> # test.plotmo.R: regression tests for plotmo
> # Stephen Milborrow, Petaluma Jan 2007
> 
> print(R.version.string)
[1] "R version 4.4.1 (2024-06-14 ucrt)"
> 
> source("test.prolog.R")
> library(earth)
Loading required package: Formula
Loading required package: plotmo
Loading required package: plotrix
> options(warn=1) # print warnings as they occur
> data(etitanic)
> make.space.for.caption <- function(caption="CAPTION")
+ {
+     oma <- par("oma")
+     needed <- 3
+     # adjust for newlines in caption
+     newlines <- grep("\n", caption)
+     if(length(newlines) > 0)
+         needed <- needed + .5 * newlines # .5 seems enough although 1 in theory
+     if(!is.null(caption) && any(nchar(caption)) && oma[3] <= needed) {
+         oma[3] <- needed
+         par(oma=oma)
+     }
+ }
> dopar <- function(nrows, ncols, caption = "")
+ {
+     cat("                             ", caption, "\n")
+     make.space.for.caption(caption)
+     par(mfrow=c(nrows, ncols))
+     par(mar = c(3, 3, 1.7, 0.5))
+     par(mgp = c(1.6, 0.6, 0))
+     par(cex = 0.7)
+ }
> example(plotmo)

plotmo> if (require(rpart)) {
plotmo+     data(kyphosis)
plotmo+     rpart.model <- rpart(Kyphosis~., data=kyphosis)
plotmo+     # pass type="prob" to plotmo's internal calls to predict.rpart, and
plotmo+     # select the column named "present" from the matrix returned by predict.rpart
plotmo+     plotmo(rpart.model, type="prob", nresponse="present")
plotmo+ }
Loading required package: rpart
 plotmo grid:    Age Number Start
                  87      4    13

plotmo> if (require(earth)) {
plotmo+     data(ozone1)
plotmo+     earth.model <- earth(O3 ~ ., data=ozone1, degree=2)
plotmo+     plotmo(earth.model)
plotmo+     # plotmo(earth.model, pmethod="partdep") # partial dependence plots
plotmo+ }
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> caption <- "basic earth test of plotmo"
> a <- earth(O3 ~ ., data=ozone1, degree=2)
> plotmo(a, degree1=2, degree2=4, caption=caption, trace=-1)
> 
> caption <- "test 5 x 5 layout"
> dopar(1,1,caption)
                              test 5 x 5 layout 
> a <- earth(O3 ~ ., data=ozone1, nk=51, pmethod="n", degree=2)
> plotmo(a, caption=caption, trace=1)
stats::predict(earth.object, NULL, type="response")
stats::fitted(object=earth.object)
got model response from model.frame(O3 ~ vh + wind + humidity + temp + ib...,
                                    data=call$data, na.action="na.fail")

 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5

> 
> caption <- "test 4 x 4 layout with ylab"
> dopar(1,1,caption)
                              test 4 x 4 layout with ylab 
> a <- earth(O3 ~ ., data=ozone1, nk=30, pmethod="n", degree=2)
> plotmo(a, caption=caption, trace=2)
plotmo trace 2: plotmo(object=a, caption=caption, trace=2)
--get.model.env for object with class earth
object call is earth(formula=O3~., data=ozone1, pmethod="n", degree=2, nk=30)
using the environment saved in $terms of the earth model: R_GlobalEnv
--plotmo_prolog for earth object 'a'
--plotmo_x for earth object

get.object.x:
object$x is NULL (and it has no colnames)

object call is earth(formula=O3~., data=ozone1, pmethod="n", degree=2, nk=30)

get.x.from.model.frame:
formula(object) is O3 ~ vh + wind + humidity + temp + ibh + dpg + ibt + vis ...
naked formula is the same
formula is valid, now looking for data for the model.frame
object$model is NULL (and it has no colnames)
object$data is NULL (and it has no colnames)
argument 2 of the call is 'data'
eval(call$data, R_GlobalEnv)
call$data is usable and has column names O3 vh wind humidity temp ibh dpg ibt vis doy
na.action(object) is "na.fail"
stats::model.frame(O3 ~ vh + wind + humidity + temp + ib..., data=call$data, na.action="na.fail")
x=model.frame[,-1] is usable and has column names vh wind humidity temp ibh dpg ibt vis doy
plotmo_x returned[330,9]:
      vh wind humidity temp  ibh dpg ibt vis doy
1   5710    4       28   40 2693 -25  87 250  33
2   5700    3       37   45  590 -24 128 100  34
3   5760    3       51   54 1450  25 139  60  35
... 5720    4       69   35 1568  15 121  60  36
330 5550    4       85   39 5000   8  44 100 390

----Metadata: plotmo_predict with nresponse=NULL and newdata=NULL
calling predict.earth with NULL newdata
stats::predict(earth.object, NULL, type="response")
predict returned[330,1]:
          O3
1   1.240608
2   3.596894
3   7.464276
... 5.282731
330 3.228830
predict after processing with nresponse=NULL is [330,1]:
          O3
1   1.240608
2   3.596894
3   7.464276
... 5.282731
330 3.228830

----Metadata: plotmo_fitted with nresponse=NULL
stats::fitted(object=earth.object)
fitted(object) returned[330,1]:
          O3
1   1.240608
2   3.596894
3   7.464276
... 5.282731
330 3.228830
fitted(object) after processing with nresponse=NULL is [330,1]:
          O3
1   1.240608
2   3.596894
3   7.464276
... 5.282731
330 3.228830

----Metadata: plotmo_y with nresponse=NULL
--plotmo_y with nresponse=NULL for earth object

get.object.y:
object$y is NULL (and it has no colnames)

object call is earth(formula=O3~., data=ozone1, pmethod="n", degree=2, nk=30)

get.y.from.model.frame:
formula(object) is O3 ~ vh + wind + humidity + temp + ibh + dpg + ibt + vis ...
formula is valid, now looking for data for the model.frame
object$model is NULL (and it has no colnames)
object$data is NULL (and it has no colnames)
argument 2 of the call is 'data'
eval(call$data, R_GlobalEnv)
call$data is usable and has column names O3 vh wind humidity temp ibh dpg ibt vis doy
na.action(object) is "na.fail"
stats::model.frame(O3 ~ vh + wind + humidity + temp + ib..., data=call$data, na.action="na.fail")
y=model.frame[,1] is usable and has column name O3
plotmo_y returned[330,1]:
    O3
1    3
2    5
3    5
...  6
330  1
plotmo_y after processing with nresponse=NULL is [330,1]:
    O3
1    3
2    5
3    5
...  6
330  1
converted nresponse=NA to nresponse=1
nresponse=1 (was NA) ncol(fitted) 1 ncol(predict) 1 ncol(y) 1

----Metadata: plotmo_y with nresponse=1
--plotmo_y with nresponse=1 for earth object

get.object.y:
object$y is NULL (and it has no colnames)

object call is earth(formula=O3~., data=ozone1, pmethod="n", degree=2, nk=30)

get.y.from.model.frame:
formula(object) is O3 ~ vh + wind + humidity + temp + ibh + dpg + ibt + vis ...
formula is valid, now looking for data for the model.frame
object$model is NULL (and it has no colnames)
object$data is NULL (and it has no colnames)
argument 2 of the call is 'data'
eval(call$data, R_GlobalEnv)
call$data is usable and has column names O3 vh wind humidity temp ibh dpg ibt vis doy
na.action(object) is "na.fail"
stats::model.frame(O3 ~ vh + wind + humidity + temp + ib..., data=call$data, na.action="na.fail")
y=model.frame[,1] is usable and has column name O3
got model response from model.frame(O3 ~ vh + wind + humidity + temp + ib...,
                                    data=call$data, na.action="na.fail")
plotmo_y returned[330,1]:
    O3
1    3
2    5
3    5
...  6
330  1
plotmo_y after processing with nresponse=1 is [330,1]:
    O3
1    3
2    5
3    5
...  6
330  1
got response name "O3" from yhat
resp.levs is NULL

----Metadata: done

number of x values: vh 53 wind 11 humidity 65 temp 63 ibh 196 dpg 128 ibt 193...

----plotmo_singles for earth object
singles: 4 temp, 5 ibh, 7 ibt, 8 vis, 9 doy 

----plotmo_pairs for earth object
pairs:
      [,1]         [,2]    
 [1,] "1 vh"       "4 temp"
 [2,] "1 vh"       "9 doy" 
 [3,] "2 wind"     "8 vis" 
 [4,] "3 humidity" "4 temp"
 [5,] "4 temp"     "5 ibh" 
 [6,] "4 temp"     "6 dpg" 
 [7,] "4 temp"     "9 doy" 
 [8,] "5 ibh"      "6 dpg" 
 [9,] "7 ibt"      "8 vis" 

graphics::par(mfrow=c(4,4), mgp=c(1.5,0.4,0), tcl=-0.3, font.main=2,
              mar=c(3,2,1.2,0.8), oma=c(0,0,3,0), cex.main=1.1, cex.lab=1,
              cex.axis=1, cex=0.66)

----Figuring out ylim
--get.ylim.by.dummy.plots
--plot.degree1(draw.plot=FALSE)
degree1 plot1 (pmethod "plotmo") variable temp
newdata[50,9]:
      vh wind humidity     temp    ibh dpg   ibt vis   doy
1   5760    5       64 25.00000 2112.5  24 167.5 120 205.5
2   5760    5       64 26.38776 2112.5  24 167.5 120 205.5
3   5760    5       64 27.77551 2112.5  24 167.5 120 205.5
... 5760    5       64 29.16327 2112.5  24 167.5 120 205.5
50  5760    5       64 93.00000 2112.5  24 167.5 120 205.5
stats::predict(earth.object, data.frame[50,9], type="response")
predict returned[50,1]:
           O3
1    8.724965
2    8.813294
3    8.901624
...  8.989953
50  18.716007
predict after processing with nresponse=1 is [50,1]:
           O3
1    8.724965
2    8.813294
3    8.901624
...  8.989953
50  18.716007
Reducing trace level for subsequent degree1 plots
degree1 plot2 (pmethod "plotmo") variable ibh
degree1 plot3 (pmethod "plotmo") variable ibt
degree1 plot4 (pmethod "plotmo") variable vis
degree1 plot5 (pmethod "plotmo") variable doy
--plot.degree2(draw.plot=FALSE)
degree2 plot1 (pmethod "plotmo") variables vh:temp
newdata[400,9]:
          vh wind humidity temp    ibh dpg   ibt vis   doy
1   5320.000    5       64   25 2112.5  24 167.5 120 205.5
2   5353.158    5       64   25 2112.5  24 167.5 120 205.5
3   5386.316    5       64   25 2112.5  24 167.5 120 205.5
... 5419.474    5       64   25 2112.5  24 167.5 120 205.5
400 5950.000    5       64   93 2112.5  24 167.5 120 205.5
stats::predict(earth.object, data.frame[400,9], type="response")
predict returned[400,1]:
          O3
1   10.41649
2   10.28902
3   10.16155
... 10.03408
400 27.17075
predict after processing with nresponse=1 is [400,1]:
          O3
1   10.41649
2   10.28902
3   10.16155
... 10.03408
400 27.17075
Reducing trace level for subsequent degree2 plots
degree2 plot2 (pmethod "plotmo") variables vh:doy
degree2 plot3 (pmethod "plotmo") variables wind:vis
degree2 plot4 (pmethod "plotmo") variables humidity:temp
degree2 plot5 (pmethod "plotmo") variables temp:ibh
degree2 plot6 (pmethod "plotmo") variables temp:dpg
degree2 plot7 (pmethod "plotmo") variables temp:doy
degree2 plot8 (pmethod "plotmo") variables ibh:dpg
degree2 plot9 (pmethod "plotmo") variables ibt:vis
--done get.ylim.by.dummy.plots

ylim c(-33.06, 31.48)    clip TRUE

--plot.degree1(draw.plot=TRUE)

 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5

graphics::plot.default(x=c(25,26.39,27.7...), y=c(8.725,8.813,8...), type="n",
                       main="1 temp", xlab="", ylab="", xaxt="s", yaxt="s",
                       xlim=c(25,93), ylim=c(-33.06,31.48))
--plot.degree2(draw.plot=TRUE)
persp(vh:temp) theta -35
persp(vh:doy) theta -35
persp(wind:vis) theta 145
persp(humidity:temp) theta -35
persp(temp:ibh) theta 235
persp(temp:dpg) theta 235
persp(temp:doy) theta 235
persp(ibh:dpg) theta 235
persp(ibt:vis) theta 235
> 
> caption <- "test 3 x 3 layout"
> dopar(1,1,caption)
                              test 3 x 3 layout 
> a <- earth(O3 ~ ., data=ozone1, nk=16, pmethod="n", degree=2)
> plotmo(a, caption=caption, trace=3)
plotmo trace 3: plotmo(object=a, caption=caption, trace=3)
--get.model.env for object with class earth
object call is earth(formula=O3~., data=ozone1, pmethod="n", degree=2, nk=16)
using the environment saved in $terms of the earth model: R_GlobalEnv
--plotmo_prolog for earth object 'a'
--plotmo_x for earth object

get.object.x:
object$x is NULL (and it has no colnames)

object call is earth(formula=O3~., data=ozone1, pmethod="n", degree=2, nk=16)

get.x.from.model.frame:
formula(object) is O3 ~ vh + wind + humidity + temp + ibh + dpg + ibt + vis ...
naked formula is the same
formula is valid, now looking for data for the model.frame
object$model is NULL (and it has no colnames)
object$data is NULL (and it has no colnames)
argument 2 of the call is 'data'
eval(call$data, R_GlobalEnv)
call$data is usable and has column names O3 vh wind humidity temp ibh dpg ibt vis doy
na.action(object) is "na.fail"
model.env is R_GlobalEnv
data[330,10]:
    O3   vh wind humidity temp  ibh dpg ibt vis doy
1    3 5710    4       28   40 2693 -25  87 250  33
2    5 5700    3       37   45  590 -24 128 100  34
3    5 5760    3       51   54 1450  25 139  60  35
...  6 5720    4       69   35 1568  15 121  60  36
330  1 5550    4       85   39 5000   8  44 100 390
stats::model.frame(O3 ~ vh + wind + humidity + temp + ib..., data=call$data, na.action="na.fail")
model.frame returned[330,10]:
    O3   vh wind humidity temp  ibh dpg ibt vis doy
1    3 5710    4       28   40 2693 -25  87 250  33
2    5 5700    3       37   45  590 -24 128 100  34
3    5 5760    3       51   54 1450  25 139  60  35
...  6 5720    4       69   35 1568  15 121  60  36
330  1 5550    4       85   39 5000   8  44 100 390
x=model.frame[,-1] is usable and has column names vh wind humidity temp ibh dpg ibt vis doy
plotmo_x returned[330,9]:
      vh wind humidity temp  ibh dpg ibt vis doy
1   5710    4       28   40 2693 -25  87 250  33
2   5700    3       37   45  590 -24 128 100  34
3   5760    3       51   54 1450  25 139  60  35
... 5720    4       69   35 1568  15 121  60  36
330 5550    4       85   39 5000   8  44 100 390

----Metadata: plotmo_predict with nresponse=NULL and newdata=NULL
calling predict.earth with NULL newdata
stats::predict(earth.object, NULL, type="response")
predict returned[330,1]:
          O3
1   1.255037
2   4.164931
3   7.585888
... 4.443360
330 1.685101
predict after processing with nresponse=NULL is [330,1]:
          O3
1   1.255037
2   4.164931
3   7.585888
... 4.443360
330 1.685101

----Metadata: plotmo_fitted with nresponse=NULL
stats::fitted(object=earth.object)
fitted(object) returned[330,1]:
          O3
1   1.255037
2   4.164931
3   7.585888
... 4.443360
330 1.685101
fitted(object) after processing with nresponse=NULL is [330,1]:
          O3
1   1.255037
2   4.164931
3   7.585888
... 4.443360
330 1.685101

----Metadata: plotmo_y with nresponse=NULL
--plotmo_y with nresponse=NULL for earth object

get.object.y:
object$y is NULL (and it has no colnames)

object call is earth(formula=O3~., data=ozone1, pmethod="n", degree=2, nk=16)

get.y.from.model.frame:
formula(object) is O3 ~ vh + wind + humidity + temp + ibh + dpg + ibt + vis ...
formula is valid, now looking for data for the model.frame
object$model is NULL (and it has no colnames)
object$data is NULL (and it has no colnames)
argument 2 of the call is 'data'
eval(call$data, R_GlobalEnv)
call$data is usable and has column names O3 vh wind humidity temp ibh dpg ibt vis doy
na.action(object) is "na.fail"
model.env is R_GlobalEnv
data[330,10]:
    O3   vh wind humidity temp  ibh dpg ibt vis doy
1    3 5710    4       28   40 2693 -25  87 250  33
2    5 5700    3       37   45  590 -24 128 100  34
3    5 5760    3       51   54 1450  25 139  60  35
...  6 5720    4       69   35 1568  15 121  60  36
330  1 5550    4       85   39 5000   8  44 100 390
stats::model.frame(O3 ~ vh + wind + humidity + temp + ib..., data=call$data, na.action="na.fail")
model.frame returned[330,10]:
    O3   vh wind humidity temp  ibh dpg ibt vis doy
1    3 5710    4       28   40 2693 -25  87 250  33
2    5 5700    3       37   45  590 -24 128 100  34
3    5 5760    3       51   54 1450  25 139  60  35
...  6 5720    4       69   35 1568  15 121  60  36
330  1 5550    4       85   39 5000   8  44 100 390
y=model.frame[,1] is usable and has column name O3
plotmo_y returned[330,1]:
    O3
1    3
2    5
3    5
...  6
330  1
plotmo_y after processing with nresponse=NULL is [330,1]:
    O3
1    3
2    5
3    5
...  6
330  1
converted nresponse=NA to nresponse=1
nresponse=1 (was NA) ncol(fitted) 1 ncol(predict) 1 ncol(y) 1

----Metadata: plotmo_y with nresponse=1
--plotmo_y with nresponse=1 for earth object

get.object.y:
object$y is NULL (and it has no colnames)

object call is earth(formula=O3~., data=ozone1, pmethod="n", degree=2, nk=16)

get.y.from.model.frame:
formula(object) is O3 ~ vh + wind + humidity + temp + ibh + dpg + ibt + vis ...
formula is valid, now looking for data for the model.frame
object$model is NULL (and it has no colnames)
object$data is NULL (and it has no colnames)
argument 2 of the call is 'data'
eval(call$data, R_GlobalEnv)
call$data is usable and has column names O3 vh wind humidity temp ibh dpg ibt vis doy
na.action(object) is "na.fail"
model.env is R_GlobalEnv
data[330,10]:
    O3   vh wind humidity temp  ibh dpg ibt vis doy
1    3 5710    4       28   40 2693 -25  87 250  33
2    5 5700    3       37   45  590 -24 128 100  34
3    5 5760    3       51   54 1450  25 139  60  35
...  6 5720    4       69   35 1568  15 121  60  36
330  1 5550    4       85   39 5000   8  44 100 390
stats::model.frame(O3 ~ vh + wind + humidity + temp + ib..., data=call$data, na.action="na.fail")
model.frame returned[330,10]:
    O3   vh wind humidity temp  ibh dpg ibt vis doy
1    3 5710    4       28   40 2693 -25  87 250  33
2    5 5700    3       37   45  590 -24 128 100  34
3    5 5760    3       51   54 1450  25 139  60  35
...  6 5720    4       69   35 1568  15 121  60  36
330  1 5550    4       85   39 5000   8  44 100 390
y=model.frame[,1] is usable and has column name O3
got model response from model.frame(O3 ~ vh + wind + humidity + temp + ib...,
                                    data=call$data, na.action="na.fail")
plotmo_y returned[330,1]:
    O3
1    3
2    5
3    5
...  6
330  1
plotmo_y after processing with nresponse=1 is [330,1]:
    O3
1    3
2    5
3    5
...  6
330  1
got response name "O3" from yhat
resp.levs is NULL

----Metadata: done

number of x values: vh 53 wind 11 humidity 65 temp 63 ibh 196 dpg 128 ibt 193...

----plotmo_singles for earth object
singles: 4 temp, 5 ibh, 8 vis, 9 doy 

----plotmo_pairs for earth object
pairs:
     [,1]         [,2]    
[1,] "2 wind"     "8 vis" 
[2,] "3 humidity" "4 temp"
[3,] "4 temp"     "6 dpg" 

do.par invoked call.dots
TRACE do.par called call.dots(par, DROP="*", KEEP="PREFIX,PAR.ARGS",
                         TRACE=if(trace>=2)trace-1e...), SCALAR=TRUE,
                         def.mfrow=c(nrows,nrows), def.mgp=mgp, def.tcl=-0.3,
                         def.font.main=def.font.main, def.mar=mar,
                         def.oma=def.oma, def.cex.main=def.cex.main,
                         def.cex.lab=cex.lab, def.cex.axis=cex.lab,
                         force.cex=cex)
PREFIX par.
DROP .*
KEEP >STANDARDPREFIXES|^force\.|^def\.|^drop\.
     >PREFIX|^par\.
     >CALLARGS|^def\.mfrow$|^def\.mgp$|^def\.tcl$|^def\.font\.main$|^def\.mar$|^def\.oma$|^def\.cex\.main$|^def\.cex\.lab$|^def\.cex\.axis$|^force\.cex$
     >EXPLICIT
     >PAR_ARGS|^adj$|^ann$|^ask$|^bg$|^bty$|^cex$|^cex\.axis$|^cex\.lab$|^cex\.main$|^cex\.sub$|^col\.axis$|^col\.lab$|^col\.main$|^col\.sub$|^crt$|^err$|^family$|^fg$|^fig$|^fin$|^font$|^font\.axis$|^font\.lab$|^font\.main$|^font\.sub$|^lab$|^las$|^lend$|^lheight$|^ljoin$|^lmitre$|^lty$|^mai$|^mar$|^mex$|^mfcol$|^mfg$|^mfrow$|^mgp$|^mkh$|^new$|^oma$|^omd$|^omi$|^pch$|^pin$|^plt$|^ps$|^pty$|^srt$|^tck$|^tcl$|^usr$|^xaxp$|^xaxs$|^xaxt$|^xlog$|^xpd$|^yaxp$|^yaxs$|^yaxt$|^ylbias$|^ylog$
input dotnames       def.mfrow def.mgp def.tcl def.font.main def.mar def.oma def.cex.main def.cex.lab def.cex.axis force.cex
after DROP and KEEP  def.mfrow def.mgp def.tcl def.font.main def.mar def.oma def.cex.main def.cex.lab def.cex.axis force.cex
return dotnames      mfrow mgp tcl font.main mar oma cex.main cex.lab cex.axis cex

graphics::par(mfrow=c(3,3), mgp=c(1.5,0.4,0), tcl=-0.3, font.main=2,
              mar=c(3,2,1.2,0.8), oma=c(0,0,3,0), cex.main=1.2, cex.lab=1,
              cex.axis=1, cex=0.66)

----Figuring out ylim
--get.ylim.by.dummy.plots
--plot.degree1(draw.plot=FALSE)
degree1 plot1 (pmethod "plotmo") variable temp
newdata[50,9]:
      vh wind humidity     temp    ibh dpg   ibt vis   doy
1   5760    5       64 25.00000 2112.5  24 167.5 120 205.5
2   5760    5       64 26.38776 2112.5  24 167.5 120 205.5
3   5760    5       64 27.77551 2112.5  24 167.5 120 205.5
... 5760    5       64 29.16327 2112.5  24 167.5 120 205.5
50  5760    5       64 93.00000 2112.5  24 167.5 120 205.5
stats::predict(earth.object, data.frame[50,9], type="response")
predict returned[50,1]:
           O3
1    5.311674
2    5.527233
3    5.742791
...  5.958350
50  29.012915
predict after processing with nresponse=1 is [50,1]:
           O3
1    5.311674
2    5.527233
3    5.742791
...  5.958350
50  29.012915
degree1 plot2 (pmethod "plotmo") variable ibh
newdata[50,9]:
      vh wind humidity temp       ibh dpg   ibt vis   doy
1   5760    5       64   62  111.0000  24 167.5 120 205.5
2   5760    5       64   62  210.7755  24 167.5 120 205.5
3   5760    5       64   62  310.5510  24 167.5 120 205.5
... 5760    5       64   62  410.3265  24 167.5 120 205.5
50  5760    5       64   62 5000.0000  24 167.5 120 205.5
stats::predict(earth.object, data.frame[50,9], type="response")
predict returned[50,1]:
           O3
1   10.870828
2   11.135522
3   11.400215
... 11.664908
50   9.845279
predict after processing with nresponse=1 is [50,1]:
           O3
1   10.870828
2   11.135522
3   11.400215
... 11.664908
50   9.845279
degree1 plot3 (pmethod "plotmo") variable vis
newdata[50,9]:
      vh wind humidity temp    ibh dpg   ibt        vis   doy
1   5760    5       64   62 2112.5  24 167.5   0.000000 205.5
2   5760    5       64   62 2112.5  24 167.5   7.142857 205.5
3   5760    5       64   62 2112.5  24 167.5  14.285714 205.5
... 5760    5       64   62 2112.5  24 167.5  21.428571 205.5
50  5760    5       64   62 2112.5  24 167.5 350.000000 205.5
stats::predict(earth.object, data.frame[50,9], type="response")
predict returned[50,1]:
          O3
1   14.86257
2   14.72553
3   14.58850
... 14.45147
50  11.88484
predict after processing with nresponse=1 is [50,1]:
          O3
1   14.86257
2   14.72553
3   14.58850
... 14.45147
50  11.88484
degree1 plot4 (pmethod "plotmo") variable doy
newdata[50,9]:
      vh wind humidity temp    ibh dpg   ibt vis       doy
1   5760    5       64   62 2112.5  24 167.5 120  33.00000
2   5760    5       64   62 2112.5  24 167.5 120  40.28571
3   5760    5       64   62 2112.5  24 167.5 120  47.57143
... 5760    5       64   62 2112.5  24 167.5 120  54.85714
50  5760    5       64   62 2112.5  24 167.5 120 390.00000
stats::predict(earth.object, data.frame[50,9], type="response")
predict returned[50,1]:
           O3
1    7.968080
2    8.746490
3    9.524900
... 10.303310
50   8.957033
predict after processing with nresponse=1 is [50,1]:
           O3
1    7.968080
2    8.746490
3    9.524900
... 10.303310
50   8.957033
--plot.degree2(draw.plot=FALSE)
degree2 plot1 (pmethod "plotmo") variables wind:vis
newdata[400,9]:
      vh       wind humidity temp    ibh dpg   ibt vis   doy
1   5760  0.0000000       64   62 2112.5  24 167.5   0 205.5
2   5760  0.5789474       64   62 2112.5  24 167.5   0 205.5
3   5760  1.1578947       64   62 2112.5  24 167.5   0 205.5
... 5760  1.7368421       64   62 2112.5  24 167.5   0 205.5
400 5760 11.0000000       64   62 2112.5  24 167.5 350 205.5
stats::predict(earth.object, data.frame[400,9], type="response")
predict returned[400,1]:
          O3
1   16.19942
2   16.04463
3   15.88983
... 15.73504
400 11.88484
predict after processing with nresponse=1 is [400,1]:
          O3
1   16.19942
2   16.04463
3   15.88983
... 15.73504
400 11.88484
degree2 plot2 (pmethod "plotmo") variables humidity:temp
newdata[400,9]:
      vh wind humidity temp    ibh dpg   ibt vis   doy
1   5760    5 19.00000   25 2112.5  24 167.5 120 205.5
2   5760    5 22.89474   25 2112.5  24 167.5 120 205.5
3   5760    5 26.78947   25 2112.5  24 167.5 120 205.5
... 5760    5 30.68421   25 2112.5  24 167.5 120 205.5
400 5760    5 93.00000   93 2112.5  24 167.5 120 205.5
stats::predict(earth.object, data.frame[400,9], type="response")
predict returned[400,1]:
           O3
1    5.311674
2    5.311674
3    5.311674
...  5.311674
400 32.296021
predict after processing with nresponse=1 is [400,1]:
           O3
1    5.311674
2    5.311674
3    5.311674
...  5.311674
400 32.296021
degree2 plot3 (pmethod "plotmo") variables temp:dpg
newdata[400,9]:
      vh wind humidity     temp    ibh dpg   ibt vis   doy
1   5760    5       64 25.00000 2112.5 -69 167.5 120 205.5
2   5760    5       64 28.57895 2112.5 -69 167.5 120 205.5
3   5760    5       64 32.15789 2112.5 -69 167.5 120 205.5
... 5760    5       64 35.73684 2112.5 -69 167.5 120 205.5
400 5760    5       64 93.00000 2112.5 107 167.5 120 205.5
stats::predict(earth.object, data.frame[400,9], type="response")
predict returned[400,1]:
           O3
1    5.311674
2    5.867588
3    6.423503
...  6.979417
400 -6.671880
predict after processing with nresponse=1 is [400,1]:
           O3
1    5.311674
2    5.867588
3    6.423503
...  6.979417
400 -6.671880
--done get.ylim.by.dummy.plots

ylim c(-6.672, 40.23)    clip TRUE

--plot.degree1(draw.plot=TRUE)

 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5

draw.degree1 invoked call.dots
TRACE draw.degree1 called call.plot(plot.default, PREFIX="degree1.",
                         TRACE=if(isingle==1&&trace...),
                         force.x=xframe[,ipred], force.y=yhat, force.type="n",
                         force.main=main, force.xlab=xlab, force.ylab=ylab,
                         force.xlim=xlim, force.ylim=ylim,
                         def.xaxt=if(xaxis.is.levs)"n"...),
                         def.yaxt=if(yaxis.is.levs)"n"...))
PREFIX degree1.
DROP .*
KEEP >STANDARDPREFIXES|^force\.|^def\.|^drop\.
     >PREFIX|^degree1\.
     >CALLARGS|^force\.x$|^force\.y$|^force\.type$|^force\.main$|^force\.xlab$|^force\.ylab$|^force\.xlim$|^force\.ylim$|^def\.xaxt$|^def\.yaxt$
     >EXPLICIT
     >PLOT_ARGS|^add$|^adj$|^bty$|^cex$|^cex\.axis$|^cex\.lab$|^cex\.main$|^cex\.sub$|^col$|^col\.axis$|^col\.lab$|^col\.main$|^col\.sub$|^crt$|^family$|^font$|^font$|^font\.axis$|^font\.lab$|^font\.main$|^font\.sub$|^lend$|^ljoin$|^lmitre$|^lty$|^lwd$|^main$|^pch$|^srt$|^xaxp$|^xaxs$|^xaxt$|^xlab$|^xlim$|^xlog$|^xpd$|^yaxp$|^yaxs$|^yaxt$|^ylab$|^ylim$|^ylog$
input dotnames       force.x force.y force.type force.main force.xlab force.ylab force.xlim force.ylim def.xaxt def.yaxt
after DROP and KEEP  force.x force.y force.type force.main force.xlab force.ylab force.xlim force.ylim def.xaxt def.yaxt
return dotnames      x y type main xlab ylab xaxt yaxt xlim ylim

graphics::plot.default(x=c(25,26.39,27.7...), y=c(5.312,5.527,5...), type="n",
                       main="1 temp", xlab="", ylab="", xaxt="s", yaxt="s",
                       xlim=c(25,93), ylim=c(-6.67,40.23))
--plot.degree2(draw.plot=TRUE)
persp(wind:vis) theta 145
TRACE plot.persp called deprefix(persp, FNAME="persp", KEEP="PREFIX,PLOT.ARGS",
                         FORMALS=persp.def.formals,
                         TRACE=if(ipair==1&&trace>=...), force.x=x1grid,
                         force.y=x2grid, force.z=yhat,
                         force.xlim=range(x1grid), force.ylim=range(x2grid),
                         force.zlim=if(is.null(ylim))yli...), force.xlab=xlab,
                         force.ylab=ylab, force.theta=theta, force.phi=30,
                         force.d=1, force.main=main2, def.cex.lab=cex.lab,
                         def.cex.axis=cex.lab, def.zlab=zlab,
                         def.ticktype="simple", def.nticks=def.nticks,
                         def.cex=cex1, force.col="lightblue", def.border=NULL,
                         def.shade=0.5)
PREFIX persp.
DROP NULL
KEEP >STANDARDPREFIXES|^force\.|^def\.|^drop\.
     >PREFIX|^persp\.
     >CALLARGS|^force\.x$|^force\.y$|^force\.z$|^force\.xlim$|^force\.ylim$|^force\.zlim$|^force\.xlab$|^force\.ylab$|^force\.theta$|^force\.phi$|^force\.d$|^force\.main$|^def\.cex\.lab$|^def\.cex\.axis$|^def\.zlab$|^def\.ticktype$|^def\.nticks$|^def\.cex$|^force\.col$|^def\.border$|^def\.shade$
     >EXPLICIT
     >PLOT_ARGS|^add$|^adj$|^bty$|^cex$|^cex\.axis$|^cex\.lab$|^cex\.main$|^cex\.sub$|^col$|^col\.axis$|^col\.lab$|^col\.main$|^col\.sub$|^crt$|^family$|^font$|^font$|^font\.axis$|^font\.lab$|^font\.main$|^font\.sub$|^lend$|^ljoin$|^lmitre$|^lty$|^lwd$|^main$|^pch$|^srt$|^xaxp$|^xaxs$|^xaxt$|^xlab$|^xlim$|^xlog$|^xpd$|^yaxp$|^yaxs$|^yaxt$|^ylab$|^ylim$|^ylog$
input dotnames       force.x force.y force.z force.xlim force.ylim force.zlim force.xlab force.ylab force.theta force.phi force.d force.main def.cex.lab def.cex.axis def.zlab def.ticktype def.nticks def.cex force.col def.border def.shade
after DROP and KEEP  force.x force.y force.z force.xlim force.ylim force.zlim force.xlab force.ylab force.theta force.phi force.d force.main def.cex.lab def.cex.axis def.zlab def.ticktype def.nticks def.cex force.col def.shade
return dotnames      x y main xlab ylab cex.lab cex.axis zlab ticktype nticks cex shade z xlim ylim zlim theta phi d col

persp(humidity:temp) theta -35
persp(temp:dpg) theta 235
> 
> caption <- "test 2 x 2 layout"
> dopar(1,1,caption)
                              test 2 x 2 layout 
> a <- earth(O3 ~ ., data=ozone1, nk=9, pmethod="n", degree=2)
> plotmo(a, caption=caption)
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> 
> caption <- "test 1 x 1 layout"
> dopar(1,1,caption)
                              test 1 x 1 layout 
> a <- earth(O3 ~ ., data=ozone1, nk=4, pmethod="n", degree=2)
> plotmo(a, caption=caption)
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> 
> caption <- "test plotmo basic params"
> a <- earth(O3 ~ ., data=ozone1, degree=2)
> dopar(3,2,caption)
                              test plotmo basic params 
> plotmo(a, do.par=FALSE, degree1=1, nrug=-1, degree2=F, caption=caption,
+         main="test main", xlab="test xlab", ylab="test ylab")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> plotmo(a, do.par=FALSE, degree1=F, degree2=4, grid.func=mean, persp.col="white", ngrid2=10, persp.phi=40)
> set.seed(2016)
> plotmo(a, do.par=FALSE, degree1=1, degree1.lty=2, degree1.lwd=4, degree1.col=2, nrug=TRUE, degree2=F, main="nrug=300")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> plotmo(a, do.par=FALSE, degree1=1, nrug=-1, degree2=F, main="nrug=TRUE")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> set.seed(2016)
> plotmo(a, do.par=FALSE, degree1=1, nrug=10, ngrid1=50, degree2=F, main="ngrid1=50 nrug=10")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> plotmo(a, do.par=FALSE, degree1=NA, degree2=1, persp.phi=60) # graph args
> 
> caption <- "test plotmo xlim and ylim"
> a <- earth(O3 ~ ., data=ozone1, degree=2)
> dopar(5,3,caption)
                              test plotmo xlim and ylim 
> plotmo(a, do.par=FALSE, degree1=2:3, degree2=4, caption=caption, xlab="ylim=default")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> plotmo(a, do.par=FALSE, degree1=2:3, degree2=4, ylim=NA, xlab="ylim=NA")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> plotmo(a, do.par=FALSE, degree1=2:3, degree2=4, ylim=c(0,20), xlab="ylim=c(0,20)")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> plotmo(a, do.par=FALSE, degree1=2:3, degree2=4, xlim=c(190,250), xlab="xlim=c(190,250)")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> plotmo(a, do.par=FALSE, degree1=2:3, degree2=4, xlim=c(190,250), ylim=c(11,18), xlab="xlim=c(190,250), ylim=c(11,18)")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> 
> # check various types of predictors with grid.func and ndiscrete
> 
> varied.type.data <- data.frame(
+     y    = 1:13,
+     num  = c(1, 3, 2, 3, 4, 5, 6, 4, 5, 6.5, 3, 6, 5), # 7 unique values (but one is non integral)
+     int  = c(1L, 1L, 3L, 3L, 4L, 4L, 3L, 5L, 3L, 6L, 7L, 8L, 10L), # 8 unique values
+     bool = c(F, F, F, F, F, T, T, T, T, T, T, T, T),
+     date = as.Date(
+            c("2018-08-01", "2018-08-02", "2018-08-03",
+              "2018-08-04", "2018-08-05", "2018-08-06",
+              "2018-08-07", "2018-08-08", "2018-08-08",
+              "2018-08-08", "2018-08-10", "2018-08-11", "2018-08-11")),
+     ord  = ordered(c("ord3", "ord3", "ord3",
+                      "ord1", "ord2", "ord3",
+                      "ord1", "ord2", "ord3",
+                      "ord1", "ord1", "ord1", "ord1"),
+                    levels=c("ord1", "ord3", "ord2")),
+     fac  = as.factor(c("fac1", "fac1", "fac1",
+                        "fac2", "fac2", "fac2",
+                        "fac3", "fac3", "fac3",
+                        "fac1", "fac2", "fac3", "fac3")),
+     str  = c("str1", "str1", "str1", # will be treated like a factor
+              "str2", "str2", "str2",
+              "str3", "str3", "str3",
+              "str3", "str3", "str3", "str3"))
> 
> varied.type.lm <- lm(y ~ ., data = varied.type.data)
> print(summary(varied.type.lm))

Call:
lm(formula = y ~ ., data = varied.type.data)

Residuals:
         1          2          3          4          5          6          7 
 9.619e-02  1.673e-01 -2.635e-01  1.297e-02 -1.297e-02 -6.592e-17 -1.029e-01 
         8          9         10         11         12         13 
 1.297e-02  5.898e-17 -8.674e-17  5.204e-17  5.772e-02  3.220e-02 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)  
(Intercept) -7192.3724  6018.6749  -1.195   0.3546  
num             0.2618     0.1919   1.364   0.3057  
int             0.6437     0.2279   2.824   0.1058  
boolTRUE       -1.7185     0.5305  -3.240   0.0835 .
date            0.4053     0.3392   1.195   0.3547  
ord.L          -0.2014     0.1726  -1.167   0.3637  
ord.Q          -1.5481     0.4045  -3.827   0.0620 .
facfac2         0.4621     1.1289   0.409   0.7219  
facfac3        -0.4299     0.5784  -0.743   0.5348  
strstr2         1.3480     0.8570   1.573   0.2564  
strstr3         5.0732     1.2534   4.048   0.0560 .
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.2471 on 2 degrees of freedom
Multiple R-squared:  0.9993,	Adjusted R-squared:  0.996 
F-statistic: 297.9 on 10 and 2 DF,  p-value: 0.003351

> set.seed(2018)
> plotres(varied.type.lm, info=TRUE)
> plotmo(varied.type.lm, pmethod="apartdep", all2=TRUE, ticktype="d", col.response="red", caption="varied.type.lm\npmethod=\"apartdep\" default grid func")
calculating apartdep for num 
calculating apartdep for int 
calculating apartdep for bool 
calculating apartdep for date 
calculating apartdep for ord 
calculating apartdep for fac 
calculating apartdep for str 
calculating apartdep for num:int 01234567890
calculating apartdep for num:bool 01234567890
calculating apartdep for num:date 01234567890
calculating apartdep for num:ord 01234567890
calculating apartdep for num:fac 01234567890
calculating apartdep for num:str 01234567890
calculating apartdep for int:bool 01234567890
calculating apartdep for int:date 01234567890
calculating apartdep for int:ord 01234567890
calculating apartdep for int:fac 01234567890
calculating apartdep for int:str 01234567890
calculating apartdep for bool:date 0123456790
calculating apartdep for bool:ord 0123456790
calculating apartdep for bool:fac 0123456790
calculating apartdep for bool:str 0123456790
calculating apartdep for date:ord 01234567890
calculating apartdep for date:fac 01234567890
calculating apartdep for date:str 01234567890
calculating apartdep for ord:fac 01234567890
calculating apartdep for ord:str 01234567890
calculating apartdep for fac:str 01234567890
> plotmo(varied.type.lm, all2=TRUE, ticktype="d", col.response="red", caption="varied.type.lm\ndefault grid func")
 plotmo grid:    num int bool       date  ord  fac  str
                   4   4 TRUE 2018-08-07 ord1 fac3 str3
> plotmo(varied.type.lm, all2=TRUE, ndiscre=1, caption="varied.type.lm\nndiscrete=1")
 plotmo grid:    num int bool       date  ord  fac  str
                   4   4 TRUE 2018-08-07 ord1 fac3 str3
> plotmo(varied.type.lm, all2=TRUE, ndiscr=2, caption="varied.type.lm\nndiscrete=2")
 plotmo grid:    num int bool       date  ord  fac  str
                   4   4 TRUE 2018-08-07 ord1 fac3 str3
> plotmo(varied.type.lm, all2=TRUE, ndis=100, caption="varied.type.lm\nndiscrete=100")
 plotmo grid:    num int bool       date  ord  fac  str
                   4   4 TRUE 2018-08-07 ord1 fac3 str3
> cat("grid.func=median:\n")
grid.func=median:
> plotmo(varied.type.lm, all2=TRUE, grid.func=median, caption="varied.type.lm\ngrid.func=median")
Warning: grid.func failed for ord, so will use the most common value of ord
Warning: grid.func failed for fac, so will use the most common value of fac
Warning: grid.func failed for str, so will use the most common value of str
Warning: grid.func failed for ord, so will use the most common value of ord
Warning: grid.func failed for fac, so will use the most common value of fac
Warning: grid.func failed for str, so will use the most common value of str
 plotmo grid:    num int bool       date  ord  fac  str
                   4   4 TRUE 2018-08-07 ord1 fac3 str3
> cat("grid.func=quantile:\n")
grid.func=quantile:
> plotmo(varied.type.lm, all2=TRUE, grid.func=function(x, ...) quantile(x, 0.5), caption="varied.type.lm\ngrid.func=function(x, ...) quantile(x, 0.5)")
Warning: grid.func failed for date, so will use the default grid.func for date
Warning: grid.func failed for ord, so will use the most common value of ord
Warning: grid.func failed for fac, so will use the most common value of fac
Warning: grid.func failed for str, so will use the most common value of str
Warning: grid.func failed for date, so will use the default grid.func for date
Warning: grid.func failed for ord, so will use the most common value of ord
Warning: grid.func failed for fac, so will use the most common value of fac
Warning: grid.func failed for str, so will use the most common value of str
 plotmo grid:    num int bool       date  ord  fac  str
                   4   4 TRUE 2018-08-07 ord1 fac3 str3
> cat("grid.func=mean:\n")
grid.func=mean:
> plotmo(varied.type.lm, all2=TRUE, grid.func=mean, caption="varied.type.lm\ngrid.func=mean")
Warning in mean.default(x, na.rm = TRUE) :
  argument is not numeric or logical: returning NA
Warning: grid.func returned NA for ord, so will use the default grid.func for ord
Warning in mean.default(x, na.rm = TRUE) :
  argument is not numeric or logical: returning NA
Warning: grid.func returned NA for fac, so will use the default grid.func for fac
Warning in mean.default(x, na.rm = TRUE) :
  argument is not numeric or logical: returning NA
Warning: grid.func returned NA for str, so will use the default grid.func for str
Warning in mean.default(x, na.rm = TRUE) :
  argument is not numeric or logical: returning NA
Warning: grid.func returned NA for ord, so will use the default grid.func for ord
Warning in mean.default(x, na.rm = TRUE) :
  argument is not numeric or logical: returning NA
Warning: grid.func returned NA for fac, so will use the default grid.func for fac
Warning in mean.default(x, na.rm = TRUE) :
  argument is not numeric or logical: returning NA
Warning: grid.func returned NA for str, so will use the default grid.func for str
 plotmo grid:    num int bool       date  ord  fac  str
            4.115385   4 TRUE 2018-08-06 ord1 fac3 str3
> 
> varied.type.earth <- earth(y ~ ., data = varied.type.data, thresh=0, penalty=-1, trace=1)
x[13,10] with colnames num int boolTRUE date ord.L ord.Q facfac2 facfac3 strstr2...
y[13,1] with colname y, and values 1, 2, 3, 4, 5, 6, 7, 8, 9, 10...
Forward pass term 1, 2, 4, 6, 8, 10, 12, 14, 16, 18
Reached maximum RSq 1.0000 at 19 terms, 13 terms used (RSq 1.0000)
After forward pass GRSq 1.000 RSq 1.000
Prune backward penalty -1 nprune null: selected 13 of 13 terms, and 9 of 10 preds
After pruning pass GRSq 1 RSq 1
> print(summary(varied.type.earth))
Call: earth(formula=y~., data=varied.type.data, trace=1, thresh=0, penalty=-1)

              coefficients
(Intercept)      9.5964912
boolTRUE        -2.0473684
ord.L            0.4986964
ord.Q            0.0859470
facfac2         -4.4157895
facfac3         -3.1526316
strstr2          3.2526316
h(4-num)         1.4105263
h(num-4)        -0.3157895
h(4-int)         2.1157895
h(int-4)         0.3421053
h(17749-date)   -3.8210526
h(date-17749)    1.4368421

Selected 13 of 13 terms, and 9 of 10 predictors
Termination condition: Reached maximum RSq 1.0000 at 13 terms
Importance: date, facfac2, facfac3, int, strstr2, boolTRUE, num, ord.L, ...
Number of terms at each degree of interaction: 1 12 (additive model)
GCV 0    RSS 0    GRSq 1    RSq 1
> set.seed(2018)
> plotres(varied.type.earth, info=TRUE)
Warning in cor(rank(x), rank(y)) : the standard deviation is zero
Warning: draw.density.along.the.bottom: cannot determine density
> plotmo(varied.type.earth, all1=TRUE, all2=TRUE, persp.ticktype="d", col.response="red")
 plotmo grid:    num int bool       date  ord  fac  str
                   4   4 TRUE 2018-08-07 ord1 fac3 str3
> 
> # term.plot calls predict.earth with an se parameter, even with termplot(se=FALSE)
> 
> caption <- "basic earth test against termplot"
> dopar(4,4,caption)
                              basic earth test against termplot 
> make.space.for.caption("test caption1")
> a <- earth(O3 ~ ., data=ozone1, degree=2)
> plotmo(a, do.par=FALSE, ylim=NA, caption=caption, degree2=FALSE)
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> cat("Ignore warning: predict.earth ignored argument \"se.fit\"\n")
Ignore warning: predict.earth ignored argument "se.fit"
> termplot(a)
Warning: predict.earth ignored argument 'se.fit'
> 
> caption <- "test change order of earth predictors and cex"
> dopar(4,4,caption)
                              test change order of earth predictors and cex 
> # minspan=1 to force two degree2 graphs for the test (wasn't necessary in old versions of earth)
> a <- earth(doy ~ humidity + temp + wind, data=ozone1, degree=2, minspan=1)
> plotmo(a, do.par=FALSE, ylim=NA, caption=caption, degree2=c(1,2), cex=1.2)
 plotmo grid:    humidity temp wind
                       64   62    5
> termplot(a)
Warning: predict.earth ignored argument 'se.fit'
> 
> caption <- "test all1=TRUE"
> a <- earth(doy ~ humidity + temp + wind, data=ozone1, degree=2)
> plotmo(a, caption=caption, all1=TRUE, persp.ticktype="d", persp.nticks=2)
 plotmo grid:    humidity temp wind
                       64   62    5
> caption <- "test all2=TRUE"
> print(summary(a))
Call: earth(formula=doy~humidity+temp+wind, data=ozone1, degree=2)

                            coefficients
(Intercept)                   150.868918
h(humidity-28)                  1.614397
h(49-temp)                     -6.984397
h(3-wind)                      50.527668
h(28-humidity) * h(temp-53)     8.123127
h(28-humidity) * h(53-temp)     1.520105
h(28-humidity) * h(temp-45)     5.390040
h(28-humidity) * h(temp-50)   -12.953206
h(41-humidity) * h(wind-3)     -0.996454

Selected 9 of 18 terms, and 3 of 3 predictors
Termination condition: Reached nk 21
Importance: wind, temp, humidity
Number of terms at each degree of interaction: 1 3 5
GCV 8954.829    RSS 2590958    GRSq 0.1805267    RSq 0.2771303
> plotmo(a, caption=caption, all2=TRUE)
 plotmo grid:    humidity temp wind
                       64   62    5
> 
> oz <- ozone1[150:200,c("O3","temp","humidity","ibh")]
> a.glob <- earth(O3~temp+humidity, data=oz, degree=2)
> ad.glob <- earth(oz[,2:3], oz[,1], degree=2)
> func1 <- function()
+ {
+     caption <- "test environments and finding the correct data"
+     dopar(4,4,caption)
+     set.seed(2016)
+ 
+     plotmo(a.glob, do.par=FALSE, main="a.glob oz",
+           degree1=1, all2=1, degree2=1, type2="im",
+           col.response=3, pt.pch=20, trace=2)
+     mtext(caption, outer=TRUE, font=2, line=1.5, cex=1)
+     plotmo(ad.glob, do.par=FALSE, main="ad.glob oz",
+           degree1=1, all2=1, degree2=1, type2="im",
+           col.response=3, pch.response=20, trace=2) # pch.response test backcompat
+ 
+     a <- earth(O3~temp+humidity, data=oz, degree=2)
+     plotmo(a, do.par=FALSE, main="a oz",
+            degree1=1, all2=1, degree2=1, type2="im",
+            col.response=3, pt.pch=20)
+ 
+     ad <- earth(oz[,2:3], oz[,1], degree=2)
+     plotmo(ad, do.par=FALSE, main="ad oz",
+            degree1=1, all2=1, degree2=1, type2="im",
+            col.response=3, pt.pch=20)
+ 
+     oz.org <- oz
+     oz10 <- 10 * oz # multiply by 10 so we can see by the axis labels if right data is being used
+     oz <- oz10      # oz is now local to this function, but multiplied by 10
+     a.oz10 <- earth(O3~temp+humidity, data=oz, degree=2)
+     a.oz10.keep <- earth(O3~temp+humidity, data=oz, degree=2, keepxy=TRUE)
+     plotmo(a.oz10, do.par=FALSE, main="a oz10",
+            degree1=1, all2=1, degree2=1, type2="im",
+            col.response=3, pt.pch=20)
+ 
+     ad.oz10 <- earth(oz[,2:3], oz[,1], degree=2)
+     ad.oz10.keep <- earth(oz[,2:3], oz[,1], degree=2, keepxy=TRUE)
+     plotmo(ad.oz10, do.par=FALSE, main="ad oz10",
+            degree1=1, all2=1, degree2=1, type2="im",
+            col.response=3, pt.pch=20)
+ 
+     func2 <- function() {
+         a.func <- earth(O3 ~ temp +   humidity, data=oz10, degree=2)
+         plotmo(a.func, do.par=FALSE, main="a.func oz10",
+                degree1=1, all2=1, degree2=1, type2="im",
+                col.response=3, pt.pch=20)
+ 
+         ad.func <- earth(oz10[,2:3], oz10[,1], degree=2)
+         plotmo(ad.func, do.par=FALSE, main="ad.func oz10",
+                degree1=1, all2=1, degree2=1, type2="im",
+                col.response=3, pt.pch=20)
+ 
+         caption <- "test environments and finding the correct data, continued"
+         dopar(4,4,caption)
+ 
+         oz <- .1 * oz.org
+         a.func <- earth(O3~temp+ humidity , data=oz, degree=2)
+         plotmo(a.func, do.par=FALSE, main="a.func oz.1",
+                degree1=1, all2=1, degree2=1, type2="im",
+                col.response=3, pt.pch=20)
+ 
+         ad.func <- earth(oz[,2:3], oz[,1], degree=2)
+         plotmo(ad.func, do.par=FALSE, main="ad.func oz.1",
+                degree1=1, all2=1, degree2=1, type2="im",
+                col.response=3, pt.pch=20)
+ 
+         plotmo(a.oz10.keep, do.par=FALSE, main="func1:a.oz10.keep",
+            degree1=1, all2=1, degree2=1, type2="im",
+            col.response=3, pt.pch=20)
+ 
+         plotmo(ad.oz10.keep, do.par=FALSE, main="func1:ad.oz10.keep",
+            degree1=1, all2=1, degree2=1, type2="im",
+            col.response=3, pt.pch=20)
+ 
+         cat("Expect error msg: formal argument \"do.par\" matched by multiple actual arguments\n")
+         expect.err(try(plotmo(a.oz10, do.par=FALSE, main="func1:a.oz10",
+            degree1=1, all2=1, degree2=1, type2="im",
+            col.response=3, pt.pch=20, do.par=FALSE)))
+     }
+     func2()
+ 
+     y  <- 3:11
+     x1 <- c(1,3,2,4,5,6,6,6,6)
+     x2 <- c(2,3,4,5,6,7,8,9,10)
+     frame <- data.frame(y=y, x1=x1, x2=x2)
+     foo <- function()
+     {
+         lm.18.out <- lm(y~x1+x2, model=FALSE)
+         x1[2] <- 18
+         y[3] <- 19
+         frame <- data.frame(y=y, x1=x1, x2=x2)
+         list(lm.18.out   = lm.18.out,
+              lm.18       = lm(y~x1+x2),
+              lm.18.keep  = lm(y~x1+x2, x=TRUE, y=TRUE),
+              lm.18.frame = lm(y~x1+x2, data=frame))
+     }
+     temp <- foo()
+         lm.18.out   <- temp$lm.18.out
+         lm.18       <- temp$lm.18
+         lm.18.keep  <- temp$lm.18.keep
+         lm.18.frame <- temp$lm.18.frame
+ 
+     # following should all use the x1 and y inside foo
+ 
+     cat("==lm.18.out\n")
+     plotmo(lm.18.out, main="lm.18.out",
+            do.par=FALSE, degree1=1, clip=FALSE, ylim=c(0,20),
+            col.response=2, pt.pch=20)
+ 
+     cat("==lm.18\n")
+     plotmo(lm.18, main="lm.18",
+            do.par=FALSE, degree1=1, clip=FALSE, ylim=c(0,20),
+            col.response=2, pt.pch=20)
+ 
+     cat("==lm.18.keep\n")
+     plotmo(lm.18.keep, main="lm.18.keep", trace=2,
+            do.par=FALSE, degree1=1, clip=FALSE, ylim=c(0,20),
+            col.response=2, pt.pch=20)
+ 
+     cat("==lm.18.frame\n")
+     plotmo(lm.18.frame, main="lm.18.frame",
+            do.par=FALSE, degree1=1, clip=FALSE, ylim=c(0,20),
+            col.response=2, pt.pch=20)
+ }
> func1()
                              test environments and finding the correct data 
plotmo trace 2: plotmo(object=a.glob, type2="im", degree1=1, degree2=1, all2=1,
                       do.par=FALSE, trace=2, main="a.glob oz", col.response=3,
                       pt.pch=20)
--get.model.env for object with class earth
object call is earth(formula=O3~temp+humidity, data=oz, degree=2)
using the environment saved in $terms of the earth model: R_GlobalEnv
--plotmo_prolog for earth object 'a.glob'
--plotmo_x for earth object

get.object.x:
object$x is NULL (and it has no colnames)

object call is earth(formula=O3~temp+humidity, data=oz, degree=2)

get.x.from.model.frame:
formula(object) is O3 ~ temp + humidity
naked formula is the same
formula is valid, now looking for data for the model.frame
object$model is NULL (and it has no colnames)
object$data is NULL (and it has no colnames)
argument 2 of the call is 'data'
eval(call$data, R_GlobalEnv)
call$data is usable and has column names O3 temp humidity ibh
na.action(object) is "na.fail"
stats::model.frame(O3 ~ temp + humidity, data=call$data, na.action="na.fail")
x=model.frame[,-1] is usable and has column names temp humidity
plotmo_x returned[51,2]:
    temp humidity
150   48       81
151   59       63
152   67       58
...   66       68
200   79       65

----Metadata: plotmo_predict with nresponse=NULL and newdata=NULL
calling predict.earth with NULL newdata
stats::predict(earth.object, NULL, type="response")
predict returned[51,1]:
           O3
1    7.990058
2   11.446254
3   13.959851
... 13.645652
51  18.207402
predict after processing with nresponse=NULL is [51,1]:
           O3
1    7.990058
2   11.446254
3   13.959851
... 13.645652
51  18.207402

----Metadata: plotmo_fitted with nresponse=NULL
stats::fitted(object=earth.object)
fitted(object) returned[51,1]:
           O3
1    7.990058
2   11.446254
3   13.959851
... 13.645652
51  18.207402
fitted(object) after processing with nresponse=NULL is [51,1]:
           O3
1    7.990058
2   11.446254
3   13.959851
... 13.645652
51  18.207402

----Metadata: plotmo_y with nresponse=NULL
--plotmo_y with nresponse=NULL for earth object

get.object.y:
object$y is NULL (and it has no colnames)

object call is earth(formula=O3~temp+humidity, data=oz, degree=2)

get.y.from.model.frame:
formula(object) is O3 ~ temp + humidity
formula is valid, now looking for data for the model.frame
object$model is NULL (and it has no colnames)
object$data is NULL (and it has no colnames)
argument 2 of the call is 'data'
eval(call$data, R_GlobalEnv)
call$data is usable and has column names O3 temp humidity ibh
na.action(object) is "na.fail"
stats::model.frame(O3 ~ temp + humidity, data=call$data, na.action="na.fail")
y=model.frame[,1] is usable and has column name O3
plotmo_y returned[51,1]:
    O3
150  2
151 12
152 22
... 17
200 14
plotmo_y after processing with nresponse=NULL is [51,1]:
    O3
150  2
151 12
152 22
... 17
200 14
converted nresponse=NA to nresponse=1
nresponse=1 (was NA) ncol(fitted) 1 ncol(predict) 1 ncol(y) 1

----Metadata: plotmo_y with nresponse=1
--plotmo_y with nresponse=1 for earth object

get.object.y:
object$y is NULL (and it has no colnames)

object call is earth(formula=O3~temp+humidity, data=oz, degree=2)

get.y.from.model.frame:
formula(object) is O3 ~ temp + humidity
formula is valid, now looking for data for the model.frame
object$model is NULL (and it has no colnames)
object$data is NULL (and it has no colnames)
argument 2 of the call is 'data'
eval(call$data, R_GlobalEnv)
call$data is usable and has column names O3 temp humidity ibh
na.action(object) is "na.fail"
stats::model.frame(O3 ~ temp + humidity, data=call$data, na.action="na.fail")
y=model.frame[,1] is usable and has column name O3
got model response from model.frame(O3 ~ temp + humidity,
                                    data=call$data, na.action="na.fail")
plotmo_y returned[51,1]:
    O3
150  2
151 12
152 22
... 17
200 14
plotmo_y after processing with nresponse=1 is [51,1]:
    O3
150  2
151 12
152 22
... 17
200 14
got response name "O3" from yhat
resp.levs is NULL

----Metadata: done

number of x values: temp 27 humidity 27

----plotmo_singles for earth object
singles: 1 temp 

----plotmo_pairs for earth object
pairs:
     [,1]     [,2]        
[1,] "1 temp" "2 humidity"

----Figuring out ylim
--get.ylim.by.dummy.plots
--plot.degree1(draw.plot=FALSE)
degree1 plot1 (pmethod "plotmo") variable temp
newdata[50,2]:
        temp humidity
1   48.00000       68
2   48.91837       68
3   49.83673       68
... 50.75510       68
50  93.00000       68
stats::predict(earth.object, data.frame[50,2], type="response")
predict returned[50,1]:
           O3
1    7.990058
2    8.278609
3    8.567159
...  8.855710
50  29.834221
predict after processing with nresponse=1 is [50,1]:
           O3
1    7.990058
2    8.278609
3    8.567159
...  8.855710
50  29.834221
--plot.degree2(draw.plot=FALSE)
degree2 plot1 (pmethod "plotmo") variables temp:humidity
newdata[400,2]:
        temp humidity
1   48.00000       33
2   50.36842       33
3   52.73684       33
... 55.10526       33
400 93.00000       90
stats::predict(earth.object, data.frame[400,2], type="response")
predict returned[400,1]:
           O3
1    7.990058
2    8.734215
3    9.478372
... 10.222529
400 33.851866
predict after processing with nresponse=1 is [400,1]:
           O3
1    7.990058
2    8.734215
3    9.478372
... 10.222529
400 33.851866
--done get.ylim.by.dummy.plots

ylim c(1.936, 33.94)    clip TRUE

--plot.degree1(draw.plot=TRUE)

 plotmo grid:    temp humidity
                   80       68

graphics::plot.default(x=c(48,48.92,49.8...), y=c(7.99,8.279,8...), type="n",
                       main="a.glob oz", xlab="", ylab="", xaxt="s", yaxt="s",
                       xlim=c(47.98,93.08), ylim=c(1.94,33.94))
--plot.degree2(draw.plot=TRUE)
plotmo trace 2: plotmo(object=ad.glob, type2="im", degree1=1, degree2=1,
                       all2=1, do.par=FALSE, trace=2, main="ad.glob oz",
                       col.response=3, pch.response=20)
--get.model.env for object with class earth
object call is earth(x=oz[, 2:3], y=oz[, 1], degree=2)
assuming the environment of the earth model is that of plotmo's caller: env(caption)
--plotmo_prolog for earth object 'ad.glob'
--plotmo_x for earth object

get.object.x:
object$x is NULL (and it has no colnames)

object call is earth(x=oz[, 2:3], y=oz[, 1], degree=2)

get.x.from.model.frame:
terms(object) did not return the terms, will look for the formula elsewhere
no formula in getCall(object)

get.data.from.object.call.field:
eval(getCall(object)$x, env(caption))
getCall(object)$x is usable and has column names temp humidity
plotmo_x returned[51,2]:
    temp humidity
150   48       81
151   59       63
152   67       58
...   66       68
200   79       65

----Metadata: plotmo_predict with nresponse=NULL and newdata=NULL
calling predict.earth with NULL newdata
stats::predict(earth.object, NULL, type="response")
predict returned[51,1]:
      oz[, 1]
1    7.990058
2   11.446254
3   13.959851
... 13.645652
51  18.207402
predict after processing with nresponse=NULL is [51,1]:
      oz[, 1]
1    7.990058
2   11.446254
3   13.959851
... 13.645652
51  18.207402

----Metadata: plotmo_fitted with nresponse=NULL
stats::fitted(object=earth.object)
fitted(object) returned[51,1]:
      oz[, 1]
1    7.990058
2   11.446254
3   13.959851
... 13.645652
51  18.207402
fitted(object) after processing with nresponse=NULL is [51,1]:
      oz[, 1]
1    7.990058
2   11.446254
3   13.959851
... 13.645652
51  18.207402

----Metadata: plotmo_y with nresponse=NULL
--plotmo_y with nresponse=NULL for earth object

get.object.y:
object$y is NULL (and it has no colnames)

object call is earth(x=oz[, 2:3], y=oz[, 1], degree=2)

get.y.from.model.frame:
terms(object) did not return the terms, will look for the formula elsewhere
no formula in getCall(object)

get.data.from.object.call.field:
eval(getCall(object)$y, env(caption))
getCall(object)$y is usable but without colnames so we will keep on searching

names(call) is "" "x" "y" "degree"
the name of argument 2 is "y" so we will not process it with argn
object$y is NULL
call$y is usable but without colnames but we will use it anyway
colname was NULL now "y"
plotmo_y returned[51,1]:
     y
1    2
2   12
3   22
... 17
51  14
plotmo_y after processing with nresponse=NULL is [51,1]:
     y
1    2
2   12
3   22
... 17
51  14
converted nresponse=NA to nresponse=1
nresponse=1 (was NA) ncol(fitted) 1 ncol(predict) 1 ncol(y) 1

----Metadata: plotmo_y with nresponse=1
--plotmo_y with nresponse=1 for earth object

get.object.y:
object$y is NULL (and it has no colnames)

object call is earth(x=oz[, 2:3], y=oz[, 1], degree=2)

get.y.from.model.frame:
terms(object) did not return the terms, will look for the formula elsewhere
no formula in getCall(object)

get.data.from.object.call.field:
eval(getCall(object)$y, env(caption))
getCall(object)$y is usable but without colnames so we will keep on searching

names(call) is "" "x" "y" "degree"
the name of argument 2 is "y" so we will not process it with argn
object$y is NULL
call$y is usable but without colnames but we will use it anyway
got model response from getCall(object)$y
colname was NULL now "y"
plotmo_y returned[51,1]:
     y
1    2
2   12
3   22
... 17
51  14
plotmo_y after processing with nresponse=1 is [51,1]:
     y
1    2
2   12
3   22
... 17
51  14
got response name "oz[, 1]" from yhat
resp.levs is NULL

----Metadata: done

number of x values: temp 27 humidity 27

----plotmo_singles for earth object
singles: 1 temp 

----plotmo_pairs for earth object
pairs:
     [,1]     [,2]        
[1,] "1 temp" "2 humidity"

----Figuring out ylim
--get.ylim.by.dummy.plots
--plot.degree1(draw.plot=FALSE)
degree1 plot1 (pmethod "plotmo") variable temp
newdata[50,2]:
        temp humidity
1   48.00000       68
2   48.91837       68
3   49.83673       68
... 50.75510       68
50  93.00000       68
stats::predict(earth.object, data.frame[50,2], type="response")
predict returned[50,1]:
      oz[, 1]
1    7.990058
2    8.278609
3    8.567159
...  8.855710
50  29.834221
predict after processing with nresponse=1 is [50,1]:
      oz[, 1]
1    7.990058
2    8.278609
3    8.567159
...  8.855710
50  29.834221
--plot.degree2(draw.plot=FALSE)
degree2 plot1 (pmethod "plotmo") variables temp:humidity
newdata[400,2]:
        temp humidity
1   48.00000       33
2   50.36842       33
3   52.73684       33
... 55.10526       33
400 93.00000       90
stats::predict(earth.object, data.frame[400,2], type="response")
predict returned[400,1]:
      oz[, 1]
1    7.990058
2    8.734215
3    9.478372
... 10.222529
400 33.851866
predict after processing with nresponse=1 is [400,1]:
      oz[, 1]
1    7.990058
2    8.734215
3    9.478372
... 10.222529
400 33.851866
--done get.ylim.by.dummy.plots

ylim c(1.931, 34)    clip TRUE

--plot.degree1(draw.plot=TRUE)

 plotmo grid:    temp humidity
                   80       68

graphics::plot.default(x=c(48,48.92,49.8...), y=c(7.99,8.279,8...), type="n",
                       main="ad.glob oz", xlab="", ylab="", xaxt="s", yaxt="s",
                       xlim=c(48,93), ylim=c(1.93,34))
--plot.degree2(draw.plot=TRUE)
 plotmo grid:    temp humidity
                   80       68
 plotmo grid:    temp humidity
                   80       68
 plotmo grid:    temp humidity
                  800      680
 plotmo grid:    temp humidity
                  800      680
 plotmo grid:    temp humidity
                  800      680
 plotmo grid:    temp humidity
                  800      680
                              test environments and finding the correct data, continued 
 plotmo grid:    temp humidity
                    8      6.8
 plotmo grid:    temp humidity
                    8      6.8
 plotmo grid:    temp humidity
                  800      680
 plotmo grid:    temp humidity
                  800      680
Expect error msg: formal argument "do.par" matched by multiple actual arguments
Error in plotmo(a.oz10, do.par = FALSE, main = "func1:a.oz10", degree1 = 1,  : 
  formal argument "do.par" matched by multiple actual arguments
Got expected error from try(plotmo(a.oz10, do.par = FALSE, main = "func1:a.oz10", degree1 = 1,     all2 = 1, degree2 = 1, type2 = "im", col.response = 3, pt.pch = 20,     do.par = FALSE))
==lm.18.out
 plotmo grid:    x1 x2
                  6  6
==lm.18
 plotmo grid:    x1 x2
                  6  6
==lm.18.keep
plotmo trace 2: plotmo(object=lm.18.keep, degree1=1, do.par=FALSE, clip=FALSE,
                       ylim=c(0,20), trace=2, main="lm.18.keep",
                       col.response=2, pt.pch=20)
--get.model.env for object with class lm
object call is lm(formula=y~x1+x2, x=TRUE, y=TRUE)
using the environment saved in $terms of the lm model: env(frame, lm.18.out, x1, y)
--plotmo_prolog for lm object 'lm.18.keep'
--plotmo_x for lm object

get.object.x:
object$x is usable and has column names (Intercept) x1 x2
dropped "(Intercept)" column from x
plotmo_x returned[9,2]:
    x1 x2
1    1  2
2   18  3
3    2  4
...  4  5
9    6 10

----Metadata: plotmo_predict with nresponse=NULL and newdata=NULL
calling predict.lm with NULL newdata
stats::predict(lm.object, NULL, type="response")
predict returned[9,1] with no column names:
             
1    8.098674
2    3.323243
3    8.792796
...  8.674176
9   10.564707
predict after processing with nresponse=NULL is [9,1] with no column names:
             
1    8.098674
2    3.323243
3    8.792796
...  8.674176
9   10.564707

----Metadata: plotmo_fitted with nresponse=NULL
stats::fitted(object=lm.object)
fitted(object) returned[9,1] with no column names:
             
1    8.098674
2    3.323243
3    8.792796
...  8.674176
9   10.564707
fitted(object) after processing with nresponse=NULL is [9,1] with no column names:
             
1    8.098674
2    3.323243
3    8.792796
...  8.674176
9   10.564707

----Metadata: plotmo_y with nresponse=NULL
--plotmo_y with nresponse=NULL for lm object

get.object.y:
object$y is usable but without colnames so we will keep on searching

object call is lm(formula=y~x1+x2, x=TRUE, y=TRUE)

get.y.from.model.frame:
formula(object) is y ~ x1 + x2
formula is valid, now looking for data for the model.frame
object$model is usable and has column names y x1 x2
y=model.frame[,1] is usable and has column name y
plotmo_y returned[9,1]:
     y
1    3
2    4
3   19
...  6
9   11
plotmo_y after processing with nresponse=NULL is [9,1]:
     y
1    3
2    4
3   19
...  6
9   11
converted nresponse=NA to nresponse=1
nresponse=1 (was NA) ncol(fitted) 1 ncol(predict) 1 ncol(y) 1

----Metadata: plotmo_y with nresponse=1
--plotmo_y with nresponse=1 for lm object

get.object.y:
object$y is usable but without colnames so we will keep on searching

object call is lm(formula=y~x1+x2, x=TRUE, y=TRUE)

get.y.from.model.frame:
formula(object) is y ~ x1 + x2
formula is valid, now looking for data for the model.frame
object$model is usable and has column names y x1 x2
y=model.frame[,1] is usable and has column name y
got model response from object$model
plotmo_y returned[9,1]:
     y
1    3
2    4
3   19
...  6
9   11
plotmo_y after processing with nresponse=1 is [9,1]:
     y
1    3
2    4
3   19
...  6
9   11
got response name "y" from yfull
resp.levs is NULL

----Metadata: done

number of x values: x1 6 x2 9

----plotmo_singles for lm object
singles: 1 x1 

----plotmo_pairs for lm object
formula(object) returned y ~ x1 + x2
formula.vars "x1" "x2"
term.labels "x1" "x2"
plotmo_pairs_from_term_labels
term.labels: "x1" "x2" "x1" "x2"
pred.names:  "x1" "x2"
considering x1
considering x2
considering x1
considering x2
no pairs

----Figuring out ylim
ylim c(0, 20)    clip FALSE

--plot.degree1(draw.plot=TRUE)

 plotmo grid:    x1 x2
                  6  6

degree1 plot1 (pmethod "plotmo") variable x1
newdata[50,2]:
           x1 x2
1    1.000000  6
2    1.346939  6
3    1.693878  6
...  2.040816  6
50  18.000000  6
stats::predict(lm.object, data.frame[50,2], type="response")
predict returned[50,1] with no column names:
             
1   10.107826
2   10.000117
3    9.892409
...  9.784700
50   4.830107
predict after processing with nresponse=1 is [50,1]:
      predict
1   10.107826
2   10.000117
3    9.892409
...  9.784700
50   4.830107
graphics::plot.default(x=c(1,1.347,1.694...), y=c(10.11,10,9.89...), type="n",
                       main="lm.18.keep", xlab="", ylab="", xaxt="s", yaxt="s",
                       xlim=c(1,18.04), ylim=c(0,20))
==lm.18.frame
 plotmo grid:    x1 x2
                  6  6
> 
> caption <- "test earth formula versus x,y model"
> # dopar(4,4,caption)
> # mtext(caption, outer=TRUE, font=2, line=1.5, cex=1)
> a <- earth(O3 ~ ., data=ozone1, degree=2)
> plotmo(a, caption="test earth formula versus xy model (formula)")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> a <- earth(ozone1[, -1], ozone1[,1], degree=2)
> plotmo(a, caption="test earth formula versus xy model (xy)")
 plotmo grid:    vh wind humidity temp    ibh dpg   ibt vis   doy
               5760    5       64   62 2112.5  24 167.5 120 205.5
> 
> # single predictor
> caption <- "test earth(O3~wind, data=ozone1, degree=2), single predictor"
> dopar(2,2,caption)
                              test earth(O3~wind, data=ozone1, degree=2), single predictor 
> a <- earth(O3~wind, data=ozone1, degree=2)
> plotmo(a)
> 
> caption = "se=2, earth(doy~humidity+temp+wind, data=ozone1) versus termplot (expect no se lines)"
> dopar(3,3,caption)
                              se=2, earth(doy~humidity+temp+wind, data=ozone1) versus termplot (expect no se lines) 
> mtext(caption, outer=TRUE, font=2, line=1.5, cex=1)
> # minspan=1 to force two degree2 graphs for the test (wasn't necessary in old versions of earth)
> a <- earth(doy~humidity + temp + wind, data=ozone1, degree=2, minspan=1)
> cat("Ignore warning: predict.earth ignored argument \"se\"\n")
Ignore warning: predict.earth ignored argument "se"
> termplot(a)
Warning: predict.earth ignored argument 'se.fit'
> plotmo(a, do.par=FALSE, ylim=NA, degree2=c(1:2), clip=FALSE, caption=caption)
 plotmo grid:    humidity temp wind
                       64   62    5
> 
> # test fix to bug reported by Joe Retzer, FIXED Dec 7, 2007
> N <- 650
> set.seed(2007)
> q_4    <- runif(N, -1, 1)
> q_2102 <- runif(N, -1, 1)
> q_2104 <- runif(N, -1, 1)
> q_3105 <- runif(N, -1, 1)
> q_3106 <- runif(N, -1, 1)
> q_4104 <- runif(N, -1, 1)
> q_6101 <- runif(N, -1, 1)
> q_6103 <- runif(N, -1, 1)
> q_7104 <- runif(N, -1, 1)
> q_3109 <- runif(N, -1, 1)
> q_4103 <- runif(N, -1, 1)
> q_2111 <- runif(N, -1, 1)
> q_3107 <- runif(N, -1, 1)
> q_3101 <- runif(N, -1, 1)
> q_3104 <- runif(N, -1, 1)
> q_7107 <- runif(N, -1, 1)
> depIndex <- sin(1.0 * q_4 + rnorm(650, sd=.8)) + sin(1.8 * q_2102 + rnorm(650, sd=.8)) + sin(1.3 * q_2104 + rnorm(650, sd=.8)) + sin(1.4 * q_3105 + rnorm(650, sd=.8)) +
+             sin(1.5 * q_3106 + rnorm(650, sd=.8)) + sin(1.6 * q_4104 + rnorm(650, sd=.8)) + sin(1.8 * q_6101 + rnorm(650, sd=.8)) + sin(1.8 * q_6103 + rnorm(650, sd=.8)) +
+             sin(1.9 * q_7104 + rnorm(650, sd=.8)) + sin(2.0 * q_3109 + rnorm(650, sd=.8))
> 
> regDatCWD <- as.data.frame(cbind(depIndex, q_4, q_2102, q_2104, q_3105, q_3106, q_4104, q_6101, q_6103, q_7104, q_3109, q_4103, q_2111, q_3107, q_3101, q_3104, q_7107))
> cat("--plotmo(earthobj5)--\n")
--plotmo(earthobj5)--
> earthobj5 <- earth(depIndex ~  q_4+q_2102+q_2104+q_3105+q_3106+q_4104+q_6101+q_6103+q_7104+q_3109+q_4103+q_2111+q_3107+q_3101+q_3104+q_7107, data=regDatCWD)
> print(summary(earthobj5, digits = 2))
Call: earth(formula=depIndex~q_4+q_2102+q_2104+q_3105+q_3106+q_4104+q_...),
            data=regDatCWD)

                     coefficients
(Intercept)                  1.79
h(0.782075-q_4)             -0.97
h(q_4-0.782075)             -5.36
h(q_2102- -0.664223)         1.19
h(q_2104- -0.954733)         0.85
h(0.83147-q_3105)           -0.77
h(0.492009-q_3106)          -0.93
h(q_4104- -0.671276)         1.02
h(0.483685-q_6101)          -1.10
h(0.914724-q_6103)          -1.12
h(0.545206-q_7104)          -1.19
h(-0.157173-q_3109)         -0.96
h(q_3109- -0.157173)         1.03

Selected 13 of 21 terms, and 10 of 16 predictors
Termination condition: RSq changed by less than 0.001 at 21 terms
Importance: q_6103, q_4104, q_2102, q_7104, q_3109, q_6101, q_2104, q_4, ...
Number of terms at each degree of interaction: 1 12 (additive model)
GCV 2.5    RSS 1509    GRSq 0.53    RSq 0.57
> plotmo(earthobj5)
 plotmo grid:    q_4     q_2102      q_2104      q_3105      q_3106     q_4104
          0.05726625 0.01725001 0.004659335 -0.01826179 -0.00913319 0.01401429
      q_6101     q_6103     q_7104      q_3109     q_4103     q_2111
 -0.04790454 0.03681165 0.01827148 -0.09899272 -0.0623349 0.01007481
      q_3107      q_3101       q_3104     q_7107
 -0.02481171 -0.07733527 -0.003053319 0.02821214
> 
> # long predictor names
> 
> a.rather.long.in.fact.very.long.name.q_4 <- q_4
> a.rather.long.in.fact.very.long.name.q_2102 <- q_2102
> a.rather.long.in.fact.very.long.name.q_2104 <- q_2104
> a.rather.long.in.fact.very.long.name.q_3105 <- q_3105
> a.rather.long.in.fact.very.long.name.q_3106 <- q_3106
> a.rather.long.in.fact.very.long.name.q_4104 <- q_4104
> a.rather.long.in.fact.very.long.name.q_6101 <- q_6101
> a.rather.long.in.fact.very.long.name.q_6103 <- q_6103
> a.rather.long.in.fact.very.long.name.q_7104 <- q_7104
> a.rather.long.in.fact.very.long.name.q_3109 <- q_3109
> a.rather.long.in.fact.very.long.name.q_4103 <- q_4103
> a.rather.long.in.fact.very.long.name.q_2111 <- q_2111
> a.rather.long.in.fact.very.long.name.q_3107 <- q_3107
> a.rather.long.in.fact.very.long.name.q_3101 <- q_3101
> a.rather.long.in.fact.very.long.name.q_3104 <- q_3104
> a.rather.long.in.fact.very.long.name.q_7107 <- q_7107
> a.rather.long.in.fact.very.long.name.for.the.response <- depIndex
> a.rather.long.in.fact.very.long.name.for.the.dataframe <-
+         as.data.frame(cbind(
+                 a.rather.long.in.fact.very.long.name.for.the.response,
+                 a.rather.long.in.fact.very.long.name.q_4,
+                 a.rather.long.in.fact.very.long.name.q_2102,
+                 a.rather.long.in.fact.very.long.name.q_2104,
+                 a.rather.long.in.fact.very.long.name.q_3105,
+                 a.rather.long.in.fact.very.long.name.q_3106,
+                 a.rather.long.in.fact.very.long.name.q_4104,
+                 a.rather.long.in.fact.very.long.name.q_6101,
+                 a.rather.long.in.fact.very.long.name.q_6103,
+                 a.rather.long.in.fact.very.long.name.q_7104,
+                 a.rather.long.in.fact.very.long.name.q_3109,
+                 a.rather.long.in.fact.very.long.name.q_4103,
+                 a.rather.long.in.fact.very.long.name.q_2111,
+                 a.rather.long.in.fact.very.long.name.q_3107,
+                 a.rather.long.in.fact.very.long.name.q_3101,
+                 a.rather.long.in.fact.very.long.name.q_3104,
+                 a.rather.long.in.fact.very.long.name.q_7107))
> 
> cat("--a.rather.long.in.fact.very.long.name.for.the...A--\n")
--a.rather.long.in.fact.very.long.name.for.the...A--
> a.rather.long.in.fact.very.long.name.for.the.modelA <-
+         earth(a.rather.long.in.fact.very.long.name.for.the.response ~
+                 a.rather.long.in.fact.very.long.name.q_4 +
+                 a.rather.long.in.fact.very.long.name.q_2102 +
+                 a.rather.long.in.fact.very.long.name.q_2104 +
+                 a.rather.long.in.fact.very.long.name.q_3105 +
+                 a.rather.long.in.fact.very.long.name.q_3106 +
+                 a.rather.long.in.fact.very.long.name.q_4104 +
+                 a.rather.long.in.fact.very.long.name.q_6101 +
+                 a.rather.long.in.fact.very.long.name.q_6103 +
+                 a.rather.long.in.fact.very.long.name.q_7104 +
+                 a.rather.long.in.fact.very.long.name.q_3109 +
+                 a.rather.long.in.fact.very.long.name.q_4103 +
+                 a.rather.long.in.fact.very.long.name.q_2111 +
+                 a.rather.long.in.fact.very.long.name.q_3107 +
+                 a.rather.long.in.fact.very.long.name.q_3101 +
+                 a.rather.long.in.fact.very.long.name.q_3104 +
+                 a.rather.long.in.fact.very.long.name.q_7107,
+                 data = a.rather.long.in.fact.very.long.name.for.the.dataframe)
> print(summary(a.rather.long.in.fact.very.long.name.for.the.modelA, digits = 2))
Call: earth(formula=a.rather.long.in.fact.very.long.name.for.the.respo...),
            data=a.rather.long.in.fact.very.long.name.for.the.da...)

                                                          coefficients
(Intercept)                                                       1.79
h(0.782075-a.rather.long.in.fact.very.long.name.q_4)             -0.97
h(a.rather.long.in.fact.very.long.name.q_4-0.782075)             -5.36
h(a.rather.long.in.fact.very.long.name.q_2102- -0.664223)         1.19
h(a.rather.long.in.fact.very.long.name.q_2104- -0.954733)         0.85
h(0.83147-a.rather.long.in.fact.very.long.name.q_3105)           -0.77
h(0.492009-a.rather.long.in.fact.very.long.name.q_3106)          -0.93
h(a.rather.long.in.fact.very.long.name.q_4104- -0.671276)         1.02
h(0.483685-a.rather.long.in.fact.very.long.name.q_6101)          -1.10
h(0.914724-a.rather.long.in.fact.very.long.name.q_6103)          -1.12
h(0.545206-a.rather.long.in.fact.very.long.name.q_7104)          -1.19
h(-0.157173-a.rather.long.in.fact.very.long.name.q_3109)         -0.96
h(a.rather.long.in.fact.very.long.name.q_3109- -0.157173)         1.03

Selected 13 of 21 terms, and 10 of 16 predictors
Termination condition: RSq changed by less than 0.001 at 21 terms
Importance: a.rather.long.in.fact.very.long.name.q_6103, ...
Number of terms at each degree of interaction: 1 12 (additive model)
GCV 2.5    RSS 1509    GRSq 0.53    RSq 0.57
> plot(a.rather.long.in.fact.very.long.name.for.the.modelA)
> plotmo(a.rather.long.in.fact.very.long.name.for.the.modelA)
 plotmo grid:    a.rather.long.in.fact.very.long.name.q_4
                                               0.05726625
 a.rather.long.in.fact.very.long.name.q_2102
                                  0.01725001
 a.rather.long.in.fact.very.long.name.q_2104
                                 0.004659335
 a.rather.long.in.fact.very.long.name.q_3105
                                 -0.01826179
 a.rather.long.in.fact.very.long.name.q_3106
                                 -0.00913319
 a.rather.long.in.fact.very.long.name.q_4104
                                  0.01401429
 a.rather.long.in.fact.very.long.name.q_6101
                                 -0.04790454
 a.rather.long.in.fact.very.long.name.q_6103
                                  0.03681165
 a.rather.long.in.fact.very.long.name.q_7104
                                  0.01827148
 a.rather.long.in.fact.very.long.name.q_3109
                                 -0.09899272
 a.rather.long.in.fact.very.long.name.q_4103
                                  -0.0623349
 a.rather.long.in.fact.very.long.name.q_2111
                                  0.01007481
 a.rather.long.in.fact.very.long.name.q_3107
                                 -0.02481171
 a.rather.long.in.fact.very.long.name.q_3101
                                 -0.07733527
 a.rather.long.in.fact.very.long.name.q_3104
                                -0.003053319
 a.rather.long.in.fact.very.long.name.q_7107
                                  0.02821214
> 
> cat("--a.rather.long.in.fact.very.long.name.for.the...C--\n")
--a.rather.long.in.fact.very.long.name.for.the...C--
> a.rather.long.in.fact.very.long.name.for.the.modelC <-
+         earth(x = a.rather.long.in.fact.very.long.name.for.the.dataframe[,-1],
+           y = a.rather.long.in.fact.very.long.name.for.the.response,
+                   degree = 3)
> print(summary(a.rather.long.in.fact.very.long.name.for.the.modelC, digits = 2))
Call: earth(x=a.rather.long.in.fact.very.long.name.for.the.dataf...),
            y=a.rather.long.in.fact.very.long.name.for.the.re..., degree=3)

                                                                                                                                                                          coefficients
(Intercept)                                                                                                                                                                       1.72
h(0.782075-a.rather.long.in.fact.very.long.name.q_4)                                                                                                                             -1.02
h(a.rather.long.in.fact.very.long.name.q_4-0.782075)                                                                                                                            -10.33
h(a.rather.long.in.fact.very.long.name.q_2102- -0.664223)                                                                                                                         1.27
h(a.rather.long.in.fact.very.long.name.q_2104- -0.954733)                                                                                                                         0.82
h(0.83147-a.rather.long.in.fact.very.long.name.q_3105)                                                                                                                           -1.00
h(0.492009-a.rather.long.in.fact.very.long.name.q_3106)                                                                                                                          -0.90
h(a.rather.long.in.fact.very.long.name.q_4104- -0.671276)                                                                                                                         1.01
h(0.483685-a.rather.long.in.fact.very.long.name.q_6101)                                                                                                                          -1.09
h(0.914724-a.rather.long.in.fact.very.long.name.q_6103)                                                                                                                          -1.18
h(0.545206-a.rather.long.in.fact.very.long.name.q_7104)                                                                                                                          -1.62
h(-0.157173-a.rather.long.in.fact.very.long.name.q_3109)                                                                                                                         -1.81
h(a.rather.long.in.fact.very.long.name.q_3109- -0.157173)                                                                                                                         1.15
h(-0.664223-a.rather.long.in.fact.very.long.name.q_2102) * h(a.rather.long.in.fact.very.long.name.q_3106- -0.148502)                                                              3.71
h(0.83147-a.rather.long.in.fact.very.long.name.q_3105) * h(a.rather.long.in.fact.very.long.name.q_7107- -0.748278)                                                                0.31
h(0.914724-a.rather.long.in.fact.very.long.name.q_6103) * h(-0.713314-a.rather.long.in.fact.very.long.name.q_3107)                                                                2.90
h(0.545206-a.rather.long.in.fact.very.long.name.q_7104) * h(a.rather.long.in.fact.very.long.name.q_2111- -0.544753)                                                               0.61
h(-0.157173-a.rather.long.in.fact.very.long.name.q_3109) * h(0.700096-a.rather.long.in.fact.very.long.name.q_2111)                                                                1.33
h(a.rather.long.in.fact.very.long.name.q_4-0.82106) * h(0.545206-a.rather.long.in.fact.very.long.name.q_7104) * h(a.rather.long.in.fact.very.long.name.q_2111- -0.544753)        15.97

Selected 19 of 33 terms, and 13 of 16 predictors
Termination condition: Reached nk 33
Importance: a.rather.long.in.fact.very.long.name.q_6103, ...
Number of terms at each degree of interaction: 1 12 5 1
GCV 2.4    RSS 1374    GRSq 0.54    RSq 0.6
> plot(a.rather.long.in.fact.very.long.name.for.the.modelC)
> plotmo(a.rather.long.in.fact.very.long.name.for.the.modelC)
 plotmo grid:    a.rather.long.in.fact.very.long.name.q_4
                                               0.05726625
 a.rather.long.in.fact.very.long.name.q_2102
                                  0.01725001
 a.rather.long.in.fact.very.long.name.q_2104
                                 0.004659335
 a.rather.long.in.fact.very.long.name.q_3105
                                 -0.01826179
 a.rather.long.in.fact.very.long.name.q_3106
                                 -0.00913319
 a.rather.long.in.fact.very.long.name.q_4104
                                  0.01401429
 a.rather.long.in.fact.very.long.name.q_6101
                                 -0.04790454
 a.rather.long.in.fact.very.long.name.q_6103
                                  0.03681165
 a.rather.long.in.fact.very.long.name.q_7104
                                  0.01827148
 a.rather.long.in.fact.very.long.name.q_3109
                                 -0.09899272
 a.rather.long.in.fact.very.long.name.q_4103
                                  -0.0623349
 a.rather.long.in.fact.very.long.name.q_2111
                                  0.01007481
 a.rather.long.in.fact.very.long.name.q_3107
                                 -0.02481171
 a.rather.long.in.fact.very.long.name.q_3101
                                 -0.07733527
 a.rather.long.in.fact.very.long.name.q_3104
                                -0.003053319
 a.rather.long.in.fact.very.long.name.q_7107
                                  0.02821214
> 
> a <- earth(survived ~ pclass+sex+age, data=etitanic, degree=2)
> print(summary(a))
Call: earth(formula=survived~pclass+sex+age, data=etitanic, degree=2)

                    coefficients
(Intercept)           0.92939850
pclass3rd            -0.45571429
pclass2nd * sexmale  -0.27354805
pclass3rd * sexmale   0.18991361
sexmale * h(age-16)   0.05497748
sexmale * h(age-25)  -0.01885057
sexmale * h(age-2)   -0.04217428

Selected 7 of 14 terms, and 4 of 4 predictors
Termination condition: Reached nk 21
Importance: sexmale, pclass3rd, pclass2nd, age
Number of terms at each degree of interaction: 1 1 5
GCV 0.1442766    RSS 146.3318    GRSq 0.4039126    RSq 0.4209023
> plotmo(a, caption="plotmo with facs: pclass+sex+age")
 plotmo grid:    pclass  sex age
                    3rd male  28
> plotmo(a, caption="plotmo with facs: pclass+sex+age, all1=T, grid.col=\"gray\"", all1=T, grid.col="gray")
 plotmo grid:    pclass  sex age
                    3rd male  28
> plotmo(a, caption="plotmo with facs: pclass+sex+age, all2=T, col.grid=\"green\"", all2=T, col.grid="green")
 plotmo grid:    pclass  sex age
                    3rd male  28
> plotmo(a, caption="plotmo with facs: pclass+sex+age, all1=T, all2=T, grid=2", all1=T, all2=T, grid.col=2)
 plotmo grid:    pclass  sex age
                    3rd male  28
> plotmo(a, clip=FALSE, degree2=FALSE, caption="plotmo (no degree2) with facs: pclass+sex+age")
 plotmo grid:    pclass  sex age
                    3rd male  28
> plotmo(a, clip=FALSE, grid.levels=list(pclass="2n", sex="ma"),
+        caption="plotmo with grid.levels: pclass+sex+age")
 plotmo grid:    pclass  sex age
                    2nd male  28
> # in above tests, all degree2 terms use facs
> # now build a model with some degree2 term that use facs, some that don't
> a <- earth(survived ~ pclass+age+sibsp, data=etitanic, degree=2)
> print(summary(a))
Call: earth(formula=survived~pclass+age+sibsp, data=etitanic, degree=2)

                       coefficients
(Intercept)              1.20590993
pclass2nd               -0.27484540
pclass3rd               -0.45765086
h(age-5)                -0.03561187
h(age-18)                0.03022469
h(18-age) * h(sibsp-2)  -0.04797511
h(18-age) * h(sibsp-3)   0.04721023

Selected 7 of 17 terms, and 4 of 4 predictors
Termination condition: Reached nk 21
Importance: pclass3rd, age, pclass2nd, sibsp
Number of terms at each degree of interaction: 1 4 2
GCV 0.2040487    RSS 206.9554    GRSq 0.1569604    RSq 0.1809888
> plotmo(a, caption="plotmo with mixed fac and non-fac degree2 terms", persp.border=NA)
 plotmo grid:    pclass age sibsp
                    3rd  28     0
> plotmo(a, caption="plotmo with mixed fac and non-fac degree2 terms and grid.levels",
+        grid.levels=list(pclass="2n", age=20), # test partial matching of grid levels, and numeric preds
+        persp.ticktype="d", persp.nticks=2)
 plotmo grid:    pclass age sibsp
                    2nd  20     0
> 
> # check detection of illegal grid.levels argument
> expect.err(try(plotmo(a, grid.levels=list(pcla="1", pclass="2"))), 'illegal grid.levels argument ("pcla" and "pclass" both match "pclass")')
Error : illegal grid.levels argument ("pcla" and "pclass" both match "pclass")
Got expected error from try(plotmo(a, grid.levels = list(pcla = "1", pclass = "2")))
> expect.err(try(plotmo(a, grid.levels=list(pclass="1", pcla="2"))), 'illegal grid.levels argument ("pclass" and "pcla" both match "pclass")')
Error : illegal grid.levels argument ("pclass" and "pcla" both match "pclass")
Got expected error from try(plotmo(a, grid.levels = list(pclass = "1", pcla = "2")))
> expect.err(try(plotmo(a, grid.levels=list(pcla="nonesuch"))), 'illegal level "nonesuch" for "pclass" in grid.levels (allowed levels are "1st" "2nd" "3rd")')
Error : illegal level "nonesuch" for "pclass" in grid.levels (allowed levels are "1st" "2nd" "3rd")
Got expected error from try(plotmo(a, grid.levels = list(pcla = "nonesuch")))
> expect.err(try(plotmo(a, grid.levels=list(pcla="1sx"))), 'illegal level "1sx" for "pclass" in grid.levels (allowed levels are "1st" "2nd" "3rd")')
Error : illegal level "1sx" for "pclass" in grid.levels (allowed levels are "1st" "2nd" "3rd")
Got expected error from try(plotmo(a, grid.levels = list(pcla = "1sx")))
> expect.err(try(plotmo(a, grid.levels=list(pcla=1))), 'illegal level for "pclass" in grid.levels (specify factor levels with a string)')
Error : illegal level for "pclass" in grid.levels (specify factor levels with a string)
Got expected error from try(plotmo(a, grid.levels = list(pcla = 1)))
> expect.err(try(plotmo(a, grid.levels=list(pcla=c("ab", "cd")))), "length(pclass) in grid.levels is not 1")
Error : length(pclass) in grid.levels is not 1
Got expected error from try(plotmo(a, grid.levels = list(pcla = c("ab", "cd"))))
> expect.err(try(plotmo(a, grid.levels=list(pcla=NA))), 'pclass in grid.levels is NA')
Error : pclass in grid.levels is NA
Got expected error from try(plotmo(a, grid.levels = list(pcla = NA)))
> expect.err(try(plotmo(a, grid.levels=list(pcla=Inf))), 'pclass in grid.levels is infinite')
Error : pclass in grid.levels is infinite
Got expected error from try(plotmo(a, grid.levels = list(pcla = Inf)))
> expect.err(try(plotmo(a, grid.levels=list(pcla=9))), 'illegal level for "pclass" in grid.levels (specify factor levels with a string)')
Error : illegal level for "pclass" in grid.levels (specify factor levels with a string)
Got expected error from try(plotmo(a, grid.levels = list(pcla = 9)))
> options(warn=2)
> expect.err(try(plotmo(a, grid.levels=list(age="ab"))), 'grid.levels returned class \"character\" for age, so will use the default grid.func for age')
Error : (converted from warning) grid.levels returned class "character" for age, so will use the default grid.func for age
Got expected error from try(plotmo(a, grid.levels = list(age = "ab")))
> options(warn=1)
> expect.err(try(plotmo(a, grid.levels=list(age=NA))), 'age in grid.levels is NA')
Error : age in grid.levels is NA
Got expected error from try(plotmo(a, grid.levels = list(age = NA)))
> expect.err(try(plotmo(a, grid.levels=list(age=Inf))), 'age in grid.levels is infinite')
Error : age in grid.levels is infinite
Got expected error from try(plotmo(a, grid.levels = list(age = Inf)))
> expect.err(try(plotmo(a, grid.lev=list(age=list(1,2)))), 'length(age) in grid.levels is not 1')
Error : length(age) in grid.levels is not 1
Got expected error from try(plotmo(a, grid.lev = list(age = list(1, 2))))
> 
> # more-or-less repeat above, but with glm models
> a <- earth(survived ~ pclass+age+sibsp, data=etitanic, degree=2, glm=list(family=binomial))
> print(summary(a))
Call: earth(formula=survived~pclass+age+sibsp, data=etitanic,
            glm=list(family=binomial), degree=2)

GLM coefficients
                         survived
(Intercept)             3.4306891
pclass2nd              -1.2012524
pclass3rd              -2.0973424
h(age-5)               -0.1769427
h(age-18)               0.1502007
h(18-age) * h(sibsp-2) -0.2887477
h(18-age) * h(sibsp-3)  0.2820357

GLM (family binomial, link logit):
 nulldev   df       dev   df   devratio     AIC iters converged
 1414.62 1045   1212.21 1039      0.143    1226     5         1

Earth selected 7 of 17 terms, and 4 of 4 predictors
Termination condition: Reached nk 21
Importance: pclass3rd, age, pclass2nd, sibsp
Number of terms at each degree of interaction: 1 4 2
Earth GCV 0.2040487    RSS 206.9554    GRSq 0.1569604    RSq 0.1809888
> plotmo(a, ylim=c(0, 1), caption="plotmo glm with mixed fac and non-fac degree2 terms")
 plotmo grid:    pclass age sibsp
                    3rd  28     0
> plotmo(a, ylim=c(0, 1), caption="plotmo glm with mixed fac and non-fac degree2 terms and grid.levels",
+        grid.levels=list(pcl="2nd")) # test partial matching of variable name in grid levels
 plotmo grid:    pclass age sibsp
                    2nd  28     0
> plotmo(a, type="earth", ylim=c(0, 1), caption="type=\"earth\" plotmo glm with mixed fac and non-fac degree2 terms")
 plotmo grid:    pclass age sibsp
                    3rd  28     0
> plotmo(a, type="link", ylim=c(0, 1), clip=FALSE, caption="type=\"link\" plotmo glm with mixed fac and non-fac degree2 terms")
 plotmo grid:    pclass age sibsp
                    3rd  28     0
> plotmo(a, type="class", ylim=c(0, 1), caption="type=\"class\" plotmo glm with mixed fac and non-fac degree2 terms")
 plotmo grid:    pclass age sibsp
                    3rd  28     0
> plotmo(a, ylim=c(0, 1), caption="default type (\"response\")\nplotmo glm with mixed fac and non-fac degree2 terms")
 plotmo grid:    pclass age sibsp
                    3rd  28     0
> # now with different type2s
> set.seed(2016)
> plotmo(a, do.par=FALSE, type2="persp", persp.theta=-20, degree1=FALSE, grid.levels=list(pclass="2nd"))
> mtext("different type2s", outer=TRUE, font=2, line=1.5, cex=1)
> plotmo(a, do.par=FALSE, type2="contour", degree1=FALSE, grid.levels=list(pclass="2nd"))
> plotmo(a, do.par=FALSE, type2="image",   degree1=FALSE, grid.levels=list(pclass="2nd"),
+        col.response=as.numeric(etitanic$survived)+2, pt.pch=20)
> plotmo(a, do.par=FALSE, type="earth", type2="image", degree1=FALSE,
+        grid.levels=list(pclass="2"))
> 
> # grid.levels with partdep
> 
> set.seed(2018)
> x1 <- (1:11) + runif(11)
> x2 <- (1:11) + runif(11)
> x3 <- as.integer((1:11) + runif(11))
> x4 <- runif(11) > .5 # logical
> y <- x1 - x2 + x3 + x4
> data <- data.frame(y=y, x1=x1, x2=x2, x3=x3, x4=x4)
> lm.x1.x2.x3 <- lm(y ~ x1 + x2 + x3 + x4 + x1*x2 + x1*x3, data=data)
> cat("summary(lm.x1.x2.x3):\n")
summary(lm.x1.x2.x3):
> print(summary(lm.x1.x2.x3))
Warning in summary.lm(lm.x1.x2.x3) :
  essentially perfect fit: summary may be unreliable

Call:
lm(formula = y ~ x1 + x2 + x3 + x4 + x1 * x2 + x1 * x3, data = data)

Residuals:
         1          2          3          4          5          6          7 
 4.445e-17 -2.215e-16  9.227e-18  2.871e-16  2.251e-16 -9.376e-17 -5.566e-16 
         8          9         10         11 
 1.746e-17  2.252e-16  3.073e-16 -2.440e-16 

Coefficients:
              Estimate Std. Error    t value Pr(>|t|)    
(Intercept)  2.142e-15  1.549e-15  1.383e+00    0.239    
x1           1.000e+00  6.608e-16  1.513e+15   <2e-16 ***
x2          -1.000e+00  1.816e-15 -5.507e+14   <2e-16 ***
x3           1.000e+00  1.818e-15  5.502e+14   <2e-16 ***
x4TRUE       1.000e+00  3.109e-16  3.216e+15   <2e-16 ***
x1:x2        3.625e-16  2.328e-16  1.557e+00    0.195    
x1:x3       -3.314e-16  2.274e-16 -1.458e+00    0.219    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 4.207e-16 on 4 degrees of freedom
Multiple R-squared:      1,	Adjusted R-squared:      1 
F-statistic: 1.326e+32 on 6 and 4 DF,  p-value: < 2.2e-16

> par(mfrow = c(5, 6), mar = c(2, 3, 2, 1), mgp = c(1.5, 0.5, 0), cex = 0.6, oma=c(0,0,8,0))
> plotmo(lm.x1.x2.x3, do.par=0, ylim=c(0,16), pt.col=2,
+        caption="row1 default\nrow2 grid.levels=list(x3=15)\nrow3 partdep\nrow4 partdetp grid.levels=list(x3=15)")
 plotmo grid:    x1       x2 x3   x4
           6.301049 6.270736  6 TRUE
> plotmo(lm.x1.x2.x3, do.par=0, ylim=c(0,16), pt.col=2, grid.levels=list(x3=15))
 plotmo grid:    x1       x2 x3   x4
           6.301049 6.270736 15 TRUE
> plotmo(lm.x1.x2.x3, do.par=0, ylim=c(0,16), pt.col=2, pmethod="partdep")
calculating partdep for x1 
calculating partdep for x2 
calculating partdep for x3 
calculating partdep for x4 
calculating partdep for x1:x2 01234567890
calculating partdep for x1:x3 01234567890
> plotmo(lm.x1.x2.x3, do.par=0, ylim=c(0,16), pt.col=2, pmethod="partdep", grid.levels=list(x3=15))
calculating partdep for x1 
calculating partdep for x2 
calculating partdep for x3 
calculating partdep for x4 
calculating partdep for x1:x2 01234567890
calculating partdep for x1:x3 01234567890
> 
> # check auto type convert in grid.levels
> plotmo(lm.x1.x2.x3, degree1="x1", degree2=0, main="x1 (x2=5L))",  ylim=c(0,16), do.par=0, pmethod="partdep", grid.levels=list(x2=15L)) # integer to numeric
calculating partdep for x1 
> plotmo(lm.x1.x2.x3, degree1="x1", degree2=0, main="x1 (x3=5))",   ylim=c(0,16), do.par=0, pmethod="partdep", grid.levels=list(x3=15))  # numeric to integer
calculating partdep for x1 
> plotmo(lm.x1.x2.x3, degree1="x1", degree2=0, main="x1 (x4=1))",   ylim=c(0,16), do.par=0, pmethod="partdep", grid.levels=list(x4=1))   # numeric to logical
calculating partdep for x1 
> expect.err(try(plotmo(lm.x1.x2.x3, degree1="x1", degree2=0, main="x1 (x4=1))",   ylim=c(0,16), do.par=0, pmethod="partdep", grid.levels=list(x4="x"))), "expected a logical value in grid.levels for x4") # char to logical
Error : expected a logical value in grid.levels for x4
Got expected error from try(plotmo(lm.x1.x2.x3, degree1 = "x1", degree2 = 0, main = "x1 (x4=1))",     ylim = c(0, 16), do.par = 0, pmethod = "partdep", grid.levels = list(x4 = "x")))
> expect.err(try(plotmo(lm.x1.x2.x3, degree1="x2", do.par=0, pmethod="partdep", grid.levels=list(x1="1"))), "the class \"character\" of \"x1\" in grid.levels does not match its class \"numeric\" in the input data")
Warning: grid.levels returned class "character" for x1, so will use the default grid.func for x1
Error : the class "character" of "x1" in grid.levels does not match its class "numeric" in the input data
Got expected error from try(plotmo(lm.x1.x2.x3, degree1 = "x2", do.par = 0, pmethod = "partdep",     grid.levels = list(x1 = "1")))
> par(org.par)
> 
> # test vector main
> 
> a20 <- earth(O3 ~ humidity + temp + doy, data=ozone1, degree=2, glm=list(family=Gamma))
> 
> dopar(2, 2)
                               
> plotmo(a20, nrug=-1)
 plotmo grid:    humidity temp   doy
                       64   62 205.5
> 
> set.seed(2016)
> plotmo(a20, nrug=10, caption="Test plotmo with a vector main (and npoints=200)",
+        main=c("Humidity", "Temperature", "Day of year", "Humidity: Temperature", "Temperature: Day of Year"),
+        col.response="darkgray", pt.pch=".", cex.response=3, npoints=200) # cex.response tests back compat
 plotmo grid:    humidity temp   doy
                       64   62 205.5
> 
> cat("Expect warning below (missing double titles)\n")
Expect warning below (missing double titles)
> plotmo(a20, nrug=-1, caption="Test plotmo with a vector main (and plain smooth)",
+        main=c("Humidity", "Temperature", "Day of year", "Humidity: Temperature", "Temp: Doy"),
+        smooth.col="indianred")
 plotmo grid:    humidity temp   doy
                       64   62 205.5
> 
> cat("Expect warning below (missing single titles)\n")
Expect warning below (missing single titles)
> plotmo(a20, nrug=-1, caption="Test plotmo with a vector main (and smooth args)",
+        main=c("Humidity", "Temperature"),
+        smooth.col="indianred", smooth.lwd=2, smooth.lty=2, smooth.f=.1,
+        col.response="gray", npoints=500)
 plotmo grid:    humidity temp   doy
                       64   62 205.5
> 
> plotmo(a20, nrug=-1, caption="Test plotmo with pt.pch=paste(1:nrow(ozone1))",
+        type2="im",
+        col.response=2, pt.cex=.8, pt.pch=paste(1:nrow(ozone1)), npoints=100)
 plotmo grid:    humidity temp   doy
                       64   62 205.5
> 
> aflip <- earth(O3~vh + wind + humidity + temp, data=ozone1, degree=2)
> 
> # test all1 and all2, with and without degree1 and degree2
> plotmo(aflip, all2=T, caption="all2=T", npoints=TRUE)
 plotmo grid:    vh wind humidity temp
               5760    5       64   62
> plotmo(aflip, all2=T, degree2=c(4, 2), caption="all2=T, degree2=c(4, 2)")
 plotmo grid:    vh wind humidity temp
               5760    5       64   62
> plotmo(aflip, all1=T, caption="all1=T")
 plotmo grid:    vh wind humidity temp
               5760    5       64   62
> plotmo(aflip, all1=T, degree1=c(3,1), degree2=NA, caption="all1=T, degree1=c(3,1), degree2=NA")
 plotmo grid:    vh wind humidity temp
               5760    5       64   62
> 
> options(warn=2)
> expect.err(try(plotmo(aflip, no.such.arg=9)), "(converted from warning) predict.earth ignored argument 'no.such.arg'")

stats::predict(earth.object, NULL, type="response", no.such.arg=9)

Error : (converted from warning) predict.earth ignored argument 'no.such.arg'
Got expected error from try(plotmo(aflip, no.such.arg = 9))
> expect.err(try(plotmo(aflip, ycolumn=1)), "(converted from warning) predict.earth ignored argument 'ycolumn'")

stats::predict(earth.object, NULL, type="response", ycolumn=1)

Error : (converted from warning) predict.earth ignored argument 'ycolumn'
Got expected error from try(plotmo(aflip, ycolumn = 1))
> expect.err(try(plotmo(aflip, title="abc")), "(converted from warning) predict.earth ignored argument 'title'")

stats::predict(earth.object, NULL, type="response", title="abc")

Error : (converted from warning) predict.earth ignored argument 'title'
Got expected error from try(plotmo(aflip, title = "abc"))
> expect.err(try(plotmo(aflip, persp.ticktype="d", persp.ntick=3, tic=3, tick=9)), "(converted from warning) predict.earth ignored argument 'tic'")

stats::predict(earth.object, NULL, type="response", tic=3, tick=9)

Error : (converted from warning) predict.earth ignored argument 'tic'
Got expected error from try(plotmo(aflip, persp.ticktype = "d", persp.ntick = 3, tic = 3,     tick = 9))
> expect.err(try(plotmo(aflip, persp.ticktype="d", ntick=3, tic=3)), "(converted from warning) predict.earth ignored argument 'ntick'")

stats::predict(earth.object, NULL, type="response", ntick=3, tic=3)

Error : (converted from warning) predict.earth ignored argument 'ntick'
Got expected error from try(plotmo(aflip, persp.ticktype = "d", ntick = 3, tic = 3))
> options(warn=1)
> # expect.err(try(plotmo(aflip, adj1=8, adj2=9))) # Error : plotmo: illegal argument "adj1"
> # expect.err(try(plotmo(aflip, yc=8, x2=9))) # "ycolumn" is no longer legal, use "nresponse" instead
> # expect.err(try(plotmo(aflip, persp.ticktype="d", ntick=3, ti=3))) # Error : "title" is illegal, use "caption" instead ("ti" taken to mean "title")
> # expect.err(try(plotmo(aflip, persp.ticktype="d", ntick=3, title=3))) # Error : "title" is illegal, use "caption" instead
> # expect.err(try(plotmo(aflip, persp.ticktype="d", ntick=3, tit=3, titl=7))) # Error : "title" is illegal, use "caption" instead ("tit" taken to mean "title")
> # expect.err(try(plotmo(aflip, zlab="abc"))) # "zlab" is illegal, use "ylab" instead
> # expect.err(try(plotmo(aflip, z="abc"))) # "zlab" is illegal, use "ylab" instead ("z" taken to mean "zlab")
> expect.err(try(plotmo(aflip, degree1=c(4,1))), "'degree1' is out of range, allowed values are 1 to 2")
Error : 'degree1' is out of range, allowed values are 1 to 2
Got expected error from try(plotmo(aflip, degree1 = c(4, 1)))
> # expect.err(try(plotmo(aflip, none.such=TRUE))) # illegal argument "all1"
> # expect.err(try(plotmo(aflip, ntick=3, type2="im"))) # the ntick argument is illegal for type2="image"
> # expect.err(try(plotmo(aflip, breaks=3, type2="persp"))) # the breaks argument is illegal for type2="persp"
> # expect.err(try(plotmo(aflip, breaks=99, type2="cont"))) #  the breaks argument is illegal for type2="contour"
> 
> # Test error handling when accessing the original data
> 
> lm.bad <- lm.fit(as.matrix(ozone1[,-1]), as.matrix(ozone1[,1]))
> expect.err(try(plotmo(lm.bad)), "'lm.bad' is a plain list, not an S3 model")
Error : 'lm.bad' is a plain list, not an S3 model
Got expected error from try(plotmo(lm.bad))
> expect.err(try(plotmo(99)), "'99' is not an S3 model")
Error : '99' is not an S3 model
Got expected error from try(plotmo(99))
> 
> x <- matrix(c(1,3,2,4,5,6,7,8,9,10,
+               2,3,4,5,6,7,8,9,8,9), ncol=2)
> 
> colnames(x) <- c("c1", "c2")
> x1 <- x[,1]
> x2 <- x[,2]
> y <- 3:12
> df <- data.frame(y=y, x1=x1, x2=x2)
> foo1 <- function()
+ {
+     a.foo1 <- lm(y~x1+x2, model=FALSE)
+     x1 <- NULL
+     expect.err(try(plotmo(a.foo1)), "cannot get the original model predictors")
+ }
> foo1()

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: invalid type (NULL) for variable 'x1'

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(plotmo(a.foo1))
> foo2 <- function()
+ {
+     a.foo2 <- lm(y~x1+x2, data=df, model=FALSE)
+     df <- 99 # note that df <- NULL here will not cause an error msg
+     y <- 99  # also needed else model.frame in plotmo will find the global y
+     expect.err(try(plotmo(a.foo2)), "cannot get the original model predictors")
+ }
> foo2()

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: variable lengths differ (found for 'x1')

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(plotmo(a.foo2))
> foo3 <- function()
+ {
+     a.foo3 <- lm(y~x) # lm() builds an lm model for which predict doesn't work
+     expect.err(try(plotmo(a.foo3)), "predict returned the wrong length (got 10 but expected 50)")
+ }
> foo3()
Warning: the variable on the right side of the formula is a matrix or data.frame
         plotmo often cannot process such variables
Warning: 'newdata' had 50 rows but variables found have 10 rows
Error : predict returned the wrong length (got 10 but expected 50)
Got expected error from try(plotmo(a.foo3))
> foo3a <- function()
+ {
+     a.foo3a <- lm(y~x) # lm() builds an lm model for which predict doesn't work
+     # this tests "ngrid1 <- ngrid1 + 1" in plotmo.R
+     expect.err(try(plotmo(a.foo3a, ngrid1=nrow(x))), "predict returned the wrong length (got 10 but expected 11)")
+ }
> foo3a()
Warning: the variable on the right side of the formula is a matrix or data.frame
         plotmo often cannot process such variables
Warning: 'newdata' had 11 rows but variables found have 10 rows
Error : predict returned the wrong length (got 10 but expected 11)
Got expected error from try(plotmo(a.foo3a, ngrid1 = nrow(x)))
> foo4 <- function()
+ {
+     a.foo4 <- lm(y~x[,1]+x[,2])  # builds an lm model for which predict doesn't work
+     # causes 'newdata' had 8 rows but variables found have 10 rows
+     expect.err(try(plotmo(a.foo4)), "predict returned the wrong length (got 10 but expected 50)")
+ }
> foo4()
Warning: Cannot determine which variables to plot in degree2 plots (use all2=TRUE?)
         Confused by variable name "x[, 1]"
Warning: 'newdata' had 50 rows but variables found have 10 rows
Error : predict returned the wrong length (got 10 but expected 50)
Got expected error from try(plotmo(a.foo4))
> foo5 <- function()
+ {
+     a.foo5 <- lm(y~x1+x2, model=FALSE)
+     x1 <- c(1,2,3)
+     # causes Error in model.frame.default: variable lengths differ (found for 'x1')
+     expect.err(try(plotmo(a.foo5)), "cannot get the original model predictors")
+ }
> foo5()

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: variable lengths differ (found for 'x1')

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(plotmo(a.foo5))
> foo6 <- function()
+ {
+     a.foo6 <- lm(y~x1+x2, model=FALSE)
+     y[1] <- NA
+     # Error in na.fail.default: missing values in object
+     expect.err(try(plotmo(a.foo6, col.response=3)), "cannot get the original model predictors")
+ }
> foo6()

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: missing values in object

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(plotmo(a.foo6, col.response = 3))
> foo7 <- function()
+ {
+     a.foo7 <- lm(y~x1+x2, model=FALSE)
+     y[1] <- Inf
+     options <- options("warn")
+     on.exit(options(warn=options$warn))
+     options(warn=2)
+     expect.err(try(plotmo(a.foo7, col.response=3)), "non-finite values returned by plotmo_y")
+ }
> foo7()
Error : (converted from warning) non-finite values returned by plotmo_y
Got expected error from try(plotmo(a.foo7, col.response = 3))
> options(warn=1)
> foo8 <- function()
+ {
+     i <- 1
+     a.foo8 <- lm(y~x[,i]+x[,2])
+     options <- options("warn")
+     on.exit(options(warn=options$warn))
+     options(warn=2)
+     expect.err(try(plotmo(a.foo8)), "Cannot determine which variables to plot in degree2 plots (use all2=TRUE?)")
+     options(warn=options$warn)
+     expect.err(try(plotmo(a.foo8)), "predict returned the wrong length (got 10 but expected 50)")
+ }
> foo8()
Error : (converted from warning) Cannot determine which variables to plot in degree2 plots (use all2=TRUE?)
         Confused by variable name "x[, i]"
Got expected error from try(plotmo(a.foo8))
Warning: Cannot determine which variables to plot in degree2 plots (use all2=TRUE?)
         Confused by variable name "x[, i]"
Warning: 'newdata' had 50 rows but variables found have 10 rows
Error : predict returned the wrong length (got 10 but expected 50)
Got expected error from try(plotmo(a.foo8))
> options(warn=1)
> foo9 <- function()
+ {
+     my.list <- list(j=2)
+     a.foo9 <- lm(y~x[,1]+x[,my.list$j])
+     expect.err(try(plotmo(a.foo9)), "cannot get the original model predictors")
+ }
> foo9()
Warning: "$" in the formula is not supported by plotmo, will try to get the data elsewhere
         formula: x[, 1] + x[, my.list$j]

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: formula(object): "$" in formula is not allowed

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(plotmo(a.foo9))
> foo9a <- function()
+ {
+     df <- data.frame(y=y, x1=x[,1], x2=x[,2])
+     a.foo9a <- lm(y~x1+x2, data=df)
+     par(mfrow = c(2, 2), oma=c(0,0,4,0))
+     set.seed(2018)
+     plotmo(a.foo9a, col.resp=2, do.par=FALSE,
+            caption="top two plots should be identical to bottom two plots")
+     x2 <- rep(99, length(x2))
+     a.foo9b <- lm(y~x1+x2, data=df)
+     x2 <- rep(199, length(x2))
+     plotmo(a.foo9b, col.resp=2, do.par=FALSE)
+ }
> foo9a()
 plotmo grid:    x1  x2
                5.5 6.5
 plotmo grid:    x1  x2
                5.5 6.5
> par(org.par)
> 
> foo20.func <- function()
+ {
+     par(mfrow = c(2, 2), oma=c(0,0,4,0))
+     foo20 <- lm(y~x1+x2)
+     set.seed(2018)
+     plotmo(foo20, degree1=1:2, col.resp=2, do.par=FALSE,
+            caption="top two plots should be identical to bottom two plots\nbecause we use saved lm$model")
+     x1 <- 99
+     plotmo(foo20, degree1=1:2, col.resp=2, do.par=FALSE)
+ }
> foo20.func()
 plotmo grid:    x1  x2
                5.5 6.5
 plotmo grid:    x1  x2
                5.5 6.5
> par(org.par)
> 
> set.seed(1235)
> tit <- etitanic
> tit <- tit[c(30:80,330:380,630:680), ]
> a <- earth(survived~., data=tit, glm=list(family=binomial), degree=2)
> plotmo(a, grid.levels=list(sex="ma"),
+        caption="smooth: survived, sex=\"m\"    jitter=1",
+        smooth.col="indianred", smooth.lwd=2,
+        col.response=as.numeric(tit$survived)+2, pt.pch=".", type2="im",
+        pt.cex=3, jitter=1) # big jitter
 plotmo grid:    pclass  sex age sibsp parch
                    1st male  29     0     0
> set.seed(1238)
> a <- earth(pclass~., data=tit)
> plotmo(a, type="class", nresponse=1,
+        grid.levels=list(sex="ma"),
+        caption="smooth: pclass, sex=\"m\"", SHOWCALL=TRUE,
+        smooth.col="indianred", smooth.lwd=2,
+        col.response=as.numeric(tit$pclass)+1, type2="im",
+        pt.pch=".", pt.cex=3)
 plotmo grid:    survived  sex age sibsp parch
                        0 male  29     0     0
> plotmo(a, type="class", nresponse=1,
+        grid.levels=list(sex="ma"),
+        caption="smooth: pclass, sex=\"m\"      jitter=.3", SHOWCALL=TRUE,
+        smooth.col="indianred", smooth.lwd=2,
+        col.response=as.numeric(tit$pclass)+1, type2="im",
+        pt.pch="x", jit=.3) # small jitter
 plotmo grid:    survived  sex age sibsp parch
                        0 male  29     0     0
> plotmo(a, nresponse=1,
+        type="class", grid.levels=list(sex="ma"),
+        caption="smooth: pclass, sex=\"m\"",  SHOWCALL=TRUE,
+        smooth.col="indianred", smooth.lwd=2,
+        col.response=as.numeric(tit$pclass)+1, type2="im",
+        pt.pch=paste(1:nrow(tit)))
 plotmo grid:    survived  sex age sibsp parch
                        0 male  29     0     0
> 
> # test the extend argument
> 
> plotmo(a, nresponse=1,             pt.col=2, degree2=0, SHOWCALL=TRUE,
+        caption="test extend: extend=0 (reference plot)")
 plotmo grid:    survived  sex age sibsp parch
                        0 male  29     0     0
> plotmo(a, nresponse=1, extend=.5, pt.col=2, SHOWCALL=TRUE,
+        caption="test extend: extend=.5")
 plotmo grid:    survived  sex age sibsp parch
                        0 male  29     0     0
> plotmo(a, nresponse=1, degree1=0, extend=.2, pt.col=2, SHOWCALL=TRUE) # nothing to plot
Warning: plotmo: nothing to plot
> 
> a <- earth(survived~pclass+age, data=etitanic, degree=2)
> # expect warning: extend=.5 not degree2 plots
> plotmo(a, extend=.5, pt.col=2, SHOWCALL=TRUE,
+        caption="test extend: extend=.5")
Warning: extend=0.5: will not plot degree2 plots (extend is not yet implemented for degree2 plots)
 plotmo grid:    pclass age
                    3rd  28
> 
> # intercept only models
> 
> dopar(2, 2, caption = "intercept-only models")
                              intercept-only models 
> set.seed(1)
> x <- 1:10
> y <- runif(length(x))
> earth.intercept.only <- earth(x, y)
> plotmo(earth.intercept.only, do.par=FALSE, main="earth intercept-only model")
> plotmo(earth.intercept.only, do.par=FALSE, col.response=1, pt.pch=20)
> # TODO following draws a plot but it shouldn't (very minor bug because int-only model with a bad degree1 spec)
> plotmo(earth.intercept.only, do.par=FALSE, degree1=3) # expect warning: 'degree1' specified but no degree1 plots
Warning: 'degree1' specified but no degree1 plots (maybe use all1=TRUE?)
> plotmo(earth.intercept.only, do.par=FALSE, degree1=0) # expect warning: plotmo: nothing to plot
Warning: plotmo: nothing to plot
> library(rpart)
> rpart.intercept.only <- rpart(y~x)
> plotmo(rpart.intercept.only, do.par=FALSE, main="rpart.plot intercept-only model")
> plotmo(rpart.intercept.only, do.par=FALSE, degree1=0)
Warning: plotmo: nothing to plot
> par(org.par)
> 
> # nrug argument
> 
> par(mfrow=c(3,3), mar=c(3,3,3,1), mgp=c(1.5, 0.5, 0))
> mod.nrug <- earth(survived~age, data=etitanic)
> set.seed(2016)
> plotmo(mod.nrug, do.par=0, nrug=-1,   main="nrug=-1")
> plotmo(mod.nrug, do.par=0, nrug=TRUE, main="nrug=TRUE")
> plotmo(mod.nrug, do.par=0, nrug=10, rug.col=2,            main="nrug=10, rug.col=2")
> plotmo(mod.nrug, do.par=0, nrug=5,  rug.col=2, rug.lwd=2, main="nrug=5, rug.col=2, rug.lwd=2")
> plotmo(mod.nrug, do.par=0, nrug="density", main="nrug=\"density\"")
> plotmo(mod.nrug, do.par=0, nrug="density", density.col=2, density.lwd=2, main="nrug=\"density\"\ndensity.col=2, density.lwd=2")
> plotmo(mod.nrug, do.par=0, nrug="density", density.adj=.2, density.col=1, main="nrug=\"density\"\ndensity.adj=.2, density.col=1")
> par(org.par)
> 
> # a <- earth(ozone1[,3]~ozone1[,1]+ozone1[,2]+ozone1[,4]+ozone1[,5]+ozone1[,6], data=ozone1)
> # # TODO fails: actual.nrows=330 expected.nrows=50 fitted.nrows=330
> # plotmo(a)
> 
> # # TODO following fails in plotmo with
> # # Error : get.earth.x from model.matrix.earth from predict.earth: x has 2 columns, expected 4 to match: 1 2 3 Girth
> # a <- earth(Volume~poly(Height, degree=3)+Girth, data=trees, subset=4:23, linpreds=TRUE)
> # plotmo(a, trace=-1, do.par=FALSE, caption="all three rows should be the same")
> 
> source("test.epilog.R")