Dane do analizy

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

Populacja badana

pacjenci z rejestru Eurocrine, którzy przebyli operację tarczycy 03.2020 - 03.2022, u których przed operacją wykonano ocenę TIRADS. Wiek pacjentów 16 lat i powyżej.

Kryteria włączenia / wykluczenia

Kolejne etapy kwalifikacji:

1. cały zbiór - 32008 przypadków
2. wiek >= 16 (31604 z 32008 przypadków, odpadło 404)
3. dostępna ocena wg EU-TIRADS (21714 z 31604 przypadków, odpadło 9890)
4. dostępna ocena hist-pat (20762 z 21714 przypadków, odpadło 952)

Kryterium wieku dodano 7.11.2022, w wyniku wcześniejszej wspólnej dyskusji autorów.

Lista zmiennych

hide

skim(df)

Table 1: Data summary

Name	df
Number of rows	20762
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	20762	0
pid	0	1.00	9	14	0	20691	0
country_id	0	1.00	1	2	0	10	0
site_id	0	1.00	1	3	0	111	0
patient_id	0	1.00	4	6	0	20691	0
size_main_cat	13084	0.37	5	11	0	4	0
clinical_risk	12855	0.38	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	2021-03-03	566

Variable type: factor

skim_variable	n_missing	complete_rate	ordered	n_unique	top_counts
diagn_main	0	1	FALSE	38	Pap: 6766, Nod: 5346, Fol: 4513, Gra: 1569
diagn_sec1	0	1	FALSE	36	(Mi: 13203, Lym: 2730, Nod: 1993, Fol: 1255
diagn_sec2	0	1	FALSE	24	(Mi: 19320, Lym: 639, Nod: 369, Fol: 156
diagn_sec3	0	1	FALSE	15	(Mi: 20575, Lym: 102, Par: 24, Nod: 19
oper_type_th	0	1	FALSE	11	Uni: 9647, Thy: 9465, Uni: 485, Ist: 457
oper_type_ln	0	1	FALSE	9	Non: 16218, Uni: 2132, Cen: 888, Bil: 877
oper_indic	0	1	FALSE	5	Exc: 8842, Com: 4318, Mal: 4235, Thy: 2817
eutirads	0	1	FALSE	5	TR4: 6831, TR5: 6157, TR3: 4133, TR2: 2412
sex	0	1	FALSE	2	Fem: 16508, Mal: 4254
tnm_t	0	1	FALSE	10	(Mi: 12704, pT1: 3739, pT1: 2285, pT2: 1278
tnm_n	0	1	FALSE	5	(Mi: 12581, pN0: 3591, pNx: 2347, pN1: 1437
tnm_m	0	1	FALSE	4	(Mi: 12639, pM0: 6749, pMx: 1276, pM1: 98
beth_class	0	1	FALSE	7	IV: 5787, Not: 5279, VI: 3505, II: 3147
age_cat	0	1	FALSE	4	(26: 10675, (53: 8671, (-0: 1046, (79: 370
oper_type_th_aggr	0	1	FALSE	3	Lob: 9647, Thy: 9465, Oth: 1650
oper_type_ln_aggr	0	1	FALSE	4	Non: 16218, CLN: 3009, CLN: 984, Oth: 551
tnm_t_orig	0	1	FALSE	10	(Mi: 12872, pT1: 3657, pT1: 2240, pT2: 1254

Variable type: logical

skim_variable	n_missing	complete_rate	mean	count
eutirads_reported	0	1	1	TRU: 20762

Variable type: numeric

skim_variable	n_missing	complete_rate	mean	sd	p0	p25	p50	p75	p100	hist
size_main	13084	0.37	15.87	14.15	0	7.0	12	20.00	150	▇▁▁▁▁
size_sec1	20258	0.02	7.03	9.51	0	2.0	4	7.25	74	▇▁▁▁▁
size_sec2	20736	0.00	6.73	8.17	1	2.0	4	8.75	40	▇▂▁▁▁
size_sec3	20759	0.00	11.33	3.51	8	9.5	11	13.00	15	▇▁▇▁▇
age	0	1.00	50.53	14.84	16	39.0	51	62.00	106	▃▇▇▂▁
eutirads_5	0	1.00	0.30	0.46	0	0.0	0	1.00	1	▇▁▁▁▃
malignant	0	1.00	0.38	0.49	0	0.0	0	1.00	1	▇▁▁▁▅
malignant_sec1	0	1.00	0.03	0.16	0	0.0	0	0.00	1	▇▁▁▁▁
malignant_sec2	0	1.00	0.00	0.04	0	0.0	0	0.00	1	▇▁▁▁▁
malignant_sec3	0	1.00	0.00	0.01	0	0.0	0	0.00	1	▇▁▁▁▁
malignant_sec	0	1.00	0.03	0.16	0	0.0	0	0.00	1	▇▁▁▁▁
fna_indicated	13084	0.37	0.46	0.50	0	0.0	0	1.00	1	▇▁▁▁▇
size_main_lt1	13084	0.37	0.46	0.50	0	0.0	0	1.00	1	▇▁▁▁▇
tnm_t1a	12872	0.38	0.46	0.50	0	0.0	0	1.00	1	▇▁▁▁▇
high_risk_profile	0	1.00	0.05	0.21	0	0.0	0	0.00	1	▇▁▁▁▁
low_risk_profile	0	1.00	0.13	0.33	0	0.0	0	0.00	1	▇▁▁▁▁
indeterminate_risk_profile	12855	0.38	0.54	0.50	0	0.0	1	1.00	1	▇▁▁▁▇
oper_count	0	1.00	1.01	0.11	1	1.0	1	1.00	3	▇▁▁▁▁

Charakterystyka pacjentów

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

hide

df1op <- df %>% 
  filter(oper_count == 1)

Wiek, płeć

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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 = 20,5261
Age [years]	51 (39, 62)
Sex
Male	4,183 (20%)
Female	16,343 (80%)
1 Median (IQR); n (%)

hide

df1op  %>%
  ggplot(aes(x=age, fill=sex)) +
  geom_histogram(binwidth = 1) 

Ocena przedoperacyjna

Wynik BAC

hide

df %>%
  select(
    beth_class
  ) %>%
  tbl_summary(
    label = list(beth_class ~ "Bethesda class")
  )  %>%
    modify_caption("**Table. Cytology results**") 

Table 3: Table. Cytology results

Characteristic	N = 20,7621
Bethesda class
Not performed	5,279 (25%)
I	517 (2.5%)
II	3,147 (15%)
III	1,351 (6.5%)
IV	5,787 (28%)
V	1,176 (5.7%)
VI	3,505 (17%)
1 n (%)

EUTIRADS.PRE

hide

df %>%
  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 = 20,7621
EU-TIRADS
TR1	1,229 (5.9%)
TR2	2,412 (12%)
TR3	4,133 (20%)
TR4	6,831 (33%)
TR5	6,157 (30%)
1 n (%)

Zabiegi

Liczba operacji z podziałem na pierwotne, wtórne

hide

df  %>% 
  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 = 20,7621
Number of surgeries
1	20,526 (99%)
2	227 (1.1%)
3	9 (<0.1%)
1 n (%)

Rodzaje zabiegów

hide

df %>%
  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 = 20,7621
Thyroid surgery
Unilateral lobectomy of thyroid gland (BAA40)	9,647 (46%)
Thyroidectomy (BAA60)	9,465 (46%)
Unilateral resection of thyroid gland (BAA20)	485 (2.3%)
Isthmus resection of thyroid gland (BAA30)	457 (2.2%)
Bilateral resection of thyroid gland (BAA25)	322 (1.6%)
Lobectomy and resection of contralateral lobe of thyroid gland (BAA50)	277 (1.3%)
Other operation on thyroid gland (BAA99)	53 (0.3%)
Percutanous thermal ablation (RFA, NWA, HIFU)	33 (0.2%)
Biopsy of thyroid gland (BAA00)	11 (<0.1%)
Incision of thyroid gland (BAA10)	8 (<0.1%)
Exploration of thyroid gland (BAA05)	4 (<0.1%)
Lymph node surgery
None	16,218 (78%)
Unilateral central lymph node dissection (PJD41)	2,132 (10%)
Central lymph node dissection (PJD41) and one-sided lat. Lymph node dissection (PJD51)	888 (4.3%)
Bilateral central lymph node dissection (PJD41)	877 (4.2%)
Extirpation of lymph nodes (PJD41)	329 (1.6%)
Exploration of lymph nodes incl. Biopsy (PJD10)	143 (0.7%)
Bilateral central lymphnode dissection AND bilateral lateral lymphnodedissection (PJD41, PJD51)	96 (0.5%)
One-sided lateral lymph node dissection (PJD51)	55 (0.3%)
Bilateral lateral lymph node dissection (PJD51)	24 (0.1%)
1 n (%)

Rodzaje zabiegów - zagregowane

hide

df %>%
  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 = 20,7621
Thyroid surgery
Lobectomy	9,647 (46%)
Thyroidectomy	9,465 (46%)
Other	1,650 (7.9%)
Lymph node surgery
None	16,218 (78%)
CLND	3,009 (14%)
CLND + LLND	984 (4.7%)
Other	551 (2.7%)
1 n (%)

Wskaznie do operacji

hide

df %>%
  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 = 20,7621
Indication
Excluding malignancy	8,842 (43%)
Compression symptom	4,318 (21%)
Malignancy	4,235 (20%)
Thyreotoxicosis	2,817 (14%)
Other	550 (2.6%)
1 n (%)

Rozpoznania hist-pat

Histological main diagnosis.F1

hide

df %>%
  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 = 20,7621
Diagnosis
Papillary cancer T-96 M-82603	6,766 (33%)
Nodular goitre T-96 M-71640	5,346 (26%)
Follicular adenoma T-96 M-83300	4,513 (22%)
Graves´ disease T-96 D-2193	1,569 (7.6%)
Hürtle cell (oxyphilic) adenoma T-96M-82900	589 (2.8%)
Follicular cancer T-96 M-83303	395 (1.9%)
Medullary cancer T-9605 M-85103	319 (1.5%)
Lymphocytic thyroiditis Hashimoto T-96 M-45810	280 (1.3%)
Hürtle cell (oxyphilic) carcinoma T-96 M-82903	183 (0.9%)
Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP)	133 (0.6%)
Other diagnosis	119 (0.6%)
Well differentiated tumour of uncertain malignant potential (WDT-UMP)	66 (0.3%)
Thyroid normal T-96 M 00110	63 (0.3%)
Thyroid nothing malignant T-96 M 0945	63 (0.3%)
Normal gland	52 (0.3%)
Anaplastic cancer T-96 M-80123	40 (0.2%)
Follicular tumour with uncertain malignant potential	40 (0.2%)
Poorly differentiated thyroid cancer	36 (0.2%)
Benign tumour UNS T-96 M-80000	32 (0.2%)
Parathyroid adenoma (T-97 M-81400)	25 (0.1%)
Subacute thyroiditis de Quervain T-96 M-44000	25 (0.1%)
Hyalinizing trabecular tumour	16 (<0.1%)
Lymph node metastasis papillary cancer T-082 M-82606	15 (<0.1%)
C-cell hyperplasia T-9605 M-72000	14 (<0.1%)
Metastasis from cancer UNS T-96 M-80106	11 (<0.1%)
Cyst, ductus thyreoglossus T-96 M-26500	8 (<0.1%)
Metastasis from malignant tumour UNS T-96 M-80006	8 (<0.1%)
Lymphoma T-96 M-95903	7 (<0.1%)
Acute thyroiditis T-96 M-41000	6 (<0.1%)
Cancer UNS T-96 M 80103	6 (<0.1%)
Parthyroid hyperplasia (T-97 M 72000)	4 (<0.1%)
Chronic fibrotic thyroiditis Riedel T-96 M-45000	4 (<0.1%)
Malignant tumour UNS T-96 M-80003	3 (<0.1%)
Lymph node metastasis medullary cancer T082 M-85106	2 (<0.1%)
Lymph node metastasis follicular cancer 1-082 M-83306	1 (<0.1%)
Parathyroid normal	1 (<0.1%)
Lymph node metastasis Hürthle cell (oxyphilic) carcinoma	1 (<0.1%)
Acute thyroiditis with abscess T-96 M-41700	1 (<0.1%)
1 n (%)

Histological secondary diagnosis 1.F1

hide

df %>%
  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 = 20,7621
Diagnosis
(Missing)	13,203 (64%)
Lymphocytic thyroiditis Hashimoto T-96 M-45810	2,730 (13%)
Nodular goitre T-96 M-71640	1,993 (9.6%)
Follicular adenoma T-96 M-83300	1,255 (6.0%)
Papillary cancer T-96 M-82603	440 (2.1%)
Parathyroid adenoma (T-97 M-81400)	257 (1.2%)
Graves´ disease T-96 D-2193	240 (1.2%)
Hürtle cell (oxyphilic) adenoma T-96M-82900	148 (0.7%)
Other diagnosis	70 (0.3%)
Parthyroid hyperplasia (T-97 M 72000)	54 (0.3%)
Subacute thyroiditis de Quervain T-96 M-44000	54 (0.3%)
Parathyroid normal	44 (0.2%)
Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP)	41 (0.2%)
Follicular cancer T-96 M-83303	35 (0.2%)
Thyroid nothing malignant T-96 M 0945	35 (0.2%)
C-cell hyperplasia T-9605 M-72000	27 (0.1%)
Lymph node metastasis papillary cancer T-082 M-82606	24 (0.1%)
Hürtle cell (oxyphilic) carcinoma T-96 M-82903	15 (<0.1%)
Normal gland	15 (<0.1%)
Benign tumour UNS T-96 M-80000	13 (<0.1%)
Chronic fibrotic thyroiditis Riedel T-96 M-45000	10 (<0.1%)
Thyroid normal T-96 M 00110	9 (<0.1%)
Medullary cancer T-9605 M-85103	6 (<0.1%)
Cyst, ductus thyreoglossus T-96 M-26500	6 (<0.1%)
Poorly differentiated thyroid cancer	5 (<0.1%)
Acute thyroiditis T-96 M-41000	5 (<0.1%)
Hyalinizing trabecular tumour	5 (<0.1%)
Well differentiated tumour of uncertain malignant potential (WDT-UMP)	4 (<0.1%)
Cancer UNS T-96 M 80103	4 (<0.1%)
Follicular tumour with uncertain malignant potential	4 (<0.1%)
Anaplastic cancer T-96 M-80123	3 (<0.1%)
Metastasis from malignant tumour UNS T-96 M-80006	3 (<0.1%)
Metastasis from cancer UNS T-96 M-80106	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%)
1 n (%)

Histological secondary diagnosis 2.F1

hide

df %>%
  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 = 20,7621
Diagnosis
(Missing)	19,320 (93%)
Lymphocytic thyroiditis Hashimoto T-96 M-45810	639 (3.1%)
Nodular goitre T-96 M-71640	369 (1.8%)
Follicular adenoma T-96 M-83300	156 (0.8%)
Parathyroid adenoma (T-97 M-81400)	95 (0.5%)
Parthyroid hyperplasia (T-97 M 72000)	29 (0.1%)
Papillary cancer T-96 M-82603	23 (0.1%)
Graves´ disease T-96 D-2193	23 (0.1%)
Other diagnosis	21 (0.1%)
Hürtle cell (oxyphilic) adenoma T-96M-82900	18 (<0.1%)
Subacute thyroiditis de Quervain T-96 M-44000	12 (<0.1%)
Parathyroid normal	10 (<0.1%)
C-cell hyperplasia T-9605 M-72000	10 (<0.1%)
Cyst, ductus thyreoglossus T-96 M-26500	10 (<0.1%)
Chronic fibrotic thyroiditis Riedel T-96 M-45000	7 (<0.1%)
Lymph node metastasis papillary cancer T-082 M-82606	6 (<0.1%)
Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP)	4 (<0.1%)
Normal gland	3 (<0.1%)
Medullary cancer T-9605 M-85103	2 (<0.1%)
Lymphoma T-96 M-95903	1 (<0.1%)
Thyroid normal T-96 M 00110	1 (<0.1%)
Metastasis from cancer UNS T-96 M-80106	1 (<0.1%)
Lymph node metastasis medullary cancer T082 M-85106	1 (<0.1%)
Benign tumour UNS T-96 M-80000	1 (<0.1%)
1 n (%)

Histological secondary diagnosis 3.F1

hide

df %>%
  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 = 20,7621
Diagnosis
(Missing)	20,575 (99%)
Lymphocytic thyroiditis Hashimoto T-96 M-45810	102 (0.5%)
Parathyroid adenoma (T-97 M-81400)	24 (0.1%)
Nodular goitre T-96 M-71640	19 (<0.1%)
Follicular adenoma T-96 M-83300	14 (<0.1%)
Parthyroid hyperplasia (T-97 M 72000)	9 (<0.1%)
Other diagnosis	8 (<0.1%)
Lymph node metastasis papillary cancer T-082 M-82606	2 (<0.1%)
Cyst, ductus thyreoglossus T-96 M-26500	2 (<0.1%)
Graves´ disease T-96 D-2193	2 (<0.1%)
Parathyroid normal	1 (<0.1%)
Benign tumour UNS T-96 M-80000	1 (<0.1%)
Normal gland	1 (<0.1%)
Follicular cancer T-96 M-83303	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, 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, 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

hide

df %>%
  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 = 20,7621
Malignant diagnosis	7,907 (38%)
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, 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, 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

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df %>%
  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 = 20,7621
Malignant secondary diagnosis	578 (2.8%)
1 n (%)

Rodzaje nowotworów złośliwych

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df %>%
  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 = 7,9071
Diagnosis
Papillary cancer T-96 M-82603	6,766 (86%)
Follicular cancer T-96 M-83303	395 (5.0%)
Medullary cancer T-9605 M-85103	319 (4.0%)
Hürtle cell (oxyphilic) carcinoma T-96 M-82903	183 (2.3%)
Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP)	133 (1.7%)
Other	111 (1.4%)
1 n (%)

TNM

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df %>%
  filter(malignant == 1) %>%
  select(
    tnm_t,
    tnm_n,
    tnm_m
  ) %>%
  tbl_summary(
    label = list(
      tnm_t ~ "T: size or direct extent of the primary tumor",
      tnm_n ~ "N: degree of spread to regional lymph nodes",
      tnm_m ~ "M: presence of distant metastasis"
    )
  )  %>%
  modify_caption("**Table. Thyroid cancer stage according to the 8<sup>th</sup> edition of AJCC/TNM**") 

Table 16: Table. Thyroid cancer stage according to the 8^th edition of AJCC/TNM

Characteristic	N = 7,9071
T: size or direct extent of the primary tumor
pT0	2 (<0.1%)
pT1a	3,502 (44%)
pT1b	2,260 (29%)
pT2	1,267 (16%)
pT3a	425 (5.4%)
pT3b	156 (2.0%)
pT4a	132 (1.7%)
pT4b	13 (0.2%)
pTx	9 (0.1%)
(Missing)	141 (1.8%)
N: degree of spread to regional lymph nodes
pN0	3,497 (44%)
pN1a	1,414 (18%)
pN1b	787 (10.0%)
pNx	2,209 (28%)
(Missing)	0 (0%)
M: presence of distant metastasis
pM0	6,535 (83%)
pM1	96 (1.2%)
pMx	1,276 (16%)
(Missing)	0 (0%)
1 n (%)

Wielkość ogniska nowotworu złośliwego

Uwaga: do poniższych zestawień włączyłem tylko przypadki z rozp. nowotworu złośliwego

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df %>% 
  filter(
    malignant == 1,
    !is.na(size_main)
  ) %>% 
  ggplot(aes(x=size_main)) + 
  geom_histogram(binwidth = 5) +
  labs(title = "Distribution of malignant tumor size",  subtitle = "n=7988 malignant thyroid tumors") +
  xlab("size [mm]") +
  theme_classic()

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df %>% 
  filter(malignant == 1) %>% 
  select(
    size_main_cat
  ) %>%
  mutate(
    size_main_cat = fct_infreq(size_main_cat)
  )%>%
  tbl_summary()  %>%
    modify_caption("**Table. Size of malignant tumors - categorized**") 

Table 17: Table. Size of malignant tumors - categorized

Characteristic	N = 7,9071
size_main_cat
<= 1cm	3,510 (46%)
(1cm - 2cm]	2,350 (31%)
(2cm - 4cm]	1,326 (17%)
> 4cm	476 (6.2%)
Unknown	245
1 n (%)