Readme files for data associated with:
Faust, CL; Crotti, M; Moses, A; Oguttu, D; Wamboko, A; Adriko, M; Adekanle, EK; Kabatereine, N; Tukahebwa, EM; Norton, AJ; Gower, CM; Webster, JP; Lamberton, PHL. Two-year longitudinal survey reveals high genetic diversity of Schistosoma mansoni with adult worms surviving praziquantel treatment at the start of mass drug administration in Uganda. Parasites & Vectors. 

FILE 1. S_mansoni_microsatellites.csv 
- csv file formatted as a genelax format:
- row 1 details 1) number of microsatellite loci, 2) number of individuals, and 3) number of populations 
- microsatellite loci are listed in separate columns but only one of the columns is labelled with the loci name
- the first column (starting on row 3) has an individual identification name per miracidia
- the second column details the infrapopulation and timepoint for each miracidia .


FILE 2: S_mansoni_metadata.csv
names and descriptions for each column in a file associating infrapopulations at a given timepoint with host data
pop_ID :  the name of the infrapopulation at a given timepoint (timepoint_child identification) - use to link to S_mansoni_microsatellite data
school_name	: primary school where individual is enrolled
school_initials : abbreviation of primary school
cid_num: truncated number of anonymised participant
cid_unique : identification number of participant (infrapopulation) appended to school (completely unique)
initials: initials of participant (used to cross reference correect individual)	
cid_alternative: unique identifier listing school, year of recruitment, age of recruitment, and id name within the age cohort
sex : sex of the participant: f = female, m = male
year_recruit : year participant was recruited (and hence PZQ treatments known)	
age_at_recruit	: participant's age at recruitment
adj_age	: participant's age at the sampling time point
time_int : sampling timpoint as an integer (1 to 11)
time_weeks : sampling timepoint as time since beginning of this genetics study (2004)
time_year_int : sampling year as integer (1 to 3)
time_year : sampling year as year (2003 to 2006)
time_char : sampling timepoint as weeks/year string
no_slides : number of Kato-Katz slides examined at the timepoint (usually duplicate slides over 3 days; 6)
sm_avg_epg	: arithmetic mean of Schistosoma mansoni (Sm) eggs per gram (epg) of all slides examined at that timepoint
sm_bin	: binary infection status at the timepoint. 1 = infected, 0 = not infected
rel_treat : short-term treatment (0 = no treatment in last 4 weeks, 1 = treatment 1 week prior, 4 = treatment 4 weeks priort)
rel_treat2: string of short term treatment (pre = no treatment in last 4 weeks; post = treatment in last 4 weeks)
rel_treat3: string of short term treatment, assuming 1 week post is from dead adults (pre = no treatment >2 weeks prior, post = treatment 4 weeks prior)
pzq_cum: total number of previous praziquantel treatments (all observed) 
last_treat_mons: the number of months a treatment was last observed