OTrecod

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

examples

Running examples in ‘OTrecod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imput_cov
> ### Title: imput_cov()
> ### Aliases: imput_cov
> 
> ### ** Examples
> 
> # Imputation of all incomplete covariates in the table simu_data:
> data(simu_data)
> 
> # Here we keep the complete variable "Gender" in the imputation model.
> # Using MICE (REP = 3):
> imput_mice <- imput_cov(simu_data,
+   indcol = 4:8, R_mice = 3,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm")
+ )
> summary(imput_mice)
            Length Class      Mode     
RAW         8      data.frame list     
IMPUTE      1      -none-     character
DATA_IMPUTE 5      data.frame list     
MICE_IMPS   3      mild       list     
> 
> 
> # Using FAMD (NB_COMP = 3):
> imput_famd <- imput_cov(simu_data,
+   indcol = 4:8,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm"),
+   missMDA = TRUE
+ )
Error in svd(A) : infinite or missing values in 'x'
Calls: imput_cov ... imputeMFA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted

tests

Running ‘testthat.R’ [43s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OTrecod)
  > 
  > test_check("OTrecod")
  Saving _problems/test-imput-cov-48.R
  Saving _problems/test-merge_dbs-73.R
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-imput-cov.R:45:3'): famd works ─────────────────────────────────
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::imput_cov(...) at test-imput-cov.R:45:3
   2.   └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   3.     └─missMDA::imputeMFA(...)
   4.       └─missMDA (local) impute(...)
   5.         └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   6.           └─irlba::irlba(X, nu = ncp, nv = ncp)
   7.             └─base::svd(A)
  ── Error ('test-merge_dbs.R:68:3'): the dimensions of the output objects are validated ──
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::merge_dbs(...) at test-merge_dbs.R:68:3
   2.   └─OTrecod::imput_cov(...)
   3.     └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   4.       └─missMDA::imputeMFA(...)
   5.         └─missMDA (local) impute(...)
   6.           └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   7.             └─irlba::irlba(X, nu = ncp, nv = ncp)
   8.               └─base::svd(A)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  Error:
  ! Test failures.
  Execution halted

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

examples

Running examples in ‘OTrecod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imput_cov
> ### Title: imput_cov()
> ### Aliases: imput_cov
> 
> ### ** Examples
> 
> # Imputation of all incomplete covariates in the table simu_data:
> data(simu_data)
> 
> # Here we keep the complete variable "Gender" in the imputation model.
> # Using MICE (REP = 3):
> imput_mice <- imput_cov(simu_data,
+   indcol = 4:8, R_mice = 3,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm")
+ )
> summary(imput_mice)
            Length Class      Mode     
RAW         8      data.frame list     
IMPUTE      1      -none-     character
DATA_IMPUTE 5      data.frame list     
MICE_IMPS   3      mild       list     
> 
> 
> # Using FAMD (NB_COMP = 3):
> imput_famd <- imput_cov(simu_data,
+   indcol = 4:8,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm"),
+   missMDA = TRUE
+ )
Error in svd(A) : infinite or missing values in 'x'
Calls: imput_cov ... imputeMFA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted

tests

Running ‘testthat.R’ [27s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OTrecod)
  > 
  > test_check("OTrecod")
  Saving _problems/test-imput-cov-48.R
  Saving _problems/test-merge_dbs-73.R
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-imput-cov.R:45:3'): famd works ─────────────────────────────────
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::imput_cov(...) at test-imput-cov.R:45:3
   2.   └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   3.     └─missMDA::imputeMFA(...)
   4.       └─missMDA (local) impute(...)
   5.         └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   6.           └─irlba::irlba(X, nu = ncp, nv = ncp)
   7.             └─base::svd(A)
  ── Error ('test-merge_dbs.R:68:3'): the dimensions of the output objects are validated ──
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::merge_dbs(...) at test-merge_dbs.R:68:3
   2.   └─OTrecod::imput_cov(...)
   3.     └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   4.       └─missMDA::imputeMFA(...)
   5.         └─missMDA (local) impute(...)
   6.           └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   7.             └─irlba::irlba(X, nu = ncp, nv = ncp)
   8.               └─base::svd(A)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  Error:
  ! Test failures.
  Execution halted

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

examples

Running examples in ‘OTrecod-Ex.R’ failed
The error most likely occurred in:

> ### Name: imput_cov
> ### Title: imput_cov()
> ### Aliases: imput_cov
> 
> ### ** Examples
> 
> # Imputation of all incomplete covariates in the table simu_data:
> data(simu_data)
> 
> # Here we keep the complete variable "Gender" in the imputation model.
> # Using MICE (REP = 3):
> imput_mice <- imput_cov(simu_data,
+   indcol = 4:8, R_mice = 3,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm")
+ )
> summary(imput_mice)
            Length Class      Mode     
RAW         8      data.frame list     
IMPUTE      1      -none-     character
DATA_IMPUTE 5      data.frame list     
MICE_IMPS   3      mild       list     
> 
> 
> # Using FAMD (NB_COMP = 3):
> imput_famd <- imput_cov(simu_data,
+   indcol = 4:8,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm"),
+   missMDA = TRUE
+ )
Error in svd(A) : infinite or missing values in 'x'
Calls: imput_cov ... imputeMFA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted

tests

Running ‘testthat.R’ [76s/203s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OTrecod)
  > 
  > test_check("OTrecod")
  Saving _problems/test-imput-cov-48.R
  Saving _problems/test-merge_dbs-73.R
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-imput-cov.R:45:3'): famd works ─────────────────────────────────
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::imput_cov(...) at test-imput-cov.R:45:3
   2.   └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   3.     └─missMDA::imputeMFA(...)
   4.       └─missMDA (local) impute(...)
   5.         └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   6.           └─irlba::irlba(X, nu = ncp, nv = ncp)
   7.             └─base::svd(A)
  ── Error ('test-merge_dbs.R:68:3'): the dimensions of the output objects are validated ──
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::merge_dbs(...) at test-merge_dbs.R:68:3
   2.   └─OTrecod::imput_cov(...)
   3.     └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   4.       └─missMDA::imputeMFA(...)
   5.         └─missMDA (local) impute(...)
   6.           └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   7.             └─irlba::irlba(X, nu = ncp, nv = ncp)
   8.               └─base::svd(A)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  Error:
  ! Test failures.
  Execution halted

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

examples

Running examples in ‘OTrecod-Ex.R’ failed
The error most likely occurred in:

> ### Name: imput_cov
> ### Title: imput_cov()
> ### Aliases: imput_cov
> 
> ### ** Examples
> 
> # Imputation of all incomplete covariates in the table simu_data:
> data(simu_data)
> 
> # Here we keep the complete variable "Gender" in the imputation model.
> # Using MICE (REP = 3):
> imput_mice <- imput_cov(simu_data,
+   indcol = 4:8, R_mice = 3,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm")
+ )
> summary(imput_mice)
            Length Class      Mode     
RAW         8      data.frame list     
IMPUTE      1      -none-     character
DATA_IMPUTE 5      data.frame list     
MICE_IMPS   3      mild       list     
> 
> 
> # Using FAMD (NB_COMP = 3):
> imput_famd <- imput_cov(simu_data,
+   indcol = 4:8,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm"),
+   missMDA = TRUE
+ )
Error in svd(A) : infinite or missing values in 'x'
Calls: imput_cov ... imputeMFA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted

tests

Running ‘testthat.R’ [68s/85s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OTrecod)
  > 
  > test_check("OTrecod")
  Saving _problems/test-imput-cov-48.R
  Saving _problems/test-merge_dbs-73.R
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-imput-cov.R:45:3'): famd works ─────────────────────────────────
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::imput_cov(...) at test-imput-cov.R:45:3
   2.   └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   3.     └─missMDA::imputeMFA(...)
   4.       └─missMDA (local) impute(...)
   5.         └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   6.           └─irlba::irlba(X, nu = ncp, nv = ncp)
   7.             └─base::svd(A)
  ── Error ('test-merge_dbs.R:68:3'): the dimensions of the output objects are validated ──
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::merge_dbs(...) at test-merge_dbs.R:68:3
   2.   └─OTrecod::imput_cov(...)
   3.     └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   4.       └─missMDA::imputeMFA(...)
   5.         └─missMDA (local) impute(...)
   6.           └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   7.             └─irlba::irlba(X, nu = ncp, nv = ncp)
   8.               └─base::svd(A)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  Error:
  ! Test failures.
  Execution halted

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

examples

Running examples in 'OTrecod-Ex.R' failed
The error most likely occurred in:

> ### Name: imput_cov
> ### Title: imput_cov()
> ### Aliases: imput_cov
> 
> ### ** Examples
> 
> # Imputation of all incomplete covariates in the table simu_data:
> data(simu_data)
> 
> # Here we keep the complete variable "Gender" in the imputation model.
> # Using MICE (REP = 3):
> imput_mice <- imput_cov(simu_data,
+   indcol = 4:8, R_mice = 3,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm")
+ )
> summary(imput_mice)
            Length Class      Mode     
RAW         8      data.frame list     
IMPUTE      1      -none-     character
DATA_IMPUTE 5      data.frame list     
MICE_IMPS   3      mild       list     
> 
> 
> # Using FAMD (NB_COMP = 3):
> imput_famd <- imput_cov(simu_data,
+   indcol = 4:8,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm"),
+   missMDA = TRUE
+ )
Error in svd(A) : infinite or missing values in 'x'
Calls: imput_cov ... imputeMFA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted

tests

Running 'testthat.R' [35s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OTrecod)
  > 
  > test_check("OTrecod")
  Saving _problems/test-imput-cov-48.R
  Saving _problems/test-merge_dbs-73.R
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-imput-cov.R:45:3'): famd works ─────────────────────────────────
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::imput_cov(...) at test-imput-cov.R:45:3
   2.   └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   3.     └─missMDA::imputeMFA(...)
   4.       └─missMDA (local) impute(...)
   5.         └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   6.           └─irlba::irlba(X, nu = ncp, nv = ncp)
   7.             └─base::svd(A)
  ── Error ('test-merge_dbs.R:68:3'): the dimensions of the output objects are validated ──
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::merge_dbs(...) at test-merge_dbs.R:68:3
   2.   └─OTrecod::imput_cov(...)
   3.     └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   4.       └─missMDA::imputeMFA(...)
   5.         └─missMDA (local) impute(...)
   6.           └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   7.             └─irlba::irlba(X, nu = ncp, nv = ncp)
   8.               └─base::svd(A)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  Error:
  ! Test failures.
  Execution halted

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

examples

Running examples in 'OTrecod-Ex.R' failed
The error most likely occurred in:

> ### Name: imput_cov
> ### Title: imput_cov()
> ### Aliases: imput_cov
> 
> ### ** Examples
> 
> # Imputation of all incomplete covariates in the table simu_data:
> data(simu_data)
> 
> # Here we keep the complete variable "Gender" in the imputation model.
> # Using MICE (REP = 3):
> imput_mice <- imput_cov(simu_data,
+   indcol = 4:8, R_mice = 3,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm")
+ )
> summary(imput_mice)
            Length Class      Mode     
RAW         8      data.frame list     
IMPUTE      1      -none-     character
DATA_IMPUTE 5      data.frame list     
MICE_IMPS   3      mild       list     
> 
> 
> # Using FAMD (NB_COMP = 3):
> imput_famd <- imput_cov(simu_data,
+   indcol = 4:8,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm"),
+   missMDA = TRUE
+ )
Error in svd(A) : infinite or missing values in 'x'
Calls: imput_cov ... imputeMFA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted

tests

Running 'testthat.R' [50s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OTrecod)
  > 
  > test_check("OTrecod")
  Saving _problems/test-imput-cov-48.R
  Saving _problems/test-merge_dbs-73.R
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-imput-cov.R:45:3'): famd works ─────────────────────────────────
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::imput_cov(...) at test-imput-cov.R:45:3
   2.   └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   3.     └─missMDA::imputeMFA(...)
   4.       └─missMDA (local) impute(...)
   5.         └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   6.           └─irlba::irlba(X, nu = ncp, nv = ncp)
   7.             └─base::svd(A)
  ── Error ('test-merge_dbs.R:68:3'): the dimensions of the output objects are validated ──
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::merge_dbs(...) at test-merge_dbs.R:68:3
   2.   └─OTrecod::imput_cov(...)
   3.     └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   4.       └─missMDA::imputeMFA(...)
   5.         └─missMDA (local) impute(...)
   6.           └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   7.             └─irlba::irlba(X, nu = ncp, nv = ncp)
   8.               └─base::svd(A)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  Error:
  ! Test failures.
  Execution halted

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

examples

Running examples in ‘OTrecod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imput_cov
> ### Title: imput_cov()
> ### Aliases: imput_cov
> 
> ### ** Examples
> 
> # Imputation of all incomplete covariates in the table simu_data:
> data(simu_data)
> 
> # Here we keep the complete variable "Gender" in the imputation model.
> # Using MICE (REP = 3):
> imput_mice <- imput_cov(simu_data,
+   indcol = 4:8, R_mice = 3,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm")
+ )
> summary(imput_mice)
            Length Class      Mode     
RAW         8      data.frame list     
IMPUTE      1      -none-     character
DATA_IMPUTE 5      data.frame list     
MICE_IMPS   3      mild       list     
> 
> 
> # Using FAMD (NB_COMP = 3):
> imput_famd <- imput_cov(simu_data,
+   indcol = 4:8,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm"),
+   missMDA = TRUE
+ )
Error in svd(A) : infinite or missing values in 'x'
Calls: imput_cov ... imputeMFA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted

tests

Running ‘testthat.R’ [41s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OTrecod)
  > 
  > test_check("OTrecod")
  Saving _problems/test-imput-cov-48.R
  Saving _problems/test-merge_dbs-73.R
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-imput-cov.R:45:3'): famd works ─────────────────────────────────
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::imput_cov(...) at test-imput-cov.R:45:3
   2.   └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   3.     └─missMDA::imputeMFA(...)
   4.       └─missMDA (local) impute(...)
   5.         └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   6.           └─irlba::irlba(X, nu = ncp, nv = ncp)
   7.             └─base::svd(A)
  ── Error ('test-merge_dbs.R:68:3'): the dimensions of the output objects are validated ──
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::merge_dbs(...) at test-merge_dbs.R:68:3
   2.   └─OTrecod::imput_cov(...)
   3.     └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   4.       └─missMDA::imputeMFA(...)
   5.         └─missMDA (local) impute(...)
   6.           └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   7.             └─irlba::irlba(X, nu = ncp, nv = ncp)
   8.               └─base::svd(A)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  Error:
  ! Test failures.
  Execution halted

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

examples

Running examples in ‘OTrecod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imput_cov
> ### Title: imput_cov()
> ### Aliases: imput_cov
> 
> ### ** Examples
> 
> # Imputation of all incomplete covariates in the table simu_data:
> data(simu_data)
> 
> # Here we keep the complete variable "Gender" in the imputation model.
> # Using MICE (REP = 3):
> imput_mice <- imput_cov(simu_data,
+   indcol = 4:8, R_mice = 3,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm")
+ )
> summary(imput_mice)
            Length Class      Mode     
RAW         8      data.frame list     
IMPUTE      1      -none-     character
DATA_IMPUTE 5      data.frame list     
MICE_IMPS   3      mild       list     
> 
> 
> # Using FAMD (NB_COMP = 3):
> imput_famd <- imput_cov(simu_data,
+   indcol = 4:8,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm"),
+   missMDA = TRUE
+ )
Error in svd(A) : infinite or missing values in 'x'
Calls: imput_cov ... imputeMFA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted

tests

Running ‘testthat.R’ [42s/73s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OTrecod)
  > 
  > test_check("OTrecod")
  Saving _problems/test-imput-cov-48.R
  Saving _problems/test-merge_dbs-73.R
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-imput-cov.R:45:3'): famd works ─────────────────────────────────
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::imput_cov(...) at test-imput-cov.R:45:3
   2.   └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   3.     └─missMDA::imputeMFA(...)
   4.       └─missMDA (local) impute(...)
   5.         └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   6.           └─irlba::irlba(X, nu = ncp, nv = ncp)
   7.             └─base::svd(A)
  ── Error ('test-merge_dbs.R:68:3'): the dimensions of the output objects are validated ──
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::merge_dbs(...) at test-merge_dbs.R:68:3
   2.   └─OTrecod::imput_cov(...)
   3.     └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   4.       └─missMDA::imputeMFA(...)
   5.         └─missMDA (local) impute(...)
   6.           └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   7.             └─irlba::irlba(X, nu = ncp, nv = ncp)
   8.               └─base::svd(A)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  Error:
  ! Test failures.
  Execution halted

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

Rd files

checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^

examples

Running examples in 'OTrecod-Ex.R' failed
The error most likely occurred in:

> ### Name: imput_cov
> ### Title: imput_cov()
> ### Aliases: imput_cov
> 
> ### ** Examples
> 
> # Imputation of all incomplete covariates in the table simu_data:
> data(simu_data)
> 
> # Here we keep the complete variable "Gender" in the imputation model.
> # Using MICE (REP = 3):
> imput_mice <- imput_cov(simu_data,
+   indcol = 4:8, R_mice = 3,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm")
+ )
> summary(imput_mice)
            Length Class      Mode     
RAW         8      data.frame list     
IMPUTE      1      -none-     character
DATA_IMPUTE 5      data.frame list     
MICE_IMPS   3      mild       list     
> 
> 
> # Using FAMD (NB_COMP = 3):
> imput_famd <- imput_cov(simu_data,
+   indcol = 4:8,
+   meth = c("logreg", "polyreg", "polr", "logreg", "pmm"),
+   missMDA = TRUE
+ )
Error in svd(A) : infinite or missing values in 'x'
Calls: imput_cov ... imputeMFA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted

tests

Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OTrecod)
  > 
  > test_check("OTrecod")
  Saving _problems/test-imput-cov-48.R
  Saving _problems/test-merge_dbs-73.R
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-imput-cov.R:45:3'): famd works ─────────────────────────────────
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::imput_cov(...) at test-imput-cov.R:45:3
   2.   └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   3.     └─missMDA::imputeMFA(...)
   4.       └─missMDA (local) impute(...)
   5.         └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   6.           └─irlba::irlba(X, nu = ncp, nv = ncp)
   7.             └─base::svd(A)
  ── Error ('test-merge_dbs.R:68:3'): the dimensions of the output objects are validated ──
  Error in `svd(A)`: infinite or missing values in 'x'
  Backtrace:
      ▆
   1. └─OTrecod::merge_dbs(...) at test-merge_dbs.R:68:3
   2.   └─OTrecod::imput_cov(...)
   3.     └─missMDA::imputeFAMD(datcov, ncp = NB_COMP, seed = seed_choice)
   4.       └─missMDA::imputeMFA(...)
   5.         └─missMDA (local) impute(...)
   6.           └─FactoMineR::svd.triplet(aux.base, row.w = row.w, ncp = 1)
   7.             └─irlba::irlba(X, nu = ncp, nv = ncp)
   8.               └─base::svd(A)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 178 ]
  Error:
  ! Test failures.
  Execution halted