I am receiving an error when using make_choose_all_table() from the tidyREDCap package and I'm hoping someone can help me understand what it means. When I export my data from REDCap using REDCapR and then run the code make_choose_all_table() the error below it pops up. The "boo_do_co_no" is my checkbox variable that I am trying to make a table with.
What does the error mean and how do I fix it?
library(REDCapR)
data <- redcap_read()
library(tidyREDCap)
make_choose_all_table(data, "boo_do_co_no")
Error: Result 1 must be a single string, not a character vector of length 0
It needs to come out like the picture below
I am guessing that you are missing an argument within data <- redcap_read() When I run that line, data contains the function code for redcap_read(), not any data output that might come from the function when all the arguments are specified.
See ?redcap_read()
Related
I am just starting to use R and there is a lot I don't know. I have a function to find irradiance in a data set based on start and end date. I made two dataframes one for the starting dates and one for the end. But when I input the name for each dataframe for the beginning and end date I get this error
Error in file(file, "rt") : invalid 'description' argument
getlightData is the function I created.
It works when I manually input the begin and end dates but now I want it to run based on the list of begin and end dates I created.
This is the line of code I run
getlightData(beginDates[1:25], endDates[1:25], product="high_low")
I was expecting to get an output of irradiance values based on each start and end date
The error message occurs when you try to insert multiple file names in a function (e.g. read.csv2()). Maybe it would be helpful to see the whole function. When functions take vectors as input, you might have to specify elements of the vectors in the function instead of using the whole vector.
I am trying to read a csv file in R using read.csv2.sql, since I would like to use a SELECT query from SQL to help me filter my data, but before I can even get to my SELECT query, I discovered that simply reading my csv file using read.csv2.sql already generates a warning message.
This is my code:
investment2 <- read.csv2.sql("investmentdata.csv")
This is the warning message:
Warning message:
In result_fetch(res#ptr, n = n) :
Column 'Capital.Investment': mixed type, first seen values of type real, coercing other values of type string
However, when I use the normal read.csv2 function, there is no error. In particular, the following code works fine with no warning messages:
investment <- read.csv2("investmentdata.csv")
Next, I tried to resolve this issue by casting the Capital.Investment column to be real as follows:
investment3 <- read.csv2.sql("investmentdata.csv", "SELECT *, CAST(Capital.Investment AS real) FROM file")
However, R now generates the following error:
Error: no such column: Capital.Investment
Thus, I have two questions. Firstly, why does using read.csv2.sql generate that warning message when read.csv2 works just fine? Secondly, why does R (or SQL) not recognise my Capital.Investment column when I try to cast it as real?
Perhaps it is also worth noting that I cannot simply ignore this warning that the read.csv2.sql function is showing, because I discovered that as a consequence of this warning, it has automatically casted some of the NA rows in my Capital.Investment column to 0, which I cannot allow - the NA rows must stay as NA. I do not seem to be having this problem with the other columns of my csv file though.
As I am quite new to R, any help and explanations will be greatly appreciated :)
Edit
The coded version of what my truncated csv file looks like is as follows. In particular, the name of the column-in-question is indeed Capital.Investment.
id;targetC;year;comp_id;homeC;Industry.Activity;Capital.Investment;Estimated;Jobs.Created;Estimated.1;Project.Type;geographic distance;SIC;listed;sales;assets;cap_structure;rnd;profit;rndintensity;polcon;homeC_gdp;targetC_gdp;homeC_gdppc;targetC_gdppc
1302;AUS;2008;FR338966385;FRA;Design, Development & Testing;33.1;Yes;36;Yes;New;15.26414042;3669;Unlisted;4333088.972;4037211.732;0;NA;-1339221.733;NA;0.489032525;2.92347E+12;1.05456E+12;45413.06571;49628.11513
1311;AUS;2008;US*190521496652;USA;Research & Development;8.4;Yes;30;No;New;15.24712914;NA;Unlisted;NA;NA;NA;NA;NA;NA;0.489032525;1.47E+13;1.05456E+12;48401.42734;49628.11513
1313;AUS;2008;GB05817296;GBR;Business Services;9.7;Yes;10;Yes;New;15.31094496;7389;Unlisted;NA;87.64187374;NA;NA;NA;NA;0.489032525;2.87546E+12;1.05456E+12;46523.26545;49628.11513
1318;AUS;2008;US129687150L;USA;Business Services;1.3;Yes;225;Yes;New;15.24712914;7373;Unlisted;NA;NA;NA;NA;NA;NA;0.489032525;1.47E+13;1.05456E+12;48401.42734;49628.11513
1351;AUS;2008;GB*P0060071;GBR;Electricity;516;No;51;Yes;New;15.31094496;NA;Unlisted;NA;NA;NA;NA;NA;NA;0.489032525;2.87546E+12;1.05456E+12;46523.26545;49628.11513
9925;AUS;2008;GB00034121;GBR;Business Services;34.8;Yes;37;Yes;New;15.31094496;4412;Unlisted;NA;2079288.611;0.355157008;NA;94320.15469;NA;0.489032525;2.87546E+12;1.05456E+12;46523.26545;49628.11513
9932;AUS;2008;CA30060NC;CAN;Sales, Marketing & Support;3.2;Yes;11;Yes;New;14.88812529;1094;Listed;NA;NA;NA;NA;NA;NA;0.489032525;1.54913E+12;1.05456E+12;46596.33599;49628.11513
9935;AUS;2008;US940890210;USA;Manufacturing;771;Yes;266;Yes;New;15.24712914;2911;Listed;NA;NA;NA;NA;NA;NA;0.489032525;1.47E+13;1.05456E+12;48401.42734;49628.11513
9938;AUS;2008;US770059951;USA;Technical Support Centre;9.1;Yes;104;Yes;Co-Locati;15.24712914;3661;Listed;34922000;53340000;0.120134983;4598000;7333000;0.086201723;0.489032525;1.47E+13;1.05456E+12;48401.42734;49628.11513
9946;AUS;2008;US010562944;USA;Extraction;535.8;Yes;198;Yes;New;15.24712914;2911;Listed;NA;NA;NA;NA;NA;NA;0.489032525;1.47E+13;1.05456E+12;48401.42734;49628.11513
9955;AUS;2008;DE5030147191;DEU;Logistics, Distribution & Transportation;21.2;Yes;134;Yes;New;14.6718338;4311;Listed;93495971.01;346629334.8;0.036629492;0;2044745.934;0;0.489032525;3.75237E+12;1.05456E+12;45699.19832;49628.11513
9958;AUS;2008;US126012192L;USA;Business Services;9.7;Yes;10;Yes;New;15.24712914;8111;Unlisted;NA;NA;NA;NA;NA;NA;0.489032525;1.47E+13;1.05456E+12;48401.42734;49628.11513
9969;AUS;2008;US135409005;USA;Extraction;NA;No;538;Yes;New;15.24712914;2911;Listed;NA;NA;NA;NA;NA;NA;0.489032525;1.47E+13;1.05456E+12;48401.42734;49628.11513
9977;AUS;2008;JP000000728JPN;JPN;ICT & Internet Infrastructure;128.6;Yes;77;Yes;New;7.0333688;3571;Listed;53255396.85;38181450.16;0.190244908;2584585.523;480589.4308;0.067692176;0.489032525;5.03791E+12;1.05456E+12;39339.29757;49628.11513
9984;AUS;2008;US841547578;USA;Sales, Marketing & Support;13.6;Yes;23;Yes;New;15.24712914;2095;Listed;NA;NA;NA;NA;NA;NA;0.489032525;1.47E+13;1.05456E+12;48401.42734;49628.11513
9993;AUS;2008;US258715604L;USA;Customer Contact Centre;1.8;No;40;No;New;15.24712914;NA;Unlisted;NA;NA;NA;NA;NA;NA;0.489032525;1.47E+13;1.05456E+12;48401.42734;49628.11513
This issue was resolved in chat, to be one of two issues:
see my original answer below, this was causing an Error; when that is fixed, we see that ...
there is a warning, informing about the fact that a column (happens to be the same column) looks numeric but has a non-numeric cell somewhere within the guts of the file.
The first is resolved below, the second is just a warning.
However, because the OP is asking to convert to numeric via SQL, the NA is converted to 0, which is not good. My recommendation is to either cast([Capital.Investment] as char) as [Capital.Investment] and use R's as.numeric to convert to numeric (preserving the NA-nature), or to just read.csv2(.) the file outright and use sqldf(.) to use its SQL querying on table-like data.
Up front: add brackets or quotes around your column name.
Rationale: Capital.Investment is seen as a dot-delimited table-column or schema-table or something similarly not what you intend. I believe in general in SQL that field names with embedded dots need this escaping. If your data has an embedded space, realize that R does not like spaces in its field names, so it is by-default using make.names when reading it in (which replaces spaces with dots).
Setup:
Save the following as "quux.csv". (I've named it csv, but since I'm changing it to be ;-delimited, it behaves the same.)
quux;Capital.Investment
1;100
2;200
(Or you can use Capital Investment, it's the same thing.)
sqldf::read.csv2.sql("quux.csv", sql='select quux, cast(Capital.Investment as real) from file')
# Error: no such column: Capital.Investment
sqldf::read.csv2.sql("quux.csv", sql='select quux, cast([Capital.Investment] as real) as CI from file')
# quux CI
# 1 1 100
# 2 2 200
sqldf::read.csv2.sql("quux.csv", sql='select quux, cast("Capital.Investment" as real) as CI from file')
# quux CI
# 1 1 100
# 2 2 200
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$well))
return(df_1)
}
normal(antitrombina_FI,Six_Plex_IID)
I get the same error mesage:
Error in preprocessCore::normalize.quantiles(mat) :
Matrix expected in normalize.quantiles
I'm completely clueless about why this is happening, why outside the function I'm obtaining a matrix and why inside the function not.
Thanks
I want to update a column value in such a way that only the part of a string after the last '.' is stored. I wrote a code that does this but it only works when it's given one input. How do I loop through all the rows of my dataframe?
One value of a row looks for example like this. I only want to store the last part ".gif"
GET /./enviro/gif/emcilogo.gif
I wrote the following code that succesfully does this.
tail(c(do.call(rbind, strsplit(as.character(sapply(strsplit("GET /./enviro/gif/emcilogo.gif", "\\s+"), `[`, 2)),"\\."))), n=1)
Output:
"gif"
However, I am using the string "GET /./enviro/gif/emcilogo.gif" as input. As soon as I change this to the column of my dataframe "df$request" I receive the error.
Error in strsplit(epa.df$request) :
argument "split" is missing, with no default
I tried writing a function that one-by-one loops through my column values and updates them. However, I cant seem to get this working.
Any help would be highly appreciated!
I want to extract "topten" values, correctly handling tie cases.
I need to use the following formula:
=INDEX($A$4:$A$12,AGGREGATE(15,7,(ROW($K$4:$K$12)-ROW($K$4)+1)/($K$4:$K$12=O4),COUNTIF($O$4:O4,O4)))
If I use this formula in my code I have a corrupted file that I can read with a text editor and that shows:
Fatal error: Uncaught PHPExcel_Calculation_Exception: Consolidation Transporteur!N4 -> Formula Error: Wrong number of arguments for INDEX() function: 5 given, between 1 and 4 expected in /home/.../PHPExcel/Cell.php:293
Stack trace:
0 /home/.../PHPExcel/Worksheet.php(754): PHPExcel_Cell->getCalculatedValue()
1 /home/.../PHPExcel/Writer/Excel2007/Worksheet.php(373): PHPExcel_Worksheet->calculateColumnWidths()
2 /home/.../PHPExcel/Writer/Excel2007/Worksheet.php(80): PHPExcel_Writer_Excel2007_Worksheet->_writeCols(Object(PHPExcel_Shared_XMLWriter),
Object(PHPExcel_Worksheet))
3 /home/.../PHPExcel/Writer/Excel2007.php(304): PHPExcel_Writer_Excel2007_Worksheet->writeWorksheet(Object(PHPExcel_Worksheet),
Array, true)
4 /home/....output.php(33): PHPExcel_Writer_Excel2007->save('/tmp/phpxltmpqF...')
5 in /home/.../PHPExcel/Cell.php on line 293
If I write the formula without the leading equal sign, I can open the Excel file, insert the equal sign and the formula gives the correct result, showing that the formula is correct with a correct number of arguments
If I use a simple MATCH function instead of the AGGREGATE one, I can get the "topten" values but tie cases are not correctly handled.
I also need to keep the setPreCalculateFormulas to true.
How can I solve this formula issue?