country iso3c name_1 urban_rural
1 Togo TGO Centre rural
2 Togo TGO Centre urban
3 Togo TGO Kara rural
4 Togo TGO Kara urban
5 Togo TGO Maritime rural
6 Togo TGO Maritime urban
7 Togo TGO Plateaux rural
8 Togo TGO Plateaux urban
9 Togo TGO Savanes rural
10 Togo TGO Savanes urbanMalariaverse Workshop Introduction
Pete Winskill
Welcome all!
Today’s aims:
- Provide a broad overview of context-specific modelling
- Site files: how to characterise a setting
- Introduce the malariaverse packages to support 📦[malariasimulation] modelling
- Exercises:
- Running a site
- Calibrating a site
- Dealing with bed nets
Not today’s aims 😄
- An introduction to the Imperial college malaria model
- Please see key publications
- An introduction to the software packages implementing the model
- 📦[malariasimulation]
- 📦[ICDMM]
- Please see websites and supporting documentation for help
- A comprehensive overview of all malariaverse packages/features
https://mrc-ide.github.io/malariasimulation https://mrc-ide.github.io/deterministic-malaria-model
Thanks 💖
Modelling philosophy
One common dichotomisation is between:
- Generic modelling
- Run the model for generic settings (e.g. Low/Medium/High PfPr2-10)
- Allows precise exploration of model behaviour and intervention impact in controlled in silico environment
- Can be challenging to translate general results
- e.g. Modelling population-level impact to inform target product profiles for childhood malaria vaccines. Hogan et al BMC Medicine, 2018.
Modelling philosophy
One common dichotomisation is between:
- Context-specific modelling
- Run the model for a specific setting/location
- Can be used to inform policy and impact assessment for specific areas
- Requires “the context” to be adequately captured 🤔
- e.g. Estimated impact of RTS,S/AS01 malaria vaccine allocation strategies in sub-Saharan Africa: A modelling study Hogan et al PLoS Medicine, 2020.
How do we characterise a setting?
Important features
- Intrinsic transmission potential (“Baseline”, “Carrying capacity”, “R0”)
- The mosquito vector
- species
- bionomics (how the 🦟 relates to its environment) & behaviour
- distribution & relative abundance
- insecticide resistance
- Rainfall seasonality ☔
- Historical interventions
- Epidemiological data (e.g. PfPr2-10, malaria cases)
- Human population & demography 🧑🤝🧑
Key data sources
- For many of these elements there are data available, for example:
- World Malaria Report
- Malaria Atlas project (burden and intervention coverage estimates)
- Vector Atlas (spatial vector data, under development and building on work by Sinka et al)
Site files
- Historically, the group has collected the required information to characterise a setting into a “Site file”.
- We have tried to formalise this approach in malariaverse
- The 📦[foresite] package contains our first-pass attempt at site-files for all countries
- They contains estimates for all of the important features needed to characterise a site
- The foresite website contains detailed information about each element of a site file
https://mrc-ide.github.io/foresite
Site files
- Site files in 📦[foresite] are defined at the first administrative unit level and further disaggregated between urban and rural populations
Site files
- We can view all the sites associated with a country site-file in 📦[foresite]
Site files
- We can also start to examine other characteristics for the sites
country iso3c name_1 urban_rural year pfpr pvpr
1 Togo TGO Centre rural 2000 0.6052841 0
2 Togo TGO Centre rural 2001 0.5733003 0
3 Togo TGO Centre rural 2002 0.5585785 0
4 Togo TGO Centre rural 2003 0.5469875 0
5 Togo TGO Centre rural 2004 0.5521835 0
6 Togo TGO Centre rural 2005 0.5470634 0
7 Togo TGO Centre rural 2006 0.5076504 0
8 Togo TGO Centre rural 2007 0.4312090 0
9 Togo TGO Centre rural 2008 0.3150650 0
10 Togo TGO Centre rural 2009 0.2370364 0
11 Togo TGO Centre rural 2010 0.2282017 0
12 Togo TGO Centre rural 2011 0.2670050 0
13 Togo TGO Centre rural 2012 0.3853727 0
14 Togo TGO Centre rural 2013 0.5225535 0
15 Togo TGO Centre rural 2014 0.5436589 0
16 Togo TGO Centre rural 2015 0.4809142 0
17 Togo TGO Centre rural 2016 0.3421906 0
18 Togo TGO Centre rural 2017 0.2384519 0
19 Togo TGO Centre rural 2018 0.2976900 0
20 Togo TGO Centre rural 2019 0.2976223 0
21 Togo TGO Centre urban 2000 0.5754777 0
22 Togo TGO Centre urban 2001 0.5221092 0
23 Togo TGO Centre urban 2002 0.4860721 0
24 Togo TGO Centre urban 2003 0.4533892 0
25 Togo TGO Centre urban 2004 0.4375488 0
26 Togo TGO Centre urban 2005 0.4260430 0
27 Togo TGO Centre urban 2006 0.3956310 0
28 Togo TGO Centre urban 2007 0.3477515 0
29 Togo TGO Centre urban 2008 0.2764904 0
30 Togo TGO Centre urban 2009 0.2354452 0
31 Togo TGO Centre urban 2010 0.2525235 0
32 Togo TGO Centre urban 2011 0.3182758 0
33 Togo TGO Centre urban 2012 0.4615116 0
34 Togo TGO Centre urban 2013 0.5983828 0
35 Togo TGO Centre urban 2014 0.5993775 0
36 Togo TGO Centre urban 2015 0.5048967 0
37 Togo TGO Centre urban 2016 0.3357021 0
38 Togo TGO Centre urban 2017 0.2133463 0
39 Togo TGO Centre urban 2018 0.2551143 0
40 Togo TGO Centre urban 2019 0.2549402 0
41 Togo TGO Kara rural 2000 0.5692016 0
42 Togo TGO Kara rural 2001 0.5652779 0
43 Togo TGO Kara rural 2002 0.5800001 0
44 Togo TGO Kara rural 2003 0.5964030 0
45 Togo TGO Kara rural 2004 0.6235924 0
46 Togo TGO Kara rural 2005 0.6416055 0
47 Togo TGO Kara rural 2006 0.6381865 0
48 Togo TGO Kara rural 2007 0.6239081 0
49 Togo TGO Kara rural 2008 0.5804334 0
50 Togo TGO Kara rural 2009 0.5419999 0
51 Togo TGO Kara rural 2010 0.5296437 0
52 Togo TGO Kara rural 2011 0.5332485 0
53 Togo TGO Kara rural 2012 0.5787800 0
54 Togo TGO Kara rural 2013 0.6085285 0
55 Togo TGO Kara rural 2014 0.5564272 0
56 Togo TGO Kara rural 2015 0.4513304 0
57 Togo TGO Kara rural 2016 0.3151321 0
58 Togo TGO Kara rural 2017 0.2271154 0
59 Togo TGO Kara rural 2018 0.2714112 0
60 Togo TGO Kara rural 2019 0.2712657 0
61 Togo TGO Kara urban 2000 0.5053127 0
62 Togo TGO Kara urban 2001 0.4976318 0
63 Togo TGO Kara urban 2002 0.5011611 0
64 Togo TGO Kara urban 2003 0.5116934 0
65 Togo TGO Kara urban 2004 0.5331335 0
66 Togo TGO Kara urban 2005 0.5475319 0
67 Togo TGO Kara urban 2006 0.5348590 0
68 Togo TGO Kara urban 2007 0.4953186 0
69 Togo TGO Kara urban 2008 0.4247267 0
70 Togo TGO Kara urban 2009 0.3625672 0
71 Togo TGO Kara urban 2010 0.3411162 0
72 Togo TGO Kara urban 2011 0.3573897 0
73 Togo TGO Kara urban 2012 0.4266210 0
74 Togo TGO Kara urban 2013 0.4951243 0
75 Togo TGO Kara urban 2014 0.4515932 0
76 Togo TGO Kara urban 2015 0.3511742 0
77 Togo TGO Kara urban 2016 0.2098442 0
78 Togo TGO Kara urban 2017 0.1454354 0
79 Togo TGO Kara urban 2018 0.2162227 0
80 Togo TGO Kara urban 2019 0.2161785 0
81 Togo TGO Maritime rural 2000 0.3898656 0
82 Togo TGO Maritime rural 2001 0.3902485 0
83 Togo TGO Maritime rural 2002 0.3932951 0
84 Togo TGO Maritime rural 2003 0.4246196 0
85 Togo TGO Maritime rural 2004 0.4774714 0
86 Togo TGO Maritime rural 2005 0.5067252 0
87 Togo TGO Maritime rural 2006 0.4844048 0
88 Togo TGO Maritime rural 2007 0.4124870 0
89 Togo TGO Maritime rural 2008 0.2820869 0
90 Togo TGO Maritime rural 2009 0.1803344 0
91 Togo TGO Maritime rural 2010 0.1450827 0
92 Togo TGO Maritime rural 2011 0.1440596 0
93 Togo TGO Maritime rural 2012 0.1998473 0
94 Togo TGO Maritime rural 2013 0.2941174 0
95 Togo TGO Maritime rural 2014 0.3489845 0
96 Togo TGO Maritime rural 2015 0.3633708 0
97 Togo TGO Maritime rural 2016 0.3407740 0
98 Togo TGO Maritime rural 2017 0.2792614 0
99 Togo TGO Maritime rural 2018 0.2409067 0
100 Togo TGO Maritime rural 2019 0.2405489 0
101 Togo TGO Maritime urban 2000 0.2879435 0
102 Togo TGO Maritime urban 2001 0.2821574 0
103 Togo TGO Maritime urban 2002 0.2679330 0
104 Togo TGO Maritime urban 2003 0.2875263 0
105 Togo TGO Maritime urban 2004 0.3214273 0
106 Togo TGO Maritime urban 2005 0.3452104 0
107 Togo TGO Maritime urban 2006 0.3351802 0
108 Togo TGO Maritime urban 2007 0.2815289 0
109 Togo TGO Maritime urban 2008 0.1977873 0
110 Togo TGO Maritime urban 2009 0.1318347 0
111 Togo TGO Maritime urban 2010 0.1063253 0
112 Togo TGO Maritime urban 2011 0.1000352 0
113 Togo TGO Maritime urban 2012 0.1211667 0
114 Togo TGO Maritime urban 2013 0.1583723 0
115 Togo TGO Maritime urban 2014 0.1717212 0
116 Togo TGO Maritime urban 2015 0.1592627 0
117 Togo TGO Maritime urban 2016 0.1280564 0
118 Togo TGO Maritime urban 2017 0.1040410 0
119 Togo TGO Maritime urban 2018 0.1240585 0
120 Togo TGO Maritime urban 2019 0.1243227 0
121 Togo TGO Plateaux rural 2000 0.5724074 0
122 Togo TGO Plateaux rural 2001 0.5473852 0
123 Togo TGO Plateaux rural 2002 0.5403351 0
124 Togo TGO Plateaux rural 2003 0.5443355 0
125 Togo TGO Plateaux rural 2004 0.5657654 0
126 Togo TGO Plateaux rural 2005 0.5741959 0
127 Togo TGO Plateaux rural 2006 0.5519000 0
128 Togo TGO Plateaux rural 2007 0.5008098 0
129 Togo TGO Plateaux rural 2008 0.4001222 0
130 Togo TGO Plateaux rural 2009 0.3163586 0
131 Togo TGO Plateaux rural 2010 0.2993224 0
132 Togo TGO Plateaux rural 2011 0.3250482 0
133 Togo TGO Plateaux rural 2012 0.4188625 0
134 Togo TGO Plateaux rural 2013 0.5273397 0
135 Togo TGO Plateaux rural 2014 0.5601973 0
136 Togo TGO Plateaux rural 2015 0.5451542 0
137 Togo TGO Plateaux rural 2016 0.4938360 0
138 Togo TGO Plateaux rural 2017 0.3995332 0
139 Togo TGO Plateaux rural 2018 0.3474873 0
140 Togo TGO Plateaux rural 2019 0.3474494 0
141 Togo TGO Plateaux urban 2000 0.4719273 0
142 Togo TGO Plateaux urban 2001 0.4193597 0
143 Togo TGO Plateaux urban 2002 0.3793888 0
144 Togo TGO Plateaux urban 2003 0.3475227 0
145 Togo TGO Plateaux urban 2004 0.3287179 0
146 Togo TGO Plateaux urban 2005 0.3110667 0
147 Togo TGO Plateaux urban 2006 0.2887998 0
148 Togo TGO Plateaux urban 2007 0.2609292 0
149 Togo TGO Plateaux urban 2008 0.2180599 0
150 Togo TGO Plateaux urban 2009 0.1901350 0
151 Togo TGO Plateaux urban 2010 0.1927515 0
152 Togo TGO Plateaux urban 2011 0.2110194 0
153 Togo TGO Plateaux urban 2012 0.2661269 0
154 Togo TGO Plateaux urban 2013 0.3336554 0
155 Togo TGO Plateaux urban 2014 0.2396851 0
156 Togo TGO Plateaux urban 2015 0.3391993 0
157 Togo TGO Plateaux urban 2016 0.4385507 0
158 Togo TGO Plateaux urban 2017 0.3096697 0
159 Togo TGO Plateaux urban 2018 0.2593552 0
160 Togo TGO Plateaux urban 2019 0.2593552 0
161 Togo TGO Savanes rural 2000 0.5710921 0
162 Togo TGO Savanes rural 2001 0.5870358 0
163 Togo TGO Savanes rural 2002 0.6301376 0
164 Togo TGO Savanes rural 2003 0.6861678 0
165 Togo TGO Savanes rural 2004 0.7617141 0
166 Togo TGO Savanes rural 2005 0.8163392 0
167 Togo TGO Savanes rural 2006 0.8372493 0
168 Togo TGO Savanes rural 2007 0.8439873 0
169 Togo TGO Savanes rural 2008 0.8272386 0
170 Togo TGO Savanes rural 2009 0.7852575 0
171 Togo TGO Savanes rural 2010 0.7255289 0
172 Togo TGO Savanes rural 2011 0.6314321 0
173 Togo TGO Savanes rural 2012 0.5273907 0
174 Togo TGO Savanes rural 2013 0.4188767 0
175 Togo TGO Savanes rural 2014 0.3344500 0
176 Togo TGO Savanes rural 2015 0.2957481 0
177 Togo TGO Savanes rural 2016 0.2996858 0
178 Togo TGO Savanes rural 2017 0.2790515 0
179 Togo TGO Savanes rural 2018 0.2188233 0
180 Togo TGO Savanes rural 2019 0.2191532 0
181 Togo TGO Savanes urban 2000 0.5168239 0
182 Togo TGO Savanes urban 2001 0.5274550 0
183 Togo TGO Savanes urban 2002 0.5660349 0
184 Togo TGO Savanes urban 2003 0.6215972 0
185 Togo TGO Savanes urban 2004 0.7089746 0
186 Togo TGO Savanes urban 2005 0.7770900 0
187 Togo TGO Savanes urban 2006 0.8045416 0
188 Togo TGO Savanes urban 2007 0.8125866 0
189 Togo TGO Savanes urban 2008 0.7920465 0
190 Togo TGO Savanes urban 2009 0.7412411 0
191 Togo TGO Savanes urban 2010 0.6713465 0
192 Togo TGO Savanes urban 2011 0.5614745 0
193 Togo TGO Savanes urban 2012 0.4413985 0
194 Togo TGO Savanes urban 2013 0.3343936 0
195 Togo TGO Savanes urban 2014 0.2580322 0
196 Togo TGO Savanes urban 2015 0.2009425 0
197 Togo TGO Savanes urban 2016 0.2054626 0
198 Togo TGO Savanes urban 2017 0.1822451 0
199 Togo TGO Savanes urban 2018 0.1358513 0
200 Togo TGO Savanes urban 2019 0.1358519 0Site files
- We can also start to examine other characteristics for the sites
iso3c name_1 urban_rural year itn_use tx_cov
1 TGO Centre rural 2000 0.042393190 0.2281398
2 TGO Centre rural 2001 0.030599122 0.2148092
3 TGO Centre rural 2002 0.021944066 0.2937525
4 TGO Centre rural 2003 0.021107161 0.3392919
5 TGO Centre rural 2004 0.143958366 0.3571002
6 TGO Centre rural 2005 0.204128371 0.3803500
7 TGO Centre rural 2006 0.151860772 0.4145958
8 TGO Centre rural 2007 0.107391349 0.4201048
9 TGO Centre rural 2008 0.268538668 0.4165851
10 TGO Centre rural 2009 0.307875383 0.4223177
11 TGO Centre rural 2010 0.255199719 0.4231978
12 TGO Centre rural 2011 0.550173241 0.4067735
13 TGO Centre rural 2012 0.708583807 0.3886981
14 TGO Centre rural 2013 0.586552827 0.3941082
15 TGO Centre rural 2014 0.509111789 0.3965702
16 TGO Centre rural 2015 0.333043216 0.4001815
17 TGO Centre rural 2016 0.232754495 0.4052033
18 TGO Centre rural 2017 0.580003451 0.4150207
19 TGO Centre rural 2018 0.735244790 0.4174946
20 TGO Centre rural 2019 0.653629806 0.4299997
21 TGO Centre rural 2020 0.580003451 0.4299997
22 TGO Centre rural 2021 0.735244790 0.4299997
23 TGO Centre rural 2022 0.653629806 0.4299997
24 TGO Centre urban 2000 0.050271022 0.2278467
25 TGO Centre urban 2001 0.033087945 0.2140736
26 TGO Centre urban 2002 0.021628087 0.2934813
27 TGO Centre urban 2003 0.020120465 0.3392148
28 TGO Centre urban 2004 0.142744971 0.3568340
29 TGO Centre urban 2005 0.204376546 0.3802322
30 TGO Centre urban 2006 0.150428159 0.4149133
31 TGO Centre urban 2007 0.100371814 0.4206556
32 TGO Centre urban 2008 0.247212826 0.4167022
33 TGO Centre urban 2009 0.283688714 0.4225606
34 TGO Centre urban 2010 0.243394104 0.4237229
35 TGO Centre urban 2011 0.565062155 0.4072412
36 TGO Centre urban 2012 0.758035470 0.3900642
37 TGO Centre urban 2013 0.660015730 0.3939430
38 TGO Centre urban 2014 0.550560314 0.3962030
39 TGO Centre urban 2015 0.357266621 0.3999768
40 TGO Centre urban 2016 0.254906266 0.4050083
41 TGO Centre urban 2017 0.612806302 0.4149835
42 TGO Centre urban 2018 0.767005700 0.4176770
43 TGO Centre urban 2019 0.684164037 0.4300674
44 TGO Centre urban 2020 0.612806302 0.4300674
45 TGO Centre urban 2021 0.767005700 0.4300674
46 TGO Centre urban 2022 0.684164037 0.4300674
47 TGO Kara rural 2000 0.048891126 0.2292877
48 TGO Kara rural 2001 0.032873734 0.2165680
49 TGO Kara rural 2002 0.021365861 0.2950579
50 TGO Kara rural 2003 0.019353105 0.3406956
51 TGO Kara rural 2004 0.134253676 0.3586754
52 TGO Kara rural 2005 0.196867560 0.3819094
53 TGO Kara rural 2006 0.164378762 0.4160803
54 TGO Kara rural 2007 0.133793179 0.4218521
55 TGO Kara rural 2008 0.324587947 0.4184337
56 TGO Kara rural 2009 0.373048658 0.4246129
57 TGO Kara rural 2010 0.313506890 0.4250521
58 TGO Kara rural 2011 0.603924818 0.4088431
59 TGO Kara rural 2012 0.741224265 0.3897915
60 TGO Kara rural 2013 0.614813761 0.3962241
61 TGO Kara rural 2014 0.582565265 0.3984946
62 TGO Kara rural 2015 0.489453607 0.4022219
63 TGO Kara rural 2016 0.348621253 0.4073006
64 TGO Kara rural 2017 0.594687499 0.4170504
65 TGO Kara rural 2018 0.659535770 0.4196187
66 TGO Kara rural 2019 0.539157282 0.4321756
67 TGO Kara rural 2020 0.594687499 0.4321756
68 TGO Kara rural 2021 0.659535770 0.4321756
69 TGO Kara rural 2022 0.539157282 0.4321756
70 TGO Kara urban 2000 0.000000000 0.0000000
71 TGO Kara urban 2001 0.000000000 0.0000000
72 TGO Kara urban 2002 0.000000000 0.0000000
73 TGO Kara urban 2003 0.000000000 0.0000000
74 TGO Kara urban 2004 0.000000000 0.0000000
75 TGO Kara urban 2005 0.000000000 0.0000000
76 TGO Kara urban 2006 0.000000000 0.0000000
77 TGO Kara urban 2007 0.131775871 0.4211407
78 TGO Kara urban 2008 0.000000000 0.0000000
79 TGO Kara urban 2009 0.381953567 0.4233347
80 TGO Kara urban 2010 0.317971272 0.4239307
81 TGO Kara urban 2011 0.619046151 0.4076106
82 TGO Kara urban 2012 0.000000000 0.0000000
83 TGO Kara urban 2013 0.664120323 0.3942262
84 TGO Kara urban 2014 0.614008676 0.3964180
85 TGO Kara urban 2015 0.000000000 0.0000000
86 TGO Kara urban 2016 0.258300404 0.4055012
87 TGO Kara urban 2017 0.530992673 0.4155376
88 TGO Kara urban 2018 0.678533968 0.4182943
89 TGO Kara urban 2019 0.590000198 0.4307619
90 TGO Kara urban 2020 0.530992673 0.4307619
91 TGO Kara urban 2021 0.678533968 0.4307619
92 TGO Kara urban 2022 0.590000198 0.4307619
93 TGO Maritime rural 2000 0.074212390 0.2314858
94 TGO Maritime rural 2001 0.045899551 0.2185223
95 TGO Maritime rural 2002 0.023949532 0.2963213
96 TGO Maritime rural 2003 0.020728550 0.3424130
97 TGO Maritime rural 2004 0.157330479 0.3597826
98 TGO Maritime rural 2005 0.235624390 0.3834832
99 TGO Maritime rural 2006 0.189475123 0.4176652
100 TGO Maritime rural 2007 0.142397194 0.4234145
101 TGO Maritime rural 2008 0.337785344 0.4196152
102 TGO Maritime rural 2009 0.385835324 0.4247077
103 TGO Maritime rural 2010 0.311037560 0.4262919
104 TGO Maritime rural 2011 0.515812636 0.4100409
105 TGO Maritime rural 2012 0.527818011 0.3949176
106 TGO Maritime rural 2013 0.396717881 0.3962011
107 TGO Maritime rural 2014 0.426595867 0.3980506
108 TGO Maritime rural 2015 0.256306456 0.4017764
109 TGO Maritime rural 2016 0.165107780 0.4066521
110 TGO Maritime rural 2017 0.565471005 0.4162716
111 TGO Maritime rural 2018 0.764828846 0.4186738
112 TGO Maritime rural 2019 0.721533233 0.4310728
113 TGO Maritime rural 2020 0.565471005 0.4310728
114 TGO Maritime rural 2021 0.764828846 0.4310728
115 TGO Maritime rural 2022 0.721533233 0.4310728
116 TGO Maritime urban 2000 0.070871676 0.2454397
117 TGO Maritime urban 2001 0.045073448 0.2351193
118 TGO Maritime urban 2002 0.024032515 0.3082170
119 TGO Maritime urban 2003 0.020445623 0.3546397
120 TGO Maritime urban 2004 0.144949082 0.3729431
121 TGO Maritime urban 2005 0.221667259 0.3941780
122 TGO Maritime urban 2006 0.189776878 0.4267764
123 TGO Maritime urban 2007 0.157402861 0.4330476
124 TGO Maritime urban 2008 0.364790332 0.4303830
125 TGO Maritime urban 2009 0.427551695 0.4363535
126 TGO Maritime urban 2010 0.360953060 0.4371414
127 TGO Maritime urban 2011 0.507473101 0.4207928
128 TGO Maritime urban 2012 0.420781739 0.4056263
129 TGO Maritime urban 2013 0.313952923 0.4060729
130 TGO Maritime urban 2014 0.474775770 0.4076157
131 TGO Maritime urban 2015 0.341780965 0.4109121
132 TGO Maritime urban 2016 0.145145831 0.4152824
133 TGO Maritime urban 2017 0.377057914 0.4242915
134 TGO Maritime urban 2018 0.570984811 0.4268715
135 TGO Maritime urban 2019 0.548288376 0.4390855
136 TGO Maritime urban 2020 0.377057914 0.4390855
137 TGO Maritime urban 2021 0.570984811 0.4390855
138 TGO Maritime urban 2022 0.548288376 0.4390855
139 TGO Plateaux rural 2000 0.058541231 0.2324051
140 TGO Plateaux rural 2001 0.035927945 0.2200053
141 TGO Plateaux rural 2002 0.020401379 0.2970646
142 TGO Plateaux rural 2003 0.018712921 0.3427912
143 TGO Plateaux rural 2004 0.136916561 0.3606750
144 TGO Plateaux rural 2005 0.196410878 0.3838494
145 TGO Plateaux rural 2006 0.144759862 0.4177921
146 TGO Plateaux rural 2007 0.097604076 0.4235012
147 TGO Plateaux rural 2008 0.235189519 0.4205762
148 TGO Plateaux rural 2009 0.269671401 0.4257664
149 TGO Plateaux rural 2010 0.232584602 0.4273779
150 TGO Plateaux rural 2011 0.515571590 0.4109700
151 TGO Plateaux rural 2012 0.659417442 0.3954189
152 TGO Plateaux rural 2013 0.550595593 0.3976380
153 TGO Plateaux rural 2014 0.521065380 0.3997876
154 TGO Plateaux rural 2015 0.362752747 0.4034863
155 TGO Plateaux rural 2016 0.276708987 0.4082291
156 TGO Plateaux rural 2017 0.637973334 0.4177128
157 TGO Plateaux rural 2018 0.755065577 0.4200366
158 TGO Plateaux rural 2019 0.668217544 0.4324217
159 TGO Plateaux rural 2020 0.637973334 0.4324217
160 TGO Plateaux rural 2021 0.755065577 0.4324217
161 TGO Plateaux rural 2022 0.668217544 0.4324217
162 TGO Plateaux urban 2000 0.000000000 0.0000000
163 TGO Plateaux urban 2001 0.000000000 0.0000000
164 TGO Plateaux urban 2002 0.000000000 0.0000000
165 TGO Plateaux urban 2003 0.000000000 0.0000000
166 TGO Plateaux urban 2004 0.000000000 0.0000000
167 TGO Plateaux urban 2005 0.000000000 0.0000000
168 TGO Plateaux urban 2006 0.000000000 0.0000000
169 TGO Plateaux urban 2007 0.000000000 0.0000000
170 TGO Plateaux urban 2008 0.000000000 0.0000000
171 TGO Plateaux urban 2009 0.000000000 0.0000000
172 TGO Plateaux urban 2010 0.000000000 0.0000000
173 TGO Plateaux urban 2011 0.000000000 0.0000000
174 TGO Plateaux urban 2012 0.000000000 0.0000000
175 TGO Plateaux urban 2013 0.000000000 0.0000000
176 TGO Plateaux urban 2014 0.629558080 0.4016104
177 TGO Plateaux urban 2015 0.000000000 0.0000000
178 TGO Plateaux urban 2016 0.367856145 0.4055034
179 TGO Plateaux urban 2017 0.771974742 0.4155048
180 TGO Plateaux urban 2018 0.867899537 0.4182492
181 TGO Plateaux urban 2019 0.781230032 0.4307126
182 TGO Plateaux urban 2020 0.771974742 0.4307126
183 TGO Plateaux urban 2021 0.867899537 0.4307126
184 TGO Plateaux urban 2022 0.781230032 0.4307126
185 TGO Savanes rural 2000 0.043963878 0.2320125
186 TGO Savanes rural 2001 0.026273719 0.2205999
187 TGO Savanes rural 2002 0.012040101 0.2975509
188 TGO Savanes rural 2003 0.009737721 0.3439539
189 TGO Savanes rural 2004 0.085446738 0.3622099
190 TGO Savanes rural 2005 0.150260313 0.3853902
191 TGO Savanes rural 2006 0.185956606 0.4190789
192 TGO Savanes rural 2007 0.169601684 0.4250272
193 TGO Savanes rural 2008 0.348788043 0.4215532
194 TGO Savanes rural 2009 0.367596394 0.4280714
195 TGO Savanes rural 2010 0.296577557 0.4279152
196 TGO Savanes rural 2011 0.550335660 0.4121874
197 TGO Savanes rural 2012 0.655148632 0.3914705
198 TGO Savanes rural 2013 0.509270969 0.3994489
199 TGO Savanes rural 2014 0.529359147 0.4017292
200 TGO Savanes rural 2015 0.560795143 0.4052111
201 TGO Savanes rural 2016 0.590055841 0.4100422
202 TGO Savanes rural 2017 0.787616814 0.4196884
203 TGO Savanes rural 2018 0.714946902 0.4221435
204 TGO Savanes rural 2019 0.526722968 0.4344188
205 TGO Savanes rural 2020 0.787616814 0.4344188
206 TGO Savanes rural 2021 0.714946902 0.4344188
207 TGO Savanes rural 2022 0.526722968 0.4344188
208 TGO Savanes urban 2000 0.000000000 0.0000000
209 TGO Savanes urban 2001 0.000000000 0.0000000
210 TGO Savanes urban 2002 0.000000000 0.0000000
211 TGO Savanes urban 2003 0.000000000 0.0000000
212 TGO Savanes urban 2004 0.000000000 0.0000000
213 TGO Savanes urban 2005 0.000000000 0.0000000
214 TGO Savanes urban 2006 0.000000000 0.0000000
215 TGO Savanes urban 2007 0.000000000 0.0000000
216 TGO Savanes urban 2008 0.000000000 0.0000000
217 TGO Savanes urban 2009 0.000000000 0.0000000
218 TGO Savanes urban 2010 0.000000000 0.0000000
219 TGO Savanes urban 2011 0.519890858 0.4074962
220 TGO Savanes urban 2012 0.000000000 0.0000000
221 TGO Savanes urban 2013 0.490939726 0.3942231
222 TGO Savanes urban 2014 0.543534324 0.3963543
223 TGO Savanes urban 2015 0.596531403 0.4003117
224 TGO Savanes urban 2016 0.661634989 0.4054393
225 TGO Savanes urban 2017 0.857723403 0.4154459
226 TGO Savanes urban 2018 0.777160781 0.4181832
227 TGO Savanes urban 2019 0.581653537 0.4306295
228 TGO Savanes urban 2020 0.857723403 0.4306295
229 TGO Savanes urban 2021 0.777160781 0.4306295
230 TGO Savanes urban 2022 0.581653537 0.4306295Using site files
- The site files in 📦[foresite] are a general attempt to collate information for all malaria-endemic settings
- They are, at best, a coarse representation of the true picture
- Please always consider your use-case carefully 🤔, it is likely you may
- Have direct or be working with people with direct knowledge of a setting
- Have more location specific data
- Have more up to date data
- Want to model at a different spatial scale
- The Malariaverse aims to provide you with the tools to be able to make necessary improvements to site files and construct new ones from scratch 🛠️
Running a site
- We can use another malariaverse 📦[site] to translate the site file information into 📦[malariasimulation] parameter input.
# Isolate a single site from a country
example_site <- site::single_site(foresite::TGO, 1)
# Create parameter inputs
site_pars <- site::site_parameters(
interventions = example_site$interventions,
demography = example_site$demography,
vectors = example_site$vectors,
seasonality = example_site$seasonality,
eir = example_site$eir$eir[1],
overrides = list(human_population = 10000)
)
# Run!
model_run <- malariasimulation::run_simulation(timesteps = site_pars$timesteps,
parameters = site_pars)Let’s give it a try!
- 📦 [mvw] has interactive tutorials. You can run code within the tutorial window (or in R/Rstudio if desired).
- Run
mvw::run_tutorial("Introduction")
