I am attempting to sum the number of atoms for each element in the chemical_formula vector:
chemical_formula <- c("CaF2", "Ca3(PO4)2", "FePO4", "KCl", "K3PO4", "K2SO4", "Mg3(PO4)2", "NaCl",
"Na3PO4", "Na2SO4", "SiO2", "CaSO4", "KAsO2", "KBr", "KI", "LiCl", "MnSO4", "CaS", "CuAsHO3",
"AlK(SO4)2", "(H2O)12", "ZnCl2", "CaCO3", "NaHCO3", "AsI3", "AuCl4Na", "Se", "K2Cr2O7")
cell_salts_atoms <- CHNOSZ::makeup(chemical_formula)
# > CHNOSZ::makeup(chemical_formula)
# [[1]]
# Ca F
# 1 2
#
# [[2]]
# Ca O P
# 3 8 2
#
# [[3]]
# Fe P O
# 1 1 4
#
# [[4]]
# K Cl
# 1 1
#
# [[5]]
# K P O
# 3 1 4
#
# [[6]]
# K S O
# 2 1 4
#
# [[7]]
# Mg O P
# 3 8 2
#
# [[8]]
# Na Cl
# 1 1
#
# [[9]]
# Na P O
# 3 1 4
#
# [[10]]
# Na S O
# 2 1 4
#
# [[11]]
# Si O
# 1 2
#
# [[12]]
# Ca S O
# 1 1 4
#
# [[13]]
# K As O
# 1 1 2
#
# [[14]]
# K Br
# 1 1
#
# [[15]]
# K I
# 1 1
#
# [[16]]
# Li Cl
# 1 1
#
# [[17]]
# Mn S O
# 1 1 4
#
# [[18]]
# Ca S
# 1 1
#
# [[19]]
# Cu As H O
# 1 1 1 3
#
# [[20]]
# Al K O S
# 1 1 8 2
#
# [[21]]
# H O
# 24 12
#
# [[22]]
# Zn Cl
# 1 2
#
# [[23]]
# Ca C O
# 1 1 3
#
# [[24]]
# Na H C O
# 1 1 1 3
#
# [[25]]
# As I
# 1 3
#
# [[26]]
# Au Cl Na
# 1 4 1
#
# [[27]]
# Se
# 1
#
# [[28]]
# K Cr O
# 2 2 7
cell_salts_atoms_matrix <- lapply(cell_salts_atoms, as.matrix)
# > cell_salts_atoms_matrix
# [[1]]
# [,1]
# Ca 1
# F 2
#
# [[2]]
# [,1]
# Ca 3
# O 8
# P 2
#
# [[3]]
# [,1]
# Fe 1
# P 1
# O 4
#
# [[4]]
# [,1]
# K 1
# Cl 1
#
# [[5]]
# [,1]
# K 3
# P 1
# O 4
#
# [[6]]
# [,1]
# K 2
# S 1
# O 4
#
# [[7]]
# [,1]
# Mg 3
# O 8
# P 2
#
# [[8]]
# [,1]
# Na 1
# Cl 1
#
# [[9]]
# [,1]
# Na 3
# P 1
# O 4
#
# [[10]]
# [,1]
# Na 2
# S 1
# O 4
#
# [[11]]
# [,1]
# Si 1
# O 2
#
# [[12]]
# [,1]
# Ca 1
# S 1
# O 4
#
# [[13]]
# [,1]
# K 1
# As 1
# O 2
#
# [[14]]
# [,1]
# K 1
# Br 1
#
# [[15]]
# [,1]
# K 1
# I 1
#
# [[16]]
# [,1]
# Li 1
# Cl 1
#
# [[17]]
# [,1]
# Mn 1
# S 1
# O 4
#
# [[18]]
# [,1]
# Ca 1
# S 1
#
# [[19]]
# [,1]
# Cu 1
# As 1
# H 1
# O 3
#
# [[20]]
# [,1]
# Al 1
# K 1
# O 8
# S 2
#
# [[21]]
# [,1]
# H 24
# O 12
#
# [[22]]
# [,1]
# Zn 1
# Cl 2
#
# [[23]]
# [,1]
# Ca 1
# C 1
# O 3
#
# [[24]]
# [,1]
# Na 1
# H 1
# C 1
# O 3
#
# [[25]]
# [,1]
# As 1
# I 3
#
# [[26]]
# [,1]
# Au 1
# Cl 4
# Na 1
#
# [[27]]
# [,1]
# Se 1
#
# [[28]]
# [,1]
# K 2
# Cr 2
# O 7
I want the result to resemble the following:
Se 1
Au 1
As 2
Ca 6
I have tried cell_salts_atoms_sum <- lapply(cell_salts_atoms, sum); however, that only provides the total sum for each list element rather than sum of each named component.
What's the best method to produce the desired result?
UPDATE
The structure of the result does not matter, I just wanted a sum of the atoms.
Thus,
Se Au As Ca
1 1 2 6
is also acceptable.
Please try
library(CHNOSZ)
cell_salts_atoms <- CHNOSZ::makeup(chemical_formula, sum=F)
data <- map(cell_salts_atoms, \(x) {
data.frame(val=x %>% as_vector()) %>% rownames_to_column(var='element')
})
data1 <- do.call(rbind, data) %>% arrange(element) %>% group_by(element) %>% summarise(sum=sum(val))
# A tibble: 24 × 2
element sum
<chr> <dbl>
1 Al 1
2 As 3
3 Au 1
4 Br 1
5 C 2
6 Ca 7
7 Cl 9
8 Cr 2
9 Cu 1
10 F 2
# ℹ 14 more rows
# ℹ Use `print(n = ...)` to see more rows