* using log directory 'd:/Rcompile/CRANpkg/local/3.6/packDAMipd.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'packDAMipd/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'packDAMipd' version '0.2.2' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'packDAMipd' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [34s] 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. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... 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 * checking for unstated dependencies in 'tests' ... OK * checking tests ... [95s] ERROR Running 'testthat.R' [95s] 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 20.274 6.762 - temperature 1 40.306 60.581 32.127 Step: AIC=4.52 expression ~ temperature Df Sum of Sq RSS AIC 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 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 63.919 182.84 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 63.840 183.68 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 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [59s] OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE