doc updates

R/mod_afs_study_beach_census.R

@@ -110,16 +110,17 @@ mod_afs_study_beach_census_server <- function(id, src, season.df, tab) {
           grepl("_count", census.names) | grepl("_sum", census.names)]
 
         validate(
-          need(all(afs.study.beach.counts %in% census.names) &
-                 all(choices.names.cs %in% afs.study.beach.counts),
+          need(all(tamatoamlr::afs.study.beach.counts %in% census.names) &
+                 all(choices.names.cs %in% tamatoamlr::afs.study.beach.counts),
                paste("The column names from afs.study.beach.counts",
                      "and names(census_df_collect()) are not identical -",
                      "please adjust the afs.study.beach.counts variable"))
         )
 
         selectInput(
           session$ns("age_sex"), tags$h5("Columns to plot"),
-          choices = afs.study.beach.counts, selected = c("pup_live_count"),
+          choices = tamatoamlr::afs.study.beach.counts,
+          selected = c("pup_live_count"),
           multiple = TRUE, selectize = TRUE
         )
       })

R/mod_season_info.R

@@ -4,7 +4,7 @@
 #'
 #' @name mod_season_info
 #'
-#' @param id character used to specify namespace, see \code{\link[shiny]{NS}}
+#' @param id character used to specify namespace, see [shiny::NS()]
 #' @param col.width integer; column width of column of UI widgets
 #'
 #' @export
@@ -25,18 +25,17 @@ mod_season_info_ui <- function(id, col.width = 7) {
 
 #' @name mod_season_info
 #'
-#' @param pool reactive; a DBI database connection pool,
-#'   intended to be the output of \code{\link{mod_database_server}}
-#' @param si.name character; name of season information table.
-#'   Default is 'season_info'
+#' @param src reactive; a DBI database connection src, intended to be the output
+#'   of `mod_database_server()`
+#' @param si.name character; name of season information table. Default is
+#'   'season_info'
 #'
-#' @returns
-#' \code{mod_season_server} returns a list with one component:
-#' a reactive of the season information data frame
+#' @returns `mod_season_server()` returns a list with one component: a reactive
+#' of the season information data frame
 #'
 #' @export
-mod_season_info_server <- function(id, pool, si.name = "season_info") {
-  stopifnot(is.reactive(pool))
+mod_season_info_server <- function(id, src, si.name = "season_info") {
+  stopifnot(is.reactive(src))
 
   moduleServer(
     id,
@@ -50,7 +49,7 @@ mod_season_info_server <- function(id, pool, si.name = "season_info") {
 
       # Get data from table
       season_info <- reactive({
-        df.out <- tbl(req(pool()), si.name) %>%
+        df.out <- tbl(req(src()), si.name) %>%
           select(-ts) %>%
           arrange(desc(season_open_date)) %>%
           collect()

R/mutate_factor_species.R

@@ -1,18 +1,20 @@
 #' Convert species column to a factor
 #'
-#' A 'wrapper' around mutate that converts the species column to a factor with the specified levels
+#' A 'wrapper' around mutate that converts the species column to a factor with
+#' the specified levels
 #'
 #' @param x data frame that at minimum contains a 'species' column
-#' @param levels character; passed to 'levels' argument of \code{\link[base]{factor}}.
-#'   Default is \code{names(\link{pinniped.sp})}
+#' @param levels character; passed to 'levels' argument of
+#'   \code{\link[base]{factor}}. Default is \code{names(\link{pinniped.sp})}
 #'
-#' @details A wrapper around \code{\link[dplyr]{mutate}} that converts
-#'   the species column to a factor with the specified levels.
-#'   This allows this function to be used directly in dplyr pipelines.
+#' @details A wrapper around \code{\link[dplyr]{mutate}} that converts the
+#'   species column to a factor with the specified levels. This allows this
+#'   function to be used directly in dplyr pipelines.
 #'
-#' @return \code{x}, with the column 'species' converted to a \link[base]{factor} that
-#'   has levels: \code{\link[base]{names}(\link{pinniped.sp})}, i.e.
-#'   \code{c("Fur seal", "Crabeater seal", etc.)}
+#' @return \code{x}, with the column 'species' converted to a
+#'   \link[base]{factor} that has levels:
+#'   \code{\link[base]{names}(\link{pinniped.sp})}, i.e. \code{c("Fur seal",
+#'   "Crabeater seal", etc.)}
 #'
 #' @examples
 #' x <- data.frame(species = c("Fur seal", "Weddell seal"), count = c(2, 1))

R/shiny-modules.R

@@ -1,17 +1,15 @@
-#' Modules for the different tabs of Tamatoa, the tamatoamlr Shiny app
+#' Tamatoa data modules
 #'
-#' Modules for the different tabs of Tamatoa, the tamatoamlr Shiny app
+#' Modules for the different tabs of Tamatoa, the `tamatoamlr` Shiny app
 #'
 #' @name shiny_modules
 #'
-#' @param id character used to specify namespace, see \code{shiny::\link[shiny]{NS}}
-#' @param src reactive; a DBI database connection.
-#'   Intended to be the output of \code{\link{mod_database_server}},
-#'   i.e. a pool object
-#' @param season.df reactive; the season info data frame.
-#'   Intended to be the first element (\code{season.df}) of
-#'   the (list) output of \code{\link{mod_filter_season_server}}
-#' @param tab reactive; the selected tab.
-#'   Used by the modules to only collect data from database if the
-#'   relevant tab is chosen
+#' @param id character used to specify namespace, see [shiny::NS()]
+#' @param src reactive; a DBI database connection. Intended to be the output of
+#'   [mod_database_server()], i.e. a pool object
+#' @param season.df reactive; the season info data frame. Intended to be the
+#'   first element (`season.df`) of the (list) output of
+#'   [mod_filter_season_server()]
+#' @param tab reactive; the selected tab. Used by the modules to only collect
+#'   data from database if the relevant tab is chosen
 NULL

R/tamatoa.R

@@ -73,6 +73,8 @@ tamatoa <- function(...,
       if (dbIsValid(pool.remote.prod)) poolClose(pool.remote.prod)
     if (isTruthy(pool.remote.test))
       if (dbIsValid(pool.remote.test)) poolClose(pool.remote.test)
+    if (isTruthy(pool.local.prod))
+      if (dbIsValid(pool.local.prod)) poolClose(pool.local.prod)
   })
 
 
@@ -161,6 +163,7 @@ tamatoa <- function(...,
     ### Quit GUI
     session$onSessionEnded(function() {
       # Close current pool object. Needed here in case working off 'other' db
+      # on.exit(dbDisconnect(conn))
       isolate({
         if (inherits(db.pool(), "Pool")) {
           if (dbIsValid(db.pool())) {

R/tamatoamlr-package.R

@@ -41,7 +41,82 @@
 #' @keywords package
 "_PACKAGE"
 
+
+
 # https://github.com/hadley/r-pkgs/issues/828
 ignore_unused_imports <- function() {
   dbplyr::sql
 }
+
+
+
+# https://github.com/r-lib/tidyselect/issues/248
+# https://r-pkgs.org/package-within.html#echo-a-working-package
+utils::globalVariables(c(
+  "where", ".",
+
+  # Commonly used variables
+  "observer", "location", "location_group", "beach_id", "species",
+  "Beach", "Beaches", "loc_lower", "loc_clean", "week_num", "header_id",
+  "capture_id",
+
+  # Plotting
+  "count_class", "count_value", "species_lty",
+
+  # season_info
+  "season_name", "season_open_date", "season_close_date", "season_days",
+  "diet_scat_date", "date_median_pupping", "ts",
+
+  # Phocid census
+  "census_phocid_header_id", "census_id", "census_type",
+  "census_date_start", "census_date_end",
+  "census_date", "time_start", "time_end",
+  "ad_female_count", "ad_male_count", "ad_unk_count",
+  "juv_female_count", "juv_male_count", "juv_unk_count",
+  "pup_live_count", "pup_dead_count",
+  "unk_female_count", "unk_male_count", "unk_unk_count",
+  "census_notes", "census_created_dt",
+
+
+  # AFS Capewide Pup Census
+  "pup_count", "pup_live_count", "pup_dead_count", "date_min",
+  "count_loc_mean", "count_loc_var", "count_loc_sd", "study_beach_count",
+  "count_mean", "count_var", "count_sd", "count_range", "group",
+  "census_date_min", "count_range_perc_diff",
+
+  # AFS Study Beach Census
+  "ad_male_count_sum", "adult_male_non_terr_count", "adult_male_terr_count",
+  "adult_male_terr_noFem_count", "adult_male_terr_wFem_count",
+  "adult_male_unk_count",
+
+
+  # Misc
+  "Code", "Day", "Hr", "ID", "Mass", "Mn", "Sig", "Yr", "action",
+  "attendance_study", "body_condition", "box_time",
+  "capt_to_release", "capt_to_reunion", "capture_date", "capture_date_rm",
+  "capture_datetime", "capture_location", "capture_time", "capture_time_rm",
+  "ccamlr_pup_weights_notes", "census_afs_capewide_pup_sort", "cohort",
+  "combined_number", "d", "datetime", "datetime_prev", "days_diff",
+  "device_inventory_id", "device_num", "device_type", "exclude_count", "freq",
+  "frequency", "gas_off", "gas_on", "gas_time", "head", "header_notes", "in_box",
+  "location_fctr", "location_lty", "m", "mass_kg", "mass_std_deviation",
+  "mass_std_error", "mass_total_kg", "max_dt", "mean_mass_kg", "min_dt", "n_records",
+  "n_resights", "n_trips", "n_weights", "name", "notes_tmp", "number_of_captures",
+  "parturition", "parturition_date", "pinniped_id", "pinniped_season_id",
+  "primary_tag", "pup_alive", "pup_mortality", "pup_mortality_date", "pup_num",
+  "pup_total_count", "release_time", "research_program", "resight_date",
+  "resight_time", "reunion_time", "round_date", "round_num", "sd", "season_date",
+  "season_info_id", "sex", "sig", "station", "std_length_cm", "tag_freq_code", "tag_letter",
+  "tag_numeric", "tag_sort", "tag_type", "tagging_date", "tare_check", "tare_kg", "time",
+  "time_diff_hr", "trip_length_hr", "trip_length_hr_mean", "trip_num",
+  "trip_num_completed", "trip_num_completed_max", "notes",
+
+  "freq_chr", "recovery_date", "deployment_date", "end_date", "tag_primary",
+  "tag_type_primary", "tag_unique_primary", "non_amlr_tag_primary",
+  "tag_sort_primary", "amlr_tag_primary", "apw_collect", "unk_group_id",
+  "deployment_season", "pinniped_sex", "arrival_date", 'twins', "status", "age",
+  "on_the_fly_id", "sample_type", "sample_type_group", "age_class",
+  "individual_seals_count", "n_adults_juveniles", "n_pups", "ad_male_sum",
+  "tag_resights_leopards_id", "id_unique", "package_count"
+))
+

README.md

@@ -5,11 +5,11 @@
 [![R-CMD-check](https://github.com/us-amlr/tamatoamlr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/us-amlr/tamatoamlr/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
-tamatoamlr and Tamatoa, the package's accompanying Shiny app, are for analyzing and visualizing data collected by the [U.S. AMLR Program's](https://www.fisheries.noaa.gov/about/antarctic-ecosystem-research-division-southwest-fisheries-science-center) [Pinniped Research Group](https://www.fisheries.noaa.gov/international/science-data/pinniped-research-antarctic).
+`tamatoamlr` and Tamatoa, the package's accompanying Shiny app, are for analyzing and visualizing data collected by the [U.S. AMLR Program's](https://www.fisheries.noaa.gov/about/antarctic-ecosystem-research-division-southwest-fisheries-science-center) [Pinniped Research Group](https://www.fisheries.noaa.gov/international/science-data/pinniped-research-antarctic).
 
 ## Installation
 
-You can install the development version of tamatoamlr from [GitHub](https://github.com/) with:
+You can install the development version of `tamatoamlr` from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")
@@ -18,7 +18,7 @@ devtools::install_github("us-amlr/tamatoamlr")
 
 ## Tamatoa: Shiny app
 
-To run Tamatoa, the tamatoamlr Shiny app, locally, you must have R and [RStudio](https://www.rstudio.com/products/rstudio/download/#download) installed. From within RStudio, install tamatoamlr as described above, and then run the following code in your RStudio console to launch the Shiny app:
+To run Tamatoa, the `tamatoamlr` Shiny app, locally, you must have R and [RStudio](https://www.rstudio.com/products/rstudio/download/#download) installed. From within RStudio, install `tamatoamlr` as described above, and then run the following code in your RStudio console to launch the Shiny app:
 
 ``` r
 tamatoamlr::tamatoa()
@@ -30,10 +30,9 @@ By default, Tamatoa attempts to connect to the database on the SWFSC server. For
 
 * `mod_database_server`, from [amlrDatabases](https://github.com/us-amlr/amlrDatabases), returns the connection to the user-specified database via a [pool](https://github.com/rstudio/pool) object that is used by the rest of the tamatoamlr Shiny App modules. Pool connections to the four possible databases (remote/local and AMLR_PINNIPEDS/AMLR_PINNIPEDS_Test) may be generated and passed to `mod_database_server`, depending on the arguments passed to `tamatoa()`. 
 
-* `mod_season_info_server` returns the season information data for the rest of the modules
+* `mod_season_info_server` returns the season information data used by the rest of the modules
 
-* The 'Database and season info' tab relies on mod_database and mod_season_info. The rest of the tabs all have a dedicated module that takes at least the pool object from mod_database, and generally season.df and season.id.list from mod_season_info_server, as inputs. These modules pass both a table and a plot to mod_output_server from  [amlrDatabases](https://github.com/us-amlr/amlrDatabases), which displays the table and plot along with associated visualization and download options. These modules generally depend on views created in the database.
-TODO: this needs a system that is more robust to changes in the SQL server views. For instance, each view has a function that checks for required column names, and returns a df with standardized capitalization things?
+* The 'Database and season info' tab relies on `mod_database` and `mod_season_info`. The rest of the tabs all have a dedicated module that takes at least the pool object from `mod_database`, and generally the season.df data frame output from `mod_season_info_server`, as inputs. These modules pass both a table and a plot to `mod_output_server` from  [amlrDatabases](https://github.com/us-amlr/amlrDatabases), which displays the table and plot along with associated visualization and download options. These modules generally depend on views created in the database.
 
 ## Disclaimer