From horacio.samaniego at gmail.com Thu Jan 13 21:14:53 2011 From: horacio.samaniego at gmail.com (Horacio Samaniego) Date: Thu, 13 Jan 2011 17:14:53 -0300 Subject: [Sdmtools-commits] predict gam model.... In-Reply-To: References: Message-ID: I just saw this great project and email list.... congrats for this much needed initiative!! Am I the first to email??? buuuhh Anyway, I've just send this question to the R-sig-geo llist but believe that this forum should be more appropriate. Here I go! Hi, I'm having some trouble on a very basic operation it seems.... I am not successful generating GAM predictions on a grid. I suspect an issue with NA's but are not sure what it is. I get the following error: > preds[["gam1"]]=predict(gam4.1,newdata=clima4.1,type="response")*100 Error in `[[<-.data.frame`(`*tmp*`, i, value = c(NA, NA, 0.259444360380994, ?: ?replacement has 88486 rows, data has 996705 Any hint on where the discrepancy between rows come from?.... basically, ?don't think that I'm fully understanding the error. Thanks, Here's a description of the dataset employed. 1st) I adjusted a gam (from mgcv's library) mod.gam1 <- gam(formula = resp ~ s(tmin_yr_3km) + s(bio4_3km) + s(bio15_3km) + s(Slope_3km) + s(Roughness_3km) + s(Bare_3km) + s(Herb_3km) + s(evi_mean) + s(srtm_3km), family = "binomial", data = data2, method = "GACV.Cp") 2nd) generated grid to hold the prediction (here's the def) > str(preds) Formal class 'SpatialGridDataFrame' [package "sp"] with 6 slots ?..@ data ? ? ? :'data.frame': 996705 obs. of ?0 variables ?..@ grid ? ? ? :Formal class 'GridTopology' [package "sp"] with 3 slots ?.. .. ..@ cellcentre.offset: Named num [1:2] -427500 3475500 ?.. .. .. ..- attr(*, "names")= chr [1:2] "x" "y" ?.. .. ..@ cellsize ? ? ? ? : num [1:2] 3000 3000 ?.. .. ..@ cells.dim ? ? ? ?: int [1:2] 621 1605 ?..@ grid.index : int(0) ?..@ coords ? ? : num [1:2, 1:2] -427500 1432500 3475500 8287500 ?.. ..- attr(*, "dimnames")=List of 2 ?.. .. ..$ : NULL ?.. .. ..$ : chr [1:2] "x" "y" ?..@ bbox ? ? ? : num [1:2, 1:2] -429000 3474000 1434000 8289000 ?.. ..- attr(*, "dimnames")=List of 2 ?.. .. ..$ : chr [1:2] "x" "y" ?.. .. ..$ : chr [1:2] "min" "max" ?..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slots ?.. .. ..@ projargs: chr " +proj=utm +south +no_defs +zone=19 +a=6378137 +rf=298.257223563 +towgs84=0.000,0.000,0.000 +to_meter=1" HERE's are the variables where this grid came from: > str(clima4.1) Formal class 'SpatialGridDataFrame' [package "sp"] with 6 slots ?..@ data ? ? ? :'data.frame': 996705 obs. of ?15 variables: ?.. ..$ tmin_yr_3km ?: int [1:996705] NA NA NA NA NA NA NA NA NA NA ... ?.. ..$ tmax_yr_3km ?: int [1:996705] NA NA NA NA NA NA NA NA NA NA ... ?.. ..$ bio1_3km ? ? : int [1:996705] NA NA NA NA NA NA NA NA NA NA ... ?.. ..$ bio4_3km ? ? : int [1:996705] NA NA NA NA NA NA NA NA NA NA ... ?.. ..$ bio12_3km ? ?: int [1:996705] NA NA NA NA NA NA NA NA NA NA ... ?.. ..$ bio15_3km ? ?: int [1:996705] NA NA NA NA NA NA NA NA NA NA ... ?.. ..$ Aspect_3km ? : num [1:996705] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... ?.. ..$ Slope_3km ? ?: num [1:996705] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... ?.. ..$ Roughness_3km: num [1:996705] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... ?.. ..$ Tree_3km ? ? : int [1:996705] NA NA NA NA NA NA NA NA NA NA ... ?.. ..$ Bare_3km ? ? : int [1:996705] NA NA NA NA NA NA NA NA NA NA ... ?.. ..$ Herb_3km ? ? : int [1:996705] NA NA NA NA NA NA NA NA NA NA ... ?.. ..$ evi_mean ? ? : num [1:996705] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... ?.. ..$ clpop2008 ? ?: num [1:996705] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... ?.. ..$ srtm_3km ? ? : int [1:996705] NA NA NA NA NA NA NA NA NA NA ... ?..@ grid ? ? ? :Formal class 'GridTopology' [package "sp"] with 3 slots ?.. .. ..@ cellcentre.offset: Named num [1:2] -427500 3475500 ?.. .. .. ..- attr(*, "names")= chr [1:2] "x" "y" ?.. .. ..@ cellsize ? ? ? ? : num [1:2] 3000 3000 ?.. .. ..@ cells.dim ? ? ? ?: int [1:2] 621 1605 ?..@ grid.index : int(0) ?..@ coords ? ? : num [1:2, 1:2] -427500 1432500 3475500 8287500 ?.. ..- attr(*, "dimnames")=List of 2 ?.. .. ..$ : NULL ?.. .. ..$ : chr [1:2] "x" "y" ?..@ bbox ? ? ? : num [1:2, 1:2] -429000 3474000 1434000 8289000 ?.. ..- attr(*, "dimnames")=List of 2 ?.. .. ..$ : chr [1:2] "x" "y" ?.. .. ..$ : chr [1:2] "min" "max" ?..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slots ?.. .. ..@ projargs: chr " +proj=utm +south +no_defs +zone=19 +a=6378137 +rf=298.257223563 +towgs84=0.000,0.000,0.000 +to_meter=1" Data to model: > str(data2) 'data.frame': ? 1252 obs. of ?18 variables: ?$ tmin_yr_3km ?: int ?1 1 1 1 1 1 0 0 1 0 ... ?$ tmax_yr_3km ?: int ?10 11 10 10 9 8 17 18 10 13 ... ?$ bio1_3km ? ? : int ?59 65 62 63 56 52 82 94 59 67 ... ?$ bio4_3km ? ? : int ?3818 3610 3717 3687 2928 2777 2413 2415 3677 3486 ... ?$ bio12_3km ? ?: int ?567 609 509 487 339 567 184 167 568 226 ... ?$ bio15_3km ? ?: int ?31 15 17 17 20 16 166 165 16 92 ... ?$ Aspect_3km ? : num ?136 200 202 112 149 ... ?$ Slope_3km ? ?: num ?8.38 2.47 5.39 5.59 1.21 ... ?$ Roughness_3km: num ?417.7 141.2 249.4 255.2 70.3 ... ?$ Tree_3km ? ? : int ?8 12 7 7 11 34 2 2 14 0 ... ?$ Bare_3km ? ? : int ?21 37 18 53 13 37 2 3 17 0 ... ?$ Herb_3km ? ? : int ?78 67 83 74 79 65 61 55 79 22 ... ?$ evi_mean ? ? : num ?0.191 0.187 0.24 0.214 0.311 ... ?$ clpop2008 ? ?: num ?0 0.628 1.04 0.339 0 ... ?$ srtm_3km ? ? : int ?675 242 389 250 208 185 3492 3288 413 2306 ... ?$ resp ? ? ? ? : num ?1 1 1 1 1 1 1 1 1 1 ... ?$ X ? ? ? ? ? ?: num ?250553 236521 243073 246358 483071 ... ?$ Y ? ? ? ? ? ?: num ?4781714 4341028 4352441 4337020 4130890 ... -- Instituto de Silvicultura Universidad Austral de Chile Isla Teja, Valdivia, Chile +56 (63) 222480 [of.] http://www.ecoinformatica.cl