From f6ec2951795461e451d9502b7b77b129d0fea253 Mon Sep 17 00:00:00 2001 From: Paula Blomquist Date: Wed, 18 Sep 2024 13:54:25 +0100 Subject: [PATCH 1/6] Adding data for salmonella outbreak in Stegen case study --- R/salmonella_outbreak_de_1998_doc.R | 26 +++ _pkgdown.yml | 4 + data-raw/stegentira_data.R | 10 + data/stegentira_data.rda | Bin 0 -> 2301 bytes inst/extdata/stegentira_data.csv | 292 ++++++++++++++++++++++++++++ inst/extdata/tableoftables.xlsx | Bin 10363 -> 10876 bytes man/stegentira_data.Rd | 32 +++ 7 files changed, 364 insertions(+) create mode 100644 R/salmonella_outbreak_de_1998_doc.R create mode 100644 data-raw/stegentira_data.R create mode 100644 data/stegentira_data.rda create mode 100644 inst/extdata/stegentira_data.csv create mode 100644 man/stegentira_data.Rd diff --git a/R/salmonella_outbreak_de_1998_doc.R b/R/salmonella_outbreak_de_1998_doc.R new file mode 100644 index 0000000..de95e2f --- /dev/null +++ b/R/salmonella_outbreak_de_1998_doc.R @@ -0,0 +1,26 @@ +#' @title Linelist for fictionalized salmonella outbreak in Stegen, Germany +#' +#' @description +#' Linelist data for fictionalized salmonella outbreak that occured in a highschool +#' in Stegen, Germany (1998) +#' +#' @details +#' This is a fake case linelist with individual level data +#' on clinical and epidemiological information, with a focus on foods +#' eaten at a cafeteria (exposures) + +#' @source +#' This case study was first designed by Alain Moren and Gilles Desve for EPIET. It is based on an investigation conducted by Anja Hauri, RKI, Berlin, 1998. +#' Data is fictional and was inspired by Nygren et al. Tick-borne encephalitis: acute clinical manifestations and severity in 581 cases from Germany, 2018-2020. Journal of Infection. 2023 Apr 1;86(4):369-75 +#' +#' This is version 1.0 (for the appliedepidata package. Earlier data versions used by EPIET are not considered) +#' +#' This dataset is English. +#' +#' This dataset is licensed under [GPL3](https://www.gnu.org/licenses/gpl-3.0.html) +#' +#' @format +#' Linelist with 291 rows and 20 columns +#' +#' @docType data +"stegentira_data" \ No newline at end of file diff --git a/_pkgdown.yml b/_pkgdown.yml index 1e1ca97..bf99a71 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -36,3 +36,7 @@ reference: contents: - mpox_linelist - mpox_aggregate_table + +- subtitle: Fictional linelist data from Salmonella outbreak in Stegen, Germany (1998) - English + contents: + - stegentira_data \ No newline at end of file diff --git a/data-raw/stegentira_data.R b/data-raw/stegentira_data.R new file mode 100644 index 0000000..8d2393d --- /dev/null +++ b/data-raw/stegentira_data.R @@ -0,0 +1,10 @@ +## code to prepare `stegentira_data` dataset goes here + +# Define the path to the Excel file in inst/extdata +file_path <- system.file("extdata", "stegentira_data.csv", package = "appliedepidata") + +# Read in the Excel file using rio +stegentira_data <- rio::import(file_path) + +# Save the data as an internal .rda file in the data/ directory +usethis::use_data(stegentira_data, overwrite = TRUE) diff --git a/data/stegentira_data.rda b/data/stegentira_data.rda new file mode 100644 index 0000000000000000000000000000000000000000..723d181308b5389542072fa9342273a0e40b8b5f GIT binary patch literal 2301 zcmaiuc~sJg7RP@ADq5O?OM)4DxRD}7niU8k8kC9^m6;+aq^4QgZl;JU3Z^Mq=1Rt- z&urK6xzgY^Zlz{sE-lk$+O*G9uiiWTH|M<1x#uq5d(Zb=ubpCdSNaYDZ%0K-LLp$S z`1XI9GTHzva#(UY2LM29gSKRI5J=d)jzdtn@mATX(Q5fR?-~QFcMSk$C4sq!?^$e+ z1c2#fU1dVCq>^SJlbx!Bql9e;JGHpmWD5*};-bsRx%Or600e~s*m2R15x{p4fI+dz zkLD-eZG4hIApqg0@J|)js^$ZS|v?NDJHf?388lDhmT=sTf9);>rV1}>mxP{c(o!wMa1FClTf zusTTlqsDL#atW3lCaqa<+1GnnD+7}@|EF|mFbw!(Fkyo-M3=HJ#D|8NXMQ{c_x`GUG|`S^d_yq zEc0$}aBWY&xj7J%95wlIQc3ocdiI$AOMGZJ8?P|}5*s^W!(uS^CjlOW{0;GjoJX`=UufkydPXGa zEBKng=VKakGYd}Ut|2ufQ0~~pqXzXiI5CwE+I-(;`st?{YV}2=t?`3`l`u~(e60KM 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+177,1,1998-06-29,1,19,1,1,0,1,,0,0,0,0,1,0,0,0,0,0 +111,1,1998-06-29,1,19,1,1,0,1,2,1,0,0,0,0,1,1,0,0,0 +242,1,1998-06-29,0,19,1,2,1,1,,0,1,1,1,1,9,9,0,1,0 +143,1,1998-06-29,1,48,0,0,1,1,1,0,0,1,0,1,0,0,1,0,1 +278,1,1998-06-29,0,19,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0 +62,1,1998-06-29,0,52,1,1,,1,1,0,0,1,0,0,0,0,1,0,0 +176,1,1998-06-29,1,19,1,1,0,0,0,0,1,1,0,0,0,0,0,0,0 +134,1,1998-06-29,0,,1,1,0,1,1,1,1,0,1,0,0,0,0,0,0 +256,0,,1,21,0,0,0,0,0,0,0,0,0,1,1,0,1,0,1 +55,0,,0,18,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1 +235,0,1998-07-05,0,20,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0 +58,0,,1,19,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1 +194,1,1998-06-27,0,39,0,0,1,1,2,0,0,1,1,0,0,0,0,0,0 +282,0,,0,17,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0 +137,0,,0,22,0,0,1,1,2,1,1,1,0,0,1,0,0,0,0 +118,0,,1,13,0,0,0,0,0,,1,0,0,0,0,0,1,1,1 +220,0,,0,20,1,1,0,0,0,1,0,0,0,0,0,0,0,0,0 +24,0,1998-07-02,1,18,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +187,0,,1,17,1,1,1,0,1,1,0,0,0,1,1,0,1,1,1 +190,0,,1,17,0,0,0,0,0,1,0,0,0,0,0,1,1,0,0 +189,0,,1,62,0,0,0,0,0,1,0,0,0,1,0,1,0,0,0 +195,0,1998-06-28,0,17,1,1,0,0,0,1,0,0,1,1,0,0,1,0,0 +231,0,,1,21,0,0,1,0,,,0,0,0,0,1,1,0,1,1 +239,0,,0,54,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +289,0,,0,20,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0 +184,0,,0,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +126,0,,0,17,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +209,0,,0,18,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +290,0,,1,22,,,,,,1,0,0,0,0,1,1,0,0,1 +67,0,1998-07-01,0,18,1,1,0,0,0,0,1,1,0,1,1,0,0,0,1 +170,0,,0,18,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +230,0,,1,,0,0,0,0,0,1,0,0,0,1,0,0,1,0,0 +151,1,1998-06-28,1,19,1,2,1,1,2,1,0,0,0,1,1,0,0,0,0 +283,0,,1,17,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +211,0,,1,20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +69,0,,0,57,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1 +35,0,,1,20,0,0,0,0,0,1,0,0,0,0,0,0,1,0,1 +233,0,,1,20,0,0,0,0,0,1,0,0,0,1,1,0,0,0,0 +208,0,1998-06-30,0,48,1,2,1,1,3,0,0,1,1,0,1,1,1,0,0 +155,0,,1,19,0,0,0,0,0,0,1,0,0,1,0,0,0,0,1 +198,0,,0,44,0,0,0,0,0,0,0,0,1,0,0,0,0,1,1 +40,0,,1,19,0,0,0,0,0,1,1,0,1,0,1,0,0,0,1 +119,0,,0,46,0,0,0,0,0,,0,0,0,0,1,1,1,0,1 +139,0,1998-06-28,0,51,1,1,,1,1,1,0,1,1,0,1,0,0,0,0 +180,0,,1,17,0,0,1,1,1,1,0,0,0,1,0,0,0,0,1 +188,0,,1,16,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0 +157,0,,1,22,0,0,1,0,1,1,0,0,0,1,1,1,0,0,0 +80,0,,1,18,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0 +203,0,,0,19,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0 +280,0,,0,20,0,0,1,1,,1,1,1,1,0,0,0,1,0,1 +37,0,,1,47,0,0,0,0,0,,0,0,1,0,1,0,0,0,0 +193,0,,0,15,0,0,,,,0,1,1,0,1,1,1,0,0,0 +53,0,,1,19,0,0,0,0,0,,0,0,0,0,0,0,0,0,0 +22,0,,0,20,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +85,0,,0,13,0,0,1,1,3,0,0,0,0,1,0,0,0,0,0 +232,0,,1,20,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1 +258,0,,0,21,0,0,0,0,0,,0,0,0,0,0,0,0,0,0 +265,0,,1,20,0,0,0,0,0,1,0,0,0,1,1,0,0,0,1 +54,0,,1,18,0,0,0,0,0,,0,0,0,0,0,0,0,0,0 +237,0,1998-07-09,1,20,0,0,0,0,0,1,0,0,1,1,1,1,0,0,1 +266,0,,1,45,0,0,0,0,0,1,0,0,1,1,0,0,1,0,1 +236,0,,1,20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +88,0,1998-06-29,1,44,1,1,0,1,2,0,1,1,0,0,1,1,0,0,0 +10,0,,1,18,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +11,0,1998-07-02,1,22,0,0,1,1,2,,1,0,0,0,1,1,0,0,0 +174,0,,1,58,0,0,0,0,0,0,0,0,1,0,0,1,1,0,0 +185,0,,1,17,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +161,0,,0,14,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1 +226,0,,0,,0,0,0,0,0,,0,0,0,0,0,0,0,0,0 +273,0,,0,20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +227,0,1998-07-06,0,20,1,1,0,1,2,1,0,0,1,0,0,0,0,0,0 +260,0,,1,,0,0,0,0,0,,0,0,1,1,1,1,0,1,0 +223,0,,1,19,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +107,0,,0,19,1,1,0,0,0,1,0,0,1,0,1,0,1,0,0 +183,0,,1,16,0,0,0,0,0,1,0,0,0,0,1,0,1,1,1 +250,0,,1,26,0,0,0,0,0,0,0,0,0,0,1,0,1,0,1 +253,0,,1,20,0,0,0,0,0,1,0,0,1,1,1,0,1,0,0 +44,0,,0,19,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +182,0,,0,17,0,0,0,0,0,,0,0,0,0,0,0,0,0,0 +228,0,,0,19,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0 +285,0,,1,57,0,0,0,0,0,0,1,1,1,1,1,1,0,1,1 +83,0,,0,18,0,0,0,1,2,0,1,0,0,0,1,0,1,0,0 +248,0,1998-06-27,0,19,0,0,0,0,0,0,0,0,1,0,1,1,0,0,1 +136,0,,0,17,0,0,0,1,1,0,0,0,0,0,0,0,0,0,1 +172,0,,1,18,1,1,0,1,1,0,0,0,0,0,0,0,0,0,0 +46,0,,0,18,1,1,0,0,0,1,0,0,0,0,0,0,0,0,0 +114,0,,0,23,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0 +166,0,,1,19,0,0,0,0,0,0,1,1,1,0,0,1,1,0,0 +164,0,1998-06-27,0,45,0,0,,1,2,0,0,1,1,1,0,1,0,0,0 +101,0,,1,15,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1 +21,0,,0,20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +158,0,,0,19,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +108,0,,0,25,0,0,1,1,2,0,1,0,1,0,1,0,1,0,0 +34,0,1998-06-28,0,20,0,0,0,0,0,,0,0,0,1,1,0,0,0,0 +276,0,,1,20,0,0,0,0,0,1,0,0,1,0,1,0,0,0,0 +222,0,,1,20,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +130,0,,0,48,0,0,0,0,0,0,0,0,0,0,1,1,0,1,0 +275,0,,0,23,,,0,0,0,0,1,1,1,0,0,0,0,0,0 +72,0,,1,17,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +218,0,1998-06-30,0,17,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +267,0,,0,46,0,0,0,0,0,0,0,0,1,0,1,0,1,0,0 +76,0,,1,19,0,0,0,0,0,0,0,0,0,0,1,1,0,1,0 +241,0,,1,21,0,0,0,0,0,,0,0,0,0,1,0,0,0,1 +171,0,,0,18,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0 +142,0,,1,24,0,0,0,0,0,1,0,0,0,0,1,1,0,1,1 +89,0,1998-06-27,1,18,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +105,0,,0,52,1,1,1,1,,0,1,0,1,0,1,0,1,0,1 +39,0,,1,50,0,0,0,1,2,1,1,1,0,0,0,0,0,0,1 +167,0,1998-06-28,1,23,1,1,1,1,1,1,0,1,1,1,1,1,0,0,1 +140,0,,1,55,1,1,0,0,0,1,0,1,0,0,1,1,0,0,1 +124,0,,0,19,0,0,1,1,2,0,0,1,0,0,1,1,1,1,0 +131,0,,0,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +17,0,,0,18,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0 +73,0,,1,19,0,0,1,0,2,1,0,0,0,0,1,0,1,0,0 +97,0,,1,50,1,3,,1,2,0,1,1,0,1,0,0,1,0,1 +5,0,,0,49,0,0,0,0,0,,1,0,0,0,0,0,1,0,0 +123,0,,1,65,0,0,0,0,0,1,0,0,1,1,0,0,1,0,1 +9,0,,1,19,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1 +99,0,,1,43,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1 +84,0,,0,43,0,0,0,0,0,1,0,0,0,1,1,0,0,0,0 +229,0,1998-06-26,0,20,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0 +116,0,,1,59,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1 +238,1,1998-06-28,0,21,1,1,,1,1,0,1,0,0,0,0,0,0,0,0 +217,0,1998-06-27,1,19,0,0,0,0,0,1,0,0,0,0,1,0,1,0,1 +122,0,,0,20,0,0,0,0,0,0,0,0,1,1,1,0,1,0,1 +240,0,,1,56,1,1,1,1,2,1,1,1,0,1,0,0,0,0,1 +95,0,,0,14,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0 +110,0,,0,55,0,0,0,0,0,0,1,1,1,1,0,0,0,1,0 +41,0,1998-06-27,0,47,0,0,0,1,1,0,1,0,0,0,0,1,0,0,0 +206,0,,0,19,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +23,0,,0,42,1,1,0,1,1,0,1,0,0,1,0,0,1,0,1 +257,0,,0,22,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1 +163,0,1998-06-27,1,49,0,0,0,1,1,0,0,0,0,0,1,1,0,0,1 +64,0,1998-07-01,0,45,1,1,,1,2,0,1,1,0,1,9,9,1,0,9 +100,0,,0,42,0,0,0,0,0,0,0,0,1,0,1,1,0,0,1 +120,0,,0,60,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0 +160,0,,1,16,0,0,1,1,1,0,0,1,0,1,0,0,0,0,1 +224,0,,1,20,1,3,0,0,0,1,0,0,0,0,0,0,1,0,0 +94,0,,0,18,1,2,,1,1,0,0,1,0,0,0,0,0,0,0 +60,0,,1,18,0,0,0,0,0,1,0,0,0,1,0,0,1,1,1 +263,0,,1,21,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +191,0,,1,19,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +147,0,,0,19,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +179,0,,0,17,0,0,1,1,2,0,0,0,0,1,0,0,0,0,1 +93,0,,0,17,0,0,0,0,0,0,0,0,1,1,0,1,0,0,0 +57,0,,0,18,1,1,1,1,3,0,1,1,1,0,0,0,0,0,0 +112,0,,1,45,0,0,0,0,0,0,0,0,1,0,1,1,0,0,0 +268,0,,0,58,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1 +243,0,,1,20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +219,0,,1,24,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +247,0,,1,57,0,0,0,0,0,1,1,1,1,1,1,0,1,1,1 +38,0,,1,19,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +33,0,,1,20,0,0,0,0,0,1,0,1,0,0,1,0,1,0,1 +68,1,,1,56,1,3,1,1,2,0,1,1,1,0,0,0,1,0,0 +4,0,,1,46,0,0,0,0,0,0,0,0,0,1,1,1,0,0,1 +150,1,1998-06-28,1,18,1,2,1,1,1,0,1,1,1,1,1,1,0,0,0 +79,0,1998-07-02,0,17,0,0,1,,1,0,0,0,1,1,0,0,0,0,0 +178,0,,1,37,0,0,0,0,0,0,0,0,1,0,1,0,0,0,1 +127,0,,1,44,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1 +153,0,,1,19,0,0,0,0,0,1,0,0,0,1,0,1,1,1,0 +261,0,,1,21,0,0,0,0,0,1,0,0,1,1,1,0,0,0,0 +92,0,1998-06-27,1,19,0,0,0,0,0,1,0,0,0,1,0,0,0,0,1 +90,0,,0,18,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1 +264,0,,1,28,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +277,0,,1,53,0,0,0,0,0,1,0,0,0,0,0,0,1,1,0 +181,0,,1,17,1,2,0,1,2,1,1,0,1,1,0,0,1,0,1 +197,0,,1,19,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +225,0,,0,19,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0 +18,0,,1,19,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1 +1,0,,0,17,1,2,1,1,1,0,1,0,0,0,0,0,0,0,0 +252,0,,1,20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +47,0,,0,18,0,0,,1,3,0,1,0,0,0,0,0,1,0,0 +245,0,,1,24,0,0,0,0,0,1,0,0,0,1,1,1,1,0,1 +78,0,1998-06-29,0,15,1,1,0,1,2,0,1,0,0,1,1,1,0,0,1 +162,0,1998-07-01,0,12,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1 +81,0,1998-06-27,1,16,0,0,0,0,0,0,0,0,0,0,1,0,1,1,1 +3,0,,0,48,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0 +82,0,1998-06-28,1,18,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +32,0,,1,21,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0 +71,0,,1,59,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0 +30,0,,1,57,,,1,1,2,1,1,1,0,1,1,1,0,0,1 +28,0,1998-07-04,0,15,0,0,0,0,0,0,0,0,0,1,0,1,1,0,0 +135,0,,1,,1,1,0,1,1,1,1,0,1,0,0,0,0,0,1 +246,0,,1,20,0,0,0,0,0,1,0,0,1,1,1,0,0,1,1 +149,0,,0,18,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +7,0,,0,18,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +19,0,,1,18,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0 +249,0,,0,,0,0,0,0,0,0,0,0,1,0,1,1,0,0,0 +128,0,,0,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +6,0,,1,20,0,0,0,0,0,1,0,0,0,1,0,0,0,0,1 +192,0,,1,16,0,0,0,0,0,1,0,0,1,0,0,0,0,0,1 +270,0,,1,51,0,0,0,0,0,0,0,0,1,1,1,0,1,0,0 +262,0,,1,18,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1 +259,0,,0,21,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0 +87,0,,1,22,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +8,0,,1,18,0,0,0,0,0,1,0,0,0,0,1,0,1,0,1 +129,0,,1,18,0,0,,1,1,0,0,0,1,0,1,0,0,1,1 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a/vignettes/adding-data.Rmd +++ b/vignettes/adding-data.Rmd @@ -3,8 +3,11 @@ title: "Adding data" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Adding data} - %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} + %\VignetteEngine{knitr::rmarkdown} +editor_options: + markdown: + wrap: 72 --- ```{r, include = FALSE} @@ -19,40 +22,22 @@ knitr::opts_chunk$set( library(appliedepidata) ``` - - # Guide to contributing new datasets -## Package folder structure +## PACKAGE FOLDER STRUCTURE -To below is a simplified explanation of the -[R packages data chapter](https://r-pkgs.org/data.html). For a fuller understanding, -read that chapter. +To below is a simplified explanation of the [R packages data +chapter](https://r-pkgs.org/data.html). For a fuller understanding, read +that chapter. +### Overview -- The following package folders are important: - - **data**: R datasets go in `data` folder - - **inst/extdata**: Non-R datasets go in `inst>extdata` folder. - - **internal data**: When you build a package, the `Rda` datasets - (from `data` folder) can become "internal" (more efficient for file storage). - These are accessed by calling `package::dataset` (e.g. - `appliedepidata::AJS_AmTiman`. They can also be imported directly from github - using link to the file in data folder e.g. 'rio()', or the - `appliedepidata::get_data` or `appliedepidata::save_data` functions. - - **data-raw**: Contains R scripts used for creating the - exported or internal data (e.g. if you have edited a dataset or used {usethis} - to internalise the dataset) - - **sysdata**: Not relevant for current package setup. In some setups you are - supposed to put *tableoftables* in sysdata (i.e. just for package usage). - However for our current setup leave in *extdata*. - - -```bash +``` bash . ├── appliedepidata.Rproj ├── _pkgdown.yml ├── data -│ └── newdata.rda +│ └── internaliseddata.rda ├── data-raw │ └── newdata.R ├── inst @@ -65,145 +50,263 @@ read that chapter. └── newdata.Rd ``` +### Folders you will edit -## Adding a file -This describes the process for adding a file to the repo. Note that the processes -for adding a non-R file (any file that is not `.rda`) and an R file (any file -already in`.rda` format) are slightly different. -If you are adding a dataset from an existing R package, you can skip to step 3 -below. - -1. Name your file appropriately - a. You can name it whatever you want, but stick to basic naming conventions. - b. Ensure that there is not already file in *tableoftables.xlsx* named the same. - c. Avoid generic names like: `linelist_cleaned.xlsx` or `survey_data.xlsx`. - d. Use consistent and descriptive names without spaces (e.g., `AJS_AmTiman`, - `sitrep_mortality_survey`). -2. Place your file in the correct folder - a. A *non-R* file (e.g. `xlsx`, `shp`, `zip`) goes in `inst/extdata` folder - i. If adding a shapefile then zip it - b. An *R* file (e.g. `rda`, `rds`) goes in `data` folder -3. Reproducibly edit dataset and internalise (see `data-raw/AJS_AmTiman.R` for example) - a. In your console run `usethis::use_data_raw()` - b. This creates an R script in the `data-raw` folder. - c. Read in the file by defining the path with `system.file`. - i. If you are editing a file already in the package (e.g. shortening the - Ebola linelist for a course), make sure you read in the original dataset here. - Document this properly with {roxygen} and in the metadata as described - below. - d. Make any edits necessary to your dataset in a reproducible way. - e. Save and internalise the dataset with `usethis::usedata()`. -4. Add documentation for each dataset added - a. This is done in an R script in the `R` folder. - b. Name the script something that will allow reviewers to find it (e.g. `AJS_chad`) and suffix with `_doc` so that it can be differentiated from functions. - c. Place all the documentation for datasets in that group within the same script. - d. Ensure to clearly document the source and license for the dataset. - e. Add in an explanation for each variable, if you have a data dictionary you - use [appliedepidata::create_desc()](https://appliedepi.github.io/appliedepidata/reference/create_desc.html) to help with this. - i. You could also create a data dictionary for use with this function, see - the [data dictionary walk-through]((https://appliedepi.github.io/appliedepidata/articles/data-dictionaries.html).) -5. Add the datasets to `_pkgdown.yml` - a. Group relevant datasets under the same subtitle (suffix with the language) - b. The names here correspond to the name in quotations at the end of your - description file from point 4 above, as well as the name of the file (without - file extension). -6. Add the dataset to the `tablesoftables.xlsx` as described below. +- **inst/extdata**: Newly added datasets go in here in their original + filetype, e.g. .xlsx, .csv, but also .rds files. These files will be + downloaded with the `save_data()` function.\ +- **data-raw**: Contains R scripts used for processing and + internalizing datasets (making them more efficient for storage), + i.e. for turning newly added datasets in `inst/extdata` to .rda + files +- **R**: Contains R scripts in Roxygen2 format which define the + functions and datasets. When run this creates the R documentation + files (.Rd files) which are saved in the **man** folder. Multiple + datasets can be defined in one script, which is sensible as some are + grouped together (e.g. part of the same outbreak) +- **vignettes**: Contains detailed instructions on how to use + particular functions. They complement the function-level + documentation in the **man** folder by giving broader explanation. - +### Folders you will not edit + +These contain files outputted by running the code in the folders above. + +- **data**: Contains internalised and processed R datasets (.rda + files). +- **man**: Contains the R documentation files for package functions + and datasets (created when running the code in the **R** folder). + Each .Rd file has information about a specific function or dataset. +- **tests**: Contains test files for developer use only. +- **internal data**: When you build a package, the `Rda` datasets + (from `data` folder) can become "internal" (more efficient for file + storage). These are accessed by calling `package::dataset` (e.g. + `appliedepidata::AJS_AmTiman`. They can also be imported directly + from github using link to the file in data folder e.g. + 'rio()', or the `appliedepidata::get_data` or + `appliedepidata::save_data` functions. +- **sysdata**: Not relevant for current package setup. In some setups + you are supposed to put *tableoftables* in sysdata (i.e. just for + package usage). However for our current setup leave in *extdata*. + +## ADDING DATA + +This describes the process for adding a file to the repo. Note that the +processes for adding a non-R file (any file that is not `.rda`) and an R +file (any file already in`.rda` format) are slightly different. + +If you are adding a dataset from an existing R package, you can skip to +step 3 below. + +1. **Name your file appropriately** + + A. You can name it whatever you want, but stick to basic naming + conventions. -# Defining dataset metadata (adding to `tablesoftables.xlsx`) + B. Ensure that there is not already file in *tableoftables.xlsx* + named the same. -Below is a table explaining how to fill in each variable in the dataset -metadata Excel sheet (`tablesoftables.xlsx`). This guide helps ensure -consistency and completeness when adding new datasets to your collection. + C. Avoid generic names like: `linelist_cleaned.xlsx` or + `survey_data.xlsx`. -- **name**: The filename of the dataset as it appears in the `inst/extdata` - directory, **without** the file extension. This should be unique within - the dataset group, and ideally also within the *tableoftables* - (i.e. avoid generic names like: `linelist_cleaned.xlsx` or `survey_data.xlsx`). - Use consistent and descriptive names without spaces (e.g., `AJS_AmTiman`, - `mortality_survey`). + D. Use consistent and descriptive names without spaces (e.g., + `AJS_AmTiman`, `sitrep_mortality_survey`). -- **type**: The category or type of the dataset (e.g., `linelist`, - `population`, `shape`, `survey`, `dictionary`). + E. Name files from the same group (e.g. from the same outbreak or + for the same case study) with the same prefix. E.g: + `examplename_data` and `examplename_population` for a case linelist + and corresponding denominator table respectively. -- **extension**: The file extension (e.g., `xlsx`, `zip`). +2. **Place your file in the correct folder** -- **type_version**: Used to identify the *original* dataset and its associated - child data. Increment when format or variables change. If there are multiple - linelists in one group, this would increment with the type. + A. A *non-rda* file (e.g. `xlsx`, `shp`, `zip`, `rds`) goes in + `inst/extdata` folder. This is what will be downloaded when running + the save_data() function. i. If adding a shapefile then zip it -- **data_version**: Used to identify the *original* dataset and its associated - child data. Increment when format or variables change. Ensure you document - changes in the appropriate 'data-raw' file. + B. An *rda* file goes in `data` folder -- **language**: Language code using [ISO 639-1 codes](https://en.wikipedia.org/wiki/List_of_ISO_639-1_codes) (e.g., `en`, `fr`). +3. **Build the package with the added data** -- **country**: Country code using [ISO 3166-1 alpha-3 codes](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) (e.g., `tcd`). + A. Press Ctrl + Shift + B to build the package with the newly added + data. This will mean the data is recognized for the next step. -- **scale**: Geographic scale (e.g., `subnational`, `national`, or `international`). + -- **subject**: Main subject of the dataset (e.g., `acute jaundice syndrome`). +4. **Reproducibly edit dataset and internalize** (see + `data-raw/AJS_AmTiman.R` for example) -- **context**: Context of the data (e.g., `outbreak`, `survey`). + A. In your console run + `usethis::use_data_raw("")`. -- **fictional**: Is the dataset fictional (`yes`) or real (`no`)? + B. This creates an R script in the `data-raw` folder. It will + already contain a comment at the top saying "code to prepare + data goes here" and a `usethis::use_data()` function + to internalise the dataset (i.e. to produce the rda file) + + C. Edit the R script to correctly read in the file using + `system.file()`, as below. Necessary edits to the dataset should + also go here. Then run this script to internalise the data, and + close. + +```{r, eval=FALSE} + +## code to prepare `examplename_linelist` dataset goes here + +# Define the path to the Excel file in inst/extdata +file_path <- system.file("extdata", "", package = "appliedepidata") + +# Read in the Excel file using rio +examplename_linelist <- rio::import(file_path) + +# Other code for editing the file can go here + + + + +# Save the data as an internal .rda file in the data/ directory +usethis::use_data(examplename_linelist, overwrite = TRUE) + + +``` -- **year**: Year the data was collected (e.g., `2016`). This is the *earliest* - year in the dataset. +5. **Add the dataset to the `tablesoftables.xlsx` as described below.** -- **description**: Brief description of the dataset. Ideally, copy from - roxygen documentation. +6. **Add documentation for each dataset added** -- **usage**: Intended usage (e.g., `{sitrep} walkthroughs`, `training`). + A. Create a new R script in the `R` folder, with one file for all + datasets in a group. The file name should be the group name + generated from tableoftables (column P), with suffix '\_doc'. Note + the easiest is to copy and edit an existing R script in the folder. -- **license**: License for dataset (e.g., `gpl3`, `mit`). + B. Ensure to clearly document the source and license for the + dataset. -- **group_identifier**: *DO NOT EDIT* - Created by concatinating function in excel. - High-level identifier combining `subject`, `context`, `country`, and `year` - (e.g.,`acute_jaundice_syndrome_outbreak_tcd_2016`). + C. Ensure to put the correct name of the dataset at the bottom of + each dataset description (under @docType). E.g. + `examplename_linelist`. -- **unique_identifier**: *DO NOT EDIT* - Combines `group_identifier`, `type`, - `type_version`, `data_version`, `context`, and `year` to create a unique - identifier (e.g. `acute_jaundice_syndrome_outbreak_tcd_2016_linelist_1`). + D. Run devtools::document() to create the actual R documentation. + This will be an .Rd file in the `man` folder, with file name + corresponding with the dataset name (e.g. `examplename_linelist.Rd`) + -For example, when adding an Ebola dataset, you would enter the information as -shown below. The original dataset (whether it's from {outbreaks} or another source) -would be considered `type_version` 1. If it’s the only linelist in its group, it -remains `type_version` 1. If a completely different linelist is added (not just an -edited version), increment the `type_version` accordingly. +6. **Add the datasets to `_pkgdown.yml`** -For any changes to the data (such as cleaning or changing nums of rows or columns), -increment the `data_version` (e.g., `data_version` 2), but the `type_version` -remains the same to indicate that it’s a derivative (or "child") of the original. -Each child dataset gets its own entry. + A. Subtitle: Describe the group of linelists. State the year in + brackets and language at the end -If a dataset is translated into a different language, create a new entry for -the translated version while keeping the `data_version` and `type_version` the same, -but editing the `language` column accordingly. -This ensures you can trace back the parent-child relationship between datasets. + B. Contents: List the datasets. Again, the names here correspond to + the name of the dataset without extension, e.g + "examplename_linelist". + C. Make sure to have correct indentation and use of dashes. See + prior examples in the file. -| **Variable** | **Example Entry** | -|-----------------------|------------------------------------| -| **name** | `ebola_linelist_cleaned` | -| **type** | `linelist` | -| **extension** | `xlsx` | -| **type_version** | `1` | -| **data_version** | `1` | -| **language** | `en` | -| **country** | `lbr` | -| **scale** | `national` | -| **subject** | `ebola` | -| **context** | `outbreak` | -| **fictional** | `yes` | -| **year** | `2014` | -| **description** | Linelist data from the Ebola virus | -| | disease outbreak in Liberia in | -| | 2014. | -| **usage** | `introexercises`, etc. | -| **license** | `gpl3` | -| **group_identifier** | `ebola_outbreak_lbr_2014` | -| **unique_identifier** | `ebola_outbreak_lbr_2014_linelist_1_1_outbreak_2014`| +## ADDING DATASET METADATA (adding to `tablesoftables.xlsx`) +Below is a table explaining how to fill in each variable in the dataset +metadata Excel sheet (`tablesoftables.xlsx`). This guide helps ensure +consistency and completeness when adding new datasets to your +collection. + +- **name**: The filename of the dataset as it appears in the + `inst/extdata` directory, **without** the file extension. This + should be unique within the dataset group, and ideally also within + the *tableoftables* (i.e. avoid generic names like: + `linelist_cleaned.xlsx` or `survey_data.xlsx`). Use consistent and + descriptive names without spaces (e.g., `AJS_AmTiman`, + `mortality_survey`). + +- **type**: The category or type of the dataset (e.g., `linelist`, + `population`, `shape`, `survey`, `dictionary`). + +- **extension**: The file extension (e.g., `xlsx`, `zip`). + +- **type_version**: Used to identify the *original* dataset and its + associated child data. Increment when format or variables change. If + there are multiple linelists in one group, this would increment with + the type. + +- **data_version**: Used to identify the *original* dataset and its + associated child data. Increment when format or variables change. + Ensure you document changes in the appropriate 'data-raw' file. + +- **language**: Language code using [ISO 639-1 + codes](https://en.wikipedia.org/wiki/List_of_ISO_639-1_codes) (e.g., + `en`, `fr`). + +- **country**: Country code using [ISO 3166-1 alpha-3 + codes](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) (e.g., + `tcd`). + +- **scale**: Geographic scale (e.g., `subnational`, `national`, or + `international`). + +- **subject**: Main subject of the dataset (e.g., + `acute jaundice syndrome`). + +- **context**: Context of the data (e.g., `outbreak`, `survey`). + +- **fictional**: Is the dataset fictional (`yes`) or real (`no`)? + +- **year**: Year the data was collected (e.g., `2016`). This is the + *earliest* year in the dataset (even if fictional). + +- **description**: Brief description of the dataset. Ideally, copy + from roxygen documentation. + +- **usage**: Intended usage (e.g., `{sitrep} walkthroughs`, + `training`). + +- **license**: License for dataset (e.g., `gpl3`, `mit`). + +- **group_identifier**: *DO NOT EDIT* - Created by concatinating + function in excel. High-level identifier combining `subject`, + `context`, `country`, and `year` + (e.g.,`acute_jaundice_syndrome_outbreak_tcd_2016`). + +- **unique_identifier**: *DO NOT EDIT* - Combines `group_identifier`, + `type`, `type_version`, `data_version`, `context`, and `year` to + create a unique identifier (e.g. + `acute_jaundice_syndrome_outbreak_tcd_2016_linelist_1`). + +For example, when adding an Ebola dataset, you would enter the +information as shown below. The original dataset (whether it's from +{outbreaks} or another source) would be considered `type_version` 1. If +it's the only linelist in its group, it remains `type_version` 1. If a +completely different linelist is added (not just an edited version), +increment the `type_version` accordingly. + +For any changes to the data (such as cleaning or changing nums of rows +or columns), increment the `data_version` (e.g., `data_version` 2), but +the `type_version` remains the same to indicate that it's a derivative +(or "child") of the original. Each child dataset gets its own entry. + +If a dataset is translated into a different language, create a new entry +for the translated version while keeping the `data_version` and +`type_version` the same, but editing the `language` column accordingly. +This ensures you can trace back the parent-child relationship between +datasets. + +| **Variable** | **Example Entry** | +|----------------------------|--------------------------------------------| +| **name** | `ebola_linelist_cleaned` | +| **type** | `linelist` | +| **extension** | `xlsx` | +| **type_version** | `1` | +| **data_version** | `1` | +| **language** | `en` | +| **country** | `lbr` | +| **scale** | `national` | +| **subject** | `ebola` | +| **context** | `outbreak` | +| **fictional** | `yes` | +| **year** | `2014` | +| **description** | Linelist data from the Ebola virus | +| | disease outbreak in Liberia in | +| | 2014\. | +| **usage** | `introexercises`, etc. | +| **license** | `gpl3` | +| **group_identifier** | `ebola_outbreak_lbr_2014` | +| **unique_identifier** | `ebola_outbreak_lbr_2014_linelist_1_1_outbreak_2014` | From 73029db4d4799f42f131769689ff57f97870dfdc Mon Sep 17 00:00:00 2001 From: Paula Blomquist Date: Tue, 24 Sep 2024 16:07:48 +0100 Subject: [PATCH 3/6] Updated instructions to clarify that any new data goes into inst/ext --- vignettes/adding-data.Rmd | 32 ++++++++++---------------------- 1 file changed, 10 insertions(+), 22 deletions(-) diff --git a/vignettes/adding-data.Rmd b/vignettes/adding-data.Rmd index 48df788..3eb603e 100644 --- a/vignettes/adding-data.Rmd +++ b/vignettes/adding-data.Rmd @@ -26,12 +26,12 @@ library(appliedepidata) ## PACKAGE FOLDER STRUCTURE -To below is a simplified explanation of the [R packages data +### Overview + +To diagram and descriptions below are a simplified explanation of the [R packages data chapter](https://r-pkgs.org/data.html). For a fuller understanding, read that chapter. -### Overview - ``` bash . ├── appliedepidata.Rproj @@ -73,27 +73,16 @@ that chapter. These contain files outputted by running the code in the folders above. - **data**: Contains internalised and processed R datasets (.rda - files). + files). These are created when internalizing the data (running code in data-raw folder), which makes them more efficient for file storage. - **man**: Contains the R documentation files for package functions and datasets (created when running the code in the **R** folder). Each .Rd file has information about a specific function or dataset. - **tests**: Contains test files for developer use only. -- **internal data**: When you build a package, the `Rda` datasets - (from `data` folder) can become "internal" (more efficient for file - storage). These are accessed by calling `package::dataset` (e.g. - `appliedepidata::AJS_AmTiman`. They can also be imported directly - from github using link to the file in data folder e.g. - 'rio()', or the `appliedepidata::get_data` or - `appliedepidata::save_data` functions. -- **sysdata**: Not relevant for current package setup. In some setups - you are supposed to put *tableoftables* in sysdata (i.e. just for - package usage). However for our current setup leave in *extdata*. + ## ADDING DATA -This describes the process for adding a file to the repo. Note that the -processes for adding a non-R file (any file that is not `.rda`) and an R -file (any file already in`.rda` format) are slightly different. +This describes the process for adding a file to the repo. Note that any original datasets need to be added to the inst/exta folder, even if already in .rda format. If you are adding a dataset from an existing R package, you can skip to step 3 below. @@ -119,11 +108,8 @@ step 3 below. 2. **Place your file in the correct folder** - A. A *non-rda* file (e.g. `xlsx`, `shp`, `zip`, `rds`) goes in - `inst/extdata` folder. This is what will be downloaded when running - the save_data() function. i. If adding a shapefile then zip it - - B. An *rda* file goes in `data` folder + A. Add into `inst/extdata` folder. This is what will be downloaded when running + the save_data() function. If a shapefile, zip first. 3. **Build the package with the added data** @@ -147,6 +133,8 @@ step 3 below. `system.file()`, as below. Necessary edits to the dataset should also go here. Then run this script to internalise the data, and close. + + D. NOTE that if you want to process the raw data to create a dataset that should also be accessible to users (e.g. via the `get_data()` or `save_data()` functions), make sure that the processed data also gets saved into inst/extdata as version 2. Make sure you internalise (with use_data) both versions of the data. ```{r, eval=FALSE} From 01c952aef8a835f8490176390b73202a8b56b99f Mon Sep 17 00:00:00 2001 From: Paula Blomquist Date: Wed, 25 Sep 2024 10:58:30 +0100 Subject: [PATCH 4/6] Revert back to old table to prevent conflict --- inst/extdata/tableoftables.xlsx | Bin 10876 -> 10696 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/inst/extdata/tableoftables.xlsx b/inst/extdata/tableoftables.xlsx index 61c019e80d801302fee7fc622699191f0997b6d6..a8b7a5c638f16fbff53655d83bff95f6addbab2b 100644 GIT binary patch delta 5482 zcmZu#byU>tww|GzLApbF00B`-K)Ra|DM2~~>Hfh0ibxM3F_d&8AR(PnI)tQrbjN^n zAHH?hI^VhH-goVHtsT#Qdp~>cwXY4n>sL?V;4?$Xb{}JcKx~Lb98Lg|m@@`biK^85 z7B%)JfJ@Q1X_3O5c-?tC-*^vL5DNFK6-R!VZ<(HEk_on5r}emfYeI0`m9+jPN=W=j z&=SV!@k*-q{K#xOT4?Ou3vtRXmO{ZcbU@4bLH~tP>4q{-HW|o3qAxQtiUXi=PHY6d`+Jj?`b)s`-^sGB*~DEA?3UIgz(5H$r7Wc zu&cb{Uf33OBpXPH)*}YK;6y45H2S&73h~x%ZkHrRNfWpQsK2u>TcqyF_C=lFs8)M= z8Vo$l3rJ)z!hLkQ$~-F!%Ss*mwdw!Ue&>9t?9vS1Ruw_t9%ghOKp3=lc& zpKhHV^2@aVHDwcY8z>TI3=D=$cuxR^FZfT(<5?{0tnZ$h3KcWPLmDypN7yclsV69k zb=mrA?N5xt-UDUWE?9~m;yHFlZGRbtyyDlbSe4;>?2j!3$y_U67k}c}3l+3B87B$W zfl3L)n4_R0&W)ycx*JMo*B*@>^pq#*rZf?Y7mmTieoY0B;yF-qZO~5fl-Tzyh)m3(S@LtBr#9wdEGF^@{ly)I5%)ZG(n$bx7iGiI?`*8uOgWnV^HQ+#@ z?e$yh>k?2~4{i~k&BC9kLvXfVKUYMYRR*T?K56*uH;Tx5sZ!&ch1sj*jslkedK2Fl z2~zTAYe4>pSv&t{HWO~^Z>Is2=>>D zL>pTcVr)k|5(OPtkALrat77Q=|qA{2P*B_)5A&!$tQ4h11NB0_rVFR}kiKI& zxkCh8H8V(ASTmM+yx20fKIi5OHf;%dyx>$@Qve|W=YFLXKsxEk@jZ&Le2R)GeqDr8 z62ff&Y&D&&u!c;yU|8@HlHj4Rvq_mk;9R`!Nvnd0=;`_jyqm z1D}7p*oC34N!m&F)-(HThg8eJz>#QC5nDdMR z&}~8AzKy#CT|gAyN=A1p1qt0%RiE$kR8Kk*{ z*{c#V^UsduMN=_4=*oV4Zfr2RY-&7#%7gO9jxNg?XXf-4)QKs6gsR8s7M=2OPLxei zk#A47^@d-b^jXR=N>+c;`ANdh`K^-Qk+Z?#600yn+NE_(Yg9)>Hec61R0R`tI>n;@ z-n-lt^Kra(wUTWWnX){aRIkozx4ofciQYznt17$PT60s?+wF8#76fx^% z=V(QWTgj+?M1u1f%B(XNcxq5k_b$p&Oa+S4VBR|(Rb@6}^e}vLEQVB!8@G9;cWGzh zQ!JXVE^gRtzvI$;jukXcF@)tlL_t}kK9epm*#I^O9miJCqK1f@Jzw<%C;V-s))A+8 zhW^M)KLuFXiwGk#1=6_3IW!ZN(H{HJup}^(V19#{3y9!nyY{@D;c$kVScpHS`!+;5-P2fB#=%%a6Ds*(8Nmld`7iK+;ee z*I07M1mL62U3I}LAfuBjBfze_!Y5o0eV^Z7EjCe>B~?ZnIy-Y6MC^D^dI|P0n->Sd z;aoLATaGi7zIxNIW^vkAk9;V6b(M~D3pKcX{{V*ioD%p!>5rBV-qN+lq?GllA3ya6 zfT@g^mCGnvsFk~Gx#q5Qe;OsGVn?t(Gv#WCj)^O4IVuT-m9UOV;UU0_tAH3U;MlT& zSq(y2v9#Yop3%zb^Bwg|`3i?S(DOmy)Y=Fg{lDE^8rKgY5>`QYxwrP}Pm`9GU0MN4 z0B>1U08)QKqL4+bse336j=Wy-u*4p{d>X>5ljEVky1Nhm&I13w^CYt6RoM3(uUVX- z*s&{KZyUtec^X-;)^X^p5;^H3Y7z|Ln8&M$hQ zQt@}qf8x&#?s-l9j8^Z!TBQ@giVY;NYR=`@sV^VU4StRfg7B;oC-ukM=8=ybUfW1q zs3Z4DTwe?c8r7D>%G*^(58ZU0GEva3b#%2#_ex~;_5|WS1eQX0?G?<^ab}G*rQOfn zo&;#FVnNg)A2@^(H-|Lx9?5@b)8HtLUMu8DROdrXAV77hlscXS*oIPQvy9BTp&4NRiJr4C!7T6wOPs&#W1bG zCzC1~TefL1aP!f&Gx-eu<@nLHmne@?8TX8%4&(cMl{FEY-Go#0V=M27Md^pCDGaq$ zevEo658>=bUp+ixe&Xp+UJ+eYBzb?4+iFSeO2kUiQ3rDrW2kM+QzSuifB)7}<<8Ye zm%W0(?g2To=eJ;Pq^RB-?(VBAMNj6wWzU7p4@rZ|`{w4iwc?ai*uc%QjUL|pW-X2f z0uh5iAYbQ49-e;AHXZ`LF3!U+GuI43ilFSeJBte>oxKVIuQ-J?Uu|Bb1X*W@t6}+z z`MVh7Ox<0Z6AM0U&THt^DaL7i(0+bTDnv6;$l~SWQi%Ysmp`wHR&Tx znqMiUaDs}L@U!whU~22i=dH^beBOn&7LUaMxmZ#ED>`0cL0EN%&`by$TJSW{_)|J@ z3AEc@_nW+4JnF1pL9f#7y&&QuJ4D5i$vZjK$w+r-%GB+fYmH#y#jfq=x?Cr)L578b z#{`xYd0rnwX5FM+F#FG#N-u{;pw!JTtKtD#K5B*G>s;*50cld6$Vg`C53NFWY%!6q z<9;WT7QHP=uF$RY8RQhh$`in@#Vu$r8RnObxH5Av1(f3qLO43uV?6llWU16})13ID z)F$^{>U2)M`{v^EHlTJj-qDWzhs(yZn5j2Y;wX+}(_P89C6hMe)F2qChf4jBqn(;nry8NSU|_8m zPzF7(tgmM&7ZDJfw^xi%pIcIp32}4h>_Iw}SFMrn7AiP$J$7)7!jk{k9M1d>q9U_< z(EOpBInQeva~i^ZC&lMD`0&=L2y^jFxMamap-gQT39tv$)SHIRvtVmKa3jJNH{v`; ze1l=(wG@R-N(%59KEfjXr0Ahm^pSoYx5>L%G{XyC>)d>>q(!IJ3>zqOEUjORa4H_j zbIE4n9HKJ(m>g!*{`EP|r^--cnf$dAbA$&4YwqNHb%jnG3R7^ z^E%GHsLLEESxFpnt_*!2%40E&RX&0xDPr!A%B59>YQu8^3>hx$ZJVs&W%3mylyt_q zDuOqfkX0RgcmJbt^Ltv{-C=@s)G@IrKsca#rhr&Mf3D*RT<(d(g!shB2&lWxi9y<^ zr|$$&CD_~34j=1?8K_^0%8I@`4)qM64eDcjjO-@B(tz?7u7dKJS>At=|9IQdpd}K`xCbpZMK0df+WiXE8IF zntpI#&iUzyI zv6_B7o@_hvhm0J(U&iPxTgaNUH%rjrs|p@{&zd=GYt>Yji^Jbd1A}xC>KJm5klX$- zpD3@hEb0<7>#=qn} zoN1&HWEl*-e5{zPfz+Kz4BY4SJV?!}0UX{&#VRW=E33h5lLM3wiGec_R(0t+NqP(D zc?csW+u9OC${;o=pe>UL1l)K3-^8Z$jSfl99cr|h-HEi%i7{sA$9I03(CD2pP{nX( z%ZGY~*)Jm4O>)Ah5i8`2CE

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A. Press Ctrl + Shift + B to build the package with the newly added data. This will mean the data is recognized for the next step. - + 4. **Reproducibly edit dataset and internalize** (see `data-raw/AJS_AmTiman.R` for example) @@ -177,7 +177,7 @@ usethis::use_data(examplename_linelist, overwrite = TRUE) This will be an .Rd file in the `man` folder, with file name corresponding with the dataset name (e.g. `examplename_linelist.Rd`) - + 6. **Add the datasets to `_pkgdown.yml`**