convert variable types when creating data frame from cor.test results
Hi
Dear list,
The below dataset and code creates a new dataset with the results from
the function cor.test being performed on each individual
('Individual_ID') from my original dataset. How do I convert each
variable from the cor.test results to a numeric data type, as it is
passed into the new dataframe? For example, 'estimate', 'p.value', and
'conf.int' should be numeric not character. Second, I would like
variable 'conf.int' to be two variables, 'lowlim' and 'uplim'.
Many Cheers,
Keith
## Create sample dataset
WW_Wing_SI <-
structure(list(Individual_ID = c("WW_08A_02", "WW_08A_02", "WW_08A_02",
"WW_08A_02", "WW_08A_02", "WW_08A_02", "WW_08A_02", "WW_08A_02",
"WW_08A_02", "WW_08A_03", "WW_08A_03", "WW_08A_03", "WW_08A_03",
"WW_08A_03", "WW_08A_03", "WW_08A_03", "WW_08A_03", "WW_08A_03"
), FeatherPosition = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 1, 2, 3, 4,
5, 6, 7, 8, 9), Delta13C = c(-18.67, -19.16, -20.38, -20.96,
-21.61, -21.65, -21.31, -20.8, -21.28, -20.06, -20.3, -21.21,
-22.9, -22.87, -21.13, -20.68, -20.58, -20.69)), .Names =
c("Individual_ID",
"FeatherPosition", "Delta13C"), row.names = c(NA, 18L), class =
"data.frame")
# split data frame according the the individual IDs
wing.list <- split(WW_Wing_SI, WW_Wing_SI$Individual_ID)
# apply cor.test() with extract to each element of the list
test <- as.data.frame(t(sapply(wing.list, function(temp)
cor.test(temp$Delta13C,
temp$FeatherPosition,
method="pearson")[c("estimate",
"p.value", "conf.int")])))
The problem is that transposing a sapply object transforms it to matrix and matrix can have only one type of values. Not very sophisticated but this result <- unlist(sapply(wing.list, function(temp) cor.test(temp$Delta13C, temp$FeatherPosition, method="pearson"))[c(3,4,9),]) gives you a numeric vector of desired values. You can change it to numeric matrix dim(result)<-c(4,2) Give the propper name to rows and columns and/or transpose according to your wish. Regards Petr
*******************************************************************************************
Keith Larson, PhD Student Evolutionary Ecology, Lund University S?lvegatan 37 223 62 Lund Sweden Phone: +46 (0)46 2229014 Mobile: +46 (0)73 0465016 Fax: +46 (0)46
2224716
Skype: sternacaspia FB: keith.w.larson at gmail.com
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