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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -23,3 +23,4 @@ allpopsamples_hlye.csv$ | |
| ^CRAN-SUBMISSION$ | ||
| ^README\.qmd$ | ||
| ^codecov\.yml$ | ||
| ^\.lintr$ | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,2 @@ | ||
| linters: linters_with_defaults() # see vignette("lintr") | ||
| encoding: "UTF-8" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| Type: Package | ||
| Package: serocalculator | ||
| Title: Estimating Infection Rates from Serological Data | ||
| Version: 1.2.0.9009 | ||
| Version: 1.2.0.9010 | ||
| Authors@R: c( | ||
| person("Peter", "Teunis", , "[email protected]", role = c("aut", "cph"), | ||
| comment = "Author of the method and original code."), | ||
|
|
@@ -49,6 +49,7 @@ Suggests: | |
| readr, | ||
| rmarkdown, | ||
| spelling, | ||
| ssdtools (>= 1.0.6.9016), | ||
| testthat (>= 3.0.0), | ||
| tidyverse | ||
| LinkingTo: | ||
|
|
@@ -60,3 +61,5 @@ LazyData: true | |
| NeedsCompilation: no | ||
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.3.2 | ||
| Remotes: | ||
| bcgov/ssdtools | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,191 @@ | ||
| get_age_var <- function(object, ...) { | ||
| age_var <- attributes(object)$age_var | ||
| return(age_var) | ||
| } | ||
|
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||
| get_age <- function(object, ...) { | ||
| age_var <- object %>% get_age_var() | ||
| age_data <- object %>% pull(age_var) | ||
| return(age_data) | ||
| } | ||
|
|
||
| get_value_var <- function(object, ...) { | ||
| value_var <- attributes(object)$value_var | ||
| return(value_var) | ||
| } | ||
|
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||
| get_value <- function(object, ...) { | ||
| value_var_name <- object %>% get_value_var() | ||
| value_data <- object %>% pull(value_var_name) | ||
| return(value_data) | ||
| } | ||
|
|
||
| get_id_var <- function(object, ...) { | ||
| id_var <- attributes(object)$id_var | ||
| return(id_var) | ||
| } | ||
|
|
||
| get_id <- function(object, ...) { | ||
| id_var_name <- object %>% get_id_var() | ||
| id_data <- object %>% pull(id_var_name) | ||
| return(id_data) | ||
| } | ||
|
|
||
| get_biomarker_levels <- function(object, ...) { | ||
| attr(object, "antigen_isos") | ||
| } | ||
|
|
||
| get_biomarker_names_var <- function(object, ...) { | ||
| # get value attribute | ||
| biomarker_var <- attributes(object)[["biomarker_var"]] | ||
|
|
||
| return(biomarker_var) | ||
| } | ||
|
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||
| get_biomarker_names <- function(object, ...) { | ||
| # get biomarker name data | ||
| biomarker_names_var <- get_biomarker_names_var(object) | ||
| biomarker_data <- object %>% pull(biomarker_names_var) | ||
|
|
||
| return(biomarker_data) | ||
| } | ||
|
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||
|
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||
| set_age <- function(object, | ||
| age = "Age", | ||
| standardize = TRUE, | ||
| ...) { | ||
| # check if age column exists | ||
| if (age %in% colnames(object)) { | ||
| attr(object, "age_var") <- age | ||
| } else { | ||
| cli::cli_warn(class = "missing variable", | ||
| 'The specified `age` column "{age}" does not exist.') | ||
|
|
||
| # search age variable from object | ||
| age_var <- | ||
| grep( | ||
| x = colnames(object), | ||
| value = TRUE, | ||
| pattern = age, | ||
| ignore.case = TRUE | ||
| ) | ||
|
|
||
| if (length(age_var) == 1) { | ||
| attr(object, "age_var") <- age_var | ||
|
|
||
| # create warning when using searched age instead of provided age | ||
| cli::cli_inform('Proceeding to use "{.var {age_var}}"') | ||
| } else if (length(age_var) == 0) { | ||
| cli::cli_abort("No similar column name was detected.") | ||
| } else if (length(age_var) > 1) { | ||
| cli::cli_warn("Multiple potential matches found: {.var {age_var}}") | ||
| cli::cli_warn("Using first match: {.var {age_var[1]}}") | ||
| attr(object, "age_var") <- age_var[1] | ||
| } else { | ||
| cli::cli_abort("{.code length(age_var)} = {.val {length(age_var)}}") | ||
| } | ||
| } | ||
|
|
||
| if (standardize) { | ||
| object <- object %>% | ||
| rename(c("age" = attr(object, "age_var"))) | ||
|
|
||
| # set age attribute | ||
| attr(object, "age_var") <- "age" | ||
| } | ||
|
|
||
| return(object) | ||
| } | ||
|
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||
|
|
||
| set_value <- function(object, | ||
| value = "result", | ||
| standardize = TRUE, | ||
| ...) { | ||
| # check if value column exists | ||
| if (value %in% colnames(object)) { | ||
| attr(object, "value_var") <- value | ||
| } else { | ||
| cli::cli_warn('The specified `value` column "{.var {value}}" | ||
| does not exist.') | ||
|
|
||
| # search value variable from pop_data | ||
| value_var <- | ||
| grep( | ||
| x = colnames(object), | ||
| value = TRUE, | ||
| pattern = value, | ||
| ignore.case = TRUE | ||
| ) | ||
|
|
||
| if (length(value_var) == 1) { | ||
| attr(object, "value_var") <- value_var | ||
|
|
||
| # create warning when using searched age instead of provided age | ||
| cli::cli_inform('Proceeding to use "{.var {value_var}}"') | ||
| } else if (length(value_var) == 0) { | ||
| cli::cli_abort("No similar column name was detected.") | ||
| } else { | ||
| # i.e. if (length(value_var) > 1) | ||
| cli::cli_warn("Multiple potential matches found: {.var {value_var}}") | ||
| cli::cli_inform("Using first match: {.var {value_var[1]}}") | ||
| attr(object, "value_var") <- value_var[1] | ||
| } | ||
| } | ||
|
|
||
| if (standardize) { | ||
| object <- object %>% | ||
| rename(c("value" = attr(object, "value_var"))) | ||
|
|
||
| # set id attribute | ||
| attr(object, "value_var") <- "value" | ||
| } | ||
|
|
||
| return(object) | ||
| } | ||
|
|
||
| set_id <- function(object, | ||
| id = "index_id", | ||
| standardize = TRUE, | ||
| ...) { | ||
| # check if id column exists | ||
| if (id %in% colnames(object)) { | ||
| attr(object, "id_var") <- id | ||
| } else { | ||
| cli::cli_warn("The specified {.var id} column {.val {id}} does not exist.") | ||
|
|
||
| # search id variable from object | ||
| id_var <- | ||
| grep( | ||
| x = colnames(object), | ||
| value = TRUE, | ||
| pattern = id, | ||
| ignore.case = TRUE | ||
| ) | ||
|
|
||
| if (length(id_var) == 1) { | ||
| attr(object, "id_var") <- id_var | ||
|
|
||
| # create warning when using searched id instead of provided id | ||
| cli::cli_inform('Proceeding to use "{id_var}"') | ||
| } else if (length(id_var) == 0) { | ||
| cli::cli_abort("No similar column name was detected.") | ||
| } else { | ||
| # if (length(id_var) > 1) | ||
| cli::cli_warn("Multiple potential matches found: {.var {id_var}}") | ||
| cli::cli_inform("Using first match: {.var {id_var[1]}}") | ||
| attr(object, "id_var") <- id_var[1] | ||
| } | ||
| } | ||
|
|
||
| if (standardize) { | ||
| object <- object %>% | ||
| rename(c("id" = attr(object, "id_var"))) | ||
|
|
||
| # set id attribute | ||
| attr(object, "id_var") <- "id" | ||
| } | ||
|
|
||
| return(object) | ||
| } |
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