From afc0c0c8274983e723076c6a78c39d65266727cf Mon Sep 17 00:00:00 2001 From: Zane Billings Date: Mon, 12 Aug 2024 11:18:44 -0400 Subject: [PATCH 1/4] chore: updates R version in renv --- renv.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/renv.lock b/renv.lock index e3a69cd..9bcd7fa 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.3.1", + "Version": "4.4.1", "Repositories": [ { "Name": "CRAN", From c61e264e01998ac767300b3ba892e3c58a4074b4 Mon Sep 17 00:00:00 2001 From: Zane Billings Date: Mon, 12 Aug 2024 11:51:47 -0400 Subject: [PATCH 2/4] chore: upgrades renv version --- renv.lock | 6 ++-- renv/activate.R | 80 ++++++++++++++++++++++++++++++++++++------------- 2 files changed, 63 insertions(+), 23 deletions(-) diff --git a/renv.lock b/renv.lock index 9bcd7fa..6daceb0 100644 --- a/renv.lock +++ b/renv.lock @@ -11,13 +11,13 @@ "Packages": { "renv": { "Package": "renv", - "Version": "1.0.3", + "Version": "1.0.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "utils" ], - "Hash": "41b847654f567341725473431dd0d5ab" + "Hash": "397b7b2a265bc5a7a06852524dabae20" } } } diff --git a/renv/activate.R b/renv/activate.R index cb5401f..d13f993 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,11 +2,13 @@ local({ # the requested version of renv - version <- "1.0.3" + version <- "1.0.7" attr(version, "sha") <- NULL # the project directory - project <- getwd() + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() # use start-up diagnostics if enabled diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") @@ -31,6 +33,14 @@ local({ if (!is.null(override)) return(override) + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + # next, check environment variables # TODO: prefer using the configuration one in the future envvars <- c( @@ -50,9 +60,22 @@ local({ }) - if (!enabled) + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + return(FALSE) + } + # avoid recursion if (identical(getOption("renv.autoloader.running"), TRUE)) { warning("ignoring recursive attempt to run renv autoloader") @@ -108,6 +131,21 @@ local({ } + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + + } + startswith <- function(string, prefix) { substring(string, 1, nchar(prefix)) == prefix } @@ -610,6 +648,9 @@ local({ # if the user has requested an automatic prefix, generate it auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + if (auto %in% c("TRUE", "True", "true", "1")) return(renv_bootstrap_platform_prefix_auto()) @@ -801,24 +842,23 @@ local({ # the loaded version of renv doesn't match the requested version; # give the user instructions on how to proceed - remote <- if (!is.null(description[["RemoteSha"]])) { + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) paste("rstudio/renv", description[["RemoteSha"]], sep = "@") - } else { + else paste("renv", description[["Version"]], sep = "@") - } # display both loaded version + sha if available friendly <- renv_bootstrap_version_friendly( version = description[["Version"]], - sha = description[["RemoteSha"]] + sha = if (dev) description[["RemoteSha"]] ) - fmt <- paste( - "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", - sep = "\n" - ) + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) FALSE @@ -1041,7 +1081,7 @@ local({ # if jsonlite is loaded, use that instead if ("jsonlite" %in% loadedNamespaces()) { - json <- catch(renv_json_read_jsonlite(file, text)) + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -1050,7 +1090,7 @@ local({ } # otherwise, fall back to the default JSON reader - json <- catch(renv_json_read_default(file, text)) + json <- tryCatch(renv_json_read_default(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -1063,14 +1103,14 @@ local({ } renv_json_read_jsonlite <- function(file = NULL, text = NULL) { - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } renv_json_read_default <- function(file = NULL, text = NULL) { # find strings in the JSON - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' locs <- gregexpr(pattern, text, perl = TRUE)[[1]] @@ -1118,14 +1158,14 @@ local({ map <- as.list(map) # remap strings in object - remapped <- renv_json_remap(json, map) + remapped <- renv_json_read_remap(json, map) # evaluate eval(remapped, envir = baseenv()) } - renv_json_remap <- function(json, map) { + renv_json_read_remap <- function(json, map) { # fix names if (!is.null(names(json))) { @@ -1152,7 +1192,7 @@ local({ # recurse if (is.recursive(json)) { for (i in seq_along(json)) { - json[i] <- list(renv_json_remap(json[[i]], map)) + json[i] <- list(renv_json_read_remap(json[[i]], map)) } } From 733d6680eabdef8d54c8a04b8e2c4547aeef1127 Mon Sep 17 00:00:00 2001 From: Zane Billings Date: Mon, 12 Aug 2024 15:35:38 -0400 Subject: [PATCH 3/4] chore: adds license --- DESCRIPTION | 16 +- LICENSE.md | 659 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 671 insertions(+), 4 deletions(-) create mode 100644 LICENSE.md diff --git a/DESCRIPTION b/DESCRIPTION index b9f45db..602b88e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,16 +1,24 @@ Package: hgp Type: Package Title: HandelGroupPackage -Version: 0.0.1 +Version: 0.0.2 Authors@R: person("Zane", "Billings", , "wz.billings@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0184-6134")) Description: Miscellaneous functions used for Handelgroup research Encoding: UTF-8 LazyData: true -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 Date: 2023-11-03 -Suggests: - ggplot2 URL: https://github.com/ahgroup/hgp BugReports: https://github.com/ahgroup/hgp/issues +Depends: + R (>= 2.10) +Suggests: + dplyr, + forcats, + ggplot2, + here, + readr, + tibble +License: AGPL (>= 3) diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..fab6548 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,659 @@ +GNU Affero General Public License +================================= + +_Version 3, 19 November 2007_ +_Copyright (C) 2007 Free Software Foundation, Inc. <>_ + +Everyone is permitted to copy and distribute verbatim copies of this +license document, but changing it is not allowed. + +## Preamble + +The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + +The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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From 2d64ce9ea9d950a31380cc6538353b3ad5959af2 Mon Sep 17 00:00:00 2001 From: Zane Billings Date: Mon, 12 Aug 2024 15:45:03 -0400 Subject: [PATCH 4/4] feat: adds strain name replacer function --- .Rbuildignore | 3 +- DESCRIPTION | 2 +- NAMESPACE | 1 + R/handelgroup_strain_names.R | 16 +++++ R/replace_strain_names.R | 89 ++++++++++++++++++++++++++ README.md | 37 ++++++----- README.qmd | 28 ++++++-- data-raw/handelgroup-strain-names.csv | 47 ++++++++++++++ data-raw/strain-names-data-prep.R | 38 +++++++++++ data/handelgroup_strain_names.rda | Bin 0 -> 1435 bytes man/handelgroup_strain_names.Rd | 26 ++++++++ man/replace_strain_names.Rd | 41 ++++++++++++ 12 files changed, 303 insertions(+), 25 deletions(-) create mode 100644 R/handelgroup_strain_names.R create mode 100644 R/replace_strain_names.R create mode 100644 data-raw/handelgroup-strain-names.csv create mode 100644 data-raw/strain-names-data-prep.R create mode 100644 data/handelgroup_strain_names.rda create mode 100644 man/handelgroup_strain_names.Rd create mode 100644 man/replace_strain_names.Rd diff --git a/.Rbuildignore b/.Rbuildignore index 21a0ea1..e42426f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -3,4 +3,5 @@ ^.*\.Rproj$ ^\.Rproj\.user$ ^LICENSE\.md$ -^README\.Rmd$ +^README\.qmd$ +^data-raw$ diff --git a/DESCRIPTION b/DESCRIPTION index 602b88e..fe60567 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Version: 0.0.2 Authors@R: person("Zane", "Billings", , "wz.billings@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0184-6134")) -Description: Miscellaneous functions used for Handelgroup research +Description: Miscellaneous functions used for Handelgroup research. Encoding: UTF-8 LazyData: true RoxygenNote: 7.3.2 diff --git a/NAMESPACE b/NAMESPACE index 65a4dec..227109d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,3 +1,4 @@ # Generated by roxygen2: do not edit by hand +export(replace_strain_names) export(theme_ms) diff --git a/R/handelgroup_strain_names.R b/R/handelgroup_strain_names.R new file mode 100644 index 0000000..d6b062d --- /dev/null +++ b/R/handelgroup_strain_names.R @@ -0,0 +1,16 @@ +#' Handelgroup Standardized Strain Names Dataset +#' +#' A dataset containing various formats of the names for the influenza strains +#' we use in our research. +#' +#' @format ## `handelgroup_strain_names` +#' A data frame with 46 rows and 6 columns: +#' \describe{ +#' \item{subtype}{Whether the strain is H1N1 or H3N2.} +#' \item{analysis_name}{Strain name format used in clean_data.Rds.} +#' \item{genbank_strain_name}{The accepted full strain name, as found in +#' genbank.} +#' \item{short_name}{The abbrevated name, usually 2-4 letters and the +#' last two digits of the year, useful for saving space in displays.} +#' } +"handelgroup_strain_names" diff --git a/R/replace_strain_names.R b/R/replace_strain_names.R new file mode 100644 index 0000000..94d5ee9 --- /dev/null +++ b/R/replace_strain_names.R @@ -0,0 +1,89 @@ +#' Replace strain names with a different format +#' +#' Using the standardized list of handelgroup strain names from +#' ["handelgroup_strain_names"], pass in a vector of strain names of arbitrary +#' length and return the same sequence of names in a different format. +#' +#' @param x A vector of strain names. +#' @param from Format of the names in the vector `x`. Should be one of +#' "analysis", "full", or "short". See ["handelgroup_strain_names"] for the +#' allowed names in each of the formats. If you want to transform a strain +#' that is not currently in the strain list, you will need to add it and +#' submit a PR to `hgp`! +#' @param to Format of the returned names. Should be one of "short", "full", +#' "analysis", or "subtype". +#' @param drop If TRUE, levels of the returned factor variable are dropped. If +#' FALSE, the level set of the factor will still contain every strain in +#' ["handelgroup_strain_names"], which is typically not desirable. +#' +#' @return A factor vector of the same length as `x`. +#' @export +#' +#' @examples +#' replace_strain_names("CA/09", from = "short", to = "analysis") +#' +#' dat <- data.frame(s = c("CA/09", "MI/15"), x = c(1, 2)) +#' transform( +#' dat, +#' s_long = replace_strain_names(s, from = "short", to = "analysis") +#' ) +replace_strain_names <- function(x, from = "analysis", to = "short", + drop = TRUE) { + # Load needed packages + requireNamespace("forcats", quietly = TRUE) + requireNamespace("tibble", quietly = TRUE) + requireNamespace("dplyr", quietly = TRUE) + requireNamespace("readr", quietly = TRUE) + + # Load the strain names data + #utils::data("handelgroup_strain_names", envir=environment()) + handelgroup_strain_names <- hgp::handelgroup_strain_names + + # Check if from and to are the same + if (from == to) { + warning("From and to are the same, returning original vector.") + return(x) + } + + # Find the right column for selecting names from + if (from == "analysis") { + from_vec <- handelgroup_strain_names$analysis_name + } else if (from == "full") { + from_vec <- handelgroup_strain_names$genbank_strain_name + } else if (from == "short") { + from_vec <- handelgroup_strain_names$short_name + } else { + stop("'from' should be 'analysis', 'full', or 'short'.") + } + + # Make sure all values of x exist in the virus info table + if (!(all(x %in% from_vec))) { + stop(paste0( + "'x' should be a vector of ", from, " names that exist in the", + ' virus-info sheet.' + )) + } + + # Now get the location in the virus info table for each element of x + locs <- match(x, from_vec) + + # Based on the names argument, get the correct names to return. + if (to == "analysis") { + vals <- handelgroup_strain_names$analysis_name[locs] + } else if (to == "full") { + vals <- handelgroup_strain_names$genbank_strain_name[locs] + } else if (to == "short") { + vals <- handelgroup_strain_names$short_name[locs] + } else if (to == "subtype") { + vals <- handelgroup_strain_names$subtype[locs] + } else { + stop("'to' should be 'analysis', 'full', 'short', or 'subtype'.") + } + + # If requested, remove unseen factor levels + if (isTRUE(drop)) { + vals <- forcats::fct_drop(vals) + } + + return(vals) +} diff --git a/README.md b/README.md index da90c57..a2b2c02 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,17 @@ - + -``` - _ _ _ _ _____ _____ _ ___ __ - | | | | | | | |/ ____| | __ \ | | / / | \ \ - | |__| | __ _ _ __ __| | ___| | | __ _ __ ___ _ _ _ __ | |__) |_ _ ___| | ____ _ __ _ ___ | || |__ __ _ _ __ | | - | __ |/ _` | '_ \ / _` |/ _ \ | | |_ | '__/ _ \| | | | '_ \| ___/ _` |/ __| |/ / _` |/ _` |/ _ \ | || '_ \ / _` | '_ \| | - | | | | (_| | | | | (_| | __/ | |__| | | | (_) | |_| | |_) | | | (_| | (__| < (_| | (_| | __/ | || | | | (_| | |_) | | - |_| |_|\__,_|_| |_|\__,_|\___|_|\_____|_| \___/ \__,_| .__/|_| \__,_|\___|_|\_\__,_|\__, |\___| | ||_| |_|\__, | .__/| | - | | __/ | \_\ __/ | | /_/ - |_| |___/ |___/|_| -``` + + _ _ _ _ _____ _____ _ + | | | | | | | |/ ____| | __ \ | | + | |__| | __ _ _ __ __| | ___| | | __ _ __ ___ _ _ _ __ | |__) |_ _ ___| | ____ _ __ _ ___ + | __ |/ _` | '_ \ / _` |/ _ \ | | |_ | '__/ _ \| | | | '_ \| ___/ _` |/ __| |/ / _` |/ _` |/ _ \ + | | | | (_| | | | | (_| | __/ | |__| | | | (_) | |_| | |_) | | | (_| | (__| < (_| | (_| | __/ + |_| |_|\__,_|_| |_|\__,_|\___|_|\_____|_| \___/ \__,_| .__/|_| \__,_|\___|_|\_\__,_|\__, |\___| + | | __/ | + |_| |___/ + # `hgp: HandelGroupPackage` @@ -20,8 +20,13 @@ `hgp` is a package for storing utility functions for use across -handelgroup. Right now, `hgp` only contains a `ggplot2` theme. But we -will update this description as we add more stuff. +handelgroup. Right now, `hgp` contains the following utilities: + +- A group-standard `ggplot2` theme function; +- A set of functions for working with HAI data; +- A function to standardize influenza strain names for the strains used + in the datasets we have available to us; along with a corresponding + data set of standardized strain names. **Because this repo is public, absolutely NO sensitive or confidential information should be stored here. This repo is strictly for shared @@ -33,8 +38,8 @@ You can install the development version of hgp from [GitHub](https://github.com/) with: ``` r -# install.packages("devtools") -devtools::install_github("ahgroup/hgp") +# install.packages("remotes") +remotes::install_github("ahgroup/hgp") ``` Or if you are in a repository with `renv` enabled (recommended): @@ -79,8 +84,6 @@ ggplot2::theme_set(hgp::theme_ms()) - Please run `devtools:check()` before merging any new functionality to the main branch and fix any resulting messages. It is unnecessary to `build` the package, we just need to ensure that any checks pass. - - Note that as of `2023-11-03`, we have not decided on a package - license, so you will get one warning in the check results for that. - `renv` is initialized for this repository using the EXPLICIT snapshot mode. - If you need to import a new package, you MUST update the `NAMESPACE` diff --git a/README.qmd b/README.qmd index 8f9103b..e66c71c 100644 --- a/README.qmd +++ b/README.qmd @@ -13,14 +13,32 @@ knitr::opts_chunk$set( ) ``` + +``` + _ _ _ _ _____ _____ _ + | | | | | | | |/ ____| | __ \ | | + | |__| | __ _ _ __ __| | ___| | | __ _ __ ___ _ _ _ __ | |__) |_ _ ___| | ____ _ __ _ ___ + | __ |/ _` | '_ \ / _` |/ _ \ | | |_ | '__/ _ \| | | | '_ \| ___/ _` |/ __| |/ / _` |/ _` |/ _ \ + | | | | (_| | | | | (_| | __/ | |__| | | | (_) | |_| | |_) | | | (_| | (__| < (_| | (_| | __/ + |_| |_|\__,_|_| |_|\__,_|\___|_|\_____|_| \___/ \__,_| .__/|_| \__,_|\___|_|\_\__,_|\__, |\___| + | | __/ | + |_| |___/ +``` + + # `hgp: HandelGroupPackage` `hgp` is a package for storing utility functions for use across handelgroup. -Right now, `hgp` only contains a `ggplot2` theme. But we will update this -description as we add more stuff. +Right now, `hgp` contains the following utilities: + +* A group-standard `ggplot2` theme function; +* A set of functions for working with HAI data; +* A function to standardize influenza strain names for the strains used in the +datasets we have available to us; along with a corresponding data set of +standardized strain names. **Because this repo is public, absolutely NO sensitive or confidential information should be stored here. This repo is strictly for shared utilities.** @@ -30,8 +48,8 @@ information should be stored here. This repo is strictly for shared utilities.** You can install the development version of hgp from [GitHub](https://github.com/) with: ``` r -# install.packages("devtools") -devtools::install_github("ahgroup/hgp") +# install.packages("remotes") +remotes::install_github("ahgroup/hgp") ``` Or if you are in a repository with `renv` enabled (recommended): @@ -75,8 +93,6 @@ should use `devtools::document()` to generate the documentation files. * Please run `devtools:check()` before merging any new functionality to the main branch and fix any resulting messages. It is unnecessary to `build` the package, we just need to ensure that any checks pass. - * Note that as of `2023-11-03`, we have not decided on a package license, - so you will get one warning in the check results for that. * `renv` is initialized for this repository using the EXPLICIT snapshot mode. * If you need to import a new package, you MUST update the `NAMESPACE` file appropriately before invoking `renv::snapshot()`. diff --git a/data-raw/handelgroup-strain-names.csv b/data-raw/handelgroup-strain-names.csv new file mode 100644 index 0000000..5e89141 --- /dev/null +++ b/data-raw/handelgroup-strain-names.csv @@ -0,0 +1,47 @@ +subtype,analysis_name,genbank_strain_name,short_name,factor_order,vaccine_strain +h1,H1N1-South Carolina-1918,A/H1N1/South Carolina/1/1918,SC/18,1,FALSE +h1,H1N1-Puerto Rico-1934,A/H1N1/Puerto Rico/8/1934,PR/34,2,FALSE +h1,H1N1-Weiss-1943,A/H1N1/Weiss/43,Wei/43,3,FALSE +h1,H1N1-Fort Monmouth-1947,A/H1N1/Fort Monmouth/1/1947,FM/47,4,FALSE +h1,H1N1-Denver-1957,A/H1N1/Denver/1957,Den/57,5,FALSE +h1,H1N1-New Jersey-1976,A/H1N1/New Jersey/8/1976,NJ/76,6,FALSE +h1,H1N1-Ussr-1977,A/H1N1/Ussr/90/1977,USSR/77,7,FALSE +h1,H1N1-Brazil-1978,A/H1N1/Brazil/11/1978,Bra/78,8,FALSE +h1,H1N1-California-1978,A/H1N1/California/10/1978,CA/78,9,FALSE +h1,H1N1-Chile-1983,A/H1N1/Chile/1/1983,Chi/83,10,FALSE +h1,H1N1-Singapore-1986,A/H1N1/Singapore/6/1986,Sing/86,11,FALSE +h1,H1N1-Texas-1991,A/H1N1/Texas/36/1991,TX/91,12,FALSE +h1,H1N1-Beijing-1995,A/H1N1/Beijing/262/1995,Bei/95,13,FALSE +h1,H1N1-New Caledonia-1999,A/H1N1/New Caledonia/20/1999,NC/99,14,FALSE +h1,H1N1-Solomon Islands-2006,A/H1N1/Solomon Islands/3/2006,SI/06,15,FALSE +h1,H1N1-Brisbane-2007,A/H1N1/Brisbane/59/2007,Bris/07,16,FALSE +h1,H1N1-California-2009,A/H1N1/California/07/2009,CA/09,17,TRUE +h1,H1N1-Michigan-2015,A/H1N1/Michigan 45/2015,MI/15,18,TRUE +h1,H1N1-Brisbane-2018,A/H1N1/Brisbane/02/2018,Bris/18,19,TRUE +h1,H1N1-Guangdong Maonan-2019,A/H1N1/Guangdong-Maonan/SWL1536/201,GD/19,20,TRUE +h1,H1N1-Victoria-2019,A/H1N1/Victoria/2570/2019,Vic/19,21,TRUE +h3,H3N2-Hong Kong-1968,A/H3N2/Hong Kong/8/1968,HK/68,22,FALSE +h3,H3N2-Port Chalmers-1973,A/H3N2/Port Chalmers/1/1973,PC/73,23,FALSE +h3,H3N2-Texas-1977,A/H3N2/Texas/1/1977,TX/77,24,FALSE +h3,H3N2-Mississippi-1985,A/H3N2/Mississippi/1/1985,MI/85,25,FALSE +h3,H3N2-Sichuan-1987,A/H3N2/Sichuan/2/1987,Sich/87,26,FALSE +h3,H3N2-Shangdong-1993,A/H3N2/Shangdong/9/1993,Shan/93,27,FALSE +h3,H3N2-Nanchang-1995,A/H3N2/Nanchang/933/1995,Nan/95,28,FALSE +h3,H3N2-Sydney-1997,A/H3N2/Sydney/5/1997,Syd/97,29,FALSE +h3,H3N2-Panama-1999,A/H3N2/Panama/2007/1999,Pan/99,30,FALSE +h3,H3N2-Fujian-2002,A/H3N2/Fujian/411/2002,Fuj/02,31,FALSE +h3,H3N2-New York-2004,A/H3N2/New York/55/2004,NY/04,32,FALSE +h3,H3N2-Brisbane-2007,A/H3N2/Brisbane/10/2007,Br/07,33,TRUE +h3,H3N2-Wisconsin-2005,A/H3N2/Wisconsin/67/2005,WI/05,34,FALSE +h3,H3N2-Uruguay-2007,A/H3N2/Uruguay/716/2007,Uru/07,35,FALSE +h3,H3N2-Perth-2009,A/H3N2/Perth/16/2009,Per/09,36,FALSE +h3,H3N2-Victoria-2011,A/H3N2/Victoria/361/2011,Vic/11,37,FALSE +h3,H3N2-Texas-2012,A/H3N2/Texas/50/2012,TX/12,38,TRUE +h3,H3N2-Switzerland-2013,A/H3N2/Switzerland/9715293/2013,Switz/13,39,TRUE +h3,H3N2-Hong Kong-2014,A/H3N2/Hong Kong/4801/2014,HK/14,40,TRUE +h3,H3N2-Singapore-2016,A/H3N2/Singapore/infimh-16-0019/2016,Sing/16,41,TRUE +h3,H3N2-Kansas-2017,A/H3N2/Kansas/14/2017,KS/17,42,TRUE +h3,H3N2-Hong Kong-2019,A/H3N2/Hong Kong/2671/2019,HK/19,43,TRUE +h3,H3N2-South Australia-2019,A/H3N2/South Australia/34/2019,SA/19,44,TRUE +h3,H3N2-Tasmania-2020,A/H3N2/Tasmania/503/2020 ,Tas/20,45,TRUE +h3,H3N2-Darwin-2021,A/H3N2/Darwin/9/2021,Dar/21,46,TRUE diff --git a/data-raw/strain-names-data-prep.R b/data-raw/strain-names-data-prep.R new file mode 100644 index 0000000..fca5c5e --- /dev/null +++ b/data-raw/strain-names-data-prep.R @@ -0,0 +1,38 @@ +### +# Code to prepare the strain names data for package inclusion +# Zane Billings +# 2024-08-12 +# The strain names data is a table of strain names, currently the ones that +# are used in UGAFluVac. We encourage updates to raw CSV file to add strain +# names that are used in other handelgroup datasets. +### + +handelgroup_strain_names <- readr::read_csv( + here::here("data-raw", "handelgroup-strain-names.csv"), + col_types = 'fcccil' +) |> + # Remove the useless columns + dplyr::select(-c(vaccine_strain)) |> + # Append a row so sorting the overall entry for CATEs is easy + tibble::add_row( + subtype = "", + analysis_name = "Overall", + short_name = "Overall", + genbank_strain_name = "Overall", + factor_order = 9999L + ) |> + # Make all of the name variables ordered factors and clean up the subtypes + dplyr::mutate( + subtype = factor( + as.character(subtype), + levels = c("h1", "h3", ""), + labels = c("H1N1", "H3N2", "") + ), + # Put the different name factors in order + dplyr::across( + c(analysis_name, genbank_strain_name, short_name), + \(x) forcats::fct_reorder(x, factor_order) + ), + ) + +usethis::use_data(handelgroup_strain_names, overwrite = TRUE) diff --git a/data/handelgroup_strain_names.rda b/data/handelgroup_strain_names.rda new file mode 100644 index 0000000000000000000000000000000000000000..0cd9b3e70bbc4d9441ee40ed3a9dec1343ff25bf GIT binary patch literal 1435 zcmV;M1!Vd{T4*^jL0KkKS+aBp#{dVi|HA+O|NsC0|KL6U-{8Oh-|#>HAOHXX&;}j} zmTuy7aXTAvKp@CTl4R0qdTE*|>Tguh=+yFnJwRv;sA-S`)Ov=DY95d=s5HXky3`+i7ZP2%lq*^(Wa_n4Nw)@UXTS)eXV z76gkBN4XLZh(_vMf<=S`kTDWTKoAfCLP=325|Wits#Pr%RV`}(cOjAoB$ZBlp;m&b zzn|IRM}c+S`m4Xi*(nevT708s+bcKqmUMJ}=NwflK>B7LL|nh(w3jOZ%-ETY3Mv#Q=X`Xi)pQW zui%9hZAkaWByvJ02t@USFUs|a@l7U>rOE0ySiK$z?G*eHH*8Mh)Izy&K?&Tb((?+1P}-yOu0}Bs)cV@ zoC1m|Y%Cbb1(FPlY%*1dNMy@UmIx9I3K9e=vo|hxku#4spFh8YKg)*L-IA1EH@hZ4 z(>_KIrm=gnWPB;C7-^0DN%mQrd?`~tZCDD45)=xveK_v!sy*S+!4y^nUwwphpft2Jbq*WYv* zjjagr*3_K4BR9#N$z)d}X@@GVhWujfQpO)V-I;t?G@mmT-EPgDToNr7S=8{h0}q&ppj%9jcm>1JUe_YFJkL2WN5Q-yV05Jdpxl% zE!=q8{Sdq~W^qnT7t)DcM$k35o_GQ`{)yuA9QOM0*ToVSXYX*k)Yb)?d zMXgy7%9WEAvi3#dMoTP0S5CM1t&x)&SCZ7ii`vx^q_v1=ytG=#h{e9xV&yZq8n01W z{Bk6zTWqarY;YDkt<$9STpDznD{gV?xdz*8+jDsA#`s~R#