[R] help with "by" function
DIGHE, NILESH [AG/2362]
nilesh.dighe at monsanto.com
Tue May 12 21:34:32 CEST 2015
Jean: Thanks a lot!! The changes you made to the code gave me what I needed. I truly appreciate your time in correcting the code.
Nilesh
From: Adams, Jean [mailto:jvadams at usgs.gov]
Sent: Tuesday, May 12, 2015 2:14 PM
To: DIGHE, NILESH [AG/2362]
Cc: r-help at r-project.org
Subject: Re: [R] help with "by" function
Nilesh,
I found a couple errors in your code. First, in your by() statement you have a function to operate on the selected subset of data, which you refer to as
x
but then, in your aov statement you refer to
data_set
not
x
Second, your funC() statement is a function of
trait_names
but to make sure that the name of the variable is included in the formula, I changed this to a character variable.
Give the code below a try and see if it works for you.
Jean
library(agricolae)
library(dplyr)
funC <- function(trait_names){
by(data_set, data_set$Isopair, function(x) {
mod <- aov(formula(paste(trait_names, "~ STGgroup*Field + Rep%in%Field")),
data=x)
out <- HSD.test(mod, "STGgroup", group=TRUE, console=TRUE)
dfout <- arrange(data.frame(out$groups), desc(trt))
})
}
funC("Trait1")
On Tue, May 12, 2015 at 1:03 PM, DIGHE, NILESH [AG/2362] <nilesh.dighe at monsanto.com<mailto:nilesh.dighe at monsanto.com>> wrote:
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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