Change proj to wintri

Why

* Wintri is available for older proj version

How

* Recreate internal spatial dataset
* Modify vignette and tmap st_transform()
* Fix doc warnings
* Prepare deliverables

issue #36

.gitignore

@@ -14,3 +14,4 @@ creds.R
 dev/00-fill-database.html
 .Renviron
 data-raw/db
+deliverables

DESCRIPTION

@@ -32,18 +32,18 @@ Imports:
     maps (>= 3.3.0),
     patchwork (>= 1.1.1),
     purrr (>= 0.3.4),
+    rmapshaper (>= 0.4.5),
     RPostgres (>= 1.3.3),
+    sf (>= 1.0.2),
     shinipsum (>= 0.1.0),
     shiny (>= 1.6.0),
     shinythemes (>= 1.2.0),
     tmap (>= 3.3.2),
     utils,
-    zeallot (>= 0.1.0),
     w3css (>= 0.0.0.9002),
-    sf (>= 1.0.2),
-    rmapshaper (>= 0.4.5),
-    dbplyr (>= 2.1.1)
+    zeallot (>= 0.1.0)
 Suggests: 
+    dbplyr,
     DiagrammeR (>= 1.0.6.1),
     DiagrammeRsvg (>= 0.1),
     knitr (>= 1.34),

R/fct_db.R

@@ -32,6 +32,7 @@ connect <- function(
 #' @export
 #'
 #' @examples
+#' get_con()
 get_con <- function(
   session = shiny::getDefaultReactiveDomain()
 ){

R/fct_species.R

@@ -29,6 +29,9 @@ get_active_species <- function(
 #' @export
 #'
 #' @examples
+#' if (interactive()){
+#'   get_conservation_status()
+#' }
 get_conservation_status <- function(
   species_id, 
   con

R/mod_a_fourth.R

@@ -81,7 +81,7 @@ mod_fourth_server <- function(id, r = r){
 
     output$raster <- tmap::renderTmap({
       req(loco$species)
-      
+
       tm_draw(
         species_latin_name = loco$species,
         spatial_type = input$square_or_division, 
@@ -92,10 +92,10 @@ mod_fourth_server <- function(id, r = r){
         ices_geom = golem::get_golem_options("ices_geom")
       )
 
-    }) %>% bindCache({
-      loco$species
-      input$square_or_division
-    })
+    }) # %>% bindCache({
+    #   loco$species
+    #   input$square_or_division
+    # })
 
     observeEvent( loco$species , {
       req(loco$species)

R/mod_a_fourth_fct_map.R

@@ -11,7 +11,6 @@
 #' @import sf
 #' @import tmap
 #'
-#' @examples
 tm_draw <- function(
   species_latin_name,
   spatial_type, 

R/mod_c_second.R

@@ -96,7 +96,7 @@ mod_second_server <- function(id, r = r){
             )), 
           aes(fill = region)
         ) +
-        coord_map() +
+        # coord_map() +
         theme_void() + 
         guides(
           fill = FALSE

R/mod_d_third.R

@@ -141,7 +141,7 @@ mod_third_server <- function(id, r = r){
             )), 
           aes(fill = region)
         ) +
-        coord_map() +
+        # coord_map() +
         theme_void() + 
         guides(
           fill = FALSE

R/mod_species.R

@@ -89,7 +89,6 @@ mod_species_server <- function(id, r, entry = "species"){
         selected = ''
       )
     })
-
   })
 }
 

R/run_app.R

@@ -8,6 +8,7 @@
 #' @importFrom shiny shinyApp
 #' @importFrom golem with_golem_options
 #' @importFrom zeallot %<-%
+#' 
 run_app <- function(
   onStart = NULL,
   options = list(), 

R/utils_helpers.R

@@ -48,7 +48,6 @@ get_dt_lg <- function(lg){
 #' @return
 #' @export
 #'
-#' @examples
 generate_datasets <- function(
   con
 ){
@@ -84,7 +83,8 @@ generate_datasets <- function(
     con, 
     query = "SELECT * FROM diadesatlas.v_ices_geom;"
   ) %>% 
-    sf::st_transform("+proj=eqearth +wktext") %>%
+    # sf::st_transform("+proj=eqearth +wktext") %>%
+    sf::st_transform("+proj=wintri") %>%
     rmapshaper::ms_simplify()
 
   species_list <- con %>%

README.Rmd

@@ -41,7 +41,7 @@ The apps needs to connect to a db.
 
 It can be set via : 
 
-```{r eval = FALSE}
+```{r eval=FALSE}
 golem::amend_golem_config(
   "POSTGRES_DBNAME",
   "diades"
@@ -60,6 +60,18 @@ Sys.setenv("POSTGRES_PASS" = "thinkrpassword")
 
 For dev purpose, please refer to the doc in the diadesdata repo on ThinkR's forge (restricted access).
 
+Verify connexion works
+```{r, eval=FALSE}
+pkgload::load_all()
+session <- new.env()
+connect(session)
+con <- get_con(session)
+
+DBI::dbListTables(con)
+DBI::dbDisconnect(con)
+```
+
+
 # Dev - vignettes
 
 Vignettes are compiled manually by developers. 

data-raw/bb-page1-catch-bycatch.Rmd

@@ -48,7 +48,7 @@ file = here::here(file.path("vignettes", vignette_file))
 ```{r setup}
 # Sys.setenv("POSTGRES_USER" = "diadesatlas_owner")
 # Sys.setenv("POSTGRES_PASS" = "thinkrpassword")
-pkgload::load_all()
+pkgload::load_all(here::here())
 library(dplyr)
 session <- new.env()
 connect(session)
@@ -109,7 +109,8 @@ catchment_geom <- st_read(
   con, 
   query =   "SELECT * FROM diadesatlas.v_basin vb"
 ) %>%
-  rmapshaper::ms_simplify()
+  rmapshaper::ms_simplify() %>% 
+  st_transform("+proj=wintri")
 
 dataALL <- dbGetQuery(
   con, 
@@ -122,7 +123,8 @@ ices_geom <- st_read(
   con, 
   query = "SELECT * FROM diadesatlas.v_ices_geom;"
 ) %>% 
-  st_transform("+proj=eqearth +wktext") %>%
+  # st_transform("+proj=eqearth +wktext") %>%
+  st_transform("+proj=wintri") %>%
   rmapshaper::ms_simplify()
 
 
@@ -169,3 +171,9 @@ tm_draw(
 )
 
 ```
+
+## Disconnect db
+```{r}
+DBI::dbDisconnect(con)
+```
+

data-raw/frontiers.R

@@ -20,7 +20,8 @@ states = c("Portugal", "Spain","France", "United Kingdom", "Ireland", "United Ki
 frontiers <- worldMap %>%  select(NAME, geometry) %>% filter(NAME %in% states)
 
 bbox <- st_bbox(c(xmin = -17.5, xmax = 19, ymax = 36, ymin = 62), crs = st_crs(4326)) 
-world_map_crs <- "+proj=eqearth +wktext"
+# world_map_crs <- "+proj=eqearth +wktext"
+world_map_crs <- "+proj=wintri"
 
 frontiers <- frontiers %>% 
   st_transform(world_map_crs)  %>%

dev/02_dev.R

@@ -27,7 +27,12 @@ usethis::use_package("sf")
 
 # Before sending to git external server
 # _deps
-attachment::att_amend_desc(extra.suggests = c("pkgload", "DiagrammeR", "DiagrammeRsvg"))
+renv::install("ThinkR-open/attachment")
+# [-] 7 package(s) removed: ggplot2, magrittr, maps, RPostgres, shinythemes, zeallot, dbplyr.
+
+attachment::att_amend_desc(
+  extra.suggests = c("pkgload", "DiagrammeR", "DiagrammeRsvg", "dbplyr"))
+
 # _renv
 custom_packages <- setdiff(
   c(attachment::att_from_description(),

dev/deliverables.R

@@ -1,13 +1,35 @@
 # Deliverables ====
 dir.create("deliverables")
 usethis::use_build_ignore("deliverables")
+usethis::use_git_ignore("deliverables")
 
 ## _pkgdown ----
 # _Compile manual vignette
-rmarkdown::render(input = here::here("data-raw/aa-data-exploration-and-preparation.Rmd"),
-                  output_format = "rmarkdown::html_vignette",
-                  output_options = list(toc = TRUE),
-                  output_file = here::here("vignettes/explo-manual.html"))
+# See readme
+rstudioapi::navigateToFile("README.Rmd")
+
+## Upgrade version Number in DESCRIPTION
+## Create a commit for the version
+## Add tag on version commit
+
+## _covr ----
+x <- covr::package_coverage()
+# Change {my-project}
+covr::report(x, file = "deliverables/codecoverage/listofcodes-codecoverage-full-report.html")
+
+
+## Update description files in app
+chameleon::create_pkg_biblio_file(
+  to = "html",
+  out.dir = "inst/app/www/about", edit = FALSE)
+chameleon::create_pkg_desc_file(
+  source = c("archive"),
+  out.dir = "inst/app/www/about", to = "html", edit = FALSE)
+
+## _add covrpage ----
+# remotes::install_github("metrumresearchgroup/covrpage")
+covrpage::covrpage(vignette = TRUE)
+file.remove("tests/README.md")
 
 # remotes::install_github("ThinkR-open/chameleon")
 # remotes::install_github("ThinkR-open/thinkrtemplate")
@@ -62,4 +84,27 @@ rsconnect::deployApp(
 setwd(origwd)
 
 
-# Clone on Irstea GitLab
+# Deploy App on rsconnect ----
+# Deploy app on connect
+appFiles <- list.files(".", recursive = TRUE)
+appFiles <- appFiles[!grepl(".Rprofile|renv|rstudio_|deliverables|dev|data-raw|docker", appFiles)]
+
+rsconnect::writeManifest(appFiles = appFiles)
+
+# Deploy App on rsconnect manually
+rsconnect::accounts()
+account_name <- rstudioapi::showPrompt("Rsconnect account", "Please enter your username:", "name")
+account_server <- rstudioapi::showPrompt("Rsconnect server", "Please enter your server name:", "1.1.1.1")
+
+appFiles <- list.files(".", recursive = TRUE)
+appFiles <- appFiles[!grepl(".Rprofile|renv|rstudio_|deliverables|dev|data-raw|docker", appFiles)]
+rsconnect::deployApp(
+  ".",                       # the directory containing the content
+  appFiles = appFiles, # the list of files to include as dependencies (all of them)
+  # appId = 478,
+  appName = "app-diades.atlas",                   # name of the endpoint (unique to your account on Connect)
+  appTitle = "app-diades.atlas",                  # display name for the content
+  account = account_name,                # your Connect username
+  server = account_server                    # the Connect server, see rsconnect::accounts()
+)
+

dev/tab1.Rmd

@@ -115,7 +115,8 @@ states = c("Portugal", "Spain","France", "United Kingdom", "Ireland", "United Ki
            'Albania', 'Bosnia and Herz.', 'Serbia', 'Montenegro', 'Macedonia', 'Kosovo',
            'Tunisia',  'Libya' ,  'Algeria' , 'Morocco' )
 
-world_map_crs <- "+proj=eqearth +wktext"
+# world_map_crs <- "+proj=eqearth +wktext"
+world_map_crs <- "+proj=wintri"
 frontiers <- worldMap %>%  
   select(NAME, geometry) %>% 
   filter(NAME %in% states) %>% 
@@ -268,7 +269,8 @@ ices_geom <- st_read(
   con, 
   query = "SELECT * FROM diadesatlas.v_ices_geom;"
 ) %>% 
-  st_transform("+proj=eqearth +wktext") %>%
+  # st_transform("+proj=eqearth +wktext") %>%
+  st_transform("+proj=wintri") %>%
   rmapshaper::ms_simplify()
 
 tm_draw(

inst/golem-config.yml

@@ -8,4 +8,4 @@ default:
 production:
   app_prod: yes
 dev:
-  golem_wd: !expr here::here()
+  golem_wd: /mnt/Data/ThinkR/Gitlab_Forge/ThinkR/Missions/diades.atlas