filter occurrences - add maxyear param

bin/10_Filter_occurrences.R

@@ -67,6 +67,7 @@ option_list <- list(
 
   ## Additional filters
   make_option("--minyear", action="store", default=1945, type='integer', help="Minimum year of occurrence (default, 1945)"),
+  make_option("--maxyear", action="store", default=NA,   type='integer', help="Maximum year of occurrence"),
   make_option("--noextinct", action="store", default=NA, type='character', help="Remove extinct species (provide a file with extinct specieskeys)"),
   make_option("--excludehuman", action="store", default=TRUE, type='logical', help="Exclude human records (genus Homo)"),
   make_option("--basisofrecordinclude",  action="store", default=NA, type='character', help="Basis of record to include from the data"),
@@ -125,7 +126,9 @@ POLYGON       <- to_na( opt$polygon )
 WGSRPD        <- to_na( opt$wgsrpd )
 WGSRPDREGIONS <- to_na( opt$regions )
 
-MINYEAR      <- as.numeric(to_na( opt$minyear) )
+MINYEAR <- as.numeric(to_na( opt$minyear) )
+MAXYEAR <- as.numeric(to_na( opt$maxyear) )
+
 EXTINCT      <- to_na( opt$noextinct )
 EXCLUDEHUMAN <- as.logical( opt$excludehuman )
 
@@ -165,6 +168,7 @@ cat(paste("WGSRPD regions: ",   WGSRPDREGIONS, "\n", sep=""))
 cat(paste("Basis of record to include: ", BASISINCL, "\n", sep=""))
 cat(paste("Basis of record to exclude: ", BASISEXCL, "\n", sep=""))
 cat(paste("Minimum year of occurrence: ", MINYEAR, "\n", sep=""))
+cat(paste("Maximum year of occurrence: ", MAXYEAR, "\n", sep=""))
 cat(paste("List of extict species: ",     EXTINCT, "\n", sep=""))
 cat(paste("Exclusion of human records: ", EXCLUDEHUMAN, "\n", sep=""))
 
@@ -291,9 +295,13 @@ if(!is.na(BASISINCL) & !is.na(BASISEXCL)){
 
 ## Year
 if(!is.na(MINYEAR)){
-  cat("..Filtering by collection date\n")
+  cat("..Filtering by collection date (min year)\n")
   dsf <- dsf %>% filter(year >= MINYEAR)
 }
+if(!is.na(MAXYEAR)){
+  cat("..Filtering by collection date (max year)\n")
+  dsf <- dsf %>% filter(year <= MAXYEAR)
+}
 
 ## Taxonomy filters
 if(!is.na(PHYLUM)){