Table 1 Estimating mutant frequencies using different methods: validation using a test dataset from Tanzania³⁹. Frequencies of the 540E mutation are estimated in 24 areas in 2 different years.

Method	Data required				Assumptions		Mean squared error	Reference for Method
Method	Mixed infections	Mean population MOI	Slide prevalence	Location	Assumption about detection of parasite clones	Other	Mean squared error	Reference for Method
5B	√			√	Imperfect MOI-dependent		0.0031	This paper extended from³²
5C	√			√	Imperfect MOI-independent		0.0037	This paper
7A	√			√	100%	mean MOI varied during fitting	0.0061	This paper extended from³¹
5A	√			√	100%		0.0062	This paper extended from³¹
6A	√			√	100%	Assume negative binomial MOI distribution	0.0071	This paper extended from³¹
3A	√	√			100%		0.0071	31
4A	√		√		100%		0.0083	This paper extended from³¹
8A				√	100%		0.0140	This paper extended from³¹

We compare frequencies estimated from the full dataset with information on MOI and resistance markers for each individual (Method 2, see Methods) with frequencies estimated from partial summary data using different methods. We show mean squared error to quantify the difference between the two sets of estimates in each comparison. The methods are ordered by increasing mean squared error; lowest indicates more similar estimates. The column ‘mixed infections’ indicates that data on the proportion of mixed wild type-resistance infections was used to estimate frequencies. ‘Slide prevalence’ indicates that mean MOI was estimated using the relationship in Fig. 4. ‘Location’ indicates that longitude and latitude of the survey location were used to obtain estimates of slide-prevalence from the Malaria Atlas Project, in order to estimate mean MOI using Fig. 4 ⁴⁵. Where imperfect detection of parasite clones was assumed, this was included when fitting to both the full and partial datasets (letters A to C after the Method number denote assumption about detection; see Methods. For example, in the first row, method 5B is compared to method 2B, in the 2^nd row method 5C is compared to method 2C etc).

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