli             3.6.2      2023-12-11 [1] CRAN (R 4.3.2)
  colorspace      2.1-0      2023-01-23 [1] CRAN (R 4.3.0)
  crayon          1.5.2      2022-09-29 [1] CRAN (R 4.3.0)
- curl            5.1.0      2023-10-02 [1] CRAN (R 4.3.1)
+ curl            5.2.0      2023-12-08 [1] CRAN (R 4.3.2)
  DBI           * 1.1.3      2022-06-18 [1] CRAN (R 4.3.0)
  dbplyr          2.4.0      2023-10-26 [1] CRAN (R 4.3.1)
  devtools        2.4.5      2022-10-11 [1] CRAN (R 4.3.0)
- digest          0.6.33     2023-07-07 [1] CRAN (R 4.3.1)
- dplyr         * 1.1.3      2023-09-03 [1] CRAN (R 4.3.1)
+ digest          0.6.34     2024-01-11 [1] CRAN (R 4.3.2)
+ dplyr         * 1.1.4      2023-11-17 [1] CRAN (R 4.3.2)
  e1071           1.7-13     2023-02-01 [1] CRAN (R 4.3.0)
  ebirdst       * 3.2022.2   2024-01-15 [1] Github (ebird/ebirdst@bd409c7)
  ellipsis        0.3.2      2021-04-29 [1] CRAN (R 4.3.0)
  evaluate        0.23       2023-11-01 [1] CRAN (R 4.3.1)
- fansi           1.0.5      2023-10-08 [1] CRAN (R 4.3.1)
+ fansi           1.0.6      2023-12-08 [1] CRAN (R 4.3.2)
  fastmap         1.1.1      2023-02-24 [1] CRAN (R 4.3.0)
  fs              1.6.3      2023-07-20 [1] CRAN (R 4.3.1)
  generics        0.1.3      2022-07-05 [1] CRAN (R 4.3.0)
  ggplot2       * 3.4.4      2023-10-12 [1] CRAN (R 4.3.1)
- glue            1.6.2      2022-02-24 [1] CRAN (R 4.3.0)
+ glue            1.7.0      2024-01-09 [1] CRAN (R 4.3.2)
  gt            * 0.10.0     2023-10-07 [1] CRAN (R 4.3.1)
  gtable          0.3.4      2023-08-21 [1] CRAN (R 4.3.1)
  hms             1.1.3      2023-03-21 [1] CRAN (R 4.3.0)
  htmltools       0.5.7      2023-11-03 [1] CRAN (R 4.3.1)
- htmlwidgets     1.6.2      2023-03-17 [1] CRAN (R 4.3.0)
+ htmlwidgets     1.6.4      2023-12-06 [1] CRAN (R 4.3.2)
  httpuv          1.6.12     2023-10-23 [1] CRAN (R 4.3.1)
  httr            1.4.7      2023-08-15 [1] CRAN (R 4.3.1)
- jsonlite        1.8.7      2023-06-29 [1] CRAN (R 4.3.1)
+ jsonlite        1.8.8      2023-12-04 [1] CRAN (R 4.3.2)
  KernSmooth      2.23-22    2023-07-10 [1] CRAN (R 4.3.1)
  knitr           1.45       2023-10-30 [1] CRAN (R 4.3.1)
  later           1.3.1      2023-05-02 [1] CRAN (R 4.3.1)
  lattice         0.22-5     2023-10-24 [4] CRAN (R 4.3.1)
- lifecycle       1.0.3      2022-10-07 [1] CRAN (R 4.3.0)
+ lifecycle       1.0.4      2023-11-07 [1] CRAN (R 4.3.2)
+ lubridate       1.9.3      2023-09-27 [1] CRAN (R 4.3.1)
  magrittr        2.0.3      2022-03-30 [1] CRAN (R 4.3.0)
  memoise         2.0.1      2021-11-26 [1] CRAN (R 4.3.0)
  mime            0.12       2021-09-28 [1] CRAN (R 4.3.0)
  miniUI          0.1.1.1    2018-05-18 [1] CRAN (R 4.3.0)
- motus         * 6.0.1.9000 2024-01-09 [1] local
+ motus         * 6.0.1.9000 2024-01-24 [1] local
  munsell         0.5.0      2018-06-12 [1] CRAN (R 4.3.0)
  naturecounts    0.4.0      2023-06-20 [1] local
  pillar          1.9.0      2023-03-22 [1] CRAN (R 4.3.0)
@@ -890,33 +901,34 @@ 
    Reproducibility
    
  Rcpp            1.0.11     2023-07-06 [1] CRAN (R 4.3.1)
  readr         * 2.1.4      2023-02-10 [1] CRAN (R 4.3.0)
  remotes         2.4.2.1    2023-07-18 [1] CRAN (R 4.3.1)
- rlang           1.1.2      2023-11-04 [1] CRAN (R 4.3.1)
+ rlang           1.1.3      2024-01-10 [1] CRAN (R 4.3.2)
  rmarkdown       2.25       2023-09-18 [1] CRAN (R 4.3.1)
  rnaturalearth * 0.3.4      2023-08-21 [1] CRAN (R 4.3.1)
  RSQLite         2.3.3      2023-11-04 [1] CRAN (R 4.3.1)
  rstudioapi      0.15.0     2023-07-07 [1] CRAN (R 4.3.1)
- sass            0.4.7      2023-07-15 [1] CRAN (R 4.3.1)
- scales          1.2.1      2022-08-20 [1] CRAN (R 4.3.0)
+ sass            0.4.8      2023-12-06 [1] CRAN (R 4.3.2)
+ scales          1.3.0      2023-11-28 [1] CRAN (R 4.3.2)
  sessioninfo     1.2.2      2021-12-06 [1] CRAN (R 4.3.0)
  sf            * 1.0-14     2023-07-11 [1] CRAN (R 4.3.1)
  shiny           1.7.5.1    2023-10-14 [1] CRAN (R 4.3.1)
  sp              2.1-1      2023-10-16 [1] CRAN (R 4.3.1)
- stringi         1.7.12     2023-01-11 [1] CRAN (R 4.3.0)
- stringr       * 1.5.0      2022-12-02 [1] CRAN (R 4.3.0)
+ stringi         1.8.3      2023-12-11 [1] CRAN (R 4.3.2)
+ stringr       * 1.5.1      2023-11-14 [1] CRAN (R 4.3.2)
  tibble        * 3.2.1      2023-03-20 [1] CRAN (R 4.3.0)
  tidyr         * 1.3.0      2023-01-24 [1] CRAN (R 4.3.0)
  tidyselect      1.2.0      2022-10-10 [1] CRAN (R 4.3.0)
+ timechange      0.2.0      2023-01-11 [1] CRAN (R 4.3.0)
  tzdb            0.4.0      2023-05-12 [1] CRAN (R 4.3.1)
  units         * 0.8-4      2023-09-13 [1] CRAN (R 4.3.1)
  urlchecker      1.0.1      2021-11-30 [1] CRAN (R 4.3.0)
  usethis         2.2.2      2023-07-06 [1] CRAN (R 4.3.1)
  utf8            1.2.4      2023-10-22 [1] CRAN (R 4.3.1)
- vctrs           0.6.4      2023-10-12 [1] CRAN (R 4.3.1)
- withr           2.5.2      2023-10-30 [1] CRAN (R 4.3.1)
+ vctrs           0.6.5      2023-12-01 [1] CRAN (R 4.3.2)
+ withr           3.0.0      2024-01-16 [1] CRAN (R 4.3.2)
  xfun            0.41       2023-11-01 [1] CRAN (R 4.3.1)
- xml2            1.3.5      2023-07-06 [1] CRAN (R 4.3.1)
+ xml2            1.3.6      2023-12-04 [1] CRAN (R 4.3.2)
  xtable          1.8-4      2019-04-21 [1] CRAN (R 4.3.0)
- yaml            2.3.7      2023-01-23 [1] CRAN (R 4.3.0)
+ yaml            2.3.8      2023-12-11 [1] CRAN (R 4.3.2)
 
  [1] /home/steffi/R/x86_64-pc-linux-gnu-library/4.3
  [2] /usr/local/lib/R/site-library
@@ -1323,12 +1335,12 @@ 
    Reproducibility
    -
    - @@ -1802,91 +1808,91 @@

    Create range plots

    -

    +

    -

    +

    -

    +

    -

    +

    -

    +

    -

    +

    -

    +

    -

    +

    -

    +

    -

    +

    -

    +

    -

    +

    -

    +

    @@ -1926,7 +1932,7 @@

    Reproducibility

    collate en_CA.UTF-8 ctype en_CA.UTF-8 tz America/Toronto - date 2024-01-17 + date 2024-01-24 pandoc 3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown) ─ Packages ─────────────────────────────────────────────────────────────────── @@ -1939,44 +1945,44 @@

    Reproducibility

    callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0) class 7.3-22 2023-05-03 [4] CRAN (R 4.3.1) classInt 0.4-10 2023-09-05 [1] CRAN (R 4.3.1) - cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0) + cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.2) codetools 0.2-19 2023-02-01 [4] CRAN (R 4.2.2) colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0) crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0) DBI * 1.1.3 2022-06-18 [1] CRAN (R 4.3.0) dbplyr 2.4.0 2023-10-26 [1] CRAN (R 4.3.1) devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0) - digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.1) - dplyr * 1.1.3 2023-09-03 [1] CRAN (R 4.3.1) + digest 0.6.34 2024-01-11 [1] CRAN (R 4.3.2) + dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.2) e1071 1.7-13 2023-02-01 [1] CRAN (R 4.3.0) ebirdst * 3.2022.2 2024-01-15 [1] Github (ebird/ebirdst@bd409c7) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0) evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.1) - fansi 1.0.5 2023-10-08 [1] CRAN (R 4.3.1) + fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.2) farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.1) generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) ggplot2 * 3.4.4 2023-10-12 [1] CRAN (R 4.3.1) - glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0) + glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.2) gt * 0.10.0 2023-10-07 [1] CRAN (R 4.3.1) gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.1) hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0) htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.1) - htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0) + htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.2) httpuv 1.6.12 2023-10-23 [1] CRAN (R 4.3.1) httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.1) - jsonlite 1.8.7 2023-06-29 [1] CRAN (R 4.3.1) + jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.2) KernSmooth 2.23-22 2023-07-10 [1] CRAN (R 4.3.1) knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1) later 1.3.1 2023-05-02 [1] CRAN (R 4.3.1) lattice 0.22-5 2023-10-24 [4] CRAN (R 4.3.1) - lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0) + lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.2) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0) mime 0.12 2021-09-28 [1] CRAN (R 4.3.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0) - motus * 6.0.1.9000 2024-01-09 [1] local + motus * 6.0.1.9000 2024-01-24 [1] local munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0) naturecounts 0.4.0 2023-06-20 [1] local pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) @@ -1994,21 +2000,21 @@

    Reproducibility

    Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.3.1) readr * 2.1.4 2023-02-10 [1] CRAN (R 4.3.0) remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.1) - rlang 1.1.2 2023-11-04 [1] CRAN (R 4.3.1) + rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.2) rmarkdown 2.25 2023-09-18 [1] CRAN (R 4.3.1) rnaturalearth * 0.3.4 2023-08-21 [1] CRAN (R 4.3.1) rnaturalearthhires 0.2.1 2023-05-31 [1] Github (ropensci/rnaturalearthhires@c3785a8) RSQLite 2.3.3 2023-11-04 [1] CRAN (R 4.3.1) rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.1) s2 1.1.4 2023-05-17 [1] CRAN (R 4.3.1) - sass 0.4.7 2023-07-15 [1] CRAN (R 4.3.1) - scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0) + sass 0.4.8 2023-12-06 [1] CRAN (R 4.3.2) + scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.2) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0) sf * 1.0-14 2023-07-11 [1] CRAN (R 4.3.1) shiny 1.7.5.1 2023-10-14 [1] CRAN (R 4.3.1) sp 2.1-1 2023-10-16 [1] CRAN (R 4.3.1) - stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0) - stringr * 1.5.0 2022-12-02 [1] CRAN (R 4.3.0) + stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.2) + stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.3.2) tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) tidyr * 1.3.0 2023-01-24 [1] CRAN (R 4.3.0) tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0) @@ -2017,15 +2023,15 @@

    Reproducibility

    urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0) usethis 2.2.2 2023-07-06 [1] CRAN (R 4.3.1) utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1) - vctrs 0.6.4 2023-10-12 [1] CRAN (R 4.3.1) + vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.2) viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.1) vroom 1.6.4 2023-10-02 [1] CRAN (R 4.3.1) - withr 2.5.2 2023-10-30 [1] CRAN (R 4.3.1) + withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.2) wk 0.9.0 2023-10-22 [1] CRAN (R 4.3.1) xfun 0.41 2023-11-01 [1] CRAN (R 4.3.1) - xml2 1.3.5 2023-07-06 [1] CRAN (R 4.3.1) + xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.2) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0) - yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0) + yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.2) [1] /home/steffi/R/x86_64-pc-linux-gnu-library/4.3 [2] /usr/local/lib/R/site-library @@ -2432,18 +2438,18 @@

    Reproducibility

    - - + @@ -117,7 +117,7 @@ - +
    -
    +

    Basic Filtering

    @@ -249,7 +255,7 @@

    Basic Filtering

    Published
    -

    January 17, 2024

    +

    January 24, 2024

    @@ -900,7 +906,7 @@

    Reproducibility