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complexities_surv_act.qmd
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## Surveillance Activities
Initially, it was mentioned that "**Field Visits, Locations, Events, Sources, Source Records, and Diagnostics usually belong to a single Surveillance Activity**. This is the Surveillance Activity that lead to the Field Visits at different Locations to document Events, collect Sources and Specimens, perform Diagnostics for a specific hazard, and provide Diagnosis for Diagnostics, Specimens, and Sources".
Furthermore, it was established that "**a Surveillance Activity usually includes Field Visits, Locations, Events, Sources, Source Records, and Diagnostics**".
Here it is explained what are the exceptions to these two general statements and how the data model can handle them.
#### Field Visits up to Specimen belong to two or more Surveillance Activities
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Two or more Surveillance Activities used the exact same methodology except for the Diagnostics (they target different hazards but the diagnostics are conducted using the same specimens). For example, the same rodents are trapped and sampled but they are tested for coronaviruses as part of Surveillance Activity 1 and Rickettsia *sp* as part of Surveillance Activity 2. In this case the Field Visits, Locations, Events, Collections, Source Records, and Specimens, belong to both Surveillance Activities. Instead, the Diagnostics and Diagnosis belong to one of them only.
#### Field Visits up to Source Records belong to two or more Surveillance Activities
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This can happen when two or more Surveillance Activities overlap in their Field Visits up to Source Records but the Specimens up to Diagnostics are different. For example, the same rodents are trapped and sampled during the same Collection but Surveillance Activity 1 uses rectal swabs to test for coronaviruses whilst Surveillance Activity 2 uses blood for Rickettsia *sp*. In this case the Field Visits, Locations, Events, Collections, and Source Records belong to both Surveillance Activities. Instead, the Specimens, Diagnostics, and Diagnosis belong to one of them only.
#### Field Visits up to Collections belong to two or more Surveillance Activities
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This can happen when two or more Surveillance Activities overlap in their Field Visits up to Collections but the Source Records up to Diagnostics are different. For example, bats are collected using the same mist nets; however, only Megabats are tested for Ebola as part of Surveillance Activity 1. Instead, only Microbats are tested for coronaviruses as part of Surveillance Activity 2. In this case the Field Visits, Locations, Events, and Collections belong to both Surveillance Activities. The Source Records, Specimens, Diagnostics, and Diagnosis belong to one of them only.
#### Field Visits up to Events belong to two or more Surveillance Activities
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This can happen when two or more Surveillance Activities overlap in their Field Visits up to Events, but the Collection up to Diagnostics are different because they have different goals. For example, water is collected from Event A as part of Surveillance Activity 1 and a mosquitos are also collected from Event A as part of Surveillance Activity 2. In this case the Field Visits, Locations, and Events belong to both Surveillance Activities. Instead, the Collections, Source Records, Specimens, Diagnostics, and Diagnosis belong to one of them only.
#### Field Visits and to Locations belong to two or more Surveillance Activities
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This can happen when two or more Surveillance Activities overlap in their Field Visits and Locations but the Events up to Diagnostics are different. For example, Surveillance Activity 1 aims to capture bats using mist nets and Surveillance Activity 1 aims to capture rodents. The Field Visit and the Locations could be the same but the capturing of the bats can occur at night and the capture of rodents can occur early morning. In this case the Field Visits and Locations belong to both Surveillance Activities. Instead, the Events, Collections, Source Records, Specimens, Diagnostics, and Diagnosis belong to one of them only.
#### Field Visits belong to two or more Surveillance Activities
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This can happen when two or more Surveillance Activities overlap in their Field Visits but the Locations up to Diagnostics are different. Field Visit can be common because it facilitates logistics. For example, coming back from the forest after collecting chimpanzee urine as part of Surveillance Activity 1 and on the way back, a visit is made to a Rehabilitation Center to sample animals as part of Surveillance Activity 2.
<!-- #### Surveillance Activity contains only Diagnostics and Diagnosis -->
<!-- This can happen when Surveillance Activity 2 uses Specimens collected as part of Surveillance Activity 1 to test them again for the same or different hazard. For example, Specimens from bats collected ten years ago will be used in a new study to test them for SARS-CoV-2. The Diagnostics are the only new entity generated as part of Surveillance Activity 2. -->
<!-- {width=100%} -->
#### Surveillance Activity contains only Specimens and Diagnostics
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This can happen when Surveillance Activity 2 uses Specimens collected as part of Surveillance Activity 1 to test them again for the same or different hazard. For example, Specimens from bats collected ten years ago will be used in a new study to test them for SARS-CoV-2. The Specimen belong to both Surveillance Activities. The Diagnostics are the only new entity generated as part of Surveillance Activity 2, and it is clear that Specimens from Surveillance Activity 1 were used in Surveillance Activity 2.
#### Surveillance Activity contains only Source Records, Specimens, Diagnostics, and Diagnosis
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This can happen when Surveillance Activity 2 generates new Specimens from carcasses of Source Records collected as part of Surveillance Activity 1 and tests these new Specimens for a hazard. For example, carcasses of bats collected ten years ago will be used in a new study, Surveillance Activity 2, to get new Specimens and test them for SARS-CoV-2. The Source Records belong to both Surveillance Activities. The new Specimens and Diagnostics are the only new entities generated as part of Surveillance Activity 2, and it is clear that Source Records (the carcasses in this particular case) from Surveillance Activity 1 were used in Surveillance Activity 2.
<!-- Moreover, Necropsies might be conducted as part of a secondary Surveillance Activity (on a Carcass that was collected under other Surveillance Activity) or new Specimens could be created from a previously unused Carcass as part of a new Surveillance Activity. In this case, the new data (Necropsy and Specimens) should receive the second Surveillance Activity only. Diagnostics using the new Specimens should receive the second Surveillance Activity only. The Carcass should receive the Surveillance Activity that lead to its collection only. -->
#### Same Source in different Surveillance Activities
The health of the same animal could be assessed under different Surveillance Activities. For example, a ranger finds a sick animal in a specific date and assess it health and potential cause of disease as part of Surveillance Activity 1. Then, the animal is taken to a rehabilitation center where its health is assessed again at admission and samples are collected for testing as part of Surveillance Activity 2. Finally, the animal health at the rehabilitation center is assessed again three months later and samples are collected again in order to learn what pathogens are circulating within the facility as part of Surveillance Activity 3.
In this case there are three Projects, Surveillance Activities, Field Visits, Events, and Collections independently of each other. There are two Locations. The Animal Source belongs to three Surveillance Activities. The Source Records and Specimens belong to a single Surveillance Activity just like the Diagnostics completed in Surveillance in Surveillance Activity 2 and 3.
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Therefore, Surveillance Activities can be interconnected through common units or the reuse of units generated by previous Surveillance Activities.
#### Sources in Surveillance Activity but not Present in any Event
Studies that track marked individuals over time could succeed in capturing all individually identified animals, so all these Sources are included as Source Records at least once during the study period. However, it is also possible that only a proportion of the individualized Sources are captured or sight during the Surveillance Activity, so these Sources are not present as Source Record of any Event. For the second possibility, it is still important to track the Sources that were part of the sampling frame and censoring them when they were nor part of any Event.
For this reason, the data model can assigned a Surveillance Activity to a Source without including any Field Visits, Location, Event, or Collection. When the study is completed, it will be possible to identify all the Sources involved in the study including those that were never captured (Source 3 in the figure below).
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#### Outbreak Investigation
An outbreak can contains elements associated with two or more Surveillance Activities. For example, the first detection of the outbreak could have been done by a citizen or by rangers patrolling a protected area. The Field Activity, Location, Event, Collection (if any), Source Records, and Specimens collected when the Outbreak is discovered belong to the "Citizen Science" or "Ranger Patrol" Surveillance Activity. However, they also belong to the "Outbreak Investigation" Surveillance Activity, together with Field Activities up to the Diagnostics associated exclusively with the Outbreak Investigation.
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#### From Group Source to Animal Source
The data model can handle the conversion of an individual in a Group Source into an Animal Source. Animal Sources have a property to identify them as previous members of a Group Source.
The decision to convert an individual of a Group Source into an Animal Source could occur because: i) it was decided to start recording animals of a Group Source at the individual level including their Specimens and Diagnostics, ii) field Necropsies are conducted with the Carcasses of animals that belong to a Group Source (Necropsy data in the data model are linked to individual animals only), iii) all or some Carcasses of a Group Source are collected and stored or exported (Carcass data in the data model are linked to individual animals only), and iv) Necropsies are conducted with the Carcasses of animals belonging to a Group Source in a facility and again, Necropsy data in the data model are linked to individual animals only. The **data model accepts Diagnostics conducted directly on a Group Source or Diagnostics conducted using Group Source Specimens**, such as body condition in the overall Groups or testing feces taken from a cage occupied by 2 animals of the same species. Therefore, in these cases, it is not necessary to convert individuals of a Group Source to Animal Sources.
In the first case, all or some of the animals of a Group Source could start being recorded at the individual level. If only some of the animals of a Group Source are recorded at the individual level, then it is possible to have an Event at time *t* with Group Source Records and Animal Source Records of animals that belonged to the Group Source at time *t'* that are considered Animal Sources at time *t*. The original Group Source does not include the animals that are converted to Animal Sources since time *t*. Therefore, the count of individuals in the Group Source Record must not include the new Animal Sources. It is also possible that starting at time *t* in a new Field Activity, all the animals of a Group Source are recorded as Animal Sources. In this case there are no more records of the Group Source since time *t*.
In the second case, a Necropsy conducted with the Carcass of an animal of a Group Source leads to the same process explained in the previous paragraph. The animal must be documented at the individual level because, in the data model, **Necropsy data are tied to Animal Sources only**.
Lastly, the collection of a Carcass of an animal of a Group Source and potential subsequent Necropsies also leads to the same process. The animal of a Group Source must be documented at the individual level because, in the data model, **Carcass and Necropsy data are tied to Animal Sources only**.
It is important to highlight that: **conversion from an individual of a Group Source to Animal Source is complete and irreversible**. This means that new Animal Source Records cannot be included in the count of animals in a Group Source, Animal Sources cannot be converted back to be part of the Group Source, and Specimens of the new Animal Sources are not Specimens of the original Group Source. Secondly, when it is decided that animals in a Group Source will be documented as Animal Sources there is a change of methodology and, most likely, the new Animal Sources should receive a new and single Surveillance Activity. It is possible to keep a connection between these Surveillance Activities in the data model (between the Group Source only one and the Groups Source - Animal Sources one). Animal sources have a property to link them to their original Group Source also. It is possible that the original Surveillance Activity methodology included an eventual change in the recording of animals in a Group Source as Animal Sources and, consequently, only a common unique Surveillance Activity is enough.