Added a function to read in EV exports without having to have the var…

… directory name

R/read_EV_exports_v2.R

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+#' read_EV_exports_v2:  Read in a directory of .csv files exported from Echoview
+#'
+#' @description Read in a directory of .csv files
+#' exported from Echoview.   The function preserves the cells by depth. 
+#' Uses packages readxl, readr, purrr, and dplyr.  This version (unlike read_EV_exports) does
+#' not need to have the directory variable
+#' @param SurveyName - name of survey
+#' @param DirNameFile excel file - contains paths and locations of files
+#' @param database is an optional argument for format of the .csv files to.  Default is database (1).  Spreadsheet =0 
+#' @param exportloc is an optional argument for using the Export_Dir or the Region_Export_dir column
+#' entry in the DirNameFile spreadsheet.  1 is Export_Dir, and 0 is Region_Export_dir
+#'
+#' @examples
+#' temp<-read_EV_exports_v2(SurveyName, DirNameFile,database=1,exportloc=1)
+#'
+#' @export
+
+read_EV_exports_v2<-function(SurveyName, DirNameFile,database=1,exportloc=1,...){
+
+DirTable <- readxl::read_excel(DirNameFile)  #load in directories/paths/ltocations
+DirTable_yr<- subset(DirTable, Survey ==SurveyName) #just year of interest
+DirTable_yr[] <- lapply(DirTable_yr, function(x) if(is.factor(x)) factor(x) else x)  #to ensure dataframe actually removed other variables in subset
+
+#setup folders to read in data
+BaseYearPath<-as.character(DirTable_yr$Base_Path[1]) #same for both surveys within year, select first one
+BaseProjPath<-as.character(DirTable_yr$Base_Path[1]) #same for both surveys within year, select first one
+
+
+if (exportloc==1){
+        CONV_exportbase <- file.path(DirTable_yr$Export_Dir) #set to export directory
+}
+else if (exportloc==0){
+        CONV_exportbase <- file.path(DirTable_yr$Region_Export_Dir) #set to region export directory
+}
+else {print("export location needs to be 0 or 1")}
+
+setwd(CONV_exportbase)
+# for spreadsheet format
+if (!database==1){  #if database does not equal 1; that is, spreadsheet
+NASC.list.to.combine <-list.files(file.path(CONV_exportbase), pattern = "*.csv") #be sure to verify correct number of files loaded
+CONV_10m_combine <- NASC.list.to.combine %>% purrr::map_df(~read_csv_addflnm(.))
+}
+
+else if(database==1){#database format
+     #load in analysis sheets
+     NASC.list.to.combine.analysis <-list.files(file.path(CONV_exportbase), pattern = "*analysis).csv") #be sure to verify correct number of files loaded
+     CONV_10m_combine_analysis <- NASC.list.to.combine.analysis %>% purrr::map_df(~read_csv_addflnm(.))
+
+     #load in cell sheets
+     NASC.list.to.combine.cells <-list.files(file.path(CONV_exportbase), pattern = "*cells).csv") #be sure to verify correct number of files loaded
+     CONV_10m_combine_cells <- NASC.list.to.combine.cells %>% purrr::map_df(~read_csv_addflnm(.))
+     #print(NASC.list.to.combine.cells)
+
+     #load in interval sheets
+     NASC.list.to.combine.intervals <-list.files(file.path(CONV_exportbase), pattern = "*intervals).csv") #be sure to verify correct number of files loaded
+     CONV_10m_combine_intervals <- NASC.list.to.combine.intervals %>% purrr::map_df(~read_csv_addflnm(.))
+
+     #load in layers sheets
+     NASC.list.to.combine.layers <-list.files(file.path(CONV_exportbase), pattern = "*layers).csv") #be sure to verify correct number of files loaded
+     CONV_10m_combine_layers <- NASC.list.to.combine.layers %>% purrr::map_df(~read_csv_addflnm(.))
+
+     #do joins
+     temp <- dplyr::inner_join(CONV_10m_combine_cells, CONV_10m_combine_intervals, by=c("Process_ID","Interval"))
+     temp <- dplyr::inner_join(temp, CONV_10m_combine_layers, by=c("Process_ID","Layer"))  
+     CONV_10m_join<- dplyr::inner_join(temp, CONV_10m_combine_analysis, by="Process_ID")
+     CONV_10m_join$Transect <- sapply(strsplit(CONV_10m_join$filename.x,"_", fixed = TRUE),`[`,1)
+     CONV_10m_join$ID <- paste(CONV_10m_join$Transect,CONV_10m_join$Interval, sep="_") 
+     CONV_10m_join$Survey <- paste(SurveyName) 
+     CONV_10m_join$Transect<-as.numeric(gsub(".*?([0-9]+).*", "\\1", CONV_10m_join$Transect))  #Make into the transect number itself (e.g. 1 instead of x1)
+     CONV_10m_join  #return result
+     }
+}
+
+