Ek Esawi
2018-Dec-20 02:32 UTC
[R] Combine recursive lists in a single list or data frame and write it to file
Thank you Bert. I don't see how unlist will help. I want to combine them but keep the "rectangular structure",e.g. list, data frame, matrix because i want to get the tables in their original form. Unlist converts the whole output to a single vector; unless i am missing something. On Wed, Dec 19, 2018 at 9:10 PM Bert Gunter <bgunter.4567 at gmail.com> wrote:> > Does ?unlist not help? Why not? > > Bert > > > On Wed, Dec 19, 2018, 5:13 PM Ek Esawi <esawiek at gmail.com wrote: >> >> Hi All? >> >> I am using the R tabulizer package to extract tables from pdf files. >> The output is a set of lists of matrices. The package extracts tables >> and a lot of extra stuff which is nearly impossible to clean with >> RegEx. So, I want to clean it manually. >> To do so I need to (1) combine all lists in a single list or data >> frame and (2) then write the single entity to a text file to edit it. >> I could not figure out how. >> >> I tried something like this but did not work. >> lapply(MyTables, function(x) >> lapply(x,write.table(file="temp.txt",append = TRUE))) >> >> Any help is greatly appreciated. >> >> Here is my code: >> >> install.packages("rJava") ;library(rJava) >> install.packages("tabulizer");library(tabulizer) >> MyPath <- "C:/Users/name/Documents/tEMP" >> ExtTable <- function (Path,CalOrd){ >> FileNames <- dir(Path, pattern =".(pdf|PDF)",full.names = TRUE) >> MyFiles <- lapply(FileNames, function(i) extract_tables(i,method = "stream")) >> if(CalOrd == "Yes"){ >> MyOFiles <- gsub("(\\s.*)|(.pdf|.PDF)","",basename(FileNames)) >> MyOFiles <- match(MyOFiles,month.name) >> MyNFiles <- MyFiles[order(MyOFiles)]} >> else >> MyFiles >> } >> MyTables <- ExtTable(Path=MyPath,CalOrd = "No") >> >> Here is cleaned portion of the output: The whole output consists of 3 >> lists, each contains 12, 15, and 12 sub-lists. >> >> [[2]][[2]] >> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] >> [1,] "" "Avg." "+_ lo" "n" "Med." "" "Avg." "+_ >> lo" "n" "Med." >> [2,] "SiOz" "44.0" "1.26" "375" "44.1" "Nb" "4.8" "6.3" >> "58" "2.7" >> [3,] "T i O 2" "0.09" "0.09" "561" "0.09" "Mo(b)" "50" "30" >> "3" "35" >> [4,] "A1203" "2.27" "1.10" "375" "2.20" "Ru(b)" "12.4" "4.1" >> "3" "12" >> [5,] "FeO total" "8.43" "1.14" "375" "8.19" "Pd(b)" "3.9" "2.1" >> "19" "4.1" >> [6,] "MnO" "0.14" "0.03" "366" "0.14" "Ag(b)" "6.8" "8.3" >> "17" "4.8" >> [7,] "MgO" "41.4" "3.00" "375" "41.2" "Cd(b)" "41" "14" >> "16" "37" >> [8,] "CaO" "2.15" "1.11" "374" "2.20" "In(b)" "12" "4" >> "19" "12" >> [9,] "Na20" "0.24" "0.16" "341" "0.21" "Sn(b)" "54" "31" >> "6" "36" >> [10,] "K20" "0.054" "0.11" "330" "0.028" "Sb(b)" "3.9" "3.9" >> "11" "3.2" >> [11,] "P205" "0.056" "0.11" "233" "0.030" "Te(b)" "11" "4" >> "18" "10" >> [12,] "Total" "98.88" "" "" "98.43" "Cs(b)" "10" "16" >> "17" "1.5" >> [13,] "" "" "" "" "" "Ba" "33" "52" >> "75" "17" >> [14,] "Mg-value" "89.8" "1.1" "375" "90.0" "La" "2.60" "5.70" >> "208" "0.77" >> [15,] "Ca/AI" "1.28" "1.6" "374" "1.35" "Ce" "6.29" "11.7" >> "197" "2.08" >> [16,] "AI/Ti" "22" "29" "361" "22" "Pr" "0.56" "0.87" >> "40" "0.21" >> [17,] "F e / M n" "60" "10" "366" "59" "Nd" "2.67" "4.31" >> "162" "1.52" >> [18,] "" "" "" "" "" "Sm" "0.47" "0.69" >> "214" "0.25" >> [19,] "Li" "1.5" "0.3" "6" "1.5" "Eu" "0.16" "0.21" >> "201" "0.097" >> [20,] "B" "0.53" "0.07" "6" "0.55" "Gd" "0.60" "0.83" >> "67" "0.31" >> [21,] "C" "110" "50" "13" "93" "Tb" "0.070" >> "0.064" "146" "0.056" >> [22,] "F" "88" "71" "15" "100" "Dy" "0.51" "0.35" >> "58" "0.47" >> [23,] "S" "157" "77" "22" "152" "Ho" "0.12" "0.14" >> "54" "0.090" >> [24,] "C1" "53" "45" "15" "75" "Er" "0.30" "0.22" >> "52" "0.28" >> [25,] "Sc" "12.2" "6.4" "220" "12.0" "Tm" "0.038" >> "0.026" "40" "0.035" >> [26,] "V" "56" "21" "132" "53" "Yb" "0.26" "0.14" >> "201" "0.27" >> [27,] "Cr" "2690" "705" "325" "2690" "Lu" "0.043" >> "0.023" "172" "0.045" >> [28,] "Co" "112" "10" "166" "111" "Hf" "0.27" "0.30" >> "71" "0.17" >> [29,] "Ni" "2160" "304" "308" "2140" "Ta" "0.40" "0.51" >> "38" "0.23" >> [30,] "Cu" "11" "9" "94" "9" "W(b)" "7.2" "5.2" >> "6" "4.0" >> [31,] "Zn" "65" "20" "129" "60" "Re(b)" "0.13" "0.11" >> "18" "0.09" >> [32,] "Ga" "2.4" "1.3" "49" "2.4" "Os(b)" "4.0" "1.8" >> "18" "3.7" >> [33,] "Ge" "0.96" "0.19" "19" "0.92" "Ir(b)" "3.7" "0.9" >> "34" "3.0" >> [34,] "As" "0.11" "0.07" "7" "0.10" "Pt(b)" "7" "-" >> "1" "-" >> [35,] "Se" "0.041" "0.056" "18" "0.025" "Au(b)" "0.65" "0.53" >> "30" "0.5" >> [36,] "Br" "0.01" "0.01" "6" "0.01" "Tl(b)" "1.2" "1.0" >> "13" "0.9" >> [37,] "Rb" "1,9" "4.8" "97" "0.38" "Pb" "0.16" "0.11" >> "17" "0.16" >> [38,] "Sr" "49" "60" "110" "20" "Bi(b)" "1.7" "0.7" >> "13" "1.6" >> [39,] "Y" "4.4" "5.5" "86" "3.1" "Th*" "0.71" "1.2" >> "71" "0.22" >> [40,] "Zr" "21" "42" "82" "8.0" "U" "0.12" "0.23" >> "48" "0.040" >> [[2]][[4]] >> [,1] [,2] [,3] [,4] [,5] >> [,6] >> [1,] "" "Spinel peridotites" "" "Garnet peridotites" >> "" "Primitive" >> [2,] "" "Avg. Meal." "M-A sp" "M-A gt B-M" >> "Jordan" "mantle" >> [3,] "SiO 2" "44.0 44.1" "44.15" "44.99 45.00" >> "45.55" "44.8" >> [4,] "TiO 2" "0.09 0.09" "0.07" "0.06 0.08" >> "0.11" "0.21" >> [5,] "A1203" "2.27 2.20" "1.96" "1.40 1.31" >> "1.43" "4.45" >> [6,] "Cr203" "0.39 0.39" "0.44" "0.32 0.38" >> "0.34" "0.43" >> [7,] "FeOtotal" "8.43 8.19" "8.28" "7.89 6.97" >> "7.61" "8.40" >> [8,] "Mn O" "0.14 0.14" "0.12" "0.11 0.13" >> "0.11" "0.14" >> [9,] "MgO" "41.4 41.2" "42.25" "42.60 44.86" >> "43.55" "37.2" >> [10,] "NiO" "0.27 0.27" "0.27" "0.26 0.29" >> "-" "0.24" >> [11,] "CaO" "2.15 2.20" "2.08" "0.82 0.77" >> "1.05" "3.60" >> [12,] "Na 20" "0.24 0.21" "0.18" "0.11 0.09" >> "0.14" "0.34" >> [13,] "K 2 0" "0.054 0.028" "0.05" "0.04 0.10" >> "0.11" "0.028" >> [14,] "P205" "0.056 0.030" "0.02" "- 0.01" >> "-" "0.022" >> [15,] "Total" "99.49 99.05" "99.87" "98.60 100.00" >> "100.00" "99.86" >> [16,] "Mg-value" "89.8 90.0" "90.1" "90.6 92.0" >> "91.1" "88.8" >> [17,] "olivine" "62 63" "67" "65 68" >> "66" "56 57" >> [18,] "opx" "24 24" "22" "28 25" >> "28" "22 17" >> [19,] "cpx" "12 11" "9" "3 2" >> "3" "19 10" >> [20,] "spinel" "2 2" "2" "- -" >> "-" "3 -" >> >> Here is portion of the output for str(MyTables): >> >> str(MyTables) >> >> List of 3 >> $ :List of 12 >> $ : chr [1:3, 1:2] "south of the artificial lake Lokka. Intrusive >> complexes" "of alkaline rocks are found at Sokli (phosphorite-bear-" >> "ing and a possible Nb-occurrence) in Finland, and at" "(Eriksson, >> 1992). During this period, Northern Europe" ... >> ..$ : chr [1:55, 1:15] "Element" "Ag" "Al" "Al_XRF" ... >> ..$ : chr [1:56, 1:2] "in the till is mainly of local origin, >> although some cob-" "bles and boulders may have been transported over >> sev-" "eral kilometres. The moraine formations in the study" "area are >> mostly gravelly and sandy tills, locally hum-" ... >> ..$ : chr [1:53, 1:2] "requisites. PCA accounts for maximum variance >> of all" "variables, while FA is based on the correlation structure" >> "of the variables. The model of factor analysis allows that" "the >> common factors do not explain the total variation of" ... >> ..$ : chr [1:54, 1:7] "lished examples of the use of factor >> analysis, it is neglec-" "ted that regional geochemical (and >> environmental) data" "almost never follow a normal distribution. >> Continuing Method" "with factor analysis in such a case must lead to >> biased" ... >> ..$ : chr [1:16, 1:2] "shows the factor loadings of the different >> variables" "entering each factor. Names of variables with an abso-" >> "lute value of the loadings <0.3 are not plotted. Fig. 5" "shows 8 >> results of factor analyses using a selection of all" ... >> ..$ : chr [1:21, 1:2] "pretable results, notwithstanding the fact >> that on the" "basis of the foregoing discussion it should probably >> not" "be used with these data. Do these results warrant the use" "of a >> quite work-intensive method? Unfortunately not," ... >> ..$ : chr [1:55, 1:8] "" "Ag" "Al" "Al_XRF" ... >> ..$ : chr [1:23, 1:2] "addition, geochemical reasoning (e.g. >> geochemical asso-" "ciations and/or pathfinder elements for different >> types of" "ore deposits) was used to select further sub-sets of vari-" >> "ables. In geochemistry, the selection of elements entered" ... >> ..$ : chr [1:55, 1:2] "Fig. 10C cuts several geological units, and >> is most likely" "indicative of alteration processes related to a >> deep-" "seated fault. It was revealed again in a factor analysis" >> "carried out with all those elements extracted by aqua" ... >> ..$ : chr [1:50, 1:2] "well justified in stating that it is not very >> scientific to" "play with the selection of elements and number of >> fac-" "tors extracted until one >> ?\200\230?\200\230finds?\200\231?\200\231 an >> ?\200\230?\200\230interesting?\200\231?\200\231 result." "On the other >> hand, even all the different results pre-" ... >> ..$ : chr [1:24, 1:2] "Niemel??, J., Ekman, I., Lukashov, A. (Eds.), >> 1993. Quaternary" "Deposits of Finland and Northwestern Part of >> Russian Fed-" "eration and Their Resources 1:1,000,000. Geological >> Survey" "of Finland, Espoo, Finland." ... >> $ :List of 15 >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code.
Jim Lemon
2018-Dec-20 02:35 UTC
[R] Combine recursive lists in a single list or data frame and write it to file
Hi Ek, Look at unlist and the argument "recursive". You can step down through the levels or a nested list to convert it to a single level list. Jim On Thu, Dec 20, 2018 at 1:33 PM Ek Esawi <esawiek at gmail.com> wrote:> > Thank you Bert. I don't see how unlist will help. I want to combine > them but keep the "rectangular structure",e.g. list, data frame, > matrix because i want to get the tables in their original form. > Unlist converts the whole output to a single vector; unless i am > missing something. > > On Wed, Dec 19, 2018 at 9:10 PM Bert Gunter <bgunter.4567 at gmail.com> wrote: > > > > Does ?unlist not help? Why not? > > > > Bert > > > > > > On Wed, Dec 19, 2018, 5:13 PM Ek Esawi <esawiek at gmail.com wrote: > >> > >> Hi All? > >> > >> I am using the R tabulizer package to extract tables from pdf files. > >> The output is a set of lists of matrices. The package extracts tables > >> and a lot of extra stuff which is nearly impossible to clean with > >> RegEx. So, I want to clean it manually. > >> To do so I need to (1) combine all lists in a single list or data > >> frame and (2) then write the single entity to a text file to edit it. > >> I could not figure out how. > >> > >> I tried something like this but did not work. > >> lapply(MyTables, function(x) > >> lapply(x,write.table(file="temp.txt",append = TRUE))) > >> > >> Any help is greatly appreciated. > >> > >> Here is my code: > >> > >> install.packages("rJava") ;library(rJava) > >> install.packages("tabulizer");library(tabulizer) > >> MyPath <- "C:/Users/name/Documents/tEMP" > >> ExtTable <- function (Path,CalOrd){ > >> FileNames <- dir(Path, pattern =".(pdf|PDF)",full.names = TRUE) > >> MyFiles <- lapply(FileNames, function(i) extract_tables(i,method = "stream")) > >> if(CalOrd == "Yes"){ > >> MyOFiles <- gsub("(\\s.*)|(.pdf|.PDF)","",basename(FileNames)) > >> MyOFiles <- match(MyOFiles,month.name) > >> MyNFiles <- MyFiles[order(MyOFiles)]} > >> else > >> MyFiles > >> } > >> MyTables <- ExtTable(Path=MyPath,CalOrd = "No") > >> > >> Here is cleaned portion of the output: The whole output consists of 3 > >> lists, each contains 12, 15, and 12 sub-lists. > >> > >> [[2]][[2]] > >> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] > >> [1,] "" "Avg." "+_ lo" "n" "Med." "" "Avg." "+_ > >> lo" "n" "Med." > >> [2,] "SiOz" "44.0" "1.26" "375" "44.1" "Nb" "4.8" "6.3" > >> "58" "2.7" > >> [3,] "T i O 2" "0.09" "0.09" "561" "0.09" "Mo(b)" "50" "30" > >> "3" "35" > >> [4,] "A1203" "2.27" "1.10" "375" "2.20" "Ru(b)" "12.4" "4.1" > >> "3" "12" > >> [5,] "FeO total" "8.43" "1.14" "375" "8.19" "Pd(b)" "3.9" "2.1" > >> "19" "4.1" > >> [6,] "MnO" "0.14" "0.03" "366" "0.14" "Ag(b)" "6.8" "8.3" > >> "17" "4.8" > >> [7,] "MgO" "41.4" "3.00" "375" "41.2" "Cd(b)" "41" "14" > >> "16" "37" > >> [8,] "CaO" "2.15" "1.11" "374" "2.20" "In(b)" "12" "4" > >> "19" "12" > >> [9,] "Na20" "0.24" "0.16" "341" "0.21" "Sn(b)" "54" "31" > >> "6" "36" > >> [10,] "K20" "0.054" "0.11" "330" "0.028" "Sb(b)" "3.9" "3.9" > >> "11" "3.2" > >> [11,] "P205" "0.056" "0.11" "233" "0.030" "Te(b)" "11" "4" > >> "18" "10" > >> [12,] "Total" "98.88" "" "" "98.43" "Cs(b)" "10" "16" > >> "17" "1.5" > >> [13,] "" "" "" "" "" "Ba" "33" "52" > >> "75" "17" > >> [14,] "Mg-value" "89.8" "1.1" "375" "90.0" "La" "2.60" "5.70" > >> "208" "0.77" > >> [15,] "Ca/AI" "1.28" "1.6" "374" "1.35" "Ce" "6.29" "11.7" > >> "197" "2.08" > >> [16,] "AI/Ti" "22" "29" "361" "22" "Pr" "0.56" "0.87" > >> "40" "0.21" > >> [17,] "F e / M n" "60" "10" "366" "59" "Nd" "2.67" "4.31" > >> "162" "1.52" > >> [18,] "" "" "" "" "" "Sm" "0.47" "0.69" > >> "214" "0.25" > >> [19,] "Li" "1.5" "0.3" "6" "1.5" "Eu" "0.16" "0.21" > >> "201" "0.097" > >> [20,] "B" "0.53" "0.07" "6" "0.55" "Gd" "0.60" "0.83" > >> "67" "0.31" > >> [21,] "C" "110" "50" "13" "93" "Tb" "0.070" > >> "0.064" "146" "0.056" > >> [22,] "F" "88" "71" "15" "100" "Dy" "0.51" "0.35" > >> "58" "0.47" > >> [23,] "S" "157" "77" "22" "152" "Ho" "0.12" "0.14" > >> "54" "0.090" > >> [24,] "C1" "53" "45" "15" "75" "Er" "0.30" "0.22" > >> "52" "0.28" > >> [25,] "Sc" "12.2" "6.4" "220" "12.0" "Tm" "0.038" > >> "0.026" "40" "0.035" > >> [26,] "V" "56" "21" "132" "53" "Yb" "0.26" "0.14" > >> "201" "0.27" > >> [27,] "Cr" "2690" "705" "325" "2690" "Lu" "0.043" > >> "0.023" "172" "0.045" > >> [28,] "Co" "112" "10" "166" "111" "Hf" "0.27" "0.30" > >> "71" "0.17" > >> [29,] "Ni" "2160" "304" "308" "2140" "Ta" "0.40" "0.51" > >> "38" "0.23" > >> [30,] "Cu" "11" "9" "94" "9" "W(b)" "7.2" "5.2" > >> "6" "4.0" > >> [31,] "Zn" "65" "20" "129" "60" "Re(b)" "0.13" "0.11" > >> "18" "0.09" > >> [32,] "Ga" "2.4" "1.3" "49" "2.4" "Os(b)" "4.0" "1.8" > >> "18" "3.7" > >> [33,] "Ge" "0.96" "0.19" "19" "0.92" "Ir(b)" "3.7" "0.9" > >> "34" "3.0" > >> [34,] "As" "0.11" "0.07" "7" "0.10" "Pt(b)" "7" "-" > >> "1" "-" > >> [35,] "Se" "0.041" "0.056" "18" "0.025" "Au(b)" "0.65" "0.53" > >> "30" "0.5" > >> [36,] "Br" "0.01" "0.01" "6" "0.01" "Tl(b)" "1.2" "1.0" > >> "13" "0.9" > >> [37,] "Rb" "1,9" "4.8" "97" "0.38" "Pb" "0.16" "0.11" > >> "17" "0.16" > >> [38,] "Sr" "49" "60" "110" "20" "Bi(b)" "1.7" "0.7" > >> "13" "1.6" > >> [39,] "Y" "4.4" "5.5" "86" "3.1" "Th*" "0.71" "1.2" > >> "71" "0.22" > >> [40,] "Zr" "21" "42" "82" "8.0" "U" "0.12" "0.23" > >> "48" "0.040" > >> [[2]][[4]] > >> [,1] [,2] [,3] [,4] [,5] > >> [,6] > >> [1,] "" "Spinel peridotites" "" "Garnet peridotites" > >> "" "Primitive" > >> [2,] "" "Avg. Meal." "M-A sp" "M-A gt B-M" > >> "Jordan" "mantle" > >> [3,] "SiO 2" "44.0 44.1" "44.15" "44.99 45.00" > >> "45.55" "44.8" > >> [4,] "TiO 2" "0.09 0.09" "0.07" "0.06 0.08" > >> "0.11" "0.21" > >> [5,] "A1203" "2.27 2.20" "1.96" "1.40 1.31" > >> "1.43" "4.45" > >> [6,] "Cr203" "0.39 0.39" "0.44" "0.32 0.38" > >> "0.34" "0.43" > >> [7,] "FeOtotal" "8.43 8.19" "8.28" "7.89 6.97" > >> "7.61" "8.40" > >> [8,] "Mn O" "0.14 0.14" "0.12" "0.11 0.13" > >> "0.11" "0.14" > >> [9,] "MgO" "41.4 41.2" "42.25" "42.60 44.86" > >> "43.55" "37.2" > >> [10,] "NiO" "0.27 0.27" "0.27" "0.26 0.29" > >> "-" "0.24" > >> [11,] "CaO" "2.15 2.20" "2.08" "0.82 0.77" > >> "1.05" "3.60" > >> [12,] "Na 20" "0.24 0.21" "0.18" "0.11 0.09" > >> "0.14" "0.34" > >> [13,] "K 2 0" "0.054 0.028" "0.05" "0.04 0.10" > >> "0.11" "0.028" > >> [14,] "P205" "0.056 0.030" "0.02" "- 0.01" > >> "-" "0.022" > >> [15,] "Total" "99.49 99.05" "99.87" "98.60 100.00" > >> "100.00" "99.86" > >> [16,] "Mg-value" "89.8 90.0" "90.1" "90.6 92.0" > >> "91.1" "88.8" > >> [17,] "olivine" "62 63" "67" "65 68" > >> "66" "56 57" > >> [18,] "opx" "24 24" "22" "28 25" > >> "28" "22 17" > >> [19,] "cpx" "12 11" "9" "3 2" > >> "3" "19 10" > >> [20,] "spinel" "2 2" "2" "- -" > >> "-" "3 -" > >> > >> Here is portion of the output for str(MyTables): > >> > >> str(MyTables) > >> > >> List of 3 > >> $ :List of 12 > >> $ : chr [1:3, 1:2] "south of the artificial lake Lokka. Intrusive > >> complexes" "of alkaline rocks are found at Sokli (phosphorite-bear-" > >> "ing and a possible Nb-occurrence) in Finland, and at" "(Eriksson, > >> 1992). During this period, Northern Europe" ... > >> ..$ : chr [1:55, 1:15] "Element" "Ag" "Al" "Al_XRF" ... > >> ..$ : chr [1:56, 1:2] "in the till is mainly of local origin, > >> although some cob-" "bles and boulders may have been transported over > >> sev-" "eral kilometres. The moraine formations in the study" "area are > >> mostly gravelly and sandy tills, locally hum-" ... > >> ..$ : chr [1:53, 1:2] "requisites. PCA accounts for maximum variance > >> of all" "variables, while FA is based on the correlation structure" > >> "of the variables. The model of factor analysis allows that" "the > >> common factors do not explain the total variation of" ... > >> ..$ : chr [1:54, 1:7] "lished examples of the use of factor > >> analysis, it is neglec-" "ted that regional geochemical (and > >> environmental) data" "almost never follow a normal distribution. > >> Continuing Method" "with factor analysis in such a case must lead to > >> biased" ... > >> ..$ : chr [1:16, 1:2] "shows the factor loadings of the different > >> variables" "entering each factor. Names of variables with an abso-" > >> "lute value of the loadings <0.3 are not plotted. Fig. 5" "shows 8 > >> results of factor analyses using a selection of all" ... > >> ..$ : chr [1:21, 1:2] "pretable results, notwithstanding the fact > >> that on the" "basis of the foregoing discussion it should probably > >> not" "be used with these data. Do these results warrant the use" "of a > >> quite work-intensive method? Unfortunately not," ... > >> ..$ : chr [1:55, 1:8] "" "Ag" "Al" "Al_XRF" ... > >> ..$ : chr [1:23, 1:2] "addition, geochemical reasoning (e.g. > >> geochemical asso-" "ciations and/or pathfinder elements for different > >> types of" "ore deposits) was used to select further sub-sets of vari-" > >> "ables. In geochemistry, the selection of elements entered" ... > >> ..$ : chr [1:55, 1:2] "Fig. 10C cuts several geological units, and > >> is most likely" "indicative of alteration processes related to a > >> deep-" "seated fault. It was revealed again in a factor analysis" > >> "carried out with all those elements extracted by aqua" ... > >> ..$ : chr [1:50, 1:2] "well justified in stating that it is not very > >> scientific to" "play with the selection of elements and number of > >> fac-" "tors extracted until one > >> ?\200\230?\200\230finds?\200\231?\200\231 an > >> ?\200\230?\200\230interesting?\200\231?\200\231 result." "On the other > >> hand, even all the different results pre-" ... > >> ..$ : chr [1:24, 1:2] "Niemel??, J., Ekman, I., Lukashov, A. (Eds.), > >> 1993. Quaternary" "Deposits of Finland and Northwestern Part of > >> Russian Fed-" "eration and Their Resources 1:1,000,000. Geological > >> Survey" "of Finland, Espoo, Finland." ... > >> $ :List of 15 > >> > >> ______________________________________________ > >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > >> and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Ek Esawi
2018-Dec-20 03:22 UTC
[R] Combine recursive lists in a single list or data frame and write it to file
Thank you Jim. I did use unlist with the recursive option which
converted the 3 levels list to a list of 38 matrices. I tried your
earlier function to join the 38 matrices, all of which have different
number of columns and rows, but i kept getting an error.
fillList<-function(x) {
+ maxrows<-max(unlist(lapply(x,length)))
+ return(lapply(x,"[",1:maxrows))
+ }>
> for (i in 1:length(MyTables)) {
+ write.table(as.data.frame(fillList(MyTables[i])),
+ file = "Temp.txt",append = TRUE,quote = TRUE)}
Error in (function (..., row.names = NULL, check.rows = FALSE,
check.names = TRUE, :
arguments imply differing number of rows: 3, 55, 56, 53, 54, 16, 21,
23, 50, 24
On Wed, Dec 19, 2018 at 9:36 PM Jim Lemon <drjimlemon at gmail.com>
wrote:>
> Hi Ek,
> Look at unlist and the argument "recursive". You can step down
through
> the levels or a nested list to convert it to a single level list.
>
> Jim
>
> On Thu, Dec 20, 2018 at 1:33 PM Ek Esawi <esawiek at gmail.com>
wrote:
> >
> > Thank you Bert. I don't see how unlist will help. I want to
combine
> > them but keep the "rectangular structure",e.g. list, data
frame,
> > matrix because i want to get the tables in their original form.
> > Unlist converts the whole output to a single vector; unless i am
> > missing something.
> >
> > On Wed, Dec 19, 2018 at 9:10 PM Bert Gunter <bgunter.4567 at
gmail.com> wrote:
> > >
> > > Does ?unlist not help? Why not?
> > >
> > > Bert
> > >
> > >
> > > On Wed, Dec 19, 2018, 5:13 PM Ek Esawi <esawiek at gmail.com
wrote:
> > >>
> > >> Hi All?
> > >>
> > >> I am using the R tabulizer package to extract tables from
pdf files.
> > >> The output is a set of lists of matrices. The package
extracts tables
> > >> and a lot of extra stuff which is nearly impossible to clean
with
> > >> RegEx. So, I want to clean it manually.
> > >> To do so I need to (1) combine all lists in a single list or
data
> > >> frame and (2) then write the single entity to a text file to
edit it.
> > >> I could not figure out how.
> > >>
> > >> I tried something like this but did not work.
> > >> lapply(MyTables, function(x)
> > >> lapply(x,write.table(file="temp.txt",append =
TRUE)))
> > >>
> > >> Any help is greatly appreciated.
> > >>
> > >> Here is my code:
> > >>
> > >> install.packages("rJava") ;library(rJava)
> > >> install.packages("tabulizer");library(tabulizer)
> > >> MyPath <- "C:/Users/name/Documents/tEMP"
> > >> ExtTable <- function (Path,CalOrd){
> > >> FileNames <- dir(Path, pattern
=".(pdf|PDF)",full.names = TRUE)
> > >> MyFiles <- lapply(FileNames, function(i)
extract_tables(i,method = "stream"))
> > >> if(CalOrd == "Yes"){
> > >> MyOFiles <-
gsub("(\\s.*)|(.pdf|.PDF)","",basename(FileNames))
> > >> MyOFiles <- match(MyOFiles,month.name)
> > >> MyNFiles <- MyFiles[order(MyOFiles)]}
> > >> else
> > >> MyFiles
> > >> }
> > >> MyTables <- ExtTable(Path=MyPath,CalOrd = "No")
> > >>
> > >> Here is cleaned portion of the output: The whole output
consists of 3
> > >> lists, each contains 12, 15, and 12 sub-lists.
> > >>
> > >> [[2]][[2]]
> > >> [,1] [,2] [,3] [,4] [,5] [,6] [,7]
[,8] [,9] [,10]
> > >> [1,] "" "Avg." "+_
lo" "n" "Med." "" "Avg."
"+_
> > >> lo" "n" "Med."
> > >> [2,] "SiOz" "44.0"
"1.26" "375" "44.1" "Nb"
"4.8" "6.3"
> > >> "58" "2.7"
> > >> [3,] "T i O 2" "0.09"
"0.09" "561" "0.09" "Mo(b)"
"50" "30"
> > >> "3" "35"
> > >> [4,] "A1203" "2.27"
"1.10" "375" "2.20" "Ru(b)"
"12.4" "4.1"
> > >> "3" "12"
> > >> [5,] "FeO total" "8.43"
"1.14" "375" "8.19" "Pd(b)"
"3.9" "2.1"
> > >> "19" "4.1"
> > >> [6,] "MnO" "0.14"
"0.03" "366" "0.14" "Ag(b)"
"6.8" "8.3"
> > >> "17" "4.8"
> > >> [7,] "MgO" "41.4"
"3.00" "375" "41.2" "Cd(b)"
"41" "14"
> > >> "16" "37"
> > >> [8,] "CaO" "2.15"
"1.11" "374" "2.20" "In(b)"
"12" "4"
> > >> "19" "12"
> > >> [9,] "Na20" "0.24"
"0.16" "341" "0.21" "Sn(b)"
"54" "31"
> > >> "6" "36"
> > >> [10,] "K20" "0.054"
"0.11" "330" "0.028" "Sb(b)"
"3.9" "3.9"
> > >> "11" "3.2"
> > >> [11,] "P205" "0.056"
"0.11" "233" "0.030" "Te(b)"
"11" "4"
> > >> "18" "10"
> > >> [12,] "Total" "98.88" ""
"" "98.43" "Cs(b)" "10"
"16"
> > >> "17" "1.5"
> > >> [13,] "" "" ""
"" "" "Ba" "33"
"52"
> > >> "75" "17"
> > >> [14,] "Mg-value" "89.8" "1.1"
"375" "90.0" "La" "2.60"
"5.70"
> > >> "208" "0.77"
> > >> [15,] "Ca/AI" "1.28" "1.6"
"374" "1.35" "Ce" "6.29"
"11.7"
> > >> "197" "2.08"
> > >> [16,] "AI/Ti" "22" "29"
"361" "22" "Pr" "0.56"
"0.87"
> > >> "40" "0.21"
> > >> [17,] "F e / M n" "60" "10"
"366" "59" "Nd" "2.67"
"4.31"
> > >> "162" "1.52"
> > >> [18,] "" "" ""
"" "" "Sm" "0.47"
"0.69"
> > >> "214" "0.25"
> > >> [19,] "Li" "1.5" "0.3"
"6" "1.5" "Eu" "0.16"
"0.21"
> > >> "201" "0.097"
> > >> [20,] "B" "0.53"
"0.07" "6" "0.55" "Gd"
"0.60" "0.83"
> > >> "67" "0.31"
> > >> [21,] "C" "110" "50"
"13" "93" "Tb" "0.070"
> > >> "0.064" "146" "0.056"
> > >> [22,] "F" "88" "71"
"15" "100" "Dy" "0.51"
"0.35"
> > >> "58" "0.47"
> > >> [23,] "S" "157" "77"
"22" "152" "Ho" "0.12"
"0.14"
> > >> "54" "0.090"
> > >> [24,] "C1" "53" "45"
"15" "75" "Er" "0.30"
"0.22"
> > >> "52" "0.28"
> > >> [25,] "Sc" "12.2" "6.4"
"220" "12.0" "Tm" "0.038"
> > >> "0.026" "40" "0.035"
> > >> [26,] "V" "56" "21"
"132" "53" "Yb" "0.26"
"0.14"
> > >> "201" "0.27"
> > >> [27,] "Cr" "2690" "705"
"325" "2690" "Lu" "0.043"
> > >> "0.023" "172" "0.045"
> > >> [28,] "Co" "112" "10"
"166" "111" "Hf" "0.27"
"0.30"
> > >> "71" "0.17"
> > >> [29,] "Ni" "2160" "304"
"308" "2140" "Ta" "0.40"
"0.51"
> > >> "38" "0.23"
> > >> [30,] "Cu" "11" "9"
"94" "9" "W(b)" "7.2"
"5.2"
> > >> "6" "4.0"
> > >> [31,] "Zn" "65" "20"
"129" "60" "Re(b)" "0.13"
"0.11"
> > >> "18" "0.09"
> > >> [32,] "Ga" "2.4" "1.3"
"49" "2.4" "Os(b)" "4.0"
"1.8"
> > >> "18" "3.7"
> > >> [33,] "Ge" "0.96"
"0.19" "19" "0.92" "Ir(b)"
"3.7" "0.9"
> > >> "34" "3.0"
> > >> [34,] "As" "0.11"
"0.07" "7" "0.10" "Pt(b)"
"7" "-"
> > >> "1" "-"
> > >> [35,] "Se" "0.041"
"0.056" "18" "0.025" "Au(b)"
"0.65" "0.53"
> > >> "30" "0.5"
> > >> [36,] "Br" "0.01"
"0.01" "6" "0.01" "Tl(b)"
"1.2" "1.0"
> > >> "13" "0.9"
> > >> [37,] "Rb" "1,9" "4.8"
"97" "0.38" "Pb" "0.16"
"0.11"
> > >> "17" "0.16"
> > >> [38,] "Sr" "49" "60"
"110" "20" "Bi(b)" "1.7"
"0.7"
> > >> "13" "1.6"
> > >> [39,] "Y" "4.4" "5.5"
"86" "3.1" "Th*" "0.71"
"1.2"
> > >> "71" "0.22"
> > >> [40,] "Zr" "21" "42"
"82" "8.0" "U" "0.12"
"0.23"
> > >> "48" "0.040"
> > >> [[2]][[4]]
> > >> [,1] [,2] [,3] [,4]
[,5]
> > >> [,6]
> > >> [1,] "" "Spinel peridotites"
"" "Garnet peridotites"
> > >> "" "Primitive"
> > >> [2,] "" "Avg. Meal."
"M-A sp" "M-A gt B-M"
> > >> "Jordan" "mantle"
> > >> [3,] "SiO 2" "44.0 44.1"
"44.15" "44.99 45.00"
> > >> "45.55" "44.8"
> > >> [4,] "TiO 2" "0.09 0.09"
"0.07" "0.06 0.08"
> > >> "0.11" "0.21"
> > >> [5,] "A1203" "2.27 2.20"
"1.96" "1.40 1.31"
> > >> "1.43" "4.45"
> > >> [6,] "Cr203" "0.39 0.39"
"0.44" "0.32 0.38"
> > >> "0.34" "0.43"
> > >> [7,] "FeOtotal" "8.43 8.19"
"8.28" "7.89 6.97"
> > >> "7.61" "8.40"
> > >> [8,] "Mn O" "0.14 0.14"
"0.12" "0.11 0.13"
> > >> "0.11" "0.14"
> > >> [9,] "MgO" "41.4 41.2"
"42.25" "42.60 44.86"
> > >> "43.55" "37.2"
> > >> [10,] "NiO" "0.27 0.27"
"0.27" "0.26 0.29"
> > >> "-" "0.24"
> > >> [11,] "CaO" "2.15 2.20"
"2.08" "0.82 0.77"
> > >> "1.05" "3.60"
> > >> [12,] "Na 20" "0.24 0.21"
"0.18" "0.11 0.09"
> > >> "0.14" "0.34"
> > >> [13,] "K 2 0" "0.054 0.028"
"0.05" "0.04 0.10"
> > >> "0.11" "0.028"
> > >> [14,] "P205" "0.056 0.030"
"0.02" "- 0.01"
> > >> "-" "0.022"
> > >> [15,] "Total" "99.49 99.05"
"99.87" "98.60 100.00"
> > >> "100.00" "99.86"
> > >> [16,] "Mg-value" "89.8 90.0"
"90.1" "90.6 92.0"
> > >> "91.1" "88.8"
> > >> [17,] "olivine" "62 63"
"67" "65 68"
> > >> "66" "56 57"
> > >> [18,] "opx" "24 24"
"22" "28 25"
> > >> "28" "22 17"
> > >> [19,] "cpx" "12 11"
"9" "3 2"
> > >> "3" "19 10"
> > >> [20,] "spinel" "2 2"
"2" "- -"
> > >> "-" "3 -"
> > >>
> > >> Here is portion of the output for str(MyTables):
> > >>
> > >> str(MyTables)
> > >>
> > >> List of 3
> > >> $ :List of 12
> > >> $ : chr [1:3, 1:2] "south of the artificial lake Lokka.
Intrusive
> > >> complexes" "of alkaline rocks are found at Sokli
(phosphorite-bear-"
> > >> "ing and a possible Nb-occurrence) in Finland, and
at" "(Eriksson,
> > >> 1992). During this period, Northern Europe" ...
> > >> ..$ : chr [1:55, 1:15] "Element" "Ag"
"Al" "Al_XRF" ...
> > >> ..$ : chr [1:56, 1:2] "in the till is mainly of local
origin,
> > >> although some cob-" "bles and boulders may have
been transported over
> > >> sev-" "eral kilometres. The moraine formations in
the study" "area are
> > >> mostly gravelly and sandy tills, locally hum-" ...
> > >> ..$ : chr [1:53, 1:2] "requisites. PCA accounts for
maximum variance
> > >> of all" "variables, while FA is based on the
correlation structure"
> > >> "of the variables. The model of factor analysis allows
that" "the
> > >> common factors do not explain the total variation of"
...
> > >> ..$ : chr [1:54, 1:7] "lished examples of the use of
factor
> > >> analysis, it is neglec-" "ted that regional
geochemical (and
> > >> environmental) data" "almost never follow a normal
distribution.
> > >> Continuing Method" "with factor analysis in such a
case must lead to
> > >> biased" ...
> > >> ..$ : chr [1:16, 1:2] "shows the factor loadings of
the different
> > >> variables" "entering each factor. Names of
variables with an abso-"
> > >> "lute value of the loadings <0.3 are not plotted.
Fig. 5" "shows 8
> > >> results of factor analyses using a selection of all" ...
> > >> ..$ : chr [1:21, 1:2] "pretable results,
notwithstanding the fact
> > >> that on the" "basis of the foregoing discussion it
should probably
> > >> not" "be used with these data. Do these results
warrant the use" "of a
> > >> quite work-intensive method? Unfortunately not," ...
> > >> ..$ : chr [1:55, 1:8] "" "Ag"
"Al" "Al_XRF" ...
> > >> ..$ : chr [1:23, 1:2] "addition, geochemical reasoning
(e.g.
> > >> geochemical asso-" "ciations and/or pathfinder
elements for different
> > >> types of" "ore deposits) was used to select further
sub-sets of vari-"
> > >> "ables. In geochemistry, the selection of elements
entered" ...
> > >> ..$ : chr [1:55, 1:2] "Fig. 10C cuts several
geological units, and
> > >> is most likely" "indicative of alteration processes
related to a
> > >> deep-" "seated fault. It was revealed again in a
factor analysis"
> > >> "carried out with all those elements extracted by
aqua" ...
> > >> ..$ : chr [1:50, 1:2] "well justified in stating that
it is not very
> > >> scientific to" "play with the selection of elements
and number of
> > >> fac-" "tors extracted until one
> > >> ?\200\230?\200\230finds?\200\231?\200\231 an
> > >> ?\200\230?\200\230interesting?\200\231?\200\231 result."
"On the other
> > >> hand, even all the different results pre-" ...
> > >> ..$ : chr [1:24, 1:2] "Niemel??, J., Ekman, I.,
Lukashov, A. (Eds.),
> > >> 1993. Quaternary" "Deposits of Finland and
Northwestern Part of
> > >> Russian Fed-" "eration and Their Resources
1:1,000,000. Geological
> > >> Survey" "of Finland, Espoo, Finland." ...
> > >> $ :List of 15
> > >>
> > >> ______________________________________________
> > >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
> > >> https://stat.ethz.ch/mailman/listinfo/r-help
> > >> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> > >> and provide commented, minimal, self-contained, reproducible
code.
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.