User defined function to do t-tests between two datasets - r

I'm a new user trying to figure out lapply.
I have two data sets with the same 30 variables in each, and I'm trying to run t-tests to compare the variables in each sample. My ideal outcome would be a table that lists each variable along with the t stat and the p-value for the difference in that variable between the two datasets.
I tried to design a function to do the t test, so that I could then use lapply. Here's my code with a reproducible example.
height<-c(2,3,4,2,3,4,5,6)
weight<-c(3,4,5,7,8,9,5,6)
location<-c(0,1,1,1,0,0,0,1)
data_test<-cbind(height,weight,location)
data_north<-subset(data_test,location==0)
data_south<-subset(data_test,location==1)
variables<-colnames(data_test)
compare_t_tests<-function(x){
model<-t.test(data_south[[x]], data_north[[x]], na.rm=TRUE)
return(summary(model[["t"]]), summary(model[["p-value"]]))
}
compare_t_tests(height)
which gets the error:
Error in data_south[[x]] : attempt to select more than one element
My plan was to use the function in lapply like this, once I figure it out.
lapply(variables, compare_t_tests)
I'd really appreciate any advice. It seems to me like I might not even be looking at this right, so redirection would also be welcome!

You're very close. There are just a few tweaks:
Data:
height <- c(2,3,4,2,3,4,5,6)
weight <- c(3,4,5,7,8,9,5,6)
location <- c(0,1,1,1,0,0,0,1)
Use data.frame instead of cbind to get a data frame with real names ...
data_test <- data.frame(height,weight,location)
data_north <- subset(data_test,location==0)
data_south <- subset(data_test,location==1)
Don't include location in the set of variables ...
variables <- colnames(data_test)[1:2] ## skip location
Use the model, not the summary; return a vector
compare_t_tests<-function(x){
model <- t.test(data_south[[x]], data_north[[x]], na.rm=TRUE)
unlist(model[c("statistic","p.value")])
}
Compare with the variable in quotation marks, not as a raw symbol:
compare_t_tests("height")
## statistic.t p.value
## 0.2335497 0.8236578
Using sapply will automatically collapse the results into a table:
sapply(variables,compare_t_tests)
## height weight
## statistic.t 0.2335497 -0.4931970
## p.value 0.8236578 0.6462352
You can transpose this (t()) if you prefer ...

Related

How to transfer multiple columns into numeric & find correlation coefficients

I have a dataset "res.sav" that I read in via haven. It contains 20 columns, called "Genes1_Acc4", "Genes2_Acc4" etc. I am trying to find a correlation coefficient between those and another column called "Condition". I want to separately list all coefficients.
I created two functions, cor.condition.cols and cor.func to do that. The first iterates through the filenames and works just fine. The second was supposed to give me my correlations which didn't work at all. I also created a new "cor.condition.Genes" which I would like to fill with the correlations, ideally as a matrix or dataframe.
I have tried to iterate through the columns with two functions. However, when I try to pass it, I get the error: "NAs introduced by conversion". This wouldn't be the end of the world (I tried also suppressWarning()). But the bigger problem I have that it seems like my function does not convert said columns into the numeric type I need for my cor() function. I receive the "y must be numeric" error when trying to run the cor() function. I tried to put several arguments within and without '' or "" without success.
When I ran str(cor.condition.cols) I only receive character strings, which makes me think that my function somehow messes up with the as.numeric function. Any suggestions of how else I could iter through these columns and transfer them?
Thanks guys :)
cor.condition.cols <- lapply(1:20, function(x){paste0("res$Genes", x, "_Acc4")})
#save acc_4 columns as numeric columns and calculate correlations
res <- (as.numeric("cor.condition.cols"))
cor.func <- function(x){
cor(res$Condition, x, use="complete.obs", method="pearson")
}
cor.condition.Genes <- cor.func(cor.condition.cols)
You can do:
cor.condition.cols <- paste0("Genes", 1:20, "_Acc4")
res2 <- as.numeric(as.matrix(res[cor.condition.cols]))
cor.condition.Genes <- cor(res2, res$Condition, use="complete.obs", method="pearson")
eventually the short variant:
cor.condition.cols <- paste0("Genes", 1:20, "_Acc4")
cor.condition.Genes <- cor(res[cor.condition.cols], res$Condition, use="complete.obs")
Here is an example with other data:
cor(iris[-(4:5)], iris[[4]])

How to write a testthat unit test for a function that returns a data frame

I am writing a script that ultimately returns a data frame. My question is around if there are any good practices on how to use a unit test package to make sure that the data frame that is returned is correct. (I'm a beginning R programmer, plus new to the concept of unit testing)
My script effectively looks like the following:
# initialize data frame
df.out <- data.frame(...)
# function set
function1 <- function(x) {...}
function2 <- function(x) {...}
# do something to this data frame
df.out$new.column <- function1(df.out)
# do something else
df.out$other.new.column <- function2(df.out)
# etc ....
... and I ultimately end up with a data frame with many new columns. However, what is the best approach to test that the data frame that is produced is what is anticipated, using unit tests?
So far I have created unit tests that check the results of each function, but I want to make sure that running all of these together produces what is intended. I've looked at Hadley Wickham's page on testing but can't see anything obvious regarding what to do when returning data frames.
My thoughts to date are:
Create an expected data frame by hand
Check that the output equals this data frame, using expect_that or similar
Any thoughts / pointers on where to look for guidance? My Google-fu has let me down considerably on this one to date.
Your intuition seems correct. Construct a data.frame manually based on the expected output of the function and then compare that against the function's output.
# manually created data
dat <- iris[1:5, c("Species", "Sepal.Length")]
# function
myfun <- function(row, col, data) {
data[row, col]
}
# result of applying function
outdat <- myfun(1:5, c("Species", "Sepal.Length"), iris)
# two versions of the same test
expect_true(identical(dat, outdat))
expect_identical(dat, outdat)
If your data.frame may not be identical, you could also run tests in parts of the data.frame, including:
dim(outdat), to check if the size is correct
attributes(outdat) or attributes of columns
sapply(outdat, class), to check variable classes
summary statistics for variables, if applicable
and so forth
If you would like to test this at runtime, you should check out the excellent ensurer package, see here. At the bottom of the page you can see how to construct a template that you can test your dataframe against, you can make it as detailed and specific as you like.
I'm just using something like this
d1 <- iris
d2 <- iris
expect_that(d1, equals(d2)) # passes
d3 <- iris
d3[141,3] <- 5
expect_that(d1, equals(d3)) # fails

Unable to Convert Chi-Squared Values into a Numeric Column in R

I've been working on a project for a little bit for a homework assignment and I've been stuck on a logistical problem for a while now.
What I have at the moment is a list that returns 10000 values in the format:
[[10000]]
X-squared
0.1867083
(This is the 10000th value of the list)
What I really would like is to just have the chi-squared value alone so I can do things like create a histogram of the values.
Is there any way I can do this? I'm fine with repeating the test from the start if necessary.
My current code is:
nsims = 10000
for (i in 1:nsims) {cancer.cells <- c(rep("M",24),rep("B",13))
malig[i] <- sum(sample(cancer.cells,21)=="M")}
benign = 21 - malig
rbenign = 13 - benign
rmalig = 24 - malig
for (i in 1:nsims) {test = cbind(c(rbenign[i],benign[i]),c(rmalig[i],malig[i]))
cancerchi[i] = chisq.test(test,correct=FALSE) }
It gives me all I need, I just cannot perform follow-up analysis on it such as creating a histogram.
Thanks for taking the time to read this!
I'll provide an answer at the suggestion of #Dr. Mike.
hist requires a vector as input. The reason that hist(cancerchi) will not work is because cancerchi is a list, not a vector.
There a several ways to convert cancerchi, from a list into a format that hist can work with. Here are 3 ways:
hist(as.data.frame(unlist(cancerchi)))
Note that if you do not reassign cancerchi it will still be a list and cannot be passed directly to hist.
# i.e
class(cancerchi)
hist(cancerchi) # will still give you an error
If you reassign, it can be another type of object:
(class(cancerchi2 <- unlist(cancerchi)))
(class(cancerchi3 <- as.data.frame(unlist(cancerchi))))
# using the ldply function in the plyr package
library(plyr)
(class(cancerchi4 <- ldply(cancerchi)))
these new objects can be passed to hist directly
hist(cancerchi2)
hist(cancerchi3[,1]) # specify column because cancerchi3 is a data frame, not a vector
hist(cancerchi4[,1]) # specify column because cancerchi4 is a data frame, not a vector
A little extra information: other useful commands for looking at your objects include str and attributes.

Extract Group Regression Coefficients in R w/ PLYR

I'm trying to run a regression for every zipcode in my dataset and save the coefficients to a data frame but I'm having trouble.
Whenever I run the code below, I get a data frame called "coefficients" containing every zip code but with the intercept and coefficient for every zipcode being equal to the results of the simple regression lm(Sealed$hhincome ~ Sealed$square_footage).
When I run the code as indicated in Ranmath's example at the link below, everything works as expected. I'm new to R after many years with STATA, so any help would be greatly appreciated :)
R extract regression coefficients from multiply regression via lapply command
library(plyr)
Sealed <- read.csv("~/Desktop/SEALED.csv")
x <- function(df) {
lm(Sealed$hhincome ~ Sealed$square_footage)
}
regressions <- dlply(Sealed, .(Sealed$zipcode), x)
coefficients <- ldply(regressions, coef)
Because dlply takes a ... argument that allows additional arguments to be passed to the function, you can make things even simpler:
dlply(Sealed,.(zipcode),lm,formula=hhincome~square_footage)
The first two arguments to lm are formula and data. Since formula is specified here, lm will pick up the next argument it is given (the relevant zipcode-specific chunk of Sealed) as the data argument ...
You are applying the function:
x <- function(df) {
lm(Sealed$hhincome ~ Sealed$square_footage)
}
to each subset of your data, so we shouldn't be surprised that the output each time is exactly
lm(Sealed$hhincome ~ Sealed$square_footage)
right? Try replacing Sealed with df inside your function. That way you're referring to the variables in each individual piece passed to the function, not the whole variable in the data frame Sealed.
The issue is not with plyr but rather in the definition of the function. You are calling a function, but not doing anything with the variable.
As an analogy,
myFun <- function(x) {
3 * 7
}
> myFun(2)
[1] 21
> myFun(578)
[1] 21
If you run this function on different values of x, it will still give you 21, no matter what x is. That is, there is no reference to x within the function. In my silly example, the correction is obvious; in your function above, the confusion is understandable. The $hhincome and $square_footage should conceivably serve as variables.
But you want your x to vary over what comes before the $. As #Joran correctly pointed out, swap sealed$hhincome with df$hhincome (and same for $squ..) and that will help.

Return multiple data frames from function R

I am trying to put together a function that will loop thru a given data frame in blocks and return a new data frame containing stuff calculated from the original. The length of x will be different each time and the actual problem will have more loops in the function. New-ish to R and have not been able to find anything helpful (I don't think using a list will help)
func<-function(x){
tmp # need to declare this here?
for (i in 1:dim(x)[1]){
tmp[i]<-ave(x[i,]) # add things to it
}
return(tmp)
}
df<-cbind(rnorm(10),rnorm(10))
means<-func(df)
This code does not work but I hope it gets across what I want to do. thanks!
Do you mean you want to loop through each row of df and return a data frame with the calculated values?
You may want to look in to the apply function:
df <- cbind(rnorm(10),rnorm(10))
# apply(df,1,FUN) does FUN(df[i,])
# e.g. mean of each row:
apply(df,1,mean)
For more complicated looping like performing some operation on a per-factor basis, I strongly recommend package plyr, and function ddply within. Quick example:
df <- data.frame( gender=c('M','M','F','F'), height=c(183,176,157,168) )
# find mean height *per gender*
ddply(df,.(gender), function(x) c(height=mean(x$height)))
# returns:
gender height
1 F 162.5
2 M 179.5

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