21  :orange_book: Malaria case study - Report #1

21.1 Introduction

21.1.1 Instructions

The data set used for this report is stored in dataset2.dta or dataset2.xlsx or dataset2.csv.

  1. Derive new variables to data frame df
  2. Describe and critically discuss the distribution of consultations by facilities depending on their characteristics (urban vs. rural, health centre vs. dispensary, district)
  3. Describe and critically discuss the demographics, clinical presentation and clinical history of patients.
  4. Describe and critically discuss the clinical assessments (fever assessment, malaria test) conducted during the consultation.
Extract of the database
child_ID CTX_month CTX_district SDC_age_in_months
1 7 Kaliua 10
2 7 Kaliua 6
3 7 Kaliua 6
4 7 Kaliua 11
5 8 Kaliua 21

21.1.2 Codebook

21.1.2.1 Numerical variables

Variable
SDC_age_in_months
CLIN_fever_onset
MEAS_temperature

21.1.2.2 Categorical variables

Variable Coding
SDC_sex

1: male

2: female

98: unknown
CLIN_fever

0: no

1: yes

98: not sure
CLIN_cough

0: no

1: yes

98: not sure
CLIN_diarrhoea

0: no

1: yes

98: not sure
RX_preconsult_antibiotics

0: no

1: yes
RX_preconsult_antimalarials

0: no

1: yes
CTX_district

Kaliua

Sengerema

Tanga
CTX_area

urban

rural
CTX_facility_type

dispensary

health centre
TEST_malaria_result 0: negative
1: positive
2: indeterminate
95: unreadable result
98: not sure
DX_malaria 0: no
1: yes
DX_malaria_severe 0: no
1: yes
RX_antimalarials 0: no
1: yes
RX_artemether 0: no
1: yes
RX_antibiotics 0: no
1: yes
MGMT_referral_src_caregiver
MGMT_referral_src_registry

21.1.3 Derive new variables

Add the following two new variables to data frame df

Variable Coding
SDC_age_category

<2 months

2-11 months

12-23 months

24-35 months

36-47 months

48-59 months
CLIN_fever_onset_category

<2 days

2-3 days

4-6 days

≥ 7 days

21.1.4 Structure of the data

Data summary
Name Piped data
Number of rows 10308
Number of columns 40
_______________________
Column type frequency:
factor 9
numeric 2
________________________
Group variables None

Variable type: factor

skim_variable n_missing complete_rate ordered n_unique top_counts
SDC_sex 4 1 FALSE 2 1: 5229, 2: 5075
CLIN_fever 0 1 FALSE 3 1: 7225, 0: 3068, 98: 15
CLIN_diarrhoea 0 1 FALSE 3 0: 7982, 1: 2306, 98: 20
CLIN_cough 0 1 FALSE 3 1: 5635, 0: 4658, 98: 15
RX_preconsult_antibiotics 0 1 FALSE 2 0: 8573, 1: 1735
RX_preconsult_antimalarials 0 1 FALSE 2 0: 9866, 1: 442
CTX_district 0 1 FALSE 3 Tan: 5176, Sen: 2703, Kal: 2429
CTX_area 0 1 FALSE 2 urb: 6220, rur: 4088
CTX_facility_type 0 1 FALSE 2 dis: 5599, hea: 4709

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
SDC_age_in_months 0 1.0 18.75 14.90 0 7 15 27 59 ▇▆▃▂▁
CLIN_fever_onset 3083 0.7 2.50 1.93 0 1 2 3 14 ▇▅▁▁▁
Data summary
Name Piped data
Number of rows 10308
Number of columns 43
_______________________
Column type frequency:
factor 12
numeric 1
________________________
Group variables None

Variable type: factor

skim_variable n_missing complete_rate ordered n_unique top_counts
TEST_malaria_done 0 1.00 FALSE 2 1: 5763, 0: 4545
TEST_malaria_type 4550 0.56 FALSE 4 1: 5371, 2: 340, 98: 45, 95: 2
TEST_malaria_result 4550 0.56 FALSE 5 0: 4665, 1: 1032, 98: 57, 95: 3
DX_severe 0 1.00 FALSE 2 0: 10054, 1: 254
DX_malaria 0 1.00 FALSE 2 0: 8508, 1: 1800
DX_malaria_severe 0 1.00 FALSE 2 0: 10160, 1: 148
RX_antimalarials 0 1.00 FALSE 2 0: 9018, 1: 1290
RX_antimalarial_parenteral 0 1.00 FALSE 2 0: 10059, 1: 249
RX_artemether 0 1.00 FALSE 2 0: 10248, 1: 60
RX_antibiotics 0 1.00 FALSE 2 1: 5430, 0: 4878
MGMT_referral_src_caregiver 0 1.00 FALSE 4 0: 10122, 1: 164, 98: 13, 97: 9
MGMT_referral_src_registry 0 1.00 FALSE 2 0: 10194, 1: 114

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
MEAS_temperature 9271 0.1 37.08 0.98 34.5 36.5 37 37.5 42.5 ▃▇▃▁▁

21.2 Facility characteristics

Describe and critically discuss the distribution of consultations by facilities depending on their characteristics (urban vs. rural, health centre vs. dispensary, district)

Characteristic N = 10,3081
CTX_facility_type
    dispensary 5,599 (54%)
    health center 4,709 (46%)
CTX_area
    rural 4,088 (40%)
    urban 6,220 (60%)
CTX_district
    Kaliua 2,429 (24%)
    Sengerema 2,703 (26%)
    Tanga 5,176 (50%)
1 n (%)

21.2.1 Urban / rural consultations

Describe the distribution of consultations in urban vs. rural facilities

Area Freq
rural 0.3965852
urban 0.6034148

21.2.2 Consultations by type of facility

Describe the distribution of consultations in dispensaries vs. health centres.

Type Freq
dispensary 0.5431704
health center 0.4568296

21.2.3 Consultations by district

Describe the distribution of consultations by district (Kaliua vs. Sengerema vs. tanga)

District Freq
Kaliua 0.2356422
Sengerema 0.2622235
Tanga 0.5021343

21.2.3.1 Number of consultations by facility within each district

Figure 21.1: ?(caption)

21.2.4 Consultations by area, type of facility and district

Area Type District Freq
rural dispensary Kaliua 1475
urban dispensary Kaliua 0
rural health center Kaliua 954
urban health center Kaliua 0
rural dispensary Sengerema 321
urban dispensary Sengerema 486
rural health center Sengerema 994
urban health center Sengerema 902
rural dispensary Tanga 344
urban dispensary Tanga 2973
rural health center Tanga 0
urban health center Tanga 1859

21.3 Patient characteristics

Describe and critically discuss the demographics, clinical presentation and clinical history of patients.

Characteristic N = 10,3081
SDC_age_category
    <2 months 597 (5.8%)
    02-11 months 3,576 (35%)
    12-23 months 2,947 (29%)
    24-35 months 1,529 (15%)
    36-47 months 980 (9.5%)
    48-59 months 679 (6.6%)
SDC_sex
    1 5,229 (51%)
    2 5,075 (49%)
    (Missing) 4
CLIN_fever
    0 3,068 (30%)
    1 7,225 (70%)
    98 15 (0.1%)
CLIN_fever_onset_category
     3,083 (30%)
    < 2 days 1,998 (19%)
    >= 7 days 343 (3.3%)
    2-3 days 4,386 (43%)
    4-6 days 498 (4.8%)
CLIN_diarrhoea
    0 7,982 (77%)
    1 2,306 (22%)
    98 20 (0.2%)
CLIN_cough
    0 4,658 (45%)
    1 5,635 (55%)
    98 15 (0.1%)
RX_preconsult_antibiotics
    0 8,573 (83%)
    1 1,735 (17%)
RX_preconsult_antimalarials
    0 9,866 (96%)
    1 442 (4.3%)
1 n (%)
Characteristic dispensary, N = 5,5991 health center, N = 4,7091
SDC_age_category

    <2 months 290 (5.2%) 307 (6.5%)
    02-11 months 1,888 (34%) 1,688 (36%)
    12-23 months 1,606 (29%) 1,341 (28%)
    24-35 months 859 (15%) 670 (14%)
    36-47 months 570 (10%) 410 (8.7%)
    48-59 months 386 (6.9%) 293 (6.2%)
SDC_sex

    1 2,810 (50%) 2,419 (51%)
    2 2,786 (50%) 2,289 (49%)
    (Missing) 3 1
CLIN_fever

    0 1,710 (31%) 1,358 (29%)
    1 3,881 (69%) 3,344 (71%)
    98 8 (0.1%) 7 (0.1%)
CLIN_fever_onset_category

     1,718 (31%) 1,365 (29%)
    < 2 days 1,167 (21%) 831 (18%)
    >= 7 days 149 (2.7%) 194 (4.1%)
    2-3 days 2,333 (42%) 2,053 (44%)
    4-6 days 232 (4.1%) 266 (5.6%)
CLIN_diarrhoea

    0 4,457 (80%) 3,525 (75%)
    1 1,135 (20%) 1,171 (25%)
    98 7 (0.1%) 13 (0.3%)
CLIN_cough

    0 2,365 (42%) 2,293 (49%)
    1 3,226 (58%) 2,409 (51%)
    98 8 (0.1%) 7 (0.1%)
RX_preconsult_antibiotics

    0 4,828 (86%) 3,745 (80%)
    1 771 (14%) 964 (20%)
RX_preconsult_antimalarials

    0 5,468 (98%) 4,398 (93%)
    1 131 (2.3%) 311 (6.6%)
1 n (%)

21.3.1 Demographics

21.3.2 Clinical presentation

21.3.2.1 Fever

21.3.2.2 Cough

21.3.2.3 Diarrhoea

21.3.2.4 Combination of symptoms

21.4 Clinical assessments conducted during the consultation

Describe and critically discuss the clinical assessments (fever assessment, malaria test) conducted during the consultation.

Characteristic N = 10,3081
CALC_temperature_measured
    0 9,271 (90%)
    1 1,037 (10%)
CALC_fever_measured
    0 711 (69%)
    1 326 (31%)
    (Missing) 9,271
CALC_fever_all
    0 3,056 (30%)
    1 7,252 (70%)
TEST_malaria_done
    0 4,545 (44%)
    1 5,763 (56%)
TEST_malaria_type
    1 5,371 (93%)
    2 340 (5.9%)
    95 2 (<0.1%)
    98 45 (0.8%)
    (Missing) 4,550
TEST_malaria_result
    0 4,665 (81%)
    1 1,032 (18%)
    2 1 (<0.1%)
    95 3 (<0.1%)
    98 57 (1.0%)
    (Missing) 4,550
DX_severe
    0 10,054 (98%)
    1 254 (2.5%)
DX_malaria
    0 8,508 (83%)
    1 1,800 (17%)
DX_malaria_severe
    0 10,160 (99%)
    1 148 (1.4%)
RX_antimalarials
    0 9,018 (87%)
    1 1,290 (13%)
RX_antimalarial_parenteral
    0 10,059 (98%)
    1 249 (2.4%)
RX_antibiotics
    0 4,878 (47%)
    1 5,430 (53%)
MGMT_referral_src_caregiver
    0 10,122 (98%)
    1 164 (1.6%)
    97 9 (<0.1%)
    98 13 (0.1%)
MGMT_referral_src_registry
    0 10,194 (99%)
    1 114 (1.1%)
1 n (%)
Characteristic dispensary, N = 5,5991 health center, N = 4,7091
CALC_temperature_measured

    0 4,843 (86%) 4,428 (94%)
    1 756 (14%) 281 (6.0%)
CALC_fever_measured

    0 507 (67%) 204 (73%)
    1 249 (33%) 77 (27%)
    (Missing) 4,843 4,428
CALC_fever_all

    0 1,699 (30%) 1,357 (29%)
    1 3,900 (70%) 3,352 (71%)
TEST_malaria_done

    0 2,589 (46%) 1,956 (42%)
    1 3,010 (54%) 2,753 (58%)
TEST_malaria_type

    1 2,836 (94%) 2,535 (92%)
    2 134 (4.5%) 206 (7.5%)
    95 1 (<0.1%) 1 (<0.1%)
    98 34 (1.1%) 11 (0.4%)
    (Missing) 2,594 1,956
TEST_malaria_result

    0 2,414 (80%) 2,251 (82%)
    1 544 (18%) 488 (18%)
    2 0 (0%) 1 (<0.1%)
    95 2 (<0.1%) 1 (<0.1%)
    98 45 (1.5%) 12 (0.4%)
    (Missing) 2,594 1,956
DX_severe

    0 5,540 (99%) 4,514 (96%)
    1 59 (1.1%) 195 (4.1%)
DX_malaria

    0 4,405 (79%) 4,103 (87%)
    1 1,194 (21%) 606 (13%)
DX_malaria_severe

    0 5,579 (100%) 4,581 (97%)
    1 20 (0.4%) 128 (2.7%)
RX_antimalarials

    0 4,923 (88%) 4,095 (87%)
    1 676 (12%) 614 (13%)
RX_antimalarial_parenteral

    0 5,562 (99%) 4,497 (95%)
    1 37 (0.7%) 212 (4.5%)
RX_antibiotics

    0 2,407 (43%) 2,471 (52%)
    1 3,192 (57%) 2,238 (48%)
MGMT_referral_src_caregiver

    0 5,528 (99%) 4,594 (98%)
    1 60 (1.1%) 104 (2.2%)
    97 6 (0.1%) 3 (<0.1%)
    98 5 (<0.1%) 8 (0.2%)
MGMT_referral_src_registry

    0 5,578 (100%) 4,616 (98%)
    1 21 (0.4%) 93 (2.0%)
1 n (%)

21.4.1 Temperature measurement

Distribution of temperature measurements and associated factors

Figure 21.2: Distribution of temperature measurements

Figure 21.3: Distribution of temperature measurements by type of facility

21.4.2 Fever assessment

Distribution of measured fever

Figure 21.4: Proportion of consultations with a temperature superior or equal to 37.5°C among children with a temperature measurement

Figure 21.5: Range of temperature measurements for children with fever (1), without fever (2) and with unkwnown fever presentation (98) by facility
Missing data analysis: MEAS_temperature Not missing Missing p
SDC_age_category <2 months 56 (9.4) 541 (90.6) 0.108
02-11 months 338 (9.5) 3238 (90.5)
12-23 months 293 (9.9) 2654 (90.1)
24-35 months 181 (11.8) 1348 (88.2)
36-47 months 108 (11.0) 872 (89.0)
48-59 months 61 (9.0) 618 (91.0)
CTX_district Kaliua 61 (2.5) 2368 (97.5) <0.001
Sengerema 573 (21.2) 2130 (78.8)
Tanga 403 (7.8) 4773 (92.2)
CTX_area rural 454 (11.1) 3634 (88.9) 0.005
urban 583 (9.4) 5637 (90.6)
CTX_facility_type dispensary 756 (13.5) 4843 (86.5) <0.001
health center 281 (6.0) 4428 (94.0)
CLIN_fever 0 238 (7.8) 2830 (92.2) <0.001
1 796 (11.0) 6429 (89.0)
98 3 (20.0) 12 (80.0)

21.4.3 Malaria tests

0 1
0 264 447
1 44 282

21.4.4 Malaria diagnoses

21.4.5 Malaria treatments

Result Diagnosis Antimalarials Freq
0 0 0 3890
1 0 0 15
2 0 0 1
95 0 0 2
98 0 0 31
0 1 0 645
1 1 0 49
2 1 0 0
95 1 0 1
98 1 0 17
0 0 1 99
1 0 1 50
2 0 1 0
95 0 1 0
98 0 1 2
0 1 1 31
1 1 1 918
2 1 1 0
95 1 1 0
98 1 1 7

21.4.5.1 Combination of treatments

21.5 Data flow from fever assessment to malaria treatment (Sankey diagrams)

21.5.1 Facility F8793

21.5.2 Facility F7729