View source: R/plot_projINLA.R

plot.SUMMERproj | R Documentation |

Plot projection output.

## S3 method for class 'SUMMERproj' plot( x, year_label = c("85-89", "90-94", "95-99", "00-04", "05-09", "10-14", "15-19"), year_med = c(1987, 1992, 1997, 2002, 2007, 2012, 2017), is.subnational = TRUE, proj_year = 2015, data.add = NULL, option.add = list(point = NULL, lower = NULL, upper = NULL, by = NULL), color.add = "black", label.add = NULL, dodge.width = 1, plot.CI = NULL, per1000 = FALSE, color.CI = NULL, alpha.CI = 0.5, ... )

`x` |
output from |

`year_label` |
labels for the periods |

`year_med` |
labels for the middle years in each period, only used when both yearly and period estimates are plotted. In that case, |

`is.subnational` |
logical indicator of whether the data contains subnational estimates |

`proj_year` |
the first year where projections are made, i.e., where no data are available. |

`data.add` |
data frame for the Comparisons data points to add to the graph. This can be, for example, the raw direct estimates. This data frame is merged to the projections by column 'region' and 'years'. Except for these two columns, this dataset should not have Comparisons columns with names overlapping the getSmoothed output. |

`option.add` |
list of options specifying the variable names for the points to plot, lower and upper bounds, and the grouping variable. This is intended to be used to add Comparisons estimates on the same plot as the smoothed estimates. See examples for details. |

`color.add` |
the color of the Comparisons data points to plot. |

`label.add` |
the label of the Comparisons data points in the legend. |

`dodge.width` |
the amount to add to data points at the same year to avoid overlap. Default to be 1. |

`plot.CI` |
logical indicator of whether to plot the error bars. |

`per1000` |
logical indicator to plot mortality rates as rates per 1,000 live births. Note that the added comparison data should always be in the probability scale. |

`color.CI` |
the color of the error bars of the credible interval. |

`alpha.CI` |
the alpha (transparency) of the error bars of the credible interval. |

`...` |
optional arguments, see details |

Examples of some arguments:

`year_label`

string of year labels, e.g.,`c("85-89", "90-94", "95-99", "00-04", "05-09", "10-14", "15-19")`

or`c(1985:2019)`

`proj_year`

the year projection starts, e.g.,`2015`

`year_med`

median of year intervals, e.g.,`c(1987, 1992, 1997, 2002, 2007, 2012, 2017)`

Zehang Richard Li

`getSmoothed`

## Not run: years <- levels(DemoData[[1]]$time) # obtain direct estimates data <- getDirectList(births = DemoData, years = years, regionVar = "region", timeVar = "time", clusterVar = "~clustid+id", ageVar = "age", weightsVar = "weights", geo.recode = NULL) # obtain direct estimates data_multi <- getDirectList(births = DemoData, years = years, regionVar = "region", timeVar = "time", clusterVar = "~clustid+id", ageVar = "age", weightsVar = "weights", geo.recode = NULL) data <- aggregateSurvey(data_multi) # national model years.all <- c(years, "15-19") fit1 <- smoothDirect(data = data, geo = NULL, Amat = NULL, year_label = years.all, year_range = c(1985, 2019), rw = 2, is.yearly=FALSE, m = 5) out1 <- getSmoothed(fit1) plot(out1, is.subnational=FALSE) # subnational model fit2 <- smoothDirect(data = data, geo = geo, Amat = mat, year_label = years.all, year_range = c(1985, 2019), rw = 2, is.yearly=TRUE, m = 5, type.st = 4) out2 <- getSmoothed(fit2) plot(out2, is.yearly=TRUE, is.subnational=TRUE) ## End(Not run)

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