,
Thibaut Jombart [aut, ccp],
Tim Taylor [ctb],
Chris Hartgerink [rev] | Title: | Tagging and Validating Epidemiological Data |
|---|---|
| Description: | Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable. |
| Authors: | Hugo Gruson [aut, cre] ,
Thibaut Jombart [aut, ccp],
Tim Taylor [ctb],
Chris Hartgerink [rev] |
| Maintainer: | Hugo Gruson <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.1.4.9000 |
| Built: | 2024-09-08 05:43:14 UTC |
| Source: | https://github.com/epiverse-trace/linelist |
The [] and [[]] operators for linelist objects behaves like for regular
data.frame or tibble, but check that tagged variables are not lost, and
takes the appropriate action if this is the case (warning, error, or ignore,
depending on the general option set via lost_tags_action()) .
## S3 method for class 'linelist' x[i, j, drop = FALSE] ## S3 replacement method for class 'linelist' x[i, j] <- value ## S3 replacement method for class 'linelist' x[[i, j]] <- value ## S3 replacement method for class 'linelist' x$name <- value## S3 method for class 'linelist' x[i, j, drop = FALSE] ## S3 replacement method for class 'linelist' x[i, j] <- value ## S3 replacement method for class 'linelist' x[[i, j]] <- value ## S3 replacement method for class 'linelist' x$name <- value
x |
a |
i |
a vector of |
j |
a vector of |
drop |
a |
value |
the replacement to be used for the entries identified in |
name |
a literal character string or a name (possibly backtick
quoted). For extraction, this is normally (see under
‘Environments’) partially matched to the |
If no drop is happening, a linelist. Otherwise an atomic vector.
lost_tags_action() to set the behaviour to adopt when tags are
lost through subsetting; default is to issue a warning
get_lost_tags_action() to check the current the behaviour
if (require(outbreaks) && require(dplyr) && require(magrittr)) { ## create a linelist x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) %>% mutate(result = if_else(is.na(date_of_death), "survived", "died")) %>% set_tags(outcome = "result") %>% rename(identifier = case_ID) x ## dangerous removal of a tagged column setting it to NULL issues a warning x[, 1] <- NULL x x[[2]] <- NULL x x$age <- NULL x }if (require(outbreaks) && require(dplyr) && require(magrittr)) { ## create a linelist x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) %>% mutate(result = if_else(is.na(date_of_death), "survived", "died")) %>% set_tags(outcome = "result") %>% rename(identifier = case_ID) x ## dangerous removal of a tagged column setting it to NULL issues a warning x[, 1] <- NULL x x[[2]] <- NULL x x$age <- NULL x }
A selector function to use in tidyverse functions
has_tag(tags)has_tag(tags)
tags |
A character vector of tags listing the variables you want to operate on |
A numeric vector containing the position of the columns with the requested tags
if (require(outbreaks) && require(dplyr)) { ## dataset we'll create a linelist from measles_hagelloch_1861 ## create linelist x <- make_linelist(measles_hagelloch_1861, id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) head(x) x %>% select(has_tag(c("id", "age"))) %>% head() }if (require(outbreaks) && require(dplyr)) { ## dataset we'll create a linelist from measles_hagelloch_1861 ## create linelist x <- make_linelist(measles_hagelloch_1861, id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) head(x) x %>% select(has_tag(c("id", "age"))) %>% head() }
This function determines the behaviour to adopt when tagged variables of a
linelist are lost e.g. through subsetting. This is achieved using options
defined for the linelist package.
lost_tags_action(action = c("warning", "error", "none"), quiet = FALSE, x) get_lost_tags_action()lost_tags_action(action = c("warning", "error", "none"), quiet = FALSE, x) get_lost_tags_action()
action |
a |
quiet |
a |
x |
deprecated |
The errors or warnings generated by linelist in case of tagged
variable loss has a custom class of linelist_error and linelist_warning
respectively.
returns NULL; the option itself is set in options("linelist")
# reset default - done automatically at package loading lost_tags_action() # check current value get_lost_tags_action() # change to issue errors when tags are lost lost_tags_action("error") get_lost_tags_action() # change to ignore when tags are lost lost_tags_action("none") get_lost_tags_action() # reset to default: warning lost_tags_action()# reset default - done automatically at package loading lost_tags_action() # check current value get_lost_tags_action() # change to issue errors when tags are lost lost_tags_action("error") get_lost_tags_action() # change to ignore when tags are lost lost_tags_action("none") get_lost_tags_action() # reset to default: warning lost_tags_action()
This function converts a data.frame or a tibble into a linelist object,
where different types of epidemiologically relevant data are tagged. This
includes dates of different events (e.g. onset of symptoms, case reporting),
information on the patient (e.g. age, gender, location) as well as other
information such as the type of case (e.g. confirmed, probable) or the
outcome of the disease. The output will seem to be the same data.frame, but
linelist-aware packages will then be able to automatically use tagged
fields for further data cleaning and analysis.
make_linelist(x, ..., allow_extra = FALSE)make_linelist(x, ..., allow_extra = FALSE)
x |
a |
... |
< |
allow_extra |
a |
Known variable types include:
id: a unique case identifier as numeric or character
date_onset: date of symptom onset (see below for date formats)
date_reporting: date of case notification (see below for date formats)
date_admission: date of hospital admission (see below for date formats)
date_discharge: date of hospital discharge (see below for date formats)
date_outcome: date of disease outcome (see below for date formats)
date_death: date of death (see below for date formats)
gender: a factor or character indicating the gender of the patient
age: a numeric indicating the age of the patient, in years
location: a factor or character indicating the location of the
patient
occupation: a factor or character indicating the professional
activity of the patient
hcw: a logical indicating if the patient is a health care worker
outcome: a factor or character indicating the outcome of the disease
(death or survival)
Dates can be provided in the following formats/types:
Date objects (e.g. using as.Date on a character with a correct date
format); this is the recommended format
POSIXct/POSIXlt objects (when a finer scale than days is needed)
numeric values, typically indicating the number of days since the first
case
The function returns a linelist object.
An overview of the linelist package
tags_names(): for a list of known tag names
tags_types(): for the associated accepted types/classes
tags(): for a list of tagged variables in a linelist
set_tags(): for modifying tags
tags_df(): for selecting variables by tags
if (require(outbreaks)) { ## dataset we will convert to linelist head(measles_hagelloch_1861) ## create linelist x <- make_linelist(measles_hagelloch_1861, id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) ## print result - just first few entries head(x) ## check tags tags(x) ## Tags can also be passed as a list with the splice operator (!!!) my_tags <- list( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) new_x <- make_linelist(measles_hagelloch_1861, !!!my_tags) ## The output is strictly equivalent to the previous one identical(x, new_x) }if (require(outbreaks)) { ## dataset we will convert to linelist head(measles_hagelloch_1861) ## create linelist x <- make_linelist(measles_hagelloch_1861, id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) ## print result - just first few entries head(x) ## check tags tags(x) ## Tags can also be passed as a list with the splice operator (!!!) my_tags <- list( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) new_x <- make_linelist(measles_hagelloch_1861, !!!my_tags) ## The output is strictly equivalent to the previous one identical(x, new_x) }
This function can be used to rename the columns a linelist, adjusting tags
as needed.
## S3 replacement method for class 'linelist' names(x) <- value## S3 replacement method for class 'linelist' names(x) <- value
x |
a |
value |
a |
a linelist with new column names
if (require(outbreaks)) { ## dataset to create a linelist from measles_hagelloch_1861 ## create linelist x <- make_linelist(measles_hagelloch_1861, id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) head(x) ## change names names(x)[1] <- "case_label" ## see results: tags have been updated head(x) tags(x) # This also works with using `dplyr::rename()` because it uses names<-() # under hood if (require(dplyr)) { x <- x %>% rename(case_id= case_label) head(x) tags(x) } }if (require(outbreaks)) { ## dataset to create a linelist from measles_hagelloch_1861 ## create linelist x <- make_linelist(measles_hagelloch_1861, id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) head(x) ## change names names(x)[1] <- "case_label" ## see results: tags have been updated head(x) tags(x) # This also works with using `dplyr::rename()` because it uses names<-() # under hood if (require(dplyr)) { x <- x %>% rename(case_id= case_label) head(x) tags(x) } }
This function prints linelist objects.
## S3 method for class 'linelist' print(x, ...)## S3 method for class 'linelist' print(x, ...)
x |
a |
... |
further arguments to be passed to 'print' |
Invisibly returns the object.
if (require(outbreaks)) { ## dataset we'll create a linelist from measles_hagelloch_1861 ## create linelist x <- make_linelist(measles_hagelloch_1861, id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) ## print object - using only the first few entries head(x) # version with a tibble if (require(tibble) && require(magrittr)) { measles_hagelloch_1861 %>% tibble() %>% make_linelist( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) } }if (require(outbreaks)) { ## dataset we'll create a linelist from measles_hagelloch_1861 ## create linelist x <- make_linelist(measles_hagelloch_1861, id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) ## print object - using only the first few entries head(x) # version with a tibble if (require(tibble) && require(magrittr)) { measles_hagelloch_1861 %>% tibble() %>% make_linelist( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) } }
![[Deprecated]](data:image/svg+xml;base64,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)
This function was equivalent to running successively tags_df() and
dplyr::select() on a linelist object.
To encourage users to understand what is going on and in order to follow the
software engineering good practice of providing just one way to do a given
task, this function is now deprecated.
select_tags(x, ...)select_tags(x, ...)
x |
a |
... |
the tagged variables to select, using |
A data.frame of tagged variables.
if (require(outbreaks)) { ## dataset we'll create a linelist from measles_hagelloch_1861 ## create linelist x <- make_linelist(measles_hagelloch_1861, id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) head(x) ## check tagged variables tags(x) # DEPRECATED! select_tags(x, "gender", "age") # Instead, use: library(dplyr) x %>% tags_df() %>% select(gender, age) }if (require(outbreaks)) { ## dataset we'll create a linelist from measles_hagelloch_1861 ## create linelist x <- make_linelist(measles_hagelloch_1861, id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) head(x) ## check tagged variables tags(x) # DEPRECATED! select_tags(x, "gender", "age") # Instead, use: library(dplyr) x %>% tags_df() %>% select(gender, age) }
![[Superseded]](data:image/svg+xml;base64,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)
This function was deprecated to ensure full compatibility with the default
dplyr::select() methods. The tag selection feature is now possible via the
has_tag() selection helper.
## S3 method for class 'linelist' select(.data, ..., tags)## S3 method for class 'linelist' select(.data, ..., tags)
.data |
a |
... |
the variables to select, using |
tags |
|
The function returns a linelist with selected columns.
tags_df() to return a data.frame of all tagged variables
This function changes the tags of a linelist object, using the same
syntax as the constructor make_linelist(). If some of the default tags are
missing, they will be added to the final object.
set_tags(x, ..., allow_extra = FALSE)set_tags(x, ..., allow_extra = FALSE)
x |
a |
... |
< |
allow_extra |
a |
The function returns a linelist object.
make_linelist() to create a linelist object
if (require(outbreaks)) { ## create a linelist x <- make_linelist(measles_hagelloch_1861, date_onset = "date_of_rash") tags(x) ## add new tags and fix an existing one x <- set_tags(x, age = "age", gender = "gender", date_onset = "date_of_prodrome" ) tags(x) ## add non-default tags using allow_extra x <- set_tags(x, severe = "complications", allow_extra = TRUE) tags(x) ## remove tags by setting them to NULL old_tags <- tags(x) x <- set_tags(x, age = NULL, gender = NULL) tags(x) ## setting tags providing a list (used to restore old tags here) x <- set_tags(x, !!!old_tags) tags(x) }if (require(outbreaks)) { ## create a linelist x <- make_linelist(measles_hagelloch_1861, date_onset = "date_of_rash") tags(x) ## add new tags and fix an existing one x <- set_tags(x, age = "age", gender = "gender", date_onset = "date_of_prodrome" ) tags(x) ## add non-default tags using allow_extra x <- set_tags(x, severe = "complications", allow_extra = TRUE) tags(x) ## remove tags by setting them to NULL old_tags <- tags(x) x <- set_tags(x, age = NULL, gender = NULL) tags(x) ## setting tags providing a list (used to restore old tags here) x <- set_tags(x, !!!old_tags) tags(x) }
This function returns the list of tags identifying specific variable types in
a linelist.
tags(x, show_null = FALSE)tags(x, show_null = FALSE)
x |
a |
show_null |
a |
Tags are stored as the tags attribute of the object.
The function returns a named list where names indicate generic
types of data, and values indicate which column they correspond to.
if (require(outbreaks)) { ## make a linelist x <- make_linelist(measles_hagelloch_1861, date_onset = "date_of_prodrome") ## check non-null tags tags(x) ## get a list of all tags, including NULL ones tags(x, TRUE) }if (require(outbreaks)) { ## make a linelist x <- make_linelist(measles_hagelloch_1861, date_onset = "date_of_prodrome") ## check non-null tags tags(x) ## get a list of all tags, including NULL ones tags(x, TRUE) }
This function returns a named list providing the default tags for a
linelist object (all default to NULL).
tags_defaults()tags_defaults()
A named list.
tags_defaults()tags_defaults()
This function returns a data.frame of all the tagged variables stored in a
linelist. Note that the output is no longer a linelist, but a regular
data.frame.
tags_df(x)tags_df(x)
x |
a |
A data.frame of tagged variables.
if (require(outbreaks) && require(magrittr)) { ## create a tibble linelist x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) x ## get a data.frame of all tagged variables tags_df(x) }if (require(outbreaks) && require(magrittr)) { ## create a tibble linelist x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) x ## get a data.frame of all tagged variables tags_df(x) }
This function returns the a character of all tag names used to designate
specific variable types in a linelist.
tags_names()tags_names()
The function returns a character vector.
tags_defaults() for a list of default values of the tags
tags_names()tags_names()
This function returns a named list providing the acceptable data types for the default tags. If no argument is provided, it returns default values. Otherwise, provided values will be used to define the defaults.
tags_types(..., allow_extra = FALSE)tags_types(..., allow_extra = FALSE)
... |
< |
allow_extra |
a |
A named list.
tags_defaults() for the default tags
validate_types() uses tags_types() for validating tags
validate_linelist() uses tags_types() for validating tags
# list default values tags_types() # change existing values tags_types(date_onset = "Date") # impose a Date class # add new types e.g. to allow genetic sequences using ape's format tags_types(sequence = "DNAbin", allow_extra = TRUE)# list default values tags_types() # change existing values tags_types(date_onset = "Date") # impose a Date class # add new types e.g. to allow genetic sequences using ape's format tags_types(sequence = "DNAbin", allow_extra = TRUE)
This function evaluates the validity of a linelist object by checking the
object class, its tags, and the types of the tagged variables. It combines
validations checks made by validate_types() and validate_tags(). See
'Details' section for more information on the checks performed.
validate_linelist(x, allow_extra = FALSE, ref_types = tags_types())validate_linelist(x, allow_extra = FALSE, ref_types = tags_types())
x |
a |
allow_extra |
a |
ref_types |
a |
The following checks are performed:
x is a linelist object
x has a well-formed tags attribute
all default tags are present (even if NULL)
all tagged variables correspond to existing columns
all tagged variables have an acceptable class
(optional) x has no extra tag beyond the default tags
If checks pass, a linelist object; otherwise issues an error.
tags_types() to change allowed types
validate_types() to check if tagged variables have the right classes
validate_tags() to perform a series of checks on the tags
if (require(outbreaks) && require(magrittr)) { ## create a valid linelist x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) x ## validation validate_linelist(x) ## create an invalid linelist - onset date is a factor x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", date_onset = "gender", age = "age" ) x ## the below issues an error ## note: tryCatch is only used to avoid a genuine error in the example tryCatch(validate_linelist(x), error = paste) }if (require(outbreaks) && require(magrittr)) { ## create a valid linelist x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) x ## validation validate_linelist(x) ## create an invalid linelist - onset date is a factor x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", date_onset = "gender", age = "age" ) x ## the below issues an error ## note: tryCatch is only used to avoid a genuine error in the example tryCatch(validate_linelist(x), error = paste) }
This function evaluates the validity of the tags of a linelist object by
checking that: i) tags are present ii) tags is a list of character iii)
that all default tags are present iv) tagged variables exist v) that no extra
tag exists (if allow_extra is FALSE).
validate_tags(x, allow_extra = FALSE)validate_tags(x, allow_extra = FALSE)
x |
a |
allow_extra |
a |
If checks pass, a linelist object; otherwise issues an error.
validate_types() to check if tagged variables have
the right classes
if (require(outbreaks) && require(magrittr)) { ## create a valid linelist x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) x ## validation validate_tags(x) ## hack to create an invalid tags (missing defaults) attr(x, "tags") <- list(id = "case_ID") ## the below issues an error ## note: tryCatch is only used to avoid a genuine error in the example tryCatch(validate_tags(x), error = paste) }if (require(outbreaks) && require(magrittr)) { ## create a valid linelist x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", date_onset = "date_of_prodrome", age = "age", gender = "gender" ) x ## validation validate_tags(x) ## hack to create an invalid tags (missing defaults) attr(x, "tags") <- list(id = "case_ID") ## the below issues an error ## note: tryCatch is only used to avoid a genuine error in the example tryCatch(validate_tags(x), error = paste) }
This function checks the class of each tagged variable in a linelist
against pre-defined accepted classes in tags_types().
validate_types(x, ref_types = tags_types())validate_types(x, ref_types = tags_types())
x |
a |
ref_types |
a |
A named list.
tags_types() to change allowed types
validate_tags() to perform a series of checks on the tags
validate_linelist() to combine validate_tags and validate_types
if (require(outbreaks) && require(magrittr)) { ## create an invalid linelist - gender is a numeric x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", gender = "infector" ) x ## the below would issue an error ## note: tryCatch is only used to avoid a genuine error in the example tryCatch(validate_types(x), error = paste) ## to allow other types, e.g. gender to be integer, character or factor validate_types(x, tags_types(gender = c("integer", "character", "factor"))) }if (require(outbreaks) && require(magrittr)) { ## create an invalid linelist - gender is a numeric x <- measles_hagelloch_1861 %>% make_linelist( id = "case_ID", gender = "infector" ) x ## the below would issue an error ## note: tryCatch is only used to avoid a genuine error in the example tryCatch(validate_types(x), error = paste) ## to allow other types, e.g. gender to be integer, character or factor validate_types(x, tags_types(gender = c("integer", "character", "factor"))) }