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The map appeared but the trajectories not. #83

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madpk opened this issue Dec 3, 2023 · 5 comments
Open

The map appeared but the trajectories not. #83

madpk opened this issue Dec 3, 2023 · 5 comments

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@madpk
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madpk commented Dec 3, 2023 •
edited

Screenshot 2023-12-03 152219 I run the following code to create a HYSPLIT backward model. However, the _trajectory_plot()_ function plots only the base map, not the trajectories.

#HYSPLIT Backtrajectory Analysis
library(splitr)
library(lubridate)

#library(devtools)
#install_github("rich-iannone/splitr")

#Prevent timing out
getOption('timeout')
options(timeout=10000)

#Build the model

trajectory_model <-hysplit_trajectory(
lat = 9.99645,
lon = 76.3427,
height = 30,
duration = 48,
met_type = "reanalysis",
direction = "backward",
days = seq(
lubridate::ymd("2023-01-01"),
lubridate::ymd("2023-01-10"),
by = "1 day"
),
daily_hours = c(8,16,24)
)

#Remove the missing values (NAs)

trajectory_model_complete <-trajectory_model[complete.cases(trajectory_model), ]

#Plot the trajectories

trajectory_plot(trajectory_model_complete)
@SGMStalin
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SGMStalin commented Mar 21, 2024 •
edited

The same problem.

I solved this by commenting on the following lines in the trajectory_plot() function

(...)

  dates <- traj_df %>% dplyr::pull(traj_dt_i) %>% unique()
  
  traj_plot <- leaflet::leaflet() %>% 
    leaflet::addProviderTiles(provider = "OpenStreetMap", 
                              group = "OpenStreetMap") %>% 
    leaflet::addProviderTiles(provider = "CartoDB.DarkMatter",
                              group = "CartoDB Dark Matter") %>%
    leaflet::addProviderTiles(provider = "CartoDB.Positron",
                              group = "CartoDB Positron") %>%
    leaflet::addProviderTiles(provider = "Esri.WorldTerrain",
                              group = "ESRI World Terrain") %>%
    # leaflet::addProviderTiles(provider = "Stamen.Toner",
    #                           group = "Stamen Toner") %>%
    leaflet::fitBounds(lng1 = min(traj_df[["lon"]]), 
                       lat1 = min(traj_df[["lat"]]), 
                       lng2 = max(traj_df[["lon"]]), 
                       lat2 = max(traj_df[["lat"]])) %>% 
    leaflet::addLayersControl(baseGroups = c("CartoDB Positron", 
                                             "CartoDB Dark Matter", "Stamen Toner", "ESRI World Terrain"), 
                              overlayGroups = c("trajectory_points", "trajectory_paths"), 
                              position = "topright")

(...)

For that, you need to extract the function, put the cursor on the function (i.e. trajectory_plot(trajectory_model_complete)) and press F2, or CTRL + left click. Copy the function and paste into a new script, assign a name to the function, comment the two lines mentioned above, run the function and prove it.

image

@Ettore91DE
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Hello everyone,

I am having the exact same issue here. Unfortunately, I am not sure I understood the solution that has been offered..

The same problem.

I solved this by commenting on the following lines in the trajectory_plot() function

(...)

  dates <- traj_df %>% dplyr::pull(traj_dt_i) %>% unique()
  
  traj_plot <- leaflet::leaflet() %>% 
    leaflet::addProviderTiles(provider = "OpenStreetMap", 
                              group = "OpenStreetMap") %>% 
    leaflet::addProviderTiles(provider = "CartoDB.DarkMatter",
                              group = "CartoDB Dark Matter") %>%
    leaflet::addProviderTiles(provider = "CartoDB.Positron",
                              group = "CartoDB Positron") %>%
    leaflet::addProviderTiles(provider = "Esri.WorldTerrain",
                              group = "ESRI World Terrain") %>%
    # leaflet::addProviderTiles(provider = "Stamen.Toner",
    #                           group = "Stamen Toner") %>%
    leaflet::fitBounds(lng1 = min(traj_df[["lon"]]), 
                       lat1 = min(traj_df[["lat"]]), 
                       lng2 = max(traj_df[["lon"]]), 
                       lat2 = max(traj_df[["lat"]])) %>% 
    leaflet::addLayersControl(baseGroups = c("CartoDB Positron", 
                                             "CartoDB Dark Matter", "Stamen Toner", "ESRI World Terrain"), 
                              overlayGroups = c("trajectory_points", "trajectory_paths"), 
                              position = "topright")

(...)

For that, you need to extract the function, put the cursor on the function (i.e. trajectory_plot(trajectory_model_complete)) and press F2, or CTRL + left click. Copy the function and paste into a new script, assign a name to the function, comment the two lines mentioned above, run the function and prove it.

image

@SGMStalin
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Can you provide us with more information about what you've done?

@Ettore91DE
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Sure, so I first crated a trajectory model using the hysplit_trajectory function:

`trajectory_model_march2019 <- hysplit_trajectory(
lat=51.36588,
lon=12.31009,
duration=168,
height = c(3,15,28,50),
met_type="gdas1",
days=seq(
lubridate::ymd("2019-03-27"),
lubridate::ymd("2019-04-02"),
by="1 day"),
direction="backward",
daily_hours=12)

trajectory_model_complete_march2019 <- trajectory_model_march2019[complete.cases(trajectory_model_march2019),]
`

then I created a new trajectory plot function:
`trajectory_plot_new <- function(x,
show_hourly = TRUE,
color_scheme = "cycle_hues") {

if (inherits(x, "trajectory_model")) {
if (!is.null(x$traj_df)) {
traj_df <- x$traj_df
} else {
stop("There is no data available for plotting.")
}
}

if (inherits(x, "data.frame")) {
if (all(c("run", "receptor", "hour_along", "traj_dt",
"lat", "lon", "height", "traj_dt_i") %in% colnames(x))) {
traj_df <- x
} else {
stop("This tibble does not contain plottable trajectory data.")
}
}

dt_runs <- traj_df$traj_dt_i %>% unique() %>% length()

if (color_scheme == "cycle_hues") {
colors <- scales::hue_pal(c = 90, l = 70)(dt_runs)
} else if (color_scheme == "increasingly_gray") {
colors <- scales::grey_pal(0.7, 0.1)(dt_runs)
}

Correct longitude values near prime meridian

traj_df$lon[which(traj_df$lon > 0)] <-
traj_df$lon[which(traj_df$lon > 0)] - (180*2)

receptors <-
traj_df %>%
dplyr::pull(receptor) %>%
unique()

dates <-
traj_df %>%
dplyr::pull(traj_dt_i) %>%
unique()

traj_plot <-
leaflet::leaflet() %>%
leaflet::addProviderTiles(
provider = "OpenStreetMap",
group = "OpenStreetMap"
) %>%
leaflet::addProviderTiles(
provider = "CartoDB.DarkMatter",
group = "CartoDB Dark Matter"
) %>%
leaflet::addProviderTiles(
provider = "CartoDB.Positron",
group = "CartoDB Positron"
) %>%
leaflet::addProviderTiles(
provider = "Esri.WorldTerrain",
group = "ESRI World Terrain"
) %>%

leaflet::fitBounds(
  lng1 = min(traj_df[["lon"]]),
  lat1 = min(traj_df[["lat"]]),
  lng2 = max(traj_df[["lon"]]),
  lat2 = max(traj_df[["lat"]])
) %>%
leaflet::addLayersControl(
  baseGroups = c(
    "CartoDB Positron", "CartoDB Dark Matter",
   "ESRI World Terrain"
  ),
  overlayGroups = c("trajectory_points", "trajectory_paths"),
  position = "topright"
)

Get different trajectories by receptor and by date

for (i in seq_along(receptors)) {

receptor_i <- receptors[i]

for (j in seq_along(dates)) {
  
  date_i <- dates[j]
  
  wind_traj_ij <-
    traj_df %>%
    dplyr::filter(
      receptor == receptor_i,
      traj_dt_i == date_i
    )
  
  popup <- 
    paste0(
      "<strong>trajectory</strong> ", wind_traj_ij[["traj_dt_i"]],
      "<br><strong>at time</strong> ", wind_traj_ij[["traj_dt"]],
      " (", wind_traj_ij[["hour_along"]],
      " h)<br><strong>height</strong> ", wind_traj_ij[["height"]],
      " <font size=\"1\">m AGL</font> / ",
      "<strong>P</strong> ", wind_traj_ij[["pressure"]],
      " <font size=\"1\">hPa</font>"
    )
  
  traj_plot <-
    traj_plot %>%
    leaflet::addPolylines(
      lng = wind_traj_ij[["lon"]],
      lat = wind_traj_ij[["lat"]],
      group = "trajectory_paths",
      weight = 2,
      smoothFactor = 1,
      color = colors[j]
    ) %>%
    leaflet::addCircles(
      lng = wind_traj_ij[["lon"]],
      lat = wind_traj_ij[["lat"]],
      group = "trajectory_points",
      radius = 250,
      fill = TRUE,
      color = colors[j],
      fillColor = colors[j], 
      popup = popup
    )
}

}

traj_plot
}
`

and plotted it:
trajectory_plot_new(trajectory_model_complete_march2019)

This way I manage to get the trajectories but these are now split:
Trajectories

is there something in my script that is causing the trajectories to split in the plot?

Thank you very much for your help!

@madpk
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madpk commented May 27, 2024 via email

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3 participants
@SGMStalin @madpk @Ettore91DE