R: Fill out data for time series (state-space) gjam

gjamFillMissingTimes {gjam}

R Documentation

Fill out data for time series (state-space) gjam

Description

Fills in predictor, response, and effort matrics for time series data where there are multiple multivariate time series. Time series gjam is here https://htmlpreview.github.io/?https://github.com/jimclarkatduke/gjam/blob/master/gjamTimeMsVignette.html

Usage

  gjamFillMissingTimes(xdata, ydata, edata, groupCol, timeCol, groupVars = groupCol,
                                 FILLMEANS = FALSE, typeNames = NULL, missingEffort = .1)

Arguments

`xdata`	`n by Q data.frame` holding predictor variables
`ydata`	`n by S matrix` holding response variables
`edata`	`n by S matrix` holding effort
`groupCol`	column name in `xdata` for group variable, i.e., observations part of the same time series
`timeCol`	column name in `xdata` for time index
`groupVars`	`character vector` of column names in `xdata` having values that are fixed for a value of `groupCol`, i.e., they do not change with time index in `timeCol`
`FILLMEANS`	fill new rows in `ydata` with mean for `groupCol` times `missingEffort`; otherwise NA
`typeNames`	typenames current limited to `'DA'` for discrete counts
`missingEffort`	effort assigned to missing values of `edata` and `ydata`

Details

Missing times in the data occur where there are gaps in timeCol column of xdata and the initial time 0 for each sequence. New versions of the data have NA (xdata) or prior values with appropriate weight (ydata). Missing times are filled in xdata, ydata, edata, including a time 0 which serves as a prior mean for ydata for time code1. The group and time indices in columns groupCol and timeCol of xdata reference the time for a given time series. Missing values in the columns groupVars of xdata are filled automatically filled in. This assumes that values for these variables are fixed for the group. If FILLMEANS, the missing values in ydata are filled with means for the group and given a low weight specified in missingEffort.

Value

A list containing the following:

`xdata`	filled version of `xdata`
`ydata`	filled version of `ydata`
`edata`	filled version of `edata`
`timeList`	time indices used for computation, including, `timeZero` (row numbers in new data where each time series begins, with times = 0), `timeLast` (row numbers in new data where each time series ends), `rowInserts` (row numbers for all inserted rows), `noEffort` (rows for which effort in `edata` is filled with `missingEffort`)

Author(s)

James S Clark, jimclark@duke.edu

References

Clark, J. S., C. L. Scher, and M. Swift. 2020. The emergent interactions that govern biodiversity change. Proceedings of the National Academy of Sciences, 117, 17074-17083.