v3.0.0

Merge branch 'beta3'

# Conflicts:
#	NEWS.md
#	R/motusUpdateTagDB.R
#	R/srvQuery.R
#	R/tagme.R
#	tests/testthat/test_server.R

.Rbuildignore

@@ -1,4 +1,6 @@
 ^data-raw$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-RELEASE.R
+RELEASE.R
+^appveyor.yml$
+^.*\SG-.*$

.gitignore

@@ -4,3 +4,4 @@ nohup.out
 .Rproj.user
 .Rhistory
 .RData
+tests/spelling.R

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: motus
 Type: Package
-Version: 2.0.0
+Version: 3.0.0
 Title: Fetch and use data from the Motus Wildlife Tracking System
 Description: Retrieve, filter, and visualize telemetry data from the Motus 
     Wildlife Tracking System http://motus.org.
@@ -14,28 +14,27 @@ Depends:
 Imports:
     DBI (>= 1.0.0),
     dplyr (>= 0.8.1),
-    dbplyr (>= 1.4.0),
+    dbplyr (>= 1.4.2),
     httr (>= 1.4.0),
     geosphere (>= 1.5.7),
     ggplot2 (>= 3.2.0),
     gridExtra (>= 2.3),
     jsonlite (>= 1.6),
-    lattice (>= 0.20.38),
     lubridate (>= 1.7.4),
+    magrittr,
     maptools (>= 0.9.5),
     methods,
     purrr (>= 0.3.0),
     rlang (>= 0.3.1),
     RSQLite (>= 2.1.1),
-    stringi (>= 1.4.3),
     stringr (>= 1.4.0),
     tidyr (>= 0.8.3),
-    magrittr
 Suggests:
-    spelling,
     ggmap (>= 3.0.0),
-    testthat,
-    roxygen2
+    RCurl,
+    roxygen2,
+    spelling,
+    testthat
 License: GPL-3 + file LICENSE
 Date: 2019-03-28
 RoxygenNote: 6.1.1

NAMESPACE

@@ -1,73 +1,39 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("$",safeSQL)
-S3method(print,safeSQL)
 export("%>%")
 export(":=")
 export(.data)
-export(RL)
 export(activity)
 export(checkVersion)
 export(clarify)
 export(createRunsFilter)
-export(dbInsertOrReplace)
 export(deleteRunsFilter)
 export(filterByActivity)
-export(getDBFilename)
-export(getLotekModel)
 export(getMotusDBSrc)
 export(getRuns)
-export(getRunsFilterID)
 export(getRunsFilters)
 export(listRunsFilters)
-export(makeAllambigsView)
-export(makeAlltagsView)
-export(makeSimpletagsView)
 export(metadata)
 export(motusLogout)
-export(motus_vars)
+export(nodeData)
 export(plotAllTagsCoord)
 export(plotAllTagsSite)
 export(plotDailySiteSum)
 export(plotRouteMap)
 export(plotSite)
 export(plotSiteSig)
 export(plotTagSig)
-export(safeSQL)
 export(simSiteDet)
 export(siteSum)
 export(siteSumDaily)
 export(siteTrans)
 export(sqliteToRDS)
-export(srvAPIinfo)
-export(srvAuth)
-export(srvBatchesForAll)
-export(srvBatchesForReceiver)
-export(srvBatchesForTagProject)
-export(srvDeviceIDForReceiver)
-export(srvGPSforReceiver)
-export(srvGPSforTagProject)
-export(srvHitsForReceiver)
-export(srvHitsForTagProject)
-export(srvMetadataForReceivers)
-export(srvMetadataForTags)
-export(srvProjectAmbiguitiesForTagProject)
-export(srvPulseCountsforReceiver)
-export(srvReceiversForProject)
-export(srvRecvMetadataForProjects)
-export(srvRunsForReceiver)
-export(srvRunsForTagProject)
-export(srvSizeOfUpdateForReceiver)
-export(srvSizeOfUpdateForTagProject)
-export(srvTagMetadataForProjects)
-export(srvTagsForAmbiguities)
 export(sunRiseSet)
 export(tagSum)
 export(tagSumSite)
 export(tagme)
 export(tellme)
 export(timeToSunriset)
-export(updateMotusDb)
 export(writeRunsFilter)
 importFrom(magrittr,"%>%")
 importFrom(rlang,":=")

NEWS.md

@@ -1,3 +1,18 @@
+# motus 3.0.0 (2019-10-16)
+
+### Big Changes
+* Switch to data version 2
+    * Includes new CTT antennas
+    * Includes `nodeData` and `nodeDeps` tables for node related data and metadata.
+
+### Small Changes
+* Replace all `cat()` with `message()` (now suppressible)
+* Add `recvUtcOffset` and `tsCorrected` to `alltags` view
+* Add `gpsID` to `gps` table, `gpsID` is now the primary key and index
+
+### Bug fixes
+* Fixed bug where `tagme(..., countOnly = TRUE)` failed
+
 # motus 2.0.0 (2019-08-12)
 
 ### Big Changes

R/Motus.R

@@ -24,7 +24,7 @@
 #' \item{myProjects}{project IDs for user at motus.org}
 #' }
 #'
-#' @export
+#' @noRd
 #'
 #' @author John Brzustowski \email{jbrzusto@@REMOVE_THIS_PART_fastmail.fm}
 

R/activity.R

@@ -1,19 +1,19 @@
 #' Add/update batch activity
 #' 
-#' Download or resume a download of the 'activity' table in an existing Motus
+#' Download or resume a download of the `activity` table in an existing Motus
 #' database. Batch activity refers to the number of hits detected during a given
 #' batch. Batches with large numbers of hits may indicate interference and thus
 #' unreliable hits.
 #'
 #' @param src src_sqlite object representing the database
-#' @param resume Logical. Resume a download? Otherwise the activity table is
+#' @param resume Logical. Resume a download? Otherwise the `activity` table is
 #'   removed and the download is started from the beginning.
 #' 
 #' @details This function is automatically run by the [tagme()] function with
 #'   `resume = TRUE`. 
 #'   
-#'   If an 'activity' table doesn't exist, it will be created prior to
-#'   downloading. If there is an existing 'activity' table, this will update the
+#'   If an `activity` table doesn't exist, it will be created prior to
+#'   downloading. If there is an existing `activity` table, this will update the
 #'   records.
 #'
 #' @examples
@@ -35,62 +35,25 @@
 #' @export
 
 activity <- function(src, resume = FALSE) {
-  # Update to include activity table
-  src <- updateMotusDb(src, src)
 
-  sql <- safeSQL(src)
-
-  # Fetch/resume activity download
-  batches <- sql("select batchID from batches")[[1]]
-  p <- sql("select val from meta where key='tagProject'")[[1]] %>%
-    as.integer()
-
-  if(resume) {
-    # If updating, start with last batch downloaded (a bit of overlap)
-    last_batch <- sql("select ifnull(max(batchID), 0) from activity")[[1]]  
-    batches <- batches[batches >= last_batch]
-  } else {
-    # Otherwise remove all rows and start again
-    DBI::dbExecute(src$con, "DELETE FROM activity")
+  getBatches <- function(src) {
+    dplyr::tbl(src$con, "batches") %>%
+      dplyr::pull(.data$batchID)
   }
 
-  if(length(batches) > 0) {
-    for(i in 1:length(batches)) {
-      batchID <- batches[i]
-      # Get first batch
-      b <- srvActivityForBatches(batchID = batchID)
-
-      # If this is the last batch, check if actually new, or just the end of the record
-      if(resume && i == 1 && identical(last_batch, batches)) {
-        t <- dplyr::tbl(src$con, "activity") %>%
-          dplyr::filter(batchID == batches[i]) %>%
-          dplyr::collect() %>%
-          as.data.frame()
-        if(identical(t, b)) break 
-      }
-
-      # Only first time
-      if(i == 1) message(sprintf("Project %5d:  %5d batch records to check", 
-                                 p, length(batches)))
-
-      # Progress messages
-      msg <- sprintf("batchID %8d (#%6d of %6d): ", batchID, i, length(batches))
-
-      # Get the rest of the data
-      while(nrow(b) > 0) {
-        # Save Previous batch
-        dbInsertOrReplace(sql$con, "activity", b)
-        message(msg, sprintf("got %6d activity records", nrow(b)))
-
-        # Page forward
-        ant <- b$ant[nrow(b)]
-        hourBin <- b$hourBin[nrow(b)]
-
-        # Try again
-        b <- srvActivityForBatches(batchID = batchID, 
-                                   ant = ant, hourBin = hourBin)
-      }
-    }
+  pageInitial <- function(batchID, projectID) srvActivityForBatches(batchID = batchID)
+
+  pageForward <- function(b, batchID, projectID) {
+    # Page forward
+    ant <- b$ant[nrow(b)]
+    hourBin <- b$hourBin[nrow(b)]
+
+    # Try again
+    srvActivityForBatches(batchID = batchID, 
+                          ant = ant, hourBin = hourBin) 
   }
-  src
+
+  pageDataByBatch(src, table = "activity", resume = resume,
+                  getBatches, pageInitial, pageForward)
+
 }