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updated un[aired stats with n_obs_complete and removed mediator vitd from sam and npa

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Tanushree Tunstall 2020-10-30 13:04:45 +00:00
parent 1b5d353060
commit a2dbecd03d
5 changed files with 165 additions and 65 deletions
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17
boxplot.R
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@ -30,12 +30,22 @@ lf_fp_npa$timepoint = paste0("t", lf_fp_npa$timepoint)
lf_fp_npa$timepoint = as.factor(lf_fp_npa$timepoint)
lf_fp_npa$obesity = as.factor(lf_fp_npa$obesity)
table(lf_fp_npa$mediator)
head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"])
lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",]
#wf_fp_sam = samm_wf[samm_wf$flustat == 1,]
lf_fp_sam = sam_lf[sam_lf$flustat == 1,]
lf_fp_sam$timepoint = paste0("t", lf_fp_sam$timepoint)
lf_fp_sam$timepoint = as.factor(lf_fp_sam$timepoint)
lf_fp_sam$obesity = as.factor(lf_fp_sam$obesity)
table(lf_fp_sam$mediator)
head(lf_fp_sam$value[lf_fp_sam$mediator == "vitd"])
lf_fp_sam = lf_fp_sam[!lf_fp_sam$mediator == "vitd",]
#wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
lf_fp_serum = serum_lf[serum_lf$flustat == 1,]
lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
@ -52,11 +62,6 @@ pdf(output_boxplot, width = 20, height = 15)
if (is.factor(lf_fp_npa$timepoint) && is.factor(lf_fp_npa$timepoint)){
cat ("PASS: required groups are factors")
}
table(lf_fp_npa$mediator)
head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"])
lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",]
#------------------------------------------
title_npa_linear = "Boxplot: NPA (Linear)"
#-----------------------------------------
@ -114,8 +119,6 @@ bxp_npa_log
if (is.factor(lf_fp_sam$timepoint) && is.factor(lf_fp_sam$timepoint)){
cat ("PASS: required groups are factors")
}
table(lf_fp_sam$mediator)
lf_fp_sam = lf_fp_sam[!lf_fp_sam$mediator == "vitd",]
#------------------------------------------
title_sam_linear = "Boxplot: sam (Linear)"