[R] help with "by" function

DIGHE, NILESH [AG/2362] nilesh.dighe at monsanto.com
Tue May 12 20:03:17 CEST 2015

I have an anonymous function called function(x) that will run anova, run HSD.test on the model, and then sort the results.  I am passing this anonymous function to the "by" function to get results by "Isopair" factor which is my index variable.  Since I want to run the anova on multiple dependent variables including "Trait1" & "Trait2", I am calling the dependent variable, "trait_names" in the model and then passing the "by" function to another function called "funC" which takes the "trait_names" as an argument to execute.

After I execute the funC(data_set$trait1), I am getting the results by Isopair but the results for the two Isopairs (Isopair-A &Isopair-B) are the same which I know is not correct.  It looks like the data is not getting split by Isopairs and so ALL data is used in anova for both Isopairs.  Any help in modifying function, funC or any other ways to achieve the desired outcome will be highly appreciated.

Thanks.  Nilesh

R code, data set, and session info is pasted below.
R code:
funC<- function(trait_names){
  by(data_set, data_set$Isopair,function(x){
  mod<- aov(trait_names~ STGgroup*Field + Rep%in%Field, data=data_set)
  dfout<- arrange(data.frame(out$groups),desc(trt))
##execute funC function for Trait1 & Trait2

data_set$Isopair: Isopair-A

      trt    means M

1 STG     776.9167 a

2 Non-STG 779.0833 a


data_set$Isopair: Isopair-B

      trt    means M

1 STG     776.9167 a

2 Non-STG 779.0833 a

data_set<- structure(list(Field = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L), .Label = c("LML6", "TZL2"), class = "factor"), Isopair = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("Isopair-A", "Isopair-B"
), class = "factor"), STGgroup = structure(c(1L, 1L, 1L, 2L,
2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L,
1L, 2L, 2L, 2L), .Label = c("Non-STG", "STG"), class = "factor"),
    Rep = structure(c(1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L,
    2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L), .Label = c("Rep1",
    "Rep2", "Rep3"), class = "factor"), Trait1 = c(686L, 641L,
    642L, 727L, 619L, 562L, 808L, 739L, 744L, 873L, 797L, 868L,
    782L, 783L, 675L, 713L, 762L, 641L, 1009L, 995L, 845L, 1186L,
    912L, 663L), Trait2 = c(45L, 65L, 70L, 35L, 20L, 80L, 70L,
    65L, 70L, 20L, 30L, 35L, 40L, 55L, 35L, 40L, 35L, 40L, 40L,
    35L, 25L, 40L, 35L, 25L)), .Names = c("Field", "Isopair",
"STGgroup", "Rep", "Trait1", "Trait2"), class = "data.frame", row.names = c(NA,

Session info:

R version 3.1.3 (2015-03-09)

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

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


[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] grid      stats     graphics  grDevices utils     datasets  methods   base

other attached packages:

 [1] gridExtra_0.9.1 Hmisc_3.16-0    Formula_1.2-1   survival_2.38-1 caret_6.0-41    ggplot2_1.0.1

 [7] lattice_0.20-30 MASS_7.3-39     dplyr_0.4.1     agricolae_1.2-1

loaded via a namespace (and not attached):

 [1] acepack_1.3-3.3     assertthat_0.1      boot_1.3-15         BradleyTerry2_1.0-6

 [5] brglm_0.5-9         car_2.0-25          cluster_2.0.1       coda_0.17-1

 [9] codetools_0.2-10    colorspace_1.2-6    combinat_0.0-8      DBI_0.3.1

[13] deldir_0.1-9        digest_0.6.8        foreach_1.4.2       foreign_0.8-63

[17] gtable_0.1.2        gtools_3.4.1        iterators_1.0.7     klaR_0.6-12

[21] latticeExtra_0.6-26 lazyeval_0.1.10     LearnBayes_2.15     lme4_1.1-7

[25] magrittr_1.5        Matrix_1.1-5        mgcv_1.8-4          minqa_1.2.4

[29] munsell_0.4.2       nlme_3.1-120        nloptr_1.0.4        nnet_7.3-9

[33] parallel_3.1.3      pbkrtest_0.4-2      plyr_1.8.1          proto_0.3-10

[37] quantreg_5.11       RColorBrewer_1.1-2  Rcpp_0.11.6         reshape2_1.4.1

[41] rpart_4.1-9         scales_0.2.4        sp_1.0-17           SparseM_1.6

[45] spdep_0.5-88        splines_3.1.3       stringr_0.6.2       tools_3.1.3

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