Summarize specific word in data table in R

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df <- data.frame(
  "Domain" = c("Euka"),
  "Kingdom" = c("An","Plan"),
  "Division" = c("20181121","20181128","20181203"),
  "Species" = c("20181115_AG25_MAGH_50_A05_CGT.TXT","20181122_AG25_MAGH_50_C05_CGT.ARR",
                "20181115_AG25_MAGH_50_G05_CGT.TXT","20181124_AG25_MAGH_50_G45_CGT.TXT",
                "20181204_AG25_MAGH_50_G05_CGT.ARR","20181205_AG25_MAGH_50_G45_CGT.TXT",
                "20181207_AG25_MAGH_50_T05_CGT.ARR","20181215_AG25_MAGH_50_F45_CGT.TXT",
                "20181223_AG25_MAGH_50_R07_CGT.GGI","20181225_TW77_MAGH_33_L06_CGT.ARR",
                "20181226_TW77_MAGH_33_S07_CGT.ARR","20181227_TW77_MAGH_33_C06_CGT.TXT")
)

I want summarize that

Division 20181121 20181128 20181203
Total_TXT 2 0 3
Total_ARR 2 3 0
Total_GGI 0 0 1

How can I achieve this in R? Thanks.

r
3 Answers

Here is a tidyverse option, where we use count to get the total for each group, then we can put it into a wide format with pivot_wider.

library(tidyverse)

df %>% 
  group_by(gr = Division) %>% 
  count(Division = str_replace_all(Species, '.*\\.', '')) %>% 
  pivot_wider(names_from = "gr", values_from = "n", values_fill = 0) %>% 
  mutate(Division = paste0("Total_", Division))

Output

  Division  `20181121` `20181128` `20181203`
  <chr>          <int>      <int>      <int>
1 Total_ARR          2          3          0
2 Total_TXT          2          1          3
3 Total_GGI          0          0          1

Or here is a data.table option:

library(data.table)

df <-
  setDT(df)[, .N, by = .(cn = Division, Division = str_replace_all(Species, '.*\\.', ''))]

dcast(df,
      paste0("Total_", Division) ~ cn,
      value.var = "N",
      fill = 0)
user_152931910

We need to extract the last three characters from Species:

x <- nchar(df$Species)
rowlbl <- substr(df$Species, x-2, x)
table(rowlbl, df$Division)
# rowlbl 20181121 20181128 20181203
#    ARR        2        3        0
#    GGI        0        0        1
#    TXT        2        1        3
user_15806450

Base R one-liner -

table(sub('.*\\.', '', df$Species), df$Division)

#     20181121 20181128 20181203
#  ARR        2        3        0
#  GGI        0        0        1
#  TXT        2        1        3

Explanation :

sub removes everything until the last "." returning

sub('.*\\.', '', df$Species)
#[1] "TXT" "ARR" "TXT" "TXT" "ARR" "TXT" "ARR" "TXT" "GGI" "ARR" "ARR" "TXT"

This is then used in table with Division values.

sub can also be replaced with tools::file_ext for a non-regex approach.

table(tools::file_ext(df$Species), df$Division)
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