Thank you Rui. Very helpful. Yolande.
On Wed, Jul 18, 2012 at 1:37 PM, Rui Barradas <ruipbarra...@sapo.pt> wrote:
> 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
>>
>> [[alternative HTML version deleted]]
>>
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>> PLEASE do read the posting guide http://www.R-project.org/**
>> posting-guide.html <http://www.r-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
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