4 Explorative Data Analysis
In this section we are going to find out more about the data and it’s variables, visualizing data and creating tables.
4.1 IHME distinct values
Let’s find out different distinct values of the variables
4.1.3 age_name
## age_name
## 1 35 to 39
## 2 40 to 44
## 3 45 to 49
## 4 50 to 54
## 5 55 to 59
## 6 60 to 64
## 7 65 to 69
## 8 70 to 74
## 9 75 to 79
## 10 80 to 84
## 11 85 to 89
## 12 90 to 94
## 13 95 plus
## 14 Under 5
## 15 5 to 9
## 16 10 to 14
## 17 15 to 19
## 18 20 to 24
## 19 25 to 29
## 20 30 to 344.1.6 cause_name
## cause_id cause_name
## 1 294 All causes
## 2 295 Communicable, maternal, neonatal, and nutritional diseases
## 3 297 Tuberculosis
## 4 298 HIV/AIDS
## 5 300 HIV/AIDS resulting in other diseases
## 6 302 Diarrheal diseases
## 7 319 Typhoid fever
## 8 320 Paratyphoid fever
## 9 321 Other intestinal infectious diseases
## 10 322 Lower respiratory infections
## 11 328 Upper respiratory infections
## 12 329 Otitis media
## 13 332 Meningitis
## 14 337 Encephalitis
## 15 338 Diphtheria
## 16 339 Whooping cough
## 17 340 Tetanus
## 18 341 Measles
## 19 342 Varicella and herpes zoster
## 20 344 Neglected tropical diseases and malaria
## 21 345 Malaria
## 22 346 Chagas disease
## 23 347 Leishmaniasis
## 24 348 Visceral leishmaniasis
## 25 349 Cutaneous and mucocutaneous leishmaniasis
## 26 350 African trypanosomiasis
## 27 351 Schistosomiasis
## 28 352 Cysticercosis
## 29 353 Cystic echinococcosis
## 30 354 Lymphatic filariasis
## 31 355 Onchocerciasis
## 32 356 Trachoma
## 33 357 Dengue
## 34 358 Yellow fever
## 35 359 Rabies
## 36 360 Intestinal nematode infections
## 37 361 Ascariasis
## 38 362 Trichuriasis
## 39 363 Hookworm disease
## 40 364 Food-borne trematodiases
## 41 365 Other neglected tropical diseases
## 42 366 Maternal disorders
## 43 367 Maternal hemorrhage
## 44 368 Maternal sepsis and other maternal infections
## 45 369 Maternal hypertensive disorders
## 46 370 Maternal obstructed labor and uterine rupture
## 47 374 Ectopic pregnancy
## 48 375 Indirect maternal deaths
## 49 376 Late maternal deaths
## 50 379 Other maternal disorders
## 51 380 Neonatal disorders
## 52 381 Neonatal preterm birth
## 53 382 Neonatal encephalopathy due to birth asphyxia and trauma
## 54 383 Neonatal sepsis and other neonatal infections
## 55 384 Hemolytic disease and other neonatal jaundice
## 56 385 Other neonatal disorders
## 57 386 Nutritional deficiencies
## 58 387 Protein-energy malnutrition
## 59 388 Iodine deficiency
## 60 389 Vitamin A deficiency
## 61 390 Dietary iron deficiency
## 62 391 Other nutritional deficiencies
## 63 393 Sexually transmitted infections excluding HIV
## 64 394 Syphilis
## 65 395 Chlamydial infection
## 66 396 Gonococcal infection
## 67 397 Trichomoniasis
## 68 398 Genital herpes
## 69 399 Other sexually transmitted infections
## 70 400 Acute hepatitis
## 71 401 Acute hepatitis A
## 72 402 Acute hepatitis B
## 73 403 Acute hepatitis C
## 74 404 Acute hepatitis E
## 75 405 Leprosy
## 76 408 Other unspecified infectious diseases
## 77 409 Non-communicable diseases
## 78 410 Neoplasms
## 79 411 Esophageal cancer
## 80 414 Stomach cancer
## 81 417 Liver cancer
## 82 418 Liver cancer due to hepatitis B
## 83 419 Liver cancer due to hepatitis C
## 84 420 Liver cancer due to alcohol use
## 85 423 Larynx cancer
## 86 426 Tracheal, bronchus, and lung cancer
## 87 429 Breast cancer
## 88 432 Cervical cancer
## 89 435 Uterine cancer
## 90 438 Prostate cancer
## 91 441 Colon and rectum cancer
## 92 444 Lip and oral cavity cancer
## 93 447 Nasopharynx cancer
## 94 450 Other pharynx cancer
## 95 453 Gallbladder and biliary tract cancer
## 96 456 Pancreatic cancer
## 97 459 Malignant skin melanoma
## 98 462 Non-melanoma skin cancer
## 99 465 Ovarian cancer
## 100 468 Testicular cancer
## 101 471 Kidney cancer
## 102 474 Bladder cancer
## 103 477 Brain and central nervous system cancer
## 104 480 Thyroid cancer
## 105 483 Mesothelioma
## 106 484 Hodgkin lymphoma
## 107 485 Non-Hodgkin lymphoma
## 108 486 Multiple myeloma
## 109 487 Leukemia
## 110 490 Other neoplasms
## 111 491 Cardiovascular diseases
## 112 492 Rheumatic heart disease
## 113 493 Ischemic heart disease
## 114 494 Stroke
## 115 495 Ischemic stroke
## 116 496 Intracerebral hemorrhage
## 117 497 Subarachnoid hemorrhage
## 118 498 Hypertensive heart disease
## 119 499 Cardiomyopathy and myocarditis
## 120 500 Atrial fibrillation and flutter
## 121 501 Aortic aneurysm
## 122 502 Peripheral artery disease
## 123 503 Endocarditis
## 124 504 Non-rheumatic valvular heart disease
## 125 508 Chronic respiratory diseases
## 126 509 Chronic obstructive pulmonary disease
## 127 510 Pneumoconiosis
## 128 511 Silicosis
## 129 512 Asbestosis
## 130 513 Coal workers pneumoconiosis
## 131 514 Other pneumoconiosis
## 132 515 Asthma
## 133 516 Interstitial lung disease and pulmonary sarcoidosis
## 134 520 Other chronic respiratory diseases
## 135 521 Cirrhosis and other chronic liver diseases
## 136 522 Cirrhosis and other chronic liver diseases due to hepatitis B
## 137 523 Cirrhosis and other chronic liver diseases due to hepatitis C
## 138 524 Cirrhosis and other chronic liver diseases due to alcohol use
## 139 525 Cirrhosis and other chronic liver diseases due to other causes
## 140 526 Digestive diseases
## 141 527 Peptic ulcer disease
## 142 528 Gastritis and duodenitis
## 143 529 Appendicitis
## 144 530 Paralytic ileus and intestinal obstruction
## 145 531 Inguinal, femoral, and abdominal hernia
## 146 532 Inflammatory bowel disease
## 147 533 Vascular intestinal disorders
## 148 534 Gallbladder and biliary diseases
## 149 535 Pancreatitis
## 150 536 Gastroesophageal reflux disease
## 151 541 Other digestive diseases
## 152 542 Neurological disorders
## 153 543 Alzheimer's disease and other dementias
## 154 544 Parkinson's disease
## 155 545 Idiopathic epilepsy
## 156 546 Multiple sclerosis
## 157 547 Migraine
## 158 548 Tension-type headache
## 159 554 Motor neuron disease
## 160 557 Other neurological disorders
## 161 558 Mental disorders
## 162 559 Schizophrenia
## 163 560 Alcohol use disorders
## 164 561 Drug use disorders
## 165 562 Opioid use disorders
## 166 563 Cocaine use disorders
## 167 564 Amphetamine use disorders
## 168 565 Cannabis use disorders
## 169 566 Other drug use disorders
## 170 567 Depressive disorders
## 171 568 Major depressive disorder
## 172 569 Dysthymia
## 173 570 Bipolar disorder
## 174 571 Anxiety disorders
## 175 572 Eating disorders
## 176 573 Anorexia nervosa
## 177 574 Bulimia nervosa
## 178 575 Autism spectrum disorders
## 179 578 Attention-deficit/hyperactivity disorder
## 180 579 Conduct disorder
## 181 582 Idiopathic developmental intellectual disability
## 182 585 Other mental disorders
## 183 587 Diabetes mellitus
## 184 588 Acute glomerulonephritis
## 185 589 Chronic kidney disease
## 186 591 Chronic kidney disease due to hypertension
## 187 592 Chronic kidney disease due to glomerulonephritis
## 188 593 Chronic kidney disease due to other and unspecified causes
## 189 594 Urinary diseases and male infertility
## 190 595 Urinary tract infections and interstitial nephritis
## 191 596 Urolithiasis
## 192 597 Benign prostatic hyperplasia
## 193 598 Male infertility
## 194 602 Other urinary diseases
## 195 603 Gynecological diseases
## 196 604 Uterine fibroids
## 197 605 Polycystic ovarian syndrome
## 198 606 Female infertility
## 199 607 Endometriosis
## 200 608 Genital prolapse
## 201 609 Premenstrual syndrome
## 202 612 Other gynecological diseases
## 203 613 Hemoglobinopathies and hemolytic anemias
## 204 614 Thalassemias
## 205 615 Sickle cell disorders
## 206 616 G6PD deficiency
## 207 618 Other hemoglobinopathies and hemolytic anemias
## 208 619 Endocrine, metabolic, blood, and immune disorders
## 209 626 Musculoskeletal disorders
## 210 627 Rheumatoid arthritis
## 211 628 Osteoarthritis
## 212 630 Low back pain
## 213 631 Neck pain
## 214 632 Gout
## 215 639 Other musculoskeletal disorders
## 216 640 Other non-communicable diseases
## 217 641 Congenital birth defects
## 218 642 Neural tube defects
## 219 643 Congenital heart anomalies
## 220 644 Orofacial clefts
## 221 645 Down syndrome
## 222 646 Turner syndrome
## 223 647 Klinefelter syndrome
## 224 648 Other chromosomal abnormalities
## 225 649 Congenital musculoskeletal and limb anomalies
## 226 650 Urogenital congenital anomalies
## 227 651 Digestive congenital anomalies
## 228 652 Other congenital birth defects
## 229 653 Skin and subcutaneous diseases
## 230 654 Dermatitis
## 231 655 Psoriasis
## 232 656 Cellulitis
## 233 657 Pyoderma
## 234 658 Scabies
## 235 659 Fungal skin diseases
## 236 660 Viral skin diseases
## 237 661 Acne vulgaris
## 238 662 Alopecia areata
## 239 663 Pruritus
## 240 664 Urticaria
## 241 665 Decubitus ulcer
## 242 668 Other skin and subcutaneous diseases
## 243 669 Sense organ diseases
## 244 670 Glaucoma
## 245 671 Cataract
## 246 672 Age-related macular degeneration
## 247 674 Age-related and other hearing loss
## 248 675 Other vision loss
## 249 679 Other sense organ diseases
## 250 680 Oral disorders
## 251 681 Caries of deciduous teeth
## 252 682 Caries of permanent teeth
## 253 683 Periodontal diseases
## 254 684 Edentulism
## 255 685 Other oral disorders
## 256 686 Sudden infant death syndrome
## 257 687 Injuries
## 258 688 Transport injuries
## 259 689 Road injuries
## 260 690 Pedestrian road injuries
## 261 691 Cyclist road injuries
## 262 692 Motorcyclist road injuries
## 263 693 Motor vehicle road injuries
## 264 694 Other road injuries
## 265 695 Other transport injuries
## 266 696 Unintentional injuries
## 267 697 Falls
## 268 698 Drowning
## 269 699 Fire, heat, and hot substances
## 270 700 Poisonings
## 271 701 Poisoning by carbon monoxide
## 272 703 Poisoning by other means
## 273 704 Exposure to mechanical forces
## 274 705 Unintentional firearm injuries
## 275 707 Other exposure to mechanical forces
## 276 708 Adverse effects of medical treatment
## 277 709 Animal contact
## 278 710 Venomous animal contact
## 279 711 Non-venomous animal contact
## 280 712 Foreign body
## 281 713 Pulmonary aspiration and foreign body in airway
## 282 714 Foreign body in eyes
## 283 715 Foreign body in other body part
## 284 716 Other unintentional injuries
## 285 717 Self-harm and interpersonal violence
## 286 718 Self-harm
## 287 721 Self-harm by firearm
## 288 723 Self-harm by other specified means
## 289 724 Interpersonal violence
## 290 725 Physical violence by firearm
## 291 726 Physical violence by sharp object
## 292 727 Physical violence by other means
## 293 729 Exposure to forces of nature
## 294 741 Maternal deaths aggravated by HIV/AIDS
## 295 837 Thalassemias trait
## 296 838 Sickle cell trait
## 297 839 G6PD trait
## 298 842 Environmental heat and cold exposure
## 299 843 Ebola
## 300 845 Acute lymphoid leukemia
## 301 846 Chronic lymphoid leukemia
## 302 847 Acute myeloid leukemia
## 303 848 Chronic myeloid leukemia
## 304 849 Non-melanoma skin cancer (squamous-cell carcinoma)
## 305 850 Non-melanoma skin cancer (basal-cell carcinoma)
## 306 854 Executions and police conflict
## 307 934 Drug-susceptible tuberculosis
## 308 935 Zika virus
## 309 936 Guinea worm disease
## 310 938 Alcoholic cardiomyopathy
## 311 941 Sexual violence
## 312 942 Myocarditis
## 313 943 Other leukemia
## 314 944 Other cardiomyopathy
## 315 945 Conflict and terrorism
## 316 946 Multidrug-resistant tuberculosis without extensive drug resistance
## 317 947 Extensively drug-resistant tuberculosis
## 318 948 HIV/AIDS - Drug-susceptible Tuberculosis
## 319 949 HIV/AIDS - Multidrug-resistant Tuberculosis without extensive drug resistance
## 320 950 HIV/AIDS - Extensively drug-resistant Tuberculosis
## 321 954 Latent tuberculosis infection
## 322 955 HIV/AIDS and sexually transmitted infections
## 323 956 Respiratory infections and tuberculosis
## 324 957 Enteric infections
## 325 958 Typhoid and paratyphoid
## 326 959 Invasive Non-typhoidal Salmonella (iNTS)
## 327 961 Other infectious diseases
## 328 962 Maternal and neonatal disorders
## 329 964 Myelodysplastic, myeloproliferative, and other hematopoietic neoplasms
## 330 965 Benign and in situ intestinal neoplasms
## 331 966 Benign and in situ cervical and uterine neoplasms
## 332 967 Other benign and in situ neoplasms
## 333 968 Non-rheumatic calcific aortic valve disease
## 334 969 Non-rheumatic degenerative mitral valve disease
## 335 970 Other non-rheumatic valve diseases
## 336 971 Cirrhosis and other chronic liver diseases due to NAFLD
## 337 972 Headache disorders
## 338 973 Substance use disorders
## 339 974 Diabetes and kidney diseases
## 340 975 Diabetes mellitus type 1
## 341 976 Diabetes mellitus type 2
## 342 977 Atopic dermatitis
## 343 978 Contact dermatitis
## 344 979 Seborrhoeic dermatitis
## 345 980 Bacterial skin diseases
## 346 981 Blindness and vision loss
## 347 992 Upper digestive system diseases
## 348 995 Maternal abortion and miscarriage
## 349 996 Liver cancer due to NASH
## 350 997 Chronic kidney disease due to diabetes mellitus type 1
## 351 998 Chronic kidney disease due to diabetes mellitus type 2
## 352 999 Refraction disorders
## 353 1000 Near vision loss
## 354 1014 Osteoarthritis hip
## 355 1015 Osteoarthritis knee
## 356 1016 Osteoarthritis hand
## 357 1017 Osteoarthritis other
## 358 1021 Liver cancer due to other causes
## 359 1022 Other malignant neoplasms
## 360 1023 Other cardiovascular and circulatory diseases
## 361 1026 Total burden related to hepatitis B
## 362 1027 Total burden related to hepatitis C
## 363 1028 Total burden related to Non-alcoholic fatty liver disease (NAFLD)
## 364 1029 Total cancers4.1.7 Calculator datas
## # A tibble: 27 × 13
## cause_id type condition OSA_severity gender multiplier OR RR PAF prevalence_base_italy direct…¹ direc…² produ…³
## <dbl> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 294 mortality All-cause mortality Severe Both 1 NA 1.54 0.075 0.003 NA NA NA
## 2 1023 mortality Cardiovascular mortality Severe Both 1 NA 2.96 0.227 0.001 NA NA NA
## 3 1029 prevalence Cancer Overall Overall Both 1 NA 1.4 0.097 0.042 5718 4581 119
## 4 669 prevalence Diabetic retinopathy Overall Both 0.124 2.01 NA 0.207 0.026 307 242 579
## 5 998 prevalence Diabetic kidney disease Overall Both 1 1.59 NA 0.135 0.015 797 NA NA
## 6 976 prevalence Type 2 diabetes Moderate-Severe Both 1 NA 1.63 0.145 0.068 3866 NA 4352
## 7 619 prevalence Metabolic syndrome Mild Both 2.06 2.39 NA 0.164 0.33 1900 NA 90
## 8 619 prevalence Metabolic syndrome Moderate-Severe Both 2.06 3.42 NA 0.232 0.33 1900 NA NA
## 9 594 prevalence Erectile dysfunction Overall Male 0.735 NA 1.82 0.228 0.1 407 NA NA
## 10 NA prevalence Female sexual dysfunction Overall Female 1 NA 2 0.153 0.29 761 NA NA
## # … with 17 more rows, and abbreviated variable names ¹direct_healthcare_cost, ²direct_nonhealthcare_cost, ³productivity_losses_cost## # A tibble: 12 × 5
## OSA_severity label gender osa_rate population
## <chr> <chr> <chr> <dbl> <chr>
## 1 Mild Mild (5≤AHI<15) Female 0.29 AGED 15-74
## 2 Moderate Moderate (15≤AHI<30) Female 0.1 AGED 15-74
## 3 Severe Severe (AHI≥30) Female 0.09 AGED 15-74
## 4 Mild Mild (5≤AHI<15) Male 0.25 AGED 15-74
## 5 Moderate Moderate (15≤AHI<30 Male 0.14 AGED 15-74
## 6 Severe Severe (AHI≥30) Male 0.22 AGED 15-74
## 7 Moderate-Severe Moderate-Severe (AHI≥15) Female 0.18 AGED 15-74
## 8 Moderate-Severe Moderate-Severe (AHI≥15) Male 0.36 AGED 15-74
## 9 Mild Mild (5≤AHI<15) Both 0.27 AGED 15-74
## 10 Moderate Moderate (15≤AHI<30) Both 0.12 AGED 15-74
## 11 Severe Severe (AHI≥30) Both 0.15 AGED 15-74
## 12 Moderate-Severe Moderate-Severe (AHI≥15) Both 0.27 AGED 15-74## # A tibble: 193 × 4
## location_name pop30_69 `Mild-Moderate-Severe` `Moderate-Severe`
## <chr> <dbl> <dbl> <dbl>
## 1 Afghanistan 8429549 0.361 0.139
## 2 Albania 1357655 0.627 0.344
## 3 Algeria 16435999 0.536 0.206
## 4 Angola 6091184 0.603 0.229
## 5 Antigua and Barbuda 42485 0.240 0.0708
## 6 Argentina 19016260 0.286 0.131
## 7 Armenia 1513141 0.508 0.252
## 8 Aruba 56900 0.244 0.0481
## 9 Australia 12110362 0.245 0.0480
## 10 Austria 4601766 0.487 0.284
## # … with 183 more rows4.2 PLOT: Population in countries
## `summarise()` has grouped output by "location_name". You can override using the `.groups` argument.
Figure 4.1: Countries population in 2019.
4.3 PLOT: Finland population 2019
Draw Finland population in 2019
## `summarise()` has grouped output by "location_name". You can override using the `.groups` argument.
Figure 4.2: Countries population in 2019.
4.4 TABLE: Prevalences
Create a table of all prevalences of disease available in the dataset from year 2019.
## `summarise()` has grouped output by "cause_id". You can override using the `.groups` argument.4.5 TABLE: Incidences
Create a table of all Incidence of disease available in the dataset from year 2019.
## `summarise()` has grouped output by "cause_id". You can override using the `.groups` argument.