error calculating with rcorr() function
Opened this issue · 2 comments
Hi,
I'm using the rcorr() example from "Package ‘Hmisc’" from November 7, 2019
if I'm trying the published example, everything ist ok. But if I want to calculate the correlation matrix for columns x and y the, I'm getting an error message. (see below)
x <- c(-2, -1, 0, 1, 2)
y <- c(4, 1, 0, 1, 4)
z <- c(1, 2, 3, 4, NA)
v <- c(1, 2, 3, 4, 5)
rcorr(cbind(x,y))
> Error in matrix(rnorm(n * d), n, d) : invalid 'nrow' value (< 0)
Further issues:
I've written an Code in R, with rcorr() to calculate a big correlation matrix. Last time it was working was around May 2019.
Recently I tried rerunning the code and I was getting this error message:
Error in rcorr(as.matrix(o_w_CSD_KSS), type = "pearson") :
unused argument (type = "pearson")
Another error message relating to rcorr():
I was learning some statistics from another example and got something like this. (dataset is coming from: https://studysites.uk.sagepub.com/dsur/study/articles.htm under chapter 6.
examData <- read.delim("Exam Anxiety.dat", header = TRUE)
# computing p-values of correlation coefficients
examMatrix<-as.matrix(examData[, c("Exam", "Anxiety")])
rcorr(examMatrix)
[20,] -0.001405012 0.15748544 -0.0729578499 0.302848404 0.157681656 -0.099289738 -0.092430213 -0.19978157
[21,] -0.062027634 0.02261721 -0.1519534279 0.180263508 0.132594815 -0.157301698 0.051600195 -0.31588050
[22,] 0.137019938 0.01987143 -0.0815079170 0.062882864 -0.016685165 -0.056887589 -0.075454718 -0.09027757
[23,] -0.074338494 -0.01589323 0.0340466644 0.102513765 -0.144096280 -0.007199578 0.136943954 -0.07506429
[24,] -0.053900968 -0.22150185 0.0725679656 0.081125188 0.523507004 0.099360897 -0.106041345 0.14067532
[25,] 0.201393705 -0.09765226 -0.2067822590 -0.146102846 0.002855684 -0.111788818 0.055571926 -0.05463886
[ reached getOption("max.print") -- omitted 15 rows ]
> # or
> # rcorr(as.matrix(examData[, c("Exam", "Anxiety", "Revise")]))
Warning message:
In matrix(rnorm(n * d), n, d) :
data length [206] is not a sub-multiple or multiple of the number of rows [40]
I'm using:
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RColorBrewer_1.1-2 scales_1.0.0 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.0.1
[6] purrr_0.3.2 readr_1.3.1 tibble_2.1.1 tidyverse_1.2.1 reshape2_1.4.3
[11] lubridate_1.7.4 anytime_0.3.3 tidyr_0.8.3 tictoc_1.0 polycor_0.7-10
[16] ggm_2.3 igraph_1.2.4.1 Hmisc_4.2-0 Formula_1.2-3 survival_2.44-1.1
[21] lattice_0.20-38 car_3.0-5 carData_3.0-3 ggplot2_3.1.1
Hi,
I'm using R3.6.1 and I have just installed Hmisc. The reported version is 4.3.0 in my Windows installation. I tried your first example and got a correct answer. I think you should update to the last version of Hmisc and retry from a clean and empty environment. In my test, I don't have that many packages loaded.
Best.
library(Hmisc) ; x <- c(-2, -1, 0, 1, 2); y <- c(4, 1, 0, 1, 4); z <- c(1, 2, 3, 4, NA); v <- c(1, 2, 3, 4, 5); rcorr(cbind(x,y)) ; sessionInfo()
#> Loading required package: lattice
#> Loading required package: survival
#> Loading required package: Formula
#> Loading required package: ggplot2
#>
#> Attaching package: 'Hmisc'
#> The following objects are masked from 'package:base':
#>
#> format.pval, units
#> x y
#> x 1 0
#> y 0 1
#>
#> n= 5
#>
#>
#> P
#> x y
#> x 1
#> y 1
#> R version 3.6.1 (2019-07-05)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 7 x64 (build 7601) Service Pack 1
#>
#> Matrix products: default
#>
#> locale:
#> [1] LC_COLLATE=English_United Kingdom.1252
#> [2] LC_CTYPE=English_United Kingdom.1252
#> [3] LC_MONETARY=English_United Kingdom.1252
#> [4] LC_NUMERIC=C
#> [5] LC_TIME=English_United Kingdom.1252
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] Hmisc_4.3-0 ggplot2_3.2.1 Formula_1.2-3 survival_2.44-1.1
#> [5] lattice_0.20-38
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.3 RColorBrewer_1.1-2 pillar_1.4.2
#> [4] compiler_3.6.1 highr_0.8 base64enc_0.1-3
#> [7] tools_3.6.1 rpart_4.1-15 digest_0.6.22
#> [10] checkmate_1.9.4 htmlTable_1.13.2 evaluate_0.14
#> [13] tibble_2.1.3 gtable_0.3.0 pkgconfig_2.0.3
#> [16] rlang_0.4.1 Matrix_1.2-17 rstudioapi_0.10
#> [19] yaml_2.2.0 xfun_0.11 gridExtra_2.3
#> [22] cluster_2.1.0 withr_2.1.2 stringr_1.4.0
#> [25] dplyr_0.8.3 knitr_1.26 htmlwidgets_1.5.1
#> [28] nnet_7.3-12 grid_3.6.1 tidyselect_0.2.5
#> [31] data.table_1.12.6 glue_1.3.1 R6_2.4.1
#> [34] foreign_0.8-71 rmarkdown_1.17 latticeExtra_0.6-28
#> [37] purrr_0.3.3 magrittr_1.5 backports_1.1.5
#> [40] scales_1.0.0 htmltools_0.4.0 splines_3.6.1
#> [43] assertthat_0.2.1 colorspace_1.4-1 stringi_1.4.3
#> [46] acepack_1.4.1 lazyeval_0.2.2 munsell_0.5.0
#> [49] crayon_1.3.4Created on 2019-11-23 by the reprex package (v0.3.0)
Hi SamGG,
Thank you for your fast reply.
Apparently the problem came from different packages I had loaded. Your hint to provide a clean environment helped me.