Simulation Results Data for 'Modelling new insecticide-treated bed nets for malaria-vector control: How to strategically manage resistance?'

GENERAL INFORMATION

1. Title of Dataset: Simulation Results Data for 'Modelling new insecticide-treated bed-nets for malaria-vector control: How to strategically manage resistance?'

2. Author Information
    A. Investigator Contact Information
        Name: Philip G. Madgwick
        Institution: Syngenta 
        Address: Jealott’s Hill International Research Centre, Bracknell, RG42 6EY, UK
        Email: philip.madgwick@syngenta.com

    B. Investigator Contact Information
        Name: Ricardo Kanitz
        Institution: Syngenta 
        Address: Syngenta Crop Protection, Rosentalstrasse 67, CH-4058 Basel, Switzerland
        Email: ricardo.kanitz@syngenta.com

3. Date of data collection (single date, range, approximate date): 2021-01-13 to 2021-02-01 

4. Geographic location of data collection: UK 

5. Information about funding sources that supported the collection of the data: 

This work was conducted during a postdoctoral research position for PGM funded by the Innovative Vector Control Consortium (IVCC).

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: NA

2. Links to publications that cite or use the data: [UPDATE]

3. Links to other publicly accessible locations of the data: NA

4. Links/relationships to ancillary data sets: NA

5. Was data derived from another source? No

6. Recommended citation for this dataset: [UPDATE]

DATA & FILE OVERVIEW

1. File List: 
PSData_random6.csv - 10^6 random samples of each of the 17 parameters in the model, where rows are samples and columns are parameters (with column names corresponding to the parameters identified in the rows of Table 1 of the manuscript; see also DATA-SPECIFIC INFORMATION)
Data_random6_maxpsMixture_Fixed_mm.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A and B are used in a mixture (at rate k=1; see manuscript) as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has mitochondrial inheritance  
Data_random6_maxpsMixture_Fixed_mn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A and B are used in a mixture (at rate k=1; see manuscript) as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_maxpsMixture_Fixed_nn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A and B are used in a mixture (at rate k=1; see manuscript) as a fixed strategy for the entire run; the resistance allele at locus 1 has nuclear inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_Mixture_Fixed_mm.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A and B are used in a mixture (at rate k; see manuscript) as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has mitochondrial inheritance  
Data_random6_Mixture_Fixed_mn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A and B are used in a mixture (at rate k; see manuscript) as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_Mixture_Fixed_nn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A and B are used in a mixture (at rate k; see manuscript) as a fixed strategy for the entire run; the resistance allele at locus 1 has nuclear inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_Mosaic_Fixed_mm.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A and B are used at 50% frequency each as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has mitochondrial inheritance  
Data_random6_Mosaic_Fixed_mn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A and B are used at 50% frequency each as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_Mosaic_Fixed_nn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A and B are used at 50% frequency each as a fixed strategy for the entire run; the resistance allele at locus 1 has nuclear inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_Rotation_Fixed_mm.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A is used first in a rotation that switch between insecticides every 36 generations as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has mitochondrial inheritance  
Data_random6_Rotation_Fixed_mn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A is used first in a rotation that switch between insecticides every 36 generations as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_Rotation_Fixed_nn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A is used first in a rotation that switch between insecticides every 36 generations as a fixed strategy for the entire run; the resistance allele at locus 1 has nuclear inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_Rotation_Fixed_revmm.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide B is used first in a rotation that switch between insecticides every 36 generations as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has mitochondrial inheritance  
Data_random6_Rotation_Fixed_revmn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide B is used first in a rotation that switch between insecticides every 36 generations as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_Rotation_Fixed_revnn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide B is used first in a rotation that switch between insecticides every 36 generations as a fixed strategy for the entire run; the resistance allele at locus 1 has nuclear inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_SoloA_Fixed_mm.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A is used solo as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has mitochondrial inheritance  
Data_random6_SoloA_Fixed_mn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A is used solo as a fixed strategy for the entire run; the resistance allele at locus 1 has nuclear inheritance and the resistance allele at locus 2 has mitochondrial inheritance  
Data_random6_SoloA_Fixed_nn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide A is used solo as a fixed strategy for the entire run; the resistance allele at locus 1 has nuclear inheritance and the resistance allele at locus 2 has nuclear inheritance  
Data_random6_SoloB_Fixed_mm.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide B is used solo as a fixed strategy for the entire run; the resistance allele at locus 1 has mitochondrial inheritance and the resistance allele at locus 2 has mitochondrial inheritance  
Data_random6_SoloB_Fixed_mn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide B is used solo as a fixed strategy for the entire run; the resistance allele at locus 1 has nuclear inheritance and the resistance allele at locus 2 has mitochondrial inheritance  
Data_random6_SoloB_Fixed_nn.csv - simulation dataset of 10^6 runs for each set of randomly sampled parameters; insecticide B is used solo as a fixed strategy for the entire run; the resistance allele at locus 1 has nuclear inheritance and the resistance allele at locus 2 has nuclear inheritance  

2. Relationship between files, if important: 

Files are named in accordance with the variables that describe each simulation setup, as described above. Each simulation dataset has 10^6 runs that correspond to the 10^6 random samples of each of the 17 parameters in the model in 'PSData_random6.csv'.

3. Additional related data collected that was not included in the current data package: NA

4. Are there multiple versions of the dataset? No

METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: Data were collected using Simulator.R, which is in the vignettes of the 'detsims' R package that accompanies the manuscript. 

2. Methods for processing the data: Data were processed using Figures.R, which is in the vignettes of the 'detsims' R package that accompanies the manuscript. 

3. Instrument- or software-specific information needed to interpret the data: Analysis was conducted in R version 4.0.3 (2020-10-10), using R packages identified in Figures.R, which is in the vignettes of the 'detsims' R package that accompanies the manuscript. 

4. Standards and calibration information, if appropriate: NA

5. Environmental/experimental conditions: NA

6. Describe any quality-assurance procedures performed on the data: NA

7. People involved with sample collection, processing, analysis and/or submission: NA 

DATA-SPECIFIC INFORMATION FOR: PSData_random6.csv

1. Number of variables: 

17 variables with column names that have the following parameter meanings (see Table 1 in the manuscript): 
Population Size    = N = starting population size (and carrying capacity in logistic model); random sample range on log-scale: 10^2 - 10^9
Intrinsic Birth Rate = b = % population growth rate (in logistic model); random sample following a standard log-normal distribution with mean=0 and sd=1
Intrinsic Death Rate = d = % breeding mosquitoes that die into next generation; random sample range: 0 - 1
Female Exposure    = x_[female-symbol] = % female mosquitoes that receive a dose; random sample range: 0 - 1
Male Exposure x_[male-symbol] = % male mosquitoes that receive a dose; random sample range: 0 - 1
Initial Frequency A = f_0,A = starting frequency of allele A; random sample range on log-scale: 10^-9 - 10^-2, limited to be within the range 1/N - N/100 where N is Population Size
Effectiveness 1    = m_1 = % dosed mosquitoes that die from insecticide 1; random sample range: 0 - 1
Resistance Restoration A = r_A = % return to baseline fitness with resistance allele A; random sample range: 0 - 1
Dominance of Resistance Restoration A = h^r_A = % resistance restoration in heterozygote with allele A; random sample range: 0 - 1
Resistance Cost A = c_A = % non-dosed mosquitoes that die from carrying allele A; random sample range on log-scale: 10^-3 - 10^-0.5
Dominance of Resistance Cost A = h^c_A = % resistance cost in heterozygote with allele A; random sample range: 0 - 1
Initial Frequency B = f_0,B = starting frequency of allele B; random sample range on log-scale: 10^-9 - 10^-2, limited to be within the range 1/N - N/100 where N is Population Size
Effectiveness 2    = m_2 = % dosed mosquitoes that die from insecticide 2; random sample range: 0 - 1
Resistance Restoration B = r_B = % return to baseline fitness with resistance allele B; random sample range: 0 - 1
Dominance of Resistance Restoration B = h^r_B = % resistance restoration in heterozygote with allele B; random sample range: 0 - 1
Resistance Cost B = c_B = % non-dosed mosquitoes that die from carrying allele B; random sample range on log-scale: 10^-3 - 10^-0.5
Dominance of Resistance Cost B = h^c_B = % resistance cost in heterozygote with allele B; random sample range: 0 - 1

2. Number of cases/rows: 

10^6, corresponding to the number of random samples 

3. Variable List: NA 

4. Missing data codes: NA

5. Specialized formats or other abbreviations used: NA

DATA-SPECIFIC INFORMATION FOR: all other dataset files (e.g. Data_random6_maxpsMixture_Fixed_mm.csv) 

1. Number of variables: 

10 variables with column names that have the following meanings:
A_t_50% = the recorded number of generations that it takes for resistance allele A to reach >50% frequency; 0 means that resistance allele A never reaches >50% frequency  
A_f_250 = the frequency of resistance allele A at the 250th generation 
A_f_bar = the mean frequency of resistance allele A over the first 250 generations  
B_t_50% = the recorded number of generations that it takes for resistance allele B to reach >50% frequency; 0 means that resistance allele B never reaches >50% frequency  
B_f_250 = the frequency of resistance allele B at the 250th generation 
B_f_bar = the mean frequency of resistance allele B over the first 250 generations 
nf_80% = the recorded number of generations that it takes for the female population size to recover to >80% of its original size in the 0th generation; 0 means that the female population size never reaches >80% recovery; 1 means that the female population size never drops below 80% of its original size in the 1st generation
nf_250 = the female population size at the 250th generation
nf_bar = the mean female population size over the first 250 generations 
nf_ext = the recorded number of generations that it takes for the female population size to drop below 1 (i.e. population extinction); 0 means that female population size never reaches <1

2. Number of cases/rows: 

10^6, corresponding to the number of random samples 

3. Variable List: NA

4. Missing data codes: all missing data is recorded as 0 

5. Specialized formats or other abbreviations used: NA