In iobis/obistools: Data Enhancement and Quality Control of Marine Species Observations

Map

tryCatch(obistools::plot_map(params$data, zoom = TRUE),
         error = function(e) e)

Issues

maxrows <- 25
qc <- obistools::report_summary(qc, maxrows = maxrows)
deps <- c()
firstOutliers <- TRUE
for (field in names(qc)) {

  if(startsWith(field, 'Outliers') & firstOutliers) {
    cat("\n\n")
    cat('<button style="margin:20px 0px 20px 0px" class="btn btn-primary" data-toggle="collapse" data-target="#outliers"> Show/Hide Outliers </button>')
    cat("\n\n## Outliers\n\n")

    #cat('<div id="outliers-div" class="collapse">')
    firstOutliers <- FALSE
  }
  cat("\n\n###", field, "\n\n")

  errors <- qc[[field]]
  if(nrow(errors) == maxrows) {
    cat(paste0("\n\nMore than **", maxrows, "** errors and warnings related to this field were found, the first **", maxrows, "** are printed below and shown on a map whenever possible.\n"))
  }
  print(knitr::kable(errors[errors$level != 'debug', c('field', 'row', 'level', 'message')], row.names = FALSE))

  mapdata <- data[stats::na.omit(errors$row),, drop=FALSE]

  if(NROW(mapdata) > 0) {
    mapplot <- NULL
    if(startsWith(field, 'Outliers ')) {
      outliers_info <- errors[errors$level == 'debug',]$extra[[1]]
      boxplots <- obistools:::plot_outliers_environmental(outliers_info)
      if(!is.null(boxplots)) {
          cat("\n\n")
          print(boxplots)
          cat("\n\n")
      }
      mapplot <- obistools:::plot_outliers_spatial(outliers_info)
      if(!is.null(mapplot)) {
        cat("\n\n")
        cat(htmltools::renderTags(mapplot)$html)
        deps <- c(deps, htmltools::renderTags(mapplot)$dependencies)
        cat("\n\n")
      }
    } else {
      try(mapplot <- obistools::plot_map(mapdata, zoom = TRUE))
      if(!is.null(mapplot)) {
        #print(paste0("plot_map ", field))
        cat("\n\n")
        print(mapplot)
        cat("\n\n")
      }
    }

  }
}

# attach the Dependencies
# since they do not get included with renderTags(...)$html
htmltools::attachDependencies(
  htmltools::tagList(),
  deps #unlist(deps,recursive=FALSE)
)

iobis/obistools documentation built on March 19, 2024, 6:27 a.m.