add_indicator_native_range_year function

[SanderDevisscher]

As suggested by @eadriaensen at issue #145 from reporting-rshiny-grofwildjacht I'll try to add the indicator_native_range_year function to the package.

• copy script from zip provided by @eadriaensen in comment 651739495
• test script in trias environment
• add relative/absolute variable

changes will be made in the add_indicator_native_range_year - branch

[SanderDevisscher]

@damianooldoni the function uses the data.table, plotly & inbotheme packages should I include these in the description file ?

[SanderDevisscher]

@eadriaensen were does the "yearToTitleString" - function originate from ? Did you make it for the app ? or is it part of a package ?

[eadriaensen]

Yes, this is made for the app:

#' Transform numeric vector with years ready to be in title
#' 
#' @param year numeric, vector of length 1 or 2
#' @param brackets logical, should the output string with years be wrapped in brackets? Defaults to TRUE 
#' @return string Numbers of the vector are separated by 'tot' in the string, 
#' brackets are put around (\code{brackets = TRUE}). If length of vector is only one, or if both elements
#' of the vector are the same, a string with the year between brackets is returned. 
#' 
#' @author Eva Adriaensen
#' @export
yearToTitleString <- function(year, brackets = TRUE) {
  
  if (!is.numeric(year) | any(is.na(year))) {
    stop("Argument is niet aanvaard.")
  }
  
	if (length(year) == 2) {
    ifelse(year[1] != year[2],
        if (brackets) paste0("(", year[1], " tot ", year[2], ")") else paste0(year[1], " tot ", year[2]),
        if (brackets) paste0("(", year[1], ")") else paste0(year[1])
    )
	} else if (length(year) == 1) {
    if (brackets) paste0("(", year[1], ")") else paste0(year[1]) 
	} else {
    stop("Kan periode niet formatteren.")
  }
}

It is part of the reporting-grofwild package

[SanderDevisscher]

How can I use it in the trias package ?

[eadriaensen]

One way would be to include it as an (exported) function of the trias package itself. I.e. just copy pasting the above function.
Alternatively, you could use it from the reporting-grofwild package, but this would mean that trias will always depend on reporting-grofwild, which is not an ideal situation.

The easiest solution would be to not include this function in trias and to exclude the concerning line from the piece of code that I shared. I.e. do not generate the plot with a title. It is kind of redundant since the years are on the x-axis anyway and the big chunks of text that serve as a title can be generated within shiny based on the data.

[eadriaensen]

So excluding this line

  title <- yearToTitleString(year = c(jaartallen[1], tail(jaartallen, 1)), brackets = FALSE)

and

removing title = title, from the layout specification of the plot:

  # Create plot
  pl <- plot_ly(data = summaryData, x = ~first_observed, y = ~value, color = ~locatie,
          colors = colors, type = "bar",  width = width, height = height) %>%
      layout(title = title,
          xaxis = list(title = "Jaar"), 
          yaxis = list(title = "Aantal", tickformat = ",d"),
          margin = list(b = 80, t = 100), 
          barmode = ifelse(nlevels(summaryData$first_observed) == 1, "group", "stack"),
          annotations = list(x = levels(summaryData$first_observed), 
              y = totalCount, 
              text = paste(ifelse(nlevels(summaryData$first_observed) == 1, "totaal:", ""), ifelse(totalCount > 0, totalCount, "")),
              xanchor = 'center', yanchor = 'bottom',
              showarrow = FALSE),
          showlegend = TRUE)  

[SanderDevisscher]

Thanks I'll remove the title portion of the graph as well as the colors as to not make trias dependant on INBOtheme

[SanderDevisscher]

@damianooldoni I think I finished the conversion. But I can't seem to find the "native_continent" value in the data. This is needed for testing on a higher level of geography.

[damianooldoni]

Hi @SanderDevisscher. I think the column you are searching for is called native_range.

[mvarewyck]

Could the function argument for data be changed from data to df for consistency with the other trias functions?
This will facilitate calling the trias functions in alien-species-portal

[Note: I don't have permission to do a PR]

[damianooldoni]

Thanks @mvarewyck! I am solving it just now. I noticed this strange behavior as well: #105. I will fix this as well. I had to pay more attention while reviewing the PR of Sander in 2020 😢