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Corrected functionality:
Updated earlier typo/change that made ukb_df incorrectly
convert all column types to character (caused by replacing
stringr::str_interp to stringr::str_c when
passing internal column type vector to data.table::fread,
without updating argument)
Bug fix:
Cleared bug in ukb_icd_freq_by for disease frequency
against a quantitative trait.
Made ukb_df column name from description regex
find/replace more general to capture all variations of “uses data
coding”
Updated functionality:
ukb_icd_keyword internal regex search
ignore.case defaults to TRUE, with and option
to set added to arguments.
Test data:
Added example UKB data ukbXXXX.tab, ukbXXXX.r, ukbXXXX.html to test
the ‘read’ and ‘summarise’ functionality ukb_df,
ukb_df_field, and ukb_context. See the section
“An example fileset” in the vignette for details.
Updated functionality:
ukb_icd_freq_by with freq.plot = TRUE plots
a barplot for categorical reference variables, and plots diagnosis
frequencies at the midpoint of each group for quantitative reference
variables.
Webpage:
The ukbtools webpage has been rebuilt with pkgdown and includes the vignette under the Articles tab.
Updated functionality:
ukb_df: Replaced readr::read_tsv with
data.table::fread for faster read. Also includes an
n_threads argument passed to
data.table::fread, which may make read faster. Column names
now include field code to ensure names are unique (UK Biobank sometimes
use the same description for more than one variable)Defunct functionality:
ukb_gen_meta,
ukb_gen_pcs, ukb_gen_excl,
ukb_gen_rel, ukb_gen_het,
ukb_gen_excl_to_na, and
ukb_gen_write_plink_excl. ukb_defunct explains
why these have become defunct and where to get UK Biobank genetic
(meta)data.New functionality:
ukb_gen_sqc_names supplies column names for the separately
downloaded sample QC file; ukb_gen_rel_count does the same
as before (a count of levels of relatedness or a plot) but with
separately downloaded relatedness data;
ukb_gen_related_with_data returns subset of relatedness
data in which both IDs have data on a phenotype of interest;
ukb_gen_samples_to_remove returns a list of individuals to
exclude in order to remove relatedness (one possible solution to a
maximal subset problem).Bug fix:
ukb_icd_freq_by: corrected order by levels of
reference.var in the optional plot. (order in the default
dataframe returned was correct.)
ukb_df: corrected tab file path update in r source
file. Specifically, made regular expression more specific (1 case
reported of regular expression matching word elsewhere in the source
file.). Also, replaced utils::read.delim with readr::read_tsv for faster
read, with progress bar.
New functionality:
ukb_icd_freq_by returns frequency for one or more
ICD diagnoses by levels of a reference variable and includes an optional
plot
ukb_df_full_join (a thin wrapper around
dplyr::full_join) recursively called on a list of UKB
datasets
ukb_df_duplicated_names to identify duplicated names
within a dataset. The variable prefix (constructed from its
description), index, and array should make the column name unique.
However, typos in UKB documentation that give two variables the do not
increment index/array have been observed. You will want to identify
these and update them appropriately. We expect the occurrence of such
duplicates will be rare.
Updated functionality:
ukb_icd_diagnosis now takes one or more individual
ids and returns a dataframe with a potential message noting ids with no
diagnoses
ukb_icd_keyword accepts a character vector of one or
more “keywords” and returns all ICD descriptions including any of the
keywords
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.