Updated sample/tutorial files

documentation/gitbook/development/python-guidelines-for-developers.md

@@ -65,15 +65,15 @@ For more details on how to use `pytest` please refer to their [usage guide](http
 
 ### Formatting
 
-We try to remain close to Python conventions and to follow the updated rules and best practices. For formatting, we use [black](https://github.com/psf/black), the _Uncompromising Code Formatter_ before submitting pull requests. It provides a consistent style, which is useful when diffing. We use a custom length of 92 characters as the baseline is short for scientific code. Here is the line to use to format your code:
+We try to remain close to Python conventions and to follow the updated rules and best practices. For formatting, we use [black](https://github.com/psf/black), the _Uncompromising Code Formatter_ before submitting pull requests. It provides a consistent style, which is useful when diffing. To get started with black please refer to their [Getting Started guide](https://black.readthedocs.io/en/stable/getting_started.html). We use a custom length of 92 characters as the baseline is short for scientific code. Here is the line to use to format your code:
 
 ```bash
 black --line-length 92 \
     --extend-exclude 'flepimop/gempyor_pkg/src/gempyor/steps_rk4.py' \
     --verbose .
 ```
 
-For those using a Mac or Linux system for development this command is also available for use by calling `./dev/lint`. Similarly, you can take advantage of the formatting pre-commit hook found at `bin/pre-commit`. To start using it copy this file to your git hooks folder:
+For those using a Mac or Linux system for development this command is also available for use by calling `./bin/lint`. Similarly, you can take advantage of the formatting pre-commit hook found at `bin/pre-commit`. To start using it copy this file to your git hooks folder:
 
 ```bash
 cp -f bin/pre-commit .git/hooks/

examples/tutorials/README.md

@@ -1 +1,3 @@
 # flepimop_sample
+
+This repository mirrors the contents in the **examples/tutorial** folder of the FlepiMoP repository ([link](https://github.com/HopkinsIDD/flepiMoP/tree/main/examples/tutorials)). It can be used to try out running simple projects using `flepimop` code and as a template for new projects. 

examples/tutorials/config_sample_2pop_inference.yml

@@ -90,7 +90,7 @@ seir_modifiers:
       method: SinglePeriodModifier
       parameter: Ro
       period_start_date: 2020-05-01
-      period_end_date: 2020-07-01
+      period_end_date: 2020-08-31
       subpop: "all"
       value: 
         distribution: truncnorm
@@ -145,7 +145,7 @@ outcome_modifiers:
     # assume that due to limitations in testing, initially the case detection probability was lower
     test_limits:
       method: SinglePeriodModifier
-      parameter: incidCase
+      parameter: incidCase::probability
       subpop: "all"
       period_start_date: 2020-02-01
       period_end_date: 2020-06-01

examples/tutorials/config_sample_2pop_modifiers.yml

@@ -61,7 +61,7 @@ seir_modifiers:
       method: SinglePeriodModifier
       parameter: Ro
       period_start_date: 2020-05-01
-      period_end_date: 2020-07-01
+      period_end_date: 2020-08-31
       subpop: "all"
       value: 0.8
     Ro_all:
@@ -105,7 +105,7 @@ outcome_modifiers:
     # assume that due to limitations in testing, initially the case detection probability was lower
     test_limits:
       method: SinglePeriodModifier
-      parameter: incidCase
+      parameter: incidCase::probability
       subpop: "all"
       period_start_date: 2020-02-01
       period_end_date: 2020-06-01

examples/tutorials/config_sample_2pop_vaccine_scenarios.yml

@@ -0,0 +1,168 @@
+name: sample_2pop
+setup_name: minimal
+start_date: 2020-02-01
+end_date: 2020-08-31
+nslots: 10
+
+subpop_setup:
+  geodata: model_input/geodata_sample_2pop.csv
+  mobility: model_input/mobility_sample_2pop.csv
+
+initial_conditions:
+  method: SetInitialConditions
+  initial_conditions_file: model_input/ic_2pop.csv
+  allow_missing_subpops: TRUE
+  allow_missing_compartments: TRUE
+
+compartments:
+  infection_stage: ["S", "E", "I", "R", "V"]
+
+seir:
+  integration:
+    method: rk4
+    dt: 1
+  parameters:
+    sigma:
+      value: 1 / 4
+    gamma:
+      value: 1 / 5
+    Ro:
+      value: 
+        distribution: truncnorm
+        mean: 2.5
+        sd: 0.1
+        a: 1.1
+        b: 3
+    omega_pess:
+        value: 0.02
+    omega_opt:
+        value: 0.01
+    nu_pess: 
+        value: 0.01
+    nu_opt: 
+        value: 0.03
+  transitions:
+    #infections
+    - source: ["S"]
+      destination: ["E"]
+      rate: ["Ro * gamma"]
+      proportional_to: [["S"],["I"]]
+      proportion_exponent: ["1","1"]
+    # progression to infectiousness
+    - source: ["E"]
+      destination: ["I"]
+      rate: ["sigma"]
+      proportional_to: ["E"]
+      proportion_exponent: ["1"]
+    # recovery
+    - source: ["I"]
+      destination: ["R"]
+      rate: ["gamma"]
+      proportional_to: ["I"]
+      proportion_exponent: ["1"]
+    #vaccination (offers complete protection)
+    - source: ["S"]
+      destination: ["V"]
+      rate: ["nu_pess + nu_opt"]
+      proportional_to: ["S"]
+      proportion_exponent: ["1"]
+    # waning of vaccine-induced protection
+    - source: ["V"]
+      destination: ["S"]
+      rate: ["omega_pess + omega_opt"]
+      proportional_to: ["V"]
+      proportion_exponent: ["1"]
+
+seir_modifiers:
+  scenarios:
+    - no_vax
+    - pess_vax
+    - opt_vax
+  modifiers:
+    pess_vax_nu: # turn off nu_opt, only nu_pess left
+      method: SinglePeriodModifier
+      parameter: nu_opt
+      period_start_date: 2020-02-01
+      period_end_date: 2020-08-31
+      subpop: "all"
+      value: 0
+    pess_vax_wane: # turn off omega_opt, only omega_pess left
+      method: SinglePeriodModifier
+      parameter: omega_opt
+      period_start_date: 2020-02-01
+      period_end_date: 2020-08-31
+      subpop: "all"
+      value: 0
+    pess_vax: # turn off all vaccination
+      method: StackedModifier
+      modifiers: ["pess_vax_nu","pess_vax_wane"]
+    opt_vax_nu: # turn off nu_pess, only nu_opt left
+      method: SinglePeriodModifier
+      parameter: nu_pess
+      period_start_date: 2020-02-01
+      period_end_date: 2020-08-31
+      subpop: "all"
+      value: 0
+    opt_vax_wane: # turn off omega_pess, only omega_opt left
+      method: SinglePeriodModifier
+      parameter: omega_pess
+      period_start_date: 2020-02-01
+      period_end_date: 2020-08-31
+      subpop: "all"
+      value: 0
+    opt_vax: # turn off all vaccination
+      method: StackedModifier
+      modifiers: ["opt_vax_nu","opt_vax_wane"]
+    no_vax: # turn off all vaccination
+      method: StackedModifier
+      modifiers: ["pess_vax","opt_vax"]
+
+
+
+outcomes:
+  method: delayframe
+  outcomes:
+    incidCase: #incidence of detected cases
+      source:
+        incidence:
+          infection_stage: "I"
+      probability:
+        value: 
+          distribution: truncnorm
+          mean: 0.5
+          sd: 0.05
+          a: 0.3
+          b: 0.7
+      delay:
+        value: 5
+    incidHosp: #incidence of hospitalizations
+      source:
+        incidence:
+          infection_stage: "I"
+      probability:
+        value: 0.05
+      delay:
+        value: 7
+      duration:
+        value: 10
+        name: currHosp # will track number of current hospitalizations (ie prevalence)
+    incidDeath: #incidence of deaths
+      source: incidHosp
+      probability:
+        value: 0.2
+      delay:
+        value: 14
+
+# outcome_modifiers:
+#   scenarios:
+#     - test_limits
+#   modifiers:
+#     # assume that due to limitations in testing, initially the case detection probability was lower
+#     test_limits:
+#       method: SinglePeriodModifier
+#       parameter: incidCase::probability
+#       subpop: "all"
+#       period_start_date: 2020-02-01
+#       period_end_date: 2020-06-01
+#       value: 0.5
+