Warning Message: in '...': Invalid Factor Level, Na Generated

Warning message: In `...` : invalid factor level, NA generated

The warning message is because your "Type" variable was made a factor and "lunch" was not a defined level. Use the stringsAsFactors = FALSE flag when making your data frame to force "Type" to be a character.

> fixed <- data.frame("Type" = character(3), "Amount" = numeric(3))
> str(fixed)
'data.frame':   3 obs. of  2 variables:
 $ Type  : Factor w/ 1 level "": NA 1 1
 $ Amount: chr  "100" "0" "0"
> 
> fixed <- data.frame("Type" = character(3), "Amount" = numeric(3),stringsAsFactors=FALSE)
> fixed[1, ] <- c("lunch", 100)
> str(fixed)
'data.frame':   3 obs. of  2 variables:
 $ Type  : chr  "lunch" "" ""
 $ Amount: chr  "100" "0" "0"

invalid factor level, NA generated error when trying to link colour information in with subgroup

Instead of doing this one by one, an option is factor

factor(pca_matrix[,"Subgroup"], levels = paste0("C", 1:6), 
      labels = c("blue", "red", "yellow", "green", "black", "white"))

invalid factor level, NA generated warning in a character column

You have the row and column indices mixed up. To change the value of CropTypeName7 (column 21) for row number 2, use EnvPerak[2,21] <- "Yam" or EnvPerak[2,"CropTypeName7"] <- "Yam", not EnvPerak[21,2] <- "Yam".

Invalid Factor Level, NA generated R

You could use ifelse() on the column, changing all values at once.

gss.s$abany <- ifelse(gss.s$abany == "YES", 1, -1)
gss.s
##    abany       advfront arrest
## 2      1          Agree     NO
## 3      1 Strongly agree    YES
## 10     1          Agree    YES
## 16     1          Agree     NO
## 21    -1 Strongly agree     NO

Warning message In `[-.factor`(`*tmp*`, iseq, value = foo) : invalid factor level, NA generated when trying to add vector to row subset

I have reduced your function based on my understanding , let me know if it gives what you want or if I have misunderstood something

addPointsToKeyRow = function(df, keyRowNum, searchString, pointsVector) {

    #Find columns which has searchString in it
    cols <- grepl(searchString, colnames(df))

    #Check if the columns with searchString and length of pointsVector is the same
    if (sum(cols) == length(pointsVector)) {
        #Assign the value
        df[keyRowNum,cols] <- pointsVector
    }
    #Return the updated dataframe
    df
}

#Convert all the variables in the column from factor to character
df[] <- lapply(df, as.character)

#define the values to be replaced
pointVals <- c("2", "2", "2", "2", "2", "2", "2", "1", "1", "1", "1","1", "1")

#Call the function
df <- addPointsToKeyRow(df, 1, "points_q", pointsval)

#Check the dataframe
df

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