Mapping health research effort

Databases:

data

    1. All RCTs registered at WHO ICTRP by Jan 1st 2016, 
    2. with start date between 2006 and 2015
    3. with study type and design corresponding to RCT
    4. with at least one country location among the 187 countries included in the GBD2010 study

replicates

    1. for each disease, replicates of the mapping of RCTs across diseases

We will:

      1. Derive uncertainty intervals for the mapping of RCTs across diseases



In [1]:

    
#Upload database
data <- read.table("/media/igna/Elements/HotelDieu/Cochrane/Mapping_Cancer/Flowchart/database_all_diseases_final_ok.txt")
N <- nrow(data)
names(data)









    





	'TrialID'
	'brief_title'
	'official_title'
	'Primary_sponsor'
	'Source_Register'
	'Recruitment_Status'
	'other_records'
	'Target_size'
	'Study_type'
	'Study_design'
	'Phase'
	'Countries'
	'condition'
	'Secondary_ID'
	'Source_Support'
	'Secondary_Sponsor'
	'year'
	'Interv'
	'Regions'
	'Nb_ctr_per_reg'
	'Sample'
	'PMID'
	'GBD28'
	'GBD171'
	'Infectious'
	'MNN'
	'Cancer'
	'Chronic'

TrialID: unique trial ID from WHOICTRP
Regions: 7 epidemiological regions from GBD 2010 study
GBD28: classification according to 28 categories defined in Atal et al. BMC Bioinformatics (2016): This classification includes the injuries category, we exclude it



In [2]:

    
#Upload traduction names/label categories
Mgbd <- read.table("/home/igna/Desktop/Programs GBD/Classifier_Trial_GBD/Databases/Taxonomy_DL/GBD_data/GBD_ICD.txt")
#And supress injuries from the causes of burden
grep("Injur",Mgbd$cause_name)
GBD27 <- sapply(strsplit(as.character(data$GBD28),"&"),function(x){paste(x[x!="28"],collapse="&")})
data$GBD27 <- GBD27

2- Estimation of number RCTs per region and disease



In [3]:

    
regs <- sort(unique(unlist(strsplit(as.character(data$Regions),"&"))))
LR <- lapply(regs,function(x){1:nrow(data)%in%grep(x,data$Regions)})
LR <- do.call('cbind',LR)



In [4]:

    
dis <- 1:27
d <- dis[1]

SMs <- list.files(paste("/media/igna/Elements/HotelDieu/Cochrane/Mapping_Cancer/Incertitude_mapping/Replicates/",as.character(d),sep=""))



In [5]:

    
ss_sp <- read.table(paste(c("/media/igna/Elements/HotelDieu/Cochrane/Mapping_Cancer/Incertitude_mapping/Replicates/",as.character(d),"/Sens_spec.txt"),collapse=""))



In [6]:

    
options(repr.plot.width=9, repr.plot.height=3)
par(mfrow=c(1,4))
for(i in 1:ncol(ss_sp)) hist(ss_sp[,i],xlim=c(0,1),main=colnames(ss_sp)[i],xlab=NULL)



In [ ]: