I wrote the following snippet of code:
b=function(x=numeric()){print(x)}
What does x=numeric() do?
b('i') and b(3) both produce the correct output.
Thanks!
You are specifying a default argument of numeric(), which I believe is just a numeric vector.
Thus, if you call the function with no arguments, that parameter will default to numeric().
If your question is about how to force arguments to be a particular type (as your title implies), then you want to look at this question.
Related
My question refers to redundant code and a problem that I've been having with a lot of my R-Code.
Consider the following:
list_names<-c("putnam","einstein","newton","kant","hume","locke","leibniz")
combined_df_putnam$fu_time<-combined_df_putnam$age*365.25
combined_df_einstein$fu_time<-combined_einstein$age*365.25
combined_df_newton$fu_time<-combined_newton$age*365.25
...
combined_leibniz$fu_time<-combined_leibniz$age*365.25
I am trying to slim-down my code to do something like this:
list_names<-c("putnam","einstein","newton","kant","hume","locke","leibniz")
paste0("combined_df_",list_names[0:7]) <- data.frame("age"=1)
paste0("combined_df_",list_names[0:7]) <- paste0("combined_df_",list_names[0:7])$age*365.25
When I try to do that, I get "target of assignment expands to non-language object".
Basically, I want to create a list that contains descriptors, use that list to create a list of dataframes/lists and use these shortcuts again to do calculations. Right now, I am copy-pasting these assignments and this has led to various mistakes because I failed to replace the "name" from the previous line in some cases.
Any ideas for a solution to my problem would be greatly appreciated!
The central problem is that you are trying to assign a value (or data.frame) to the result of a function.
In paste0("combined_df_",list_names[0:7]) <- data.frame("age"=1), the left-hand-side returns a character vector:
> paste0("combined_df_",list_names[0:7])
[1] "combined_df_putnam" "combined_df_einstein" "combined_df_newton"
[4] "combined_df_kant" "combined_df_hume" "combined_df_locke"
[7] "combined_df_leibniz"
R will not just interpret these strings as variables that should be created and be referenced to. For that, you should look at the function assign.
Similarily, in the code paste0("combined_df_",list_names[0:7])$age*365.25, the paste0 function does not refer to variables, but simply returns a character vector -- for which the $ operator is not accepted.
There are many ways to solve your problem, but I will recommend that you create a function that performs the necessary operations of each data frame. The function should then return the data frame. You can then re-use the function for all 7 philosophers/scientists.
I created a small function to process a dataframe to be able to use the function:
preprocessCore::normalize.quantiles()
Since normalize.quintles() can only use a matrixc object, and I need to rearrange my data, I create a small function that takes a specific column (variable) in a especific data frame and do the following:
normal<-function(boco,df){
df_p1<-subset(df,df$Plate==1)
df_p2<-subset(df,df$Plate==2)
mat<-cbind(df_p1$boco,df_p2$boco)
norm<-preprocessCore::normalize.quantiles(mat)
df_1<-data.frame(var_1=c(norm[,1],norm[,2]),well=c(df_p1$well,df_p2$well))
return(df_1)
}
However, "mat" should be a matrix, but it seems the cbind() does not do its job since I'm obtaining the following Error:
normal(antitrombina_FI,Six_Plex_IID)
Error in preprocessCore::normalize.quantiles(mat) :
Matrix expected in normalize.quantiles
So, it is clear that the cbind() is not creating a matrix. I don't understand why this is happening.
Most likely you are binding two NULL objects together, yielding NULL, which is not a matrix. If your df objects are data.frame, then df_p1$boco is interpreted as "extract the variable named boco", not "extract the variable whose name is the value of an object having the symbol boco". I suspect that your data does not contain a variable literally named "boco", so df_p1$boco is evaluated as NULL.
If you want to extract the column that is given as the value to the formal argument boco in function normal() then you should use [[, not $:
normal<-function(boco,df){
df_p1<-subset(df,df$Plate==1)
df_p2<-subset(df,df$Plate==2)
mat<-cbind(df_p1[[boco]],df_p2[[boco]])
norm<-preprocessCore::normalize.quantiles(mat)
df_1<-data.frame(var_1=c(norm[,1],norm[,2]),well=c(df_p1$well,df_p2$well))
return(df_1)
}
Thanks for your help bcarlsen. However I have found some errors:
First, I believe you need to introduce quotes in
mat<-cbind(df_p1[["boco"]],df_p2[["boco"]])
If I run this script outside of a function works erally perfectly:
df_p1<-subset(Six_Plex_IID,Six_Plex_IID$Plate==1)
df_p2<-subset(Six_Plex_IID,Six_Plex_IID$Plate==2)
mat<-cbind(df_p1[["antitrombina_FI"]],df_p2[["antitrombina_FI"]])
norm<-preprocessCore::normalize.quantiles(mat)
However If I introduce this now in a function and try to run it like a function:
normal<-function(boco,df){
df_p1<-subset(df,df$Plate==1)
df_p2<-subset(df,df$Plate==2)
mat<-cbind(df_p1[["boco"]],df_p2[["boco"]])
norm<-preprocessCore::normalize.quantiles(mat)
df_1<-data.frame(var_1=c(norm[,1],norm[,2]),well=c(df_p1$well,df_p2$well))
return(df_1)
}
normal(antitrombina_FI,Six_Plex_IID)
I get the same error mesage:
Error in preprocessCore::normalize.quantiles(mat) :
Matrix expected in normalize.quantiles
I'm completely clueless about why this is happening, why outside the function I'm obtaining a matrix and why inside the function not.
Thanks
I am trying to iterate over a character vector "outcomes"
results <- map(outcomes, run("Female", ., predictors))
"run" is a user-defined function and "Female" and predictors are additional arguments I pass to the function. Period does not seem to work as a placeholder for each element of outcomes :
Error in .f(.x[[i]], ...) : object '.' not found
I would really like to use map instead of a loop.
it does not identify . as a valid parameter for your run function. Here, is a sample code which works well:
run<-function(outcome,gender,key,predictor){
paste0(outcome," ",gender," ",key," ",predictor)
}
and then call it by map:
outcome=c(8:11)
library(purrr)
map(outcome,run,gender="Female",key=1,predictor=5 )
if your run function has multiple argument, all of the parameters of run, are the parameters of map now. But, in your code, you did not follow it.
For complete explanation, please find this link.
There has been discussion on how to get a variable from a string. Indeed, get works for, say, the data.table function: get("data.table") returns data.table. However,
> get("data.table::data.table")
Error in get("data.table::data.table") :
object 'data.table::data.table' not found
Is there a way to do this that preserves the reference to the package name? I.e., I do NOT want to simply do a split on "::" and get the second half of the string.
You could just use the envir argument to get the function from the namespace.
get("data.table", envir = getNamespace("data.table"))
Or more simply as #joran notes, getFromNamespace() can be used.
getFromNamespace("data.table", "data.table")
Trying to get into Julia after learning python, and I'm stumbling over some seemingly easy things. I'd like to have a function that takes strings as arguments, but uses one of those arguments as a regular expression to go searching for something. So:
function patterncount(string::ASCIIString, kmer::ASCIIString)
numpatterns = eachmatch(kmer, string, true)
count(numpatterns)
end
There are a couple of problems with this. First, eachmatch expects a Regex object as the first argument and I can't seem to figure out how to convert a string. In python I'd do r"{0}".format(kmer) - is there something similar?
Second, I clearly don't understand how the count function works (from the docs):
count(p, itr) → Integer
Count the number of elements in itr for which predicate p returns true.
But I can't seem to figure out what the predicate is for just counting how many things are in an iterator. I can make a simple counter loop, but I figure that has to be built in. I just can't find it (tried the docs, tried searching SO... no luck).
Edit: I also tried numpatterns = eachmatch(r"$kmer", string, true) - no go.
To convert a string to a regex, call the Regex function on the string.
Typically, to get the length of an iterator you an use the length function. However, in this case that won't really work. The eachmatch function returns an object of type Base.RegexMatchIterator, which doesn't have a length method. So, you can use count, as you thought. The first argument (the predicate) should be a one argument function that returns true or false depending on whether you would like to count a particular item in your iterator. In this case that function can simply be the anonymous function x->true, because for all x in the RegexMatchIterator, we want to count it.
So, given that info, I would write your function like this:
patterncount(s::ASCIIString, kmer::ASCIIString) =
count(x->true, eachmatch(Regex(kmer), s, true))
EDIT: I also changed the name of the first argument to be s instead of string, because string is a Julia function. Nothing terrible would have happened if we would have left that argument name the same in this example, but it is usually good practice not to give variable names the same as a built-in function name.