#**************************************************************************
# project: LTBI screening
# N Green
# Oct 2016
#
# partial correlation coefficients
library(ppcor)
# library(pse)
# all pairwise partial correlation
# pcor(design_matrix[ ,c("Agree", "Start", "Complete", "Effective")], method = "spearman")
# pcc of screening
pcor_screen <- pcor.test(x = sim_matrix$NMB,
y = sim_matrix$policy,
z = sim_matrix[ ,c("Agree", "Start", "Complete", "Effective")], #controlling for
method = "spearman")
# pcc of each step
dm_screen <- subset(sim_matrix, policy == "screened")
pcor_agree <- pcor.test(x = dm_screen$NMB,
y = dm_screen$Agree,
z = dm_screen[ ,c("Start", "Complete", "Effective")],
method = "spearman")
pcor_start <- pcor.test(x = dm_screen$NMB,
y = dm_screen$Start,
z = dm_screen[ ,c("Agree", "Complete", "Effective")],
method = "spearman")
pcor_complete <- pcor.test(x = dm_screen$NMB,
y = dm_screen$Complete,
z = dm_screen[ ,c("Agree", "Start", "Effective")],
method = "spearman")
pcor_effective <- pcor.test(x = dm_screen$NMB,
y = dm_screen$Effective,
z = dm_screen[ ,c("Agree", "Start", "Complete")],
method = "spearman")
out <- cbind(var = c("screen", "agree", "start", "complete", "effective"),
rbind(pcor_screen, pcor_agree, pcor_start, pcor_complete, pcor_effective))
# save --------------------------------------------------------------------
write.csv(out, file = paste(diroutput, "pcc_table.csv", sep = "/"))
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