Lara Dutra Silva
2017-Oct-21 00:11 UTC
[R] Help_urgent_how to calculate mean and sd in biomod 2
Hello I am new in R. I am trying to implement Biomod 2 package. However, I have a doubt. I want to calculate the mean and sd of "Testing.data" (ROC and TSS)> # let's print the ROC scores of all selected models> myBiomodModelEval_55["ROC","Testing.data",,,]RUN1 RUN2 RUN3 RUN4 RUN5 RUN6 RUN7 RUN8 RUN9 RUN10 0.938 0.938 0.926 0.931 0.939 0.918 0.920 0.914 0.935 0.919>> # let's print the TSS scores> myBiomodModelEval_55["TSS","Testing.data",,,]RUN1 RUN2 RUN3 RUN4 RUN5 RUN6 RUN7 RUN8 RUN9 RUN10 0.746 0.763 0.717 0.758 0.754 0.704 0.700 0.725 0.742 0.721>I try to use "apply" apply(myBiomodModelEval_55["TSS","Testing.data",,,], 1, mean) apply(myBiomodModelEval_55["ROC","Testing.data",,,],1, mean) apply(myBiomodModelEval_55["ROC","Testing.data",,,], 1, sd) apply(myBiomodModelEval_55["TSS","Testing.data",,,], 1, sd) I can not figure it out because it runs error. The problem is in the dimension? Error in apply(myBiomodModelEval_55["TSS", "Testing.data", , , ], 1, mean) : dim(X) must have a positive length>How can I solve this? This is the structure of object> dimnames(myBiomodModelEval_55)[[1]] [1] "ROC" "TSS" [[2]] [1] "Testing.data" "Cutoff" "Sensitivity" "Specificity" [[3]] [1] "GAM" [[4]] [1] "RUN1" "RUN2" "RUN3" "RUN4" "RUN5" "RUN6" "RUN7" "RUN8" "RUN9" [10] "RUN10" [[5]] Acacia_AllData "AllData" Regards, Silva [[alternative HTML version deleted]]
Rui Barradas
2017-Oct-21 04:40 UTC
[R] Help_urgent_how to calculate mean and sd in biomod 2
Hello, This is because myBiomodModelEval_55["ROC","Testing.data",,,] is a vector not an array or matrix. What the error message is saying is that dim() is not returning a value (it's length is not positive, since it cannot be negative length(dim(.)) must be zero). Try it. Or see the class of those objects. class(myBiomodModelEval_55["ROC","Testing.data",,,]) class(myBiomodModelEval_55["TSS","Testing.data",,,]) You do not apply(), simply do mean(myBiomodModelEval_55["ROC","Testing.data",,,]) And the same for sd(). Hope this helps, Rui Barradas Em 21-10-2017 01:11, Lara Dutra Silva escreveu:> Hello > > I am new in R. I am trying to implement Biomod 2 package. > > However, I have a doubt. I want to calculate the mean and sd of > "Testing.data" > (ROC and TSS) > > >> # let's print the ROC scores of all selected models > >> myBiomodModelEval_55["ROC","Testing.data",,,] > > RUN1 RUN2 RUN3 RUN4 RUN5 RUN6 RUN7 RUN8 RUN9 RUN10 > > 0.938 0.938 0.926 0.931 0.939 0.918 0.920 0.914 0.935 0.919 > >> > >> # let's print the TSS scores > >> myBiomodModelEval_55["TSS","Testing.data",,,] > > RUN1 RUN2 RUN3 RUN4 RUN5 RUN6 RUN7 RUN8 RUN9 RUN10 > > 0.746 0.763 0.717 0.758 0.754 0.704 0.700 0.725 0.742 0.721 > >> > > > > I try to use "apply" > > apply(myBiomodModelEval_55["TSS","Testing.data",,,], 1, mean) > > apply(myBiomodModelEval_55["ROC","Testing.data",,,],1, mean) > > apply(myBiomodModelEval_55["ROC","Testing.data",,,], 1, sd) > > apply(myBiomodModelEval_55["TSS","Testing.data",,,], 1, sd) > > > > I can not figure it out because it runs error. > The problem is in the dimension? > > Error in apply(myBiomodModelEval_55["TSS", "Testing.data", , , ], 1, mean) : > > dim(X) must have a positive length > >> > > > How can I solve this? > > This is the structure of object > >> dimnames(myBiomodModelEval_55) > [[1]] > [1] "ROC" "TSS" > > [[2]] > [1] "Testing.data" "Cutoff" "Sensitivity" "Specificity" > > [[3]] > [1] "GAM" > > [[4]] > [1] "RUN1" "RUN2" "RUN3" "RUN4" "RUN5" "RUN6" "RUN7" "RUN8" "RUN9" > [10] "RUN10" > > [[5]] > Acacia_AllData > "AllData" > > > Regards, > Silva > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >
Rui Barradas
2017-Oct-26 20:47 UTC
[R] Help_urgent_how to calculate mean and sd in biomod 2
Ol?, Please keep this in the list, I'm cc-ing r-help at r-project.org. And yes, I am Portuguese but R-Help is a mailing list in the English language. As for your new question, I believe that you should start a new thread. This is completely different from the question on computing mean and sd. Ask a new question. Font "arial" is a Microsoft font and as far as I know is not supported by R. And 'size' is not a graphical parameter. To see the font families supported by R see the help page ?par. Note that width and height are arguments to function ?windows not to function plot. windows(width = 6, height = 5) # open a new window plot(1:10, main = "Teste", family = "serif") #----------- sessionInfo() R version 3.4.2 (2017-09-28) 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=Portuguese_Portugal.1252 LC_CTYPE=Portuguese_Portugal.1252 [3] LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C [5] LC_TIME=Portuguese_Portugal.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ggplot2_2.2.1 lubridate_1.6.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.13 digest_0.6.12 grid_3.4.2 plyr_1.8.4 [5] gtable_0.2.0 magrittr_1.5 scales_0.5.0 rlang_0.1.2 [9] stringi_1.1.5 lazyeval_0.2.0 labeling_0.3 tools_3.4.2 [13] stringr_1.2.0 munsell_0.4.3 compiler_3.4.2 colorspace_1.3-2 [17] tibble_1.3.4 Hope this helps, Rui Barradas Em 26-10-2017 21:09, Lara Dutra Silva escreveu:> Boa noite, > > N?o sei se portugu?s. > > Estou a ter algumas dificuldades na altera??o do tamanho, letra de um > plot, ou seja, as altera??es b?sicas. > Em anexo envio o plot > > O c?digo que estou a utilizar ? o seguinte: > > > plot(proj90PT$Acacia_EMmeanByTSS_mergedAlgo_mergedRun_mergedData, > main= "Present", xlab ="a", ylab="b",width=6,height=5) > > 1) Queria alterar o tipo de letra para "arial" > family = "arial" - ocorreu erro > > 2) O tamanho da letra > size =14 - ocorreu erro > > 3) font > > 4) Tamanho do plot > (width=6,height=5) > > > N?o sei se poder? ajudar-me. Sei que s?o quest?es muito b?sicas. > Tentei enviar um e-mail para r-help at r-project.org > <mailto:r-help at r-project.org> > Cumprimentos, > > Lara Silva > > > > 2017-10-21 13:46 GMT+00:00 Lara Dutra Silva <laradutrasilva at gmail.com > <mailto:laradutrasilva at gmail.com>>: > > Thank you for the information. > > Regards, > > Lara Silva > > 2017-10-21 4:40 GMT+00:00 Rui Barradas <ruipbarradas at sapo.pt > <mailto:ruipbarradas at sapo.pt>>: > > Hello, > > This is because myBiomodModelEval_55["ROC","Testing.data",,,] is > a vector not an array or matrix. What the error message is > saying is that dim() is not returning a value (it's length is > not positive, since it cannot be negative length(dim(.)) must be > zero). Try it. > Or see the class of those objects. > > class(myBiomodModelEval_55["ROC","Testing.data",,,]) > class(myBiomodModelEval_55["TSS","Testing.data",,,]) > > > You do not apply(), simply do > > mean(myBiomodModelEval_55["ROC","Testing.data",,,]) > > And the same for sd(). > > Hope this helps, > > Rui Barradas > > > Em 21-10-2017 01:11, Lara Dutra Silva escreveu: > > Hello > > I am new in R. I am trying to implement Biomod 2 package. > > However, I have a doubt. I want to calculate the mean and sd of > "Testing.data" > (ROC and TSS) > > > # let's print the ROC scores of all selected models > > > myBiomodModelEval_55["ROC","Testing.data",,,] > > > RUN1 RUN2 RUN3 RUN4 RUN5 RUN6 RUN7 RUN8 RUN9 RUN10 > > 0.938 0.938 0.926 0.931 0.939 0.918 0.920 0.914 0.935 0.919 > > > > # let's print the TSS scores > > > myBiomodModelEval_55["TSS","Testing.data",,,] > > > RUN1 RUN2 RUN3 RUN4 RUN5 RUN6 RUN7 RUN8 RUN9 RUN10 > > 0.746 0.763 0.717 0.758 0.754 0.704 0.700 0.725 0.742 0.721 > > > > > > I try to use "apply" > > apply(myBiomodModelEval_55["TSS","Testing.data",,,], 1, mean) > > apply(myBiomodModelEval_55["ROC","Testing.data",,,],1, mean) > > apply(myBiomodModelEval_55["ROC","Testing.data",,,], 1, sd) > > apply(myBiomodModelEval_55["TSS","Testing.data",,,], 1, sd) > > > > I can not figure it out because it runs error. > The problem is in the dimension? > > Error in apply(myBiomodModelEval_55["TSS", "Testing.data", , > , ], 1, mean) : > > dim(X) must have a positive length > > > > > How can I solve this? > > This is the structure of object > > dimnames(myBiomodModelEval_55) > > [[1]] > [1] "ROC" "TSS" > > [[2]] > [1] "Testing.data" "Cutoff" "Sensitivity" "Specificity" > > [[3]] > [1] "GAM" > > [[4]] > [1] "RUN1" "RUN2" "RUN3" "RUN4" "RUN5" "RUN6" > "RUN7" "RUN8" "RUN9" > [10] "RUN10" > > [[5]] > Acacia_AllData > "AllData" > > > Regards, > Silva > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org <mailto:R-help at r-project.org> mailing > list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > <https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > <http://www.R-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible > code. > > > > > -- > > /Lara Dutra da Silva/ > > > > > -- > > /Lara Dutra da Silva/