I'm getting the following error message when using qualtRics::fetch_survey function together with purrr::partial:
library(tidyverse)
library(qualtRics)
fetch_new_survey <- partial(fetch_survey,
force_request = TRUE)
fetch_new_survey(some_survey_id)
Error in vapply(match.call(), deparse, "character") : `values must be
length 1, but FUN(X[[1]]) result is length 68
Am I using partial incorrectly, or is there something else going on here?
Related
I know this is a very basic question. So you might wonder why this is even bothering.
But, I have an issue with rounding numbers up.
I tried this but none of this worked.
mode(RNA_data) <- 'numeric'
Error in mde(x) : (list) object cannot be coerced to type 'double'
RNA_data<-as.numeric(RNA_data)
Error: (list) object cannot be coerced to type 'double'
round(P7_N02_RNA, digits=0)
Error in Math.data.frame(list(P07_N02_RNA.genes.V5 = c(326L, 1L, 851L, :
non-numeric variable(s) in data frame: P07_N02_RNA.genes.V5
Error: unexpected symbol in "non-numeric variable"
P7_N02_RNA <- round(P7_N02_RNA, digits=0)
Error in Math.data.frame(list(P07_N02_RNA.genes.V5 = c(326L, 1L, 851L, :
non-numeric variable(s) in data frame: P07_N02_RNA.genes.V5
Error: unexpected symbol in "non-numeric variable"
trimmed_RNA <- round(RNA_data$p07_N01,digit = 0)
Error in round(RNA_data$p07_N01, digit = 0) :
non-numeric argument to mathematical function
Error: unexpected symbol in "non-numeric argument"
trimmed_RNA <- round(RNA_data[-1,], digits=0)
Error in Math.data.frame(list(geneID = 2:58639, p07_N01 = c(2175L, 9753L, : non-numeric variable(s) in data frame: geneID, p07_N01, p07_T01, p07_N02, p07_T02, p08_N01, p08_T01, p08_N02, p08_T02, p09_N01, p09_T01, p09_N02, p09_T02
RNA_data <-data.frame(RNA_data)
trimmed_RNA <- data.frame(round(as.numeric(levels(RNA_data)[RNA_data])))
got a reault with 0 obs.
rm(trimmed_RNA)
require(data.table)
setDT(RNA_data)
RNA_data[, RNA_data:=round(as.numeric(levels(RNA_data)[RNA_data]))]
Error in [.data.table(RNA_data, , :=(RNA_data, round(as.numeric(levels(RNA_data)[RNA_data])))) : RHS of assignment to existing column 'RNA_data' is zero length but not NULL. If you intend to delete the column use NULL. Otherwise, the RHS must have length > 0; e.g., NA_integer_. If you are trying to change the column type to be an empty list column then, as with all column type changes, provide a full length RHS vector such as vector('list',nrow(DT)); i.e., 'plonk' in the new column.**
This is how data looks like with 58639 rows.
I also tried to export files into csv file and trim them in excel but, also had a circular reference error, and didn't work.
Now I have no idea what can I do.
Can anybody help me with rounding up those numbers?
Its hard to tell from your question, but first convert your variables to numeric like this:
mtcars$mpg <- as.numeric( as.character( mtcars$mpg))
And is this what you mean by rounding up
ceiling( mtcars$qsec )
round( mtcars$disp , -1 )
I'll explain the end goal, and what I'm trying as a test first. (Because I'm likely going about it the wrong way.)
I am using the phyloseq package to visualize microbiome data. I want to "automate" it to an extent by having users choose levels of analysis and have my script generate the visualizations without someone hand typing in each combination.
The issue is passing variables into the subset function. I get these errors primarily (depending on what combinations of paste0, eval, parse, as.logical, expression, noquote....etc that i've tried):
Error in subset.data.frame(oldDF, ...) : 'subset' must be logical
Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent
A user would set the levels of analysis. So lets say for now there are two levels, and selecting the second level automatically means you want the first level as well. (I haven't worked on that part yet, but I wanted to explain it upfront.
#Set lineage level
lin_level <- 1
lin_list <- c("k__Kingdom", "p__Phylum","c__Class", "o__Order","f__Family")
lin_select <- lin_list[lin_level]
sub_lin <- lin_list[(lin_level +1)]
#Kingdom
king_list <- "k__Bacteria"
#set Phylum list
if (lin_select == "p__Phylum"){
phylum_list <- c("p__Firmicutes","p__Proteobacteria","p__Bacteroidetes","p__Actinobacteria","p__Tenericutes")
}
subgroup <- "All"
From here, the script would ultimately get to the graphing section. If lin_level is set to 1, it would look like this:
FIXED
gphic = subset_taxa(physeq1, Kingdom=="k__Bacteria")
title = paste0(subgroup," ", "Bacteria-only")
plot_bar(gpsfb, "Phylum", "Abundance", "Phylum",
title=title, facet_grid="Type~.")
AUTOMATED
gphic = subset_taxa(physeq1, (substring(lin_select,4)) == king_list)
title = paste0(subgroup," ", (substring(king_list,4)),"-only")
plot_bar(gpsfb, (substring(sub_lin,4)), "Abundance", (substring(sub_lin,4)),
title=title, facet_grid="Type~.")
But, trying to pass (substring(lin_select,4)) == king_list as an argument results in errors.
I've searched through the various threads on this issue, but haven't been able to get the different answers to work. Ultimately I need to run the graphing section once for Kingdom, and then again each time for each item in the Phylum list. But before i can get there, I need to be able to pass the arguments into the subset function.
Things I've tried:
test <- paste0(substring(lin_select,4),"==","\"","p__Bacteroidetes","\"")
noquote(test)
[1] Phylum=="p__Bacteroidetes"
gphic = subset_taxa(physeq1, noquote(test))
Error in subset.data.frame(oldDF, ...) : 'subset' must be logical
gphic = subset_taxa(physeq1, paste0(substring(lin_select,4),"==","\"","p__Bacteroidetes","\""))
Error in subset.data.frame(oldDF, ...) : 'subset' must be logical
gphic = subset_taxa(physeq1, as.logical(test))
Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent
as.logical(noquote(test))
[1] NA
gphic = subset_taxa(physeq1, as.logical(noquote(test)))
Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent
noquote(test)
[1] Phylum=="p__Bacteroidetes"
as.logical(noquote(test))
[1] NA
as.logical(as.character(noquote(test)))
[1] NA
test2 <- eval(parse(text= test))
Error in eval(parse(text = test)) : object 'Phylum' not found
test2 <- eval(test)
gphic = subset_taxa(physeq1, as.logical(test2))
Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent
as.logical(test2)
[1] NA
And a lot of other permutations trying to sub in different things, but you get the idea.
gphic = subset_taxa(physeq1, eval(as.name(level_tax)) == king_list)
Here , level_tax is the variable in a loop. Say level_tax = "Order", then we convert the string "Order" into variable name by as.name(level_tax) or as.symbol(level_tax). Then we use eval(), which takes an expression and evaluates in the specified environment
I am trying to convert a dgcMatrix to datatable in R using following piece of code:
feats <- as.data.table(as.matrix(dtm_text))
But it throws an error like this:
Error in nchar(collabs) : invalid multibyte string, element 149
Does anyone have the reason for this error or another way to achieve the same??
A small part of the code before the problem line
bow <- itoken(trte_data$Description, preprocessor = tolower ,tokenizer =
word_tokenizer, ids = trte_data$User_ID)
bow_vocab <- create_vocabulary(bow)
pruned_bow <- prune_vocabulary(bow_vocab, term_count_min = 100)
vovec <- vocab_vectorizer(pruned_bow)
dtm_text <- create_dtm(bow, vovec)
I am currently facing an error mentioned below which is related to NULL values being coerced to a data frame. The data set does contain nulls, however I have tried both is.na() and is.null() functions to replace the null values with something else. The data is stored on hdfs and is stored in a pig.hive format. I have also attached the code below. The code works fine if I remove v[,25] from the key.
Code:
AM = c("AN");
UK = c("PP");
sample.map <- function(k,v){
key <- data.frame(acc = v[!which(is.na(v[,1],1],
year = substr(v[!which(is.na(v[,1]),2],1,4),
month = substr(v[!which(is.na(v[,1]),2],5,6))
value <- data.frame(v[,3],count=1)
keyval(key,value)
}
sample.reduce <- function(key,v){
AT <- sum(v[which(v[,1] %in% AM=="TRUE"),2])
UnknownT <- sum(v[which(v[,1] %in% UK=="TRUE"),2])
Total <- AT + UnknownT
d <- data.frame(AT,UnknownT,Total)
keyval(key,d)
}
out <- mapreduce(input ="/user/hduser/input",
output = "/user/hduser/output",
input.format = make.input.format("pig.hive", sep = "\u0001")
output.format = make.output.format("csv", sep = ","),
map= sample.map)
reduce = sample.reduce)
Error:
Warning in asMethod(object) : NAs introduced by coercion
Warning in split.default(1:rmr.length(y), unique(ind), drop = TRUE) : data length is not a multiple of split variable
Warning in rmr.split(x, x, FALSE, keep.rownames = FALSE) : number of items to replace is not a multiple of replacement length Warning in split.default(1:rmr.length(y), unique(ind), drop = TRUE) :
data length is not a multiple of split variable
Warning in rmr.split(v, ind, lossy = lossy, keep.rownames = TRUE) : number of items to replace is not a multiple of replacement length
Error in as(x, class(k)) :
no method or default for coercing “NULL” to “data.frame”
Calls: <Anonymous> ... apply.reduce -> c.keyval -> reduce.keyval -> lapply -> FUN -> as No traceback available
UPDATE
I have added the sample data and edited the code above. Hope this helps!
Sample Data:
NULL,"2014-03-14","PP"
345689202,"2014-03-14","AN"
234539390,"2014-03-14","PP"
123125444,"2014-03-14","AN"
NULL,"2014-03-14","AN"
901828393,"2014-03-14","AN"
There are some issues with as which have been identified recently. I don't see why as can't handle this by default, but you can modify coerce which handles the conversion with an S4 method to call as.data.frame.
setMethod("coerce",c("NULL","data.frame"), function(from, to, strict=TRUE) as.data.frame(from))
[1] "coerce"
as(NULL,"data.frame")
data frame with 0 columns and 0 rows
I have a loop that reads HTML table data from ~ 440 web pages. The code on each page is not exactly the same, so sometimes I need table node 1 and sometime I need node 2. Right now I've just been setting the node number manually in a list and feeding it into the loop. My problem is that the page nodes have started changing and updating the node # list is getting to be a hassle.
If the loop encounters the wrong node # (ie: 1 instead of 2, or reverse) it gives an error and shuts down. Is there a way to have the loop replace the erroneous node number to the correct one if it encounters an error, and then keep running the loop as if nothing happened?
Here's the readHTML portion of the code in my loop with an example url:
url <- "http://espn.go.com/nba/player/gamelog/_/id/2991280/year/2013/"
html.page <- htmlParse(url)
tableNodes <- getNodeSet(html.page, "//table")
x <- as.numeric(Players$Nodes[s])
tbl = readHTMLTable(tableNodes[[x]], colClasses = c("character"),stringsAsFactors = FALSE)
Here's the error I get when the node # is wrong:
"Error in readHTMLTable(tableNodes[[x]], colClasses = c("character"), stringsAsFactors = FALSE) : error in evaluating the argument 'doc' in selecting a method for function 'readHTMLTable': Error in tableNodes[[x]] : subscript out of bounds"
Example code:
A <- c("dog", "cat")
Nodes <- as.data.frame(1:1)
#)Nodes <- as.data.frame(1:2) <-- This works without errors
colnames(Nodes)[1] <- "Col1"
Nodes2 <- 2
url <-c("http://espn.go.com/nba/player/gamelog/_/id/6639/year/2013/","http://espn.go.com/nba/player/gamelog/_/id/6630/year/2013/")
for (i in 1:length(A))
{
html.page <- htmlParse(url[i])
tableNodes <- getNodeSet(html.page, "//table")
x <- as.numeric(Nodes$Col1[i])
df = readHTMLTable(tableNodes[[x]], colClasses = c("character"),stringsAsFactors = FALSE)
#tryCatch(df) here.....no clue
assign(paste0("", A[i]), df)
}
If you get subscript out of bounds error msg, then you should try to with a lower x for sure. General demo with tryCatch based on the demo code you posted in the original question (although I have replaced x with 2 as I have no idea what is Players and s):
> msg <- tryCatch(readHTMLTable(tableNodes[[2]], colClasses = c("character"),stringsAsFactors = FALSE), error = function(e)e)
> str(msg)
List of 2
$ message: chr "error in evaluating the argument 'doc' in selecting a method for function 'readHTMLTable': Error in tableNodes[[2]] : subscript"| __truncated__
$ call : language readHTMLTable(tableNodes[[2]], colClasses = c("character"), stringsAsFactors = FALSE)
- attr(*, "class")= chr [1:3] "simpleError" "error" "condition"
> msg$message
[1] "error in evaluating the argument 'doc' in selecting a method for function 'readHTMLTable': Error in tableNodes[[2]] : subscript out of bounds\n"
> grepl('subscript out of bounds', msg$message)
[1] TRUE