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LandsatTS

An R package to facilitate retrieval, cleaning, cross-calibration, and phenological modeling of Landsat time-series data.
https://github.com/logan-berner/landsatts

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LandsatTS is an R package to facilitate retrieval, cleaning, cross-calibration, and phenological modeling of Landsat time-series data.

README

        

---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# LandsatTS

# LandsatTS: an R package to facilitate retrieval, cleaning, cross-calibration, and phenological modeling of Landsat time-series data

**Logan T. Berner, Jakob J. Assmann, Signe Normand and Scott Goetz**

The **LandsatTS** package helps you to:

- Export whole Landsat 5, 7, and 8 time series records based on point coordinates ("sites").
- Quality screen surface reflectance measurements from Landsat.
- Cross-calibrate surface reflectance measurements and vegetation indices among Landsat sensors.
- Quantify growing season characteristics using Landsat time series (e.g., annual maximum NDVI).

## Content
1. [Installation](#1-installation)
2. [Prepare sites and extract Landsat data](#2-prepare-sites-and-extract-Landsat-data)
3. [Clean and cross-calibrate Landsat data](#3-clean-and-cross-calibrate-Landsat-data)
4. [Quantify growing season characteristics](#4-quantify-growing-season-characteristics)
5. [Citation](#5-citation)
6. [Contact](#6-contact)
7. [Contributions](#7-contributions)
8. [References](#8-references)
9. [License](#9-license)
10. [Funding](#10-funding)

## 1. Installation

You can install the package using `devtools` as follows:

``` r
# install.packages("devtools")
devtools::install_github("logan-berner/LandsatTS", build_vignettes = TRUE)
```

For the preparation and extractions scripts you will also have to make sure you have the `rgee` package installed, fully configured and the Earth Engine initialized for the current R session. You can find out how to do that on the [rgee website](https://r-spatial.github.io/rgee/).

*Tip: All functions are designed to run in a non-interactive R Session. The only exception is `lsat_get_pixel_centers()`, which optionally allows the user to view and export a map. For this to work the function may have to be run in an interactive session in RStudio (not tested outside) and you may also have to install the external program PhantomJS. If so, you will be prompted to do so using `webshot::install_phantomjs()`. You can find out more [here](https://wch.github.io/webshot/articles/intro.html).*

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## 2. Prepare sites and extract Landsat data

Before you start you will have to determine whether you will extract data for point coordinates or for a polygon area. See flow chart below.

The time-series extraction from the Google Earth Engine with `lsat_export_ts()` will __*only*__ work for point coordinates. If you have a polygon you can use `lsat_get_pixel_centers()` to generate point coordinates based on all Landsat 8 pixel centers that fall within your polygon.

This section illustrates how to use the two functions. Please note that while the other sections below will always run well in a non-interactive session some of the optional functionality in this section may require R Studio. This includes for example generating the map views and using the access to the Google Drive via `rgee`.

![](man/figures/fig_1_prep_and_extraction.jpg)

**Setting up the environment**

Let's prepare the environment for the extractions:

``` {r eval = FALSE}
# Load packages for data handling etc.
library(sf)
library(dplyr)
library(purrr)
library(data.table)
library(stringr)
library(rgee)

# Load LandsatTS package
library(LandsatTS)

# Intialize the Earth Engine with rgee
ee_Initialize()

```
Note: If you have trouble initializing the Earth Engine, please consult the rgee website or forum. Some `LandsatTS` users have reported that they need to initialize by specifying their email address and using the `drive` option: `ee.Initialize(email = "myemail", drive = TRUE)`

**Getting pixel centers using lsat_get_pixel_centers()**

Next, we assume you have no point coordinates ready yet, but would like to extract the Landsat time-series for a polygon. So we start with `lsat_get_pixel_centers()`. This function is a convenience helper function that determines the Landsat 8 grid pixel centers within a polygon (adding an optional buffer). Below are two examples that show how it works.

**Important:** It is not advisable to determine pixel centers for very large polygons. See `?lsat_get_pixel_centers` for more on this.

*Tip: You can download the WRS2 scene boundaries kml file from USGS and specify it in the function call to avoid downloading it every time the function is called. See `?lsat_get_pixel_centers` for more info.*

**First**, for a single polygon:

``` {r eval = FALSE}
# Specify a region
test_poly <- st_polygon(
list(matrix(c(-138.90125, 69.58413,
-138.88988, 69.58358,
-138.89147, 69.58095,
-138.90298, 69.57986,
-138.90125, 69.58413),
ncol = 2, byrow = TRUE)))
test_poly_sf <- st_sfc(test_poly, crs = 4326) %>% st_sf()

# Use lsat_get_pixel_centers to retrieve pixel centers and plot to a file that can be added to this documentation.
# We set plot_map to a file path (or just TRUE) to view
pixel_list_test_poly <- lsat_get_pixel_centers(test_poly_sf, plot_map = "man/figures/lsat_get_pixel_centers.png")

```
Here is a capture of what you would see in the map view port of R Studio:

![](man/figures/lsat_get_pixel_centers.png)

**Second**, for multiple polygons:

``` {r eval = FALSE}

## Ge pixel centers for multiple regions
# Create multi-polygon sf
ellesmere <- st_polygon(list(matrix(c(-75.78526, 78.86973,
-75.78526, 78.87246,
-75.77116, 78.87246,
-75.77116, 78.86973,
-75.78526, 78.86973),
ncol = 2, byrow = TRUE)))
zackenberg <- st_polygon(list(matrix(c(-20.56254, 74.47469,
-20.56254, 74.47740,
-20.55242, 74.47740,
-20.55242, 74.47469,
-20.56254, 74.47469),
ncol = 2, byrow = TRUE)))
toolik <- st_polygon(list(matrix(c(-149.60686, 68.62364,
-149.60686, 68.62644,
-149.59918, 68.62644,
-149.59918, 68.62364,
-149.60686, 68.62364),
ncol = 2, byrow = TRUE)))
test_regions_sf <- st_sfc(ellesmere, zackenberg, toolik, crs = 4326) %>% st_sf() %>%
mutate(region = c("ellesmere", "zackenberg", "toolik"))

# Split and map lsat_get_pixel_centers using dplyr and purrr wihout plotting
pixel_list <- test_regions_sf %>%
split(.$region) %>%
map(lsat_get_pixel_centers,
pixel_prefix_from = "region") %>%
bind_rows()

# Let's look at the returned sf object:
pixel_list
```

**Exporting time-series from the Earth Engine using lsat_export_ts()**

Now that we have point coordinates ready we can use `lsat_export_ts()` to extract the Landsat time-series from the Earth Engine. See the code examples below for how this is done. For this tutorial we only use a small number of points to speed things up a bit.

The `lsat_export_ts()` function will accept any sf object that contains a point feature collection. It also requires one column with unique identifiers for each "site" (i.e. a pixel identifier) these can be specified with `site_id_from =`. If you have an attribute column called "site_id" such as that generated by `lsat_get_pixel_centers()` you will not have to specify anything extra.

`lsat_export_ts()` issues one or more tasks to the Earth Engine that export the data to your Google Drive. The default output folder is `/lsatTS_export/` you can change the output folder and file name using the relevant arguments (see `?lsat_export_ts`).

Importantly to note is that for larger data sets of points the time-series will have to be export in chunks. You can a) let the function chunk the data automatically (no arguments needed), b) set the chunk size (ue `max_chunk_size = `) or c) define the chunks based on a column in the dataset (use `chunks_from = `). Examples for all are shown below.

**Please note:** There is a reason we decided to export the data in small chunks. For the exports there are two important bottlenecks: 1) transfer of the point data to the Earth Engine and 2) export of time-series from the Earth Engine. The latter is particularly important. Larger chunks are prone to cause more errors and exceed the user limit set on exports by Google. It is safer and perhaps more efficient to issue smaller chunks and bind them back together later rather than exporting one big mass of time-series. We found that 250 points is a happy medium (at time of writing a chunck of that size took about 3h to export).

``` {r eval = FALSE}
# Generate test points
test_points_sf <- st_sfc(sf::st_point(c(-149.6026, 68.62574)),
sf::st_point(c(-149.6003, 68.62524)),
sf::st_point(c(-75.78057, 78.87038)),
sf::st_point(c(-75.77098, 78.87256)),
sf::st_point(c(-20.56182, 74.47670)),
sf::st_point(c(-20.55376, 74.47749)), crs = 4326) %>%
st_sf() %>%
mutate(sample_id = c("toolik_1",
"toolik_2",
"ellesmere_1",
"ellesmere_1",
"zackenberg_1",
"zackenberg_2"),
region = c("toolik", "toolik",
"ellesmere", "ellesmere",
"zackenberg", "zackenberg"))
# Export time-series using lsat_export_ts()
task_list <- lsat_export_ts(test_points_sf)

## Further examples:
# Export time-series using with a chunk size of 2
# task_list <- lsat_export_ts(test_points_sf, max_chunk_size = 2)

# Export time-series in chunks by column
# task_list <- lsat_export_ts(test_points_sf, chunks_from = "region")

```

The function returns the task objects generated by rgee for each chunk to be exported. You can monitor progress of the task using rgee's ee_monitoring() or the GEE WebAPI.

*Tip: Should the export of a chunk fail for some reason you can reissue the export task using the `this_chunk_only =` option. See below.*

``` {r eval = FALSE}
# re-export a chunk
# reexport_task <- lsat_export_ts(test_points_sf, chunks_from = "region", this_chunk_only = "yamal")
```

Once the tasks are completed, open your Google Drive and check the `/lsatTS_export/` folder (or the folder you specified) and retrieve the data to process it in Sections 3 and 4 below. For example, you could use the Google Drive Backup tool or rgee's `ee_drive_to_local()` [function](https://r-spatial.github.io/rgee/reference/ee_drive_to_local.html) to copy the data automatically to a local drive:

``` {r eval = FALSE}
# Monitor export progress, waiting for last export to have finished
map(task_list, ee_monitoring)

# Copy exported file(s) to tempfolder in R using ee_drive_to_local()
temp_files <- map(task_list, ee_drive_to_local)
```

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## 3. Clean and cross-calibrate Landsat data

![](man/figures/fig_2_cross_calibration.jpg)

**Prepare the exported Landsat data for analysis using lsat_format_data()**

After exporting Landsat data from Earth Engine, it is then necessary prepare the data for analysis. First, read the exported data into R using `data.table::fread()` and then use the `lsat_format_data()` function to parse necessary information, rename columns, and scale band values.

*Please note:* All LandsatTS functions depend on there being a column called "sample.id" that uniquely identifies each location. If this column is not called 'sample.id' in your dataset, then make sure to modify your column name accordingly.

``` {r eval = FALSE}
lsat.dt <- do.call("rbind", lapply(files_exported_from_EE, fread))

# setnames(lsat.dt, 'my_unique_location_column','sample.id')

lsat.dt <- lsat_format_data(lsat.dt)
```

**Clean the surface reflectance data using lsat_clean_data()**

For most analyses you'll want to use high-quality surface reflectance measurements that were acquired under clear-sky conditions. You can filter surface reflectance measurements using `lsat_clean_data()`. This function allows you to filter measurements based on pixel quality flags and scene criteria. The USGS provides pixel quality flags based on the CFMask algorithm and provides information on each scene (e.g., cloud cover). The default settings from `lsat_clean_data()` will filter out snow and water. Addition water masking is provided based on the maximum surface water extent variable from the JRC Global Surface Water Dataset that was derived from Landsat.

``` {r eval = FALSE}
lsat.dt <- lsat_clean_data(lsat.dt, geom.max = 15, cloud.max = 80, sza.max = 60, filter.cfmask.snow = T, filter.cfmask.water = T, filter.jrc.water = T)
```

**Optional: Compute average surface reflectance among neighboring pixels using lsat_neighborhood_mean()**

If each of your sites is actually a neightborhood of Landsat pixels (e.g., 3 x 3 pixels), then `lsat_neighborhood_mean()` will compute the mean reflectance across this neighborhood of pixels.

``` {r eval = FALSE}
lsat.dt <- lsat_neighborhood_mean(lsat.dt)
```

**Optional: Summarize the availability of Landsat data for each site using lsat_summarize_data()**

The function `lsat_summarize_data()` creates a summary table that provides information on the time period of observations and number of observations available for each site. It also generates a figure showing the density of observations across years, which combines data across all sites.

``` {r eval = FALSE}
data.summary.dt <- lsat_summarize_data(lsat.dt)
data.summary.dt
```

**Calculate spectral indices using lsat_calc_spectral_index()**

The function `lsat_calc_spectral_index()` allows users to easily calculate some widely used spectral indices. These include NDVI, EVI, and currently nine other spectral indices (EVI2, kNDVI, MSI, NBR, NIRv, NDII, NDWI, PSRI, SATVI). Note that only one index can be computed at a time.
``` {r eval = FALSE}
# Compute NDVI or other vegetation index
lsat.dt <- lsat_calc_spectral_index(lsat.dt, si = 'ndvi')
```

**Cross-calibrate spectral reflectance or index using lsat_calibrate_rf()**

There are systematic differences in surface reflectance and spectral indices among Landsat sensors. If you are working with data from multiple sensors, then it is very important to further cross-calibrate data among sensors. The function `lsat_calibrate_rf()` will calibrate individual bands or spectral indices from Landsat 5/8 to match Landsat 7. Landsat 7 is used as a benchmark because it temporally overlaps with the other two sensors. Cross-calibration can only be performed on one band or spectral index at a time and requires having data from 100s to preferably many 1,000s of sample sites. The approach involves determining the typical reflectance at a site during a portion of the growing season using Landsat 7 and Landsat 5/8 data that were collected the same years. A Random Forest model is then trained to predict Landsat 7 reflectance from Landsat 5/8 reflectance. If your data include both Landsat 5 and 8, then the function will train a Random Forest model for each sensor. Please note that for analyses focused on Arctic or boreal regions, there in an option to train the Random Forest models use an internal dataset of reflectance measurements from ~6,000 random sample sites. This is accomplished by setting train.with.highlat.data = T. By default, `lsat_calibrate_rf()` will add a new column with the cross-calibrated data ([band].xcal); however, the function will overwrite the existing column if you set the option overwrite.col = T (as used in the example below). The function will optionally also create an output directory that contains (1) trained Random Forest models, (2) a spreadsheet with model evaluation metrics, and (3) a multi-panel figure comparing sensors pre- and post-calibration.

*Note: If you use the default setting that adds a new column with the cross-calibrated data, then you'll either want to use those data in the subsequent functions (e.g., ndvi.xcal) or, once satisfied, manually overwrite the uncalibrated data to simplify subsuquent column names.*
``` {r eval = FALSE}
# Cross-calibrate NDVI among sensors using an approach based on Random Forest machine learning
lsat.dt <- lsat_calibrate_rf(lsat.dt,
band.or.si = 'ndvi',
doy.rng = 151:242,
min.obs = 5,
frac.train = 0.75,
overwrite.col = T,
write.output = F)

# If needed, then manually overwrite the uncalibrated data with the calibrated data, then drop the duplicate column
# lsat.dt <- lsat.dt[, ndvi := ndvi.xcal]
# lsat.dt <- lsat.dt[, ndvi.xcal := NULL)

```

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## 4. Quantify growing season characteristics

![](man/figures/fig_3_define_growing_season.jpg)

**Fit phenological curves to vegetation greenness time series using lsat_fit_phenological_curves()**

The function `lsat_fit_phenological_curves()` characterizes seasonal land surface phenology at each sampling site using vegetation greenness (e.g., NDVI) time series from Landsat satellite observations. The function was construted as a stepping stone to estimating annual maximum vegetation greenness (e.g., NDVImax). The function iteratively fits cubic splines to seasonal vegetation greenness time series and returns information about the timing and magnitude of individual vegetation greenness observation relative to a multi-year seasonal phenology at each site.

*Note: The function was designed for spectral indices that are typically positive (e.g., NDVI). If you are working with a spectral index that is typically negative (e.g., NDWI) then multiply your index by -1 before running the `lsat_fit_phenological_curves()` and `lsat_summarize_growing_seasons()` functions and backtransform afterwards.*

``` {r eval = FALSE}
# Fit phenological models (cubic splines) to each time series
lsat.pheno.dt <- lsat_fit_phenological_curves(lsat.dt, si = 'ndvi', window.yrs = 5, window.min.obs = 10, vi.min = 0, spl.fit.outfile = F, progress = T)
```

**Derived annual growing season metrics using lsat_summarize_growing_seasons()**

The function `lsat_summarize_growing_seasons()` estimates several annual growing season metrics from vegetation greenness time series derived from Landsat satellite observations. The metrics include annual mean, median, and 90th percentile vegetation greenness of observations during each growing season, as well as phenologically-modeled estimates of annual maximum vegetation greenness and the seasonal timing (Day of Year) of maximum vegetation greenness. This function relies on output from `lsat_fit_phenological_curves()`.

``` {r eval = FALSE}
lsat.gs.dt <- lsat_summarize_growing_seasons(lsat.pheno.dt, si = 'ndvi', min.frac.of.max = 0.75)
```

**Optional: Evaluate how raw and modeled estimates of annual max NDVI vary with scene availability using lsat_evaluate_phenological_max()**

Estimates of annual maximum vegetation greenness are sensitive to the number of observations available from a growing season. The function `lsat_evaluate_phenological_max()` is a tool for assessing how the number of annual Landsat observations impacts estimates of annual maximum vegetation greenness derived from raw observations and after phenological modeling. The algorithm computes a "true" annual maximum vegetation greenness using site x years with a user-specific number of observations and then compares these with estimates derived when using progressively smaller subsets of observations. This lets you determine the degree to which annual estimates of maximum vegetation greenness are impacted by the number of available observations.

``` {r eval = FALSE}
lsat.gs.eval.dt <- lsat_evaluate_phenological_max(lsat.pheno.dt, si = 'ndvi', min.obs = 10, reps = 5, min.frac.of.max = 0.75, outdir = NA)

```

**Compute trends in annual vegetation greenness using lsat_calc_trend()**

Th function `lsat_calc_trend()` computes a temporal trend in annual time series of vegetation greenness for each sampling site over a user-specificed time period. This is a wrapper for the zyp.yuepilon() function from the zyp package. This function will iteratively pre-whiten a time series (i.e., remove temporal autocorrelation) and then compute Mann-Kendall trend tests and Theil-Sen slope indicators.

``` {r eval = FALSE}
lsat.trnds.dt <- lsat_calc_trend(lsat.gs.dt, si = 'ndvi.max', 2000:2020, sig = 0.1)
```

[\[to top\]](#content)

## 5. Citation
When using this package please cite:

Berner, L.T., Assmann, J.J., Normand, S. and Goetz, S.J. 2023. LandsatTS: an R package to facilitate retrieval, cleaning, cross-calibration, and phenological modeling of Landsat time-series data. Ecography, e06768, http://doi.org/10.1111/ecog.06768.

[\[to top\]](#content)

## 6. Contact
Logan T. Berner and Jakob J. Assmann

Email Logan at: [[email protected]](mailto:[email protected])

Email Jakob at: [[email protected]](mailto:[email protected])

[\[to top\]](#content)

## 7. Contributions

Logan T. Berner wrote the analysis functions (Sections 3 and 4). Jakob J. Assmann facilitated package development and wrote the extraction and preparation functions (Section 2). Richard Massey wrote the original Python code for the `lsat_export_ts()` function, later refined and translated first to JavaScript and then rgee code by Jakob J. Assmann. Singe Normand and Scott Goetz provided funding and mentorship for this project. Logan T. Berner and Jakob J. Assmann prepared the code for publication and wrote the documentation.

Thank you to all the testers: Jeff Kerby, Adrianna Foster, Sarah Elmendorf, Russell Wong, and others!

[\[to top\]](#content)

## 8. References

**rgee**

Aybar C, Wu Q, Bautista L, Yali R and Barja A (2020) rgee: An R package for interacting with Google Earth Engine, Journal of Open Source Software, https://github.com/r-spatial/rgee/.


**Peer-reviewed publications that have used `LandsatTS` functions:**

***2022***

Berner, L.T., Goetz, S.J., 2022. Satellite observations document trends consistent with a boreal forest biome shift. Global Change Biology 28, 3275–3292.

Foster et al, 2022. Disturbances in North American boreal forest and Arctic tundra: impacts, interactions, and responses.
Environmental Research Letters 17, 113001.

***2021***

Boyd, M.A., Berner, L.T., Foster, A.C., Goetz, S.J., Rogers, B.M., Walker, X.J., Mack, M.C., 2021. Historic declines in growth portend trembling aspen death during a contemporary leaf miner outbreak in Alaska. Ecosphere 12, e03569.

Gaglioti, B., Berner, L.T., Jones, B.M., Orndahl, K.M., Williams, A.P., Andreu‐Hayles, L., D’Arrigo, R., Goetz, S.J., Mann, D.H., 2021. Tussocks enduring or shrubs greening: Alternate responses to changing fire regimes in the Noatak River Valley, Alaska. Journal of Geophysical Research: Biogeosciences 126, e2020JG006009.

Mekonnen, Z.A., Riley, W.J., Berner, L.T., Bouskill, N.J., Torn, M.S., Iwahana, G., Breen, A.L., Myers-Smith, I.H., Criado, M.G., Liu, Y., Euskirchen, E.S., Goetz, S.J., Mack, M.C., Grant, R.F., 2021. Arctic tundra shrubification: a review of mechanisms and impacts on ecosystem carbon balance. Environmental Research Letters 16, 053001.

Walker, X.J., Alexander, H.D., Berner, L.T., Boyd, M.A., Loranty, M.M., Natali, S.M., Mack, M.C., 2021. Positive response of tree productivity to warming is reversed by increased tree density at the Arctic tundra-taiga ecotone. Canadian Journal of Forest Research 51, 1323-1338.

***2020 and earlier***

Berner, L.T., Massey, R., Jantz, P., Forbes, B.C., Macias-Fauria, M., Myers-Smith, I.H., Kumpula, T., Gauthier, G., Andreu-Hayles, L., Gaglioti, B., Burns, P.J., Zetterberg, P., D'Arrigo, R., Goetz, S.J., 2020. Summer warming explains widespread but not uniform greening in the Arctic tundra biome. Nature Communications 11, 4621.

Boyd, M.A., Berner, L.T., Doak, P., Goetz, S.J., Rogers, B.M., Wagner, D., Walker, X.J., Mack, M.C., 2019. Impacts of climate and insect herbivory on productivity and physiology of trembling aspen (Populus tremuloides) in Alaskan boreal forests. Environmental Research Letters 14, 085010.

Verdonen, M., Berner, L.T., Forbes, B.C., Kumpula, T., 2020. Periglacial vegetation dynamics in Arctic Russia: decadal analysis of tundra regeneration on landslides with time series satellite imagery. Environmental Research Letters 15, 105020.

## 9. License

[MIT LICENSE](LICENSE)

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## 10. Funding
Software development was supported by the National Aeronautics and Space Administration (NASA) Arctic Boreal Vulnerability Experiment (Grant No. 80NSSC19M0112) and NASA New Investigator Program (Grant No. 80NSSC21K1364). Further support was provided by the National Science Foundation Navigating the New Arctic Big Idea (Grant No. 2127273), the Independent Research Fund of Denmark (Grant No. 7027-00133B), and the EU Horizon 2020 CHARTER project (Grant No. 869471).


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Dependencies

DESCRIPTION cran
  • R >= 3.50 depends
  • R.utils * imports
  • broom * imports
  • crayon * imports
  • data.table * imports
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  • geojsonio * imports
  • ggplot2 * imports
  • ggpubr * imports
  • magrittr * imports
  • mapview * imports
  • purrr * imports
  • ranger * imports
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  • sf * imports
  • stats * imports
  • stringr * imports
  • zoo * imports
  • zyp * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests

Score: 5.241747015059643