spelling check + minor + bump version 0.7

Rafnuss · Rafnuss · commit 2bc60d56981b · 2022-10-29T11:38:54.000-04:00
diff --git a/.RDataTmp b/.RDataTmp
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,12 @@
 Package: GeoPressureTemplate
 Title: These are the Goal of my Study (One Line, Title Case)
-Version: 0.6
+URL: https://github.com/Rafnuss/GeoPressureTemplate
+Description: More detailed description of my research objective with my dataset available (one paragraph).
 Authors@R: 
     person("Raphaël", "Nussbaumer", , "rafnuss@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-8185-1020"))
-Description: More detailed description of my research objective with my dataset available (one paragraph).
 License: GPL (>= 3)
-URL: https://github.com/Rafnuss/GeoPressureTemplate
+Version: 0.7
 Depends: 
     R (>= 3.5.0)
 Imports: 
@@ -35,4 +35,4 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # GeoPressureTemplate
 
-Analysing geolocator data with pressure is full of potential, but the the path is long and the journey can be challenging. `GeoPressureTemplate` is a [Github repository template](https://docs.github.com/articles/creating-a-repository-from-a-template/) for a startup R project to make that journey easier.
+Analyzing geolocator data with pressure is full of potential, but the the path is long and the journey can be challenging. `GeoPressureTemplate` is a [Github repository template](https://docs.github.com/articles/creating-a-repository-from-a-template/) for a start-up R project to make that journey easier.
 
 ## What is this template and who is it for? :mag_right:
 
@@ -11,7 +11,7 @@ In essence, it contains the code from all the [GeoPressureManual](https://raphae
 ## What do you need to use this template? :computer:
 
 - Geolocator data containing pressure, light and activity data.
-- Have read the [GeoPressureManual](https://raphaelnussbaumer.com/GeoPressureManual) (:warning: You should be familar with the **full process involved** before starting with your own project)
+- Have read the [GeoPressureManual](https://raphaelnussbaumer.com/GeoPressureManual) (:warning: You should be familiar with the **full process involved** before starting with your own project)
 - Basic R experience (I'm using the [tidyverse](https://www.tidyverse.org/) syntax here).
 - A [Github account](https://github.com/signup).
 
@@ -20,7 +20,7 @@ In essence, it contains the code from all the [GeoPressureManual](https://raphae
 
 Following the recommendations of [rrrpkg](https://github.com/ropensci/rrrpkg), the project contains:
 1. Standard description files at the root (`DESCRIPTION`, `.Rproj`, `README.md`, `LICENCES`,...).
-2. `data/` folder containing the raw geolocator data, the pressure and light labelled files and the data generated with the code from `analysis/`. Note that you could instead keep the geolocator and labelization files seperately in a `raw-data/` folder, following `usethis()` standard.
+2. `data/` folder containing the raw geolocator data, the pressure and light labelled files and the data generated with the code from `analysis/`. Note that you could instead keep the geolocator and labelization files separately in a `raw-data/` folder, following `usethis()` standard.
 3. `analysis/` contains all the `.R` code used for your project.
 4. `report/` reads the data generated and produces sharable results (figures, html page, manuscript, etc...).
 <details>
@@ -113,7 +113,7 @@ devtools::install()
 
 ## Start analysing the data :chart_with_upwards_trend:
 
-Now that you are set-up, it's time to start the serious work. :grimacing: Follow the order of the `.R` code in the `analysis/` folder. They follow the same order as the GeoPressureManual (but with different numerotation to be able to analyse multiple track at the same time).
+Now that you are set-up, it's time to start the serious work. :grimacing: Follow the order of the `.R` code in the `analysis/` folder. They follow the same order as the GeoPressureManual (but with different numeration to be able to analyse multiple track at the same time).
 
 |  GeoPressureTemplate analysis |  GeoPressureManual  |
 |---|---|
@@ -126,7 +126,7 @@ Now that you are set-up, it's time to start the serious work. :grimacing: Follow
 |  `5-3-wind-graph_analyse.R` |  [5. Wind graph - Outputs](https://raphaelnussbaumer.com/GeoPressureManual/wind-graph.html#compute-the-transition-probability-1) |
 |  `99-combined.R` |  Run all steps for multiple tracks. |
 
-In order to keep your code clean, we isolate all the key paramters used in all functions in the `gpr_setting.xlsx` spreadsheet located in the `data/` folder. You can adjust these parameters seperatly for each track or add any informations on your individuals bird that might be useful for your analysis. 
+In order to keep your code clean, we isolate all the key parameters used in all functions in the `gpr_setting.xlsx` spreadsheet located in the `data/` folder. You can adjust these parameters separately for each track or add any information on your individuals bird that might be useful for your analysis. 
 
 <details>
   <summary>Click to see explanations on the parameters of <code>gpr_setting.xlsx</code></summary>
@@ -145,12 +145,12 @@ In order to keep your code clean, we isolate all the key paramters used in all f
 |map_max_sample     |300                      |see [`geopressure_map()`](https://raphaelnussbaumer.com/GeoPressureR/reference/geopressure_map.html)                   |
 |map_margin         |30                       |see [`geopressure_map()`](https://raphaelnussbaumer.com/GeoPressureR/reference/geopressure_map.html)                   |
 |prob_map_s         |1                        |see [`geopressure_prob_map()`](https://raphaelnussbaumer.com/GeoPressureR/reference/geopressure_prob_map.html)         |
-|prob_map_s_calib   |                         |Alternative value for  `prob_map_s` for calibration site. Useful for species living in moutain only during calibration. |
+|prob_map_s_calib   |                         |Alternative value for  `prob_map_s` for calibration site. Useful for species living in mountain only during calibration. |
 |prob_map_thr       |0.9                      |see [`geopressure_prob_map()`](https://raphaelnussbaumer.com/GeoPressureR/reference/geopressure_prob_map.html)         |
 |shift_k            |0                        |see [`find_twilights()`](https://raphaelnussbaumer.com/GeoPressureR/reference/find_twilights.html)                     |
 |kernel_adjust      |1.4                      |see [Calibration of light data](https://raphaelnussbaumer.com/GeoPressureManual/light-map.html#calibrate-zenith-angles)        |
 |calib_lon          |17.05                    |Longitude of the calibration site.                                                                                     |
-|calib_lat          |48.9                     |Latitude of the calibrataion site.                                                                                      |
+|calib_lat          |48.9                     |Latitude of the calibration site.                                                                                      |
 |calib_1_start      |2017-06-20               |Start date of the first calibration period.                                                                             |
 |calib_1_end        |2017-08-05               |End date of the first calibration period.                                                                               |
 |calib_2_start      |                         |Start date of the second calibration period.                                                                           |
@@ -162,7 +162,6 @@ In order to keep your code clean, we isolate all the key paramters used in all f
 |thr_gs             |120                      |see [`graph_create()`](https://raphaelnussbaumer.com/GeoPressureR/reference/graph_create.html)                         |
 |thr_as             |100                      |see [`graph_add_wind()`](https://raphaelnussbaumer.com/GeoPressureR/reference/graph_add_wind.html)                     |
 |low_speed_fix      |15                       |see [`flight_prob()`](https://raphaelnussbaumer.com/GeoPressureR/reference/flight_prob.html)                           |
-|ringNo             |                         |Ring number if available (not used).                                                                                                                        |
 |scientific_name    |Acrocephalus arundinaceus|see [`flight_bird()`](https://raphaelnussbaumer.com/GeoPressureR/reference/flight_bird.html)                           |
 |common_name        |Great Reed Warbler       |                                                                                                                       |
 |mass               |                         |see [`flight_bird()`](https://raphaelnussbaumer.com/GeoPressureR/reference/flight_bird.html)                           |
@@ -182,12 +181,12 @@ The main idea is to produce report templates (`_name_of_the_report_template.Rmd`
 3. Look at `make_reports.R` script to see how you can generate the HTML for multiple tracks and reports templates at once. 
 4. Edit `index.Rmd` as you wishes
 5. Run `{r} render_site('./reports')` (also provided at the bottom of  `make_reports.R`) to generate the full website in `docs/`.
-6. Push your changes on Gihub and create your [Github Page](https://rstudio.github.io/distill/publish_website.html#github-pages).
+6. Push your changes on Github and create your [Github Page](https://rstudio.github.io/distill/publish_website.html#github-pages).
 
 
 ## Advanced options :link:
 
 - Generate your DOI with [Zenodo](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content) (e.g., https://zenodo.org/record/6720386)
 - Generate a citation file with [`usethis::use_citation`](https://usethis.r-lib.org/reference/use_citation.html) and [`cffr`](https://github.com/ropensci/cffr).
-- Use [`renv`](https://rstudio.github.io/renv/index.html) to make your work reproducable.
+- Use [`renv`](https://rstudio.github.io/renv/index.html) to make your work reproducible.
 - Export your data on [Movebank](https://www.movebank.org/cms/movebank-content/import-custom-tabular-data).
diff --git a/analysis/1-pressure.R b/analysis/1-pressure.R
@@ -108,7 +108,7 @@ if (debug) {
 
 
 # Filter stationary period based on the number of pressure datapoint available
-thr_dur <- gpr$thr_dur # 24*4 # duration in hour. Decrease this value down to gpr$thr_dur
+thr_dur <- gpr$thr_dur # duration in hour. Decrease this value zero if possible
 res <- as.numeric(difftime(pam$pressure$date[2], pam$pressure$date[1], units = "hours"))
 sta_id_keep <- pam$pressure %>%
   filter(!isoutlier & sta_id > 0) %>%
@@ -122,7 +122,6 @@ pam_short$pressure <- pam_short$pressure %>%
   mutate(sta_id = ifelse(sta_id %in% sta_id_keep, sta_id, NA))
 
 # Query pressure map
-# We overwrite the setting parameter for resolution to make query faster at first
 pressure_maps <- geopressure_map(pam_short$pressure,
   extent = c(gpr$extent_N, gpr$extent_W, gpr$extent_S, gpr$extent_E),
   scale = gpr$map_scale,
diff --git a/analysis/3-static.R b/analysis/3-static.R
@@ -18,7 +18,7 @@ gdl <- "18LX"
 load(paste0("data/1_pressure/", gdl, "_pressure_prob.Rdata"))
 load(paste0("data/2_light/", gdl, "_light_prob.Rdata"))
 
-# Defint the threashold of the stationay period to consider
+# Define the threshold of the stationary period to consider
 thr_sta_dur <- gpr$thr_dur # in hours
 
 sta_pres <- unlist(lapply(pressure_prob, function(x) raster::metadata(x)$sta_id))
@@ -52,11 +52,6 @@ static_prob <- mapply(function(light, pressure, flight) {
   # define static prob as the product of light and pressure prob
   static_prob <- light * pressure
 
-  # replace na by zero
-  # tmp <- values(static_prob)
-  # tmp[is.na(tmp)] <- 0
-  # values(static_prob) <- tmp
-
   # define metadata
   metadata(static_prob) <- metadata(pressure)
   metadata(static_prob)$flight <- flight
@@ -84,7 +79,7 @@ tmp[!is.na(tmp)] <- 0
 tmp[lat_calib_id, lon_calib_id] <- 1
 values(static_prob[[1]]) <- tmp
 
-if (!is.na(gpr$calib_2_start) & abs(difftime(gpr$calib_2_end, gpr$crop_end, units = "days"))<3) {
+if (!is.na(gpr$calib_2_start) & abs(difftime(gpr$calib_2_end, gpr$crop_end, units = "days")) < 3) {
   if (!is.na(gpr$calib_2_lat)) {
     lon_calib_id <- which.min(abs(gpr$calib_2_lon - lon))
     lat_calib_id <- which.min(abs(gpr$calib_2_lat - lat))
@@ -123,7 +118,7 @@ if (debug) {
   # impact your code
   pam_diff <- pam
   pam_diff$pressure <- pam_diff$pressure %>%
-    left_join(path_modified_ts_bind %>% dplyr::select(c("date","pressure0")), by="date") %>%
+    left_join(path_modified_ts_bind %>% dplyr::select(c("date", "pressure0")), by = "date") %>%
     rename(obs_ref = pressure0)
 
   trainset_write(pam_diff, "data/1_pressure/labels/", filename = paste0(pam$id, "_act_pres"))
@@ -135,7 +130,8 @@ if (debug) {
   twl_path <- left_join(twl, path_modified) %>%
     mutate(
       twilight = twilight(twilight,
-                          lon = lon, lat = lat, rise = rise, zenith = 96)
+        lon = lon, lat = lat, rise = rise, zenith = 96
+      )
     ) %>%
     filter(!is.na(twilight))
 
@@ -145,14 +141,14 @@ if (debug) {
         series = ifelse(twl$rise, "Rise", "Set"),
         timestamp = strftime(twl$twilight, "%Y-%m-%dT00:00:00Z", tz = "UTC"),
         value = (as.numeric(format(twl$twilight, "%H")) * 60 + as.numeric(format(twl$twilight, "%M"))
-                 + gpr$shift_k / 60 + 60 * 12) %% (60 * 24),
+          + gpr$shift_k / 60 + 60 * 12) %% (60 * 24),
         label = ifelse(is.na(twl$delete), "", ifelse(twl$delete, "Delete", ""))
       ),
       data.frame(
         series = ifelse(twl_path$rise, "Set_ref", "Rise_ref"),
         timestamp = strftime(twl_path$twilight, "%Y-%m-%dT00:00:00Z", tz = "UTC"),
         value = (as.numeric(format(twl_path$twilight, "%H")) * 60 + as.numeric(format(twl_path$twilight, "%M"))
-                 + gpr$shift_k / 60 + 60 * 12) %% (60 * 24),
+          + gpr$shift_k / 60 + 60 * 12) %% (60 * 24),
         label = ""
       )
     ),
diff --git a/analysis/5-1-wind-graph_download.R b/analysis/5-1-wind-graph_download.R
@@ -1,24 +1,22 @@
+library(GeoPressureR)
 library(ecmwfr)
 
 # Define which track to work with
 gdl <- "18LX"
 
 # Load
+load(paste0("data/1_pressure/", gdl, "_pressure_prob.Rdata"))
 load(paste0("data/3_static/", gdl, "_static_prob.Rdata"))
 
 # Set credential
-Sys.setenv( cds_key="Insert_your_CDS_API_KEY_here")
-Sys.setenv( cds_user="Insert_your_CDS_UID_here")
+Sys.setenv(cds_key = "Insert_your_CDS_API_KEY_here")
+Sys.setenv(cds_user = "Insert_your_CDS_UID_here")
 
 # You can see them with
 # usethis::edit_r_environ()
 # cds_key <- Sys.getenv("cds_key")
 # cds_user <- Sys.getenv("cds_user")
 
-graph_download_wind(pam,
-                    area = static_prob,
-                    # cds_key="Insert_your_CDS_API_KEY_here"
-                    # cds_user="Insert_your_CDS_UID_here"
-                    )
+graph_download_wind(pam, area = static_prob)
 
 # Check request at https://cds.climate.copernicus.eu/cdsapp#!/yourrequests
diff --git a/analysis/99-combined.R b/analysis/99-combined.R
@@ -35,7 +35,7 @@ dir.create("data/5_wind_graph", showWarnings = FALSE)
 for (i in seq(1, length(gdl_list))) {
   gdl <- gdl_list[i]
   source("analysis/5-1-wind-graph_download.R")
-  # Use job to avoid blocking your console.
+  # You can also make this request with a background job in Rstudio (https://solutions.rstudio.com/r/jobs/)
   # rstudioapi::jobRunScript("analysis/5-1-wind-graph_download.R",
   #                          name = paste0("wind_graph_download_", gdl),
   #                          workingDir = ".",
diff --git a/data/gpr_settings.xlsx b/data/gpr_settings.xlsx
