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comparison obisindicators.r @ 1:d7b6ff32d072 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit d1d3e8640457c30349b842ea05de64b9312890f4
author ecology
date Wed, 25 Jan 2023 16:01:52 +0000
parents 1015a0070bac
children
comparison
equal deleted inserted replaced
0:1015a0070bac 1:d7b6ff32d072
30 longitude <- as.numeric(args[4]) 30 longitude <- as.numeric(args[4])
31 latitude <- as.numeric(args[5]) 31 latitude <- as.numeric(args[5])
32 spe <- as.numeric(args[6]) 32 spe <- as.numeric(args[6])
33 rec <- as.numeric(args[7]) 33 rec <- as.numeric(args[7])
34 crs <- as.numeric(args[8]) 34 crs <- as.numeric(args[8])
35 source(args[9]) 35 reso <- as.numeric(args[9])
36 source(args[10]) 36 source(args[10])
37 source(args[11]) 37 source(args[11])
38 source(args[12])
38 } 39 }
39 40
40 if (hr == "false") { 41 if (hr == "false") {
41 hr <- FALSE 42 hr <- FALSE
42 }else { 43 }else {
61 colnames(occ)[rec] <- c("records") 62 colnames(occ)[rec] <- c("records")
62 63
63 #Create a discrete global grid 64 #Create a discrete global grid
64 #Create an ISEA discrete global grid of resolution 9 using the dggridR package: 65 #Create an ISEA discrete global grid of resolution 9 using the dggridR package:
65 66
66 dggs <- dggridR::dgconstruct(projection = "ISEA", topology = "HEXAGON", res = 9) 67 dggs <- dggridR::dgconstruct(projection = "ISEA", topology = "HEXAGON", res = reso)
67 68
68 #Then assign cell numbers to the occurrence data 69 #Then assign cell numbers to the occurrence data
69 occ$cell <- dggridR::dgGEO_to_SEQNUM(dggs, occ$decimalLongitude, occ$decimalLatitude)[["seqnum"]] 70 occ$cell <- dggridR::dgGEO_to_SEQNUM(dggs, occ$decimalLongitude, occ$decimalLatitude)[["seqnum"]]
70 71
71 #Calculate indicators 72 #Calculate indicators