Hi,
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$trait1), I am getting the results by Isopair
but the results for the two Isopairs (Isopair-A &Isopair-B) are the same which
I know is not correct. It looks like the data is not getting split by Isopairs
and so ALL data is used in anova for both Isopairs. Any help in modifying
function, funC or any other ways to achieve the desired outcome will be highly
appreciated.
Thanks. Nilesh
R code, data set, and session info is pasted below.
R code:
library(agricolae)
funC<- function(trait_names){
by(data_set, data_set$Isopair,function(x){
mod<- aov(trait_names~ STGgroup*Field + Rep%in%Field, data=data_set)
out<-HSD.test(mod,"STGgroup",group=TRUE,console=TRUE)
dfout<- arrange(data.frame(out$groups),desc(trt))
})
}
Results:
##execute funC function for Trait1 & Trait2
funC(data_set$Trait1)
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:
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,
-24L))
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
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] 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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