[R] spatial adjustment using checks
DIGHE, NILESH [AG/2362]
nilesh.dighe at monsanto.com
Thu Oct 22 19:10:29 CEST 2015
Hi,
I have yield data for several varieties and a randomly placed check (1 in every 8 column or "cols") in a field test arranged in a rows*cols grid format (see image attached). Both "rows" & "cols" are variables in the data set. I like to adjust "yield" variable for each row listed as "variety" in variable "linecode" by dividing its yield with the average yield of four nearest "check" (on the rows*cols field grid) in variable "linecode". I like to have two checks on the same row where one check is on the left and the other is on the right side of a given variety. The other two checks should come from the two neighboring columns ("cols"). If a check is missing on one or more sides of a given variety, then I like to proceed with the calculation with only the available checks around that given variety. If two checks on the neighboring column are equidistance from a given variety then use position of the variety to choose which one to use (If variety is in cols 1-8 then use check from those cols; if variety is in cols 9-16 then use check from cols 9-16).
Below is the function I wrote which adjust yield values for each "variety" (variable "linecode") by dividing its yield with the average yield of all checks in the field. Instead of using average check across the whole field, I like to use the four neighboring checks to make this adjustment. I am struggling with specifying the four nearest checks in this loop. I played around using "dist" function but without any success. I tried searching for any packages that can do these nearest check adjustments without any success. Any help will be appreciated.
-------------------function------------------------------------------
function (dataset, trait, control) {
m <- c()
x <- length(trait)
chkmean <- tapply(trait, control, mean, na.rm = T)
for (i in 1:x) {
m[i] <- ifelse(control[i] == "variety", trait[i]/chkmean[1],
trait[i]/trait[i])
}
head(as.data.frame(m))
}
---------------------data----------------------------------------------------------------------
dput(dat)
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, 2L, 3L, 4L, 5L,
6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 16L, 15L,
14L, 13L, 12L, 11L, 10L, 9L, 8L, 7L, 6L, 5L, 4L, 3L, 2L, 1L,
1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L,
15L, 16L, 16L, 15L, 14L, 13L, 12L, 11L, 10L, 9L, 8L, 7L, 6L,
5L, 4L, 3L, 2L, 1L), .Label = c("1", "2", "3", "4", "5", "6",
"7", "8", "9", "10", "11", "12", "13", "14", "15", "16"), class = "factor"),
plotid = c(289L, 290L, 291L, 292L, 293L, 294L, 295L, 296L,
297L, 298L, 299L, 300L, 301L, 302L, 303L, 304L, 369L, 370L,
371L, 372L, 373L, 374L, 375L, 376L, 377L, 378L, 379L, 380L,
381L, 382L, 383L, 384L, 385L, 386L, 387L, 388L, 389L, 390L,
391L, 392L, 393L, 394L, 395L, 396L, 397L, 398L, 399L, 400L,
465L, 466L, 467L, 468L, 469L, 470L, 471L, 472L, 473L, 474L,
475L, 476L, 477L, 478L, 479L, 480L), yield = c(5.1, 5.5,
5, 5.5, 6.2, 5.1, 5.5, 5.2, 5, 5, 3.9, 4.6, 5, 4.4, 5.1,
4.3, 4.4, 4.2, 3.9, 4.6, 4.8, 5.4, 4.7, 5.5, 5.3, 4.8, 5.8,
4.6, 5.8, 5.5, 5.3, 5.6, 5.6, 5, 4.8, 4.9, 5.2, 5.3, 4.6,
4.8, 5.3, 4.2, 4.6, 4.2, 4.2, 4, 3.9, 4.5, 5.4, 4.8, 4.6,
5.2, 4.9, 5.1, 4.5, 5.8, 5.2, 4.7, 4.8, 5.3, 5.8, 4.9, 5.9,
4.5), line = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
9L, 1L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L,
20L, 1L, 21L, 22L, 1L, 23L, 24L, 25L, 26L, 27L, 28L, 29L,
30L, 31L, 32L, 33L, 1L, 34L, 35L, 36L, 37L, 38L, 39L, 40L,
41L, 42L, 1L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 1L,
51L, 52L, 53L, 54L, 1L, 55L, 56L, 57L), .Label = c("CHK",
"V002", "V003", "V004", "V005", "V006", "V007", "V008", "V009",
"V010", "V011", "V012", "V013", "V014", "V015", "V016", "V017",
"V018", "V019", "V020", "V021", "V022", "V023", "V024", "V025",
"V026", "V027", "V028", "V029", "V030", "V031", "V032", "V033",
"V034", "V035", "V036", "V037", "V038", "V039", "V040", "V041",
"V042", "V043", "V044", "V045", "V046", "V047", "V048", "V049",
"V050", "V051", "V052", "V053", "V054", "V055", "V056", "V057"
), class = "factor"), linecode = structure(c(1L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L,
2L), .Label = c("check", "variety"), class = "factor")), .Names = c("rows",
"cols", "plotid", "yield", "line", "linecode"), row.names = c(NA,
-64L), class = "data.frame")
-------------------------------------------------------------------------------------------------
My expected output is in column "adj_yield" below:
rows cols plotid yield line linecode adj_yield
1 1 1 289 5.1 CHK check check
2 1 2 290 5.5 V002 variety 1.071
3 1 3 291 5.0 V003 variety 0.974
4 1 4 292 5.5 V004 variety 1.071
5 1 5 293 6.2 V005 variety 1.208
6 1 6 294 5.1 V006 variety 0.994
7 1 7 295 5.5 V007 variety 1.071
8 1 8 296 5.2 V008 variety 1.013
9 1 9 297 5.0 V009 variety 0.974
10 1 10 298 5.0 CHK check check
11 1 11 299 3.9 V010 variety 0.750
12 1 12 300 4.6 V011 variety 0.885
13 1 13 301 5.0 V012 variety 0.962
14 1 14 302 4.4 V013 variety 0.846
15 1 15 303 5.1 V014 variety 0.981
16 1 16 304 4.3 V015 variety 0.827
17 2 16 369 4.4 V016 variety check
18 2 15 370 4.2 V017 variety 0.881
19 2 14 371 3.9 V018 variety 0.818
20 2 13 372 4.6 V019 variety 0.965
21 2 12 373 4.8 V020 variety 1.007
22 2 11 374 5.4 CHK check check
23 2 10 375 4.7 V021 variety 0.959
24 2 9 376 5.5 V022 variety 1.053
25 2 8 377 5.3 CHK check check
26 2 7 378 4.8 V023 variety 0.923
27 2 6 379 5.8 V024 variety 1.115
28 2 5 380 4.6 V025 variety 0.885
29 2 4 381 5.8 V026 variety 1.115
30 2 3 382 5.5 V027 variety 1.058
31 2 2 383 5.3 V028 variety 1.019
32 2 1 384 5.6 V029 variety 1.077
-----------------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
other attached packages:
[1] rlist_0.4.5.1 mapplots_1.5 agridat_1.12
loaded via a namespace (and not attached):
[1] magrittr_1.5 plyr_1.8.3 tools_3.2.1 reshape2_1.4.1 Rcpp_0.12.0 stringi_0.5-5
[7] grid_3.2.1 data.table_1.9.4 stringr_1.0.0 chron_2.3-47 lattice_0.20-31
Nilesh Dighe
(806)-252-7492 (Cell)
(806)-741-2019 (Office)
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