We assume

• the input shown reproducibly in the Note at the end
• that we want to sort by the prefix (part before dot)
• we wish to maintain the same order for the suffix (part after the dot)

Note that the tools package comes with R so it does not have to be installed.

library(dplyr)
library(tools)

ix <- dat %>% names %>% file_path_sans_ext %>% order
dat %>% select(all_of(ix))

##   cd.2013 cd.2012 cd.2011 pr.2013 pr.2012 pr.2011
## 1       4       5       6       1       2       3

Note

Input data frame shown reproducibly.

dat <- data.frame(pr.2013 = 1L, pr.2012 = 2L, pr.2011 = 3L, 
  cd.2013 = 4L, cd.2012 = 5L, cd.2011 = 6L)

You can use order + sub like below

> x <- c("pr.2013", "pr.2012", "pr. 2011", "cd.2013", "cd.2012", "cd.2011")

> x[order(sub("\..*", "", x))]
[1] "cd.2013"  "cd.2012"  "cd.2011"  "pr.2013"  "pr.2012"  "pr. 2011"

If there’s really lots of columns, it might be better to create a separate sorting vector and then simply select accordingly. Try this:

# Pkgs (stringr, tibble, dplyr) -------------------------------------------
library(tidyverse)

# Toy data ----------------------------------------------------------------
my_df <- tibble::tribble(
  ~pr.2013, ~pr.2012, ~pr.2011, ~cd.2013, ~cd.2012, ~cd.2011,
        1L,       2L,       3L,       4L,       5L,       6L)

# Sort --------------------------------------------------------------------
# Make a tibble with colnames
# Arrange it by letters fist and descending numbers last
aux <- tibble(value = colnames(my_df)) %>% 
  arrange(str_extract(value, "\D+"), desc(str_extract(value, "\d+$"))) %>% 
  pull(value)

# Sort the tibble/df with selection-helper `all_of` or `any_of`
new_df <- select(my_df, all_of(aux))
rm(aux)

# Output ------------------------------------------------------------------
new_df
#> # A tibble: 1 × 6
#>   cd.2013 cd.2012 cd.2011 pr.2013 pr.2012 pr.2011
#>     <int>   <int>   <int>   <int>   <int>   <int>
#> 1       4       5       6       1       2       3

^{Created on 2024-09-16 with reprex v2.1.0}

If this is your data

  pr.2012 pr.2011 pr.2013 cd.2012 cd.2013 cd.2011
1       1       2       3       4       5       6
2       2       3       4       5       6       7
3       3       4       5       6       7       8

Using the strsplit by . and arranged colnames to select the variables in the right order.

library(dplyr)

df[,match(data.frame(t(data.frame(strsplit(colnames(df), "\.")))) %>% 
    arrange(X1, desc(X2)) %>% 
    reframe(paste0(X1, ".", X2)) %>% 
    unlist(use.names=F), colnames(df))]
  cd.2013 cd.2012 cd.2011 pr.2013 pr.2012 pr.2011
1       5       4       6       3       1       2
2       6       5       7       4       2       3
3       7       6       8       5       3       4

Data

df <- structure(list(pr.2012 = 1:3, pr.2011 = 2:4, pr.2013 = 3:5, cd.2012 =
 4:6, cd.2013 = 5:7, cd.2011 = 6:8), class = "data.frame", row.names =
 c(NA, -3L))

Here is a base R solution:

df <- data.frame(
  pr.2012 = letters[1:10],
  pr.2013 = letters[11:20],
  cd.2012 = LETTERS[1:10],
  cd.2013 = LETTERS[11:20]
)

print(df)

   pr.2012 pr.2013 cd.2012 cd.2013
1        a       k       A       K
2        b       l       B       L
3        c       m       C       M
4        d       n       D       N
5        e       o       E       O
6        f       p       F       P
7        g       q       G       Q
8        h       r       H       R
9        i       s       I       S
10       j       t       J       T


# order column names alphabetically & reverse order
df <- df[,order(sort(colnames(df),decreasing = T))]

print(df)


   cd.2013 cd.2012 pr.2013 pr.2012
1        K       A       k       a
2        L       B       l       b
3        M       C       m       c
4        N       D       n       d
5        O       E       o       e
6        P       F       p       f
7        Q       G       q       g
8        R       H       r       h
9        S       I       s       i
10       T       J       t       j