Error in reading files using reprex

General
1

I keep getting the same error - despite checking that the file name is correct and has been imported. Here's my code:

# Setting up the RStudio environment
#~~~~~~~~~~~
# Libraries
#~~~~~~~~~~
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(ggplot2)
#> Registered S3 methods overwritten by 'ggplot2':
#>   method         from 
#>   [.quosures     rlang
#>   c.quosures     rlang
#>   print.quosures rlang
library(tidyr)

#~~~~~~~~~~~
# Functions
#~~~~~~~~~~

rescale_01 <-function(x) (x-min(x))/(max(x)-min(x)) -1/2
z_stand<-function(x) (x-mean(x))/sd(x)
ExpectedBrix <- function(x) (x*0.21084778699754 + 4.28455310831511)

#~~~~~~~~~~~~
# Thresholds
#~~~~~~~~~~~
Thresh.Brix.min <- 15
Thresh.Brix.max <- 30

Thresh.Pol.min <- 50
Thresh.Pol.max <- 105
ExpectedBrix.delta <- 1

Thresh.Fibre.min <- 4
Thresh.Fibre.max <- 25
Thresh.Fibre.delta <- .25

Thresh.Ash.min <- 0
Thresh.Ash.max <- 8


# Import the Fibre data into a data table called “Lab_Fibre_Data”

Lab_Fibre_Data <- read.table("Lab_Fibre_Weights.csv", header=TRUE, sep=",", dec =".")
#> Warning in file(file, "rt"): cannot open file 'Lab_Fibre_Weights.csv': No
#> such file or directory
#> Error in file(file, "rt"): cannot open the connection


# Calculate Percentage Fibre Variables using direct assignment
# Name the resulting variable “Fibre1” and add this new variable to the “Lab_Fibre_Data” data table, using direct assignment
# Fibre% = 100 * (InitialSampleCanWeight – FinalSampleCanWeight) / SampleWeight

Lab_Fibre_Data$Fibre1 <- 100 * (Lab_Fibre_Data$InitialSampleCanWeight_1 - Lab_Fibre_Data$FinalSampleCanWeight_1) / Lab_Fibre_Data$SampleWeight_1
#> Error in eval(expr, envir, enclos): object 'Lab_Fibre_Data' not found


# Calculate Percentage Fibre Variables using the mutate() function from the dplyr package, call it “Fibre2”
# Add “Fibre2” as a new variable to the “Lab_Fibre_Data” data table

Lab_Fibre_Data <- Lab_Fibre_Data %>% mutate(Fibre2 = 100 *(InitialSampleCanWeight_2 - FinalSampleCanWeight_2) / SampleWeight_2)
#> Error in eval(lhs, parent, parent): object 'Lab_Fibre_Data' not found


# Use the filter() function to remove samples (rows) that contain a missing value

Lab_Fibre_Filtered <- Lab_Fibre_Data %>% filter(InitialSampleCanWeight_1 >0 & 
                                                InitialSampleCanWeight_2 >0 &
                                                FinalSampleCanWeight_1 >0 &
                                                FinalSampleCanWeight_2 >0 &
                                                SampleWeight_1 >0 &
                                                SampleWeight_2 >0)                                              
#> Error in eval(lhs, parent, parent): object 'Lab_Fibre_Data' not found


# UPDATE code in table 5 to include maximum fibre difference limit as an additional filtering criteria
# Absolute difference between the two estimates (computed variables “Fibre1”  and “Fibre2”) = or > 0.25 units
# UPDATE your code in table 5 to include this maximum fibre difference limit as an additional filtering criteria

Lab_Fibre_Filtered <- Lab_Fibre_Filtered %>% filter(!(abs(Fibre1 - Fibre2) >= 0.25))
#> Error in eval(lhs, parent, parent): object 'Lab_Fibre_Filtered' not found


# Calculate the final fibre estimates by averaging the replicate fibre measurements, “Fibre1” and “Fibre2”
# Use mutate() to calculate the average fibre and add it as a new variable named “Fibre” to the Lab_Fibre_Filtered data table

Lab_Fibre_Filtered <- Lab_Fibre_Filtered %>% mutate(Fibre = (Fibre1 + Fibre2)/2)
#> Error in eval(lhs, parent, parent): object 'Lab_Fibre_Filtered' not found


# Use a PIPE to sequentially filter the measurements in Lab_Fibre_Filtered to remove the out-of-range fibre values
# Keeping only the rows of the data table for which “Fibre” is greater than Thresh.Fibre.min
# Keeping only the resulting rows for which “Fibre” is less than Thresh.Fibre.max.  Save the resulting data into the Lab_Fibre_Filtered table

Lab_Fibre_Filtered <- Lab_Fibre_Filtered %>% filter(Fibre > Thresh.Fibre.min & Fibre < Thresh.Fibre.max)
#> Error in eval(lhs, parent, parent): object 'Lab_Fibre_Filtered' not found


# Use select() to save the LabID and Fibre variables (1st and last columns) from Lab_Fibre_Filtered to a new data table called Lab_Fibre

Lab_Fibre <- Lab_Fibre_Filtered %>% select(LabID,Fibre)
#> Error in eval(lhs, parent, parent): object 'Lab_Fibre_Filtered' not found


#  Import the Ash data into a data table called “Lab_Ash_Data”

Lab_Ash_Data <- read.table("Lab_Ash_Weights.csv", header=TRUE, sep=",", dec =".")
#> Warning in file(file, "rt"): cannot open file 'Lab_Ash_Weights.csv': No
#> such file or directory
#> Error in file(file, "rt"): cannot open the connection


# Calculate Ash Variables
# Use a PIPE to filter out the missing values using filter()
# Sequentially calculate “InitialWeight”, “FinalWeight” and “Ash” as new variables using mutate()
# TinWeight (column 2), InitialSampleInTinWeight (column 3), FinalSampleInTinWeight (column 4)
# Ash = 100*FinalWeight/InitialWeight
# InitialWeight=InitialSampleInTinWeight-TinWeight, FinalWeight=FinalSampleInTinWeight-TinWeight 

Lab_Ash_Calculated$Ash <- Lab_Ash_Data %>% 
                          filter(InitialSampleInTinWeight ==0 &                                                  
                                 FinalSampleInTinWeight ==0) &
                          mutate(InitialWeight = InitialSampleInTinWeight) &
                          mutate(FinalWeight = FinalSampleInTinWeight) &
                          mutate(Ash = 100 *(FinalWeight/InitialWeight)) 
#> Error in eval(lhs, parent, parent): object 'Lab_Ash_Data' not found



# Filtering Ash Variables
# Threshold values for ash are: Thresh.Ash.min and Thresh.Ash.max.
# Update pipe to filter out any out-of-range Ash values. Add the additional filter at the end of the pipe.

Lab_Ash_Calculated <- Lab_Ash_Calculated %>% filter(Ash > Thresh.Ash.min & Ash < Thresh.Ash.max)
#> Error in eval(lhs, parent, parent): object 'Lab_Ash_Calculated' not found


# Summarising Ash Variables
# Use a PIPE with the grouped_by() and summarize() functions to produce a data table called Lab_Ash 
# Grouped by LabID and summarises variable Ash by taking its grouped mean values
# Resulting table, Lab_Ash, must then have two variables, LabID and Ash, where LabID now contains unique values (no replicates)

Lab_Ash<-Lab_Ash_Calculated %>% grouped_by(LabID) %>% summarize(Ash=mean(Ash))
#> Error in eval(lhs, parent, parent): object 'Lab_Ash_Calculated' not found


# Import the Pol and Brix data into a data table called “Lab_PB_Data”

Lab_PB_Data <- read.table("Lab_Pol_Brix.csv", header=TRUE, sep=",", dec =".") 
#> Warning in file(file, "rt"): cannot open file 'Lab_Pol_Brix.csv': No such
#> file or directory
#> Error in file(file, "rt"): cannot open the connection


# Use the mutate() function to add to the data table Lab_PB_Data a new variable, PredBrix, which uses the ExpectedBrix function with Pol as input

Lab_PB_Data <-mutate(Lab_PB_Data,PredBrix=ExpectedBrix(Pol))  
#> Error in mutate(Lab_PB_Data, PredBrix = ExpectedBrix(Pol)): object 'Lab_PB_Data' not found

Created on 2019-06-01 by the reprex package (v0.3.0)

However, these files do exist in the environment:
image

Can someone please explain why I am getting the error?

2

If you mean why you are getting those errors while using the reprex package, then it's because reprex() executes your code on a separate R process and in a temporary working directory where your file doesn't exists, the reason for this is to ensure reproducibility, since most likely other people is not going to have access to your local files.

1 Like
3

Thank you, that makes sense. I have another error I am trying sort out which was the original reason for creating the reprex. It relates to ggplot but not sure how I can represent this error if reprex() can't read the files, unless I can redirect R to the actual directory whilst using reprex()? Is that possible? Alternatively, I could screen shot the executed code but then someone will tell me to create a reprex(). Any suggestions on how to get around this?

4

You can set the option outfile = NA to force reprex() to execute in your current working directory, but if you do this no one is going to be able to reproduce your problem unless you share the csv file too using some cloud service like Dropbox for example.
Ideally you should try to make a reprex with a small subset of your data using something like dput or datapasta.

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