Could not find function "gstat.randtest"

[D.Garrett]

Hi all,

I am having a lot of difficulty trying to use gstat.randtest in RStudio. All packages are in (ade4, adegenet, hierfstat) and data is in genind. Latest version of R (4.0.3).

#script:
gtest <- gstat.randtest(obj2,nsim=99)
gtest
plot(gtest)

Console:

gtest <- gstat.randtest(obj2,nsim=99)
Error in gstat.randtest(obj2, nsim = 99) :
could not find function "gstat.randtest"

Even using the nancycats genind, I still get the same error.

I am working through the basic tutorial for adegenet. Closed RStudio and loaded everything again but to no avail.

Any help or tips would be really appreciated.

Thank you

[nirgrahamuk]

Libraries need to be loaded into R sessions

library(adegenet)

[D.Garrett]

Hi,

Sorry if I wasn't clear. Libraries of these have been loaded.

install.packages("devtools")
library(usethis)
library("devtools")

install.packages("ade4")
library("ade4")
install.packages("adegenet")
library("adegenet")
install.packages("hierfstat")
library("hierfstat")

All loaded correctly without errors and get:

gtest <- gstat.randtest(obj2,nsim=99)
Error in gstat.randtest(obj2, nsim = 99) :
could not find function "gstat.randtest"

[nirgrahamuk]

getAnywhere(gstat.randtest)
sessionInfo()

[D.Garrett]

Hi nigrahamuk,

This is what I get back from those commands:

Console:

gtest <- gstat.randtest(obj2,nsim=99)
Error in gstat.randtest(obj2, nsim = 99) :
could not find function "gstat.randtest"
gtest
Error: object 'gtest' not found
getAnywhere(gstat.randtest)
no object named ‘gstat.randtest’ was found
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

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] pegas_0.14 ape_5.4-1 adegenet_2.1.3 readxl_1.3.1
[5] hierfstat_0.5-7 ade4_1.7-16

loaded via a namespace (and not attached):
[1] splines_4.0.3 gtools_3.8.2 shiny_1.5.0
[4] assertthat_0.2.1 expm_0.999-5 sp_1.4-4
[7] cellranger_1.1.0 LearnBayes_2.15.1 progress_1.2.2
[10] pillar_1.4.7 lattice_0.20-41 glue_1.4.2
[13] digest_0.6.27 promises_1.1.1 colorspace_2.0-0
[16] htmltools_0.5.0 httpuv_1.5.4 Matrix_1.2-18
[19] plyr_1.8.6 pkgconfig_2.0.3 raster_3.4-5
[22] gmodels_2.18.1 purrr_0.3.4 xtable_1.8-4
[25] scales_1.1.1 gdata_2.18.0 later_1.1.0.1
[28] tibble_3.0.4 mgcv_1.8-33 generics_0.1.0
[31] ggplot2_3.3.2 ellipsis_0.3.1 cli_2.2.0
[34] magrittr_2.0.1 crayon_1.3.4 mime_0.9
[37] deldir_0.2-3 fansi_0.4.1 nlme_3.1-150
[40] MASS_7.3-53 class_7.3-17 vegan_2.5-6
[43] tools_4.0.3 prettyunits_1.1.1 hms_0.5.3
[46] lifecycle_0.2.0 stringr_1.4.0 munsell_0.5.0
[49] cluster_2.1.0 compiler_4.0.3 e1071_1.7-4
[52] rlang_0.4.8 classInt_0.4-3 units_0.6-7
[55] grid_4.0.3 rstudioapi_0.13 igraph_1.2.6
[58] boot_1.3-25 gtable_0.3.0 codetools_0.2-18
[61] DBI_1.1.0 reshape2_1.4.4 R6_2.5.0
[64] dplyr_1.0.2 utf8_1.1.4 fastmap_1.0.1
[67] seqinr_4.2-4 spdep_1.1-5 KernSmooth_2.23-18
[70] permute_0.9-5 stringi_1.5.3 parallel_4.0.3
[73] Rcpp_1.0.5 vctrs_0.3.5 sf_0.9-6
[76] spData_0.3.8 tidyselect_1.1.0 coda_0.19-4

[nirgrahamuk]

According to this

commenting all

. That function was removed from that package back in 2015. Supposedly would be in hierfstat, but not in that name, perhaps it got renamed along the way. Perhaps contact / raise an issue with the package developer...

[D.Garrett]

Right, that would make sense. I will see what it may have been renamed to and, failing that, will contact the package developer.

Thank you very much for your help.