could not find function "getClades2"

[johnsnowgo]

Hi, I got this Error could not find function "getClades2" when I run the command myclades=getClades2(tree,MinTotalSize=5, MinTrimSize=5, OverlapCutoff=1, TimeFrame=3) in code/Data_5_1_3.R to compute the features. And I have already import all packages and function this R script need. Could you please help me to solve this problem?

These are my R sessionInfo(): R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] seqinr_4.2-30 treeCentrality_0.1.0 devtools_2.4.5 usethis_2.1.6
[5] moments_0.14.1 phyloTop_2.1.2 igraph_1.3.5 apTreeshape_1.5-0
[9] phangorn_2.11.1 ape_5.7-1

loaded via a namespace (and not attached): [1] httr_1.4.4 tidyr_1.2.1 pkgload_1.3.1 splines_4.2.2 carData_3.0-5
[6] shiny_1.7.3 assertthat_0.2.1 stats4_4.2.2 progress_1.2.2 remotes_2.4.2
[11] sessioninfo_1.2.2 pillar_1.8.1 lattice_0.20-45 quantreg_5.94 glue_1.6.2
[16] quadprog_1.5-8 uuid_1.1-0 digest_0.6.30 promises_1.2.0.1 htmltools_0.5.3
[21] httpuv_1.6.6 Matrix_1.5-1 plyr_1.8.8 XML_3.99-0.14 pkgconfig_2.0.3
[26] rncl_0.8.7 SparseM_1.81 purrr_0.3.5 phylobase_0.8.10 xtable_1.8-4
[31] NHPoisson_3.3 processx_3.8.0 later_1.3.0 cubature_2.1.0 MatrixModels_0.5-1 [36] tibble_3.1.8 generics_0.1.3 car_3.1-1 ellipsis_0.3.2 withr_2.5.0
[41] cachem_1.0.6 pbapply_1.6-0 cli_3.4.1 survival_3.4-0 magrittr_2.0.3
[46] crayon_1.5.2 mime_0.12 memoise_2.0.1 ps_1.7.2 fs_1.5.2
[51] fansi_1.0.3 nlme_3.1-160 MASS_7.3-58.1 xml2_1.3.3 pkgbuild_1.3.1
[56] profvis_0.3.7 tools_4.2.2 prettyunits_1.1.1 hms_1.1.2 lifecycle_1.0.3
[61] stringr_1.4.1 callr_3.7.3 ade4_1.7-22 compiler_4.2.2 RNeXML_2.4.11
[66] rlang_1.0.6 grid_4.2.2 rstudioapi_0.14 htmlwidgets_1.5.4 miniUI_0.1.1.1
[71] codetools_0.2-18 curl_4.3.3 abind_1.4-5 DBI_1.1.3 reshape2_1.4.4
[76] R6_2.5.1 dplyr_1.0.10 fastmap_1.1.0 utf8_1.2.2 fastmatch_1.1-4
[81] stringi_1.7.8 parallel_4.2.2 Rcpp_1.0.9 vctrs_0.5.0 tidyselect_1.2.0
[86] urlchecker_1.0.1 coda_0.19-4

[HayatiMar]

Hello,

I have updated "Tree_Statistics.R", so it includes "getClades2". Please try it again.

Thanks, Maryam

On Tue, Nov 7, 2023 at 11:14 PM johnsnowgo @.***> wrote:

Hi, I got this Error could not find function "getClades2" when I run the command myclades=getClades2(tree,MinTotalSize=5, MinTrimSize=5, OverlapCutoff=1, TimeFrame=3) in code/Data_5_1_3.R to compute the features. And I have already import all packages and function this R script need. Could you please help me to solve this problem?

These are my R sessionInfo(): R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] seqinr_4.2-30 treeCentrality_0.1.0 devtools_2.4.5 usethis_2.1.6 [5] moments_0.14.1 phyloTop_2.1.2 igraph_1.3.5 apTreeshape_1.5-0 [9] phangorn_2.11.1 ape_5.7-1

loaded via a namespace (and not attached): [1] httr_1.4.4 tidyr_1.2.1 pkgload_1.3.1 splines_4.2.2 carData_3.0-5 [6] shiny_1.7.3 assertthat_0.2.1 stats4_4.2.2 progress_1.2.2 remotes_2.4.2 [11] sessioninfo_1.2.2 pillar_1.8.1 lattice_0.20-45 quantreg_5.94 glue_1.6.2 [16] quadprog_1.5-8 uuid_1.1-0 digest_0.6.30 promises_1.2.0.1 htmltools_0.5.3 [21] httpuv_1.6.6 Matrix_1.5-1 plyr_1.8.8 XML_3.99-0.14 pkgconfig_2.0.3 [26] rncl_0.8.7 SparseM_1.81 purrr_0.3.5 phylobase_0.8.10 xtable_1.8-4 [31] NHPoisson_3.3 processx_3.8.0 later_1.3.0 cubature_2.1.0 MatrixModels_0.5-1 [36] tibble_3.1.8 generics_0.1.3 car_3.1-1 ellipsis_0.3.2 withr_2.5.0 [41] cachem_1.0.6 pbapply_1.6-0 cli_3.4.1 survival_3.4-0 magrittr_2.0.3 [46] crayon_1.5.2 mime_0.12 memoise_2.0.1 ps_1.7.2 fs_1.5.2 [51] fansi_1.0.3 nlme_3.1-160 MASS_7.3-58.1 xml2_1.3.3 pkgbuild_1.3.1 [56] profvis_0.3.7 tools_4.2.2 prettyunits_1.1.1 hms_1.1.2 lifecycle_1.0.3 [61] stringr_1.4.1 callr_3.7.3 ade4_1.7-22 compiler_4.2.2 RNeXML_2.4.11 [66] rlang_1.0.6 grid_4.2.2 rstudioapi_0.14 htmlwidgets_1.5.4 miniUI_0.1.1.1 [71] codetools_0.2-18 curl_4.3.3 abind_1.4-5 DBI_1.1.3 reshape2_1.4.4 [76] R6_2.5.1 dplyr_1.0.10 fastmap_1.1.0 utf8_1.2.2 fastmatch_1.1-4 [81] stringi_1.7.8 parallel_4.2.2 Rcpp_1.0.9 vctrs_0.5.0 tidyselect_1.2.0 [86] urlchecker_1.0.1 coda_0.19-4

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[johnsnowgo]

Hello again, I found new Clade_featurs() function was created in code/Data_5_1_3.R. It contained Epitop features but lack of funtion of getEpitopeDist and Error happended for could not find function "getEpitopeDist". Could you please updated function getEpitopeDist . Thanks a lot.

[HayatiMar]

Hello,

Please try the updated file "Data_5_1_3.R" and let me know if it works.

Thanks, Maryam

On Wed, Nov 8, 2023 at 7:10 PM johnsnowgo @.***> wrote:

Hello again, I found new Clade_featurs() function was created in code/Data_5_1_3.R. It contained Epitop features but lack of funtion of getEpitopeDist and Error happended for could not find function "getEpitopeDist". Could you please updated function getEpitopeDist . Thanks a lot.

— Reply to this email directly, view it on GitHub https://github.com/HayatiMar/flu_vaccine/issues/1#issuecomment-1803095292, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5UWFMFYPIIQ5EKD6B3BF3LYDRCT7AVCNFSM6AAAAAA7CMIZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBTGA4TKMRZGI . You are receiving this because you commented.Message ID: @.***>

[johnsnowgo]

Hello, I am happy to tell you that it works! I have to say this part really takes time. And I am sorry to bother you again. I want to know what does the Labels colunm in the last of code/Data_5_1_3.R use for, and how do you clarrify the outcome in the data 2020/mycurrentdata2020_NA.csv ? Thank you so much.