HIV disease transmission within relationships report¶
The HIV relationship transmission report is a CSV-formatted output file which provides detailed information about each transmission event and relationship members, evaluated at the time of disease transmission within the relationship. Includes the time/date of transmission and information about the transmitter and recipient (age, gender, current and lifetime number of relationships, infection stage, circumcision status for males, co-infections, and disease- specific biomarkers if applicable). The filename is TransmissionReport.csv.
To generate the report, set the configuration parameter Report_Transmission to 1.
Report structure and data channel descriptions¶
The file contains the following data channels:
Data channel |
Data type |
Description |
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SIM_TIME |
integer |
The time in days during the simulation that the infection was transmitted. |
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YEAR |
float |
The time of the simulation time-steps in units of calendar year. For STI simulations, this is the simulation time divided by 365. For HIV simulations, this is the simulation time divided by 365 plus the configuration parameter Base_Year. |
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NODE_ID |
integer |
The identifying number of the node. |
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SRC_ID |
integer |
The unique identifying number of the transmitting individual. |
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SRC_INFECTED |
boolean |
Describes whether or not the transmitting individual is infected; 0 for not infected, 1 for infected. |
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SRC_GENDER |
enum |
Describes the gender of the transmitting individual: 0 for male, 1 for female. |
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SRC_AGE |
float |
The age of the transmitting individual, in days (including fractions of time). |
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SRC_current_relationship_count |
integer |
The total number of relationships (of all types) that the transmitting individual was in at the time of transmission. |
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SRC_lifetime_relationship_count |
integer |
The total number of relationships (of all types) that the transmitting individual has had until the current time. |
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SRC_relationships_in_last_6_months |
integer |
The number of relationships (of all types) that the transmitting individual has had in the previous 6 months. |
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SRC_FLAGS |
enum |
Indicates which types of relationships that individuals are allowed to have when they have more than one active relationship. These are encoded in a 3-digit bitmask. In order, the digits correspond to commercial, marital, informal, and transitory relationships. The following table lists some of the possible combinations:
|
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SRC_CIRCUMCISED |
boolean |
Describes whether or not the transmitting individual is circumcised; 0 for not circumcised, 1 for circumcised. |
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SRC_STI |
boolean |
Describes whether or not the transmitting individual has an STI co-infection. 0 for no STI co-infection, 1 for having an STI co-infection at the time of the transmission event. |
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SRC_SUPERSPREADER |
boolean |
Describes whether or not the transmitting individual is a superspreader. 0 for not a superspreader, 1 for the transmitting individual is a superspreader. Whether or not an individual is a superspreader is determined by the demographics parameter Probability_Person_Is_Behavioral_Super_Spreader. |
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SRC_INF_AGE |
integer |
Not currently supported; this will always display as -42. |
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DEST_ID |
integer |
The unique identifying number of the infected individual. |
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DEST_INFECTED |
boolean |
Describes whether or not the receiving individual is infected. 0 for not infected, 1 for infected (this should always be 1). |
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DEST_GENDER |
enum |
Describes the gender of the receiving individual: 0 for male, 1 for female. |
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DEST_AGE |
float |
The age of the receiving individual, in days (including fractions of time). |
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DEST_current_relationship_count |
integer |
The total number of relationships (of all types) that the receiving individual was in at the time of transmission. |
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DEST_lifetime_relationship_count |
integer |
The total number of relationships (of all types) that the receiving individual has had until the current time. |
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DEST_relationships_in_last_6_months |
integer |
The number of relationships (of all types) that the receiving individual has had in the previous 6 months. |
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DEST_FLAGS |
enum |
Indicates which types of relationships that individuals are allowed to have when they have more than one active relationship. See SRC_FLAGS for an explanation of the bitmask. |
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DEST_CIRCUMCISED |
boolean |
Describes whether or not the receiving individual is circumcised; 0 for not circumcised, 1 for circumcised. |
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DEST_STI |
boolean |
Describes whether or not the receiving individual has an STI co-infection. 0 for no STI co-infection, 1 for having an STI co-infection at the time of the transmission event. |
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DEST_SUPERSPREADER |
boolean |
Describes whether or not the receiving individual is a superspreader. 0 for not a superspreader, 1 for the transmitting individual is a superspreader. Whether or not an individual is a superspreader is determined by the demographics parameter Probability_Person_Is_Behavioral_Super_Spreader. |
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SRC_CD4 |
float |
The current CD4 count of the transmitting individual. This column will be included for HIV simulations only. |
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SRC_VIRAL_LOAD |
float |
Not currently supported; 10000 implies that the individual is infected. This column will be included for HIV simulations only. |
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SRC_STAGE |
enum |
The stage of infection for the transmitting indivdiual. 0 for uninfected, 1 for untreated acute HIV, 2 for untreated latent HIV, 3 for untreated late/AIDS stage, 4 for on ART, -1 implies the transmitting individual does not have HIV. This column will be included for HIV simulations only. |
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DEST_CD4 |
float |
The current CD4 count of the receiving individual. This column will be included for HIV simulations only. |
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DEST_VIRAL_LOAD |
float |
Not currently supported; 10000 implies that the individual is infected. This column will be included for HIV simulations only. |
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DEST_STAGE |
enum |
The stage of infection for the receiving individual. 0 for uninfected, 1 for untreated acute HIV, 2 for untreated latent HIV, 3 for untreated late/AIDS stage, 4 for on ART, -1 implies the receiving individual does not have HIV. This column will be included for HIV simulations only. |
Example¶
The following is an example of a TransmissionReport.csv report:
SIM_TIME |
YEAR |
NODE_ID |
SRC_ID |
SRC_INFECTED |
SRC_GENDER |
SRC_AGE |
SRC_current_relationship_count |
SRC_lifetime_relationship_count |
SRC_relationships_in_last_6_months |
SRC_FLAGS |
SRC_CIRCUMSIZED |
SRC_STI |
SRC_SUPERSPREADER |
SRC_INF_AGE |
DEST_ID |
DEST_INFECTED |
DEST_GENDER |
DEST_AGE |
DEST_current_relationship_count |
DEST_lifetime_relationship_count |
DEST_relationships_in_last_6_months |
DEST_FLAGS |
DEST_CIRCUMSIZED |
DEST_STI |
DEST_SUPERSPREADER |
SRC_CD4 |
SRC_VIRAL_LOAD |
SRC_STAGE |
DEST_CD4 |
DEST_VIRAL_LOAD |
DEST_STAGE |
7320 |
2020.05 |
1 |
3304 |
1 |
1 |
21039 |
4 |
17 |
2 |
15 |
0 |
0 |
1 |
-42 |
8 |
1 |
0 |
11427.9 |
5 |
18 |
1 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
10102 |
1 |
0 |
7140 |
2 |
11 |
0 |
15 |
0 |
0 |
1 |
-42 |
254 |
1 |
1 |
27166 |
2 |
11 |
0 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
305 |
1 |
1 |
15460.5 |
2 |
11 |
0 |
15 |
0 |
0 |
1 |
-42 |
376 |
1 |
0 |
24153.8 |
5 |
14 |
1 |
15 |
0 |
0 |
1 |
530.289 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
4067 |
1 |
0 |
20249.3 |
2 |
14 |
1 |
15 |
0 |
0 |
1 |
-42 |
400 |
1 |
1 |
10791.4 |
3 |
11 |
0 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
8806 |
1 |
1 |
19393.9 |
3 |
15 |
1 |
15 |
0 |
0 |
1 |
-42 |
401 |
1 |
0 |
11479 |
3 |
13 |
1 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
5277 |
1 |
0 |
16866.5 |
2 |
12 |
0 |
15 |
0 |
0 |
1 |
-42 |
675 |
1 |
1 |
18830.7 |
3 |
18 |
1 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
9690 |
1 |
1 |
22120.2 |
2 |
13 |
0 |
15 |
0 |
0 |
1 |
-42 |
694 |
1 |
0 |
22312.4 |
2 |
15 |
0 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
9786 |
1 |
1 |
25615.4 |
2 |
18 |
0 |
15 |
0 |
0 |
1 |
-42 |
1038 |
1 |
0 |
23414.3 |
2 |
18 |
1 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
2791 |
1 |
0 |
13911.6 |
3 |
12 |
0 |
15 |
0 |
0 |
1 |
-42 |
1202 |
1 |
1 |
24019.9 |
2 |
14 |
0 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
1309 |
1 |
1 |
22660 |
5 |
16 |
2 |
15 |
0 |
0 |
1 |
-42 |
1219 |
1 |
0 |
8558.16 |
4 |
17 |
0 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
13319 |
1 |
0 |
2190 |
4 |
7 |
2 |
15 |
0 |
0 |
1 |
-42 |
1296 |
1 |
1 |
22208.7 |
3 |
13 |
1 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
13396 |
1 |
1 |
2070 |
2 |
3 |
0 |
15 |
0 |
0 |
1 |
-42 |
1394 |
1 |
0 |
15821.8 |
2 |
19 |
0 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
172 |
1 |
1 |
16421.3 |
2 |
17 |
0 |
15 |
0 |
0 |
1 |
-42 |
1562 |
1 |
0 |
17737.1 |
2 |
15 |
0 |
15 |
0 |
0 |
1 |
532.182 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
13657 |
1 |
1 |
1740 |
3 |
8 |
0 |
15 |
0 |
0 |
1 |
-42 |
1909 |
1 |
0 |
24805.4 |
2 |
14 |
0 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
1665 |
1 |
1 |
13339.3 |
3 |
19 |
0 |
15 |
0 |
0 |
1 |
-42 |
1968 |
1 |
0 |
23197.1 |
2 |
16 |
0 |
15 |
0 |
0 |
1 |
502.227 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
2999 |
1 |
1 |
23923.2 |
2 |
18 |
0 |
15 |
0 |
0 |
1 |
-42 |
1991 |
1 |
0 |
13858.2 |
3 |
17 |
0 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
1788 |
1 |
1 |
9191.84 |
2 |
10 |
0 |
15 |
0 |
0 |
1 |
-42 |
2124 |
1 |
0 |
24729.1 |
2 |
15 |
0 |
15 |
0 |
0 |
1 |
532.935 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
5205 |
1 |
1 |
10807.5 |
3 |
18 |
1 |
15 |
0 |
0 |
1 |
-42 |
2329 |
1 |
0 |
19987.5 |
3 |
16 |
1 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
2724 |
1 |
0 |
10120.4 |
3 |
17 |
0 |
15 |
0 |
0 |
1 |
-42 |
2618 |
1 |
1 |
13123.5 |
5 |
23 |
2 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |
7320 |
2020.05 |
1 |
6458 |
1 |
1 |
16463.5 |
4 |
21 |
0 |
15 |
0 |
0 |
1 |
-42 |
2836 |
1 |
0 |
16741.4 |
4 |
23 |
0 |
15 |
0 |
0 |
1 |
540.55 |
10000 |
1 |
540.55 |
10000 |
1 |