do_many,do_any, and final_model

[eliascherenet]

I was running the following code:
final_model(species_name = species[1],
algorithms = NULL, #if null it will take all the algorithms in disk
models_dir = test_folder,
which_models = c("raw_mean",
"bin_mean",
"bin_consensus"),
consensus_level = 0.5,
uncertainty = TRUE,
overwrite = TRUE)

ens <- ensemble_model

However, I found the following error
Error in final_model(species_name = species[1], algorithms = NULL, models_dir = test_folder, :
could not find function "final_model"
Error in ensemble_model(species_name = species[1], occurrences = occs, :
could not find function "ensemble_model"

I need your help on how to fix this issue.

[AndreaSanchezTapia]

Hello @eliascherenet can you provide more details about your code? It seems as though modleR wasn't installed on your computer, or not loaded correctly.

[eliascherenet]

dear Andrea, Please find attached my code and i need your help where to set the code in order to calculate the uncertainty and sensitivity analysis. Elias

…

On Wed, Oct 7, 2020 at 8:03 AM AndreaSanchezTapia ***@***.***> wrote: Hello @eliascherenet <https://github.com/eliascherenet> can you provide more details about your code? It seems as though modleR wasn't installed on your computer, or not loaded correctly. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#79 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD4I2LCVI7YVF6JPIJ2QOD3SJPZBHANCNFSM4SENBPZQ> .

-- +++++++++++++++++++++++++++++++++++++++++++++ Elias Cherenet Weldemariam(MSc, BSc) Lecturer(GIS and Remote Sensing) Coordinator, Department of Geo-information Science (GIS) Haramaya University, Ethiopia Email: eliachent@gmail.com, elubdu1999@yahoo.com Skype: elias.weld, +251(0)966429087 ++++++++++++++++++++++++++++++++++++++++++++++

[eliascherenet]

dear Andrea,, I hope you have got my attachment file in my previous email. Looking your help soon. regards

…

On Wed, Oct 7, 2020 at 8:28 AM Elias Cherenet ***@***.***> wrote: dear Andrea, Please find attached my code and i need your help where to set the code in order to calculate the uncertainty and sensitivity analysis. Elias On Wed, Oct 7, 2020 at 8:03 AM AndreaSanchezTapia < ***@***.***> wrote: > Hello @eliascherenet <https://github.com/eliascherenet> can you provide > more details about your code? It seems as though modleR wasn't installed on > your computer, or not loaded correctly. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#79 (comment)>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AD4I2LCVI7YVF6JPIJ2QOD3SJPZBHANCNFSM4SENBPZQ> > . > -- +++++++++++++++++++++++++++++++++++++++++++++ Elias Cherenet Weldemariam(MSc, BSc) Lecturer(GIS and Remote Sensing) Coordinator, Department of Geo-information Science (GIS) Haramaya University, Ethiopia Email: ***@***.***, ***@***.*** Skype: elias.weld, +251(0)966429087 ++++++++++++++++++++++++++++++++++++++++++++++

-- +++++++++++++++++++++++++++++++++++++++++++++ Elias Cherenet Weldemariam(MSc, BSc) Lecturer(GIS and Remote Sensing) Coordinator, Department of Geo-information Science (GIS) Haramaya University, Ethiopia Email: eliachent@gmail.com, elubdu1999@yahoo.com Skype: elias.weld, +251(0)966429087 ++++++++++++++++++++++++++++++++++++++++++++++

[AndreaSanchezTapia]

Hello Elias, GitHub does not allow for attachments.
Can you post a reproducible example of your code? Are you sure that modleR is correctly installed on your computer?

[eliascherenet]

dear Andrea, I found this " modelr" from the installation but didn't get the one mentioned in the GitHub" modleR " . I do not know if this is the same and have similar function. please find also my code here: library(maptools) ## For wrld_simpl library(raster) library(dismo) library(rgdal) library(raster) library(ggplot2) library(parallel) library(tidyr) library(dplyr) file <- paste(system.file(package="dismo"), "/ex/sena.csv", sep="") file sp<- read.csv("C:/Users/user/Desktop/ex/sena.csv") head(sp) colnames(sp) class(sp)## this is data frame not spatial point, to change from datafram to spatial... setwd("C:/Users/user/Desktop/ex/wc2.1_10m_elev") #sp$species<- 1 # to add new columun #sp<-sp[,c('lon','lat','species')]## to combine the new column and other column from original data #head(sp) #class(sp) #coordinates(sp)<- ~lon + lat #class(sp) #head(sp) sp library(maptools) data(wrld_simpl) plot(wrld_simpl, xlim=c(27,27), ylim=c(-35,35), axes=TRUE,col="light yellow") # restore the box around the map box() # plot points points(sp$long, sp$lat, col='orange', pch=20, cex=0.75) # plot points again to add a border, for better visibility points(sp$long, sp$lat, col='red', cex=0.75) coordinates(sp) <- ~long+lat crs(sp) <- crs(wrld_simpl) class(sp) #class(wrld_simpl) #ovr <- over(sp, wrld_simpl) #head(ovr) #tail(ovr) #cntr <- ovr$NAME #i <- which(is.na(cntr)) #i #j <- which(cntr != sp$country) #cbind(cntr, sp$country)[j,] #plot(sp) #plot(wrld_simpl, add=T, border='blue', lwd=1) #points(sp[j, ], col='yellow', pch=20, cex=2) sp<-sp[c('species')] class(sp) head(sp) bio1 <- raster::getData('worldclim', var='bio', res=5) bio <- stack(bio1) bio #plot(bio) elev <- raster("wc2.1_5m_elev.tif") elev #plot(elev) bio <- stack(bio1,elev) bio <- raster::stack(bio1) #plot(bio) bio e <- extent(bio) p <- as(e, 'SpatialPolygons') projection(p) <- crs(bio) mask_raster <- function(raster, shape){ outr <- crop(raster, extent(shape)) outr <- mask(outr, p) return(outr) } bio<- mask_raster(raster= bio1, shape = p) elev <- mask_raster(raster= elev, shape = p) bio2 <- stack(bio1,elev) bio2 #plot(bio2) names(bio2) ####################### r <- bio2[[c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20)]] names(r) #names(r) <- c("Temp","Prec") ############ myshp <- readOGR("C:/Users/user/Desktop/ex/Africa.shp") #plot(myshp) bion2 <- raster(r, crs=proj4string(myshp)) r2 <- crop(r, extent(myshp)) bion3 <- mask(r2, myshp) #plot(bion3) #plot(myshp, add=TRUE, lwd=2) bion3 <- stack(bion3) bion3 ################################# myshp <- readOGR("C:/Users/user/Desktop/ex/Africa.shp") plot(myshp) bion2 <- raster(r, crs=proj4string(myshp)) r2 <- crop(r, extent(myshp)) bion3 <- mask(r2, myshp) #plot(bion3) plot(myshp, add=TRUE, lwd=2) bion3 <- stack(bion3) bion3 plot(bion3) plot(bion3[[1]]) ############ install.packages("rgeos") e<-drawExtent() sp<-crop(sp,e) points(sp,col='red') biok<-crop(bion3,e) plot(biok) plot(biok[[1]]) #install.packages("usdm") library(usdm) ex<- raster::extract(biok,sp) head(ex) v1<- vifstep(ex) #v2<- vifcor(bion3, th=0.7) v1 #v2 bm2<-exclude(biok,v1) head(bm2) plot(bm2[[1]]) vif(bion3) ##################### #e<-drawExtent() #sp<-crop(sp,e) #points(sp,col='blues9') #bio #install.packages("usdm") library(usdm) #ex<- raster::extract(bio2,sp) #head(ex) v1<- vifstep(bion3, th=10) v2<- vifcor(bion3, th=0.7) v1 v2 bm2<-exclude(bion3,v1) #plot(bm2[[1]]) ###### to select important variables after VIF #bm2<- bio2[[c('bio2','bio3','bio4','bio8','bio12','bio13','bio14','bio16','bio18','wc2.1_10m_elev')]] #names(bm2) <- c('bio2','bio3','bio4','bio8','bio12','bio13','bio14','bio16','bio18','wc2.1_10m_elev') #bm2 #plot(bm2) #bm2<- bio2[[c('bio1','bio2','bio4','bio12','bio13','bio14','bio17','bio18','wc2.1_10m_elev')]] #names(bm2) <- c('bio1','bio2','bio4','bio12','bio13','bio14','bio17','bio18','wc2.1_10m_elev') #bm2 #plot(bm2) ##############333 #bm2<- bio2[[c('bio1','bio3','bio8','bio9','bio10','bio12','bio14','bio17','wc2.1_10m_elev')]] #names(bm2) <- c('bio1','bio3','bio8','bio9','bio10','bio12','bio14','bio17','wc2.1_10m_elev') #bm2 #plot(bm2) ################3333 #bm2<- bio2[[c('bio1','bio3','bio7','bio9','bio10','bio12','bio14','bio15','bio17','wc2.1_10m_elev')]] #names(bm2) <- c('bio1','bio3','bio7','bio9','bio10','bio12','bio14','bio15','bio17','wc2.1_10m_elev') #bm2 #plot(bm2) ###################### bm2<- bion3[[c('bio1','bio6','bio8','bio9','bio12','bio14','bio17','bio18','wc2.1_5m_elev')]] names(bm2) <- c('bio1','bio6','bio8','bio9','bio12','bio14','bio17','bio18','wc2.1_5m_elev') bm2 #plot(bm2) vif(bm2) ###cliping raster myshp <- readOGR("C:/Users/user/Desktop/ex/Africa.shp") plot(myshp) biom2 <- raster(bm2, crs=proj4string(myshp)) r2 <- crop(bm2, extent(myshp)) biom3 <- mask(r2, myshp) #plot(biom3) #plot(myshp, add=TRUE, lwd=2) biom3 <- stack(biom3) ## crop points(sp,cex=0.5,pch=16) proj4string(sp)<-projection(raster()) mapview(sp) install.packages('mapview') library(mapview) getmethodNames() mapview(wrld_simpl) installAll() library(sdm) d <- sdmData(species~.,sp,predictors = bm2, bg=list(n=800), method='gRandom',remove=TRUE,seed=47) d m <- sdm(species~.,d, methods = c('glm','svm','rf','brt','gam','fda','mars','mda'), replications= c('boot'),n=10, parallelSetting=list(ncore=4, method='parallel'),seed=47) m p <-predict(m,bion3,'prediction2020.img', overwrite=TRUE) p plot(p) rcurve(m) plot(sdm::getVarImp(m,1:80)) getVarImp(m) install.packages("shiny") library(shiny) installAll() gui(m) library(rgdal) # for vector work; sp package should always load with rgdal. library (raster) en<- ensemble(m,p,'ens2020.img',setting = list(method='weighted',stat='TSS',opt=2),overwrite=TRUE,uncertainty = TRUE,sensitivity = 0.9,consensus_level = 0.5) en plot(en) biof2<-raster::getData('CMIP5',var='bio',res=5,rcp=45, year=70,model='AC') biof <- stack(biof2,elev) names(bio2) names(biof) names(biof)<-names(bio2) names(biof)<-names(bio2) names(biof) ########################## ##################### #elev #plot(elev) #biof <- stack(biof2,elev) #biof #names(biof) #biok <- raster::stack(biof2) #plot(biok) #e <- extent(biok) #p <- as(e, 'SpatialPolygons') #projection(p) <- crs(biok) #mask_raster <- function(raster, shape){ # outr <- crop(raster, extent(shape)) #outr <- mask(outr, p) #return(outr) #} #biok<- mask_raster(raster= biof2, shape = p) #elev <- mask_raster(raster= elev, shape = p) #biol <- stack(biox,elev) #biol #plot(biol) ##############3 ###cliping to afrcia extent myshp <- readOGR("C:/Users/user/Desktop/ex/Africa.shp") #plot(myshp) biof3 <- raster(biof, crs=proj4string(myshp)) r2 <- crop(biof, extent(myshp)) biof3 <- mask(r2, myshp) #plot(biof3) names(biof3) #plot(myshp, add=TRUE, lwd=2) ###end of clipping pf<-predict(m,biof3,'predictf4570.img',overwrite=TRUE) #plot(pf) ##plot(stack(p,pf)) #pf5<-calc(pf,mean) #plot(pf5, main='predicted future') enf5<-ensemble(m,pf,'RCP 4.5 2070.img',overwrite=TRUE, setting = list(methods='weighted',stat='TSS',opt=2)) #plot(enf5, main='average ensf') #enf55<-calc(enf5,mean) #plot(enf55, main= 'mean of ensf') plot(stack(en,enf5)) plot(en) plot(enf5) plot(stack(en,enf5)) ch<-enf5-en plot(ch, main= 'Change') getEvaluation(m,stat='AUC') ##or ev<-getEvaluation(m,stat=c('AUC','TSS','threshold'), opt = 2) mean(ev$threshold) pa<-raster(en) pa[]<-ifelse(en[]>='0.4821103',1,0) plot(pa) pf<-raster(enf5) pf[]<-ifelse(enf5[]>='0.4821103',1,0) plot(pf,main='prediction70 after mean') pac<-pf-pa plot(pac, main='Pf-PA') cl<-colorRampPalette(c('red','gray','darkgreen')) plot(pac,col=cl(3),main='PF-PA') library(sp) library(raster) #z<-raster::writeRaster(pac, "changemap.tif") #z <- raster(z) writeRaster(pac, filename="changemap.tif", overwrite=TRUE) rcurve(m,id=2) plot(sdm::getVarImp(m,9)) getVarImp(m) Elias

…

On Fri, Oct 9, 2020 at 10:01 PM AndreaSanchezTapia ***@***.***> wrote: Hello Elias, GitHub does not allow for attachments. Can you post a reproducible example of your code? Are you sure that modleR is correctly installed on your computer? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#79 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD4I2LCCJYAHS4Q75DTAW7DSJ5MY7ANCNFSM4SENBPZQ> .

-- +++++++++++++++++++++++++++++++++++++++++++++ Elias Cherenet Weldemariam(MSc, BSc) Lecturer(GIS and Remote Sensing) Coordinator, Department of Geo-information Science (GIS) Haramaya University, Ethiopia Email: eliachent@gmail.com, elubdu1999@yahoo.com Skype: elias.weld, +251(0)966429087 ++++++++++++++++++++++++++++++++++++++++++++++

[eliascherenet]

dear Andrea,
devtools::load_all("../../1_modleR") failed to run in my machine. and also the loading "modleR " package refused. I need your help in fixing these issues.

[AndreaSanchezTapia]

Hello Elias, when reading your script I can see that you are not using modleR but other packages, such as sdm and usdm.
As far as modleR goes, if
library(modleR)
tells you there is no package, you must install it, via remotes::install_github()
Check the README for installation:

remotes::install_github("Model-R/modleR",
                        build = TRUE,
                        dependencies = TRUE,
                        build_opts = c("--no-resave-data", "--no-manual"),
                        build_vignettes = TRUE)

devtools::load_all() is a command used for development and it is not meant to be run, you can skip that.

[eliascherenet]

final_model(species_name = species[1],
algorithms = NULL, #if null it will take all the algorithms in disk
models_dir = test_folder,
which_models = c("raw_mean",
"bin_mean",
"bin_consensus"),
consensus_level = 0.5,
uncertainty = TRUE,
overwrite = TRUE)
I tried to run the above code for testing purpose and i found the following error,

Abarema_langsdorffii
Reading evaluation files for Abarema_langsdorffii in present
Extracting data for Abarema_langsdorffii bioclim
Reading models from .tif files
Error in x[[1]] : subscript out of bounds
Your help on how to fix this is appreciated!!!!!!

[eliascherenet]

dear Andrea, Good afternoon, when i tried to run the final_model script I got this error. I would like to ask your quick help , on how to fix this problem. I tried to shorten the path but failed to execute. Elias [image: image.png]

…

On Mon, Oct 12, 2020 at 6:54 PM AndreaSanchezTapia ***@***.***> wrote: Hello Elias, when reading your script I can see that you are not using modleR but other packages, such as sdm and usdm. As far as modleR goes, if library(modleR) tells you there is no package, you must install it, via remotes::install_github() Check the README for installation: remotes::install_github("Model-R/modleR", build = TRUE, dependencies = TRUE, build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE) devtools::load_all() is a command used for development and it is not meant to be run, you can skip that. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#79 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD4I2LFLX3SGUNPXHP6TBBDSKMRD5ANCNFSM4SENBPZQ> .

-- +++++++++++++++++++++++++++++++++++++++++++++ Elias Cherenet Weldemariam(MSc, BSc) Lecturer(GIS and Remote Sensing) Coordinator, Department of Geo-information Science (GIS) Haramaya University, Ethiopia Email: eliachent@gmail.com, elubdu1999@yahoo.com Skype: elias.weld, +251(0)966429087 ++++++++++++++++++++++++++++++++++++++++++++++

[AndreaSanchezTapia]

Hi Elias, your attachment is not coming through. Could you send a .zip file with your example data to andreasancheztapia@gmail.com, please? Occurrences for one species, scripts and one or two explanatory variables should be enough. I would like to examine a reproducible example of your code.