R/occs_history.R

In luismurao/nichetoolbox: From getting biodiversity data to evaluating species distribution models in a friendly GUI environment

#' Function to visualize GIBIF data using googleVis
#' @description Visualize history of GBIF records
#' @param data A data.frame with GBIF data
#' @return Returns a list with googleVis motin chart and a data.frame
#' @export

occs_history <- function(data){

  # Data atributes

  namesDB <- c("name","country","year","month","day")

  data <- data[,namesDB]
  s <-data %>% group_by(name,country,year) %>% summarise(count = n())
  dat_byY <- group_by(ungroup(s),name) %>% mutate(prop = count/sum(count))
  dat_byY <- dat_byY %>% mutate(year1=year)
  dat_byY <- ungroup(dat_byY)


  myStateSettings <-'{"xZoomedDataMin":1199145600000,"colorOption":"2",
  "duration":{"timeUnit":"Y","multiplier":1},"yLambda":1,
  "yAxisOption":"4","sizeOption":"_UNISIZE",
  "iconKeySettings":[],"xLambda":1,"nonSelectedAlpha":0,
  "xZoomedDataMax":1262304000000,"iconType":"LINE",
  "dimensions":{"iconDimensions":["dim0"]},
  "showTrails":false,"uniColorForNonSelected":false,
  "xAxisOption":"_TIME","orderedByX":false,"playDuration":25000,
  "xZoomedIn":false,"yZoomedDataMin":0,
  "yZoomedIn":false,"orderedByY":false,"yZoomedDataMax":100}
  '
  dat_byY <- dat_byY[ !duplicated(dat_byY[,c("country","year")]), ]

  mot <- gvisMotionChart(dat_byY, idvar="country", timevar="year",
                         xvar="year1", yvar="count",
                         sizevar="prop",
                         options=list(myStateSettings))



  return(list(mot=mot,data=data))
  }