Module 8: Data Wrangling - Chris Okitondo
Setup
Load needed packages.
Data loading
# path to data
data_location<- here::here("fluanalysis", "data", "SympAct_Any_Pos.Rda")
# load data
data <- readRDS(data_location)Looking at the data
dplyr::glimpse(data)Rows: 735
Columns: 63
$ DxName1 <fct> "Influenza like illness - Clinical Dx", "Acute tonsi…
$ DxName2 <fct> NA, "Influenza like illness - Clinical Dx", "Acute p…
$ DxName3 <fct> NA, NA, NA, NA, NA, NA, NA, NA, "Fever, unspecified"…
$ DxName4 <fct> NA, NA, NA, NA, NA, NA, NA, NA, "Other fatigue", NA,…
$ DxName5 <fct> NA, NA, NA, NA, NA, NA, NA, NA, "Headache", NA, NA, …
$ Unique.Visit <chr> "340_17632125", "340_17794836", "342_17737773", "342…
$ ActivityLevel <int> 10, 6, 2, 2, 5, 3, 4, 0, 0, 5, 9, 1, 3, 6, 5, 2, 2, …
$ ActivityLevelF <fct> 10, 6, 2, 2, 5, 3, 4, 0, 0, 5, 9, 1, 3, 6, 5, 2, 2, …
$ SwollenLymphNodes <fct> Yes, Yes, Yes, Yes, Yes, No, No, No, Yes, No, Yes, Y…
$ ChestCongestion <fct> No, Yes, Yes, Yes, No, No, No, Yes, Yes, Yes, Yes, Y…
$ ChillsSweats <fct> No, No, Yes, Yes, Yes, Yes, Yes, Yes, Yes, No, Yes, …
$ NasalCongestion <fct> No, Yes, Yes, Yes, No, No, No, Yes, Yes, Yes, Yes, Y…
$ CoughYN <fct> Yes, Yes, No, Yes, No, Yes, Yes, Yes, Yes, Yes, No, …
$ Sneeze <fct> No, No, Yes, Yes, No, Yes, No, Yes, No, No, No, No, …
$ Fatigue <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Ye…
$ SubjectiveFever <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, No, Yes…
$ Headache <fct> Yes, Yes, Yes, Yes, Yes, Yes, No, Yes, Yes, Yes, Yes…
$ Weakness <fct> Mild, Severe, Severe, Severe, Moderate, Moderate, Mi…
$ WeaknessYN <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Ye…
$ CoughIntensity <fct> Severe, Severe, Mild, Moderate, None, Moderate, Seve…
$ CoughYN2 <fct> Yes, Yes, Yes, Yes, No, Yes, Yes, Yes, Yes, Yes, Yes…
$ Myalgia <fct> Mild, Severe, Severe, Severe, Mild, Moderate, Mild, …
$ MyalgiaYN <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Ye…
$ RunnyNose <fct> No, No, Yes, Yes, No, No, Yes, Yes, Yes, Yes, No, No…
$ AbPain <fct> No, No, Yes, No, No, No, No, No, No, No, Yes, Yes, N…
$ ChestPain <fct> No, No, Yes, No, No, Yes, Yes, No, No, No, No, Yes, …
$ Diarrhea <fct> No, No, No, No, No, Yes, No, No, No, No, No, No, No,…
$ EyePn <fct> No, No, No, No, Yes, No, No, No, No, No, Yes, No, Ye…
$ Insomnia <fct> No, No, Yes, Yes, Yes, No, No, Yes, Yes, Yes, Yes, Y…
$ ItchyEye <fct> No, No, No, No, No, No, No, No, No, No, No, No, Yes,…
$ Nausea <fct> No, No, Yes, Yes, Yes, Yes, No, No, Yes, Yes, Yes, Y…
$ EarPn <fct> No, Yes, No, Yes, No, No, No, No, No, No, No, Yes, Y…
$ Hearing <fct> No, Yes, No, No, No, No, No, No, No, No, No, No, No,…
$ Pharyngitis <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, No, No, No, Yes, …
$ Breathless <fct> No, No, Yes, No, No, Yes, No, No, No, Yes, No, Yes, …
$ ToothPn <fct> No, No, Yes, No, No, No, No, No, Yes, No, No, Yes, N…
$ Vision <fct> No, No, No, No, No, No, No, No, No, No, No, No, No, …
$ Vomit <fct> No, No, No, No, No, No, Yes, No, No, No, Yes, Yes, N…
$ Wheeze <fct> No, No, No, Yes, No, Yes, No, No, No, No, No, Yes, N…
$ BodyTemp <dbl> 98.3, 100.4, 100.8, 98.8, 100.5, 98.4, 102.5, 98.4, …
$ RapidFluA <fct> Presumptive Negative For Influenza A, NA, Presumptiv…
$ RapidFluB <fct> Presumptive Negative For Influenza B, NA, Presumptiv…
$ PCRFluA <fct> NA, NA, NA, NA, NA, NA, Influenza A Not Detected, N…
$ PCRFluB <fct> NA, NA, NA, NA, NA, NA, Influenza B Not Detected, N…
$ TransScore1 <dbl> 1, 3, 4, 5, 0, 2, 2, 5, 4, 4, 2, 3, 2, 5, 3, 5, 1, 5…
$ TransScore1F <fct> 1, 3, 4, 5, 0, 2, 2, 5, 4, 4, 2, 3, 2, 5, 3, 5, 1, 5…
$ TransScore2 <dbl> 1, 2, 3, 4, 0, 2, 2, 4, 3, 3, 1, 2, 2, 4, 2, 4, 1, 4…
$ TransScore2F <fct> 1, 2, 3, 4, 0, 2, 2, 4, 3, 3, 1, 2, 2, 4, 2, 4, 1, 4…
$ TransScore3 <dbl> 1, 1, 2, 3, 0, 2, 2, 3, 2, 2, 0, 1, 1, 3, 1, 3, 1, 3…
$ TransScore3F <fct> 1, 1, 2, 3, 0, 2, 2, 3, 2, 2, 0, 1, 1, 3, 1, 3, 1, 3…
$ TransScore4 <dbl> 0, 2, 4, 4, 0, 1, 1, 4, 3, 3, 2, 2, 2, 4, 3, 4, 0, 4…
$ TransScore4F <fct> 0, 2, 4, 4, 0, 1, 1, 4, 3, 3, 2, 2, 2, 4, 3, 4, 0, 4…
$ ImpactScore <int> 7, 8, 14, 12, 11, 12, 8, 7, 10, 7, 13, 17, 11, 13, 9…
$ ImpactScore2 <int> 6, 7, 13, 11, 10, 11, 7, 6, 9, 6, 12, 16, 10, 12, 8,…
$ ImpactScore3 <int> 3, 4, 9, 7, 6, 7, 3, 3, 6, 4, 7, 11, 6, 8, 4, 4, 5, …
$ ImpactScoreF <fct> 7, 8, 14, 12, 11, 12, 8, 7, 10, 7, 13, 17, 11, 13, 9…
$ ImpactScore2F <fct> 6, 7, 13, 11, 10, 11, 7, 6, 9, 6, 12, 16, 10, 12, 8,…
$ ImpactScore3F <fct> 3, 4, 9, 7, 6, 7, 3, 3, 6, 4, 7, 11, 6, 8, 4, 4, 5, …
$ ImpactScoreFD <fct> 7, 8, 14, 12, 11, 12, 8, 7, 10, 7, 13, 17, 11, 13, 9…
$ TotalSymp1 <dbl> 8, 11, 18, 17, 11, 14, 10, 12, 14, 11, 15, 20, 13, 1…
$ TotalSymp1F <fct> 8, 11, 18, 17, 11, 14, 10, 12, 14, 11, 15, 20, 13, 1…
$ TotalSymp2 <dbl> 8, 10, 17, 16, 11, 14, 10, 11, 13, 10, 14, 19, 13, 1…
$ TotalSymp3 <dbl> 8, 9, 16, 15, 11, 14, 10, 10, 12, 9, 13, 18, 12, 16,…summary(data) DxName1
Influenza like illness - Clinical Dx :328
Influenza - Virus Identified :131
Fever, unspecified :101
Cough : 66
Acute pharyngitis, unspecified : 50
Acute upper respiratory infection, unspecified: 22
(Other) : 37
DxName2
Influenza - Virus Identified :126
Influenza like illness - Clinical Dx:115
Fever, unspecified : 45
Cough : 41
Acute pharyngitis, unspecified : 31
(Other) : 97
NA's :280
DxName3
Influenza - Virus Identified : 23
Influenza like illness - Clinical Dx: 14
Cough : 10
Fever, unspecified : 6
Acute pharyngitis, unspecified : 4
(Other) : 52
NA's :626
DxName4
Influenza - Virus Identified : 3
Acute upper respiratory infection, unspecified: 2
Encounter for immunization : 2
Influenza like illness - Clinical Dx : 2
Acute pharyngitis, unspecified : 1
(Other) : 9
NA's :716
DxName5
Acute suppurative otitis media without spontaneous rupture of ear drum, right ear : 0
Encounter for immunization : 0
Headache : 1
Other infectious mononucleosis without complication : 0
Strain of other flexor muscle, fascia and tendon at forearm level, right arm, subsequent encounter: 0
NA's :734
Unique.Visit ActivityLevel ActivityLevelF SwollenLymphNodes
Length:735 Min. : 0.000 3 :125 No :421
Class :character 1st Qu.: 3.000 5 : 97 Yes:314
Mode :character Median : 4.000 4 : 95
Mean : 4.463 2 : 80
3rd Qu.: 6.000 7 : 68
Max. :10.000 6 : 66
(Other):204
ChestCongestion ChillsSweats NasalCongestion CoughYN Sneeze Fatigue
No :326 No :131 No :170 No : 75 No :340 No : 64
Yes:409 Yes:604 Yes:565 Yes:660 Yes:395 Yes:671
SubjectiveFever Headache Weakness WeaknessYN CoughIntensity CoughYN2
No :230 No :115 None : 49 No : 49 None : 47 No : 47
Yes:505 Yes:620 Mild :224 Yes:686 Mild :156 Yes:688
Moderate:341 Moderate:360
Severe :121 Severe :172
Myalgia MyalgiaYN RunnyNose AbPain ChestPain Diarrhea EyePn
None : 79 No : 79 No :211 No :642 No :501 No :636 No :622
Mild :214 Yes:656 Yes:524 Yes: 93 Yes:234 Yes: 99 Yes:113
Moderate:327
Severe :115
Insomnia ItchyEye Nausea EarPn Hearing Pharyngitis Breathless
No :316 No :553 No :477 No :573 No :705 No :121 No :438
Yes:419 Yes:182 Yes:258 Yes:162 Yes: 30 Yes:614 Yes:297
ToothPn Vision Vomit Wheeze BodyTemp
No :569 No :716 No :656 No :514 Min. : 97.20
Yes:166 Yes: 19 Yes: 79 Yes:221 1st Qu.: 98.20
Median : 98.50
Mean : 98.94
3rd Qu.: 99.30
Max. :103.10
NA's :5
RapidFluA
Positive for Influenza A :169
Presumptive Negative For Influenza A:159
NA's :407
RapidFluB PCRFluA
Positive for Influenza B : 26 Influenza A Detected :120
Presumptive Negative For Influenza B:302 Influenza A Not Detected: 33
NA's :407 Assay Invalid : 0
Indeterminate : 1
NA's :581
PCRFluB TransScore1 TransScore1F TransScore2
Influenza B Detected : 9 Min. :0.000 0: 13 Min. :0.000
Influenza B Not Detected:145 1st Qu.:3.000 1: 53 1st Qu.:2.000
Assay Invalid : 0 Median :4.000 2:107 Median :3.000
NA's :581 Mean :3.473 3:157 Mean :2.917
3rd Qu.:5.000 4:210 3rd Qu.:4.000
Max. :5.000 5:195 Max. :4.000
TransScore2F TransScore3 TransScore3F TransScore4 TransScore4F
0: 13 Min. :0.000 0: 24 Min. :0.000 0: 50
1: 89 1st Qu.:1.000 1:166 1st Qu.:2.000 1:103
2:138 Median :2.000 2:222 Median :3.000 2:154
3:201 Mean :2.148 3:323 Mean :2.576 3:230
4:294 3rd Qu.:3.000 3rd Qu.:4.000 4:198
Max. :3.000 Max. :4.000
ImpactScore ImpactScore2 ImpactScore3 ImpactScoreF ImpactScore2F
Min. : 2.000 Min. : 2.000 Min. : 0.00 8 :105 7 :107
1st Qu.: 8.000 1st Qu.: 7.000 1st Qu.: 3.00 9 :104 8 :102
Median : 9.000 Median : 8.000 Median : 5.00 10 : 88 9 : 90
Mean : 9.514 Mean : 8.581 Mean : 5.06 7 : 84 10 : 86
3rd Qu.:11.000 3rd Qu.:10.000 3rd Qu.: 7.00 11 : 82 6 : 85
Max. :18.000 Max. :17.000 Max. :13.00 12 : 58 11 : 59
(Other):214 (Other):206
ImpactScore3F ImpactScoreFD TotalSymp1 TotalSymp1F TotalSymp2
4 :134 8 :105 Min. : 5.00 12 : 86 Min. : 4.00
5 :112 9 :104 1st Qu.:11.00 13 : 84 1st Qu.:10.00
3 :108 10 : 88 Median :13.00 14 : 80 Median :12.00
6 :102 7 : 84 Mean :12.99 11 : 72 Mean :12.43
7 : 66 11 : 82 3rd Qu.:15.00 10 : 62 3rd Qu.:15.00
2 : 64 12 : 58 Max. :23.00 15 : 61 Max. :22.00
(Other):149 (Other):214 (Other):290
TotalSymp3
Min. : 3.00
1st Qu.:10.00
Median :12.00
Mean :11.66
3rd Qu.:14.00
Max. :21.00
head(data) DxName1
1 Influenza like illness - Clinical Dx
2 Acute tonsillitis, unspecified
3 Influenza like illness - Clinical Dx
4 Influenza like illness - Clinical Dx
5 Acute pharyngitis, unspecified
6 Influenza like illness - Clinical Dx
DxName2 DxName3 DxName4 DxName5
1 <NA> <NA> <NA> <NA>
2 Influenza like illness - Clinical Dx <NA> <NA> <NA>
3 Acute pharyngitis, unspecified <NA> <NA> <NA>
4 Unspecified asthma with (acute) exacerbation <NA> <NA> <NA>
5 Influenza like illness - Clinical Dx <NA> <NA> <NA>
6 <NA> <NA> <NA> <NA>
Unique.Visit ActivityLevel ActivityLevelF SwollenLymphNodes ChestCongestion
1 340_17632125 10 10 Yes No
2 340_17794836 6 6 Yes Yes
3 342_17737773 2 2 Yes Yes
4 342_17806002 2 2 Yes Yes
5 342_17610918 5 5 Yes No
6 343_17543967 3 3 No No
ChillsSweats NasalCongestion CoughYN Sneeze Fatigue SubjectiveFever Headache
1 No No Yes No Yes Yes Yes
2 No Yes Yes No Yes Yes Yes
3 Yes Yes No Yes Yes Yes Yes
4 Yes Yes Yes Yes Yes Yes Yes
5 Yes No No No Yes Yes Yes
6 Yes No Yes Yes Yes Yes Yes
Weakness WeaknessYN CoughIntensity CoughYN2 Myalgia MyalgiaYN RunnyNose
1 Mild Yes Severe Yes Mild Yes No
2 Severe Yes Severe Yes Severe Yes No
3 Severe Yes Mild Yes Severe Yes Yes
4 Severe Yes Moderate Yes Severe Yes Yes
5 Moderate Yes None No Mild Yes No
6 Moderate Yes Moderate Yes Moderate Yes No
AbPain ChestPain Diarrhea EyePn Insomnia ItchyEye Nausea EarPn Hearing
1 No No No No No No No No No
2 No No No No No No No Yes Yes
3 Yes Yes No No Yes No Yes No No
4 No No No No Yes No Yes Yes No
5 No No No Yes Yes No Yes No No
6 No Yes Yes No No No Yes No No
Pharyngitis Breathless ToothPn Vision Vomit Wheeze BodyTemp
1 Yes No No No No No 98.3
2 Yes No No No No No 100.4
3 Yes Yes Yes No No No 100.8
4 Yes No No No No Yes 98.8
5 Yes No No No No No 100.5
6 Yes Yes No No No Yes 98.4
RapidFluA RapidFluB
1 Presumptive Negative For Influenza A Presumptive Negative For Influenza B
2 <NA> <NA>
3 Presumptive Negative For Influenza A Presumptive Negative For Influenza B
4 Presumptive Negative For Influenza A Presumptive Negative For Influenza B
5 <NA> <NA>
6 <NA> <NA>
PCRFluA PCRFluB TransScore1 TransScore1F TransScore2 TransScore2F TransScore3
1 <NA> <NA> 1 1 1 1 1
2 <NA> <NA> 3 3 2 2 1
3 <NA> <NA> 4 4 3 3 2
4 <NA> <NA> 5 5 4 4 3
5 <NA> <NA> 0 0 0 0 0
6 <NA> <NA> 2 2 2 2 2
TransScore3F TransScore4 TransScore4F ImpactScore ImpactScore2 ImpactScore3
1 1 0 0 7 6 3
2 1 2 2 8 7 4
3 2 4 4 14 13 9
4 3 4 4 12 11 7
5 0 0 0 11 10 6
6 2 1 1 12 11 7
ImpactScoreF ImpactScore2F ImpactScore3F ImpactScoreFD TotalSymp1 TotalSymp1F
1 7 6 3 7 8 8
2 8 7 4 8 11 11
3 14 13 9 14 18 18
4 12 11 7 12 17 17
5 11 10 6 11 11 11
6 12 11 7 12 14 14
TotalSymp2 TotalSymp3
1 8 8
2 10 9
3 17 16
4 16 15
5 11 11
6 14 14skimr::skim(data)| Name | data |
| Number of rows | 735 |
| Number of columns | 63 |
| _______________________ | |
| Column type frequency: | |
| character | 1 |
| factor | 50 |
| numeric | 12 |
| ________________________ | |
| Group variables | None |
Variable type: character
| skim_variable | n_missing | complete_rate | min | max | empty | n_unique | whitespace |
|---|---|---|---|---|---|---|---|
| Unique.Visit | 0 | 1 | 10 | 12 | 0 | 735 | 0 |
Variable type: factor
| skim_variable | n_missing | complete_rate | ordered | n_unique | top_counts |
|---|---|---|---|---|---|
| DxName1 | 0 | 1.00 | FALSE | 25 | Inf: 328, Inf: 131, Fev: 101, Cou: 66 |
| DxName2 | 280 | 0.62 | FALSE | 42 | Inf: 126, Inf: 115, Fev: 45, Cou: 41 |
| DxName3 | 626 | 0.15 | FALSE | 37 | Inf: 23, Inf: 14, Cou: 10, Fev: 6 |
| DxName4 | 716 | 0.03 | FALSE | 14 | Inf: 3, Acu: 2, Enc: 2, Inf: 2 |
| DxName5 | 734 | 0.00 | FALSE | 1 | Hea: 1, Acu: 0, Enc: 0, Oth: 0 |
| ActivityLevelF | 0 | 1.00 | FALSE | 11 | 3: 125, 5: 97, 4: 95, 2: 80 |
| SwollenLymphNodes | 0 | 1.00 | FALSE | 2 | No: 421, Yes: 314 |
| ChestCongestion | 0 | 1.00 | FALSE | 2 | Yes: 409, No: 326 |
| ChillsSweats | 0 | 1.00 | FALSE | 2 | Yes: 604, No: 131 |
| NasalCongestion | 0 | 1.00 | FALSE | 2 | Yes: 565, No: 170 |
| CoughYN | 0 | 1.00 | FALSE | 2 | Yes: 660, No: 75 |
| Sneeze | 0 | 1.00 | FALSE | 2 | Yes: 395, No: 340 |
| Fatigue | 0 | 1.00 | FALSE | 2 | Yes: 671, No: 64 |
| SubjectiveFever | 0 | 1.00 | FALSE | 2 | Yes: 505, No: 230 |
| Headache | 0 | 1.00 | FALSE | 2 | Yes: 620, No: 115 |
| Weakness | 0 | 1.00 | FALSE | 4 | Mod: 341, Mil: 224, Sev: 121, Non: 49 |
| WeaknessYN | 0 | 1.00 | FALSE | 2 | Yes: 686, No: 49 |
| CoughIntensity | 0 | 1.00 | FALSE | 4 | Mod: 360, Sev: 172, Mil: 156, Non: 47 |
| CoughYN2 | 0 | 1.00 | FALSE | 2 | Yes: 688, No: 47 |
| Myalgia | 0 | 1.00 | FALSE | 4 | Mod: 327, Mil: 214, Sev: 115, Non: 79 |
| MyalgiaYN | 0 | 1.00 | FALSE | 2 | Yes: 656, No: 79 |
| RunnyNose | 0 | 1.00 | FALSE | 2 | Yes: 524, No: 211 |
| AbPain | 0 | 1.00 | FALSE | 2 | No: 642, Yes: 93 |
| ChestPain | 0 | 1.00 | FALSE | 2 | No: 501, Yes: 234 |
| Diarrhea | 0 | 1.00 | FALSE | 2 | No: 636, Yes: 99 |
| EyePn | 0 | 1.00 | FALSE | 2 | No: 622, Yes: 113 |
| Insomnia | 0 | 1.00 | FALSE | 2 | Yes: 419, No: 316 |
| ItchyEye | 0 | 1.00 | FALSE | 2 | No: 553, Yes: 182 |
| Nausea | 0 | 1.00 | FALSE | 2 | No: 477, Yes: 258 |
| EarPn | 0 | 1.00 | FALSE | 2 | No: 573, Yes: 162 |
| Hearing | 0 | 1.00 | FALSE | 2 | No: 705, Yes: 30 |
| Pharyngitis | 0 | 1.00 | FALSE | 2 | Yes: 614, No: 121 |
| Breathless | 0 | 1.00 | FALSE | 2 | No: 438, Yes: 297 |
| ToothPn | 0 | 1.00 | FALSE | 2 | No: 569, Yes: 166 |
| Vision | 0 | 1.00 | FALSE | 2 | No: 716, Yes: 19 |
| Vomit | 0 | 1.00 | FALSE | 2 | No: 656, Yes: 79 |
| Wheeze | 0 | 1.00 | FALSE | 2 | No: 514, Yes: 221 |
| RapidFluA | 407 | 0.45 | FALSE | 2 | Pos: 169, Pre: 159 |
| RapidFluB | 407 | 0.45 | FALSE | 2 | Pre: 302, Pos: 26 |
| PCRFluA | 581 | 0.21 | FALSE | 3 | In: 120, In: 33, Ind: 1, Ass: 0 |
| PCRFluB | 581 | 0.21 | FALSE | 2 | In: 145, In: 9, Ass: 0 |
| TransScore1F | 0 | 1.00 | FALSE | 6 | 4: 210, 5: 195, 3: 157, 2: 107 |
| TransScore2F | 0 | 1.00 | FALSE | 5 | 4: 294, 3: 201, 2: 138, 1: 89 |
| TransScore3F | 0 | 1.00 | FALSE | 4 | 3: 323, 2: 222, 1: 166, 0: 24 |
| TransScore4F | 0 | 1.00 | FALSE | 5 | 3: 230, 4: 198, 2: 154, 1: 103 |
| ImpactScoreF | 0 | 1.00 | FALSE | 17 | 8: 105, 9: 104, 10: 88, 7: 84 |
| ImpactScore2F | 0 | 1.00 | FALSE | 16 | 7: 107, 8: 102, 9: 90, 10: 86 |
| ImpactScore3F | 0 | 1.00 | FALSE | 14 | 4: 134, 5: 112, 3: 108, 6: 102 |
| ImpactScoreFD | 0 | 1.00 | FALSE | 17 | 8: 105, 9: 104, 10: 88, 7: 84 |
| TotalSymp1F | 0 | 1.00 | FALSE | 19 | 12: 86, 13: 84, 14: 80, 11: 72 |
Variable type: numeric
| skim_variable | n_missing | complete_rate | mean | sd | p0 | p25 | p50 | p75 | p100 | hist |
|---|---|---|---|---|---|---|---|---|---|---|
| ActivityLevel | 0 | 1.00 | 4.46 | 2.64 | 0.0 | 3.0 | 4.0 | 6.0 | 10.0 | ▆▇▆▅▂ |
| BodyTemp | 5 | 0.99 | 98.94 | 1.20 | 97.2 | 98.2 | 98.5 | 99.3 | 103.1 | ▇▇▂▁▁ |
| TransScore1 | 0 | 1.00 | 3.47 | 1.31 | 0.0 | 3.0 | 4.0 | 5.0 | 5.0 | ▂▅▆▇▇ |
| TransScore2 | 0 | 1.00 | 2.92 | 1.11 | 0.0 | 2.0 | 3.0 | 4.0 | 4.0 | ▁▂▃▆▇ |
| TransScore3 | 0 | 1.00 | 2.15 | 0.88 | 0.0 | 1.0 | 2.0 | 3.0 | 3.0 | ▁▅▁▆▇ |
| TransScore4 | 0 | 1.00 | 2.58 | 1.21 | 0.0 | 2.0 | 3.0 | 4.0 | 4.0 | ▂▃▆▇▇ |
| ImpactScore | 0 | 1.00 | 9.51 | 2.84 | 2.0 | 8.0 | 9.0 | 11.0 | 18.0 | ▂▇▇▅▁ |
| ImpactScore2 | 0 | 1.00 | 8.58 | 2.78 | 2.0 | 7.0 | 8.0 | 10.0 | 17.0 | ▂▇▆▃▁ |
| ImpactScore3 | 0 | 1.00 | 5.06 | 2.34 | 0.0 | 3.0 | 5.0 | 7.0 | 13.0 | ▂▇▃▂▁ |
| TotalSymp1 | 0 | 1.00 | 12.99 | 3.41 | 5.0 | 11.0 | 13.0 | 15.0 | 23.0 | ▂▇▇▅▁ |
| TotalSymp2 | 0 | 1.00 | 12.43 | 3.22 | 4.0 | 10.0 | 12.0 | 15.0 | 22.0 | ▁▇▇▅▁ |
| TotalSymp3 | 0 | 1.00 | 11.66 | 3.10 | 3.0 | 10.0 | 12.0 | 14.0 | 21.0 | ▁▇▇▅▁ |
Checking variable names
names(data) [1] "DxName1" "DxName2" "DxName3"
[4] "DxName4" "DxName5" "Unique.Visit"
[7] "ActivityLevel" "ActivityLevelF" "SwollenLymphNodes"
[10] "ChestCongestion" "ChillsSweats" "NasalCongestion"
[13] "CoughYN" "Sneeze" "Fatigue"
[16] "SubjectiveFever" "Headache" "Weakness"
[19] "WeaknessYN" "CoughIntensity" "CoughYN2"
[22] "Myalgia" "MyalgiaYN" "RunnyNose"
[25] "AbPain" "ChestPain" "Diarrhea"
[28] "EyePn" "Insomnia" "ItchyEye"
[31] "Nausea" "EarPn" "Hearing"
[34] "Pharyngitis" "Breathless" "ToothPn"
[37] "Vision" "Vomit" "Wheeze"
[40] "BodyTemp" "RapidFluA" "RapidFluB"
[43] "PCRFluA" "PCRFluB" "TransScore1"
[46] "TransScore1F" "TransScore2" "TransScore2F"
[49] "TransScore3" "TransScore3F" "TransScore4"
[52] "TransScore4F" "ImpactScore" "ImpactScore2"
[55] "ImpactScore3" "ImpactScoreF" "ImpactScore2F"
[58] "ImpactScore3F" "ImpactScoreFD" "TotalSymp1"
[61] "TotalSymp1F" "TotalSymp2" "TotalSymp3" Step 1: Removing all variables that have Score or Total or FluA or FluB or Dxname or Activity in their name
data1 <- data %>% dplyr:: select(-matches("Score|Total|FluA|FluB|Dxname|Activity"))Step 2: Removing the variable Unique.Visit.
data2 <- data1[,-1]Step 3: Removing all NA observations in the dataset
data3 <- na.omit(data2)Naming the newly processed data as cleaned_data
cleaned_data <- data3Saving the cleaned data
save_data_location <- here::here("fluanalysis", "data", "cleaned_data.rds")
saveRDS(cleaned_data, file = save_data_location)Addition for Module 11: Preparing data for Machine Learning
Loading the previous cleaned data for additional cleaning
cleaned_data <- readRDS(here("fluanalysis", "data", "cleaned_data.rds"))We are getting rid of repetitive variables
cleaned_data_v2 <- cleaned_data %>% select(-CoughYN,-WeaknessYN,-CoughYN2,-MyalgiaYN)We are getting rid of hearing and vision variables since they have less than 5- entries (Y/N)
cleaned_data_v3 <- cleaned_data_v2 %>% select(-Vision,-Hearing)Our data is now made of 730 observations and 26 variables. This is what we will use for Module 11.
saveRDS(cleaned_data_v3, file = here("fluanalysis", "data", "cleaned_data_mod11.rds"))