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fixing to work with the test
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Meghan Avolio authored and Ian Carroll committed Apr 17, 2018
1 parent 37ff5da commit e6b41de
Showing 1 changed file with 15 additions and 15 deletions.
30 changes: 15 additions & 15 deletions R/curve_difference_test.R
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Original file line number Diff line number Diff line change
Expand Up @@ -108,12 +108,12 @@ curve_difference_test <- function(df, time.var=NULL,

#rank species in each replicate and calculate relative rank and cumulative abundance
rep_trt <- unique(subset(df, select = c(replicate.var, treatment.var, block.var)))
relrankdf <- relrank(df, species.var, abundance.var, replicate.var)
relrankdf <- relrank_test(df, species.var, abundance.var, replicate.var)
relrankdf1 <- merge(relrankdf, rep_trt, by=replicate.var)

#split by block and calculate curve difference
X <- split(relrankdf1, relrankdf1[[block.var]])
out <- lapply(X, FUN = curve_diff, treatment.var, relrank, cumabund)
out <- lapply(X, FUN = curve_diff_test, treatment.var, relrank, cumabund)
ID <- unique(names(out))
out <- mapply(function(x, y) "[<-"(x, block.var, value = y) ,
out, ID, SIMPLIFY = FALSE)
Expand All @@ -124,7 +124,7 @@ curve_difference_test <- function(df, time.var=NULL,
#rank species in each replicate and time and calculate relative rank and cumulative abundance
rep_trt <- unique(subset(df, select = c(replicate.var, treatment.var, block.var)))
X <- split(df, df[[time.var]])
out <- lapply(X, FUN = relrank, species.var, abundance.var, replicate.var)
out <- lapply(X, FUN = relrank_test, species.var, abundance.var, replicate.var)
ID <- unique(names(out))
out <- mapply(function(x, y) "[<-"(x, time.var, value = y) ,
out, ID, SIMPLIFY = FALSE)
Expand All @@ -134,7 +134,7 @@ curve_difference_test <- function(df, time.var=NULL,
#split by block and time and calcualte curve difference
relrankdf1$splitvariable <- paste(relrankdf1[[block.var]], relrankdf1[[time.var]], sep = "##")
X <- split(relrankdf1, relrankdf1$splitvariable)
out <- lapply(X, FUN = curve_diff, treatment.var, relrank, cumabund)
out <- lapply(X, FUN = curve_diff_test, treatment.var, relrank, cumabund)
ID <- unique(names(out))
out <- mapply(function(x, y) "[<-"(x, "splitvariable", value = y) ,
out, ID, SIMPLIFY = FALSE)
Expand Down Expand Up @@ -168,7 +168,7 @@ curve_difference_test <- function(df, time.var=NULL,
relrankdf1<-relrank(spave, species.var, abundance.var, treatment.var)

#calcualte curve difference
output <- curve_diff (relrankdf1, treatment.var, relrank, cumabund)
output <- curve_diff_test (relrankdf1, treatment.var, relrank, cumabund)

} else {

Expand All @@ -192,15 +192,15 @@ curve_difference_test <- function(df, time.var=NULL,

#rank each species by treatment, time
X <- split(spave, spave[[time.var]])
out <- lapply(X, FUN = relrank, species.var, abundance.var, treatment.var)
out <- lapply(X, FUN = relrank_test, species.var, abundance.var, treatment.var)
ID <- unique(names(out))
out <- mapply(function(x, y) "[<-"(x, time.var, value = y) ,
out, ID, SIMPLIFY = FALSE)
relrankdf1 <- do.call("rbind", out)

#split by time and calcualte curve difference
X <- split(relrankdf1, relrankdf1[[time.var]])
out <- lapply(X, FUN = curve_diff, treatment.var, relrank, cumabund)
out <- lapply(X, FUN = curve_diff_test, treatment.var, relrank, cumabund)
ID <- unique(names(out))
out <- mapply(function(x, y) "[<-"(x, time.var, value = y) ,
out, ID, SIMPLIFY = FALSE)
Expand All @@ -213,24 +213,24 @@ curve_difference_test <- function(df, time.var=NULL,

if(is.null(time.var)) {
#rank species in each replicate and time and calculate relative rank and cumulative abundance
relrankdf1 <- relrank(df, species.var, abundance.var, replicate.var)
relrankdf1 <- relrank_test(df, species.var, abundance.var, replicate.var)

#split by time and calcualte curve difference
output <- curve_diff (relrankdf1, replicate.var, relrank, cumabund)
output <- curve_diff_test (relrankdf1, replicate.var, relrank, cumabund)

} else {

#rank species in each replicate and time and calculate relative rank and cumulative abundance
X1 <- split(df, df[[time.var]])
out1 <- lapply(X1, FUN=relrank, species.var, abundance.var, replicate.var)
out1 <- lapply(X1, FUN=relrank_test, species.var, abundance.var, replicate.var)
ID1 <- unique(names(out1))
out1 <- mapply(function(x, y) "[<-"(x, time.var, value = y) ,
out1, ID1, SIMPLIFY = FALSE)
relrankdf1 <- do.call("rbind", out1)

#split by time and calcualte curve difference
X <- split(relrankdf1, relrankdf1[[time.var]])
out <- lapply(X, FUN=curve_diff, replicate.var, relrank, cumabund)
out <- lapply(X, FUN=curve_diff_test, replicate.var, relrank, cumabund)
ID <- unique(names(out))
out <- mapply(function(x, y) "[<-"(x, time.var, value = y) ,
out, ID, SIMPLIFY = FALSE)
Expand All @@ -249,10 +249,10 @@ curve_difference_test <- function(df, time.var=NULL,
if(is.null(time.var)){

#rank species in each replicate and time and calculate relative rank and cumulative abundance
relrankdf1 <- relrank(df, species.var, abundance.var, replicate.var)
relrankdf1 <- relrank_test(df, species.var, abundance.var, replicate.var)

#split by time and calcualte curve difference
output <- curve_diff (relrankdf1, replicate.var, relrank, cumabund)
output <- curve_diff_test (relrankdf1, replicate.var, relrank, cumabund)

#merge in trt info
output <- merge(output, rep_trt, by = replicate.var)
Expand All @@ -262,15 +262,15 @@ curve_difference_test <- function(df, time.var=NULL,

#rank species in each replicate and time and calculate relative rank and cumulative abundance
X1 <- split(df, df[[time.var]])
out1 <- lapply(X1, FUN=relrank, species.var, abundance.var, replicate.var)
out1 <- lapply(X1, FUN=relrank_test, species.var, abundance.var, replicate.var)
ID1 <- unique(names(out1))
out1 <- mapply(function(x, y) "[<-"(x, time.var, value = y) ,
out1, ID1, SIMPLIFY = FALSE)
relrankdf1 <- do.call("rbind", out1)

#split by time and calcualte curve difference
X <- split(relrankdf1, relrankdf1[[time.var]])
out <- lapply(X, FUN=curve_diff, replicate.var, relrank, cumabund)
out <- lapply(X, FUN=curve_diff_test, replicate.var, relrank, cumabund)
ID <- unique(names(out))
out <- mapply(function(x, y) "[<-"(x, time.var, value = y) ,
out, ID, SIMPLIFY = FALSE)
Expand Down

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