chore: restore order

main.Rmd

@@ -0,0 +1,159 @@
+---
+title: "Topic 8"
+output:
+  pdf_document: default
+  html_document: default
+date: "`r Sys.Date()`"
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+# Load Library
+```{r preamble, echo=FALSE}
+library(dplyr)
+library(lubridate)
+library(readr)
+library(utils)
+library(openSkies)
+library(dotenv)
+library(httr)
+library(jsonlite)
+```
+# Download flights 
+```{r include=FALSE}
+#
+#time_now <- Sys.time()
+#time_one_hour_ago <- time_now - 3600
+#
+## get departures from frankfurt airport
+#flights <- getAirportDepartures(airport = "EDDF", startTime = time_one_hour_ago, endTime = time_now)
+#
+#print(paste("Found flights:", length(flights)))
+#head(flights)
+```
+
+
+```{r openskies, include=FALSE}
+load_dot_env()
+my_client_id     <- Sys.getenv("OPENSKY_CLIENT_ID")
+my_client_secret <- Sys.getenv("OPENSKY_CLIENT_SECRET")
+
+token_url <- "https://auth.opensky-network.org/auth/realms/opensky-network/protocol/openid-connect/token"
+
+token_resp <- POST(
+  token_url,
+  body = list(
+    grant_type = "client_credentials",
+    client_id = my_client_id,
+    client_secret = my_client_secret
+  ),
+  encode = "form"
+)
+
+if (status_code(token_resp) == 200) {
+  my_token <- content(token_resp)$access_token
+  message("Token successfully generated")
+} else {
+  stop(paste("Error while collecting token:", content(token_resp, as = "text")))
+}
+
+time_now <- as.numeric(Sys.time())
+time_one_hour_ago <- time_now - 3600
+
+api_url <- paste0("https://opensky-network.org/api/flights/departure?airport=EDDF&begin=", 
+                  round(time_one_hour_ago), "&end=", round(time_now))
+
+data_resp <- GET(
+  api_url, 
+  add_headers(Authorization = paste("Bearer", my_token))
+)
+
+if (status_code(data_resp) == 200) {
+  departures_df <- fromJSON(content(data_resp, as = "text", encoding = "UTF-8"))
+  print(head(departures_df))
+} else {
+  print(paste("API Error:", status_code(data_resp)))
+  print(content(data_resp, as = "text"))
+}
+
+```
+
+```{r last5}
+
+icao24 <- "4bcdf9"
+
+time_now <- as.numeric(Sys.time())
+time_then <- time_now - (1 * 24 * 60 * 60) 
+
+api_url_aircraft <- paste0("https://opensky-network.org/api/flights/aircraft?icao24=", 
+                           icao24, "&begin=", round(time_then), "&end=", round(time_now))
+
+aircraft_resp <- GET(
+  api_url_aircraft, 
+  add_headers(Authorization = paste("Bearer", my_token))
+)
+
+if (status_code(aircraft_resp) == 200) {
+  all_flights <- fromJSON(content(aircraft_resp, as = "text", encoding = "UTF-8"))
+  
+  if (length(all_flights) > 0) {
+    all_flights <- all_flights[order(all_flights$firstSeen, decreasing = TRUE), ]
+    
+    last_5_flights <- head(all_flights, 5)
+    
+    last_5_flights$firstSeen <- as.POSIXct(last_5_flights$firstSeen, origin="1970-01-01")
+    last_5_flights$lastSeen <- as.POSIXct(last_5_flights$lastSeen, origin="1970-01-01")
+    
+    print(last_5_flights[, c("icao24", "firstSeen", "estDepartureAirport", "estArrivalAirport")])
+  } else {
+    print("No flights in this timespan for this airplane")
+  }
+} else {
+  print(paste("Error:", status_code(aircraft_resp)))
+}
+```
+
+# Plot the flights 
+
+```{r route}
+target_icao <- all_flights$icao24[1]
+
+target_time <- as.numeric(all_flights$firstSeen[1]) 
+
+api_url_track <- paste0("https://opensky-network.org/api/tracks/all?icao24=", 
+                        target_icao, "&time=", target_time)
+
+track_resp <- GET(
+  api_url_track, 
+  add_headers(Authorization = paste("Bearer", my_token))
+)
+
+if (status_code(track_resp) == 200) {
+  track_data <- fromJSON(content(track_resp, as = "text", encoding = "UTF-8"))
+  
+  if (!is.null(track_data$path) && length(track_data$path) > 0) {
+    
+    route_df <- as.data.frame(track_data$path)
+    colnames(route_df) <- c("time", "lat", "lon", "alt", "heading", "on_ground")
+    
+    message("Loading of route successfull! Points: ", nrow(route_df))
+    
+    plot(route_df$lon, route_df$lat, type="o", pch=20, col="blue", 
+         main=paste("Geographic route from", target_icao),
+         xlab="Longitude", ylab="Latitude")
+    
+    plot(route_df$time, route_df$alt, type="l", col="red", lwd=2,
+         main=paste("Altitude profile of", target_icao),
+         xlab="Time (Unix)", ylab="Height (Meter)")
+    
+  } else {
+    print("No path points from api")
+  }
+  
+} else {
+  print(paste("Error while getting the route. Status:", status_code(track_resp)))
+  print(content(track_resp, as = "text"))
+}
+```

renv.lock

@@ -58,42 +58,6 @@
       "Maintainer": "Kirill Müller <kirill@cynkra.com>",
       "Repository": "https://packagemanager.posit.co/cran/latest"
     },
-    "MASS": {
-      "Package": "MASS",
-      "Version": "7.3-65",
-      "Source": "Repository",
-      "Priority": "recommended",
-      "Date": "2025-02-19",
-      "Revision": "$Rev: 3681 $",
-      "Depends": [
-        "R (>= 4.4.0)",
-        "grDevices",
-        "graphics",
-        "stats",
-        "utils"
-      ],
-      "Imports": [
-        "methods"
-      ],
-      "Suggests": [
-        "lattice",
-        "nlme",
-        "nnet",
-        "survival"
-      ],
-      "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Brian.Ripley@R-project.org\"), person(\"Bill\", \"Venables\", role = c(\"aut\", \"cph\")), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\", comment = \"support functions for polr\"))",
-      "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).",
-      "Title": "Support Functions and Datasets for Venables and Ripley's MASS",
-      "LazyData": "yes",
-      "ByteCompile": "yes",
-      "License": "GPL-2 | GPL-3",
-      "URL": "http://www.stats.ox.ac.uk/pub/MASS4/",
-      "Contact": "<MASS@stats.ox.ac.uk>",
-      "NeedsCompilation": "yes",
-      "Author": "Brian Ripley [aut, cre, cph], Bill Venables [aut, cph], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb] (support functions for polr)",
-      "Maintainer": "Brian Ripley <Brian.Ripley@R-project.org>",
-      "Repository": "CRAN"
-    },
     "R6": {
       "Package": "R6",
       "Version": "2.6.1",
@@ -1933,13 +1897,12 @@
     },
     "openSkies": {
       "Package": "openSkies",
-      "Version": "1.2.1",
+      "Version": "1.2.2",
-      "Source": "GitHub",
+      "Source": "Repository",
       "Type": "Package",
       "Title": "Retrieval, Analysis and Visualization of Air Traffic Data",
-      "Date": "2024-04-03",
+      "Date": "2025-08-20",
-      "Author": "Rafael Ayala, Daniel Ayala, David Ruiz, Aleix Sellés, Lara Sellés Vidal",
+      "Authors@R": "c( person(\"Rafael\", \"Ayala\", email = \"rafaelayalahernandez@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9332-4623\")), person(\"Daniel\", \"Ayala\", email = \"dayala1@us.es\", role = \"aut\", comment = c(ORCID = \"0000-0003-2095-1009\")), person(\"David\", \"Ruiz\", email = \"druiz@us.es\", role = \"aut\", comment = c(ORCID = \"0000-0003-4460-5493\")), person(\"Aleix\", \"Sellés\", role = \"aut\"), person(\"Lara\", \"Selles Vidal\", email = \"lara.selles@oist.jp\", role = \"aut\", comment = c(ORCID = \"0000-0003-2537-6824\")))",
-      "Maintainer": "Rafael Ayala <rafael.ayala@oist.jp>",
       "Description": "Provides functionalities and data structures to retrieve, analyze and visualize aviation  data. It includes a client interface to the 'OpenSky' API <https://opensky-network.org>. It allows  retrieval of flight information, as well as aircraft state vectors.",
       "Acknowledgements": "The development of this software is supported by the Spanish Ministry of Science and Innovation (grant code PID2019-105471RB-I00) and the Regional Government of Andalusia (grant code P18-RT-1060).",
       "License": "CC BY-NC 4.0",
@@ -1965,7 +1928,6 @@
         "knitr",
         "BiocStyle",
         "RUnit",
-        "BiocGenerics",
         "rmarkdown",
         "markdown"
       ],
@@ -1973,13 +1935,9 @@
       "BugReports": "https://github.com/Rafael-Ayala/openSkies/issues",
       "NeedsCompilation": "no",
       "Encoding": "UTF-8",
-      "Repository": "CRAN",
+      "Repository": "https://packagemanager.posit.co/cran/latest",
-      "RemoteType": "github",
+      "Author": "Rafael Ayala [aut, cre] (ORCID: <https://orcid.org/0000-0002-9332-4623>), Daniel Ayala [aut] (ORCID: <https://orcid.org/0000-0003-2095-1009>), David Ruiz [aut] (ORCID: <https://orcid.org/0000-0003-4460-5493>), Aleix Sellés [aut], Lara Selles Vidal [aut] (ORCID: <https://orcid.org/0000-0003-2537-6824>)",
-      "RemoteHost": "api.github.com",
+      "Maintainer": "Rafael Ayala <rafaelayalahernandez@gmail.com>"
-      "RemoteUsername": "eneller",
-      "RemoteRepo": "openSkies",
-      "RemoteRef": "main",
-      "RemoteSha": "ea794da413c3c2ef86f7ca73306e5da50682cd79"
     },
     "openssl": {
       "Package": "openssl",
@@ -2095,30 +2053,6 @@
       "NeedsCompilation": "no",
       "Repository": "https://packagemanager.posit.co/cran/latest"
     },
-    "plotrix": {
-      "Package": "plotrix",
-      "Version": "3.8-13",
-      "Source": "Repository",
-      "Title": "Various Plotting Functions",
-      "Authors@R": "c( person(\"Jim\", \"Lemon\", role = \"aut\"), person(\"Ben\", \"Bolker\", role = \"ctb\"), person(\"Sander\", \"Oom\", role = \"ctb\"), person(\"Eduardo\", \"Klein\", role = \"ctb\"), person(\"Barry\", \"Rowlingson\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Anupam\", \"Tyagi\", role = \"ctb\"), person(\"Olivier\", \"Eterradossi\", role = \"ctb\"), person(\"Gabor\", \"Grothendieck\", role = \"ctb\"), person(\"Michael\", \"Toews\", role = \"ctb\"), person(\"John\", \"Kane\", role = \"ctb\"), person(\"Rolf\", \"Turner\", role = \"ctb\"), person(\"Carl\", \"Witthoft\", role = \"ctb\"), person(\"Julian\", \"Stander\", role = \"ctb\"), person(\"Thomas\", \"Petzoldt\", role = \"ctb\"), person(\"Remko\", \"Duursma\", role = \"ctb\"), person(\"Elisa\", \"Biancotto\", role = \"ctb\"), person(\"Ofir\", \"Levy\", role = \"ctb\"), person(\"Christophe\", \"Dutang\", role = \"ctb\"), person(\"Peter\", \"Solymos\", role = \"ctb\"), person(\"Robby\", \"Engelmann\", role = \"ctb\"), person(\"Michael\", \"Hecker\", role = \"ctb\"), person(\"Felix\", \"Steinbeck\", role = \"ctb\"), person(\"Hans\", \"Borchers\", role = \"ctb\"), person(\"Henrik\", \"Singmann\", role = \"ctb\"), person(\"Ted\", \"Toal\", role = \"ctb\"), person(\"Derek\", \"Ogle\", role = \"ctb\"), person(\"Darshan\", \"Baral\", role = \"ctb\"), person(\"Ulrike\", \"Groemping\", role = \"ctb\"), person(\"Bill\", \"Venables\", role = \"ctb\"), person(family = \"The CRAN Team\", role = \"ctb\"), person(\"Duncan\", \"Murdoch\", email = \"murdoch.duncan@gmail.com\", role = c(\"ctb\", \"cre\")))",
-      "Imports": [
-        "grDevices",
-        "graphics",
-        "stats",
-        "utils"
-      ],
-      "Description": "Lots of plots, various labeling, axis and color scaling functions. The author/maintainer died in September 2023.",
-      "License": "GPL (>= 2)",
-      "NeedsCompilation": "no",
-      "Depends": [
-        "R (>= 3.5.0)"
-      ],
-      "Repository": "CRAN",
-      "URL": "https://plotrix.github.io/plotrix/, https://github.com/plotrix/plotrix",
-      "BugReports": "https://github.com/plotrix/plotrix/issues",
-      "Author": "Jim Lemon [aut], Ben Bolker [ctb], Sander Oom [ctb], Eduardo Klein [ctb], Barry Rowlingson [ctb], Hadley Wickham [ctb], Anupam Tyagi [ctb], Olivier Eterradossi [ctb], Gabor Grothendieck [ctb], Michael Toews [ctb], John Kane [ctb], Rolf Turner [ctb], Carl Witthoft [ctb], Julian Stander [ctb], Thomas Petzoldt [ctb], Remko Duursma [ctb], Elisa Biancotto [ctb], Ofir Levy [ctb], Christophe Dutang [ctb], Peter Solymos [ctb], Robby Engelmann [ctb], Michael Hecker [ctb], Felix Steinbeck [ctb], Hans Borchers [ctb], Henrik Singmann [ctb], Ted Toal [ctb], Derek Ogle [ctb], Darshan Baral [ctb], Ulrike Groemping [ctb], Bill Venables [ctb], The CRAN Team [ctb], Duncan Murdoch [ctb, cre]",
-      "Maintainer": "Duncan Murdoch <murdoch.duncan@gmail.com>"
-    },
     "plyr": {
       "Package": "plyr",
       "Version": "1.8.9",
@@ -2607,37 +2541,6 @@
       "Maintainer": "Thomas Lin Pedersen <thomas.pedersen@posit.co>",
       "Repository": "https://packagemanager.posit.co/cran/latest"
     },
-    "signal": {
-      "Package": "signal",
-      "Version": "1.8-1",
-      "Source": "Repository",
-      "Title": "Signal Processing",
-      "Date": "2024-06-13",
-      "Authors@R": "c(person(\"Uwe\", \"Ligges\", role = c(\"aut\", \"cre\"), email=\"ligges@statistik.tu-dortmund.de\", comment = \"new maintainer\"), person(\"Tom\", \"Short\", role = \"aut\", email = \"tshort@eprisolutions.com\", comment=\"port to R\"), person(\"Paul\", \"Kienzle\", role = \"aut\", comment=\"majority of the original sources\"), person(\"Sarah\", \"Schnackenberg\", role = \"ctb\", comment=\"various test cases and bug fixes\"), person(\"David\", \"Billinghurst\", role = \"ctb\"), person(\"Hans-Werner\", \"Borchers\", role = \"ctb\"), person(\"Andre\", \"Carezia\", role = \"ctb\"), person(\"Pascal\", \"Dupuis\", role = \"ctb\"), person(\"John W.\", \"Eaton\", role = \"ctb\"), person(\"E.\", \"Farhi\", role = \"ctb\"), person(\"Kai\", \"Habel\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"ctb\"), person(\"Sebastian\", \"Krey\", role = \"ctb\"), person(\"Bill\", \"Lash\", role = \"ctb\"), person(\"Friedrich\", \"Leisch\", role = \"ctb\"), person(\"Olaf\", \"Mersmann\", role = \"ctb\"), person(\"Paulo\", \"Neis\", role = \"ctb\"), person(\"Jaakko\", \"Ruohio\", role = \"ctb\"), person(\"Julius O.\", \"Smith III\", role = \"ctb\"),                   \t    person(\"Doug\", \"Stewart\", role = \"ctb\"), person(\"Andreas\", \"Weingessel\", role = \"ctb\"))",
-      "Depends": [
-        "R (>= 3.5.0)"
-      ],
-      "Imports": [
-        "MASS",
-        "graphics",
-        "grDevices",
-        "stats",
-        "utils"
-      ],
-      "Suggests": [
-        "pracma"
-      ],
-      "Enhances": [
-        "matlab"
-      ],
-      "Description": "A set of signal processing functions originally written for 'Matlab' and 'Octave'. Includes filter generation utilities, filtering functions, resampling routines, and visualization of filter models. It also includes interpolation functions.",
-      "License": "GPL-2",
-      "URL": "https://signal.R-forge.R-project.org",
-      "NeedsCompilation": "yes",
-      "Author": "Uwe Ligges [aut, cre] (new maintainer), Tom Short [aut] (port to R), Paul Kienzle [aut] (majority of the original sources), Sarah Schnackenberg [ctb] (various test cases and bug fixes), David Billinghurst [ctb], Hans-Werner Borchers [ctb], Andre Carezia [ctb], Pascal Dupuis [ctb], John W. Eaton [ctb], E. Farhi [ctb], Kai Habel [ctb], Kurt Hornik [ctb], Sebastian Krey [ctb], Bill Lash [ctb], Friedrich Leisch [ctb], Olaf Mersmann [ctb], Paulo Neis [ctb], Jaakko Ruohio [ctb], Julius O. Smith III [ctb], Doug Stewart [ctb], Andreas Weingessel [ctb]",
-      "Maintainer": "Uwe Ligges <ligges@statistik.tu-dortmund.de>",
-      "Repository": "CRAN"
-    },
     "ssh": {
       "Package": "ssh",
       "Version": "0.9.4",
@@ -3009,48 +2912,6 @@
       "Maintainer": "Yihui Xie <xie@yihui.name>",
       "Repository": "https://packagemanager.posit.co/cran/latest"
     },
-    "trajr": {
-      "Package": "trajr",
-      "Version": "1.5.1",
-      "Source": "Repository",
-      "Type": "Package",
-      "Title": "Animal Trajectory Analysis",
-      "Date": "2023-11-28",
-      "Authors@R": "person(\"Jim\", \"McLean\", email = \"jim_mclean@optusnet.com.au\", role = c(\"aut\", \"cre\"))",
-      "Description": "A toolbox to assist with statistical analysis of animal trajectories. It provides simple access to algorithms for calculating and assessing a variety of  characteristics such as speed and acceleration, as well as multiple measures of  straightness or tortuosity. Some support is provided for 3-dimensional trajectories.  McLean & Skowron Volponi (2018) <doi:10.1111/eth.12739>.",
-      "License": "MIT + file LICENSE",
-      "URL": "https://github.com/JimMcL/trajr",
-      "BugReports": "https://github.com/JimMcL/trajr/issues",
-      "Encoding": "UTF-8",
-      "Imports": [
-        "signal",
-        "utils",
-        "stats",
-        "graphics",
-        "plotrix",
-        "grDevices"
-      ],
-      "RoxygenNote": "7.2.3",
-      "Suggests": [
-        "knitr",
-        "rmarkdown",
-        "testthat",
-        "readr",
-        "tcltk",
-        "sp",
-        "MASS",
-        "covr"
-      ],
-      "VignetteBuilder": "knitr",
-      "BuildVignettes": "true",
-      "NeedsCompilation": "no",
-      "Author": "Jim McLean [aut, cre]",
-      "Maintainer": "Jim McLean <jim_mclean@optusnet.com.au>",
-      "Depends": [
-        "R (>= 3.5.0)"
-      ],
-      "Repository": "CRAN"
-    },
     "tzdb": {
       "Package": "tzdb",
       "Version": "0.5.0",

src/main.Rmd

@@ -1,66 +0,0 @@
----
-title: "Topic 8"
-output:
-  pdf_document: default
-  html_document: default
-date: "`r Sys.Date()`"
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
-
-```{r preamble, message=FALSE}
-# Load Libraries
-library(dplyr)
-library(lubridate)
-library(readr)
-library(utils)
-library(openSkies)
-library(dotenv)
-library(httr)
-library(jsonlite)
-library(trajr)
-```
-
-# Download flights 
-```{r opensky}
-
-time_now <- Sys.time()
-creds <- getCredentials(
-  client_id = Sys.getenv('OPENSKY_CLIENT_ID'),
-  client_secret = Sys.getenv('OPENSKY_CLIENT_SECRET'))
-
-# get departures from Frankfurt airport
-departures <- getAirportDepartures(airport = "EDDF", startTime = time_now - hours(1), endTime = time_now, credentials = creds )
-
-getFlights <- function(icao, time, creds){
-  flights <-getAircraftFlights(icao, startTime =  time - days(1), endTime = time, credentials = creds )
-  return(flights)
-}
-icao <- departures[[1]][["ICAO24"]]
-flights <- getFlights(icao,Sys.time(), creds)
-# TODO map from all available flights to tracks
-query <- list(icao24= icao, time=as.numeric(flights[[1]][["departure_time"]]))
-
-response <-makeAuthenticatedRequest('tracks/all',query, creds)
-track_data <- fromJSON(content(response, as = "text", encoding = "UTF-8"))
-if (!is.null(track_data$path) && length(track_data$path) > 0) {
-    
-    route_df <- as.data.frame(track_data$path)
-    colnames(route_df) <- c("time", "lat", "lon", "alt", "heading", "on_ground")
-    
-    message("Loading of route successfull! Points: ", nrow(route_df))
-    
-    plot(route_df$lon, route_df$lat, type="o", pch=20, col="blue", 
-         main=paste("Geographic route of", icao),
-         xlab="Longitude", ylab="Latitude")
-    
-    plot(route_df$time, route_df$alt, type="l", col="red", lwd=2,
-         main=paste("Altitude profile of", icao),
-         xlab="Time (Unix)", ylab="Height (Meter)")
-    
-  } else {
-    print("No path points from api")
-  }
-```

src/slides.Rmd

@@ -1,33 +0,0 @@
----
-title: "Topic 8"
-date: "`r Sys.Date()`"
-output: beamer_presentation
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = FALSE)
-# {cat, child="../README.md"}
-```
-
-## Task
-Develop an R-based software, which will perform the following tasks:
-
-1.  download from the OpenSky Network online database the observations of the trajectory of a randomly selected aircraft on a randomly selected flight over at least five days, in uninterrupted continuity (1)
-
-2.  perform the selections in the graphical user interface (GUI) of your R script,
-
-3.  determine the characteristics of each trajectory according to the parameters: diffusion distance, straightness, duration of travel, mean travel velocity and fractal dimension (2),
-
-4.  using the R library trajr, (4) perform basic statistical analysis of the parameters of daily trajectories from (3): arithmetic mean, variance, quartiles, boxplot, estimate of the density function of the experimental statistical distribution, analyze and interpret them.
-
-
-## Methodology
-
-1. acquire data using the OpenSky API
-
-2. use 
-
-## Contribution
-
-- extended functionality of the `openSkies` R package and created a merge request
-