clean_data.RdThis function loads and parses a mark recapture data set. It assumes that three files are available, specifying capture, survey, and (optional) translocation data.
clean_data( captures, surveys, translocations = NA, removals = NA, capture_formula = ~1, survival_formula = ~1, survival_fill_value = NA )
| captures | Data frame containing capture-recapture data. Necessary columns include `pit_tag_id` and `survey_date`. |
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| surveys | Data frame containing survey data. Necessary columns include `survey_date`, `primary_period`, and `secondary_period`. Secondary periods for which individuals are added or removed from a population should be set to zero, and must occur on their own primary period (because of the assumption that individuals cannot change states within primary periods). |
| translocations | Optional data frame with translocation data. Necessary columns include `pit_tag_id` and `release_date`. If nothing is provided to this argument, the `clean_data` function assumes that there are no translocations of individuals into the population. |
| removals | Optional data frame with removal data. Necessary columns include `pit_tag_id` and `removal_date`. If nothing provided, `clean_data` assumes there are no removals from the population. This can be used to account for individuals being pulled out of a population (e.g., for translocation), and for tagged indivuals whose carcasses are found. |
| capture_formula | An optional formula specifying the structure of survey-level capture probability covariates. Any variables in this formula must be columns in the `surveys` data frame. The formula must start with `~` and can be provided unquoted, e.g., `capture_formula = ~ temperature`. It is advisable to ensure that any continuous covariates provided in this formula are appropriately scaled (ideally, with mean = 0, and standard deviation = 1). |
| survival_formula | An optional formula specifying the structure of individual-level survival covariates. Any variables in this formula must be columns in the `captures` data.frame, and if there are translocations, these variables must also exist as columns in the `translocations` data.frame. The formula must start with `~` and can be provided unquoted. It is advisable to ensure that any continuous covariates provided in this formula are appropriately scaled (ideally, with mean = 0, and standard deviation = 1). Variables specified in this formula cannot be time-varying. They must be fixed for each individual over the entire study. |
| survival_fill_value | A fill value to use for individual-level covariates. This argument is only required when using the `survival_formula` argument`. |
A list containing the data frames resulting from the capture, translocation, and survey data, along with a list of data formatted for use in a mark recapture model (with name 'stan_d').