Code
library(tidyverse)
# result <- read.csv(file = 'total_elements_mindat.csv')
result <- read.csv(file = 'total_elements_mindat.csv')MY DATASET
This dataset is generated based on the elements coexistence counts from Mindat.org database. The original data source is retrieved via Mindat API and stored in JSON format. Then after data pre-process and data cleaning steps, the retrieved data is cured and stored in CSV format. The dataset can be accessed at the Github repository, in the name of total_elements_mindat.csv.
Note
The CSV file of dataset is a concatenated version of 72 separate spread sheets of element triplets coexistence values. Each spread sheet has 2 + 72 columns, the first column indicates the background element, which should remain the same throughout each separate sheet. The second column records the second dimension of the element triplets Then the third dimension of elements are listed by the remaining columns. The value of cell \((i, j)\) indicating the coexistence amount of three elements: the first two elements in \((i, 0)\) and \((i, 1)\), and the third element in \((0, j)\).
Data Collection
The dataset was retrieved via Mindat API as a JSON file. In the data preprocessing step, the elements information are extracted and statistically recorded in a new JSON file. Then I reorganized the data into 72 spread sheets as CSV formats.
IMPORTING THE DATA
I’m going to use the built-in read.csv package to import CSV file.
The glimpse command in the Tidyverse package is a nice way to summarize the data frame:
Code
glimpse(result)Rows: 5,184
Columns: 74
$ zaxis <chr> "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H",…
$ yaxis <chr> "H", "Li", "Be", "B", "C", "N", "O", "F", "Na", "Mg", "Al", "Si"…
$ H <int> 3228, 51, 66, 193, 330, 128, 3205, 141, 643, 472, 817, 1023, 524…
$ Li <int> 51, 51, 4, 8, 2, 0, 51, 4, 19, 6, 25, 39, 9, 1, 1, 6, 8, 0, 6, 0…
$ Be <int> 66, 4, 66, 3, 1, 0, 66, 1, 13, 4, 8, 31, 27, 0, 0, 4, 34, 0, 0, …
$ B <int> 193, 8, 3, 193, 13, 3, 192, 10, 50, 55, 52, 73, 3, 8, 24, 9, 89,…
$ C <int> 330, 2, 1, 13, 330, 23, 317, 12, 65, 55, 50, 46, 17, 30, 19, 11,…
$ N <int> 128, 0, 0, 3, 23, 128, 118, 5, 23, 13, 22, 10, 18, 48, 23, 6, 8,…
$ O <int> 3205, 51, 66, 192, 317, 118, 3205, 138, 643, 472, 817, 1021, 524…
$ F <int> 141, 4, 1, 10, 12, 5, 138, 141, 54, 22, 79, 58, 30, 24, 8, 14, 5…
$ Na <int> 643, 19, 13, 50, 65, 23, 643, 54, 643, 106, 182, 356, 89, 102, 3…
$ Mg <int> 472, 6, 4, 55, 55, 13, 472, 22, 106, 472, 147, 161, 86, 61, 28, …
$ Al <int> 817, 25, 8, 52, 50, 22, 817, 79, 182, 147, 817, 401, 169, 135, 3…
$ Si <int> 1023, 39, 31, 73, 46, 10, 1021, 58, 356, 161, 401, 1023, 15, 36,…
$ P <int> 524, 9, 27, 3, 17, 18, 524, 30, 89, 86, 169, 15, 524, 21, 1, 32,…
$ S <int> 531, 1, 0, 8, 30, 48, 531, 24, 102, 61, 135, 36, 21, 531, 27, 53…
$ Cl <int> 210, 1, 0, 24, 19, 23, 204, 8, 39, 28, 33, 36, 1, 27, 210, 26, 5…
$ K <int> 287, 6, 4, 9, 11, 6, 287, 14, 82, 50, 81, 162, 32, 53, 26, 287, …
$ Ca <int> 918, 8, 34, 89, 97, 8, 918, 58, 187, 131, 269, 424, 134, 84, 53,…
$ Sc <int> 8, 0, 0, 0, 0, 0, 8, 0, 1, 3, 0, 4, 3, 0, 0, 0, 5, 8, 0, 0, 0, 0…
$ Ti <int> 145, 6, 0, 3, 2, 0, 145, 18, 81, 11, 9, 116, 9, 2, 2, 30, 32, 0,…
$ V <int> 181, 0, 0, 3, 6, 8, 180, 2, 28, 24, 31, 27, 14, 12, 3, 10, 55, 0…
$ Cr <int> 40, 0, 0, 4, 5, 0, 40, 2, 7, 11, 4, 13, 2, 6, 3, 3, 11, 0, 1, 2,…
$ Mn <int> 406, 4, 9, 15, 17, 2, 406, 14, 81, 42, 70, 185, 98, 23, 17, 28, …
$ Fe <int> 663, 11, 9, 18, 22, 18, 663, 15, 130, 78, 136, 216, 176, 122, 32…
$ Co <int> 35, 0, 0, 0, 4, 1, 35, 0, 3, 0, 1, 1, 1, 12, 2, 0, 4, 0, 0, 1, 0…
$ Ni <int> 63, 0, 0, 0, 12, 4, 62, 0, 2, 1, 6, 7, 2, 15, 5, 1, 4, 0, 0, 2, …
$ Cu <int> 359, 1, 0, 4, 36, 10, 358, 6, 16, 16, 39, 29, 40, 87, 61, 16, 50…
$ Zn <int> 208, 0, 3, 0, 15, 1, 208, 1, 11, 16, 23, 32, 44, 46, 7, 7, 29, 0…
$ Ga <int> 4, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0…
$ Ge <int> 10, 0, 0, 0, 1, 0, 10, 0, 0, 0, 3, 1, 0, 4, 0, 0, 2, 0, 0, 0, 0,…
$ As <int> 397, 0, 3, 2, 4, 5, 397, 3, 36, 40, 42, 17, 9, 21, 14, 12, 112, …
$ Se <int> 26, 0, 0, 0, 0, 0, 26, 0, 2, 1, 4, 1, 0, 3, 2, 1, 3, 0, 0, 0, 0,…
$ Br <int> 3, 0, 0, 0, 0, 1, 3, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Rb <int> 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Sr <int> 77, 1, 0, 9, 12, 0, 77, 6, 23, 4, 30, 30, 15, 5, 2, 4, 20, 0, 8,…
$ Y <int> 54, 1, 1, 2, 27, 0, 54, 5, 18, 1, 13, 21, 6, 6, 2, 2, 18, 0, 2, …
$ Zr <int> 70, 1, 3, 2, 9, 0, 70, 3, 56, 2, 1, 58, 9, 1, 10, 10, 31, 0, 1, …
$ Nb <int> 54, 0, 0, 0, 4, 0, 54, 4, 26, 4, 1, 32, 4, 1, 2, 12, 17, 0, 7, 1…
$ Mo <int> 49, 0, 0, 0, 0, 1, 49, 0, 6, 4, 3, 0, 6, 5, 0, 4, 9, 0, 0, 0, 0,…
$ Ru <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Rh <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Pd <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Ag <int> 3, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 1, 2, 1, 0, 0, 0, 0, 0, 0…
$ Cd <int> 12, 0, 0, 0, 0, 0, 12, 1, 0, 0, 1, 0, 2, 8, 0, 1, 0, 0, 0, 0, 0,…
$ In <int> 2, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Sn <int> 21, 0, 2, 1, 0, 1, 20, 0, 2, 2, 2, 8, 0, 1, 2, 0, 7, 1, 0, 0, 0,…
$ Sb <int> 32, 0, 0, 0, 0, 0, 32, 0, 4, 2, 5, 2, 0, 10, 3, 2, 5, 0, 2, 0, 0…
$ Te <int> 52, 0, 0, 0, 2, 0, 52, 0, 0, 8, 1, 0, 0, 9, 7, 0, 6, 0, 0, 0, 1,…
$ I <int> 12, 0, 0, 0, 0, 1, 12, 0, 3, 3, 0, 0, 0, 1, 3, 2, 3, 0, 0, 0, 2,…
$ Cs <int> 12, 0, 1, 1, 0, 0, 12, 2, 4, 0, 2, 8, 1, 0, 0, 1, 4, 0, 2, 1, 0,…
$ Ba <int> 134, 2, 3, 4, 12, 0, 134, 16, 42, 11, 34, 76, 32, 5, 9, 8, 18, 1…
$ La <int> 29, 0, 0, 0, 7, 0, 29, 0, 3, 1, 14, 15, 3, 0, 0, 0, 10, 0, 1, 1,…
$ Ce <int> 77, 0, 2, 5, 16, 0, 77, 8, 17, 10, 25, 47, 8, 4, 1, 1, 28, 0, 13…
$ Nd <int> 19, 0, 1, 0, 8, 0, 19, 1, 1, 0, 3, 5, 3, 2, 0, 0, 5, 0, 0, 0, 0,…
$ Sm <int> 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Gd <int> 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0…
$ Dy <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Er <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Yb <int> 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Hf <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Ta <int> 5, 0, 0, 0, 0, 0, 5, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0…
$ W <int> 22, 0, 0, 0, 1, 0, 22, 0, 5, 1, 2, 3, 1, 0, 0, 0, 7, 0, 0, 1, 0,…
$ Re <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Os <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Ir <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Pt <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Au <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ Hg <int> 11, 0, 0, 0, 3, 4, 10, 0, 0, 0, 1, 0, 1, 1, 4, 0, 0, 0, 0, 0, 0,…
$ Tl <int> 7, 0, 0, 0, 0, 0, 7, 0, 0, 0, 1, 0, 0, 4, 2, 2, 0, 0, 0, 2, 0, 0…
$ Pb <int> 229, 0, 1, 5, 28, 3, 228, 6, 3, 7, 27, 32, 27, 54, 39, 3, 13, 0,…
$ Bi <int> 42, 0, 0, 0, 0, 2, 41, 0, 1, 1, 1, 1, 11, 4, 1, 0, 1, 0, 0, 5, 1…
$ Th <int> 15, 0, 0, 1, 2, 0, 15, 2, 2, 0, 2, 4, 5, 0, 0, 1, 3, 0, 1, 0, 0,…
$ U <int> 272, 1, 0, 0, 41, 12, 272, 8, 33, 24, 21, 20, 51, 61, 2, 27, 54,…DESCRIBE THE DATA
Data Set Type
The dataset is stored as a great Flat Table, the items are arranged as each of the 72 elements, with the attributes of element triplets coexistence in the cells of corresponding sheets.
Element list
c('H', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Cs', 'Ba', 'La', 'Ce', 'Nd', 'Sm', 'Gd', 'Dy', 'Er', 'Yb', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Th', 'U') [1] "H" "Li" "Be" "B" "C" "N" "O" "F" "Na" "Mg" "Al" "Si" "P" "S" "Cl"
[16] "K" "Ca" "Sc" "Ti" "V" "Cr" "Mn" "Fe" "Co" "Ni" "Cu" "Zn" "Ga" "Ge" "As"
[31] "Se" "Br" "Rb" "Sr" "Y" "Zr" "Nb" "Mo" "Ru" "Rh" "Pd" "Ag" "Cd" "In" "Sn"
[46] "Sb" "Te" "I" "Cs" "Ba" "La" "Ce" "Nd" "Sm" "Gd" "Dy" "Er" "Yb" "Hf" "Ta"
[61] "W" "Re" "Os" "Ir" "Pt" "Au" "Hg" "Tl" "Pb" "Bi" "Th" "U" Attribute Types
The attributes of the data are recorded in a 2-dimensional format, therefore the data frame rows will looks similar to the result of glimpse function.
Code
head(result) zaxis yaxis H Li Be B C N O F Na Mg Al Si P S Cl K
1 H H 3228 51 66 193 330 128 3205 141 643 472 817 1023 524 531 210 287
2 H Li 51 51 4 8 2 0 51 4 19 6 25 39 9 1 1 6
3 H Be 66 4 66 3 1 0 66 1 13 4 8 31 27 0 0 4
4 H B 193 8 3 193 13 3 192 10 50 55 52 73 3 8 24 9
5 H C 330 2 1 13 330 23 317 12 65 55 50 46 17 30 19 11
6 H N 128 0 0 3 23 128 118 5 23 13 22 10 18 48 23 6
Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Rb Sr Y Zr Nb Mo Ru
1 918 8 145 181 40 406 663 35 63 359 208 4 10 397 26 3 1 77 54 70 54 49 0
2 8 0 6 0 0 4 11 0 0 1 0 0 0 0 0 0 0 1 1 1 0 0 0
3 34 0 0 0 0 9 9 0 0 0 3 0 0 3 0 0 0 0 1 3 0 0 0
4 89 0 3 3 4 15 18 0 0 4 0 0 0 2 0 0 1 9 2 2 0 0 0
5 97 0 2 6 5 17 22 4 12 36 15 0 1 4 0 0 0 12 27 9 4 0 0
6 8 0 0 8 0 2 18 1 4 10 1 0 0 5 0 1 0 0 0 0 0 1 0
Rh Pd Ag Cd In Sn Sb Te I Cs Ba La Ce Nd Sm Gd Dy Er Yb Hf Ta W Re Os Ir
1 0 0 3 12 2 21 32 52 12 12 134 29 77 19 1 1 0 0 1 0 5 22 0 0 0
2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3 0 0 0 0 0 2 0 0 0 1 3 0 2 1 0 0 0 0 1 0 0 0 0 0 0
4 0 0 0 0 0 1 0 0 0 1 4 0 5 0 0 0 0 0 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0 2 0 0 12 7 16 8 0 1 0 0 0 0 0 1 0 0 0
6 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Pt Au Hg Tl Pb Bi Th U
1 0 0 11 7 229 42 15 272
2 0 0 0 0 0 0 0 1
3 0 0 0 0 1 0 0 0
4 0 0 0 0 5 0 1 0
5 0 0 3 0 28 0 2 41
6 0 0 4 0 3 2 0 12Question
Note
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