> # test.linmod.R: test example S3 model at http://www.milbo.org/doc/linmod.R
> 
> source("test.prolog.R")
> source("linmod.R")         # linear model code (http://www.milbo.org/doc/linmod.R)
> source("linmod.methods.R") # additional method functions for linmod
> options(warn=1) # print warnings as they occur
> 
> almost.equal <- function(x, y, max=1e-8)
+ {
+     stopifnot(max >= 0 && max < .01)
+     length(x) == length(y) && max(abs(x - y)) < max
+ }
> # check that linmod model matches reference lm model in all essential details
> check.lm <- function(fit, ref, newdata=trees[3:5,],
+                      check.coef.names=TRUE,
+                      check.casenames=TRUE,
+                      check.newdata=TRUE,
+                      check.sigma=TRUE)
+ {
+     check.names <- function(fit.names, ref.names)
+     {
+         if(check.casenames &&
+         # lm always adds rownames even if "1", "2", "3": this seems
+         # wasteful and not particulary helpful, so linmod doesn't do
+         # this, hence the first !isTRUE(all.equal) below
+            !isTRUE(all.equal(ref.names, paste(1:length(ref.names)))) &&
+            !isTRUE(all.equal(fit.names, ref.names))) {
+             print(fit.names)
+             print(ref.names)
+             stop(deparse(substitute(fit.names)), " != ",
+                  deparse(substitute(ref.names)))
+         }
+     }
+     cat0("check ", deparse(substitute(fit)), " vs ",
+          deparse(substitute(ref)), "\n")
+ 
+     stopifnot(coef(fit) == coef(ref))
+     if(check.coef.names)
+         stopifnot(identical(names(coef(fit)), names(coef(ref))))
+ 
+     stopifnot(identical(dim(fit$coefficients), dim(ref$coefficients)))
+     stopifnot(length(fit$coefficients) == length(ref$coefficients))
+     stopifnot(almost.equal(fit$coefficients, ref$coefficients))
+ 
+     stopifnot(identical(dim(fit$residuals), dim(ref$residuals)))
+     stopifnot(length(fit$residuals) == length(ref$residuals))
+     stopifnot(almost.equal(fit$residuals, ref$residuals))
+ 
+     stopifnot(identical(dim(fit$fitted.values), dim(ref$fitted.values)))
+     stopifnot(length(fit$fitted.values) == length(ref$fitted.values))
+     stopifnot(almost.equal(fit$fitted.values, ref$fitted.values))
+ 
+     stopifnot(identical(fit$rank, ref$rank))
+ 
+     if(!is.null(fit$vcov) && !is.null(ref$vcov)) {
+         stopifnot(identical(dim(fit$vcov), dim(ref$vcov)))
+         stopifnot(length(fit$vcov) == length(ref$vcov))
+         stopifnot(almost.equal(fit$vcov, ref$vcov))
+     }
+     if(check.sigma) {
+         ref.sigma <- ref$sigma
+         if(is.null(ref.sigma)) # in lm models, sigma is only available from summary()
+             ref.sigma <- summary(ref)$sigma
+         stopifnot(almost.equal(fit$sigma, ref.sigma))
+     }
+     stopifnot(almost.equal(fit$df.residual, ref$df.residual))
+ 
+     stopifnot(almost.equal(fitted(fit), fitted(ref)))
+     check.names(names(fitted(fit)), names(fitted(ref)))
+ 
+     stopifnot(almost.equal(residuals(fit), residuals(ref)))
+     check.names(names(residuals(fit)), names(residuals(ref)))
+ 
+     stopifnot(almost.equal(predict(fit), predict(ref)))
+     check.names(names(predict(fit)), names(predict(ref)))
+     if(check.newdata) {
+         stopifnot(almost.equal(predict(fit, newdata=newdata),
+                                predict(ref, newdata=newdata)))
+         check.names(names(predict(fit, newdata=newdata)),
+                     names(predict(ref, newdata=newdata)))
+     }
+ }
> tr <- trees # trees data but with rownames
> rownames(tr) <- paste("tree", 1:nrow(trees), sep="")
> 
> linmod.form.Volume.tr <- linmod(Volume~., data=tr)
> cat0("==print(summary(linmod.form.Volume.tr))\n")
==print(summary(linmod.form.Volume.tr))
> print(summary(linmod.form.Volume.tr))
Call: linmod.formula(formula = Volume ~ ., data = tr)

               Estimate    StdErr   t.value      p.value
(Intercept) -57.9876589 8.6382259 -6.712913 2.749507e-07
Girth         4.7081605 0.2642646 17.816084 8.223304e-17
Height        0.3392512 0.1301512  2.606594 1.449097e-02
> lm.Volume.tr <- lm(Volume~., data=tr)
> check.lm(linmod.form.Volume.tr, lm.Volume.tr)
check linmod.form.Volume.tr vs lm.Volume.tr
> stopifnot(almost.equal(predict(linmod.form.Volume.tr, newdata=data.frame(Girth=10, Height=80)),
+                        16.234045, max=1e-5))
> stopifnot(almost.equal(predict(linmod.form.Volume.tr, newdata=as.matrix(tr[1:3,])),
+                        c(4.8376597, 4.5538516, 4.8169813), max=1e-5))
> # character new data (instead of numeric)
> newdata.allchar <- as.data.frame(matrix("blank", ncol=3, nrow=3))
> colnames(newdata.allchar) <- colnames(trees)
> expect.err(try(predict(lm.Volume.tr, newdata=newdata.allchar)),
+                "variables 'Girth', 'Height' were specified with different types from the fit")
Error : variables 'Girth', 'Height' were specified with different types from the fit
Got expected error from try(predict(lm.Volume.tr, newdata = newdata.allchar))
> expect.err(try(predict(linmod.form.Volume.tr, newdata=newdata.allchar)),
+               "variables 'Girth', 'Height' were specified with different types from the fit")
Error : variables 'Girth', 'Height' were specified with different types from the fit
Got expected error from try(predict(linmod.form.Volume.tr, newdata = newdata.allchar))
> 
> linmod.xy.Volume.tr <- linmod(tr[,1:2], tr[,3,drop=FALSE])                         # x=data.frame y=data.frame
> cat0("==print(summary(linmod.xy.Volume.tr))\n")
==print(summary(linmod.xy.Volume.tr))
> print(summary(linmod.xy.Volume.tr))
Call: linmod.default(x = tr[, 1:2], y = tr[, 3, drop = FALSE])

               Estimate    StdErr   t.value      p.value
(Intercept) -57.9876589 8.6382259 -6.712913 2.749507e-07
Girth         4.7081605 0.2642646 17.816084 8.223304e-17
Height        0.3392512 0.1301512  2.606594 1.449097e-02
> newdata.2col <- trees[3:5,1:2]
> check.lm(linmod.xy.Volume.tr, lm.Volume.tr, newdata=newdata.2col)
check linmod.xy.Volume.tr vs lm.Volume.tr
> stopifnot(almost.equal(predict(linmod.xy.Volume.tr, newdata=data.frame(Girth=10, Height=80)),
+                        16.234045, max=1e-5))
> stopifnot(almost.equal(predict(linmod.xy.Volume.tr, newdata=tr[1:3,1:2]),
+                        c(4.8376597, 4.5538516, 4.8169813), max=1e-5))
> 
> linmod50.xy.Volume.tr <- linmod(as.matrix(tr[,1:2]), as.matrix(tr[,3,drop=FALSE])) # x=matrix y=matrix
> check.lm(linmod50.xy.Volume.tr, lm.Volume.tr, newdata=newdata.2col)
check linmod50.xy.Volume.tr vs lm.Volume.tr
> linmod51.xy.Volume.tr <- linmod(tr[,1:2], tr[,3])                                  # x=data.frame y=vector
> check.lm(linmod51.xy.Volume.tr, lm.Volume.tr, newdata=newdata.2col)
check linmod51.xy.Volume.tr vs lm.Volume.tr
> linmod52.xy.Volume.tr <- linmod(as.matrix(tr[,1:2]), tr[,3])                       # x=matrix y=vector
> check.lm(linmod52.xy.Volume.tr, lm.Volume.tr, newdata=newdata.2col)
check linmod52.xy.Volume.tr vs lm.Volume.tr
> 
> # newdata can be a vector
> stopifnot(almost.equal(predict(linmod.xy.Volume.tr, newdata=c(8.3, 70)),
+                        4.8376597, max=1e-5))
> stopifnot(almost.equal(predict(linmod.xy.Volume.tr,
+                        newdata=c(8.3, 8.6, 70, 65)), # 4 element vector, byrow=FALSE
+                        c(4.8376597, 4.5538516), max=1e-5))
> options(warn=1) # print warnings as they occur
> # expect Warning: data length [3] is not a sub-multiple or multiple of the number of rows [2]
> stopifnot(almost.equal(predict(linmod.xy.Volume.tr, newdata=c(8.3, 9, 70)), # 3 element vector
+                       c(4.8376597, -12.7984291), max=1e-5))
Warning in matrix(newdata, ncol = length(object$coefficients) - 1) :
  data length [3] is not a sub-multiple or multiple of the number of rows [2]
> options(warn=2) # treat warnings as errors
> 
> stopifnot(almost.equal(predict(linmod.xy.Volume.tr, newdata=as.matrix(data.frame(Girth=10, Height=80))),
+                        16.234045, max=1e-5))
> # column names in newdata are ignored for linmod.default models
> stopifnot(almost.equal(predict(linmod.xy.Volume.tr, newdata=data.frame(name1.not.in.orig.data=10, name2.not.in.orig.datax2=80)),
+                        16.234045, max=1e-5))
> # note name reversed below but names still ignored, same predict result as c(Girth=10, Height=80)
> stopifnot(almost.equal(predict(linmod.xy.Volume.tr, newdata=data.frame(Height=10, Girth=80)),
+                        16.234045, max=1e-5))
> 
> cat0("==print.default(linmod.form.Volume.tr)\n")
==print.default(linmod.form.Volume.tr)
> print.default(linmod.form.Volume.tr)
$coefficients
(Intercept)       Girth      Height 
-57.9876589   4.7081605   0.3392512 

$residuals
      tree1       tree2       tree3       tree4       tree5       tree6 
 5.46234035  5.74614837  5.38301873  0.52588477 -1.06900844 -1.31832696 
      tree7       tree8       tree9      tree10      tree11      tree12 
-0.59268807 -1.04594918  1.18697860 -0.28758128  2.18459773 -0.46846462 
     tree13      tree14      tree15      tree16      tree17      tree18 
-0.06846462  0.79384587 -4.85410969 -5.65220290  2.21603352 -6.40648192 
     tree19      tree20      tree21      tree22      tree23      tree24 
-4.90097760 -3.79703501  0.11181561 -4.30831896  0.91474029 -3.46899800 
     tree25      tree26      tree27      tree28      tree29      tree30 
-2.27770232  4.45713224  3.47624891  4.87148717 -2.39932888 -2.89932888 
     tree31 
 8.48469518 

$rank
[1] 3

$fitted.values
    tree1     tree2     tree3     tree4     tree5     tree6     tree7     tree8 
 4.837660  4.553852  4.816981 15.874115 19.869008 21.018327 16.192688 19.245949 
    tree9    tree10    tree11    tree12    tree13    tree14    tree15    tree16 
21.413021 20.187581 22.015402 21.468465 21.468465 20.506154 23.954110 27.852203 
   tree17    tree18    tree19    tree20    tree21    tree22    tree23    tree24 
31.583966 33.806482 30.600978 28.697035 34.388184 36.008319 35.385260 41.768998 
   tree25    tree26    tree27    tree28    tree29    tree30    tree31 
44.877702 50.942868 52.223751 53.428513 53.899329 53.899329 68.515305 

$vcov
            (Intercept)       Girth      Height
(Intercept)  74.6189461  0.43217138 -1.05076889
Girth         0.4321714  0.06983578 -0.01786030
Height       -1.0507689 -0.01786030  0.01693933

$sigma
[1] 3.881832

$df.residual
[1] 28

$call
linmod.formula(formula = Volume ~ ., data = tr)

$terms
Volume ~ Girth + Height
attr(,"variables")
list(Volume, Girth, Height)
attr(,"factors")
       Girth Height
Volume     0      0
Girth      1      0
Height     0      1
attr(,"term.labels")
[1] "Girth"  "Height"
attr(,"order")
[1] 1 1
attr(,"intercept")
[1] 1
attr(,"response")
[1] 1
attr(,".Environment")
<environment: R_GlobalEnv>
attr(,"predvars")
list(Volume, Girth, Height)
attr(,"dataClasses")
   Volume     Girth    Height 
"numeric" "numeric" "numeric" 

$xlevels
named list()

attr(,"class")
[1] "linmod"
> 
> cat0("==check single x variable\n")
==check single x variable
> linmod1a.form <- linmod(Volume~Height, data=tr)
> cat0("==print(summary(linmod1a.form))\n")
==print(summary(linmod1a.form))
> print(summary(linmod1a.form))
Call: linmod.formula(formula = Volume ~ Height, data = tr)

             Estimate     StdErr   t.value      p.value
(Intercept) -87.12361 29.2731221 -2.976232 0.0058346689
Height        1.54335  0.3838693  4.020509 0.0003783823
> lma.tr <- lm(Volume~Height, data=tr)
> check.lm(linmod1a.form, lma.tr)
check linmod1a.form vs lma.tr
> 
> stopifnot(almost.equal(predict(linmod1a.form, newdata=data.frame(Height=80)),
+                        36.34437, max=1e-5))
> stopifnot(almost.equal(predict(linmod1a.form, newdata=data.frame(Girth=99, Height=80)),
+                        36.34437, max=1e-5))
> stopifnot(almost.equal(predict(linmod1a.form, newdata=as.matrix(tr[1:3,])),
+                        c(20.91087, 13.19412, 10.10742), max=1e-5))
> 
> linmod1a.xy <- linmod(tr[,2,drop=FALSE], tr[,3])
> cat0("==print(summary(linmod1a.xy))\n")
==print(summary(linmod1a.xy))
> print(summary(linmod1a.xy))
Call: linmod.default(x = tr[, 2, drop = FALSE], y = tr[, 3])

             Estimate     StdErr   t.value      p.value
(Intercept) -87.12361 29.2731221 -2.976232 0.0058346689
Height        1.54335  0.3838693  4.020509 0.0003783823
> check.lm(linmod1a.xy, lma.tr, newdata=trees[3:5,2,drop=FALSE])
check linmod1a.xy vs lma.tr
> check.lm(linmod1a.xy, lma.tr, newdata=trees[3:5,2,drop=TRUE],
+          check.newdata=FALSE) # needed because predict.lm gives 'data' must be a data.frame, environment, or list
check linmod1a.xy vs lma.tr
> stopifnot(almost.equal(predict(linmod1a.xy, newdata=trees[3:5,2,drop=FALSE]),
+                        predict(linmod1a.xy, newdata=trees[3:5,2,drop=TRUE])))
> stopifnot(almost.equal(predict(linmod1a.xy, newdata=data.frame(Height=80)),
+                        36.34437, max=1e-5))
> stopifnot(almost.equal(predict(linmod1a.xy, newdata=tr[1:3,2]),
+                        c(20.91087, 13.19412, 10.10742), max=1e-5))
> stopifnot(almost.equal(predict(linmod1a.xy, newdata=as.matrix(data.frame(Height=80))),
+                        36.34437, max=1e-5))
> 
> # check that extra fields in predict newdata are ok with formula models
> stopifnot(almost.equal(predict(linmod.form.Volume.tr, newdata=data.frame(Girth=10, Height=80, extra=99)),
+                        predict(lm.Volume.tr,          newdata=data.frame(Girth=10, Height=80))))
> stopifnot(almost.equal(predict(linmod.form.Volume.tr, newdata=data.frame(Girth=10, Height=80, extra=99)),
+                        predict(lm.Volume.tr,          newdata=data.frame(Girth=10, Height=80, extra=99))))
> # check that extra fields in predict newdata are not ok with x,y models
> expect.err(try(predict(linmod.xy.Volume.tr, newdata=data.frame(Girth=10, Height=80, extra=99))),
+               "ncol(newdata) is 3 but should be 2")
Error in predict.linmod(linmod.xy.Volume.tr, newdata = data.frame(Girth = 10,  : 
  ncol(newdata) is 3 but should be 2
Got expected error from try(predict(linmod.xy.Volume.tr, newdata = data.frame(Girth = 10,     Height = 80, extra = 99)))
> 
> # missing variables in newdata
> expect.err(try(predict(linmod.form.Volume.tr, newdata=data.frame(Girth=10))),
+                "object 'Height' not found")
Error in eval(predvars, data, env) : object 'Height' not found
Got expected error from try(predict(linmod.form.Volume.tr, newdata = data.frame(Girth = 10)))
> expect.err(try(predict(linmod.form.Volume.tr, newdata=c(8.3, 70))),
+                "object 'Girth' not found")
Error in eval(predvars, data, env) : object 'Girth' not found
Got expected error from try(predict(linmod.form.Volume.tr, newdata = c(8.3, 70)))
> expect.err(try(predict(lm.Volume.tr,          newdata=data.frame(Girth=10))),
+                "object 'Height' not found")
Error in eval(predvars, data, env) : object 'Height' not found
Got expected error from try(predict(lm.Volume.tr, newdata = data.frame(Girth = 10)))
> expect.err(try(predict(linmod.xy.Volume.tr,            newdata=data.frame(Girth=10))),
+                "ncol(newdata) is 1 but should be 2")
Error in predict.linmod(linmod.xy.Volume.tr, newdata = data.frame(Girth = 10)) : 
  ncol(newdata) is 1 but should be 2
Got expected error from try(predict(linmod.xy.Volume.tr, newdata = data.frame(Girth = 10)))
> 
> # check that rownames got propagated
> stopifnot(names(linmod.form.Volume.tr$residuals)[1] == "tree1")
> stopifnot(names(linmod.form.Volume.tr$fitted.values)[3] == "tree3")
> stopifnot(names(linmod.xy.Volume.tr$residuals)[1] == "tree1")
> stopifnot(names(linmod.xy.Volume.tr$fitted.values)[3] == "tree3")
> stopifnot(!is.null(names(linmod.xy.Volume.tr$residuals)))
> stopifnot(!is.null(names(linmod.xy.Volume.tr$fitted.values)))
> cat0("==print.default(linmod.xy.Volume.tr)\n")
==print.default(linmod.xy.Volume.tr)
> print.default(linmod.xy.Volume.tr)
$coefficients
(Intercept)       Girth      Height 
-57.9876589   4.7081605   0.3392512 

$residuals
      tree1       tree2       tree3       tree4       tree5       tree6 
 5.46234035  5.74614837  5.38301873  0.52588477 -1.06900844 -1.31832696 
      tree7       tree8       tree9      tree10      tree11      tree12 
-0.59268807 -1.04594918  1.18697860 -0.28758128  2.18459773 -0.46846462 
     tree13      tree14      tree15      tree16      tree17      tree18 
-0.06846462  0.79384587 -4.85410969 -5.65220290  2.21603352 -6.40648192 
     tree19      tree20      tree21      tree22      tree23      tree24 
-4.90097760 -3.79703501  0.11181561 -4.30831896  0.91474029 -3.46899800 
     tree25      tree26      tree27      tree28      tree29      tree30 
-2.27770232  4.45713224  3.47624891  4.87148717 -2.39932888 -2.89932888 
     tree31 
 8.48469518 

$rank
[1] 3

$fitted.values
    tree1     tree2     tree3     tree4     tree5     tree6     tree7     tree8 
 4.837660  4.553852  4.816981 15.874115 19.869008 21.018327 16.192688 19.245949 
    tree9    tree10    tree11    tree12    tree13    tree14    tree15    tree16 
21.413021 20.187581 22.015402 21.468465 21.468465 20.506154 23.954110 27.852203 
   tree17    tree18    tree19    tree20    tree21    tree22    tree23    tree24 
31.583966 33.806482 30.600978 28.697035 34.388184 36.008319 35.385260 41.768998 
   tree25    tree26    tree27    tree28    tree29    tree30    tree31 
44.877702 50.942868 52.223751 53.428513 53.899329 53.899329 68.515305 

$vcov
            (Intercept)       Girth      Height
(Intercept)  74.6189461  0.43217138 -1.05076889
Girth         0.4321714  0.06983578 -0.01786030
Height       -1.0507689 -0.01786030  0.01693933

$sigma
[1] 3.881832

$df.residual
[1] 28

$call
linmod.default(x = tr[, 1:2], y = tr[, 3, drop = FALSE])

attr(,"class")
[1] "linmod"
> 
> # check that we don't artificially add rownames when no original rownames
> linmod1a.xy <- linmod(trees[,1:2], trees[,3])
> stopifnot(is.null(names(linmod1a.xy$residuals)))
> stopifnot(is.null(names(linmod1a.xy$fitted.values)))
> 
> cat0("==example plots\n")
==example plots
> 
> library(plotmo)
Loading required package: Formula
Loading required package: plotrix
> data(trees)
> 
> linmod.form.Volume.trees <- linmod(Volume~., data=trees)
> print(linmod.form.Volume.trees)
Call: linmod.formula(formula = Volume ~ ., data = trees)

(Intercept)       Girth      Height 
-57.9876589   4.7081605   0.3392512 
> print(summary(linmod.form.Volume.trees))
Call: linmod.formula(formula = Volume ~ ., data = trees)

               Estimate    StdErr   t.value      p.value
(Intercept) -57.9876589 8.6382259 -6.712913 2.749507e-07
Girth         4.7081605 0.2642646 17.816084 8.223304e-17
Height        0.3392512 0.1301512  2.606594 1.449097e-02
> 
> linmod1.xy <- linmod(trees[,1:2], trees[,3])
> print(linmod1.xy)
Call: linmod.default(x = trees[, 1:2], y = trees[, 3])

(Intercept)       Girth      Height 
-57.9876589   4.7081605   0.3392512 
> print(summary(linmod1.xy))
Call: linmod.default(x = trees[, 1:2], y = trees[, 3])

               Estimate    StdErr   t.value      p.value
(Intercept) -57.9876589 8.6382259 -6.712913 2.749507e-07
Girth         4.7081605 0.2642646 17.816084 8.223304e-17
Height        0.3392512 0.1301512  2.606594 1.449097e-02
> 
> plotmo(linmod.form.Volume.trees)
 plotmo grid:    Girth Height
                  12.9     76
> plotmo(linmod1.xy)
 plotmo grid:    Girth Height
                  12.9     76
> 
> plotres(linmod.form.Volume.trees)
> plotres(linmod1.xy)
> 
> cat0("==test keep arg\n")
==test keep arg
> 
> trees1 <- trees
> linmod.form.Volume.trees.keep <- linmod(Volume~., data=trees1, keep=TRUE)
> print(summary(linmod.form.Volume.trees.keep))
Call: linmod.formula(formula = Volume ~ ., data = trees1, keep = TRUE)

               Estimate    StdErr   t.value      p.value
(Intercept) -57.9876589 8.6382259 -6.712913 2.749507e-07
Girth         4.7081605 0.2642646 17.816084 8.223304e-17
Height        0.3392512 0.1301512  2.606594 1.449097e-02
> print(head(linmod.form.Volume.trees.keep$data))
  Girth Height Volume
1   8.3     70   10.3
2   8.6     65   10.3
3   8.8     63   10.2
4  10.5     72   16.4
5  10.7     81   18.8
6  10.8     83   19.7
> stopifnot(dim(linmod.form.Volume.trees.keep$data) == c(nrow(trees1), ncol(trees1)))
> trees1 <- NULL # destroy orginal data so plotmo has to use keep data
> plotmo(linmod.form.Volume.trees.keep, pt.col=3)
 plotmo grid:    Girth Height
                  12.9     76
> plotres(linmod.form.Volume.trees.keep)
> 
> linmod.xy.keep <- linmod(trees[,1:2], trees[,3], keep=TRUE)
> print(summary(linmod.xy.keep))
Call: linmod.default(x = trees[, 1:2], y = trees[, 3], keep = TRUE)

               Estimate    StdErr   t.value      p.value
(Intercept) -57.9876589 8.6382259 -6.712913 2.749507e-07
Girth         4.7081605 0.2642646 17.816084 8.223304e-17
Height        0.3392512 0.1301512  2.606594 1.449097e-02
> print(head(linmod.xy.keep$x))
     Girth Height
[1,]   8.3     70
[2,]   8.6     65
[3,]   8.8     63
[4,]  10.5     72
[5,]  10.7     81
[6,]  10.8     83
> stopifnot(dim(linmod.xy.keep$x) == c(nrow(trees), 2))
> stopifnot(class(linmod.xy.keep$x)[1] == "matrix")
> print(head(linmod.xy.keep$y))
     trees[,3]
[1,]      10.3
[2,]      10.3
[3,]      10.2
[4,]      16.4
[5,]      18.8
[6,]      19.7
> stopifnot(dim(linmod.xy.keep$y) == c(nrow(trees), 1))
> stopifnot(class(linmod.xy.keep$y)[1] == "matrix")
> linmod.xy.keep$call <- NULL # trick to force use of x and y in plotmo
> plotmo(linmod.xy.keep, pt.col=3)
 plotmo grid:    Girth Height
                  12.9     76
> plotres(linmod.xy.keep)
> 
> check.lm(linmod.form.Volume.trees.keep, linmod.xy.keep, check.casenames=FALSE, check.newdata=FALSE)
check linmod.form.Volume.trees.keep vs linmod.xy.keep
> 
> cat0("==test keep arg with vector x\n")
==test keep arg with vector x
> 
> n <- 20
> linmod.vecx.form.keep <- linmod(Volume~Height, data=trees[1:n,], keep=TRUE)
> print(summary(linmod.vecx.form.keep))
Call: linmod.formula(formula = Volume ~ Height, data = trees[1:n, ], keep =
      TRUE)

               Estimate     StdErr   t.value     p.value
(Intercept) -19.3368332 11.9072601 -1.623953 0.121767815
Height        0.5318092  0.1597269  3.329491 0.003730259
> print(head(linmod.vecx.form.keep$data))
  Girth Height Volume
1   8.3     70   10.3
2   8.6     65   10.3
3   8.8     63   10.2
4  10.5     72   16.4
5  10.7     81   18.8
6  10.8     83   19.7
> stopifnot(dim(linmod.vecx.form.keep$data) == c(n, ncol(trees)))
> stopifnot(class(linmod.vecx.form.keep$data) == class(trees))
> plotmo(linmod.vecx.form.keep, pt.col=3)
> plotres(linmod.vecx.form.keep)
> 
> linmod.vecx.xy.keep <- linmod(trees[1:n,2], trees[1:n,3], keep=TRUE)
> print(summary(linmod.vecx.xy.keep))
Call: linmod.default(x = trees[1:n, 2], y = trees[1:n, 3], keep = TRUE)

               Estimate     StdErr   t.value     p.value
(Intercept) -19.3368332 11.9072601 -1.623953 0.121767815
V1            0.5318092  0.1597269  3.329491 0.003730259
> print(head(linmod.vecx.xy.keep$x))
     [,1]
[1,]   70
[2,]   65
[3,]   63
[4,]   72
[5,]   81
[6,]   83
> stopifnot(dim(linmod.vecx.xy.keep$x) == c(n, 1))
> stopifnot(class(linmod.vecx.xy.keep$x)[1] == "matrix")
> print(head(linmod.vecx.xy.keep$y))
     trees[1:n,3]
[1,]         10.3
[2,]         10.3
[3,]         10.2
[4,]         16.4
[5,]         18.8
[6,]         19.7
> stopifnot(dim(linmod.vecx.xy.keep$y) == c(n, 1))
> stopifnot(class(linmod.vecx.xy.keep$y)[1] == "matrix")
> linmod.vecx.xy.keep$call <- NULL # trick to force use of x and y in plotmo
> plotmo(linmod.vecx.xy.keep, pt.col=3)
> plotres(linmod.vecx.xy.keep)
> 
> check.lm(linmod.vecx.form.keep, linmod.vecx.xy.keep, newdata=trees[3:5,2,drop=FALSE],
+          check.coef.names=FALSE, check.casenames=FALSE)
check linmod.vecx.form.keep vs linmod.vecx.xy.keep
> 
> cat0("==test model building with assorted numeric args\n")
==test model building with assorted numeric args
> 
> x <- tr[,1:2]
> y <- tr[,3]
> cat0("class(x)=", class(x), " class(y)=", class(y), "\n") # class(x)=data.frame class(y)=numeric
class(x)=data.frame class(y)=numeric
> linmod2.xy <- linmod(x, y)
> check.lm(linmod2.xy, lm.Volume.tr, newdata=newdata.2col)
check linmod2.xy vs lm.Volume.tr
> 
> # check consistency with lm
> expect.err(try(linmod(y~x)), "invalid type (list) for variable 'x'")
Error in model.frame.default(formula = formula, data = data, na.action = na.pass) : 
  invalid type (list) for variable 'x'
Got expected error from try(linmod(y ~ x))
> expect.err(try(lm(y~x)),     "invalid type (list) for variable 'x'")
Error in model.frame.default(formula = y ~ x, drop.unused.levels = TRUE) : 
  invalid type (list) for variable 'x'
Got expected error from try(lm(y ~ x))
> 
> linmod3.xy <- linmod(as.matrix(x), as.matrix(y))
> check.lm(linmod3.xy, lm.Volume.tr, newdata=newdata.2col)
check linmod3.xy vs lm.Volume.tr
> 
> linmod4.form <- linmod(y ~ as.matrix(x))
> lm4 <- lm(y ~ as.matrix(x))
> check.lm(linmod4.form, lm4, check.newdata=FALSE)
check linmod4.form vs lm4
> stopifnot(coef(linmod4.form)  == coef(lm.Volume.tr),
+           gsub("as.matrix(x)", "", names(coef(linmod4.form)), fixed=TRUE)  == names(coef(lm.Volume.tr)))
> 
> xm <- as.matrix(x)
> cat0("class(xm)=", class(xm), " class(y)=", class(y), "\n") # class(xm)=matrix class(y)=numeric
class(xm)=matrixarray class(y)=numeric
> linmod5.form <- linmod(y ~ xm)
> lm5 <- lm(y ~ xm)
> check.lm(linmod5.form, lm5, check.newdata=FALSE)
check linmod5.form vs lm5
> stopifnot(coef(linmod5.form)  == coef(lm.Volume.tr),
+           gsub("xm", "", names(coef(linmod5.form)), fixed=TRUE)  == names(coef(lm.Volume.tr)))
> 
> cat0("==test correct use of global x1 and y1, and of predict error handling\n")
==test correct use of global x1 and y1, and of predict error handling
> x1 <- tr[,1]
> y1 <- tr[,3]
> cat0("class(x1)=", class(x1), " class(y1)=", class(y1), "\n") # class(x1)=numeric class(y1)=numeric
class(x1)=numeric class(y1)=numeric
> linmod.y1.x1 <- linmod(y1~x1)
> lm1 <- lm(y1~x1)
> linmod6.xy <- linmod(x1, y1)
> 
> newdata.x1 <- trees[3:5,1,drop=FALSE]
> colnames(newdata.x1) <- "x1"
> stopifnot(almost.equal(predict(linmod.y1.x1, newdata=newdata.x1),
+           c(7.63607739644657, 16.24803331528098, 17.26120459984973)))
> 
> check.lm(linmod6.xy, linmod.y1.x1, newdata=x1[3:5],
+          check.newdata=FALSE, # TODO needed because linmod.y1.x1 ignores newdata(!)
+          check.coef.names=FALSE, check.casenames=FALSE)
check linmod6.xy vs linmod.y1.x1
> print(predict(linmod6.xy, newdata=x1[3:5]))
[1]  7.636077 16.248033 17.261205
> stopifnot(almost.equal(predict(linmod6.xy, newdata=x1[3]), 7.63607739644657))
> 
> stopifnot(coef(linmod6.xy) == coef(linmod.y1.x1)) # names(coef(linmod.y1.x1) are "(Intercept)" "x1"
> stopifnot(names(coef(linmod6.xy)) == c("(Intercept)", "V1"))
> 
> # following checks some confusing behaviour of predict.lm
> options(warn=2) # treat warnings as errors
> expect.err(try(predict(lm1,    newdata=trees[3:5,1,drop=FALSE])),
+            "'newdata' had 3 rows but variables found have 31 rows")
Error : (converted from warning) 'newdata' had 3 rows but variables found have 31 rows
Got expected error from try(predict(lm1, newdata = trees[3:5, 1, drop = FALSE]))
> expect.err(try(predict(lm1,    newdata=trees[3:5,1,drop=TRUE])),
+            "'data' must be a data.frame, environment, or list")
Error in model.frame.default(Terms, newdata, na.action = na.action, xlev = object$xlevels) : 
  'data' must be a data.frame, environment, or list
Got expected error from try(predict(lm1, newdata = trees[3:5, 1, drop = TRUE]))
> 
> # following checks messages when missing variables in newdata
> 
> options(warn=2) # treat warnings as errors to check that we get a warning in stats::model.frame
> expect.err(try(predict(linmod.y1.x1, newdata=trees[3:5,1,drop=FALSE])),
+            "(converted from warning) 'newdata' had 3 rows but variables found have 31 rows")
Error : (converted from warning) 'newdata' had 3 rows but variables found have 31 rows
Got expected error from try(predict(linmod.y1.x1, newdata = trees[3:5, 1, drop = FALSE]))
> expect.err(try(predict(lm1, newdata=trees[3:5,1,drop=FALSE])),
+            "(converted from warning) 'newdata' had 3 rows but variables found have 31 rows")
Error : (converted from warning) 'newdata' had 3 rows but variables found have 31 rows
Got expected error from try(predict(lm1, newdata = trees[3:5, 1, drop = FALSE]))
> expect.err(try(predict(linmod.y1.x1, newdata=trees[3:5,1,drop=TRUE])),
+            "(converted from warning) 'newdata' had 3 rows but variables found have 31 rows")
Error : (converted from warning) 'newdata' had 3 rows but variables found have 31 rows
Got expected error from try(predict(linmod.y1.x1, newdata = trees[3:5, 1, drop = TRUE]))
> 
> # following checks predict.linmod error messages when missing variables
> # (it tries to give better error messages than predict.lm)
> 
> options(warn=1) # print warnings as they occur to test stop() in linmod.R::process.newdata.formula
> expect.err(try(predict(linmod.y1.x1, newdata=trees[3:5,1,drop=FALSE])),
+            "newdata has 3 rows but model.frame returned 31 rows (variable 'x1' may be missing from newdata)")
Warning: 'newdata' had 3 rows but variables found have 31 rows
Error in process.newdata.formula(object, newdata) : 
  newdata has 3 rows but model.frame returned 31 rows (variable 'x1' may be missing from newdata)
Got expected error from try(predict(linmod.y1.x1, newdata = trees[3:5, 1, drop = FALSE]))
> expect.err(try(predict(linmod.y1.x1, newdata=trees[3:5,1,drop=TRUE])),
+            "newdata has 3 rows but model.frame returned 31 rows (variable 'x1' may be missing from newdata)")
Warning: 'newdata' had 3 rows but variables found have 31 rows
Error in process.newdata.formula(object, newdata) : 
  newdata has 3 rows but model.frame returned 31 rows (variable 'x1' may be missing from newdata)
Got expected error from try(predict(linmod.y1.x1, newdata = trees[3:5, 1, drop = TRUE]))
> options(warn=2) # back to treating warnings as errors
> 
> # test old version of linmod.R (pre Sep 2020)
> #
> # expect.err(try(predict(linmod.y1.x1, newdata=trees[3:5,1,drop=FALSE])),
> #            "variable 'x1' is missing from newdata")
> # expect.err(try(predict(lm1, newdata=trees[3:5,1,drop=FALSE])),
> #            "(converted from warning) 'newdata' had 3 rows but variables found have 31 rows")
> # expect.err(try(predict(linmod.y1.x1, newdata=trees[3:5,1,drop=TRUE])),
> #            "variable 'x1' is missing from newdata")
> 
> linmod6.form <- linmod(y1~x1)
> check.lm(linmod6.form, linmod.y1.x1, check.newdata=FALSE)
check linmod6.form vs linmod.y1.x1
> 
> newdata <- trees[5:6,]
> colnames(newdata) <- c("Girth", "Height", "Volume999") # doesn't matter what we call the response
> stopifnot(identical(predict(linmod.form.Volume.tr, newdata=newdata),
+                     predict(linmod.form.Volume.tr, newdata=trees[5:6,])))
> newdata <- trees[5:6,3:1] # reverse columns and their colnames
> colnames(newdata) <- c("Volume", "Height", "Girth")
> stopifnot(identical(predict(linmod.form.Volume.tr, newdata=newdata),
+                     predict(linmod.form.Volume.tr, newdata=trees[5:6,])))
> newdata <- trees[5:6,2:1] # reverse columns and their colnames, delete response column
> colnames(newdata) <- c("Height", "Girth")
> stopifnot(identical(predict(linmod.form.Volume.tr, newdata=newdata),
+                     predict(linmod.form.Volume.tr, newdata=trees[5:6,])))
> stopifnot(identical(predict(linmod.form.Volume.tr, newdata=as.matrix(trees[5:6,])), # allow matrix newdata
+                     predict(linmod.form.Volume.tr, newdata=trees[5:6,])))
> newdata <- trees[5:6,]
> colnames(newdata) <- c("Girth99", "Height", "Volume")
> expect.err(try(predict(linmod.form.Volume.tr, newdata=newdata)),
+            "object 'Girth' not found")
Error in eval(predvars, data, env) : object 'Girth' not found
Got expected error from try(predict(linmod.form.Volume.tr, newdata = newdata))
> colnames(newdata) <- c("Girth", "Height99", "Volume")
> expect.err(try(predict(linmod.form.Volume.tr, newdata=newdata)),
+            "object 'Height' not found")
Error in eval(predvars, data, env) : object 'Height' not found
Got expected error from try(predict(linmod.form.Volume.tr, newdata = newdata))
> 
> cat0("==check integer input (sibsp is an integer)\n")
==check integer input (sibsp is an integer)
> 
> library(earth) # for etitanic data
> data(etitanic)
> tit <- etitanic[seq(1, nrow(etitanic), by=60), ] # small set of data for tests (18 cases)
> tit$survived <- tit$survived != 0 # convert to logical
> rownames(tit) <- paste("pas", 1:nrow(tit), sep="")
> cat0(paste(colnames(tit), "=", sapply(tit, class), sep="", collapse=", "), "\n")
pclass=factor, survived=logical, sex=factor, age=numeric, sibsp=integer, parch=integer
> 
> linmod7.xy <- linmod(tit$age, tit$sibsp)
> lm7 <- lm.fit(cbind(1, tit$age), tit$sibsp)
> stopifnot(coef(linmod7.xy) == coef(lm7)) # coef names will differ
> 
> linmod7.form <- linmod(sibsp~age, data=tit)
> lm7.form  <- lm(sibsp~age, data=tit)
> check.lm(linmod7.form, lm7.form, newdata=tit[3:5,])
check linmod7.form vs lm7.form
> 
> linmod8.xy <- linmod(tit$sibsp, tit$age)
> lm8 <- lm.fit(cbind(1, tit$sibsp), tit$age)
> stopifnot(coef(linmod8.xy) == coef(lm8)) # coef names will differ
> 
> linmod8.form <- linmod(age~sibsp, data=tit)
> lm8.form  <- lm(age~sibsp, data=tit)
> check.lm(linmod8.form, lm8.form, newdata=tit[3:5,])
check linmod8.form vs lm8.form
> 
> # drop=FALSE so response is a data frame
> linmod1a.xy <- linmod(trees[,1:2], trees[, 3, drop=FALSE])
> print(linmod1a.xy)
Call: linmod.default(x = trees[, 1:2], y = trees[, 3, drop = FALSE])

(Intercept)       Girth      Height 
-57.9876589   4.7081605   0.3392512 
> print(summary(linmod1a.xy))
Call: linmod.default(x = trees[, 1:2], y = trees[, 3, drop = FALSE])

               Estimate    StdErr   t.value      p.value
(Intercept) -57.9876589 8.6382259 -6.712913 2.749507e-07
Girth         4.7081605 0.2642646 17.816084 8.223304e-17
Height        0.3392512 0.1301512  2.606594 1.449097e-02
> plotres(linmod1a.xy) # plot caption shows response name "Volume"
> 
> cat0("==test model building with assorted non-numeric args\n")
==test model building with assorted non-numeric args
> 
> library(earth) # for etitanic data
> data(etitanic)
> etit <- etitanic[seq(1, nrow(etitanic), by=60), ] # small set of data for tests (18 cases)
> etit$survived <- etit$survived != 0 # convert to logical
> rownames(etit) <- paste("pas", 1:nrow(etit), sep="")
> cat0(paste(colnames(etit), "=", sapply(etit, class), sep="", collapse=", "), "\n")
pclass=factor, survived=logical, sex=factor, age=numeric, sibsp=integer, parch=integer
> 
> lm9 <- lm(survived~., data=etit)
> linmod9.form <- linmod(survived~., data=etit)
> check.lm(linmod9.form, lm9, newdata=etit[3:5,])
check linmod9.form vs lm9
> 
> # change class of pclass to numeric
> etit.pclass.numeric <- etit
> etit.pclass.numeric$pclass <- as.numeric(etit$pclass)
> expect.err(try(predict(lm9,       newdata=etit.pclass.numeric)),
+               "(converted from warning) variable 'pclass' is not a factor")
Error in model.frame.default(Terms, newdata, na.action = na.action, xlev = object$xlevels) : 
  (converted from warning) variable 'pclass' is not a factor
Got expected error from try(predict(lm9, newdata = etit.pclass.numeric))
> expect.err(try(predict(linmod9.form, newdata=etit.pclass.numeric)),
+               "(converted from warning) variable 'pclass' is not a factor")
Error in model.frame.default(terms, newdata, na.action = na.pass, xlev = object$xlevels) : 
  (converted from warning) variable 'pclass' is not a factor
Got expected error from try(predict(linmod9.form, newdata = etit.pclass.numeric))
> 
> # change class of age to factor
> etit.age.factor <- etit
> etit.age.factor$age <- etit$pclass
> expect.err(try(predict(lm9,       newdata=etit.age.factor)),
+               "variable 'age' was fitted with type \"numeric\" but type \"factor\" was supplied")
Error : variable 'age' was fitted with type "numeric" but type "factor" was supplied
Got expected error from try(predict(lm9, newdata = etit.age.factor))
> expect.err(try(predict(linmod9.form, newdata=etit.age.factor)),
+               "variable 'age' was fitted with type \"numeric\" but type \"factor\" was supplied")
Error : variable 'age' was fitted with type "numeric" but type "factor" was supplied
Got expected error from try(predict(linmod9.form, newdata = etit.age.factor))
> 
> # predict for formula model ignores extra column(s) in newdata
> etit.extra.col <- etit
> etit.extra.col$extra <- etit$sibsp
> stopifnot(identical(predict(lm9, newdata=etit), predict(lm9, newdata=etit.extra.col)))
> stopifnot(identical(predict(linmod9.form, newdata=etit), predict(linmod9.form, newdata=etit.extra.col)))
> etit.extra.col$extra2 <- etit$sibsp
> stopifnot(identical(predict(lm9, newdata=etit), predict(lm9, newdata=etit.extra.col)))
> stopifnot(identical(predict(linmod9.form, newdata=etit), predict(linmod9.form, newdata=etit.extra.col)))
> 
> # predict for formula model doesn't care if columns in different order
> etit.different.col.order <- etit[,ncol(etit):1] # reverse order of columns
> stopifnot(identical(predict(lm9, newdata=etit), predict(lm9, newdata=etit.different.col.order)))
> stopifnot(identical(predict(linmod9.form, newdata=etit), predict(linmod9.form, newdata=etit.different.col.order)))
> 
> # linmod.default, non numeric x (factors in x)
> expect.err(try(linmod(etit[c(1,3,4,5,6)], etit[,"survived"])),
+               "non-numeric column in 'x'")
Error in check.linmod.x(x) : non-numeric column in 'x'
Got expected error from try(linmod(etit[c(1, 3, 4, 5, 6)], etit[, "survived"]))
> expect.err(try(linmod.fit(etit[c(1,3,4,5,6)], etit[,"survived"])),
+               "'x' is not a matrix or could not be converted to a matrix")
Error in check.linmod.x(x) : 
  'x' is not a matrix or could not be converted to a matrix
Got expected error from try(linmod.fit(etit[c(1, 3, 4, 5, 6)], etit[, "survived"]))
> # lousy error message from lm.fit
> expect.err(try(lm.fit(etit[,c(1,3,4,5,6)], etit[,"survived"])),
+               "INTEGER() can only be applied to a 'integer', not a 'NULL'")
Error in lm.fit(etit[, c(1, 3, 4, 5, 6)], etit[, "survived"]) : 
  INTEGER() can only be applied to a 'integer', not a 'NULL'
Got expected error from try(lm.fit(etit[, c(1, 3, 4, 5, 6)], etit[, "survived"]))
> 
> expect.err(try(linmod(data.matrix(cbind("(Intercept)"=1, etit[,c(1,3,4,5,6)])), etit[,"survived"])),
+               "column name \"(Intercept)\" in 'x' is duplicated")
Error in check.linmod.x(x) : 
  column name "(Intercept)" in 'x' is duplicated
Got expected error from try(linmod(data.matrix(cbind(`(Intercept)` = 1, etit[, c(1, 3,     4, 5, 6)])), etit[, "survived"]))
> linmod9a.xy <- linmod(data.matrix(etit[,c(1,3,4,5,6)]), etit[,"survived"])
> lm9.fit <- lm.fit(data.matrix(cbind("(Intercept)"=1, etit[,c(1,3,4,5,6)])), etit[,"survived"])
> stopifnot(coef(linmod9a.xy) == coef(lm9.fit))
> stopifnot(names(coef(linmod9a.xy)) == names(coef(lm9.fit)))
> expect.err(try(predict(linmod9a.xy, newdata=etit.age.factor[,c(1,3,4,5,6)])), "non-numeric column in 'newdata'")
Error in predict.linmod(linmod9a.xy, newdata = etit.age.factor[, c(1,  : 
  non-numeric column in 'newdata' (after processing)
Got expected error from try(predict(linmod9a.xy, newdata = etit.age.factor[, c(1, 3,     4, 5, 6)]))
> expect.err(try(predict(linmod9a.xy, newdata=etit[,c(1,3,4,5)])), "ncol(newdata) is 4 but should be 5")
Error in predict.linmod(linmod9a.xy, newdata = etit[, c(1, 3, 4, 5)]) : 
  ncol(newdata) is 4 but should be 5
Got expected error from try(predict(linmod9a.xy, newdata = etit[, c(1, 3, 4, 5)]))
> expect.err(try(predict(linmod9a.xy, newdata=etit[,c(1,3,4,5,6,6)])), "ncol(newdata) is 6 but should be 5")
Error in predict.linmod(linmod9a.xy, newdata = etit[, c(1, 3, 4, 5, 6,  : 
  ncol(newdata) is 6 but should be 5
Got expected error from try(predict(linmod9a.xy, newdata = etit[, c(1, 3, 4, 5, 6, 6)]))
> 
> # linmod.formula, logical response
> data.logical.response <- data.frame(etit[1:6,c("age","sibsp","parch")], response=c(TRUE, TRUE, FALSE, TRUE, FALSE, FALSE))
> linmod9b.form <- linmod(response~., data=data.logical.response)
> print(linmod9b.form)
Call: linmod.formula(formula = response ~ ., data = data.logical.response)

 (Intercept)          age        sibsp        parch 
 1.102508872 -0.007261985 -0.182883049 -0.569470942 
> lm9b.form <- lm(response~., data=data.logical.response)
> check.lm(linmod9b.form, lm9b.form, newdata=data.logical.response[2,,drop=FALSE])
check linmod9b.form vs lm9b.form
> 
> # linmod.formula, factor response (not allowed)
> data.fac.response <- data.frame(etit[1:6,c("age","sibsp","parch")], response=factor(c("a", "a", "b", "a", "b", "b")))
> expect.err(try(linmod(response~., data=data.fac.response)), "'y' is not numeric or logical")
Error in check.linmod.y(x, y) : 'y' is not numeric or logical
Got expected error from try(linmod(response ~ ., data = data.fac.response))
> # lm.formula
> expect.err(try(lm(response~., data=data.fac.response)),
+               "(converted from warning) using type = \"numeric\" with a factor response will be ignored")
Error in model.response(mf, "numeric") : 
  (converted from warning) using type = "numeric" with a factor response will be ignored
Got expected error from try(lm(response ~ ., data = data.fac.response))
> 
> # linmod.formula, string response (not allowed)
> data.string.response <- data.frame(etit[1:6,c("age","sibsp","parch")], response=c("a", "a", "b", "a", "b", "b"))
> expect.err(try(linmod(response~., data=data.string.response)), "'y' is not numeric or logical")
Error in check.linmod.y(x, y) : 'y' is not numeric or logical
Got expected error from try(linmod(response ~ ., data = data.string.response))
> # lm.formula
> expect.err(try(lm(response~., data=data.string.response)),
+               "(converted from warning) NAs introduced by coercion")
Error in storage.mode(v) <- "double" : 
  (converted from warning) NAs introduced by coercion
Got expected error from try(lm(response ~ ., data = data.string.response))
> 
> # linmod.default, logical response
> linmod9b.xy <- linmod(etit[1:6,c("age","sibsp","parch")], c(TRUE, TRUE, FALSE, TRUE, FALSE, FALSE))
> print(linmod9b.xy)
Call: linmod.default(x = etit[1:6, c("age", "sibsp", "parch")], y = c(TRUE,
      TRUE, FALSE, TRUE, FALSE, FALSE))

 (Intercept)          age        sibsp        parch 
 1.102508872 -0.007261985 -0.182883049 -0.569470942 
> # lm.fit, logical response (lousy error message from lm.fit)
> expect.err(try(lm.fit(etit[1:6,c("age","sibsp","parch")], c(TRUE, TRUE, FALSE, TRUE, FALSE, FALSE))),
+               "INTEGER() can only be applied to a 'integer', not a 'NULL'")
Error in lm.fit(etit[1:6, c("age", "sibsp", "parch")], c(TRUE, TRUE, FALSE,  : 
  INTEGER() can only be applied to a 'integer', not a 'NULL'
Got expected error from try(lm.fit(etit[1:6, c("age", "sibsp", "parch")], c(TRUE, TRUE,     FALSE, TRUE, FALSE, FALSE)))
> # linmod.default, factor response
> expect.err(try(linmod(etit[1:6,c("age","sibsp","parch")], factor(c("a",
+               "a", "b", "a", "b", "b")))), "'y' is not numeric or logical")
Error in check.linmod.y(x, y) : 'y' is not numeric or logical
Got expected error from try(linmod(etit[1:6, c("age", "sibsp", "parch")], factor(c("a",     "a", "b", "a", "b", "b"))))
> # linmod.default, string response
> expect.err(try(linmod(etit[1:6,c("age","sibsp","parch")], c("a",
+               "a", "b", "a", "b", "b"))), "'y' is not numeric or logical")
Error in check.linmod.y(x, y) : 'y' is not numeric or logical
Got expected error from try(linmod(etit[1:6, c("age", "sibsp", "parch")], c("a", "a",     "b", "a", "b", "b")))
> # lm.fit, string and factor responses (lousy error messages from lm.fit)
> expect.err(try(lm.fit(etit[1:6,c("age","sibsp","parch")], factor(c("a",
+               "a", "b", "a", "b", "b")))), "INTEGER() can only be applied to a 'integer', not a 'NULL'")
Error in lm.fit(etit[1:6, c("age", "sibsp", "parch")], factor(c("a", "a",  : 
  INTEGER() can only be applied to a 'integer', not a 'NULL'
Got expected error from try(lm.fit(etit[1:6, c("age", "sibsp", "parch")], factor(c("a",     "a", "b", "a", "b", "b"))))
> expect.err(try(lm.fit(etit[1:6,c("age","sibsp","parch")], c("a",
+               "a", "b", "a", "b", "b"))), "INTEGER() can only be applied to a 'integer', not a 'NULL'")
Error in lm.fit(etit[1:6, c("age", "sibsp", "parch")], c("a", "a", "b",  : 
  INTEGER() can only be applied to a 'integer', not a 'NULL'
Got expected error from try(lm.fit(etit[1:6, c("age", "sibsp", "parch")], c("a", "a",     "b", "a", "b", "b")))
> 
> options(warn=2) # treat warnings as errors
> expect.err(try(lm(pclass~., data=etit)), "using type = \"numeric\" with a factor response will be ignored")
Error in model.response(mf, "numeric") : 
  (converted from warning) using type = "numeric" with a factor response will be ignored
Got expected error from try(lm(pclass ~ ., data = etit))
> expect.err(try(linmod(pclass~., data=etit)), "'y' is not numeric or logical")
Error in check.linmod.y(x, y) : 'y' is not numeric or logical
Got expected error from try(linmod(pclass ~ ., data = etit))
> 
> options(warn=1) # print warnings as they occur
> lm10 <- lm(pclass~., data=etit) # will give warnings
Warning in model.response(mf, "numeric") :
  using type = "numeric" with a factor response will be ignored
Warning in Ops.factor(y, z$residuals) : '-' not meaningful for factors
> options(warn=2) # treat warnings as errors
> linmod10.form <- linmod(as.numeric(pclass)~., data=etit)
> stopifnot(coef(linmod10.form) == coef(lm10))
> stopifnot(names(coef(linmod10.form)) == names(coef(lm10)))
> # check.lm(linmod10.form, lm10) # fails because lm10 fitted is all NA
> 
> expect.err(try(linmod(pclass~., data=etit)), "'y' is not numeric or logical")
Error in check.linmod.y(x, y) : 'y' is not numeric or logical
Got expected error from try(linmod(pclass ~ ., data = etit))
> expect.err(try(linmod(etit[,-1], etit[,1])), "non-numeric column in 'x'")
Error in check.linmod.x(x) : non-numeric column in 'x'
Got expected error from try(linmod(etit[, -1], etit[, 1]))
> expect.err(try(linmod(1:10, paste(1:10))), "'y' is not numeric or logical")
Error in check.linmod.y(x, y) : 'y' is not numeric or logical
Got expected error from try(linmod(1:10, paste(1:10)))
> 
> linmod10a.form <- linmod(survived~pclass, data=etit)
> lm10a <- lm(survived~pclass, data=etit)
> check.lm(linmod10a.form, lm10a, newdata=etit[3:5,])
check linmod10a.form vs lm10a
> 
> expect.err(try(linmod(etit[,"pclass"], etit[,"age"])), "non-numeric column in 'x'")
Error in check.linmod.x(x) : non-numeric column in 'x'
Got expected error from try(linmod(etit[, "pclass"], etit[, "age"]))
> 
> expect.err(try(linmod(paste(1:10), 1:10)), "non-numeric column in 'x'")
Error in check.linmod.x(x) : non-numeric column in 'x'
Got expected error from try(linmod(paste(1:10), 1:10))
> 
> lm11 <- lm(as.numeric(pclass)~., data=etit)
> linmod11.form <- linmod(as.numeric(pclass)~., data=etit)
> check.lm(linmod11.form, lm11, newdata=etit[3:5,])
check linmod11.form vs lm11
> 
> # logical data (not numeric)
> bool.data <- data.frame(x=rep(c(TRUE, FALSE, TRUE), length.out=10),
+                         y=rep(c(TRUE, FALSE, FALSE), length.out=10))
> lm12 <- lm(y~x, data=bool.data)
> linmod12.form <- linmod(y~x, data=bool.data)
> check.lm(linmod12.form, lm12, newdata=bool.data[3:5,1],
+          check.newdata=FALSE) # needed because predict.lm gives invalid type (list) for variable 'x'
check linmod12.form vs lm12
> linmod12.xy <- linmod(bool.data$x, bool.data$y)
> # hack: delete mismatching names so check.lm() doesn't fail
> names(lm12$coefficients) <- NULL     # were "(Intercept)" "xTRUE"
> names(linmod12.xy$coefficients) <- NULL # were "(Intercept)" "V1"
> check.lm(linmod12.xy, lm12, newdata=bool.data[3:5,1],
+          check.newdata=FALSE, # needed because predict.lm gives invalid 'envir' argument of type 'logical'
+          check.casenames=FALSE)
check linmod12.xy vs lm12
> 
> cat0("==check use of functions in arguments to linmod\n")
==check use of functions in arguments to linmod
> 
> identfunc <- function(x) x
> lm10 <- lm(        sqrt(survived) ~ I(age^2) + as.numeric(sex), data=identfunc(etit))
> linmod10 <- linmod(sqrt(survived) ~ I(age^2) + as.numeric(sex), data=identfunc(etit))
> print(summary(lm10))

Call:
lm(formula = sqrt(survived) ~ I(age^2) + as.numeric(sex), data = identfunc(etit))

Residuals:
    Min      1Q  Median      3Q     Max 
-0.6959 -0.2665 -0.2302  0.3427  0.8261 

Coefficients:
                  Estimate Std. Error t value Pr(>|t|)  
(Intercept)      1.101e+00  4.223e-01   2.608   0.0198 *
I(age^2)        -5.389e-05  1.190e-04  -0.453   0.6571  
as.numeric(sex) -3.881e-01  2.508e-01  -1.547   0.1426  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.4855 on 15 degrees of freedom
Multiple R-squared:  0.1736,	Adjusted R-squared:  0.06346 
F-statistic: 1.576 on 2 and 15 DF,  p-value: 0.2392

> print(summary(linmod10))
Call: linmod.formula(formula = sqrt(survived) ~ I(age^2) + as.numeric(sex),
      data = identfunc(etit))

                     Estimate       StdErr    t.value    p.value
(Intercept)      1.101499e+00 0.4223245953  2.6081808 0.01977424
I(age^2)        -5.389047e-05 0.0001189838 -0.4529226 0.65708686
as.numeric(sex) -3.880912e-01 0.2507927081 -1.5474582 0.14258876
> check.lm(linmod10, lm10, newdata=etit[3:5,])
check linmod10 vs lm10
> set.seed(2020)
> plotmo(lm10,     pt.col="green", do.par=2)
 plotmo grid:    age  sex
                32.5 male
> set.seed(2020)
> plotmo(linmod10, pt.col="green", do.par=0)
 plotmo grid:    age  sex
                32.5 male
> par(org.par)
> 
> cat0("==data.frame with strings\n")
==data.frame with strings
> 
> df.with.string <-
+     data.frame(1:5,
+                c(1,2,-1,4,5),
+                c("a", "b", "a", "a", "b"),
+                stringsAsFactors=FALSE)
> colnames(df.with.string) <- c("num1", "num2", "string")
> 
> linmod30.form <- linmod(num1~num2, df.with.string)
> lm30       <- lm(num1~num2, df.with.string)
> check.lm(linmod30.form, lm30, check.newdata=FALSE)
check linmod30.form vs lm30
> 
> linmod31.form <- linmod(num1~., df.with.string)
> lm31       <- lm(num1~., df.with.string)
> check.lm(linmod31.form, lm31, check.newdata=FALSE)
check linmod31.form vs lm31
> 
> expect.err(try(linmod(string~., df.with.string)), "'y' is not numeric or logical")
Error in check.linmod.y(x, y) : 'y' is not numeric or logical
Got expected error from try(linmod(string ~ ., df.with.string))
> 
> vec <- c(1,2,3,4,3)
> expect.err(try(linmod(df.with.string, vec)), "non-numeric column in 'x'")
Error in check.linmod.x(x) : non-numeric column in 'x'
Got expected error from try(linmod(df.with.string, vec))
> expect.err(try(linmod(etit$pclass, etit$survived)), "non-numeric column in 'x'")
Error in check.linmod.x(x) : non-numeric column in 'x'
Got expected error from try(linmod(etit$pclass, etit$survived))
> 
> cat0("==x is singular\n")
==x is singular
> 
> set.seed(1)
> x2 <- matrix(rnorm(6), nrow=2)
> y2 <- c(1,2)
> expect.err(try(linmod(y2~x2)), "'x' is singular (it has 4 columns but its rank is 2)")
Error in do.linmod.fit(x, y) : 
  'x' is singular (it has 4 columns but its rank is 2)
  colnames(x): (Intercept) x21 x22 x23
Got expected error from try(linmod(y2 ~ x2))
> 
> x3 <- matrix(1:10, ncol=2)
> y3 <- c(1,2,9,4,5)
> expect.err(try(linmod(y3~x3)), "'x' is singular (it has 3 columns but its rank is 2)")
Error in do.linmod.fit(x, y) : 
  'x' is singular (it has 3 columns but its rank is 2)
  colnames(x): (Intercept) x31 x32
Got expected error from try(linmod(y3 ~ x3))
> 
> expect.err(try(linmod(trees[1,1:2], trees[1,3])), "'x' is singular (it has 3 columns but its rank is 1)")
Error in do.linmod.fit(x, y) : 
  'x' is singular (it has 3 columns but its rank is 1)
  colnames(x): (Intercept) Girth Height
Got expected error from try(linmod(trees[1, 1:2], trees[1, 3]))
> 
> x2a <- matrix(1:6, nrow=3)
> y2a <- c(1,2,3)
> expect.err(try(linmod(y2a~x2a)), "'x' is singular (it has 3 columns but its rank is 2)")
Error in do.linmod.fit(x, y) : 
  'x' is singular (it has 3 columns but its rank is 2)
  colnames(x): (Intercept) x2a1 x2a2
Got expected error from try(linmod(y2a ~ x2a))
> 
> cat0("==perfect fit (residuals are zero)\n")
==perfect fit (residuals are zero)
> 
> set.seed(1)
> x2b <- matrix(rnorm(6), nrow=3)
> y2b <- c(1,2,3)
> data.x2b <- data.frame(x2b, y2b)
> colnames(data.x2b) <- c("x1", "x2", "y")
> linmod.x2b <- linmod(y~., data=data.x2b)
> print(summary(linmod.x2b)) # will have "Residual degrees-of-freedom is zero" comment
Call: linmod.formula(formula = y ~ ., data = data.x2b)

               Estimate StdErr t.value p.value
(Intercept)  2.28088400    Inf       0       0
x1          -0.05211945    Inf       0       0
x2          -0.82338760    Inf       0       0
> lm.x2b <- lm(y~., data=data.x2b)
> print(summary(lm.x2b)) # will have "ALL 3 residuals are 0" comment

Call:
lm(formula = y ~ ., data = data.x2b)

Residuals:
ALL 3 residuals are 0: no residual degrees of freedom!

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept)  2.28088        NaN     NaN      NaN
x1          -0.05212        NaN     NaN      NaN
x2          -0.82339        NaN     NaN      NaN

Residual standard error: NaN on 0 degrees of freedom
Multiple R-squared:      1,	Adjusted R-squared:    NaN 
F-statistic:   NaN on 2 and 0 DF,  p-value: NA

> check.lm(linmod.x2b, lm.x2b, newdata=data.x2b[1:2,]+1, check.sigma=FALSE)
check linmod.x2b vs lm.x2b
> 
> x2c <- 1:10
> y2c <- 11:20
> data.x2c <- data.frame(x2c, y2c)
> colnames(data.x2c) <- c("x", "y")
> linmod.x2c <- linmod(y~., data=data.x2c)
> print(summary(linmod.x2c))
Call: linmod.formula(formula = y ~ ., data = data.x2c)

            Estimate StdErr t.value p.value
(Intercept)       10      0     Inf       0
x                  1      0     Inf       0
> lm.x2c <- lm(y~., data=data.x2c)
> options(warn=1) # print warnings as they occur
> print(summary(lm.x2c)) # will have "essentially perfect fit: summary may be unreliable" comment
Warning in summary.lm(lm.x2c) :
  essentially perfect fit: summary may be unreliable

Call:
lm(formula = y ~ ., data = data.x2c)

Residuals:
       Min         1Q     Median         3Q        Max 
-3.635e-15 -3.541e-16  3.225e-16  9.411e-16  1.721e-15 

Coefficients:
             Estimate Std. Error   t value Pr(>|t|)    
(Intercept) 1.000e+01  1.100e-15 9.088e+15   <2e-16 ***
x           1.000e+00  1.773e-16 5.639e+15   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.611e-15 on 8 degrees of freedom
Multiple R-squared:      1,	Adjusted R-squared:      1 
F-statistic: 3.18e+31 on 1 and 8 DF,  p-value: < 2.2e-16

> options(warn=2) # treat warnings as errors
> check.lm(linmod.x2c, lm.x2c, newdata=data.x2c[1:2,]+1, check.sigma=FALSE)
check linmod.x2c vs lm.x2c
> 
> par(mfrow=c(2,2)) # all plots on same page so can compare
> plot(linmod.x2b, main="linmod.x2b\nall residuals are zero")
> plot(lm.x2b, which=1, main="lm.x2b")
> plot(linmod.x2c, main="linmod.x2c")
> plot(lm.x2c, which=1, main="lm.x2c")
> par(org.par)
> 
> cat0("==nrow(x) does not match length(y)\n")
==nrow(x) does not match length(y)
> 
> x4 <- matrix(1:10, ncol=2)
> y4 <- c(1,2,9,4)
> expect.err(try(linmod(x4, y4)), "nrow(x) is 5 but length(y) is 4")
Error in check.linmod.y(x, y) : nrow(x) is 5 but length(y) is 4
Got expected error from try(linmod(x4, y4))
> 
> x5 <- matrix(1:10, ncol=2)
> y5 <- c(1,2,9,4,5,9)
> expect.err(try(linmod(x5, y5)), "nrow(x) is 5 but length(y) is 6")
Error in check.linmod.y(x, y) : nrow(x) is 5 but length(y) is 6
Got expected error from try(linmod(x5, y5))
> 
> cat0("==y has multiple columns\n")
==y has multiple columns
> 
> vec <- c(1,2,3,4,3)
> y2 <- cbind(c(1,2,3,4,9), vec^2)
> expect.err(try(linmod(vec, y2)), "nrow(x) is 5 but length(y) is 10")
Error in check.linmod.y(x, y) : nrow(x) is 5 but length(y) is 10
Got expected error from try(linmod(vec, y2))
> expect.err(try(linmod(y2~vec)), "nrow(x) is 5 but length(y) is 10")
Error in check.linmod.y(x, y) : nrow(x) is 5 but length(y) is 10
Got expected error from try(linmod(y2 ~ vec))
> 
> cat0("==NA in x\n")
==NA in x
> 
> x <- tr[,1:2]
> y <- tr[,3]
> x[2,2] <- NA
> expect.err(try(linmod(x, y)), "NA in 'x'")
Error in check.linmod.x(x) : NA in 'x'
Got expected error from try(linmod(x, y))
> 
> x <- tr[,1:2]
> y <- tr[,3]
> y[9] <- NA
> expect.err(try(linmod(x, y)), "NA in 'y'")
Error in check.linmod.y(x, y) : NA in 'y'
Got expected error from try(linmod(x, y))
> 
> # Following added Sep 2020 (prior to this, predict.linmod gave an incorrect error message)
> cat0("==test formulas that use functions on rhs variables, like Volume~sqrt(Girth)\n")
==test formulas that use functions on rhs variables, like Volume~sqrt(Girth)
> 
> linmod.sqrt1 <- linmod(Volume~sqrt(as.numeric(Girth)), data=tr)
> cat0("==print(summary(linmod.sqrt1))\n")
==print(summary(linmod.sqrt1))
> print(summary(linmod.sqrt1))
Call: linmod.formula(formula = Volume ~ sqrt(as.numeric(Girth)), data = tr)

                          Estimate   StdErr   t.value      p.value
(Intercept)             -103.40058 7.706018 -13.41816 5.733634e-14
sqrt(as.numeric(Girth))   36.94188 2.117135  17.44900 6.396229e-17
> lm.sqrt1 <- lm(Volume~sqrt(as.numeric(Girth)), data=tr)
> check.lm(linmod.sqrt1, lm.sqrt1)
check linmod.sqrt1 vs lm.sqrt1
> stopifnot(almost.equal(predict(linmod.sqrt1, newdata=data.frame(Girth=10, Height=80)),
+                        predict(lm.sqrt1,     newdata=data.frame(Girth=10, Height=80))))
> stopifnot(almost.equal(predict(linmod.sqrt1, newdata=as.matrix(tr[1:3,])),
+                        predict(lm.sqrt1,     newdata=tr[1:3,])))
> par(mfrow=c(2,2)) # all plots on same page so can compare
> plotmo(linmod.sqrt1, do.par=FALSE)
> plotmo(lm.sqrt1,     do.par=FALSE)
> par(org.par)
> 
> linmod.sqrt2 <- linmod(Volume~sqrt(Girth)+Height+Girth, data=tr)
> cat0("==print(summary(linmod.sqrt2))\n")
==print(summary(linmod.sqrt2))
> print(summary(linmod.sqrt2))
Call: linmod.formula(formula = Volume ~ sqrt(Girth) + Height + Girth, data =
      tr)

                Estimate      StdErr   t.value      p.value
(Intercept)  132.4266671 33.03008713  4.009274 4.318421e-04
sqrt(Girth) -106.5505058 18.19173301 -5.857084 3.085730e-06
Height         0.4030722  0.08863082  4.547765 1.026574e-04
Girth         19.0489443  2.45495604  7.759383 2.410443e-08
> lm.sqrt2 <- lm(Volume~sqrt(Girth)+Height+Girth, data=tr)
> check.lm(linmod.sqrt2, lm.sqrt2)
check linmod.sqrt2 vs lm.sqrt2
> stopifnot(almost.equal(predict(linmod.sqrt2, newdata=data.frame(Girth=10, Height=80)),
+                        predict(lm.sqrt2,     newdata=data.frame(Girth=10, Height=80))))
> stopifnot(almost.equal(predict(linmod.sqrt2, newdata=as.matrix(tr[1:3,])),
+                        predict(lm.sqrt2,     newdata=tr[1:3,])))
> par(mfrow=c(2,2)) # all plots on same page so can compare
> plotmo(linmod.sqrt2, do.par=FALSE)
 plotmo grid:    Girth Height
                  12.9     76
> plotmo(lm.sqrt2,     do.par=FALSE)
 plotmo grid:    Girth Height
                  12.9     76
> par(org.par)
> 
> lm.sqrt.as.numeric <- lm(survived~sqrt(age)+as.numeric(pclass), data=etit)
> linmod.sqrt.as.numeric <- linmod(survived~sqrt(age)+as.numeric(pclass), data=etit)
> check.lm(linmod.sqrt.as.numeric, lm.sqrt.as.numeric, newdata=etit[3:5,])
check linmod.sqrt.as.numeric vs lm.sqrt.as.numeric
> expect.err(try(predict(linmod.sqrt.as.numeric, newdata=data.frame(age=30))), # pclass missing
+            "object 'pclass' not found")
Error in eval(predvars, data, env) : object 'pclass' not found
Got expected error from try(predict(linmod.sqrt.as.numeric, newdata = data.frame(age = 30)))
> par(mfrow=c(2,2)) # all plots on same page so can compare
> plotmo(linmod.sqrt.as.numeric, do.par=FALSE)
 plotmo grid:    age pclass
                32.5    3rd
> plotmo(lm.sqrt.as.numeric,     do.par=FALSE)
 plotmo grid:    age pclass
                32.5    3rd
> par(org.par)
> 
> y.age    <- etit[,"age"]
> x.pclass <- etit[,"pclass"]
> x.sex    <- etit[,"sex"]
> linmod.y.age.sex.pclass <- linmod(y.age ~ as.numeric(x.pclass) + x.sex)
> lm.y.age.sex.pclass     <- lm(    y.age ~ as.numeric(x.pclass) + x.sex)
> stopifnot(identical(linmod.y.age.sex.pclass$coef, lm.y.age.sex.pclass$coef))
> options(warn=1) # print warnings as they occur to test stop() in linmod.R::process.newdata.formula
> # TODO following says variable 'as.numeric(x.pclass)' may be missing
> #      it should say  variable 'x.pclass' may be missing
> expect.err(try(predict(linmod.y.age.sex.pclass, newdata=etit[3:5,1,drop=FALSE])),
+            "newdata has 3 rows but model.frame returned 18 rows (variable 'as.numeric(x.pclass)' may be missing from newdata)")
Warning: 'newdata' had 3 rows but variables found have 18 rows
Error in process.newdata.formula(object, newdata) : 
  newdata has 3 rows but model.frame returned 18 rows (variable 'as.numeric(x.pclass)' may be missing from newdata)
Got expected error from try(predict(linmod.y.age.sex.pclass, newdata = etit[3:5, 1, drop = FALSE]))
> options(warn=2) # back to treating warnings as errors
> 
> cat0("==misc tests with different kinds of data\n")
==misc tests with different kinds of data
> 
> data3 <- data.frame(s=c("a", "b", "a", "c", "a"), num=c(1,5,1,9,2), y=c(1,3,2,5,3), stringsAsFactors=F)
> stopifnot(sapply(data3, class) == c("character", "numeric", "numeric"))
> a40 <- linmod(y~., data=data3)
> print(summary(a40))
Call: linmod.formula(formula = y ~ ., data = data3)

                 Estimate    StdErr       t.value   p.value
(Intercept) -1.390219e-15 1.2247449 -1.135109e-15 1.0000000
sb          -4.500000e+00 3.2787193 -1.372487e+00 0.4008582
sc          -8.500000e+00 6.6895441 -1.270640e+00 0.4244770
num          1.500000e+00 0.8660254  1.732051e+00 0.3333333
> stopifnot(almost.equal(a40$coefficients, c(0, -4.5, -8.5, 1.5), max=0.001))
> stopifnot(almost.equal(predict(a40, newdata=data3[2:3,]),
+                        c(3.0, 1.5), max=0.001))
> 
> data4 <- data.frame(s=c("a", "b", "a", "c", "a"), num=c(1,5,1,9,2), y=c(1,3,2,5,3), stringsAsFactors=T)
> stopifnot(sapply(data4, class) == c("factor", "numeric", "numeric"))
> expect.err(try(linmod(data4[,1:2], data4[,3])), "non-numeric column in 'x'")
Error in check.linmod.x(x) : non-numeric column in 'x'
Got expected error from try(linmod(data4[, 1:2], data4[, 3]))
> 
> # following gives no error (and matches lm) even though col 1 of data3 is character not factor
> a41 <- linmod(y~., data=data4)
> print(summary(a41))
Call: linmod.formula(formula = y ~ ., data = data4)

                 Estimate    StdErr       t.value   p.value
(Intercept) -1.390219e-15 1.2247449 -1.135109e-15 1.0000000
sb          -4.500000e+00 3.2787193 -1.372487e+00 0.4008582
sc          -8.500000e+00 6.6895441 -1.270640e+00 0.4244770
num          1.500000e+00 0.8660254  1.732051e+00 0.3333333
> stopifnot(almost.equal(predict(a41, newdata=data3[2:3,]),
+                        c(3.0, 1.5), max=0.001))
> 
> data5 <- data.frame(s=c("a", "b", "c", "a", "a"), num=c(1,9,4,2,6), y=c(1,2,3,5,3), stringsAsFactors=F)
> stopifnot(almost.equal(predict(a41, newdata=data5[1:3,1:2]),
+                         c(1.5, 9.0, -2.5), max=0.001))
> 
> data6 <- data.frame(s=c("a", "b", "c", "a9", "a"),
+                     num=c(1,9,4,2,6),
+                     num2=c(1,9,4,2,7),
+                     y=c(1,2,3,5,3), stringsAsFactors=T)
> expect.err(try(predict(a41, newdata=data6[1:3,1])), "object 's' not found")
Error in eval(predvars, data, env) : object 's' not found
Got expected error from try(predict(a41, newdata = data6[1:3, 1]))
> expect.err(try(predict(a41, newdata=data6[1:3,c(1,1)])), "object 'num' not found")
Error in eval(predvars, data, env) : object 'num' not found
Got expected error from try(predict(a41, newdata = data6[1:3, c(1, 1)]))
> 
> expect.err(try(predict(a41, newdata=data.frame(s=1, num=2, y=3))), "variable 's' is not a factor")
Error in model.frame.default(terms, newdata, na.action = na.pass, xlev = object$xlevels) : 
  (converted from warning) variable 's' is not a factor
Got expected error from try(predict(a41, newdata = data.frame(s = 1, num = 2, y = 3)))
> 
> expect.err(try(predict(a41, newdata=1:9)),
+            "object 's' not found")
Error in eval(predvars, data, env) : object 's' not found
Got expected error from try(predict(a41, newdata = 1:9))
> 
> expect.err(try(predict(a41, newdata=data.frame())), "'newdata' is empty")
Error in predict.linmod(a41, newdata = data.frame()) : 'newdata' is empty
Got expected error from try(predict(a41, newdata = data.frame()))
> 
> # perfect fit (residuals are all zero)
> linmod.data6 <- linmod(y~s+num, data=data6)
> print(summary(linmod.data6))
Call: linmod.formula(formula = y ~ s + num, data = data6)

            Estimate StdErr t.value p.value
(Intercept)      0.6    Inf       0       0
sa9              3.6    Inf       0       0
sb              -2.2    Inf       0       0
sc               0.8    Inf       0       0
num              0.4    Inf       0       0
> lm.data6 <- lm(y~s+num, data=data6)
> print(summary(lm.data6))

Call:
lm(formula = y ~ s + num, data = data6)

Residuals:
ALL 5 residuals are 0: no residual degrees of freedom!

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept)      0.6        NaN     NaN      NaN
sa9              3.6        NaN     NaN      NaN
sb              -2.2        NaN     NaN      NaN
sc               0.8        NaN     NaN      NaN
num              0.4        NaN     NaN      NaN

Residual standard error: NaN on 0 degrees of freedom
Multiple R-squared:      1,	Adjusted R-squared:    NaN 
F-statistic:   NaN on 4 and 0 DF,  p-value: NA

> check.lm(linmod.data6, lm.data6, newdata=data6[2,,drop=FALSE], check.sigma=FALSE)
check linmod.data6 vs lm.data6
> 
> expect.err(try(linmod(y~., data=data6)), "'x' is singular (it has 6 columns but its rank is 5)")
Error in do.linmod.fit(x, y) : 
  'x' is singular (it has 6 columns but its rank is 5)
  colnames(x): (Intercept) sa9 sb sc num num2
Got expected error from try(linmod(y ~ ., data = data6))
> 
> tr.na <- trees
> tr.na[9,3] <- NA
> expect.err(try(linmod(Volume~.,data=tr.na)), "NA in 'y'")
Error in check.linmod.y(x, y) : NA in 'y'
Got expected error from try(linmod(Volume ~ ., data = tr.na))
> expect.err(try(linmod(tr.na[,1:2], tr.na[,3])), "NA in 'y'")
Error in check.linmod.y(x, y) : NA in 'y'
Got expected error from try(linmod(tr.na[, 1:2], tr.na[, 3]))
> 
> tr.na <- trees
> tr.na[10,1] <- NA
> expect.err(try(linmod(Volume~.,data=tr.na)), "NA in 'x'")
Error in check.linmod.x(x) : NA in 'x'
Got expected error from try(linmod(Volume ~ ., data = tr.na))
> expect.err(try(linmod(tr.na[,1:2], tr.na[,3])), "NA in 'x'")
Error in check.linmod.x(x) : NA in 'x'
Got expected error from try(linmod(tr.na[, 1:2], tr.na[, 3]))
> 
> a42 <- linmod(trees[,1:2], trees[, 3])
> newdata1 <- data.frame(Girth=20)
> expect.err(try(predict(a42, newdata=newdata1)), "ncol(newdata) is 1 but should be 2")
Error in predict.linmod(a42, newdata = newdata1) : 
  ncol(newdata) is 1 but should be 2
Got expected error from try(predict(a42, newdata = newdata1))
> newdata3 <- data.frame(Girth=20, extra1=21, extra2=22)
> expect.err(try(predict(a42, newdata=newdata3)), "ncol(newdata) is 3 but should be 2")
Error in predict.linmod(a42, newdata = newdata3) : 
  ncol(newdata) is 3 but should be 2
Got expected error from try(predict(a42, newdata = newdata3))
> expect.err(try(predict(a42, newdata=data.frame())), "'newdata' is empty")
Error in predict.linmod(a42, newdata = data.frame()) : 'newdata' is empty
Got expected error from try(predict(a42, newdata = data.frame()))
> newdata.with.NA <- data.frame(Girth=20, Height=NA)
> expect.err(try(predict(a42, newdata=newdata.with.NA)), "NA in 'newdata'")
Error in predict.linmod(a42, newdata = newdata.with.NA) : NA in 'newdata'
Got expected error from try(predict(a42, newdata = newdata.with.NA))
> 
> a43 <- linmod(Volume~.,data=trees)
> expect.err(try(predict(a43, newdata=newdata.with.NA)), "NA in 'newdata'")
Error in process.newdata.formula(object, newdata) : NA in 'newdata'
Got expected error from try(predict(a43, newdata = newdata.with.NA))
> lm43 <- lm(Volume~.,data=trees)
> # message from predict.lm could be better
> expect.err(try(predict(lm43, newdata=newdata.with.NA)),
+               "variable 'Height' was fitted with type \"numeric\" but type \"logical\" was supplied")
Error : variable 'Height' was fitted with type "numeric" but type "logical" was supplied
Got expected error from try(predict(lm43, newdata = newdata.with.NA))
> 
> y6 <- 1:5
> x6 <- data.frame()
> options(warn=1) # print warnings as they occur
> expect.err(try(linmod(x6, y6)), "'x' is empty")
Warning in cbind(`(Intercept)` = 1, xmat) :
  number of rows of result is not a multiple of vector length (arg 1)
Error in check.linmod.x(x) : 'x' is empty
Got expected error from try(linmod(x6, y6))
> options(warn=2) # treat warnings as errors
> 
> y7 <- data.frame()
> x7 <- 1:5
> expect.err(try(linmod(x7, y7)), "'y' is empty")
Error in check.linmod.y(x, y) : 'y' is empty
Got expected error from try(linmod(x7, y7))
> 
> # duplicated column names
> data7 <- matrix(1:25, ncol=5)
> colnames(data7) <- c("y", "x1", "x1", "x3", "x4")
> expect.err(try(linmod(data7[,-1], data7[,1])), "column name \"x1\" in 'x' is duplicated")
Error in check.linmod.x(x) : column name "x1" in 'x' is duplicated
Got expected error from try(linmod(data7[, -1], data7[, 1]))
> 
> colnames(data7) <- c("y", "x1", "x2", "x2", "x4")
> expect.err(try(linmod(data7[,-1], data7[,1])), "column name \"x2\" in 'x' is duplicated")
Error in check.linmod.x(x) : column name "x2" in 'x' is duplicated
Got expected error from try(linmod(data7[, -1], data7[, 1]))
> 
> colnames(data7) <- c("y", "x1", "x2", "x2", "x2")
> expect.err(try(linmod(data7[,-1], data7[,1])), "column name \"x2\" in 'x' is duplicated")
Error in check.linmod.x(x) : column name "x2" in 'x' is duplicated
Got expected error from try(linmod(data7[, -1], data7[, 1]))
> 
> # column name V2 will be created but it clashes with the existing column name
> colnames(data7) <- c("y", "V2", "", "V3", "V4")
> expect.err(try(linmod(data7[,-1], data7[,1])), "column name \"V2\" in 'x' is duplicated")
Error in check.linmod.x(x) : column name "V2" in 'x' is duplicated
Got expected error from try(linmod(data7[, -1], data7[, 1]))
> 
> # missing column names
> trees1 <- trees
> colnames(trees1) <- NULL
> cat0("a52\n")
a52
> a52 <- linmod(trees1[,1:2], trees1[,3])
> print(summary(a52))
Call: linmod.default(x = trees1[, 1:2], y = trees1[, 3])

               Estimate    StdErr   t.value      p.value
(Intercept) -57.9876589 8.6382259 -6.712913 2.749507e-07
V1            4.7081605 0.2642646 17.816084 8.223304e-17
V2            0.3392512 0.1301512  2.606594 1.449097e-02
> 
> trees1 <- trees
> colnames(trees1) <- c("", "Height", "Volume") # was Girth Height Volume
> cat0("linmod.form.Volume.trees1\n")
linmod.form.Volume.trees1
> linmod.form.Volume.trees1 <- linmod(trees1[,1:2], trees1[,3])
> print(summary(linmod.form.Volume.trees1))
Call: linmod.default(x = trees1[, 1:2], y = trees1[, 3])

               Estimate    StdErr   t.value      p.value
(Intercept) -57.9876589 8.6382259 -6.712913 2.749507e-07
V1            4.7081605 0.2642646 17.816084 8.223304e-17
Height        0.3392512 0.1301512  2.606594 1.449097e-02
> cat0("linmod.form.Volume.trees1.formula\n")
linmod.form.Volume.trees1.formula
> expect.err(try(linmod(Volume~., data=trees1)), "attempt to use zero-length variable name")
Error in terms.formula(formula, data = data) : 
  attempt to use zero-length variable name
Got expected error from try(linmod(Volume ~ ., data = trees1))
> 
> # very long names to test formatting in summary.linmod
> trees1 <- trees
> colnames(trees1) <- c("Girth.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name",
+                       "Height.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name",
+                       "Volume.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name")
> cat0("a55\n")
a55
> a55 <- linmod(Volume.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name~
+               Girth.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name+
+               Height.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name,
+               data=trees1)
> print(summary(a55))
Call: linmod.formula(formula =
      Volume.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name
      ~
      Girth.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name
      +
      Height.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name,
      data = trees1)

                                                                                          Estimate
(Intercept)                                                                            -57.9876589
Girth.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name    4.7081605
Height.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name   0.3392512
                                                                                          StdErr
(Intercept)                                                                            8.6382259
Girth.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name  0.2642646
Height.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name 0.1301512
                                                                                         t.value
(Intercept)                                                                            -6.712913
Girth.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name  17.816084
Height.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name  2.606594
                                                                                            p.value
(Intercept)                                                                            2.749507e-07
Girth.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name  8.223304e-17
Height.a.very.long.name.in.fact.an.exceptionally.exceptionally.exceptionally.long.name 1.449097e-02
> 
> # intercept-only model
> intonly.form <- linmod(Volume~1, data=trees)
> print(summary(intonly.form))
Call: linmod.formula(formula = Volume ~ 1, data = trees)

            Estimate   StdErr  t.value      p.value
(Intercept) 30.17097 2.952324 10.21939 2.753323e-11
> stopifnot(length(coef(intonly.form)) == 1)
> try(plotmo(intonly.form)) # Error in plotmo(intonly.form) : x is empty
Error in plotmo(intonly.form) : x is empty
> plotres(intonly.form)
> expect.err(try(plotmo(intonly.form)), "x is empty")
Error in plotmo(intonly.form) : x is empty
Got expected error from try(plotmo(intonly.form))
> expect.err(try(linmod(rep(1, length.out=nrow(trees)), trees$Volume)),
+               "'x' is singular (it has 2 columns but its rank is 1)")
Error in do.linmod.fit(x, y) : 
  'x' is singular (it has 2 columns but its rank is 1)
  colnames(x): (Intercept) V1
Got expected error from try(linmod(rep(1, length.out = nrow(trees)), trees$Volume))
> 
> # various tests for bad args
> expect.err(try(linmod(trees[,1:2])), "no 'y' argument")
Error in as.matrix(y) : no 'y' argument
Got expected error from try(linmod(trees[, 1:2]))
> 
> # test stop.if.dot.arg.used
> expect.err(try(linmod(Volume~., data=trees, nonesuch=99)),
+               "unused argument (nonesuch = 99)")
Error in stop.if.dot.arg.used(...) : unused argument (nonesuch = 99)
Got expected error from try(linmod(Volume ~ ., data = trees, nonesuch = 99))
> expect.err(try(linmod(trees[,1:2], trees[,3], nonesuch=linmod)),
+               "unused argument (nonesuch = function (...)")
Error in stop.if.dot.arg.used(...) : 
  unused argument (nonesuch = function (...) 
UseMethod("linmod"))
Got expected error from try(linmod(trees[, 1:2], trees[, 3], nonesuch = linmod))
> expect.err(try(summary(linmod(trees[,1:2], trees[,3]), nonesuch=linmod)),
+               "unused argument (nonesuch = function (...)")
Error in stop.if.dot.arg.used(...) : 
  unused argument (nonesuch = function (...) 
UseMethod("linmod"))
Got expected error from try(summary(linmod(trees[, 1:2], trees[, 3]), nonesuch = linmod))
> expect.err(try(print(linmod(trees[,1:2], trees[,3]), nonesuch=linmod)),
+               "unused argument (nonesuch = function (...)")
Error in stop.if.dot.arg.used(...) : 
  unused argument (nonesuch = function (...) 
UseMethod("linmod"))
Got expected error from try(print(linmod(trees[, 1:2], trees[, 3]), nonesuch = linmod))
> expect.err(try(predict(linmod.form.Volume.tr, nonesuch=99)),
+               "unused argument (nonesuch = 99)")
Error in stop.if.dot.arg.used(...) : unused argument (nonesuch = 99)
Got expected error from try(predict(linmod.form.Volume.tr, nonesuch = 99))
> 
> # check partial matching on type argument
> stopifnot(identical(predict(linmod.form.Volume.tr, type="r"),    predict(linmod.form.Volume.tr)))
> stopifnot(identical(predict(linmod.form.Volume.tr, type="resp"), predict(linmod.form.Volume.tr)))
> expect.err(try(predict(linmod.form.Volume.tr, type="nonesuch")), "'arg' should be \"response\"")
Error in match.arg(type, "response") : 'arg' should be "response"
Got expected error from try(predict(linmod.form.Volume.tr, type = "nonesuch"))
> 
> # test additional method functions (see linmod.methods.R)
> 
> check.lm(linmod.form.Volume.tr, lm.Volume.tr, newdata=trees[3,1:2])
check linmod.form.Volume.tr vs lm.Volume.tr
> stopifnot(almost.equal(coef(linmod.form.Volume.tr), coef(lm.Volume.tr)))
> stopifnot(identical(names(coef(linmod.form.Volume.tr)), names(coef(lm.Volume.tr))))
> stopifnot(almost.equal(fitted(linmod.form.Volume.tr), fitted(lm.Volume.tr)))
> stopifnot(identical(names(fitted(linmod.form.Volume.tr)), names(fitted(lm.Volume.tr))))
> stopifnot(identical(na.action(linmod.form.Volume.tr), na.action(lm.Volume.tr)))
> stopifnot(almost.equal(residuals(linmod.form.Volume.tr), residuals(lm.Volume.tr)))
> stopifnot(identical(names(residuals(linmod.form.Volume.tr)), names(residuals(lm.Volume.tr))))
> stopifnot(identical(names(case.names(linmod.form.Volume.tr)), names(case.names(lm.Volume.tr))))
> stopifnot(identical(variable.names(linmod.form.Volume.tr), variable.names(lm.Volume.tr)))
> stopifnot(identical(nobs(linmod.form.Volume.tr), nobs(lm.Volume.tr)))
> stopifnot(identical(weights(linmod.form.Volume.tr), weights(lm.Volume.tr)))
> stopifnot(almost.equal(df.residual(linmod.form.Volume.tr), df.residual(lm.Volume.tr)))
> stopifnot(identical(names(df.residual(linmod.form.Volume.tr)), names(df.residual(lm.Volume.tr))))
> stopifnot(almost.equal(deviance(linmod.form.Volume.tr), deviance(lm.Volume.tr)))
> stopifnot(identical(names(deviance(linmod.form.Volume.tr)), names(deviance(lm.Volume.tr))))
> stopifnot(identical(weights(linmod.form.Volume.tr), weights(lm.Volume.tr)))
> stopifnot(identical(model.frame(linmod.form.Volume.tr), model.frame(lm.Volume.tr)))
> stopifnot(identical(model.matrix(linmod.form.Volume.tr), model.matrix(lm.Volume.tr)))
> stopifnot(identical(model.matrix(linmod.form.Volume.tr, data=tr[1:2,]),
+                     model.matrix(lm.Volume.tr,          data=tr[1:2,])))
> stopifnot(almost.equal(logLik(linmod.form.Volume.tr), logLik(lm.Volume.tr)))
> expect.err(try(logLik(linmod.form.Volume.tr, REML=TRUE)), "!REML is not TRUE")
Error in logLik.linmod(linmod.form.Volume.tr, REML = TRUE) : 
  !REML is not TRUE
Got expected error from try(logLik(linmod.form.Volume.tr, REML = TRUE))
> library(sandwich) # for estfun.lm
> stopifnot(almost.equal(estfun(linmod.form.Volume.tr), estfun(lm.Volume.tr)))
> 
> linmod.form.Volume.tr.update <- update(linmod.form.Volume.tr, formula.=Volume~Height)
> lm.Volume.tr.update          <- update(lm.Volume.tr, formula.=Volume~Height)
> check.lm(linmod.form.Volume.tr.update, lm.Volume.tr.update)
check linmod.form.Volume.tr.update vs lm.Volume.tr.update
> 
> check.lm(linmod.xy.Volume.tr, lm.Volume.tr, newdata=trees[3,1:2])
check linmod.xy.Volume.tr vs lm.Volume.tr
> stopifnot(almost.equal(coef(linmod.xy.Volume.tr), coef(lm.Volume.tr)))
> stopifnot(identical(names(coef(linmod.xy.Volume.tr)), names(coef(lm.Volume.tr))))
> stopifnot(almost.equal(fitted(linmod.xy.Volume.tr), fitted(lm.Volume.tr)))
> stopifnot(identical(names(fitted(linmod.xy.Volume.tr)), names(fitted(lm.Volume.tr))))
> stopifnot(identical(na.action(linmod.xy.Volume.tr), na.action(lm.Volume.tr)))
> stopifnot(almost.equal(residuals(linmod.xy.Volume.tr), residuals(lm.Volume.tr)))
> stopifnot(identical(names(residuals(linmod.xy.Volume.tr)), names(residuals(lm.Volume.tr))))
> stopifnot(identical(case.names(linmod.xy.Volume.tr), case.names(lm.Volume.tr)))
> stopifnot(identical(variable.names(linmod.xy.Volume.tr), variable.names(lm.Volume.tr)))
> stopifnot(identical(nobs(linmod.xy.Volume.tr), nobs(lm.Volume.tr)))
> stopifnot(identical(weights(linmod.xy.Volume.tr), weights(lm.Volume.tr)))
> stopifnot(almost.equal(df.residual(linmod.xy.Volume.tr), df.residual(lm.Volume.tr)))
> stopifnot(identical(names(df.residual(linmod.xy.Volume.tr)), names(df.residual(lm.Volume.tr))))
> stopifnot(almost.equal(deviance(linmod.xy.Volume.tr), deviance(lm.Volume.tr)))
> stopifnot(identical(names(deviance(linmod.xy.Volume.tr)), names(deviance(lm.Volume.tr))))
> stopifnot(identical(weights(linmod.xy.Volume.tr), weights(lm.Volume.tr)))
> expect.err(try(model.frame(linmod.xy.Volume.tr)),  "model.frame cannot be used on linmod models built without a formula")
Error in model.frame.linmod(linmod.xy.Volume.tr) : 
  model.frame cannot be used on linmod models built without a formula
Got expected error from try(model.frame(linmod.xy.Volume.tr))
> expect.err(try(model.matrix(linmod.xy.Volume.tr)),
+               "model.frame cannot be used on linmod models built without a formula")
Error in model.frame.linmod(object) : 
  model.frame cannot be used on linmod models built without a formula
Got expected error from try(model.matrix(linmod.xy.Volume.tr))
> stopifnot(almost.equal(logLik(linmod.xy.Volume.tr), logLik(lm.Volume.tr)))
> 
> par(mfrow=c(2,2))
> plot(linmod.form.Volume.tr)
> plot(lm.Volume.tr, which=1, main="lm.Volume.tr")
> plot(linmod.xy.Volume.tr)
> plot(linmod.form.Volume.tr, xlim=c(0,80), ylim=c(-10,10), pch=20, main="linmod.form.Volume.tr: test plot args")
> par(org.par)
> 
> cat0("==test one predictor model\n")
==test one predictor model
> 
> linmod.onepred.form <- linmod(Volume~Girth, data=tr) # one predictor
> lm.onepred.form <- lm(Volume~Girth, data=tr)
> check.lm(linmod.onepred.form, lm.onepred.form, newdata=trees[3,1:2])
check linmod.onepred.form vs lm.onepred.form
> linmod.onepred.xy <- linmod(tr[,1,drop=FALSE], tr[,3]) # one predictor
> print(summary(linmod.onepred.xy))
Call: linmod.default(x = tr[, 1, drop = FALSE], y = tr[, 3])

              Estimate   StdErr   t.value      p.value
(Intercept) -36.943459 3.365145 -10.97827 7.621449e-12
Girth         5.065856 0.247377  20.47829 8.644334e-19
> check.lm(linmod.onepred.xy, lm.onepred.form, newdata=trees[3,1,drop=FALSE])
check linmod.onepred.xy vs lm.onepred.form
> 
> par(mfrow=c(2,2))
> plot(linmod.onepred.form)
> plot(lm.onepred.form, which=1, main="lm.onepred.form")
> plot(linmod.onepred.xy)
> par(org.par)
> plotres(linmod.onepred.form)
> plotmo(linmod.onepred.form, pt.col=2)
> 
> cat0("==test no intercept model\n")
==test no intercept model
> # no intercept models are only supported with the formula interface (not x,y interface)
> 
> linmod.noint <- linmod(Volume~.-1, data=trees) # no intercept
> print(summary(linmod.noint))
Call: linmod.formula(formula = Volume ~ . - 1, data = trees)

         Estimate    StdErr   t.value      p.value
Girth   5.0440083 0.4118733 12.246506 5.519859e-13
Height -0.4773192 0.0734721 -6.496605 4.118004e-07
> lm.noint <- lm(Volume~.-1, data=trees) # no intercept
> check.lm(linmod.noint, lm.noint)
check linmod.noint vs lm.noint
> linmod.noint.keep <- linmod(Volume~.-1, data=trees, keep=TRUE)
> print(summary(linmod.noint.keep))
Call: linmod.formula(formula = Volume ~ . - 1, data = trees, keep = TRUE)

         Estimate    StdErr   t.value      p.value
Girth   5.0440083 0.4118733 12.246506 5.519859e-13
Height -0.4773192 0.0734721 -6.496605 4.118004e-07
> 
> check.lm(linmod.noint, lm.noint)
check linmod.noint vs lm.noint
> stopifnot(class(linmod.noint.keep$data)   == class(linmod.form.Volume.trees.keep$data))
> stopifnot(all(dim(linmod.noint.keep$data) == dim(linmod.form.Volume.trees.keep$data)))
> stopifnot(all(linmod.noint.keep$data == linmod.form.Volume.trees.keep$data))
> stopifnot(class(linmod.noint.keep$y)   == class(linmod.form.Volume.trees.keep$y))
> stopifnot(all(dim(linmod.noint.keep$data) == dim(linmod.form.Volume.trees.keep$data)))
> stopifnot(all(linmod.noint.keep$data == linmod.form.Volume.trees.keep$data))
> 
> # check method functions in no-intercept model
> stopifnot(almost.equal(coef(linmod.noint), coef(lm.noint)))
> stopifnot(identical(names(coef(linmod.noint)), names(coef(lm.noint))))
> stopifnot(almost.equal(fitted(linmod.noint), fitted(lm.noint)))
> stopifnot(identical(names(fitted(linmod.noint)), names(fitted(lm.noint))))
> stopifnot(identical(na.action(linmod.noint), na.action(lm.noint)))
> stopifnot(almost.equal(residuals(linmod.noint), residuals(lm.noint)))
> stopifnot(identical(names(residuals(linmod.noint)), names(residuals(lm.noint))))
> stopifnot(identical(case.names(linmod.noint), case.names(lm.noint)))
> stopifnot(identical(variable.names(linmod.noint), variable.names(lm.noint)))
> stopifnot(identical(nobs(linmod.noint), nobs(lm.noint)))
> stopifnot(identical(weights(linmod.noint), weights(lm.noint)))
> stopifnot(almost.equal(df.residual(linmod.noint), df.residual(lm.noint)))
> stopifnot(identical(names(df.residual(linmod.noint)), names(df.residual(lm.noint))))
> stopifnot(almost.equal(deviance(linmod.noint), deviance(lm.noint)))
> stopifnot(identical(names(deviance(linmod.noint)), names(deviance(lm.noint))))
> stopifnot(identical(weights(linmod.noint), weights(lm.noint)))
> stopifnot(identical(model.frame(linmod.noint), model.frame(lm.noint)))
> stopifnot(identical(model.matrix(linmod.noint), model.matrix(lm.noint)))
> stopifnot(identical(model.matrix(linmod.noint, data=tr[1:2,]),
+                     model.matrix(lm.noint,     data=tr[1:2,])))
> stopifnot(almost.equal(logLik(linmod.noint), logLik(lm.noint)))
> stopifnot(almost.equal(estfun(linmod.noint), estfun(lm.noint)))
> 
> # check error messages with bad newdata in no-intercept model
> expect.err(try(predict(linmod.noint, newdata=NA)),
+               "object 'Girth' not found")
Error in eval(predvars, data, env) : object 'Girth' not found
Got expected error from try(predict(linmod.noint, newdata = NA))
> expect.err(try(predict(linmod.noint, newdata=data.frame(Height=c(1,NA), Girth=c(3,4)))),
+               "NA in 'newdata'")
Error in process.newdata.formula(object, newdata) : NA in 'newdata'
Got expected error from try(predict(linmod.noint, newdata = data.frame(Height = c(1,     NA), Girth = c(3, 4))))
> expect.err(try(predict(linmod.noint, newdata=trees[0,])), "'newdata' is empty")
Error in predict.linmod(linmod.noint, newdata = trees[0, ]) : 
  'newdata' is empty
Got expected error from try(predict(linmod.noint, newdata = trees[0, ]))
> expect.err(try(predict(linmod.noint, newdata=trees[3:5,"Height"])), "object 'Girth' not found")
Error in eval(predvars, data, env) : object 'Girth' not found
Got expected error from try(predict(linmod.noint, newdata = trees[3:5, "Height"]))
> # check that extra fields in predict newdata are ok with (formula) models without intercept
> stopifnot(almost.equal(predict(linmod.noint, newdata=data.frame(Girth=10, Height=80, extra=99)),
+                        predict(lm.noint,  newdata=data.frame(Girth=10, Height=80, extra=99))))
> 
> par(mfrow=c(2,2))
> plot(linmod.noint)
> plot(lm.noint, which=1, main="lm.noint")
> par(org.par)
> 
> plotres(linmod.noint)
> plotmo(linmod.noint)
 plotmo grid:    Girth Height
                  12.9     76
> 
> cat0("==test one predictor no intercept model\n")
==test one predictor no intercept model
> # no intercept models are only supported with the formula interface (not x,y interface)
> 
> linmod.onepred.noint <- linmod(Volume~Girth-1, data=trees) # one predictor, no intercept
> print(summary(linmod.onepred.noint))
Call: linmod.formula(formula = Volume ~ Girth - 1, data = trees)

      Estimate    StdErr  t.value    p.value
Girth 2.420943 0.1253311 19.31637 1.7813e-18
> lm.onepred.noint <- lm(Volume~Girth-1, data=trees) # one predictor, no intercept
> check.lm(linmod.onepred.noint, lm.onepred.noint)
check linmod.onepred.noint vs lm.onepred.noint
> linmod.onepred.noint.keep <- linmod(Volume~.-1, data=trees, keep=TRUE)
> print(summary(linmod.onepred.noint.keep))
Call: linmod.formula(formula = Volume ~ . - 1, data = trees, keep = TRUE)

         Estimate    StdErr   t.value      p.value
Girth   5.0440083 0.4118733 12.246506 5.519859e-13
Height -0.4773192 0.0734721 -6.496605 4.118004e-07
> 
> check.lm(linmod.onepred.noint, lm.onepred.noint)
check linmod.onepred.noint vs lm.onepred.noint
> stopifnot(class(linmod.onepred.noint.keep$data)   == class(linmod.form.Volume.trees.keep$data))
> stopifnot(all(dim(linmod.onepred.noint.keep$data) == dim(linmod.form.Volume.trees.keep$data)))
> stopifnot(all(linmod.onepred.noint.keep$data == linmod.form.Volume.trees.keep$data))
> stopifnot(class(linmod.onepred.noint.keep$y)   == class(linmod.form.Volume.trees.keep$y))
> stopifnot(all(dim(linmod.onepred.noint.keep$data) == dim(linmod.form.Volume.trees.keep$data)))
> stopifnot(all(linmod.onepred.noint.keep$data == linmod.form.Volume.trees.keep$data))
> 
> # check method functions in one predictor no-intercept model
> stopifnot(almost.equal(coef(linmod.onepred.noint), coef(lm.onepred.noint)))
> stopifnot(identical(names(coef(linmod.onepred.noint)), names(coef(lm.onepred.noint))))
> stopifnot(almost.equal(fitted(linmod.onepred.noint), fitted(lm.onepred.noint)))
> stopifnot(identical(names(fitted(linmod.onepred.noint)), names(fitted(lm.onepred.noint))))
> stopifnot(identical(na.action(linmod.onepred.noint), na.action(lm.onepred.noint)))
> stopifnot(almost.equal(residuals(linmod.onepred.noint), residuals(lm.onepred.noint)))
> stopifnot(identical(names(residuals(linmod.onepred.noint)), names(residuals(lm.onepred.noint))))
> stopifnot(identical(case.names(linmod.onepred.noint), case.names(lm.onepred.noint)))
> stopifnot(identical(variable.names(linmod.onepred.noint), variable.names(lm.onepred.noint)))
> stopifnot(identical(nobs(linmod.onepred.noint), nobs(lm.onepred.noint)))
> stopifnot(identical(weights(linmod.onepred.noint), weights(lm.onepred.noint)))
> stopifnot(almost.equal(df.residual(linmod.onepred.noint), df.residual(lm.onepred.noint)))
> stopifnot(identical(names(df.residual(linmod.onepred.noint)), names(df.residual(lm.onepred.noint))))
> stopifnot(almost.equal(deviance(linmod.onepred.noint), deviance(lm.onepred.noint)))
> stopifnot(identical(names(deviance(linmod.onepred.noint)), names(deviance(lm.onepred.noint))))
> stopifnot(identical(weights(linmod.onepred.noint), weights(lm.onepred.noint)))
> stopifnot(identical(model.frame(linmod.onepred.noint), model.frame(lm.onepred.noint)))
> stopifnot(identical(model.matrix(linmod.onepred.noint), model.matrix(lm.onepred.noint)))
> stopifnot(identical(model.matrix(linmod.onepred.noint, data=tr[1:2,]),
+                     model.matrix(lm.onepred.noint,     data=tr[1:2,])))
> stopifnot(almost.equal(logLik(linmod.onepred.noint), logLik(lm.onepred.noint)))
> stopifnot(almost.equal(estfun(linmod.onepred.noint), estfun(lm.onepred.noint)))
> 
> # check error messages with bad newdata in one predictor no-intercept model
> expect.err(try(predict(linmod.onepred.noint, newdata=99)), "object 'Girth' not found")
Error in eval(predvars, data, env) : object 'Girth' not found
Got expected error from try(predict(linmod.onepred.noint, newdata = 99))
> expect.err(try(predict(linmod.onepred.noint, newdata=data.frame(Girth=NA))), "NA in 'newdata'")
Error in process.newdata.formula(object, newdata) : NA in 'newdata'
Got expected error from try(predict(linmod.onepred.noint, newdata = data.frame(Girth = NA)))
> expect.err(try(predict(linmod.onepred.noint, newdata=trees[0,1])), "'newdata' is empty")
Error in predict.linmod(linmod.onepred.noint, newdata = trees[0, 1]) : 
  'newdata' is empty
Got expected error from try(predict(linmod.onepred.noint, newdata = trees[0, 1]))
> expect.err(try(predict(linmod.onepred.noint, newdata=trees[3:5,"Height"])), "object 'Girth' not found")
Error in eval(predvars, data, env) : object 'Girth' not found
Got expected error from try(predict(linmod.onepred.noint, newdata = trees[3:5, "Height"]))
> # check that extra fields in predict newdata are ok with (formula) models without intercept
> stopifnot(almost.equal(predict(linmod.onepred.noint, newdata=data.frame(Girth=10, extra=99)),
+                        predict(lm.onepred.noint,     newdata=data.frame(Girth=10, extra=99))))
> 
> par(mfrow=c(2,2))
> plot(linmod.onepred.noint)
> plot(lm.onepred.noint, which=1, main="lm.onepred.noint")
> par(org.par)
> 
> plotres(linmod.onepred.noint)
> plotmo(linmod.onepred.noint)
> 
> expect.err(try(linmod(Volume~nonesuch, data=trees)), "object 'nonesuch' not found")
Error in eval(predvars, data, env) : object 'nonesuch' not found
Got expected error from try(linmod(Volume ~ nonesuch, data = trees))
> expect.err(try(linmod(Volume~0, data=trees)),   "'x' is empty") # no predictor
Error in check.linmod.x(x) : 'x' is empty
Got expected error from try(linmod(Volume ~ 0, data = trees))
> expect.err(try(linmod(Volume~-1, data=trees)), "'x' is empty") # no predictor, no intercept
Error in check.linmod.x(x) : 'x' is empty
Got expected error from try(linmod(Volume ~ -1, data = trees))
> 
> cat0("==check model with many variables\n")
==check model with many variables
> 
> set.seed(2018)
> p <- 300 # number of variables
> n <- floor(1.1 * p)
> bigdat <- as.data.frame(matrix(rnorm(n * (p+1)), ncol=p+1))
> colnames(bigdat) <- c("y", paste0("var", 1:p))
> lm.bigdat <- lm(y~., data=bigdat)
> linmod.bigdat <- linmod(y~., data=bigdat)
> check.lm(linmod.form.Volume.tr, lm.Volume.tr)
check linmod.form.Volume.tr vs lm.Volume.tr
> print(linmod.bigdat)
Call: linmod.formula(formula = y ~ ., data = bigdat)

  (Intercept)          var1          var2          var3          var4 
-0.0074874141 -0.0156168166 -0.0323375299 -0.0680410620 -0.1784176655 
         var5          var6          var7          var8          var9 
 0.0970839766 -0.2420079781  0.0068052116  0.0605142551  0.1563114625 
        var10         var11         var12         var13         var14 
-0.0705547201  0.0661388031  0.0753290388 -0.0595687675 -0.1972523829 
        var15         var16         var17         var18         var19 
-0.0928371617  0.1400015667  0.0349750202  0.0990295749 -0.0806465990 
        var20         var21         var22         var23         var24 
-0.0005353688 -0.1384821496 -0.0405121324 -0.0181462061 -0.2133498970 
        var25         var26         var27         var28         var29 
-0.0186244683 -0.2593737746 -0.0589964475 -0.0537252842 -0.0594401821 
        var30         var31         var32         var33         var34 
 0.0934989343  0.0244371962  0.1403544230  0.2619465745  0.0159354057 
        var35         var36         var37         var38         var39 
-0.0210109954 -0.0328618036 -0.1371912460 -0.0649163643  0.0595217563 
        var40         var41         var42         var43         var44 
-0.0682175594 -0.1103821881 -0.0508841621 -0.1392364303 -0.0103981103 
        var45         var46         var47         var48         var49 
-0.1196682294 -0.1534327142 -0.0754141872  0.1426175022  0.0011406008 
        var50         var51         var52         var53         var54 
 0.0379811394  0.0320275730 -0.0532598495 -0.1410085314  0.1519143039 
        var55         var56         var57         var58         var59 
-0.0228233810  0.3170130760 -0.1044797851 -0.0035954154  0.1479556565 
        var60         var61         var62         var63         var64 
 0.0122428193 -0.0253431378 -0.0180440355 -0.1794590898  0.0131447015 
        var65         var66         var67         var68         var69 
-0.1720319639  0.1526605311  0.0771868987 -0.2418787630  0.0447156252 
        var70         var71         var72         var73         var74 
-0.1105368627  0.0567936200  0.0424605198 -0.0881098654  0.0092876782 
        var75         var76         var77         var78         var79 
-0.0716540798 -0.1255361536 -0.0071680571 -0.1208344391 -0.0735928839 
        var80         var81         var82         var83         var84 
 0.2324224976 -0.1849522151  0.0694052039  0.1390729406 -0.0617270270 
        var85         var86         var87         var88         var89 
 0.0850926211  0.1221016487  0.0233354163  0.0075718550 -0.0032554103 
        var90         var91         var92         var93         var94 
 0.1209443561  0.2292860177  0.1347583831  0.0781827877 -0.1541547464 
        var95         var96         var97         var98         var99 
 0.1337171223 -0.1163422961 -0.0966724692 -0.2182129213 -0.1204830968 
       var100        var101        var102        var103        var104 
-0.0619465323 -0.1113710701  0.0594579753  0.0955361014 -0.0519687498 
       var105        var106        var107        var108        var109 
-0.0346599073  0.2181197633  0.0332996851 -0.0969131172  0.1736014017 
       var110        var111        var112        var113        var114 
-0.1714974837 -0.0056002152  0.1393566962 -0.0972988693  0.0475762687 
       var115        var116        var117        var118        var119 
 0.2364360899 -0.0985131354 -0.0894394214 -0.2355018204  0.0025381197 
       var120        var121        var122        var123        var124 
-0.1427340796 -0.0565016310 -0.0455466677  0.1579742783  0.1290270638 
       var125        var126        var127        var128        var129 
 0.0735269010 -0.0074354274 -0.0202350963  0.0921409434  0.0578351619 
       var130        var131        var132        var133        var134 
 0.0457446540 -0.0497481279 -0.0716169797 -0.0834890066  0.0078486400 
       var135        var136        var137        var138        var139 
 0.0569885547 -0.0880888941  0.0931535379  0.0029921816  0.0215558011 
       var140        var141        var142        var143        var144 
 0.0379439385  0.1288009147 -0.0627699322  0.1471235930  0.0418985129 
       var145        var146        var147        var148        var149 
 0.1581333558  0.2109672906 -0.1305882685  0.1715603371 -0.0674028658 
       var150        var151        var152        var153        var154 
-0.1809329622 -0.0618254790 -0.0644645613 -0.0185217288  0.0963509748 
       var155        var156        var157        var158        var159 
 0.0669555139  0.1341679917  0.0014091507  0.1912096659  0.1049270995 
       var160        var161        var162        var163        var164 
 0.1407325985 -0.0149350788 -0.1567496204  0.0881458138 -0.0429862791 
       var165        var166        var167        var168        var169 
 0.0080105136 -0.0374778798  0.1385838635 -0.0734288141 -0.1266495195 
       var170        var171        var172        var173        var174 
 0.0071467393 -0.0255859731  0.1516581037 -0.2106472762 -0.0308347530 
       var175        var176        var177        var178        var179 
 0.0076295054  0.1793572809  0.1064141211  0.0906223259  0.0435110825 
       var180        var181        var182        var183        var184 
-0.1264325305 -0.0968032660  0.1430811907  0.0307419406 -0.0319429988 
       var185        var186        var187        var188        var189 
 0.0461719964 -0.2385322379  0.0850810205  0.3949689631  0.1245166753 
       var190        var191        var192        var193        var194 
 0.1720563316  0.2144640136  0.0501975420  0.1174708714 -0.1943912402 
       var195        var196        var197        var198        var199 
 0.0202300723  0.0210580247  0.0726236855  0.1064539412 -0.0767767634 
       var200        var201        var202        var203        var204 
-0.0624521254  0.0028300645 -0.1715330103  0.2115665862  0.0338181429 
       var205        var206        var207        var208        var209 
 0.0167958834 -0.0590878112 -0.1653100651 -0.0740487318 -0.0043391023 
       var210        var211        var212        var213        var214 
 0.3393487726  0.2223498489  0.0213281741  0.2230110595 -0.1228075434 
       var215        var216        var217        var218        var219 
-0.0104634410  0.0326754989 -0.4439139348 -0.1087432871 -0.0107897918 
       var220        var221        var222        var223        var224 
-0.0296175151  0.1091241015  0.0909297736 -0.3485310127  0.0832890933 
       var225        var226        var227        var228        var229 
-0.0042697108  0.0593458113 -0.0182956931  0.0572344159 -0.1231669279 
       var230        var231        var232        var233        var234 
 0.0492497234 -0.2862525037  0.1834105207  0.2081280243  0.1641204059 
       var235        var236        var237        var238        var239 
 0.2472694582  0.0683823801  0.1891842675 -0.0489319878  0.1490499844 
       var240        var241        var242        var243        var244 
-0.0095798604  0.0721964545 -0.0126839937 -0.2221525719 -0.0829084901 
       var245        var246        var247        var248        var249 
-0.0318090335 -0.0425994225  0.0033944363  0.0984076551 -0.2148911884 
       var250        var251        var252        var253        var254 
-0.1875432344 -0.1735721485  0.2886948591  0.1467087046 -0.0834815473 
       var255        var256        var257        var258        var259 
-0.0635576566 -0.0346030600 -0.1224921370 -0.2423169128 -0.0021922047 
       var260        var261        var262        var263        var264 
-0.0818789537 -0.0707600938 -0.3301726263 -0.2602526557 -0.1427837485 
       var265        var266        var267        var268        var269 
-0.1315034492  0.1292166855  0.0265412839  0.1111883441  0.1302021867 
       var270        var271        var272        var273        var274 
-0.0923837589 -0.0680064479 -0.1776069310 -0.0374118346  0.0877037245 
       var275        var276        var277        var278        var279 
-0.0016240717  0.1670149940  0.1542172653 -0.0108006893  0.1334885400 
       var280        var281        var282        var283        var284 
 0.1637485211  0.0649039066 -0.0277897733  0.1978208690  0.0984930229 
       var285        var286        var287        var288        var289 
-0.1113854013  0.0770616839 -0.0634971052  0.1652137421 -0.0984475187 
       var290        var291        var292        var293        var294 
 0.1166070472 -0.0682754836  0.1016526112 -0.2976518291 -0.1119627963 
       var295        var296        var297        var298        var299 
 0.2734232937 -0.1054927068 -0.2151298321  0.0208265210  0.0882009038 
       var300 
 0.1604547308 
> print(summary(linmod.bigdat))
Call: linmod.formula(formula = y ~ ., data = bigdat)

                 Estimate    StdErr      t.value   p.value
(Intercept) -0.0074874141 0.1800205 -0.041592015 0.9671090
var1        -0.0156168166 0.2371393 -0.065855031 0.9479451
var2        -0.0323375299 0.2074053 -0.155914683 0.8771805
var3        -0.0680410620 0.2135121 -0.318675467 0.7522565
var4        -0.1784176655 0.2765676 -0.645114193 0.5239245
var5         0.0970839766 0.2705479  0.358842112 0.7223126
var6        -0.2420079781 0.2227204 -1.086599878 0.2861632
var7         0.0068052116 0.2638035  0.025796522 0.9795963
var8         0.0605142551 0.2672763  0.226410883 0.8224702
var9         0.1563114625 0.2173700  0.719103064 0.4778324
var10       -0.0705547201 0.2298045 -0.307020683 0.7610215
var11        0.0661388031 0.2511706  0.263322181 0.7941642
var12        0.0753290388 0.2012531  0.374300073 0.7109041
var13       -0.0595687675 0.3550150 -0.167792238 0.8679114
var14       -0.1972523829 0.2246975 -0.877857612 0.3872362
var15       -0.0928371617 0.2113127 -0.439335409 0.6636749
var16        0.1400015667 0.2435983  0.574723062 0.5699107
var17        0.0349750202 0.1917603  0.182389223 0.8565463
var18        0.0990295749 0.2216047  0.446874974 0.6582850
var19       -0.0806465990 0.1909595 -0.422323087 0.6759040
var20       -0.0005353688 0.2338494 -0.002289374 0.9981890
var21       -0.1384821496 0.2015467 -0.687097048 0.4974799
var22       -0.0405121324 0.2477545 -0.163517220 0.8712455
var23       -0.0181462061 0.2375000 -0.076405072 0.9396215
var24       -0.2133498970 0.2363631 -0.902636318 0.3741555
var25       -0.0186244683 0.2254941 -0.082594047 0.9347418
var26       -0.2593737746 0.2564927 -1.011232508 0.3202685
var27       -0.0589964475 0.2340174 -0.252102832 0.8027398
var28       -0.0537252842 0.2245610 -0.239245826 0.8125978
var29       -0.0594401821 0.2027951 -0.293104596 0.7715294
var30        0.0934989343 0.2367895  0.394860933 0.6958348
var31        0.0244371962 0.3424643  0.071356924 0.9436035
var32        0.1403544230 0.2135245  0.657322481 0.5161571
var33        0.2619465745 0.2640503  0.992032890 0.3293872
var34        0.0159354057 0.2044152  0.077956052 0.9383984
var35       -0.0210109954 0.2844938 -0.073853956 0.9416337
var36       -0.0328618036 0.2399793 -0.136936018 0.8920276
var37       -0.1371912460 0.2537454 -0.540664966 0.5928674
var38       -0.0649163643 0.1799295 -0.360787712 0.7208731
var39        0.0595217563 0.2022310  0.294325542 0.7706057
var40       -0.0682175594 0.2554638 -0.267034184 0.7913327
var41       -0.1103821881 0.2331126 -0.473514393 0.6393915
var42       -0.0508841621 0.2752612 -0.184857767 0.8546273
var43       -0.1392364303 0.2495550 -0.557938843 0.5811682
var44       -0.0103981103 0.2209398 -0.047063086 0.9627856
var45       -0.1196682294 0.3048932 -0.392492323 0.6975645
var46       -0.1534327142 0.2572114 -0.596523861 0.5554538
var47       -0.0754141872 0.2600154 -0.290037393 0.7738514
var48        0.1426175022 0.2254117  0.632697751 0.5318886
var49        0.0011406008 0.2120596  0.005378679 0.9957453
var50        0.0379811394 0.2310918  0.164355174 0.8705918
var51        0.0320275730 0.2767792  0.115715247 0.9086758
var52       -0.0532598495 0.2458433 -0.216641439 0.8300046
var53       -0.1410085314 0.1977205 -0.713171114 0.4814399
var54        0.1519143039 0.2314816  0.656269545 0.5168246
var55       -0.0228233810 0.2350910 -0.097083173 0.9233282
var56        0.3170130760 0.3614265  0.877116184 0.3876321
var57       -0.1044797851 0.2183847 -0.478420881 0.6359379
var58       -0.0035954154 0.2751337 -0.013067882 0.9896631
var59        0.1479556565 0.2123298  0.696820184 0.4914637
var60        0.0122428193 0.2293630  0.053377487 0.9577972
var61       -0.0253431378 0.2313604 -0.109539665 0.9135290
var62       -0.0180440355 0.1981508 -0.091062144 0.9280693
var63       -0.1794590898 0.1901054 -0.943998047 0.3529695
var64        0.0131447015 0.2083418  0.063092011 0.9501261
var65       -0.1720319639 0.2428857 -0.708283494 0.4844239
var66        0.1526605311 0.2147799  0.710776774 0.4829003
var67        0.0771868987 0.3130362  0.246575008 0.8069742
var68       -0.2418787630 0.2493599 -0.969998540 0.3400684
var69        0.0447156252 0.2115566  0.211364798 0.8340810
var70       -0.1105368627 0.1705161 -0.648248782 0.5219242
var71        0.0567936200 0.2117084  0.268263375 0.7903957
var72        0.0424605198 0.2223151  0.190992539 0.8498623
var73       -0.0881098654 0.2502169 -0.352133982 0.7272839
var74        0.0092876782 0.1725946  0.053812095 0.9574539
var75       -0.0716540798 0.2042502 -0.350815262 0.7282627
var76       -0.1255361536 0.2032681 -0.617588945 0.5416660
var77       -0.0071680571 0.2245031 -0.031928539 0.9747478
var78       -0.1208344391 0.2171811 -0.556376521 0.5822217
var79       -0.0735928839 0.2758883 -0.266748816 0.7915503
var80        0.2324224976 0.2178554  1.066865690 0.2948340
var81       -0.1849522151 0.2494518 -0.741434562 0.4643923
var82        0.0694052039 0.2244402  0.309236945 0.7593522
var83        0.1390729406 0.2408728  0.577370810 0.5681449
var84       -0.0617270270 0.2172721 -0.284100080 0.7783524
var85        0.0850926211 0.2263187  0.375985799 0.7096640
var86        0.1221016487 0.2563207  0.476362843 0.6373855
var87        0.0233354163 0.1872097  0.124648512 0.9016619
var88        0.0075718550 0.1673231  0.045252884 0.9642159
var89       -0.0032554103 0.1788632 -0.018200555 0.9856035
var90        0.1209443561 0.2560722  0.472305640 0.6402436
var91        0.2292860177 0.1858306  1.233844321 0.2271674
var92        0.1347583831 0.2565987  0.525171749 0.6034562
var93        0.0781827877 0.2780298  0.281202951 0.7805515
var94       -0.1541547464 0.2788393 -0.552844434 0.5846067
var95        0.1337171223 0.2598042  0.514684249 0.6106743
var96       -0.1163422961 0.2154543 -0.539986000 0.5933295
var97       -0.0966724692 0.1949970 -0.495763812 0.6237974
var98       -0.2182129213 0.2123535 -1.027592541 0.3126367
var99       -0.1204830968 0.2005145 -0.600869627 0.5525946
var100      -0.0619465323 0.1976115 -0.313476390 0.7561624
var101      -0.1113710701 0.2468408 -0.451185779 0.6552116
var102       0.0594579753 0.2864292  0.207583470 0.8370051
var103       0.0955361014 0.2438856  0.391725115 0.6981251
var104      -0.0519687498 0.1991270 -0.260982906 0.7959502
var105      -0.0346599073 0.2657151 -0.130440121 0.8971189
var106       0.2181197633 0.2335975  0.933741705 0.3581471
var107       0.0332996851 0.2262542  0.147178175 0.8840098
var108      -0.0969131172 0.2404953 -0.402973070 0.6899235
var109       0.1736014017 0.2382727  0.728582793 0.4720999
var110      -0.1714974837 0.2789115 -0.614881303 0.5434281
var111      -0.0056002152 0.2405138 -0.023284378 0.9815829
var112       0.1393566962 0.2713318  0.513602510 0.6114211
var113      -0.0972988693 0.2237430 -0.434868813 0.6668767
var114       0.0475762687 0.2010286  0.236664132 0.8145811
var115       0.2364360899 0.1812356  1.304578743 0.2022950
var116      -0.0985131354 0.1918563 -0.513473612 0.6115102
var117      -0.0894394214 0.2173996 -0.411405563 0.6837999
var118      -0.2355018204 0.2043250 -1.152584287 0.2584937
var119       0.0025381197 0.2468950  0.010280159 0.9918682
var120      -0.1427340796 0.2098195 -0.680270750 0.5017283
var121      -0.0565016310 0.2247369 -0.251412320 0.8032684
var122      -0.0455466677 0.2003293 -0.227358982 0.8217399
var123       0.1579742783 0.2883202  0.547912675 0.5879449
var124       0.1290270638 0.2496442  0.516843926 0.6091846
var125       0.0735269010 0.2161412  0.340180001 0.7361728
var126      -0.0074354274 0.2214263 -0.033579687 0.9734424
var127      -0.0202350963 0.2301697 -0.087913801 0.9305495
var128       0.0921409434 0.1946116  0.473460579 0.6394294
var129       0.0578351619 0.1972534  0.293202402 0.7714554
var130       0.0457446540 0.1811477  0.252526816 0.8024152
var131      -0.0497481279 0.2395549 -0.207669049 0.8369389
var132      -0.0716169797 0.2264069 -0.316319726 0.7540255
var133      -0.0834890066 0.2330487 -0.358247063 0.7227531
var134       0.0078486400 0.2177636  0.036042020 0.9714958
var135       0.0569885547 0.2341690  0.243365105 0.8094359
var136      -0.0880888941 0.2153686 -0.409014568 0.6855340
var137       0.0931535379 0.2469843  0.377163735 0.7087980
var138       0.0029921816 0.2751486  0.010874785 0.9913978
var139       0.0215558011 0.2147867  0.100359093 0.9207499
var140       0.0379439385 0.2406773  0.157654833 0.8758214
var141       0.1288009147 0.2085225  0.617683396 0.5416046
var142      -0.0627699322 0.2098144 -0.299168892 0.7669448
var143       0.1471235930 0.2412491  0.609841087 0.5467163
var144       0.0418985129 0.2434882  0.172076181 0.8645729
var145       0.1581333558 0.2214480  0.714088092 0.4808812
var146       0.2109672906 0.2233900  0.944389874 0.3527727
var147      -0.1305882685 0.2529765 -0.516207076 0.6096237
var148       0.1715603371 0.2701917  0.634957851 0.5304342
var149      -0.0674028658 0.2036219 -0.331019746 0.7430096
var150      -0.1809329622 0.2498705 -0.724106996 0.4748015
var151      -0.0618254790 0.2176185 -0.284100247 0.7783522
var152      -0.0644645613 0.2754214 -0.234057917 0.8165845
var153      -0.0185217288 0.2208211 -0.083876614 0.9337309
var154       0.0963509748 0.2313142  0.416537290 0.6800839
var155       0.0669555139 0.1933443  0.346302031 0.7316158
var156       0.1341679917 0.2524602  0.531442178 0.5991599
var157       0.0014091507 0.2640273  0.005337141 0.9957781
var158       0.1912096659 0.1695380  1.127827842 0.2686376
var159       0.1049270995 0.2414864  0.434505156 0.6671377
var160       0.1407325985 0.2455352  0.573166587 0.5709501
var161      -0.0149350788 0.2301044 -0.064905660 0.9486945
var162      -0.1567496204 0.2009329 -0.780109241 0.4416476
var163       0.0881458138 0.1865732  0.472446196 0.6401445
var164      -0.0429862791 0.1842946 -0.233247688 0.8172076
var165       0.0080105136 0.2145006  0.037344952 0.9704659
var166      -0.0374778798 0.2318411 -0.161653296 0.8726999
var167       0.1385838635 0.2867304  0.483324640 0.6324945
var168      -0.0734288141 0.3050426 -0.240716561 0.8114685
var169      -0.1266495195 0.2501795 -0.506234633 0.6165190
var170       0.0071467393 0.2711878  0.026353468 0.9791559
var171      -0.0255859731 0.1960230 -0.130525331 0.8970520
var172       0.1516581037 0.2794876  0.542629017 0.5915315
var173      -0.2106472762 0.2586949 -0.814269164 0.4221271
var174      -0.0308347530 0.1917615 -0.160797399 0.8733679
var175       0.0076295054 0.3046328  0.025044924 0.9801907
var176       0.1793572809 0.2037214  0.880404570 0.3858783
var177       0.1064141211 0.2557243  0.416128313 0.6803797
var178       0.0906223259 0.1983712  0.456832105 0.6511953
var179       0.0435110825 0.2579405  0.168686498 0.8672143
var180      -0.1264325305 0.2161180 -0.585016152 0.5630615
var181      -0.0968032660 0.2302398 -0.420445421 0.6772593
var182       0.1430811907 0.2453891  0.583078722 0.5643475
var183       0.0307419406 0.2604510  0.118033506 0.9068549
var184      -0.0319429988 0.2463878 -0.129645214 0.8977422
var185       0.0461719964 0.2008406  0.229893732 0.8197882
var186      -0.2385322379 0.2385500 -0.999925395 0.3256175
var187       0.0850810205 0.2238337  0.380108258 0.7066348
var188       0.3949689631 0.2554732  1.546028733 0.1329419
var189       0.1245166753 0.2747638  0.453177206 0.6537938
var190       0.1720563316 0.1879732  0.915323611 0.3675705
var191       0.2144640136 0.2413709  0.888524686 0.3815695
var192       0.0501975420 0.2506340  0.200282260 0.8426578
var193       0.1174708714 0.1746616  0.672562616 0.5065496
var194      -0.1943912402 0.3087673 -0.629571991 0.5339036
var195       0.0202300723 0.1915222  0.105627803 0.9166049
var196       0.0210580247 0.2176811  0.096737972 0.9235999
var197       0.0726236855 0.2177147  0.333572658 0.7411020
var198       0.1064539412 0.2261034  0.470819639 0.6412918
var199      -0.0767767634 0.2594113 -0.295965345 0.7693656
var200      -0.0624521254 0.2431441 -0.256852333 0.7991064
var201       0.0028300645 0.2063768  0.013713095 0.9891528
var202      -0.1715330103 0.2434880 -0.704482359 0.4867518
var203       0.2115665862 0.2486851  0.850740856 0.4018833
var204       0.0338181429 0.2280774  0.148274859 0.8831521
var205       0.0167958834 0.2489778  0.067459374 0.9466790
var206      -0.0590878112 0.1959422 -0.301557386 0.7651414
var207      -0.1653100651 0.2678547 -0.617163149 0.5419429
var208      -0.0740487318 0.2976417 -0.248784829 0.8052807
var209      -0.0043391023 0.2286282 -0.018978862 0.9849879
var210       0.3393487726 0.2358674  1.438726974 0.1609341
var211       0.2223498489 0.2661974  0.835281675 0.4103882
var212       0.0213281741 0.2315918  0.092093805 0.9272568
var213       0.2230110595 0.2581936  0.863735666 0.3948210
var214      -0.1228075434 0.2065047 -0.594696099 0.5566586
var215      -0.0104634410 0.2454306 -0.042632989 0.9662863
var216       0.0326754989 0.1978876  0.165121515 0.8699940
var217      -0.4439139348 0.3244134 -1.368358977 0.1817084
var218      -0.1087432871 0.2499652 -0.435033655 0.6667585
var219      -0.0107897918 0.2111081 -0.051110265 0.9595881
var220      -0.0296175151 0.2005449 -0.147685200 0.8836133
var221       0.1091241015 0.2479581  0.440090806 0.6631341
var222       0.0909297736 0.2382558  0.381647734 0.7055049
var223      -0.3485310127 0.2994113 -1.164054343 0.2538897
var224       0.0832890933 0.2243884  0.371182680 0.7131995
var225      -0.0042697108 0.3003295 -0.014216755 0.9887544
var226       0.0593458113 0.2310813  0.256817880 0.7991327
var227      -0.0182956931 0.1938017 -0.094404189 0.9254374
var228       0.0572344159 0.2343684  0.244207074 0.8087900
var229      -0.1231669279 0.2605563 -0.472707582 0.6399602
var230       0.0492497234 0.2111087  0.233290802 0.8171745
var231      -0.2862525037 0.1914503 -1.495179287 0.1456712
var232       0.1834105207 0.1939787  0.945519089 0.3522060
var233       0.2081280243 0.1632040  1.275263095 0.2123381
var234       0.1641204059 0.2272942  0.722061495 0.4760391
var235       0.2472694582 0.1902445  1.299745561 0.2039253
var236       0.0683823801 0.2231440  0.306449594 0.7614518
var237       0.1891842675 0.2214505  0.854295987 0.3999433
var238      -0.0489319878 0.2340164 -0.209096383 0.8358349
var239       0.1490499844 0.2429465  0.613509393 0.5443221
var240      -0.0095798604 0.2533123 -0.037818383 0.9700916
var241       0.0721964545 0.1969929  0.366492592 0.7166580
var242      -0.0126839937 0.2087745 -0.060754522 0.9519715
var243      -0.2221525719 0.1983111 -1.120222514 0.2718109
var244      -0.0829084901 0.2055738 -0.403302790 0.6896837
var245      -0.0318090335 0.2292748 -0.138737596 0.8906165
var246      -0.0425994225 0.2283779 -0.186530377 0.8533276
var247       0.0033944363 0.2129927  0.015936864 0.9873939
var248       0.0984076551 0.2343675  0.419886173 0.6776632
var249      -0.2148911884 0.2120962 -1.013177766 0.3193544
var250      -0.1875432344 0.2503294 -0.749185930 0.4597794
var251      -0.1735721485 0.2906428 -0.597200849 0.5550079
var252       0.2886948591 0.2512542  1.149015262 0.2599386
var253       0.1467087046 0.2485217  0.590325564 0.5595449
var254      -0.0834815473 0.2384597 -0.350086644 0.7288036
var255      -0.0635576566 0.2733631 -0.232502667 0.8177807
var256      -0.0346030600 0.3391339 -0.102033634 0.9194322
var257      -0.1224921370 0.1991311 -0.615133252 0.5432640
var258      -0.2423169128 0.2163175 -1.120191176 0.2718240
var259      -0.0021922047 0.2169919 -0.010102701 0.9920085
var260      -0.0818789537 0.2213754 -0.369864799 0.7141707
var261      -0.0707600938 0.2111357 -0.335140308 0.7399315
var262      -0.3301726263 0.2521985 -1.309177801 0.2007530
var263      -0.2602526557 0.2351244 -1.106872336 0.2774464
var264      -0.1427837485 0.2547866 -0.560405290 0.5795071
var265      -0.1315034492 0.2038109 -0.645222811 0.5238552
var266       0.1292166855 0.1857550  0.695629819 0.4921980
var267       0.0265412839 0.2291648  0.115817440 0.9085955
var268       0.1111883441 0.2630197  0.422737718 0.6756049
var269       0.1302021867 0.2400981  0.542287436 0.5917637
var270      -0.0923837589 0.2552903 -0.361877334 0.7200673
var271      -0.0680064479 0.2072222 -0.328181232 0.7451325
var272      -0.1776069310 0.2287416 -0.776452095 0.4437692
var273      -0.0374118346 0.2277425 -0.164272515 0.8706562
var274       0.0877037245 0.2180473  0.402223481 0.6904689
var275      -0.0016240717 0.2913139 -0.005574988 0.9955900
var276       0.1670149940 0.2327284  0.717639018 0.4787213
var277       0.1542172653 0.2293724  0.672344500 0.5066864
var278      -0.0108006893 0.2634879 -0.040991220 0.9675838
var279       0.1334885400 0.2086489  0.639775940 0.5273407
var280       0.1637485211 0.2134740  0.767065523 0.4492427
var281       0.0649039066 0.1972117  0.329107849 0.7444393
var282      -0.0277897733 0.2630854 -0.105630223 0.9166030
var283       0.1978208690 0.1913322  1.033913324 0.3097222
var284       0.0984930229 0.2972660  0.331329592 0.7427780
var285      -0.1113854013 0.2238975 -0.497483952 0.6225990
var286       0.0770616839 0.2067096  0.372801690 0.7120070
var287      -0.0634971052 0.2337652 -0.271627762 0.7878326
var288       0.1652137421 0.2168261  0.761964380 0.4522341
var289      -0.0984475187 0.2827889 -0.348130788 0.7302565
var290       0.1166070472 0.1940659  0.600863259 0.5525988
var291      -0.0682754836 0.2270118 -0.300757444 0.7657452
var292       0.1016526112 0.2081493  0.488363972 0.6289646
var293      -0.2976518291 0.2175924 -1.367932916 0.1818403
var294      -0.1119627963 0.2411543 -0.464278710 0.6459147
var295       0.2734232937 0.2291048  1.193442092 0.2423685
var296      -0.1054927068 0.2409970 -0.437734561 0.6648217
var297      -0.2151298321 0.3031934 -0.709546479 0.4836518
var298       0.0208265210 0.2160796  0.096383564 0.9238789
var299       0.0882009038 0.2477594  0.355994206 0.7244217
var300       0.1604547308 0.2218983  0.723100206 0.4754104
> expect.err(try(predict(linmod.bigdat, newdata=bigdat[,1:(p-3)])), "object 'var297' not found")
Error in eval(predvars, data, env) : object 'var297' not found
Got expected error from try(predict(linmod.bigdat, newdata = bigdat[, 1:(p - 3)]))
> plot(linmod.bigdat)
> # plotmo(linmod.bigdat) # works, but commented out because slow(ish)
> # plotres(linmod.bigdat) # ditto
> 
> cat0("==check use of matrix as data in linmod.form\n")
==check use of matrix as data in linmod.form
> # linmod.form allows a matrix, lm doesn't TODO is this inconsistency what we want?
> tr.mat <- as.matrix(tr)
> cat0("class(tr.mat)=", class(tr.mat), "\n") # class(tr.mat)=matrix
class(tr.mat)=matrixarray
> expect.err(try(lm(Volume~., data=tr.mat)), "'data' must be a data.frame, not a matrix or an array")
Error in model.frame.default(formula = Volume ~ ., data = tr.mat, drop.unused.levels = TRUE) : 
  'data' must be a data.frame, not a matrix or an array
Got expected error from try(lm(Volume ~ ., data = tr.mat))
> linmod.form.Volume.mat.tr <- linmod(Volume~., data=tr.mat)
> check.lm(linmod.form.Volume.mat.tr, linmod.form.Volume.tr)
check linmod.form.Volume.mat.tr vs linmod.form.Volume.tr
> cat0("==print(summary(linmod.form.Volume.mat.tr))\n")
==print(summary(linmod.form.Volume.mat.tr))
> print(summary(linmod.form.Volume.mat.tr))
Call: linmod.formula(formula = Volume ~ ., data = tr.mat)

               Estimate    StdErr   t.value      p.value
(Intercept) -57.9876589 8.6382259 -6.712913 2.749507e-07
Girth         4.7081605 0.2642646 17.816084 8.223304e-17
Height        0.3392512 0.1301512  2.606594 1.449097e-02
> plotres(linmod.form.Volume.mat.tr)
> 
> tr.mat.no.colnames <- as.matrix(tr)
> colnames(tr.mat.no.colnames) <- NULL
> expect.err(try(linmod(Volume~., data=tr.mat.no.colnames)), "object 'Volume' not found")
Error in eval(predvars, data, env) : object 'Volume' not found
Got expected error from try(linmod(Volume ~ ., data = tr.mat.no.colnames))
> linmod.form.Volume.mat.tr.no.colnames <- linmod(V3~., data=tr.mat.no.colnames)
> check.lm(linmod.form.Volume.mat.tr.no.colnames, linmod.form.Volume.tr,
+          check.coef.names=FALSE, check.newdata=FALSE) # no check.newdata else object 'V1' not found
check linmod.form.Volume.mat.tr.no.colnames vs linmod.form.Volume.tr
> 
> # Check what happens when we change the original data used to build the model.
> # Use plotres as an example function that must figure out residuals from predict().
> 
> pr <- function(model, main=deparse(substitute(model)))
+ {
+     plotres(model, which=3, main=main) # which=3 for just the residuals plot
+ }
> cat0("==linmod.formula: change data used to build the model\n")
==linmod.formula: change data used to build the model
> 
> trees1 <- trees
> linmod.trees1 <- linmod(Volume~., data=trees1)
> # delete the saved residuals and fitted.values so plotres has to use the saved
> # call etc. to get the x and y used to build the model, and rely on predict()
> linmod.trees1$residuals <- NULL
> linmod.trees1$fitted.values <- NULL
> par(mfrow=c(3,3))
> pr(linmod.trees1)
> trees1 <- trees[, 3:1]                      # change column order in original data
> pr(linmod.trees1, "change col order")
> trees1 <- trees[1:3, ]                      # change number of rows in original data
> pr(linmod.trees1, "change nbr rows")        # TODO wrong residuals! (lm has the same issue)
> cat("call$data now refers to the changed data:\n") # lm has the same problem if called with model=FALSE
call$data now refers to the changed data:
> print(eval(linmod.trees1$call$data))
  Girth Height Volume
1   8.3     70   10.3
2   8.6     65   10.3
3   8.8     63   10.2
> cat("model.frame now returns the changed data:\n")
model.frame now returns the changed data:
> print(model.frame(linmod.trees1))
  Volume Girth Height
1   10.3   8.3     70
2   10.3   8.6     65
3   10.2   8.8     63
> trees1 <- trees[nrow(tr):1, ]               # change row order (but keep same nbr of rows)
> pr(linmod.trees1, "change row order")
> colnames(trees1) <- c("x1", "x2", "x3")     # change column names in original data
> expect.err(try(pr(linmod.trees1,
+               "change colnames")), "cannot get the original model predictors")

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: object 'Volume' not found

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(pr(linmod.trees1, "change colnames"))
> trees1 <- "garbage"
> expect.err(try(pr(linmod.trees1,
+               "trees1=\"garbage\"")), "cannot get the original model predictors")

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: object 'Volume' not found

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(pr(linmod.trees1, "trees1=\"garbage\""))
> trees1 <- 1:1000
> expect.err(try(pr(linmod.trees1,
+               "trees1=1:1000")), "cannot get the original model predictors")

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: object 'Volume' not found

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(pr(linmod.trees1, "trees1=1:1000"))
> trees1 <- NULL                              # original data no longer available
> expect.err(try(pr(linmod.trees1,
+               "trees1=NULL")), "cannot get the original model predictors")

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: object 'Volume' not found

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(pr(linmod.trees1, "trees1=NULL"))
> remove(trees1)
> expect.err(try(pr(linmod.trees1,
+               "remove(trees1)")), "cannot get the original model predictors")
Error in eval(expr, envir, enclos) : object 'trees1' not found

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: object 'Volume' not found

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(pr(linmod.trees1, "remove(trees1)"))
> 
> # similar to above, but don't delete the saved residuals and fitted.values
> trees1 <- trees
> linmod2.trees1 <- linmod(Volume~., data=trees1)
> trees1 <- trees[1:3, ]                      # change number of rows in original data
> expect.err(try(plotmo(linmod2.trees1)), "plotmo_y returned the wrong length (got 3 but expected 31)")
Error : plotmo_y returned the wrong length (got 3 but expected 31)
Got expected error from try(plotmo(linmod2.trees1))
> 
> par(org.par)
> 
> cat0("==linmod.formula(keep=TRUE): change data used to build the model\n")
==linmod.formula(keep=TRUE): change data used to build the model
> par(mfrow=c(3,3))
> trees1 <- trees
> linmod.trees1.keep <- linmod(Volume~., data=trees1, keep=TRUE)
> # delete the saved residuals and fitted.values so plotres has to use the saved
> # call etc. to get the x and y used to build the model, and rely on predict()
> linmod.trees1.keep$residuals <- NULL
> linmod.trees1.keep$fitted.values <- NULL
> pr(linmod.trees1.keep)
> trees1 <- trees[, 3:1]                      # change column order in original data
> pr(linmod.trees1.keep, "change col order")
> trees1 <- trees[1:3, ]                      # change number of rows in original data
> pr(linmod.trees1.keep, "change nbr rows")
> trees1 <- trees[nrow(tr):1, ]               # change row order (but keep same nbr of rows)
> pr(linmod.trees1.keep, "change row order")
> colnames(trees1) <- c("x1", "x2", "x3")     # change column names in original data
> pr(linmod.trees1.keep, "change colnames")
> trees1 <- NULL                              # original data no longer available
> pr(linmod.trees1.keep, "trees1=NULL")
> remove(trees1)
> pr(linmod.trees1.keep, "remove(trees1)")
> par(org.par)
> 
> cat0("==linmod.default: change data used to build the model\n")
==linmod.default: change data used to build the model
> trees1 <- trees
> x1 <- trees1[,1:2]
> y1 <- trees1[,3]
> linmod.xy <- linmod(x1, y1)
> # delete the saved residuals and fitted.values so plotres has to use the saved
> # call etc. to get the x1 and y1 used to build the model, and rely on predict()
> linmod.xy$residuals <- NULL
> linmod.xy$fitted.values <- NULL
> par(mfrow=c(3,3))
> pr(linmod.xy)
> x1 <- trees1[,2:1]                 # change column order in original x1
> pr(linmod.xy, "change col order")
> x1 <- trees1[1:3, 1:2]                      # change number of rows in original x1
> expect.err(try(pr(linmod.xy, "change nbr rows")),
+               "plotmo_y returned the wrong length (got 31 but expected 3)") # TODO different behaviour to linmod.trees1
Error : plotmo_y returned the wrong length (got 31 but expected 3)
Got expected error from try(pr(linmod.xy, "change nbr rows"))
> cat("call$x1 now refers to the changed x1:\n") # lm has the same problem if called with model=FALSE
call$x1 now refers to the changed x1:
> print(eval(linmod.xy$call$x1))
NULL
> x1 <- trees1[nrow(tr):1, 1:2]               # change row order (but keep same nbr of rows)
> pr(linmod.xy, "change row order")
> x1 <- trees1[,1:2]
> colnames(x1) <- c("x1", "x2")     # change column names in original x1
> pr(linmod.xy, "change colnames")
> x1 <- "garbage"
> expect.err(try(pr(linmod.xy, "x1=\"garbage\"")), "cannot get the original model predictors")

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: no formula in getCall(object)

(3) getCall(object)$x: garbage

Error : cannot get the original model predictors
Got expected error from try(pr(linmod.xy, "x1=\"garbage\""))
> x1 <- 1:1000
> expect.err(try(pr(linmod.xy, "x1=1:1000")), "ncol(newdata) is 1 but should be 2")

stats::predict(linmod.object, data.frame[3,1], type="response")

Error in predict.linmod(structure(list(coefficients = c(`(Intercept)` = -57.987658918381,  : 
  ncol(newdata) is 1 but should be 2
Got expected error from try(pr(linmod.xy, "x1=1:1000"))
> x1 <- NULL                              # original x1 no longer available
> expect.err(try(pr(linmod.xy, "x1=NULL")), "cannot get the original model predictors")

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: no formula in getCall(object)

(3) getCall(object)$x: NULL

Error : cannot get the original model predictors
Got expected error from try(pr(linmod.xy, "x1=NULL"))
> remove(x1)
> expect.err(try(pr(linmod.xy, "remove(x1)")), "cannot get the original model predictors")

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: no formula in getCall(object)

(3) getCall(object)$x: object 'x1' not found

Error : cannot get the original model predictors
Got expected error from try(pr(linmod.xy, "remove(x1)"))
> 
> # similar to above, but don't delete the saved residuals and fitted.values
> trees1 <- trees
> x1 <- trees1[,1:2]
> y1 <- trees1[,3]
> linmod.xy <- linmod(x1, y1)
> x1 <- trees1[1:3, 1:2]                      # change number of rows in original x1
> expect.err(try(plotmo(linmod2.x1)), "object 'linmod2.x1' not found") # TODO error message misleading?
Error : object 'linmod2.x1' not found
Got expected error from try(plotmo(linmod2.x1))
> 
> par(org.par)
> 
> cat0("==linmod.default(keep=TRUE): change data used to build the model\n")
==linmod.default(keep=TRUE): change data used to build the model
> par(mfrow=c(3,3))
> trees1 <- trees
> x1 <- trees1[,1:2]
> linmod.xy <- linmod(x1, y1, keep=TRUE)
> # delete the saved residuals and fitted.values so plotres has to use the saved
> # call etc. to get the x1 and y1 used to build the model, and rely on predict()
> linmod.xy$residuals <- NULL
> linmod.xy$fitted.values <- NULL
> pr(linmod.xy.keep)
> x1 <- trees1[, 2:1]                 # change column order in original x1
> pr(linmod.xy.keep, "change col order")
> x1 <- trees1[1:3, 1:2]                      # change number of rows in original x1
> pr(linmod.xy.keep, "change nbr rows")
> x1 <- trees1[nrow(tr):1, 1:2]               # change row order (but keep same nbr of rows)
> pr(linmod.xy.keep, "change row order")
> x1 <- trees1[,1:2]
> colnames(x1) <- c("x1", "x2")     # change column names in original x1
> pr(linmod.xy.keep, "change colnames")
> x1 <- NULL                              # original x1 no longer available
> pr(linmod.xy.keep, "x1=NULL")
> remove(x1)
> pr(linmod.xy.keep, "remove(x1)")
> par(org.par)
> 
> cat("==test processing a model created in a function with local data\n")
==test processing a model created in a function with local data
> 
> # pr <- function(model, main=deparse(substitute(model)))
> # {
> #     plotmo(model, degree1=1, degree2=0, pt.col=2, do.par=FALSE, main=main)
> # }
> pr <- function(model, main=deparse(substitute(model)))
+ {
+     plotres(model, which=3, main=main) # which=3 for just the residuals plot
+ }
> lm.form.func <- function(keep=FALSE)
+ {
+     local.tr <- trees[1:20,]
+     lm(Volume~., data=local.tr, model=keep)
+ }
> linmod.form.func <- function(keep=FALSE)
+ {
+     local.tr <- trees[1:20,]
+     model <- linmod(Volume~., data=local.tr, keep=keep)
+     # delete the saved residuals and fitted.values so plotres has to use the saved
+     # call etc. to get the x and y used to build the model, and rely on predict()
+     model$residuals <- NULL
+     model$fitted.values <- NULL
+     model
+ }
> linmod.xy.func <- function(keep)
+ {
+     xx <- trees[1:20,1:2]
+     yy <- trees[1:20,3]
+     model <- linmod(xx, yy, keep=keep)
+     # delete the saved residuals and fitted.values so plotres has to use the saved
+     # call etc. to get the x and y used to build the model, and rely on predict()
+     model$residuals <- NULL
+     model$fitted.values <- NULL
+     model
+ }
> par(mfrow=c(3,2))
> 
> lm.form <- lm.form.func(keep=FALSE)
> pr(lm.form)
> 
> lm.form.keep <- lm.form.func(keep=TRUE)
> pr(lm.form.keep)
> 
> linmod.form <- linmod.form.func(keep=FALSE)
> pr(linmod.form)
> 
> linmod.form.keep <- linmod.form.func(keep=TRUE)
> pr(linmod.form.keep)
> 
> linmod.xy <- linmod.xy.func(keep=FALSE)
> expect.err(try(pr(linmod.xy)), "cannot get the original model predictors")

Looked unsuccessfully for the original predictors in the following places:

(1) object$x: NULL

(2) model.frame: no formula in getCall(object)

(3) getCall(object)$x: object 'xx' not found

Error : cannot get the original model predictors
Got expected error from try(pr(linmod.xy))
> 
> linmod.xy.keep <- linmod.xy.func(keep=TRUE)
> pr(linmod.xy.keep)
> 
> par(org.par)
> 
> # test xlevels (predict with newdata using a string to represent a factor)
> data(iris)
> linmod.Sepal.Length <- linmod(Sepal.Length~Species,data=iris)
> lm.Sepal.Length     <- lm(Sepal.Length~Species,data=iris)
> predict.linmod <- predict(linmod.Sepal.Length, newdata=data.frame(Species="setosa"))
> predict.lm     <- predict(lm.Sepal.Length,     newdata=data.frame(Species="setosa"))
> stopifnot(all.equal(predict.linmod, predict.lm))
> 
> source("test.epilog.R")
