Running 'testthat.R' [101s]
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