Dr Augustina Badu-Peprah - PTB Analysis

Author

Dr Samuel Blay Nguah

First read in the data

Code

df_ptb <- 
    readxl::read_xlsx("./Data/PTB Response.xlsx") %>% 
    janitor::clean_names() %>% 
    select(-c(timestamp, question, dropdown, stephanie_janet_badu_peprah)) %>% 
    rename(
        ghon_focus = question_persistent_calcification_ghons_focus,
        tuberculoma = question_tuberculoma,
        miliary = question_miliary_nodules, 
        peribronchial_fibrosis = question_peribronchial_fibrosis,
        consolidation = question_consolidation,
        cavitation = question_cavitation,
        perihilar_lymphadenopathy = question_perihilar_lymphadenopathy,
        reticulonodular_infiltrates = question_reticulonodular_infiltrates,
        reticular_infiltrates = question_reticular_infiltrates,
        lung_volume_loss = question_lung_volume_loss,
        cxr_conclusion = based_on_xtics_above_cxr_signifies,
        extent_of_lung_involved_segment = extent_of_lung_involved,
        extent_of_effusion_minimal = extent_of_effusion,
        pleural_effusion_present_unilateral = pleural_effusion_present
        ) %>% 
    mutate(
        consolid_rul = case_when(
            str_detect(consolidation, "Right upper lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        consolid_lul = case_when(
            str_detect(consolidation, "Left upper lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        consolid_rml = case_when(
            str_detect(consolidation, "Right middle lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        consolid_lml = case_when(
            str_detect(consolidation, "Left middle")~"Yes", 
            TRUE ~ "No") %>% factor(),
        consolid_rll = case_when(
            str_detect(consolidation, "Right lower lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        consolid_lll = case_when(
            str_detect(consolidation, "Left lower lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        cavit_rul = case_when(
            str_detect(cavitation, "Right upper lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        cavit_lul = case_when(
            str_detect(cavitation, "Left upper lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        cavit_rml = case_when(
            str_detect(cavitation, "Right middle lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        cavit_lml = case_when(
            str_detect(cavitation, "Left middle")~"Yes", 
            TRUE ~ "No") %>% factor(),
        cavit_rll = case_when(
            str_detect(cavitation, "Right lower lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        cavit_lll = case_when(
            str_detect(cavitation, "Left lower lobe")~"Yes", 
            TRUE ~ "No") %>% factor(levels = c("No", "Yes")),
        tuberculoma = case_when(
            str_detect(tuberculoma, ".")~"Yes", 
            TRUE ~ "No") %>% factor(levels = c("No", "Yes")),
        miliary = case_when(
            str_detect(miliary, ".")~"Yes", 
            TRUE ~ "No") %>% factor(levels = c("No", "Yes")),
        peri_lymph_rml = case_when(
            str_detect(perihilar_lymphadenopathy, "Right middle")~"Yes", 
            TRUE ~ "No") %>% factor(),
        peri_lymph_lml = case_when(
            str_detect(perihilar_lymphadenopathy, "Left middle")~"Yes", 
            TRUE ~ "No") %>% factor(),
        
        ret_nod_rul = case_when(
            str_detect(reticulonodular_infiltrates, "Right upper lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        ret_nod_lul = case_when(
            str_detect(reticulonodular_infiltrates, "Left upper lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        ret_nod_rml = case_when(
            str_detect(reticulonodular_infiltrates, "Right middle lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        ret_nod_lml = case_when(
            str_detect(reticulonodular_infiltrates, "Left middle")~"Yes", 
            TRUE ~ "No") %>% factor(),
        ret_nod_rll = case_when(
            str_detect(reticulonodular_infiltrates, "Right lower lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        ret_nod_lll = case_when(
            str_detect(reticulonodular_infiltrates, "Left lower lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        
        ret_rul = case_when(
            str_detect(reticular_infiltrates, "Right upper lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        ret_lul = case_when(
            str_detect(reticular_infiltrates, "Left upper lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        ret_rml = case_when(
            str_detect(reticular_infiltrates, "Right middle lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        ret_lml = case_when(
            str_detect(reticular_infiltrates, "Left middle")~"Yes", 
            TRUE ~ "No") %>% factor(),
        ret_rll = case_when(
            str_detect(reticular_infiltrates, "Right lower lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        ret_lll = case_when(
            str_detect(reticular_infiltrates, "Left lower lobe")~"Yes", 
            TRUE ~ "No") %>% factor(),
        
        total_lung_damaged = factor(
            total_lung_damaged, 
            levels = c("None", "Small", "Moderate", "Large")
            ),
        ghon_focus = ifelse(is.na(ghon_focus), "None", ghon_focus),
        lung_volume_loss = ifelse(
            is.na(lung_volume_loss), "None", lung_volume_loss
            ),
        peribronchial_fibrosis = ifelse(
            is.na(peribronchial_fibrosis), "None", peribronchial_fibrosis
            ),
        cxr_conclusion = ifelse(
            cxr_conclusion == "Previous/Chronic TB", "Active TB", cxr_conclusion
            ) %>% factor(),
        extent_of_lung_involved_segment = ifelse(
            is.na(extent_of_lung_involved_segment), 
            "No", 
            extent_of_lung_involved_segment
            ),
        extent_of_lung_involved_one_lobe = ifelse(
            is.na(extent_of_lung_involved_one_lobe), 
            "No", 
            extent_of_lung_involved_one_lobe
            ),
        extent_of_lung_involved_two_lobes = ifelse(
            is.na(extent_of_lung_involved_two_lobes), 
            "No", 
            extent_of_lung_involved_two_lobes
            ),
        extent_of_lung_involved_more_than_2lobes = ifelse(
            is.na(extent_of_lung_involved_more_than_2lobes), 
            "No", 
            extent_of_lung_involved_more_than_2lobes
            ),
        extent_of_lung_involved_none = ifelse(
            is.na(extent_of_lung_involved_none), 
            "No", 
            extent_of_lung_involved_none
            ),
        extent_of_effusion_minimal = ifelse(
            is.na(extent_of_effusion_minimal), 
            "No", 
            extent_of_effusion_minimal
            ),
        extent_of_effusion_up_to_middle_lung_zone = ifelse(
            is.na(extent_of_effusion_up_to_middle_lung_zone), 
            "No", 
            extent_of_effusion_up_to_middle_lung_zone
            ),
        extent_of_effusion_massive = ifelse(
            is.na(extent_of_effusion_massive), 
            "No", 
            extent_of_effusion_massive
            ) %>% factor(levels = c("No", "Yes")),
        extent_of_effusion_none = ifelse(
            is.na(extent_of_effusion_none), 
            "No", 
            extent_of_effusion_none
            ) %>% factor(levels = c("No", "Yes")),
        pleural_effusion_present_unilateral = ifelse(
            is.na(pleural_effusion_present_unilateral), 
            "No", 
            pleural_effusion_present_unilateral
            ) %>% factor(levels = c("No", "Yes")),
        pleural_effusion_present_bilateral = ifelse(
            is.na(pleural_effusion_present_bilateral), 
            "No", 
            pleural_effusion_present_bilateral
            ) %>% factor(levels = c("No", "Yes")),
        pleural_effusion_present_none = ifelse(
            is.na(pleural_effusion_present_none), 
            "No", 
            pleural_effusion_present_none
            ) %>% factor(levels = c("No", "Yes"))
        )

df_ptb <-
    df_ptb %>% 
    labelled::set_variable_labels(
        consolid_rul = "Consolidation: Right Upper Lobe",
        consolid_rml = "Consolidation: Right Middle Lobe",
        consolid_rll = "Consolidation: Right Lower Lobe",
        consolid_lul = "Consolidation: Left Upper Lobe",
        consolid_lml = "Consolidation: Left Middle Lung Zone",
        consolid_lll = "Consolidation: Left Lower Lobe",
        #---------------------------------------------
        cavit_rul = "Cavitation: Right Upper Lobe",
        cavit_rml = "Cavitation: Right Middle Lobe",
        cavit_rll = "Cavitation: Right Lower Lobe",
        cavit_lul = "Cavitation: Left Upper Lobe",
        cavit_lml = "Cavitation: Left Middle Lung Zone",
        cavit_lll = "Cavitation: Left Lower Lobe",
        #----------------------------------------------
        tuberculoma = "Tuberculoma",
        miliary = "Miliary",
        #----------------------------------------------
        peri_lymph_lml = "Perihilar Lymphadenopathy: Left Middle Lung Zone",
        peri_lymph_rml = "Perihilar Lymphadenopathy: Right Middle Lobe",
        #----------------------------------------------
        ret_nod_rul = "Ret. Nodular Infiltrates: Right Upper Lobe",
        ret_nod_rml = "Ret. Nodular Infiltrates: Right Middle Lobe",
        ret_nod_rll = "Ret. Nodular Infiltrates: Right Lower Lobe",
        ret_nod_lul = "Ret. Nodular Infiltrates: Left Upper Lobe",
        ret_nod_lml = "Ret. Nodular Infiltrates: Left Middle Lung Zone",
        ret_nod_lll = "Ret. Nodular Infiltrates: Left Lower Lobe",
        #---------------------------------------------
        ret_rul = "Reticular Infiltrates: Right Upper Lobe",
        ret_rml = "Reticular Infiltrates: Right Middle Lobe",
        ret_rll = "Reticular Infiltrates: Right Lower Lobe",
        ret_lul = "Reticular Infiltrates: Left Upper Lobe",
        ret_lml = "Reticular Infiltrates: Left Middle Lung Zone",
        ret_lll = "Reticular Infiltrates: Left Lower Lobe",
        #---------------------------------------------
        total_lung_damaged = "Total Lung Damage",
        ghon_focus = "Persistent Calcification Ghon Focus",
        cxr_conclusion = "CXR conclusion",
        extent_of_lung_involved_segment = "Extent of lung involved: Segment",
        extent_of_lung_involved_one_lobe = "Extent of lung involved: One Lobe",
        extent_of_lung_involved_two_lobes = "Extent of lung involved: Two Lobes",
        extent_of_lung_involved_more_than_2lobes = "Extent of lung involved: > Two Lobes",
        extent_of_lung_involved_none = "Extent of lung involved: None",
        extent_of_effusion_minimal = "Extent of Effusion: Minimal",
        extent_of_effusion_up_to_middle_lung_zone = "Extent of Effusion: Up to middle lung zone",
        extent_of_effusion_massive = "Extent of Effusion: Massive",
        extent_of_effusion_none = "Extent of Effusion: None",
        pleural_effusion_present_unilateral = "Pleural Effusion Present: Unilateral",
        pleural_effusion_present_bilateral = "Pleural Effusion Present: Bilateral",
        pleural_effusion_present_none = "Pleural Effusion Present: None",
        lung_volume_loss = "Lung volume loss",
        peribronchial_fibrosis = "Peribronchail Fibrosis"
        )

# df_ptb %>% summarytools::dfSummary(labels.col = F, graph.col = F)
df_ptb2 <- df_ptb
df_ptb <- 
    df_ptb %>% 
    filter(!is.na(cxr_conclusion))

write_rds(x = df_ptb, file = "ptb_data.rds")

Table 1

Reticular nodular

Code

gtsummary::theme_gtsummary_compact()

Setting theme `Compact`

Code

ret_nod <- 
    df_ptb %>% 
    select(starts_with("ret_nod"),
        cxr_conclusion
        ) %>% 
    gtsummary::tbl_summary(
        by = cxr_conclusion,
        digits = gtsummary::all_categorical()~ c(0, 1),
        statistic = gtsummary::all_categorical() ~ "{n}({p})"
        ) %>% 
    gtsummary::bold_labels() %>% 
    gtsummary::modify_spanning_header(
        gtsummary::all_stat_cols() ~ "**Tuberculosis Status**"
        ) %>% 
    gtsummary::add_overall(last = T) %>% 
    gtsummary::add_p(pvalue_fun = ~ gtsummary::style_pvalue(.x, digits = 3))

ret_nod

Characteristic	Tuberculosis Status		Overall, N = 154¹	p-value²
Characteristic	Active TB, N = 97¹	Latent TB, N = 57¹	Overall, N = 154¹	p-value²
Ret. Nodular Infiltrates: Right Upper Lobe	13(13.4)	1(1.8)	14(9.1)	0.015
Ret. Nodular Infiltrates: Left Upper Lobe	13(13.4)	0(0.0)	13(8.4)	0.002
Ret. Nodular Infiltrates: Right Middle Lobe	26(26.8)	0(0.0)	26(16.9)	<0.001
Ret. Nodular Infiltrates: Left Middle Lung Zone	26(26.8)	0(0.0)	26(16.9)	<0.001
Ret. Nodular Infiltrates: Right Lower Lobe	11(11.3)	0(0.0)	11(7.1)	0.007
Ret. Nodular Infiltrates: Left Lower Lobe	10(10.3)	0(0.0)	10(6.5)	0.014
¹ n(%)
² Pearson’s Chi-squared test; Fisher’s exact test

Reticular

Code

ret_only <- 
    df_ptb %>% 
    select(ret_rul, ret_lul, ret_rll, ret_lll, ret_rml, ret_lml, 
        cxr_conclusion
        ) %>% 
    gtsummary::tbl_summary(
        by = cxr_conclusion,
        digits = gtsummary::all_categorical()~ c(0, 1),
        statistic = gtsummary::all_categorical() ~ "{n}({p})"
        ) %>% 
    gtsummary::bold_labels() %>% 
    gtsummary::modify_spanning_header(
        gtsummary::all_stat_cols() ~ "**Tuberculosis Status**"
        ) %>% 
    gtsummary::add_overall(last = T) %>% 
    gtsummary::add_p(pvalue_fun = ~ gtsummary::style_pvalue(.x, digits = 3))

ret_only

Characteristic	Tuberculosis Status		Overall, N = 154¹	p-value²
Characteristic	Active TB, N = 97¹	Latent TB, N = 57¹	Overall, N = 154¹	p-value²
Reticular Infiltrates: Right Upper Lobe	8(8.2)	0(0.0)	8(5.2)	0.026
Reticular Infiltrates: Left Upper Lobe	8(8.2)	0(0.0)	8(5.2)	0.026
Reticular Infiltrates: Right Lower Lobe	7(7.2)	0(0.0)	7(4.5)	0.047
Reticular Infiltrates: Left Lower Lobe	7(7.2)	0(0.0)	7(4.5)	0.047
Reticular Infiltrates: Right Middle Lobe	14(14.4)	0(0.0)	14(9.1)	0.003
Reticular Infiltrates: Left Middle Lung Zone	10(10.3)	0(0.0)	10(6.5)	0.014
¹ n(%)
² Fisher’s exact test; Pearson’s Chi-squared test

Cavitation

Code

cavit_only <- 
    df_ptb %>% 
    select(
        cavit_rul, 
        cavit_lul, 
        cavit_rll, 
        cavit_lll, 
        cavit_rml, 
        cavit_lml,
        cxr_conclusion
        ) %>% 
    gtsummary::tbl_summary(
        by = cxr_conclusion,
        digits = gtsummary::all_categorical()~ c(0, 1),
        statistic = gtsummary::all_categorical() ~ "{n}({p})"
        ) %>% 
    gtsummary::bold_labels() %>% 
    gtsummary::modify_spanning_header(
        gtsummary::all_stat_cols() ~ "**Tuberculosis Status**"
        ) %>% 
    gtsummary::add_overall(last = T) %>% 
    gtsummary::add_p(pvalue_fun = ~ gtsummary::style_pvalue(.x, digits = 3))

cavit_only

Characteristic	Tuberculosis Status		Overall, N = 154¹	p-value²
Characteristic	Active TB, N = 97¹	Latent TB, N = 57¹	Overall, N = 154¹	p-value²
Cavitation: Right Upper Lobe	8(8.2)	0(0.0)	8(5.2)	0.026
Cavitation: Left Upper Lobe	8(8.2)	0(0.0)	8(5.2)	0.026
Cavitation: Right Lower Lobe	3(3.1)	0(0.0)	3(1.9)	0.296
Cavitation: Left Lower Lobe	0(0.0)	0(0.0)	0(0.0)	>0.999
Cavitation: Right Middle Lobe	13(13.4)	0(0.0)	13(8.4)	0.002
Cavitation: Left Middle Lung Zone	7(7.2)	0(0.0)	7(4.5)	0.047
¹ n(%)
² Fisher’s exact test

Consolidation

Code

consolid_only <- 
    df_ptb %>% 
    select(
        consolid_rul, 
        consolid_lul, 
        consolid_rll, 
        consolid_lll, 
        consolid_rml, 
        consolid_lml,
        cxr_conclusion
        ) %>% 
    gtsummary::tbl_summary(
        by = cxr_conclusion,
        digits = gtsummary::all_categorical()~ c(0, 1),
        statistic = gtsummary::all_categorical() ~ "{n}({p})"
        ) %>% 
    gtsummary::bold_labels() %>% 
    gtsummary::modify_spanning_header(
        gtsummary::all_stat_cols() ~ "**Tuberculosis Status**"
        ) %>% 
    gtsummary::add_overall(last = T) %>% 
    gtsummary::add_p(pvalue_fun = ~ gtsummary::style_pvalue(.x, digits = 3))

consolid_only

Characteristic	Tuberculosis Status		Overall, N = 154¹	p-value²
Characteristic	Active TB, N = 97¹	Latent TB, N = 57¹	Overall, N = 154¹	p-value²
Consolidation: Right Upper Lobe	19(19.6)	1(1.8)	20(13.0)	0.001
Consolidation: Left Upper Lobe	17(17.5)	0(0.0)	17(11.0)	<0.001
Consolidation: Right Lower Lobe	6(6.2)	0(0.0)	6(3.9)	0.085
Consolidation: Left Lower Lobe	9(9.3)	0(0.0)	9(5.8)	0.027
Consolidation: Right Middle Lobe	15(15.5)	0(0.0)	15(9.7)	0.002
Consolidation: Left Middle Lung Zone	10(10.3)	0(0.0)	10(6.5)	0.014
¹ n(%)
² Pearson’s Chi-squared test; Fisher’s exact test

Lung involvement

Code

lung_involve <- 
    df_ptb %>% 
    select(
        extent_of_lung_involved_none, 
        extent_of_lung_involved_segment,
        extent_of_lung_involved_one_lobe,
        extent_of_lung_involved_two_lobes,
        extent_of_lung_involved_more_than_2lobes,
        cxr_conclusion
        ) %>% 
    gtsummary::tbl_summary(
        by = cxr_conclusion,
        digits = gtsummary::all_categorical()~ c(0, 1),
        statistic = gtsummary::all_categorical() ~ "{n}({p})"
        ) %>% 
    gtsummary::bold_labels() %>% 
    gtsummary::modify_spanning_header(
        gtsummary::all_stat_cols() ~ "**Tuberculosis Status**"
        ) %>% 
    gtsummary::add_overall(last = T) %>% 
    gtsummary::add_p(pvalue_fun = ~ gtsummary::style_pvalue(.x, digits = 3))

lung_involve

Characteristic	Tuberculosis Status		Overall, N = 154¹	p-value²
Characteristic	Active TB, N = 97¹	Latent TB, N = 57¹	Overall, N = 154¹	p-value²
Extent of lung involved: None	2(2.1)	55(96.5)	57(37.0)	<0.001
Extent of lung involved: Segment	17(17.5)	0(0.0)	17(11.0)	<0.001
Extent of lung involved: One Lobe	19(19.6)	2(3.5)	21(13.6)	0.005
Extent of lung involved: Two Lobes	32(33.0)	0(0.0)	32(20.8)	<0.001
Extent of lung involved: > Two Lobes	38(39.2)	0(0.0)	38(24.7)	<0.001
¹ n(%)
² Pearson’s Chi-squared test

Perihilar lymphadenopathy

Code

perihilar_lymph <- 
    df_ptb %>% 
    select(
        peri_lymph_rml,
        peri_lymph_lml,
        cxr_conclusion
        ) %>% 
    gtsummary::tbl_summary(
        by = cxr_conclusion,
        digits = gtsummary::all_categorical()~ c(0, 1),
        statistic = gtsummary::all_categorical() ~ "{n}({p})"
        ) %>% 
    gtsummary::bold_labels() %>% 
    gtsummary::modify_spanning_header(
        gtsummary::all_stat_cols() ~ "**Tuberculosis Status**"
        ) %>% 
    gtsummary::add_overall(last = T) %>% 
    gtsummary::add_p(pvalue_fun = ~ gtsummary::style_pvalue(.x, digits = 3))

perihilar_lymph

Characteristic	Tuberculosis Status		Overall, N = 154¹	p-value²
Characteristic	Active TB, N = 97¹	Latent TB, N = 57¹	Overall, N = 154¹	p-value²
Perihilar Lymphadenopathy: Right Middle Lobe	25(25.8)	0(0.0)	25(16.2)	<0.001
Perihilar Lymphadenopathy: Left Middle Lung Zone	16(16.5)	0(0.0)	16(10.4)	0.001
¹ n(%)
² Pearson’s Chi-squared test

Pleural Effusion

Code

pleural_eff <- 
    df_ptb %>% 
    select(
        pleural_effusion_present_none,
        pleural_effusion_present_unilateral, 
        pleural_effusion_present_bilateral,
                cxr_conclusion
        ) %>% 
    gtsummary::tbl_summary(
        by = cxr_conclusion,
        digits = gtsummary::all_categorical()~ c(0, 1),
        statistic = gtsummary::all_categorical() ~ "{n}({p})"
        ) %>% 
    gtsummary::bold_labels() %>% 
    gtsummary::modify_spanning_header(
        gtsummary::all_stat_cols() ~ "**Tuberculosis Status**"
        ) %>% 
    gtsummary::add_overall(last = T) %>% 
    gtsummary::add_p(pvalue_fun = ~ gtsummary::style_pvalue(.x, digits = 3))

pleural_eff

Characteristic	Tuberculosis Status		Overall, N = 154¹	p-value²
Characteristic	Active TB, N = 97¹	Latent TB, N = 57¹	Overall, N = 154¹	p-value²
Pleural Effusion Present: None	85(87.6)	57(100.0)	142(92.2)	0.004
Pleural Effusion Present: Unilateral	11(11.3)	0(0.0)	11(7.1)	0.007
Pleural Effusion Present: Bilateral	0(0.0)	0(0.0)	0(0.0)	>0.999
¹ n(%)
² Fisher’s exact test

Extent of Effusion

Code

extent_eff <- 
    df_ptb %>% 
    select(
        extent_of_effusion_none, 
        extent_of_effusion_minimal,
        extent_of_effusion_up_to_middle_lung_zone,
        extent_of_effusion_massive,
        cxr_conclusion
        ) %>% 
    gtsummary::tbl_summary(
        by = cxr_conclusion,
        digits = gtsummary::all_categorical()~ c(0, 1),
        statistic = gtsummary::all_categorical() ~ "{n}({p})"
        ) %>% 
    gtsummary::bold_labels() %>% 
    gtsummary::modify_spanning_header(
        gtsummary::all_stat_cols() ~ "**Tuberculosis Status**"
        ) %>% 
    gtsummary::add_overall(last = T) %>% 
    gtsummary::add_p(pvalue_fun = ~ gtsummary::style_pvalue(.x, digits = 3))

extent_eff

Characteristic	Tuberculosis Status		Overall, N = 154¹	p-value²
Characteristic	Active TB, N = 97¹	Latent TB, N = 57¹	Overall, N = 154¹	p-value²
Extent of Effusion: None	86(88.7)	57(100.0)	143(92.9)	0.007
Extent of Effusion: Minimal	6(6.2)	0(0.0)	6(3.9)	0.085
Extent of Effusion: Up to middle lung zone	5(5.2)	0(0.0)	5(3.2)	0.158
Extent of Effusion: Massive	0(0.0)	0(0.0)	0(0.0)	>0.999
¹ n(%)
² Fisher’s exact test

Extent of Effusion

Code

other_features <- 
    df_ptb %>% 
    select(
        total_lung_damaged,
        miliary,
        tuberculoma,
        ghon_focus,
        lung_volume_loss,
        peribronchial_fibrosis,
        cxr_conclusion
        ) %>% 
    gtsummary::tbl_summary(
        by = cxr_conclusion,
        digits = gtsummary::all_categorical()~ c(0, 1),
        statistic = gtsummary::all_categorical() ~ "{n}({p})"
        ) %>% 
    gtsummary::bold_labels() %>% 
    gtsummary::modify_spanning_header(
        gtsummary::all_stat_cols() ~ "**Tuberculosis Status**"
        ) %>% 
    gtsummary::add_overall(last = T) %>% 
    gtsummary::add_p(pvalue_fun = ~ gtsummary::style_pvalue(.x, digits = 3))

There was an error in 'add_p()/add_difference()' for variable 'peribronchial_fibrosis', p-value omitted:
Error in stats::chisq.test(x = structure(c("None", "None", "None", "None", : 'x' and 'y' must have at least 2 levels

Code

other_features

Characteristic	Tuberculosis Status		Overall, N = 154¹	p-value²
Characteristic	Active TB, N = 97¹	Latent TB, N = 57¹	Overall, N = 154¹	p-value²
Total Lung Damage				<0.001
None	0(0.0)	55(96.5)	55(35.7)
Small	20(20.6)	2(3.5)	22(14.3)
Moderate	38(39.2)	0(0.0)	38(24.7)
Large	39(40.2)	0(0.0)	39(25.3)
Miliary	0(0.0)	0(0.0)	0(0.0)	>0.999
Tuberculoma	0(0.0)	0(0.0)	0(0.0)	>0.999
Persistent Calcification Ghon Focus				0.370
None	97(100.0)	56(98.2)	153(99.4)
Right middle lobe	0(0.0)	1(1.8)	1(0.6)
Lung volume loss				0.531
None	95(97.9)	57(100.0)	152(98.7)
Right upper lobe	2(2.1)	0(0.0)	2(1.3)
Peribronchail Fibrosis
None	97(100.0)	57(100.0)	154(100.0)
¹ n(%)
² Pearson’s Chi-squared test; Fisher’s exact test