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Export R Objects to Several Markup Languages
Coerce R object to 'asciidoc', 'txt2tags', 'restructuredText', 'org', 'textile' or 'pandoc' syntax. Package comes with a set of drivers for 'Sweave'.
Helper Functions for Rmd Documents
A series of functions to aid in repeated tasks for Rmd documents. All details are to my personal preference, though I am happy to add flexibility if there are use cases I am missing. I will continue updating with new functions as I add utility functions for myself.
Calculate the Dutch Air Quality Index (LKI)
Calculates the dutch air quality index (LKI). This index was created on the basis of scientific studies of the health effects of air pollution. From these studies it can be deduced at what concentrations a certain percentage of the population can be affected. For more information see: < https://www.rivm.nl/bibliotheek/rapporten/2014-0050.pdf>.
Separate Metabolites into Likely Measurement Artifacts and True Metabolites
Split an untargeted metabolomics data set into a set of likely true metabolites and a set of likely measurement artifacts. This process involves comparing missing rates of pooled plasma samples and biological samples. The functions assume a fixed injection order of samples where biological samples are randomized and processed between intermittent pooled plasma samples. By comparing patterns of missing data across injection order, metabolites that appear in blocks and are likely artifacts can be separated from metabolites that seem to have random dispersion of missing data. The two main metrics used are: 1. the number of consecutive blocks of samples with present data and 2. the correlation of missing rates between biological samples and flanking pooled plasma samples.
Data Correction and Imputation Using Deductive Methods
Attempt to repair inconsistencies and missing values in data records by using information from valid values and validation rules restricting the data.
Print Maps, Draw on Them, Scan Them Back in
Enables preparation of maps to be printed and drawn on. Modified maps can then be scanned back in, and hand-drawn marks converted to spatial objects.
Data Validation Infrastructure
Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. Supports checks implied
by an SDMX DSD file as well. See also Van der Loo
and De Jonge (2018)
Modify Data Using Externally Defined Modification Rules
Data cleaning scripts typically contain a lot of 'if this change that' type of statements. Such statements are typically condensed expert knowledge. With this package, such 'data modifying rules' are taken out of the code and become in stead parameters to the work flow. This allows one to maintain, document, and reason about data modification rules as separate entities.
Smoothing tools
Tools rewritten in C for various smoothing tasks
Estimate Aerosol Particle Collection Through Sample Lines
Estimate ideal efficiencies of aerosol sampling through sample
lines. Functions were developed consistent with the approach described in
Hogue, Mark; Thompson, Martha; Farfan, Eduardo; Hadlock, Dennis, (2014),
"Hand Calculations for Transport of Radioactive Aerosols through Sampling
Systems" Health Phys 106, 5, S78-S87,