Dane do analizy

Opis zbioru danych do analizy. Kryteria włączenia. Charakterystyka grupy badanej. Lista zmiennych.

Piotr Wiśniewski
2023-09-11

Grupa badana

Wszyscy pacjenci z rejestru Eurocrine, którzy przebyli operację tarczycy 03.2020 - 03.2022.

Kryteria włączenia / wykluczenia

Kolejne etapy kwalifikacji:

  1. cały zbiór - 32008 przypadków

Lista zmiennych

hide 
skim(df_unfiltered)
Table 1: Data summary
Name df_unfiltered
Number of rows 32008
Number of columns 44
_______________________
Column type frequency:
character 7
Date 1
factor 17
logical 1
numeric 18
________________________
Group variables None

Variable type: character

skim_variable n_missing complete_rate min max empty n_unique whitespace
oper_id 0 1.00 9 11 0 32008 0
pid 0 1.00 9 14 0 31703 0
country_id 0 1.00 1 2 0 10 0
site_id 0 1.00 1 3 0 113 0
patient_id 0 1.00 4 6 0 31703 0
size_main_cat 22095 0.31 5 11 0 4 0
clinical_risk 21754 0.32 3 12 0 3 0

Variable type: Date

skim_variable n_missing complete_rate min max median n_unique
oper_date 0 1 2020-03-01 2022-03-01 2021-02-22 589

Variable type: factor

skim_variable n_missing complete_rate ordered n_unique top_counts
diagn_main 0 1 FALSE 41 Nod: 9563, Pap: 8581, Fol: 5527, Gra: 2827
diagn_sec1 0 1 FALSE 38 (Mi: 22012, Lym: 3394, Nod: 2631, Fol: 1559
diagn_sec2 0 1 FALSE 28 (Mi: 30276, Lym: 743, Nod: 422, Fol: 187
diagn_sec3 0 1 FALSE 19 (Mi: 31796, Lym: 107, Par: 26, Nod: 22
oper_type_th 0 1 FALSE 11 Thy: 15419, Uni: 13742, Uni: 979, Ist: 572
oper_type_ln 0 1 FALSE 10 Non: 25709, Uni: 2574, Cen: 1193, Bil: 1172
oper_indic 0 1 FALSE 5 Exc: 12914, Com: 6643, Mal: 5657, Thy: 5397
eutirads 0 1 FALSE 7 Not: 8476, TR4: 7126, TR5: 6578, TR3: 4428
sex 0 1 FALSE 2 Fem: 24950, Mal: 7058
tnm_t 0 1 FALSE 10 (Mi: 21427, pT1: 4894, pT1: 2834, pT2: 1712
tnm_n 0 1 FALSE 5 (Mi: 21239, pN0: 4408, pNx: 3531, pN1: 1773
tnm_m 0 1 FALSE 4 (Mi: 21332, pM0: 8245, pMx: 2275, pM1: 156
beth_class 0 1 FALSE 7 Not: 11621, IV: 6790, II: 4548, VI: 4249
age_cat 0 1 FALSE 4 (26: 15695, (53: 13659, (-0: 2002, (79: 652
oper_type_th_aggr 0 1 FALSE 3 Thy: 15419, Lob: 13742, Oth: 2847
oper_type_ln_aggr 0 1 FALSE 4 Non: 25709, CLN: 3746, CLN: 1344, Oth: 1209
tnm_t_orig 0 1 FALSE 10 (Mi: 21688, pT1: 4778, pT1: 2770, pT2: 1665

Variable type: logical

skim_variable n_missing complete_rate mean count
eutirads_reported 0 1 0.68 TRU: 21925, FAL: 10083

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
size_main 22095 0.31 16.52 15.33 0 7 12 21 150 ▇▁▁▁▁
size_sec1 31164 0.03 6.53 9.09 0 2 4 7 74 ▇▁▁▁▁
size_sec2 31962 0.00 6.04 7.83 1 2 3 6 40 ▇▁▁▁▁
size_sec3 32003 0.00 7.80 5.54 1 4 8 11 15 ▇▇▇▇▇
age 0 1.00 50.57 15.73 0 39 51 62 106 ▁▅▇▃▁
eutirads_5 0 1.00 0.21 0.40 0 0 0 0 1 ▇▁▁▁▂
malignant 0 1.00 0.32 0.47 0 0 0 1 1 ▇▁▁▁▃
malignant_sec1 0 1.00 0.03 0.17 0 0 0 0 1 ▇▁▁▁▁
malignant_sec2 0 1.00 0.00 0.04 0 0 0 0 1 ▇▁▁▁▁
malignant_sec3 0 1.00 0.00 0.01 0 0 0 0 1 ▇▁▁▁▁
malignant_sec 0 1.00 0.03 0.17 0 0 0 0 1 ▇▁▁▁▁
fna_indicated 22095 0.31 0.36 0.48 0 0 0 1 1 ▇▁▁▁▅
size_main_lt1 22095 0.31 0.45 0.50 0 0 0 1 1 ▇▁▁▁▆
tnm_t1a 21688 0.32 0.46 0.50 0 0 0 1 1 ▇▁▁▁▇
high_risk_profile 0 1.00 0.04 0.20 0 0 0 0 1 ▇▁▁▁▁
low_risk_profile 0 1.00 0.10 0.31 0 0 0 0 1 ▇▁▁▁▁
indeterminate_risk_profile 21754 0.32 0.54 0.50 0 0 1 1 1 ▇▁▁▁▇
oper_count 0 1.00 1.02 0.14 1 1 1 1 3 ▇▁▁▁▁

Charakterystyka pacjentów

Uwaga: tutaj uwzględniono tylko 1 rekord per pacjent (pierwszą operację u danego pacjenta)

hide 
df1op <- df_unfiltered %>% 
  filter(oper_count == 1)

Wiek, płeć

hide 
df1op %>% 
  select(age,sex) %>% 
  tbl_summary(
    label = list(
      age ~ "Age [years]",
      sex ~ "Sex"
    )
  ) %>%
  modify_caption("**Table. Patient characteristics**")
Table 2: Table. Patient characteristics
Characteristic N = 31,4031
Age [years] 51 (39, 62)
Sex
    Male 6,871 (22%)
    Female 24,532 (78%)
1 Median (IQR); n (%)
hide 
df1op  %>%
  ggplot(aes(x=age, fill=sex)) +
  geom_histogram(binwidth = 1)

Ocena przedoperacyjna

Wynik BAC

hide 
df_unfiltered %>%
  select(
    beth_class
  ) %>%
  tbl_summary(
    label = list(beth_class ~ "Bethesda class")
  )  %>%
    modify_caption("**Table. Cytology results**")
Table 3: Table. Cytology results
Characteristic N = 32,0081
Bethesda class
    Not performed 11,621 (36%)
    I 840 (2.6%)
    II 4,548 (14%)
    III 2,222 (6.9%)
    IV 6,790 (21%)
    V 1,738 (5.4%)
    VI 4,249 (13%)
1 n (%)

EUTIRADS.PRE

hide 
df_unfiltered %>%
  select(
    eutirads
  ) %>%
  tbl_summary(
    label = list(eutirads ~ "EU-TIRADS")
  )  %>%
    modify_caption("**Table. Pre-operative ultrasound results**")
Table 4: Table. Pre-operative ultrasound results
Characteristic N = 32,0081
EU-TIRADS
    (Missing) 1,607 (5.0%)
    TR1 1,289 (4.0%)
    TR2 2,504 (7.8%)
    TR3 4,428 (14%)
    TR4 7,126 (22%)
    TR5 6,578 (21%)
    Not classified 8,476 (26%)
1 n (%)

Zabiegi

Liczba operacji z podziałem na pierwotne, wtórne

hide 
df_unfiltered  %>% 
  select(oper_count) %>% 
  tbl_summary(
    label = list( oper_count ~ "Number of surgeries")
  ) %>%
  modify_caption("**Table. Number of surgeries per 1 patient**")
Table 5: Table. Number of surgeries per 1 patient
Characteristic N = 32,0081
Number of surgeries
    1 31,403 (98%)
    2 590 (1.8%)
    3 15 (<0.1%)
1 n (%)

Rodzaje zabiegów

hide 
df_unfiltered %>%
  select(
    oper_type_th,
    oper_type_ln
  ) %>%
  mutate(
    oper_type_th = fct_infreq(oper_type_th),
    oper_type_ln = fct_infreq(oper_type_ln)   
  ) %>%
  tbl_summary(
    label = list(oper_type_th ~ "Thyroid surgery",
                 oper_type_ln ~ "Lymph node surgery")
  )  %>%
    modify_caption("**Table. Type of surgery**")
Table 6: Table. Type of surgery
Characteristic N = 32,0081
Thyroid surgery
    Thyroidectomy (BAA60) 15,419 (48%)
    Unilateral lobectomy of thyroid gland (BAA40) 13,742 (43%)
    Unilateral resection of thyroid gland (BAA20) 979 (3.1%)
    Isthmus resection of thyroid gland (BAA30) 572 (1.8%)
    Bilateral resection of thyroid gland (BAA25) 534 (1.7%)
    Lobectomy and resection of contralateral lobe of thyroid gland (BAA50) 512 (1.6%)
    Other operation on thyroid gland (BAA99) 169 (0.5%)
    Percutanous thermal ablation (RFA, NWA, HIFU) 41 (0.1%)
    Biopsy of thyroid gland (BAA00) 24 (<0.1%)
    Incision of thyroid gland (BAA10) 10 (<0.1%)
    Exploration of thyroid gland (BAA05) 6 (<0.1%)
Lymph node surgery
    None 25,709 (80%)
    Unilateral central lymph node dissection (PJD41) 2,574 (8.0%)
    Central lymph node dissection (PJD41) and one-sided lat. Lymph node dissection (PJD51) 1,193 (3.7%)
    Bilateral central lymph node dissection (PJD41) 1,172 (3.7%)
    Extirpation of lymph nodes (PJD41) 652 (2.0%)
    Exploration of lymph nodes incl. Biopsy (PJD10) 382 (1.2%)
    Bilateral central lymphnode dissection AND bilateral lateral lymphnodedissection (PJD41, PJD51) 151 (0.5%)
    One-sided lateral lymph node dissection (PJD51) 126 (0.4%)
    Bilateral lateral lymph node dissection (PJD51) 43 (0.1%)
    (Missing) 6 (<0.1%)
1 n (%)

Rodzaje zabiegów - zagregowane

hide 
df_unfiltered %>%
  select(
    oper_type_th_aggr,
    oper_type_ln_aggr
  ) %>%
  mutate(
    oper_type_th_aggr = fct_infreq(oper_type_th_aggr),
    oper_type_ln_aggr = fct_infreq(oper_type_ln_aggr)   
  ) %>%
  tbl_summary(
    label = list(oper_type_th_aggr ~ "Thyroid surgery",
                 oper_type_ln_aggr ~ "Lymph node surgery")
  )  %>%
    modify_caption("**Table. Type of surgery**")
Table 7: Table. Type of surgery
Characteristic N = 32,0081
Thyroid surgery
    Thyroidectomy 15,419 (48%)
    Lobectomy 13,742 (43%)
    Other 2,847 (8.9%)
Lymph node surgery
    None 25,709 (80%)
    CLND 3,746 (12%)
    CLND + LLND 1,344 (4.2%)
    Other 1,209 (3.8%)
1 n (%)

Wskaznie do operacji

hide 
df_unfiltered %>%
  select(
    oper_indic
  ) %>%
  mutate(
    oper_indic = fct_infreq(oper_indic)   
  ) %>%
  tbl_summary(
    label = list(oper_indic ~ "Indication")
  )  %>%
    modify_caption("**Table. Main indications**")
Table 8: Table. Main indications
Characteristic N = 32,0081
Indication
    Excluding malignancy 12,914 (40%)
    Compression symptom 6,643 (21%)
    Malignancy 5,657 (18%)
    Thyreotoxicosis 5,397 (17%)
    Other 1,397 (4.4%)
1 n (%)

Rozpoznania hist-pat

Histological main diagnosis.F1

hide 
df_unfiltered %>%
  select(
    diagn_main 
  ) %>%
  mutate(
    diagn_main = fct_infreq(diagn_main)
  ) %>%
  tbl_summary(
    label = list(diagn_main ~ "Diagnosis")
  )  %>%
    modify_caption("**Table. Histological main diagnosis**")
Table 9: Table. Histological main diagnosis
Characteristic N = 32,0081
Diagnosis
    Nodular goitre T-96 M-71640 9,563 (30%)
    Papillary cancer T-96 M-82603 8,581 (27%)
    Follicular adenoma T-96 M-83300 5,527 (17%)
    Graves´ disease T-96 D-2193 2,827 (8.8%)
    (Missing) 1,401 (4.4%)
    Hürtle cell (oxyphilic) adenoma T-96M-82900 749 (2.3%)
    Follicular cancer T-96 M-83303 593 (1.9%)
    Lymphocytic thyroiditis Hashimoto T-96 M-45810 522 (1.6%)
    Medullary cancer T-9605 M-85103 423 (1.3%)
    Hürtle cell (oxyphilic) carcinoma T-96 M-82903 241 (0.8%)
    Other diagnosis 236 (0.7%)
    Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) 217 (0.7%)
    Thyroid nothing malignant T-96 M 0945 179 (0.6%)
    Normal gland 167 (0.5%)
    Thyroid normal T-96 M 00110 143 (0.4%)
    Well differentiated tumour of uncertain malignant potential (WDT-UMP) 79 (0.2%)
    Benign tumour UNS T-96 M-80000 74 (0.2%)
    Poorly differentiated thyroid cancer 64 (0.2%)
    Anaplastic cancer T-96 M-80123 62 (0.2%)
    Follicular tumour with uncertain malignant potential 58 (0.2%)
    C-cell hyperplasia T-9605 M-72000 37 (0.1%)
    Parathyroid adenoma (T-97 M-81400) 36 (0.1%)
    Lymph node metastasis papillary cancer T-082 M-82606 34 (0.1%)
    Subacute thyroiditis de Quervain T-96 M-44000 34 (0.1%)
    Acute thyroiditis T-96 M-41000 24 (<0.1%)
    Metastasis from cancer UNS T-96 M-80106 23 (<0.1%)
    Chronic fibrotic thyroiditis Riedel T-96 M-45000 19 (<0.1%)
    Lymphoma T-96 M-95903 17 (<0.1%)
    Hyalinizing trabecular tumour 16 (<0.1%)
    Cyst, ductus thyreoglossus T-96 M-26500 15 (<0.1%)
    Metastasis from malignant tumour UNS T-96 M-80006 13 (<0.1%)
    Cancer UNS T-96 M 80103 10 (<0.1%)
    Mixed medullary /follicular carcinoma 83463 5 (<0.1%)
    Parthyroid hyperplasia (T-97 M 72000) 5 (<0.1%)
    Malignant tumour UNS T-96 M-80003 5 (<0.1%)
    Lymph node metastasis medullary cancer T082 M-85106 3 (<0.1%)
    Parathyroid normal 2 (<0.1%)
    Lymph node metastasis follicular cancer 1-082 M-83306 1 (<0.1%)
    Lymph node metastasis Hürthle cell (oxyphilic) carcinoma 1 (<0.1%)
    Acute thyroiditis with abscess T-96 M-41700 1 (<0.1%)
    Lymph node metastasis anaplastic cancer T082 M-80126 1 (<0.1%)
1 n (%)

Histological secondary diagnosis 1.F1

hide 
df_unfiltered %>%
  select(
    diagn_sec1 
  ) %>%
  mutate(
    diagn_sec1 = fct_infreq(diagn_sec1)
  ) %>%
  tbl_summary(
    label = list(diagn_sec1 ~ "Diagnosis")
  )  %>%
    modify_caption("**Table. Histological secondary diagnosis**")
Table 10: Table. Histological secondary diagnosis
Characteristic N = 32,0081
Diagnosis
    (Missing) 22,012 (69%)
    Lymphocytic thyroiditis Hashimoto T-96 M-45810 3,394 (11%)
    Nodular goitre T-96 M-71640 2,631 (8.2%)
    Follicular adenoma T-96 M-83300 1,559 (4.9%)
    Papillary cancer T-96 M-82603 765 (2.4%)
    Parathyroid adenoma (T-97 M-81400) 336 (1.0%)
    Graves´ disease T-96 D-2193 325 (1.0%)
    Hürtle cell (oxyphilic) adenoma T-96M-82900 188 (0.6%)
    Other diagnosis 108 (0.3%)
    Parthyroid hyperplasia (T-97 M 72000) 103 (0.3%)
    Parathyroid normal 78 (0.2%)
    C-cell hyperplasia T-9605 M-72000 71 (0.2%)
    Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) 66 (0.2%)
    Subacute thyroiditis de Quervain T-96 M-44000 59 (0.2%)
    Lymph node metastasis papillary cancer T-082 M-82606 48 (0.1%)
    Follicular cancer T-96 M-83303 47 (0.1%)
    Thyroid nothing malignant T-96 M 0945 38 (0.1%)
    Normal gland 30 (<0.1%)
    Chronic fibrotic thyroiditis Riedel T-96 M-45000 22 (<0.1%)
    Benign tumour UNS T-96 M-80000 20 (<0.1%)
    Hürtle cell (oxyphilic) carcinoma T-96 M-82903 19 (<0.1%)
    Medullary cancer T-9605 M-85103 12 (<0.1%)
    Thyroid normal T-96 M 00110 12 (<0.1%)
    Cyst, ductus thyreoglossus T-96 M-26500 9 (<0.1%)
    Acute thyroiditis T-96 M-41000 8 (<0.1%)
    Well differentiated tumour of uncertain malignant potential (WDT-UMP) 7 (<0.1%)
    Poorly differentiated thyroid cancer 7 (<0.1%)
    Follicular tumour with uncertain malignant potential 7 (<0.1%)
    Hyalinizing trabecular tumour 5 (<0.1%)
    Cancer UNS T-96 M 80103 5 (<0.1%)
    Anaplastic cancer T-96 M-80123 4 (<0.1%)
    Metastasis from malignant tumour UNS T-96 M-80006 4 (<0.1%)
    Metastasis from cancer UNS T-96 M-80106 3 (<0.1%)
    Lymphoma T-96 M-95903 2 (<0.1%)
    Malignant tumour UNS T-96 M-80003 1 (<0.1%)
    Lymph node metastasis anaplastic cancer T082 M-80126 1 (<0.1%)
    Lymph node metastasis medullary cancer T082 M-85106 1 (<0.1%)
    Lymph node metastasis follicular cancer 1-082 M-83306 1 (<0.1%)
1 n (%)

Histological secondary diagnosis 2.F1

hide 
df_unfiltered %>%
  select(
    diagn_sec2 
  ) %>%
  mutate(
    diagn_sec2 = fct_infreq(diagn_sec2)
  ) %>%
  tbl_summary(
    label = list(diagn_sec2 ~ "Diagnosis")
  )  %>%
    modify_caption("**Table. Histological secondary diagnosis**")
Table 11: Table. Histological secondary diagnosis
Characteristic N = 32,0081
Diagnosis
    (Missing) 30,276 (95%)
    Lymphocytic thyroiditis Hashimoto T-96 M-45810 743 (2.3%)
    Nodular goitre T-96 M-71640 422 (1.3%)
    Follicular adenoma T-96 M-83300 187 (0.6%)
    Parathyroid adenoma (T-97 M-81400) 106 (0.3%)
    Papillary cancer T-96 M-82603 41 (0.1%)
    Parthyroid hyperplasia (T-97 M 72000) 37 (0.1%)
    Graves´ disease T-96 D-2193 32 (<0.1%)
    Other diagnosis 32 (<0.1%)
    Hürtle cell (oxyphilic) adenoma T-96M-82900 24 (<0.1%)
    Parathyroid normal 17 (<0.1%)
    C-cell hyperplasia T-9605 M-72000 17 (<0.1%)
    Subacute thyroiditis de Quervain T-96 M-44000 14 (<0.1%)
    Chronic fibrotic thyroiditis Riedel T-96 M-45000 13 (<0.1%)
    Cyst, ductus thyreoglossus T-96 M-26500 10 (<0.1%)
    Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) 10 (<0.1%)
    Lymph node metastasis papillary cancer T-082 M-82606 8 (<0.1%)
    Normal gland 5 (<0.1%)
    Medullary cancer T-9605 M-85103 3 (<0.1%)
    Thyroid normal T-96 M 00110 2 (<0.1%)
    Benign tumour UNS T-96 M-80000 2 (<0.1%)
    Lymphoma T-96 M-95903 1 (<0.1%)
    Metastasis from cancer UNS T-96 M-80106 1 (<0.1%)
    Hyalinizing trabecular tumour 1 (<0.1%)
    Acute thyroiditis with abscess T-96 M-41700 1 (<0.1%)
    Lymph node metastasis medullary cancer T082 M-85106 1 (<0.1%)
    Thyroid nothing malignant T-96 M 0945 1 (<0.1%)
    Anaplastic cancer T-96 M-80123 1 (<0.1%)
1 n (%)

Histological secondary diagnosis 3.F1

hide 
df_unfiltered %>%
  select(
    diagn_sec3 
  ) %>%
  mutate(
    diagn_sec3 = fct_infreq(diagn_sec3)
  ) %>%
  tbl_summary(
    label = list(diagn_sec3 ~ "Diagnosis")
  )  %>%
    modify_caption("**Table. Histological secondary diagnosis**")
Table 12: Table. Histological secondary diagnosis
Characteristic N = 32,0081
Diagnosis
    (Missing) 31,796 (99%)
    Lymphocytic thyroiditis Hashimoto T-96 M-45810 107 (0.3%)
    Parathyroid adenoma (T-97 M-81400) 26 (<0.1%)
    Nodular goitre T-96 M-71640 22 (<0.1%)
    Follicular adenoma T-96 M-83300 19 (<0.1%)
    Parthyroid hyperplasia (T-97 M 72000) 10 (<0.1%)
    Other diagnosis 9 (<0.1%)
    Parathyroid normal 3 (<0.1%)
    Lymph node metastasis papillary cancer T-082 M-82606 3 (<0.1%)
    C-cell hyperplasia T-9605 M-72000 2 (<0.1%)
    Cyst, ductus thyreoglossus T-96 M-26500 2 (<0.1%)
    Graves´ disease T-96 D-2193 2 (<0.1%)
    Subacute thyroiditis de Quervain T-96 M-44000 1 (<0.1%)
    Benign tumour UNS T-96 M-80000 1 (<0.1%)
    Normal gland 1 (<0.1%)
    Lymph node metastasis medullary cancer T082 M-85106 1 (<0.1%)
    Follicular cancer T-96 M-83303 1 (<0.1%)
    Papillary cancer T-96 M-82603 1 (<0.1%)
    Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) 1 (<0.1%)
1 n (%)

nowa zmienna: malignant

hide 
tar_load(malignant_codes)
Malignant = 1 Malignant = 0
gdy Histological main diagnosis.F1 przyjmuje wartość: gdy Histological main diagnosis.F1 przyjmuje wartość:
Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP), Papillary cancer T-96 M-82603, Anaplastic cancer T-96 M-80123, Follicular cancer T-96 M-83303, Medullary cancer T-9605 M-85103, Hürtle cell (oxyphilic) carcinoma T-96 M-82903, Mixed medullary /follicular carcinoma 83463, Lymphoma T-96 M-95903, Poorly differentiated thyroid cancer, Metastasis from malignant tumour UNS T-96 M-80006, Cancer UNS T-96 M 80103, Malignant tumour UNS T-96 M-80003, Metastasis from cancer UNS T-96 M-80106 Nodular goitre T-96 M-71640, Follicular adenoma T-96 M-83300, Normal gland, Graves´ disease T-96 D-2193, Lymphocytic thyroiditis Hashimoto T-96 M-45810, Hürtle cell (oxyphilic) adenoma T-96M-82900, Thyroid normal T-96 M 00110, (Missing), Well differentiated tumour of uncertain malignant potential (WDT-UMP), Thyroid nothing malignant T-96 M 0945, Other diagnosis, Cyst, ductus thyreoglossus T-96 M-26500, Benign tumour UNS T-96 M-80000, Lymph node metastasis papillary cancer T-082 M-82606, Parathyroid adenoma (T-97 M-81400), Follicular tumour with uncertain malignant potential, C-cell hyperplasia T-9605 M-72000, Acute thyroiditis T-96 M-41000, Hyalinizing trabecular tumour, Lymph node metastasis follicular cancer 1-082 M-83306, Subacute thyroiditis de Quervain T-96 M-44000, Parthyroid hyperplasia (T-97 M 72000), Chronic fibrotic thyroiditis Riedel T-96 M-45000, Parathyroid normal, Lymph node metastasis Hürthle cell (oxyphilic) carcinoma, Lymph node metastasis medullary cancer T082 M-85106, Acute thyroiditis with abscess T-96 M-41700, Lymph node metastasis anaplastic cancer T082 M-80126

Wątpliwosci: co z niftp ? tump ? co z secondary diagnosis ?

hide 
df_unfiltered %>%
  select(
    malignant 
  ) %>%
  tbl_summary(
    label = list(malignant ~ "Malignant diagnosis")
  )  %>%
    modify_caption("**Table. Histological main diagnosis category**")
Table 13: Table. Histological main diagnosis category
Characteristic N = 32,0081
Malignant diagnosis 10,254 (32%)
1 n (%)

nowa zmienna: malignant_sec

malignant_sec = 1 malignant_sec = 0
gdy dowolna z 3 zmiennych Histological secondary diagnosis.F1 przyjmuje wartość: gdy wszystkie 3 zmienne Histological secondary diagnosis.F1 przyjmują wartość:
Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP), Papillary cancer T-96 M-82603, Anaplastic cancer T-96 M-80123, Follicular cancer T-96 M-83303, Medullary cancer T-9605 M-85103, Hürtle cell (oxyphilic) carcinoma T-96 M-82903, Mixed medullary /follicular carcinoma 83463, Lymphoma T-96 M-95903, Poorly differentiated thyroid cancer, Metastasis from malignant tumour UNS T-96 M-80006, Cancer UNS T-96 M 80103, Malignant tumour UNS T-96 M-80003, Metastasis from cancer UNS T-96 M-80106 Nodular goitre T-96 M-71640, Follicular adenoma T-96 M-83300, Normal gland, Graves´ disease T-96 D-2193, Lymphocytic thyroiditis Hashimoto T-96 M-45810, Hürtle cell (oxyphilic) adenoma T-96M-82900, Thyroid normal T-96 M 00110, (Missing), Well differentiated tumour of uncertain malignant potential (WDT-UMP), Thyroid nothing malignant T-96 M 0945, Other diagnosis, Cyst, ductus thyreoglossus T-96 M-26500, Benign tumour UNS T-96 M-80000, Lymph node metastasis papillary cancer T-082 M-82606, Parathyroid adenoma (T-97 M-81400), Follicular tumour with uncertain malignant potential, C-cell hyperplasia T-9605 M-72000, Acute thyroiditis T-96 M-41000, Hyalinizing trabecular tumour, Lymph node metastasis follicular cancer 1-082 M-83306, Subacute thyroiditis de Quervain T-96 M-44000, Parthyroid hyperplasia (T-97 M 72000), Chronic fibrotic thyroiditis Riedel T-96 M-45000, Parathyroid normal, Lymph node metastasis Hürthle cell (oxyphilic) carcinoma, Lymph node metastasis medullary cancer T082 M-85106, Acute thyroiditis with abscess T-96 M-41700, Lymph node metastasis anaplastic cancer T082 M-80126
hide 
df_unfiltered %>%
  select(
    malignant_sec
  ) %>%
  tbl_summary(
    label = list(malignant_sec ~ "Malignant secondary diagnosis")
  )  %>%
    modify_caption("**Table. Histological secondary diagnosis category**")
Table 14: Table. Histological secondary diagnosis category
Characteristic N = 32,0081
Malignant secondary diagnosis 978 (3.1%)
1 n (%)

Rodzaje nowotworów złośliwych

hide 
df_unfiltered %>%
  filter(malignant == 1) %>%
  select(
    diagn_main 
  ) %>%
  mutate(
    diagn_main = fct_infreq(diagn_main),
    diagn_main = fct_lump_prop(diagn_main, prop = 0.01)
  ) %>%
  tbl_summary(
    label = list(diagn_main ~ "Diagnosis")
  )  %>%
    modify_caption("**Table. Histological main diagnosis**")
Table 15: Table. Histological main diagnosis
Characteristic N = 10,2541
Diagnosis
    Papillary cancer T-96 M-82603 8,581 (84%)
    Follicular cancer T-96 M-83303 593 (5.8%)
    Medullary cancer T-9605 M-85103 423 (4.1%)
    Hürtle cell (oxyphilic) carcinoma T-96 M-82903 241 (2.4%)
    Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) 217 (2.1%)
    Other 199 (1.9%)
1 n (%)