Analyse your data

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Analyse your data

When you start to use Armadillo as a backend for DataSHIELD you can use the DSMolgenisArmadillo package for research purposes. There is a default workflow in DataSHIELD to do analysis. These are the steps that you need to take:

Authenticate

First obtain a token from the authentication server to authenticate in DataSHIELD.

# Load the necessary packages.
library(dsBaseClient)
library(DSMolgenisArmadillo)

# specify server url
armadillo_url <- "https://armadillo-demo.molgenis.net"

# get token from central authentication server
token <- armadillo.get_token(armadillo_url)
#> [1] "We're opening a browser so you can log in with code 5FW3FV"

Then build a login dataframe and perform the login on the Armadillo server. The important part is to specify the driver. This should be ArmadilloDriver.

# build the login dataframe
builder <- DSI::newDSLoginBuilder()
builder$append(
  server = "armadillo",
  url = armadillo_url,
  token = token,
  driver = "ArmadilloDriver",
  profile = "xenon",
  )

# create loginframe
login_data <- builder$build()

# login into server
conns <- DSI::datashield.login(logins = login_data, assign = FALSE)

You can append multiple servers to the login frame to perform an analysis across multiple cohorts.

Assign data

To work with DataSHIELD you need to be able to query data. You can do this by assigning data in the Armadillo service.

Assign data using expressions

You can assign values from expressions to symbols.

# assign some data to 'K'
datashield.assign.expr(conns = conns, symbol = "K", "c(10,50,100)")

# calculate the mean of 'K' to see that the assignment has worked
ds.mean("K", datasources = conns)
#> $Mean.by.Study
#>           EstimatedMean Nmissing Nvalid Ntotal
#> armadillo      53.33333        0      3      3
#> 
#> $Nstudies
#> [1] 1
#> 
#> $ValidityMessage
#>           ValidityMessage 
#> armadillo "VALID ANALYSIS"

Assign data from tables

You can check which tables (data.frame’s) are available on the Armadillo.

datashield.tables(conns)
#> $armadillo
#>  [1] "study1/2_1-core-1_0/nonrep"               "study1/2_1-core-1_0/yearlyrep"           
#>  [3] "study1/1_1-outcome-1_0/yearlyrep"         "gecko/2_1-core-1_0/trimesterrep"         
#>  [5] "gecko/2_1-core-1_0/nonrep"                "gecko/2_1-core-1_0/yearlyrep"            
#>  [7] "gecko/2_1-core-1_0/monthlyrep"            "gecko/1_1-outcome-1_0/nonrep"            
#>  [9] "gecko/1_1-outcome-1_0/yearlyrep"          "test/data/LT-example-dataset_long-format"
#> [11] "test/data/d"                              "trajectories/data/alspac"                
#> [13] "trajectories/data/chs"                    "trajectories/data/bib"                   
#> [15] "trajectories/data/bcg"                    "trajectories/data/d"                     
#> [17] "trajectories/data/probit"                 "inma/1_2_urban_ath_1_0/yearly_rep"       
#> [19] "inma/1_2_urban_ath_1_0/trimester_rep"     "inma/1_2_urban_ath_1_0/non_rep"          
#> [21] "inma/1_1_outcome_ath_1_0/trimester_rep"   "inma/1_1_outcome_ath_1_0/non_rep"        
#> [23] "inma/1_0_outcome_ath_1_0/trimester_rep"   "inma/1_0_outcome_ath_1_0/non_rep"        
#> [25] "longitools/testparquet/LT_example_data"   "longitools/mydata/nonrep"

And load data from one of these tables.

# assign table data to a symbol
datashield.assign.table(
  conns = conns,
  table = "gecko/2_1-core-1_0/nonrep",
  symbol = "core_nonrep"
)

# check the columns in the non-repeated data
ds.colnames("core_nonrep", datasources = conns)
#> $armadillo
#>   [1] "row_id"              "child_id"            "mother_id"           "cohort_id"           "preg_no"            
#>   [6] "child_no"            "coh_country"         "recruit_age"         "cob_m"               "ethn1_m"            
#>  [11] "ethn2_m"             "ethn3_m"             "agebirth_m_y"        "agebirth_m_d"        "death_m"            
#>  [16] "death_m_age"         "prepreg_weight"      "prepreg_weight_mes"  "prepreg_weight_ga"   "latepreg_weight"    
#>  [21] "latepreg_weight_mes" "latepreg_weight_ga"  "preg_gain"           "preg_gain_mes"       "height_m"           
#>  [26] "height_mes_m"        "prepreg_dia"         "preg_dia"            "preg_thyroid"        "preg_fever"         
#>  [31] "preeclam"            "preg_ht"             "asthma_m"            "prepreg_psych"       "preg_psych"         
#>  [36] "ppd"                 "prepreg_smk"         "prepreg_cig"         "preg_smk"            "preg_cig"           
#>  [41] "prepreg_alc"         "prepreg_alc_unit"    "preg_alc"            "preg_alc_unit"       "folic_prepreg"      
#>  [46] "folic_preg12"        "folic_post12"        "parity_m"            "preg_plan"           "mar"                
#>  [51] "ivf"                 "outcome"             "mode_delivery"       "plac_abrup"          "cob_p"              
#>  [56] "cob_p_fath"          "ethn1_p"             "ethn2_p"             "ethn3_p"             "ethn_p_fath"        
#>  [61] "agebirth_p_y"        "agebirth_p_d"        "agebirth_p_fath"     "death_p"             "death_p_age"        
#>  [66] "death_p_fath"        "weight_f1"           "weight_mes_f1"       "weight_f1_fath"      "height_f1"          
#>  [71] "height_mes_f1"       "height_f1_fath"      "dia_bf"              "asthma_bf"           "psych_bf"           
#>  [76] "smk_p"               "smk_cig_p"           "smk_fath"            "birth_month"         "birth_year"         
#>  [81] "apgar"               "neo_unit"            "sex"                 "plurality"           "ga_lmp"             
#>  [86] "ga_us"               "ga_mr"               "ga_bj"               "birth_weight"        "birth_length"       
#>  [91] "birth_head_circum"   "weight_who_ga"       "plac_weight"         "con_anomalies"       "major_con_anomalies"
#>  [96] "cer_palsy"           "sibling_pos"         "death_child"         "death_child_age"     "breastfed_excl"     
#> [101] "breastfed_any"       "breastfed_ever"      "solid_food"          "childcare_intro"     "cats_preg"          
#> [106] "dogs_preg"           "cats_quant_preg"     "dogs_quant_preg"

Assign data at login time

You can also specify a table in the login frame and assign the data when you login.

# build the login dataframe
builder <- DSI::newDSLoginBuilder()
builder$append(
  server = "armadillo",
  url = armadillo_url,
  token = token,
  driver = "ArmadilloDriver",
  table = "gecko/2_1-core-1_0/nonrep",
  profile = "xenon",
  )

# create loginframe
login_data <- builder$build()

# login into server
conns <- DSI::datashield.login(logins = login_data, assign = TRUE, symbol="core_nonrep")

Subsetting data

Before you are working with the data you can subset to a specific range of variables you want to use in the set.

# assign the repeated data to reshape
datashield.assign.table(
  conns = conns,
  table = "gecko/2_1-core-1_0/yearlyrep",
  symbol = "core_yearlyrep"
)

# check dimensions of repeatead measures
ds.dim("core_yearlyrep", datasources = conns)
#> $`dimensions of core_yearlyrep in armadillo`
#> [1] 19000    34
#> 
#> $`dimensions of core_yearlyrep in combined studies`
#> [1] 19000    34

# subset the data to the first 2 years
ds.dataFrameSubset(
  df.name = "core_yearlyrep",
  newobj = "core_yearlyrep_1_3",
  V1.name = "core_yearlyrep$age_years",
  V2.name = "2",
  Boolean.operator = "<="
)
#> $is.object.created
#> [1] "A data object <core_yearlyrep_1_3> has been created in all specified data sources"
#> 
#> $validity.check
#> [1] "<core_yearlyrep_1_3> appears valid in all sources"

# check the columns
ds.colnames("core_yearlyrep_1_3", datasources = conns)
#> $armadillo
#>  [1] "row_id"            "child_id"          "age_years"         "cohab_"            "occup_m_"         
#>  [6] "occupcode_m_"      "edu_m_"            "occup_f1_"         "occup_f1_fath"     "occup_f2_"        
#> [11] "occup_f2_fath"     "occupcode_f1_"     "occupcode_f1_fath" "occupcode_f2_"     "occupcode_f2_fath"
#> [16] "edu_f1_"           "edu_f1_fath"       "edu_f2_"           "edu_f2_fath"       "childcare_"       
#> [21] "childcarerel_"     "childcareprof_"    "childcarecentre_"  "smk_exp"           "pets_"            
#> [26] "cats_"             "cats_quant_"       "dogs_"             "dogs_quant_"       "mental_exp"       
#> [31] "hhincome_"         "fam_splitup"       "famsize_child"     "famsize_adult"

# check dimensions again
ds.dim("core_yearlyrep_1_3", datasources = conns)
#> $`dimensions of core_yearlyrep_1_3 in armadillo`
#> [1] 3000   34
#> 
#> $`dimensions of core_yearlyrep_1_3 in combined studies`
#> [1] 3000   34

# strip the redundant columns
ds.dataFrame(
  x = c("core_yearlyrep_1_3$child_id",
        "core_yearlyrep_1_3$age_years",
        "core_yearlyrep_1_3$dogs_",
        "core_yearlyrep_1_3$cats_",
        "core_yearlyrep_1_3$pets_"),
  completeCases = TRUE,
  newobj = "core_yearlyrep_1_3_stripped",
  datasources = conns
)
#> $is.object.created
#> [1] "A data object <core_yearlyrep_1_3_stripped> has been created in all specified data sources"
#> 
#> $validity.check
#> [1] "<core_yearlyrep_1_3_stripped> appears valid in all sources"

Transform data

In general you need 2 methods to work with data that is stored in long format, the reshape and merge functions in DataSHIELD. You can reshape data with the Armadillo to transform data from wide-format to long-format and vice versa.

You can do this using the ds.reshape function:

# reshape the data for the wide-format variables (yearlyrep)
ds.reShape(
  data.name = "core_yearlyrep_1_3_stripped",
  timevar.name = "age_years",
  idvar.name = "child_id",
  v.names = c("pets_", "cats_", "dogs_"),
  direction = "wide",
  newobj = "core_yearlyrep_1_3_wide",
  datasources = conns
)
#> $is.object.created
#> [1] "A data object <core_yearlyrep_1_3_wide> has been created in all specified data sources"
#> 
#> $validity.check
#> [1] "<core_yearlyrep_1_3_wide> appears valid in all sources"

# show the reshaped columns of the new data frame
ds.colnames("core_yearlyrep_1_3_wide", datasources = conns)
#> $armadillo
#>  [1] "child_id" "pets_.0"  "cats_.0"  "dogs_.0"  "pets_.1"  "cats_.1"  "dogs_.1"  "pets_.2"  "cats_.2"  "dogs_.2"

When you reshaped and subsetted the data you often need to merge your dataframe with others to get your analysis dataframe. You can do this using the ds.merge function:

# merge non-repeated table with wide-format repeated table
# make sure the disclosure measure regarding stringshort is set to '100'
ds.merge(
  x.name = "core_nonrep",
  y.name = "core_yearlyrep_1_3_wide",
  by.x.names = "child_id",
  by.y.names = "child_id",
  newobj = "analysis_df",
  datasources = conns
)
#> $is.object.created
#> [1] "A data object <analysis_df> has been created in all specified data sources"
#> 
#> $validity.check
#> [1] "<analysis_df> appears valid in all sources"

ds.colnames("analysis_df", datasources = conns)
#> $armadillo
#>   [1] "child_id"            "row_id"              "mother_id"           "cohort_id"           "preg_no"            
#>   [6] "child_no"            "coh_country"         "recruit_age"         "cob_m"               "ethn1_m"            
#>  [11] "ethn2_m"             "ethn3_m"             "agebirth_m_y"        "agebirth_m_d"        "death_m"            
#>  [16] "death_m_age"         "prepreg_weight"      "prepreg_weight_mes"  "prepreg_weight_ga"   "latepreg_weight"    
#>  [21] "latepreg_weight_mes" "latepreg_weight_ga"  "preg_gain"           "preg_gain_mes"       "height_m"           
#>  [26] "height_mes_m"        "prepreg_dia"         "preg_dia"            "preg_thyroid"        "preg_fever"         
#>  [31] "preeclam"            "preg_ht"             "asthma_m"            "prepreg_psych"       "preg_psych"         
#>  [36] "ppd"                 "prepreg_smk"         "prepreg_cig"         "preg_smk"            "preg_cig"           
#>  [41] "prepreg_alc"         "prepreg_alc_unit"    "preg_alc"            "preg_alc_unit"       "folic_prepreg"      
#>  [46] "folic_preg12"        "folic_post12"        "parity_m"            "preg_plan"           "mar"                
#>  [51] "ivf"                 "outcome"             "mode_delivery"       "plac_abrup"          "cob_p"              
#>  [56] "cob_p_fath"          "ethn1_p"             "ethn2_p"             "ethn3_p"             "ethn_p_fath"        
#>  [61] "agebirth_p_y"        "agebirth_p_d"        "agebirth_p_fath"     "death_p"             "death_p_age"        
#>  [66] "death_p_fath"        "weight_f1"           "weight_mes_f1"       "weight_f1_fath"      "height_f1"          
#>  [71] "height_mes_f1"       "height_f1_fath"      "dia_bf"              "asthma_bf"           "psych_bf"           
#>  [76] "smk_p"               "smk_cig_p"           "smk_fath"            "birth_month"         "birth_year"         
#>  [81] "apgar"               "neo_unit"            "sex"                 "plurality"           "ga_lmp"             
#>  [86] "ga_us"               "ga_mr"               "ga_bj"               "birth_weight"        "birth_length"       
#>  [91] "birth_head_circum"   "weight_who_ga"       "plac_weight"         "con_anomalies"       "major_con_anomalies"
#>  [96] "cer_palsy"           "sibling_pos"         "death_child"         "death_child_age"     "breastfed_excl"     
#> [101] "breastfed_any"       "breastfed_ever"      "solid_food"          "childcare_intro"     "cats_preg"          
#> [106] "dogs_preg"           "cats_quant_preg"     "dogs_quant_preg"     "pets_.0"             "cats_.0"            
#> [111] "dogs_.0"             "pets_.1"             "cats_.1"             "dogs_.1"             "pets_.2"            
#> [116] "cats_.2"             "dogs_.2"

Save your work

When you finished building your analysis frame you can save it using workspaces.

Performing analysis

There are a variety of analysis you can perform in DataSHIELD. You can perform basic methods such as summary statistics and more advanced methods such as GLM.

Simple statistical methods

You execute a summary on the a variable within you analysis frame. It will return summary statistics.

ds.summary("analysis_df$pets_.1", datasources = conns)
#> $armadillo
#> $armadillo$class
#> [1] "numeric"
#> 
#> $armadillo$length
#> [1] 1000
#> 
#> $armadillo$`quantiles & mean`
#>      5%     10%     25%     50%     75%     90%     95%    Mean 
#>   8.000  15.000  32.750  61.000  90.000 108.000 113.000  60.954

Advanced statistical methods

When you finished the analysis dataframe, you can perform the actual analysis. You can use a wide variety of functions. The example below is showing the glm.

datashield.assign.table(
  conns = conns,
  table = "gecko/1_1-outcome-1_0/nonrep",
  symbol = "outcome_nonrep"
)

armadillo_glm <- ds.glm(
  formula = "asthma_ever_CHICOS~pets_preg",
  data = "outcome_nonrep",
  family = "binomial",
  datasources = conns
)

Do the meta analysis and install prerequisites.

if (!require('metafor')) install.packages('metafor')

yi <- c(armadillo_glm$coefficients["pets_preg", "Estimate"])
sei <- c(armadillo_glm$coefficients["pets_preg", "Std. Error"])

res <- metafor::rma(yi, sei = sei)
res
#> 
#> Random-Effects Model (k = 1; tau^2 estimator: REML)
#> 
#> tau^2 (estimated amount of total heterogeneity): 0
#> tau (square root of estimated tau^2 value):      0
#> I^2 (total heterogeneity / total variability):   0.00%
#> H^2 (total variability / sampling variability):  1.00
#> 
#> Test for Heterogeneity:
#> Q(df = 0) = 0.0000, p-val = 1.0000
#> 
#> Model Results:
#> 
#> estimate      se     zval    pval    ci.lb   ci.ub    
#>  -0.1310  0.1267  -1.0343  0.3010  -0.3793  0.1173    
#> 
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
metafor::forest(res, xlab = "OR", transf = exp, refline = 1, slab = c("armadillo_glm"))

plot of chunk meta-analysis

Creating figures

You can directly create figures with the DataSHIELD methods. For example:

# create histogram
ds.histogram(x = "core_nonrep$coh_country", datasources = conns)

plot of chunk create-a-histogram

#> $breaks
#>  [1]  35.31138 116.38319 197.45500 278.52680 359.59861 440.67042 521.74222 602.81403 683.88584 764.95764 846.02945
#> 
#> $counts
#>  [1] 106 101  92 103 106 104 105 101 113  69
#> 
#> $density
#>  [1] 0.0013074829 0.0012458092 0.0011347965 0.0012704787 0.0013074829 0.0012828134 0.0012951481 0.0012458092 0.0013938261
#> [10] 0.0008510974
#> 
#> $mids
#>  [1]  75.84729 156.91909 237.99090 319.06271 400.13451 481.20632 562.27813 643.34993 724.42174 805.49355
#> 
#> $xname
#> [1] "xvect"
#> 
#> $equidist
#> [1] TRUE
#> 
#> attr(,"class")
#> [1] "histogram"

# create a heatmap
ds.heatmapPlot(x = "analysis_df$pets_.1", y = "analysis_df$dogs_.1", datasources = conns)

plot of chunk create-a-heatmap

# logout
datashield.logout(conns)

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.