ShipsDataPackage

Edward Gillian 27/05/2021

---

The shipsdatapackage has a number of goals:

Firstly, this package uses shiny.semantic package from Appsilon to provide the ui interface.

Secondly, this package uses reactivity to get ship type and ship name input from the ui to display data about ship maximum distance and the start and end of ship movements.

Lastly, automated testing is done through chained test functions using testthat. These functions allow the developer to add different input files to test the functions stored in the R folder to be tested for reliable outputs. The functions use expect_known_value to generate the test outputs.

Installation

You can install the released version of shipsdatapackage with:

devtools::install_github("EdwardJGillian/shipsdatapackage")

Embedded Application

You can see the shipsdatapackage embedded in this document:

#> Loading required package: shiny
#> Warning: package 'shiny' was built under R version 4.0.5
#> Warning: package 'shiny.semantic' was built under R version 4.0.5
#> 
#> Attaching package: 'shiny.semantic'
#> The following objects are masked from 'package:shiny':
#> 
#>     actionButton, checkboxInput, dateInput, fileInput, flowLayout,
#>     icon, incProgress, modalDialog, numericInput, Progress,
#>     removeModal, removeNotification, selectInput, setProgress,
#>     showNotification, sliderInput, splitLayout, textAreaInput,
#>     textInput, updateActionButton, updateSelectInput,
#>     updateSliderInput, verticalLayout, withProgress
#> The following object is masked from 'package:graphics':
#> 
#>     grid
#> The following object is masked from 'package:utils':
#> 
#>     menu
#> Warning: package 'leaflet' was built under R version 4.0.5
#> Warning: package 'geosphere' was built under R version 4.0.5
#> 
#> Attaching package: 'geosphere'
#> The following object is masked from 'package:shiny':
#> 
#>     span
#> Warning: package 'dplyr' was built under R version 4.0.5
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
#> 
#> Listening on http://127.0.0.1:3230

Testing the package

As shown by the code below, a chained function using purrr::map is created to loop through a file list of example data to test the core functions to be tested for reliable outputs. This function creates a series of reference files automatically

library(shipsdatapackage)
library(testthat)

test_chained_functions <- function(csv_file) {
  test_that("check file values for parameters", {
    # naming helper
    tname <- function(n) {
      paste0(home,
             "/data/known_value/",
             csv,
             ".",
             n,
             ".test"
      )
    }

    # create file path to csv file examples

    csv_path <-
      paste0(home, "/data/csv_examples/", csv_file)
    csv <- stringr::str_remove(csv_file, ".csv")
    df1 <- readr::read_csv(file=csv_path, col_names=TRUE, col_types = readr::cols())
    parameter_list <- shipsdatapackage::general_data_preprocess(df1)

    # SuppressWarnings used as expect_known_value is a deprecated function
    suppressWarnings(testthat::expect_known_value(
      parameter_list, tname("param_list")))

    frame_with_next_values <- cbind(df1[parameter_list$ranks,], next_lat = parameter_list$next_lat, next_lon = parameter_list$next_lon)

    frame_without_na <- frame_with_next_values[0:(nrow(frame_with_next_values)-1),]

    # rename columns by index to ensure column names are different
    frame_without_na <- frame_without_na %>%
      dplyr::rename(next_lat = 21, next_lon = 22)

    calc_distance <- mapply(shipsdatapackage::calculate_distance, frame_without_na$LON, frame_without_na$LAT, frame_without_na$next_lon, frame_without_na$next_lat)

    # SuppressWarnings used as expect_known_value is a deprecated function
    suppressWarnings(testthat::expect_known_value(
      calc_distance, tname("calc_dist")))


  })
}

# create the ALS file path
home <- setwd(Sys.getenv("HOME"))

csv_file_path <- file.path(home, "data/csv_examples")

csv_files_list <- list.files(path = csv_file_path, pattern = "*.csv$", full.names = FALSE)

# apply 1 list vector to the function
purrr::map(csv_files_list, test_chained_functions)

Testthat results:

library(testthat)
#> Warning: package 'testthat' was built under R version 4.0.5
#> 
#> Attaching package: 'testthat'
#> The following object is masked from 'package:dplyr':
#> 
#>     matches
library(dplyr)
library(magrittr)
#> Warning: package 'magrittr' was built under R version 4.0.3
#> 
#> Attaching package: 'magrittr'
#> The following objects are masked from 'package:testthat':
#> 
#>     equals, is_less_than, not
library(shipsdatapackage)
test_results_raw <- testthat::test_file("tests/testthat/test-chained_function_known_value.R", reporter = testthat::ListReporter)

test_results_individual <- test_results_raw %>%
  as_tibble() %>%
  dplyr::rename(Test = test) %>%
  dplyr::group_by(file, context, Test) %>%
  dplyr::summarise(NumTests = first(nb),
            Passed   = sum(passed),
            Failed   = sum(failed),
            Warnings = sum(warning),
            Errors   = sum(as.numeric(error)),
            Skipped  = sum(as.numeric(skipped)),
            .groups = "drop")

summarise_results <- function(res) {
  res %>% dplyr::summarise_if(is.numeric, sum) %>% knitr::kable()
  }

summarise_results(test_results_individual)

NumTests	Passed	Failed	Warnings	Errors	Skipped
2	8	0	0	0	0

Running the package

You can run shipsdatapackage by opening global.R in shipsdatapackage/inst/shiny-examples/ships_app/

or type in the console: shipsdatapackage::run_ship_example()