Panoramica y US

require(tidyverse)

Loading required package: tidyverse
Loading tidyverse: ggplot2
Loading tidyverse: tibble
Loading tidyverse: tidyr
Loading tidyverse: readr
Loading tidyverse: purrr
Loading tidyverse: dplyr
Conflicts with tidy packages --------------------------------------------------------------------------------------
filter(): dplyr, stats
lag():    dplyr, stats

require(meta)

Loading required package: meta
Loading 'meta' package (version 4.5-0).

library("mada")

Loading required package: mvtnorm
Loading required package: ellipse
Loading required package: mvmeta
This is mvmeta 0.4.7. For an overview type: help('mvmeta-package').

Attaching package: ‘mada’

The following object is masked from ‘package:meta’:

    forest

The following object is masked from ‘package:readr’:

    spec

dataset

df <- read_csv("pano_us.csv")

Missing column names filled in: 'X1' [1]Parsed with column specification:
cols(
  .default = col_character(),
  X1 = col_integer(),
  Año = col_integer(),
  `Total Pacientes` = col_integer(),
  `Total carótidas examinadas` = col_integer(),
  `Edad mínina (años)` = col_integer(),
  `Edad máxima (años)` = col_integer(),
  `Edad promedio (años)` = col_double(),
  `Verdaderos positivos` = col_integer(),
  `Total positivos` = col_integer(),
  `Verdaderos negativos` = col_integer(),
  `Total negativos` = col_integer()
)
See spec(...) for full column specifications.

summary(df)

       X1         Estudio               Año           País           Total Pacientes Total carótidas examinadas
 Min.   :2.00   Length:2           Min.   :2014   Length:2           Min.   :35.00   Min.   : 70.0             
 1st Qu.:3.25   Class :character   1st Qu.:2014   Class :character   1st Qu.:38.75   1st Qu.: 77.5             
 Median :4.50   Mode  :character   Median :2014   Mode  :character   Median :42.50   Median : 85.0             
 Mean   :4.50                      Mean   :2014                      Mean   :42.50   Mean   : 85.0             
 3rd Qu.:5.75                      3rd Qu.:2014                      3rd Qu.:46.25   3rd Qu.: 92.5             
 Max.   :7.00                      Max.   :2014                      Max.   :50.00   Max.   :100.0             
   Mujeres            Hombres          Edad mínina (años) Edad máxima (años) Edad promedio (años)
 Length:2           Length:2           Min.   :18         Min.   :60         Min.   :41.17       
 Class :character   Class :character   1st Qu.:26         1st Qu.:66         1st Qu.:46.99       
 Mode  :character   Mode  :character   Median :34         Median :72         Median :52.81       
                                       Mean   :34         Mean   :72         Mean   :52.81       
                                       3rd Qu.:42         3rd Qu.:78         3rd Qu.:58.63       
                                       Max.   :50         Max.   :84         Max.   :64.45       
 Equipo Pano         Equipo US         Criterio Dx Pano   Criterio Dx US     Observadores Pano  Observadores US   
 Length:2           Length:2           Length:2           Length:2           Length:2           Length:2          
 Class :character   Class :character   Class :character   Class :character   Class :character   Class :character  
 Mode  :character   Mode  :character   Mode  :character   Mode  :character   Mode  :character   Mode  :character  
                                                                                                                  
                                                                                                                  
                                                                                                                  
   K intra            K inter          Verdaderos positivos Total positivos Verdaderos negativos Total negativos
 Length:2           Length:2           Min.   :11           Min.   :25      Min.   :39.00        Min.   :41.0   
 Class :character   Class :character   1st Qu.:13           1st Qu.:26      1st Qu.:47.75        1st Qu.:49.5   
 Mode  :character   Mode  :character   Median :15           Median :27      Median :56.50        Median :58.0   
                                       Mean   :15           Mean   :27      Mean   :56.50        Mean   :58.0   
                                       3rd Qu.:17           3rd Qu.:28      3rd Qu.:65.25        3rd Qu.:66.5   
                                       Max.   :19           Max.   :29      Max.   :74.00        Max.   :75.0   
 Sensibilidad Pano  Especificidad US  
 Length:2           Length:2          
 Class :character   Class :character  
 Mode  :character   Mode  :character  
                                      
                                      
                                      

colnames(df)

 [1] "X1"                         "Estudio"                    "Año"                       
 [4] "País"                       "Total Pacientes"            "Total carótidas examinadas"
 [7] "Mujeres"                    "Hombres"                    "Edad mínina (años)"        
[10] "Edad máxima (años)"         "Edad promedio (años)"       "Equipo Pano"               
[13] "Equipo US"                  "Criterio Dx Pano"           "Criterio Dx US"            
[16] "Observadores Pano"          "Observadores US"            "K intra"                   
[19] "K inter"                    "Verdaderos positivos"       "Total positivos"           
[22] "Verdaderos negativos"       "Total negativos"            "Sensibilidad Pano"         
[25] "Especificidad US"          

Confidence intervals por diagnostic measures

Sensitivity

metaprop(df$`Verdaderos positivos`, df$`Total positivos`, 
         comb.fixed = FALSE, 
         comb.random = FALSE, 
         studlab = paste(df$Estudio, df$Año))

                proportion           95%-CI
Khambete 2014       0.7600 [0.5487; 0.9064]
Brasileiro 2014     0.3793 [0.2069; 0.5774]

Number of studies: k = 2

Quantifying heterogeneity:
tau^2 = 1.1704; H = 2.72; I^2 = 86.5%

Details on meta-analytical method:
- Inverse variance method
- Logit transformation
- Clopper-Pearson confidence interval for individual studies

Specificity

metaprop(df$`Verdaderos negativos`, df$`Total negativos`, 
         comb.fixed = FALSE, 
         comb.random = FALSE, 
         studlab = paste(df$Estudio, df$Año))

                proportion           95%-CI
Khambete 2014       0.9867 [0.9279; 0.9997]
Brasileiro 2014     0.9512 [0.8347; 0.9940]

Number of studies: k = 2

Quantifying heterogeneity:
tau^2 = 0.1197; H = 1.07; I^2 = 13.5%

Details on meta-analytical method:
- Inverse variance method
- Logit transformation
- Clopper-Pearson confidence interval for individual studies

Meta-analisis Diagnostic

Odds ratio

m1

                      OR              95%-CI
Khambete 2014   149.0000 [23.5681; 941.9933]
Brasileiro 2014   9.8216 [ 2.2471;  42.9292]

Number of studies: k = 2

Quantifying heterogeneity:
tau^2 = 2.9724; H = 2.26; I^2 = 80.4%

Details on meta-analytical method:
- Mantel-Haenszel method
- Continuity correction of 0.5 in all studies

Likelihood ratio

md1 <- madad(df)

There are very few primary studies!

Muy pocos estudios para calcular el LR

Citations

citation()

To cite R in publications use:

  R Core Team (2016). R: A language and environment for statistical computing. R Foundation for
  Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2016},
    url = {https://www.R-project.org/},
  }

We have invested a lot of time and effort in creating R, please cite it when using it for data
analysis. See also ‘citation("pkgname")’ for citing R packages.

citation(package = "tidyverse", lib.loc = NULL, auto = NULL)

To cite package ‘tidyverse’ in publications use:

  Hadley Wickham (2016). tidyverse: Easily Install and Load 'Tidyverse' Packages. R package version
  1.0.0. https://CRAN.R-project.org/package=tidyverse

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {tidyverse: Easily Install and Load 'Tidyverse' Packages},
    author = {Hadley Wickham},
    year = {2016},
    note = {R package version 1.0.0},
    url = {https://CRAN.R-project.org/package=tidyverse},
  }

citation(package = "meta", lib.loc = NULL, auto = NULL)

To cite package ‘meta’ in publications use:

  Guido Schwarzer (2016). meta: General Package for Meta-Analysis. R package version 4.5-0.
  https://CRAN.R-project.org/package=meta

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {meta: General Package for Meta-Analysis},
    author = {Guido Schwarzer},
    year = {2016},
    note = {R package version 4.5-0},
    url = {https://CRAN.R-project.org/package=meta},
  }

citation(package = "mada", lib.loc = NULL, auto = NULL)

To cite package ‘mada’ in publications use:

  Philipp Doebler (2015). mada: Meta-Analysis of Diagnostic Accuracy. R package version 0.5.7.
  https://CRAN.R-project.org/package=mada

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {mada: Meta-Analysis of Diagnostic Accuracy},
    author = {Philipp Doebler},
    year = {2015},
    note = {R package version 0.5.7},
    url = {https://CRAN.R-project.org/package=mada},
  }

ATTENTION: This citation information has been auto-generated from the package DESCRIPTION file and may
need manual editing, see ‘help("citation")’.