rentrez in R
Cari Lewis
2022-12-07
‘rentrez’ Assignment
1. Create a search of a topic, organism, etc.
# load the necessary packages
library(rentrez)
library(tidyverse)## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.3.6 ✔ purrr 0.3.5
## ✔ tibble 3.1.8 ✔ dplyr 1.0.10
## ✔ tidyr 1.2.1 ✔ stringr 1.4.1
## ✔ readr 2.1.3 ✔ forcats 0.5.2
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()library(ggplot2)
library(glue)
# create an object to hold the search information
cl_search <- entrez_search(db = "pubmed",
term = "cimex lectularius[ORGN] and 2018:2022[PDAT]",
retmax = 100)
cl_search## Entrez search result with 247 hits (object contains 100 IDs and no web_history object)
## Search term (as translated): ("bedbugs"[MeSH Terms] OR "bedbugs"[All Fields] OR ...2. Use the summary or fetch arguement to extract relevant information to your search.
# get the summary information
cl_multi_sum <- entrez_summary(db= "pubmed", id = cl_search$ids)
# extract elements from the summary using the
extract_from_esummary(cl_multi_sum,
c("title","pubtype","pubdate","authors"),
simplify = TRUE)## 36421963
## title "Characterizing Repellencies of Methyl Benzoate and Its Analogs against the Common Bed Bug, Cimex le" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Nov 17"
## authors data.frame,3
## 36400831
## title "Household perception and infestation dynamics of bedbugs among residential communities and its pote" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Nov 18"
## authors data.frame,3
## 36397113
## title "Systemic veterinary drugs for control of the common bed bug, Cimex lectularius, in poultry farms."
## pubtype "Journal Article"
## pubdate "2022 Nov 17"
## authors data.frame,3
## 36396986
## title "Comparative analysis of detoxification-related gene superfamilies across five hemipteran species."
## pubtype "Journal Article"
## pubdate "2022 Nov 17"
## authors data.frame,3
## 36232802
## title "Characterization of New Defensin Antimicrobial Peptides and Their Expression in Bed Bugs in Respons" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Sep 29"
## authors data.frame,3
## 36226901
## title "Perspective on Biology and Management of Bed Bugs: Introduction."
## pubtype "Journal Article"
## pubdate "2022 Sep 14"
## authors data.frame,3
## 36198396
## title "Historical and Contemporary Control Options Against Bed Bugs, Cimex spp."
## pubtype character,2
## pubdate "2022 Oct 5"
## authors data.frame,3
## 36194505
## title ""Bed bugs live in dirty places"-How Using Live Animals in Teaching Contributes to Reducing Stigma, " [truncated]
## pubtype "Journal Article"
## pubdate "2022 Dec"
## authors data.frame,3
## 36135475
## title "Comparative Efficacy of a Fungal Entomopathogen with a Broad Host Range against Two Human-Associate" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Aug 26"
## authors data.frame,3
## 36127851
## title "'When the bedbugs come, that's another problem': exploring the lived experiences of bedbug infestat" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Sep 20"
## authors data.frame,3
## 36124973
## title "Effect of Bed Bug (Hemiptera: Cimicidae) Aldehydes on Efficacy of Fungal Biopesticides."
## pubtype "Journal Article"
## pubdate "2022 Sep 19"
## authors data.frame,3
## 36086827
## title "Histamine Excretion by the Common Bed Bug (Hemiptera: Cimicidae)."
## pubtype "Journal Article"
## pubdate "2022 Nov 16"
## authors data.frame,3
## 36000777
## title "Comparative Insecticide Uptake Characteristics of Chlorfenapyr Suggests an Additional Reason Why Be" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Oct 12"
## authors data.frame,3
## 30844155
## title "Bedbug Bites."
## pubtype list,0
## pubdate "2022 Jan"
## authors data.frame,3
## 35900244
## title "Analysis of Patients With Bed Bugs in the Emergency Department."
## pubtype "Journal Article"
## pubdate "2022 Jul-Sep 01"
## authors data.frame,3
## 35895369
## title "Identification of Knockdown Resistance Mutations in the Cimex hemipterus (Hemiptera: Cimicidae) in " [truncated]
## pubtype "Journal Article"
## pubdate "2022 Jul 13"
## authors data.frame,3
## 35781682
## title "Bed bugs on ship: a French review."
## pubtype character,2
## pubdate "2022"
## authors data.frame,3
## 35715692
## title "Effects of Wolbachia elimination and B-vitamin supplementation on bed bug development and reproduct" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Jun 17"
## authors data.frame,3
## 35703110
## title "Morphometrics of the Tropical Bed Bug (Hemiptera: Cimicidae) From Cape Coast, Ghana."
## pubtype "Journal Article"
## pubdate "2022 Sep 14"
## authors data.frame,3
## 35671220
## title "Quantification of Fecal Spot Production as a Measure of Environmental Contamination Based on Common" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Oct 12"
## authors data.frame,3
## 35663609
## title "Staphylococcus aureus native mitral valve endocarditis associated with bed bug bites - A case repor" [truncated]
## pubtype list,0
## pubdate "2022"
## authors data.frame,3
## 35640206
## title "The Efficacy of a Pyrethroid-impregnated Mattress Liner on Multiple International Strains of Cimex " [truncated]
## pubtype "Journal Article"
## pubdate "2022 May 29"
## authors data.frame,3
## 35639556
## title "Performance of Pyrethroid-Neonicotinoid Mixture Formulations Against Field-Collected Strains of the" [truncated]
## pubtype "Journal Article"
## pubdate "2022 May 26"
## authors data.frame,3
## 35623470
## title "Bed bug infestation in a French university hospital: control strategy, financial impact and perspec" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Aug"
## authors data.frame,3
## 35617203
## title "Spatiotemporal trends in bed bug metrics: New York City."
## pubtype "Journal Article"
## pubdate "2022"
## authors data.frame,3
## 35607829
## title "Comparative Efficacy of Superheated Dry Steam Application and Insecticide Spray against Common Bed " [truncated]
## pubtype "Journal Article"
## pubdate "2022 May 24"
## authors data.frame,3
## 35597739
## title "Cimex lectularius and Cimex hemipterus (bed bugs)."
## pubtype "Journal Article"
## pubdate "2022 Oct"
## authors data.frame,3
## 35524788
## title "Geographical patterns and mechanisms of Cimex lectularius Linnaeus, 1758, and Cimex hemipterus Fabr" [truncated]
## pubtype character,3
## pubdate "2022 Jul"
## authors data.frame,3
## 35495968
## title "Bed bug (Cimex spp.) colonization of human host."
## pubtype list,0
## pubdate "2022 May"
## authors data.frame,3
## 35391489
## title "Prevalence of Cockroaches, Bed Bugs, and House Mice in Low-Income Housing and Evaluation of Baits f" [truncated]
## pubtype "Journal Article"
## pubdate "2022 May 11"
## authors data.frame,3
## 35384689
## title "A Comparative Study of Body Lice and Bed Bugs Reveals Factors Potentially Involved in Differential " [truncated]
## pubtype "Journal Article"
## pubdate "2022 May 19"
## authors data.frame,3
## 35348633
## title "Elevated Temperature Reduces Overwintering Survival of an Avian Ectoparasite, the Swallow Bug (Hemi" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Apr 22"
## authors data.frame,3
## 35318403
## title "Bacterial symbionts influence host susceptibility to fenitrothion and imidacloprid in the obligate " [truncated]
## pubtype "Journal Article"
## pubdate "2022 Mar 22"
## authors data.frame,3
## 35286393
## title "Morphological, Molecular and MALDI-TOF MS Identification of Bedbugs and Associated Wolbachia Specie" [truncated]
## pubtype "Journal Article"
## pubdate "2022 May 11"
## authors data.frame,3
## 35274683
## title "Morphological and Molecular Identification of Cimex hemipterus Fabricius, 1803 (Hemiptera: Cimicida" [truncated]
## pubtype "Journal Article"
## pubdate "2022 May 11"
## authors data.frame,3
## 35199182
## title "Characteristic Linear and Zigzag Purpuric Lesions in a Patient with Long-term and Repeated Exposure" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Mar 8"
## authors data.frame,3
## 34981990
## title "A Francisella tularensis-Like Bacterium in Tropical Bed Bugs from Madagascar."
## pubtype "Journal Article"
## pubdate "2022 Jan"
## authors data.frame,3
## 34897482
## title "Procurement Competence and Framework Agreements for Upgraded Bed Bug Control [Cimex lectularius (He" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Feb 9"
## authors data.frame,3
## 34880281
## title "Human skin triglycerides prevent bed bug (Cimex lectularius L.) arrestment."
## pubtype "Journal Article"
## pubdate "2021 Dec 8"
## authors data.frame,3
## 34838119
## title "Molecular and MALDI-TOF MS identification of swallow bugs Cimex hirundinis (Heteroptera: Cimicidae)" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Nov 27"
## authors data.frame,3
## 34821827
## title "The Impact of Bedbug (Cimex spp.) Bites on Self-Rated Health and Average Hours of Sleep per Day: A " [truncated]
## pubtype "Journal Article"
## pubdate "2021 Nov 14"
## authors data.frame,3
## 34787287
## title "Evaluation of the insecticide susceptibility profile in Cimex lectularius (Hemiptera: Cimicidae) in" [truncated]
## pubtype "Journal Article"
## pubdate "2021"
## authors data.frame,3
## 34765758
## title "Investigating the association of bed bugs with infectious diseases: A retrospective case-control st" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Oct"
## authors data.frame,3
## 34758597
## title "[Bed bug bites]."
## pubtype "Journal Article"
## pubdate "2021 Nov 9"
## authors data.frame,3
## 34693975
## title "Multiple Mechanisms Conferring Broad-Spectrum Insecticide Resistance in the Tropical Bed Bug (Hemip" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Dec 6"
## authors data.frame,3
## 34644597
## title "Time- and tissue-specific antimicrobial activity of the common bed bug in response to blood feeding" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Nov-Dec"
## authors data.frame,3
## 34639855
## title "A Survey of Potentially Pathogenic-Incriminated Arthropod Vectors of Health Concern in Botswana."
## pubtype "Journal Article"
## pubdate "2021 Oct 8"
## authors data.frame,3
## 34523872
## title "Pilot study: specific immunotherapy in patients with Papular urticaria by Cimex lectularius."
## pubtype character,2
## pubdate "2022 Nov"
## authors data.frame,3
## 34521460
## title "High levels of pyrethroid resistance and super-kdr mutations in the populations of tropical bed bug" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Sep 14"
## authors data.frame,3
## 34498401
## title "Respiratory diseases in patients with bed bugs."
## pubtype "Journal Article"
## pubdate "2022 Jan"
## authors data.frame,3
## 34486193
## title "Seminal fluid and sperm diluent affect sperm metabolism in an insect: Evidence from NAD(P)H and fla" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Jan"
## authors data.frame,3
## 34479609
## title "Latrocimicinae completes the phylogeny of Cimicidae: meeting old morphologic data rather than moder" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Sep 3"
## authors data.frame,3
## 34468070
## title "Characterization of heat exposure-associated escape behaviors and HSP gene expression in bed bugs (" [truncated]
## pubtype "Journal Article"
## pubdate "2022 Jan"
## authors data.frame,3
## 34454015
## title "Common substitution mutation F348Y of acetylcholinesterase gene contributes to organophosphate and " [truncated]
## pubtype "Journal Article"
## pubdate "2021 Nov"
## authors data.frame,3
## 34434117
## title "The Olfactory Chemosensation of Hematophagous Hemipteran Insects."
## pubtype character,2
## pubdate "2021"
## authors data.frame,3
## 34410423
## title "Behavioral Response of the Tropical Bed Bug, Cimex hemipterus (Hemiptera: Cimicidae) to Carbon Diox" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Oct 13"
## authors data.frame,3
## 34330972
## title "Male diet affects female fitness and sperm competition in human- and bat-associated lineages of the" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Jul 30"
## authors data.frame,3
## 34327537
## title "Bed Bugs (Cimex spp. (Hemiptera: Cimicidae)) as Permanent Ectoparasites: A Rare But Potentially Sig" [truncated]
## pubtype "Letter"
## pubdate "2021 Nov 9"
## authors data.frame,3
## 34312971
## title "Detection and monitoring of bed bugs (Hemiptera: Cimicidae): review of the underlying science, exis" [truncated]
## pubtype character,2
## pubdate "2021 Dec"
## authors data.frame,3
## 34272799
## title "Cuticle thickening associated with fenitrothion and imidacloprid resistance and influence of voltag" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Nov"
## authors data.frame,3
## 34202079
## title "Bed Bugs (Hemiptera: Cimicidae) Population Diversity and First Record of Cimex hemipterus in Paris."
## pubtype "Journal Article"
## pubdate "2021 Jun 25"
## authors data.frame,3
## 34185547
## title "Pesticides Misused for Bed Bug Control: Comparing Professional and Nonprofessional Applications Rep" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Aug"
## authors data.frame,3
## 34184043
## title "Toxicity of Methyl Benzoate and Analogs to Adult Aedes aegypti."
## pubtype "Journal Article"
## pubdate "2021 Jun 1"
## authors data.frame,3
## 34136318
## title "Associations Between Bed Bugs and Mental Illness Among Emergency Department Patients."
## pubtype "Journal Article"
## pubdate "2021 May 14"
## authors data.frame,3
## 34074914
## title "Common pediatric infestations: update on diagnosis and treatment of scabies, head lice, and bed bug" [truncated]
## pubtype character,2
## pubdate "2021 Aug 1"
## authors data.frame,3
## 33993977
## title "Plant essential oil constituents enhance deltamethrin toxicity in a resistant population of bed bug" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Jun"
## authors data.frame,3
## 33948981
## title "Early evidence of establishment of the tropical bedbug (Cimex hemipterus) in Central Europe."
## pubtype "Journal Article"
## pubdate "2021 Sep"
## authors data.frame,3
## 33899212
## title "Cutaneous reactions to bedbug bites."
## pubtype "Letter"
## pubdate "2022 Feb"
## authors data.frame,3
## 33899103
## title "The Common Bed Bug (Hemiptera: Cimicidae) Does Not Commonly Use Canines and Felines as a Host in Lo" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Nov 9"
## authors data.frame,3
## 33884648
## title "Experimental infection of bed bugs (Cimex lectularius L.) with Burkholderia multivorans."
## pubtype "Journal Article"
## pubdate "2021 Sep"
## authors data.frame,3
## 33875727
## title "Characterization of bacterial communities associated with blood-fed and starved tropical bed bugs, " [truncated]
## pubtype "Journal Article"
## pubdate "2021 Apr 19"
## authors data.frame,3
## 33872787
## title "Rapid control method of bed bugs infestation by freezing."
## pubtype "Letter"
## pubdate "2021 Jul-Aug"
## authors data.frame,3
## 33831435
## title "Bedbug salivation patterns during hematophagy in the skin of a mammalian host."
## pubtype "Journal Article"
## pubdate "2021 May-Jun"
## authors data.frame,3
## 33822124
## title "Assessment of Tropical Bed Bug (Hemiptera: Cimicidae), Infestations in Cape Coast, Ghana: Household" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Jul 16"
## authors data.frame,3
## 33822102
## title "Resistance to Fipronil in the Common Bed Bug (Hemiptera: Cimicidae)."
## pubtype "Journal Article"
## pubdate "2021 Jul 16"
## authors data.frame,3
## 33802315
## title "Effects of Chemical Insecticide Residues and Household Surface Type on a Beauveria bassiana-Based B" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Mar 3"
## authors data.frame,3
## 33704797
## title "Association between bed bugs and allergic reactions."
## pubtype "Journal Article"
## pubdate "2021 Jul"
## authors data.frame,3
## 33704449
## title "The Behavioral Response to Heat in the Common Bed Bug, Cimex lectularius (Hemiptera: Cimicidae)."
## pubtype "Journal Article"
## pubdate "2021 Jul 16"
## authors data.frame,3
## 33704428
## title "Field Evaluations of Sulfuryl Fluoride Fumigation for Control of the Common Bed Bug (Hemiptera: Cim" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Apr 13"
## authors data.frame,3
## 33670065
## title "Behavioral Responses of the Common Bed Bug to Essential Oil Constituents."
## pubtype "Journal Article"
## pubdate "2021 Feb 21"
## authors data.frame,3
## 33644237
## title "The Phylogenetic Analysis of Cimex hemipterus (Hemiptera: Cimicidae) Isolated from Different Region" [truncated]
## pubtype "Journal Article"
## pubdate "2020 Sep"
## authors data.frame,3
## 33599802
## title "[Parasitoses in childhood]."
## pubtype character,2
## pubdate "2021 Mar"
## authors data.frame,3
## 33559752
## title "Molecular analysis of the blood meals and bacterial communities of bed bugs (Cimex lectularius L.) " [truncated]
## pubtype "Journal Article"
## pubdate "2021 Apr"
## authors data.frame,3
## 33557124
## title "Magnitude and Spread of Bed Bugs (Cimex lectularius) throughout Ohio (USA) Revealed by Surveys of P" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Feb 4"
## authors data.frame,3
## 33533822
## title "New pandemic, old bugs: A case of cimicosis (Bed Bug) in a neglected elderly patient during the cor" [truncated]
## pubtype "Journal Article"
## pubdate "2021"
## authors data.frame,3
## 33528356
## title "Insecticidal efficacy of afoxolaner against bedbugs, Cimex lectularius, when administered orally to" [truncated]
## pubtype "Journal Article"
## pubdate "2021"
## authors data.frame,3
## 33479298
## title "Mating and starvation modulate feeding and host-seeking responses in female bed bugs, Cimex lectula" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Jan 21"
## authors data.frame,3
## 33424811
## title "Transmission, Tropism, and Biological Impacts of Torix Rickettsia in the Common Bed Bug Cimex lectu" [truncated]
## pubtype "Journal Article"
## pubdate "2020"
## authors data.frame,3
## 33420500
## title "Methods for Testing Repellents Against Bed Bugs (Hemiptera: Cimicidae)."
## pubtype "Journal Article"
## pubdate "2021 Feb 9"
## authors data.frame,3
## 33419204
## title "Widespread Mutations in Voltage-Gated Sodium Channel Gene of Cimex lectularius (Hemiptera: Cimicida" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Jan 6"
## authors data.frame,3
## 33378530
## title "Four Species of Under-reported Parasitic Arthropods in Mexico and their Potential Role as Vectors o" [truncated]
## pubtype "Journal Article"
## pubdate "2020 Nov 12"
## authors data.frame,3
## 33310450
## title "Detection of target-site and metabolic resistance to pyrethroids in the bed bug Cimex lectularius i" [truncated]
## pubtype "Journal Article"
## pubdate "2020 Dec"
## authors data.frame,3
## 33282107
## title "ATYPICAL LINEAR CONFIGURATION OF BEDBUG BITES IN AN EIGHT-YEAR-OLD BOY: A Case Report and Overview " [truncated]
## pubtype list,0
## pubdate "2020 Jun"
## authors data.frame,3
## 33239286
## title "The immune and circulatory systems are functionally integrated across insect evolution."
## pubtype "Journal Article"
## pubdate "2020 Nov"
## authors data.frame,3
## 33221110
## title "Bed bugs are associated with anemia."
## pubtype "Journal Article"
## pubdate "2021 Aug"
## authors data.frame,3
## 33210364
## title "Modification of footed pajamas to confirm arthropod bites: The Modified Onesie Biting Bug Assessmen" [truncated]
## pubtype "Journal Article"
## pubdate "2021 Mar"
## authors data.frame,3
## 33167323
## title "Ontogenesis of Aldehyde Pheromones in Two Synanthropic Bed Bug Species (Heteroptera: Cimicidae)."
## pubtype "Journal Article"
## pubdate "2020 Nov 5"
## authors data.frame,3
## 33159287
## title "Isolation and characterization of human DNA recovered from Cimex hemipterus (F.) (Hemiptera:Cimicid" [truncated]
## pubtype "Journal Article"
## pubdate "2020 Dec"
## authors data.frame,3
## 33144950
## title "Reproductive compatibility among populations and host-associated lineages of the common bed bug (Ci" [truncated]
## pubtype "Journal Article"
## pubdate "2020 Oct"
## authors data.frame,3
## 33140831
## title "Repellency of Novel Catnip Oils Against the Bed Bug (Hemiptera: Cimicidae)."
## pubtype "Journal Article"
## pubdate "2021 Mar 12"
## authors data.frame,33. Create a plot to see how this topic has been reported on over a particular time span.
# create an object for searching in glue
year <- 1950:2022
clec_search <- glue("cimex lectularius[ORGN] AND {year}[PDAT]")
# create a second search to compare change over time in publications
search_counts <- tibble(year = year,
clec_search = clec_search) %>%
mutate(C_lec = map_dbl(clec_search, ~entrez_search(db = "pubmed",
term = .x)$count))
# plot the number of publications for AMV and tomato viruses from 1950 to 2022
search_counts %>%
select(year, C_lec) %>%
pivot_longer(-year) %>%
ggplot(aes(x = year,
y = value,
group = name,
color = name))+
geom_line(size = 1)+
geom_smooth(color = "light blue")+
theme_bw()## `geom_smooth()` using method = 'loess' and formula 'y ~ x'