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loop searching the id corresponding to the given index (timestamp)
5 messages · Yolande Tra, Jean V Adams, Rui Barradas
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Hello,
Try the following.
for(i in 1:dim(diveData_2008)[1]){
# Which dive is this observation from
thisIndex <- as.character(index(diveData_2008[i,]))
thisIndex <- as.POSIXct(thisIndex)
dive_id <- diveCond_all$dive_id[diveCond_all$timestamp == thisIndex]
#
[... etc ...]
And the same in the 2009 loop.
I think this is it.
Good luck,
Rui Barradas
Em 18-07-2012 14:47, Yolande Tra escreveu:
Hello,
I have the following loop for two data sets: diveData_2008 and
diveData_2009. It uses two other data: diveCond_all and fishTable. The
problem is at the point to identify the dive_id for the given index (index
is timestamp). It keeps on saying
for the1st loop
Error in fishReport$dive_id[i] <- dive_id : replacement has length zero
for the 2nd loop
Error in fishReport$dive_id[i + j] <- dive_id :
replacement has length zero
That is where the only problem resides.
Here is the code and below are the first 15 lines of data
N <- dim(diveData_2009)[1] + dim(diveData_2008)[1]
fishReport <- data.frame(matrix(0, nrow=N, ncol=11))
names(fishReport) <- c("dive_id", "site", "section", "level", "transect",
"depth", "species", "count", "size")
for(i in 1:dim(diveData_2008)[1]){
# Which dive is this observation from
thisIndex <- as.character(index(diveData_2008[i,]))
dive_id <-
diveCond_all$dive_id[diveCond_all$timestamp==thisIndex]
cat(dive_id, thisIndex, "\n")
# Store the pertinent data in the fish report data.frame
fishReport$dive_id[i] <- dive_id
fishReport$site[i] <-
diveData_2008[i,"site"]
fishReport$level[i] <-
diveData_2008[i,"level"]
fishReport$section[i] <- 0
fishReport$transect[i] <-
as.numeric(diveData_2008[i,"TRANSECT"])
fishReport$depth[i] <-
as.numeric(diveData_2008[i,"depth"])
fishReport$species[i] <-
fishTable$name_2009[fishTable$name_2008==as.character(diveData_2008[i,"species"])
][1]
fishReport$count[i] <-
as.numeric(diveData_2008[i,"count"])
fishReport$size[i] <-
as.numeric(diveData_2008[i,"size"])
fishReport$visibility[i] <-
as.numeric(diveData_2008[i,"VIS_M"])
fishReport$swell[i] <-as.numeric(diveData_2008[i,"swell_URSKI"])
}
j<-i
## The 2009 dives
for(i in i+1:dim(diveData_2009)[1]){
thisIndex <- as.character(index(diveData_2009[i,]))
dive_id <-
diveCond_all$dive_id[diveCond_all$timestamp==thisIndex]
cat(dive_id, thisIndex, "\n")
fishReport$dive_id[i+j] <- dive_id
fishReport$site[i+j] <- "Hopkins"
fishReport$level[i+j] <-
diveData_2009[i,"level"]
fishReport$transect[i+j] <-
as.numeric(diveData_2009[i,"TRANSECT"])
fishReport$depth[i+j] <-
as.numeric(diveData_2009[i,"depth"])
fishReport$species[i+j] <-
diveData_2009[i,"species"]
fishReport$count[i+j] <-
as.numeric(diveData_2008[i,"count"])
fishReport$size[i+j] <-
as.numeric(diveData_2009[i,"size"])
fishReport$visibility[i+j] <-
as.numeric(diveData_2008[i,"VIS_M"])
}
diveData_2008 (first 15 lines)
structure(c(" 1", " 1", " 1", " 1", " 1", " 1", " 1", " 1", " 1",
" 2", " 2", " 2", " 2", " 2", " 2", "8/6/2008", "8/6/2008", "8/6/2008",
"8/6/2008", "8/6/2008", "8/6/2008", "8/6/2008", "8/6/2008", "8/6/2008",
"8/6/2008", "8/6/2008", "8/6/2008", "8/6/2008", "8/6/2008", "8/6/2008",
"8:49", "8:49", "8:49", "8:49", "8:49", "8:49", "8:49", "8:49",
"8:49", "10:03", "10:03", "10:03", "10:03", "10:03", "10:03",
"S. OYT", "S. atrovirens", "S. atrovirens", "S. atrovirens",
"O. pictus", "C. nicholsii", "C. nicholsii", "D. vacca", "No organisms",
"S. OYT", "S. atrovirens", "S. atrovirens", "S. atrovirens",
"S. chrysomelas", "O. pictus", " 15", " 1", " 1", " 1",
" 1", " 1", " 1", " 1", " 1", " 1", " 1", " 1",
" 1", " 1", " 1", " 6", "23", "27", "29", " 8", " 8", " 9",
"18", NA, " 6", "23", "28", "35", "32", " 8", "Hopkins", "Hopkins",
"Hopkins", "Hopkins", "Hopkins", "Hopkins", "Hopkins", "Hopkins",
"Hopkins", "Hopkins", "Hopkins", "Hopkins", "Hopkins", "Hopkins",
"Hopkins", "15", "15", "15", "15", "15", "15", "15", "15", "15",
"10", "10", "10", "10", "10", "10", "B", "B", "B", "B", "B",
"B", "B", "B", "M", "B", "B", "B", "B", "B", "B", " 1", " 1",
" 1", " 1", " 1", " 1", " 1", " 1", " 1", " 2", " 2", " 2", " 2",
" 2", " 2", " 3.5", " 3.5", " 3.5", " 3.5", " 3.5", " 3.5", " 3.5",
" 3.5", " 3.5", " 3.5", " 3.5", " 3.5", " 3.5", " 3.5", " 3.5",
"13.9", "13.9", "13.9", "13.9", "13.9", "13.9", "13.9", "13.9",
"13.9", "13.9", "13.9", "13.9", "13.9", "13.9", "13.9", "1.0686708",
"1.0686708", "1.0686708", "1.0686708", "1.0686708", "1.0686708",
"1.0686708", "1.0686708", "1.0686708", "1.1111950", "1.1111950",
"1.1111950", "1.1111950", "1.1111950", "1.1111950"), .indexCLASS =
c("POSIXct",
"POSIXt"), tclass = c("POSIXct", "POSIXt"), .indexTZ = "", tzone = "",
class = c("xts",
"zoo"), index = structure(c(1218026940, 1218026940, 1218026940,
1218026940, 1218026940, 1218026940, 1218026940, 1218026940, 1218026940,
1218031380, 1218031380, 1218031380, 1218031380, 1218031380, 1218031380
), tzone = "", tclass = c("POSIXct", "POSIXt")), .Dim = c(15L,
13L), .Dimnames = list(NULL, c("dive_id", "date", "time", "species",
"count", "size", "site", "depth", "level", "TRANSECT", "VIS_M",
"TEMP_C", "swell_URSKI")))
diveData_2009 (first 15 lines)
structure(c("62", "62", "62", "62", "62", "62", "62", "62", "62",
"62", "62", "62", "62", "62", "62", "10/12/2009", "10/12/2009",
"10/12/2009", "10/12/2009", "10/12/2009", "10/12/2009", "10/12/2009",
"10/12/2009", "10/12/2009", "10/12/2009", "10/12/2009", "10/12/2009",
"10/12/2009", "10/12/2009", "10/12/2009", "12:44", "12:44", "12:44",
"12:44", "12:44", "12:44", "12:44", "12:44", "12:44", "12:44",
"12:44", "12:44", "12:44", "12:44", "12:44", "E. lateralis",
"E. lateralis", "E. lateralis", "E. lateralis", "O. pictus",
"S. OYT", "S. OYT", "S. atrovirens", "S. atrovirens", "S. atrovirens",
"S. atrovirens", "S. carnatus", "S. carnatus", "S. carnatus",
"S. carnatus", " 2", " 1", " 1", " 1", " 1", " 3", " 1", " 3",
" 2", " 1", " 1", " 1", " 2", " 1", " 1", "15", "22", "25", "27",
" 4", " 6", " 8", " 5", "20", "23", "25", " 5", "20", "26", "30",
"Hopkins", "Hopkins", "Hopkins", "Hopkins", "Hopkins", "Hopkins",
"Hopkins", "Hopkins", "Hopkins", "Hopkins", "Hopkins", "Hopkins",
"Hopkins", "Hopkins", "Hopkins", "15", "15", "15", "15", "15",
"15", "15", "15", "15", "15", "15", "15", "15", "15", "15", "B",
"B", "B", "B", "B", "B", "B", "B", "B", "B", "B", "B", "B", "B",
"B", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1",
"1", "1", "1", "4.0000", "4.0000", "4.0000", "4.0000", "4.0000",
"4.0000", "4.0000", "4.0000", "4.0000", "4.0000", "4.0000", "4.0000",
"4.0000", "4.0000", "4.0000"), class = c("xts", "zoo"), .indexCLASS =
c("POSIXct",
"POSIXt"), tclass = c("POSIXct", "POSIXt"), .indexTZ = "", tzone = "",
index = structure(c(1255365840,
1255365840, 1255365840, 1255365840, 1255365840, 1255365840, 1255365840,
1255365840, 1255365840, 1255365840, 1255365840, 1255365840, 1255365840,
1255365840, 1255365840), tzone = "", tclass = c("POSIXct", "POSIXt"
)), .Dim = c(15L, 11L), .Dimnames = list(NULL, c("dive_id", "date",
"time", "species", "count", "size", "site", "depth", "level",
"TRANSECT", "VIS_M")))
diveCond_all (first 15 lines)
structure(list(dive_id = structure(1:15, .Label = c(" 1", " 2",
" 3", " 4", " 5", " 6", " 7", " 8", " 9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24",
"25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35",
"36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46",
"47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57",
"58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68",
"69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79",
"80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90",
"91", "92", "93", "94", "95", "96", "97"), class = "factor"),
timestamp = structure(c(1218026940, 1218031380, 1218032700,
1218202920, 1218207180, 1218213720, 1218478320, 1218478320,
1218463800, 1218463800, 1218466860, 1218467760, 1218634260,
1218638100, 1218639720), class = c("POSIXct", "POSIXt"), tzone = ""),
visability = structure(c(5L, 5L, NA, 6L, NA, NA, NA, NA,
NA, NA, 11L, 10L, NA, NA, NA), .Label = c(" 1.5", " 2.0",
" 2.5", " 3.0", " 3.5", " 4.0", " 5.0", " 5.5", " 6.0", " 6.5",
" 7.0", " 7.5", " 8.0", " 9.0", "10.0", "12.0", "13.0", "3.0000",
"4.0000", "5.0000", "5.4864", "6.0000", "6.0960"), class = "factor"),
r_wvht = c(0.91, 1, 1.02, 0.76, 0.78, 0.78, 1.35, 1.35, 1.57,
1.57, 1.53, 1.53, 1.51, 1.53, 1.69), r_dpd = c(14.29, 4.35,
4.35, 13.33, 13.33, 8.33, 8.33, 8.33, 8.33, 8.33, 8.33, 8.33,
9.09, 9.09, 8.33), r_apt = c(4.59, 4.45, 4.26, 5.87, 6.27,
6.58, 6.7, 6.7, 6.67, 6.67, 6.66, 6.5, 6.99, 6.95, 7.19),
r_mwd = c(229, 291, 297, 226, 228, 260, 287, 287, 291, 291,
290, 290, 294, 292, 298), r_wtmp = c(12.6, 12.6, 12.5, 12.7,
12.6, 12.6, 12.8, 12.8, 12.7, 12.7, 12.7, 12.7, 13.4, 13.4,
13.5), l_salinity = c("33.513", "33.513", "33.513", "33.513",
"33.513", "33.513", "33.513", "33.513", "33.513", "33.513",
"33.513", "33.513", "33.513", "33.513", "33.513"), l_o2 = c("0",
"0", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0",
"0", "0"), l_hs = c("54.926", "54.926", "54.926", "54.926",
"54.926", "54.926", "54.926", "54.926", "54.926", "54.926",
"54.926", "54.926", "54.926", "54.926", "54.926"), l_tp = c("340.0",
"340.0", "340.0", "340.0", "340.0", "340.0", "340.0", "340.0",
"340.0", "340.0", "340.0", "340.0", "340.0", "340.0", "340.0"
), l_wdir = c("1.600", "1.600", "1.600", "1.600", "1.600",
"1.600", "1.600", "1.600", "1.600", "1.600", "1.600", "1.600",
"1.600", "1.600", "1.600"), l_along = c(NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_), l_cross = c(NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_), l_mab = c(".",
".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".",
".", "."), l_depth = c(" 9.090", " 9.090", " 9.090", " 9.090",
" 9.090", " 9.090", " 9.090", " 9.090", " 9.090", " 9.090",
" 9.090", " 9.090", " 9.090", " 9.090", " 9.090"), l_temp1 =
c("11.288",
"11.288", "11.288", "11.288", "11.288", "11.288", "11.288",
"11.288", "11.288", "11.288", "11.288", "11.288", "11.288",
"11.288", "11.288"), l_temp7 = c("13.675", "13.675", "13.675",
"13.675", "13.675", "13.675", "13.675", "13.675", "13.675",
"13.675", "13.675", "13.675", "13.675", "13.675", "13.675"
), l_temp14 = c("13.743", "13.743", "13.743", "13.743", "13.743",
"13.743", "13.743", "13.743", "13.743", "13.743", "13.743",
"13.743", "13.743", "13.743", "13.743")), .Names = c("dive_id",
"timestamp", "visability", "r_wvht", "r_dpd", "r_apt", "r_mwd",
"r_wtmp", "l_salinity", "l_o2", "l_hs", "l_tp", "l_wdir", "l_along",
"l_cross", "l_mab", "l_depth", "l_temp1", "l_temp7", "l_temp14"
), row.names = c(" 1", " 2", " 3", " 4", " 5", " 6", " 7", " 8",
" 9", "10", "11", "12", "13", "14", "15"), class = "data.frame")
fishTable (first 15 lines)
structure(list(name_2009 = c("E. lateralis", "O. pictus", "S. atrovirens",
"S. carnatus", "S. caurinus", "S. chrysomelas", "S. miniatus",
"S. mystinus", "S. OYT", "S. pinniger", "S. serriceps", "E. jacksoni",
"B. frenatus", "H. decagrammus", "S. rastrelliger"), name_2008 = c("ELAT",
"OPIC", "SATR", "SCAR", "SCAU", "SCHR", "SMIN", "SMYS", "OYT",
"SPIN", "STRE", "EJAC", "BFRE", "HDEC", "SRAS"), description = c("Striped
Surfperch,",
"Painted Greenling,", "kelp rockfish,", "gopher rockfish,", "copper
rockfish,",
"black and yellow rockfish,", "vermilion rockfish,", "blue rockfish,",
"OYT (Olive/Yellowtail) Rockfish, This species group includes Sebastes
serranoides and Sebastes flavidus (Olive/Yellowtail)",
"canary rockfish,", "treefish,", "Black Surfperch,", "Kelp Surfperch,",
"Kelp Greenling,", "grass rockfish,")), .Names = c("name_2009",
"name_2008", "description"), row.names = c(NA, 15L), class = "data.frame")
Thank you for your insight and help,
Yolande
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