CRAN Package Check Results for Package packDAMipd

Last updated on 2021-03-09 03:53:47 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.2 28.91 358.44 387.35 OK
r-devel-linux-x86_64-debian-gcc 0.2.2 22.55 261.65 284.20 OK
r-devel-linux-x86_64-fedora-clang 0.2.2 448.18 NOTE
r-devel-linux-x86_64-fedora-gcc 0.2.2 448.61 NOTE
r-devel-windows-ix86+x86_64 0.2.2 69.00 370.00 439.00 OK
r-devel-windows-x86_64-gcc10-UCRT 0.2.2 NOTE
r-patched-linux-x86_64 0.2.2 25.64 336.97 362.61 OK
r-patched-solaris-x86 0.2.2 601.30 NOTE
r-release-linux-x86_64 0.2.2 26.02 338.03 364.05 OK
r-release-macos-x86_64 0.2.2 NOTE
r-release-windows-ix86+x86_64 0.2.2 53.00 427.00 480.00 OK
r-oldrel-macos-x86_64 0.2.2 ERROR
r-oldrel-windows-ix86+x86_64 0.2.2 38.00 320.00 358.00 ERROR

Check Details

Version: 0.2.2
Check: package dependencies
Result: NOTE
    Imports includes 29 non-default packages.
    Importing from so many packages makes the package vulnerable to any of
    them becoming unavailable. Move as many as possible to Suggests and
    use conditionally.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.2
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 0.2.2
Check: installed package size
Result: NOTE
     installed size is 5.1Mb
     sub-directories of 1Mb or more:
     extdata 3.8Mb
Flavor: r-patched-solaris-x86

Version: 0.2.2
Check: R code for possible problems
Result: NOTE
    plot_return_residual_cox: no visible global function definition for
     ‘plot’
    plot_return_residual_survival: no visible global function definition
     for ‘plot’
    Undefined global functions or variables:
     plot
    Consider adding
     importFrom("graphics", "plot")
    to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2.2
Check: examples
Result: ERROR
    Running examples in ‘packDAMipd-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: microcosting_liquids_long
    > ### Title: Function to estimate the cost of liquids when IPD is in long
    > ### format
    > ### Aliases: microcosting_liquids_long
    >
    > ### ** Examples
    >
    > med_costs_file <- system.file("extdata", "average_unit_costs_med_brand.csv",
    + package = "packDAMipd")
    > data_file <- system.file("extdata", "medication_liq.xlsx",
    + package = "packDAMipd")
    > ind_part_data <- load_trial_data(data_file)
    > med_costs <- load_trial_data(med_costs_file)
    > conv_file <- system.file("extdata", "Med_calc.xlsx",
    + package = "packDAMipd")
    > table <- load_trial_data(conv_file)
    > names <- colnames(ind_part_data)
    > ending <- length(names)
    > ind_part_data_long <- tidyr::gather(ind_part_data, measurement, value,
    + names[2]:names[ending], factor_key = TRUE)
    > the_columns <- c("measurement", "value")
    > res <- microcosting_liquids_long(the_columns,
    + ind_part_data_long = ind_part_data_long,
    + name_med = "liq_name", brand_med = NULL, dose_med = "liq_strength",
    + unit_med = NULL, bottle_size = "liq_bottle_size",bottle_size_unit = NULL,
    + bottle_lasts = "liq_lasts",bottle_lasts_unit = NULL,preparation_dose = NULL,
    + preparation_unit = NULL,timeperiod = "4 months",unit_cost_data = med_costs,
    + unit_cost_column = "UnitCost",cost_calculated_per = "Basis",
    + strength_column = "Strength",list_of_code_names = NULL,
    + list_of_code_brand = NULL,list_of_code_dose_unit = NULL,
    + list_of_code_bottle_size_unit = NULL,list_of_code_bottle_lasts_unit = NULL,
    + list_preparation_dose_unit = NULL,eqdose_covtab = table,
    + basis_strength_unit = NULL)
    Error in microcosting_liquids_wide(ind_part_data_wide, name_med, brand_med, :
     The used dosage is not in costing table
    Calls: microcosting_liquids_long -> microcosting_liquids_wide
    Execution halted
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2.2
Check: tests
Result: ERROR
     Running ‘testthat.R’ [71s/71s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     ans$brand not equal to "a".
     'current' is not a factor
     ── Failure (test-help_cost_analysis_functions.R:15:4): testing to get the subset of data compared to list of string ──
     ans$brand not equal to "a".
     'current' is not a factor
     ── Failure (test-help_cost_analysis_functions.R:24:3): testing to get the subset of data compared to list of string ──
     ans$xx not equal to c("bb", "aa").
     'current' is not a factor
     ── Failure (test-help_parameter_estimation_survival.R:94:3): testing creating a new dataset based on given one ──
     unique(new$check) not equal to "no".
     'current' is not a factor
    
     [ FAIL 9 | WARN 0 | SKIP 0 | PASS 994 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 0.2.2
Check: tests
Result: ERROR
     Running 'testthat.R' [81s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(packDAMipd)
     >
     > test_check("packDAMipd")
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
    
     Call:
     lm(formula = gre ~ gpa, data = dataset)
    
     Residuals:
     Min 1Q Median 3Q Max
     -302.394 -62.789 -2.206 68.506 283.438
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) 192.30 47.92 4.013 7.15e-05 ***
     gpa 116.64 14.05 8.304 1.60e-15 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     Residual standard error: 106.8 on 398 degrees of freedom
     Multiple R-squared: 0.1477, Adjusted R-squared: 0.1455
     F-statistic: 68.95 on 1 and 398 DF, p-value: 1.596e-15
    
    
     ASSESSMENT OF THE LINEAR MODEL ASSUMPTIONS
     USING THE GLOBAL TEST ON 4 DEGREES-OF-FREEDOM:
     Level of Significance = 0.05
    
     Call:
     gvlma::gvlma(x = fit)
    
     Value p-value Decision
     Global Stat 2.7853 0.5944 Assumptions acceptable.
     Skewness 0.1510 0.6975 Assumptions acceptable.
     Kurtosis 0.9735 0.3238 Assumptions acceptable.
     Link Function 0.3578 0.5497 Assumptions acceptable.
     Heteroscedasticity 1.3030 0.2537 Assumptions acceptable.
     [1] "i= 1 and j = 1"
     [1] "i= 1 and j = 2"
     [1] "i= 2 and j = 1"
     [1] "i= 2 and j = 2"
     [1] "i= 3 and j = 1"
     [1] "i= 3 and j = 2"
     $stats
     [,1] [,2]
     [1,] 35.62186 37.20490
     [2,] 47.35844 48.63362
     [3,] 52.71848 51.79091
     [4,] 55.90675 58.49112
     [5,] 63.60830 65.19133
    
     $n
     [1] 109 91
    
     $conf
     [,1] [,2]
     [1,] 51.42481 50.15822
     [2,] 54.01215 53.42360
    
     $out
     numeric(0)
    
     $group
     numeric(0)
    
     $names
     [1] "female" "male"
    
    
     Call:
     lm(formula = admit ~ gpa, data = dataset)
    
     Residuals:
     Min 1Q Median 3Q Max
     -0.4507 -0.3312 -0.2531 0.5908 0.8942
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) -0.42238 0.20606 -2.050 0.041037 *
     gpa 0.21826 0.06041 3.613 0.000341 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     Residual standard error: 0.4592 on 398 degrees of freedom
     Multiple R-squared: 0.03176, Adjusted R-squared: 0.02933
     F-statistic: 13.05 on 1 and 398 DF, p-value: 0.0003412
    
    
     ASSESSMENT OF THE LINEAR MODEL ASSUMPTIONS
     USING THE GLOBAL TEST ON 4 DEGREES-OF-FREEDOM:
     Level of Significance = 0.05
    
     Call:
     gvlma::gvlma(x = fit)
    
     Value p-value Decision
     Global Stat 66.0026 1.582e-13 Assumptions NOT satisfied!
     Skewness 37.1456 1.096e-09 Assumptions NOT satisfied!
     Kurtosis 28.0492 1.183e-07 Assumptions NOT satisfied!
     Link Function 0.5683 4.509e-01 Assumptions acceptable.
     Heteroscedasticity 0.2394 6.247e-01 Assumptions acceptable.
     Start: AIC=6.76
     expression ~ temperature + treatment
    
     Df Sum of Sq RSS AIC
     - treatment 4 5.255 25.529 4.523
     <none> 20.274 6.762
     - temperature 1 40.306 60.581 32.127
    
     Step: AIC=4.52
     expression ~ temperature
    
     Df Sum of Sq RSS AIC
     <none> 25.529 4.523
     + treatment 4 5.255 20.274 6.762
     - temperature 1 219.509 245.038 59.063
    
     Call:
     lm(formula = expression ~ temperature + treatment, data = dataset)
    
     Residuals:
     Min 1Q Median 3Q Max
     -2.3417 -0.5409 0.0743 0.5725 1.6273
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) -8.0714 1.5734 -5.130 5.95e-05 ***
     temperature 0.8168 0.1329 6.146 6.59e-06 ***
     treatmentB 0.2796 0.6539 0.428 0.674
     treatmentC 0.4602 0.6573 0.700 0.492
     treatmentD 1.3629 0.6814 2.000 0.060 .
     treatmentE 1.7445 1.1304 1.543 0.139
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     Residual standard error: 1.033 on 19 degrees of freedom
     Multiple R-squared: 0.9173, Adjusted R-squared: 0.8955
     F-statistic: 42.13 on 5 and 19 DF, p-value: 1.232e-09
    
    
     ASSESSMENT OF THE LINEAR MODEL ASSUMPTIONS
     USING THE GLOBAL TEST ON 4 DEGREES-OF-FREEDOM:
     Level of Significance = 0.05
    
     Call:
     gvlma::gvlma(x = fit)
    
     Value p-value Decision
     Global Stat 11.02282 0.02631 Assumptions NOT satisfied!
     Skewness 0.44187 0.50622 Assumptions acceptable.
     Kurtosis 0.01247 0.91109 Assumptions acceptable.
     Link Function 9.42560 0.00214 Assumptions NOT satisfied!
     Heteroscedasticity 1.14288 0.28504 Assumptions acceptable.
     Start: AIC=486.34
     admit ~ gpa + gre
    
     Df Deviance AIC
     <none> 480.34 486.34
     - gpa 1 486.06 490.06
     - gre 1 486.97 490.97
     [1] "i= 1 and j = 1"
     [1] "i= 1 and j = 2"
     [1] "i= 2 and j = 1"
     [1] "i= 2 and j = 2"
     [1] "i= 3 and j = 1"
     [1] "i= 3 and j = 2"
     [1] "i= 1 and j = 1"
     [1] "i= 1 and j = 2"
     [1] "i= 2 and j = 1"
     [1] "i= 2 and j = 2"
     [1] "i= 3 and j = 1"
     [1] "i= 3 and j = 2"
     [1] "i= 1 and j = 1"
     [1] "i= 1 and j = 2"
     [1] "i= 2 and j = 1"
     [1] "i= 2 and j = 2"
     [1] "i= 3 and j = 1"
     [1] "i= 3 and j = 2"
     [1] "i= 1 and j = 1"
     [1] "i= 1 and j = 2"
     [1] "i= 2 and j = 1"
     [1] "i= 2 and j = 2"
     [1] "i= 3 and j = 1"
     [1] "i= 3 and j = 2"
     [1] "i= 1 and j = 1"
     [1] "i= 1 and j = 2"
     NULL
     NULL
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_well_to_dead2 1 well 4 dead2
     5: 5 prob_disabled_to_disabled 2 disabled 2 disabled
     6: 6 prob_disabled_to_dead 2 disabled 3 dead
     7: 7 prob_disabled_to_dead2 2 disabled 4 dead2
     8: 8 prob_dead_to_dead 3 dead 3 dead
     9: 9 prob_dead_to_dead2 3 dead 4 dead2
     10: 10 prob_dead2_to_dead2 4 dead2 4 dead2
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_well_to_well 1 well 1 well
     2: 2 prob_well_to_disabled 1 well 2 disabled
     3: 3 prob_well_to_dead 1 well 3 dead
     4: 4 prob_disabled_to_disabled 2 disabled 2 disabled
     5: 5 prob_disabled_to_dead 2 disabled 3 dead
     6: 6 prob_dead_to_dead 3 dead 3 dead
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_B_to_B 2 B 2 B
     5: 5 prob_B_to_C 2 B 3 C
     6: 6 prob_C_to_C 3 C 3 C
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_B_to_B 2 B 2 B
     5: 5 prob_B_to_C 2 B 3 C
     6: 6 prob_C_to_C 3 C 3 C
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_B_to_B 2 B 2 B
     5: 5 prob_B_to_C 2 B 3 C
     6: 6 prob_C_to_C 3 C 3 C
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_A_to_D 1 A 4 D
     5: 5 prob_B_to_B 2 B 2 B
     6: 6 prob_B_to_C 2 B 3 C
     7: 7 prob_B_to_D 2 B 4 D
     8: 8 prob_C_to_C 3 C 3 C
     9: 9 prob_C_to_D 3 C 4 D
     10: 10 prob_D_to_D 4 D 4 D
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_B_to_B 2 B 2 B
     5: 5 prob_B_to_C 2 B 3 C
     6: 6 prob_C_to_C 3 C 3 C
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_B_to_B 2 B 2 B
     5: 5 prob_B_to_C 2 B 3 C
     6: 6 prob_C_to_C 3 C 3 C
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_B_to_B 2 B 2 B
     5: 5 prob_B_to_C 2 B 3 C
     6: 6 prob_C_to_C 3 C 3 C
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_A_to_A 1 A 1 A
     2: 2 prob_A_to_B 1 A 2 B
     3: 3 prob_A_to_C 1 A 3 C
     4: 4 prob_B_to_B 2 B 2 B
     5: 5 prob_B_to_C 2 B 3 C
     6: 6 prob_C_to_C 3 C 3 C
     [1] "The transition matrix as explained"
     transition number probability name from from state to to state
     1: 1 prob_Healthy_to_Healthy 1 Healthy 1 Healthy
     2: 2 prob_Healthy_to_Dead 1 Healthy 2 Dead
     3: 3 prob_Dead_to_Healthy 2 Dead 1 Healthy
     4: 4 prob_Dead_to_Dead 2 Dead 2 Dead
     [1] "For the distributions other than gamma,the code is not equipped to\n estimate the parameters"
     [1] "For the distributions other than gamma,the code is not equipped to\n estimate the parameters"
    
     Call:
     lm(formula = admit ~ gre, data = dataset)
    
     Residuals:
     Min 1Q Median 3Q Max
     -0.4755 -0.3415 -0.2522 0.5989 0.8966
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) -0.1198407 0.1190510 -1.007 0.314722
     gre 0.0007442 0.0001988 3.744 0.000208 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     Residual standard error: 0.4587 on 398 degrees of freedom
     Multiple R-squared: 0.03402, Adjusted R-squared: 0.03159
     F-statistic: 14.02 on 1 and 398 DF, p-value: 0.0002081
    
    
     ASSESSMENT OF THE LINEAR MODEL ASSUMPTIONS
     USING THE GLOBAL TEST ON 4 DEGREES-OF-FREEDOM:
     Level of Significance = 0.05
    
     Call:
     gvlma::gvlma(x = fit)
    
     Value p-value Decision
     Global Stat 65.312437 2.212e-13 Assumptions NOT satisfied!
     Skewness 36.445627 1.570e-09 Assumptions NOT satisfied!
     Kurtosis 28.227938 1.078e-07 Assumptions NOT satisfied!
     Link Function 0.002174 9.628e-01 Assumptions acceptable.
     Heteroscedasticity 0.636699 4.249e-01 Assumptions acceptable.
    
     Call:
     lm(formula = admit ~ gre, data = dataset)
    
     Residuals:
     Min 1Q Median 3Q Max
     -0.4755 -0.3415 -0.2522 0.5989 0.8966
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) -0.1198407 0.1190510 -1.007 0.314722
     gre 0.0007442 0.0001988 3.744 0.000208 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     Residual standard error: 0.4587 on 398 degrees of freedom
     Multiple R-squared: 0.03402, Adjusted R-squared: 0.03159
     F-statistic: 14.02 on 1 and 398 DF, p-value: 0.0002081
    
    
     ASSESSMENT OF THE LINEAR MODEL ASSUMPTIONS
     USING THE GLOBAL TEST ON 4 DEGREES-OF-FREEDOM:
     Level of Significance = 0.05
    
     Call:
     gvlma::gvlma(x = fit)
    
     Value p-value Decision
     Global Stat 65.312437 2.212e-13 Assumptions NOT satisfied!
     Skewness 36.445627 1.570e-09 Assumptions NOT satisfied!
     Kurtosis 28.227938 1.078e-07 Assumptions NOT satisfied!
     Link Function 0.002174 9.628e-01 Assumptions acceptable.
     Heteroscedasticity 0.636699 4.249e-01 Assumptions acceptable.
     Start: AIC=65.77
     mpg ~ hp + wt + drat + disp
    
     Df Sum of Sq RSS AIC
     - disp 1 0.844 183.68 63.919
     <none> 182.84 65.772
     - drat 1 12.153 194.99 65.831
     - hp 1 60.916 243.75 72.974
     - wt 1 70.508 253.35 74.209
    
     Step: AIC=63.92
     mpg ~ hp + wt + drat
    
     Df Sum of Sq RSS AIC
     - drat 1 11.366 195.05 63.840
     <none> 183.68 63.919
     + disp 1 0.844 182.84 65.772
     - hp 1 85.559 269.24 74.156
     - wt 1 107.771 291.45 76.693
    
     Step: AIC=63.84
     mpg ~ hp + wt
    
     Df Sum of Sq RSS AIC
     <none> 195.05 63.840
     + drat 1 11.366 183.68 63.919
     + disp 1 0.057 194.99 65.831
     - hp 1 83.274 278.32 73.217
     - wt 1 252.627 447.67 88.427
    
     Call:
     lm(formula = mpg ~ hp + wt + drat + disp, data = dataset)
    
     Residuals:
     Min 1Q Median 3Q Max
     -3.5077 -1.9052 -0.5057 0.9821 5.6883
    
     Coefficients:
     Estimate Std. Error t value Pr(>|t|)
     (Intercept) 29.148738 6.293588 4.631 8.2e-05 ***
     hp -0.034784 0.011597 -2.999 0.00576 **
     wt -3.479668 1.078371 -3.227 0.00327 **
     drat 1.768049 1.319779 1.340 0.19153
     disp 0.003815 0.010805 0.353 0.72675
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     Residual standard error: 2.602 on 27 degrees of freedom
     Multiple R-squared: 0.8376, Adjusted R-squared: 0.8136
     F-statistic: 34.82 on 4 and 27 DF, p-value: 2.704e-10
    
    
     ASSESSMENT OF THE LINEAR MODEL ASSUMPTIONS
     USING THE GLOBAL TEST ON 4 DEGREES-OF-FREEDOM:
     Level of Significance = 0.05
    
     Call:
     gvlma::gvlma(x = fit)
    
     Value p-value Decision
     Global Stat 13.93816 0.007495 Assumptions NOT satisfied!
     Skewness 4.31310 0.037820 Assumptions NOT satisfied!
     Kurtosis 0.01378 0.906542 Assumptions acceptable.
     Link Function 8.71658 0.003153 Assumptions NOT satisfied!
     Heteroscedasticity 0.89470 0.344207 Assumptions acceptable.
     == Failed tests ================================================================
     -- Failure (test-3a_trialdata_analysis_input_functions.R:154:3): testing get the coding values of a column in data --
     ans$variable not equal to "arm".
     'current' is not a factor
     -- Failure (test-3a_trialdata_analysis_input_functions.R:155:3): testing get the coding values of a column in data --
     ans$nonrescode not equal to "999".
     'current' is not a factor
     -- Failure (test-3a_trialdata_analysis_input_functions.R:161:3): testing get the coding values of a column in data --
     ans$variable not equal to "arm".
     'current' is not a factor
     -- Error (test-3c_costing_medication_functions.R:1288:1): (code run outside of `test_that()`) --
     Error: The used dosage is not in costing table
     Backtrace:
     x
     1. \-packDAMipd::microcosting_liquids_wide(...) test-3c_costing_medication_functions.R:1288:0
     -- Failure (test-4a_deterministic_sensitivity_analysis_functions.R:233:3): testing plotting deterministic sensitivity analysis --
     the_plot$data$parameters not equal to c("cost_direct_med_B", "cost_comm_care_C").
     'current' is not a factor
     -- Failure (test-help_cost_analysis_functions.R:7:3): testing to get the subset of data compared to a string --
     ans$brand not equal to "a".
     'current' is not a factor
     -- Failure (test-help_cost_analysis_functions.R:15:4): testing to get the subset of data compared to list of string --
     ans$brand not equal to "a".
     'current' is not a factor
     -- Failure (test-help_cost_analysis_functions.R:24:3): testing to get the subset of data compared to list of string --
     ans$xx not equal to c("bb", "aa").
     'current' is not a factor
     -- Failure (test-help_parameter_estimation_survival.R:94:3): testing creating a new dataset based on given one --
     unique(new$check) not equal to "no".
     'current' is not a factor
    
     [ FAIL 9 | WARN 0 | SKIP 0 | PASS 994 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64