The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

Type: Package
Title: Clinical and Laboratory Standards Institute (CLSI) EP15-A3 Calculations
Version: 0.1.0
Maintainer: Claucio Antonio Rank Filho <claucio.filho@hitechnologies.com.br>
Description: Calculations of "EP15-A3 document. A manual for user verification of precision and estimation of bias" CLSI (2014, ISBN:1-56238-966-1).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Depends: R (≥ 4.0)
Imports: stats, dplyr, tidyr
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2023-11-10 13:01:20 UTC; claucio
Author: Claucio Antonio Rank Filho [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-10 19:43:23 UTC

Calculate bias validation interval

Description

Calculate bias validation interval

Usage

bias_validation_interval(TV, m, se_c)

Arguments

TV

True value

m

factor

se_c

SE Combined

Value

named list with the interval


Calculate the UVL factor

Description

Calculate the UVL factor

Usage

calculate_F_uvl(nsamp = 1, df, alpha = 0.05)

Arguments

nsamp

n samples in the study

df

degres of freedom

alpha

confidence level

Value

Uvl factor


Calculate ANOVA Results and Imprecision Estimates

Description

Calculate ANOVA Results and Imprecision Estimates

Usage

calculate_aov_infos(ep_15_table)

Arguments

ep_15_table

table generated from create_table_ep_15()

Value

Named list with ANOVA Results and Imprecision Estimates

Examples

calculate_aov_infos(create_table_ep_15(CLSIEP15::ferritin_long, data_type = 'long'))

Calculate bias interval from TV

Description

Calculate bias interval from TV

Usage

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

Arguments

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

Value

a named list with the defined mean, the interval significance (user mean should be in for approval), and total bias (user mean - TV)

Examples

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

Calculate degres of freedom within-lab as specified in appendix B

Description

Calculate degres of freedom within-lab as specified in appendix B

Usage

calculate_dfWL(cvr_manufacture, cvwl_manufacture, k, n0, N)

Arguments

cvr_manufacture

CV repeatability informed by the manufacturer

cvwl_manufacture

CV within-lab informed by the manufacturer

k

the number of runs

n0

the “average” number of results per run

N

the total number of replicates

Value

dfwl


Calculate degrees of freedom of SE C (SE combined) given a selected scenario and additional parameters necessary for the scenario

Description

Calculate degrees of freedom of SE C (SE combined) given a selected scenario and additional parameters necessary for the scenario

Usage

calculate_df_combined(scenario, ...)

Arguments

scenario

Scenario (A, B, C, D, E)

...

additional parameters necessary for the scenario

Value

DF


Calculate M

Description

Calculate M

Usage

calculate_m(df, conf.level = 95, nsamples = 1)

Arguments

df

degrees of freedom

conf.level

confidence interval

nsamples

number of samples

Value

m factor


Calculate n0

Description

Calculate n0

Usage

calculate_n0(long_result_table)

Arguments

long_result_table

table generated by create_table_ep_15 function

Value

The n0 number which refers to Number of Results per Run


Calculate SE combined based on SE X and SE RM

Description

Calculate SE combined based on SE X and SE RM

Usage

calculate_se_c(se_x, se_rm)

Arguments

se_x

SE X

se_rm

SE RM

Value

SE C


Calculate SE RM given a scenario and a list of additional args that can change based on the selected scenario or sub scenario

Description

Calculate SE RM given a scenario and a list of additional args that can change based on the selected scenario or sub scenario

Usage

calculate_se_rm(scenario, additional_args)

Arguments

scenario

scenario (A, B, C, D, E)

additional_args

additional arguments list

Value

SE RM


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,

Description

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,

Usage

calculate_se_rm_a_Ucoverage(U, coverage)

Arguments

U

expanded uncertainty

coverage

coverage

Value

SE RM


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”)

Description

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”)

Usage

calculate_se_rm_a_Uk(U, k)

Arguments

U

expanded uncertainty

k

coverage factor

Value

SE RM


Calculate SE RM for scenario A when f the manufacturer supplies lower and upper limits and coverage confidence interval (95 or 99...)

Description

Calculate SE RM for scenario A when f the manufacturer supplies lower and upper limits and coverage confidence interval (95 or 99...)

Usage

calculate_se_rm_a_lowerupper(upper, lower, coverage)

Arguments

upper

upper limit

lower

lower limit

coverage

coverage

Value

SE RM


Calculate SE RM for scenario A when “standard error” or “standard uncertainty” (abbreviated by lowercase “u”) or “combined standard uncertainty” (often denoted by “uC ”)

Description

Calculate SE RM for scenario A when “standard error” or “standard uncertainty” (abbreviated by lowercase “u”) or “combined standard uncertainty” (often denoted by “uC ”)

Usage

calculate_se_rm_a_u(u)

Arguments

u

“standard error” or “standard uncertainty” (abbreviated by lowercase “u”) or “combined standard uncertainty” (often denoted by “uC ”)

Value

SE RM


Calculate SE RM for scenario B or C If the reference material has a TV determined by PT or peer group results

Description

Calculate SE RM for scenario B or C If the reference material has a TV determined by PT or peer group results

Usage

calculate_se_rm_scenario_b_c(sd_rm, nlab)

Arguments

sd_rm

SD RM

nlab

number of lab or peer group results

Value

SE RM


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 estimated

Description

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 estimated

Usage

calculate_se_rm_scenario_d_e()

Value

SE RM


Calculate SE x

Description

Calculate SE x

Usage

calculate_se_x(nrun, nrep, SWL, SR)

Arguments

nrun

Run number

nrep

Number of repetitions per run n0

SWL

SWL from aov table

SR

SR from aov table

Value

SE X


Calculate upper verification limit

Description

Generic function for calculating UVL the return is a named list and cv_uvl_r and cv_uvl_wl depends on what is the input (S or CV) if the input is SR and SWL the returns is S

Usage

calculate_uvl_info(aov_return, nsamp = 1, cvr_or_sr, cvwl_or_swl)

Arguments

aov_return

Return of calculate_aov_info()

nsamp

number of samples in the experiment

cvr_or_sr

Desirable CV or S repetability

cvwl_or_swl

Desirable CV or S within-lab

Value

Named list with UVL params

Examples

 data <- create_table_ep_15(ferritin_wider)
 aov_t <- calculate_aov_infos(data)
 calculate_uvl_info(aov_t, nsamp = 5, cvr_or_sr = .43, cvwl_or_swl = .7)

Create table for precision calculations

Description

Create table for precision calculations

Usage

create_table_ep_15(data, data_type = "wider")

Arguments

data

a long or a wider data.frame with the same structure of CLSIEP15::ferritin_long or CLSIEP15::ferritin_wider

data_type

c('wider', 'long')

Value

a data.frame with renamed columns and structure adjustments

Examples

data <- create_table_ep_15(ferritin_long, data_type = "longer")

Reference of degrees of freedon based on tau given in the CLSI Manual

Description

Reference of degrees of freedon based on tau given in the CLSI Manual

Usage

dfc_references

Format

'dfc_references' A data frame with 390 rows and 4 columns:

tau

tau

df

degrees of freedon

labs

number of labs or peers

runs

number of runs

...

Source

CLSI EP15-A3


Ferrtin data used in CLSI document examples in wide format

Description

Ferrtin data used in CLSI document examples in wide format

Usage

ferritin_long

Format

'ferritin_long' A data frame with 25 rows and 3 columns:

rep

Repetition of sample

name

Run of the Runs obtained from 5 distinct days

value

result of the observation

...

Source

CLSI EP15-A3


Ferrtin data used in CLSI document examples in wide format

Description

Ferrtin data used in CLSI document examples in wide format

Usage

ferritin_wider

Format

'ferritin_wider' A data frame with 5 rows and 6 columns:

rep

Repetition of sample

Run_1, Run_2, Run_3, Run_4, Run_5

Runs from 5 distinct days

...

Source

CLSI EP15-A3

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.