Last updated on 2025-03-13 15:51:44 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.3.5 | 6.41 | 72.26 | 78.67 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.3.5 | 4.01 | 49.84 | 53.85 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.3.5 | 136.55 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.3.5 | 163.75 | ERROR | |||
| r-devel-macos-arm64 | 0.1.3.5 | 116.00 | OK | |||
| r-devel-macos-x86_64 | 0.1.3.5 | 220.00 | NOTE | |||
| r-devel-windows-x86_64 | 0.1.3.5 | 9.00 | 88.00 | 97.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.3.5 | ERROR | ||||
| r-release-linux-x86_64 | 0.1.3.5 | 6.81 | 68.14 | 74.95 | ERROR | |
| r-release-macos-arm64 | 0.1.3.5 | 127.00 | OK | |||
| r-release-macos-x86_64 | 0.1.3.5 | 220.00 | OK | |||
| r-release-windows-x86_64 | 0.1.3.5 | 9.00 | 88.00 | 97.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.1.3.5 | OK | ||||
| r-oldrel-macos-x86_64 | 0.1.3.5 | 230.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.3.5 | 11.00 | 293.00 | 304.00 | ERROR |
Version: 0.1.3.5
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘summary.spjctest.R’ ‘summary.spqtest.R’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64, r-devel-windows-x86_64
Version: 0.1.3.5
Check: examples
Result: ERROR
Running examples in ‘spqdep-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.map.test
> ### Title: Compute the QE and QI tests of Equivalence and Independence
> ### between maps
> ### Aliases: Q.map.test
>
> ### ** Examples
>
>
> # Case 1:
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> x <- cbind(cx,cy)
> listw <- spdep::nb2listw(spdep::knn2nb(
+ spdep::knearneigh(cbind(cx,cy), k = 4)))
> p <- c(1/6, 3/6, 2/6)
> rho = 0.5
> QY1 <- dgp.spq(p = p, listw = listw, rho = rho)
> rho = 0.8
> QY2 <- dgp.spq(p = p, listw = listw, rho = rho)
> dt = data.frame(QY1,QY2)
> m = 3
> r = 1
> formula <- ~ QY1 + QY2
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 264.54, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 63.928, df = 81, p-value = 0.9186
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap, ci=.6)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> summary(qmap[[1]]$mh)
Characteristics of m-surrounding:
Number of m-surrounding (R): 90
Length of m-surrounding (m): 3
Number no-symbolized observations: 12
List of no-symbolized observations:
8 62 66 69 80 85 117 122 130 146 191 199
List of the degree overlaping:
There are 2 m-surrounding that have intersection with 0 m-surrounding
There are 12 m-surrounding that have intersection with 1 m-surrounding
There are 76 m-surrounding that have intersection with 2 m-surrounding
Mean degree of overlaping: 1.8222
>
> control <- list(dtmaxknn = 20)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="permutations", control = control)
Warning in Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r, :
The ratio between the number of symbolized observations and the number of symbols is lower than 5.
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QE = 287.89, df = 26, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QI = 238.55, df = 676, p-value = 1
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations")
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QE = 292, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QI = 66.633, df = 81, p-value = 0.875
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 264.54, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 63.928, df = 81, p-value = 0.9186
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
>
> # Case 2:
> data(provinces_spain)
> # sf::sf_use_s2(FALSE)
> m = 3
> r = 1
>
> provinces_spain$Mal2Fml <- factor(provinces_spain$Mal2Fml > 100)
> levels(provinces_spain$Mal2Fml) = c("men","woman")
> provinces_spain$Coast <- factor(provinces_spain$Coast)
> levels(provinces_spain$Coast) = c("no","yes")
> formula <- ~ Coast + Mal2Fml
> qmap <- Q.map.test(formula = formula, data = provinces_spain, m = m, r = r,
+ type ="combinations")
Error in UseMethod("units") :
no applicable method for 'units' applied to an object of class "NULL"
Calls: Q.map.test -> m.surround -> rbind -> rbind -> units
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.3.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘user-guide.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 30100 bytes
Input file size = 30214 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22188
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22188
Output IDAT size = 22188 bytes (7912 bytes decrease)
Output file size = 22266 bytes (7948 bytes = 26.31% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29819 bytes
Input file size = 29933 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27237
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27237
Output IDAT size = 27237 bytes (2582 bytes decrease)
Output file size = 27315 bytes (2618 bytes = 8.75% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh prune-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28643 bytes
Input file size = 28757 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25872
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25872
Output IDAT size = 25872 bytes (2771 bytes decrease)
Output file size = 25950 bytes (2807 bytes = 9.76% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27669 bytes
Input file size = 27783 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20259
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20259
Output IDAT size = 20259 bytes (7410 bytes decrease)
Output file size = 20337 bytes (7446 bytes = 26.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21628 bytes
Input file size = 21730 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16151
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16151
Output IDAT size = 16151 bytes (5477 bytes decrease)
Output file size = 16229 bytes (5501 bytes = 25.32% decrease)
Quitting from lines 273-279 [unnamed-chunk-11] (user-guide.Rmd)
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
no applicable method for 'units' applied to an object of class "NULL"
--- failed re-building ‘user-guide.Rmd’
SUMMARY: processing the following file failed:
‘user-guide.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.3.5
Check: examples
Result: ERROR
Running examples in ‘spqdep-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.map.test
> ### Title: Compute the QE and QI tests of Equivalence and Independence
> ### between maps
> ### Aliases: Q.map.test
>
> ### ** Examples
>
>
> # Case 1:
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> x <- cbind(cx,cy)
> listw <- spdep::nb2listw(spdep::knn2nb(
+ spdep::knearneigh(cbind(cx,cy), k = 4)))
> p <- c(1/6, 3/6, 2/6)
> rho = 0.5
> QY1 <- dgp.spq(p = p, listw = listw, rho = rho)
> rho = 0.8
> QY2 <- dgp.spq(p = p, listw = listw, rho = rho)
> dt = data.frame(QY1,QY2)
> m = 3
> r = 1
> formula <- ~ QY1 + QY2
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 282.76, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 45.214, df = 81, p-value = 0.9996
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap, ci=.6)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> summary(qmap[[1]]$mh)
Characteristics of m-surrounding:
Number of m-surrounding (R): 90
Length of m-surrounding (m): 3
Number no-symbolized observations: 12
List of no-symbolized observations:
8 62 66 69 80 85 117 122 130 146 191 199
List of the degree overlaping:
There are 2 m-surrounding that have intersection with 0 m-surrounding
There are 12 m-surrounding that have intersection with 1 m-surrounding
There are 76 m-surrounding that have intersection with 2 m-surrounding
Mean degree of overlaping: 1.8222
>
> control <- list(dtmaxknn = 20)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="permutations", control = control)
Warning in Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r, :
The ratio between the number of symbolized observations and the number of symbols is lower than 5.
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QE = 292.63, df = 26, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QI = 167.17, df = 676, p-value = 1
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations")
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QE = 301.82, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QI = 49.713, df = 81, p-value = 0.9976
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 282.76, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 45.214, df = 81, p-value = 0.9996
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
>
> # Case 2:
> data(provinces_spain)
> # sf::sf_use_s2(FALSE)
> m = 3
> r = 1
>
> provinces_spain$Mal2Fml <- factor(provinces_spain$Mal2Fml > 100)
> levels(provinces_spain$Mal2Fml) = c("men","woman")
> provinces_spain$Coast <- factor(provinces_spain$Coast)
> levels(provinces_spain$Coast) = c("no","yes")
> formula <- ~ Coast + Mal2Fml
> qmap <- Q.map.test(formula = formula, data = provinces_spain, m = m, r = r,
+ type ="combinations")
Error in UseMethod("units") :
no applicable method for 'units' applied to an object of class "NULL"
Calls: Q.map.test -> m.surround -> rbind -> rbind -> units
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.3.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘user-guide.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29408 bytes
Input file size = 29522 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21786
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21786
Output IDAT size = 21786 bytes (7622 bytes decrease)
Output file size = 21864 bytes (7658 bytes = 25.94% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29819 bytes
Input file size = 29933 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27237
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27237
Output IDAT size = 27237 bytes (2582 bytes decrease)
Output file size = 27315 bytes (2618 bytes = 8.75% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh prune-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28643 bytes
Input file size = 28757 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25872
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25872
Output IDAT size = 25872 bytes (2771 bytes decrease)
Output file size = 25950 bytes (2807 bytes = 9.76% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28050 bytes
Input file size = 28164 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20490
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20490
Output IDAT size = 20490 bytes (7560 bytes decrease)
Output file size = 20568 bytes (7596 bytes = 26.97% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21573 bytes
Input file size = 21675 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16149
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16149
Output IDAT size = 16149 bytes (5424 bytes decrease)
Output file size = 16227 bytes (5448 bytes = 25.13% decrease)
Quitting from lines 273-279 [unnamed-chunk-11] (user-guide.Rmd)
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
no applicable method for 'units' applied to an object of class "NULL"
--- failed re-building ‘user-guide.Rmd’
SUMMARY: processing the following file failed:
‘user-guide.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.3.5
Check: examples
Result: ERROR
Running examples in ‘spqdep-Ex.R’ failed
The error most likely occurred in:
> ### Name: Q.map.test
> ### Title: Compute the QE and QI tests of Equivalence and Independence
> ### between maps
> ### Aliases: Q.map.test
>
> ### ** Examples
>
>
> # Case 1:
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> x <- cbind(cx,cy)
> listw <- spdep::nb2listw(spdep::knn2nb(
+ spdep::knearneigh(cbind(cx,cy), k = 4)))
> p <- c(1/6, 3/6, 2/6)
> rho = 0.5
> QY1 <- dgp.spq(p = p, listw = listw, rho = rho)
> rho = 0.8
> QY2 <- dgp.spq(p = p, listw = listw, rho = rho)
> dt = data.frame(QY1,QY2)
> m = 3
> r = 1
> formula <- ~ QY1 + QY2
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 268.44, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 71.283, df = 81, p-value = 0.7714
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap, ci=.6)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> summary(qmap[[1]]$mh)
Characteristics of m-surrounding:
Number of m-surrounding (R): 90
Length of m-surrounding (m): 3
Number no-symbolized observations: 12
List of no-symbolized observations:
8 62 66 69 80 85 117 122 130 146 191 199
List of the degree overlaping:
There are 2 m-surrounding that have intersection with 0 m-surrounding
There are 12 m-surrounding that have intersection with 1 m-surrounding
There are 76 m-surrounding that have intersection with 2 m-surrounding
Mean degree of overlaping: 1.8222
>
> control <- list(dtmaxknn = 20)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="permutations", control = control)
Warning in Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r, :
The ratio between the number of symbolized observations and the number of symbols is lower than 5.
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QE = 288.98, df = 26, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QI = 232.61, df = 676, p-value = 1
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations")
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QE = 295.63, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QI = 74.091, df = 81, p-value = 0.6937
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 268.44, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 71.283, df = 81, p-value = 0.7714
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
>
> # Case 2:
> data(provinces_spain)
> # sf::sf_use_s2(FALSE)
> m = 3
> r = 1
>
> provinces_spain$Mal2Fml <- factor(provinces_spain$Mal2Fml > 100)
> levels(provinces_spain$Mal2Fml) = c("men","woman")
> provinces_spain$Coast <- factor(provinces_spain$Coast)
> levels(provinces_spain$Coast) = c("no","yes")
> formula <- ~ Coast + Mal2Fml
> qmap <- Q.map.test(formula = formula, data = provinces_spain, m = m, r = r,
+ type ="combinations")
Error in UseMethod("units") :
no applicable method for 'units' applied to an object of class "NULL"
Calls: Q.map.test -> m.surround -> rbind -> rbind -> units
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.3.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘user-guide.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29802 bytes
Input file size = 29916 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21381
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21381
Output IDAT size = 21381 bytes (8421 bytes decrease)
Output file size = 21459 bytes (8457 bytes = 28.27% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29738 bytes
Input file size = 29852 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27111
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27111
Output IDAT size = 27111 bytes (2627 bytes decrease)
Output file size = 27189 bytes (2663 bytes = 8.92% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh prune-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28569 bytes
Input file size = 28683 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25713
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25713
Output IDAT size = 25713 bytes (2856 bytes decrease)
Output file size = 25791 bytes (2892 bytes = 10.08% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27745 bytes
Input file size = 27859 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19605
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19605
Output IDAT size = 19605 bytes (8140 bytes decrease)
Output file size = 19683 bytes (8176 bytes = 29.35% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21079 bytes
Input file size = 21181 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15069
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15069
Output IDAT size = 15069 bytes (6010 bytes decrease)
Output file size = 15147 bytes (6034 bytes = 28.49% decrease)
Quitting from lines 273-279 [unnamed-chunk-11] (user-guide.Rmd)
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
no applicable method for 'units' applied to an object of class "NULL"
--- failed re-building ‘user-guide.Rmd’
SUMMARY: processing the following file failed:
‘user-guide.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.3.5
Check: examples
Result: ERROR
Running examples in ‘spqdep-Ex.R’ failed
The error most likely occurred in:
> ### Name: Q.map.test
> ### Title: Compute the QE and QI tests of Equivalence and Independence
> ### between maps
> ### Aliases: Q.map.test
>
> ### ** Examples
>
>
> # Case 1:
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> x <- cbind(cx,cy)
> listw <- spdep::nb2listw(spdep::knn2nb(
+ spdep::knearneigh(cbind(cx,cy), k = 4)))
> p <- c(1/6, 3/6, 2/6)
> rho = 0.5
> QY1 <- dgp.spq(p = p, listw = listw, rho = rho)
> rho = 0.8
> QY2 <- dgp.spq(p = p, listw = listw, rho = rho)
> dt = data.frame(QY1,QY2)
> m = 3
> r = 1
> formula <- ~ QY1 + QY2
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 263.92, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 76.423, df = 81, p-value = 0.6232
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap, ci=.6)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> summary(qmap[[1]]$mh)
Characteristics of m-surrounding:
Number of m-surrounding (R): 90
Length of m-surrounding (m): 3
Number no-symbolized observations: 12
List of no-symbolized observations:
8 62 66 69 80 85 117 122 130 146 191 199
List of the degree overlaping:
There are 2 m-surrounding that have intersection with 0 m-surrounding
There are 12 m-surrounding that have intersection with 1 m-surrounding
There are 76 m-surrounding that have intersection with 2 m-surrounding
Mean degree of overlaping: 1.8222
>
> control <- list(dtmaxknn = 20)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="permutations", control = control)
Warning in Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r, :
The ratio between the number of symbolized observations and the number of symbols is lower than 5.
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QE = 291.46, df = 26, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QI = 215.39, df = 676, p-value = 1
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: No shared levels found between `names(values)` of the manual scale and the
data's fill values.
Warning: No shared levels found between `names(values)` of the manual scale and the
data's fill values.
Warning: No shared levels found between `names(values)` of the manual scale and the
data's fill values.
> plot(qmap[[1]]$mh)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations")
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QE = 290.69, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QI = 81.871, df = 81, p-value = 0.452
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 263.92, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 76.423, df = 81, p-value = 0.6232
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
>
> # Case 2:
> data(provinces_spain)
> # sf::sf_use_s2(FALSE)
> m = 3
> r = 1
>
> provinces_spain$Mal2Fml <- factor(provinces_spain$Mal2Fml > 100)
> levels(provinces_spain$Mal2Fml) = c("men","woman")
> provinces_spain$Coast <- factor(provinces_spain$Coast)
> levels(provinces_spain$Coast) = c("no","yes")
> formula <- ~ Coast + Mal2Fml
> qmap <- Q.map.test(formula = formula, data = provinces_spain, m = m, r = r,
+ type ="combinations")
Error in UseMethod("units") :
no applicable method for 'units' applied to an object of class "NULL"
Calls: Q.map.test -> m.surround -> rbind -> rbind -> units
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.3.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘user-guide.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28861 bytes
Input file size = 28975 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20889
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20889
Output IDAT size = 20889 bytes (7972 bytes decrease)
Output file size = 20967 bytes (8008 bytes = 27.64% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29738 bytes
Input file size = 29852 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27111
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27111
Output IDAT size = 27111 bytes (2627 bytes decrease)
Output file size = 27189 bytes (2663 bytes = 8.92% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh prune-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28569 bytes
Input file size = 28683 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25713
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25713
Output IDAT size = 25713 bytes (2856 bytes decrease)
Output file size = 25791 bytes (2892 bytes = 10.08% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27839 bytes
Input file size = 27953 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19630
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19630
Output IDAT size = 19630 bytes (8209 bytes decrease)
Output file size = 19708 bytes (8245 bytes = 29.50% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21502 bytes
Input file size = 21604 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15356
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15356
Output IDAT size = 15356 bytes (6146 bytes decrease)
Output file size = 15434 bytes (6170 bytes = 28.56% decrease)
Quitting from lines 273-279 [unnamed-chunk-11] (user-guide.Rmd)
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
no applicable method for 'units' applied to an object of class "NULL"
--- failed re-building ‘user-guide.Rmd’
SUMMARY: processing the following file failed:
‘user-guide.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.3.5
Check: examples
Result: ERROR
Running examples in 'spqdep-Ex.R' failed
The error most likely occurred in:
> ### Name: Q.map.test
> ### Title: Compute the QE and QI tests of Equivalence and Independence
> ### between maps
> ### Aliases: Q.map.test
>
> ### ** Examples
>
>
> # Case 1:
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> x <- cbind(cx,cy)
> listw <- spdep::nb2listw(spdep::knn2nb(
+ spdep::knearneigh(cbind(cx,cy), k = 4)))
> p <- c(1/6, 3/6, 2/6)
> rho = 0.5
> QY1 <- dgp.spq(p = p, listw = listw, rho = rho)
> rho = 0.8
> QY2 <- dgp.spq(p = p, listw = listw, rho = rho)
> dt = data.frame(QY1,QY2)
> m = 3
> r = 1
> formula <- ~ QY1 + QY2
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 262.38, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 63.021, df = 81, p-value = 0.9305
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap, ci=.6)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> summary(qmap[[1]]$mh)
Characteristics of m-surrounding:
Number of m-surrounding (R): 90
Length of m-surrounding (m): 3
Number no-symbolized observations: 12
List of no-symbolized observations:
8 62 66 69 80 85 117 122 130 146 191 199
List of the degree overlaping:
There are 2 m-surrounding that have intersection with 0 m-surrounding
There are 12 m-surrounding that have intersection with 1 m-surrounding
There are 76 m-surrounding that have intersection with 2 m-surrounding
Mean degree of overlaping: 1.8222
>
> control <- list(dtmaxknn = 20)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="permutations", control = control)
Warning in Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r, :
The ratio between the number of symbolized observations and the number of symbols is lower than 5.
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QE = 284.9, df = 26, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QI = 220.69, df = 676, p-value = 1
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: No shared levels found between `names(values)` of the manual scale and the
data's fill values.
Warning: No shared levels found between `names(values)` of the manual scale and the
data's fill values.
Warning: No shared levels found between `names(values)` of the manual scale and the
data's fill values.
> plot(qmap[[1]]$mh)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations")
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QE = 284.37, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QI = 66.164, df = 81, p-value = 0.8834
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 262.38, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 63.021, df = 81, p-value = 0.9305
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
>
> # Case 2:
> data(provinces_spain)
> # sf::sf_use_s2(FALSE)
> m = 3
> r = 1
>
> provinces_spain$Mal2Fml <- factor(provinces_spain$Mal2Fml > 100)
> levels(provinces_spain$Mal2Fml) = c("men","woman")
> provinces_spain$Coast <- factor(provinces_spain$Coast)
> levels(provinces_spain$Coast) = c("no","yes")
> formula <- ~ Coast + Mal2Fml
> qmap <- Q.map.test(formula = formula, data = provinces_spain, m = m, r = r,
+ type ="combinations")
Error in UseMethod("units") :
no applicable method for 'units' applied to an object of class "NULL"
Calls: Q.map.test -> m.surround -> rbind -> rbind -> units
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.1.3.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'user-guide.Rmd' using rmarkdown
Quitting from lines 273-279 [unnamed-chunk-11] (user-guide.Rmd)
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
no applicable method for 'units' applied to an object of class "NULL"
--- failed re-building 'user-guide.Rmd'
SUMMARY: processing the following file failed:
'user-guide.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.1.3.5
Check: examples
Result: ERROR
Running examples in ‘spqdep-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.map.test
> ### Title: Compute the QE and QI tests of Equivalence and Independence
> ### between maps
> ### Aliases: Q.map.test
>
> ### ** Examples
>
>
> # Case 1:
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> x <- cbind(cx,cy)
> listw <- spdep::nb2listw(spdep::knn2nb(
+ spdep::knearneigh(cbind(cx,cy), k = 4)))
> p <- c(1/6, 3/6, 2/6)
> rho = 0.5
> QY1 <- dgp.spq(p = p, listw = listw, rho = rho)
> rho = 0.8
> QY2 <- dgp.spq(p = p, listw = listw, rho = rho)
> dt = data.frame(QY1,QY2)
> m = 3
> r = 1
> formula <- ~ QY1 + QY2
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 281.5, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 64.877, df = 81, p-value = 0.9047
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap, ci=.6)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> summary(qmap[[1]]$mh)
Characteristics of m-surrounding:
Number of m-surrounding (R): 90
Length of m-surrounding (m): 3
Number no-symbolized observations: 12
List of no-symbolized observations:
8 62 66 69 80 85 117 122 130 146 191 199
List of the degree overlaping:
There are 2 m-surrounding that have intersection with 0 m-surrounding
There are 12 m-surrounding that have intersection with 1 m-surrounding
There are 76 m-surrounding that have intersection with 2 m-surrounding
Mean degree of overlaping: 1.8222
>
> control <- list(dtmaxknn = 20)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="permutations", control = control)
Warning in Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r, :
The ratio between the number of symbolized observations and the number of symbols is lower than 5.
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QE = 308.8, df = 26, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QI = 221.95, df = 676, p-value = 1
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations")
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QE = 308.81, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QI = 54.928, df = 81, p-value = 0.9883
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 281.5, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 64.877, df = 81, p-value = 0.9047
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
>
> # Case 2:
> data(provinces_spain)
> # sf::sf_use_s2(FALSE)
> m = 3
> r = 1
>
> provinces_spain$Mal2Fml <- factor(provinces_spain$Mal2Fml > 100)
> levels(provinces_spain$Mal2Fml) = c("men","woman")
> provinces_spain$Coast <- factor(provinces_spain$Coast)
> levels(provinces_spain$Coast) = c("no","yes")
> formula <- ~ Coast + Mal2Fml
> qmap <- Q.map.test(formula = formula, data = provinces_spain, m = m, r = r,
+ type ="combinations")
Error in UseMethod("units") :
no applicable method for 'units' applied to an object of class "NULL"
Calls: Q.map.test -> m.surround -> rbind -> rbind -> units
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.1.3.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘user-guide.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29214 bytes
Input file size = 29328 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21494
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21494
Output IDAT size = 21494 bytes (7720 bytes decrease)
Output file size = 21572 bytes (7756 bytes = 26.45% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29819 bytes
Input file size = 29933 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27237
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27237
Output IDAT size = 27237 bytes (2582 bytes decrease)
Output file size = 27315 bytes (2618 bytes = 8.75% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh prune-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28643 bytes
Input file size = 28757 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25872
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25872
Output IDAT size = 25872 bytes (2771 bytes decrease)
Output file size = 25950 bytes (2807 bytes = 9.76% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28090 bytes
Input file size = 28204 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20527
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20527
Output IDAT size = 20527 bytes (7563 bytes decrease)
Output file size = 20605 bytes (7599 bytes = 26.94% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21599 bytes
Input file size = 21701 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16211
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16211
Output IDAT size = 16211 bytes (5388 bytes decrease)
Output file size = 16289 bytes (5412 bytes = 24.94% decrease)
Quitting from lines 273-279 [unnamed-chunk-11] (user-guide.Rmd)
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
no applicable method for 'units' applied to an object of class "NULL"
--- failed re-building ‘user-guide.Rmd’
SUMMARY: processing the following file failed:
‘user-guide.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.1.3.5
Check: examples
Result: ERROR
Running examples in ‘spqdep-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.map.test
> ### Title: Compute the QE and QI tests of Equivalence and Independence
> ### between maps
> ### Aliases: Q.map.test
>
> ### ** Examples
>
>
> # Case 1:
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> x <- cbind(cx,cy)
> listw <- spdep::nb2listw(spdep::knn2nb(
+ spdep::knearneigh(cbind(cx,cy), k = 4)))
> p <- c(1/6, 3/6, 2/6)
> rho = 0.5
> QY1 <- dgp.spq(p = p, listw = listw, rho = rho)
> rho = 0.8
> QY2 <- dgp.spq(p = p, listw = listw, rho = rho)
> dt = data.frame(QY1,QY2)
> m = 3
> r = 1
> formula <- ~ QY1 + QY2
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 260.05, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 92.202, df = 81, p-value = 0.1856
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap, ci=.6)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> summary(qmap[[1]]$mh)
Characteristics of m-surrounding:
Number of m-surrounding (R): 90
Length of m-surrounding (m): 3
Number no-symbolized observations: 12
List of no-symbolized observations:
8 62 66 69 80 85 117 122 130 146 191 199
List of the degree overlaping:
There are 2 m-surrounding that have intersection with 0 m-surrounding
There are 12 m-surrounding that have intersection with 1 m-surrounding
There are 76 m-surrounding that have intersection with 2 m-surrounding
Mean degree of overlaping: 1.8222
>
> control <- list(dtmaxknn = 20)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="permutations", control = control)
Warning in Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r, :
The ratio between the number of symbolized observations and the number of symbols is lower than 5.
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QE = 276.13, df = 26, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QI = 213.62, df = 676, p-value = 1
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations")
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QE = 285.17, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QI = 82.711, df = 81, p-value = 0.4263
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 260.05, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 92.202, df = 81, p-value = 0.1856
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
>
> # Case 2:
> data(provinces_spain)
> # sf::sf_use_s2(FALSE)
> m = 3
> r = 1
>
> provinces_spain$Mal2Fml <- factor(provinces_spain$Mal2Fml > 100)
> levels(provinces_spain$Mal2Fml) = c("men","woman")
> provinces_spain$Coast <- factor(provinces_spain$Coast)
> levels(provinces_spain$Coast) = c("no","yes")
> formula <- ~ Coast + Mal2Fml
> qmap <- Q.map.test(formula = formula, data = provinces_spain, m = m, r = r,
+ type ="combinations")
Error in UseMethod("units") :
no applicable method for 'units' applied to an object of class "NULL"
Calls: Q.map.test -> m.surround -> rbind -> rbind -> units
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.1.3.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘user-guide.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29846 bytes
Input file size = 29960 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22064
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22064
Output IDAT size = 22064 bytes (7782 bytes decrease)
Output file size = 22142 bytes (7818 bytes = 26.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29819 bytes
Input file size = 29933 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27237
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27237
Output IDAT size = 27237 bytes (2582 bytes decrease)
Output file size = 27315 bytes (2618 bytes = 8.75% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh prune-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28643 bytes
Input file size = 28757 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25872
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25872
Output IDAT size = 25872 bytes (2771 bytes decrease)
Output file size = 25950 bytes (2807 bytes = 9.76% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28173 bytes
Input file size = 28287 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20549
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20549
Output IDAT size = 20549 bytes (7624 bytes decrease)
Output file size = 20627 bytes (7660 bytes = 27.08% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21561 bytes
Input file size = 21663 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16129
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16129
Output IDAT size = 16129 bytes (5432 bytes decrease)
Output file size = 16207 bytes (5456 bytes = 25.19% decrease)
Quitting from lines 273-279 [unnamed-chunk-11] (user-guide.Rmd)
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
no applicable method for 'units' applied to an object of class "NULL"
--- failed re-building ‘user-guide.Rmd’
SUMMARY: processing the following file failed:
‘user-guide.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.1.3.5
Check: examples
Result: ERROR
Running examples in 'spqdep-Ex.R' failed
The error most likely occurred in:
> ### Name: Q.map.test
> ### Title: Compute the QE and QI tests of Equivalence and Independence
> ### between maps
> ### Aliases: Q.map.test
>
> ### ** Examples
>
>
> # Case 1:
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> x <- cbind(cx,cy)
> listw <- spdep::nb2listw(spdep::knn2nb(
+ spdep::knearneigh(cbind(cx,cy), k = 4)))
> p <- c(1/6, 3/6, 2/6)
> rho = 0.5
> QY1 <- dgp.spq(p = p, listw = listw, rho = rho)
> rho = 0.8
> QY2 <- dgp.spq(p = p, listw = listw, rho = rho)
> dt = data.frame(QY1,QY2)
> m = 3
> r = 1
> formula <- ~ QY1 + QY2
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 268.68, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 66.162, df = 81, p-value = 0.8835
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap, ci=.6)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> summary(qmap[[1]]$mh)
Characteristics of m-surrounding:
Number of m-surrounding (R): 90
Length of m-surrounding (m): 3
Number no-symbolized observations: 12
List of no-symbolized observations:
8 62 66 69 80 85 117 122 130 146 191 199
List of the degree overlaping:
There are 2 m-surrounding that have intersection with 0 m-surrounding
There are 12 m-surrounding that have intersection with 1 m-surrounding
There are 76 m-surrounding that have intersection with 2 m-surrounding
Mean degree of overlaping: 1.8222
>
> control <- list(dtmaxknn = 20)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="permutations", control = control)
Warning in Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r, :
The ratio between the number of symbolized observations and the number of symbols is lower than 5.
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QE = 285.57, df = 26, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QI = 194.85, df = 676, p-value = 1
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations")
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QE = 291.17, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QI = 62.022, df = 81, p-value = 0.9421
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 268.68, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 66.162, df = 81, p-value = 0.8835
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
>
> # Case 2:
> data(provinces_spain)
> # sf::sf_use_s2(FALSE)
> m = 3
> r = 1
>
> provinces_spain$Mal2Fml <- factor(provinces_spain$Mal2Fml > 100)
> levels(provinces_spain$Mal2Fml) = c("men","woman")
> provinces_spain$Coast <- factor(provinces_spain$Coast)
> levels(provinces_spain$Coast) = c("no","yes")
> formula <- ~ Coast + Mal2Fml
> qmap <- Q.map.test(formula = formula, data = provinces_spain, m = m, r = r,
+ type ="combinations")
Error in UseMethod("units") :
no applicable method for 'units' applied to an object of class "NULL"
Calls: Q.map.test -> m.surround -> rbind -> rbind -> units
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.1.3.5
Check: examples
Result: ERROR
Running examples in 'spqdep-Ex.R' failed
The error most likely occurred in:
> ### Name: Q.map.test
> ### Title: Compute the QE and QI tests of Equivalence and Independence
> ### between maps
> ### Aliases: Q.map.test
>
> ### ** Examples
>
>
> # Case 1:
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> x <- cbind(cx,cy)
> listw <- spdep::nb2listw(spdep::knn2nb(
+ spdep::knearneigh(cbind(cx,cy), k = 4)))
> p <- c(1/6, 3/6, 2/6)
> rho = 0.5
> QY1 <- dgp.spq(p = p, listw = listw, rho = rho)
> rho = 0.8
> QY2 <- dgp.spq(p = p, listw = listw, rho = rho)
> dt = data.frame(QY1,QY2)
> m = 3
> r = 1
> formula <- ~ QY1 + QY2
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 265.62, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 55.612, df = 81, p-value = 0.986
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap, ci=.6)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> summary(qmap[[1]]$mh)
Characteristics of m-surrounding:
Number of m-surrounding (R): 90
Length of m-surrounding (m): 3
Number no-symbolized observations: 12
List of no-symbolized observations:
8 62 66 69 80 85 117 122 130 146 191 199
List of the degree overlaping:
There are 2 m-surrounding that have intersection with 0 m-surrounding
There are 12 m-surrounding that have intersection with 1 m-surrounding
There are 76 m-surrounding that have intersection with 2 m-surrounding
Mean degree of overlaping: 1.8222
>
> control <- list(dtmaxknn = 20)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="permutations", control = control)
Warning in Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r, :
The ratio between the number of symbolized observations and the number of symbols is lower than 5.
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QE = 284.03, df = 26, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QI = 221.1, df = 676, p-value = 1
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: No shared levels found between `names(values)` of the manual scale and the
data's fill values.
Warning: No shared levels found between `names(values)` of the manual scale and the
data's fill values.
Warning: No shared levels found between `names(values)` of the manual scale and the
data's fill values.
> plot(qmap[[1]]$mh)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations")
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QE = 292.13, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QI = 55.301, df = 81, p-value = 0.9871
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 265.62, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 55.612, df = 81, p-value = 0.986
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
>
> # Case 2:
> data(provinces_spain)
> # sf::sf_use_s2(FALSE)
> m = 3
> r = 1
>
> provinces_spain$Mal2Fml <- factor(provinces_spain$Mal2Fml > 100)
> levels(provinces_spain$Mal2Fml) = c("men","woman")
> provinces_spain$Coast <- factor(provinces_spain$Coast)
> levels(provinces_spain$Coast) = c("no","yes")
> formula <- ~ Coast + Mal2Fml
> qmap <- Q.map.test(formula = formula, data = provinces_spain, m = m, r = r,
+ type ="combinations")
Error in UseMethod("units") :
no applicable method for 'units' applied to an object of class "NULL"
Calls: Q.map.test -> m.surround -> rbind -> rbind -> units
Execution halted
Flavor: r-oldrel-windows-x86_64