From 1c416665302a8484b6c6f95e7188d87aabf7abd4 Mon Sep 17 00:00:00 2001
From: Alejandro Ruete <alejandro@greensway.se>
Date: Fri, 15 Jan 2021 15:08:24 +0100
Subject: [PATCH] fix uniqueSpillover and example orgDate

---
 R/organizeBirds.R   |  5 ++++-
 R/overlayBirds.R    |  5 +++++
 R/summarizeBirds.R  | 36 ++++++++++++++++++------------------
 man/organizeDate.Rd |  5 ++++-
 4 files changed, 31 insertions(+), 20 deletions(-)

diff --git a/R/organizeBirds.R b/R/organizeBirds.R
index b1e889a..9510c3b 100644
--- a/R/organizeBirds.R
+++ b/R/organizeBirds.R
@@ -45,7 +45,10 @@ findCols <- function(pattern, df, exact=FALSE, value = TRUE){
 #' @export
 #' @examples
 #' ymd<-as.Date(Sys.Date())+1:5
-#' organizeDate(as.data.frame(ymd), "ymd")
+#' id<-1:5
+#' organizeDate(data.frame("id"=id,
+#'                         "ymd"=as.character(ymd)),
+#'              "ymd")
 #' @keywords internal
 organizeDate <- function(x, columns){
   if (!length(columns) %in% c(1,3)) stop("Could not create date, please specify either one or three column names")
diff --git a/R/overlayBirds.R b/R/overlayBirds.R
index 5d874ca..04ed8af 100644
--- a/R/overlayBirds.R
+++ b/R/overlayBirds.R
@@ -76,6 +76,11 @@ includeUniqueSpillover <- function(birdData, grid, visitCol){
     stop("Organized data and grid do not share the same CRS")
   }
 
+  ## rename grids id no have integers
+  for(i in 1:length(grid)){
+    slot(slot(grid, "polygons")[[i]], "ID") <- as.character(i)
+  }
+
   #Extract the unique ID from the polygons in the spdf
   ids <- data.frame(
     matrix(
diff --git a/R/summarizeBirds.R b/R/summarizeBirds.R
index 9f35fc5..45c6473 100644
--- a/R/summarizeBirds.R
+++ b/R/summarizeBirds.R
@@ -70,21 +70,24 @@ getSpatial<-function(birdOverlay, visitCol=NULL){
 
   cols2use<-c("scientificName", "year", "month", "day", visitCol)
 
-  dataRes<-lapply(dataList[birdOverlay$nonEmptyGridCells], function(x){
-
-    x<-x[,cols2use]
-    colnames(x) <- c("scientificName", "year", "month", "day", "visitCol")
-
-    return(c("nObs"=length(x[,"scientificName"]),
-             "nVis"=length(unique(x[,"visitCol"])),
-             "nSpp"=length(unique(x[,"scientificName"])),
-             "avgSll"= median(summarise(group_by(x, visitCol),
-                                       avgSLL=n_distinct(.data$scientificName))$avgSLL),
-             "nDays"=length(unique( paste0(x[,"year"],"-", as.numeric(x[,"month"]), "-", as.numeric(x[,"day"]))) ),
-             "nYears"=length(unique(x[,"year"])),
-             "visitsUID"= paste0(unique(x[,"visitCol"]), collapse = ",")
-             ))
-  })
+  dataRes<-lapply(dataList[birdOverlay$nonEmptyGridCells],
+                  function(x){
+                    x<-x[,cols2use]
+                    colnames(x) <- c("scientificName", "year", "month", "day", "visitCol")
+
+                    tmp <- c("nObs"=length(x[,"scientificName"]),
+                             "nVis"=length(unique(x[,"visitCol"])),
+                             "nSpp"=length(unique(x[,"scientificName"])),
+                             "avgSll"= median(summarise(group_by(x, .data$visitCol),
+                                                        avgSLL=n_distinct(.data$scientificName))$avgSLL),
+                             "nDays"=length(unique( paste0(x[,"year"],"-",
+                                                           as.numeric(x[,"month"]), "-",
+                                                           as.numeric(x[,"day"]))) ),
+                             "nYears"=length(unique(x[,"year"])),
+                             "visitsUID"= paste0(unique(x[,"visitCol"]), collapse = ",")
+                             )
+                    return(tmp)
+                    })
 
   dataRes<-data.frame(matrix(unlist(dataRes),
                              nrow=length(dataRes), byrow=TRUE),
@@ -314,7 +317,6 @@ summarizeBirds.OrganizedBirds<-function(x, grid, spillOver = NULL){
       stop("The variable grid can only be of class SpatialPolygonsDataFrame, or NULL")
     }
   }else{
-
     areaGrid <- OB2Polygon(x)
     bTOver <- overlayBirds(x, grid=areaGrid, spillOver = spillOver)
     warning("To get the most out of summarizeBirds you should have a grid.")
@@ -322,7 +324,6 @@ summarizeBirds.OrganizedBirds<-function(x, grid, spillOver = NULL){
 
   #Here we use a modifyed version of bOver where the grid is only one single cell.
   temporal <- getTemporal(bTOver)
-
   if(useSpatial){
     #If we have spatial grid data:
     spatial <- getSpatial(bOver)
@@ -333,7 +334,6 @@ summarizeBirds.OrganizedBirds<-function(x, grid, spillOver = NULL){
     spatioTemporal <- getSpatioTemporal(bTOver, visitCol=visitCol)
     wNonEmptyCells <- bTOver$nonEmptyGridCells
   }
-
   res <- list("temporal" = temporal,
               "spatial" = spatial,
               "spatioTemporal" = spatioTemporal$resYM,
diff --git a/man/organizeDate.Rd b/man/organizeDate.Rd
index c7ac8c7..3e677f5 100644
--- a/man/organizeDate.Rd
+++ b/man/organizeDate.Rd
@@ -23,6 +23,9 @@ Organize the date-column(s) in a dataframe to three columns
 }
 \examples{
 ymd<-as.Date(Sys.Date())+1:5
-organizeDate(as.data.frame(ymd), "ymd")
+id<-1:5
+organizeDate(data.frame("id"=id,
+                        "ymd"=as.character(ymd)),
+             "ymd")
 }
 \keyword{internal}