Paragonimiasis Statistical Analysis

Data Sets

The full data set was created by combining two different data sets: actively collected (9355 individuals) and passively collected (3046 individuals). Columns that only appeared in one data set were added to the other data set then filled with blank entries.

There was an overlap in the values of Serial_No between the two data sets. To remain the values being unique, we add 1,000,000 to each serial in the passive data set. This also allows us to differentiate which data set the individual came from.

The following columns were removed:

• Name_of_the_study_participant
• Date_of_the_interview
• Tube_No_Spot_Fresh_sputum_sample_without_fixative
• Date_Collection_Spot_Fresh_sputum_sample_without_fixative
• Date_sent_to_Lab_Spot_Fresh_sputum_sample_without_fixative
• Date_Collection_Overnight_Fresh_sputum_sample_without_fixative
• Date_sent_to_Lab_Overnight_Fresh_sputum_sample_without_fixative
• Tube_No_Spot_Fresh_sputum_sample_with_preservative
• Date_Collection_Spot_Fresh_sputum_sample_with_preservative
• Date_sent_to_Lab_Spot_Fresh_sputum_sample_with_preser
• Tube_No_Spot_sputum_sample_with_Ethanol_Sol
• Date_Collection_Spot_sputum_sample_with_Ethanol_Soln
• Date_sent_to_Lab_Spot_sputum_sample_with_Ethanol_Soln
• Tube_No_Overnight_Stool_sample
• Date_Collection_of_Overnight_stool_sample
• Date_Sent_to_lab_of_Overnight_stool_sample
• Tube_No_Spot_Whole_Blood_sample
• Date_Collection_Spot_whole_blood_sample
• Scrutinize_Filled_all_questions
• Scrutinize_Sputum_collected
• Scrutinize_Stool_collected
• Scrutinize_Blood_collected
• Field_Investigator_name
• Date_checked_Field_investigator
• Checked_by_name
• Checked_by
• Designation

Statistical Analysis: Continuous Variables

We start by investigating for significant differences in the age, weight and height of individuals who tested ELISA positive/negative. A common approach is to use a two-sample t-test, which determines if there is a statistical difference between the means of two samples.

Running the t-test on these columns results in the following table:

	Age	Height (cm)	Weight (kg)
Positive Mean	32.0184	149.043	44.2147
Negative Mean	35.9002	149.262	46.8544
t-stat	-3.13453	-0.220966	-2.74948
p-value	0.00172535	0.825122	0.00597772

The $p$-value represents the probability of receiving the two samples under the assumption that they are independent. Using the golden standard of <0.05, we see that the average age and average weight of ELISA positive individuals is significantly lower than ELISA negative individuals.

Statistical Analysis: Categorical Variables

The majority of the data set is categorical, e.g. sex, marital status, religion, etc. For categorical data, we cannot use a t-test. Instead, we use another common test, the chi-squared two sample test. The chi-squared test provides a $p$-value measuring the significance in the differences between the proportions of responses between two groups.

For example, consider the responses in regards to marital status:

	Positive	Negative
Married	305	11574
Unmarried	21	430

Running a chi-squared test on this table results in a $p$-value of 0.0103. The $p$-value being less than 0.05 suggests that there is significant differences in the proportions of responses between ELISA positive and ELISA negative individuals. We can see this visually by creating bar-charts:

The red bars represent the percentage of ELISA positive individuals who gave a particular response. Likewise, the blue bars are the percentage of ELISA negative individuals who gave a particular response.

We get a similar result in terms of expectoration ($p=0.0378$) and chest pain ($p=0.01002)$:

	Positive	Negative
Had Expectoration	53	2540
No Expectoration	273	9461

	Positive	Negative
Had Chest Pain	51	2610
No Chest Pain	275	9391

Or in bar chart form:

In terms of pathogen factors, we also find a strong significant difference in the consumption of cray fish ($p=0.000017$).

	Positive	Negative
Consumes cray fish	4	15
Does not consume cray fish	322	11989

In summary, we found statistically significant differences between ELISA positive and ELISA negative in the following variables:

• Marital status
• Expectoration
• Chest pain
• Consumption of cray fish

The remaining columns had no statistical significant differences. The breakdown of the remaining columns are included at the end of this document.

Future Work

There is a large difference in the sample sizes, 326 ELISA positive and 12075 ELISA negative. The chi-squared test is very sensitive to sample size which may result in false identification of statistically significant differences. More work needs to be done to take into account the large disparity between sample sizes.

Not all columns have been tested. For example, it may be beneficial to test the durations of symptoms with a t-test. Before doing so, some cleanup of the data is necessary as it is incomplete.

Full Breakdown

Host Factors:

Sex_of_the_study_participant p-value: 0.6600516932794341

	Positive	Negative
Female	180	6345
Male	146	5654
Transgender	0	5

Marital_status_of_the_participant p-value: 0.010338783754939688

	Positive	Negative
Married	305	11574
Unmarried	21	430

Religion_of_the_participant p-value: 0.8420839699727036

	Positive	Negative
Chistianity	0	5
Hindu	325	11941
Islam	1	58

Belongs_to_tribal_community p-value: 1.0

	Positive	Negative
No	326	12004

Educational_qualification_of_the_study_participant p-value: 0.1896305167122306

	Positive	Negative
Graduate/Degree/Diploma	74	2558
Illiterate	90	3004
Post-graduate	72	2439
Secondary	90	4003

Occupation_of_the_study_participant p-value: 0.07118126521529632

	Positive	Negative
Agri. Laborer	38	1222
Construction laborer	26	1050
Forest products	12	483
Housewife	1	42
Livestock	0	14
MNREGA work only	18	455
Others	1	13
Own cultivation	1	129
Own cultivation and laborer	70	1882
Private	2	63
Small business/Petti/Tea shop	30	986
Student	127	5665

Which_health_facility_do_you_access_when_you_are_sick p-value: 0.5154638395142579

	Positive	Negative
Government	300	10992
Health centers run by NGO	0	44
Private	25	841
Self-treatment	0	39
Traditional healer	1	88

Have_you_had_Cough p-value: 0.37789035913987745

	Positive	Negative
No	242	8556
Yes	84	3352

Have_you_had_Expectoration p-value: 0.037877357849456596

	Positive	Negative
No	273	9461
Yes	53	2540

Have_you_had_Chest_pain p-value: 0.010026969615090838

	Positive	Negative
No	275	9391
Yes	51	2610

Have_you_had_fever p-value: 1.0

	Positive	Negative
No	3	105
Yes	323	11896

Have_you_lost_appetite p-value: 0.15609852522410084

	Positive	Negative
No	300	10732
Yes	26	1269

Have_you_had_blood_in_sputum p-value: 0.430210821210259

	Positive	Negative
No	326	11947
Yes	0	54

Have_you_had_night_sweats p-value: 0.6305612868045478

	Positive	Negative
No	282	10248
Yes	44	1753

Have_you_lost_weight p-value: 1.0

	Positive	Negative
No	315	11595
Yes	10	386

Have_you_had_shortness_of_breath p-value: 0.22037504598491625

	Positive	Negative
No	267	9474
Yes	59	2527

Have_you_had_tiredness p-value: 0.8687320660144218

	Positive	Negative
No	252	9342
Yes	74	2659

Other_symptoms p-value: 1.0

	Positive	Negative
No	325	11951
Yes	1	50

Have_you_taken_any_treatment_or_actions p-value: 0.6159132422548381

	Positive	Negative
No	312	11597
Yes	0	38

Have_you_ever_been_treated_for_TB p-value: 0.6160488670397868

	Positive	Negative
No	312	11600
Yes Currently on ATT	0	38

Pathogen Factors:

Consumption_of_fresh_water_crabs p-value: 1.0

	Positive	Negative
No	0	5
Yes	326	11999

Duration_of_consumption_of_fresh_water_crabs p-value: 0.6758771337543388

	Positive	Negative
1-3 years	0	3
3-11 months	0	2
<3 months	0	51
>5 years	326	11948

Frequency_of_consumption_of_fresh_water_crabs p-value: 0.22952043999118324

	Positive	Negative
More than once in a week	18	511
Occasionally	37	1135
Once in a month	19	961
Once in a week	252	9397

Raw_fresh_water_crabs p-value: 1.0

	Positive	Negative
No	315	11585
Yes	11	419

Roasted_fresh_water_crabs p-value: 0.32006920638339187

	Positive	Negative
No	324	11980
Yes	2	24

Smoked_fresh_water_crabs p-value: 1.0

	Positive	Negative
No	326	12002
Yes	0	2

Soup_fresh_water_crabs p-value: 0.3020510534208001

	Positive	Negative
No	5	101
Yes	321	11903

Pickled_fresh_water_crabs p-value: 1.0

	Positive	Negative
No	326	12004

Cooked_fresh_water_crabs p-value: 1.0

	Positive	Negative
No	0	5
Yes	260	9231

Consumption_of_cray_fishes p-value: 1.78890200369268e-05

	Positive	Negative
No	322	11989
Yes	4	15

Duration_of_consumption_of_cray_fishes p-value: 1.0

	Positive	Negative
1-3 years	3	15

Frequency_of_consumption_of_cray_fishes p-value: 1.0

	Positive	Negative
Occasionally	3	15

Raw_cray_fish p-value: 1.0

	Positive	Negative
No	326	12004

Roasted_cray_fish p-value: 1.0

	Positive	Negative
No	326	12004

Smoked_cray_fish p-value: 1.0

	Positive	Negative
No	326	12004

Soup_cray_fish p-value: 1.0

	Positive	Negative
No	325	11985
Yes	1	19

Pickled_cray_fish p-value: 1.0

	Positive	Negative
No	326	12004

Cooked_cray_fish p-value: 1.0

	Positive	Negative
No	326	12004

Consumption_of_wlid_boar_meat p-value: 0.06804177212239208

	Positive	Negative
No	323	11975
Yes	3	29

Duration_of_consumption_of_wild_boar_meat p-value: 0.9585895848817743

	Positive	Negative
1-3 years	0	1
3-11 months	0	1
<3 months	0	1
>5 years	3	29

Frequency_of_consumption_of_wild_boar_meat p-value: 1.0

	Positive	Negative
Occasionally	3	31
Once in a month	0	1

Raw_wild_boar_meat p-value: 1.0

	Positive	Negative
No	260	9236

Roasted_wild_boar_meat p-value: 1.0

	Positive	Negative
No	260	9236

Smoked_wild_boar_meat p-value: 1.0

	Positive	Negative
No	260	9236

Soup_wild_boar_meat p-value: 1.0

	Positive	Negative
No	260	9236

Pickled_wild_boar_meat p-value: 1.0

	Positive	Negative
No	260	9236

Cooked_wild_boar_meat p-value: 1.0

	Positive	Negative
No	260	9233
Yes	0	3

Consumption_of_Rodents_Rats_etc p-value: 1.0

	Positive	Negative
No	260	9236

Duration_of_consumption_of_rodents p-value: error

Positive	Negative

Frequency_of_consumption_of_rodents p-value: error

Positive	Negative

Raw_rodents p-value: 1.0

	Positive	Negative
No	260	9236

Roasted_rodents p-value: 1.0

	Positive	Negative
No	260	9236

Smoked_rodents p-value: 1.0

	Positive	Negative
No	260	9236

Soup_rodents p-value: 1.0

	Positive	Negative
No	260	9236

Pickled_rodents p-value: 1.0

	Positive	Negative
No	260	9236

Cooked_rodents p-value: 1.0

	Positive	Negative
No	260	9236