R summarise by group sum giving NA

问题

I have a data frame like this

Observations: 2,190,835
Variables: 13
$ patientid      <int> 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489…
$ preparationid  <dbl> 1000307, 1000307, 1000307, 1000307, 1000307, 1000307, 1000307, 1000307, 1000307, 1000307, 1000307, 1…
$ doseday        <int> 90, 90, 91, 91, 92, 92, 92, 92, 93, 93, 93, 93, 94, 94, 94, 94, 95, 95, 95, 95, 99, 99, 100, 100, 10…
$ route          <fct> enteral., enteral., enteral., enteral., enteral., enteral., enteral., enteral., enteral., enteral., …
$ enteral        <fct> t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t, t…
$ energy_kcal_kg <dbl> 0.00, 13.56, 0.00, 13.56, 0.00, 13.49, 0.00, 13.49, 0.00, 13.35, 0.00, 13.35, 0.00, 12.95, 0.00, 12.…
$ prot_g_kg      <dbl> 0.000, 0.366, 0.000, 0.366, 0.000, 0.365, 0.000, 0.365, 0.000, 0.361, 0.000, 0.361, 0.000, 0.350, 0.…
$ lipids_g_kg    <dbl> 0.000, 0.495, 0.000, 0.495, 0.000, 0.492, 0.000, 0.492, 0.000, 0.487, 0.000, 0.487, 0.000, 0.472, 0.…
$ K_mmol_kg      <dbl> 0.000, 0.385, 0.000, 0.385, 0.000, 0.383, 0.000, 0.383, 0.000, 0.379, 0.000, 0.379, 0.000, 0.368, 0.…
$ Na_mmol_kg     <dbl> 0.0000, 0.1832, 0.0000, 0.1832, 0.0000, 0.1823, 0.0000, 0.1823, 0.0000, 0.1804, 0.0000, 0.1804, 0.00…
$ Ca_mg_kg       <dbl> 0.00, 10.99, 0.00, 10.99, 0.00, 10.94, 0.00, 10.94, 0.00, 10.82, 0.00, 10.82, 0.00, 10.50, 0.00, 10.…
$ P_mg_kg        <dbl> 0.00, 8.25, 0.00, 8.25, 0.00, 8.20, 0.00, 8.20, 0.00, 8.12, 0.00, 8.12, 0.00, 7.88, 0.00, 7.88, 0.00…
$ Pi_mmol_kg     <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
>

And I would need to calculate for each patient the daily sum of nutrient intakes. And I´ve been using the code below.

nutrient_intake <- nutrient_data %>% group_by(patientid, doseday, enteral) %>% summarise(energy_kcal_kg_d=sum(energy_kcal_kg), protein_g_kg_d=sum(prot_g_kg), lipids_g_kg_d=sum(lipids_g_kg), na_total_mmol_kg_d=sum(Na_mmol_kg), K_total_mmol_kg_d=sum(K_mmol_kg), Ca_mg_total_kg_d=sum(Ca_mg_kg), P_mg_kg_d=sum(P_mg_kg), Pi_mmol_kg_d=sum(Pi_mmol_kg))

The code seems to be working in someway since the grouping seems fine, however the daily sums are missing, result is NA. What is wrong here?

Variables: 11
Groups: patientid, doseday [30,991]
$ patientid          <int> 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, 4489, …
$ doseday            <int> 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 13, 13, 14, …
$ enteral            <fct> f, t, f, t, f, t, f, t, f, t, f, t, f, t, f, t, f, t, f, t, f, t, f, t, f, t, f, t, f, t, f, t, …
$ energy_kcal_kg_d   <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
$ protein_g_kg_d     <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
$ lipids_g_kg_d      <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
$ na_total_mmol_kg_d <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
$ K_total_mmol_kg_d  <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
$ Ca_mg_total_kg_d   <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
$ P_mg_kg_d          <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
$ Pi_mmol_kg_d       <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
> ```

回答1:

By default, sum does not consider NA.

Try this:

nutrient_intake <- nutrient_data %>% 
  group_by(patientid, doseday, enteral) %>% 
  summarise(
    energy_kcal_kg_d=sum(energy_kcal_kg, na.rm=T),
    protein_g_kg_d=sum(prot_g_kg, na.rm=T),
    lipids_g_kg_d=sum(lipids_g_kg, na.rm=T),
    na_total_mmol_kg_d=sum(Na_mmol_kg, na.rm=T),
    K_total_mmol_kg_d=sum(K_mmol_kg, na.rm=T),
    Ca_mg_total_kg_d=sum(Ca_mg_kg, na.rm=T),
    P_mg_kg_d=sum(P_mg_kg, na.rm=T),
    Pi_mmol_kg_d=sum(Pi_mmol_kg, na.rm=T)
  )

来源：https://stackoverflow.com/questions/59283479/r-summarise-by-group-sum-giving-na

标签

group-by

dplyr

sum

summarize