Columns with different line numbers, how to join?

You can join several bases with only the base R. Since the merge function only accepts two data.frame 's when more than two have to be put in a list and the Reduce function is called merge .

With the example of the question data, I will assume that the bases are in .GlobalEnv and therefore I will first create a list with them.

df_list <- ls(pattern = "^df\d+$")  # Encontra os nomes das df's
df_list <- mget(df_list)             # Vai buscar os objetos com esses nomes

Now it's just a line of code.

Reduce(function(x, y) merge(x, y, all = TRUE), df_list)
#        data v1234 v7827  v3698
#1 2016-10-01    NA 12.36     NA
#2 2016-11-01    NA 12.37 3.3420
#3 2016-12-01  1.12 11.84 3.3523
#4 2017-01-01  1.09 11.11 3.1966
#5 2017-02-01  0.87 10.53 3.1042
#6 2017-03-01  1.05  9.85 3.1279
#7 2017-04-01  0.79    NA 3.1362
#8 2017-05-01  0.08    NA     NA

Data.

Note that in the question the first df has no column header, I used data and v followed by any number.

df1 <- read.table(text = "
    data           v1234
228 2016-12-01      1.12
229 2017-01-01      1.09
230 2017-02-01      0.87
231 2017-03-01      1.05
232 2017-04-01      0.79
233 2017-05-01      0.08
", header = TRUE)

df2 <- read.table(text = "
    data       v7827
206 2016-10-01 12.36
207 2016-11-01 12.37
208 2016-12-01 11.84
209 2017-01-01 11.11
210 2017-02-01 10.53
211 2017-03-01  9.85
", header = TRUE)

df3 <- read.table(text = "
  data          v3698
227 2016-11-01 3.3420
228 2016-12-01 3.3523
229 2017-01-01 3.1966
230 2017-02-01 3.1042
231 2017-03-01 3.1279
232 2017-04-01 3.1362
", header = TRUE)

df1$data <- as.Date(df1$data)
df2$data <- as.Date(df2$data)
df3$data <- as.Date(df3$data)

I have simulated some bases to illustrate what you want, please let me know if there is any inconsistency:

The bases with 3 and 4 lines, where the equal values are a1 and a2 (in their case are the dates):

df1 <- data.frame(
  data=c("a1", "a2", "a3"),
  b=c("b1", "b2", "b3"),
  stringsAsFactors = F
)

df2 <- data.frame(
  data=c("a1", "a2", "a4", "a5"),
  c=c("c1", "c2", "c3", "c4"),
  stringsAsFactors = F
)

Now I extract the single dates and I make a left_join() of dplyr to add the columns:

datas <- as.data.frame(unique(c(df1$data, df2$data)), stringsAsFactors = F)
colnames(datas) <- "data"

df <- left_join(datas, df1) %>%
  left_join(., df2)

Run:

x<-c(1:9)
y<-c(1:10)

library(qpcR)
qpcR:::cbind.na(x,y)

or

qpcR:::rbind.na(x,y) # para linhas