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convert variable types when creating data frame from cor.test results

3 messages · Keith Larson, PIKAL Petr, Jean V Adams

Keith Larson
# 
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")])))

*******************************************************************************************
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
PIKAL Petr
# 
Hi
c("Individual_ID",
"data.frame")
temp$FeatherPosition,
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
*******************************************************************************************
2224716
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