Reading a csv file in R

Question

I am trying to read some data written in R from a csv file instead using the data frame.

I used read.csv to extract the data from the file but I got always this error In read.table(file = file, header = header, sep = sep, quote = quote, : line 1 appears to contain embedded nulls .

This is a piece of the code in R using the data frame:

COL <- c("Fallow" = "slategray", "Mustard" = "red3" , "Mix4" = "orchid3", "Mix12"= "orange4")
SHP <- c("Fallow"=21,"Mustard"=22,"Mix4"=23, "Mix12"=24)


# generate data frame with original data
data <- data.frame(cc_variant = structure(c(1L, 1L, 1L, 3L, 4L, 2L, 3L, 4L, 2L, 2L, 4L, 3L), .Label = c("Fallow", "Mustard", "Mix4", "Mix12"), class = "factor"),
                   Date = structure(c(17092, 17093, 17098, 17092, 17092, 17092, 17093, 17093, 17093, 17098, 17098, 17098), class = "Date"),
                   NEE = c(52.3186092, 36.752742, 34.590816, -516.868370737168, -617.110003978854, -182.24567563611, -102.63776100067, -431.558870280712, -139.041211720174, -114.099387563412, -400.212603947375, -175.332083704246)
)


lm_NEE <- lmer(NEE ~ cc_variant + (1|Date), data=data)
df_NEE <- cld(emmeans(lm_NEE, specs ="cc_variant"), Letters=letters, sort=FALSE)

# Plot for BFS
ggplot(data, aes(x= cc_variant, y=NEE, fill= cc_variant))+
  geom_boxplot()+
  scale_fill_manual(values = COL, guide=FALSE)+
  geom_text(data= df_NEE ,aes(y=-600,x=cc_variant, label=.group))+
  labs(x="Catch crop variant",  y=expression("NEE (mg CO"[2]~"- C"~m^{-2}~h^{-1}~")"), fill="")+
  theme_myBW

ggsave("Fig1.png", width = 84, height = 70, units = "mm", dpi = 600)

This how the data frame looks:

 cc_variant       Date        NEE
1      Fallow 2016-10-18   52.31861
2      Fallow 2016-10-19   36.75274
3      Fallow 2016-10-24   34.59082
4        Mix4 2016-10-18 -516.86837
5       Mix12 2016-10-18 -617.11000
6     Mustard 2016-10-18 -182.24568
7        Mix4 2016-10-19 -102.63776
8       Mix12 2016-10-19 -431.55887
9     Mustard 2016-10-19 -139.04121
10    Mustard 2016-10-24 -114.09939
11      Mix12 2016-10-24 -400.21260
12       Mix4 2016-10-24 -175.33208

This is my try:

# set vector with colors and label
COL <- c("Fallow" = "slategray", "Mustard" = "red3" , "Mix4" = "orchid3", "Mix12"= "orange4")
SHP <- c("Fallow"=21,"Mustard"=22,"Mix4"=23, "Mix12"=24)


# generate data frame with original data
data <- read.csv("C:\\Users\\aganfoud\\Desktop\\orkg-stencila\\Gentsch2020\\data.csv", header=T, sep = ';')
datalm_NEE <- lmer(NEE ~ cc_variant + (1|Date), data=data)
df_NEE <- cld(emmeans(lm_NEE, specs ="cc_variant"), Letters=letters, sort=FALSE)

# Plot for BFS
  fig1 <- ggplot(data, aes(x= cc_variant, y=NEE, fill= cc_variant))+
  geom_boxplot()+
  scale_fill_manual(values = COL, guide=FALSE)+
  geom_text(data= df_NEE ,aes(y=-600,x=cc_variant, label=.group))+
  labs(x="Catch crop variant",  y=expression("NEE (mg CO"[2]~"- C"~m^{-2}~h^{-1}~")"), fill="")+
  theme_myBW

ggsave("Fig1.png", width = 84, height = 70, units = "mm", dpi = 600)

and finally this is how I create my csv file:

I suspect there's a mismatched quotation mark in there somewhere, but it's difficult to tell. Can you edit the question - I don't think we need anything after "This is my try", and indicate where the error occurs. — neilfws, Nov 03 '20 at 22:54
@neilfws the line of read the csv data, so shall I delete my try — Anouar, Nov 03 '20 at 22:58
Sounds like a [file encoding issue](https://stackoverflow.com/questions/24734911/warning-message-line-appears-to-contain-embedded-nulls/36346228). — neilfws, Nov 03 '20 at 23:08
@neilfws I added an utf-16 enconding as suggested in the answer but it doesn't work and I am getting an error that no lines available in input — Anouar, Nov 03 '20 at 23:14
Your file isn't necessarily utf-16. You need to work out what the encoding is. You could try `library(readr)` - install readr if required - then use `guess_encoding()`. In fact `readr::read_csv` may work better than `read.csv` - give it a try. — neilfws, Nov 03 '20 at 23:17
@neilfws I just add the `library(readr)´and the `guess_encoding()´directly after `read.csv´but it doesn't work for me, I am getting an argument "file" is missing for guess-encoding without standard value — Anouar, Nov 03 '20 at 23:25
You need to pass the full path and file name to `guess_encoding`, as you do for `read.csv`. Just do it in the console first, check the result. — neilfws, Nov 03 '20 at 23:59
Thanks for your rectifying, no I have this output of encoding : `! Multiple files in zip: reading ''[Content_Types].xml'' # A tibble: 1 x 2 encoding confidence 1 ASCII 1`´ — Anouar, Nov 04 '20 at 00:07

Spyrolix · Answer 1 · 2020-11-03T23:29:52.327

1

Does it help if you try to change:

data <- read.csv("C:\\Users\\aganfoud\\Desktop\\orkg-stencila\\Gentsch2020\\data.csv", header=T, sep = ';')

to

data <- read.csv("C:\\Users\\aganfoud\\Desktop\\orkg-stencila\\Gentsch2020\\data.csv", header=T, sep = ';',fileEncoding="utf-16")

UPDATE:

try to changeread.csv() to read_csv()

edited Nov 03 '20 at 23:29

answered Nov 03 '20 at 23:09

Spyrolix

40
5

Thanks for your answer but it doesn't work, I am getting an error that no lines available in input – Anouar Nov 03 '20 at 23:13
1

does it help now? – Spyrolix Nov 03 '20 at 23:30
unfortuantly no – Anouar Nov 03 '20 at 23:35

score 0 · Accepted Answer · answered Nov 04 '20 at 11:30

0

The problem was the file is saved as csv file but not exported to csv. So the exportation is necessary for the encoding of the file.

answered Nov 04 '20 at 11:30

Anouar

191
4
14

Reading a csv file in R

2 Answers2