View source: R/contact_matrix.r

contact_matrix | R Documentation |

Samples a contact survey using a bootstrap

contact_matrix( survey, countries = c(), survey.pop, age.limits, filter, n = 1, bootstrap, counts = FALSE, symmetric = FALSE, split = FALSE, sample.participants = FALSE, estimated.participant.age = c("mean", "sample", "missing"), estimated.contact.age = c("mean", "sample", "missing"), missing.participant.age = c("remove", "keep"), missing.contact.age = c("remove", "sample", "keep", "ignore"), weights = c(), weigh.dayofweek = FALSE, weigh.age = FALSE, weight.threshold = NA, sample.all.age.groups = FALSE, return.part.weights = FALSE, return.demography = NA, per.capita = FALSE, ... )

`survey` |
a |

`countries` |
limit to one or more countries; if not given, will use all countries in the survey; these can be given as country names or 2-letter (ISO Alpha-2) country codes |

`survey.pop` |
survey population – either a data frame with columns 'lower.age.limit' and 'population', or a character vector giving the name(s) of a country or countries from the list that can be obtained via |

`age.limits` |
lower limits of the age groups over which to construct the matrix |

`filter` |
any filters to apply to the data, given as list of the form (column=filter_value) - only contacts that have 'filter_value' in 'column' will be considered. If multiple filters are given, they are all applied independently and in the sequence given. |

`n` |
deprecated; number of bootstrap samples to generate |

`bootstrap` |
deprecated; whether to bootstrap contact matrices |

`counts` |
whether to return counts (instead of means) |

`symmetric` |
whether to make matrix symmetric, such that c_ijN_i = cjiN_j. |

`split` |
whether to split the number of contacts and assortativity |

`sample.participants` |
whether to sample participants randomly (with replacement); done multiple times this can be used to assess uncertainty in the generated contact matrices. See the "Bootstrapping" section in the vignette for how to do this.. |

`estimated.participant.age` |
if set to "mean" (default), people whose ages are given as a range (in columns named "..._est_min" and "..._est_max") but not exactly (in a column named "..._exact") will have their age set to the mid-point of the range; if set to "sample", the age will be sampled from the range; if set to "missing", age ranges will be treated as missing |

`estimated.contact.age` |
if set to "mean" (default), contacts whose ages are given as a range (in columns named "..._est_min" and "..._est_max") but not exactly (in a column named "..._exact") will have their age set to the mid-point of the range; if set to "sample", the age will be sampled from the range; if set to "missing", age ranges will be treated as missing |

`missing.participant.age` |
if set to "remove" (default), participants without age information are removed; if set to "keep", participants with missing age are kept and treated as a separate age group |

`missing.contact.age` |
if set to "remove" (default), participants that have contacts without age information are removed; if set to "sample", contacts without age information are sampled from all the contacts of participants of the same age group; if set to "keep", contacts with missing age are kept and treated as a separate age group; if set to "ignore", contact with missing age are ignored in the contact analysis |

`weights` |
column names(s) of the participant data of the |

`weigh.dayofweek` |
whether to weigh social contacts data by the day of the week (weight (5/7 / N_week / N) for weekdays and (2/7 / N_weekend / N) for weekends) |

`weigh.age` |
whether to weigh social contacts data by the age of the participants (vs. the populations' age distribution) |

`weight.threshold` |
threshold value for the standardized weights before running an additional standardisation (default 'NA' = no cutoff) |

`sample.all.age.groups` |
what to do if bootstrapping fails to sample participants from one or more age groups; if FALSE (default), corresponding rows will be set to NA, if TRUE the sample will be discarded and a new one taken instead |

`return.part.weights` |
boolean to return the participant weights |

`return.demography` |
boolean to explicitly return demography data that corresponds to the survey data (default 'NA' = if demography data is requested by other function parameters) |

`per.capita` |
wheter to return a matrix with contact rates per capita (default is FALSE and not possible if 'counts=TRUE' or 'split=TRUE') |

`...` |
further arguments to pass to |

a contact matrix, and the underlying demography of the surveyed population

Sebastian Funk

data(polymod) contact_matrix(polymod, countries = "United Kingdom", age.limits = c(0, 1, 5, 15))

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