[R] subset data using a vector

Mon Nov 23 17:05:32 CET 2015

Dear R users,
                I like to split my data by a vector created by using variable "ranges".  This vector will have the current range (ranges), preceding range (ranges - 1), and post range (ranges + 1) for a given plotid.  If the preceding or post ranges in this vector are outside the levels of ranges in the data set then I like to drop those ranges and only include the ranges that are available.  Variable "rangestouse" includes all the desired ranges I like to subset a given plotid.  After I subset these dataset using these desired ranges, then I like to extract the yield data for checks in those desired ranges and adjust yield of my data by dividing yield of a given plotid with the check average for the desired ranges.

I have created this function (fun1) but when I run it, I get the following error:

Error in m1[[i]] : subscript out of bounds

Any help will be highly appreciated!
Thanks, Nilesh

Dataset:
dput(mydata)
structure(list(rows = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c("1", "2", "3",
"4"), class = "factor"), cols = structure(c(1L, 10L, 11L, 12L,
13L, 14L, 15L, 16L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 1L, 10L,
11L, 12L, 13L, 14L, 15L, 16L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L,
1L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 2L, 3L, 4L, 5L, 6L, 7L,
8L, 9L, 1L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 2L, 3L, 4L, 5L,
6L, 7L, 8L, 9L), .Label = c("1", "2", "3", "4", "5", "6", "7",
"8", "9", "10", "11", "12", "13", "14", "15", "16"), class = "factor"),
    plotid = c(289L, 298L, 299L, 300L, 301L, 302L, 303L, 304L,
    290L, 291L, 292L, 293L, 294L, 295L, 296L, 297L, 384L, 375L,
    374L, 373L, 372L, 371L, 370L, 369L, 383L, 382L, 381L, 380L,
    379L, 378L, 377L, 376L, 385L, 394L, 395L, 396L, 397L, 398L,
    399L, 400L, 386L, 387L, 388L, 389L, 390L, 391L, 392L, 393L,
    480L, 471L, 470L, 469L, 468L, 467L, 466L, 465L, 479L, 478L,
    477L, 476L, 475L, 474L, 473L, 472L), yield = c(5.1, 5, 3.9,
    4.6, 5, 4.4, 5.1, 4.3, 5.5, 5, 5.5, 6.2, 5.1, 5.5, 5.2, 5,
    5.6, 4.7, 5.4, 4.8, 4.6, 3.9, 4.2, 4.4, 5.3, 5.5, 5.8, 4.6,
    5.8, 4.8, 5.3, 5.5, 5.6, 4.2, 4.6, 4.2, 4.2, 4, 3.9, 4.5,
    5, 4.8, 4.9, 5.2, 5.3, 4.6, 4.8, 5.3, 4.5, 4.5, 5.1, 4.9,
    5.2, 4.6, 4.8, 5.4, 5.9, 4.9, 5.8, 5.3, 4.8, 4.7, 5.2, 5.8
    ), linecode = structure(c(1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L,
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
    1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
    2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 1L), .Label = c("check",
    "variety"), class = "factor"), ranges = c(1L, 1L, 1L, 1L,
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L,
    3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L,
    4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L
    ), rangestouse = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L,
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L,
    3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L,
    4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c("1,2",
    "1,2,3", "2,3,4", "3,4"), class = "factor")), .Names = c("rows",
"cols", "plotid", "yield", "linecode", "ranges", "rangestouse"

), class = "data.frame", row.names = c(NA, -64L))

Function:

fun1<- function (dataset, plot.id, ranges2use, control)

{

    m1 <- strsplit(as.character(dataset$ranges2use), ",")

    dat1 <- data.frame()

    m2 <- c()

    row_check_mean <- c()

    row_check_adj_yield <- c()

    x <- length(plot.id)

    for (i in (1:x)) {

        m2[i] <- m1[[i]]

        dat1 <- dataset[dataset$ranges %in% m2[i], ]

        row_check_mean[i] <- tapply(dat1$trait, dat1$control,

            mean, na.rm = TRUE)[1]

        row_check_adj_yield[i] <- ifelse(control[i] == "variety",

            trait[i]/dataset$row_check_mean[i], trait[i]/trait[i])

    }

    data.frame(dataset, row_check_adj_yield)

}

Apply function:
fun1(mydata, plot.id=mydata$plotid, ranges2use = mydata$rangestouse,control=mydata$linecode)

Error:

Error in m1[[i]] : subscript out of bounds

Session info:

R version 3.2.1 (2015-06-18)

Platform: i386-w64-mingw32/i386 (32-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252

[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):

 [1] magrittr_1.5    plyr_1.8.3      tools_3.2.1     reshape2_1.4.1  Rcpp_0.12.1     stringi_1.0-1

 [7] grid_3.2.1      agridat_1.12    stringr_1.0.0   lattice_0.20-31

Nilesh Dighe
(806)-252-7492 (Cell)
(806)-741-2019 (Office)

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