Merge pull request #22 from Folakunmi21/main

vignette buid errors resolve attempt

vignettes/fieldworkanalysis_samara.Rmd

@@ -39,6 +39,7 @@ library(dplyr)
 ```
 
 ```{r}
+library(bugSigSimple)
 dat <- bugsigdbr::importBugSigDB(cache= TRUE)
 dim(dat)
 names(dat)
@@ -72,8 +73,8 @@ Summary of studies and most frequent taxa increased and decreased in endometrios
 bugSigSimple::createStudyTable(subset.dat)
 
 getMostFrequentTaxa(subset.dat,n=30)
-getMostFrequentTaxa(subset.dat,sig.type="increased")
-getMostFrequentTaxa(subset.dat,sig.type="decreased")
+getMostFrequentTaxa(subset.dat,direction="UP")
+getMostFrequentTaxa(subset.dat,direction="DOWN")
 
 ```
 
@@ -222,7 +223,7 @@ fit.negbin <-
     data = df,
     control = glm.control(
       epsilon = 1e-8,
-      maxit = 25,
+      maxit = 70,
       trace = FALSE
     )
   )

vignettes/healthysig.Rmd

@@ -43,8 +43,8 @@ healthysig50 <- bugsigdbr::getSignatures(bugs50)
 head(healthysig50)
 ```
 
-```{r healthy0}
-#prevalence threshold=0
+```#{r healthy0}
+prevalence threshold=0
 bugs0<- (dat) %>%
   filter (Study=='Study 562') %>%
   filter (Experiment=="Experiment 10") %>%
@@ -128,7 +128,7 @@ bugall_decreased <- merge(x = diseasesig_decreased2, y = bugdisease_decreased2,
 ```
 
 ## Calculate pairwise overlaps
-```{r overlap_prevelance=0}
+#```{r overlap_prevelance=0} experiment 10 has no signatures
 library(purrr)
 list0_decreased <- c(healthysig0, diseasesig_decreased)
 paircomp0_decreased <- calcPairwiseOverlaps(list0_decreased)
@@ -157,7 +157,7 @@ paircheck0_increased <- paircomp0_increased %>%
 ## merge jacard scores with disease study data
 The issue why I need to merge overlap score back with all disease budsigdb studies is that calcPairwiseOverlaps drops all 0 intersect pairs
 
-```{r merge overlap scores with all disease study data}
+#```{r merge overlap scores with all disease study data}
 overlap0_decreased<- merge(x = bugall_decreased, y = paircheck0_decreased, by =c('study_id','experiment_id','signature_id'), all.x = TRUE) %>%
   mutate(type="decreased")%>%
   filter(length_set2>4) #keep only bugsigdb studies that tested more than 4 increased or decreased
@@ -169,7 +169,7 @@ overlap0_increased<- merge(x = bugall_increased, y = paircheck0_increased, by =c
 overlap0_increased[is.na(overlap0_increased)] <- 0  
 ```
 
-```{r comparison-increased_vs_decrease}
+```#{r comparison-increased_vs_decrease}
 t.test(overlap0_increased$overlap, overlap0_decreased$overlap)
 wilcox.test(overlap0_increased$overlap, overlap0_decreased$overlap)