Package: CLSIEP15 0.1.0

Claucio Antonio Rank Filho

CLSIEP15: Clinical and Laboratory Standards Institute (CLSI) EP15-A3 Calculations

Calculations of "EP15-A3 document. A manual for user verification of precision and estimation of bias" CLSI (2014, ISBN:1-56238-966-1).

Authors:Claucio Antonio Rank Filho [aut, cre]

CLSIEP15_0.1.0.tar.gz
CLSIEP15_0.1.0.tar.gz(r-4.5-noble)CLSIEP15_0.1.0.tar.gz(r-4.4-noble)
CLSIEP15_0.1.0.tgz(r-4.4-emscripten)CLSIEP15_0.1.0.tgz(r-4.3-emscripten)
CLSIEP15.pdf |CLSIEP15.html✨
CLSIEP15/json (API)

# Install 'CLSIEP15' in R:
install.packages('CLSIEP15', repos = 'https://cloud.r-project.org')
Datasets:
  • dfc_references - Reference of degrees of freedon based on tau given in the CLSI Manual
  • ferritin_long - Ferrtin data used in CLSI document examples in wide format
  • ferritin_wider - Ferrtin data used in CLSI document examples in wide format

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 202 downloads 4 exports 21 dependencies

Last updated 1 years agofrom:d3f73244b6. Checks:2 OK, 1 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 04 2025
R-4.5-linuxNOTEMar 04 2025
R-4.4-linuxOKMar 04 2025

Exports:calculate_aov_infoscalculate_bias_intervalcalculate_uvl_infocreate_table_ep_15

Dependencies:clicpp11dplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithr

CLSIEP15

Rendered fromCLSIEP15.Rmdusingknitr::rmarkdownon Mar 04 2025.

Last update: 2023-11-10
Started: 2023-11-10

Citation

To cite package ‘CLSIEP15’ in publications use:

Rank Filho C (2023). CLSIEP15: Clinical and Laboratory Standards Institute (CLSI) EP15-A3 Calculations. R package version 0.1.0, https://CRAN.R-project.org/package=CLSIEP15.

Corresponding BibTeX entry: 

  @Manual{,
    title = {CLSIEP15: Clinical and Laboratory Standards Institute
      (CLSI) EP15-A3 Calculations},
    author = {Claucio Antonio {Rank Filho}},
    year = {2023},
    note = {R package version 0.1.0},
    url = {https://CRAN.R-project.org/package=CLSIEP15},
  }

Readme and manuals

CLSIEP15

This package aims on Clinical and Laboratory Standards Institute (CLSI) EP15-A3 Calculations

CLSI EP15-A3 provides guidance on the user verification of precision and the estimation of bias for laboratory test methods. It outlines the steps and procedures that clinical laboratories should follow to evaluate the performance of a test method they intend to implement.

This package is a R implementation of the calculations used in the document

Install

devtools::install_github('clauciorank/CLSIEP15')

library(CLSIEP15)

Usage

Create a table in the specified format
Wider Format
rep Run_1 Run_2 Run_3 Run_4 Run_5
1 140 140 140 141 139
2 139 143 138 144 140
3 138 141 136 142 141
4 138 143 141 143 138
5 140 137 136 144 141
Long Format
rep name value
1 Run_1 140
1 Run_2 140
1 Run_3 140
1 Run_4 141
1 Run_5 139
2 Run_1 139
2 Run_2 143
2 Run_3 138
2 Run_4 144
2 Run_5 140
... ... ...

ferritin_long and ferritin_wider are provided as data in the package and can be used as example

For long format

data <- create_table_ep_15(ferritin_long, data_type = 'long')

For wide format

data <- create_table_ep_15(ferritin_wider)

Precision

Calculate Anova parameters and Imprecision Estimates

aov_t <- calculate_aov_infos(data)

If user repetibility(SR or CVR) < repetibility claim and Within-lab(SWL or CVWL) < Within-lab claim the user has verified manufacture's precision claims if not the upper verification limit (UVL) should be checked

uvl_info <- calculate_uvl_info(aov_return = aov_t, cvr_or_sr = .43, cvwl_or_swl = .7)

Where arguments are the follow:

  • aov_return: Return of calculate_aov_info()

  • nsamp: number of samples in the experiment. Default is 1

  • cvr_or_sr: Desirable CV or S repetability

  • cvwl_or_swl: Desirable CV or S within-lab

Rechek If user repetibility(SR or CVR) < UVL repetibility claim and Within-lab(SWL or CVWL) < UVL Within-lab claim

Bias

For calculating a range for acceptable bias different scenarios and subscenarios are provided by the document

calculate_bias_interval is the function used:

calculate_bias_interval( scenario, nrun, nrep, SWL, SR, nsamples, expected_mean, user_mean, ... )

These are the mandatory parameters:

  • scenario: Choosed scenario from section 3.3 of EP15-A3

  • nrun: Number of runs

  • nrep: number of repetitions per run (n0)

  • SWL: S within laboratory (obtained from anova)

  • SR: S repetability (obtained from anova)

  • nsamples: total number of samples tested usual 1

  • expected_mean: Expected mean or TV

  • user_mean: Mean of all samples (obtained from anova)

  • ... : additional parameters necessary for processing the choosed scenario

Scenario A:

Bona fide reference materials, can vary depending on the information provided by the manufacturer.

  • Sub scenario "u":
    • manufacturer supplies a "standard error," "standard uncertainty" (u), or "combined standard uncertainty" (often denoted as uC ) for the TV
  • Sub scenario "Uk":
    • manufacturer provides an "expanded uncertainty" (U) for the TV and a "coverage factor" (k)
  • Sub scenario "Ucoverage":
    • manufacturer provides an "expanded uncertainty" (U) for the TV and a "coverage percentage"
  • Sub scenario "lowerupper":
    • manufacturer provides an lower and upper limits and a "coverage percentage" (CI)
Example

calculate_bias_interval('A', subscenario = 'Uk', nrun = 7, nrep = 5, SWL = .042, SR = .032, nsamples = 2, exppected_mean = 1, user_mean = .94)

Will return

Error in calculate_se_rm(scenario, additional_args) : For the choosed scenario U and k must be supplied

So we need to pass the requested parameters:

calculate_bias_interval('A', subscenario = 'Uk', nrun = 7, nrep = 5, SWL = .042, SR = .032, nsamples = 2, expected_mean = 1, user_mean = .94, U = 140, k = 1.96)

Scenario B and C

When a reference material's total uncertainty (TV) is determined based on Proficiency Testing (PT) (B) or peer group results from an interlaboratory QC program (C)

Additional parameters necessary are sd_rm and nlab

Example

calculate_bias_interval('C', nrun = 7, nrep = 5, SWL = .042, SR = .032, nsamples = 2, expected_mean = 1, user_mean = .94, sd_rm = .05, nlab = 43)

Scenario D and E

If the TV represents a conventional quantity value (D) or When working with a commercial QC material supplied with a TV for which the standard error cannot be estimated (E)

calculate_bias_interval('E', nrun = 7, nrep = 5, SWL = .042, SR = .032, nsamples = 2, expected_mean = 1, user_mean = .94)

Bias conclusion

If the mean is inside interval object returned in calculate_bias_interval() the result is not significant and the observed bias is inside the manufacture claims

Help Manual

Help pageTopics
Calculate bias validation intervalbias_validation_interval
Calculate ANOVA Results and Imprecision Estimatescalculate_aov_infos
Calculate bias interval from TVcalculate_bias_interval
Calculate degrees of freedom of SE C (SE combined) given a selected scenario and additional parameters necessary for the scenariocalculate_df_combined
Calculate degres of freedom within-lab as specified in appendix Bcalculate_dfWL
Calculate the UVL factorcalculate_F_uvl
Calculate Mcalculate_m
Calculate n0calculate_n0
Calculate SE combined based on SE X and SE RMcalculate_se_c
Calculate SE RM given a scenario and a list of additional args that can change based on the selected scenario or sub scenariocalculate_se_rm
Calculate SE RM for scenario A when f the manufacturer supplies lower and upper limits and coverage confidence interval (95 or 99...)calculate_se_rm_a_lowerupper
Calculate SE RM for scenario A when “standard error” or “standard uncertainty” (abbreviated by lowercase “u”) or “combined standard uncertainty” (often denoted by “uC ”)calculate_se_rm_a_u
Calculate SE RM for scenario A when f the manufacturer supplies an “expanded uncertainty” (abbreviated by uppercase “U”) for the TV and coverage e.g. 95 or 99,calculate_se_rm_a_Ucoverage
Calculate SE RM for scenario A when f the manufacturer supplies an “expanded uncertainty” (abbreviated by uppercase “U”) for the TV and the “coverage factor” (abbreviated by “k”)calculate_se_rm_a_Uk
Calculate SE RM for scenario B or C If the reference material has a TV determined by PT or peer group resultscalculate_se_rm_scenario_b_c
Calculate SE RM for scenario D or E If the TV represents a conventional quantity value or When working with a commercial QC material supplied with a TV for which the standard error cannot be estimatedcalculate_se_rm_scenario_d_e
Calculate SE xcalculate_se_x
Calculate upper verification limitcalculate_uvl_info
Create table for precision calculationscreate_table_ep_15
Reference of degrees of freedon based on tau given in the CLSI Manualdfc_references
Ferrtin data used in CLSI document examples in wide formatferritin_long
Ferrtin data used in CLSI document examples in wide formatferritin_wider