added example data, modified functions to work independently with exa…

…mple data
rubenpp7 · Feb 18, 2021 · 8e66709 · 8e66709
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diff --git a/.gitignore b/.gitignore
@@ -3,4 +3,4 @@
 .RData
 .Ruserdata
 /data-raw
-/data
+/data-RB
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -12,7 +12,7 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
-Imports:   dplyr,
+Imports: dplyr,
   ggplot2,
   googlesheets4,
   leaflet,
@@ -26,3 +26,6 @@ Imports:   dplyr,
   htmltools
 Depends: 
     R (>= 2.10)
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -6,11 +6,11 @@ export(divesite_depths)
 export(divetypes)
 export(divetypes_platform)
 export(divewatch)
+export(example_data)
 export(logbook_highlights)
 export(logbook_map)
 export(logged_depths)
 export(prep_data)
-export(test_data)
 import(dplyr)
 import(forcats)
 import(ggplot2)

diff --git a/R/cum_dives.R b/R/cum_dives.R
@@ -17,9 +17,19 @@
 
 
 
-cum_dives <- function(){
-
-load("data/scuba_map.RData")
+cum_dives <- function(path = getwd()){
+
+  if(dir.exists(paste0(path, "/divewatchr_data"))){
+
+    load('divewatchr_data/scuba_map.RData')
+  }
+
+  # } else {
+  #   
+  #   load('data/scuba_map.RData')  
+  # }
+
+
 scuba_map_cum <- scuba_map %>% mutate(cum_dives = seq(1, nrow(scuba_map)))                     
 
 ggplot(scuba_map_cum, 

diff --git a/R/divecount_reg.R b/R/divecount_reg.R
@@ -16,10 +16,12 @@
 
 #.........................................................
 
-divecount_reg <- function (){
+divecount_reg <- function (path = getwd()){
 
-  # Plot dives per country and region
-  load("data/scuba_clean.RData")
+  if(dir.exists(paste0(path, "/divewatchr_data"))){
+
+    load('divewatchr_data/scuba_clean.RData')
+  }
 
   ggplot(scuba_clean, aes(x = country, fill = paste0(region, ", " ,country))) +
     geom_bar(alpha = 0.7, position = "dodge2") +

diff --git a/R/divesite_depths.R b/R/divesite_depths.R
@@ -21,9 +21,12 @@
 
 #.........................................................
 
-divesite_depths <- function (toofew = 1){
-
-  load("data/scuba_map.RData")
+divesite_depths <- function (toofew = 1, path = getwd()){
+
+  if(dir.exists(paste0(path, "/divewatchr_data"))){
+
+    load('divewatchr_data/scuba_map.RData')
+  }
 
 # Drop locations where there is only 1 dive since the point of this plot is showing variation
   y <- scuba_map %>% filter (locationID %in% (scuba_map %>%

diff --git a/R/divetypes.R b/R/divetypes.R
@@ -19,9 +19,12 @@
 
 #.........................................................
 
-divetypes <- function (n.other = 4){
+divetypes <- function (n.other = 4, path = getwd()){
 
-  load("data/scuba_clean.RData")
+  if(dir.exists(paste0(path, "/divewatchr_data"))){
+
+    load('divewatchr_data/scuba_clean.RData')
+  }
   # Plot platformTypes
 types <-  count(scuba_clean, diveType, diveClass) %>%
           mutate(diveType = ifelse(n < n.other, "Other", diveType),

diff --git a/R/divetypes_platform.R b/R/divetypes_platform.R
@@ -15,9 +15,12 @@
 
 #.........................................................
 
-divetypes_platform <- function (){
-
-  load("data/scuba_clean.RData")
+divetypes_platform <- function (path = getwd()){
+
+  if(dir.exists(paste0(path, "/divewatchr_data"))){
+
+    load('divewatchr_data/scuba_clean.RData')
+  }
   # Plot platformTypes
   ggplot(scuba_clean, aes(x = platformType, fill = paste0(region, ", " ,country))) +
     geom_bar(alpha = 0.7, position = "dodge2") +

diff --git a/R/test_data.R → R/example_data.R b/R/test_data.R → R/example_data.R
@@ -1,10 +1,10 @@
-#' Creates a fake dataset
+#' Creates a example dataset
 #'
-#' Creates a fake dataset with the basic data to perform the visualizations of the package
+#' Creates a example dataset with the basic data to perform the visualizations of the package
 #'
-#' This function creates a model dataset with the structure 
+#' This function creates an example dataset with the structure 
 #' needed to perform the visualization functions from the divewatchr package.
-#' It can be used to test the other functions and to show the user how the data must look like.
+#' It can be used to run the other functions and to show the user how the data must look like.
 #' The output dataset must be copypasted in a google sheets spreadsheet and the user
 #' needs to make sure that the data is formatted as character/text
 #' 
@@ -15,14 +15,14 @@
 #' @import dplyr
 #' 
 #' @export
-#' @return 2 csv files with fake data.
+#' @return 4 csv files with example data.
 #' @examples
-#' test_data()
+#' example_data()
 
 
-test_data <- function(path = getwd()){
+example_data <- function(path = getwd()){
 
-test_data_logbook <- data.frame (eventDate = sample(seq(as.Date('1999/01/01'),
+example_data_logbook <- data.frame (eventDate = sample(seq(as.Date('1999/01/01'),
                                                   as.Date('2020/01/01'),
                                                   by="day"), 500),
                          eventTime = NA,
@@ -83,7 +83,7 @@ test_data_logbook <- data.frame (eventDate = sample(seq(as.Date('1999/01/01'),
 
 
 
-test_data_coordinates <- data.frame (locationID	= c("Piscina ZOEA"	,
+example_data_coordinates <- data.frame (locationID	= c("Piscina ZOEA"	,
                                                     "Marina del Este"	,
                                                     "La Cueva de la Virgen"	,
                                                     "Chocolate Island"	,
@@ -180,7 +180,7 @@ test_data_coordinates <- data.frame (locationID	= c("Piscina ZOEA"	,
                                      caveType = NA)
 
 
-test_data_divetypes <- data.frame (diveType = c("Advanced Open Water Diver Course"	,
+example_data_divetypes <- data.frame (diveType = c("Advanced Open Water Diver Course"	,
                                                 "Cleaning Dive Leading"	,
                                                 "PADI AOWD Assistance"	,
                                                 "PADI DSD Assistance"	,
@@ -227,7 +227,7 @@ test_data_divetypes <- data.frame (diveType = c("Advanced Open Water Diver Cours
                                                     "Training"))
 
 
-test_data_certifications <- data.frame (diverID = c("XXXXXX",
+example_data_certifications <- data.frame (diverID = c("XXXXXX",
                                                     "XXXXXX",
                                                     "XXXXXX",
                                                     "XXXXXX"
@@ -254,9 +254,9 @@ test_data_certifications <- data.frame (diverID = c("XXXXXX",
 
 
 
-if(!dir.exists(paste0(path, "/test_data"))) {dir.create("test_data")}
-write.csv(test_data_logbook, paste0(path, "/test_data/logbook.csv"), row.names = FALSE, na = "")
-write.csv(test_data_coordinates, paste0(path, "/test_data/coordinates.csv"), row.names = FALSE, na = "")
-write.csv(test_data_divetypes, paste0(path, "/test_data/divetypes.csv"), row.names = FALSE, na = "")
-write.csv(test_data_certifications, paste0(path, "/test_data/certifications.csv"), row.names = FALSE, na = "")
+if(!dir.exists(paste0(path, "/data-raw"))) {dir.create("data-raw")}
+write.csv(example_data_logbook, paste0(path, "/data-raw/logbook.csv"), row.names = FALSE, na = "")
+write.csv(example_data_coordinates, paste0(path, "/data-raw/coordinates.csv"), row.names = FALSE, na = "")
+write.csv(example_data_divetypes, paste0(path, "/data-raw/divetypes.csv"), row.names = FALSE, na = "")
+write.csv(example_data_certifications, paste0(path, "/data-raw/certifications.csv"), row.names = FALSE, na = "")
           }
diff --git a/R/logbook_highlights.R b/R/logbook_highlights.R
@@ -19,9 +19,19 @@
 
 #.........................................................
 
-logbook_highlights <- function(){
+logbook_highlights <- function(path = getwd()){
+
+  if(dir.exists(paste0(path, "/divewatchr_data"))){
+
+    load('divewatchr_data/scuba_clean.RData')
+  }
+
+  # } else {
+  #   
+  #   load('data/scuba_clean.RData')  
+  # }
+
 
-load('data/scuba_clean.RData')
 
 highlights <- gather(data.frame("Number_of_dives" = as.character(nrow(scuba_clean)),
                   "Number_of_dive_sites" = paste0(nrow(distinct(select(scuba_clean, locationID))),

diff --git a/R/logbook_map.R b/R/logbook_map.R
@@ -18,10 +18,13 @@
 
 #.........................................................
 
-logbook_map <- function (){
-
-  load("data/scuba_map.RData")
-  load("data/scuba_clean.RData")
+logbook_map <- function (path = getwd()){
+
+  if(dir.exists(paste0(path, "/divewatchr_data"))){
+
+    load('divewatchr_data/scuba_clean.RData')
+    load('divewatchr_data/scuba_map.RData')
+  }
 ### MAKING MAP
 #--------------------
 

diff --git a/R/logged_depths.R b/R/logged_depths.R
@@ -20,9 +20,12 @@
 #-----------------------------------------------------------------------------------------------------
 
 
-logged_depths <- function (){
-
-  load("data/scuba_map.RData")
+logged_depths <- function (path = getwd()){
+
+  if(dir.exists(paste0(path, "/divewatchr_data"))){
+
+    load('divewatchr_data/scuba_map.RData')
+  }
 # The problem of making the previous function is that scuba_map does not get generated
 
 # Plot date against max depths https://www.neonscience.org/dc-time-series-plot-ggplot-r

diff --git a/R/prep_data.R b/R/prep_data.R
@@ -41,12 +41,12 @@ if(!is.na(data)){
 (scuba_typ <- read_sheet(data, sheet = "divetypes", na = ""))
 (scuba_cert <- read_sheet(data, sheet = "certifications", na = ""))  
 } else {
-test_data()
+example_data() # not necessary this line because data will be a permanent shared folder and downloadable -- see later
 # From the test_data (in case sheets don't work)
-(scuba_log <- read.csv(paste0(path, "/test_data/logbook.csv") ))
-(scuba_geo <- read.csv(paste0(path, "/test_data/coordinates.csv") ))
-(scuba_typ <- read.csv(paste0(path, "/test_data/divetypes.csv") ))
-(scuba_cert <- read.csv(paste0(path, "/test_data/certifications.csv") ))  
+(scuba_log <- read.csv(paste0(path, "/data-raw/logbook.csv") ))
+(scuba_geo <- read.csv(paste0(path, "/data-raw/coordinates.csv") ))
+(scuba_typ <- read.csv(paste0(path, "/data-raw/divetypes.csv") ))
+(scuba_cert <- read.csv(paste0(path, "/data-raw/certifications.csv") ))  
 }
 #.........................................................
 ### DATA PROCESSING
@@ -98,10 +98,17 @@ print(st_crs(scuba_map))
 scuba_cert <- scuba_cert %>% mutate(certificationDate = as.character(certificationDate))
 
 
-if(!dir.exists(paste0(path, "/data"))) {dir.create("data")}
-save(scuba_map, file = paste0(path, "/data/scuba_map.RData"))
-save(scuba_clean, file = paste0(path, "/data/scuba_clean.RData"))
-save(scuba_cert, file = paste0(path, "/data/scuba_cert.RData"))
+if(!is.na(data)){ 
+  if(!dir.exists(paste0(path, "/divewatchr_data"))) {dir.create("divewatchr_data")}
+    save(scuba_map, file = paste0(path, "/divewatchr_data/scuba_map.RData"))
+    save(scuba_clean, file = paste0(path, "/divewatchr_data/scuba_clean.RData"))
+    save(scuba_cert, file = paste0(path, "/divewatchr_data/scuba_cert.RData"))
+} else {
+  if(!dir.exists(paste0(path, "/data"))) {dir.create("data")}
+    save(scuba_map, file = paste0(path, "/data/scuba_map.RData"))
+    save(scuba_clean, file = paste0(path, "/data/scuba_clean.RData"))
+    save(scuba_cert, file = paste0(path, "/data/scuba_cert.RData"))
+}
 
 #save(scuba_map, file = paste0(path, "/data/scuba_map.rda"))
 #save(scuba_clean, file = paste0(path, "/data/scuba_clean.rda"))

diff --git a/data-original/TSD.xls.xlsx b/data-original/TSD.xls.xlsx
diff --git a/data-original/TSRCP Spring 2017-20200509T234651Z-001.zip b/data-original/TSRCP Spring 2017-20200509T234651Z-001.zip
diff --git a/data-original/ZOEA/2018-08.xlsx b/data-original/ZOEA/2018-08.xlsx
diff --git a/data-original/ZOEA/2018-09.xlsx b/data-original/ZOEA/2018-09.xlsx
diff --git a/data-original/ZOEA/Planning 2016-07.xlsx b/data-original/ZOEA/Planning 2016-07.xlsx
diff --git a/data-original/ZOEA/Planning 2016-08.xlsx b/data-original/ZOEA/Planning 2016-08.xlsx
diff --git a/data-original/ZOEA/Planning 2016-09.xlsx b/data-original/ZOEA/Planning 2016-09.xlsx
diff --git a/data-original/ZOEA/Planning 2017-07.xlsx b/data-original/ZOEA/Planning 2017-07.xlsx
diff --git a/data-original/ZOEA/Planning 2017-08.xlsx b/data-original/ZOEA/Planning 2017-08.xlsx
diff --git a/data-original/ZOEA/Planning 2017-09.xlsx b/data-original/ZOEA/Planning 2017-09.xlsx
diff --git a/data-original/ZOEA/Planning 2017-09b.xlsx b/data-original/ZOEA/Planning 2017-09b.xlsx
diff --git a/data-original/logbook_data.csv b/data-original/logbook_data.csv
@@ -0,0 +1,44 @@
+eventID,eventDate,eventTime,locationID,locality,decimalLatitude,decimalLongitude
+D-2,2011-08,,La Cresta,"Isla del Fraile, Aguilas (Murcia)",37.407457,-1.548604
+D-1,2011-10-21,,"""frente al centro scubasur""",Almunecar (Granada),36.733577,-3.70523
+D0,2011-10-21,,"""frente al centro scubasur""",Almunecar (Granada),36.733578,-3.705231
+D1,2011-10-22,11:45,Chambao de Joaquin,La Herradura (Granada),36.728883,-3.736961
+D2,2011-10-22,14:04,La Piedra del Hombre,La Herradura (Granada),36.725076,-3.736712
+D3,2011-10-23,13:08,La Calita,La Herradura (Granada),36.721808,-3.735178
+D4,2011-10-23,14:34,La Calita,La Herradura (Granada),36.721808,-3.735178
+D5,2012-04-02,12:26,La Cresta,"Isla del Fraile, Aguilas (Murcia)",37.407457,-1.548604
+D6,2012-04-03,11:27,Pared Sur,"Isla del Fraile, Aguilas (Murcia)",37.407431,-1.547101
+D7,2012-05,,Marina del Este,Almunecar (Granada),36.722489,-3.728296
+D8,2012-06,,Marina del Este,Almunecar (Granada),36.72249,-3.728297
+D9,2012-06-16,,El Hornillo,Aguilas (Murcia),37.406587,-1.559013
+D10,2012-06-16,,La Cabeza del Caballo,Aguilas (Murcia),37.42452,-1.500005
+D11,2012-06-16,,El Hornillo,Aguilas (Murcia),37.406587,-1.559013
+D12,2012-06-17,,La Cresta,"Isla del Fraile, Aguilas (Murcia)",37.407457,-1.548604
+D13,2012-06-17,,El Fontanet,Cabo de Cope (Murcia),37.42451,-1.500005
+D14,2012-06-17,,La Cresta,"Isla del Fraile, Aguilas (Murcia)",37.407457,-1.548604
+D15,2013-04-22,,Marina del Este,Almunecar (Granada),36.72249,-3.728297
+D16,2014-04-09,,Marina del Este,Almunecar (Granada),36.72249,-3.728297
+D17,2014-06-19,,El Penhon,Salobrenha (Granada),36.736497,-3.593632
+D18,2014-07-28,,Exiles,Sliema (Malta),35.918614,14.498422
+D19,2014-07-30,,Exiles,Sliema (Malta),35.918614,14.498422
+D20,2017-08-01,,Exiles,Sliema (Malta),35.918614,14.498422
+D21,2017-08-02,,Exiles,Sliema (Malta),35.918614,14.498422
+D22,2017-08-04,,Exiles,Sliema (Malta),35.918614,14.498422
+D23,2017-08-04,,Exiles,Sliema (Malta),35.918614,14.498422
+D24,2017-08-05,,Exiles,Sliema (Malta),35.918614,14.498422
+D25,2017-08-08,,Exiles,Sliema (Malta),35.918614,14.498422
+D26,2017-08-08,,Exiles,Sliema (Malta),35.918614,14.498422
+D27,2017-08-11,,"Tug 2, Exiles",Sliema (Malta),35.919331,14.498331
+D28,2017-08-12,,"Tug 2, Exiles",Sliema (Malta),35.919331,14.498331
+D29,2017-08-13,,Exiles,Sliema (Malta),35.918614,14.498422
+D30,2017-08-14,,Exiles,Sliema (Malta),35.918614,14.498422
+D31,2018-05-28,,A catedral,Sagres (Portugal),37.006141,-8.92733
+D32,2018-05-28,,A catedral,Sagres (Portugal),37.006141,-8.92733
+D33,2019-07-06,10:58,Grevelingenmeer,"Zeeland, Netherland",51.747398,3.89119
+D34,2019-07-06,14:02,Grevelingenmeer,"Zeeland, Netherland",51.747398,3.89119
+D35,2019-08-10,10:36,La Cueva de la Virgen,Cabo de Cope (Murcia),37.424511,-1.500004
+D36,2019-08-11,12:16,El Mindanao,Cabo de Cope (Murcia),37.424511,-1.500005
+D37,2019-08-15,10:23,La Cresta,"Isla del Fraile, Aguilas (Murcia)",37.407457,-1.548604
+D38,2019-08-15,11:58,Pared Sur,"Isla del Fraile, Aguilas (Murcia)",37.407431,-1.547101
+D39,2019-10-05,14:30,Oesterdam,"Zeeland, Netherland",51.516707,4.17167
+D40,2019-10-05,15.14,Oesterdam,"Zeeland, Netherland",51.516708,4.171671
diff --git a/data-original/malapascua-data.xlsx b/data-original/malapascua-data.xlsx
diff --git a/data/scuba_cert.RData b/data/scuba_cert.RData
diff --git a/data/scuba_clean.RData b/data/scuba_clean.RData
diff --git a/data/scuba_map.RData b/data/scuba_map.RData
diff --git a/files/overview.Rmd b/files/overview.Rmd
@@ -141,7 +141,7 @@ knitr::kable(logbook_highlights())
 This data frame shows the diving logbook used. Personal information such as eventRemarks are omitted from this data frame
 
 ```{r echo=FALSE, rows.print=15}
-load('data/scuba_clean.RData')
+load('divewatchr_data/scuba_clean.RData')
 
 
 transmute (scuba_clean, eventDate, locationID, locality, maximumDepth = maximumDepthInMeters, bottomTime, diveType, diveClass, platformType, region, country)
@@ -154,7 +154,7 @@ transmute (scuba_clean, eventDate, locationID, locality, maximumDepth = maximumD
 ## Certifications 
 
 ```{r echo=FALSE, rows.print=15}
-load('data/scuba_cert.RData')
+load('divewatchr_data/scuba_cert.RData')
 
 knitr::kable(scuba_cert %>% select (-instructorID))
 ```

diff --git a/man/cum_dives.Rd b/man/cum_dives.Rd
diff --git a/man/divecount_reg.Rd b/man/divecount_reg.Rd
diff --git a/man/divesite_depths.Rd b/man/divesite_depths.Rd
diff --git a/man/divetypes.Rd b/man/divetypes.Rd